Abstract: Hepatocyte growth factor (HGF) and macrophage stimulatory protein (MSP) are cytokines containing 728 and 711 amino acid residues, respectively. This poster will describe the generation of three-dimensional models of the serine protease-like domains of the two proteins, which contain 234 and 228 residues respectively, using homology modeling techniques. Structural aspects of the presumed binding sites of HGF and MSP are discussed. Speculation about the possible structure of a peptide-based binding partner is also given.
Abstract:
The conformational analysis of cis 1,3 cyclohexane diol as a function of solvent dielectric has recently been
extensively studied by Abrahams et al. They concluded that in non polar solvents, a large proportion of the di-axial
conformer exists, whereas in polar solvents, only the di-equatorial form can be detected. We felt
this system was an excellent candidate for testing theoretical solvation models such as the COSMO
hamiltonian. A series of 2D energy contour maps were calculated as a
function of the two OH dihedral angles using
COSMO/MOPAC/PM3. This left us with the requirement of representing this data
as a function of the defined solvent permittivity.
We chose to make use of the extensive facilities of the
World-Wide-Web system, which we have previously demonstrated is suitable not only for chemical
electronic publishing but for presenting talks,
posters and conference workshops.
The multidimensional molecular potential energy surfaces were converted to a MPEG
animations in which the time dimension is mapped onto the solvent dielectric. To
illustrate key geometries within these maps, context sensitive ISmapping was used to establish
hyperlinks to the optimised MOPAC coordinates, and chemical MIME types were defined to
enable transfer
of these coordinates to local viewers such as XMol. This enables others to readily acquire the
relevant coordinates, and view the system under local control, or even repeat the MOPAC
calculations if desired. In an extension of this concept, Explorer EyeChem maps
can be defined with MIME types and used to initiate real-time chemical and video conferencing
and "remote-picking" editing sessions of the molecular coordinates via Internet links using
ATM technology. We believe this has particular importance for collaborative projects between
remote sites.
Our MOPAC results show that particular ridges in the potential surfaces appear as a function of dielectric,
and the coordinate mapping clearly reveals that these geometries are associated with intramolecular
hydrogen bonds that are disrupted by polar solvents. Having calibrated our system against
the known experimental results, we then went on to study the effects resulting from putative
pi-facial hydrogen bonding in 1-phenyl-3-cyclohexanol, and 1-ethynyl-3-cyclohexanol; systems
hitherto unstudied experimentally. These effects appear weaker than conventional OH...O
hydrogen bonding interactions, but should be detectable experimentally.
We conclude that the analysis and presentation of complex potential energy maps containing subtle
structural features is particularly well suited for the rich features present in hypermedia
systems such as world-wide-web, and that suitable application of such technology has the potential
to revolutionise chemical information delivery.
Abstract:
Full geometry optimization studies at HF/6-31G*, MP2/6-31G* and LDF-JMW
levels all predict a planar trans-azobenzene instead of a twisted one
seen in the gas-phase electron diffraction experiment and in several
semi-empirical calculations.
Energy profiles of phenyl rotations with both C2 and Ci symmetries are
obtained by torsion constrained HF/6-31G* optimization. They clearly
show that the planar trans-azobenzene is indeed the lowest energy
conformer. However it only costs ~0.7 kcal/mol to twist a phenyl ring
by 30 degree. This could reconcile the difference between the
exeperimental result obtained around 450 K and our theoretical results
at 0 K.
The vibrational frequencies for both trans and cis azobenzenes are
calculated at the HF/6-31G* level. As expected, the lowest vibrational
mode of trans-azobenzene is related to phenyl rotation and its frequency
is only 22 cm(-1).
The calculated energy difference between cis and trans conformers
at LDF-JMW level is 13.5 cal/mol, which agrees reasonably with the
related experimental enthalpy difference of 11.7 kcal/mol in nonpolar
solvent. The corresponding HF/6-31G* result is 17.3 kcal/mol, still
about 5 kcal/mol too high than the experimental enthalpy value.
# Present address : High-Resolution NMR center, V.U.B., Pleinlaan 2, 1050
Brussels, Belgium
Abstract:
Cytochrome c551 is a 80 residue peptide from the extreme
halophilic bacterium Ectothiorhodospira abdelmalekii [1]. It is thought to
be the primary electron acceptor in the photocycle of this bacterium. Here
we present the identification of all secondary structure elements and a
preliminary structure of this cytochrome.
The proton resonances (also these of the heme moiety) of the
reduced form (Fe(II)) were assigned on the basis of 2D DQF-COSY,
CLEAN-TOCSY and NOESY spectra with the PRONTO program [2]. In a first
stage we were able to assign unambiguously 1097 NOE contacts. From typical
medium range NOE's we identified alpha helices between residues 3-10,
16-22, 42-53 and 65-79. The NOE constraints were used to calculate
preliminary structures using the distance geometry program DGII [3].
The alpha helices, identified on the basis of medium range NOE's,
were evidenced by these preliminary structures. This result is in good
agreement with data from the cytochromes c551 from Pseudomonas aeruginosa
and Pseudomonas stutzeri, for which 3D structures are known [4,5].
Additional NOE's, assigned with the help of this preliminary
structures, together with more precise distance restraints from IRMA
calculations should allow us to further refine the structure. A fully
refined structure will allow us to compare it with that of the structure
of the oxidized form and draw conclusions about a possible working
mechanism. The structure of the oxidized form is determined in an ongoing
parallel study.
1. J.F. Imhoff and H.G. Truper, Zbl. Bakt. Hyg., I. Abt. Orig. C 2,228-234
(1981).
2. Pronto/3D, Pronto Software- Development and Distribution, Copenhagen,
Denmark.
3. T.F. Havel, Prog. Mol. Biol. Biophys., 56, 43-78 (1991).
Abstract:
The ground 2A'' and 4A' surfaces for the reaction of NH2 with O
have been characterized by calculating energies, geometries, and frequencies
for all important stationary points connecting reactants with products. The
Gaussian 2 methodology was used for all calculations with further refinement
for transition state properties made by calculating energies using QCISD/
6-311G(d,p) geometries and frequencies. The results predict that, on the
2A'' surface, an H2NO intermediate is formed which is 87.6 kcal/mole below
the separated NH2 + O reactants. This intermediate may either fragment to
form H + HNO or H2 + NO, or undergo a 1,2 hydrogen shift to form trans-HNOH.
This second intermediate may dissociate to either NH + OH or H + HNO, or
isomerize to cis-HNOH, which, in turn, may dissociate into the same products.
The abstraction reaction NH2 + O -> NH + OH was found to have a transition
state 6.7 kcal/mole above the energy of the separated reactants.
Abstract:
Structure-activity relationships (SARs) are methods for predicting properties of
substances from chemical structure information and are playing an increasingly
important role in the field of risk assessment of hazardous chemicals. For
example, SARs can provide data in the absence of experimental values for
prioritisation schemes for toxicity testing and improve testing efficiency.
Ultimately, well-validated SARs would be used in knowledge based information
systems for guidance in hazard and risk assessment procedures. Furthermore
SARs can provide insights into the mechanism of action of toxic substances where
such information is lacking or ill-defined.
This work describes two approaches to prediction of toxicity: the first is based
on artificial neural networks (ANN) which are used to assist in the automated
derivation of new prediction rules. The second method is the identification of
structural alerts (substructures associated with a particular toxicological
endpoint) and relevant physicochemical descriptors (e.g. octanol-water partition
coefficient), based on mechanistic considerations combined with analysis of
databases. These features can then be incorporated as rules into knowledge-based
systems (KBS) capable of recognising chemical structures. The KBS used for our
work is DEREK, managed by LHASA UK, School of Chemistry, University of Leeds, U.K.
ANNs and the KBS approach have been used to investigate the following
toxicological effects: mutagenicity and skin sensitisation.
* ANNs: back-propagation and Kohonen networks - mutagenicity.
The results of the analysis of skin sensitisation and mutagenicity data for
structural alerts and relevant physicochemical parameters will be discussed and
the current state of the knowledge-base for predicting these and other toxicological
effects will be summarised. Potential future directions in enhancing the
knowledge-base will be described.
Abstract:
It is shown that the foundation of the density functional theory (DFT)
is approximate, in general, and invalid for polyatomic systems in electronic
degenerate or pseudo degenerate states. For these systems the main assumption
of DFT that the electron-nuclear interaction may be considered as an external
potential to the electronic subsystem is not valid (even approximately) because
of the special coupling between the electronic and nuclear motions resulting
in their non-separability; the linear vibronic E-e problem is used as an
illustrative example.
Also DFT does not include transition densities and hence it is not
applicable to phenomena and physical magnitudes described by off-diagonal
matrix elements that depend essentially on the interference of two different
wavefunctions. By way of example, the correlation-polarization effect revealed
earlier in the adiabatic approximation calculations for the Li atom is
discussed. Qualitatively equivalent to the admixture of p configurations in
CI calculations (which is not included in DFT), this effect is shown to
contribute significantly to transition probabilities in atoms and to the
understanding of the origin of non-nuclear attractors in the Li2 molecule.
Abstract:
The strong electronic heterogeneity introduced by the d electrons of
the transition metal in the nsnp (mainly 2s2p) organic part of organometallic
(OM) compounds and other transition metal systems (TMS) (e.g. metallobio-
chemical systems (MBS)) makes the existing methods of molecular mechanics (MM),
in general, invalid in application to these systems. The three main specific
features of TMS which are of prime importance in this respect, are [1]:
non-transferability of metal-ligand bond parameters, ligand excitation by
coordination, and vibronic coupling with consequent electron-conformational
transitions (the latter is of special importance to MBS).
The method of modeling TMS we worked out includes these new features
introduced by d electrons and preserves as much as possible the advantages of
simplicity achieved in MM. For this purpose the TMS is divided into fragments,
one of which contains the metal center with minimal possible environment (or
several such fragments in case of multi-center compounds), the others
including the organic part. Then the central fragment is calculated by
a semi-empirical MO-LCAO method with geometry optimization (e.g. from the
ZINDO package [2]), while the ligands and the system as a whole with the fixed
central fragment are optimized by MM. The rules of fragmentation and the
methods of calculation of the consequent interfragment interactions are based
on an earlier publication of one of us [3] and include a double (intrafragment
and interfragment) self-consistent procedure. The interface between
the fragments is realized by means of calculating the charges at the border
atoms (or the density matrices) with the LCAO coefficients from both fragments.
As an illustrative example, Collman's picket-fence porphyrin [4] is
optimized by the new method: the central (iron porphyrin) fragment is
calculated by INDO/1 and the five ligand fragments, as well as the system as
a whole, are optimized by Sybyl [5].
[1] I. B. Bersuker, Electronic Structure and Properties of Transition Metal
Compounds, in press; I. B. Bersuker and R. S. Pearlman, Fifteenth Austin
Symposium on Molecular Structure, The University of Texas, 1994, P5.
[2] M. C. Zerner, ZINDO, Dept. Chem., Univ. Florida, Gainesville, Florida 32611.
[3] I. B. Bersuker, Teor. i Eksp. Khim. 9, 3 (1973) (English transl.: Theoret.
Exp. Chem., 9, 1 (1973)).
[4] J. P. Collman, J. I. Brauman, E. Rose, and K. S. Suslick, Proc. Natl.
Acad. Sci. USA, 75, 1052 (1978).
[5] Sybyl, Tripos Associates, 1699 S.Hanley Road, Suite 303, St. Louis, MO.
63144.
Abstract:
A full geometry optimization at HF level has been carried out for the
fullerene platinum complexes [Pt(PH3)2]nC60 n=1, 2 and 6, and for the
hexasubstituted derivative palladium [Pd(PH3)2]6C60. The computed
geometries are in good agreement with those determined by X-ray
diffraction. When there is just one platinum bound to C60 the binding
energy is found to be 11 Kcal/mol higher than the calculated Pt-ethylene
binding energy. The interaction between the metal and C60 is basically
local. As a matter of fact, the dissociation energy of the first metal
group in [Pt(PH3)2]2C60 is just 2.7 Kcal/mol lower than the dissociation
energy of the Pt(PH3)2 fragment in the monosubstituted derivative. The
total binding energy of the six platinum groups in [Pt(PH3)2]6C60 has
been computed to be 178.5 Kcal/mol (29.7 kcal/mol per group). An
important charge transfer from the metal group to the C60 core has been
detected, about 0.5 e for the monosubstituted derivative and 2.2 e for
the hexasubstituted platinum complex. The Pd(PH3)2 group has been
determined to be more labile than the corresponding platinum group.
The M-C60 bond strength is noticeably weakened if the complex is
reduced. Hence, the loss of C60- from [Pt(PH3)2]2(C60)- is
12.5 Kcal/mol more favorable than the loss of C60 from its neutral
partner.
Abstract:
The possibility of addressing the question of hydrogen bond
strength by means of isotope effects is explored theoretically using
intramolecular hydrogen bond of 3-carboxy-4-hydroxy-1,2-benzisoxazole
as a model. Calculations are carried out using AM1 and PM3
Hamiltonians and COSMO solvent model for decarboxylation of this
compound. Kinetic isotope effects of hydrogen strongly increase with
decreasing solvent polarity while for heavy atoms the differences between
isotope effects calculated for low and high polarity are small (for eps=2.0 to
eps=80.0).
Abstract:
Continuing in our investigations of the pericyclic reactions of phosphaalkenes
and phosphaalkynes, we report an ab initio study of the Diels-Alder reaction of
phosphaethene and phosphaethyne with butadiene. Limited experimental studies of
these reactions indicate that they are quite facile, however, no determination
of activation energies or stereoselection has been reported.
We have optimized the structures of the reactants, transition states, and products
for Reactions 1-3 at the HF/6-31G* and MP2/6-31G* levels. Single point energy
calculations at MP4SDQ/6-31G*//MP2/6-31G* were performed to correct for the
underestimation of activation energies at MP2. ZPE correction were made using the
HF/6-31G* analytical frequencies scaled by 0.89.
(Aqui hi va una figura. Si la vols veure conectat al servidor del congres. cb)
These reaction are exothermic, ranging from -39.0 kcal/mol for Reaction 1 to
-43.1 kcal/mol for Reaction 3. The activation energies for all three reactions
are small -- Reaction 1, 19.3 kcal/mol; Reaction 2, 13.0 kcal/mol; Reaction 3,
15.50 kcal/mol -- considerably less than their hydrocarbon analogues. The low
activation energies are due to the very reactive P=C bond, as evidenced by its
high HOMO and low LUMO.
The reaction of phosphaethene display regioselectivity. The orientation with the
phosphorus lone pair exo is favored, both kinetically and thermodynamically. This
orientation reduces the lone-pair pi-system interaction. The geometry of the TSs
shows a twisting of the phosphaethene fragment to minimize this interaction in both
TSs. This regioselectivity is similar to that found for the reaction of butadiene
with formaldimine.
Topological electron density analysis was used to gauge the bond orders in the TSs.
As we have found for a number of pericyclic reactions involving heteroatoms, the
TSs examined here display a remarkable degree of synchronicity. Further, bond order
appears to be conserved during the course of the reaction.
Abstract:
Clustering methods play an important part in the selection of compounds from chemical
databases for both purchase and biological screening. These clustering methods
usually rely on descriptors which encode the structural features of the molecules in
the databases. Structural descriptors allow the similarities of pairs of molecules
to be calculated from the co-occurrence of these features. Clusters may then be
assembled on the basis of the similarity measures. A number of methods exist
within commercially available database searching software to produce these descriptors.
In this paper the relative merits of some of these descriptors, which
variously describe the two-dimensional and three-dimensional content of molecules, are
examined. Two commercially available clustering algorithms are also compared. All
comparisons are based on the ability of the methods to produce sets of clusters
in which biologically active and inactive structures do not occur in the same clusters.
Abstract:
The gas-phase nucleophilic attack of the hydroxyl ion on the carbon
atom in the carbonyl group of the beta-lactam ring was studied by using
the PM3 semi-empirical and ab initio methods.
It is well known that the presence of solvent molecules can alter
considerably the potential-energy surfaces of reactions involving
charged products and intermediates. To quantitatively asses the effect
of the solvent on the reaction studied, we used two different models:
the AMSOL (a model dealing with the solvent as a continuum) and the
super-molecule approach (surrounding the system with 20 water
molecules
+ Centro Svizzero di Calcolo Scientifico (CSCS), Via Cantonale,
CH-6928 Manno, Switzerland
Abstract:
The electronic structure of bond-centered hydrogen and muonium in
silicon and diamond crystals has been calculated using clusters of
various sizes containing up to 44 host atoms.
The potential energy surface around the hydrogen and the hyperfine
coupling constants (hfcc) have been calculated using the configuration
interaction (CI) and density functional methods (DFT). Averaging the
hfcc over the spread of the probability distribution for proton and
muon the residual isotope effect was found.
The values are compaired to other results and are found to agree well
with experimental data obtained by uSR expriments.
Abstract:
Distribution Biased Monte Carlo (DBMC), a recently developed
efficient conformational sampling method [1], is extended here to
all-atom potentials. The method is used to conformationally sample the
lipid head group molecule, Glycerolphosphatidylcholine (GPC),
using sampling functions constructed from the CHARMM parm22
force-field [2]. Additionally, Langevin Dynamics (LD) simulations
of 50 ns each at collision frequencies of 2, 5, 10 and 25 ps-1 were
carried out with the same potential. The conformational populations
were examined through evaluation of the joint potentials of mean force
for the 6 pairs of adjacent backbone torsions. Convergence of the
torsional densities was analysed using the concepts of conformational
similarity and statistical inefficiency.
The LD simulation which had the highest transition rates and
fastest convergence of torsional densities was, somewhat surprisingly,
that carried out at the lowest collision frequency. GPC exhibited
significant flexibility in its backbone torsions and moved between
limited regions of high occupational probability in the joint
potentials of mean force. Backbone torsions were strongly coupled
to each other and numerous concerted transitions were observed.
The inherent flexibility in GPC is consistent with the notion of
an entropic driving force for dissolution of an individual lipid
molecule from the membrane phase into solution.
DBMC sampling functions were constructed based on 1) adiabatic
potentials constructed from energy minimization of single torsion
fragments and, 2) potentials of mean force from LD simulations of the
same fragments. However, due to strong local electrostatic
interactions, the single torsional potentials of several torsions
were inefficient sampling functions; better performance required
the use of conditional distributions. Using a segmental sampling
procedure consisting of 1-, 2-, and 3-torsion moves, the DBMC simulations
were able to closely reproduce the potentials of mean force
obtained from 200 ns of LD, and did so with significantly greater
efficiency. Residual differences are attributed to the neglect
of bond-angle flexibility in the MC procedure. The latter problem can be
overcome by either compensating for fixing angles in the parametrization
of the MC force-field or by the incorporation of bond-angle sampling
functions in the MC procedure.
References
1. B.J. Hardy and R.W. Pastor, J. Comp. Chem., 15, 208 (1994).
2. Alex D MacKerell Jr. and Michael Schlenkrick.
Abstract:
The pi* <- n transition of acetone is known to be strongly solvent
dependent [1]. In particular, blue shifts are found in polar solvents, such
as water, and red shifts in nonpolar solvents, such as tetrachloromethane.
Computation of solvent-induced shifts of electronic transitions require a
quantum mechanical description of at least the chromophore. The
surroundings will necessarily have to be described at a classical level.
The solvent models developed over the last decade have proven useful in
many cases but have failed in the computation of red shifts.
This failure is due to the fact that the red shifts are a result of
dispersion interactions between solute and solvent, and these are not
included in the solvent-solute interaction Hamiltonian. This is true for
both dielectric and explicit solvent models, although the dielectric model
was recently improved in this sense [2]. The explicit solvent models [3]
fail because electronic polarisabilities are accounted for in an average
sense only and are not described explicitly.
Our direct reaction field (DRF) solvent model [4] does, however, contain
explicit electronic polarisabilities on explicit solvent molecules.
Moreover, it gives a dispersion energy estimate, based on the second order
dispersion expression for interacting polarisabilities, requiring as input
parameters the mean excitation energies of solute and solvent [5].
With our solvent model the solvent-induced pi* < - n blue shift in
water as well as the red shift in tetrachloromethane were successfully
calculated, but only by treating the first solvent shells explicitly (26
surrounding solvent molecules were added to the quantum mechanically
treated acetone molecule). The dielectric-only solvent model failed for
both water and tetrachloromethane when applied consistently.
[1] W.P. Hayes and C.J. Timmons, Spectrochim. Acta 21, 529 (1955)
[2] N. Roesch and M.C. Zerner, J. Phys. Chem. 98, 5817 (1994)
[3] J. Gao and X. Xia, Science 258, 631 (1992)
[4] P.Th. van Duijnen, A.H. Juffer and J.P. Dijkman, J. Mol. Struct
(Theochem) 260, 195 (1992)
[5] B.T. Thole and P.Th. van Duijnen, Theor. Chim. Acta 55 307 (1980)
Abstract:
An analysis of the classical dynamics of unimolecular reaction will be
presented, focussing on two and three mode models of the dissociation
of hydrazoic acid, HNNN, along the central N-N bond. Previous work by
our group on a fully-dimensional model of this reaction indicates that
the reaction occurs via specific dynamics for several vibrational
periods on the approach to the transition state. During this time,
the phase of the HNN-N stretch is carefully correlated with the
approach of the HN-NN stretch to its last inner turning point before
reaction, producing large-scale, impulsive energy transfer into the
reactive mode from the HNN-N stretch. Our two-mode model of this
reaction, which contains the HN-NN and HNN-N stretches, reproduces the
essential behavior of the six-mode model, indicating that only those
two modes are necessary for reaction. Examining the phase space of
the trajectories just prior to crossing the transition state reveals
that all trajectories enter a "reactive cylinder", as described by De
Leon and coworkers, which leads through a region of large coupling and
thus produces the impulse of energy into the reaction coordinate.
Viewed in reverse time, the path of the cylinder as it leaves the
transition state is governed by the near-adiabaticity of the reactive
mode during the last half-vibrational period before reaction,
producing a convergence of phase in the non-reactive HNN-N stretch.
Our study of the three-mode model of this reaction, which includes the
H-NNN stretch, reveals that there is no such constraint on the motions
of the H-NNN stretch.
(+) Departament de Qumica Fsica, Facultat de Qumica, Universitat de Barcelona, C/ Mart i Franqus 1, 08028 Barcelona (Spain)
Abstract:
A comparative and systematic study of the chemisorption of
alkali metals, Li to Cs, on diferent sites of the Si(111) surface has
been carried out using an ab initio cluster model approach. Several
tools of analysis of the nature of the bond have been used. These
techniques include the analysis of the energetic of the interaction by
means of the Constrained Space Orbital Variation, CSOV, method , the
analysis of the ionicity by means of the dipole moment curves and their
CSOV decomposition and the analysis of the SCF wavefunction. In this
later case we have used a projection technique which, starting
from a purely ionic picture, permits to obtain the contribution of this
ionic wavefunction to the cluster SCF wavefunction.
In all cases we have found a highly ionic bond with a small
participation of covalent effects to the interaction energy which
ranges from 20 % for chemisorbed Li to less than 10% for Rb and Cs.
We show that the dipole moment for chemisorbed alkali metals is smaller than the one expected from an
ionic bond because of the substrate polarization. Consequently we argue
that changes in the measured work function are not adequate to extract
information about the ionicity of a given interaction. This is in
agreement with previous works considering a metal substrate. Here, we
show that the same mechanism holds for semiconductor surfaces as well.
Abstract:
An approach called the Hypersurface Iterative Projection
(HIP) method uses 3-D computer graphics to extrapolate from
existing structure-activity relationship (SAR) information
to new synthetic targets. By updating the SAR data set at
each stage of a molecular design project, regions of
parameter space worth exploring can be identified. The
method can also show when all of parameter space is
reasonably well filled to the extent that synthetic
chemistry allows.
The method will be illustrated for improving the biological
activity of bicyclic pyrazolidinones. This is a class of
synthetic antibacterial agents in which the beta-lactam
ring of carbapenems is replaced by a five-membered
pyrazolidinone ring. Lipophilicity and electron-
withdrawing properties of the substituent on the 3 position
are shown to strongly influence minimum inhibitory
concentrations (MIC).
The HIP method can also be used to analyze other
multidimensional data. The dependence of one property on
two or more descriptors can be determined visually. The
method provides a way of rationally using existing data to
decide what further information to acquire. Unlike many
prior quantitative structure-activity or structure-property
approaches that are used for post facto analysis of static
data sets, the HIP method is intended to be used
dynamically while new compounds are still being made in a
series.
Abstract:
The Raman spectra of three triphenylmethane dyes (Crystal Violet,
Malachite Green, Parafuchsine) have been calculated with the PM3
Hamiltonian. The calculated normal coordinates are displayed
graphically. The use of these pictures, as well as the symmetry and
frequency data from the calculation, allows to assign the bands in
the experimental spectra to calculated normal vibrations.
This combination of experiment and theory helps to explain several
features of the spectra.
Abstract:
In the fluorescence spectra of para-Dimethylaminobenzonitrile (p-DMABN)
in solvents of medium polarity two emission bands are observed.
While the higher energetic band shows almost no dependence on the
solvent polarity, the other band at a larger wavelength has a large
solvatochromic shift. This is indicative for the emission from an
excited state that has a large dipole moment.
Usually this behaviour is explained by the so called TICT-model.
In contrast, our self-consistent reaction field studies, using
the semi-empirical program package VAMP, suggest a novel
interpretation of dual fluorescence.
Abstract:
A new Software Toolkit, based on the SPROUT program, is under development.
It is an interactive system that assists the chemists in several steps of
the structure based rational drug design process. The system is modularised
and offers automatic methods for solving a number of problems in drug design.
However, the user maintains control and is able to guide each module and
modify its decisions as required. Six modules of the Toolkit are described
below. Each module name is an acronym and (sometimes misspelt) animal name.
The module CANGAROO detects potential binding pockets of protein
structures by detecting large inward-facing regions in the solvent-accessible
surface of the protein.
HIPPO identifies favourable hydrogen bonding and hydrophobic regions
within a binding pocket. The hydrogen bonding sites are directional and
are used to define target sites for the position of potential ligand atoms.
The module ELEFANT will select functional groups and position them at
the target sites to form starting fragments for structure generation.
SPIDER generates skeletons that satisfy the steric constraints of a
binding pocket by growing spacer fragments onto the start fragments
and then connecting the resulting part skeletons together.
MARABOU substitutes hetero
atoms into the skeletons to generate molecules with the electrostatic
properties that are complementary to those of the receptor site.
Finally, ALLIGATOR will cluster and score the solutions to provide the
user with an efficient tool for evaluating and navigating through the results.
The capability of the system for generating thought provoking ideas
is demonstrated by examples.
Abstract:
The bonding and electronic structure of an electron-deficient solid
Na1.9Cu2Se2Cu2O are analyzed with the extended H ckel tight-binding method.
This solid consists of three kinds of layers: a Cu2O layer with square-
coordinated oxygen atoms, an anti-PbO type Cu2Se2 layer, and a cationic Na layer.
The Cu2O layer has a closed-shell electronic structure, whereas the Cu2Se2 layer
needs two more electrons per Cu2Se2 to complete a closed-shell configuration.
Thus charge transfer takes place mainly from the Na layer to the Cu2Se2
layer. The holes created by the incomplete occupancy at the Na sites reside in
the Cu2Se2 layer.
(2) Department of Chemistry, Princeton University Princeton, NJ 08544
Abstract:
Derivatives of vibrational frequencies are calculated with respect to molecular
mechanics force field parameters, and with respect to atomic Cartesian coordinate
displacements. In the former case the implicit dependence of the minimum-energy
configuration upon the parameters is accounted for. The frequency derivatives
require the availability of third derivatives of the force field with respect
to atomic Cartesian coordinates, and these have been obtained analytically.
Application is made to a small and a moderate sized molecule as illustrations
of the frequency derivative capability. A principal components analysis is
performed for each structure, and for each type of derivative, thereby
identifying the most important parameters and atomic displacements. The
results are interpreted in terms of molecular size, the localized nature of
specific vibrational modes, and interactions known to be important in
producing realistic molecular force fields. Implications of the findings for
molecular mechanics and vibrational spectroscopy are discussed.
Abstract:
We have implemented extensions to the Brookhaven Protein Data Bank
(PDB) file format for incorporating scene information such as
viewing parameters, additional molecular information (e.g., van
der Waals radii and atom colors) and user-defined graphics. These
extensions were made in conformance with the PDB standard and
provide sufficient information to render the scene in various styles
such as space-filling images and ribbon diagrams. For the past
five years these extensions have been used in the MidasPlus molecular
modeling system and have proved both powerful and sufficient for
generating complex molecular images. We propose that the extensions
to the PDB presented here be adopted by the molecular modeling
community for incorporation into visualization programs.
Abstract:
We describe an effective Hamiltonian for an electronically
excited molecular ion embedded in a neutral cluster. The model uses
ab-initio electronic eigenfunctions for several states of the isolated ion
as basis functions for the effective Hamiltonian; matrix elements of
the ion-cluster interaction potential are expressed in terms of
distributed charges on the cluster and distributed multipoles on the
ion. The model is applied to excited ICl- ions in CO2 clusters, and the
results are compared to experimental data from W. C. Lineberger and coworkers.
Abstract:
AM1 calculations have been performed to gain insight into the
thermal racemization process of hexa- and octahelicenes.
For octahelicene a symmetrical (mirror plane) transition state
was found. Starting from this point IRC calculations gave a series of
intermediate structures between TS and the two enantiomeric
helices.
From these structures an MPEG movie has been constructed, and
a file with z-matrices which can be loaded into a local
molecule viewer.
Apart from the visualization of the process the paper gives an
analysis in terms of torsional angles.
For 1,16-dimethylhexahelicene the racemization follows a similar
path; the methyl groups have the same steric effect as the extra
benzene rings. However, the thermodynamic data are different, the
entropy contribution in particular.
An attempt was made to compute the entropy contribution to the
total energy, for structures on both sides of the symmetrical
structure in which one methyl group is more or less stuck
under the opposite part of the helix.
No conclusive result could be obtained, so I would like to
sollicit comment on this part.
A preliminary poster can be accessed through Henry Rzepa's
compilation of hyperactive molecules, #14.
Abstract:
A semiempirical AM1 theoretical study was carried out to examine the very low
reactivity of thiophene, on the one hand, and high reactivity of thiophene
1-oxide as a diene in Diels Alder reactions. The reactivity of cyclopentadiene,
thiophene, thiophene 1-oxide, and thiophene 1,1-dioxide was studied as a diene
in reaction with ethylene, cyclopropene, and benzoquinone. Ethylene was chosen
as a standard while cyclopropene with its high strain energy released in the
course of a reaction making it relatively reactive. The benzoquinone has a lower
LUMO energy that make it very reactive dienophile for the Diels-Alder reaction.
Frontier molecular orbital energy gap between the reactants was considered, and
the disadvantage of this approach in studying the reactivity was demonstrated.
For all combinations the corresponding transition structures are generated and
the activation energies are estimated. The estimated activation barrier for
sulfur dioxide elimination from the adduct was used to explain the failure to
accumulate the cycloadduct in the reaction mixture. The obtained results are
compared with experimental data when available. An excellent agreement of
theory and experiment was obtained.
Abstract:
AM1 semiempirical method was used for theoretical searching of activation of
thiophene as diene for Diels-Alder reaction. The reactivity of thiophene, electron-withdrawing and electron-donating substituted thiophenes, as well as S-methylthiophenium ion were studied as diene for Diels-Alder reactions by
evaluating their frontier orbital energies and by calculating reaction
barriers with activated and deactivated dienophiles. It was demonstrated
that slight activation of thiophene ring can be obtained with both
electron-donating and electron-withdrawing groups attached to the thiophene
ring. It was predicted that the actual transformation of thiophenes into
corresponding S-methylthiophenium anions is the best means of activating
the thiophenes. The calculated activation energies for normal (nonactivated)
dienophiles are moderate so mild reaction conditions are predicted. If
dienophiles are activated with electron-donating substituents, AM1
calculations predict a two step cycloaddition reaction with a very small
activation barrier.
Abstract:
Transition structures for azide anion 1,3-polar addition to hydrogen cyanide,
formaldimine, nitrogen, cis- and trans-diazene, ethylene, and
acetylene were obtained at the MP2/6-31+G* theoretical model. The additions
can be divided into two groups: addition to triple bond giving rise to an
aromatic heterocyclic product and addition to double bond forming a
non-aromatic product. All transition structures correspond to a concerted
mechanism for the polar cycloaddition. Symmetrical dienophiles, except
cis-diazene, give rise to synchronous transition structures. The
anomaly is explained in terms of strong n-n repulsion of the reactants in
the transition structure. The reactivity of the compounds can be
rationalized in terms of the bond orders of the newly forming bonds, from
the frontier orbital energy differences and the charge transfer from the
azide anion to the dienophile. Quantitative correlation of the reactivity
was judged on the basis of the activation energies of the reactions
calculated at MP2/6-31+G* and MP3/6-31+G*. It was predicted that the
addition of azide to nitrogen is the slowest, while the additions to
hydrogen cyanide and acetylene are with the lowest barriers, in agreement
with literature data.
Abstract:
An ab initio theoretical study of the reactivity of tetrazole tautomers,
on the example of the ethylene cycloaddition reactions, was undertaken. The
geometries of the reactants, the transition structures, and the products for
the three tetrazole tautomers were generated at RHF/3-21G*, RHF/6-31G*, and
MP2/6-31G*. The energies were evaluated up to the MP4/6-31G*//MP2/6-31G*
level. The relative stabilities of the tetrazole tautomers were studied,
and their relative reactivity were predicted from their frontier molecular
orbitals (FMO), the charge transfer between the reactants in the transition
structures, the extent of the reaction calculated from the bond orders, and
electronic location of transition state calculated from fraction of the
overall charge transferred in the transition state. It was demonstrated
that FMO and the charge transferred in transition states are not reliable
methods for evaluation of relative reactivity of tetrazole tautomers.
However the percentage of charge transferred, and percentage of reaction
advance can be useful in the case when energies of reactants and products
are available. The calculated activation energies predict that the most
reactive tetrazole tautomer is one that is not aromatic (1T) while the
least reactive is aromatic aromatic tautomer (2T). It was predicted that
the cycloaddition reaction with tautomer 1T is experimentally
achievable but other side reactions with either tautomer 1T or the
cycloadduct product might prevent the accumulation of the primary
cycloaddition product in the reaction mixture.
Abstract:
The geometries of cis and trans-nitrosoethylene and their O- and N-borane
complexes were optimized with the RHF/6-31G* and MP2/6-31G* theoretical model,
while the transition states and products with RHF/6-31G*. On all species
involved in the reaction the energy was evaluated up to the MP3/6-31G* level
at the RHF/6-31G* geometries. The stability of the geometric isomers of
nitrosoethylene and their borane complexes were evaluated on the basis of
their total energies and by comparing the bond orders. The reactivity is
discussed in terms of frontier orbital energies, bond orders in the
reactants and the transition states, charge transfer from ethylene to
nitrosoethylene moiety in the transition states, and activation barriers.
It is predicted that the reaction is inverse electron demand Diels-Alder
cycloaddition and borane as a catalyst has a profound influence. Because
the predicted activation energies are small the borane catalyzed reaction
should be experimentally feasible
(2) Laboratory of Medicinal Chemistry, Developmental Therapeutics Program, Division of Cancer Treatment, National Cancer Institute, NIH, Bethesda, MD 20892
Abstract:
We have recently described the creation of a searchable 3D database of
over 400,000 structures ( Milne, GWA, et al. J. Chem. Inf. Comput. Sci.,
in press, 1994) from connection tables that have been collected in the NCI Drug
Information System. There were several aspects of that build that we felt could
be improved and in this presentation we will describe the improvements and their
application to the 17229 compounds registered at the NCI since our first build.
One problem in the first build was the inability to handle
organometallic compounds. The program we use, Chem-X ( Chemical Design ),
allows user modification of parameter and build libraries so we attempted to use
this approach to build platinum compounds. The approach allowed us
to successfully build 3D structures for about 80% of the platinum compounds, but
the work involved makes it hard to justify using this approach to include many
more elements.
In the first build there was no capability to build rings with more than
seven members. This problem was handled by passing the compounds that failed
the Chem-X build to the CONCORD 3.0 program. Chem-X built 95.1% of the
structures in the update with valid connection tables, somewhat less than the
96.5% success rate in the first build. CONCORD 3.0 was able to build 87% of the
compounds that failed, giving us an overall success rate on the update build of
99.4%.
In the first build, approximately 6% of the 3D structures were found
to be effectively unsearchable in the conformational analysis and keying step.
The reasons for these failures were about evenly divided between an upper limit
of 15 rotatable bonds imposed on the structures and the failure to find a
conformation that passed the Chem-X rules. In the first case, we implemented a
random conformational search for very flexible structures and increased the
maximum number of rotatable bonds to 99, thus exluding only 0.04% of the
compounds in the update database. In the second case, we implemented a small
pre-key conformational search in order to find a better starting point for
the full conformational search. In our update database this resulted in
only 0.5% of the structures having no conformations that pass the Chem-X rules.
We have searched the update database with a pharmacophore for
Protein Kinase C binding based on phorbol. An analysis of the hits of this
search suggest that the improvements described above also improve the
quality of the databases searches.
Abstract:
A novel method, based on genetic algorithms, has been developed and applied
to the solution of differential equations. The new approach is based on the
use of real numbers to form the candidate solutions which are improved
iteratively by a suitable breeding process. The algorithm was tested in the
calculation of the bound states of a double well potential and
in the nonlinear density functional calculation.
Comparison of the results with those obtained using
the direct relaxation method shows excellent agreement.
Abstract:
In this paper we present a method for locating transition states and
higher-order saddles on potential energy surfaces using
double-ended classical trajectories. We then apply
this method to 7- and 8-atom
Lennard-Jones clusters,
finding one previously unreported
transition state for the 7-atom cluster and two for the 8-atom
cluster.
Abstract:
Ab initio Perturbed Ion cluster-in-the-lattice calculations are
done to determine the local properties of Cu(+)-doped alkali halides.
In those calculations the crystal is divided into two separated
regions: (a) the cluster containing the impurity, for which the
electronic structure is self-consistently solved; and (b) the lattice,
that contains the rest of the crystal, represented by a rigid
wavefunction obtained from a previous Hartree-Fock calculation on the
pure host.
We first examine the results of several models of Cu(+):NaF having
from 7 to 33 ions in the cluster region. When substituting Na(+), the
Cu(+) ion induces an inward relaxation on the nearest-neighbor (nn)
shell. The 7-ion model predicts an exaggerated relaxation,
significantly larger than the other models, evidencing the danger of
allowing a geometrical movement of the ions that lie in the frontier
between the cluster and the lattice.
To avoid those undesirable frontier effects, a large model,
containing 179 ions in the cluster region, is used to predict the local
geometry and stability of Cu(+) in nine alkali halides (AX; A=Li,Na,K;
X=F,Cl,Br). Up to four shells of neighbors are allowed to relax around
Cu(+). To prevent systematic errors, models of Cu:AX and A:AX are
simultaneously solved. Our results show qualitatively different nn
relaxations depending on the cation being substituted. Negligible or
very small inwards relaxations are found on Cu:LiX, large inwards
relaxations around -0.1 A are encountered on Cu:NaX, and very large
relaxations of about -0.3 A are predicted for Cu:KX. The nn relaxation
on Cu:NaCl is predicted to be -0.10 A, in excellent agreement with
recent EXAFS measurements. These results largely separate from "common
wisdom" usually based upon Pauling's ionic radii, but are in qualitative
agreement with topological Shannon's radii.
Finally, the resonant vibrations of Cu(+) and its first four shells
of neighbbors in NaF have been determined by numerically computing the
138 independent Oh force constants. The 179-ion model of both the
impurity center and the pure host have been examined concurrently,
and, from the comparison between them, we have determined that the
only modes truly characteristic of the impurity center are the lowest
a1g, eg, and t1u vibrations. These results are discussed in relation
with the experimental visible and UV spectra of Cu:NaF.
Abstract:
In this contribution we discuss two techniques for determining
interionic potentials (IP's) from quantum-mechanical descriptions of
ions in crystals. The first one is based on the use of the energy
expressions supplied by the Theory of the Electronic Separability
(TES), as implemented in the ab initio Perturbed Ion (aiPI) model.
The second one relies on the aiPI ionic electron densities and uses
the Electron Gas (EG) theory of Gordon and Kim to generate the IP's.
The many body contributions to the energy of ionic solids mainly
arise due to the changes of the electronic densities in passing from
the gas-phase to the crystal. For the TES based IP's we have recently
shown that this terms can be meaningfully separated into pairwise
contributions and straighforwardly incorporated in the pairwise part
of the IP's. Regarding the EG model based IP's, the many body
contributions can be neglected or modeled by means of a term that
explicitly depends on the crystal geometry. In the first case, the
pairwise part of the IP's are crystal geometry independent (rigid).
In the second case, the IP between a pair of ions, say A and B,
depend both on their relative separation and the geometry of the
crystal. These IP's are called relaxed.
We have applied the EG model and the TES strategies to generate IP's
for several test crystals, including halides and oxides. Their
relative merits are explored by computing the crystal energy, static
equation of state, and elastic behaviour using pairpot3, a fortran
code that allows of the use of very general forms (numerical or
analytical) of the potentials.
Abstract:
We have used molecular modeling to investigate the enantioselective separation of the unsaturated hydrocarbon alpha-pinene on permethylated beta-cyclodextrin. Using the CVFF forcefield from Insight/Discover, we have carried out molecular dynamics and systematic rigid- body docking grid searches on each of the optical antipodes of alpha-pinene interacting with permethylated beta-cyclodextrin. Both methods show an energy difference in the binding of the (+) and (-) enantiomers of less than 1.0 kcal/mol, with the (-) enantiomer binding more favorably. This result corresponds well with experimental results. In this paper we discuss the nature of the interactions that lead to the differential energy of binding.
Abstract:
Recently, Roterman et al. [J. Biomol. Struct. Dynam. 7, 421 453 (1989)] have
determined the PHI PSI maps of N-acetyl-N -methylalanineamide (blocked single
residue of Ala) to compare three force fields: CHARMM, AMBER, and ECEPP/2.
However, with the publication of many other force fields and commercial
molecular modeling software, there is a need to extend this evaluation. We
have used the Insight/Discover force fields (CVFF, CFF91, and AMBER), the
HyperChem forcefields (MM+ and BIO+), and the SPARTAN forcefields (Sybil,
MM2, and MM3) to determine and compare the phi psi maps of blocked Ala of
these various forcefields. We have used these maps to calculate the
characteristic ratios of poly-L-alanine using a modified Flory method.
(2) Dept. Pharmacology, School of Medicine, Iran University of Medical Sciences, Tehran, IRAN
Abstract:
Dopamine-beta-hydroxylase (DBH) is a very important enzyme in the
biosynthesis of norepinephrine and epinephrine, which are very potent
neurotransmitters in the regulation of many biologically essential processes
like blood pressure. So, inhibition of DBH seems to be an effective approach
to control of hypertension.
Phenyl-propene and its substituted analogues are among the best known
mechanism-based inhibitors of this enzyme. Two mechanisms have been proposed
for the inhibitory effect of these agents; one of them suggests for a cationic
intermediate and the other for a radical one. Both mechanisms involve a
reactive intermediate which bounds covalently to the enzyme molecule and tends
to inhibition of DBH.
The inhibitors were constructed graphically by the use of PCMODEL (Serena
Software) on a DOS-based PC. The structures were minimized energetically using
the MMX subroutine implemented in the program. In the next step these molecular
mechanically-optimized geometries were introduced to MOPAC 6.0 (QCPE), running
on a VAX 6000 computer. The corresponding radicals and cations were defined by
deletion of the appropriate hydrogen from parent structures and assigning the
relevant charge to them. The PM3 method was used for geometry optimizations and
energy calculations.
The differences between the energies of parent structures with their
intermediates was used as a measure of evaluation of suggested mechanisms for
DBH inhibition. Our results suggest that the radicallic intermediate is
energetically more stble and therefore it seems that the radicallic pathway is
the prefered mechanism for DBH inhibition.
QSAR analysis of the structures with the classic and our self-defined
parameters show that there is a high correlation (r > 0.90) between biological
activity and hydrophobicity of molecules. The obtained results have been
interpreted on the basis of experimental and biological evidence.
Abstract:
A non-empirical all-electron SCF method is presented which exploits an
Atom-in-Molecule picture and allows for a localized treatment of large and
extended systems. The method is derived by projecting out atomic
(single-centered) subspaces from within a molecular or periodically
extended system and iteratively solving perturbed atomic-like subsystems
until a self-consistent Atom-in-Molecule picture is obtained. The
partitioning leads to a familiar non-local energy-dependent pseudopotential
formalism, but the use of a pseudometric and truncated (renormalized)
pseudoeigenfunctions keeps the problem energy-independent and locally
tractable.
This localized approach enables the use of self-consistently derived
single-center effective atom potentials that are then used in the
inter-atomic Coulomb interactions which reduces the N**4 multi-center
two-electron Coulomb integrals to less than N**2 two-center one-electron
integrals. The universal form of the effective atom potentials are based
on the analytic solution to a generalized Thomas-Fermi model. Further use
of projection techniques likewise reduces the inter-atomic exchange to a
non-local expression involving only two-center one-electron integrals.
This reduction to two-center one-electron integrals allows the entire
method to be based on STO's.
To properly treat embedded atomic-like subsystems, a statistically based
Grand Canonical Unrestricted Hartree-Fock (GCUHF) formalism is employed,
which permits the use of fractional occupation numbers and the flow of
electrons between subsystems. The occupations are determined
self-consistently within a chemical potential equalization procedure.
Due to the Atom-in-Molecule nature of this method, an Alternating Spin
Valence Bond (ASVB) approach is taken in defining the initial molecular
state from constituent atomic states. This allows for proper separation in
bond breaking and offers a unique approach to understanding non-alternate
or unconventional spin systems and diabatic state representations.
This approach is outlined for surface chemisorption, but its application
to polymers, solvation, and other extended systems can also be discussed.
Abstract:
A computer aided modelling study was undertaken on agonists and antagonists acting at the rho1 protein. The rho1 protein has been cloned from the retina and forms an homooligomeric GABA receptor which regulates chloride channels. This receptor is distinct from the GABAa and GABAb receptors as it displays insensitivity to both bicuculline and baclofen. As a result, it is one of the receptors that was classified as GABAc receptors. The most potent agonist and antagonists for the rho1 receptor is TACA and 3-APMPA respectively. Due to the competitive nature of the antagonism the volume where the rho1 agonists and antagonists bind is probably common, centring on the amino group because this moiety is common to both the agonists and antagonists. The gamma-carboxylic acid or its bioisosteric replacements bind to different loci in the homooligomeric GABA receptor. Our studies indicated that the binding of the antagonists was dependent on the orienation of large hydrophobic side-chains. Studies also showed that activity was dependent upon the charge at the acidic and basic groups of the active compounds.
Abstract:
An initial study [1], considered the nonlinear resonant interaction resulting
from kinematic coupling between the torsional mode and other modes in
sequentially bonded ABBA type tetra-atomic molecules. It was found that the
nonlinear resonant interactions were most likely to involve the symmetric
bending mode.
In order to facilitate a quantum study [2] of the nonlinear resonance between
the symmetric bend and torsion modes a reduced dimensional model was employed.
The low dimensionality of the system also makes it amenable to the methods used
commonly in the study of ergodic properties of nonlinear classical dynamical
systems [3] e.g. surfaces of section, phase space plots. The rate of torsional
isomerization is compared to the prediction of Transition State Theory, and
related to the observed intramolecular vibrational energy redistribution (IVR).
The dependence of the nonlinear resonance on the relevant kinematic terms in the
Hamiltonian is clearly demonstrated in both the quantum and classical studies.
While the mechanisms for the nonlinear resonance is essentially the same, the
exact frequency matching required, and strength and timescales of the resulting
energy transfer can be significantly different. The extent to which classical
studies of IVR can be used to make quantitative predictions will be discussed.
REFERENCES
[1] H. W. Schranz and M. A. Collins, J. Chem. Phys. 98
(1993) 1132.
[2] M. A. Collins and H. W. Schranz, J. Chem. Phys.100
(1994) 2089.
[3] H. W. Schranz and M. A. Collins, J. Chem. Phys.101
(1994) 307.
Abstract:
The Isoinversion principle, based on the Eyring theory, is a very general
selectivity model that can be applied to various types of selectivity.
It takes into account the changes in selectivity depending on
temperature or pressure, respectively. By calculating the isoinversion
temperature of a reaction class, the synthetic chemist obtains a good
starting point for the optimization of the examined reaction.
In order to support chemists in applying the Isoinversion principle, we
are currently developing a computer system that will perform the
necessary calculations and serve as a database for experiment data. We
intend to use the WWW as an interface to the system, thus allowing
chemists from various places to share their findings.
Abstract:
Recently, we investigated with the DFT method the electronic and vibrational
properties of Aluminium and Lithium carbonyl complexes which were observed
in matrix isolation experiments.
A rather good agreement was obtained between the experimental and calculated
vibrational spectra.
On the contrary, the MP2 and MP4 calculations carried out on MCO and M(CO)2
(M= Al, Li) predicted wrong binding energies by nearly 10 Kcal/mol, and were
not able to reproduce the experimental vibrational spectra.
The DFT calculations on Bn(CO)m species (n,m = 1,2) give results which are
completly different from the MP2 ones and are better in line with the
experimental results.
Abstract:
A 3 * 3 * 3 cubic grid of oxygen atoms has 54 internal bonds
and this can be an idealised model of a completely hydrogen bonded water
cluster (H2O)27. A combinatorial study gave 456 distinct isomers
of such ideal structures, each of which should have similar energies.
Computer simulation of (H2O)27 with a realistic intermolecular
potential has produced such structures with energies of -237 kcal/mol.
Similar cubic structures, but with a few external O-H bonds have also
been found and these have the slightly lower energy of -241 kcal/mol.
Pictures, hyperactive molecules and graphs
will be provided with the paper.
Abstract:
Several 1 ns length molecular dynamics simulations have been performed
for linear and disulphide-bridged versions of the peptides
Ac-Pen-Arg-Gly-Asp-Cys-NH2 (RGD1) and Tyr-D-Pen-Gly-Phe-D-Pen (DPDPE)
in aqueous solution. Analysis of the trajectories yields the conformations
explored by the studied peptides in solution as well as time scales and
amplitudes of structural fluctuations. The results lead to quantitative
measures of the influence of peptide sequence and presence of disulphide
bond constraints on structural flexibility. The molecular dynamics
trajectories are also used to calculate features of NMR spectra of the
studied peptides. Chemical and biological consequences of decreased
flexibility of cyclic peptides are discussed.
Abstract:
A simple procedure to check whether a whether a finite set of basis functions
is consistent with the Kohn-Sham potential in a density functional calculation
is discussed. The method is simple to implement and can be used to provide
information on the regions in space where the basis functions are reasonable
and where improvements may be required.
Abstract:
The experimental NMR data is not sufficient to determine the 3D structure of
a protein. Therefore the experimental data is complemented by general protein
structure data, which is further collected into a potential energy function
(penalty function). Genetic algorithm (GA) is then used to search for the
global optimum of the penalty function. The general protein folding problem
has been shown to be NP-hard. In practise this means that in the general case
it is quite impossible to find the global optimum in reasonable time. Genetic
algorithms are a heuristics, which are known to be good in solving hard
problems and finding good solutions, if not the global optimum, to them. In
this work we compare the efficiency of the GA approach to the more videly
known simulated annealing (SA) approach. In good agreement with the other
comparisons of GAs and SA in other hard problems, GAs seems to be superior
to the SA approach. The authors think that this is perhaps because GAs are
more global and parallel in nature capable of (re)combining different
solution alternatives concurrently.
Abstract:
The performance of Generalized Gradient Approximation Density Functional Theory
(GGA DFT) methods with gaussian basis sets is examined by studying 5 small
molecules. The geometries are optimized by HF, MP2 and DFT methods. We apply
four different DFT methods. The combinations of the functionals were as
follows:
(i) B-P86 or Becke-Perdew method, in which Becke's gradient corrected
exchange functional is combined with Perdew's gradient corrected correlation
functional.
(ii) B3-P86 is a hybrid method. It is a linear combination of various
exchange and correlational functionals in the form:
A*Ex[Slater] + (1-A)*Ex[HF] + B*Ex[Becke]+Ec[VWN]+C*Ec[P86].
where Ex[Slater], Ex[HF] and Ex[Becke] are the Slater, HF and Becke exchange
functionals; and Ec[VWN] and Ec[P86] are the Vosko, Wilk and Nussair and Perdew
correlation functionals respectively. The constants A, B and C are those
determined by Becke by fitting heats of formation.
(iii) B-LYP method, in which Becke's gradient corrected exchange
functional [16] is combined with the gradient corrected correlation functional
of Lee, Yang and Parr.
(iv) B3-LYP method, in which Becke's three parameter gradient corrected
exchange functional is combined with the gradient corrected correlation
functional of Lee, Yang and Parr.
The gradual improvement of basis sets gradually decrease the bond lengths and
increase the bond angles. Accidentally the HF/6-311G(d) results are close to
the experimental results and the improvement of the basis sets to 6-311G(2d,f)
worsen the agreement with the experiment. The inclusion of the electron
correlation effect increase the bond lengths considerably. The various GGA DFT
results agree qualitatively with each other and with the MP2 results, however
some functional provide exaggerated effects and poor agreement with the
experiment while others yield reasonable results.
Abstract:
Pople et al. have recently published the results of a series of extensive
tests on 55 molecules with accurately known experimental atomisation energies.
In the order of appearance the tested methods are Gaussian-1 (G1),
Gaussian-2 (G2), G2(MP2) and G2(MP3).[1] These methods include
QCISD(T)/6-311G(d,p), MP4, MP3 and MP2 calculations with a series of
extended basis sets up to 6-311+G(3df,2p). The most expensive G2 method
yielded the best test results. However, the computationally most intensive
steps, the QCISD(T) and MP4 calculations make these methods prohibitively
expensive for larger molecules.
In this work the possibility of the reduction of the basis sets will be
presented. The result suggest, that the QCISD(T) calculations are necessary
only in some specific cases, and there exist a well defined area where the
MP2 results approximate well the QCISD(T) and CCSD(T) results. Our results
show that this is particularly true for the basis set extension effects
arising from the addition of p-polarisation functions to the basis set for
the Hydrogen atoms. Some examples of the speed increase (5-20 times) will
be presented where there is no loss in the precision of the calculated
results, and the predictive force of the method is conserved. Generalize
d Gradient Approximation Density Functional Theory basis set effects will
be also presented.
[1] Curtiss,L. A., Raghavachari, K and Pople, J. A. J. Chem. Phys. 98, 1293
(1993) and references cited therein.
Abstract:
As a first step in investigating the dynamics of the 2-hydroxy-acid
dehydrogenase family of enzymes, a set of in vacuo molecular dynamics
trajectories have been calculated for pig heart, dog fish muscle, and
Bacillus stearotherophilus lactate dehydrogenase. The RMS deviation of
each conformation from the average trajectory conformation was used to
monitor the overall conformation of the proteins. Here we present
information indicating that the RMS deviation is a good indicator of
overall structural changes. We also present initial results of the
dynamics simulations. Averages from subsets of trajectory conformations
and single conformations were considered as reference points for the RMS
deviation calculations. We have found that the average over the complete
trajectory was the most useful reference because it did not weight any of
the trajectory conformations more heavily than others. From one of our
simulations with the NEV(constant number, energy, and volume) ensemble, we
have found that although the simulation is equilibrated within 20 ps; as
judged by the average temperature, kinetic, potential, and total energy
remaining constant; conformational equilibrium does not appear to be
reached until around 40 ps when considering the RMS deviation. This
suggests that care must be taken when judging that a simulation is
equilibrated. Finally, the results indicate that over the course of the
simulation the structures move from one general conformation to another.
This is consistent with the notion of conformational substates.
Abstract:
The evaluation of functions of square matrices can be
based on either the Taylor series of the function, or
on diagonalization techniques. In the present contribution
it is shown that suitable extrapolation techniques enhance
the efficiency of the Taylor series approach. As an
important example, the exponential of a matrix can be
obtained via this method. The exponential of matrices has to
be calculated frequently in recursive methods for the solution of
linear systems of ordinary differential equations, as occur in
the solution of evolution equations, and also in the solution of
the heat-conduction equation or the time-dependent Schroedinger
equation after suitable discretization [Yung-Ya Lin and Lian-Pin
Hwang, Computers Chem. 16 (1992), 285]. Several extrapolation
methods will be compared. It is discussed whether these methods
may also be useful for the extrapolation of vector
sequences which occur for instance in iterative solutions
of nonlinear equations. Examples for the latter are for instance
ab initio SCF and MCSCF equations.
Abstract:
A novel molecular dynamics method has been developed in
which the partial charges in the simulation are themselves treated as
dynamic variables, and allowed to respond to their charge environment
as the simulation proceeds. The charge degrees of freedom are
propagated in time along with the atomic positions by using an
extended Lagrangian method, similar to the treatment of the electronic
degrees of freedom in a Car-Parrinello ab-initio MD simulation. The
potential in which the charges move is determined by the principle of
electronegativity equalization, with forces acting on the charges to
make the electronegativity (or, equivalently, the chemical potential)
equal at all points in the system. This method is completely general,
and could be used on any molecular system with partial charges. In
the work presented here, the system studied is liquid water.
Fluctuating-charge water models based on the simple point charge (SPC)
and four-point transferable intermolecular potential (TIP4P) model
geometries have been developed and tested, and the results are
compared to a range of commonly-used water models. Both gas- and
liquid-phase properties, including the liquid structure, diffusion
constant, and dielectric constant, compare favorably with fixed-charge
and dipole-polarizable models. This is achieved at an added
compuational cost of only 10% over the corresponding fixed-charge
models.
Abstract:
An overview is given of the computational quantum chemistry code MOLFDIR,
the Molecular Dirac-Fock-CI Program Package developed at the University of
Groningen. A brief description of the theoretical background on
relativistic quantum chemistry will be given. The structure and the
possibilities of the MOLFDIR Package are shown together with some technical
and theoretical aspects dealing with the implementation of the
four-component Dirac-Fock-Breit Hamiltonian and the Restricted Active Space
Configuration Interaction (RASCI) equations. A summary is given of the
results of relativistic ab initio calculations that have been performed
with MOLFDIR.
The Program Package is currenly being used for calculations on the UF6
molecule and for large correlation calculations on the (EuO6)9- cluster. An
overview of the results can be found on this poster.
(2) DRAL, Chemical Database Service, Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, UK
Abstract:
Will WWW rationalise or aggravate the present chaotic state of
chemical- structure file formats? This poster illustrates typical
problems encountered with stereochemical representation and transfer
using familiar, so called 2.5D, chemical-drawing packages and 3D
molecular modelling software.
Abstract:
A wide theoretical framework has been recently proposed for the ab initio
study of the mechanisms of pressure induced phase transformations in
ionic solids. So far, it has been used to investigate the B1-B2 transition
in alkali halides. In brief, if a path connecting the two phases is assumed
on a high dimensional space, one may construct a set of models of greater
and greater complexity and follow simple prescriptions to study the connections
among symmetry, stability, and topological considerations. A clear picture
of the important role that symmetry plays in the establishment of the topology
of the energetic hypersurface at both the end points and along the transition
path has emerged. It has ultimately led to the discovery of interphase
universal relations among phase transitions. The relation between phase
stability and the critical points of the electronic density has also proven to
be fruitful. By defining topological ionic radii, the classical arguments
regarding the stability of ionic phases in terms of cation to anion size ratios
are recovered.
Abstract:
Two different theoretical approaches to compute the total energy of
solids have been applied to describe the equations of state (EOS) of ionic
halides and oxides. The first one is the ab initio Perturbed Ion (aiPI)
model, a quantum-mechanical technique that solves the Hartree-Fock
equations of a crystal in a localize Fock space. The second one is an
interatomic force model implemented in a new computational code (PAIRPOT)
that calculates static thermodynamic properties of pure crystalis using
non-polarizable many-body interionic potentials.
Our focus in this contribution will cover both the technical aspects of
the two simulation tools, and the discussion of the main results obtained
in the systems explored. Specifically, the following topics are addressed:
(i) Computational implementation of the aiPI and PAIRPOT models;
(ii) Relative performance of the quantum-mechanical and the atomistic
strategies in total energy and global geometry optimizations;
(iii) Calculation of static cohesive, elastic and mechanical properties in
ionic halides and oxides; (iv) Structural phase transitions induced by
hydrostatic pressure; and (v) Relative merits of empirical EOS in the
description of the crystal response to pressure.
Abstract:
Aromatic nitrenium ions have been postulated as carcinogenic species
derived from the in vivo catabolism of aromatic amines. Nitrenium ions
incorporate a disubstituted, positively charged nitrogen atom, and may
thus have either singlet or triplet spin multiplicity. The former spin
state is implicated in carcinogenesis. We have calculated singlet-triplet
gaps for a number of small nitrenium ions, such as nitrenium, imenium,
methylnitrenium, aziridinium, and phenylnitrenium; similar calculations
have also been done for the analogous isoelectronic carbenes. Calculations
have been performed at several levels of theory, including multi-
configurational self consistent field, multi-reference configuration
interaction, and density functional theory. The electronic and steric
factors that influence the singlet-triplet gaps for these species are
discussed, and the levels of theory are compared. Density functional
theory appears to hold promise for larger, biologically relevant
nitrenium ions.
Abstract:
The model of lone pair electrons is an extremely important
and useful tool and yet the nature of these lone pair electrons
remains elusive. In this paper we examine the electron density and
electrostatic potential around the water molecule using ab initio
electronic structure techniques. Scientific visualization is used to
examine the behavior of these observables in the region to the "rear"
of the water molecule, where electron lone pairs are depicted. We
find that the electron density exhibits no significant structure which
might indicate the presence or location of electron lone pairs.
However, the electrostatic potential reveals more structure and exhibits
two minima in the regions where tetrahedrally arranged lone pairs would
be expected.
Abstract:
The linear and non-linear molecular response tensors of urea and thiourea
are partitioned into atomic and functional groups contributions using
sub-system quantum mechanics as implemented in Bader's Theory of Atoms in
Molecules [1]. The equations for generalized spatial partitioning of
molecular polarization densities are developed in analogy to those for
the molecular multipole moments [2,3]. As a demonstration of the method,
the first and second hyperpolarizabilities of urea and thiourea will be
discussed in terms of the atomic and functional group contributions to
the molecular properties.
[1] Bader, R. F. W. "Atoms in Molecules: A Quantum Theory", Claredon
Press, Oxford, 1990.
[2] Laidig, K. E. J. Phys. Chem., 1993, 97, 12760
[3] Laidig, K. E. "A General Expression for the Spatial Partitioning of
Molecular Mulitpole Polarizabilities" (in preparation).
Abstract:
RETROSYN (1) is a complete (and in a sense, expert system) tool to
aid the organic chemist in searching databases of reactions for
synthesis planning. The program has basically two major parts, one
for the user for synthesis planning and one for the automatic analysis
of a database of reactions to set up a hierarchial structured database
for searching.
A typical usage by a chemist would be to draw in
a molecule through the X-Window interface, choose a bond that is to be
retrosynthetically broken and the system would search for existing
reactions in its database for 'similar' reactions.
To set up the reaction database within the system, learn algorithms are used
to extract the essential characteristics of the individual reactions.
The most important characteristic is the reaction center.
The reaction centers are the basis of the similarity between reactions and form
the basis of the search algorithm.
RETROSYN itself is made up of a set of modules utilizing a wide range
of multidisiplinary techniques in artificial intelligence (learning
and search), software engineering (database management, user
interface, X-windows), mathematics (graph theory), physical chemistry
(molecular property calculations), computer chemistry (representation
of molecules and reactions) and, of course, organic chemistry.
Work is currently underway to document the system for release into
public domain at the beginning of 1995. The documentation project has
several goals:
Abstract:
REACTION is a software system for modeling a mechanistic system of
reactions. The key to the model is the reaction pattern which
represents a class of reactions. The techniques used are a result of
the experience gained in the synthesis planning program RETROSYN, the
only difference being that the analysis in this case goes in the
reaction direction and not in the retro-synthetic direction.
The reaction patterns representing reaction prototypes, i.e. classes
of reactions, act on a specific molecule to generate a specific
reaction. Given a set of molecules the iterative action of the
reaction patterns on the set of molecules produces a set of reactions
representing a model of the mechanistic system. It main use is in the
generation and then analysis of complex reactive systems, such as
combustion, where the structure of the molecule plays a large role.
Given a set of molecules under study, the system can 'react' them
under similar conditions (i.e. using the same mechanisms). The
automatic generation ensures that all reaction sequences stem from the
same mechanism. The user can concentrate on the set of reaction
mechansim prototypes and the details as to how it is applied to each
molecule is left to the system.
This is meant to be the first stage in a larger project concerning
combustion modeling. Due to the complexity of combustion modeling, it
has been necessary to reduce the detailed set of reactions for a given
system to a managable size. A discussion of the role of reaction
patterns and automatic generation in this simplification process will
also be discussed. Currently, analysis of the generated reaction
sequences is done through the numeric solution of the concentration
dependence of the species. Work is starting on the more complete
modeling including time dependent temperature evolution.
The paper presented will be a hypertext document in which more details
about the structure of the system and specific experiments performed than
can be given in a normal publication.
Abstract:
Technological advances in networked virtual environments and the World-Wide
Web now permit an effective medium for electronic conferencing which
facilitates communication in real time and concurrent display of multi-media
information. Our poster will present a link to a networked virtual
environment in which ECCC participants may communicate with other participants
in real time while viewing the data presented in the posters with their Mosaic
clients.
Abstract:
The atomization heat (per atom, if clusters of different dimensions are
concerned) is suggested as a reasonable stability measure when comparing
species of X60 and related types (attempts to use a mere heat of formation
for the purpose are analyzed). Semiempirical quantum-chemical methods
(AM1, MNDO) are used with homo-clusters C60, Si60, Ge60, N60, B60, hetero-
clusters B36N24, B36P24, Al36N24, Al36P24, and various BmNn
(m + n < 60, m + n > 60). For example, the following stability order is
predicted: B36N24 > B36P24 > Al36N24 > Al36P24. Geometrical rules and
bond-energy contributions are discussed. In addition to the conventional
pentagon-hexagon fullerene pattern, the square-hexagon route is considered
as an alternative. A particular interest is given to tetrahedral-symmetry
cages B36N24, B28N28, and B36N36. On a selected example, effects of
temperature on inter-cluster relative stabilities are studied in conjunction
with a full computational vibrational analysis. Temperature interchanges in
the relative stabilities are pointed out. Attention is also paid to a usage
of the HOMO-LUMO gap and effects of the Jahn-Teller distortion.
Abstract:
Recently the AlH4 anion was identified by considering IR Matrix Isolation
Spectroscopy results together with quantum chemical calculations. This
anion was found to be nearly 3eV more stable than the neutral AlH2(H2)
parent species.
In this paper the energy, the structure and the vibrational
properties of the GaH4 anion are investigated with the CCSD(T) and DFT
methods and are compared to those of the GaH4 neutral.
Abstract:
Nafion belongs to the wide class of solid superacids catalysts,
in that it exhibits acid stength greater than that
of pure H2SO4. It has hydrophobic (-CF2-CF2-) and hydrophilic (-SO3H)
regions in its polimeric structure, and its supeacidity
is attributed to the electron-withdrawing effect of the
perfluorocarbon chain acting on the sulfonic acid group.
It is able to catalyze various reactions, such as alkylation,
disproportionation, and esterification.
A quantum mechanical ab-initio study has been undertaken
on the smallest molecular model of the active site found in Nafion,
namely triflic acid, CF3-SO3H (T).
To study the effect of the fluorine atoms on its propensity
to form hydrogen bonds, we have also considered
the methanesulfonic acid, CH3-SO3H (M).
Structures and vibrational spectra of a number of H-bonded
aggregates, have been computed, namely the dimer of triflic
acid (TT), the complex between triflic acid and water
(TW), the dimer of methanesulfonic acid, (MM), the complex
between methanesulfonic acid and water (MW) and finally,
the complex between triflic acid and methanesulfonic acid, (TM).
All the calculations have been done at Hartree-Fock
self-consistent field level with the Dunning double zeta
plus a set of polarization functions (d and p) basis set (SCF/DZP).
Full geometry optimization has been carried out for the monomers
and the corresponding aggregates. The only symmetry constraint
(Ci point group) has been imposed for the geometry of the
TT and MM dimers. Due to the nature of the -SO3H groups,
cyclic structures are formed for all aggregates.
Harmonic vibrational frequencies have been computed for all
structures at SCF/DZP level, showing that all aggregates
are full minima (the calculation for the TM species is
still in progress). The SCF/DZP binding energies are (kcal/mol):
19.1 (MM), 18.4 (MT), 16.3 (TT), 13.6 (TW) and 12.4 (MW), respectively.
Calculations of the basis set superposition error and of the
electron correlation corrections (MP2) to the binding energies
are still in progress and will be reported in the full paper.
In order to understand the nature of the bond between different
structures a pure electrostatic model has been adopted.
SCF/DZP molecular electrostatic potential derived charges (PED)
have been computed for T, M and W molecules.
Using the SCF optimized geometries of the various aggregates
the interaction energy based on the simple Coulombic scheme
has been computed with the PED charges. The resulting binding
energies are (kcal/mol): 21.1 (MT), 21.7 (MM), 19.4 (TT),
16.0 (TW) and 14.4 (MW), respectively.
Clearly, the simple electrostatic model is able to parallel
the full ab-initio results with great accuracy.
It is noterworthy, that no inversion in the order of stability
is computed with the electrostatic model.
From these data it results that the flourine electron
withdrawing ability increase the acidity of the proton of
the -SO3H group but decreases, at the same time,
the ability of the nearby basic oxygen to behave as donor
with respect to the hydrogen of the partner molecule.
This delicate interplay of effects is clearly shown in
the MW and TW structures; indeed, in the TW structure
water forms a non-cyclic structure acting mainly as a
hydrogen acceptor. Instead, a cyclic structure
is computed for the corresponding MW structure.
The corresponding shifts in the SO3(O-H) vibrational
frequency parallel the values of the binding: -496 cm(-1)
and -385 cm(-1) for the TW and MW respectively.
Our data also show that the formation of hydronioum ion, H3O(+) is
energetically unfavoured with respect to the neutral H-bonded complex for both TW and MW structures.
Abstract:
High level ab initio calculations (MP2/6-31+G**//
MP2/6-31+G*) are used to characterize the reactions of methyl-
oxirane with HO- and methylthiirane with HO- and HS-. Addition
and elimination pathways are investigated as well as attack at
the sulfur of thiirane. The results are compared to acyclic
analogs and discussed in terms of ring strain release. The
results suggest that much of the strain is released early
on the reaction coordinate of ring openings.
Abstract:
Ab initio calculations have been carried out to investigate the
interactions between singlet carbenes and fluoroalkanes. The carbenes
studied were singlet methylene, CH2, and singlet carbomethoxycarbene,
CHCO2Me, interacting with CH3F and CF4. Geometry optimizations at the
RHF and MP2 levels employing 3-21G and 6-31G* basis sets indicate that
stable complexes are formed between the carbenes and fluoroalkanes, with
binding energies (measured relative to the separated species) in the range
of 5-20 kcal/mol. The complexes formed between CHCO2Me and the
fluoroalkanes are more strongly bound than complexes formed between CH2
and the same fluoroalkanes. These ab initio results suggest one possible
origin of an experimentally observed solvent effect in the reaction of
singlet carboethoxycarbene, CHCO2Et, with 2,3-dimethylbutane [J. M.
Swanson, C. A. Dvorak, J. P. DeLuca, and J. M. Standard, J. Org. Chem. 59,
3026 (1994)]. A greater preference for tertiary insertion over primary
insertion was observed in 1:1 pentane-perfluorohexane solvent versus
2,3-dimethylbutane solvent. No such solvent effect was observed in
similar reactions involving singlet methylene.
(2) Bundesinstitut fuer Arzneimittel und Medizinprodukte, (Federal Institute of Drugs and Medical Products), Seestr. 10-11, 13353 Berlin, Germany
Abstract:
The addition reaction of three substituted 1-(1-cyan-1-methylethyl) urea to
form three substituted 5,5-dimethyl-4-imino-imidazolidin-2-ones was examined
using semi-empirical quantum mechanical calculations. The solvent effect
was considered using the COSMO model as implemented in MOPAC 93. The
Hamiltonians AM1 and PM3 were applied. Comparing the reaction enthalpies
obtained through AM1 and PM3 with our experimental findings shows that PM3
is superior to AM1. This observation was confirmed through further
calculations on the solvent dependent tautomeric equilibrium of
1-methylcytosine. The predominant tautomer of this system can be predicted
through the COSMO model. But the theoretical restriction of the COSMO
model becomes significant when looking at the ratios of the tautomeres.
This ratio is not predicted correctly if compared to the experimental value.
Despite this restriction is the PM3 Hamiltonian in combination with the COSMO
model suited in modelling reactions of compounds with urea partial structure.
Abstract:
Density functional theory is used in conjunction with cluster models
to calculate the activation energies for H2 desorption from Si(100)-2x1
surface and for intra-dimer and intra-row diffusion of H atoms on this
surface. Diffusion of H atoms along the surface dimer rows is predicted
to have an activation energy of about 52 kcal/mol. This is comparable
to recent estimates of the activation energy for H2 desorption,
suggesting that hydrogen mobility on the surface may be important in the
desorption process. The mechanism of H2 desorption from Si(100)-2x1 is
discussed in light of calculated H-atom diffusion barriers. We propose a
mechanism in which surface defects are converted into a dihydride (SiH2)
species, from which H2 desorption occurs. The barrier for defect migration
is predicted to be only 14 kcal/mol, so that a single defect can account
for the desorption of H2 from a large number of monohydride sites.
Abstract:
The CRYSTAL[1] suite of programs has been generalised in order to apply
DFT LCAO methods as well as the HF LCAO technique to bulk crystals, slabs,
as models of surfaces, polymers and molecules.
The LDA energy correlation functional used in this work is the Perdew-
Zunger [2] parametrization of the numerical results obtained by Ceperley
and Alder for the electron gas[3]. Gradient dependent functionals are
also tested, as defined by the Generalized Gradient Approximation (GGA),
formulated by Becke for exchange energy (BEC)[4] and by Perdew for
correlation (P91)[5].
Three ionic surfaces have been considered, ranging from perfect ionicity
(MgO, LiF), to partially ionic bond situations (alpha Alumina): the H-form
of a 1:3 form of a Si/Al chabazite has been studied as a model of realistic
zeolites. The band structures and the electronic charge distributions
calculated at the DFT and HF levels are compared.
The electrostatic potential has been calculated using the quantum
mechanical electronic densities: the effect of the Hartree-Fock , the local
and the gradient DFT Exchange operators have been analyzed. The correlation
effects on the electrostatic fields have been estimated using local and GGA
DFT correlation operators. The intensity of the electrostatic fields,
calculated in the different approximations, have been compared to the shift
of the vibrational frequencies of CO molecules periodically adsorbed on the
surfaces and interacting with an acidic site of the zeolitic cavity.
[1] R. Dovesi, C. Pisani, C. Roetti, M. Causa', and V.R. Saunders,
CRYSTAL 88. AN AB-INITIO ALL-ELECTRON LCAO-HARTREE-FOCK PROGRAM FOR
PERIODIC SYSTEMS., QCPE Pgm N. 577, Quantum Chemistry Program exchange,Indiana
University,Bloomington, Indiana (1989); R. Dovesi, V.R. Saunders and C. Roetti,
CRYSTAL92 User's Manual., Gruppo di Chimica Teorica, Univ. Torino, and
Daresbury SERC Lab.
[2] John P. Perdew and Alex Zunger, Phys. Rev. B 23, 50.
[3] D. M. Ceperley and B. J. Alder, Phys. Rev. Lett. 45, 566(1980).
[4] A. Becke , Phys. Rev. A 88, 1053(1988).
[5] P. Perdew and Y. Wang, , Phys. Rev. B 45, 13244 (1991); J. P. Perdew,
J.A. Chevary, S.H. Vosko, M.R. Pederson, D.J. Singh, and C. Fiolhais, Phys.
Rev. B 46, 6671(1992).
Abstract:
An interaction potential for the methanol-He system has been calculated at
the MP2 level for use in scattering calculations on the collisional
excitation of the internal rotation in methanol. The basis set was
equivalent to the "D3-gamma" basis described by Palma, et. al. [J. Chem.
Phys. 89, 1401 (1988)] for their water-He interaction potential,
consisting of C,O:[10s,6p]->(5s,4p), H:[5s]->(4s), and He: [10s]->(5s),
augmented with C,O: s,p,2d, H: s,2p, and He: 2p diffuse and polarization
functions. The methanol geometry was taken from the Lees and Baker
determination and was held rigid except for rotation of the (symmetrical)
methyl group about its symmetry axis. Interaction energies were computed
on a grid of He positions (R,theta,phi) relative to the methanol center
of mass, namely 11 R values between 4 and 12 bohrs, 9 theta values, and 7
(or 13) phi values for symmetrical (or unsymmetrical) conformations of
the methanol. The grid for the internal rotation angle was gamma=0
(staggered), 30, and 60 (eclipsed). The BSSE was corrected using the
counterpoise method. The minimum in the potential occurs for a near
T-shaped complex in which the He is 3.5 Ang. from the staggered methanol
center of mass, along an axis perpendicular to the methyl symmetry axis
and parallel (syn) to the OH bond, similar to the geometry found for the
methanol-Ar complex by Suenram, et. al. [J. Mol. Spectrosc. 137, 127
(1989)]. The binding energy is 28 cm^-1. The barrier to internal
rotation in this complex is only 20 cm^-1 higher than the barrier in free
methanol. The barrier to the overall rotation of the methanol relative
to the He is approximately 15 cm^-1. The MP2 potential is less
anisotropic than the HFD potential used in earlier scattering calculations
[S.L. Davis, J. Chem. Phys. 97, 6291(1992)].
(2) Department Medicinal Chemistry, University of Minnesota
Abstract:
A molecular mechanics potential energy function is developed and
parameterized to study the folding and unfolding pathways of several
protein structures. To bring the numerical problems in reach, a
tethered-bead model was adopted that reduces each amino acid to a
single sphere centered at the C_alpha position. Local interactions
in the chain are captured using a suitable spline function fit to
reproduce known C_alpha torsion and angle distributions taken from a
crystal structure database. To effectively model the complex geometries
of peptide backbones using C_alpha beads only, the torsion and angle
terms were coupled during the fitting process. Long range forces are
captured using a Lennard-Jones 10-12 function parameterized from
residue contact energies reported by Miyazawa & Jernigan (Macromolecules
18:534, 1985). This particular function was chosen since it decays
quite rapidly ,minimizing artifacts produced by residues outside the
near-contact distance (6.5 angstroms). The interaction potential was
then implemented as part of a Langevin dynamics/simulated annealing
scheme to examine the folding process and low energy structures of a
de novo designed 4-helix bundle (Regan & DeGrado, Science 241:976, 1988).
Remarkably, the 74 residue sequence folds to produce the "correct"
structure observed experimentally using fairly straightforward annealing
protocols. To further examine the applicability and limitations of the
new force field, two other small proteins have been simulated under both
conditions of gradual heating and cooling to probe the folding and
unfolding process. The limited data collected so far indicates that the
crystal structure is indeed a fairly deep minimum on the simplified
potential energy surface providing encouragement for more detailed studies
of the folding process and low energy structures.
Abstract:
The fact that several compounds with biological activity contain
N-C-C=O units makes it of interest to develop an accurate molecular
mechanics force field for their study. On the structure of simple
molecules containing this kind of unit very little experimental research
has been carried out. Therefore ab initio MO results are necessary in
order to start the parameterization of this force field.
A comparative study of 2-aminoethanal [1], the smaller compound with
the N-C-C=O unit, and its methylated derivatives has been carried out by
HONDO 8.4 [2] and GAUSSIAN92 [3] using the 3-21G and 6-31G** basis sets.
The effect that mono- and di-methylation in several positions of
2-aminoethanal has on the relative stabilities of the conformers and on
the principal geometrical trends will be discussed. These results are
being compared with MM392 [4] calculations.
For doing this, the barriers of rotation of the N-C-C=O torsion has
been calculated for the series of methylated compounds and the minima
found along these paths have been unrestrained optimized. The results
obtained have been compared with the similar ones obtained for
2-aminoethanal [5]. The effect of electron correlation has been also
considered. Taking these results into account, we shall construct the
projected molecular mechanics force field.
1. L. Van den Enden, C. Van Alsenoy, et al., J. Mol. Struct., 105, 407-415
(1983).
2. M. Dupuis, S.tChin and A. M rquez, "CHEM-Station and HONDO" in
"Relativistic and Electron Correlation Effects in Molecules and Clusters",
G.L. Malli Editor, NATO ASI Series, Plenum Press, New York, 1992.
3. Gaussian 92, Revision A, M.J. Frisch and others, Gaussian, Inc.,
Pittsburgh PA, 1992.
4. N.L. Allinger, Y.H. Yuh and J.-H. Lii, MM3-1992 Version, J. Am. Chem.
Soc., 111, 8551 (1989).
5. L. Carballeira and I. Perez-Juste, J. Mol. Struct. THEOCHEM, 309, 267
(1994).
Abstract:
The structures and properties of complexes of a range of carbonyl
compounds with dialkyl boron fluorides and chlorides were examined
by ab initio methods. Based on these results it is suggested that the
observed enantioselectivity of reduction of ketones with diisopinocampheyl
boron chloride can be directly related to which group on the ketone
prefers to be coordinated cis to the boron. An extension to the MM2
force field was developed to allow molecular modelling of these complexes.
Jeffrey L.
Krause,
Mike
Messina,
Bret J.
Naylor,
Daniel
A. Olshove,
Amandeep
K. Shergill,
Robert M.
Whitnell,
Kent R.
Wilson,
Vladislav V.
Yakovlev, and Yijing
Yan(#)
(#) Department of Chemistry, Hong Kong Science and Technology University, Kowloon Hong Kong
Abstract:
The evolution of a quantum system can be guided to
a desired target in phase (position/momentum) space by use of tailored light
fields. Our pursuit of this goal involves a
close collaboration between theory and
experiment. On the theoretical side we must determine the light field
that best drives a quantum system to the desired final
outcome. We have developed a theory in the weak response limit
that enables us to compute the globally optimal light field to attain a
chosen goal. On the experimental side we use these theoretically
determined light pulses as a guide to control the evolution of
molecular systems in the laboratory.
We present theoretical and experimental results on control of
the vibrational dynamics of the iodine molecule. The desired target is
a minimum uncertainty wavepacket on the excited state
of I_2. Results are presented for a pump-probe experiment
on this system. The pump pulse is the light field that drives the
iodine molecule to the desired outcome and the probe pulse
measures how well we have achieved this outcome. We also compare the
theoretically and experimentally determined laser induced fluorescence
spectra as a function of the delay time between the pump and probe
pulses.
Daniel
A. Olshove,
Amandeep
K. Shergill,
Robert M.
Whitnell and
Kent R.
Wilson
Abstract:
Multimedia education allows students to see, in three dimensions, many of
the chemical concepts that are inadequately represented in 2-D chemical
textbooks. Our all-digital physical chemistry course relaces the clackboard
and chalk with a seamless mix of words, equations, images, computer animation
and video displayed on a 20-foot wide screen in back of the lecturer. The World
Wide Web is a means to make these still and moving images available to many
students simultaneously as well as to distribute them around the world. A free
CD-ROM of this multimedia imagery will also soon be available. Currently, we
are preparing similar material for an upcoming general chemistry course.
Video compression, fast Macintsoh computers, high capacity hard drives, and
high resolution LCD projection make our multimedia presentations possible.
Abstract:
The cellular machine weaves together literally thousands of parts, each with unique
structural and functional properties. Both understanding how the cell works and
engineering cells with novel properties requires the description and analysis of the
components and their interactions. In this presentation we describe our work on
representing biochemical compounds using a layered graph grammar, Klotho, written in the
logic programming language Prolog. Our approach is to capture the ``natural language'' of
biochemistry in a rule which describes the stereochemical configuration of a compound, and
then use the graph grammar to generate a representation equivalent to a graph edge/node
description. This is one of a family of stereochemically specific equivalent
representations which can be automatically generated for particular computations as
useful. Isomeric SMILES strings are automatically generated and passed to CONCORD, which
in turn calculates an approximately minimized three-dimensional structure and returns a
pdb file. The results can be viewed in the World-Wide Web manifestation of Klotho at
http://ibc.wustl.edu/klotho/. The WWW version includes for each compound its Prolog rule,
synonyms if available, a Fischer projection if nonaromatic, a static GIF image and the pdb
file. Klotho supports the proposed Chemical MIME type, so this last can be viewed
interactively over Mosaic.
Paper 2
EMail discussions
Potential Energy Surfaces as a Function of Solvent Dielectric: Application of Hypermedia Concepts
By: Omer Casher, Christopher Leach and Henry S. Rzepa
From: Department of Chemistry, Imperial College, London, SW7 2AY
Email: h.rzepa@ic.ac.uk
Paper 3
EMail discussions
Theoretical Study of Trans and Cis Azobezenes
By: Zhengwei Peng
From: Biosym Technologies, Inc., 9685 Scraton Road, San Diego, CA 92121
Email: zxp@iris31.biosym.com
Paper 4
EMail discussions
Preliminary solution structure of the cytochrome c551 from Ectothiorhodospira abdelmalekii by homonuclear NMR and distance geometry
By: K. Boulez, M. Budesinsky, J. Martins(#), F. Fant, W. Vranken and F.A.M. Borremans
From: Biomolecular NMR unit, University of Gent, Krijgslaan 281/S4bis, 9000 Gent, Belgium
Email: kris@bionmr1.rug.ac.be
Paper 5
EMail discussions
The reaction of NH2 with O: A theoretical study employing Gaussian 2 theory
By: D.L. Yang, M.L. Koszykowski, and J.L. Durant, Jr
From: Center for Combustion and Materials Science and Technology, Sandia National Laboratories, Livermore, California, 94551-0969
Email: dlyang@ca.sandia.gov
Paper 6
EMail discussions
Structure-Activity Relationships for Prediction of Toxicity using Artificial Neural Networks and Knowledge-Based Systems
By: M Brinn, PT Walsh and MP Payne
From: Health and Safety Laboratory, Health and Safety Executive, Broad Lane Sheffield S3 7HQ, U.K.
Email: Nick@cis-hsl.demon.co.uk
Paper 7
EMail discussions
On the Limitations of the Density Functional Theory in Electronic Structure Calculations
By: Isaac B. Bersuker
From: Department of Chemistry & Biochemistry and College of Pharmacy, The University of Texas at Austin, Austin, Texas 7871
EMail: cmao771@charon.cc.utexas.edu
Paper 8
EMail discussions
A Method of Modelling Transition Metal System with an Interface Between Quantum-Mechanical Calculations and Molecular Mechanics
By: Isaac B. Bersuker(a,b), Max K. Leong(a), James E. Boggs(a), and Robert S. Pearlman(b)
From: (a) Department of Chemistry & Biochemistry and (b) College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712
EMail: cmao771@charon.cc.utexas.edu & max@eeyore.cm.utexas.edu
Paper 9
EMail discussions
Multiple Metal Additions to C60. An Ab Initio Study of [M(PH3)2]nC60 (M=Pt and Pd; n=1,2 and 6)
By: Carles Bo, Miquel Costas, Jose Carlos Ortiz, Josep M. Poblet (*)
From: Departament de Quimica. Universitat Rovira i Virgili. Plaa Imperial Tarraco, 1. 43005 Tarragona. Spain
EMail: bo@quimica.urv.es
Paper 10
EMail discussions
Semiempirical Calculations of Kinetic Isotope Effects on Decarboxylation of 3-Carboxy-4-hydroxy-1,2-benzisoxazole
By: Przemyslaw Czyryca and Piotr Paneth*
From: Institute of Applied Radiation Chemistry, Technical University of Lodz, Zwirki 36, 90-924 Lodz, Poland
EMail: ppaneth1@itr1.p.lodz.pl
Paper 11
EMail discussions
Ab Initio Study of the Diels-Alder Reaction of Phosphaethene and Phosphaethyne with Butadiene
By: Debbie C. Mulhearn and Steven M. Bachrach*
From: Department of Chemistry, Northern Illinois University, DeKalb, IL 60115
EMail: smb@smb.chem.niu.edu
Paper 12
EMail discussions
A Comparison of Some Commercially Available Structural
Descriptors and Clustering Algorithms
By: Robert D. Brown, Mark G. Bures, Yvonne C. Martin
From: Pharmaceutical Products Division, Abbott Laboratories
EMail: brownr@kekule.abbott.com
Paper 13
EMail discussions
Nucleophilic attack on beta-lactam rings
By: J. Frau, Francisco Munoz, and J. Donoso
From: Chemistry Department, Universitat de les Illes Balears, 07071 Plma de Mallorca, Spain
EMail: dqufmi0@ps.uib.es
Paper 14
EMail discussions
The Hyperfine Structure of Muons in Silicon and Diamond Crystals
By: H.U. Suter*+, N. Paschedag*, D.M. Maric+ and P.F. Meier*
From: * Physik--Institut der Universit\"at Z\"urich,
Winterthurerstrasse 190, CH-8057 Z\"urich, Switzerland
EMail: noe@physik.unizh.ch
Paper 15
EMail discussions
Conformational Sampling of Glycerolphosphatidylcholine using Distribution Biased Monte Carlo and Langevin Dynamics Methods
By: Barry J. Hardy
From: Computer-Aided Molecular Design Group, Physical Chemistry Lab, Oxford University, Oxford, OX1 3QZ, U.K.
EMail: bhardy@convex.ox.ac.uk
Paper 16
EMail discussions
Combined Quantum Mechanical - Classical Mechanical Calculations on Solvent-induced Blue and Red Shifts of the =BC*<-n Transition of Acetone
By: Alex H. de Vries and Piet Th. van Duijnen
From: OMAC, Dept. of Chemistry, State University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
EMail: alexxx@chem.rug.nl
Paper 17
EMail discussions
Impulsive Energy Transfer During Unimolecular Reaction via Reactive Cylinders in Phase Space
By: Joanna R. Fair, Karin R. Wright and John S. Hutchinson
From: Department of Chemistry, Rice University
EMail: jshutch@hbar.rice.edu
Paper 18
EMail discussions
Ab Initio Study of the Chemisorption of Alkali Metals on the Si(111) Surface
By: A. Clotet, J. C. Ortiz, J. M. Ricart (*), J. Rubio(+) and F. Illas(+)
From: Departament de Qumica, Facultat de Qumica, Universitat Rovira i Virgili Pl. Imperial Trraco 1, 43005 Tarragona (Spain)
EMail: ricart@quimica.urv.es
Paper 19
EMail discussions
A Tool for Negotiating Through Structure-Activity Relationship Space: the Hypersurface Iterative Projection Method
By: Donald B. Boyd
From: Department of Chemistry, Indiana University-Purdue University at Indianapolis, Indianapolis, Indiana 46202-3274
EMail: boyd@chem.iupui.edu
Paper 20
EMail discussions
Interpretation of Raman spectra using semi-empirical calculations
By: Peter Freunscht
From: Institut fur Physikalische Chemie I, Uni Erlangen-Nurnberg, Egerlandstr. 3, Germany
EMail: freunsch@pctc.chemie.uni-erlangen.de
Paper 21
EMail discussions
Self-consistent reaction field study of dual fluorescence in p-DMABN
By: Peter Gedeck
From: Institut fur Physikalische Chemie I, Uni Erlangen-Nurnberg, Egerlandstr. 3, Germany
EMail: gedeck@pctc.chemie.uni-erlangen.de
Paper 22
EMail discussions
A Software Toolkit for de Novo Ligand Design
By: Z. Zsoldos, A.P. Johnson, V. Gillet, G.J. Myatt, D. Bayada
From: ICAMS, The University of Leeds, UK
EMail: zsolt@mi.leeds.ac.uk
Paper 23
EMail discussions
Investigation of Bonding and Interlayer Charge Transfer in the Solid State Compound Na1.9Cu2Se2Cu2O by the Tight-Binding Extended Huckel Method
By: Gerardo Chacon, Xiangyun Long and Chong Zheng
From: Department of Chemistry, Northern Illinois University, DeKalb IL 60115
EMail: zheng@cz2.chem.niu.edu
Paper 24
EMail discussions
Analytical Derivatives of Molecular Vibrational Frequencies with Respect to Coordinates and Model Potential Parameters
By: Adam Helman,(1) Thomas Thacher,(1) and Herschel Rabitz(2)
From: 1) Biosym Technologies, Inc. San Diego, California 92126 (All correspondence should be made with Dr.Helman)
EMail: adam@iris22.biosym
Paper 25
EMail discussions
Annotating PDB Files with Scene Information
By: Gregory S. Couch, Eric F. Pettersen, Conrad C. Huang, and Thomas E. Ferrin
From: Computer Graphics Laboratory
University of California
San Francisco, California 94143-0446
EMail: gregc@cgl.ucsf.edu
Paper 26
EMail discussions
Electronic Structure of Solvated Molecular Anions
By: Paul Maslen, James Faeder, and Robert Parson
From: Department of Chemistry and Biochemistry, University of Colorado, and Joint Institute for Laboratory Astrophysics, University of Colorado and National Institute of Standards and Technology, Boulder, CO
80309-0440
EMail: rparson@jila02.colorado.edu
Paper 27
EMail discussions
Modelling the Racemization of Helicenes
By: Hens Borkent
From: CAOS/CAMM Center, University of Nijmegen, P.O. Box 9010, Nijmegen, The Netherlands
EMail: borkent@camms1.caos.kun.nl
Paper 28
EMail discussions
Comparison of Reactivity of Thiophene, Thiophene 1-Oxide, and Thiophene 1,1-Dioxide as Diene for Diels-Alder Reactions.
An AM1 Semiempirical Study
By: Branko S. Jursic* and Don Coupe
From: Department of Chemistry, University of New Orleans, New Orleans,
Louisiana 70148
EMail: bsjcm@uno.edu
Paper 29
EMail discussions
AM1 Semiempirical Searching for Suitable Thiophene Derivation that
will Enable Thiophene to Act as Diene for Diels-Alder Reactions
By: Branko S. Jursic* and Don Coupe
From: Department of Chemistry, University of New Orleans, New Orleans,
Louisiana 70148
EMail: bsjcm@uno.edu
Paper 30
EMail discussions
Theoretical Study of Azide Anion Addition to Nonpolar and
Polar Double and Triple Bonds
By: Branko S. Jursic* and Zoran Zdravkovski
From: Department of Chemistry, University of New Orleans, New Orleans,
Louisiana 70148
EMail: bsjcm@uno.edu
Paper 31
EMail discussions
Why is Tetrazole not Practical as a Diene in Diels-Alder Reactions?
An Ab Initio Theoretical Study
By: Branko S. Jursic* and Zoran Zdravkovski
From: Department of Chemistry, University of New Orleans, New Orleans,
Louisiana 70148
EMail: bsjcm@uno.edu
Paper 32
EMail discussions
Theoretical Study of BH3 Catalyzed Hetero Diels-Alder Reaction
Between Ethylene and Nitrosoethylene
By: Branko S. Jursic* and Zoran Zdravkovski
From: Department of Chemistry, University of New Orleans, New Orleans,
Louisiana 70148
EMail: bsjcm@uno.edu
Paper 33
EMail discussions
An update to the NCI Drug Information System 3D Database
By: Daniel W. Zaharevitz(1), Xinjian Yan,(2) Shaomeng Wang,(2) G.W.A. Milne(2)
From: (1) PRI/Dyncorp, Inc., NCI/Frederick Cancer R&D Center, Frederick, MD 21702
EMail: ZAHAREVITZ@dtpax2.ncifcrf.gov
Paper 34
EMail discussions
Application of Genetic Algorithm to the Calculation
of Bound States and Local Density Approximations
By: Yehuda Zeiri, Eyal Fattal and Ronnie Kosloff
From: Department of Physical Chemistry and The Fritz Haber Research
Center for Molecular Dynamics, The Hebrew University Jerusalem
91904 Israel
EMail: ronnie@grid.fh.huji.ac.il
Paper 35
EMail discussions
Locating Transition States Using Double-ended Classical Trajectories
By: A. Matro, D.L. Freeman and J.D. Doll
From: University of Rhode Island and Brown University
EMail: matro@haydn.chm.uri.edu
Paper 36
EMail discussions
Stability, local geometry and resonant vibrations of Cu(+) inmpurity in alkali halides
By: V. Luana, M.A. Blanco, M. Florez, and L. Pueyo
From: Departamento de Quimica Fisica y Analitica, Universidad de Oviedo, E-33006 Oviedo, Spain
EMail: victor@hobbit.quimica.uniovi.es
Paper 37
EMail discussions
Strategies for Determining Interionic Potentials from Ab Initio Calculations of Ionic Crystals
By: M.A. Blanco, E. Francisco, J.M. Recio, A.M. Pendas, and V. Luana.
From: Departamento de Quimica Fisica y Analitica, Facultad de Quimica, Universidad de Oviedo, 33006-Oviedo, SPAIN.
EMail: evelio@hobbit.quimica.uniovi.es
Paper 38
EMail discussions
Modeling Enantioselective Chromatographic Separation of alpha-Pinene Racemates on Permethylated beta-Cyclodextrin
By: Delbert R. Black, Craig G. Parker, S. Scott Zimmerman,* and Milton L. Lee
From: Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
EMail: szimmer@molmod.byu.edu
Paper 39
EMail discussions
Calculations of the Phi-Psi Conformational Contour Maps on N-Acetyl-N'-methylalanineamide (Blocked ala) and of the Characteristic Ratios of Poly-L-Alanine using Various Molecular Mechanics Force Fields
By: Chui Hong Lee and S. Scott Zimmerman
From: Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
EMail: szimmer@molmod.byu.edu
Paper 40
EMail discussions
A quantum chemical study of mechanism and QSAR analysis of dopamine-beta-hydroxylase inhibitors using PM3 method
By: Emadeddin Tajkhorshid(1), Massoud Mahmoudian (2) and Daryoush Khodaverdi (2)
From: (1) Dept. Medicinal Chemistry, School of Pharmacy, Tehran University of Medical Sciences, P.O.Box 14155/6451, Tehran, IRAN
EMail: emadtajk@IREARN.BITNET
Paper 41
EMail discussions
A Localized Projected Atom Approach to Large and Extended Systems
By: Jack A. Smith
From: Union Carbide Corporation, Catalyst Skills Center, P.O. Box 8361,
South Charleston, WV 25303, USA
EMail: jas@medinah.atc.ucarb.com
Paper 42
EMail discussions
Proposed Topography of Compounds Acting at the rho1 Receptor
By: Capper, H.R., Collins, M., Gillies, M.B. & Johnston, G.A.R.
From: Department of Pharmacology, The University of Sydney
EMail: hughc@extro.ucc.su.oz.au
Paper 43
EMail discussions
Intramolecular Vibrational Energy Redistribution and Torsional Isomerization: A Model Classical and Quantum Study
By: Dr. Harold W. Schranz and Michael A. Collins
From: Research School of Chemistry, Australian National University, Canberra, Australia
EMail: Harold.Schranz@anu.edu.au
Paper 44
EMail discussions
Computer Support for the Isoinversion Principle
By: Stefanie Kethers
From: Lehrstuhl V fuer Informatik, RWTH Aachen, Germany
EMail: neysa@picasso.informatik.rwth-aachen.de
Paper 45
EMail discussions
Theoretical electronic and vibrational study of Bn(CO)m (n,m =1,2) with the Density Functional Method : Preliminary Results
By: Pullumbi Pluton, Bouteiller Yves
From: University Paris VI
EMail: pullumbi@ccr.jussieu.fr
Paper 46
EMail discussions
Water clusters - a speculation
By: Dr. Bernd R. Eggen
From: University of Sussex at Brighton (UK)
EMail: B.R.Eggen@Sussex.ac.uk
Paper 47
EMail discussions
Molecular Dynamics Study of Peptide Flexibility
By: Yan Wang and Krzysztof Kuczera
From:
EMail: kuczera@tedybr.chem.ukans.edu
Paper 48
EMail discussions
A check on basis functions in density functional calculations
By: Daniel P. Joubert
From: Physics Department, University of the Witwatersrand,
PO Wits 2050, Johannesburg, South Africa
EMail: joubert@physnet.phys.wits.ac.za
Paper 49
EMail discussions
Application of Genetic Algorithms to the Determination of Protein 3D Structure from NMR Spectroscopy Data
By: Jarmo T. Alander and Jari Ylinen
From: Department of Computer Science and Production Economics, University of Vaasa, P. O. Box 700, FIN-65101 Vaasa, Finland
EMail: jal@uwasa.fi
Paper 50
EMail discussions
The Performance of Generalized Gradient Approximation DFT Methods with Gaussian Basis Sets: Sulfur and Chlorine-containing Molecules
By: Gabor I. Csonka, N. Anh and J. Reffy
From: Department of Inorganic Chemistry, Technical University of Budapest H-1521 Budapest, Hungary
EMail: csonka@iris.inc.bme.hu
Paper 51
EMail discussions
The Ability of the MP2 Method to Model the QCISD(T) Basis Set Extension Effects for the Hydrogen Atoms in Molecules
By: Gabor I. Csonka, N. Anh
From: Department of Inorganic Chemistry, Technical University of Budapest H-1521 Budapest, Hungary
EMail: csonka@iris.inc.bme.hu
Paper 52
EMail discussions
The Evolution of Lactate Dehydrogenase Conformation During Molecular Dynamics Simulations
By: C. A. Letner and G. M. Alter
From: Wright State University, Department of Molecular Biology and
Biochemistry, Dayton, Ohio 45435
EMail: cletner@remcure.bmb.wright.edu
Paper 53
EMail discussions
On the Computation of Functions of Matrices
By: Herbert H. H. Homeier
From: Institut fuer Physikalische und Theoretische Chemie, Universitaet
Regensburg, D-93040 Regensburg, Germany
EMail: Herbert.Homeier@chemie.uni-regensburg.de
Paper 54
EMail discussions
Fluctuating-Charge Molecular Dynamics of Liquid Water
By: Steven J. Stuart
From: Columbia University
EMail: steve@chem.columbia.edu
Paper 55
EMail discussions
Relativistic Molecular Ab Initio Electronic Structure Calculations with the MOLFDIR Program Package
By: W.A. de Jong, F.Dijkstra, L.Visscher, P.J.C. Aerts, W.C.Nieuwpoort
From:
University of Groningen, Department of Chemistry, Theoretical Chemistry Group
EMail: bert@chem.rug.nl
Paper 56
EMail discussions
WWW - Chemist's Friend or Foe? Problems with Electronic Chemical Data Exchange
By: Bernard Blessington(1) and Don Parkin(2)
From: (1) Bradford University, Department of Pharmaceutical Chemistry, Bradford BD7 1DP, UK
EMail: B.Blessington@bradford.ac.uk
Paper 57
EMail discussions
From Electronic Structure to Phase Stability Through Topological Arguments: The Alkali Halide Example
By: A. Martin Pendas, V. Luana, J. M. Recio, M. A. Blanco, E. Francisco, and M. Florez
From: Departamento de Quimica Fisica y Analitica. Facultad de Quimica. Universidad de Oviedo. 33006-Oviedo. SPAIN
EMail: angel@hobbit.quimica.uniovi.es
Paper 58
EMail discussions
Computing Equations of State for Ionic Solids
By: J. M. Recio, A. Martin Pendas, E. Francisco, M. Florez, R. Franco, M. A. Blanco, M. Bermejo, V. Luaqa, and L. Pueyo
From: Departamento de Quimica Fisica y Analitica. Universidad de Oviedo. E-33006 Oviedo. SPAIN
EMail: mateo@hobbit.quimica.uniovi.es
Paper 59
EMail discussions
The Electronic Structure of Singlet and Triplet Nitrenium Ions from MCSCF and DFT Calculations
By: Sharon E. Worthington, Christopher J. Cramer, Frederic J. Dulles and Joey W. Storer
From: Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis MN 55455-0431
EMail: worth@prometheus.chem.umn.edu
Paper 60
EMail discussions
Lone Pairs and the Molecular Electrostatic Potential of Water
By: David Young and James F. Harrison
From: Department of Chemistry, Center for Fundamental Materials Research, Michigan State University, East Lansing, MI 48824-1322
EMail: young@slater.cem.msu.edu
Paper 61
EMail discussions
Atomic and Functional Groups Origins of Non-linear Response Tensors in Urea and Thiourea
By: Keith E. Laidig
From: Department of Medicinal Chemistry, University of Washington,
Seattle, WA 98195
EMail: laidig@fitz.mchem.washington.edu
Paper 62
EMail discussions
RETROSYN: A (Soon to be Public Domain) Tool for Computer Aided Synthesis Design
By: Edward S. Blurock
From: Research Institute for Symbolic Computation, University of Linz, A-4040 LINZ, Austria
EMail: blurock@risc.uni-linz.ac.at
Experimentation is underway to present the documentation not only in
traditional written form, but also in searchable and organized
hypertext. Attempts will be made to automate the documentation
procedure as much as possible. The main thrust of the presentation
will be the the hypertext documentation as of the date of the
conference.
Paper 63
EMail discussions
REACTION: A tool for the Generation and Analysis of Reactive Systems
By: Edward S. Blurock
From: Research Institute for Symbolic Computation, University of Linz, A-4040 LINZ, Austria
EMail: blurock@risc.uni-linz.ac.at
Paper 64
Withdrawn
Paper 65
EMail discussions
Networked Virtual Environments and Electronic Conferencing
By: John Towell,Paul Hansen, Eric Mercer, Martin Leach, Irit Rubin, Jaime Prilusky and Gustavo Glusman
From: Administrators, BioMOO, bioinformatics.weizmann.ac.il 8888
EMail: m50jft1@hayek.cob.niu.edu
Paper 66
EMail discussions
Computing the Fullerene Neighbors
By: Zdenek Slanina and Shyi-Long Lee
From: Department of Chemistry, National Chung-Cheng University, Ming-Hsiung, Chia-Yi 621, Taiwan
EMail: zds@ipp-garching.mpg.de
Paper 68
EMail discussions
Theoretical investigation of the structure, energy and vibrational properties of GaH4 anion
By: Pullumbi Pluton, Bouteiller Yves
From: University Pierre and Marie Curie. (Paris VI)
EMail: pullumbi@ccr.jussieu.fr
Paper 69
EMail discussions
Triflic Acid as a Model for the Acidic Site of the Superacid Catalyst Nafion: an Ab-initio Study of its Hydrogen Bond Propensity
By: G. Ricchiardi and P. Ugliengo
From: Dipartiemnto di Chimica Inorganica, Chimica Fisica e Chimica dei Materiali. Via P. Giuria, 7 I-10125 Torino ITALY
EMail: ugliengo@silver.ch.unito.it
Paper 70
EMail discussions
The Reactions of Methyloxirane and Methylthiirane with Nucleophiles
By: Scott Gronert and Joseph M. Lee
From: San Francisco State University
EMail: gronerts@lewis.sfsu.edu
Paper 71
EMail discussions
Ab Initio Studies of Carbene-Fluoroalkane Complexes
By: Jean M. Standard
From: Department of Chemistry, Illinois State University, Normal, IL 61790-4160
EMail: standard@krypton.che.ilstu.edu
Paper 72
EMail discussions
Study of Addition Reaction to Form Cyclic Urea Derivatives
By: Joerg R.P. Heuer (1) and Harald G. Schweim(1,2)
From: (1) Department of Chemistry and Pharmacy,University of Hamburg, Bundesstr. 45, 20146 Hamburg, Germany
EMail: heuer@chemie.uni-hamburg.de
Paper 73
EMail discussions
Theoretical Study of the Mechanism of Recombinative Hydrogen Desorption from the Si(100) Surface
By: Petr Nachtigall, Carlos Sosa, and Kenneth D. Jordan
From: University of Pittsburgh and Cray Research, Inc.
EMail: petr@theoryg.chem.pitt.edu
Paper 74
EMail discussions
Electrostatic Fields over Ionic Surfaces and into Zeolitic
Cavities: Comparison between LCAO Periodic Calculations in the
Hartree Fock and the Density Functional Approximations
By: M. Causa`
From: Department of Inorganic, Physical and Materials Chemistry,
University of Torino, Via P. Giuria 5 - 10125 , Torino, Italy
EMail: causa@ch.unito.it
Paper 75
EMail discussions
Torsional Dependence of the Methanol-He Interaction Potential
By: Han Thai and Stephen L. Davis
From: Chemistry Department, George Mason University, Fairfax, VA 22030
EMail: sdavis@gmuvax.gmu.edu
Paper 76
EMail discussions
Langevin Dynamics of Simplified Protein Models
By: John M. Troyer(1), Fred E. Cohen(1), and David Ferguson(2)
From: (1) Department Pharmaceutical Chemistry,University of California, San Francisco
EMail: troyer@cgl.ucsf.edu
Paper 77
EMail discussions
Conformational Analysis of 2-Aminoethanal and Methylated Derivatives
By: Luis Carballeira and Ignacio Perez-Juste
From: Laboratorio de Quimica Fisica, Facultad de Ciencias, Universidad de Vigo Apdo, 874, Vigo, SPAIN
EMail: uviqpipj@cesga.es
Paper 78
EMail discussions
Insights into the Mechanism of the Asymmetric Reduction of Ketones with Diisopinoampheyl Boron Chloride
By: Mark D. Mackey and Jonathan M. Goodman
From: Department of Chemistry, Cambridge University
EMail: mdm1004@cus.cam.ac.uk
Paper 79
EMail discussions
Quantum Control of Molecular Dynamics with Tailored Light Pulses
By: Jianwei
Che,
Eric A.
Fernandes,
Bern
Kohler,
From: Department of Chemistry, University of California at Sab Diego, La Jolla, Ca 92093-0339
EMail: krwilson@ucsd.edu
Paper 80
EMail discussions
Multimedia Chemistry and Education
By: Eric A.
Fernandes,
Mike
Messina,
Bret J.
Naylor,
From: Senses Bureau, University of California, Department of Chemistry 0339,La Jolla, CA 92093-0339
EMail: ashergil@chem.UCSD.EDU
Paper 81
EMail discussions
Klotho
By: Brian Dunford-Shore, Francis Fabrizio, Jason Holcomb, William Wise and Toni Kazic
From: Institute for Biomedical Computing
Washington University, St. Louis MO 63110
EMail: toni@athe.wustl.edu