bluuebunny/crossref_metadata_2025 huggingface dataset:
Normal coordinates–finite elements calculation of 3D vibrational energy levels: Henon—Heiles and Eckart potentials, H molecule
Authors: Alvarez–collado J. R.
Published: January 2005

Theoretical and numerical results related to the calculation of multidimensional vibrational levels are presented. A description of the methodological details of a very general method (normal coordinates–finite elements, NC–FEM) is provided. Several representative three‐dimensional (3D) systems (Henon–Heiles and Eckart potentials, and the H molecule) are studied, and NC–FEM results are compared with those published by other authors. For the H, a vibrational Hamiltonian expressed in terms of the three internuclear distances is integrated, and the results obtained are compared with the experimental ones. © 1994 by John Wiley & Sons, Inc.
Modulation of intramolecular proton transfer by electronic excitation and environment: 2‐Pyridone as a case study
Authors: Barone Vincenzo , Adamo Carlo
Published: January 2005

The kinetics and thermodynamics of lactam/lactim tautomerization in 2‐pyridone have been investigated, with special attention to direct and assisted proton transfer mechanisms in the ground and first excited electronic state. Specific interactions with a single water molecule strongly enhance the reaction rate and shift the equilibrium toward the lactam form. The effect of bulk solvent is comparatively negligible, although the lactam form is further stabilized. Electron excitation strongly destabilizes the saddle point for proton transfer and, especially, the lactim form with respect to the lactam species. As a consequence, the direct reaction barrier is increased, but the reverse barrier is lowered. Nonpotential energy effects are relatively small and do not modify the aforementioned general trends. © 1994 by John Wiley & Sons, Inc.
MRD‐CI studies of vertical excitation energies of unsaturated hydrocarbon molecules
Authors: Grimme S.
Published: January 2005

Systematic MRD‐CI calculations using the AM1 Hamiltonian have been carried out for two polyenes and eight aromatic hydrocarbons ranging from benzene to ovalene (C32H14). Twenty singlet–singlet excitation energies in these compounds were calculated and compared with experimental data and ab initio STO‐3G results. On an absolute scale, the AM1/MRD‐CI approach underestimates the excitation energies to states with dominant covalent character by an average of 1.1 eV, whereas the errors for ionic states are between −1.0 and 1.0 eV. The STO‐3G calculated data are much too high by ≈ 1 eV and ≈ 5 eV, respectively. The inclusion of σπ‐correlation effects through second‐order Epstein–Nesbet perturbation theory combined with the use of localized orbitals leads to a significant improvement of the ab initio calculated state energies. In an analogous AM1 treatment, negligible corrections for the σπ correlations are found, which is attributed to the implicit account in the parameters and approximation of the semiempirical Hamiltonian. The possible error sources of the calculational methods are discussed. © 1994 by John Wiley & Sons, Inc.
Atomic orbital basis sets for molecular interactions
Authors: Da Costa Herbert F. M. , Micha David A.
Published: January 2005

We describe a general approach to the parametrization of linear combinations of Gaussian atomic orbitals, useful for atomic and molecular interactions. We use a Gaussian transform method and Gauss‐Legendre quadratures to express hydrogenic atomic orbitals, with varying effective charges, in terms of Gaussian‐type orbitals. This procedure provides well‐defined rules for calculating exponent factors and combination coefficients of the linear combinations of Gaussians in problems where nuclear distances may vary over large ranges during interactions. © 1994 by John Wiley & Sons, Inc.
An optimized AM1/MST method for the MST‐SCRF representation of solvated systems
Authors: Luque F. J. , Bachs M. , Orozco Modesto
Published: January 2005

The AM1/MST strategy for the computation of hydrated neutral molecules has been optimized. For this purpose, we have systematically explored the best cavity definition, the most suitable strategy to compute the molecular electrostatic potential (MEP), and the use of MEP scaling factors to correct the semiempirical MEPs. As a result, we have developed an optimized version of the AM1/MST method, which allows us to reproduce well the experimental free energies of hydration (root mean square, rms, deviation in the range of 1 kcal/mol) as well as the water‐induced dipoles computed at the 6‐31G*/MST level (rms deviations in the range of 0.3 D). © 1994 by John Wiley & Sons, Inc.
Study of localized molecular orbitals using group theory methods and its approach to the many‐electron correlation problem. IV. The symmetry‐adaptation of many‐center integrals and hamiltonian matrix elements in MCSCF calculations
Authors: Zhou Taijin , Liu Aimin
Published: January 2005

Group theoretic methods are presented for the transformations of integrals and the evaluation of matrix elements encountered in multiconfigurational self‐consistent field (MCSCF) and configuration interaction (CI) calculations. The method has the advantages of needing only to deal with a symmetry unique set of atomic orbitals (AO) integrals and transformation from unique atomic integrals to unique molecular integrals rather than with all of them. Hamiltonian matrix element is expressed by a linear combination of product terms of many‐center unique integrals and geometric factors. The group symmetry localized orbitals as atomic and molecular orbitals are a key feature of this algorithm. The method provides an alternative to traditional method that requires a table of coupling coefficients for products of the irreducible representations of the molecular point group. Geometric factors effectively eliminate these coupling coefficients. The saving of time and space in integral computations and transformations is analyzed. © 1994 by John Wiley & Sons, Inc.
Molecular mechanics (MM3) parameterization of hydroxylamine and methyl derivatives
Authors: Liang Guyan , Bowen J. Phillip , Bentley James A.
Published: January 2005

Based on results of electron diffraction, gas phase infrared spectroscopy (IR), and MP2/6‐31 + G* ab initio calculations, a set of molecular mechanics (MM3) parameters was developed for molecules containing the N(sp3)—O(sp3) moiety. Using this set of parameters, MM3 is able to reproduce structures (bond lengths and bond angles) and vibrational spectra satisfactorily. © 1994 by John Wiley & Sons, Inc.
Triazene proton affinities: A comparison between density functional, Hartree–Fock, and post‐Hartree–Fock methods
Authors: Schmiedekamp Ann M. , Topol Igor A. , Burt Stanley K. , Razafinjanahary Holy , Chermette Henry , Pfaltzgraff Timothy , Michejda Christopher J.
Published: January 2005

The consistency of three density functional computational implementations (DMol, DGauss, and deMon) are compared with high‐level Hartree–Fock and Møller–Plesset (MP) calculations for triazene (HNNNH2) and formyl triazene (HNNNHCOH). Proton affinities on all electronegative sites are investigated as well as the geometries of the neutral and protonated species. Density functional calculations employing the nonlocal gradient corrections show agreement with MP calculations for both proton affinities and geometries of neutral and protonated triazenes. Local spin density approximation DMol calculations using numerical basis sets must employ an extended basis to agree with other density functional codes using analytic Gaussian basis sets. The lowest energy conformation of triazene was found to be nonplanar; however, the degree of nonplanarity, as well as some bond lengths, is dependent on the basis set, electron correlation treatment, and methods used for the calculation. © 1994 by John Wiley & Sons, Inc.

This article is a U.S. Government work and, as such, is in the public domain in the United States of America.
Structure of disiloxane: A semiempirical and Post‐Hartree–Fock study
Authors: Csonka Gábor I. , Erdösy Miklós , Réffy József
Published: January 2005

The semiempirical (MNDO, AM1, and PM3) and ab initio predicted structure of disiloxane is studied with a series of basis sets and inclusion of electron correlation at MP2, MP3, MP4, CCD, CCSD, and CCSD(T) levels. The calculated molecular geometry and barrier to linearization of the SiOSi bond angle are compared with previous theoretical and experimental values. Our results show that the calculated barrier to linearization is very sensitive to the number of polarization functions in the basis set. We also investigate the coupling between the SiOSi bond angle and the SiO bond length and calculate the Mulliken and electrostatic potential‐derived charges. For comparison purposes we also calculate the molecular geometry, the barrier to linearization of the SiOSi bond angle, and the atomic charges in hexamethyldisiloxane. © 1994 by John Wiley & Sons, Inc.
Potential energy surfaces for RhCO from DFT calculations
Authors: Biemolt W. , Jansen A. P. J.
Published: January 2005

We present potential energy surfaces for RhCO obtained from density functional theory for two electronic states of RhCO. We have performed local spin‐density calculations including relativistic as well as gradient corrections. The construction of a reasonably accurate atom–atom potential for RhCO is not possible. We were much more successful in constructing the potential energy surfaces by representing the potential as a spherical expansion. The expansion coefficients, which are functions of the distance between the rhodium atom and the carbon monoxide center of mass, can be represented by Lennard‐Jones, Buckingham, or Morse functions, with an error of the fit within 10 kJ/mol. The potential energy surfaces, using Morse functions, predict that the electronic ground state of RhCO is 2Σ+ or 2Δ. This is a linear structure with an equilibrium distance of rhodium to the carbon monoxide center of mass of 0.253 nm. The bonding energy is −184 kJ/mol. Further, Morse functions predict that the first exicted state is 4A′. This is a bent structure (∠RhCO = 14°) with an equilibrium distance of rhodium to the carbon monoxide center of mass of 0.298 nm. The bonding energy of this state is −60 kJ/mol. Both these predictions are in good agreement with the actual density functional calculations. We found 0.250 nm with −205 kJ/mol for 2Σ+ and 0.253 nm with −199 kJ/mol for 2Δ. For 4A′, we found 0.271 nm, ∠RhCO = 30°, with −63 kJ/mol. The larger deviation for 4A′ than for 2Σ+ or 2Δ is a consequence of the fact that the minimum for 4A′ is a very shallow well. © 1994 by John Wiley & Sons, Inc.
The natural atomic orbital point charge model for PM3: Multipole moments and molecular electrostatic potentials
Authors: Beck Bernd , Rauhut Guntram , Clark Timothy
Published: January 2005

The natural atomic orbital/point (NAO‐PC) model originally developed to calculate molecular electrostatic potentials (MEPs) and multiple moments based on the AM1 wave function has been extended to PM3. As for AM1, NAO‐PC/PM3 reproduces dipole moments calculated by the standard PM3 method very well. There is also a surprisingly good correlation between experimental and calculated quadrupole moments. The MEPs calculated using PM3/NAO‐PC are found to be in better agreement with those given by RHF/6‐31G* than those obtained from the PM3 wave function using Coulson charges. On the other hand, the NAO‐PC model is often slightly worse then the method implemented in MOPAC‐ESP. The MEPs calculated using our model based on the PM3 wave function are often in better agreement with those given by RHF/6‐31G* than those obtain with AM1. © 1994 by John Wiley & Sons, Inc.
Conformational sensitivity analysis of FKBP–FK506/rapamycin complexes
Authors: Susnow Roberta , Senko Nancie , Ocain Timothy
Published: January 2005

Sensitivity analysis techniques are applied to the FKBP–FK506 and FKBP–rapamycin complexes to quantify the conformational relationships between FKBP and its ligands. Crystal structures of the two FKBP complexes are energy minimized in the Amber force field using a continuum solvent model, and derived Green's function sensitivity coefficients are developed to describe the relationship between the ϕ, ψ, and χ1 torsional angles of the FKBP residues and the bound ligand macrocycle torsional angles. Sensitivity analysis is applied to the entire FKBP structure and reveals that the local conformation of the residues of the 80s and 50s loops and of the active site are sensitive to the ligand conformation. The analysis also reveals that the torsional angles controlling the orientation of the amide and keto carbonyls of FK506 are sensitive to the aromatic side chains in the FKBP carbonyl binding pocket. © 1994 by John Wiley & Sons, Inc.
Efficient parallelization of the energy, surface, and derivative calculations for internal coordinate mechanics
Authors: Totrov Maxim , Abagyan Ruben
Published: January 2005

An efficient algorithm for parallelization of a molecular mechanics program operating in the space of internal coordinates such as dihedral angles, bond angles, and bond lengths is described. The iterative procedure to calculate analytical energy derivatives with respect to the internal coordinates was modified to allow parallelization. Computationally intensive modules that calculate energy and its derivatives, solvent‐accessible surface, electrostatic polarization energy and that update lists of interactions were parallelized with nearly 100% efficiency. The proposed strategy for the shared‐memory computer architecture is easily scalable and requires minimum changes in a program code. The overall speedup for a realistic calculation minimizing the energy of a myoglobin reaches a factor of 3 for 4 processors. © 1994 by John Wiley & Sons, Inc.
The use of Fraga's potential with AM1 atomic point charges in the evaluation of spectral shifts: Application to TICT molecules
Authors: Gorse Alain‐Dominique , Pesquer Michel
Published: January 2005

Fraga potential calculations with atomic point charges and geometrical parameters calculated from AM1 calculations have been used to calculate spectral shifts upon electronic excitation in twisted intramolecular charge transfer (TICT) systems due to intermolecular interactions. Changes of atomic polarizabilities have also been taken into account. Present calculations deal with absorption transitions of the p‐N,N‐dimethylaminobenzonitrile (DMABN) surrounded by methane, water, acetone, or acetonitrile solvent molecules. The methodology permits us to evaluate the influence of the solvent molecule on DMABN dimethylamino motions and to find the most stable conformation of a cluster configuration which can lead to a blue or red shift. The results have been compared with the experimental work of Warren et al.7 and confirm their analysis. © 1994 by John Wiley & Sons, Inc.
A computational study of azine, azoethene, and diimine linkages in the poly/oligoazine system
Authors: Schmitz Brian K. , Euler William B.
Published: January 2005

Hartree‐Fock (HF) and molecular mechanics calculations were performed on linear azine oligomers and model compounds. The rotational energy curves for the model compounds formaldazine, H2C = NN = CH2, ethenyl diazene, H2C = CHN = NH, and ethanediimine, HN = CHCH = NH were calculated for a variety of basis sets at the HF and MP2 level. In all of these cases the rotational energy barriers are quite different from butadienes or aza‐substituted butadienes because of the lone pair–lone pair interaction of the adjacent nitrogen atoms. The results on the model compounds were used to generate a set of molecular mechanics (MM) parameters that are appropriate for linear oligo‐ and polyazines. Comparison of the geometries of the HF results and MM results for the oligoazines showed that the two methods gave comparable results. © 1994 by John Wiley & Sons, Inc.
A variational biorthogonal valence bond method
Authors: Malcolm Nathaniel O. J. , McDouall Joseph J. W.
Published: January 2005

The details of a simple and efficient scheme for performing variational biorthogonal valence bond calculations are presented. A variational bound on the energy functional is obtained through the use of a complete configuration expansion in a well‐chosen subset of orbitals. The resultant wave functions are clearly dominated by the covalent (spin‐coupled) structures, with a negligible contribution from ionic structures. The orbitals obtained compare favorably with overlap enhanced atomic orbitals obtained by other valence bond approaches. The method is illustrated by calculations on water and dioxygen difluoride. © 1994 by John Wiley & Sons, Inc.
Implementation of artificial intelligence for automatic drug design. I. Stepwise computation of the interactive drug‐design sequence
Authors: Cohen Alexander A. , Shatzmiller Shimon E.
Published: January 2005

In this article we represent the development of an artificial‐intelligence‐based method for the automatic design of valid chemical structures (AISD). The key feature of the proposed algorithm is its ability to mimic many decision‐making processes carried by the human drug designer during a design session. The manual drug‐design process is analyzed and transformed into a computerized form by associating a weight factor with each term. These weights enable the translation of the drug designer's intution into probabilities that control the flow of the design process. The input required to initiate a design session might be as minimal as the geometry of a previously existed pharmacophoric model, up to the three‐dimensional geometry of the host receptor. A design application is demonstrated by the implementation of the proposed algorithm for the design of new potent sweeteners. © 1994 by John Wiley & Sons, Inc.
ToBaD: A method for the estimation of torsion barriers from crystal structure data; conformational analysis of N,N‐dimethylaniline and derivatives
Authors: Verdonk M. L. , Tjerkstra R. W. , Ridder I. S. , Kanters J. A. , Kroon J. , van der Kemp W. J. M.
Published: January 2005

A new method for the estimation of torsion barriers and its application to conformational analysis is presented. This method, the ToBaD method (method of the torsion barrier derivative), makes use of crystal structure data. It is based on the assumption that the conformation of a compound in the crystalline phase must be very close to a (local) minimum energy conformation of this compound in the gas phase. The ToBaD method is demonstrated for the rotation of the phenyl‐N bond in N,N‐dimethylaniline. Two geometries of this compound are handled separately: one in which the nitrogen substituents are in a pyramidal or sp3 geometry, and the other in which the nitrogen atom and its substituents are coplanar (the sp2 geometry). It is predicted, by means of the ToBaD method, that for both geometries the conformation in which the nitrogen lone pair or p orbital is perpendicular to the aromatic ring is the lowest energy conformation. © 1994 by John Wiley & Sons, Inc.
Propella[34] prismane and its congeners: A MO‐theoretical study
Authors: Gleiter Rolf , Pfeifer Karl‐Heinz , Koch Wolfram
Published: January 2005

The geometries of a fourfold bridged tricyclo[4.2.0.02,5]octa‐3,7‐diene (1) and its photoproducts 2 and 3 were calculated by Hartree‐Fock ab initio (3‐21G and DZP basis) and semiempirical (MNDO, AM1, MINDO /3) methods. It was found that due to the smaller distance between the double bonds in 1 (2.65 Å) as compared to the parent tricyclo[4.2.0.02,5]octa‐3,7‐diene (4) (2.91 Å), the sequence of the frontier orbitals is different. In the case of 1, the photochemical [2 + 2]cycloaddition is allowed, whereas in 4 it is forbidden. © 1995 by John Wiley & Sons, Inc.
Implementation of reaction field methods in quantum chemistry computer codes
Authors: De Vries A. H. , Van Duijnen P. Th. , Juffer A. H. , Rullmann J. A. C. , Dijkman J. P. , Merenga H. , Thole B. T.
Published: January 2005

The embedding of a quantum mechanically described subsystem by classical representations of its surroundings is reviewed. The choices for a distributed monopole representation and a distributed (group) polarizability representation, as well as the continuum approach to model bulk effects, are discussed. Focus is on the practical implementation of the classical description in quantum chemistry codes (in particular, HONDO8.1). Expressions are given for the self‐consistent coupling between the classical partitions (dipole polarizabilities and boundary surface dipoles and charges) and for the coupling between classical and quantum partitions. The latter is mediated through expanded, rather than exact, potentials and fields. In this way, the computation of only a limited number of formal interactions between unit charge distributions located at the expansion centers suffices to evaluate the reaction field contributions. The electronic part of the coupling can be included in the Hamiltonian via the Fock matrix. The field operators, as well as the one‐ and two‐electron matrix elements over the basis functions, are simple. The expressions for these are given explicitly.

Nonequilibrium potentials and Monte Carlo sampling over classical degrees of freedom have been added to better mimic experimental conditions. © 1995 by John Wiley & Sons, Inc.
Force field parameters for sulfates and sulfamates based onab initiocalculations: Extensions of AMBER and CHARMm fields
Authors: Huige Cornelis J. M. , Altona Cornelis
Published: January 2005

Ab initioself‐consistent field (SCF) Hartree‐Fock calculations of sulfatesROSO3(−1) (R= Me, Et, i‐Pr) and sulfamatesRNHSO3(−1) (R= H, Me, Et, i‐Pr) were performed at the 4‐31G(*S*N) //3‐21G(*S*N) basis set levels, where asterisks indicatedfunctions on sulfur and nitrogen atoms. These standard levels were determined by comparing calculation results with several basis sets up to MP2/6‐31G*//6‐31G*. Several conformations per compound were studied to obtain molecular geometries, rotational barriers, and potential derived point charges. In methyl sulfate, the rotational barrier around the CO bond is 1.6 kcal/mol at the MP2 level and 1.4 kcal/mol at the standard level. Its ground state has one of three HCOS torsion angles trans and one of three COSO torsion angles trans. Rotation over 60° around the single OS bond in the sulfate group costs 2.5 kcal/mol at the MP2 and 2.1 kcal/mol at the standard level. For ethyl sulfate, the calculated rotational barrier in going from the ground state, which has its CCOS torsion angle trans, to the syn‐periplanar conformation (CCOS torsion angle cis) is 4.8 kcal/mol. However, a much lower barrier of 0.7 kcal/mol leads to a secondary gauchelike conformation about 0.4 kcal/mol above the ground state, with the CCOS torsion angle at 87.6°. Again, one of the COSO torsion angles is trans in the ground state, and the rotational barrier for a 60° rotation of the sulfate group amounts to 1.8 kcal/mol. For methyl sulfamate, the rotational barriers are 2.5 kcal/mol around the CN bond and 3.3 kcal/mol around the NS bond. This is noteworthy because sulfamate itself has a calculated rotational barrier around the NS bond of only 1.7 kcal/mol. These and other data were used to parameterize the well‐known empirical force fields AMBER and CHARMm. When the new fields were tested by means of vibrational frequency calculations at the 6‐31G*//6‐31G* level for methyl sulfate, sulfamate, and methyl sulfamate ground states, the frequencies compared favorably with the AMBER and CHARMm calculated frequencies. The transferability of the force parameters to β‐D‐glucose‐6‐sulfate and isopropyl sulfate appears to be better than to isopropyl sulfamate. © 1995 by John Wiley & Sons, Inc.
The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies
Authors: Eisenhaber Frank , Lijnzaad Philip , Argos Patrick , Sander Chris , Scharf Michael
Published: January 2005

The double cubic lattice method (DCLM) is an accurate and rapid approach for computing numerically molecular surface areas (such as the solvent accessible or van der Waals surface) and the volume and compactness of molecular assemblies and for generating dot surfaces. The algorithm has no special memory requirements and can be easily implemented. The computation speed is extremely high, making interactive calculation of surfaces, volumes, and dot surfaces for systems of 1000 and more atoms possible on single‐processor workstations. The algorithm can be easily parallelized. The DCLM is an algorithmic variant of the approach proposed by Shrake and Rupley (J. Mol. Biol., 79, 351–371, 1973). However, the application of two cubic lattices—one for grouping neighboring atomic centers and the other for grouping neighboring surface dots of an atom—results in a drastic reduction of central processing unit (CPU) time consumption by avoiding redundant distance checks. This is most noticeable for compact conformations. For instance, the calculation of the solvent accessible surface area of the crystal conformation of bovine pancreatic trypsin inhibitor (entry 4PTI of the Brookhaven Protein Data Bank, 362‐point sphere for all 454 nonhydrogen atoms) takes less than 1 second (on a single R3000 processor of an SGI 4D/480, about 5 MFLOP). The DCLM does not depend on the spherical point distribution applied. The quality of unit sphere tesselations is discussed. We propose new ways of subdivision based on the icosahedron and dodecahedron, which achieve constantly low ratios of longest to shortest arcs over the whole frequency range. The DCLM is the method of choice, especially for large molecular complexes and high point densities. Its speed has been compared to the fastest techniques known to the authors, and it was found to be superior, especially when also taking into account the small memory requirement and the flexibility of the algorithm. The program text may be obtained on request. © 1995 by John Wiley & Sons, Inc.
Uncoupled Hartree–Fock calculations of the polarizability and hyperpolarizabilities of nitrophenols
Authors: Bursi R. , Lankhorst M. , Feil D.
Published: January 2005

The polarizability and hyperpolarizabilities of nitrophenols as model compounds for studying nonlinear optics have been investigated at the Hartree‐Fock level of approximation by means of the Dalgarno Uncoupled Hartree‐Fock (DUHF) or Sum Over Orbitals (SOO) method. The additive character and the charge transfer effects in α, β, and γ have been analyzed in terms of the σ and π molecular orbital contributions, the contribution of the individual π molecular orbitals, and the contribution of the highest occupied and the lowest unoccupied molecular orbitals. Within the SOO approach, the reliability of the Two‐Level Model has been tested and the influence of the rotation of the nitro group and of the presence of the intramolecular hydrogen bonding in ortho‐nitrophenol have been studied. The results show that the present method is a reliable and efficient tool for the prediction of trends in the molecular polarizability and hyperpolarizabilities of large molecules. © 1995 by John Wiley & Sons, Inc.
INDO parameters for the elements of the I and II transition rows
Authors: Sizova O. V. , Baranovski V. I.
Published: January 2005

It is shown that with the use of published one‐center INDO parameters for transition metals M, it is not possible to reproduce experimental relative energies of the electronic states of M, M+, and M2+ accurately enough. Two new sets of INDO parameters for the elements of the I and II transition rows are developed. These parameters are obtained by the method which ensures that the calculated energy differences between atomic electron states are in agreement with the experimental data. The results of some molecular test calculations are presented. © 1995 by John Wiley & Sons, Inc.
Conformational memories and a simulated annealing program that learns: Application to LTB4
Authors: Guarnieri Frank , Wilson Stephen R.
Published: January 2005

The use of computer simulations in all areas of chemistry is growing rapidly because of the powerful insights that they have provided into many interesting phenomena. As investigators continuously examine more sophisticated problems, they need increasingly more powerful tools. Hence, much effort has gone into the development of algorithms which might extend the scope and power of standard dynamic and Monte Carlo techniques. In the Monte Carlo regime, the most common area subject to improvement is the choice of a trial move. In the ordinary case, trial moves are generated uniformly at random. In the extended and hopefully improved case, trial moves are generated randomly but not uniformly. In this article we present a new and totally general method of biased sampling which is applicable to any flexible molecule. In our method, multiple simulated annealing runs are performed to reveal populated and unpopulated regions of the multidimensional conformation space. The second phase of the simulation is done at a fixed temperature with sampling only from populated regions found in the first phase. Because the simulated annealing runs quickly reveal unpopulated regions of the conformation space, the volume of conformation space that needs to be sampled in the second phase of the algorithm is reduced by many orders of magnitude. Additionally, because no energy minimization is used, these populations represent a canonical ensemble which may be used to estimate conformational free energies. © 1995 by John Wiley & Sons, Inc.
A simple yet accurate boundary element method for continuum dielectric calculations
Authors: Purisima Enrico O. , Nilar Shahul H.
Published: January 2005

A simple yet accurate method for calculating electrostatic potentials using the boundary element continuum dielectric method is presented. It is shown that the limiting factor in accuracy is not the evaluation of integrals involving the interaction between boundary elements but rather a proper estimation of the self‐polarization of a patch upon itself. We derive a sum rule that allows us to calculate this important self‐polarization term in a self‐consistent and simple way. Intricate integration schemes used in previous treatments are consequently rendered unnecessary while concurrently achieving at least comparable accuracy over earlier methods. In some model systems for which analytic solutions are available, the computed surface polarization charge and reaction field energy are correct to better than six significant figures. An application of the method to the calculation of hydration free energies is presented. Good agreement with experimental values is obtained.
Genetic algorithms: A robust scheme for geometry optimizations and global minimum structure problems
Authors: Mestres Jordi , Scuseria Gustavo E.
Published: January 2005

A Genetic Algorithm for Geometry Optimizations (GALGO) program has been developed to study the efficiency of this method of finding global minimum structures. Using a semiempirical tight‐binding potential, the behavior of different genetic algorithm (GA) operators has been tested for the linear chain isomer of a C8 cluster. An optimum set of parameters for the GA operators is proposed for this problem and afterward is used to obtain the global minimum structure of rare‐gas atomic clusters of up to 13 atoms using the 12–6 Lennard‐Jones interatomic pair potential. © 1995 by John Wiley & Sons, Inc.
Force field studies of cholesterol and cholesteryl acetate crystals and cholesterol–cholesterol intermolecular interactions
Authors: Liang Congxin , Yan Liqun , Hill Jörg‐R. , Ewig Carl S. , Stouch Terry R. , Hagler Arnold T.
Published: January 2005

To model the physical properties of sterols and related species, an all‐atom Class II force field has been derived based on the recently reported CFF93 force field for hydrocarbons. It has been tested using both energy minimization and molecular dynamics (MD) simulations of the low‐temperature neutron‐diffraction structure of cholesteryl acetate crystals and the X‐ray diffraction crystal structure of cholesterol. Thus these studies test the techniques and limitations of high‐accuracy crystal simulations as well. Employing energy minimization, all cell vectors and volumes were reproduced to within 2.4% of experimental values. For cholesteryl acetate, the root mean square (rms) deviations between the calculated and experimental bond lengths, angles, and torsions of nonhydrogen atoms are 0.013 Å, 1.2°, and 2.4°, respectively. The corresponding maximum deviations are also very small: 0.027 Å for bond length, 3.2° for angle, and 7.6° for torsion. For cholesterol, good agreement between the calculated and experimental structures was found only when the comparison was limited to atoms with relatively small thermal factors (Beq < 15 Å2). It was found that for both systems, the MD averaged structures were in better agreement with the experimental ones than the energy minimized structures, since the rms deviations in atom positions are smaller for the MD‐averaged structures (0.064 Å for cholesteryl acetate and 0.152 Å for cholesterol) than those for the minimized structures (0.178 Å for cholesteryl acetate and 0.189 Å for cholesterol). The force field was then applied to isolated molecules focusing on the rigidity of the cholesteryl ring and cholesterol–cholesterol interaction energies. It is concluded that the cholesteryl ring is fairly rigid since no major conformational change was observed during an MD simulation of a single cholesterol molecule in vacuo at 500 K, in agreement with condensed phase experiments. Calculations of cholesterol–cholesterol pairs suggest that there are only four low‐energy configurations and that it is more useful to describe each molecule as having a plane (flat face) and two grooves rather than as having two (one flat and one rough) faces. This provides some insight into the equilibrium crystal structures. Limited results from a modified Class I (CVFF) force field are presented for comparison. © 1995 by John Wiley & Sons, Inc.
An improved molecular modeling method for the prediction of enantioselectivity
Authors: Aerts J.
Published: January 2005

An improved method for the calculation of enantioselectivity by molecular mechanics is presented. This method does not use any a priori assumption on the conformation of the molecules in the complex and is equally applicable to weak as well as very strong complexes. High‐temperature molecular dynamics is used for the creation of a large number (5000–20,000) of random conformations and configurations of a 1:1 (or 1:2) complex of chiral molecules with a chiral selector. All configurations are energy minimized. The data set is only accepted if all lowest‐energy complexes occur at least five times in the minimized data set. The enantioselectivity is then calculated from the free energies of the diasteromeric complexes (chiral chromatography) or from the ratio of the sum of the Boltzmann weights (distribution of enantiomers over a chiral organic phase and a nonchiral water phase). This approach has been successfully applied to a range of chiral compounds. These include a weakly bonded Pirkle chiral stationary phase (CSP) system, a strong complex of diprotonated 1,2‐diphenyl‐1,2‐diamino‐ethane with two molecules of R,R‐tartrate, and the intermediate‐strength complexes of protonated and of neutral norephedrine with R,R‐tartrate. © 1995 by John Wiley & Sons, Inc.
An improved description of the molecular charge density in force fields with atomic multipole moments
Authors: Koch Uwe , Egert Ernst
Published: January 2005

Atomic multipole moments, calculated from ab initio wave functions, offer an attractive way toward an improvement of the description of electrostatic interactions in force‐field programs. Accordingly, we have implemented the formulas for calculation of energies, forces, and torques resulting from the interactions of multipoles up to quadrupole–quadrupole interactions in our force‐field program MOMO. The method was successfully applied to various problems, including conformational analysis, hydrogen bonding, and π–π interactions. © 1995 by John Wiley & Sons, Inc.
Parallel direct implementations of second‐order perturbation theories
Authors: Nielsen Ida M. B. , Seidl Edward T.
Published: January 2005

Two algorithms are presented for parallel direct computation of energies with second‐order perturbation theory. Closed‐shell MP2 theory as well as the open‐shell perturbation theories OPT2(2) and ZAPT2 have been implemented. The algorithms are designed for distributed memory parallel computers. The first algorithm exhibits an excellent load balance and scales well when relatively few processors are used, but a large communication overhead reduces the efficiency for larger numbers of processors. The other algorithm employs very little interprocessor communication and scales well for large systems. In both implementations the memory requirement has been reduced by allowing the two‐electron integral transformation to be performed in multiple passes and by distributing the (partially) transformed integrals between processors. Results are presented for systems with up to 327 basis functions. © 1995 John Wiley & Sons, Inc.
Density functional theory and molecular clusters
Authors: Hobza Pavel , šponer Jiří , Reschel Tomáš
Published: January 2005

Density functional theory (DFT) methods, including nonlocal density gradient terms in the exchange and correlation energy functionals, were applied to various types of molecular clusters: H‐bonded, ionic, electrostatic, and London. Reliable results on the structure and stabilization energy were obtained for the first two types of cluster as long as Becke3LYP and Becke3P86 functionals and basis sets of at least DZ + P quality were used. DFT methods with currently available functionals failed completely, however, for London‐type clusters, for which no minimum was found on the potential energy surfaces. DFT interaction energy exhibits the same basis set extension dependence as the Hartree‐Fock (HF) interaction energy. Therefore, the Boys‐Bernardi function counterpoise procedure should be employed for elimination of the DFT basis set superposition error. © 1995 John Wiley & Sons, Inc.
A molecular dynamics study of the inhibition of chicken dihydrofolate reductase by a phenyl triazine
Authors: Leach Andrew R. , Klein Teri E.
Published: January 2005

Molecular dynamics simulations have been used to investigate the ternary complex formed between chicken liver dihydrofolate reductase, a phenyl triazine inhibitor, and reduced nicotinamide adenine dinucleotide phosphate (NADPH). The solvent was represented by a sphere of water molecules encompassing the system. We report the results of quantum mechanical calculations of the rotational barrier in the pyrophosphate link and the barrier to inversion of the triazine ring. AMBER parameters for NADPH and the triazine are provided. Over the course of a 300‐ps molecular dynamics simulation of the ternary complex in water, the triazine inhibitor maintains the same hydrogen bonding and hydrophobic interactions with the enzyme that are observed in the X‐ray crystal structure. Despite the low calculated barrier to inversion of the triazine ring, a single puckered conformation is observed throughout the simulation. It is proposed that this is primarily due to interactions with Phe34, which maintains an approximately parallel orientation to the triazine ring. The nicotinamide portion of NADPH maintains the interactions observed in the crystal structure, but more conformational change is observed at the adenine end together with associated changes in the protein. Two conformations for the sidechain of Tyr31 are present in the X‐ray structure. The main simulation reported here corresponds to the conformation characterized by (χ1 = − 161°, χ2 = − 103°). A separate simulation was also performed in which the sidechain of Tyr31 was initially set to the other conformation present in the crystal structure (χ1 = 139°, χ2 = −99°). During this simulation, χ1 of this sidechain gradually changed until it occupied the region characterized by χ1 = −160°, thereby suggesting that this is the preferred conformation for this residue. The simulation required 200 ps to reach structural equilibrium (as measured by the root mean square, rms, deviation from the initial crystal structure), thus reinforcing the view that simulations of at least several hundreds of picoseconds are desirable when studying such systems. © 1995 John Wiley & Sons, Inc.
Energy minimization of peptide analogues using genetic algorithms
Authors: Herrmann Frank , Suhai Sándor
Published: January 2005

A genetic algorithm is used to minimize the energy of peptide analogues in the dihedral angle space. It is interfaced to MOPAC, which computes the energy employing the AM1 Hamiltonian. The genetic algorithm identified the global energy minimum of glycine dipeptide analogue, alanine dipeptide analogue, diglycine, and dialanine. It identified three low‐energy conformations of tetraalanine, including the reported global minimum, all of which contained three hydrogen bonds. A structure with a lower energy than the reported global minimum has been generated in which one hydrogen bond is replaced by another one. © 1995 John Wiley & Sons, Inc.
Bond energies in chloroethanes and chloroethyl radicals
Authors: Frankin J. A. , Huybrechts G. H.
Published: January 2005

CCl and CC bond energies in the chloroethanes and CH, CCl, and CC bond energies in the chloroethyl radicals are calculated from known heats of formation of chloroethanes and chloroethylenes and known CH bond energies in chloroethanes.

The results obtained show a dependence of bond energy on the isomeric structure of the molecules and radicals and on the type of bond broken (primary, secondary, or tertiary). Heats of formation and bond energies estimated from group property additivity rules are in close agreement with experimental values.
Methylene radical reaction with cis‐butene‐2
Authors: Ring D. F. , Rabinovitch B. S.
Published: January 2005

A study of the pressure dependence of the C5 products from the reaction of cis‐butene‐2 and methylene is reported. Methylene was produced by the photolysis of diazomethane with 4358 Å light at 23° or 56°, and by photolysis of ketene with 3200 Å radiation at 23° or 100°. The change with increasing pressure of the relative amounts of the characteristically “triplet products” (trans‐1,2‐dimethylcyclopropane, trans‐pentene‐2 (TP2), and 3‐methylbutene‐1 (3MB1)) and “singlet products” (cis‐1,2‐dimethylcyclopropane (CDMC) and cis‐pentene‐2 (CP2)) are discussed. The behavior is reminiscent of that found in 3CH2‐cis‐butene‐2 systems and can be interpreted in terms of the rapid rate of rearrangement of an initial triplet diradical product component, due to 3CH2, relative to the slower rate and readier collisional stabilization of an initial vibrationally‐excited dimethyl cyclopropane product component, due to 1CH2. Relative rates of reactions of 1CH2 with allylic CH:vinyl CH:CC in the neat liquid were, for diazomethane, 1:1.1:7.2 and, for ketene, 1:1.2:6.7.
Peresters XIII. Solvent effects in the decomposition of t‐butylperoxy α‐phenylisobutyrate with special reference to the cage effect
Authors: Herkes Frank E. , Friedman Juliette , Bartlett Paul D.
Published: January 2005

t‐Butylperoxy α‐phenylisobutyrate (I) decomposes thermally by concerted formation of carbon dioxide, t‐butoxy, and cumyl radicals. Radical pair return in the solvent cage therefore does not affect the observed rate of decomposition, but is readily determined by means of galvinoxyl and other scavengers. In a series of 15 solvents the rate constant varies over a 2.8 fold range, being fastest in aromatic solvents. In the same solvent series the relative rates of diffusion and combination of radicals, measured by the cage effect, change by tenfold and are largely determined by the viscosity of the solvent. In all solvents of η > 8 mP, the reciprocal of the cage effect is a linear function of (T1/2/η), as recently observed for trifluoromethyl and methyl radicals [16]. This property of the cage effect provides a test by which it can be distinguished from other processes that reduce the efficiency of free‐radical production from an initiator.
Kinetics and rate constants for the reaction of tri‐n‐butylgermanium hydride with methyl iodide and carbon tetrachloride. The combination of methyl and trichloromethyl radicals in solution.
Authors: Carlsson D. J. , Ingold K. U. , Bray L. C.
Published: January 2005

The kinetics of the photoinitiated reductions of methyl iodide and carbon tetrachloride by tri‐n‐butylgermanium hydride in cyclohexane at 25°C have been studied and absolute rate constants have been measured. Rate constants for the combination of CH3ċ and CCl3ċ radicals are equal within experimental error and are also equal to the values found for the self‐reactions of most non‐polymeric radicals in low viscosity solvents, i.e. ∼1–3 × 109 M−1 sec−1.

Rate constants for hydrogen atom abstraction by CH3ċ and CCl3ċ radicals are both ∼1−2 × 105 M−1 sec−1. Tri‐n‐butyltin hydride is about 10–20 times as good a hydrogen donor to alkyl radicals as is tri‐n‐butylgermanium hydride.

The strength of the germanium–hydrogen bond, D(n‐Bu3Ge–H) is estimated to be approximately 84 kcal/mole.
Kinetics of the reaction of cyclopentane with trichloroethylene
Authors: Hardwick T. J.
Published: January 2005

The kinetics of the thermally and radiation initiated chain reaction between trichloroethylene and cyclopentane to produce 1,1‐dichlorovinylcyclopentane and hydrogen chloride have been investigated in the temperature range 250–360°C at high pressure in the gas phase. The rate governing step in the chain is (k3 = 3.3 × 109 exp −(4800/RT) cc mole−1 sec −1). The rate of the unimolecular decomposition of trichloroethylene is 1.4 × 1014 exp −(61,200/RT) sec−1.
Activating effects of unsaturated and cyclopropyl groups in gas phase pyrolysis of acetates. Paper XVIII
Authors: Lum Kin K. , Smith Grant Gill
Published: January 2005

The activating effects of a number of unsaturated groups and a cyclopropyl group have been evaluated in a solvent free system by determining the absolute rate constants, and energies and entropies of activation in the vapor phase pyrolysis of secondary and tertiary esters of the type RC(R′CH3) OAc where R′ = H or CH3 and R = c‐Pr, i‐Pr, CH3, CH2CH, CH2CHCH2, C6H5; the cyclopropyl showed only a moderate activating effect. The results are in contrast to the very significant activating effect of a cyclopropyl group in solvolysis of cyclopropylcarbinyl derivatives. Apparently marked activation by this group occurs only when a highly developed positive center forms adjacent to it. The lack of marked activation by the cyclopropyl group supports a mechanism for ester pyrolysis which involves a modest, but detectable, charge separation in the transition state [2] but questions a mechanism in which an intimate ion‐pair was proposed [3].
The photolysis of pentafluoroacetone
Authors: Pritchard G. O. , Perona M. J.
Published: January 2005

The photolysis of pentafluoroacetone has been investigated in the 3130 Å region, from room temperature to 360°C. The ΦCO varies from 0.7 to 0.9 over this range, and the decomposition is represented by CF2HCOCF3 → CF2H + CO + CF3. The disproportionation/combination ratio for CF3 and CF2H (→ CF3H + CF2) radicals is found to be 0.09. Arrhenius parameters for hydrogen atom abstraction from the ketone are log10A = 12.7 (units are mole−1 cc sec−1) and E = 14.3 kcal mole−1 for CF2H, and log10A = 12.1 and E = 11.8, for CF3 radicals. At low pressures HF elimination reactions are observed from the vibrationally excited fluoroethanes, C2F5H* and C2F4H2*, formed in the system. A rough estimate of the activation energy for the process C2F5H → C2F4 + HF of 60–65 kcal mole−1 is made.