bluuebunny/crossref_metadata_2025 huggingface dataset:
On the use of conformationally dependent geometry trends from ab initio dipeptide studies to refine potentials for the empirical force field CHARMM
Authors: Momany Frank A. , Klimkowski Valentine J. , Schäfer Lothar
Published: January 2005

Previous 4‐21G ab initio geometry optimizations of various conformations of the model dipeptides (N‐acetyl N'methyl amides) of glycine (GLY) and the alanine (ALA) have been used to help refine the empirical force constants and equilibrium geometry in the CHARMM force field for peptides. Conformationally dependent geometry trends from ab initio calculations and positions of energy minima on the ab initio energy surfaces have been used as guides in the parameter refinement, leading to modifications in the bond stretch, angle bending, and some torsional parameters. Preliminary results obtained with these refined empirical parameters are presented for the protein Crambin. Results for the cyclic (Ala‐Pro‐DPhe)2 are compared with those from other calculations. It seems that the dihedral angle fit achieved by the new parameters is significantly improved compared with results from force fields whose derivation does not include ab initio geometry trends.
Simulations of internal rotation potential energies for substituted ethanes
Authors: Chung‐Phillips Alice , Stevenson Thomas A.
Published: January 2005

Two approaches to the simulation of internal rotation potential energies in substituted ethanes are formulated for general applications. Called the vicinal Fourier coefficient and vicinal pair energy methods, they differ only in form. The latter procedure has the advantage of yielding energy terms that represent pairwise interactions between vicinal substitutents. As numerical examples, the potential energies of ethane and five of its simple methyl and chloro derivatives are employed to simulate the corresponding energies of two higher derivatives of the series. The initial energy data were calculated by the molecular mechanics method (MM2) with geometry optimizations and the ab initio MO procedure (STO‐3G) with standard geometries. Results indicate that simulated energies are reasonably accurate for the flexible‐rotor model (MM2) and extremely accurate for the rigid‐rotor model (STO‐3G). Deviations appear to be systematic and may be rationalized on the basis of molecular structure.
Different approaches to conformational analysis: A comparison of completeness, efficiency, and reliability based on the study of a nine‐membered lactam
Authors: Böhm Hans‐Joachim , Klebe Gerhard , Lorenz Thomas , Mietzner Thomas , Siggel Lorenz
Published: January 2005

Different methods such as molecular dynamics, systematic, or stochastic search and a special “generic shape” algorithm have been employed in the conformational analysis of a nine‐membered lactam. Furthermore, crystal data were used to generate conformations of the compound under consideration. The various methods are compared in terms of their efficiency and completeness in the search for conformations with an energy content of up to 60 kJ/mol above the global minimum. Additionally, the generated conformations have been optimized by different techniques, molecular mechanics and quantum chemical calculations, to compare the number of existing local minima and their relative energies and geometries.
A boundary element method for molecular electrostatics with electrolyte effects
Authors: Yoon Byung Jun , Lenhoff A. M.
Published: January 2005

A boundary element method is developed to compute the electrostatic potential inside and around molecules in an electrolyte solution. A set of boundary integral equations are derived based on the integral formulations of the Poisson equation and the linearized Poisson‐Boltzmann equation. The boundary integral equations are then solved numerically after discretizing the molecular surface into a number of flat triangular elements. The method is applied to a spherical molecule for which analytical solutions are available. Use is made of both constant and linearly varying unknowns over the boundary elements, and the method is tested for various values of parameters such as the dielectric constant of the molecule, ionic strength, and the location of the interior point charge. The use of the boundary integral method incorporating the nonlinear Poisson‐Boltzmann equation is also briefly discussed.
Conserving energy during molecular dynamics simulations of water, proteins, and proteins in water
Authors: Kitchen Douglas B. , Hirata Fumio , Westbrook John D. , Levy Ronald , Kofke David , Yarmush Martin
Published: January 2005

Molecular dynamics simulations have been carried out for a series of systems of increasing complexity including: pure water, a model polypeptide (α‐helical decaglycine) in vacuo, a protein (Pancreatic Trypsin Inhibitor, PTI) in vacuo, and a fully solvated protein (PTI in water). The equations of motion were integrated using Andersen's velocity version of the Verlet algorithm with internal contraints (the RATTLE algorithm). The accuracy with which the equations of motion are integrated has been analyzed for several different simulation conditions. The effects of various nonbonded interaction truncation schemes on the conservation of energy have been examined, including the use of atomic cutoffs, and (neutral group) residue cutoffs. The use of a smoothing function to eliminate the discontinuities in the potential at the cutoff leads to a significant improvement in the accuracy of the integration for each of the systems studied. The accuracy with which the equations of motion are integrated using the RATTLE algorithm for pure water and for the solvated protein are found to be comparable when the nonbonded interactions are tapered with a smoothing function at the cutoff.
The nature of the N  H…︁OC hydrogen bond: An intermolecular perturbation theory study of the formamide/formaldehyde complex
Authors: Mitchell John B. O. , Price Sarah L.
Published: January 2005

We have used Hayes‐Stone Intermolecular Perturbation Theory (IMPT) to study the variation with distance and orientation of the various components of the interaction energy of the N  H…︁O = C hydrogen bonded trans‐ formamide/formaldehyde complex, a model system for hydrogen bonding in proteins. The directionality of the total interaction energy is similar to that of the electrostatic component alone. We have analysed our data in terms of two model atom‐atom intermolecular potentials, using an isotropic functional form and an anisotropic one. The anisotropic form gives an excellent representation of the IMPT potential energy surface, considerably better than the isotropic model, and is comprised entirely of theoretically justified, physically meaningful terms.
Exo‐exo and endo‐endo vicinal proton spin‐spin coupling constants in norbornane and norbornene. An IPPP‐CLOPPA analysis
Authors: Cavasotto C. N. , Giribet C. G. , de Azúa M. C. Ruiz , Contreras R. H.
Published: January 2005

The IPPP‐CLOPPA method is used to study the origin of the difference between exo‐exo and endo‐endo vicinal interproton couplings in norbornane and norbornene. The main pathway defining such couplings is found to be determined by the corresponding CH bonds and antibonds. For this reason they can be considered to be transmitted through space. Contributions from excitations involving MOs of bridge 7 and the CH endo and exo bonds and antibonds are found to be negligible in both compounds. Even though bridges 5–6 and 7 are not included in the coupling pathway, they influence the structure of endo and exo CH bonds, and thus cause the nonequivalence of endo‐endo and exo‐exo couplings. Results obtained with the NNBI method are compared to those of IPPP‐CLOPPA.
Geometry optimization in semiempirical SCF‐MO‐CI calculations
Authors: Pötter T. , Klessinger M.
Published: January 2005

It is shown that up to 50% of the computer time needed for geometry optimization on the (semiempirical) CI level by means of gradients calculated as finite differences can be saved by using “corrected noncentral gradients” in combination with a judiciously chosen first estimate of the Hessian in order to assure fast convergence of the procedure.
A simple approximation for the vibrational partition function of a hindered internal rotation
Authors: Truhlar Donald G.
Published: January 2005

A simple formula is presented for calculating the approximate partition function of a hindered internal rotational mode of a polyatomic molecule. The formula gives useful accuracy over the whole range from harmonic oscillator to hindered rotator to free rotator.
A simple method for calculating atomic charges in charged molecular systems of biochemical interest
Authors: Mullay John
Published: January 2005

A previously developed method for calculating atomic charge in neutral molecules is modified so as to account for charged molecular species. The method is based on the orbital electronegativity (EN) concept and utilizes an EN equalization principal. Since only one linear equation is required per bond in the molecule, the scheme is extremely simple to use and thus is readily applicable to larger molecules of interest to biochemistry. Atom charge results are compared to ab initio calculations as well as experimental data from NMR and X‐ray diffraction studies. It is shown that the method compares very well even with higher level theoretical methods for a variety of charged molecules including alanine and protonated adenine. It is also shown that NMR chemical shift data for charged amino acids are correlated quite well with atomic charges from the present method. In addition charges obtained from X‐ray diffraction data for both ionic alanine and 2′‐deoxycytidine‐5′‐monophosphate are also reproduced very well.
Algorithms for calculating excluded volume and its derivatives as a function of molecular conformation and their use in energy minimization
Authors: Kundrot Craig E. , Ponder Jay W. , Richards Frederic M.
Published: January 2005

A numerical method for calculating the volume of a macromolecule and its first and second derivatives as a function of atomic coordinates is presented. For N atoms, the method requires about 0.3 N ln(N) seconds of CPU time on a VAX‐8800 to evaluate the volume and derivatives. As a test case, the method was used to evaluate a pressure‐volume energy term in energy minimizations of the protein lysozyme at 1000 atm (1 atm = 1.013 × 105 Pa). R.m.s. gradients of 10−4 kcal/mol/Å were obtained at convergence. The calculated structures exhibited pressure‐induced changes which were qualitatively similar to the changes observed in the 1000 atm structure determined by X‐ray crystallography.
Molecular mechanics (MM) and MM‐EHMO conformational analysis of the diastereoisomers of 3‐amino‐1,2,3‐triphenyl‐1‐propyl chloride
Authors: Ivanov Petko M. , Momchilova Tatyana G. , Pojarlieff Ivan G.
Published: January 2005

The conformations of simple alkyl substituted 1,2‐diphenylethanes and the diastereoisomers of 3‐amino‐1,2,3‐triphenyl‐1‐propyl chloride were studied by the MM2 force field with the addition of electrostatic corrections to the aromatic force field as proposed recently by Allinger and Lii (dipole‐dipole interactions) and independently by Pettersson and Liljefors (charge‐charge interactions). Computations were also carried out with a modified version of the MM2 program utilizing the MM3 van der Waals potential function and parameters for C (type 2, sp2 hybridized) and H (type 5). The inclusion of dipole moments for the Csp2Csp3 and Csp2H bonds significantly improves the results. A lower value for the V1 parameter for the torsional unit CarCalCalCar had to be used instead of the MM2 value of 2.1 kcal/mol. Computations were carried out also with the hybrid MM‐EHMO procedure. The latter method appears to work correctly also with 1,2,3‐triphenylpropane systems.
Molecular topology. IV. Regressive vertex degrees (new graph invariants) and derived topological indices
Authors: Diudea Mircea V. , Minailiuc Ovidiu , Balaban Alexandru T.
Published: January 2005

New local graph invariants, “regressive vertex degrees” (which are slightly augmented vertex degrees) are introduced on the basis of decreasing contributions of more remote vertexes to the classical vertex degrees. Several such invariants are proposed (BR, ER, SR) where t (either t = 1 or t = 2) is an operator expressing the attenuation with increasing topological distance, according to formula (1) or (2). With the aid of these new local invariants, new topological indices (global graph invariants), Y (namely BY, EY or SY) are introduced and exemplified. Their ability to express the branching and to order alkanes is investigated. An appendix gives some recursive relationships for computing these indices.
The incorporation of hydration forces determined by continuum electrostatics into molecular mechanics simulations
Authors: Zauhar R. J.
Published: January 2005

A new technique is presented for incorporating hydration forces into molecular mechanics simulations. The method assumes the classical continuum approximation, where a solvated molecule is represented as a low‐dielectric cavity of arbitrary shape embedded in a continuous region of high dielectric constant. Electrostatic effects are computed by first calculating the distribution of polarization charge (induced by the configuration of solute fixed charges) at the molecular surface. The hydration force at a particular atom is then found as the sum of the coulombic interaction with the induced surface charge, plus a purely mechanical contribution that arises from the pressure of the polarized solvent as it is pulled toward the solute. A procedure is developed to use the computed hydration forces in conjunction with the CHARMM molecular mechanics package to carry out energy minimizations in which the effects of solvation are explicitly included. This new technique also allows a detailed analysis of the relative balance of coulombic, hydration, and steric energies as a function of molecular conformation. The method is applied to the test case of a zwitterionic tripeptide (LYS‐GLY‐GLU), and the computational results suggest that hydration effects can play a significant role in determining a stable conformation for a solvated polar molecule. The future application to larger molecules is discussed.
A comparative study of the simulated‐annealing and Monte Carlo‐with‐minimization approaches to the minimum‐energy structures of polypeptides: [Met]‐enkephalin
Authors: Nayeem Akbar , Vila Jorge , Scheraga Harold A.
Published: January 2005

A comparison of two methods for surmounting the multiple‐minima problem, Simulated Annealing (SA) and Monte Carlo with Minimization (MCM), is presented with applications to [Met]‐enkephalin in the absence and in the presence of water. SA explores a continuous space of internal variables, while MCM explores a discrete space consisting of the local energy minima on that space. Starting from random conformations chosen from the whole conformational space in both cases, it is found that, while SA converges to low‐energy structures significantly faster than MCM, the former does not converge to a unique minimum whereas the latter does. Furthermore, the behavior of the RMS deviations with respect to the apparent global minimum (for enkephalin in the absence of water) shows no correlation with the observed overall energy decrease in the case of SA, whereas such a correlation is quite evident with MCM; this implies that, even though the potential energy decreases in the annealing process, the Monte Carlo SA trajectory does not proceed towards the global minimum. Possible reasons for these differences between the two methods are discussed. It is concluded that, while SA presents attractive prospects for possibly improving or refining given structures, it must be considered inferior to MCM, at least in problems where little or no structural information is available for the molecule of interest.
Molecular simulations of DD‐peptidase, a model ß‐lactam‐binding protein: Synergy between X‐ray crystallography and computational chemistry
Authors: Boyd Donald B. , Snoddy John D. , Lin Ho‐Shen
Published: January 2005

Using computer model building, the three‐dimensional structure of an enzyme from Streptomyces R61 that is inhibited by ß‐lactam antibiotics has been constructed starting from incomplete X‐ray crystallographic data for this 37.4 kDa protein. The so‐called DD‐peptidase catalyzes transpeptidation and hydrolysis of peptides terminating in D‐Ala‐D‐Ala and is a model for bacterial transpeptidases and carboxypeptidases essential in the biosynthesis of the peptidoglycan layer of the cell wall. The structure, which was completed with the SYBYL molecular modeling package, has been refined by energy minimization and molecular dynamics using Quanta/CHARMm software. A simulation of 105 ps was run with waters of solvation in the active site. From these computations, the interatomic distances between the active serine and key residues around the active site were determined. Inadequacies at reproducing geometric details of the ß‐lactam ring of a cephalosporin are pointed out which are typical of most commercially available force fields.
A semiempirical theoretical study of the molecular interaction of cocaine with the biological substrate glycine
Authors: Wu C. S. , Neely W. C. , Worley S. D.
Published: January 2005

Semiempirical SCFMO computations of the MNDO and AM1 varieties have been employed to model possible interaction processes for cocaine with the biological substrate glycine. It was found for the gas‐phase species that the most likely interactions occurred as nucleophilic attack of the nitrogen lone pair of glycine on the two carbonyl groups of cocaine. These reactions led to intermediates which further decomposed exothermically to amide and alcohol species. The activation enthalpies for the gas‐phase reactions were predicted to be high (39–46 kcal/mol), but it is believed that such processes could possibly occur by reaction pathways with considerably lower activation energies in the liquid state in the presence of mucus containing olfactory binding protein in vertebrate olfactory reception.
Principal component analysis of dipole moment derivative signs of chloroform
Authors: Suto Elisabete , Ferreira M. M. C. , Bruns Roy E.
Published: January 2005

The use of principal components as a basis for a graphical procedure to analyze polar tensor data is proposed. Molecular orbital and experimental polar tensor data for all possible sign combinations of the ∂p/∂Qj of CHCl3 and CDCl3 are represented graphically as principal component scores facilitating sign selection for the ∂p/∂Qj. The graphs are particularly useful in analyzing an apparent conflict in ∂p/∂Qj sign choices based on the isotopic invariance criterion and molecular orbital results for the A1 symmetry species of these molecules. The numerical impacts of individual sign ambiguities for the ∂p/∂Qj on the polar tensor data are measured by the variances associated with the principal components. Assuming the ∂p/∂Qj sign sets with indeterminate signs provide replicated results for the polar tensor elements, their errors are estimated and compared with errors obtained previously by propagating intensity uncertainties through the polar tensor equations.
Free energy calculations on calcium and magnesium complexes: Protein and phospholipid model systems
Authors: Charifson Paul S. , Hiskey Richard G. , Pedersen Lee G. , Kuyper Lee F.
Published: January 2005

Free energy calculations have been performed on a variety of calcium (Ca(II)) and magnesium (Mg(II)) complexes as model systems for protein‐metal, phospholipid‐metal, and protein‐metal‐phospholipid interactions. The major goal of this work was to advance our understanding of Ca(II) ion selectivity in the blood coagulation proteins. The limitations of present force field methods as applied to divalent metal ion‐containing systems is discussed. The effects of different water models, varying nonbond cutoff values, and counterions are evaluated. Additionally, the effects of complete charge transformation between predetermined quantum mechanical states is evaluated in which all of the charges of the metal complexes as well as the van der Waals radii of the metals are perturbed. Protein models include formate, malonate, ethylene‐diaminetetraacetate, and 1,1,4,4 ‐butanetetracarboxylic acid. Phospholipid mimics included methylphosphatidylserine, methylphosphatidylcholine, dimethyl phosphate, and trans‐cyclohexane‐1,3‐diphosphate. The present set of calculations tends to overestimate Mg(II) binding in the various test systems for which experimental results exist, an effect which may in part be due to the lack of explicit polarization/charge transfer terms for all molecules, including water, in the force field. However, these calculations support the notion that coagulation protein selectivity towards Ca(II) is likely due to a greater ease of desolvation of Ca(II) over Mg(II).
Charges derived from distributed multipole series
Authors: Ferenczy György G.
Published: January 2005

A novel method to calculate electrostatic charges is proposed. Partial charges are fitted to reproduce the electrostatic potential of a distributed multipole series without explicitly evaluating electrostatic potentials. The calculation is economical and results in charges reflecting the symmetry properties of charge centers and being independent of molecular orientation.
Basis sets for geometry optimizations of second‐row transition metal inorganic and organometallic complexes
Authors: Sargent Andrew L. , Hall Michael B.
Published: January 2005

Modest‐sized basis sets for the second‐row transition metal atoms are developed for use in geometry optimization calculations. Our method is patterned after previous work on basis sets for first‐row transition metal atoms. The basis sets are constructed from the minimal basis sets of Huzinaga and are augmented with a set of diffuse p and d functions. The exponents of these diffuse functions are chosen to minimize both the difference between the calculated and experimental equilibrium geometries and the total molecular energies for several second‐row transition metal inorganic and organon etallic complexes. Slightly smaller basis sets, based on the same Huzinaga minimal sets but augmented with a set of diffuse s and p functions rather than diffuse p and d functions, are also presented. The performance of these basis sets is tested on a wide variety of second‐row transition metal inorganic and organometallic complexes and is compared to pseudopotential basis sets incorporating effective core potentials.
A computer automated structure evaluation (CASE) approach to calculation of partition coefficient
Authors: Klopman Gilles , Wang Shaomeng
Published: January 2005

A Computer Automated Structure Evaluation (CASE) approach to the calculation of partition coefficient (log P) has been developed. A linear regression equation was obtained linking the log P value of molecules to some of their fragments as identified by a CASE analysis. The relationship was obtained for a database consisting of 935 compounds (r2 = 0.93, s = 0.39, F(39, 895, 0.05) = 316.5). It was found that this approach produced accurate log P estimations even for complex molecules and, in general, gave better results than previously described techniques.
An unbounded systematic search of conformational space
Authors: Goodman Jonathan M. , Still W. Clark
Published: January 2005

A new method for searching internal coordinate conformational space systematically via a continuous‐process procedure is described. Unlike previous systematic search methods, the new scheme generates torsionally remote conformers early in the search. It is also unbounded in that the extent of the search need not be specified at the outset. The search begins at low resolution (120° in torsion angle space) and then goes to higher and higher resolution as all points in space at a given resolution have been searched. The search may run without end or be terminated when new conformers cease to be found or when all space at some maximum allowable resolution has been explored. Conformational searches on several medium‐ and large‐ring molecules using the new method are described and the results are compared with those from certain previously described search methods. It is found that the new method is significantly more efficient than previous procedures at finding all low energy conformers of organic molecules.
An ab initio study of the proton affinities of some heteroatomic rings: Imidazole, oxazole, and thiazole
Authors: Kabir Shahrzad , Sapse Anne‐Marie
Published: January 2005

The proton affinities of imidazole, oxazole, and thiazole rings, relevant to the binding of lexitropsins that contain these rings to the minor groove of DNA, are calculated using ab initio (Hartree–Fock) calculations. It is found that the proton affinities decrease in the order imidazole, oxazole, thiazole and that a methyl group substituent increases the proton affinity of imidazole, while a peptidic group decreases it.
A Monte Carlo simulation of free energy relationships for the electron transfer reaction between Fe+ and Fe2+ in water
Authors: González‐Lafont Angels , Lluch José M. , Oliva Antonio , Bertrán Juan
Published: January 2005

A free energy barrier ΔF≠ = 174.2 kJ/mol for the self‐exchange electron transfer reaction model Fe+/Fe2+ in water has been calculated by combining Monte Carlo simulations and the statistical perturbation theory. We have shown that, even for those electron transfer reactions that present a very high free energy barrier of activation, the free energy curve behaves parabolically versus the reaction coordinate, which justifies the quadratic expression for the activation free energy done by Marcus.
Sixty‐atom carbon cages
Authors: Liu X. , Klein D. J. , Seitz W. A. , Schmalz T. G.
Published: January 2005

The enumeration of all 60‐atom carbon cages associated to trivalent polyhedra with five‐and six‐sided faces is addressed. This isomer problem is computationally solved to give 1790 cages, with a further resolution into subclasses of cages with differing numbers p of abutting pairs of pentagonal faces. The individual cages are generated, and then there are computed various graph‐theoretic invariants, including Hückel MO energies, HOMO‐LUMO gaps, Kekulé structure counts, and conjugated‐circuit counts. Associated properties as a function of p are reported and found to be in concert with earlier qualitative arguments. It is found that the most stable of these cages is the unqiue p = 0 Buckminsterfullerene structure.
Conformational sampling and ensemble generation by molecular dynamics simulations: 18‐Crown‐6 as a test case
Authors: Sun Yaxiong , Kollman Peter A.
Published: January 2005

Using the crown ether 18‐crown‐6 as a test system, molecular dynamics has been evaluated as a technique for conformational searching and thermodynamic ensemble generation. By running a series of 200 ps and 2 ns simulations, an “optimum” temperature range for conformational searching, i.e., the temperature at which one finds the largest number of low energy structures, was demonstrated to be dependent on the time interval at which one examines the structure. By considering conformational degeneracy and entropy with the rigid rotor harmonic oscillator approximation we have been able to demonstrate that the ensemble generated approaches thermodynamic equilibrium in about 6 ns of simulation. To our knowledge this is the first time this has been demonstrated for a complex organic molecule and it highlights the power and usefulness of molecular dynamics as a method for thermodynamic ensemble generation and conformational searching.
Conformational analysis of trehalose disaccharides and analogues using MM3
Authors: Dowd Michael K. , Reilly Peter J. , French Alfred D.
Published: January 2005

Energy surfaces for the relative orientations of the pyranosyl rings of α,α‐, α,β‐, and β,β‐trehalose and analogues were generated with MM3. Sixteen starting conformations of the rotatable side groups of α,β‐trehalose were considered, while only 10 conformations were needed for α,α‐ and β,β‐trehalose because of molecular symmetry. Energies were calculated at 20° increments of the two torsional angles of the glycosidic linkage, but otherwise the molecules were fully relaxed. The structure at the overall minimum for α,α‐trehalose agrees well with that found in crystal structures, and also agrees with interpretations of NMR and optical rotation data. The energy surfaces for the three trehaloses differ greatly from each other, but are each similar to those for the corresponding three 2‐(6‐methyltetrahydropyran‐2‐yloxy)6‐methyltetrahydropyrans. This suggests that linkage type (axial or equatorial) is more important than exocyclic substituents in determining trehalose conformations. A comparison with surfaces from the corresponding 5a‐carba trehalose analogues illustrates that the exo‐anomeric effect is important in determining disaccharide conformation.
Basis set and correlation energy dependence of geometry and harmonic frequencies of difluoroethane, CHF2CH3
Authors: Speis Martin , Buss Volker
Published: January 2005

Optimum geometries and harmonic frequencies calculated at the Hartree–Fock and the MP2 level are reported for the fluorohydrocarbon CHF2CH3; basis sets employed range from STO‐3G to 6‐311G**. The significantly shortened CC distance of 1.50 Å is reproduced already with the simplest split‐valence basis set; the CF distance of 1.36 Å on the other hand needs MP2 correction at least at the double‐ζ or 6‐311G* level. Symmetry coordinates defined in terms of internal coordinates are in qualitative agreement with available experimental evidence. Even the best basis set yields frequencies that differ from experimental (anharmonic) values by up to 200 cm−1 indicating the well‐known necessity of including higher‐order force constants if quantitative agreement with experiment is to be achieved.
A concurrent algorithm for parallel calculation of eigenvalues and eigenvectors of real symmetric matrices
Authors: Carbo Ramon , Molino Lluís , Calabuig Blanca
Published: January 2005

Elementary Jacobi Rotations are used as the basic tools to obtain eigenvalues and eigenvectors of arbitrary real symmetric matrices. The proposed algorithm has a complete concurrent structure, that is: every eigenvalue‐eigenvector pair can be obtained in any order and in an independent way from the rest. Examples based on diagonally dominant real symmetric matrices are given.
Calculated structures and relative stabilities of furoxan, some 1,2‐dinitrosoethylenes and other isomers
Authors: Seminario Jorge M. , Concha Monica C. , Politzer Peter
Published: January 2005

The structures and relative stabilities of furoxan and some of its isomers, e.g., the 1,2‐dinitrosoethylenes, have been determined by means of ab initio Hartee–Fock and Møller–Plesset calculations. Geometries were optimized at the HF/3‐21G, HF/6‐31G* and MP2/6‐31G* levels, and subsequently used for computing MP2/6‐31G*, MP3/6‐31G*, and MP4/6‐31G* energies. The results are markedly affected by the inclusion of electronic correlation, which renders three of the isomers unstable. It also emphasizes the importance of a zwitterionic contribution to the structure of furoxan, which promotes ring‐opening through a cis 1,2‐dinitrosoethylene intermediate/transition state that has an MP4/6‐31G*//MP2/6‐31G* energy that is 31.6 kcal/mol above furoxan.
Davydov soliton dynamics: Initial state, boundary conditions, and numerical procedure
Authors: Förner Wolfgang
Published: January 2005

The performance of a Runge‐Kutta method of fourth order in dynamic simulations within Davydov's so‐called |D2〉 state ansatz is studied by comparison with analytical solutions available for two special cases. Further, the Runge–Kutta method is compared with the one‐step procedure used by Su and Schrieffer. A detailed analysis of the structure and energetics of Davydov solitons is given. The differences in the dynamics between open chain ends and periodic boundary conditions are also discussed. The properties of the soliton detector plot introduced by Lomdahl and Kerr are studied. Finally, three widely used initial states for Davydov soliton dynamics are compared.
Floating functions satisfying the hellmann—feynman theorem: Single floating scheme
Authors: Hirao K. , Mogi K.
Published: January 2005

The electrostatic calculation for molecules using approximated variational wave functions leads to well known difficulties connected with the application of the Hellmann‐Feynman (HF) theorem. This is due to the basis set inadequacies in the underlying calculations. This defect can easily be remedied by floating functions, whose centers are optimized in space. We can keep almost everything of the traditional wave function with a nuclear‐fixed basis set, but we apply single floating to ensure the HF theorem. Then, one can obtain a wave function obeying the HF theorem. This provides a great conceptual simplification and may lead to practical advantages. The single floating scheme, which retains one expansion center per nucleus, is successfully applied to a series of small molecules using SCF and CASSCF wave functions with sufficiently polarized basis sets.
Comparison of ab initio, semiempirical, and molecular mechanics calculations for the conformational analysis of ring systems
Authors: Ferguson David M. , Gould Ian R. , Glauser William A. , Schroeder Stefan , Kollman Peter A.
Published: January 2005

The potential energy surfaces of four cyclic alkanes have been examined using molecular mechanics, semiempirical, and ab initio methods to determine if they produce mutually consistent results and investigate the source of any errors between the methods. The C5  C8 cyclic alkanes were chosen since these structures present a finite set of conformations and transition‐state geometries and are still within the computational time and memory limits of the quantum mechanical approaches. We also examined several conformations of 1,2‐dideoxyribose to determine the effect of heteroatoms on the results for the 5‐membered ring. The molecular mechanics and ab initio calculations are consistent in the relative energies and geometries determined for the conformers of all ring systems. While the semiempirical calculations yielded geometries consistent with the other methods (except for 5‐membered rings), the relative energies often deviated substantially. A decomposition analysis of the semiempirical and molecular mechanics energies revealed that the disparities are mainly due to errors in the 1‐center energies of the semiempirical calculations. The 2‐center bonding and nonbonding energies followed reasonable trends for the conformers. The core‐repulsion function, however, is suspected of producing anomalies. A minimum in the attractive Gaussian of this term at 2.1 Å for HH interactions partly explains the propensity of the 5‐membered rings to optimize to near planarity (decreasing 1,2‐diaxial hydrogen distances to 2.3 Å) and the underestimation of the relative energy of the boat structure of cyclohexane.
Locally implicit solution of a reaction‐diffusion system with stiff kinetics
Authors: Vasquez Desiderio A.
Published: January 2005

The Tyson‐Fife reaction‐diffusion equations are solved numerically using a locally implicit approach. Since the variables evolve at very different time scales, the resulting system of equations is stiff. The reaction term is responsible for the stiffness and the time step is increased by using an implicit method. The diffusion operator is evaluated explicitly and the system of implicit nonlinear equations is decoupled. The method is particularly useful for parameter values in which the equations are very stiff, such as the values obtained directly from the experimental reaction rate constants. Previous efforts modified the parameters on the equations to avoid stiffness. The equations then become a simplified model of excitable media and, for those cases, the locally implicit method gives a faster although less accurate solution. Nevertheless, since the modified equations no longer represent a particular chemical system an accurate solution is not as important. The algorithm is applied to observe the transition from simple motion to compound motion of a spiral tip.
Artificial redox enzymes. II. A computational chemistry study1
Authors: Tong Weida , Ye Hongping , Rong Ding , D'Souza Valerian T.
Published: January 2005

A computational chemistry study of the artificial redox enzyme synthesized by covalently attaching flavin to cyclodextrins explains some of its properties. Calculations indicate that the flavin moiety covalently attached to cyclodextrin is not within the cavity of cyclodextrin. This result is consistent with the UV‐vis spectrum of the artificial enzyme. The calculations also indicate hydrogen bonds formed between the carbonyl groups of the catalytic functionality and the hydroxyl groups of cyclodextrin play a role in their most stable conformation. This explains the observed overall stability of these artificial enzymes compared to riboflavin. Electrostatic energies and solvation energies play a major role in the stability of the hosts and the orientation of guests included within the artificial enzymes. The rates of oxidation of various thiols catalyzed by the artificial enzyme can be explained by the relative distances between the sulfur atom of the substrates and C(4a) of the flavin moiety.
Conformational preferences for hydroxyl groups in substituted tetrahydropyrans
Authors: Zheng Ya‐Jun , Le Grand Scott M. , Merz Kenneth M.
Published: January 2005

Quantum mechanical (ab initio and semiempirical) and force field calculations are reported for representative torsion potentials in several tetrahydropyran derivatives. The overall agreement between the various methods is quite good except that the AMBER torsion profiles are sensitive to the choice of atomic point charges. Using electrostatic potential (ESP) derived atomic point charges determined with the STO‐3G basis set we find that AMBER is able to match the best quantum mechanical results quite well. However, when the point charges are derived using the 6‐31G* basis set we find that scaling the intramolecular electrostatic nonbond interactions is necessary. AM1 does not work very well for these compounds when compared to the ab initio methods and, therefore, should only be used in cases when ab initio calculations would be prohibitive. Based upon our results we feel that any force field that makes use of 6‐31G* ESP derived atomic point charges will need to scale intramolecular interactions. Implications of scaling intramolecular interactions to the development of force fields based on 6‐31G* ESP derived atomic point charges are discussed. © 1992 by John Wiley & Sons, Inc.
Molecular electrostatic potentials and partial atomic charges from correlated wave functions: Applications to the electronic ground and excited states of 3‐methylindole
Authors: Westbrook John D. , Levy Ronald M. , Krogh‐Jespersen Karsten
Published: January 2005

Procedures have been developed to generate molecular electrostatic potentials based on correlated wave function from ab initio or semiempirical electronic structure programs. A new algorithm for point‐wise sampling of the potential is described and used to obtain partial atomic charges via a linear, least squares fit between classical and quantum mechanical electrostatic potentials. The proposed sampling algorithm is efficient and promises to introduce less rotational variance in the potential derived partial charges than algorithms applied previously. Electrostatic potentials and fitted atomic charges from ab initio (HF/6–31G* and MP2/6‐31G*) and semiempirical (INDO/S; HF, SECI, and SDCI) wave functions are presented for the electronic ground (S0) and excited (1Lb, 1La) states of 3‐methylindole. © 1992 by John Wiley & Sons, Inc.
Rapid estimation of charge distribution. II. Heteroatoms
Authors: Houser John J. , Klopman Gilles
Published: January 2005

A rapid method for estimating CNDO charges in large data bases using a reparameterized Del Re method has been described previously. In this article the method is extended to saturated compounds containing B, N, O, F, Si, P, S, and Cl. Good results are obtained by forcing the Del Re δo parameter for each element to be linearly related to its Pauling electronegativity, but with the slopes and intercepts being different for second‐ and third‐row elements. With a test set of 17 compounds and 71 atoms, the CNDO charge was reproduced with an average deviation of ±0.03. The largest deviations, up to ±0.2, were observed for carbons having multiple F or Cl substituents and for sterically hindered atoms. © 1992 by John Wiley & Sons, Inc.
Molecular dynamics on a distributed‐memory multiprocessor
Authors: Lin S.L. , Mellor‐Crummey J. , Pettitt B.M. , Phillips G.N.
Published: January 2005

Dynamics simulations of molecular systems are notoriously computationally intensive. Using parallel computers for these simulations is important for reducing their turnaround time. In this article we describe a parallelization of the simulation program CHARMM for the Intel iPSC/860, a distributed memory multiprocessor. In the parallelization, the computational work is partitioned among the processors for core calculations including the calculation of forces, the integration of equations of motion, the correction of atomic coordinates by constraint, and the generation and update of data structures used to compute nonbonded interactions. Processors coordinate their activity using synchronous communication to exchange data values. Key data structures used are partitioned among the processors in nearly equal pieces, reducing the memory requirement per node and making it possible to simulate larger molecular systems. We examine the effectiveness of the parallelization in the context of a case study of a realistic molecular system. While effective speedup was achieved for many of the dynamics calculations, other calculations fared less well due to growing communication costs for exchanging data among processors. The strategies we used are applicable to parallelization of similar molecular mechanics and dynamics programs for distributed memory multiprocessors. © 1992 by John Wiley & Sons, Inc.
Analysis of the gas‐phase addition of water to formaldehyde: A semiempirical and ab initio study of bifunctional catalysis by H2O
Authors: Ventura Oscar N. , CoitiñO Elena L. , Lledós Agustí , Bertran Juan
Published: January 2005

Semiempirical AM1, MNDO‐PM3, and MNDO/M, as well as ab initio Hartree–Fock and Möller–Plesset calculations using the 4‐31G, 6‐31G(d,p), and 6‐31 +G(d,p) basis sets have been done on the water‐assisted addition of water to formaldehyde. ab initio methods predict a reduction of 30% of the bimolecular ΔG0,‡ (from 48 to 33 kcal/mol) when an ancillary water molecule is used as catalyst. AM1 and MNDO‐PM3 predict anticatalysis instead; ΔG0,‡ for the termolecular addition is larger than the one for the bimolecular reaction. MNDO/M predicts a modest decrease, from 42 to 39 kcal/mol. We conclude that, as predicted by the ab initio calculations, there is a bifunctional catalysis caused by the ancillary water. Two of the semiempirical methods are qualitatively (and all of them quatitatively) in disagreement with this conclusion. © 1992 by John Wiley & Sons, Inc.
Ab Initio investigation of the structures and stabilities of CH2N2, CHFN2, and CF2N2 isomers: Important consequences of MP2 optimizations
Authors: Boldyrev Alexander I. , Schleyer Paul v. R. , Higgins D. , Thomson Colin , Kramarenko Sofia S.
Published: January 2005

Ab initio calculations of the potential energy surfaces of CH2N2, CHFN2, and CF2N2 at MP4SDTQ/6‐31G*//MP2(full)/6‐31G* reveal several surprising features. While diazomethane is more stable than diazirine, only the three‐membered ring forms of the fluorine‐substituted isomers are known experimentally. We find fluorodiazomethane and difluorodiazomethane not to be viable species: They have no barriers toward exothermic dissociation into N2 and CHF or CF2, respectively. In contrast, the three‐membered ring isomers, fluorodiazirine and difluorodiazirine, have high barriers toward dissociation despite being high in energy. Diazomethane bends easily; a nonplanar Cs minimum is found at MP2(full)/6‐31G* but C2v symmetry is preferred at QCISD/6‐31G*. © 1992 by John Wiley & Sons, Inc.
General expression for the density dependence of the mori coefficients
Authors: Morales Juan J. , Nuevo María J.
Published: January 2005

The particular expression that relates the first Mori coefficients of the solvent particles with the solute particles as a function of their masses m1 and m2 is generalized to the case of the solute particle also having a different volume. The resulting density relationship, in terms of the mass factor M(m2) and coupling constants CD, is also valid for the second Mori coefficients and for two‐ and three‐dimensional system. © 1992 by John Wiley & Sons, Inc.
Study of hydrogen bonding interactions relevant to biomolecular structure and function
Authors: Zheng Ya‐Jun , Merz Kenneth M.
Published: January 2005

Ab initio molecular orbital calculations were used to study hydrogen bonding interactions and interatomic distances of a number of hydrogen bonded complexes that are germane to biomolecular structure and function. The calculations were carried out at the STO‐3G, 3‐21G, 6‐31G*, and MP2/6‐31G* levels (geometries were fully optimized at each level). For anionic species, 6‐31 + G* and MP2/6‐31 + G* were also used. In some cases, more sophisticated calculations were also carried out. Whenever possible, the corresponding enthalpy, entropy, and free energy of complexation were calculated. The agreement with the limited quantity of experimental data is good. For comparison, we also carried out semiempirical molecular orbital calculations. In general, AM1 and PM3 give lower interaction enthalpies than the best ab initio results. With regard to structural results, AM1 tends to favor bifurcated structures for OH‐O and NHO types of hydrogen bonds, but not for hydrogen bonds involving O‐HS and S‐HO, where the usual hydrogen bond patterns are observed. Overall, AM1 geometries are in general in poor agreement with ab initio structural results. On the other hand, PM3 gives geometries similar to the ab initio ones. Hence, from the structural point of view PM3 does show some improvement over AM1. Finally, insights into the formation of cyclic or open formate–water hydrogen bonded complexes are presented. © 1992 by John Wiley & Sons, Inc.
Molecular dynamics simulation of a poly(oxyethylene) chain dissolved in benzene
Authors: Depner M. , Schürmann B.L.
Published: January 2005

Molecular dynamics simulations of pure benzene and a poly(oxyethylene) chain in benzene are performed. The simulation of pure benzene is found to agree excellently with previous simulations despite using a different force field. A comparison is made between the results of simulations of the poly(oxyethylene) chain in benzene and in water and of stochastic simulations with respect to mean torsional angles, trans/gauche fractions, and transition rates. Characteristic deviations are found for the simulation in water and explained by specific atomic interactions, while there is satisfactory agreement with a stochastic simulation based upon the simple Langevin equation using a friction coefficient of 1 ps−1. The characteristic ratio of poly(oxyethylene) in benzene is calculated on the basis of the rotational isomeric state model. © 1992 by John Wiley & Sons, Inc.
An electron repulsion integral compression algorithm
Authors: Fülscher Markus P. , Widmark Per‐Olof
Published: January 2005

A data compression algorithm for packing/unpacking floating point numbers is presented. The method has been used to compress large volumes of data commonly generated in ab initio quantum mechanical calculations. To retain an accuracy of 10−6 Hartree on the final energy, the required file space needed is approximately half its original size whereas the CPU time required to solve the Hartree–Fock self‐consistent field equations increases with 30–60%. © 1993 John Wiley & Sons, Inc.