bluuebunny/crossref_metadata_2025 huggingface dataset:
Theoretical studies of organometallic compounds. III. Structures and bond energies of FeCHn and FeCH (n = 1, 2, 3)
Authors: Veldkamp Achim , Frenking Gernot
Published: January 2005

The geometries and dissociation energies for the FeC and CH bonds of FeCHn and FeCH (n = 1, 2, 3) have been calculated by ab initio quantum mechanical methods using different effective core potential models and Møller–Plesset perturbation theory. The HW3 ECP model, which has a configuration [core] (n−1)s2, (n−1)p6, (n−1)d1, (n)sm for the transition metals, is clearly superior to the larger core LANL1DZ ECP model with the configuration [core] (n−1)d1, (n)sm. The FeC bond energies calculated at correlated levels using the HW3 ECP are in much better agreement with experiment than the LANL1DZ results. This effect is mainly due to the higher number of correlated electrons rather than the inclusion of the outermost core electrons in the Hartree–Fock calculation. At the PMP4/HW3TZ/6‐31G(d)//MP2/HW3TZ/6‐31G(d) level, the theoretically predicted FeC bond energies for FeCH are in the range of 80% of the experimental values and have nearly the same accuracy as all‐electron calculations using large valence basis sets and the MCPF method for the correlation energy. © 1992 by John Wiley & Sons, Inc.
Conformational sampling by a general linearized embedding algorithm
Authors: Crippen Gordon M. , Smellie Andrew S. , Richardson Wendy W.
Published: January 2005

Linearized embedding is a variant on the usual distance geometry methods for finding atomic Cartesian coordinates given constraints on interatomic distances. Instead of dealing primarily with the matrix of interatomic distances, linearized embedding concentrates on properties of the metric matrix, the matrix of inner products between pairs of vectors defining local coordinate systems within the molecule. We developed a pair of general computer programs that first convert a given arbitrary conformation of any covalent molecule from atomic Cartesian coordinates representation to internal local coordinate systems enforcing rigid valence geometry and then generate a random sampling of conformers in terms of atomic Cartesian coordinates that satisfy the rigid local geometry and a given list of interatomic distance constraints. We studied the sampling properties of this linearized embedding algorithm vs. a standard metric matrix embedding program, DGEOM, on cyclohexane, cycloheptane, and a cyclic pentapeptide. Linearized embedding always produces exactly correct bond lengths, bond angles, planarities, and chiralities; it runs at least two times faster per structure generated, and is successful as much as four times as often at refining these structures to full agreement with the constraints. It samples the full range of allowed conformations broadly, although not perfectly uniformly. Because local geometry is rigid, linearized embedding's sampling in terms of torsion angles is more restricted than that of DGEOM, but it finds in some instances conformations missed by DGEOM. © 1992 by John Wiley & Sons, Inc.
Rotational barrier in phosphatriafulvene: An MCSCF study
Authors: Schoeller Wolfgang W. , Strutwolf Jörg , Haug Wilfried , Busch Thilo
Published: January 2005

As probed by ab initio calculations at SCF and MCSCF levels, the rotational barrier of the PC double bond in the title compound is similar in magnitude to the corresponding one in methylenephosphane. The transition state for rotation is dipolaric in nature. On this basis, a combination of electron releasing and electron accepting substituents reduces the magnitude of the rotational barrier in phosphatriafulvene. It is supported by experimental investigations. © 1993 John Wiley & Sons, Inc.
Supplementary d and f functions in molecular wave functions: Optimum and nonoptimum exponents
Authors: Magnusson Eric
Published: January 2005

Energy optimization calculations have been carried out to determine the variability of optimum p, d, and f polarization function exponents in molecules containing first‐ and second‐row elements and in normal valency and hypercoordinate species. Optimum exponents were determined for single sets of higher‐order functions at both Hartree–Fock and correlated (Moller–Plesset) levels of theory using the Dunning–Hay double zeta and the McLean–Chandler triple zeta basis sets. More detailed calculations were used to test the response to nonoptimum d and f function exponents of the total energy, the optimum geometry, and harmonic stretching frequencies. The variability in optimum exponents and the size of the energy penalties incurred by adopting nonoptimum values reduces the utility of standard exponents for p, d, and f polarization functions. © 1993 John Wiley & Sons, Inc.
Supplementary d and f functions in molecular wave functions at large and small internuclear separations
Authors: Magnusson Eric
Published: January 2005

The CO, CO2, CS, CIF, and SO2 molecules were used to test the dependence of supplementary d and f function exponents to changes in bond lengths and bond angles in MO calculations utilizing Gaussian basis sets in Hartree–Fock and Moller–Plesset calculations. Using Dunning–Hay double zeta basis sets, optimizations were performed at internuclear separations from 100–200 pm and beyond. The energy cost of not reoptimizing d function exponents when bonds are stretched or compressed is much smaller for correlated calculations than for those at the Hartree–Fock level and is greatest at the lower end of the range of internuclear distances. The problem is much less serious at all levels when multiple sets of d functions are used. © 1993 John Wiley & Sons, Inc.
Comparison of computational methods applied to oxazole, thiazole, and other heterocyclic compounds
Authors: Shaffer Alan A. , Wierschke Scott G.
Published: January 2005

A variety of computational methods, including the semiempirical techniques AM1, PM3, and MNDO, and the thermochemical basis sets of Benson and Stine, was used to calculate and compare heats of formation (ΔHf°) data for optimized geometries of a variety of aromatic and nonaromatic heterocycles. Detailed analyses, including 6‐31G* and MP2/6‐31G* ab initio calculations, were performed for the oxazole and thiazole heterocycles. The results indicate a scatter among the methods sensitive to the nature of the heterocycle. This was in particular evident in the oxazole molecule, where AM1 gave a singularly high value of ΔHf° consistent with longer calculated bond lengths, particularly about the oxygen atom. Aromatic stabilization energy appears to be addressed differently among the employed methods. Implications of this contrast applied to calculation of macromolecular systems containing heterocyclic units are discussed.
Ability of the PM3 quantum‐mechanical method to model intermolecular hydrogen bonding between neutral molecules
Authors: Jurema Marcus W. , Shields George C.
Published: January 2005

The PM3 semiempirical quantum‐mechanical method was found to systematically describe intermolecular hydrogen bonding in small polar molecules. PM3 shows charge transfer from the donor to acceptor molecules on the order of 0.02–0.06 units of charge when strong hydrogen bonds are formed. The PM3 method is predictive; calculated hydrogen bond energies with an absolute magnitude greater than 2 kcal mol−1 suggest that the global minimum is a hydrogen bonded complex; absolute energies less than 2 kcal mol−1 imply that other van der Waals complexes are more stable. The geometries of the PM3 hydrogen bonded complexes agree with high‐resolution spectroscopic observations, gas electron diffraction data, and high‐level ab initio calculations. The main limitations in the PM3 method are the underestimation of hydrogen bond lengths by 0.1–0.2 Å for some systems and the underestimation of reliable experimental hydrogen bond energies by approximately 1–2 kcal mol−1. The PM3 method predicts that ammonia is a good hydrogen bond acceptor and a poor hydrogen donor when interacting with neutral molecules. Electronegativity differences between F, N, and O predict that donor strength follows the order F > O > N and acceptor strength follows the order N > O > F. In the calculations presented in this article, the PM3 method mirrors these electronegativity differences, predicting the F‐H‐‐‐N bond to be the strongest and the N‐H‐‐‐F bond the weakest. It appears that the PM3 Hamiltonian is able to model hydrogen bonding because of the reduction of two‐center repulsive forces brought about by the parameterization of the Gaussian core–core interactions. The ability of the PM3 method to model intermolecular hydrogen bonding means reasonably accurate quantum‐mechanical calculations can be applied to small biologic systems. © 1993 John Wiley & Sons, Inc.
Benzene is not very rigid
Authors: Lipkowitz Kenny B. , Peterson Michael A.
Published: January 2005

The concept of molecular kurtosis as a dynamic molecular shape descriptor is introduced and used to compare the relative flexibilities of benzene and cyclohexane. For small torsional deformations (<15°) the potential energy surfaces are similar, indicating both molecules are flexible. Using molecular kurtosis, the stiffness of benzene and cyclohexane are compared from gas‐phase stochastic dynamics simulations and validated by distributions found in the Cambridge Structural Database. © 1993 John Wiley & Sons, Inc.
Parallelization strategies for molecular simulation using the Monte Carlo algorithm
Authors: Jones Douglas M. , Goodfellow Julia M.
Published: January 2005

We describe the development of Metropolis Monte Carlo algorithms for a general network of multiple instruction multiple data (MIMD) parallel processors. The implementation of farm, event, and systolic parallel algorithms on transputer‐based computers is detailed and their relative performance discussed. Although the emphasis is on methodology, the application of such parallel algorithms will be important for addressing computational problems such as the determination of free energy differences in complex biologically important molecular systems. © 1993 John Wiley & Sons, Inc.
Rapid empirical calculation of the first (n or π) ionization potential of organic molecules
Authors: Hanebeck W. , Gasteiger J.
Published: January 2005

The first ionization potential of an organic molecule containing electrons in nonbonding or π‐type molecular orbitals can rapidly be calculated using parameters describing physical and chemical effects. These parameters include effective polarizability, resonance stabilization of a cation, π‐ and σ‐charges, and electronegativity and are directly calculated from the structure of the compound. Correlation analyses with the first ionization potentials were carried out on various data sets classified into five groups to cover a wide range of organic molecules. The equations thus obtained were integrated into a system that automatically calculates the ionization potential of an organic compound from a connection table as obtained by a graphic input program. © 1993 John Wiley & Sons, Inc.
MORMIN: A quasi‐Newtonian energy minimizer fitting the nuclear overhauser data
Authors: Pothier JoëL , Gabarro‐Arpa Jacques , Bret Marc Le
Published: January 2005

In this article, we describe the program MORMIN, which can simultaneously minimize the mechanical energy of a given macromolecular structure, together with a weighted quadratic penalty function of the difference between the observed and computed nuclear Overhauser effect (nOe) peaks. The gradient of the nOe penalty function relatively to the proton coordinates is computed from an exact closed formula of a matrix exponential derivative. To cut CPU time, the molecular system is partitioned into nonoverlapping subsets containing the protons involved in the observed peaks. The algorithm is no longer exact, but if a 1% relative error is accepted it can be run, on a scalar computer, in about the same CPU time as needed for the calculation of the mechanical energy. We have successfully run the program in more than 1000 situations, including cases where the hybrid method failed because of the occurrence of negative eigenvalues. In some cases, the optimization of the Cartesian coordinates could be successfully extended to individual atomic diffusion times. © 1993 John Wiley & Sons, Inc.
Observations concerning the treatment of long‐range interactions in molecular dynamics simulations
Authors: Tasaki K. , McDonald S. , Brady J.W.
Published: January 2005

Molecular dynamics simulations of pure water employing two different empirical water models have been used to study the effects of different methods for truncation of long‐range interactions in molecular mechanics calculations. As has been observed previously in integral equation studies, “shifting” these interactions on an atom‐by‐atom basis was found to produce artificial structuring in the water and affect diffusion rates. In cases where some form of short‐range truncation must be used, the ST2 switching function applied on a group‐by‐group basis was found to be the most realistic procedure. If atom‐based shifting must be employed, a cutoff distance greater than or equal to 12.0 Å was found to be required to produce realistic results. © 1993 John Wiley & Sons, Inc.
Conformational and energetic effects of truncating nonbonded interactions in an aqueous protein dynamics simulation
Authors: Guenot Jeanmarie , Kollman Peter A.
Published: January 2005

In a previous aqueous protein dynamics study, we compared the rms deviation relative to the crystal structure for distance‐dependent and constant dielectric models with and without a nonbonded cutoff. The structures obtained from a constant dielectric simulation with a cutoff were substantially different from the structures obtained from a distance‐dependent dielectric simulation, with and without cutoff, and a constant dielectric model without a cutoff. In fact, structures from the distance‐dependent dielectric simulations were insensitive to the nonbonded cutoff and in good agreement with the structures generated from the constant dielectric simulation without a cutoff. In addition, the solute‐solvent temperature differential and solvent evaporation artifacts, characteristic of the constant dielectric simulation with a cutoff, were not present for the distance‐dependent dielectric simulations. In this current work, we explore whether this dielectric‐dependent cutoff‐sensitive behavior for a constant dielectric model arises from the discontinuities in the forces at the nonbonded cutoff or from neglecting the structure‐stabilizing interactions beyond the nonbonded cutoff. We also examine the origin of the dielectric‐dependent artifacts, and its potential influence on the structural disparity. Several protocols for protein dynamics simulations are compared using both constant and distance‐dependent dielectric models, including implementation of a switching function and a nonbonded cutoff and two different temperature coupling algorithms. We show that the distance‐dependent dielectric model conserves energy in the SPASMS molecular mechanics and dynamics software for the time steps and nonbonded cutoffs commonly used in macromolecule simulations. Although the switching function simulation also conserved energy over a range of commonly used cutoffs, the constant dielectric model with a switching function yielded conformational results more similar to a constant dielectric simulation without a switching function than to a constant dielectric model without a nonbonded cutoff. Therefore, the conformational disparity between the dielectric models arises from neglecting important structure‐stabilizing interactions beyond the cutoff, rather than differences in energy conservation. © 1993 John Wiley & Sons, Inc.
Conformational dependence of the electrostatic potential‐derived charges of dopamine: Ramifications in molecular mechanics force field calculations in the gas phase and in aqueous solution
Authors: Urban Joseph J. , Famini George R.
Published: January 2005

The electrostatic potential‐derived charges for the catecholamine neurotransmitter dopamine were calculated at the STO‐3G and 6‐31G* basis sets for six different molecular conformations. The degree of variance of the charges with changing conformations was examined. The 6‐31G* basis set produced charges that were more sensitive to changes in conformation than those derived from the STO‐3G electrostatic potentials. The implication of the charge variations in molecular mechanics calculations was also investigated. The molecular mechanics results in the gas phase exhibited a variance depending upon the charge set used. The force field calculations varied much less when aqueous solvation was included in the calculations through a continuum model. © 1993 John Wiley & Sons, Inc.
Yammp: Development of a molecular mechanics program using the modular programming method
Authors: Tan Robert K.‐Z. , Harvey Stephen C.
Published: January 2005

Molecular mechanics is a fast developing discipline with new methods and potential fields appearing every year. A versatile molecular mechanics program supports many methods and potential fields that make it unavoidably large. There are problems writing and maintaining large programs with traditional methods because of data and other dependencies. Modular programming provides a solution. A program is developed as a collection of highly independent modules containing only related data structures and procedures. These entities are isolated in the module and access to them is provided through a well‐defined and controlled interface. The high degree of independence circumscribes programming errors. Most of all, it reduces the cost of revising the program as only a small part of the program needs to be read and understood for each revision. We implemented a molecular mechanics program, yammp, using the modular programming method. © 1993 John Wiley & Sons, Inc.
Minimization of empirical energy functions in proteins including hydrophobic surface area effects
Authors: Freyberg Berthold Von , Braun Werner
Published: January 2005

We present analytical expressions to calculate the gradient of the water‐accessible surface area of proteins with respect to Cartesian coordinates and dihedral angles. A detailed mathematical analysis leads to corrected equations for the gradient calculation used previously in the ANAREA program. To study the hydrophobic effect of solvent‐protein interactions, our expressions have been implemented to further improve the program package FANTOM. We used this version of FANTOM to minimize the ECEPP/2 and the hydrophobic energy of tendamistat. © 1993 John Wiley & Sons, Inc.
Comparative study between ab initio and semiempirical electrostatic potentials on molecular surfaces
Authors: Alkorta Ibon , Villar Hugo O. , Arteca Gustavo A.
Published: January 2005

The electrostatic potentials of 21 molecules containing different functional groups has been computed at the ab initio RHF/6‐31G* level on a series of solvent accessible surfaces and compared with MNDO, AM1, and PM3‐derived pontentials. We analyzed in detail the distribution of electrostatic potentials on the surfaces around their maximum and minimum values and found out that consistently MNDO gives results similar to ab initio potentials. The actual values of the MNDO electrostatic potentials show a systematic deviation from the “correct” results, but the pattern of the MEP distribution on the surface is similar to that of the ab initio results. In contrast, PM3 fails in some cases to give even the correct number or distribution of “hot spots” of potential (low MEP) on the surface. AM1 behaves somewhere between these two semiempirical methods. As a conclusion, MNDO would be suggested as the best approach to analyses requiring a fast and efficient mapping of electrostatic potentials on simplified models of molecular surfaces. © 1993 John Wiley & Sons, Inc.
Techniques for the compression of sequences of integer numbers and real numbers with fixed absolute precision
Authors: Stradella Omar G. , Corongiu Giorgina , Clementi Enrico
Published: January 2005

Algorithms to reduce the space needed to store information either in memory or magnetic media are presented. These algorithms were designed to pack and unpack two common kinds of data types: sequences of sets of integers that change in a regular fashion and real numbers of fixed absolute precision. One typical application of these techniques is in the storage of electron repulsion integrals in ab initio calculations, where the indices of the basis functions are a good example of data of the first type and the integrals of the second type. In this case, savings in storage space of 50% or more can be obtained with reasonable accuracies in the energies. FORTRAN subroutines are presented for packing/unpacking indices and integrals both in the IBM and IEEE 754 64‐bit floating point formats. © 1993 John Wiley & Sons, Inc.
Sprouting side chain conformations in X‐PLOR simulations of peptides
Authors: David Carl W.
Published: January 2005

A scheme for sprouting peptide side chains using X‐PLOR is introduced using an example from the collagen system to show how reasonable starting structures for minimization studies may be created. © 1993 John Wiley & Sons, Inc.
Chiral force constants: Recommendations for the presentation of internal coordinate force constants
Authors: Polavarapu P.L.
Published: January 2005

Some force constants associated with the internal coordinates that sense handedness or chirality can have opposite signs in the enantiomers of chiral molecules. Examples of such force constants include interaction force constants between a torsional and stretching or bending internal coordinates. The sign reversal for these force constants in the enantiomers of chiral molecules or in opposite‐handed molecular segments is best recognized by labeling them as chiral force constants. Recognition of chiral force constants suggests that certain guidelines are to be followed in the presentation of internal coordinate force constants. © 1993 by John Wiley & Sons, Inc. © John Wiley & Sons, Inc.
Beyond the MNDO model: Methodical considerations and numerical results
Authors: Kolb Matthias , Thiel Walter
Published: January 2005

It is suggested to improve the MNDO model by the explicit inclusion of valence‐shell orthogonalization corrections, penetration integrals, and effective core potentials (ECPs) in the one‐center part of the core Hamiltonian matrix. Guided by analytic formulas and numerical ab initio results, the orthogonalization corrections are expressed in terms of the resonance integrals that are represented by a new empirical parametric function. All two‐center Coulomb interactions and ECP integrals are evaluated analytically in a Gaussian basis followed by a uniform Klopman–Ohno scaling. One particular implementation of the proposed NDDO SCF approach is described and parameterized for the elements H, C, N, O, and F. In a statistical evaluation of ground‐state properties, this implementation shows slight but consistent improvements over MNDO, AM1, and PM3. Significant improvements are found for excited states, transition states, and strong hydrogen bonds. Possible further enhancements of the current implementation are discussed. © 1993 John Wiley & Sons, Inc.
Suitability of the PM3‐derived molecular electrostatic potentials
Authors: Alemán Carlos , Luque F.J. , Orozco M.
Published: January 2005

A systematic study of the suitability of PM3‐derived molecular electrostatic potentials (MEPs) is presented. Forty‐six MEP minima, 81 electrostatic charges, and 17 electrostatic dipoles were determined at the PM3 level and compared with those obtained from the ab initio 6‐31G* wave function, as well as from the semiempirical MNDO and AM1 wave functions. The statistical results of the comparison analysis between semiempirical and ab initio 6‐31G* MEPs show that PM3 is in general reliable for the study of the MEP minima but a mediocre method as a source of electrostatic charges. © 1993 John Wiley & Sons, Inc.
Ab initio study of bond stretching: Implications in force‐field parametrization for molecular mechanics and dynamics
Authors: Orozco Modesto , Luque F.J.
Published: January 2005

We report a theoretical study of the stretching of chemical bonds and its implications on the force‐field parametrization. Computations were performed at the SCF and MCSCF levels by using minimal, split‐valence, and large extended and polarized basis sets. The stretching energy profiles were determined considering up to 25 perturbed geometries of 11 different bonds (6 singles, 2 doubles, and 3 triples). The energy profiles and stretching parameters are compared with the experimental data compiled in the most popular force fields. MCSCF stretching energy profiles are mainly anharmonic and can be only roughly reproduced by quadratic equations. The use of Allinger's MM2 quasiharmonic expression appears as the best choice because it fits with reasonable accuracy a large percentage of the stretching profile without increasing the complexity of the formalism and of the parametrization procedure. MCSCF computations are needed to obtain reliable stretching force parameters. In this respect, MCSCF calculations considering as active space only the bonded and nonbonded orbitals of the perturbed bond seems to be the best strategy to obtain good results at a minimum computational cost, especially if small split‐valence basis sets like the 3‐21G are used. Results obtained at this level of sophistication are completely comparable to stretching parameters compiled on empirical force fields. © 1993 John Wiley & Sons, Inc.
Analysis of the core‐repulsion functions used in AM1 and PM3 semiempirical calculations: Conformational analysis of ring systems
Authors: Csonka G.I.
Published: January 2005

The AM1 and PM3 potential energy surfaces of cyclopentane have been compared and the energy difference between two (boat and chair) cyclohexane conformers analyzed. The effects of reparameterization and different core‐repulsion functions (CRFs) have been studied. The HH, CH, and CC CRF energy contributions have been calculated separately. The results show that the CRF energy corrections stabilize the correct (MM2 and ab initio) geometries. The PM3 equilibrium geometry of cyclopentane is closer to the MM2 and ab initio results than the AM1 geometry. It is known that above 190 pm the AM1 HH CRF curve is smooth and negative but the PM3 HH CRF curve has a trough and a shoulder. It has been shown that this latter oscillation is not damped by other parameters. As a result, the HH PM3 energy gradient curve is different from the quasilinear AM1 and ab initio gradient curves. © 1993 John Wiley & Sons, Inc.
Quantitative comparison of molecular electrostatic potential distributions from several semiempirical and ab initio wave functions
Authors: Rodríguez Jesús , Manaut Francesc , Sanz Ferran
Published: January 2005

A quantitative comparative analysis of molecular electrostatic potential (MEP) distributions generated from different wave functions was carried out. Wave functions were computed by using MNDO, AMl, STO‐3G, 3‐21G, 4‐31G, 6‐31G, 4‐31G*, 6‐31G*, and 6‐31G** methods. Ten different compounds, which include usual atoms and groups of biomolecules, such as hydroxyl, carbonyl, amine, amide, imine, double and triple bonds, and heteroaromatic rings, were studied. For each compound, MEP values in the points of a common 3‐D grid were computed; thereafter, the similarity between each pair of MEP distributions generated by different methods was assessed. Similarities were measured using the Spearman rank correlation coefficient. A similarity matrix was obtained for each compound. Similarity matrices were averaged and a hierarchical cluster analysis was carried out to classify the different quantum chemical methods. In the compounds studied, the main conclusion is the negligible difference between the pattern of MEP distributions generated from all split valence basis sets (with and without polarization functions). © 1993 John Wiley & Sons, Inc.
Modified MM2 scheme for computation of OCN‐containing systems
Authors: Senderowitz Hanoch , Aped Pinchas , Fuchs Benzion
Published: January 2005

A modification of Allinger's MM2 force field for the anomeric effect in OCN systems is presented. For optimal consistency, it was parameterized by alternate use of ab initio (3‐21G level) and X‐ray results to account for the energetic and structural manifestations of the effect in the gas or condensed phase, respectively. The results obtained with the modified force field are in good agreement with those from both theoretical and experimental methods. The parameterization scheme explicitly treats all structural parameters of the COCNC moiety as well as CN bond lengths in tertiary amines contained within an anomeric unit. In addition, it includes directional H‐bond type interactions. A limited number of parameters is put forward, in accord with the general MM2 force‐field approach. © 1993 John Wiley & Sons, Inc.
Application of parallel processing techniques to improving the efficiency of MM2 molecular mechanics calculations
Authors: Schweitzer Robert C. , Small Gary W.
Published: January 2005

The application of parallel processing techniques to molecular mechanics calculations is evaluated. Using the standard molecular mechanics package, MM2, four different parallel versions of the program are implemented in a four‐processor computing environment. A set of 529 test structures is used to compare the efficiency of the parallel versions of MM2 to a standard serial version of the program. Statistics describing execution times and program execution cycles are gathered and analyzed. The effects of parallel processing overhead and computer system load are explored, and the practical utility of parallel processing in molecular mechanics is estimated. The results of these parallelization experiments indicate that for geometry optimizations requiring significant amounts of computing time an improvement in program execution speed approaching 50% is realizable. © 1993 John Wiley & Sons, Inc.
Conformational searching methods for small molecules. I. Study of the sybyl search method
Authors: Ghose A.K. , Jaeger E.P. , Kowalczyk P.J. , Peterson M.L. , Treasurywala A.M.
Published: January 2005

Several methods are available in the literature for the conformational analysis of small molecules. Each of these methods has some advantages and some disadvantages. Also, each of these methods may be expected to perform better or worse on different types of molecules. There is no clear calibration of each of these methods against a “standardized” set of molecules available in the literature. Such a reference work would be useful to the community because it would allow the choice of methods to be based on some facts. We attempted to provide a start to such a calibration in this article with an examination of the SYBYL SEARCH method. Methods for evaluating the performance of this method are described in detail and will be applied to all other available conformational analysis methods in future papers. © John Wiley & Sons, Inc.
Calculation of the interaction energy in a localized representation for a trimer (Ne3) system
Authors: Kozmutza C. , Kapuy E. , Evleth E.M.
Published: January 2005

We studied the transferability of the localized orbitals (LOs) of interacting Ne atoms using several basis sets. Both at SCF and at MP2 and MP3 levels, the contributions of the LOs have been calculated and discussed for the Ne2 and Ne3 systems. It was shown that for the LOs the transferability is satisfied to a good extent and due to the transferability the interaction energy at the correlated level can be calculated by using only the LOs of the supermolecule. The basis set superposition error (BSSE) is simply extracted from the intramolecular parts of the correlation energy. The two‐ and three‐body interaction energies have been investigated for the studied systems. © John Wiley & Sons, Inc.
Parallel direct SCF and gradient program for workstation clusters
Authors: Brode Stefan , Horn Hans , Ehrig Michael , Moldrup Diane , Rice Julia E. , Ahlrichs Reinhart
Published: January 2005

A parallel direct SCF and gradient program for workstation clusters has been implemented on the basis of the ab initio program package TURBOMOLE. Applications on large molecular systems monitor an appreciable speedup in residence time. © John Wiley & Sons, Inc.
Divide‐and‐conquer, pattern matching, and relaxation methods in interpretation of 2‐D NMR spectra of polypeptides
Authors: Soo Von‐Wun , Hwang Jan‐Fu , Chen Tung‐Bo , Yu Chin
Published: January 2005

One task in the interpretation of the 2‐D nuclear magnetic resonance (NMR) spectrum is to assign its signal patterns to their corresponding amino acids in proteins or polypeptides. To carry out this task of interpretation, one requires sufficient chemical knowledge and expertise to reason from a set of highly noisy data. We present a system called RUBIDIUM (a Rule‐Based Identification in 2‐D NMR Spectrum) to formulate the expertise and automate the process of interpretation. Given a protein or polypeptide with a known amino acid sequence and the 2‐D NMR spectra (both COSY and NOESY), RUBIDIUM yields plausible assignments of lines that account for most signals observed in the spectrum and conform to prior chemical knowledge. Rules of pattern matching are used to detect plausible signal patterns. The expertise of the sequence‐specific assignment task is formulated to assign a signal pattern to amino acids. To cope with ambiguities and noise, RUBIDIUM adopts various low‐level data preprocessing techniques, the strategy of divide and conquer, and the relaxation technique to decrease the complexity and recover from overconstrained conditions. The polypeptides oxytocin and vasopressin are used to illustrate the performance of RUBIDIUM. © John Wiley & Sons, Inc.
Lattice representations of globular proteins: How good are they?
Authors: Godzik Adam , Kolinski Andrzej , Skolnick Jeffrey
Published: January 2005

Using a number of different lattice models of proteins, the problems introduced by the discretization of a protein backbone are discussed and examples of the most typical errors arising in low coordination number lattices presented. The geometric properties of different lattices used in the literature are compiled, and for all of them the resulting α‐carbon models of proteins are described in detail and compared to the original structures obtained from experiment. © John Wiley & Sons, Inc.
Long‐Range multicenter integrals with slater functions: Gauss transform‐based methods
Authors: Rico J. Fernández
Published: January 2005

The separation of the short‐ and long‐range terms in the potentials generated by pairs of Slater functions is reformulated in the context of the Gauss transform method. Analytic expressions of the long‐range potentials (in closed form) are derived for equal exponents and generalized (as expansion series) for different exponents. Additionally, the representation of these potentials from small sets of charges or lowest‐order multipoles is examined, paying special attention to their values and optimal positions. Finally, numerical tests of the formal developments are presented. It is concluded that the long‐range three‐ and four‐center integrals can be calculated with high accuracy in a simple and relatively inexpensive manner. © John Wiley & Sons, Inc.
Self‐Similarity of solvent‐accessible surfaces of biological and synthetical macromolecules
Authors: Zachmann Carl‐Dieter , Kast Stefan Michael , Sariban Alla , Brickmann Jürgen
Published: January 2005

The quantification of surface roughness of globular proteins and synthetical macromolecules in the globular state is discussed using the concept of fractality. The Hausdorff dimension as a measure for local and global fractality of surfaces is applied. To calculate the Hausdorff dimension of any surface at a high level of accuracy, a new algorithm is presented that is based on a triangulated solvent‐accessible molecular surface. It can be demonstrated that protein surfaces (as calculated on the basis of experimentally determined structures) as well as surfaces of globular polyethylene (PE) conformers (calculated on the basis of structural information basing on extensive Monte Carlo and molecular dynamics simulations) in fact show self‐similarity within a reasonable yardstick range, at least in a global statistical sense. The same is true for parts of a protein surface provided that these regions are not too small. The concept of self‐similarity breaks down when individual surface points are considered. The results obtained for the fractal dimension of PE surfaces (average fractal dimension D = 2.23) lead to the conclusion that protein surfaces probably do not exhibit a unique and specific degree of geometrical complexity (or surface roughness) characterized by a fractal dimension of approximately D = 2.2 as was argued in the past. It is clear that the concept of self‐similarity is helpful for the classification of surface roughness of large molecules, but it seems questionable whether this concept is useful for the identification of active sites or other questions related to the field of molecular recognition. © John Wiley & Sons, Inc.
Critical reevaluation of proximity effects in the barton oxidation and related intramolecular reactions
Authors: Smith Douglas A. , Smith Douglas A. , Vijayakumar S.
Published: January 2005

The limiting factor to account for the increased rate of intramolecular reactions between functional groups as opposed to their intermolecular counterparts can and has been explained both by proximity effects and by activation energy. Neither explanation has emerged as the single most important reason in all or even the majority of cases studied. We have therefore reexamined the spatiotemporal hypothesis of Menger and the transition‐state energy approach of Houk on a consistent set of compounds subjected to the Barton oxidation or related reactions in an effort to more clearly define the reasons for the proximity effect. For the 26 structures studied, neither hypothesis provides a consistent, quantitative explanation although the transitionstate energy hypothesis offered the most promise. © John Wiley & Sons, Inc.
Simulation of the electronic and vibrational structure of hydrogenated amorphous silicon using cluster models
Authors: Clare B.W. , Jennings P.J. , Cornish J.C.L. , Talukder G. , Lund C.P. , Hefter G.T.
Published: January 2005

A set of simple models of hydrogenated amorphous silicon (a‐Si:H) consisting of hypothetical silane molecules with diamond or similar lattices was studied by the semiempirical AM1 method. Densities of states and infrared spectra were calculated for the silane molecules and similar molecules with dangling bonds disorder, and with boron or phosphorus substitution to simulate doping. Some examples are presented, and a comparison is made with experimental properties of a‐Si:H. It is proposed to use these models in a study of the Staebler–Wronski photodegradation of a‐Si:H and other aspects of amorphous silicon technology. © John Wiley & Sons, Inc.
Conformational analysis of HIV protease inhibitors. I. Rotation of the amide group adjacent to the P′1 decahydroisoquinoline ring system in ro 31‐8959 and related systems
Authors: Murcko Mark A. , Rao B. Govinda
Published: January 2005

Pipecolic acid derivatives have proven to be effective P′1 groups in a series of highly potent inhibitors of the enzyme HIV protease. One such inhibitor, Ro 31‐8959, contains the saturated bicyclic ring system decahydroisoquinoline (DIQ) in the P′1 position. The binding orientation of Ro 31‐8959 is known from X‐ray crystallography. However, the bound conformation of the S‐hydroxy diastereomer has not been studied, and for this molecule there are at least two different possible binding conformations. Specifically, the N‐alkyl substituents may be equatorial or axial and the 3‐carboxamide may be rotated into several different orientations. To gain a better understanding of the relative energies of these various conformations, ab initio molecular orbital calculations have been carried out on a series of pipecolic acid and DIQ derivatives. The results indicate that the lowest‐energy N‐equatorial rotamer is always at least 3 kcal/mol more stable than the lowest‐energy N‐axial rotamer. The presence of the second ring, as in the DIQ system, considerably raises the equatorial–axial difference to nearly 7 kcal/mol. Also, the preferred rotation angle of the amide group is different for the N‐equatorial and N‐axial cases. When the molecular dynamics‐averaged conformation of the bound S‐hydroxy inhibitor is considered, the energy difference between the N‐equatorial and N‐axial conformers drops to 4–5 kcal/mol. The preferred amide rotations in these systems are compared to those found in proline‐containing peptides. Finally, some observations are made with respect to the large conformational energy penalty necessary for binding Ro 31‐8959. © John Wiley & Sons, Inc.
Evaluation of AM1‐calculated radical cation ion‐neutral complexes
Authors: Griffin Lawrence L. , McAdoo David J. , Olivella Santiago
Published: January 2005

AM1 semiempirical molecular orbital calculations are reported for 20 ion‐neutral complexes, including hydrogen‐bonded complexes, presumably involved in the gas‐phase unimolecular decomposition of simple organic radical cations. The systems investigated are [C2H4O2]˙+, [C2H5NO]˙+, [C2H6O]˙+, [C2H6O2]˙+, [C3H6O]˙+, [C3H6O2]˙+, [C3H8O]˙+, and [C3H8O2]˙+. The AM1 results are compared with ab initio molecular orbital calculations at different levels of theory up to MP3/6‐31G(d, p)//SCF/6‐31G(d) + ZPVE and the available experimental data. AM1 fails to predict some local minima and the equilibrium geometries calculated for several complexes are found to be qualitatively different from those predicted by the ab initio calculations. However, reasonable agreement is generally found for the stabilization energies of the complexes toward dissociation into their loosely bound components. © John Wiley & Sons, Inc.
Theoretical investigation into the potential of halogenated methanes to undergo reductive metabolism
Authors: Waller Chris L. , McKinney James D.
Published: January 2005

The density‐functional theory (DFT)‐based computational chemistry software package DMol was used to provide insight into the reductive potentials of a series of halomethanes. It is known that certain members of this series are readily reduced in vivo via catalysis by cytochrome P450. DMol was used to calculate the electron affinities of these molecules to be used as measures of their reduction potentials. Our results are consistent with experimental electrochemical reduction potentials and indicate that electron affinity is dependent upon the number and type of halogens present in the molecule. Calculated bond lengths and angles also compared favorably with experimental results and estimates derived from other ab initio methods of calculation. Concurrent with this study was the observation of a linear empirical relationship between electron affinity and the lowest unoccupied molecular orbital energy. It is possible that these values could be used as indicators of reductive potentials and ultimately of metabolic rates for use in PB–PK models designed to predict the dose associated with the toxicity of molecules of this and other classes. © John Wiley & Sons, Inc.
Updated Hessian matrix and the restricted step method for locating transition structures
Authors: Bofill Josep Maria
Published: January 2005

A family of the updated Hessian matrices for locating transition structures is presented. An analysis and improvement of the restricted step algorithm described by Culot et al. is proposed. The efficiency of the latter method is compared with other well‐established methods for locating transition structures. © 1994 by John Wiley & Sons, Inc.
Free energy derivatives: A new method for probing the convergence problem in free energy calculations
Authors: Pearlman David A.
Published: January 2005

The convergence behavior of free energy calculations has been explored in more detail than in any previously reported work, using a model system of two neon atoms in a periodic box of water. We find that for thermodynamic integration‐type free energy calculations as much as a nanosecond or more molecular dynamics sampling is required to obtain a fully converged value for a single λ point of the integrand. The concept of “free energy derivatives” with respect to the individual parameters of the force field is introduced. This formalism allows the total convergence of the simulation to be deconvoluted into components. A determination of the statistical “sampling ratio” from these simulations indicates that for window‐type free energy calculations carried out in a periodic waterbox of typical size at least 0.6 ps of sampling should be performed at each window (0.7 ps if constraint contributions to the free energy are being determined). General methods to estimate and reduce the error in thermodynamic integration and free energy perturbation calculations are discussed. We show that the difficulty in applying such methods is determining a reliable estimate of the correlation length from a short series of data. © 1994 by John Wiley & Sons, Inc.
Utilization of shape data in molecular mechanics using a potential based on spherical harmonic surfaces
Authors: Malhotra Arun , Tan Robert K.‐Z. , Harvey Stephen C.
Published: January 2005

This article introduces a novel potential function that allows the use of topographical information in molecular modeling. Quantitative shape data are provided by techniques such as electron‐microscopy–based three‐dimensional image reconstruction for large macromolecular assemblies. Such data can provide important constraints for molecular mechanics. We represent topographical data by spherical harmonic surfaces, first used by Max and Getzoff21 for displaying molecular surfaces. A simple harmonic potential is used to constrain atoms within these spherical harmonic surfaces. This potential was implemented in the yammp molecular mechanics package.27 Implementation details and results of several test cases are discussed here. © 1994 by John Wiley & Sons, Inc.
Conformational sampling of hydrocarbon and lipid chains in an orienting potential
Authors: Hardy Barry J. , Pastor Richard W.
Published: January 2005

A Distribution Biased Monte Carlo (DBMC) sampling procedure is developed for the efficient generation of chain conformations in the oriented environment of lipid membranes and other liquid crystalline systems. Conformations of the sn‐1 chain of dipalmitoyl phosphatidylcholine (DPPC) were generated by independently sampling torsion angles from continuous distributions in an orienting potential based on a Marcelja mean field; depending on the chain position, the convergence in the deuterium order parameters (SCD) was 100 to 3000 times more efficient with DBMC than with Brownian dynamics. Optimization using joint distribution and torsional potentials of mean force yielded a further threefold increase in sampling efficiency. Overall chain tilt was included using Euler angle rotations and a separate field strength for the anchor. A segmental DBMC procedure was used to generate a set of complete DPPC conformations with well‐converged conformationally averaged SCD consistent with experimental values. These conformations show considerable flexibility, not only in the hydrocarbon tails, but additionally in both the glycerol and head‐group portions of the lipid. An appendix compares DBMC with a number of other Monte Carlo and stochastic dynamics algorithms using the example of a bistable oscillator, and illustrates the tuning of parameters for optimal convergence. © 1994 by John Wiley & Sons, Inc.

This article is a US Government work and, as such, is in the public domain in the United States of America.