bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of computational methods applied to oxazole, thiazole, and other heterocyclic compounds
Authors: Shaffer Alan A. , Wierschke Scott G. 
Published: January 2005

AbstractA 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

AbstractThe 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

AbstractThe 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

AbstractWe 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

AbstractThe 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

AbstractIn 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

AbstractMolecular 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

AbstractIn 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

AbstractThe 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

AbstractMolecular 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

AbstractWe 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

AbstractThe 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

AbstractAlgorithms 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.
Chiral force constants: Recommendations for the presentation of internal coordinate force constants
Authors: Polavarapu P.L. 
Published: January 2005

AbstractSome 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

AbstractIt 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

AbstractA 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

AbstractWe 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

AbstractThe 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

AbstractA 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

AbstractA 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.