bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular electrostatic potential of substituted aromatic compounds: Factors affecting the differences between Ab Initio and semiempirical results
Authors: Bonati L. , Cosentino U. , Fraschini E. , Moro G. , Pitea D. 
Published: January 2005

AbstractThe molecular electrostatic potential (MEP) distribution of anisole, chlorobenzene, and fluorobenzene obtained from STO‐3G, 3‐21G, and 6‐31G* basis set ab initio and MNDO and AM1 semiempirical wave functions is investigated to explain the differences among the MEP features obtained for polychlorodibenzo‐p‐dioxins. The main topological features as well as the absoltue and relative minima location obtained from ab initio calculations are independent from the choice of the basis set. MNDO calculations are in good agreement with the ab initio ones in the case of anisole and fluorobenzene, while they incorrectly describe the MEP of chlorobenzene. The AM1 fails to localize the absolute minimum of fluorobenzene and does not find the minimum above the chlorobenzene chlorine atom. The poor agreement of both semiempirical methods with ab initio for any kind of chlorinated compounds is confirmed by results obtained for chloreothylene and chloroethane. We hypothesize that the main problem concerning these methods is that they freeze a too large amount of electrons in the atomic core of elements belonging to the second row, which makes for a wrong description of the core–valence electron interactions. Results obtained by modifying the AM1 parameters related to these interactions confirm our hypothesis. © 1992 by John Wiley & Sons, Inc.
Cumulative atomic multipole moments complement any atomic charge model to obtain more accurate electrostatic properties
Authors: Sokalski W.A. , Shibata M. , Rein R. , Ornstein R.L. 
Published: January 2005

AbstractThe quality of several atomic charge models based on different definitions has been analyzed using cumulative atomic multipole moments (CAMM). This formalism can generate higher atomic moments starting from any atomic charges, while preserving the corresponding molecular moments. The atomic‐charge contribution to the higher molecular moments, as well as to the electrostatic potentials, has been examined for CO and HCN molecules at several different levels of theory. The results clearly show that the electrostatic potential obtained from CAMM expansion is convergent up to the R−5 term for all atomic charge models used. This illustrates that higher atomic moments can be used to supplement any atomic charge model to obtain more accurate description of electrostatic properties. © 1992 by John Wiley & Sons, Inc.
Validation of the general purpose QUANTA ®3.2/CHARMm® force field
Authors: Momany Frank A. , Rone Rebecca 
Published: January 2005

AbstractAn evaluation of the CHARMm force field for small molecules is described. Using different force field conditions and computational techniques, a wide variety of compounds are analyzed. rms deviations of Cartesian coordinates for 49 diverse organic molecules taken from the Cambridge Crystallographic Data Base and internal coordinate geometries for 28 other molecules are reported. Results are described with different dielectrics, dihedral constraints, and crystal packing to allow analysis of deviations from experimental data and give precise statements of the reliability of the parameters used in the force field. Torsional barriers (rms = 0.4) and conformational energy differences (rms = 0.4) are examined and comparisons made to other force fields such as MM2, Tripos, and DREIDING. The results confirm that CHARMm is an internally consistent all purpose force field with energy terms for bonds, angles, dihedrals, and out‐of‐plane motions, as well as nonbonded electrostatic and van der Waals interactions. Reported CHARMm results (rms = 0.006 Å for bonds, rms = 1.37° for angles, and rms = 3.2° for dihedrals) are in excellent agreement with high quality electron diffraction data. © 1992 by John Wiley & Sons, Inc.
Improvements on the protein–dipole Langevin–dipole model
Authors: Xu Y.W. , Wang C.X. , Shi Y.Y. 
Published: January 2005

AbstractThe protein–dipole Langevin–dipole (PDLD) model developed by Warshel and co‐workers is an approach to evaluate electrostatic interactions in protein systems from microscopic sights. This model grasped the main physical factors and required little computations. But it might need the tests from every aspect. In the present work, we have chosen the solvation energies of Asp3, Glu7, Glu49, and Asp50 in bovine pancreatic trypsin inhibitor (BPTI) as a calibration to discuss the influences of parameters and conditions on the simulation results in the PDLD model. Some improvements have been proposed. The calculated solvation energies associated with ionizing the four acidic groups in BPTI and aspartic acid in solution are found in good agreement with the corresponding observed results if the improved PDLD approach and computational methods are used. © 1992 by John Wiley & Sons, Inc.
Solving the finite‐difference non‐linear Poisson–Boltzmann equation
Authors: Luty Brock A. , Davis Malcolm E. , McCammon J. Andrew 
Published: January 2005

AbstractThe Poisson–Boltzmann equation can be used to calculate the electrostatic potential field of a molecule surrounded by a solvent containing mobile ions. The Poisson–Boltzmann equation is a non‐linear partial differential equation. Finite‐difference methods of solving this equation have been restricted to the linearized form of the equation or a finite number of non‐linear terms. Here we introduce a method based on a variational formulation of the electrostatic potential and standard multi‐dimensional maximization methods that can be used to solve the full non‐linear equation. © 1992 by John Wiley & Sons, Inc.
Intensities of infrared bands in molecular mechanics (MM3)
Authors: Lii Jenn‐Huei , Allinger Norman L. 
Published: January 2005

AbstractThe MM3 molecular mechanics program calculates a fair representation of vibrational frequencies for molecules. To make this information more useful, a qualitative intensity calculation has been added, as is described herein. Because each bond in the molecule is assigned a dipole moment, and the vibrational amplitudes are known from the frequency calculation, the change in dipole moment corresponding to each normal mode is readily calculated. In some cases a charge flux has to be added empirically for bond stretchings. This relatively simple calculation has been applied to a number of different functional groups, and gives band intensities adequate for dividing the bands into very strong, strong, medium, weak, or very weak (forbidden) categories. © 1992 by John Wiley & Sons, Inc.
Ab Initio prediction of possible crystal structures for general organic molecules
Authors: Karfunkel H.R. , Gdanitz R.J. 
Published: January 2005

AbstractThe performance of a new crystal packing procedure for the ab initio prediction of possible molecular crystal structures is presented. The method is based upon only molecular information, i.e., no unit cell parameters are assumed to be known. The search for the global crystal energy minimum and all local minima inside an energy window is derived from Monte Carlo simulated annealing methods and has been applied to various organic molecules containing heteroatoms and polar groups. A systematic evaluation of the search method and of the quality of the potential energy function has been established. It is demonstrated that the packing of general organic molecules is possible even with standard force fields like CHARMM provided that the charges defining the electrostatic interactions are based upon physical models rather than transferable empirical parameters. Concepts of crystal packing that were based till now upon assumptions and speculations could be proved or disproved by solving directly the extended global optimization problem related to crystal packing. Crystal structures of molecules as complex as those treated in this article have not been, till now, predicted by a computational approach. In one case, a disagreement between the predicted and experimental structure was evident and, based upon the computations, we suspect that the published structure is the wrong one. © 1992 by John Wiley & Sons, Inc.
Critical analysis of electric field modeling: Formamide
Authors: Colonna François , Evleth Earl , Ángyán János G. 
Published: January 2005

AbstractA detailed analysis of ab initio derived electric field and multipole modeling is presented using formamide as an example. Penetration effects, a problem encountered with most currently used modeling methods, are avoided using the Overlap Multipolar Expansion (OME) technique computed up to the hexadecapole level. This method is shown to be grid insensitive. The OME fields and subsequent atomic charge modeling are found to be more sensitive to correlation effects than to basis sets changes. Three different types of error analysis are applied to test the accuracy of regenerated fields from various multipole descriptions. It is shown that atom centered charge models, those most commonly used in the literature, have significant errors. Considerable improvement can be made by using various combinations of charge, dipole, and quadrupole atom‐ or bond‐centered models. For molecular dynamic programs it is argued that the best compromise between accuracy and efficiency is to use both atom and fictive atom charge models calculated from MP2 level density matrices using at least DZP level basis sets. © 1992 by John Wiley & Sons, Inc.
Ab Initio computed molecular structures and energies of the conformers of glucose
Authors: Polavarapu P.L. , Ewig C.S. 
Published: January 2005

AbstractAb initio computations indicate the existence of several stable and some unstable conformers in isolated α and β glucose molecules. All of the lower‐energy conformers exhibit a strikingly regular pattern of internal hydrogen bonding. Five such stable structures have been identified for each of the α and β anomers, differing primarily in the orientation of the CH2OH group. In each conformer, the α anomer is predicted to be lower in energy than the corresponding conformers of β anomer. The difference is about 2 kcal/mol in the 4‐31G basis but only 0.4 kcal/mol in the 6‐31G* basis. It is found that the electronic contributions to the free energy difference stabilize the α anomer while the nuclear motion contributions stabilize the β anomer. The implications of these predictions and the future investigations required to understand the relative stabilities of the two anomers are pointed out. © 1992 by John Wiley & Sons, Inc.
Search for nondegenerate real vertex invariants and derived topological indexes
Authors: Balaban Alexandru T. , Catana Cornel 
Published: January 2005

AbstractTwo new types of real (i.e., noninteger) local vertex invariants (LOVIs), denoted by ci and c′i and called distance‐enhanced exponential connectivities, are defined via eqs. (1)–(3) and (1′)–(3′), respectively. Only the case when the exponent z equals 1 in eqs. (3) and (3′) is discussed in detail. Both these LOVIs span the range from 0–1, but their dependence upon topology is fairly different, as seen from Table II, where ci and c′i values for all heptane and octane isomers are displayed. From these LOVIs, by simple summation over all graph vertices two new topological indexes (TIs), denoted by XC and XC′, respectively, are obtained. Their intermolecular ordering of all alkanes with four to nine carbon atoms is discussed. On their basis, correlations with boiling points and critical pressures of alkanes are presented. © 1993 John Wiley & Sons, Inc.
Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs
Authors: Lee Frederick S. , Chu Zhen Tao , Warshel Arieh 
Published: January 2005

AbstractDifferent microscopic and semimicroscopic approaches for calculations of electrostatic energies in macromolecules are examined. This includes the Protein Dipoles Langevin Dipoles (PDLD) method, the semimicroscopic PDLD (PDLD/S) method, and a free energy perturbation (FEP) method. The incorporation of these approaches in the POLARIS and ENZYMIX modules of the MOLARIS package is described in detail. The PDLD electrostatic calculations are augmented by estimates of the relevant hydrophobic and steric contributions, as well as the effects of the ionic strength and external pH. Determination of the hydrophobic energy involves an approach that considers the modification of the effective surface area of the solute by local field effects. The steric contributions are analyzed in terms of the corresponding reorganization energies. Ionic strength effects are studied by modeling the ionic environment around the given system using a grid of residual charges and evaluating the relevant interaction using Coulomb's law with the dielectric constant of water. The performance of the FEP calculations is significantly enhanced by using special boundary conditions and evaluating the long‐range electrostatic contributions using the Local Reaction Field (LRF) model. A diverse set of electrostatic effects are examined, including the solvation energies of charges in proteins and solutions, energetics of ion pairs in proteins and solutions, interaction between surface charges in proteins, and effect of ionic strength on such interactions, as well as electrostatic contributions to binding and catalysis in solvated proteins. Encouraging results are obtained by the microscopic and semimicroscopic approaches and the problems associated with some macroscopic models are illustrated. The PDLD and PDLD/S methods appear to be much faster than the FEP approach and still give reasonable results. In particular, the speed and simplicity of the PDLD/S method make it an effective strategy for calculations of electrostatic free energies in interactive docking studies. Nevertheless, comparing the results of the three approaches can provide a useful estimate of the accuracy of the calculated energies. © 1993 John Wiley & Sons, Inc.
Analytical density‐dependent representation of Hartree—Fock atomic potentials
Authors: Pacios L. Fernandez 
Published: January 2005

AbstractA procedure to represent atomic electron charge densities [L. Fernandez Pacios,J. Phys. Chem.,95, 10653 (1991);J. Phys. Chem.,96, 7294 (1992)] is here generalized to obtain simple analytical functions for potential energy contributions. Based upon suitable functions to describe atomic electron densities in a physically meaningful form, the procedure is developed to define density‐dependent analytical expressions for the electrostatic (classical) and exchange (quantum) potentials by means of proper approximate functionals. Calculations of correlation energies by using various density‐functional approaches are also performed. The whole scheme is used to represent Hartree–Fock limit atomic wave functions by Clementi–Roetti. This way, a set of analytically simple, nonbasis set‐dependent functions are defined with the aim to be further implemented in energy decomposition schemes for molecular interactions studies using atomic instead of electronic building blocks. © 1993 John Wiley & Sons, Inc.
Development of a restricted Hartree—Fock program INDMOL on PARAM: A highly parallel computer
Authors: Shirsat Rajendra N. , Limaye Ajay C. , Gadre Shridhar R. 
Published: January 2005

AbstractParallelization of the SCF method for closed‐shell molecules on the highly parallel transputer‐based system PARAM is described. The parallelization has been implemented on three different hardware and software environments: (1) a network of bare 64 transputers; (2) configuration 1 plus a back‐end file system (BFS); and (3) configuration 2 with one INTEL i860 processor. The evaluation of electron repulsion integrals (ERIs) and setting up of the Fock matrix is carried out in parallel on 64 nodes using minimal communication strategies. A good load balance is achieved for ERI evaluation with the help of bounds, local symmetry features, and the shell concept, as well as a data randomization technique, resulting into almost linear speedup (for ERI evaluation). In configurations 2 and 3, BFS is used for parallel storage and retrieval of ERIs. Further, in 3 matrix operations are implemented as remote procedure calls on the i860 processor. Routine techniques of level shifting and extrapolation are used for accelerating SCF convergence. The resulting package, INDMOL, has been tested for some randomly selected molecules having up to 255 contractions. Using configuration 3, a factor of 2 to 5 in computation time is obtained over 1, for the systems for which the ERIs cannot be stored in the distributed core memory. In summary, a heterogeneous system, as in configuration 3, can indeed be optimally exploited for programming peculiar diverse requirements of the SCF procedure. © 1993 John Wiley & Sons, Inc.
Computer generation of Hadamard matrices
Authors: Balasubramanian K. 
Published: January 2005

AbstractWe develop a computer code that uses elegant bit‐manipulation techniques for matrix multiplication and thus facilitates exhaustive generation of Skew‐Hadamard matrices. Hadamard matrices are useful in spectroscopic applications (Hadamard transform spectroscopy) and in balanced chemical designs. Application of our code yields several Skew‐Hadamard matrices up to order 100 × 100, although the combinatorial complexity of exhaustive generation increases exponentially. Our bit‐manipulation‐based codes took 124 h of CPU time to perform 7.79344 × 1011 matrix multiplications on an IBM RS 6000/560 system to generate all 100 × 100 matrices. This amounts to 5.7 × 10−7 s of CPU time per matrix multiplication. © 1993 John Wiley & Sons, Inc.
Madelung fields from optimized point charges for ab initio cluster model calculations on ionic systems
Authors: Sousa C. , Casanovas J. , Rubio J. , Illas F. 
Published: January 2005

AbstractA simple procedure devised to obtain optimized point charges to represent the Madelung potential is reported and applied to six different crystal structures occurring in ionic systems. Their use in ab initio cluster model calculations is discussed through some selected examples and results compared with those arising from the use of the well‐known Evjen method. © 1993 John Wiley & Sons, Inc.
Relative basicities of carboxylate lone pairs in aqueous solution
Authors: Pranata Julianto 
Published: January 2005

AbstractRelative basicities of the lone pairs of the acetate ion have been determined using ab initio calculations for the gas phase and Monte Carlo simulations for the aqueous phase. The syn lone pair is found to be more basic by only 1.25 pKa units. This small difference is the result of a large intrinsic preference for the syn conformer of the conjugate acid in the gas phase, offset by an almost equally large preferential solvation of the anti conformer in the aqueous phase. The better solvation of the anti conformer is due to stronger solute–solvent interactions. © 1993 John Wiley & Sons, Inc.
Conformational analysis of cocaine, the potent analog 2β‐carbomethoxy‐3β‐(4‐fluorophenyl)tropane (CFT), and other dopamine reuptake blockers
Authors: Froimowitz Mark 
Published: January 2005

AbstractUsing the MM2‐87 program and parameter set, conformational analyses have been performed on cocaine (1), the potent analog 2β‐carbomethoxy‐3β‐(4‐fluorophenyl)tropane (CFT, 2), and a group of dopamine reuptake blockers that contain two phenyl rings. The latter includes LU 19‐005 (3), a 1‐amino‐4‐phenyltetralin (4), a hexahydropyrrolo[2,1‐a]isoquinoline (5), diclofensine (6), and a hexahydro[1,2‐b]pyridine (7). Using different values for the dielectric constant, the global minimum of 1 and 2 is a conformer in which there is a favorable electrostatic interaction between the ammonium hydrogen and the carbonyl of the carbomethoxy group. The N‐methyl groups in 1 and 2 are found to strongly prefer the equatorial position of the piperidine ring. These results were also related to four crystal structures of 1 and its close derivatives. Compounds 3–7 are found to have a common conformation that was used to define the pharmacophore for dopamine reuptake blockers including the required orientation of the ammonium hydrogen. The pharmacophore provides an explanation for why the tertiary amine analogs of 3 and 4 are less potent than the secondary amines because the added N‐methyl group occupies the position required for the ammonium hydrogen. This explanation, however, does not work for 7, in which the tertiary amine is again less active than the secondary amine. However, this last series appears to have a number of anomalous features. Superposition of 2 with the pharmacophore suggests that its carbomethoxy may occupy the same region of the receptor as the second phenyl ring in compounds 3–7. © 1993 John Wiley & Sons, Inc.
Continuous similarity measure between nonoverlapping X‐ray powder diagrams of different crystal modifications
Authors: Karfunkel H.R. , Rohde B. , Leusen F.J.J. , Gdanitz R.J. , Rihs G. 
Published: January 2005

AbstractThe problem of quantifying similarity between crystal structures is transformed into the problem of comparing the associated X‐ray powder diagrams. A smooth similarity measure between two powder diagrams, termed a “fold,” is defined. In contrast to conventional comparison methods, the introduced method is still applicable when the peaks of the spectra to be compared have no overlap. The main areas of application of the method are the construction of a molecular crystal structure when only the experimental powder diagram is available and the analysis of possible crystal packings predicted on the basis of molecular information only. A suitable empirical parameterization of the fold has been derived from a large set of experimental and force‐field‐generated crystals. The analysis of the outcome of an ab initio packing of a flexible molecule is given as an example. The algorithmic details of the method are given as a FORTRAN 77 code. © John Wiley & Sons, Inc.
Shape groups of the electronic isodensity surfaces for small molecules: Shapes of 10‐electron hydrides
Authors: Walker P. Duane , Arteca Gustavo A. , Mezey Paul G. 
Published: January 2005

AbstractAn algorithm for a detailed 3‐D characterization of the shapes of molecular charge distributions is implemented in the form of a comprehensive package of computer programs, GSHAPE, and applied to a series of 10‐electron hydrides to critically evaluate the methodology. Attention is paid to the effects of nuclear geometry and the size of basis on the molecular shape. The characterization is performed by computing a number of topological invariants (“shape groups”) associated with a continuum of molecular surfaces: the complete family of all electronic isodensity contours for the given molecules. These shape groups (the homology groups of truncated surfaces derived from isodensity contours) depend on two continuous parameters: a density value defining the density contour and a reference curvature value, to which the local curvatures of the isodensity contours are compared. The electronic charge distribution is calculated at the ab initio level using basis sets ranging from STO‐3G to 6‐31G**. No visual inspection is required for the characterization and comparison of shapes of molecular charge densities, as these are done algorithmically by the computer. However, visualization of the results is one option of our program using Application Visualization Software (AVS). For a given molecule, in a given nuclear geometry, the technique provides a 2‐D shape map, displaying the distribution of the shape gruops as a function of the local curvature and the level set value (the value of the charge density at the contour). The computer program GSHAPE performs the analysis automatically. This feature makes it potentially useful in the context of computer‐aided drug design, where unbiased, automated shape characterization methods are valuable tools. As examples, a variety of 2‐D shape maps are discussed. © John Wiley & Sons, Inc.