bluuebunny/crossref_metadata_2025_split huggingface dataset:
An analysis of the structural and energetic properties of deoxyribose by potential energy methods
Authors: Schlick Tamar , Peskin Charles , Broyde Suse , Overton Michael 
Published: January 2005

AbstractWe discuss the three fundamental issues of a computational approach in structure prediction by potential energy minimization, and analyze them for the nucleic acid component deoxyribose. Predicting the conformation of deoxyribose is important not only because of the molecule's central conformational role in the nucleotide backbone, but also because energetic and geometric discrepancies from experimental data have exposed some underlying uncertainties in potential energy calculations. The three fundamental issues examined here are: (i) choice of coordinate system to represent the molecular conformation; (ii) construction of the potential energy function; and (iii) choice of the minimization technique. For our study, we use the following combination. First, the molecular conformation is represented in cartesian coordinate space with the full set of degrees of freedom. This provides an opportunity for comparison with the pseudorotation approximation. Second, the potential energy function is constructed so that all the interactions other than the nonbonded terms are represented bypolynomialsof the coordinate variables. Third, two powerful Newton methods that are globally and quadratically convergent are implemented: Gill and Murray's Modified Newton method and a Truncated Newton method, specifically developed for potential energy minimization. These strategies have produced the two experimentally‐observed structures of deoxyribose with geometric data (bond angles and dihedral angles) in very good agreement with experiment. More generally, the application of these modeling and minimization techniques to potential energy investigations is promising. The use of cartesian variables and polynomial representation of bond length, bond angle and torsional potentials promotes efficient second‐derivative computation and, hence, application of Newton methods. The truncated Newton, in particular, is ideally suited for potential energy minimization not only because the storage and computational requirements of Newton methods are made manageable, but also because it contains an important algorithmic adaptive feature: the minimization search is diverted from regions where the function is nonconvex and is directed quickly toward physically interesting regions.
Molecular mechanics parameters for organosilicon compounds calculated from ab initio computations
Authors: Grigoras Stelian , Lane Thomas H. 
Published: January 2005

AbstractMolecular structures of 26 organosilicon compounds have been optimized using ab initio calculations at the 3‐21G* (modified) level. From these optimized structures, the internal coordinates have been deformed and the variation of the total molecular energy has been studied. Parameters for stretching and bending deformations are reported herein. The bending potential for the SiOSi bond which has an unusual flexibility is also included. Nonbonding interactions are described in terms of steric and electrostatic potentials. For systems which do not include bond resonance effects, torsional behavior is well described by steric potentials with van der Waals radii 20% larger than the previous values and simple electrostatic potential (monopole‐monopole) with net atomic charges obtained from ab initio or Extended Huckel Theory calculations. The nonbonding potentials, as defined in this study, have an advantage in that they allow for the computation of torsional barriers without torsional potentials, in the case of single bonds where no additional electronic effects interfere. As an example, it is shown that no torsional potentials are necessary to estimate the torsional barriers in the case of ethane. The newly defined potentials are used to study the torsional barrier in hexamethyldisiloxane and the conformation of octamethylcyclotetrasiloxane (D4). The most stable calculated conformation of D4, coincides with the experimentally determined structure. This study shows that the most stable conformation is determined by the steric repulsion of methyl groups.
A conformational study of a biologically active conjugated syn‐oxime
Authors: Venanzi Thomas J. , Venanzi Carol A. 
Published: January 2005

AbstractThe conjugated system (E)‐tiglaldoxime is the simplest example of a perillartine analog which exhibits sweetness with a taste potency greater than sucrose with almost no bitter aftertaste. In previous studies, the structure of this biologically active compound has been assumed to be planar with the CC double bond trans to the CN bond of the oxime moiety. In this article a conformational analysis of this molecule is reported. The results indicate that, although the trans conformer of the planar molecule is indeed the global minimum, other conformers lie within a few kilocalories of this minimum. Hence, other accessible conformations may be available for interaction with the receptor and, therefore, may be biologically active. The structural parameters obtained for this conjugated syn‐oxime are nearly identical to those of (E)‐acetaldoxime. This fact has implications for the transferability of these parameters to the more complicated perillartine analogs.
Ab initio vibrational transition dipole moments and intensities of formaldehyde
Authors: Hsieh Hsiuchin C. , Ermler Walter C. 
Published: January 2005

AbstractVibrational transition dipole moments and absorption band intensities for the ground state of formaldehyde, including the deuterated isotopic forms, are calculated. The analysis is based on ab initio SCF and CI potential energy and dipole moment surfaces. The formalism derives from second‐order perturbation theory and involves the expansion of the dipole moment in terms of normal coordinates, as well as the incorporation of point group symmetry in the selection of the dipole moment components for the allowed transitions. Dipole moment expansion coefficients for the three molecule‐fixed Cartesian coordinates of formaldehyde are calculated for internal and normal coordinate representations. Transition dipole moments and absorption band intensities of the fundamental, first overtone, combination, and second overtone transitions are reported. The calculated intensities and dipole moment derivatives are compared to experiment and discussed in the context of molecular orbital and bond polarization theory.
Contraction of the well‐tempered Gaussian basis sets: The first‐row diatomic molecules
Authors: Dingle T. W. , Huzinaga S. , Klobukowski M. 
Published: January 2005

AbstractThe well‐tempered Gaussian basis sets (14s 10p) for atoms from lithium to neon were contracted and used in restricted Hartree–Fock calculations on 13 systems: Li2(Σ), B2(Σ), C2(Σ), N2(Σ), O2(Σ), F2(Σ), Ne2(Σ), LiF(Σ), BeO(Σ), BF(Σ), CN−(Σ), CO(Σ), and NO+(Σ). Spectroscopic constants (Re, ωe, ωexe, Be, αe, and ke) and one‐electron properties (dipole, quadrupole, and octupole moments at the center of mass and electric field, electric field gradient, potential, and electron density at the nuclei) were evaluated and compared with the Hartree–Fock results. The largest contracted basis set (7s6p3d) gives results very close to the Hartree–Fock values; the remaining differences are attributed to the absence of the f functions in the present basis sets. For Ne2, the interaction energy was calculated; the magnitude of the basis‐set superposition error was found to be very small (less than 3 μEh at 2.8 a0 and less than 2 μEh at 5.0 a0).
Chlorosilanes: Development and application of MM2 force field parameters
Authors: Cho Soo Gyeong , Unwalla Rayomand J. , Cartledge Frank K. , Profeta Salvatore 
Published: January 2005

AbstractThe geometries, relative conformational energies, and dipole moments of mono and polychlorosilanes have been calculated using ab initio molecular orbital (MO) theory. Calculations at the HF/3–21G(*) level, with the exception of dipole moments, give reasonable agreement with experimental data. A new MM2 force field for chlorosilanes, which includes terms for bond length shortening and bond angle compression due to the attachment of electronegative Cl atoms, has been developed on the basis of experimental and ab initio results. The new force field is generally successful in predicting structural parameters, but is unable to reproduce the dipole moments of several model systems. While dipole moment predictions are not the authors' main interest, this failure defines a shortcoming in the MM2 method. The new parameters have been applied to problems in the prediction of stereochemistries of cyclic systems, and compared with experimental results where data are available.
Molecular mechanics conformational analysis of cyclononane using the RIPS method and comparison with quantum‐mechanical calculations
Authors: Ferguson David M. , Glauser William A. , Raber Douglas J. 
Published: January 2005

AbstractThe recently reported Random Incremental Pulse Search (RIPS) technique has been used to probe the conformational energy surface of cyclononane. The stochastic method permits searching of the potential energy surface for all minimum‐energy conformations. The search located all previously reported structures together with three additional conformations that were not found by earlier, primitive searching techniques. Two of these structures are high‐nergy skew forms, and the third is a low‐energy conformer that should contribute significantly to the overall equilibrium set of cyclononane conformations. The global minimum has been found to be the D3 symmetrical twist chair‐boat (TBC) form in accordance with previous studies. The newly discovered low‐energy structure, which lies only 2.2 kcal/mol above the global minimum, has been designated twist chair‐twist chair (TCTC). The two higher energy conformers are skewed chair‐chair (SCC) and skewed boat‐boat (SBB) forms that are 5.7 kcal/mol and 10.4 kcal/mol above the global minimum, respectively. The seven reported conformations were reanalyzed quantum mechanically (AM1), and a comparison between MM2 and AM1 results is presented.
Coupled cluster method with first‐order correlation orbitals versus multireference configuration interaction method. Accurate calculations for HF, H2O, and NH3
Authors: Adamowicz Ludwik 
Published: January 2005

AbstractThis article shows that with our Hylleras‐functional based method1 for generating correlation orbitals, we can determine electronic structures for small polyatomic systems very accurately. The procedure is ab initio, uses conventional Gaussian basis sets, and solves the electronic Schrödinger equation with the coupled cluster method. A comparison is made with MRCI results obtained in equivalent basis sets for the HF, H2O, and NH3 molecules.
Characters for symmetric and antisymmetric higher powers of representations: Application to the number of anharmonic force constants in symmetrical molecules
Authors: Zhou Xue‐Feng , Pulay Peter 
Published: January 2005

AbstractExplicit formulas are given for the characters of symmetric and antisymmetric powers of an arbitrary representation up to the sixth, and a general method for obtaining the higher ones is described. The results allow, among others, the determination of nonvanishing higher force constants in symmetrical molecules. The benzene molecule, for instance, has 237 nonvanishing cubic and 1890 quartic force constants. Other potential applications are a general method for the symmetry species of vibrational overtones, the determination of the number of independent centrifugal distortion constants, and the symmetry classification of vibrational multiplets.
A recipe for evaluating and differentiating cos ϕ expressions
Authors: Schlick Tamar 
Published: January 2005

AbstractWe present a simple recipe for calculating and differentiating cosine of bond angle and dihedral angle expressions. The resulting formulas can be incorporated in a straightforward manner into the bond angle and dihedral angle components of potential energy functions. These formulas rely only on expressions and derivatives of dot products, and, in particular, they avoid cross products as well as excessive Fortran function references. Consequently, the expressions derived in this article can be written compactly and evaluated rapidly.
The dynamics of gallamine: A potent neuromuscular blocker. A determination by quantum mechanics and molecular dynamics (i) in vacuo studies
Authors: Saldanha José W. , Howlin Brendan , Toit Louis Du , Palmer Rex A. 
Published: January 2005

AbstractThe potent neuromuscular blocker, gallamine, possesses three chemically equivalent, flexible side chains, the motion of which has been proposed as important in its mode of action on the acetylcholine receptor in vivo. The flexibility of the side chains has been investigated in the present initial study by a combination of quantum mechanics and molecular dynamics on the isolated, unsolvated molecule. Net atomic charges for the gallamine molecule have been calculated using the semiempirical program MOPAC for use in the molecular dynamics simulation. The flexibility of the side chains has been shown to correlate with the range of fluctuations in torsion angles observed in the crystal structure of gallamine.
Validation of the general purpose tripos 5.2 force field
Authors: Clark Matthew , Cramer Richard D. , Van Opdenbosch Nicole 
Published: January 2005

AbstractA molecular mechanics force field implemented in the Sybyl program is described along with a statistical evaluation of its efficiency on a variety of compounds by analysis of internal coordinates and thermodynamic barriers. The goal of the force field is to provide good quality geometries and relative energies for a large variety of organic molecules by energy minimization. Performance in protein modeling was tested by minimizations starting from crystallographic coordinates for three cyclic hexapeptides in the crystal lattice with rms movements of 0.019 angstroms, 2.06 degrees, and 6.82 degrees for bond lengths, angles, and torsions, respectively, and an rms movement of 0.16 angstroms for heavy atoms. Isolated crambin was also analyzed with rms movements of 0.025 angstroms, 2.97 degrees, and 13.0 degrees for bond lengths, angles, and torsions respectively, and an rms movement of 0.42 angstroms for heavy atoms. Accuracy in calculating thermodynamic barriers was tested for 17 energy differences between conformers, 12 stereoisomers, and 15 torsional barriers. The rms errors were 0.8, 1.7, and 1.13 kcal/mol, respectively, for the three tests. Performance in general purpose applications was assessed by minimizing 76 diverse complex organic crystal structures, with and without randomization by coordinate truncation, with rms movements of 0.025 angstroms, 2.50 degrees, and 9.54 degrees for bond lengths, angles and torsions respectively, and an average rms movement of 0.192 angstroms for heavy atoms.
Computational chemistry applied to the design of chiral stationary phases for enantiomeric separation
Authors: Däppen Richard , Karfunkel Heinrich R. , Leusen Frank J. J. 
Published: January 2005

AbstractA general computational scheme for the rational design of chiral stationary phases for the chromatographic separation of enantiomers has been established. The developed scheme was based on applying different interaction models (force field methods versus semi empirical quantum chemical methods), different docking algorithms (systematic grid search methods versus interactive methods guided by rules based on binding modes) and different levels of approximations (rigid versus flexible docking) to a representative test problem containing the 3,5‐dinitrobenzoyl group. The computational methods in use covered the most sophisticated methods which could presently be applied to problems of such a size (about 80 atoms). It has been shown that the current computational approaches using rigid body approximations for the docked molecules and simple molecular mechanics (not taking pi‐“effects” into account) are invalid in view of the required predictive precision of about 1–2 Kcal/mole for the differential binding energy. Another surprising result was the failure of the commonly used systematic search methods in determining the most favorable binding modes. Based on our calculations on the representative test problem we propose a new arrangement for the most stable complexes without parallel stacking of the aromatic pi‐donor and the 3,5‐dinitrobenzoyl pi‐acceptor systems.
η5‐P‐ or η4‐P‐Coordination in apically oxygenated phosphoranes? An ab initio study of PH4O−, PH4O− · E (E = Li+, NH4+, and HF) and related fluorinated oxyphosphoranes
Authors: Glaser Rainer , Streitwieser Andrew 
Published: January 2005

AbstractStructural optimizations of the apically substituted isomer of PH4O− and the diapically substituted isomer of PH3FO− with diffuse‐function augmented 3–21G* basis sets and with the 6–31 + G* and 6–31 + + G* basis sets result in P‐η4‐coordination in these anions. The structures obtained are those of a hydride or fluoride ion “solvated” by or complexed with phosphine oxide, rather than phosphoranes. In contrast, 3–21G* basis sets without diffuse functions on the atom in the trans‐apical position with regard to the oxy‐substituent yield P‐η5‐phosphorane structures that appear to be computational artifacts of the small basis set; the formation of the P‐η4‐geometries is curtailed by the insufficient functional description of the potential trans‐apical nucleophilic leaving group. The overall neutral apical isomers of PH4O− · E(E = Li+, NH4+), the diapical isomer of PH3FO−Li+, as well as the model‐solvated apical isomer of PH4O− · HF favor P‐η5‐phosphorane geometries at all of these computational levels. The mechanism by which the E‐group alters the electronic structures within PH4Oa− is discussed based on the geometries, the molecular orbitals, and electron density analysis techniques.
Partial electrostatic charges for the active center of Cu, Zn superoxide dismutase
Authors: Shen Jian , Wong Chung F. , Subramaniam Shankar , Albright Thomas A. , McCammon J. Andrew 
Published: January 2005

AbstractAtomic partial charges for three model systems that mimic the metal‐ligand moiety of the active site in the enzyme Cu, Zn superoxide dismutase (SOD) have been calculated at the ab initio level. The model systems include copper and zinc complexes with imidazole, formate and ammonia ligands. The partial charges thus obtained have been incorporated into force fields for molecular simulations. Simulations carried out with these force fields justify the need for specialized charge assignments for the metals and their ligands.
Comparative study of the molecular electrostatic potential obtained from different wavefunctions. Reliability of the semiempirical MNDO wavefunction
Authors: Luque F. J. , Illas F. , Orozco M. 
Published: January 2005

AbstractA systematic analysis of the molecular electrostatic potential (MEP) is presented. This study has been performed with a twofold purpose: first, to study the MEP dependence with regard to the quality of the basis set used to compute the ab initio SCF wavefunction and second, to develop and to assess a new strategy for computing isoelectrostatic potential maps using the semiempirical MNDO wavefunction. The only differences between this procedure and the ab initio SCF MEP computation lie in the freezing of the inner electrons and in the origin of the first‐order density matrix. The statistical analysis of MEPs computed for a large number of molecules from MNDO wavefunction and ab initio SCF wavefunctions obtained using STO‐3G, 4‐31G, 6‐31G, 4‐31G*, 6‐31G*, and 6‐31G** basis sets points out the ability of any wavefunction to reproduce the general topological characteristics of the MEP surfaces. Nevertheless, split‐valence basis sets including polarization functions are necessary to obtain accurate MEP minimum energy values. MNDO wavefunction tends to overestimate the MEP minima depth by a constant factor and shows an excellent ability to reflect the relative variation of MEP minima energies derived from a rather sophisticated (6‐31G*) basis set, lacking of the shortcomings detected in the semiempirical CNDO approximation.
A structural approach to calculate physical properties of pure organic substances: The critical temperature, critical volume and related properties
Authors: Grigoras Stelian 
Published: January 2005

AbstractA new approach based on computation of the molecular surface interactions (MSI) to estimate several physical properties of pure organic substances is described. MSI are derived from molecular structural data and consist of total molecular surface area, electrostatic molecular surface interactions, and a hydrogen bonding term. This new approach estimates the critical temperature and the molar critical volume of pure organic substances with molecular weights in the range of 40–500 a.u‥ In addition, the following properties can be calculated: the critical pressure, the boiling temperature, the molar volume in liquid state at normal pressure and temperature. The method can be used to predict physical properties of compounds having flexible or rigid, symmetric or asymmetric, polar or nonpolar molecular structures, and compounds with or without hydrogen bonding groups.
H/He Molecules in strong electric fields
Authors: Gründler W. , Steinke T. , Walther P. 
Published: January 2005

AbstractFloating spherical Gaussian orbitals are used within a split‐shell description to calculate the properties of H, He, He+, H2, H+2, HeH+, and H+3 in a strong uniform electric field. Accurate polarizabilities including their field strength dependence are obtained with two basis functions at most. Critical field strengths for ionization and deprotonation are determined for different orientations of molecules. Electron tunneling is described within the time dependent approach using floating Gaussian orbitals also.
Solvent effect and librational entropy calculations on N‐acetylalanylglycine amide
Authors: Sapse Anne‐Marie , Jain Duli C. , De Gale Denyse , Wu T. C. 
Published: January 2005

AbstractEntropy and solvent effects are calculated for some conformations of Ala‐Gly. The inclusion of these effects in energy calculations show the βII type structure to be the most stable.
Computer generation of character tables of generalized wreath product groups
Authors: Liu Xiaoyu , Balasubramanian K. 
Published: January 2005

AbstractAlgorithms and computer codes in FORTRAN 77 are developed for the computation of characters of generalized wreath product groups through generating function methods. Characters of generalized wreath product groups of symmetric groups are computed in terms of the characters of much smaller composing groups using plethysms of S‐functions. The developed codes were tested for many generalized wreath product groups. The character tables of generalized wreath products, S2[S3, S2, S2] (NMR group of hexane) and S4[S3] containing 576 and 31,104 elements, respectively, were constructed as examples.
Effect of basic set quality and electron correlation on the scale factors of a harmonic force field
Authors: Bock C. W. , Panchenko Y. N. , Pupyshev V. I. 
Published: January 2005

AbstractThe completely optimized structure and harmonic force field of s‐trans‐buta‐1,3‐diene are reported at the MP2/6‐31G and MP2/6‐31G* levels of computation. Sets of empirical scale factors for the calculated force fields are derived and compared with the corresponding values computed at the RHF/4‐31G and RHF/6‐31G levels. Changes in the scale factors for this series of force fields are discussed. The vibrational frequencies are also reported for thirteen isotopomers of s‐trans‐buta‐1,3‐diene using the MP2/6‐31G* force field. Some characteristics of the gauche and cis forms of buta‐1,3‐diene are also given.