bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ab initio calculations on CO4 centers in silicon dioxide
Authors: McEachern R. J. , Rao P. S. , Weil J. A. 
Published: January 2005

AbstractAb initio SCF‐MO Hartree–Fock calculations were performed using the STO‐3G, 6‐31G, and 6‐31G* basis sets to model hypothetical substitutional carbon impurities in silicon dioxide. We utilized nine‐atom clusters, [C(OH)4]qt, with charge number qt = 0 and + 1. The positions of the C and O atoms were varied to achieve minimum total energies, while the fixed protons served to simulate the rigid crystal surroundings. In the optimized configuration of the neutral cluster, the CO bond lengths are appreciably longer than typical CO bonds, indicating relatively weak bonds for a carbon impurity at a silicon site. For comparison, the relative positions of all nine atoms in the [C(OH)4]0 model were allowed to vary. This unconstrained model yielded more normal bond lengths and was lower in energy than the fixed‐proton model by 6.80 eV with the 6‐31G* basis set. The free‐H model compared favorably with the x‐ray diffraction data for an analogous orthocarbonate. Our results are in concert with the lack of reports of any substitutional carbon impurity in α‐quartz. In the fixed‐H models, the twofold local symmetry was found to be retained when qt is 0 but not when qt is + 1. For the latter ion, the unrestricted H‐F calculations indicate that this paramagnetic center has its spin population almost entirely on one oxygen ion and is high in energy (5.31 eV with 6‐31G) compared to the diamagnetic neutral one. Conclusions reached with the nine‐atom clusters were confirmed by a series of calculations on the extended model [C(OSiH3)4]0.
Standard‐geometry chains fitted to X‐ray derived structures: Validation of the rigid‐geometry approximation. I. Chain closure through a limited search of “loop” conformations
Authors: Palmer Kathleen A. , Scheraga Harold A. 
Published: January 2005

AbstractThe Gō–Scheraga algorithm to produce rigid‐geometry chain closures for polypeptide chains (N. Gō and H.A. Scheraga, Macromolecules, 3, 178, 1970) has been updated to allow each residue in the chain to adopt different bond lengths or bond angles. A treatment of five‐residue local chain deformations is presented in detail. For chain sections shorter than five residues in length, it is shown that satisfactory closures may be obtained by direct fitting, indicating that the rigid‐geometry approximation is adequate to model even short sections of chains having perturbed local geometry. The new implementation of the algorithm has been applied to several problems in protein structure determination and molecular modeling. The first of these is the problem of finding standard‐geometry closures for short regions of chains having irregular geometry. It is shown that standard‐geometry closures which superimpose well upon the coordinates of the irregular structures may be obtained routinely for chain sections that are five amino acid residues or more in length. Another application of the algorithm is to generate a large number of closures for a short segment of a protein chain, as a method to search the conformational space of this segment. The latter application should prove useful in studies in which the conformation of some region of a given protein has not been determined experimentally. Such applications include the modeling of proteins which have a sequence homology to a crystallized protein, and modeling regions of crystallized proteins which are not well‐defined in electron density maps.
The Hylleraas‐CI method in molecular calculations. III. Implementation and numerical verification of a three‐electron many‐center theory
Authors: Frye D. , Preiskorn A. , Clementi E. 
Published: January 2005

AbstractThe general theory of three‐electron Hylleraas‐Configuration‐Interaction method using linear correlation factors of the form rij has been implemented for molecular systems using cartesian Gaussians as basis sets. A brief review of the theory and the form of the three‐electron integrals is presented. Additionally, a table of numerical values of some selected three‐electron integrals is given. Results from test calculations on H3 using the full form of the theory are presented for some simple basis sets. A discussion of the computational problems that need to be overcome before this approach is competitive with traditional methods is included.
Geometry optimization in cartesian coordinates: The end of the Z‐matrix?
Authors: Baker Jon , Hehre Warren J. 
Published: January 2005

AbstractGeometry optimization directly in Cartesian coordinates using the EF and GDIIS algorithms with standard Hessian updating techniques is compared and contrasted with optimization in internal coordinates utilizing the well known Z‐matrix formalism. Results on a test set of 20 molecules show that, with an appropriate initial Hessian, optimization in Cartesians is just as efficient as optimization in internals, thus rendering it unnecessary to construct a Z‐matrix in situations where Cartesians are readily available, for example from structural databases or graphical model builders.
PM3 study of the proton affinities of 2‐, 3‐, and 4‐monosubstituted pyridines in the gas phase
Authors: Szafran Miroslaw , Koput Jacek 
Published: January 2005

AbstractHeats of formation (ΔHf) and proton affinities (PA) of 2‐, 3‐, and 4‐monosubstituted pyridines in the gas phase are calculated using the AM1 and PM3 semiempirical methods. The following substitutents are considered: NO2, CN, CF3, CHO, F, Cl, COCH3, H, CH3, OCH3, SCH3, NH2, and N(CH3)2. The results are compared with the experimental data. Both methods reproduce the ΔHf with comparble accuracy; the rms deviations are 4.1 (AM1) and 4.5 kcal/mol (PM3) for the free bases and 9.5 (AM1) and 9.7 kcal/mol (PM3) for their conjugated acids. The PA are systematically underestimated by both methods, but AM1 appears to be clearly better than PM3 for reproducing the experimental values. The rms deviations for AM1 and PM3 are 5.1 and 9.6 kcal/mol, respectively. This is due to a cancellation of systematic errors in the calculated ΔHf in the AM1 case and to a summation of the errors in the PM3 case. Both methods correctly reproduce conformations of the molecules under consideration.
The use of ultraviolet resonance Raman intensities to test proposed molecular force fields for nucleic acid bases
Authors: Lagant Philippe , Derreumaux Philippe , Vergoten Gerard , Peticolas Warner 
Published: January 2005

AbstractThe harmonic molecular force fields for the nucleic acid bases, cytosine, and guanine, that have been previously published by several investigators are tested by the calculation of the relative intensities of the in‐plane modes in the ultraviolet resonance Raman (UVRR) effect from the two lowest lying absorption bands using a theoretical approach devised previously.1–3 Since only a fraction of the 2N – 3 in‐plane vibrations of a molecule are active in the UVRR, the two criteria that are taken for the adjustment of the force constant are: (1) the closest possible agreement between the observed and calculated frequencies of the 2N – 3 in‐plane vibrations, and (2) the closest possible agreement between the calculated and observed intensities of those few vibrations that are strongly active in the ultraviolet resonance Raman effect. In particular it is necessary that the force constants be adjusted to avoid the calculation of intense Raman lines with frequencies that are not observed in the UVRR spectrum. Using this criteria, a new force field has been developed that appears to give better agreement with the observed UVRR intensities than previously published ones. It is suggested that this calculation of the UVRR intensities can be used to refine molecular force fields in combination with other methods such as isotopic replacement currently in use to refine force constants.
Grid‐search molecular accessible surface algorithm for solving the protein docking problem
Authors: Wang Huajun 
Published: January 2005

AbstractAn algorithm for solving the protein docking problem is presented. Many tentative dockings are first generated by requiring a hole on the surface of one protein to match a knob on the surface of the other. All the tentative dockings are then applied. The initial configurations thus generated are further optimized. The optimization is facilitated by giving a discrete representation to the protein interior and a double‐layer discrete representation to the protein surface. The algorithm presented correctly predicts the association of trypsin with its inhibitor as well as that of the α and β subunits in hemoglobin.
Parallel algorithm for the computation of characteristic polynomials of chemical graphs
Authors: Venuvanalingam P. , Thangavel P. 
Published: January 2005

AbstractA parallel algorithm is developed for the first time based on Frame's method to compute the characteristic polynomials of chemical graphs. This algorithm can handle all types of graphs: ordinary, weighted, directed, and signed. Our algorithm takes only linear time in the CRCW PRAM model with O(n3) processors whereas the sequential algorithm takes O(n4) time. Especially when the number of vertices of the graph is large this method will be more efficient than the recently developed vectorized Frame and Givens–Householder methods.
Dispersion and repulsion contributions to the solvation energy: Refinements to a simple computational model in the continuum approximation
Authors: Floris F. M. , Tomasi J. , Ahuir J. L. Pascual 
Published: January 2005

AbstractA computational method for the evaluation of dispersion and repulsion contributions to the solvation energy is here presented in a formulation which makes use of a continuous distribution of the solvent, without introducing additional assumptions (e.g., local isotropy in the solvent distribution). The analysis is addressed to compare the relative importance of the various components of the dispersion energy (n = 6, 8, 10) and of the repulsion term, to compare several molecular indicators (molecular surface and volume, number of electrons) which may be put in relation to the dispersion‐repulsion energy, and to define simplified computational strategies. The numerical examples refer to saturated hydrocarbons in water, treated with the homogeneous approximation of the distribution function which for this type of solution appears to be acceptable.
A molecular orbital study of amiloride
Authors: Venanzi Carol A. , Plant Christopher , Venanzi Thomas J. 
Published: January 2005

AbstractMolecular orbital calculations with geometry optimization in the 3‐21G(*) basis set were carried out for the acylimino (A, 1a) and the isoimino (E, 1b) tautomers of the free base form of amiloride, and for the protonated form (F, 1c) of amiloride. The results showed the E1 tautomer to be 16.8 kcal/mol higher in energy than the A conformer of lowest energy, A1. The protonation energy of the A1 species was found to be 269.4 kcal/mol. Similar results were obtained using the AM1 method. These results are in agreement with the NMR results of Smith et al. which show the A and F species to be predominant in solution. The 3‐21G(*) rotational barrier for the acylimino tautomer was found to be 19.0 kcal/mol, with the A4 conformer 2.50 kcal/mol higher in energy than the A1.
Conformational studies of 2‐methylbutyronitrile and 3‐methyl‐1‐pentyne by vibrational spectroscopy and molecular mechanics
Authors: Crowder G. A. , Carlisle G. O. 
Published: January 2005

AbstractVibrational spectra were obtained for the structurally similar compounds 2‐methylbutyronitrile and 3‐methyl‐1‐pentyne, and vibrational assignments were made with the aid of normal coordinate calculations. Molecular mechanics calculations were also made, and each compound was shown to exist as a mixture of three conformers, with the most stable conformer being the one with the two methyl groups trans to each other. Results of the calculations are given.
Dielectric boundary smoothing in finite difference solutions of the poisson equation: An approach to improve accuracy and convergence
Authors: Davis Malcolm E. , McCammon J. Andrew 
Published: January 2005

AbstractFinite difference methods are becoming very popular for calculating electrostatic fields around molecules. Due to the large amount of computer memory required, grid spacings cannot be made extremely small in relation to the size of the van der Waals radii of the atoms. As a result, the calculations make a rather crude approximation to the molecular surface by defining grid line midpoints discontinuously as either interior or exterior. We present a method which “smoothes” the boundary, but more accurately models the potential from the analytic solution of the discontinuous dielectric problem and improves convergence in electrostatic energy calculations. In addition, a small improvement in convergence rate is observed.
Molecular geometries and heats of formation of C60 and C70 as computed by MM2‐87
Authors: Froimowitz Mark 
Published: January 2005

AbstractMM2‐87 calculations have been performed on C60 (buckminsterfullerence; footballene) and C70 with full energy minimization. The steric energies for C60 and C70 were computed to be 179.9 and 177.9 kcal/mol, respectively. The heats of formation for C60 is found to be more stable than C60. The two bond lengths for C60 were computed to be 1.393 and 1.444 Å. Eight different bond lengths were found for C70 ranging from 1.386 to 1.452 Å. Bond angles, dihedral angles, and moments of inertia are also reported for the compounds.
Approximate STO functions for the first‐row transition metal atoms
Authors: de la Vega J. M. García , Miguel B. 
Published: January 2005

AbstractSlater type orbital (STO) basis sets for the atoms Sc‐Zn have been derived using a technique based on the distance between subspaces. The accuracy for several properties of these basis sets has been tested. Basis sets studied are of both single‐ and double‐zeta sizes, although this technique can be generalized for any size. Uniform quality criteria through the series of atoms Sc‐Zn are difficulty to establish due to the varying number of d electrons. A comparative study at the atomic level of the quality of STO basis sets (both the two new basis sets and Clementi's basis sets) for the first‐row transition elements has been carried out. Results show that the new basis sets provide better simulation for several properties. Molecular calculations on compounds with these atoms using a Gaussian expansion fitted according to the new values of optimized STOs are also included. The results obtained are similar to those reported when STO‐3G basis set is used.
The graph isomorphism problem
Authors: Liu X. , Klein D. J. 
Published: January 2005

AbstractA chemically and graph‐theoretically relevant problem is that of determining whether a pair of graphs G and G′ are isomorphic. A two‐stage computational test is developed. In the first stage an “eigenvalue‐eigenprojector” tabular graph‐theoretic invariant is computed, whence if the two tables differ, G and G′ must be nonisomorphic. The second stage, utilizing the tables of the first stage, orders the vertices, thereby leading to a special labeling for them, whence if the associated adjacency matrices for G and G′ are equal, it must be that G and G′ are isomorphic. The computational implementation, and testing of the algorithm is described.
Extension of SINDO1 to transition metal compounds
Authors: Li Jian , De Mello Paulo Correa , Jug Karl 
Published: January 2005

AbstractThe semiempirical MO method SINDO1, originally suitable for first‐ and second‐row atoms, is extended to transition metals from scandium to zinc. The core Hamiltonian elements in a symmetrically orthogonalized atomic orbital (OAO) basis set are modified and the parameters are optimized to reproduce the experimental geometries, heats of formation, and ionization potentials. An application of the method to a selected number of molecules, as well as a comparison between calculated and experimental data is reported.
Analysis of an intermediate in a 1,3‐dipolar cycloaddition of methylsulfonyl azide
Authors: Sustmann Reiner , Sicking Willi , Quast Helmut 
Published: January 2005

AbstractMNDO‐PM3 calculations, carried out on an experimentally determined structure of an intermediate in the cycloaddition of an electrophilic azide and a nucleophilic 1,3‐dipolarophile, show that the semiempirical MO scheme models this structure closely. Transition structures for formation of the intermediate and ring closure of the latter are described.
Charge distributions of phosphorylcholine and its derivatives
Authors: Schaumberger M. , Köhler J. 
Published: January 2005

AbstractHartree–Fock self‐consistent field calculations on the 3‐21G(*) level of approximation have been performed to phosphorylcholine and its derivatives in a geometry close to an X‐ray structure of an antibody/antigen complex. Wave functions have been analyzed using different methods for derivation of atomic charges used as Coulomb charges in empirical force fields for molecular dynamics simulations. Among the three applied methods—Mulliken population analysis, natural population analysis, and electrostatical fit—the natural population analysis seems to give best results for these molecules.
A conformational analysis of 3′‐azido‐3′‐deoxythymidine
Authors: Sabio Michael , Topiol Sid 
Published: January 2005

AbstractAn extensive conformational analysis of 3′‐azido‐3′‐deoxythymidine (AZT) was performed at the semiempirical AM1 level with full relaxation of all geometric parameters and careful consideration of furan puckering and the rotational states of the thymine—furan, furan—azide, furan—methylene, and methylene—hydroxyl bonds. The search located 70 conformers, 21 of which have relative energies within 2.5 kcal/mol of the global minimum. Several geometric features, including various forms of hydrogen bonding, within this selected lowenergy subset were examined in terms of their relative contributions to the conformational states of AZT. Hydrogen bonding of thymine's position 2 carbonyl oxygen atom to the hydroxymethyl group (O2;HO), which until recently has not been mentioned in the literature, is observed in a few low‐energy AM1 conformations; however, this form is less favored at the AM1 level than the usually depicted modes involving the thymine moiety with the oxygen atoms of the hydroxyl and furan groups (H6;OH and H6Ofur, as observed in the two crystallographically independent structures), as well as that involving the hydroxyl hydrogen and furan oxygen atoms (OHOfur, which also has not been mentioned for AZT in the literature until recently). The AM1‐optimized geometries agree more closely with nuclear magnetic resonance data than with crystallographic structures and bear little resemblance to molecular mechanics results. The present study shows no evidence of a single dominant conformation or single structural parameter that determines AZT's conformational states. In contrast to our previous analogous study of cGMP, this computational study of AZT does not show strong evidence of a syn conformation with hydrogen bonding involving the base.
Automated docking with grid‐based energy evaluation
Authors: Meng Elaine C. , Shoichet Brian K. , Kuntz Irwin D. 
Published: January 2005

AbstractThe ability to generate feasible binding orientations of a small molecule within a site of known structure is important for ligand design. We present a method that combines a rapid, geometric docking algorithm with the evaluation of molecular mechanics interaction energies. The computational costs of evaluation are minimal because we precalculate the receptor‐dependent terms in the potential function at points on a three‐dimensional grid. In four test cases where the components of crystallographically determined complexes are redocked, the “force field” score correctly identifies the family of orientations closest to the experimental binding geometry. Scoring functions that consider only steric factors or only electrostatic factors are less successful. The force field function will play an important role in our efforts to search databases for potential lead compounds.
Pathways for ring inversion in 9, 10‐dihydroanthracene, 9, 10‐dihydrophenanthrene, and 7, 12‐dihydropleiadene: Combined molecular orbital and molecular mechanics study
Authors: Sygula Andrzej , Rabideau Peter W. 
Published: January 2005

AbstractThe combined semiempirical AM1 and MM2 study of the ring inversion processes in 9, 10‐dihydroanthracene (1), 9, 10‐dihydrophenanthrene (2), and 7, 12‐dihydropleiadene (3) predicts planar transition states for 1 and 2, in accord with earlier assumptions. In the case of 3, however, a nonplanar, chair‐like transition state is located on the potential energy surface in contrast with previous conclusions. Implications of the nonplanar TS on the rationalization of available experimental data are discussed. The calculated barriers for ring inversion in 1–3 are in reasonable agreement with both experiment and previous theoretical results. In general, AM1 is found to slightly underestimate the barriers as compared to the MM2 calculations.
Theoretical study of some nitriles: Intramolecular hydrogen bonds and anomeric effect
Authors: Fernández Berta , Vázquez Saulo A. , Ríos Miguel A. 
Published: January 2005

AbstractAn ab initio study of 3‐chloro‐, 3‐hydroxy‐, 3‐mercapto‐, and 3‐amino‐propanenitrile and 4‐chloro‐bu‐ tanenitrile was carried out at several levels of theory. The calculated stabilities and geometrical trends are interpreted in terms of the effects of intramolecular hydrogen bonds and anomeric interactions, and compared with available experimental data.
Stiffness‐Adaptive Taylor method for the integration of non‐stiff and stiff kinetic models
Authors: Baeza J. J. Baeza , Ramos G. Ramis , Plá F. Pérez 
Published: January 2005

AbstractA systematic derivation procedure that greatly facilitates the application of the Taylor method to the integration of kinetic models is developed. In addition, an algorithm that gives the integration step as a function of the required level of accuracy is proposed. Using the Taylor method, application of this algorithm is immediate and largely reduces the integration time. In addition, a new method of integration of kinetic models, whose most important feature is the self‐adaptability to the stiffness of the system along the integration process, is developed. This “stiffness‐adaptive” Taylor method (SAT method) makes use of several algorithms, combining them to meet the particular requirements of the integration of each species along the integration process. In comparison with the Runge–Kutta–Felhberg, Runge–Kutta–Calahan, Taylor, and Gear methods, the SAT method is the best to integrate non‐stiff and stiff kinetic systems, giving the best accuracy and the smallest computing time. © 1992 by John Wiley & Sons, Inc.