bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stationary points on the potential energy surface of O2−HF and O2−H2O
Authors: Lopez Jesus P. 
Published: January 2005

AbstractThe determination of minima and saddle points on the potential energy surfaces of the hydrogen bonded species O2−HF and O2−H2O is performed with unrestricted Hartree‐Fock calculations. Geometries, electron density distributions, and relative energies for every stationary point are reported. Only one true minimum is found for O2−HF and for O2−H2O, and this approximately corresponds to a structure where the partially positive hydrogen atom is located along one of the superoxide ion electron lone‐pair directions. Calculated ΔH, ΔS, and ΔG values for the reaction between O2− and H2O are in good agreement with experimental data.
Improvements on the direct SCF method
Authors: Häser Marco , Ahlrichs Reinhart 
Published: January 2005

AbstractThree improvements on the direct self‐consistent field method are proposed and tested which together increase CPU‐efficiency by about 50%: (i) selective storage of costly integral batches; (ii) improved integral bond for prescreening; (iii) decomposition of the current density matrix into a linear combination of previous density matrices—for which the two‐electron contributions to the Fock matrix are available—and a remainder ΔD, which is minimized; construction of the current Fock matrix only requires processing of the small ΔD which enhances prescreening.
The density integration approach to populations. A critical comparison of projection populations to populations defined by the theory of atoms in molecules
Authors: Glaser Rainer 
Published: January 2005

AbstractThe theory of atoms in molecules defines an unambiguous partitioning of the three‐dimensional electron density into atomic basins based on the zero‐flux surfaces of the gradient of the electron density, ∇(r). Integrations of the electron density within such basins yield integrated Bader populations (IBP) that have a rigorous foundation in quantum mechanics. In the density integration technique based on the two‐dimensional electron density projection function, P(x,z), integrated projection populations (IPP) are obtained by integration within regions demarked by steepest descent lines Dp of P(x,z). These density integration techniques are compared by an analysis of the electron density of diatomic molecules that is based on the properties of the zero‐flux surface that partitions the electron density between the atoms. The conventional method for the partitioning of regions of P(x,z) approximates the virial partitioning. Differences between IPP and IBP can be quantitatively described by two terms. One term reflects the error intrinsic to projection populations as a result of the loss of all information about the electron distribution in the third dimension in the calculation of P(x,z). The second term accounts for the effects of the displacement of the demarcation lines Dp toward the less polarizable atom compared with the cross‐section of the density with the plane of projection, Dd. The analysis suggests the definition of a projection population IPP2 that is based on the cross‐section Dd instead of the demarcation lines Dp. Relations between the populations IPP, IPP2, and IBP are derived for diatomic molecules and numerical results are presented for a series of diatomic molecules. Several polyatomic anions are also discussed. The values of IPP are found to be good approximations of IBP in highly polar diatomic molecules. In cases where the bonding involves comparatively little intramolecular charge transfer IPP2 is the better and equally satisfactory projection population. In the intermediate semipolar bonding situations projection populations provide qualitatively correct descriptions of the charge distributions but the numerical agreement with the IBP values is less satisfactory.
The calculation of molar polarizabilities by the CNDO/2 method: Correlation with the hydrophobic parameter, log P
Authors: Lewis David F. V. 
Published: January 2005

AbstractResults of molecular orbital (MO) calculations by the complete neglect of differential overlap (CNDO/2) method on 50 small molecules are reported. The summation of calculated atomic polarizabilities are equated with molecular polarizabilities, and these are compared with experimentally determined values. It is found that there is very good agreement between calculated and experimental molecular polarizability. This provides a reliable method for the determination of molecular polarizabilities for compounds for which experimental values are not known. The relationship between log P and polarizability is discussed and analyzed in terms of contributions from electronic components to the partitioning energy.
AM1 studies on the potential energy surface for the proton transfer in protonated water clusters, H+(H2O)n
Authors: Choi Jae Young , Davidson Ernest R. , Lee Ikchoon 
Published: January 2005

AbstractThe potential energy surfaces for the proton transfer processes in H+(H2O)n with n=2 ∼ 11 have been studied using the semiempirical AM1 method. Two model systems were adopted: branched and linear systems. The branched system showed a tendency to form a bulk cluster, while the linear system showed a tendency toward a constant barrier height with increasing number of water molecules in the model system. The potential energy surfaces were discussed using Marcus theory. In the case of H+ (H2O)n with n=10 and 11, the intrinsic barrier to the proton transfer was found to be around 1.0 kcal/mol.
Guanidinium‐Type resonance stabilization and its biological implications. 2. The doubly‐extended‐guanidine series
Authors: Jordan Meredith J. , Gready Jill E. 
Published: January 2005

Abstractπ‐Electron delocalization in neutral and protonated “doubly‐extended‐guanidine,” (H2N)2CNCHN—CHNH, has been studied by ab initio methods at the self‐consistent field (SCF) STO‐3G and 3‐21G levels for a large number of tautomeric, rotameric, pseudocyclic, and monocyclic (disubstituted triazine) forms. These π systems have been characterized in terms of a number of structural and energetic parameters: degree of single/bond character from bond lengths and π bond orders, electron distributions, and tautomer, rotamer, and protonation energies. The acyclic neutral forms exhibit largely alternant single–double bond patterns as predicted by classical bonding structures but with, however, significant deviations due to conjugation. The acyclic protonated forms exhibit bond patterns consistent with resonance delocalized structures extending over the whole molecule (“doubly‐extended guanidinium”) or part of the molecule (“extended‐guanidinium”) or guanidinium . All systems showed alternant charge distributions with electron‐deficient carbons. The energy results have been analyzed in terms of possible contributions from steric interactions, lone‐pair repulsions, purportive electrostatic interactions in pseudocyclic forms, overall π‐system conformation (extended, kinked, or folded), and specific through‐space π‐overlap interactions in some pseudocyclic forms. It was found that these other interactions usually dominate the specifically π effects so that the general concept of preferential π delocalization in straight lines does not hold for the acyclic systems. Some interesting examples of pseudocyclic forms exhibiting strongly stabilizing intramolecular interactions attributed to π through‐space coupling are identified. These systems with incipient‐ring characteristics present intermediate bonding models between the acyclic and closed‐ring π systems. The extent of stabilization of the guanidinium‐type cations by resonance delocalization in cyclic systems depended on whether it reinforced or interfered with the overall ring delocalization.
Probing the anomeric effect. The diaminomethylene group: Calculations of NCN‐containing molecular systems1
Authors: Aped Pinchas , Schleifer Leah , Fuchs Benzion , Wolfe Saul 
Published: January 2005

AbstractA study of systems containing the title moiety is described, with special reference to the anomeric effect. We have calculated ab initio, using Gaussian‐80 with the 3‐21G basis set, all basic conformations of methylene‐diamine (H2NCH2NH2) and its N‐methyl derivative with full geometry optimization of energy minima and barriers. The structural data thus obtained, were then employed to parameterize Allinger's MM2‐80 force field in a procedure similar to that described for oxygen derivatives, including hydrogen‐bonding effects and CN bond shortening in tertiary amines. This modification, termed MM2‐AE was then used to calculate larger molecules, including N,N′‐di‐ and N,N,N′,N′‐tetramethyl‐methylenediamine, various 1,3‐diazane systems, and 1,4,5,8‐tetraazadecalin derivatives of established (x‐ray) structures. The results are discussed in light of their verificative and predictive power and appear to validate MM2‐AE as a useful computational procedure.
Multiple solutions of unrestricted Hartree‐Fock equations: The SNH+ radical as an example
Authors: Redondo P. , Flores J. R. , Largo‐Cabrerizo J. 
Published: January 2005

AbstractA case of appearance of multiple unrestricted Hartree‐Fock (UHF) solutions in the SNH+ (2A') radical is reported. This kind of solution does not arise from different electron configurations or symmetry breaking effects and seem to be exclusive of the UHF method. Three solutions are found and studied on the basis of wave function stability tests and several conclusions about their origin are given.
Solving the finite difference linearized Poisson‐Boltzmann equation: A comparison of relaxation and conjugate gradient methods
Authors: Davis M. E. , McCammon J. A. 
Published: January 2005

AbstractComparisons have been made between relaxation methods and certain preconditioned conjugate gradient techniques for solving the system of linear equations arising from the finite‐difference form of the linearized Poisson‐Boltzmann equation. The incomplete Cholesky conjugate gradient (ICCG) method of Meijerink and van der Vorst has been found to be superior to relaxation methods, with at least a factor of two improvement in speed, and only a 50% increase in storage.
The rate of convergence of the S matrix for the renormalized Numerov and log‐derivative methods
Authors: Braga J. P. 
Published: January 2005

AbstractThe convergence of the S matrix for the renormalized Numerov method, the original log‐derivative method, and one recent version of this method is studied. A single‐ and a two‐channel problem are analyzed and the percent relative errors for the S matrix and transition probabilities are calculated.
Theoretical study of the proton affinities of 2‐, 3‐, and 4‐monosubstituted pyridines in the gas phase by means of MINDO/3, MNDO, and AM1
Authors: Voets R. , François J.‐P. , Martin J. M. L. , Mullens J. , Yperman J. , Van Poucke L. C. 
Published: January 2005

AbstractProton affinities (PAs) of 2‐, 3‐, and 4‐monosubstituted pyridines in the gas phase are calculated using the MINDO/3, MNDO, and AM1 methods. The following substituents are considered: F, Cl, CN, CH3, CF3, CHO, NO2, NH2, N(CH3)2, OCH3, and SCH3. The results are compared with experimental values. It is found that all MINDO/3 PAs are ca. 6% too high (mean value) compared to the experimental results; on the other hand, the MNDO values are ca. 7% too low (mean value). However, a much better agreement has been observed for the AM1 method where the theoretical values are only ca. 2.4% too low (mean value). Correlations between the calculated proton affinities on one hand and the charges on the acid H atom and Hammett constants on the other hand are studied. Particularly good linear relationships are found for the 4‐monosubstituted compounds within the AM1 formalism.
Nitrogen inversion barriers in three‐membered rings. An ab initio molecular orbital study
Authors: Alcamí M. , De Paz J. L. G. , Yáñez M. 
Published: January 2005

AbstractPolarization and correlation effects on the nitrogen inversion barrier of some three‐membered rings have been investigated. The characteristics of the barrier have been analyzed in terms of perturbation theory arguments. This analysis shows that the HOMO is the orbital that changes more dramatically along the inversion barrier. As a consequence, there is a good linear correlation between the destabilization undergone by the HOMO along the pyramidalization process and the barrier height. To obtain quantitatively meaningful barriers it is necessary to use polarized basis sets. Although polarization effects at the inverting center are dominant, a proper polarization of the remaining atoms of the ring seems also necessary. In general, with the only exception of 1H‐diazirine, correlation effects on the barrier height are small if a polarized basis set is used.
Monte Carlo simulations for the study of hemoglobin‐fragment conformations
Authors: Chen R. S. 
Published: January 2005

AbstractMonte Carlo simulations have been performed to study the conformations of the pentapeptide fragments of normal adult (Thr‐Pro‐Glu‐Glu‐Lys) and sickle‐like anemia hemoglobin (Thr‐Pro‐Val‐Glu‐Lys). The results show that the energy optimized conformation of normal adult hemoglobin‐fragment agrees with the X‐ray experiment and the theoretically determined conformation of the sickle‐like anemia hemoglobin‐fragment is identical with the conformation of the normal adult hemoglobin‐fragment.
Calculation of number and free energy of the conformers of linear alkanes with medium and long chains. Implications for catalysis
Authors: Fǎrcaşiu Dan , Walter Patrick , Sheils Kelly 
Published: January 2005

AbstractA method for calculating the number of rotamers of a linear alkane and of the number of rotamers with a given number of gauche conformations along the chain as a function of the total number of atoms in the chain, using general equations, is presented. A graphical method for generating individual rotamers was applied to the homologs up to decane, which has 1134 rotamers. The steric energies calculated by molecular mechanics (MM2 force field) were used as measures of the heat of formation for the coiled conformations relative to the anti conformer for each molecule, whereas the statistical entropy differences were calculated for classes of coiled rotamers grouped by the number of gauche bonds and steric energy. The free energy values calculated from these components show that already at 400 K hexane exists preferentially in conformations containing gauche bonds. For larger chains the free energy advantage for the coiled chains increases very steeply. The implications for the question of reactions of linear alkanes occurring on the surface or inside the channels of small‐ and medium‐pore zeolites are briefly examined.
A method for fitting a smooth ribbon to curved DNA
Authors: Darden Tom 
Published: January 2005

AbstractA method for fitting a smooth ribbon representation of DNA structures is proposed. Following a review of the relevant definitions for classical linear helical DNA and generalizations to curving helices, a parameterization of smooth ribbons is given, which leads to tractable expressions. In addition it suggests a new way to define twist, tilt, and roll for a base step that is free of the ambiguities caused by noncommutativity of finite rotations. A least squares fitting criterion for ribbons is then proposed. In some cases the optimal ribbon with respect to this criterion is not unique. This problem is analyzed, and the circumstances in which it can occur are specified. To resolve the nonuniqueness problem, a variational description of the optimal ribbon is proposed, namely the ribbon of lowest elastic energy achieving a specified level of fit with respect to the least squares criterion. The appropriate level of fit is decided using distances of backbone atoms from fitted ribbon axes. Theoretical tests of the fitting methodology are presented, and as a sample application a smooth ribbon is fit to an existing experimental structure.
An ab initio distributed multipole study of the electrostatic potential around an undecapeptide cyclosporin derivative and a comparison with point charge electrostatic models
Authors: Price S. L. , Harrison R. J. , Guest M. F. 
Published: January 2005

AbstractAn SCF calculation has been performed on C63H113N11O12, a derivative of the immuno‐suppressive drug cyclosporin, using a 3‐21G basis set and a Direct SCF method. A distributed multipole analysis has been performed on the resulting charge density to give a set of multipoles at each atomic site, which are used to calculate the electrostatic potential around the molecule. The potential maxima and minima on the accessible surface of the molecule are compared with those predicted using the corresponding Mulliken charges, and also using a potential‐derived point‐charge model based on the force‐field of Kollman et al. The Mulliken charges give a misleading picture of the electrostatic potential around this peptide. The potential‐derived charges give results which are in far better agreement with the ab initio distributed multipole model, despite being derived from calculations on smaller molecules with different basis sets and geometries. The limitations of point‐charge models for describing the electrostatic interactions of polypeptides are discussed.
A molecular mechanics (MM2) study of Furan, Thiophene, and related compounds
Authors: Tai Julia C. , Lii Jenn‐Huei , Allinger Norman L. 
Published: January 2005

AbstractThe molecular mechanics calculations reported earlier for nitrogen heterocycles have now been extended to include the title compounds, and related molecules. It is in general possible to calculate these structures with an accuracy that compares favorably with experiment.
Voronoi binding site models: Calculation of binding modes and influence of drug binding data accuracy
Authors: Boulu Laurent G. , Crippen Gordon M. 
Published: January 2005

AbstractA new and accurate method for calculating the geometrically allowed modes of binding of a ligand molecule to a Voronoi site model is reported. It is shown that the feasibility of the binding of a group of atoms to a Voronoi site reduces to a simple set of linear and quadratic inequalities and quadratic equalities which can be solved by minimization of a simple function. Newton's numerical method of solution coupled to a line search proved to be successful. Moreover, we have developed efficient molecular and site data bases to discard quickly infeasible binding modes without time‐consuming numerical calculation. The method is tested with a data set consisting of the binding constants for a series of biphenyls binding to prealbumin. After determination of the conformation space of the molecules and proposal of a Voronoi site geometry, the geometrically feasible modes are calculated and the energy interaction parameters determined to fit the observed binding energies to the site within experimental error ranges. We actually allowed these ranges to vary in order to study the influence of their broadness on the site geometry and found that as they increase, one can first model the receptor as a three‐region site then as a single region site, but never as a two‐region site.
Computational algorithms for matching polynomials of graphs from the characteristic polynomials of edge‐weighted graphs
Authors: Hosoya Haruo , Balasubramanian K. 
Published: January 2005

AbstractComputational algorithms are described which provide for constructing the set of associated edge‐weighted directed graphs such that the average of the characteristic polynomials of the edge‐weighted graphs gives the matching polynomial of the parent graph. The weights were chosen to be unities or purely imaginary numbers so that the adjacency matrix is hermitian. The computer code developed earlier by one of the authors (K.B.) is generalized for complex hermitian matrices. Applications to bridged and spirographs, some lattices and all polycyclic graphs containing up to four cycles are considered.
Electrostatic interactions in host‐guest complexes 2
Authors: Bruning H. , Feil D. 
Published: January 2005

AbstractIn this article the quantum chemically calculated charge density distribution of 18‐crown‐6 and the K+ …18‐crown‐6 complex are compared with the charge density distribution of smaller molecules and corresponding complexes which can be considered as fragments of the 18‐crown‐6 molecule. An analysis of the charge density distribution in terms of atomic charge distribution according to the stockholder recipe gives accurate rules for the transferability of the charge density distribution. This gives us the possibility to construct the charge density distribution of large molecules out of accurate large basis set results on small molecules.
Interaction of Lysine‐Alanine‐Alanine tripeptide with a fragment of DNA: An empirical potential study
Authors: Hobza Pavel , Nachtigallová Dana , Havlas Zdeněk , Maloň Petr , Šponar Jaroslav 
Published: January 2005

AbstractInteraction of a rigid fragment of B‐DNA (polyanionic as well as screened by Na+ cations) with the flexible tripeptide Lys‐Ala‐Ala (in both L and D configurations) were investigated with the aid of an empirical potential. The potential consists of intramolecular (MM2 potential) and intermolecular (pair potential described in reference 1) parts; hence total energy is formed by intra‐ and intermolecular components. The results demonstrate that intramolecular relaxation of the peptide results in a considerable decrease in total energy. While energies of DNA complexes with L‐Lys‐L‐Ala‐L‐Ala were comparable to those with D‐Lys‐D‐Ala‐D‐Ala the respective geometries exhibit considerable differences.
Tautomeric equilibria of heterocyclic molecules. A test of the semiempirical AM1 and MNDO‐PM3 methods
Authors: Fabian Walter M. F. 
Published: January 2005

AbstractTautomeric equilibria (mainly of the lactam‐lactim type) for a rather large number of six‐membered heterocyclic molecules are calculated by the semiempirical AM1, MNDO‐PM3, and MNDO methods. Except for compounds with adjacent pyridine‐like lone pairs both AM1 as well as MNDO‐PM3 give rather reliable predictions for relative stabilities of the various tautomeric species–comparable to quite high level ab initio calculations. The known errors associated with MNDO in the treatment of heterocyclic tautomerism are thus largely corrected in AM1 as well as MNDO‐PM3. For 2‐hydroxypyridine‐pyrid‐2(1H)‐one the effect of self‐association is less satisfactorily described by MNDO‐PM3 than by AM1. MNDO‐PM3 calculated relative stabilities of methylated derivatives are, however, in considerably closer agreement with experimental values than those obtained by AM1. Ionization potentials, especially those for lone‐pair orbitals, are overestimated by all three semiempirical methods. MNDO‐PM3 results for nitrogen lone‐pair orbital energies are slightly better than those obtained by the AM1 or MNDO method.