bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimization of parameters for semiempirical methods II. Applications
Authors: Stewart James J. P. 
Published: January 2005

AbstractMNDO/AM1‐type parameters for twelve elements have been optimized using a newly developed method for optimizing parameters for semiempirical methods. With the new method, MNDO‐PM3, the average difference between the predicted heats of formation and experimental values for 657 compounds is 7.8 kcal/mol, and for 106 hypervalent compounds, 13.6 kcal/mol. For MNDO the equivalent differences are 13.9 and 75.8 kcal/mol, while those for AM1, in which MNDO parameters are used for aluminum, phosphorus, and sulfur, are 12.7 and 83.1 kcal/mol, respectively. Average errors for ionization potentials, bond angles, and dipole moments are intermediate between those for MNDO and AM1, while errors in bond lengths are slightly reduced.
Spatial geometric arrangements of disulfide‐crosslinked loops in nonplanar proteins
Authors: Kikuchi Takeshi , Némethy George , Scheraga Harold A. 
Published: January 2005

AbstractThe method presented earlier [T. Kikuchi, G. Némethy, and H.A. Scheraga, (1986) J. Comput. Chem. 7, 67] for the classification of patterns of the three‐dimensional folding of a covalently crosslinked polypeptide chain has been extended to nonplanar proteins. The procedure described earlier was applicable only to proteins termed planar, i.e., with a connexity of the crosslinks (e.g., disulfide bonds) that can be represented in a planar diagram. The procedure described in the present work is applicable to any (planar or nonplanar) pattern of crosslinking. The classification is based on a systematic and objective method of enumeration of spatial geometric arrangements of loops (SGAL) using no information other than the location of the disulfide bonds in the amino acid sequence. Various SGAL classes correspond to the presence of different ways of mutual penetration of loops, called thrustings and entanglements. Information on SGAL classes can be of use in structural predictions of folding patterns of proteins.
On the computation of matrix elements between numerical wave functions: The canonical functions method
Authors: Kobeissi H. , Dagher M. , El‐Hajj A. , Kobeissi M. 
Published: January 2005

AbstractThe problem of the computation of the matrix elements

is considered when Ψv(r) and Ψv(r) are eigenfunctions related to a diatomic potential of the RKR type (defined by the coordinates of its turning points Pi with polynomial interpolations). The eigenfunction Ψ(r) is computed by the canonical functions method making use of the abscissas ri of Pi uniquely. This limited number of points allows the storage of ψv(ri) for all the required levels v, and reduces greatly the computational effort when v, ν′, and k are varying. The present method maintains all the advantages of a highly accurate numerical method (even for levels near the dissociation), and reduces greatly the computing time. Furthermore, it is shown that it may be extended to analytical potentials like Morse and Lennard‐Jones functions, to vibrational‐rotational eigenfunctions and to matrix elements between eigenfunctions related to two different potentials. Numerical applications are presented and discussed.
The effect of electron correlation on the topological and atomic properties of the electron density distributions of molecules
Authors: Boyd Russell J. , Wang Liang‐Chen 
Published: January 2005

AbstractThe topological properties of the electron density and the properties of an atom in a molecule are calculated by means of second‐order Møller‐Plesset perturbation theory (MP2) and compared with the results of configuration interaction calculations (C12) which include all single and double substitutions from the Hartree‐Fock reference configuration. A software package for analyzing the effects of electron correlation on the topological properties of the electron density of molecules is described. H2CO is used to provide a numerical example and to indicate that the number of bond critical points is unaffected by the inclusion of electron correlation. Correlation leads to only a small shift in the positions of bond critical points and a small change in the electron density at bond critical points. It is further shown that the energy of an atom in a molecule can be calculated to an accuracy of 1 kcal/mol and the electron population of an atom to about 0.001e. A statistical method is used to show that the deviation of the MP2 correlation correction relative to the CI2 correlation correction for a variety of atomic properties is about 25%.
Algorithm for rapid calculation of excluded volume of large molecules
Authors: Higo Jun'Ichi , Gō Nobuhiro 
Published: January 2005

AbstractAn algorithm is described for rapid calculation of excluded volume of large molecules. The excluded volume is defined based on coordinates of constituent atoms as the volume of overlapping spheres, each standing for a space around an atom inaccessible for a solvent molecule. A computer program based on the algorithm has been tested on a protein, ovomucoid. The accuracy of the numerical calculation is discussed.
Topological electron density analysis of phosphines, phosphaalkenes and phosphaalkynes
Authors: Bachrach Steven M. 
Published: January 2005

AbstractA general survey of the topological properties of various phospines, phosphaalkenes, and phosphaalkynes is presented. Fifteen compounds containing carbon‐phosphorus single, aromatic, double, and triple bonds were optimized at the Hartree‐Fock‐self‐consistent field (HF‐SCF) level using the 3‐21G, 3‐21G(*) and 6‐31G* basis sets. Inclusion of d‐orbitals was necessary to obtain reasonable structures. The electron densities of these compounds were analyzed using the topological method of Bader, revealing a number of trends. The value of the electron density at the PC bond critical point correlates strongly with the bond distance and bond order. Integrated electron populations correlate with coordination number. The integrated charge indicates a strongly polarized CP bond in all compounds. Comparisons with five CN compounds are made.
Conformational analysis. 48. A molecular mechanics (MMP2) approach to the conformational analysis of methyl‐, dimethyl‐ and trimethylisochromanes
Authors: Olefirowicz Edward M. , Eliel Ernest L. 
Published: January 2005

AbstractConformational equilibria of mono‐, di‐, and trimethylisochromanes substituted in the heterocyclic ring are calculated by the MMP2(85) force field program. The results are in generally good agreement with the experimental findings of Pihlaja et al. The accuracy of experimental studies based on vicinal coupling constants is examined.
The tautomerism of 1,2,3‐triazole, 3(5)‐methylpyrazole and their cations
Authors: Catalán Javier , Sánchez‐Cabezudo Marta , De Paz José Luis G. , Elguero José , Taft Robert W. , Anvia Frederick 
Published: January 2005

AbstractThe annular tautomerism of 1,2,3‐triazole and 3(5)‐methylpyrazole is discussed by means of a combination of theoretical calculations and experimental (ICR) gas‐phase basicities and acidities. In the gas phase 1,2,3‐triazole exists as the 2H‐tautomer, whereas both tautomers of 3(5)‐methylpyrazole are of similar energy. The solvent effects on these prototropic equilibria are discussed taking into account solvent properties as polarity/polarizability, acidity, and basicity. In nonhydrogen bonding solvents, the difference in dipole moments between both tautomers plays a role that has usually been underestimated.
Basis set quality versus size II. Approximate GTO wave functions for second row transition metal atoms
Authors: Faegri Knut , Biran Gil 
Published: January 2005

AbstractBasis sets ranging in size from (16, 10, 7) to (20, 14, 11) have been derived for the atoms Y–Cd. Separate sets represent the energy optimized wave functions for each of the s2dn, s1dn+1, and s0dn+2 configurations. The energies from the largest sets are within 3 mhartrees of the values obtained in numerical Hartree–Fock calculations. Reasonable Hartree–Fock s2dn– s1dn+1 and s2dn– s0dn+2 excitation energies may be obtained either using the largest basis sets, or using d‐orbitals optimized for the s0dn+2 configurations. The basis sets are slightly unbalanced in favor of the s‐functions and in disfavor of the d‐functions, but various alternative basis sets may be derived by combining parts of the five parent sets. The convergence of radial expectation values is discussed.
Application of various population methods to some oxygenated compounds
Authors: Bachrach Steven M. , Streitwieser Andrew 
Published: January 2005

AbstractThe charge on oxygen for a series of compounds was obtained using Mulliken population, natural population analysis (NPA), integrated projected electron population (IPP) analysis, and Bader's topological density analysis, “integrated Bader populations” (IBP). The orbital‐based methods (Mulliken and NPA) predict oxygen charges of about –0.6 whereas the spatial‐based methods (IPP and IBP) predict charges of about – 1.2 to – 1.3. The differences are ascribed primarily to the nuclear‐centered basis sets used in the orbital methods that minimize local atomic polarization effects. Accordingly, such population analyses should be used for electronic structure considerations only with due circumspection. The IPP method as an approximation to IBP shows gross similarities; small but significant differences vary in a nonsystematic manner and IPP values must also be used with care.
An MNDO molecular orbital study of the reactions of protonated oxirane derivatives (XCHCH2OH+, X = CN, Cl, CH3, Ph) with simple nucleophiles. Implications for regioselectivity in the reactions of electrophiles with nucleic acid bases
Authors: Ford George P. , Smith Christopher T. 
Published: January 2005

AbstractThe gas‐phase analogs of the classical SN1 and SN2 reactions of nucleophiles with a series of protonated oxiranes bearing the substituents CN, Cl, Me, and Ph were studied using MNDO semiempirical molecular orbital theory. The transition states for nucleophilic attack on the intact rings are calculated to become progressively more “SN1‐like,” as the ability of the substituent group to stabilize the corresponding ring opened carbenium ion increases. At the same time the activation barriers become progressively smaller and their relative values for different nucleophiles approach the order expected on the basis of a purely electrostatic attraction between the reacting moieties. Exactly the opposite trends are calculated for the transition states for nucleophilic attack on the intermediate carbenium ions. As the stabilities of the latter increase the extent of bond formation, and transfer of charge to the incoming nucleophile also increase. Here, the relative barriers for attack by different nucleophiles approach the order expected on the basis of a superposition of both covalent and electrostatic interactions in which the former dominate. These results support a previously suggested rationalization for the enhanced reactivities of certain alkylating agents towards the exocyclic oxygen atoms, rather than the ring nitrogens, of the nucleic acid bases. They also suggest a new explanation for the tendencies of aralkylating electrophiles to modify the exocyclic amino groups of the nucleic acid bases: sites which are unreactive towards simple alkylating agents.
Theoretical studies in molecular recognition: Rebek's cleft
Authors: Lipkowitz Kenny B. , Zegarra Richard 
Published: January 2005

AbstractMolecular recognition in Rebek's cleft was studied with the MM2 force field. A new computational protocol was used to determine the free energies of substrate binding to this topologically unique model receptor. The energies and structural features of substrate‐receptor complexes reveal that molecular recognition involves ammonium ion binding to the interior of the cleft and aromatic π‐stacking on the exterior of the cleft.
Evaluation of the dispersion contribution to the solvation energy. A simple computational model in the continuum approximation
Authors: Floris F. , Tomasi J. 
Published: January 2005

AbstractWe present a simple computational method for the evaluation of solute‐solvent dispersion energy contributions in dilute isotropic solutions, supplementing the method with an analysis of its sensitivity with respect to several parameters (or features of the solvation model) which are left free in the general formulation. The method is a natural complement of the electrostatic solvation procedure described in preceding articles.
An algorithm for the representation and computation of supermolecular surfaces and volumes
Authors: Karfunkel Heinrich R. , Eyraud Veronique 
Published: January 2005

AbstractAn algorithm for the computation and representation of van der Waals surfaces and volumes of supermolecules (several overlapping molecules) by a set of grid points originating from an equidistant lattice is described in detail. The grid points in this set belong either to the “outer” surface of the van der Waals body or to a layer just below that outer surface. By means of this double layer (outer and inner) it is possible to represent the volume via the surface without referring to grid points lying inside the body. The algorithm is based on the octree concept, which means that the final relevant lattice points are derived by the successive refinement of an initial coarse lattice. The main features of the algorithm are the automatic elimination of inner atoms irrelevant for the surface definition and the association of any surface point with only those atoms which define the surface in the vicinity of these points. The most remarkable consequence of these features is that the amount of computation is almost independent of the number of atoms in the supermolecule. The algorithm can be used in solving problems arising in drug design, protein folding, molecular graphics, etc.
On the construction of the matching polynomial for unbranched catacondensed benzenoids
Authors: Randić Milan , Hosoya Haruo , Polansky Oskar E. 
Published: January 2005

AbstractAn algorithm for obtaining the matching polynomial of an arbitrary catacondensed unbranched benzenoid molecule is presented. It is based on multiplication of only three 5 x 5 transfer matricesI,J,K, and an appropriate terminal vector. The choice of the matrices is dictated by the history of the growth of the hexagonal “animals” (i.e., by the pattern of the successive fusions of the benzene rings). The approach also gives the number of Kekule valance structures, the count of conjugated circuits, the values of the topological indexZ, and the characteristic polynomials.
Theoretical studies in molecular recognition: Enantioselectivity in chiral chromatography
Authors: Lipkowitz Kenny B. , Baker Brian , Zegarra Richard 
Published: January 2005

AbstractThe enantioselective binding of optical analytes on chiral stationary phases used in column chromatography is investigated with molecular modeling techniques. By rolling the analytes over the van der Waals surface of the phase, configurations are sampled and free energies of transient diastereomeric complexes are computed. These free energies allow us to compute chromatographic separability factors and a linear relationship between computed and observed values is found. The intermolecular potential energy surfaces of these diastereomeric complexes are flat with gentle rolling hills and multiple minima. The binding sites are ill‐defined and the analytes are found to freely slide over the chiral stationary phases. An energy partitioning algorithm is used to determine how much of the total binding energy is attributable to a given molecular fragment on the phase. It is found that the fragments of the phase bearing the stereogenic carbons are the least cognizant of differences between optical antipodes.
Methods for the Fourier‐series expansion of torsional energies
Authors: Chung‐Phillips Alice 
Published: January 2005

AbstractSeveral general procedures for the derivation and analysis of a Fourier‐series expansion V(ϕ) over computed torsional energies E(ϕi) are formulated. STO‐3G energy values in n‐butane, 1‐chloropropane, and 1,2‐dichloroethane are used as test data for deriving V(ϕ) with the numerical methods of interpolation and least squares. The accuracy of each derived V(ϕ) is assessed on the basis of calculated conformational properties, mean and rms deviations, and an error curve, V(ϕ)–V(ϕ)ref, where V(ϕ)ref represents a reference set of E(ϕi). Results indicate that given the same number of expansion terms, interpolation and least squares yield functions of comparable accuracy; however, interpolation is a more efficient procedure for monitoring the accuracy of a function in regions of interest. In cases where there are too few input energies to achieve the desired accuracy, energy derivatives can be employed effectively for expanding the input set. In designing special‐purpose functions, the error curve can be used meaningfully as a guide; an example for producing functions that are especially well behaved in regions for gauche conformations is provided. The present study continues to add systematics and rigor to the fitting of an internal rotation potential function from energy data.
Force related atomic multipoles in planar molecules. Derivation of atomic quadrupole and octupole moments
Authors: Dinur Uri 
Published: January 2005

AbstractAtomic multipoles as defined by current methods generally do not account for forces in molecules that arise from external electrostatic fields. It is pointed out that such forces and the electrostatic potential that the molecule itself generates are both determined by the molecular multipolar tensors. The latter constitute therefore the fundamental molecular constants that determine the molecular electrostatics apart from polarization. In general the multipolar tensors include contributions from the atomic multipoles and their fluxes. In planar molecules, however, the perpendicular charge flux is zero by symmetry. This gives rise to a (previously introduced) formalism that extracts analytical, force‐related, atomic multipoles from the molecular multipolar tensors. This formalism is extended in this work to include force‐related (FR) atomic quadrupoles and octupoles in planar molecules. The properties of the FR atomic multipoles, including their perpendicular fluxes, are discussed and some formal theoretical and computational advantages that characterize them are indicated. As an example, the electrostatics of OCS, including the molecular electrostatic potential and the forces on the nuclei due to an external point charge, is discussed.
Theoretical calculation of the steric effects of ortho substituents by the AM1 method
Authors: Sotomatsu Tomoko , Murata Yoshiyuki , Fujita Toshio 
Published: January 2005

AbstractThe AM1 calculation was done for ortho‐substituted toluenes (o‐X‐C6H4‐CH3) and ortho‐substituted tert‐butylbenzenes (o‐X‐C6H4‐t‐Bu). The difference in the calculated heat of formation between o‐X‐C6H4‐CH3 and o‐X‐C6H4‐t‐Bu was used as a theoretical steric index for ortho‐X. The correlation of this theoretical steric index with the empirical steric parameter sets such as our recently defined Es(AMD) and the Taft–Kutter–Hansch (TKH) Es was examined. In spite of the simplicity of the model system, the theoretical index was linear with the Es(AMD) constant with a correlation coefficient of r = 0.972 for 17 substituents of various structures. Including the phenyl group, the correlation with the TKH Es constant was r = 0.948. The theoretically calculated index was shown to serve as a measure of the ortho steric effect.
Upregulation of clusterin/apolipoprotein J in lactacystin‐treated SH‐SY5Y cells
Authors: Carreras Isabel , Garrett‐Young Rosemary , Ullman M. David , Eisenhauer Patricia B. , Fine Richard E. , Wells John M. , Conn Kelly J. 
Published: January 2005

AbstractClusterin (apolipoprotein J) is a highly conserved, multifunctional, vertebrate glycoprotein. Several isoforms of clusterin have been described including the predominant secreted isoform (sCLU) and several nuclear isoforms (nCLU) associated with cell death. sCLU has been shown to bind a variety of partly unfolded, stressed proteins including those associated with Lewy bodies (LBs) in patients with Parkinson's disease (PD). The development of familial and sporadic PD has been associated with the ubiquitin‐proteasome system (UPS) dysfunction and aberrant protein degradation. This suggests that failure of the UPS to degrade abnormal proteins may underlie nigral degeneration and LB formation in PD. The effects of toxin‐mediated proteasomal impairment on changes in gene expression and cell viability were studied in differentiated SH‐SY5Y cells. Clusterin expression was increased in cells exposed for 24 hr to the proteasomal inhibitor lactacystin (10 μM) as determined by gene microarray analysis. RT‐PCR showed that sCLU, not nCLU, was the major clusterin isoform expressed in both control and lactacystin‐treated cells. Western blot analysis identified statistically significant increases in sCLU in total cell lysates after 24 hr of lactacystin exposure and showed that sCLU fractionates with the endoplasmic reticulum. Time‐course studies demonstrated that maximal decreases in proteasome activity (4 hr) preceded maximal increases in clusterin expression (24 hr). Together these data suggest that proteasome impairment results in the upregulation of sCLU in SH‐SY5Y cells, supporting the hypothesis that the association of clusterin with LBs in PD may be related to UPS failure. © 2005 Wiley‐Liss, Inc.
Mitogen‐ and stress‐activated protein kinase 1: Convergence of the ERK and p38 pathways in Alzheimer's disease
Authors: Webber Kate M. , Smith Mark A. , Lee Hyoung‐gon , Harris Peggy L. , Moreira Paula , Perry George , Zhu Xiongwei 
Published: January 2005

AbstractTwo of the earliest manifestations of the selective neurodegeneration that occurs in Alzheimer's disease (AD) involve the oxidative modification of various biomacromolecules and the reexpression of a multitude of cell cycle‐related proteins. Taken together with the proximal and ectopic increases in activated components of the ERK and p38 pathways, involved in mitotic and cellular stress signaling, respectively, there is a clear and important role for mitotic and oxidative insults in the pathogenesis of AD. Despite the mounting evidence, however, for the causal role of mitogenic abnormalities and oxidative stress in AD pathogenesis, the effect of the converging relevant pathways due to chronic stimulation in AD remains largely unknown. To delineate further the mechanism by which mitogenic and stress signaling cascades converge, we focused on one of the downstream effectors of activated ERK and p38, mitogen‐ and stress‐activated kinase 1 (MSK1). Activated MSK1, phosphorylated at residues Ser376 and Thr581, was upregulated in vulnerable neurons in AD when compared to that in age‐matched controls, whereas MSK1 phosphorylated at residue Ser360 was not increased in AD. Furthermore, activated MSK1 phosphorylated at Thr581 colocalized strongly with activated p38 but only weakly with activated ERK, whereas MSK1 phosphorylated at Ser376 colocalized strongly with activated ERK but only weakly with activated p38, suggesting potential preferential phosphorylation sites for the two upstream effectors. © 2005 Wiley‐Liss, Inc.