bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vectorizable algorithm for green function and many‐body perturbation methods
Authors: Zakrzewski Vyacheslav G. , von Niessen Wolfgang 
Published: January 2005

AbstractThe principles of an efficient, fast algorithm for the calculation of diagrams appearing in Green function and many‐body perturbation methods are discussed and timing examples are given. Within the suggested algorithm, the third order‐diagrams required in the Green function approach are evaluated by arranging computations in such a way that the most inner loops contain only simple scalar products and multiplication of vector by scalar operations. The molecular symmetry is taken into account for abelian groups. © 1993 John Wiley & Sons, Inc.
Use of effective core potentials forab initiocalculations on molecular siloxanes and silicates
Authors: Earley Clarke W. 
Published: January 2005

AbstractA series ofab initioelectronic structure calculations have been performed on the (H3Si)2O molecule using a range of basis sets. The accuracy of these calculations was evaluated by comparison with several experimental measurements. These calculations support earlier results indicating that polarization functions on the bridging oxygen atom are usually required to obtain a bent geometry for the Si‐O‐Si linkage in disiloxane. It was found thatab initiocalculations utilizing effective core potentials and a double‐ζ valence description augmented with polarization functions (CEP‐31G*) provide results comparable in quality to those obtained using the all‐electron 6‐31G* basis set. To demonstrate the general utility of these effective core potential basis sets for theoretical studies of molecular silicates, calculations were performed on the (HO)3SiOSi(OH)3molecule. The results obtained are in excellent agreement with previous experimental andab initiocalculations using all‐electron basis sets. © 1993 John Wiley & Sons, Inc.
Is tetrahedral H42+ a minimum? Anomalous behavior of popular basis sets with the standard p exponents on hydrogen
Authors: Glukhovtsev Mikhail N. , Schleyer Paul Von Ragué , van Eikema Hommes Nicolaas J.R. , De M. Carneiro Jose Walkimar , Koch Wolfram 
Published: January 2005

AbstractThe nature of the tetrahedral H42+ stationary point (minimum or triply degenerate saddle) depends remarkably upon the theoretical level employed. Harmonic vibrational analyses with, e.g., the 6‐31G** (and 6‐31 + +G**) and Dunning's [4s2p1d;2s1p] [D95(d,p)] basis sets using the standard p exponent suggest (erroneously) that the Td geometry is a minimum at both the HF and MP2 levels. This is not the case at definitive higher levels. The C3H42+ structure with an apical H is another example of the failure of the calculations with the 6‐31G**, 6‐311G**, and D95(d,p) basis sets. Even at MP2/6‐31G** and MP2/ cc‐pVDZ levels, the C3v structure has no negative eigenvalues of the Hessian. Actually, this form is a second‐order saddle point as shown by the MP2/6‐31G** calculation with the optimized exponent. The D4h methane dication structure is also an example of the misleading performance of the 6‐31G** basis set. In all these cases, energy‐optimized hydrogen p exponents give the correct results, i.e., those found with more extended treatments. Optimized values of the hydrogen polarization function exponents eliminate these defects in 6‐31G** calculations. Species with higher coordinate hydrogens may also be calculated reliably by using more than one set of p functions on hydrogen [e.g., the 6‐31G(d,2p) basis set]. Not all cases are critical. A survey of examples, also including some boron compounds, provides calibration. © 1993 John Wiley & Sons, Inc.
Rapid approximation to molecular surface area via the use of Boolean logic and look‐up tables
Authors: Le Grand Scott M. , Merz Kenneth M. 
Published: January 2005

AbstractWe report the development of a new approximate method of calculating molecular surface areas. Our technique is based upon the method of Sharake and Rupley but incorporates several major advances. First, we represent the state of surface points as bits in a bit string so we can utilize Boolean operations to simultaneously turn off multiple test points in one Boolean AND operation. Second, we use a series of Boolean mask look‐up tables to reduce the time complexity of the calculation of molecular surface area down to the same magnitude as doing a potential energy evaluation. When we use a 256 surface point sphere for all of the atoms in BPTI, a 454 nonhydrogen atom protein, and a 1.4‐Å solvent probe, we in general underestimate the total solvent‐accessible surface area (SASA) by approximately 1.25% with a correlation coefficient of 0.9990 over a wide range of conformations. The average CPU time required to calculate the SASA of a BPTI conformer is 0.58 s on an SGI 4D/220 workstation. We also describe a method by which we can calculate an approximate finite difference SASA gradient for BPTI in 0.79 of CPU time. © 1993 John Wiley & Sons, Inc.
Molecular orbital studies of enzyme mechanisms. II. Catalytic oxidation of alcohols by liver alcohol dehydrogenase
Authors: von Onciul Andreas Ritter , Clark Timothy 
Published: January 2005

AbstractSemiempirical (AM1) molecular orbital theory has been used to investigate the oxidation of alcohols at the active site of liver alcohol dehydrogenase (LADH). The model active site consists of a zinc dication coordinated to two methyl‐mercaptans (Cys‐46, Cys‐176), an imidazole (His‐67), and a water. An imidazole (His‐51) hydrogen bonded to a hydroxy‐acetate (Ser‐48) forms the remote base. AM1 calculations that address the two distinct steps in the catalytic mechanism of ethanol oxidation by LADH are reported. These two steps are: (1) the deprotonation of ethanol by imidazole (His‐51) via hydrogen‐bonded hydroxy‐acetate (Ser‐48), creating a proton relay system; and (2) the rate‐limiting hydride transfer step from ethanol C1 to nicotinamide adenine dinucleotide (NAD+), leading to product formation. Detailed calculations have been used to resolve the unsolved problems of mechanisms that have been suggested on the basis of kinetic data and crystal structures of several LADH complexes. We investigated two possible mechanisms for the deprotonation of ethanol, by zinc‐bound OH− and by direct deprotonation of zinc‐bound ethanol by imidazole via hydroxyacetate (Ser‐48). Our calculations show that there is no need for LADH to activate a water molecule at the active site as in many other zinc enzymes. This result agrees with experimental evidence. Our calculations also indicate that substrates are bound in an inner‐sphere‐pentacoordinated complex to the active site zincion. In this case, spectroscopic investigations agree with our results but crystallographic data do not. The highest activation energy is found for the hydride transfer, in agreement with the experiment. Finally, we proposed an alternative mechanism for the mode of action of LADH based upon our results. © 1993 John Wiley & Sons, Inc.
Prediction of possible crystal structures for C‐, H‐, N‐, O‐, and F‐containing organic compounds
Authors: Holden James R. , Du Zuyue , Ammon Herman L. 
Published: January 2005

AbstractA procedure is reported for the prediction of dense crystal structures of C‐, H‐, N‐, O‐, and F‐containing organic compounds in the primitive triclinic, monoclinic, and orthorhombic space groups with Z ≤ 4. The crystal environments of molecules in 242 crystal structures have been analyzed to determine the common coordination sphere pattens. This led to the development of the MOLPAK (MOLecular PAcKing) program, which uses a rigid‐body molecular structure probe to build packing arrangements (possible crystal structures) in the various space groups. A MOLPAK search, which involves the investigation of all unique orientations of a central molecule and the construction of the appropriate coordination patterns about the central molecule, provides a 3‐D map of minimum unit cell volume as a function of the orientation of the central molecule. MOLPAK uses a repulsion‐only potential and a preset threshold to place molecules in contact with each other. The 5–10 smallest volume packing arrangements from a search are subjected to a lattice energy minimization refinement with the WMIN program to yield possible crystal structures. The results are described from the analyses of several known compounds starting with the crystal molecular structures as the MOLPAK search probes in the P1, P21, P21/c, and P212121 space groups. In addition, several examples are given in which the search probes were created by AM1 geometry optimization of preliminary molecular models. More extensive data are given in supplementary tables. © 1993 John Wiley & Sons, Inc.
The ethylene group as a peptide bond mimicking unit: A theoretical conformational analysis
Authors: Bagińki Maciej , Piela Lucjan , Skolnick Jeffrey 
Published: January 2005

AbstractOne of the features of the polypeptide backbone is that it represents a flexible chain that contains almost rigid CONH peptide bonds. One may try to substitute one or more such bonds by another relatively rigid unit to maintain the overall conformational properties of the backbone and at the same time modify some other properties of the molecule (“pseudopeptide”), such as the ability to form hydrogen bonds. By a detailed conformational analysis, it is shown that the carboncarbon double bond is quite isosteric with the peptide bond and for this reason suitable for such a substitution. This is accomplished by applying molecular mechanics in calculation of the ϕ, ψ maps for pseudopeptide analogs of the N‐acetyl‐Ala‐NHMe molecule. © 1993 John Wiley & Sons, Inc.
Finite element approach to the electrostatics of macromolecules with arbitrary geometries
Authors: You Tony J. , Harvey Stephen C. 
Published: January 2005

AbstractA new treatment of macromolecular electrostatics has been developed using the 3‐D finite element method to numerically solve the linear Poisson–Boltzmann equation. The procedure is based upon a model where the macromolecule is represented at an atomic level of detail, while the solvent is treated in a continuum approximation. The finite element method has two major advantages over previous methods based upon the finite difference approach. First, charges are located on atomic centers rather than being distributed onto grid points. Second, an isoparameter model allows the use of noncubic grids, providing a more accurate description of molecular shape. The principal disadvantage of the finite element method has been its computational complexity, which arises from the use of large matrices. To overcome this difficulty, a new matrix representation has been formulated and an iterative solution procedure has been adopted. The combination of these two techniques drastically reduces the size of the system matrix and increases the overall computational efficiency of the algorithm, making the new treatment computationally competitive with the finite difference approach. Because of the mathematical rigor and physical sophistication of the finite element algorithm, the new treatment is able to give an accurate description of the electrostatic potential distribution in a macromolecular system. Results on test cases with simple geometries show that the new treatment is able to reach the same level of accuracy achieved by the finite difference method while using a lower grid density. Near changes and surfaces, our method is more accurate than the finite difference method. The overall maximum deviation between computed and analytic potentials is less than 3% except in regions surrounding charges. The applicaions of both the finite element and finite difference methods to the same biomolecular systems produce similar potential distributions that would become identical in the limit of infinitely fine grids. © 1993 John Wiley & Sons, Inc.
Study of localized molecular orbitals using group theory methods and its approach to the many‐electron correlation problem. III. Orthogonal bonded functions
Authors: Zhou Taijin 
Published: January 2005

AbstractBy using the group symmetrical localized molecular orbitals (SLMOs) as configuration‐generating orbitals (CGOs) of many‐electron wave functions, the symmetry adaptation of many‐electron spaces is greatly simplified, and novel orthogonal bonded functions (OBFs), as complete space‐ and spin‐adapted antisymmetrized products, are introduced. The corresponding programs for the solutions of OBFs are developed. © 1993 John Wiley & Sons, Inc.
Are most of the stationary points in a molecular association minima? Application of Fraga's potential to benzene–benzene
Authors: Rubio Mercedes , Torrens Francisco , Sánchez‐Marín José 
Published: January 2005

AbstractThe importance of characterizing the stationary points of the intermolecular potential by means of Hessian eigenvalues is illustrated for the calculation of the benzene–benzene interaction using an atom‐to‐atom pair potential proposed by Fraga (FAAP). Two models, the standard one‐center‐per atom and another using three‐centers‐per atom due to Hunter and Sanders, are used to evaluate the electrostatic contributions and the results are compared. It is found in both cases that although using low‐gradient thresholds allows optimization procedures to avoid many stationary points that are not true minima computing time considerations makes the usual procedure of using high‐gradient thresholds [say, 10−2 kj/(mol Å)] as the most efficient. Moreover, this later procedure can be recommended because the actual minima can be characterized by means of Hessian eigenvalues even if these high‐gradient thresholds are used, and further decreasing of the convergence criterion does not imply significant modifications in the geometric parameters of the minima. The possible advantages of using the three‐centers‐per‐atom model for the calculation of molecular associations between delocalized systems are also discussed on the basis of the agreement of the benzene–benzene results with experimental and theoretical data taken from the literature. © 1993 John Wiley & Sons, Inc.
Torsional flexing: Conformational searching of cyclic molecules in biased internal coordinate space
Authors: Kolossváry István , Guida Wayne C. 
Published: January 2005

AbstractA new stochastic (Monte Carlo) procedure, termed torsional flexing, has been devised for searching the conformational space of cyclic molecules. Torsional flexing causes a local, torsion angle‐biased, distortion of a ring bond in a cyclic molecule. Because torsional flexing does not cause large atomic movements, even when it is applied to several bonds simultaneously, subsequent energy minimization generally proceeds rapidly. Nevertheless, the torsional flexing method is prone to generate structures that cross energy barriers so that the structure resulting after energy minimization is frequently a different conformer of the cyclic molecule. Conformational searches on cycloheptadecane, oxobrefeldin A, cyclopenta‐L‐alanine, and rifamycin SV based upon torsional flexing indicated that torsional flexing is among the best methods yet devised for searching the conformational space of flexible cyclic molecules. © 1993 John Wiley & Sons, Inc.
Molecular dynamics simulation of cellobiose in water
Authors: Hardy B.J. , Sarko A. 
Published: January 2005

AbstractThe conformational behavior of cellobiose was studied by molecular dynamics simulation in a periodic box of waters. Several different initial conformations were used and the results compared with equivalent vacuum simulations. The average positions and rms fluctuations within single torsional conformations of cellobiose were affected only slightly by the solvent. However, water damped local torsional librations and transitions. The conformational energies of the solute and their fluctuations were also sensitive to the presence of solvent. Intramolecular hydrogen bonding was weakened relative to that observed in vacuo due to competition with solvating waters. All cellobiose hydroxyl groups participated in intermolecular hydrogen bonds with water, with approximately eight hydrogen bonds formed per glucose ring. The hydrogen bonding was predominantly between water hydrogens and solute hydroxyl oxygens. Intermolecular hydrogen bonding to ring and bridge oxygens was seldom present. The diffusion coefficients of both water and solute agree closely with experimental values. Water interchanged rapidly between the solvating first shell and the bulk on the picosecond time scale. © 1993 John Wiley & Sons, Inc.
Semidirect MP2 gradient evaluation on workstation computers: The MPGRAD program
Authors: Haase Frank , Ahlrichs Reinhart 
Published: January 2005

AbstractA semidirect implementation of the closed‐shell MP2 gradient for efficient use on workstation computers is presented. The approach is based on the algorithm proposed by Frisch and coworkers but includes several modifications to reduce disk storage requirements and exploits nonabelian point group symmetry. The performance of the resulting program MPGRAD (BIOSYM Corp., San Diego, CA) is demonstrated in applications to the molecules [AlSi(CH3)3]4 and ferrocene. The largest calculation involved 492 basis functions and was carried out on IBM RS/6000 workstations with memory sizes of 32 and 128 Mb. The ratio of CPU to wallclock time exceeds 90% in all typical applications. © 1993 John Wiley & Sons, Inc.
Techniques for geometry optimization: A comparison of cartesian and natural internal coordinates
Authors: Baker Jon 
Published: January 2005

AbstractA comparison is made between geometry optimization in Cartesian coordinates, using an appropriate initial Hessian, and natural internal coordinates. Results on 33 different molecules covering a wide range of symmetries and structural types demonstrate that both coordinate systems are of comparable efficiency. There is a marked tendency for natural internals to converge to global minima whereas Cartesian optimizations converge to the local minimum closest to the starting geometry. Because they can now be generated automatically from input Cartesians, natural internals are to be preferred over Z‐matrix coordinates. General optimization strategies using internal coordinates and/or Cartesians are discussed for both unconstrained and constrained optimization. © John Wiley & Sons, Inc.
CONCEPTS: New dynamic algorithm for de novo drug suggestion
Authors: Pearlman David A. , Murcko Mark A. 
Published: January 2005

AbstractWe describe a new method for de novo design of molecules that bind to protein active sites. The method, CONCEPTS (Creation of Novel Compounds by Evaluation of Particles at Target Sites), places a group of atom‐like particles in the site. The particles are free to move within the site to improve binding to the protein. A key innovation of this technique is that covalent connections are made among the particles in a stochastic and dynamically reversible manner. These changes in the topology are either accepted or rejected depending on their ability to improve the total energy of the enzyme–inhibitor complex. The method is applied to two test systems: The FK506 binding protein (FKBP‐12) and HIV‐1 aspartyl protease. In both cases, we are able to predict, de novo, drugs that have striking similarities to known potent inhibitors and that can successfully be used to generate “hits” of the known inhibitors from a data base. © John Wiley & Sons, Inc.
Ab initio molecular orbital calculations for 3,6‐dihydro‐1,2‐dithiin and 3,6‐dihydro‐1,2‐dioxin
Authors: Po Henry N. , Freeman Fillmore , Lee Choonsun , Hehre Warren J. 
Published: January 2005

AbstractOptimized geometries and total energies for the conformers of 3,6‐dihydro‐1,2‐dithiin (2) and 3,6‐dihydro‐1,2‐dioxin (3) were calculated at several ab initio MO levels: RHF/3‐21G(*), RHF/6‐31G*, MP2/6‐31G*, and MP2/6‐31G*/ /RHF/3‐21G(*). For the dioxin, in addition to the above levels the corresponding nonextended basis sets ab initio methods were also carried out. The dithiin results are compared with those of simple disulfanes, HSSH and (CH3)2S2, whose optimized geometries agree closely with the observed structures, which is the gauche (C2 symmetry). For the disulfanes, the gauche geometries from RHF/3‐21G(*) are in good agreement with the observed structure while the RHF/3‐21G results best fit the dioxin. Pertinent structural data at the RHF/3‐21G(*) for the half‐chair (C2) dithiin are: bond lengths, SS, CS, CC, and CC, 2.050, 1.817, 1.515, and 1.317 Å, respectively; bond angles, CSS, CCS, and CCS, 98.0, 114.2, and 127.8°, respectively; CSSC dihedral angle of 63.2°; and twist angle of 36.5°. The total energy for half‐chair dithiin at MP2/6‐31G*//RHF/3‐21G(*) is less than the planar (C2v) and the half‐boat (Cs) structures by 69.67 and 29.05 kJ/mol, respectively. The calculated structural data (vs. observed) at RHF/3‐21G for the half‐chair dioxin are: bond lengths, OO, CO, CC, and CC, 1.464 (1.463), 1.454, 1.509, and 1.313 Å (1.338 Å), respectively; bond angles, COO, CCO, and CCO, 105.0, 109.8 (110.3), and 120.7° (119.9°), respectively; COOC dihedral angle of 79.7° (80 ± 2°); and twist angle of 39.0 (38.3°). The total energy for half‐chair dioxin at MP2/6‐31G//RHF/3‐21G is less than the planar and the half‐boat structures by 70.35 and 42.85 kJ/mol, respectively. The total energies calculated at the extended basis sets (*) ab initio levels for the C2 symmetry dioxin are much lower than those of the nonextended basis sets. © John Wiley & Sons, Inc.
Distributed data parallel coupled‐cluster algorithm: Application to the 2‐hydroxypyridine/2‐pyridone tautomerism
Authors: Rendell Alistair P. , Guest Martyn F. , Kendall Rick A. 
Published: January 2005

AbstractThe recently developed parallel coupled‐cluster algorithm of Rendell, Lee, and Lindh [Chem. Phys. Lett., 194, 84 (1992)] is extended to allow four‐indexed quantities containing one or two indices in the virtual orbital space to be stored across the global memory of distributed‐memory parallel processors. Quantities such as the double‐excitation amplitudes can now be distributed over multiple nodes, with blocks of data retrieved from remote nodes by the use of interrupt handlers. As an application of the new code, we have investigated the potential energy surface of the 2‐hydroxypyridine/2‐pyridone tautomers. Using large basis sets, the structure of each tautomer and the transition state connecting the two minima has been determined at the SCF level. The relative energy difference and the activation energy were then redetermined using the MP2, CCSD, and CCSD(T) methods. All calculations have been performed on Intel distributed‐memory supercomputers. The largest coupled‐cluster calculations contained over 2 million double‐excitation amplitudes. © John Wiley & Sons, Inc.
Electric dipole polarity of diatomic molecules
Authors: Huzinaga S. , Miyoshi E. , Sekiya M. 
Published: January 2005

AbstractThe restricted SCF (single‐configuration SCF) and MCSCF (multiconfiguration SCF) calculations are performed to compute the ground‐state electric dipole moments of four pairs of diatomic molecules—(1) CO and BF; (2) SiO and AlF; (3) CS and BCl; and (4) SiS and AlCl—at a number of internuclear distances on both sides of the equilibrium position. Near Hartree–Fock accuracy is obtained in the SCF calculations. All eight molecules have a range of internuclear distance in which electric dipole moments are of the polarity of A−B+. The shapes of computed electric dipole moment functions are discussed in the language of the molecular orbital method and in relationship to electronegativities of atoms. The present study gives us deeper understanding of electron transfer inside molecules and consequently of the apparent contradiction between electronegativity and the dipole polarity of some molecules. © John Wiley & Sons, Inc.