bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transport Properties of Macromolecules by Brownian Dynamics Simulation: Vectorization of Brownian Dynamics on the Cyber‐205
Authors: Ganti Girija , Andrew McCammon J. 
Published: January 2005

AbstractTime consuming portions in the computation of transport properties of rigid and flexible molecules are the evaluation of subunit hydrodynamic interaction tensors Q and σ, and the procedure for satisfying subunit‐subunit distance constraints. Vector algorithms to speed up these parts of the computation are given. Using these algorithms, a vector version of the Ermak‐McCammon Brownian dynamics code has been developed on a Cyber‐205. To demonstrate the order of speedups that can be achieved, the code was tested on a rigid “trimer” system comprising 24 spherical subunits with a fixed geometry. A speedup of about 14 times for the whole program, and of 45, 6, and 18 times for the computation of Q, σ, and for the procedure to enforce the constraints, respectively, were obtained.
A Comparison of the Rotational Potential Functions in Butane, Propylsilane, Ethylmethylsilane, and 1,2‐Disilylethane: Ab Initio and MM2 Results
Authors: Profeta Salvatore , Unwalla Rayomand J. , Nguyen Binh T. , Cartledge Frank K. 
Published: January 2005

AbstractAb initio calculations at several basis set levels were used to examine the rotational potential energy function around the CC bond of 1,2‐disilylethane, also known as disilabutane (DSB). The best basis set for this system was found to be the 3‐21G(*) basis, which was also used to verify the potential function around the CH2—SiH2 segment in ethylmethylsilane (EMS). The torsional parameters developed by Frierson and Allinger for the CSiCC fragments were shown to yield a potential in excellent agreement with those from the 3‐21G(*) basis. Full 3‐21G(*) geometry optimizations were performed on the 0°, gauche (60°), and 180° conformers of DSB and EMS. Data derived from the ab initio calculations on DSB were used to establish MM2 torsional and bond length parameters for the SiCCSi fragment. The MM2 and ab initio structures agree well. A detailed comparison of rotational potentials and the steric energy components is presented. We also report the torsional potential of propylsilane (PS) and compare the MM2 calculated structure with experiment. Our findings suggest that the similarity of the torsional potentials of butane and DSB and the dissimilarity between butane and EMS arise from the same phenomenon—van der Waals interactions that are attractive rather than repulsive dominant.
Implementation and applications of Gaussian 82 on a CDC Cyber 205
Authors: Rauk Arvi , Dutler Remo 
Published: January 2005

AbstractThe implementation of the GAUSSIAN 82 system of quantum chemistry codes on the CDC Cyber 205 supercomputer required approximately 1 1/2 man years of effort. Idiosyncracies of the Cyber 205 architecture, operating system, and compiler in so far as they affect the conversion and operation of large quantum chemistry codes on the machine are described. While advantage has not been taken of the powerful vector processor, the high intrinsic speed of the scalar processor and the large virtual storage capacity of the Cyber 205 make it a very powerful research tool for computational chemistry. The impact of the GAUSSIAN 82/Cyber 205 combination on computational chemistry research at the University of Calgary is illustrated by brief descriptions of a range of applications from highly accurate calculations on small systems to semiempirical studies of large molecular aggregates. Complete geometry optimizations and harmonic frequency analyses, for the most part, have become routine.
Generalized potential surfaces under inclusion of nuclear motion
Authors: Krüger Thomas , Jug Karl 
Published: January 2005

AbstractA new method for the solution of the vibronic Schrödinger equation is presented. The proposed approach allows the preservation of the concept of potential surfaces under inclusion of nuclear motion. The dynamical interaction of electrons and nuclei is partially included in the equation determining the potential surfaces. The corresponding electronic wave functions can be used as a basis for a generalized representation. Since the variation principle is involved for the determination of the potential surfaces, the proposed representation may be considered as a generalization of the adiabatic one. As a consequence the vibrational wave equation and the calculation of radiationless transition probabilities is simplified.
Linear notations and molecular graph similarity
Authors: Herndon William C. , Bertz Steven H. 
Published: January 2005

AbstractTwo simple linear notation systems are suggested to encode molecular structure including stereochemical elements. Both systems give rise to a unique numbering of the molecular graph, and thus also lead to a unique linear notation. Both linear notation systems are extremely compact and require only standard chemical symbols. A string comparison technique is developed to measure the similarity of two molecular linear notations. This procedure allows one to define a molecular similarity index with values that range from zero to unity, the zero value characterizing complete dissimilarity and the value of unity denoting identity. The notation and similarity index procedures are applied to several small molecular structures.
Application of the MuMATH computer algebra system to sets of first order kinetic equations of significance in chemistry
Authors: Trindle Carl 
Published: January 2005

AbstractAnalytical solutions to systems of first order differential equations have long been available; however, they become so involved that they are seldom used. Numerical simulations are preferred in practice, although they produce bulky output that is difficult to interpret. Even worse, they are occasionally seriously in error owing to “stiffness” in the equations, intrinsic instability, or other pathological behavior. Computer algebra systems can handle the complicated manipulations that make the analytical solutions of first order kinetic systems inconvenient and can serve as a check on numerical simulations. We show applications of the small MuMATH(R) computer algebra package to a variety of first‐order process, including relaxation kinetics and the analysis of stability of steady states in nonlinear kinetic systems.
On the SCF calculation of excited states: Singlet states in the two‐electron problem
Authors: McCourt Mary , McIver James W. 
Published: January 2005

AbstractThe problem of determining SCF wave functions for excited electronic states is examined for singlet states of two‐electron systems using a Lowdin natural orbital transformation of the full CI wave function. This analysis facilitates the comparison of various SCF methods with one another. The distribution of the full CI states among the natural orbital MCSCF states is obtained for the S states of helium using a modest Gaussian basis set. For SCF methods that are not equivalent to the full CI wave functions, it is shown that the Hartree‐Fock plus all single excitation wave functions are equivalent to that of Hartree‐Fock plus one single excitation. It is further shown that these wave functions are equivalent to the perfect pair or TCSCF wave functions in which the CI expansion coefficients are restricted to have opposite signs. The case of the natural orbital MCSCF wave function for two orbitals is examined in greater detail. It is shown that the first excited state must always be found on the lower natural orbital MCSCF CI root, thus precluding the use of the Hylleras‐Undeim‐MacDonald (HUM) theorem in locating this state. It is finally demonstrated that the solution obtained by applying the HUM theorem (minimizing the upper MCSCF CI root with respect to orbital mixing parameters) is an artifact of the MCSCF method and does not correspond to any of the full CI states.
Column design. 3. Theoretical studies of a chiral stationary phase used in column chromatography
Authors: Lipkowitz Kenny B. , Demeter David A. , Parish Carol A. , Landwer Jo M. , Darden Thomas 
Published: January 2005

AbstractConformational features of a chiral stationary phase used in column chromatography are discussed. The syn forms invoked in chiral recognition models are consistent with MNDO and MM2 calculations. It is speculated that the inherent flexibility of the syn form makes these phases effective templates for analyte binding.
Electrostatic interaction of a solute with a continuum. Improved description of the cavity and of the surface cavity bound charge distribution.
Authors: Pascual‐Ahuir J. L. , Silla E. , Tomasi J. , Bonaccorsi R. 
Published: January 2005

AbstractAlgorithms for a finer description of cavities in continuous media and for a more efficient selection of sampling points on the cavity surface are described. Applications to the evaluation of solute surface and volume and to the calculation of the solute‐solvent electrostatic interaction energy, as well as of the cavitation energy are shown as examples.
Theoretical studies on the acid hydrolysis of methyl carbamate
Authors: Lee Ikchoon , Kim Chang Kon , Lee Byung Choon 
Published: January 2005

AbstractThe mechanism of the A2 acid hydrolysis of methyl carbamate was investigated using MNDO method. The reaction was found to proceed in two steps: (1) the rate‐determining nucleophilic attack of water on the carbonyl carbon of the N‐protonated tautomer involving the tetrahedral TS; and (2) the fast subsequent proton abstraction by the leaving group, NH3, to form products. The mechanism is similar to that involved in the A2 hydrolysis of acetamide. Effects of substituents, R1, R2, and R3 in R1OCONR2R3, on rates can be predicted by the changes in electron densities on alkoxy oxygen and N, in complete agreement with the experimental results. We concluded that there is no need for invoking two different mechanisms for amides and carbamates since a common mechanism can easily accommodate all the experimental results.
Molecular mechanics study of myelin basic protein
Authors: Gilliom Richard D. , Stoner Gerald L. 
Published: January 2005

AbstractMyelin basic protein (MBP) is the major extrinsic protein of the myelin sheath in the central nervous system. We have examined the predicted structure of segments of MBP using the molecular mechanics program ECEPP83 developed by Scheraga and coworkers as modified by Chuman, Momany, and Schafer. We have focused upon segments containing the Pro‐Pro‐Pro sequence (residues 100‐102), which have been predicted from standard algorithms to exist in a hairpin loop connecting anti‐parallel beta‐strands. Both the shorter (98‐105, 99‐105, and 100‐105) and longer segments (87‐109, 87‐118, and 87‐120) have been examined. These results indicate potential for a chain reversal in this region. The shorter segments have been studied by others using NMR techniques and the results are compared.
Combined bond‐polarization basis sets for accurate determination of dissociation energies. II. Basis set superposition error as a function of the parent basis set
Authors: Martin J. M. L. , François J. P. , Gijbels R. 
Published: January 2005

AbstractThe effect of the parent basis set on the basis set superposition error caused by bond functions is investigated systematically. An important difference between BSSE at the SCF and correlated levels is pointed out. Three new basis sets are defined, denoted 6‐311 + G(d,p)B, 6‐311 + G(2d,p)B, and 6‐311 + G(2df,p)B. BSSE for the first‐row hydrides seems to increase uniformly with increasing atomic number of the central atom. Expansion of the valence part of the basis set from 6‐31G to 6‐311G, as well as adding f functions, has a significant effect on the BSSE. Additional BSSEs incurred by bond functions are less than or equal to 1 kcal/mol for the 6‐311 + G(2df,p)B basis set. For the dissociation energies of the first‐row hydride species, agreement with experiment within only a few kcal/mol can be obtained even without resorting to isogyric reaction cycles. For high‐quality calculations, adding bond functions seems to have definite advantages over expanding the polarization space beyond the [2d1f] level.
Long‐Range proton‐proton coupling constants. I. Propanic coupling involving a methyl group 4JMeH
Authors: Esteban Angel L. , Galache Maria P. , Mora Francisco , Diez Ernesto , Fabian Jesus San 
Published: January 2005

AbstractAn equation is formulated on the basis of theoretical INDO/FPT calculations which describes the angular dependence of the propanic long‐range coupling constant 4JMeH in substituted HCCCH3 fragments. This equation is a truncated Fourier series in the torsion angle ϕ, HCCMe, which takes into account the dependence of the Fourier coefficients on the bond angle θ, CCMe. The substituent effects are assumed to be additive. Some parameters in the equation may be obtained from the 4JMeH couplings in propane and neopentane derivatives. The calculated effect upon 4JMeH of changes in the bond angle θ is significant and it seems to be in part the cause of some effects which have been attributed to conformational dependence.
On the evaluation of the characteristic polynomial of a chemical graph
Authors: Živković Tomislav P. 
Published: January 2005

AbstractThe evaluation of the characteristic polynomial of a chemical graph is considered. It is shown that the operation count of the Le Verrier–Faddeev–Frame method, which is presently considered to be the most efficient method for the calculation of the characteristic polynomial, is of the order n4. Here n is the order of the adjacency matrix A or equivalently, the number of vertices in the graph G. Two new algorithms are described which both have the operation count of the order n3. These algorithms are stable, fast, and efficient. A related problem of finding a characteristic polynomial from the known eigenvalues λi of the adjacency matrix is also considered. An algorithm is described which requires only n(n − 1)/2 operations for the solution of this problem.
Determining atom‐centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis
Authors: Breneman Curt M. , Wiberg Kenneth B. 
Published: January 2005

AbstractAn improved method for computing potential‐derived charges is described which is based upon the CHELP program available from QCPE.1 This approach (CHELPG) is shown to be considerably less dependent upon molecular orientation than the original CHELP program. In the second part of this work, the CHELPG point selection algorithm was used to analyze the changes in the potential‐derived charges in formamide during rotation about the CN bond. In order to achieve a level of rotational invariance less than 10% of the magnitude of the electronic effects studied, an equally‐spaced array of points 0.3 Å apart was required. Points found to be greater than 2.8 Å from any nucleus were eliminated, along with all points contained within the defined VDW distances from each of the atoms. The results are compared to those obtained by using CHELP. Even when large numbers of points (ca. 3000) were sampled using the CHELP selection routine, the results did not indicate a satisfactory level of rotatational invariance. On the basis of these results, the original CHELP program was found to be inadequate for analyzing internal rotations.
Efficient formulation of the large generator matrices required for computation of the higher moments, and mixed moments, of conformation‐dependent properties of chain molecules with independent bonds
Authors: Galiatsatos V. , Mattice Wayne L. 
Published: January 2005

AbstractDimensionless ratios of various moments of conformation‐dependent physical properties play an important role in the evaluation of the behavior of chain molecules. For example, the correlation coefficient, ρxy, between two conformation‐dependent physical properties, denoted here as x and y, is determined by the three dimensionless ratios 〈x2〉/〈x〉2, 〈y2〉/〈y〉2, and 〈xy〉/〈x〉〈y〉. Angle brackets denote the statistical mechanical average of the enclosed property. In the rotational isomeric state approximation, generator matrices of modest size can often be used for calculation of 〈x〉 and 〈y〉. The dimensions of the matrices grow rapidly upon going to higher moments or to mixed moments, such as 〈xy〉. Formulation of these large matrices, while straight‐forward, has been extremely tedious for chains with independent bonds, arbitrary rotational potentials, and arbitrary bond angles (which need not be fixed). Here we describe an approach that quickly and accurately solves this problem for all cases in which the generator matrices required for 〈x〉 and 〈y〉 are known. The algorithm is validitated by successful use for the computation of ρr2s2 for r2 and s2 for freely jointed chains of various n, a case for which an exact analytical result in closed form is available in the literature. Here r2 and s2 denote the squared end‐to‐end distance and squared radius of gyration for a specified conformation, and n denotes the number of bonds.
Atomic charges derived from semiempirical methods
Authors: Besler Brent H. , Merz Kenneth M. , Kollman Peter A. 
Published: January 2005

AbstractIt is demonstrated that semiempirical methods give electrostatic potential (ESP) derived atomic point charges that are in reasonable agreement with ab initio ESP charges. Furthermore, we find that MNDO ESP charges are superior to AM1 ESP charges in correlating with ESP charges derived from the 6‐31G* basis set. Thus, it is possible to obtain 6‐31G* quality point charges by simply scaling MNDO ESP charges. The charges are scaled in a linear (y = Mx) manner to conserve charge. In this way researchers desiring to carry out force field simulations or minimizations can obtain charges by using MNDO, which requires much less computer time than the corresponding 6‐31G* calculation.
On proper dissociation configurations of a molecule
Authors: Krishna M. V. Rama 
Published: January 2005

AbstractAn analytical procedure is presented for the determination of the proper dissociation configurations of a molecule. We illustrate this procedure by determining the proper dissociation configurations of many electronic states of the first‐row diatomic molecules and ozone. Finally, a few simple guidelines are provided to help in the identification of the important configurations needed for proper dissociation of a molecule.
A conformational study of cocaine and its diastereomers
Authors: Villar Hugo O. , Loew Gilda H. 
Published: January 2005

AbstractA conformational study of cocaine and its three diastereomers, pseudococaine, allococaine, and allopseu‐dococaine was carried out using molecular mechanics and quantum mechanical semiempirical techniques. Molecular dynamics simulations were performed at high temperature to scan their conformational space. Additional molecular dynamics at 312 K were used to explore the conformational flexibility of the compounds around the minimum energy conformation at physiologically relevant temperatures. The AM1 technique was used to refine the description of the minimum energy structures obtained with the molecular mechanics technique and to compute the electronic properties of cocaine and its diastereoisomers. Comparison of the results obtained with previous NMR and X‐ray structural data was carried out. The structural information obtained was then used to discuss some aspects of the pharmacology of cocaine and other compounds that bind at the site recognized by it on the dopamine transporter.
The MM3 force field for amides, polypeptides and proteins
Authors: Lii Jenn‐Huei , Allinger Norman L. 
Published: January 2005

AbstractThe potential functions for simple amides, several peptides and a small protein have been worked out for the MM3 force field. Structures and energies were fit as previously with MM2, but additionally, we fit the vibrational spectra of the simple amides (average rms error over four compounds, 34 cm−1), and examined more carefully electrostatic interactions, including charge‐charge and charge‐dipole interactions. The parameters were obtained and tested by examining four simple amides, five electrostatic model complexes, two dipeptides, six crystalline cyclic peptides, and the protein Crambin. The average root‐mean‐square deviation from the X‐ray structures for the six cyclic peptide crystals was only 0.10 Å for the nonhydrogen atomic positions, and 0.011 Å, 1.0°, and 4.9° for bond lengths, bond angles, and torsional angles, respectively. The parameter set was then further tested by minimizing the high resolution crystal structure of the hydrophobic protein Crambin. The resultant root‐mean‐square deviations for the non‐hydrogen atomic data, in the presence of the crystal lattice, are 0.22 Å, 0.023 Å, 2.0°, and 6.4° for coordinates, bond lengths, bond angles, and torsional angles, respectively.
ORAL: All purpose molecular mechanics simulator and energy minimizer
Authors: Zimmermann Karel 
Published: January 2005

AbstractA molecular mechanics energy minimizer is presented whose main features are the “floating blocks” and “isles” option, the “a‐NOE” distance inequality constraints and the variable storage first derivative minimization method. The program possibilities are illustrated by examples of molecular docking, energy barrier estimation, modeling of infinite structures, and DNA bending simulations.
A metropolis Monte Carlo method for computing microcanonical statistical rate constants
Authors: Dumont Randall S. 
Published: January 2005

AbstractA new method of computing microcanonical statistical rate constants is presented. The method utilizes the Metropolis Monte Carlo algorithm in a manner which circumvents some of the numerical inefficiency associated with other Metropolis and “shot‐gun” Monte Carlo based schemes. It is therefore expected to be useful in studies of many degree of freedom systems where numerical efficiency is crucial. Optimization of the method efficiency with respect to its adjustable parameters is examined in detail, both theoretically and in a numerical study of the T‐shaped Ar3 “inversion” process. The energy dependence of the T‐shaped Ar3 inversion rate is studied in a sample application of the method. An application to full three dimensional Ar3 will be presented in a future study.
Splicing I: Using mixed basis sets in ab initio calculations
Authors: Jensen Jan H. , Gordon Mark S. 
Published: January 2005

AbstractThe effect of mixing (or “splicing”) extended and minimal basis sets on molecular properties such as geometries, Mulliken charges, dipoles, and internal rotation barriers was studied for several test molecules. The effect is gauged by comparison with full extended basis set calculations. It is found that splicing improves most properties relative to full minimal basis set calculations, and little accuracy is lost if the splicing is done in a judicious manner.
Conformational energies and rotational barriers in 3‐methyl‐1‐butene and 1‐butene: An ab initio and molecular mechanics study
Authors: Pettersson Ingrid , Gundertofte Klaus 
Published: January 2005

AbstractThe calculated result obtained with MM2(87) for the rotation of the isopropyl group in 3‐methyl‐1‐butene is not in agreement with experimental data. In order to reparametrize the Csp2‐Csp3‐Csp‐Csp3 torsional angle, 3‐methyl‐1‐butene and 1‐butene have been studied by molecular mechanics (MM2(87)) and ab initio (MP2/6‐31G* and MP3/6‐31G*) calculations. The reparametrization of the torsional angle gives calculated results from MM2(87) in agreement with experimental data and ab initio calculations for both 3‐methyl‐1‐butene and 1‐butene. The calculated barriers for the rotation of alkyl groups in alkylbenzenes are improved with these new parameters.