bluuebunny/crossref_metadata_2025_split huggingface dataset:
Empirical energy functions for energy minimization and dynamics of nucleic acids
Authors: Nilsson Lennart , Karplus Martin 
Published: January 2005

AbstractAn improved empirical energy function for energy minimization and dynamics calculations of nucleic acids is developed and evaluated by an examination of its representation of both static and dynamic properties of model systems. Among the properties studied and used for parameter optimization are base pairing interactions, sugar and phosphate energy surfaces, small crystal heats of sublimation, base, phosphate and sugar analogue vibration spectra, and the overall behavior of a DNA hexamer duplex in vacuum molecular dynamics simulations. The results obtained are compared with those from two other energy functions that have been used recently for nucleic acids. Parameters for two energy functions are given; one includes heavy atoms and only polar hydrogens and the other includes all atoms.
The Computer System G R A P H: A Useful Tool in Chemical Graph Theory
Authors: Cvetković Dragos̆ , Gutman Ivan 
Published: January 2005

AbstractThe interactive programming system GRAPH, implemented at the Faculty of Electrical Engineering in Belgrade, is described. This system has been designed to treat a great variety of problems of graph theory. In the present article we point out the applicability of the system GRAPH in chemical investigations and illustrate it by two examples.
Computer Simulation of Metabolic Transformation
Authors: Tinker John F. , Gelernter Herbert 
Published: January 2005

AbstractSYNCHEM2 is a large knowledge‐based domain‐specific heuristic problem solving system that applies the methodology of artificial intelligence to the problem domain of synthetic organic chemistry. The program may be used for both synthetic and retrosynthetic exploration of the reaction transform space. We describe some experiments that might lead to the development of a special purpose version of the program for the investigation and prediction of environmental and metabolic processes undergone by chemicals that are released into the biosphere or directly ingested. The test system was used to predict the metabolites of three molecules of considerable biochemical interest, benzo[a]pyrene (known to be metabolically transformed into an active carcinogen), paramethyl substituted phenylalanine (which undergoes the NIH‐shift when metabolized), and haloperidol (an important and widely used neuroleptic). In the case of the benzo[a]pyrene, the program predicted all of the known metabolites, as well as several others. All of the 11 compounds predicted as metabolites of 4‐methylphenylalanine, which included the major known metabolite that exhibits the NIH‐shift, were reasonable. Contained among the predicted metabolic pathways for haloperidol was a credible explanation for the occurrence of a known haloperidol metabolite derived from a substituted phenylacetic acid, but for which no intermediates have been isolated. The program was able to bridge the problem space between haloperidol and the derived hippuric acid by using an unsuspected, but metabolically sound pinacol rearrangement.
On the importance of size‐consistency corrections in semiempirical MNDOC calculations
Authors: Cremer Dieter , Thiel Walter 
Published: January 2005

AbstractEnergies obtained by configuration interaction calculations including all double excitations with regard to the Hartree‐Fock reference determinant can empirically be corrected to size consistency using either the Langhoff‐Davidson (LD) formula or a formula suggested by Pople, Seeger, and Krishnan (PSK). Semiempirical MNDOC calculations suggest that for molecular systems with a large number of electrons and important correlation effects the PSK correction is superior to the LD correction.
Converged calculations of rotational energy transfer in HFHF collisions
Authors: Schwenke David W. , Truhlar Donald G. 
Published: January 2005

AbstractWe have performed large‐scale close coupling calculations of rotational‐to‐rotational energy transfer in HFHF collisions for the realistic potential energy surface of Brobjer and Murrell. We employ up to 525 angular terms in the expansion of the potential and up to 440 coupled channels in the rotational‐orbital basis set. The results for zero total angular momentum are well converged for relative translational energies up to over 0.6 eV, and they show extensive rotational excitation.
Time step error in diffusion Monte Carlo simulations: An empirical study
Authors: Rothstein Stuart M. , Patil Narayan , Vrbik Jan 
Published: January 2005

AbstractDiffusion Monte Carlo (DMC) is a random walk computational method for solving the ground‐state Schrödinger equation for atoms or molecules. One obtains a biased simulated energy which is used to estimate the exact energy, where the bias increases with the time step used in the simulation. We present six new DMC algorithms, all of which have the same theoretical justification. Yet, when applied to the LiH and H2 molecules, the algorithms give results with markedly different error. Furthermore, algorithms which exhibit a small error when applied to one molecule show significantly greater error for the other. The explanation for these results relates to sampling of configuration space in the neighborhood of the nuclei. We investigate this issue hoping that our results will aid in the design of more efficient DMC algorithms.
Theoretical study of the addition of hydrogen halides to olefins: A comparison between (HCl)2 and (HF)2 additions to ethylene
Authors: Clavero Carmen , Duran Miquel , Lledós Agustí , Ventura Oscar N. , Bertrán Juan 
Published: January 2005

AbstractThe addition of HCl and (HCl)2 to ethylene is theoretically studied by means of ab initio SCF techniques using the 3‐21G basis set. A statistical thermodynamics analysis is also carried out. When a comparison is made with the HF and (HF)2 additions to ethylene, the general fact of the catalytic action of the second HX molecule in the (HX)2 complex is revealed. The behavior of HF, however, is very different from that of HCl, since in the former case the driving force in the termolecular transition state is the bonding between fluorine and carbon, while in the latter case the driving force is the bonding between carbon and hydrogen, as generally accepted for electrophilic reactions. The use of density plots of the transition states on the plane of the cycle allows us to conclude that, while both HF and HCl termolecular transition states are hexacyclic, the bimolecular transition state of the HCl addition is bicentric and not tetracentric as previously reported.
Innate degree of freedom of a graph
Authors: Klein D. J. , Randić M. 
Published: January 2005

AbstractFor a Kekulé structure we consider the smallest number of placements of double bonds such that the full Kekulé structure on the given parent graph is fully determined. These numbers for each Kekulé structure of the parent graph sum to a novel structural invariant F, called the degree of freedom of the graph. Some qualitative characteristics are identified, and it is noted that apparently it behaves differently from a couple of other invariants related to Kekulé structures.
Ab initio study of the He(1S)‐Li2(X̃, 1∑) interaction by the SCF and MP2 methods
Authors: Matías M. A. , Varandas A. J. C. 
Published: January 2005

AbstractAb initio electronic structure calculations have been carried out for the He(1S)‐Li2 (X̃, 1∑) interaction both by the single‐configuration SCF and correlated second‐order MP2 methods using an extended basis set. From these calculations, an estimate of the isotropic (V0) and first two anisotropic (V2 and V4) terms of the He‐Li2 potential surface has been obtained. An assessment of the leading induced‐dipole‐induced‐dipole dispersion energy is presented from the MP2 energies. Where possible, a comparison is made with previous unpublished ab initio calculations by Staemmler and Stahl using the CEPA method.
Improvement of the hydrogen bonding correction to MNDO for calculations of biochemical interest
Authors: Goldblum Amiram 
Published: January 2005

AbstractRecent suggestions for correcting HAcceptor interactions within MNDO, together with results of crystallographic analysis, were used to modify this SCF semiempirical calculation for multiple hydrogen bonded associations. Thermodynamic profiles for model systems of biochemical interest such as H2OH2O, hydration of neutral and charged molecules, dimerizations and proton transfers show the advantages of this method. Its treatment of charges, bonding, geometries, energetics and vibrational frequencies is shown to be comparable to ab initio calculations with various basis sets. However, basic MNDO deficiencies and criteria applied for H‐bonding result in some too high barriers for proton transfers.
Topology of conical intersections and Jahn‐Teller crossing: Application to the standard model for XY4 molecules in T2 ground states
Authors: Liotard D. , Roche M. 
Published: January 2005

AbstractThe topological understanding of a potential function requires a knowledge of its critical points and indices. These concepts are mathematically meaningless if the potential function is not twice continuously differentiable. When conical intersections or Jahn–Teller crossings are encountered, the adiabatic potential, defined as the lowest eigenvalue of a Hamiltonian, can be smoothed everywhere. Moreover, the limiting properties of the smoothed critical points for vanishing values of a smoothing parameter lead to a unambiguous definition of a pseudo critical point of the limiting potential. Therefore, Morse theory is readily applicable to the ground state potential function in spite of the first order discontinuities. The regularization procedure is formally and numerically applied to the simplest Hamiltonian matrix of order 3 describing the Jahn–Teller effect of XY4 molecules in the T2 ground states. Various kinds of pseudo‐critical points are encountered and are shown to satisfy the Morse theory.
Monte Carlo study of the aqueous hydration of dimethylphosphate conformations
Authors: Jayaram B. , Mezei M. , Beveridge D. L. 
Published: January 2005

AbstractMonte Carlo computer simulations were performed on dilute aqueous solutions of the dimethylphosphate anion and the sodium dimethylphosphate ion pair, with the two phosphodiester torsional angles in the gauche–gauche, gauche–trans, and trans–trans conformations. The structural and energetic aspects of the aqueous hydration of each molecule were analyzed in terms of quasi component distribution functions based on the proximity criterion and partitioned into ionic, hydrophilic, and hydrophobic contributions to facilitate an understanding of the hydration pattern and conformational trends in these multifunctional solutes. Special attention was also paid to methodological issues affecting hydration, such as statistical uncertainty in the determined hydration indices, choice of partial atomic charges for the solute atoms, and solute–water interaction potentials adopted in the simulations. The results showed that gauche–trans and gauche–gauche forms are equally favorable for the dimethylphosphate anion with the trans extended form destabilized by hydration. The sodium dimethylphosphate ion pair hydration energetically favors the trans–trans conformation.
Application of SINDO1 to chlorine and sodium compounds
Authors: Jug Karl , Schulz Joachim 
Published: January 2005

AbstractSINDO1 calculations are presented for ground state geometries, heats of formation, ionization potentials and dipole moments of chlorine and sodium compounds. These calculations are based on a new parametrization of SINDO1 for second‐row elements which features inclusion of 3d orbitals and zero point energies. The comparison shows a substantial improvement over MNDO in geometries and heats of formation of hypervalent compounds and ionization potentials, whereas other properties are of similar quality.
On the use of constraints in molecular mechanics. II. The Lagrange multiplier method and non‐full‐matrix Newton‐Raphson minimization
Authors: Dillen Jan L.M. 
Published: January 2005

AbstractIt is shown how the Lagrange Multiplier method for constrained minimization can be implemented in a molecular mechanics program using the common approximations to the full‐matrix Newton‐Raphson minimization. The method reduces the number of cycles to achieve convergence, and also stabilizes the refinement process. Increases in computer memory requirements are small. As an application, the conformational surface of cycloheptane is calculated.
Semi‐empirical calculations of molecular trajectories: Method and applications to some simple molecular systems
Authors: Stewart James J.P. , Davis Larry P. , Burggraf Larry W. 
Published: January 2005

AbstractThe MNDO Hamiltonian as incorporated within MOPAC has been utilized to predict dynamics for some simple reactions. In one option, the intrinsic reaction coordinate has been followed along the path of steepest descent from the transition state backward to reactants and forward to products. In a second option, dynamics of isolated molecular systems have been calculated. In each case, the potential surface (as predicted by the MNDO Hamiltonian) is calculated in situ as the atomic trajectories are calculated from Newton's Laws of Motion. Several specific examples are given and discussed.
Ab initio program for treatment of related molecules. II. Integral transformation in extended systems
Authors: Kozmutza C. 
Published: January 2005

AbstractAn integral transformation procedure is reported as a part of an ab initio program (named SYCETY) developed recently for spatially extended molecules. It is shown that all advantages of the program SYCETY can be kept. The procedure is especially suitable to transform the integrals to a localized basis set. By using the MBPT with localized basis the most important part of the correlation can be calculated even for large (spatially extended) systems.
A molecular mechanics‐NMR pseudoenergy approach to the solution conformation of glycolipids
Authors: Scarsdale J. N. , Ram P. , Prestegard J. H. , Yu R. K. 
Published: January 2005

AbstractWe present here a protocol for the determination of oligosaccharide solution conformation from a combination of molecular mechanics calculations and NMR distance constraints treated as pseudoenergies. As an illustration of our methodology we have chosen the determination of the solution conformation of the tetrasaccharide headgroup of the glycolipid globoside. In order to test the ability of our methodology to avoid becoming trapped in local minima, we have chosen three starting structures, well displaced from one another in conformational space. The structures obtained upon convergence of the calculations with distance constraint pseudoenergies were quite similar to one another. For two of the three glycosidic linkages in globoside, the results from the calculations were virtually identical for each of the three starting structures. We also apply our protocol to a model which allows for the existence of multiple conformers in an effort to explore the possibility of conformational flexibility in the oligosaccharide headgroup of globoside.
Parallel computation of the Moller–Plesset second‐order contribution to the electronic correlation energy
Authors: Watts John D. , Dupuis Michel 
Published: January 2005

AbstractWe report herein, the implementation of a second‐order Moller–Plesset perturbation theory (MP2) program on the IBM LCAP parallel supercomputers. The LCAP systems comprise IBM 308X hosts and 10 FPS‐X64 attached processing units (APs). The APs are interconnected by a 512 Mbyte shared memory which allows rapid interprocessor communication. All the computationally demanding steps of the MP2 procedure execute efficiently in parallel. Parallel computation of two‐electron integrals is accomplished by distributing the loop over shell blocks among the APs. Parallel Fock matrix formation is achieved by having each AP evaluate the contribution of its own integral sublist to the total Fock matrix. The contributions are added together on the host, and the sum diagonalized either on the host or on a single AP. The parallel implementations of the integral transformation and the MP2 calculation are less straightforward. In each case, the use of the shared memory is essential for an efficient implementation. Details of the implementations and performance data are given.
Steric effects on reaction rates. XI. Solvolysis of tertiary carbon substrates rationalized by molecular mechanics calculations
Authors: Müller Paul , Mareda Jiri 
Published: January 2005

AbstractThe steric energy difference (ΔEst) between tertiary carbenium ions (R+) and the corresponding alcohols has been calculated by MM2 for a series of tertiary nonbridgehead substrates and correlated with their rate of solvolytic reactivity. Satisfactory correlation is obtained, except for p‐nitrobenzoates of highly congested substrates. The slope and intercept of the correlations remain almost unchanged if bridge‐head substrates are included in the plot. However, the quality of the fit is better for bridgehead substrates alone.
Computational strategies for the optimization of equilibrium geometries and transition‐state structures at the semiempirical level
Authors: Cummins Peter L. , Gready Jill E. 
Published: January 2005

AbstractSeveral improvements have been made to the gradient algorithms commonly used to optimize equilibrium and transition‐state geometries at the semiempirical level. A gradient algorithm derived from a combination of a variable metric method (Davidon–Fletcher–Powell/Broyden–Fletcher–Goldfarb–Shanno) and Pulay's direct inversion in the iterative subspace method for geometry optimization (GDIIS) is compared with the variable metric method combined with an accurate linear search algorithm. The latter method is used routinely in the standard semiempirical program packages, MNDO, MOPAC, and AMPAC. The combined variable metric and GDIIS algorithm is also compared with GDIIS which uses a static metric. The performance of these algorithms is examined for a wide range of systems with respect to both choice of coordinate system (for cyclic molecules) and guess for the initial Hessian. The results show that the GDIIS method is up to ca. 40% more efficient than the variable metric combined with accurate line search algorithm: however, the exact savings vary depending on the coordinate system and initial Hessian. For noncyclic systems, variable‐metric GDIIS is usually equal or superior to static‐metric GDIIS, and consistently performs ca. 30% more efficiently than the variable metric combined with accurate line search algorithm. For the optimization of cyclic molecules, an improved estimate of the initial Hessian has increased the efficiency by at least a factor of two. Greater efficiencies (usually >40%) are also obtained when static‐metric GDIIS is used to refine the geometry after the initial application of a transition‐state search based on the variable metric combined with line search algorithm. On the basis of these results, we recommend several changes to the algorithms as currently implemented in the standard semiempirical program packages.
A molecular mechanics analysis of molecular recognition by cyclodextrin mimics of α‐chymotrypsin
Authors: Venanzi Carol A. , Canzius Preston M. , Zhang Zhifeng , Bunce Jeffrey D. 
Published: January 2005

AbstractThe method of molecular mechanics is used to investigate the structural and electrostatic features of molecular recognition by β‐cyclodextrin and capped β‐cyclodextrin models of α‐chymotrypsin. Since capped β‐cyclodextrin has been shown to be the more effective biomimetic catalyst, these features of molecular recognition can be interpreted in terms of the relationship between molecular structure and catalytic function. Calculations in vacuo show that the addition of an N‐methylformamide “cap” substituent to each glucose unit appears to change the relative orientation of some glucose fragments from that found in the X‐ray structure of the β‐cyclodextrin macrocycle. These results indicate that certain structural components of molecular recognition, such as the orientation of the secondary hydroxyls and the related orientation of the caps, may be implicated in the catalysis. In addition, the electrostatic component of molecular recognition was investigated by the analysis of molecular electrostatic potential maps calculated in planes parallel to the average plane of the glycosidic oxygen atoms. The results indicate that the addition of the caps to the β‐cyclodextrin macrocycle subtly alters the pattern of the maps in each plane. However, the general qualitative features of electrostatic recognition by β‐cyclodextrin and capped β‐cyclodextrin are similar.
SCF, MP2, and CEPA‐1 calculations on the OH ‥ O hydrogen bonded complexes (H2O)2 and (H2O‐H2CO)
Authors: Vos R. J. , Hendriks R. , Van Duijneveldt F. B. 
Published: January 2005

AbstractCounterpoise corrected ab initio calculations are reported for (H2O)2 and H2O‐H2CO. Geometry searches were done in the moment‐optimized basis DZP' at the SCF, MP2, and CEPA‐1 levels of theory, followed by more accurate single‐point calculations in basis ESPB, which includes bondfunctions to saturate the dispersion energy. The final equilibrium binding energies obtained are −4.7 ±0.3 kcal/mol for a near‐linear (H2O)2 structure and −4.6 ±0.3 kcal/mol for a strongly bent HOH ‥ OCH2 structure. The energy difference between these systems is much smaller than in all previous ab initio work. Cyclic (C2h) and bifurcated (C2v) transition structures for (H2O)2 are located at 1.0 ±0.1 kcal/mol and 1.9 ±0.3 kcal/mol above the global minimum, respectively. A new partitioning scheme is presented that rigorously partitions the MP2 correlation interaction energy in intra and intermolecular (dispersion) contributions. These terms are large (up to 2 kcal/mol) but of opposite sign for most geometries studied and hence their overall effect upon the final structures is relatively small. The relative merits of the MP2 and CEPA‐1 approaches are discussed are discussed and it is concluded that for economical reasons MP2 is to be preferred, especially for larger systems.
Partial optimization of large molecules and clusters
Authors: Head John D. 
Published: January 2005

AbstractBy examining the displacement coordinate metric three modes of constrained optimization for large molecules and clusters are suggested. The first method corresponds to a conventional optimization using internal coordinates. The second mode has applications with respect to both internal and cartesian coordinates. The final mode is particularly interesting because it can result in computational savings. A mixture of both internal and cartesian coordinates is specified where these coordinates are usually a subset of the molecules or clusters total coordinate set. In the optimization only a subset of the energy derivatives need be evaluated reducing the computational effort associated with the gradient calculation.
Hydration free energy calculations by the acceptance ratio method
Authors: Saito Minoru , Nakamura Haruki 
Published: January 2005

AbstractThe hydration energy difference between the alanine and glycine zwitter ions was calculated by both the free energy perturbation method and the acceptance ratio method. The calculations were carried out by using different increments of the mutation parameter λ, δλ = − 0.05, −0.10, and −0.20. The free energy difference calculated by the acceptance ratio method was found to be approximately the same as an average of the two free energy differences in the forward and the backward directions calculated by the perturbation method. The results by the perturbation method were significantly affected by large δλ as compared with that by the acceptance ratio method. The statistical error caused by decreasing the simulation time for sampling equilibrium configurations is discussed.