bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combined molecular mechanical and quantum mechanical potential study of a nucleophilic addition reaction in solution
Authors: Liu Haiyan , Shi Yunyu 
Published: January 2005

AbstractThe procedure of combined semiempirical quantum mechanical (AM1) and molecular mechanical potential7 was used to study the nucleophilic addition of hydroxide to formaldehyde in solution. The gas phase AM1 potential surface is approximately 26 kcal/mol more exothermic than the corresponding ab initio 6‐31 + G* calculation results. The free energy profile for the reaction in solution was determined by means of molecular dynamic simulations. The resulting free energy of activation is approximately 5 kcal/mol. The difference of the free energy of solvation between the reactant and the product states is about 38 kcal/mol. As the reaction goes on, the number of hydrogen bonds formed by the hydroxide oxygen with the surrounding water molecules decreases, whereas the number of hydrogen bonds formed by the carbonyl oxygen increases. There is no significant change in the total number of hydrogen bonds between the solute and the solvent molecules, and the average number of these hydrogen bonds is between five and six during the entire reaction process. These results are consistent with previous studies using a model based on ad initio 6‐31 + G* calculations in the gas phase. The reaction path in solution is different from the gas phase minimum energy reaction path. When the two reactants are at a large distance, the attack route of the hydroxide anion in solution is close to perpendicular to the formaldehyde plane, whereas in the gas phase the route is collinear with the carbonyl group. These results suggests that although AM1 does not yield accurate energies in the gas phase, valuable insights into the solvent effects can be obtained through computer simulations with this combined potential. This combined procedure could be applied to chemical reactions within macromolecules, in which a quantitative estimation of the effects of the environment would not be easily attainable by another technique. © 1994 by John Wiley & Sons, Inc.
Algorithms for clustering molecular dynamics configurations
Authors: Torda Andrew E. , van Gunsteren Wilfred F. 
Published: January 2005

AbstractTwo traditional clustering algorithms are applied to configurations from a long molecular dynamics trajectory and compared using two sets of test data. First, a subset of atoms was chosen to present conformations which naturally fall into a number of clusters. Second, a subset of atoms was selected to span a relatively continuous region of conformational space rather than form discrete conformational classes. Of the two algorithms used, the single linkage method is inappropriate for this kind of data. The divisive hierarchical method, based on minimizing the difference between cluster centroids and extrema, is successful but also prone to imposing clustering hierarchy where none can be justified. © 1994 by John Wiley & Sons, Inc.
Path integral molecular dynamics methods: Application to neon
Authors: Morales Juan J. , Nuevo María J. 
Published: January 2005

AbstractFeynman's path integral formulation of quantum statistical mechanics, which has commonly been applied be Monte Carlo methods, is now also implemented by traditional molecular dynamics simulations of the microcanonical ensemble and in the Nosé‐Hoover method simulating the isothermal‐isobaric ensemble. In this article these two methods are applied to solid and liquid neon, in which quantum effects are not negligible. The validity of the procedure is shown by comparison with Monte Carlo and Brownian Dynamics computer simulations and with experiment. © 1995 by John Wiley & Sons, Inc.
Ab initio SCF calculations on low‐energy conformers of cyclohexaglycine
Authors: Böhm Hans‐Joachim , Brode Stefan 
Published: January 2005

AbstractResults from ab initio self‐consistent field (SCF) calculations with a 3‐21G and a double‐zeta‐plus polarization (DZP) basis set on four low‐energy conformations of cyclohexaglycine are reported. In agreement with results from semiempirical and molecular mechanics force field calculations, the lowest‐energy conformation found at the DZP level is a conformation forming six C7 turns. However, the energy difference to the β‐turn conformers is significantly smaller at the ab initio DZP level than calculated by the other methods. In contrast to the results obtained with some of the other methods, the present ab initio calculations show that both the double‐type‐I β turn and the double‐type‐II β‐turn conformer of cyclohexaglycine are stable low‐energy structures. © 1995 by John Wiley & Sons, Inc.
Conformational analysis and flexibility of carbohydrates using the CICADA approach with MM3
Authors: Koča Jaroslav , Pérez Serge , Imberty Anne 
Published: January 2005

AbstractThe potential energy hypersurfaces (PES) of several carbohydrate molecules were studied with a new algorithm for conformational searches, CICADA (Channels in Conformational Space Analyzed by Driver Approach) interfaced with the molecular mechanics program MM3(92). The method requires (1) one or a few low‐energy conformations as starting points; and (2) designation of the torsion angles important for understanding the conformational behavior of the molecule. The PES is explored by driving separately each selected torsion angle (in both directions) with a concomitant full‐geometry optimization at each increment (except for the driven angle). When a minimum has been detected, the molecule is freely optimized, and the minima so detected are then stored if not encountered previously. The new minima serve as starting structures for further explorations. The results from CICADA permit prediction of relative and absolute flexibility and conformational softness for both the entire molecule as well as for individual group rotations and local minima. The carbohydrates analyzed were Me‐α‐D‐glucopyranoside, β‐D‐GlcNAc(1‐2)α‐D‐Man, and α‐D‐GalNAc(1‐3)[α‐L‐Fuc(1‐2)]Gal‐O‐Me. All the low‐energy conformers along with the transition states and flexibilities features were characterized. CICADA found all minima and low‐energy conversion pathways for the disaccharide that were found by a traditional grid search. In contrast to the grid search method, CICADA concentrates mostly on the exploration of the low‐energy regions of the PES, thereby saving a significant amount of computational time. The performance of the method opens new routes for exploring conformational space of larger molecules, such as oligosaccharides. © 1995 by John Wiley & Sons, Inc.
Numerical solution of the nonlinear Poisson–Boltzmann equation: Developing more robust and efficient methods
Authors: Holst Michael J. , Saied Faisal 
Published: January 2005

AbstractWe present a robust and efficient numerical method for solution of the nonlinear Poisson‐Boltzmann equation arising in molecular biophysics. The equation is discretized with the box method, and solution of the discrete equations is accomplished with a global inexact‐Newton method, combined with linear multilevel techniques we have described in an article appearing previously in this journal. A detailed analysis of the resulting method is presented, with comparisons to other methods that have been proposed in the literature, including the classical nonlinear multigrid method, the nonlinear conjugate gradient method, and nonlinear relaxation methods such as successive overrelaxation. Both theoretical and numerical evidence suggests that this method will converge in the case of molecules for which many of the existing methods will not. In addition, for problems which the other methods are able to solve, numerical experiments show that the new method is substantially more efficient, and the superiority of this method grows with the problem size. The method is easy to implement once a linear multilevel solver is available and can also easily be used in conjunction with linear methods other than multigrid. © 1995 by John Wiley & Sons, Inc.
Calculation of binding energy differences for receptor–ligand systems using the Poisson‐Boltzmann method
Authors: Shen Jian , Quiocho Florante A. 
Published: January 2005

AbstractAn approach using the finite difference solution of the Poisson‐Boltzmann equation to estimate binding free energy changes for two receptor–ligand systems, arabinose binding protein and sulfate binding protein, is presented. The eight calculated binding free energy changes agree with experiment, showing a correlation coefficient of 0.92 and energy deviations of 1 kcal/mol or less. More importantly, the decomposition of solvation and assembly energies in this approach provides an understanding of binding mechanisms and therefore could suggest directions to alter binding affinities. The method is demonstrated to be useful in analyzing experimental binding structures and predicting binding effects of mutants or modified ligands for macromolecular systems, in which the electrostatic forces dominate the overall interaction and the structural perturbations upon modifications are small. © 1995 by John Wiley & Sons, Inc.
Theoretical investigation of the relative stabilities of XSSX and X2SS isomers (X = F, Cl, H, and CH3)
Authors: Bickelhaupt F. Matthias , Solà Miquel , von Ragué Schleyer Paul 
Published: January 2005

AbstractThe structures and relative stabilities of a series of disulfide (XSSX) and thiosulfoxide (X2SS) isomers have been studied for X = F, Cl, CH3, and H, using various levels of conventional ab initio and density functional theory (DFT). The XSSX isomers are more stable than the X2SS isomers for all substituents. The energy gap ΔE(X) between the two isomers increases (i.e., XSSX becomes more stable with respect to X2SS), and the SS bond contracts in the series for X = F, Cl, CH3, H. The results are interpreted by means of natural population analysis (NPA) (e.g., the interaction between the disulfide moiety S and the two substituents X·). The bonding in the hypervalent X2SS species is similar to the bonding in the nonhypervalent XSSX and does not involve a special role for sulfur‐3d orbitals. These orbitals acquire only minimal populations and are not to be conceived as valence orbitals. The DFT and conventional ab initio results, Xα/DZP and MP2/6‐31G** optimized structures and isomerization energies (at the highest levels of both methods), agree well. © 1995 by John Wiley & Sons, Inc.
Determination of C‐terminal structure of human CHaras oncogenic protein
Authors: Yoon Jeong Hyeok , Shin Jae Kwang , Jhon Mu Shik 
Published: January 2005

AbstractThe three‐dimensional structure of the carboxyl‐terminal region of the human ras oncogenic protein (called p21) has been determined using the HDMC (High‐directional Monte Carlo) method combined with MD (molecular dynamics) simulation. A truncated p21 containing residues 1–171 without the carboxyl‐terminal end was analyzed using X‐ray crystallography by Kim et al. It has been well documented that the carboxyl‐terminal region of p21 is flexible and plays an important role in transmitting a signal from the membrane‐attached domain. We have carried out the theoretical calculation for 18 undefined residues, which correspond to residues 172–189 of intact p21, in addition to seven residues (165–171) from X‐ray coordinates of the C‐terminal end of human CHaras protein. In this calculation, the main‐chain atoms of residues 165–169 have been fitted to X‐ray structure, and the remaining region has been allowed to move during the conformational analysis. We have confirmed that revised HDMC can easily alter the local minima of the polypeptide chains as the internal vibrations of molecules are allowed by MD simulation. Throughout this study, we suggest that the C‐terminal end of human CHaras p21 protein has structures in the forms of an α helix for 165–172, a loop for 173–180, and an α helix for 181–187 regions, like the helical hairpin. © 1995 by John Wiley & Sons, Inc.
An empirical force field. II. Crystalline alkanes
Authors: Dillen Jan L. M. 
Published: January 2005

AbstractThe EFF'93 force field is used to study crystalline alkanes. In addition to detailed molecular geometries, the sublimation enthalpy, heat capacity, and lattice vibrations for a number of saturated hydrocarbons are reported and compared with experiment. © 1995 by John Wiley & Sons, Inc.
Nonlocal density functional calculation of gas phase heats of formation
Authors: Habibollahzadeh Dariush , Grice M. Edward , Concha Monica C. , Murray Jane S. , Politzer Peter 
Published: January 2005

AbstractA general procedure is presented for computing the gas phase heats of formation of a wide variety of organic compounds. ΔE for the formation of the molecule from its elements at 0 K is obtained from density functional calculations (Gaussian 92/DFT) for optimized geometries. This result is converted to ΔH at 298 K by assuming ideal behavior and adding the translational, rotational, and vibrational energies. Additive correction terms corresponding to the various coordination states of the carbons, nitrogens, and oxygens were developed using a database of 54 compounds. The experimental ΔH values of these compounds are then reproduced with an average absolute error of 3 kcal/mol and a standard deviation of 4 kcal/mol. For a group of 10 test cases that were not part of the database, the average absolute error is 3.5 kcal/mol and the standard deviation is 4.1 kcal/mol. © 1995 by John Wiley & Sons, Inc.
An improved algorithm for the analytical computation of solvent‐excluded volume. The treatment of singularities in solvent‐accessible surface area and volume functions
Authors: Gogonea Valentin , Ōsawa Eiji 
Published: January 2005

AbstractAn algorithm for the analytical computation of solvent‐excluded volume is presented as part of our efforts to develop an improved computational model for a solvent effect term, in which the work required to create a cavity in the solvent is expressed as a function of the solvent‐excluded volume. In this article we describe mathematical developments in the analytical integration of solvent‐accessible surface (SAS) area, the singularities in SAS area and volume functions, and the procedures required to detect and treat singularities. Techniques to increase algorithm performance are presented, which improve computational speed by about five times, on the average. The accuracy of the analytical method for volume computation is compared with the accuracy of two numerical methods: the numerical integration of SAS area and the point‐by‐point scanning method. This algorithm calculates the volume of the spheres confined among their intersection planes and resembles a numerical integration of surface area by summing up volume layers. These characteristics make the algorithm useful in analytically calculating the work required to create a convex cavity in a solvent and the work (pΔV) associated with a change in the solvent‐excluded volume of the solute due to solvent pressure. © 1995 by John Wiley & Sons, Inc.
Electrostatic bonding models: A test on group 1 and 2 metal complexes with H2O, NH3, H2S, PH3, and related ligands
Authors: Magnusson Eric 
Published: January 2005

AbstractElectrostatic models frequently proposed to describe ion–molecule interactions have been tested on the adducts formed by Group 1 and 2 cations with H2O, NH3, H2S, PH3, their methyl analogs, and their anions. The results from the model calculations were compared with all‐electron calculations (geometry optimized, MP2, TZP basis sets) carried out on adducts formed with Li+, Na+, K+, Ca2+, and Mg2+. The electrostatic potential model was utilized in two ways: The attraction of the point charge was calculated with and without relaxation of the ligand. A third model allowed relaxation of the ligand but treated the cation as a frozen core. The final model was the crude point charge/point dipole approximation. At long range, the models satisfactorily track the effects on energy of gross changes in the ion–ligand interaction (monovalent versus divalent ions, neutral ligands versus anions, parent ligands versus methyl derivatives), but correlation at close range is poor, especially for binding by divalent cations. The hypothesis that the calculated strength of cation–dipole binding is dependent on calculated dipole moment could not be verified. © 1995 by John Wiley & Sons, Inc.
Ab initio molecular orbital studies of nonidentity allyl transfer reactions
Authors: Lee Ikchoon , Kim Chang Kon , Lee Bon‐Su 
Published: January 2005

AbstractAb initio molecular orbital (MO) calculations are carried out on the nonidentity allyl transfer processes, X− + CH2CHCH2Y ⇌ CH2CHCH2 X + Y−, with X− = H, F, and Cl and Y = H, NH2, OH, F, PH2, SH, and Cl. The Marcus equation applies well to the allyl transfer reactions. The transition state (TS) position along the reaction coordinate and the TS structure are strongly influenced by the thermodynamic driving force, whereas the TS looseness is originated from the intrinsic barrier. The intrinsic barrier, ΔE, looseness, %L‡, and absolute asymmetry, %AS‡, are well correlated with the percentage bond elongation, %CY‡ = [(d − d)/d] × 100 and/or %CX‡. The %CY‡ and the bond orders indicate that a stronger nucleophile and/or a stronger nucleofuge (or a better leaving group) leads to an earlier TS on the reaction coordinate with a lesser degree of bond making as well as bond breaking. These are consistent with the Bell‐Evans‐Polanyi principle and the Leffler‐Hammond postulate. © 1995 by John Wiley & Sons, Inc.
On the existence of SH3, SeH3, and TeH3: Discrepancies between all‐electron and pseudopotential calculations
Authors: Smart Bruce A. , Schiesser Carl H. 
Published: January 2005

AbstractAb initio calculations using both pseudopotential and double and triple‐ζ all‐electron basis sets, with and without electron correlation (MP2, QCISD), have been performed on the λ4‐sulfanyl (SH3), λ4‐selanyl (SeH3), and λ4‐tellanyl (TeH3) radicals. All‐electron basis sets of double‐ζ quality predict that SH3 and SeH3 correspond to transition states on their respective potential energy surfaces. In contrast, the pseudopotentials of Hay and Wadt predict that SH3 and SeH3 correspond to local minima at the QCISD level of theory while the pseudopotentials of Christiansen and Stevens predict transition states. By comparison, TeH3 proved to be a local minimum at all levels of theory. Interestingly, when a very large (triple‐ζ) all‐electron basis set was used, SH3 proved to be a transition state; however, in this instance the potential energy surface was found to be much flatter than in the case for which a double‐ζ basis set was used, suggesting that further improvements in the basis set may lead to a local minimum. Further improvements in the all‐electron selenium basis also led to a local minimum for SeH3 at the QCISD level of theory. © 1995 by John Wiley & Sons, Inc.
A density functional treatment of organolithium compounds: Comparison to ab initio, semiempirical, and experimental results
Authors: Pratt Lawrence M. , Khan Ishrat M. 
Published: January 2005

AbstractDensity functional calculations on several classes of organolithium compounds are described. The compounds studied include lithium bonds to carbon, oxygen, and nitrogen and are representative of most types of organolithium compounds that have appeared in the recent literature. The computational results are compared to those using MNDO, which has been shown to have some serious deficiencies in compounds involving carbon–lithium bonds, and to PM3 results, which offer some improvement over MNDO for many organolithium compounds. Most of the density functional calculations with a large basis set are in good agreement with available ab initio and experimental data. Calculated carbon–lithium bond lengths were slightly shorter than those calculated by other ab initio methods and were substantially longer than those calculated by MNDO, which is known to underestimate carbon–lithium bond lengths severely. Dimerization energies of methyllithium, calculated by DMol, were also in good agreement with those of other ab initio calculations. Lithium–nitrogen bonds in lithium amides were calculated to be slightly shorter by DMol than by MNDO, although the two methods were in qualitative agreement for this type of compound. © 1995 by John Wiley & Sons, Inc.
Error evaluation in the design of a special‐purpose processor that calculates nonbonded forces in molecular dynamics simulations
Authors: Amisaki Takashi , Fujiwara Takaji , Kusumi Akihiro , Miyagawa Hiroo , Kitamura Kunihiro 
Published: January 2005

AbstractSpecial‐purpose parallel machines that are plugged into a workstation to accelerate molecular dynamics (MD) simulations are attracting a considerable amount of interest. These machines comprise scalable homogeneous multiprocessors for calculating nonbonded forces (Coulombic and van der Waals forces), which consume more than 99% of the central processing unit (CPU) time in standard MD simulations. Each processor element in the machine has a pipeline architecture to calculate the total nonbonded force exerted on a particle by all of the other particles using information regarding the coordinates, the electric charge, and the species of each particle broadcast by the host computer. The processor then sends the calculated force back to the host computer. This article addresses the precision of the calculated nonbonded forces in the design of a processor LSI with minimal complexity. The precision of the arithmetic inside the processor that is required to calculate forces for MD simulations using Verlet's procedure was critically evaluated. Forward and backward error analysis, coupled with numerical MD experiments on one‐dimensional systems, was performed, and the following results were obtained: (1) Each element of the position vector which the processor receives from the host computer should have a precision of at least 25 bits; and (2) the pairwise forces should be calculated using floating point numbers with at least 29 bits of mantissa in the processor. Calculation of a pairwise force, which involves second‐order polynomial interpolation using a table‐driven algorithm, requires a key which contains a duplicate of at least 11 most significant bits of mantissa of the squared pairwise distance. The final result was that (3) the total force that acts on a particle, which is obtained by summing the forces exerted by all of the other particles, should be calculated using an accumulator that has a mantissa of at least 48 bits. © 1995 by John Wiley & Sons, Inc.
Hydrophobic solvation of methane and nonbond parameters of the TIP3P water model
Authors: Sun Yaxiong , Kollman Peter A. 
Published: January 2005

AbstractIn the process of studying the solvation of simple hydrocarbons, we found that the nonbond van der Waals (vdw) parameters for the TIP3P water model could be adjusted without significantly changing its liquid water properties. By increasing the van der Waals well depth ϵ from 0.152 kcal/mol for the TIP3P model to 0.190 kcal/mol (model TIP3P_MOD), the solvation free energy of all‐atom methane changed from 2.5 kcal/mol to 2.1 kcal/mol, much closer to the experimental value of 2.0 kcal/mol. This change of van der Waals parameters does not change hydrophilic solvation, since calculations using either water model lead to the same relative solvation free energy between ethane and methanol. The solvation free‐energy differences between methane and ethane and between ethane and propane have also been calculated with both models, and results found with the two water models are similar. For the united‐atom hydrocarbon model, however, the solvation free energy of methane changed from 2.1 kcal/mol with TIP3P to 1.8 kcal/mol with TIP3P_MOD. © 1995 by John Wiley & Sons, Inc.