bluuebunny/crossref_metadata_2025_split huggingface dataset:
Precision of free energies calculated by molecular dynamics simulations of peptides in solution
Authors: Hermans Jan , Yun R.H. , Anderson Amil G. 
Published: January 2005

AbstractErrors in free energies for molecular replacement and for conformation change of a small model peptide have been determined empirically by repeated simulations from different starting points. All calculations have been done using thermodynamic integration, in which the system's potential energy is coupled to a parameter λ, that is increased or decreased by a small amount at each step of the simulation. The effects of several factors that may alter the precision are evaluated. These factors include: the length of the simulation, the dependence of the potential energy on λ, the use of conformational restraints, and their magnitude and form. The methods used for restraint and conformational forcing are described in detail. The free energy change, calculated as the mean from several successive simulations with alternately increasing and decreasing λ, is found to be independent of the length of the simulations. As expected, longer simulations produce more precise results. The variation of the calculated free energies is found to consist of two parts, a random error and a systematic hysteresis, i.e., a dependence on the direction in which λ changes. The hysteresis varies as the inverse of the length of the simulation and the random error as the inverse square root The advantage of the use of a different (nonlinear) dependence of the attractive and repulsive parts of the nonbonded potential energy on the coupling parameter when “creating” particles in solution is found to be very large. This nonlinear coupling was found to be superior to the use of linear coupling and a nonlinear change of the coupling parameter with the simulation time. The hysteresis in conformational free energy calculations is found to increase markedly if too weak a forcing restraint is chosen. It is shown how to deconvolute the contribution of a torsional restraint from the dependence of the free energy on a torsion angle.
Relative log P and solution structure for small organic solutes in the chloroform/water system using monte carlo methods
Authors: Dunn William J. , Nagy Peter I. 
Published: January 2005

AbstractRelative log P values of dimethylether to methanol and dimethylamine to methylamine were calculated in the chloroform/water system using Monte Carlo simulations and statistical perturbation theory. Correct ordering of the calculated relative log Ps was obtained for the two pairs although the method leads to an overestimation of these values. In aqueous solution, both dimethyl ether and dimethylamine solutes are proton acceptors forming a single hydrogen bond to water. Dimethylamine forms a stable NH‐Ow hydrogen bond while the water hydrogen is poorly localized in the OH‐Ow bond to the ether. In chloroform, the solvent molecules are less ordered around the solutes than was found around methanol and methylamine.
Structural studies of aromatic amines and the dna intercalating compounds m‐amsa and o‐amsa: Comparison of mndo, am1, and pm3 to experimental and ab initio results
Authors: Smith Douglas A. , Ulmer Charles W. , Gilbert Matthew J. 
Published: January 2005

AbstractThe ability of the MNDO, AM1, and PM3 semiempirical methods to reproduce pyramidalization at the nitrogen in 15 aromatic amines has been examined and compared to experimental and other theoretical results. AM1 consistently gives the best agreement. We have therefore reexamined the DNA intercalating compounds m‐AMSA and o‐AMSA using AM1.
MO‐Studies of enzyme reaction mechanisms. I. Model molecular orbital study of the cleavage of peptides by carboxypeptidase A
Authors: Alex Alexander , Clark Timothy 
Published: January 2005

AbstractAb initio and semiempiridal (AM1) molecular orbital theory has been used to model the cleavage of formamide at the active site of carboxypeptidase A. The model active site consists of a zinc dication coordinated to two imidazoles, an acetate, a water with a hydrogen‐bonded formate, and a formamide molecule as model substrate. AM1 has been compared with ab initio theory for the coordination of water and formamide to Zn++ and found to give excellent energetic results. The course of the amide cleavage was therefore calculated with AM1. The first step of the reaction is the dissociation of the zinc‐coordinated water to give an active ZnOH+ species. The remote formate acts as proton acceptor. This process has an activation energy of only 4.6 kcal mol−1. The next and rate‐determining step is the concerted addition of the ZnOH+ moiety to the formamide CO bond. The ZnO distance in the transition state is more than 3 Å. In four further steps, the amide nitrogen is protonated and the CN bond cleaved. The net activation energy for the entire process is 15.5 kcal mol−1 relative to the active site model and 19.6 kcal mol−1 relative to the most stable point on the calculated reaction profile.
Vibrational Stark effect: Theoretical determination through the semiempirical AM1 method
Authors: Martí Josep , Lledós Agustí , Bertrán Juan , Duran Miquel 
Published: January 2005

AbstractThe vibrational Stark effect of a series of small molecules has been calculated by means of the semiempirical AM1 method through addition of the electron–field interaction term in the one‐electron Hamiltonian. Optimized geometrical parameters along with harmonic frequencies and line intensities are determined for different strengths of the applied uniform electric field. The perturbed spectra are compared with theoretical studies carried out at the ab initio level and with experimental results. The vibrational Stark effect of the retinal molecule is also computed, showing that this kind of study is feasible in systems of biochemical interest. © 1992 by John Wiley & Sons, Inc.
Theoretical studies of organometallic compounds. II. All electron and pseudopotential calculations of M(CH3)nCl4 − n (M = C, Si, Ge, Sn, Pb; n = 0–4)
Authors: Jonas Volker , Frenking Gernot , Reetz Manfred T. 
Published: January 2005

AbstractThe performance of effective core potentials (ECP) for the main group elements of group IV has been studied by calculating the geometries and reaction energies of isodesmic reactions for the molecules M(CH3)nCl4 − n (M = C, Si, Ge, Sn, Pb; n = 0–4) at the Hartree–Fock level of theory. The results are compared with data from all electron calculations and experimental results as far as available. The all electron calculations were performed with a 3‐21G(d) and a 6‐31G(d) basis set for Si, a (43321/4321/41) basis set for Ge, and a (433321/43321/431) basis set for Sn. For the ECP calculations the potentials developed by Hay and Wadt with a configuration (n)sa(n)pb and the valence basis set (21/21), extended by a set of d functions, are employed. © 1992 by John Wiley & Sons, Inc.
Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
Authors: Miyamoto Shuichi , Kollman Peter A. 
Published: January 2005

AbstractAn analytical algorithm, called SETTLE, for resetting the positions and velocities to satisfy the holonomic constraints on the rigid water model is presented. This method is still based on the Cartesian coordinate system and can be used in place of SHAKE and RATTLE. We implemented this algorithm in the SPASMS package of molecular mechanics and dynamics. Several series of molecular dynamics simulations were carried out to examine the performance of the new algorithm in comparison with the original RATTLE method. It was found that SETTLE is of higher accuracy and is faster than RATTLE with reasonable tolerances by three to nine times on a scalar machine. Furthermore, the performance improvement ranged from factors of 26 to 98 on a vector machine since the method presented is not iterative. © 1992 by John Wiley & Sons, Inc.
MNDO parameters for helium: Optimization, tests, and application to endohedral fullerene—helium complexes
Authors: Kolb Matthias , Thiel Walter 
Published: January 2005

AbstractMNDO parameters for helium are derived from an optimization that employs only atomic and diatomic reference data. Comparisons with published high‐level ab initio results indicate that MNDO correctly predicts the existence of covalently bonded helium compounds and normally reproduces the geometries of these small charged molecules reasonably well. Endohedral fullerene–helium complexes and the transition states for their formation are studied for C60, C60, and C. The calculated barriers are discussed and compared with those for the passage of helium through C6H6, C6H, and C6H. © 1993 John Wiley & Sons, Inc.
Ab initio study of the ground and excited states of HCP and its isomer HPC
Authors: Goldstein Elisheva , Jin Suqian , Carrillo M. Robyn , Cave Robert J. 
Published: January 2005

AbstractThe potential energy surface of HCP converting to HPC in its ground electronic state has been investigated with ab initio methods at levels up to MP2/6‐311G**//MP4/6‐311G** as well as TZV + + ** CASSCF. All geometries are fully optimized and compare favorably to previous theoretical and experimental values. The HCP molecule is predicted to be 85.4 kcal/mol lower in energy than its linear isomer at the‐MP2/6‐31G*//MP2/6‐31G* level. The energy barrier for hydrogen rearrangement is found to be merely 2.3 kcal from the HPC end. CASSCF studies were initiated to clarify the low barrier and lent support to a flat surface as HPC converts to stable, linear HCP at the TZV + + ** level. CASSCF also predicts that HPC is unstable with respect to bending. Harmonic vibrational frequencies for HCP results in 5% accuracy or better. A bent triplet is found to be the lowest excited state using the CASSCF method. © 1993 John Wiley & Sons, Inc.
Monte Carlo simulations of pure liquid substituted benzenes with OPLS potential functions
Authors: Jorgensen William L. , Laird Ellen R. , Nguyen Toan B. , Tirado‐Rives Julian 
Published: January 2005

AbstractIntermolecular potential functions have been developed for use in computer simulations of substituted benzenes. Previously reported optimized potentials for liquid simulations (OPLS) for benzene and organic functional groups were merged and tested in Monte Carlo statistical mechanics simulations for the pure liquids of toluene, m‐cresol, anisole, aniline, and benzonitrile at 25°C at 1 atm. The merged potential functions yielded acceptable thermodynamic results for the liquids except in the case of aniline, for which the error in the heat of vaporization was 12%. This was remedied by enhancing the polarity of the model to be more consistent with the observed dipole moment of aniline. Overall, the average errors in computed heats of vaporization and densities were then 2 and 1%, respectively. The structures of the liquids were characterized through energy and radial distribution functions. For m‐cresol and aniline, the molecules participate in averages of 1.6 and 1.4 hydrogen bonds, respectively. Condensed phase effects on the torsional energies for anisole, m‐cresol, and aniline were found to be small; m‐cresol has a slightly enhanced tendency to be nonplanar in the liquid than in the gas phase, while anisole shows the opposite pattern. © 1993 John Wiley & Sons, Inc.
Fast generation of molecular surfaces from 3D data fields with an enhanced “marching cube” algorithm
Authors: Heiden W. , Goetze T. , Brickmann J. 
Published: January 2005

AbstractAn improved version of the “marching cubes” algorithm [W. Lorensen and H. Cline, Comp. Graph. 21, (1987)] for the generation of isosurfaces from 3D data fields is presented and applied to molecular surfaces. The new algorithm avoids inconsistent pattern definitions of the original one, which lead to artificial gaps. The advantage of a logarithmic interpolation procedure, in particular for data fields typically occurring in molecular science, is demonstrated. An example is the generation of molecular surfaces based upon electron density data. © 1993 John Wiley & Sons, Inc.
Vibrational molecular force field of model compounds with biologic interest. II. Harmonic dynamics of both anomers of glucose in the crystalline state
Authors: Dauchez Manuel , Derreumaux Philippe , Vergoten Gérard 
Published: January 2005

AbstractCombining the modified Urey–Bradley–Shimanouchi intramolecular potential energy function with an appropriate intermolecular energy function, normal coordinate calculations have been performed for both α and β anomers of glucose and for some deuterated analogs in the crystalline state. The overall agreement between the observed and calculated frequencies leads to an average error on the order of 3 and 5 cm−1 for α and β glucose, respectively. In both cases, it is shown that the intermolecular potential energy terms are essential to reproduce perfectly the whole spectra, in particular for the hydroxyl stretching region, the anomeric and crystalline spectral regions, and the low‐frequency range. Moreover, the intermolecular interactions have a nonnegligible influence on the value of the intramolecular force constants. But, the potential energy distribution of vibrational modes are in accord with previous works performed for an isolated molecule. It is also important to point out that approximately the same set of force constants has been used for both molecules, differences existing only for the atoms involved in the anomeric configuration. Likewise, different charge distributions have been calculated and tested with different value of the dielectric constant. Charges determined by the AM1 quantum mechanical procedure with a value of 3 for the dielectric constant have the merit to reproduce quite well the whole spectra and in particular the frequency range below 200 cm−1. © 1993 John Wiley & Sons, Inc.
Fitting of nonlinear regressions by orthogonalized power series
Authors: Randić Milan 
Published: January 2005

AbstractWe outline a procedure that resolves ambiguities in fitting nonlinear data by power series. As is well known, the coefficients in the regression equations depend upon the truncation of the power series. We outline the procedure in which the coefficients of the regression using a power expansion are independent of the degree of the polynomials used. This is achieved by considering mutual regression of descriptors and using residuals as novel variables. The derived regression equations show unusual numerical stability, i.e., the coefficients of the regression equations are constant and independent of the truncation of the power series. The process is illustrated in an example to show all details and facilitate duplicating the process for interested readers. The method described here complements recently outlined procedures for construction of orthogonal descriptors for use in multivariate regression analysis. © 1993 John Wiley & Sons, Inc.
Loop closure via bond scaling and relaxation
Authors: Zheng Qiang , Rosenfeld Rakefet , Vajda Sandor , Delisi Charles 
Published: January 2005

AbstractWe describe, test, and apply a new computational algorithm for generating protein loop conformations subject to distance and secondary structure constraints. The algorithm is based upon initial scaling and subsequent relaxation of covalent bond lengths. The scaling‐relaxation procedure needs no additional energy terms and can be readily incorporated into existing molecular modeling packages. The algorithm uses an all‐atom energy function from the outset in a straightforward way so that about 60% of the generated loop conformations are free of severe distortions of covalent bond lengths and angles. An extensive application to the major loop conformations of TFIIIA‐type zinc fingers (Zif268 and ADR1) is presented, as well as preliminary calculations on hypervariable loops of two immunoglobulins (MCPC603 and Bence‐Jones). © 1993 John Wiley & Sons, Inc.
FORTRAN routine to compute Born–Oppenheimer potential energy curves directly from spectroscopic data
Authors: Battaglia Franco , Gallicchio Emilio 
Published: January 2005

AbstractA computer program that calculates Born–Oppenheimer potential energy curves of diatomic molecules directly from spectroscopic data is presented. Rather than performing the usual preliminary fitting of the experimental data to a single polynomial in the variable (v + 1/2), where v is the vibrational quantum number, the program contains an accurate built‐in interpolation routine by which each experimental input point belongs to its own polynomial. The program is tested on the ground state of the H2 molecule and results are compared with the most accurate ab initio calculations available. © 1993 John Wiley & Sons, Inc.
Comparison of methods to estimate the free energy of solvation:Importance in the modulation of the affinity of 3‐benzazepines for the D1receptor
Authors: Alkorta Ibon , Villar Hugo O. , Perez Juan J. 
Published: January 2005

AbstractWe computed the free energy of solvation for a series of ions and neutral molecules using two different continuum approaches. First, we used the AM1–SM1 technique, where the AM1 Fock matrix is modified to include a generalized Born contribution. Second, we applied the DelPhi approach, where the electrostatic component of the free energy of solvation is evaluated by resolving the Poisson–Boltzman equation by a finite difference method. Both methods appear equally reliable for ionic systems. For neutral compounds, AM1–SM1 performs better than DelPhi; however, the differences become less pronounced for compounds with larger free energies of solvation. In parallel, both methods were applied to study the influence of the solvation process in the overall drug receptor interaction for a series of closely related ligands for the D1 dopamine receptor. An inverse linear relationship was found between the free energy of solvation and the logarithm of the affinity of the ligands; nevertheless, electrostatic properties are likely to modulate affinity as well. © 1993 John Wiley & Sons, Inc.
Treatment of hydrogen bonding in SINDO1
Authors: Jug Karl , Geudtner Gerald 
Published: January 2005

AbstractFor the treatment of hydrogen bonding in SINDO1, 2p orbitals are introduced on hydrogen. The optimization of the orbital exponent together with the generation of approximate formulas for the core attraction integrals is sufficient to obtain good geometries and binding energies in hydrogen bonded systems. The method is applied to the dimers (H2O)2, (NH3)2, (HF)2, (HCOOH)2, (HCN)2, (H2S)2, and (HCI)2, mixed dimers NH3 · H2O and H2O · HCN, and cyclic polymers (HF)n(n = 3, 4, 6). © 1993 John Wiley & Sons, Inc.
Theoretical study of “protonated pyruvate”: A methylhydroxycarbene—carbon dioxide complex—implications for the decarboxylation of pyruvic acid
Authors: Norris Kathryn E. , Bacskay George B. , Gready Jill E. 
Published: January 2005

AbstractTwo conformers of protonated pyruvate, CH3C+(OH)COO, with the OH group either trans or cis to the methyl group and the carboxylate group in the CCC plane have been studied using the ab initio SCF/3‐21G method, as well as by some semiempirical AM1 calculations. Both ab initio SCF and AM1 curves for the potential energy as a function of the CCOO distance exhibit a minimum corresponding to a complex of methylhydroxycarbene, CH3COH, associated with carbon dioxide, but only the AM1 curves predict an inner minimum corresponding to a covalently bonded protonated pyruvate molecule with a CCOO distance of 1.6–1.7 Å. The two models also disagree on the dissociation pathway for pyruvic acid, with the AM1 calculations predicting formation of acetyl and HOCO radicals while the ab initio method predicts dissociation into methylhydroxycarbene and carbon dioxide following an initial intramolecular proton transfer. The weakly bound complexes of methylhydroxycarbene and carbon dioxide have been studied in some detail using ab initio SCF and MP2 methods in conjunction with 6‐311G** basis sets, obtaining equilibrium geometries and vibrational frequencies. In addition, the lactone‐type isomer of protonated pyruvate, which contains a CCO ring, was also studied. The conclusions of these calculations are consistent with those from earlier work using the smaller 3‐21G basis set. The most stable complex is predicted to occur between trans‐methylhydroxycarbene and carbon dioxide where substantial stabilization is provided by an OH ⃛ OC hydrogen bond. © 1993 John Wiley & Sons, Inc.
Comparison of the boys and Pipek–Mezey localizations in the local correlation approach and automatic virtual basis selection
Authors: Boughton James W. , Pulay Peter 
Published: January 2005

AbstractOur implementation of Pipek–Mezey population localization is described. It is compared with other localization schemes and its use in the framework of the local correlation method is discussed. For such use, this localization is shown to be clearly superior to Boys in the case of physically well‐localized systems. Our current algorithm for selection of local virtual spaces is also described. © 1993 John Wiley & Sons, Inc.
Hydrolytic degradation of α‐substituted polyglycolic acids: A semiempirical computational study
Authors: Pratt Lawrence M. , Chu C.C. 
Published: January 2005

AbstractThe two‐step hydrolyses of substituted polyglycolic acids are modeled by the semiempirical MNDO Hamiltonian using small molecule analogs to determine the effect of the alkyl substituents on the reaction and activation enthalpies. Reaction enthalpies remain reasonably constant up to three carbons, before becoming less exothermic for large alkyl substituents. Activation enthalpies show patterns that can be explained by steric effects. © 1993 John Wiley & Sons, Inc.
Conformational analysis and molecular dynamics simulation of cellobiose and larger cellooligomers
Authors: Hardy B.J. , Sarko A. 
Published: January 2005

AbstractThe conformational behavior of cellobiose (D‐glc‐ß(1→4)‐D‐glc), cellotetraose, and cellooctaose was studied by a combination of energy minimization and molecular dynamics simulations in vacuo at 400 K. These diand oligosaccharide models have considerable flexibility and exhibit a variety of different motions in glycosidic and exocyclic torsions. The glycosidic ϕ, ψ torsions moved frequently between two local minima on the cellobiose energy surface in the region of known crystal structures. Transitions of the hydroxymethyl side chain were observed between gt,gg, and tg conformations accompanied by changes in intramolecular hydrogen bonding patterns. A reasonable fit to the experimental optical rotation and nuclear magnetic resonance vicinal coupling data of cellobiose in solution required a distribution of its conformations. The oligomers, although generally extended, assumed a more coiled or twisted shape than is observed in the crystalline state of cellulose and exhibited considerable backbone motion due to local ring rotations about the glycosidic bonds. Long‐lived transitions to structures having torsion angles 180° from the major minima (ring flips) introduced kinks and bends into the tetramer and octamer. While the glucose rings of the structures remained primarily in the 4C1 conformation, twist and boat structures were also observed in the tetramer and octamer structures. Reducing the simulation temperature to 300 K eliminated some of the transitions seen at 400 K. © 1993 John Wiley & Sons, Inc.