bluuebunny/crossref_metadata_2025_split huggingface dataset:
PVM‐AMBER: A parallel implementation of the AMBER molecular mechanics package for workstation clusters
Authors: Swanson Eric , Lybrand Terry P. 
Published: January 2005

AbstractA parallel version of the popular molecular mechanics package AMBER suitable for execution on workstation clusters has been developed. Computer‐intensive portions of molecular dynamics or free‐energy perturbation computations, such as nonbonded pair list generation or calculation of nonbonded energies and forces, are distributed across a collection of Unix workstations linked by Ethernet or FDDI connections. This parallel implementation utilizes the message‐passing software PVM (Parallel Virtual Machine) from Oak Ridge National Laboratory to coordinate data exchange and processor synchronization. Test simulations performed for solvated peptide, protein, and lipid bilayer systems indicate that reasonable parallel efficiency (70–90%) and computational speedup (2–5 × serial computer runtimes) can be achieved with small workstation clusters (typically six to eight machines) for typical biomolecular simulation problems. PVM‐AMBER is also easily and rapidly portable to different hardware platforms due to the availability of PVM for numerous computers. The current version of PVM‐AMBER has been tested successfully on Silicon Graphics, IBM RS6000, DEC ALPHA, and HP 735 workstation clusters and heterogeneous clusters of these machines, as well as on CRAY T3D and Kendall Square KSR2 parallel supercomputers. Thus, PVM‐AMBER provides a simple and cost‐effective mechanism for parallel molecular dynamics simulations on readily available hardware platforms. Factors that affect the efficiency of this approach are discussed. © 1995 by John Wiley & Sons, Inc.
Evaluating polarizable potentials on distributed memory parallel computers: Program development and applications
Authors: Bernardo Dan N. , Ding Yanbo , Krogh‐Jespersen Karsten , Levy Ronald M. 
Published: January 2005

AbstractThe efficient evaluation of polarizable molecular mechanics potentials on distributed memory parallel computers is discussed. The program executes at 7–10 Mflops/node on a 32‐node CM‐5 partition and is 19 times faster than comparable code running on a single‐processor HP 9000/735. On the parallel computer, matrix inversion becomes a practical alternative to the commonly used iterative method for the calculation of induced dipole moments. The former method is useful in cases such as free‐energy perturbation (FEP) simulations, which require highly accurate induced dipole moments. Matrix inversion is performed 110 times faster on the CM‐5 than on the HP. We show that the accuracy which is needed for FEP calculations with polarization can be obtained by either matrix inversion or by performing a large number of iteration cycles to satisfy convergence tolerances that are less than 10−6 D. © 1995 by John Wiley & Sons, Inc.
Implementation of the ECEPP algorithm, the Monte Carlo minimization method, and the electrostatically driven Monte Carlo method on the Kendall square research KSR1 computer
Authors: Ripoll D. R. , Pottle M. S. , Gibson K. D. , Scheraga H. A. , Liwo A. 
Published: January 2005

AbstractIn this article the adaptation of the Empirical Conformational Energy Program for Peptides (ECEPP/3) and two conformational search methods [viz., the Monte Carlo minimization (MCM) method and the electrostatically driven Monte Carlo (EDMC) method] to the Kendall Square Research KSR1 computer is described. The MCM and EDMC methods were developed to surmount the multiple‐minima problem in protein folding. Parallelization of these codes led to substantial speedups (expressed as the ratio between the mean time per energy evaluation in one processor and the mean time per energy evaluation in a set of processors) over the serial versions of these codes. A comparison of the performance of these algorithms on the KSR1 and on the IBM ES9000 computers is presented. © 1995 by John Wiley & Sons, Inc.
Discrete, dynamic polymer modeling: A pseudo‐diatomic model of lignin
Authors: Roussel Marc R. , Lim Carmay 
Published: January 2005

AbstractWe have developed a novel simulation strategy based on cellular automata methods which can be used to simulate a variety of physicochemical processes, including those involved in polymerization. Our approach leads to dynamic, parallel models. This strategy can address several classes of questions in technologically or scientifically important systems for which only limited structural or dynamical information is available by current experimental techniques. We illustrate the use of our methods by creating a model of lignification in vivo. The monomers are represented by pseudo‐diatomic molecules as a refinement to the usual point‐particle geometry normally used in such models. Our lignification model captures the essence of the underlying physical processes, as evidenced by the fact that it reproduces satisfactorily many experimentally determined properties of lignin. Due to the inherent efficiency of parallel cellular automata, our simulation strategy shows great promise, particularly for modeling species of very high molecular weight (over 106 daltons). © 1995 John Wiley & Sons, Inc.
Gradient SHAKE: An improved method for constrained energy minimization in macromolecular simulations
Authors: Duan Yong , Kumar Shankar , Rosenberg John M. , Kollman Peter A. 
Published: January 2005

AbstractCurrent macromolecular energy minimization algorithms become inefficient and prone to failure when bond length constraints are imposed. They are required to relieve steric stresses in biomolecules prior to a molecular dynamics simulation. Unfortunately, the latter often require constraints, leading to difficulties in initiating trajectories from unconstrained energy minima. This difficulty was overcome by requiring that the components of the energy gradient vanish along the constrained bonds. The modified energy minimization algorithm converges to a lower energy in a fewer number of iterations and is more robust than current implementations. The method has been successfully applied to the Dickerson DNA dodecamer, CGCGAATTCGCG. © 1995 John Wiley & Sons, Inc.
An efficient approach to calculation of zero‐flux atomic surfaces and generation of atomic integration data
Authors: Stefanov Boris B. , Cioslowski Jerzy 
Published: January 2005

AbstractA new robust method for variational determination of atomic zero‐flux surfaces is presented. The zero‐flux surface sheets are expressed in terms of variational trial functions in prolate spheroidal coordinates. The trial functions are optimized with a Newton procedure to satisfy the zero‐flux condition on a grid. The data required for radial integrations are generated by an adaptive quadrature procedure that employs model electron densities and utilizes an original third‐order algorithm for linear search. Results of test calculations involving variational determination of atomic surfaces are presented for a representative set of 20 molecules. The new approach is both less time consuming and substantially more accurate than the previously published algorithms. © 1995 John Wiley & Sons, Inc.
Docking flexible molecules: A case study of three proteins
Authors: Judson R. S. , Tan Y. T. , Mori E. , Melius C. , Jaeger E. P. , Treasurywala A. M. , Mathiowetz A. 
Published: January 2005

AbstractA genetic algorithm (GA) conformation search method is used to dock a series of flexible molecules into one of three proteins. The proteins examined are thermolysin (tmn), carboxypeptidase A (cpa), and dihydrofolate reductase (dfr). In the latter two proteins, the crystal ligand was redocked. For thermolysin, we docked eight ligands into a protein conformation derived from a single crystal structure. The bound conformations of the other ligands in tmn are known. In the cpa and dfr cases, and in seven of the eight tmn ligands, the GA docking method found conformations within 1.6 Å root mean square (rms) of the relaxed crystal conformation. © 1995 John Wiley & Sons, Inc.
A highly portable parallel implementation of AMBER4 using the message passing interface standard
Authors: Vincent James J. , Merz Kenneth M. 
Published: January 2005

AbstractWe have implemented a portable parallel version of the macromolecular modeling package AMBER4. The message passing paradigm was used. All message passing constructs are compliant with the Message Passing Interface (MPI) standard. The molecular dynamics/minimization module MINMD and the free‐energy perturbation module Gibbs have been implemented in parallel on a number of machines, including a Cray T3D, an IBM SP1/SP2, and a collection of networked workstations. In addition, the code has been tested with an MPI implementation from Argonne National Laboratories/Mississippi State University which runs on many parallel machines. The goal of this work is to decrease the amount of time required to perform molecular dynamics simulations. Performance results for a lipid bilayer molecular dynamics simulation on a Cray T3D, an IBM SP1/SP2, and a Cray C90 are compared. © 1995 John Wiley & Sons, Inc.
Effects of the cutoff center on the mean potential and pair distribution functions in liquid water
Authors: Gabdoulline Razif R. , Zheng Chong 
Published: January 2005

AbstractMolecular dynamics simulations of extended simple point charge (SPC/E) water have been performed to study the effects of the truncation of long‐range interactions on some calculated bulk properties of the liquid. The mean potential calculated in liquid water is sensitive to the choice of the cutoff center in the water molecule. The pair distribution function is also dependent on this choice, although not as strongly as the mean potential. An analysis is carried out to understand the origin of these effects. A common cutoff center is at the oxygen atom in the water molecule, but our study shows that this choice does not yield a mean potential value consistent with a more accurate estimate when no cutoff is applied. © 1995 John Wiley & Sons, Inc.
Harmonic analysis of large systems. II. Comparison of different protein models
Authors: Janežič Dšanka , Brooks Bernard R. 
Published: January 2005

AbstractA series of normal mode analyses of bovine pancreatic trypsin inhibitor (BPTI) has been performed. The results of modifying the long‐range truncation of electrostatics, reducing the conformational space of the system (reduced basis normal mode analysis), and using different parameter sets and models for the potential function are reported. Both explicit (904 atoms) and polar hydrogen (580 atoms) representations of BPTI were examined and produced nearly identical normal mode vectors but slightly modified vibrational frequencies. The truncation methods—no cutoff, shift, and switch—were examined, and the use of a short switching function was found to alter harmonic motion greatly. A table relating the different cutoff methods to several previously published frequencies for BPTI indicates that the diversity of published lowest frequencies is due to the use of different electrostatic models rather than to inherent differences in the models or energy parameters. Examining reduced basis results demonstrates that a dihedral basis yields similar normal mode vectors, though the vibrational frequencies are shifted to higher values. The analysis of BPTI harmonic dynamics using a spherical harmonic reduced basis set yields significantly altered dynamics, indicating that BPTI is not well represented as a homogeneous object at low temperatures. © 1995 John Wiley & Sons, Inc.This article is a U.S. Government work and, as such, is in the public domain in the United States of America.
The relaxation spectra of nickel(II) and cobalt(II) arginine complexes
Authors: Davies G. , Kustin K. , Pasternack R. F. 
Published: January 2005

AbstractThe temperature‐jump method has been used to determine the nickel(II)‐ and cobalt(II)‐arginine complexation kinetics. In the pH range studied, the neutral form of the ligand, HL, is the attacking, as well as the complexed, ligand species. The reactions reported on are of the type
equation image
where n = 1, 2, 3 and M is Ni or Co. At 25° and ionic strength 0.1M the association rate constants are: for nickel(II) k1 = 2.3 × 103(±20%), k2 = 2.4 × 104(±20%), k3 = 3.5 × 104(±40%) M−1 sec−1; for cobalt(II) k1 = 1.5 × 105(±20%), k2 = 8.7 × 105(±20%), k3 = 2.0 × 105(±40%) M−1 sec−1. Arginine binds to metal ions less well than homologous chelating agents due to the electrostatic repulsion arising from the positively charged terminus of the zwitterion. Kinetically, the effect appears in the association rate constants with nickel reactions more strongly influenced than cobalt.
Molecular‐modulation spectrometry: CH3ONO photolysis and detection of nitroxyl
Authors: McGraw G. E. , Johnston H. S. 
Published: January 2005

AbstractThe method of molecular‐modulation spectrometry for studying photochemical reactions has been applied to methyl nitrite photolysis. The infrared absorption of the nitroxyl radical HNO has been observed in the gas phase at 3300 cm−1. Under the present experimental conditions the steady‐state concentration of HNO under steady illumination was 1.1 × 1012 particles/cc, and the observed modulation amplitude was 4.5 × 1010 particles/cc. At 25°C and 1 atm of nitrogen, the cross section for infrared absorption by HNO at 3300 cm−1 is 1.7 × 10−19 cm2. The rate constant ratio b/c
equation image
was found to be 8.0. From the literature value of the rate constant d
equation image
, the observed rate constant for the reaction
equation image
is e = (5 ± 1) × 10−11 cc/particle sec.
Pressure Effects in the Solvolysis of Benzyl Chlorides
Authors: Laidler K. J. , Martin R. 
Published: January 2005

AbstractRates of solvolysis of benzyl chloride and of substituted benzyl chlorides have been measured in an acetone‐water mixture (acetone mole fraction 0.147) at pressures ranging from atmospheric to 1 kbar. Pressure studies have also been made for p‐methyl benzyl chloride in various acetone‐water mixtures. Measurements have also been made of the partial molar volumes of the reactants. The plots of log k against pressure are fitted to a second‐degree polynomial in P, and values of ΔV‡ and (δΔV//δP)T are obtained. The ΔV‡ values are all negative, having values ranging from −18 to −24 cc/mole. The results are interpreted on the view that the mechanisms are SN2(1), i.e. are towards the SN1 end of the SN2 spectrum of behavior. The ΔV‡ values steadily become more negative in the series pCH3, H, pCl, pNO2, and this is interpreted in terms of the greater spreading of positive charge in the pCH3 case and in terms of greater SN2(2) character in the pNO2 case. The ΔV‡ values go through a minimum as the solvent composition is varied, a result that is related to the existence of a corresponding maximum in the partial molar volumes of the reactant. The (δΔV‡/δP)T values show a negative correlation with ΔV‡, suggesting, as expected, that the more compact activated complexes are the least compressible.
Thermal unimolecular isomerization of 1,4‐dimethylbicyclo[2.2.0]hexane, 1,4‐dimethylbicyclo[2.1.1]hexane, and 1,4‐dimethylbicyclo[2.1.0]pentane
Authors: Srinivasan R. 
Published: January 2005

AbstractThe thermal isomerization of the title compounds was studied in the vapor phase. Over the temperature range from 445.1 to 477.5°K, 1,4‐dimethylbicyclo[2.2.0]hexane underwent a homogeneous unimolecular reaction to 2,5‐dimethyl‐1,5‐hexadiene, the rate constants being represented by the equation: k = 1.86 × 1011 exp (−31000 ± 1800/RT) sec−1. Over the temperature range from 630.0 to 662.2°K, 1,4‐dimethylbicyclo[2.1.1]‐hexane also underwent a unimolecular isomerization to the same product, the rate constants being given by the equation: k = 8.91 × 1014 exp (−56000 ± 900/RT) sec−1. The pyrolysis of 1,4‐dimethylbicyclo[2.1.0]pentane gave 1,3‐dimethylcyclopentene‐1 and 2,4‐dimethyl‐1,4‐pentadiene in the ratio of 9:1. The former reaction was influenced by surface effects but the latter was not. The rate constants for the formation of 2,4‐dimethyl‐1,4‐pentadiene fitted the equation: k = 1.66 × 1017 exp (−57400 ± 3100/RT) sec−1. The effect of the two methyl groups at the bridgehead positions in these molecules in influencing the rate of decomposition is discussed in terms of the non‐bonded repulsive forces between the substituents.
The thermal decomposition of azomethane‐d6
Authors: Chang Do‐Ren , Rice O. K. 
Published: January 2005

AbstractThe thermal decomposition of azomethane‐d6 has been studied. There is a short chain reaction, and measurements have been made of the rate of production of N2, CD4, and C2D6. A mechanism is suggested which accounts for these results fairly well. A comparison is made with some similar results of Forst for azomethane. Measurements have also been made of the reaction inhibited by NO. It is believed that the N2 production, extrapolated to zero NO pressure, measures the rate of the initial step CD3N2CD3 → 2 CD3 + N2. This has an activation energy at high pressures of 50.7 kcal per mole and an Arrhenius A·factor of 1015.49 sec−1. This is to be compared to values of 55.5 and 1017.3 found by Forst and Rice for CH3N2CH3 → 2 CH3 + N2. The pressure fall‐off behavior for CD3N2CD3 → 2 CD3 + N2 has also been investigated and compared to the theoretical curves, which seem to fit satisfactorily except at the lowest pressure, where experimental errors may be large. Unexpectedly, the fall‐off curve crosses that for CH3N2CH3 → 2 CH3 + N2. It is suggested that the extrapolation to zero NO pressure may not be entirely correct in the CH3N2CH3 case where the chain is longer than with CD3N2CD3. It is believed that the decomposition of azomethane‐d6 is a better example for unimolecular‐rate theory than is that of azomethane.
Thermal decomposition of 3,4‐dimethylpentene‐1, 2,3,3‐trimethylpentane, 3,3‐dimethylpentane, and isobutylbenzene in a single pulse shock tube
Authors: Tsang Wing 
Published: January 2005

AbstractSeveral hydrocarbons have been pyrolyzed in a single pulse shock tube. Rate parameters for the main bond breaking step have been found to be

In combination with similar studies carried out earlier and through application of the well‐established experimental rule (k(AB)/kr(AA)kr(BB))1/2 ∼ 2 where A and B are radicals and the rate constants are for the combination of these radicals, rate parameters for the thermal decomposition of all the hydrocarbons formed from any pair of the following radicals: methyl, ethyl, isopropyl, t‐butyl, t‐amyl, allyl, methylallyl, and benzyl have been calculated. The available calculated and experimental values of the decomposition rate constants are in excellent agreement. It appears that, with the possible exception of reactions involving the ejection of methyl radicals, the frequency factors per bond are nearly constant, depending only upon the type of carbon–carbon bond that is being broken. These values are all lower than those expected from the radical recombination rates.Heats of formation of ethyl, t‐amyl, benzyl, methylallyl, n‐propyl, s‐butyl, isobutyl, neopentyl, and 3‐pentyl radicals have been derived.Rate parameters for the decomposition of some simple ketones and ethers have also been estimated.
The nitric oxide catalyzed positional isomerization of 3‐methylene‐1,5,5‐trimethylcyclohexene and the stabilization energy in the 3‐methylenecyclohexenyl radical
Authors: Egger Kurt W. 
Published: January 2005

AbstractThe gas phase, nitric oxide catalyzed positional isomerization of 3‐methylene‐1,5,5‐trimethylcyclohexene (MTC) into 1,3,5,5‐tetramethyl‐1,3‐cyclohexadiene (TECD) has been studied for temperatures ranging between 296° and 425°C. The major reaction was first order with respect to nitric oxide and to MTC.The major side product, mesitylene, usually amounted to less than 10% of the TECD isomer formed. Only at high temperatures and large conversions has up to 20% been observed.Conditioned pyrex or quartz vessels coated with KCl have been used. The nitric oxide catalyzed isomerization is apparently a homogeneous process, as demonstrated by the insensitivity of the observed rate constants towards a 15‐fold increase in the surface to volume ratio of the reaction vessels. However, a residual, presumably heterogeneous, thermal isomerization of the starting material could not be eliminated. Good mass balances were obtained for both NO and hydrocarbons.After correcting for the thermally induced conversion the observed rate constants for the nitric oxide catalyzed isomerization yield log k1 (1 mole−1 sec−1) = (10.7 ± 0.2) – (37.3 ± 0.9)/θ where θ is 2.303 × 10−3 RT (kcal mole−1). Plotting log k1 versus the ratio of the starting materials (MTC/NO)0 it was found that for temperatures ≥ 365°C the rate constants were systematically too high.Using extrapolated values for the higher temperature range yields the more reliable corrected Arrhenius equation
log k = 8.6 – 31.7/θ.
The reaction mechanism is outlined and the implications with respect to the stabilization energy generated in the MTCċ radical intermediate and the activation energy of the backreaction MTCċ + HNO are discussed.Using for the activation energy E−1 of the backreaction (Rċ + HNO) a literature value of 9.2 ± 0.9 kcal mole−1 reported for the cyclohexadiene1,3system, this yields 23.4 ± 2 kcal mole−1 for the stabilization energy in the methylenecyclohexenyl radical, which is to be compared with the corresponding values for the allyl (10.2 ± 1.4), methallyl (12.6 ± 1) pentadienyl (15.4 ± 1) and cyclohexadienyl (24.6 ± 0.7) radicals.The pre‐exponential factor agrees well with the value of (8.4 ± 0.2) reported by Shaw and co‐workers for the similar reaction of NO with 1,3‐cyclohexadiene. It is noteworthy that HNO, acting as sole hydrogen donor in the system, is surprisingly stable under the reaction conditions used. Nitrous oxide, HCN, H2O and N2 are observed in the product mixture of experiments carried out to high conversions at higher temperatures.
The carbon–hydrogen bond strength in dimethyl ether and some properties of iodomethyl methyl ether
Authors: Cruickshank F. R. , Benson S. W. 
Published: January 2005

AbstractThe kinetics and mechanism of the reaction between iodine and dimethyl ether (DME) have been studied spectrophotometrically from 515–630°K over the pressure ranges, I2 3.8–18.9 torr and DME 39.6–592 torr in a static system. The rate‐determining step is,
equation image
where k1 is given by log (k1/M−1 sec−1) = 11.5 ± 0.3 – 23.2 ± 0.7/θ, with θ = 2.303RT in kcal/mole. The ratio k2/k−1,
equation image
is given by log (k2/k−1) = −0.05 ± 0.19 + (0.9 ± 0.45)/θ, whence the carbon‐hydrogen bond dissociation energy, DH° (HCH2OCH3) = 93.3 ± 1 kcal/mole. From this, ΔH°f(CH2OCH3) = −2.8 kcal and DH°(CH3OCH2) = 9.1 kcal/mole.Some nmr and uv spectral features of iodomethyl ether are reported.