bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational memories and a simulated annealing program that learns: Application to LTB4
Authors: Guarnieri Frank , Wilson Stephen R. 
Published: January 2005

AbstractThe use of computer simulations in all areas of chemistry is growing rapidly because of the powerful insights that they have provided into many interesting phenomena. As investigators continuously examine more sophisticated problems, they need increasingly more powerful tools. Hence, much effort has gone into the development of algorithms which might extend the scope and power of standard dynamic and Monte Carlo techniques. In the Monte Carlo regime, the most common area subject to improvement is the choice of a trial move. In the ordinary case, trial moves are generated uniformly at random. In the extended and hopefully improved case, trial moves are generated randomly but not uniformly. In this article we present a new and totally general method of biased sampling which is applicable to any flexible molecule. In our method, multiple simulated annealing runs are performed to reveal populated and unpopulated regions of the multidimensional conformation space. The second phase of the simulation is done at a fixed temperature with sampling only from populated regions found in the first phase. Because the simulated annealing runs quickly reveal unpopulated regions of the conformation space, the volume of conformation space that needs to be sampled in the second phase of the algorithm is reduced by many orders of magnitude. Additionally, because no energy minimization is used, these populations represent a canonical ensemble which may be used to estimate conformational free energies. © 1995 by John Wiley & Sons, Inc.
A simple yet accurate boundary element method for continuum dielectric calculations
Authors: Purisima Enrico O. , Nilar Shahul H. 
Published: January 2005

AbstractA simple yet accurate method for calculating electrostatic potentials using the boundary element continuum dielectric method is presented. It is shown that the limiting factor in accuracy is not the evaluation of integrals involving the interaction between boundary elements but rather a proper estimation of the self‐polarization of a patch upon itself. We derive a sum rule that allows us to calculate this important self‐polarization term in a self‐consistent and simple way. Intricate integration schemes used in previous treatments are consequently rendered unnecessary while concurrently achieving at least comparable accuracy over earlier methods. In some model systems for which analytic solutions are available, the computed surface polarization charge and reaction field energy are correct to better than six significant figures. An application of the method to the calculation of hydration free energies is presented. Good agreement with experimental values is obtained.
Genetic algorithms: A robust scheme for geometry optimizations and global minimum structure problems
Authors: Mestres Jordi , Scuseria Gustavo E. 
Published: January 2005

AbstractA Genetic Algorithm for Geometry Optimizations (GALGO) program has been developed to study the efficiency of this method of finding global minimum structures. Using a semiempirical tight‐binding potential, the behavior of different genetic algorithm (GA) operators has been tested for the linear chain isomer of a C8 cluster. An optimum set of parameters for the GA operators is proposed for this problem and afterward is used to obtain the global minimum structure of rare‐gas atomic clusters of up to 13 atoms using the 12–6 Lennard‐Jones interatomic pair potential. © 1995 by John Wiley & Sons, Inc.
Force field studies of cholesterol and cholesteryl acetate crystals and cholesterol–cholesterol intermolecular interactions
Authors: Liang Congxin , Yan Liqun , Hill Jörg‐R. , Ewig Carl S. , Stouch Terry R. , Hagler Arnold T. 
Published: January 2005

AbstractTo model the physical properties of sterols and related species, an all‐atom Class II force field has been derived based on the recently reported CFF93 force field for hydrocarbons. It has been tested using both energy minimization and molecular dynamics (MD) simulations of the low‐temperature neutron‐diffraction structure of cholesteryl acetate crystals and the X‐ray diffraction crystal structure of cholesterol. Thus these studies test the techniques and limitations of high‐accuracy crystal simulations as well. Employing energy minimization, all cell vectors and volumes were reproduced to within 2.4% of experimental values. For cholesteryl acetate, the root mean square (rms) deviations between the calculated and experimental bond lengths, angles, and torsions of nonhydrogen atoms are 0.013 Å, 1.2°, and 2.4°, respectively. The corresponding maximum deviations are also very small: 0.027 Å for bond length, 3.2° for angle, and 7.6° for torsion. For cholesterol, good agreement between the calculated and experimental structures was found only when the comparison was limited to atoms with relatively small thermal factors (Beq < 15 Å2). It was found that for both systems, the MD averaged structures were in better agreement with the experimental ones than the energy minimized structures, since the rms deviations in atom positions are smaller for the MD‐averaged structures (0.064 Å for cholesteryl acetate and 0.152 Å for cholesterol) than those for the minimized structures (0.178 Å for cholesteryl acetate and 0.189 Å for cholesterol). The force field was then applied to isolated molecules focusing on the rigidity of the cholesteryl ring and cholesterol–cholesterol interaction energies. It is concluded that the cholesteryl ring is fairly rigid since no major conformational change was observed during an MD simulation of a single cholesterol molecule in vacuo at 500 K, in agreement with condensed phase experiments. Calculations of cholesterol–cholesterol pairs suggest that there are only four low‐energy configurations and that it is more useful to describe each molecule as having a plane (flat face) and two grooves rather than as having two (one flat and one rough) faces. This provides some insight into the equilibrium crystal structures. Limited results from a modified Class I (CVFF) force field are presented for comparison. © 1995 by John Wiley & Sons, Inc.
An improved molecular modeling method for the prediction of enantioselectivity
Authors: Aerts J. 
Published: January 2005

AbstractAn improved method for the calculation of enantioselectivity by molecular mechanics is presented. This method does not use any a priori assumption on the conformation of the molecules in the complex and is equally applicable to weak as well as very strong complexes. High‐temperature molecular dynamics is used for the creation of a large number (5000–20,000) of random conformations and configurations of a 1:1 (or 1:2) complex of chiral molecules with a chiral selector. All configurations are energy minimized. The data set is only accepted if all lowest‐energy complexes occur at least five times in the minimized data set. The enantioselectivity is then calculated from the free energies of the diasteromeric complexes (chiral chromatography) or from the ratio of the sum of the Boltzmann weights (distribution of enantiomers over a chiral organic phase and a nonchiral water phase). This approach has been successfully applied to a range of chiral compounds. These include a weakly bonded Pirkle chiral stationary phase (CSP) system, a strong complex of diprotonated 1,2‐diphenyl‐1,2‐diamino‐ethane with two molecules of R,R‐tartrate, and the intermediate‐strength complexes of protonated and of neutral norephedrine with R,R‐tartrate. © 1995 by John Wiley & Sons, Inc.
An improved description of the molecular charge density in force fields with atomic multipole moments
Authors: Koch Uwe , Egert Ernst 
Published: January 2005

AbstractAtomic multipole moments, calculated from ab initio wave functions, offer an attractive way toward an improvement of the description of electrostatic interactions in force‐field programs. Accordingly, we have implemented the formulas for calculation of energies, forces, and torques resulting from the interactions of multipoles up to quadrupole–quadrupole interactions in our force‐field program MOMO. The method was successfully applied to various problems, including conformational analysis, hydrogen bonding, and π–π interactions. © 1995 by John Wiley & Sons, Inc.
Parallel direct implementations of second‐order perturbation theories
Authors: Nielsen Ida M. B. , Seidl Edward T. 
Published: January 2005

AbstractTwo algorithms are presented for parallel direct computation of energies with second‐order perturbation theory. Closed‐shell MP2 theory as well as the open‐shell perturbation theories OPT2(2) and ZAPT2 have been implemented. The algorithms are designed for distributed memory parallel computers. The first algorithm exhibits an excellent load balance and scales well when relatively few processors are used, but a large communication overhead reduces the efficiency for larger numbers of processors. The other algorithm employs very little interprocessor communication and scales well for large systems. In both implementations the memory requirement has been reduced by allowing the two‐electron integral transformation to be performed in multiple passes and by distributing the (partially) transformed integrals between processors. Results are presented for systems with up to 327 basis functions. © 1995 John Wiley & Sons, Inc.
Density functional theory and molecular clusters
Authors: Hobza Pavel , šponer Jiří , Reschel Tomáš 
Published: January 2005

AbstractDensity functional theory (DFT) methods, including nonlocal density gradient terms in the exchange and correlation energy functionals, were applied to various types of molecular clusters: H‐bonded, ionic, electrostatic, and London. Reliable results on the structure and stabilization energy were obtained for the first two types of cluster as long as Becke3LYP and Becke3P86 functionals and basis sets of at least DZ + P quality were used. DFT methods with currently available functionals failed completely, however, for London‐type clusters, for which no minimum was found on the potential energy surfaces. DFT interaction energy exhibits the same basis set extension dependence as the Hartree‐Fock (HF) interaction energy. Therefore, the Boys‐Bernardi function counterpoise procedure should be employed for elimination of the DFT basis set superposition error. © 1995 John Wiley & Sons, Inc.
A molecular dynamics study of the inhibition of chicken dihydrofolate reductase by a phenyl triazine
Authors: Leach Andrew R. , Klein Teri E. 
Published: January 2005

AbstractMolecular dynamics simulations have been used to investigate the ternary complex formed between chicken liver dihydrofolate reductase, a phenyl triazine inhibitor, and reduced nicotinamide adenine dinucleotide phosphate (NADPH). The solvent was represented by a sphere of water molecules encompassing the system. We report the results of quantum mechanical calculations of the rotational barrier in the pyrophosphate link and the barrier to inversion of the triazine ring. AMBER parameters for NADPH and the triazine are provided. Over the course of a 300‐ps molecular dynamics simulation of the ternary complex in water, the triazine inhibitor maintains the same hydrogen bonding and hydrophobic interactions with the enzyme that are observed in the X‐ray crystal structure. Despite the low calculated barrier to inversion of the triazine ring, a single puckered conformation is observed throughout the simulation. It is proposed that this is primarily due to interactions with Phe34, which maintains an approximately parallel orientation to the triazine ring. The nicotinamide portion of NADPH maintains the interactions observed in the crystal structure, but more conformational change is observed at the adenine end together with associated changes in the protein. Two conformations for the sidechain of Tyr31 are present in the X‐ray structure. The main simulation reported here corresponds to the conformation characterized by (χ1 = − 161°, χ2 = − 103°). A separate simulation was also performed in which the sidechain of Tyr31 was initially set to the other conformation present in the crystal structure (χ1 = 139°, χ2 = −99°). During this simulation, χ1 of this sidechain gradually changed until it occupied the region characterized by χ1 = −160°, thereby suggesting that this is the preferred conformation for this residue. The simulation required 200 ps to reach structural equilibrium (as measured by the root mean square, rms, deviation from the initial crystal structure), thus reinforcing the view that simulations of at least several hundreds of picoseconds are desirable when studying such systems. © 1995 John Wiley & Sons, Inc.
Energy minimization of peptide analogues using genetic algorithms
Authors: Herrmann Frank , Suhai Sándor 
Published: January 2005

AbstractA genetic algorithm is used to minimize the energy of peptide analogues in the dihedral angle space. It is interfaced to MOPAC, which computes the energy employing the AM1 Hamiltonian. The genetic algorithm identified the global energy minimum of glycine dipeptide analogue, alanine dipeptide analogue, diglycine, and dialanine. It identified three low‐energy conformations of tetraalanine, including the reported global minimum, all of which contained three hydrogen bonds. A structure with a lower energy than the reported global minimum has been generated in which one hydrogen bond is replaced by another one. © 1995 John Wiley & Sons, Inc.
Bond energies in chloroethanes and chloroethyl radicals
Authors: Frankin J. A. , Huybrechts G. H. 
Published: January 2005

AbstractCCl and CC bond energies in the chloroethanes and CH, CCl, and CC bond energies in the chloroethyl radicals are calculated from known heats of formation of chloroethanes and chloroethylenes and known CH bond energies in chloroethanes.The results obtained show a dependence of bond energy on the isomeric structure of the molecules and radicals and on the type of bond broken (primary, secondary, or tertiary). Heats of formation and bond energies estimated from group property additivity rules are in close agreement with experimental values.
Methylene radical reaction with cis‐butene‐2
Authors: Ring D. F. , Rabinovitch B. S. 
Published: January 2005

AbstractA study of the pressure dependence of the C5 products from the reaction of cis‐butene‐2 and methylene is reported. Methylene was produced by the photolysis of diazomethane with 4358 Å light at 23° or 56°, and by photolysis of ketene with 3200 Å radiation at 23° or 100°. The change with increasing pressure of the relative amounts of the characteristically “triplet products” (trans‐1,2‐dimethylcyclopropane, trans‐pentene‐2 (TP2), and 3‐methylbutene‐1 (3MB1)) and “singlet products” (cis‐1,2‐dimethylcyclopropane (CDMC) and cis‐pentene‐2 (CP2)) are discussed. The behavior is reminiscent of that found in 3CH2‐cis‐butene‐2 systems and can be interpreted in terms of the rapid rate of rearrangement of an initial triplet diradical product component, due to 3CH2, relative to the slower rate and readier collisional stabilization of an initial vibrationally‐excited dimethyl cyclopropane product component, due to 1CH2. Relative rates of reactions of 1CH2 with allylic CH:vinyl CH:CC in the neat liquid were, for diazomethane, 1:1.1:7.2 and, for ketene, 1:1.2:6.7.
Peresters XIII. Solvent effects in the decomposition of t‐butylperoxy α‐phenylisobutyrate with special reference to the cage effect
Authors: Herkes Frank E. , Friedman Juliette , Bartlett Paul D. 
Published: January 2005

Abstractt‐Butylperoxy α‐phenylisobutyrate (I) decomposes thermally by concerted formation of carbon dioxide, t‐butoxy, and cumyl radicals. Radical pair return in the solvent cage therefore does not affect the observed rate of decomposition, but is readily determined by means of galvinoxyl and other scavengers. In a series of 15 solvents the rate constant varies over a 2.8 fold range, being fastest in aromatic solvents. In the same solvent series the relative rates of diffusion and combination of radicals, measured by the cage effect, change by tenfold and are largely determined by the viscosity of the solvent. In all solvents of η > 8 mP, the reciprocal of the cage effect is a linear function of (T1/2/η), as recently observed for trifluoromethyl and methyl radicals [16]. This property of the cage effect provides a test by which it can be distinguished from other processes that reduce the efficiency of free‐radical production from an initiator.
Kinetics and rate constants for the reaction of tri‐n‐butylgermanium hydride with methyl iodide and carbon tetrachloride. The combination of methyl and trichloromethyl radicals in solution.
Authors: Carlsson D. J. , Ingold K. U. , Bray L. C. 
Published: January 2005

AbstractThe kinetics of the photoinitiated reductions of methyl iodide and carbon tetrachloride by tri‐n‐butylgermanium hydride in cyclohexane at 25°C have been studied and absolute rate constants have been measured. Rate constants for the combination of CH3ċ and CCl3ċ radicals are equal within experimental error and are also equal to the values found for the self‐reactions of most non‐polymeric radicals in low viscosity solvents, i.e. ∼1–3 × 109 M−1 sec−1.Rate constants for hydrogen atom abstraction by CH3ċ and CCl3ċ radicals are both ∼1−2 × 105 M−1 sec−1. Tri‐n‐butyltin hydride is about 10–20 times as good a hydrogen donor to alkyl radicals as is tri‐n‐butylgermanium hydride.The strength of the germanium–hydrogen bond, D(n‐Bu3Ge–H) is estimated to be approximately 84 kcal/mole.
Kinetics of the reaction of cyclopentane with trichloroethylene
Authors: Hardwick T. J. 
Published: January 2005

AbstractThe kinetics of the thermally and radiation initiated chain reaction between trichloroethylene and cyclopentane to produce 1,1‐dichlorovinylcyclopentane and hydrogen chloride have been investigated in the temperature range 250–360°C at high pressure in the gas phase. The rate governing step in the chain is (k3 = 3.3 × 109 exp −(4800/RT) cc mole−1 sec −1). The rate of the unimolecular decomposition of trichloroethylene is 1.4 × 1014 exp −(61,200/RT) sec−1.
Activating effects of unsaturated and cyclopropyl groups in gas phase pyrolysis of acetates. Paper XVIII
Authors: Lum Kin K. , Smith Grant Gill 
Published: January 2005

AbstractThe activating effects of a number of unsaturated groups and a cyclopropyl group have been evaluated in a solvent free system by determining the absolute rate constants, and energies and entropies of activation in the vapor phase pyrolysis of secondary and tertiary esters of the type RC(R′CH3) OAc where R′ = H or CH3 and R = c‐Pr, i‐Pr, CH3, CH2CH, CH2CHCH2, C6H5; the cyclopropyl showed only a moderate activating effect. The results are in contrast to the very significant activating effect of a cyclopropyl group in solvolysis of cyclopropylcarbinyl derivatives. Apparently marked activation by this group occurs only when a highly developed positive center forms adjacent to it. The lack of marked activation by the cyclopropyl group supports a mechanism for ester pyrolysis which involves a modest, but detectable, charge separation in the transition state [2] but questions a mechanism in which an intimate ion‐pair was proposed [3].
The photolysis of pentafluoroacetone
Authors: Pritchard G. O. , Perona M. J. 
Published: January 2005

AbstractThe photolysis of pentafluoroacetone has been investigated in the 3130 Å region, from room temperature to 360°C. The ΦCO varies from 0.7 to 0.9 over this range, and the decomposition is represented by CF2HCOCF3 → CF2H + CO + CF3. The disproportionation/combination ratio for CF3 and CF2H (→ CF3H + CF2) radicals is found to be 0.09. Arrhenius parameters for hydrogen atom abstraction from the ketone are log10A = 12.7 (units are mole−1 cc sec−1) and E = 14.3 kcal mole−1 for CF2H, and log10A = 12.1 and E = 11.8, for CF3 radicals. At low pressures HF elimination reactions are observed from the vibrationally excited fluoroethanes, C2F5H* and C2F4H2*, formed in the system. A rough estimate of the activation energy for the process C2F5H → C2F4 + HF of 60–65 kcal mole−1 is made.
The thermal isomerization of 1,1‐dimethyl‐2‐vinylcyclopropane to cis‐2‐methylhexa‐1,4‐diene via 1,5‐hydrogen migration
Authors: Frey H. M. , Solly R. K. 
Published: January 2005

AbstractThe gas phase isomerization of 1,1‐dimethyl‐2‐vinylcyclopropane to cis‐2‐methylhexa‐1,4‐diene has been studied in a static system. The isomerization is homogeneous and kinetically first order. The rate constants were independent of initial reactant pressure in the range 0.6 to 2 torr and of added nitrogen up to 180 torr. Rate constants determined at 10 temperatures in the range 200 to 254°C fitted the Arrhenius equation
k = 1011.41±0.02 exp (−33,540 ± 47 cal/RT) sec−1The low A factor and activation energy are consistent with a concerted 1,5‐hydrogen migration via a “tight” cyclic transition complex.
New differential techniques for evaluating rate constants and ratios of rate constants. The behaviors of irreversible first‐and pseudo‐first‐order reactions
Authors: Meites Louis , Meites Thelma 
Published: January 2005

AbstractA record of the time dependence of the difference between two signals, one proportional to the concentration of a reactant or product in one reaction mixture and the other proportional to the concentration of the same or a corresponding substance in another mixture in which the reaction is initiated at the same time as the first, makes it possible to obtain not only the ratio, but also the individual values, of the rate constants for the two reactions. The effects of the experimental variables on a number of measurable parameters are examined, the errors associated with a number of different ways of evaluating the rate constants and their ratio are discussed, and it is shown how conditions can be selected that should provide values whose precisions compare favorably with those attainable by other techniques.
Reaction of O(1D) with N2O
Authors: Greenberg Raymond I. , Heicklen Julian 
Published: January 2005

AbstractO(1D), produced from the photolysis of N2O at 2139 Å, reacts with N2O in accord with:

We have used the method of chemical difference to obtain an accurate measure of k2/k3 = 0.59 ± 0.01. Furthermore, the quantum yield of production of O(3P), either on direct photolysis or on deactivation of O(1D) by N2O, is less than 0.02 and probably zero.
A Quantitative study of alkyl radical reactions by kinetic spectroscopy. Part I. Mutual combination of methyl radicals and combination of methyl radicals with nitric oxide
Authors: Basco N. , James D. G. L. , Suart R. D. 
Published: January 2005

AbstractCombination reactions of the methyl radical have been studied by following the decay of the absorbance of the methyl radical during the course of the reaction by means of kinetic spectroscopy. The limiting values of the second‐order rate constants at high pressure were determined for two reactions at room temperature:

The extinction coefficient of the methyl radical was found to have a maximum value of (1.02 ± 0.06) X 104 1 mole−1 cm−1 at 216.4 nm. Integration of the extinction coefficient over the absorption band of the methyl radical gave an oscillator strength of 1.0 X 10−2.
Reaction of CF3 radicals with group IV tetramethyls
Authors: Bell T. N. , Platt A. E. 
Published: January 2005

AbstractArrhenius parameters have been measured for the abstraction of hydrogen from the C Si, Ge, and Sn tetramethyls:

The rate constants correlate with the proton chemical shift, which is related to a polar effect. In all cases except carbon, a hot‐molecule β‐fluorine rearrangement‐elimination reaction occurs following radical combination:

We suggest the occurrence of a radical exchange reaction for the Si, Sn, and Ge systems,

with kexchange (CF3 + Sn(Me)4) ∼ 107 ml m−1 s−1.