bluuebunny/crossref_metadata_2025 huggingface dataset:
The geometry of pyrazole: A test for ab initio calculations
Authors: Llamas‐Saiz Antonio L. , Foces‐Foces Concepción , Mó Otilia , Yáñez Manuel , Elguero Eric , Elguero José
Published: January 2005

Ab initio calculations on the structure of pyrazole have been carried out at different levels of accuracy. At the Hartree‐Fock (HF) level, the performance of several basis sets, namely 3‐21G, 6‐31G, 6‐31G**, and 6–311G** was investigated. The influence of electron correlation effects also was studied by carrying out geometry optimizations at the MP2, MP4, and QCISD levels. The performance of a density functional method also was evaluated. We have also investigated the possible influence of the frozen core approximation on the final optimized geometry. Three different statistical analyses were considered in determining which geometry is closest to the experimental microwave geometry—namely Paul Curtin's diagrams, cluster analysis, and multidimensional scaling. From these analyses, we conclude that there is no asymptotic approach to the experimental geometry by increasing the quality of the theoretical model, although, as expected, the more reliable structures are those obtained at the MP2, MP4, and QCISD levels, as well as those obtained by the B3LYP density functional method. We have also found that the values of the rotational constants are a tight criterion to define the quality of a molecular geometry. © 1995 by John Wiley & Sons, Inc.
Small‐amplitude protein conformational dynamics: Second‐order analytic relation between cartesian coordinates and dihedral angles
Authors: Sunada Shinji , Go Nobuhiro
Published: January 2005

An analytic expression for protein atomic displacements in Cartesian coordinate space (CCS) against small changes in dihedral angles is derived. To study time‐dependent dynamics of a native protein molecule in CCS from dynamics in the internal coordinate space (ICS), it is necessary to convert small changes of internal coordinate variables to Cartesian coordinate variables. When we are interested in molecular motion, six degrees of freedom for translational and rotational motion of the molecule must be eliminated in this conversion, and this conversion is achieved by requiring the Eckart condition to hold. In this article, only dihedral angles are treated as independent internal variables (i.e., bond angles and bond lengths are fixed), and Cartesian coordinates of atoms are given analytically by a second‐order Taylor expansion in terms of small deviations of variable dihedral angles. Coefficients of the first‐order terms are collected in the K matrix obtained previously by Noguti and Go (1983) (see ref. 2). Coefficients of the second‐order terms, which are for the first time derived here, are associated with the (newly termed) L matrix. The effect of including the resulting quadratic terms is compared against the precise numerical treatment using the Eckart condition. A normal mode analysis (NMA) in the dihedral angle space (DAS) of the protein bovine pancreatic trypsin inhibitor (BPTI) has been performed to calculate shift of mean atomic positions and mean square fluctuations around the mean positions. The analysis shows that the second‐order terms involving the L matrix have significant contributions to atomic fluctuations at room temperature. This indicates that NMA in CCS involves significant errors when applied for such large molecules as proteins. These errors can be avoided by carrying out NMA in DAS and by considering terms up to second order in the conversion of atomic motion from DAS to CCS. © 1995 by John Wiley & Sons, Inc.
Parallel computation of the MP2 energy on distributed memory computers
Authors: Márquez Antonio M. , Dupuis Michel
Published: January 2005

A parallel distributed implementation of the second‐order Møller‐Plesset perturbation theory method, widely used in quantum chemistry, is presented. Parallelization strategy and performance for the HONDO quantum chemistry program running on a network of Unix computers are also discussed. Superlinear speedups are obtained through a combined use of the CPU and memory of the different processors. Performance for standard and direct algorithms are presented and discussed. A superdirect algorithm that eliminates the communication bottleneck during the integral transformation step is also proposed. © 1995 by John Wiley & Sons, Inc.
SINDO1 study of the photoreaction of tetramethylene sulfone
Authors: Gerwens Heiko , Jug Karl
Published: January 2005

The mechanism of the photoreaction of tetramethylene sulfone (TMSO2) was investigated by the semiempirical molecular orbital (MO) method SINDO1. The relevant low‐lying potential energy surfaces, which were calculated with limited configuration interaction (CI), were studied by optimizing intermediates and transition structures and by introducing linear interpolations between these stationary points. The main initial reaction step for all important products is an α cleavage of one CS bond. This leads to an intermediate that can be classified as an excited singlet diradical. Its electronic structure is described with a two‐electron, three‐orbital model. Starting from this initially generated intermediate, the reaction branches into several pathways leading to various products. Feasible reaction pathways were established for all important products consistent with experiments. © 1995 by John Wiley & Sons, Inc.
Fast, fuzzy c‐means clustering of data sets with many features
Authors: Alsberg Bjørn K.
Published: January 2005

A fuzzy c‐means clustering algorithm is presented which is much faster than the traditional algorithm for data sets in which the number of features is significantly larger than the number of feature vectors. The algorithm is constructed by utilizing the covariance structure of feature vectors and cluster centers. By using results from a previous clustering, modified versions of the new algorithm achieve additional reductions in floating point operations. © 1995 by John Wiley & Sons, Inc.
Force and virial of torsional‐angle‐dependent potentials
Authors: Bekker H. , Berendsen H. J. C. , van Gunsteren W. F.
Published: January 2005

Simple expressions for the forces due to dihedral‐angle interactions are derived using first principles of mechanics. The expressions require significantly fewer numerical operations than those generally used in the literature and provide insight into the physics of dihedral‐angle interactions. It is also shown that the scalar virial due to angle‐dependent interactions is zero. © 1995 by John Wiley & Sons, Inc.
An empirical force field. I. Alkanes
Authors: Dillen Jan L. M.
Published: January 2005

A new empirical force field for saturated hydrocarbons is presented. It is applicable to gaseous and crystalline alkanes that do not contain four‐ or three‐membered rings. The force field allows the calculation of structural, thermodynamic, and vibrational properties of both simple and highly strained molecules to an accuracy comparable to experiment. Vibrational frequencies are improved considerably as compared to MM3. © 1995 by John Wiley & Sons, Inc.
Theoretical study of the gas‐phase addition of HF and HCl to ethylene: Analysis of the catalytic action of dimeric halides
Authors: Menéndez M. I. , Suárez D. , Sordo J. A. , Sordo T. L.
Published: January 2005

Ab initioMP2/6‐31G** calculations render the same mechanism for the gas‐phase addition of HF and HCl to ethylene in contrast with previous HF/3‐21G calculations. The leading interaction is in both cases the electrophilic attachment of the hydrogen atom in the hydrogen halide to a carbon atom in ethylene. The presence of a second molecule of hydrogen halide causes a catalytic effect by allowing an alternative mechanism for electron density rearrangement through ethylene polarization. © 1995 by John Wiley & Sons, Inc.
Efficient conformational space sampling for nucleosides using internal coordinate Monte Carlo simulations and a modified furanose description
Authors: Gabb H. A. , Lavery R. , Prévost C.
Published: January 2005

Internal coordinates can be very helpful in modeling large biomacromolecules because freezing stiffer degrees of freedom, such as bond lengths, strongly reduces the number of variables describing the system. This, however, leads to difficulties in treating flexible rings such as the furanose sugars of nucleic acids or the proline residues of proteins, for which internal coordinates are an overcomplete description. We present here a new, internal coordinate furanose model based on the pseudorotational variables phase and amplitude which avoids having to solve a ring closure problem. The choice of a two‐ rather than a four‐variable description is justified by a detailed analysis of molecular dynamic simulations. The efficiency and accuracy of the method are also demonstrated using extensive Monte Carlo simulations. This method of ring treatment is fast and well adapted to macromolecular simulations. © 1995 by John Wiley & Sons, Inc.
Potential energy function for cation–peptide interactions: An ab initio study
Authors: Roux Benoît , Karplus Martin
Published: January 2005

A potential energy function is developed to represent the interaction of small monovalent cations, Li+, Na+, and K+, with the backbone of polypeptides. The results are based on ab initio calculations up to the 6‐31G* level of the interactions of the ions with acetamide and N‐methylacetamide. Basis set superposition errors are corrected with the counterpoise method. A systematic overestimate of the bond polarities is taken into account by an empirical scaling procedure that uses the ratio of the experimental to ab initio dipole moment. The calculated binding energies obtained with this procedure show consistent convergence with different basis sets and are in good agreement with experimental data on cation–water and cation–dimethylformamide systems. Investigations of the calculated ab initio potential energy surface indicate that the cation–peptide interaction is dominated by electrostatics and includes a nonnegligible contribution from polarization of the peptide group by the ion. The induced polarization results in a steeper‐than‐Coulombic interaction and cannot be described by fixed ion–peptide partial charges electrostatics. Atomic polarizabilities located on the atoms of the ligand molecule are introduced to account for the induced polarization in the empirical energy function. A ∼1/r4 attractive interaction appears in the potential function. The resulting radial and angular dependence of the potential energy surface is well reproduced. © 1995 by John Wiley & Sons, Inc.
Dynamic load balancing algorithms for replicated data molecular dynamics
Authors: Young William S. , Brooks Charles L.
Published: January 2005

Algorithms to enhance parallel performance of molecular dynamics simulations on parallel computers by dynamic load balancing are described. Load balancing is achieved by redistribution of work based on either a history of time spent computing per processor or on the number of pair interactions computed per processor. The two algorithms we detail are designed to yield optimal load balancing on both workstation clusters and parallel supercomputers. We illustrate these methods using a small molecular dynamics kernel developed for the simulation of rigid molecular solvents. In addition, we discuss our observation regarding global communications performance on workstation clusters with a fiber distributed data interface (FDDI) using a high‐speed point‐to‐point switch (Gigaswitch) and the k‐ary 3‐cube of the Cray T3D. © 1995 by John Wiley & Sons, Inc.
The electronic structure of weakly bound systems. I. Rare‐gas bimolecular cations
Authors: López Gustavo E.
Published: January 2005

A general perspective is presented of bimolecular positive ions formed from two rare gases that share a positive charge. These species, which are important in ionospheric processes, arise when neutral van der Waals species are ionized. A general theoretical program based on standard theoretical techniques (e.g., various configuration interaction and Møller‐Plesset techniques and quadratic configuration interaction) is outlined, and results for the geometry, stability, and vibrational frequencies for a set of rare gas dimers, AB+, are presented. Specifically, the molecules HeHe+, HeNe+, HeAr+, NeNe+, NeAr+, and ArAr+ are considered; the equilibrium geometry of the ground electronic state is determined at several levels of approximation. Then binding energies are calculated in several ways, and these binding energies are compared to experimental and other sophisticated theoretical results. In general, the agreement with experiment is good, within a few kcal/mol. Harmonic vibrational frequencies at the MP2 level are also computed. © 1995 by John Wiley & Sons, Inc.
Conformational analysis of jet‐cooled tryptophan analogs and Histamine using the MM3(94) force field: Comparison with experiment
Authors: Sulkes Mark
Published: January 2005

MM3(94) has been used to predict the conformers of nitrogen‐containing aromatic heterocycles with polar aliphatic sidechains. Computations were done for cases in which experimental gas‐phase rotational constants have been determined and include histamine and analogs of tryptophan. The agreement with experiment for the tryptophan analogs is better than earlier MM2(87) computations but still not complete. A fairly good match can be made to experimental rotational constants of four histamine conformers, but other conformers are also predicted that may not be important experimentally. A comparison can be made with ab initio calculations undertaken for histamine. Similar structures were generally predicted, but there were significant discrepancies with MM3 in relative conformer energies. © 1995 by John Wiley & Sons, Inc.
A rapid method for calculating derivatives of solvent accessible surface areas of molecules
Authors: Sridharan S. , Nicholls Anthony , Sharp Kim A.
Published: January 2005

A novel method to calculate the derivatives of solvent accessible surface areas is presented. Unlike earlier analytic methods, which require the molecular topology and the use of global Gauss‐Bonnet theorem, this method requires only the fractional accessibilities of surface arcs. We developed an efficient numerical algorithm to calculate the surface arcs by creating a uniform set of points on the circles of intersection between surface atoms. A hierarchical point density doubling scheme led to a logarithmic dependence of Central Processing Unit (CPU) time on the number of points used. This algorithm calculated area derivatives for a 1000‐atom protein in 1.5 s on an SGI INDIGO2 which were within 2% of the analytic area derivatives calculated with the program ANAREA. This algorithm scales linearly with the number of atoms for large molecules and is easily parallelizable. © 1995 by John Wiley & Sons, Inc.
PVM‐AMBER: A parallel implementation of the AMBER molecular mechanics package for workstation clusters
Authors: Swanson Eric , Lybrand Terry P.
Published: January 2005

A 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

The 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

In 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

We 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

Current 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

A 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

A 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

We 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

Molecular 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

A 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

The 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

The 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

Rates 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

The 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

The 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

Several 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

The 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

The 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.
The kinetics of the gas phase intramolecular elimination of isobutene from 2‐d1‐triisobutylaluminum and the deuterium isotope effect in reactions involving cyclic transition states
Authors: Egger Kurt W.
Published: January 2005

The intramolecular elimination of isobutene from 2‐d1‐triisobutylaluminum has been studied in the gas phase for temperatures ranging between 102.4 and 184.6°C. The reaction is apparently homogeneous and obeys the first order rate law, yielding the following Arrhenius relationship:

Excess ethylene was added to the starting material in order to avoid complications from the backreaction. The cyclic 4‐center nature of the transition state proposed earlier has been unequivocally demonstrated by deuterium labelling. Mass‐spectral analyses show that the isobutene formed contains no deuterium. The hydrolyses products of the mixed trialkylaluminum formed during the reaction consist of monodeuteroethane and 2‐d1‐isobutane. The observed negative entropy of activation of ∼12 cal/°‐mole agrees with prediction and implies a reasonably tight transition state structure. Combined with the corresponding data for the non deuterized Al(i‐bu)3 reported earlier, these data result in a primary kinetic deuterium isotope effect of kH/kD = 1.3 × 100.6/θ corresponding to a ratio of the isotopic rate constants of 3.7 at 25°C. This result is in excellent agreement with a predicted value of 1.4 × 100.7/θ and it is in line with literature data on similar reactions involving cyclic transition state complexes.
Chemical kinetics of hydrogen halide lasers. 1. The H2Cl2 system
Authors: Cohen N. , Jacobs T. A. , Emanuel G. , Wilkins R. L.
Published: January 2005

A detailed kinetic model of the HCl chemical laser produced by the flash photolytically initiated H2Cl2 explosion is described, and the results of computer calculations on such a system are discussed. It is shown that currently accepted values of the various rate constants, supplemented in a few cases by reasonable estimates of previously unmeasured rate constants, are adequate to approximate the observed laser behavior of this system. It is also shown that the chemistry of such a system is extremely complex, and exhibits a high degree of coupling between one reaction and another; therefore, great care is required to extract kinetic data from the optical behavior of such laser systems. It is further argued that different hydrogen halide lasers may behave quite differently from each other, depending on the relative magnitudes of the various rate constants involved.
Semi‐empirical potential energy surfaces for hydrogen‐atom transfer reactions
Authors: Salomon Mark
Published: January 2005

A method for constructing potential energy surfaces previously proposed by the author has been extended to hydrogen transfer reactions between halide, oxygen, and carbon atoms. A qualitative relation was found between the repulsive energy and the number of anti‐bonding electrons. In general, the calculated kinetic isotope effect is in satisfactory agreement with observed values and the contributions by H‐atom tunneling to the rate of reaction is smaller than that obtained from other surfaces.
The Kinetics of the gas‐phase isomerization of 1,trans‐3,trans‐5‐heptatriene into the cis‐5‐isomer catalyzed by Nitric Oxide and the stabilization energy in the pentadienyl radical
Authors: Egger Kurt W. , Jola M.
Published: January 2005

The kinetics of the nitric oxide catalyzed, homogeneous, gas‐phase isomerization of 1,trans‐3,trans‐5‐heptatriene have been studied for temperatures ranging between 130°C and 241°C. The very clean reaction involves exclusive geometrical isomerization about the 5,6‐π‐bond. The observed rate constants for \documentclass{article}\pagestyle{empty}\begin{document}$ {\rm NO} + trans - {\rm 3,}trans{\rm - 5}\stackrel{1}{\rightarrow}trans - 3,cis - 5 + {\rm NO} $\end{document} can be represented (with standard errors) by log k1 = (7.18 ± 0.06) – (16.75 ± 0.12)/θ, where θ = 2.303 RT in kcal/mole. The consecutive‐step reaction mechanism involves addition of NO to the double bond (Ka, b = ka/kb), followed by rotation of the 5,6‐CC bond in the adduct radical (kc.)

Analysis of the observed activation parameters shows, that kc is rate‐controlling and consequently k1 = kcKa, b. Estimates of kc and Ka, b lead to a value of k1 in good agreement with experiment.

Comparing our data with those previously obtained for the similar 1,3‐pentadiene system results in a value for the extra stabilization energy generated in the 1,3‐heptadienyl radical of 18.5 ± 1.7 kcal/mole. This value is discussed in view of comparable data in the literature.
Diffusion of a trace gas into a flowing carrier
Authors: Brown Robert L.
Published: January 2005

Numerical Methods were used to solve the differential equation for diffusion of a trace gas into a flowing carrier gas having a parabolic velocity profile in a cylindrical tube. Steady state solutions are given in the form of contour diagrams of constant trace gas concentration.
The reactions of CF3 radicals with cyclanes and the determination of CH bond dissociation energies in cyclanes
Authors: Jones S. H. , Whittle E.
Published: January 2005

The reactions of CF3 radicals with the C3 to C7 cyclanes and spiropentane were studied and the following Arrhenius parameters were obtained for the reaction CF3 + c‐RH → CF3H + c‐R:

c‐RH
log A (cm3mole−1sec−1)
E (kcal/mole)
D(c‐R—H) (kcal/mole)

Cyclopropane
11.54
8.73
100.7

Cyclobutane
11.66
6.48
95.7

Cyclopentane
12.30
6.18
94.3

Cyclohexane
12.12
6.26
94.9

Cycloheptane
12.43
5.89
94.0

Spiropentane
11.91
8.12
98.8

The CF3 radicals were generated by photolysis of hexafluoroacetone or CF3I and a comparison is made of the utility of the two compounds as radical sources. The Arrhenius parameters are compared with those for corresponding reactions of CH3 radicals with cyclanes, and the general reactivity of cyclic compounds toward free radicals is discussed. An Evans‐Polanyi treatment is used to derive CH bond dissociation energies in cyclanes; and these results, based on the reactions of CF3 with cyclanes, agree well with those previously obtained using CH3 plus cyclanes. The final mean values are shown above.
Computer simulation of cage processes and some difficulties with present models
Authors: Walling Cheves , Lepley Arthur R.
Published: January 2005

A simple model involving random displacements of particles in a cubic lattice is used to evaluate the importance of primary and secondary recombination in cage processes and leads to estimates of the lifetime of cage pehnomena. However, it is pointed out that all such models, and treatments which attempt to relate processes at the molecular level with bulk viscosity or diffusion constants, are inherently qualitative since they ignore the important correlation between motions of neighboring molecules.
Rotating sector study of the gas phase photolysis of the carbon tetrachloride–cyclohexane system
Authors: White Merle L. , Kuntz Robert R.
Published: January 2005

The rate constant for the combination of trichloromethyl radicals in the gas phase has been measured by applying the rotating sector technique to the gas phase carbon tetrachloride–cyclohexane photochemical system. A temperature‐independent rate constant, k5, of 3.9 ± 1.0 × 1012 cc mole−1 sec−1 was found. Arrhenius parameters for the reaction

were found to be given by the expression log k4 = 11.79 – (10,700/2.3 RT).
The addition of methyl radicals to hexafluoropropylene
Authors: Thynne J. C. J.
Published: January 2005

The addition of methyl radicals to hexafluoropropylene has been studied over the temperature range 81°–203°C using a mass‐balance technique involving the photolysis of biacetyl in the presence of hexafluoropropylene–isobutane mixtures. For the reaction

the rate constant is given by the equation

The result suggests that methyl radicals are very unselective in their behavior reacting with tetrafluoroethylene and hexafluoropropylene at similar rates. This is in marked contrast to the behavior of oxygen atoms with these olefins.
The arrhenius factors for some six‐center unimolecular reactions
Authors: Blades A. T. , Sandhu H. S.
Published: January 2005

The Pyrolysis of ethyl formate has been carried out in the temperature range 557°–630° and the rate expression k = 1012.34 e−48,100±500/RT sec−1 was obtained, in agreement with the prediction of O'Neal and Benson [1]. Calculated Arrhenius A‐factors and experimental rate constants have been used to obtain the activation energies for the decomposition of the following compounds by the six‐center molecular mechanism (in kcal/mole): 2‐pentanone 59; methoxyacetone, 58; 2,4‐pentanedione, 51; methyl butyrate, ≥ 70; 1‐heptene, 54, and 4‐methyl‐1‐hexene, 54–55.
The photolysis of N2O at 1470 Å
Authors: Dodge Marcia C. , Heicklen Julian
Published: January 2005

The photolysis of pure N2O, N2O and N2, and N2O and C3H6 mixtures at 1470 Å and room temperature has been studied to determine the relative importance of the primary processes. The results are
equation image
where ϕ{O(1D)} = 0.515 represents both the O(1D) produced in the primary act and that produced by collisional quenching of O(1S); ϕ{N2(3Σ)} = 0.084 represents only that portion of N2(3ϕ) which dissociates N2O on deactivation; and ϕ{O(1S)} = 0.38 – ±{N(2D)} represents only that portion of O(1S) which enters into chemical reaction with N2O. If the reaction of O(1S) with N2O yields only N2 and O2 as products, which seems likely from potential‐energy curve considerations then ±{O(1S)} = 0.135 ± 0.06 and ϕ{N(2D)} = 0.245 ± 0.06. Young and coworkers [4] have found from spectroscopic observations that the total quantum yield of O(1S) is about 0.5. Thus it can be concluded that collisional removal of O(1S) by N2O yields mainly O(1D) with chemical reaction being less important. Furthermore, most of the O(1D) is produced this way, and the true primary yield of O(1D) is about 0.15. The metastable N(2D) is not deactivated by N2O, but is removed by chemical reaction to produce N2 and NO. The results further indicate that N2(3Σ) dissociates N2O at least 80% of the time during quenching. The relative efficiency of N2O compared to N2 is about 2 for the removal of O(1D). O(1S) is removed about 90 times as efficiently by C3H6 as by N2O.
Some hydrogen abstraction reactions of the trichloromethyl radical
Authors: Wampler Fred B. , Kuntz Robert R.
Published: January 2005

The gas phase photolysis of CCl4 in the presence of several alkanes has been used to obtain Arrhenius parameters for the abstraction of hydrogen atoms by the CCl3 radical: magnified image The following log k4 values were obtained:

RH
log k4

c‐C5H10,

n‐C6H14

2,3‐Dimethylbutane

c‐C7H14

Methylcyclohexane

c‐C8H16

The results are compared to those for CH3 and CF3 radicals.