bluuebunny/crossref_metadata_2025 huggingface dataset:
Decomposition analyses of the intermolecular interaction energies in two ππ stacking complexes: Quinhydrone and N,N,N′, N′‐tetramethyl‐P‐diaminobenzene‐chloranil complex
Authors: Kurita Yasuyuki , Takayama Chiyozo , Tanaka Shizuya
Published: January 2005

Although there is a similarity in the orbital interaction scheme between quinhydrone and N,N,N′,N′‐tetramethyl‐p‐diaminobenzene‐chloranil complex, the stacking conformations are different from each other. The former prefers the half‐stacked conformation, whereas the latter prefers the completely stacked conformation. We have done ab initio molecular orbital calculations and decomposition analyses of the intermolecular interaction energies to clarify the origin of the different stacking conformations. It was concluded that the main origin is the difference in the steric part of the interaction energies. © 1994 by John Wiley & Sons, Inc.
Conformation energy around the N(sp3)O single bond
Authors: Tronchet Jean M. J. , Komaromi Istvan
Published: January 2005

A detailed conformational analysis was performed on simple substituted hydroxylamines using either ab initio (from HF/6‐31G* to RQCISD/6‐311G**) or popular semiempirical (MNDO, AM1, PM3) methods to ascertain the allowed conformations and to establish the influence of the level of theory on the results. All the ab initio results (provision being made for their expected divergences) are similar and show a simple twofold character for the > NO rotational energy, without any appreciable populations of the cis conformer. On the other hand, the predictive value of the semiempirical methods for structural and energetical parameters of molecules bearing > NO moieties is limited, a situation like that prevailing for peptide bonds. The inversional barriers for the methyl‐substituted hydroxylamines were also calculated and compared to the corresponding rotational energy barriers. Rotation is generally favored over inversion for hydroxylamine and its methylated derivatives. © 1994 by John Wiley & Sons, Inc.
Stable conformations of CH3CH2OCH2CH2OH: A comparison of theoretical methods
Authors: Luke Brian T.
Published: January 2005

This article presents the results of an extensive examination of the stable conformations of CH3CH2OCH2CH2OH at various levels of theory. In particular, 41 initial conformations are optimized using the MM2 force field in BIGSTRN‐3; the MINDO/3, MNDO, and AM1 Hamiltonians in AMPAC 2.2; the PM3 Hamiltonian in MOPAC 7.0; and at the HF/STO‐3G and HF/3‐21G levels using Gaussian 92. The optimized HF/3‐21G structures are reoptimized at the HF/6‐31G(d) level, and the unique structures are optimized again at the MP2 = FULL/6‐31G(d) level. In addition, single‐point MP2/6‐31G(d) calculations are performed using the HF/6‐31G(d) geometries. The goal is to determine the relative accuracy of each method and discuss their strengths and weaknesses. © 1994 by John Wiley & Sons, Inc.
A rapidly convergent simulation method: Mixed Monte Carlo/stochastic dynamics
Authors: Guarnieri Frank , Still W. Clark
Published: January 2005

Although Monte Carlo and molecular dynamics are the primary methods used for free energy simulations of molecular systems, their application to molecules that have multiple conformations separated by energy barriers of ≥ 3 kcal/mol is problematic because of slow rates of convergence. In this article we introduce a hybrid simulation method termed MC‐SD which mixes Monte Carlo (MC) and stochastic dynamics (SD). This new method generates a canonical ensemble via alternating MC and SD steps and combines the local exploration strengths of dynamics with the barrier‐crossing ability of large‐step Monte Carlo. Using calculations on double‐well potentials and long simulations (108 steps of MC and 1 μs of SD) of the simple, conformationally flexible molecule n‐pentane, we find that MC‐SD simulations converage faster than either MC or SD alone and generate ensembles which are equivalent to those created by classical MC or SD. Using pure SD at 300 K, the conformational populations of n‐pentane are shown to be poorly converged even after a full microsecond of simulation. © 1994 by John Wiley & Sons, Inc.
Molecular mechanics calculations (MM2 and MM3) on enamines and aniline derivatives
Authors: Allinger N. L. , Yan Liqun , Chen Kuohsiang
Published: January 2005

The MM2 and MM3 force fields have been extended to cover this class of compounds. Structures, vibrational spectra, and other data for 13 compounds were examined and can be reproduced satisfactorily by MM3. Except for the spectra, the other data can be reproduced somewhat less well by MM2. © 1994 by John Wiley & Sons, Inc.
Atomic radii scales and electron properties deduced from the charge density
Authors: Pacios L. Fernández
Published: January 2005

A procedure to represent Hartree‐Fock electron densities in atoms [L. Fernandez Pacios,J. Comp. Chem.,14, 410 (1993)] defines ρ(r) as a reduced expansion of exponential functions. These analytically modeled densities (AMDs) are used in this article to develop a simple computational procedure for analyzing different atomic radii scales implemented in the commercial software system MATHEMATICA. The analysis is focused on the physical information associated to a given atomic radius as deduced from calculations depending on ρ(r). The amount of electron charge contained in the sphere of the given radius as well as the distinct contributions to the potential energy integrated up to that radius are obtained within the AMD formulation for main‐group atoms H—Kr. The ASCII file needed to run the procedure within MATHEMATICA is also presented. © 1995 by John Wiley & Sons, Inc.
Geometry‐dependent atomic charges: Methodology and application to alkanes, aldehydes, ketones, and amides
Authors: Dinur U. , Hagler A. T.
Published: January 2005

A general methodology for deriving geometry‐dependent atomic charges is presented. The main ingredient of the method is a model that describes the molecular dipole moment in terms of geometry‐dependent point charges. The parameters of the model are determined from ab initio calculations of molecular dipole moments and their Cartesian derivatives at various molecular geometries. Transferability of the parameters is built into the model by fitting ab initio calculations for various molecules simultaneously. The results show that charge flux along the bonds is a major contributing factor to the geometry dependence of the atomic charges, with additional contributions from fluxes along valence angles and adjacent bonds. Torsion flux is found to be smaller in magnitude than the bond and valence angle fluxes but is not always unimportant. A set of electrostatic parameters is presented for alkanes, aldehydes, ketones, and amides. Transferability of these parameters for a host of molecules is established to within 3 −5% error in the predicted dipole moments. A possible extension of the method to include atomic dipoles is outlined. With the inclusion of such atomic dipoles and with the set of transferable point charges and charge flux parameters, it is demonstrated that molecular electrostatic potentials as well as electrostatic forces on nuclei can be reproduced much better than is possible with other models (such as potential derived charges). © 1995 by John Wiley & Sons, Inc.
Poling: Promoting conformational variation
Authors: Smellie Andrew , Teig Steven L. , Towbin Peter
Published: January 2005

This article introduces several methods of assessing the extent to which a collection of conformations represents or covers conformational space. It also describes poling: a novel technique for promoting conformational variation that can be applied to any method of conformational analysis that locally minimizes a penalty or energy function. The function being minimized is modified to force similar conformers away from each other. The method is independent of the origin of the initial conformers and of the particular minimization method used. It is found that, with the modification of the penalty function, clustering of the resulting conformers is generally unnecessary because the conformers are forced to be dissimilar. The functional form of the poling function is presented, and the merits are discussed with reference to (1) efficacy at promoting variation and (2) perturbation of the unmodified function. Results will be presented using conformers obtained from distance geometry with and without poling. It will be shown that the addition of poling eliminates much redundancy in conformer generation and improves the coverage of the conformational space. © 1995 by John Wiley & Sons, Inc.
Parallel implementation of a mesh‐based density functional electronic structure code
Authors: Li Y. S. , Wrinn M. C. , Newsam J. M. , Sears M. P.
Published: January 2005

We describe the implementation of the mesh‐based first‐principles density functional code DMol on nCUBE 2 parallel computers. The numerical mesh nature of DMol makes it naturally suited for a massively parallel computational environment. Our parallelization strategy consists of a domain decomposition of mesh points. This evenly distributes mesh points to all available processors and leads to a substantial computational speedup with limited communication overhead and good node balancing. To achieve better performance and circumvent memory storage limitations, the torus wrap method is used to distribute both the Hamiltonian and overlap matrices, and a parallel matrix diagonalization routine is employed to calculate eigenvalues and eigenvectors. Benchmark calculations on a 128‐node nCUBE 2 are presented. © 1995 by John Wiley & Sons, Inc.
Evaluation of moment statistics for molecular modeling
Authors: Lipkowitz Kenny B. , Peterson Michael A.
Published: January 2005

The concept of moment statistics for evaluating conformations of molecules derived from molecular dynamics simulations is presented. A comparison of the rigidity of tetralin with benzene and cyclohexane, the effect of “tooth thickness” in geared systems, the fluctional motion of a linear alkane, and the differences between dynamical motions of hydrogen‐bonded systems in gas versus solution phases were studied. The strengths and weaknesses of implementing moment statistics as a tool for data reduction are described. © 1995 by John Wiley & Sons, Inc.
Prediction of LUMO energy and rate constant by comparative molecular field analysis (CoMFA)
Authors: Yoo Sung‐Eun , Cha Ok Ja
Published: January 2005

We used the comparative molecular field analysis (CoMFA) method to correlate the rate constant (log k) for the SN2 reaction of benzyl benzenesulfonates and p‐methoxybenzylamines. Molecular fields calculated with a C+ probe produced a good correlation with a small standard deviation and a high correlation coefficient with cross validation. This study demonstrated that CoMFA is an excellent method in predicting the physicochemical properties of the molecule such as LUMO energy and rate constants. © 1995 by John Wiley & Sons, Inc.
Parameterization and evaluation of a flexible water model
Authors: Ferguson David M.
Published: January 2005

The thermodynamic, dielectric, and dynamic properties of a newly parameterized flexible water model are studied using molecular dynamics simulations. The potential function developed is based on the popular simple point charge (SPC) rigid model with the addition of appropriate harmonic and anharmonic energy terms for stretching and bending. Care was taken to account for the self‐polarization and gas‐phase monomer energy corrections during the parameterization, which have typically been ignored in past studies. The results indicate that an increased Lennard‐Jones repulsive coefficient and slightly scaled partial charges are required when adding flexibility to the rigid model potential to reliably reproduce the experimental density, energy, and O ⃛ O radial distribution function of water at 298 K and 1 atm. Analysis of the power spectrum derived from the H‐velocity autocorrelation function allowed the water potential to be evaluated further and refined by adjusting the valence forces to fit the vibrational frequencies of the gas and liquid. Once a consistent set of parameters was determined, the static dielectric properties of the water model were calculated at two temperatures using the reaction field method to treat long‐range forces and correlations. The dielectric constant of 75 ± 7 calculated at 300 K is in good agreement with the experimental value of 78.5. The Kirkwood g factor was also examined for temperature dependence and showed the correct increasing behavior with decreasing T. As a final check of the water potential, the free energies of solvation of a flexible water molecule and neon were predicted using thermodynamic perturbation methods. The calculated solvation energies of −7.0 ± 0.8 for water and 2.7 ± 0.7 for neon are both consistent with the experimental values of −6.3 and 2.7 kcal/mol. Comparisons are made throughout the study with the results of previous rigid and flexible model simulations. © 1995 by John Wiley & Sons, Inc.
The true diatomic potential as a perturbed Morse function
Authors: Dagher Mounzer , Kobersi Mounif , Kobeissi Hafez
Published: January 2005

The problem of representing a diatomic (true) Rydberg‐Klein‐Rees potential Ut by an analytical function Ua is discussed. The perturbed Morse function is in the form Ua = UM + ∑bnyn, where the Morse potential is UM = Dy2, y = 1 −exp(−;a(r − re)). The problem is reduced to determination of the coefficients bn so Ua(r) = Ut(r). A standard least‐squares method is used, where the number N of bn is given and the average discrepancy ΔU = |(Ut − Ua)/Ut| is observed over the useful range of r. N is varied until ΔU is stable. A numerical application to the carbon monoxide X1∑ state is presented and compared to the results of Huffaker1 using the same function with N = 9. The comparison shows that the accuracy obtained by Huffaker is reached in one model with N = 5 only and that the best ΔU is obtained for N = 7 with a gain in accuracy. Computation of the vibrational energy Ev and the rotational constant Bv, for both potentials, shows that the present method gives values of ΔE and ΔB that are smaller than those found by Huffaker. The dissociation energy obtained here is 2.3% from the experimental value, which is an improvement over Huffaker's results. Applications to other molecules and other states show similar results. © 1995 by John Wiley & Sons, Inc.
An analytical algorithm for the rapid determination of the solvent accessibility of points in a three‐dimensional lattice around a solute molecule
Authors: You Tony , Bashford Donald
Published: January 2005

We address the problem of marking points on a grid lattice of arbitrary size and spacing as either accessible or inaccessible to a solvent‐sized spherical probe. It is shown that an analytical description of the solvent‐accessible volume suitable for rapidly testing a large number of lattice points can be constructed from relatively simple geometric elements. By first constructing these basic analytical elements and storing them in suitable data structures, any number of subsequent lattice markings can be carried out. This approach leads to increased computational efficiency whenever a multiple calculation using different lattice sizes and scales is necessary on the same molecular geometry. We also present an algorithm for determining the analytical volume elements. Some aspects of this algorithm, particularly the method for finding all sterically allowed probe positions in which the probe simultaneously contacts three atoms, may also be useful for improving the speed and reliability of analytical surface area calculations. An object‐oriented implementation of these algorithms written in C + + is freely available via Internet. © 1995 by John Wiley & Sons, Inc.
The fast multipole boundary element method for molecular electrostatics: An optimal approach for large systems
Authors: Bharadwaj Ranganathan , Windemuth Andreas , Sridharan S. , Honig Barry , Nicholls Anthony
Published: January 2005

We propose a fast implementation of the boundary element method for solving the Poisson equation, which approximately determines the electrostatic field around solvated molecules of arbitrary shape. The method presented uses computational resources of order O(N) only, where N is the number of elements representing the dielectric boundary at the molecular surface. The method is based on the Fast Multipole Algorithm by Rokhlin and Greengard, which is used to calculate the Coulombic interaction between surface elements in linear time. We calculate the solvation energies of a sphere, a small polar molecule, and a moderately sized protein. The values obtained by the boundary element method agree well with results from finite difference calculations and show a higher degree of consistency due to the absence of grid dependencies. The boundary element method can be taken to a much higher accuracy than is possible with finite difference methods and can therefore be used to verify their validity. © 1995 by John Wiley & Sons, Inc.
Molecular dynamics simulation with a continuum electrostatic model of the solvent
Authors: Gilson Michael K. , McCammon J. Andrew , Madura Jeffry D.
Published: January 2005

The accuracy and simplicity of the Poisson‐Boltzmann electrostatics model has led to the suggestion that it might offer an efficient solvent model for use in molecular mechanics calculations on biomolecules. We report a successful merger of the Poisson‐Boltzmann and molecular dynamics approaches, with illustrative calculations on the small solutes dichloroethane and alanine dipeptide. The algorithm is implemented within the program UHBD. Computational efficiency is achieved by the use of rather coarse finite difference grids to solve the Poisson‐Boltzmann equation. Nonetheless, the conformational distributions generated by the new method agree well with reference distributions obtained as Boltzmann distributions from energies computed with fine finite difference grids. The conformational distributions also agree well with the results of experimental measurements and conformational analyses using more detailed solvent models. We project that when multigrid methods are used to solve the finite difference problem and the algorithm is implemented on a vector supercomputer, the computation of solvent electrostatic forces for a protein of modest size will add only about 0.1 s computer time per simulation step relative to a vacuum calculation. © 1995 by John Wiley & Sons, Inc.
Internal motions of carbohydrates as probed by comparative molecular modeling and nuclear magnetic resonance of ethyl β‐lactoside
Authors: Engelsen Søren Balling , Pérez Serge , Braccini Isabelle , Du Penhoat Catherine Hervé
Published: January 2005

The realization that conformational flexibility must be incorporated into the description of the structural and dynamical behavior of carbohydrates has stimulated the quest for an appropriate force field and associated parameterization capable of dealing with the many specific features of these molecules. Accordingly, we set out to evaluate the capacity of very different force fields to reproduce a series of experimental spectral data such as optical rotatory dispersion, coupling constants, and nuclear Overhauser effects. NOESY volumes and long‐range homonuclear and heteronuclear vicinal coupling constants were measured at 400.13 MHz. Optical rotation measurements were also performed on ethyl β‐lactoside. The conformational behavior of ethyl β‐lactoside was investigated in three different molecular mechanics force fields leading to three complete ensembles of theoretical conformations, which were used for evaluating these statistically averaged observables. The calculations of optical rotation followed a recent model based on interacting oscillators. Coupling constants were calculated using the appropriate sets of Karplus‐type equations, and theoretical nuclear magnetic resonance (NMR) relaxation data were obtained for models which account for either slow or fast internal motions. The calculated potential energy surfaces were shown to be dependent on the type of force field, even in the case of such a simple disaccharide. They differ in several respects, including the number and location of low‐energy conformers and the shallowness of the dominant primary region. It was possible to assess the different time‐averaged orientations about the glycosidic linkage of the three force fields from the fit obtained for the interglycosidic heteronuclear coupling constants. Poor fits between theoretical and experimental NOESY volumes were observed for all three force fields when the slow internal motion model was used, while a greatly improved fit was obtained when the fast internal motions model was applied. It has been shown that the motional model established from NOESY data is analogous to the one obtained from molecular dynamics simulations. The quality of the fit for the NOESY data varies with the force fields and corroborates the classification obtained from heteronuclear coupling. © 1995 by John Wiley & Sons, Inc.
IMOMM: A new integrated ab initio + molecular mechanics geometry optimization scheme of equilibrium structures and transition states
Authors: Maseras Feliu , Morokuma Keiji
Published: January 2005

A new computational scheme integrating ab initio and molecular mechanics descriptions in different parts of the same molecule is presented. In contrast with previous approaches, this method is especially designed to allow the introduction of molecular mechanics corrections in full geometry optimizations concerning problems usually studied through ab initio calculations on model systems. The scheme proposed in this article intends to solve some of the systematic error associated with modeling through the use of molecular mechanics corrections. This method, which does not require any new parameter, evaluates explicitly the energy derivatives with respect to geometrical parameters and therefore has a straightforward application to geometry optimization. Examples of its performance on two simple cases are provided: the equilibrium geometry of cyclopropene and the energy barriers on SN2 reactions of alkyl chloride systems. Results are in satisfactory agreement with those of full ab initio calculations in both cases. © 1995 by John Wiley & Sons, Inc.
Flexible ligand docking without parameter adjustment across four ligand–receptor complexes
Authors: Clark Kevin P. , Ajay
Published: January 2005

Understanding molecular recognition is one of the fundamental problems in molecular biology. Computationally, molecular recognition is formulated as a docking problem. Ideally, a molecular docking algorithm should be computationally efficient, provide reasonably thorough search of conformational space, obtain solutions with reasonable consistency, and not require parameter adjustments. With these goals in mind, we developed DIVALI (Docking wIth eVolutionary AlgorIthms), a program which efficiently and reliably searches for the possible binding modes of a ligand within a fixed receptor. We use an AMBER‐type potential function and search for good ligand conformations using a genetic algorithm (GA). We apply our system to study the docking of both rigid and flexible ligands in four different complexes. Our results indicate that it is possible to find diverse binding modes, including structures like the crystal structure, all with comparable potential function values. To achieve this, certain modifications to the standard GA recipe are essential. © 1995 John Wiley & Sons, Inc.
Ab initio calculations of the ultraviolet resonance Raman spectra of uracil
Authors: Peticolas Warner L. , Rush Thomas
Published: January 2005

An equation been derived to calculate, ab initio, the frequencies and intensities of a resonant Raman spectrum from the transform theory of resonance Raman scattering. This equation has been used to calculate the intensities of the ultraviolet resonance Raman spectra from the first π‐π* excited state of uracil and 1,3‐dideuterouracil. The protocol for this calculation is as follows: (1) The force constant matrix elements in Cartesian coordinate space, the vibrational frequencies, and the minimum energy ground and excited state geometries of the molecule are calculated ab initio using the molecular orbital program Gaussian 92, (2) the force constants in Cartesian coordinates are transformed into force constants in the space of a set of 3N – 6 nonredundant symmetrized internal coordinates, (3) the G matrix is constructed from the energy minimized ground state Cartesian coordinates and the GFL = LΛ eigenvalue equation is solved in internal coordinate space, (4) the elements of the L and L−1 matrices are calculated, (5) the changes in all of the internal coordinates in going from the ground to the excited state are calculated, and (6) these results are used in combination with the transform theory of resonance Raman scattering to calculate the relative intensities of each of the 3N – 6 vibrations as a function of the exciting laser frequency. There are no adjustable parameters in this calculation, which reproduces the experimental frequencies and intensities with remarkable fidelity. This indicates that the Dushinsky rotation of the modes in the excited state of these molecules is not important and that the simplest form of the transform theory is adequate. © 1995 John Wiley & Sons, Inc.
Reduced variable molecular dynamics
Authors: Turner James , Weiner Paul , Robson Barry , Venugopal Ravi , Schubele Harry , Singh Ramen
Published: January 2005

This article describes an extension to previously developed constraint techniques. These enhanced constraint methods will enable the study of large computational chemistry problems that cannot be easily handled with current constrained molecular dynamics (MD) methods. These methods are based on an O(N) solution to the constrained equations of motion. The benefits of this approach are that (1) the system constraints are solved exactly at each time step, (2) the solution algorithm is noniterative, (3) the algorithm is recursive and scales as O(N), (4) the algorithm is numerically stable, (5) the algorithm is highly amenable to parallel processing, and (6) potentially greater integration step sizes are possible. It is anticipated that application of this methodology will provide a 10‐ to 100‐improvement in the speed of a large molecular trajectory as compared with the time required to run a conventional atomistic unconstrained simulation. It is, therefore, anticipated that this methodology will provide an enabling capacity for pursuing the drug discovery process for large molecular systems. © 1995 John Wiley & Sons, Inc.
Incorporating the protein – dipole Langevin – dipole model into Tanford‐Kirkwood theory
Authors: Zhexin Xiang , Fuhua Huang , Yunyu Shi , Yinwu Xu
Published: January 2005

A new technique incorporating the protein–dipole Langevin–dipole (PDLD) model into the Tanford‐Kirkwood (TK) formula has been proposed which provides a rather detailed description of solvent and ionic strength effects on the electrostatic energies. Applications of this method to realistic problems have been performed and concern the solvation energies of four residues of bovine pancreatic trypsin inhibitor (BPTI) and the pK shift of His‐64 of mutant subtilisin BPN′. We focus our calculation on the back‐field effects of bulk solvent.

The determination of protein‐induced dipoles is cumbersome due to the solvent screening effects. The protein‐induced dipoles are dependent on their local electric fields, which come from the protein net charges, the surrounding water molecules, and bulk solvent. The bulk solvent will usually screen the electric fields from the protein net charges and dipoles, which are defined here as the back‐field effects of bulk solvent on protein net charges and dipoles, respectively.

Our calculations indicate that the back‐field effects of bulk solvent on protein dipoles can simply be ignored, introducing a relative error less than 3%; whereas such back field‐effects on protein net charges are relatively important and cannot simply be ignored, especially when considering a system of highly charged species. © 1995 John Wiley & Sons, Inc.
Iodine monochloride as a thermal source of chlorine atoms: The reaction of chlorine atoms with hydrogen
Authors: Benson S. W. , Cruickshank F. R. , Shaw R.
Published: January 2005

The use of iodine monochloride (ICl) as a thermal source of chlorine atoms in known concentration is discussed with particular reference to the suppression, by large excesses of iodine, of the chain processes normally associated with chlorine atom reactions. The kinetics and mechanism of the reaction of ICl with hydrogen are presented in a study covering the temperature range 205–337°C, and the pressure ranges: ICl, 6–20 torr; I2, 3–13 torr; and H2, 9–520 torr. The reaction, followed spectrophotometrically in a static system, is shown to be homogeneous, first order in ICl and in H2, and inverse half‐order in I2, over several half‐lifetimes of the ICl, yielding HCl as the sole product. The rate data obtained in this work for the reaction
equation image
are combined with the critically evaluated results of other workers in an Arrhenius plot covering the temperature range 286–730°C, and three orders‐of‐magnitude in the rate constant, yielding the results, log k1/(1/mole sec) = 10.68–5.26/θ, where θ = 2.303RT in kcal/mole. This value of k1 is lower by a factor of about two than that proposed in a recent review by Fettis and Knox, and is clearly at variance by a factor of two or more with the most recent data of Clyne and Stedman.
Cleavage of vinylic mercuric halides by aqueous acids
Authors: Kreevoy Maurice M. , Landholm Richard A.
Published: January 2005

Isotope effects, general acid catalysis, and relative reactivities show that proton transfer to one of the unsaturated carbon atoms is rate determining for the acidolysis of unsaturated alkylmercuric halides. For compounds, R1R2CCHHgX, substitution of CH3 for H at R1 or R2 leads to an acceleration of a factor of ∼ 30. This relatively small acceleration, the relative facility of the reactions, and the magnitude of the Br− catalytic terms, suggests an olefin–mercuric halide complex as the product of the rate‐determining step, rather than a simple carbonium ion.

The Brøonsted catalysis law is obeyed with a variety of carboxylic acids, giving an ∝ of 0.69 ± 0.04, but acids of other structures give substantially deviant catalytic coefficients, in a pattern similar to that generated by other A‐SE2 reactions. The acetic acid catalytic coefficient is larger by a factor of 102 than that predicted if it were due to specific hydronium ion–general base catalysis instead of true general acid catalysis.

The overall solvent isotope effect, kH/kD, is 2.55 ± 0.10. The competitive isotope effect, κH/κD, is 6.84 ± 0.06. Taken with a model in which the proton is transferred directly from the H3O+ unit of the aquated proton to the substrate, these are sufficient to successfully predict the rate at all intermediate isotopic compositions.
Entropies and heat capacities of free radicals
Authors: O'Neal H. E. , Benson S. W.
Published: January 2005

Methods are presented for rapidly estimating the entropies and heat capacities of free radicals from the known S0 and C of structurally similar compounds. The methods consist of estimating the differences due to changes in mass, vibration frequencies, spin, symmetry, and changes in rotational barriers. Tables of contributions to S0 and C by different frequencies over the temperature range 300–1500°K are presented to facilitate the tabulation of the above differences. Conjugated radicals, such as benzyl and allyl, are included. It is shown that the greatest uncertainties in the estimates arise from uncertainties in the barriers to rotation in the radicals.

The results are applied to kinetic data on the pyrolysis of branched hydrocarbons and the reverse reactions of radical recombination. Major discrepancies exist in these data which can be nearly reconciled by postulating improbably high rotational barriers of 8 kcal for CH3 rotation in isopropyl and t‐butyl radicals.

It is shown that radical thermochemistry can be fitted into group schemes and tables of groups values are given for the rapid estimation of ΔH, S0, and C for different organic radicals, including those containing sulfur, oxygen, and nitrogen.
The addition of methyl radicals to tetrafluoroethylene
Authors: Sangster J. M. , Thynne J. C. J.
Published: January 2005

The addition of methyl radicals to tetrafluoroethylene in the gas phase has been studied over the temperature range 80–180°C, using a material balance method.

Arrhenius parameters of 1011.95±0.23 (mole−1 cm3 sec−1) and 5.7 ± 0.4 (kcal/mole) have been measured for the addition reaction.

Electrophilic reagents such as O or CF3 appear to react almost equally readily with ethylene and tetrafluoroethylene but methyl radicals add much more rapidly to tetrafluoroethylene than to ethylene, the difference in reactivity being principally due to an activation energy difference of ∼2 kcal/mole.
Kinetic study of the gas‐phase reaction c‐C5H10 + I2 ⇄ c‐C5H8 + 2HI the heat of formation of cyclopentyl radical
Authors: Furuyama Shozo , Golden David M. , Benson Sidney W.
Published: January 2005

The kinetics of the gas‐phase dehydrogenation of cyclopentane to cyclopentene is found to be consistent with a slow attack by an I atom (step 4, text) on cyclopentane in the range 282–382°C. The measured rate constants fit the Arrhenius equation, log k4 = 11.95 ± 0.08 – (24.9 ± 0.23)/θ 1 mole−1 sec−1, where θ = 2.303RT in kcal/mole. This leads to a value of ΔH magnified image = 24.3 ± 1 kcal/mole and a bond dissociation energy DHmagnified image = 94.9 ± 1 kcal/mole. The latter value is identical with DH0(i‐Pr‐H) = 95 ± 1 kcal/mole and signifies that cyclopentane and the cyclopentyl radical have the same strain energy. Arrhenius parameters are deduced for all six steps in the reaction mechanism. Surface reactions are shown to be unimportant.

Cyclopentyl iodide is an unstable intermediate in the reaction and the rate constant for its bimolecular formation from HI + cyclopentene is found to be log k6 = 8.40 ± 0.29 ‐ (26.9 ± 0.8)/θ 1 mole−1 sec−1. Together with the equilibrium constant, this yields for the unimolecular elimination of HI from cyclopentyl iodide, the rate constant, log k5 = 13.3 ± 0.3 – (42.8 ± 1.2)/θ sec−1.
Pyrolysis of 1,2‐dichloropropane
Authors: Martens G. J. , Godfroid M. , Ramoisy L.
Published: January 2005

The thermal decomposition of 1,2‐dichloropropane at atmospheric pressure has been studied in the temperature range 227–590°C, in a flow system. Above 450°C, the reaction is homogenous and unimolecular with a rate constant:

Below 450°C, a low activation energy, probably heterogenous process competes with the gas phase reaction

The primary reaction products are HCl and the monochloropropene isomers; the relative amounts of each isomer depend on the temperature in the low but not in the high temperature region. The direction of the HCl elimination is discussed in terms of substituent effects at the α‐ and β‐carbon positions and compared with literature data on similar reactions

Secondary products are formed principally by further pyrolysis of allyl chloride. The first‐order rate constant of this reaction is given by:

.
A simple, self‐consistent electrostatic model for quantitative prediction of the activation energies of four‐center reactions. II.*
Authors: Haugen G. R. , Benson S. W.
Published: January 2005

A simple electrostatic model of point dipoles is used which permits direct calculation of the activation energies for the addition of the molecules H2O, H2S, H3N, and H3P to olefins. These calculated values agree with the known experimental data to within ±2 kcal/mole on the average. It was found that the best fit could be obtained with a polar transition state that corresponded to a reduction in bond order from 1 to ½ for the bond‐breaking coordinates and an increase in bond order from 0 to 0.18 for the bond‐forming coordinates. The replacement of a hydrogen atom of the species H2O, H2S, H3N, or H3P by a polarizable methyl group is expected to stabilize the charge on the central atoms. The following stabilization energies for the pairs H2OCH3OH, H2SCH3SH, H3NCH3NH2, H3PCH3PH2 were calculated: −4.8 kcal/mole, −0.7 kcal/mole, −1.9 kcal/mole, −0.8 kcal/mole, respectively.
A thermochemical and kinetic analysis of the mechanisms of pyrolysis of polycyclic molecules
Authors: O'Neal H. E. , Benson Sidney W.
Published: January 2005

The quantitative kinetics of pyrolysis of some cyclic and polycyclic compounds are examined from the point of view of biradical intermediates. Transition state methods for estimating the Arrhenius parameters of the lowest free energy biradical pathway to products in cyclic and polycyclic compound reactions are described and illustrated. A large number of the polycyclic reactions are found to have Arrhenius parameters consistent with the biradical mechanism estimates. Other reactions are found to have much faster experimental rates and must therefore be concerted. The value of activation energy and activation entropy estimates as discriminatory tests of mechanism, i.e., single step (concertedness) or consecutive step processes, is discussed.
The reaction of the hydroxyl radical with acetylene
Authors: Breen J. E. , Glass G. P.
Published: January 2005

The reaction of OH with acetylene was studied in a discharge flow system at room temperature. OH was generated by the reaction of atomic hydrogen with NO2and was monitored throughout the reaction using ESR spectroscopy. Mass‐spectrometric analysis of the reaction products yielded the following results: (1) less than 3 molecules of OH were consumed, and less than 2 molecules of H2O were formed for every molecule of acetylene that reacted; (2) CO was identified as the major carbon‐containing product; (3) NO, formed in the generation of OH, reacted with a reaction intermediate to give among other products N2O. These observations placed severe limitations on the choice of a reaction mechanism. A mechanism containing the reaction OH + C2H2→ HC2O + H2better accounted for the experimental results than one involving the abstraction reaction OH + C2H2→ C2H + H2O. The rate constant for the initial reaction was measured as 1.9 ± 0.6 × 10−13cm3molecule−1sec−1.
Orientation of addition of hydrogen atoms to propylene, butene‐1, and isobutene
Authors: Falconer W. E. , Sunder W. A.
Published: January 2005

The orientation of addition of H atoms to the asymmetric olefins propylene, butene‐1, and isobutene has been determined as a function of atom concentration, olefin concentration, hydrogen pressure, total pressure, and olefin conversion. Conditions have been determined for which complicating secondary processes are believed to be unimportant. The percentage of nonterminal addition is 5.7, 5.7, and 0.48 for propylene, butene‐1, and isobutene, respectively. From these data activation energy differences between nonterminal and terminal addition of 1.7 and 3.2 kcal/mole for the linear olefins and isobutene, respectively, may be calculated. For D atom addition to propylene, a small isotope effect was observed, nonterminal addition being 5.4%. These observations are consistent with a predominantly free radical or electroneutral character for H atoms.
A kinetic study of the thermal elimination of hydrogen fluoride from 1,2‐difluoroethane. Determination of the bond dissociation energies D(CH2FCH2F) and D(CH2FH).
Authors: Kerr J. A. , Timlin D. M.
Published: January 2005

The kinetics of the thermal elimination of HF from 1,2‐difluoroethane

have been studied in a static system over the temperature range 734–820°K. The reaction was shown to be first order and homogeneous, with a rate constant of

where θ = 2.303RT in kcal/mole. The A‐factor falls within the normal range for such reactions and is in line with transition state theory; the activation energy is similarly consistent with an estimate based on data for the analogous reactions of ethyl fluoride and other alkyl halides. The above activation energy has been compared with values of the critical energy calculated from data on the decomposition of chemically activated 1,2‐difluoroethane by the RRKM theory and the bond dissociation energy, D(CH2FCH2F) = 88 ± 2 kcal/mole, derived. It follows from thermochemistry that ΔHf0(CH2F) = ‐7.8 and D(CH2FH) = 101 ± 2 kcal/mole. Bond dissociation energies in fluoromethanes and fluoroethanes are discussed.
Iron (II) and iron (III) isotope exchange in water–dimethyl sulfoxide mixtures
Authors: Henry Marian S. , Reynolds Warren L.
Published: January 2005

The rate of the isotope exchange reaction between iron(II) and iron(III) perchlorates has been measured in a solvent mixture containing a 3:2 mole ratio of water to dimethyl sulfoxide over the temperature range from 25° to −98°C. In this temperature range, the reactants can diffuse together faster than they can undergo isotope exchange. The activation enthalpy and entropy for the acid‐independent reaction were 6.0 ± 1.2 kcal/mole and −38 ± 17 cal/deg mole, respectively. Below −22°C, the acid‐dependent exchange reaction did not contribute significantly to the exchange. In liquid media at −112° and −117°C and in a solid glass at −136°C, no isotope exchange was observed over the period of a calculated half‐life for the reaction. At these temperatures, the rate at which the reactants diffuse together is slower than the calculated rate of isotope exchange. In a solid glass at −196°C, no isotope exchange was observed over the period of one week.
A study of the intersystem crossing reaction induced in gaseous sulfur dioxide molecules by collisions with nitrogen and cyclohexane at 27°C
Authors: Horowitz Abraham , Calvert Jack G.
Published: January 2005

The quantum yields of the sulfur dioxide triplet (3SO2)‐sensitized phosphorescence of biacetyl (Φsens) were determined in experiments with N2–SO2–Ac2 and c‐C6H12–SO2–Ac2 mixtures excited at 2875 Å at 27°C. The fraction of the biacetyl triplets which reacts homogeneously by radiative or nonradiative decay reactions was determined in a series of runs at constant [SO2]/[M] and [SO2]/[Ac2] ratios but at varied total pressure. A kinetic treatment of the Φsens results and singlet sulfur dioxide (1SO2) quenching rate constant data gave the following new kinetic estimates: 1SO2 + M → (SO2–M) (1b) 1SO2 + M → 3SO2 + M (2b); for 1SO2–N2 collisions, k2b/(k1b + k2b) = 0.033 ± 0.008; for 1SO2–c‐C6H12 collisions, k2b/(k1b ± k2b) = 0.073 ± 0.024; previous studies have shown this ratio to be 0.095 ± 0.005 for 1SO2–SO2 collisions. It was concluded that the inter‐system crossing ratio in 1SO2 induced by collision is relatively insensitive to the nature of the collision partner M. However, the individual rate constants for the collision‐induced spin inversion of 1SO2 (k2b) and the total 1SO2‐quenching constants (k1b + k2b) are quite sensitive to the nature of M: k2b/k2a varies from 0.10 ± 0.03 for M = N2 to 1.11 ± 0.37 for M = c‐C6H12, and (k1b + k2b)/(k1a + k2a) varies from 0.29 for M = N2 to 1.44 for M = c‐C6H12; k1a and k1b are the rate constants for the reactions 1SO2 ‐ SO2 → (2SO2) (1a) and 1SO2 + SO2 → 3SO2 + SO2 (2a), respectively.
A comparative kinetic study of the N‐Nitrosation of sulfanilamide by cyclohexyl nitrite and by nitrous acid
Authors: Shenton A. J. , Johnson R. M.
Published: January 2005

A comparative study of the kinetics of the N‐nitrosation of sulfanilamide by cyclohexyl nitrite and by nitrous acid has been made, using an automated technique. The results indicate that a common nitrosating species is effective in analogous reactions involving cyclohexyl nitrite or nitrous acid. The N‐nitrosation reaction has been followed spectrophotometrically by coupling the diazotized product with 1‐naphthol. Under certain conditions a competitive reaction takes place in which coupling occurs with unreacted sulfanilamide.
The reaction of C2F5 radicals with H2S
Authors: Bassett J. E. , Whittle E.
Published: January 2005

The reaction of C2F5 radicals with H2S

was studied over the range 1°−123°C using C2F5 radicals generated by photolysis of perfluoropropionic anhydride. The rate constant kH for reaction (2) is given by

where θ = 2.303RT/cal mole−1. The relevance of this result to conflicting published data on the analogous reaction between CF3 radicals and H2S is discussed. It is concluded that there is little difference in the Arrhenius parameters for reaction of CF3 and C2F5 radicals with H2S.
The radiolysis of mixtures of carbon dioxide and hydrogen
Authors: Beattie W. H.
Published: January 2005

The self‐radiolysis of CO2 in excess tritium (3H2) has been studied at pressures of 0.1 to 1.0 atm, temperatures of −80° to +100°C, and in the presence of added H2O, He, or Ar. The primary products of decomposition are CO and 3H2O. Secondary products are C3H4, C23H4, and a white polymer. The rates of disappearance of CO2 and formation of products and G‐;values were measured. The disappearance of CO2 initially obeys first‐order kinetics, then slows down with time at a rate depending upon the initial pressure of 3H2. The initial rates are proportional to pressures of CO2 and 3H2. They are independent of temperature, decreased by addition of H2O vapor, and increased by addition of He or Ar. The proposed mechanism of decomposition of CO2 and formation of products involves ionization of CO2 followed by dissociative recombination forming CO and O. Then the O reacts with a hydrogen‐containing species forming OH and H2O, and a back reaction forms CO2 from CO and OH.
The reaction of OH with NO2 and the deactivation of O(1D) by CO
Authors: Simonaitis R. , Heicklen Julian
Published: January 2005

NO2 was photolyzed with 2288 Å radiation at 300° and 423°K in the presence of H2O, CO, and in some cases excess He. The photolysis produces O(1D) atoms which react with H2O to give HO radicals

or are deactivated by CO to O(3P) atoms

The ratio k5/k3 is temperature dependent, being 0.33 at 300°K and 0.60 at 423°K. From these two points, the Arrhenius expression is estimated to be k5/k3 = 2.6 exp(−1200/RT) where R is in cal/mole – °K. The OH radical is either removed by NO2

or reacts with CO

The ratio k2/kα is 0.019 at 300°K and 0.027 at 423°K, and the ratio k2/k0 is 1.65 × 10−5M at 300°K and 2.84 × 10−5M at 423°K, with H2O as the chaperone gas, where kα = k1 in the high‐pressure limit and k0[M] = k1 in the low‐pressure limit. When combined with the value of k2 = 4.2 × 108 exp(−1100/RT) M−1sec−1, kα = 6.3 × 109 exp (−340/RT)M−1sec−1 and k0 = 4.0 × 1012M−2sec−1, independent of temperature for H2O as the chaperone gas. He is about 1/8 as efficient as H2O.
Kinetics of the reactions of singlet molecular oxygen (O21Δg) with organic compounds in the gas phase
Authors: Huie Robert E. , Herron John T.
Published: January 2005

The reactions of singlet molecular oxygen (O21Δg) with a series of organic compounds have been studied in the gas phase at 298°K. The concentration of singlet molecular oxygen was determined by titration with 2,5‐dimethylfuran. The titration technique was checked using a photoionization technique. Absolute rate constants were measured on the basis of the loss of organic reactant and, in some cases, of singlet molecular oxygen. It was found that the usual method of producing singlet molecular oxygen in the gas phase can also, under some conditions, allow reactive species other than singlet molecular oxygen to enter the reactor, leading to serious errors in the determination of rate constants. This problem was eliminated by carrying out the rate measurements in the presence of a small amount of nitrogen dioxide a radical scavenger.
Kinetics of the gas‐phase reaction of allyl alcohol with iodine. The heat of formation and stabilization energy of the hydroxyallyl radical
Authors: Alfassi Ze'ev B. , Golden David M.
Published: January 2005

The reaction of iodine with allyl alcohol has been studied in a static system, following the absorption of visible light by iodine, in the temperature range 150‐190°C and in the pressure range 10‐200 torr. The rate‐determining step has been found to be
equation image
and k3 is consistent with the equation
equation image
From the activation energy and the assumption E‐3 = 1 ± 1 kcal mol−1, it has been calculated that
equation image
kcal mol−1. The stabilization energy of the hydroxyallyl radical has been found to be 11.4 ± 2.2 kcal mol−1.