bluuebunny/crossref_metadata_2025 huggingface dataset:
On the evaluation of the solvent polarization apparent charges in the polarizable continuum model: A new formulation
Authors: Coitiño Elena L. , Tomasi Jacopo , Cammi Roberto
Published: January 2005

A new formulation (CLS‐PCM) for the calculation of the apparent surface charges in the framework of the ab initio polarizable continuum model of the solvent (PCM) is introduced. Its performance is compared with that of the original iterative version (ITER‐PCM) of the method as well as with a matricial alternative formulation (matrix‐BEM‐PCM) of the same problem. Both CLS‐PCM and matrix‐BEM‐PCM have shown to be computationally more efficient than ITER‐PCM without presenting any problems associated with the convergence of the process. Although for small and medium‐size solutes the use of matrix‐BEM‐PCM is recommended, for neutral solutes of larger size the use of CLS2 becomes computationally more convenient. Finally, for very large‐size systems, compromise between matrix storage requirements, time of calculation, and exactness of the results may make preferable the use of the more approximate CLS1 formalism, possibly in conjunction with semiempirical or semiclassical descriptions of the solute. © 1995 by John Wiley & Sons, Inc.
A vibrational molecular force field of model compounds with biological interest. IV. Parameters for the different glycosidic linkages of oligosaccharides
Authors: Dauchez Manuel , Derreumaux Philippe , Lagant Philippe , Vergoten Gérard
Published: January 2005

The force field previously obtained for both anomers of glucose has been applied to six disaccharides that are molecules of D‐glucopyranosyl residues. These six disaccharides have different types of glycosidic linkages—that is, α, α trehalose dihydrate (1‐1), sophorose monohydrate (β, 1‐2), laminarabiose (β, 1‐3), maltose monohydrate (α, 1‐4) and cellobiose (β, 1‐4), and gentiobiose (β, 1‐6). From a careful analysis of the infrared and Raman spectra and from harmonic dynamics calculations in the crystalline state, the results show the reliability and the transferability of the set of parameters previously obtained for different carbohydrates. Below 1500 cm−1, observed data and the corresponding calculated frequencies agreed within 5 cm−1 for each of the six disaccharides. The vibrational density of states are well reproduced by these calculations for each molecule, particularly for the fingerprint regions. Moreover, as found by other workers who used sophisticated potential energy functions, no additional terms are needed to express the exoanomeric effect. Specific force constants characteristic of each glycosidic linkage have been derived, particularly for the glycosidic angle bending. More interesting are the values of the internal rotation barriers. It is shown that they are of the same size for both sides of the glycosidic linkage: VC1O1 = VO1Cx′ = 3.29 kcal/mol for an alpha residue and 2.64 kcal/mol for a beta unit (x = 1–6 depends on the position of the glycosidic linkages of the considered disaccharide). © 1995 by John Wiley & Sons, Inc.
Generalized alteration of structure and parameters: A new method for free‐energy perturbations in systems containing flexible degrees of freedom
Authors: Severance Daniel L. , Essex Jonathan W. , Jorgensen William L.
Published: January 2005

A modified derivation of the free energy perturbation (FEP) equation leads to a more general interpretation of the procedures for generating the geometry of a perturbed molecule from the reference one in FEP simulations of flexible systems. Using this form of the equation, it is possible to implement a wide variety of procedures which heretofore would have been considered impossible. A new method, generalized alteration of structure and parameters (GASP), has been implemented in the BOSS program and has been found to be more efficient for perturbations of harmonic degrees of freedom than the commonly adopted procedure. Additionally, an extreme example for which the new procedure proves less satisfactory is presented, and a more efficient method which is also derived from the new form of the FEP equation is devised and tested. It is concluded that the key to a convergent FEP method is efficient sampling of low‐energy configurations of the perturbed state; the new form of the equation suggests ways of generating such configurations. © 1995 by John Wiley & Sons, Inc.
Symplectic integrators and the conservation of angular momentum
Authors: Zhang Mei‐Qing , Skeel Robert D.
Published: January 2005

In this article we observe that generally symplectic integrators conserve angular momentum exactly, whereas nonsymplectic integrators do not. We show that this observation extends to multiple timesteps and to constrained dynamics. Both of these devices are important for efficient molecular dynamics simulations. © 1995 by John Wiley & Sons, Inc.
Ab initiocalculation of molar volumes: Comparison with experiment and use in solvation models
Authors: Wong Ming Wah , Wiberg Kenneth B. , Frisch Michael J.
Published: January 2005

A simple and efficient procedure of calculating molecular volume (VM) based on the Monte Carlo method is presented. The volume of a molecule is defined by the volume occupied by the 0.001‐au electron density envelope. We have employed this method to compute the molecular volumes (VM) of a large selection of organic molecules and compare them with the corresponding molar volumes (Vm) measured in the liquid state. A strong correlation is found to exist between theVMandVmvalues (VM/Vm≈ 0.75). Using this linear relationship, the calculated molecular volume may provide an estimate of the cavity‐volume parameter in solvent‐effect calculations. As a chemical application of molecular volume, we have investigated the conformational equilibrium of 1,2‐difluoroethane in the liquid state using the self‐consistent reaction field theory. © 1995 by John Wiley & Sons, Inc.
The extended law of corresponding states and the intermolecular potentials for HeHe and NeNe
Authors: Behnejad H. , Maghari A. , Najafi M.
Published: January 2005

A direct inversion procedure is used to obtain the pair interaction potentials for He and Ne from the extended law of corresponding states over the temperature range from absolute zero to the onset of ionization. We have used the experimentally reduced viscosity collision integrals obtained from the corresponding states correlation and performed an INVERT to determine the reduced potential energy curve corresponding to the collision integral. This directly determined potential is in excellent agreement with the potential independently obtained from molecular beam scattering measurements. © 1995 by John Wiley & Sons, Inc.
A molecular mechanics/grid method for evaluation of ligand–receptor interactions
Authors: Luty Brock A. , Wasserman Zelda R. , Stouten Pieter F. W. , Hodge C. Nicholas , Zacharias Martin , McCammon J. Andrew
Published: January 2005

We present a computational method for prediction of the conformation of a ligand when bound to a macromolecular receptor. The method is intended for use in systems in which the approximate location of the binding site is known and no large‐scale rearrangements of the receptor are expected upon formation of the complex. The ligand is initially placed in the vicinity of the binding site and the atomic motions of the ligand and binding site are explicitly simulated, with solvent represented by an implicit solvation model and using a grid representation for the bulk of the receptor protein. These two approximations make the method computationally efficient and yet maintain accuracy close to that of an all‐atom calculation. For the benzamidine/trypsin system, we ran 100 independent simulations, in many of which the ligand settled into the low‐energy conformation observed in the crystal structure of the complex. The energy of these conformations was lower than and well‐separated from that of others sampled. Extensions of this method are also discussed. © 1995 by John Wiley & Sons, Inc.
The exponents method for calculating equilibrium concentrations of complex species in solution
Authors: Campos Frederico F. , Rollett John S.
Published: January 2005

The exponents method for calculating the concentrations of species in multimetal‐multiligand systems is introduced. This method uses the Newton‐Raphson method with restricted step iteration, which guarantees a monotonically decreasing objective function. Variable transformation and scaling are performed to avoid underflows and overflows during the calculations. A special linear solver using the eigenvalues and eigenvectors of the Jacobian matrix is implemented for overcoming disastrous singularity of this matrix, and the singular value decomposition method is applied for setting the initial guess. In addition, polynomial extrapolation is used for improving the performance when simulating a diagram of concentrations of species. The method was tested with 14 systems of different sizes over the whole pH range and presented robust and efficient behavior. © 1995 by John Wiley & Sons, Inc.
Development of optimized MST/SCRF methods for semiempirical calculations: The MNDO and PM3 Hamiltonians
Authors: Orozco Modesto , Bachs M. , Luque F. J.
Published: January 2005

The self‐consistent reaction field (SCRF) method proposed by Miertus, Scrocco, and Tomasi (MST) has been optimized for MNDO and PM3 semiempirical Hamiltonians. Different algorithms used to compute the molecular electrostatic potential (MEP) and different solute cavities have been investigated. The ability of the optimized models to reproduce experimental free energies of solvation and to mimic the solvent effect in several chemical processes has been compared with the ab initio and AM1 versions of the MST method as well as with experimental data. © 1995 by John Wiley & Sons, Inc.
The role of the carboxylate ion in models of acyl‐chymotrypsin
Authors: Tong Weida , D'Souza Valerian T.
Published: January 2005

Two exquisite models of the acyl‐chymotrypsin intermediate, one designed by Bruice and another by Bender, were studied to elucidate the role of the carboxylate ion in the catalytic triad of serine proteases. However, opposing conclusions were drawn from these studies. Computational chemistry analysis of these models indicates that the carboxylate ion plays an insignificant role in the former model because of the correct orientation and the distance of the imidazole group without the carboxylate ion. However, in the latter model, the carboxylate ion serves to orient and place the imidazole group at the correct position. This analysis suggests that an important role of the carboxylate ion in serine proteases is to position the imidazole group to be an effective general base catalyst. © 1995 by John Wiley & Sons, Inc.
The electronic structure of weakly bound systems. II. NeX+ and ArX+(X = H2O, HCl, and HF) bimolecular cations
Authors: López Gustavo E.
Published: January 2005

The theoretical framework developed and tested in our previous study of weakly bound systems is applied to a sequence of bimolecular cations: (NeX)+ and (ArX)+, where X = HF, H2O, and HCl. The equilibrium structure, binding energies, and vibrational frequencies for this sequence of bimolecular cations are computed using several post‐Hartree‐Fock methods and triple zeta basis sets. In all cases, the absolute minima in the potential energy surface involves a hydrogen bond. The existence and stability of the aforementioned systems are established with binding energies ranging from 0.1 eV to 1.0 eV. The stability for the systems is explained in terms of the possible dissociative channels and changes in the electron density of the constituent monomers. © 1995 by John Wiley & Sons, Inc.
Comparison of potential‐derived charge and atomic multipole models in calculating electrostatic potentials and energies of some nucleic acid bases and pairs
Authors: Ritchie James P. , Copenhaver Ann S.
Published: January 2005

We compare the electrostatic potential surrounding several natural and synthetic nucleic acid bases calculated using an atom‐centered multiple expansion (ACME) derived from integration of the charge distribution with that from potential‐derived charges (PDCs) obtained using the CHELPG procedure. When the multipole expansions are carried out to octapoles, the root mean square (rms) error in the potential is always less than that from PDCs. Electrostatic interactions in pairs of these nucleic acid bases were also evaluated using ACMEs up to octapoles and PDCs. The electrostatic interaction energies from ACMEs were found always to be larger than those from PDCs or the total self‐consistent field (SCF) interaction energy. The value of the electrostatic energy differs by as much as approximately 19 or as little as approximately 8 kJ/mol between the ACME and PDC methods. The rank ordering provided by the electrostatic models is grossly similar but differs in the ranking of systems with two and three hydrogen bonds. A rigid twist about the NH ⃛ N axis of the pairs was examined using SCF calculations and the electrostatic models. It was found that with ACMEs the energy required for a 90‐degree rotation was always higher than that found from SCF calculations. With PDCs, similar results are obtained, except with the adenine/thymine and 9‐methyl‐adenine/1‐methyl‐thymine pairs. In these instances, the barrier is about 4 kJ/mol lower than that found with SCF calculations. These results demonstrate that integration of the charge density can provide convergent multipole expansions that provide a more accurate description of the electrostatic potential than the commonly used PDC model. In addition, the description of electrostatic interactions during twisting of AT and mAmT given by this model is shown to be somewhat anomalous. © 1995 by John Wiley & Sons, Inc.
An empirical boundary potential for water droplet simulations
Authors: Essex Jonathan W. , Jorgensen William L.
Published: January 2005

An empirical modified boundary potential has been derived to correct the structural perturbations arising from the presence of the vacuum boundary in the simulation of spherical TIP4P water systems. The potential is parameterized for a 12.0‐Å sphere of TIP4P water and gives improved number density and orientational sampling behavior. It is also transferable to both larger and smaller simulation systems with only a moderate degradation in performance. Free‐energy calculations have been conducted for the perturbation of a TIP4P water molecule to methane under aqueous conditions, and the modified boundary potential gives results consistent with those from simulations using periodic boundary conditions. However, simple half‐harmonic boundary potentials give unsatisfactory number density, orientational sampling, and free‐energy results. Moreover, use of the modified boundary potential results in a negligible increase in simulation time. It is envisaged that the modified boundary potential will find use in free‐energy perturbation calculations on proteins with a solvent sphere centered on the active site. © 1995 by John Wiley & Sons, Inc.
Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. IV. Application to hypervalent sulfur‐ and phosphorus‐containing molecules
Authors: Park Je Myung , Kwon Oh Young , No Kyoung Tai , Jhon Mu Shik , Scheraga Harold A.
Published: January 2005

The parameters for an empirical point charge calculation method, Mulliken Population Constrained Potential Derived–Modified Partial Equalization of Orbital Electronegativity (MPCPD–MPEOE) method, for hypervalent sulfur, phosphorus, and the atoms bonded to these atoms, were determined. A new empirical method, MPCPD, which has inherent advantages over both the Mulliken population and potential derived methods, is proposed here. The MPCPD net atomic charges are transferable and reproduce the electrostatic potential. The electrical properties were calculated with the MPCPD and MPCPD–MPEOE charges. These properties agreed well with experimental results and with 6‐31G** ab initio results. The MPEOE parameters for the sulfur atom in aromatic molecules and trivalent phosphorus in phosphite molecules were also determined. The dipole moments calculated with the MPCPD–MPEOE point charges agreed well with experimental results. All the parameters obtained in this work are consistent with those obtained in our previous work. © 1995 by John Wiley & Sons, Inc.
A comparative quantum mechanical study of bond separation energies as a measure of cyclic conjugation
Authors: Chesnut D. B.
Published: January 2005

Restricted Hartree‐Fock (RHF), second‐order Møller‐Plesset (MP2), and density functional calculations [using the Becke/Lee‐Yang‐Parr (B‐LYP) exchange/correlation gradient‐corrected functionals] employing the 6‐311G(d, p) and 6‐311 + + G(d, p) basis sets have been carried out to calculate isodesmic bond separation energies for reactions involving a number of representative five‐ and six‐membered ring organic compounds. The MP2 and density functional approaches yield reasonably good energies; the density functional method agrees particularly well with experiment, exhibiting a root‐mean‐square error of only 2.5 kcal/mol. Ring geometries are calculated satisfactorily in all approaches but are given particularly accurately by the MP2 approach. A comparison of the B‐LYP bond separation energies with several other definitions of resonance energy shows that these different approaches correlate with each other in a reasonable fashion. © 1995 John Wiley & Sons, Inc.
Approaches to large‐scale parallel self‐consistent field calculations
Authors: Wong Adrian T. , Harrison Robert J.
Published: January 2005

The availability of massively parallel computers with high computation rates but limited memory and input/output bandwidth prompts the reevaluation of appropriate solution schemes for the self‐consistent field (SCF) equations. Several algorithms are considered which exhibit between linear and quadratic convergence using various approximations to the orbital Hessian. A prototype is developed to understand the computational expense of each approach. The optimal choice is found to be a conjugate–gradient method preconditioned with a level‐shifted approximation to the orbital Hessian. This is a compromise between efficiency, stability, and low memory usage. Sample benchmarks on two parallel supercomputers are also reported. © 1995 John Wiley & Sons, Inc.
Analysis of the updated Hessian matrices for locating transition structures
Authors: Bofill Josep Maria , Comajuan Móanica
Published: January 2005

We present an analysis of the behavior of different updating Hessian formulas when they are used for the location and optimization of transition structures. The analysis is based on the number of iterations, the minimum of the weighted Euclidean matrix norm, and first‐order perturbation theory applied to each type of Hessian correction. Finally, we give a derivation of a family of updated Hessians from the variational method proposed by Greenstadt. We conclude that the proposed family of updated Hessians is useful for the optimization of transition structures. © 1995 John Wiley & Sons, Inc.
Multidimensional free‐energy calculations using the weighted histogram analysis method
Authors: Kumar Shankar , Rosenberg John M. , Bouzida Djamal , Swendsen Robert H. , Kollman Peter A.
Published: January 2005

The recently formulated weighted histogram analysis method (WHAM)1 is an extension of Ferrenberg and Swendsen's multiple histogram technique for free‐energy and potential of mean force calculations. As an illustration of the method, we have calculated the two‐dimensional potential of mean force surface of the dihedrals gamma and chi in deoxyadenosine with Monte Carlo simulations using the all‐atom and united‐atom representation of the AMBER force fields. This also demonstrates one of the major advantages of WHAM over umbrella sampling techniques. The method also provides an analysis of the statistical accuracy of the potential of mean force as well as a guide to the most efficient use of additional simulations to minimize errors. © 1995 John Wiley & Sons, Inc.
Application of the shape group method to conformational processes: Shape and conjugation changes in the conformers of 2‐phenyl pyrimidine
Authors: Walker P. Duane , Mezey Paul G. , Maggiora Gerald M. , Johnson Mark A. , Petke James D.
Published: January 2005

The shape group method (SGM) and the associated (a,b)‐parameter maps provide a detailed shape characterization of molecular charge distributions. This method is applied to the study of the variations of shape and conjugation of conformers of 2‐phenyl pyrimidine in their electronic ground state. Within the SGM framework, the method of (a,b)‐parameter maps provides a concise, nonvisual, algorithmic technique for shape characterization of molecules with fixed nuclear geometries. Moreover, shape codes derived from the (a,b)‐parameter maps afford a practical means for efficiently storing the shape properties of molecules in an electronic database. The shape codes of two or more charge distributions can be compared directly, and numerical measures of molecular shape similarity can be computed using a technique that is simple, fast, and inexpensive, especially in relation to direct, pairwise comparisons of electronic charge densities. The quantitative and automated nature of the method suggests applications in the field of computer‐aided molecular design. In this study, the method is used for the first time to determine detailed numerical shape codes and shape similarity measures for a nontrivial conformational problem involving changes in energy and in conjugation. Numerical shape similarity measures of eight conformers of 2‐phenyl pyrimidine are determined and correlated with variations in conformational energy and conjugation. The competing effects of steric repulsion and conjugation lead to important correlations between conformational energy and shape. © 1995 John Wiley & Sons, Inc.
Harmonic analysis of large systems. III. Comparison with molecular dynamics
Authors: Janežič Dušanka , Venable Richard M. , Brooks Bernard R.
Published: January 2005

Atomic motions in bovine pancreatic trypsin inhibitor (BPTI), derived from molecular dynamics, harmonic analysis, and quasiharmonic analysis, are compared when a single protein model, energy parameters, and environment are employed. Molecular dynamics (MD) was carried out for 2 nanoseconds. An average structure was determined from the last nanosecond of the MD simulation, when no major structural changes were observed. This structure was used for several harmonic analysis calculations as well as for a reference structure for the quasiharmonic analysis, for both full basis and reduced basis sets. In contrast to the harmonic analysis results, the quasiharmonic reduced basis calculation using a spherical harmonics reduced basis provided good agreement with the full basis calculation, suggesting that when anharmonic effects are considered, BPTI can behave as a homogeneous object. An extensive analysis of the normal modes from a diverse set of 201 minimized MD simulation frames was performed. On only the sub‐picosecond time scale were energy minima revisited after a transition to another state. This analysis shows that the dynamics average structure is not representative of the simulation frames in terms of energy and vibrational frequencies. For this model of BPTI, 42% of the motion (mean‐squared fluctuation) can be attributed to harmonic limit behavior. A spectral analysis of the correlation function of deformation for a particular normal mode or quasiharmonic mode can be used to determine the time scales of motions which correspond to harmonic vibration, large‐scale drift, or sharp transitions between local substrates. © 1995 John Wiley & Sons, Inc.
Kinetics of the pyrolysis of 1,2‐diiodoethylene
Authors: Furuyama Shozo , Golden David M. , Benson Sidney W.
Published: January 2005

The spectrophotometric determination of the rate of pyrolysis of 1,2‐diiodoethylene from 305.8 to 435.0° (with additional data on the addition of iodine to acetylene from 198.1 to 331.6°) has resulted in the observation of both a (in part heterogeneous) unimolecular process (A), and an iodine atom catalyzed process (B). For the homogeneous unimolecular process, log (kA/sec−1) ≈ 12.5–46/θ would appear to be reasonable, while log (kB/M−1 sec−1) = 11.8–23.9/θ, where θ = 2.303RT in kcal/mole.

It is suggested that a donor–acceptor complex intermediate may explain the observed rate constant of process B and analogous reactions in other systems.
Kinetics of molecular motions in liquids and its correlation with kinetics of radical liquid–phase reactions
Authors: Buchachenko A. L. , Wasserman A. M. , Kovarskii A. L.
Published: January 2005

Stable nitroxide radicals and ESR techniques have been used to investigate rotational and translational motions of molecules in the liquid state. It is found that for hydrocarbons and molecules with low polarity the rotational frequencies are about an order of magnitude faster than translational encounters. Arrhenius parameters are reported for the rates of both types of processes. A scheme is given for the relation of these motions to radical recombination in solution and also to reactions requiring activation energy. The consequences of this scheme are examined.

Such important properties as hydrodynamic fluidity, thermal conductivity, processes of extraction and solution, occurring in the liquid phase as well as at the interface are determined by mobility of particles in the liquid. The problem of molecular mobility is of essential significance for the kinetics of chemical and chemico‐physical processes in the liquid phase.

Application of both ESR techniques and stable nitroxide radicals for kinetic studies of molecular motions in liquids and the correlation between molecular mobility and the kinetic parameters of liquid‐phase radical reactions have been studied in the present paper.
Exchange and decomposition reactions of isobutyl iodide with iodine
Authors: Nakashima Masato , Noyes Richard M.
Published: January 2005

In the presence of elementary iodine, isobutyl iodide (2‐methyl‐1‐iodopropane) undergoes isotopic exchange and also decomposes with production of additional iodine. Both reactions are approximately first order in isobutyl iodide and half order in iodine molecules. In degassed hexachlorobutadiene at 160°, the rate constants for exchange and decomposition are 7.5 × 10−6 and 11.4 × 10−6 (liter/mole)1/2sec−1, respectively. The decomposition is probably initiated by iodine atom abstraction of a β hydrogen atom, but comparison with rates for related compounds indicates that this hydrogen abstraction does not contribute significantly to the mechanism of exchange.
Kinetics of the gas‐phase reaction of acetone with iodine: Heat of formation and stabilization energy of the acetonyl radical
Authors: Solly R. K. , Golden D. M. , Benson S. W.
Published: January 2005

The kinetics of the gas‐phase reaction CH3COCH3 + I2 ⇄ CH3COCH2I + HI have been measured spectrophotometrically in a static system over the temperature range 340–430°. The pressure of CH3COCH3 was varied from 15 to 330 torr and of I2 from 4 to 48 torr, and the initial rate of the reaction was found to be consistent with \documentclass{article}\pagestyle{empty}\begin{document}$ {\rm CH}_3 {\rm COCH}_3 + {\rm I}^{\rm .} \stackrel{1}{\rightarrow}{\rm CH}_{\rm 3} {\rm COCH} + {\rm HI} $\end{document} as the rate‐determining step. An Arrhenius plot of the variation of k1 with temperature showed considerable scatter of the points, depending on the conditioning of the reaction vessel. After allowance for surface catalysis, the best line drawn by inspection yielded the Arrhenius equation, log [k1/(M−1 sec−1)] = (11.2 ± 0.8) – (27.7 θ 2.3)/θ, where θ = 2.303 RT in kcal/mole. This activation energy yields an acetone CH bond strength of 98 kcal/mole and δH (CH3COĊH2) radical = −5.7 ± 2.6 kcal/mole. As the acetone bond strength is the same as the primary CH bond strength in isopropyl alcohol, there is no resonance stabilization of the acetonyl radical due to delocalization of the radical site. By contrast, the isoelectronic allyl resonance energy is 10 kcal/mole, and reasons for the difference are discussed in terms of the π‐bond energies of acetone and propene.
Reactions of Cl2P3/2: Absolute rate constants for reaction with H2, CH4, C2H6, CH2Cl2, C2Cl4, and cC6H12
Authors: Davis D. D. , Braun W. , Bass A. M.
Published: January 2005

The absolute rate constants have been measured for several gas‐phase chlorine atom‐molecule reactions at 25°C by resonance fluorescence. These reactions and their corresponding rate constants in units of cm3 mole−1 sec−1 are: magnified image

The effects of varying the substrate pressure, total pressure, light intensity and chlorine‐atom source on the value of the bimolecular rate constants have been investigated for all these reactions. Conditions under which no competing side reaction occurs were established and the reported rate constants were measured under these conditions. For reactions (2), (5), (6), (7), and 8, there is a discrepancy of a factor of two between the rate constants measured in this work and values in the literature; it is suggested that this is due to an error in the previously measured value of k/k upon which the relative measurements in the literature ultimately depend.
The pyrolysis of acetaldehyde in the presence of nitric oxide
Authors: Schuchmann H.‐P. , Laidler K. J.
Published: January 2005

The kinetics of the acetaldehyde pyrolysis have been studied at temperatures from 450° to 525°C, at an acetaldehyde pressure of 176 torr and at 0 to 40 torr of added nitric oxide. The following products were identified and their rates of formation measured: CH4, H2, CO, CO2, C2H4, C2H6, H2O, C3H6, C2H5CHO, CH3COCH3, CH3COOCHCH2, N2, N2O, HCN, CH3NCO, and C2H5NCO. Acetaldehyde vapor was found to react with nitric oxide slowly in the dark at room temperature, the products being H2O, CH3COOCH3, CO, CO2, N2, NO2, HCN, CH3NO2, and CH3ONO2. The rates of formation of N2and C2H5NCO depend on how long the CH3CHO‐NO mixture is kept at room temperature before pyrolysis; the rates of formation of the other products depend only slightly on the mixing period.

The pyrolysis of “clean” CH3CHO–NO mixtures (i.e., the results extrapolated to zero mixing time, which are independent of products formed in the cold reaction) are interpreted as follows: (1) There are two chain carriers, CH3and CH2CHO, their concentrations being interdependent and influenced by NO in different ways: the CH3radical is both generated and removed by reactions directly involving NO, whereas CH2CHO is generated only indirectly from CH3but is also removed by direct reaction with NO. (2) An important mode of initiation by NO is its addition to the carbonyl group with the formation ofmagnified imagewhich is converted intomagnified image; this splits off OH with the formation of CH3NCO or CH3+ OCN. (3) Important modes of termination areThe steady‐state equations derived from the mechanism are shown to give a good fit to the experimental rate versus [NO] curves and, in particular, explain why there is enhancement of rate by NO at higher CH3CHO pressures and, at lower CH3CHO pressures, inhibition at low [NO] followed by enhancement at higher [NO].

The cold reaction is explained in terms of chain‐propagating and chain‐branching steps resulting from the addition of several NO molecules to CH3CHO and the CH3CO radical. In the “unclean” reaction it is found that the rates of N2and C2N5NCO formation are increased by CH3NO2, CH3ONO, and CH3ONO2formed during the cold reaction. A mechanism is proposed, involving the participation of α‐nitrosoethyl nitrite, CH3CH(NO)ONO.

It is suggested that there are two modes of behavior in pyrolyses in the presence of NO: (1) In the paraffins, ethers, and ketones, the effects are attributed to the addition of NO to a radical with the formation of an oxime‐like compound. (2) In the aldehydes and alkenes, where there is a hydrogen atom attached to a double‐bonded carbon atom, the behavior is explained in terms of addition of NO to the double bond followed by the formation of an oxime‐like species.
Kinetics and thermochemistry of the gas phase reaction of methyl ethyl ketone with iodine. II. The heat of formation and unimolecular decomposition of 2‐iodo‐3‐butanone
Authors: Solly Richard K. , Golden David M. , Benson Sidney W.
Published: January 2005

Equilibrium constants for the reaction CH3COCH2CH3 + I2 ⇌ CH3COCHICH3 + HI have been computed to fit the kinetics of the reaction of iodine atoms with methyl ethyl ketone. From a calculated value of S(CH3COCHICH3) = 93.9 ± 1.0 gibbs/mole and the experimental equilibrium constants, ΔH(CH3COCHICH3) is found to be −38.2 ± 0.6 kcal/mole. The Δ(ΔH) value on substitution of a hydrogen atom by an iodine atom in the title compound is compared with that for isopropyl iodide. The relative instability of 2‐iodo‐3‐butanone (3.4 kcal/mole) is presented as further evidence for intramolecular coulombic interaction between partial charges in polar molecules. The unimolecular decomposition of 2‐iodo‐3‐butanone to methyl vinyl ketone and hydrogen iodide was also measured in the same system. This reaction is relatively slow compared to the formation of the above equilibrium. Rate constants for the reaction over the temperature range 281°–355°C fit the Arrhenius equation:

where θ = 2.303RT kcal/mole. The stability of both the ground and transition states is discussed in comparing this activation energy with that reported for the unimolecular elimination of hydrogen iodide from other secondary iodides. The kinetics of the reaction of hydrogen iodide with methyl vinyl ketone were also measured. The addition of HI to the double bond is not rate controlling, but it may be shown that the rate of formation of 1‐iodo‐3‐butanone is more rapid than that for 2‐iodo‐3‐butanone. Both four‐ and six‐center transition complexes and iodine atom‐catalyzed addition are discussed in analyzing the relative rates.
Hydrogen abstraction reactions from organosilicon compounds. The reactions of fluoromethyl radicals with trichlorosilane. The photolyses of di‐ and tetrafluoroacetone
Authors: Kerr J. A. , Timlin D. M.
Published: January 2005

The photolyses of 1,3‐difluoro‐ and 1,1,3,3‐tetrafluoroacetone have been reinvestigated as sources of fluoromethyl radicals, and the following rate constant ratios were determined magnified image

θ= 2.303 RT in kcal/mole.

The results are in substantial agreement with the original investigations. The photolyses of the fluoroacetones were used as sources of CH2F and CHF2 radicals, and the following Arrhenius parameters were obtained for the hydrogen abstraction reactions R + SiHCl3 → RH + SiCl3:

R
T(°K)
E (kcal/mole)
log A (mole−1 cc sec−1)
log k (400°K) (mole−1 cc sec−1)

CH2F
335–443
6.06 ± 0.15
10.79 ± 0.08
7.48 CHF2

CHF2
334–442
6.82 ± 0.09
11.32 ± 0.05
7.59

The rates of reactions of CH2F and CHF2 radicals toward hydrogen abstraction from SiHCl3 are an order of magnitude lower than the corresponding rates for the CH3, C2H5, and CF3 radicals as a result of increased activation energies for the CH2F and CHF2 reactions. The interpretation of the results is hindered by a lack of accurate thermochemical data on the radicals. The activation energies, as they stand, can be rationalized in terms of a polar repulsion between SiHCl3 and the radicals, increasing regularly and leading to a progressive increase in activation energy with increasing fluorine substitution in the radical. This interpretation is consistent with the estimates D(CH2FH) ∝ D(CHF2H) ∝ 97 kcal/mole. On the other hand, there is some indication, from the spread of A‐factors in the series of fluoromethyl radicals reacting with SiHCl3, that internal compensation of Arrhenius parameters is occurring in some of the reactions; and when this is taken into account, the interpretation of activation energies is more difficult.
The thermal isomerization of cyclobutenes. XVI. 1,2‐bis(trimethylsiloxy)cyclobutene
Authors: Bloomfield J. J. , Frey H. M. , Metcalfe J.
Published: January 2005

The gas phase thermal isomerization of 1,2‐bis(trimethylsiloxy)cyclobutene has been studied in the temperature range 172°–204°C. The reaction is homogeneous, kinetically first order, and yields 2,3‐bis(trimethylsiloxy)buta‐1,3‐diene as the only product. The rate constants fit the Arrhenius equation

These results, taken with those obtained previously, demonstrate the insensitivity of the kinetics of the reaction to the nature of the groups substituted on the 1‐ and/or 2‐positions of the cyclobutene ring.
The mercury‐sensitized oxidation of carbon monoxide
Authors: Simonaitis R. , Heicklen Julian
Published: January 2005

The mercury‐photosensitized oxidation of CO was studied at 275°C over a wide range of [O2]/[CO] ratios in the absence and presence of the oxygen atom scavenger 2‐trifluoromethylpropene (TMP) and at 25°C at low [O2]/[CO] ratios in the presence of TMP. By following the quantum yield of CO2 production, Φ {CO2}, as a function of the [O2]/[CO] ratio, the reactions of vibrationally excited CO (v υ 9) and electronically excited O2, probably in the c1Σ−u state, were studied. At low [O2]/[CO] ratios the predominant reactions are of vibrationally excited CO (v υ 9). Relative rate constants for chemical reaction versus deactivation of CO (v υ 9) were obtained. At higher [O2]/[CO] ratios, the principal reactions are of electronically excited O2. Relative rate constants for chemical reactions and deactivation of this electronically excited O2 with CO, O2, and TMP were obtained. From the effect of total pressure on Φ {CO2}, it is proposed that an intermediate CO3 is formed in the reaction of electronically excited O2 with CO.
The free‐radical reaction of tri‐n‐butyltin hydride with peroxides
Authors: Brokenshire J. L. , Ingold K. U.
Published: January 2005

Rate constants for the tri‐n‐butyltin radical (Sn ·) induced decomposition of a number of peroxides have been measured in benzene at 10°C. The values range from ∼100 M−1 sec−1 for di‐t‐butyl peroxide to 2.6 × 107 M−1 sec−1 for di‐t‐butyl diperoxyisophthalate. The majority of the peroxides, including diethyl peroxide, diacetyl peroxide, and t‐butyl peracetate, have rate constants of ∼105 M−1 sec−1. It is shown that di‐n‐alkyl disulfides are ten times as reactive toward Sn · as di‐n‐alkyl peroxides, although the exothermicities of these reactions are ∼15 and ∼39 kcal/mole, respectively. The enhanced reactivity of the disulfides is attributed to the easier formation of an intermediate or transition state with 9 electrons around sulfur, compared with an analogous species with 9 electrons around oxygen.

The following bond strengths (kcal/mole) have been estimated: D[SnOR] = 77; D[SnH] = 82; D[SnSR] = 83; and D[SnOC(O)R] = 86, where R = alkyl. Rate constants for reaction of Sn · with some benzyl esters have also been measured. It has been found that t‐butoxy radicals can add to benzene and abstract hydrogen from benzene at ambient temperatures.
Reactions of radicals. XXVI. On the use of activation parameters as a test for concerted decomposition of initiators
Authors: Pryor William A. , Smith Kennedy
Published: January 2005

In 1958, Bartlett and Hiatt [1] suggested that the number of bonds which are rotationally “frozen” at the transition state for decomposition of peresters can be determined from the magnitude of the values of ΔH‡ and ΔS‡. In recent years, other workers have extended this hypothesis to include the use of the magnitude of ΔH‡ and ΔS‡ values to determine the number of bonds which undergo synchronous scission in the decomposition of initiators. This criterion for separating one‐bond from two ‐or three‐bond initiators is discussed in the light of all of the data now reported in the literature. It is probable that the correlation of ΔH‡ and ΔS‡ in an isokinetic plot cannot be used to distinguish either the number of bonds which are rotationally frozen at the transition state or the number that are undergoing scission, except in limited and rather imprecise ways. However, the insights and principles of Bartlett and Hiatt still are extremely useful as qualitative tools.
The rate of dissociation of allyl iodide in shock waves
Authors: Maloney K. L. , Palmer H. B. , Seery D. J.
Published: January 2005

The rate of decomposition of allyl iodide has been measured from 742plusmn;K to 1068±K and from 169 to 1429 torr using a shock tube method in which the disappearance of allyl iodide and the appearance of iodine are followed simultaneously. The kinetics are first order in allyl iodide and probably are slightly dependent upon total pressure. Mathematical modeling shows that they are compatible with a mechanism consisting of three reactions:

equation image

The experiments yield the rate constant k1, the high‐pressure limiting value of which is found to be

in reasonable agreement with that predicted using the methods of Benson and O'Neal [1].
Very low‐pressure pyrolysis. VII. The decomposition of methylhydrazine, 1,1‐dimethylhydrazine, 1,2‐dimethylhydrazine, and tetramethylhydrazine. Concerted deamination and dehydrogenation of methylhydrazine
Authors: Golden D. M. , Solly R. K. , Gac N. A. , Benson S. W.
Published: January 2005

The rate constants (kuni) for the first‐order disappearance of the title molecules have been determined under VLPP conditions. The kuni are not the rate constants of ultimate interest since they reflect the fact that energy transfer competes with the chemical decomposition. Use of the Rice‐Ramsperger‐Kassel‐(Marcus) [RRK(M)] theory allows the determination of the high‐pressure rate constants (kα), if the mode of decomposition is known. The heats of formation of the radicals NH2, CH3NH, and (CH3)2N are known. These values should be usable for prediction of the activation energy for NN bond homolysis in the hydrazines. Measured rate constants for UDMH and TMH bear this out, but the rate constant for MMH does not. This and other evidence lead to the conclusion that MMH decomposes via molecular concerted elimination of NH3 and H2 not and by NN bond scission. The following values are preferred from this work (θ = 2.303RT in kcal/mole). Mode of decomposition is N—N bond scission unless noted otherwise in parenthesis:

.
The rate of the gas phase iodination of cyclobutane. The heat of formation of the cyclobutyl radical
Authors: McMillen D. F. , Golden D. M. , Benson S. W.
Published: January 2005

The gas phase iodination of cyclobutane was studied spectrophotometrically in a static system over the temperature range 589° to 662°K. The early stage of the reaction was found to correspond to the general mechanism

where the Arrenius parameters describing k1 are given by log k1/M−1 sec−1 = 11.66 ± 0.11 – 26.83 ± .31/θ, θ = 2.303RT in kcal/mole. The measured value of E1, together with the fact that E−1 = 1 ± 1 kcal/mole, provides ΔH(c‐C4H7.) = 51.14 ± 1.0 kcal/mole, and the corresponding bond dissociation energy, D(c‐C4H7H) = 96.8 ± 1.0 kcal/mole. A bond dissociation energy of 1.8 kcal/mole higher than that for a normal secondary CH bond corresponds to one half of the extra strain energy in cyclobutene compared to cyclobutane and is in excellent agreement with the recent value of Whittle, determined in a completely different system. Estimates of ΔH and entropy of cyclobutyl iodide are in very good agreement with the equilibrium constant K12 deduced from the kinetic data. Also in good agreement with estimates of Arrhenius parameters is the rate of HI elimination from cyclobutyl iodide.
Reaction of methyl radicals with atomic oxygen
Authors: Morris E. D. , Niki H.
Published: January 2005

The reaction of hydrogen atoms with diazomethane was used as a source of methyl radicals to study the reaction of oxygen atoms with methyl radicals. This investigation verifies directly the earlier results that formaldehyde is a major product and that the rate constant is greater than 3×10−11cm3 molecule−1 sec−1.
The compilation and evaluation of chemical kinetics data; a descriptive survey of current efforts
Authors: Gevantman Lewis H. , Garvin David
Published: January 2005

A description of the current range of activities being pursued in the compilation and evaluation of chemical kinetic data is given. The roles of individual scientists, professional groups, and national and international programs are detailed. The special problems attending on kinetic parameters are enumerated and discussed. An appendix is included which gives a comprehensive list of compilations and evaluations extant in the field of chemical kinetics.
The very low‐pressure dehydrogenation of cis‐2‐butene. The activation energy for 1,4‐H2 elimination
Authors: Alfassi Ze'ev B. , Golden David M. , Benson Sidney W.
Published: January 2005

Pyrolysis of cis‐butene‐2 under conditions of very low pressure (VLPP) has been studied in the range of 1100–1300°K. The principal products are butadiene and H2, obtained in a unimolecular reaction. A competing reaction to form butene‐l accounts for from 10% to 40% of the overall decomposition over the range. Using a «tight» model for the transition state and RRKM theory yields a high‐pressure, unimolecular rate constant for the 1,4‐H2 elimination of

where θ = 2.303RT in kcal/mol. There is some surface reaction of butadiene at these temperatures to yield H2 + nonvolatile residue. Butene‐l proceeds to decompose irreversibly to allyl + methyl radicals which have been observed directly. Comparison with related reactions leads to the conclusion that orbital symmetry‐forbidden, 1,2‐H2 elimination from saturated organic compounds will have activation energies too high to observe.
Kinetic isotope effect in the protonation of anthracenide salts by MeOH and MeOD role of counterions and solvents
Authors: Rainis A. , Szwarc M.
Published: January 2005

Kinetics of protonation of Li+, Na+, K+, and Cs+ salts of anthracene radical anions (A−·,Cat+) and dianions (A2−, 2Cat+) by MeOH and MeOD in tetrahydrofuran (THF) and dimethoxyethane (DME) led to the determination of the isotope effect (kH/kD) in the following reactions:

Studies of cation and solvent influence on the rate constants of these reactions and on the magnitude of the isotope effect permitted us to draw some conclusions about the structure of the pertinent transition states. It seems that only the tight A−·,Na+ pairs participate in the protonation, and on this basis the fraction of tight ion paris of A−·,Na+ in DME was estimated. Our results have been compared with data reported in the literature.
The reaction of OH with NO
Authors: Sie B. K. T. , Simonaitis R. , Heicklen J.
Published: January 2005

Mixtures of N2O, CO, and NO in excess H2 were photolyzed at 213.9 nm and 298°K. The initially formed O(1D) atoms from the photolysis of N2O abstract an H atom from H2 permitting a study of the competition:

equation image

From the CO2 yield the relative rate coefficient k1/k2 is obtained. It is found to be slightly dependent on pressure for total pressures (mainly H2) of 95.5 to 768 torr. However, the values are near the high‐pressure limiting value which is found by extrapolation to give k1∞ = 1.2 × 10−11 cm3/sec based on k2∞ = 3.55 × 10−13 cm3/sec.
H2 formation in the reaction of O(1D) with CH4
Authors: Jayanty R. K. M. , Simonaitis R. , Heicklen Julian
Published: January 2005

The reaction of O(1D) with CH4 was studied to determine the efficiency of H2 production in a direct process, and it was found to be 0.11 ± 0.02. Thus the two channels which account for all of the reaction between O(1D) and CH4 in the gas phase are

equation image
Gas‐phase hydrogen abstraction from asymmetrically halogenated ethanes by chlorine atoms
Authors: Martens G. J. , Godfroid M. , Delvaux J. , Verbeyst J.
Published: January 2005

The hydrogen abstraction from asymmetrically fluorinated and chlorofluorinated ethanes by chlorine atoms has been investigated in the gas phase between 264 and 333°K using the competition method. Arrhenius parameters for the reaction on both sites of the molecules are discussed.