bluuebunny/crossref_metadata_2025 huggingface dataset:
Algorithms for clustering molecular dynamics configurations
Authors: Torda Andrew E. , van Gunsteren Wilfred F.
Published: January 2005

Two traditional clustering algorithms are applied to configurations from a long molecular dynamics trajectory and compared using two sets of test data. First, a subset of atoms was chosen to present conformations which naturally fall into a number of clusters. Second, a subset of atoms was selected to span a relatively continuous region of conformational space rather than form discrete conformational classes. Of the two algorithms used, the single linkage method is inappropriate for this kind of data. The divisive hierarchical method, based on minimizing the difference between cluster centroids and extrema, is successful but also prone to imposing clustering hierarchy where none can be justified. © 1994 by John Wiley & Sons, Inc.
Path integral molecular dynamics methods: Application to neon
Authors: Morales Juan J. , Nuevo María J.
Published: January 2005

Feynman's path integral formulation of quantum statistical mechanics, which has commonly been applied be Monte Carlo methods, is now also implemented by traditional molecular dynamics simulations of the microcanonical ensemble and in the Nosé‐Hoover method simulating the isothermal‐isobaric ensemble. In this article these two methods are applied to solid and liquid neon, in which quantum effects are not negligible. The validity of the procedure is shown by comparison with Monte Carlo and Brownian Dynamics computer simulations and with experiment. © 1995 by John Wiley & Sons, Inc.
Ab initio SCF calculations on low‐energy conformers of cyclohexaglycine
Authors: Böhm Hans‐Joachim , Brode Stefan
Published: January 2005

Results from ab initio self‐consistent field (SCF) calculations with a 3‐21G and a double‐zeta‐plus polarization (DZP) basis set on four low‐energy conformations of cyclohexaglycine are reported. In agreement with results from semiempirical and molecular mechanics force field calculations, the lowest‐energy conformation found at the DZP level is a conformation forming six C7 turns. However, the energy difference to the β‐turn conformers is significantly smaller at the ab initio DZP level than calculated by the other methods. In contrast to the results obtained with some of the other methods, the present ab initio calculations show that both the double‐type‐I β turn and the double‐type‐II β‐turn conformer of cyclohexaglycine are stable low‐energy structures. © 1995 by John Wiley & Sons, Inc.
Conformational analysis and flexibility of carbohydrates using the CICADA approach with MM3
Authors: Koča Jaroslav , Pérez Serge , Imberty Anne
Published: January 2005

The potential energy hypersurfaces (PES) of several carbohydrate molecules were studied with a new algorithm for conformational searches, CICADA (Channels in Conformational Space Analyzed by Driver Approach) interfaced with the molecular mechanics program MM3(92). The method requires (1) one or a few low‐energy conformations as starting points; and (2) designation of the torsion angles important for understanding the conformational behavior of the molecule. The PES is explored by driving separately each selected torsion angle (in both directions) with a concomitant full‐geometry optimization at each increment (except for the driven angle). When a minimum has been detected, the molecule is freely optimized, and the minima so detected are then stored if not encountered previously. The new minima serve as starting structures for further explorations. The results from CICADA permit prediction of relative and absolute flexibility and conformational softness for both the entire molecule as well as for individual group rotations and local minima. The carbohydrates analyzed were Me‐α‐D‐glucopyranoside, β‐D‐GlcNAc(1‐2)α‐D‐Man, and α‐D‐GalNAc(1‐3)[α‐L‐Fuc(1‐2)]Gal‐O‐Me. All the low‐energy conformers along with the transition states and flexibilities features were characterized. CICADA found all minima and low‐energy conversion pathways for the disaccharide that were found by a traditional grid search. In contrast to the grid search method, CICADA concentrates mostly on the exploration of the low‐energy regions of the PES, thereby saving a significant amount of computational time. The performance of the method opens new routes for exploring conformational space of larger molecules, such as oligosaccharides. © 1995 by John Wiley & Sons, Inc.
Numerical solution of the nonlinear Poisson–Boltzmann equation: Developing more robust and efficient methods
Authors: Holst Michael J. , Saied Faisal
Published: January 2005

We present a robust and efficient numerical method for solution of the nonlinear Poisson‐Boltzmann equation arising in molecular biophysics. The equation is discretized with the box method, and solution of the discrete equations is accomplished with a global inexact‐Newton method, combined with linear multilevel techniques we have described in an article appearing previously in this journal. A detailed analysis of the resulting method is presented, with comparisons to other methods that have been proposed in the literature, including the classical nonlinear multigrid method, the nonlinear conjugate gradient method, and nonlinear relaxation methods such as successive overrelaxation. Both theoretical and numerical evidence suggests that this method will converge in the case of molecules for which many of the existing methods will not. In addition, for problems which the other methods are able to solve, numerical experiments show that the new method is substantially more efficient, and the superiority of this method grows with the problem size. The method is easy to implement once a linear multilevel solver is available and can also easily be used in conjunction with linear methods other than multigrid. © 1995 by John Wiley & Sons, Inc.
Calculation of binding energy differences for receptor–ligand systems using the Poisson‐Boltzmann method
Authors: Shen Jian , Quiocho Florante A.
Published: January 2005

An approach using the finite difference solution of the Poisson‐Boltzmann equation to estimate binding free energy changes for two receptor–ligand systems, arabinose binding protein and sulfate binding protein, is presented. The eight calculated binding free energy changes agree with experiment, showing a correlation coefficient of 0.92 and energy deviations of 1 kcal/mol or less. More importantly, the decomposition of solvation and assembly energies in this approach provides an understanding of binding mechanisms and therefore could suggest directions to alter binding affinities. The method is demonstrated to be useful in analyzing experimental binding structures and predicting binding effects of mutants or modified ligands for macromolecular systems, in which the electrostatic forces dominate the overall interaction and the structural perturbations upon modifications are small. © 1995 by John Wiley & Sons, Inc.
Theoretical investigation of the relative stabilities of XSSX and X2SS isomers (X = F, Cl, H, and CH3)
Authors: Bickelhaupt F. Matthias , Solà Miquel , von Ragué Schleyer Paul
Published: January 2005

The structures and relative stabilities of a series of disulfide (XSSX) and thiosulfoxide (X2SS) isomers have been studied for X = F, Cl, CH3, and H, using various levels of conventional ab initio and density functional theory (DFT). The XSSX isomers are more stable than the X2SS isomers for all substituents. The energy gap ΔE(X) between the two isomers increases (i.e., XSSX becomes more stable with respect to X2SS), and the SS bond contracts in the series for X = F, Cl, CH3, H. The results are interpreted by means of natural population analysis (NPA) (e.g., the interaction between the disulfide moiety S and the two substituents X·). The bonding in the hypervalent X2SS species is similar to the bonding in the nonhypervalent XSSX and does not involve a special role for sulfur‐3d orbitals. These orbitals acquire only minimal populations and are not to be conceived as valence orbitals. The DFT and conventional ab initio results, Xα/DZP and MP2/6‐31G** optimized structures and isomerization energies (at the highest levels of both methods), agree well. © 1995 by John Wiley & Sons, Inc.
Determination of C‐terminal structure of human CHaras oncogenic protein
Authors: Yoon Jeong Hyeok , Shin Jae Kwang , Jhon Mu Shik
Published: January 2005

The three‐dimensional structure of the carboxyl‐terminal region of the human ras oncogenic protein (called p21) has been determined using the HDMC (High‐directional Monte Carlo) method combined with MD (molecular dynamics) simulation. A truncated p21 containing residues 1–171 without the carboxyl‐terminal end was analyzed using X‐ray crystallography by Kim et al. It has been well documented that the carboxyl‐terminal region of p21 is flexible and plays an important role in transmitting a signal from the membrane‐attached domain. We have carried out the theoretical calculation for 18 undefined residues, which correspond to residues 172–189 of intact p21, in addition to seven residues (165–171) from X‐ray coordinates of the C‐terminal end of human CHaras protein. In this calculation, the main‐chain atoms of residues 165–169 have been fitted to X‐ray structure, and the remaining region has been allowed to move during the conformational analysis. We have confirmed that revised HDMC can easily alter the local minima of the polypeptide chains as the internal vibrations of molecules are allowed by MD simulation. Throughout this study, we suggest that the C‐terminal end of human CHaras p21 protein has structures in the forms of an α helix for 165–172, a loop for 173–180, and an α helix for 181–187 regions, like the helical hairpin. © 1995 by John Wiley & Sons, Inc.
An empirical force field. II. Crystalline alkanes
Authors: Dillen Jan L. M.
Published: January 2005

The EFF'93 force field is used to study crystalline alkanes. In addition to detailed molecular geometries, the sublimation enthalpy, heat capacity, and lattice vibrations for a number of saturated hydrocarbons are reported and compared with experiment. © 1995 by John Wiley & Sons, Inc.
Nonlocal density functional calculation of gas phase heats of formation
Authors: Habibollahzadeh Dariush , Grice M. Edward , Concha Monica C. , Murray Jane S. , Politzer Peter
Published: January 2005

A general procedure is presented for computing the gas phase heats of formation of a wide variety of organic compounds. ΔE for the formation of the molecule from its elements at 0 K is obtained from density functional calculations (Gaussian 92/DFT) for optimized geometries. This result is converted to ΔH at 298 K by assuming ideal behavior and adding the translational, rotational, and vibrational energies. Additive correction terms corresponding to the various coordination states of the carbons, nitrogens, and oxygens were developed using a database of 54 compounds. The experimental ΔH values of these compounds are then reproduced with an average absolute error of 3 kcal/mol and a standard deviation of 4 kcal/mol. For a group of 10 test cases that were not part of the database, the average absolute error is 3.5 kcal/mol and the standard deviation is 4.1 kcal/mol. © 1995 by John Wiley & Sons, Inc.
An improved algorithm for the analytical computation of solvent‐excluded volume. The treatment of singularities in solvent‐accessible surface area and volume functions
Authors: Gogonea Valentin , Ōsawa Eiji
Published: January 2005

An algorithm for the analytical computation of solvent‐excluded volume is presented as part of our efforts to develop an improved computational model for a solvent effect term, in which the work required to create a cavity in the solvent is expressed as a function of the solvent‐excluded volume. In this article we describe mathematical developments in the analytical integration of solvent‐accessible surface (SAS) area, the singularities in SAS area and volume functions, and the procedures required to detect and treat singularities. Techniques to increase algorithm performance are presented, which improve computational speed by about five times, on the average. The accuracy of the analytical method for volume computation is compared with the accuracy of two numerical methods: the numerical integration of SAS area and the point‐by‐point scanning method. This algorithm calculates the volume of the spheres confined among their intersection planes and resembles a numerical integration of surface area by summing up volume layers. These characteristics make the algorithm useful in analytically calculating the work required to create a convex cavity in a solvent and the work (pΔV) associated with a change in the solvent‐excluded volume of the solute due to solvent pressure. © 1995 by John Wiley & Sons, Inc.
Electrostatic bonding models: A test on group 1 and 2 metal complexes with H2O, NH3, H2S, PH3, and related ligands
Authors: Magnusson Eric
Published: January 2005

Electrostatic models frequently proposed to describe ion–molecule interactions have been tested on the adducts formed by Group 1 and 2 cations with H2O, NH3, H2S, PH3, their methyl analogs, and their anions. The results from the model calculations were compared with all‐electron calculations (geometry optimized, MP2, TZP basis sets) carried out on adducts formed with Li+, Na+, K+, Ca2+, and Mg2+. The electrostatic potential model was utilized in two ways: The attraction of the point charge was calculated with and without relaxation of the ligand. A third model allowed relaxation of the ligand but treated the cation as a frozen core. The final model was the crude point charge/point dipole approximation. At long range, the models satisfactorily track the effects on energy of gross changes in the ion–ligand interaction (monovalent versus divalent ions, neutral ligands versus anions, parent ligands versus methyl derivatives), but correlation at close range is poor, especially for binding by divalent cations. The hypothesis that the calculated strength of cation–dipole binding is dependent on calculated dipole moment could not be verified. © 1995 by John Wiley & Sons, Inc.
Ab initio molecular orbital studies of nonidentity allyl transfer reactions
Authors: Lee Ikchoon , Kim Chang Kon , Lee Bon‐Su
Published: January 2005

Ab initio molecular orbital (MO) calculations are carried out on the nonidentity allyl transfer processes, X− + CH2CHCH2Y ⇌ CH2CHCH2 X + Y−, with X− = H, F, and Cl and Y = H, NH2, OH, F, PH2, SH, and Cl. The Marcus equation applies well to the allyl transfer reactions. The transition state (TS) position along the reaction coordinate and the TS structure are strongly influenced by the thermodynamic driving force, whereas the TS looseness is originated from the intrinsic barrier. The intrinsic barrier, ΔE, looseness, %L‡, and absolute asymmetry, %AS‡, are well correlated with the percentage bond elongation, %CY‡ = [(d − d)/d] × 100 and/or %CX‡. The %CY‡ and the bond orders indicate that a stronger nucleophile and/or a stronger nucleofuge (or a better leaving group) leads to an earlier TS on the reaction coordinate with a lesser degree of bond making as well as bond breaking. These are consistent with the Bell‐Evans‐Polanyi principle and the Leffler‐Hammond postulate. © 1995 by John Wiley & Sons, Inc.
On the existence of SH3, SeH3, and TeH3: Discrepancies between all‐electron and pseudopotential calculations
Authors: Smart Bruce A. , Schiesser Carl H.
Published: January 2005

Ab initio calculations using both pseudopotential and double and triple‐ζ all‐electron basis sets, with and without electron correlation (MP2, QCISD), have been performed on the λ4‐sulfanyl (SH3), λ4‐selanyl (SeH3), and λ4‐tellanyl (TeH3) radicals. All‐electron basis sets of double‐ζ quality predict that SH3 and SeH3 correspond to transition states on their respective potential energy surfaces. In contrast, the pseudopotentials of Hay and Wadt predict that SH3 and SeH3 correspond to local minima at the QCISD level of theory while the pseudopotentials of Christiansen and Stevens predict transition states. By comparison, TeH3 proved to be a local minimum at all levels of theory. Interestingly, when a very large (triple‐ζ) all‐electron basis set was used, SH3 proved to be a transition state; however, in this instance the potential energy surface was found to be much flatter than in the case for which a double‐ζ basis set was used, suggesting that further improvements in the basis set may lead to a local minimum. Further improvements in the all‐electron selenium basis also led to a local minimum for SeH3 at the QCISD level of theory. © 1995 by John Wiley & Sons, Inc.
A density functional treatment of organolithium compounds: Comparison to ab initio, semiempirical, and experimental results
Authors: Pratt Lawrence M. , Khan Ishrat M.
Published: January 2005

Density functional calculations on several classes of organolithium compounds are described. The compounds studied include lithium bonds to carbon, oxygen, and nitrogen and are representative of most types of organolithium compounds that have appeared in the recent literature. The computational results are compared to those using MNDO, which has been shown to have some serious deficiencies in compounds involving carbon–lithium bonds, and to PM3 results, which offer some improvement over MNDO for many organolithium compounds. Most of the density functional calculations with a large basis set are in good agreement with available ab initio and experimental data. Calculated carbon–lithium bond lengths were slightly shorter than those calculated by other ab initio methods and were substantially longer than those calculated by MNDO, which is known to underestimate carbon–lithium bond lengths severely. Dimerization energies of methyllithium, calculated by DMol, were also in good agreement with those of other ab initio calculations. Lithium–nitrogen bonds in lithium amides were calculated to be slightly shorter by DMol than by MNDO, although the two methods were in qualitative agreement for this type of compound. © 1995 by John Wiley & Sons, Inc.
Error evaluation in the design of a special‐purpose processor that calculates nonbonded forces in molecular dynamics simulations
Authors: Amisaki Takashi , Fujiwara Takaji , Kusumi Akihiro , Miyagawa Hiroo , Kitamura Kunihiro
Published: January 2005

Special‐purpose parallel machines that are plugged into a workstation to accelerate molecular dynamics (MD) simulations are attracting a considerable amount of interest. These machines comprise scalable homogeneous multiprocessors for calculating nonbonded forces (Coulombic and van der Waals forces), which consume more than 99% of the central processing unit (CPU) time in standard MD simulations. Each processor element in the machine has a pipeline architecture to calculate the total nonbonded force exerted on a particle by all of the other particles using information regarding the coordinates, the electric charge, and the species of each particle broadcast by the host computer. The processor then sends the calculated force back to the host computer. This article addresses the precision of the calculated nonbonded forces in the design of a processor LSI with minimal complexity. The precision of the arithmetic inside the processor that is required to calculate forces for MD simulations using Verlet's procedure was critically evaluated. Forward and backward error analysis, coupled with numerical MD experiments on one‐dimensional systems, was performed, and the following results were obtained: (1) Each element of the position vector which the processor receives from the host computer should have a precision of at least 25 bits; and (2) the pairwise forces should be calculated using floating point numbers with at least 29 bits of mantissa in the processor. Calculation of a pairwise force, which involves second‐order polynomial interpolation using a table‐driven algorithm, requires a key which contains a duplicate of at least 11 most significant bits of mantissa of the squared pairwise distance. The final result was that (3) the total force that acts on a particle, which is obtained by summing the forces exerted by all of the other particles, should be calculated using an accumulator that has a mantissa of at least 48 bits. © 1995 by John Wiley & Sons, Inc.
Hydrophobic solvation of methane and nonbond parameters of the TIP3P water model
Authors: Sun Yaxiong , Kollman Peter A.
Published: January 2005

In the process of studying the solvation of simple hydrocarbons, we found that the nonbond van der Waals (vdw) parameters for the TIP3P water model could be adjusted without significantly changing its liquid water properties. By increasing the van der Waals well depth ϵ from 0.152 kcal/mol for the TIP3P model to 0.190 kcal/mol (model TIP3P_MOD), the solvation free energy of all‐atom methane changed from 2.5 kcal/mol to 2.1 kcal/mol, much closer to the experimental value of 2.0 kcal/mol. This change of van der Waals parameters does not change hydrophilic solvation, since calculations using either water model lead to the same relative solvation free energy between ethane and methanol. The solvation free‐energy differences between methane and ethane and between ethane and propane have also been calculated with both models, and results found with the two water models are similar. For the united‐atom hydrocarbon model, however, the solvation free energy of methane changed from 2.1 kcal/mol with TIP3P to 1.8 kcal/mol with TIP3P_MOD. © 1995 by John Wiley & Sons, Inc.
Algorithms for constrained molecular dynamics
Authors: Barth Eric , Kuczera Krzysztof , Leimkuhler Benedict , Skeel Robert D.
Published: January 2005

In molecular dynamics simulations, the fastest components of the potential field impose severe restrictions on the stability and hence the speed of computational methods. One possibility for treating this problem is to replace the fastest components with algebraic length constraints. In this article the resulting systems of mixed differential and algebraic equations are studied. Commonly used discretization schemes for constrained Hamiltonian systems are discussed. The form of the nonlinear equations is examined in detail and used to give convergence results for the traditional nonlinear solution technique SHAKE iteration and for a modification based on successive overrelaxation (SOR). A simple adaptive algorithm for finding the optimal relaxation parameter is presented. Alternative direct methods using sparse matrix techniques are discussed. Numerical results are given for the new techniques, which have been implemented in the molecular modeling software package CHARMM and show as much as twofold improvement over SHAKE iteration. © 1995 John Wiley & Sons, Inc.
Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins
Authors: Cieplak Piotr , Cornell Wendy D. , Bayly Christopher , Kollman Peter A.
Published: January 2005

We present the derivation of charges of ribo‐ and deoxynucleosides, nucleotides, and peptide fragments using electrostatic potentials obtained from ab initio calculations with the 6‐31G* basis set. For the nucleic acid fragments, we used electrostatic potentials of the four deoxyribonucleosides (A, G, C, T) and four ribonucleosides (A, G, C, U) and dimethylphosphate. The charges for the deoxyribose nucleosides and nucleotides are derived using multiple‐molecule fitting and restrained electrostatic potential (RESP) fits,1,2 with Lagrangian multipliers ensuring a net charge of 0 or ± 1. We suggest that the preferred approach for deriving charges for nucleosides and nucleotides involves allowing only C1′ and H1′ of the sugar to vary as the nucleic acid base, with the remainder of sugar and backbone atoms forced to be equivalent. For peptide fragments, we have combined multiple conformation fitting, previously employed by Williams3 and Reynolds et al.,4 with the RESP approach1,2 to derive charges for blocked dipeptides appropriate for each of the 20 naturally occuring amino acids. Based on our results for propyl amine,1,2 we suggest that two conformations for each peptide suffice to give charges that represent well the conformationally dependent electrostatic properties of molecules, provided that these two conformations contain different values of the dihedral angles that terminate in heteroatoms or hydrogens attached to heteroatoms. In these blocked dipeptide models, it is useful to require equivalent N—H and CO charges for all amino acids with a given net charge (except proline), and this is accomplished in a straightforward fashion with multiple‐molecule fitting. Finally, the application of multiple Lagrangian constraints allows for the derivation of monomeric residues with the appropriate net charge from a chemically blocked version of the residue. The multiple Lagrange constraints also enable charges from two or more molecules to be spliced together in a well‐defined fashion. Thus, the combined use of multiple molecules, multiple conformations, multiple Lagrangian constraints, and RESP fitting is shown to be a powerful approach to deriving electrostatic charges for biopolymers. © 1995 John Wiley & Sons, Inc.
Remarks on the use of the apparent surface charges (ASC) methods in solvation problems: Iterative versus matrix‐inversion procedures and the renormalization of the apparent charges
Authors: Cammi R. , Tomasi J.
Published: January 2005

We present a formal and numerical comparison between the iterative and matrix‐inversion approaches of the polarizable continuum model. The formal analysis shows completely the equivalence of the two approaches. Numerical equivalence is also recovered, introducing in both methods the proper boundary conditions on the apparent charge distribution. © 1995 John Wiley & Sons, Inc.
Harmonic analysis of large systems. I. Methodology
Authors: Brooks Bernard R. , Janežič Dušanka , Karplus Martin
Published: January 2005

Methods have been developed for the determination of vibrational frequencies and normal modes of large systems in the full conformational space (including all degrees of freedom) and in a reduced conformational space (reducing the number of degrees of freedom). The computational method, which includes Hessian generation and storage, full and iterative diagonalization techniques, and the refinement of the results, is presented. A method is given for the quasiharmonic analysis and the reduced basis quasiharmonic analysis. The underlying principle is that from the atomic fluctuations, an effective harmonic force field can be determined relative to the dynamic average structure. Normal mode analysis tools can be used to characterize quasiharmonic modes of vibration. These correspond to conventional normal modes except that anharmonic effects are included. Numerous techniques for the analyses of vibrational frequencies and normal modes are described. Criteria for the analysis of the similarity of low‐frequency normal modes is presented. The approach to determining the natural frequencies and normal modes of vibration described here is general and applicable to any large system. © 1995 John Wiley & Sons, Inc.

This article is a U.S. Government work and, as such, is in the public domain in the United States of America.
Carbon–hydrogen bond strengths in methyl formate and the kinetics of the reaction with iodine
Authors: Solly Richard K. , Benson Sidney W.
Published: January 2005

The gas phase reaction I2 + HCOOCH3 → HI + CH3I + CO2 has been studied spectrophotometrically in a static system over the pressure ranges I2 (6–39 torr) and HCOOMe (28–360 torr). In the temperature range 293–356°, the initial rate of disappearance of I2 is first order in [HCOOMe] and half‐order in [I2]. The rate determining step is
equation image
where k1 is given by

where θ = 2.303 RT in kcal/mole. This activation energy gives a carbonyl CH bond strength of 92.7 kcal/mole. At 356° there was no evidence of abstraction of a methoxy hydrogen, so a lower limit of 100 kcal/mole may be placed on this CH bond strength. These ester CH bond strengths are discussed in relation to comparable values in aldehydes and ethers.
Kinetics of the HBr‐catalyzed photoisomerization of the allyl halides
Authors: Abell Paul I. , Adolf Paul K.
Published: January 2005

The kinetics of the gas phase bond isomerization of allyl fluoride, allyl chloride and allyl bromide, catalyzed by HBr and ultraviolet light, has been studied in the temperature range of 150–250° and at pressures of 3.5 to 50 mm. The reactions are very clean, first order in allyl halide and HBr, and have a light intensity exponent of unity. A quantum yield for allyl chloride of 3200 indicates a chain reaction. Dilution with inert gases is almost without effect, indicating that excited state intermediates are not involved. A small wall effect is observed. The evidence indicates a free radical reaction, involving hydrogen abstractions by bromine atoms, with replacement at the other end of the allylic radical.
A Complication in the thermal reactions of 1,1,2,2‐tetramethylcyclopropane
Authors: Blumstein C. , Henfling D. , Sharts C. M. , O'Neal H. E.
Published: January 2005

Reinvestigation of the gas phase thermal reaction of 1,1,2,2‐tetramethylcyclopropane (699‐759°K) gave for the unimolecular disappearance of reactant, k(TMC) = 1015.27–63.93/θ sec−1, in good agreement with the original results of Frey and Marshall. However, evidence for a high activation energy (E = 79 ± 5 kcal/mole), competitive unimolecular decomposition to 2,3‐dimethyl‐1 and ‐2‐butenes was also obtained. It is proposed that the serious discrepancy noted [1] between the experimentally observed Arrhenius parameters for the overall reaction kinetics, and those predicted by transition state calculations assuming a biradical mechanism for the isomerization reactions (previously believed to be the only primary reaction mode) can be explained in terms of the increasing importance of the decomposition reactions at higher reaction temperatures.
The pyrolysis of ethane in the presence of nitric oxide
Authors: Esser Joseph , Laidler Keith J.
Published: January 2005

The kinetics of the ethane pyrolysis have been studied at temperatures from 550 to 596°C and with 0 to 62% of added nitric oxide. The rates of production of various products were studied by gas chromatography; ethylene, hydrogen, methane, nitrogen, water, nitrous oxide and acetonitrile were found as primary products, with hydrogen cyanide, carbon monoxide, acetaldehyde, n‐butane, 1‐butene, cis‐ and trans‐2‐butene and 1,3‐butadiene as secondary products. For all the primary products the orders with respect to C2H6and NO were determined, as were the activation energies at two different percentages of NO (15.7 and 45.5%).

Nitric oxide was found to be rapidly consumed with a finite initial rate, and the rate of production of H2O was close to that of C2H4 at higher nitric oxide pressures.

A mechanism is proposed which gives good agreement with all of the observed results. Its main features are: (1) Initiation takes place mainly by the unimolecular dissociation of ethane; there is no evidence for or against the process NO + C2H6 → HNO + C2H5; (2) NO scavenges ethyl radicals to form acetaldoxime which decomposes, and in this way the breakdown of C2H5 is hastened; (3) termination takes place mainly by the unimolecular decomposition of acetaldoxime to give inactive products. Some of the relevant rate parameters are evaluated. Reactions are proposed to account for the formation of the secondary products observed.
Kinetic study of the gas‐phase reaction c‐C5H8 + I2 ⇄ c‐C5H6 + 2HI the heat of formation and the stabilization energy of the cyclopentenyl radical
Authors: Furuyama Shozo , Golden David M. , Benson Sidney W.
Published: January 2005

The gas‐phase dehydrogenation of cyclopentene to cyclopentadiene catalyzed by iodine in the range 178–283°C has been found to obey a rate law consistent with the slow rate‐determining step, \documentclass{article}\pagestyle{empty}\begin{document}$ {\rm I} + {\rm c} - {\rm C}_5 {\rm H}_8 \stackrel{4}{\rightarrow}{\rm HI} + {\rm c} - {\rm C}_5 {\rm H}_7 $\end{document}, log [k4/(1 mole−1 sec−1)] = 10.25 ± 0.08 ‐ (12.26 ± 0.18)/θ, where θ = 2.303RT in kcal/mole. Surface effects are not important. This value of E4 leads to a value of DHmagnified image = 82.3 ± 1 kcal/mole and ΔHf298magnified image = 38.4 ± 1 kcal/mole. From difference in bond strengths in the alkane and the alkene, the allylic resonance stabilization in the cyclopentenyl radical is 12.6 ± 1.0 kcal/mole, in excellent agreement with the value for the butenyl radical.

Arrhenius parameters for the other steps in the mechanism are evaluated. The low value of A4 (compared with A4 for cyclopentane) suggests a “tighter” transition state for H‐atom abstraction from alkenes than from alkanes.
H2S inhibition of the pyrolysis of ethane
Authors: Scacchi G. , Dzierzynski M. , Martin R. , Niclause M.
Published: January 2005

At 540°C, H2S (0.1 to 5 mm Hg) diminishes the initial rate of pyrolysis of C2H6 (50 mm Hg) into C2H4 + H2 and, even more strongly, the rate of appearance of the traces of nC4H10; on the contrary, the initial rate of formation of the traces of CH4 is practically not modified.

A mechanism is proposed in order to interpret these experimental facts.
The free‐radical reaction of tri‐n‐butyltin hydride with disulfides
Authors: Spanswick J. , Ingold K. U.
Published: January 2005

The kinetics and absolute rate constants for the free‐radical chain reaction of tri‐n‐butyltin hydride with di‐t‐butyl disulfide have been measured in cyclohexane at 30°. The rate controlling step for chain propagation involves the cleavage of the disulfide bond by an attacking tributyltin radical. The rate constant for this bimolecular homolytic substitution at sulfur is ∼8 × 104 Mole−1 sec−1. Chain termination involves the self‐reaction of two tributyltin radicals.

The rate constants for attack of tributyltin radicals on some other disulfides and on elemental sulfur have also been measured. The results are compared with literature data for homolytic substitutions on these compounds by a variety of radicals which have their unpaired electron centered on carbon.
Stern–volmer plots in the photolysis of perfluoroazoethane
Authors: Pritchard G. O. , Mattinen W. A. , Dacey J. R.
Published: January 2005

Nitrogen quantum yields are reported for the photolysis of C2F5NNC2F5 at 3660 Å over the pressure range 2–10 cm from 25° to 150°c. The Stern–Volmer plots obtained are discussed and compared with those obtained with azoethane and azoisopropane.
Comparative rate single‐pulse shock tube studies on the thermal decomposition of cyclohexene, 2,2,3‐trimethylbutane, isopropyl bromide, and ethylcyclobutane
Authors: Tsang Wing
Published: January 2005

A check of the data from comparative rate single‐pulse shock tube experiments have been carried out through the use of a new standard reaction, the decyclization reaction of ethylcyclobutane. The rate expressions for cyclohexene and 2,2,3‐trimethylbutane have been found to be

in excellent agreement with previously published results. Most of the small discrepancy that does exist is apparently due to the differences between the present and earlier (decomposition of isopropyl bromide) "standard" reaction. For the latter process, the present study yields

These results confirm the correctness of previously published comparative rate single‐pulse shock tube experiments. They demonstrate once again that for the decomposition of paraffin hydrocarbons, calculated preexponential factors are at least an order of magnitude higher than the directly measured number and that the accepted value of the heat of formation of t‐butyl radicals ΔHf300(tC4H9·) = 29 kJ (6.8 kcals) is at least 10 kJ too low. Finally, attention is called to recent studies on neopentane decomposition in flow and static systems which are in complete agreement with the present conclusions.
The thermal unimolecular isomerization of cis‐hepta‐1,3‐diene
Authors: O'Neal H. E. , Frey H. M.
Published: January 2005

The reversible isomerization of cis‐hepta‐1,3‐diene to cis‐2‐trans‐4‐heptadiene via a 1,5 hydrogen shift has been investigated kinetically at nine temperatures in the range of 475° to 531°K. Equilibrium is reached near 94% reaction. Some cis‐2‐cis‐4‐heptadiene is also formed, but at a rate some 60 times slower than the cis,trans isomer. A least‐squares analysis of the data yielded the Arrhenius equation for the isomerization of the cis‐hepta‐1,3‐diene:

Possible errors in the equilibrium constant measurements are discussed, and employing an equilibrium constant calculated by using group additivity estimates together with the values of k1, we obtained for the reverse reaction

where

.
Kinetics and thermochemistry of the gas phase reaction of methyl ethyl ketone with iodine. I. The resonance energy of the methylacetonyl radical
Authors: Solly Richard K. , Golden David M. , Benson Sidney W.
Published: January 2005

The gas phase reaction of iodine (2.8–43.3 torr) with methyl ethyl ketone (MEK) (7.4–303.4 torr) has been studied over the temperature range 280–355°C in a static system. The initial rate of disappearance of I2 is first order in MEK and half order in I2. The rate‐determining step is the abstraction of a secondary hydrogen atom by an iodine atom:

where k1 is given by

and θ = 2.303RT in kcal/mole. This activation energy is equivalent to a secondary CH bond strength of 92.3 ± 1.4 kcal/mole and ΔH of the methylacetonyl radical = ‐16.8 ± 1.7 kcal/mole. By comparison with 95 kcal/mole for the secondary CH bond strength, when delocalization of the unpaired electron with a pi bond is not possible, the resonance stabilization of the methylacetonyl radical is calculated to be 2.7 ± 1.7 kcal/mole. This value is 10 kcal/mole less than the stabilization energy of the isoelectronic methylallyl radical. The difference in pi bond energies in the canonical forms of the methylacetonyl radical is shown to account for the variation in stabilization energies.
Mechanism of the bimolecular reactions of ethylene and propylene
Authors: Back M. H.
Published: January 2005

Rate constants for the bimolecular reactions of ethylene and propylene to form radicals and to form cyclobutane or its derivatives have been calculated using thermodynamic and kinetic data. Comparison of these rates with the kinetics of the thermal reactions of ethylene and propylene show that cyclobutane and its derivatives are probably not important intermediates in the processes forming radicals.
Hydrogen abstraction from organosilicon compounds. The reactions of fluoromethyl radicals with tetramethylsilane. Polar effects in gas phase reactions
Authors: Kerr J. A. , Timlin D. M.
Published: January 2005

The photolysis of 1,1,3,3‐tetrafluoroacetone has been reinvestigated as a source of CHF2 radicals at temperatures up to 578°K, and the following rate constant ratio was determined for the reactions magnified image

θ= 2.303 RT in kcal/mole.

1,1‐Difluoro‐ and 1,1,3,3‐tetrafluoroacetone were photolyzed in the presence of tetramethylsilane, and Arrhenius parameters were measured for the hydrogen abstraction reactions: R + Me4Si → RH + Me3SiCH2

R
T(°K)
E (kcal/mole)
log A (mole−1cc sec−1)
log k (500°K) (mole−1cc sec−1)

CH2F
473–586
12.00 ± 0.30
11.68 ± 0.12
6.44

CHF2
416–526
10.18 ± 0.33
11.65 ± 0.15
7.21

By comparing with previous data on the CH3 and CF3 reactions, the activation energies were interpreted in terms of the enthalpy changes for the reactions and a polar effect operative between the attacking fluoromethyl radicals and the substrate which tends to reduce the activation energy progressively as the fluorine content of the radical increases. This polar effect, which decreases the activation energy for hydrogen abstraction from SiMe4 along the series CH3, CH2F, CHF2, and CF3, is in marked contrast to the polar repulsion between the fluorinated radicals and SiHCl3 which was tentatively proposed to explain the increase in activation energy observed in the same series of reactions with SiHCl3.
The kinetics and thermochemistry of the gas phase reaction of cyclopentadiene and iodine. Relevance to the heat of formation of cyclopentadienyl iodide and cyclopentadienyl radical
Authors: Furuyama Shozo , Golden David M. , Benson Sidney W.
Published: January 2005

The rate of the reaction of cyclopentadiene with iodine has been followed spectrophotometrically over the temperature range 171.7° to 276.5°C. The reaction first proceeds almost to the point of equilibrium with cyclopentadienyl iodide and HI, although the final products are fulvalene and HI. Equilibrium constants obtained are those predicted by bond additivity. A third‐law value of δH0f 298 (c‐C5H5I,g) = 49 kcal/mole is obtained. Rate studies of the reaction up to the iodide equilibrium, yield values for the rate constant magnified image. Uncertainty in the Arrhenius parameters, as well as doubts as to the applicability of the usual assumption that E3 = 1 ± 1 kcal/mole, make difficult an evaluation of total cyclopentadienyl stabilization energy (TSE) from these data. However, the value is probably 15 < TSE < 20.
Kinetics of the gas‐phase reaction of cyclopropylcarbinyl iodide and hydrogen iodide. Heat of formation and stabilization energy of the cyclopropylcarbinyl radical
Authors: McMillen Donald F. , Golden David M. , Benson Sidney W.
Published: January 2005

The rate of the gas phase reaction

has been measured spectrophotometrically over the range 480°–550°K. The rate constant fits the equation

where θ = 2.303RT in kcal/mole. This result, together with the assumption that the activation energy for the back reaction is 0 ± 1 kcal/mole, allows calculation of DH (ΔCH2H) = 97.4 ± 1.6 kcal/mole and ΔH (ΔCH2·) = 51.1 ± 1.6 kcal/mole. These values correspond to a stabilization energy of 0.4 ± 1.6 kcal/mole in the cyclopropylcarbinyl radical.
Kinetics of the thermal gas phase reactions of 1,2‐epoxy‐2‐methylpropane
Authors: Flowers M. C. , Parker R. M.
Published: January 2005

The kinetics of the gas phase decomposition of 1,2‐epoxy‐2‐methylpropane has been studied over the temperature range 377°–436°C at pressures between 5.3 and 61.6 torr. Isomerization reactions to give isobutyraldehyde, isopropenyl methyl ether, and 2‐methyl‐prop‐2‐en‐l‐ol account for over 95% of the epoxide decomposition. These isomerizations are homogeneous first‐order, nonradical processes:
Chemically activated 3‐methyl‐l‐butene and 2‐methyl‐l‐butene from photolysis of diazomethane–isobutene–neopentane–oxygen mixtures
Authors: Taylor G. W. , Simons J. W.
Published: January 2005

An experimental study of the decomposition kinetics of chemically activated 2‐methyl‐l‐butene and 3‐methyl‐l‐butene produced from photolysis of diazomethane‐isobutene‐neopentane‐oxygen mixtures is reported. The experimental rate constants for 3‐methyl‐l‐butene decomposition were 1.74 ± 0.44 × 108 sec−1 and 1.01 ± 0.25 × 108 sec−1 at 3660 and 4358 Å, respectively. 2‐Methyl‐l‐butene experimental decomposition rate constants were found to be 5.94 ± 0.59 × 107 sec−1 at 3660 Å and 3.42 ± 0.34 × 107 sec−1 at 4358 Å. Activated complex structures giving Arrhenius A‐factors calculated from absolute rate theory of 1016.6 ± 0.5 sec−1 for 3‐methyl‐l‐butene and 1016.2 ± 0.4 sec−1 for 2‐methyl‐l‐butene, both calculated at 1000°K, were required to fit RRKM theory calculated rate constants to the experimental rate constants at reasonable E0 and E* values. Corrected calculations (adjusted E0 values) on previous results for 2‐pentene decomposition gave an Arrhenius A‐factor of 1016.45 ± 0.35 sec−1 at 1000°K. The predicted A‐factors for these three alkene decompositions giving resonance‐stabilized methylully radicals are in good internal agreement. The fact that these A‐factors are only slightly less than those for related alkane decompositions indicates that methylallylic resonance in the decomposition products leads to only a small amount of tightening in the corresponding activated complexes. This tightening is a significantly smaller factor than the large reduction in the critical energy due to resonance stabilization.
Some hydrogen abstraction reactions of the CF3CCl2 radical
Authors: Wampler Fred B. , Kuntz Robert R.
Published: January 2005

The gas phase photolysis of CF3CCl3 in the presence of several alkanes has been used to obtain Arrhenius parameters for the abstraction of hydrogen atoms by the CF3CCl2 radical:

Activation energies of 9.6 and 8.0 kcal/mole are found for abstraction from secondary and tertiary C–H bonds, respectively. The Arrhenius parameters are compared to those for CCl3 and CF3 radicals.
The reactions of C2F5 radicals with benzene in the vapor phase
Authors: Chamberlain G. A. , Whittle E.
Published: January 2005

C2F5 radicals were generated in the presence of benzene vapor by the reaction

The radicals react with the benzene by addition and pseudo H abstraction

equation image

The rate constant kadd for the addition reaction (7) is given by

where θ = 2.303RT cal/mole and kc is the rate constant for combination of C2F5 radicals. The addition becomes reversible above 110°C. The reactions of CF3 and C2F5 radicals with benzene vapor are compared.
The kinetics of the reactions of O(3P) atoms with dimethyl ether and methanol
Authors: Lefevre Henry F. , Meagher James F. , Timmons Richard B.
Published: January 2005

The kinetics of the reaction of O + CH3OCH3 were investigated using fast‐flow apparatus equipped with ESR and mass‐spectrometric detection. The concentration of O(3P) atoms to CH3OCH3 was varied over an unusually large range. The rate constant for reaction

was found to be k = (5.0 ± 1.0) × 1012 exp [(−2850 ± 200/RT)] cm3 mole−1 sec−1. The reaction O + CH3OH was studied using ESR detection. Based on an assumed stoichiometry of two oxygen atoms consumed per molecule of CH3OH which reacts, we obtain a value of k = (1.70 ± 0.66) × 1012 exp [(−2,280 ± 200/RT)] cm3 mole−1 sec−1 for the reaction

The results obtained in this study are compared with the results from other workers on these reactions. The observation of essentially equal activation energies in these two reactions is indicative of approximately equal CH bond strengths in CH3OCH3 and CH3OH. This is in agreement with recent measurements of these bond energies.
Rate constants for alkyl radical recombination. II. The isopropyl radical
Authors: Hiatt R. , Benson S. W.
Published: January 2005

Products of radical combination from the free‐radical buffer system \documentclass{article}\usepackage{amssymb}\pagestyle{empty}\begin{document}$${{\rm R}^{\rm .} + {\rm R}^{\rm '} {\rm I}\mathop {\leftrightharpoons}\limits^{{\rm K}_{{\rm RR}}}{\rm RI} + {\rm R}^{'}}$$\end{document}. have been analyzed for the two cases, R = Me, R′ = iPr and R = Et, R′ = iPr. Results are consistent with the previously examined system where R = Me, R′ = Et, and give a value of kP for iPr· combination of 108.6±1.1 M−1 sec−1.
The Gas‐phase thermal unimolecular isomerization of n‐propylidenecyclopropylamine to 5‐ethyl‐1‐pyrroline
Authors: Cocks Alan T. , Egger Kurt W.
Published: January 2005

The gas‐phase thermal isomerization of N‐propylidenecyclopropylamine has been studied in the temerature range of 573° to 635°K. The reaction is homogeneous and kinetically first order and yields 5‐ethyl‐1‐pyrroline as the sole product. The rate constants are independent of pressure in the range of 2.5 to 55 torr and fit the Arrhenius relationship log k(sec−1) = (14.05 ± 0.06) ‐ (47.77 ± 0.16)/θ where θ = 2.303 RT in units of kcal/mole, or log k(sec−1) = (14.05 ± 0.06) ‐ (199.9 ± 0.7)/θ, where θ = 2.303RT in kJ/mole. From considerations of a biradical pathway it is concluded that the resonance stabilization energy of the substituted 2‐aza‐allyl radical is very similar to that of the methallyl radical.
Thermal decomposition of 3‐chloro‐3‐trichloromethyldiazirine in solution
Authors: Liu Michael T. H. , Toriyama K.
Published: January 2005

The thermal decomposition of 3‐chloro‐3‐trichloromethyldizairine in carbon tetrachloride and iso‐octane has been investigated over the temperature range 75–115°C. The products, tetrachloroethylene and nitrogen, are formed quantitatively by a first‐order reaction which is probably unimolecular:
magnified image
The results yielded the following Arrhenius equations:

.