bluuebunny/crossref_metadata_2025_split huggingface dataset:
Algorithms for constrained molecular dynamics
Authors: Barth Eric , Kuczera Krzysztof , Leimkuhler Benedict , Skeel Robert D. 
Published: January 2005

AbstractIn 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

AbstractWe 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

AbstractWe 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

AbstractMethods 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

AbstractThe 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

AbstractThe 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

AbstractReinvestigation 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

AbstractThe 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

AbstractThe 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

AbstractAt 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

AbstractThe 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

AbstractNitrogen 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

AbstractA 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

AbstractThe 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

AbstractThe 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

AbstractRate 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

AbstractThe 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 imageθ= 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

AbstractThe 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

AbstractThe 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

AbstractThe 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

AbstractAn 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

AbstractThe 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

AbstractC2F5 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.