bluuebunny/crossref_metadata_2025_split huggingface dataset:
An empirical boundary potential for water droplet simulations
Authors: Essex Jonathan W. , Jorgensen William L. 
Published: January 2005

AbstractAn 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

AbstractThe 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

AbstractRestricted 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

AbstractThe 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

AbstractWe 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

AbstractThe 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

AbstractThe 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

AbstractAtomic 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

AbstractThe 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

AbstractStable 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

AbstractIn 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

AbstractThe 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

AbstractThe 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 imageThe 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

AbstractThe 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

AbstractEquilibrium 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

AbstractThe 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 imageθ= 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

AbstractThe 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

AbstractThe 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.