The Experts below are selected from a list of 213 Experts worldwide ranked by ideXlab platform
Jeong Hee Moon - One of the best experts on this subject based on the ideXlab platform.
-
efficient and reliable calculation of rice ramsperger kassel marcus Unimolecular Reaction rate constants for biopolymers modification of beyer swinehart algorithm for degenerate vibrations
Journal of the American Society for Mass Spectrometry, 2007Co-Authors: Jeong Hee Moon, Meiling Sun, Myung Soo KimAbstract:The Beyer-Swinehart (BS) algorithm, which calculates vibrational state density and sum, was modified for simultaneous treatment of degenerate vibrations. The modified algorithm was used in the grouped-frequency mode of the Rice-Ramsperger-Kassel-Marcus (RRKM) Unimolecular Reaction rate constant calculation for proteins with relative molecular mass as large as 100,000. Compared to the original BS method, reduction in computation time by a factor of around 3000 was achieved. Even though large systematic errors arising from frequency grouping were observed for state densities and sums, they more or less canceled each other, thus enabling reliable rate constant calculation. The present method is thought to be adequate for efficient and reliable RRKM calculations for any macromolecule in the gas phase such as the molecular ions of proteins, nucleic acids, and carbohydrates generated inside a mass spectrometer. The algorithm can also be used to calculate the internal energy distribution of a macromolecule at thermal equilibrium.
-
Efficient and reliable calculation of rice-ramsperger—kassel-marcus Unimolecular Reaction rate constants for biopolymers: Modification of beyer-swinehart algorithm for degenerate vibrations
Journal of the American Society for Mass Spectrometry, 2007Co-Authors: Jeong Hee MoonAbstract:The Beyer-Swinehart (BS) algorithm, which calculates vibrational state density and sum, was modified for simultaneous treatment of degenerate vibrations. The modified algorithm was used in the grouped-frequency mode of the Rice-Ramsperger-Kassel-Marcus (RRKM) Unimolecular Reaction rate constant calculation for proteins with relative molecular mass as large as 100,000. Compared to the original BS method, reduction in computation time by a factor of around 3000 was achieved. Even though large systematic errors arising from frequency grouping were observed for state densities and sums, they more or less canceled each other, thus enabling reliable rate constant calculation. The present method is thought to be adequate for efficient and reliable RRKM calculations for any macromolecule in the gas phase such as the molecular ions of proteins, nucleic acids, and carbohydrates generated inside a mass spectrometer. The algorithm can also be used to calculate the internal energy distribution of a macromolecule at thermal equilibrium.
-
improved whitten rabinovitch approximation for the rice ramsperger kassel marcus calculation of Unimolecular Reaction rate constants for proteins
Journal of Physical Chemistry B, 2007Co-Authors: Meiling Sun, Jeong Hee Moon, Myung Soo KimAbstract:The Whitten−Rabinovitch (WR) approximation used in the semi-classical calculation of the Rice−Ramsperger−Kassel−Marcus (RRKM) Unimolecular Reaction rate constant was improved for reliable application to protein Reactions. The state sum data for the 10-mer of each amino acid calculated by the accurate Beyer−Swinehart (BS) algorithm were used to obtain the residue-specific correction functions (w). The correction functions were obtained down to a much lower internal energy range than reported in the original work, and the cubic, rather than quadratic, polynomial was used for data fitting. For a specified sequence of amino acid residues in a protein, an average was made over these functions to obtain the sequence-specific correction function to be used in the rate constant calculation. Reliability of the improved method was tested for dissociation of various peptides and proteins. Even at low internal energies corresponding to the RRKM rate constant as small as 0.1 s-1, the rate constant calculated by the pr...
Myung Soo Kim - One of the best experts on this subject based on the ideXlab platform.
-
efficient and reliable calculation of rice ramsperger kassel marcus Unimolecular Reaction rate constants for biopolymers modification of beyer swinehart algorithm for degenerate vibrations
Journal of the American Society for Mass Spectrometry, 2007Co-Authors: Jeong Hee Moon, Meiling Sun, Myung Soo KimAbstract:The Beyer-Swinehart (BS) algorithm, which calculates vibrational state density and sum, was modified for simultaneous treatment of degenerate vibrations. The modified algorithm was used in the grouped-frequency mode of the Rice-Ramsperger-Kassel-Marcus (RRKM) Unimolecular Reaction rate constant calculation for proteins with relative molecular mass as large as 100,000. Compared to the original BS method, reduction in computation time by a factor of around 3000 was achieved. Even though large systematic errors arising from frequency grouping were observed for state densities and sums, they more or less canceled each other, thus enabling reliable rate constant calculation. The present method is thought to be adequate for efficient and reliable RRKM calculations for any macromolecule in the gas phase such as the molecular ions of proteins, nucleic acids, and carbohydrates generated inside a mass spectrometer. The algorithm can also be used to calculate the internal energy distribution of a macromolecule at thermal equilibrium.
-
improved whitten rabinovitch approximation for the rice ramsperger kassel marcus calculation of Unimolecular Reaction rate constants for proteins
Journal of Physical Chemistry B, 2007Co-Authors: Meiling Sun, Jeong Hee Moon, Myung Soo KimAbstract:The Whitten−Rabinovitch (WR) approximation used in the semi-classical calculation of the Rice−Ramsperger−Kassel−Marcus (RRKM) Unimolecular Reaction rate constant was improved for reliable application to protein Reactions. The state sum data for the 10-mer of each amino acid calculated by the accurate Beyer−Swinehart (BS) algorithm were used to obtain the residue-specific correction functions (w). The correction functions were obtained down to a much lower internal energy range than reported in the original work, and the cubic, rather than quadratic, polynomial was used for data fitting. For a specified sequence of amino acid residues in a protein, an average was made over these functions to obtain the sequence-specific correction function to be used in the rate constant calculation. Reliability of the improved method was tested for dissociation of various peptides and proteins. Even at low internal energies corresponding to the RRKM rate constant as small as 0.1 s-1, the rate constant calculated by the pr...
Donald L. Thompson - One of the best experts on this subject based on the ideXlab platform.
-
interpolating moving least squares methods for fitting potential energy surfaces an application to the h2cn Unimolecular Reaction
Journal of Chemical Physics, 2007Co-Authors: Yin Guo, Lawrence B Harding, Albert F Wagner, Michael Minkoff, Donald L. ThompsonAbstract:Classical trajectories have been used to compute rates for the Unimolecular Reaction H2CN→H+HCN on a fitted ab initio potential energy surface (PES). The ab initio energies were obtained from CCSD(T)/aug-cc-pvtz electronic structure calculations. The ab initio energies were fitted by the interpolating moving least-squares (IMLS) method. This work continues the development of the IMLS method for producing ab initio PESs for use in molecular dynamics simulations of many-atom systems. A dual-level scheme was used in which the preliminary selection of data points was done using a low-level theory and the points used for fitting the final PES were obtained at the desired higher level of theory. Classical trajectories were used on various low-level IMLS fits to tune the fit to the Unimolecular Reaction under study. Procedures for efficiently picking data points, selecting basis functions, and defining cutoff limits to exclude distant points were investigated. The accuracy of the fitted PES was assessed by compa...
-
Predicting nonstatistical Unimolecular Reaction rates using Kramers’ theory
The Journal of Chemical Physics, 1999Co-Authors: Yin Guo, Dmitrii V. Shalashilin, Justin A. Krouse, Donald L. ThompsonAbstract:A method for computing Unimolecular Reaction rate constants in the IVR-limited regime is presented. It is based on Kramers’ energy diffusion theory, with the Reaction coordinate taken as the subsystem and the rest of the vibrational modes as the bath. Applications to some bond fission Reactions demonstrate that the method accurately predicts the rate constants for wide range of energies by using the result of a dynamical calculation of the Reaction rate at a single energy to determine the friction coefficient. Examination of the energy exchange in the Reaction coordinate provides a qualitative understanding of the validity of the approach for treating Unimolecular Reactions. Thus, the method provides a practical means of calculating Reaction rates in the IVR-limited regime at considerable savings of computer time than that required by standard classical trajectory calculations.
-
method for predicting ivr limited Unimolecular Reaction rate coefficients
Journal of Chemical Physics, 1997Co-Authors: Dmitrii V. Shalashilin, Donald L. ThompsonAbstract:We present a method based on diffusion theory (i.e., a classical master equation) for calculating Unimolecular Reaction rates at high energies where Reaction is limited by the IVR (intramolecular vibrational energy redistribution) rate. The method, which we refer to as intramolecular dynamics diffusion theory (IDDT), uses short-time (a few fs) classical trajectory results to determine the characteristic times for the evolution of an initial microcanonical distribution, or, more specifically, the rate of IVR between the Reaction coordinate and the “bath” modes of the molecule. The IDDT method accurately predicts the rate of Si–Si bond fission in Si2H6 in the nonstatistical, IVR-controlled regime, as demonstrated by comparisons with the results of a standard classical trajectory simulation. The method requires much less computer time than do the standard classical trajectory calculations. The method can be used to obtain results from the dynamical regime down to the statistical regime (near threshold), wher...
-
intrinsic non rrk behavior classical trajectory statistical theory and diffusional theory studies of a Unimolecular Reaction
Journal of Chemical Physics, 1996Co-Authors: Dmitrii V. Shalashilin, Donald L. ThompsonAbstract:The nonstatistical behavior of a Unimolecular Reaction at energies well in excess of the threshold is examined. This behavior is sometimes referred to as ‘‘intrinsically non‐Rice–Ramsperger–Kassel–Marcus’’ (RRKM). It is well known that microcanonical Unimolecular rates computed by using classical mechanics can deviate from the predictions of statistical theories, particularly at high energies. The simplest manifestation of this behavior is that rate constants as a function of energy cannot be represented by simple expressions such as the RRK equation, k(E)=ν(1−E*/E)s−1, with a single set of parameter values over a wide energy range; more specifically, fits of the classical RRK expression to trajectory results frequently yield values for the effective number of degrees of freedom s that are significantly smaller than the ‘‘theoretical’’ values 3N−6. In the present study, rates were calculated for the Unimolecular dissociation of dimethylnitramine, (CH3)2NNO2, by simple N–N bond rupture over wide energy ran...
Meiling Sun - One of the best experts on this subject based on the ideXlab platform.
-
efficient and reliable calculation of rice ramsperger kassel marcus Unimolecular Reaction rate constants for biopolymers modification of beyer swinehart algorithm for degenerate vibrations
Journal of the American Society for Mass Spectrometry, 2007Co-Authors: Jeong Hee Moon, Meiling Sun, Myung Soo KimAbstract:The Beyer-Swinehart (BS) algorithm, which calculates vibrational state density and sum, was modified for simultaneous treatment of degenerate vibrations. The modified algorithm was used in the grouped-frequency mode of the Rice-Ramsperger-Kassel-Marcus (RRKM) Unimolecular Reaction rate constant calculation for proteins with relative molecular mass as large as 100,000. Compared to the original BS method, reduction in computation time by a factor of around 3000 was achieved. Even though large systematic errors arising from frequency grouping were observed for state densities and sums, they more or less canceled each other, thus enabling reliable rate constant calculation. The present method is thought to be adequate for efficient and reliable RRKM calculations for any macromolecule in the gas phase such as the molecular ions of proteins, nucleic acids, and carbohydrates generated inside a mass spectrometer. The algorithm can also be used to calculate the internal energy distribution of a macromolecule at thermal equilibrium.
-
improved whitten rabinovitch approximation for the rice ramsperger kassel marcus calculation of Unimolecular Reaction rate constants for proteins
Journal of Physical Chemistry B, 2007Co-Authors: Meiling Sun, Jeong Hee Moon, Myung Soo KimAbstract:The Whitten−Rabinovitch (WR) approximation used in the semi-classical calculation of the Rice−Ramsperger−Kassel−Marcus (RRKM) Unimolecular Reaction rate constant was improved for reliable application to protein Reactions. The state sum data for the 10-mer of each amino acid calculated by the accurate Beyer−Swinehart (BS) algorithm were used to obtain the residue-specific correction functions (w). The correction functions were obtained down to a much lower internal energy range than reported in the original work, and the cubic, rather than quadratic, polynomial was used for data fitting. For a specified sequence of amino acid residues in a protein, an average was made over these functions to obtain the sequence-specific correction function to be used in the rate constant calculation. Reliability of the improved method was tested for dissociation of various peptides and proteins. Even at low internal energies corresponding to the RRKM rate constant as small as 0.1 s-1, the rate constant calculated by the pr...
Henri Edouard Audier - One of the best experts on this subject based on the ideXlab platform.
-
A Hidden Hydrogen Transfer in the Unimolecular Reaction of 1,2-Dimethoxyethane•+
Journal of Physical Chemistry A, 1999Co-Authors: Roland Thissen, Christian Alcaraz, ‡ And J. Chamot-rooke, Philippe Mourgues, Odile Dutuit, Henri Edouard AudierAbstract:The metastable dimethoxyethane radical cation 1 eliminates methanal to give the CH3O+(H)CH2C•H2 distonic ion 2 (m/z 60, 80%) and methanol to yield the C3H6O•+ (m/z 58, 20%) fragment. The first process is well-known, beginning with the transfer of a hydrogen from a methoxy group to the oxygen of the other to yield the intermediate distonic ion •CH2OCH2CH2O+(H)CH3, 3. It is shown, from FTICR experiments, that the m/z 58 fragment possesses the CH3OCHCH2•+ structure 5. From energetic studies, it can be established that both fragmentations involve the same intermediate 3. The existence of a hidden 1,4-H transfer from carbon to carbon in the formation of 5 is shown. The energy profile is elucidated by the behavior of metastably decomposing stable isotopically labeled 1,2-dimethoxyethane radical cation 1.
-
Unimolecular Reaction of the (H3CO)3C+ cation
Rapid Communications in Mass Spectrometry, 1995Co-Authors: Viet Nguyen, Henri Edouard Audier, A. Milliet, Philippe MourguesAbstract:From metastable ion studies, Fourier transform ion cyclotron resonance experiments and semi-empirical calculations, the Unimolecular Reaction of the (H3CO)3C+ cation 1 is discussed. The first step of the Reaction is an irreversible, 1,3-CH transfer giving the H3COC(O)O(CH3) ion, 2. This ion either cleaves or isomerizes into the ion-neutral complex [H3COCO+, CH3OCH3], 3. Since the H3COCO+ cation is a very good CH donor, a CH transfgr then occurs within the complex, 3, to yield the predominant fragment (CH3)3O+.
