scholarly journals Subsite mapping of enzymes. Application of the depolymerase computer model to two α-amylases

1976 ◽  
Vol 159 (1) ◽  
pp. 121-132 ◽  
Author(s):  
J D Allen ◽  
J A Thoma
Keyword(s):  
Experimental Data ◽  
Computer Model ◽  
Rate Coefficient ◽  
Bond Cleavage ◽  
Preceding Paper ◽  
Rate Coefficients ◽  
Binding Region ◽  
Enzyme Binding ◽  
Chain Lengths ◽  
Subsite Mapping

In the preceding paper (Allen and Thoma, 1976) we developed a depolymerase computer model, which uses a minimization routine to establish a subsite map for a depolymerase. In the present paper we show how the model is applied to experimental data for two alpha-amylases. Michaelis parameters and bond-cleavage frequencies for substrates of chain lengths up to twelve glucosyl units have been reported for Bacillus amyloliquefaciens, and a subsite map has been proposed for this enzyme [Thoma et al. (1971) J. Biol. Chem. 246, 5621-5635]. By applying the computer model to the experimental data, we have arrived at a ten-subsite map. We find that a significant improvement in this map is achieved by allowing the hydrolytic rate coefficient to vary as a function of the number of occupied subsites comprising the enzyme-binding region. The bond-cleavage frequencies, the enzyme is found to have eight subsites. A partial subsite map is arrived at, but the entire binding region cannot be mapped because Michaelis parameters are complicated by transglycosylation reactions. The hydrolytic rate coefficients for this enzyme are not constant.

scholarly journals Subsite mapping of enzymes. Depolymerase computer modelling

1976 ◽  
Vol 159 (1) ◽  
pp. 105-120 ◽  
Author(s):  
J D Allen ◽  
J A Thoma
Keyword(s):  
Goodness Of Fit ◽  
Computer Modelling ◽  
Bond Cleavage ◽  
Calculated Data ◽  
Simulated Data ◽  
Binding Energies ◽  
Rate Coefficients ◽  
Minimization Procedure ◽  
Squared Residuals ◽  
Subsite Mapping

We have developed a depolymerase computer model that uses a minimization routine. The model is designed so that, given experimental bond-cleavage frequencies for oligomeric substrates and experimental Michaelis parameters as a function of substrate chain length, the optimum subsite map is generated. The minimized sum of the weighted-squared residuals of the experimental and calculated data is used as a criterion of the goodness-of-fit for the optimized subsite map. The application of the minimization procedure to subsite mapping is explored through the use of simulated data. A procedure is developed whereby the minimization model can be used to determine the number of subsites in the enzymic binding region and to locate the position of the catalytic amino acids among these subsites. The degree of propagation of experimental variance into the subsite-binding energies is estimated. The question of whether hydrolytic rate coefficients are constant or a function of the number of filled subsites is examined.

scholarly journals Effect of ammonia and water molecule on OH + CH3OH reaction under tropospheric condition

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mohamad Akbar Ali ◽  
M. Balaganesh ◽  
Faisal A. Al-Odail ◽  
K. C. Lin
Keyword(s):  
Water Molecule ◽  
Energy Surface ◽  
Rate Coefficient ◽  
Water Concentration ◽  
State Theory ◽  
Rate Coefficients ◽  
Hydrogen Atoms ◽  
Experimental And Theoretical Studies ◽  
Effective Reaction ◽  
Effective Reaction Rate

AbstractThe rate coefficients for OH + CH3OH and OH + CH3OH (+ X) (X = NH3, H2O) reactions were calculated using microcanonical, and canonical variational transition state theory (CVT) between 200 and 400 K based on potential energy surface constructed using CCSD(T)//M06-2X/6-311++G(3df,3pd). The results show that OH + CH3OH is dominated by the hydrogen atoms abstraction from CH3 position in both free and ammonia/water catalyzed ones. This result is in consistent with previous experimental and theoretical studies. The calculated rate coefficient for the OH + CH3OH (8.8 × 10−13 cm3 molecule−1 s−1), for OH + CH3OH (+ NH3) [1.9 × 10−21 cm3 molecule−1 s−1] and for OH + CH3OH (+ H2O) [8.1 × 10−16 cm3 molecule−1 s−1] at 300 K. The rate coefficient is at least 8 order magnitude [for OH + CH3OH(+ NH3) reaction] and 3 orders magnitude [OH + CH3OH (+ H2O)] are smaller than free OH + CH3OH reaction. Our calculations predict that the catalytic effect of single ammonia and water molecule on OH + CH3OH reaction has no effect under tropospheric conditions because the dominated ammonia and water-assisted reaction depends on ammonia and water concentration, respectively. As a result, the total effective reaction rate coefficients are smaller. The current study provides a comprehensive example of how basic and neutral catalysts effect the most important atmospheric prototype alcohol reactions.

Rapid relaxation NMR measurements to predict rate coefficients in ionic liquid mixtures. An examination of reaction outcome changes in a homologous series of ionic liquids

2021 ◽  
Author(s):  
Daniel C Morris ◽  
Stuart W Prescott ◽  
Jason B Harper
Keyword(s):  
Ionic Liquid ◽  
Ionic Liquids ◽  
Homologous Series ◽  
Rate Coefficient ◽  
Liquid Mixtures ◽  
Solvent Mixture ◽  
Rate Coefficients ◽  
Substitution Process

A series of ionic liquids based on the 1-alkyl-3-methylimidazolium cations were examined as components of the solvent mixture for a bimolecular substitution process. The effects on both the rate coefficient...

scholarly journals The calculation of TV, VT, VV, VV' − rate coefficients for the collisions of the main atmospheric components

1998 ◽  
Vol 16 (7) ◽  
pp. 838-846 ◽  
Author(s):  
A. S. Kirillov
Keyword(s):  
Experimental Data ◽  
Energy Transfer ◽  
Vibrational Energy ◽  
Relaxation Times ◽  
Atmospheric Composition ◽  
Rate Coefficients ◽  
Frequency Change ◽  
Vibrational Energy Transfer ◽  
Ion Chemistry ◽  
Vibrationally Excited

Abstract. The first-order perturbation approximation is applied to calculate the rate coefficients of vibrational energy transfer in collisions involving vibrationally excited molecules in the absence of non-adiabatic transitions. The factors of molecular attraction, oscillator frequency change, anharmonicity, 3-dimensionality and quasiclassical motion have been taken into account in the approximation. The analytical expressions presented have been normalized on experimental data of VT-relaxation times in N2 and O2 to obtain the steric factors and the extent of repulsive exchange potentials in collisions N2-N2 and O2-O2. The approach was applied to calculate the rate coefficients of vibrational-vibrational energy transfer in the collisions N2-N2, O2-O2 and N2-O2. It is shown that there is good agreement between our calculations and experimental data for all cases of energy transfer considered.Key words. Ionosphere (Auroral ionosphere; ion chemistry and composition). Atmospheric composition and structure (Aciglow and aurora).

scholarly journals On apparent barrier-free reactions

2020 ◽  
Vol 3 (1) ◽  
pp. 3-8
Author(s):  
Maikel Ballester
Keyword(s):  
Low Temperature ◽  
Chemical Reactions ◽  
Rate Constant ◽  
Kinetic Models ◽  
Rate Coefficient ◽  
Minimum Energy ◽  
Temperature Limit ◽  
Rate Coefficients ◽  
Minimum Energy Path ◽  
Full Dimension

Rate coefficients of bi-molecular chemical reactions are fundamental for kinetic models. The rate coefficient dependence on temperature is commonly extracted from the analyses of the reaction minimum energy path. However, a full dimension study of the same reaction may suggest a different asymptotic low-temperature limit in the rate constant than the obtained from the energetic profile.

Excitation of Ne VIII by electron impact

1976 ◽  
Vol 54 (20) ◽  
pp. 2019-2023 ◽  
Author(s):  
W. L. van Wyngaarden ◽  
Ronald J. W. Henry
Keyword(s):  
Electron Impact ◽  
Born Approximation ◽  
Experimental Error ◽  
Rate Coefficient ◽  
Impact Excitation ◽  
Rate Coefficients ◽  
Electron Impact Excitation ◽  
Close Coupling ◽  
Coupling Approximation ◽  
Made In

Collision strengths for electron impact excitation of Ne VIII are calculated at 14, 18, and 30 Ry in a 5-state close coupling expansion and the unitarized Coulomb–Born approximation. To assess the importance of exchange and coupling beyond the 5 states, additional calculations are made at 18 Ry in 5-state and 8-state close coupling expansions without exchange. For the 2s–2p excitation, calculations below the 3s threshold at 10.0 Ry are made in a 2-state close coupling expansion at 1.6, 3.2, and 8.0 Ry. In most instances the close coupling method gives results which differ by 15% or less from those of the unitarized Coulomb–Born approximation and by 20–70% from the CBI (Coulomb–Born) results of Bely. Rate coefficients which are calculated from the results obtained in the close coupling approximation agree within experimental error with the experimental results of Kunze and Johnston and Haddad and McWhirter with the exception of the rate coefficient for the 2p → 3d excitation.

The metachors of polyvalent and associated electrolytes in aqueous solutions

1984 ◽  
Vol 49 (5) ◽  
pp. 1079-1089
Author(s):  
Jiří Čeleda ◽  
Stanislav Škramovský ◽  
Jana Žilková
Keyword(s):  
Experimental Data ◽  
Surface Tension ◽  
Oxalic Acid ◽  
Organic Acids ◽  
Aqueous Solutions ◽  
Preceding Paper ◽  
Weak Electrolytes ◽  
Direct Proportionality ◽  
Very High

The quantity metachor introduced in the preceding paper was evaluated from the experimental data on surface tension of the aqueous solutions for a set of polyvalent and weak electrolytes. The almost complete concentration independence of the metachor and its direct proportionality to the number of the free charges in a dissociated molecule (observed and theoretically substantiated in the above cited paper for strong 1,1-, 1,2- and 2,1-valent electrolytes) has been verified in the present paper also for electrolytes of the higher valency types. The metachor values of fully dissociated 1,1-, 1,2-, 1,3- and 1,4-valent electrolytes follow a ratio (5 ± 1) : (10 ± 1.5) : 15 : 22 cm3 mol-1. Association of the electrolytes decreases correspondingly the metachor value as one can see on the case of electrolytes with bulky ions (NH4SCN, KCH3COO, Na2S2O3, hexacyanoferrates(II) or with the free acids H2SO4, H2CrO4, H3PO4 etc. A weak, in the investigated concentration range neglibility dissociated oxalic acid, consisting of small hydrated hydrophilic molecules, exhibits metachor values close to zero. Dibasic organic acids with a larger number of hydrophobic CH2 groups reach very high negative metachor values, however, their salts again possess metachor values close to 10 cm3 mol-1 - in accordance with the values found for strong 1,2-valent electrolytes. The metachors of ZnCl2 and CdCl2 decrease sharply from the last mentioned value, with increasing concentration while the metachor value of zinc perchlorate remains unchanged at the level corresponding to the fully dissociated salt. This is in agreement with the well known sequence of tendency of the d10-cations to form complexes with the Cl- and ClO-4 anions. All these facts have verified that the metachor can be, in principle, applied for a diagnostic states of the electrolytes in aqueous solutions.

Dissection of the multichannel reaction of acetylene with atomic oxygen: from the global potential energy surface to rate coefficients and branching dynamics

2019 ◽  
Vol 21 (3) ◽  
pp. 1408-1416 ◽  
Author(s):  
Junxiang Zuo ◽  
Qixin Chen ◽  
Xixi Hu ◽  
Hua Guo ◽  
Daiqian Xie
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Atomic Oxygen ◽  
Energy Surface ◽  
Rate Coefficient ◽  
Branching Ratio ◽  
Classical Trajectory ◽  
Rate Coefficients ◽  
Product Branching

A global potential energy surface for the O(3P) + C2H2reaction is developed and the quasi-classical trajectory study on the potential energy surface reproduce the rate coefficient and product branching ratio.

scholarly journals Low temperature gas phase reaction rate coefficient measurements: Toward modeling of stellar winds and the interstellar medium

2019 ◽  
Vol 15 (S350) ◽  
pp. 382-383
Author(s):  
Niclas A. West ◽  
Edward Rutter ◽  
Mark A. Blitz ◽  
Leen Decin ◽  
Dwayne E. Heard
Keyword(s):  
Low Temperature ◽  
Interstellar Medium ◽  
Gas Phase ◽  
Low Temperatures ◽  
Reaction Rate ◽  
Rate Coefficient ◽  
Building Blocks ◽  
Rate Coefficients ◽  
Stellar Winds ◽  
Phase Reaction

AbstractStellar winds of Asymptotic Giant Branch (AGB) stars are responsible for the production of ∼85% of the gas molecules in the interstellar medium (ISM), and yet very few of the gas phase rate coefficients under the relevant conditions (10 – 3000 K) needed to model the rate of production and loss of these molecules in stellar winds have been experimentally measured. If measured at all, the value of the rate coefficient has often only been obtained at room temperature, with extrapolation to lower and higher temperatures using the Arrhenius equation. However, non-Arrhenius behavior has been observed often in the few measured rate coefficients at low temperatures. In previous reactions studied, theoretical simulations of the formation of long-lived pre-reaction complexes and quantum mechanical tunneling through the barrier to reaction have been utilized to fit these non-Arrhenius behaviours of rate coefficients.Reaction rate coefficients that were predicted to produce the largest change in the production/loss of Complex Organic Molecules (COMs) in stellar winds at low temperatures were selected from a sensitivity analysis. Here we present measurements of rate coefficients using a pulsed Laval nozzle apparatus with the Pump Laser Photolysis - Laser Induced Fluorescence (PLP-LIF) technique. Gas flow temperatures between 30 – 134 K have been produced by the University of Leeds apparatus through the controlled expansion of N2 or Ar gas through Laval nozzles of a range of Mach numbers between 2.49 and 4.25.Reactions of interest include those of OH, CN, and CH with volatile organic species, in particular formaldehyde, a molecule which has been detected in the ISM. Kinetics measurements of these reactions at low temperatures will be presented using the decay of the radical reagent. Since formaldehyde and the formal radical (HCO) are potential building blocks of COMs in the interstellar medium, low temperature reaction rate coefficients for their production and loss can help to predict the formation pathways of COMs observed in the interstellar medium.

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