Molecular transition states

Halgren T A and Lipscomb W N 1977 The synchronous transit method for determining reaction pathways and locating molecular transition states Chem. Phys. Lett. 49 225... 

The Synchronous-Transit Method for determining Reaction Pathways and Locating Molecular Transition States Thomas A. Halgren and William N. Lipscomb Chemical Physics Letters 49 (1977) 225-232... 

Optimizations of saddle points such as molecular transition states and excited electronic states are usually more difficult than minimizations. First, the methods to determine saddle points are less developed and less stable than methods for minimizations. Second, it is usually less clear where to start an optimization of a saddle point than a minimization. 

I. Burhardt, P. Gaspard, Molecular transition state, resonances, and periodic orbit theory, J. Chem. Phys. 100 (1994) 6395. 

Halgren, T. A., and W. N. Lipscomb (1977), The Synchronous-Transit Method for Determining Reaction Pathways and Locating Molecular Transition States, Chem. 

Transit Method for Determining Reaction Pathways and Locating Molecular Transition States. 

Halasz GJ, Vibok A, Mayer I (1999) Comparison of basis set superposition error corrected perturbation theories for calculating intermolecular interaction energies. J Comput Chem 20 274-283 Halgren TA, Lipscomb WN (1977) The synchronous-transit method for determining reaction pathways and locating molecular transition states. (3hem Phys Lett 49 225-232 Hammond GS (1955) A correlation of reaction rates. J Am Chem Soc 77 334-338... 

The localization of first-order saddle points corresponding to molecular transition states is a much more difficult problem. Indeed, transition state searches cannot yet be called routine. There are several reasons for this situation. First, there is apparently little interest in the subject of saddle points outside the area of quantum chemistry. Thus, the above... 

The most important feature of enzyme molecules is their specific three-dimensional configuration with a molecular cavity including an active site which is suitable for a special sort of substrate molecule. At this site, the reaction of the substrate molecule during the formation of a product takes place. The enzyme molecule recognizes the substrate sterically, i.e. by following the lock-and-key principle. The active site makes up only a small part of the overall molecular volume. Its primary function is to stabilize the activated complex, i.e. the molecular transition state which is formed between enzyme and substrate... 

Sequences such as the above allow the formulation of rate laws but do not reveal molecular details such as the nature of the transition states involved. Molecular orbital analyses can help, as in Ref. 270 it is expected, for example, that increased strength of the metal—CO bond means decreased C=0 bond strength, which should facilitate process XVIII-55. The complexity of the situation is indicated in Fig. XVIII-24, however, which shows catalytic activity to go through a maximum with increasing heat of chemisorption of CO. Temperature-programmed reaction studies show the presence of more than one kind of site [99,1(K),283], and ESDIAD data show both the location and the orientation of adsorbed CO (on Pt) to vary with coverage [284]. 

It is important to recognize that the time-dependent behaviour of tire correlation fimction during the molecular transient time seen in figure A3.8.2 has an important origin [7, 8]. This behaviour is due to trajectories that recross the transition state and, hence, it can be proven [7] that the classical TST approximation to the rate constant is obtained from A3.8.2 in the t —> 0 limit ... 

Bennett C H 1977 Molecular dynamics and transition state theory the simulation of infrequent events Algorithms for Chemical Computation (ACS Symposium Series No 46) ed R E Christofferson (Washington, DC American Chemical Society)... 

A situation that arises from the intramolecular dynamics of A and completely distinct from apparent non-RRKM behaviour is intrinsic non-RRKM behaviour [9], By this, it is meant that A has a non-random P(t) even if the internal vibrational states of A are prepared randomly. This situation arises when transitions between individual molecular vibrational/rotational states are slower than transitions leading to products. As a result, the vibrational states do not have equal dissociation probabilities. In tenns of classical phase space dynamics, slow transitions between the states occur when the reactant phase space is metrically decomposable [13,14] on the timescale of the imimolecular reaction and there is at least one bottleneck [9] in the molecular phase space other than the one defining the transition state. An intrinsic non-RRKM molecule decays non-exponentially with a time-dependent unimolecular rate constant or exponentially with a rate constant different from that of RRKM theory. 

At any geometry g.], the gradient vector having components d EjJd Q. provides the forces (F. = -d Ej l d 2.) along each of the coordinates Q-. These forces are used in molecular dynamics simulations which solve the Newton F = ma equations and in molecular mechanics studies which are aimed at locating those geometries where the F vector vanishes (i.e. tire stable isomers and transition states discussed above). 

Hammes-Schiffer S and Tully J C 1995 Nonadiabatic transition state theory and multiple potential energy surfaces molecular dynamics of infrequent events J. Chem. Phys. 103 8528... 

Tripos a molecular mechanics force field, also the name of a company that sells computational chemistry software TST (transition state theory) method for computing rate constants UHF (unrestricted Hartree-Fock)... 

UFF (universal force field) a molecular mechanics force field unrestricted (spin unrestricted) calculation in which particles of different spins are described by different spatial functions VTST (variational transition state theory) method for predicting rate constants... 

His data suggested values for y of — 12 and — 6 kcal mol for molecular chlorination and nitration respectively, indicating that the transition states in nitration resemble the reactants more than do the transition states in chlorination. 

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