Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins

2016 ◽  
pp. 31-55
Author(s):  
A.K. Das ◽  
M. Meuwly
Keyword(s):  
Chemical Reactions ◽  
Force Fields ◽  
Mechanistic Studies

Analysis of Chemical Oscillations

1998 ◽  
Author(s):  
Irving R. Epstein ◽  
John A. Pojman
Keyword(s):  
Chemical Reactions ◽  
Mass Action ◽  
Dust Particles ◽  
Rate Equations ◽  
Mechanistic Studies ◽  
Chemical Oscillations ◽  
Chemical Oscillators ◽  
Oscillating Reactions ◽  
Persuasive Argument ◽  
Special Rules

Many of the most remarkable achievements of chemical science involve either synthesis (the design and construction of molecules) or analysis (the identification and structural characterization of molecules). We have organized our discussion of oscillating reactions along similar lines. In the previous chapter, we described how chemists have learned to build chemical oscillators. Now, we will consider how to dissect an oscillatory reaction into its component parts—the question of mechanism. A persuasive argument can be made that it was progress in unraveling the mechanism of the prototype BZ reaction in the 1970s that gave the study of chemical oscillators the scientific respectability that had been denied it since the discovery of the earliest oscillating reactions. The formulation by Field, Körös, and Noyes (Field et al., 1972) of a set of chemically and thermodynamically plausible elementary steps consistent with the observed “exotic” behavior of an acidic solution of bromate and cerium ions and malonic acid was a major breakthrough. Numerical integration (Edelson et al., 1975) of the differential equations corresponding to the FKN mechanism demonstrated beyond a doubt that chemical oscillations in a real system were consistent with, and could be explained by, the same physicochemical principles that govern "normal" chemical reactions. No special rules, no dust particles, and no vitalism need be invoked to generate oscillations in chemical reactions. All we need is an appropriate set of uni- and bimolecular steps with mass action kinetics to produce a sufficiently nonlinear set of rate equations. Just as the study of molecular structure has benefited from new experimental and theoretical developments, mechanistic studies of complex chemical reactions, including oscillating reactions, have advanced because of new techniques. Just as any structural method has its limitations (e.g., x-ray diffraction cannot achieve a resolution that is better than the wavelength of the x-rays employed), mechanistic studies, too, have their limitations. The development of a mechanism, however, has an even more fundamental and more frustrating limitation, sometimes referred to as the fundamental dogma of chemical kinetics. It is not possible to prove that a reaction mechanism is correct. We can only disprove mechanisms.

Nebulization prior to ionization for mechanistic studies of chemical reactions

2020 ◽  
Vol 1107 ◽  
pp. 107-112
Author(s):  
Hong Zhang ◽  
Lina Qiao ◽  
Wenxin Wang ◽  
Jing He ◽  
Kai Yu ◽  
...  
Keyword(s):  
Chemical Reactions ◽  
Mechanistic Studies

Use of the Magnetostatic Analogue In Electromagnetic Lens Engineering

1970 ◽  
Vol 28 ◽  
pp. 360-361
Author(s):  
John W. Coleman
Keyword(s):  
Boundary Conditions ◽  
High Performance ◽  
Force Fields ◽  
Optical Design ◽  
Direct Conversion ◽  
Design Engineering ◽  
Design Data ◽  
Scalar Potentials ◽  
Geometric Elements ◽  
At Will

In the design engineering of high performance electromagnetic lenses, the direct conversion of electron optical design data into drawings for reliable hardware is oftentimes difficult, especially in terms of how to mount parts to each other, how to tolerance dimensions, and how to specify finishes. An answer to this is in the use of magnetostatic analytics, corresponding to boundary conditions for the optical design. With such models, the magnetostatic force on a test pole along the axis may be examined, and in this way one may obtain priority listings for holding dimensions, relieving stresses, etc..The development of magnetostatic models most easily proceeds from the derivation of scalar potentials of separate geometric elements. These potentials can then be conbined at will because of the superposition characteristic of conservative force fields.

Sign in / Sign up

Export Citation Format

Share Document