Molecular dynamics time based definition

The main goal of data treatment in conventional mass spectrometry (MS) is to facilitate identification and quantification of analytes. The focus of time-resolved mass spectrometry (TRMS) is to track variations of identities and quantities of analytes and products over time. In many chemical reactions, the concentrations of reactants decrease and those of products increase with time. In more complex reactions, reaction intermediates exist and their concentrations may increase and decrease within certain periods of time. The evolution of reaction intermediates is distinct from that of reactants and products. TRMS provides an insight into the progress of reactions by identifying molecules based on their mass-to-charge (m/z) ratios. It also determines concentrations of molecules based on signal intensities of ions. Thus, it is important for TRMS to interpret MS data on highly complex and dynamic systems correctly. This chapter will first introduce definitions of various technical terms, and then discuss how to predict molecular compositions of complex mixtures based on the information contained in mass spectra. 

We can now give precise definitions of some words and phrases that are often used loosely. A reaction rate is a rate of change of the concentration of some chemical species at a particular moment it is derived from a set of observations, in which the course of a reaction is monitored over a period of time. Such observations are the basic experimental data. By analysing the relation between these rates and the corresponding concentrations, one obtains a rate law that fits both the data and (often) some standard form (e.g., first-order, in which the rate is proportional to the concentration of one of the reactants). These rate laws, along with known structural data, may be given some interpretation in terms of reaction kinetics, one would describe a scheme of molecular motions that would explain the rate law. Often there are several alternative schemes that would be consistent with a particular set of data further experimentation would then be needed in order to choose between them. Such schemes in terms of chemical kinetics describe events on the microscopic scale, involving atoms and molecules, as distinct from rate laws which are expressed in terms of macromolecular quantities (time and concentration). The schemes may in turn be interpreted in terms of a reaction mechanism, which relates them to chemical dynamics, i.e., to theories of how molecules behave, in terms either of some particular model with limited scope (such as collison theory, or transition-state theory) or of the more fundamental body of theory based upon quantum mechanics. 

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