Molecular systems experimental probing

The use of computer simulations to study internal motions and thermodynamic properties is receiving increased attention. One important use of the method is to provide a more fundamental understanding of the molecular information contained in various kinds of experiments on these complex systems. In the first part of this paper we review recent work in our laboratory concerned with the use of computer simulations for the interpretation of experimental probes of molecular structure and dynamics of proteins and nucleic acids. The interplay between computer simulations and three experimental techniques is emphasized (1) nuclear magnetic resonance relaxation spectroscopy, (2) refinement of macro-molecular x-ray structures, and (3) vibrational spectroscopy. The treatment of solvent effects in biopolymer simulations is a difficult problem. It is not possible to study systematically the effect of solvent conditions, e.g. added salt concentration, on biopolymer properties by means of simulations alone. In the last part of the paper we review a more analytical approach we have developed to study polyelectrolyte properties of solvated biopolymers. The results are compared with computer simulations. 

In recent years, there have been many significant advances in our models for the dynamics for proton transfer. However, only a limited number of experimental studies have served to probe the validity of these models for bimolecular systems. The proton-transfer process within the benzophenone-AL A -di methyl aniline contact radical IP appears to be the first molecular system that clearly illustrates non-adiabatic proton transfer at ambient temperatures in the condensed phase. The studies of Pines and Fleming on napthol photoacids-carboxylic base pairs appear to provide evidence for adiabatic proton transfer. Clearly, from an experimental perspective, the examination of the predictions of the various theoretical models is still in the very early stages of development. 

Vibrational dephasing provides us with a powerful method to probe the interaction of a chemical bond with the surrounding medium. Over the years, many experimental techniques have been developed to study dephasing of bonds in many molecular systems at various temperatures, pressures, and concentrations [122-124]. One popular experimental technique is the isotropic Raman lineshape. The other methods involve a coherent excitation of the vibration with a laser pulse and monitoring the decay of the phase coherence,... 

There are many studies of the transfer of electrons from enzymes to substrates, across biological membranes, to (or from) electrodes from (or to) substrates, between adsorbed molecular dyes and semiconductor particles, within synthetic films and nano-scale arrays, within molecular wires , and so on. Only a few, general comments will be offered on these topics here. The basic physics of molecular electron transfer does not change with the scale of the system, as long as identifiable molecular moieties are present with at least partly localized electronic configurations. The nature of the properties observed, the experimental probes available, and the level of theoretical treatment that is useful may be very different. Different approaches, different limiting models are used for extended arrays (or lattices) of very strongly coupled moieties. 

A standard experimental probe of this motion is infrared spectroscopy. We may use the results of Sections 7,5 and 8.2.3 to examine the effect of interaction with the thermal environment on the absorption lineshape. The simplest model for the coupling of a molecular system to the radiation field is expressed by a term —fi S in the Hamiltonian, where is the molecular dipole, and (t) is the oscillating electric field (see Section 3.1). For a one-dimensional oscillator, assuming that /r is proportional to the oscillator displacement from its equilibrium position and taking cos((uZ), we find that the coupling of the oscillator to the thermal environment and the radiation field can be modeled by Eq. (8.31) supplemented by a term (F/ni where F denotes the radiation induced driving force. We can... 

It is well known that water-mediated interaction stabilizes structure of biomolecules [1, 138, 247-250]. Therefore, several model molecular systems have been chosen to probe the water-mediated interactions in biomolecules and a large amount of experimental and theoretical work has been published over the years on this subject [78, 138, 251-258]. Since phenol is the simplest aromatic alcohol resembling chromophore of an aromatic amino acid, hydration of phenol molecules has been studied to understand H-bonding and solute-solvent interaction in biological systems. Several experimental and theoretical calculations have been made on the phenol-water clusters [259-273]. Recently, we have made a comprehensive analysis on structure, stability, and H-bonding interaction in phenol (P1-4), water (W1-4), and phenol-water (PmW (w = 1-3, n = 1-3, w + n < 4)) clusters using ab initio and DFT methods [245]. In this section, electronic structure calculations combined with AIM analysis on phenol-water clusters are presented. 

The chapter is organized as follows. In the remainder of the introduction the investigated molecular systems are introduced. The experimental section describes a typical pump-probe setup for experiments with a very high time resolution. Then the transient absorption and the contributing processes are discussed. In the fourth section a model of the reaction mechanism is developed from the experimental findings. Then we discuss briefly the situation of parallel reaction channels, and finally the results and conclusion are summarized. 

Progress in any field requires information on the state of well-defined systems as a function of conditions. Advancement is thus intimately linked to the availability of experimental probes capable of providing accurate and detailed information. Important metrics of biomolecules at interfaces include the interfacial composition distributions in molecular orientation, molecular spatial arrangement, and intramolecular conformation and biological activity. In this section, several experimental techniques probing the physical properties of biomolecules at interfaces are introduced these are grouped into optical, piezoelectric, and scanning probe methods. Further details can be found in other excellent reviews (62,188,189). 

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