Showing papers in "Annual Review of Physical Chemistry in 1978"

The Description of Chemical Bonding From AB Initio Calculations

Abstract: Concepts, such as hybridization and electronegativity, developed by Linus Pauling (1), Robert Mulliken (2), John Slater (3), and others in the 1930s have been powerful in rationalizing and predicting molecular structure, bond energies, and some aspects of reactivity. The power of these concepts is exemplified in the classic exposition, Nature of the Chemical Bond, by Linus Pauling (4). In recent years experimental and theoretical studies of numerous radicals have provided an assembly of quantitative information concerning bond energies, excitation energies, relative ordering of states, and shapes of potential curves, much of which is not explained by the older ideas. However, it has recently become possible to abstract from ab initio calculations qualitative concepts that rationalize many of the observed properties in such a way as to allow quantitative predictions for related systems. Currently the basis and application of this approach is distributed over a number of papers (5-9). Here we draw these ideas together with applications to number of related systems so as to indicate the utility and force of these methods. For simplicity of presentation we use Si and its hydrides (SiH, SiH_2, SiH_3, SiH_4) as prototypes for outlining the various concepts. These ideas are then extended to other molecules by replacing Si with Be through F and Mg through C1, and other related nontransition metal elements, and by replacing H with halogens such as F and C1.

Information theory approach to molecular reaction dynamics

Abstract: The information theoretic approach was introduced (1-7) as a procedure to compact, codify, and correlate the large amounts of data that were becoming available from experimental and computational studies of molecular collisions. In so doing, a large number of papers, presenting the theory and its diverse application, were generated. The purpose of this review is to compact, codify, and correlate the litera­ ture of the first five years ( 1972-1977). The initial objectives of the formalism were rapidly augmented. Links are forged with a thermodynamic point of view (6, 8,9, 10), predictive capabilities were explored (1 1 -16), the analysis of energy disposal (2-8) was complemented by a corresponding analysis of energy consumption ( 17, 18), and a formulation as a dynamical theory (be it quantal or classical) was provided ( 19, 20). This review, however, does not stray from its avowed purpose. It thus cannot replace the "handbooks" for would-be practitioners (21, 22) nor the detailed presen­ tations aimed at a systematic introduction with illustrative applications (23-25). A survey of actual applications to molecular collisions is provided in two tables and in two sections divided along the traditional lines of inelastic (energy transfer) and rearrangement (reactive) collisions. The literature coverage in these two sections is fairly exhaustive. Potential directions for future work conclude the review.

Structures of Molecular Liquids

Abstract: The phrase "liquid structures" refers to how molecules arrange themselves relative to one another in a liquid (the static structure), and how they move around in a liquid (the dynamic structure). A large volume of experimental and theoretical work has been directed at understanding these physical processes. Relatively complete bibliographies of the field have been compiled in this series of volumes alone (1-3). In addition, two excellent texts have appeared recently (4, 5). A survey of these reviews and texts shows that our undcrstanding of liquid structures is very advanced. Approximate and simple theories are now available which can be used successfully to interpret most experiments that probe the structures of nonassociated liquids. The purpose of this article is to discuss the strengths and limitations of the experi­ ments and ideas that form the foundation for this advanced state of the art.

Atom and Radical Recombination Reactions

Abstract: Radical recombination reactions are rarely reviewed as a separate field. They are either included in general surveys of reaction kinetics, or they are considered in dis­ cussions of the reverse dissociation processes. It is therefore attractive to present the subject from the less common "recombination point of view" instead of the normal unimolecular reaction side. The intimate relationship between the recombination and the reverse dissociation processes, nevertheless, remains a most important fact. The present review considers the recombination of atoms and the combination or association of atoms or poly atomic species with molecules in the gas phase. Many experimental examples have already been included either in earlier reviews in this series (1-4) or in other earlier reviews and compilations (e.g. 5-18). Various aspects of the theoretical analysis have been described for the cases of atom recombination (19) and combination of poly atomic species in reviews of modern unimolecular rate theory ( 16, 17, 20). Since these references include fairly exhaustive collections of experimental data, only a few are cited in the following pages. Instead we intend to present characteristic experiments for the reactions under a wide variety of conditions and to compare these with theoretical models. Only for a qualitative orientation do we first consider the simple energy transfer mechanism with association, dissociation, and collisional energy transfer steps. Two species, A and B, associate and form highly excited unstable molecules AB* that then either redissociate or are collisionally stabilized in collisions with arbitrary particles M:

NMR Studies of Membrane Structure and Dynamics

Abstract: Over the past decade, there has been considerable interest in the motional state of the phospholipid bilayer membrane. The motivation underlying these efforts has been the contention that the phospholipid bilayer is the basic matrix in which membrane proteins are embedded to form the biological membrane, and that the permeability and mechanical properties of the membrane, as well as the enzymatic activity of membrane proteins, are dependent upon the fluidity of the bilayer, especially the motional state of the hydrocarbon chains.

Light Energy Transduction in Visual Pigments and Bacteriorhodopsin

Abstract: The study of visual pigments and related molecules has become an area of consider­ able interest for physical chemists. Rhodopsin, which is a name now applied to all visual pigments, consists of a chromophore covalently bound to the apoprotein, opsin. Both in vertebrate and in invertebrate systems the chromophore has always been found to be the ll-cis isomer of retinal, the aldehyde of vitamin A (1). Visual pigments are membrane proteins that are located in photoreceptor cells: the rods and cones of the vertebrates and the rhabdomeres of invertebrates. The role of photoreceptors in the visual process is one of transduction; they convert the energy of an absorbed photon into a change in electrical potential in the cell membrane that is thcn transmitted to the nervous system through standard synaptic processes. The primary role of visual pigments is light absorption at the proper wavelengths, followed by activation of an as yet poorly defined mechanism that eventually leads to the change in the membrane potential. II-cis retinal and related molecules have been studied in great detail both in solution and when bound to the protein in the form of a protonated Schiff base. A significant part of this article is devoted to reviewing the properties of the protein­ bound chromophore and to a discussion of its biological function. However, in addition to their biological relevance, the photophysical properties of visual pig­ ments have turned out to be of great chemical interest, and the application of new physical techniques has resulted in significant advances during the past few years. In parallel, there have been extremely important gains in the understanding of photoreceptor physiology, which are briefly discussed in the following section. The recent discovery of a new retinal-based pigment, bacteriorhodopsin (2), has caused a great deal of excitement among researchers in many different fields. The

Kinetic Processes on Metal Single-Crystal Surfaces

Abstract: Chemical interactions between gas molecules and solid surfaces manifest themselves as crucial considerations in such diverse areas as wall effects in fusion reactors, heterogeneous catalysis (including electrocatalysis), corrosion, and molecular cos­ mology. In each of these fields the resolution of important questions rests on a more fundamental understanding of molecular transformations that occur at solid surfaces. Each process in question is characterizcd by thc sequence of molecular events (a) adsorption, (b) surface reaction, and (c) desorption (except when the reac­ tion product is nonvolatile). The purpose of this article is to review the recent work that utilizes single-crystal surfaces to understand these elementary processes, in­ cluding the effects of surface structure and composition. Excellent review articles are available concerning adsorption-desorption and surface reaction phenomena (82, 106, 108, 118, 141) and the interested reader should consult these for further information. In addition to these kinetic events, the current knowledge of the nature of the adsorbed state is also briefly reviewed. Surface oxidation processes which involve the surface as a final reaction product are not discussed.

Circular Dichroism Spectroscopy and the Vacuum Ultraviolet Region

Abstract: Circular dichroism (CD) is a special kind of electronic absorption spectroscopy that uses circularly polarized light rather than isotropic light. CD is a particularly useful technique because it is sensitive to the conformation of a molecule, and because it can be applied to randomly oriented molecules in solution and in the gas phase. For a molecule to exhibit a CD spectrum it must be asymmetric, that is, it must contain no plane or center of symmetry. Since most biological molecules are asymmetric, CD spectroscopy has been used extensively to investigate their conformation. It has also been used to investigate the electronic properties of chromophores when simple asymmetric derivatives of known conformation are available. Most readers will be familiar with plane-polarized light. With this type of polarization the direction of the electric field vector is constant to within a sign, while the magnitude of the electric vector is modulated. Circularly polarized light is the antithesis of plane-polarized light. A snapshot of circularly polarized light is depicted in Figure 1 where we see that the magnitude of the electric vector is

NMR Relaxation Studies of Solute-Solvent Interactions

Abstract: This review focuses on the application of nuclear magnetic resonance relaxation measurements to the study of solvent-solute interactions. It primarily deals with solutions of low molecular weight solutes and with aqueous protein solutions in an attempt to compare the approaches to these rather different systems. Magnetic resonance has been so widely used to characterize solution chemistry of all sorts that it is difficult to distinguish clearly between those experiments that deal directly with solvent-solute interactions and those that do not. This review therefore omits major areas of activity and makes no attempt to be comprehensive. Discussion of solvent or solute relaxation measurements in systems containing liquid crystals, lipids, polynucleotides, polysaccharides, inorganic solids such as clay, and most of the data on whole tissues is largely omitted for lack of space, not interest. Fundamental aspects of NMR have previously been presented (1-7). Reviews of magnetic resonance appear regularly in several series (8-12). Discussions of NMR relaxation and related topics appear in related review series (13-15). Grandly stated, the goal is to understand solutions. Unfortunately one is limited by the observations that are possible and the preconceived notions that are brought to the problem. For example, the existence of a solvent in the first coordination sphere of the transition metal ions is clearly documented. The first coordination sphere water molecules remain bonded to chromium(III) ions in water for times exceeding a day at room temperature, while other metal ions exchange solvent more rapidly (16). In either case the first coordination sphere is included in formu­ lating the chemistry of these ions; we write Cr(H20)�+, rather than Cr3+. The situation is less clear for other electrolyte ions such as the halide or alkali metal ions. One may expect to discover the coordination number for an ion by using a new experimental approach; however, if the solvent lifetime in the first coordination sphere region of the ion at a temperature of interest is not significantly longer than the time required for a solvent molecule to translate one jump length in the pure

High-resolution, solid state NMR

Abstract: : A review of the experimental capabilities presently available for the modification of spin Hamiltonians normally encountered in solids has been presented to illustrate the control the still-developing high-resolution, solid state NMR techniques furnish. Examples have been discussed to furnish insight into how such schemes can be used to control the time developemnt of a nuclear spin system to allow a detailed characterization of both the electronic and molecular-frame structure near a nuclear site. While the examples specifically discussed have been chosen from areas of current activity, they are only examples of present efforts, and future developments in this field will undoubtedly furnish many more such examples since the concepts upon which these techniques are based are quite general, and there exists great flexibility for the development of specific experimental schemes for a given problem. (Author)

Coherent energy transfer in solids

Abstract: Periodicity is the property of crystalline solids that makes possible the propagation of electronic excitation in solids as coherent wavepackets in the limit of weak exciton-lattice interactions. In this review, we briefly discuss the theoretical founda­ tion of coherent energy migration in the various limits of the exciton-lattice inter­ action. In addition, we revicw and evaluate experimental evidence for coherence from a variety of sources. This latter area is the focus of this review because the experimental detection and characterization of coherent energy transfer has been a field of such great interest and moderate controversy in recent years. In the last dozen years several general reviews on the properties of molecular solids have been published. These include those written by Hochstrasser (1), Robinson (2), Kopelman (3), and El-Sayed (4). Soos (5) has reviewed excitation in organic charge-transfer crystals. More recently, Silbey (6) has written an excellent review on electronic energy transfer processes in molecular crystals. Although his review has much in common with ours, he focused on formal developments in the theory of exciton-phonon interactions while we are concerned primarily with the theory and its relation to experimental observations of coherence and exciton­ phonon coupling. While experimental evidence is of recent vintage, the prediction of coherence in molecular solids dates back to the work of Frenkel in 1931. In his original paper on excitons (7), Frenkel develops three important insights. First, he pointed out that the electronic excitation can be delocalized and, as a result, be described by a series of Bloch wave functions in analogy to the lattice modes of the crystal. Second, as a consequence of delocalization, the superposition of several of the modes will form a localized wavepacket that propagates through the lattice with a group velocity

High Resolution NMR Studies of the Structure and Dynamics of tRNA in Solution

Abstract: Ribonucleic acids are composed of a sugar-phosphate backbone with bases attached at position l' of the sugar ring (Fig. 1). The backbone consists of six rotatable bonds defined by the angles 0/, cp', 1/1', 1/1, cp, and w, while the base and sugar rings are joined by the rotatable glycosidic bond, x. The four major bases are the purines guanine· (G) and adenine (A), and the pyrimidines cytosine (C) and uracil (U). Polynucleotide strands can interact with each other to form duplex structures by formation of complementary Watson-Crick adenine-uracil and guanine· cytosine base pairs. tRNA is composed of a single ribonucleic acid chain that ranges between 73 and 93 nucleotides in length with a terminal phosphate at its 5' end (residue 1). The nucleotide sequence of known tRNAs (2, 3) suggests that the polynucleotide chain can fold back on itself to generate double-stranded helical regions, as well as single­ stranded loop regions of the hairpin (chain reversal) and bulge types (Fig. 2)_ There are three hairpin loops defined as the D loop (contains the dihydrouracil base), the anticodon loop (contains the trinucleotide sequence complementary to the trinucleotide codon on messenger RNA), and the TljlC loop (contains the common sequence ribothymine-pseudouridine-cytosine). Each of these three loops is asso­ ciated with its corresponding double helical region called the stem. There is in addition a variable loop whose length depends on individual tRNAs and the acceptor stem whose 3' terminus is the site of aminoacylation. A survey of the known tRNA sequences demonstrates the presence of invariant and semi-invariant bases and they are defined in Figure 2 with purines and pyrimidines designated by Y and R, respectively (4, 5).

High resolution electron microscopy of crystal defects and surfaces

Abstract: Claims that single heavy atoms have been seen in high resolution electron microscope images have become commonplace in recent years. The accumulated experimental experience and theoretical contrast calculations suggest that in many cases these claims are fully justified. The performance of modern electron microscopes, when used at the limits of their capabilities, is such that one can begin to contemplate the use of "atomic resolution electron microscopy" as a fun damentally new and enor­ mously powerful method for the study of the structure of matter in terms of the detailed arrangements of the constituent atoms. In this review we report the initial applications of this new level of electron micros­ copy to a range of topics of particular relevance for physical chemistry; namely, the atom configurations on the surfaces of solids and in the defects within thin crystals. In some cases inf ormation at the level of atomic resolution has already been achieved. In many cases enough has been accomplished to suggest that a flood of information on atomic arrangements will follow from the use of the next generation of high resolution microscopes now under construction or being planned. In other cases we must rely on extrapolation beyond our present technical capabilities for initial results that appear feasible on the basis of theoretical analyses. It is our purpose to call attention to the range of exciting possibilities for new developments in this area in order to stimulate interest and support for the efforts being made.