Showing papers in "Annual Review of Physical Chemistry in 1985"

Chemical Reaction Dynamics in Solution

Abstract: An impressive renaissance in the study of chemical reactions in solution has occurred during the past decade. Although many of the reactions of interest to chemists occur in solution, most attention in the physical chemistry community has tended in the past 30 or so years to focus, with understandable cause, on gas phase chemical dynamics. But with the advent of experimental techniques such as picosecond spectroscopy, the accessibility of large-scale computer simulation, and the creation of new theories, solution phase reaction theory and experiment have now come into their own. As a consequence, at least a glimmering of understanding (and sometimes more) is now emerging in our appreciation of key features of various reaction types in solution. But it is an important measure of the rate of progress in this frontier in chemistry that new questions are often generated faster than are definitive answers. In contrast to the situation in the gas phase, where reactants (usually) follow their route to products in splendid isolation, the ubiquitous solvent molecules in solution continually perturb the reactants in their course. The first way in which a solvent medium can affect a reaction rate is via a modification of the activation (free) energy. This can be a substantial influence, since a change of only 2 kcal can modify the room temperature rate by a factor of 30. Good examples here are ionic and polar reactions in polar solvents. Calculations based on Transition State Theory (TST) and continuum dielectric picture of the solvent are well known, but have long been recognized as not being very reliable. As a result of progress in theory and computation of the microscopic properties of polar solvents, workers have been able to find more accurate activation parameters. TST predic-

Relativistic Effects in Chemical Systems

Abstract: Although the velocity of light c is finite in the real world, most calculations of theoretical chemistry make the approximation c = 00. This is usually a satisfactory approximation for systems of light atoms H, C, N, 0, etc, and for most properties of chemical interest. Where heavy elements are involved, however, the nonrelativistic (c = 00) approximation is not adequate. This review concerns the area where relativistic equations must be used for accurate calculations of properties of chemical interest. Only in the last decade have a large and diverse array of relativistic quantum chemical calculations been made. We define relativistic effects as the differences between calculations for the correct value ofthe velocity oflight and the results for c = 00. To obtain correct results even for c = 00, one must either use the Dirac equation, which yields electron spin, or supplement the Schr6dinger equation with an ad hoc assumption about spin. Both of these procedures yield the same

Chemical kinetics of soot particle growth

Abstract: The light given off by a candle flame and the black smoke from wood­ burning fireplaces, diesel engines, and industrial furnaces have a common origin: tiny carbonaceous soot particles. The light of a candle comes from incandescent soot particles that ultimately burn up in the air at the top of the flame. (But a cold object placed in the flame will quickly become covered with black soot.) In the other cases, however, the soot may be emitted into the atmosphere as a pollutant. In spite of generations of effort, soot emission from many practical combustion systems remains a serious problem, and the viability of the fuel-efficient passenger car diesel engine may rest on our ability to make significant reductions in soot emissions. The morphology of soot particles can be best observed with electron micrographs such as that shown in Figure 1. We see 10 to 30 nm spherical units attached in necklace-like chains, with each sphere containing the order of 105 carbon atoms and 104-105 hydrogen atoms, putting the spheres somewhat above molecular in size. The structure in Figure 1 is nearly the same for soot generated on a bunsen burner and in a diesel engine. A great deal of work has been reported that correlates soot formation with fuel type, flame temperature, or flow fields (1), yielding an extensive and very useful body of engineering data, but these data have provided little insight into the detailed chemistry of soot formation. Soot formation involves some interesting and unusual chemistry. First, soot formation represents growth from species the size of fuel molecules, with perhaps 1 to 10 carbon atoms, to particles with hundreds of thousands of carbon atoms. Such growth takes place at flame temperatures, generally between 1000 K

Theory of Hydrophobic Effects

Abstract: The subject of this review is the solution environment of nonpolar molecules dissolved in liquid water, and the molecular description of the most likely encounters between such solutes in aqueous solution. These subjects have been traditionally discussed under the name, "hydrophobic effects." Several reviews have been written previously about hydrophobic effects, and from a variety of different perspectives. The perspectives include the peculiarities of solution thermodynamic properties (la,b, 2), the formation of membranes and micelles (3, 4), and the influence of solution environment on the structure of proteins (5, 6). These are problems of obvious importance, and they have been the subject of research over many decades. This research has produced a rich array of thermodynamic and spectroscopic data on aqueous solutions and evolved speculations about the molecular-level structure of the systems. In fact, until the late 1970s these topics were often discussed in much the same ways as they were decades previously. However, at about that time a new category of molecular-level information bearing on hydrophobic effects began to be available. The new pieces of information were predominately theoretical in character. In the majority of cases, the new results were obtained from computationally demanding Monte Carlo or molecular dynamics calcu­ lations on model aqueous solutions. However, those calculations were carried out during a period of rapid maturation of the theory of molecular liquids. This combined theoretical impulse produced a demand for new experiments, and considerable progress has been achieved over the last several years. It is these developments that are reviewed here. Despite renewed activity, the recent developments have not quite

Fluorescence correlation spectroscopy and photobleaching recovery

Abstract: Fluorescence correlation spectroscopy (FCS) and fluorescence photo­ bleaching recovery (FPR)l are closely related methods that can be used to measure rates of molecular transport and chemical reaction via observations of fluorescence changes in small open regions of a system. In FCS the fluorescence from the observation region is recorded over time while the sample rests in thermodynamic equilibrium. Spontaneous microscopic fluctuations of the numbers of fluorescent molecules in the observation region yield corresponding fluctuations in the measured fluorescence. The lifetimes of the fluctuations are determined in a statistical scnse by the rates of molecular transport (diffusion, drift, or flow) into and out of the observation region and by the rates of chemical reactions among the system components. The amplitudes of the fluctuations depcnd on the mean numbers of the various kinds of molecules in the observation region

Molecular Dynamics Beyond the Adiabatic Approximation: New Experiments and Theory

Abstract: At the heart of the quantum mechanical description of molecular structure and dynamics lies the adiabatic or Born-Oppenheimer approximation (1 , 2). Starting with an assumption of separability of time scales for nuclear and electronic motion, a familiar picture emerges of nuclei subject to well­ defined forces corresponding to the potential energy surface for a particular electronic state. Although the well-established success of these ideas in the areas of molecular spectroscopy (3-5) and reaction dynamics (6-9) is likely to secure the adiabatic approximation as a continuing foundation of molecular science, the range of dynamical processes that lies within its scope is far from complete. Recent experimental and theoretical advances in particular are beginning to yield a coherent understanding of several phenomena that, far from requiring minor corrections to the adiabatic approximation for their explanation, by their very nature exist entirely outside its framework. Examples of importance in diverse areas of chemistry and physics range from the dynamics of radiationless decay (1015) and nonadiabatic processes in chemical reactions (16-19) to the spectroscopy of excited (20-23) and ionized (24-26) states of isolated molecules, from single collision electronic energy transfer (27--41) to exciton (42) and soliton (43) dynamics and spin-lattice relaxation (44). Specialized reviews on these topics are available.

Infrared Induced Photochemical Processes in Matrices

Abstract: Solid inert gases at cryogenic temperatures (matrices) containing a trapped guest molecule provide an environment characterized by extremely weak coupling between the guest and the solid lattice. This is most obviously manifested by the small frequency shifts and the narrow band widths of guest vibrational frequencies. More relevant to our interest here, this weak coupling implies that intramolecular vibrational relaxation within the guest molecule degrees of freedom can be much faster than transfer of energy among the "supermolecule" degrees of freedom of the guest plus lattice. Such a difference may, in some instances, permit study of vibrational initiation of chemical events that are characteristic of the guest molecule in absence of the matrix. Reactions with activation energies in the range of 1 to 5 kcaljmole are generally too rapid to be studied easily at room temperature. In contrast, the extremely low thermal energy available in a cryogenic matrix implies that such a reaction can be completely suppressed. Then the reaction might be induced by absorption of an infrared photon since a mid-infrared photon adds a few kcal/mole of energy to the absorbing molecule. If so, this technique allows tight control of the reaction progress. It opens the possibility, for example, of exciting selectively and converting quantita­ tively a stable conformer of a flexible molecule into an unstable form for subsequent leisurely spectroscopic study. In addition, stimulation of chemical reactions (unior bimolecular) by selective excitation of funda­ mental or low overtone vibrations holds promise for mode-specific

The Structure of Polar Molecular Liquids

Abstract: The importance of the solvent environment to chemistry in solution is widely appreciated; hence, the motivation for development of detailed molecular descriptions of chemically relevant liquids and their solutions is substantial. At the same time, the area of liquid state theory continues to evolve rapidly, with realistic descriptions of complex chemical systems becoming increasingly accessible to theoretical analysis. Reviews in this series alone show the steady progression of our theoretical understanding of liquid state molecular organization during the last ten years (1-6). Nevertheless, the theory of liquids remains an active area of study for systems that involve strong attractive forces in addition to the ubiquitous, short-range repulsive forces usually referred to as molecular "shape." The latter forces contribute to liquid structure through the packing requirements for molecular species in the dense liquid phase (4), and are a necessary consideration, whether or not strong polar forces are present or effectively competitive. The purpose of the present review is to discuss elements of liquid structure studies for systems in which both types of forces are present. Such is the case for most solutions of chemical interest. I include in this discussion both an outline of current techniques and a description of general features of structure that have emerged from recent studies. When we discuss liquid "structure," we mean the statistical distribution of relative molecular separations and orientations in the fluid, and of intramolecular coordinates, if the molecules are flexible. These are typically described through equilibrium probability distributions or correlation functions (providing relative probabilities, compared to spatially uncor-

Computer simulation studies of solids

Abstract: PROLOGUE Computers influence our lives in more ways than we care to admit, and simulation or modeling is just one facet of a vast activity that will inevitably continue to grow even larger. Nowadays, computer simulation is used routinely in fields as diverse as econometrics and meteorology. The successes that have been achieved to date are such that, whatever the field of application, a healthy scepticism is warranted in assessing the predictions based upon any particular computer model. In this respect, computer studies on "real" systems, be they solid or liquid, have much in common with the modeling of the economy or the weather. That is, although in principle one can now obtain exact numerical results, we cannot thereby evade the question of how faithfully the model mimics reality. I devote this article to the recent advances in the modeling of condensed matter, with particular emphasis on the properties of solids and the structural transitions that can arise with changes in temperature and pressure. I am not concerned here with "exact" numerical studies of mathematical models, which is an autonomous field of endeavour. Rather, I concentrate instead on the study of atoms and molecules that interact with what are believed to be "realistic" potentials. The degree of simplification in the modeling is necessarily related to the complexity of the system of interest. Computer simulation in statistical mechanics dates from the very birth of

Theory of Chain Packing in Amphiphilic Aggregates

Abstract: Amphiphilic molecules in aqueous solutions cluster together into diverse aggregates organized in a variety of macroscopic phases (1-5). Extreme examples are the small globular micelles of surfactant molecules such as sodium-dodecyl-sulfate (sds), and the large bilayers of biological phos­ pholipids such as lecithin. The former are dispersed in an isotropic solution, whereas the latter may be organized into finite vesicles or as ordered macroscopic lamellae. Many other structures and phases have been ob­ served, depending on the nature of the amphiphiles and their concentra­ tion as well as on the temperature and composition (e.g. salinity) of the surrounding solution. A common characteristic of all the aggregates is that they comprise two regions: a hydrophobic core composed of the hydro­ carbon tails (typically alkyl chains) of the amphiphiles, and a hydrophilic mantle containing their polar (ionic, nonionic or zwitter-ionic) heads. Intercst in amphiphile solutions and micellar aggregates is wide and interdisciplinary, involving basic questions in physics, biology, medicine, and chemistry, as well as having practical applications in the oil,

High Resolution NMR Studies of Nucleic Acids and Proteins

Abstract: It has long been recognized that NMR can be used to investigate the solution structure and dynamics of biological polymers and to monitor many different parts of the molecule simultaneously. However, as recently as five years ago, even decapeptides presented a formidable challenge to the NMR spectroscopist. The major limitations have been three-fold: the great difficulty in assigning resonances to particular nuclei in the molecule, the lack of resolution in the spectrum due to the multitude of resonances from even a moderately small biopolymer, and the relatively low sensitivity of NMR. All of these limitations have been alleviated by the introduction of two-dimensional NMR (2DNMR) methods and the development of higher field strength spectrometers. 2DNMR spreads the spectral information into two frequency dimensions and allows simultaneous collection of infor­ mation about all resonances, thus improving the effective resolution and sensitivity. Methods for systematically obtaining reliable resonance assign­ ments using 2DNMR were first developed for proteins by Wuthrich and co­ workers, and later extended to other biopolymers. In the present review, we restrict ourselves to a discussion of the basic principles of the most important 2DNMR experiments and present some recent examples ; however, this article is not intended to be a comprehensive survey of all the recently published protein and nucleic acid NMR literature.

Periodic Perturbations of Chemical Oscillators: Experiments

Abstract: Periodic perturbations of chemical reactions have been the subject of many experimental studies in the past. Recall the early and exciting reports of submicrosecond relaxation times measured in ultrasonic adsorption, or in dielectric loss experiments in the 1950s and 1960s (1, 2). All these methods applied small periodic (or transient) pressure or electric field variations to chemical equilibria, in order to determine relaxation times and rate constants of elementary chemical steps. Because of its potential for increased yield, periodic operation of chemical reactions, particularly of polymerizations, has been studied extensively by chemical engineers (3-5) by the use of flow methods such as continuous flow-stirred tank reactor (CSTR). In the aforementioned systems the forcing perturbations were applied either to chemical equilibria or stable stationary states about which a small perturbation decays exponentially. In many a Gottingen tea hour iIi the 1960s a new question was raised: namely, how do chemical non­ sinusoidal limit cycles behave when they are periodically perturbed? Which type of response do they display? It had long been known then that a chemical oscillator that is damped should show "normal resonance" behavior. This was actually tested in a specifically designed experiment only recently (6). To sustain any oscillatory behavior the system has to be continuously replenished by reactants. By being open with respect to the influx of matter or energy (light, for example), the chemical oscillator is guaranteed to be far from chemical equilibrium in a defined nonequilibrium state characterized by a non-zero affinity. The 1970s saw a surge in the

High Resolution Infrared Studies of Molecular Dynamics

Abstract: Reaction dynamics is one of the principal subjects of chemistry. The traditional way of studying this problem relies on inspection of changes in concentration of reactants and products as the reaction proceeds; the result of chemical analysis is employed to infer the details of intermediate processes. Chemical reactions are obviously not as simple as explained merely by means of classical methods of chemical analysis. Many workers have closely examined the individual steps of gas phase reaction processes, i.e. elementary reactions. Such efforts have resulted in the detection of quite a large number of short-lived molecules as reaction intermediates. Identification of these species is a sort of prerequisite for understanding the reaction mechanism. Because most reaction intermediates involve un­ paired electrons, they have attracted a lot of attention in many fields of molecular science. Increasing development of spectroscopic tools has enabled workers to characterize many of them. The high-resolution spectra of reaction intermediates are extremely valuable in examining, in real time, distributions over quantum states of molecules taking part in reac­ tions, which can deviate considerably from the Boltzmann distribution. High resolution molecular spectroscopy and kinetic studies have thus collaborated closely to bring about recent remarkable progress in the study of reaction dynamics. Electronic spectroscopy in the visible and ultraviolet regions, combined with flash photolysis, has been most widely employed in the study of transient molecules as reaction intermediates (1). The development of the dye laser has accelerated this trend, because this light source has made laser-induced fluorescence (UF) easy to apply. This method provides us

Multiple Quantum NMR: Studies of Molecules in Ordered Phases

Abstract: The object of this article is to describe recent applications of multiple quantum spectroscopy to the study of molecular systems in ordered phases. I make no attempt to review the phenomenon of multiple quantum spectroscopy comprehensively since several general reviews have already appeared in the literature (1, 2). For the purposes of this article, it is necessary only to discuss that class of nonselective multiple quantum experiments commonly employed by several groups to elucidate molecular structure and dynamics in ordered media. In conventional NMR spectroscopy one observes only transitions for which the change in the absolute value of the magnetic quantum number is one. Such transitions are referred to as single quantum transitions. Multiple quantum transitions occur when states in nonadjacent Zeeman manifolds are placed in coherent superposition. These various transitions are illustrated in Figure 1, which shows, in schematic form, the energy level diagram of a system of N spin 1/2 nuclei. In this paper I discuss how, in such a system, multiple quantum transitions from order zero to N may be excited and detected. Although it is possible to observe multiple quantum transitions in slow passage experiments (3, 4), all of the work described in this review involves the use of pulsed techniques to excite and detect multiple quantum transitions. Therefore I confine theoretical discussion to pulsed techniques. Attention is also confined to those experiments in which the objective is to obtain physical information through an analysis of the multiple quantum