Annual Review of Physical Chemistry - Volume 46,

Over the past 25 years, astronomers have discovered a large number of gas-phase molecules in space, ranging in size up to more than 10 atoms. The molecules, which are mainly organic in nature and comprise both normal and abnormal species, are located between stars, in regions known as interstellar clouds, which contain both gaseous material and material in the form of dust particles. The gas is well characterized by high-resolution spetroscopy, whereas the dust is less well characterized by low-resolution infrared spectroscopy and the scattering of visible radiation. The gaseous molecules are synthesized in situ from precursor atomic material, which derives from the mass loss of previous generations of stars. The chemical reactions involved in this synthesis are discussed in some detail as are the models that seek to reproduce the observed abundances of molecules.

Experimental studies of gas-phase chemical reactions and molecular energy transfer at very low temperatures and between electrically neutral species are reviewed. Although work of collisionally induced vibrational and rotational transfer is described, emphasis is placed on very recent results on the rates of free radical reactions obtained by applying the pulsed laser photolysis (PLP)–laser-induced fluorescence (LIF) technique in a CRESU (Cinétique de Réactions en Ecoulement Supersonique Uniforme) apparatus at temperatures as low as 13 K. These measurements demonstrate that quite a wide variety of reactions—including those between two radicals, those between radicals and unsaturated molecules, and even some of those between radicals and saturated molecules—remain rapid at very low temperatures. Theoretical efforts to explain some of these results are described, as is their impact on attempts to model the synthesis of molecules in interstellar clouds.

Current concepts in heteronuclear multidimensional NMR spectroscopy are reviewed. Methods to improve the sensitivity and the efficiency of data collection include constant time, compression through the overlap of chemical shift evolution and dephasing and rephasing periods, and dual or time-shared evolution. Two classes of three-dimensional and fourdimensional triple-resonance experiments applied to proteins are considered. The first class correlates ¹H, ¹⁵N, and ¹³C signals of the protein backbone. The second class correlates both backbone and side-chain signals. Application of triple resonance to RNA is also discussed. Heteronuclear cross polarization (HCP) is considered as an alternative to INEPT transfer, and its application to nucleic acids is presented. Finally, two methods of employing pulsed field gradients (PFGs) are reviewed.

We describe recent advances in the theoretical description of bimolecular reactions involving four or more atoms based on quantum scattering theory and quasiclassical trajectory methods. The application of these methods to several reactions is described in detail along with relevant experimental results. The discussion emphasizes the use of reduced dimensionality quantum scattering methods and quasiclassical trajectory methods to describe quantum state-resolved effects, including state-specific reaction rate enhancements and product state distributions. Also considered are thermal rate constants, the lifetimes of intermediate complexes, and the branching between multiple reaction pathways.

This review covers the field of excited electronic-state chemical reactions in small clusters. The clusters emphasized are those comprised of an organic chromophore that is electronically excited to initiate the reaction and of various coreactant molecules ranging from water and ammonia to ethers, amines, aromatics, alkanes, alkenes, and diatomics. The reactions discussed include vibrational relaxation, vibrational predissociation, electron transfer, proton transfer, and radical additions. The reactions are analyzed based on laser-induced fluorescence excitation, dispersed emission, mass-resolved excitation spectroscopy, stimulated emission pumping, and picosecond time-resolved implementation of these spectroscopies.

The importance of collective motions in proteins, such as hinge-bending motions or motions involving domains, has been recognized. Occurrence of such motions and their experimental and theoretical studies are reviewed. Normal-mode analysis and principal component analysis are powerful theoretical tools for studying such motions. The former is based on the assumption of harmonicity of the dynamics, while the latter is valid even when the dynamics is highly anharmonic. The results of the latter analysis indicate that most important conformational events are taking place in a conformational subspace spanned by a rather small number of principal modes, and this important subspace is also spanned by a small number of normal modes. The normal-mode refinement method of protein X-ray crystallography, which is developed based on the concept of the above important subspace, is discussed.

The use of wave packets in time-dependent quantum mechanical studies of chemical reaction dynamics is examined. The basic priniciples of time­dependent scattering theory are reviewed. The Fourier-grid method and various propagation schemes are discussed. A number of useful methodologies are examined, such as discrete variable representations and close­coupling expansions, multiconfiguration self-consistent field formulations, and the mixing of classical with quantum variables. Numerous applications to gas-surface scattering are considered. The dissociative adsorption of diatomic molecules on metal surfaces and the Eley-Rideal recombination of gas-phase atoms with atoms adsorbed on surfaces are discussed in detail. Applications to gas-phase reactions are also examined, with emphasis on three-body A+BC and four-body AB+CD reactions.

Rotationally resolved photoelectron spectra can provide significant insight into the underlying dynamics of molecular photoionization. Here, we discuss and compare results of recent theoretical studies of rotationally resolved photoelectron spectra with measurements for molecules such as HBr, OH, NO, N2, CO, H20, H2CO, and CH3. These studies reveal the rich dynamics of quantum-state-specific studies of molecular photoionization and provide a robust description of key spectral features resulting from Cooper minima, autoionization, alignment, partial-wave mixing, and interference in related experimental studies.

The theory and practice of external infrared reflection absorption spectrometry (IRRAS) as applied to monomolecular films at the air-water interface are reviewed. The observed IR frequencies for films of amphiphilic species provide information about the conformational states of the hydrocarbon chains and the hydrogen bonding and ionization states of the polar head groups, under conditions of controlled surface pressure. Determination of molecular orientation is also feasible and requires detailed consideration of the reflection-absorption properties of the three­ phase (air-monolayer-water) system. Current theoretical approaches are described.

Applications of IRRAS to the study of single- and double-chain amphiphiles and proteins are reviewed, and initial excursions into biochemistry (interfacial enzyme catalysis) and physiology (pulmonary surfactant function) are reported.

Many-body potential energy surfaces (PESs) for describing atomic interactions in gas-solid and surface reaction dynamics are reviewed in this work. Initial PESs from the 1960s-1970s were restricted to a diatomic molecule interacting with a solid surface. Since the 1980s, a multitude of many-body reactive PESs, their parameterization, and their applications have been reported in the literature. Although we mention most of the PESs in general, we have chosen to describe only those that either have had general utility or have had staying power, i.e. they have been used widely by other research groups. The potentials discussed in the most detail are the Stillinger-Weber and Tersoff Si PESs, the Brenner hydrocarbon PES, and the embedded-atom method (EAM) style potentials for metals. We conclude that although these PESs have been used successfully in large-scale computer simulations, further development is needed in many-body PESs. In particular, the development of new functional forms for multicomponent reactive systems is required.

At present, two main types of algebraic methods are employed for analysis of molecular spectra. The first goes back to the early days of molecular spectroscopy. The second, developed recently by Iachello and coworkers, grew out of nuclear physics and makes use of classical Lie algebras such as SU(4). In this review, the standard spectroscopic fitting Hamiltonian for molecular vibrations, including resonance interactions, is first described. Then, new developments in the application of the standard approach are surveyed. In particular, the question of how one determines the true nature of molecular motions in highly excited spectra is investigated. Next, the recent algebraic approach of Iachello and coworkers is discussed. Application of ideas of molecule-like modes and algebraic methods to the analysis of the electronic spectra of atoms is discussed. Finally, prospects for future development of algebraic methods are discussed.

Advances in laser cooling of neutral atoms have made possible a new form of high-resolution laser spectroscopy: photoassociation of ultracold atoms. Colliding neutral atoms, confined in a laser trap, are photoassociated to bound excited states of the dimer molecule by absorbing a photon from a tunable laser. The technique can probe long range and “purely long range” molecular states that are difficult or impossible to detect by traditional means and, because of the extremely low energy of the colliding atoms (<1 mK), is capable of high resolution (<0.001 cm^-1). The spectra are useful for atomic lifetime measurements, determination of atomic ground-state scattering information, and measurement of curve-crossing probabilities. Theoretical and experimental work in the field, including multiple resonance techniques and photo association line shapes, are reviewed.

The factors that govern efficient electron transfer in the initial steps of photosynthetic charge separation are discussed. The dependence of the electron transfer rate constant on free energy, temperature, and distance are described both in theory and in numerous experiments on photosynthetic and macromolecular systems, with particular attention to those aspects of macromolecular charge transfer systems that show strong analogy to characteristics of photosynthetic charge transfer reactions. The unique features of the primary charge separation reaction in photosynthesis are emphasized in light of recent experimental data, including time-resolution of excited state vibrational motion, the electric field dependence of the quantum yield, and resonance Raman and hole-burning experiments that probe the nature of the initially formed excited state. The experimental results indicate the need for further development of electron transfer theory to include nonequilibrium vibrational populations and more explicit models of higher-order electronic coupling.

New experiments have succeeded in measuring actual rates of nucleation and are revealing the shortcomings of classical nucleation theory, which assumes that the molecular-scale regions of the new phase may be treated using bulk thermodynamics and planar surface free energies. In response to these developments, new theories have been developed that incorporate information about molecular interactions in a more realistic fashion. This article reviews recent experimental and theoretical advances in the study of nucleation of liquids from the vapor and of crystals from the melt, with particular emphasis on phenomena that relate to particle formation in the atmosphere.