Showing papers in "Annual Review of Physical Chemistry in 1995"

Density-Functional Theory of the Electronic Structure of Molecules

Abstract: Recent fundamental advances in the density-functional theory of electronic structure are summarized. Emphasis is given to four aspects of the subject: (a) tests of functionals, (b) new methods for determining accurate exchange-correlation functionals, (c) linear scaling methods, and (d) developments in the description of chemical reactivity.

External infrared reflection absorption spectrometry of monolayer films at the air-water interface

Abstract: 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.

Chemistry in the Interstellar Medium

Abstract: 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

NUCLEATION: Measurements, Theory, and Atmospheric Applications

Abstract: 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.

Imaging techniques for the study of chemical reaction dynamics.

Abstract: In recent years the development of new techniques to study gas-phase reaction dynamics of full and half collisions has been tremendous. The ultimate goal in this field of research is to achieve control of chemical reactions. Levine & Bernstein ( 1) have outlined desiderata for the study of molecular reaction dynamics, stating that in the ultimate experiment one would like to determine the total cross section at specified collision energies; measure the internal-state, angular and velocity distributions, and alignment of the products; and prepare selectively the internal state, alignment, and orientation of the reactants. So far no experiment has simultaneously implemented all of these desiderata. Levine & Bernstein considered many experiments in which determination of a few of the desiderata has been achieved simultaneously. Considerable advances have been made since their review. Some of these are highlighted in this review. The majority of studies of chemical reactions focus on the asymptotic properties of the reaction, measuring the quantum-state or velocity (speed and angle) distributions of the products. Newly developed techniques for the simultaneous measurement of these properties are the subject of this review. Simultaneous measurement is important so that correlated quan­ tities (e.g. the quantum state of one product correlated with that of the other or the velocities of fragments correlated with the particular quantum

Salt-nucleic acid interactions

Abstract: Coulombic interactions of salt ions with polymeric and oligomeric nucleic acids in solution have large and distinctive effects on ion distributions, on thermodynamic coefficients, and hence on equilibrium processes involving nucleic acids, such as their conformational transitions and binding interactions. In experimental or theoretical studies where an oligonucleotide is taken to represent the corresponding polynucleotide, the impact of coulombic end effects on molecular and thermodynamic properties must be taken into account. Observable consequences of coulombic interactions in nucleic acid solutions have been calculated by using models with varying degrees of detail and methods formulated at varying levels of rigor. From comparisons of experimental results with predictions of the prevalent theoretical approaches, this review concludes that the more rigorous methods have proved capable of accounting for thermodynamic (and some molecular) consequences of coulombic interactions with a minimal number of preaveraged parameters that represent the most important structural features of the nucleic acid solution.

Collective Variable Description of Native Protein Dynamics

Abstract: 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.

High-pressure structural transformations in semiconductor nanocrystals.

Abstract: Pressure-induced structural transformations in semiconductor nanocrystals are examined. High-pressure Raman spectroscopy, EXAFS, X­ray diffraction, and optical absorption are discussed as methods for studying these transformations in CdSe, CdS, and Si nanocrystals. In these nanocrystal systems, each technique shows an elevation in solid-solid structural transformation pressure as crystallite size decreases. By analogy with melting in nanocrystals, this elevation in transformation pressure is explained in terms of an increase in surface energy in the newly formed high-pressure phase crystallites. The increase in surface energy is in turn the result of transition path-induced changes in the shape of the nanocrystals. These changes convert spherical nanocrystals with low-index, low-energy surfaces into oblate or prolate crystallites with higher-index, higher-energy surfaces. The elevation in structural transformation pressure in nanocrystals is thus a kinetic rather than a thermodynamic phenomenon.

Theoretical studies of polyatomic bimolecular reaction dynamics.

Abstract: 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.

Orientation and Alignment in Reactive Beam Collisions: Recent Progress

Abstract: The concept of directional axis distributions and orientation-dependent reaction cross sections is used to describe the effect of the mutual orientation of reagents on the outcome of reactive beam collisions. The axis distributions and cross sections are expanded in series of Legendre polynomials and real spherical harmonics, respectively, and characterized by the expansion coefficients (moments). The interrelations between the moments of the cross sections and the directionally dependent experimental data (steric effects) on the one hand and the anisotropic properties of the potential energy surfaces on the other hand are presented. Recent progress in the field of dynamical stereochemistry results from the prep­ aration of molecular orientation and alignment by using the novel brute force technique and an optical method, respectively. The theories of both methods are summarized, and typical experimental arrangements are presented. All experimental results based on these techniques are reviewed. Among the...

Algebraic Methods in Spectroscopy

Abstract: 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.

Gas-phase reactions and energy transfer at very low temperatures

Abstract: 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 (Cinetique de Reactions 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.

Femtosecond pulse shaping, multiple-pulse spectroscopy, and optical control.

Abstract: A review is presented of femtosecond pulse-shaping methods and their application to spectroscopy of atoms, molecules, and condensed materials. Pulse shaping can be used to generate femtosecond pulse sequences and other optical waveforms whose time-dependent amplitude, phase, frequency, and polarization profiles are all specified precisely. The light­matter interaction mechanisms through which such waveforms can be used for optical control over molecular and material responses are discussed. Most of the spectroscopic experiments conducted to date that involve shaped femtosecond waveforms are reviewed. These have involved control over coherent electronic responses of atoms, small molecules, and multiple quantum wells and control over coherent molecular and lattice vibrations. A selective review is presented of theoretical predictions and qualitative discussions of optical control possibilities involving complex ultrafast waveforms

Photoassociative spectroscopy of laser-cooled atoms.

Abstract: 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.

Dynamics and Photochemistry of Neutral van der Waals Clusters

Abstract: 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.

Potential energy surfaces for chemical reactions at solid surfaces.

Abstract: 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.

Spectroscopy and Quantum Mechanics of the Hydrogen Molecular Cation: A Test of Molecular Quantum Mechanics

Abstract: The hydrogen molecular cation is the simplest molecule, consisting of two protons and one electron. It provides a unique opportunity for accurate theoretical calculations, which may be compared with experimental measurements. In addition to Hi, its isotopomers HD+ and Di are included in this review. We concentrate on the developments that have taken place in the last five years and that demonstrate the interaction between experimental and theoretical studies. We describe recent experi­ ments that provide a stringent test for theory and show that the current most accurate calculations can reproduce the experimental results extremely closely. For more details of earlier work, the reader is referred to the reviews by Carrington & Kennedy (1) and by Carrington et al (2). Because the hydrogen molecular ion has only one electron, electron correlation is not of concern; indeed some might dismiss the hydrogen molecular ion as being irrelevant to this central problem of molecular quantum mechanics. However, theory has concentrated instead on non­ adiabatic, relativistic, and radiative effects, all of which must be included in the calculations if experimental results are to be reproduced. Kolos (3) has recently reviewed the hydrogen molecule and addressed the problem of more than one electron as well as nonadiabatic and other effects.

High-resolution photoelectron spectroscopy of molecules.

Abstract: 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.

Time-dependent wave-packet approach to quantum reactive scattering

Abstract: 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.

Some Spectroscopic Reminiscences

Abstract: We review a number of essentially spectroscopic problems in this personal account. The structure of high-temperature species remains a topic of considerable broad interest. The binary fluorides of essentially every element are stable as the isolated gas-phase molecular species. As such they provide a means of comparing bonding with the entire periodic table. The structural characterization of the binary fluorides, although still incomplete, has provided a considerable insight into a variety of bonding types. The formation of molecules in the interstellar medium has been a model for abiotic synthesis of complex species. A kinetic model based upon ion­molecule reactions as the predominant reaction class appears to fit many of the observations, such as the polyatomic ion HCO+. The high abundance of carbon-chain compounds is attributed to the efficient formation of C+ by the reaction CO+He+ →C+ +O+He. The spectroscopic characterization of weakly bonded species has led to a detailed knowledge of intermolecular...

Ion reaction dynamics.

Abstract: This article reviews recent progress in the study of ion reaction dynamics in which product energy disposal studies provide detailed information about the potential energy surfaces mediating chemical rea ction. We emphasize product state-resolved studies of the proton tran sfer and hydro­ gen atom tran sfer reactions of 0-. We also discuss several critical experi­ ments that test the validity of the double minimum potential energy surf ace model in describing the bimolecular nucleophilic substitution (SN2) reac­ tion. Photo ionization methods for producing vibrational and vibrational­ rotational state selecti ons of ions are also discussed, and recent examples with Hi and Nt are presented. The role of these state-selection methods in elucidating mode-s elective chemistry in the reactions of NHt and C2Ht are also discussed.

Effective hamiltonian theory and molecular dynamics.

Abstract: The theory of effective Hamiltonians was developed within nuclear physics in the 1960s by Bloch (I) and Des Cloizeaux (2) as a method for determining the effective interactions between nucleons. Subsequently it was adapted to quantum chemistry (3, 4a,b) and used to overcome some limitations of both ab initio and semiempirical methods (5, 6). A more recent application of the theory is in molecular dynamics, where the basic processes studied are full collisions, in which energy transfers and structural modifications appear between molecular bound states and molecular continua (7), and half colli­ sions, in which one participating continuum is a photon continuum and the other one is an ionization or dissociation continuum (7a). Most of the recent theoretical treatments of collisions discretize the molecular continua by adding absorbing spatial boundaries and by working with a bounded range of radial coordinates in conjunction with finite basis sets of square integrable functions. Wave packet propagation methods have often been used to integrate these systems by using discrete representations (8). Because the required computer processor unit CPU time rapidly becomes prohibitively long when wave packets are propagated on multidimensional grids, new attempts have been made to derive time-independent treatments from the time-dependent ones. A solution within the framework of the Floquet theory

Design and regulation of efficient photoinduced electron transfer in macromolecular and photosynthetic systems.

Abstract: 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 mo...

Heteronuclear NMR Pulse Sequences Applied to Biomolecules

Abstract: 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.