Showing papers in "Annual Review of Physical Chemistry in 1997"
TL;DR: The energy landscape theory of protein folding suggests that the most realistic model of a protein is a minimally frustrated heteropolymer with a rugged funnel-like landscape biased toward the native structure.
Abstract: ▪ Abstract The energy landscape theory of protein folding is a statistical description of a protein's potential surface. It assumes that folding occurs through organizing an ensemble of structures rather than through only a few uniquely defined structural intermediates. It suggests that the most realistic model of a protein is a minimally frustrated heteropolymer with a rugged funnel-like landscape biased toward the native structure. This statistical description has been developed using tools from the statistical mechanics of disordered systems, polymers, and phase transitions of finite systems. We review here its analytical background and contrast the phenomena in homopolymers, random heteropolymers, and protein-like heteropolymers that are kinetically and thermodynamically capable of folding. The connection between these statistical concepts and the results of minimalist models used in computer simulations is discussed. The review concludes with a brief discussion of how the theory helps in the interpre...
2,040 citations
TL;DR: Although it has been proposed that strong, short, low-barrier hydrogen bonds are important in enzymatic reactions, it is concluded that the evidence for them in small molecules and in biomolecules is inconclusive.
Abstract: Hydrogen bonds are a key feature of chemical structure and reactivity. Recently there has been much interest in a special class of hydrogen bonds called "strong" or "low-barrier" and characterized by great strength, short distances, a low or vanishing barrier to hydrogen transfer, and distinctive features in the NMR spectrum. Although the energy of an ordinary hydrogen bond is ca 5 kcal mol-1, the strength of these hydrogen bonds may be > or = 10 kcal mol-1. The properties of these hydrogen bonds have been investigated by many experimental techniques, as well as by calculation and by correlations among those properties. Although it has been proposed that strong, short, low-barrier hydrogen bonds are important in enzymatic reactions, it is concluded that the evidence for them in small molecules and in biomolecules is inconclusive.
705 citations
TL;DR: A generally useful method for obtaining electronic and vibrational Stark spectra that does not require sophisticated equipment is described and applications to donor-acceptor polyenes, transition metal complexes, and nonphotosynthetic biological systems are reviewed.
Abstract: Stark spectroscopy has been applied to a wide range of molecular systems and materials. A generally useful method for obtaining electronic and vibrational Stark spectra that does not require sophisticated equipment is described. By working with frozen glasses it is possible to study nearly any molecular system, including ions and proteins. Quantitative analysis of the spectra provides information on the change in dipole moment and polarizability associated with a transition. The change in dipole moment reflects the degree of charge separation for a transition, a quantity of interest to a variety of fields. The polarizability change describes the sensitivity of a transition to an electrostatic field such as that found in a protein or an ordered synthetic material. Applications to donor-acceptor polyenes, transition metal complexes (metal-to-ligand and metal-to-metal mixed valence transitions), and nonphotosynthetic biological systems are reviewed.
560 citations
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TL;DR: How an alternative "model-free" approach to kinetic analysis, which is based on the isoconversional method, can overcome some of these limitations of the widely practiced force fitting of experimental data to simple reaction-order kinetic models is discussed.
Abstract: ▪ Abstract The kinetics of solid state reactions generally cannot be assumed to follow simple rate laws that are applicable to gas-phase reactions. Nevertheless, a widely practiced method for extracting Arrhenius parameters from thermal analysis experiments involves force fitting of experimental data to simple reaction-order kinetic models. This method can produce significant errors in predicted rates outside the experimental range of temperatures, and it is of limited utility for drawing mechanistic conclusions about reactions. In this review, we discuss how an alternative “model-free” approach to kinetic analysis, which is based on the isoconversional method, can overcome some of these limitations.
511 citations
TL;DR: Experimental progress in controlling the population of specific quantum states, in manipulating the dynamics of bound wave packets, and in the control of chemical reactions are reviewed, and current problems in the field are summarized.
Abstract: ▪ Abstract There has been much progress in the control of chemical reactions since methods of active control were first proposed by Brumer & Shapiro and by Tannor & Rice ten years ago. This chapter reviews both theoretical and experimental advances in the field. Control schemes based on quantum mechanical interference between competing paths and the manipulation of wave packets with tailored laser pulses are discussed. The theory of optimal control, the limitations of control theory applied to many-body dynamics, and the effects of constraints on the trajectory of the controlled observable are presented. Experimental progress in controlling the population of specific quantum states, in manipulating the dynamics of bound wave packets, and in the control of chemical reactions are reviewed, and current problems in the field are summarized.
320 citations
TL;DR: Applications of VOA now include all major classes of biological and pharmaceutical molecules, and its importance as a diagnostic tool will likely grow as the control of molecular chirality increases in research and industrial areas.
Abstract: ▪ Abstract Advances in the field of vibrational optical activity (VOA) are reviewed over the past decade. Topics are surveyed with an emphasis on the theoretical and instrumental progress in both vibrational circular dichroism (VCD) and Raman optical activity (ROA). Applications of VOA to stereochemical and biological problems are reviewed, with a bias toward new kinds of experiments made possible by theoretical and instrumental advances. In the field of VCD, the most notable advances have taken place in the quality and size of ab initio calculations of VOA intensities and in the quality of step-scan Fourier transform instrumentation. For ROA, the most dramatic progress has occurred in the areas of theoretical formulation and high-throughput instrumentation. Applications of VOA now include all major classes of biological and pharmaceutical molecules. VOA's importance as a diagnostic tool will likely grow as the control of molecular chirality increases in research and industrial areas.
286 citations
TL;DR: There are indications that the rates of key heterogeneous reactions have not yet been established with sufficient accuracy to enable a reliable diagnosis of observed ozone losses by means of global models.
Abstract: Liquid and solid particles in polar stratospheric clouds are of central importance for the depletion of stratospheric ozone. Surface-catalyzed reactions on these particles, and diffusion-controlled processes in the bulk of the particles, convert halogens, which derive from compounds of mainly anthropogenic origin, from relatively inert reservoir species into forms that efficiently destroy ozone. The microphysics of these particles under cold stratospheric conditions is still uncertain in many respects, in particular concerning phase transitions such as freezing nucleation and deposition nucleation. Furthermore, there are indications that the rates of key heterogeneous reactions have not yet been established with sufficient accuracy to enable a reliable diagnosis of observed ozone losses by means of global models. The present paper reviews the current (late 1996) knowledge of the physico-chemistry of polar stratospheric clouds and evaluates the remaining uncertainties with respect to their ozone depletion potential.
279 citations
TL;DR: The structural, dynamical, and electrical properties of the interface between two immiscible liquids are described and a proper account of the molecular structure of the interfaces is important for understanding solvation and charge transfer processes at the interface.
Abstract: The structural, dynamical, and electrical properties of the interface between two immiscible liquids are described. The adsorption of solute molecules and the processes of ion transfer across the interface and of electron transfer at the interface are discussed. The microscopic perspective is emphasized by focusing on selected recent experimental results and on results obtained from molecular dynamics and Monte Carlo computer simulations. The validity of some of the existing models of the interface is examined. A proper account of the molecular structure of the interface is important for understanding solvation and charge transfer processes at the interface.
267 citations
TL;DR: Observations from these studies have provided many new insights into the fundamental interactions in electrostatic bonding.
Abstract: Weakly bound metal ion complexes are produced in molecular beams and studied with mass-selected laser photodissociation spectroscopy. The metal ions Mg+ and Ca+ are the focus of these studies because they have a single valence electron and strong atomic resonance lines in convenient wavelength regions. Weakly bound complexes of these ions with rare-gas atoms and small molecules are prepared with laser vaporization in a pulsed nozzle cluster source. The vibrationally and rotationally resolved electronic spectra obtained for these complexes help to determine the complexes' structures and bonding energetics. Observations from these studies have provided many new insights into the fundamental interactions in electrostatic bonding.
241 citations
TL;DR: A review of single-molecule spectroscopy in solids can be found in this paper, where the emphasis is on physical results and their interpretation, followed by a general introduction.
Abstract: ▪ Abstract Recent experimental and theoretical studies concerning single-molecule spectroscopy in solids are discussed. Pure quantum effects—such as photon bunching, antibunching, and spectral jumps—and more classical phenomena—such as near-field excitation, saturation, ac/dc Stark shifts, spectral diffusion, two-photon excitation, and customary spectroscopic analysis—are considered. The emphasis of this review is on physical results and their interpretation. This is preceded by a general introduction, where fundamentals of single-molecule spectroscopy are explained.
241 citations
TL;DR: Thin oxide films (from one to tens of monolayers) of SiO2, MgO, NiO, Al2O3, FexOy, and TiO2 supported on refractory metal substrates have been prepared by depositing the oxide metal precursor in a background of oxygen.
Abstract: Thin oxide films (from one to tens of monolayers) of SiO2, MgO, NiO, Al2O3, FexOy, and TiO2 supported on refractory metal substrates have been prepared by depositing the oxide metal precursor in a background of oxygen (ca 1 x 10(-5) Torr). The thinness of these oxide samples facilitates investigation by an array of surface techniques, many of which are precluded when applied to the corresponding bulk oxide. Layered and mixed binary oxides have been prepared by sequential synthesis of dissimilar oxide layers or co-deposition of two different oxides. Recent work has shown that the underlying oxide substrate can markedly influence the electronic and chemical properties of the overlayer oxide. The structural, electronic, and chemical properties of these ultrathin oxide films have been probed using Auger electron spectroscopy (AES), X-ray photoelectron spectroscopy (XPS), electron energy loss spectroscopy (ELS), ion-scattering spectroscopy (ISS), high-resolution electron energy loss spectroscopy (HREELS), infrared reflectance absorption spectroscopy (IRAS), temperature-programmed desorption (TPD), scanning tunneling microscopy (STM), and scanning tunneling spectroscopy (STS).
TL;DR: Time- and momentum-resolved two-photon photoemission spectra as a function of layer thickness fully determine the conduction band dynamics at the interface.
Abstract: ▪ Abstract Two-photon photoemission is a promising new technique that has been developed for the study of electron dynamics at interfaces. A femtosecond laser is used to both create an excited electronic distribution at the surface and eject the distribution for subsequent energy analysis. Time- and momentum-resolved two-photon photoemission spectra as a function of layer thickness fully determine the conduction band dynamics at the interface. Earlier clean surface studies showed how excited electron lifetimes are affected by the crystal band structure and vacuum image potential. Recent studies of various insulator/metal interfaces show that the dynamics of excess electrons are largely determined by the electron affinity of the adsorbate. In general, electron dynamics at the interface are influenced by the substrate and adlayer band structures, dielectric screening, and polaron formation in the two-dimensional overlayer lattice.
TL;DR: This review implements the kinetic analysis for evaluating the properties of small cavities in proteins and the diffusion of protons within narrow channels and discusses how the clustering of proton-binding sites on a surface can endow the surface with enhanced capacity to attract protons and to funnel them toward a specific site.
Abstract: The dynamics of proton dissociation from an acidic moiety and its subsequent dispersion in the bulk is regulated by the physical chemical properties of the solvent. The solvent has to provide a potential well to accommodate the discharged proton, screen it from the negative charge of the conjugated base, and provide an efficient mode for the diffusion of the proton to the bulk. On measuring the dynamics of proton dissociation in the time-resolved domain, the kinetic analysis of the reaction can quantitate the properties of the immediate environment. In this review we implement the kinetic analysis for evaluating the properties of small cavities in proteins and the diffusion of protons within narrow channels. On the basis of this analysis,we discuss how the clustering of proton-binding sites on a surface can endow the surface with enhanced capacity to attract protons and to funnel them toward a specific site.
TL;DR: This review summarizes recent progress in the understanding of the properties of high molecular Rydberg states and gives an overview of recent chemical applications of these states.
Abstract: ▪ Abstract The unusual properties of high molecular Rydberg states with principal quantum number have enabled the development of new research tools for the study of molecules and ions in the gas phase. These tools range from spectroscopic techniques such as zero kinetic energy (ZEKE) photoelectron spectroscopy and mass-analyzed threshold ionization (MATI) spectroscopy to techniques that are suited to the investigation of photodissociation processes, bimolecular reactions, and state-selected ion-molecule reactions. This review summarizes recent progress in the understanding of the properties of high molecular Rydberg states and gives an overview of recent chemical applications of these states.
TL;DR: Significance and specificity of the results achieved for charge separation in photosynthetic reaction centers and donor-acceptor model complexes indicate highly promising perspectives in photochemical research.
Abstract: Some of the significant advances in time-resolved multifrequency electron paramagnetic resonance (EPR) methods are reviewed, with the explicit focus on studies of light-driven processes and photoreactions in real time. Prominent examples are excited state electron transfer reactions with transient charge-separated radical pairs playing a central role. Paramagnetic intermediates and products are key functional states; thus EPR is the method of choice for their characterization. Photogenerated spin polarization and coherences as process-inherent features add the practical advantage of compensation in the trade-off between sensitivity and time resolution. Additionally, they provide detailed structural and dynamic information on the photoreactive system. Significance and specificity of the results achieved for charge separation in photosynthetic reaction centers and donor-acceptor model complexes indicate highly promising perspectives in photochemical research.
TL;DR: This chapter includes higher-order spectroscopy, and a limited number of three- and four-photon studies are discussed.
Abstract: ▪ Abstract Nonresonant two-photon electronic spectroscopy of polyatomic molecules is reviewed for the period since 1979. Emphasis is placed on studies that expose patterns in the two-photon fluorescence (also ionization, optoacoustic) excitation spectra of aromatic hydrocarbons and the effect of vibrations and substitution, particularly within the framework of pseudoparity rules. A section is devoted to biological molecules and the emerging use of two-photon–induced fluorescence anisotropy. Relevant theoretical results are discussed, with emphasis on quantum chemical predictions of vibronic coupling and substituent effects on two-photon absorptivity and tensor properties of individual molecules. This chapter includes higher-order spectroscopy, and a limited number of three- and four-photon studies are discussed.
TL;DR: In this article, a review of state-to-state studies of collision-induced electronic quenching and energy transfer processes is presented, which provides examples of both perturbation-assisted and nonadiabatic gateways between the initial and final electronic states.
Abstract: Laser and molecular beam techniques have enabled researchers to determine the rovibrational levels populated in collision-induced electronic transitions from specified initial levels of several diatomic molecules. As exemplified by the N2+- and CN-rare-gas systems, such measurements, in combination with theoretical calculations of cross sections for these state-to-state collisional processes, provide a means to understand in detail the dynamics of these electronic quenching and energy transfer processes. The present article reviews state-to-state studies of collision-induced electronic transitions. The various collision systems studied provide examples of both perturbation-assisted "gateways" between the initial and final electronic states and perturbation-independent transitions enabled by nonadiabatic mixing induced by the collision partner.
TL;DR: In this article, a beam of low divergence and small cross-sectional area is used to study dissociative recombination of cold molecules with respect to cross sections, branching ratios, and angular distibutions at an unprecedented luminosity.
Abstract: ▪ Abstract The development of heavy-ion storage-cooler rings for atomic physics has made it possible to produce high-quality beams of molecular ions that are internally cold. The stored molecular-ion beam is immersed in a cold electron bath, which gives a beam of low divergence and small cross-sectional area. The electron cooler also serves as a target for electron–molecular ion collision experiments. This allows the study of dissociative recombination of cold molecules with respect to cross sections, branching ratios, and angular distibutions at an unprecedented luminosity.
TL;DR: The entrance channel to the OH+H2-->H2O+H hydrogen abstraction reaction has been investigated from several different experimental approaches and complementary theoretical calculations and photodetachment of an electron from the H3O- anion enabled the neutral reaction to be probed in conformations sampled by the two isomeric forms of the anion.
Abstract: The entrance channel to the OH+H2-->H2O+H hydrogen abstraction reaction has been investigated from several different experimental approaches and complementary theoretical calculations. Weakly bound complexes between the hydroxyl radical and molecular hydrogen have been stabilized within a shallow well in the entrance channel and characterized via electronic spectroscopy on the OH A2Sigma+-X2Pi transition. Laser-induced fluorescence and fluorescence depletion experiments have revealed the binding energy of H2/D2 with ground state OH X2Pi radicals, the intermolecular energy levels supported by the OH A2Sigma+ (v'=0,1)+H2/D2 potential, and the OH-H2/D2 excited state dissociation limit. The OH X2Pi + H2 potentials have also been examined through inelastic scattering measurements on Lambda-doublet state-selected OH with normal or para-H2. Finally, photodetachment of an electron from the H3O- anion enabled the neutral reaction to be probed in conformations sampled by the two isomeric forms of the anion.
TL;DR: The fundamental quantum mechanics, group theory, and spectroscopy of methyl torsional structure accompanying electronic transitions is presented and the origin of barriers to internal rotation and the interaction of the methyl with the pi system via hyperconjugation are discussed.
Abstract: ▪ Abstract The fundamental quantum mechanics, group theory, and spectroscopy of methyl torsional structure accompanying electronic transitions is presented. The origin of barriers to internal rotation and the interaction of the methyl with the π system via hyperconjugation are discussed. Because of the relationship between the methyl barrier and the π system, measurement of the CH3 properties provides structural information about the molecule. In para′-substituted p-methyl-t-stilbenes, barriers in the S1 state show a strong dependence on the substituent, substituent conformation, and involvement of the substituent in hydrogen bonding interaction. The methyl torsional barrier reflects these changes despite the distance of the substitution site, 10 atoms away.
TL;DR: This review focuses on the insights provided by ab initio-based molecular dynamics that are currently unavailable from experimental studies and discusses current techniques and limitations.
Abstract: We review the young field of ab initio molecular dynamics applied to molecule-surface reactions. The techniques of ab initio molecular dynamics include methods that use an analytic potential energy function fit to ab initio data and those that are fully ab initio. In this review, we focus on the insights provided by ab initio-based molecular dynamics that are currently unavailable from experimental studies and discuss current techniques and limitations. As an example of how different aspects of a problem can be tackled with state-of-the-art theoretical tools, we consider the well-studied case of H2 desorption and adsorption from the Si(100)-2 x 1 surface.
TL;DR: This work discusses both theoretical and experimental results in atomic and molecular ionization and dissociation with applications to femtochemistry, and introduces the subfemtosecond time scale into strong-field dynamics through time-dependent Born-Oppenheimer surfaces.
Abstract: Strong field atomic and molecular interactions can be understood by following electronic dynamics inside the laser cycle. This quasistatic perspective introduces the subfemtosecond time scale into strong-field dynamics through time-dependent Born-Oppenheimer surfaces. We discuss both theoretical and experimental results in atomic and molecular ionization and dissociation with applications to femtochemistry. An all-optical Coulomb explosion method for determining time-dependent molecular structure and properties is demonstrated. The concept of time-dependent Born-Oppenheimer surfaces is used to study molecular dissociation and exchange reactions in infrared fields.
TL;DR: Underlying common basic concepts and fundamental mechanisms such as adiabaticity and nonadiabatic transition are extracted and discussed in order to facilitate a comprehensive understanding of chemical dynamics.
Abstract: ▪ Abstract Recent remarkable progress in theoretical studies of (a) quantum dynamics of chemical reactions, (b) characteristics and dynamics of superexcited states of molecules, (c) nonadiabatic transitions at potential curve crossings, and (d) multidimensional tunneling is reviewed briefly. Underlying common basic concepts and fundamental mechanisms such as adiabaticity and nonadiabatic transition are extracted and discussed in order to facilitate a comprehensive understanding of chemical dynamics. Not only the basic theoretical methodologies but also the intriguing dynamical aspects of each subject are explained as simply as possible.
TL;DR: Techniques for time-resolved natural and magnetic circular dichroism spectroscopy covering the picosecond to millisecond time regimes and their applications are reviewed, with particular emphasis on quasi-null ellipsometric techniques for nanosecond multichannel measurements of circular dichROism.
Abstract: The addition of circular or, more generally, elliptical polarization state detection to fast optical absorption spectroscopy can increase the amount of electronic and nuclear conformational information obtained about transient molecular species. To accomplish this, fast circular dichroism methods have emerged over the past decade that overcome the millisecond limit on time resolution associated with conventional modulation techniques and enable structural studies of excited states and kinetic intermediates. This article reviews techniques for time-resolved natural and magnetic circular dichroism spectroscopy covering the picosecond to millisecond time regimes and their applications, with particular emphasis on quasi-null ellipsometric techniques for nanosecond multichannel measurements of circular dichroism. Closely related quasi-null polarimetric techniques for nanosecond optical rotatory dispersion and linear dichroism measurements are also discussed.
TL;DR: A narrative account of the ingredients in the making of a young scientist, his wartime science in England, and subsequent career in France, where he has grown older and has expanded his horizons to address problems of astrophysical, nonlinear optical, and biological interest, using a variety of techniques.
Abstract: A narrative account of the ingredients in the making of a young scientist, his wartime science in England, and subsequent career in France, where, starting in molecular electronic spectroscopy, he has grown older and has expanded his horizons to address problems of astrophysical, nonlinear optical, and biological interest, using, with the aid of many good scientists, a variety of techniques, mainly of optical and mass spectroscopies and with synchrotron radiation as an important excitation source. He has plans to continue.