Interfacial energy exchange and reaction dynamics in collisions of gases on model organic surfaces

Molecular beam scattering experiments and molecular dynamics simulations have been combined to develop an atomic-level understanding of energy transfer, accommodation, and reactions during collisions between gases and model organic surfaces. The work highlighted in this progress report has been motivated by the scientific importance of understanding fundamental interfacial chemical reactions and the relevance of reactions on organic surfaces to many areas of environmental chemistry. The experimental investigations have been accomplished by molecular beam scattering from ω-functionalized self-assembled monolayers (SAMs) on gold. Molecular beams provide a source of reactant molecules with precisely characterized collision energy and flux; SAMs afford control over the order, structure, and chemical nature of the surface. The details of molecular motion that affect energy exchange and scattering have been elucidated through classical-trajectory simulations of the experimental data using potential energy surfaces derived from ab initio calculations. Our investigations began by employing rare-gas scattering to explore how alkanethiol chain length and packing density, terminal group relative mass, orientation, and chemical functionality influence energy transfer and accommodation at organic surfaces. Subsequent studies of small molecule scattering dynamics provided insight into the influence of internal energy, molecular orientation, and gas–surface attractive forces in interfacial energy exchange. Building on the understanding of scattering dynamics in non-reactive systems, our work has recently explored the reaction probabilities and mechanisms for O₃ and atomic fluorine in collisions with a variety of functionalized SAM surfaces. Together, this body of work has helped construct a more comprehensive understanding of reaction dynamics at organic surfaces.     

Advanced Techniques for Quantum-State Specific Reaction Dynamics of Gas Phase Metal Atoms?

One of the themes of modern molecular reaction dynamics is to characterize elementary chemical reactions from "quantum state to quantum state", and the study of molecular reaction dynamics in excited states can help test the validity of modern chemical theories and provide methods to control chemical reactions. The subject of this review is to describe the recent experimental techniques used to study the reaction dynamics of metal atoms in the gas phase. Through these techniques, information such as the internal energy distribution and angular distribution of the nascent products or the three-dimensional stereodynamic reactivity can be obtained. In addition, by preparing metal atoms with specific excited electronic states or orbital arrangements, information about the reactivity of the electronic states enriches the relevant understanding of the electron transfer mechanism in metal reaction dynamics.      

Molecular structure and dynamics of liquids: aqueous urea solutions

In this review a multi-technical approach to the analysis of the structure and dynamics of the urea/water system is described. The reorientational movement of the solute molecule is investigated by the analysis of spectral band-shapes, as well as with the use of the optical Kerr effect (OKE) and molecular dynamics simulation (MDS). The effect of solute concentration on the structure and dynamics of the aqueous solutions (aggregation, orientational distribution, solvation...) is studied by molecular dynamics simulation and neutron scattering. The results obtained by other techniques are included to provide a critical analysis. Finally, the low-frequency Raman spectra of the system are interpreted on the basis of the semi-quantitative information obtained by molecular dynamics simulation.     

A mini review of the crossed molecular beam apparatus in molecular reaction dynamics

This review has introduced some experimental techniques of crossed molecular beam apparatus in chemical reaction dynamics. First of all, the history of crossed molecular beam equipment is retrospected in this paper. The detectors of both the universal crossed molecular beam machine and Hydrogen-atom Rydberg-tagging apparatus have been discussed. Other types of crossed molecular beam instruments have also been reviewed. Each experimental apparatus makes a compromise among the resolution, sensibility and universality. As a matter of fact, it is these equipments that make many breakthroughs happen in chemical reaction dynamics. This review aims to provide the readers and researchers with some information about the experiments in molecular reaction dynamics. We believe that new types of experimental techniques can emerge and contribute to the development of molecular reaction dynamics and relevant research fields.     

Molecular beams and chemical dynamics at surfaces

The use of molecular beams to study chemical dynamics at surfaces is outlined. The techniques is briefly introduced and its applications are given in a few areas. Scattering experiments give detailed information about the first steps toward a chemical reaction at a surface. Beams with enhanced population of specific quantum states make an even more detailed analysis possible. Adsorption at surfaces can be studied very well using beam methods, especially in the case of activated processes. Beams can be used to grow novel structures. Beams allow the study of chemical reactions at surfaces, and in particular those where product are directly ejected into the gas phase, or where reactions take place upon impact. Finally the study of liquid surfaces is briefly introduced.     

Spatiotemporal Kinetics in Solution Studied by Time‐Resolved X‐Ray Liquidography (Solution Scattering)

Information about temporally varying molecular structure during chemical processes is crucial for understanding the mechanism and function of a chemical reaction. Using ultrashort optical pulses to trigger a reaction in solution and using time‐resolved X‐ray diffraction (scattering) to interrogate the structural changes in the molecules, time‐resolved X‐ray liquidography (TRXL) is a direct tool for probing structural dynamics for chemical reactions in solution. TRXL can provide direct structural information that is difficult to extract from ultrafast optical spectroscopy, such as the time dependence of bond lengths and angles of all molecular species including short‐lived intermediates over a wide range of times, from picoseconds to milliseconds. TRXL elegantly complements ultrafast optical spectroscopy because the diffraction signals are sensitive to all chemical species simultaneously and the diffraction signal from each chemical species can be quantitatively calculated from its three‐dimensional atomic coordinates and compared with experimental TRXL data. Since X‐rays scatter from all the atoms in the solution sample, solutes as well as the solvent, the analysis of TRXL data can provide the temporal behavior of the solvent as well as the structural progression of all the solute molecules in all the reaction pathways, thus providing a global picture of the reactions and accurate branching ratios between multiple reaction pathways. The arrangement of the solvent around the solute molecule can also be extracted. This review summarizes recent developments in TRXL, including technical innovations in synchrotron beamlines and theoretical analysis of TRXL data, as well as several examples from simple molecules to an organometallic complex, nanoparticles, and proteins in solution. Future potential applications of TRXL in femtosecond studies and biologically relevant molecules are also briefly mentioned.     

Universal and state-resolved imaging of chemical dynamics

We showcase the use of high-resolution ion imaging with complementary state-resolved and "universal" vacuum ultraviolet probes to address a broad range of fundamental problems in chemical reaction dynamics. Examples from our recent work include applications in state-correlated unimolecular reactions, ion pair dissociation dynamics and spectroscopy, crossed-beam reactive scattering, and atomic angular momentum polarization in photodissociation. These studies are all directed to achieving a detailed understanding of atomic and molecular interactions, with particular emphasis on reaction mechanisms outside the scope of transition state theory; on spectroscopy and dynamics of highly excited, transient species; on nonadiabatic reaction mechanisms; and on chemical dynamics in polyatomic systems.     

Single Molecules as Optical Nanoprobes for Soft and Complex Matter

The optical signals of single molecules provide information about structure and dynamics of their nanoscale environment, free from space and time averaging. These new data are particularly useful whenever complex structures or dynamics are present, as in polymers or in porous oxides, but also in many other classes of materials, where heterogeneity is less obvious. We review the main uses of single molecules in studies of condensed matter at nanometer scales, especially in the fields of soft matter and materials science. We discuss several examples, including the orientation distribution of molecules in crystals, rotational diffusion in glass‐forming molecular liquids, polymer studies with probes and labeled chains, porous and heterogeneous oxide materials, blinking of single molecules and nanocrystals, and the potential of surface‐enhanced Raman scattering for local chemical analysis. All these examples show that static and dynamic heterogeneities and the spread of molecular parameters are much larger than previously imagined.     

Theories of reactive scattering

This paper is an overview of the theory of reactive scattering, with emphasis on fully quantum mechanical theories that have been developed to describe simple chemical reactions, especially atom-diatom reactions. We also describe related quasiclassical trajectory applications, and in all of this review the emphasis is on methods and applications concerned with state-resolved reaction dynamics. The review first provides an overview of the development of the theory, including a discussion of computational methods based on coupled channel calculations, variational methods, and wave packet methods. Choices of coordinates, including the use of hyperspherical coordinates are discussed, as are basis set and discrete variational representations. The review also summarizes a number of applications that have been performed, especially the two most comprehensively studied systems, H+H2 and F+H2, along with brief discussions of a large number of other systems, including other hydrogen atom transfer reactions, insertion reactions, electronically nonadiabatic reactions, and reactions involving four or more atoms. For each reaction we describe the method used and important new physical insight extracted from the results.     

Ab initio studies of ultrafast x-ray scattering of the photodissociation of iodine

We computationally examine various aspects of the reaction dynamics of the photodissociation and recombination of molecular iodine. We use our recently proposed formalism to calculate time-dependent x-ray scattering signal changes from first principles. Different aspects of the dynamics of this prototypical reaction are studied, such as coherent and noncoherent processes, features of structural relaxation that are periodic in time versus nonperiodic dissociative processes, as well as small electron density changes caused by electronic excitation, all with respect to x-ray scattering. We can demonstrate that wide-angle x-ray scattering offers a possibility to study the changes in electron densities in nonperiodic systems, which render it a suitable technique for the investigation of chemical reactions from a structural dynamics point of view.     

Time-Resolved Photoacoustic Calorimetry: From Carbenes to Proteins

Why have molecules only been seen but not heard? For over a century chemists have probed reactions with various spectroscopic methods to learn about structures, dynamics, and reactivities of their molecules. What they have not done is to listen to their molecules react. Although the photoacoustic phenomenon has been known since 1880, it is only in the last twenty years that technology has developed to the point where sound waves produced by reacting molecules can be time resolved and the information contained within the waves deciphered. The information content within the photoacoustic wave is indeed rich, for one can learn about the dynamics and the magnitude of enthalpy changes associated with the reaction as well as the changes in molecular volume. This review article chronicles the development of time-resolved photoacoustic calorimetry and its application to a variety of reactions encountered in organic and organometallic chemistry and biochemistry.     

Reaction Dynamics with Molecular Beams and Oriented Molecular Beams: A Tool for Looking Closer to Chemical Reactions and Photodissociations

Experimental studies on reaction dynamics by use of molecular beams and oriented molecular beams are reviewed in order for looking closer to chemical reactions as well as photodissociations at the molecular level. We discuss about versatility and usefulness of the electrostatic hexapole sate‐selector as a non‐destructive selector for molecular structure analysis. Some experimental evidences on novel reaction dynamics in photodissociation and stereodynamics are presented followed by concluding remarks and future perspectives for controlling chemical reactions from the point of view of green chemistry, by manipulating molecular orientation without any catalyst nor by applying any external forces like intense electromagnetic field.     

燃料电池电极表界面催化氧还原反应的STM研究进展

催化氧还原反应的电催化剂是燃料电池的一个重要组成部分. 从分子尺度研究催化氧还原反应中所涉及的表界面反应机理,不仅有利于深入理解催化机理,更有利于指导人们合理地设计新型的电催化剂. 本文结合近年来国内外的研究工作,概述了通过扫描隧道显微镜研究燃料电池内部催化氧还原反应过程中所涉及的表面形貌变化、单分子结构变化、中间体的观测以及反应产物调控等方面最新进展,并展望了该研究领域的发展趋势.     

Local Control Theory in Trajectory Surface Hopping Dynamics Applied to the Excited‐State Proton Transfer of 4‐Hydroxyacridine

The application of local control theory combined with nonadiabatic ab initio molecular dynamics to study the photoinduced intramolecular proton transfer reaction in 4‐hydroxyacridine was investigated. All calculations were performed within the framework of linear‐response time‐dependent density functional theory. The computed pulses revealed important information about the underlying excited‐state nuclear dynamics highlighting the involvement of collective vibrational modes that would normally be neglected in a study performed on model systems constrained to a subset of the full configuration space. This study emphasizes the strengths of local control theory for the design of pulses that can trigger chemical reactions associated with the population of a given molecular excited state. In addition, analysis of the generated pulses can help to shed new light on the photophysics and photochemistry of complex molecular systems.     

A recent development in computational chemistry: chemical reactions from first principles molecular dynamics simulations

First-principles molecular dynamics simulations have recently been found an effective tool to study a large variety of chemical problems. Finite temperature simulations reveal unique information, including explicit dynamical effects and the evaluation of proper free energy differences. Moreover, dynamics simulations reveal information on the flexibility of molecular systems, and elucidate, often otherwise inaccessible, mechanistic details of chemical reactions. In addition this methodology allows the study of larger, periodic, systems, revealing computationally unique information which may be directly compared to experiments on realistic chemical systems. A variety of examples will be given, although most focus on the important field of catalysis.     

Classical Reactive Molecular Dynamics Implementations: State of the Art

Reactive molecular dynamics (RMD) implementations equipped with force field approaches to simulate both the time evolution as well as chemical reactions of a broad class of materials are reviewed herein. We subdivide the RMD approaches developed during the last decade as well as older ones already reviewed in 1995 by Srivastava and Garrison and in 2000 by Brenner into two classes. The methods in the first RMD class rely on the use of a reaction cutoff distance and employ a sudden transition from the educts to the products. Due to their simplicity these methods are well suited to generate equilibrated atomistic or material‐specific coarse‐grained polymer structures. In connection with generic models they offer useful qualitative insight into polymerization reactions. The methods in the second RMD class are based on empirical reactive force fields and implement a smooth and continuous transition from the educts to the products. In this RMD class, the reactive potentials are based on many‐body or bond‐order force fields as well as on empirical standard force fields, such as CHARMM, AMBER or MM3 that are modified to become reactive. The aim with the more sophisticated implementations of the second RMD class is the investigation of the reaction kinetics and mechanisms as well as the evaluation of transition state geometries. Pure or hybrid ab initio, density functional, semi‐empirical, molecular mechanics, and Monte Carlo methods for which no time evolution of the chemical systems is achieved are excluded from the present review. So are molecular dynamics techniques coupled with quantum chemical methods for the treatment of the reactive regions, such as Car–Parinello molecular dynamics.     

The many facets of Raman spectroscopy for biomedical analysis

A critical review is presented on the use of linear and nonlinear Raman microspectroscopy in biomedical diagnostics of bacteria, cells, and tissues. This contribution is combined with an overview of the achievements of our research group. Linear Raman spectroscopy offers a wealth of chemical and molecular information. Its routine clinical application poses a challenge due to relatively weak signal intensities and confounding overlapping effects. Nonlinear variants of Raman spectroscopy such as coherent anti-Stokes Raman scattering (CARS) and stimulated Raman scattering (SRS) have been recognized as tools for rapid image acquisition. Imaging applications benefit from the fact that contrast is based on the chemical composition and molecular structures in a label-free and nondestructive manner. Although not label-free, surface enhanced Raman scattering (SERS) has also been recognized as a complementary biomedical tool to increase sensitivity. The current state of the art is evaluated, illustrative examples are given, future developments are pointed out, and important reviews and references from the current literature are selected. The topics are identification of bacteria and single cells, imaging of single cells, Raman activated cell sorting, diagnosis of tissue sections, fiber optic Raman spectroscopy, and progress in coherent Raman scattering in tissue diagnosis. The roles of networks—such as Raman4clinics and CLIRSPEC on a European level—and early adopters in the translation, dissemination, and validation of new methods are discussed.     

Local angular momentum-local impact parameter analysis: derivation and properties of the fundamental identity, with applications to the F+H2, H+D2, and Cl+HCl chemical reactions

The technique of local angular momentum-local impact parameter (LAM-LIP) analysis has recently been shown to provide valuable dynamical information on the angular scattering of chemical reactions under semiclassical conditions. The LAM-LIP technique exploits a nearside-farside (NF) decomposition of the scattering amplitude, which is assumed to be a Legendre partial wave series. In this paper, we derive the "fundamental NF LAM identity," which relates the full LAM to the NF LAMs (there is a similar identity for the LIP case). Two derivations are presented. The first uses complex variable techniques, while the second exploits an analogy between the motion of the scattering amplitude in the Argand plane with changing angle and the classical mechanical motion of a particle in a plane with changing time. Alternative forms of the fundamental LAM-LIP identity are described, one of which gives rise to a CLAM-CLIP plot, where CLAM denotes (Cross section) x LAM and CLIP denotes (Cross section) x LIP. Applications of the NF LAM theory, together with CLAM plots, are reported for state-to-state transitions of the benchmark reactions F+H2-->FH+H, H+D2-->HD+D, and Cl+HCl-->ClH+Cl, using as input both numerical and parametrized scattering matrix elements. We use the fundamental LAM identity to explain the important empirical observation that a NF cross section analysis and a NF LAM analysis provide consistent (and complementary) information on the dynamics of chemical reactions.