Simulations of Gas-Phase Chemical Reactions: Applications to SN2 Nucleophilic Substitution

Computer simulations and animations of the motion of atoms as a chemical reaction proceeds give a detailed picture of how the reaction occurs at a microscopic level. This information is particularly useful for testing the accuracy of statistical models, which are used to calculate various attributes of chemical reactions. Such simulations and animations, in concert with experimental and ab initio studies, have begun to provide a microscopic picture of the intimate details of a particular class of gas-phase ion-molecule bimolecular reactions known as S(N)2 nucleophilic substitution. In these reactions, a nucleophile is displaced from a molecule by another nucleophile. The dynamical model of S(N)2 reactions that emerges from the computer studies, and its relation to statistical theories, is discussed here.     

The validity of the "diradical" hypothesis: direct femtoscond studies of the transition-state structures

Direct studies of diradicals, the molecular species hypothesized to be archetypal of chemical bond transformations in many classes of reactions, have been made using femtosecond laser techniques with mass spectrometry in a molecular beam. These studies are aimed at "freezing" the diradicals in time and in the course of the reaction. The passage of these species through the transition-state region was observed and the effect of total energy and alkyl substitution on the rates of bond closure and cleavage was examined. The results establish the nature of these intermediates and define their existence during reactions.     

High-resolution and analytical transmission electron microscopy of mineral disorder and reactions

Crystal defects and chemical reactions occurring at scales beyond the resolution of light microscopes have major effects on the chemical and physical properties of rocks and minerals. High-resolution imaging, diffraction, and chemical analysis in the transmission electron microscope have become important methods for exploring mineral defect structures and reaction mechanisms and for studying the distribution of phases resulting from reactions. These techniques have shown that structural disorder is common in some rock-forming minerals but rare in others. They have also established mechanisms by which many reactions occur at the atomic cluster scale. These data thus provide an atomistic basis for understanding the kinetics of geological reactions. Furthermore, apparent major-element, minor-element, and trace-element chemistry of minerals can be influenced by submicroscopic inclusions or intergrowths, which commonly form as products of solid-state reactions.     

Steric control of the reaction of CH stretch-excited CHD3 with chlorine atom

Exciting the CH-stretching mode of CHD(3) (where D is deuterium) is known to promote the C-H bond's reactivity toward chlorine (Cl) atom. Conventional wisdom ascribes the vibrational-rate enhancement to a widening of the cone of acceptance (i.e., the collective Cl approach trajectories that lead to reaction). A previous study of this reaction indicated an intriguing alignment effect by infrared laser-excited reagents, which on intuitive grounds is not fully compatible with the above interpretation. We report here an in-depth experimental study of reagent alignment effects in this reaction. Pronounced impacts are evident not only in total reactivity but also in product state and angular distributions. By contrasting the data with previously reported stereodynamics in reactions of unpolarized, excited CHD(3) with fluorine (F) and O((3)P), we elucidate the decisive role of long-range anisotropic interactions in steric control of this chemical reaction.     

Laser probing of chemical reaction dynamics

Lasers are used in increasingly sophisticated ways to carry out reactions between molecules in selected vibrational, rotational, and electronic states and to probe the product states of chemical reactions. Such investigations are providing unprecedented insights into chemical reaction dynamics, the study of the detailed motions that molecules undergo in simple chemical reactions. In many cases it is possible to describe the influence that specific types of molecular excitation have on reactive events. Experiments are also being carried out to leam about chemical reactivity as a function of the alignment of reagents. There is increasing excitement concerning the potential of laser methods to interrogate the transition states of molecular reactions.     

Direct Br?nsted analysis of the restoration of activity to a mutant enzyme by exogenous amines

A true Br?nsted analysis of proton transfer in an enzyme mechanism is made possible by the chemical rescue of an inactive mutant of aspartate aminotransferase, where the endogenous general base, Lys258, is replaced with Ala by site-directed mutagenesis. Catalytic activity is restored to this inactive mutant by exogenous amines. The eleven amines studied generate a Br?nsted correlation with beta of 0.4 for the transamination of cysteine sulfinate, when steric effects are included in the regression analysis. Localized mutagenesis thus allows the classical Br?nsted analysis of transition-state structure to be applied to enzyme-catalyzed reactions.     

Water catalysis of a radical-molecule gas-phase reaction

There has been considerable speculation about the role of water and water complexes in chemical gas-phase reactions, including the conjecture that water may act as a molecular catalyst through its ability to form hydrogen bonds. Here, we present kinetic studies in which the effect of water on the rate of the reaction between hydroxyl radicals and acetaldehyde has been measured directly in Laval nozzle expansions at low temperatures. An increasing enhancement of the reaction rate by added water was found with decreasing temperatures between 300 and 60 kelvin. Quantum chemical calculations and statistical rate theory support our conclusions that this observation is due to the reduction of an intrinsic reaction barrier caused by specific water aggregation. The results suggest that even single water molecules can act as catalysts in radical-molecule reactions.     

Pi electron systems at high pressure

In the paper "Pi electron systems at high pressure" [Science 156, 1183 (1967)] a mechanism is suggested for the high-pressure reactions of perylene and azulene complexes with tetracyanoethylene (Figs. lOb and lOc) which is clearly impossible as drawn. What I had meant to suggest is the reaction shown below (with Fig. lOb as an example), which is at least conceivable, if not very probable from the chemical viewpoint. A similar modification would apply to Fig. lOc. As indicated in the paper, any serious study of the reaction requires the synthesis of enough product for more complete analysis, as well as a fairly detailed knowledge of the crystal geometry of the unreacted complex. See pdf for figure.     

农药基准物——苯取代基定位效应的量子化学研究

采用混合密度泛函理论的B3LYP方法,在6-311G**水平上对10种取代基所形成的化合物进行结构优化,计算出苯环上各个碳原子的电荷数及各种化合物HOMO轨道中各个原子轨道系数,提出依据电子密度和HOMO轨道中原子轨道系数判断取代基定位效应的方法,并依此给出了10种取代基的定位效应。这种方法避免了依据化学反应来判断取代基定位效应所带来的环境污染问题,同时对芳香化合物的亲电取代反应具有一定的预见性。     

Steric effects and solvent effects in ionic reactions

Rates of SN2 reactions of chloride ion with methyl- and tert-butyl-substituted chloroacetonitrile were measured by using Fourier transform-ion cyclotron resonance spectrometry to follow the isotopic exchange reaction. Barrier heights for these reactions indicate that steric effects in the gas phase are diminished relative to apparent steric effects in solution. We attribute the increased barrier in solution to a solvation effect. Monte Carlo simulations done using statistical perturbation theory confirm that steric hindrance to solvation contributes to SN2 barriers in solution.     

Ostwald ripening of clays and metamorphic minerals

Analyses of particle size distributions indicate that clay minerals and other diagenetic and metamorphic minerals commonly undergo recrystallization by Ostwald ripening. The shapes of their particle size distributions can yield the rate law for this process. One consequence of Ostwald ripening is that a record of the recrystallization process is preserved in the various particle sizes. Therefore, one can determine the detailed geologic history of clays and other recrystallized minerals by separating, from a single sample, the various particle sizes for independent chemical, structural, and isotopic analyses.     

Reactions of aromatic and sulfur amino acids in ribonuclease with hydrogen atoms in water solution

Neutral hydrogen atoms are simple, one-electron-equivalent reagents and their reactions are of fundamental interest for chemical kinetics. Functional correlation between aromatic and divalent-sulfur amino acids in ribonuclease is shown in the reaction of ribonuclease with hydrogen atoms in aqueous solution. Products of the reaction are partially characterized.     

Synthesis of carbenes through substitution reactions at a carbene center

An (amino)(phosphino) carbene can be transformed into (amino)(phosphonio) carbenes, which undergo nucleophilic intermolecular as well as intramolecular substitution reactions at the carbene center. A variety of carbenes can be synthesized starting from a single carbene precursor. The resulting gamut of electronic and steric effects possible should open the way not only to a detailed study of the mechanism, but also to the subsequent improvement of catalytic reactions that involve carbene-transition metal complexes.     

Interval analysis on non-linear monotonic systems as an efficient tool to optimise fresh food packaging

When few data or information are available, the validity of studies performing uncertainty analysis or robust design optimisation (i.e., parameter optimisation under uncertainty) with a probabilistic approach is questionable. This is particularly true in some agronomical fields, where parameter and variable uncertainties are often quantified by a handful of measurements or by expert opinions. In this paper, we propose a simple alternative approach based on interval analysis, which avoids the pitfalls of a classical probabilistic approach. We propose simple methods to achieve uncertainty propagation, parameter optimisation and sensitivity analysis in cases where the model satisfies some monotonic properties. As a real-world case study, we interest ourselves to the application developed in our laboratory that has motivated the present work, that is the design of sustainable food packaging preserving fresh fruits and vegetables as long as possible.     

Atmospheric dynamics of the outer planets

Despite major differences in the solar and internal energy inputs, the atmospheres of the four Jovian planets all exhibit latitudinal banding and high-speed jet streams. Neptune and Saturn are the windiest planets, Jupiter is the most active, and Uranus is a tipped-over version of the others. Large oval storm systems exhibit complicated time-dependent behavior that can be simulated in numerical models and laboratory experiments. The largest storm system, the Great Red Spot of Jupiter, has survived for more than 300 years in a chaotic shear zone where smaller structures appear and dissipate every few days. Future space missions will add to our understanding of small-scale processes, chemical composition, and vertical structure. Theoretical hypotheses about the interiors provide input for fluid dynamical models that reproduce many observed features of the winds, temperatures, and cloud patterns. In one set of models the winds are confined to the thin layer where clouds form. In other models, the winds extend deep into the planetary fluid interiors. Hypotheses will be tested further as observations and theories become more exact and detailed comparisons are made.     

Automatic segmentation of relevant textures in agricultural images

One important issue emerging strongly in agriculture is related with the automatization of tasks, where the optical sensors play an important role. They provide images that must be conveniently processed. The most relevant image processing procedures require the identification of green plants, in our experiments they come from barley and corn crops including weeds, so that some types of action can be carried out, including site-specific treatments with chemical products or mechanical manipulations. Also the identification of textures belonging to the soil could be useful to know some variables, such as humidity, smoothness or any others. Finally, from the point of view of the autonomous robot navigation, where the robot is equipped with the imaging system, some times it is convenient to know not only the soil information and the plants growing in the soil but also additional information supplied by global references based on specific areas. This implies that the images to be processed contain textures of three main types to be identified: green plants, soil and sky if any. This paper proposes a new automatic approach for segmenting these main textures and also to refine the identification of sub-textures inside the main ones. Concerning the green identification, we propose a new approach that exploits the performance of existing strategies by combining them. The combination takes into account the relevance of the information provided by each strategy based on the intensity variability. This makes an important contribution. The combination of thresholding approaches, for segmenting the soil and the sky, makes the second contribution; finally the adjusting of the supervised fuzzy clustering approach for identifying sub-textures automatically, makes the third finding. The performance of the method allows to verify its viability for automatic tasks in agriculture based on image processing.     

Theoretical chemistry comes alive: full partner with experiment

During the last decade, advances in computational techniques and in the extraction of chemically useful concepts from electronic wave functions have put theorists into the mainstream of chemistry. Some recent examples of the prediction of spectroscopic quantities and the elucidation of catalytic processes for homogeneous and heterogeneous reactions from theoretical calculations are used to illustrate how theory and experiment are now full partners in chemical research. It is expected that during the next decade the thrust of theoretical chemistry will be to combine the knowledge of fundamental chemical steps and fundamental interactions with advances in chemical dynamics and irreversible statistical mechanics and in computer technology to produce simulations of chemical systems with competing reactions taking place simultaneously at various reaction sites. The promise of such simulation is illustrated by a study of the enzyme thermolysin.     

Quantum theory of chemical reaction dynamics

It is now possible to use rigorous quantum scattering theory to perform accurate calculations on the detailed state-to-state dynamics of chemical reactions in the gas phase. Calculations on simple reactions, such as H + D2 --> HD + D and F + H2 --> HF + H, compete with experiment in their accuracy. Recent advances in theory promise to extend such accurate predictions to more complicated reactions, such as OH + H2 --> H2O + H, and even to reactions of molecules on solid surfaces. New experimental techniques for probing reaction transition states, such as negative-ion photodetachment spectroscopy and pump-probe femtosecond spectroscopy, are stimulating the development of new theories.     

van der waals interactions in the Cl + HD reaction

The van der Waals forces in the entrance valley of the Cl + HD reaction are shown here to play a decisive role in the reaction's dynamics. Exact quantum mechanical calculations of reactive scattering on a potential energy surface without Cl-HD van der Waals forces predict that the HCl and DCl products will be produced almost equally, whereas the same calculations on a new ab initio potential energy surface with van der Waals forces show a strong preference for the production of DCl. This preference is also seen in crossed molecular beam experiments on the reaction. The study of chemical reaction dynamics has now advanced to the stage where even comparatively weak van der Waals interactions can no longer be neglected in calculations of the potential energy surfaces of chemical reactions.