Data Formats for Elementary Gas‐Phase Kinetics: Part 2. Unique Representations of Reactions

A method of extending the IUPAC International Chemical Identifier (InChI) to describe and identify elementary reactions in a standard computer‐readable notation is developed. Denoted InChI‐ER, the method is based on the existing InChI formalism, with certain refinements for the better identification of molecular entities as proposed in Part 1 published previously in this journal. Using this base notation, an identifier for elementary reactions on a molecular level is created by adding additional layers in a conceptually similar and extensible manner. Two of the layers describe the atoms involved in the transition state and the connectivity changes that occur during the reaction. Additional layers classify the reactions on the basis of the connectivity changes, providing chemical information useful in organizing and searching kinetic data sets found in databases or used in detailed kinetic modeling. Important aspects of the method are that the proposed layers are optional, that they do not interfere with existing InChI specifications, and that they retain extensibility should further refinements be desired in the future.     

Interacting Quantum Atoms Analysis of the Reaction Force: A Tool to Analyze Driving and Retarding Forces in Chemical Reactions

The analysis of the reaction force and its topology has provided a wide range of fruitful concepts in the theory of chemical reactivity over the years, allowing to identify chemically relevant regions along a reaction profile. The reaction force (RF), a projection of the Hellmann-Feynman forces acting on the nuclei of a molecular system onto a suitable reaction coordinate, is partitioned using the interacting quantum atoms approach (IQA). The exact IQA molecular energy decomposition is now shown to open a unique window to identify and quantify the chemical entities that drive or retard a chemical reaction. The RF/IQA coupling offers an extraordinarily detailed view of the type and number of elementary processes that take reactants into products, as tested on two sets of simple reactions.     

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.      

yaInChI: modified InChI string scheme for line notation of chemical structures

A modified InChI (International Chemical Identifier) string scheme, yaInChI (yet another InChI), is suggested as a method for including the structural information of a given molecule, making it straightforward and more easily readable. The yaInChI theme is applicable for checking the structural identity with higher sensitivity and generating three-dimensional (3-D) structures from the one-dimensional (1-D) string with less ambiguity than the general InChI method. The modifications to yaInChI provide non-rotatable single bonds, stereochemistry of organometallic compounds, allene and cumulene, and parity of atoms with a lone pair. Additionally, yaInChI better preserves the original information of the given input file (SDF) using the protonation information, hydrogen count +1, and original bond type, which are not considered or restrictively considered in InChI and SMILES. When yaInChI is used to perform a duplication check on a 3D chemical structure database, Ligand.Info, it shows more discriminating power than InChI. The structural information provided by yaInChI is in a compact format, making it a promising solution for handling large chemical structure databases.     

Solar‐Energy‐Driven Photoelectrochemical Biosensing Using TiO2 Nanowires

Photoelectrochemical sensing represents a unique means for chemical and biological detection, with foci of optimizing semiconductor composition and electronic structures, surface functionalization layers, and chemical detection methods. Here, we have briefly discussed our recent developments of TiO₂ nanowire‐based photoelectrochemical sensing, with particular emphasis on three main detection mechanisms and corresponding examples. We have also demonstrated the use of the photoelectrochemical sensing of real‐time molecular reaction kinetic measurements, as well as direct interfacing of living cells and probing of cellular functions.     

5,10-CH+-THF向邻苯二胺转移一碳单元反应的理论研究

叶酸辅酶在酶催化的一碳单元转移过程中具有重要的作用,已有大量的实验及实验模拟对其生物学功能进行了研究分析.本文用PM3半经验方法对5,10-CH⁺-THF向邻苯二胺转移一碳单元的反应进行了理论研究.结果表明,5,10-CH⁺-THF中的咪唑啉环有两种开环方式,从而使得该反应可以通过两种途径实现,每一种途径都经历了6个反应步骤,其中包括限制速度的两次质子转移步骤.优化计算了每个步骤所有可能的中间体和过渡态的结构和能量,并通过比较分析得到了各反应阶段的最优中间体和过渡态结构.     

Mechanistic and spectroscopic identification of initial reaction intermediates for prenal decomposition on a platinum model catalyst

The prediction of a reaction mechanism and the identification of the corresponding chemical intermediates is a major challenge in surface science and heterogeneous catalysis, due to a complex network of elementary steps and surface species. Here we demonstrate how to overcome this difficulty by tracking the temperature dependent formation of the initial reaction intermediates and identifying the decomposition pathways in the case of prenal, an α,β-unsaturated aldehyde, on the Pt(111) model catalyst surface by combining vibrational spectroscopy, thermal reaction/desorption spectroscopy (TPRS) experiments and detailed theoretical analysis. TPRS characterization of this reaction up to 600 K shows a series of desorption states of H(2) (～280 K, 410 K and 473 K) and CO (～414 K), giving valuable insights into the sequence of elementary steps suggesting that the loss of hydrogen and the carbonyl functions are among the first elementary steps. HREELS experiments recorded after annealing to specific temperatures result in complex spectra, which can be assigned to several subsequently formed and transformed surface intermediates. Starting from stable prenal adsorption structures, complementary DFT calculations allow the determination of the most likely reaction pathway for the initial decomposition steps and the identification of the corresponding intermediates by comparison with HREELS. The decomposition occurs from the strongly bonded prenal adsorption structures via a dehydro-η(3)-triσ(CCC)-H1 intermediate to the highly stable η(1)-isobutylidyne species at high temperatures.     

First-principles determination of molecular conformations of indolizidine (−)-235B′ in solution

Indolizidine (?)-235B′ is a particularly interesting natural product, as it is the currently known, most potent and subtype-selective open-channel blocker of the α4β2 nicotinic acetylcholine receptor (nAChR). In the current study, extensive first-principles electronic structure calculations have been carried out in order to determine the stable molecular conformations and their relative free energies of the protonated and deprotonated states of (?)-235B′ in the gas phase, in chloroform, and in aqueous solution. The ¹H and ¹³C NMR chemical shifts calculated using the computationally determined dominant molecular conformation of the deprotonated state are all consistent with available experimental NMR spectra of (?)-235B′ in chloroform, which suggests that the computationally determined molecular conformations are reasonable. Our computational results reveal for the first time that two geminal H atoms on carbon-3 (C3) of (?)-235B′ have remarkably different chemical shifts (i.e., 3.24 and 2.03 ppm). The computational results help one to better understand and analyze the experimental ¹H NMR spectra of (?)-235B′. The finding of remarkably different chemical shifts of two C3 geminal H atoms in a certain molecular conformation of (?)-235B′ may also be valuable in analysis of NMR spectra of other related ring-containing compounds. In addition, the pK _a of (?)-235B′ in aqueous solution is predicted to be ~9.7. All of the computational results provide a solid basis for future studies of the microscopic and phenomenological binding of various receptor proteins with the protonated and deprotonated structures of this unique open-channel blocker of α4β2 nAChRs. This computational study also demonstrates how one can appropriately use computational modeling and spectroscopic analysis to address the structural and spectroscopic problems that cannot be addressed by experiments alone.     

SemanticEye: a semantic web application to rationalize and enhance chemical electronic publishing

SemanticEye, an ontology with associated tools, improves the classification and open accessibility of chemical information in electronic publishing. In a manner analogous to digital music management, RDF metadata encoded as Adobe XMP can be extracted from a variety of document formats, such as PDF, and managed in an RDF repository called Sesame. Users upload electronic documents containing XMP to a central server by "dropping" them into WebDAV folders. The documents can then be navigated in a Web browser via their metadata, and multiple documents containing identical metadata can then be aggregated. SemanticEye does not actually store any documents. By including unique identifiers within the XMP, such as the DOI, associated documents can be retrieved from the Web with the help of resolving agents. The power of this metadata driven approach is illustrated by including, within the XMP, InChI identifiers for molecular structures and finding relationships between articles based on their InChIs. SemanticEye will become increasingly more comprehensive as usage becomes more widespread. Furthermore, following the Semantic Web architecture enables the reuse of open software tools, provides a "semantically intuitive" alternative to search engines, and fosters a greater sense of trust in Web-based scientific information.     

A combined experimental and theoretical study on the effect of doping and interface formation on Ppv-ether copolymer

We present a detailed optoelectronic and vibrational study devoted to the transformation from neutral to doped PPV-ether copolymer in both powder and thin film states. The full geometries were optimized with the density functional theory (DFT) for neutral and doped states, where a comparative geometric study was established. The lowest singlet excited-state geometries have been investigated by using the configuration interaction single (CIS/3-21G(d)) method. The absorption spectra are then calculated respectively on the basis of the ground- and excited-state geometries. Our calculation results are in close agreement with those available from experiments. The charge distribution and excitation energies of singly charged PPV-ether are calculated, where two subgap absorption features are found to dominate the optical spectrum correlated with the polaron picture. These theoretical results are compared to experimental optical data illustrated by iodine-doped PPV-ether. Next, we have performed a simulation to model the conformations and the electronic structure modifications of interface formation of PPV-ether copolymer thin film with calcium (Ca), magnesium (Mg), and aluminum (Al) metal as a cathode and indium tin oxide (ITO) as anode in polymer LEDs. By providing the optical parameter obtained and the chemical reaction at the interface, we present the energetic diagram near the interface and the energy position of the lowest occupied molecular orbital with respect to the electrode Fermi level.     

Accurate specification of molecular structures: the case for zero-order bonds and explicit hydrogen counting

Most data structures used to represent molecular entities for cheminformatics are underspecified for purposes of representing nonorganic chemical species. Two extensions are proposed: allowing bond orders of 0 and adding an atom property to control the number of inferred attached hydrogen atoms. The case for these two extensions is made by demonstrating the effective representation of a number of unconventional bonding types that cannot be effectively represented by data structures currently in common use. A set of enhancements to the industry standard MDL CTfile format is proposed, which includes a backward compatibility mechanism to maximize interpretability by software that has not been updated to make use of the extensions.     

Diastereofacial solid phase synthesis and self-promoted cleavage of a [2.2.1] bicyclic diversity scaffold

[reaction: see text]. We have previously described a diastereofacially selective 1,3-dipolar cycloaddition reaction of isomünchnones with vinyl ethers. While adapting this methodology for solid phase synthesis, we discovered a chemoselective and self-promoted linker aminolysis that provides liberated product in high purity, at a significantly enhanced rate. Herein we describe the implementation of a chiral auxiliary as a solid-phase linker, the detailed investigation of its unique aminolysis, and the utility of this cleavage within a chemical diversity format.     

Effect of diabatic correlation on the reactions of O(2 3P, 2 1D) with N2 O and CO2

Although correlation diagrams based upon the application of spin and angular momentum conservation have been shown to be a useful device in interpreting the chemistry of electronically excited atoms, experimental observations suggest that a more complete understanding of such chemical processes requires some insight into the electronic structure of the collision complex. In the absence of such information, it is possible to consider the role of diabatic correlations on the energetics of elementary processes with a view toward analyzing the behavior of the reactants along the reaction coordinate. Here, the aeronomically interesting reactions of ground state and electronically excited oxygen atoms with N₂ O and CO₂ are analyzed and the effects of low-lying molecular excited states on the reactivity of these molecules assessed.     

化学反应过渡态的结构和动力学

化学反应过渡态决定了包括反应速率和微观反应动力学在内的化学反应的基本特性,而无论是从理论还是实验上研究和观测化学反应过渡态都是极具挑战性的课题.近年来,我国科学家们利用交叉分子束-里德堡氢原子飞行时间谱仪,结合高精度的量子动力学计算,对H＋H2和F＋H2这两个教科书式的典型反应体系进行了全量子态分辨的反应动力学研究,从中得出了关于这两个反应体系的过渡态的结构和动力学性质的结论性的研究成果.     

Thermodynamics, Transport and Kinetics of Equilibrium and Non-Equilibrium Plasmas: A State-to-State Approach

Thermal non-equilibrium plasmas have been deeply investigated theoretically by means of the state-to-state approach, offering the unique opportunity of a detailed information about internal distributions affecting thermodynamics, transport coefficients and kinetics, properly accounting for the presence of excited states. The efforts made in the construction of knowledge on the dynamics of elementary processes occurring in the plasma with resolution on internal degrees of freedom, required by the method, are discussed. Boltzmann equation is solved for electrons self-consistently coupled to the chemical species collisional dynamics, reproducing very interesting features of strongly non-equilibrium internal distributions, characterizing plasmas.     

Comparison of Thiophene–Pyrrole Oligomers with Oligothiophenes: A Joint Experimental and Theoretical Investigation of Their Structural and Spectroscopic Properties

We have prepared a new series of mixed thiophene–pyrrole oligomers to investigate the electronic benefits arising from the combination of these two heterocycles. The oligomers are functionalized with several hexyl and aryl groups to improve both processability and chemical robustness. An analysis of their spectroscopic (absorption and emission), photophysical, electrochemical, solid state, and vibrational properties is performed in combination with quantum‐chemical calculations. This analysis provides relevant information regarding the use of these materials as organic semiconductors. The balance between the high aromatic character of pyrrole and the moderate aromaticity of thiophene allows us to address the impact of the coupling of these heterocycles in conjugated systems. The data are interpreted on the basis of the aromaticity, molecular conformations, ground and excited electronic state structures, frontier orbital topologies and energies, oxidative states, and quinoidal versus aromatic competition.     

Enhancing Hydrogen Evolution Activity of Au(111) in Alkaline Media through Molecular Engineering of a 2D Polymer

The electrochemical splitting of water holds promise for the storage of energy produced intermittently by renewable energy sources. The evolution of hydrogen currently relies on the use of platinum as a catalyst—which is scarce and expensive—and ongoing research is focused towards finding cheaper alternatives. In this context, 2D polymers grown as single layers on surfaces have emerged as porous materials with tunable chemical and electronic structures that can be used for improving the catalytic activity of metal surfaces. Here, we use designed organic molecules to fabricate covalent 2D architectures by an Ullmann‐type coupling reaction on Au(111). The polymer‐patterned gold electrode exhibits a hydrogen evolution reaction activity up to three times higher than that of bare gold. Through rational design of the polymer on the molecular level we engineered hydrogen evolution activity by an approach that can be easily extended to other electrocatalytic reactions.     

The Royal Society of Chemistry and the delivery of chemistry data repositories for the community

Since 2009 the Royal Society of Chemistry (RSC) has been delivering access to chemistry data and cheminformatics tools via the ChemSpider database and has garnered a significant community following in terms of usage and contribution to the platform. ChemSpider has focused only on those chemical entities that can be represented as molecular connection tables or, to be more specific, the ability to generate an InChI from the input structure. As a structure centric hub ChemSpider is built around the molecular structure with other data and links being associated with this structure. As a result the platform has been limited in terms of the types of data that can be managed, and the flexibility of its searches, and it is constrained by the data model. New technologies and approaches, specifically taking into account a shift from relational to NoSQL databases, and the growing importance of the semantic web, has motivated RSC to rearchitect and create a more generic data repository utilizing these new technologies. This article will provide an overview of our activities in delivering data sharing platforms for the chemistry community including the development of the new data repository expanding into more extensive domains of chemistry data.