Molecular Photochemistry: Recent Developments in Theory

Photochemistry is a fascinating branch of chemistry that is concerned with molecules and light. However, the importance of simulating light‐induced processes is reflected also in fields as diverse as biology, material science, and medicine. This Minireview highlights recent progress achieved in theoretical chemistry to calculate electronically excited states of molecules and simulate their photoinduced dynamics, with the aim of reaching experimental accuracy. We focus on emergent methods and give selected examples that illustrate the progress in recent years towards predicting complex electronic structures with strong correlation, calculations on large molecules, describing multichromophoric systems, and simulating non‐adiabatic molecular dynamics over long time scales, for molecules in the gas phase or in complex biological environments.     

A Collection of Fullerenes for Synthetic Access Toward Oriented Charge‐Transfer Cascades in Triple‐Channel Photosystems

The development of synthetic methods to build complex functional systems is a central and current challenge in organic chemistry. This goal is important because supramolecular architectures of highest sophistication account for function in nature, and synthetic organic chemistry, contrary to high standards with small molecules, fails to deliver functional systems of similar complexity. In this report, we introduce a collection of fullerenes that is compatible with the construction of multicomponent charge‐transfer cascades and can be placed in triple‐channel architectures next to stacks of oligothiophenes and naphthalenediimides. For the creation of this collection, modern fullerene chemistry—methanofullerenes and 1,4‐diarylfullerenes—is combined with classical Nierengarten–Diederich–Bingel approaches.     

有机化学进展(2011~2012)

本文综述了中国大陆地区有机化学研究人员2011至2012年两年内在合成方法学、有机合成化学、元素有机化学以及天然产物化学等领域获得的重要成果。文章中共引用参考文献355篇,其中110多篇手性金属配合物和有机小分子催化的不对称反应、金属催化的碳氢键活化等合成方法学论文和30余篇氟有机化学论文基本来源于德国《应用化学》(国际版)和《美国化学杂志》。本文汇集了中国有机化学家两年中合成的150多个具有生物活性和化学结构多样性的天然产物,其中不乏具有高度挑战性的复杂天然分子。在近两年中中国有机化学家从陆地和海洋的生物体内发现各种不同类型新天然产物90多个。     

Inverse quantum chemistry: Concepts and strategies for rational compound design

The rational design of molecules and materials is becoming more and more important. With the advent of powerful computer systems and sophisticated algorithms, quantum chemistry plays a decisive role in the design process. While traditional quantum chemical approaches predict the properties of a predefined molecular structure, the goal of inverse quantum chemistry is to find a structure featuring one or more desired properties. Herein, we review inverse quantum chemical approaches proposed so far and discuss their advantages as well as their weaknesses. © 2014 Wiley Periodicals, Inc.     

Computer-Assisted Molecular Design (CAMD)—An Overview

A new instrument, long established as CAD in engineering, is beginning to make its presence felt in chemical research laboratories: Computer-Assisted Molecular Design (CAMD). The combined use of computer graphics and theoretical chemistry is opening up new perspectives in molecular research. Structures and properties of molecules such as spacefilling, charge distribution, or dynamic behavior can be determined and used for comparison. For research on complex systems like biomolecules (protein engineering), this new approach turns out to be indispensable.     

Ketenes in polymer-assisted synthesis

Since its inception, ketene chemistry has developed into a unique and well-established source of useful transformations for conventional synthetic organic chemistry. It is, therefore, not surprising that soon after their movement from the realm of peptide and peptoid libraries to that of small molecules, combinatorial chemists have sought the benefits of ketene chemistry to satisfy their own synthetic needs. The ability of these versatile molecules to undergo reactions with nucleophiles, and to participate in cycloadditions and cyclocondensations, has been utilized for the preparation of diverse heterocyclic compounds, and has added to the advantages of polymer-assisted synthesis for rapid purification. Different types of ketenes and different methods for their generation have been involved, which illustrates the potential diversity of the chemistry. There is now a better grasp of the effect of the fragility of these sometimes transient molecules on the reactions involving solid supports, and this augurs well for the application of some of the more recent developments in ketene chemistry to the generation of small-molecule libraries.     

Par-delà la synthèse : l’auto-organisation

The evolution of the universe from the particle to the thinking organism has taken place through self-organization. Chemistry has a major role to play in understanding these processes leading to the generation of complex matter. Chemistry has developed a highly powerful molecular synthetic chemistry, mastering the combination and recombination of atoms into increasingly complex molecules through selective chemical reactions. Supramolecular chemistry is harnessing intermolecular forces for the generation of informed supramolecular systems and processes through supramolecular synthetic chemistry implementing molecular information carried by electromagnetic interactions. Supramolecular chemistry has been actively exploring systems undergoing self-organization, i.e., systems capable of spontaneously generating well-defined functional supramolecular architectures by self-assembly from their components, under the control of interactional molecular recognition events, thus behaving as programmed chemical systems. Molecular chemistry may similarly take advantage of the selectivity of covalent reactions to assemble complex molecular architectures through self-organization processes implementing functional molecular recognition. Supramolecular/non-covalent and molecular/covalent SELF-ORGANIZATION may thus be considered as the ULTIMATE SYNTHETIC CHEMISTRY, whereby chemical objects at both levels are generated on the basis of recognition processes involving either interactional or reactional features. Illustrations from the supramolecular domain will serve as illustrations. Supramolecular entities as well as molecules containing reversible bonds are able to undergo a continuous change in constitution by reorganization and exchange of building blocks. This capability defines a Constitutional Dynamic Chemistry (CDC) on both the molecular and supramolecular levels. CDC introduces a paradigm shift with respect to constitutionally static chemistry. It takes advantage of dynamic constitutional diversity to allow variation and selection and thus leads towards the emergence of adaptive and evolutive chemistry.     

Molecular Recognition with Model Systems

How structures fit together is the principal domain of molecular recognition, and current studies are evolving from the host–guest chemistry of ions to interactions between two molecules. Recent advances in the synthesis of sizable concave molecules, especially those featuring convergent functional groups, make it possible to bind smaller convex structures with considerable selectivity. One result is that hydrogen bonding can be addressed in model systems. The present review emphasizes the use of cleftlike structures as a means of probing the forces involved in nucleic acid recognition. The application of such molecules to the catalysis of chemical reactions, particularly those involved in self-replicating systems, is also described. Some implications for future pharmaceutical agents are suggested as a result of access to synthetic receptors for biologically relevant targets.     

计算(机)化学学科进展(2011-2013)

计算(机)化学已成为化学学科的重要组成部分,在理论计算、分子模拟、数据挖掘以及复杂体系分析中发挥了重要作用。本文总结了近年来化学信息学的研究进展,包括化学信息学方法、软件及数据库技术以及化学信息学在结构、性质、相互作用、反应机理,蛋白质及功能材料的性能研究,复杂体系化学数据分析中的应用。共引用参考文献78篇。     

Supramolecular Chemistry in Microflow Fields: Toward a New Material World of Precise Kinetic Control

Constructing new and versatile self‐assembling systems in supramolecular chemistry is much like the development of new reactions or new catalysts in synthetic organic chemistry. As one such new technology, conventional supramolecular assembly systems have been combined with microflow techniques to control intermolecular or interpolymer interactions through precise regulation of a flowing self‐assembly field. The potential of the microflow system has been explored by using various simple model compounds. Uniform solvent diffusion in the microflow leads to rapid activation of molecules in a nonequilibrium state and, thereby, enhanced interactions. All of these self‐assembly processes begin from a temporally activated state and proceed in a uniform chemical environment, forming a synchronized cluster and resulting in effective conversion to supramolecules, with precise tuning of molecular (or polymer) interactions. This approach allows the synthesis of a variety of discrete microstructures (e.g., fibers, sheets) and unique supramolecules (e.g., hierarchical assemblies, capped fibers, polymer networks, supramolecules with time‐delayed action) that have previously been inaccessible.     

Click Chemistry: Diverse Chemical Function from a Few Good Reactions

Examination of nature's favorite molecules reveals a striking preference for making carbon–heteroatom bonds over carbon–carbon bonds—surely no surprise given that carbon dioxide is nature's starting material and that most reactions are performed in water. Nucleic acids, proteins, and polysaccharides are condensation polymers of small subunits stitched together by carbon–heteroatom bonds. Even the 35 or so building blocks from which these crucial molecules are made each contain, at most, six contiguous C−C bonds, except for the three aromatic amino acids. Taking our cue from nature's approach, we address here the development of a set of powerful, highly reliable, and selective reactions for the rapid synthesis of useful new compounds and combinatorial libraries through heteroatom links (C−X−C), an approach we call “click chemistry”. Click chemistry is at once defined, enabled, and constrained by a handful of nearly perfect “spring‐loaded” reactions. The stringent criteria for a process to earn click chemistry status are described along with examples of the molecular frameworks that are easily made using this spartan, but powerful, synthetic strategy.     

Advances in the study of the host-guest interaction by using coronene as the guest molecule

This review supplied direct insight of host-guest molecule system by using COR as the guest molecule.     

Real‐time quantum chemistry

Significant progress in the development of efficient and fast algorithms for quantum chemical calculations has been made in the past two decades. The main focus has always been the desire to be able to treat ever larger molecules or molecular assemblies—especially linear and sublinear scaling techniques are devoted to the accomplishment of this goal. However, as many chemical reactions are rather local, they usually involve only a limited number of atoms so that models of about 200 (or even less) atoms embedded in a suitable environment are sufficient to study their mechanisms. Thus, the system size does not need to be enlarged, but remains constant for reactions of this type that can be described by less than 200 atoms. The question then arises how fast one can obtain the quantum chemical results. This question is not directly answered by linear‐scaling techniques. In fact, ideas such as haptic quantum chemistry (HQC) or interactive quantum chemistry require an immediate provision of quantum chemical information which demands the calculation of data in “real time.” In this perspective, we aim at a definition of real‐time quantum chemistry, explore its realm and eventually discuss applications in the field of HQC. For the latter, we elaborate whether a direct approach is possible by virtue of real‐time quantum chemistry. © 2012 Wiley Periodicals, Inc.     

Gas-phase ion chemistry in XH4--C3H4--ZH3 (X==Si, Ge; Z==N, P) mixtures

The gas-phase ion chemistry of silane-allene-ammonia, germane-allene (or propyne)-ammonia (or phosphine) systems was studied by ion trap mass spectrometry. Reaction sequences were determined and rate constants were measured for the main processes observed. The mixture containing silane displays higher reactivity with respect to that with germane. Comparison with analogous systems provides useful information about the reactivity of different hydrocarbon molecules and the different affinities of silicon and germanium towards nitrogen and phosphorus. The most interesting product ions observed are those containing Si (or Ge), C and N (or P) elements together, as these ion species may be considered precursors of doped amorphous carbides, which are widely used in semiconductor devices.     

Template Syntheses

Although the principle of template synthesis has been known since the sixties, surprising discoveries and new applications in the field of supramolecular chemistry over the last decade have provoked a boom in the subject. The synthesis of supramolecular species has been made much more efficient, or even in some cases possible, by the introduction of template ions or molecules. It is not just metal ions that can act as templates. Neutral molecules, electrostatic interactions, and hydrogen bonds also support the formation of binary and tertiary complexes. Energetically favorable conformations then lead to the formation of a specific desired product in high yield. In addition to the discussion of metal ions and neutral molecules as templates, covalent, positive, and negative templates are differentiated. Kinetic and thermodynamic aspects will also be considered in this review, together with the influence of templates on the phenomenon of self-organization. Further developments and applications include the synthesis of oligonucleotides, peptide blocks capable of forming secondary structure, and template polymers. Template synthesis of defined molecular cavities ultimately leads to “inclusion chemistry on a nanometer scale.”     

Supramolecular Inorganic Chemistry: Small Guests in Small and Large Hosts

A key reaction in the biological and material world is the controlled linking of simple (molecular) building blocks, a reaction with which one can create mesoscopic structures, which, for example, contain cavities and display specifically desired properties, but also compounds that exhibit typical solid-state structures. The best example in this context is the chemistry of host–guest interactions, which spans the entire range from three- and two-dimensional to one- and “zero-dimensional”, discrete host structures. Members of the class of multidimensional compounds have been classified as such for a long time, for example, clathrates and intercalation compounds. Thus far, however, there are no classifications for discrete inorganic host–guest compounds. The first systematic approach can be applied to novel polyoxometalates, a class of compounds which has only recently become known. Molecular recognition; tailor-made, molecular engineering; control of fragment linkage of spin organization and crystallization; cryptands and coronands as “cages” for cations, anions or anion–cation aggregates as sections of ionic lattices; anions within anions, receptors; host–guest interactions; complementarity, as well as the dialectic terms reduction and emergence are important terms and concepts of supramolecular inorganic chemistry. Of particular importance for future research is the comprehension of the mesoscopic area (molècular assemblies)—that between individual molecules and solids (“substances”)—which acts in the biological world as carrier of function and information and for which interesting material properties are expected. This area is accessible through certain variations of “controlled” self-organization processes, which can be demonstrated by using examples from the chemistry of polyoxometalates. The comprehension of the laws that rule the linking of simple polyhedra to give complex systems enables one to deal with numerous interdisciplinary areas of research: crystal physics and chemistry, heterogeneous catalysis, bioinorganic chemistry (biomineralization), and materials science. In addition, conservative self-organization processes, for example template-directed syntheses, are of importance for natural philosophy in the context of the question about the inherent properties of material systems.     

Computational Chemistry to the Rescue: Modern Toolboxes for the Assignment of Complex Molecules by GIAO NMR Calculations

The calculations of NMR properties of molecules using quantum chemical methods have deeply impacted several branches of organic chemistry. They are particularly important in structural or stereochemical assignments of organic compounds, with implications in total synthesis, stereoselective reactions, and natural products chemistry. In studying the evolution of the strategies developed to support (or reject) a structural proposal, it becomes clear that the most effective and accurate ones involve sophisticated procedures to correlate experimental and computational data. Owing to their relatively high mathematical complexity, such calculations (CP3, DP4, ANN‐PRA) are often carried out using additional computational resources provided by the authors (such as applets or Excel files). This Minireview will cover the state‐of‐the‐art of these toolboxes in the assignment of organic molecules, including mathematical definitions, updates, and discussion of relevant examples.     

Photochemical Reactions in the Synthesis of Protein–Drug Conjugates

The ability to modify biologically active molecules such as antibodies with drug molecules, fluorophores or radionuclides is crucial in drug discovery and target identification. Classic chemistry used for protein functionalisation relies almost exclusively on thermochemically mediated reactions. Our recent experiments have begun to explore the use of photochemistry to effect rapid and efficient protein functionalisation. This article introduces some of the principles and objectives of using photochemically activated reagents for protein ligation. The concept of simultaneous photoradiosynthesis of radiolabelled antibodies for use in molecular imaging is introduced as a working example. Notably, the goal of producing functionalised proteins in the absence of pre-association (non-covalent ligand-protein binding) introduces requirements that are distinct from the more regular use of photoactive groups in photoaffinity labelling. With this in mind, the chemistry of thirteen different classes of photoactivatable reagents that react through the formation of intermediate carbenes, electrophiles, dienes, or radicals, is assessed.