Organic Chemistry as a Language and the Implications of Chemical Linguistics for Structural and Retrosynthetic Analyses

Methods of computational linguistics are used to demonstrate that a natural language such as English and organic chemistry have the same structure in terms of the frequency of, respectively, text fragments and molecular fragments. This quantitative correspondence suggests that it is possible to extend the methods of computational corpus linguistics to the analysis of organic molecules. It is shown that within organic molecules bonds that have highest information content are the ones that 1) define repeat/symmetry subunits and 2) in asymmetric molecules, define the loci of potential retrosynthetic disconnections. Linguistics‐based analysis appears well‐suited to the analysis of complex structural and reactivity patterns within organic molecules.     

Connecting Discrete Stereoclusters by Using DFT and NMR Spectroscopy: The Case of Nivariol

The structural determination of small organic molecules is mainly undertaken by using NMR techniques, although it is increasingly supplemented by using computational methods. NMR parameters, such as chemical shifts and coupling constants, are extremely sensitive indicators of local molecular conformation and are a source of structural evidence. However, their interpretation is fairly challenging in many circumstances, such as the case of the new polyether squalene derivative nivariol, the structure of which was elucidated by means of NMR spectroscopy and DFT calculations. The potential flexibility of this molecule and the high number of quaternary carbon atoms that it contains make its configurational assignment very difficult. Moreover, the relative configuration of four separated stereoclusters was established and subsequently connected by using NOE and J‐based analysis, as well as by a comparison of its experimental ¹³C NMR chemical shifts with the corresponding population‐weighted values, as calculated by using DFT methods. Limitations of these used approaches became apparent but were overcome by combining the two methods.     

Determination of Complex Small‐Molecule Structures Using Molecular Alignment Simulation

Correct structural assignment of small molecules and natural products is critical for drug discovery and organic chemistry. Anisotropy‐based NMR spectroscopy is a powerful tool for the structural assignment of organic molecules, but it relies on the utilization of a medium that disrupts the isotropic motion of molecules in organic solvents. Here, we establish a quantitative correlation between the atomic structure of the alignment medium, the molecular structure of the small molecule, and molecule‐specific anisotropic NMR parameters. The quantitative correlation uses an accurate three‐dimensional molecular alignment model that predicts residual dipolar couplings of small molecules aligned by poly(γ‐benzyl‐l ‐glutamate). The technique facilitates reliable determination of the correct stereoisomer and enables unequivocal, rapid determination of complex molecular structures from extremely sparse NMR data.     

Non-empirical LCAO-MO-SCF-CI calculations on organic molecules with Gaussian type functions

This paper (Part I) describes the theoretical and computational bases of some non-empirical calculations on small organic molecules to be reported in later papers (Parts II et seq). Approximate solutions for the usual fixed nucleus electronic Hamiltonian, in the term of wave functions composed of Slater determinants, are discussed, with particular emphasis on their computational utility. Possible choices of basis functions, from which to form the determinants are examined, and the advantages of Gaussian type functions (GTF) centered on the component atoms are pointed out. Some of the properties of molecules which can be calculated using such approximate wave functions are outlined. Finally an attempt is made to discuss the current limitations of non-empirical calculations of the type described here, and some guesses are made about their future. Brief outlines as a set of appendices are given of the mathematical formalism and computational details of the calculations.     

含氮基团修饰β-环糊精量子化学研究

用PM3半经验方法优化了5种不同含氮基团修饰环糊精的结构,并用HF方法在STO-3G和3-21G*两种基组水平上计算了它们的单点能.首次给出了这5种修饰环糊精的优化结构,同时计算结果采用极性基团会增加修饰环糊精的偶极距,优化的结构及计算出的物理性质表明修饰后产物明显与β-环糊精有明显的差别.     

Organic Superhalogens

Using first‐principles calculations with predictive capability we show that organic molecules having negative electron affinity can be transformed to superhalogens with electron affinities far exceeding that of chlorine, once its core and ligand atoms are suitably replaced. The discovery of organic superhalogens could have significant impact in chemistry, allowing the synthesis of new materials and compounds.     

Polyhalogen and Polyinterhalogen Anions from Fluorine to Iodine

This Review deals with the evolving field of polyhalogen chemistry, specifically polyhalogen anions (polyhalides). In addition to a historical outline, current progress in synthetic approaches towards the formation of polyfluorides, polychlorides, polybromides, and polyinterhalides is also illustrated. The structural diversity of polyhalides has substantially increased in the past decade, especially for polychlorides and polybromides, which are commonly characterized by single‐crystal X‐ray diffraction, Raman spectroscopy, and quantum‐chemical calculations. Polyfluorides have been examined by sophisticated state‐of‐the‐art quantum‐chemical calculations and investigated spectroscopically in noble gas matrix‐isolation experiments under cryogenic conditions at 4 K. The bonding in such polyhalide systems is also discussed. The last Section deals with applications of polyhalides in halogenation reactions and electrochemistry as well as their use as reactive ionic liquids, emphasizing the promising future of polyhalogen chemistry.     

Dendrimer‐Type Peptoid‐Decorated Hexaphenylxylenes and Tetraphenylmethanes: Synthesis and Structure in Solution and in the Gas Phase

Branched organic nanostructures are useful scaffolds that find multiple applications in a variety of fields. Here, we present a novel approach to dendrimer‐like structures. Our design contains a rigid hydrocarbon‐based core (hexaphenylxylylene/tetraethynylphenylmethane) combined with a library of N‐substituted oligoglycines (so‐called peptoids) providing a flexible shell. The use of click chemistry allows rapid assembly of the nanostructures. The possibility of tuning the size and the solubility of this new type of nanostructure will be advantageous for future applications such as heterogeneous catalysis.     

Linear‐scaling self‐consistent field calculations based on divide‐and‐conquer method using resolution‐of‐identity approximation on graphical processing units

Graphical processing units (GPUs) are emerging in computational chemistry to include Hartree?Fock (HF) methods and electron‐correlation theories. However, ab initio calculations of large molecules face technical difficulties such as slow memory access between central processing unit and GPU and other shortfalls of GPU memory. The divide‐and‐conquer (DC) method, which is a linear‐scaling scheme that divides a total system into several fragments, could avoid these bottlenecks by separately solving local equations in individual fragments. In addition, the resolution‐of‐the‐identity (RI) approximation enables an effective reduction in computational cost with respect to the GPU memory. The present study implemented the DC‐RI‐HF code on GPUs using math libraries, which guarantee compatibility with future development of the GPU architecture. Numerical applications confirmed that the present code using GPUs significantly accelerated the HF calculations while maintaining accuracy. © 2014 Wiley Periodicals, Inc.     

Ethers on Si(001): A Prime Example for the Common Ground between Surface Science and Molecular Organic Chemistry

By using computational chemistry it has been shown that the adsorption of ether molecules on Si(001) under ultrahigh vacuum conditions can be understood with classical concepts of organic chemistry. Detailed analysis of the two‐step reaction mechanism—1) formation of a dative bond between the ether oxygen atom and a Lewis acidic surface atom and 2) nucleophilic attack of a nearby Lewis basic surface atom—shows that it mirrors acid‐catalyzed ether cleavage in solution. The O−Si dative bond is the strongest of its kind, and the reactivity in step 2 defies the Bell–Evans–Polanyi principle. Electron rearrangement during C−O bond cleavage has been visualized with a newly developed method for analyzing bonding, which shows that the mechanism of nucleophilic substitutions on semiconductor surfaces is identical to molecular S_N2 reactions. Our findings illustrate how surface science and molecular chemistry can mutually benefit from each other and unexpected insight can be gained.     

From a Si3‐Cyclopropene to a Si3S‐Bicyclo[1.1.0]butane to a Si3S‐Cyclopropene to a Si3S2‐Bicyclo[1.1.0]butane: Back‐and‐Forth,and In‐Between

Compact and highly reactive bicyclo[1.1.0]butanes constitute one of the most fascinating classes of organic compounds. Furthermore, interplay of bicyclo[1.1.0]butanes with their valence isomers, such as buta‐1,3‐dienes and cyclobutenes, is among the fundamental pericyclic transformations in organic chemistry. Herein we report the back‐and‐forth interconversion between the cyclotrisilenes and thiatrisilabicyclo[1.1.0]butanes, allowing for the synthesis of novel representatives of such classes of highly reactive organometallics. The peculiar structural and bonding features of the newly synthesized compounds, as well as the mechanism of their isomerization, were verified both experimentally and computationally.     

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.     

Insights into Structure Direction of Microporous Aluminophosphates: Competition between Organic Molecules and Water

A combination of experimental characterisation techniques and computational modelling has allowed us to gain insight into the molecular features governing structure direction in the synthesis of microporous aluminophosphates. The occlusion of three different structure‐directing agents (SDAs), triethylamine (TEA), benzylpyrrolidine (BP) and (S )‐(?)‐N‐benzylpyrrolidine‐2‐methanol (BPM), within the AFI structure during its crystallisation, together with the simultaneous incorporation of water, has been experimentally measured. We found a higher incorporation of organic molecules in the structure obtained with BPM, while a higher water (and lower organic) content is found for the ones obtained with TEA and BP as SDAs. The computational study provides a thermodynamic explanation for the observed behaviour in terms of the relative stabilisation energy of the SDAs and water molecules within the AFI framework compared with when they are in aqueous solution, and demonstrates that a competition for preferential occupation exists between water and organic SDAs, which is a function of the interaction with the inorganic framework. The lower interaction of TEA and BP molecules with the AFI structure promotes the simultaneous incorporation of water molecules in the 12‐membered‐ring (MR) channel, to increase the host–guest interaction energy and thus the thermodynamic stability. The presence of strongly interacting methanol groups in the BPM molecules leads to the incorporation of only organic molecules within the 12‐MR channels. Our results demonstrate the essential role that water molecules play in the stabilisation of hydrophilic microporous aluminophosphates; a minimum amount of organic SDA is, however, essential for a templating role of the microporous architecture.     

The Huisgen Reaction: Milestones of the 1,3‐Dipolar Cycloaddition

The concept of 1,3‐dipolar cycloadditions was presented by Rolf Huisgen 60 years ago. Previously unknown reactive intermediates, for example azomethine ylides, were introduced to organic chemistry and the (3+2) cycloadditions of 1,3‐dipoles to multiple‐bond systems (Huisgen reaction) developed into one of the most versatile synthetic methods in heterocyclic chemistry. In this Review, we present the history of this research area, highlight important older reports, and describe the evolution and further development of the concept. The most important mechanistic and synthetic results are discussed. Quantum‐mechanical calculations support the concerted mechanism always favored by R. Huisgen; however, in extreme cases intermediates may be involved. The impact of 1,3‐dipolar cycloadditions on the click chemistry concept of K. B. Sharpless will also be discussed.     

Metal‐Directed Self‐Assembly of a Polyoxometalate‐Based Molecular Triangle: Using Powerful Analytical Tools to Probe the Chemical Structure of Complex Supramolecular Assemblies

A polyoxometalate‐based molecular triangle has been synthesized through the metal‐driven self‐assembly of covalent organic/inorganic hybrid oxo‐clusters with remote pyridyl binding sites. The new metallomacrocycle was unambiguously characterized by using a combination of ¹H NMR spectroscopy, 2D diffusion NMR spectroscopy (DOSY), electrospray ionization travelling wave ion mobility mass spectrometry (ESI‐TWIM‐MS), small‐angle X‐ray scattering (SAXS) and molecular modelling. The collision cross‐sections obtained from TWIM‐MS and the hydrodynamic radii derived from DOSY are in good agreement with the geometry‐optimized structures obtained by using theoretical calculations. Furthermore, SAXS was successfully employed and proved to be a powerful technique for characterizing such large supramolecular assemblies.     

Bayesian inference of conformational state populations from computational models and sparse experimental observables

We present a Bayesian inference approach to estimating conformational state populations from a combination of molecular modeling and sparse experimental data. Unlike alternative approaches, our method is designed for use with small molecules and emphasizes high‐resolution structural models, using inferential structure determination with reference potentials, and Markov Chain Monte Carlo to sample the posterior distribution of conformational states. As an application of the method, we determine solution‐state conformational populations of the 14‐membered macrocycle cineromycin B, using a combination of previously published sparse Nuclear Magnetic Resonance (NMR) observables and replica‐exchange molecular dynamic/Quantum Mechanical (QM)‐refined conformational ensembles. Our results agree better with experimental data compared to previous modeling efforts. Bayes factors are calculated to quantify the consistency of computational modeling with experiment, and the relative importance of reference potentials and other model parameters. © 2014 Wiley Periodicals, Inc.     

Functionalization of Pyrene To Prepare Luminescent Materials—Typical Examples of Synthetic Methodology

Pyrene‐based π‐conjugated materials are considered to be an ideal organic electro‐luminescence material for application in semiconductor devices, such as organic light‐emitting diodes (OLEDs), organic field‐effect transistors (OFETs) and organic photovoltaics (OPVs), and so forth. However, the great drawback of employing pyrene as an organic luminescence material is the formation of excimer emission, which quenches the efficiency at high concentration or in the solid‐state. Thus, in order to obtain highly efficient optical devices, scientists have devoted much effort to tuning the structure of pyrene derivatives in order to realize exploitable properties by employing two strategies, 1) introducing a variety of moieties at the pyrene core, and 2) exploring effective and convenient synthetic strategies to functionalize the pyrene core. Over the past decades, our group has mainly focused on synthetic methodologies for functionalization of the pyrene core; we have found that formylation/acetylation or bromination of pyrene can selectly lead to functionalization at K‐region by Lewis acid catalysis. Herein, this Minireview highlights the direct synthetic approaches (such as formylation, bromination, oxidation, and de‐tert‐butylation reactions, etc.) to functionalize the pyrene in order to advance research on luminescent materials for organic electronic applications. Further, this article demonstrates that the future direction of pyrene chemistry is asymmetric functionalization of pyrene for organic semiconductor applications and highlights some of the classical asymmetric pyrenes, as well as the latest breakthroughs. In addition, the photophysical properties of pyrene‐based molecules are briefly reviewed. To give a current overview of the development of pyrene chemistry, the review selectively covers some of the latest reports and concepts from the period covering late 2011 to the present day.     

主族元素AB4型含氧酸根的成键分析——推荐一个研究型计算化学实验

介绍了一个面向高年级本科生的研究型计算化学实验。主族元素AB4型含氧酸根是无机和结构化学理论课程中讨论化学键类型的例子,然而其结果却存在争议。本实验利用常用量子化学软件,通过计算化学方法分析化学成键,验证猜测,并得出结论。旨在通过本实验,锻炼学生对量子化学计算方法的运用,进而加深对化学基础知识的理解。     

On the algebraic construction of chemistry from quantum mechanics. A fundamental valency vector field defined on the euclidean 3-space and its relation to the Hilbert space

To obtain from quantum mechanics directly the qualitative deductions of chemistry, a mathematical machinery is set up. A single vector space, and a dyad space relate different molecules or spatial configurations of an isomeric set of atoms to each other. Different electronic Hamiltonians belong to the dyad space and are treated so as to be used directly without the intermediary of orbitals, parameter choices, or variational calculations.