Special Collection: Computational Chemistry

Chemists know well the value of an experimental or a theoretical result, but what is the value of a computational result? Simulation is neither theory nor experience, nor a mere calculation tool, but a genuine way of approaching reality that is transforming the scientific method. In some cases, it offers explanations to observations or experiments that seem incomprehensible because they are too complex. In this case, the computation serves as a relief. An experiment that converges with a certain computation has more scientific value than an experiment that does not converge with anything at all. In other cases, contribution of computational chemistry is essential because there is no experimental manner to determine what happens during a chemical process; for instance, in the path from reactants to products in (fast) reactions. Now, computational chemistry provides additional information that is not possible to obtain from experiments, so it is a valuable complement to them. Indeed, fruitful synergy between computation and experiment has led to the approach of theory-driven experimentation. Finally, computational chemistry helps to legitimize models or theories that have little opportunity to be contrasted with reality. In this situation, computational chemistry is not experience, but it does substitute it in relation to theory. In the present special collection, we have examples of the different ways computational chemistry helps chemists to interpret the electronic and molecular structure of molecules and their reactivity.     

Perceiving molecular themes in the structures and bonding of intermetallic phases: the role of Hückel theory in an ab initio era

Qualitative molecular orbital theory is central to our understanding of the bonding and reactivity of molecules and materials across chemistry. Advances in computational technology and methodology, however, have made ab initio or density functional theory calculations a simpler alternative, offering reliable results on increasingly large systems in a reasonable time-scale without the need for concerns about the approximations and parameterization of semi-empirical one-electron based methods. In this perspective, we illustrate how the availability of higher-level computational results can augment, rather than supplant, the insights provided by approaches such as the simple and extended Hückel methods. We begin by describing a way to parameterize Hückel-type Hamiltonians against DFT results for intermetallic systems. The potential for chemical understanding embodied by such orbital-based models is then demonstrated with two schemes of bonding analysis that originated in them (but can be extended to DFT results): the μ(3)-acid/base model and the μ(2)-Hückel chemical pressure analysis, which translate the molecular concepts of acidity and electronic/steric competition, respectively, into the context of intermetallic chemistry.     

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.     

Organic Dications: Gas Phase Experiments and Theory in Concert

Knowledge of structure and bonding are integral parts in the understanding of the chemistry of neutral, radicaloid and positively or negatively charged species. The interplay of molecular bonding and the inherent electrostatic repulsion in doubly-charged molecules expands our insight in the versatility of bonding in electron deficient molecules. Small organic dications are now routinely detected in the gas phase by a variety of mass spectrometric techniques. Ab initio molecular orbital theory has advanced to the stage of accurately predicting potential energy surfaces. This review highlights the symbiotic relationship between gas-phase ion and computational studies and gives a rationale for the salient bonding features in doubly-charged organic cations.     

Chemical and biochemical sensing with modified single walled carbon nanotubes

The nano dimensions, graphitic surface chemistry and electronic properties of single walled carbon nanotubes make such a material an ideal candidate for chemical or biochemical sensing. Carbon nanotubes can be nondestructively oxidized along their sidewalls or ends and subsequently covalently functionalized with colloidal particles or polyamine dendrimers via carboxylate chemistry. Proteins adsorb individually, strongly and noncovalently along nanotube lengths. These nanotube-protein conjugates are readily characterized at the molecular level by atomic force microscopy. Several metalloproteins and enzymes have been bound on both the sidewalls and termini of single walled carbon nanotubes. Though coupling can be controlled, to a degree, through variation of tube oxidative pre-activation chemistry, careful control experiments and observations made by atomic force microscopy suggest that immobilization is strong, physical and does not require covalent bonding. Importantly, in terms of possible device applications, protein attachment appears to occur with retention of native biological structure. Nanotube electrodes exhibit useful voltammetric properties with direct electrical communication possible between a redox-active biomolecule and the delocalized pi system of its carbon nanotube support.     

Chemical Concepts from Density Functional TheorySCI北大核心CSCD

Chemical concepts such as structure,bonding,reactivity,etc.have been widely used in the literature and text books to appreciate molecular properties and chemical transformations.Even though modern theoretical and computational chemistry is well established from the perspective of accuracy and complexity,how to quantify these concepts is a still unresolved task.Conceptual density functional theory and its related recent developments provide unique opportunities to tackle this problem.In this Special Issue,27 contributions from top investigators over the world are collected to highlight the state-of-art research on this topic,which not only showcases the status of where we are now but also unveils a number to possible future directions to be pursued.     

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.     

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。     

Using Molecular Modeling in the Organic Chemistry Course for Majors

Molecular modeling provides a way to correlate theoretical concepts with experimental data; therefore, we have introduced organic chemistry students to molecular modeling early in the first semester. This approach provides students with additional skills for clarifying chemical and theoretical concepts by means of demonstrations in the classroom and hands-on tutorial modules. In this manner the impact of the active-learning process is increased. In addition, this tool allows us to further enhance laboratory experiments already developed using a guided-inquiry approach and to design new experiments. Chemical concepts such as conformational analysis, stereochemistry, IR spectra, molecular and electronic properties, molecular orbitals, and chemical reactivity are emphasized through this approach.     

Structure and reactivity of radical ions: new twists on old concepts

Electron transfer is the simplest reaction possible, yet it has a profound impact on the structure and reactivity of organic compounds. These changes allow a new look at some of the fundamental concepts that are used to explain organic chemistry, such as symmetry, aromaticity, and bonding. The results from high-level electronic structure calculations are used to analyze the mechanistic differences in the pericyclic reactions of simple hydrocarbons and their radical cation counterparts. The importance of state symmetry correlation, Jahn-Teller distortions, delocalization, and fractional bonding for the reaction pathways of hydrocarbon radical cations is discussed.     

"Non-VSEPR" Structures and Bonding in d(0) Systems

Under certain circumstances, metal complexes with a formal d(0) electronic configuration may exhibit structures that violate the traditional structure models, such as the VSEPR concept or simple ionic pictures. Some examples of such behavior, such as the bent gas-phase structures of some alkaline earth dihalides, or the trigonal prismatic coordination of some early transition metal chalcogenides or pnictides, have been known for a long time. However, the number of molecular examples for "non-VSEPR" structures has increased dramatically during the past decade, in particular in the realm of organometallic chemistry. At the same time, various theoretical models have been discussed, sometimes controversially, to explain the observed, unusual structures. Many d(0) systems are important in homogeneous and heterogeneous catalysis, biocatalysis (e.g. molybdenum or tungsten enzymes), or materials science (e.g. ferroelectric perovskites or zirconia). Moreover, their electronic structure without formally nonbonding d orbitals makes them unique starting points for a general understanding of structure, bonding, and reactivity of transition metal compounds. Here we attempt to provide a comprehensive view, both of the types of deviations of d(0) and related complexes from regular coordination arrangements, and of the theoretical framework that allows their rationalization. Many computational and experimental examples are provided, with an emphasis on homoleptic mononuclear complexes. Then the factors that control the structures are discussed in detail. They are a) metal d orbital participation in sigma bonding, b) polarization of the outermost core shells, c) ligand repulsion, and d) pi bonding. Suggestions are made as to which of the factors are the dominant ones in certain situations. In heteroleptic complexes, the competition of sigma and pi bonding of the various ligands controls the structures in a complicated fashion. Some guidelines are provided that should help to better understand the interrelations. Bent's rule is of only very limited use in these types of systems, because of the paramount influence of pi bonding. Finally, computed and measured structures of multinuclear complexes are discussed, including possible consequences for the properties of bulk solids.     

Size-dependent structural evolution and chemical reactivity of gold clusters.

Ground-state structures and other experimentally relevant isomers of Au(15) (-) to Au(24) (-) clusters are determined through joint first-principles density functional theory and photoelectron spectroscopy measurements. Subsequent calculations of molecular O(2) adsorption to the optimal cluster structures reveal a size-dependent reactivity pattern that agrees well with earlier experiments. A detailed analysis of the underlying electronic structure shows that the chemical reactivity of the gold cluster anions can be elucidated in terms of a partial-jellium picture, where delocalized electrons occupying electronic shells move over the ionic skeleton, whose geometric structure is strongly influenced by the directional bonding associated with the highly localized "d-band" electrons.     

Sorption of chlorhexidine on cellulose: mechanism of binding and molecular recognition

Chlorhexidine (CH) is an effective antimicrobial agent. There has been very little work published concerning the interactions of CH with, and its adsorption mechanism on, cellulose. In this paper, such physical chemistry parameters are examined and related to computational chemistry studies. Adsorption isotherms were constructed following application of CH to cellulose. These were typical of a Langmuir adsorption isotherm, but at higher concentrations displayed good correlation also with a Freundlich isotherm. Sorption was attributed to a combination of electrostatic (major contribution) and hydrogen bonding forces, which endorsed computational chemistry proposals: electrostatic interactions between CH and carboxylic acid groups in the cellulose dominate with a contribution to binding through hydrogen bonding of the biguanide residues and the p-chlorophenol moieties (Yoshida H-bonding) with the cellulose hydroxyl groups. At high CH concentrations, there is evidence of monolayer and bilayer aggregation. Differences in sorption between CH and another antimicrobial agent previously studied, poly(hexamethylenebiguanide) (PHMB), are attributed to higher molecular weight of PHMB and higher charge density of biguanide residues in CH (due to the relative electron withdrawing effect of the p-chlorophenol moiety).     

Methyl Complexes of the Transition Metals

Organometallic chemistry can be considered as a wide area of knowledge that combines concepts of classic organic chemistry, that is, based essentially on carbon, with molecular inorganic chemistry, especially with coordination compounds. Transition‐metal methyl complexes probably represent the simplest and most fundamental way to view how these two major areas of chemistry combine and merge into novel species with intriguing features in terms of reactivity, structure, and bonding. Citing more than 500 bibliographic references, this review aims to offer a concise view of recent advances in the field of transition‐metal complexes containing M?CH₃ fragments. Taking into account the impressive amount of data that are continuously provided by organometallic chemists in this area, this review is mainly focused on results of the last five years. After a panoramic overview on M?CH₃ compounds of Groups 3 to 11, which includes the most recent landmark findings in this area, two further sections are dedicated to methyl‐bridged complexes and reactivity.     

Asymmetric Reduction of Acetophenone with (−)-β-chlorodiisopinocampheylborane, and Derivatization with (−)-Menthyl Chloroformate. An Undergraduate Organic Synthesis, GC Analysis, and Molecular Modeling Project

Molecular vibration plays an important role in chemistry, both in chemical reactions and in the characterization and measurement of molecular structure and bonding. Normal modes provide the conceptual framework for understanding molecular vibrations. For example, the analysis of infrared spectra, an important tool for chemists, relies heavily on the concept of normal modes; yet, undergraduate students, even chemistry majors, seldom gain a thorough understanding of normal modes through the traditional chemistry curriculum. In fact, the most commonly used physical chemistry textbooks give only a cursory introduction to this concept, leaving out the substantive development. This occurs presumably because normal modes emerge from a multistepped mathematical analysis of the molecular dynamics. While the mathematical skill needed for each step typically has been covered in an introductory calculus course, the full development is a lengthy process and skipped in the texts. Thus, students have little opportunity to develop a sound conceptual understanding of vibrational modes and fundamental vibrational frequencies, even though they inevitably encounter these terms in their future work.     

计算化学在分子轨道教学中的应用

分子轨道理论是理解分子电子结构与微观性质的重要理论之一,也是本科生与研究生结构化学教学中的重点与难点。学生对原子轨道组合形成分子轨道、分子轨道能级交叉混合等知识的理解缺乏形象直观、定量的认识。本文通过基于量子化学或密度泛函理论的Gaussian 03计算软件,计算、绘制并分析了F_2、O_2、N_2、HF、CO等的分子轨道能级图,将学生较难理解的内容定量、直观地呈现出来,形象地解释了分子轨道成键原则与电子填充原则等分子轨道理论中的重难点,加深了学生对分子轨道理论的理解,特别是sp轨道混杂导致的σ_(2p_z)与π_(2p)轨道能级交叉这一难点,激发了学生学习的主动性和积极性,提高了教学质量。在此基础上,利用分子轨道理论分析了CO_2的电子结构,使学生学会应用分子轨道理论解决实际问题,巩固了相关课堂理论知识。     

Putting anion-π interactions into perspective

Supramolecular chemistry is a field of scientific exploration that probes the relationship between molecular structure and function. It is the chemistry of the noncovalent bond, which forms the basis of highly specific recognition, transport, and regulation events that actuate biological processes. The classic design principles of supramolecular chemistry include strong, directional interactions like hydrogen bonding, halogen bonding, and cation-π complexation, as well as less directional forces like ion pairing, π-π, solvophobic, and van der Waals potentials. In recent years, the anion-π interaction (an attractive force between an electron-deficient aromatic π system and an anion) has been recognized as a hitherto unexplored noncovalent bond, the nature of which has been interpreted through both experimental and theoretical investigations. The design of selective anion receptors and channels based on this interaction represent important advances in the field of supramolecular chemistry. The objectives of this Review are 1) to discuss current thinking on the nature of this interaction, 2) to survey key experimental work in which anion-π bonding is demonstrated, and 3) to provide insights into the directional nature of anion-π contact in X-ray crystal structures.