Particle formation and surface processes on atmospheric aerosols: A review of applied quantum chemical calculations

Aerosols significantly influence atmospheric processes such as cloud nucleation, heterogeneous chemistry, and heavy-metal transport in the troposphere. The chemical and physical complexity of atmospheric aerosols results in large uncertainties in their climate and health effects. In this article, we review recent advances in scientific understanding of aerosol processes achieved by the application of quantum chemical calculations. In particular, we emphasize recent work in two areas: new particle formation and heterogeneous processes. Details in quantum chemical methods are provided, elaborating on computational models for prenucleation, secondary organic aerosol formation, and aerosol interface phenomena. Modeling of relative humidity effects, aerosol surfaces, and chemical kinetics of reaction pathways is discussed. Because of their relevance, quantum chemical calculations and field and laboratory experiments are compared. In addition to describing the atmospheric relevance of the computational models, this article also presents future challenges in quantum chemical calculations applied to aerosols.     

Use of Quantum Chemical Methods to Study Cyclodextrin Chemistry

Studies of cyclodextrin chemistry by quantum chemical methods are briefly surveyed. Emphases are put on what types of quantum chemical methods can be used for cyclodextrin chemistry, how to use quantum chemical methods to find the global minimum, to study the structures, binding energies, driving forces for cyclodextrin complexes, as well as chemical reactions occurring inside cyclodextrin cavities. Problems associated with the application of quantum chemical methods in cyclodextrin chemistry are also discussed.     

Application of quantum calculations in the chemical industry—An overview

The field of quantum chemistry experienced huge progress in the past two decades. The drivers for this have been the availability of more and more powerful computer hardware, the development and implementation of improved methods with a better balanced compromise between accuracy and efficiency, as well as pioneering work how these methods are successfully applied to real‐world problems. Thus, quantum calculations, in particular via density functional theory, became an essential tool in many branches of chemical research. This article tries to give an overview how quantum chemical modeling is used in chemical industry, which is done by reviewing papers written by authors from chemical companies. Various topics of particular industrial relevance are introduced together with strategies how to address them via quantum calculations. Examples are the computation of reaction thermodynamics and kinetics as the key ingredients to understand and predict chemical reactivity, but also solvation models as well as methods to describe electronically excited states. © 2014 Wiley Periodicals, Inc.     

Ground and excited electronic states of azobenzene: a quantum Monte Carlo study

Large-scale quantum Monte Carlo (QMC) calculations of ground and excited singlet states of both conformers of azobenzene are presented. Remarkable accuracy is achieved by combining medium accuracy quantum chemistry methods with QMC. The results not only reproduce measured values with chemical accuracy but the accuracy is sufficient to identify part of experimental results which appear to be biased. Novel analysis of nodal surface structure yields new insights and control over their convergence, providing boost to the chemical accuracy electronic structure methods of large molecular systems.     

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。     

Quantum chemical calculation of vibrational spectra of large molecules--Raman and IR spectra for Buckminsterfullerene

In this work we demonstrate how different modern quantum chemical methods can be efficiently combined and applied for the calculation of the vibrational modes and spectra of large molecules. We are aiming at harmonic force fields, and infrared as well as Raman intensities within the double harmonic approximation, because consideration of higher order terms is only feasible for small molecules. In particular, density functional methods have evolved to a powerful quantum chemical tool for the determination of the electronic structure of molecules in the last decade. Underlying theoretical concepts for the calculation of intensities are reviewed, emphasizing necessary approximations and formal aspects of the introduced quantities, which are often not explicated in detail in elementary treatments of this topic. It is shown how complex quantum chemistry program packages can be interfaced to new programs in order to calculate IR and Raman spectra. The advantages of numerical differentiation of analytical gradients, dipole moments, and static, as well as dynamic polarizabilities, are pointed out. We carefully investigate the influence of the basis set size on polarizabilities and their spatial derivatives. This leads us to the construction of a hybrid basis set, which is equally well suited for the calculation of vibrational frequencies and Raman intensities. The efficiency is demonstrated for the highly symmetric C(60), for which we present the first all-electron density functional calculation of its Raman spectrum.     

Experimental and quantum chemical studies of structure and reaction mechanisms of dioxouranium(VI) complexes in solution

This perspective article describes the combination of experimental data and quantum chemical methods for the determination of structure and reaction mechanisms of uranyl(vi) complexes in aqueous solution. The first part assesses the accuracy of the chemical and thermodynamic properties of solvated uranyl(vi) complexes as obtained by various quantum chemical methods. The second part discusses structure determination, mechanisms for ligand exchange and the lability of coordinated water molecules for various uranyl(vi) complexes using a combination of NMR and quantum chemical data.     

Application of semiempirical quantum chemical methods as a scoring function in docking

A crucial point in docking simulations is the scoring function used for estimation of the target-ligand interaction energy. The usual practice is to employ fast but simplified empirical scoring functions. Rigorous quantum chemical methods are too slow to screen virtual combinatorial libraries consisting of thousands of molecules, but they can be used in the final step of the simulations for assessing the results obtained. At this stage quantum chemical calculations can be performed only for the 10–100 top binders predicted by simplified scoring functions, and only using linear-scaling semiempirical quantum chemical methods such as MOZYME. The possibilities and potentialities of the quantum chemical methods for estimation of the binding affinities in docking simulations are a largely unexplored area, so the main goal of this study is a detailed evaluation of the potential and limitations of the MOZYME methodology for estimation of the target-ligand binding energies and its comparison with available experimental data.Proceedings of the 11th International Congress of Quantum Chemistry satellite meeting in honor of Jean-Louis Rivail     

Holographic electron density shape theorem and its role in drug design and toxicological risk assessment

Each complete, boundaryless molecular electron density is fully determined by any nonzero volume piece of the electron density cloud. This inherent feature of molecules, called the "holographic" property of molecular electron densities, provides a strong foundation for the local, quantum chemical shape analysis of various functional groups, pharmacophores, and other local molecular moieties. A proof is presented for the relevant molecular shape theorem, the "holographic electron density shape theorem", and the role of this theorem in quantum chemical, quantitative shape-activity relations (QShAR) is discussed. The quantum chemical methods of molecular shape analysis can be extended to ab initio quality electron densities of macromolecules, such as proteins, as well as to local molecular moieties, such as functional groups or pharmacophores, based on the transferability and additivity of local, fuzzy density fragments and the associated local density matrixes within the framework of the ADMA (Adjustable Density Matrix Assembler) approach. In addition to new results on chemical bonding and the development of macromolecular force methods, the new methodologies are also applicable to QShAR studies in computer-aided drug discovery and in toxicological risk assessment.     

Theoretical prediction and assignment of vicinal 1H-1H coupling constants of diastereomeric 3-alkoxy-6,7-epoxy-2-oxabicyclo[3.3.0]octanes

Spin-spin coupling constants between nuclei in NMR spectroscopy reflect their spatial arrangement. A number of calculation methods, applying different levels of theory, have been developed to support the stereochemical assignment of novel compounds. Nevertheless, revisions of the assignment of structures in the literature are not rare. In the present work, the reliability of the calculation methods amenable for a theoretical prediction of spin-spin coupling constants of vicinal protons to support correct stereochemical assignment of substitution at five-membered rings of 3-alkoxy-6,7-epoxy-2-oxabicyclo[3.3.0]octanes was studied. Experimental (3)J(H,H) coupling constants were compared with the coupling constants calculated for all possible diastereomers. The fully quantum chemical approach provided theoretical (3)J(H,H) coupling constants with an absolute deviation of no more than 1.1 Hz for 91% of the experimentally studied coupled spins, whereas the methods without quantum chemical geometry optimization resulted in completely unreliable predictions. Consequently, for a reliable stereochemical assignment of small and medium size molecules, the protocol for calculating the coupling constants based on the results of the quantum chemical geometry optimization is recommended.     

基于量子化学计算方法的天然气水合物稳定性研究进展

天然气水合物以资源丰富、优质、洁净等特点,被视为21世纪新能源。天然气水合物稳定性的研究对天然气水合物资源勘探开发具有重要意义。本文简述了微观、介观、宏观、矿藏四个尺度天然气水合物稳定性的研究,重点从微观量子尺度介绍了量子化学计算方法对水合物晶体结构及其稳定性以及水合物宏观物理特性微观表征的计算研究。应用量子化学计算方法可以对天然气水合物的晶体结构、电子轨道分布、振动光谱、成键特性及主客体相互作用进行计算研究,其结果能够为天然气水合物在油气储运、水合物成藏、开采及其综合利用等方面的研究提供理论支持。目前,量子化学计算方法的优化与分子动力学模拟、分子力学模拟等方法的结合将有助于水合物形成和分解微观机理研究的发展,提升计算精度和扩大研究体系,为矿场尺度的天然气水合物资源开采利用提供理论支持。     

Conformers of diheteroaryl ketones and thioketones: a quantum chemical study of their properties and fundamental intramolecular energetic effects

The conformational behavior of ten diheteroaryl ketones and thioketones is investigated using various quantum chemical methods. These ketones and thioketones are formed by the disubstitution of formaldehyde and thioformaldehyde with such a heteroaryl group as 2-furanyl, 2-thiophenyl, 2-selenophenyl, 2-pyrrolyl or 1-methyl-2-pyrrolyl. For these compounds, their conformational preference and the energetic ordering of their conformers are determined at the MP2 and B3LYP levels of theory. Energetic barriers resulting from the interconversion between conformations are also estimated. The natural bond orbital (NBO) and interacting quantum atoms (IQA) methods are used to study fundamental intramolecular energetic effects influencing the stability of individual conformers. The results of the two methods indicate the great significance of the effect associated with electron delocalization (in the form of either NBO donor–acceptor interactions or the IQA interatomic exchange–correlation interaction energy) in governing the conformational behavior of the investigated diheteroaryl ketones and thioketones.     

Role of quantum chemical calculations in molecular biophysics with a historical perspective

We discuss how the basic principles of quantum chemistry and quantum mechanics can be and have been applied to a variety of problems in molecular biophysics. First, the historical development of quantum concepts in biophysics is discussed. Next, we describe a series of interesting applications of quantum chemical methods for studying biologically active molecules, molecular structures, and some of the important processes which play a role in living organisms. We discuss the application of quantum chemistry to such processes as energy storage and transformation, and the transmission of genetic information. Quantum chemical approaches are essential to comprehend and understand the molecular nature of these processes. To conclude our work, we present a short discussion of the perspectives of quantum chemical methods in modern biophysics, the field of experimental and theoretical chiral vibrational and electronic spectroscopy.     

Quantum chemical methods for the investigation of photoinitiated processes in biological systems: theory and applications.

With the advent of modern computers and advances in the development of efficient quantum chemical computer codes, the meaningful computation of large molecular systems at a quantum mechanical level became feasible. Recent experimental effort to understand photoinitiated processes in biological systems, for instance photosynthesis or vision, at a molecular level also triggered theoretical investigations in this field. In this Minireview, standard quantum chemical methods are presented that are applicable and recently used for the calculation of excited states of photoinitiated processes in biological molecular systems. These methods comprise configuration interaction singles, the complete active space self-consistent field method, and time-dependent density functional theory and its variants. Semiempirical approaches are also covered. Their basic theoretical concepts and mathematical equations are briefly outlined, and their properties and limitations are discussed. Recent successful applications of the methods to photoinitiated processes in biological systems are described and theoretical tools for the analysis of excited states are presented.     

有机二硫化物润滑添加剂抗磨极压性能的密度泛函理论研究

用量子化学的密度泛函理论计算了12种有机二硫化物和铁原子簇的分子轨道指数及其与铁原子簇的化学吸附作用能, 探讨了这种作用能与抗磨性能的关系; 运用轨道能量近似原则讨论了有机二硫化物与铁原子的作用方式; 以前线电子密度、超离域性指数和原子净电荷作为判据分析了12种有机二硫化物与铁原子间键合的强弱、反应性的大小等表征有机二硫化物与金属作用强弱的参数。结果表明: 有机二硫化物与铁接触时, 在较缓和条件下, SS键优先断裂与金属发生化学吸附形成配位键, 起到抗磨作用; 在高负荷下, 与金属发生常规条件下不能发生的化学反应, 即CS键断裂生成无机膜, 起到极压作用; 且随着碳链的增长, 有机二硫化物的抗磨性能愈来愈好, 但极压性能愈来愈差; 运用量子化学计算得到的预测结果与摩擦学试验结果具有良好的一致性, 可为同类极压添加剂化合物的分子设计提供较为可靠的参考依据和理论方法。     

Three-dimensional structural features and the toxicity of aminobenzenes and phenols

There are many organic pollutants in the environment, such as polychlorinated biphenyl, polycyclic aromatic hydrocarbons, dichlorodiphenyl-trichloroethane (DDT), and polychlorinated naphthalene. These organic pollutants are persistent,liposoluble and easily cumulated in organism; consequently, the potential toxicity will be high. Risk assessment of industrial chemicals is currently carried out using scanty experimental data, because many of these chemicals have very little or no test data. S…     

聚丙烯酸酯类Tg的量子化学-神经网络研究

用密度泛函方法在6-31G(d)基组上优化了38种聚丙烯酸酯类的结构单元, 得到了其单元的量子化学参数, 探讨了这些参数与聚丙烯酸酯类玻璃化温度(Tg)的关系. 计算表明, 影响聚丙烯酸酯类Tg的主要因素有结构单元的侧链长度、侧链的分支数、最高占据轨道能级、极化率、偶极矩、等体积热容和热力学能等参数. 用模式识别方法(偏最小二乘法)讨论了这些参数与Tg的定性关系, 两类Tg大小不同的聚合物基本分布在不同区域, 用逐步回归和人工神经网络方法建立了这些参数与Tg的定量关系, 2种方法的预测结果与实验值的相关系数分别为0.9753、0.9985, 标准偏差分别为18.42、4.25, 预报结果与实验值基本一致.     

Quantum chemical definition and calculation of oxidation number

A new quantum chemical definition of oxidation number is proposed, in the present paper, as a direct generalization of the corresponding classical definition. According to the proposed general definition, the oxidation number can be calculated by use of molecular orbital data and a population analysis method or by use of other quantum chemical methods. For the practical calculation, we present a corresponding concrete calculation procedure within the framework of the maximum overlap population principle, which is very simple and very easy to use. The calculated numerical results are, on the whole, in good agreement with chemists' intuitive concepts of chemical bonding.