On the non-existence of parallel universes in chemistry

This treatise presents thoughts on the divide that exists in chemistry between those who seek their understanding within a universe wherein the laws of physics apply and those who prefer alternative universes wherein the laws are suspended or ‘bent’ to suit preconceived ideas. The former approach is embodied in the quantum theory of atoms in molecules (QTAIM), a theory based upon the properties of a system’s observable distribution of charge. Science is experimental observation followed by appeal to theory that, upon occasion, leads to new experiments. This is the path that led to the development of the molecular structure hypothesis—that a molecule is a collection atoms with characteristic properties linked by a network of bonds that impart a structure—a concept forged in the crucible of nineteenth century experimental chemistry. One hundred and fifty years of experimental chemistry underlie the realization that the properties of some total system are the sum of its atomic contributions. The concept of a functional group, consisting of a single atom or a linked set of atoms, with characteristic additive properties forms the cornerstone of chemical thinking of both molecules and crystals and Dalton’s atomic hypothesis has emerged as the operational theory of chemistry. We recognize the presence of a functional group in a given system and predict its effect upon the static, reactive and spectroscopic properties of the system in terms of the characteristic properties assigned to that group. QTAM gives physical substance to the concept of a functional group.     

Toward universal substituent constants: Model chemistry sensitivity of descriptors from the quantum theory of atoms in molecules

The quantum theory of atoms in molecules (QTAIM) provides a theoretical foundation to determine the properties of functional groups through additive atomic contributions. Many studies have used QTAIM in their analyses with a variety of electronic structure methods, but it is unknown if the properties measured using one model chemistry, the combination of the electronic structure method and basis set, can be compared to those measured by another. Here, we evaluate the sensitivity of QTAIM functional group and bond critical point properties using six functionals and seven basis sets. High-level B2PLYPD3-BJ/aug-cc-pV5Z reference values are provided for 116 functional groups and the property sensitivity with respect to these values are evaluated based on absolute deviations and by assessing linear relationships. Functional group properties, including charges, dipoles, quadrupoles and volumes, were found to be mostly insensitive to choice of computational model chemistry. However, due to structural and topological inconsistencies, the 6-31G(d) basis set is not recommended for use. Bond critical point properties varied with choice of model chemistry, but models incorporating hybrid functionals and triple-ζ basis sets provided values suitable for use in regression studies.     

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.     

ER-BOC calculations of crystal bulk properties from smallest-cluster models

Ab initio calculation of bulk properties of crystals with a high accuracy, which is a long-time goal of solid chemistry and physics, is still difficult and expensive because a large cluster is required as a crystal structure model. This article proposes a model based on density functional theory (DFT) quantum chemistry calculations and the assumption that the bond order of a given atom with its nearest atoms in a compound is conserved over the entire range from its diatomic molecules to clusters and further to crystals. This entire range bond order conservation (ER-BOC) provides an effective way to correlate bulk properties of crystals with those of the corresponding molecules and small clusters. By combining this ER-BOC principle with hybrid DFT quantum chemistry calculations, accurate predictions of the bulk bond lengths of a crystal can be made using calculations on small clusters.     

How big are atoms in crystals?

Atoms and bonds are central concepts in structural chemistry, but neither are concepts that arise naturally from the physics of condensed phases. It is ironic that the internuclear distances in crystals that are readily measured depend on the sizes of atoms, but since atoms in crystals can be defined in many different ways, all of them arbitrary and often incompatible, there is no natural way to express atomic size. I propose a simple coherent picture of Atoms-in-Crystals which combines properties selected from three different physically sound definitions of atoms and bonds. The charge density of the free atom that is used to construct the procrystal is represented by a sphere of constant charge density having the quantum theory of atoms in molecules (QTAIM) bonded radius. The sum of these radii is equal to the bond length that correlates with the bond flux (bond valence) in the flux theory of the bond. The use of this model is illustrated by answering the question: How big are atoms in crystals? The QTAIM bonded radii are shown to be simple functions of two properties, the number of quantum shells in the atomic core and the flux of the bond that links neighbouring atoms. Various radii can be defined. The univalent bonded radius measures the intrinsic size of the atom and is the same for all cations in a given row of the periodic table, but the observed bonded radius depends also on the bond flux that reflects the chemical environment.     

The Quantum Mechanical Basis of Conceptual Chemistry

Summary. An experimentalist approaching theory for an understanding of conceptual chemistry that can be related to measurable properties, focuses on the electron density distribution. One finds in the topology of the electron density the definition of an atom, of the bonding between atoms, and of the boundary condition for the extension of quantum mechanics to an open system – to an atom in a molecule. This paper describes this approach, as it evolved from the failure of existing models to a study of molecular charge distributions and of how these studies resulted in the extension of quantum mechanics to an open system using the action principle.     

The Quantum Mechanical Basis of Conceptual Chemistry

An experimentalist approaching theory for an understanding of conceptual chemistry that can be related to measurable properties, focuses on the electron density distribution. One finds in the topology of the electron density the definition of an atom, of the bonding between atoms, and of the boundary condition for the extension of quantum mechanics to an open system – to an atom in a molecule. This paper describes this approach, as it evolved from the failure of existing models to a study of molecular charge distributions and of how these studies resulted in the extension of quantum mechanics to an open system using the action principle.     

Is there a quantum definition of a molecule?

The paper surveys how chemistry has developed over the past two centuries starting from Lavoisier’s classification of the chemical elements at the end of the eighteenth century; the subsequent development of the atomic–molecular model of matter preoccupied chemists throughout the nineteenth century, while the results of the application of quantum theory to the molecular model has been the story of this century. Whereas physical chemistry originated in the nineteenth century with the measurement of the physical properties of groups of chemical compounds that chemists identified as families, the goal of chemical physics is the explanation of the facts of chemistry in terms of the principles and theories of physics. Chemical physics as such was only possible after the discovery of the quantum theory in the 1920’s. By then the first of the sub‐atomic particles had been discovered and seemingly it is no longer possible to discuss chemical facts purely in terms of atoms and molecules – one has to recognize the electron and the nucleus, the parts of atoms. The combination of classical molecular structure with the quantum properties of the electron has given us a tremendously successful account of chemistry called ‘quantum chemistry’. Yet from the perspective of the quantum theory the deepest part of chemistry, the existence of chemical isomers and the very idea of molecular structure that rationalizes it, remains a central problem for chemical physics. This revised version was published online in July 2006 with corrections to the Cover Date.     

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.     

Nematic compounds and mixtures with high negative dielectric anisotropy

Syntheses, mesogenic and dielectric properties of three-ring alkylcyclohexyl, alkoxy and alkylphenyl benzoates substituted with four fluorine atoms or with two fluorine atoms and simultaneously a cyano group or two cyano groups are described. Their properties are compared with analogous three-ring phenyl tolanes. Conformation analysis and the calculation of dipole moments with the quantum chemistry method are performed to explain the experimental results. Several four fluorine-substituted two-ring tolanes and biphenyls are also prepared, which are used as a solvent decreasing viscosity, melting point and clearing point of the formulated mixtures. Examples of mixtures prepared from the esters and tolanes with high dielectric anisotropy are given. Curiosity is observed that 4?-(4-ethoxyphenyl)-4-pentyloxy-2,2?,3,3?-tetrafluorotolane is not the mesogenic compound, while analogous ester 4?-ethoxy-2,3-difluorobiphenyl-4-yl 2,3-difluoro-4-pentyloxybenzoate exhibits a broad temperature range of the nematic phase.     

Starburst® dendrimers: A conceptual approach to nanoscopic chemistry and architecture

The nanoscopic domain of structural complexity, which ranges from 1 to 100 run on a particle size scale includes a relatively unexplored area of science which resides between classical chemistry and molecular biology. This rapidly growing area of science is referred to as nanoscopic chemistry and architecture. Concepts evolving in this area lead to a rich variety of precise structures, architecture and properties. These concepts are based on dendritic macromolecules in general and on Starburst® dendrimers in particular. They envision dendrimers as fundamental building blocks which may be used to synthesize nanoscopic compounds, clusters, polymers, etc. Accordingly, dendrimers are regarded architecturally as functional analogues of atoms; therefore, their potential role in nanoscopic chemistry may be compared to that of the atoms in classical chemistry.     

Specific quantum mechanical/molecular mechanical capping-potentials for biomolecular functional groups

We present a series of capping-potentials designed as link atoms to saturate dangling bonds at the quantum/classical interface within density functional theory-based hybrid QM/MM calculations. We aim at imitating the properties of different carbon-carbon bonds by means of monovalent analytic pseudopotentials. These effective potentials are optimized such that the perturbations of the quantum electronic density are minimized. This optimization is based on a stochastic scheme, which helps to avoid local minima trapping. For a series of common biomolecular groups, we find capping-potentials that outperform the more common hydrogen-capping in view of structural and spectroscopic properties. To demonstrate the transferability to complex systems, we also benchmark our potentials with a hydrogen-bonded dimer, yielding systematic improvements in structural and spectroscopic parameters.     

Molecular model with quantum mechanical bonding information

The molecular structure can be defined quantum mechanically thanks to the theory of atoms in molecules. Here, we report a new molecular model that reflects quantum mechanical properties of the chemical bonds. This graphical representation of molecules is based on the topology of the electron density at the critical points. The eigenvalues of the Hessian are used for depicting the critical points three-dimensionally. The bond path linking two atoms has a thickness that is proportional to the electron density at the bond critical point. The nuclei are represented according to the experimentally determined atomic radii. The resulting molecular structures are similar to the traditional ball and stick ones, with the difference that in this model each object included in the plot provides topological information about the atoms and bonding interactions. As a result, the character and intensity of any given interatomic interaction can be identified by visual inspection, including the noncovalent ones. Because similar bonding interactions have similar plots, this tool permits the visualization of chemical bond transferability, revealing the presence of functional groups in large molecules.     

最小二乘支持向量机方法用于提高低水平量子化学方法计算吸收能的精度

运用B3LYP/STO-3G和ZINDO两种低水平的量子化学方法计算了160个有机分子的UV-Vis吸收光谱, 然后提取合适的物理参数, 并以实验值为基础, 引入最小二乘支持向量机方法以提高吸收能的计算值精度. 结果表明, 最小二乘支持向量机方法可有效提高量子化学计算精度, 体系的吸收能误差均方根分别从0.95和0.46 eV降低到0.16和0.15 eV. 最小二乘支持向量机校正方法的引入可在较少的机时和计算资源下得到比单一的量子化学计算方法更为稳定和精确的计算结果, 且可在现有计算条件下预测现有计算能力达不到的精度. 因此, 将最小二乘支持向量机方法用于量子化学数据分析, 为化学研究准确、 快捷地预测分子性质提供了一种新的研究手段.     

Bonding of the chain structure for novel boranes B_(3k+)H_(5k+p+3)~-

The molecular orbitals obtained from conventional quantum chemistry calculations, are expressed in terms of symmetrized valence bond functions of fragment, and a direct picture of chemical bonding can be drawn easily. This method is utilized, together with extended Huckel calculations, to interpret the bonding properties of a centipede-like chain structure for novel laser-producing boranes B3k+pH5k+p+3- which is constructed from the repeated unit B3H5 linked to each other by three B-H-B bonds.     

多齿配体三(2-苯并咪唑亚甲基)胺(C_6H_4NNHCCH_2)_3N·H_2O的合成、晶体结构及PM3量子化学计算

报道了含一个结晶水的多齿配体三（２－苯并咪唑亚甲基）胺（ＮＴＢ·Ｈ２Ｏ）的合成、红外光谱及晶体结构和理论化学计算。该化合物（Ｃ２４Ｈ２３Ｎ７Ｏ）属单斜晶系,空间群Ｐ２１／ｎ,ａ＝９．９６１（２）,ｂ＝１２．３１８（２）,ｃ＝１８．１９１（３）,β＝９１．３７（１）°,Ｖ＝２２３２（１）,Ｚ＝４,Ｆ（０００）＝８９６,Ｄｘ＝１．２６６ｇ／ｃｍ３,Ｍｒ＝４２５．５,μ（ＭｏＫα）＝０．７７ｃｍ－１。用ＣＡＤ４四圆衍射仪,ＭｏＫα射线收集数据,结构由直接法解出,全矩阵最小二乘修正,最终偏离因子Ｒ＝０．０５４,Ｒｗ＝０．０６３。量子化学计算结果也证明了ＮＴＢ具有由三个扇叶构成的螺旋桨式构型,一些氮原子上有负电荷,有利于金属离子进行配位     

含氮杂环并苯类高聚物结构与能带规律的从头算和半经验量子化学研究

采用从头算ＨＦ和半经验量子化学方法,对含氮杂环并苯类高聚物体系进行几何结构优化．比较不同方法下它们的电子性质的差异,揭示聚并苯、聚并吡啶、聚并吡嗪的能带分布特征和规律．为深入研究导电、发光等功能材料及能带匹配器件的分子设计提供依据．     

The role of the organic layer functionalization in the formation of silicon/organic layer/metal junctions with coinage metals

The design of silicon/alkyl layer/metal junctions for the formation of optimal top metal contacts requires knowledge of the mechanistic and energetic aspects of the interactions of metal atoms with the modified surface. This involves (a) the interaction of the metal with the terminal groups of the organic layer, (b) the diffusion of metal atoms through the organic layer and (c) the reactions of metal atoms with the silicon surface atoms. The diffusion through the monolayer and the metal catalyzed breakage of Si-C bonds must be avoided to obtain high quality junctions. In this work, we performed a comprehensive density functional theory investigation to identify the reaction pathways of all these processes. In the absence of a reactive terminal group, gold atoms may penetrate through a compact alkyl monolayer on Si(111) with no energy barrier. However, the presence of thiol terminal groups introduces a high energy barrier which blocks the diffusion of metals into the monolayer. The diffusion barriers increase in the order Ag < Au < Cu and correlate with the stability of metal-thiolate complexes whereas the barriers for the formation of metal silicides increase in the order Cu < Au < Ag in correlation with the increasing metallic radii. The reactivity of gold clusters with functionalized Si(111) surfaces was also investigated. Metal silicide formation can only be avoided by a compact monolayer terminated by a reactive functional group. The mechanistic and energetic picture obtained in this work contributes to understanding of the factors that influence the quality of top metal contacts during the formation of silicon/organic layer/metal junctions.