Theoretical Definition of a Functional Group and the Molecular Orbital Paradigm

It is the purpose of this review to demonstrate that the empirical classification of the observations of chemistry in terms of the properties assigned to functional groups is a consequence of and is predicted by physics. This is accomplished by showing that the atoms and functional groups of chemistry can be identified with bounded space-filling objects whose properties are defined by quantum mechanics. The quantum mechanical definition of a group is combined with a new pictorial representation of its form to obtain a unified picture which should make it eminently recognizable to chemists. This picture, when combined with the demonstrated ability of these groups to recover the measured properties of atoms in molecules, is offered as one which meets the expectations a chemist associates with the concept of a functional group. The manner in which this physical definition of a group differs fundamentally from models of functional groups based upon molecular orbital theory is discussed.     

Molecular modeling of intercalation complexes of antitumor active 9-aminoacridine and a [d,e]-anellated isoquinoline derivative with base paired deoxytetranucleotides

Summary Intercalators are molecules capable of sliding between DNA base pairs without breaking up the hydrogen bonds between the DNA bases. On the basis of molecular mechanics calculations structural, models of B-DNA tetranucleotide intercalation complexes of some cytostatic active 9-aminoacridines and of a [d, e]-anellated isoquinoline derivative are presented. The drug complexes are stabilized by energetically favouredvan der Waals interactions and by selective hydrogen bonds between the side chains of the drugs and the DNA bases. Semiempirical quantum chemistry calculations revealed that the chromophoric system of the intercalators is able to form ,-charge-transfer interactions with the purine bases of the base paired deoxytetranucleotides. The theoretical findings are of interest for a more specific drug design of cytostatically active agents.

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Molecular Modeling von Interkalationskomplexen antitumoraktiver 9-Aminoacridine sowie eines [d, e]-anellierten Isochinolinderivates mit basengepaarten Desoxytetranukleotiden

Zusammenfassung Interkalatoren sind Moleküle, die in der Lage sind, sich zwischen DNA-Basenpaare einzulagern, ohne die Wasserstoffbrücken zwischen den DNA-Basen aufzubrechen. Auf der Basis von molekülmechanischen Rechnungen werden Tetranukleotid-Interkalationskomplexe von verschiedenen zytostatisch aktiven 9-Aminoacridinen und von einem [d, e]-anellierten Isochinolinderivat präsentiert. Die Komplexe werden durch energetisch günstigevan der Waals-Interaktionen sowie durch selektive Wasserstoffbrückenbindungen zwischen den Seitenketten der Wirkstoffe und den DNA-Basen stabilisiert. Semiempirische quantenchemische Rechnungen ergaben, daß der Chromophor der Interkalatoren in der Lage ist, ,-charge-transfer Wechselwirkungen mit den Purinbasen der basengepaarten Desoxytetranukleotide auszubilden. Die theoretischen Ergebnisse sind für ein spezifischeres Wirkstoffdesign zytostatisch aktiver Verbindungen von Interesse.

     

Models for the binding of amiodarone to the thyroid hormone receptor

Summary The antiarrhythmic drug amiodarone has recently been characterized as the first known thyroid hormone antagonist. Its mode of interaction with the thyroid hormone receptor is therefore of interest. A computational analysis of the conformational flexibility of amiodarone using molecular mechanics and the semiempirical molecular orbital method AM1 has been performed. The molecular mechanics studies show that the low-energy conformations of the benzoylbenzofuran portion of amiodarone can be grouped into 4 distinct classes, while the diethylaminoethoxy side chain is extremely flexible. Conformers representative of the 4 low-energy classes were fitted to an extended thyroid hormone receptor model. Four independent modes in which amiodarone could bind to the thyroid hormone receptor site were evaluated.     

简单Hückel分子轨道理论判断H4分子及离子的几何构型

简单Hückel分子轨道理论是结构化学课程内容的主要知识点之一,主要用于计算π电子成平面分布的离域体系的电子结构和轨道能量。本文把该理论推广到H_4非离域体系,定性地计算H_4非离域体系的轨道能量,帮助学生理解Walsh规则应用举例中难以理解的H_4构型为直线型,但H_4~+为四面体构型的原因。     

The Fock Matrix Analysis for Atomic Orbitals in Molecular Orbitals II. The Electronic Structure of N2 Molecules

Weinhold's natural hybrid orbitals can be chosen as the molecular adapted atomic orbitals to build the canonical molecular orbitals of N₂ molecules. The molecular Fock matrix expanded in the natural hybrid orbitals can reveal deeper insight of the electronic structure and reaction of the N₂ molecule. For example, the magnitude of F_ab can signify the bonding character of the paired electrons as well as the diradical character of the unpaired electrons for both σ‐ and π‐types. Discarding the concept of the overlap between non‐orthogonal atomic orbitals, the different orbitals for different spins in the unrestricted Hartree‐Fock wavefunction reveal that there are three pairs of opposite spin density flows between two atoms, which proceed until the bonding molecular orbitals form.     

Predictive Molecular Orbital Calculations in Organic Chemistry

The utility and importance of predictive, rather than correlative, molecular orbital calculations in organic chemistry are discussed. Examples of the predictive approach to organic synthesis and the study of organic reaction mechanisms are presented.     

Molecular Structures from Density Functional Calculations with Simulated Annealing

The geometrical structure of any aggregate of atoms is one of its basic properties and, in principle, straightforward to predict. One chooses a structure, determines the total energy E of the system of electrons and ions, and repeats the calculation for all possible geometries. The ground state structure is that with the lowest energy. A quantum mechanical calculation of the exact wave function Ψ would lead to the total energy, but this is practicable only in very small molecules. Furthermore, the number of local minima in the energy surface increases dramatically with increasing molecular size. While traditional ab initio methods have had many impressive successes, these difficulties have meant that they have focused on systems with relatively few local minima, or have used experiment or experience to limit the range of geometries studied. On the other hand, calculations for much larger molecules and extended systems are often forced to use simplifying assumptions about the interatomic forces that limit their predictive capability. The approach described here avoids both of these extremes: Total energies of predictive value are calculated without using semi-empirical force laws, and the problem of multiple minima in the energy surface is addressed. The density functional formalism, with a local density approximation for the exchange-correlation energy, allows one to calculate the total energy for a given geometry in an efficient, if approximate, manner. Calculations for heavier elements are not significantly more difficult than for those in the first row and provide an ideal way to study bonding trends. When coupled with finite-temperature molecular dynamics, this formalism can avoid many of the energetically unfavorable minima in the energy surface. We show here that the method leads to surprising and exciting results.     

Molecular Mechanics Calculations in Organic Chemistry: Examples of the Usefulness of this Simple Non-Quantum Mechanical Model

Various problems arising in experimental organic chemistry can be clarified by molecular mechanics or force field calculations: molecular dynamics (conformational analysis and internal rotation), the search for the most stable isomer of various polycyclic hydrocarbons, reactivity calculations, including solvolysis of bridgehead substituted systems. Such calculations are shown to be useful in elucidating the mechanism of multistep carbonium ion rearrangement, for predicting the structure and stability of anti-Bredt olefins, and also offer an explanation for the selectivity observed in the hydrogenolysis of strained polycyclic smallring hydrocarbons, for the identification of long bonds and electronic effects, for the analysis of late transition states, and for the product distribution in complex reactions.     

Localized Orbitals vs. Pseudopotential-Plane Waves Basis Sets: Performances and Accuracy for Molecular Magnetic Systems

 Density functional theory, in combination with a) a careful choice of the exchange-correlation part of the total energy and b) localized basis sets for the electronic orbitals, has become the method of choice for calculating the exchange-couplings in magnetic molecular complexes. Orbital expansion on plane waves can be seen as an alternative basis set especially suited to allow optimization of newly synthesized materials of unknown geometries. However, little is known on the predictive power of this scheme to yield quantitative values for exchange coupling constants J as small as a few hundredths of eV (50–300 cm⁻¹). We have used density functional theory and a plane waves basis set to calculate the exchange couplings J of three homodinuclear Cu-based molecular complexes with experimental values ranging from +40 cm⁻¹ to −300 cm⁻¹. The plane waves basis set proves as accurate as the localized basis set, thereby suggesting that this approach can be reliably employed to predict and rationalize the magnetic properties of molecular-based materials. Corresponding author. E-mail: Carlo.Massobrio@ipcms.u-strasbg.fr Received August 5, 2002; accepted August 9, 2002     

The Special Nodal Structure of the Rydberg Orbitals

A new scheme to account for the special nodal structure of the orbitals for Rydberg states is proposed. The scheme shows that in order to compute higher Rydberg states a new formula for choosing Gaussian exponentials is needed.     

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。     

Fundamentals of Silicon Chemistry: Molecular States of Silicon-Containing Compounds

Silicon and its compounds have made possible the design of new materials, which, from computers to space travel, have helped to shape the technology of our 20th century. Conversely, the demands of new technology have stimulated the fast development of silicon chemistry as part of the “renaissance” of inorganic chemistry. This article uses selected examples of predominantly organosilicon compounds to discuss in simplified terms the measurement and assignment of suitable spectroscopic “molecular fingerprints” as well as the resulting benefit for the preparative chemist. The comparison of “equivalent” states of “chemically related” molecules is emphasized, based on perturbation arguments and supporting quantum-chemical models. Special attention is given to the relation between structure and energy, which allows us to understand and to predict the connectivity between and the spatial arrangement of silicon “building blocks”, the energy-dependent electron distribution over the effective nuclear potentials of a molecular framework, and, especially, the partly considerable effects of “silicon substituents” on molecular properties. Future-directed extensions and applications include polysilane band structures, Rydberg states of chromophores containing silicon centers, redox reactions and ion-pair formation of silicon-substituted π systems, and molecular dynamic phenomena in solution or on thermal fragmentation in the gas phase. The main objective is a set of clear and practical rules for interpreting measurements and planning experiments.     

The Valence Orbitals of the Alkaline-Earth Atoms

Quantum chemical calculations of the alkaline-earth oxides, imides and dihydrides of the alkaline-earth atoms (Ae=Be, Mg, Ca, Sr, Ba) and the calcium cluster Ca₆H₉[N(SiMe₃)₂]₃(pmdta)₃ (pmdta=N,N,N′,N′′,N′′-pentamethyldiethylenetriamine) have been carried out by using density functional theory. Analysis of the electronic structures by charge and energy partitioning methods suggests that the valence orbitals of the lighter atoms Be and Mg are the (n)s and (n)p orbitals. In contrast, the valence orbitals of the heavier atoms Ca, Sr and Ba comprise the (n)s and (n−1)d orbitals. The alkaline-earth metals Be and Mg build covalent bonds like typical main-group elements, whereas Ca, Sr and Ba covalently bind like transition metals. The results not only shed new light on the covalent bonds of the heavier alkaline-earth metals, but are also very important for understanding and designing experimental studies.     

The Fock Matrix Analysis for Atomic Orbitals in Molecular Orbitals I. A New Look on the Covalent Bond in H2?

The character of the molecular orbitals can be better accounted for in terms of molecular adapted atomic orbitals and the Fock matrix expanded in these atomic orbital sets. A clean‐cut and unique criterion for the diradicals and the covalent bonds can be given for the molecular orbitals in both restricted and unrestricted Hartree‐Fock wavefunctions. Instead of the picture that overlap charge migrates into the bonding region, the new analysis displays another picture that the charge densities for the electrons with α and β spins give rise to two opposite spin density shifts. If the α one shifts from atom A toward atom B then it is vice versa for the β one. The spin density shifts proceed until the bonding molecular orbitals form.     

Structure and Bonding in Cyclic Sulfur-Nitrogen Compounds—Molecular Orbital Considerations

The molecular structures of monocyclic sulfur-nitrogen ring systems, such as S₂N₂, S₃N, S₄N and S₅N, can be considered as examples of electron rich (4n + 2)π systems. The structures of S₄N₄, S₄N, P₄S₄, As₄S₄ and the bicyclic structures S₄N, S₄N as well as S₅N₆ can be rationalized on the basis of a planar tetrasulfur tetranitride with 12π electrons.     

Fuzzy Symmetries for Linear Molecules and their Molecular Orbitals

In this paper, the fuzzy symmetry of some prototypical linear molecules has been analyzed. The results show that some molecular orbitals (MOs) are less symmetrical but some others are more symmetrical than the molecular skeleton, which the MOs correspond to. The membership functions of space inversion for MOs are closely related to the chemical characteristics of the MOs. Sometimes, although the symmetry of a molecular skeleton is not obvious, however that of some MO is quite obvious. The membership functions of the fuzzy inversion symmetry depend on the choice of the position of the center of inversion. As compared to those of diatomic molecules and linear tri-atomic molecules, the linear polyatomic molecules in which a distinctive fuzzy symmetry of space translation may exist, and thus a significant effect on their properties can be expected.     

超价分子中的d轨道

通过对一些典型超价分子进行计算和分析,得出了超价分子"d轨道参与"(即外层d轨道杂化和d-pπ键概念)不尽合理的结论,并提出了能与实验事实相符的解释方法。此外,本文还阐述了计算化学中基组d函数与d轨道的关系:二者并不等价。     

Theory and range of modern semiempirical molecular orbital methods

Semiempirical molecular orbital methods have a long history. They serve to tackle large systems and complicated processes beyond the reach of ab initio or density functional methods. Although their setup is derived from Hartree–Fock theory, the design of approximate energy expressions and the empirical parameters are used to achieve higher accuracy than the underlying ab initio theory. In this way the effect of larger basis sets or correlation can be partially simulated. All widely used semiempirical methods establish their accuracy by error statistics for molecular properties with experimental and high-level ab initio or density functional theory calculations as a reference. Their computational efficiency makes them suitable for the study of biochemical systems and solid materials. The present review presents a variety of applications which demonstrate the need for and success of semiempirical methods.