Atoms and bonds in molecules and chemical explanations

The concepts of atoms and bonds in molecules which appeared in chemistry during the nineteenth century are unavoidable to explain the structure and the reactivity of the matter at a chemical level of understanding. Although they can be criticized from a strict reductionist point of view, because neither atoms nor bonds are observable in the sense of quantum mechanics, the topological and statistical interpretative approaches of quantum chemistry (quantum theory of atoms in molecules, electron localization function and maximum probability domain) provide consistent definitions which accommodate chemistry and quantum mechanics.     

Photophysical processes and the photodissociation of chemical bonds in polyatomic molecules

The main concepts of the nature of electronically excited states in polyatomic molecules and the intramolecular and intermolecular processes of their evolution are reported. The dependence of the probabilities of these processes on the electronic structure of the molecule is considered. Possible mechanisms of the dissociation of electronically excited molecules with bond cleavage are discussed, and the theoretical results of this consideration are given. The experimental data obtained by the authors are interpreted. In this case, attention is focused on C-H-bond photodissociation processes in a condensed phase, which are the best studied processes. The dissociation of other bonds is briefly discussed.     

烷基锂分子中化学键的 ab initio 研究

本文用6-13G基函对3-12G基优化构型进行单点ab initio (从头计算法) 计算, 并根据轨道的组合系数、电荷密度图和键强参数等详尽地分析了烷基锂分子的成键情况。烷基锂的易挥发、易聚合、聚合物易溶于烃类溶剂中等物理、化学性质主要是其C－Li键具有显著的共价性缘故。由于烷基锂的C-Li键比C－H和C－C键的强度要小,故C-Li键易于断裂,使烷基锂表现有高的化学反应活性。     

Charge fluctuations and correlation strength in chemical bonds: First-row homonuclear diatomic molecules

We investigate, by means of ab initio calculations, the strength of electron correlations within covalent bonds: the first-row homonuclear diatomics serve as test cases. As an appropriate measure of the correlation strength, we introduce the reduction of the mean-square deviations of the electronic charges in localized orbitals forming a bond. A recently developed population analysis in terms of local operators derived from localized molecular orbitals is thereby used. The correlation-strength parameter depends only weakly on dynamical correlations as test calculations demonstrate. Therefore, the full-valence complete active space self-consistent field (CASSCF) approximation is applied in order to study the changes in the correlation strength with changing bond length for different types of bonds. A number of simple rules emerge from this discussion. In addition, we show that charge fluctuations are not only a reliable measure of intrabond correlation effects, but also can be used to monitor intraatomic quasi-degeneracy effects as well as the interdependence within multiple bonds. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 67: 157–173, 1998     

Empirical model of orbital relaxation and interatomic distances in molecules with polar chemical bonds

Orbital relaxation is treated as one of the reasons for shortening of chemical bonds with respect to the sum of the covalent radii of interacting atoms. The C-O, Si-O, Si-C, Si-H, Si-F, and Si-Cl bond lengths in organic and inorganic silicon compounds and of E-H and E-F bonds in diatomic hydrides and absolute-valent fluorides (E is a second-period element) are considered in terms of a simple empirical model of orbital relaxation. In all cases under study, orbital relaxation is an important factor affecting the length of the chemical bond. Translated fromZhumal Struktumoi Khimii, Vol. 38, No. 3, pp. 438–446, May–June, 1997.     

Covalent palladium-zinc bonds and their reactivity

Photolysis of ((F)PNP)Pd-Et in the presence of Et(2)Zn leads to the formation of ((F)PNP)Pd-Zn-Pd(PNP(F)), the first example of a compound with a covalent Pd-Zn bond.     

Electron pairing and chemical bonds: Bonding in hypervalent molecules from analysis of Fermi holes

Bonding in the hypervalent molecules SF₄, BrF₅, PF₅, and SF₆ was studied using multicenter bond order indices and examination of the eigenvalues and the eigenvectors of the Fermi holes of the constituent atoms. Diagonalization of the Fermi holes provided quantitative validation of Musher's categorization of hypervalency with SF₄ and BrF₅ representative of type I, and PF₅ and SF₆ belonging to type II. The eigenvalues and eigenvectors of type I molecules distinguished between classic two-center two-electron bonds and three-center four-electron bonds, whereas the results of diagonalization for type II molecules demonstrated the presence of substantial reorganization of the valence state of the central atom leading to equivalent bonds and the highest expected symmetry of the molecule. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 760–771, 1999     

Non-identical electronic characters of the internucleotidic phosphates in RNA modulate the chemical reactivity of the phosphodiester bonds

We here show that the electronic properties and the chemical reactivities of the internucleotidic phosphates in the heptameric ssRNAs are dissimilar in a sequence-specific manner because of their non-identical microenvironments, in contrast with the corresponding isosequential ssDNAs. This has been evidenced by monitoring the delta H8(G) shifts upon pH-dependent ionization (pK(a1)) of the central 9-guaninyl (G) to the 9-guanylate ion (G-), and its electrostatic effect on each of the internucleotidic phosphate anions, as measured from the resultant delta 31P shifts (pKa2) in the isosequential heptameric ssRNAs vis-à-vis ssDNAs: [d/r(5'-Cp1Ap2Q1p3Gp4Q2p5Ap6C-3'): Q1 = Q2 = A (5a/5b) or C (8a/8b), Q(1) = A, Q(2) = C (6a/6b), Q1 = C, Q2 = A (7a/7b)]. These oligos with single ionizable G in the centre are chosen because of the fact that the pseudoaromatic character of G can be easily modulated in a pH-dependent manner by its transformation to G- (the 2'-OH to 2-O- ionization effect is not detectable below pH 11.6 as evident from the N(1-Me)-G analog), thereby modulating/titrating the nature of the electrostatic interactions of G to G- with the phosphates, which therefore constitute simple models to interrogate how the variable pseudoaromatic characters of nucleobases under different sequence context (J. Am. Chem. Soc., 2004, 126, 8674-8681) can actually influence the reactivity of the internucleotide phosphates as a result of modulation of sequence context-specific electrostatic interactions. In order to better understand the impact of the electrostatic effect of the G to G- on the tunability of the electronic character of internucleotidic phosphates in the heptameric ssRNAs 5b, 6b, 7b and 8b, we have also performed their alkaline hydrolysis at pH 12.5 at 20 degrees C, and have identified the preferences of the cleavage sites at various phosphates, which are p2, p3 and p4 (Fig.3). The results of these alkaline hydrolysis studies have been compared with the hydrolysis of analogous N(1-Me)-G heptameric ssRNA sequences 5c, 7c and 8c under identical conditions in order to establish the role of the electrostatic effect of the 9-guanylate ion (and the 2'-OH to 2-O- ionization) on the internucleotidic phosphate. It turned out that the relative alkaline hydrolysis rate at those particular phosphates (p2, p3 and p4) in the N(1-Me)-G heptamers was reduced from 16-78% compared to those in the native counterparts [Fig. 4, and ESI 2 (Fig. S11)]. Thus, these physico-chemical studies have shown that those p2, p3 and p4 phosphates in the native heptameric RNAs, which show pKa2 as well as more deshielding (owing to weaker 31P screening) in the alkaline pH compared to those at the neutral pH, are more prone to the alkaline hydrolysis because of their relatively enhanced electrophilic character resulting from weaker 31P screening. This screening effect originates as a result of the systematic charge repulsion effect between the electron cloud in the outermost orbitals of phosphorus and the central guanylate ion, leading to delocalization of the phosphorus p(pi) charge into its dpi orbitals. It is thus likely that, just as in the non-enzymatic hydrolysis, the enzymatic hydrolysis of a specific phosphate in RNA by general base-catalysis in RNA-cleaving proteins (RNase A, RNA phosphodiesterase or nuclease) can potentially be electrostatically influenced by tuning the transient charge on the nucleobase in the steric proximity or as a result of specific sequence context owing to nearest-neighbor interactions.     

Synthesis and reactivity of germanium heterocycles containing germanium-tin bonds

Previously unknown stannyl-substituted germanium heterocycles, 1, 1 -bis(trimethylstannyl) 2,3,4,5-tetraphenyl-l-germacyclopenta-2,4-dienc and 1,1-bis(trimethylstannyl)-3,4-dimethyl-1-germacyclopent-3-ene were synthesized, and their photolysis and chemical transformations were Studied.Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 11, pp 2764–2767, November, 1996.     

Diamagnetism and chemical bonds in semiconductors

The formulation of the Langevin and the van Vleck components in terms of a Kirkwood—Vinti-like expression and bond/band parameters respectively enables us to obtain accurate values for the lattice magnetic susceptibility of intrinsic diamond-like semiconductors and to understand coherently the nature of its variation from compound to compound in terms of structural modifications of the electron-density distribution between the interacting atoms.     

DNA-templated organic synthesis: nature's strategy for controlling chemical reactivity applied to synthetic molecules

In contrast to the approach commonly taken by chemists, nature controls chemical reactivity by modulating the effective molarity of highly dilute reactants through macromolecule-templated synthesis. Nature's approach enables complex mixtures in a single solution to react with efficiencies and selectivities that cannot be achieved in conventional laboratory synthesis. DNA-templated organic synthesis (DTS) is emerging as a surprisingly general way to control the reactivity of synthetic molecules by using nature's effective-molarity-based approach. Recent developments have expanded the scope and capabilities of DTS from its origins as a model of prebiotic nucleic acid replication to its current ability to translate DNA sequences into complex small-molecule and polymer products of multistep organic synthesis. An understanding of fundamental principles underlying DTS has played an important role in these developments. Early applications of DTS include nucleic acid sensing, small-molecule discovery, and reaction discovery with the help of translation, selection, and amplification methods previously available only to biological molecules.     

Atoms and bonds in molecules from radial densities

Radial densities are explored as an alternative method for partitioning the molecular density into atomic regions and bonding regions. The radial densities for atoms in molecules are similar to those of an isolated atom. The method may also provide an alternative to Bragg-Slater radii.     

Hydrophobic interactions and chemical reactivity

This perspective describes how kinetic studies of organic reactions can be used to increase our understanding of hydrophobic interactions. In turn, our understanding of hydrophobic interactions can be used as a tool to influence chemical reactions.     

Synthesis of epoxyquinol A and related molecules: probing chemical reactivity of epoxyquinol dimers and 2H-pyran precursors

Total syntheses of the epoxyquinoid dimers, epoxyquinols A, B, and epoxytwinol A (RKB-3564 D), have been accomplished employing [4 + 2] and [4 + 4] dimerization of 2H-pyran epoxyquinol monomers. Modifications of 2H-pyran precursors have been explored, including alteration of epoxy alcohol and diene stereochemistry. A stable 2H-pyran prepared by alteration of the epoxyquinol 2H-pyran nucleus was evaluated as a diene in Diels-Alder cycloaddition with reactive dienophiles. Extensive studies for improving the [4 + 4] dimerization of selectively protected 2H-pyran monomers to afford the novel epoxyquinoid dimer epoxytwinol A were carried out, and valuable insight regarding competitive [4 + 2] and [4 + 4] dimerization processes has been obtained. In addition, chemical reactivities and structural modifications of epoxyquinol dimers have been evaluated, including [2 + 2] photocycloaddition and [3,3] sigmatropic rearrangement, indicating the possibility for production of novel structural diversity from dimeric epoxyquinoid natural product frameworks.     

Synthesis and chemical reactivity of indenoisoxazoles

Treatment of 2-pivaloyl-1,3-indandione ( 1 ) with hydroxylamine under acidic conditions, results in formation of 8-t-butylindeno[1,2-c]isoxazol-7-one ( 2 ) while treatment of the triketone with hydroxylamine at neutral or basic pH gave 6 which upon cyclization gave the isomeric 3-t-butylindeno[1,2-c]isoxazol-4-one ( 7 ). Compound 7 was readily reduced to amine 12 by treatment with hydrazine or hydrogen over platinum. The amine, although quite unreactive, was converted to 3-t-butylindeno[1,2-c]pyrazol-4-one ( 13 ) with hydrazine or reduced to 15 and 16 with sodium in liquid ammonia and alcohol. Surprisingly, the amine 3 obtained from isoxazole 2 gave reduction product 15 from a sodium-liquid ammonia reduction and not the expected product 18. Spectral evidence for each of the structures is discussed.     

Quantum chemical study of the substituent effect on pKa of molecules with conjugated bonds using the PPP method

It is shown that the change of pK_a of unsubstituted heterocyclic compounds on substitution is proportional to the difference of the residual -electron charges at the position where the functional group is introduced in the unsubstituted heterobase and its conjugated acid.Translated from Teoreticheskaya i éksperimental'naya Khimiya, Vol. 24, No. 1, pp. 13–20, January–February, 1988.The author expresses his gratitude to M. M. Mestechkin and N. G. Korzhenevskaya for the discussion.     

Electronic structure of long molecules with conjugated bonds

The -electron system in a long molecule of the polyene type was calculated according to the Hartree-Fock self-consistent field method in which electrons with different spins are located on different molecular orbitals. The ground state of the -electron system in a long molecule is found to be antiferromagnetic and possesses a gap in the one-particle excitation spectrum. The calculated value of the first -electron transition as a function of the number of atoms in the polyene chain is in good agreement with experiment.