Biomedical subjects

Philippe C Hiberty

Publications and source records attributed to Philippe C Hiberty.

12 recordsLinked to original sources

PubMed2007

A survey of recent developments in ab initio valence bond theory.

Starting from the 1980s and onwards, Valence Bond theory has been enjoying renaissance that is characterized by the development of a growing number of ab initio methods, and by many applications to chemical reactivity and to the central paradigms of chemistry. Owing the increase of computational power of modern computers and to significant advances in the methodology, valence bond theory begins to offer a sound and attractive alternative to Molecular Orbital theory. This review aims at summarizing the most important developments of ab initio valence bond methods during the last two or three decades, and is primarily devoted to a description of what the various methods can actually achieve within their specific scopes and limitations. Key available softwares are surveyed.

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PubMed2007

A valence bond study of the dioxygen molecule.

The dioxygen molecule has been the subject of valence bond (VB) studies since 1930s, as it was considered as the first "failure" of VB theory. The object of this article is to provide an unambiguous VB interpretation for the nature of chemical bonding of the molecule by means of modern VB computational methods, VBSCF, BOVB, and VBCI. It is shown that though the VBSCF method can not provide quantitative accuracy for the strongly electronegative and electron-delocalized molecule because of the lack of dynamic correlation, it still gives a correct qualitative analysis for wave function of the molecule and provides intuitive insights into chemical bonding. An accurate quantitative description for the molecule requires higher levels of VB methods that incorporate dynamic correlation. The potential energy curves of the molecule are computed at the various VB levels. It is shown that there exists a small hump in the PECs of VBSCF for the ground state, as found in previous studies. However, higher levels of VB methods dissolve the hump. The BOVB and VBCI methods reproduce the dissociation energies and other physical properties of the ground state and the two lowest excited states in very good agreement with experiment and with sophisticated MO based methods, such as the MRCI method.

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PubMed2007

Classical and distonic radical cations: a valence bond approach.

The conventional radical cations arising from the ionization of CH(3)CH(2)X (X=F, OH, NH(2), Cl, SH, PH(2)), and their distonic isomers, CH(2)CH(2)XH(.+), were studied by means of standard Møller-Plesset and G2 methods, and by an ab initio valence bond method. Among the conventional structures, two distinct states are considered. In the so-called c' states, the unpaired electron is in an orbital that lies in the plane of the heavy atoms, while the c'' states have their unpaired electron in an orbital lying out of the plane. It is shown that c' states are, as a rule, more stable than the c'' states, by up to approximately 20 kJ mol(-1) depending on the nature of X, owing to a stabilizing interplay of resonating structures. While the geometries of the c'' states are rather similar to those of the neutral molecules, some of the c' states display very different geometries, characterized by elongated C--C bonds, particularly when X=F or, to a lesser extent, when X=OH or Cl. These peculiar geometric features are rationalized by the valence bond analysis, which reveals that the C--C bond in these species is better viewed as a two-center, one-electron bond. The distonic radical cations are generally more stable than the conventional ones (by 20-100 kJ mol(-1)), except for the less electronegative X groups of the series, namely X=SH and PH(2). In these two cases, together with X=NH(2), the radical cation displays a classical distonic structure, as regards the geometry and electronic state. On the other hand, considerable C--X elongation is found for X=F or Cl. In these last cases, the valence bond analysis shows that the radical cation is better viewed as an ion-molecule complex between an ionized ethylene and a neutral HX molecule. The electronic structure of the distonic radical cation with X=OH lies between the two previous limiting descriptions.

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PubMed2006

Identity SN2 reactions X- + CH3X --> XCH3 + X- (X=F, Cl, Br, and I) in vacuum and in aqueous solution: a valence bond study.

The recently developed (L. Song, W. Wu, Q. Zhang, S. Shaik, J. Phys. Chem. A 2004, 108, 6017) valence bond method coupled with a polarized continuum model (VBPCM) has been applied to the identity SN2 reaction of halides in the gas phase and in aqueous solution. The barriers computed at the level of the breathing orbital VB method (P. C. Hiberty, J. P. Flament, E. Noizet, Chem. Phys. Lett. 1992, 189, 259), BOVB and VBPCM//BOVB, are comparable to CCSD(T) and CCSD(T)//PCM results and to experimentally derived barriers in solution (W. J. Albery, M. M. Kreevoy, Adv. Phys. Org. Chem. 1978, 16, 85). The reactivity parameters needed to apply the valence bond state correlation diagram (VBSCD) method (S. Shaik, J. Am. Chem. Soc. 1984, 106, 1227), were also determined by VB calculations. It has been shown that the reactivity parameters along with their semiempirical derivations provide a satisfactory qualitative and quantitative account of the barriers.

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PubMed2006

Barriers of hydrogen abstraction vs halogen exchange: an experimental manifestation of charge-shift bonding.

This paper shows that the differences between the barriers of the halogen exchange reactions, in the H + XH systems, and the hydrogen abstraction reactions, in the X + HX systems (X = F, Cl, Br), measure the covalent-ionic resonance energies of the corresponding X-H bonds. These processes are investigated using CCSD(T) calculations as well as the breathing-orbital valence bond (BOVB) method. Thus, the VB analysis shows that (i) at the level of covalent structures the barriers are the same for the two series and (ii) the higher barriers for halogen exchange processes originate solely from the less efficient mixing of the ionic structures into the respective covalent structures. The barrier differences, in the HXH vs XHX series, which decrease as X is varied from F to I, can be estimated as one-quarter of the covalent-ionic resonance energy of the H-X bond. The largest difference (22 kcal/mol) is calculated for X = F in accord with the finding that the H-F bond possesses the largest covalent-ionic resonance energy, 87 kcal/mol, which constitutes the major part of the bonding energy. The H-F bond belongs to the class of "charge-shift" bonds (Shaik, S.; Danovich, D.; Silvi, B.; Lauvergnat, D. L.; Hiberty, P. C. Chem. Eur. J. 2005, 21, 6358), which are all typified by dominant covalent-ionic resonance energies. Since the barrier difference between the two series is an experimental measure of the resonance energy quantity, in the particular case of X = F, the unusually high barrier for the fluorine exchange reaction emerges as an experimental manifestation of charge-shift bonding.

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PubMed2005

Charge-shift bonding--a class of electron-pair bonds that emerges from valence bond theory and is supported by the electron localization function approach.

This paper deals with a central paradigm of chemistry, the electron-pair bond. Valence bond (VB) theory and electron-localization function (ELF) calculations of 21 single bonds demonstrate that along the two classical bond families of covalent and ionic bonds, there exists a class of charge-shift bonds (CS bonds) in which the fluctuation of the electron pair density plays a dominant role. In VB theory, CS bonding manifests by way of a large covalent-ionic resonance energy, RE(CS), and in ELF by a depleted basin population with large variances (fluctuations). CS bonding is shown to be a fundamental mechanism that is necessary to satisfy the equilibrium condition, namely the virial ratio of the kinetic and potential energy contributions to the bond energy. The paper defines the atomic propensity and territory for CS bonding: Atoms (fragments) that are prone to CS bonding are compact electronegative and/or lone-pair-rich species. As such, the territory of CS bonding transcends considerations of static charge distribution, and involves: a) homopolar bonds of heteroatoms with zero static ionicity, b) heteropolar sigma and pi bonds of the electronegative and/or electron-pair-rich elements among themselves and to other atoms (e.g., the higher metalloids, Si, Ge, Sn, etc), c) all hypercoordinate molecules. Several experimental manifestations of charge-shift bonding are discussed, such as depleted bonding density, the rarity of ionic chemistry of silicon in condensed phases, and the high barriers of halogen-transfer reactions as compared to hydrogen-transfers.

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PubMed2004

What makes the trifluoride anion F3 - so special? A breathing-orbital valence bond ab initio study.

The ground states of the F(3)(-) and H(3)(-) hypercoordinated anions are investigated and analyzed in terms of valence bond structures by means of the breathing-orbital valence bond method. While H(3)(-) is described reasonably well as the interplay of two major Lewis structures, H(2) + H(-) and its mirror image, the description of F(3)(-) requires a further structure, of the type F(*)F(-)F(*), which strongly stabilizes the trimer relative to the dissociation products, and endows the F(3)(-) ground state with a predominant three-electron bond character. It follows that the simple picture that is closest to the true nature of F(3)(-) is a resonating combination of F(2)(-) + F(*) and its mirror image. This peculiarity of the F(3)(-) electronic structure is at the origin of its preferred dissociation channel leading to F(2)(-) + F(*) rather than to the most stable product F(2) + F(-), at high collision energies. The three-electron bond character of F(3)(-) is also the root cause for the failure of the Hartree-Fock and density functional methods for this species, and for its strong tendency to artifactual symmetry-breaking. As an alternative to the Rundle-Pimentel model, the origins of the stability of F(3)(-), as opposed to the instability of H(3)(-), CH(5)(-), and other S(N)2 transition states, are analyzed in the framework of valence bond state correlation diagrams [Shaik, S.; Shurki, A. Angew. Chem., Int. Ed. 1999, 38, 586]. It is found that a fundamental factor of stability for X(3)(-) is the presence of lone pairs on the X fragment. The explanation carries over to other trihalide anions, and to isoelectronic 22-valence electron hypercoordinated anions.

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PubMed2004

Valence bond calculations of hydrogen transfer reactions: a general predictive pattern derived from theory.

Hydrogen abstraction reactions of the type X(*) + H-H' --> X-H + H'(*) (X = F, Cl, Br, I) are studied by ab initio valence bond methods and the VB state correlation diagram (VBSCD) model. The reaction barriers and VB parameters of the VBSCD are computed by using the breathing orbital valence bond and valence bond configuration interaction methods. The combination of the VBSCD model and semiempirical VB theory leads to analytical expressions for the barriers and other VB quantities that match the ab initio VB calculations fairly well. The barriers are influenced by the endo- or exothermicity of the reaction, but the fundamental factor of the barrier is the average singlet-triplet gap of the bonds that are broken or formed in the reactions. Some further approximations lead to a simple formula that expresses the barrier for nonidentity and identity hydrogen abstraction reactions as a function of the bond strengths of reactants and products. The semiempirical expressions are shown to be useful not only for the model reactions that are studied in this work, but also for other nonidentity and identity hydrogen abstraction reactions that have been studied in previous articles.

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PubMed2003

An accurate barrier for the hydrogen exchange reaction from valence bond theory: is this theory coming of age?

One of the landmark achievements of quantum chemistry, specifically of MO-based methods that include electron correlation, was the precise calculation of the barrier for the hydrogen-exchange reaction (B. Liu, J. Chem. Phys. 1973, 58, 1925; P. Siegbahn, B. Liu, J. Chem. Phys. 1978, 68, 2457). This paper reports an accurate calculation of this barrier by two recently developed VB methods that use only the eight classical VB structures. To our knowledge, the present work is the first accurate ab initio VB barrier that matches an experimental value. Along with the accurate barrier, the VB method provides accurate bond energies and diabatic quantities that enable the barrier height to be analyzed by the VB state correlation diagram approach, VBSCD (S. Shaik, A. Shurki, Angew. Chem. 1999, 111, 616; Angew. Chem. Int. Ed. Engl. 1999, 38, 586). This is a proof of principal that VB theory with appropriate account of dynamic electron correlation can achieve quantitative accuracy of reaction barriers, and still retain a compact and interpretable wave function. A sample of S(N)2 barriers and dihalogen bonding energies, which are close to CCSD(T) and G2(+) values, show that the H(3) problem is not an isolated case, and while it is premature to conclude that VB theory has come of age, the occurrence of this event is clearly within sight.

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PubMed2003

A conversation on VB vs MO theory: a never-ending rivalry?

Quantum mechanics has provided chemistry with two general theories, valence bond (VB) theory and molecular orbital (MO) theory. The two theories were developed at about the same time, but quickly diverged into rival schools that have competed, sometimes fervently, on charting the mental map and epistemology of chemistry. Three practitioners of MO and VB theory talk - fighting a little, trying to understand - of the past and present of these two approaches to describing bonding in molecules.

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PubMed2002

Stability, metastability, and unstability of three-electron-bonded radical anions. A model ab initio theoretical study.

The stability of O therefore O, N therefore N, S therefore S, P therefore P, and Si therefore Si three-electron bonds in anionic radicals isoelectronic to dihalogen radical anions is studied by means of ab initio calculations on model systems. The difficulty of generating the dissociation energy profiles of such anions and their rearrangement to neutral species is solved by a practical method which consists of calculating the neutral and anionic energy profiles separately and shifting the curves with respect to each other to match the experimental energy gap between the asymptotes. Here the neutral and anionic reaction profiles are calculated at the CASPT2 and MP2 levels, respectively. The calculations predict that the O therefore O bond is likely to be observed in anions of the type [RO therefore OR](*-), where R is any alkyl substituent or carbon chain. The anion Si(2)H(6)(*-) is found to be a metastable species, with a fair barrier to electron detachment. The barrier is much smaller for N(2)H(4)(*-) and P(2)H(4)(*-), thus precluding experimental observation. However, these species can be stabilized by electron-attractor substituents, the effect of which can be quantitatively estimated by means of the parent anion's diagrams and some fast complementary calculations. An example is given with the [CF(3)HN therefore NHCF(3)](*-) anionic complex.

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PubMed2002

Methyl substituent effects in [H(n)X...XH(n)](+) three-electron-bonded radical cations (X = F, O, N, Cl, S, P; n = 1 - 3). An ab initio theoretical study.

The effects of methyl substitution on the geometries and bonding energies of a systematic series of three-electron-bonded radical cations of the type [H(n)X...XH(n)](+), covering all possible symmetrical three-electron bonds that may take place between atoms of the second and third rows of the periodic table, have been investigated at the level of Møller-Plesset perturbation theory. Methyl substitution leads to significant weakening and lengthening of the X...X bond when X is a second-row atom. The effects increase with the number of substitutions and are more and more important in the series X = N, O, F. By contrast, methyl substitution leaves the bonding energies between third-row atoms practically unchanged but leads to a surprising bond shortening in the S...S and P...P cases. These seemingly contradictory effects are rationalized through a qualitative analysis based on an elementary molecular orbital description of three-electron bonding.

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