CNRS Theoretical Chemistry Laboratory

Paris, France

CNRS Theoretical Chemistry Laboratory

Paris, France

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Braida B.,CNRS Theoretical Chemistry Laboratory | Hiberty P.C.,University Paris - Sud
Nature Chemistry | Year: 2013

Hypervalency in XeF 2 and isoelectronic complexes is generally understood in terms of the Rundle-Pimentel model (which invokes a three-centre/four- electron molecular system) or its valence bond version as proposed by Coulson, which replaced the old expanded octet model of Pauling. However, the Rundle-Pimentel model is not always successful in describing such complexes and has been shown to be oversimplified. Here using ab initio valence bond theory coupled to quantum Monte Carlo methods, we show that the Rundle-Pimentel model is insufficient by itself in accounting for the great stability of XeF 2, and that charge-shift bonding, wherein the large covalent-ionic interaction energy has the dominant role, is a major stabilizing factor. The energetic contribution of the old expanded octet model is also quantified and shown to be marginal. Generalizing to isoelectronic systems such as ClF 3, SF 4, PCl 5 and others, it is suggested that charge-shift bonding is necessary, in association with the Rundle-Pimentel model, for hypervalent analogues of XeF 2 to be strongly bonded. © 2013 Macmillan Publishers Limited.


Braida B.,CNRS Theoretical Chemistry Laboratory | Walter C.,Institute For Organische Chemie | Engels B.,Institute For Organische Chemie | Hiberty P.C.,University Paris - Sud
Journal of the American Chemical Society | Year: 2010

A series of nine 1,3-dipoles, belonging to the families of diazonium betaines, nitrilium betaines, and azomethine betaines, has been studied by means of the breathing-orbital valence bond ab initio method. Each 1,3-dipole is described as a linear combination of three valence bond structures, two zwitterions and one diradical, for which the weights in the total wave function can be quantitatively estimated. In agreement with an early proposition of Harcourt, the diradical character of 1,3-dipoles is shown to be a critical feature to favor 1,3-dipolar cycloaddition. Within each family, a linear relationship is evidenced between the weight of the diradical structure in the 1,3-dipole and the barrier to cycloaddition to ethylene or acetylene, with correlation coefficients of 0.98-1.00. The barrier heights also correlate very well with the transition energies from ground state to pure diradical states of the 1,3-dipoles at equilibrium geometry. Moreover, the weight of the diradical structure is shown to increase significantly in all 1,3-dipoles from their equilibrium geometries to their distorted geometries in the transition states. A mechanism for 1,3-dipolar cycloaddition is proposed, in which the 1,3-dipole first distorts so as to reach a reactive state that possesses some critical diradical character and then adds to the dipolarophile with little or no barrier. This mechanism is in line with the recently proposed distortion/interaction energy model of Ess and Houk and their finding that the barrier heights for the cycloaddition of a given 1,3-dipole to ethylene and acetylene are nearly the same, despite the exothermicity difference (Ess, D. H. and Houk, K. N. J. Am. Chem. Soc. 2008, 130, 10187). © 2010 American Chemical Society.


Duke R.E.,Wayne State University | Starovoytov O.N.,Wayne State University | Piquemal J.-P.,CNRS Theoretical Chemistry Laboratory | Cisneros G.A.,Wayne State University
Journal of Chemical Theory and Computation | Year: 2014

GEM*, a force field that combines Coulomb and Exchange terms calculated with Hermite Gaussians with the polarization, bonded, and modified van der Waals terms from AMOEBA is presented. GEM* is tested on an initial water model fitted at the same level as AMOEBA. The integrals required for the evaluation of the intermolecular Coulomb interactions are efficiently evaluated by means of reciprocal space methods. The GEM* water model is tested by comparing energies and forces for a series of water oligomers and MD simulations. Timings for GEM* compared to AMOEBA are presented and discussed. © 2014 American Chemical Society.


Zhang J.,University of Texas at Austin | Yang W.,Florida State University | Piquemal J.-P.,CNRS Theoretical Chemistry Laboratory | Ren P.,University of Texas at Austin
Journal of Chemical Theory and Computation | Year: 2012

As the second most abundant cation in the human body, zinc is vital for the structures and functions of many proteins. Zinc-containing matrix metalloproteinases (MMPs) have been widely investigated as potential drug targets in a range of diseases ranging from cardiovascular disorders to cancers. However, it remains a challenge in theoretical studies to treat zinc in proteins with classical mechanics. In this study, we examined Zn 2+ coordination with organic compounds and protein side chains using a polarizable atomic multipole-based electrostatic model. We find that the polarization effect plays a determining role in Zn 2+ coordination geometry in both matrix metalloproteinase (MMP) complexes and zinc-finger proteins. In addition, the relative binding free energies of selected inhibitors binding with MMP13 have been estimated and compared with experimental results. While not directly interacting with the small molecule inhibitors, the permanent and polarizing field of Zn 2+ exerts a strong influence on the relative affinities of the ligands. The simulation results also reveal that the polarization effect on binding is ligand-dependent and thus difficult to incorporate into fixed-charge models implicitly. © 2012 American Chemical Society.


Liu H.-J.,University of California at Berkeley | Raynaud C.,Charles Gerhardt Institute | Raynaud C.,CNRS Theoretical Chemistry Laboratory | Eisenstein O.,Charles Gerhardt Institute | Tilley T.D.,University of California at Berkeley
Journal of the American Chemical Society | Year: 2014

The synthesis of the cyclometalated complexes CpRu(IXy-H) (2) [IXy = 1,3-bis(2,6-dimethylphenyl)imidazol-2-ylidene; IXy-H = 1-(2-CH2C 6H3-6-methyl)-3-(2,6-dimethylphenyl)imidazol-2-ylidene-1- yl (the deprotonated form of IXy); Cp* = η5-C 5Me5] and CpRu(IXy-H)(N2) (3) was achieved by dehydrochlorination of CpRu(IXy)Cl (1) with KCH2Ph. Complexes 2 and 3 activate primary silanes (RSiH3) to afford the silyl complexes Cp(IXy-H)(H)RuSiH2R [R = p-Tol (4), Mes (5), Trip (6)]. Density functional theory studies indicated that these complexes are close in energy to the corresponding isomeric silylene species Cp(IXy)(H)Ru=SiHR. Indeed, reactivity studies indicated that various reagents trap the silylene isomer of 6, Cp(IXy)(H)Ru=SiHTrip (6a). Thus, benzaldehyde reacts with 6 to give the [2 + 2] cycloaddition product 7, while 4-bromoacetophenone reacts via C-H bond cleavage and formation of the enolate Cp(IXy)(H)2RuSiH[OC(=CH 2)C6H4Br]Trip (8). Addition of the O-H bond of 2,6-dimethylphenol across the Ru=Si bond of 6a gives Cp(IXy)(H) 2RuSiH(2,6-Me2C6H3O)Trip (9). Interestingly, CuOTf and AgOTf also react with 6 to provide unusual Lewis acid-stabilized silylene complexes in which MOTf bridges the Ru-Si bond. The AgOTf complex, which was crystallographically characterized, exhibits a structure similar to that of [Cp(iPr3P)Ru(μ-H) 2SiHMes]+, with a three-center, two-electron Ru-Ag-Si interaction. Natural bond orbital analysis of the MOTf complexes supported this type of bonding and characterized the donor interaction with Ag (or Cu) as involving a delocalized interaction with contributions from the carbene, silylene, and hydride ligands of Ru. © 2014 American Chemical Society.


Lane J.R.,University of Waikato | Contreras-Garcia J.,CNRS Theoretical Chemistry Laboratory | Piquemal J.-P.,CNRS Theoretical Chemistry Laboratory | Miller B.J.,University of Otago | Kjaergaard H.G.,Copenhagen University
Journal of Chemical Theory and Computation | Year: 2013

Atoms in Molecules (AIM) theory is routinely used to assess hydrogen bond formation; however its stringent criteria controversially exclude some systems that otherwise appear to exhibit weak hydrogen bonds. We show that a regional analysis of the reduced density gradient, as provided by the recently introduced Non-Covalent Interactions (NCI) index, transcends AIM theory to deliver a chemically intuitive description of hydrogen bonding for a series of 1,n-alkanediols. This regional definition of interactions overcomes the known caveat of only analyzing electron density critical points. In other words, the NCI approach is a simple and elegant generalization of the bond critical point approach, which raises the title question. Namely, is it the presence of an electron density bond critical point that defines a hydrogen bond or the general topology in the region surrounding it? © 2013 American Chemical Society.


Contreras-Garcia J.,Duke University | Johnson E.R.,University of California at Merced | Keinan S.,Duke University | Chaudret R.,CNRS Theoretical Chemistry Laboratory | And 3 more authors.
Journal of Chemical Theory and Computation | Year: 2011

Noncovalent interactions hold the key to understanding many chemical, biological, and technological problems. Describing these noncovalent interactions accurately, including their positions in real space, constitutes a first step in the process of decoupling the complex balance of forces that define noncovalent interactions. Because of the size of macromolecules, the most common approach has been to assign van der Waals interactions (vdW), steric clashes (SC), and hydrogen bonds (HBs) based on pairwise distances between atoms according to their vdW radii. We recently developed an alternative perspective, derived from the electronic density: the non-covalent interactions (NCI) index [J. Am. Chem. Soc. 2010, 132, 6498 ]. This index has the dual advantages of being generally transferable to diverse chemical applications and being very fast to compute, since it can be calculated from promolecular densities. Thus, NCI analysis is applicable to large systems, including proteins and DNA, where analysis of noncovalent interactions is of great potential value. Here, we describe the NCI computational algorithms and their implementation for the analysis and visualization of weak interactions, using both self-consistent fully quantum-mechanical as well as promolecular densities. A wide range of options for tuning the range of interactions to be plotted is also presented. To demonstrate the capabilities of our approach, several examples are given from organic, inorganic, solid state, and macromolecular chemistry, including cases where NCI analysis gives insight into unconventional chemical bonding. The NCI code and its manual are available for download at http://www.chem.duke.edu/ ∼yang/software.htm. © 2011 American Chemical Society.


Gould T.,Griffith University | Toulouse J.,CNRS Theoretical Chemistry Laboratory
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2014

Within exact electron density-functional theory, we investigate Kohn-Sham (KS) potentials, orbital energies, and noninteracting kinetic energies of the fractional ions of Li, C, and F. We use quantum Monte Carlo densities as input, which are then fitted, interpolated at noninteger electron numbers N, and inverted to produce accurate KS potentials vsN(r). We study the dependence of the KS potential on N, and in particular we numerically reproduce the theoretically predicted spatially constant discontinuity of vsN(r) as N passes through an integer. We further show that, for all the cases considered, the inner orbital energies and the noninteracting kinetic energy are nearly piecewise linear functions of N. This leads us to propose a simple approximation of the KS potential vsN(r) at any fractional electron number N which uses only quantities of the systems with the adjacent integer electron numbers. © 2014 American Physical Society.


Calatayud M.,CNRS Theoretical Chemistry Laboratory
Catalysis Today | Year: 2010

The present paper describes the interaction of ethylene glycol CH 2OH-CH2OH with alkaline earth oxide basic catalysts MO (M = Mg, Ca, Sr, Ba) from periodic DFT calculations. The geometry of adsorption depends on the nature of the metallic site: on MgO the alcohol groups bind to the metal sites on quasitop positions, while on CaO, SrO and BaO the molecule is located on bridging positions. The adsorption is exothermic and the strength correlates with the basicity of the alkaline earth oxide, the more basic the substrate, the more exothermic the adsorption energy: MgO < CaO < SrO < BaO. The glycol molecule deprotonates to form surface alkoxy groups bound to the metal sites. The extent of such deprotonation is also correlated to the basicity of MO:MgO (completely protonated) < CaO (partially protonated) < SrO (completely deprotonated) = BaO (completely deprotonated). Defects, modeled for a stepped CaO slab, are found to enhance the strength of the interaction and the deprotonation extent, inducing a different adsorption mode. The step is found to be more reactive than the most basic BaO regular surface, in agreement with experimental observations on glycerol. The implications of these aspects in chemical reactivity are discussed. © 2009 Elsevier B.V. All rights reserved.


Hadzic M.,CNRS Theoretical Chemistry Laboratory | Braida B.,CNRS Theoretical Chemistry Laboratory | Volatron F.,CNRS Theoretical Chemistry Laboratory
Organic Letters | Year: 2011

The traditional resonance model for electrophilic attacks on substituted aromatic rings is revisited using high level valence bond (VB) calculations. A large π-donation is found in the X = NH2 case and a weaker one for the X = Cl case, not only for ortho and para isomers but also for the meta case, which can be explained by considering five (not three) fundamental VB structures. No substantial ?-effect is found in the X = NO2 case, generally viewed as π-attractive. © 2011 American Chemical Society.

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