Theoretical basis of the empirical reaction field approximations through continuum model

We derive from exact integral equations of classical electrostatics some approximate expressions of the interaction energy of a point charge distribution with a dielectric medium. We show how they can be used for computing the wave functions of solvated species imbedded in cavities formed by interlocking spheres in a polarizable continuum. We discuss the relation between these formulae and the ones proposed earlier on empirical basis and we especially emphasize the improvement that they bring out.     

Computer generation of chemical structures from known fragments

The interactive generation of chemical structures from given fragments is described and discussed. It is implemented as a part of our expert system CARBON, based on C-13 NMR spectra. As it is designed, this program can also be a useful tool in the structure elucidation process when information on parts of the structure is obtained by other means (IR, mass and other spectrometries, chemical analysis, other relevant information). The topological characteristics of candidate fragments are first chosen interactively and then the elements are connected in all topologically possible ways. In the following step, the topological building blocks are substituted by chemical structural fragments resulting in a set of all chemical structures consistent with the input information.     

Preferred Binding of Carboxylates by Chiral Urea Derivatives Containing α‐Phenylethyl Group

An efficient, simple protocol for the synthesis of a new family of chiral ureas 1 – 4 is described. The binding properties of 1 – 4 toward different anion (acetate, benzoate, fluoride, and chloride) have been studied by ¹H‐NMR titration and have been observed in the case of 4 is a selective receptor for acetate. The theoretical calculation M06/6‐311+G(d,p) helped us explain the binding properties observed. The most interesting observation is that this calculated structure is consistent with expected, based on the concept of allylic 1,3‐strain (A^1,3 strain). When chiral caboxylates were studied, urea 1 was the best in discriminating between enantiomers.     

A highly efficient hybrid method for calculating the hydration free energy of a protein

We develop a new method for calculating the hydration free energy (HFE) of a protein with any net charge. The polar part of the energetic component in the HFE is expressed as a linear combination of four geometric measures (GMs) of the protein structure and the generalized Born (GB) energy plus a constant. The other constituents in the HFE are expressed as linear combinations of the four GMs. The coefficients (including the constant) in the linear combinations are determined using the three‐dimensional reference interaction site model (3D‐RISM) theory applied to sufficiently many protein structures. Once the coefficients are determined, the HFE and its constituents of any other protein structure are obtained simply by calculating the four GMs and GB energy. Our method and the 3D‐RISM theory give perfectly correlated results. Nevertheless, the computation time required in our method is over four orders of magnitude shorter.     

Recasting wave functions into valence bond structures: A simple projection method to describe excited states

A method is proposed to obtain coefficients and weights of valence bond (VB) determinants from multi configurational wave functions. This reading of the wave functions can apply to ground states as well as excited states. The method is based on projection operators. Both energetic and overlap‐based criteria are used to assess the quality of the resulting VB wave function. The approach gives a simple access to a VB rewriting for low‐lying states, and it is applied to the allyl cation, to the allyl radical and to the ethene (notably to the V‐state). For these states, large overlap between VB and multi reference wave functions are easily obtained. The approach proves to be useful to propose an interpretation of the nature of the V‐state of ethene. © 2015 Wiley Periodicals, Inc.     

Quantum chemical mass spectrometry: ab initio prediction of electron ionization mass spectra and identification of new fragmentation pathways

The electron ionization mass spectra of four organic compounds are predicted based on the results of quantum chemical calculations at the DFT/B3LYP/6‐311 + G* level of theory. This prediction is performed ‘ab initio’, i.e. without any prior knowledge of the thermodynamics or kinetics of the reactions under consideration. Using a set of rules determining which routes will be followed, the fragmentation of the molecules' bonds and the complete resulting fragmentation pathways are studied. The most likely fragmentation pathways are identified based on calculated reaction energies ΔE when bond cleavage is considered and on activation energies ΔE^? when rearrangements are taken into account; the final intensities of the peaks in the spectrum are estimated from these values. The main features observed in the experimental mass spectra are correctly predicted, as well as a number of minor peaks. In addition, the results of the calculations allow us to propose fragmentation pathways new to empirical mass spectrometry, which have been experimentally verified using tandem mass spectrometry measurements. Copyright © 2016 John Wiley & Sons, Ltd.     

Adsorption and Decomposition of NH3 on Ni/Pt(111) and Ni/WC(001) Surfaces: A First-Principles Study

Density functional theory was used to study the NH₃ behavior on Ni monolayer covered Pt(111) and WC(001). The electronic structure of the surfaces, and the adsorption and decomposition of NH₃ were calculated and compared. Ni atoms in the monolayer behave different from that in Ni(111). More dz2 electrons of Ni in monolayer covered systems were shifted to other regions compared to Ni(111), charge density depletion on this orbital is crucial to NH₃ adsorption. NH₃ binds more stable on Ni/Pt(111) and Ni/WC(001) than on Ni(111), the energy barriers of the first N-H bond scission were evidently lower on Ni/Pt(111) and Ni/WC(001) than on Ni(111), these are significant to NH₃ decomposition. N recombination is the rate-limiting step, high reaction barrier implies that N₂ is produced only at high temperatures. Although WC has similar properties to Pt, differences of the electronic structure and catalytic activities are observed for Ni/Pt(111) and Ni/WC(001), the energy barrier for the rate-determined step increases on Ni/WC(001) instead of decreasing on Ni/Pt(111) when compared to Ni(111). To design cheaper and better catalysts, reducing the N recombination barrier by modifying Ni/WC(001) is a critical question to be solved.     

Molecular dynamics simulation and density functional theory insight into the cocrystal explosive of hexaazaisowurtzitane/nitroguanidine

Theoretical methods involving molecular dynamics (MD) simulation and density functional theory were performed to investigate the different molecular ratios, mechanical Properties, structure, trigger bond, and intermolecular interaction of hexaazaisowurtzitane (CL‐20)/nitroguanidine (NQ) cocrystal explosive. Results of MD simulation show that CL‐20 and NQ packed in ratios of 1:1 present the larger binding energy and better mechanical properties than any other molecular ratios, which indicates 1:1 cocrystal can form the stable crystal structure. Shorter length and larger dissociation energy of trigger bond in composite structure than in isolated CL‐20 component suggests that the cocrystal may exhibit less sensitive than CL‐20. Analyses of atoms in molecules, reduced density gradient, and natural bond orbital confirm that intermolecular interactions are mainly derived from a series of weak hydrogen bond and strong vdW forces, involving of NH···O, CH···O, CH···N, O···N, and O···O. Additionally, composite structures of 2 and 3 bringing us more attractive performance will act as a key role in constructing of CL‐20/NQ cocrystal explosive. © 2015 Wiley Periodicals, Inc.     

Novel application of quantum chemical investigation in terms of substituent parameters: Statistical comparison of dual and single substituent parameter treatments

The correlation analysis of Mulliken charge (Q_M) calculated by using density functional theory (B3LYP/STO-3G) calculations of 1-(4-azido-5-hydroxymethyl-tetrahydro-selenophen-2-ylmethyl)-5-substituted-1H-pyrimidine-2,4-dione, were done by using mono substituent parameter (Hammett’s model), and dual substituent parameter (Taft’s, Reynolds’, and Swain’s models). The dual substituent parameter correlations of the Q_M data gave no significant improvement over single parameter correlations, the best correlation observed with the Taft’s Model as compared with the Swain’s and Reynolds’ Models, respectively. The correlation analysis of Mulliken charge can be used successfully to demonstrate the existence or absence of the interaction between the oxygen of the carbonyl group and selenium atom.     

Structural evolution of (Ca0.35Sr0.65)TiO3 perovskite at high pressures

Lattice parameters of a synthetic powder sample of Ca_0.35Sr_0.65TiO₃ perovskite have been determined by the method of Le Bail refinement, using synchrotron X-ray diffraction patterns collected at pressures up to 15.5 GPa with a membrane-driven diamond anvil cell. At ambient conditions, diffraction data were consistent with the I4/mcm structure reported previously in the literature for the same composition. Diffraction data collected at high pressures were consistent with tetragonal (or, at least, pseudo-tetragonal) lattice geometry, and no evidence was found for the development of any of the orthorhombic structures identified in other studies of (Ca, Sr)TiO₃ perovskites. Additional weak reflections, which could not be accounted for by the normal I4/mcm perovskite structure, were detected in diffraction patterns collected at pressures of 0.9-2.5 GPa, and above ∼13.5 GPa, however. Small anomalies in the evolution of unit cell volume and tetragonal strain were observed near 3 GPa, coinciding approximately with breaks in slope with increasing pressure of bulk and shear moduli for a sample with the same composition which had previously been reported. The anomalies could be due either to new tetragonal↔tetragonal/pseudo-tetragonal phase transitions or to subtle changes in compression mechanism of the tetragonal perovskite structure.