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New insights on reaction pathway selectivity promoted by crown ether phase-transfer catalysis: Model ab initio calculations of nucleophilic fluorination

Pliego, Josefredo R., Jr.; Riveros, Jose M.
Fonte: ELSEVIER SCIENCE BV; AMSTERDAM Publicador: ELSEVIER SCIENCE BV; AMSTERDAM
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
26.18%
Crown ethers have the ability of solubilizing inorganic salts in apolar solvents and to promote chemical reactions by phase-transfer catalysis. However, details on how crown ethers catalyze ionic S(N)2 reactions and control selectivity are not well understood. In this work, we have used high level theoretical calculations to shed light on the details of phase-transfer catalysis mechanism of KF reaction with alkyl halides promoted by 18-crown-6. A complete analysis of the of the model reaction between KF(18-crown-6) and ethyl bromide reveals that the calculations can accurately predict the product ratio and the overall kinetics. Our results point out the importance of the K* ion and of the crown ether ring in determining product selectivity. While the K* ion favors the S(N)2 over the E2 anti pathway, the crown ether ring favors the S(N)2 over E2 syn route. The combination effects lead to a predicted 94% for the S(N)2 pathway in excellent agreement with the experimental value of 92%. A detailed analysis of the overall mechanism of the reaction under phase-transfer conditions also reveals that the KBr product generated in the nucleophilic fluorination acts as an inhibitor of the 18-crown-6 catalyst and it is responsible for the observed slow reaction rate. (C) 2012 Elsevier B.V. All rights reserved.; Brazilian Research Council (CNPq); Brazilian Research Council (CNPq); Brazilian Office of Higher Education (CAPES); Brazilian Office of Higher Education (CAPES); Fundacao de Amparo a Pesquisa do Estado de Minas Gerais (FAPEMIG); Fundacao de Amparo a Pesquisa do Estado de Minas Gerais (FAPEMIG); Institute for Science and Technology of Materials (INOMAT); Institute for Science and Technology of Materials (INOMAT)

The X3LYP extended density functional for accurate descriptions of nonbond interactions, spin states, and thermochemical properties

Xu, Xin; Goddard, William A.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
26.18%
We derive the form for an exact exchange energy density for a density decaying with Gaussian-like behavior at long range. Based on this, we develop the X3LYP (extended hybrid functional combined with Lee–Yang–Parr correlation functional) extended functional for density functional theory to significantly improve the accuracy for hydrogen-bonded and van der Waals complexes while also improving the accuracy in heats of formation, ionization potentials, electron affinities, and total atomic energies [over the most popular and accurate method, B3LYP (Becke three-parameter hybrid functional combined with Lee–Yang–Parr correlation functional)]. X3LYP also leads to a good description of dipole moments, polarizabilities, and accurate excitation energies from s to d orbitals for transition metal atoms and ions. We suggest that X3LYP will be useful for predicting ligand binding in proteins and DNA.

Doubly hybrid density functional for accurate descriptions of nonbond interactions, thermochemistry, and thermochemical kinetics

Zhang, Ying; Xu, Xin; Goddard, William A.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
46.62%
We develop and validate a density functional, XYG3, based on the adiabatic connection formalism and the Görling–Levy coupling-constant perturbation expansion to the second order (PT2). XYG3 is a doubly hybrid functional, containing 3 mixing parameters. It has a nonlocal orbital-dependent component in the exchange term (exact exchange) plus information about the unoccupied Kohn–Sham orbitals in the correlation part (PT2 double excitation). XYG3 is remarkably accurate for thermochemistry, reaction barrier heights, and nonbond interactions of main group molecules. In addition, the accuracy remains nearly constant with system size.

Properties of water along the liquid-vapor coexistence curve via molecular dynamics simulations using the polarizable TIP4P-QDP-LJ water model

Bauer, Brad A.; Patel, Sandeep
Fonte: American Institute of Physics Publicador: American Institute of Physics
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
26.33%
We present an extension of the TIP4P-QDP model, TIP4P-QDP-LJ, that is designed to couple changes in repulsive and dispersive nonbond interactions to changes in polarizability. Polarizability is intimately related to the dispersion component of classical force field models of interactions, and we explore the effect of incorporating this connection explicitly on properties along the liquid-vapor coexistence curve of pure water. Parametrized to reproduce condensed-phase liquid water properties at 298 K, the TIP4P-QDP-LJ model predicts density, enthalpy of vaporization, self-diffusion constant, and the dielectric constant at ambient conditions to about the same accuracy as TIP4P-QDP but shows remarkable improvement in reproducing the liquid-vapor coexistence curve. TIP4P-QDP-LJ predicts critical constants of Tc=623 K, ρc=0.351 g∕cm3, and Pc=250.9 atm, which are in good agreement with experimental values of Tc=647.1 K, ρc=0.322 g∕cm3, and Pc=218 atm, respectively. Applying a scaling factor correction (obtained by fitting the experimental vapor-liquid equilibrium data to the law of rectilinear diameters using a three-term Wegner expansion) the model predicts critical constants (Tc=631 K and ρc=0.308 g∕cm3). Dependence of enthalpy of vaporization...

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

Huang, Jing; MacKerell, Alexander D.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
26.8%
Protein structure and dynamics can be characterized on the atomistic level with both nuclear magnetic resonance (NMR) experiments and molecular dynamics (MD) simulations. Here we quantify the ability of the recently presented CHARMM36 (C36) force field (FF) to reproduce various NMR observables using MD simulations. The studied NMR properties include backbone scalar couplings across hydrogen bonds, residual dipolar couplings (RDCs) and relaxation order parameter, as well as scalar couplings, RDCs and order parameters for side chain amino- and methyl- containing groups. It is shown that the C36 force field leads to better correlation with experimental data compared to the CHARMM22/CMAP force field, and suggest using C36 in protein simulations. While both CHARMM FFs contains the same nonbond parameters, our results show how the changes in the internal parameters associated with the peptide backbone via CMAP and the χ1 and χ2 dihedral parameters leads to improved treatment of the analyzed nonbond interactions. This highlights the importance of proper treatment of the internal covalent components in modeling nonbond interactions with molecular mechanics FFs.

Water modeled as an intermediate element between carbon and silicon

Molinero, Valeria; Moore, Emily B.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 16/09/2008 Português
Relevância na Pesquisa
16.28%
Water and silicon are chemically dissimilar substances with common physical properties. Their liquids display a temperature of maximum density, increased diffusivity on compression, they form tetrahedral crystals and tetrahedral amorphous phases. The common feature to water, silicon and carbon is the formation of tetrahedrally coordinated units. We exploit these similarities to develop a coarse-grained model of water (mW) that is essentially an atom with tetrahedrality intermediate between carbon and silicon. mW mimics the hydrogen-bonded structure of water through the introduction of a nonbond angular dependent term that encourages tetrahedral configurations. The model departs from the prevailing paradigm in water modeling: the use of long-ranged forces (electrostatics) to produce short-ranged (hydrogen-bonded) structure. mW has only short-range interactions yet it reproduces the energetics, density and structure of liquid water, its anomalies and phase transitions with comparable or better accuracy than the most popular atomistic models of water, at less than 1% of the computational cost. We conclude that it is not the nature of the interactions but the connectivity of the molecules that determines the structural and thermodynamic behavior of water. The speedup in computing time provided by mW makes it particularly useful for the study of slow processes in deeply supercooled water...

Studies of fullerenes and carbon nanotubes by an extended bond order potential

Che, Jianwei; Çağin, Tahir; Goddard, William A., III
Fonte: Institute of Physics Publicador: Institute of Physics
Tipo: Article; PeerReviewed Formato: application/pdf
Publicado em /09/1999 Português
Relevância na Pesquisa
26.7%
We present a novel approach to combine bond order potentials with long-range nonbond interactions. This extended bond order potential consistently takes into account bond terms and nonbond terms. It not only captures the advantages of the bond order potentials (i.e. simulating bond forming and breaking), but also systematically includes the nonbond contributions to energy and forces in studying the structure and dynamics of covalently bonded systems such as graphite, diamond, nanotubes, fullerenes and hydrocarbons, in their crystal and melt forms. Using this modified bond order potential, we studied the structure and thermal properties (including thermal conductivity) of C60 crystal, and the elastic properties and plastic deformation processes of the single-walled and double-walled nanotubes. This extended bond order potential enables us to simulate large deformations of a nanotube under tensile and compressive loads. The basic formulation in this paper is transferable to other bond order potentials and traditional valence force fields.

Universal Correction of Density Functional Theory to Include London Dispersion (up to Lr, Element 103)

Kim, Hyungjun; Choi, Jeong-Mo; Goddard, William A., III
Fonte: American Chemical Society Publicador: American Chemical Society
Tipo: Article; PeerReviewed Formato: application/pdf
Publicado em 02/02/2012 Português
Relevância na Pesquisa
16.28%
Conventional density functional theory (DFT) fails to describe accurately the London dispersion essential for describing molecular interactions in soft matter (biological systems, polymers, nucleic acids) and molecular crystals. This has led to several methods in which atom-dependent potentials are added into the Kohn–Sham DFT energy. Some of these corrections were fitted to accurate quantum mechanical results, but it will be tedious to determine the appropriate parameters to describe all of the atoms of the periodic table. We propose an alternative approach in which a single parameter in the low-gradient (lg) functional form is combined with the rule-based UFF (universal force-field) nonbond parameters developed for the entire periodic table (up to Lr, Z = 103), named as a DFT-ulg method. We show that DFT-ulg method leads to a very accurate description of the properties for molecular complexes and molecular crystals, providing the means for predicting more accurate weak interactions across the periodic table.

An extended hybrid density functional (X3LYP) with improved descriptions of nonbond interactions and thermodynamic properties of molecular systems

Xu, Xin; Zhang, Qingsong; Muller, Richard P.; Goddard, William A., III
Fonte: Instituto de Tecnologia da Califórnia Publicador: Instituto de Tecnologia da Califórnia
Tipo: Article; PeerReviewed Formato: application/pdf
Publicado em 01/01/2005 Português
Relevância na Pesquisa
36.33%
We derive here the form for the exact exchange energy density for a density that decays with Gaussian-type behavior at long range. This functional is intermediate between the B88 and the PW91 exchange functionals. Using this modified functional to match the form expected for Gaussian densities, we propose the X3LYP extended functional. We find that X3LYP significantly outperforms Becke three parameter Lee–Yang–Parr (B3LYP) for describing van der Waals and hydrogen bond interactions, while performing slightly better than B3LYP for predicting heats of formation, ionization potentials, electron affinities, proton affinities, and total atomic energies as validated with the extended G2 set of atoms and molecules. Thus X3LYP greatly enlarges the field of applications for density functional theory. In particular the success of X3LYP in describing the water dimer (with Re and De within the error bars of the most accurate determinations) makes it an excellent candidate for predicting accurate ligand–protein and ligand–DNA interactions.

The X3LYP extended density functional for accurate descriptions of nonbond interactions, spin states, and thermochemical properties

Xu, Xin; Goddard, William A., III
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Article; PeerReviewed Formato: application/pdf
Publicado em 02/03/2004 Português
Relevância na Pesquisa
26.18%
We derive the form for an exact exchange energy density for a density decaying with Gaussian-like behavior at long range. Based on this, we develop the X3LYP (extended hybrid functional combined with Lee-Yang-Parr correlation functional) extended functional for density functional theory to significantly improve the accuracy for hydrogen-bonded and van der Waals complexes while also improving the accuracy in heats of formation, ionization potentials, electron affinities, and total atomic energies [over the most popular and accurate method, B3LYP (Becke three-parameter hybrid functional combined with Lee-Yang-Parr correlation functional)]. X3LYP also leads to a good description of dipole moments, polarizabilities, and accurate excitation energies from s to d orbitals for transition metal atoms and ions. We suggest that X3LYP will be useful for predicting ligand binding in proteins and DNA.

Doubly hybrid density functional for accurate descriptions of nonbond interactions, thermochemistry, and thermochemical kinetics

Zhang, Ying; Xu, Xin; Goddard, William A., III
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Article; PeerReviewed Formato: application/pdf; application/pdf
Publicado em 31/03/2009 Português
Relevância na Pesquisa
46.62%
We develop and validate a density functional, XYG3, based on the adiabatic connection formalism and the Görling–Levy coupling-constant perturbation expansion to the second order (PT2). XYG3 is a doubly hybrid functional, containing 3 mixing parameters. It has a nonlocal orbital-dependent component in the exchange term (exact exchange) plus information about the unoccupied Kohn–Sham orbitals in the correlation part (PT2 double excitation). XYG3 is remarkably accurate for thermochemistry, reaction barrier heights, and nonbond interactions of main group molecules. In addition, the accuracy remains nearly constant with system size.