Home About us Contact
|
Home About us Contact | ||
|
|
||
Reaction Coordinate (reaction + coordinate)
Kinds of Reaction Coordinate Selected AbstractsMultidimensional Reaction Coordinate for the Excited-state H-atom Transfer in Perylene Quinones: Importance of the 7-Membered Ring in Hypocrellins A and BPHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 2 2000Anindya Datta ABSTRACT The excited-state intramolecular H-atom transfer reactions of hypocrellins B and A are compared by using time-resolved absorption and fluorescence upconversion techniques. The hypocrellin B photophysics are well described by a simple model involving one ground-state species and excited-state forward and reverse H-atom transfer with a nonfluorescent excited state. We suggest that excited-state conformational changes are coupled to the H-atom transfer in hypocrellin B just as gauche/anti changes are coupled to the H-atom transfer in hypocrellin A. [source] Transition-State Energy and Position along the Reaction Coordinate in an Extended Activation Strain Model,CHEMPHYSCHEM, Issue 8 2007G. Theodoor de Jong Dr. Abstract We investigate palladium-induced activation of the CH, CC, CF, and CCl bonds in methane, ethane, cyclopropane, fluoromethane, and chloromethane, using relativistic density functional theory (DFT) at ZORA-BLYP/TZ2P. Our purpose is to arrive at a qualitative understanding, based on accurate calculations, of the trends in activation barriers and transition state (TS) geometries (e.g. early or late along the reaction coordinate) in terms of the reactants' properties. To this end, we extend the activation strain model (in which the activation energy ,E, is decomposed into the activation strain ,E,strain of the reactants and the stabilizing TS interaction ,E,int between the reactants) from a single-point analysis of the TS to an analysis along the reaction coordinate ,, that is, ,E(,)=,Estrain(,)+,Eint(,). This extension enables us to understand qualitatively, trends in the position of the TS along , and, therefore, the values of the activation strain ,E,strain=,Estrain(,TS) and TS interaction ,E,int=,Eint(,TS) and trends therein. An interesting insight that emerges is that the much higher barrier of metal-mediated CC versus CH activation originates from steric shielding of the CC bond in ethane by CH bonds. Thus, before a favorable stabilizing interaction with the CC bond can occur, the CH bonds must be bent away, which causes the metal,substrate interaction ,Eint(,) in CC activation to lag behind. Such steric shielding is not present in the metal-mediated activation of the CH bond, which is always accessible from the hydrogen side. Other phenomena that are addressed are anion assistance, competition between direct oxidative insertion (OxIn) versus the alternative SN2 pathway, and the effect of ring strain. [source] On the Enantioselectivity of Transition Metal-Catalyzed 1,3-Cycloadditions of 2-Diazocyclohexane-1,3-dionesHELVETICA CHIMICA ACTA, Issue 9 2003Paul Müller The formal 1,3-cycloaddition of 2-diazocyclohexane-1,3-diones 1a,1d to acyclic and cyclic enol ethers in the presence of RhII -catalysts to afford dihydrofurans has been investigated. Reaction with a cis/trans mixture of 1-ethoxyprop-1-ene (13a) yielded the dihydrofuran 14a with a cis/trans ratio of 85,:,15, while that with (Z)-1-ethoxy-3,3,3-trifluoroprop-1-ene (13b) gave the cis -product 14b exclusively. The stereochemical outcome of the reaction is consistent with a concerted rather than stepwise mechanism for cycloaddition. The asymmetric cycloaddition of 2-diazocyclohexane-1,3-dione (1a) or 2-diazodimedone (=2-diazo-5,5-dimethylcyclohexane-1,3-dione; 1b) to furan and dihydrofuran was investigated with a representative selection of chiral, nonracemic RhII catalysts, but no significant enantioselectivity was observed, and the reported enantioselective cycloadditions of these diazo compounds could not be reproduced. The absence of enantioselectivity in the cycloadditions of 2-diazocyclohexane-1,3-diones is tentatively explained in terms of the Hammond postulate. The transition state for the cycloaddition occurs early on the reaction coordinate owing to the high reactivity of the intermediate metallocarbene. An early transition state is associated with low selectivity. In contrast, the transition state for transfer of stabilized metallocarbenes occurs later, and the reactions exhibit higher selectivity. [source] A linear three-center four electron bonding identity nucleophilic substitution at carbon, boron, and phosphorus.INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 7 2010A theoretical study in combination with van't Hoff modeling Abstract We studied various identity nucleophilic substitution reactions based on an SN2 reaction profile. With calculations and experimental geometries concerning the nature of the various complexes indicated as stable, intermediate, and transition state we were able to show the additional value of van't Hoff 's tetrahedron by changing its geometry via a trigonal pyramid into a trigonal bipyramid. The ratio of the apical and the corresponding tetrahedral bond distance is then 1.333. This value has been used in general as a calibration point for the understanding of the (in)stabilities of the complex formation on the SN2 reaction coordinate. The relevance of this approach has been also proved for enzymatic reactions focused on carbon and phosphorus substrates. Furthermore, it could be established that identity proton-in-line displacements are fully comparable with the relocation of carbon in a nucleophilic substitution reaction as Cl, + CH3Cl. The significance of this information will afford new insight in the dynamics of a linear three-center four-electron complex. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Adiabatic decoupling of the reaction coordinateINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 10 2008J. C. Lorquet Abstract When the dynamics is constrained by adiabatic invariance, a reactive process can be described as a one-dimensional motion along the reaction coordinate in an effective potential. This simplification is often valid for central potentials and for the curved harmonic valley studied in the reaction path Hamiltonian model. For an ion,molecule reaction, the action integral ,P,, = (1/2,),P,d, is an adiabatic invariant. The Poisson bracket of ,P,,2 with Hamiltonians corresponding to a great variety of long-range electrostatic interactions is found to decrease with the separation coordinate r, faster than the corresponding potential. This indicates that the validity of the adiabatic approximation is not directly related to the shape of the potential energy surface. The leading role played by the translational momentum is accounted for by Jacobi's form of the least action principle. However, although the identification of adiabatic regions by this procedure is limited to a specific range of coordinate configurations, equivalent constraints must persist all along the reaction coordinate and must operate during the entire reaction, as a result of entropy conservation. The study of the translational kinetic energy released on the fragments is particularly appropriate to detect restrictions on energy exchange between the reaction coordinate and the bath of internal degrees of freedom. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Mechanisms and kinetics for preparing carbohydrazide by reacting dimethyl carbonate with hydrazine: A theoretical studyINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 9 2008Jianguo Zhang Abstract The mechanism and kinetic modeling for preparing carbohydrazide from dimethyl carbonate and hydrazine has been declared. The geometries of all the stationary points (reactants, intermediates, transition states, and products) are optimized by using the B3LYP method with the cc-pVDZ basis set, and the harmonic vibrational frequencies as well as infrared intensities are predicted with the same method. The minimum-energy paths are obtained by using the intrinsic reaction coordinate (IRC) theory at the B3LYP/cc-pVDZ level of theory with the step length 0.02 (amu)1/2·bohr. The rate constants are evaluated by using the TST, TST/Eckart, and RRKM (T)/Eckart methods. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Calculated spectral properties of perylene orange, perylene red, and their complex with sodium azideINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2007Anuar Aldongarov Abstract Using the method of density functional theory in approximating B3LYP with the basis set 6-31G(d) the computations of structures of the following dyes 2,2,- N - N,-di(1,3-diisopropylbenzene)-diimide 3,4,9,10-perylenetethracarbon acid (Perylene Orange-PO) and 1,6,7,12-tethraphenyl ether 2,2,- N,N,-di(1,3-diisopropylbenzene)-diimide 3,4,9,10-perylenetethracarbon acid (Perylene Red-PR) were performed. It was revealed that PO and PR have nonplanar structures. On the basis of the predicted geometrical structures and molecular orbitals of S0 ground state their theoretical UV-vis spectra, which are in good agreement with experiment, were obtained by applying time-dependent DFT (TDDFT) method. In addition, the calculations of complex [PR , NaN3] and its UV-vis spectrum, which was compared with the observed electron spectrum of PR ethanol solution in the presence of NaN3 under the laser irradiation at 532 nm, were carried out. By using DFT method at B3LYP level the calculations of the assumed complex were made where the reaction coordinate was the distance between Na+ and carbonyl group O atom. It was suggested that [PR , NaN3] complex formation involves transition of PR to the triplet state which brings about formation of PR anion. New peak at 793 nm in UV-vis spectrum of this solution under the laser irradiation at 532 nm is supposed to be a PR anion band. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] Charge and Mass Transfer Across the Metal/Solution InterfaceISRAEL JOURNAL OF CHEMISTRY, Issue 3-4 2008Eliezer Gileadi Electrode reactions are characterized by charge transfer across the interface. The charge can be carried by electrons or by ions. It is shown here that when both mass and charge cross the interface, the charge must be carried by the ionic species, not by the electrons, as a result of the very large difference in the time scale for electron and ion transfer. A prime example of charge transfer by ions is metal deposition. It is proposed that ion transfer occurs by migration of the ions across the interface, under the influence of the high electrostatic field in the double layer. The rate constants observed for metal deposition are comparable to those for outer-sphere charge transfer. These unexpectedly high rate constants for metal deposition are explained by a model in which removal of the solvation shell and reduction of the effective charge on the metal ion occur in many small steps, and a make-before-break mechanism exists, which lowers the total Gibbs energy of the system as it moves along the reaction coordinate from the initial to the final state. [source] Mode-selective stereomutation tunneling as compared to parity violation in hydrogen diselenide isotopomers 1,2,3H280Se2ISRAEL JOURNAL OF CHEMISTRY, Issue 3-4 2003Michael Gottselig We present quantitative calculations of the mode-selective stereomutation tunneling in the chiral hydrogen diselenide isotopomers X2Se2 with X = H, D, and T. The torsional tunneling stereomutation dynamics were investigated with a quasi-adiabatic channel quasi-harmonic reaction path Hamiltonian approach, which treats the torsional motion anharmonically in detail and all remaining coordinates as harmonic (but anharmonically coupled to the reaction coordinate). We also investigated the influence of the excitation of fundamental modes on the stereomutation dynamics and predict which modes should be promoting or inhibiting. Our stereomutation dynamics results and the influence of parity violation on these are discussed in relation to our recent investigations for the analogous molecules H2O2, HSOH, H2S2, and Cl2S2. The electronic potential energy barrier heights for the torsional motion of hydrogen diselenide are similar to those of HSOH, whereas the torsional tunneling splittings are similar to the corresponding values of HSSH. The ground-state torsional tunneling splittings calculated here for D2Se2 are of the same order as the parity-violating energy difference reported by Laerdahl and Schwerdtfeger (Phys. Rev. A 1999, 60, 4439), whereas for T2Se2 the corresponding tunneling splitting is about three orders of magnitude smaller. [source] Application of QM simulations and multivariate analysis in the study of alkene reactivity in the zeolite H-ZSM5JOURNAL OF CHEMOMETRICS, Issue 6 2008Duangkamol Gleeson Abstract Reported herein are the results of an investigation into the effect of the extended framework of the zeolite ZSM-5 on the reaction energetics and structures of (a) the physisorbed complex formed between the zeolite and six alkenes, (b) the corresponding chemisorbed alkoxide intermediate and (c) the transition states (TS) connecting the two. For this, quantum mechanical (QM) simulations of ZSM-5 in the presence and absence of the zeolite framework have been employed. A 46T density functional theory (DFT) cluster model and a 3T:46T DFT:UFF ONIOM model are used to represent the former scenario and a simple 3T DFT cluster model for the latter. The structural implications of neglecting the zeolite framework have been rigorously compared using the multivariate statistical method principal components analysis (PCA). This method allows one to assess the correlated nature of the changes in structure along the reaction coordinate, for multiple different alkenes, in a facile, reliable way. Copyright © 2008 John Wiley & Sons, Ltd. [source] Formation of 8-nitroguanine and 8-oxoguanine due to reactions of peroxynitrite with guanineJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2007N. R. Jena Abstract Reactions of peroxynitrite with guanine were investigated using density functional theory (B3LYP) employing 6-31G** and AUG-cc-pVDZ basis sets. Single point energy calculations were performed at the MP2/AUG-cc-pVDZ level. Genuineness of the calculated transition states (TS) was tested by visually examining the vibrational modes corresponding to the imaginary vibrational frequencies and applying the criterion that the TS properly connected the reactant and product complexes (PC). Genuineness of all the calculated TS was further ensured by intrinsic reaction coordinate (IRC) calculations. Effects of aqueous media were investigated by solvating all the species involved in the reactions using the polarizable continuum model (PCM). The calculations reveal that the most stable nitro-product complex involving the anion of 8-nitroguanine and a water molecule i.e. 8NO2G, + H2O can be formed according to one reaction mechanism while there are two possible reaction mechanisms for the formation of the oxo-product complex involving 8-oxoguanine and anion of the NO2 group i.e. 8OG + NO2,. The calculated relative stabilities of the PC, barrier energies of the reactions and the corresponding enthalpy changes suggest that formation of the complex 8OG + NO2, would be somewhat preferred over that of the complex 8NO2G, + H2O. The possible biological implications of this result are discussed. © 2007 Wiley Periodicals, Inc. J Comput Chem 2007 [source] Ab initio investigation on the reaction path and rate for the gas-phase reaction of HO + H2O , H2O + OHJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2003Tadafumi Uchimaru Abstract This article describes an ab initio investigation on the potential surfaces for one of the simplest hydrogen atom abstraction reactions, that is, HO + H2O , H2O + OH. In accord with the findings in the previously reported theoretical investigations, two types of the hydrogen-bonding complexes [HOHOH] and [H2OHO] were located on the potential energy surface. The water molecule acts as a hydrogen donor in the [HOHOH] complex, while the OH radical acts as a hydrogen donor in the [H2OHO] complex. The energy evaluations at the MP2(FC) basis set limit, as well as those through the CBS-APNO procedure, have provided estimates for enthalpies of association for these complexes at 298 K as ,2.1 , ,2.3 and ,4.1 , ,4.3 kcal/mol, respectively. The IRC calculations have suggested that the [H2OHO] complex should be located along the reaction coordinate for the hydrogen abstraction. Our best estimate for the classical barrier height for the hydrogen abstraction is 7.8 kcal/mol, which was obtained from the CBS-APNO energy evaluations. After fitting the CBS-APNO potential energy curve to a symmetrical Eckart function, the rate constants were calculated by using the transition state theory including the tunneling correction. Our estimates for the Arrhenius parameters in the temperature region from 300 to 420 K show quite reasonable agreement with the experimentally derived values. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1538,1548, 2003 [source] A computational study of conformational interconversions in 1,4-dithiacyclohexane (1,4-dithiane)JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2003Fillmore Freeman Abstract Ab initio molecular orbital theory with the 6-31G(d), 6-31G(d,p), 6-31+G(d), 6-31+G(d,p), 6-31+G(2d,p), 6-311G(d), 6-311G(d,p), and 6-311+G(2d,p) basis sets and density functional theory (BLYP, B3LYP, B3P86, B3PW91) have been used to locate transition states involved in the conformational interconversions of 1,4-dithiacyclohexane (1,4-dithiane) and to calculate the geometry optimized structures, relative energies, enthalpies, entropies, and free energies of the chair and twist conformers. In the chair and 1,4-twist conformers the CHax and CHeq bond lengths are equal at each carbon, which suggest an absence of stereoelectronic hyperconjugative interactions involving carbon,hydrogen bonds. The 1,4-boat transition state structure was 9.53 to 10.5 kcal/mol higher in energy than the chair conformer and 4.75 to 5.82 kcal/mol higher in energy than the 1,4-twist conformer. Intrinsic reaction coordinate (IRC) calculations showed that the 1,4-boat transition state structure was the energy maximum in the interconversion of the enantiomers of the 1,4-twist conformer. The energy difference between the chair conformer and the 1,4-twist conformer was 4.85 kcal/mol and the chair-1,4-twist free energy difference (,G°c-t) was 4.93 kcal/mol at 298.15 K. Intrinsic reaction coordinate (IRC) calculations connected the transition state between the chair conformer and the 1,4-twist conformer. This transition state is 11.7 kcal/mol higher in energy than the chair conformer. The effects of basis sets on the 1,4-dithiane calculations and the relative energies of saturated and unsaturated six-membered dithianes and dioxanes are also discussed. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 909,919, 2003 [source] The mechanism of alkaline hydrolysis of amides: a comparative computational and experimental study of the hydrolysis of N -methylacetamide, N -methylbenzamide, and acetanilideJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 6 2009Diana Cheshmedzhieva Abstract Theoretical computations and experimental kinetic measurements were applied in studying the mechanistic pathways for the alkaline hydrolysis of three secondary amides: N -methylbenzamide, N -methylacetamide, and acetanilide. Electronic structure methods at the HF/6-31+G(d,p) and B3LYP/6-31+G(d,p) levels of theory are employed. The energies of the stationary points along the reaction coordinate were further refined via single point computations at the MP2/6-31+G(d,p) and MP2/6-311++G(2d,2p) levels of theory. The role of water in the reaction mechanisms is examined. The theoretical results show that in the cases of N -methylbenzamide and N -methylacetamide the process is catalyzed by an ancillary water molecule. The influence of water is further assessed by predicting its role as bulk solvent. The alkaline hydrolysis process in aqueous solution is characterized by two distinct free energy barriers: the formation of a tetrahedral adduct and its breaking to products. The results show that the rate-determining stage of the process is associated with the second transition state. The entropy terms evaluated from theoretical computations referring to gas-phase processes are significantly overestimated. The activation barriers for the alkaline hydrolysis of N -methylbenzamide and acetanilide were experimentally determined. Quite satisfactory agreement between experimental values and computed activation enthalpies was obtained. Copyright © 2008 John Wiley & Sons, Ltd. [source] A chemical understanding for the enhanced hydrogen tunnelling in hydroperoxidation of linoleic acid catalysed by soybean lipoxygenase-1JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 7-8 2008Monica Barroso Abstract The reaction path of the Interacting-State Model (ISM) is used with the Transition-State Theory (TST) and the semiclassical correction for tunnelling (ISM/scTST) to calculate the rates of H-atom abstraction from C(11) of linoleic acid catalysed by soybean lipoxygenase-1 (SLO), as well as of an analogous uncatalysed reaction in solution. The calculated hydrogen-atom transfer rates, their temperature dependency and kinetic isotope effect (KIE) are in good agreement with the experimental data. ISM/scTST calculations reveal the hypersensitivity of the rate to protein dynamics when the hydrogen bonding to a carbon atom is present in the reaction coordinate. Copyright © 2008 John Wiley & Sons, Ltd. [source] Computational study of the chair,chair interconversion and stereoelectronic interactions in 1,2,3-trithiacyclo-hexane (1,2,3-trithiane)JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 1 2004Fillmore Freeman Abstract Ab initio theory, density functional theory (DFT) and Møller,Plesset perturbation theory (MP2) with the 6,31G(d), 6,31++G(d), 6,31G(d,p), 6,31+G(d,p), 6,31++G(d,p), 6,311G(d,p) and 6,311+G(d,p) basis sets were used to study stereoelectronic hyperconjugative interactions and the mechanism of the chair,chair conformational interconversion in 1,2,3-trithiacyclohexane (1,2,3-trithiane). The relative energies, enthalpies, entropies, free energies and structural parameters of the chair, 1,4-twist and 2,5-twist conformers, a distorted 1,4-boat transition state and a 2,5-boat transition state were calculated. The HF calculated energy difference (,E) between the chair conformer of 1,2,3-trithiane and the distorted 1,4-boat transition state was 10.59,kcal,mol,1 (1 kcal=4.184,kJ). The 1,4-twist conformer and the 2,5-boat transition state are close in energy, as are the 2,5-twist conformer and the distorted 1,4-boat transition state. B3LYP/6,311+G(d,p) calculated the chair conformer of 1,2,3-trithiane to be 5.83, 10.09, and 5.96,kcal,mol,1, respectively, lower in energy than the 1,4-twist conformer, 2,5-twist conformer and 2,5-boat transition state. Intrinsic reaction coordinate (IRC) calculations were used to connect the transition state between the chair conformer and the 1,4-twist conformer. B3LYP/6,31+G(d,p) and B3LYP/6,311+G(d,p) calculated this transition state to be 14.25,kcal,mol,1 higher in energy than the chair conformer. In the chair conformer, the respective C4,H and C6,H bond lengths are equal, but the C5,Heq bond is longer than the C5,Hax bond. In the 1,4-twist conformer, the C4,Hiso bond lengths are equal, the C5,H,eq bond is longer than the C5,H,ax bond and the C6,H bond lengths are equal. In the 2,5-twist conformer, equal C,H bond lengths are found at C4 and at C5, but the C6,H,eq bond is longer than the C6,H,ax bond. Copyright © 2003 John Wiley & Sons, Ltd. Additional material for this paper is available in Wiley Intersciene [source] Efficient Intramolecular Hydroalkoxylation of Unactivated Alkenols Mediated by Recyclable Lanthanide Triflate Ionic Liquids: Scope and MechanismCHEMISTRY - A EUROPEAN JOURNAL, Issue 11 2010Alma Dzudza Dr. Abstract Lanthanide triflate complexes of the type [Ln(OTf)3] (Ln=La, Sm, Nd, Yb, Lu) serve as effective, recyclable catalysts for the rapid intramolecular hydroalkoxylation (HO)/cyclization of primary/secondary and aliphatic/aromatic hydroxyalkenes in imidazolium-based room-temperature ionic liquids (RTILs) to yield the corresponding furan, pyran, spirobicyclic furan, spirobicyclic furan/pyran, benzofuran, and isochroman derivatives. Products are straightforwardly isolated from the catalytic solution, conversions exhibit Markovnikov regioselectivity, and turnover frequencies are as high as 47,h,1 at 120,°C. The ring-size rate dependence of the primary alkenol cyclizations is 5>6, consistent with a sterically controlled transition state. The hydroalkoxylation/cyclization rates of terminal alkenols are slightly more rapid than those of internal alkenols, which suggests modest steric demands in the cyclic transition state. Cyclization rates of aryl-functionalized hydroxyalkenes are more rapid than those of the linear alkenols, whereas five- and five/six-membered spirobicyclic skeletons are also regioselectively closed. In cyclization of primary, sterically encumbered alkenols, turnover-frequency dependence on metal-ionic radius decreases by approximately 80-fold on going from La3+ (1.160,Å) to Lu3+ (0.977,Å), presumably reflecting steric impediments along the reaction coordinate. The overall rate law for alkenol hydroalkoxylation/cyclization is v,k[catalyst]1[alkenol]1. An observed ROH/ROD kinetic isotope effect of 2.48 (9) is suggestive of a catalytic pathway that involves kinetically significant intramolecular proton transfer. The present activation parameters,enthalpy (,H,)=18.2 (9),kcal,mol,1, entropy (,S,)=,17.0 (1.4),eu, and energy (Ea)=18.2 (8),kcal,mol,1,suggest a highly organized transition state. Proton scavenging and coordinative probing results suggest that the lanthanide triflates are not simply precursors of free triflic acid. Based on the kinetic and mechanistic evidence, the proposed catalytic pathway invokes hydroxyl and olefin activation by the electron-deficient Ln3+ center, and intramolecular H+ transfer, followed by alkoxide nucleophilic attack with ring closure. [source] Transport Processes at ,-Quartz,Water Interfaces: Insights from First-Principles Molecular Dynamics SimulationsCHEMPHYSCHEM, Issue 7 2008Waheed A. Adeagbo Dr. Abstract Car,Parrinello molecular dynamics (CP,MD) simulations are performed at high temperature and pressure to investigate chemical interactions and transport processes at the ,-quartz,water interface. The model system initially consists of a periodically repeated quartz slab with O-terminated and Si-terminated (1000) surfaces sandwiching a film of liquid water. At a temperature of 1000 K and a pressure of 0.3 GPa, dissociation of H2O molecules into H+ and OH, is observed at the Si-terminated surface. The OH, fragments immediately bind chemically to the Si-terminated surface while Grotthus-type proton diffusion through the water film leads to protonation of the O-terminated surface. Eventually, both surfaces are fully hydroxylated and no further chemical reactions are observed. Due to the confinement between the two hydroxylated quartz surfaces, water diffusion is reduced by about one third in comparison to bulk water. Diffusion properties of dissolved SiO2 present as Si(OH)4 in the water film are also studied. We do not observe strong interactions between the hydroxylated quartz surfaces and the Si(OH)4 molecule as would have been indicated by a substantial lowering of the Si(OH)4 diffusion coefficient along the surface. No spontaneous dissolution of quartz is observed. To study the mechanism of dissolution, constrained CP,MD simulations are done. The associated free energy profile is calculated by thermodynamic integration along the reaction coordinate. Dissolution is a stepwise process in which two SiO bonds are successively broken. Each bond breaking between a silicon atom at the surface and an oxygen atom belonging to the quartz lattice is accompanied by the formation of a new SiO bond between the silicon atom and a water molecule. The latter loses a proton in the process which eventually leads to protonation of the oxygen atom in the cleaved quartz SiO bond. The final solute species is Si(OH)4. [source] Transition-State Energy and Position along the Reaction Coordinate in an Extended Activation Strain Model,CHEMPHYSCHEM, Issue 8 2007G. Theodoor de Jong Dr. Abstract We investigate palladium-induced activation of the CH, CC, CF, and CCl bonds in methane, ethane, cyclopropane, fluoromethane, and chloromethane, using relativistic density functional theory (DFT) at ZORA-BLYP/TZ2P. Our purpose is to arrive at a qualitative understanding, based on accurate calculations, of the trends in activation barriers and transition state (TS) geometries (e.g. early or late along the reaction coordinate) in terms of the reactants' properties. To this end, we extend the activation strain model (in which the activation energy ,E, is decomposed into the activation strain ,E,strain of the reactants and the stabilizing TS interaction ,E,int between the reactants) from a single-point analysis of the TS to an analysis along the reaction coordinate ,, that is, ,E(,)=,Estrain(,)+,Eint(,). This extension enables us to understand qualitatively, trends in the position of the TS along , and, therefore, the values of the activation strain ,E,strain=,Estrain(,TS) and TS interaction ,E,int=,Eint(,TS) and trends therein. An interesting insight that emerges is that the much higher barrier of metal-mediated CC versus CH activation originates from steric shielding of the CC bond in ethane by CH bonds. Thus, before a favorable stabilizing interaction with the CC bond can occur, the CH bonds must be bent away, which causes the metal,substrate interaction ,Eint(,) in CC activation to lag behind. Such steric shielding is not present in the metal-mediated activation of the CH bond, which is always accessible from the hydrogen side. Other phenomena that are addressed are anion assistance, competition between direct oxidative insertion (OxIn) versus the alternative SN2 pathway, and the effect of ring strain. [source] Theoretical Studies on the Isomerizations of CH3NO2CHINESE JOURNAL OF CHEMISTRY, Issue 6 2009Lijuan YANG Abstract The isomerizations of CH3NO2 (NM) have been investigated by density function theory (DFT) and electron density topological analysis methods. Nine isomers and eight isomerization channels were found. The connection relationship between the transition state (TS) and the isomers was confirmed by intrinsic reaction coordinate (IRC) tracing calculation. The calculation results show that in the CH3NO2,CH3ONOt process, the TS is a tight one (CH3NO2 does not break into CH3 and NO2 throughout the reaction), which is consistent with Arenass' results. A long structure transition region, which contains a four-numbered ring , a five-numbered ring , a four-numbered ring , a five-numbered ring structure, exists in CH3NOOc,CH2NOOH process. And it is the first time that a five-numbered ring TS was found in reaction. [source] The existence of secondary orbital interactionsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2007Chaitanya S. Wannere Abstract B3LYP/6-311+G** (and MP2/6-311+G**) computations, performed for a series of Diels-Alder (DA) reactions, confirm that the endo transition states (TS) and the related Cope-TSs are favored energetically over the respective exo -TSs. Likewise, the computed magnetic properties (nucleus-independent chemical shifts and magnetic susceptibililties) of the endo - (as well as the Cope) TS's reveal their greater electron delocalization and greater aromaticity than the exo -TS's. However, Woodward and Hoffmann's original example is an exception: their endo -TS model, involving the DA reaction of a syn - with an anti -butadiene (BD), actually is disfavored energetically over the corresponding exo -TS; magnetic criteria also do not indicate the existence of SOI delocalization in either case. Instead, a strong energetic preference for endo -TSs due to SOI is found when both BDs are in the syn conformations. This is in accord with Alder and Stein's rule of "maximum accumulation of double bonds:" both the dienophile and the diene should have syn conformations. Plots along the IRC's show that the magnetic properties typically are most strongly exalted close to the energetic TS. Because of SOI, all the points along the endo reaction coordinates are more diatropic than along the corresponding exo pathways. We find weak SOI effects to be operative in the endo -TSs involved in the cycloadditions of cyclic alkenes, cyclopropene, aziridine, cyclobutene, and cyclopentene, with cyclopentadiene. While the endo -TSs are only slightly lower in energy than the respective exo -TSs, the magnetic properties of the endo -TS's are significantly exalted over those for the exo -TS's and the Natural Bond Orbitals indicate small stabilizing interactions between the methylene cycloalkene hydrogen orbitals (and lone pairs in case of aziridine) with ,-character and the diene , MOs. © 2006 Wiley Periodicals, Inc. J Comput Chem 2007 [source] Systematic and statistical error in histogram-based free energy calculationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2003Mark N. Kobrak Abstract A common technique for the numerical calculation of free energies involves estimation of the probability density along a given coordinate from a set of configurations generated via simulation. The process requires discretization of one or more reaction coordinates to generate a histogram from which the continuous probability density is inferred. We show that the finite size of the intervals used to construct the histogram leads to quantifiable systematic error. The width of these intervals also determines the statistical error in the free energy, and the choice of the appropriate interval is therefore driven by the need to balance the two sources of error. We present a method for the construction of the optimal histogram for a given system, and show that the use of this technique requires little additional computational expense. We demonstrate the efficacy of the technique for a model system, and discuss how the principles governing the choice of discretization interval could be used to improve extended sampling techniques. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1437,1446, 2003 [source] Resonance Raman spectra and excited state structural dynamics of ethylene trithiocarbonate in the A - and B -band absorptionsJOURNAL OF RAMAN SPECTROSCOPY, Issue 9 2009Huigang Wang Abstract A - and B -band resonance Raman spectra were acquired for ethylene trithiocarbonate in cyclohexane solution. The results indicate that the S3 state structural dynamics is mostly along vibrational motions of the CS stretch ,11, while the S4 state one has motions mainly via the SCS symmetric stretch ,18, CS stretch ,11, and the HCH rock + SCS antisymmetric stretch ,14 reaction coordinates. The very different excited state structural dynamics were briefly discussed in terms of vibronic couplings using local symmetry point group. Copyright © 2009 John Wiley & Sons, Ltd. [source] Mass spectrometric characterization of 4-oxopentanoic acid and gas-phase ion fragmentation mechanisms studied using a triple quadrupole and time-of-flight analyzer hybrid system and density functional theoryRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 14 2008Basem Kanawati 4-Oxopentanoic acid was characterized experimentally by electrospray ionization using a triple quadrupole and time-of-flight analyzer hybrid system. This compound was chosen as a model substance for small organic compounds bearing an acetyl and a carboxyl group. Collision-induced dissociation experiments at different activation energies were performed to elucidate possible fragmentation pathways. These pathways were also studied on the theoretical level using density functional theory (DFT) B3LYP/6-311++G(3df,3pd)//B3LYP/6-31+G(d)+ZPVE calculations. CO2 ejection from the [M,H], anion of 4-oxopentanoic acid was observed and the fragmentation pathway studied by DFT reveals a new concerted mechanism for CO2 elimination accompanied by an intramolecular proton transfer within a pentagonal transition state structure. Successive elimination of water and CO from the [M,H], anion of 4-oxopentanoic acid was also observed. A rearrangement in the primary deprotonated ketene anion produced after water elimination was found on the theoretical level and leads to CO elimination from the primary product anion [M,H,H2O],. Energy diagrams along the reaction coordinates of the fragmentation pathways are presented and discussed in detail. Mulliken charge distributions of some important structures are presented. Copyright © 2008 John Wiley & Sons, Ltd. [source] | ||||||||||||||||||||||