Alexis T Bell

Publications of Alexis T Bell

• Efficient exploration of reaction paths via a freezing string method.

  Authors: Andrew Behn, Paul M Zimmerman, Alexis T Bell, Martin Head-Gordon

  The Journal of chemical physics. 12/2011; 135(22):224108.

  The ability to efficiently locate transition states is critically important to the widespread adoption of theoretical chemistry techniques for their ability to accurately predict kinetic constants.The ability to efficiently locate transition states is critically important to the widespread adoption of theoretical chemistry techniques for their ability to accurately predict kinetic constants. Existing surface walking techniques to locate such transition states typically require an extremely good initial guess that is often beyond human intuition to estimate. To alleviate this problem, automated techniques to locate transition state guesses have been created that take the known reactant and product endpoint structures as inputs. In this work, we present a simple method to build an approximate reaction path through a combination of interpolation and optimization. Starting from the known reactant and product structures, new nodes are interpolated inwards towards the transition state, partially optimized orthogonally to the reaction path, and then frozen before a new pair of nodes is added. The algorithm is stopped once the string ends connect. For the practical user, this method provides a quick and convenient way to generate transition state structure guesses. Tests on three reactions (cyclization of cis,cis-2,4-hexadiene, alanine dipeptide conformation transition, and ethylene dimerization in a Ni-exchanged zeolite) show that this "freezing string" method is an efficient way to identify complex transition states with significant cost savings over existing methods, particularly when high quality linear synchronous transit interpolation is employed.

• Comparison of cobalt-based nanoparticles as electrocatalysts for water oxidation.

  Authors: Nam Hawn Chou, Philip N Ross, Alexis T Bell, T Don Tilley

  ChemSusChem. 11/2011; 4(11):1566-9.

• A study of the acid-catalyzed hydrolysis of cellulose dissolved in ionic liquids and the factors influencing the dehydration of glucose and the formation of humins.

  Authors: Sean J Dee, Alexis T Bell

  ChemSusChem. 08/2011; 4(8):1166-73.

  An investigation was carried out into the hydrolysis of cellulose dissolved in 1-ethyl-3-methylimidazolium chloride ([Emim][Cl]) and 1-butyl-3-methylimidazolium chloride ([Bmim][Cl]) catalyzed byAn investigation was carried out into the hydrolysis of cellulose dissolved in 1-ethyl-3-methylimidazolium chloride ([Emim][Cl]) and 1-butyl-3-methylimidazolium chloride ([Bmim][Cl]) catalyzed by mineral acids. Glucose, cellobiose, and 5-hydroxymethylfurfural (5-HMF) were observed as the primary reaction products. The initial rate of glucose formation was determined to be of first order in the concentrations of dissolved glucan and protons and of zero order in the concentration of water. The absence of a dependence on water concentration suggests that cleavage of the β-1,4-glycosidic linkages near chain ends is irreversible. The apparent activation energy for glucose formation is 96 kJ mol(-1). The absence of oligosaccharides longer than cellobiose suggests that cleavage of interior glycosidic bonds is reversible due to the slow diffusional separation of cleaved chains in the highly viscous glucan/ionic liquid solution. Progressive addition of water during the course of glucan hydrolysis inhibited the rate of glucose dehydration to 5-HMF and the formation of humins. The inhibition of glucose dehydration is attributed to stronger interaction of protons with water than the 2-OH atom of the pyranose ring of glucose, the critical step in the proposed mechanism for the formation of 5-HMF. The reduction in humin formation associated with water addition is ascribed to the lowered concentration of 5-HMF, since the formation of humins is suggested to proceed through the condensation polymerization of 5-HMF with glucose.

• Enhanced activity of gold-supported cobalt oxide for the electrochemical evolution of oxygen.

  Authors: Boon Siang Yeo, Alexis T Bell

  Journal of the American Chemical Society. 03/2011; 133(14):5587-93.

  Scanning electron microscopy, linear sweep voltammetry, chronoamperometry, and in situ surface-enhanced Raman spectroscopy were used to investigate the electrochemical oxygen evolution reaction (OER)Scanning electron microscopy, linear sweep voltammetry, chronoamperometry, and in situ surface-enhanced Raman spectroscopy were used to investigate the electrochemical oxygen evolution reaction (OER) occurring on cobalt oxide films deposited on Au and other metal substrates. All experiments were carried out in 0.1 M KOH. A remarkable finding is that the turnover frequency for the OER exhibited by ∼0.4 ML of cobalt oxide deposited on Au is 40 times higher than that of bulk cobalt oxide. The activity of small amounts of cobalt oxide deposited on Pt, Pd, Cu, and Co decreased monotonically in the order Au > Pt > Pd > Cu > Co, paralleling the decreasing electronegativity of the substrate metal. Another notable finding is that the OER turnover frequency for ∼0.4 ML of cobalt oxide deposited on Au is nearly three times higher than that for bulk Ir. Raman spectroscopy revealed that the as-deposited cobalt oxide is present as Co(3)O(4) but undergoes progressive oxidation to CoO(OH) with increasing anodic potential. The higher OER activity of cobalt oxide deposited on Au is attributed to an increase in fraction of the Co sites present as Co(IV) cations, a state of cobalt believed to be essential for OER to occur. A hypothesis for how Co(IV) cations contribute to OER is proposed and discussed.

• Quantum mechanical modeling of catalytic processes.

  Authors: Alexis T Bell, Martin Head-Gordon

  Annual review of chemical and biomolecular engineering. 01/2011; 2:453-77.

  Advances in quantum chemical methods in combination with exponential growth in the computational speed of computers have enabled researchers in the field of catalysis to apply electronic structureAdvances in quantum chemical methods in combination with exponential growth in the computational speed of computers have enabled researchers in the field of catalysis to apply electronic structure calculations to a wide variety of increasingly complex problems. Such calculations provide insights into why and how changes in the composition and structure of catalytically active sites affect their activity and selectivity for targeted reactions. The aim of this review is to survey the recent advances in the methods used to make quantum chemical calculations and to define transition states as well as to illustrate the application of these methods to a selected series of examples taken from the authors' recent work.

• Quantum chemical modeling of benzene ethylation over H-ZSM-5 approaching chemical accuracy: a hybrid MP2:DFT study.

  Authors: Niels Hansen, Torsten Kerber, Joachim Sauer, Alexis T Bell, Frerich J Keil

  Journal of the American Chemical Society. 08/2010; 132(33):11525-38.

  The alkylation of benzene by ethene over H-ZSM-5 is analyzed by means of a hybrid MP2:DFT scheme. Density functional calculations applying periodic boundary conditions (PBE functional) are combinedThe alkylation of benzene by ethene over H-ZSM-5 is analyzed by means of a hybrid MP2:DFT scheme. Density functional calculations applying periodic boundary conditions (PBE functional) are combined with MP2 energy calculations on a series of cluster models of increasing size which allows extrapolation to the periodic MP2 limit. Basis set truncation errors are estimated by extrapolation of the MP2 energy to the complete basis set limit. Contributions from higher-order correlation effects are accounted for by CCSD(T) coupled cluster calculations. The sum of all contributions provides the "final estimates" for adsorption energies and energy barriers. Dispersion contributes significantly to the potential energy surface. As a result, the MP2:DFT potential energy profile is shifted downward compared to the PBE profile. More importantly, this shift is not the same for reactants and transition structures due to different self-interaction correction errors. The final enthalpies for ethene, benzene, and ethylbenzene adsorption on the Brønsted acid site at 298 K are -46, -78, and -110 kJ/mol, respectively. The intrinsic enthalpy barriers at 653 K are 117 and 119/94 kJ/mol for the one- and two-step alkylation, respectively. Intrinsic rate coefficients calculated by means of transition state theory are converted to apparent Arrhenius parameters by means of the multicomponent adsorption equilibrium. The simulated apparent activation energy (66 kJ/mol) agrees with experimental data (58-76 kJ/mol) within the uncertainty limit of the calculations. Adsorption energies obtained by adding a damped dispersion term to the PBE energies (PBE+D), agree within +/-7 kJ/mol, with the "final estimates", except for physisorption (pi-complex formation) and chemisorption of ethene (ethoxide formation) for which the PBE+D energies are 12.4 and 26.0 kJ/mol, respectively larger than the "final estimates". For intrinsic energy barriers, the PBE+D approach does not improve pure PBE results.

• Improved United-Atom Force Field for 1-Alkyl-3-methylimidazolium Chloride.

  Authors: Zhiping Liu, Ting Chen, Alexis T Bell, Berend Smit

  The journal of physical chemistry. B. 08/2010; 114(32):10692.

• Identification of hydroperoxy species as reaction intermediates in the electrochemical evolution of oxygen on gold.

  Authors: Boon Siang Yeo, Shannon L Klaus, Philip N Ross, Richard A Mathies, Alexis T Bell

  Chemphyschem : a European journal of chemical physics and physical chemistry. 06/2010; 11(9):1854-7.

• Viscosities of the mixtures of 1-ethyl-3-methylimidazolium chloride with water, acetonitrile and glucose: a molecular dynamics simulation and experimental study.

  Authors: Ting Chen, Mandan Chidambaram, Zhiping Liu, Berend Smit, Alexis T Bell

  The journal of physical chemistry. B. 04/2010; 114(17):5790-4.

  A recently improved ionic liquid force field was used to compute the viscosity for binary and ternary mixtures of 1-ethyl-3-methylimidazolium chloride ([emim][Cl]) with water, acetonitrile, andA recently improved ionic liquid force field was used to compute the viscosity for binary and ternary mixtures of 1-ethyl-3-methylimidazolium chloride ([emim][Cl]) with water, acetonitrile, and glucose. For the same systems, experimental viscosity data are provided. The simulation and experimental results were in reasonable agreement. Simulations consistently overestimate the viscosities for the mixtures of [emim][Cl] and glucose while the viscosities of the mixtures of glucose and water are well reproduced. Both experiments and simulations show that the addition of acetonitrile reduces the viscosity of a solution of [emim][Cl] and glucose by more than an order of magnitude.

• Are pressure fluctuation-based equilibrium methods really worse than nonequilibrium methods for calculating viscosities?

  Authors: Ting Chen, Berend Smit, Alexis T Bell

  The Journal of chemical physics. 12/2009; 131(24):246101.

• Spectroscopic investigation of the species involved in the rhodium-catalyzed oxidative carbonylation of toluene to toluic acid.

  Authors: Joseph Zakzeski, Sarah Burton, Andrew Behn, Martin Head-Gordon, Alexis T Bell

  Physical chemistry chemical physics : PCCP. 11/2009; 11(42):9903-11.

  A spectroscopic investigation of complexes used to catalyze the oxidative carbonylation of toluene to p-toluic acid was conducted. Rhodium complexes were analyzed by (103)Rh and (13)C NMR, UV-visibleA spectroscopic investigation of complexes used to catalyze the oxidative carbonylation of toluene to p-toluic acid was conducted. Rhodium complexes were analyzed by (103)Rh and (13)C NMR, UV-visible spectroscopy, and infrared spectroscopy. In the presence of vanadium and oxygen, the resting state of the Rh-catalyst was found to exist as a Rh(iii) complex with carbonyl and trifluoroacetate ligands, consistent with the structure Rh(CO)(2)(TFA)(3). The (13)C NMR spectrum of Rh((13)CO)(2)(TFA)(3) complex exhibited a carbonyl peak with an unusual degree of shielding, which resulted in the appearance of the carbonyl peak at an unprecedented upfield position in the (13)C NMR spectrum. This shielding was caused by interaction of the carbonyl group with the trifluoroacetate ligand. In the absence of oxygen, the Rh(iii) complex reduced to Rh(i), and the reduced form exhibited properties resembling the catalyst precursor. Structures and spectroscopic properties calculated using density functional theory agreed closely with the experimental results. The vanadium co-catalyst used to reoxidize Rh(i) to Rh(iii) was similarly characterized by (51)V NMR and UV-visible spectroscopy. The oxidized species corresponded to [(VO(2))(TFA)](2), whereas the reduced species corresponded to (VO)(TFA)(2). The spectroscopic results obtained in this study confirm the identity of the species that have been proposed to be involved in the Rh-catalyzed oxidative carbonylation of toluene to toluic acid.

• Effects of Ligand Composition on the Oxidative Carbonylation of Toluene to Toluic Acid Catalyzed by Rh(III) Complexes.

  Authors: Joseph Zakzeski, Andrew Behn, Martin Head-Gordon, Alexis T Bell

  Journal of the American Chemical Society. 08/2009;

  Experimental and theoretical studies were conducted to investigate the influence of anionic ligands (e.g., CF(3)COO(-), CH(3)SO(3)(-)) on the catalytic activity and selectivity of Rh(III) in theExperimental and theoretical studies were conducted to investigate the influence of anionic ligands (e.g., CF(3)COO(-), CH(3)SO(3)(-)) on the catalytic activity and selectivity of Rh(III) in the oxidative carbonylation of toluene to toluic acid. The catalyst activity was found to pass through a maximum as the pK(a) of the conjugate Brønsted acid decreases from 4.63 to -2.00, with the maximum activity occurring at pK(a) = 0.35, corresponding to CClF(2)COOH. The theoretical analysis showed that the strength of toluene coordination increases with decreasing basicity of the anion (i.e., decreasing pK(a) of the corresponding acid). In contrast, the activation barrier for C-H activation increases with decreasing ligand pK(a). The experimentally observed effect of anion composition on catalyst activity can be explained using calculations of the apparent rate coefficient for toluene activation based on density functional theory and transition state theory. The ratio of p- to m-toluic acid formed increases with decreasing acid pK(a) and passes through a maximum for pK(a) = 0, corresponding to CF(3)COOH. The effect of anion composition on the isomer selectivity is attributed to changes in the charge density on the Rh(III) cation, which in turn affect the distribution of charge on the para and meta carbon atoms of the aromatic ring.

• Transition state-finding strategies for use with the growing string method.

  Authors: Anthony Goodrow, Alexis T Bell, Martin Head-Gordon

  The Journal of chemical physics. 07/2009; 130(24):244108.

  Efficient identification of transition states is important for understanding reaction mechanisms. Most transition state search algorithms require long computational times and a good estimate of theEfficient identification of transition states is important for understanding reaction mechanisms. Most transition state search algorithms require long computational times and a good estimate of the transition state structure in order to converge, particularly for complex reaction systems. The growing string method (GSM) [B. Peters et al., J. Chem. Phys. 120, 7877 (2004)] does not require an initial guess of the transition state; however, the calculation is still computationally intensive due to repeated calls to the quantum mechanics code. Recent modifications to the GSM [A. Goodrow et al., J. Chem. Phys. 129, 174109 (2008)] have reduced the total computational time for converging to a transition state by a factor of 2 to 3. In this work, three transition state-finding strategies have been developed to complement the speedup of the modified-GSM: (1) a hybrid strategy, (2) an energy-weighted strategy, and (3) a substring strategy. The hybrid strategy initiates the string calculation at a low level of theory (HF/STO-3G), which is then refined at a higher level of theory (B3LYP/6-31G(*)). The energy-weighted strategy spaces points along the reaction pathway based on the energy at those points, leading to a higher density of points where the energy is highest and finer resolution of the transition state. The substring strategy is similar to the hybrid strategy, but only a portion of the low-level string is refined using a higher level of theory. These three strategies have been used with the modified-GSM and are compared in three reactions: alanine dipeptide isomerization, H-abstraction in methanol oxidation on VO(x)/SiO(2) catalysts, and C-H bond activation in the oxidative carbonylation of toluene to p-toluic acid on Rh(CO)(2)(TFA)(3) catalysts. In each of these examples, the substring strategy was proved most effective by obtaining a better estimate of the transition state structure and reducing the total computational time by a factor of 2 to 3 compared to the modified-GSM. The applicability of the substring strategy has been extended to three additional examples: cyclopropane rearrangement to propylene, isomerization of methylcyclopropane to four different stereoisomers, and the bimolecular Diels-Alder condensation of 1,3-butadiene and ethylene to cyclohexene. Thus, the substring strategy used in combination with the modified-GSM has been demonstrated to be an efficient transition state-finding strategy for a wide range of types of reactions.

• Vapor-Phase Carbonylation of Dimethoxymethane over H-Faujasite.

  Authors: Fuat E Celik, Tae-Jin Kim, Alexis T Bell

  Angewandte Chemie (International ed. in English). 06/2009;

• Mechanistic studies of the hydroamination of norbornene with electrophilic platinum complexes: the role of proton transfer.

  Authors: Jennifer L McBee, Alexis T Bell, T Don Tilley

  Journal of the American Chemical Society. 01/2009; 130(49):16562-71.

  Hydroaminations of norbornene with arylsulfonamides and weakly basic anilines were achieved using electrophilic Pt(II) bis(triflate) complexes of the type L2Pt(OTf)2 (L2 = (t)Bu2bpy, (t)BuC6H4N==Hydroaminations of norbornene with arylsulfonamides and weakly basic anilines were achieved using electrophilic Pt(II) bis(triflate) complexes of the type L2Pt(OTf)2 (L2 = (t)Bu2bpy, (t)BuC6H4N== C(CH3)C(CH3)==NC6H4(t)Bu, (C6H5)2PCH2CH2P(C6H5)2, (C6F5)2PCH2CH2P(C6F5)2, S-BINAP). Pseudo-first-order kinetics reveal little to no dependence of the reaction rate on the ancillary ligand. Mechanistic studies do not favor an olefin coordination mechanism but are instead consistent with a mechanism involving sulfonamide coordination and generation of an acidic proton that is transferred to the norbornene. It is postulated that the resulting norbornyl cation is then attacked by free sulfonamide, and loss of proton from this adduct completes the hydroamination. The platinum-sulfonamide complex readily undergoes deprotonation to give a mu-amido platinum-bridged dimer that was isolated from the reaction solution. These studies also involve use of Me3SiPh and Me3SnPh as non-nucleophilic proton traps. Cleavage of the Ph-E bonds was used to detect the acidic, catalytically active species.

• Electron Donation in the Water-Water Hydrogen Bond.

  Authors: Rustam Z Khaliullin, Alexis T Bell, Martin Head-Gordon

  Chemistry (Weinheim an der Bergstrasse, Germany). 01/2009;

• Development and application of a hybrid method involving interpolation and ab initio calculations for the determination of transition states.

  Authors: Anthony Goodrow, Alexis T Bell, Martin Head-Gordon

  The Journal of chemical physics. 12/2008; 129(17):174109.

  Transition state search algorithms, such as the nudged elastic band can fail, if a good initial guess of the transition state structure cannot be provided. The growing string method (GSM) [J. Chem.Transition state search algorithms, such as the nudged elastic band can fail, if a good initial guess of the transition state structure cannot be provided. The growing string method (GSM) [J. Chem. Phys. 120, 7877 (2004)] eliminates the need for an initial guess of the transition state. While this method only requires knowledge of the reactant and product geometries, it is computationally intensive. To alleviate the bottlenecks in the GSM, several modifications were implemented: Cartesian coordinates were replaced by internal coordinates, the steepest descent method for minimization of orthogonal forces to locate the reaction path was replaced by the conjugate gradient method, and an interpolation scheme was used to estimate the energy and gradient, thereby reducing the calls to the quantum mechanical (QM) code. These modifications were tested to measure the reduction in computational time for four cases of increasing complexity: the Muller-Brown potential energy surface, alanine dipeptide isomerization, H abstraction in methanol oxidation, and C-H bond activation in oxidative carbonylation of toluene to p-toluic acid. These examples show that the modified GSM can achieve two- to threefold speedups (measured in terms of the reduction in actual QM gradients computed) over the original version of the method without compromising accuracy of the geometry and energy of the final transition state. Additional savings in computational effort can be achieved by carrying out the initial search for the minimum energy pathway (MEP) using a lower level of theory (e.g., HF/STO-3G) and then refining the MEP using density functional theory at the B3LYP level with larger basis sets (e.g., 6-31G( *), LANL2DZ). Thus, a general strategy for determining transition state structures is to initiate the modified GSM using a low level of theory with minimal basis sets and then refining the calculation at a higher level of theory with larger basis sets.

• Analysis of charge transfer effects in molecular complexes based on absolutely localized molecular orbitals.

  Authors: Rustam Z Khaliullin, Alexis T Bell, Martin Head-Gordon

  The Journal of chemical physics. 06/2008; 128(18):184112.

  A new method based on absolutely localized molecular orbitals (ALMOs) is proposed to measure the degree of intermolecular electron density delocalization (charge transfer) in molecular complexes.A new method based on absolutely localized molecular orbitals (ALMOs) is proposed to measure the degree of intermolecular electron density delocalization (charge transfer) in molecular complexes. ALMO charge transfer analysis (CTA) enables separation of the forward and backward charge transfer components for each pair of molecules in the system. The key feature of ALMO CTA is that all charge transfer terms have corresponding well defined energetic effects that measure the contribution of the given term to the overall energetic stabilization of the system. To simplify analysis of charge transfer effects, the concept of chemically significant complementary occupied-virtual orbital pairs (COVPs) is introduced. COVPs provide a simple description of intermolecular electron transfer effects in terms of just a few localized orbitals. ALMO CTA is applied to understand fundamental aspects of donor-acceptor interactions in borane adducts, synergic bonding in classical and nonclassical metal carbonyls, and multiple intermolecular hydrogen bonds in a complex of isocyanuric acid and melamine. These examples show that the ALMO CTA results are generally consistent with the existing conceptual description of intermolecular bonding. The results also show that charge transfer and the energy lowering due to charge transfer are not proportional to each other, and some interesting differences emerge which are discussed. Additionally, according to ALMO CTA, the amount of electron density transferred between molecules is significantly smaller than charge transfer estimated from various population analysis methods.

• Unravelling the origin of intermolecular interactions using absolutely localized molecular orbitals.

  Authors: Rustam Z Khaliullin, Erika A Cobar, Rohini C Lochan, Alexis T Bell, Martin Head-Gordon

  The journal of physical chemistry. A. 10/2007; 111(36):8753-65.

  An energy decomposition analysis (EDA) method is proposed to isolate physically relevant components of the total intermolecular interaction energies such as the contribution from interacting frozenAn energy decomposition analysis (EDA) method is proposed to isolate physically relevant components of the total intermolecular interaction energies such as the contribution from interacting frozen monomer densities, the energy lowering due to polarization of the densities, and the further energy lowering due to charge-transfer effects. This method is conceptually similar to existing EDA methods such as Morokuma analysis but includes several important new features. The first is a fully self-consistent treatment of the energy lowering due to polarization, which is evaluated by a self-consistent field calculation in which the molecular orbital coefficients are constrained to be block-diagonal (absolutely localized) in the interacting molecules to prohibit charge transfer. The second new feature is the ability to separate forward and back-donation in the charge-transfer energy term using a perturbative approximation starting from the optimized block-diagonal reference. The newly proposed EDA method is used to understand the fundamental aspects of intermolecular interactions such as the degree of covalency in the hydrogen bonding in water and the contributions of forward and back-donation in synergic bonding in metal complexes. Additionally, it is demonstrated that this method can be used to identify the factors controlling the interaction of the molecular hydrogen with open metal centers in potential hydrogen storage materials and the interaction of methane with rhenium complexes.

• Theoretical study of solvent effects on the thermodynamics of iron(III) [tetrakis(pentafluorophenyl)]porphyrin chloride dissociation.

  Authors: Rustam Z Khaliullin, Martin Head-Gordon, Alexis T Bell

  The journal of physical chemistry. B. 10/2007; 111(37):10992-8.

  A quasichemical method that combines ab initio treatment of explicit solvent with dielectric continuum models has been used to study the origin of a strong effect of methanol on the extent ofA quasichemical method that combines ab initio treatment of explicit solvent with dielectric continuum models has been used to study the origin of a strong effect of methanol on the extent of iron(III) [tetrakis(pentafluorophenyl)]porphyrin chloride dissociation in acetonitrile-methanol solutions. It is shown that the dissociation is energetically more favorable in methanol than in acetonitrile primarily because of the strong specific interactions between the chloride anion and the solvent methanol molecules in its first solvation shell. These interactions are weaker in acetonitrile. The final estimate for the difference in the dissociation free energies in methanol and acetonitrile is -23 kJ/mol, in a good agreement with the experimental value of -21 kJ/mol. Energy decomposition analysis of chloride-solvent interactions suggests that stronger chloride-methanol binding is a result of the contribution of charge delocalization effects to the chloride-methanol interactions.