Donald Truhlar - Academia.edu (original) (raw)
Papers by Donald Truhlar
Inorganic chemistry, May 16, 2016
We report electronic, vibrational, and magnetic properties, together with their structural depend... more We report electronic, vibrational, and magnetic properties, together with their structural dependences, for the metal-organic framework Fe2(dobdc) (dobdc(4-) = 2,5-dioxido-1,4-benzenedicarboxylate) and its derivatives, Fe2(O)2(dobdc) and Fe2(OH)2(dobdc)-species arising in the previously proposed mechanism for the oxidation of ethane to ethanol using N2O as an oxidant. Magnetic susceptibility measurements reported for Fe2(dobdc) in an earlier study and reported in the current study for Fe(II)0.26[Fe(III)(OH)]1.74(dobdc)(DMF)0.15(THF)0.22, which is more simply referred to as Fe2(OH)2(dobdc), were used to confirm the computational results. Theory was also compared to experiment for infrared spectra and powder X-ray diffraction structures. Structural and magnetic properties were computed by using Kohn-Sham density functional theory both with periodic boundary conditions and with cluster models. In addition, we studied the effects of different treatments of the exchange interactions on t...
PLoS biology, 2016
Nucleoside-based cofactors are presumed to have preceded proteins. The Rossmann fold is one of th... more Nucleoside-based cofactors are presumed to have preceded proteins. The Rossmann fold is one of the most ancient and functionally diverse protein folds, and most Rossmann enzymes utilize nucleoside-based cofactors. We analyzed an omnipresent Rossmann ribose-binding interaction: a carboxylate side chain at the tip of the second β-strand (β2-Asp/Glu). We identified a canonical motif, defined by the β2-topology and unique geometry. The latter relates to the interaction being bidentate (both ribose hydroxyls interacting with the carboxylate oxygens), to the angle between the carboxylate and the ribose, and to the ribose's ring configuration. We found that this canonical motif exhibits hallmarks of divergence rather than convergence. It is uniquely found in Rossmann enzymes that use different cofactors, primarily SAM (S-adenosyl methionine), NAD (nicotinamide adenine dinucleotide), and FAD (flavin adenine dinucleotide). Ribose-carboxylate bidentate interactions in other folds are not ...
Physical Review B, 1995
We calculate surface-diffusion coefficients for hydrogen on the (100) face of nickel over a tempe... more We calculate surface-diffusion coefficients for hydrogen on the (100) face of nickel over a temperature range from 40 to 1000 K. The calculations include tunneling contributions from discrete-energy states. The results are in very good agreement with experiment. We find a dramatic leveling off of the Arrhenius plot at approximately 66 K, below which temperature the diffusion coefficient is virtually independent of temperature. The existence and magnitude of such a transition temperature agrees well with experimental findings and also with previous theoretical work based on path-integral transitionstate theory. The present treatment provides insight into the origin of the effect. We evaluate the transition temperature analytically in terms of local quadratic approximations to the potential and find it to correspond approximately to the temperature at which the various low-energy bound-reactant states contribute equally to the diffusion coefficient. The nearly temperature-independent diffusion rate below the transition temperature corresponds to tunneling primarily from the ground state. The analytical expression for the transition temperature depends strongly on the magnitude of the frequency at the top of the potential barrier. We also demonstrate that this transition temperature does not correspond to a transition from over-barrier activated diffusion to tunneling diffusion, which has been previously proposed, and that the surface-diffusion process proceeds largely by a tunneling mechanism even well above the transition temperature. 'Christmann, Schober, Ertl, and Neumann, Ref. 42.
Journal of chemical theory and computation, Jan 14, 2015
Time-dependent density functional theory (TDDFT) with conventional local and hybrid functionals s... more Time-dependent density functional theory (TDDFT) with conventional local and hybrid functionals such as the local and hybrid generalized gradient approximations (GGA) seriously underestimates the excitation energies of Rydberg states, which limits its usefulness for applications such as spectroscopy and photochemistry. We present here a scheme that modifies the exchange-enhancement factor to improve GGA functionals for Rydberg excitations within the TDDFT framework while retaining their accuracy for valence excitations and for the thermochemical energetics calculated by ground-state density functional theory. The scheme is applied to a popular hybrid GGA functional and tested on data sets of valence and Rydberg excitations and atomization energies, and the results are encouraging. The scheme is simple and flexible. It can be used to correct existing functionals, and it can also be used as a strategy for the development of new functionals.
![Research paper thumbnail of Comment on "Fe2: As simple as a Herculean labour. Neutral (Fe2), cationic (Fe2 (+)), and anionic (Fe2 (-)) species" [J. Chem. Phys. 142, 244304 (2015)]](https://attachments.academia-assets.com/108052311/thumbnails/1.jpg)
](The Journal of chemical physics, Jan 14, 2016
A recent paper on Fe2 [A. Kalemos, J. Chem. Phys. 142, 244304 (2015)] critiqued our previous work... more A recent paper on Fe2 [A. Kalemos, J. Chem. Phys. 142, 244304 (2015)] critiqued our previous work on the system [Hoyer et al., J. Chem. Phys. 141, 204309 (2014)]. In this comment, we explain the nature of our previously reported potential energy curve for Fe2 and we discuss our computed properties for Fe2. Additionally, we fix a labeling error that was present in our previous work, although this error is unrelated to the main point of discussion.
Journal of the American Chemical Society, Jan 3, 2016
Pressure-dependent reactions are ubiquitous in combustion and atmospheric chemistry mechanisms. H... more Pressure-dependent reactions are ubiquitous in combustion and atmospheric chemistry mechanisms. Here we employ a new calibration procedure for quantum Rice-Ramsperger-Kassel (QRRK) unimolecular rate theory within a chemical activation mechanism to calculate the pressure-falloff effect of a radical association with an aromatic ring, including anharmonicity. This allows the radical association to be treated conveniently at a level of dynamical theory consistent with the treatment of bimolecular atom transfer reactions. The first application, of the new theoretical framework is a calculation of the kinetics of the reaction of H with toluene, which is a prototypical reaction in the combustion chemistry of aromatic hydrocarbons, which are present in most fuels. Both the hydrogen abstraction reactions and the hydrogen addition reactions are calculated. In our QRRK approach, we adjust QRRK theory with system-specific (SS) parameters to agree with multistructural canonical variational trans...
Theoretical Chemistry Accounts, 2007
Diabatic potential energy surfaces are a convenient starting point for dynamics calculations of p... more Diabatic potential energy surfaces are a convenient starting point for dynamics calculations of photochemical processes, and they can be calculated by the fourfold way direct diabatization scheme. Here we present an improved definition of the reference orbital for applying the fourfold way direct diabatization scheme to ammonia. The improved reference orbital is a geometry-dependent hybrid orbital that allows one to define consistent dominant configuration lists at all geometries important for photodissociation. Using diabatic energies calculated with the new reference orbital and consistent dominant configuration lists, we have refitted the analytical representations of the ground and the first electronically excited singlet-state potential energy surfaces and the diabatic coupling surface. Improved functional forms were used to reproduce the experimental dissociation energies and excitation energies, which will be important for subsequent simulations of photochemical dynamics. We find that the lowestenergy conical intersection point is at 5.16 eV, with C 2v symmetry.
Protein Science, 2004
A subject of great practical importance that has not received much attention is the question of t... more A subject of great practical importance that has not received much attention is the question of the sensitivity of molecular dynamics simulations to the initial X‐ray structure used to set up the calculation. We have found two cases in which seemingly similar structures lead to quite different results, and in this article we present a detailed analysis of these cases. The first case is acyl‐CoA dehydrogenase, and the chief difference of the two structures is attributed to a slight shift in a backbone carbonyl that causes a key residue (the proton‐abstracting base) to be in a bad conformation for reaction. The second case is xylose isomerase, and the chief difference of the two structures appears to be the ligand sphere of a Mg2+ metal cofactor that plays an active role in catalysis.
Physical Chemistry Chemical Physics, 2011
We present M06-2X density functional calculations of the chloroform/water partition coefficients ... more We present M06-2X density functional calculations of the chloroform/water partition coefficients of cytosine, thymine, uracil, adenine, and guanine and calculations of the free energies of association of selected unsubstituted and alkylated nucleotide base pairs in chloroform and water. Both hydrogen bonding and p-p stacking interactions are considered. Solvation effects are treated using the continuum solvent models SM8, SM8AD, and SMD, including geometry optimization in solution. Comparison of theoretical results with available experimental data indicates that all three of these solvation models predict the chloroform-water partition coefficients for the studied nucleobases qualitatively well, with mean unsigned errors in the range of 0.4-1.3 log units. All three models correctly predict the preference for hydrogen bonding over stacking for nucleobase pairs solvated in chloroform, and SM8, SM8AD, and SMD show similar accuracy in predicting the corresponding free energies of association. The agreement between theory and experiment for the association free energies of the dimers in water is more difficult to assess, as the relevant experimental data are indirect. Theory predicts that the stacking interaction of nucleobases in water is more favorable than hydrogen bonding for only two out of three tested hetero-dimers.
Journal of Computational Chemistry, 2006
This essay provides a perspective on several issues in valence bond theory: the physical signific... more This essay provides a perspective on several issues in valence bond theory: the physical significance of semilocal bonding orbitals, the capability of valence bond concepts to explain systems with multireferences character, the use of valence bond theory to provide analytical representations of potential energy surfaces for chemical dynamics by the method of semiempirical valence bond potential energy surfaces (an early example of specific reaction parameters), by multiconfiguration molecular mechanics, by the combined valence bond‐molecular mechanics method, and by the use of valence bond states as coupled diabatic states for describing electronically nonadiabatic processes (photochemistry). The essay includes both ab initio and semiempirical approaches. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2007
Journal of Chemical Theory and Computation, 2007
Journal of Chemical Theory and Computation, 2007
The electrostatically embedded many-body expansion (EE-MB), previously applied to the total elect... more The electrostatically embedded many-body expansion (EE-MB), previously applied to the total electronic energy, is here applied only to the electronic correlation energy (CE), combined with a Hartree-Fock calculation on the entire system. The separate treatment of the Hartree-Fock and correlation energies provides an efficient way to approximate correlation energy for extended systems. We illustrate this here by calculating accurate MØller-Plesset second-order perturbation theory (MP2) energies for a series of clusters ranging in size from 5 to 20 water molecules. In this new method, called EE-MB-CE, where MB is pairwise additive (PA) or three-body (3B), the full Hartree-Fock energy of a system of N monomers is calculated (i.e., the many-body expansion is carried out to N th order), while the EE-MB method is used to calculate the correlation energy of the system. We find that not only does this new method lead to better energetics than the original EE-MB method, but that one is able to obtain excellent agreement with full MP2 calculations by considering only a two-body expansion of the correlation energy, leading to a considerable savings in computational time as compared to the three-body expansion. Additionally, we propose the use of a cutoff to further reduce the number of two-body terms that must be calculated, and we show that if a cutoff of 6 Å is used one can eliminate up to 44% of the pairs and still calculate energies to within 0.1% of the net interaction energy of the full cluster.
The Journal of Chemical Physics, 2004
The most widely used algorithm for Monte Carlo sampling of electronic transitions in trajectory s... more The most widely used algorithm for Monte Carlo sampling of electronic transitions in trajectory surface hopping (TSH) calculations is the so-called anteater algorithm, which is inefficient for sampling low-probability nonadiabatic events. We present a new sampling scheme (called the army ants algorithm) for carrying out TSH calculations that is applicable to systems with any strength of coupling. The army ants algorithm is a form of rare event sampling whose efficiency is controlled by an input parameter. By choosing a suitable value of the input parameter the army ants algorithm can be reduced to the anteater algorithm (which is efficient for strongly coupled cases), and by optimizing the parameter the army ants algorithm may be efficiently applied to systems with low-probability events. To demonstrate the efficiency of the army ants algorithm, we performed atom–diatom scattering calculations on a model system involving weakly coupled electronic states. Fully converged quantum mech...
The Journal of Chemical Physics, 2001
The photodissociation of Li⋯FH and Na⋯FH van der Waals complexes is studied using Tully’s fewest-... more The photodissociation of Li⋯FH and Na⋯FH van der Waals complexes is studied using Tully’s fewest-switches surface-hopping and the natural decay of mixing semiclassical trajectory methods for coupled-state dynamics. The lifetimes of the predissociated excited-state complex (exciplex), as well as the branching ratio into reactive and nonreactive arrangements and the internal energy distribution of the products are reported at several excitation energies. The semiclassical trajectory methods agree with each other only qualitatively, and the results are strongly dependent on the choice of electronic representation. In general, the lifetime of the LiFH exciplex is shorter and less dependent on the excitation energy than the lifetime of the NaFH exciplex. The semiclassical dynamics of LiFH and NaFH are interpreted in terms of the features of their coupled potential energy surfaces.
The Journal of Chemical Physics, 2010
The adsorption of small molecules such as NO or CO on surfaces of magnetic oxides containing tran... more The adsorption of small molecules such as NO or CO on surfaces of magnetic oxides containing transition metals is difficult to model by current density functional approximations. Two such oxides are NiO(100) and Ni-doped MgO(100). Here we compare the results of a theoretical model of the Ni-doped MgO(100) surface with experimental results on NiO(100), which introduces some uncertainty into a quantitative theory-experiment comparison. In the present work, we tested seven meta-GGA and hybrid metafunctionals, in particular, three developed by the Minnesota group (M05, M06-L, and M06), and TPSS, TPSSh, TPSSKCIS, and B1B95; six GGA functionals, including BP86, PBE, and four other functionals that are modifications of PBE (PBEsol, SOGGA, revPBE, and RPBE); five hybrid GGA functionals (B3LYP, PBE0, B97–2, B97–3, and MPWLYP1M); and one unconventional functional of the generalized gradient type with scaled correlation called MOHLYP. The Minnesota meta-GGA functionals were found in the past t...
The Journal of Chemical Physics, 2009
As gold clusters increase in size, the preferred structure changes from planar to three-dimension... more As gold clusters increase in size, the preferred structure changes from planar to three-dimensional and, for anionic clusters, Aun−, the two-dimensional(2D)→three-dimensional (3D) transition is found experimentally to occur between n=11 and n=12. Most density functionals predict that planar structures are preferred up to higher n than is observed experimentally, an exception being the local spin density approximation. Here we test four relatively new functionals for this feature, in particular, M05, M06-L, M06, and SOGGA. We find that M06-L, M06, and SOGGA all predict the 2D→3D transition at the correct value of n. Since the M06-L and M06 functionals have previously been shown to be reasonably accurate for transition metal bond energies, main group atomization energies, barrier heights, and noncovalent interaction energies, and, since they are here shown to perform well for the s-d excitation energy and ionization potential of Au atoms and for the size of Aun− clusters at which the ...
The Journal of Chemical Physics, 2009
Using previously developed potential energy surfaces and their couplings, non-Born–Oppenheimer tr... more Using previously developed potential energy surfaces and their couplings, non-Born–Oppenheimer trajectory methods are used to study the state-selected photodissociation of ammonia, prepared with up to six quanta of vibrational excitation in the symmetric (ν1) or antisymmetric (ν3) stretching modes of NH3(Ã). The predicted dynamics is mainly electronically nonadiabatic (that is, it produces ground electronic state amino radicals). The small probability of forming the excited-state amino radical is found, for low excitations, to increase with total energy and to be independent of whether the symmetric or antisymmetric stretch is excited; however some selectivity with respect to exciting the antisymmetric stretch is found when more than one quantum of excitation is added to the stretches, and more than 50% of the amino radical are found to be electronically excited when six quanta are placed in the antisymmetric stretch. These results are in contrast to the mechanism inferred in recen...
The Journal of Chemical Physics, 2008
The adsorption of CO on Mg(001) constitutes a challenge for current density functional approximat... more The adsorption of CO on Mg(001) constitutes a challenge for current density functional approximations because of its weak interaction character. In the present work we show that the M06-2X and M06-HF exchange-correlation functionals are the first ones to provide a simultaneously satisfactory description of adsorbate geometry, vibrational frequency shift, and adsorption energy of CO on MgO(001). For a sufficiently large embedded cluster model, the three functionals of the M06 family—which contain a nonzero percentage of Hartree–Fock exchange (M06, M06-2X, and M06-HF)—all predict positive C–O vibrational shifts, in agreement with the experimental findings, while the local M06-L functional gives large negative shifts. Moreover, the shifts computed with the M06-2X and M06-HF potentials are in good agreement with the experimental shift of +14 cm−1. The interaction energy (De) calculated with M06-2X and M06-HF is ∼6.0 kcal/mol, which agrees well with the De value (∼4 kcal/mol) deduced fro...
The Journal of Chemical Physics, 2008
The performance of the M06 family of exchange-correlation potentials for describing the electroni... more The performance of the M06 family of exchange-correlation potentials for describing the electronic structure and the Heisenberg magnetic coupling constant (J) is investigated using a set of representative open-shell systems involving two unpaired electrons. The set of molecular systems studied has well defined structures, and their magnetic coupling values are known experimentally. As a general trend, the M06 functional is about equally as accurate as B3LYP or PBE0. The performance of local functionals is important because of their economy and convenience for large-scale calculations; we find that M06-L local functional of the M06 family largely improves over the local spin density approximation and the generalized gradient approximation.
The Journal of Chemical Physics, 2008
The CCSD, CCSD(T), and CR-CC(2,3) coupled cluster methods, combined with five triple-zeta basis s... more The CCSD, CCSD(T), and CR-CC(2,3) coupled cluster methods, combined with five triple-zeta basis sets, namely, MG3S, aug-cc-pVTZ, aug-cc-pV(T+d)Z, aug-cc-pCVTZ, and aug-cc-pCV(T+d)Z, are tested against the DBH24 database of diverse reaction barrier heights. The calculations confirm that the inclusion of connected triple excitations is essential to achieving high accuracy for thermochemical kinetics. They show that various noniterative ways of incorporating connected triple excitations in coupled cluster theory, including the CCSD(T) approach, the full CR-CC(2,3) method, and approximate variants of CR-CC(2,3) similar to the triples corrections of the CCSD(2) approaches, are all about equally accurate for describing the effects of connected triply excited clusters in studies of activation barriers. The effect of freezing core electrons on the results of the CCSD, CCSD(T), and CR-CC(2,3) calculations for barrier heights is also examined. It is demonstrated that to include core correlati...
Inorganic chemistry, May 16, 2016
We report electronic, vibrational, and magnetic properties, together with their structural depend... more We report electronic, vibrational, and magnetic properties, together with their structural dependences, for the metal-organic framework Fe2(dobdc) (dobdc(4-) = 2,5-dioxido-1,4-benzenedicarboxylate) and its derivatives, Fe2(O)2(dobdc) and Fe2(OH)2(dobdc)-species arising in the previously proposed mechanism for the oxidation of ethane to ethanol using N2O as an oxidant. Magnetic susceptibility measurements reported for Fe2(dobdc) in an earlier study and reported in the current study for Fe(II)0.26[Fe(III)(OH)]1.74(dobdc)(DMF)0.15(THF)0.22, which is more simply referred to as Fe2(OH)2(dobdc), were used to confirm the computational results. Theory was also compared to experiment for infrared spectra and powder X-ray diffraction structures. Structural and magnetic properties were computed by using Kohn-Sham density functional theory both with periodic boundary conditions and with cluster models. In addition, we studied the effects of different treatments of the exchange interactions on t...
PLoS biology, 2016
Nucleoside-based cofactors are presumed to have preceded proteins. The Rossmann fold is one of th... more Nucleoside-based cofactors are presumed to have preceded proteins. The Rossmann fold is one of the most ancient and functionally diverse protein folds, and most Rossmann enzymes utilize nucleoside-based cofactors. We analyzed an omnipresent Rossmann ribose-binding interaction: a carboxylate side chain at the tip of the second β-strand (β2-Asp/Glu). We identified a canonical motif, defined by the β2-topology and unique geometry. The latter relates to the interaction being bidentate (both ribose hydroxyls interacting with the carboxylate oxygens), to the angle between the carboxylate and the ribose, and to the ribose's ring configuration. We found that this canonical motif exhibits hallmarks of divergence rather than convergence. It is uniquely found in Rossmann enzymes that use different cofactors, primarily SAM (S-adenosyl methionine), NAD (nicotinamide adenine dinucleotide), and FAD (flavin adenine dinucleotide). Ribose-carboxylate bidentate interactions in other folds are not ...
Physical Review B, 1995
We calculate surface-diffusion coefficients for hydrogen on the (100) face of nickel over a tempe... more We calculate surface-diffusion coefficients for hydrogen on the (100) face of nickel over a temperature range from 40 to 1000 K. The calculations include tunneling contributions from discrete-energy states. The results are in very good agreement with experiment. We find a dramatic leveling off of the Arrhenius plot at approximately 66 K, below which temperature the diffusion coefficient is virtually independent of temperature. The existence and magnitude of such a transition temperature agrees well with experimental findings and also with previous theoretical work based on path-integral transitionstate theory. The present treatment provides insight into the origin of the effect. We evaluate the transition temperature analytically in terms of local quadratic approximations to the potential and find it to correspond approximately to the temperature at which the various low-energy bound-reactant states contribute equally to the diffusion coefficient. The nearly temperature-independent diffusion rate below the transition temperature corresponds to tunneling primarily from the ground state. The analytical expression for the transition temperature depends strongly on the magnitude of the frequency at the top of the potential barrier. We also demonstrate that this transition temperature does not correspond to a transition from over-barrier activated diffusion to tunneling diffusion, which has been previously proposed, and that the surface-diffusion process proceeds largely by a tunneling mechanism even well above the transition temperature. 'Christmann, Schober, Ertl, and Neumann, Ref. 42.
Journal of chemical theory and computation, Jan 14, 2015
Time-dependent density functional theory (TDDFT) with conventional local and hybrid functionals s... more Time-dependent density functional theory (TDDFT) with conventional local and hybrid functionals such as the local and hybrid generalized gradient approximations (GGA) seriously underestimates the excitation energies of Rydberg states, which limits its usefulness for applications such as spectroscopy and photochemistry. We present here a scheme that modifies the exchange-enhancement factor to improve GGA functionals for Rydberg excitations within the TDDFT framework while retaining their accuracy for valence excitations and for the thermochemical energetics calculated by ground-state density functional theory. The scheme is applied to a popular hybrid GGA functional and tested on data sets of valence and Rydberg excitations and atomization energies, and the results are encouraging. The scheme is simple and flexible. It can be used to correct existing functionals, and it can also be used as a strategy for the development of new functionals.
The Journal of chemical physics, Jan 14, 2016
A recent paper on Fe2 [A. Kalemos, J. Chem. Phys. 142, 244304 (2015)] critiqued our previous work... more A recent paper on Fe2 [A. Kalemos, J. Chem. Phys. 142, 244304 (2015)] critiqued our previous work on the system [Hoyer et al., J. Chem. Phys. 141, 204309 (2014)]. In this comment, we explain the nature of our previously reported potential energy curve for Fe2 and we discuss our computed properties for Fe2. Additionally, we fix a labeling error that was present in our previous work, although this error is unrelated to the main point of discussion.
Journal of the American Chemical Society, Jan 3, 2016
Pressure-dependent reactions are ubiquitous in combustion and atmospheric chemistry mechanisms. H... more Pressure-dependent reactions are ubiquitous in combustion and atmospheric chemistry mechanisms. Here we employ a new calibration procedure for quantum Rice-Ramsperger-Kassel (QRRK) unimolecular rate theory within a chemical activation mechanism to calculate the pressure-falloff effect of a radical association with an aromatic ring, including anharmonicity. This allows the radical association to be treated conveniently at a level of dynamical theory consistent with the treatment of bimolecular atom transfer reactions. The first application, of the new theoretical framework is a calculation of the kinetics of the reaction of H with toluene, which is a prototypical reaction in the combustion chemistry of aromatic hydrocarbons, which are present in most fuels. Both the hydrogen abstraction reactions and the hydrogen addition reactions are calculated. In our QRRK approach, we adjust QRRK theory with system-specific (SS) parameters to agree with multistructural canonical variational trans...
Theoretical Chemistry Accounts, 2007
Diabatic potential energy surfaces are a convenient starting point for dynamics calculations of p... more Diabatic potential energy surfaces are a convenient starting point for dynamics calculations of photochemical processes, and they can be calculated by the fourfold way direct diabatization scheme. Here we present an improved definition of the reference orbital for applying the fourfold way direct diabatization scheme to ammonia. The improved reference orbital is a geometry-dependent hybrid orbital that allows one to define consistent dominant configuration lists at all geometries important for photodissociation. Using diabatic energies calculated with the new reference orbital and consistent dominant configuration lists, we have refitted the analytical representations of the ground and the first electronically excited singlet-state potential energy surfaces and the diabatic coupling surface. Improved functional forms were used to reproduce the experimental dissociation energies and excitation energies, which will be important for subsequent simulations of photochemical dynamics. We find that the lowestenergy conical intersection point is at 5.16 eV, with C 2v symmetry.
Protein Science, 2004
A subject of great practical importance that has not received much attention is the question of t... more A subject of great practical importance that has not received much attention is the question of the sensitivity of molecular dynamics simulations to the initial X‐ray structure used to set up the calculation. We have found two cases in which seemingly similar structures lead to quite different results, and in this article we present a detailed analysis of these cases. The first case is acyl‐CoA dehydrogenase, and the chief difference of the two structures is attributed to a slight shift in a backbone carbonyl that causes a key residue (the proton‐abstracting base) to be in a bad conformation for reaction. The second case is xylose isomerase, and the chief difference of the two structures appears to be the ligand sphere of a Mg2+ metal cofactor that plays an active role in catalysis.
Physical Chemistry Chemical Physics, 2011
We present M06-2X density functional calculations of the chloroform/water partition coefficients ... more We present M06-2X density functional calculations of the chloroform/water partition coefficients of cytosine, thymine, uracil, adenine, and guanine and calculations of the free energies of association of selected unsubstituted and alkylated nucleotide base pairs in chloroform and water. Both hydrogen bonding and p-p stacking interactions are considered. Solvation effects are treated using the continuum solvent models SM8, SM8AD, and SMD, including geometry optimization in solution. Comparison of theoretical results with available experimental data indicates that all three of these solvation models predict the chloroform-water partition coefficients for the studied nucleobases qualitatively well, with mean unsigned errors in the range of 0.4-1.3 log units. All three models correctly predict the preference for hydrogen bonding over stacking for nucleobase pairs solvated in chloroform, and SM8, SM8AD, and SMD show similar accuracy in predicting the corresponding free energies of association. The agreement between theory and experiment for the association free energies of the dimers in water is more difficult to assess, as the relevant experimental data are indirect. Theory predicts that the stacking interaction of nucleobases in water is more favorable than hydrogen bonding for only two out of three tested hetero-dimers.
Journal of Computational Chemistry, 2006
This essay provides a perspective on several issues in valence bond theory: the physical signific... more This essay provides a perspective on several issues in valence bond theory: the physical significance of semilocal bonding orbitals, the capability of valence bond concepts to explain systems with multireferences character, the use of valence bond theory to provide analytical representations of potential energy surfaces for chemical dynamics by the method of semiempirical valence bond potential energy surfaces (an early example of specific reaction parameters), by multiconfiguration molecular mechanics, by the combined valence bond‐molecular mechanics method, and by the use of valence bond states as coupled diabatic states for describing electronically nonadiabatic processes (photochemistry). The essay includes both ab initio and semiempirical approaches. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2007
Journal of Chemical Theory and Computation, 2007
Journal of Chemical Theory and Computation, 2007
The electrostatically embedded many-body expansion (EE-MB), previously applied to the total elect... more The electrostatically embedded many-body expansion (EE-MB), previously applied to the total electronic energy, is here applied only to the electronic correlation energy (CE), combined with a Hartree-Fock calculation on the entire system. The separate treatment of the Hartree-Fock and correlation energies provides an efficient way to approximate correlation energy for extended systems. We illustrate this here by calculating accurate MØller-Plesset second-order perturbation theory (MP2) energies for a series of clusters ranging in size from 5 to 20 water molecules. In this new method, called EE-MB-CE, where MB is pairwise additive (PA) or three-body (3B), the full Hartree-Fock energy of a system of N monomers is calculated (i.e., the many-body expansion is carried out to N th order), while the EE-MB method is used to calculate the correlation energy of the system. We find that not only does this new method lead to better energetics than the original EE-MB method, but that one is able to obtain excellent agreement with full MP2 calculations by considering only a two-body expansion of the correlation energy, leading to a considerable savings in computational time as compared to the three-body expansion. Additionally, we propose the use of a cutoff to further reduce the number of two-body terms that must be calculated, and we show that if a cutoff of 6 Å is used one can eliminate up to 44% of the pairs and still calculate energies to within 0.1% of the net interaction energy of the full cluster.
The Journal of Chemical Physics, 2004
The most widely used algorithm for Monte Carlo sampling of electronic transitions in trajectory s... more The most widely used algorithm for Monte Carlo sampling of electronic transitions in trajectory surface hopping (TSH) calculations is the so-called anteater algorithm, which is inefficient for sampling low-probability nonadiabatic events. We present a new sampling scheme (called the army ants algorithm) for carrying out TSH calculations that is applicable to systems with any strength of coupling. The army ants algorithm is a form of rare event sampling whose efficiency is controlled by an input parameter. By choosing a suitable value of the input parameter the army ants algorithm can be reduced to the anteater algorithm (which is efficient for strongly coupled cases), and by optimizing the parameter the army ants algorithm may be efficiently applied to systems with low-probability events. To demonstrate the efficiency of the army ants algorithm, we performed atom–diatom scattering calculations on a model system involving weakly coupled electronic states. Fully converged quantum mech...
The Journal of Chemical Physics, 2001
The photodissociation of Li⋯FH and Na⋯FH van der Waals complexes is studied using Tully’s fewest-... more The photodissociation of Li⋯FH and Na⋯FH van der Waals complexes is studied using Tully’s fewest-switches surface-hopping and the natural decay of mixing semiclassical trajectory methods for coupled-state dynamics. The lifetimes of the predissociated excited-state complex (exciplex), as well as the branching ratio into reactive and nonreactive arrangements and the internal energy distribution of the products are reported at several excitation energies. The semiclassical trajectory methods agree with each other only qualitatively, and the results are strongly dependent on the choice of electronic representation. In general, the lifetime of the LiFH exciplex is shorter and less dependent on the excitation energy than the lifetime of the NaFH exciplex. The semiclassical dynamics of LiFH and NaFH are interpreted in terms of the features of their coupled potential energy surfaces.
The Journal of Chemical Physics, 2010
The adsorption of small molecules such as NO or CO on surfaces of magnetic oxides containing tran... more The adsorption of small molecules such as NO or CO on surfaces of magnetic oxides containing transition metals is difficult to model by current density functional approximations. Two such oxides are NiO(100) and Ni-doped MgO(100). Here we compare the results of a theoretical model of the Ni-doped MgO(100) surface with experimental results on NiO(100), which introduces some uncertainty into a quantitative theory-experiment comparison. In the present work, we tested seven meta-GGA and hybrid metafunctionals, in particular, three developed by the Minnesota group (M05, M06-L, and M06), and TPSS, TPSSh, TPSSKCIS, and B1B95; six GGA functionals, including BP86, PBE, and four other functionals that are modifications of PBE (PBEsol, SOGGA, revPBE, and RPBE); five hybrid GGA functionals (B3LYP, PBE0, B97–2, B97–3, and MPWLYP1M); and one unconventional functional of the generalized gradient type with scaled correlation called MOHLYP. The Minnesota meta-GGA functionals were found in the past t...
The Journal of Chemical Physics, 2009
As gold clusters increase in size, the preferred structure changes from planar to three-dimension... more As gold clusters increase in size, the preferred structure changes from planar to three-dimensional and, for anionic clusters, Aun−, the two-dimensional(2D)→three-dimensional (3D) transition is found experimentally to occur between n=11 and n=12. Most density functionals predict that planar structures are preferred up to higher n than is observed experimentally, an exception being the local spin density approximation. Here we test four relatively new functionals for this feature, in particular, M05, M06-L, M06, and SOGGA. We find that M06-L, M06, and SOGGA all predict the 2D→3D transition at the correct value of n. Since the M06-L and M06 functionals have previously been shown to be reasonably accurate for transition metal bond energies, main group atomization energies, barrier heights, and noncovalent interaction energies, and, since they are here shown to perform well for the s-d excitation energy and ionization potential of Au atoms and for the size of Aun− clusters at which the ...
The Journal of Chemical Physics, 2009
Using previously developed potential energy surfaces and their couplings, non-Born–Oppenheimer tr... more Using previously developed potential energy surfaces and their couplings, non-Born–Oppenheimer trajectory methods are used to study the state-selected photodissociation of ammonia, prepared with up to six quanta of vibrational excitation in the symmetric (ν1) or antisymmetric (ν3) stretching modes of NH3(Ã). The predicted dynamics is mainly electronically nonadiabatic (that is, it produces ground electronic state amino radicals). The small probability of forming the excited-state amino radical is found, for low excitations, to increase with total energy and to be independent of whether the symmetric or antisymmetric stretch is excited; however some selectivity with respect to exciting the antisymmetric stretch is found when more than one quantum of excitation is added to the stretches, and more than 50% of the amino radical are found to be electronically excited when six quanta are placed in the antisymmetric stretch. These results are in contrast to the mechanism inferred in recen...
The Journal of Chemical Physics, 2008
The adsorption of CO on Mg(001) constitutes a challenge for current density functional approximat... more The adsorption of CO on Mg(001) constitutes a challenge for current density functional approximations because of its weak interaction character. In the present work we show that the M06-2X and M06-HF exchange-correlation functionals are the first ones to provide a simultaneously satisfactory description of adsorbate geometry, vibrational frequency shift, and adsorption energy of CO on MgO(001). For a sufficiently large embedded cluster model, the three functionals of the M06 family—which contain a nonzero percentage of Hartree–Fock exchange (M06, M06-2X, and M06-HF)—all predict positive C–O vibrational shifts, in agreement with the experimental findings, while the local M06-L functional gives large negative shifts. Moreover, the shifts computed with the M06-2X and M06-HF potentials are in good agreement with the experimental shift of +14 cm−1. The interaction energy (De) calculated with M06-2X and M06-HF is ∼6.0 kcal/mol, which agrees well with the De value (∼4 kcal/mol) deduced fro...
The Journal of Chemical Physics, 2008
The performance of the M06 family of exchange-correlation potentials for describing the electroni... more The performance of the M06 family of exchange-correlation potentials for describing the electronic structure and the Heisenberg magnetic coupling constant (J) is investigated using a set of representative open-shell systems involving two unpaired electrons. The set of molecular systems studied has well defined structures, and their magnetic coupling values are known experimentally. As a general trend, the M06 functional is about equally as accurate as B3LYP or PBE0. The performance of local functionals is important because of their economy and convenience for large-scale calculations; we find that M06-L local functional of the M06 family largely improves over the local spin density approximation and the generalized gradient approximation.
The Journal of Chemical Physics, 2008
The CCSD, CCSD(T), and CR-CC(2,3) coupled cluster methods, combined with five triple-zeta basis s... more The CCSD, CCSD(T), and CR-CC(2,3) coupled cluster methods, combined with five triple-zeta basis sets, namely, MG3S, aug-cc-pVTZ, aug-cc-pV(T+d)Z, aug-cc-pCVTZ, and aug-cc-pCV(T+d)Z, are tested against the DBH24 database of diverse reaction barrier heights. The calculations confirm that the inclusion of connected triple excitations is essential to achieving high accuracy for thermochemical kinetics. They show that various noniterative ways of incorporating connected triple excitations in coupled cluster theory, including the CCSD(T) approach, the full CR-CC(2,3) method, and approximate variants of CR-CC(2,3) similar to the triples corrections of the CCSD(2) approaches, are all about equally accurate for describing the effects of connected triply excited clusters in studies of activation barriers. The effect of freezing core electrons on the results of the CCSD, CCSD(T), and CR-CC(2,3) calculations for barrier heights is also examined. It is demonstrated that to include core correlati...