Donald Truhlar - Profile on Academia.edu (original) (raw)
Papers by Donald Truhlar
Observing Molecular Collisions
Science, Dec 17, 1982
The Journal of chemical physics, Jan 21, 2016
Metal-organic frameworks (MOFs) have many potential uses for separations, storage, and catalysis,... more Metal-organic frameworks (MOFs) have many potential uses for separations, storage, and catalysis, but their use as intercalation hosts for batteries has been scarce. In this article, we examine the mechanism of Li insertion in a MOF to provide guidance to future design efforts in this area. As a model system, we choose UiO-66, a MOF with the formula (Zr6O4(OH)4)4(1,4-benzenedicarboxylate)6, as an electrode material for lithium-ion batteries; this MOF is of special interest because the zirconium is not redox active. We report both quantum mechanical characterization of the mechanism and experimental studies in which the material is synthesized as nanoparticles to reduce diffusion lengths for lithium ions and increase the contact area with a conductive carbon phase. The calculated changes in the IR spectra of UiO-66 and lithiated UiO-66 are consistent with the experimental FTIR results. We found experimentally that this MOF can maintain a specific discharge capacity of at least 118 mA...
Journal of chemical theory and computation, Jan 9, 2014
Partial atomic charges are widely used for the description of charge distributions of molecules a... more Partial atomic charges are widely used for the description of charge distributions of molecules and solids. These charges are useful to indicate the extent of charge transfer and charge flow during chemical reactions in batteries, fuel cells, and catalysts and to characterize charge distributions in capacitors, liquid-phase electrolytes, and solids and at electrochemical interfaces. However, partial atomic charges given by various charge models differ significantly, especially for systems containing metal atoms. In the present study, we have compared various charge models on both molecular systems and extended systems, including Hirshfeld, CM5, MK, ChElPG, Mulliken, MBS, NPA, DDEC, LoProp, and Bader charges. Their merits and drawbacks are compared. The CM5 charge model is found to perform well on the molecular systems, with a mean unsigned percentage deviation of only 9% for the dipole moments. We therefore formulated it for extended systems and applied it to study charge flow durin...
Kinetics of the Hydrogen Abstraction Reaction From 2-Butanol by OH Radical
The Journal of Physical Chemistry A, 2015
The kinetics of the hydrogen abstraction from 2-butanol by hydroxyl radical have been studied usi... more The kinetics of the hydrogen abstraction from 2-butanol by hydroxyl radical have been studied using multipath variational transition-state theory with the multidimensional small curvature tunneling approximation. The rate constants for each of the five hydrogen abstraction sites (C1, C2, C3, C4, and O) and the overall reaction have been computed by direct dynamics based on M08-HX/6-311+G(2df,2p) electronic structure calculations. We show that multistructural torsional anharmonicity, anharmonicity differences of high-frequency modes between the transition structures and the reactants, and reaction-path dependence of multiple reaction paths are all important factors for determining accurate reaction rates and branching fractions for this problem. The reaction barrier heights for abstraction from various sites follow the order C2 < C3 < C4 < C1 < O, but the reactivities of the various sites do not precisely follow the inverse order of barrier heights, and the order of reactivities depends on temperature. The abstractions from C2 and C3 have the largest contribution to the total reaction rate from 200 to 2000 K.
The Journal of chemical physics, Jan 7, 2015
Accurate modeling of high-temperature hypersonic flows in the atmosphere requires consideration o... more Accurate modeling of high-temperature hypersonic flows in the atmosphere requires consideration of collision-induced dissociation of molecular species and energy transfer between the translational and internal modes of the gas molecules. Here, we describe a study of the N2 + N2⟶N2 + 2N and N2 + N2⟶4N nitrogen dissociation reactions using the quasiclassical trajectory (QCT) method. The simulations used a new potential energy surface for the N4 system; the surface is an improved version of one that was presented previously. In the QCT calculations, initial conditions were determined based on a two-temperature model that approximately separates the translational-rotational temperature from the vibrational temperature of the N2 diatoms. Five values from 8000 K to 30 000 K were considered for each of the two temperatures. Over 2.4 × 10(9) trajectories were calculated. We present results for ensemble-averaged dissociation rate constants as functions of the translational-rotational tempera...
The journal of physical chemistry. B, Jan 18, 2015
Theoretical studies on the electrode materials in lithium-ion batteries provide information on th... more Theoretical studies on the electrode materials in lithium-ion batteries provide information on the structural changes during the charging and discharging processes. In the present study, we tested the M06-L and N12 exchange-correlation functionals on some well-studied lithium-containing materials. These functionals, which have already shown good performance for a variety of databases, outperform the widely used PBE functional for reproducing the experimental structures and averaged intercalation potentials. It is especially noteworthy that the M06-L functional gives voltages as accurate as those provided by the Heyd-Scuseria-Ernzerhof (HSE06) hybrid functional, but with less computational cost.
Journal of the American Chemical Society, 2015
Free energy calculations for eight enol isomers of malonaldehyde (MA) and simulation of the ultra... more Free energy calculations for eight enol isomers of malonaldehyde (MA) and simulation of the ultraviolet (UV) absorption spectrum in both the gas phase and water (pH = 3, where the molecule exists in neutral undeprotonated form) show that in water the two s-trans nonchelated enol conformers of MA become thermodynamically more stable than the internally hydrogen-bonded ("chelated enol") conformer (CE). The pure CE conformer in water has a slightly red-shifted UV spectrum with respect to that in the gas phase, but the blue-shifted spectrum observed in water at pH 3 is dominated by solvent-stabilized conformations that have negligible populations in the gas phase. Density functional calculations with the solvation model based on density (SMD) and an ensemble-averaged vertical excitation model explain the experimental observations in detail.
The Journal of Physical Chemistry Letters, 2013
Endohedral fullerences have great potential for a variety of techological applications. Here we c... more Endohedral fullerences have great potential for a variety of techological applications. Here we consider B@C 60 and show that the amount of charge transfer from the semimetal boron atom to the cage is a strong function of the radial distance of the atom from the center of the fullerene, and it is controlled by multistate conical intersections whose associated ridge of avoided crossings has the topology of a Euclidean sphere. The potential energy surfaces of B@C 60 are characterized by two kinds of local minima: those with a boron atom located in the geometric center of the fullerene, and those with a boron atom bound to the fullerene inner wall. At the lowestenergy minimum, at the center, the boron atom is neutral, whereas the transition to the wall is accompanied by an electron transfer from boron to the fullerene cage. The two kinds of minima are separated by a ridge of avoided crossings that forms a surface with a nearly spherical shape. The properties of such systems may be altered by controlling the populations of the two kinds of minima, for example, by application of an external field. Such switchable atom-cage charge transfer may find applications in novel molecular devices.
Environmental Science & Technology, 1997
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
Observing Molecular Collisions
Science, Dec 17, 1982
The Journal of chemical physics, Jan 21, 2016
Metal-organic frameworks (MOFs) have many potential uses for separations, storage, and catalysis,... more Metal-organic frameworks (MOFs) have many potential uses for separations, storage, and catalysis, but their use as intercalation hosts for batteries has been scarce. In this article, we examine the mechanism of Li insertion in a MOF to provide guidance to future design efforts in this area. As a model system, we choose UiO-66, a MOF with the formula (Zr6O4(OH)4)4(1,4-benzenedicarboxylate)6, as an electrode material for lithium-ion batteries; this MOF is of special interest because the zirconium is not redox active. We report both quantum mechanical characterization of the mechanism and experimental studies in which the material is synthesized as nanoparticles to reduce diffusion lengths for lithium ions and increase the contact area with a conductive carbon phase. The calculated changes in the IR spectra of UiO-66 and lithiated UiO-66 are consistent with the experimental FTIR results. We found experimentally that this MOF can maintain a specific discharge capacity of at least 118 mA...
Journal of chemical theory and computation, Jan 9, 2014
Partial atomic charges are widely used for the description of charge distributions of molecules a... more Partial atomic charges are widely used for the description of charge distributions of molecules and solids. These charges are useful to indicate the extent of charge transfer and charge flow during chemical reactions in batteries, fuel cells, and catalysts and to characterize charge distributions in capacitors, liquid-phase electrolytes, and solids and at electrochemical interfaces. However, partial atomic charges given by various charge models differ significantly, especially for systems containing metal atoms. In the present study, we have compared various charge models on both molecular systems and extended systems, including Hirshfeld, CM5, MK, ChElPG, Mulliken, MBS, NPA, DDEC, LoProp, and Bader charges. Their merits and drawbacks are compared. The CM5 charge model is found to perform well on the molecular systems, with a mean unsigned percentage deviation of only 9% for the dipole moments. We therefore formulated it for extended systems and applied it to study charge flow durin...
Kinetics of the Hydrogen Abstraction Reaction From 2-Butanol by OH Radical
The Journal of Physical Chemistry A, 2015
The kinetics of the hydrogen abstraction from 2-butanol by hydroxyl radical have been studied usi... more The kinetics of the hydrogen abstraction from 2-butanol by hydroxyl radical have been studied using multipath variational transition-state theory with the multidimensional small curvature tunneling approximation. The rate constants for each of the five hydrogen abstraction sites (C1, C2, C3, C4, and O) and the overall reaction have been computed by direct dynamics based on M08-HX/6-311+G(2df,2p) electronic structure calculations. We show that multistructural torsional anharmonicity, anharmonicity differences of high-frequency modes between the transition structures and the reactants, and reaction-path dependence of multiple reaction paths are all important factors for determining accurate reaction rates and branching fractions for this problem. The reaction barrier heights for abstraction from various sites follow the order C2 < C3 < C4 < C1 < O, but the reactivities of the various sites do not precisely follow the inverse order of barrier heights, and the order of reactivities depends on temperature. The abstractions from C2 and C3 have the largest contribution to the total reaction rate from 200 to 2000 K.
The Journal of chemical physics, Jan 7, 2015
Accurate modeling of high-temperature hypersonic flows in the atmosphere requires consideration o... more Accurate modeling of high-temperature hypersonic flows in the atmosphere requires consideration of collision-induced dissociation of molecular species and energy transfer between the translational and internal modes of the gas molecules. Here, we describe a study of the N2 + N2⟶N2 + 2N and N2 + N2⟶4N nitrogen dissociation reactions using the quasiclassical trajectory (QCT) method. The simulations used a new potential energy surface for the N4 system; the surface is an improved version of one that was presented previously. In the QCT calculations, initial conditions were determined based on a two-temperature model that approximately separates the translational-rotational temperature from the vibrational temperature of the N2 diatoms. Five values from 8000 K to 30 000 K were considered for each of the two temperatures. Over 2.4 × 10(9) trajectories were calculated. We present results for ensemble-averaged dissociation rate constants as functions of the translational-rotational tempera...
The journal of physical chemistry. B, Jan 18, 2015
Theoretical studies on the electrode materials in lithium-ion batteries provide information on th... more Theoretical studies on the electrode materials in lithium-ion batteries provide information on the structural changes during the charging and discharging processes. In the present study, we tested the M06-L and N12 exchange-correlation functionals on some well-studied lithium-containing materials. These functionals, which have already shown good performance for a variety of databases, outperform the widely used PBE functional for reproducing the experimental structures and averaged intercalation potentials. It is especially noteworthy that the M06-L functional gives voltages as accurate as those provided by the Heyd-Scuseria-Ernzerhof (HSE06) hybrid functional, but with less computational cost.
Journal of the American Chemical Society, 2015
Free energy calculations for eight enol isomers of malonaldehyde (MA) and simulation of the ultra... more Free energy calculations for eight enol isomers of malonaldehyde (MA) and simulation of the ultraviolet (UV) absorption spectrum in both the gas phase and water (pH = 3, where the molecule exists in neutral undeprotonated form) show that in water the two s-trans nonchelated enol conformers of MA become thermodynamically more stable than the internally hydrogen-bonded ("chelated enol") conformer (CE). The pure CE conformer in water has a slightly red-shifted UV spectrum with respect to that in the gas phase, but the blue-shifted spectrum observed in water at pH 3 is dominated by solvent-stabilized conformations that have negligible populations in the gas phase. Density functional calculations with the solvation model based on density (SMD) and an ensemble-averaged vertical excitation model explain the experimental observations in detail.
The Journal of Physical Chemistry Letters, 2013
Endohedral fullerences have great potential for a variety of techological applications. Here we c... more Endohedral fullerences have great potential for a variety of techological applications. Here we consider B@C 60 and show that the amount of charge transfer from the semimetal boron atom to the cage is a strong function of the radial distance of the atom from the center of the fullerene, and it is controlled by multistate conical intersections whose associated ridge of avoided crossings has the topology of a Euclidean sphere. The potential energy surfaces of B@C 60 are characterized by two kinds of local minima: those with a boron atom located in the geometric center of the fullerene, and those with a boron atom bound to the fullerene inner wall. At the lowestenergy minimum, at the center, the boron atom is neutral, whereas the transition to the wall is accompanied by an electron transfer from boron to the fullerene cage. The two kinds of minima are separated by a ridge of avoided crossings that forms a surface with a nearly spherical shape. The properties of such systems may be altered by controlling the populations of the two kinds of minima, for example, by application of an external field. Such switchable atom-cage charge transfer may find applications in novel molecular devices.
Environmental Science & Technology, 1997
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