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Reports on the topology of the molecular electrostatic potential of 18 molecules, calculated in the framework of Kohnn-Sham density functional theory. Application of a search algorithm for location of the different kinds of critical points; Poincare-Hopf relationship for the molecular electrostatic potential.

Vibrational frequencies of three niobium normal modes of triniobium dicarbide neutral and cation have been determined from pulsed field ionization-zero electron kinetic energy photoelectron spectra. The niobium stretching mode has a frequency of 326 cm[SUP-1]in the neutral and 339 cm[SUP-1]in the ion. The two deformation modes have frequencies of 238 and 82 cm[SUP-1]in the neutral and a degenerate frequency of 258 cm[SUP-1]in the ion. The geometry of the triniobium dicarbide has been established by comparing the experimental spectra with theoretical calculations. The cluster has a trigonal bipyramid geometry with carbon atoms capping on each face of the metal frame. The cation cluster has D[SUB3h] symmetry whereas the neutral cluster has lower symmetry resulting from a Jahn-Teller distortion. A second low-lying structure with doubly bridging carbon atoms has been identified by the calculations but has not yet been observed. [ABSTRACT FROM AUTHOR]

The geometrical structures of the ground states of triniobium monoxide, Nb3O, and its cation, Nb3O+, have been determined by an experimental and theoretical study. Vibrationally resolved photoelectron spectra of an Nb3O cluster beam were obtained at 100 and 300 K using the pulsed field ionization-zero electron kinetic energy technique. The spectra were simulated by calculating multidimensional Franck–Condon factors using the geometries and harmonic vibrational frequencies obtained from density functional theory for the minimum energy structures of the ion and neutral molecule. The rather remarkable agreement between the experiment and the simulated spectra establishes that Nb3O and Nb3O+ have planar C2v structures with the oxygen atom bridging two niobium atoms. These are the most complex transition metal cluster structures to date to be characterized by gas phase spectroscopic techniques. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The isotropic and anisotropic hyperfine (hf) structures of a set of anionic, neutral and cationic radicals are investigated by means of local and nonlocal gradient-corrected density functional theory (DFT). The molecules under study are formed by H, C, N, O, F, and Cl atoms, and the hf structures are computed at both the experimental (where present) and various DFT and CI optimized geometries. The agreement with experiment and with results from previous CI or MRCI calculations is generally very satisfactory. The anisotropic hf couplings are relatively insensitive to basis set effects and functional form, whereas the isotropic hf couplings are highly dependent on the form of the nonlocal corrections to the exchange functional, particularly for heteroatoms. Using the functional by Perdew and Wang (‘‘PW86’’), an excellent agreement with experiment is obtained for all neutral and cationic radicals, whereas for the halide containing anions somewhat elongated bond lengths, and thus less accurate hf structures, are obtained. [ABSTRACT FROM AUTHOR]

Equilibrium geometries, bond dissociation energies, dipole moments, harmonic vibrational frequencies, and infrared intensities were calculated for a set of ten neutral nitrogen oxides (NO, NO2, NO3, N2O, sym N2O2, asym N2O3, sym N2O3, sym N2O4, asym N2O4, and N2O5) by applying one local and two gradient-corrected nonlocal functionals in a Gaussian-type-orbital density functional method. Comparison with available experimental data shows that, except for the bond dissociation energies, the local functional gives very accurate molecular properties. Nonlocal functionals considerably improve the bond dissociation energies, but the results still overestimate the experimental values by about 10 kcal/mol on average. For the other properties, the results obtained with nonlocal functionals are not necessarily superior to those calculated with the local functional. The properties of two molecules (sym N2O3 and asym N2O4) are predicted for the first time and several reassignments are proposed in the vibrational spectra of di-nitrogen oxides. [ABSTRACT FROM AUTHOR]

The hyperfine (hf) structures of radical cations are calculated using first principles density functional theory. Within the local spin density (LSD) approximation, the isotropic hyperfine coupling constants (Fermi contact terms) are computed for a set of linear (nonbranched) alkane and alkene radical cations with up to four carbon atoms. The results are as a whole in very good agreement with experimental data, obtained from low temperature matrix isolation electron-spin resonance (ESR) measurements, and with results from previous configuration interaction calculations. [ABSTRACT FROM AUTHOR]

Abstract: Exemplars of the state of the art in modeling enzymes are reviewed through a selection of works from leading schools using QM‐only cluster models, QM/MM models and QM/MM/MD models. A computational protocol is proposed, intended to guide neophytes through the myriad of methodological choices that are necessary for the successful study of chemical reactions in the complex enzymatic environment. [ABSTRACT FROM AUTHOR]

Quantum mechanical cluster model and quantum mechanical/molecular mechanical (QM/MM) calculations have been performed on series of natural and artificial carbonic anhydrases. Insight is gained into the promiscuous nature of the enzymatic activity upon metal-ion substitution (Zn-, Co-, Cd-CA hydrating CO 2 ), substrate substitution (Zn-CA hydrating carbodiiimide) and reaction substitution (Rh-CA hydrogenating CO 2 to formic acid). Substituting Zn for Co slightly increases the efficiency while Cu decreases the activity of the enzyme. The Cd variant, which has two cysteine residues in its first coordination shell, chooses a different reaction mechanism from the native Zn enzyme, Cd preferring a bidentate mode of binding bicarbonate. Carbodiimide acts as a competitive inhibitor. Rh-CA is predicted to be an effective catalyst for the hydrogenation of CO 2 , aided by two explicit water molecules that lower the activation barrier of the rate-limiting step, the release of the product. [ABSTRACT FROM AUTHOR]

The efficient conversion of carbon dioxide into useful products is a prime challenge to modern chemistry. An alternative route to address this challenge based on a rhodium-substituted human carbonic anhydrase is described that can be considered the first cofactor-independent reductase. This artificial enzyme is able to convert CO2 into formic acid, with potential applications in renewable energy. Our quantum mechanical investigation (QM/QM′ method), which considers the entire catalytic pocket (390 atoms), provides evidence that the catalytic process is governed by an energetically favored σ-bond-metathesis mechanism and the rate-limiting step is the release of formic acid (11.7 kcal mol−1). Water molecules are found to play an active role during the chemical process by contributing to reduce dramatically the energy of the rate-limiting step and favoring an efficient regeneration of the catalyst. [ABSTRACT FROM AUTHOR]

Hydrogenation reactions catalyzed by transition-metal-containing nanoparticles represent an important type of reaction in chemical industry. However, the modeling of these reactions in their working conditions requires much longer simulation times than what could usually be achieved with ab initio or first-principle methods. To address this problem, in this work, the density-functional-based tight-binding (DFTB) method was parameterized for hydrogenation reactions on molybdenum carbide catalysts, involving the elements C, H, Mo, O and Si. The overall quality of the DFTB parameters was tested with band structure/molecular orbital energies, molecular/crystal structures, chemisorption bond strengths, hydrogen adsorption energies, hydrogenation reaction energies, molecular vibrational frequencies, energy barriers and the structures of the transition states for systems of interest. The parameterized DFTB method gave errors of <1.45 % for bond distances of hydrocarbons and 4.86 % for non-hydrocarbons. It could reproduce the structure and vibrational frequencies (with errors of about 100 cm−1) of selected hydrocarbon–molybdenum carbide complexes obtained from DFT calculations. Good agreement was reached between DFTB and DFT on the dissociative adsorption of hydrogen on the α-Mo2C (0001) surface. For most of the hydrogenation reactions examined, DFTB showed errors of ~2 kcal/mol compared to DFT/PBE, with a few exceptions of ~5 kcal/mol. It could also describe the reaction energies, the forward and reverse energy barriers and the transition-state structures for the benzene hydrogenation reaction on a Mo38C19 cluster. [ABSTRACT FROM AUTHOR]

This Review presents an overview of the most common numerical simulation approaches for the investigation of electron transfer (ET) in proteins. We try to highlight the merits of the different approaches but also the current limitations and challenges. The article is organized into three sections. Section 2 deals with direct simulation algorithms of charge migration in proteins. Section 3 summarizes the methods for testing the applicability of the Marcus theory for ET in proteins and for evaluating key thermodynamic quantities entering the reaction rates (reorganization energies and driving force). Recent studies interrogating the validity of the theory due to the presence of non-ergodic effects or of non-linear responses are also described. Section 4 focuses on the tunneling aspects of electron transfer. How can the electronic coupling between charge transfer states be evaluated by quantum chemistry approaches and rationalized? What interesting physics regarding the impact of protein dynamics on tunneling can be addressed? We will illustrate the different sections with examples taken from the literature to show what types of system are currently manageable with current methodologies. We also take care to recall what has been learned on the biophysics of ET within proteins thanks to the advent of atomistic simulations. [ABSTRACT FROM AUTHOR]

Transition-state theory (TST) is a widely accepted paradigm for rationalizing the kinetics of chemical reactions involving one potential energy surface (PES). Multiple PES reaction rate constants can also be estimated within semiclassical approaches provided the hopping probability between the quantum states is taken into account when determining the transmission coefficient. In the Marcus theory of electron transfer, this hopping probability was historically calculated with models such as Landau-Zener theory. Although the hopping probability is intimately related to the question of the transition from the fully quantum to the semiclassical description, this issue is not adequately handled in physicochemical models commonly in use. In particular, quantum nuclear effects such as decoherence or dephasing are not present in the rate constant expressions. Retaining the convenient semiclassical picture, we include these effects through the introduction of a phenomenological quantum decoherence function. A simple modification to the usual TST rate constant expression is proposed: in addition to the electronic coupling, a characteristic decoherence time τdec now also appears as a key parameter of the rate constant. This new parameter captures the idea that molecular systems, although intrinsically obeying quantum mechanical laws, behave semiclassically after a finite but nonzero amount of time (τdec). This new degree of freedom allows a fresh look at the underlying physics of chemical reactions involving more than one quantum state. The ability of the proposed formula to describe the main physical lines of the phenomenon is confirmed by comparison with results obtained from density functional theory molecular dynamics simulations for a triplet to singlet transition within a copper dioxygen adduct relevant to the question of dioxygen activation by copper monooxygenases. [ABSTRACT FROM AUTHOR]

The structures and stabilities of the glycerol (G) and glycerol 3-phosphate (G3P) isomers have been calculated in the gas phase, using an ab initio density functional theory (DFT) method. The different conformational structures are shown to be at the origin of the various phospholipid conformers, except, obviously, for the alkyl chain torsions. The G3P conformations have been examined taking into account the experimental structures of the complexation sites in the glycerol kinase (GK) and glycerol 3-phosphate acyl transferase (G3PAT) enzymes, which correspond to the first and second steps of the “de novo” phospholipid biogenesis, respectively. The conformational analysis of the glycerophosphate skeleton is shown to determine most of the structural characteristics of the phosphatidyl choline lipids, which differ by the length of their diacyl chains, i.e., dilauroyl (DL), dimyristoyl (DM), and dipalmitoyl (DP) phosphatidylcholines (PC). Higher energy conformers with kinks in the acyl chains have been found, in preparation for molecular dynamics studies of the chain melting phase transformation. [ABSTRACT FROM AUTHOR]

Most known DNA-dependent RNA polymerases (RNAPs) share a universal heptapeptide, called the NADFDGD motif. The crystal structures of RNAPs indicate that in all cases this motif forms a loop with an embedded triad of aspartic acid residues. This conserved loop is the key part of the active site. Based on the crystal structures of the yeast RNAP II, we have studied this common active site for three cases: (1) single RNAP, (2) pre-translocation elongation complex, and (3) post-translocation elongation complex. Here we have applied two different modeling methods, the GGA density functional theory method (PBE) of quantum mechanics (QM) and the ReaxFF reactive force field. The QM calculations indicate that the loop shrinks from pre- to post-translocation and expands from post- to pre- translocation. In addition, PBE MD simulations in the gas phase at 310 K shows that the loop in the single-RNAP case is tightly connected to a catalytic Mg 2+ ion and that there is an ordered hydrogen bond network in the loop. The corresponding ReaxFF MD simulation presents a less stable loop structure, suggesting that ReaxFF may underestimate the coordinating interactions between carbonyl oxygen and magnesium ion compared to the gas phase QM. However, with ReaxFF it was practical to study the dynamics for a much more detailed model for the post-translocational case, including the complete loop and solvent. This leads to a plausible reactant-side model that may explain the large difference in efficiency of NTP polymerization between RNA and DNA polymerases. [ABSTRACT FROM AUTHOR]

Standard density functional theory (DFT) is augmented with a damped empirical dispersion term. The damping function is optimized on a small, well balanced set of 22 van der Waals (vdW) complexes and verified on a validation set of 58 vdW complexes. Both sets contain biologically relevant molecules such as nucleic acid bases. Results are in remarkable agreement with reference high-level wave function data based on the CCSD(T) method. The geometries obtained by full gradient optimization are in very good agreement with the best available theoretical reference. In terms of the standard deviation and average errors, results including the empirical dispersion term are clearly superior to all pure density functionals investigated—B-LYP, B3-LYP, PBE, TPSS, TPSSh, and BH-LYP—and even surpass the MP2/cc-pVTZ method. The combination of empirical dispersion with the TPSS functional performs remarkably well. The most critical part of the empirical dispersion approach is the damping function. The damping parameters should be optimized for each density functional/basis set combination separately. To keep the method simple, we optimized mainly a single factor, sR, scaling globally the vdW radii. For good results, a basis set of at least triple-ζ quality is required and diffuse functions are recommended, since the basis set superposition error seriously deteriorates the results. On average, the dispersion contribution to the interaction energy missing in the DFT functionals examined here is about 15 and 100% for the hydrogen-bonded and stacked complexes considered, respectively. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 555–569, 2007 [ABSTRACT FROM AUTHOR]

Kohn and Sham introduced orbitals into density–functional theory (DFT) as a set of physically meaningless auxiliary quantities useful only for calculating the total energy and charge density. While the traditional view is that Kohn–Sham orbitals do not approximate anything, Duffy et al. [Phys. Rev. A 50 (1994) 4707] showed that Kohn–Sham orbitals calculated using approximate exchange-correlation (xc) potentials could provide excellent approximations to spherically averaged momentum distributions, despite the fact that the corresponding Kohn–Sham orbital energies do not provide good approximations to ionization potentials when typical common present-day functionals are used. Since the original conclusions were based upon approximate xc potentials, the question arises as to how these conclusions might change when the same orbitals and orbital energies are calculated using an exact (or nearly exact) xc potential. For example, it has long been known that the highest occupied molecular orbital energy should give the exact ionization potential when the DFT xc functional is exact, but that this is not observed for approximate potentials. What about the other orbital energies? Long regarded as artifactual, we show that (1) Kohn–Sham orbital energies calculated using the exact Kohn–Sham exchange potential are actually better approximations to experimental ionization potentials than are Hartree–Fock orbital energies calculated via Koopmans’ theorem. We also show that (2) there are only negligable differences between spherically averaged momentum distributions calculated from HF orbitals and from Kohn–Sham orbitals calculated using the exact Kohn–Sham exchange potential, thus partially addressing the question of how the use of the exact Kohn–Sham potential will affect predictions for electron momentum spectroscopy. In addition to the two numbered observations above can be added that (3) it is quite remarkable that a nominally initial state theory such as DFT can do so well in describing ionization, a phenomenon which one expects to be sensitive to both initial and final states (before and after the ionization event). [Copyright &y& Elsevier]

Density functional calculations of neutral and cationic vanadium trimers are presented. The all-electron calculations employed a gradient-corrected exchange-correlation functional and a newly developed vanadium basis set optimized for gradient-corrected density functional calculations. For both neutral and charged systems, different isomers were studied in order to determine the lowest energy structures. A vibrational analysis was performed in order to characterize these isomers. We found an equilateral triangle [sup 2]A[sub 1][sup ′] ground state for V[sub 3] and an equilateral triangle [sup 3]A[sub 2][sup ′] ground state for V[sub 3][sup +]. The experimental pulsed-field ionization zero-electron-kinetic energy spectrum was simulated by calculating multidimensional Franck-Condon factors, using the geometries and harmonic frequencies of the calculated minima of V[sub 3] and V[sub 3][sup +]. The excellent agreement between the experimental and theoretical spectra allows the unequivocal determination of the ground state structure of V[sub 3]. This work provides a final answer to the controversy in the literature about the ground state structure of V[sub 3] and yields deeper insight into the electronic structure of the neutral and cationic systems. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The structures of different neutral and cationic isomers of Nb[sub 3]O, Nb[sub 3]S and Nb[sub 3]Se were optimized within the framework of Kohn-Sham density functional theory. For Nb[sub 3]O, neutral and cationic, the lowest minimum is a planar C[sub 2v] structure with an edge-bound oxygen atom. The binding energy of the oxygen to the Nb[sub 3] cluster is 184.9 kcal/mol, 185.4 kcal/mol for the cationic system. For Nb[sub 3]S and Nb[sub 3]Se, neutral and cationic, the lowest minima are three-dimensional structures. The corresponding binding energies are 137.9, 138.1, 131.8 and 132.3 kcal/mol for Nb[sub 3]S, Nb[sub 3]S[sup +], Nb[sub 3]Se and Nb[sub 3]Se[sup +], respectively. In order to explain the different ground state structures of Nb[sub 3]O, on the one hand, and Nb[sub 3]S and Nb[sub 3]Se, on the other, in terms of the nature of the bonding in each of them a topological analysis of the molecular electrostatic potential was performed. The different relative stabilities of two- and three-dimensional structures can be explained on the basis of bond critical points in the molecular electrostatic potential. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]

deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program implements an additive QM/MM (quantum mechanics/molecular mechanics) module relying either on non-polarizable or polarizable force fields. QM/MM methodologies available in deMon2k include ground-state geometry optimizations, ground-state Born–Oppenheimer molecular dynamics simulations, Ehrenfest non-adiabatic molecular dynamics simulations, and attosecond electron dynamics. In addition several electric and magnetic properties can be computed with QM/MM. We review the framework implemented in the program, including the most recently implemented options (link atoms, implicit continuum for remote environments, metadynamics, etc.), together with six applicative examples. The applications involve (i) a reactivity study of a cyclic organic molecule in water; (ii) the establishment of free-energy profiles for nucleophilic-substitution reactions by the umbrella sampling method; (iii) the construction of two-dimensional free energy maps by metadynamics simulations; (iv) the simulation of UV-visible absorption spectra of a solvated chromophore molecule; (v) the simulation of a free energy profile for an electron transfer reaction within Marcus theory; and (vi) the simulation of fragmentation of a peptide after collision with a high-energy proton. [ABSTRACT FROM AUTHOR]