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The ground states of the neutral and anionic tetrafluoride and hexafluoride series of 3d-metal atoms from Sc to Zn were assigned by using a double-check approach in which the pure and hybrid density functional methods were interchangeably used. It was confirmed that all these neutral fluorides are superhalogens except for TiF4. The electron affinities of the hexafluorides were shown to be consistently higher than those of the tetrafluorides in accordance with the superhalogen conception of the extra electron delocalization over a larger number of the electronegative ligands. In the search for mononuclear fluorides possessing higher electron affinities, we considered the M(F2)6- and M(F3)6- series where M = Sc-Zn. We found that the optimized geometrical structures in both series may be described as MF6-- k(F2), k = 3 and 6, of which the geometry of the MF6- core mimics that of the corresponding hexafluoride anion and the F2 dimers are kept in a bound state by polarizing forces. In these cases, the electron affinity is decreased by tenths of eV with respect to the electron affinity of the core hexafluorides due to a confinement of the extra electron by the F2 environment.

The mercury dihalides show a remarkable diversity in the structural preferences in their minimum energy structure types, spanning molecular to strongly bound ionic solids. A challenge in the development of density functional methods for extended systems is to arrive at strategies that serve equally well such a broad range of bonding modes or structural preferences. The chemical bonding and the stabilities of mercury dihalides and the general utility and reliability of the van der Waals density functional with C09 exchange (vdW-DF-C09) in predicting or describing the energetics and structural preferences in these metal dihalides is examined. We show that, in contrast with the uncorrected generalized gradient approximation of the Perdew-Burke-Erzenhoff (PBE) exchange-correlation functional, qualitative and quantitative patterns in the bonding of the mercury dihalide solids are well reproduced with vdW-DF-C09 for the full series of HgX2 systems for X = F, Cl, Br, and I. The possible existence of a low-temperature cotunnite polymorph for HgF2 and PbF2 is posited.

Quantum chemical calculations using density functional methods were performed for complexes of type L2C2 with L = NHCMe (1), SNHCMe (2) (S = saturated), cAACMe (3), and diamidocarbene (DACMe) (4). ...

Tri-coordinated Fe single sites on the (111)n surface of γ-alumina have been investigated by the carefully calibrated density functional methods (M12-L/SV) using periodic boundary conditions. For a...

Two methods to calculate negative electron affinities systematically from ground-state density functional methods are presented. One makes use of the lowest unoccupied molecular orbital energy shift provided by approximate inclusion of derivative discontinuity in the nearly correct asymptotic potential (NCAP) nonempirical, constraint-based generalized gradient approximation exchange functional. The other uses a second-order perturbation calculation of the derivative discontinuity based on the NCAP exchange-correlation potential. On a set of thirty-eight molecules, NCAP leads to a rather accurate description that is improved further through the perturbation correction. The results presented show the importance of the asymptotic behavior of the exchange-correlation potential in the calculation of negative electron affinities as well as demonstrating the versatility of the NCAP functional.

The broken symmetry method is a standard approach for the calculation of isotropic exchange coupling constants in oligonuclear transition-metal compounds with density functional methods. It is most...

We explore the suitability of three popular density functionals (B97-D3, B3LYP-D3, M05-2X) for producing accurate equilibrium geometries of van der Waals (vdW) complexes with diverse binding motifs. For these functionals, optimizations using Dunning's aug-cc-pVDZ basis set best combine accuracy and a reasonable computational expense. Each DFT/aug-cc-pVDZ combination produces optimized equilibrium geometries for 21 small vdW complexes of organic molecules (up to four non-hydrogen atoms total) that agree with high-level CCSD(T)/CBS reference geometries to within ±0.1 Å for the averages of the center-of-mass displacement and the mean least root-mean-squared displacement. The DFT/aug-cc-pVDZ combinations are also able to reproduce the optimal center-of-mass displacements interpolated from CCSD(T)/CBS radial potential energy surfaces in both NBC7x and HBC6 test sets to within ±0.1 Å. We therefore conclude that each of these denisty functional methods, together with the aug-cc-pVDZ basis set, is suitable for producing equilibrium geometries of generic nonbonded complexes.

We report an alternative quantum mechanical:quantum mechanical (QM:QM) method to the currently used periodic density functional calculations including dispersion and investigate its performance with respect to main structural and energetic properties of the X23 set of molecular crystals. By setting the goal of reproducing reference periodic BLYP+D3 values and by embedding BLYP+D3 into DFTB, we obtain results similar to those of periodic BLYP+D3-typically within 1-2% in lattice energies and ∼0.4% in cell volumes. The accuracy of this QM:QM method in comparison to DFTB+D and DFT+D for the X23 set of molecular crystals is discussed.

Adsorption of the TaSi16 cluster on highly oriented pyrolytic graphite (HOPG) is studied using density functional methods. These calculations resolve some of the issues raised by the recent experiments of Shubita et al. (Shibuta, M.; Ohta, T.; Nakaya, M.; Tsunoyama, H.; Eguchi, T.; Nakajima, A. Chemical Characterization of an Alkali-Like Superatom Consisting of a Ta-Encapsulating Si16 Cage. J. Am. Chem. Soc. 2015, 137, 14015−14018) and provide additional insights into the system. For the first time, the ground-state structure of TaSi16 is obtained through a global search employing an evolutionary algorithm. A symmetric structure of the Si cage, together with a small charge transfer from Ta to the Si atoms, explains the observed core-level photoemission spectra. The ground-state isomer is deposited on HOPG at different points and in different random orientations. The cluster is found to be physisorbed on HOPG and retains the Ta-encapsulating cage structure, with little charge transfer between the cluster a...

Halogen-substituted pyrimidines, such as 5-bromouracil and 5-iodouracil, have been used as radio therapeutic (RT) agents in cancer treatment. The radiosensitizer activity of 5-bromouracil is attributed to its reaction with electron which produce the highly reactive uracil-5-yl radical by dissociating the C5-Br bond. Using density functional methods and highly accurate Gaussian 4 (G4) theory, herein, we show that 5-bromocytosine (5-Brcyt) after reaction with electron, also, leads to the formation of cytosine-5-yl radical. However, our results show that this species can subsequently undergo a base catalyzed tautomerization reaction to form the π-aminyl radical followed by a second tautomerization to the thermodynamically most stable σ-iminyl radical (cytN•) (see scheme 1). From the present theoretical calculations, we infer that the mechanism of the formation of cytN• by one-electron reduction of 5-Brcyt is straightforward and may take place in 5-BrCyt labeled DNA in competition with the usual reactions expected for the cytosine-5-yl radical such as abstraction and water addition.

The failure of available density functional methods to compute accurate reaction enthalpies of common organic reactions is well documented. Herein, we demonstrate that the disparate results from different functionals stem from the systematic errors in the underlying elementary reactions that represent the changes in the bonding environment between reactants and products. We develop a rigorous protocol to correct for these systematic errors and obtain dramatically improved results with deviations of only 1-2 kcal/mol for most functionals.

The M4(CO)12 molecules Co4(CO)12, Rh4(CO)12, and Ir4(CO)12 have two low-lying structures, the all-terminal structure with Td symmetry and the triply bridged structure with C3v symmetry. A total of 45 density functional theory (DFT) methods have been used to predict structures and vibrational frequencies for Co4(CO)12, Rh4(CO)12, and Ir4(CO)12. The different DFT methods show a broad range of energy differences ΔE = E(Td) - E(C3v). For Rh4(CO)12, none of the 45 DFT predictions is within 11 kcal/mol of the 2005 experimental value of 5.1 ± 0.6 kcal/mol reported by Allian and Garland (Dalton Trans. 2005, 1957 - 1965). For the challenging Ir4(CO)12 molecule, 21 DFT methods predict the correct Td structure, while 24 DFT methods predict the C3v structure to lie lower in energy. This research reveals many peculiar problems in the computation of the vibrational frequencies for the all-terminal structure.

We present an implementation of a time-dependent density functional theory (TD-DFT) linear response module in NWChem for unrestricted DFT calculations and apply it to the calculation of resonant Raman spectra in open-shell molecular systems using the short-time approximation. The new source code was validated and applied to simulate Raman spectra on several doublet organic radicals (e.g., benzyl, benzosemiquinone, TMPD, trans-stilbene anion and cation, and methyl viologen) and the metal complex copper phthalocyanine. We also introduce a divide-and-conquer approach for the evaluation of polarizabilities in relatively large systems (e.g., copper phthalocyanine). The implemented tool gives comparisons with experiment that are similar to what is commonly found for closed-shell systems, with good agreement for most features except for small frequency shifts, and occasionally large deviations for some modes that depend on the molecular system studied, experimental conditions not being accounted in the modeling such as solvation effects and extra solvent-based peaks, and approximations in the underlying theory. The approximations used in the quantum chemical modeling include (i) choice of exchange-correlation functional and basis set; (ii) harmonic approximation used in the frequency analysis to determine vibrational normal modes; and (iii) short-time approximation (omission of nuclear motion effects) used in calculating resonant Raman spectra.

A number of commonly available density functionals have been tested for their ability to describe the energetics and the geometry at conical intersections in connection with the spin-restricted ensemble referenced Kohn–Sham (REKS) method. The minimum energy conical intersections have been optimized for several molecular systems, which are widely used as paradigmatic models of photochemical rearrangements and models of biological chromophores. The results of the calculations are analyzed using the sign-change theorem of Longuet-Higgins and a method of elementary reaction coordinates of Haas et al. The latter approach helps to elucidate the differences between the geometries at conical intersections as predicted by the multireference wave function ab initio methods and by the density functional methods. Overall, the BH&HLYP density functional yields the best results for the conical intersection geometries and energetics.

Crystalline oxalyl dihydrazide has five experimentally known polymorphs whose energetics are governed by subtle balances between intra- and intermolecular interactions, providing a severe challenge for theoretical crystal structure modeling. Previous work has shown that many common density functional methods that neglect van der Waals dispersion cannot correctly describe this system, but it has been argued that empirically dispersion-corrected DFT-D performs much better. Here, we examine these crystals with second-order Møller-Plesset perturbation theory (MP2) and related levels of theory using the fragment-based hybrid many-body interaction method. The energetics prove sensitive to the treatment of electron-electron correlation, the basis set, many-body induction, three-body dispersion, and zero-point contributions. Nevertheless, our best predictions for the polymorph energy ordering based on dispersion-corrected MP2C calculations agree with the available experimental data. In contrast, lower levels of theory, including the common B3LYP-D* and D-PW91 dispersion-corrected density functional approximations, fail to reproduce experimental observations and/or the high-level calculations.

Ab initio and density functional methods have been employed to study the structure, stability, and spectral properties of various ethylene glycol (EG(m)) and ethylene glycol-water (EG(m)W(n)) (m = 1-3, n = 1-4) clusters. The effective fragment potential (EFP) approach was used to explore various possible EG(m)W(n) clusters. Calculated interaction energies of EG(m)W(n) clusters confirm that the hydrogen-bonding interaction between EG molecules is perturbed by the presence of water molecules and vice versa. Further, energy decomposition analysis shows that both electrostatic and polarization interactions predominantly contribute to the stability of these clusters. It was found from the same analysis that ethylene glycol-water interaction is predominant over the ethylene glycol-ethylene glycol and water-water interactions. Overall, the results clearly illustrate that the presence of water disrupts the ethylene glycol-ethylene glycol hydrogen bonds.

This study provides comprehensive benchmark calculations for the thermochemical properties of the common α-amino acids. Calculated properties include the proton affinity, gas-phase basicity, protonation entropy, ΔH°(acid), ΔG°(acid), and enthalpies of formation for the protonated and deprotonated α-amino acids. In order to determine the performance at various levels of theory, including density functional methods and composite methods, the calculated thermochemical properties are compared to experimental results. For all the common α-amino acids investigated, the thermochemical properties computed with the Gaussian-n theories were found to be quite consistent with each other in terms of mean absolute deviation from experiment. While all Gaussian-n theory values can serve as benchmarks, we focus on the G3MP2 values as it is the least resource-intensive of the Gaussian-n theories considered.

Coordinative polymerization of fluorinated olefins is still a challenging task. We analyzed the catalytic properties of diimido chromium VI compounds computationally by density functional methods. It was found that reactivity predictions depend strongly on the density functional chosen for the computations. Therefore, DFT calculations were calibrated to high level wave function theory calculations. Then geometrical parameters, which can be tuned by a ligand, were scanned to elucidate their influence on the catalytic activity. Having arrived at an optimal parameter set, we randomly assembled chromium complexes from a fragments database and automatically checked for their activities. This led to the proposal of three exemplary catalyst candidates.

In this work, we have revisited the mechanism of the formic acid + OH radical reaction assisted by a single water molecule. Density functional methods are employed in conjunction with large basis sets to explore the potential energy surface of this radical-molecule reaction. Computational kinetics calculations in a pseudo-second-order mechanism have been performed, taking into account average atmospheric water concentrations and temperatures. We have used this method recently to study the single water molecule assisted H-abstraction by OH radicals (Iuga, C.; Alvarez-Idaboy, J. R.; Reyes, L.; Vivier-Bunge, A. J. Phys. Chem. Lett. 2010, 1, 3112; Iuga, C.; Alvarez-Idaboy, J. R.; Vivier-Bunge, A. Chem. Phys. Lett. 2010, 501, 11; Iuga, C.; Alvarez-Idaboy, J. R.; Vivier-Bunge, A. Theor. Chem. Acc. 2011, 129, 209), and we showed that the initial water complexation step is essential in the rate constant calculation. In the formic acid reaction with OH radicals, we find that the water-acid complex concentration is small but relevant under atmospheric conditions, and it could in principle be large enough to produce a measurable increase in the overall rate constant. However, the water-assisted process occurs according to a formyl hydrogen abstraction, rather than abstraction of carboxylic hydrogen as in the water-free case. As a result, the overall reaction rate constant is considerably smaller. Products are different in the water-free and water-assisted processes.

The three smallest symmetrical paracyclophanes, having tethers with two, three, or four methylene groups, have been examined with four density functional methods (B3LYP, M06-2x, B97-D, ωB97X-D). The geometries predicted by functionals accounting for medium-range correlation or long-range exchange and/or dispersion are in close agreement with experiment. In addition, these methods provide similar estimates of the strain energy of the paracylcophanes, which decrease with increasing tether length. [4.4]Paracyclophane is nearly strain-free, reflecting the small out-of-plane distortion of its phenyl rings. Lastly, the barrier for interconversion of the conformers of [3.3]paracylcophane is computed in close agreement with experiment, and an estimate for phenyl rotation in [4.4]paracyclophane of about 19 kcal mol(-1) is predicted by the DFT methods employed.

Electric fields have been claimed to influence intrinsic acidity on zeolites, and in this work, we try to establish a relation between the electric field and Bronsted acidity. In this study, we use experimental data from commercial samples of mordenite (Si/Al ≈ 4−8) and we make periodic first-principles calculations of the infrared OH stretching bands with periodic density functional methods on several reliable models of a mordenite unit cell with a composition of Si40Al8O96H8 (Si/Al = 5). Experiments show a high-frequency band at 3610 cm−1 and a low-frequency band at 3585 cm−1, and the computational results give frequencies in the range of 3600−3510 cm−1, slightly lower due to the PAW-GGA methodology employed. A rationalization of the IR frequencies found has been attempted on the basis of physicochemical properties of the microporous material. No correlation has been found with geometrical parameters, such as SiO(H)Al angles, or chemical parameters, such as the number of Al neighbors. No clear relation ...

Trends for R-X bond dissociation energies have been examined with density functional methods of B3LYP, BMK, M06-2X, MC3MPW, B2PLYP, MCG3-MPW, and XYG3, as well as G3, MCG3/3, G3X, and G4 theories as functions of alkylation (i.e., R(•) = Me, Et, i-Pr, t-Bu) and X(•) substitution (i.e., X(•) = H, Me, Cl, OH). The results highlight the physical origin of success or failure of each method and demonstrate the good agreement with experimental results for G4, MCG3-MPW, and XYG3. The last holds great promise as a reliable method that is applicable to larger systems.

Electronic structure, charge distribution, and vibrational frequencies of cucurbit[n]uril, CB[n] (n = 5-12), hosts have been derived using the density functional methods. CB[n] conformers with different orientations of methylene group connecting glycouril units have been investigated. The conformers that possess uniform CB[n] cavity turn out to be of lowest energy, and molecular electrostatic potential (MESP) herein engender shallow minima near ureido oxygens along the series. MESP topography has been utilized to estimate the cavity height and diameter; the ratio of which governs the shape (circular or elliptical) of the cavity. When this ratio is larger than unity (for CB[n] with nor= 8), an elliptical host cavity is noticed. Calculated vibrational spectra reveal that carbonyl stretching frequency shift in successive CB[n] homologue decreases steadily from 1760 cm(-1) in CB[5] to 1742 cm(-1) in CB[12]. An increase in glycouril units along the CB[n] series influences significantly the intensity profile of C horizontal lineO and C-N stretching vibrations in the calculated infrared spectra. Furthermore, calculated (1)H chemical shifts predict that one of methylene protons directing outside the host cavity are deshielded, whereas the remaining proton near the carbonyl group exhibits downshifted signal in the NMR spectra.

Hydrogen chemisorption and diffusion on Pt and Pd decorated MoO3(010) surfaces were examined using periodic density functional methods. The deposition of Pt and Pd on MoO3 was first carefully investigated. The strong metal−support interactions were found to greatly reduce the catalytic activity of Pt and Pd atoms anchored at their most favorable binding sites. On the other hand, the energies and activation barriers along selected diffusion pathways indicate that hydrogen dissociation and diffusion on the supported Pt5 and Pd5 clusters are feasible, whereas Pt clusters exhibit better catalytic activity than Pd clusters. Subsequently, the dissociated hydrogen atoms tend to directly diffuse onto the sublayer oxygen atoms instead of the surface oxygen atoms.

An improved direct correlation function is proposed and applied to construct an accurate free energy functional. The theoretical method is extended to analyze the pore size distributions (PSDs) of both slit- and cylindrical-shaped carbonaceous materials. With the same parameters for the fluid and material as in the simulation, the model is much more advantageous than the known density functional methods for calculating the adsorption isotherms in individual pores. The overall PSDs for two model carbons are evaluated for CH4, CF4, and SF6 absorbates, and good results are obtained. The results are reliable because the two model carbons have structures that are exactly known. Encouraged by the success with slit pores, we further extend the model to the internal cylindrical space of a single-walled carbon nanohorn. The PSDs of the carbon nanohorn are evaluated, and satisfactory results are again obtained.

The conformational study on N-acetyl- N'-methylamide of l-lactic acid (Ac-Lac-NHMe, the Lac dipeptide) is carried out using ab initio HF and density functional methods with the self-consistent reaction field method to explore its backbone conformational preferences and cis-trans isomerization for the depsipeptide with an ester bond in the gas phase and in solution. In the gas phase and in chloroform, the conformation tB with a trans depsipeptide bond is most preferred for the Lac dipeptide, whose backbone torsion angles are phi approximately -150 degrees and psi approximately -5 degrees , juxtaposed to those of the 3 10-helical structure. The larger shift in phi is brought to reduce the repulsion between the two carbonyl carbons of the acetyl and NHMe groups. However, the polyproline II-like tF conformation becomes more populated and the relative stability of conformation tB decreases significantly as the solvent polarity increases. This may be ascribed to weakening a C(5) hydrogen bond between the depsipeptidyl oxygen and the carboxyl amide hydrogen that plays a role in stabilizing the conformation tB in the gas phase and in chloroform. The cis populations about the depsipeptide bond are nearly negligible in the gas phase and in solution. The rotational barriers to the cis-trans isomerization of the depsipeptide bond for the Lac dipeptide are calculated to be about 11 kcal/mol, which is about half of those for the Ala dipeptide, although they increase somewhat with the increase of solvent polarity. The cis-trans isomerization of the depsipeptide bond proceeds through either clockwise or anticlockwise rotations with torsion angles of about +90 degrees or -90 degrees , respectively, in the gas phase and in solution, whereas it has been known that the isomerization proceeds through only the clockwise rotation for alanyl and prolyl peptide bonds. The pertinent distances between the depsipeptidyl oxygen and the carboxyl amide hydrogen can describe the role of this hydrogen bond in stabilizing the transition state structures in the gas phase and in solution.

A systematic theoretical study on several models of Zn(II) complexes has been carried out employing both ab initio correlated wave function and density functional methods. The performance of five different functionals namely PW91, PBE, B3LYP, MPWLYP1M, and TPSS in the prediction of metal-ligand bond distances, binding energies, and proton affinities has been assessed comparing the results to those obtained with the MP2 and CCSD(T) wave function methodologies. Several basis sets ranging from double-ζ up to quintuple-ζ quality have been used, including the recently developed all-electron correlation consistent basis sets for zinc. It is shown that all the tested functionals overestimate both the metal-ligand bond distances and the binding energies, being that the B3LYP and TPSS functionals are the ones that perform the best. An analysis of the metal-ligand interaction energy shows that induction and charge-transfer effects play a prominent role in the bonding of these systems, even for those complexes with the less polarizable ligands. This finding highlights the importance of a correct description of the polarization of the monomers' charge densities by any theoretical method which aims to be applied to the study of Zn(II) complexes.

We test a few ways to improve atomization energies of CHON molecules and found that the best way to do it is simply by correcting the atom energies of the participating atoms. Extraordinary improvement on the average errors is obtained. For the HF/6-31G** level of theory an average error of 271.2 kcal/mol on 115 molecules is improved to 6.7 kcal/mol simply by correcting the atomic energy of the four chon atoms. The corrections to density functional methods allow us to reach a chemical accuracy of 2 kcal/mol.

In recent years, BN fullerenes have been synthesized experimentally. As their carbon counterparts, these BN fullerenes could be assembled in molecular solids, but this possibility has been studied little in the literature. In this work, we focus on the smallest synthesized BN fullerene, B12N12, which is built by squares and hexagons. First, the interaction between two of these fullerenes has been analyzed, using the hybrid B3LYP and MPW1PW91 density functional methods. Two different interactions have been studied in the dimer, a square facing a square (S−S) and a hexagon facing a hexagon (H−H). In both cases, a B is facing a N. The most stable dimer was found to be S−S facing, with covalent interactions between the monomers, but other dimers with weak interactions have been found as well, which opens possibilities of new systems, as in the case of fullerene dimers and solids. The solids resulting from the infinite repetition of the characterized dimers were optimized, finding two different solids, with co...

The potential energy surfaces involved in the insertion of diazomethane species R2CN2 (R = H, Ph) into the Zr−CH3 bonds of Cp2Zr(CH3)2 are examined using density functional methods. The first insertion leads to the experimentally observed mono-hydrazonato complex Cp2Zr(CH3)(CH3−N−NCPh2), for which the reaction energy is calculated to be −37 kcal/mol. Insertion of a second diazomethane molecule into the remaining Zr−Me bond leads to the bis-hydrazonato complex Cp2Zr(CH3−N−NCPh2)2, which is calculated to be a stable species with an overall reaction exothermicity of −27 kcal/mol. While the first insertion proceeds with a small activation barrier (2−7 kcal/mol), a more substantial activation barrier (25 kcal/mol) is found for the second insertion, but not sufficiently large to preclude formation of the bis-hydrazonato complex. This formally 20-valence-electron species is hence predicted to be a target for synthesis. The bonding in the bis-hydrazonato complexes shows significant Zr 4d admixture in the MOs invo...

The electronic structures of Lindqvist type functionalized polyoxometalates (POM) ([Mo6O18R]n- R=O, NO, NAr, NNAr, NNAr2; n=2, 3) have been investigated using density functional methods. We discuss the role of the replacement of terminal oxo ligands by pi-donor/acceptor multiple-bonded nitrogenous ligands on the basis of geometrical parameters, charge analyses, reactivity indexes, and vibrational spectra. The calculated reactivity indexes (chemical potential, electronegativity, hardness, and electrophilicity) indicate that the most reactive functionalized POMs are those substituted by pi-acceptor ligands. These pi-acceptor ligands induce a decrease in the hardness and an increase in the chemical potential and electrophilicity, thus increasing the reactivity. Our calculations are in reasonable agreement with reported experimental data.

Potassium sulfate crystals orient and overgrow 2-aminobenzenesulfonate (OSA), and many other sulfonated aromatic compounds, on particular facets during growth from solution. The energetics associated with adsorption of OSA and benzenesulfonate (BS) were calculated using both molecular mechanical and density functional methods, in order to assess the surface binding effectiveness of these compounds on various faces of potassium sulfate. It was found that both theoretical techniques predicted that OSA and BS bind to potassium sulfate to a similar extent. The surface binding capacities were also assessed experimentally by studying the growth rates of individual faces of K2SO4, with results showing similar findings to those from the computational studies.

Several reaction pathways on the potential energy surface (PES) for the reaction of CH 3 O 2 radicals with Br atoms are examined using both ab initio and density functional methods. Analysis of the PES suggests the presence of the stable intermediates CH 3 OOBr and CH 3 OBrO. CH 3 OOBr is calculated to be more stable than CH 3 OBrO by 9.7 kcal mol -1 with a significant barrier preventing formation of CH 3 OBrO via isomerization of CH 3 OOBr. The relative importance of bi- and termolecular product channels resulting from the initially formed CH 3 OOBr adduct are assessed based on calculated barriers to the formation of CH 2 OO + HBr, CH 3 O + BrO, CH 3 Br + O 2 , and CH 2 O + HOBr.

Five multilevel model chemistries (CBS-QB3, G3B3, G3MP2B3, MCG3/3, and MC-QCISD/3) and seven hybrid density functional methods (PBE0, B1B95, B3LYP, MPW1KCIS, PBE1KCIS, and MPW1B95) have been applied to the calculation of gas-phase basicity and proton affinity values for a series of 17 molecules relevant to the study of biological phosphoryl transfer. In addition, W1 calculations were performed on a subset of molecules. The accuracy of the methods was assessed and the nature of systematic errors was explored, leading to the introduction of a set of effective bond enthalpy and entropy correction terms. The multicoefficient correlation methods (MCG3/3 and MC-QCISD), with inclusion of specific zero-point scale factors, slightly outperform the other multilevel methods tested (CBS-QB3, G3B3, and G3MP2B3), with significantly less computational cost, and in the case of MC-QCISD, slightly less severe scaling. Four density functional methods, PBE1KCIS, MPW1B95, PBE0, and B1B95 perform nearly as well as the multilevel methods. These results provide an important set of benchmarks relevant to biological phosphoryl transfer reactions.

We employed four newly developed density functional theory (DFT) methods for the calculation of five pi hydrogen bonding systems, namely, H2O-C6H6, NH3-C6H6, HCl-C6H6, H2O-indole, and H2O-methylindole. We report new coupled cluster calculations for HCl-C6H6 that support the experimental results of Gotch and Zwier. Using the best available theoretical and experimental results for all five systems, our calculations show that the recently proposed MPW1B95, MPWB1K, PW6B95, and PWB6K methods give accurate energetic and geometrical predictions for pi hydrogen bonding interactions, for which B3LYP fails and PW91 is less accurate. We recommend the most recent DFT method, PWB6K, for investigating larger pi hydrogen bonded systems, such as those that occur in molecular recognition, protein folding, and crystal packing.

Bond distances, vibrational frequencies, electron affinity, ionization potential, and dissociation energies of the title molecules were studied by use of density functional methods B3LYP, B3P86, B3PW91, BHLYP, BLYP, BP86, mPW1PW91, and PBE1PBE. It was found that the ground electronic state is doublet for neutral species, singlet for the anion, and triplet for the cation, in agreement with experiments and previous theoretical studies. The calculated properties are highly dependent on the functionals employed, in particular for the dissociation energy. The predicted bond distances and vibrational frequencies are in agreement with experiments and previous theoretical results. BP86 and BLYP have relatively good performance in reproducing the experimental results, while BHLYP is the worst functional method compared with the other density functional methods used for the title molecules.

The coordination of Cu2+ by glyoxilic acid oxime (gao)--the oxime analogue of glycine amino acid--and its deprotonated (gao- and gao2-) species has been studied with different density functional methods. Single-point calculations have also been carried out at the single- and double- (triple) excitation coupled-cluster (CCSD(T)) level of theory. The isomers studied involve coordination of Cu2+ to electron-rich sites (O,N) of neutral, anionic, and dianionic gao species in different conformations. In contrast to Cu2+-glycine, for which the ground-state structure is bidentate with the CO2(-) terminus of zwitterionic glycine, for Cu2+-gao the most stable isomer shows monodentate binding of Cu2+ with the carbonylic oxygen of the neutral form. The most stable complexes of Cu2+ interacting with deprotonated gao species (gao- and gao2-) also take place through the carboxylic oxygens but in a bidentate manner. The results with different functionals show that, for these open shell (Cu2+-L) systems, the relative stability of complexes with different coordination environments (and so, different spin distribution) can be quite sensitive to the amount of "Hartree-Fock" exchange included in the functional. Among all the functionals tested in this work, the BHandHLYP is the one that better compares to CCSD(T) results.

There are a large number of helices in proteins that contain the Cδ−H···OC hydrogen bonds involving Pro. Ab initio and density functional methods at HF/6-31G*, B3LYP/6-31+G**, B3LYP/6-311+G**, and MP2/6-31+G** levels are used to determine the factors that may lead to the stabilization (destabilization) of these Cδ−H···OC hydrogen bonds. The calculations are performed for 16 helical models with their structures generated from the X-ray structures of proteins. The direct Cδ−H and OC interaction is not stabilizing for the cases where the Cδ−H···OC hydrogen bond immediately precedes a peptide hydrogen bond between (i+1)NH and (i−3)CO groups (here i is the Pro residue number). The direct Cδ−H and OC interaction is generally stabilizing for the cases where this peptide hydrogen bond is absent. Therefore, the formation of the (i+1)NH···(i−3)CO peptide hydrogen bond is likely to force the C−H and OC moieties into less favorable positions for the interaction. The strength of the Cδ−H···OC hydrogen bonds is signifi...

The homolytic dissociation enthalpies of various bonds (C−H, N−H, O−H, S−H, X−H, C−C, C−N, C−O, C−S, and C−halogen) have been computed by using five density functional methods (B3LYP, MPW1PW91, B3PW91, B3P86, and MPW1P86). The quality of these methods is comprehensively evaluated on the basis of the available experimental bond dissociation enthalpies, and it is found that the MPW1P86 has the best agreement, while B3LYP performs the largest deviations. Large deviations also are found at the sophisticated CCSD(T) level of theory. The restricted open-shell method underestimates the radical stability.

Equilibrium structures and harmonic vibrational frequencies were computed for adamantane (Ad), the 1- and 2-adamantyl radicals (1-Ad•, 2-Ad•), cations (1-Ad+, 2-Ad+), and anions (1-Ad-, 2-Ad-). Ionization potentials and electron affinities of Ad, 1-Ad• and 2-Ad• have been predicted using four different density functional and hybrid Hartree−Fock/density functional methods. The equilibrium structure of adamantane (Td symmetry) is in excellent agreement with electron diffraction experiments. 1-Ad• and 1-Ad- are predicted to lie about 4 kJ mol-1 below their 2-isomers, while 1-Ad+ is predicted to lie 47 kJ mol-1 below 2-Ad+. For 1-Ad•, 1-Ad+, and 1-Ad-, C3v structures are found to be the minima, while a Cs structure lies lowest for 2-Ad•, 2-Ad+, and 2-Ad-. The final predicted adiabatic ionization potentials for the radicals are 6.22 (1-Ad•) and 6.70 eV (2-Ad•). The vertical radical ionization potentials are necessarily larger: 6.85 (1-Ad•) and 7.08 eV (2-Ad•). The predicted adiabatic electron affinities are a...

We have studied clusters containing two sulfuric acid (SA) molecules and 0−8 water molecules using density functional methods. Our main interest was to study the energies and structures of the formed clusters. We are interested in the SA-assisted nucleation of water, and the formation free energies of the clusters will help to understand the first steps of this process. Also, the deprotonation of SA is interesting. For single SA, the first deprotonations happen when three waters are present. Here, the second SA will replace the water, and the deprotonation will happen when two waters are present. The second SA will deprotonate in clusters containing four waters. At the larger cluster (n = 5−8) both of the acids are singly deprotonated. We did not observe any doubly deprotonated sulfuric acids, SO42-. We also obtained several stable structures of these clusters. The most stable structures contain solvent separated acid-hydronium ion pairs whenever it is was possible.

The electron delocalization in isocyanates, amides, and ureas has been studied using ab initio MO and density functional methods. The observed trends in the CN rotational barriers and N-inversion barriers in these systems have been explained in terms of orbital interactions. NBO analysis indicates that there is nN → π*[C-X] electron delocalization in amides, which increases with a decrease in the energy difference (ΔE) between the two interacting orbitals. This phenomenon, rather than electronegativity, is responsible for the observed increase in the CN rotational barrier in amides XC(R)NH2 (R = H, NH2) in the order X = O < S < Se.

The enthalpy of formation of methanethial-S,S-dioxide (CH 2 SO 2 ) has been determined by the use of isodesmic and nonisodesmic reactions, with individual enthalpies calculated by employing density functional methods and the CBS-QB3 model chemistry. After assessing the possible errors in the methodology, it was concluded that this value can be expressed as Δ f H° 2 9 8 (CH 2 SO 2 ) = -144.7 ′ 8.4 kJ/mol.

Possible molecular implementations of quantum-dot cellular automata (QCA) with mixed-valence ruthenium complexes are discussed. A study of the geometric and electronic structures of three mixed-valence ruthenium dimers has been done using ab initio Hartree-Fock and hybrid density functional methods at the HF/3-21G and B3LYP/3-21G levels of theory. These complexes are representatives of Robin and Day classes I, II, and III. Predicted geometries are compared to experimental data, as well as previous computational studies, where available. The B3LYP method predicts structures in better agreement with experiment than the HF method. The analysis of the orbital energies and localization provides insights into the degree of localization and the Robin-Day classification. They are therefore useful tools for the design of mixed valence compounds for use in molecular QCA.

The biomimic reactions of N-phosphoryl amino acids are very important in the study of many biochemical processes, such as origin of proteins and phosphorylation of amino acid residues in the proteins. The differences in reactivities between α-COOH and γ-COOH in phosphoryl amino acids were studied by ab initio and density functional methods. The pentacoordinate phosphoric intermediates 2 containing five-membered rings were predicted to be more stable than 3 with seven-membered rings. For intermediates 3, the isomers with apical-equatorial ring spanning arrangement were predicted to be more stable than those with diequatorial ring spanning arrangement. At the B3LYP/6-31G** level, intermediates 2 were 66.56 kJ/mol lower in energy than 3. It was shown that the transition states 4 and 5 involving an α-COOH or γ-COOH group had energy barriers of ΔE = 57.59 kJ mol-1 and 120.93 kJ mol-1, respectively. The theoretical calculations suggested that the α-COOH group could be differentiated from the γ-COOH intramolecul...

A theoretical study has been carried out for the detailed mechanism of Rh-catalyzed alkane borylation reaction with the density functional methods of B3LYP and B3PW91 and the MP2 methods. The pathw...

The structure and bonding in alpha and beta octamolybdate anions have been investigated using density functional methods. In general, good computational-experimental agreement for the geometrical parameters has been obtained. The electronic structure of the anions has been probed with molecular orbital and Mulliken-Mayer methods. All Mo-O interactions have been found to be predominantly d(Mo)-p(O) in character. Several multicentered molecular orbitals can be described as sigma or pi closed-loop structures, but the proposed connection with the stability of the polyanions is not completely supported by the calculations. Mayer indexes correspond to fractional multiple character for terminal bonds and approximately single or low-order character for bridging bonds, in accordance with structural and bond valence results. The valency analysis has yielded similar overall bonding capacity for the various oxygen atoms. A distribution of the negative charge over all types of oxygen sites and metal charges considerably smaller than the formal oxidation states have been obtained from the Mulliken analysis.

The magnetic behavior of the oxo-bridged Cu(II) dinuclear complexes has been investigated using hybrid density functional methods (B3LYP) and a post-Hartree-Fock approach (difference-dedicated configuration interaction method, DDCI). Both methods confirm the strong ferromagnetic coupling predicted for such complexes at geometries close to the energy minimum. For large Cu-O-Cu bridging angles, the DFT calculations predict an increase, whereas the DDCI method predicts a decrease of the ferromagnetic interaction, a result that is associated with the different weight of the excited charge-transfer configurations.

We have carried out a theoretical study of the migratory insertion step in the cationic Ni(II) [(dppp)Ni(CH3)(CO)]+ complex by means of both static and dynamic density functional methods to shed light on the mechanistic aspects of the migratory insertion and in particular on the role played by five-coordinate species. We find the addition-insertion pathway, taking place via a five-coordinate complex, to be thermodynamically and kinetically favored, with a highest energy barrier of 7.9 kcal mol-1, in agreement with the experimental data. Dynamics simulations have shown that the migratory insertion reaction takes place by a methyl attack on the resting carbonyl group.

Reaction energies for the deprotonation of Al3+·6(H2O), Fe3+·6(H2O), and Si(OH)4 were calculated using Hartree−Fock and density functional methods with 6-311+G(d,p) (for Al3+ and Si4+) and 6-311G(d) (for Fe3+) basis sets. Theoretical energies were calculated using a supermolecule approach (i.e., explicit hydration of the solute) combined with the Integral Equation Formalism Polarized Continuum Model (IEFPCM; Cances et al., 1997, J. Chem. Phys. 107, 3032) and the Self-Consistent Isodensity Polarized Continuum Model (SCIPCM; Keith and Frisch, 1994, ACS Symp. Ser. 56, 22) in Gaussian 98. Tests on the effects of increasing the number of water molecules explicitly included in the supermolecule were also carried out. Additional water molecules in the energy minimizations of Al(OH)3, Fe(OH)3, and [Si(OH)3(OH2)]+ resulted in 5-coordinate complexes for all three species. Correlations of deprotonation energies with observed ln(Ka) values are good for individual cations. These correlations suggest that the combined ...