Journal of Theoretical and Computational Chemistry

On the basis of the generalized nonadiabatic transition state theory recently introduced to remedy the crucial deficiencies of the conventional transition state theory, we have presented a new formula for electron transfer rate, which can cover the whole range from adiabatic to nonadiabatic regime in the absence of solvent dynamics control. The rate is expressed as a product of the well-known Marcus theory and a new coefficient that represents the effects of nonadiabatic transition at the crossing seam surface. The numerical comparisons are performed with different approaches and the present approach shows an excellent agreement with the quantum mechanical numerical solutions from weak to strong electronic coupling. The explanation of the experimental data of Nelsen et al. manifests the potential applicability of the present theory.

In this paper, the partial potential energy surface (PPESs) of the Br + HBr and Br^- + HBr systems including the minimum energy path and the vibrational potential curves were constructed at MP2/6-311++G** level, based on the conception and constructing approach of the PPESs previously proposed. These results obtained from the PPESs were compared with those from the high resolved threshold photodetachment spectrum of the BrHBr^- anion measured by Neumark et al., J Phys Chem94, 1377–1388, 1990. On the basis of the PPESs, the scattering resonance states of the Br + HBr(v) → BrH(v′) + Br state-to-state reaction were studied and the satisfactory results were obtained. Subsequently, we calculated the width and lifetime of the resonance states in this reaction by the one-dimensional square potential well model, and obtained some results consistent to the experiments.

The mechanism of hole charge transfer in DNA of various lengths and sequences is investigated based on a partially coherent tunneling theory (Zhang et al., J Chem Phys117:4578, 2002), where the effects of phase-breaking in adenine–thymine and guanine–cytosine base pairs are treated on equal foot. This work aims at providing a self-consistent microscopic interpretation for rate experiments on various DNA systems. We will also clarify the condition under which the simple superexchange-mediated-hopping picture is valid, and make some comments on the further development of present theory.

The cooperative chirality for an ensemble of molecules is analyzed with the Dicke model in which the chiral molecules are described by the two-state systems and their interactions are simply characterized by the couplings to external fields due to their collective motion. It is shown that when the temperature is sufficiently low, a phase transition from the achiral state to the chiral one is possible, which is concomitant with emergence of the superradiance. Some physical properties such as the chiralization are calculated in the thermodynamic limit. The results are used to clarify the localization of pyramidal molecules.

On the basis of atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM), we have constructed the effective Fe²⁺ and Fe³⁺ ion-water potential by fitting to ab initio structures and binding energies for ionic clusters, where Fe²⁺ and Fe³⁺ ions are in their high spin state. We then apply the ion-water interaction potential in combination with the ABEEM-7P water model to molecular dynamic simulations of single-ion Fe²⁺(aq) and Fe³⁺(aq) solutions, managing to reproduce many experimental, structural and dynamical properties of the solutions. The effects of ionic charges on structural and dynamical properties of water molecules in the hydration shells are discussed.

In the present work, the new formulations describing spectral shifts by the authors have been introduced and employed to investigate two dye molecules, 6-propanoyl-2-(N,N-dimethylamino) naphthalene and 4-(N,N-dimethylamino) benzonitrile. From the viewpoints of the authors, the cavity radii were overestimated owing to the errors existing in the traditional models. Slightly differing from the results by other authors in the past, this work fits the cavity radii to the values of ~4.5 Å for 6-propanoyl-2-(N,N-dimethylamino) naphthalene and ~3.2 Å for 4-(N,N-dimethylamino) benzonitrile. In the fittings, both point dipole approximation and multipole expansion methods are employed. The calculations of the excited states are performed by means of the time-dependent density functional theory. Comparing the fitted cavity radii from the experimental spectra with those estimated from the molecular volumes by some well-known procedures such as COSMO and PCM, we find that the new formulations give fairly satisfactory results. By taking an atomic ion as an example, the authors argue that the Onsager radii recommended by some popular procedures are greatly exaggerated. The cavity radius derived simply from the volume encompassed by the solvent-accessible surface, without any addition of other parts, is suggested for application.

Green fluorescent protein (GFP) is a spontaneously fluorescent protein due to its p-hydroxylbenzylideneimidazolidinone chromophore. In this work, we have investigated the electronic structures, liquid structures, and solvent shifts of the GFP chromophore model compounds 4′-hydroxylbenzylidene-2,3-dimethylimidazolin-5-one (HBDI) and 4′-hydroxylbenzylidene-2-methyl-imidazoin-5-one-3-acetate (HBMIA) in NaOH/aqueous solutions, in which both compounds are protonated at anionic state. The electronic structure calculations predict that both model compounds could adopt both cis and trans conformations in solutions. Moreover, liquid simulations elucidate an extensive well-defined hydrogen-bonding network between the solvent and the solute in the ground state. Furthermore, solvent shifts calculations indicate that contributions from the specific solute-solvent hydrogen-bonding interactions are negligible for the solvatochromatic shifts observed in the absorption spectrum of the model compounds in solutions; rather, the solvent shifts are dominated by the dipolar solvation in which both permanent charge–charge interactions and many-body polarizations contribute significantly. Self-Consistent Reaction-Field (SCRF) approach could be the efficient method for studying the unusual optical properties of the GFP chromophore in solutions and proteins.

The excited states structure, essential in determining the light-emitting properties, in a correlated electron system behaves differently from the one-electron system. Previous investigations show that upon proper chemical substitution, the non-emissive polyacetylene (PA) can be designed to be strongly light-emitting materials. On the basis of the correlated quantum chemical calculations within the INDO/EOM-CCSD approach, we systematically studied both the pristine and substituted polydiacetylene (PDA) about the low-lying excited states orderings. PDA possesses high mobility, but it is non-emissive. We predict that it is impossible to cause PDA to be light-emitting. From these numerical results, we propose a simple and practical rule to design conjugated light-emitting polymers, which require only a molecular orbital calculation instead of sophisticated correlated calculations. This rule is derived from physical pictures of correlated electron model, and is found to be in agreement with the existing experiments for various substituted PA and poly(p-phenylenebutadiynylene) (PPPB).

We report on a quantum-chemical study of the electronic and optical properties of Mercury(II) complexes HgTFT (1) and its electron-withdrawing substitutent HgTFOT (2), HgTFCNT (3) [where TFT = diethynylfluorenyl, TFOT = diethynylfluorenone and TFCNT = diethynyl-(9-(dicyanomethylene)fluorene)]. Our theoretical calculations indicate that the substitution of -CO, -C(CN)₂ for -CH in HgTFT significantly decreases the bond length alternation and increases the electron affinity, which would qualify HgTFOT2 and HgTFCNT3, especially 3, as candidates for n-type electrical conductors. The vertical transition energy associated with the low-lying excited state has been examined within the time-dependent DFT formalism for mercury diethynylfluorenyl derivatives. It is found that the electron-withdrawing substitutions lead to remarkable red shift in transition energy and alter the corresponding charge transfer manner.

We show that an economic basis set, in which the polarization functions are considered only for oxygen and nitrogen atoms of strong electronegativity, can be used to determine reliable structures of nucleic acid base pairs. Mulliken charge analysis and the HOMO-LUMO gap in single-point energy calculations using standard basis sets on the geometric structures optimized with the economic basis set found reasonable agreements with the ones of standard calculations. This study is expected to provide a general guideline for basis set selection in the computation of large biological systems being performed with considerable high accuracy, using a low cost computation resource.

The neutral hydrolysis mechanisms of a simple β-phospholactam with and without water-assisted reaction have been studied by using quantum chemical method at HF/6-31G**, MP2/6-31G** and B3LYP/6-31G** levels, respectively. The reaction can proceed by two different mechanisms: concerted and stepwise. There are two pathways in stepwise, i.e. pathway a and b, and the energy barriers of them are close. The energy barriers of water-assisted hydrolysis of β-phospholactam are obviously lower than those of no-water-assisted hydrolysis system. The energy barriers of stepwise mechanism are much lower than those of the concerted pathway in both cases. The solvent effects have been considered by means of a polarizable continuum model. The hydrolysis mechanism of β-phospholactam with that of the β-lactam and β-sultam was compared.

By means of the Homology modeling and the known structure of cyannogenic β-glycosidase from white clover (1CBG, EC 3.2.1.21), we construct a 3D model of the β-primeverosidase (EC 3.2.1.149) and search for the binding site of substrate. The 3D model is then refined by using molecular mechanics (optimization and molecular dynamics) simulation. Finally, the refined model is further assessed by Profile-3D and PROCHECK, and the results showed that the final model is reliable. Furthermore, the docking of the substrates into the active site of the protein indicates that β-primeverosidase is able to hydrolyze β-primeverosides, but not act on 2-phenylethyl β-D-glucopyranoside. These results suggest that β-primeverosidase shows broad substrate specificity with respect to the disaccharide glycon moiety (subsite -2). This is consistent with the experimental observation. Thr271 and Thr415 play important roles in subsite -2 of β-primeverosidase. Our results may be helpful for further experimental investigations.

Density functional calculations are employed to investigate the mechanisms of all elementary reaction steps involved in the catalytic reaction of pyruvate dehydrogenase multienzyme complex E1 (PDHc E1). We have obtained the free energy profiles for all reaction steps, and have demonstrated the importance of some key residues (Glu571, Glu522, His640 and a water molecule) near the active center in each individual step. Glu571 plays an essential role in the ylide formation, the addition of pyruvate, and the release of acetaldehyde. Glu522 helps to orientate the carboxyl of pyruvate in favor of the addition reaction of pyruvate. The protonation of the enamine is found to proceed through a concerted double proton transfer transition state involving His640 and a water molecule. All reaction steps are calculated to be thermodynamically favorable, except for the release of acetaldehyde which is slightly endothermic. The protonation of the enamine is a rate-limiting step with a barrier of 24.5 kcal/mol in the protein environment. Comparing the energetics of the catalytic reaction in PDHc E1 with that in PDC, we find that the relative orientation of some conserved residues and the conformation of the cofactor ThDP have a significant impact on the reaction rates of individual steps.

Quantum chemical density functional theory (DFT) calculations using B3LYP and BP86 functionals have been carried out for the di-metallocene complexes. The equilibrium geometries and the bond characters have been reported. The calculations of Cp₂Zn₂, Cp₂Cd₂ and Cp₂Hg₂ demonstrate that the di-metallocene complexes slightly favor D_5h conformations for the free molecules, where Cp is C₅H₅. The predicted Cd-Cd distance of 2.723 Å and Hg-Hg distance of 2.826 Å are indicative of substantial Cd-Cd and Hg-Hg bonds. In this work, we have reported DFT MO energy level diagrams for the di-metallocene complexes. The strong interaction between Cp and Zn atoms is mainly due to the π orbital of the Cp and the s and dz² orbitals of the Zn atom. The metal–metal bonds were studied in detail. The results indicated that there are two δ, one σ and two π interactions between five d orbitals and one σ interaction between s orbitals of the two metal atoms. The electron configurations are pictured as , and so the bond order is determined by the molecular orbital theory, which is in agreement with the NBO analysis that shows that each metal atom has one covalent bond (to the other metal atom) and a nearly pure s character of metal–metal bonds. At last, from the behavior of the HOMO and HOMO-LUMO gap, the order of the stability of those di-metallocene complexes is Cp₂Zn₂ > Cp₂Cd₂ > Cp₂Hg₂.

The first structural characterization for the twelve binuclear alkaline-earth metal compounds M₂(ηⁿ-N₅)₂ (M=Be, Mg; n = 1, 2) and Ca₂(ηⁿ-N₅)₂(n = 2, 5) have been optimized with local energy minimum by density functional theory (DFT). The most energetically favored structures in M₂(ηⁿ-N₅)₂(M=Be, Mg, Ca) are of D_2d symmetry Be₂(η¹-N₅)₂, Mg₂(η²-N₅)₂ and Ca₂(η²-N₅)₂ and the metal–metal distances are 2.03 Å for Be-Be, 2.77 Å for Mg-Mg and 3.72 Å for Ca-Ca, which are significantly shorter than the experiment values of weakly bound bare diatomic Be₂, Mg₂ and Ca₂.^1,2Ca₂(η⁵-N₅)₂ (D_5d or D_5h) is the only stable specie with sandwiched structure, bearing an even shorter Ca-Ca distance of 3.66 Å, and lying 24 kcal/mol higher in energy than the D_2d structure. The dissociation enthalpies of the twelve M₂(ηⁿ-N₅)₂(M=Be, Mg, Ca) to two M(ηⁿ-N₅) fragments are predicted to be 72.6–73.1, 41.2–43.8, and 27.4–29.7 kcal/mol, respectively, implying a substantial metal–metal bonding. Natural bond orbital (NBO) analysis suggests that metal–metal bonds are of σ-bond. The natural charge of the alkali earth metal atom in the twelve M₂(ηⁿ-N₅)₂ species is larger than +0.88, which is consistent with the +1 oxidation state of the metal atoms. Nucleus-independent chemical shift (NICS) values confirm that the planar exhibits characteristics of aromaticity for these M₂(ηⁿ-N₅)₂ species.

Density functional theory calculations at the level of B3LYP have been performed to systematically study the linear and bent structures of the end-on FeN₂. The linear structure was found to be more stable than the bent one and the lowest bonding state was concluded to be a linear 1³Σ^-. The geometric structure and vibrational frequency for each electronic state were reported. The bonding properties were analyzed in terms of natural electronic configurations, natural charges, and spin densities, etc. The results revealed that the interaction between N₂ and the ground state Fe atom is a weak van der Waals interaction; covalently bonded FeN₂ may be formed by using the excited states of Fe atom where the N₂ unit remains almost intact.

The magnetic exchange interactions for five representative triangular Copper(II) complexes: antiferromagnetic Cu₃(TiPB)₆ (1), [Cu₃(μ₃-OH)(aaat)₃(H₂O)₃]²⁺ (2), [PPN]₂ [Cu₃(μ₃-O)(μ-pz)₃Cl₃] (3), [PPN][Cu₃(μ₃-OH)(μ-pz)₃Cl₃] (4) and ferromagnetic [Cu₃(2-CH₃C₆H₄CO₂)₄{(C₂H₅)₂NC₂H₄O}₂H₂O] (5) are investigated by using density functional theory combined with broken-symmetry approach (DFT-BS) and ab initio CASPT2 method. Our calculated results show that DFT-BS has remarkable dependence on the particular chosen XC functionals and is system-dependent, while the calculations at CASPT2 level of theory are able to give the accurate magnetic coupling constants. Qualitatively, the two theoretical methods reproduce consistently the linear correlation between the magnetic coupling constants and the departure of the (μ₃-O) oxygen atom from the {Cu3} plane in the complexes (3) and (4). Spin population analyses reveal that the DFT-BS method overestimates the spin electronic delocalization from the Cu(II) center to the bridging ligands.

The electronic and magnetic properties of Na_0.5CoO₂ are studied within the hybrid density functional methods. A charge-ordered antiferromagnetic insulating state is unambiguously identified as the ground state of Na_0.5CoO₂. The electronic structures of the ground state are very similar to our previous GGA+U (U = 4eV) results, except for the large band gap discrepancy. Our results suggest that the hybrid density functional methods capture the main physics of the strong correlation in Na_xCoO₂ system.