Journal of Theoretical and Computational Chemistry

Relativistic energy-consistent small-core lanthanide pseudopotentials of the Stuttgart–Köln variety and corresponding valence basis sets have been used for the investigation of the ground state (¹Σ⁺) lanthanum monohalides LaF, LaCl, LaBr, and LaI. The molecular constants were derived from coupled-cluster calculations, taking into account corrections for atomic spin-orbit splitting as well as basis set superposition errors. With the exception of the binding energies for LaI the theoretical values for LaF (R_e = 2.034 Å, D_e = 6.73eV, ω_e = 574cm^-1), LaCl (R_e = 2.517 Å, D_e = 5.11eV, ω_e = 339cm^-1), LaBr (R_e = 2.664 Å, D_e = 4.47eV, ω_e = 236cm^-1), and LaI (R_e = 2.891 Å, D_e = 3.65eV, ω_e = 186cm^-1) show good agreement with the experimental data. The calculated binding energy (3.65 eV) for LaI is in-between the two conflicting estimated experimental data (2.97 eV, 4.29 eV).

The structure of the FeMo cofactor with the central X ligand (X = C^4-, C^2-, N^3-, N^-, or O^2-) has been determined by the density functional approach. The FeMo cluster with one of the proposed central atoms C^4-, C^2-, N^3-, or N^- has an optimized geometry, comparable with the high-resolution X-Ray crystallographic structure of the nitrogenase FeMo cofactor. When the O^2- species is present, the FeMo cofactor has an expanded cage. Calculations in the gas phase show that an >Fe₄ facet of the FeMo cluster binds NO and CO in end-on coordination with an exothermicity of 25 and 8 kcal mol^-1, respectively, while the singlet O₂ coordinates to the FeMo cluster with an endothermicity of 12 kcal mol^-1. Deoxygenization of the bound NO and CO by the proton-electron addition is favored energetically, which leads to penetration of the C or N atom into the FeMo cage and yields the FeMo(μ₆-X) cluster. Antiferromagnetic coupling between the Fe sites and vibrational properties of the FeMo(μ₆-X) cluster, as well as the Mo-bound homocitrate ligand ring opening, have been explored theoretically. Present results suggest that O^2- is unlikely as a central anion and the central ligands are identifiable by their IR spectra. Predicted energetics indicates that the protonation opening of the homocitrate ligand ring at the Mo site is feasible.

We have implemented the Coupled-Cluster Equation of Motion (CC-EOM) with single and double excitations coupled with semiempirical parameterizations, Pariser–Parr–Pople model and INDO Hamiltonians, to investigate the optical and nonlinear optical properties, electronic structures and the excited states properties for the conjugated polymers. The semiempirical parameters allow us to study the conjugated systems with extensive sizes. Firstly, by comparing with the quasi-exact Density Matrix Renormalization Group theory for the 1D conjugated chain, we find that the CC-EOM approach can give satisfactory results for both the ground state and the excited states energies. We demonstrate that our approach can be adopted to evaluate linear and nonlinear response. We find that both the real and imaginary parts of the third-order polarizability can be solved either for static and dynamic responses. Then we apply the CC-EOM approach to study the optical signatures for the polarons in conjugated polymers. We have established a solid relationship between the rigidity of a polymer and its optical signature of the polarons.

The reaction mechanisms for the formations of halo-sulfonic acids from sulfur trioxide and hydrogen halides are investigated using density functional theory. Two channels of reaction are considered: the binary SO₃ + HX reaction pathway and the ternary SO₃ + 2HX pathway. Equilibrium geometries, harmonic frequencies, and relative energies of the reactant, transition state, and product clusters are calculated at the B3LYP/6-311++G** level. Hydrogen fluoride was found to have a particularly strong interaction with SO₃, forming an electron donor acceptor complex. Similarities to the hydrolysis of SO₃ to form sulfuric acid are discussed and the relative acidities of the halo-sulfonic acid series are evaluated and compared in the same context to sulfuric and perchloric acids.

We present an extended self-consistent charge density-functional tight-binding (SCC-DFTB) method that allows for computing vibrational infrared spectra. The extension is based on introducing an additional term in the SCC-DFTB energy formula that describes effectively the interaction of external electric field with molecular electron density distribution. The extended SCC-DFTB method is employed to model vibrational infrared spectra of 16 organic molecules. The calculated spectra are compared to experiment and to spectra obtained with density functional theory. For most of the molecules, the SCC-DFTB method reproduces the experimental spectra in a very satisfactory manner. We discuss the drawbacks and possible applications of this new scheme.

The effects of various metal intercalations (Li, Na and Be) on the electronic structures and the field emission properties of single-wall carbon nanotubes (SWNT) were investigated using the periodic plane-wave DFT method. We found that intercalations of metal tend to shift the conductive characteristics of the SWNT from those of a semiconductor to those of a quasi-metallic conductor. The Fermi levels for all metal-intercalated in SWNT are moved toward the conduction band, induced by the charge transfer from the metal to the SWNT. Intercalations of Li and Na atoms increase the field emission current, whereas Be intercalation does not affect the field emission current due to the absence of high density of states around the Fermi level. The correlation between the electronic structures for the metal-intercalated nanowires with field emission properties is further discussed in light of the above results.

The isolobal relationship has been applied computationally to create a new family of positively charged boron carbonyls. These are generated by replacing one or more of the CH's in carbocations by BCO groups. The boron carbonyl cations can be hypercoordinated (e.g. H₄BCO⁺, isolobal with ), hydrogen bridged (e.g. (BCO)₂H⁺, isolobal with the bridged vinyl cation ), carbon bridged (e.g. , isolobal with the 2-norbornyl cation), and polyhedral (e.g. , isolobal with C₄v). Furthermore, the BCO analogs have geometries and electronic structures similar to those of their carbocation counterparts, for example, characterized by 3c-2e multicenter and aromatic six interstitial electron bonding. The nucleus-independent chemical shifts (NICS) at the centers of three-membered rings or the pyramidal clusters are highly diatropic, ranging from -28 to -45 ppm. The replacement of CH by BCO favors the hypercoordinate bonding characteristic of boron compounds due to the more diffuse orbitals and lower electronegativity of boron.

Using N-Methylacetamide (NMA) dimer and NMA–water as model complexes, the solvent effect on the protein inter- N–H⋯O=C and intra- N –H⋯OH₂, and C=O⋯H₂O hydrogen bonding have been studied by the polarizable continuum model (PCM) ab initio calculations in the four media (vacuum, ether, nitromethane and water). In contrast to the empirical approaches, we suggested using the direction interaction energies (DE) to consider the solvent polarization, which can be derived from PCM ab initio calculations. The DEs of the model compounds in solvents are larger than their in vacuo binding energies, which reflect the solvent polarization effect. As the solvents become increasingly polar, the binding free energies decrease while DEs increase. The increasing DE is consistent with the increasing hydrogen bond length. Considering the protein environment, the DEs of NMA-NMA dimer in ether, 9.14 and 9.41 kcal/mol for NMADI and NMADII, are recommended for the intra N–H⋯O=C hydrogen bonding. The DEs of NMA–water complex in water, -5.47 (NMAWI) and -5.41 kcal/mol (NMAWI'), -8.44 (NMAWII) and -8.68 kcal/mol (NMAWII'), respectively, are suggested for the inter- N–H⋯OH₂ and C–O⋯H₂O hydrogen bonding of proteins. Using the same approach, we have also computed the DE of water dimer in liquid water. The computed DE of water dimer (-5.63 kcal/mol) is larger than the in vacuo water dimerization energy (-5.14 kcal/mol) and in reasonable agreement with the dimerization energies (ranging from –6.0 to 6.8 kcal/mol) of polarization-included empirical water models.

The electronic ground state and first excited state (òΣ⁺) of phosphaethyne cation (HCP⁺) have been systematically investigated using ab initio electronic structure theory. The total energies, geometries, rotational constants, dipole moments, harmonic vibrational frequencies, and parameters for Renner–Teller splittings were determined using self-consistent-field (SCF), configuration interaction with single and double excitations (CISD), coupled cluster (CC) with single and double excitations (CCSD), CCSD with perturbative triple excitations [CCSD(T)], CC with single, double, and iterative partial triple excitations (CCSDT-3), and CC with single, double, and full triple excitations (CCSDT) methods and eight different basis sets. Some of the largest full triples coupled cluster computations to date are reported. Degenerate bending frequencies for the òΣ⁺ state were determined using the equation-of-motion (EOM)-CCSD technique. The two states have been confirmed to have linear equilibrium structures. At the full CCSDT level of theory with the correlation-consistent polarized valence quadruple zeta (cc-pVQZ) basis set, the classical splitting (T_e value) is predicted to be 47.7 kcal/mol (2.07 eV, 16,700 cm^-1) and the quantum mechanical splitting (T₀ value) to be 48.1 kcal/mol (2.08 eV, 16,800 cm^-1), which are in excellent agreement with the experimental values of T_e = 47.77 kcal/mol (2.072 eV, 16,708 cm^-1) and T₀ = 47.94 kcal/mol (2.079 eV, 16,766 cm^-1). The excitation energies predicted by the CCSDT-3 and CCSD(T) methods differ from the full triples CCSDT result by 0.38 and 0.45 kcal/mol, respectively. With the aug-cc-pVQZ CCSDT-3 method the Renner parameter and the averaged harmonic bending vibrational frequency are determined to be ∊= -0.0390 and for the ground state of HCP⁺, which are reasonably consistent with the experimental values of ∊=-0.0415 and . The predicted dipole moments are 1.30 Debye ( state, polarity-hydrogen atom positive) and 0.06 Debye (òΣ⁺ state, polarity-phosphorus atom positive).

The potential energy surfaces of isomerization, decarboxylation, and decarbonylation reactions of glyoxylic acid have been characterized by the B3LYP/cc-pVTZ, B3LYP/aug-cc-pVTZ, and MP2/cc-pVTZ calculations. There is a relatively high barrier on the isomerization pathway from Tc to Tt, due to existence of the intramolecular H-bond in the Tc to Tt structures. The decarboxylation reaction proceeds mainly through a stepwise mechanism. The singlet hydroxyl carbene and carbon dioxide are formed in the first step, which is followed by isomerization of the carbene to formaldehyde in the second step. The thermal decarbonylation reaction of glyoxylic acid may take place at high temperature, due to a barrier of ~52 kcal/mol on the pathway.

Theoretical calculations have been carried out to study the mechanism of intermolecular hydroacylation of acetylene with acetaldehyde. The results indicate that the generally accepted mechanism, C–H oxidative addition followed by hydrometallation and reductive elimination, is the most favorable pathway. The intermolecular hydroacylation reaction of acetylene is shown to suffer from three problems: (1) the formation of a stable bis-acetylene intermediate, which leads to a facile dimerization side-reaction; (2) higher activation barrier of the rate-determining C–H (carbonyl) bond activation; and (3) "fatal" easy decarbonylation from hydrometalated intermediate and subsequent reductive elimination to give decarbonylation product. Our calculations indicate that the above three problems can all be overcome by the use of a tethered carbonyl substrate with a chelation-forming basic donor ligand such as alkylthio group.