Journal of Theoretical and Computational Chemistry

The structure and stability of the still experimentally unknown M⁺-C_nH_2n+1O₂ (M = H, Li, Na, K; n = 1 ~ 3) complexes were theoretically investigated via density function theory at the B3LYP/6-311+G(3df,2p)//B3LYP/6-311G(d,p) level. The addition of alkali metal ions (Li, Na, and K) to C_nH_2n+1O₂ are found to form only one stable structure, while proton transfer reactions with C_nH_2n+1O₂ produce two isomers except for CH₃CH₂CH₂O₂. The optimized geometries and Mulliken population analysis indicate that the M⁺ (M = Li, Na, K)-C_nH_2n+1O₂ complexes exist as ion-dipole molecules. Our prediction for the affinity energies of M⁺ to C_nH_2n+1O₂ are 165.4, 178.0, 181.9 and 176.8 kcal/mol (H⁺); 34.3, 36.4, 37.5, and 38.4 kcal/mol (Li⁺); 24.4, 26.1, 26.9, and 27.5 kcal/mol (Na⁺); and 17.5, 19.2, 19.6, and 20.0 kcal/mol (K⁺), respectively. Thus, these values suggest that C_nH_2n+1O₂-M⁺ (M = H, Li, Na, K) complexes could be detected as stable species in gas phase at room temperature by ion attachment mass spectrometry.

In order to investigate the substituting effects on the two-photon absorption (TPA) cross-section and the position of the TPA peak, the one- and two-photon absorption properties of a series of symmetric molecules with bis(stilbene)diethylene π-conjugated bridge have been studied using ZINDO-SOS method. The transition moments from the ground state to the lowest excited state (M_0k) and from the lowest excited state to the TPA final state (M_kn), together with the detuning energy ΔE = E_0k - E_kn/2, were calculated using the INDO1 method included in the ZINDO program. The results indicate that bis-donor and bis-acceptor substitutions mainly affect the transition dipole moments M_0k and M_kn, and that donor or acceptor side groups have a strong influence on the detuning energy. Meanwhile, it was found that the molecules with the bis-donor structure possess enhanced TPA cross sections, and the molecules with cyano or methoxy side groups have a large red-shift with respect to molecules without side groups.

Accurate, post-Hartree–Fock calculations have been carried out for a broad range of geometries in order to obtain an extended description of the orientational anisotropy and radial strength of the interaction of OH⁺ and OH^- ions with the unit species of a weak quantum solvent as that provided by ⁴He droplets. The potential energy surfaces (PES) are obtained for the smallest complex system with one ⁴He atom, and the possible role and importance of many-body effects is also investigated. The energetics and shapes of the OH⁺-⁴He and OH^--⁴He internal bound states are obtained and analyzed in detail.

The relationship between the topological indices and the Neutral Endopeptidase (NEP) inhibitory activity and Angiotensin-Converting Enzyme (ACE) inhibitory activity of mercaptoacyldipeptides has been investigated. Three topological indices — the Wiener index (a distance-based topological index), the molecular connectivity index (an adjacency-based topological index), and the eccentric connectivity index (an adjacency-cum-distance-based topological index), were presently used for investigation. A data set comprising 39 differently substituted mercaptoacyldipeptides was selected for the present study. The values of the Wiener index, molecular connectivity index, and eccentric connectivity index for each of the 39 compounds comprising the data set were computed using an in-house computer program. Resultant data were analyzed and suitable models were developed after identification of the active ranges. Subsequently, a biological activity was assigned to each compound using these models, and the biological activity was then compared with the reported NEP and ACE inhibitory activity of each compound. Accuracy of prediction up to a maximum of ~91% was obtained using these models.

Molecular dynamics, density functional with correlation, as well as docking studies of inhibitors of HIV-1 reverse transcriptase (RT) are reported. We propose in this work a novel potential HIV-1 RT inhibitor (RTI), which theoretically appears to bind in a similar mode as other nucleoside reverse transcriptase inhibitors, and in addition, it introduces a new hydrogen bond interaction with Trp229. Our novel RTI has high docking scores and the molecular dynamics studies, as well as the analysis of the ligand-receptor interactions in the active site and the ADMET properties suggest advantages and specificities for this potential RTI.

We studied two three-dimensional off-lattice protein models with two species of monomers, hydrophobic and hydrophilic. Low energy configurations in both models were optimized using the energy landscape paving (ELP) method and subsequent gradient descent. The numerical results show that the proposed methods are very promising for finding the ground states of proteins. For all sequences with lengths 13 ≤ n ≤ 55, the algorithm finds states with lower energy than previously proposed putative ground states.

The structural and energetic properties of polyfluorene and its derivatives were investigated, using quantum chemical calculations. Conformational analysis of bifluorene was performed by using ab initio (HF/6-31G* and MP2/6-31G*) and density functional theory (B3LYP/6-31G*) calculations. The results showed that the local energy minimum of bifluorene lies between the coplanar and perpendicular conformation, and the B3LYP/6-31G* calculations led to the overestimation of the stability of the planar pi systems. The HOMO-LUMO energy differences of fluorene oligomers and its derivatives — 9,9-dihexylfluorene (DHPF), 9,9-dioctylfluorene (PFO), and bis(2-ethylhexyl)fluorene (BEHPF) — were calculated at the B3LYP/6-31G* level. Energy gaps and effective conjugation lengths of the corresponding polymers were obtained by extrapolating HOMO-LUMO energy differences and the lowest excitation energies to infinite chain length. The lowest excitation energies and the maximum absorption wavelength of polyfluorene were also performed, employing the time-dependent density functional theory (TDDFT) and ZINDO methods. The extrapolations, based on TDDFT and ZINDO calculations, agree well with experimental results. These theoretical methods can be useful for the design of new polymeric structures with a reducing energy gap.

The structure and stability of pyrazine dimer in different orientations have been investigated using second- and fourth-order Møller–Plesset perturbation theory (MP2, MP4) and coupled-cluster singles and doubles with non-iterative perturbative triples method [CCSD(T)] with various basis sets (6-31G*, 6-311G**, 6-311++G**, cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, and aug-cc-pVTZ). With the largest basis set (aug-cc-pVTZ) at the MP2 level of theory, the calculated binding energies (basis set superposition error corrected) for the sandwich, N–N axial-displaced, lateral-displaced, cross-displaced, T-shaped (T_N-ring and T_H-ring), and wedge-shaped (W_N–C and W_C–C) geometries are found to be 3.01, 4.18, 4.63, 5.92, 4.54, 2.78, 2.89, and 3.23 kcal/mol, respectively. Although MP2 calculations predict the cross-displaced geometry to be the most stable one, MP4 and CCSD(T) calculations show the most stable geometry to be T-shaped (T_N-ring), with a center-of-mass separation of 4.2 Å. Dispersion interaction seems to be the major source of attraction in all the geometries considered, while the nature of electrostatic interaction depends on the mutual orientation of the two rings.

The nature of weak van der Waals interactions in different complexes of some atmospheric molecules such as CO₂, N₂O, and N₂ was examined. Ab initio calculation was carried out at MP2 level of theory using Dunning's aug-cc-pVTZ basis set. Bader's theory of atoms in molecules (AIM) was employed to analyze electron density and to characterize the nature and properties of van der Waals interactions. A set of criteria, having been proposed in the context of AIM theory, was examined for these complexes. In spite of the parameter kinetics energy, per electron density is expected to be greater than unity for closed-shell interactions; we obtained values less than unity for many of these polyatomic systems. A set of limitations has also been outlined for the values of two AIM quantities: total energy density, H(r), and Laplacian of electron density, ∇²ρ, which correspond to different bond natures.

In this work, the proton transfer between carbon acids and amine bases was investigated using computational methods. The effect of substitutions on the interaction between 1-nitro-1-(4-nitrophenyl) alkanes (with R = H, CH₃) and 1-5-7-triazabicyclo[4,4,0]dec-5-ene) (TBD) was investigated. The solvent effects on proton transfer reaction between 1-nitro-1-(4-nitrophenyl) alkanes (in which R = H, CH₃) and TBD have been calculated in acetonitrile and water solvents. The products of proton transfer reactions between C-acids and 7-methyl-1-5-7-triazabicyclo[4,4,0]dec-5-ene (MTBD) were dissociated into free ions, while those of the TBD reaction contained a comparable amount of ions and ion pairs. In addition, the free energy of activation for proton transfer reaction between C-acids with R = H, CH₃ and TBD was calculated. The intermolecular hydrogen bonding formation between 4-nitrophenylnitromethane and TBD was investigated using the Hartree–Fock method, density functional theory (DFT), and atoms in molecules (AIM) theory. The effects of hydrogen bonding on structural parameters of model systems were also studied. The results are in agreement with the results of AIM theory.

Complete conformational analysis of all possible keto and enol forms of thenoyltrifluoroacetone (TTFA) was carried out using density functional theory with the B3LYP functional and the 6-31G**, 6-311G**, and 6-311++G** basis sets. In addition, the geometries and energies of the four most stable chelated conformers and their corresponding open structures were obtained at the MP2/6-31G** level of theory. The energy differences between the four stable chelated enol conformers, in the gas phase, calculated at the B3LYP levels are negligible. However, calculations at the MP2 level indicate that the B2 conformer (the hydroxyl group in the -CF₃ side) is significantly more stable than others, in agreement with the X-ray diffraction results. The calculated intramolecular hydrogen bond (IHB) energy E_HB and the strength of the bond have been compared, and an imperfection in the prevalent method of evaluating E_HB has been perceived. The IHB of TTFA was compared with those in several β-dicarbonyls.

In this paper, the structures and energetics of porphyrin-fullerene supramolecular complexes have been investigated theoretically via molecular mechanics calculations on complexes having different porphyrins. The results of the calculations allow us to delineate the effect of the substituents on the porphyrin ring on the porphyrin-fullerene interaction energies. The calculations also allow us to understand how the van der Waals force affects the structures of the 2:1, 2:2, and 3:1 supramolecular complexes.

The effect of solvation on ET rate processes has been investigated on the basis of the exact theory constructed in J. Phys. Chem. B110:11438, 2006. The nature of solvation has been studied in close relation with the mechanism of ET processes. The resulting Kramers' turnover and Marcus' inversion characteristics have been analyzed accordingly. The classical picture of solvation has been found to be invalid when the solvent longitudinal relaxation time is short compared with the inverse temperature.