Journal of Theoretical and Computational Chemistry

Three endohedral fullerenes C₂H₂–C₆₀, C₂H₄–C₆₀, and C₂H₆–C₆₀ are investigated theoretically using density functional theory. Their electronic and structural properties are studied. The calculations suggest that the formations of these complexes are endothermic; the dopant and C₆₀ cage affect each other rarely except for the slight distortion of C₆₀ cage and compression of the hydrocarbon molecules. A small quantity of electron transfer from C₆₀ to the hydrocarbon molecule was also observed. Accordingly, C₆₀ could theoretically be a good container for some small hydrocarbon molecules.

The cooperativity between hydrogen bonds and halogen bonds in X–HCN–Y(X: C₂H₂, H₂O, NH₃, HCI, HCN, HF; Y: HF, BrF, Br₂ is analyzed with MP2/6-311++G(d, p) and DFT/6-311++G(d, p) calculations using the B3LYP and mPW1PW91 hybrid functionals. The results from the quantum chemical calculations are typically clustered in groups according to the Y-ligand. By choosing the X–HCN–HF group as reference it is possible to describe the interaction between the hydrogen and the halogen bond with a two-parameter model. The value of the first parameter of the model describes the contribution of the X-ligand to the interbond cooperativity in the reference cluster. The second parameter of our model quantifies the changes in interbond cooperativity upon varying the Y-ligand. This simple model can be used to predict the cooperativity in X–HCN–Y trimers with reasonable accuracy and thereby to organize the results systematically. It is further shown that the conclusions drawn from this ordering scheme are independent from the computational method and thereby generally applicable.

¹⁵N and ¹³C NMR chemical shifts for four radiosensitizers have been calculated and compared with experimental data. The thermal and solvent effects on NMR spectra were simulated with the polarizable continuum model and an alternative molecular dynamics/quantum mechanics methodology. Magnetic shielding tensors were evaluated at the GIAO-B3LYP and GIAO-OPBE level using II' and 6-311+(2D,P) basis sets, showing that it is essential to incorporate the dynamics and solvent effects on NMR calculations in condensed phases.

PES as functions of the trans-angle (θ) and the dihedral angle (ε) for optimized bond length is calculated. It is found that the most unstrained stable conformation of the is D_2d at θ = 129.45° and ε = 90.0°. Calculated EPR g values change smoothly and in a logarithmic manner in the experimental range. The g₃₃ value varies from 2.1287 (D_4h) to 2.2836 (T_d), and g₁₁ = g₂₂ from 2.035 to 2.1001. The Cu hyperfine values of the D_4h are A₁₁ = -196.455 and A₂₂ = A₃₃ = -17.533. At the most stable D_2d conformation, the values are A₁₁ = -177.606 and A₂₂ = A₃₃ = 2.6266, all in the 10^-4 cm^-1 unit.

The variation of EPR g values with molecular charge in the range of -2.0 to -2.8 were studied, and it was found that by increasing molecular charge, both components of g values are increased. For the D_2d conformation with molecular charge of -2.6, g⊥ = 2.085 (expt. = 2.094) and g|| = 2.243 (expt. = 2.238). For the D_4h conformation, calculated g|| values with increasing molecular charge improved, but g⊥ values deviated increasingly from experimental values. Frequencies are also calculated in the range of D_2d to D_4h.

Quantitative structure–property relationship (QSPR) modeling is a powerful approach for predicting environmental behavior of organic pollutants with their structure descriptors. This study reports an optimal QSPR model for estimating logarithmic soil sorption coefficients (log K_OC) of polycyclic aromatic hydrocarbons (PAHs). Quantum chemical descriptors computed using density functional theory at the B3LYP/6-31G(d) level and partial least squares (PLS) analysis with an optimizing procedure were used to generate QSPR models for log K_OC of PAHs. The correlation coefficient of the optimal model was 0.993, and the results of a cross-validation test () showed this optimal model had high fitting precision and good predicting ability. The log K_OC values predicted by the optimal model are very close to those observed. The PLS analysis indicated that PAHs with larger electronic spatial extent tend to more easily adsorb and accumulate in soils and sediments, whereas those with higher molecular total energy and larger energy gap between the lowest unoccupied and the highest occupied molecular orbital adsorb and accumulate in soils and sediments less readily.

In this paper, we suggested a theoretical relationship between the property of molecular atomization energy and energy transfer rate in explosive detonation. According to the theory of Dlott and Fayer (J Chem Phys92(6):3798, 1990) some explosives are stable molecules with large energy barriers to chemical reaction in shock or impact initiation, so, a sizable amount of phonon energy must be converted to the molecular internal higher vibrations by multiphonon up pumping. To investigate the relationship between atomization energies and energy transfer rate, the number of doorway modes of explosives is estimated by their theory in which the rate is proportional to the number of normal mode vibrations. We evaluated frequencies of normal mode vibrations of TNB, TNAP, TNA, DATB, TATB, 2,4,6-trinitro-benzylalcohol (C₇H₅N₃O₇), and TNR by means of density functional theory (DFT) at the B3P86/6-31G(d, p) level. It is found that the number of doorway modes shows a linearly correlation to the atomization energies also calculated by means of DFT at the B3P86/6-31G(d, p) level. Besides, we studied the relation between the number of atoms and atomization energies for these molecules, and confirmed that for those secondary explosives molecules with similar molecular structure and similar molecular weight, the correlation between the atomization energy and the number of doorway modes is higher. This relationship is beneficial to the understanding of the property of explosive in detonation.

The transfer of energy perturbations within protein structure is an important phenomenon in many biological processes. In particular, the transfer of energy perturbations within a molecule in the absence of electron transfer is critical to the understanding of such processes as signaling involving receptors, channels, and enzymes among others, and to the design and development of relevant conducting materials. In this work, we have proposed a mechanism to explain this nonradiative, nonelectron energy transfer based on the π-orbital interactions of aromatic amino acids. Additionally, some theoretical background and possible computational approaches are presented as support for the proposal.

Visualized theoretical evidence for successively switching from ligand-to-ligand charge transfer (LLCT) to intraligand charge transfer (ILCT) and then to metal-to-ligand charge transfer (MLCT) excited states in platinum(II) terpyridyl acetylide (PTA) complexes in low-energy absorption by sequential protonations has been given with charge transfer density, based on recently experimental report (Han X. et al., Chem Eur J13:1231, 2007). The sequential protonations have shown significant influence on the molecular geometries, ionization potential, affinity potential, and band gap of PTA. The protonations on the amino group of the ligands result in the shift of the molecular orbital energy levels of PTA. The physical mechanism of switching from LLCT to ILCT and then to MLCT excited states by sequential protonations is interpreted with the theory of molecular orbital transitions.

A mathematical model of amperometric response for a polymer-modified electrode system has been developed. The model is based on nonstationary diffusion equations containing a nonlinear term related to Michaelis–Menten kinetics of the enzymatic reaction. In particular, the interplay between chemical reaction and substrate diffusion is specifically taken into account. The limiting situations of catalytic site unsaturation and site saturation are considered. The analytical solutions for substrate concentration and transient current for both steady and nonsteady-state are obtained using Danckwerts' relation and variable and separable method. An excellent agreement with the previous analytical results are noted. The combined analytical set of solution of steady-state current in all the nearest sites is also described in a case diagram. A general simple analytical approximate solution for steady-state current for all values of α is also given. A two-point Padé approximation is also derived for the nonsteady-state current for all values of saturation parameter α. Limiting case results (α ≪ 1 and α ≫ 1) are compared with Padé approximation results and are found to be in good agreement.

Six isomers with C_2v, D_3h, C_5v, D_2d, O_h, and C_4v symmetries of and two isomers with C_3v and C_2v symmetries of are investigated at the high ab initio level combined with the natural bond orbital and the atoms-in-molecules theorems. The hyperconjugative interaction and the electron topological analyses indicate that the multiple three-center two-electron (3c-2e) hyperbond is the common chemical-bonding basis for and species. In contrast to the planar 3c-2e (triangle structure) and planar four-center four-electron (4c-4e) hyperbonds in isomeric species, the 3c-2e hyperbond in (C_4v) is linear while the 4c-4e hyperbonds in (C_5v, D_2d, O_h) are unplanar. (C_2v) and (C_3v) as the global minima have many resonance structures predicted by the natural bond resonance theory, indicating the high possibility of the hydrogen scrambling which is similar to the scenario of .

In the present work, a set of cyclooctane and cyclohexane molecular surfaces were used to solvate excess electrons using hydrogen sulfide (H₂S). The compounds implemented have been constructed with OH groups on one side of the hydrocarbon surfaces and hydrogen atoms on the opposite side. These OH groups increased the dipole moment of systems. Simultaneously the hydrogen atoms on the opposite side of the surface for a pocket of positive charge that can attach excess electrons via dipole-bound states. The solvated anions formed between the molecular surfaces and hydrogen sulfide are stable with respect to vertical electron detachment (VDE). The effect of basis sets was also addressed in the context of VDE calculations.

Geometric optimizations of neutral Al_n (n = 2–11) clusters at B3LYP/6-31+G(d) level of theory demonstrate that small aluminum clusters are spin-polarized in ground state. Specifically, Al_n (n = 3, 5, 7, 9, and 11) clusters are spin doublets, Al_n (n = 2, 4, 6, and 8) are triplets, whereas Al₁₀ is a singlet. The spin polarizability decreases as the size of the cluster increases. The electronic spin polarization is mainly attributed to the atomic 3p electrons of aluminum atoms each of which has a nonzero orbital and spin angular momenta, respectively. Among all the clusters, Al₂ is the most spin-polarized; its evident triplet stability and electronic structural properties are partially ascribed to its nuclear spins, based on the calculations of indirect nuclear spin–spin coupling constants at B3LYP/6-311+G(3df) level of theory. As the size of the cluster increases, the influence of nuclear spins on electronic spin polarization declines due to the multiple couplings.