Journal of Theoretical and Computational Chemistry

The accurate prediction of the strength of protein–ligand interactions is a very difficult problem despite impressive advances in the field of biomolecular modeling. There are good reasons to believe that quantum mechanical methods can help with this task, but the application of such methods in the context of scoring is still in its infancy. Here we benchmark several wave function theory (WFT), density functional theory (DFT) and semiempirical quantum mechanical (SQM) approaches against high-level theoretical references for realistic test cases. Based on our findings for systematically generated model systems of real protein/ligand complexes from the PDB-bind database, we can recommend SCS-MP2 and B2-PLYP-D3 as reference methods, TPSS-D3+D_abc/def-TZVPP as the best DFT approach and PM6-DH+ as a fast and accurate alternative to full ab initio treatments.

Density functional theory (DFT) using PBE, PBE1PBE, B3P86, B97-1, and BHandHLYP functionals as well as MP2 calculations employing the TZVP basis set were used to study the formation of four host–guest complexes with formula [H₃L⋯X]²⁺ (X = F^-, Cl^-, Br^-, and I^-). The result of calculations on the structural parameters of [H₃L⋯Cl]²⁺ shows that the calculated data with BHandHLYP functional have the best agreement with the experimental data and all five DFT methods give the better result than MP2. The largest amounts of interaction energies between the halide anions and protonated macrocycle were also calculated by PBE functional. The results show the following trend for the formation of complexes in the gas phase: [H₃L⋯F]²⁺ > [H₃L⋯Cl]²⁺ > [H₃L⋯Br]²⁺ > [H₃L⋯I]²⁺. Formation of the complexes in solution also shows the above trend where the [H₃L⋯Br]²⁺ and [H₃L⋯I]²⁺ complexes have positive values and probably cannot be formed.

Multimetallocene complexes (Cp–M_n–Cp) of Be, Mg and Ca have been considered for the theoretical study of static second hyperpolarizability using a number of DFT functionals. Owing to the cooperative effect in bonding, beryllium forms multiberyllocene complexes (Cp–Be_n–Cp) which have sufficient thermal stability with respect to dissociation into neutral fragments up to n = 10. On the other hand, multimetallocene complexes of Mg and Ca are found to be stable for n ≤ 5 which may be due to the weaker covalent bonding interaction between the larger metal atoms. The rather small variation of linear and cubic polarizabilities of Cp–Be_n–Cp complexes beyond n = 5 arises from the rather weaker charge transfer transitions. The difference in NLO property among the investigated metal complexes arises from the extent of charge transfer from the terminal metal atoms and the distance between them. The charge transfer at longer distances in the ground state of Mg and Ca complexes leads to more intense electronic transition — the spectroscopic parameters of which strongly favors the enhancement of second hyperpolarizability.

The present work deals with the theoretical investigation of electronic structure features and stability of adenine–thymine (AT) and rare tautomer of adenine–thymine (rAT) base pairs along with their complexes with Cu²⁺ cation and their interactions with BN doped fullerene (C₅₈BN). All the calculations have been performed with density functional theory using B3LYP functional. Electronic structures of the two base pairs are almost identical. Hence, it is rather difficult to distinguish between the two base pairs on the basis of their electronic properties. As per our theoretical calculations, we have observed that, BN modified fullerene could act as a nano-biosensor for detection of mispairing between these two complementary bases as well as their Cu²⁺ complexes.

The structures of the germylenoid H₂GeFMgF and its insertion reactions with RH (R = F, OH, NH₂) were studied using the DFT B3LYP and QCISD approaches for the first time. The geometries of all of the stationary points were optimized at the B3LYP/6-311+G (d, p) level of theory. And then the QCISD/6-311++G (d, p) single-point energies were calculated. The solvent effects on the geometries and insertion reactions were also computed using the PCM model. The calculated results suggested that H₂GeFMgF had three equilibrium configurations, in which the p-complex structure had the lowest energy and was the most stable structure. The isomerization reactions among the three complexes had been studied. For the insertion reactions of H₂GeFMgF with RH (R = F, OH, NH₂), along the potential energy surface, there were one transition state and one intermediate which connected the reactants and the products. For the three insertion reactions the mechanisms are identical. However, under the same conditions the insertion reactions should occur easily in the order of H-F > H-OH > H-NH₂. The solvent effect calculations suggested the larger the solvent polarity is, the easier the reaction will be.

Based on the non-equilibrium Green's function (NEGF) method combined with the density functional theory (DFT), we have studied the gate-modulated electronic properties of a graphene nanoribbon (GNR) which is composed of two GNRs of different widths. The results show that the charge transport is greatly modulated by the applied gate. Negative differential resistance (NDR) behaviors is found in such a system. With the increase in the gate, the NDR behaviors will disappear and reappear. Furthermore, under certain gate voltages multiple NDR behavior is found, the origin of which is attributed to the change of the number of effective transport channels and the variation of delocalization degree of the orbitals within the bias window. Interestingly, low bias NDR behavior is obtained which is desirable for integrated circuits from the point view of power consumption.

Azpy (2-phenylazopyridine), Nazpy (2-pyridylazonaphtol), Mazpy (2,6-diméthyl-2-phenylazopyridine) and Dazpy (2-phenylazo-4,6-dimethylpyridine) are four pyridylazo ligands that are characterized by density functional theory (DFT) theoretical investigation either in gas or in condensed phases. As they display at least three heteroatoms donors of electrons, hydrogen bond basicity has been experimented via energy and geometrical descriptors to determine which of the donors will link to metal so as to form metallic complexes. The pyridinic Nitrogen (N_py) and that close to the substituent linked to azo group (N₂) are the most available with almost the same energy to authorize coordination with metal. Before, prediction of Azpy synthesis was undertaken. ¹H NMR was also performed. They showed that the conformational trans or E₂-azpy was the most stable existing ligand. Nonetheless, this structure undergoes a modification on behalf of the conformational cis or E₁-azpy that is the suitable ligand to provide with two nitrogen atoms with the same energy. Regarding this observation, all calculations were undertaken on the conformational E₁ of each pyridylazo ligand. Therefore, the results obtained were consistent with the experimental analysis confirming that all of the four ligands are bidentates. In consequence, all the pyridylazo ligands can be assumed to connect to the metal by two nitrogen atoms forming five membered ring regardless the azo group's substituent nature.

The combination of cations with octahedral coordinated d⁰ transition metal ions has been proved to be an effective way for designing new polar materials. So we investigate the second-order nonlinear optical (NLO) properties of Strandberg-type polyoxometalates (POMs) with alkali metal cations M₆Mo₅X₂O₂₃ (M = K⁺, Rb⁺, Cs⁺; X = P, As) and M₄Mo₅X₂O₂₁ (M = K⁺, Rb⁺, Cs⁺; X = S, Se, Te) by density functional theory (DFT) method. The calculated results show that this kind of Strandberg-type POMs possesses remarkably large molecular second-order NLO polarizability, especially for the Cs₆Mo₅P₂O₂₃ (system Ic), which has a computed β₀ value of 12526 a.u. and might be an excellent second-order NLO material. Moreover, the cations have important impact on the second-order NLO polarizabilities. Therefore, a careful choice of appropriate cations may allow the control of the second-order NLO response on these Strandberg-type POMs, which may provide a new route to design efficient NLO materials.