Theoretical investigation to characterize the inclusion complex of α-lipoic acid and β-cyclodextrin

We simulated the docking of α-lipoic acid (α-LA) in β-cyclodextrin (β-CD) using two models. We considered in this study complexes formed by 1:1 host–guest stoichiometry in vacuo and in aqueous phase, using PM6, DFT and ONIOM2 hybrid calculations. The results obtained with PM6 method clearly indicate that the complexes formed are energetically favored with or without solvent, model 2 (α-LA entering the cavity of β-CD from its wide side by COOH group) is found more favored than model 1 (α-LA entering into the cavity of β-CD from its wide side by cyclic group), the preference being greater in the case of ONIOM2 calculations. In addition, NBO analysis gives that mutual interactions between the donor and acceptor orbitals of α-lipoic acid and β-CD plays an important role to the stabilization of such a complex. Finally, ¹H nuclear magnetic resonance (NMR) chemical shifts of free and complexed α-LA were calculated by the Gauge-Including Atomic Orbital (GIAO) method and compared with available experimental data. The results of GIAO calculations were analyzed and discussed.     

Elongation method with intermediate mechanical and electrostatic embedding for geometry optimizations of polymers

The elongation method with intermediate mechanical and electrostatic embedding (ELG-IMEE) is proposed. The electrostatic embedding uses atomic charges generated by a charge sensitivity analysis (CSA) method and parameterized for three different population analyses, namely, the Merz–Singh–Kollman scheme, the charge model 5, and the atomic polar tensor. The obtained CSA models were tested on two model systems. Test calculations show that the electrostatic embedding provides several times of decrease in the difference of energies of testing and reference calculations in comparison with the conventional elongation approach (ELG). The mechanical embedding is implemented in a combination of the conventional elongation method and the ONIOM approach. Moreover, it was demonstrated that the geometry optimization with the ELG-IMEE reduces the errors in the optimized structures by about one order in root-mean-square deviation, when compared to ELG.     

Comparative ONIOM modeling of 1,3-butadiene polymerization using Nd(III) and Gd(III) Ziegler–Natta catalyst systems

On the base of structural and thermodynamic data using modern methods of quantum chemistry, a comparative theoretical study of the elementary acts of initiation and growth of a polymer chain during the polymerization of 1,3-butadiene was carried out. Ziegler–Natta catalysts based on Nd(III) and Gd(III) were used as polymerization initiators. It was shown that the higher stereospecificity of the action of gadolinium catalytic complexes in comparison with neodymium complexes is due to the increased stability of the anti-form of the π-allylic terminal structure of the growing polymer chain, and the reduced activity is due to the higher activation energy of the processes of initiation and chain growth.     

The theoretical study of one-carbon unit transfer with H_2O participation from imidazolidine to dUMP analogue

The ONIOM quantum mechanics method is used to study the reaction of one-carbon unit transfer from an imidazolidine to 6- aminouracil model with the participation of water molecules.The computation results show that in this reaction the participation of H_2O molecule makes the energy barrier lower because of the H-bond interaction.     

A case study in performance evaluation of Density Functional Tight Binding method in two-layer ONIOM method

A performance evaluation of Density Functional Tight Binding (DFTB) in the two-layer ONIOM method is presented in an effort to estimate DFTB effectiveness as an inexpensive low level quantum mechanical layer. Ground state geometries, geometry error, S-values and energy error for: (H₂O)_x(MeOH)_y, [(η⁵-C₅Me_nH_5−n)₂Ti]₂(μ₂, η²,η²-N₂), n = 4, and complexes of Cu⁺ with tyrosine, were compared to target calculations at B3LYP level of theory for all three of the systems and second order Moller-Plesset (MP2) target level of theory for the first two systems. The calculated root-mean-square errors (RMS) of the ONIOM optimized geometries relative to the target are found to be small. The DFTB level of theory was unable to reproduce the target geometry structure for one of the isomers of tyrosine–Cu⁺ complex, while the ONIOM combinations were able to reproduce all target structures. The absolute value of the geometry error was determined to be smaller then the corresponding energy error except for the (H₂O)_x(MeOH)_y system at the ONIOM(MP2/6-31G(d,p):DFTB) level of theory. The S-values were relatively small and close in value contributing to relatively small energy errors. Both method combinations ONIOM(MP2:DFTB) and ONIOM(DFT:DFTB) show similar performance compared to the corresponding target level of theory. The results also suggest that it is safe to use ONIOM(DFT:DFTB) for investigations of [(η⁵-C₅Me_nH_5−n)₂Ti]₂(μ₂, η²,η²-N₂) complexes.     

QM/MM study of the interaction between zigzag SnC nanotube and small toxic gas molecules

Adsorptions of small toxic molecules such as CO, N₂, HCN, SO₂, H₂CO, and NH₃ on a single‐walled (6,0) SnC nanotube (SnCNT) are investigated using Quantum Mechanics/Molecular Mechanics (QM/MM) methodology. The calculations are carried out at the B3LYP/6‐311++G(d,p)//LANL2DZ:UFF level of theory. The high layer of the model consists of a pyrene‐type ring on the nanotube surface as the adsorption site, where one gas molecule is allowed to interact. Conversely, for the adsorption of the two molecules, a larger site like a coronene ring is used for the high layer. Adsorption energy, Gibbs free energy change, Mulliken charge transfer, and total electron‐density maps are computed in each case. The adsorption strength of the gas molecule on the SnCNT surface is also analyzed from the density of states projected to different atoms (PDOS) of the nanotube–adsorbate complexes. The adsorptions of CO and N₂ on the (6,0) SnCNT surface require to cross potential barriers, and the corresponding transition structures are identified by ONIOM‐IRC calculations. For the remaining four molecules, the processes of adsorption are predicted to be barrier‐less. The calculations for the adsorption of H₂CO on (5,0) and (7,0) SnCNT surfaces are extended to study the effect of the size of the nanotube. Results for the adsorption of a single molecule on (6,0) SnCNT using B3LYP functional are compared with those obtained from a dispersion corrected functional such as M06‐2X. © 2015 Wiley Periodicals, Inc.     

Testing the ONIOM G2R3 model against donor-acceptor dissociation energies of group 13-15 complexes: accuracy comparable to CCSD(T)/aug-CC-pVTZ at a fraction of the resource cost

The ability of the composite three-layer ONIOM G2R3 (OG2R3) method to match experimental dissociation energies for group 13-15 donor-acceptor complexes was examined for a database of 34 complexes. The composite approach provides energies that agree reasonably with experiment, performing nearly as well as both the CCSD(T)/aug-CC-pVTZ and CCSD(T)/6-311+G(2df, 2p) models for small molecules and nearly as well as the latter for slightly larger ones. Broadly, all three models exhibit average absolute errors of ～3 kcal mol(-1) , and root mean square errors of ～4 kcal mol(-1) . The average signed error suggest that the OG2R3 approach systematically underbinds by ～2.3 kcal mol(-1) ; if this is used as a general correction, the approach performs as well or better than the pure CCSD(T) models. However, the OG2R3 model can be applied to molecules too large to be studied by the other CCSD(T) methods, as it requires only a fraction of the time and computer resources.     

Quantum chemical study on the one-carbon unit transfer of imidazolinium

One-carbon unit transfer reaction of folate cofactor model compound, 1-acetyl-2-methyl-imidazolinium, with 1,2-diaminobenzene has been studied theoretically with ONIOM method. The result shows that there are two pathways to complete this reaction because the imidazolinium ring has two breaking patterns. Both the two pathways have six steps. They are combination of two reactants, proton migration, break of five-membered ring, formation of benzimidazole derivate, another proton migration, and formation of final products. In each of the above pathways, the two proton migration steps have higher energy, which illuminate that the reaction is catalyzed by general acid-base. This fact agrees with the experimental results of enzymatic one-carbon unit transfer at oxidation level of formate.     

A comparative study of various computational approaches in calculating the structure of pyridoxal 5'-phosphate (PLP)-dependent beta-lyase protein. The importance of protein environment

Various computational approaches, using molecular mechanics (Amber), semiempirical (AM1), density functional (B3LYP), and various ONIOM methods, have been comparatively investigated for the structure of Escherichia coli NifS CsdB protein. The structure of the entire monomer containing 407 amino acid residues and 579 surrounding water molecules has been optimized. The full geometry optimization in the "active site-only" approach (including only active site atoms) has been found to give the largest root-mean-square (RMS) deviation from the X-ray structure; a much better agreement has been achieved by keeping the atoms leading to the backbones of some amino acids frozen in their positions in the X-ray structure. The best agreement has been attained by including the surrounding protein in the calculations using the two-layer ONIOM (B3LYP:Amber) approach. The results presented in this study conclusively demonstrate the importance of the protein/active-site interaction on the active-site structure of the enzyme. The present theoretical study represents the largest system studied at the ONIOM level to date, containing 7992 atoms, including 84 atoms in the QM region and rest in the MM region.