Electronic structure of GaN nanotubes

Nanotube properties are strongly dependent on their structures. In this study, gallium nitride nanotubes (GaNNTs) are analyzed in armchair and zigzag conformations. The wurtzite GaN (0001) surface is used to model the nanotubes. Geometry optimization is performed at the PM7 semiempirical level, and subsequent single-point energy calculations are carried out via Hartree–Fock and B3LYP methods, using the 6-311G basis set. Semiempirical and ab initio methods are used to obtain strain energy, charge distribution, dipole moment, |HOMO-LUMO| gap energy, density of states and orbital contribution. The gap energy of the armchair structure is 3.82 eV, whereas that of the zigzag structure is 3.92 eV, in agreement with experimental data.     

Hexavalent symmetric graphs of order 9p

A graph is symmetric if its automorphism group acts transitively on the set of arcs of the graph. In this paper, we classify hexavalent symmetric graphs of order $9p$ for each prime $p$.     

Minimum MD simulation length required to achieve reliable results in free energy perturbation calculations: Case study of relative binding free energies of fructose‐1,6‐bisphosphatase inhibitors

In an attempt to establish the criteria for the length of simulation to achieve the desired convergence of free energy calculations, two studies were carried out on chosen complexes of FBPase‐AMP mimics. Calculations were performed for varied length of simulations and for different starting configurations using both conventional‐ and QM/MM‐FEP methods. The results demonstrate that for small perturbations, 1248 ps simulation time could be regarded a reasonable yardstick to achieve convergence of the results. As the simulation time is extended, the errors associated with free energy calculations also gradually tapers off. Moreover, when starting the simulation from different initial configurations of the systems, the results are not changed significantly, when performed for 1248 ps. This study carried on FBPase‐AMP mimics corroborates well with our previous successful demonstration of requirement of simulation time for solvation studies, both by conventional and ab initio FEP. The establishment of aforementioned criteria of simulation length serves a useful benchmark in drug design efforts using FEP methodologies, to draw a meaningful and unequivocal conclusion. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Methylation of zebularine investigated using density functional theory calculations

Deoxyribonucleic acid (DNA) methylation is an epigenetic phenomenon, which adds methyl groups into DNA. This study reveals methylation of a nucleoside antibiotic drug 1‐(β‐D ‐ribofuranosyl)‐2‐pyrimidinone (zebularine or zeb) with respect to its methylated analog, 1‐(β‐D ‐ribofuranosyl)‐5‐methyl‐2‐pyrimidinone (d5) using density functional theory calculations in valence electronic space. Very similar infrared spectra suggest that zeb and d5 do not differ by types of the chemical bonds, but distinctly different Raman spectra of the nucleoside pair reveal that the impact caused by methylation of zeb can be significant. Further valence orbital‐based information details on valence electronic structural changes caused by methylation of zebularine. Frontier orbitals in momentum space and position space of the molecules respond differently to methylation. Based on the additional methyl electron density concentration in d5, orbitals affected by the methyl moiety are classified into primary and secondary contributors. Primary methyl contributions include MO8 (57a), MO18 (47a), and MO37 (28a) of d5, which concentrates on methyl and the base moieties, suggest certain connection to their Frontier orbitals. The primary and secondary methyl affected orbitals provide useful information on chemical bonding mechanism of the methylation in zebularine. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

An efficient parallel algorithm for the calculation of unrestricted canonical MP2 energies

We present details of our efficient implementation of full accuracy unrestricted open‐shell second‐order canonical Møller–Plesset (MP2) energies, both serial and parallel. The algorithm is based on our previous restricted closed‐shell MP2 code using the Saebo–Almlöf direct integral transformation. Depending on system details, UMP2 energies take from less than 1.5 to about 3.0 times as long as a closed‐shell RMP2 energy on a similar system using the same algorithm. Several examples are given including timings for some large stable radicals with 90+ atoms and over 3600 basis functions. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Long Distance Electronic Effects on the Rotational Potential Barriers Around the Caromatic-Cethylenic Bond

A systematic study of the rotational activation free energy around the C_aromatic-C_ethylenic bond of para-substituted styrene systems is carried out in the present work from a quantum chemistry point of view.

Calculations of the rotational potential barriers in the AM1 approach are developed as function of the electron-donor groups localized on the aromatic ring. Based on these calculations and thermodynamical data, we predict changes in the activation free energy barriers due to the long distance electronic effects of the substituents in acetophenones, cinnamaldehydes and benzalketones according to the following equation:

Our results agree the experimental measurements registered up to date and the standard deviations are similar to experimental determinations.     

13C-NMR and Molecular Orbital Studies of Protonation to Formanilides

The effect of protonation to formanilides was studied by measurements of ¹³C-NMR chemical shifts in CDCl₃ and methanesulfonic acid. It was found that the ¹³C shift of the ring carbon, to which the amide group is attached, exhibits an upfield shift by the protonation, whereas the peaks of the rest of ring carbons and carbonyl carbon shift downfield. The protonation-induced shifts of the ring carbons were found to be roughly correlated with the differences of the total electron densities between formanilides and their monocations. From the comparison between the protonation-induced shifts and the differences of the total electron densities at the carbons, especially at the carbonyl carbon, it is suggested that N-protonation is partly involved, although O-protonation seems to be dominant.