Journal of Theoretical and Computational Chemistry

Aromatic stabilization energies (ASE) for a set of 29 five-membered heteroaromatic compounds are calculated using molecular descriptors such as magnetic susceptibility exaltation (Λ), nucleus-independent chemical shifts (NICS), and electrotopological indices (EI) via linear, quadratic and cubic fitting polynomials. Theoretical estimations compare fairly well with experimental data when three variables multilinear regression equations are employed.

In a manner analogous to the definition of Stirling numbers of the first and second kind we define a set of numbers for restricted random walks of finite memory. These two sequences of counting numbers should be useful in the exact enumeration of properties of simple and restricted random walks.

Now that the problems surrounding ab initio calculations over a Slater Type Orbital basis have been solved, it is available in several software packages.

For general structures the STOP package (Slater Type Orbital Package) has offered ab initio SCF molecular properties since 1996, the requisite integrals all being evaluated analytically, including the four center term available since 1994. SMILES (Slater Molecular Integrals for Large Electronic Systems) has offered various basis sets, geometry optimization and CI since 2001. For density functional work, ADF, the Amsterdam Density Functional suite of programs, is a project dating from the 1970s with a 2003 edition.

In this work the preferred ETOs (Exponential Type Orbitals) will be shown to be the hydrogenic orbitals and similar Coulomb Sturmians. Slater Type Functions (STFs) will be compared to them and suitable equivalent combinations, which are rarely used, given.

The correct shielding of the nucleus, resulting from radial factors of hydrogenic orbitals is shown to be essential in the evaluation of precise nuclear shielding tensors for NMR spectroscopy of molecules using ab initio or DFT methods.

The case study of benzothiazoles using natural abundance ¹⁵N is re-examined and compared with previous work including measurements.

We present a dual origin Cartesian multipole expansion for continuous and discrete charge distributions. The remainder term for the truncated expansion is analyzed and formulas for translating and clustering are derived. The analysis of the remainder term, and the formulas for translating and clustering are equally applicable to one and two center Cartesian expansions.

This work signifies the next step in our way in the magnetic properties simulation of spin clusters and extended networks containing quantum spins, by original FORTRAN codes based on Heisenberg–Dirac–VanVleck (HDVV) or Ising approaches, using Full Diagonalization Heisenberg Matrix (FDHM) or Monte Carlo–Metropolis (MCM) procedure, respectively.

We present the results of magnetic Monte Carlo studies on a magnetite type lattice, Ising model ferrimagnet that provide insight into the exchange interactions involved in Cubic Ferrospinels. We have demonstrated that a comparatively simple model can reproduce ferrimagnetic behavior of ferrospinels, particularly for magnetite.

Boron isosteres [CH₃-CO-BH-CH(R)-CONHCH₃; R=CH₃,CH₂OH,CH₂SH] of natural amino acids have been designed as inhibitors of serine protease based on boron's ability to mimic the transition state of the normal enzyme catalyzed reaction. The conformation and electronic properties of these isosteres have been determined by ab initio calculations at the HF/6-31G** level of theory. The global minimum energy structures of the boron isosteres (which are all identical) and the natural amino acids are radically different. Interestingly, the boron isosteres have favorable conformations with positive values for the ϕ dihedral, which are "disallowed states" for the natural amino acids. This is possible because of the smaller atomic size of boron compared to nitrogen. The molecular electrostatic potential of the boron isosteres is also very different from the natural amino acids. There is a positive potential around the boron atom, which provokes the attack of the Ser¹⁹⁵–OH group in the enzyme, resulting in formation of an irreversible enzyme-inhibitor adduct.

Methyl substituents are introduced into solvated ammonium perchlorate (AP) systems to explicate the effects of methylation on localized hydrogen-bonding. Methylation systems are modeled using density functional theory (DFT) B3LYP type with 4-31G(d, p), 6-311+(2d, p) basis set methods, indicating that whichever methyl group is substituted at the proton site in an ammonium ion or solvent, both methyl groups cease to H-bond, as evidence by elongation of the neighboring bond and characteristic red-shifts in the frequency of vibration. The energy barriers to the conversion from reactants to products in solvated AP systems are also discussed herein to help to elucidate the relationship solubility and H-bonding.

A numerical method based on the transfer matrix method is developed to calculate the critical temperature of two-layer Ising ferromagnet with a weak inter-layer coupling. The reduced internal energy per site has been accurately calculated for symmetric ferromagnetic case, with the nearest neighbor coupling K₁=K₂=K (where K₁ and K₂ are the nearest neighbor interaction in the first and second layers, respectively) with inter-layer coupling J. The critical temperature as a function of the inter-layer coupling , is obtained for very weak inter-layer interactions, ξ<0.1. Also a different function is given for the case of the strong inter-layer interactions (ξ>1). The importance of these relations is due to the fact that there is no well tabulated data for the critical points versus J/K. We find the value of the shift exponent ϕ=γ is 1.74 for the system with the same intra-layer interaction and 0.5 for the system with different intra-layer interactions.

Theoretical calculations have been carried out to investigate the effect of the 4(R)-substituents (OH, F, NH₂, and ) in proline on the stability of the collagen triple helix. A series of substituted proline models were studied first with density functional (B3LYP/6-31+G*) calculations. The solvent effect was studied using the SCIPCM method. While the F, OH and NH₂ groups increase the stability of the trans-up conformation with respect to the trans-down conformation, appears to favor the trans-down conformation in an aqueous solution. Second, the triple helices of the tripeptide models, Ac–Pro–Pro(X)–Gly–H with the two proline residues in the down/down and down/up puckering conformations, were optimized with a repeating unit approach using the HF/6-31G* method. For the Ac–Pro–Pro–Gly–H model peptide, the calculated binding energies of the two triple helices with the different puckering modes are similar. All four substituents, F, OH, NH₂, and , considerably increased the binding energy of the down/up helix, but only stabilizes the down/down triple helix. Our calculations indicate that the inter-chain electrostatic interactions involving the 4(R)-substituents play an important role in stabilizing triple helical collagen models and allow the rationalization of all available experimental observations. Further model studies indicate that the substituent effects by the F, OH and NH₂ substituents are local while the effect of is long-range in nature.

The relationship between Wiener's index — a distance-based topological descriptor, Zagreb group parameter — M₁, an adjacency-based topological descriptor, and eccentric connectivity index — an adjacency-cum-distance based topological descriptor, with the alpha-1 adrenoceptor antagonistic activity of arylpiperazines has been investigated. A training set, comprising 30 analogues, of substituted arylpiperazines was selected for the present investigations. The values of the Wiener's index, Zagreb group parameter and eccentric connectivity index and each of 30 analogues comprising the data set were computed. Resulting data was analyzed and suitable models developed after identification of active range. Subsequently, a biological activity was assigned to each analogue involved in the data set using these models, which was then compared with the reported adrenoceptor antagonistic activity. High accuracy of prediction ranging from 90–93% was observed using these models.

In previous work,¹ we presented a one center two range expansion method for the evaluation of the two-center overlap-like quantum similarity integrals over Slater type orbitals which are four orbitals overlap integrals.

In this work, to improve the accuracy and to reduce the calculation times, the above integrals are developed using the Fourier transform approach and the so-called B functions. With the help of angular momentum selection rules, two-center overlap-like quantum similarity integrals are expressed as combinations of usual overlap integrals (e.g. two-orbitals) which could be evaluated very accurately using the Fourier transform method combinated with B functions.