Authors:Kemoabetswe R. N. Serobatse, Mwadham M. Kabanda Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. A theoretical study on the antioxidant properties of two chalcone derivatives, kanakugiol and pedicellin, is performed by considering their Fe[math] and Fe[math] coordination ability. The objective of the study is to elucidate the factors influencing the stability of the isolated conformers, the nature of the complexes, metal[math]ligand stability, metal ion affinities (MIA) and electronic properties of the cations before and after coordination to the ligand. The study is performed using the B3LYP/6–311[math]G(2d,p)//B3LYP/6–31[math]G(d,p) method. The LANL2DZ pseudopotential is selected to describe the Fe[math] ions. Time-dependent density functional theory (TDDFT) method is used to assess the electronic UV–Vis spectra of the isolated chalcones and their complexes with Fe[math] ions. The results suggest that the preferred complexes are those in which the Fe ion is coordinated at the hydroxyl-methoxy and hydroxyl-keto sites for kanakugiol and methoxy-keto site for pedicellin. Both kanakugiol and pedicellin have potential to chelate iron ions as demonstrated by their high MIA values in vacuo and in water solution. However, the ability of pedicellin to chelate iron is slightly lower than that of kanakugiol, indicating that the presence of the hydroxyl group has an effect of enhancing the metal binding abilities of the chalcone derivatives. In all the complexes obtained in vacuo, kanakugiol and pedicellin exhibit the ability to reduce the Fe[math] ion. In water solution (which mimics the environment in biological systems or studies performed in vivo), Fe[math] is reduced to Fe[math] upon coordination to the ligand while the oxidation number of Fe[math] upon coordination to the ligand remains virtually unchanged. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-07-15T05:34:04Z DOI: 10.1142/S0219633616500486

Authors:Muhammad Jawwad Saif, Matloob Ahmad, Nazeran Idrees Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. This study presents structural features of an important benzothiazine derivative -[math]2-(5,5-Dioxido-3-phenylpyrazolo[4,3-c][1,2]benzothiazin-4(2H)-yl)-N[math]-[(3-nitrophenyl)methylidene]acetohydrazide. Molecular structure is characterized by single crystal XRD and compared with optimized geometry at B3LYP/6-31G(d,p) and PBE0/6-31G(d,p) levels of density functional theory (DFT). Simulated properties (1H-NMR & IR) are in good correlation with experimental results. Electronic properties (coefficients of HOMO and LUMO) are also presented. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-07-11T06:58:31Z DOI: 10.1142/S0219633616500383

Authors:Siti Fatimah Zaharah Mustafa, Hasmerya Maarof, Mohammed Abu Naser, Hassan H. Abdallah, Ahmad Irfan, Rashid Ahmed Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The urea inclusion compounds, a unique polar organic crystalline complex, are considered as a potential candidate for a molecular separator of long chain alkane molecule. A well-defined structure of the crystalline channel systems constructed from hydrogen bonding arrangement of the urea molecules, can be used to understand the fundamental aspects of the processes involving ions or molecules transportation. To do so, in our work, molecular dynamics approach is implemented to understand the behavioral pattern of the hexadecane-1,16-diol and hexadecane guests’ related to translational and rotational orientation along the urea tunnel. Our obtained results reveal that high interaction of hexadecane-1,16-diol with urea host molecules offers a restricted environment inside urea tunnel, resulting in slowing down the guest movement. Hexadecane guest system, on the contrary, exhibits lower interaction whereby the translational and rotational movement is faster. Moreover, as the distance increases (along [math]-axis) in the urea tunnel, both guest systems favor a clockwise rotational orientation. Preference of the respected orientation indicates the influence of chiral urea tunnel on achiral guests that is clathrate inside the tunnel structure. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-07-07T11:14:58Z DOI: 10.1142/S0219633616500474

Authors:Nadia G. Haress, Devarasu Manimaran, Isaac Hubert Joe, Aida A. EL-Azzouny, Reem I. Al-Wabli, Mohamed I. Attia Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Indole derivatives represent an important class of privileged structures. Spectroscopic (Fourier transform infrared (FT-IR), FT-Raman, 1H and [math]C nuclear magnetic resonance (NMR)) investigations of the indole-bearing title compound, namely 5-methoxy-1-[(5-methoxy-1[math]-indol-2-yl)methyl]-1[math]-indole (MMIMI) have been carried out. The corresponding data of the MMIMI molecule were analyzed to understand its optimized geometry, and inter/intra-molecular interactions. The equilibrium geometry, harmonic vibrational wavenumbers, Frontier orbital energy, and natural bond orbital (NBO) analyses have been performed with the help of density functional theory (DFT) with B3LYP/6-311[math]G([math],[math]) level of theory. The vibrational modes have been unequivocally assigned using potential energy distribution analysis. The theoretically predicted wavenumbers have good agreement with the experimental values. NBO has confirmed the intra-molecular charge transfer interactions. HOMO–LUMO analysis was carried out to explore charge delocalization on the MMIMI molecule. The immunomodulatory activity of the title molecule was predicted using molecular docking approach. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-07-07T11:14:58Z DOI: 10.1142/S0219633616500462

Authors:Elham Tazikeh-Lemeski Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. In this study, we estimated the optimum concentration of copper ions that are effective in the stability and the structural changes of human growth hormone (hGH) protein in the combination of different concentrations of these ions at the molecular level using molecular dynamics simulation by Gromacs 4.6.5 software. Moreover, to estimate the binding affinity of copper ions to hGH protein, binding free energies is calculated by the molecular mechanics Poisson–Boltzmann Surface Area (MM-PBSA). The analysis of molecular dynamics (MD) trajectories as dictionary of the secondary structure of protein (DSSP), solvent accessible surface area (SASA) and binding free energy calculations show that hGH protein structure is more stabilized by increasing a limited concentration of copper ions. These findings align with our previous experimental studies. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-06-21T08:14:46Z DOI: 10.1142/S0219633616500450

Authors:Sohail Nadeem, Saad Tariq, M. Imran Jamil, Ejaz Ahmad, S. M. Sohail Gilani, Khurram Shahzad Munawar Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. In this paper, computations based on generalized gradient approximations were carried out to investigate the structural, electronic and thermo-elastic properties of LaTiO3 within the frame work of Density Functional Theory. In structural properties, the ground state structural parameters have been found to be in good agreement with those cited in recent literature. For electronic properties, in-depth analysis of quantum degenerate electronic states of LaTiO3 have been explained on the grounds of Projected Density of States. Elastic properties corresponds to anisotropy, elastic moduli’s, phase stability, elastic wave velocities, thermal stability and Debye temperature were calculated and elaborated that has not yet been found in literature. In this observation, LaTiO3 exhibited ductile nature and physically stable indirect bandgap semiconductor behavior with quasi metallic nature near Fermi level due to La-Ti degenerate states. Moreover, longitudinal mode of vibration is observed to be maximum along [100] direction than transverse mode of vibration. A plausible reason of superconductivity may arise in LaTiO3 below Debye temperature. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-06-21T08:14:46Z DOI: 10.1142/S0219633616500449

Authors:Aleksey E. Kuznetsov Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. A large variety of metalloporphyrin arrays, including stacks, have been synthesized and extensively explored for their numerous applications in molecular devices. Motivated by the phenomenon of formation of stacks by regular metalloporphyrins, we performed the computational check of the stack formation between the MP(P)4 species without any linkers or substituents. For this we chose the ZnP(P)4 species as the simplest MP(P)4 compound. Three modes of binding or coordination were found to be possible between the monomeric ZnP(P)4 units. The “convexity-to-convexity” dimer I generally is the most stable compound with the highest binding energy. The dimers II and III are generally bound significantly weaker than the “convexity-to-convexity” dimer I. In the dimer I, the strongly convex shape of both monomer units was demonstrated. The Zn–Zn distances in the dimer I, ca. 3.5[math]Å, were computed to be significantly shorter than in two other dimers. This could lead to additional interactions between the metal centers with unpaired d-electrons involved in the formation of such a dimer. In the dimer I significant decrease of the charge was found on the Zn-centers, along with slight decrease of the positive charge on the P-centers coordinated to the Zn-centers of another monomer, and slight buildup of the positive charge on the P-centers not coordinated to the Zn-centers of another monomer. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-06-17T06:21:57Z DOI: 10.1142/S0219633616500437

Authors:Sheeraz Ahmad Bhat, Shabbir Ahmad Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The FTIR (4000–400[math]cm[math]) and the FT-Raman spectra (4000–50[math]cm[math]) of 4-Hydroxy-7-methyl-1,8-naphthyridine-3-carboxylic acid are recorded and investigated. The spectra are interpreted using anharmonic frequency computations by VPT2, VSCF and PT2-VSCF methods within DFT/6-311G(d,p) framework. The root mean square (RMS) values indicate that VSCF computed frequencies are in close agreement with the observed frequencies. The combination and overtone bands are also identified in the FTIR spectrum. The intermolecular O-H[math]O hydrogen bonding interactions are discussed in the dimer structure of the molecule. The magnitudes of the coupling between pair of modes are also computed. The electronic spectra in water and ethanol solvents are analyzed using TD-B3LYP/6-311[math]G(d,p) level of theory. Molecular electrostatic potential (MEP) and HOMO-LUMO analysis are also performed. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-06-14T08:24:07Z DOI: 10.1142/S0219633616500425

Authors:Ambareesh Kumar Singh, Meenakshi Singh Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Molecular imprinting is one of few general, nonbiological methods for creating molecular receptors, but the progress in molecular imprinting calls for the predictive tools capable of understanding molecular level complexities of these processes. Thus, computational chemistry which predicts the suitability of functional monomer in designing the sensor for a particular analyte was attempted to design an amino acid (L-serine) sensor based on the molecular imprinting approach using density functional theory (DFT). Here, the computations were carried out to check the feasibility of best suited monomers for imprinting an amino acid (L-serine) in water and allied solvents. DFT method was utilized at B3LYP/6-31[math]G(d,p) level to optimize template, monomers and template-monomer complexes and basis set superposition error (BSSE) was corrected by means of the counterpoise (CP) method for complexes in gas phase. All monomers can be utilized for imprinting. 2-vinyl pyridine and acrylamide were found to be good for imprinting serine in water but toluene was found to be good porogen for imprinting serine with functional monomer acrylamide. This study will aid in designing a water-compatible MIP sensor for serine molecules, which could be a biomarker for certain neurological disorders. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-06-14T08:24:04Z DOI: 10.1142/S0219633616500413

Authors:Kaushik Hatua, Prasanta K. Nandi Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. In the present work, electronic structure and second hyperpolarizability of a number of alkaline earth metals (M [math] Be, Mg and Ca) complexes with carbon nanotube (CNT) has been studied by using different DFT functional. The complexes have sufficient thermal stability. Significant amount of charge transfer from metal to CNT results in stronger ground state polarization. The second hyperpolarizability obtained at different DFT functional (BHHLYP, CAM-B3LYP, B2PLYP, [math]B97XD) showed a consistent trend. The magnitude of second hyperpolarizability of M@CNT[3,0] complexes enhances rather appreciably when a second metal atom is introduced into other mouth position. The longitudinal component of second hyperpolarizability of M@CNT[3,0]@M complexes increases with increasing size of metal atom. The magnitude of second hyperpolarizability of Ca@CNT[3,0]@Ca complex is comparable with Fe([math]-C[math]B[math]. However, widening/lengthening of CNT markedly reduces the cubic responses. The two state model can qualitatively explain the variation of second hyperpolarizability. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-06-10T04:16:42Z DOI: 10.1142/S0219633616500401

Authors:T. Kavitha, G. Velraj Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The theoretical and computational analysis of two isoxazole derivatives 3,5-dimethylisoxazole and 4-chloromethyl-3,5-dimethylisoxazole were carried out along with some of the experimental evidences. The density functional theory calculations of these compounds were done with DFT/B3LYP/6-31+G(d,p) basis set using Gaussian 09 software. From the DFT calculations, the optimization geometry, vibrational analysis, electronic properties, local reactivity descriptors, natural bond orbitals, and other structural properties of the title compounds were elucidated. The chemical shifts of every C and H atom of the title compounds were calculated using Gauge Independent Atomic orbitals (GIAO) method for both proton and carbon NMR spectra. The molecular electrostatic potential of DMI has been found out and the difference in MEP on addition of chloromethyl group is also discussed. The hyperpolarizability calculations of the investigated molecules shows that the nonlinear optical activity of CDMI is greater when compared to DMI. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-06-10T04:16:42Z DOI: 10.1142/S0219633616500395

Authors:Fen He, Xin Yang, Zhi-Yue Tian, Han-Guang Wang, Ying Xue Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The density functional theory (DFT) has been applied for the analysis of the bond between group 10 metals and N-heterocyclic carbene (NHC) in complexes (MCl(L-X): M [math] Pd(II), Pt(II), and Ni(II), L-X[math][2-(3-methylimidazolin-4,5-bisX-2-yliden-1-yl)-4-phenyl] amido, X [math]H, Cl and CN). Full geometry optimizations have been performed for all the ligands (L-X[math] anions), MCl[math] cations, and the complexes. In the ligands, the energy levels of the carbon [math] lone-pair orbitals suggest the trend L-H[math] L-Cl[math] L-CN[math] for the donor strength. The role of the M–NHC interaction in complexes was investigated by natural bond orbital (NBO) analysis. The results show that the NHC–M bond consists of the components originating from the L[math]M donation and the M[math]Carbene C back-donation and the metal[math]the ring of NHC back-donation. The transition-metal strongly affects the donation and back-donation. The interaction between the metal and the NHC ligand can be influenced by the central metal and the substituent on the ring of NHC. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-05-27T06:04:21Z DOI: 10.1142/S0219633616500371