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: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:Kamal Ziadi, Abdelhamid Bouldjedri Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. In this paper, an accurate and efficient algebraic technique is used to compute linear tetra-atomic molecules stretching and bending vibration modes. Namely, several collective energy levels of linear XYYX molecules N[math]C[math]C[math]N[math] and N[math]C[math]C[math]N[math] have been described in the framework of the algebraic approach based on U[math] Lie algebra. The results are compared to experimental data, good agreement has been obtained. The potential energy function of the two molecules is analyzed and the dissociation energies are derived. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-06-01T03:25:17Z DOI: 10.1142/S021963361650036X

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

Authors:Tsung-Lung Li, Wen-Cai Lu Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The structural and electronic characteristics of the intercalated monopotassium–rubrene (K1Rub) are studied. In the intercalated K1Rub, one of the two pairs of phenyl groups of rubrene is intercalated by potassium, whereas the other pair remains pristine. This structural feature facilitates the comparison of the electronic structures of the intercalated and pristine pairs of phenyl groups. It is found that, in contrast to potassium adsorption to rubrene, the potassium intercalation promotes the carbon [math] orbitals of the intercalated pair of phenyls to participate in the electronic structures of HOMO. Additionally, this intercalated K1Rub is used as a testing vehicle to study the performance of a commodity computing cluster built to run the General Atomic and Molecular Electronic Structure System (GAMESS) simulation package. It is shown that, for many frequently encountered simulation tasks, the performance of the commodity computing cluster is comparable with a massive computing cluster. The high performance-cost-ratio of the computing clusters constructed with commodity hardware suggests a feasible alternative for research institutes to establish their computing facilities. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-05-17T03:19:54Z DOI: 10.1142/S0219633616500358

Authors:Tarek A. Mohamed, Ibrahim A. Shaaban, Usama A Soliman, Lee D. Wilson Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The Raman (3500[math]cm[math]100[math]cm[math] and IR spectra (4000[math]cm[math]400[math]cm[math] of liquid trimethylacetonitrile (C5H9N, TMA) have been obtained. In addition, the 1H and [math]C NMR spectra of TMA were obtained in DMSO-[math] and CDCl3. The staggered conformer (C[math] was favored using MP2 and DFT(B3LYP/[math]B97XD) quantum mechanical calculations utilizing a 6-311[math]G(d,p) basis set. High energy difference estimates of 4534[math]cm[math]5338[math]cm[math] (12.96[math]kcal/mol[math]15.26[math]kcal/mol) were predicted, along with three imaginary torsion frequencies for the eclipsed conformer, therefore considered a transition state. The 1H and [math]C NMR chemical shifts were predicted with B3LYP and [math]B97XD methods using the GIAO approximation and 6-311[math]G(d,p) basis set. B3LYP frequencies calculation is favored herein owing to the relatively good compilation with the experimental measurements. The computed structural parameters are well correlated to those reported from electron diffraction and microwave studies. Moreover, the [math]C[math]H coupling constant was estimated and found consistent with that observed for the sample dissolved in DMSO-[math]/CDCl3 solvents. Using the observed methyl torsion at 266[math]cm[math] in gas phase and the kinetic parameter F number, a potential function (V[math] of [math][math]cm[math]([math][math]kcal/mol) was obtained, this barrier to internal rotation is well correlated to 1527[math]cm[math] (4.37[math]kcal/mol) predicted from MP2/6-311[math]G(d,p) potential surface scan. Aided by the predicted wavenumbers and their IR intensity/Raman activity, the observed IR/Raman bands were intensively discussed and therefore assigned to their corresponding fundamentals, in agreement with novel normal coordinate analysis and potential energy distributions (PEDs). Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-05-13T08:09:03Z DOI: 10.1142/S0219633616500346

Authors:Bing-Qiang Wang, Xiao-Fen Yin, Yan-Yun Dong, Cai-Yun Zhang Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. We have performed a series of calculations using density functional theory (DFT) and time-dependent density functional theory (TD-DFT) for 1-methylamideanthraquinone (MAAQ). In the S0 state of MAAQ, amide group is coplanar with anthraquinone, and an intramolecular hydrogen bond [math] is formed. The S[math] transition has an intramolecular charge transfer character. Two stable structures (planar nMAAQ and twisted tMAAQ) have been obtained in the S1 state of MAAQ. Thereinto, nMAAQ is lower by 0.105[math]eV than tMAAQ in energy, so nMAAQ is the dominant conformation in the S1 state of MAAQ and the emission spectra of tMAAQ cannot be observed in the solution of MAAQ. Excited state intramolecular proton transfer (ESIPT) between C[math]O and N–H was not observed in the S1 state of MAAQ. Upon addition of fluoride anion, only twisted conformations were obtained in both S0 and S1 states of MAAQ-F[math]. An intermolecular hydrogen bond [math] is formed in the S0 state, and intermolecular proton transfer happens in the S1 state for MAAQ-F[math]. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-04-26T08:41:39Z DOI: 10.1142/S0219633616500334

Authors:Davood Farmanzade, Leila Tabari Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The electronic and field emission properties of the fullerene end-functionalized zinc oxide nanotube (ZnONT) are investigated by density functional theory (DFT) to search for novel field emitter nano material. The interaction energies of ZnONT/fullerenes complexes gradually increase, with increasing the nanotube lengths which indicate that ZnONTs with higher lengths could improve the stability of the complexes. The band gaps of connected construction of fullerene molecules with ZnONTs gradually reduced by increasing the tube length, but were not sensitive to the tubes diameter. It is found that the ionization potentials of ZnONT/fullerenes complexes mainly decrease compared to that of pristine nanotube in the presence of 0, 0.002, 0.004[math]a.u. electric field. The reduction of the ionization potential means the enhancement of the field emission properties of ZnONT/fullerenes complexes compared with simple ZnONT and fullerene molecules. The calculations show that the combination of ZnONT with fullerene molecules indeed improves the field emission by controlling the tube size and electric field strength. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-04-26T08:41:39Z DOI: 10.1142/S0219633616500310

Authors:Mehdi Bayat, Fatemeh Amraie, Sadegh Salehzadeh Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. A theoretical study on the structure, formation and nature of E[math]E and C–E bonds (E[math][math][math]Si, Ge, Sn) in catenated compounds of the group 14 elements including disila-, digerma- and distannacyclobutene ring formed from the reaction of 1-thiacyclohept-4-yne and E(NR)2SiR2 molecules [E[math][math][math]Si, Ge, Sn, R[math][math][math]t-Bu, H, F, Cl, Br] in 1:2 mole ratio has been investigated at the M06/def2-TZVPP level of theory. The results showed that the formation energy of the products of the reaction above with Si(NBr)2SiBr2 and Sn(NF)2SiF2 reactants has greatest and the smallest value, respectively. In agreement with the values of formation energies, both the calculated Wiberg bond indices (WBI) for E—E and C—E bonds and [math](BCP) of E—E bond in the products of two above reactants have largest and smallest values, respectively. The nature of E—E bond in the products was also studied with atoms in molecules (AIM) and natural bond orbital (NBO) analyses. The data confirmed that the E—E bond is partly covalent. In addition, the nature of C—E bond was investigated with energy decomposition analysis (EDA) and it was shown that the covalent contribution is in the range 48[math]53% depending on the types of E atom and corresponding substituents. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-04-26T08:41:38Z DOI: 10.1142/S0219633616500322

Authors:Mohamed Ali Boughdiri, Bahoueddine Tangour, Taoufik Boubaker Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. DFT/B3LYP theoretical study has been performed in order to interpret the kinetic-thermodynamic competition between compounds obtained by reaction of the methoxide ion on the 7-methyl 4-nitro benzofuroxan. Geometry, atomic charge distribution, transition states, IRC path, thermodynamic, and kinetic parameters ([math], [math], [math], [math]*, [math]*, and [math]*) have been calculated for all possible products. In gaseous state or in the presence of water as solvent, all [math] values were found to be negative, ranging from [math]12.54[math]kcal mol[math] to [math]29.85[math]kcal mol[math] in water, indicating that all possible products should form spontaneously. Those values indicated the possible observation of all products but experimenters only detect simultaneously two [math]-complexes in C5 and C7 among three possibilities. The Fukui indices obtained by NBO atomic charge distribution confirm the super electrophilicity of those two sites. For transition states barriers, [math]* ranged from 18.98[math]kcal mol[math] to 42.12[math]kcal mol[math] in gaseous state and from 18.59[math]kcal mol[math] to 24.22[math]kcal mol[math] in water. The unexpected result of our calculations is that the most stable compound is the unobserved carbanion but it also exhibits the highest activation barrier. Our results indicated the existence of two consecutive kinetic/thermodynamic competitions that occur in separate periods. The simultaneous observation of the three compounds is impossible because compound 4 occurs as a trace at the time compound 2 disappears completely. Experimental reinvestigation of the studied reaction leads by a very slow process to the earlier unobserved carbanion. Reaction mechanisms were also discussed on the basis of IRC calculations. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-04-14T07:31:22Z DOI: 10.1142/S0219633616500309

Authors:Nuha Ahmed Wazzan Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. This work reports density functional theory (DFT) calculations on the molecular structures, electronic distribution, and UV-Vis and IR spectroscopy analysis of charge transfer complexes between aminopyridines (APYs), namely 2-APY, 3-APY and 4-APY, as electron-donors and some [math]-electron-acceptors, namely chloranil (CHL), tetracyanoethylene (TCNE) and picryl chloride (PC), formed in the gas phase at the B3LYP/6-31[math]G(d,p) method/basis set, and in chloroform at the same method/basis set using PCM as solvation model. Good correspondence was generally obtained between the calculated parameters and the experimental ones. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-04-05T06:52:53Z DOI: 10.1142/S0219633616500292

Authors:Romesh Borgohain, Jyotirekha G. Handique, Ankur Kanti Guha, Sanjay Pratihar Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Phenolic compounds play a very crucial role as antioxidant that can prevent various diseases caused by free radicals in human body. Although, lots of natural phenolic compounds having antioxidant activity are available nowadays, the modeling of compounds with naturally available phenolics as building blocks is very important in order to get enhanced antioxidant activity. In this study, Ferulic acid (FA), one natural phenolic acid present in coffee, apples, orange, etc., is taken as building block and its ester derivatives with different alkyl groups are subjected to measure the antioxidant activity by using density functional theory (DFT). Various parameters like bond dissociation enthalpy (BDE), vertical ionization potential (IP[math]), reactivity descriptors, metal chelation ability, etc. are used to measure the antioxidant activity. All the parameters suggest that the ester derivatives are superior antioxidants to the parent FA. Since FA has been reported to be present as esters in many herbs and plants, hence our study provides a route to study the structure activity relationship of this class of natural phenolics with antioxidant activity. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-04-05T06:52:53Z DOI: 10.1142/S0219633616500280