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: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

Authors:Meng Liang, Jun Yin, Kadali Chaitanya, Xue-Hai Ju Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The charge transport properties of perylene diimide (PDI) and its fluorinated derivatives were explored by density functional theory (DFT) coupled with the incoherent charge-hopping model. The geometric structure, reorganization energy, frontier molecule orbital, electron affinity (EA), ionization potential (IP), transfer integral as well as the anisotropic mobility were discussed. By attaching fluorine atoms to the bay region of PDI, the p-type material converts to the n-type or ambipolar ones (difluorinated-perylene diimide (DF-PDI) and tetraflurinated-perylene diimide (TF-PDI)). The electron mobility of difluorinated-perylene diimide (DF-PDI) (0.33[math]cm2 V[math] s[math] is much larger than its corresponding hole mobility (0.0008[math]cm2 V[math] s[math] due to its lower LUMO energy and more efficient pack-stacking, hence it could be a candidate of n-type organic semiconductor (OSC). The introduction of strong electron-withdrawing substituents (such as fluorine) to the perylene-based OSC materials is a promising strategy for the high-performance n-type OSCs. Besides, the three molecules exhibit remarkable anisotropic behaviors. Both the hole and electron maximal mobilities occur in the parallel [math]–[math] stacking dimers. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-04-05T06:52:53Z DOI: 10.1142/S0219633616500279

Authors:Atanu Basak, Kuheli Chakrabarty, Animesh Ghosh, Gourab Kanti Das Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Biosynthesis of polyterpenoid and related molecules are largely accomplished via mevalonate pathway. One of the vital steps in this pathway is the inter-conversion of two intermediates isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) catalyzed by IPP:DMAPP isomerase (IDI). The crystal structure of the enzyme, bound to the substrate analogues and inhibitors, revealed possible mechanism of this inter-conversion; however, none of them could affirm the true nature of the transition state through which the process is taking place. Our DFT study on the pathway of this isomerization reaction at the active site of the enzyme suggests a favorable concerted mechanism that occurs through a single transition structure without generating any carbocation intermediate. In this mechanism, the Cys-67 residue acts as proton donor whereas Glu-116 acts as proton acceptor. The mechanism also reveals the active involvement of other two components present at the active site. A crystallographic water molecule (Wat508) and Glu-87 assist to reprotonate the conjugate base of cysteine residue through a proton shuttle mechanism while forming the transition structure of the isomerization reaction. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-03-15T10:38:48Z DOI: 10.1142/S0219633616500255

Authors:Qing-Hai Hao, Qian Chen, Zhen Zheng, Li-Yan Liu, Tie-Ju Liu, Xiao-Hui Niu, Qing-Gong Song, Hong-Ge Tan Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Molecular dynamics simulations are applied to investigate the cylindrical polyelectrolyte brushes in monovalent and multivalent salt solutions. By varying the salt valence and concentration, the brush thickness, shape factor of grafted chains, and distributions of monomers and ions in the solutions are studied. The simulation results show that the single osmotic pressure effect in the brush leads to changes in conformation in the presence of monovalent salt, while the ion exchange effect induces the collapse of the brushes in the multivalent salt solutions. Furthermore, the snapshots combined with the distributions of the end-monomers and the mean bond angles demonstrate a nonuniform stretching picture of the grafted chains, which is different with the chains tethered on the planar surface. The charge ratios between the ions trapped in the brush and the monomers are also calculated to elucidate the details of ion exchange process. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-03-15T10:38:48Z DOI: 10.1142/S0219633616500267

Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. A variety of organic donor–acceptor–donor materials based on thienylbenzothiadiazole (BTD[math]–5) combined with different [math]-conjugated systems are studied by density functional theory (DFT) and time-dependent DFT (TD-DFT) for the ground- and excited-state properties, respectively, using B3LYP and the 6-31G(d, p) basis set. The effect of different electron-donor groups on the structural, electronic and optoelectronic properties is studied. To provide for the bandgap and to guide the synthesis of novel low bandgap materials, we applied quantum chemistry techniques to calculate the difference in the highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital LUMO energies. However, we have studied the effect of the reduction and oxidation properties on the electronic excitation transitions for all compounds. The emission energies have been obtained from TD-DFT calculations performed on the excited-state optimized S1 geometries. The theoretical results suggest that both the introduction of electron-donor groups and the doping process contribute significantly to the electronic and optoelectronic properties of the alternating donor–acceptor–donor conjugated systems studied. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-03-09T08:01:26Z DOI: 10.1142/S0219633616500231

Authors:Kenneth Osondu Monago, Charles Otobrise Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. This work describes a procedure for the numerical calculation of third virial coefficients of simple linear molecules. The method is applied to nitrogen using a site–site model pair-potential and the triple dipole term. Values of volumetric and acoustic second and third virial coefficients of nitrogen are reported over a wide range of temperature and compared with experimental data of several authors. The effect of including the quadrupole–quadrupole energy to the pair potential is investigated and the results suggest that the contributions of the quadrupole moment to second and third virial coefficients are non-negligible at low temperatures. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-03-07T04:24:20Z DOI: 10.1142/S0219633616500243

Authors:Ming-Xia Zhang, Bing-Fei Yan, Wen-Zuo Li, Qing-Zhong Li, Jian-Bo Cheng Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The addition reaction of germylenoid H2GeFMgF with ethylene (C2H4) was first investigated in this work. All of the stationary points were optimized using the M062X method in conjunction with the 6-311[math]G (d, p) basis set and the corresponding energies were calculated using the QCISD method with the 6-311[math]G (d, p) basis set. The calculated results demonstrated that there are two different channels in the addition reaction of H2GeFMgF with C2H4, while only the channel I is feasible once the C2H4 approaches H2GeFMgF in the proper conditions. The solvent effect upon the addition reaction was also investigated using PCM model. The results demonstrated that the tetrahydrofuran (THF) solvent could accelerate the addition reaction. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-03-02T11:55:27Z DOI: 10.1142/S021963361650022X

Authors:M. G. Khrenova, B. L. Grigorenko, J.-P. Zhang, P. Wang, A. V. Nemukhin Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The all-atom model of the photosynthetic core complex composed of the light-harvesting system (LH1) and the reaction center (RC) from a thermophilic purple bacterium Thermochromatium tepidum is constructed. We compare the structural parameters of this complex embedded into the lipid bilayer to those reported for the recently resolved crystal structure of the LH1–RC. We focus on the local structure of the binding sites of the calcium ions regulating stability and optical spectra of the core complex. We show the differences between the computationally derived model and the crystal structure at the extramembrane region of the LH1 polypeptides where the calcium binding sites are located. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-02-22T08:53:32Z DOI: 10.1142/S0219633616500206

Authors:Toufik Salah, Salah Belaidi, Nadjib Melkemi, Ismail Daoud, Salima Boughdiri Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Current knowledge about Chagas disease, the potentially life-threatening illness caused by the protozoan parasite (Trypanosoma cruzi), has led to the development of new drugs and the understanding of their mode of action. The Conceptual Density-Functional Theory was applied to determine the active center sites of trypanocidal compounds, extended by the Molecular Docking analysis to identify the most favorable ligand conformation when bound to the active site of cruzain. Results such as CHELPG charges, Fukui function, MESP, and Molecular Docking analysis are reported and discussed in the present investigation. Whereas, a close agreement with experimental results was found to explain the possibility of studying the receptor-binding mode using these different axes. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-02-18T07:08:15Z DOI: 10.1142/S0219633616500218

Authors:Qingxi Meng, Peiying Su, Fen Wang, Shuhua Zhu Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Density functional theory (DFT) was used to investigate the reaction mechanisms of ruthenium(II)-catalyzed hydroacylation of isoprene with benzaldehyde, and o-methoxyl, m-methoxyl and p-methoxyl benzaldehyde. All intermediates and transition states were entirely optimized at the B3LYP/6-31G(d,p) level (LANL2DZ(f) for Ru). The results demonstrated that the hydroacylation had two different catalytic cycles (path I and II), path II was more favorable than path I. Ru(II)-catalyzed hydroacylation began from the first catalytic cycle, and the nucleophilic reaction was the rate-determining step. The activation barriers of hydrogen migration were the highest in two catalytic cycles, so the hydrogen migration was the rate-determining step. The activation barrier of hydrogen migration could be broken down to two parts: the free energy of exchange ([math]) and the relative free energy of transition state ([math]). The ligand exchange energy ([math]) had more contribution to the activation barrier than the relative free energy of transition state ([math]), so the ligand exchange would control these hydroacylation. Furthermore, our calculations also described the substituent effect, and the results indicated that four aldehydes showed different chemical reactivity, and benzaldehyde and m-methoxyl benzaldehyde were predicted to have the best reactivity in ruthenium hydride-catalyzed hydroacylation. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-02-18T07:08:14Z DOI: 10.1142/S021963361650019X