Volume 20; Issue 3

Journal of Molecular Modeling

Volume 20; Issue 3

1

2D-QSPR/DFT studies of aryl-substituted PNP-Cr-based catalyst systems for highly selective ethylene oligomerization

Tang, Siyang, Liu, Zhen, Zhan, Xingwen, Cheng, Ruihua, He, Xuelian, Liu, Boping

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 826 KB

english, 2014

2

Density functional theory and molecular dynamics study of the uranyl ion (UO2)2+

Rodríguez-Jeangros, Nicolás, Seminario, Jorge M.

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 1.71 MB

english, 2014

3

Ab-initio study of structural, electronic, and transport properties of zigzag GaP nanotubes

Srivastava, Anurag, Jain, Sumit Kumar, Khare, Purnima Swarup

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 1.59 MB

english, 2014

4

Encapsulation of sodium radio-iodide in fullerene C60

Valderrama, Alejandro, Guzman, José

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 2.94 MB

english, 2014

5

Self-consistent field convergence for proteins: a comparison of full and localized-molecular-orbital schemes

Wick, Christian R., Hennemann, Matthias, Stewart, James J. P., Clark, Timothy

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 385 KB

english, 2014

6

Different proton transfer channels for the transformation of zwitterionic alanine–(H2O)n=2-4to nonzwitterionic alanine–(H2O)n=2-4: a density functional theory study

Ojha, Animesh K., Bhunia, Snehasis

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 690 KB

english, 2014

7

In pursuit of negative Fukui functions: molecules with very small band gaps

Echegaray, Eleonora, Rabi, Sandra, Cárdenas, Carlos, Zadeh, Farnaz Heidar, Rabi, Nataly, Lee, Sungmin, Anderson, James S. M., Toro-Labbe, Alejandro, Ayers, Paul W.

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 594 KB

english, 2014

8

Reaction mechanism of methylamine decomposition on Ru(0001): a density functional theory study

Lv, Cun-Qin, Liu, Jian-Hong, Song, Xiao-fei, Guo, Yong, Wang, Gui-Chang

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 470 KB

english, 2014

9

A density functional theory study of paramagnetic cyclopentadienylcobalt(III) derivatives: fluoride versus cyanide

Gao, Xiaozhen, Zhang, Xiuhui, Li, Qian-shu, King, R. Bruce, Schaefer, Henry F.

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 560 KB

english, 2014

10

In silico analysis on structure and DNA binding mode of AtNAC1, a NAC transcription factor fromArabidopsis thaliana

Zhu, Qiankun, Zou, Jiaxin, Zhu, Mengli, Liu, Zubi, Feng, Peichun, Fan, Gaotao, Wang, Wanjun, Liao, Hai

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 908 KB

english, 2014

11

Targeted studies on the interaction of nicotine and morin molecules with amyloid β-protein

Boopathi, Subramaniam, Kolandaivel, Ponmalai

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 1.35 MB

english, 2014

12

Quantum chemical DFT study of the interaction between molecular oxygen and FeN4complexes, and effect of the macrocyclic ligand

Silva, Adilson Luís Pereira, Almeida, Luciano Farias, Marques, Aldaléa Lopes Brandes, Costa, Hawbertt Rocha, Tanaka, Auro Atsushi, Silva, Albérico Borges Ferreira, Varela Júnior, Jaldyr

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 532 KB

english, 2014

13

3D-dynamic representation of DNA sequences

Wąż, Piotr, Bielińska-Wąż, Dorota

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 401 KB

english, 2014

14

Encapsulation of alkyl and aryl derivatives of quaternary ammonium cations within cucurbit[n]uril (n = 6,7) and their inverted diastereomers: density functional investigations

Raja, Ishita A., Gobre, Vivekanand V., Pinjari, Rahul V., Gejji, Shridhar P.

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 1.25 MB

english, 2014

15

Theoretical study of absorption of 2,2,6,6-tetramethylpiperidine-1-oxoammonium cation (TEMPO) on TiO2(110) rutile surface

Nieto-López, Israel, Hernández-García, Luis, Bonilla-Cruz, José, Sanchez, Mario

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 353 KB

english, 2014

16

A theoretical study on ascorbic acid dissociation in water clusters

Demianenko, Eugeniy, Ilchenko, Mykola, Grebenyuk, Anatoliy, Lobanov, Victor, Tsendra, Oksana

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 378 KB

english, 2014

17

Scytonin, a novel cyanobacterial photoprotective pigment: calculations of Raman spectroscopic biosignatures

Varnali, Tereza, Edwards, Howell G. M.

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 291 KB

english, 2014

18

ReaxFF molecular dynamics simulations of the initial pyrolysis mechanism of unsaturated triglyceride

Zhang, Zhiqiang, Yan, Kefeng, Zhang, Jilong

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 810 KB

english, 2014

19

Effect of protonation and hydrogen bonding on 2, 4, 6-substituted pyrimidine and its salt complex-experimental and theoretical evidence

Pillai, Chithra Neelakanda, Chellapan, James

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 691 KB

english, 2014

20

The influence of anharmonic and solvent effects on the theoretical vibrational spectra of the guanine–cytosine base pairs in Watson–Crick and Hoogsteen configurations

Bende, Attila, Muntean, Cristina M.

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 717 KB

english, 2014

21

Small cobalt clusters encapsulated inside Si30C30nanocages: electronic and magnetic properties

Javan, Masoud Bezi

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 1.76 MB

english, 2014

22

Homology modeling, molecular dynamics and atomic level interaction study of snake venom 5′ nucleotidase

Arafat, A. Syed Yasir, Arun, A., Ilamathi, M., Asha, J., Sivashankari, P. R., D’Souza, Cletus J. M., Sivaramakrishnan, V., Dhananjaya, B. L.

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 828 KB

english, 2014

23

Mechanistic insights into mode of actions of novel oligopeptidase B inhibitors for combating leishmaniasis

Goyal, Sukriti, Grover, Sonam, Dhanjal, Jaspreet Kaur, Goyal, Manisha, Tyagi, Chetna, Chacko, Sajeev, Grover, Abhinav

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 713 KB

english, 2014

24

Theoretical study of the solvent effect on the aromaticity of benzene: a NICS analysis

Junqueira, Georgia M. A., Santos, Hélio F. Dos

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 1.08 MB

english, 2014

25

Virtual screening of potential inhibitors from TCM for the CPSF30 binding site on the NS1A protein of influenza A virus

Ai, Haixin, Zhang, Li, Chang, Alan K., Wei, Hongyun, Che, Yuchen, Liu, Hongsheng

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 677 KB

english, 2014

26

Experimental and theoretical study of the mechanism of hydrolysis of substituted phenyl hexanoates catalysed by globin in the presence of surfactant

Ercan, Selami, Arslan, Nevin, Kocakaya, Safak Ozhan, Pirinccioglu, Necmettin, Williams, Andrew

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 691 KB

english, 2014

27

Nanomechanics of β-rich proteins related to neuronal disorders studied by AFM, all-atom and coarse-grained MD methods

Mikulska, Karolina, Strzelecki, Janusz, Nowak, Wiesław

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 617 KB

english, 2014

28

Insights into the influence of 5-HT2c aminoacidic variants with the inhibitory action of serotonin inverse agonists and antagonists

Galeazzi, Roberta, Massaccesi, Luca, Piva, Francesco, Principato, Giovanni, Laudadio, Emilioano

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 1.21 MB

english, 2014

29

Experimental and theoretical assignment of the vibrational spectra of triazoles and benzotriazoles. Identification of IR marker bands and electric response properties

Aziz, Saadullah G., Elroby, Shabaan A., Alyoubi, Abdulrahman, Osman, Osman I., Hilal, Rifaat

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 1.00 MB

english, 2014

30

A B3LYP and MP2(full) theoretical investigation on the cooperativity effect between hydrogen-bonding and cation-molecule interactions and thermodynamic property in the 1: 2 (Na+: N-(Hydroxymethyl)acetamide) ternary complex

Feng, Guo-rui, Qi, Ting-ye, Shi, Wen-jing, Guo, Yu-xia, Zhang, Yu-jiang, Guo, Jun, Kang, Li-xun

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 730 KB

english, 2014

31

Stereodynamic study of the reaction H(2S) + ClO(2

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 744 KB

english, 2014

32

A computational model of the glycine tautomerization reaction in aqueous solution

Tolosa, Santiago, Hidalgo, Antonio, Sansón, Jorge A.

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 590 KB

english, 2014

33

Charge distribution analysis in( {mathbf{Ag}}_{mathbf{n}}^{mathbf{m}+} )clusters: molecular modeling and DFT calculations

Milek, Theodor, Döpper, Tibor, Neiss, Christian, Görling, Andreas, Zahn, Dirk

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 1020 KB

english, 2014

34

An all-atom force field developed for Zn4O(RCO2)6metal organic frameworks

Sun, Yingxin, Sun, Huai

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 981 KB

english, 2014

35

Homology modeling and virtual screening for antagonists of protease from yellow head virus

Unajak, Sasimanas, Sawatdichaikul, Orathai, Songtawee, Napat, Rattanabunyong, Siriluk, Tassnakajon, Anchalee, Areechon, Nontawith, Hirono, Ikuo, Kondo, Hidehiro, Khunrae, Pongsak, Rattanarojpong, Triw

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 1.14 MB

english, 2014

36

UV–vis absorption spectrum of a novel Ru(II) complex intercalated in DNA: [Ru(2,2′-bipy)(dppz)(2,2′-ArPy)]+

Chantzis, Agisilaos, Very, Thibaut, Despax, Stéphane, Issenhuth, Jean-Thomas, Boeglin, Alex, Hébraud, Pascal, Pfeffer, Michel, Monari, Antonio, Assfeld, Xavier

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 790 KB

english, 2014

37

In silico and in vivo studies of molecular structures and mechanisms of AtPCS1 protein involved in binding arsenite and/or cadmium in plant cells

Nahar, Noor, Rahman, Aminur, Moś, Maria, Warzecha, Tomasz, Ghosh, Sibdas, Hossain, Khaled, Nawani, Neelu N., Mandal, Abul

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 1.26 MB

english, 2014

38

Homodimers of Cytosine and 1-MethylCytosine. A DFT study of geometry, relative stability and H-NMR shifts in gas-phase and selected solvents

Paytakov, Guvanchmyrat, Gorb, Leonid, Stepanyugin, Andriy, Samiylenko, Svitlana, Hovorun, Dmytro, Leszczynski, Jerzy

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 296 KB

english, 2014

39

Ab initio study of the structures and electronic states of small neutral and ionic DABCO – Arnclusters

Mathivon, Kevin, Linguerri, Roberto, Hochlaf, Majdi

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 753 KB

english, 2014

40

A new AMBER-compatible force field parameter set for alkanes

Nikitin, Alexei M., Milchevskiy, Yury V., Lyubartsev, Alexander P.

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 448 KB

english, 2014

41

Theoretical investigation on the healing mechanism of divacancy defect in CNT growth by C2H2and C2H4

Xiao, Bo, Yu, Xue-fang, Ding, Yi-hong

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 593 KB

english, 2014

42

Steered molecular dynamics identifies critical residues of the Nodamura virus B2 suppressor of RNAi

Allen, William J., Wiley, Michael R., Myles, Kevin M., Adelman, Zach N., Bevan, David R.

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 859 KB

english, 2014

43

The X∙∙∙Au interactions in the CF3X (X = Cl, Br) ∙∙∙Aun(n = 2, 3, and 4) complexes

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 279 KB

english, 2014

44

Water-mediated potassium acetate intercalation in kaolinite as revealed by molecular simulation

Ható, Zoltán, Makó, Éva, Kristóf, Tamás

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 841 KB

english, 2014

45

Investigation of plausible mechanistic pathways in hydrogenation of η5-(C5H5)2Ta(H)=CH2: an analysis using DFT and AIM techniques

Neogi, Soumya Ganguly, Das, Anita, Chaudhury, Pinaki

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 547 KB

english, 2014

46

The unrestricted local properties: application in nanoelectronics and for predicting radicals reactivity

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 382 KB

english, 2014

47

Theoretical study of the ring expansion reaction mechanism of cyclopropenylidene with azetidine

Tan, Xiaojun, Wang, Weihua, Sun, Qiao, Jing, Ying, Li, Ping

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 628 KB

english, 2014

48

Density functional theory study of small X-doped Mgn(X = Fe, Co, Ni,n = 1–9) bimetallic clusters: equilibrium structures, stabilities, electronic and magnetic properties

Kong, Fanjie, Hu, Yanfei

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 635 KB

english, 2014

49

Electronic and ionization spectra of 1,1-diamino-2,2-dinitroethylene, FOX-7

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 376 KB

english, 2014

50

Insights from quantum chemistry into piperazine-based ionic liquids and their behavior with regard to CO2

Sanz, Virginia, Alcalde, Rafael, Atilhan, Mert, Aparicio, Santiago

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 1.26 MB

english, 2014

51

Quantum chemical investigations of the water exchange mechanism on [AlIII(H2O)5(L)]2+as a function of the donor strength of the anionic L

Alzoubi, Basam M., Weber, Immo, Hanauer, Hans, Puchta, Ralph, van Eldik, Rudi

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 731 KB

english, 2014

52

Accurate simulation of geometry, singlet-singlet and triplet-singlet excitation of cyclometalated iridium(III) complex

Wang, Jian, Bai, Fu-Quan, Xia, Bao-Hui, Zhang, Hong-Xing, Cui, Tian

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 401 KB

english, 2014

53

Atomistic simulation studies of theα/β-glucoside and galactoside in anhydrous bilayers: effect of the anomeric and epimeric configurations

Ahmadi, Sara, Manickam Achari, Vijayan, Nguan, HockSeng, Hashim, Rauzah

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 2.98 MB

english, 2014

54

Stimulation of N−glycoside transfer in deoxythymidine glycol: mechanism of the initial step in base excision repair

Chen, Ze-qin, Liu, Xiao-qiang, Xue, Ying

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 2.06 MB

english, 2014

55

Rational design of organoboron derivatives as chemosensors for fluoride and cyanide anions and charge transport and luminescent materials for organic light-emitting diodes

Jin, Ruifa, Tang, Shanshan, Luo, Dongmei

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 1.14 MB

english, 2014

56

Sequence and 3D structure based analysis of TNT degrading proteins inArabidopsis thaliana

Bhattacherjee, Amrita, Mandal, Rahul Shubhra, Das, Santasabuj, Kundu, Sudip

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 1.82 MB

english, 2014

57

First-principles study of Carbz-PAHTDDT dye sensitizer and two Carbz-derived dyes for dye sensitized solar cells

Mohammadi, Narges, Wang, Feng

Journal:

Journal of Molecular Modeling

Year:

2014

Language:

english

File:

PDF, 748 KB

english, 2014