Volume 19; Issue 9

Journal of Molecular Modeling

Volume 19; Issue 9

1

A new theoretical analysis of the cooperative effect in T-shaped hydrogen complexes of CnHm∙∙∙HCN∙∙∙HW with n = 2, m = 2 or 4, and W = F or CN

Oliveira, Boaz G., Costa, Tamires F., AraÃºjo, Regiane C. M. U.

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 744 KB

english, 2013

2

Oxygen doped SiC nanocrystals: first principles study of the optical properties

Bezi Javan, Masoud

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 793 KB

english, 2013

3

Theoretical investigation of the selectivity in intramolecular cyclizations of some 2’–aminochalcones to dihydroquinolin–8–ones and indolin–3–ones

Reyes, Andres, Cuervo, Paola Andrea, Orozco, Fabian, Abonia, Rodrigo, Duque-NoreÃ±a, Mario, PÃ©rez, Patricia, Chamorro, Eduardo

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 249 KB

english, 2013

4

Theoretical study on isomerization and peptide bond cleavage at aspartic residue

Sang-aroon, Wichien, Ruangpornvisuti, Vithaya

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 770 KB

english, 2013

5

A coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation

Li, Yongxiu, Gao, Ya, Zhang, Xuqiang, Wang, Xingyu, Mou, Lirong, Duan, LiLi, He, Xiao, Mei, Ye, Zhang, John Z. H.

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 1.05 MB

english, 2013

6

DFT and MP2 study of low barrier proton transfer in hydrazide schiff base tautomers via water bridges and in the gas

Tavakol, Hossein, Farrokhpour, Hossein

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 454 KB

english, 2013

7

DFT studies of acrolein molecule adsorption on pristine and Al- doped graphenes

Rastegar, Somayeh F., Hadipour, Nasser L., Tabar, Mohammad Bigdeli, Soleymanabadi, Hamed

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 558 KB

english, 2013

8

Synthetic and quantum chemical study on the regioselective addition of amines to methyl maleamate

RÃ¡cz, Ãkos, VÃ¡radi, AndrÃ¡s, MazÃ¡k, KÃ¡roly, KÃ¶kÃ¶si, JÃ³zsef, NoszÃ¡l, BÃ©la

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 494 KB

english, 2013

9

NH3on a BC3nanotube: effect of doping and decoration of aluminum

Peyghan, Ali Ahmadi, Tabar, Mohammad Bigdeli, Kakemam, Jamal

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 450 KB

english, 2013

10

Monte Carlo simulations of a polymer chain conformation. The effectiveness of local moves algorithms and estimation of entropy

MaÅka, Agnieszka, Nowicki, Waldemar, Nowicka, GraÅ¼yna

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 395 KB

english, 2013

11

Homology modeling and structural comparison of leucine rich repeats of toll like receptors 1-10 of ruminants

Swathi, Anandan, Dhinakar Raj, Gopal, Raja, Angamuthu, Tirumurugaan, Krishnaswamy Gopalan

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 547 KB

english, 2013

12

Revealing substitution effects on the strength and nature of halogen-hydride interactions: a theoretical study

Esrafili, Mehdi D., Solimannejad, Mohammad

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 459 KB

english, 2013

13

A theoretical study on the halogen bonding interactions of C6F5I with a series of group 10 metal monohalides

Cheng, Na, Liu, Yongjun, Zhang, Changqiao, Liu, Chengbu

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 364 KB

english, 2013

14

DFT study on crystalline 1,1-diamino-2,2-dintroethylene under high pressures

Wu, Qiong, Zhu, Weihua, Xiao, Heming

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 826 KB

english, 2013

15

Modeling and molecular dynamics of the intrinsically disordered e7 proteins from high- and low-risk types of human papillomavirus

Nicolau-Junior, Nilson, Giuliatti, Silvana

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 943 KB

english, 2013

16

The effect of cross linking density on the mechanical properties and structure of the epoxy polymers: molecular dynamics simulation

Shokuhfar, Ali, Arab, Behrouz

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 932 KB

english, 2013

17

Theoretical study on the antioxidant properties of 2′-hydroxychalcones: H-atom vs. electron transfer mechanism

Xue, Yunsheng, Zheng, Youguang, Zhang, Ling, Wu, Wenya, Yu, Ding, Liu, Yi

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 724 KB

english, 2013

18

A theoretical study on the gas-phase protonation of pyridine and phosphinine derivatives

Zielinski, FranÃ§ois, Tognetti, Vincent, Joubert, Laurent

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 366 KB

english, 2013

19

Effects of protein binding on a lipid bilayer containing local anesthetic articaine, and the potential of mean force calculation: a molecular dynamics simulation approach

Amjad-Iranagh, Sepideh, Yousefpour, Abbas, Haghighi, Parto, Modarress, Hamid

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 904 KB

english, 2013

20

Effects of organic solvents and substrate binding on trypsin in acetonitrile and hexane media

Meng, Yanyan, Yuan, Yuan, Zhu, Yanyan, Guo, Yanzhi, Li, Menglong, Wang, Zhimeng, Pu, Xuemei, Jiang, Lin

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 1.38 MB

english, 2013

21

Theoretical study of the pre- and post-translational effects of adenine and thymine tautomers and methyl derivatives

Gardner, Noel, Magers, David, Hill, Glake

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 336 KB

english, 2013

22

Fluorination of BC3nanotubes: DFT studies

Peyghan, Ali Ahmadi, Noei, Maziar

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 412 KB

english, 2013

23

Simulations on the possibility of formation of complexes between fluorouracil drug and cucurbit[n]urils: ab initio van der Waals DFT study

Mahsa Sabet, M. Darvish Ganji

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 1.22 MB

english, 2013

24

Spin-flip reactions of Zr + C2H6researched by relativistic density functional theory

Yi Xiao, Xian-Yang Chen, Yi-Xiang Qiu, Shu-Guang Wang

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 502 KB

english, 2013

25

The effects of external electric field: creating non-zero first hyperpolarizability for centrosymmetric benzene and strongly enhancing first hyperpolarizability for non-centrosymmetric edge-modified graphene ribbon H2N-(3,3)ZGNR-NO2

Yang Bai, Zhong-Jun Zhou, Jia-Jun Wang, Ying Li, Di Wu…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 374 KB

english, 2013

26

High temperature unfolding of a truncated hemoglobin by molecular dynamics simulation

Ravi Datta Sharma, Rajnee Kanwal, Andrew M. Lynn…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 2.13 MB

english, 2013

27

Computationally designed prodrugs of statins based on Kirby’s enzyme model

Rafik Karaman, Wajd Amly, Laura Scrano, Gennaro Mecca…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 693 KB

english, 2013

28

Protophilicity index and protofelicity equalization principle: new measures of Brønsted-Lowry-Lewis acid–base interactions

Francisco Méndez, Julio A. Alonso, Arlette Richaud

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 205 KB

english, 2013

29

Equilibrium and folding simulations of NS4B H2 in pure water and water/2,2,2-trifluoroethanol mixed solvent: examination of solvation models

Man Guo, Ye Mei

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 760 KB

english, 2013

30

Variations of the tautomeric preferences and π-electron delocalization for the neutral and redox forms of purine when proceeding from the gas phase (DFT) to water (PCM)

Ewa D. Raczyńska, Beata Kamińska

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 389 KB

english, 2013

31

Temperature dependence of the polarization and the dielectric constant near the paraelectric-ferroelectric transitions in BaTiO3

H. Yurtseven, A. Kiraci

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 497 KB

english, 2013

32

Screening of different computational models for the preparation of sol–gel imprinted materials

Elmer-Rico E. Mojica

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 648 KB

english, 2013

33

Molecular dynamics simulations of void defects in the energetic material HMX

Xiao Hui Duan, Wen Peng Li, Chong Hua Pei, Xiao Qing Zhou

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 563 KB

english, 2013

34

An information-theoretic classification of amino acids for the assessment of interfaces in protein–protein docking

Christophe Jardin, Arno G. Stefani, Martin Eberhardt…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 614 KB

english, 2013

35

Enhanced hybrid search algorithm for protein structure prediction using the 3D-HP lattice model

Changjun Zhou, Caixia Hou, Qiang Zhang, Xiaopeng Wei

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 1.04 MB

english, 2013

36

Theoretical study of photophysical properties of 1,4-dihydropyrrolo[3,2-b]pyrrole-cored branched molecules with thienylenevinylene arms toward broad absorption spectra for solar cells

Shanshan Tang, Binbin Tang, Dadong Liang, Guang Chen…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 318 KB

english, 2013

37

A DFT study on the sensing behavior of a BC2N nanotube toward formaldehyde

Maziar Noei, Ali Ahmadi Peyghan

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 589 KB

english, 2013

38

Electronic structure and optical properties of Cu-doping and Zn vacancy impurities in ZnTe

Qing-Fang Li, Ge Hu, Qing She, Jing Yao, Wen-Jiang Feng

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 893 KB

english, 2013

39

Molecular dynamics simulations of hydrogen storage capacity of few-layer graphene

Cheng-Da Wu, Te-Hua Fang, Jian-Yuan Lo, Yu-Lun Feng

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 557 KB

english, 2013

40

Electron density reactivity indexes of the tautomeric/ionization forms of thiamin diphosphate

Gonzalo A. Jaña, Eduardo J. Delgado

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 271 KB

english, 2013

41

Structural and phylogenetic basis for the classification of group III phospholipase A2

Gururao Hariprasad, Alagiri Srinivasan, Reema Singh

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 1.40 MB

english, 2013

42

The symmetric and asymmetric thiophene-fused benzocarborane: structures and first hyperpolarizabilities

Yong Li, Heng-Qing Wu, Hong-Liang Xu, Shi-Ling Sun…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 306 KB

english, 2013

43

A structural modeling approach for the understanding of initiation and elongation of ALS-linked superoxide dismutase fibrils

Mattia Falconi, Federico Iacovelli, Alessandro Desideri

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 749 KB

english, 2013

44

Computational study of decomposition mechanisms and thermodynamic properties of molecular-type cracking patterns for the highly energetic molecule GZT

Sou-Ro Cheng, Ken-Fa Cheng, Min-Hsien Liu, Yaw-Shun Hong…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 1.05 MB

english, 2013

45

Natural velvet antler polypeptide conformation prediction and molecular docking study with TGF-β1 complex

Yu-Dong Shang, Ji-Long Zhang, Qing-Chuan Zheng

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 737 KB

english, 2013

46

Anomeric and rotameric preferences of glucopyranose in vacuo, water and organic solvents

Sedat Karabulut, Jerzy Leszczynski

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 459 KB

english, 2013

47

Predicting the preferred conformations of luteolin-4′-O-β-D-glucoside in gas phase: a comparison of two computational approaches

Yongzhi Li, Xiuhua Liu, Dong Chen, Zhichao Wei, Bo Liu

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 549 KB

english, 2013

48

Molecular modeling of the piezoelectric effect in the ferroelectric polymer poly(vinylidene fluoride) (PVDF)

Vladimir S. Bystrov, Ekaterina V. Paramonova…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 851 KB

english, 2013

49

PPIcons: identification of protein-protein interaction sites in selected organisms

Brijesh K. Sriwastava, Subhadip Basu, Ujjwal Maulik…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 606 KB

english, 2013

50

Structure guided inhibitor designing of CDK2 and discovery of potential leads against cancer

Arun Kumar V.A, Keshav Mohan, Syed Riyaz

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 569 KB

english, 2013

51

DFT calculation of the electronic properties of fluorene-1,3,4-thiadiazole oligomers

Nora Aydeé Sánchez-Bojorge, Luz María Rodríguez-Valdez…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 296 KB

english, 2013

52

Modeling the physisorption of bisphenol A on graphene and graphene oxide

Diego Cortés-Arriagada, Luis Sanhueza…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 1.08 MB

english, 2013

53

A comparative study of the aromaticity of pyrrole, furan, thiophene, and their aza-derivatives

Kalbinur Najmidin, Ablikim Kerim, Paruza Abdirishit…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 371 KB

english, 2013

54

In silico discrimination of nsSNPs inhTERTgene by means of local DNA sequence context and regularity

C. George Priya Doss, Chiranjib Chakraborty, B. Rajith…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 814 KB

english, 2013

55

Computational nanochemistry study of the molecular structure and properties of ethambutol

Guillermo Salgado-Morán, Samuel Ruiz-Nieto…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 535 KB

english, 2013

56

Reaction mechanism of CH3M≡MCH3(M=C, Si, Ge) with C2H4: [2+1] or [2+2] cycloaddition?

Suhong Huo, Xiaoyan Li, Yanli Zeng, Shijun Zheng…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 376 KB

english, 2013

57

Looking for high energy density compounds among polynitraminepurines

Ting Yan, Guangdong Sun, Weijie Chi, Butong Li, Haishun Wu

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 224 KB

english, 2013

58

A method for in silico identification of SNAIL/SLUG DNA binding potentials to the E-box sequence using molecular dynamics and evolutionary conserved amino acids

Jeremy W. Prokop, Yuanjie Liu, Amy Milsted…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 386 KB

english, 2013

59

Thermal, electronic and ductile properties of lead-chalcogenides under pressure

Dinesh C. Gupta, Idris Hamid Bhat

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 804 KB

english, 2013

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