Volume 19; Issue 1

Journal of Molecular Modeling

Volume 19; Issue 1

1

Theoretical studies on the crystal structure, thermodynamic properties, detonation performance and thermal stability of cage-tetranitrotetraazabicyclooctane as a novel high energy density compound

Guo-zheng Zhao, Ming Lu

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 280 KB

english, 2013

2

Quantum chemical investigation of the intra- and intermolecular proton transfer reactions and hydrogen bonding interactions in 4-amino-5-(2-hydroxyphenyl)-2H-1,2,4-triazole-3(4H)-thione

Namık Özdemir

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 342 KB

english, 2013

3

Computer simulation based selection of optimal monomer for imprinting of tri-O-acetiladenosine in polymer matrix: vacuum calculations

Viatcheslav V. Barkaline, Yana V. Douhaya, Andreas Tsakalof

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 481 KB

english, 2013

4

Molecular modeling to investigate the binding of Congo red toward GNNQQNY protofibril and in silico virtual screening for the identification of new aggregation inhibitors

Jian-Hua Zhao, Hsuan-Liang Liu, Pavadai Elumalai, Wei-Hsi Chen, Lee-Chung Men, Kung-Tien Liu

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 705 KB

english, 2013

5

In silico structural and functional analysis of the human TOPK protein by structure modeling and molecular dynamics studies

Palani Kirubakaran, Muthusamy Karthikeyan, Kh. Dhanachandra Singh, Selvaraman Nagamani, Kumpati Premkumar

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 1.08 MB

english, 2013

6

Density functional theory study on the reaction mechanism of synthesizing 1,3-dimethyl-2-imidazolidinone by urea method

Shujuan Yao, Huayong Chen, Shu Jiang, Xin Shao, Shouxin Cui

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 422 KB

english, 2013

7

Dependence of the optical absorption and Na+binding energies of coumarin-crown ethers on the size and attachment position of ether ring: density functional investigation

Esra Kasapbasi, Mine Yurtsever

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 266 KB

english, 2013

8

MD simulation of self-diffusion and structure in somen-alkanes over a wide temperature range at high pressures

Huajie Feng, Wei Gao, Jingjing Nie, Jing Wang, Xiaojuan Chen, Liuping Chen, Xin Liu, Hans-Dietrich Lüdemann, Zhenfan Sun

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 360 KB

english, 2013

9

Theoretical investigations on the structure, density, thermodynamic and performance properties of amino-, methyl-, nitroso- and nitrotriazolones

P. Ravi, Bonige K. Babu, Suyra P. Tewari

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 317 KB

english, 2013

10

Theoretical study of the triangular bonding complex formed by carbon tetrabromide, a halide, and a solvent molecule in the gas phase

Xiao Ran Zhao, Yu Jie Wu, Juan Han, Qian Jin Shen, Wei Jun Jin

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 1.87 MB

english, 2013

11

Characterization of the structures and dynamics of phosphoric acid doped benzimidazole mixtures: a molecular dynamics study

Minal More, Swagata Pahari, Sudip Roy, Arun Venkatnathan

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 722 KB

english, 2013

12

A DFT study on the mechanisms for the cycloaddition reactions between 1−aza-2-azoniaallene cations and acetylenes

Jing-mei Wang, Zhi-ming Li, Quan-rui Wang, Feng-gang Tao

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 576 KB

english, 2013

13

Rectifying behavior of charge transfer complexes of tetrakis(dimethylamino)ethene with acceptor molecules: a theoretical study

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 363 KB

english, 2013

14

Theoretical investigation on the structure and thermodynamic properties of the 2,4-dinitroimidazole complex with methanol

Shu-sen Zhao, Wen-jing Shi, Jian-long Wang

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 532 KB

english, 2013

15

Electric field effect on thezigzag(6,0) single-wall BC2N nanotube for use in nano-electronic circuits

Mohammad T. Baei, Ali Ahmadi Peyghan, Masoumeh Moghimi, Saeede Hashemian

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 555 KB

english, 2013

16

Structural and chemical basis for enhanced affinity to a series of mycobacterial thymidine monophosphate kinase inhibitors: fragment-based QSAR and QM/MM docking studies

Renata V. Bueno, Ney R. Toledo, Bruno J. Neves, Rodolpho C. Braga, Carolina H. Andrade

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 723 KB

english, 2013

17

Structure-based design of nitrogen-linked macrocyclic kinase inhibitors leading to the clinical candidate SB1317/TG02, a potent inhibitor of cyclin dependant kinases (CDKs), Janus kinase 2 (JAK2), and Fms-like tyrosine kinase-3 (FLT3)

Anders Poulsen, Anthony William, Stéphanie Blanchard, Harish Nagaraj, Meredith Williams, Haishan Wang, Angeline Lee, Eric Sun, Ee-Ling Teo, Evelyn Tan, Kee Chuan Goh, Brian Dymock

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 704 KB

english, 2013

18

Theoretical design study on photophysical property on oligomers based on spirobifluorene and carbazole-triphenylamine for PLED applications

Xiao-Hua Xie, Wei Shen, Rong-Xing He, Ming Li

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 625 KB

english, 2013

19

Anion recognition by azophenol thiourea-based chromogenic sensors: a combined DFT and molecular dynamics investigation

Ming Wah Wong, Huifang Xie, Soo Tin Kwa

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 608 KB

english, 2013

20

Performance comparison of computational methods for modeling alpha-helical structures

Alexandru Lupan, Attila-Zsolt Kun, Francisco Carrascoza, Radu Silaghi-Dumitrescu

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 558 KB

english, 2013

21

Computational investigation on the new high energy density material of aluminum enriched 1, 1-diamino-2, 2-dinitroethylene

Liang Bian, Yuanjie Shu, Jinbao Xu, Lei Wang

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 578 KB

english, 2013

22

Density functional study on the adsorption of the drug isoniazid onto pristine and B-doped single wall carbon nanotubes

Nabanita Saikia, Ramesh C. Deka

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 807 KB

english, 2013

23

A plausible explanation for enhanced bioavailability of P-gp substrates in presence of piperine: simulation for next generation of P-gp inhibitors

Durg Vijay Singh, Madan M. Godbole, Krishna Misra

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 840 KB

english, 2013

24

Density functional investigation of CO adsorption on Ni-doped single-walled armchair (5,5) boron nitride nanotubes

Sarawut Tontapha, Vithaya Ruangpornvisuti, Banchob Wanno

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 676 KB

english, 2013

25

A new interaction mechanism of LiNH2with MgH2: magnesium bond

Xin Yang, Qingzhong Li, Jianbo Cheng, Wenzuo Li

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 242 KB

english, 2013

26

A density functional theory analysis for the adsorption of the amine group on graphene and boron nitride nanosheets

Ernesto Chigo Anota, Alejandro Rodríguez Juárez, Miguel Castro, Heriberto Hernández Cocoletzi

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 753 KB

english, 2013

27

Hydrogen dissociation on diene-functionalized carbon nanotubes

Javad Beheshtian, Ali Ahmadi Peyghan, Zargham Bagheri

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 430 KB

english, 2013

28

A comparative study of semi-squaraine and squaraine dyes using computational techniques: tuning the charge transfer/biradicaloid character by substitution

Avinash L. Puyad, Gunturu Krishna Chaitanya, Chetti Prabhakar, Kotamarthi Bhanuprakash

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 1.28 MB

english, 2013

29

Probing the structural and electronic properties of aluminum-sulfur AlnSm(2 ≤ n + m ≤ 6) clusters and their oxides

Ming-Min Zhong, Xiao-Yu Kuang, Zhen-Hua Wang, Peng Shao, Li-Ping Ding

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 617 KB

english, 2013

30

Theoretical study of the decomposition of ethyl and ethyl 3-phenyl glycidate

Daniela Josa, Angeles Peña-Gallego, Jesús Rodríguez-Otero, Enrique M. Cabaleiro-Lago

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 192 KB

english, 2013

31

Conformational entropy of a polymer chain grafted to rough surfaces

Waldemar Nowicki, Grażyna Nowicka, Marcin Dokowicz, Agnieszka Mańka

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 470 KB

english, 2013

32

Periodic density functional theory study of the high-pressure behavior of energetic crystalline 1,4-dinitrofurazano[3, 4-b]piperazine

Wentao Wang, Weihua Zhu, Jinshan Li, Bibo Cheng, Heming Xiao

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 944 KB

english, 2013

33

Modeling the structure and proton transfer pathways of the mutant His-107-Tyr of human carbonic anhydrase II

Puspita Halder, Srabani Taraphder

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 598 KB

english, 2013

34

Ab initio study of weakly bound halogen complexes: RX⋯PH3

Herbert C. Georg, Eudes E. Fileti, Thaciana Malaspina

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 366 KB

english, 2013

35

Insight into substituent effects in Cal-B catalyzed transesterification by combining experimental and theoretical approaches

Zhong Ni, Xianfu Lin

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 483 KB

english, 2013

36

Prodrugs of fumarate esters for the treatment of psoriasis and multiple sclerosis—a computational approach

Rafik Karaman, Ghadeer Dokmak, Maryam Bader, Hussein Hallak, Mustafa Khamis, Laura Scrano, Sabino Aurelio Bufo

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 634 KB

english, 2013

37

A flexible-protein molecular docking study of the binding of ruthenium complex compounds to PIM1, GSK-3β, and CDK2/Cyclin A protein kinases

Yingting Liu, Neeraj J. Agrawal, Ravi Radhakrishnan

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 734 KB

english, 2013

38

Sequence selectivity of azinomycin B in DNA alkylation and cross-linking: a QM/MM study

Dhurairajan Senthilnathan, Anbarasan Kalaiselvan, Ponnambalam Venuvanalingam

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 771 KB

english, 2013

39

Discovery of novel low-molecular-weight HIV-1 inhibitors interacting with cyclophilin A using in silico screening and biological evaluations

Yu-Shi Tian, Chris Verathamjamras, Norihito Kawashita, Kousuke Okamoto, Teruo Yasunaga, Kazuyoshi Ikuta, Masanori Kameoka, Tatsuya Takagi

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 830 KB

english, 2013

40

Low-energy conformers of pamidronate and their intramolecular hydrogen bonds: a DFT and QTAIM study

Masoud Arabieh, Mohammad Hossein Karimi-Jafari, Mohammad Ghannadi-Maragheh

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 756 KB

english, 2013

41

Structural phase transition of CdTe: an ab initio study

Sebahaddin Alptekin

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 384 KB

english, 2013

42

Carbon nanotube functionalization with carboxylic derivatives: a DFT study

Javad Beheshtian, Ali Ahmadi Peyghan, Zargham Bagheri

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 403 KB

english, 2013

43

A B3LYP and MP2(full) theoretical investigation into the strength of the C-NO2bond upon the formation of the molecule-cation interaction between Na+and the nitro group of nitrotriazole or its methyl derivatives

Qing-guo Wei, Wen-jing Shi, Fu-de Ren, Yong Wang, Jun Ren

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 616 KB

english, 2013

44

Stress-induced activation of decomposition of organic explosives: a simple way to understand

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 383 KB

english, 2013

45

Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters

James J. P. Stewart

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 686 KB

english, 2013

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