Volume 19; Issue 11

Journal of Molecular Modeling

Volume 19; Issue 11

1

Computational and experimental studies of the electronic excitation spectra of EDTA and DTPA substituted tetraphenylporphyrins and their Lu complexes

Valiev, Rashid R., Ermolina, Elena G., Kuznetsova, Rimma T., Cherepanov, Victor N., Sundholm, Dage

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 314 KB

english, 2013

2

Can Satraplatin be hydrated before the reduction process occurs? The DFT computational study

Bradáč, Ondřej, Zimmermann, Tomáš, Burda, Jaroslav V.

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 464 KB

english, 2013

3

Theoretical study of electronic absorptions in aminopyridines – TCNE CT complexes by quantum chemical methods, including solvent

Mach, Pavel, Juhász, György, Kyseľ, Ondrej

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 421 KB

english, 2013

4

Theoretical description of halogen bonding – an insight based on the natural orbitals for chemical valence combined with the extended-transition-state method (ETS-NOCV)

Mitoraj, Mariusz P., Michalak, Artur

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 547 KB

english, 2013

5

Halogen bond tunability II: the varying roles of electrostatic and dispersion contributions to attraction in halogen bonds

Riley, Kevin E., Murray, Jane S., FanfrlÃk, JindÅich, ÅezÃ¡Ä, Jan, SolÃ¡, Ricardo J., Concha, Monica C., Ramos, Felix M., Politzer, Peter

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 713 KB

english, 2013

6

Interaction of organic solvents with protein structures at protein-solvent interface

Khabiri, Morteza, Minofar, Babak, BrezovskÃ½, Jan, DamborskÃ½, JiÅÃ, Ettrich, Rudiger

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 659 KB

english, 2013

7

The use of supramolecular structures as protein ligands

Barbara Stopa, Anna Jagusiak, Leszek Konieczny…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 780 KB

english, 2013

8

Effect of the aminoacid composition of model α-helical peptides on the physical properties of lipid bilayers and peptide conformation: a molecular dynamics simulation

Milan Melicherčík, Alžbeta Holúbeková, Tibor Hianik…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 499 KB

english, 2013

9

Regulation of the transient receptor potential channel TRPA1 by its N-terminal ankyrin repeat domain

Vasilina Zayats, Abdul Samad, Babak Minofar…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 843 KB

english, 2013

10

Non-covalent interactions – QTAIM and NBO analysis

Sławomir J. Grabowski

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 312 KB

english, 2013

11

Congratulations to Professor Pavel Mach on the occasion of his 60th birthday

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 101 KB

english, 2013

12

Ligation of water to magnesium chelates of biological importance

Dorota Rutkowska-Zbik, Małgorzata Witko, Leszek Fiedor

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 218 KB

english, 2013

13

Theoretical study on cooperative effects between X⋯N and X⋯Carbene halogen bonds (X = F,Cl,Br and I)

Esrafili, Mehdi D., Mohammdain-Sabet, Fariba, Esmailpour, Parvin

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 230 KB

english, 2013

14

A theoretical investigation on the conformation and the interaction of CHF2OCF2CHF2(desflurane II) with one water molecule

Sutradhar, Dipankar, Zeegers-Huyskens, Therese, Chandra, Asit K.

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 347 KB

english, 2013

15

A DFT study of the Al2Cl6-catalyzed Friedel–Crafts acylation of phenyl aromatic compounds

Melissen, Sigismund T. A. G., Tognetti, Vincent, Dupas, Georges, Jouanneau, Julien, LÃª, Guillaume, Joubert, Laurent

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 804 KB

english, 2013

16

DFT and docking studies of rhodostreptomycins A and B and their interactions with solvated/nonsolvated Mg2+and Ca2+ions

JardÃnez, Christiaan, NicolÃ¡s-VÃ¡zquez, Ines, Cruz-Borbolla, Julian, GonzÃ¡lez-RamÃrez, Cesar A., Cepeda, Miguel, Correa-Basurto, Jose, Pandiyan, Thangarasu, Miranda, Rene

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 1.28 MB

english, 2013

17

Molecular dynamics simulation of cross-linked urea-formaldehyde polymers for self-healing nanocomposites: prediction of mechanical properties and glass transition temperature

Arab, Behrouz, Shokuhfar, Ali

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 767 KB

english, 2013

18

DFT model cluster studies of O2 adsorption on hydrogenated titania sub-nanoparticles

Andreev, Alexey S., Kuznetsov, Vyacheslav N., Chizhov, Yuri V.

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 619 KB

english, 2013

19

Easy methods to study the smart energetic TNT/CL-20 co-crystal

Li, Huarong, Shu, Yuanjie, Gao, Shijie, Chen, Ling, Ma, Qing, Ju, Xuehai

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 546 KB

english, 2013

20

A comparative DFT study on aquation and nucleobase binding of ruthenium (II) and osmium (II) arene complexes

Wang, Hanlu, Zeng, Xingye, Zhou, Rujin, Zhao, Cunyuan

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 340 KB

english, 2013

21

Structure and spectral characteristics of diquat-cucurbituril complexes from density functional theory

Peerannawar, Swarada R., Gejji, Shridhar P.

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 1.58 MB

english, 2013

22

Conformational analysis and intramolecular hydrogen bonding ofcis-3-aminoindan-1-ol: a quantum chemical study

Kheffache, Djaffar, Guemmour, Hind, Dekhira, Azzedine, Benaboura, Ahmed, Ouamerali, Ourida

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 431 KB

english, 2013

23

International conference on “Modeling interaction in biomolecules 2011”, in Kutná Hora, September 4th–9th, 2011

Burda, Jaroslav V., Sokalski, Andrzej W.

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 51 KB

english, 2013

24

Theoretical investigation on the kinetics and branching ratio of the gas phase reaction of sevoflurane with Cl atom

Singh, Hari Ji, Gour, Nand Kishor, Rao, Pradeep Kumar, Tiwari, Laxmi

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 353 KB

english, 2013

25

Design of Lewis acid–base complex: enhancing the stability and first hyperpolarizability of large excess electron compound

Ma, Fang, Miao, Tifang, Zhou, Zhongjun, Sun, Dengming

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 439 KB

english, 2013

26

Thiophenic compounds adsorption on Na(I)Y and rare earth exchanged Y zeolites: a density functional theory study

Gao, Xionghou, Geng, Wei, Zhang, Haitao, Zhao, Xuefei, Yao, Xiaojun

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 495 KB

english, 2013

27

Influence of doped nitrogen and vacancy defects on the thermal conductivity of graphene nanoribbons

Yang, Haiying, Tang, Yunqing, Gong, Jie, Liu, Yu, Wang, Xiaoliang, Zhao, Yanfang, Yang, Ping, Wang, Shuting

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 504 KB

english, 2013

28

Molecular basis of lateral force spectroscopy nano-diagnostics: computational unbinding of autism related chemokine MCP-1 from IgG antibody

Gogolinska, Anna, Nowak, Wieslaw

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 564 KB

english, 2013

29

Stereoselectivity of chalcone isomerase with chalcone derivatives: a computational study

Yao, Yuan, Zhang, Hui, Li, Ze-Sheng

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 683 KB

english, 2013

30

Do coinage metal anions interact with substituted benzene derivatives?

Aliakbar Tehrani, Zahra, Jamshidi, Zahra, Farhangian, Hossein

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 612 KB

english, 2013

31

Theoretical studies on the structure, thermochemical and detonation properties of amino and nitroso substituted 1,2,4-triazol-5-one-N-oxides

Ravi, P., Venkatesan, V., Tewari, Surya P.

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 449 KB

english, 2013

32

Binding selectivity studies of PKBα using molecular dynamics simulation and free energy calculations

Chen, Shi-Feng, Cao, Yang, Chen, Jiong-Jiong, Chen, Jian-Zhong

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 4.93 MB

english, 2013

33

Gas phase acidities of N-substituted amine-boranes

Adamson, Aiko, Guillemin, Jean-Claude, Burk, Peeter

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 197 KB

english, 2013

34

Optimized CGenFF force-field parameters for acylphosphate and N-phosphonosulfonimidoyl functional groups

Hegazy, Lamees, Richards, Nigel G. J.

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 713 KB

english, 2013

35

Theoretical investigations on the synthesis mechanism of cyanuric acid from NH3and CO2

Cheng, Xueli, Zhao, Yanyun, Zhu, Weiqun, Liu, Yongjun

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 461 KB

english, 2013

36

Competition and interplay between the lithium bonding and hydrogen bonding: R3C···HY···LiY and R3C···LiY···HY triads as a working model (R=H, CH3; Y=CN, NC)

Solimannejad, Mohammad, Rezaei, Zahra, Esrafili, Mehdi D.

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 165 KB

english, 2013

37

A knowledge-based halogen bonding scoring function for predicting protein-ligand interactions

Liu, Yingtao, Xu, Zhijian, Yang, Zhuo, Chen, Kaixian, Zhu, Weiliang

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 1.33 MB

english, 2013

38

The competition of C-X⋯O=P halogen bond and π-hole⋯O=P bond between halopentafluorobenzenes C6F5X (X=F, Cl, Br, I) and triethylphosphine oxide

Zhao, Xiao Ran, Wang, Hui, Jin, Wei Jun

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 566 KB

english, 2013

39

The study of interactions between DNA and PcrA DNA helicase by using targeted molecular dynamic simulations

Wang, Hao, Cui, Jiajia, Hong, Wei, Paterson, Ian C., Laughton, Charles A.

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 844 KB

english, 2013

40

Armchair BN nanotubes—levothyroxine interactions: a molecular study

Anota, E. Chigo, Cocoletzi, Gregorio H., Ramírez, J. F. Sánchez

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 554 KB

english, 2013

41

Destabilization of the MutSα’s protein-protein interface due to binding to the DNA adduct induced by anticancer agent carboplatin via molecular dynamics simulations

Negureanu, Lacramioara, Salsbury, Freddie R.

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 2.15 MB

english, 2013

42

Effect of surface hydroxyls on dimethyl ether synthesis over the γ-Al2O3in liquid paraffin: a computational study

Zuo, Zhi-jun, Wang, Le, Han, Pei-de, Huang, Wei

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 767 KB

english, 2013

43

Conformational flexibility of the leucine binding protein examined by protein domain coarse-grained molecular dynamics

Siuda, Iwona, Thøgersen, Lea

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 937 KB

english, 2013

44

Molecular interactions between fenoterol stereoisomers and derivatives and the β2-adrenergic receptor binding site studied by docking and molecular dynamics simulations

Plazinska, Anita, Kolinski, Michal, Wainer, Irving W., Jozwiak, Krzysztof

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 751 KB

english, 2013

45

The intrinsic helical propensities of the helical fragments in prion protein under neutral and low pH conditions: a replica exchange molecular dynamics study

Lu, Xiaoliang, Zeng, Juan, Gao, Ya, Zhang, John Z. H., Zhang, Dawei, Mei, Ye

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 1.11 MB

english, 2013

46

Exploring surface reactivity of phosphorous-doped (6,0) and (4,4) BC3 nanotubes: a DFT study

Alizadeh, Mohammad, Esrafili, Mehdi D., Vessally, Esmail

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 676 KB

english, 2013

47

Discovery of σ-hole interactions involving ylides

Ji, Jiannan, Zeng, Yanli, Zhang, Xueying, Zheng, Shijun, Meng, Lingpeng

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 642 KB

english, 2013

48

Insight into the structural stability of wild type and mutants of the tobacco etch virus protease with molecular dynamics simulations

Wang, Yu, Zhu, Guo-Fei, Ren, Si-Yan, Han, Yong-Guang, Luo, Yue, Du, Lin-Fang

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 1.35 MB

english, 2013

49

Redox and Lewis acid–base activities through an electronegativity-hardness landscape diagram

Das, Ranjita, Vigneresse, Jean-Louis, Chattaraj, Pratim Kumar

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 330 KB

english, 2013

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