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Journal of Molecular Modeling

Jianchun Zhang, Tao Ji
Oncogenic BRaf V600E mutation is involved in the development, invasion and metastasis of colon cancer. Selective inhibition of BRaf(V600E) mutant has been recognized as a therapeutic strategy for the cancer. Here, we carried out atomistic molecular dynamics (MD) simulations to characterize the structural basis, energetic property, and dynamics behavior of conformational change in BRaf activation loop upon the mutation. It is found that V600E mutation destabilizes inactive DFG-out conformation of activation loop and promotes its conversion to the active DFG-in conformation, thus conferring constitutive activity for BRaf kinase...
January 2017: Journal of Molecular Modeling
Ahmed Taki Eddine Ardjani, Sidi Mohamed Mekelleche
In the present work, the molecular structure and the antioxidant activity of 4-(5-chloro-2-hydroxyphenylamino)-4-oxobut-2-enoic acid (A) and its derivatives (B-E) have been studied at the B3LYP/6-31++G(2d,2p) computational level. The obtained results indicate that the hydrogen atom transfer (HAT mechanism) is thermodynamically more favored in gas phase; whereas, the sequential proton loss-electron transfer (SPLET mechanism) is more preferred in polar solvents. The antioxidant activity of compounds A-E is also analyzed by the calculation of atomic spin densities, chemical hardnesses, dipole moments, and lipophilicity indexes...
December 2016: Journal of Molecular Modeling
Malek Boukallaba, Boutheïna Kerkeni, Christine Lepetit, Dorothée Berthomieu
A quantum chemistry study of mononuclear metal coordination with four 4-methylimidazole ligands (4-MeIm) was investigated. The four complexes [Cu(4-MeIm)4](2+), [Cu(4-MeIm)4, H2O](2+), [Zn(4-MeIm)4](2+) and [Zn(4-MeIm)4, H2O](2+) were studied with particular attention to the Nπ or Nτ possible coordinations of the 4-MeIm ring with the metals, using different DFT methods. The results suggest that the Nτ coordination of 4-MeIm ring to Zn(II) or Cu(II) is more favorable whatever the level of calculation. In contrast, the addition of one water molecule in the first coordination sphere of the metal ions provides five-coordinated complexes showing no Nπ or Nτ preferences...
December 2016: Journal of Molecular Modeling
Jingjing Wang, Lixin Mo, Xiaoyan Li, Zongke Geng, Yanli Zeng
The σ-hole and π-hole of the protonated 2-halogenated imidazolium cation (XC3H4N2(+); X = F, Cl, Br, I) were investigated and analyzed. The monomers of (CH3)3SiY(Y=F, Cl, Br, I), considered as the Lewis base, were combined with the σ-hole and π-hole of XC3H4N2(+) to form the σ-hole and π-hole interactions in the bimolecular complexes (CH3)3SiY · · · XC3H4N2(+) and (CH3)3SiY · · · C3(X)H4N2(+)(X/Y=F, Cl, Br, I), respectively. For both the σ-hole and π-hole interactions, the equilibrium geometries of complexes show regular changes according to the sequence of heavy sequence of the noncovalent interaction acceptors and donors...
December 2016: Journal of Molecular Modeling
Bing Zhang, Jia Xu, Shu-Fan Mo, Jian-Xi Yao, Song-Yuan Dai
Electron transfer between cytochrome c (Cytc) and electrodes can be influenced greatly by the orientation of protein on the surface of the electrodes. In the present study, different initial orientations of Cytc on the surface of five types of single-walled carbon nanotubes (SWNTs), with different diameters and chirality, were constructed. Properties of the orientations of proteins on the surface of these tubes were first investigated through molecular dynamics simulations. It was shown that variations in SWNT diameter do not significantly affect the orientation; however, the chirality of the SWNTs is crucial to the orientation of the heme embedded in Cytc, and the orientation of the protein can consequently be influenced by the heme orientation...
December 2016: Journal of Molecular Modeling
S Ajori, R Ansari, H Parsapour
Functionalized carbon nanotubes (CNTs) can be used for improving the mechanical properties and load transfer in nanocomposites. In this research, the buckling behavior of perfect and defective cross-linked functionalized CNTs with polyethylene (PE) chains is studied employing molecular dynamics (MD) simulations. Two different configurations with the consideration of vacancy defects, namely mapped and wrapped, are selected. According to the results, critical buckling force of cross-linked functionalized CNTs with PE chains increases as compared to pure CNTs, especially in the case of double-walled carbon nanotubes (DWCNTs)...
December 2016: Journal of Molecular Modeling
Le Yang, Peng Jin, Qinghua Hou, Lanlan Li
For the first time, the structures, stabilities and electronic properties of alkaline-earth metal doped B44 fullerenes were investigated by means of density functional theory calculations. Our results reveal that M@B44 (M = Ca, Sr, Ba) possess endohedral configurations as their lowest energy structures, whereas the exohedral form is favored when metal is Be or Mg. The large binding energies and sizable HOMO-LUMO gap energies of Ca@B44, Sr@B44 and Ba@B44 suggest the considerable possibility to achieve these novel endohedral borofullerenes experimentally...
December 2016: Journal of Molecular Modeling
Christiaan Jardínez, Alberto Vela, Julián Cruz-Borbolla, Rodrigo J Alvarez-Mendez, José G Alvarado-Rodríguez
The relationship between the chemical structure and biological activity (log IC50) of 40 derivatives of 1,4-dihydropyridines (DHPs) was studied using density functional theory (DFT) and multiple linear regression analysis methods. With the aim of improving the quantitative structure-activity relationship (QSAR) model, the reduced density gradient s( r) of the optimized equilibrium geometries was used as a descriptor to include weak non-covalent interactions. The QSAR model highlights the correlation between the log IC50 with highest molecular orbital energy (E HOMO), molecular volume (V), partition coefficient (log P), non-covalent interactions NCI(H4-G) and the dual descriptor [Δf(r)]...
December 2016: Journal of Molecular Modeling
Bruno S Leite, Cristiano C Bastos, Antonio C Pavão
The infrared spectrum of water observed in sunspots is complex and dense, with bands separated by approximately 0.01 cm(-1). For top asymmetrical molecules, there is no theoretical approach that allows for the calculation of rotovibrational energy with such precision. Experimentally derived rotovibracional energy levels of water at high temperatures combined with variational calculations have been used for the band assignments. These energy levels are employed to refine the analysis of a small portion of the infrared absorption spectrum...
December 2016: Journal of Molecular Modeling
Jingwen Zhu, Emilie-Laure Zins, Mohammad Esmaïl Alikhani
For over a decade, amine-borane has been considered as a potential chemical hydrogen vector in the context of a search for cleaner energy sources. When catalyzed by organometallic complexes, the reaction mechanisms currently considered involve the formation of β-BH agostic intermediates. A thorough understanding of these intermediates may constitute a crucial step toward the identification of ideal catalysts. Topological approaches such as QTAIM and ELF revealed to be particularly suitable for the description of β-agostic interactions...
December 2016: Journal of Molecular Modeling
M Prakash, V Subramanian
The structure, stability and infrared spectral signatures of triflic acid (TA) with water clusters (Wn) and protonated water clusters (TAH(+)Wn, n = 1 - 6) were computed using DFT and MP2 methods. Our calculations show that a minimum of three water molecules are necessary to stabilize the dissociated zwitterionic form of TA. It can be seen from the results that there is no significant movement of protons in smaller (n = 1 and 2) and linear (n = 1 - 6) types of water clusters. Further, the geometries of TAWn clusters first form a neutral pair (NP) to contact ion pair (CIP), then form a solvent separated ion pair (SSIP) in a water hexamer...
December 2016: Journal of Molecular Modeling
Yamei Cheng, Xueye Wang, Weiwei Li, Dan Chang
The conversion of 2-phenylbenzimidazole using o-phenylenediamine and benzaldehyde can be improved significantly under β-cyclodextrin (β-CD). The density functional theory (DFT) method was applied to study the whole process. According to energy parameters (binding energy, deformation energy) and structural deformation, entry models and the reaction process can be pinpointed, with o-phenylenediamine embedding β-CD from a wide rim, and then benzaldehyde passing into the inclusion from the narrow rim. Subsequently, natural bonding orbital (NBO), Mulliken charge, frontier orbital, FuKui function and nuclear magnetic resonance (NMR) methods were employed to reveal the mechanism of electron transfer...
December 2016: Journal of Molecular Modeling
Li-Qiang Feng, Hang Liu, Wenliang Li, Rich-Samuel Castle
Molecular high-order harmonic generation (HHG) spectra from H2(+) and its application to the generation of the isolated attosecond pulses (IAPs) have been numerically investigated. Results show that (i) the 7th harmonic order is enhanced with the nuclei around the equilibrium internuclear, and as the internuclear distance increased, this enhanced harmonic produces a red-shift (even disappearance). Theoretical analyses show that the electronic transition between the ground and the 1st excited states is responsible for the red-shift enhanced harmonic...
December 2016: Journal of Molecular Modeling
Siti Fatimah Zaharah Mustafa, Hasmerya Maarof, Rashid Ahmed, Hassan Hadi Abdallah
Diffusion at the atomic or molecular level is a source of many physical, chemical, and biological processes taking place in plentiful materials. This work is an endeavor toward investigating the diffusional behavior of two different type of guests, hexadecane-1,16-diol and hexadecane enclathration in urea tunnel architecture, whereby the correlation of the diffusion mechanism with the guest's structural and conformational properties is explored. To carry out this study, molecular dynamics simulation approach is adopted...
December 2016: Journal of Molecular Modeling
Michael Wykes, Fabrice Odobel, Carlo Adamo, Ilaria Ciofini, Frédéric Labat
We present hybrid, periodic, spin-polarized density functional theory calculations of antiferromagnetic NiO bulk, of its clean (100) surface and of the binding on this latter of four different organic ligands, relevant for p-type dye-sensitized solar cells (p-DSSC) applications. We find evidence for a strong chemisorption of all ligands to the NiO surface in the form of short interatomic distances between surface Ni atoms and ligand atoms, confirmed by high binding energies. Although the analysis of the impact of the ligand adsorption on the density of states of the NiO substrate reveals significant modifications, the overall picture obtained is in line with the operation principles of p-DSSC in all cases...
December 2016: Journal of Molecular Modeling
A Levet, C Bordes, Y Clément, P Mignon, C Morell, H Chermette, P Marote, P Lantéri
To limit in vivo experiments, the use of quantitative structure-activity relationships (QSARs) is advocated by REACH regulation to predict the required fish, invertebrate, and algae EC50 for chemical registration. The aim of this work was to develop reliable QSARs in order to model both invertebrate and algae EC50 for organic solvents, regardless of the mechanism of toxic action involved. EC50 represents the concentration producing the 50 % immobilization of invertebrates or the 50 % growth inhibition of algae...
December 2016: Journal of Molecular Modeling
Mariagrazia Fortino, Tiziana Marino, Nino Russo, Emilia Sicilia
This paper illustrates the outcomes of a density functional theory investigation aimed at unraveling mechanistic aspects of the 5'-outer ring deiodination process of thyroxine (T4) assisted by the sterically protected organoselenol compound BpqSeH. BpqSeH, which was previously synthesized and tested for its deiodinase activity, is able to afford the active hormone 3,5,3'-tetraiodothyronine (T3) by selective outer-ring deiodination of T4, and to protect the SeH moiety inside the nano-sized molecular cavity from further reactivity, allowing its isolation and characterization...
December 2016: Journal of Molecular Modeling
Gabriela C Araujo, Ricardo H T Silva, Luis P B Scott, Alexandre S Araujo, Fatima P Souza, Ronaldo Junio de Oliveira
The human respiratory syncytial virus (hRSV) is the major cause of lower respiratory tract infection in children and elderly people worldwide. Its genome encodes 11 proteins including SH protein, whose functions are not well known. Studies show that SH protein increases RSV virulence degree and permeability to small compounds, suggesting it is involved in the formation of ion channels. The knowledge of SH structure and function is fundamental for a better understanding of its infection mechanism. The aim of this study was to model, characterize, and analyze the structural behavior of SH protein in the phospholipids bilayer environment...
December 2016: Journal of Molecular Modeling
Loïc Barnes, Baptiste Schindler, Isabelle Compagnon, Abdul-Rahman Allouche
We have developed and tested a new time-effective and accurate hybrid QM//MM generalized second-order vibrational perturbation theory (GVPT2) approach. In this approach, two different levels of theory were used, a high level one (DFT) for computing the harmonic spectrum and a lower fast one (Molecular Mechanic) for the anharmonic corrections. To validate our approach, we used B2PLYP/def2-TZVPP as the high-level method, and the MMFF94 method for the anharmonic corrections as the low-level method. The calculations were carried out on 28 molecules (containing from 2 to 47 atoms) covering a broad range of vibrational modes present in organic molecules...
November 2016: Journal of Molecular Modeling
Juan Sanz García, Fabienne Alary, Martial Boggio-Pasqua, Isabelle M Dixon, Jean-Louis Heully
The factors that explain the competition between intramolecular NO linkage photoisomerization and NO photorelease in five ruthenium nitrosyl complexes were investigated. By applying DFT-based methods, it was possible to characterize the ground states and lowest triplet potential energy surfaces of these species, and to establish that both photoisomerization and photorelease processes can occur in the lowest triplet state of each species. This work highlights the crucial role of the sideways-bonded isomer, a metastable state also known as the MS2 isomer, in the photochemical loss of NO, while the results obtained also indicate that the population of the triplet state of this isomer is compulsory for both processes and show how photoisomerization and photorelease interfere...
November 2016: Journal of Molecular Modeling
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