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Journal of Molecular Modeling

Diego Chaparro, Jorge Alí-Torres
Molecular phenomena involving electron transfer and reduction/oxidation processes are of the utmost importance in chemistry. However, accurate computational calculations of standard reduction potentials (SRPs) for transition metal complexes are still challenging. For this reason, some computational strategies have been proposed in order to overcome the main limitations in SRP calculations for copper complexes. However, these strategies are limited to particular coordination spheres and do not represent a general methodology...
September 21, 2017: Journal of Molecular Modeling
Minh Thao Nguyen, Quoc Tri Tran, Van Tan Tran
In this work, the low-lying states of several isomers of ScSi n(-/0) (n = 4-6) were investigated with the B3LYP functional and CASPT2 method. The ground states of the anionic clusters were predicted to be the singlet states of the trigonal bipyramid ScSi4(-) (A-ScSi4(-)), the face-capped trigonal bipyramid ScSi5(-) (A-ScSi5(-)), and the pentagonal bipyramid ScSi6(-) (A-ScSi6(-)) isomer. Based on the anionic ground states, all the relevant electron detachment processes were identified. The corresponding adiabatic and vertical detachment energies (ADEs and VDEs) of the anionic clusters were computed at the CASPT2 level...
September 20, 2017: Journal of Molecular Modeling
Gui-Yun Hang, Wen-Li Yu, Tao Wang, Jin-Tao Wang, Zhen Li
To investigate and compare the differences of structures and properties of CL-20/TNT cocrystal and composite explosives, the CL-20/TNT cocrystal and composite models were established. Molecular dynamics simulations were performed to investigate the structures, mechanical properties, sensitivity, stabilities and detonation performance of cocrystal and composite models with COMPASS force field in NPT ensemble. The lattice parameters, mechanical properties, binding energies, interaction energy of trigger bond, cohesive energy density and detonation parameters were determined and compared...
September 19, 2017: Journal of Molecular Modeling
Song Yu, Jiang Bo, Li Jiahong
The mechanism for the competitive adsorption of CH4 and CO2 on coal vitrinite (DV-8, maximum vitrinite reflectance R o,max = 0.58%) was revealed through simulation and experimental methods. A saturated state was reached after absorbing 17 CH4 or 22 CO2 molecules per DV-8 molecule. The functional groups (FGs) on the surface of the vitrinite can be ranked in order of decreasing CH4 and CO2 adsorption ability as follows: [-CH3] > [-C=O] > [-C-O-C-] > [-COOH] and [-C-O-C-] > [-C=O] > [-CH3] > [-COOH]...
September 16, 2017: Journal of Molecular Modeling
Huanjie Wang, Fancui Meng
The stratum corneum (SC), the outermost layer of skin, represents the primary barrier to molecules penetrating the skin. Menthol is widely used in clinical medicine as a penetration enhancer due to its high efficiency and relative safety. In this study, molecular dynamics simulations have been performed to investigate the effect of menthol molecules on the structural and permeability of both single component and ternary mixed bilayers. The lipid matrix is modeled as pure ceramide (CER2) or as a 2:2:1 mixture of CER2, cholesterol (CHOL), and free fatty acid (FFA)...
September 15, 2017: Journal of Molecular Modeling
Tayeb Aissaoui, Yacine Benguerba, Mohamed Khalid AlOmar, Inas M AlNashef
Recently, there has been significant interest in the possibility of using deep eutectic solvents (DESs) as novel green media and alternatives to conventional solvents and ionic liquids (ILs) in many applications. Due to their attractive properties, such as their biodegradability, low cost, easy preparation, and nontoxicity, DESs appear to be very promising solvents for use in the field of green chemistry. This computational study investigated six glycerol-based DESs: DES1 (glycerol:methyl triphenyl phosphonium bromide), DES2 (glycerol:benzyl triphenyl phosphonium chloride), DES3 (glycerol:allyl triphenyl phosphonium bromide), DES4 (glycerol:choline chloride), DES5 (glycerol:N,N-diethylethanolammonium chloride), and DES6 (glycerol:tetra-n-butylammonium bromide)...
September 14, 2017: Journal of Molecular Modeling
Tsvetan G Gantchev, Peicho St Petkov, Darel J Hunting
The major structural aberrations of DNA induced by a cis-diammineplatinum (II) 1,2-d(GG) intrastrand cross-link (CPT) have been known for decades. To gain deeper insights into the structural dynamics of the sequence-dependent DNA distortions adjacent to the CPT adduct, we employed molecular modeling and molecular dynamics (MD) simulations. The structural dynamics of native (N-DNA) and cisPt 1,2-d(GG) crosslinked (CPT-DNA) in the form of symmetric 36 nt d(G2T15G*G*T15G2)●C2A15CCA15C2) oligonucleotide duplexes is compared...
September 14, 2017: Journal of Molecular Modeling
Liliana Mammino
Arzanol (C22H26O7) is a naturally occurring acylphloroglucinol largely responsible for the anti-inflammatory, anti-oxidant, antibiotic and antiviral activities of Helichrysum italicum. Like all acylphloroglucinols, the molecule contains a carboxylic substituent (-COR group); for arzanol, this is a -COCH3 group. The molecule is further characterized by the presence of an α-pyrone ring bonded in meta to -COR through a methylene bridge, and of a prenyl chain bonded to the other meta position. The molecule can form up to three intramolecular hydrogen bonds (IHB) simultaneously, and their presence and patterns are the major stabilizing factors...
September 12, 2017: Journal of Molecular Modeling
He-Hou Zong, Lei Zhang, Wei-Bin Zhang, Sheng-Li Jiang, Yi Yu, Jun Chen
In this work, we report the structure, mechanical properties, and vibrational spectra of 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105), an energetic molecular crystal, with a first-principles method based on density functional theory (DFT) using the recentely developped HASEM package. The elastic constants, acoustic velocity, and parameters of equations of state were calculated, and the predicted ordering of stiffness constants is C 33 (38.5 GPa) > C 11 (24.0 GPa) > C 22 (17.7 GPa). We also investigated the structure and equation of state of LLM-105 under hydrostatic pressure up to 100 GPa...
September 10, 2017: Journal of Molecular Modeling
Shinya Iwata, Hiroaki Uehara, Tatsuo Takada
Polyethylene (PE) is widely used as an electrical insulating material. Acetophenone (AP) is a major residue in PE and is considered one of the causes of insulation deterioration. However, the physicochemical explanation of the influence of AP is still unknown. Therefore, in the present study, the behavior of AP molecules in amorphous PE was investigated using molecular dynamics (MD) simulations and quantum chemical calculation. First, the basic properties of the AP molecule were evaluated from the viewpoint of molecular electrostatic potential (MEP), molecular orbitals, and energy levels...
September 8, 2017: Journal of Molecular Modeling
Oscar Parravicini, M Lucrecia Bogado, Sebastián Rojas, Emilio L Angelina, Sebastián A Andujar, Lucas J Gutierrez, Nuria Cabedo, M Jesús Sanz, M Pilar López-Gresa, Diego Cortes, Ricardo D Enriz
A series of tetrahydroisoquinolines functionalized with carbamates is reported here as highly selective ligands on the dopamine D2 receptor. These compounds were selected by means of a molecular modeling study. The studies were carried out in three stages: first an exploratory study was carried out using combined docking techniques and molecular dynamics simulations. According to these results, the bioassays were performed; these experimental studies corroborated the results obtained by molecular modeling. In the last stage of our study, a QTAIM analysis was performed in order to determine the main molecular interactions that stabilize the different ligand-receptor complexes...
September 2, 2017: Journal of Molecular Modeling
Zhanhang Shen, Kelly A Mulholland, Yujun Zheng, Chun Wu
DNA G-quadruplex structures are emerging cancer-specific targets for chemotherapeutics. Ligands that bind to and stabilize DNA G-quadruplexes have the potential to be anti-cancer drugs. Lack of binding selectivity to DNA G-quadruplex over DNA duplex remains a major challenge when attempting to develop G-quadruplex ligands into successful anti-cancer drugs. Thorough understanding of the binding nature of existing non-selective ligands that bind to both DNA quadruplex and DNA duplex will help to address this challenge...
September 2017: Journal of Molecular Modeling
Rupendeep Kaur, Noorinder Kaur
It is worth remarking that the C20 cage like isomer has been the topic of concentrated theoretical research. C20 single fullerene molecular devices gained a lot of popularity in the field of nano research due to their superlative doping dependent conductive properties. In this work, the double fullerene device has been considered. Here double fullerene molecular junction is created when two C20 fullerene molecules, one in pristine form and other in doped form, are positioned between gold electrodes. Doping was done firstly by second period elements, boron, nitrogen, oxygen, and fluorine and then by group 14 tetragens, silicon, germanium, tin, and lead...
September 2017: Journal of Molecular Modeling
Qiong Wu, Bo Kou, Zewu Zhang, Zusheng Hang, Weihua Zhu
In this study, employing a new high oxygen balance energetic 3,3'-dinitro-5,5'-bis-1,2,4-triazole-1,1'-diolate anion (DNBTDO) as the bidentate ligand, NH3 and NH2NO2 as short energetic ligands, and Cu/Ni as the metal atoms, two series of novel energetic metal complexes were computationally designed. Their structures and properties were studied by density functional theory, electrostatic potential data, and molecular mechanics methods. The results showed that the designed metal complexes have high detonation performance and acceptable sensitivity: Cu/Ni(DNBTDO)(NH2NO2)2 (A3/B3) have better detonation properties and lower sensitivity than the most powerful CHNO explosive hexanitrohexaazaisowurtzitane, Cu/Ni(DNBTDO)(NH3)(NH2NO2) (A2/B2) have comparable energetic performance and sensitivity with 1,3,5,7-tetranitro-1,3,5,7-tetrazocane, Ni(DNBTDO)(NH3)2 (B1) has comparative energy level and sensitivity with 1,3,5-trinitro-1,3,5-triazinane...
September 2017: Journal of Molecular Modeling
Caio Lima Firme, Diógenes Mendes Araújo
Although there are a multitude of aromaticity indexes, only a few have a widespread usage. All famous aromaticity indexes are limited: HOMA and FLU are reference-dependent; ELF is π-bond-dependent; PDI is structurally dependent and NICS is ring size dependent. These limitations stimulate the continuous search for better (i.e., having no dependency), more flexible (i.e., applied to any aromatic system) and more effective (i.e., with excellent correlations with other indexes) aromaticity indexes. The D3BIA was our first topological aromaticity index...
September 2017: Journal of Molecular Modeling
Rajendran Niranjana Devi, Maria G Khrenova, Samuel Israel, Chellam Anzline, Andrey A Astakhov, Vladimir G Tsirelson
A combined molecular docking, QM, and QM/MM dynamics modeling complemented with electron-density based descriptors computed at the B3LYP/6-311G++(d,p) level of theory have been carried out in order to understand the ability of the drugs rhodanine (RD) and 2,4-thiazolidinedione (TZD) in the effective treatment of type 2 diabetes mellitus. The global HOMO/LUMO descriptors provided just a very rough estimate of the chemical reactivity of both molecules, while the features of electron density studied in terms of its Laplacian and electrostatic potential allowed identifying the local electron rich/poor sites which were associated with the regions of electrophilic/nucleophilic attacks in RD and TZD...
September 2017: Journal of Molecular Modeling
Nargis Tabassum, Qianyun Ma, Guanzhao Wu, Tao Jiang, Rilei Yu
Nicotinic acetylcholine receptors (nAChRs) belong to the Cys-loop receptor family and are important drug targets for the treatment of neurological diseases. However, the precise determinants of the binding efficacies of ligands for these receptors are unclear. Therefore, in this study, the binding energy profiles of various ligands (full agonists, partial agonists, and antagonists) were quantified by docking those ligands with structural ensembles of the α7 nAChR exhibiting different degrees of C-loop closure...
September 2017: Journal of Molecular Modeling
Keunhong Jeong, YongGoon Jeon, Soonmo Kwon
B3LYP, PBE, M06-2X, B2PLYP, BN2PLYP-D, ωB97X-D, and MP2 levels of theory, in combination with the 6-311++G(d,p) and cc-pVTZ basis sets were comprehensively assessed for their ability to reproduce experimental FOX-7 structural and detonation data. ωB97X-D/cc-pVTZ, B3LYP/cc-pVTZ, and M06-2X/cc-pVTZ provided highly accurate optimized structure predictions. M06-2X/cc-pVTZ and ωB97X-D/cc-pVTZ reproduced experimentally determined detonation properties (detonation velocity and detonation pressure) with high accuracy...
September 2017: Journal of Molecular Modeling
Gülşen Öztürk, Salih Subari, Sevil Şeker, Mahmut Toğrul, Şafak Özhan Kocakay, Selami Ercan, Necmettin Pirinççioğlu
Two novel amide-based receptors were synthesized under microwave irradiation. Their chemical structures were confirmed by IR, (1)H NMR, (13)C NMR, and elemental analysis. The binding properties of these amide-based receptors to various anions (H2PO4(-), HSO4(-), C6H5CO2(-), CH3CO2(-), ClO4(-), F(-), Cl(-), and Br(-)) were examined by UV titration in THF at 20 °C. The results indicated that the receptors form 1:1 complexes with anions and they have the strongest affinity for fluoride (F(-)) among the anions considered...
September 2017: Journal of Molecular Modeling
Xuehua Zheng, Siyuan Zhou, Chen Zhang, Deyan Wu, Hai-Bin Luo, Yinuo Wu
Recently, a series of xanthone analogues has been identified as α-glucosidase inhibitors. To provide deeper insight into the three-dimensional (3D) structural requirements for the activities of these molecules, CoMFA and CoMSIA approaches were employed on 54 xanthones to construct 3D-QSAR models. Their bioactive conformations were first investigated by docking studies and optimized by subsequent molecular dynamics (MD) simulations using the homology modeled structure of the target protein. Based on the docking/MD-determined conformers, 3D-QSAR studies generated several significant models in terms of 47 molecules as the training set...
August 31, 2017: Journal of Molecular Modeling
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