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Journal of Molecular Modeling

G E Balatti, M F Martini, M Pickholz
In the present work we investigated the differential interactions of the antimicrobial peptides (AMPs) aurein 1.2 and maculatin 1.1 with a bilayer composed of a mixture of the lipids 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE). We carried out molecular dynamics (MD) simulations using a coarse-grained approach within the MARTINI force field. The POPE/POPG mixture was used as a simple model of a bacterial (prokaryotic cell) membrane...
July 17, 2018: Journal of Molecular Modeling
Nazish U Tanoli, Sheraz A K Tanoli, Antonio G Ferreira, Mazhar Mehmood, Sana Gul, Julia L Monteiro, Lucas C C Vieira, Tiago Venâncio, Arlene G Correa, Zaheer Ul-Haq
Alzheimer's disease (AD) is one of the most common forms of dementia and a significant threat to the elderly populations, especially in the Western world. The rapid hydrolysis of the principal neurotransmitter into choline and acetate by acetylcholinesterase (AChE) at synapses causes the loss of cognitive response that becomes the real cause of AD. Therefore, inhibition of AChE is the most fundamental therapy among currently available treatments for AD. In this context, we designed and performed molecular recognitions studies of coumarin-based inhibitors towards AChE...
July 14, 2018: Journal of Molecular Modeling
Meral Ayan, Sebnem Essiz
While ~30% of the human genome encodes membrane proteins, only a handful of structures of membrane proteins have been resolved to high resolution. Here, we studied the structure of a member of the Cys-loop ligand gated ion channel protein superfamily of receptors, human type A γ2 α1 β2 α1 β2 gamma amino butyric acid receptor complex in a lipid bilayer environment. Studying the correlation between the structure and function of the gamma amino butyric acid receptor may enhance our understanding of the molecular basis of ion channel dysfunctions linked with epilepsy, ataxia, migraine, schizophrenia and other neurodegenerative diseases...
July 14, 2018: Journal of Molecular Modeling
Tang-Mi Yuan, Shao-Li Liu, Zhen-Bo Liu, Xiao Wang, Wen-Zuo Li, Jian-Bo Cheng, Qing-Zhong Li
Aluminum nitride nanotubes (AlNNTs) doped by the excess electron, e@AlNNT and M@N-AlNNT (M = Li, Na, K), have been designed and their geometrical, electronic, and nonlinear optical (NLO) properties have been explored theoretically. The results showed that the excess electron narrows the energy gap between HOMO and LUMO values (EH-L ) of the doped systems in the range of 3.42-5.37 eV, which is due to a new energy level HOMO formed for the doped excess electron, with higher energy than the original HOMO of AlNNT...
July 14, 2018: Journal of Molecular Modeling
Debolina Paul, Jyotirmoy Deb, Barnali Bhattacharya, Utpal Sarkar
Utilizing first-principles calculations, we studied the electronic and optical properties of C24 , C12 X6 Y6 , and X12 Y12 fullerenes (X = B, Al; Y = N, P). These fullerenes are energetically stable, as demonstrated by their negative cohesive energies. The energy gap of C24 may be tuned by doping, and the B12 N12 fullerene was found to have the largest energy gap. All of the fullerenes had finite optical gaps, suggesting that they are optical semiconductors, and they strongly absorb UV radiation, so they could be used in UV light protection devices...
July 14, 2018: Journal of Molecular Modeling
Gabriel F S Fernandes, Francisco B C Machado, Luiz F A Ferrão
The present work focuses on establishing a function to rank the stability of small silicon clusters to characterize their magic numbers. This function is composed by a thermodynamic descriptor, the atomization Gibbs free energy, and indirect kinetic descriptors, the highest occupied molecular orbital energy and the lowest excitation energy of each system. The silicon clusters geometries were optimized using density functional theory within a hybrid meta-GGA approximation (M06), while the electronic energy was corrected by single-point calculation using CASPT2 level of theory to obtain the molecular properties...
July 13, 2018: Journal of Molecular Modeling
Juan David Ospina-Villa, Juan García-Contreras, Jorge Luis Rosas-Trigueros, Esther Ramírez-Moreno, César López-Camarillo, Beatriz Zamora-López, Laurence A Marchat, Absalom Zamorano-Carrillo
The CFIm25 subunit of the heterotetrameric cleavage factor Im (CFIm) is a critical factor in the formation of the poly(A) tail at mRNA 3' end, regulating the recruitment of polyadenylation factors, poly(A) site selection, and cleavage/polyadenylation reactions. We previously reported the homologous protein (EhCFIm25) in Entamoeba histolytica, the protozoan causing human amoebiasis, and showed the relevance of conserved Leu135 and Tyr236 residues for RNA binding. We also identified the GUUG sequence as the recognition site of EhCFIm25...
July 12, 2018: Journal of Molecular Modeling
Arnaldo F Silva, Paul L A Popelier
When electronic correlation energy is partitioned topologically, a detailed picture of its distribution emerges, both within atoms and between any two atoms. This methodology allows one to study dispersion beyond its more narrow definition in long-range Rayleigh-Schrödinger perturbation theory. The interacting quantum atoms (IQA) method was applied to MP2/6-31G(d,p) (uncontracted) wave functions of a wide variety of systems: glycine…water (hydration), the ethene dimer (π-π interactions), benzene (aromaticity), cyclobutadiene (antiaromaticity), and NH3 BH3 (dative bond)...
July 11, 2018: Journal of Molecular Modeling
Xiaonan Zheng, Yang Liu, Ya Wang
It has been extensively observed in experiments that nanoparticle additives can efficiently inhibit the electrical tree growth of the cross-linked polyethylene (XLPE) matrix of power cables. Inspired by this, the first-principles calculations employing the density functional theory (DFT) method were performed in this study to investigate the significant role of SiO2 nanosized fillers as a voltage stabilizer for power cable insulation. Several different types of α-SiO2 fillers, including hydroxylated, reconstructed, doped or oxygen vacancy surface structures, were constructed to model the interfacial interaction for SiO2 /XLPE nanocomposites...
July 9, 2018: Journal of Molecular Modeling
Chao Shen, Zhenyu Gong, Lei Gao, Minglong Gu, Long Huan, Sicong Wang, Ju Xie
In order to systematically explore the general rule of the host-guest chemistry for pillararenes, this work investigates the weak interactions between pillar[4]arene and some typical guests (anions, cations, and dumbbell-shaped molecules) by using density functional theory (DFT) calculations at the ωB97XD/6-311G(d,p) level. The strong molecular recognition ability of pillar[4]arene has been discussed based on the geometry structure, electronic structure, and thermodynamic properties of the host-guest complexes...
July 9, 2018: Journal of Molecular Modeling
Monia Chebbi, Youssef Arfaoui
The N-alkylation reaction of pyrazole derivatives with halomethanes was studied using density functional theory (DFT). The hybrid method B3LYP was employed, along with an ECP basis set such as LANL2DZ for halogen atoms (X = Cl, Br, I) and the 6-311 + G(d,p) basis set for all other atoms. In order to predict the specific site at which the pyrazole derivatives interact with halomethanes, local reactivity descriptors such as the Fukui functions were calculated. Detailed analysis of transition-state energies showed that alkylation occurred at the nitrogen atom N2 in the pyrazole derivatives, in agreement with the chemical reactivity results...
July 9, 2018: Journal of Molecular Modeling
Bárbara M T C Peluzo, Breno R L Galvão
The gas-phase mechanisms of UF4 and UF5 conversion into UF6 at different electronic states have been investigated using density functional theory (DFT) calculations, including relativistic effects and without the frozen core approximation. New geometries and electronic states of the isolated molecules were obtained, and their reactions were predicted to occur without a potential energy barrier. Our calculations show that UF4 +F2 collision will most likely produce UF5 +F in the gas phase. Relevant surface crossings between different electronic states are also obtained and their roles in collision dynamics are discussed...
July 7, 2018: Journal of Molecular Modeling
M X Silva, F T Silva, B R L Galvão, J P Braga, J C Belchior
The DFT potential energy hypersurfaces of closed-shell nitrogen clusters up to ten atoms are explored via a genetic algorithm (GA). An atom-atom distance threshold parameter, controlled by the user, and an "operator manager" were added to the standard evolutionary procedure. Both B3LYP and PBE exchange-correlation functionals with 6-31G basis set were explored using the GA. Further evaluation of the structures generated were performed through reoptimization and vibrational analysis within MP2 and CCSD(T) levels employing larger correlation consistent basis set...
July 7, 2018: Journal of Molecular Modeling
Beatriz Angulo, Clara I Herrerías, Zoel Hormigón, José Antonio Mayoral, Luis Salvatella
The mechanism of the copper(I)-catalyzed cyclopropanation reaction for methyl diazoacetate with both (Z)- and (E)-but-2-ene stereoisomers has been studied using the 6-311++G(d,p) basis set by means of M06-2X and O3LYP functionals. According to both methods, the rate-limiting step is the formation of a copper-carbene intermediate, formed by association between methyl diazoacetate and bis(acetonitrile)-copper(I) ion with the concomitant extrusion of dinitrogen. Cis/trans diastereoselectivity for the cyclopropanation reaction of a 1,2-disubstituted alkene ((Z)-but-2-ene) has been theoretically studied for the first time through the proper location of transition states on the potential-energy surface with the O3LYP method, since no transition structures could be found with the M06-2X functional due to the extreme flatness of the potential-energy surface...
July 5, 2018: Journal of Molecular Modeling
Zahra Rostami, Fatemeh Firoznasab
Recent exploration of the boron fullerenes has raised exciting new prospects for boron applications. Here, the endohedral X/X+ @B40 complexes (X = Li, Na, and K) were explored by means of density functional theory calculations. By increasing the atomic number, the interaction of alkali metals with the B40 nanocage is unusually weakened. It was concluded that by increasing the alkali metals' size, their electrons repel those of the cage, and the interaction weakens. The interaction of X with B40 is more favorable than that of X+ ...
July 5, 2018: Journal of Molecular Modeling
Caio Caetano Ribeiro, Jaldyr de Jesus Gomes Varela, Silvete Guerini
The structural and electronic properties of FeCl3 and CrO3 interacting with (10,0) GaNNT were obtained using first principles calculations based on the density functional theory. The results show that for the CrO3 interacting with the GaNNT, the structure was locally deformed. However, in case of FeCl3 adsorbed with the GaNNT, the structure remained practically the same with the negligible deformation observed on tube surface. The projected density of states for the pristine GaNNT was modified with adsorption of FeCl3 molecule by the appearance of three strongly localized states in gap region...
July 4, 2018: Journal of Molecular Modeling
Andrey M Kuznetsov, Alexey N Masliy, Gregory V Korshin
Thermodynamic and structural aspects of the hydration of Pb(II) ions were explored based on DFT calculations combined with the supermolecular/continuum solvent model. Hydration of Pb(II) was considered as the formation of Pb(H2 O)n 2+ aqua complexes (n=6-9) from the gas phase Pb(II) ion. Hexa- and hepta-aqua Pb(II) complexes were shown to exhibit the hemidirected symmetry, while those containing eight and nine water molecules are characterized by the holodirected symmetry. The calculations showed that because Pb(H2 O)n 2+ complexes with six to nine water molecules have comparable thermodynamic stabilities, such complexes are likely to coexist in aqueous solutions...
July 4, 2018: Journal of Molecular Modeling
Katelynn J Edgehouse, David W Ball
In a continuing effort to evaluate the properties of new possible high energy density materials, we have calculated the optimized geometries and thermodynamic properties of a series of nitro derivatives of triazetidine, c-CH2 (NH)3 . After evaluating approximately 50 different levels of NO2 substitution and conformations, we predict that several nitrotriazetidine compounds show some significantly desirable HEDM properties. Graphical abstract The triazetidine molecule, the parent structure for a series of new hypothetical high energy densitymaterials with various NO2 content...
July 3, 2018: Journal of Molecular Modeling
Katarzyna Kulczycka-Mierzejewska, Joanna Sadlej, Joanna Trylska
Clindamycin, a lincosamide antibiotic, binds to 23S ribosomal RNA and inhibits protein synthesis. The A2058G mutation in 23S RNA results in bacterial resistance to clindamycin. To understand the influence of this mutation on short-range interactions of clindamycin with 23S RNA, we carried out full-atom molecular dynamics simulations of a ribosome fragment containing clindamycin binding site. We compared the dynamical behavior of this fragment simulated with and without the A2058G mutation. Molecular dynamics simulations suggest that clindamycin in the native ribosomal binding site is more internally flexible than in the A2058G mutant...
July 3, 2018: Journal of Molecular Modeling
Ann-Christin Andres, Julian Beckmann, Lukas Klemmer, Stephan Muth, David Scheschkewitz, Michael Springborg
Propellane-like structures are an important building block for group-14 compounds. Therefore, in the present work, we study theoretically various such structures of the form E[Formula: see text] starting with the pure molecules for which E = E' = E″ = C, Si, Ge, or Sn. Subsequently, we study the systems with E ≠ E' = E″ and finally, we consider some selected cases molecules for which E, E' , and E″ all are different. Special emphasis is put on identifying structural trends for the molecules with at least two different group-14 elements...
July 3, 2018: Journal of Molecular Modeling
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