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Journal of Molecular Modeling

Johannes T Margraf, Pavlo O Dral
We elucidate the approaches used to incorporate electron correlation in existing semiempirical molecular orbital theory (SEMO) methods and compare them with the techniques used in other quantum chemical methods. After analyzing expressions for electron correlation in ab initio wavefunction theory, density functional theory, and density functional-based tight-binding (TB) methods, we suggest a framework for developing hybrid TB-SEMO methods. We provide a numerical proof-of-concept for such a method based on the OM2 method...
April 16, 2019: Journal of Molecular Modeling
Yiding Yu, Xiyan Wang, Yawen Gao, Yanan Yang, Lin Sun, Guizhen Wang, Xuming Deng, Xiaodi Niu
The treatment of bacterial infections is currently threatened by the emergence of pathogenic bacteria producing β-lactamase, which catalyzes the hydrolysis of β-lactams. Although the hydrolysis of the substrate nitrocefin by a metallo-β-lactamase, namely β-lactamase N1 from USA300 (a typical methicillin-resistant Staphylococcus aureus), has previously been reported in the literature, its mechanism remains elusive. Here, we show that molecular modeling and quantum-mechanical/molecular mechanics (QM/MM) calculations describing the complex of β-lactamase N1 with nitrocefin (the substrate of β-lactamase N1) can predict the catalytic mechanism of nitrocefin hydrolysis by β-lactamase N1...
April 13, 2019: Journal of Molecular Modeling
Luz Palomino-Asencio, Alfredo Ramírez-Torres, Joana Avelar, Jorge Garza, Erwin García-Hernández
Eleven adducts for the interaction between imidacloprid (IMI) and some activated carbon (AC) pieces are proposed in this work. Activated carbon pieces were obtained by using a finite zig-zag graphene structure saturated with hydrogen atoms on the edges giving a pristine model with 70 carbon atoms and 22 hydrogen atoms. The zig-zag graphene structure was oxidized with -O, -COOH, -OH, and -O- groups. In this process, two identical groups were inserted over selected sites of the pristine model. All of these structures yielded ten IMI-AC adducts by using the PBE0-D3/6-31G* method, which predicts stable adducts at 0 K, and six of our models give negative free energies changes at room temperature...
April 13, 2019: Journal of Molecular Modeling
Ingrid Vieira, Lilian T F M Camargo, Luciano Ribeiro, Allane C C Rodrigues, Ademir J Camargo
Alzheimer's disease is a widespread type of neurodegenerative dementia that mainly affects the elderly. Currently, this disease can only be treated palliatively. Existing drugs can only improve patients' symptoms. The search for new drugs that can effectively treat this disease is an important field of research in medicinal chemistry. Here we report a structure-activity relationship study of tacrine and some of its analogues in relation to their inhibitory activities against Alzheimer's disease. All of the molecular descriptors were calculated at the M062X/6-311++G(d,p) level of theory...
April 11, 2019: Journal of Molecular Modeling
Andreas Lynge Vishart, Nicolai Ree, Kurt V Mikkelsen
Creating input files to atomistic simulations and quantum chemical calculations in the CP2K software package can be a challenge. Here, we present a new graphical user interface to reduce the complexity of the work needed to run a CP2K calculation as well as the risk for making mistakes. The program is called CP2K Editor, and it provides a user-friendly interface for both new and experienced users. CP2K Editor keeps the construction of the input file simple and manageable. The input files are similarly structured, so they are easy to recognize and adjust if more advanced configurations are needed...
April 10, 2019: Journal of Molecular Modeling
Paweł Śliwa, Rafał Kurczab, Rafał Kafel, Anna Drabczyk, Jolanta Jaśkowska
The complexes of selected long-chain arylpiperazines with homology models of 5-HT1A , 5-HT2A , and 5-HT7 receptors were investigated using quantum mechanical methods. The molecular geometries of the ligand-receptor complexes were firstly optimized with the Our own N-layered Integrated molecular Orbital and molecular Mechanics (ONIOM) method. Next, the fragment molecular orbitals method with an energy decomposition analysis scheme (FMO-EDA) was employed to estimate the interaction energies in binding sites. The results clearly showed that orthosteric binding sites of studied serotonin receptors have both attractive and repulsive regions...
April 6, 2019: Journal of Molecular Modeling
Francesca Grisoni, Claudia S Neuhaus, Miyabi Hishinuma, Gisela Gabernet, Jan A Hiss, Masaaki Kotera, Gisbert Schneider
Membranolytic anticancer peptides (ACPs) are drawing increasing attention as potential future therapeutics against cancer, due to their ability to hinder the development of cellular resistance and their potential to overcome common hurdles of chemotherapy, e.g., side effects and cytotoxicity. In this work, we present an ensemble machine learning model to design potent ACPs. Four counter-propagation artificial neural-networks were trained to identify peptides that kill breast and/or lung cancer cells. For prospective application of the ensemble model, we selected 14 peptides from a total of 1000 de novo designs, for synthesis and testing in vitro on breast cancer (MCF7) and lung cancer (A549) cell lines...
April 5, 2019: Journal of Molecular Modeling
C Siouani, S Mahtout, F Rabilloud
The structural, electronic and magnetic properties of niobium- and tantalum-doped germanium clusters MGen (M = Nb, Ta and n = 1-19) were investigated by first principles calculations within the density functional theory (DFT) approach. Growth pattern behaviors, stabilities, and electronic properties are presented and discussed. Endohedral cage-like structures in which the metal atom is encapsulated are favored for n ≥ 10. The doping metal atom contributes largely to strengthening the stability of the germanium cage-like structures, with binding energy ordered as follows BE(Gen + 1 ) < BE (VGen ) < BE(NbGen ) < BE(TaGen )...
April 5, 2019: Journal of Molecular Modeling
Jun Li, Qiang Fu, Yang Liang, Biao Cheng, Xiaolong Li
Glycogen synthase kinase 3β (GSK3β), a serine/threonine protein kinase, is involved in several human diseases, including type II diabetes, mood disorders, prostate cancer, and Alzheimer's disease, representing a potential therapeutic target. GSK3β has a unique specificity, with its primed substrates binding to the primed phosphate binding site, which is critical for the catalytic activity of GSK3β. An L343R mutation located at the C-lobe of GSK3β, remote from the catalytic site, causes kinase inactivation...
April 4, 2019: Journal of Molecular Modeling
Karl M García-Ruiz, Andrés F Marmolejo-Valencia, Augusto González-Navejas, Laura Dominguez, Carlos Amador-Bedolla
Organic photovoltaics (OPV) have been theoretically studied within the usual parameters: open circuit voltage (Voc ), short circuit current (Jsc ), and fill factor (FF). The first two refer mostly to electronic properties, whereas the last contains all other possible contributions to cell efficiency, importantly including molecular geometrical and topological structures, both within a single molecule as amongst a system of molecules. In order to study the effects of molecular morphology of the heterostructures used in OPVs, molecular dynamic simulations (MDS) are imperative, and therefore parameterization of force fields to account for the description of planarity between aromatic rings, both intra- and inter-molecules, is of key importance...
April 3, 2019: Journal of Molecular Modeling
Rubí Zarmiento-García, Jonathan Guerrero-Sánchez, Noboru Takeuchi
Organic functionalization of nanomaterials offers exceptional flexibility in materials design, and applications in molecular sensors and molecular electronics are expected. However, more studies should be conducted to understand the interaction between nanomaterials and organic molecules. In this work, we studied the functionalization of silicene and silicane with benzaldehyde, performing nudged elastic band calculations within density functional theory. We calculated the structural changes of the adsorption process, electronic properties of the main states, and the energetics...
April 3, 2019: Journal of Molecular Modeling
Jiapu Zhang
On 2018-01-17 two electron crystallography structures (with PDB entries 6AXZ, 6BTK) on a prion protofibril of bank vole PrP(168-176) (a segment in the PrP β2-α2 loop) were released into the PDB Bank. The paper published by Gallagher-Jones et al. (Nat Struct Mol Biol 25(2):131-134, 2018) reports some polar clasps for these two crystal structures, and "an intersheet hydrogen bond between Tyr169 and the backbone carbonyl of Asn171 on an opposing strand."-this hydrogen bond is not directly between the neighboring chain B and chain A...
April 2, 2019: Journal of Molecular Modeling
Dmitry Khakimov, Victor Zelenov, Nikita Baraboshkin, Tatyana Pivina
The thermodynamic stability of the furoxan ring annullated with 1,2,3,4-tetrazine 1,3-dioxide cycle was studied. Crystal structure prediction based on global energy minimization in the framework of the atom-atom potential functions method was performed for isomeric furoxano-tetrazinedioxides (FuxTDOs): [1,2,5]oxadiazolo[3,4-e][1,2,3,4]tetrazine 1,5,7-trioxide (1) and [1,2,5]oxadiazolo[3,4-e][1,2,3,4]tetrazine 1,4,6-trioxide (2). The Coulomb energy was calculated with advanced point charge models fitted with high accuracy to the molecular electrostatic potentials of these molecules...
April 1, 2019: Journal of Molecular Modeling
Hanlu Wang, Mei Yu, Zhigeng Lin
The catalytic mechanism of Ti-MWW in oxidative desulfurization with H2 O2 was investigated by quantum chemical calculations. A defect model (Ti-d) and a perfect model (Ti-p) were proposed for Ti-MWW, and two possible reaction pathways starting from Ti-d and Ti-p were considered. On Ti-d, the hydroperoxy bidentate intermediate TiOOH (η2 ) was formed by activating H2 O2 at the Ti center. Afterwards, aromatic sulfides were oxidized to sulfoxides and to ultimate sulfones by TiOOH (η2 ). The order of oxidation reactivity was benzothiophene > dibenzothiophene > thiophene, conforming to experimental observations...
March 30, 2019: Journal of Molecular Modeling
S Haghighi, R Ansari, S Ajori
The average pull-out force and interaction energy of polyethylene (PE) cross-linked functionalized carbon nanotubes (cfCNTs) embedded in polymer matrices (PE-cfCNTs@polymers) was studied using molecular dynamics (MD) simulations. Accordingly, the pull-out process of PE-cfCNTs from inside polymer matrices, i.e., Aramid and PE, was performed under displacement control. The results obtained were compared with those of pure carbon nanotube (CNT) incorporated into polymer matrices (pure CNT@polymers). The influence on the pull-out force and interaction energy between the CNT and polymer of the structure of polymer matrices, the weight percentage and two types of distribution patterns of cross-linked PE chains, namely mapped and wrapped, was investigated...
March 29, 2019: Journal of Molecular Modeling
Camilla F Silva, Keyller B Borges, Clebio S Nascimento
In the present work we investigate, through DFT calculations, the mechanism of formation of a molecular imprinted polymer for the acetamiprid (ACT) insecticide, using four different functional monomers, four molar ratios attempts, and considering eight distinct solvents. As the main result we obtain the following theoretical protocol for the MIP synthesis: methacrylic acid (MMA) as functional monomer, 1:4 M ratio, i.e., one ACT to four MMAs, and chloroform as solvent. This DFT calculated condition shows more favorable energies for the formed complexes...
March 28, 2019: Journal of Molecular Modeling
Eduardo N Maciel, Iuri N Soares, Sebastião C da Silva, Gabriel L C de Souza
The strategy of investigating the antioxidant potential of flavonols through the explicit modeling of chemical reactions (initiated to be employed in a previous work from our group) was taken further in this work. Therefore, a theoretical investigation on the reaction between fisetin and 2,2-diphenyl-1-picrylhydrazyl (DPPH) is presented. All the computations were performed using the density functional theory with the B3LYP functional along with the 6-31G(d,p) basis set. Structural, energetic quantities (ΔG and ΔG++ ), and reaction rates were probed in order to provide information on the antioxidant activity and to explore the contributions of each hydroxyl group to the referred property...
March 28, 2019: Journal of Molecular Modeling
Paulo Eduardo de Brito, Bernhard Georg Enders, Luiz Antonio Ribeiro, Hugo Nicolas Nazareno
We investigated the dynamics of an electron subjected to a uniform electric field in the scope of a tight-binding electron-phonon interacting approach. We aimed at describing the transport in a one-dimensional lattice in which the on-site energies are distributed according to a Fibonacci sequence. Within this physical picture, we obtained a novel dynamical process with no counterpart in ordered lattices. Our findings showed that in low-disorder limit, the electron performs spatial Bloch oscillations, generating, in the turning points of its trajectory, composite quasi-particles-namely, polarons...
March 28, 2019: Journal of Molecular Modeling
Jane S Murray, Peter Politzer
We report a computational study of two series of molecules, one having the Si-O-N linkage and the other with the Si-(CH2 )n -N linkage, where n = 1-4. The silicons have various substituents-combinations of H, CH3 , F, Cl and CF3 . Many of these compounds have been prepared and characterized experimentally. The Si···N distances were found to be relatively short, which may denote a noncovalent interaction or may simply be dictated by the molecular structures. This and the nature of the interaction (if any) were the subjects of our study...
March 27, 2019: Journal of Molecular Modeling
Philipp Ectors, Dirk Zahn
We present an ab initio based molecular mechanics model for prominent additives used in lubricants to moderate oil-steel interfaces. The force field is created for zinc dialkyldithiophosphate and calcium sulfonate charge neutral ligand-ion-ligand complexes and benchmarked to the widely spread generalized amber force field (GAFF). For the latter, comparison to quantum chemical calculations shows significant errors in terms of complex structure and formation energy. This is corrected by the newly created force field that is commensurate with GAFF but uses tailor-made ion-ligand van der Waals parameters...
March 25, 2019: Journal of Molecular Modeling
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