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Journal of Molecular Modeling

A A Safonov, A A Bagaturyants, V A Sazhnikov
The applicabilities of various CIS- and TDDFT-based procedures to the calculation of the fluorescence spectra of DBMBF2 exciplexes with aromatic hydrocarbons are analyzed. It is shown that a reasonable agreement between the calculated and experimental fluorescence spectra is obtained when a combined procedure is used. In this combined procedure, the geometries of the exciplexes are optimized beforehand using the CIS method with an empirical dispersion correction, while the exciplex transition energies are calculated at the optimized geometries using the CIS(D) method or the TDDFT approach with double-hybrid B2PLYP and mPW2PLYP functionals...
May 2017: Journal of Molecular Modeling
Benjamin Schweitzer, Chantal Daniel, Christophe Gourlaouen
A topological analysis based on density functional electronic and spin densities of the bonding characteristics in a series of Fe, Ru, Os, Tc and Rh dimers and trimers bridged, respectively, by μ-1,8-naphthyridine (nap) and μ-2,2'-dipyridylamine (dpa) is presented. By this simple qualitative analysis, we were able to determine the electronic ground state and correlated bonding order for a number of complexes potentially involved in extended metal atom chains (EMAC). Furthermore, we showed in the Ru dimer that it was possible to control the spin state simply by changing the bonded counter-anion...
May 2017: Journal of Molecular Modeling
Milan Senćanski, Ivana Djordjević, Sonja Grubišić
Selenium has been increasingly recognized as an important element in biological systems, which participates in numerous biochemical processes in organisms, notably in enzyme reactions. Selenium can substitute sulfur of cysteine and methionine to form their selenium analogues, selenocysteine (Sec) and selenomethionine (SeM). The nature of amino acid pockets in proteins is dependent on their composition and thus different non-covalent forces determine the interactions between selenium of Sec or SeM and other functional groups, resulting in specific biophysical behavior...
May 2017: Journal of Molecular Modeling
Aldo Cervantes-Flores, Heriberto Cruz-Martínez, Omar Solorza-Feria, Patrizia Calaminici
A first-principle investigation of structures and properties of Ni n Pd n (n=1-5) clusters is presented. For this study, the linear combination of Gaussian-type orbitals auxiliary density functional theory (LCGTO-ADFT) method has been employed. In order to determine the lowest energy structures, several isomers in different spin multiplicities were studied, for each cluster size. Initial structures, for which successive geometry optimization was computed without any constrain, were taken along Born-Oppenheimer molecular dynamics (BOMD) trajectories...
May 2017: Journal of Molecular Modeling
E Broclawik, K Góra-Marek, M Radoń, T Bučko, A Stępniewski
This work is focused on the donor properties of cobalt-exchanged cationic sites in zeolites. It is based on cluster and periodic density functional theory modeling for relevant {[Co(II)(NH3)n]-NO} adducts, where Co(II) means a cobalt cation embedded either in a periodic model of chabasite (CHA) zeolite or in model clusters. NO stretching frequencies were derived from MD trajectories and compared to harmonic values from cluster calculations. By relating calculated NO frequencies to experimental FTIR spectra, it was shown that the forms of {Co(II)-NO} adducts comprising three or four ammonia co-ligands dominate the spectrum taken in ammonia-saturation conditions while forms with two NH3 ligands prevail under intermediate ammonia saturation...
May 2017: Journal of Molecular Modeling
Á Nagy, E Romera
The nonidempotency measure of Löwdin is found to be proportional to the disequilibrium. It is shown that there exists a simple relationship between the LMC (López-Ruiz-Mancini-Calbet) and the generalized statistical complexities and the generalized nonidempotency measure of Löwdin. Results are illustrated for an exactly solvable two-electron model atom.
May 2017: Journal of Molecular Modeling
Abbas Yousefpour, Hamid Modarress, Fatemeh Goharpey, Sepideh Amjad-Iranagh
The anti-hypertensive drugs amlodipine, atenolol and lisinopril, in ordinary and PEGylated forms, with different combined-ratios, were studied by molecular dynamics simulations using GROMACS software. Twenty simulation systems were designed to evaluate the interactions of drug mixtures with a dimyristoylphosphatidylcholine (DMPC) lipid bilayer membrane, in the presence of water molecules. In the course of simulations, various properties of the systems were investigated, including drug location, diffusion and mass distribution in the membrane; drug orientation; the lipid chain disorder as a result of drug penetration into the DMPC membrane; the number of hydrogen bonds; and drug surface area...
May 2017: Journal of Molecular Modeling
Hamidreza Jouypazadeh, Hossein Farrokhpour, Mohammad Solimannejad
This work evaluated the reliability of the one-dimensional potential energy surface for calculating the spectroscopic properties (rovibrational constants and rotational line energies) of hydrogen bonds in linear bonded complexes by comparing theoretical results with the corresponding experimental results. For this purpose, two hydrogen bonded complexes were selected: the HCN···HCN homodimer and the HCN···HF heterodimer. The one-dimensional potential energy surfaces related to the hydrogen bonds in these complexes were calculated using different computational methods and basis sets...
May 2017: Journal of Molecular Modeling
Xingtao Ma, Li Zhang, Hong Wu, Xingdong Zhang, Mingli Yang
Biphasic calcium phosphate (BCP) bioceramics, the mixture of hydroxyapatite (HA) and beta- tricalcium phosphate (β-TCP), are widely used as bone repair materials. Optimization of its composition and mixing pattern is crucial for its design and preparation. A series of BCP structures with a HA/β-TCP mass ratio of 0/100, 30/70, 50/50, 70/30, and 100/0 were constructed and studied with a simulated annealing molecular dynamics method. On the basis of equilibrated BCP structures, their elastic constants and moduli were computed and analyzed...
May 2017: Journal of Molecular Modeling
Yuli Liu, Anand H G Patel, Steven K Burger, Paul W Ayers
Three different pKa prediction methods were used to calculate the pKa of Lys115 in acetoacetate decarboxylase (AADase): the empirical method PROPKA, the multiconformation continuum electrostatics (MCCE) method, and the molecular dynamics/thermodynamic integration (MD/TI) method with implicit solvent. As expected, accurate pKa prediction of Lys115 depends on the protonation patterns of other ionizable groups, especially the nearby Glu76. However, since the prediction methods do not explicitly sample the protonation patterns of nearby residues, this must be done manually...
May 2017: Journal of Molecular Modeling
James J P Stewart
The catalytic cycle for the serine protease α-chymotrypsin was investigated in an attempt to determine the suitability of using the semiempirical method PM7 in the program MOPAC for investigating enzyme-catalyzed reactions. All six classical intermediates were modeled using standard methods, and were characterized as stable minima on the potential energy surface. Using a modified saddle point optimization method, five transition states were located and verified both by vibrational and by intrinsic reaction coordinate analysis...
May 2017: Journal of Molecular Modeling
Luciano Almeida Leal, Rafael Timóteo de Souza Júnior, Antonio Luciano de Almeida Fonseca, Luiz Antonio Ribeiro Junior, Stefan Blawid, Demetrio Antonio da Silva Filho, Wiliam Ferreira da Cunha
Pentacene is an organic semiconductor that draws special attention from the scientific community due to the high mobility of its charge carriers. As electron-hole interactions are important aspects in the regard of such property, a computationally inexpensive method to predict the coupling between these quasi-particles is highly desired. In this work, we propose a hybrid methodology of combining Uncoupled Monte Carlo Simulations (UMC) and Density functional Theory (DFT) methodologies to obtain a good compromise between computational feasibility and accuracy...
May 2017: Journal of Molecular Modeling
Siba Shanak, Ozlem Ulucan, Volkhard Helms
DNA methylation plays a major role in organismal development and the regulation of gene expression. Methylation of cytosine bases and the cellular roles of methylated cytosine in eukaryotes are well established, as well as methylation of adenine bases in bacterial genomes. Still lacking, however, is a general mechanistic understanding, in structural and thermodynamic terms, of how proteins recognize methylated DNA. Toward this aim, we present the results of molecular dynamics simulations, alchemical free energy perturbation, and MM-PBSA calculations to explain the specificity of the R...
May 2017: Journal of Molecular Modeling
Chun-Yi Chang, Shin-Pon Ju, Li-Fang Wang, Chien-Chia Chen, Ying-Chen Chuang, Hong-Lin Wu, Hsin-Tsung Chen
Coarse-grained molecular dynamics (CGMD) simulation was employed to investigate how stable chondroitin sulfate-graft-polycaprolactone (CS-PCL, CP) copolymers self-assemble into micelles in an aqueous environment. Three types of CP containing low (2.4%), medium (6.3%), and high (18.7%) PCL contents (denoted L-CP, M-CP, and H-CP, respectively) in which PCL molecules consisting of 63 monomers were grafted onto each CS molecule consisting of 120 monomers were considered. L-CP and M-CP were found to display spheroidal micellar structures, while H-CP presented a rod-like structure, in agreement with previous experimental observations...
May 2017: Journal of Molecular Modeling
Berkay Sütay, Mine Yurtsever
Weak interactions of graphene surface with reactive molecular impurities are the subject of many studies since noncovalent functionalization of surface via molecular doping is a powerful tool for tuning the electronic properties of graphene layers. In this work, the adsorption of diatomic halogen gas molecules, F2, Cl2, Br2, I2 onto bilayer and multilayer pristine graphene surfaces were studied comparatively by Monte Carlo (MC) and molecular dynamics (MD) simulation techniques in canonical ensemble. The adsorption sites, adsorption capacity, coverage factors, adsorption isotherms, and adsorption kinetics were investigated and the adsorption energies were calculated for all adsorbates...
May 2017: Journal of Molecular Modeling
Dongsheng Zhang, Jingjing Liu, Teng Wang, Liping Sun
β-Cyclodextrin (β-CD), which resides in the α-hemolysin (αHL) protein pore, can act as a molecular adapter in single-molecule exonuclease DNA sequencing approaches, where the different nucleotide binding behavior of β-CD is crucial for base discrimination. In the present contribution, the inclusion modes of β-CD towards four 2'-deoxyribonucleoside 5'-monophosphates (dNMPs) were investigated using quantum mechanics (QM) calculations. The calculated binding energy suggests that the binding affinity of dAMP to β-CD are highest among all the dNMPs in solution, in agreement with experimental results...
April 2017: Journal of Molecular Modeling
Mustafa U Kucukkal, Steven J Stuart
Single-walled carbon nanotubes show promise as nanoscale transistors for nanocomputing applications. This use will require appropriate methods for creating electrical connections between distinct nanotubes, analogous to welding of metallic wires at larger length scales, but methods for performing nanoscale chemical welding are not yet sufficiently understood. This study examines the effect of Ar bombardment on the junction of two crossed single-walled carbon nanotubes, to understand the value and limitations of this method for generating connections between nanotubes...
April 2017: Journal of Molecular Modeling
Robenilson F Santos, Ana Carla P Bitencourt, Mirco Ragni, Frederico V Prudente, Cecilia Coletti, Annalisa Marzuoli, Vincenzo Aquilanti
The Wigner 9j symbols of the first kind-also known as Fano X-coefficients-serve to connect different addition schemes of four angular momenta, widely known examples being the LS and the jj couplings in atomic, molecular, and nuclear spectroscopies. Here, we also consider alternative sequences of binary couplings of four angular momenta, which are dealt through the 9j symbols of the second kind, and are explicitly given by the pentagonal (or Biedenharn-Elliott) identity. These coefficients are essential ingredients in the quantum-mechanical treatments of rotational and polarization phenomena in reaction dynamics and photoinduced processes...
April 2017: Journal of Molecular Modeling
Washington Barbosa da Silva, Alessandra F Albernaz, Patricia R P Barreto, Eberth Correa
The addition of C2 to HCN is of relevant interest in astrochemistry. We studied the pathways of this addition to produce CCCN and estimated its reaction rate using the Master Equation in the circumstellar environment. From the results of this study, it was possible to show that a different pathway in the Surface Potential Energy-PES can also be investigated. In a circumstellar envelop environment, with temperatures varying between 1000 K and 2000 K, the abundances of these species are favorable to this kind of addition, and our branching ratio for the rate constant showed that the new pathway is more favorable in comparison with other possibilities for this range of temperatures in this environment, and must be taken into account in any computation of the rate constant...
April 2017: Journal of Molecular Modeling
Eduardo C Aguiar, Ricardo L Longo, João Bosco P da Silva
Density functional theory (B3LYP, B3LYP-D2 and wB97XD functionals) was used in finite models of zigzag carbon nanotubes (CNT), (n,0)×k with n = 6-9 and k = 2-4, to systematically investigate the effects of size on their structural and electronic properties. We found that the ratio between the length (L t) and the diameter (d t) of the pristine CNT has to be larger than 2, i.e., L t/d t > 2, in order to provide the observed experimental trends of C=C bond distances, as well as to maintain the atomic charges nearly constant and zero around the center of the tube...
April 2017: Journal of Molecular Modeling
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