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Daniel Bonhenry, François Dehez, Mounir Tarek
The low bioavailability of most therapeutic compounds is often counterbalanced by association with molecular vectors capable of crossing cell membranes. Previous studies demonstrated that for vectors bearing titratable chemical groups, the translocation process might be accompanied by a change in the protonation state. For simple compounds e.g. a lysine analog, free energy calculations, using a single collective variable, namely the insertion depth, suggest that such a transition could only take place if the amino acid diffuses deep enough into the hydrophobic core of the membrane, a situation thermodynamically unfavorable...
March 22, 2018: Physical Chemistry Chemical Physics: PCCP
Konda Reddy Karnati, Yixuan Wang
Two widely used anticancer drugs, doxorubicin (DOX) and paclitaxel (PTX), possess distinct physical properties and chemotherapy specificity. In order to investigate their interaction mechanism with single-walled carbon nanotubes (SWCNTs), co-loading and releasing from the SWCNTs, all-atom molecular dynamics (MD) simulations were firstly carried out for different SWCNT systems, followed by binding free energy calculation with MM-PBSA. The results indicate that the co-loading of DOX and PTX onto the pristine SWCNT is exothermic and spontaneous...
March 22, 2018: Physical Chemistry Chemical Physics: PCCP
Chia-Hua Wu, Yu Zhang, Krista van Rickley, Judy I Wu
Textbook explanations for the associations of multipoint hydrogen-bonded arrays have long hinged on the secondary electrostatic interaction (SEI) model, which suggests that array association strengths depend on the proton donor (D) and acceptor (A) patterns of the interacting units. Here, computational results based on the block-localized wavefunction (BLW) method reveal limitations of the SEI model, demonstrating instead that, in the gas-phase (and in implicit chloroform solvation), the inherent free-energies of associations of multipoint hydrogen-bonded arrays correlate with the degree of "aromaticity gain" (i...
March 22, 2018: Chemical Communications: Chem Comm
Waheed Khan, Qun Wang, Xin Jin
We report the first results of functional properties of nitrogenized silver-permalloy thin films deposited on polyethylene terephthalic ester {PETE (C10 H₈O₄)n } flexible substrates by magnetron sputtering. These new soft magnetic thin films have magnetization that is comparable to pure Ni81 Fe19 permalloy films. Two target compositions (Ni76 Fe19 Ag₅ and Ni72 Fe18 Ag10 ) were used to study the effect of compositional variation and sputtering parameters, including nitrogen flow rate on the phase evolution and surface properties...
March 17, 2018: Materials
Yuki Mitsuta, Takashi Kawakami, Mitsutaka Okumura, Shusuke Yamanaka
We present a new approach for automated exploration of free energy landscapes on the basis of the umbrella integration (UI) method. The method to search points in the landscape relies on the normal distributions and gradients of the potential of mean force (PMF) obtained from UI calculations. We applied this approach to the alanine dipeptide in solution and demonstrated that the equilibrium and the transition states were efficiently found in the ascending order of the PMF values.
March 21, 2018: International Journal of Molecular Sciences
Songling Ma, Sungbo Hwang, Sehan Lee, William Acree, Kyoung Tai No
To describe the physically realistic solvation free energy surface of a molecule in a solvent, a generalized version of the solvation free energy density (G-SFED) calculation method has been developed. In the G-SFED model, the contribution from the hydrogen bond (HB) between a solute and a solvent to the solvation free energy was calculated as the product of the acidity of the donor and the basicity of the acceptor of an HB pair. The acidity and basicity parameters of a solute were derived using the summation of acidities and basicities of the respective acidic and basic functional groups of the solute, and that of the solvent was experimentally determined...
March 21, 2018: Journal of Chemical Information and Modeling
Ming Zheng, Fang-Yuan Chen, Jia-Nan Tian, Qing-Jiang Pan
To provide deep insight into cation-cation interactions (CCIs) involving hexavalent actinyl species that are major components in spent nuclear fuel and pose important implications for the effective removal of radiotoxic pollutants in the environment, a series of homo- and heterobimetallic actinide complexes supported by cyclopentadienyl (Cp) and polypyrrolic macrocycle (H4 L) ligands were systematically investigated using relativistic density functional theory. The metal sort in both parts of (THF)(H2 L)(OAnVI O) and (An')III Cp3 from U to Np to Pu, as well as the substituent bonding to Cp from electron-donating Me to H to electron-withdrawing Cl, SiH3 , and SiMe3 , was changed...
March 21, 2018: Inorganic Chemistry
Qiuyan Yu, Jinglei Hu, Yi Hu, Rong Wang
Assembly of nanoparticles (NPs) coated with complementary DNA strands leads to novel crystals with nanosized basic units rather than classic atoms, ions or molecules. The assembly process is mediated by hybridization of DNA via specific base pairing interaction, and is kinetically linked to the disassociation of DNA duplexes. DNA-level physiochemical quantities, both thermodynamic and kinetic, are key to understanding this process and essential for the design of DNA-NP crystals. The melting transition properties are helpful to judge the thermostability and sensitivity of relative DNA probes or other applications...
March 21, 2018: Soft Matter
Laura Pérez-Benito, Henrik Keränen, Herman van Vlijmen, Gary Tresadern
A congeneric series of 21 phosphodiesterase 2 (PDE2) inhibitors are reported. Crystal structures show how the molecules can occupy a 'top-pocket' of the active site. Molecules with small substituents do not enter the pocket, a critical leucine (Leu770) is closed and water molecules are present. Large substituents enter the pocket, opening the Leu770 conformation and displacing the waters. We also report an X-ray structure revealing a new conformation of the PDE2 active site domain. The relative binding affinities of these compounds were studied with free energy perturbation (FEP) methods and it represents an attractive real-world test case...
March 20, 2018: Scientific Reports
Yoshio Okiyama, Tatsuya Nakano, Chiduru Watanabe, Kaori Fukuzawa, Shigenori Tanaka
In this study, an ab initio fragment molecular orbital (FMO) methodology was developed to evaluate the solvent effects on electrostatic interactions, which make a significant contribution to the physical and chemical processes occurring in biological systems. Here, a fully polarizable solute consisting of the FMO electron density was electrostatically coupled with an implicit solvent based on the Poisson-Boltzmann (PB) equation; in addition, the nonpolar contributions empirically obtained from the molecular surface area (SA) were added...
March 20, 2018: Journal of Physical Chemistry. B
André Luiz Sehnem, Doreen Niether, Simone Wiegand, Antonio Martins Figueiredo Neto
The ionic Soret effect induced by temperature gradients is investigated in organic electrolytes (tetramethylammonium and tetrabutylammonium hydroxides) dispersed in water using a holographic grating experiment. We report the influences of temperature and salt concentrations on the Soret, diffusion and thermal diffusion coefficients. Experimental results to the thermal diffusion coefficient are compared with a theoretical description for thermodiffusion of Brownian particles in liquids based in the thermal expansion of the liquid solution...
March 20, 2018: Journal of Physical Chemistry. B
Gurkamaljit Kaur, Bharati Pandey, Arbind Kumar, Naina Garewal, Abhinav Grover, Jagdeep Kaur
The lipolytic protein LipU was conserved in mycobacterium sp. including M. tuberculosis (MTB LipU) and M. leprae (MLP LipU). The MTB LipU was identified in extracellular fraction and was reported to be essential for the survival of mycobacterium. Therefore to address the problem of drug resistance in pathogen, LipU was selected as a drug target and the viability of finding out some FDA approved drugs as LipU inhibitors in both the cases was explored. Three dimensional (3D) model structures of MTB LipU and MLP LipU were generated and stabilized through molecular dynamics (MD)...
March 20, 2018: Journal of Biomolecular Structure & Dynamics
P Petkov, R Marinova, V Kochev, N Ilieva, E Lilkova, L Litov
Antimicrobial peptides (AMPs) play crucial role as mediators of the primary host defence against microbial invasion. They are considered a promising alternative to antibiotics for multidrug resistant bacterial strains. For complete understanding of the antimicrobial defence mechanism, a detailed knowledge of the dynamics of peptide-membrane interactions, including atomistic studies on AMPs geometry and both peptide and membrane structural changes during the whole process is a prerequisite. We aim at clarifying the conformation dynamics of small linear AMPs in solution as a first step of in silico protocol for establishing a correspondence between certain amino-acid sequence motifs, secondary-structure elements, conformational dynamics in solution and the intensity and mode of interaction with the bacterial membrane...
March 20, 2018: Journal of Biomolecular Structure & Dynamics
So-Yoen Kim, Yang-Jin Cho, Ho-Jin Son, Dae Won Cho, Sang Ook Kang
We report the results of photoinduced electron transfer (PET) in a novel dyad, in which a boron dipyrromethene (BODIPY) dye is covalently linked to o-carborane (o-Cb). In this dyad, BODIPY and o-Cb act as electron donor and acceptor, respectively. PET dynamics were investigated using a femtosecond time-resolved transient absorption spectroscopic method. The free energy dependence of PET in the S1 and S2 states was examined on the basis of Marcus theory. PET in the S1 state occurs in the Marcus normal region...
March 19, 2018: Journal of Physical Chemistry. A
Shalini Awasthi, Shalini Gupta, Ravi Tripathi, Nisanth N Nair
Enhanced sampling of large number of collective variables (CVs) is inevitable in molecular dynamics (MD) simulations of complex chemical processes such as enzymatic reactions. Due to the computational overhead of hybrid quantum mechanical/molecular mechanical (QM/MM) based (MD) simulations, especially together with density functional theory (DFT), predictions of reaction mechanism and estimation of free energy barriers have to be carried out within few tens of picoseconds. We show here that the recently developed Temperature Accelerated Sliced Sampling (TASS) method allows one to sample large number of CVs, thereby enabling us to obtain rapid convergence in free energy estimates in QM/MM MD simulation of enzymatic reactions...
March 19, 2018: Journal of Physical Chemistry. B
Sandro Bottaro, Pavel Banáš, Jiří Šponer, Giovanni Bussi
No abstract text is available yet for this article.
March 19, 2018: Journal of Physical Chemistry Letters
Robert B Wexler, John Mark P Martirez, Andrew M Rappe
The activity of Ni2 P catalysts for the hydrogen evolution reaction (HER) is currently limited by strong H adsorption at the Ni3 -hollow site. We investigate the effect of surface nonmetal doping on the HER activity of the Ni3 P2 termination of Ni2 P(0001), which is stable at modest electrochemical conditions. Using density functional theory (DFT) calculations, we find that both 2 p nonmetals and heavier chalcogens provide nearly thermoneutral H adsorption at moderate surface doping concentrations. We also find, however, that only chalcogen substitution for surface P is exergonic...
March 19, 2018: Journal of the American Chemical Society
Alexander Kyrychenko, Nathan M Lim, Victor Vasquez-Montes, Mykola V Rodnin, J Alfredo Freites, Linh P Nguyen, Douglas J Tobias, David L Mobley, Alexey S Ladokhin
Dynamic disorder of the lipid bilayer presents a challenge for establishing structure-function relationships in membranous systems. The resulting structural heterogeneity is especially evident for peripheral and spontaneously inserting membrane proteins, which are not constrained by the well-defined transmembrane topology and exert their action in the context of intimate interaction with lipids. Here, we propose a concerted approach combining depth-dependent fluorescence quenching with Molecular Dynamics simulation to decipher dynamic interactions of membrane proteins with the lipid bilayers...
March 17, 2018: Journal of Membrane Biology
Anand Mohan Verma, Harshal D Kawale, Kushagra Agrawal, Nanda Kishore
In the pyrolysis of Sphagnum moss species, p-isopropenylphenol (p-IPP) is a major product which has been considered in this density functional theory based computational study for its conversion to various products such as benzene, phenol, 4-propenylphenol, indan-5-ol, 4-propylcyclohexanone, 4-cyclopropylphenol, etc. In order to achieve these products, eight different reaction schemes are performed using B3LYP/6-311 + g (d,p) level of theory. Further, thermodynamic properties such as reaction free energies and reaction enthalpies associated with these eight reaction schemes are developed in the temperature range of 298-898 K...
March 9, 2018: Journal of Molecular Graphics & Modelling
Xinwei Ge, Yunxiang Sun, Feng Ding
Accumulating evidence suggests that soluble oligomers are more toxic than final fibrils of amyloid aggregations. Among the mixture of inter-converting intermediates with continuous distribution of sizes and secondary structures, oligomers in the β-barrel conformation - a common class of protein folds with a closed β-sheet - have been postulated as the toxic species with well-defined three-dimensional structures to perform pathological functions. A common mechanism for amyloid toxicity, therefore, implies that all amyloid peptides should be able to form β-barrel oligomers as the aggregation intermediates...
March 14, 2018: Biochimica et Biophysica Acta
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