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Wenlan Liu, Sofia Canola, Andreas Köhn, Bernd Engels, Fabrizia Negri, Reinhold F Fink
On the example of an aggregate of two perylenebisimide (PBI) molecules the character of the lowest excited electronic states in terms of charge transfer (CT) and Frenkel exciton (FE) configurations is investigated as a function of the intermolecular arrangement. A minimal model Hamiltonian based on two FE and two CT configurations at the frontier-orbitals CIS (FOCIS) level is shown to represent a simple and comprehensible approach providing insight into the physical significance of the model Hamiltonian matrix elements...
September 15, 2018: Journal of Computational Chemistry
Honghong Lyu, Jingchun Tang, Boxiong Shen, Tariq Siddique
A sequential chem-bio hybrid process was developed using a novel biochar supported carboxymethyl cellulose-stabilized nanoscale iron sulfide (CMC-FeS@biochar) as a chemical remover and Corynebacterium variabile HRJ4 as a biological agent for trichloroethylene (TCE) degradation. Compared with CMC-FeS, FeS@biochar600, bare FeS and biochar600, the CMC-FeS@biochar600 composite displayed better physiochemical properties (smaller hydrodynamic diameter and higher stability) and demonstrated excellent removal capacity for TCE from aqueous phase...
September 29, 2018: Water Research
Yang Jiao, Elsebeth Schröder, Per Hyldgaard
The vdW-DF-cx0 exchange-correlation hybrid design [K. Berland et al. , J. Chem. Phys. 146 , 234106 (2017)] has a truly nonlocal correlation component and aims to facilitate concurrent descriptions of both covalent and non-covalent molecular interactions. The vdW-DF-cx0 design mixes a fixed ratio, a , of the Fock exchange into the consistent-exchange van der Waals density functional, vdW-DF-cx [K. Berland and P. Hyldgaard, Phys. Rev. B 89 , 035412 (2014)]. The mixing value a is sometimes taken as a semi-empirical parameter in hybrid formulations...
May 21, 2018: Journal of Chemical Physics
Elad Harel
A fundamental goal of chemical physics is an understanding of microscopic interactions in liquids at and away from equilibrium. In principle, this microscopic information is accessible by high-order and high-dimensionality nonlinear optical measurements. Unfortunately, the time required to execute such experiments increases exponentially with the dimensionality, while the signal decreases exponentially with the order of the nonlinearity. Recently, we demonstrated a non-uniform acquisition method based on radial sampling of the time-domain signal [W...
May 21, 2018: Journal of Chemical Physics
Congyue Wang, Nariman Piroozan, Leili Javidpour, Muhammad Sahimi
Protein folding in confined media has attracted wide attention over the past 15 years due to its importance to both in vivo and in vitro applications. It is generally believed that protein stability increases by decreasing the size of the confining medium, if the medium's walls are repulsive, and that the maximum folding temperature in confinement is in a pore whose size D 0 is only slightly larger than the smallest dimension of a protein's folded state. Until recently, the stability of proteins in pores with a size very close to that of the folded state has not received the attention it deserves...
May 21, 2018: Journal of Chemical Physics
Fei Wu, Changhui Xu, Claudio J Margulis
In a set of recent publications [C. J. Margulis et al. , J. Am. Chem. Soc. 133 , 20186 (2011); C. H. Xu et al. , J. Am. Chem. Soc. 135 , 17528 (2013); C. H. Xu and C. J. Margulis, J. Phys. Chem. B 119 , 532 (2015); and K. B. Dhungana et al. , J. Phys. Chem. B 121 , 8809 (2017)], we explored for selected ionic liquids the early stages of excess charge localization and reactivity relevant both to electrochemical and radiation chemistry processes. In particular, Xu and Margulis [J. Phys. Chem. B 119 , 532 (2015)] explored the dynamics of an excess electron in 1-methyl-1-butyl-pyrrolidinium dicyanamide...
May 21, 2018: Journal of Chemical Physics
Emmy C Wijaya, Frances Separovic, Calum J Drummond, Tamar L Greaves
There has been a substantial increase in enzyme applications within the biochemical and pharmaceutical industries, for example, as industrial biocatalysts. However, enzymes have narrow marginal stability which makes them prone to become inactive and/or denature with a slight change in the solvent environment. Typically industrial applications require harsher solvent environments than enzyme native environments, and hence there is a need to understand solvent-protein interactions in order to develop strategies to maintain, or enhance, the enzymatic activity under industrially relevant solvent conditions...
May 21, 2018: Journal of Chemical Physics
Kento Suzuki, Takaaki Miyazaki, Toshiyuki Takayanagi, Motoyuki Shiga
The direct photoionization of pure helium clusters, Hen (n = 100, 200 and 300), and its subsequent short-time process have been studied by path integral molecular dynamics (PIMD) and ring-polymer molecular dynamics (RPMD) simulations that can effectively describe the nuclear quantum effects in large systems. The modified diatomics-in-molecule (DIM) model [Calvo et al., J. Chem. Phys., 2011, 135, 124308] has been used to describe the electronic structures of Hen+ clusters. The PIMD simulations were able to reproduce the experimental ionization spectra having a broad and asymmetric nature, which can be ascribed to the inhomogeneity of the energy levels of He atoms in the inner and outer regions of the cluster...
October 11, 2018: Physical Chemistry Chemical Physics: PCCP
Eshan Gurung, Dujuan Meng, Lianjie Xue, George Tamas, Ruth M Lynden-Bell, Edward L Quitevis
A comparative study of the intermolecular dynamics of CS2 in monocationic and dicationic ionic liquids (ILs) was performed using optical heterodyne-detected Raman-induced Kerr effect spectroscopy (OHD-RIKES). The reduced spectral densities (RSDs) of mixtures of CS2 in 1-alkyl-3-methylimidazolium bis[(trifluoromethane)sulfonyl]amide ([CnC1im][NTf2] for n = 3-5) and 1,2n-bis(3-methylimidazolium-1-yl) alkane bis[(trifluoromethane)sulfonyl]amide ([(C1im)2C2n][NTf2]2 for n = 3-5) were investigated as a function of concentration at 295 K...
October 11, 2018: Physical Chemistry Chemical Physics: PCCP
Thi H Ho, Yoshiyuki Kawazoe, Hung M Le
Correction for 'Penetrating probability and cross section of the Li+-C60 encapsulation process through an ab initio molecular dynamics investigation' by Thi H. Ho et al., Phys. Chem. Chem. Phys., 2018, 20, 7007-7013.
October 11, 2018: Physical Chemistry Chemical Physics: PCCP
Adam K Sieradzan, Artur Giełdoń, Yanping Yin, Yi He, Harold A Scheraga, Adam Liwo
Based on the coarse-grained UNRES and NARES-2P models of proteins and nucleic acids, respectively, developed in our laboratory, in this work we have developed a coarse-grained model of systems containing proteins and nucleic acids. The UNRES and NARES-2P effective energy functions have been applied to the protein and nucleic-acid components of a system, respectively, while protein-nucleic-acid interactions have been described by the respective coarse-grained potentials developed in our recent work (Yin et al...
October 11, 2018: Journal of Computational Chemistry
Chao Huang, Wenjian Liu
The recently proposed iterative vector interaction (iVI) method for large Hermitian eigenvalue problems (Huang et al., J. Comput. Chem. 2017, 38, 2481) is extended to generalized eigenvalue problems, HC = SCE, with the metric S being either positive definite or not. Although, it works with a fixed-dimensional search subspace, iVI can converge quickly and monotonically from above to the exact exterior/interior roots. The algorithms are further specialized to nonrelativistic and relativistic time-dependent density functional theories (TD-DFT) by taking the orbital Hessian as the metric (i...
October 11, 2018: Journal of Computational Chemistry
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October 15, 2018: Angewandte Chemie
Asim Najibi, Lars Goerigk
The development of van-der-Waals density functional approximations (vdW-DFAs) has gained considerable interest over the past decade. While in a strictest sense, energy calculations with vdW-DFAs should be carried out fully self-consistently, we demonstrate conclusively for a total of 11 methods that such a strategy only increases the computational time effort without having any significant effect on energetic properties, electron densities or orbital-energy differences. The strategy to apply a non-local vdW-DFA kernel as an additive correction to a fully converged conventional DFA result is therefore justified and more efficient...
October 9, 2018: Journal of Chemical Theory and Computation
Caspar J Schattenberg, Toni M Maier, Martin Kaupp
Hyperfine couplings (HFCs) of open-shell transition-metal centers are known to often depend crucially on core-shell spin polarization (CSSP). The latter is typically underestimated by semi-local density functionals, while admixture of exact exchange (EXX) in (global) hybrid functionals enhances CSSP. Unfortunately, a metal-ligand antibonding character of one or more of the singly occupied molecular orbitals of the complex will cause substantial valence-shell spin polarization (VSSP), which for global hybrids with higher EXX admixtures may lead to substantial spin contamination, thereby deteriorating the overall electronic structure and the dipolar couplings...
October 9, 2018: Journal of Chemical Theory and Computation
Antonio Francés-Monerris, Cécilia Hognon, Miguel A Miranda, Virginie Lhiaubet-Vallet, Antonio Monari
Nucleic acids are constantly exposed to external agents that can induce chemical and photochemical damage. In spite of the great advances achieved in the last years, some molecular mechanisms of DNA damage are not completely understood yet. A recent experimental report (I. Aparici-Espert et al., ACS Chem. Biol. 2018, 13, 542) proved the ability of 5-formyluracil (ForU), a common oxidatively generated product of thymine, to act as an intrinsic sensitizer of nucleic acids, causing single strand breaks and cyclobutane pyrimidine dimers in plasmid DNA...
October 9, 2018: Physical Chemistry Chemical Physics: PCCP
Wei-Yu Li, Chuan-Shuo Wu, Zhou Wang, Luo Yang
Correction for 'Fe-Catalyzed three-component carboazidation of alkenes with alkanes and trimethylsilyl azide' by Wei-Yu Li et al., Chem. Commun., 2018, DOI: 10.1039/c8cc05090b.
October 9, 2018: Chemical Communications: Chem Comm
Roheeth Kumar Pavana, Khushbu Shah, Taylor Gentile, Nicholas F Dybdal-Hargreaves, April L Risinger, Susan L Mooberry, Ernest Hamel, Aleem Gangjee
The discovery, synthesis and biological evaluations of a series of nine N5-substituted-pyrrolo[3,2-d]pyrimidin-4-amines are reported. Novel compounds with microtubule depolymerizing activity were identified. Some of these compounds also circumvent clinically relevant drug resistance mechanisms (expression of P-glycoprotein and βIII tubulin). Compounds 4, 5, and 8-13 were one to two-digit nanomolar (IC50 ) inhibitors of cancer cells in culture. Contrary to recent reports (Banerjee et al. J. Med. Chem.2018, 61, 1704-1718), the conformation of the most active compounds determined by 1 H NMR and molecular modeling are similar to that reported previously and in keeping with recently reported X-ray crystal structures...
September 21, 2018: Bioorganic & Medicinal Chemistry
Katharina M Rund, Annika I Ostermann, Laura Kutzner, Jean-Marie Galano, Camille Oger, Claire Vigor, Sabine Wecklein, Nina Seiwert, Thierry Durand, Nils Helge Schebb
Misregulation of oxidative and antioxidative processes in the organism - oxidative stress - contributes to the pathogenesis of different diseases, e.g. inflammatory or neurodegenerative diseases. Oxidative stress leads to autoxidation of polyunsaturated fatty acids giving rise to prostaglandin-like isoprostanes (IsoP) and isofurans (IsoF). On the one hand they could serve as biomarker of oxidative stress and on the other hand may act as lipid mediators, similarly as the enzymatically formed oxylipins. In the present paper we describe the development of an LC-ESI(-)-MS/MS method allowing the parallel quantification of 27 IsoP and 8 IsoF derived from 6 different PUFA (ALA, ARA, EPA, AdA, n6-DPA, DHA) within 12 min...
December 11, 2018: Analytica Chimica Acta
Amit K Paul, Niclas A West, Joshua D Winner, Rodney D W Bowersox, Simon W North, William L Hase
A chemical dynamics simulation was performed to model experiments [N. A. West et al. , J. Chem. Phys. 145 , 014308 (2016)] in which benzene molecules are vibrationally excited to 148.1 kcal/mol within a N2 -benzene bath. A significant fraction of the benzene molecules are excited, resulting in heating of the bath, which is accurately represented by the simulation. The interesting finding from the simulations is the non-statistical collisional energy transfer from the vibrationally excited benzene C6 H6 * molecules to the bath...
October 7, 2018: Journal of Chemical Physics
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