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Chemical Physics Letters

Christopher Arntsen, Chen Chen, Gregory A Voth
We present two new multiscale molecular dynamics (MS-RMD) models for the hydrated excess proton in water developed directly from ab initio molecular dynamics (AIMD) simulation data of the same system. The potential of mean force along the proton transfer reaction coordinate and radial distribution functions for the MS-RMD models are shown faithfully reproduce those of AIMD. The models are developed using an algorithm based on relative entropy minimization, thus demonstrating the ability of the method to rapidly generate accurate and highly efficient reactive MD force fields...
September 1, 2017: Chemical Physics Letters
Matthew C Patterson, Mark F DiTusa, Cheri A McFerrin, R L Kurtz, Randall W Hall, E D Poliakoff, P T Sprunger
Environmentally persistent free radicals (EPFRs) have significant environmental and public health impacts. In this study, we demonstrate that EPFRs formed on ZnO nanoparticles provide two significant surprises. First, EPR spectroscopy shows that phenoxy radicals form readily on ZnO nanoparticles at room temperature, yielding EPR signals similar to those previously measured after 250°C exposures. Vibrational spectroscopy supports the conclusion that phenoxy-derived species chemisorb to ZnO nanoparticles under both exposure temperatures...
February 16, 2017: Chemical Physics Letters
Laleh Majari Kasmaee, Asghar Aryanfar, Zarui Chikneyan, Michael R Hoffmann, Agustín J Colussi
Understanding the mechanism of formation of solid-electrolyte interphases (SEI) is key to the prospects of lithium metal batteries (LMB). Here, we investigate via cyclic voltammetry, impedance spectroscopy and chronoamperometry the role of kinetics in controlling the properties of the SEI generated from the reduction of propylene carbonate (PC, a typical solvent in LMB). Our observations are consistent with the operation of a radical chain PC electropolymerization into polymer units whose complexity increases at lower initiation rates...
September 16, 2016: Chemical Physics Letters
Elizabeth A Jolley, Michael Lewis, Brent M Znosko
A computational model for predicting RNA nearest neighbor free energy rankings has been expanded to include the nonstandard nucleotide inosine. The model uses average fiber diffraction data and molecular dynamic simulations to generate input geometries for Quantum mechanic calculations. This resulted in calculated intrastrand stacking, interstrand stacking, and hydrogen bonding energies that were combined to give total binding energies. Total binding energies for RNA dimer duplexes containing inosine were ranked and compared to experimentally determined free energy ranks for RNA duplexes containing inosine...
October 16, 2015: Chemical Physics Letters
Chad A Thibodeaux, E D Poliakoff, Orhan Kizilkaya, Matthew C Patterson, Mark F DiTusa, Richard L Kurtz, P T Sprunger
Environmentally persistent free radicals (EPFRs) are toxic organic/metal oxide composite particles that have been discovered to form from substituted benzenes chemisorbed to metal oxides. Here, we perform photoelectron spectroscopy, electron energy loss spectroscopy, and low energy electron diffraction of phenol chemisorbed to ZnO(1 0 1̱ 0) and (0 0 0 1̱)-Zn to observe electronic structure changes and charge transfer as a function adsorption temperature. We show direct evidence of charge transfer from the ZnO surfaces to the phenol...
October 1, 2015: Chemical Physics Letters
Albert M Lund, Gabriel I Pagola, Anita M Orendt, Marta B Ferraro, Julio C Facelli
Here we present the results of our unbiased searches of glycine polymorphs obtained using the Genetic Algorithms search implemented in Modified Genetic Algorithm for Crystals coupled with the local optimization and energy evaluation provided by Quantum Espresso. We demonstrate that it is possible to predict the crystal structures of a biomedical molecule using solely first principles calculations. We were able to find all the ambient pressure stable glycine polymorphs, which are found in the same energetic ordering as observed experimentally and the agreement between the experimental and predicted structures is of such accuracy that the two are visually almost indistinguishable...
April 17, 2015: Chemical Physics Letters
Min Yao, Xi Chen, Chang-Guo Zhan
To accurately predict the free energy barrier for urea elimination in aqueous solution, we examined the reaction coordinates for the direct and water-assisted elimination pathways, and evaluated the corresponding free energy barriers by using the surface and volume polarization for electrostatics (SVPE) model-based first-principles electronic-structure calculations. Based on the computational results, the water-assisted elimination pathway is dominant for urea elimination in aqueous solution, and the corresponding free energy barrier is 25...
April 1, 2015: Chemical Physics Letters
Li Xiao, Qin Cai, Zhilin Li, Hongkai Zhao, Ray Luo
A multi-scale framework is proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent. This article reports our initial efforts to formulate the physical concepts necessary for coupling the two mechanics and develop a 3D numerical algorithm to simulate the solvent fluid via the Navier-Stokes equation. The numerical algorithm was validated with multiple test cases. The validation shows that the algorithm is effective and stable, with observed accuracy consistent with our design...
November 25, 2014: Chemical Physics Letters
Francesco Musumeci, Gerald H Pollack
The discharge of a platinum parallel-plate capacitor filled with ultrapure water has been measured. The observed discharge trend can be described by a Modified Poisson-Boltzmann Equation (MPB) only when the voltage is very low. Increasing the applied voltage creates an "exclusion zone," in which the MPB equation no longer fits, and the system capacitance shows a dependence on the spacing between the two platinum plates. The permittivity of water, calculated considering the system as a plane capacitor, appears to be very high...
October 3, 2014: Chemical Physics Letters
Tomaz Urbic
Knowledge of water-water potential is important for an accurate description of water. Potential between two molecules depends upon the distance, relative orientation of each molecule and local environment. In simulation, water-water hydrogen bonds are handled by point-charge water potentials and by polarizable models. These models produce good results for bulk water being parameterized for such environment. Water around surfaces and in channels, however is different from bulk water. Using quantum-mechanical methods, hydrogen bond strength was calculated in the vicinity of different monoions...
August 28, 2014: Chemical Physics Letters
Mathieu Frenette, Maryam Hatamimoslehabadi, Stephanie Bellinger-Buckley, Samir Laoui, Seema Bag, Olivier Dantiste, Jonathan Rochford, Chandra Yelleswarapu
The nonlinear optical properties of a series of pyrrolic compounds consisting of BODIPY and aza-BODIPY systems are investigated using 532 nm nanosecond laser and the Z-scan technique. Results show that 3,5-distyryl extension of BODIPY to the red shifted MeO2BODIPY dye has a dramatic impact on its nonlinear absorption properties changing it from a saturable absorber to an efficient reverse saturable absorbing material with a nonlinear absorption coefficient of 4.64 × 10(-10) m/W. When plotted on a concentration scale per mole of dye in solution MeO2BODIPY far outperforms the recognized zinc(II) phthalocyanine dye and is comparable to that of zinc(II) tetraphenylporphyrin...
July 21, 2014: Chemical Physics Letters
Nikki M Magdaong, Dariusz M Niedzwiedzki, Jordan A Greco, Hongbin Liu, Koki Yano, Takayuki Kajikawa, Kazuhiko Sakaguchi, Shigeo Katsumura, Robert R Birge, Harry A Frank
C29-peridinin is a synthetic analogue of the important, naturally-occurring carotenoid, peridinin, found in several marine algal species. C29-peridinin has five conjugated carbon-carbon double bonds compared to eight possessed by peridinin and also lacks the methyl group functionalities typically present along the polyene chain of carotenoids. These structural modifications lead to unique excited state properties and important insights regarding the factors controlling the photophysics of peridinin and other carbonyl-containing carotenoids, which are critical components of the light-harvesting systems of many photosynthetic organisms...
February 11, 2014: Chemical Physics Letters
Jong Seol Yuk, Ernest F Guignon, Michael A Lynes
We describe a novel approach to enhance the sensitivity of a grating-based surface plasmon-coupled emission (SPCE) sensor by increasing the thickness of the metal film used in this system. The calculated optical properties of grating-based SPR spectra were significantly affected by both grating depth and by gold thickness. Higher angular sensitivity could be achieved at short wavelengths and under in situ measurement (analysis under aqueous condition). We confirmed the predicated enhancements of SPCE response using Alexa Fluor 647-labeled anti-mouse IgG immobilized on the SPCE sensor chips...
January 20, 2014: Chemical Physics Letters
Alan K Soper
The structure of water confined in MCM41 silica cylindrical pores is studied to determine whether confined water is simply a version of the bulk liquid which can be substantially supercooled without crystallisation. A combination of total neutron scattering from the porous silica, both wet and dry, and computer simulation using a realistic model of the scattering substrate is used. The water in the pore is divided into three regions: core, interfacial and overlap. The average local densities of water in these simulations are found to be about 20% lower than bulk water density, while the density in the core region is below, but closer to, the bulk density...
December 18, 2013: Chemical Physics Letters
Amanda J Taylor, Elizabeth Rendina, Brenda J Smith, Donghua H Zhou
Bone minerals possess two primary hydrogen sources: hydroxide ions in the nanocrystalline core and structural water in the amorphous surface layer. In order to accurately measure their concentrations using hydrogen to phosphorus cross polarization NMR spectroscopy, it is necessary to analyze the dependence of signal intensities on serial contact times, namely, cross polarization kinetics. A reliable protocol is developed to iteratively decompose the severely overlapped spectra and to analyze the cross-polarization kinetics, leading to measurement of hydroxyl and structural water concentrations...
November 19, 2013: Chemical Physics Letters
Thomas J Measey, Beatrice N Markiewicz, Feng Gai
Peptide hydrogels are promising candidates for a wide range of medical and biotechnological applications. To further expand the potential utility of peptide hydrogels, herein we demonstrate a simple yet effective strategy to render peptide hydrogels photodegradable, making controlled disassembly of the gel structure of interest feasible. In addition, we find that the high-frequency amide I' component (i.e., the peak at ~1685 cm(-1)) of the photodegradable peptide hydrogel studied shows an unusually large enhancement, in comparison to that of other peptide fibrils consisting of antiparallel β-sheets, making it a good model system for further study of the coupling-structure relationship...
August 6, 2013: Chemical Physics Letters
Gian Giacomo Guerreschi, Markus Tiersch, Ulrich E Steiner, Hans J Briegel
The yield of radical pair reactions is influenced by magnetic fields well beyond the levels expected from energy considerations. This dependence can be traced back to the microscopic dynamics of electron spins and constitutes the basis of chemical compasses. Here we propose a new experimental approach based on molecular photoswitches to achieve additional control on the chemical reaction and allow short-time resolution of the spin dynamics. Our proposal enables experiments to test some of the standard assumptions of the radical pair model and improves the sensitivity of a paradigmatic model of chemical magnetometer by up to two orders of magnitude...
May 30, 2013: Chemical Physics Letters
Sy Redding, Eric C Greene
Many aspects of biology depend on the ability of DNA-binding proteins to locate specific binding sites within the genome. Interest in this target search problem has been reinvigorated through the recent development of microscopy-based technologies capable of tracking individual proteins in real-time as they search for binding sites. In this review we discuss how two different proteins, lac repressor and RNA polymerase, have solved the target search problem through seemingly different mechanisms, with an emphasis on how recent in vitro single-molecule studies have influenced our understanding of these reactions...
May 10, 2013: Chemical Physics Letters
Ileana M Pazos, Rachel M Roesch, Feng Gai
To expand the spectroscopic utility of the non-natural amino acid p-cyanophenylalanine (PheCN), we examine the quenching efficiencies of a series of commonly encountered anions toward its fluorescence. We find that iodide exhibits an unusually large Stern-Volmer quenching constant, making it a convenient choice in PheCN fluorescence quenching studies. Indeed, using the villin headpiece subdomain as a testbed we demonstrate that iodide quenching of PheCN fluorescence offers a convenient means to reveal protein conformational heterogeneity...
March 20, 2013: Chemical Physics Letters
Sangram L Raut, Dmytro Shumilov, Rahul Chib, Ryan Rich, Zygmunt Gryczynski, Ignacy Gryczynski
In this short letter, we have synthesized the BSA protected Au25 nanoclusters and studied their two photon luminescence behavior. We demonstrate that BSA Au25 nanoclusters can be used as a probe with two photon excitation capability. Our results show a quadratic relation between excitation power and emission intensity whereas with one photon excitation shows a linear dependence. The emission spectrum of BSA Au25 nanoclusters with one photon and two photon excitation shows no appreciable change. Due to its long wavelength emission (650 nm) and two photon excitation, BSA Au25 can be potentially used as a probe for deep tissue imaging...
March 13, 2013: Chemical Physics Letters
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