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Chemical Physics Letters

Oleg Kovtun, Ian D Tomlinson, Danielle M Bailey, Lucas B Thal, Emily J Ross, Lauren Harris, Michael P Frankland, Riley S Ferguson, Zachary Glaser, Jonathan Greer, Sandra J Rosenthal
The use of nanometer-sized semiconductor crystals, known as quantum dots, allows us to directly observe individual biomolecular transactions through a fluorescence microscope. Here, we review the evolution of single quantum dot tracking over the past two decades, highlight key biophysical discoveries facilitated by quantum dots, briefly discuss biochemical and optical implementation strategies for a single quantum dot tracking experiment, and report recent accomplishments of our group at the interface of molecular neuroscience and nanoscience...
August 16, 2018: Chemical Physics Letters
Pavol Jusko, Aude Simon, Gabi Wenzel, Sandra Brünken, Stephan Schlemmer, Christine Joblin
The fragment of the 1-methylpyrene cation, <mml:math xmlns:mml=""> <mml:mrow> <mml:msub> <mml:mtext>C</mml:mtext> <mml:mrow> <mml:mn>17</mml:mn> </mml:mrow> </mml:msub> <mml:msubsup> <mml:mtext>H</mml:mtext> <mml:mrow> <mml:mn>11</mml:mn> </mml:mrow> <mml:mo>+</mml:mo> </mml:msubsup> <mml:mo>,</mml:mo> </mml:mrow> </mml:math> is expected to exist in two isomeric forms, 1-pyrenemethylium <mml:math xmlns:mml="http://www...
April 16, 2018: Chemical Physics Letters
Mary Rose Hilaire, Debopreeti Mukherjee, Thomas Troxler, Feng Gai
Several cyanotryptophans have been shown to be useful biological fluorophores. However, how their fluorescence lifetimes vary with solvent has not been examined. In this regard, herein we measure the fluorescence decay kinetics as well as the absorption and emission spectra of six cyanoindoles in different solvents. In particular, we find, among other results, that only 4-cyanoindole affords a long fluorescence lifetime and hence high quantum yield in H2 O. Therefore, our measurements provide not only a guide for choosing which cyanotryptophan to use in practice but also data for computational modeling of the substitution effect on the electronic transitions of indole...
October 1, 2017: Chemical Physics Letters
Michael J Robertson, Julian Tirado-Rives, William L Jorgensen
DFT calculations have been used to develop improved descriptions of the torsional energetics for nucleosides and nucleotides in the OPLS-AA force field. Scans of nucleotide dihedral angles (γ, χ, and β) and methyl phosphates provided the bases for the new torsional parameters. In addition, the angle-bending parameters of phosphodiesters and ribose were updated, and adjustments were made to existing carbohydrate torsions to better capture the sugar puckering landscape of ribose. MD simulations of nucleosides with the new parameters demonstrate a significant improvement in the ribose sugar puckering and χ angle distributions...
September 1, 2017: Chemical Physics Letters
Rachel M Abaskharon, Stephen P Brown, Wenkai Zhang, Jianxin Chen, Amos B Smith, Feng Gai
Because of their negatively charged carboxylates, aspartate and glutamate are frequently found at the active or binding site of proteins. However, studying a specific carboxylate in proteins that contain multiple aspartates and/or glutamates via infrared spectroscopy is difficult due to spectral overlap. We show, herein, that isotopic-labeling of the aspartate sidechain can overcome this limitation as the resultant 13 C=O asymmetric stretching vibration resides in a transparent region of the protein IR spectrum...
September 1, 2017: 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
Liliya Vugmeyster, Dmitry Ostrovsky
We compared the dynamics of key methionine methyl groups in the water-accessible hydrophobic cavity of amyloid fibrils and Fluorenylmethyloxycarbonyl-Methionine (FMOC-Met), which renders general hydrophobicity to the environment without the complexity of the protein. Met35 in the hydrated cavity was recently found to undergo a dynamical cross-over from the dominance of methyl rotations at low temperatures to the dominance of diffusive motion of methyl axis at high temperatures. Current results indicate that in FMOC-Met this cross-over is suppressed, similar to what was observed for the dry fibrils, indicating that hydration of the cavity is driving the onset of the dynamical transition...
April 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
Chandana Kasireddy, Jonathan M Ellis, James G Bann, Katie R Mitchell-Koch
Ribonuclease A is the oldest model for studying enzymatic mechanisms, yet questions remain about proton transfer within the active site. Seminal work by Jackson et al. (Science, 1994) labeled Ribonuclease A with 4-fluorohistidine, concluding that active-site histidines act as general acids and bases. Calculations of 4-fluorohistidine indicate that the π-tautomer is predominant in all simulated environments (by ~17 kJ/mol), strongly suggesting that fluoro-labeled ribonuclease A functions with His119 in π-tautomer...
December 1, 2016: 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
Makoto Hatakeyama, Koji Ogata, Katsushi Fujii, Vittal K Yachandra, Junko Yano, Shinichiro Nakamura
The S3 state of the Mn4 CaO5 -cluster in photosystem II was investigated by DFT calculations and compared with EXAFS data. Considering previously proposed mechanism; a water molecule is inserted into an open coordination site of Mn upon S2 to S3 transition that becomes a substrate water, we examined if the water insertion is essential for the S3 formation, or if one cannot eliminate other possible routes that do not require a water insertion at the S3 stage. The novel S3 state structure consisting of only short 2...
May 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
D Skouteris, V Barone
We report the main features of a new implementation of the Gaussian Multi-Configuration Time-Dependent Hartree (G-MCTDH) model. The code allows effective computations of time-dependent phenomena, including calculation of vibronic spectra (in one or more electronic states), relative state populations etc., with the possibility of a multilayer formulation. We have validated the code on the diabatic surfaces recently published by Truhlar and coworkers to study the nonadiabatic photodynamics of phenol. Using an Ehrenfest-like, single-nuclear-configuration (but in a fully quantum formalism) model we calculate the optical spectrum and relative state populations of the system as a function of time...
September 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
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