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Journal of Physical Chemistry. B

Pierre Lucas, Garrett J Coleman, Manga Venkateswara Rao, Angharad Naomi Edwards, Chrishani Devaadithya, Shuai Wei, Abduljabar Qassem Alsayoud, Barrett G Potter, Krishna Muralidharan, Pierre A Deymier
The fraction of edge- and corner-sharing tetrahedra in liquid ZnCl2 is quantified as a function of temperature using Raman spectroscopy and ab initio molecular dynamic simulations. Two distinct regimes are found in the temperature dependence of the change in these structural units. This behavior is consistent with the existence of a fragile-to-strong transition in liquid ZnCl2 suggested by calorimetric and viscosity measurements. The structural origin of this transition is rationalized in terms of a constraint counting formalism...
November 22, 2017: Journal of Physical Chemistry. B
Kelsey A Stoerzinger, Marco Favaro, Philip N Ross, Junko Yano, Zhi Liu, Zahid Hussain, Ethan J Crumlin
Understanding the surface chemistry of electrocatalysts in operando can bring insight into the reaction mechanism, and ultimately the design of more efficient materials for sustainable energy storage and conversion. Recent progress in synchrotron based X-ray spectroscopies for in operando characterization allows us to probe the solid/liquid interface directly while applying an external potential, applied here to the model system of Pt in alkaline electrolyte for the hydrogen evolution reaction (HER). We employ ambient pressure X-ray photoelectron spectroscopy (AP-XPS) to identify the oxidation and reduction of Pt-oxides and hydroxides on the surface as a function of applied potential, and further assess the potential for hydrogen adsorption and absorption (hydride formation) during and after the HER...
November 22, 2017: Journal of Physical Chemistry. B
Changhao Wang, Pengyu Ren, Ray Luo
Solvent-mediated electrostatic interactions were well recognized to be important in the structure and function of molecular systems. Ionic interaction is an important component in electrostatic interactions, especially in highly charged molecules, such as nucleic acids. Here we focus on the quality of the widely used PBSA continuum models in modeling ionic interactions by comparing with both explicit solvent simulations and experiment. In this work, the molality-dependent chemical potentials for sodium chloride (NaCl) electrolyte were first simulated in the SPC/E explicit solvent...
November 22, 2017: Journal of Physical Chemistry. B
Jing Zhang, Qing Tang, Zhong-Zheng Gao, Ying Huang, Xin Xiao, Zhu Tao
Two supramolecular assemblies between twisted cucurbit[14]uril and hemicyanine dyes have been successfully constructed based on host-guest recognition. These supramolecular assemblies could be reversibly switched under acidic and neutral conditions. Furthermore, it responded to selected chemical stimuli such as MV2+, thereby exhibiting potential analysis application.
November 22, 2017: Journal of Physical Chemistry. B
Lin-Na Wang, Chen Cai, Yun-Hong Zhang
No abstract text is available yet for this article.
November 22, 2017: Journal of Physical Chemistry. B
Xinzhi Cao, Remi Casier, Hunter Little, Jean Duhamel
Evidence is provided showing that global Model Free Analysis (MFA) of monomer and excimer fluorescence decays of pyrene dissolved in aqueous solutions of sodium dodecyl sulfate (SDS) provides the same structural and dynamic information on SDS micelles as the well-established Micelle Model (MM) does. Both MFA and MM were employed to characterize the quenching kinetics between dyes and quenchers located in surfactant micelles and the aggregation number of surfactant micelles. However, contrary to the MM which assumes that dyes and quenchers distribute themselves among SDS micelles according to a Poisson distribution and react with a rate constant that is proportional to the number of reactants in a micelle, the MFA accomplishes this task without making any assumption about the process of pyrene excimer formation in SDS micelles...
November 21, 2017: Journal of Physical Chemistry. B
John S Bender, John T Fourkas, Benoit Coasne
Ultrafast optical Kerr effect (OKE) spectroscopy is a widely used method for studying the depolarized, Raman-active intermolecular dynamics of liquids. Through appropriate manipulation of OKE data, it is possible to determine the reduced spectral density (RSD), which is the Bose-Einstein-corrected, low-frequency Raman spectrum with the contribution of diffusive reorientation removed. OKE RSDs for van der Waals liquids can often be fit well to an empirical function that is the sum of a Bucaro-Litovitz function and an antisymmetrized Gaussian (AG)...
November 21, 2017: Journal of Physical Chemistry. B
Tatyana G Karabencheva-Christova, Christo Z Christov, Gregg B Fields
Matrix metalloproteinase-1 (MMP-1) is a zinc-dependent protease that catalyzes hydrolysis of interstitial collagens. A previously reported X-ray crystallographic structure revealed specific interactions between a triple-helical peptide (THP) model of interstitial collagen and the hemopexin-like (HPX) and catalytic (CAT) domains of MMP-1. An NMR-based structure of MMP-1 in complex with a different THP was also solved, where docking was used to model the MMP-1•THP interactions and develop a mechanism for the early stages of collagenolysis...
November 21, 2017: Journal of Physical Chemistry. B
Osamu Takahashi, Mathias P Ljungberg, Lars G M Pettersson
The X-ray emission spectrum of liquid ethanol was calculated using density functional theory and a semi-classical approximation to the Kramers-Heisenberg formula including core-hole-induced dynamics. Our spectrum agrees well with the experimental spectrum. We found that the intensity ratio between the two peaks at 526 and 527 eV assigned as 10a' and 3a" depends not only on the hydrogen bonding network around the target molecule, but also on the intramolecular conformation. This effect is absent in liquid methanol and demonstrates the high sensitivity of X-ray emission to molecular structure...
November 21, 2017: Journal of Physical Chemistry. B
Amy L Stevens, Neeraj Kumar Joshi, Matthew F Paige, Ronald Paul Steer
Dimeric and multimeric aggregates of a model metalloporphyrin, zinc tetraphenylporphyrin (ZnTPP), have been produced in a controlled manner by incrementally increasing the water content of dilute aqueous ethanol solutions. Steady state absorption, fluorescence emission and fluorescence excitation spectra have been measured to identify the aggregates present as a function of solvent composition. The dynamics of the excited states of the aggregates produced initially by excitation in the Soret region have been measured by ultrafast fluorescence upconversion techniques...
November 21, 2017: Journal of Physical Chemistry. B
Andre Portz, Christoph R Gebhardt, Michael Dürr
The kinetics of the H/D exchange reaction in angiotensin II (ATII), hexaglycine (Gly6), Co(II)Tetra(3-carboxyphenyl)porphyrin (CoTCPP), and tetra(4-carboxyphenyl)\-porphyrin (H2TCPP) were followed in real-time by mass spectrometry employing desorption/ionization induced by neutral SO2 clusters (DINeC). The change of the isotope patterns with increasing degree of deuteration was recorded as a function of D2O exposure and the underlying H/D exchange kinetics, i.e., the dependence of the different degrees of deuteration on time, were deduced...
November 21, 2017: Journal of Physical Chemistry. B
Christoph J Sahle, Johannes Niskanen, Christian Schmidt, Johannes Stefanski, Keith Gilmore, Yury Forov, Sandro Jahn, Max Wilke, Christian Sternemann
We present a study of the local atomic environment of the oxygen atoms in aqueous solutions of NaOH and HCl under simultaneous high temperature and high pressure conditions. Experimental non-resonant X-ray Raman scattering core-level spectra at the oxygen K-edge show systematic changes as a function of temperature and pressure. These systematic changes are distinct for the two different solutes and are described well by calculations within the Bethe-Salpeter formalism for snapshots from {\it ab initio} molecular dynamics simulations...
November 21, 2017: Journal of Physical Chemistry. B
Miguel Ponce-Vargas, Cloé Azarias, Denis Jacquemin, Boris Le Guennic
A set of 13 bis(difluoroboron)-1,2-bis((pyrrol-2-yl)methylene)hydrazine (BOPHY) dyes is studied through a hybrid time-dependent density functional theory (TD-DFT)-scaled opposite spin-configuration interaction singles with a double correction [SOS-CIS(D)] approach accounting for solvent effects, to shed light onto the structure-property relationships of these recently developed chromophores. In the first step, we calculate the absorption-fluorescence crossing points with refined TD-DFT models considering the influences of both vibrational and solvent contributions...
November 21, 2017: Journal of Physical Chemistry. B
Samantha R Summers, K G Sprenger, Jim Pfaendtner, Jan Marchant, Michael F Summers, Joel L Kaar
The ability of ionic liquids (ILs) to solubilize cellulose has sparked interest in their use for enzymatic biomass processing. However, this potential is yet to be realized, primarily because ILs inactivate requisite cellulases by mechanisms that are yet to be identified. We used a combination of enzymology, circular dichroism (CD), nuclear magnetic resonance (NMR), and molecular dynamics (MD) methods to investigate the molecular basis for the inactivation of the endocellulase 1 (E1) from Acidothermus cellulolyticus by the imidazolium IL 1-butyl-3-methylimidazolium chloride ([BMIM][Cl])...
November 21, 2017: Journal of Physical Chemistry. B
Pratyush Tiwary
Biotin-streptavidin is a very popular system used to gain insight into protein-ligand interactions. In its tetrameric form, it is well-known for its exceptionally high kinetic stability, being one of the strongest known noncovalent interactions in nature, and it is heavily used across the biotechnological industry. In this work, we gain understanding of the molecular determinants and bottlenecks in the dissociation of the dimeric biotin-streptavidin system in wild type and with a point mutation. Using recently proposed enhanced sampling methods with full atomistic resolution, we reproduce the experimentally reported effect of the mutation on the dissociation rate...
November 21, 2017: Journal of Physical Chemistry. B
Vojtěch Mlýnský, Petra Kührová, Petr Jurečka, Jiří Šponer, Michal Otyepka, Pavel Banáš
Ribozymes utilize diverse catalytic strategies. We report systematic quantum chemical calculations mapping the catalytic space of RNA cleavage by comparing all chemically feasible reaction mechanisms of RNA self-cleavage, using appropriate model systems including those chemical groups that may directly participate in ribozyme catalysis. We calculated the kinetics of uncatalyzed cleavage reactions proceeding via both monoanionic and dianionic pathways, and explicitly probed effects of various groups acting as general bases (GBs) and/or general acids (GAs), or electrostatic transition state stabilizers...
November 21, 2017: Journal of Physical Chemistry. B
Myungjin Lee, Vesselin Kolev, Arieh Warshel
Simulating the nature of voltage activated systems is a problem of major current interest, covering the action of voltage gated ion channels to energy storage batteries. However, fully microscopic converging molecular simulations of external voltage effects present a major challenge and macroscopic models are associated with major uncertainties about the dielectric treatment and the underlying physical basis. Recently we developed a coarse grained (CG) model that represents explicit the electrodes, the electrolytes and the membrane / protein system...
November 20, 2017: Journal of Physical Chemistry. B
James McClory, David J Timson, Warispreet Singh, Jian Zhang, Meilan Huang
Isopentenyl phosphate kinase (IPK) catalyzes the Mg2+-ATP dependent phosphorylation reactions to produce isopentenyl diphosphate, an important precursor in the synthesis of isopentenols. However, the position of the divalent metal ion in the crystal structures of IPK in complex with ATP and its native substrate IP has not been definitively resolved, and as a result ambiguity surrounds the catalytic mechanism of IP, limiting its exploitation as a biofuel and in drug design. Here we report the conformational change caused by substrate binding and the catalytically competent structure in complex with the metal ion Mg2+ using molecular dynamic simulations and density functional theory-based quantum mechanics/molecular mechanics calculations (B97d/AMBER99)...
November 20, 2017: Journal of Physical Chemistry. B
Lingyi Meng, Shanshan He, Xin Sheng Zhao
Fluorescence correlation spectroscopy (FCS) encodes the information of the equilibrium constant (K), the relative fluorescence brightness of fluorophore (Q), and the forward and backward reaction rate constants (k+ and k-) on a physical or chemical relaxation. However, it has been a long-standing problem to completely resolve the FCS data to get the thermodynamic and kinetic information. Recently, we have solved the problem for fluorescence auto-correlation spectroscopy (FACS). Here, we extend the method to fluorescence cross-correlation spectroscopy (FCCS), which appears when FCS is coupled with fluorescence resonance energy transfer (FRET)...
November 20, 2017: Journal of Physical Chemistry. B
Grzegorz Nawrocki, Po-Hung Wang, Isseki Yu, Yuji Sugita, Michael Feig
For a long time the effect of crowded cellular environment on protein dynamics has been largely ignored. Recent experiments indicate that proteins diffuse much slower in a living cell than in a diluted solution and further studies suggest that the diffusion depends on the local surrounding. Here, detailed insight into how diffusion depends on protein-protein contacts is presented based on extensive all-atom molecular dynamics simulations of concentrated villin head piece solutions. After force field adjustments in the form of increased protein-water interactions to reproduce experimental data, translational and rotational diffusion was analyzed in detail...
November 20, 2017: Journal of Physical Chemistry. B
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