Journal of Physical Chemistry Letters

Publications in this journal

• Article: Surface-Enhanced Infrared Spectroscopic Study of a CO-Covered Pt Electrode in Room-Temperature Ionic Liquid

  Yao-Yue Yang †, Li-Na Zhang †, Masatoshi Osawa ‡, Wen-Bin Cai *†
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  ABSTRACT: ATR-SEIRAS is extended for the first time to study potential-induced surface and interface structure variation of a CO-covered Pt electrode in a room-temperature ionic liquid of N-butyl-N-methyl-piperidinium bis((trifluoromethyl)sulfonyl)imide (or [Pip14][TNf2]). Owing to a wide effective potential window of [Pip14][TNf2], a gradual conversion from bridged COad (COB) to terminal COad (COL) is observed in response to positively going potentials, suggesting that [Pip14]+ may be involved in a strong electrostatic interaction with the COad. This site conversion enables the ratio of the apparent absorption coefficient of COL to that of COB to be determined. Also, the spectral results reveal the potential-dependent COad frequency variations as well as the potential-induced interfacial ionic reorientation and movement at the Pt/CO/[Pip14][TNf2] interface.
  Journal of Physical Chemistry Letters 04/2013; 4:1582.
• Article: Atom-Scale Reaction pathways and Free-Energy Landscapes in Oxygen Plasma Etching of Graphene

  Kenichi Koizumi, Mauro Boero, Yasuteru Shigeta, Atsushi Oshiyama
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  ABSTRACT: We report first-principles molecular dynamics calculations combined with rare events sampling techniques that clarify atom-scale mechanisms of oxygen plasma etching of graphene. The obtained reaction pathways and associated free-energy landscapes show that the etching proceeds near vacancies via a two-step mechanism, formation of precursor lactone structures and the subsequent exclusive CO2 desorption. We find that atomic oxygen among the plasma components is most efficient for etching, providing a guidline in tuning the plasma conditions.
  Journal of Physical Chemistry Letters 04/2013; 4(10):1592.
• Article: Measurement of an Electronic Resonance in a Ground-State, Gas-Phase Acetophenone Cation via Strong-Field Mass Spectrometry

  Timothy Bohinski, Katharine Moore Tibbetts, Maryam Tarazkar, Dmitri Romanov, Spiridoula Matsika, Robert J. Levis
  Journal of Physical Chemistry Letters 04/2013;
• Article: Molecular Dynamics Simulation at High Sodium Chloride Concentration: Toward the Inactive Conformation of the Human Adenosine A2A Receptor

  Balázs Jójárt, Róbert Kiss, Béla Viskolcz, István Kolossváry, Gyoergy M. KeserHu
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  ABSTRACT: The recently solved crystal structure of the human adenosine A2A receptor (hA2AR) shows the characteristics of a partially activated state. Experimental data suggests that high sodium chloride concentration shifts hA2AR to the inactive state. We found that molecular dynamics simulations at high sodium chloride concentration result in an inactive form of hA2AR reflected in the reformation of the "ionic lock" (Arg(102)(3.50)-Glu(228)(6.30)) as well as in the reduction of the alpha C-alpha C distance between the intracellular sides of transmembrane, helices 3 and 6 (TM3 and TM6). Interestingly, no such stabilization effect was observed at physiological concentrations. Our results suggest that the effect of high sodium chloride concentration might be exploited to generate an inactive state of hA2AR, which is more favorable for identifying pharmacologically relevant antagonists or inverse agonists.
  Journal of Physical Chemistry Letters 04/2013; 1(6):1008-1013.
• Article: Piezoelectric Effects of Applied Electric Fields on Hydrogen-Bond Interactions: First-Principles Electronic Structure Investigation of Weak Electrostatic Interactions

  Keith A Werling, Geoffrey Hutchison, Daniel S Lambrecht
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  ABSTRACT: The piezoelectric properties of 2-methyl-4-nitroaniline crystals were explored qualitatively and quantitatively using an electrostatically embedded many-body (EE-MB) expansion scheme for the correlation energies of a system of monomers within the crystal. The results demonstrate that hydrogen bonding is an inherently piezoelectric interaction, deforming in response to the electrostatic environment. We obtain piezo- coefficients in excellent agreement with the experimental values. This approach reduces computational cost and reproduces the total resolution of the identity (RI)-Møller−Plesset second-order perturbation theory (RI-MP2) energy for the system to within 1.3 × 10−5%. Furthermore, the results suggest novel ways to self-assemble piezoelectric solids and suggest that accurate treatment of hydrogen bonds requires precise electrostatic evaluation. Considering the ubiquity of hydrogen bonds across chemistry, materials, and biology, a new electromechanical view of these interactions is required.
  Journal of Physical Chemistry Letters 04/2013; 4(9):1365-1370.
• Article: Unusual Bonding in Platinum Carbido Clusters

  D.J. Harding, C. Kerpal, G. Meijer, A. Fielicke
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  ABSTRACT: Vibrational spectroscopy and density functional theory calculations are used to determine the structures of small gas-phase platinum carbido clusters PtnC+, n = 3–5. The carbon atom is found to prefer three-coordinate binding sites near the center of the cluster, in contrast to most previously investigated adatoms on transition metal clusters. The Pt3C unit is particularly stable, and binding of the carbon atom also leads to significant rearrangement of the metal framework when compared to the bare clusters.
  Journal of Physical Chemistry Letters 03/2013; 4:892.
• Article: Conductivity and Solvation Dynamics in Ionic Liquids

  Xin-Xing Zhang †‡, Min Liang §, Nikolaus P. Ernsting ‡, Mark Maroncelli *§
  Journal of Physical Chemistry Letters 03/2013;
• Article: Two-Dimensional Hexagonal Transition-Metal Oxide for Spintronics

  Erjun Kan, Ming Li, Shuanglin Hu, Chuanyun Xiao, Hongjun Xiang, Kaiming Deng
  Journal of Physical Chemistry Letters 03/2013; 4(7):1120.
• Article: What Stabilizes the LinPn Inorganic Double Helices?

  Jissy A. K, Ayan Datta
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  ABSTRACT: Recently, inorganic double helical structures based on simple lithium and phosphorus salts were demonstrated. In this communication, we have analyzed the nature of bonding in these double helices of LinPn (n = 7–9). Similar to DNA, non-covalent interactions and co-operativity play an important role in stabilizing the inorganic double helices. Cooperativity imparts an additional stabilization of 4.5 kcal/mol to 10.1 kcal/mol per Li-P pair. In addition, the ionicity of Li-P units further augments to stability of these inorganic double helix structures in contrast to the canonical base pairs in DNA where non-covalent interactions determine the duplex stability. Unwinding is shown to be unfavourable and cleavage of a few edge Li – P bonds led to spontaneous self – healing into the intact double helix tract.
  Journal of Physical Chemistry Letters 03/2013;
• Article: Towards Accurate Prediction of Protonation Equilibrium of Nucleic Acids.

  Garrett B Goh, Jennifer L Knight, Charles L Brooks
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  ABSTRACT: The role of protonated nucleotides in modulating the pH-dependent properties of nucleic acids is one of the emerging frontiers in the field of nucleic acid biology. The recent development of a constant pH molecular dynamics simulation (CPHMD(MSλD)) framework for simulating nucleic acids has provided a tool for realistic simulations of pH-dependent dynamics. We enhanced the CPHMD(MSλD) framework with pH-based replica exchange (pH-REX), which significantly improves the sampling of both titration and spatial coordinates. The results from our pKa calculations for the GAAA tetraloop, which was predicted with lower accuracy previously due to sampling challenges, demonstrates that pH-REX reduces the average unsigned error (AUE) to 0.7 pKa units, and the error of the most poorly predicted residue A17 was drastically reduced from 2.9 to 1.2 pKa unit. Lastly, we show that pH-REX CPHMD(MSλD) simulations can be used to identify the dominant conformation of nucleic acid structures in alternate pH environments. This work suggests that pH-REX CPHMD(MSλD) simulations provide a practical tool for predicting nucleic acid protonation equilibrium from first-principles, and offering structural and mechanistic insight into the study of pH-dependent properties of nucleic acids.
  Journal of Physical Chemistry Letters 03/2013; 4(5):760-766.
• Article: Dynamic Trap Formation and Elimination in Colloidal Quantum Dots

  Oleksandr Voznyy, Susanna Thon, Alex Ip, Edward Sargent
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  ABSTRACT: Using first-principles simulations on PbS and CdSe colloidal quantum dots, we find that surface defects form in response to electronic doping and charging of the nanoparticles. We show that electronic trap states in nanocrystals are dynamic entities, in contrast with the conventional picture wherein traps are viewed as stable electronic states that can be filled or emptied, but not created or destroyed. These traps arise from the formation or breaking of atomic dimers at the nanoparticle surface. The dimers’ energy levels can reside within the bandgap, in which case a trap is formed. Fortunately, we are also able to identify a number of shallow-electron-affinity cations that stabilize the surface, working to counter dynamic trap formation and allowing for trap-free doping.
  Journal of Physical Chemistry Letters 03/2013;