Coupled-cluster, Möller Plesset (MP2), density fitted local MP2, and density functional theory examination of the energetic and structural features of hydrophobic solvation: Water and pentane

Yasaman Ghadar and Aurora E. Clark

In this work, the interaction energy of water–pentane dimer has been determined using coupled-cluster theory with single double (triple) excitations [CCSD(T)], 2nd order Möller Plesset perturbation theory (MP2), density fitted local MP2 (DF-LMP2), as well as density functional theory using a wide variety of density functionals and several different basis sets.

J. Chem. Phys. 136, 054305 (2012)

Modeling simple amphiphilic solutes in a Jagla solvent

Zhiqiang Su, Sergey V. Buldyrev, Pablo G. Debenedetti, Peter J. Rossky, and H. Eugene Stanley

An exploration of the amphiphilic behavior of a Jagla solvent, which has been previously shown to exhibit many of the anomalous properties of water. The authors consider two models of an amphiphilic solute: (i) a "dimer" model, which consists of one hydrophobic hard sphere linked to a Jagla particle with a permanent bond, and (ii) a "monomer" model, which is a limiting case of the dimer, formed by concentrically overlapping a hard sphere and a Jagla particle.

J. Chem. Phys. 136, 044511 (2012)

(PbS)₃₂: A baby crystal

B. Kiran, Anil K. Kandalam, Rameshu Rallabandi, Pratik Koirala, Xiang Li, Xin Tang, Yi Wang, Howard Fairbrother, Gerd Gantefoer, and Kit Bowen

Theoretical calculations based on density functional theory have found (PbS)₃₂ to be the smallest cubic cluster for which its inner (PbS)₄ core enjoys bulk-like coordination. Experiments in which mass-selected (PbS)₃₂ clusters were soft-landed onto a highly ordered pyrolytic graphite surface and the resulting aggregates imaged by scanning tunneling microscopy provide evidence in direct support of the computational results.

J. Chem. Phys. 136, 024317 (2012) | Read the press release.

Understanding the EF-hand closing pathway using non-biased interatomic potentials

L. Dupuis and Normand Mousseau

The authors simulated the folding pathway, from Ca²⁺-unbound open holo conformations to closed apo states, of two well-studied EF-hand: the NT domains of calmodulin and Troponin C. Trajectories were generated using an activated algorithm, ART nouveau, along with the multi-scale holographic method, which lead to an unbiased sampling of the conformation space with a focus on the flexible regions.

J. Chem. Phys. 136, 035101 (2012)

The effects of shape and flexibility on bio-engineered fd-virus suspensions

M. Dennison, M. Dijkstra, and R. van Roij

The authors present a theoretical model to describe binary mixtures of semi-flexible colloidal rods applying it to fd-virus systems with different diameter (thick-thin) and length (long-short) ratios. The authors find the behavior of fd-virus systems to be very sensitive to the stiffness of the constituent particles, with only small changes in particle stiffness required to give dramatic changes in the observed phase behavior.

J. Chem. Phys. 135, 144106 (2011)