Adaptive resolution molecular dynamics simulation through coupling to an internal particle reservoir

For simulation studies of (macro) molecular liquids it would be of significant interest to be able to adjust or increase the level of resolution within one region of space, while allowing for the free exchange of molecules between open regions of different resolution or representation. We generalize the adaptive resolution idea and suggest an interpretation in terms of an effective generalized grand canonical approach. The method is applied to liquid water at ambient conditions.     

Dual-scale modeling of benzene adsorption onto Ni(111) and Au(111) surfaces in explicit water.

We present a multiscale modeling approach for studying interactions of organic molecules with metal surfaces in explicit water. The approach is based on combining adsorption energies of isolated molecules on transition metal surfaces calculated by ab initio density functional methods and classical molecular dynamics simulations using atomistically detailed force fields. The interaction of benzene with Ni(111) and Au(111) surfaces was studied. It is shown that a strong affinity of water for the hydrophilic surfaces makes benzene adsorption on Au thermodynamically unfavorable, while on Ni there is no preference. The work presented here serves as a first step in modeling the interactions of larger organic molecules with metal surfaces.     

Classical kinetic energy,quantum fluctuation terms and kinetic-energy functionals

We employ a recently formulated dequantization procedure to obtain an exact expression for the kinetic energy which is applicable to all kinetic-energy functionals. We express the kinetic energy of an N-electron system as the sum of an N-electron classical kinetic energy and an N-electron purely quantum kinetic energy arising from the quantum fluctuations that turn the classical momentum into the quantum momentum. This leads to an interesting analogy with Nelson’s stochastic approach to quantum mechanics, which we use to conceptually clarify the physical nature of part of the kinetic-energy functional in terms of statistical fluctuations and in direct correspondence with Fisher Information Theory. We show that the N-electron purely quantum kinetic energy can be written as the sum of the (one-electron) Weizsäcker term and an (N?1)-electron kinetic correlation term. We further show that the Weizsäcker term results from local fluctuations while the kinetic correlation term results from the nonlocal fluctuations. We then write the N-electron classical kinetic energy as the sum of the (one-electron) classical kinetic energy and another (N?1)-electron kinetic correlation term. For one-electron orbitals (where kinetic correlation is neglected) we obtain an exact (albeit impractical) expression for the noninteracting kinetic energy as the sum of the classical kinetic energy and the Weizsäcker term. The classical kinetic energy is seen to be explicitly dependent on the electron phase, and this has implications for the development of accurate orbital-free kinetic-energy functionals. Also, there is a direct connection between the classical kinetic energy and the angular momentum and, across a row of the periodic table, the classical kinetic energy component of the noninteracting kinetic energy generally increases as Z increases. Finally, we underline that, although our aim in this paper is conceptual rather than practical, our results are potentially useful for the construction of improved kinetic-energy functionals.     

DNA vaccine containing the mycobacterial hsp65 gene prevented insulitis in MLD-STZ diabetes

Background  

Our group previously demonstrated that a DNA plasmid encoding the mycobacterial 65-kDa heat shock protein (DNA-HSP65) displayed prophylactic and therapeutic effect in a mice model for tuberculosis. This protection was attributed to induction of a strong cellular immunity against HSP65. As specific immunity to HSP60 family has been detected in arthritis, multiple sclerosis and diabetes, the vaccination procedure with DNA-HSP65 could induce a cross-reactive immune response that could trigger or worsen these autoimmune diseases.     

Polymers near metal surfaces: selective adsorption and global conformations

We study the properties of a polycarbonate melt near a nickel surface as a model system for the interaction of polymers with metal surfaces by employing a multiscale modeling approach. For bulk properties, a suitably coarse-grained bead-spring model is simulated by molecular dynamics methods with model parameters directly derived from quantum chemical calculations. The surface interactions are parametrized and incorporated by extensive quantum mechanical density functional calculations using the Car-Parrinello method. We find strong chemisorption of chain ends, resulting in significant modifications of the melt composition when compared to an inert wall.     

Bader's interatomic surfaces are unique

 In this work we comment on the statement about the nonuniqueness of the solution of Bader's equation for defining atoms in molecules reported in the article of P. Cassam-Chena? and D. Jayatilaka in Theoretical Chemistry Accounts (2001) 105: 213–218 Received: 10 May 2001 / Accepted: 7 September 2001 / Published online: 3 June 2002     

氨工质的新简明状态方程

本文根据新导得的当量分子作用势函数和分子自由体积理论,建立一组形式简便、精度高的氨工质新三次维里状态方程、蒸气压方程及其液相密度方程,具有显著的工程应用价值。     

A macromolecule in a solvent: adaptive resolution molecular dynamics simulation

The authors report adaptive resolution molecular dynamics simulations of a flexible linear polymer in solution. The solvent, i.e., a liquid of tetrahedral molecules, is represented within a certain radius from the polymer's center of mass with a high level of detail, while a lower coarse-grained resolution is used for the more distant solvent. The high resolution sphere moves with the polymer and freely exchanges molecules with the low resolution region through a transition regime. The solvent molecules change their resolution and number of degrees of freedom on the fly. The authors show that their approach correctly reproduces the static and dynamic properties of the polymer chain and surrounding solvent.     

Access to Bis(σ-B−H) Complexes of Ruthenium Bearing Monoaryl Borate and Borane Ligands

A series of ruthenium bis(σ-B−H) borate complexes 1 – 4 have been prepared by a salt-elimination protocol using lithium monoaryl trihydroborates Li[ArBH₃] (R=Ph, 3,5-(CF₃)₂C₆H₃, o-tol or Mes) and the corresponding metal halide Cp*Ru(PCy₃)Cl. All of these bis(σ-B−H) borate complexes are stable at room temperature and isolated in good yields (70–92 %). Additionally, treatment of 4 with the hydride abstracting agent B(C₆F₅)₃ generated rare cationic bis(σ-B−H) borane complex 5 . Crystallographic characterization data are provided for 3 and 5 . All these new complexes were fully characterized by multinuclear NMR spectroscopy and elemental analysis.     

Lone pair versus bonding pair electrons: the mechanism of electronic polarization of water in the presence of positive ions

It is commonly accepted that the water molecules in the first solvation shell of a positive ion are strongly polarized because of an elongation of the oxygen lone pair orbitals along the ion-oxygen direction and this is commonly considered the dominant effect. Recent experimental and theoretical works have instead suggested that this is not the dominant aspect and that the problem is by far more complicated. Consistent with the picture given above, here we show that, in particular, an equally important role into the polarization process is played by the bonding pair electrons located along the internal oxygen-hydrogen bond. We also provide some arguments which suggest that the main reason of such a behavior is due to the distortion of the molecular orbitals caused by the interaction between non-hydrogen-bonded water molecules in the first solvation shell of the ion.