Interaction of liquid water with the rutile TiO2 (110) surface

A force-field which describes the interaction between the TiO2 (110) rutile surface and a modified TIP3P water [P. Mark and L. Nilsson, J. Phys. Chem. A, 105, 9954, (200 1)] is tested against periodic density functional theory (PDFT). Optimizations of water on the non-hydroxylated and hydroxylated surfaces are performed using PDFT and the geometries are compared with optimizations of modified TIP3P water on the TiO2 surface using the force-field. The surface hydroxyl torsional profile is also compared using PDFT and force-field calculations as well as molecular dynamics (MD) simulations of the surface. MD simulations of liquid TIP3P water, containing dissolved Na+ and Cl- ions, on six TiO2 (110) surfaces at 298 K and 1 atm are performed for neutral surfaces and negatively-charged surfaces. Axial density and angular distributions show good agreement with results of Predota et al. [J. Phys. Chem. B, 108, 12049 (2004)] and X-ray crystal truncation rod experiments [Z. Zhang et al., Langmuir, 20, 4954 (2004)]

Analysis of polarization in QM/MM modelling of biologically relevant hydrogen bonds

Combined quantum mechanics/molecular mechanics (QM/MM) methods are increasingly important for the study of chemical reactions and systems in condensed phases. Here, we have tested the accuracy of a density functional theory-based QM/MM implementation (B3LYP/6-311+G(d,p)/CHARMM27) on a set of biologically relevant interactions by comparison with full QM calculations. Intermolecular charge transfer due to hydrogen bond formation is studied to assess the severity of spurious polarization of QM atoms by MM point charges close to the QM/MM boundary. The changes in total electron density and natural bond orbital atomic charges due to hydrogen bond formation in selected complexes obtained at the QM/MM level are compared with full QM results. It is found that charge leakage from the QM atoms to MM atomic point charges close to the QM/MM boundary is not a serious problem, at least with limited basis sets. The results are encouraging in showing that important properties of key biomolecular interactions can be treated well at the QM/MM level employing good-quality levels of QM theory

Side chain-positioning as an integer programming problem

Abstract. An important aspect of homology modeling and protein design algorithms is the correct positioning of protein side chains on a fixed backbone. Homology modeling methods are necessary to complement large scale structural genomics projects. Recently it has been shown that in automatic protein design it is of the uttermost importance to find the global solution to the side chain positioning problem [1]. If a suboptimal solution is found the difference in free energy between different sequences will be smaller than the error of the side chain positioning. Several different algorithms have been developed to solve this problem. The most successful methods use a discrete representation of the conformational space. Today, the best methods to solve this problem, are based on the dead end elimination theorem. Here we introduce an alternative method. The problem is formulated as a linear integer program. This programming problem can then be solved by efficient polynomial time methods, using linear programming relaxation. If the solution to the relaxed problem is integral it corresponds to the global minimum energy conformation (GMEC). In our experimental results, the solution to the relaxed problem has always been integral.