Yaoquan Tu

The electronic properties of water molecules in water clusters and liquid water

Abstract A novel, self-consistent approach, applicable both for ground and excited electronic states, is introduced to calculate molecular properties in clusters and liquids. Using the method, carried out here at the second-order Moller–Plesset perturbation theory (MP2) level, we obtain an average dipole moment of 2.65 D for water in liquid. Significant changes in quadrupole moment and polarizability, due to surrounding molecules, are also found along the water plane in the direction perpendicular to the axis bisecting the H–O–H bond angle.

Modulation of iridium(III) phosphorescence via photochromic ligands : a density functional theory study

The photochromic iridium(iii) complex (Py-BTE)(2)Ir(acac) synthesized by Tan et al. [W. Tan et al., Org. Lett. 2009, 11, 161-164] has shown distinct photo-reactivity and photo-controllable phosphorescence. We here present a density functional theory study on the (Py-BTE)(2)Ir(acac) complex to explore the mechanism at the molecular level and to help further design of photochromic iridium(iii) complexes with the desirable properties. The hybrid functional PBE0, with 25% Hartree-Fock exchange, is found to give an optimal structure compared with X-ray crystallographic data. The absorption bands are well reproduced by using time-dependent density functional theory calculations, lending the possibility to assign the metal-to-ligand and intra-ligand charge transfer transitions. The radiative and nonradiative deactivation rate constants, k(r) and k(nr), are rationalized for both the open-ring and closed-ring forms of the complex. The very large k(nr) and small k(r) make the closed-ring form of the complex non-emissive. The triplet reactivity of the Py-BTE ligand is also studied by performing density functional theory calculations on the potential energy surfaces of the ground state and the lowest triplet state.

On the effect of Lennard-Jones parameters on the quantum mechanical and molecular mechanical coupling in a hybrid molecular dynamics simulation of liquid water

Combined quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations have been carried out to study liquid water. The QM forces are evaluated at the Hartree–Fock level. The QM/MM coupling potentials, constructed from the flexible TIP3P Lennard-Jones parameters, and from those modified according to the corresponding QM/MM calculations of the water dimer, are examined based on the structure of liquid water, polarization effects of the QM water molecule from the surrounding classical MM water molecules, and the interactions between the QM molecule and the MM molecules. Our simulations show that when the flexible TIP3P Lennard-Jones parameters are used, the QM/MM coupling is too strong. However, when the Lennard-Jones parameters on the QM water molecule are modified according to the corresponding QM/MM calculations of the water dimer, the coupling between the QM water molecule and MM water molecules becomes too weak. In general, our work shows that the Lennard-Jones parameters on the QM ato...

The adsorption of xyloglucan on cellulose: effects of explicit water and side chain variation

The interaction between para-crystalline cellulose and the cross-linking glycan xyloglucan (XG) plays a central role for the strength and extensibility of plant cell walls. The coating of XGs on cellulose surfaces is believed to be one of the most probable interaction patterns. In this work, the effects of explicit water and side chain variation on the adsorption of XGs on cellulose are investigated by means of atomistic molecular dynamics simulations. The adsorption properties are studied in detail for three XGs on cellulose Iβ 1-10 surface in aqueous environment, namely GXXXGXXXG, GXXLGXXXG, and GXXFGXXXG, which differ in the length and composition of one side chain. Our work shows that when water molecules are included in the theoretical model, the total interaction energies between the adsorbed XGs and cellulose are considerably smaller than in vacuo. Furthermore, in water environment the van der Waals interactions prevail over the electrostatic interactions in the adsorption. Variation in one side chain does not have significant influence on the interaction energy and the binding affinity, but does affect the equilibrium structural properties of the adsorbed XGs to facilitate the interaction between both the backbone and the side chain residues with the cellulose surface. Together, this analysis provides new insights into the nature of the XG-cellulose interaction, which helps to further refine current molecular models of the composite plant cell wall.

Molecular dynamics simulations of the surface tension and structure of salt solutions and clusters.

Sodium halides, which are abundant in sea salt aerosols, affect the optical properties of aerosols and are active in heterogeneous reactions that cause ozone depletion and acid rain problems. Interfacial properties, including surface tension and halide anion distributions, are crucial issues in the study of the aerosols. We present results from molecular dynamics simulations of water solutions and clusters containing sodium halides with the interatomic interactions described by a conventional force field. The simulations reproduce experimental observations that sodium halides increase the surface tension with respect to pure water and that iodide anions reach the outermost layer of water clusters or solutions. It is found that the van der Waals interactions have an impact on the distribution of the halide anions and that a conventional force field with optimized parameters can model the surface tension of the salt solutions with reasonable accuracy.

Working Mechanism for a Redox Switchable Molecular Machine Based on Cyclodextrin: A Free Energy Profile Approach

This paper reports the working mechanism for a redox-responsive bistable [2]rotaxane incorporating an alpha-cyclodextrin (alpha-CD) ring (J. Am. Chem. Soc. 2008, 130, 11294-11296), based on free energy profiles obtained from all-atom molecular dynamics simulations. Employing an umbrella sampling technique, the free energy profiles (potential of mean force, PMF) were calculated for the shuttling motion of the alpha-CD ring between a tetrathiafulvalene (TTF) recognition site and a triazole (TZ) unit on the dumbbell of the rotaxane for three oxidation states (0, +1, +2) of the TTF unit. These calculated free energy profiles verified the experimentally observed binding preference for each state. Analysis of the free energy components reveals that, for these alpha-CD-based rotaxanes with charged TTF units, the real driving force for the shuttling in the oxidized states is actually the interactions between water and the rotaxane components, which overwhelms the attractive interactions between the alpha-CD ring and the charged dumbbell. In this work, we put forward a feasible approach to correctly describe the complexation behavior of CD with charged species, that is, free energy profiles obtained from all-atom molecular dynamics simulation.

Two-photon absorption of hydrogen-bonded octupolar molecule clusters.

Charge-transfer octupolar molecules can form clusters in solution through intermolecular hydrogen bonds. In the present work we explore the role of such clustering on two-photon absorption (TPA) spectra assuming 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) as a model system. Using density functional quadratic response theory we examine different cluster structures of TATB dimers, trimers, and tetramers taken from snapshots of molecular dynamics simulations. In comparison with the TPA spectrum of a monomer, significant red shifts of charge-transfer states are predicted for all chosen clusters, which mainly is the result of the distortion of the structures induced by the aggregation. The TPA spectra for dimers and trimers show strong conformation dependence, whereas they turn out to be more stable for tetramers. Enhancements of TPA absorption have also been found for clusters containing less distorted molecules connected by hydrogen bonds.

Effects of Graphene Nanopore Geometry on DNA Sequencing

In this Letter we assess the effect of graphene nanopore geometries on DNA sequencing by considering DNA fragments including A, T, C, G, and 5-methylcytosine (MC) pulled out of graphene nanopores of different geometries with diameters down to ∼1 nm. Using steered molecular dynamics simulations it is demonstrated that the bases (A, T, C, G, and MC) can be indentified at single-base resolution through the characteristic peaks on the force profile in a circular graphene nanopore but not in nanopores with other asymmetric geometries. Our study suggests that the graphene nanopore surface should be modified as symmetrically as possible in order to sequence DNA by atomic force microscopy or optical tweezers.

Combined Hartree–Fock quantum mechanical and molecular mechanical molecular dynamics simulations of water at ambient and supercritical conditions

Combined ab initio Hartree–Fock quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations have been carried out for water at ambient and supercritical conditions. The QM/MM coupling potential is optimized for ambient water by scaling down the original MM charges in the MM potential model. Simulation results show that the modified QM/MM coupling potential behaves well in the studied water system. The evolution of the water structure from ambient to the supercritical conditions is studied and compared to the available experimental results. Our simulation results suggest that, at supercritical conditions, the data refined from the experiment by neutron diffraction with the isotopic substitution technique probably overestimate the hydrogen bonding interactions.

Residues remote from the binding pocket control the antagonist selectivity towards the corticotropin-releasing factor receptor-1

The corticotropin releasing factors receptor-1 and receptor-2 (CRF1R and CRF2R) are therapeutic targets for treating neurological diseases. Antagonists targeting CRF1R have been developed for the potential treatment of anxiety disorders and alcohol addiction. It has been found that antagonists targeting CRF1R always show high selectivity, although CRF1R and CRF2R share a very high rate of sequence identity. This has inspired us to study the origin of the selectivity of the antagonists. We have therefore built a homology model for CRF2R and carried out unbiased molecular dynamics and well-tempered metadynamics simulations for systems with the antagonist CP-376395 in CRF1R or CRF2R to address this issue. We found that the side chain of Tyr6.63 forms a hydrogen bond with the residue remote from the binding pocket, which allows Tyr6.63 to adopt different conformations in the two receptors and results in the presence or absence of a bottleneck controlling the antagonist binding to or dissociation from the receptors. The rotameric switch of the side chain of Tyr3566.63 allows the breaking down of the bottleneck and is a perquisite for the dissociation of CP-376395 from CRF1R.