As the two-dimensional square ice in graphene nanocapillaries 10 was observed by transmission electron microscopy (TEM), a variety of theoretical methods have been applied to explore this phenomenon. However, a satisfactory model has not yet been described. Here, we investigate the structural properties and phase behavior of the confined water in graphene nanocapillaries by using the ABEEM sigma pi polarizable force field (PFF) with the ABEEM-7P water model and ABEEM sigma pi graphene model. The ordered AB-stacked bilayer and ABA-stacked trilayer square ice samples are acquired in 8.0 and 10.2 angstrom graphene nanocapillaries, respectively, at 298 K at a constant volume. Furthermore, the bilayer and trilayer ices demonstrate rhombus-square-triangular ice as the graphene nanocapillary changes from 7.8 to 8.6 and 10.0 to 11.0 angstrom, respectively. The results yielded by using a fixed charge force field with the SPC/E water model are different from those obtained by ABEEM sigma pi PFF. By changing the constant pressure from 0.5 to 1.5 GPa, the monolayer (bilayer) triangular ice is transformed to bilayer (trilayer) square ice in a 6.5 (9.0) angstrom graphene nanocapillary system. Additionally, the van der Waals interactions, density of the confined water, confinement width, polarization effects, and pressure all play decisive roles in the distribution of the confined water. Our study provides some clues for clarifying the experimental consequences of TEM.

How the receptor and ligand recognise each other is a challenging subject in explaining the mechanism of recognition at the molecular level. As a starting point, here, a synthesised RS receptor and its RGD ligand were investigated as a proper model to simulate their recognition process in terms of ABEEMσπ/MM polarisable force field. It is found that a switch of forming up a salt bridge in the ligand triggers the recognition of the receptor and ligand. Through the salt-bridge switch that undergoes several cycles from on-state with parallel hydrogen bonds to off-state with bifurcated hydrogen bonds, the active site of ligand can flex easily to interact with the active site of the receptor. In addition, the water molecules form a decisive bridge connecting the active sites of the bound system. The salt-bridge switch and water-mediated movement are cooperative as the important factors for the receptor-ligand recognition. In addition, the properties, such as binding free energy, conformational flexibility and solvent accessible surface area have been calculated to provide adequate evidence for the whole recognition process. According to the simulation, a detailed mechanism was derived involving diffusion, a switch triggered cooperative water-mediated movement, and conformational folding, for the flexible recognition.

Continuum solvent models have shown to be very efficient for calculating solvation energy of biomolecules in solution. However, in order to produce accurate results, besides atomic radii or volumes, an appropriate set of partial charges of the molecule is needed. Here, a set of partial charges produced by a fluctuating charge model-the atom-bond electronegativity equalization method model (ABEEMσπ) fused into molecular mechanics is used to fit for the analytical continuum electrostatics model of generalized-Born calculations. Because the partial atomic charges provided by the ABEEMσπ model can well reflect the polarization effect of the solute induced by the continuum solvent in solution, accurate and rapid calculations of the solvation energies have been performed for series of compounds involving 105 small neutral molecules, twenty kinds of dipeptides and several protein fragments. The solvation energies of small neutral molecules computed with the combination of the GB model with the fluctuating charge protocol (ABEEMσπ∕GB) show remarkable agreement with the experimental results, with a correlation coefficient of 0.97, a slope of 0.95, and a bias of 0.34 kcal∕mol. Furthermore, for twenty kinds of dipeptides and several protein fragments, the results obtained from the analytical ABEEMσπ∕GB model calculations correlate well with those from ab initio and Poisson-Boltzmann calculations. The remarkable agreement between the solvation energies computed with the ABEEMσπ∕GB model and PB model provides strong motivation for the use of ABEEMσπ∕GB solvent model in the simulation of biochemical systems.

This paper reports an effective way to improve the accuracy of the generalized Born(GB)model in use of a fluctuating charge(FQ)model-the ABEEMσπ model(atom-bond electronegativity equalization method).The GB model is a continuum model which treats the solvent as a continuous medium having the average properties of the real solvent,so the calculation of solvation free energy with this model is simple and rapid.However,the accuracy of this model requires some improvements.The charge regions of one molecule in ABEEMσπ model are explicitly presented by different sites:atoms,single bonds,double bonds,and lone-pairs,especially for double bonds with one σ and four π bond sites.Moreover,the partial atomic charges provided by the ABEEMσπ model can flow through chemical bonds from one atomic center to another based on the local electrostatic environment surrounding each atom,so accurate and rapid calculations have been performed for series of compounds involving several alkane molecules by ABEEMσπ-GB/SA method.

Atom-bond electronegativity equalization method fused into molecular mechanics(ABEEMσπ/MM)as a fluctuating charge(FQ)force field,was combined with the Generalized Born Solvent Accessible surface area(GB/SA)to calculate the binding free energy of receptor and ligand.The binding free energy is divided into molecular mechanical energy(involving internal energy,van der Waals energy,and Columbic energy),solvation energy and entropic effect.Because the charges on atomic,bond and lone pair's sites are variable in response to the environment,the binding free energies were well reproduced by the present method compared to the experimental values errors being within 0.5 kJ/mol.

Structures, binding energies, and vibrational frequencies of (NH(3))(n) (n=2-5) isomers and dynamical properties of liquid ammonia have been explored using a transferable intermolecular potential eight point model including fluctuating charges and flexible body based on a combination of the atom-bond electronegativity equalization and molecular (ABEEM) mechanics (ABEEM ammonia-8P) in this paper. The important feature of this model is to divide the charge sites of one ammonia molecule into eight points region containing four atoms, three sigma bonds, and a lone pair, and allows the charges in system to fluctuate responding to the ambient environment. Due to the explicit descriptions of charges and special treatment of hydrogen bonds, the results of equilibrium geometries, dipole moments, cluster interaction energies, vibrational frequencies for the gas phase of small ammonia clusters, and radial distribution function for liquid ammonia calculated with the ABEEM ammonia-8P potential model are in good agreement with those measured by available experiments and those obtained from high level ab initio calculations. The properties of ammonia dimer are studied in detail involving the structure and one-dimensional, two-dimensional potential energy surface. As for interaction energies, the root mean square deviation is 0.27 kcal/mol, and the linear correlation coefficient reaches 0.994.