Development and Comprehensive Benchmark of a High-Quality AMBER-Consistent Small Molecule Force Field with Broad Chemical Space Coverage for Molecular Modeling and Free Energy Calculation.

Biomolecular simulations have become an essential tool in contemporary drug discovery, and molecular mechanics force fields (FFs) constitute its cornerstone. Developing a high quality and broad coverage general FF is a significant undertaking that requires substantial expert knowledge and computing resources, which is beyond the scope of general practitioners. Existing FFs originate from only a limited number of groups and organizations, and they either suffer from limited numbers of training sets, lower than desired quality because of oversimplified representations, or are costly for the molecular modeling community to access. To address these issues, in this work, we developed an AMBER-consistent small molecule FF with extensive chemical space coverage, and we provide Open Access parameters for the entire modeling community. To validate our FF, we carried out benchmarks of quantum mechanics (QM)/molecular mechanics conformer comparison and free energy perturbation calculations on several benchmark data sets. Our FF achieves a higher level of performance at reproducing QM energies and geometries than two popular open-source FFs, OpenFF2 and GAFF2. In relative binding free energy calculations for 31 protein-ligand data sets, comprising 1079 pairs of ligands, the new FF achieves an overall root-mean-square error of 1.19 kcal/mol for ΔΔG and 0.92 kcal/mol for ΔG on a subset of 463 ligands without bespoke fitting to the data sets. The results are on par with those of the leading commercial series of OPLS FFs.

Prediction of self-assemblies of sodium dodecyl sulfate and fragrance additives using coarse-grained force fields.

Coarse-grained force field (CGFF) methods were applied to study the self-assembly of sodium dodecyl sulfate with fragrance additives. The CGFF parameters were parameterized and validated using experimental and all-atom simulation data. Direct molecular dynamics simulations were carried out to characterize the initial aggregation, partitioning of fragrances, and chemical potentials of the surfactant and fragrance molecules in aggregates of different sizes. The equilibrium critical micelle concentrations (CMCs) and micelle size distributions, which could not be obtained by direct simulation, were predicted using the calculated chemical potentials in combination with a thermodynamic model. The predicted partitioning of fragrances, CMCs, micelle sizes, and micelle structures agree well with previously reported experimental data. Graphical abstract Enhancement of micelle size distribution using thermodynamic model.

Rose-like I-doped Bi2O2CO3 microspheres with enhanced visible light response: DFT calculation, synthesis and photocatalytic performance.

Based on the crystal structure and the DFT calculation of Bi2O2CO3, I- can partly replace the CO32-in Bi2O2CO3 to narrow its bandgap and to enhance its visible light absorption. With this in mind, rose-like I-doped Bi2O2CO3 microspheres were prepared via a hydrothermal process. This method can also be extended to synthesize rose-like Cl- or Br-doped Bi2O2CO3 microspheres. Photoelectrochemical test supports the DFT calculation result that I- doping narrows the bandgap of Bi2O2CO3 by forming two intermediate levels in its forbidden band. Further study reveals that I-doped Bi2O2CO3 microspheres with optimized composition exhibit the best photocatalytic activity. Rhodamine B can be completely degraded within 6min and about 90% of Cr(VI) can be reduced after 25min under the irradiation of visible light (λ>400nm).

Free Energy-Based Coarse-Grained Force Field for Binary Mixtures of Hydrocarbons, Nitrogen, Oxygen, and Carbon Dioxide.

The free energy based Lennard-Jones 12-6 (FE-12-6) coarse-grained (CG) force field developed for alkanes1 has been extended to model small molecules of light hydrocarbons (methane, ethane, propane, butane, and isobutane), nitrogen, oxygen, and carbon dioxide. The adjustable parameters of the FE-12-6 potential are determined by fitting against experimental vapor-liquid equilibrium (VLE) curves and heat of vaporization (HOV) data for pure substance liquids. Simulations using the optimized FE-12-6 parameters correctly reproduced experimental measures of the VLE, HOV, density, vapor pressure, compressibility, critical point, and surface tension for pure substances over a wide range of thermodynamic states. The force field parameters optimized for pure substances were tested on methane/butane, nitrogen/decane, and carbon dioxide/decane binary mixtures to predict their vapor-liquid equilibrium phase diagrams. It is found that for nonpolar molecules represented by different sized beads, a common scaling factor (0.08) that reduces the strength of the interaction potential between unlike beads, generated using Lorentz-Berthelot (LB) combination rules, is required to predict vapor-liquid phase equilibria accurately.

Hierarchical atom type definitions and extensible all-atom force fields.

The extensibility of force field is a key to solve the missing parameter problem commonly found in force field applications. The extensibility of conventional force fields is traditionally managed in the parameterization procedure, which becomes impractical as the coverage of the force field increases above a threshold. A hierarchical atom-type definition (HAD) scheme is proposed to make extensible atom type definitions, which ensures that the force field developed based on the definitions are extensible. To demonstrate how HAD works and to prepare a foundation for future developments, two general force fields based on AMBER and DFF functional forms are parameterized for common organic molecules. The force field parameters are derived from the same set of quantum mechanical data and experimental liquid data using an automated parameterization tool, and validated by calculating molecular and liquid properties. The hydration free energies are calculated successfully by introducing a polarization scaling factor to the dispersion term between the solvent and solute molecules. © 2015 Wiley Periodicals, Inc.

Transferability and nonbond functional form of coarse grained force field - tested on linear alkanes.

Whether or not a coarse grained force field (CGFF) can be made to be transferrable is an important question to be addressed. By comparing potential energy with potential of mean force (PMF) of a molecular dimer, we proposed to use a free energy function (FE-12-6) with the parameters in entropic and energetic terms explicitly to represent the nonbond interactions in CGFF. Although the FE-12-6 function cannot accurately describe the PMF curves, a cancelation of short radii and strong repulsion makes the function a good approximation. For nonpolar molecules represented by linear alkanes, FE-12-6 is demonstrated to be highly effective in representing the nonbond interactions in CGFF. The force field parameters are well transferrable among different alkane molecules, in different thermodynamic states and for predicting various thermodynamic properties including heats of vaporization, vapor-liquid-equilibrium coexistence curves, surface tensions, and liquid densities.

Exploring the important role of nanocrystals orientation in TiO2 superstructure on photocatalytic performances.

Efficient charge separation has been widely accepted as one of the important factors responsible for the photocatalytic water splitting, organic oxidation, and solar cell, etc. TiO2 mesocrystal is a superstructure which could largely enhance charge separation, where TiO2 nanocrystals with parallel crystallographic alignment assemble in a form of oriented aggregation. Here, the intercrystal misorientation in TiO2 superstructure was first concerned and evaluated on the influence of photocatalytic efficiency. Our results showed that the intercrystal misorientation in TiO2 superstructures had a harmful effect on the charge separation efficiency.

Plant uptake-assisted round-the-clock photocatalysis for complete purification of aquaculture wastewater using sunlight.

A novel reactor equipped with solar batteries, Bi2O3/TiO2 film photocatalyst, and celery plant was designed and used for purification of aquaculture wastewater. The Bi2O3/TiO2 film photocatalyst started photocatalytic degradation of organonitrogen compounds under irradiation of sunlight. Meanwhile, the solar batteries absorbed and converted excess sunlight into electric energy and then started UV lamps at night, leading to round-the-clock photocatalysis. Subsequently, the inorganic nitrogen species including NH4(+), NO2(-), and NO3(-) resulting from photocatalytic degradation of the organonitrogen compounds could subsequently be uptaken by the celery plant as the fertilizer to reduce the secondary pollution. It was found that, after 24 h circulation, both organonitrogen compounds and NO2(-) species were completely removed, while NH4(+) and NO3(-) contents also decreased by 30% and 50%, respectively. The reactor could be used repetitively, showing a good potential in practical application.

π-π interaction of aromatic groups in amphiphilic molecules directing for single-crystalline mesostructured zeolite nanosheets.

One of the challenges in material science has been to prepare macro- or mesoporous zeolite. Although examples of their synthesis exist, there is a need for a facile yet versatile approach to such hierarchical structures. Here we report a concept for designing a single quaternary ammonium head amphiphilic template with strong ordered self-assembling ability through π-π stacking in hydrophobic side, which stabilizes the mesostructure to form single-crystalline mesostructured zeolite nanosheets. The concept is demonstrated for the formation of a new type of MFI (zeolite framework code by International Zeolite Association) nanosheets joined with a 90° rotational boundary, which results in a mesoporous zeolite with highly specific surface area even after calcination. Low binding energies for this self-assembling system are supported by a theoretical analysis. A geometrical matching between the arrangement of aromatic groups and the zeolitic framework is speculated for the formation of single-crystalline MFI nanosheets.

Ultrafine single-crystal TiOF2 nanocubes with mesoporous structure, high activity and durability in visible light driven photocatalysis.

Single crystal TiOF2 nanocubes assembled into a mesoporous structure were synthesized by alcoholysis of TiF4 under solvothermal conditions, which displayed spectral response in the visible area owing to the intrinsic narrow energy band gap. Mechanism studies revealed that TiOF2 was formed via consecutive hydrolysis reactions and the H2O produced by condensation between two alcohols played a key role in determining the TiOF2 crystal growth and its transformation to anatase TiO2. The TiOF2 nanocube size could be easily adjusted by changing either alcoholysis time, or solvothermal temperature, or alcohol kind owing to the different H2O production rate and amount. The small-sized TiOF2 nanocubes with large surface area exhibited high activity in photocatalytic degradation of Rhodamine B (RhB) and 4-chlorophenol (4-CP) owing to the enhanced adsorption for reactant molecules and the reduced photoelectron-hole recombination rate. Meanwhile, they also showed strong durability since the mesoporous structure enhanced the stability against either the phase transformation from TiOF2 crystal to anatase TiO2 or the agglomeration of TiOF2 nanocubes.

A three-dimensional microporous metal-organic framework with large hydrogen sorption hysteresis.

A three-dimensional microporous metal-organic framework [Cd(2)(Tzc)(2)](n), which is dehydrated from [Cd(2)(Tzc)(2)(H(2)O)(2)](n), exhibits selective gas adsorption and large hydrogen sorption hysteresis.

Solvothermal synthesis of well-defined TiO(2) mesoporous nanotubes with enhanced photocatalytic activity.

High efficiency TiO(2) photocatalyst in porous nanotubes were prepared by solvothermal alcoholysis of TiOSO(4) in the presence of carbon nanotube template.

On the kinetic mechanism of the hydrogen abstraction reactions of the hydroxyl radical with CH3CF2Cl and CH3CFCl2: a dual level direct dynamics study.

By means of the dual-level direct dynamics method, the mechanisms of the reactions, CH(3)CF(2)Cl + OH --> products (R1) and CH(3)CFCl(2) + OH --> products (R2), are studied over a wide temperature range 200-2000 K. The optimized geometries and frequencies of the stationary points are calculated at the MP2/6-311G(d,p) level, and then the energy profiles of the reactions are refined with the interpolated single-point energy method at the G3(MP2) level. The canonical variational transition-state theory with the small-curvature tunneling (SCT) correction method is used to calculate the rate constants. For the title reactions, three reaction channels are identified and the H-abstraction channel is the major pathway. The results indicate that F substitution has a significant (reductive) effect on hydrochlorofluorocarbon reactivity. Also, for all H-abstraction reaction channels the variational effect is small and the SCT effect is only important in the lower temperature range on the rate constants calculation.

Boron nitride nanotubes functionalized by a series of carbenes.

We systematically studied the structural, energetic and electronic properties of zigzag boron nitride nanotubes (BNNTs) functionalized by a class of substituted carbenes (CR(2)) where R = H, F, Cl, CH(3), CN and NO(2) on different absorption sites using density functional theory. For R = H, F and Cl, the open structure is preferred with a BNNT sidewall bond cleavage, while for R = CH(3) and CN, a competition between the open and closed cyclopropane-like three-membered ring (3MR) structure occurs. Interestingly, for R = NO(2) we find a novel double five-membered ring (5MR) structure with high reaction stability. This new structure cannot be found in BNNTs' alternative carbon nanotubes (CNTs). In addition, the electronic properties of BNNTs functionalized with carbenes are hardly changed for R = H, F, Cl, CH(3) and CN, but are significantly affected when R = NO(2) due to the heterocyclic double 5MR structure.

In situ encapsulation of Au nanoparticles in mesoporous core-shell TiO(2) microspheres with enhanced activity and durability.

An active and durable Au/TiO(2) photocatalyst was prepared by in situ encapsulation of Au particles into core-shell TiO(2) spheres based on consecutive solvothermal and hydrothermal treatments.

The structural and electronic properties of amine-functionalized boron nitride nanotubes via ammonia plasmas: a density functional theory study.

The reaction behavior of the chemical modification of boron nitride nanotubes (BNNTs) with ammonia plasmas has been investigated by density functional theory (DFT) calculations. Unlike previously studied functionalization with NH(3) and amino functional groups, we found that NH(2)(*) radicals involved in the ammonia plasmas can be covalently incorporated to BNNTs through a strong single B-N bond. Subsequently, the H(*) radicals also involved in the ammonia plasmas would prefer to combine with the N atoms neighboring the NH(2)-functionalized B atoms. Our study revealed that this reaction behavior can be elucidated using the frontier orbital theory. The calculated band structures and density of states (DOS) indicate that this modification is an effective method to modulate the electronic properties of BNNTs. We have discussed various defects on the surface of BNNTs generated by collisions of N(2)(+) ions. For most defects considered, the reactivity of the functionalization of BNNTs with NH(2)(*) are enhanced. Our conclusions are independent of the chirality, and the diameter dependence of the reaction energies is presented.