Fullrmc,a rigid body reverse monte carlo modeling package enabled with machine learning and artificial intelligence

A new Reverse Monte Carlo (RMC) package “fullrmc” for atomic or rigid body and molecular, amorphous, or crystalline materials is presented. fullrmc main purpose is to provide a fully modular, fast and flexible software, thoroughly documented, complex molecules enabled, written in a modern programming language (python, cython, C and C++ when performance is needed) and complying to modern programming practices. fullrmc approach in solving an atomic or molecular structure is different from existing RMC algorithms and software. In a nutshell, traditional RMC methods and software randomly adjust atom positions until the whole system has the greatest consistency with a set of experimental data. In contrast, fullrmc applies smart moves endorsed with reinforcement machine learning to groups of atoms. While fullrmc allows running traditional RMC modeling, the uniqueness of this approach resides in its ability to customize grouping atoms in any convenient way with no additional programming efforts and to apply smart and more physically meaningful moves to the defined groups of atoms. In addition, fullrmc provides a unique way with almost no additional computational cost to recur a group's selection, allowing the system to go out of local minimas by refining a group's position or exploring through and beyond not allowed positions and energy barriers the unrestricted three dimensional space around a group. © 2016 Wiley Periodicals, Inc.     

Inelastic collisions of ultracold polar LiCs molecules with caesium atoms in an optical dipole trap

We investigate collisions of ultracold polar LiCs molecules and ultracold caesium atoms. LiCs molecules are formed in an optical dipole trap by photoassociation of caesium and lithium atoms via the B(1)Π excited state followed by spontaneous emission to the X(1)Σ(+) ground state and the lowest triplet state a(3)Σ(+). The molecules are then stored together with caesium atoms in the same optical trap. Rate coefficients for the loss of molecules induced by collisions with surrounding Cs atoms are measured for molecular ensembles produced via different photoassociation resonances. The results are analyzed in terms of the unitarity limit for the inelastic rates and predictions from the universal model of Idziaszek and Julienne (Phys. Rev. Lett., 2010, 104, 113202).     

Orientational correlations in molecular liquid SnI4

The total scattering structure factor of liquid tin tetraiodide (SnI(4)) has been interpreted by means of reverse Monte Carlo (RMC) modeling. From the sets of particle coordinates provided by RMC, which are consistent with experimental results within errors, partial radial distribution functions as well as correlation functions characterizing mutual orientations of molecules as a function of distance between molecular centers can be calculated. Interestingly and very much in contrast to liquids of symmetric XCl(4) molecules, the corner-to-face (or "Apollo")-type orientation of neighboring molecules has a significant (about 20%) occurrence in liquid SnI(4). Via comparison with a reference system, obtained by hard sphere Monte Carlo simulation, we demonstrate that intermolecular two-body correlations in liquid SnI(4) are determined largely by excluded volume (steric) effects; that is, intermolecular two-body interactions play only a minor role. On the other hand, as it is manifested in the large difference between the reference and "real" systems in terms of the orientational correlations, higher order interactions are indispensable. This feature can explain the extremely rich phase behavior of SnI(4) at high pressures.     

Efficient simultaneous reverse Monte Carlo modeling of pair-distribution functions and extended x-ray-absorption fine structure spectra of crystalline disordered materials

An efficient implementation of simultaneous reverse Monte Carlo (RMC) modeling of pair distribution function (PDF) and EXAFS spectra is reported. This implementation is an extension of the technique established by Krayzman et al. [J. Appl. Cryst. 42, 867 (2009)] in the sense that it enables simultaneous real-space fitting of x-ray PDF with accurate treatment of Q-dependence of the scattering cross-sections and EXAFS with multiple photoelectron scattering included. The extension also allows for atom swaps during EXAFS fits thereby enabling modeling the effects of chemical disorder, such as migrating atoms and vacancies. Significant acceleration of EXAFS computation is achieved via discretization of effective path lengths and subsequent reduction of operation counts. The validity and accuracy of the approach is illustrated on small atomic clusters and on 5500-9000 atom models of bcc-Fe and α-Fe(2)O(3). The accuracy gains of combined simultaneous EXAFS and PDF fits are pointed out against PDF-only and EXAFS-only RMC fits. Our modeling approach may be widely used in PDF and EXAFS based investigations of disordered materials.     

无定形碳的逆向蒙特卡洛法建模

作为一种很有前景的建模方法，逆向蒙特卡洛法（Reverse Monte Carlo 简称RMC 法）在无定形碳结构研究中得到了广泛应用。本文阐述了RMC 法对于无定形碳材料结构识别的意义，简介了该法的基本原理，同时针对使用RMC 法建立无定形碳结构模型时遇到的两大难点：即模拟结构的真实性问题和大尺寸孔网络的建模问题，综述了该方法的改进和发展趋势。几何约束和能量约束的使用，提高了模拟结构的真实性；具有介孔的多孔碳模型的建立，将成为今后研究的热点。     

Detailed intermolecular structure of molecular liquids containing slightly distorted tetrahedral molecules with C(3v) symmetry: chloroform, bromoform, and methyl-iodide

Analyses of the intermolecular structure of molecular liquids containing slightly distorted tetrahedral molecules of the CXY(3)-type are described. The process is composed of the determination of several different distance-dependent orientational correlation functions, including ones that are introduced here. As a result, a complete structure classification could be provided for CXY(3) molecular liquids, namely for liquid chloroform, bromoform, and methyl-iodide. In the present work, the calculations have been conducted on particle configurations resulting from reverse Monte Carlo computer modeling: these particle arrangements have the advantage that they are fully consistent with structure factors from neutron and x-ray diffraction measurements. It has been established that as the separation between neighboring molecules increases, the dominant mutual orientations change from face-to-face to edge-to-edge, via the edge-to-face arrangements. Depending on the actual liquid, these geometrical elements (edges and faces of the distorted tetrahedra) were found to contain different atoms. From the set of liquids studied here, the structure of methyl-iodide was found to be easiest to describe on the basis of pure steric effects (molecular shape, size, and density) and the structure of liquid chloroform seems to be the furthest away from the corresponding "flexible fused hard spheres" like reference system.     

Molecular Recognition in Organic Crystals: Directed Intermolecular Bonds or Nonlocalized Bonding?

Molecules are held together mainly by forces acting between individual atoms. Does the same apply to molecular clusters? Does intermolecular cohesion depend on weak bonds between individual atoms in different molecules or on less localized, more diffuse interactions between molecules? We discuss these questions from several viewpoints and in particular compare interpretations based on the extension of Bader's atoms in molecules (AIM) theory to cover closed‐shell intermolecular interactions with interpretations based on the new pixel method for the calculation of coulombic, polarization, dispersion, and repulsion energies from the electron density of molecular clusters.     

Macroporous Poly(Acrylamide) Hydrogels: Swelling and Shrinking Behaviors

Macroporous poly(acrylamide) hydrogels have been synthesized by using poly(ethylene glycol) (PEG) with three different molecular weights as the pore‐forming agent. Scanning electron microscope graphs reveal that the macroporous network structure of the hydrogels can be adjusted by applying different molecular weights of PEG during the polymerization reaction. The swelling ratios of the PEG‐modified hydrogels were much higher than those for the same type of hydrogel prepared via conventional method. However, the swelling/deswelling ratios of the PEG‐modified hydrogels were affected slightly by the change in the amount of the PEG. Scanning electron microscopy experiments, together with swelling ratio studies, reveal that the PEG‐modified hydrogels are characterized by an open structure with more pores and higher swelling ratio, but lower mechanical strength, compared the conventional hydrogel. PAAm has potential applications in controlled release of macromolecular active agents.     

On‐Surface Metalation and 2D Self‐Assembly of Pyrphyrin Molecules Into Metal‐Coordinated Networks on Cu(111)

The metalation of the tetradentate molecule pyrphyrin by copper substrate atoms on a Cu(111) surface is studied. Pyrphyrin, in contrast to porphyrin, consists of four fused pyridine groups instead of pyrrol groups. Using thermal desorption spectroscopy (TDS ) and N 1s X‐ray photoelectron spectroscopy (XPS ), we show that metalation of the monolayer of pyrphyrin with Cu atoms from the Cu(111) surface occurs at 377 K. The formation of an extended two‐dimensional (2D) network is observed with scanning tunneling microscopy (STM ). A honeycomb‐like lattice of metalated pyrphyrin molecules is formed by intermolecular connection via the two cyano groups at the periphery of pyrphyrin as well as Cu adatoms. Dehydrogenation at the periphery of the molecule is observed during annealing at 520 K. The surface‐adsorbed metal‐pyrphyrin has the potential to serve as a molecular catalyst.     

eQE: An open‐source density functional embedding theory code for the condensed phase

In this work, we present the main features and algorithmic details of a novel implementation of the frozen density embedding (FDE) formulation of subsystem density functional theory (DFT) that is specifically designed to enable ab initio molecular dynamics (AIMD) simulations of large‐scale condensed‐phase systems containing 1000s of atoms. This code (available at http://eqe.rutgers.edu ) has been given the moniker of embedded Quantum ESPRESSO (eQE) as it is a generalization of the open‐source Quantum ESPRESSO (QE) suite of programs. The strengths of eQE reside in a hierarchical parallelization scheme that allows for an efficient and fully self‐consistent treatment of the electronic structure (via the addition of an additional DIIS extrapolation layer) while simultaneously exploiting the inherent symmetries and periodicities in the system (via sampling of subsystem‐specific first Brillouin zones and utilization of subsystem‐specific basis sets). While bulk liquids and molecular crystals are two classes of systems that exemplify the utility of the FDE approach (as these systems can be partitioned into weakly interacting subunits), we show that eQE has significantly extended this regime of applicability by outperforming standard semilocal Kohn–Sham DFT (KS‐DFT) for large‐scale heterogeneous catalysts with quite different layer‐specific electronic structure and intrinsic periodicities. eQE features very favorable strong parallel scaling for a model system of bulk liquid water composed of 256 water molecules, which allows for a significant decrease in the overall time to solution when compared to KS‐DFT. We show that eQE achieves speedups greater than one order of magnitude ( ) when performing AIMD simulations of such large‐scale condensed‐phase systems as: (1) molecular liquids via bulk liquid water represented by 1024 independent water molecules (3072 atoms with a 25.3× speedup over KS‐DFT), (2) polypeptide/biomolecule solvation via (gly )₆ solvated in (H₂O)₃₉₅ (1230 atoms with a 38.6× speedup over KS‐DFT), and (3) molecular crystals via a 3 × 3 × 3 periodic supercell of pentacene (1940 atoms with a 12.0× speedup over KS‐DFT). These results represent a significant improvement over the current state‐of‐the‐art and now enable subsystem DFT‐based AIMD simulations of realistically sized condensed‐phase systems of interest throughout chemistry, physics, and materials science.     

(E)‐Methyl 2‐[(2‐fluorophenyl)aminomethylene]‐3‐oxobutanoate: X‐ray and density functional theory (DFT) study

The title compound, C₁₂H₁₂FNO₃, a potential precursor for fluoroquinoline synthesis, is essentially planar, with the most outlying atoms displaced from the best‐plane fit through all non‐H atoms by 0.163 (2) and 0.118 (2) Å. Molecules are arranged in layers oriented parallel to the (011) plane. The arrangement of the molecules in the structure is controlled mainly by electrostatic interactions, as the dipole moment of the molecule is 5.2 D. In addition, the molecules are linked by a weak C—H...O hydrogen bond which gives rise to chains with the base vector [1,1,1]. Electron transfer within the molecule is analysed using natural bond orbital (NBO) analysis. Deviations from the ideal molecular geometry are explained by the concept of non‐equivalent hybrid orbitals.     

Molecular Modeling of Interactions of the Benzolactam-V8 Modulators with the Cys2 Domain of Protein Kinase Cδ

Molecular modeling of interactions of four 7- or 8-substituted benzolactam-V8 （BLV） molecules with the cys2 activator-binding domain of protein kinase C （PKCδ） was carried out using molecular docking program Autodock. The docked models reveal that the hydroxymethyl group at the C（5） atom of the eight-membered ring of each BLV is bound at the bottom of the binding groove of the cys2 domain of PKCδ The BLV molecules make hydrogen bonds and hydrophobic interactions with PKCδ, which are similar to those in the crystal structure of the cys2 domain of PKCδ in complex with phorbol 13-acetate. BLV-1 does not contain a long side chain that is hydrophobic and necessary for membrane insertion, so that it would not be a potent modulator of PKCδ. The other three BLV molecules have long side chains substituted at C（7） or C（8） atoms, and it was predicted, based on the docking results, that they had the PKCδ-binding affinity in the order of BLV-2〉BLV-4〉BLV-3, and BLV-2 would be a potent activator of PKCδ.     

Automatic perception of organic molecules based on essential structural information

Format conversion is very common in structure preparation in molecular modeling studies. Unfortunately, format conversion cannot always be executed precisely. We have developed an automatic method, called I-interpret (available on-line at http://www.sioc-ccbg.ac.cn/software/I-interpret/), for interpreting the chemical structure of a given organic molecule merely from its essential structural information, including element identities and three-dimensional coordinates of its component atoms. I-interpret uses standard geometrical parameters of organic molecules in atom/bond-type assignment. A series of elaborate considerations are arranged in a logical sequence for this purpose. I-interpret was tested on a set of 179 small organic molecules from the Protein Data Bank and a set of 1990 organic molecules from the NCI diversity set. On both sets, it achieved a success rate of over 95% in interpreting the correct chemical structures, outperforming other programs under our evaluation. I-interpret also provides users some optional functions, which makes it more flexible and powerful in practice. It may serve as a valuable tool for processing chemical structures in molecular modeling.     

Molecular modeling of porous carbons using the hybrid reverse Monte Carlo method

We apply a simulation protocol based on the reverse Monte Carlo (RMC) method, which incorporates an energy constraint, to model porous carbons. This method is called hybrid reverse Monte Carlo (HRMC), since it combines the features of the Monte Carlo and reverse Monte Carlo methods. The use of the energy constraint term helps alleviate the problem of the presence of unrealistic features (such as three- and four-membered carbon rings), reported in previous RMC studies of carbons, and also correctly describes the local environment of carbon atoms. The HRMC protocol is used to develop molecular models of saccharose-based porous carbons in which hydrogen atoms are taken into account explicitly in addition to the carbon atoms. We find that the model reproduces the experimental pair correlation function with good accuracy. The local structure differs from that obtained with a previous model (Pikunic, J.; Clinard, C.; Cohaut, N.; Gubbins, K. E.; Guet, J. M.; Pellenq, R. J.-M.; Rannou, I.; Rouzaud, J. N. Langmuir 2003, 19 (20), 8565). We study the local structure by calculating the nearest neighbor distribution, bond angle distribution, and ring statistics.     

Crystal and molecular structure of pyridazine-3-carboxylic acid hydrochloride and zinc(II) pyridazine-3-carboxylate tetrahydrate

Crystals of pyridazine-3-carboxylic acid hydrochloride contain almost planar molecular sheets in which the cations, composed of acid molecules each with a hydrogen atom attached to one of the ring-nitrogen atoms, interact with chloride anions via a network of weak hydrogen bonds. Van der Waals interactions between sheets are indicated by the intersheet spacing of 3.47?Å. The crystal structure of di(aqua-O)bis(trans-pyridazine-3-carboxylato-N,O)zinc(II) dihydrate is composed of monomeric molecules in which the zinc(II) ion at the center of symmetry is coordinated by two ligand molecules each via its N,O bonding moiety. The ligand molecules and the metal ion form a trans-planar configuration. Two water oxygen atoms, above and below the plane, complete a distorted octahedron. A network of weak hydrogen bonds holds the monomers together.     

Methods for refining interactively established models of ribosomal RNA towards a physico‐chemically plausible structure

A computational multiscale modeling approach that was used for the refinement of the structure of the bacterial ribosome is presented. Though designed for the ribosome, the methods are applicable to other large biomolecules as well. Algorithms were developed, allowing defined groups of atoms to be clustered into rigid objects, which greatly reduces the number of parameters in the molecular dynamics approach and thus speeds up the computational process considerably (clustered molecular dynamics). The energy potential function, which is used in molecular dynamics to describe structural details of a particle, was extended to include terms that describe high‐level biochemical constraints resulting from crosslinking techniques and cryo‐electron microscopy. High‐ and low‐level features of the potential function were specified, and the clustered molecular dynamics technique was integrated into the interactive model‐building process, to establish a physico‐chemically plausible structure of the bacterial ribosomal RNA. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 407–417, 2001     

2-巯基苯并噻唑对铜缓蚀行为的表面增强红外光谱研究

2-巯基苯并噻唑(MBT)是Cu的高效缓蚀剂,但是缓蚀机理存在较大争议.本文通过电化学极化曲线从宏观角度对缓蚀效率进行评估,并利用原位衰减全反射-表面增强红外光谱技术结合理论计算研究了电位控制下的微观吸附构型.结果表明:在较高电位(大于0 V,相对饱和甘汞电极(SCE))下,MBT和金属Cu之间发生电子转移,MBT以硫醇式的环外S和N与金属Cu(I)离子配位在表面形成聚合物膜;在较低电位(小于0 V,vs SCE)下,MBT通过环外S原子以硫醇离子形式在金属Cu表面直立吸附.表面膜阻止了腐蚀介质的侵蚀,起到了较好的缓蚀效果.     

Fitting atomic correlation parameters for RECEP (rapid estimation of correlation energy from partial charges) method to estimate molecular correlation energies within chemical accuracy

The accuracy of the RECEP method [Chem Phys 1997, 224, 33 and Chem Phys Lett 1999, 307, 469] has been increased considerably by the use of fitted atomic correlation parameters. This method allows an extremely rapid, practically prompt calculation of the correlation energy of molecules after an HF‐SCF calculation. The G2 level correlation energy and HF‐SCF charge distribution of 41 closed‐shell neutral molecules (composed of H, C, N, O, and F atoms) of the G2 thermochemistry database were used to obtain the fitted RECEP atomic correlation parameters. Four different mathematical definitions of partial charges, as a multiple choice, were used to calculate the molecular correlation energies. The best results were obtained using the natural population analysis, although the other three are also recommended for use. For the 41 molecules, the G2 results were approached within a 1.8 kcal/mol standard deviation (the mean absolute difference was 1.5 kcal/mol). The RECEP atomic correlation parameters were also tested on a different, nonoverlapping set of other 24 molecules from the G2 thermochemistry database. The G2 results of these 24 molecules were approached within a 2.3 kcal/mol standard deviation (the mean absolute difference was 1.9 kcal/mol). This method is recommended to estimate total correlation energies of closed shell ground‐state neutral molecules at stationary (minimums and transition states) points on the potential surface. Extension of the work for charged molecules, radicals, and molecules containing other atoms is straightforward. Numerical example as a recipe is also provided. © 2000 John Wiley & Sons, Inc. J Comput Chem 22: 241–254, 2001     

Molecular Spoked Wheels: Synthesis and Self‐Assembly Studies on Rigid Nanoscale 2D Objects

We present the efficient synthesis of a new molecular spoked‐wheel structure ( MSW‐3 ). Two derivatives with diameters of approximately 4 nm have been prepared. By highlighting the importance of pseudo‐high‐dilution conditions during cyclization, we were able to access the compounds on a several hundred milligram scale. In addition to the standard characterization (NMR spectroscopy, MS), we describe a detailed investigation of the optical properties of the fluorescent MSWs by comparison with appropriate model chromophores. Furthermore, a comprehensive study of the structure in solution by means of light‐ and X‐ray scattering experiments has been conducted. Scanning tunneling microscopy (STM) revealed the two‐dimensional organization of the molecules on highly oriented pyrolytic graphite and emphasized the spoked‐wheel structure. The diameter of these molecules measured by small‐angle X‐ray scattering is in very good agreement with that obtained from STM and matches the results of molecular modeling. This confirms the rigidifying effect of the spokes, which results in highly shape‐persistent nanometer‐sized oblate organic compounds.