GRID: A high‐resolution protein structure refinement algorithm

The energy‐based refinement of protein structures generated by fold prediction algorithms to atomic‐level accuracy remains a major challenge in structural biology. Energy‐based refinement is mainly dependent on two components: (1) sufficiently accurate force fields, and (2) efficient conformational space search algorithms. Focusing on the latter, we developed a high‐resolution refinement algorithm called GRID. It takes a three‐dimensional protein structure as input and, using an all‐atom force field, attempts to improve the energy of the structure by systematically perturbing backbone dihedrals and side‐chain rotamer conformations. We compare GRID to Backrub, a stochastic algorithm that has been shown to predict a significant fraction of the conformational changes that occur with point mutations. We applied GRID and Backrub to 10 high‐resolution (≤ 2.8 Å) crystal structures from the Protein Data Bank and measured the energy improvements obtained and the computation times required to achieve them. GRID resulted in energy improvements that were significantly better than those attained by Backrub while expending about the same amount of computational resources. GRID resulted in relaxed structures that had slightly higher backbone RMSDs compared to Backrub relative to the starting crystal structures. The average RMSD was 0.25 ± 0.02 Å for GRID versus 0.14 ± 0.04 Å for Backrub. These relatively minor deviations indicate that both algorithms generate structures that retain their original topologies, as expected given the nature of the algorithms. © 2012 Wiley Periodicals, Inc.     

Crystallization of tetrahedral patchy particles in silico

We investigate the competition between glass formation and crystallization of open tetrahedral structures for particles with tetrahedral patchy interactions. We analyze the outcome of such competition as a function of the potential parameters. Specifically, we focus on the separate roles played by the interaction range and the angular width of the patches, and show that open crystal structures (cubic and hexagonal diamond and their stacking hybrids) spontaneously form when the angular width is smaller than about 30°. Evaluating the temperature and density dependence of the chemical potential of the fluid and of the crystal phases, we find that adjusting the patch width affects the fluid and crystal in different ways. As a result of the different scaling, the driving force for spontaneous self-assembly rapidly grows as the fluid is undercooled for small-width patches, while it only grows slowly for large-width patches, in which case crystallization is pre-empted by dynamic arrest into a network glass.     

Molecular Alignment-Induced Chemically Patchy Uniaxial Nanoparticles and Their Applications in Anti-Counterfeiting and Self-Assembled Superstructures

We report an unusual strategy for synthesizing patchy nanoparticles (NPs) by controlling the orientation of the molecules that form the NPs. This is realized by synchronous polymerization and crystallization of liquid crystal (LC) monomers during scalable precipitation polymerization. The resulting NPs are cylinders with highly uniform shapes and have only a single LC domain. The patchy properties originate from the discrepancy of surface chemical compositions on flat and side surfaces and can be switched on and off by solvent. Extra colloidal blocks can be grown onto the patches, resulting in highly uniform triblock patchy dumbbells, which have integrated optical properties, and as demonstrated, show triple-mode optical authentication in anti-counterfeiting labels or patterns. We also demonstrate that the triblock patchy cylinders are attractive building blocks for long LC rods or porous colloidal materials through polymerization-induced self-assembly.     

Crystallization,Vitrification, and Gelation of Patchy Colloidal Particles

We present the phase diagrams for neutral patchy colloidal particles whose surface is decorated by different number of identical patches, where each patch serves as an associating site. The hard-core Lennard-Jones (LJ) potential and associating interaction are incorpo-rated into the free energies of patchy particles in phases of the fluid (F), random close packing (RCP), and face-centered-cubic (FCC) crystal. A rich phase structure of patchy particles with F-F, F-RCP, and F-FCC transitions can be observed. Meanwhile, the sol-gel transition (SGT) characterizing the connectivity of patchy particles is also investigated. It is shown that, depending on the number of patches and associating energy, the F-F transition might be metastable or stable with respect to the F-RCP and F-FCC transitions. Meanwhile, the critical temperatures, critical densities, triple points, and SGT can be significantly regulated by these factors.     

DOX: A new computational protocol for accurate prediction of the protein–ligand binding structures

Molecular docking techniques have now been widely used to predict the protein–ligand binding modes, especially when the structures of crystal complexes are not available. Most docking algorithms are able to effectively generate and rank a large number of probable binding poses. However, it is hard for them to accurately evaluate these poses and identify the most accurate binding structure. In this study, we first examined the performance of some docking programs, based on a testing set made of 15 crystal complexes with drug statins for the human 3‐hydroxy‐3‐methylglutaryl coenzyme A reductase (HMGR). We found that most of the top ranking HMGR–statin binding poses, predicted by the docking programs, were energetically unstable as revealed by the high theoretical‐level calculations, which were usually accompanied by the large deviations from the geometric parameters of the corresponding crystal binding structures. Subsequently, we proposed a new computational protocol, DOX, based on the joint use of molecular Docking, ONIOM, and eXtended ONIOM (XO) methods to predict the accurate binding structures for the protein–ligand complexes of interest. Our testing results demonstrate that the DOX protocol can efficiently predict accurate geometries for all 15 HMGR‐statin crystal complexes without exception. This study suggests a promising computational route, as an effective alternative to the experimental one, toward predicting the accurate binding structures, which is the prerequisite for all the deep understandings of the properties, functions, and mechanisms of the protein–ligand complexes. © 2015 Wiley Periodicals, Inc.     

ChemInform Abstract: Novel Structures and Superconductivities of Calcium—Lithium Alloys at High Pressures: A First‐Principles Study.

The crystal structures of Ca—Li alloys are investigated in the pressure range 0—200 GPa using a structure search method based on particle‐swarm optimization algorithms in combination with DFT calculations.     

Quantitative description of the self-assembly of patchy particles into chains and rings

We numerically study a simple fluid composed of particles having a hard-core repulsion complemented by two patchy attractive sites on the particle poles. An appropriate choice of the patch angular width allows for the formation of ring structures which, at low temperatures and low densities, compete with the growth of linear aggregates. The simplicity of the model makes it possible to compare simulation results and theoretical predictions based on the Wertheim perturbation theory, specialized to the case in which ring formation is allowed. Such a comparison offers a unique framework for establishing the quality of the analytic predictions. We find that the Wertheim theory describes remarkably well the simulation results.     

Flexible ligand docking using a robust evolutionary algorithm

A flexible ligand docking protocol based on evolutionary algorithms is investigated. The proposed approach incorporates family competition and adaptive rules to integrate decreasing‐based mutations and self‐adaptive mutations to act as global and local search strategies, respectively. The method is applied to a dihydrofolate reductase enzyme with the anticancer drug methotrexate and two analogues of antibacterial drug trimethoprim. Conformations and orientations closed to the crystallographically determined structures are obtained, as well as alternative structures with low energy. Numerical results indicate that the new approach is very robust. The docked lowest‐energy structures have root‐mean‐square derivations ranging from 0.67 to 1.96 Å with respect to the corresponding crystal structures. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 988–998, 2000     

Starting point to molecular design: efficient automated 3D model builder Key3D

Obtaining three-dimensional (3D) structures from structural formulae is a crucial process in molecular design. We have developed a new 3D model builder, Key3D, in which the simplified distance geometry technique and structure optimization based on the MMFF force field are combined. In an evaluation study using 598 crystal structures, the high performance and accuracy of Key3D were demonstrated. In the "flexible-fitting" test, which is focused on practical usefulness in the molecular design process, 88% of the Key3D structures acceptably reproduced the reference crystal structures (root-mean-square deviation <0.6 A) upon rotation of acyclic bonds. These results indicate that Key3D will be very effective in providing starting points for practical molecular design.     

Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field

This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC distributed computing framework includes a series of tightly integrated computer programs for generating the molecule's force field, sampling crystal structures using a distributed parallel genetic algorithm and local energy minimization of the structures followed by the classifying, sorting, and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Structure rationalization and topology prediction of two-distinct-component organic crystals: the role of volume fraction and interface topology

We consider here small-length-scale crystal structures with two clearly different molecular components (e.g., hydrophobic and hydrophilic). Using a perspective developed by studies on large-length-scale block copolymers and liquid crystals, we focus on the crystalline interface between the two components. We examine four types of two-component crystals: aromatic ammonium carboxylates, aromatic oligo(ethylene oxides), cyclohexylammonium carboxylates, and ether-thioether compounds. Of the 111 crystal structures found in the Cambridge Structure Database (CSD), 108 adopt one of the five generic topologies found in diblock copolymers: spheres, columns, perforated layers, layers, and bicontinuous structures. As in diblock copolymers, a key factor controlling the interfacial topology is shown to be the volume ratio of the two components. When the volume fraction of one component is less than 30% of the whole, more than five-sixths of the examined crystal structures are of columnar or spherical type. For volume fractions between 40 and 50% more than three-quarters are of lamellar or bicontinuous type. We use this model to predict the topologies of small-length-scale two-component crystals. We predict the crystal topolgies of six new crystal structures: three are predicted to be columnar, and the other three, lamellar or bicontinuous. The crystal structures of these systems were then determined by single-crystal X-ray methods. Five of the structures form in topologies consistent with the predictions: three in columns and two in layers. The remaining one forms as a perforated layer instead of the predicted columnar structure. Such predictive accuracy is consistent with the statistics of the CSD investigation.     

Recent progress on discovery and properties prediction of energy materials:Simple machine learning meets complex quantum chemistry

In nature,the properties of matter are ultimately governed by the electronic structures.Quantum chemistry(QC)at electronic level matches well with a few simple physical assumptions in solving simple problems.To date,machine learning(ML)algorithm has been migrated to this field to simplify calculations and improve fidelity.This review introduces the basic information on universal electron structures of emerging energy materials and ML algorithms involved in the prediction of material properties.Then,the structure-property relationships based on ML algorithm and QC theory are reviewed.Especially,the summary of recently reported applications on classifying crystal structure,modeling electronic structure,optimizing experimental method,and predicting performance is provided.Last,an outlook on ML assisted QC calculation towards identifying emerging energy materials is also presented.     

Examination of stabilty of molecular agglomerates in molecular crystals

We report an examination algorithm of stability of molecular aggregates based on the estimation of rigidity of intermolecular contacts in a crystal structure. The algorithm includes the intermolecular interaction energy calculation (in the atom-atom potential approximation) of a pair of molecules selected in the crystal structure. Further, the energy is minimized using a least-squares technique by varying the position and orientation of one of the molecules. The contact rigidity is quantitatively assessed by the minimized rms difference between the positions of the atoms in the original and optimized structures (Zorkii’s criterion). Every rigid contact revealed in the structure determines finite or infinite stable agglomerates. The paper presents the results of testing the computer program based on this algorithm with a number of real crystal structures previously determined by single crystal X-ray diffraction, and also the examples of the most common stable molecular agglomerates found with the aid of the program.     

Nucleation barriers in tetrahedral liquids spanning glassy and crystallizing regimes

Crystallization and vitrification of tetrahedral liquids are important both from a fundamental and a technological point of view. Here, we study via extensive umbrella sampling Monte Carlo computer simulations the nucleation barriers for a simple model for tetrahedral patchy particles in the regime where open tetrahedral crystal structures (namely, cubic and hexagonal diamond and their stacking hybrids) are thermodynamically stable. We show that by changing the angular bond width, it is possible to move from a glass-forming model to a readily crystallizing model. From the shape of the barrier we infer the role of surface tension in the formation of the crystalline clusters. Studying the trends of the nucleation barriers with the temperature and the patch width, we are able to identify an optimal value of the patch size that leads to easy nucleation. Finally, we find that the nucleation barrier is the same, within our numerical precision, for both diamond crystals and for their stacking forms.     

Theoretical investigations of candidate crystal structures for β-carbonic acid

Using multiple computational tools, we examine five candidate crystal structures for β-carbonic acid, a molecular crystal of environmental and astrophysical significance. These crystals comprise of hydrogen bonded molecules in either sheetlike or chainlike topologies. Gas phase quantum calculations, empirical force field based crystal structure search, and periodic density functional theory based calculations and finite temperature simulations of these crystals have been carried out. The infrared spectrum calculated from density functional theory based molecular dynamics simulations compares well with experimental data. Results suggest crystals with one-dimensional hydrogen bonding topologies (chainlike) to be more stable than those with two-dimensional (sheetlike) hydrogen bonding networks. We predict that these structures can be distinguished on the basis of their far infrared spectra.     

An evaluation of molecular models of the cytochrome P450 Streptomyces griseolus enzymes P450SU1 and P450SU2

Summary P450SU1 and P450SU2 are herbicide-inducible bacterial cytochrome P450 enzymes from Streptomyces griseolus. They have two of the highest sequence identities to camphor hydroxylase (P450cam from Pseudomonas putida), the cytochrome P450 with the first known crystal structure. We have built several models of these two proteins to investigate the variability in the structures that can occur from using different modeling protocols. We looked at variability due to alignment methods, backbone loop conformations and refinement methods. We have constructed two models for each protein using two alignment algorithms, and then an additional model using an identical alignment but different loop conformations for both buried and surface loops. The alignments used to build the models were created using the Needleman-Wunsch method, adapted for multiple sequences, and a manual method that utilized both a dotmatrix search matrix and the Needleman-Wunsch method. After constructing the initial models, several energy minimization methods were used to explore the variability in the final models caused by the choice of minimization techniques. Features of cytochrome P450cam and the cytochrome P450 superfamily, such as the ferredoxin binding site, the heme binding site and the substrate binding site were used to evaluate the validity of the models. Although the final structures were very similar between the models with different alignments, active-site residues were found to be dependent on the conformations of buried loops and early stages of energy minimization. We show which regions of the active site are the most dependent on the particular methods used, and which parts of the structures seem to be independent of the methods.     

Crystal assembly based on 3,5-bis(2′-benzimidazole) pyridine and its complexes

Imdazole, pyridine and their derivatives have been considered as excellent ligands in supramolecular self-assembly. In this paper, a ligand molecule 3,5-bis (2′-benzimidazole) pyridine (BBP) was prepared, and two different crystal architectures based on the ligand molecule were self-assembled by diffusion/solvothermal ways. Furthermore, several crystal architectures of several relative complexes were also successfully assembled. These crystal structures were well defined by X-ray diffractions. Structural resolutions indicated that, as building blocks, this bibenzimidazole pyridine molecules exhibited coordination varieties in constructing the crystal architectures based on its related complexes.