A5006061942- X-ray Diffraction in Crystallography
- Crystallography and molecular interactions
- Crystallization and Solubility Studies
- Organic Electronics and Photovoltaics
- Computational Drug Discovery Methods
- Molecular Junctions and Nanostructures
- Machine Learning in Materials Science
- Thermal and Kinetic Analysis
- Molecular spectroscopy and chirality
- Energetic Materials and Combustion
- Chemical Thermodynamics and Molecular Structure
- bioluminescence and chemiluminescence research
- Luminescence and Fluorescent Materials
- Enzyme Structure and Function
- Natural product bioactivities and synthesis
- Carbon Nanotubes in Composites
- Catalysis and Oxidation Reactions
- Microstructure and Mechanical Properties of Steels
- Pharmacological Effects of Natural Compounds
- Perovskite Materials and Applications
- High-Velocity Impact and Material Behavior
- Solid-state spectroscopy and crystallography
- Synthesis and Properties of Aromatic Compounds
- Synthesis of β-Lactam Compounds
- Inflammatory mediators and NSAID effects
Toyohashi University of Technology
2013-2024
National Institute of Advanced Industrial Science and Technology
2010-2013
University of Edinburgh
2008
University of Göttingen
2008
University of Southampton
2008
The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, polymorphic former drug candidate, chloride salt hydrate, co-crystal and bulky flexible molecule. This seen substantial growth in the number participants, broad range giving unique insight into state art field. Significant progress treating molecules, usage hierarchical approaches to ranking structures, application density-functional...
A seventh blind test of crystal structure prediction was organized by the Cambridge Crystallographic Data Centre featuring seven target systems varying complexity: a silicon and iodine-containing molecule, copper coordination complex, near-rigid cocrystal, polymorphic small agrochemical, highly flexible drug candidate, morpholine salt. In this first two parts focusing on generation methods, many (CSP) methods performed well for but agrochemical compound, successfully reproducing...
A seventh blind test of crystal structure prediction has been organized by the Cambridge Crystallographic Data Centre. The results are presented in two parts, with this second part focusing on methods for ranking structures order stability. exercise involved standardized sets seeded from a range generation methods. Participants 22 groups applied several periodic DFT-D methods, machine learned potentials, force fields derived empirical data or quantum chemical calculations, and various...
We theoretically investigate the energetically favorable orientation of poly(3-hexylthiophene) (P3HT) on self-assembled monolayers (SAMs) using molecular dynamics simulations. The effects different kinds SAMs are studied by examining a CH3-terminated SAM with hydrophobic surface and an NH2-terminated hydrophilic surface. also dynamic behavior systems limited numbers P3HT molecules surfaces. important factors in controlling elucidated from these results. demonstrate that edge-on is more than...
Prediction of material properties newly designed molecules is a long-term goal in organic electronics. In general, it difficult problem, because the are dominated by unknown packing structure. We present practical method to obtain charge transport single crystals, without use experimental single-crystal data. As demonstration, we employ promising molecule C
Anhydrous 5-aminotetrazole (5-amino-1H-tetrazole, 5-ATZ) is an energetic material that produces a large amount of nitrogen gas by thermal decomposition and often used as generator agent. Although it widely air bag inflator, its crystal structure has not been determined yet. Thus, we performed powder X-ray diffraction experiment, Rietveld analysis, the density functional theory calculation to investigate be orthorhombic P212121 with 1H-form molecule. We also investigated high-pressure...
We examined the characteristics and behaviors of carbon nanotube (CNT) surfactants complexes in an aqueous environment using computational techniques to elucidate effects used disperse CNTs toxicity studies CNTs. found that cohesive energy per one adsorbed surfactant molecule CNT–surfactants complex depends on type amount molecules CNT surface. The CNT–dipalmitoyl phosphatidylcoline (DPPC; a primary component human lung surfactants) was more energetically stable than CNT–Tween 80 (an...
We theoretically predict crystal structures and molecular arrangements for rubrene molecule using CONFLEX program compare them with the experimental ones. The most, second-most, fourth-most stable predicted show good agreement triclinic, orthorhombic, monoclinic polymorphs of rubrene, respectively. change in conformation is also between crystalline gas phases: tetracene backbone takes flat phase as observed structure. Meanwhile, it twisted phase. theoretical prediction method used this work...
We developed a master-worker type parallel algorithm for allocating tasks of crystal structure optimizations to distributed compute nodes, in order improve performance simulations predictions. The experiments were demonstrated on TUT-ADSIM supercomputer system (HITACHI HA8000-tc/HT210). experimental results show that our could achieve speed-ups 214 and 179 times using 256 processor cores predictions structures 3-aza-bicyclo(3.3.1)nonane-2,4-dione 2-diazo-3,5-cyclohexadiene-1-one,...
計算化学技術による結晶構造解析は、機能材料や医薬品の開発など広範囲な研究分野において重要な役割が期待されている。一般に結晶計算では、計算対象となる結晶モデルを大きくするとより実在系に近づき、より高精度な計算結果を期待できるが、それに伴う分子間相互作用の計算量は爆発的に増加する。このため、利用可能な計算機の演算性能に応じて計算できる結晶モデルの大きさは制限されてしまう。そこで本研究では、我々が開発してきた結晶構造最適化プログラムKESSHOUの結晶計算法を、汎用分子計算プログラムCONFLEXに導入したCONFLEX/KESSHOUにおいて、分子間相互作用の計算部分に並列分散処理技術を適用することによって、結晶構造のエネルギー計算や構造最適化の効率的な高速化を実現した。また、結晶モデルの大規模化に伴う分子間相互作用エネルギーの加算誤差を最小限に抑えるため、Kahanの加算アルゴリズムを適用した。並列分散計算環境を利用して、アスピリン結晶の構造最適化を行なったところ、その並列化効率が90%以上に達することを確認した。また、結晶モデルの大きさ(有効結晶半径)に依存した結晶エネルギー揺ら...
本研究では,アスピリン結晶の配座多形の可能性を調べるため,効率的な配座空間探索が可能な分子計算プログラムCONFLEXに,結晶計算プログラムKESSHOUの機能を導入したCONFLEX/KESSOUを用いて,立体配座解析と配座多形解析を行った.MMFF94を用いてアスピリン単分子の徹底的な配座探索を行ったところ,10種類の配座異性体を見つけた.得られた配座異性体をMM3,およびab initio法(MP2/6-31+G**)で構造最適化を行ったところ,MMFF94構造はMP2構造とよく一致するが,MM3構造は側鎖のねじれ角が異なっていた.また,配座エネルギーについて,MMFF94はMP2よりも高く,MM3は低く評価する傾向にあった.一方,X線結晶構造を結晶格子最適化(LOPT: Lattice Optimization)法で最適化したところ,MM3が極めて高い精度で既知のアスピリン結晶の構造を再現できることがわかった.さらに,20種類の配座多形を解析したところ,...
Abstract Heating crystal samples of 9,10-diphenylanthracene endoperoxide (1) and its deuterated derivative (1-d10) to 200 °C led singlet-oxygen chemiluminescence (CL) from the mixtures crystalline molten states. To understand events in heated samples, reactions 1 1-d10 crystals were investigated by powder X-ray diffraction measurements thermal analyses. The used obtained a mixture ethyl acetate (EA) n-hexane contained EA. Other slow recrystallization with same solvents had solvent-free...
The phase transition behavior of the 5-aminotetrazole (5-ATZ) crystal was studied in range room temperature to melting point by differential scanning calorimetry and powder X-ray diffraction techniques investigate dehydration phenomenon obtain physical state high phase. We found that 5-ATZ has one monohydrate three anhydrous phases (I, II, III) up its point. reaction occurred at about 50 °C. enthalpy 12.2 kcal/mol. required activation energy calculated using Kissinger method, yielding value...
Abstract Computational approaches to elucidate the phase transitions in lanthanide complexes will support understanding their electronic structure changes by weak stimuli such as gas adsorptions. There are no examples molecular models of Ln for defining parameters, due various shapes with unexpected coordination numbers resulting different packings ions. Here, we succeeded determining force field parameters (van der Waals; vdW = Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er and Tm; torsion ligand)...
We studied the effects of regioregularity poly(3-hexylthiophene) (P3HT) molecules on order molecular arrangement in P3HT lamellar structure using dynamics simulations. found that RR-P3HT molecule shows aligned ordered structure, while RRa-P3HT produces disorders π-π interchain stacking due to formation disordered network intermolecular interactions between alkyl side chains molecules. gains more stabilization energy with respect than former system. The is considered be controlled by chains.
The chemiluminescence (CL) feature and reactivity of the aromatic endoperoxide 9-phenyl-10-(2-phenylethynyl)anthracene (PPEA-O2) were investigated in crystalline state. For this, PPEA-O2 crystals prepared using dichloromethane n-hexane. These exhibited an α-phase structure containing n-hexane as a crystal solvent. nonperoxidic anthracene (i.e., PPEA) was also confirmed. After optimizing heating conditions to 120 °C for thermolytic reaction while maintaining solid state, its CL characteristic...
Force field parameters around Au atom that have been lacking in standard parameter set of the MMFF94s were temporarily determined to reproduce molecular crystal structure phenyl(phenylisocyanide)gold(I) complex by classical force calculations. It was confirmed two polymorphic forms optimized CONFLEX software with these are good agreement experimental structures. Application other derivatives also gives results but Au..Au distances some structures longer than those experimental. Therefore,...
Abstract Using molecular dynamics simulations, we theoretically investigate the orientation of poly(3-hexylthiophene) (P3HT) on hydrophobic and hydrophilic self-assembled monolayers (SAMs). In particular, study effects roughness at SAM surfaces P3HT molecules put surface. The energetically preferable does not change by introduced. induces more frequent transition between edge-on face-on orientations, when a small number are SAM. Keywords: Molecular simulationmolecular orientationorganic...
Sessions3 1 corrected rather easily by changing the residue name, deleting surplus atoms or editing LINK CONECT records.Other problems, however, require more sophisticated methods to fix them.To e.g.stereochemistry have be relocated.In some instances, e.g. when wrong stereochemistry is involved in glycosidic linkages, entire residues might rearranged, which involves refinement of 3d structure.Here, we present an approach combine a tool for carbohydrate validation (pdb-care [3],...
Crystal structure prediction(CSP)is one of the important studies what are expected computational chemistry and CSP methods have steadily advanced against a background an improvement performance, many academic interests, needs from industry. The goal is to propose possible crystal structures target molecule based only on its structural formula. In this article, short introduction current discussions remaining obstacles in described. We also present our prediction method including calculation...
Crystal structure prediction is one of the useful theoretical tools for designing and synthesizing new materials in pharmaceutical therapeutics industrial electronics. Furthermore, can provide immense valuable scientific knowledge on a crystal growth, polymorphism many properties organic molecular crystals. Therefore, we have started development high-speed high-accurate method structures [1,2]. In this work, demonstrate predictions fourteen target molecules that were used international...
Computational techniques for crystal structure prediction (CSP) of organic molecules have received much attention as a useful theoretical tool designing new materials with desirable properties in pharmaceutical and functional material industries been steadily established by many efforts.The Cambridge Crystallographic Data Center has periodically organized international scientific workshop on predicting structures that is known CSP blind test promoting development improvement the...