Parallelization of Crystal Calculation for Large-Scale Molecular Crystal Structure Analysis

Obata, Shigeaki; Goto, Hitoshi

doi:10.2751/jcac.9.8

Cited by 15 publications

(7 citation statements)

References 14 publications

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“…Energetic stability of α- and β-forms was estimated by performing calculations of intermolecular interaction energy (lattice energy) based on CONFLEX 8 Rev. C − with the MMFF94s force field (Table ). − The calculations were carried out on molecular structures determined from the respective single-crystal analysis after the optimization of only hydrogens in the crystals.…”

Section: Resultsmentioning

confidence: 99%

Selective Formation and SHG Intensity of Noncentrosymmetric and Centrosymmetric 1,1,2,2-Tetramethyl-1-(4-(N,N-dimethylamino)phenyl)-2-(2′-cyanophenyl)disilane Crystals under External Stimuli

et al. 2020

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In this paper, selective formation of noncentrosymmetric (Cc; α-crystal) and centrosymmetric (P2 1 /c; 1) was reported and both crystals were characterized by single-crystal X-ray diffraction (XRD) analysis, indicating multiple CH−π interactions created the crystal packing. The second harmonic generation (SHG) activity was attributed to the crystal packing and the orientation of dipole moment. Noncentrosymmetric crystal packing in a parallel manner exhibited SHG activity (intensity: 2.1 times vs urea). On the contrary, centrosymmetric structure in an antiparallel form showed no SHG activity (intensity: 0.0 times vs urea). As the calculated crystal energies of two polymorphs were very close to each other, the regulation of αand β-crystals is succeeded through supercooled liquid-to-crystal and crystal-to-crystal phase transitions, controlling the SHG activity. Powder XRD and solid-state 13 C NMR spectroscopy were applied for the qualitative analysis of αor β-polymorphs.

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Section: Resultsmentioning

confidence: 99%

Selective Formation and SHG Intensity of Noncentrosymmetric and Centrosymmetric 1,1,2,2-Tetramethyl-1-(4-(N,N-dimethylamino)phenyl)-2-(2′-cyanophenyl)disilane Crystals under External Stimuli

et al. 2020

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“…Considering the fact that only alkanes with C7–C9 main chains formed this type of inclusion crystals among the alkanes tested, only guest molecules that can stabilize the capsule structure by CH−π interactions with both the calixarene molecules, as seen in the inclusion crystal of heptane, seem to induce the structural change from the self-inclusion to the capsule type and form this type of inclusion crystals. This was supported by the calculation of crystal structures using CONFLEX − with the MMFF94S force field. The X-ray structure of 2 ·(Et 2 NH) 1.5 ·(heptane) 0.5 ·H 2 O was well reproduced by the minimum-energy structure calculated from the X-ray structure (Figure S6a).…”

Section: Resultsmentioning

confidence: 85%

“…Crystal structures were calculated by the spherical crystal model using CONFLEX 8. − The effective crystal radius was set to 40 Å. The space groups of the crystal structures of 2 ·Et 2 NH·(hexane) 0.5 and 2 ·(Et 2 NH) 1.5 ·(heptane) 0.5 ·H 2 O were converted to P 1 ( Z = 1) and P 2 1 2 1 2 1 ( Z = 4), respectively, and the structures were optimized with MMFF94S force field.…”

Section: Experimental Sectionmentioning

confidence: 99%

Inclusion of Alkanes with a Crystal Consisting of Exocavity Complexes of p-tert-Butylthiacalix[4]arene with Diethylamine: Extension of Guest Scope by Changing the Structure of Inclusion Crystals

Morohashi

Miyoshi

Sasaki

et al. 2019

Crystal Growth & Design

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A crystal of the exocavity complex of p-tert-butylthiacalix[4]arene (2) with diethylamine (2·Et2NH) includes alkanes that cannot be included in a crystal of compound 2 alone and produces two types of inclusion crystals. X-ray crystallographic analysis of inclusion crystals 2·Et2NH·(hexane)0.5 and 2·(Et2NH)1.5·(heptane)0.5·H2O, which were chosen as representatives of the two types, reveals that hexane and heptane are captured in a space surrounded by four self-inclusion dimers of the exocavity complex and in a capsule constructed by two exocavity complexes, respectively. The crystal of 2·Et2NH selectively includes hexane, heptane, and octane from mixtures with their branched isomers.

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“…The molecular clusters may first decompose in the reaction process of the thermal decomposition, since the reaction paths of the molecular complex show lower energetic barriers than the barriers of the monomolecular reaction paths . We believe that a new approach based on computational chemistry techniques , for crystal structure prediction is needed for determining the crystal structures of phases II and III. The development of the new approach and the structural analyses of phases II and III are in progress and will be reported later.…”

Section: Discussionmentioning

confidence: 99%

Phase Transition Analysis of 5-Aminotetrazole from Room Temperature to the Melting Point

et al. 2010

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The phase transition behavior of the 5-aminotetrazole (5-ATZ) crystal was studied in the range of room temperature to the melting point by the differential scanning calorimetry and powder X-ray diffraction techniques to investigate the dehydration phenomenon and to obtain the physical state of the high temperature phase. We found that 5-ATZ has one monohydrate crystal phase and three anhydrous crystal phases (I, II, and III) up to its melting point. The dehydration reaction of the monohydrate crystal occurred at about 50 °C. The dehydration enthalpy was 12.2 kcal/mol. The required activation energy was calculated using the Kissinger method, yielding the value of 27.1 kcal/mol. The phase transitions accompanying the sublimation from phase I to phase II and from phase II to phase III were observed during the prolonged heating at 175 °C. The dehydration phenomenon was also examined through quantum chemical calculations, and the calculated energy to eliminate a water molecule from the monohydrate crystal by the density functional theory at the M06/cc-pVTZ level basically agreed with the experimentally determined dehydration enthalpy.

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Parallelization of Crystal Calculation for Large-Scale Molecular Crystal Structure Analysis

Cited by 15 publications

References 14 publications

Selective Formation and SHG Intensity of Noncentrosymmetric and Centrosymmetric 1,1,2,2-Tetramethyl-1-(4-(N,N-dimethylamino)phenyl)-2-(2′-cyanophenyl)disilane Crystals under External Stimuli

Selective Formation and SHG Intensity of Noncentrosymmetric and Centrosymmetric 1,1,2,2-Tetramethyl-1-(4-(N,N-dimethylamino)phenyl)-2-(2′-cyanophenyl)disilane Crystals under External Stimuli

Inclusion of Alkanes with a Crystal Consisting of Exocavity Complexes of p-tert-Butylthiacalix[4]arene with Diethylamine: Extension of Guest Scope by Changing the Structure of Inclusion Crystals

Phase Transition Analysis of 5-Aminotetrazole from Room Temperature to the Melting Point

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