scholarly journals 4-Phenylnaphtho[2,3-c]furan-1(3H)-one, 9-Phenylnaphtho[2,3-c]furan-1(3H)-one and 3a,4-Dihydro-9-phenylnaphtho[2,3-c]furan-1(3H)-one Crystal Structures

Crystals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 857
Author(s):  
Nabyl Merbouh ◽  
Simon Cassegrain ◽  
Wen Zhou
Keyword(s):  
Crystal Structures ◽  
Unit Cell ◽  
Geometrical Parameters ◽  
Type I ◽  
Type Ii ◽  
Asymmetric Unit ◽  
Asymmetric Unit Cell

The crystal structures are reported for two unsubstituted arylnaphthalene lactones, 4-phenylnaphtho[2,3-c]furan-1(3H)-one (2), 9-phenylnaphtho[2,3-c]furan-1(3H)-one (3) and a non-aromatic dihydro arylnaphthene lactone, 3a,4-dihydro-9-phenylnaphtho[2,3-c]furan-1(3H)-one (5). There are only minor differences in the geometrical parameters of these structures. However, in certain cases, both isomers of arylnaphthalene lactones (termed Type I and Type II) were found in the same asymmetric unit cell.

scholarly journals aCHESYM: standardized placement of macromolecular models in the unit cell

2014 ◽  
Vol 70 (a1) ◽  
pp. C336-C336
Author(s):  
Marcin Kowiel ◽  
Mariusz Jaskolski ◽  
Andrzej Gzella ◽  
Zbigniew Dauter
Keyword(s):  
Crystal Structures ◽  
Molecular Model ◽  
Unit Cell ◽  
Asymmetric Unit ◽  
Space Groups ◽  
Reflection Data ◽  
Interpretation Errors ◽  
Structure Solution ◽  
Asymmetric Unit Cell ◽  
Atomic Coordinates

Unique choice of the unit cell and the asymmetric unit are well defined and described in the International Tables for Crystallography vol. A. Unfortunately, the placement of molecules within the unit cell is not standardized. Since structure solution programs often use random numbers in their algorithms, the selected set of atomic coordinates may be different even with successive runs of the same program. Although formally correct, an arbitrary choice of molecular placement within the unit cell is confusing and may lead to interpretation errors [1]. With the use of the anti-Cheshire unit cell introduced by Dauter [2], for all space groups without inversion symmetry, it is possible to transform the molecular model such that its center of gravity falls within the anti-Cheshire asymmetric unit cell. It means that for macromolecular crystal structures it should be possible to standardize the placement of the molecules within the unit cell. In consequence, it should be easier for crystallographers and non-crystallographers to compare similar or related crystal structures. An implementation of the anti-Cheshire concept has been programmed in Python as a web service, aCHESYM. The aCHESYM program takes a PDB file as input and transforms the macromolecular model into the desired anti-Cheshire region. The program can also handle structure factor CIF files if the transformation used requires reindexing of the reflection data. The unit cell, coordinates and displacement parameters of all atoms after transformation are saved in a new PDB file. All the calculated transformations are reversible, so there is no danger of data loss. Moreover, the program helps the user to find the most compact assembly of the molecules (chains) in the structure when there are several chains in the asymmetric unit.

scholarly journals Crystal structures of aconitase X enzymes from bacteria and archaea provide insights into the molecular evolution of the aconitase superfamily

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Seiya Watanabe ◽  
Yohsuke Murase ◽  
Yasunori Watanabe ◽  
Yasuhiro Sakurai ◽  
Kunihiko Tajima
Keyword(s):  
Molecular Evolution ◽  
Agrobacterium Tumefaciens ◽  
Crystal Structures ◽  
Epr Spectroscopy ◽  
Binding Sites ◽  
Active Sites ◽  
Type I ◽  
Type Ii ◽  
Thermococcus Kodakarensis ◽  
Evolutionary Scenario

AbstractAconitase superfamily members catalyze the homologous isomerization of specific substrates by sequential dehydration and hydration and contain a [4Fe-4S] cluster. However, monomeric and heterodimeric types of function unknown aconitase X (AcnX) have recently been characterized as a cis-3-hydroxy-L-proline dehydratase (AcnXType-I) and mevalonate 5-phosphate dehydratase (AcnXType-II), respectively. We herein elucidated the crystal structures of AcnXType-I from Agrobacterium tumefaciens (AtAcnX) and AcnXType-II from Thermococcus kodakarensis (TkAcnX) without a ligand and in complex with substrates. AtAcnX and TkAcnX contained the [2Fe-2S] and [3Fe-4S] clusters, respectively, conforming to UV and EPR spectroscopy analyses. The binding sites of the [Fe-S] cluster and substrate were clearlydifferent from those that were completely conserved in other aconitase enzymes; however, theoverall structural frameworks and locations of active sites were partially similar to each other.These results provide novel insights into the evolutionary scenario of the aconitase superfamilybased on the recruitment hypothesis.

scholarly journals Structural Transformations in Crystals Induced by Radiation and Pressure. Part 7. Molecular and Crystal Geometries as Factors Deciding about Photochemical Reactivity under Ambient and High Pressures

Crystals ◽  
2018 ◽  
Vol 8 (7) ◽  
pp. 299 ◽  
Author(s):  
Krzysztof Konieczny ◽  
Arkadiusz Ciesielski ◽  
Julia Bąkowicz ◽  
Tomasz Galica ◽  
Ilona Turowska-Tyrk
Keyword(s):  
High Pressures ◽  
Unit Cell ◽  
Geometrical Parameters ◽  
Isopropyl Group ◽  
Unit Cell Parameters ◽  
Photochemical Reactivity ◽  
Space Group ◽  
Cell Parameters ◽  
Pressure Part ◽  
Asymmetric Unit Cell

We studied the photochemical reactivity of salts of 4-(2,4,6-triisopropylbenzoyl)benzoic acid with propane-1,2-diamine (1), methanamine (2), cyclohexanamine (3), and morpholine (4), for compounds (1), (3), and (4) at 0.1 MPa and for compounds (1) and (2) at 1.3 GPa and 1.0 GPa, respectively. The changes in the values of the unit cell parameters after UV irradiation and the values of the intramolecular geometrical parameters indicated the possibility of the occurrence of the Norrish–Yang reaction in the case of all the compounds. The analysis of the intramolecular geometry and free spaces revealed which o-isopropyl group takes part in the reaction. For (1), the same o-isopropyl group should be reactive at ambient and high pressures. In the case of (2), high pressure caused the phase transition from the space group I2/a with one molecule in the asymmetric unit cell to the space group P1¯ with two asymmetric molecules. The analysis of voids indicated that the Norrish–Yang reaction is less probable for one of the two molecules. For the other molecule, the intramolecular geometrical parameters showed that except for the Norrish–Yang reaction, the concurrent reaction leading to the formation of a five-membered ring can also proceed. In (3), both o-isopropyl groups are able to react; however, the bigger volume of a void near 2-isopropyl may be the factor determining the reactivity. For (4), only one o-isopropyl should be reactive.

The theory of the crystallography of deformation twinning

1965 ◽  
Vol 288 (1413) ◽  
pp. 240-255 ◽  
Keyword(s):  
Crystal Structures ◽  
Deformation Twinning ◽  
Type I ◽  
Lattice Structures ◽  
Type Ii ◽  
Orientation Relationships ◽  
Tensor Calculus ◽  
Moving Interface ◽  
Twinning Shear ◽  
Crystallographic Characteristics

The crystallographic characteristics of deformation twinning are derived by considering the atomic movements which occur at the moving interface as a twin propagates. This is facilitated by making use of the notation of the tensor calculus, and general expressions, valid for all crystal structures, are obtained giving the magnitude of the twinning shear and relating the twinning elements for both type I and type II twinning. The atomic shuffles, which in general must accompany the twinning shear in both single and multiple lattice structures, are examined in detail and expressions are derived for their magnitudes and directions for the cases of the four classical orientation relationships associated with deformation twinning. The use of these expressions in predicting operative twinning modes is described and the relations between this theory and other recent theories of the crystallography of deformation twinning are discussed.

scholarly journals Plasmonic terahertz detection by a double-grating-gate field-effect transistor structure with an asymmetric unit cell

2011 ◽  
Vol 99 (24) ◽  
pp. 243504 ◽  
Author(s):  
V. V. Popov ◽  
D. V. Fateev ◽  
T. Otsuji ◽  
Y. M. Meziani ◽  
D. Coquillat ◽  
...  
Keyword(s):  
Field Effect ◽  
Field Effect Transistor ◽  
Unit Cell ◽  
Asymmetric Unit ◽  
Transistor Structure ◽  
Terahertz Detection ◽  
Effect Transistor ◽  
Asymmetric Unit Cell

scholarly journals Acemetacin cocrystal structures by powder X-ray diffraction

IUCrJ ◽  
2017 ◽  
Vol 4 (3) ◽  
pp. 206-214 ◽  
Author(s):  
Geetha Bolla ◽  
Vladimir Chernyshev ◽  
Ashwini Nangia
Keyword(s):  
Crystal Structures ◽  
Molecular Electrostatic Potential ◽  
Acid Group ◽  
Mutual Orientation ◽  
Type I ◽  
Type Ii ◽  
Melt Crystallization ◽  
X Ray Diffraction ◽  
X Ray ◽  
Hydrogen Bond Interactions

Cocrystals of acemetacin drug (ACM) with nicotinamide (NAM),p-aminobenzoic acid (PABA), valerolactam (VLM) and 2-pyridone (2HP) were prepared by melt crystallization and their X-ray crystal structures determined by high-resolution powder X-ray diffraction. The powerful technique of structure determination from powder data (SDPD) provided details of molecular packing and hydrogen bonding in pharmaceutical cocrystals of acemetacin. ACM–NAM occurs in anhydrate and hydrate forms, whereas the other structures crystallized in a single crystalline form. The carboxylic acid group of ACM forms theacid–amide dimer three-point synthonR32(9)R22(8)R32(9) with three differentsynamides (VLM, 2HP and caprolactam). The conformations of the ACM molecule observed in the crystal structures differ mainly in the mutual orientation of chlorobenzene fragment and the neighboring methyl group, beinganti(type I) orsyn(type II). ACM hydrate, ACM—NAM, ACM–NAM-hydrate and the piperazine salt of ACM exhibit the type I conformation, whereas ACM polymorphs and other cocrystals adopt the ACM type II conformation. Hydrogen-bond interactions in all the crystal structures were quantified by calculating their molecular electrostatic potential (MEP) surfaces. Hirshfeld surface analysis of the cocrystal surfaces shows that about 50% of the contribution is due to a combination of strong and weak O...H, N...H, Cl...H and C...H interactions. The physicochemical properties of these cocrystals are under study.

Laser generation on weak modes in graphene structure with asymmetric unit cell

2021 ◽  
Author(s):  
K.V. Mashinsky ◽  
V.V. Popov ◽  
D.V. Fateev
Keyword(s):  
Single Layer ◽  
Resonance Mode ◽  
Unit Cell ◽  
Single Layer Graphene ◽  
Laser Generation ◽  
Asymmetric Unit ◽  
Plasmonic Resonance ◽  
Layer Graphene ◽  
Asymmetric Unit Cell ◽  
Plasmon Resonance Mode

Problem formulating. Lasing on strong («radiative») plasmon resonance mode in graphene structure with dual grating gate with asymmetric unit cell requires strong gain. It is possible to achieve lasing in a weak ("non-radiative") mode at a lower gain rate. Goal. Theoretical study of laser generation on weak plasmonic resonance mode in single layer graphene structure screened by dual grating gate with asymmetric unit cell. Result. Laser generation on weak plasmonic resonance mode in single layer graphene structure screened by dual grating gate with asymmetric unit cell is reached. Excitation of a weak plasmon resonance mode requires less gain than excitation of a radiative one. Practical meaning. Results can be used to create sources of terahertz waves.

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