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Structural and vibrational studies have been carried out for the most stable conformer of 3,3′-ethane-1,2-diyl-bis-1,3,5-triazabicyclo[3.2.1]octane (ETABOC) at the DFT/B3LYP/6-31G(dp) level using the Gaussian 03 software. In light of the computed vibrational parameters, the observed IR Bolhmann bands for the C2V, C2, and Ci symmetrical structures of ETABOC have been analyzed. Hyperconjugative interaction was done by Natural Bond Orbital Analysis. Interpretation of hyperconjugative interaction involving the lone pairs on the bridgehead nitrogen atoms with the neighboring C–N and C–C bonds defines the conformational preference of the title compound. The recorded X-ray diffraction bond parameters were compared with theoretical values calculated at B3LYP/6-31G(d,p) and HF/6-31G(d,p) level of theory showed that ETABOC adopts a chair conformation and possesses an inversion center.
Synthesis, crystal structure and structure–property relations of strontium orthocarbonate, Sr2CO4
(2021)
Carbonates containing CO4 groups as building blocks have recently been discovered. A new orthocarbonate, Sr2CO4 is synthesized at 92 GPa and at a temperature of 2500 K. Its crystal structure was determined by in situ synchrotron single-crystal X-ray diffraction, selecting a grain from a polycrystalline sample. Strontium orthocarbonate crystallizes in the orthorhombic crystal system (space group Pnma) with CO4, SrO9 and SrO11 polyhedra as the main building blocks. It is isostructural to Ca2CO4. DFT calculations reproduce the experimental findings very well and have, therefore, been used to predict the equation of state, Raman and IR spectra, and to assist in the discussion of bonding in this compound.
Synthesis and crystal structure of 2-(2-hydroxyphenyl)-1,3-bis(4-methoxybenzyl)-1,3-diazinan-5-ol
(2022)
The redetermined structure of 2-(2-hydroxyphenyl)-1,3-bis(4-methoxybenzyl)-1,3-diazinan-5-ol, C26H30N2O4, at 173 K has orthorhombic (Pbca) symmetry. It was previously described by Bolte et al. [ Private Communication (refcode EWICEV). CCDC, Cambridge, England]. The title compound resulted from the condensation reaction between 1,3-bis{[(4-methoxyphenyl)methyl]amino}propan-2-ol and 2-hydroxybenzaldehyde in CH3OH. The structure exhibits disorder. One of the 4-methoxybenzyl groups, the hydroxy group bonded to the 1,3-diazinan ring, and the methyl group of the methoxy residue are disordered over two orientations, with occupancies of 0.807 (3)/0.193 (3), 0.642 (5)/0.358 (5), and 0.82 (4)/0.18 (4), respectively. The dihedral angles between the mean planes of the central 1,3-diazinan-5-ol and the 4-methoxyphenyl rings (both occupancy components of the disordered ring) are 88.65 (13), 85.79 (14) and 83.4 (7)°. The crystal packing is sustained by C—H...O and O—H...π interactions, giving rise to infinite chains running along the b-axis direction.
The title thiourea was synthesized by reaction of 3,4,5-trimethoxybenzoyl isothiocyante with 3-fluoroaniline. The 3,4,5-trimethoxybenzoyl isothiocyante was produced in situ by reaction of 3,4,5-trimethoxybenzoyl chloride with ammonium thiocyanate in dry acetonitrile. The structure was confirmed by the spectroscopic, elemental analysis and single crystal X-ray diffraction data. It crystallizes in the monoclinic space group P21/c with unit cell dimensions a = 13.0966(9), b = 16.6460(13), c = 7.8448(5), β = 106.721(5)°, V 1637.9(2) ų, Z = 4.
We have encountered two polymorphs of the title compound, C24H16B2OS2, both of which display almost the same unit-cell parameters. Compound (I) crystallizes in the non-centrosymmetric space group P21 with four molecules in the asymmetric unit. These molecules are related by pseudosymmetry. As a result, the space group looks like P21/c, but the structure cannot be refined successfully in that space group. Compound (II) on the other hand crystallizes in the centrosymmetric space group P21/c with only two molecules in the asymmetric unit. The crystals studied for (I) and (II) were both non-merohedral twins.
Solvent-free treatment of 1,3,6,8-tetraazatricyclo[4.3.1.13,8]undecano (TATU) with 4-chloro-3,5-dimethylphenol led to the formation of the title co-crystal, C7H14N4·2C8H9ClO. The asymmetric unit contains one aminal cage molecule and two phenol molecules linked via two O-H...N hydrogen bonds. In the aminal cage, the N-CH2-CH2-N unit is slightly distorted from a syn periplanar geometry. Aromatic [pi]-[pi] stacking between the benzene rings from two different neighbouring phenol molecules [centroid-centroid distance = 4.0570 (11) Å] consolidates the crystal packing.
Mechanism of Na+-dependent citrate transport from the structure of an asymmetrical CitS dimer
(2015)
The common human pathogen Salmonella enterica takes up citrate as a nutrient via the sodium symporter SeCitS. Uniquely, our 2.5 Å x-ray structure of the SeCitS dimer shows three different conformations of the active protomer. One protomer is in the outside-facing state. Two are in different inside-facing states. All three states resolve the substrates in their respective binding environments. Together with comprehensive functional studies on reconstituted proteoliposomes, the structures explain the transport mechanism in detail. Our results indicate a six-step process, with a rigid-body 31° rotation of a helix bundle that translocates the bound substrates by 16 Å across the membrane. Similar transport mechanisms may apply to a wide variety of related and unrelated secondary transporters, including important drug targets.
Iodo(triphenyl)silane
(2019)
The molecular structure of the title compound, C18H15ISi, which crystallizes in the space group C2/c, does not exhibit any unusual features. Two weak C—H⋯π interactions may help to consolidate the packing. The present structure is not isostructural with the known Ph3SiX (X = F, Cl or Br) compounds.
The title compound, C8H16N4·2C11H16O, was synthesized from the corresponding sterically crowded phenol by treatment with the aminal cage polyamine. Single-crystal X-ray diffraction structural analysis revealed the three-molecule aggregate to crystallize in the monoclinic space group P2/c with one half of a 1,3,6,8-tetraaztricyclo[4.4.1.13,8]dodecane (TATD) molecule and one 2-tert-butyl-4-methylphenol molecule per asymmetric unit. The crystal structure features intermolecular O—H...N and C—H...O hydrogen bonds, as well as intermolecular C—H...π interactions.
We have determined the crystal structures of two decachlorocyclopentasilanes, namely bis(tetra-n-butylammonium) dichloride decachlorocyclopentasilane dichloromethane disolvate, 2C16H36N+·2Cl−·Si5Cl10·2CH2Cl2, (I), and bis(tetraethylammonium) dichloride decachlorocyclopentasilane dichloromethane disolvate, 2C8H20N+·2Cl−·Si5Cl10·2CH2Cl2, (II), both of which crystallize with discrete cations, anions, and solvent molecules. In (I), the complete decachlorocyclopentasilane ring is generated by a crystallographic twofold rotation axis. In (II), one cation is located on a general position and the other two are disordered about centres of inversion. These are the first structures featuring the structural motif of a five-membered cyclopentasilane ring coordinated from both sides by a chloride ion. The extended structures of (I) and (II) feature numerous C—H⋯Cl interactions. In (II), the N atoms are located on centres of inversion and as a result, the ethylene chains are disordered over equally occupied orientations.
The asymmetric unit of the title compound, C18H18I2N2O2, consists of one half-molecule, completed by the application of inversion symmetry. The molecule adopts the typical structure for this class of bis-benxozazines, characterized by an anti orientation of the two benzoxazine rings around the central C—C bond. The oxazinic ring adopts a half-chair conformation. In the crystal, molecules are linked by C—I⋯N short contacts [I⋯N = 3.378 (2) Å], generating layers lying parallel to the bc plane.
Large crystals of the methyl ester of the N-a-benzyloxycarbonyl protected Ala-Phe dipeptide (Z-AF-OMe) were obtained after the very slow evaporation of a solution of the corresponding carboxylic acid (Z-AF-OH) in methanol containing an excess of HCl. The structure was confirmed by single crystal X-ray diffraction data. It crystallizes in the orthorhombic space group P212121 with unit cell dimensions a = 5.0655(6) Å, b = 8.4614(8) Å, c = 46.856(5) Å, V = 2008.3(4) Å3, Z = 4. In the crystal, the molecules form hydrogen bonded chains running along the a axis of the unit cell. Other secondary interactions are also discussed.
The title compound, C21H26Cl2N2O2, was prepared in a solvent-free microwave-assisted synthesis, and crystallizes in the orthorhombic space group Pna21. The imidazolidine ring adopts an envelope conformation and its mean plane is almost perpendicular to the two pendant aromatic rings [dihedral angles = 84.61 (9) and 86.54 (9)°]. The molecular structure shows the presence of two intramolecular O—H⋯N hydrogen bonds between the phenolic hydroxy groups and imidazolidine N atoms. The two 3-chloro-6-hydroxy-2,4-dimethylbenzyl groups are located in a cis orientation with respect to the imidazolidine fragment. As a result, the lone pairs of electrons on the N atoms are presumed to be disposed in a syn conformation. This is therefore the first example of an exception to the `rabbit-ears' effect in such 2,2′-[imidazolidine-1,3-diylbis(methylene)]diphenol derivatives.
The asymmetric unit of the title co-crystalline adduct, 1,3,6,8-tetraazatricyclo[4.4.1.13,8]dodecane (TATD)–4-iodophenol (1/2), C8H16N4·2C6H5IO, comprises a half molecule of the aminal cage polyamine plus a 4-iodophenol molecule. A twofold rotation axis generates the other half of the adduct. The components are linked by two intermolecular O—H⋯N hydrogen bonds. The adducts are further linked into a three-dimensional framework structure by a combination of N⋯I halogen bonds and weak non-conventional C—H⋯O and C—H⋯I hydrogen bonds.
In the crystal of the title co-crystalline adduct, C8H16N4·C8H9ClO, (I), prepared by solid-state reaction, the molecules are linked by intermolecular O—H⋯N hydrogen bonds, forming a D motif. The azaadamantane structure in (I) is slightly distorted, with N—CH2—CH2—N torsion angles of 10.4 (3) and −9.0 (3)°. These values differ slightly from the corresponding torsion angles in the free aminal cage (0.0°) and in related co-crystalline adducts, which are not far from a planar geometry and consistent with a D2d molecular symmetry in the tetraazatricyclo structure. The structures also differ in that there is a slight elongation of the N—C bond lengths about the N atom that accepts the hydrogen bond in (I) compared with the other N—C bond lengths. In the crystal, the two molecules are not only linked by a classical O—H⋯N hydrogen bond but are further connected by weak C—H⋯π interactions, forming a two-dimensional supramolecular network parallel to the bc plane.
The structure of the 1:2 co-crystalline adduct C8H16N4·2C6H5BrO, (I), from the solid-state reaction of 1,3,6,8-tetraazatricyclo[4.4.1.13,8]dodecane (TATD) and 4-bromophenol, has been determined. The asymmetric unit of the title co-crystalline adduct comprises a half molecule of aminal cage polyamine plus a 4-bromophenol molecule. A twofold rotation axis generates the other half of the adduct. The primary inter-species association in the title compound is through two intermolecular O—H⋯N hydrogen bonds. In the crystal, the adducts are linked by weak non-conventional C—H⋯O and C—H⋯Br hydrogen bonds, giving a two-dimensional supramolecular structure parallel to the bc plane.
In the title compound, C7H14N4·2C6H5ClO, which crystallized with two crystallographically independent 4-chlorophenol molecules and one 1,3,6,8-tetraazatricyclo[4.3.1.13,8]undecane (TATU) molecule in the asymmetric unit, the independent components are linked by two O-H...N hydrogen bonds. The hydrogen-bond acceptor sites are two non-equivalent N atoms from the aminal cage structure, and the tricyclic system distorts by changing the C-N bond lengths. In the crystal, these hydrogen-bonded aggregates are linked into chains along the c axis by C-H...N hydrogen bonds. The crystal structure also features C-H...[pi] contacts.
In the title ternary co-crystalline adduct, C7H14N4·2C6H5NO3, molecules are linked by two intermolecular O—H⋯N hydrogen bonds, forming a tricomponent aggregates in the asymmetric unit. The hydrogen-bond formation to one of the N atoms is enough to induce structural stereoelectronic effects in the normal donor→acceptor direction. In the title adduct, the two independent nitrophenol molecules are essentially planar, with maximum deviations of 0.0157 (13) and 0.0039 (13) Å. The dihedral angles between the planes of the nitro group and the attached benzene rings are 4.04 (17) and 5.79 (17)°. In the crystal, aggregates are connected by C—H⋯O hydrogen bonds, forming a supramolecular dimer enclosing an R66(32) ring motif. Additional C—H⋯O intermolecular hydrogen-bonding interactions form a second supramolecular inversion dimer with an R22(10) motif. These units are linked via C—H⋯O and C—H⋯N hydrogen bonds, forming a three-dimensional network.
In the title salt, [Ag(C27H36N2)2]Cl·C4H8O, the AgI atom is coordinated by two 1,3-bis(2,6-dimethylphenyl)imidazol-2-ylidene ligands. The imidazole rings are inclined to one another by 46.69 (13)° and the benzene rings in each ligand are almost normal to the imdazole ring to which they are attached, with dihedral angles varying from 82.39 (13) to 88.27 (12)°. There are C—H⋯π interactions present in the cation, involving the two ligands, and the solvent molecule is linked to the cation via a C—H⋯O hydrogen bond. In the crystal, molecules are linked by trifurcated C—H⋯(Cl,Cl,Cl) hydrogen bonds, forming slabs parallel to (101). One isopropyl group is disordered over two sets of sites with an occupancy ratio of 0.447 (17):0.553 (17) and the THF molecule is disordered over two positions with an occupancy ratio of 0.589 (6):0.411 (6).
The title compound, di-μ3-chlorido-tetra-μ2-chlorido-tetrakis(diethyl ether-κO)bis(1,1-dimethylethyl)tetramagnesium, [Mg4(C4H9)2Cl6(C4H10O)4], features an Mg4Cl6 open-cube cluster. The two four-coordinate Mg2+ ions show an almost tetrahedral coordination, whereas the two six-coordinate Mg2+ ions have their ligands in an octahedral environment. The Mg—Cl bond lengths differ depending on the coordination number (2 or 3) of the bridging μ-Cl− ligands. There are few comparable structures deposited in the Cambridge Structural Database.