Crystal Packing Modes Research Articles

Synthesis and X-Ray Crystal Structure of the First Pure and Air-Stable Salt of Peroxymonosulphuric Acid: (Ph)4PHSO5

In this paper we describe the synthesis of tetraphenylphosphonium peroxymonosulphate, its crystal structure and packing mode. The asymmetric unit accomodates two independent molecules of the monopersulphate anion, which are held together by hydrogen bonds. In the packing mode, rows of such dimers are surrounded by four rows of tetraphenyl cations. The consequence is that the highly water sensitive HSO5¯ anions are segregated inside hydrophobic channels composed by the lipophilic cations. This circumstance presumably accounts for the exceptional stability of the title compound.

Channel-Type Crystal Packing in the Very Rare Space Group P4212 with Z' = 3/4: Crystal Structure of the Complex γ-Cyclodextrin–Methanol–n-Hydrate

The crystal structure of the title compound is discussed with focus on its unusual crystal packing mode. The γ-cyclodextrin molecules stack in columns which have internal channels and additional large channels are formed between the columns. Both types of channels are so wide that more or less free diffusion of water and small guest molecules is possible, preventing characterization of the solvent and guest arrangements. Although the space group P4212 (no. 90) and the unit-cell content Z′ = 3\over 4 are extremely rare in general, this is the favorite crystal packing arrangement of γ-cyclodextrin inclusion complexes. This space group has not been observed as yet for other purely organic compounds.

Structural Variability and New Intermolecular Interactions of Z-DNA in Crystals of d(pCpGpCpGpCpG)

We have determined the single crystal x-ray structure of the synthetic DNA hexamer d(pCpGpCpGpCpG) in two different crystal forms. The hexamer pCGCGCG has the Z-DNA conformation and in both cases the asymmetric unit contains more than one Z-DNA duplex. Crystals belong to the space group C2221 with a=69.73, b=52.63, and c=26.21Å, and to the space group P21 with a=49.87, b=41.26, c=21.91Å, and γ=97.12°. Both crystals show new crystal packing modes. The molecules also show striking new features when compared with previously determined Z-DNA structures: 1) the bases in one duplex have a large inclination with respect to the helical axis, which alters the overall shape of the molecule. 2) Some cytosine nitrogens interact by hydrogen bonding with phosphates in neighbor molecules. Similar base-phosphate interactions had been previously detected in some B-DNA crystals. 3) Basepair stacking between the ends of neighbor molecules is variable and no helical continuity is maintained between contiguous hexamer duplexes.

The Role of Water-Solvation in the Optical Resolution of Dl-Leucine with (S)-(−)-1-Phenylethanesulfonic Acid. Characterization and X-Ray Crystal Structures of Their Diastereomeric Salts

Abstract In the optical resolution by diasteromeric salt formation of Dl-leucine with (S)-(−)-1-phenylethanesulfonic acid (PES), the less-soluble l-Leu·(−)-PES salt preferentially crystallized from acetonitrile–methanol and, in contrast, the same resolution from acetonitrile–water afforded the monohydrated d-salt [d-Leu·(−)-PES·H2O]. The role of the water of crystallization formed during this resolution system has been explored through a comparison of the crystalline characteristics of d-, monohydrated d-, and l-Leu·(−)-PES by thermoanalysis (DSC) and spectroscopy. The DSC indicated that d-Leu·(−)-PES had a polymorphic form with the water of crystallization; that is, d-Leu·(−)-PES·H2O was thoroughly dehydrated at 60—90 °C and simultaneously converted into the d-Leu·(−)-PES form. However, l-Leu·(−)-PES does not have the water of crystallization even in 75% relative humidity. Detailed comparisons among the X-ray crystal structures of three salts have revealed that in all of the salts the conformations of the PES anion and the Leu cation, respectively, were approximately the same, and their crystal structures comprised specific interaction modes having characteristic hydrogen-bond networks. In particular, in d-Leu·(−)-PES·H2O the PES and Leu ions are cross-linked to each other through water molecules. These observations suggested that the water of crystallization, together with the formation of a stable crystal-packing mode by cross-linking the PES and Leu ions, presumably plays an important role in the selective crystallization in the resolution.

Molecular structure of 2-chloro-2′-deoxyadenosine an agent used in therapy for multiple sclerosis and its unusual crystal packing mode

The X-ray crystal structure of 2-chloro-2′-deoxyadenosine was determined at low temperature [space group orthorhombic P2 12 12, a = 7.493(6), b = 16.894(4), c = 9.065(4) → A, V = 1147.6(11) →A 3, 4097 unique reflections, R = 0.050]. The ribose unit is in 2 3T conformation, and the orientation around the Cl′-N glycosylic bond is syn with respect to the base. The 2-chloro-substitution leads to small but significant changes of the covalent geometry of the base at the substitution site, particularly to widening of the endocyclic angle at C2. The crystal packing is unusual foradenine nucleosides: molecules form stacks with parallel bases which are aligned by chains of short chlorine-chlorine contacts.

Packing Modes in Nitrobenzene Derivatives. I. The Single Stacks

The crystal packing modes of nitrobenzene derivatives, compounds classified as BCLASS = 15 by the Cambridge Structural Database (CSD), have been analysed. Several packing modes have been observed, although two of them, the so-called stacks and pseudo-herringbone, appear as the most populated ones. In 28.4% of the 169 structures that fulfilled the conditions of the search, the molecules are packed to form columns, with the aromatic planes almost parallel. Different ways of stacking within the columns and the way in which these columns pack together to give the whole crystal have been analysed.

Preferences and exceptions in organic crystal packing modes

Preferences and exceptions in organic crystal packing modes

Morphological studies on a novel poly(aryl ether ketone)

AbstractThe morphology of a novel poly(aryl ether ketone) [PEDEKmK] was investigated via polarizing optical microscopy (POM), TEM, DSC, SAXS and electron diffraction (ED). A distinct change in lamellar thickness, orientation, and spherulitic morphology was observed due to crystal melting and recrystallization. However, the crystal packing mode is found to be identical before and after the recrystallization process.

The crystal packing modes of three sterically overcrowded imidazole derivatives

The crystal packing of racemic 4-cyclohexylamino-5-hydroxy-1,5-diphenyl-Δ3-imidazolin-2-one resembles the bilayered packing arrangements with alternating hydrophilic and hydrophobic layers observed in the crystal structures of lipids. The hydrophobic layers of the imidazolinone are built up individually by phenyl and cyclohexyl groups. In contrast, the corresponding 4-tert-butylamino derivative crystallizes optically resolved in a non-bilayer layer structure. This crystal packing is similar to the host-lattice of the inclusion compound formed by 9-(4-tert-butylphenyl)fluoren-9-ol and dioxane [Csöregh, Weber, Nassimbeni, Gallardo, Dörpinghaus, Ertan & Bourne (1993). J. Chem. Soc. Perkin Trans. 2, pp. 1775–1781]. The major building units of 4-tert-butylamino-1,5-diphenylimidazole are centrosymmetrical dimers in which the molecules display a `yin-and-yang'-like self-complementarity. The dimers pack in columns, which form a distorted hexagonal pattern.

Chiral Discrimination in the Solid and the Solution States

Abstract Crystal packing modes were compared for the active and the corresponding racemic crystals obtained for various representative compounds. In the case of 1,1′-binaphthyl, the molecular conformation itself was different in the two crystal forms. For metal complexes of D3 symmetry with three-bladed propeller shape, there appear to be only a few favoured crystal packing modes, which is in good agreement with our dispersion energy calculations. Using CD spectroscopy and X-ray crystallography, chiral discriminations of optically labile chromium complexes of D3 symmetry have been investigated in the solid and the solution states.

The Crystal Structure of r(CCCCGGGG) in Two Distinct Lattices

The structure of the RNA octamer r(C4G4) has been determined in two different crystal forms. The conformations of the RNA duplex in the rhombohedral and hexagonal lattices display only minimal deviations, demonstrating that the RNA double helix is considerably less deformable than the DNA double helix. For the first time the crystal structures of an A-RNA and an A-DNA with identical sequence can now be compared. The large number of ordered water molecules observed in the minor groove of the RNA duplex suggests that an important contribution to its higher rigidity derives from the improved hydration due to the presence of the 2'-hydroxyl groups. Our finding that the conformation of the RNA double helix is virtually unaffected by different crystal packing modes provides evidence that proteins may not alter the conformation of RNA stem regions in a significant way.

ChemInform Abstract: Aliphatic Amino Acid‐Metal Ion‐Aromatic Amine Ternary Complexes. Crystal Structures of Aqua(L‐leucinato)(1,10‐phenanthroline)copper(II) Nitrate and Aqua(DL‐leucinato)(1,10‐phenanthroline)copper(II) Nitrate

Abstract The crystal structures of the two aliphatic amino acid-metal ion-aromatic diamine ternary complexes, [Cu( L -Leu)( o -phen)(H 2 O)]NO 3 (1) and [Cu( DL -Leu)( o -phen) (H 2 O)]NO 3 (2) (Leu=leucinato and o -phen=1,10-phenanthroline), have been determined by X-ray diffraction. Complex 1 crystallizes in the triclinic space group P 1 with a =12.362(2), b =11.593(2), c =7.311(2) A, α=107.82(2), β=76.05(2), γ=93.62(2)°, Z =2, D calc =1.557 g cm −3 , and R =0.045 for 3184 unique observed reflections. Complex 2 crystallizes in triclinic space group P 1 with a =12.368(4), b =11.608(4), c =7.280(3) A, α=107.16(3), β=75.98(3), γ=93.54(3)°, Z =2, D calc =1.556 g cm −3 , and R =0.052 for 2579 unique observed reflections. The L -Leu complex (1) involves two crystallographically independent molecules, which are related by a pseudo center of symmetry except for the C β atoms. Both the 1 and 2 structures are essentially identical, including the crystal packing mode, except for the existence of an exact crystallographic center of symmetry in 2. In 2 the C β atom of Leu is disordered at two positions corresponding to D - and L -configurations, respectively. In each complex, the copper atom is coordinated in a distorted squarepyramidal geometry by the bidentate Leu and o -phen ligands at the equatorial sites and water at an axial position. The isopropyl side chain of each Leu extends away from the aromatic ring system of o -phen, thus there is no intramolecular ligand-ligand interaction between them, in contrast to a ring-aliphatic hydrophobic interaction in solution for this ternary system. Factors affecting the formation of a folded structure having such an interligand interaction are considered from the structural viewpoint.

Chiral discriminations of complexes with D3symmetry. Molecular structure and crystal-packing mode of (–)589-tris[(–)-O,O′-1(R),2(R)-dimethylethylene dithiophosphato]chromium(III), [Cr{(–)bdtp}3

The molecular structure and crystal-packing mode of [Cr{(–)bdtp}3][bdtp =O,O′-1(R),2(R)-dimethylethylene dithiophosphate] have been determined from single-crystal X-ray diffraction data and refined by full-matrix least-squares methods to R 0.0435. The optically active crystal has unit-cell dimensions a= 11.699(1), b= 12.738(2), c= 16.827(2)Å, space group P212121 and Z= 4. The ligand has two ring planes: an inner four-membered chelate ring and an outer five-membered ring. The complex exhibits approximate D3 symmetry and the three inner rings and the three outer rings each form a propeller of opposite handedness. The crystal-packing mode and the chiral recognitions have been compared with those of D3 tris(chelate)metal complexes involving a single propeller system.

Aliphatic amino acid-metal ion-aromatic amine ternary complexes. Crystal structures of aqua( L-leucinato)(1,10-phenanthroline)copper(II) nitrate and aqua( DL-leucinato)(1,10-phenanthroline)copper(II) nitrate

The crystal structures of the two aliphatic amino acid-metal ion-aromatic diamine ternary complexes, [Cu( L-Leu)( o-phen)(H 2O)]NO 3 (1) and [Cu( DL-Leu)( o-phen) (H 2O)]NO 3 (2) (Leu=leucinato and o-phen=1,10-phenanthroline), have been determined by X-ray diffraction. Complex 1 crystallizes in the triclinic space group P1 with a=12.362(2), b=11.593(2), c=7.311(2) Å, α=107.82(2), β=76.05(2), γ=93.62(2)°, Z=2, D calc=1.557 g cm −3, and R=0.045 for 3184 unique observed reflections. Complex 2 crystallizes in triclinic space group P 1 with a=12.368(4), b=11.608(4), c=7.280(3) Å, α=107.16(3), β=75.98(3), γ=93.54(3)°, Z=2, D calc=1.556 g cm −3, and R=0.052 for 2579 unique observed reflections. The L-Leu complex (1) involves two crystallographically independent molecules, which are related by a pseudo center of symmetry except for the C β atoms. Both the 1 and 2 structures are essentially identical, including the crystal packing mode, except for the existence of an exact crystallographic center of symmetry in 2. In 2 the C β atom of Leu is disordered at two positions corresponding to D- and L-configurations, respectively. In each complex, the copper atom is coordinated in a distorted squarepyramidal geometry by the bidentate Leu and o-phen ligands at the equatorial sites and water at an axial position. The isopropyl side chain of each Leu extends away from the aromatic ring system of o-phen, thus there is no intramolecular ligand-ligand interaction between them, in contrast to a ring-aliphatic hydrophobic interaction in solution for this ternary system. Factors affecting the formation of a folded structure having such an interligand interaction are considered from the structural viewpoint.

Synthesis and characterization of bis[salicylideneaminato] palladium(II) complexes. Molecular structure of bis[ N-(n-butyl)(3-benzyloxy)-2-salicylideneaminato]-palladium(II), pd(C 18H 20NO 2) 2

Transition metal compounds having liquid crystalline properties can be interesting materials for practical applications. Attempting to correlate mesomorphic properties with molecular structure and crystal packing mode, we have investigated some complexes obtained from Schiff bases of long chain aliphatic amines and salicylaldehyde or 2,3-dihydroxybenzaldehyde derivatives. The X-ray structural analysis of bis[ N-(n-butyl)(3-benzyloxy)-2-salicylideneaminato] palladium [II] is also reported.

Crystal and molecular structures of tetrathia[7]heterohelicene: racemate and enantiomer

The crystal and molecular structures of the racemate and enantiomer tetrathia[7]heterohelicene have been determined in order to elucidate their molecular geometries and crystal packing modes. The racemate and enantiomer both crystallize from benzene in the orthorhombic form with Z= 4. The former belongs to the space group Pbcn with a= 15.383(2), b= 14.195(2), c= 7.767(1)A, and the latter belongs to the space group P212121 with a= 16.975(2), b= 11.236(1), c= 9.186(1)A. The racemate molecule retains C2 symmetry in the crystal, while the enantiomer lacks this symmetry, primarily because of differences in the dihedral angles between the successive aromatic rings. In the racemate, the molecules are stacked in a column with alternating chirality, while in the enantiomer the molecules are confined orthogonally to each other, resulting in strain. These packing modes are consistent with the observed geometrical deformation of the enantiomer, and provide a clue to the problem of chirality recognition.

ChemInform Abstract: CRYSTAL AND MOLECULAR STRUCTURE OF (5)HELICENE: CRYSTAL PACKING MODES

Chemischer InformationsdienstVolume 13, Issue 40 Physical Organic Chemistry ChemInform Abstract: CRYSTAL AND MOLECULAR STRUCTURE OF (5)HELICENE: CRYSTAL PACKING MODES R. KURODA, R. KURODASearch for more papers by this author R. KURODA, R. KURODASearch for more papers by this author First published: October 5, 1982 https://doi.org/10.1002/chin.198240067AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat No abstract is available for this article. Volume13, Issue40October 5, 1982 RelatedInformation

Crystal and molecular structure of [5]helicene: crystal packing modes

The crystal and molecular structure of two crystal habits of [5]helicene, forms A and B, have been determined and their respective crystal packing modes are compared, together with those of other members of the helicene series. Form A crystallizes from n-pentane in the space group P21/c with a= 5.8150(7), b= 14.178(1), c= 17.498(1)A, β= 94.41(1)°, Z= 4, while form B from ethanol solution belongs to the space group A2/a with a= 26.013(2), b= 8.898(1), c=19.494(2)A, β= 103.94(1)°, Z=12.

ChemInform Abstract: CONFORMATIONAL POLYMORPHISM. THE INFLUENCE OF CRYSTAL STRUCTURE ON MOLECULAR CONFORMATION

A methodology for the study of the influence of crystal forces on molecular conformation has been developed and ap- plied. As part of this study the phenomenon of conformationalpolymorphism, in which a molecule adopts significantly differ- ent conformations in different crystal polymorphs, is elucidated. A combination of quantitative analysis of the molecular pack- ing in different space groups along with ab initio molecular orbital calculations is used to analyze these phenomena. The model system p-(N-chlorobenzy1idene)-p-chloroaniline (a Schiff base) was chosen for study. Lattice energy calculations involving the minimization of the energy of the triclinic and orthorhombic crystal forms of this molecule were carried out in order to ex- plain the stability of the former lattice in which the unstable planar conformation of the molecule obtains. Three different po- tential functions were employed (6-9, 6- 12, and 6-exp), in order to avoid potential-dependent conclusions. All potentials yielded lower (more negative), for the triclinic lattice, in agreement with the experimental observation. The conforma- tional energy of the isolated molecule was studied by molecular orbital methods using both minimal and split valance basis sets. The energy differences obtained from these calculations are in good agreement with the differences in lattice obtained from the crystal calculations. A of the lattice energy into partial atomic energies was performed in order to carry out a detailed analysis of the packing differences between the polymorphs. The introduction of this partitioning proved to be a powerful probe for analyses of the energetics of different crystal packing modes. The approach employed, including packing analysis and crystal energetic studies to conformational polymorphs, yields much information as to the nature of the crystal forces in the different polymorphs and promises to be a useful tool in the investigation of the role of these forces in in- fluencing molecular conformation.

Conformational polymorphism. The influence of crystal structure on molecular conformation

A methodology for the study of the influence of crystal forces on molecular conformation has been developed and ap- plied. As part of this study the phenomenon of conformationalpolymorphism, in which a molecule adopts significantly differ- ent conformations in different crystal polymorphs, is elucidated. A combination of quantitative analysis of the molecular pack- ing in different space groups along with ab initio molecular orbital calculations is used to analyze these phenomena. The model system p-(N-chlorobenzy1idene)-p-chloroaniline (a Schiff base) was chosen for study. Lattice energy calculations involving the minimization of the energy of the triclinic and orthorhombic crystal forms of this molecule were carried out in order to ex- plain the stability of the former lattice in which the unstable planar conformation of the molecule obtains. Three different po- tential functions were employed (6-9, 6- 12, and 6-exp), in order to avoid potential-dependent conclusions. All potentials yielded lower (more negative), for the triclinic lattice, in agreement with the experimental observation. The conforma- tional energy of the isolated molecule was studied by molecular orbital methods using both minimal and split valance basis sets. The energy differences obtained from these calculations are in good agreement with the differences in lattice obtained from the crystal calculations. A of the lattice energy into partial atomic energies was performed in order to carry out a detailed analysis of the packing differences between the polymorphs. The introduction of this partitioning proved to be a powerful probe for analyses of the energetics of different crystal packing modes. The approach employed, including packing analysis and crystal energetic studies to conformational polymorphs, yields much information as to the nature of the crystal forces in the different polymorphs and promises to be a useful tool in the investigation of the role of these forces in in- fluencing molecular conformation.