On the relationships between molecular conformations and intermolecular contacts toward crystal self-assembly of mono-, di-, tri-, and tetra-oxygenated xanthone derivatives

Oxygenated xanthones have been extensively investigated over the years, but there are few reports concerning their crystal structure. Our chemical investigations of Brazilian plants resulted in the isolation of four natural products named 1-hydroxyxanthone (I), 1-hydroxy-7-methoxyxanthone (II), 1,5-dihydroxy-3-methoxyxanthone (III), and 1,7-dihydroxy-3,8-dimethoxyxanthone (IV). The structures of these compounds were established on the basis of single crystal X-ray diffraction. The xanthone nucleus conformation is essentially planar with the substituents adopting the orientations less sterically hindered. In addition, classical intermolecular hydrogen bonds (O-H center dot center dot center dot O) present in III and IV give rise to infinite ribbons. However, the xanthone I does not present any intermolecular hydrogen bonds, meanwhile the xanthone II presents only a non-classical one (C-H center dot center dot center dot O). The crystal packing of all xanthone structures is also stabilized by pi-pi interactions. The fingerprint plots, derived from the Hirshfeld surfaces, exhibited significant features of each crystal structures.

Molecular engineering strategies to control photo-induced birefringence and surface-relief gratings on layer-by-layer films from an azopolymer

The interactions governing adsorption of layer-by-layer (LBL) films from an azopolymer, PS-119(R), and poly(allylamine hydrochloride) (PAH) have been controlled by modifying the pH of the solutions used to form the films. The thickness per bilayer was varied by one order of magnitude, from 10 to 240 A, as the pH changed from 4 to 10. Thick layers were formed at higher pHs because in this case the PAH is only partially charged adopting a loopy conformation. This change in molecular conformation caused the kinetics of isomerization and mass transport to be much slower than at lower pHs. The writing time defined as the time to achieve 50% of maximum birefringence dropped from 110 to 18 min for films prepared from solutions with pH 10 and pH 4, respectively. This decrease is probably due to the higher free volume for isomerization in the films prepared at lower pHs, in which PAH molecules are less coiled than at higher pHs. For the same reason, the rate of inscription of surface-relief gratings with an interference pattern of p-polarized light was also much slower at higher pHs. (C) 2003 Elsevier B.V. All rights reserved.

Eletrônica molecular via método híbrido DFT/FGNE em anéis fenilas acoplados a eletrodos metálicos de nanotubos de carbono: a regra de conformação e quiralidade molecular

Nesta tese, investigamos detalhadamente as propriedades de transporte eletrônico, conformacional e de simetria de estruturas de Nanotubos de Carbono de Parede Simples zigzag (9,0), NCPS zz9, acopladas a anéis fenilas (2, 3, 4 e 5) sob influência de campo elétrico externo (voltagem) via método híbrido da Teoria do Funcional Densidade (DFT) do tipo B3LYP 6-311G(d,p) combinado com Função de Green de Não Equilíbrio (FGNE) e Teoria de Grupo. Verificamos uma boa relação entre: 1- o índice quiral () por Teoria de Grupo e a lei do cos2 (, ângulo diedral) por geometria sob a influência de campo elétrico externo, pois  só depende das posições atômicas (), das conformações, e também está fortemente correlacionada a corrente que passa através do sistema; 2- a condutância normalizada (G/Go) é proporcional a cos2 na região do gap (EHOMO-ELUMO), isto é, nas regiões onde ocorre a ressonância e a resistência diferencial negativa (RDN); 3- o gráfico Fowler-Northeim (FN) exibe mínimo de voltagem (Vmin) que ocorre sempre que a cauda de um pico de transmissão ressonante entra na janela de voltagem, isto é, quando nessas estruturas ocorre uma RDN, pois o número de RDN na curva I-V está associado ao número de Vmin no gráfico FN e pode ser explicado pelo modelo de transporte molecular coerente; 4- a altura da barreira (EF - EHOMO e ELUMO - EF) como função do comprimento molecular; 5- Vmin como função da altura da barreira (EF - EHOMO) e do comprimento molecular. Assim, 1 implica que a conformação molecular desempenha um papel preponderante na determinação das propriedades de transporte da junção; 2 sugere que a lei do cos2 tem uma aplicabilidade mais geral independentemente da natureza dos eletrodos; 3 serve como um instrumento espectroscópico e também para identificar a molécula na junção; 4 e 5 a medida que o comprimento molecular atinge um certo valor (1,3nm) o Vmin permanece praticamente inalterado. Os resultados mostraram que as propriedades estruturais sofrem alterações significativas com o aumento da voltagem que estão em boa concordância com os valores encontrados na literatura. O comportamento das curvas IxV e G/GoxV perdem sua dependência linear para dar origem a um comportamento não linear com aparecimento de RDN. Tal ponto revela a modificação estrutural sofrida pelo sistema. A curva IxV confirmou as afirmações que foram feitas através da análise estrutural para o sistema considerado e mostrou como se dá o fluxo de carga nos sistemas analisados.

NMR (1H, 13C) and MO (ab initio, CNDO/2, EHT) studies on basic and N-protonated hydrazinecarbothioamide

The conformational preferences of hydrazinecarbothioamide (HCTA, H2NNHCSNH2) in its basic and N-protonated (PHCTA, H3NNNHCSNH2) forms have been studied by 1H and 13C NMR spectroscopy and by theoretical LCAO-MO methods (ab initio, CNDO/2 and EHT). The hindered rotation around the C---N bond has been investigated by a total line shape analysis for the thioamide protons and by the three MO methods. Changes in the molecular conformation and electronic structure on protonation are briefly discussed.

1-Benzoyl-3-methyl-2,6-diphenyl-4-piperidone

In the title moleclue, C25H23NO2, the 4-piperidone ring adopts a boat conformation. The molecular conformation is stabilized by an intramolecular C-H center dot center dot center dot O hydrogen bond. In the crystal, molecules are connected through weak intermolecular C-H center dot center dot center dot O hydrogen bonds.

1-(3,5-Dimethyl-1H-pyrazol-1-yl)-3-phenylisoquinoline

The molecular conformation of the title compound, C20H17N3, is stabilized by an intramolecular C-H center dot center dot center dot N interaction. The crystal structure shows intermolecular C-H center dot center dot center dot pi interactions. The dihedral angle between the isoquinoline unit and the phenyl ring is 11.42 (1)degrees whereas the isoquinoline unit and the pendent dimethyl pryrazole unit form a dihedral angle of 50.1 (4)degrees. Furthermore, the angle between the mean plane of the phenyl ring and the dimethyl pyrazole unit is 47.3 (6)degrees.

Ethyl 3-oxo-2-[(4-sulfamoylphenyl)hydrazono]butyrate

In the title compound, C12H15N3O5S, an intramolecular N-H center dot center dot center dot O hydrogen bond between the hydrazine unit and one of the carbonyl groups may influence the molecular conformation. In the crystal structure, intermolecular N-H center dot center dot center dot O hydrogen bonds, including one which is bifurcated, link the molecules into a two-dimensional network.

Ethyl 4-(4-chlorophenyl)-6-methyl-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate

In the title compound, C14H15ClN2O2S, the tetrahydropyrimidine ring adopts a twisted boat conformation with the carbonyl group in an s-trans conformation with respect to the C C double bond of the six-membered tetrahydropyrimidine ring. The molecular conformation is determined by an intramolecular C-H center dot center dot center dot pi interaction. The crystal structure is further stabilized by intermolecular N-H center dot center dot center dot O molecular chains and centrosymmetric N-H center dot center dot center dot S dimers.

2-[2-(Hydroxymethyl)phenyl]-1-(1-naphthyl)ethanol

The molecular conformation of the title compound, C19H18O2, is stabilized by an intramolecular O-H-O hydrogen bond. In addition, intermolecular O-H-O interactions link the molecules into zigzag chains running along the c axis.

2-[(E)-(4-hydroxy-3-methoxybenzylidene)amino]-N-(2-methylphenyl)-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide

The title compound, C24H24N2O3S, exhibits antifungal and antibacterial properties. The compound crystallizes with two molecules in the asymmetric unit, with one molecule exhibiting 'orientational disorder' in the crystal structure with respect to the cyclohexene ring. The o-toluidine groups in both molecules are noncoplanar with the respective cyclohexene-fused thiophene ring. In both molecules, there is an intramolecular N-H...N hydrogen bond forming a pseudo-six-membered ring which locks the molecular conformation and eliminates conformational flexibility. The crystal structure is stabilized by O-H...O hydrogen bonds; both molecules in the asymmetric unit form independent chains, each such chain consisting of alternating 'ordered' and 'disordered' molecules in the crystal lattice.

Disorder Induced Concomitant Polymorphism in 3-Fluoro-N-(3-fluorophenyl)benzamide

The occurrence of concomitant polymorphism in 3-fluoro-N-(3-fluorophenyl) benzamide has been identified to be due to the disorder in the crystal structure. Of the two modifications, the plate form (Form I) crystallizes in the monoclinic centrosymmetric space group C2/c with Z = 4, and the needle form (Form II) crystallizes in the noncentrosymmetric space group P21 with Z = 2. An interesting positional disorder at the bridging atoms in both forms holds the molecular conformation identical, while subtle variations brought by N−H···O hydrogen bonds along with weak C−H···F and F···F interactions result in packing polymorphism.

Stereochemical Analysis of Higher α,α-Dialkylglycine Containing Peptides. Characterization of Local Helical Conformations at Dipropylglycine Residues and Observation of a Novel Hydrated Multiple β-Turn Structure in Crystals of a Glycine Rich Peptide

The peptide Boc-Gly-Dpg-Gly-Gly-Dpg-Gly-NHMe (1) has been synthesized to examine the conformational preferences of Dpg residues in the context of a poor helix promoting sequence. Single crystals of 1 were obtained in the space group P21/c with a = 13.716(2) Å, b = 12.960(2) Å, c = 22.266(4) Å, and β = 98.05(1)°; R = 6.3% for 3660 data with |Fo| > 4σ. The molecular conformation in crystals revealed that the Gly(1)-Dpg(2) segment adopts φ, ψ values distorted from those expected for an ideal type II‘ β-turn (φGly(1) = +72.0°, ψGly(1) = −166.0°; φDpg(2) = −54.0°, ψDpg(2) = −46.0°) with an inserted water molecule between Boc-CO and Gly(3)NH. The Gly(3)-Gly(4) segment adopts φ, ψ values which lie broadly in the right handed helical region (φGly(3) = −78.0°, ψGly(3) = −9.0°; φGly(4) = −80.0°, ψGly(4) = −18.0°). There is a chiral reversal at Dpg(5) which takes up φ, ψ values in the left handed helical region. The Dpg(5)-Gly(6) segment closely resembles an ideal type I‘ β-turn (φDpg(5) = +56.0°, ψDpg(5) = +32.0°; φGly(6) = +85.0°, ψGly(6) = −3.0°). Molecules of both chiral senses are found in the centrosymmetric crystal. The C-terminus forms a hydrated Schellman motif, with water insertion into the potential 6 → 1 hydrogen bond between Gly(1)CO and Gly(6)NH. NMR studies in CDCl3 suggest substantial retention of the multiple turn conformation observed in crystals. In solution the observed NOEs support local helical conformation at the two Dpg residues.

5-(4-Chlorophenyl)-3-(2,4-dimethylthiazol-5-yl)-1,2,4-triazolo[3,4-a]isoquinoline

In the title molecule, C21H15ClN4S, the triazoloisoquinoline ring system is approximately planar, with an r.m.s. deviation of 0.054 (2) angstrom and a maximum deviation of 0.098 (2) angstrom from the mean plane for the triazole ring C atom that is bonded to the thiazole ring. The thiazole and benzene rings are twisted by 66.36 (7) and 56.32 (7)degrees respectively, with respect to the mean plane of the triazoloisoquinoline ring system. In the crystal structure, molecules are linked by intermolecular C-H center dot center dot center dot N interactions along the a axis. The molecular conformation is stabilized by a weak intramolecular pi-pi interaction involving the thiazole and benzene rings, with a centroid-centroid distance of 3.6546 (11) angstrom . In addition, two other intermolecular pi-pi stacking interactions are observed, between the triazole and benzene rings and between the dihydropyridine and benzene rings [centroid-centroid distances = 3.6489 (11) and 3.5967 (10) angstrom, respectively].

Structural studies of model peptides containing beta-, gamma- and delta-amino acids

The crystal structures of five model peptides Piv-Pro-Gly-NHMe (1), Piv-Pro-beta Gly-NHMe (2), Piv-Pro-beta Gly-OMe (3), Piv-Pro-delta Ava-OMe (4) and Boc-Pro-gamma Abu-OH (5) are described (Piv:pivaloyl; NHMe: N-methylamide; beta Gly:beta-glycine; OMe:O-methyl ester; delta Ava:delta-aminovaleric acid; gamma Abu:gamma-aminobutyric acid). A comparison of the structures of peptides 1 and 2 illustrates the dramatic consequences upon backbone homologation in short sequences. 1 adopts a type II beta-turn conformation in the solid state, while in 2, the molecule adopts an open conformation with the beta-residue being fully extended. Piv-Pro-beta Gly-OMe (3), which differs from 2 by replacement of the C-terminal NH group by an O-atom, adopts an almost identical molecular conformation and packing arrangement in the solid state. In peptide 4, the observed conformation resembles that determined for 2 and 3, with the delta Ava residue being fully extended. In peptide 5, the molecule undergoes a chain reversal, revealing a beta-turn mimetic structure stabilized by a C-H center dot center dot center dot O hydrogen bond.

1-(3,5-Diethyl-1H-pyrazol-1-yl)-3-phenylisoquinoline

In the title molecule, C22H21N3, the isoquinoline ring is almost planar maximum deviation = 0.046 (1) A] and makes dihedral angles of 52.01 (4) and 14.61 (4)degrees with the pyrazole and phenyl rings, respectively. The phenyl ring and the pyrazole ring are twisted by 44.20 (6)degrees with respect to each other. The terminal C atoms of both of the ethyl groups attached to the pyrazole ring are disordered over two sites with occupancy ratios of 0.164 (7):0.836 (7) and 0.447 (16):0.553 (16). A weak intramolecular C-H...N contact may influence the molecular conformation. The crystal structure is stabilized by C-H...pi contacts involving the phenyl and pyrazole rings, and by pi-pi stacking interactions involving the pyridine and benzene rings centroid-centroid distance = 3.5972 (10) A].