Combined experimental powder X-ray diffraction and DFT data to obtain the lowest energy molecular conformation of friedelin

Friedelin molecular conformers were obtained by Density Functional Theory (DFT) and by ab initio structure determination from powder X-ray diffraction. Their conformers with the five rings in chair-chair-chair-boat-boat, and with all rings in chair, are energy degenerated in gas-phase according to DFT results. The powder diffraction data reveals that rings A, B and C of friedelin are in chair, and rings D and E in boat-boat, conformation. The high correlation values among powder diffraction data, DFT and reported single-crystal data indicate that the use of conventional X-ray diffractometer can be applied in routine laboratory analysis in the absence of a single-crystal diffractometer.

Molecular conformation of the racemic indan derivative (+/-)-1-trans-3-(3,4-dichlorophenyl)-2,3-dihydro-1H-indene-1-carboxamide

This paper presents the structural characterization of the indan derivative (+/-)-1-trans-3-(3,4-dichlorophenyl)-2,3-dihydro-1H-indene-1-carboxamide, which was unambiguously determined by X-ray diffraction (XRD) to be a racemate (R/S: 50/50) crystallizing in an achiral crystal structure (P2(1)/c, a = 9.3180(1) , b = 7.9070(2) , c = 19.7550(4) , beta = 103.250(1)A degrees, V = 1416.75(5) (3) and Z = 4). The diastereomers are related by the inversion symmetry and linked by H bond forming a dimer. The crystal packing is stabilized by hydrogen bonds, including the classical one responsible for the formation of centrosymmetric dimers, and non-classical ones involving C-H center dot center dot center dot O and C-H center dot center dot center dot pi-aryl interactions. The intra and intermolecular geometry of the title compound is compared to the (+/-)-1-trans-3-(3,4-dichlorophenyl)-2,3-dihydro-1H-indene-1-carboxylic acid one, which also present an achiral crystal structure from racemates (R/S: 50/50). The two indan derivatives crystallize in a very similar unit cell.

Correlation Between Molecular Conformation, Packing, and Dynamics in Oligofluorenes: A Theoretical/Experimental Study

Fluorene-based systems have shown great potential as components in organic electronics and optoelectronics (organic photovoltaics, OPVs, organic light emitting diodes, OLEDs, and organic transistors, OTFTs). These systems have drawn attention primarily because they exhibit strong blue emission associated with relatively good thermal stability. It is well-known that the electronic properties of polymers are directly related to the molecular conformations and chain packing of polymers. Here, we used three oligofluorenes (trimer, pentamer, and heptamer) as model systems to theoretically investigate the conformational properties of fluorene molecules, starting with the identification of preferred conformations. The hybrid exchange correlation functional, OPBE, and ZINDO/S-CI showed that each oligomer exhibits a tendency to adopt a specific chain arrangement, which could be distinguished by comparing their UV/vis electronic absorption and C-13 NMR spectra. This feature was used to identify the preferred conformation of the oligomer chains in chloroform-cast films by comparing experimental and theoretical UV/vis and C-13 NMR spectra. Moreover, the oligomer chain packing and dynamics in the films were studied by DSC and several solid state NMR techniques, which indicated that the phase behavior of the films may be influenced by the tendency that each oligomeric chain has to adopt a given conformation.

The Role of Molecular Conformation and Polarizable Embedding for One- and Two-Photon Absorption of Disperse Orange 3 in Solution

Solvent effects on the one- and two-photon absorption (IPA and 2PA) of disperse orange 3 (DO3) in dimethyl sulfoxide (DMSO) are studied using a discrete polarizable embedding (PE) response theory. The scheme comprises a quantum region containing the chromophore and an atomically granulated classical region for the solvent accounting for full interactions within and between the two regions. Either classical molecular dynamics (MD) or hybrid Car-Parrinello (CP) quantum/classical (QM/MM) molecular dynamics simulations are employed to describe the solvation of DO3 in DMSO, allowing for an analysis of the effect of the intermolecular short-range repulsion, long-range attraction, and electrostatic interactions on the conformational changes of the chromophore and also the effect of the solute-solvent polarization. PE linear response calculations are performed to verify the character, solvatochromic shift, and overlap of the two lowest energy transitions responsible for the linear absorption spectrum of DO3 in DMSO in the visible spectral region. Results of the PE linear and quadratic response calculations, performed using uncorrelated solute-solvent configurations sampled from either the classical or hybrid CP QM/MM MD simulations, are used to estimate the width of the line shape function of the two electronic lowest energy excited states, which allow a prediction of the 2PA cross-sections without the use of empirical parameters. Appropriate exchange-correlation functionals have been employed in order to describe the charge-transfer process following the electronic transitions of the chromophore in solution.

Probing the relationships between molecular conformation and intermolecular contacts in N,N-dibenzyl-N '-(furan-2-carbonyl)thiourea

In the crystal structure of the title compound, C20H18N2O2S, molecules are linked by bifurcated C-H center dot center dot center dot O hydrogen-bond interactions, giving rise to chains whose links are composed of alternating centrosymmetrically disposed pairs of molecules and characterized by R-2(2)(10) and R-2(2)(20) hydrogen-bonding motifs. Also, N-H center dot center dot center dot S hydrogen bonds form infinite zigzag chains along the [010] direction, which exhibit the C(4) motif. Hirshfeld surface and fingerprint plots were used to explore the intermolecular interactions in the crystal structure. This analysis confirms the important role of C-H center dot center dot center dot O hydrogen bonds in the molecular conformation and in the crystal structure, providing a potentially useful tool for a full understanding of the intermolecular interactions in acylthiourea derivatives.

Experimental and theoretical investigation of molecular structure and conformation of the 4-isopropylthioxanthone

In this study, the molecular structure and conformational analyses of the 4-isopropylthioxanthone (4-ITX) are reported according to experimental and theoretical results. The compound crystallizes in the centrosymmetric P (1) over bar space group with only one molecule in the asymmetric unit, presenting the most stable conformation, in which the three fused-rings adopt a planar geometry, and the isopropyl group assumes a torsional angle with less sterical hindrance. The structural and conformational analyses were performed using theoretical calculations such as Hartree-Fock (HF), DFT method in combination with 6-311G(d,p) and 6-31++G(d,p) and the results were compared with infrared spectroscopy (FT-IR) and X-ray diffraction (XRD). The supramolecular assembly of 4-ITX is kept by non-classical C-H center dot center dot center dot O hydrogen bonds and weak interactions such as pi-pi stacking. 4-ITX was also studied by (1)H and (13)C NMR spectroscopy. UV-Vis absorption spectroscopic properties of the 4-ITX showed the long-wavelength maximum shifts towards high energy when the solvent polarity increases. (C) 2011 Elsevier B.V. All rights reserved.

Interaction of alpha-melanotropin with central dopamine systems: role of hormonal state and molecular structure

The tubero-infundibular and nigrostriatal DA neurone systems of rats respond to systemic (i.p.) injection of alpha-MSH (2-100 microgram/kg). The response of the tubero-infundibular (arcuate) DA neurones, an increase in cellular fluorescence intensity which can be interpreted as a sign of increased neuronal activity, is essentially the same in males, estrogen-progesterone-pretreated ovariectomized females and hypophysectomized males, whereas the type of response elicited by alpha-MSH in the nigral DA neurones depends upon the hormonal state of the animal. Differences between the two DA neurone groups exist also with regard to the effects of peptide fragments containing the two active sites of the alpha-MSH molecule. Results of lesion experiments in the lower brainstem (area postrema) and of blockade of muscarinic mechanisms by atropine further point to differences in the mechanisms underlying the peptide effects on the two neurone systems. The reaction of the tubero-infundibular DA system (which controls the pars intermedia of the pituitary) can be considered to reflect the activation of a feedback mechanism on MSH secretion, while the functional counterpart of the changes observed in the nigral system remains unknown at the present time.

Formation of a one-dimensional helical alignment of water molecules within a water-mediated supramolecular helix using molecular self-assembly of a water-soluble short pseudopeptide

The reported pseudopeptide 1 adopts a double turn molecular conformation consisting of an intramolecular 9-membered turn together with a water-mediated 11-atom turn and this pseudopeptide 1 self-assembles to form a water-mediated supramolecular helical structure with internal water molecules, which are aligned in a ID helical array. (c) 2006 Elsevier Ltd. All rights reserved.

First crystallographic signature of an acyclic peptide nanorod: molecular mechanism of nanorod formation by a self-assembled tetrapeptide

A terminally protected acyclic tetrapeptide Boc-Aib-Val-Aib-beta-Ala-OMe 1 (Aib: alpha-aminoisobutyric acid, beta-Ala: beta-Alanine) self-assembles into a continuous hydrogen-bonded supramolecular helix with an average diameter of 10Angstrom (1nm) starting from a double bend molecular conformation in crystals and further self-assembly of this supramolecular architecture leads to the formation of polydisperse nanorods of diameters 10-40 nm.

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.

A New Platinum Complex With Tryptophan: Synthesis, Structural Characterization, Dft Studies And Biological Assays In Vitro Over Human Tumorigenic Cells.

A new platinum(II) complex with the amino acid L-tryptophan (trp), named Pt-trp, was synthesized and characterized. Elemental, thermogravimetric and ESI-QTOF mass spectrometric analyses led to the composition [Pt(C11H11N2O2)2]⋅6H2O. Infrared spectroscopic data indicate the coordination of trp to Pt(II) through the oxygen of the carboxylate group and also through the nitrogen atom of the amino group. The (13)C CP/MAS NMR spectroscopic data confirm coordination through the oxygen atom of the carboxylate group, while the (15)N CP/MAS NMR data confirm coordination of the nitrogen of the NH2 group to the metal. Density functional theory (DFT) studies were applied to evaluate the cis and trans coordination modes of trp to platinum(II). The trans isomer was shown to be energetically more stable than the cis one. The Pt-trp complex was evaluated as a cytotoxic agent against SK-Mel 103 (human melanoma) and Panc-1 (human pancreatic carcinoma) cell lines. The complex was shown to be cytotoxic over the considered cells.

Organic molecule assembled between carbon nanotubes: A highly efficient switch device

We report a highly efficient switch built from an organic molecule assembled between single-wall carbon nanotube electrodes. We theoretically show that changes in the distance between the electrodes alter the molecular conformation within the gap, affecting in a dramatic way the electronic and charge transport properties, with an on/off ratio larger than 300. This opens up the perspective of combining molecular electronics with carbon nanotubes, bringing great possibilities for the design of nanodevices.

Low-temperature study of a new nevirapine pseudopolymorph

The title compound (systematic name: 11-cyclopropyl-4-methyl-5,11-dihydro-6H-dipyrido[3,2-b: 2',3'-e][1,4] diazepin-6-one butanol 0.3-solvate), C15H14N4O center dot 0.3C(4)H(9)OH, was crystallized in a new triclinic pseudopolymorphic form, a butanol solvate, and the crystal structure determined at 150 K. The molecular conformation of this new form differs from that reported previously, although the main intermolecular hydrogen-bond pattern remains the same. N-H center dot center dot center dot O hydrogen bonds [N center dot center dot center dot O = 2.957 (3) angstrom] form centrosymmetric dimers and the crystal packing of this new pseudopolymorph generates infinite channels along the b axis.