Crystal structure of (2Z,5Z)-3-(4-meth­oxy­phen­yl)-2-[(4-meth­oxy­phenyl)­imino]-5-[(E)-3-(2-nitro­phen­yl)allyl­idene]-1,3-thia­zolidin-4-one

PubMed Central

Rahmani, Rachida; Djafri, Ahmed; Daran, Jean-Claude; Djafri, Ayada; Chouaih, Abdelkader; Hamzaoui, Fodil

2016-01-01

In the title compound, C26H21N3O5S, the thia­zole ring is nearly planar with a maximum deviation of 0.017 (2) Å, and is twisted with respect to the three benzene rings, making dihedral angles of 25.52 (12), 85.77 (12) and 81.85 (13)°. In the crystal, weak C—H⋯O hydrogen bonds and C—H⋯π inter­actions link the mol­ecules into a three-dimensional supra­molecular architecture. Aromatic π–π stacking is also observed between the parallel nitro­benzene rings of neighbouring mol­ecules, the centroid-to-centroid distance being 3.5872 (15) Å. PMID:26958377

Synthesis and bioelectrochemical behavior of aromatic amines.

PubMed

Shabbir, Muhammad; Akhter, Zareen; Ahmad, Iqbal; Ahmed, Safeer; Bolte, Michael; McKee, Vickie

2017-12-01

Four aromatic amines 1-amino-4-phenoxybenzene (A 1 ), 4-(4-aminophenyloxy) biphenyl (A 2 ), 1-(4-aminophenoxy) naphthalene (A 3 ) and 2-(4-aminophenoxy) naphthalene (A 4 ) were synthesized and characterized by elemental, spectroscopic (FTIR, NMR), mass spectrometric and single crystal X-ray diffraction methods. The compounds crystallized in monoclinic crystal system with space group P2 1 . Intermolecular hydrogen bonds were observed between the amine group and amine/ether acceptors of neighboring molecules. Electrochemical investigations were done using cyclic voltammetry (CV), square wave voltammetry (SWV) and differential pulse voltammetry (DPV). CV studies showed that oxidation of aromatic amines takes place at about 0.9 V (vs. Ag/AgCl) and the electron transfer (ET) process has irreversible nature. After first scan reactive intermediate were generated electrochemically and some other cathodic and anodic peaks also appeared in the succeeding scans. DPV study revealed that ET process is accompanied by one electron. DNA binding study of aromatic amines was performed by CV and UV-visible spectroscopy. These investigations revealed groove binding mode of interaction of aromatic amines with DNA. Copyright © 2017 Elsevier Inc. All rights reserved.

Crystallization and preliminary crystallographic analysis of the catechol 2,3-dioxygenase PheB from Bacillus stearothermophilus BR219

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sugimoto, Keisuke; Matsufuzi, Kazuki; Ohnuma, Hiroaki

2006-02-01

PheB, an extradiol-cleaving catecholic dioxygenase, was crystallized by the hanging-drop vapour-diffusion method using PEG 4000 as a precipitant. The crystal belongs to the orthorhombic system, space group P2{sub 1}2{sub 1}2{sub 1}, and diffracts to 2.3 Å resolution. Class II extradiol-cleaving catecholic dioxygenase, a key enzyme of aromatic compound degradation in bacteria, cleaves the aromatic ring of catechol by adding two O atoms. PheB is one of the class II extradiol-cleaving catecholic dioxygenases and shows a high substrate specificity for catechol derivatives, which have one aromatic ring. In order to reveal the mechanism of the substrate specificity of PheB, PheB hasmore » been crystallized by the hanging-drop vapour-diffusion method using PEG 4000 as a precipitant. The space group of the obtained crystal was P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 65.5, b = 119.2, c = 158.7 Å. The crystal diffracted to 2.3 Å resolution.« less

Investigation of Y/SBA Composite Molecular Sieves Morphology Control and Catalytic Performance for n-Pentane Aromatization

PubMed Central

Shi, Chun-Wei; Wu, Wen-Yuan; Li, Shuai; Bian, Xue; Zhao, Shan-lin; Pei, Ming-Yuan

2016-01-01

Using Y molecular sieve as the core, Y/SBA-15 composite molecular sieves were prepared by different crystallization methods in the paper. The growth process and morphologies of the composite molecular sieves were controlled by adjusting the synthesis factors. The structures and acidity of two kinds of composite molecular sieves were characterized by X-ray diffraction (XRD), N2 adsorption/desorption, transmission electron microscopy (TEM), and NH3-TPD. The catalysis performances of the composite molecular sieves were investigated in the aromatization reaction of n-pentane. The results indicated that the desired core-shell composite molecular sieves were obtained when the crystallization conditions were 36 hours, 100 °C and secondary crystallization. The aromatization results showed that core-shell composite molecular sieves had better selectivity for producing high application value xylenes compared to mixed-crystal composite molecular sieves. PMID:27029526

Crystal Structure, Conformational Analysis, and Charge Density Distribution for Eng-Epifisetinidol: An Explanation for Regiospecific Aromatic Substitution of 5-Deoxyflavan

Treesearch

Fred L. Tobiason; Frank R. Fronczek; Jan P. Steynberg; Elizabeth C. Steynberg; Richard W. Hemingway; Wayne L. Mattice

1993-01-01

Molecular modeling and molecular orbital analyses of ent-epifisetinidol gave &ood predictions of the approximate "reverse half-chair" conformation found for the crystal structure. MNDO and AM1 analyses of HOMO electron densities provided an explanation for the stereospecific electrophilic aromatic substitution at C(6) in 5-deoxy-flavans...

Diazotisation of Weakly Basic Aromatic and Heterocyclic Amines in Strongly Acid Media

NASA Astrophysics Data System (ADS)

Godovikova, Tamara I.; Rakitin, Oleg A.; Khmel'nitskii, Lenor I.

1983-05-01

The review is devoted to the diazotisation of weakly basic aromatic amines. The methods of synthesis of diazonium salts based on these amines by non-traditional methods are examined. Data on the mechanism of the diazotisation reaction in strongly acid media are surveyed. Reactions of diazonium salts leading to the synthesis of new compounds are presented. The bibliography includes 75 references.

Crystal structure of 4-fluoro-N-[2-(4-fluoro-benzo-yl)hydra-zine-1-carbono-thio-yl]benzamide.

PubMed

Firdausiah, Syadza; Salleh Huddin, Ameera Aqeela; Hasbullah, Siti Aishah; Yamin, Bohari M; Yusoff, Siti Fairus M

2014-09-01

In the title compound, C15H11F2N3O2S, the dihedral angle between the fluoro-benzene rings is 88.43 (10)° and that between the central semithiocarbazide grouping is 47.00 (11)°. The dihedral angle between the amide group and attached fluoro-benzene ring is 50.52 (11)°; the equivalent angle between the carbonyl-thio-amide group and its attached ring is 12.98 (10)°. The major twists in the mol-ecule occur about the C-N-N-C bonds [torsion angle = -138.7 (2)°] and the Car-Car-C-N (ar = aromatic) bonds [-132.0 (2)°]. An intra-molecular N-H⋯O hydrogen bond occurs, which generates an S(6) ring. In the crystal, the mol-ecules are linked by N-H⋯O and N-H⋯S hydrogen bonds, generating (001) sheets. Weak C-H⋯O and C-H⋯F inter-actions are also observed.

Acyclic cucurbit[n]uril-type molecular containers: influence of glycoluril oligomer length on their function as solubilizing agents.

PubMed

Gilberg, Laura; Zhang, Ben; Zavalij, Peter Y; Sindelar, Vladimir; Isaacs, Lyle

2015-04-07

We present the synthesis of a series of six new glycoluril derived molecular clips and acyclic CB[n]-type molecular containers (1–3) that all feature SO3(−) solubilizing groups but differ in the number of glycoluril rings between the two terminal dialkoxyaromatic sidewalls. We report the X-ray crystal structure of 3b which shows that its dialkoxynaphthalene sidewalls actively define a hydrophobic cavity with high potential to engage in π–π interactions with insoluble aromatic guests. Compounds 1–3 possess very good solubility characteristics (≥38 mM) and undergo only very weak self-association (Ks < 92 M(−1)) in water. The weak self-association is attributed to unfavorable SO3(−)···SO3(−) electrostatic interactions in the putative dimers 12–42. Accordingly, we created phase solubility diagrams to study their ability to act as solubilizing agents for four water insoluble drugs (PBS-1086, camptothecin, β-estradiol, and ziprasidone). We find that the containers 3a and 3b which feature three glycoluril rings between the terminal dialkoxy-o-xylylene and dialkoxynaphthalene sidewalls are less efficient solubilizing agents than 4a and 4b because of their smaller hydrophobic cavities. Containers 1 and 2 behave as molecular clip type receptors and therefore possess the ability to bind to and thereby solubilize aromatic drugs like camptothecin, ziprasidone, and PBS-1086.

Acyclic Cucurbit[n]uril-Type Molecular Containers: Influence of Glycoluril Oligomer Length on their Function as Solubilizing Agents

PubMed Central

Gilberg, Laura; Zhang, Ben; Zavalij, Peter Y.; Sindelar, Vladimir; Isaacs, Lyle

2015-01-01

We present the synthesis of a series of six new glycoluril derived molecular clips and acyclic CB[n]-type molecular containers (1 – 3) that all feature SO3− solubilizing groups but differ in the number of glycoluril rings between the two terminal dialkoxyaromatic sidewalls. We report the x-ray crystal structure of 3b which shows that its dialkoxynaphthalene sidewalls actively define a hydrophobic cavity with high potential to engage in π–π interactions with insoluble aromatic guests. Compounds 1 – 3 possess very good solubility characteristics (≥ 38 mM) and undergo only very weak self-association (Ks < 92 M−1) in water. The weak self-association is attributed to unfavorable SO3−•••SO3− electrostatic interactions in the putative dimers 12 – 42. Accordingly, we created phase solubility diagrams to study their ability to act as solubilizing agents for four water insoluble drugs (PBS-1086, camptothecin, β-estradiol, and ziprasidone). We find that the containers 3a and 3b which feature three glycoluril rings between the terminal dialkoxy-o-xylylene and dialkoxynaphthalene sidewalls are less efficient solubilizing agents than 4a and 4b because of their smaller hydrophobic cavities. Containers 1 and 2 behave as molecular clip type receptors and therefore possess the ability to bind to and thereby solubilize aromatic drugs like camptothecin and ziprasidone, and PBS-1086. PMID:25731639

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuz'mina, L. G., E-mail: kuzmina@igic.ras.ru; Gunina, M. A.; Churakov, A. V.

Two aromatic esters with the formulas C{sub 6}H{sub 13}-O-C{sub 6}H{sub 4}-C(O)O-C{sub 6}H{sub 4}-O-C{sub 7}H{sub 15} (1) and C{sub 7}H{sub 15}-O-C{sub 6}H{sub 4}-C(O)O-C{sub 6}H{sub 4}-O-C{sub 4}H{sub 9} (2) belonging to nematic liquid-crystal compounds were studied by X-ray diffraction. Compound 1 crystallizes in two modifications: monoclinic (1-m) and triclinic (1-tr). The crystal packing of 1 and 2 is built from alternating loosely packed aliphatic regions and closely packed aromatic regions. In crystal structures 1-m and 2, the aromatic regions are linked into chains by hydrogen bonds with the participation of the carbonyl oxygen atom of the ester group and the C-H fragmentmore » of the benzene ring, but these hydrogen bonds in 1-m are much weaker than in 2. In 1-m there are {pi}-stacking interactions between the molecules, resulting in the formation of centrosymmetric dimers with an interplanar distance of 3.45 A. In 1-tr, the aromatic fragments form a herringbone packing motif favorable for a two-dimensional network of directional C-H...{pi}-system interactions.« less

Phase Behavior of Pyrene and Vinyl Polymers with Aromatic Side Groups

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kangovi, Gagan N.; Lee, Sangwoo

The phase behavior and thermodynamic properties of mixtures of pyrene and model vinyl polymers with and without aromatic side groups are investigated using differential scanning calorimetry (DSC) measurements. The melting temperature and associated heat of melting of the pyrene crystals in the mixtures are utilized to extract the effective interaction parameters χ and the composition of polymer-rich phases, respectively. The χ of pyrene mixed with polymers with aromatic side groups investigated in this study, polystyrene, poly(2-vinylpyridine), and poly(3-vinylanisole), is less than 0.5 at the melting point of the pyrene crystals, suggesting that pyrene and the polymers with aromatic sides groupsmore » are enthalpically compatible, likely due to aromatic π–π interactions. In contrast, the χ of pyrene mixed with poly(1,4-isoprene) or poly(ethylene-alt-propylene) is larger than 0.5. The DSC measurements also enable characterization of the composition of polymer-rich phases. Interestingly, the polymers with aromatic side groups are found to have more pronounced miscibility with pyrene at symmetric compositions.« less

Bulkiness or aromatic nature of tyrosine-143 of actin is important for the weak binding between F-actin and myosin-ADP-phosphate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gomibuchi, Yuki; Uyeda, Taro Q.P.; Wakabayashi, Takeyuki, E-mail: tw007@nasu.bio.teikyo-u.ac.jp

2013-11-29

Highlights: •The effect of mutation of Tyr143 that becomes more exposed on assembly was examined. •Mutation of tyrosine-143 of Dictyostelium actin changed actin polymerizability. •The bulkiness or aromatic nature of Tyr143 is important for the weak binding. •The weak interaction between myosin and actin strengthened by Tyr143Trp mutation. -- Abstract: Actin filaments (F-actin) interact with myosin and activate its ATPase to support force generation. By comparing crystal structures of G-actin and the quasi-atomic model of F-actin based on high-resolution cryo-electron microscopy, the tyrosine-143 was found to be exposed more than 60 Å{sup 2} to the solvent in F-actin. Because tyrosine-143more » flanks the hydrophobic cleft near the hydrophobic helix that binds to myosin, the mutant actins, of which the tyrosine-143 was replaced with tryptophan, phenylalanine, or isoleucine, were generated using the Dictyostelium expression system. It polymerized significantly poorly when induced by NaCl, but almost normally by KCl. In the presence of phalloidin and KCl, the extents of the polymerization of all the mutant actins were comparable to that of the wild-type actin so that the actin-activated myosin ATPase activity could be reliably compared. The affinity of skeletal heavy meromyosin to F-actin and the maximum ATPase activity (V{sub max}) were estimated by a double reciprocal plot. The Tyr143Trp-actin showed the higher affinity (smaller K{sub app}) than that of the wild-type actin, with the V{sub max} being almost unchanged. The K{sub app} and V{sub max} of the Tyr143Phe-actin were similar to those of the wild-type actin. However, the activation by Tyr143Ile-actin was much smaller than the wild-type actin and the accurate determination of K{sub app} was difficult. Comparison of the myosin ATPase activated by the various mutant actins at the same concentration of F-actin showed that the extent of activation correlates well with the solvent-accessible surface areas (ASA) of the replaced amino acid molecule. Because 1/K{sub app} reflects the affinity of F-actin for the myosin–ADP-phosphate intermediate (M.ADP.Pi) through the weak binding, these data suggest that the bulkiness or the aromatic nature of the tyrosin-143 is important for the initial binding of the M.ADP.Pi intermediate with F-actin but not for later processes such as the phosphate release.« less

Two unprecedented aromatic guanidines supramolecular chains self-assembled by hydrogen bonding interaction

NASA Astrophysics Data System (ADS)

Zhang, Yunshen; Huang, Yichao; Zhang, Jiangwei; Zhu, Li; Chen, Kun; Hao, Jian

2015-10-01

Two aromatic guanidine derivatives, C6H5N = C(NHCy)2 (1), (n-TBA)C6H5NHC(NHCy)2Mo2O7 (2) (Cy = cyclohexyl), were synthetized with high yields. Both of them self-assembled into supramolecules via H-bond interactions. Single crystal XRD indicated that crystal 1 showed helix chains combining pseudo four-fold and pseudo six-fold symmetries, while crystal 2 presented ladder chains with alternate ring structures. In this paper, a novel way to design ladder-like supramolecular chains from helix chains was presented, using POMs (polyoxometalates) to provide protons to help assembly.

Preferential deprotonation and conformational stability of dicarboxylic acids: A packing effect

NASA Astrophysics Data System (ADS)

Barooah, Nilotpal; Singh, W. Marjit; Baruah, Jubaraj B.

2008-03-01

Crystal structures of a series of salts of (6-carboxymethyl-1,3,5,7-tetraoxo-3,5,6,7-tetrahydro-1 H-pyrrolo[3,4- f]isoindol-2-yl)-acetic acid ( 1) and 2-carboxymethyl-1,3-dioxo-2,3-dihydro-1 H-isoinodole-5-carboxylic acid ( 2) with different polynuclear nitrogen containing heterocyclic compounds, namely, quinoline, 1,10-phenanthroline and 8-hydroxyquinoline are determined. In the case of salt of 1 with quinolinium and 1,10-phenanthrolinium cations syn disposition between the carboxylate anion and carboxylic acid groups is observed; whereas in the case of the 8-hydroxyquinolinium salt of 1, it is the anti disposition. It is also found that the solid state structure of 1,10-phenanthrolinium salt of 2 has deprotonation at the aromatic end, whereas in 8-hydroxy-quinolinium salt of 2 is formed by deprotonation of carboxylic acid group on the aliphatic side. The dicarboxylic acid 2 forms 1:2 co-crystals with quinoline. From crystallographic study it is shown that the weak interactions become prominent in stabilising the observed conformers and also in stabilising specific deprotonated species.

Crystal structure of 4-fluoro-N-[2-(4-fluoro­benzo­yl)hydra­zine-1-carbono­thio­yl]benzamide

PubMed Central

Firdausiah, Syadza; Salleh Huddin, Ameera Aqeela; Hasbullah, Siti Aishah; Yamin, Bohari M.; Yusoff, Siti Fairus M.

2014-01-01

In the title compound, C15H11F2N3O2S, the dihedral angle between the fluoro­benzene rings is 88.43 (10)° and that between the central semithiocarbazide grouping is 47.00 (11)°. The dihedral angle between the amide group and attached fluoro­benzene ring is 50.52 (11)°; the equivalent angle between the carbonyl­thio­amide group and its attached ring is 12.98 (10)°. The major twists in the mol­ecule occur about the C—N—N—C bonds [torsion angle = −138.7 (2)°] and the Car—Car—C—N (ar = aromatic) bonds [−132.0 (2)°]. An intra­molecular N—H⋯O hydrogen bond occurs, which generates an S(6) ring. In the crystal, the mol­ecules are linked by N—H⋯O and N—H⋯S hydrogen bonds, generating (001) sheets. Weak C—H⋯O and C—H⋯F inter­actions are also observed. PMID:25309250

Effects of Coke Deposits on the Catalytic Performance of Large Zeolite H-ZSM-5 Crystals during Alcohol-to-Hydrocarbon Reactions as Investigated by a Combination of Optical Spectroscopy and Microscopy

PubMed Central

Nordvang, Emily C; Borodina, Elena; Ruiz-Martínez, Javier; Fehrmann, Rasmus; Weckhuysen, Bert M

2015-01-01

The catalytic activity of large zeolite H-ZSM-5 crystals in methanol (MTO) and ethanol-to-olefins (ETO) conversions was investigated and, using operando UV/Vis measurements, the catalytic activity and deactivation was correlated with the formation of coke. These findings were related to in situ single crystal UV/Vis and confocal fluorescence micro-spectroscopy, allowing the observation of the spatiotemporal formation of intermediates and coke species during the MTO and ETO conversions. It was observed that rapid deactivation at elevated temperatures was due to the fast formation of aromatics at the periphery of the H-ZSM-5 crystals, which are transformed into more poly-aromatic coke species at the external surface, preventing the diffusion of reactants and products into and out of the H-ZSM-5 crystal. Furthermore, we were able to correlate the operando UV/Vis spectroscopy results observed during catalytic testing with the single crystal in situ results. PMID:26463581

Cooperativity of anion⋯π and π⋯π interactions regulates the self-assembly of a series of carbene proligands: Towards quantitative analysis of intermolecular interactions with Hirshfeld surface

NASA Astrophysics Data System (ADS)

Samanta, Tapastaru; Dey, Lingaraj; Dinda, Joydev; Chattopadhyay, Shyamal Kumar; Seth, Saikat Kumar

2014-06-01

The cooperative effect of weak non-covalent forces between anions and electron deficient aromatics by π⋯π stacking of a series of carbene proligands (1-3) have been thoroughly explored by crystallographic studies. Structural analysis revealed that the anion⋯π and π⋯π interactions along with intermolecular hydrogen bonding mutually cooperate to facilitate the assembling of the supramolecular framework. The π⋯π and corresponding anion⋯π interactions have been investigated in the title carbene proligands despite their association with counter ions. The presence of the anion in the vicinity of the π-system leads to the formation of anion⋯π/π⋯π/π⋯anion network for an inductive stabilization of the assemblies. To assess the dimensionality of the supramolecular framework consolidated by cooperative anion⋯π/π⋯π interactions and hydrogen bonding, different substituent effects in the carbene backbone have been considered to tune these interactions. These facts show that the supramolecular framework based on these cooperative weak forces may be robust enough for application in molecular recognition. The investigation of close intermolecular interactions between the molecules via Hirshfeld surface analyses is presented in order to reveal subtle differences and similarities in the crystal structures. The decomposition of the fingerprint plot area provides a percentage of each intermolecular interaction, allowing for a quantified analysis of close contacts within each crystal.

AROMATIC AMINES IN AND NEAR THE BUFFALO RIVER

EPA Science Inventory

Three sediment samples taken from the Buffalo River and two soil samples taken near its bank have been analyzed for 2-propanol-extractable, basic organic compounds by using GC/MS. Eleven aromatic amines related to the commercial production of malachite green and crystal violet we...

(E)-1-(2,4-Di-nitro-phen-yl)-2-(3-eth-oxy-4-hy-droxy-benzyl-idene)hydrazine.

PubMed

Fun, Hoong-Kun; Chantrapromma, Suchada; Ruanwas, Pumsak; Kobkeatthawin, Thawanrat; Chidan Kumar, C S

2014-01-01

The mol-ecule of the title hydrazine derivative, C15H14N4O6, is essentially planar, the dihedral angle between the substituted benzene rings being 2.25 (9)°. The eth-oxy and hy-droxy groups are almost coplanar with their bound benzene ring [r.m.s. deviation = 0.0153 (2) Å for the ten non-H atoms]. Intra-molecular N-H⋯O and O-H⋯Oeth-oxy hydrogen bonds generate S(6) and S(5) ring motifs, respectively. In the crystal, mol-ecules are linked by O-H⋯Onitro hydrogen bonds into chains propagating in [010]. Weak aromatic π-π inter-actions, with centroid-centroid distances of 3.8192 (19) and 4.0491 (19) Å, are also observed.

(S)-N-{1-[5-(4-Chloro-benzyl-sulfanyl)-1,3,4-oxadiazol-2-yl]eth-yl}-4-methyl-benzene-sulfonamide.

PubMed

Syed, Tayyaba; Hameed, Shahid; Jones, Peter G

2011-10-01

The title compound, C(18)H(18)ClN(3)O(3)S(2), adopts by folding the form of a distorted disc. Inter-planar angles are 29.51 (7) and 63.43 (7)° from the five-membered ring to the aromatic systems and 34.80 (6)° between these two latter rings. The absolute configuration was confirmed by determination of the Flack parameter. In the crystal, the mol-ecules are linked by four hydrogen bonds, one classical (N-H⋯N) and three 'weak' (C-H⋯O), forming layers parallel to the ac plane; these are in turn linked in the third dimension by Cl⋯N [3.1689 (16) Å] and Cl⋯O [3.3148 (13) Å] contacts to the heterocyclic ring.

Aqua-(3-fluoro-benzoato-κO)(3-fluoro-benzoato-κO,O')(1,10-phenanthroline-κN,N')cobalt(II).

PubMed

Wang, Xiao-Hui; Sun, Li-Mei

2012-01-01

In the title compound, [Co(C(7)H(4)FO(2))(2)(C(12)H(8)N(2))(H(2)O)], the Co(II) ion is coordinated by two O atoms from one 3-fluoro-benzoate (fb) ligand and one O atom from another fb ligand, two N atoms from the 1,10-phenanthroline ligand and a water mol-ecule in a distorted octa-hedral geometry. An intra-molecular O-H⋯O hydrogen bond occurs. Inter-molecular O-H⋯O hydrogen bonds link pairs of mol-ecules into centrosymmetric dimers. Weak inter-molecular C-H⋯O and C-H⋯F hydrogen bonds and π-π inter-actions between the aromatic rings [shortest centroid-centroid distance = 3.4962 (2) Å] further stabilize the crystal packing.

Time-Dependent Solid State Polymorphism of a Series of Donor-Acceptor Dyads

PubMed Central

Peebles, Cameron; Alvey, Paul M.; Lynch, Vincent; Iverson, Brent L.

2014-01-01

In order to exploit the use of favorable electrostatic interactions between aromatic units in directing the assembly of donor-acceptor (D-A) dyads, the present work examines the ability of conjugated aromatic D-A dyads with symmetric side chains to exhibit solid-state polymorphism as a function of time during the solid formation process. Four such dyads were synthesized and their packing in the solid-state from either slower (10-20 days) or faster (1-2 days) evaporation from solvent was investigated using single crystal X-ray analysis and powder X-ray diffraction. Two of the dyads exhibited tail-to-tail (A-A) packing upon slower evaporation from solvent and head-to-tail (D-A) packing upon faster evaporation from solvent. A combination of single crystal analysis and XRD patterns were used to create models wherein a packing model for the other two dyads is proposed. Our findings suggest that while side chain interactions in asymmetric aromatic dyads can play an important role in enforcing segregated D-A dyad assembly, slowly evaporating symmetrically substituted aromatic dyads allows for favorable electrostatic interactions between the aromatic moieties to facilitate the organization of the dyads in the solid-state. PMID:24678269

Study on four polymorphs of bifendate based on X-ray crystallography.

PubMed

Nie, Jinju; Yang, Dezhi; Hu, Kun; Lu, Yang

2016-05-01

Bifendate, a synthetic anti-hepatitis drug, exhibits polycrystalline mode phenomena with 2 polymorphs reported (forms A and B). Single crystals of the known crystalline form B and 3 new crystallosolvates involving bifendate solvated with tetrahydrofuran (C), dioxane (D), and pyridine (E) in a stoichiometric ratio of 1:1 were obtained and characterized by X-ray crystallography, thermal analysis, and Fourier transform infrared (FT-IR) spectroscopy. The differences in molecular conformation, intermolecular interaction and crystal packing arrangement for the four polymorphs were determined and the basis for the polymorphisms was investigated. The rotation of single bonds resulted in different orientations for the biphenyl, methyl ester and methoxyl groups. All guest solvent molecules interacted with the host molecule via an interesting intercalative mode along the [1 0 0] direction in the channel formed by the host molecules through weak aromatic stacking interactions or non-classical hydrogen bonds, of which the volume and planarity played an important role in the intercalation of the host with the guest. The incorporation of solvent-augmented rotation of the C-C bond of the biphenyl group had a striking effect on the host molecular conformation and contributed to the formation of bifendate polymorphs. Moreover, the simulated powder X-ray diffraction (PXRD) patterns for each form were calculated on the basis of the single-crystal data and proved to be unique. The single-crystal structures of the four crystalline forms are reported in this paper.

Weak crystallization theory of metallic alloys

DOE PAGES

Martin, Ivar; Gopalakrishnan, Sarang; Demler, Eugene A.

2016-06-20

Crystallization is one of the most familiar, but hardest to analyze, phase transitions. The principal reason is that crystallization typically occurs via a strongly first-order phase transition, and thus rigorous treatment would require comparing energies of an infinite number of possible crystalline states with the energy of liquid. A great simplification occurs when crystallization transition happens to be weakly first order. In this case, weak crystallization theory, based on unbiased Ginzburg-Landau expansion, can be applied. Even beyond its strict range of validity, it has been a useful qualitative tool for understanding crystallization. In its standard form, however, weak crystallization theorymore » cannot explain the existence of a majority of observed crystalline and quasicrystalline states. Here we extend the weak crystallization theory to the case of metallic alloys. In this paper, we identify a singular effect of itinerant electrons on the form of weak crystallization free energy. It is geometric in nature, generating strong dependence of free energy on the angles between ordering wave vectors of ionic density. That leads to stabilization of fcc, rhombohedral, and icosahedral quasicrystalline (iQC) phases, which are absent in the generic theory with only local interactions. Finally, as an application, we find the condition for stability of iQC that is consistent with the Hume-Rothery rules known empirically for the majority of stable iQC; namely, the length of the primary Bragg-peak wave vector is approximately equal to the diameter of the Fermi sphere.« less

Single crystal, liquid crystal, and hybrid organic semiconductors

NASA Astrophysics Data System (ADS)

Twieg, Robert J.; Getmanenko, Y.; Lu, Z.; Semyonov, A. N.; Huang, S.; He, P.; Seed, A.; Kiryanov, A.; Ellman, B.; Nene, S.

2003-07-01

The synthesis and characterization of organic semiconductors is being pursued in three primary structure formats: single crystal, liquid crystal and organic-inorganic hybrid. The strategy here is to share common structures, synthesis methods and fabrication techniques across these formats and to utilize common characterization tools such as the time of flight technique. The single crystal efforts concentrate on aromatic and heteroaromatic compounds including simple benzene derivatives and derivatives of the acenes. The structure-property relationships due to incorporation of small substituents and heteroatoms are being examined. Crystals are grown by solution, melt or vapor transport techniques. The liquid crystal studies exploit their self-organizing properties and relative ease of sample preparation. Though calamitic systems tha deliver the largest mobilities are higher order smectics, even some unusual twist grain boundary phases are being studied. We are attempting to synthesize discotic acene derivatives with appropriate substitution patterns to render them mesogenic. The last format being examined is the hybrid organic-inorganic class. Here, layered materials of alternating organic and inorganic composition are designed and synthesized. Typical materials are conjugated aromatic compounds, usually functinalized with an amine or a pyridine and reacted with appropriate reactive metal derivatives to incorporate them into metal oxide or sulfide layers.

(E)-1-(2,4-Di­nitro­phen­yl)-2-(3-eth­oxy-4-hy­droxy­benzyl­idene)hydrazine

PubMed Central

Fun, Hoong-Kun; Chantrapromma, Suchada; Ruanwas, Pumsak; Kobkeatthawin, Thawanrat; Chidan Kumar, C. S.

2014-01-01

The mol­ecule of the title hydrazine derivative, C15H14N4O6, is essentially planar, the dihedral angle between the substituted benzene rings being 2.25 (9)°. The eth­oxy and hy­droxy groups are almost coplanar with their bound benzene ring [r.m.s. deviation = 0.0153 (2) Å for the ten non-H atoms]. Intra­molecular N—H⋯O and O—H⋯Oeth­oxy hydrogen bonds generate S(6) and S(5) ring motifs, respectively. In the crystal, mol­ecules are linked by O—H⋯Onitro hydrogen bonds into chains propagating in [010]. Weak aromatic π–π inter­actions, with centroid–centroid distances of 3.8192 (19) and 4.0491 (19) Å, are also observed. PMID:24527018

Orphenadrinium picrate picric acid.

PubMed

Fun, Hoong-Kun; Hemamalini, Madhukar; Siddaraju, B P; Yathirajan, H S; Narayana, B

2010-02-24

The asymmetric unit of the title compound N,N-dimethyl-2-[(2-methyl-phen-yl)phenyl-meth-oxy]ethanaminium picrate picric acid, C(18)H(24)NO(+)·C(6)H(2)N(3)O(7) (-)·C(6)H(3)N(3)O(7), contains one orphenadrinium cation, one picrate anion and one picric acid mol-ecule. In the orphenadrine cation, the two aromatic rings form a dihedral angle of 70.30 (7)°. There is an intra-molecular O-H⋯O hydrogen bond in the picric acid mol-ecule, which generates an S(6) ring motif. In the crystal structure, the orphenadrine cations, picrate anions and picric acid mol-ecules are connected by strong inter-molecular N-H⋯O hydrogen bonds, π⋯π inter-actions between the benzene rings of cations and anions [centroid-centroid distance = 3.5603 (9) Å] and weak C-H⋯O hydrogen bonds, forming a three-dimensional network.

Evidence of C-F-P and aromatic π-F-P weak interactions in imidazolium ionic liquids and its consequences

NASA Astrophysics Data System (ADS)

Panja, Sumit Kumar; Srivastava, Nitin; Srivastava, Jyoti; Prasad, Namburi Eswara; Noothalapati, Hemanth; Shigeto, Shinsuke; Saha, Satyen

2018-04-01

A simple change from alkyl group to alkene in side chain of imidazolium cation with same anion resulted in a drastic impact on physical properties (e.g., melting point) from bmimPF6 IL to cmimPF6 IL. The underlying reasons have been elucidated by structural and interaction studies with the help of DSC, SCXRD, vibrational and multi-nuclear NMR spectroscopic techniques. Experiments reveal existence of new weak interactions involving the carbon and π cloud of the imidazolium aromatic ring with fluoride of PF6 anion (i.e., C2-F-P and π-F-P) in cmimPF6 but are absent in structurally similar prototype IL, bmimPF6. Though weak, these interactions helped to form ladder type supramolecular arrangement, resulting in quite high melting point for cmimPF6 IL compared to bmimPF6 IL. These findings emphasize that an IL system can behave uniquely because of the existence of uncommon weak interactions.

Crystal structures of HIV-1 nonnucleoside reverse transcriptase inhibitors: N-benzyl-4-methyl-benzimidazoles

NASA Astrophysics Data System (ADS)

Ziółkowska, Natasza E.; Michejda, Christopher J.; Bujacz, Grzegorz D.

2009-07-01

HIV-1 nonnucleoside reverse transcriptase inhibitors are potentially specific and effective drugs in AIDS therapy. The presence of two aromatic systems with an angled orientation in the molecule of the inhibitor is crucial for interactions with HIV-1 RT. The inhibitor drives like a wedge into the cluster of aromatic residues of RT HIV-1 and restrains the enzyme in a conformation that blocks the chemical step of nucleotide incorporation. Structural studies provide useful information for designing new, more active inhibitors. The crystal structures of four NNRTIs are presented here. The investigated compounds are derivatives of N-benzyl-4-methyl-benzimidazole with various aliphatic and aromatic substituents at carbon 2 positions and a 2,6-dihalogeno-substituted N-benzyl moiety. Structural data reported here show that the conformation of the investigated compounds is relatively rigid. Such feature is important for the nonnucleoside inhibitor binding to HIV-1 reverse transcriptase.

Models of S/π interactions in protein structures: Comparison of the H2S–benzene complex with PDB data

PubMed Central

Ringer, Ashley L.; Senenko, Anastasia; Sherrill, C. David

2007-01-01

S/π interactions are prevalent in biochemistry and play an important role in protein folding and stabilization. Geometries of cysteine/aromatic interactions found in crystal structures from the Brookhaven Protein Data Bank (PDB) are analyzed and compared with the equilibrium configurations predicted by high-level quantum mechanical results for the H2S–benzene complex. A correlation is observed between the energetically favorable configurations on the quantum mechanical potential energy surface of the H2S–benzene model and the cysteine/aromatic configurations most frequently found in crystal structures of the PDB. In contrast to some previous PDB analyses, configurations with the sulfur over the aromatic ring are found to be the most important. Our results suggest that accurate quantum computations on models of noncovalent interactions may be helpful in understanding the structures of proteins and other complex systems. PMID:17766371

Luminescent Li-based metal-organic framework tailored for the selective detection of explosive nitroaromatic compounds: direct observation of interaction sites.

PubMed

Kim, Tae Kyung; Lee, Jae Hwa; Moon, Dohyun; Moon, Hoi Ri

2013-01-18

A luminescent lithium metal-organic framework (MOF) is constructed from the solvothermal reaction of Li(+) and a well-designed organic ligand, bis(4-carboxyphenyl)-N-methylamine (H(2)CPMA). A Li-based MOF can detect an explosive aromatic compound containing nitro groups as an explosophore, by showing a dramatic color change with concurrent luminescence quenching in the solid state. The detection sites are proven directly through single-crystal-to-single-crystal transformations, which show strong interactions between the aromatic rings of the electron-rich CPMA(2-) molecules and the electron-deficient nitrobenzene.

Mechanochemical synthesis and structural characterization of three novel cocrystals of dimethylglyoxime with N-heterocyclic aromatic compounds and acetamide

NASA Astrophysics Data System (ADS)

Abidi, Syed Sibte Asghar; Azim, Yasser; Gupta, Abhishek Kumar; Pradeep, Chullikkattil P.

2017-12-01

With an aim to explore the interactions of (RR'Cdbnd Nsbnd OH) oxime moiety of dimethylglyoxime (DMG) with pyridyl ring of N-heterocyclic aromatic compounds and acetamide, three novel cocrystals of dimethylglyoxime with acridine (ACR), 1,10-phenanthroline monohydrate (PT) and acetamide (ACT) are reported. These three cocrystals were obtained with a mechanochemical synthesis approach and were characterized by single crystal X-ray diffraction (SCXRD), powder X-ray diffraction (PXRD), fourier transform-infrared spectroscopy (FT-IR), differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). Additionally, Hirshfeld surface analysis is used to investigate the intermolecular interaction and the crystal packing of cocrystals.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pang, Xiaoyun; Xu, Feng, E-mail: xuf@xtal.tsinghua.edu.cn; Bell, Stephen G.

The cytochrome P450 enzyme CYP203A1 from Rhodopseudomonas palustris binds a wide range of highly substituted aromatic compounds and may play an important role in the astonishing metabolic diversity of this organism. Crystals of CYP203A1 that diffract to 2.0 Å resolution have been obtained. Cytochrome P450 enzymes constitute a large family of haemoproteins that catalyze the monooxygenation of a great variety of endogenous and exogenous organic compounds. Cytochrome P450 203A1 (CYP203A1, RPA1009) from the metabolically versatile organism Rhodopseudomonas palustris binds a broad range of substrates, in particular substituted aromatic compounds. Crystals of CYP203A1 suitable for X-ray crystallography have been obtained andmore » diffraction data were collected in-house to 2.0 Å resolution from a single crystal. The crystals belong to space group P222, with unit-cell parameters a = 40.1, b = 95.1, c = 99.0 Å, α = β = γ = 90°. There is one protein molecule per asymmetric unit.« less

2,4,5-trihydroxy-3-methylacetophenone: A cellulosic chromophore as a case study of aromaticity

Treesearch

Nele Sophie Zwirchmayr; Thomas Elder; Markus Bacher; Andreas Hofinger-Horvath; Paul Kosma; Thomas Rosenau

2017-01-01

The title compound (2,4,5-trihydroxy-3-methylacetophenone, 1) was isolated as chromophore from aged cellulosic pulps. The peculiar feature of the compound is its weak aromatic system that can be converted into nonaromatic (quinoid or cyclic aliphatic) tautomers, depending on the conditions and reaction partners. In alkaline media, the participation of quinoid canonic...

Crystallization of a salt of a weak organic acid and base: solubility relations, supersaturation control and polymorphic behavior.

PubMed

Jones, H P; Davey, R J; Cox, B G

2005-03-24

Control of crystallization processes for organic salts is of importance to the pharmaceutical industry as many active pharmaceutical materials are marketed as salts. In this study, a method for estimating the solubility product of a salt of a weak acid and weak base from measured pH-solubility data is described for the first time. This allows calculation of the supersaturation of solutions at known pH. Ethylenediammonium 3,5-dinitrobenzoate is a polymorphic organic salt. A detailed study of the effects of pH, supersaturation, and temperature of crystallization on the physical properties of this salt shows that the desired polymorph may be produced by appropriate selection of the pH and supersaturation of crystallization. Crystal morphology is also controlled by these crystallization conditions.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gianetto, A.; Farag, H.I.; Blasetti, A.P.

Changes of the relative importance of intradiffusion on USY zeolite crystals were studied as a way of affecting selectivity of catalytic cracking reactions. Zeolite crystals were synthesized (Si/Al = 2.4), activated and stabilized using ion exchange and steam calcination to obtain USSY (Ultra Stable Submicron Y) zeolites. After the activation the zeolites were pelletized (45--60 [mu]m particles). USSYs were tested in a novel Riser Simulator. Results obtained show that total aromatics (BTX), benzene, C[sub 4] olefins, and coke were significantly affected with the change of zeolite crystal sizes. Gasolines produced with USSY zeolites contain less aromatics and particularly lower benzenemore » levels. Experimental results were analyzed with a model including several lumps: unconverted gas oil, gasoline, light gases, and coke. This model also accounts for catalyst deactivation as a function of coke on catalyst. Various kinetic parameters were determined with their corresponding spans for the 95% level of confidence.« less

Non-isothermal crystallization of poly(etheretherketone) aromatic polymer composite

NASA Technical Reports Server (NTRS)

Cebe, Peggy

1988-01-01

The nonisothermal crystallization kinetics of PEEK APC-2 and of 450G neat resin PEEK material were compared using a differential scanning calorimeter to monitor heat flow during crystallization; the effects of cooling rate on the crystallization temperature, the degree of crystallinity, and the conversion rate were investigated. A modified Avrami (1940) analysis was used to describe nonisothermal crystallization kinetics. It was found that, compared with the 450G neat resin PEEK, the nonisothermal crystallization of the PEEK APC-2 composite is characterized by higher initiation temperature, higher heat flow maximum temperature, and greater relative conversion by primary processes.

Crystal structures of bis-(phen-oxy)silicon phthalocyanines: increasing π-π inter-actions, solubility and disorder and no halogen bonding observed.

PubMed

Lessard, Benoît H; Lough, Alan J; Bender, Timothy P

2016-07-01

We report the syntheses and characterization of three solution-processable phen-oxy silicon phthalocyanines (SiPcs), namely bis-(3-methyl-phen-oxy)(phthalocyanine)silicon [(3MP)2-SiPc], C46H30N8O2Si, bis-(2-sec-butyl-phen-oxy)(phthalocyanine)silicon [(2secBP)2-SiPc], C44H24I2N8O2Si, and bis-(3-iodo-phen-oxy)(phthalocyanine)silicon [(3IP)2-SiPc], C52H42N8O2Si. Crystals grown of these compounds were characterized by single-crystal X-ray diffraction and the π-π inter-actions between the aromatic SiPc cores were studied. It was determined that (3MP)2-SiPc has similar inter-actions to previously reported bis-(3,4,5-tri-fluoro-phen-oxy)silicon phthalocyanines [(345 F)2-SiPc] with significant π-π inter-actions between the SiPc groups. (3IP)2-SiPc and (2secBP)2-SiPc both experienced a parallel stacking of two of the peripheral aromatic groups. In all three cases, the solubility of these mol-ecules was increased by the addition of phen-oxy groups while maintaining π-π inter-actions between the aromatic SiPc groups. The solubility of (2secBP)2-SiPc was significantly higher than other bis-phen-oxy-SiPcs and this was exemplified by the higher observed disorder within the crystal structure.

Global low-energy weak solution and large-time behavior for the compressible flow of liquid crystals

NASA Astrophysics Data System (ADS)

Wu, Guochun; Tan, Zhong

2018-06-01

In this paper, we consider the weak solution of the simplified Ericksen-Leslie system modeling compressible nematic liquid crystal flows in R3. When the initial data are of small energy and initial density is positive and essentially bounded, we prove the existence of a global weak solution in R3. The large-time behavior of a global weak solution is also established.

Rationalizing the photophysical properties of BODIPY laser dyes via aromaticity and electron-donor-based structural perturbations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Waddell, Paul G.; Liu, Xiaogang; Zhao, Teng

2015-05-01

The absorption and fluorescence properties of six boron dipyrromethene (BODIPY) laser dyes with simple non-aromatic substituents are rationalized by relating them to observable structural perturbations within the molecules of the dyes. An empirical relationship involving the structure and the optical properties is derived using a combination of single-crystal X-ray diffraction data, quantum chemical calculations and electronic constants: i.e. the tendency of the pyrrole bond lengths towards aromaticity and the UV-vis absorption and fluorescence wavelengths correlating with the electron-donor properties of the substituents. The effect of molecular conformation on the solid-state optical properties of the dyes is also discussed. The findingsmore » in this study also demonstrate the usefulness and limitations of using crystal structure data to develop structure-property relationships in this class of optical materials, contributing to the growing effort to design optoelectronic materials with tunable properties via molecular engineering.« less

Supramolecular features of 2-(chlorophenyl)-3-[(chlorobenzylidene)-amino]-2,3-dihydroquinazolin-4(1H)-ones: A combined experimental and computational study

NASA Astrophysics Data System (ADS)

Mandal, Arkalekha; Patel, Bhisma K.

2018-03-01

The molecular structures of two isomeric 2-(chlorophenyl)-3-[(chlorobenzylidene)-amino] substituted 2,3-dihydroquinazolin-4(1H)-ones have been determined via single crystal XRD. Both isomers contain chloro substitutions on each of the phenyl rings and as a result a broad spectrum of halogen mediated weak interactions are viable in their crystal structures. The crystal packing of these compounds is stabilized by strong N-H⋯O hydrogen bond and various weak, non-classical hydrogen bonds acting synergistically. Both the molecules contain a chiral center and the weak interactions observed in them are either chiral self-discriminatory or chiral self-recognizing in nature. The weak interactions and spectral features of the compounds have been studied through experimental as well as computational methods including DFT, MEP, NBO and Hiresfeld surface analyses. In addition, the effect of different weak interactions to dictate either chiral self-recognition or self-discrimination in crystal packing has been elucidated.

Evidence for a strong sulfur-aromatic interaction derived from crystallographic data.

PubMed

Zauhar, R J; Colbert, C L; Morgan, R S; Welsh, W J

2000-03-01

We have uncovered new evidence for a significant interaction between divalent sulfur atoms and aromatic rings. Our study involves a statistical analysis of interatomic distances and other geometric descriptors derived from entries in the Cambridge Crystallographic Database (F. H. Allen and O. Kennard, Chem. Design Auto. News, 1993, Vol. 8, pp. 1 and 31-37). A set of descriptors was defined sufficient in number and type so as to elucidate completely the preferred geometry of interaction between six-membered aromatic carbon rings and divalent sulfurs for all crystal structures of nonmetal-bearing organic compounds present in the database. In order to test statistical significance, analogous probability distributions for the interaction of the moiety X-CH(2)-X with aromatic rings were computed, and taken a priori to correspond to the null hypothesis of no significant interaction. Tests of significance were carried our pairwise between probability distributions of sulfur-aromatic interaction descriptors and their CH(2)-aromatic analogues using the Smirnov-Kolmogorov nonparametric test (W. W. Daniel, Applied Nonparametric Statistics, Houghton-Mifflin: Boston, New York, 1978, pp. 276-286), and in all cases significance at the 99% confidence level or better was observed. Local maxima of the probability distributions were used to define a preferred geometry of interaction between the divalent sulfur moiety and the aromatic ring. Molecular mechanics studies were performed in an effort to better understand the physical basis of the interaction. This study confirms observations based on statistics of interaction of amino acids in protein crystal structures (R. S. Morgan, C. E. Tatsch, R. H. Gushard, J. M. McAdon, and P. K. Warme, International Journal of Peptide Protein Research, 1978, Vol. 11, pp. 209-217; R. S. Morgan and J. M. McAdon, International Journal of Peptide Protein Research, 1980, Vol. 15, pp. 177-180; K. S. C. Reid, P. F. Lindley, and J. M. Thornton, FEBS Letters, 1985, Vol. 190, pp. 209-213), as well as studies involving molecular mechanics (G. Nemethy and H. A. Scheraga, Biochemistry and Biophysics Research Communications, 1981, Vol. 98, pp. 482-487) and quantum chemical calculations (B. V. Cheney, M. W. Schulz, and J. Cheney, Biochimica Biophysica Acta, 1989, Vol. 996, pp.116-124; J. Pranata, Bioorganic Chemistry, 1997, Vol. 25, pp. 213-219)-all of which point to the possible importance of the sulfur-aromatic interaction. However, the preferred geometry of the interaction, as determined from our analysis of the small-molecule crystal data, differs significantly from that found by other approaches. Copyright 2000 John Wiley & Sons, Inc.

(E)-1,2-Bis(4-fluoro­phen­yl)ethane-1,2-dione

PubMed Central

Fun, Hoong-Kun; Kia, Reza

2008-01-01

The title compound, C14H8F2O2, is a substituted benzil with an s-trans conformation of the dicarbonyl unit. This conformation is also shown by the O—C—C—O torsion angle of −110.65 (12)°. An unusual feature of the structure is the length, 1.536 (2) Å, of the central C—C bond connecting the carbonyl units, which is significantly longer than a normal Csp 2—Csp 2 single bond. This is probably the result of decreasing the unfavourable vicinal dipole–dipole inter­actions by increasing the distance between the two electronegative O atoms [O⋯O = 3.1867 (12) Å] and allowing orbital overlap of the dione with the π system of the benzene rings. The dihedral angle between the aromatic rings is 64.74 (5)°. In the crystal structure, neighbouring mol­ecules are linked together by weak inter­molecular C—H⋯O (× 2) hydrogen bonds. In addition, the crystal structure is further stabilized by inter­molecular π–π inter­actions with centroid–centroid distances in the range 3.6416 (6)–3.7150 (7) Å. PMID:21203308

Synthesis, structure and research on quasi-aromaticity of a new organically templated aluminoborate: [NH0.5C4H4NH0.5][AlB12O14(OH)12

NASA Astrophysics Data System (ADS)

Hu, HengBin; Chen, XiangYi; Deng, Song; Cai, Feng; Sun, YanQiong; Chen, YiPing

2012-02-01

By employing hydrothermal method, we identify a new organically templated aluminoborate [NH0.5C4H4NH0.5][AlB12O14(OH)12] which is structurally determined by single crystal X-ray diffraction and characterized by simulated and experimental IR, 2D IR COS (two-dimensional infrared correlation spectroscopy), NICS (nucleus-independent chemical shifts) and Mulliken charges calculations. Although the cluster anions [AlB12O14(OH)12]- is identical to the counterpart of compound reported by Lin et al. at 2008, we firstly bring up its quasi-aromaticity, discuss and confirm it by NICS, Mulliken charges calculations and magnetic-induced 2D IR COS, and conclude that three isolated and non-coplanar four-center six-electron π bonds of cluster could cooperate and interact with each other to form a closed conjugated large π orbital system, endowing the cluster anions with quasi-aromaticity. Thus, a one-dimensional chain is constructed by π-π stacked interaction between quasi-aromatic clusters and aromatic pyrazine along [1 0¯ 1] direction. The title compound crystallizes in monoclinic space group C2/c with a = 18.397(4), b = 12.0670(16), c = 11.075(2) Å, α = 90.00, β = 116.483(11), γ = 90.00°, Z = 4, V = 2200.6(7) Å, R = 0.0442 and wR = 0.1128 for 2689 observed reflections.

Influence of spacer moiety and length of end chain for the phase stability in complementary, double hydrogen bonded liquid crystals, MA:nOBAs

NASA Astrophysics Data System (ADS)

Ashok Kumar, A. V. N.; Chalapathi, P. V.; Srinivasulu, M.; Muniprasad, M.; Potukuchi, D. M.

2015-01-01

Supra molecular liquid crystals formed by the Hydrogen Bonding interaction between a non-mesogenic aliphatic dicarboxylic acid viz., COOHsbnd CH2sbnd COOH (Malonic Acid, MA); and mesogenic aromatic, N-(p-n-alkoxy benzoic)Acids, (i.e., nOBAs) for n = 3, 4, 5, 7, 8, 9, 10, 11 and 12, labeled as nOBA:COOHsbnd [CH2]msbnd COOH:nOBAs, abbreviated as MA:nOBAs are reported. 1H NMR and 13C NMR studies confirm the formation of HBLC complexes. Infrared (IR) studies confirm the complementary, double, alternative type of HB. Polarized Optical Microscopy (POM) and Differential Scanning Calorimetry (DSC) studies infer N, SmC, SmX, SmCRE, SmF, SmG LC phase variance. SmX phase exhibiting finger print texture grows in MA:nOBAs for n = 10, 11 and 12 by the interruption of SmC phase with decreasing temperature. Re-Entrant SmC (SmCRE) grows by the cooling of SmX. I-N, N-C, X-CRE, C-G, CRE-F, F-G and G-Solid transitions exhibit first order nature. C-X is found to be second order nature in n = 10 and 11. C-X in n = 12 and X-CRE and CRE-F transitions are found to be weak first order nature. Influence of lengths of end chain (n) and spacer (m) for the overall LC phase [ΔT]LC; tilted phase [ΔT]Tilt; SmC phase [ΔT]C and SmX phase [ΔT]X stabilities is discussed in the wake of data on other HBLCs with similar molecular structure. Prevalence of SmX phase in MA:nOBAs with m = 1 infers repulsive interaction between the π-electronic cloud of aromatic boards of nOBAs. Model molecule predicts a twisted configuration of π-cloud around the molecular long axis. Finger print texture of SmX validates the model.

(E)-2-[4-(Diethyl­amino)­styr­yl]-1-methyl­pyridinium 4-chloro­benzene­sulfonate monohydrate

PubMed Central

Fun, Hoong-Kun; Kaewmanee, Narissara; Chanawanno, Kullapa; Karalai, Chatchanok; Chantrapromma, Suchada

2011-01-01

In the title hydrated mol­ecular salt, C18H23N2 +·C6H4ClO3S−·H2O, which shows moderate biological activity against methicillin-resistant Staphylococcus aureus (MRSA), one ethyl group of the 2-[4-(diethyl­amino)­styr­yl]-1-methyl­pyridinium cation is disordered over two orientations in a 0.604 (13):0.396 (13) ratio. The main part of the cation is nearly planar with a dihedral angle of 4.50 (10)° between the pyridinium and benzene rings. In the crystal, the components are linked by O—H⋯O hydrogen bonds and C—H⋯O weak inter­actions. Aromatic π–π stacking inter­actions with centroid–centroid separations of 3.7363 (12) and 3.7490 (13) Å also occur. PMID:22059040

Anion-π interaction in metal-organic networks formed by metal halides and tetracyanopyrazine

NASA Astrophysics Data System (ADS)

Rosokha, Sergiy V.; Kumar, Amar

2017-06-01

Co-crystallization of tetracyanopyrazine, TCP, with the tetraalkylammonium salts of linear [CuBr2]-, planar [PtCl4]2- or [Pt2Br6]2-, or octahedral [PtBr6]2- complexes resulted in formation of the alternating [MlXn]m-/TCP stacks separated by the Alk4N+ cations. These hybrid stacks showed multiple short contacts between halide ligands of the [MlXn]m- complexes and carbon atoms of the TCP acceptor indicating strong anion-π bonding between these species. It confirmed that the anion-π interaction is sufficiently strong to bring together such disparate components as ionic metal complexes and neutral aromatic molecules regardless of the geometry of the coordination compound. Structural features of the solid-state stacks and [MlXn]m-·TCP dyads resulted from the quantum-mechanical computations suggests that the molecular-orbital (weakly-covalent) component play an important role in association of the [MlXn]m- complexes with the TCP acceptor.

Orphenadrinium picrate picric acid

PubMed Central

Fun, Hoong-Kun; Hemamalini, Madhukar; Siddaraju, B. P.; Yathirajan, H. S.; Narayana, B.

2010-01-01

The asymmetric unit of the title compound N,N-dimethyl-2-[(2-methyl­phen­yl)phenyl­meth­oxy]ethanaminium picrate picric acid, C18H24NO+·C6H2N3O7 −·C6H3N3O7, contains one orphenadrinium cation, one picrate anion and one picric acid mol­ecule. In the orphenadrine cation, the two aromatic rings form a dihedral angle of 70.30 (7)°. There is an intra­molecular O—H⋯O hydrogen bond in the picric acid mol­ecule, which generates an S(6) ring motif. In the crystal structure, the orphenadrine cations, picrate anions and picric acid mol­ecules are connected by strong inter­molecular N—H⋯O hydrogen bonds, π⋯π inter­actions between the benzene rings of cations and anions [centroid–centroid distance = 3.5603 (9) Å] and weak C—H⋯O hydrogen bonds, forming a three-dimensional network. PMID:21580426

Adsorption and separation of reactive aromatic isomers and generation and stabilization of their radicals within cadmium(II)-triazole metal-organic confined space in a single-crystal-to-single-crystal fashion.

PubMed

Liu, Qi-Kui; Ma, Jian-Ping; Dong, Yu-Bin

2010-05-26

A series of reactive group functionalized aromatics, namely 2-furaldehyde, 3-furaldehyde, 2-thenaldehyde, 3-thenaldehyde, o-toluidine, m-toluidine, p-toluidine, and aniline, can be absorbed by a CdL(2) (1; L = 4-amino-3,5-bis(4-pyridyl-3-phenyl)-1,2,4-triazole) porous framework in both vapor and liquid phases to generate new G(n) [symbol: see text] CdL(2) (n = 1, 2) host-guest complexes. In addition, the CdL(2) framework can be a shield to protect the active functional group (-CHO and -NH(2)) substituted guests from reaction with the outside medium containing their reaction partners. That is, aldehyde-substituted guests within the CdL(2) host become "stable" in the aniline phase and vice versa. Moreover, 1 displays a very strict selectivity for these reactive group substituted aromatic isomers and can completely separate these guest isomers under mild conditions (i.e., 2-furaldehyde vs 3-furaldehyde, 2-thenaldehyde vs 3-thenaldehyde, and o-toluidine vs m-toluidine vs p-toluidine). All adsorptions and separations are directly performed on the single crystals of 1. More interestingly, these reactive group substituted aromatics readily transform to the corresponding radicals within the CdL(2) host upon ambient light or UV light (355 nm) irradiation. Furthermore, the generated organic radicals are alive for 1 month within the interior cavity in air under ambient conditions. Simple organic radicals are highly reactive short-lived species, and they cannot be generally isolated and conserved under ambient conditions. Thus, the CdL(2) host herein could be considered as a radical generator and storage vessel.

European Scientific Notes. Volume 35. Number 1.

DTIC Science & Technology

1981-01-31

thermotropic polymers, primar- formed smectic phases. She also studied ily with aromatic polyesters. Dr. R.W. the orientation of liquid crystal ...booster synchrotron and Linac are switched studies of crystals where a very good off and the electrons are allowed to approximation to a point source...compounds in the temperature Cr in a MgO host crystal in magnetic range of 1 to 25 K and as a function of fields up to 2*S T at temperatures between

An excellent fluorescent dye with a twistable aromatic chain and its axially chiral crystals.

PubMed

Ma, Yan; Hao, Rui; Shao, Guangsheng; Wang, Yuan

2009-04-30

A new organic fluorescent dye, 2,4-dichloro-6-[p-(N,N-diethylamino)biphenylyl]-1,3,5-triazine (DBQ), with an electron withdrawing-donating pair bridged by a twistable aromatic chain has been synthesized. DBQ exhibits high fluorescence quantum yields (0.96 in hexane and 0.71 in THF), high extinction coefficients, and an excitation window extending up to approximately 480 nm. Due to the strong intramolecular charge transfer character, DBQ shows obviously solvent-dependent Stokes shifts with a value as high as 6360 cm(-1) in THF and controllable fluorescence emission in the visible region from "blue" to "orange". The axially chiral structures of DBQ crystals were clearly revealed by the X-ray analyses and CD spectroscopy measurements. Two enantiomers of DBQ were obtained by spontaneous resolution upon crystallization without any chiral auxiliary. The low rotation barriers around the interannular bonds in DBQ molecules resulted in an efficient and selective multiplication of each of the chiral structures when DBQ crystallized in THF at room temperature in the presence of an enantiopure crystal seed, leaving racemized DBQ molecules in the solution. The special crystalline properties of DBQ provided a new approach to the design and synthesis of organic chiral crystals. The photophysical properties of DBQ make it promising in the preparation of new fluorescent probes with high sensitivity.

1-(Hydroxy­meth­yl)pyrene

PubMed Central

Gruber, Tobias; Seichter, Wilhelm; Weber, Edwin

2010-01-01

The asymmetric unit of the title compound, C17H12O, contains two molecules, in which the fused aromatic ring systems are almost planar [maximum deviations = 0.0529 (9) and 0.0256 (9) Å]. In the crystal, aromatic π–π stacking inter­actions (perpendicular distance of centroids of about 3.4 Å) and strong O—H⋯O hydrogen bonds result in a helical arrangement of pyrenyl dimers. PMID:21579858

Syntheses and structure characterization of ten acid-base hybrid crystals based on N-containing aromatic brønsted bases and mineral acids

NASA Astrophysics Data System (ADS)

Lin, Zhihao; Jin, Shouwen; Li, Xiaoliang; Xiao, Xiao; Hu, Kaikai; Guo, Ming; Chi, Xinchen; Liu, Hui; Wang, Daqi

2017-10-01

Cocrystallization of the aromatic brønsted bases with a series of mineral acids gave a total of ten hybrid salts with the compositions: (2-methylquinoline)2: (hydrochloride acid): 3H2O [(HL1)+. (L1)·· (Cl-) · (H2O)3] (1), (6-bromobenzo[d]thiazol-2-amine): (hydrochloride acid) [(HL2)+. (Cl-)] (2), (6-bromobenzo[d]thiazol-2-amine): (nitric acid) [(HL2)+. (NO3-)] (3), (6-bromobenzo[d]thiazol-2-amine): (sulfuric acid) [(HL2)+ · (HSO4)-] (4), (6-bromobenzo[d]thiazol-2-amine): (phosphoric acid) [(HL2)+ · (H2PO4)-] (5), (5,7-dimethyl-1,8-naphthyridine-2-amine): (hydrochloride acid): 3H2O [(HL3)+ · (Cl-) (H2O)3] (6), (5,7-dimethyl-1,8-naphthyridine-2-amine): (hydrobromic acid): CH3OH [(HL3)+ · (Br)- · CH3OH] (7), (5,7-dimethyl-1,8-naphthyridine-2-amine): (sulfuric acid): H2O [(HL3)+ · (HSO4)- · H2O] (8), (2-aminophenol): (phosphoric acid) [(HL4)+ · (H2PO4)-] (9), and (2-amino-4-chlorophenol): (phosphoric acid) [(HL5)+ · (H2PO4)-] (10). The ten salts have been characterized by X-ray diffraction analysis, IR, and elemental analysis, and the melting points of all the salts were also reported. And their structural and supramolecular aspects are fully analyzed. The result reveals that among the ten investigated crystals the ring N of the heterocycle or the NH2 in the aminophenol are protonated when the acids are deprotonated, and the crystal packing is interpreted in terms of the strong charge-assisted classical hydrogen bonds between the NH+/NH3+ and deprotonated acidic groups. Further analysis of the crystal packing of the salts indicated that a different family of additional CHsbnd O, CHsbnd Cl, CH3sbnd N, CH3sbnd O, CHsbnd Br, CH3sbnd Br, Brsbnd Cl, Clsbnd S, Osbnd S, Osbnd O, Brsbnd S, Hsbnd H, and π-π associations contribute to the stabilization and expansion of the total high-dimensional frameworks. For the coexistence of the various weak nonbonding interactions these structures adopted homo or hetero supramolecular synthons or both. Some classical supramolecular synthons, such as R22(8), R42(8), R43(10) and R44(12), usually observed in the organic solids, were again shown to be involved in constructing most of these H-bonding networks.

Frozen Chirality of Tertiary Aromatic Amides: Access to Enantioenriched Tertiary α-Amino Acid or Amino Alcohol without Chiral Reagent.

PubMed

Mai, Thi Thoa; Viswambharan, Baby; Gori, Didier; Guillot, Régis; Naubron, Jean-Valère; Kouklovsky, Cyrille; Alezra, Valérie

2017-04-27

One of the fundamental and intriguing aspects of life is the homochirality of the essential molecules. In this field, the absolute asymmetric synthesis of α-amino acids is a major challenge. Herein, we report access, by chemical means, to tertiary α-amino acid derivatives in up to 96 % ee without using any chiral reagent. In our strategy, the dynamic axial chirality of tertiary aromatic amides is frozen in a crystal and is responsible for the stereoselectivity of the subsequent steps. Furthermore, we could control the configuration of the final product by manually sorting and selecting the initial crystals. Based on vibrational circular dichroism studies, we could rationalize the observed stereoselectivity. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Kinetic stabilization of Bacillus licheniformis alpha-amylase through introduction of hydrophobic residues at the surface.

PubMed

Machius, Mischa; Declerck, Nathalie; Huber, Robert; Wiegand, Georg

2003-03-28

It is generally assumed that in proteins hydrophobic residues are not favorable at solvent-exposed sites, and that amino acid substitutions on the surface have little effect on protein thermostability. Contrary to these assumptions, we have identified hyperthermostable variants of Bacillus licheniformis alpha-amylase (BLA) that result from the incorporation of hydrophobic residues at the surface. Under highly destabilizing conditions, a variant combining five stabilizing mutations unfolds 32 times more slowly and at a temperature 13 degrees C higher than the wild-type. Crystal structure analysis at 1.7 A resolution suggests that stabilization is achieved through (a) extension of the concept of increased hydrophobic packing, usually applied to cavities, to surface indentations, (b) introduction of favorable aromatic-aromatic interactions on the surface, (c) specific stabilization of intrinsic metal binding sites, and (d) stabilization of a beta-sheet by introducing a residue with high beta-sheet forming propensity. All mutated residues are involved in forming complex, cooperative interaction networks that extend from the interior of the protein to its surface and which may therefore constitute "weak points" where BLA unfolding is initiated. This might explain the unexpectedly large effect induced by some of the substitutions on the kinetic stability of BLA. Our study shows that substantial protein stabilization can be achieved by stabilizing surface positions that participate in underlying cooperatively formed substructures. At such positions, even the apparently thermodynamically unfavorable introduction of hydrophobic residues should be explored.

Altering the Polymorphic Accessibility of Polycyclic Aromatic Hydrocarbons with Fluorination

DOE PAGES

Hiszpanski, Anna M.; Woll, Arthur R.; Kim, Bumjung; ...

2017-04-25

Here, substituting hydrogen with fluorine is an extensively employed strategy to improve the macroscopic properties of compounds for use in fields as diverse as pharmaceutics and optoelectronics. The role fluorine substitution plays on polymorphism—the ability of a compound to adopt more than one crystal structure—has not been previously studied. Yet, this understanding is important as different polymorphs of the same compound can result in drastically different bulk properties (e.g., solubility, absorptivity, and conductivity). Strategies to either promote or suppress the crystallization of particular polymorphs are thus desired. Here, we show that substituting hydrogen with fluorine affects the polymorphic behavior ofmore » contorted hexabenzocoronene (cHBC). A polycyclic aromatic hydrocarbon and molecular semiconductor, cHBC exhibits two polymorphs (i.e., P2 1/c crystal structure which we refer to as polymorph I and a triclinic crystal structure which we refer to as polymorph II) that are accessible through postdeposition processing of amorphous films. While the same two polymorphs remain accessible in fluorinated derivatives of cHBC, fluorination appears to favor the formation of polymorph I, with progressively smaller energy barrier for transformation from polymorph II to polymorph I with fluorination.« less

Altering the Polymorphic Accessibility of Polycyclic Aromatic Hydrocarbons with Fluorination

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hiszpanski, Anna M.; Woll, Arthur R.; Kim, Bumjung

Here, substituting hydrogen with fluorine is an extensively employed strategy to improve the macroscopic properties of compounds for use in fields as diverse as pharmaceutics and optoelectronics. The role fluorine substitution plays on polymorphism—the ability of a compound to adopt more than one crystal structure—has not been previously studied. Yet, this understanding is important as different polymorphs of the same compound can result in drastically different bulk properties (e.g., solubility, absorptivity, and conductivity). Strategies to either promote or suppress the crystallization of particular polymorphs are thus desired. Here, we show that substituting hydrogen with fluorine affects the polymorphic behavior ofmore » contorted hexabenzocoronene (cHBC). A polycyclic aromatic hydrocarbon and molecular semiconductor, cHBC exhibits two polymorphs (i.e., P2 1/c crystal structure which we refer to as polymorph I and a triclinic crystal structure which we refer to as polymorph II) that are accessible through postdeposition processing of amorphous films. While the same two polymorphs remain accessible in fluorinated derivatives of cHBC, fluorination appears to favor the formation of polymorph I, with progressively smaller energy barrier for transformation from polymorph II to polymorph I with fluorination.« less

Crystal structure of a four-copper laccase complexed with an arylamine: insights into substrate recognition and correlation with kinetics.

PubMed

Bertrand, Thomas; Jolivalt, Claude; Briozzo, Pierre; Caminade, Eliane; Joly, Nathalie; Madzak, Catherine; Mougin, Christian

2002-06-11

Laccases are multicopper oxidases that catalyze the oxidation of a wide range of phenols or arylamines, and their use in industrial oxidative processes is increasing. We purified from the white rot fungus Trametes versicolor a laccase that exists as five different isozymes, depending on glycosylation. The 2.4 A resolution structure of the most abundant isozyme of the glycosylated enzyme was solved. The four copper atoms are present, and it is the first crystal structure of a laccase in its active form. The crystallized enzyme binds 2,5-xylidine, which was used as a laccase inducer in the fungus culture. This arylamine is a very weak reducing substrate of the enzyme. The cavity enclosing 2,5-xylidine is rather wide, allowing the accommodation of substrates of various sizes. Several amino acid residues make hydrophobic interactions with the aromatic ring of the ligand. In addition, two charged or polar residues interact with its amino group. The first one is an histidine that also coordinates the copper that functions as the primary electron acceptor. The second is an aspartate conserved among fungal laccases. The purified enzyme can oxidize various hydroxylated compounds of the phenylurea family of herbicides that we synthesized. These phenolic substrates have better affinities at pH 5 than at pH 3, which could be related to the 2,5-xylidine binding by the aspartate. This is the first high-resolution structure of a multicopper oxidase complexed to a reducing substrate. It provides a model for engineering laccases that are either more efficient or with a wider substrate specificity.

Soliton self-frequency shift controlled by a weak seed laser in tellurite photonic crystal fibers.

PubMed

Liu, Lai; Meng, Xiangwei; Yin, Feixiang; Liao, Meisong; Zhao, Dan; Qin, Guanshi; Ohishi, Yasutake; Qin, Weiping

2013-08-01

We report the first demonstration of soliton self-frequency shift (SSFS) controlled by a weak continuous-wave (CW) laser, from a tellurite photonic crystal fiber pumped by a 1560 nm femtosecond fiber laser. The control of SSFS is performed by the cross-gain modulation of the 1560 nm femtosecond laser. By varying the input power of the weak CW laser (1560 nm) from 0 to 1.17 mW, the soliton generated in the tellurite photonic crystal fiber blue shifts from 1935 to 1591 nm. The dependence of the soliton wavelength on the operation wavelength of the weak CW laser is also measured. The results show the CW laser with a wavelength tunable range of 1530-1592 nm can be used to control the SSFS generation.

Adsorption of aromatic hydrocarbons and ozone at environmental aqueous surfaces.

PubMed

Vácha, Robert; Cwiklik, Lukasz; Rezác, Jan; Hobza, Pavel; Jungwirth, Pavel; Valsaraj, Kalliat; Bahr, Stephan; Kempter, Volker

2008-06-05

Adsorption of environmentally important aromatic molecules on a water surface is studied by means of classical and ab initio molecular dynamics simulations and by reflection-absorption infrared spectroscopy. Both techniques show strong activity and orientational preference of these molecules at the surface. Benzene and naphthalene, which bind weakly to water surface with a significant contribution of dispersion interactions, prefer to lie flat on water but retain a large degree of orientational flexibility. Pyridine is more rigid at the surface. It is tilted with the nitrogen end having strong hydrogen bonding interactions with water molecules. The degree of adsorption and orientation of aromatic molecules on aqueous droplets has atmospheric implications for heterogeneous ozonolysis, for which the Langmuir-Hinshelwood kinetics mechanism is discussed. At higher coverages of aromatic molecules the incoming ozone almost does not come into contact with the underlying aqueous phase. This may rationalize the experimental insensitivity of the ozonolysis on the chemical nature of the substrate on which the aromatic molecules adsorb.

New Molecular Detections in TMC-1 with the Green Bank Telescope: Carbon-Chain and Aromatic Molecules

NASA Astrophysics Data System (ADS)

Burkhardt, Andrew Michael

2018-01-01

Polycyclic aromatic hydrocarbons (PAHs) and polycyclic aromatic nitrogen heterocycles PA(N)Hs are believed to be widespread throughout the Universe, and are likely responsible for the unidentified infrared bands. However, the individual detection of aromatic molecules has been limited to a single weak absorption feature of an infrared bending mode of benzene (c-C6H6). The cold core TMC-1 has long been a source of new molecular detections, particularly for unsaturated carbon-rich molecules that are appealing potential precursors of PA(N)Hs. Through deep observations with the Green Bank Telescope of TMC-1, we report the first rotational detection of an aromatic molecule, benzonitrile (c-C6H5CN), along with 8 new isotopologues of HC5N and HC7N and an entirely new molecular family (HC5O, HC7O). These new detections provide crucial insights to the formation of PAHs and the underlying carbon-chain chemistry of dark clouds.

Aromatic dipeptides and their salts—Solid-state linear-dichroic infrared (IR-LD) spectral analysis and ab initio calculations

NASA Astrophysics Data System (ADS)

Ivanova, Bojidarka B.

2008-07-01

Stereo-structural analysis and IR-bands assignment of the aromatic dipeptides L-tryrosyl- L-phenylalanine ( Tyr-Phe), L-phenylalanyl- L-tyrosine ( Phe-Tyr) and their hydrochloride salts have been carried out by means of IR-LD spectroscopy of oriented as nematic liquid crystal suspension solid samples. The experimental data are compared with known crystallographic ones and theoretical predicted geometries at RHF/ and UHF/6-31G**.

Single-particle spectroscopy on large SAPO-34 crystals at work: methanol-to-olefin versus ethanol-to-olefin processes.

PubMed

Qian, Qingyun; Ruiz-Martínez, Javier; Mokhtar, Mohamed; Asiri, Abdullah M; Al-Thabaiti, Shaeel A; Basahel, Suliman N; van der Bij, Hendrik E; Kornatowski, Jan; Weckhuysen, Bert M

2013-08-19

The formation of hydrocarbon pool (HCP) species during methanol-to-olefin (MTO) and ethanol-to-olefin (ETO) processes have been studied on individual micron-sized SAPO-34 crystals with a combination of in situ UV/Vis, confocal fluorescence, and synchrotron-based IR microspectroscopic techniques. With in situ UV/Vis microspectroscopy, the intensity changes of the λ=400 nm absorption band, ascribed to polyalkylated benzene (PAB) carbocations, have been monitored and fitted with a first-order kinetics at low reaction temperatures. The calculated activation energy (Ea ) for MTO, approximately 98 kJ mol(-1) , shows a strong correlation with the theoretical values for the methylation of aromatics. This provides evidence that methylation reactions are the rate-determining steps for the formation of PAB. In contrast for ETO, the Ea value is approximately 60 kJ mol(-1) , which is comparable to the Ea values for the condensation of light olefins into aromatics. Confocal fluorescence microscopy demonstrates that during MTO the formation of the initial HCP species are concentrated in the outer rim of the SAPO-34 crystal when the reaction temperature is at 600 K or lower, whereas larger HCP species are gradually formed inwards the crystal at higher temperatures. In the case of ETO, the observed egg-white distribution of HCP at 509 K suggests that the ETO process is kinetically controlled, whereas the square-shaped HCP distribution at 650 K is indicative of a diffusion-controlled process. Finally, synchrotron-based IR microspectroscopy revealed a higher degree of alkylation for aromatics for MTO as compared to ETO, whereas high reaction temperatures favor dealkylation processes for both the MTO and ETO processes. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Design of weak link channel-cut crystals for fast QEXAFS monochromators

DOE Office of Scientific and Technical Information (OSTI.GOV)

Polheim, O. von, E-mail: vonpolheim@uni-wuppertal.de; Müller, O.; Lützenkirchen-Hecht, D.

2016-07-27

A weak link channel-cut crystal, optimized for dedicated Quick EXAFS monochromators and measurements, was designed using finite element analysis. This channel-cut crystal offers precise detuning capabilities to enable suppression of higher harmonics in the virtually monochromatic beam. It was optimized to keep the detuning stable, withstanding the mechanical load, which occurs during oscillations with up to 50 Hz. First tests at DELTA (Dortmund, Germany), proved the design.

[Macromolecular aromatic network characteristics of Chinese power coal analyzed by synchronous fluorescence and X-ray diffraction].

PubMed

Ye, Cui-Ping; Feng, Jie; Li, Wen-Ying

2012-07-01

Coal structure, especially the macromolecular aromatic skeleton structure, has a strong influence on coke reactivity and coal gasification, so it is the key to grasp the macromolecular aromatic skeleton coal structure for getting the reasonable high efficiency utilization of coal. However, it is difficult to acquire their information due to the complex compositions and structure of coal. It has been found that the macromolecular aromatic network coal structure would be most isolated if small molecular of coal was first extracted. Then the macromolecular aromatic skeleton coal structure would be clearly analyzed by instruments, such as X-ray diffraction (XRD), fluorescence spectroscopy with synchronous mode (Syn-F), Gel permeation chromatography (GPC) etc. Based on the previous results, according to the stepwise fractional liquid extraction, two Chinese typical power coals, PS and HDG, were extracted by silica gel as stationary phase and acetonitrile, tetrahydrofuran (THF), pyridine and 1-methyl-2-pyrollidinone (NMP) as a solvent group for sequential elution. GPC, Syn-F and XRD were applied to investigate molecular mass distribution, condensed aromatic structure and crystal characteristics. The results showed that the size of aromatic layers (La) is small (3-3.95 nm) and the stacking heights (Lc) are 0.8-1.2 nm. The molecular mass distribution of the macromolecular aromatic network structure is between 400 and 1 130 amu, with condensed aromatic numbers of 3-7 in the structure units.

2-[(4-Chloro­phen­yl)selan­yl]-3,4-di­hydro-2H-benzo[h]chromene-5,6-dione: crystal structure and Hirshfeld analysis

PubMed Central

Prado, Karinne E.; Name, Luccas L.; Jotani, Mukesh M.

2017-01-01

The title organoselenium compound, C19H13ClO3Se {systematic name: 2-[(4-chloro­phen­yl)selan­yl]-2H,3H,4H,5H,6H-naphtho­[1,2-b]pyran-5,6-dione}, has the substituted 2-pyranyl ring in a half-chair conformation with the methyl­ene-C atom bound to the methine-C atom being the flap atom. The dihedral angle between the two aromatic regions of the mol­ecule is 9.96 (9)° and indicates a step-like conformation. An intra­molecular Se⋯O inter­action of 2.8122 (13) Å is noted. In the crystal, π–π contacts between naphthyl rings [inter-centroid distance = 3.7213 (12) Å] and between naphthyl and chloro­benzene rings [inter-centroid distance = 3.7715 (13) Å], along with C—Cl⋯π(chloro­benzene) contacts, lead to supra­molecular layers parallel to the ab plane, which are connected into a three-dimensional architecture via methyl­ene-C—H⋯O(carbon­yl) inter­actions. The contributions of these and other weak contacts to the Hirshfeld surface is described. PMID:28638659

From dense monomer salt crystals to CO2 selective microporous polyimides via solid-state polymerization.

PubMed

Unterlass, Miriam M; Emmerling, Franziska; Antonietti, Markus; Weber, Jens

2014-01-14

Fully aromatic polyimides are synthesized via solid-state polymerization of the corresponding monomer salts. The crystal structure of salts shows strong hydrogen bonding of the reactive groups and thereby paves the way for solid-state transformations. The polycondensation yields copies of the initial salt crystallite habits, accompanied by the development of a porosity especially suited for CO2.

Amination of electrophilic aromatic compounds by vicarious nucleophilic substitution

DOEpatents

Mitchell, Alexander R.; Pagoria, Philip F.; Schmidt, Robert D.

2000-01-01

The present invention relates to a process to aminate electrophilic aromatic compounds by vicarious nucleophilic substitution of hydrogen using quaternary hydrazinium salts. The use of trialkylhydrazinium halide, e.g., trimethylhydrazinium iodide, as well as hydroxylamine, alkoxylamines, and 4-amino-1,2,4-triazole to produce aminated aromatic structures, such as 1,3-diamino-2,4,6-trinitrobenzene (DATB), 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) and 3,5-diamino-2,4,6-trinitrotoluene (DATNT), is described. DATB and TATB are useful insensitive high explosives. TATB is also used for the preparation of benzenehexamine, a starting material for the synthesis of novel materials (optical imaging devices, liquid crystals, ferromagnetic compounds).

Crystal structure of 3-(2,5-di-meth-oxy-phen-yl)propionic acid.

PubMed

Bugenhagen, Bernhard; Al Jasem, Yosef; AlAzani, Mariam; Thiemann, Thies

2015-05-01

In the crystal of the title compound, C11H14O4, the aromatic ring is almost coplanar with the 2-position meth-oxy group with which it subtends a dihedral of 0.54 (2)°, while the 5-position meth-oxy group makes a corresponding dihedral angle of just 5.30 (2)°. The angle between the mean planes of the aromatic ring and the propionic acid group is 78.56 (2)°. The fully extended propionic side chain is in a trans configuration with a C-C-C-C torsion angle of -172.25 (7)°. In the crystal, hydrogen bonding is limited to dimer formation via R 2 (2)(8) rings. The hydrogen-bonded dimers are stacked along the b axis. The average planes of the two benzene rings in a dimer are parallel to each other, but at an offset of 4.31 (2) Å. Within neighbouring dimers along the [101] direction, the average mol-ecular benzene planes are almost perpendicular to each other, with a dihedral angle of 85.33 (2)°.

Impact of speciation on the electron charge transfer properties of nanodiamond drug carriers

NASA Astrophysics Data System (ADS)

Sun, Baichuan; Barnard, Amanda S.

2016-07-01

Unpassivated diamond nanoparticles (bucky-diamonds) exhibit a unique surface reconstruction involving graphitization of certain crystal facets, giving rise to hybrid core-shell particles containing both aromatic and aliphatic carbon. Considerable effort is directed toward eliminating the aromatic shell, but persistent graphitization of subsequent subsurface-layers makes perdurable purification a challenge. In this study we use some simple statistical methods, in combination with electronic structure simulations, to predict the impact of different fractions of aromatic and aliphatic carbon on the charge transfer properties of the ensembles of bucky-diamonds. By predicting quality factors for a variety of cases, we find that perfect purification is not necessary to preserve selectivity, and there is a clear motivation for purifying samples to improve the sensitivity of charge transfer reactions. This may prove useful in designing drug delivery systems where the release of (selected) drugs needs to be sensitive to specific conditions at the point of delivery.Unpassivated diamond nanoparticles (bucky-diamonds) exhibit a unique surface reconstruction involving graphitization of certain crystal facets, giving rise to hybrid core-shell particles containing both aromatic and aliphatic carbon. Considerable effort is directed toward eliminating the aromatic shell, but persistent graphitization of subsequent subsurface-layers makes perdurable purification a challenge. In this study we use some simple statistical methods, in combination with electronic structure simulations, to predict the impact of different fractions of aromatic and aliphatic carbon on the charge transfer properties of the ensembles of bucky-diamonds. By predicting quality factors for a variety of cases, we find that perfect purification is not necessary to preserve selectivity, and there is a clear motivation for purifying samples to improve the sensitivity of charge transfer reactions. This may prove useful in designing drug delivery systems where the release of (selected) drugs needs to be sensitive to specific conditions at the point of delivery. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr03068h

Molecular recognition in chiral smectic liquid crystals: the effect of core-core interactions and chirality transfer on polar order.

PubMed

Lemieux, Robert P

2007-12-01

This critical review focuses on the induction of polar order in smectic liquid crystal phases by dopants with axially chiral cores, and should be of interest to all practitioners of supramolecular chemistry. The variations in polarization power of these dopants with the core structure of the liquid crystal hosts is a manifestation of molecular recognition that reflects the nanosegregation of aromatic cores from paraffinic side-chains in smectic phases, and the collective effect of core-core interactions that enable the propagation of chiral perturbations.

Self-Assembly of New Arene-Ruthenium Rectangles Containing Triptycene Building Block and Their Application in Fluorescent Detection of Nitro Aromatics

PubMed Central

Dubey, Abhishek; Mishra, Anurag; Min, Jin Wook; Lee, Min Hyung; Kim, Hyunuk; Stang, Peter J.; Chi, Ki-Whan

2014-01-01

A suite of two new tetraruthenium metallarectangles 5 and 6 have been obtained from [2 + 2] self-assemblies between dipyridylethynyltriptycene 2 and one of the two dinuclear arene ruthenium clips, [Ru2 (μ-η4-OO∩OO) (η6-p-cymene)2][OTf]2 ; (OO∩OO = oxalate 3; 6,11-dihydroxy-5,12-naphthacenedionato (dotq) 4; OTf = triflate). These molecular rectangles are fully characterized by 1H NMR spectroscopy, electrospray mass spectrometry. A single crystal of 6 was suitable for X-ray diffraction structural characterization. These new metallarectangles showed fluorescence behavior in solution, have been examined for emission quenching effects with various aromatic compounds, and show high quenching selectivity and sensitivity towards nitroaromatics, particularly picric acid and trinitrotoluene. Excited-state charge transfer from the rectangles to nitro aromatic substrates can be used to develop selective fluorescent sensors for nitro aromatics. PMID:26321767

Likelihood of atom-atom contacts in crystal structures of halogenated organic compounds.

PubMed

Jelsch, Christian; Soudani, Sarra; Ben Nasr, Cherif

2015-05-01

The likelihood of occurrence of intermolecular contacts in crystals of halogenated organic compounds has been analysed statistically using tools based on the Hirshfeld surface. Several families of small halogenated molecules (containing organic F, Cl, Br or I atoms) were analysed, based on chemical composition and aromatic or aliphatic character. The behaviour of crystal contacts was also probed for molecules containing O or N. So-called halogen bonding (a halogen making short interactions with O or N, or a π interaction with C) is generally disfavoured, except when H is scarce on the molecular surface. Similarly, halogen⋯halogen contacts are more rare than expected, except for molecules that are poor in H. In general, the H atom is found to be the preferred partner of organic halogen atoms in crystal structures. On the other hand, C⋯C interactions in parallel π-stacking have a high propensity to occur in halogenated aromatic molecules. The behaviour of the four different halogen species (F, Cl, Br, I) is compared in several chemical composition contexts. The analysis tool can be refined by distinguishing several types for a given chemical species, such as H atoms bound to O or C. Such distinction shows, for instance, that C-H⋯Cl and O-H⋯O are the preferred interactions in compounds containing both O and Cl.

The Triplet State

NASA Astrophysics Data System (ADS)

Zahlan, A. B.

2010-01-01

Preface; List of participants; Part I. Spin-orbit Coupling and Intersystem Crossing: 1. Spin-orbit interactions in organic molecules; 2. Singlet-triplet transitions in organic molecules; 3. Triplet decay and intersystem crossing in aromatic hydrocarbons; 4. Statistical aspects of resonance energy transfer; Discussion; Part II. Magnetic Resonance and Magnetic Interactions: 5. Magnetic resonance spectra of organic molecules in triplet states in single crystals; 6. Magnetic interactions related to phosphorescence; 7. ESR investigations of naphthalene-d8:Naphthalene-h8 mixed crystals; 8. Biradicals and polyradicals in the nitroxide series; 9. Changes induced in the phosphorescent radiation of aromatic molecules by paramagnetic resonance in their metastable triplet states; 10. Paramagnetic resonance of the triplet state of tetramethylpyrazine; 11. On magnetic dipole contributions to the intrinsic S0 = T1 transition in simple aromatics; Discussion; Part III. Photochemistry: 12. The kinetics of energy transfer from the triplet state in rigid solutions; 13. Triplet states in gas-phase photochemistry; 14. Biphotonic photochemistry, involving the triplet state: polarisation of the effective T-T transition and solvent effects; 15. Direct and sensitised photo-oxidation of aromatic hydrocarbons in boric acid glass; Discussion; Part IV. Radiationless Transitions: 16. Radiationless transitions in gaseous benzene; 17. Low-lying excited triplet states and intersystem crossing in aromatic hydrocarbons; 18. De-excitation rates of triplet states in condensed media; 19. Lifetimes of the triplet state of aromatic hydrocarbons in the vapour phase; Discussion; Part V. Triplet Excitons: 20. Some comments on the properties of triplet excitons in molecular crystals; 21. Exact treatment of coherent and incoherent triplet exciton migration; 22. Magnetic susceptibility of a system of triplet excitons: Würster's Blue Perchlorate; 23. A study of triplet excitons in anthracene crystals under laser excitation; 24. The electronic states in crystaline anthracene; Discussion; Part VI. Delayed Fluorescent and Phosphorescence: 25. Delayed fluorescence of solutions; 26. The kinetics of the excited states of anthracene and phenanthrene vapor; 27. Optical investigations of the triplet states of naphthalene in different crystalline environments; 28. Excitation of the triplet states of organic molecules; 29. The delayed luminescence and triplet quantum yields of pyrene solutions; 30. Triplet state studies of some polyphenyls in rigid glasses; 31. Decay time of delayed fluorescence of anthracene as a function of temperature (2-30ºK); 32. Energy transfer between benzene and biacetyl and the lifetime of triplet benzene in the gas phase; 33. Charge transfer triplet state of molecular complexes. 34. Flash-photolytic detection of triplet acridine formed by energy transfer from biacetyl; 35. Extinction coefficients of triplet-triplet transitions between 3000 and 8800 A in anthracene; 36. Anthracene triplet-triplet annihilation rate constant; Discussion; Part VII. Triplet State Related to Biology: 37. ESR and optical studies of some triplet states of biological interest; 38. The triplet state of DNA; 39. Some characteristics of the triplet states of the nucleic bases; Discussion; Indexes.

Cation-π Interactions: Computational Analyses of the Aromatic Box Motif and the Fluorination Strategy for Experimental Evaluation

PubMed Central

Davis, Matthew R.; Dougherty, Dennis A.

2015-01-01

Cation-π interactions are common in biological systems, and many structural studies have revealed the aromatic box as a common motif. With the aim of understanding the nature of the aromatic box, several computational methods were evaluated for their ability to reproduce experimental cation-π binding energies. We find the DFT method M06 with the 6-31G(d,p) basis set performs best of several methods tested. The binding of benzene to a number of different cations (sodium, potassium, ammonium, tetramethylammonium, and guanidinium) was studied. In addition, the binding of the organic cations NH4+ and NMe4+ to ab initio generated aromatic boxes as well as examples of aromatic boxes from protein crystal structures were investigated. These data, along with a study of the distance dependence of the cation-π interaction, indicate that multiple aromatic residues can meaningfully contribute to cation binding, even with displacements of more than an angstrom from the optimal cation-π interaction. Progressive fluorination of benzene and indole was studied as well, and binding energies obtained were used to reaffirm the validity of the “fluorination strategy” to study cation-π interactions in vivo. PMID:26467787

Cation-π interactions: computational analyses of the aromatic box motif and the fluorination strategy for experimental evaluation.

PubMed

Davis, Matthew R; Dougherty, Dennis A

2015-11-21

Cation-π interactions are common in biological systems, and many structural studies have revealed the aromatic box as a common motif. With the aim of understanding the nature of the aromatic box, several computational methods were evaluated for their ability to reproduce experimental cation-π binding energies. We find the DFT method M06 with the 6-31G(d,p) basis set performs best of several methods tested. The binding of benzene to a number of different cations (sodium, potassium, ammonium, tetramethylammonium, and guanidinium) was studied. In addition, the binding of the organic cations NH4(+) and NMe4(+) to ab initio generated aromatic boxes as well as examples of aromatic boxes from protein crystal structures were investigated. These data, along with a study of the distance dependence of the cation-π interaction, indicate that multiple aromatic residues can meaningfully contribute to cation binding, even with displacements of more than an angstrom from the optimal cation-π interaction. Progressive fluorination of benzene and indole was studied as well, and binding energies obtained were used to reaffirm the validity of the "fluorination strategy" to study cation-π interactions in vivo.

Deducing 2D crystal structure at the liquid/solid interface with atomic resolution: a combined STM and SFG study.

PubMed

McClelland, Arthur A; Ahn, Seokhoon; Matzger, Adam J; Chen, Zhan

2009-11-17

Sum frequency generation vibrational spectroscopy (SFG) has been applied to study two-dimensional (2D) crystals formed by an isophthalic acid diester on the surface of highly oriented pyrolytic graphite, providing complementary measurements to scanning tunneling microscopy (STM) and computational modeling. SFG results indicate that both aromatic and C=O groups in the 2D crystal tilt from the surface. This study demonstrates that a combination of SFG and STM techniques can be used to gain a more complete picture of 2D crystal structure, and it is necessary to consider solvent-2D crystal interactions and dynamics in the computer models to achieve an accurate representation of interfacial structure.

Noncovalent Polymerization of Mesogens Crystallizes Lysozyme: Correlation between Nonamphiphilic Lyotropic Liquid Crystal Phase and Protein Crystal Formation

PubMed Central

Simon, Karen A.; Shetye, Gauri S.; Englich, Ulrich; Wu, Lei; Luk, Yan-Yeung

2011-01-01

Crystallization of proteins is important for fundamental studies and biopharmaceutical development but remains largely an empirical science. Here, we report the use of organic salts that can form a class of unusual non-amphiphilic lyotropic liquid crystals to crystallize the protein lysozyme. Certain non-amphiphilic organic molecules with fused aromatic rings and two charges can assemble into stable thread-like noncovalent polymers that may further form liquid crystal phases in water, traditionally termed chromonic liquid crystals. Using five of these mesogenic molecules as additives to induce protein crystallization, we discover that molecules that can form liquid crystal phases in water are highly effective at inducing the crystal formation of lysozyme, even at concentrations significantly lower than that required for forming liquid crystal phases. This result reveals an example of inducing protein crystallization by the molecular assembly of the additives, and is consistent with a new mechanism by which the strong hydration of an assembly process provides a gradual means to compete for the water molecules to enable solvated proteins to form crystals. PMID:21786812

Quantitative study of interactions between oxygen lone pair and aromatic rings: substituent effect and the importance of closeness of contact.

PubMed

Gung, Benjamin W; Zou, Yan; Xu, Zhigang; Amicangelo, Jay C; Irwin, Daniel G; Ma, Shengqian; Zhou, Hong-Cai

2008-01-18

Current models describe aromatic rings as polar groups based on the fact that benzene and hexafluorobenzene are known to have large and permanent quadrupole moments. This report describes a quantitative study of the interactions between oxygen lone pair and aromatic rings. We found that even electron-rich aromatic rings and oxygen lone pairs exhibit attractive interactions. Free energies of interactions are determined using the triptycene scaffold and the equilibrium constants were determined by low-temperature 1H NMR spectroscopy. An X-ray structure analysis for one of the model compounds confirms the close proximity between the oxygen and the center of the aromatic ring. Theoretical calculations at the MP2/aug-cc-pVTZ level corroborate the experimental results. The origin of attractive interactions was explored by using aromatic rings with a wide range of substituents. The interactions between an oxygen lone pair and an aromatic ring are attractive at van der Waals' distance even with electron-donating substituents. Electron-withdrawing groups increase the strength of the attractive interactions. The results from this study can be only partly rationalized by using the current models of aromatic system. Electrostatic-based models are consistent with the fact that stronger electron-withdrawing groups lead to stronger attractions, but fail to predict or rationalize the fact that weak attractions even exist between electron-rich arenes and oxygen lone pairs. The conclusion from this study is that aromatic rings cannot be treated as a simple quadrupolar functional group at van der Waals' distance. Dispersion forces and local dipole should also be considered.

Free energy surfaces for the interaction of D-glucose with planar aromatic groups in aqueous solution

NASA Astrophysics Data System (ADS)

Wohlert, Jakob; Schnupf, Udo; Brady, John W.

2010-10-01

Multidimensional potentials of mean force for the interactions in aqueous solution of both anomers of D-glucopyranose with two planar aromatic molecules, indole and para-methyl-phenol, have been calculated using molecular dynamics simulations with umbrella sampling and were subsequently used to estimate binding free energies. Indole and para-methyl-phenol serve as models for the side chains of the amino acids tryptophan and tyrosine, respectively. In all cases, a weak affinity between the glucose molecules and the flat aromatic surfaces was found. The global minimum for these interactions was found to be for the case when the pseudoplanar face of β-D-glucopyranose is stacked against the planar surfaces of the aromatic residues. The calculated binding free energies are in good agreement with both experiment and previous simulations. The multidimensional free energy maps suggest a mechanism that could lend kinetic stability to the complexes formed by sugars bound to sugar-binding proteins.

In-situ study on growth units of Ba2Mg(B3O6)2 crystal

NASA Astrophysics Data System (ADS)

Lv, X. S.; Sun, Y. L.; Tang, X. L.; Wan, S. M.; Zhang, Q. L.; You, J. L.; Yin, S. T.

2013-05-01

BMBO (Ba2Mg(B3O6)2 crystal) is an excellent birefringent crystal and a potential stimulated Raman scattering (SRS) crystal. In this paper, high temperature Raman spectroscopy was used to in-situ study the melt structure near a BMBO crystal-melt interface. [B3O6]3- groups were found in this region. The result reveals that both of BaO bonds and MgO bonds are the weak bonds in the BMBO crystal structure. During the melting process, the crystal structure broke into Ba2+ ions, Mg2+ ions and [B3O6]3- groups. Our experimental results confirmed that the well-developed faces of BMBO crystals are the (001), (101) and (012) faces. Based on attachment energy theory, the crystal growth habit was discussed. The (001) (101) and (012) crystal faces linked by the weak BaO bonds and MgO bonds have smaller attachment energies and slower growth rates, and thus present in the final morphology. The (012) crystal face has a multi-terrace structure, which suggests that BMBO crystal grows with a layer-by-layer mode.

Role of Urea-Aromatic Stacking Interactions in Stabilizing the Aromatic Residues of the Protein in Urea-Induced Denatured State.

PubMed

Goyal, Siddharth; Chattopadhyay, Aditya; Kasavajhala, Koushik; Priyakumar, U Deva

2017-10-25

A delicate balance of different types of intramolecular interactions makes the folded states of proteins marginally more stable than the unfolded states. Experiments use thermal, chemical, or mechanical stress to perturb the folding equilibrium for examining protein stability and the protein folding process. Elucidation of the mechanism by which chemical denaturants unfold proteins is crucial; this study explores the nature of urea-aromatic interactions relevant in urea-assisted protein denaturation. Free energy profiles corresponding to the unfolding of Trp-cage miniprotein in the presence and absence of urea at three different temperatures demonstrate the distortion of the hydrophobic core to be a crucial step. Exposure of the Trp6 residue to the solvent is found to be favored in the presence of urea. Previous experiments showed that urea has a high affinity for aromatic groups of proteins. We show here that this is due to the remarkable ability of urea to form stacking and NH-π interactions with aromatic groups of proteins. Urea-nucleobase stacking interactions have been shown to be crucial in urea-assisted RNA unfolding. Examination of these interactions using microsecond-long unrestrained simulations shows that urea-aromatic stacking interactions are stabilizing and long lasting. Further MD simulations, thermodynamic integration, and quantum mechanical calculations on aromatic model systems reveal that such interactions are possible for all the aromatic amino acid side-chains. Finally, we validate the ubiquitous nature of urea-aromatic stacking interactions by analyzing experimental structures of urea transporters and proteins crystallized in the presence of urea or urea derivatives.

Proton nuclear magnetic resonance characterization of the aromatic residues in the variant-3 neurotoxin from Centruroides sculpturatus Ewing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krishna, N.R.; Nettesheim, D.G.; Klevit, R.E.

1989-02-21

The amino acid sequence for the variant-3 (CsE-v3) toxin from the venom of the scorpion Centruroides sculpturatus Ewing contains eight aromatic residues. By use of 2D NMR spectroscopic methods, the resonances from the individual protons (NH, C{sup alpha}H, C{sup beta}H{prime}, H{double prime}, and the ring) for each of the individual aromatic residues have been completely assigned. The spatial arrangement of the aromatic ring systems with respect to each other has been qualitatively analyzed by 2D-NOESY techniques. The results show that Trp-47, Tyr-4, and Tyr-42 are in close spatial proximity to each other. The NOESY contacts and the ring current inducedmore » shifts in the resonances of the individual protons of Tyr-4 and Trp-47 suggest that the aromatic ring planes of these residues are in an orthogonal arrangement. A comparison with the published crystal structure suggests that there is a minor rearrangement of the aromatic rings in the solution phase. No 2D-NOESY contacts involving Phe-44 and Tyr-14 to any other aromatic ring protons have been observed. The pH dependence of the aromatic ring proton chemical shifts has also been studied. These results suggest that the Tyr-58 phenolic group is experiencing a hydrogen-bonding interaction with a positively charged group, while Tyr-4, -14, -38, and -40 are experiencing through-space interactions with proximal negatively charged groups. These studies define the microenvironment of the aromatic residues in the variant-3 neurotoxin in aqueous solution.« less

Towards vaporized molecular discrimination: a quartz crystal microbalance (QCM) sensor system using cobalt-containing mesoporous graphitic carbon.

PubMed

Tang, Jing; Torad, Nagy L; Salunkhe, Rahul R; Yoon, Jang-Hee; Al Hossain, Md Shahriar; Dou, Shi Xue; Kim, Jung Ho; Kimura, Tatsuo; Yamauchi, Yusuke

2014-11-01

A recent study on nanoporous carbon based materials (J. Am. Chem. Soc. 2012, 134, 2864) showed that the presence of abundant graphitized sp(2) carbon species in the frameworks led to higher affinity for aromatic hydrocarbons than their aliphatic analogues. Herein, improved understanding of the sensitive and selective detection of aromatic substances by using mesoporous carbon (MPC)-based materials, combined with a quartz crystal microbalance (QCM) sensor system, was obtained. MPCs were synthesized by direct carbonization of mesoporous polymers prepared from resol through a soft templating approach with Pluronic F127. The carbon-based frameworks can be graphitized through the addition of a cobalt source to the precursor solution, according to the catalytic activity of the cobalt nanoparticles formed during the carbonization process. From the Raman data, the degree of the graphitization was clearly increased by increasing the cobalt content and elevating the carbonization temperature. From a QCM study, it was proved that the highly graphitized MPCs exhibited a higher affinity for aromatic hydrocarbons than their aliphatic analogues. By increasing the degree of graphitization in the carbon-based pore walls, the MPCs showed both larger adsorption uptake and faster sensor response towards toxic benzene and toluene vapors. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evolution of molecular crystal optical phonons near structural phase transitions

NASA Astrophysics Data System (ADS)

Michki, Nigel; Niessen, Katherine; Xu, Mengyang; Markelz, Andrea

Molecular crystals are increasingly important photonic and electronic materials. For example organic semiconductors are lightweight compared to inorganic semiconductors and have inexpensive scale up processing with roll to roll printing. However their implementation is limited by their environmental sensitivity, in part arising from the weak intermolecular interactions of the crystal. These weak interactions result in optical phonons in the terahertz frequency range. We examine the evolution of intermolecular interactions near structural phase transitions by measuring the optical phonons as a function of temperature and crystal orientation using terahertz time-domain spectroscopy. The measured orientation dependence of the resonances provides an additional constraint for comparison of the observed spectra with the density functional calculations, enabling us to follow specific phonon modes. We observe crystal reorganization near 350 K for oxalic acid as it transforms from dihydrate to anhydrous form. We also report the first THz spectra for the molecular crystal fructose through its melting point.

Crystal structure of zwitterionic bisimidazolium sulfonates

NASA Astrophysics Data System (ADS)

Kohmoto, Shigeo; Okuyama, Shinpei; Yokota, Nobuyuki; Takahashi, Masahiro; Kishikawa, Keiki; Masu, Hyuma; Azumaya, Isao

2012-05-01

Crystal structures of three zwitterionic bisimidazolium salts 1-3 in which imidazolium sulfonate moieties were connected with aromatic linkers, p-xylylene, 4,4'-dimethylenebiphenyl, and phenylene, respectively, were examined. The latter two were obtained as hydrates. An S-shaped molecular structure in which the sulfonate moiety was placed on the imidazolium ring was observed for 1. A helical array of hydrated water molecules was obtained for 2 while a linear array of hydrated water molecules was observed for 3.

Structure of complex of N-methylpiperidine betaine with p-hydroxybenzoic acid studied by X-ray, FT-IR and DFT methods

NASA Astrophysics Data System (ADS)

Dega-Szafran, Z.; Dutkiewicz, G.; Kosturkiewicz, Z.; Szafran, M.

2008-03-01

Crystal structure of the complex of N-methylpiperidine betaine ( N-carboxymethyl- N-methylpiperidinium inner salt, MPB) with p-hydroxybenzoic acid (HBA) has been determined by X-ray diffraction. The crystals are triclinic, space group Pī, with a = 6.1156(5), b = 10.6869(10), c = 12.0320(10) Å, α = 109.55(1)°, β = 95.25(1)°, γ = 99.22(1)°, Z = 2, R = 0.034. Two molecules of p-hydroxybenzoic acid and two molecules of N-methylpiperidine betaine are linked together forming a centrosymmetric dimer, (MPB·HBA) 2, by four O-H···O hydrogen bonds of lengths 2.622(1) and 2.617(1) Å, between the carboxylic and hydroxy groups of HBA and both oxygen atoms of the carboxylate group of MPB, respectively. The piperidine ring has a chair conformation with the CH 2COO - substituent in the axial position and the CH 3 group in the equatorial one. Two parallel aromatic rings in (MPB·HBA) 2 are distanced by 3.457 Å. In the crystals the complexes form "islands" related to the neighboring complexes by the inversion centers, weak C-H···O bonds and van der Waals forces. A broad band in the 3100-2400 cm -1 region and two bands attributed to the νC dbnd O (1689 cm -1) and νasCOO (1607 cm -1) vibrations in the FT-IR spectrum confirm the structure of the title complex. The two structures of MPB·HBA, denoted as A and B, have been optimized by the B3LYP/6-31G(d,p) method. In A, MPB forms a O-H···O hydrogen bond (2.562 Å) with the carboxylic group of HBA shorter than in the crystals, while in B it interacts with the phenolic group of HBA by a longer O-H···O hydrogen bond (2.661 Å) than in the crystals. Complex A is slightly more stable than B (0.15 kcal/mol).

Invited Review Article: Development of crystal lenses for energetic photons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smither, Robert K.

2014-08-15

This paper follows the development of crystal diffraction lenses designed to focus energetic photons. It begins with the search for a solution to the astrophysics problem of how to detect weak astrophysics sources of gamma rays and x-rays. This led to the basic designs for a lens and to the understanding of basic limitations of lens design. The discussion of the development of crystal diffraction lenses is divided into two parts: lenses using crystals with mosaic structure, and lenses that use crystals with curved crystal planes. This second group divides into two sub-groups: (1) Curved crystals that are used tomore » increase the acceptance angle of the diffraction of a monochromatic beam and to increase the energy bandwidth of the diffraction. (2) Curved crystals used to focus gamma ray beams. The paper describes how these two types of crystals affect the design of the corresponding crystal lenses in different fields: astrophysics, medical imaging, detection of weak, distant, gamma-ray sources, etc. The designs of crystal lenses for these applications are given in enough detail to allow the reader to design a lens for his own application.« less

Self-Assembly and Drug Release Capacities of Organogels via Some Amide Compounds with Aromatic Substituent Headgroups

PubMed Central

Zhang, Lexin; Jiao, Tifeng; Ma, Kai; Xing, Ruirui; Liu, Yamei; Xiao, Yong; Zhou, Jingxin; Zhang, Qingrui; Peng, Qiuming

2016-01-01

In this work, some amide compounds with different aromatic substituent headgroups were synthesized and their gelation self-assembly behaviors in 22 solvents were characterized as new gelators. The obtained results indicated that the size of aromatic substituent headgroups in molecular skeletons in gelators showed crucial effect in the gel formation and self-assembly behavior of all compounds in the solvents used. Larger aromatic headgroups in molecular structures in the synthesized gelator molecules are helpful to form various gel nanostructures. Morphological investigations showed that the gelator molecules can self-assembly and stack into various organized aggregates with solvent change, such as wrinkle, belt, rod, and lamella-like structures. Spectral characterizations suggested that there existed various weak interactions including π-π stacking, hydrogen bonding, and hydrophobic forces due to aromatic substituent headgroups and alkyl substituent chains in molecular structures. In addition, the drug release capacities experiments demonstrated that the drug release rate in present obtained gels can be tuned by adjusting the concentrations of dye. The present work would open up enormous insight to design and investigate new kind of soft materials with designed molecular structures and tunable drug release performance. PMID:28773663

CH-π Interaction Driven Macroscopic Property Transition on Smart Polymer Surface

NASA Astrophysics Data System (ADS)

Li, Minmin; Qing, Guangyan; Xiong, Yuting; Lai, Yuekun; Sun, Taolei

2015-10-01

Life systems have evolved to utilize weak noncovalent interactions, particularly CH-π interaction, to achieve various biofunctions, for example cellular communication, immune response, and protein folding. However, for artificial materials, it remains a great challenge to recognize such weak interaction, further transform it into tunable macroscopic properties and realize special functions. Here we integrate monosaccharide-based CH-π receptor capable of recognizing aromatic peptides into a smart polymer with three-component “Recognition-Mediating-Function” design, and report the CH-π interaction driven surface property switching on smart polymer film, including wettability, adhesion, viscoelasticity and stiffness. Detailed studies indicate that, the CH-π interaction induces the complexation between saccharide unit and aromatic peptide, which breaks the initial amphiphilic balance of the polymer network, resulting in contraction-swelling conformational transition for polymer chains and subsequent dramatic switching in surface properties. This work not only presents a new approach to control the surface property of materials, but also points to a broader research prospect on CH-π interaction at a macroscopic level.

CH-π Interaction Driven Macroscopic Property Transition on Smart Polymer Surface.

PubMed

Li, Minmin; Qing, Guangyan; Xiong, Yuting; Lai, Yuekun; Sun, Taolei

2015-10-29

Life systems have evolved to utilize weak noncovalent interactions, particularly CH-π interaction, to achieve various biofunctions, for example cellular communication, immune response, and protein folding. However, for artificial materials, it remains a great challenge to recognize such weak interaction, further transform it into tunable macroscopic properties and realize special functions. Here we integrate monosaccharide-based CH-π receptor capable of recognizing aromatic peptides into a smart polymer with three-component "Recognition-Mediating-Function" design, and report the CH-π interaction driven surface property switching on smart polymer film, including wettability, adhesion, viscoelasticity and stiffness. Detailed studies indicate that, the CH-π interaction induces the complexation between saccharide unit and aromatic peptide, which breaks the initial amphiphilic balance of the polymer network, resulting in contraction-swelling conformational transition for polymer chains and subsequent dramatic switching in surface properties. This work not only presents a new approach to control the surface property of materials, but also points to a broader research prospect on CH-π interaction at a macroscopic level.

Nitrogen: A New Class of π-Bonding Partner in Hetero π-Stacking Interaction.

PubMed

Ramanathan, N; Sankaran, K; Sundararajan, K

2017-11-30

Spectroscopy under isolated conditions at low temperatures is an excellent tool to characterize the aggregates stabilized through weak interactions. Within the framework of weak interactions, the π-stacking interactions are considered unconventional with the limited experimental proofs, wherein the bonding associates are either aromatic and heterocyclic compounds or their combinations. Besides aromatic compounds, π-stacking networks can even be realized with molecules possessing electron rich π-clouds. In this work, the N 2 molecule as a possible π-bonding partner is explored for the first time in which hetero π-stacking was achieved between pyrrole and N 2 precursors. The matrix isolation experiments performed by seeding pyrrole and N 2 mixtures in an Ar matrix at low temperatures with subsequent infrared spectral characterization revealed the generation of adducts stabilized through a π(pyrrole)···π(N 2 ) interaction. Under identical conditions with the likelihood of two competing π-stacking and hydrogen-bonding interactions in pyrrole-N 2 associates, π-stacking dominates energetically over hydrogen-bonding interaction.

Aromatic Polythiourea Dielectrics with High Energy Density, High Breakdown Strength, and Low Dielectric Loss

NASA Astrophysics Data System (ADS)

Wu, Shan; Burlingame, Quinn; Lin, Minren; Zhang, Qiming

2013-03-01

There is an increasing demand on dielectric materials with high electric energy density and low loss for a broad range of applications in modern electronics and electrical power systems such as hybrid electric vehicles (HEV), medical defibrillators, filters, and switched-mode power supplies. One major challenge in developing dielectric polymers is how to achieve high energy density Ue while maintaining low dielectric loss, even at very high-applied electric fields. Here we show that amorphous polar-polymers with very low impurity concentration can be promising for realizing such a dielectric polymer. Polar-polymer with high dipole moment and weak dipole coupling can provide relatively high dielectric constant for high Ue, eliminate polarization and conduction losses due to weak dipolar coupling and strong polar-scattering to charge carriers. Indeed, an aromatic polythiourea thin film can maintain low loss to high fields (>1 GV/m) with a high Ue (~ 24 J/cm3) , which is very attractive for energy storage capacitors.

Architecture of the hydrophobic and hydrophilic layers as found from crystal structure analysis of N-benzyl-N,N-dimethylalkylammonium bromides.

PubMed

Hodorowicz, Maciej; Stadnicka, Katarzyna; Czapkiewicz, Jan

2005-10-01

The molecular and crystal structures of N-benzyl-N,N-dimethylalkylammonium bromides monohydrates with chain length n=8-10 have been determined. The crystals are isostructural with the N-benzyl-N,N-dimethyldodecylammonium bromide monohydrate. The structures consist of alternated hydrophobic and hydrophilic layers perpendicular to [001]. The attraction between N+ of the cation head-groups and Br- anions is achieved through weak C_H...Br interactions. The water molecules incorporated into ionic layers are donors for two O_H...Br hydrogen bonds and serve as the acceptors in two weak interactions of C_H...O type. The methylene chains, with the slightly curved general shape, have the extended all-trans conformation. The mutual packing of the chains in the hydrophobic layers is governed by weak C_H...pi interactions.

Infrared and Raman spectra of N-acetyl- L-amino acid methylamides with aromatic side groups

NASA Astrophysics Data System (ADS)

Matsuura, Hiroatsu; Hasegawa, Kodo; Miyazawa, Tatsuo

Infrared and Raman spectra of N-acetyl- L-phenylalanine methylamide, N-acetyl- L-tyrosine methylamide and N-acetyl- L-tryptophan methylamide, as model compounds of aromatic amino acid residues in proteins, were measured in the solid state and in methanol solutions. Vibrational assignments of the spectra were made by utilizing the deuteration effect and by comparison with the spectra of related compounds which include toluene, p-cresol and 3-methylindole. The amide I, III and IV bands were strong in Raman scattering, but other characteristic amide bands were ill-defined. In the Raman spectra of methanol solutions, only the bands due to the aromatic side group vibrations were markedly observed, but those due to the peptide backbone vibrations were very weak, suggesting the coexistence of various molecular conformations in solution.

High-resolution electron microscopy and its applications.

PubMed

Li, F H

1987-12-01

A review of research on high-resolution electron microscopy (HREM) carried out at the Institute of Physics, the Chinese Academy of Sciences, is presented. Apart from the direct observation of crystal and quasicrystal defects for some alloys, oxides, minerals, etc., and the structure determination for some minute crystals, an approximate image-contrast theory named pseudo-weak-phase object approximation (PWPOA), which shows the image contrast change with crystal thickness, is described. Within the framework of PWPOA, the image contrast of lithium ions in the crystal of R-Li2Ti3O7 has been observed. The usefulness of diffraction analysis techniques such as the direct method and Patterson method in HREM is discussed. Image deconvolution and resolution enhancement for weak-phase objects by use of the direct method are illustrated. In addition, preliminary results of image restoration for thick crystals are given.

Nature of the anomalies in the supercooled liquid state of the mW model of water.

PubMed

Holten, Vincent; Limmer, David T; Molinero, Valeria; Anisimov, Mikhail A

2013-05-07

The thermodynamic properties of the supercooled liquid state of the mW model of water show anomalous behavior. Like in real water, the heat capacity and compressibility sharply increase upon supercooling. One of the possible explanations of these anomalies, the existence of a second (liquid-liquid) critical point, is not supported by simulations for this model. In this work, we reproduce the anomalies of the mW model with two thermodynamic scenarios: one based on a non-ideal "mixture" with two different types of local order of the water molecules, and one based on weak crystallization theory. We show that both descriptions accurately reproduce the model's basic thermodynamic properties. However, the coupling constant required for the power laws implied by weak crystallization theory is too large relative to the regular backgrounds, contradicting assumptions of weak crystallization theory. Fluctuation corrections outside the scope of this work would be necessary to fit the forms predicted by weak crystallization theory. For the two-state approach, the direct computation of the low-density fraction of molecules in the mW model is in agreement with the prediction of the phenomenological equation of state. The non-ideality of the "mixture" of the two states never becomes strong enough to cause liquid-liquid phase separation, also in agreement with simulation results.

Nature of the anomalies in the supercooled liquid state of the mW model of water

NASA Astrophysics Data System (ADS)

Holten, Vincent; Limmer, David T.; Molinero, Valeria; Anisimov, Mikhail A.

2013-05-01

The thermodynamic properties of the supercooled liquid state of the mW model of water show anomalous behavior. Like in real water, the heat capacity and compressibility sharply increase upon supercooling. One of the possible explanations of these anomalies, the existence of a second (liquid-liquid) critical point, is not supported by simulations for this model. In this work, we reproduce the anomalies of the mW model with two thermodynamic scenarios: one based on a non-ideal "mixture" with two different types of local order of the water molecules, and one based on weak crystallization theory. We show that both descriptions accurately reproduce the model's basic thermodynamic properties. However, the coupling constant required for the power laws implied by weak crystallization theory is too large relative to the regular backgrounds, contradicting assumptions of weak crystallization theory. Fluctuation corrections outside the scope of this work would be necessary to fit the forms predicted by weak crystallization theory. For the two-state approach, the direct computation of the low-density fraction of molecules in the mW model is in agreement with the prediction of the phenomenological equation of state. The non-ideality of the "mixture" of the two states never becomes strong enough to cause liquid-liquid phase separation, also in agreement with simulation results.

Cocrystals of kaempferol, quercetin and myricetin with 4,4‧-bipyridine: Crystal structures, analyses of intermolecular interactions and antibacterial properties

NASA Astrophysics Data System (ADS)

Zhang, Yu-Nan; Yin, He-Mei; Zhang, Yu; Zhang, Da-Jun; Su, Xin; Kuang, Hai-Xue

2017-02-01

With an aim to explore the interactions of Osbnd H⋯N between hydroxyl moiety of the flavonoids and the pyridyl ring of N-containing aromatic amines, three flavonols with varying B-ring-hydroxyl groups (kaempferol, quercetin, and myricetin) were selected to combine with 4,4‧-bipyridine. As a result, three new cocrystals of flavonols were obtained with a solution evaporation approach. These three cocrystals were characterized by single crystal X-ray diffraction, XPRD, IR and NMR methods. The resulting cocrystals were kaempferol: 4,4‧-bipyridine (2:1) (KAE·BPY·2H2O), quercetin: 4,4‧-bipyridine (1:1.5) (QUE·BPY), and myricetin: 4,4‧-bipyridine (1:2) (MYR·BPY·H2O). Structural analyses show that an array of hydrogen bonds and π-π stacking interactions interconnect the molecules to form a two-dimensional (2D) supramolecular layer in KAE·BPY·2H2O, QUE·BPY, and MYR·BPY·H2O. In the three cocrystals, they present as three different synthons-ⅠR88(58), Ⅳ R44(42) and, Ⅶ R66(29) with 4,4‧-bipyridine, respectively-which may yield a strategy for constructing the supramolecule. Cocrystals of flavonols combined with N-containing aromatic amines, 7-OH, B-ring-hydroxyl number and/or the location of the flavonols to play a significant part in extending the dimensionality of the cocrystals. The resulting motif formation and crystal packing in these flavonols cocrystals has combined with N-containing aromatic amines. Additionally, the antibacterial properties of the three cocrystals against Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) have been investigated.

Band gaps and the possible effect on impact sensitivity for some nitro aromatic explosive materials

NASA Astrophysics Data System (ADS)

Zhang, Hong; Cheung, Frankie; Zhao, Feng; Cheng, Xin-Lu

The first principle density functional theory method SIESTA has been used to compute the band gap of several polynitroaromatic explosives, such as TATB, DATB, TNT, and picric acid. In these systems, the weakest bond is the one between an NO2 group and the aromatic ring. The bond dissociation energy (BDE) alone cannot predicate the relative sensitivity to impact of these four systems correctly. It was found that their relative impact sensitivity could be explained by considering the BDE and the band gap value of the crystal state together.

Supramolecular aromaticity

NASA Astrophysics Data System (ADS)

Karabıyık, Hande; Sevinçek, Resul; Karabıyık, Hasan

2014-05-01

We report experimental and theoretical evidences for supramolecular aromaticity as a new concept to be widely used in researches about molecular crystals. CSD survey regarding frequently encountered resonance-assisted H-bonds (RAHBs) in formic acid, formamide, formimidamide, formic acid-formamide, and formamide-formimidamide dimers shows that supramolecular quasirings formed by RAHBs have remarkable electronic delocalization within themselves, which is reminiscent of aromaticity at supramolecular level. This study criticizes and reevaluates the validity of conventional judgment which states that ring systems formed by intermolecular H-bonds cannot be aromatic. Thus, the term aromaticity can be extended to supramolecular systems formed by RAHBs. Supramolecular aromaticity has a multi-fold nature involving both σ- and π-delocalization, and σ-delocalization through RAHBs takes on a task of compensating σ-deficiency within quasirings. Atomic composition in donor-acceptor set of the dimers is descriptive for supramolecular aromaticity. We revised bond-valence parameters for RAHBs and they suggest that hypervalent character of H atoms is more pronounced than their hypovalent character in RAHBs. The σ-delocalized bonding within H-bonded quasirings necessitates hypervalent character of H atoms. Quantum chemical calculations based on adiabatic Hydrogen Atom Transfer (HAT) between the monomers reveal that topological parameters at ring critical points (RCPs) of the quasirings correlate well with Shannon's entropic aromaticity index. The presence of additional LP orbital on O atoms implying more diffused LP-orbitals in donor-acceptor set leads to the formation of resonance-disabling states reducing supramolecular aromaticity of a quasiring and energetic cost of the electron transfer between the monomers. There is a nonignorable electron transfer between the monomers even in the cases where H atoms are close to donor or acceptor atom. NBO analyses have revealed that formally vacant LP* orbitals on H-atoms in TS geometries mediate intermolecular electron transfer as a result of the hyperconjugative stereoelectronic interactions.

Di-μ-acetato-bis­[(acetato-κ2 O,O′)bis­(iso­nicotinamide-κN)copper(II)

PubMed Central

Perec, Mireille; Baggio, Ricardo

2010-01-01

The title centrosymmetric bimetallic complex, [Cu2(C2H3O2)4(C6H6N2O)4], is composed of two copper(II) cations, four acetate anions and four isonicotinamide (INA) ligands. The asymmetric unit contains one copper cation to which two acetate units bind asymmetrically; one of the Cu—O distances is rather long [2.740 (2) Å], almost at the limit of coordination. These Cu—O bonds define an equatorial plane to which the Cu—N bonds to the INA ligands are almost perpendicular, the Cu—N vectors subtending angles of 2.4 (1) and 2.3 (1)° to the normal to the plane. The metal coordination geometry can be described as a slightly distorted trigonal bipyramid if the extremely weak Cu—O bond is disregarded, or as a highly distorted square bipyramid if it is not. The double acetate bridge between the copper ions is not coplanar with the CuO4 equatorial planes, the dihedral angle between the (O—C—O)2 and O—Cu—O groups being 34.3 (1)°, resulting in a sofa-like conformation for the 8-member bridging loop. In the crystal, N—H⋯O hydrogen bonds occur, some of which generate a head-to tail-linkage between INA units, giving raise to chains along [101]; the remaining ones make inter-chain contacts, defining a three-dimensional network. There are in addition a number of C—H⋯O bonds involving aromatic H atoms. Probably due to steric hindrance, the aromatic rings are not involved in significant π⋯π inter­actions. PMID:21580223

On the Interaction between Carbon Dioxide and Nanomaterials with High Accuracy ab initio and DFT Calculations

NASA Astrophysics Data System (ADS)

Vogiatzis, Konstantinos D.; Mavrandonakis, Antreas; Klopper, Wim; Froudakis, George

2009-08-01

The separation, capture and storage of carbon dioxide from the flue gas is an environmental and economical problem of significant importance. Zeolites and activated carbons have been used from the industries in order to reduce the emissions of CO2. A new family of materials, the metal-organic frameworks (MOFs), has been recently proposed as an efficient substitute of the abovementioned materials. In particular, materials based on zinc complexes with imidazo-like aromatic compounds which builds frameworks similar with those of Zeolites (Zeolite-Imidazolium Frameworks, ZIFs), have the potential for efficient separation of CO2 from CO and CH4. [1]. Weak interactions between carbon dioxide and heterocyclic aromatic compounds are being examined with high accuracy ab initio methods. CO2 has zero dipole moment but a significant quadrupole moment enables it to operate as a weak acid or weak base, according to his environment. Nitrogen-containing aromatic compounds act as electron donors, while CO2 acts as an electron acceptor. Electrostatic interactions induce a non-permanent dipole moment on CO2 and the complex is stabilized by in-plane hydrogen bonds between the charged oxygens of CO2 and nearby hydrogen of the aromatic molecule. In addition, dispersion forces from the electron correlation contribute to the interaction energy. By using explicitly correlated methods (MP2-F12/aug-cc-pVTZ) [2] and by adding the contribution from the triples excitations, calculated with a smaller basis (6-311++G**), we reach to an approximate CCSD(T) complete basis set result. [3] Extrapolation schemes were used in order to reach the MP2 basis set limit and compare it with the CCSD(T)/CBS result. Those results are in excellent agreement with the explicitly correlated MP2-F12. In addition, our complexes are being investigated with DFT methods that calculate separately the dispersion energy (DFT-D) [4] and modified MP2 which scaling of spin pair correlation [5]. DFT-D results are in good agreement with CCSD(T)/CBS results, providing us a computational cheap method with high accuracy. The quantization of the interaction is examined by changing the aromaticity of the heterocyclic molecules and by talking into account the electron correlation. [6] The electron density of the nitrogen that binds CO2 is gradually decreasing by substituting carbons with nitrogens in pyridine (pyrimidine, pyrazine, triazine), leading to lower binding energy.

Optical coherence of 166Er:7LiYF4 crystal below 1 K

NASA Astrophysics Data System (ADS)

Kukharchyk, N.; Sholokhov, D.; Morozov, O.; Korableva, S. L.; Kalachev, A. A.; Bushev, P. A.

2018-02-01

We explore optical coherence and spin dynamics of an isotopically purified 166Er:7LiYF4 crystal below 1 K and at weak magnetic fields < 0.3T. Crystals were grown in our lab and demonstrate narrow inhomogeneous optical broadening down to 16 MHz. Solid-state atomic ensembles with such narrow linewidths are very attractive for implementing of off-resonant Raman quantum memory and for the interfacing of superconducting quantum circuits and telecom C-band optical photons. Both applications require a low magnetic field of ∼10 mT. However, at conventional experimental temperatures T > 1.5 K, optical coherence of Er:LYF crystal attains ≃ 10 μ {{s}} time scale only at strong magnetic fields above 1.5 T. In the present work, we demonstrate that the deep freezing of Er:LYF crystal below 1 K results in the increase of optical coherence time to ≃ 100 μ {{s}} at weak fields.

Continuous structural evolution of calcium carbonate particles: a unifying model of copolymer-mediated crystallization.

PubMed

Kulak, Alex N; Iddon, Peter; Li, Yuting; Armes, Steven P; Cölfen, Helmut; Paris, Oskar; Wilson, Rory M; Meldrum, Fiona C

2007-03-28

Two double-hydrophilic block copolymers, each comprising a nonionic block and an anionic block comprising pendent aromatic sulfonate groups, were used as additives to modify the crystallization of CaCO3. Marked morphological changes in the CaCO3 particles were observed depending on the reaction conditions used. A poly(ethylene oxide)-b-poly(sodium 4-styrenesulfonate) diblock copolymer was particularly versatile in effecting a morphological change in calcite particles, and a continuous structural transition in the product particles from polycrystalline to mesocrystal to single crystal was observed with variation in the calcium concentration. The existence of this structural sequence provides unique insight into the mechanism of polymer-mediated crystallization. We propose that it reflects continuity in the crystallization mechanism itself, spanning the limits from nonoriented aggregation of nanoparticles to classical ion-by-ion growth. The various pathways to polycrystalline, mesocrystal, and single-crystal particles, which had previously been considered to be distinct, therefore all form part of a unifying crystallization framework based on the aggregation of precursor subunits.

Study on Japanese Cornmint in Mississippi

USDA-ARS?s Scientific Manuscript database

Japanese cornmint (Mentha canadensis L.) is a subtropical essential oil crop grown in Asia and South America. The essential oil of Japanese cornmint is the source for production of crystal (-)-menthol, which is a major aromatic agent used as a flavor, fragrance, and cooling sensation vector in the ...

Crystal structures of a therapeutic single chain antibody in complex with two drugs of abuse—Methamphetamine and 3,4-methylenedioxymethamphetamine

PubMed Central

Celikel, Reha; Peterson, Eric C; Owens, S Michael; Varughese, Kottayil I

2009-01-01

Methamphetamine (METH) is a major drug threat in the United States and worldwide. Monoclonal antibody (mAb) therapy for treating METH abuse is showing exciting promise and the understanding of how mAb structure relates to function will be essential for future development of these important therapies. We have determined crystal structures of a high affinity anti-(+)-METH therapeutic single chain antibody fragment (scFv6H4, KD= 10 nM) derived from one of our candidate mAb in complex with METH and the (+) stereoisomer of another abused drug, 3,4-methylenedioxymethamphetamine (MDMA), known by the street name “ecstasy.” The crystal structures revealed that scFv6H4 binds to METH and MDMA in a deep pocket that almost completely encases the drugs mostly through aromatic interactions. In addition, the cationic nitrogen of METH and MDMA forms a salt bridge with the carboxylate group of a glutamic acid residue and a hydrogen bond with a histidine side chain. Interestingly, there are two water molecules in the binding pocket and one of them is positioned for a C—H⋯O interaction with the aromatic ring of METH. These first crystal structures of a high affinity therapeutic antibody fragment against METH and MDMA (resolution = 1.9 Å, and 2.4 Å, respectively) provide a structural basis for designing the next generation of higher affinity antibodies and also for carrying out rational humanization. PMID:19760665

Crystal structures of a therapeutic single chain antibody in complex with two drugs of abuse-Methamphetamine and 3,4-methylenedioxymethamphetamine.

PubMed

Celikel, Reha; Peterson, Eric C; Owens, S Michael; Varughese, Kottayil I

2009-11-01

Methamphetamine (METH) is a major drug threat in the United States and worldwide. Monoclonal antibody (mAb) therapy for treating METH abuse is showing exciting promise and the understanding of how mAb structure relates to function will be essential for future development of these important therapies. We have determined crystal structures of a high affinity anti-(+)-METH therapeutic single chain antibody fragment (scFv6H4, K(D)= 10 nM) derived from one of our candidate mAb in complex with METH and the (+) stereoisomer of another abused drug, 3,4-methylenedioxymethamphetamine (MDMA), known by the street name "ecstasy." The crystal structures revealed that scFv6H4 binds to METH and MDMA in a deep pocket that almost completely encases the drugs mostly through aromatic interactions. In addition, the cationic nitrogen of METH and MDMA forms a salt bridge with the carboxylate group of a glutamic acid residue and a hydrogen bond with a histidine side chain. Interestingly, there are two water molecules in the binding pocket and one of them is positioned for a C--H...O interaction with the aromatic ring of METH. These first crystal structures of a high affinity therapeutic antibody fragment against METH and MDMA (resolution = 1.9 A, and 2.4 A, respectively) provide a structural basis for designing the next generation of higher affinity antibodies and also for carrying out rational humanization.

Enhancement of the orientational order parameter of nematic liquid crystals in thin cells.

PubMed

Dhara, Surajit; Madhusudana, N V

2004-04-01

Abstract. We report measurements of birefringence (Delta n) of several nematic liquid crystals having transverse as well as longitudinal dipole moments in thin (1.4 to 2.3 microm) and thick (7 to 16 microm) cells. Rubbed polyimide-coated glass plates are used to get planar alignment of the nematic director in these cells. We find significant enhancement (6 to 18%) of Delta n (proportional to S, where S is the orientational order parameter) in thin cells in all compounds with aromatic cores even at temperatures far approximately 20 degrees C) below the nematic-isotropic transition point. The enhancement is larger in compounds having several phenyl rings and lower if the number of phenyl rings is reduced. In a compound that does not have an aromatic core no significant enhancement is observed, implying that the strength of the surface potential depends on the aromaticity of the cores. Assuming a perfect orientational order at the surface, calculations based on the Landau-de Gennes theory show that the thickness averaged enhancement of S is sharply reduced as the temperature is lowered in the nematic phase. The measured order parameter S is further enhanced in thin cells because of the stiffening of the elastic constant which reduces the thermal fluctuations of the nematic director. The combined effect is however too small at low temperatures to account for the experimental data.

13C NMR spectroscopy of the insoluble carbon of carbonaceous chondrites

NASA Technical Reports Server (NTRS)

Cronin, J. R.; Pizzarello, S.; Frye, J. S.

1987-01-01

13C NMR spectra have been obtained of the insoluble carbon residues resulting from HF-digestion of three carbonaceous chondrites, Orgueil (C1), Murchison (CM2), and Allende (CV3). Spectra obtained using the cross polarization magic-angle spinning technique show two major features attributable respectively to carbon in aliphatic/olefinic structures. The spectrum obtained from the Allende sample was weak, presumably as a consequence of its low hydrogen content. Single pulse excitation spectra, which do not depend on 1H-13C polarization transfer for signal enhancement were also obtained. These spectra, which may be more representative of the total carbon in the meteorite samples, indicate a greater content of carbon in aromatic/olefinic structures. These results suggest that extensive polycyclic aromatic sheets are important structural features of the insoluble carbon of all three meteorites. The Orgueil and Murchison materials contain additional hydrogenated aromatic/olefinic and aliphatic groups.

Catalytic upgrading of oil fractions separated from food waste leachate.

PubMed

Heo, Hyeon Su; Kim, Sang Guk; Jeong, Kwang-Eun; Jeon, Jong-Ki; Park, Sung Hoon; Kim, Ji Man; Kim, Seung-Soo; Park, Young-Kwon

2011-02-01

In this work, catalytic cracking of biomass waste oil fractions separated from food waste leachate was performed using microporous catalysts, such as HY, HZSM-5 and mesoporous Al-MCM-48. The experiments were carried out using pyrolysis gas chromatography/mass spectrometry (Py-GC/MS) to allow the direct analysis of the pyrolytic products. Most acidic components, especially oleic acid, contained in the food waste oil fractions were converted to valuable products, such as oxygenates, hydrocarbons and aromatics. High yields of hydrocarbons within the gasoline-range were obtained when microporous catalysts were used; whereas, the use of Al-MCM-48, which exhibits relatively weak acidity, resulted in high yields of oxygenated and diesel-range hydrocarbons. The HZSM-5 catalyst produced a higher amount of valuable mono aromatics due to its strong acidity and shape selectivity. Especially, the addition of gallium (Ga) to HZSM-5 significantly increased the aromatics content. Copyright © 2010 Elsevier Ltd. All rights reserved.

A Naphtho- p-quinodimethane Exhibiting Baird’s (Anti)Aromaticity, Broken Symmetry, and Attractive Photoluminescence

DOE PAGES

Shokri, Siamak; Li, Jingbai; Manna, Manoj K.; ...

2017-08-24

In this paper, we report a novel reductive desulfurization reaction involving π-acidic naphthalene diimides 1 (NDI) using thionating agents such as Lawesson’s reagent. Along with the expected thionated NDI derivatives 2-6, new heterocyclic naphtho-p-quinodimethane compounds 7 depicting broken/reduced symmetry were successfully isolated and fully characterized. Empirical studies and theoretical modeling suggest that was formed via a six-membered ring oxathiaphosphenine intermediate rather than the usual four-membered ring oxathiaphosphetane of 2-6. Aside from the reduced symmetry in 7 as confirmed by single-crystal XRD analysis, we established that the ground state UV-vis absorption of 7 is red-shifted in comparison to the parent NDImore » 1. This result was expected in the case of thionated polycyclic diimides. However, unusual low energy transitions originate from Baird 4nπ aromaticity of compounds 7 in lieu of the intrinsic Huckel (4n + 2)π aromaticity as encountered in NDI 1. Moreover, complementary theoretical modeling results also corroborate this change in aromaticity of 7. Consequently, photophysical investigations show that, compared to parent NDI 1, 7 can easily access and emit from its T 1 state with a phosphorescence 3(7a)* lifetime of τ P = 395 μs at 77 K indicative of the formation of the corresponding “aromatic triplet” species according to the Baird’s rule of aromaticity.« less

Sequence-specific 1H-NMR assignments for the aromatic region of several biologically active, monomeric insulins including native human insulin.

PubMed

Roy, M; Lee, R W; Kaarsholm, N C; Thøgersen, H; Brange, J; Dunn, M F

1990-06-12

The aromatic region of the 1H-FT-NMR spectrum of the biologically fully-potent, monomeric human insulin mutant, B9 Ser----Asp, B27 Thr----Glu has been investigated in D2O. At 1 to 5 mM concentrations, this mutant insulin is monomeric above pH 7.5. Coupling and amino acid classification of all aromatic signals is established via a combination of homonuclear one- and two-dimensional methods, including COSY, multiple quantum filters, selective spin decoupling and pH titrations. By comparisons with other insulin mutants and with chemically modified native insulins, all resonances in the aromatic region are given sequence-specific assignments without any reliance on the various crystal structures reported for insulin. These comparisons also give the sequence-specific assignments of most of the aromatic resonances of the mutant insulins B16 Tyr----Glu, B27 Thr----Glu and B25 Phe----Asp and the chemically modified species des-(B23-B30) insulin and monoiodo-Tyr A14 insulin. Chemical dispersion of the assigned resonances, ring current perturbations and comparisons at high pH have made possible the assignment of the aromatic resonances of human insulin, and these studies indicate that the major structural features of the human insulin monomer (including those critical to biological function) are also present in the monomeric mutant.

Oxygen transport as a structure probe for heterogeneous polymeric systems

NASA Astrophysics Data System (ADS)

Hu, Yushan

Although permeability of small molecules is often measured as an important performance property, deeper analysis of the transport characteristics provides insight into polymer structure, especially if used in combination with other characterization techniques. Transport of small gas molecules senses the permeable amorphous structure and probes the nature of free volume. This work focuses on oxygen transport, supplemented with other methods of physical analysis, as a probe for: (1) the nature of free volume and crystalline morphology in the crystallized glassy state, (2) the nature of free volume and hierarchical structure in liquid crystalline polymers, and (3) the role of dispersed polyamide phase geometry on oxygen barrier properties of poly(ethylene terephthalate) (PET)/polyamide blends. In the first part, the improvement in oxygen-barrier properties of glassy polyesters by crystallization was examined. Examples included poly(ethylene naphthalate) (PEN), and a copolymer based on PET in which 55 mol% terephthalate was replaced with 4,4'-bibenzoate. Explanation of the unexpectedly high solubility of crystallized PEN required a two-phase transport model consisting of an impermeable crystalline phase of constant density and a permeable amorphous phase of variable density. The resulting relationship between oxygen solubility and amorphous phase density was consistent with free volume concepts of gas sorption. In the second part, oxygen barrier properties of liquid crystalline (LC) polyesters based on poly(diethylene glycol 4,4'-bibenzoate) (PDEGBB) were studied. This study extended the 2-phase transport model for oxygen transport of non-LC crystalline polymers to a smectic LCP. It was possible to systematically vary the solid state structure of (PDEGBB) from LC glass to crystallized LC glass. The results were consistent with a liquid crystalline state intermediate between the permeable amorphous glass and the impermeable 3-dimensional crystal. In this interpretation, LC order naturally led to inherently low gas solubility. In the third part, improvement of gas-barrier properties of poly(ethylene terephthalate) (PET) by blending with an aromatic polyamide, either poly(m-xylylene adipamide) (MXD6) or a copolyamide based on MXD6 in which 12 mol% adipamide was replaced with isophthalamide (MXD6-12I), was studied. Aromatic polyamides provided higher barrier than aliphatic polyamides, and unlike aliphatic polyamides, the aromatic polyamides retained high barrier under conditions of high humidity, making them more suitable for beverage packaging applications. (Abstract shortened by UMI.)

1-(2,4-Di-nitro-phen-yl)-2-[(E)-(3,4,5-tri-meth-oxy-benzyl-idene)]hydrazine.

PubMed

Chantrapromma, Suchada; Ruanwas, Pumsak; Boonnak, Nawong; Chidan Kumar, C S; Fun, Hoong-Kun

2014-02-01

Mol-ecules of the title compound, C16H16N4O7, are not planar with a dihedral angle of 5.50 (11)° between the substituted benzene rings. The two meta-meth-oxy groups of the 3,4,5-tri-meth-oxy-benzene moiety lie in the plane of the attached ring [Cmeth-yl-O-C-C torsion angles -0.1 (4)° and -3.7 (3)°] while the para-meth-oxy substituent lies out of the plane [Cmeth-yl-O-C-C, -86.0 (3)°]. An intra-molecular N-H⋯O hydrogen bond involving the 2-nitro substituent generates an S(6) ring motif. In the crystal structure, mol-ecules are linked by weak C-H⋯O inter-actions into screw chains, that are arranged into a sheet parallel to the bc plane. These sheets are connected by π-π stacking inter-actions between the nitro and meth-oxy substituted aromatic rings with a centroid-centroid separation of 3.9420 (13) Å. C-H⋯π contacts further stabilize the two-dimensional network.

Bis(acetato-κ2 O,O′)(4,4′-dimethyl-2,2′-bipyridine-κ2 N,N′)­zinc

PubMed Central

Harvey, Miguel A.; Suarez, Sebastian A.; Ibañez, Andres; Doctorovich, Fabio; Baggio, Ricardo

2012-01-01

The mol­ecular structure of the title compound, [Zn(CH3COO)2(C12H12N2)], consists of isolated mol­ecules bis­ected by a twofold rotation axis which goes through the ZnII cation and halves the organic base through the central C—C bond. The ZnII ion is coordinated by two N atoms from one mol­ecule of the aromatic base and four O atoms from two bidentate, symmetry-related acetate anions, which coordinate asym­metrically [Zn—O distances of 2.058 (2) and 2.362 (3) Å], while the two Zn—N bond distances are equal as imposed by symmetry [2.079 (2) Å]. The crystal structure is supported by a number of weak C—H⋯O inter­actions and C—H⋯π contacts, with no π–π inter­actions present, mainly hindered by the substituent methyl groups and the relative mol­ecular orientation. The result is a three-dimensional structure in which each mol­ecule is linked to eight different neighbors. PMID:23284355

Selective Ring Opening of 1-Methylnaphthalene Over NiW-Supported Catalyst Using Dealuminated Beta Zeolite.

PubMed

Kim, Eun-Sang; Lee, You-Jin; Kim, Jeong-Rang; Kim, Joo-Wan; Kim, Tae-Wan; Chae, Ho-Jeong; Kim, Chul-Ung; Lee, Chang-Ha; Jeong, Soon-Yong

2016-02-01

Nanoporous Beta zeolite was dealuminated by weak acid treatment for reducing the acidity. Bi-functional catalysts were prepared using commercial Beta zeolites and the dealuminated zeolites for acidic function, NiW for metallic function. 1-Methylnaphthalene was selected as a model compound for multi-ring aromatics in heavy oil, and its selective ring opening reaction has been investigated using the prepared bi-functional catalysts with different acidity in fixed bed reaction system. The dealuminated Beta zeolites, which crystal structure and nanoporosity were maintained, showed the higher SiO2/Al2O3 ratio and smaller acidity than their original zeolite. NiW-supported catalyst using the dealuminated Beta zeolite with SiO2/Al203 mole ratio of 55 showed the highest performance for the selective ring opening. The acidity of catalyst seemed to play an important role as active sites for the selective ring opening of 1-methylnaphthalene but there should be some optimum catalyst acidity for the reaction. The acidity of Beta zeolite could be controlled by the acid treatment and the catalyst with the optimum acidity for the selective ring opening could be prepared.

Crystal Structures of Apo and Liganded 4-Oxalocrotonate Decarboxylase Uncover a Structural Basis for the Metal-Assisted Decarboxylation of a Vinylogous β-Keto Acid.

PubMed

Guimarães, Samuel L; Coitinho, Juliana B; Costa, Débora M A; Araújo, Simara S; Whitman, Christian P; Nagem, Ronaldo A P

2016-05-10

The enzymes in the catechol meta-fission pathway have been studied for more than 50 years in several species of bacteria capable of degrading a number of aromatic compounds. In a related pathway, naphthalene, a toxic polycyclic aromatic hydrocarbon, is fully degraded to intermediates of the tricarboxylic acid cycle by the soil bacteria Pseudomonas putida G7. In this organism, the 83 kb NAH7 plasmid carries several genes involved in this biotransformation process. One enzyme in this route, NahK, a 4-oxalocrotonate decarboxylase (4-OD), converts 2-oxo-3-hexenedioate to 2-hydroxy-2,4-pentadienoate using Mg(2+) as a cofactor. Efforts to study how 4-OD catalyzes this decarboxylation have been hampered because 4-OD is present in a complex with vinylpyruvate hydratase (VPH), which is the next enzyme in the same pathway. For the first time, a monomeric, stable, and active 4-OD has been expressed and purified in the absence of VPH. Crystal structures for NahK in the apo form and bonded with five substrate analogues were obtained using two distinct crystallization conditions. Analysis of the crystal structures implicates a lid domain in substrate binding and suggests roles for specific residues in a proposed reaction mechanism. In addition, we assign a possible function for the NahK N-terminal domain, which differs from most of the other members of the fumarylacetoacetate hydrolase superfamily. Although the structural basis for metal-dependent β-keto acid decarboxylases has been reported, this is the first structural report for that of a vinylogous β-keto acid decarboxylase and the first crystal structure of a 4-OD.

A Two-Tailed Phosphopeptide Crystallizes to Form a Lamellar Structure.

PubMed

Pellach, Michal; Mondal, Sudipta; Harlos, Karl; Mance, Deni; Baldus, Marc; Gazit, Ehud; Shimon, Linda J W

2017-03-13

The crystal structure of a designed phospholipid-inspired amphiphilic phosphopeptide at 0.8 Å resolution is presented. The phosphorylated β-hairpin peptide crystallizes to form a lamellar structure that is stabilized by intra- and intermolecular hydrogen bonding, including an extended β-sheet structure, as well as aromatic interactions. This first reported crystal structure of a two-tailed peptidic bilayer reveals similarities in thickness to a typical phospholipid bilayer. However, water molecules interact with the phosphopeptide in the hydrophilic region of the lattice. Additionally, solid-state NMR was used to demonstrate correlation between the crystal structure and supramolecular nanostructures. The phosphopeptide was shown to self-assemble into semi-elliptical nanosheets, and solid-state NMR provides insight into the self-assembly mechanisms. This work brings a new dimension to the structural study of biomimetic amphiphilic peptides with determination of molecular organization at the atomic level. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural and spectral comparisons between isomeric benzisothiazole and benzothiazole based aromatic heterocyclic dyes

NASA Astrophysics Data System (ADS)

Wang, Yin-Ge; Wang, Yue-Hua; Tao, Tao; Qian, Hui-Fen; Huang, Wei

2015-09-01

A pair of isomeric heterocyclic compounds, namely 3-amino-5-nitro-[2,1]-benzisothiazole and 2-amino-6-nitrobenzothiazole, are used as the diazonium components to couple with two N-substituted 4-aminobenzene derivatives. As a result, two pairs of isomeric aromatic heterocyclic azo dyes have been produced and they are structurally and spectrally characterized and compared including single-crystal structures, electronic spectra, solvatochromism and reversible acid-base discoloration, thermal stability and theoretically calculations. It is concluded that both benzisothiazole and benzothiazole based dyes show planar molecular structures and offset π-π stacking interactions, solvatochromism and reversible acid-base discoloration. Furthermore, benzisothiazole based aromatic heterocyclic dyes exhibit higher thermal stability, larger solvatochromic effects and maximum absorption wavelengths than corresponding benzothiazole based ones, which can be explained successfully by the differences of their calculated isomerization energy, dipole moment and molecular band gaps.

A divergent route to core- and peripherally functionalized diazacoronenes that act as colorimetric and fluorescence proton sensors

DOE PAGES

He, Bo; Dai, Jing; Zherebetskyy, Danylo; ...

2015-03-31

Combining core annulation and peripheral group modification, we have demonstrated a divergent synthesis of a family of highly functionalized coronene derivatives from a readily accessible dichlorodiazaperylene intermediate. Various reactions, such as aromatic nucleophilic substitution, Kumada coupling and Suzuki coupling proceed effectively on α-positions of the pyridine sites, giving rise to alkoxy, thioalkyl, alkyl or aryl substituted polycyclic aromatic hydrocarbons. In addition to peripheral group modulation, the aromatic core structures can be altered by annulation with thiophene or benzene ring systems. Corresponding single crystal X-ray diffraction and optical studies indicate that the heteroatom linkages not only impact the solid state packing,more » but also significantly influence the optoelectronic properties. Moreover, these azacoronene derivatives display significant acid-induced spectroscopic changes, suggesting their great potential as colorimetric and fluorescence proton sensors.« less

Hofmeister effect on the interfacial free energy of aliphatic and aromatic surfaces studied by chemical force microscopy.

PubMed

Patete, Jonathan; Petrofsky, John M; Stepan, Jeffery; Waheed, Abdul; Serafin, Joseph M

2009-01-15

This work describes chemical force microscopy (CFM) studies of specific-ion effects on the aqueous interfacial free energy of hydrophobic monolayers. CFM measurements allow for the characterization of interfacial properties on length scales below 100 nm. The ions chosen span the range of the Hofmeister series, from the kosmotropic Na(2)SO(4) to the chaotropic NaSCN. The salt concentrations used are typical of many laboratory processes such as protein crystallization, 2-3 M. Both aliphatic (terminal methyl) and aromatic (terminal phenyl) monolayers were examined, and rather pronounced differences were observed between the two cases. The specific-ion dependence of the aliphatic monolayer closely follows the Hofmeister series, namely the chaotropic ions lowered the interfacial free energy and the kosmotropic ions increased the interfacial free energy. However, the aromatic monolayer had significant deviations from the Hofmeister series. Possible origins for this difference are discussed.

Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases

ERIC Educational Resources Information Center

Rzepa, Henry S.

2016-01-01

Three new examples are presented illustrating three-dimensional chemical information searches of the Cambridge structure database (CSD) from which basic core concepts in organic and inorganic chemistry emerge. These include connecting the regiochemistry of aromatic electrophilic substitution with the geometrical properties of hydrogen bonding…

NMR analysis of cross strand aromatic interactions in an 8 residue hairpin and a 14 residue three stranded β-sheet peptide.

PubMed

Sonti, Rajesh; Rai, Rajkishor; Ragothama, Srinivasarao; Balaram, Padmanabhan

2012-12-13

Cross strand aromatic interactions between a facing pair of phenylalanine residues in antiparallel β-sheet structures have been probed using two structurally defined model peptides. The octapeptide Boc-LFV(D)P(L)PLFV-OMe (peptide 1) favors the β-hairpin conformation nucleated by the type II' β-turn formed by the (D)Pro-(L)Pro segment, placing Phe2 and Phe7 side chains in proximity. Two centrally positioned (D)Pro-(L)Pro segments facilitate the three stranded β-sheet formation in the 14 residue peptide Boc-LFV(D)P(L)PLFVA(D)P(L)PLFV-OMe (peptide 2) in which the Phe2/Phe7 orientations are similar to that in the octapeptide. The anticipated folded conformations of peptides 1 and 2 are established by the delineation of intramolecularly hydrogen bonded NH groups and by the observation of specific cross strand NOEs. The observation of ring current shifted aromatic protons is a diagnostic of close approach of the Phe2 and Phe7 side chains. Specific assignment of aromatic proton resonances using HSQC and HSQC-TOCSY methods allow an analysis of interproton NOEs between the spatially proximate aromatic rings. This approach facilitates specific assignments in systems containing multiple aromatic rings in spectra at natural abundance. Evidence is presented for a dynamic process which invokes a correlated conformational change about the C(α)-C(β)(χ(1)) bond for the pair of interacting Phe residues. NMR results suggest that aromatic ring orientations observed in crystals are maintained in solution. Anomalous temperature dependence of ring current induced proton chemical shifts suggests that solvophobic effects may facilitate aromatic ring clustering in apolar solvents.

Crystallographic Phasing from Weak Anomalous Signals

PubMed Central

Liu, Qun; Hendrickson, Wayne A.

2015-01-01

The exploitation of anomalous signals for biological structural solution is maturing. Single-wavelength anomalous diffraction (SAD) is dominant in de novo structure analysis. Nevertheless, for challenging structures where the resolution is low (dmin ≥ 3.5 Å) or where only lighter atoms (Z ≤ 20) are present, as for native macromolecules, solved SAD structures are still scarce. With the recent rapid development in crystal handling, beamline instrumentation, optimization of data collection strategies, use of multiple crystals and structure determination technologies, the weak anomalous diffraction signals are now robustly measured and should be used for routine SAD structure determination. The review covers these recent advances on weak anomalous signals measurement, analysis and utilization. PMID:26432413

Crystallographic phasing from weak anomalous signals.

PubMed

Liu, Qun; Hendrickson, Wayne A

2015-10-01

The exploitation of anomalous signals for biological structural solution is maturing. Single-wavelength anomalous diffraction (SAD) is dominant in de novo structure analysis. Nevertheless, for challenging structures where the resolution is low (dmin≥3.5Å) or where only lighter atoms (Z≤20) are present, as for native macromolecules, solved SAD structures are still scarce. With the recent rapid development in crystal handling, beamline instrumentation, optimization of data collection strategies, use of multiple crystals and structure determination technologies, the weak anomalous diffraction signals are now robustly measured and should be used for routine SAD structure determination. The review covers these recent advances on weak anomalous signals measurement, analysis and utilization. Copyright © 2015 Elsevier Ltd. All rights reserved.

Weak ferromagnetism along the third-order axis of the FeBO3 crystals caused by Fe2+ impurity ions

NASA Astrophysics Data System (ADS)

Ovchinnikov, S. G.; Rudenko, V. V.; Vorotynov, A. M.

2018-05-01

Using the single-ion approximation, the weak ferromagnetic moment σZ(Fe2+) along the third-order axis of FeBO3 crystals, which is caused by the contribution of Fe2+ ions, has been investigated in the framework of the model Fe2+ impurity ion -BO3 vacancy. The extreme low-temperature behavior of the total magnetic moment due to the strong dependence of the Fe2+ion contribution is predicted.

Advanced Biosensors for Amino Acid Detection. Phase 1

DTIC Science & Technology

1989-12-31

dissolved in CHCl 3 , where it was found effective for extracting phenylethylamine (C 6 H5 CH2 NH2 ) and dt-phenylglycine ethyl ester (C 6 H6 (NH2...promoted. Since resonance effects are important in aromatic amines and since p-nitroani- line is an extremely weak nucleophile, the lack of

Advanced Biosensors for Amino Acid Detection

DTIC Science & Technology

1990-04-18

when (II) was dissolved in CHCl 3 , and found effective for extracting phenylethylamine (C 6 H5CH2 CH2 NH)) and di-phenylglycine ethyl ester (C 6 H6...reaction was promoted. Since reson nce effects are important in aromatic amines and since p-nitroanilive is an extremely weak nucleophile, lack of

Catalytic pyrolysis of oil fractions separated from food waste leachate over nanoporous acid catalysts.

PubMed

Kim, Seung-Soo; Heo, Hyeon Su; Kim, Sang Guk; Ryoo, Ryong; Kim, Jeongnam; Jeon, Jong-Ki; Park, Sung Hoon; Park, Young-Kwon

2011-07-01

Oil fractions, separated from food waste leachate, can be used as an energy source. Especially, high quality oil can be obtained by catalytic cracking. In this study, nanoporous catalysts such as Al-MCM-41 and mesoporous MFI type zeolite were applied to the catalytic cracking of oil fractions using the pyrolysis gas chromatography/mass spectrometry. Mesoporous MFI type zeolite showed better textural porosity than Al-MCM-41. In addition, mesoporous MFI type zeolite had strong Brönsted acidity while Al-MCM-41 had weak acidity. Significant amount of acid components in the food waste oil fractions were converted to mainly oxygenates and aromatics. As a result of its well-defined nanopores and strong acidity, the use of a mesoporous MFI type zeolite produced large amounts of gaseous and aromatic compounds. High yields of hydrocarbons within the gasoline range were also obtained in the case of mesoporous MFI type zeolite, whereas the use of Al-MCM-41, which exhibits relatively weak acidity, resulted in high yields of oxygenates and diesel range hydrocarbons.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mikhlina, Ya. A., E-mail: altik@inbox.ru; Bolotin, B. M.; Kuz'mina, L. G., E-mail: kuzmina@igic.ras.ru

Two crystal modifications (1o and 1y) of N-butyl-2-cyano-3-[4-(dimethylamino)phenyl]-2-propenamide, which differ in the color of crystals and the color of luminescence, have been studied by X-ray diffraction and spectral-luminescence methods. The corresponding bond lengths and bond angles in the molecules of two crystal modifications are virtually identical. In both crystal structures, there are two systems of weak intermolecular interactions: {pi}-stacking interactions and -CN Horizontal-Ellipsis H-N hydrogen bonds involving nitrile and NH groups. In the crystal structures, two hydrogen bonds connect pairs of molecules into centrosymmetric dimers. The N Horizontal-Ellipsis H distances are 2.21 and 2.41 A in 1o and 1y, respectively.more » The interplanar distances in the {pi}-stacked systems of 1o and 1y are 3.33 and 3.41 A, respectively. Both types of weak interactions are stronger in 1o than in 1y, which accounts for a larger shift of absorption and luminescence bands for the former compound.« less

Enhanced intersystem crossing in core-twisted aromatics.

PubMed

Nagarajan, Kalaivanan; Mallia, Ajith R; Muraleedharan, Keerthi; Hariharan, Mahesh

2017-03-01

We describe the design, bottom-up synthesis and X-ray single crystal structure of systematically twisted aromatics 1c and 2d for efficient intersystem crossing. Steric congestion at the cove region creates a nonplanar geometry that induces a significant yield of triplet excited states in the electron-poor core-twisted aromatics 1c and 2d . A systematic increase in the number of twisted regions in 1c and 2d results in a concomitant enhancement in the rate and yield of intersystem crossing, monitored using femtosecond and nanosecond transient absorption spectroscopy. Time-resolved absorption spectroscopic measurements display enhanced triplet quantum yields ( Φ T = 10 ± 1% for 1c and Φ T = 30 ± 2% for 2d ) in the twisted aromatics when compared to a negligible Φ T (<1%) in the planar analog 3c . Twist-induced spin-orbit coupling via activated out-of-plane C-H/C 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 C vibrations can facilitate the formation of triplet excited states in twisted aromatics 1c and 2d , in contrast to the negligible intersystem crossing in the planar analog 3c . The ease of synthesis, high solubility, access to triplet excited states and strong electron affinity make such imide functionalized core-twisted aromatics desirable materials for organic electronics such as solar cells.

1-(4-Chloro­benzyl­ideneamino)pyridinum iodide

PubMed Central

Cui, Yong-Tao; Wang, Jian-Qiang; Ji, Chun-Xiang; Wang, Hai-Bo; Cheng, Guo

2009-01-01

In the title compound, C12H10ClN2 +·I−, the aromatic rings are oriented at a dihedral angle of 54.55 (3)°. In the crystal structure, inter­molecular C—H⋯I and C—H⋯Cl hydrogen bonds link the mol­ecules. PMID:21581845

4-[(3-Chloro-2-methyl-phen-yl)imino-meth-yl]phenol.

PubMed

Manjunath, B C; Abdoh, M M M; Mallesha, L; Mohana, K N; Lokanath, N K

2012-11-01

In the title compound, C(14)H(12)ClNO, the dihedral angle between the aromatic rings is 39.84 (7)°. In th crystal, mol-ecules are connected by O-H⋯N hydrogen bonds into chains parallel to [001]. In addition, a C-H⋯π contact occurs.

Selectivity of hexaphenylbenzene-based hydrocarbon stationary phase with propeller-like conformation for aromatic and aliphatic isomers.

PubMed

Yang, Yinhui; Chang, Zhengfeng; Yang, Xiaohong; Qi, Meiling; Wang, Jinliang

2018-08-03

Herein we report a propeller-like hexaphenylbenzene-based hydrocarbon material (denoted as BT) as the stationary phase for capillary gas chromatography (GC). The statically-coated BT capillary column showed a high column efficiency of 4340 plates m -1 and weak polarity. Owing to its unique conformation, π-electron toroidal delocalization and intrinsic microporosity, the BT stationary phase exhibited interesting selectivity for aromatic compounds over alkanes. Compared with the graphene (G) column, the BT column showed much prolonged retention and high selectivity for aromatic isomers, especially methylnaphthalenes, dimethylnaphthalenes and phenanthrene/anthracene, mainly because of its propeller-like conformation with rich intercalation effects. Moreover, it exhibited good column repeatability (intra-day, inter-day) and reproducibility (between-column) with RSD values on the retention times less than 0.08% for intra-day, 0.32% for inter-day and 3.8% for between-column, respectively. Also, it showed good potential for determination of minor isomer impurities in real samples. To the best of our knowledge, this work presents the first example of employing an neat aromatic hydrocarbon material as the GC stationary phase with high selectivity for analytes of a wide ranging polarity. Copyright © 2018 Elsevier B.V. All rights reserved.

Evidence for weakly bound electrons in non-irradiated alkane crystals: The electrons as a probe of structural differences in crystals.

PubMed

Pietrow, M; Gagoś, M; Misiak, L E; Kornarzyński, K; Szurkowski, J; Rochowski, P; Grzegorczyk, M

2015-02-14

It is generally assumed that weakly bound (trapped) electrons in organic solids come only from radiolytical (or photochemical) processes like ionization caused by an excited positron entering the sample. This paper presents evidence for the presence of these electrons in non-irradiated samples of docosane. This can be due to the triboelectrification process. We argue that these electrons can be located (trapped) either in interlamellar gaps or in spaces made by non-planar conformers. Electrons from the former ones are bound more weakly than electrons from the latter ones. The origin of Vis absorption for the samples is explained. These spectra can be used as a probe indicating differences in the solid structures of hydrocarbons.

Nonlinear Raman spectroscopy of liquid crystals: orientational alignment and switching behaviour in a ferroelectric liquid crystal mixture

NASA Astrophysics Data System (ADS)

Grofcsik, Andras

Picosecond inverse Raman spectroscopy has been employed to probe the alignment behaviour and switching characteristics of a 6 mum thick ferroelectric liquid crystal based on a host mixture of fluorinated phenyl biphenylcarboxylates and a chiral dopant. Optical bistability is observed in the Raman signal on application of dc electric fields of opposite polarity. For particular polarities of the applied field, the Raman signals display a cos4theta dependence on the angle of rotation around the beam direction. Reorientational rate constants of 300 mus and 590 mus are observed for the aromatic core at the high-voltage limit for the rise and decay of the 1600 cm-1 Raman signal on application of a switching ac electric field.

Crystal Structure and Substrate Specificity of Drosophila 3,4-Dihydroxyphenylalanine Decarboxylase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han, Q.; Ding, H; Robinson, H

2010-01-01

3,4-Dihydroxyphenylalanine decarboxylase (DDC), also known as aromatic L-amino acid decarboxylase, catalyzes the decarboxylation of a number of aromatic L-amino acids. Physiologically, DDC is responsible for the production of dopamine and serotonin through the decarboxylation of 3,4-dihydroxyphenylalanine and 5-hydroxytryptophan, respectively. In insects, both dopamine and serotonin serve as classical neurotransmitters, neuromodulators, or neurohormones, and dopamine is also involved in insect cuticle formation, eggshell hardening, and immune responses. In this study, we expressed a typical DDC enzyme from Drosophila melanogaster, critically analyzed its substrate specificity and biochemical properties, determined its crystal structure at 1.75 Angstrom resolution, and evaluated the roles residues T82more » and H192 play in substrate binding and enzyme catalysis through site-directed mutagenesis of the enzyme. Our results establish that this DDC functions exclusively on the production of dopamine and serotonin, with no activity to tyrosine or tryptophan and catalyzes the formation of serotonin more efficiently than dopamine. The crystal structure of Drosophila DDC and the site-directed mutagenesis study of the enzyme demonstrate that T82 is involved in substrate binding and that H192 is used not only for substrate interaction, but for cofactor binding of drDDC as well. Through comparative analysis, the results also provide insight into the structure-function relationship of other insect DDC-like proteins.« less

DNA–protein π-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar

PubMed Central

Wilson, Katie A.; Kellie, Jennifer L.; Wetmore, Stacey D.

2014-01-01

Four hundred twenty-eight high-resolution DNA–protein complexes were chosen for a bioinformatics study. Although 164 crystal structures (38% of those searched) contained no interactions, 574 discrete π–contacts between the aromatic amino acids and the DNA nucleobases or deoxyribose were identified using strict criteria, including visual inspection. The abundance and structure of the interactions were determined by unequivocally classifying the contacts as either π–π stacking, π–π T-shaped or sugar–π contacts. Three hundred forty-four nucleobase–amino acid π–π contacts (60% of all interactions identified) were identified in 175 of the crystal structures searched. Unprecedented in the literature, 230 DNA–protein sugar–π contacts (40% of all interactions identified) were identified in 137 crystal structures, which involve C–H···π and/or lone–pair···π interactions, contain any amino acid and can be classified according to sugar atoms involved. Both π–π and sugar–π interactions display a range of relative monomer orientations and therefore interaction energies (up to –50 (–70) kJ mol−1 for neutral (charged) interactions as determined using quantum chemical calculations). In general, DNA–protein π-interactions are more prevalent than perhaps currently accepted and the role of such interactions in many biological processes may yet to be uncovered. PMID:24744240

Aromatic as well as aliphatic hydrocarbon solvent axonopathy.

PubMed

Spencer, Peter S; Kim, Min Sun; Sabri, Mohammad I

2002-03-01

Superfund sites that contain mixtures of aromatic and aliphatic solvents represent an undefined health hazard. After prolonged exposure to relatively high levels of certain aliphatic solvents (e.g. n-hexane, 2-hexanone), humans and animals develop a dose-dependent neurodegeneration that occurs clinically as a symmetrical peripheral neuropathy. This is triggered by the action of 2,5-hexanedione (1,2-diacetylethane), a 1,4-diketone (gamma-diketone) metabolite that targets proteins required for the maintenance of neuronal (and testicular Sertoli cell) integrity. Certain aromatic solvents (1,2-diethylbenzene, 1,2,4-triethylbenzene) cause electrophysiological changes consistent with sensorimotor neuropathy in rodents, but the underlying mechanisms and pathogenesis are unclear. Our recent studies show that the o-diacetyl derivative and likely metabolite of 1,2-diethylbenzene, 1,2-diacetylbenzene, behaves as a neurotoxic (aromatic) gamma-diketone of high neurotoxic potency. Rats treated with 1,2-diacetylbenzene develop limb weakness associated with proximal, neurofilament-filled giant axonal swellings comparable to those seen in animals treated with the potent 3,4-dimethyl derivative of 2,5-hexanedione. The blue chromogen induced by treatment with 1,2-diacetylbenzene is under study as a possible urinary biomarker of exposure to aromatic solvents (e.g. 1,2-diethylbenzene, tetralin) with neurotoxic potential. Development and validation of sensitive new biomarkers, especially for non-cancer endpoints, will aid in assessing the health risk associated with exposure to hazardous substances at Superfund sites.

Stability and molecular properties of the boron-nitrogen alternating analogs of azulene and naphthalene: a computational study.

PubMed

Catão, Anderson José Lopes; López-Castillo, Alejandro

2017-04-01

In this work, the spectroscopic information, stability and aromaticity of the boron-nitrogen azulene and naphthalene molecules are provided by the use of CC2 (geometry optimization, dipole moment, UV-vis spectrum calculations) and DFT (vibrational spectrum and NMR calculations) methodologies. One isomer of the investigated boron-nitrogen naphthalene (boroazanaphthalene) and two isomers of boron-nitrogen azulene, 1,3,4,6,8-pentaaza-2,3a,5,7,8a-pentaboraazulene (BN-azulene) and 2,3a,5,7,8a-pentaaza-1,3,4,6,8- pentaboraazulene (NB-azulene), are stable systems. However, these molecules have different properties, i.e., different stability, dipole moment, and aromaticity based on the NICS approach. BN-naphthalene has a high dipole moment magnitude showing high polar character, while naphthalene is apolar. BN- and NB-azulene are weakly polar, while ordinary azulene is highly polar in character. Also, substitution of C atoms by B and N atoms decreases the aromaticity. In the case of NB-azulene, the seven-membered ring has anti-aromaticity behavior while both rings of BN-azulene exhibit aromaticity. We expect that the new theoretical data provided in this work will be useful in identifying and characterizing experimentally the compounds investigated, and in helping our understanding of the chemistry of boron-nitrogen molecules. Graphical abstract Boron-nitrogen alternating analogs of azulene. Spectral distinction between isomers.

In situ STM investigation of aromatic poly(azomethine) arrays constructed by "on-site" equilibrium polymerization.

PubMed

Tanoue, Ryota; Higuchi, Rintaro; Ikebe, Kiryu; Uemura, Shinobu; Kimizuka, Nobuo; Stieg, Adam Z; Gimzewski, James K; Kunitake, Masashi

2012-10-02

Two-dimensional (2D) arrays of π-conjugated aromatic polymers produced by surface-selective Schiff base coupling reactions between an aromatic diamine and an aromatic dialdehyde were investigated in detail using in situ scanning tunneling microscopy. Surface-selective coupling was achieved for almost all diamine/dialdehyde combinations attempted, although several combinations did not proceed even in homogeneous aqueous alkaline solution. Most of the combinations of an aromatic diamine and a dialdehyde, except the combinations of 4,4'-azodianiline with mono/bithiophenedicarboxaldehyde, formed highly ordered π-conjugated polymer arrays on an iodine-modified Au(111) surface in aqueous solution at a suitable pH. The simplest polymer of the various combinations tested, obtained from the combination of 1,4-diaminobenzene with terephthaldicarboxaldehyde, gave a 2D array consisting of linearly connected benzene units. Poly(azomethine) adlayers caused a positive shift in the electrochemical potential of the butterfly shaped oxidative adsorption and reductive desorption of iodine. The acceleration of the reductive desorption of iodine suggests the existence of a weak interaction between the polymer layer and iodine. Not only the first polymer adlayers but also partially adsorbed secondary adlayers with "on-top" epitaxial behavior were frequently observed for all polymer systems. The alignment of the polymer chains in the adlayers possessed a certain regularity in terms of a regular interval between polymer chains because of repulsive interpolymer interactions.

The shikimate pathway: review of amino acid sequence, function and three-dimensional structures of the enzymes.

PubMed

Mir, Rafia; Jallu, Shais; Singh, T P

2015-06-01

The aromatic compounds such as aromatic amino acids, vitamin K and ubiquinone are important prerequisites for the metabolism of an organism. All organisms can synthesize these aromatic metabolites through shikimate pathway, except for mammals which are dependent on their diet for these compounds. The pathway converts phosphoenolpyruvate and erythrose 4-phosphate to chorismate through seven enzymatically catalyzed steps and chorismate serves as a precursor for the synthesis of variety of aromatic compounds. These enzymes have shown to play a vital role for the viability of microorganisms and thus are suggested to present attractive molecular targets for the design of novel antimicrobial drugs. This review focuses on the seven enzymes of the shikimate pathway, highlighting their primary sequences, functions and three-dimensional structures. The understanding of their active site amino acid maps, functions and three-dimensional structures will provide a framework on which the rational design of antimicrobial drugs would be based. Comparing the full length amino acid sequences and the X-ray crystal structures of these enzymes from bacteria, fungi and plant sources would contribute in designing a specific drug and/or in developing broad-spectrum compounds with efficacy against a variety of pathogens.

Crystal structure of [propane-1,3-diylbis(piperidine-4,1-di-yl)]bis-[(pyridin-4-yl)methanone]-4,4'-oxydi-benzoic acid (1/1).

PubMed

Low, Emily M; LaDuca, Robert L

2014-09-01

In the title co-crystal, C25H32N4O2·C14H10O5, mol-ecules are connected into supra-molecular chains aligned along [102] by O-H⋯N hydrogen bonding. These aggregate into supra-molecular layers oriented parallel to (20-1) by C-H⋯O inter-actions. These layers then stack in an ABAB pattern along the c crystal direction to give the full three-dimensional crystal structure. The central chain in the dipyridylamide has an anti-anti conformation. The dihedral angle between the aromatic ring planes is 29.96 (3)°. Disorder is noted in some of the residues in the structure and this is manifested in two coplanar dispositions of one statistically disordered carb-oxy-lic acid group.

Crystallization and preliminary crystallographic analysis of an acridone-producing novel multifunctional type III polyketide synthase from Huperzia serrata

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morita, Hiroyuki; Kondo, Shin; Kato, Ryohei

2007-07-01

An acridone-producing novel type III polyketide synthase from H. serrata has been overexpressed in E. coli, purified and crystallized. Diffraction data have been collected to 2.0 Å. Polyketide synthase 1 (PKS1) from Huperzia serrata is a plant-specific type III polyketide synthase that shows an unusually versatile catalytic potential, producing various aromatic tetraketides, including chalcones, benzophenones, phlorogulucinols and acridones. Recombinant H. serrata PKS1 expressed in Escherichia coli was crystallized using the hanging-drop vapour-diffusion method. The crystals belonged to space group I222 or I2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 73.3, b = 85.0, c = 137.7 Å, α =more » β = γ = 90.0°. Diffraction data were collected to 2.0 Å resolution using synchrotron radiation at BL24XU of SPring-8.« less

Non-Fullerene Electron Acceptors for Use in Organic Solar Cells

PubMed Central

2015-01-01

Conspectus The active layer in a solution processed organic photovoltaic device comprises a light absorbing electron donor semiconductor, typically a polymer, and an electron accepting fullerene acceptor. Although there has been huge effort targeted to optimize the absorbing, energetic, and transport properties of the donor material, fullerenes remain as the exclusive electron acceptor in all high performance devices. Very recently, some new non-fullerene acceptors have been demonstrated to outperform fullerenes in comparative devices. This Account describes this progress, discussing molecular design considerations and the structure–property relationships that are emerging. The motivation to replace fullerene acceptors stems from their synthetic inflexibility, leading to constraints in manipulating frontier energy levels, as well as poor absorption in the solar spectrum range, and an inherent tendency to undergo postfabrication crystallization, resulting in device instability. New acceptors have to address these limitations, providing tunable absorption with high extinction coefficients, thus contributing to device photocurrent. The ability to vary and optimize the lowest unoccupied molecular orbital (LUMO) energy level for a specific donor polymer is also an important requirement, ensuring minimal energy loss on electron transfer and as high an internal voltage as possible. Initially perylene diimide acceptors were evaluated as promising acceptor materials. These electron deficient aromatic molecules can exhibit good electron transport, facilitated by close packed herringbone crystal motifs, and their energy levels can be synthetically tuned. The principal drawback of this class of materials, their tendency to crystallize on too large a length scale for an optimal heterojunction nanostructure, has been shown to be overcome through introduction of conformation twisting through steric effects. This has been primarily achieved by coupling two units together, forming dimers with a large intramolecular twist, which suppresses both nucleation and crystal growth. The generic design concept of rotationally symmetrical aromatic small molecules with extended π orbital delocalization, including polyaromatic hydrocarbons, phthalocyanines, etc., has also provided some excellent small molecule acceptors. In most cases, additional electron withdrawing functionality, such as imide or ester groups, can be incorporated to stabilize the LUMO and improve properties. New calamitic acceptors have been developed, where molecular orbital hybridization of electron rich and poor segments can be judiciously employed to precisely control energy levels. Conformation and intermolecular associations can be controlled by peripheral functionalization leading to optimization of crystallization length scales. In particular, the use of rhodanine end groups, coupled electronically through short bridged aromatic chains, has been a successful strategy, with promising device efficiencies attributed to high lying LUMO energy levels and subsequently large open circuit voltages. PMID:26505279

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuz'mina, L. G., E-mail: kuzmina@igic.ras.ru; Kucherepa, N. S.; Rodnikova, M. N.

The molecular and crystal structures of two p-alkoxybenzylidene)-p'-toluidines C{sub 2}H{sub 5}O-C{sub 6}H{sub 4}-CH=N-C{sub 6}H{sub 4}-CH{sub 3} (1) and C{sub 4}H{sub 9}O-C{sub 6}H{sub 4}-CH=N-C{sub 6}H{sub 4}-CH{sub 3} (2) are determined by X-ray diffraction. Crystals 1 and 2 contain four and two crystallographically independent molecules, respectively. In 1, the geometry of the independent molecules is almost identical. In 2, the independent molecules differ in the conformation of the alkyl chain, which is disordered in one of them. An analysis of the crystal packing of 2 reveals the alternation of spacious layers formed by loosely packed aliphatic fragments of molecules and layers ofmore » closely packed aromatic fragments, which ensures the formation of the mesogenic phase in the course of melting of crystals 2. In crystal 1, loose aliphatic layers are absent.« less

Supernucleation and Orientation of Poly(butylene terephthalate) Crystals in Nanocomposites Containing Highly Reduced Graphene Oxide

PubMed Central

2017-01-01

The ring-opening polymerization of cyclic butylene terephthalate into poly(butylene terephthalate) (pCBT) in the presence of reduced graphene oxide (RGO) is an effective method for the preparation of polymer nanocomposites. The inclusion of RGO nanoflakes dramatically affects the crystallization of pCBT, shifting crystallization peak temperature to higher temperatures and, overall, increasing the crystallization rate. This was due to a supernucleating effect caused by RGO, which is maximized by highly reduced graphene oxide. Furthermore, combined analyses by differential scanning calorimetry (DSC) experiments and wide-angle X-ray diffraction (WAXS) showed the formation of a thick α-crystalline form pCBT lamellae with a melting point of ∼250 °C, close to the equilibrium melting temperature of pCBT. WAXS also demonstrated the pair orientation of pCBT crystals with RGO nanoflakes, indicating a strong interfacial interaction between the aromatic rings of pCBT and RGO planes, especially with highly reduced graphene oxide. PMID:29296028

UV LED lighting for automated crystal centring

PubMed Central

Chavas, Leonard M. G.; Yamada, Yusuke; Hiraki, Masahiko; Igarashi, Noriyuki; Matsugaki, Naohiro; Wakatsuki, Soichi

2011-01-01

A direct outcome of the exponential growth of macromolecular crystallography is the continuously increasing demand for synchrotron beam time, both from academic and industrial users. As more and more projects entail screening a profusion of sample crystals, fully automated procedures at every level of the experiments are being implemented at all synchrotron facilities. One of the major obstacles to achieving such automation lies in the sample recognition and centring in the X-ray beam. The capacity of UV light to specifically react with aromatic residues present in proteins or with DNA base pairs is at the basis of UV-assisted crystal centring. Although very efficient, a well known side effect of illuminating biological samples with strong UV sources is the damage induced on the irradiated samples. In the present study the effectiveness of a softer UV light for crystal centring by taking advantage of low-power light-emitting diode (LED) sources has been investigated. The use of UV LEDs represents a low-cost solution for crystal centring with high specificity. PMID:21169682

Aromatic Ring Currents Illustrated--NMR Spectra of Tin(IV) Porphyrin Complexes. An Advanced Undergraduate Experiment.

ERIC Educational Resources Information Center

Arnold, Dennis P.

1988-01-01

Attempts to show that in the closed loops of cyclic structures the protons situated in conic regions above and below the ring will be shielded. Uses the diamagnetic and air stable octahedral tin(IV) complexes of porphyrins for study. Notes complexes crystallize easily and offer spectacular purple colors. (MVL)

4-[(3-Chloro-2-methyl­phen­yl)imino­meth­yl]phenol

PubMed Central

Manjunath, B. C.; Abdoh, M. M. M; Mallesha, L.; Mohana, K. N.; Lokanath, N. K.

2012-01-01

In the title compound, C14H12ClNO, the dihedral angle between the aromatic rings is 39.84 (7)°. In th crystal, mol­ecules are connected by O—H⋯N hydrogen bonds into chains parallel to [001]. In addition, a C—H⋯π contact occurs. PMID:23284502

Normal coordinate analysis of the vibrational spectrum of benzil molecule

NASA Astrophysics Data System (ADS)

Volovšek, V.; Colombo, L.

1993-03-01

Normal coordinate analysis is performed for the benzil molecule. Force constants of phenyl rings are transferred from earlier studies on binuclear aromatic molecules. The existance of some low-frequency internal modes have been proved, thus eliminating the earlier explanations of the excess of the bands observed in the low-frequency Raman and FIR spectra of benzil crystal.

Stereodynamics and edge-to-face CH-π aromatic interactions in imino compounds containing heterocyclic rings.

PubMed

González-Rosende, M Eugenia; Castillo, Encarna; Jennings, W Brian; Malone, John F

2017-02-07

By comparison with close contact interactions between benzene rings there is a paucity of experimental data available for attractive interactions involving aromatic heterocyclic rings, especially for small molecules in solution. Herein we describe aromatic heterocyclic and carbocyclic edge-to face interactions and conformational stereodynamics of N-1,2-diphenylethyl imines bearing a phenyl group and either a 2-pyridyl, 3-pyridyl, 2-thiophene or 2-furanyl moiety on the imino carbon. X-ray crystal structures have been determined for two compounds. Slow rotation about the phenyl-imino bond in the E-isomers and around the heterocycle-imino bond in the Z-isomers of the pyridyl compounds was observed at low temperatures by NMR. Abnormally large shielding of one ortho hydrogen indicates that both the imino phenyl and heterocycle rings can engage in an edge-to-face interaction with the N-terminal phenyl moiety in the appropriate isomer. Some rotational barriers around the phenyl-imino and heterocycle-imino bonds were measured.

Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-coumaric acid and related aromatic acids.

PubMed

Tan, Kemin; Chang, Changsoo; Cuff, Marianne; Osipiuk, Jerzy; Landorf, Elizabeth; Mack, Jamey C; Zerbs, Sarah; Joachimiak, Andrzej; Collart, Frank R

2013-10-01

Lignin comprises 15-25% of plant biomass and represents a major environmental carbon source for utilization by soil microorganisms. Access to this energy resource requires the action of fungal and bacterial enzymes to break down the lignin polymer into a complex assortment of aromatic compounds that can be transported into the cells. To improve our understanding of the utilization of lignin by microorganisms, we characterized the molecular properties of solute binding proteins of ATP-binding cassette transporter proteins that interact with these compounds. A combination of functional screens and structural studies characterized the binding specificity of the solute binding proteins for aromatic compounds derived from lignin such as p-coumarate, 3-phenylpropionic acid and compounds with more complex ring substitutions. A ligand screen based on thermal stabilization identified several binding protein clusters that exhibit preferences based on the size or number of aromatic ring substituents. Multiple X-ray crystal structures of protein-ligand complexes for these clusters identified the molecular basis of the binding specificity for the lignin-derived aromatic compounds. The screens and structural data provide new functional assignments for these solute-binding proteins which can be used to infer their transport specificity. This knowledge of the functional roles and molecular binding specificity of these proteins will support the identification of the specific enzymes and regulatory proteins of peripheral pathways that funnel these compounds to central metabolic pathways and will improve the predictive power of sequence-based functional annotation methods for this family of proteins. Copyright © 2013 Wiley Periodicals, Inc.

Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-coumaric acid and related aromatic acids

PubMed Central

Tan, Kemin; Chang, Changsoo; Cuff, Marianne; Osipiuk, Jerzy; Landorf, Elizabeth; Mack, Jamey C.; Zerbs, Sarah; Joachimiak, Andrzej; Collart, Frank R.

2013-01-01

Lignin comprises 15.25% of plant biomass and represents a major environmental carbon source for utilization by soil microorganisms. Access to this energy resource requires the action of fungal and bacterial enzymes to break down the lignin polymer into a complex assortment of aromatic compounds that can be transported into the cells. To improve our understanding of the utilization of lignin by microorganisms, we characterized the molecular properties of solute binding proteins of ATP.binding cassette transporter proteins that interact with these compounds. A combination of functional screens and structural studies characterized the binding specificity of the solute binding proteins for aromatic compounds derived from lignin such as p-coumarate, 3-phenylpropionic acid and compounds with more complex ring substitutions. A ligand screen based on thermal stabilization identified several binding protein clusters that exhibit preferences based on the size or number of aromatic ring substituents. Multiple X-ray crystal structures of protein-ligand complexes for these clusters identified the molecular basis of the binding specificity for the lignin-derived aromatic compounds. The screens and structural data provide new functional assignments for these solute.binding proteins which can be used to infer their transport specificity. This knowledge of the functional roles and molecular binding specificity of these proteins will support the identification of the specific enzymes and regulatory proteins of peripheral pathways that funnel these compounds to central metabolic pathways and will improve the predictive power of sequence-based functional annotation methods for this family of proteins. PMID:23606130

Evidence for weakly bound electrons in non-irradiated alkane crystals: The electrons as a probe of structural differences in crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pietrow, M., E-mail: mrk@kft.umcs.lublin.pl; Misiak, L. E.; Gagoś, M.

2015-02-14

It is generally assumed that weakly bound (trapped) electrons in organic solids come only from radiolytical (or photochemical) processes like ionization caused by an excited positron entering the sample. This paper presents evidence for the presence of these electrons in non-irradiated samples of docosane. This can be due to the triboelectrification process. We argue that these electrons can be located (trapped) either in interlamellar gaps or in spaces made by non-planar conformers. Electrons from the former ones are bound more weakly than electrons from the latter ones. The origin of Vis absorption for the samples is explained. These spectra canmore » be used as a probe indicating differences in the solid structures of hydrocarbons.« less

Efficiency of surface plasmon excitation at the photonic crystal – metal interface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuznetsova, T I; Raspopov, N A

2015-11-30

We report the results of a theoretical investigation of light wave transformation in a one-dimensional photonic crystal. The scheme considered comprises an incident wave directed in parallel with layers of the photonic crystal under an assumption that the wave vector is far from a forbidden zone. Expressions for propagating and evanescent electromagnetic waves in a periodic medium of the photonic crystal are obtained. It is found that the transverse structure of the propagating wave comprises a strong constant component and a weak oscillating component with a period determined by that of the photonic crystal. On the contrary, the dependence ofmore » evanescent waves on transverse coordinates is presented by a strong oscillating component and a weak constant component. The process of transformation of propagating waves to evanescent waves at a crystal – metal interface is investigated. Parameters of the photonic crystal typical for synthetic opals are used in all numerical simulations. The theoretical approach elaborated yields in an explicit form the dependence of the amplitude of a generated surface wave on the period of the dielectric function modulation in the photonic crystal. The results obtained show that in the conditions close to plasmon resonance the amplitude of the surface wave may be on the order of or even exceed that of the initial incident wave. (light wave transformation)« less

A theoretical perspective of the nature of hydrogen-bond types - the atoms in molecules approach

NASA Astrophysics Data System (ADS)

Vijaya Pandiyan, B.; Kolandaivel, P.; Deepa, P.

2014-06-01

Hydrogen bonds and their strength were analysed based on their X-H proton-donor bond properties and the parameters of the H-Y distance (Y proton acceptor). Strong, moderate and weak interactions in hydrogen-bond types were verified through the proton affinities of bases (PA), deprotanation enthalpies of acids (DPE) and the chemical shift (σ). The aromaticity and anti-aromaticity were analysed by means of the NICS (0) (nucleus-independent chemical shift), NICS (1) and ΔNICS (0), ΔNICS (1) of hydrogen-bonded molecules. The strength of a hydrogen bond depends on the capacity of hydrogen atom engrossing into the electronegative acceptor atom. The correlation between the above parameters and their relations were discussed through curve fitting. Bader's theory of atoms in molecules has been applied to estimate the occurrence of hydrogen bonds through eight criteria reported by Popelier et al. The lengths and potential energy shifts have been found to have a strong negative linear correlation, whereas the lengths and Laplacian shifts have a strong positive linear correlation. This study illustrates the common factors responsible for strong, moderate and weak interactions in hydrogen-bond types.

Exploring contribution of intermolecular interactions in supramolecular layered assembly of naphthyridine co-crystals: Insights from Hirshfeld surface analysis of their crystalline states

NASA Astrophysics Data System (ADS)

Seth, Saikat Kumar; Das, Nirmal Kumar; Aich, Krishnendu; Sen, Debabrata; Fun, Hoong-Kun; Goswami, Shyamaprasad

2013-09-01

Co-crystals of 1a and 1b have been prepared by slow evaporation of the solutions of mixtures of 2,7-dimethyl-1,8-naphthyridine (1), urea (a) and thiourea (b). The structures of the complexes are determined by the single crystal X-ray diffraction and a detailed investigation of the crystal packing and classification of intermolecular interactions is presented by means of Hirshfeld surface analysis which is of considerable current interest in crystal engineering. The X-ray study reveals that the co-crystal formers are envisioned to produce N-H⋯N hydrogen bond as well as N-H⋯O/N-H⋯S pair-wise hydrogen bonds and also the weaker aromatic π⋯π interactions which cooperatively take part in the crystal packing. The recurring feature of the self-assembly in the compounds is the appearance of the molecular ribbon through multiple hydrogen bonding which are further stacked into molecular layers by π⋯π stacking interactions. Hirshfeld surface analysis for visually analyzing intermolecular interactions in crystal structures employing molecular surface contours and 2D Fingerprint plots have been used to examine molecular shapes. Crystal structure analysis supported with the Hirshfeld surface and fingerprint plots enabled the identification of the significant intermolecular interactions.

1-(2,4-Di­nitro­phen­yl)-2-[(E)-(3,4,5-tri­meth­oxy­benzyl­idene)]hydrazine

PubMed Central

Chantrapromma, Suchada; Ruanwas, Pumsak; Boonnak, Nawong; Chidan Kumar, C. S.; Fun, Hoong-Kun

2014-01-01

Mol­ecules of the title compound, C16H16N4O7, are not planar with a dihedral angle of 5.50 (11)° between the substituted benzene rings. The two meta-meth­oxy groups of the 3,4,5-tri­meth­oxy­benzene moiety lie in the plane of the attached ring [Cmeth­yl–O–C–C torsion angles −0.1 (4)° and −3.7 (3)°] while the para-meth­oxy substituent lies out of the plane [Cmeth­yl—O—C—C, −86.0 (3)°]. An intra­molecular N—H⋯O hydrogen bond involving the 2-nitro substituent generates an S(6) ring motif. In the crystal structure, mol­ecules are linked by weak C—H⋯O inter­actions into screw chains, that are arranged into a sheet parallel to the bc plane. These sheets are connected by π–π stacking inter­actions between the nitro and meth­oxy substituted aromatic rings with a centroid–centroid separation of 3.9420 (13) Å. C—H⋯π contacts further stabilize the two-dimensional network. PMID:24764900

Diamond, aromatic, aliphatic components of interstellar dust grains: Random covalent networks in carbonaceous grains

NASA Astrophysics Data System (ADS)

Duley, W. W.

1995-05-01

A formalism based on the theory of random covalent networks (RCNs) in amorphous solids is developed for carbonaceous dust grains. RCN solutions provide optimized structures and relative compositions for amorphous materials. By inclusion of aliphatic, aromatic, and diamond clusters, solutions specific to interstellar materials can be obtained and compared with infrared spectral data. It is found that distinct RCN solutions corresponding to diffuse cloud and molecular cloud materials are possible. Specific solutions are derived for three representative objects: VI Cyg No. 12, NGC 7538 (IRS 9), and GC IRS 7. While diffuse cloud conditions with a preponderance of sp2 and sp3 bonded aliphatic CH species can be reproduced under a variety of RCN conditions, the presence of an abundant tertiary CH or diamond component is highly constrained. These solutions are related quantitatively to carbon depletions and can be used to provide a quantitative estimate of carbon in these various dust components. Despite the abundance of C6 aromatic rings in many RCN solutions, the infrared absorption due to the aromatic stretch at approximately 3.3 micrometers is weak under all conditions. The RCN formalism is shown to provide a useful method for tracing the evolutionary properties of interstellar carbonaceous grains.

Combined Experimental and Theoretical Investigations on Optical Activities of Möbius Aromatic and Möbius Antiaromatic Hexaphyrin Phosphorus Complexes.

PubMed

Mori, Tadashi; Tanaka, Takayuki; Higashino, Tomohiro; Yoshida, Kota; Osuka, Atsuhiro

2016-06-23

Intrinsically chiral Möbius aromatic [28]hexaphyrin monophosphorus(V) and Möbius antiaromatic [30]hexaphyrin bisphosphorus(V) complexes have been optically resolved and their absolute configurations (ACs) were determined by combined experimental and theoretical investigations on their circular dichroisms (CDs). First elutes in chiral HPLC exhibited strong positive Cotton effects (CEs) at the B-band, characteristic for the ML configurations in their Möbius strips. Weak CEs at the Q-band, if attainable, complemented their AC assignment. The whole CD pattern and intensity were well reproduced by time-dependent approximate coupled cluster theory using model systems that omit five outward meso-aryl substituents (inward-meso-retained model), providing a solid basis for AC assignment. The cost efficient TD-DFT method with appropriate functionals for fully substituted (nontruncated) complexes well reproduced CEs around the B-band (but less satisfactory at the Q-band), also allows the rapid AC estimation for their Möbius strips. Observed difference in CDs between aromatic and antiaromatic hexaphyrins were better interpreted by their shifts in energy levels and altered interactions of relevant molecular orbitals, rather than small differences in Möbius geometries nor aromatic/antiaromatic character, despite the correlations recently claimed in planar π-systems.

1-(Benzyl­ideneamino)pyridinum iodide

PubMed Central

Cui, Yong-Tao; Wang, Jian-Qiang; Ji, Chun-Xiang; Wu, Cong-Ren; Guo, Cheng

2009-01-01

In the title compound, C12H11N2 +·I−, the aromatic rings are oriented at a dihedral angle of 73.40 (3)°. In the crystal structure, π–π contacts between the pyridine rings and the benzene and pyridine rings [centroid–centroid distances = 3.548 (3) and 4.211 (3) Å] may stabilize the structure. PMID:21581846

Meso-Decorated Switching-Knot Gels

NASA Astrophysics Data System (ADS)

Gong, Jin; Sawamura, Kensuke; Makino, Masato; Kabir, M. H.; Furukawa, Hidemitsu

Gels are a new material having three-dimensional network structures of macromolecules. They possess excellent properties as swellability, high permeability and biocompatibility, and have been applied in various fields of daily life, food, medicine, architecture, and chemistry .In this study, we tried to prepare new multi-functional and high-strength gels by using Meso-Decoration (Meso-Deco), one new method of structure design at intermediate mesoscale. High-performance rigid-rod aromatic polymorphic crystals. The strengthening of gels can be realized by meso-decorating the gels' structure using high-performance polymorphic crystals. New gels with good mechanical properties, novel optical properties and thermal properties are expected to be developed.

Gelatin Nano-coating for Inhibiting Surface Crystallization of Amorphous Drugs.

PubMed

Teerakapibal, Rattavut; Gui, Yue; Yu, Lian

2018-01-05

Inhibit the fast surface crystallization of amorphous drugs with gelatin nano-coatings. The free surface of amorphous films of indomethacin or nifedipine was coated by a gelatin solution (type A or B) and dried. The coating's effect on surface crystallization was evaluated. Coating thickness was estimated from mass change after coating. For indomethacin (weak acid, pK a  = 4.5), a gelatin coating of either type deposited at pH 5 and 10 inhibited its fast surface crystal growth. The coating thickness was 20 ± 10 nm. A gelatin coating deposited at pH 3, however, provided no protective effect. These results suggest that an effective gelatin coating does not require that the drug and the polymer have opposite charges. The ineffective pH 3 coating might reflect the poor wetting of indomethacin's neutral, hydrophobic surface by the coating solution. For nifedipine (weak base, pK a  = 2.6), a gelatin coating of either type deposited at pH 5 inhibited its fast surface crystal growth. Gelatin nano-coatings can be conveniently applied to amorphous drugs from solution to inhibit fast surface crystallization. Unlike strong polyelectrolyte coatings, a protective gelatin coating does not require strict pairing of opposite charges. This could make gelatin coating a versatile, pharmaceutically acceptable coating for stabilizing amorphous drugs.

Wave function delocalization and large-amplitude vibrations of helium on corrugated aromatic microsurfaces: tetracene.He and pentacene.He van der Waals complexes.

PubMed

Xu, Minzhong; Bacić, Zlatko

2007-08-09

We report accurate quantum three-dimensional calculations of highly excited intermolecular vibrational states of the van der Waals (vdW) complexes tetracene.He and pentacene.He in the S1 excited electronic state. The aromatic molecules were taken to be rigid and the intermolecular potential energy surfaces (IPESs) were modeled as a sum of atom-atom Lennard-Jones pair potentials. The IPESs are corrugated in the direction of the long (x) axis of the aromatic molecules, due to the presence of the symmetrically equivalent global double minimum for tetracene.He, and a triple minimum (central global minimum and two equivalent local minima) for pentacene.He, on each side of the aromatic plane. Both IPESs have two additional minor equivalent local minima further away from the center of the molecule. The vdW vibrational states analyzed in this work cover about 80% of the well depths of the IPESs. The mode coupling is generally weak for those states whose out-of-plane (z) mode is unexcited. However, the z-mode fundamental is strongly coupled to the short-axis (y) in-plane mode, so that the pure z-mode excitation could not be identified. The He atom exhibits large in-plane spatial delocalizaton already in the ground vdW vibrational state, which increases rapidly upon the excitation of the in-plane x and y modes, with little hindrance by the corrugation of the aromatic microsurfaces. For the vdW vibrational energies considered, the He atom spatial delocalization reaches Deltax and Deltay values of approximately 5 and 4 A, respectively, and is limited only by the finite size of the aromatic substrates. Side-crossing delocalization of the wave functions on both sides of the molecular plane is found at excitation energies >30 cm(-1), giving rise to the energy splittings of the pairs of states symmetric/antisymmetric with respect to the aromatic plane; the splittings show strong vdW vibrational mode specificity.

The anomalous 3.43 and 3.53 micron emission features toward HD 97048 and Elias 1 - C-C vibrational modes of polycyclic aromatic hydrocarbons?

NASA Technical Reports Server (NTRS)

Schutte, W. A.; Tielens, A. G. G. M.; Allamandola, L. J.; Wooden, D. H.; Cohen, M.

1990-01-01

The 5-8 micron spectra obtained toward the two protostellar sources, HD 97048 and Elias 1 exhibit strong anomalous emission features at 3.43 and 3.53 microns. Combining these results with earlier data established that the emission in the general IR features is extended on at least a 20-arcsec scale. In view of the high energy density in the emission zone, as well as the apparent correspondence of the anomalous 3.43 and 3.53 micron features with weak emission shoulders associated with the general family of IR emission bands, an explanation for these observations in terms of C-C overtones and combination tones of large or dehydrogenated polycyclic aromatic hydrocarbons is judged to be provisionally suitable.

Peak effect in untwinned YBa 2Cu 3O 7-δ single crystals

NASA Astrophysics Data System (ADS)

D'Anna, G.; André, M.-O.; Indenbom, M. V.; Benoit, W.

1994-12-01

We report on the observation of a weak effect of the critical current density in untwinned YBa 2Cu 3O 7-δ single crystals of different purity, using a low frequency torsion pendulum. We construct the peak effect line and the irreversibility line.

A new method for solid surface topographical studies using nematic liquid crystals

NASA Astrophysics Data System (ADS)

Baber, N.; Strugalski, Z.

1984-03-01

A new simple method has been developed to investigate the topography of a wide range of solid surfaces using nematic liquid crystals. Polarizing microscopy is employed. The usefulness of the method for detecting weak mechanical effects has been demonstrated. An application in criminology is foreseen.

Acyclic Cucurbit[n]uril-type Molecular Containers: Influence of Aromatic Walls on their Function as Solubilizing Excipients for Insoluble Drugs

PubMed Central

2015-01-01

We studied the influence of the aromatic sidewalls on the ability of acyclic CB[n]-type molecular containers (1a–1e) to act as solubilizing agents for 19 insoluble drugs including the developmental anticancer agent PBS-1086. All five containers exhibit good water solubility and weak self-association (Ks ≤ 624 M–1). We constructed phase solubility diagrams to extract Krel and Ka values for the container·drug complexes. The acyclic CB[n]-type containers generally display significantly higher Ka values than HP-β-CD toward drugs. Containers 1a–1e bind the steroidal ring system and aromatic moieties of insoluble drugs. Compound 1b displays highest affinity toward most of the drugs studied. Containers 1a and 1b are broadly applicable and can be used to formulate a wider variety of insoluble drugs than was previously possible with cyclodextrin technology. For drugs that are solubilized by both HP-β-CD and 1a–1e, lower concentrations of 1a–1e are required to achieve identical [drug]. PMID:25369565

Acyclic cucurbit[n]uril-type molecular containers: influence of aromatic walls on their function as solubilizing excipients for insoluble drugs.

PubMed

Zhang, Ben; Isaacs, Lyle

2014-11-26

We studied the influence of the aromatic sidewalls on the ability of acyclic CB[n]-type molecular containers (1a-1e) to act as solubilizing agents for 19 insoluble drugs including the developmental anticancer agent PBS-1086. All five containers exhibit good water solubility and weak self-association (Ks ≤ 624 M(-1)). We constructed phase solubility diagrams to extract Krel and Ka values for the container·drug complexes. The acyclic CB[n]-type containers generally display significantly higher Ka values than HP-β-CD toward drugs. Containers 1a-1e bind the steroidal ring system and aromatic moieties of insoluble drugs. Compound 1b displays highest affinity toward most of the drugs studied. Containers 1a and 1b are broadly applicable and can be used to formulate a wider variety of insoluble drugs than was previously possible with cyclodextrin technology. For drugs that are solubilized by both HP-β-CD and 1a-1e, lower concentrations of 1a-1e are required to achieve identical [drug].

Comparative analysis of the electrostatic potentials of some structural analogues of 2,3,7,8-tetrachlorodibenzo-p-dioxin and of related aromatic systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murray, J.S.; Evans, P.; Politzer, P.

1990-01-01

An ab initio STO-5G computational analysis of the electrostatic potentials of four structural analogs of the highly toxic 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and four related aromatic systems (benzo(a)pyrene, benz(a)anthracene and two isomeric benzoflavones) was carried out. The systems, to varying degrees, induce aryl hydrocarbon hydroxylase activity and are believed to interact with the same cytosolic receptor in initiating their biochemical responses. It was found that a high degree of activity appears to require negative potentials that are non-overlapping above all or most of the lateral regions, with an observed optimum range of magnitudes. In systems with central oxygens, it is required thatmore » the negative oxygen potentials be small and weak; however, oxygen negative regions in the molecule are not necessary for high activity. The observed differences between the potential patterns of the four aromatic systems and those of TCDD and its active analogs may reflect an inherent dissimilarity in the nature of their interactions with the cytosolic receptor.« less

In silico Analysis of Conformational Changes Induced by Mutation of Aromatic Binding Residues: Consequences for Drug Binding in the hERG K+ Channel

PubMed Central

Knape, Kirsten; Linder, Tobias; Wolschann, Peter; Beyer, Anton; Stary-Weinzinger, Anna

2011-01-01

Pharmacological inhibition of cardiac hERG K+ channels is associated with increased risk of lethal arrhythmias. Many drugs reduce hERG current by directly binding to the channel, thereby blocking ion conduction. Mutation of two aromatic residues (F656 and Y652) substantially decreases the potency of numerous structurally diverse compounds. Nevertheless, some drugs are only weakly affected by mutation Y652A. In this study we utilize molecular dynamics simulations and docking studies to analyze the different effects of mutation Y652A on a selected number of hERG blockers. MD simulations reveal conformational changes in the binding site induced by mutation Y652A. Loss of π-π-stacking between the two aromatic residues induces a conformational change of the F656 side chain from a cavity facing to cavity lining orientation. Docking studies and MD simulations qualitatively reproduce the diverse experimentally observed modulatory effects of mutation Y652A and provide a new structural interpretation for the sensitivity differences. PMID:22194911

Controlling Chirality of Entropic Crystals

NASA Astrophysics Data System (ADS)

Damasceno, Pablo F.; Karas, Andrew S.; Schultz, Benjamin A.; Engel, Michael; Glotzer, Sharon C.

2015-10-01

Colloidal crystal structures with complexity and diversity rivaling atomic and molecular crystals have been predicted and obtained for hard particles by entropy maximization. However, thus far homochiral colloidal crystals, which are candidates for photonic metamaterials, are absent. Using Monte Carlo simulations we show that chiral polyhedra exhibiting weak directional entropic forces self-assemble either an achiral crystal or a chiral crystal with limited control over the crystal handedness. Building blocks with stronger faceting exhibit higher selectivity and assemble a chiral crystal with handedness uniquely determined by the particle chirality. Tuning the strength of directional entropic forces by means of particle rounding or the use of depletants allows for reconfiguration between achiral and homochiral crystals. We rationalize our findings by quantifying the chirality strength of each particle, both from particle geometry and potential of mean force and torque diagrams.

Cracking a chemical conundrum

NASA Astrophysics Data System (ADS)

Adams, James M.; Ivanov, Alexandre S.; Johnson, Mark R.; Stride, John A.

2004-07-01

An everyday laboratory chemical, hexamethylbenzene (HMB) has assumed an important role in the history of molecular structure and crystallography. It was one of the first organic crystal structures to be solved and provided direct experimental proof for the hypothesis of planarity in aromatic systems. Very soon after this, HMB was found to undergo a phase transition at 117K, resulting in crystal shattering. Since then, many attempts have been made to obtain the low-temperature structure, but none have succeeded until now. Making use of the unique properties of the neutron, we have performed powder diffraction measurements to obtain the low-temperature crystal structure and inelastic measurements to determine the dynamics of the system. These experiments have been augmented by the use of ab initio calculations and molecular modelling to obtain a complete picture of HMB in the solid state.

Crystal structure of a new amine nitrate: 4-dimethylaminopyridinium nitrate (C{sub 7}H{sub 11}N{sub 2})NO{sub 3}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Benhassan, D., E-mail: houcine-naili@yahoo.com; Rekik, W.; Naïli, H.

2015-12-15

The title compound (C{sub 7}H{sub 11}N{sub 2})NO{sub 3} (I) was obtained by the slow evaporation method at room temperature. Its crystal structure consists of organic cations (C{sub 7}H{sub 11}N{sub 2}){sup +} and nitrate anions (NO{sub 3}){sup –} linked by two types of hydrogen bonds. Each monoprotonated nitrogen atom, called bifurcated, is engaged in two N–H···O hydrogen bonds with two symmetric oxygen atoms. In addition, the crystal structure stability is established by C–H···O hydrogen bonds that ensure the formation of infinite layers, parallel to (001) plane. These layers are related together through π···π interactions established between aromatic amines.

Organic/inorganic-doped aromatic derivative crystals: Growth and properties

NASA Astrophysics Data System (ADS)

Stanculescu, F.; Ionita, I.; Stanculescu, A.

2014-09-01

Results of a comparative study on the growth from melt by the Bridgman-Stockbarger method of meta-dinitrobenzene (m-DNB) and benzil (Bz) crystals in the same experimental set-up and the same experimental conditions are presented. The incorporation of an inorganic (iodine) dopant in m-DNB was analyzed in the given experimental conditions from the point of view of the solid-liquid interface stability. The limits for a stable growth and the conditions that favor the generation of morphological instability are emphasized. These limits for m-DNB are compatible with those previously determined for Bz, and therefore, even for a high gradient concentration at the growth interface, it is possible to grow m-DNB and Bz crystals in the same experimental conditions characterized by a high ΔT and v. The optical properties were investigated in relation with the dopant incorporation in the crystal in the mentioned experimental conditions. Effects of the dopant (m-DNB/iodine in Bz and iodine in m-DNB) on the optical band gap and optical non-linear properties of the crystals are discussed.

Modeling the intermolecular interactions: molecular structure of N-3-hydroxyphenyl-4-methoxybenzamide.

PubMed

Karabulut, Sedat; Namli, Hilmi; Kurtaran, Raif; Yildirim, Leyla Tatar; Leszczynski, Jerzy

2014-03-01

The title compound, N-3-hydroxyphenyl-4-methoxybenzamide (3) was prepared by the acylation reaction of 3-aminophenol (1) and 4-metoxybenzoylchloride (2) in THF and characterized by ¹H NMR, ¹³C NMR and elemental analysis. Molecular structure of the crystal was determined by single crystal X-ray diffraction and DFT calculations. 3 crystallizes in monoclinic P2₁/c space group. The influence of intermolecular interactions (dimerization and crystal packing) on molecular geometry has been evaluated by calculations performed for three different models; monomer (3), dimer (4) and dimer with added unit cell contacts (5). Molecular structure of 3, 4 and 5 was optimized by applying B3LYP method with 6-31G+(d,p) basis set in gas phase and compared with X-ray crystallographic data including bond lengths, bond angles and selected dihedral angles. It has been concluded that although the crystal packing and dimerization have a minor effect on bond lengths and angles, however, these interactions are important for the dihedral angles and the rotational conformation of aromatic rings. Copyright © 2013 Elsevier Inc. All rights reserved.

Air-stable n-type semiconductor: core-perfluoroalkylated perylene bisimides.

PubMed

Li, Yan; Tan, Lin; Wang, Zhaohui; Qian, Hualei; Shi, Yubai; Hu, Wenping

2008-02-21

A series of core-perfluoroalkylated perylene bisimides (PBIs) have been efficiently synthesized by copper-mediated perfluoroalkylation of dibrominated PBIs. Their aromatic cores are highly twisted due to the steric encumbrance in the bay regions as revealed by single-crystal X-ray analysis. The organic field-effect transistors (OFETs) incorporating these new n-type semiconductors show remarkable air-stability and good field effect mobility.

Porphyrin-Embedded Silicate Materials for Detection of Hydrocarbon Solvents

DTIC Science & Technology

2011-01-14

Sensors 2011, 11, 886-904; doi:10.3390/s110100886 sensors ISSN 1424-8220 www.mdpi.com/journal/ sensors Article Porphyrin-Embedded Silicate...Prescribed by ANSI Std Z39-18 Sensors 2011, 11 887 1. Introduction Mesoporous silicates have been widely described in sensing...absorption spectroscopy, quartz crystal microbalance ( QCM ), and FTIR have been utilized for aromatic hydrocarbon sensing applications based on these

Reduced Iron Sulfide Systems for Removal of Heavy Metal Ions from Groundwater

DTIC Science & Technology

2009-07-01

be gleaned from higher magnification of these samples. Each set of lattice fringes represents a single crystal of mackinawite (Ohfuji and Ricard...diffractograms, the diffraction peaks are broad and weak, indicating a poor degree of crystallization or a small crystallite size. For the non-magnetic...the lattice spacings of synthetic mackinawite in this study are shorter. The 3-day aging in this study resulted in a higher degree of crystallization

Aniline-containing guests recognized by α,α',δ,δ'-tetramethyl-cucurbit[6]uril host.

PubMed

Lin, Rui-Lian; Fang, Guo-Sheng; Sun, Wen-Qi; Liu, Jing-Xin

2016-12-13

The host-guest complexation of symmetrical α,α',δ,δ'-tetramethyl-cucurbit[6]uril (TMeQ[6]) and cucurbit[7]uril (Q[7]) with a series of aniline-containing guests has been investigated by various experimental techniques including NMR, ITC, and X-ray crystallography. Experimental results indicate that both TMeQ[6] and Q[7] hosts can encapsulate aniline-containing guests to form stable inclusion complexes. However, the oval cavity of TMeQ[6] is more complementary in size and shape to the aromatic ring of the guests than the spherical cavity of Q[7]. Shielding and deshielding effects of the aromatic ring on guests lead to the remarkable chemical shifts of the TMeQ[6] host protons. The rotational restriction of the guests in the oval cavity of TMeQ[6] results in the large negative values of entropy. The X-ray crystal structure of the 1:1 inclusion complex between TMeQ[6] and N,N'-diethyl-benzene-1,4-diamine unambiguously reveals that the aromatic ring of the guest resides in the oval cavity of TMeQ[6].

Diketopyrrolopyrrole Polymers with Thienyl and Thiazolyl Linkers for Application in Field-Effect Transistors and Polymer Solar Cells.

PubMed

Yu, Yaping; Wu, Yang; Zhang, Andong; Li, Cheng; Tang, Zheng; Ma, Wei; Wu, Yonggang; Li, Weiwei

2016-11-09

Conjugated polymers consisting of diketopyrrolopyrrole (DPP) units have been successfully applied in field-effect transistors (FETs) and polymer solar cells (PSCs), while most of the DPP polymers were designed as symmetric structures containing identical aromatic linkers. In this manuscript, we design a new asymmetric DPP polymer with varied aromatic linkers in the backbone for application in FETs and PSCs. The designation provides the chance to finely adjust the energy levels of conjugated polymers so as to influence the device performance. The asymmetric polymer exhibits highly crystalline properties, high hole mobilities of 3.05 cm 2 V -1 s -1 in FETs, and a high efficiency of 5.9% in PSCs with spectra response from 300 to 850 nm. Morphology investigation demonstrates that the asymmetric polymer has a large crystal domain in blended thin films, indicating that the solar cell performance can be further enhanced by optimizing the microphase separation. The study reveals that the asymmetric design via adjusting the aromatic linkers in DPP polymers is a useful route toward flexible electronic devices.

Electronic distributions within protein phenylalanine aromatic rings are reflected by the three-dimensional oxygen atom environments.

PubMed Central

Thomas, K A; Smith, G M; Thomas, T B; Feldmann, R J

1982-01-01

The atomic environments of 170 phenylalanine-residue aromatic rings from 28 protein crystal structures are transformed into a common orientation and combined to calculate an average three-dimensional environment. The spatial distribution of atom types in this environment reveals a preferred interaction between oxygen atoms and the edge of the planar aromatic rings. From the difference in frequency of interaction of oxygen atoms with the edge and the top of the ring, an apparent net free energy difference of interaction favoring the edge of the ring is estimated to be about -1 kcal/mol (1 cal = 4.184 J). Ab initio quantum mechanical calculations, performed on a model consisting of benzene and formamide, indicate that the observed geometry is stabilized by a favorable enthalpic interaction. Although benzene rings are considered to be nonpolar, the electron distribution is a complex multipole with no net dipole moment. The observed interaction orientation frequencies demonstrate that these multipolar electron distributions, when occurring at the short distances encountered in densely packed protein molecules, are significant determinants of internal packing geometries. PMID:6956896

Structure, optical and phonon properties of bulk and nanocrystalline Al2-xScx(WO4)3 solid solutions doped with Cr3+

NASA Astrophysics Data System (ADS)

Mączka, M.; Hermanowicz, K.; Pietraszko, A.; Yordanova, A.; Koseva, I.

2014-01-01

Pure and Cr3+ doped nanosized Al2-xScx(WO4)3 solid solutions were prepared by co-precipitation method as well as Al2-xScx(WO4)3 single crystals were grown by high-temperature flux method. The obtained samples were characterized by X-ray, Raman, IR, absorption and luminescence methods. Single crystal X-ray diffraction showed that AlSc(WO4)3 is orthorhombic at room temperature with space group Pnca and trivalent cations are statistically distributed. Raman and IR studies showed that Al2-xScx(WO4)3 solid solutions show "two mode" behavior. They also showed that vibrational properties of nanosized samples have been weakly modified in comparison with the bulk materials. The luminescence and absorption spectra revealed that chromium ions occupy two sites of weak and strong crystal field strength.

Molecular association via halogen bonding and other weak interactions in the crystal structures of 11-bromo-12-oxo-5β-cholan derivatives

NASA Astrophysics Data System (ADS)

Salunke, Deepak B.; Hazra, Braja G.; Gonnade, Rajesh G.; Pore, Vandana S.; Bhadbhade, Mohan M.

2008-12-01

Methyl 3α,7α-diacetoxy-12-oxo-5β-cholan-24-oate 2, methyl 11α-bromo-3α,7α-diacetoxy-12-oxo-5β-cholan-24-oate 3, methyl 11β-bromo-3α,7α-diacetoxy-12-oxo-5β-cholan-24-oate 4 and methyl 11,11-dibromo-3α,7α-diacetoxy-12-oxo-5β-cholan-24-oate 5 were synthesized. The crystal structures of these molecules were resolved to study the effect of bulky bromine atom in the steroid skeleton of cholic acid with different stereo-chemical orientations at C-11 on the two-dimensional arrangement of molecules and solid-state properties. All the molecules associate only via weak intermolecular interactions in their crystal structures, notable one being the Halogen Bonded assembly (C-Br…O) in 5.

The effect of an electric field on the morphological stability of the crystal-melt interface of a binary alloy. III - Weakly nonlinear theory

NASA Technical Reports Server (NTRS)

Wheeler, A. A.; Mcfadden, G. B.; Coriell, S. R.; Hurle, D. T. J.

1990-01-01

The effect of a constant electric current on the crystal-melt interface morphology during directional solidification at constant velocity of a binary alloy is considered. A linear temperature field is assumed, and thermoelectric effects and Joule heating are neglected; electromigration and differing electrical conductivities of crystal and melt are taken into account. A two-dimensional weakly nonlinear analysis is carried out to third order in the interface amplitude, resulting in a cubic amplitude equation that describes whether the bifurcation from the planar state is supercritical or subcritical. For wavelengths corresponding to the most dangerous mode of linear theory, the demarcation between supercritical and subcritical behavior is calculated as a function of processing conditions and material parameters. The bifurcation behavior is a sensitive function of the magnitude and direction of the electric current and of the electrical conductivity ratio.

Morphological diversity of nitroguanidine crystals with enhanced mechanical performance and thermodynamic stability

NASA Astrophysics Data System (ADS)

Luo, Zhilong; Cui, Yingdan; Dong, Weibing; Xu, Qipeng; Zou, Gaoxing; Kang, Chao; Hou, Baohong; Chen, Song; Gong, Junbo

2017-12-01

Nitroguanidine (NQ) is a commonly used explosive, which has been widely used for both civilian and military explosive applications. However, the weak flowability and mechanical performance limit its application. In this work, mechanical performance and thermodynamic stability of NQ crystals were improved by controlling crystal morphologies in the crystallization process. Typical NQ crystals with multiple morphologies and single crystal form were obtained in the presence of additives during the cooling crystallization. The morphology controlled NQ crystals showed higher density, unimodal crystal size distribution and enhanced flowability. The additives showed the inhibitory effect on the nucleation of NQ crystals by in-situ FBRM and PVM determination, and the mechanism was analyzed by means of morphological prediction and molecular simulation. Furthermore, the morphology controlled NQ crystals suggested higher thermodynamic stability according to the calculation of entropy, enthalpy, Gibbs free energy and apparent activation energy on the basis of DSC results.

Industry - Military Energy Symposium, held 21-23 October 1980, San Antonio, Texas

DTIC Science & Technology

1980-10-21

unless the best available technology is applied to many sources including those the size of airports . Further discussion of these issues will hopefully...particularly with naphthenic fuels. A similar weakness applies to correlations of net heat of combustion. Some additional correlating parameters...Viscosity Boost pump power Line size and weight Thermal Stability Gum, deposits, nozzle coking Specific Heat Avionics and engine oil cooling Aromatics

Electron-hole diffusion lengths >175 μm in solution-grown CH 3NH 3PbI 3 single crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dong, Qingfeng; Fang, Yanjun; Shao, Yuchuan

Long, balanced electron and hole diffusion lengths greater than 100 nanometers in the polycrystalline organolead trihalide compound CH 3NH 3PbI 3 are critical for highly efficient perovskite solar cells. We found that the diffusion lengths in CH 3NH 3PbI 3 single crystals grown by a solution-growth method can exceed 175 micrometers under 1 sun (100 mW cm –2) illumination and exceed 3 millimeters under weak light for both electrons and holes. The internal quantum efficiencies approach 100% in 3-millimeter-thick single-crystal perovskite solar cells under weak light. These long diffusion lengths result from greater carrier mobility, longer lifetime, and much smallermore » trap densities in the single crystals than in polycrystalline thin films. As a result, the long carrier diffusion lengths enabled the use of CH 3NH 3PbI 3 in radiation sensing and energy harvesting through the gammavoltaic effect, with an efficiency of 3.9% measured with an intense cesium-137 source.« less

Dislocation dynamics and crystal plasticity in the phase-field crystal model

NASA Astrophysics Data System (ADS)

Skaugen, Audun; Angheluta, Luiza; Viñals, Jorge

2018-02-01

A phase-field model of a crystalline material is introduced to develop the necessary theoretical framework to study plastic flow due to dislocation motion. We first obtain the elastic stress from the phase-field crystal free energy under weak distortion and show that it obeys the stress-strain relation of linear elasticity. We focus next on dislocations in a two-dimensional hexagonal lattice. They are composite topological defects in the weakly nonlinear amplitude equation expansion of the phase field, with topological charges given by the standard Burgers vector. This allows us to introduce a formal relation between the dislocation velocity and the evolution of the slowly varying amplitudes of the phase field. Standard dissipative dynamics of the phase-field crystal model is shown to determine the velocity of the dislocations. When the amplitude expansion is valid and under additional simplifications, we find that the dislocation velocity is determined by the Peach-Koehler force. As an application, we compute the defect velocity for a dislocation dipole in two setups, pure glide and pure climb, and compare it with the analytical predictions.

Electron-hole diffusion lengths >175 μm in solution-grown CH 3NH 3PbI 3 single crystals

DOE PAGES

Dong, Qingfeng; Fang, Yanjun; Shao, Yuchuan; ...

2015-02-27

Long, balanced electron and hole diffusion lengths greater than 100 nanometers in the polycrystalline organolead trihalide compound CH 3NH 3PbI 3 are critical for highly efficient perovskite solar cells. We found that the diffusion lengths in CH 3NH 3PbI 3 single crystals grown by a solution-growth method can exceed 175 micrometers under 1 sun (100 mW cm –2) illumination and exceed 3 millimeters under weak light for both electrons and holes. The internal quantum efficiencies approach 100% in 3-millimeter-thick single-crystal perovskite solar cells under weak light. These long diffusion lengths result from greater carrier mobility, longer lifetime, and much smallermore » trap densities in the single crystals than in polycrystalline thin films. As a result, the long carrier diffusion lengths enabled the use of CH 3NH 3PbI 3 in radiation sensing and energy harvesting through the gammavoltaic effect, with an efficiency of 3.9% measured with an intense cesium-137 source.« less

Survival condition for low-frequency quasi-one-dimensional breathers in a two-dimensional strongly anisotropic crystal

NASA Astrophysics Data System (ADS)

Savin, A. V.; Zubova, E. A.; Manevitch, L. I.

2005-06-01

We investigate a two-dimensional (2D) strongly anisotropic crystal (2D SAC) on substrate: 2D system of coupled linear chains of particles with strong intrachain and weak interchain interactions, each chain being subjected to the sine background potential. Nonlinear dynamics of one of these chains when the rest of them are fixed is reduced to the well known Frenkel-Kontorova (FK) model. Depending on strengh of the substrate, the 2D SAC models a variety of physical systems: polymer crystals with identical chains having light side groups, an array of inductively coupled long Josephson junctions, anisotropic crystals having light and heavy sublattices. Continuum limit of the FK model, the sine-Gordon (sG) equation, allows two types of soliton solutions: topological solitons and breathers. It is known that the quasi-one-dimensional topological solitons can propagate also in a chain of 2D system of coupled chains and even in a helix chain in a three-dimensional model of polymer crystal. In contrast to this, numerical simulation shows that the long-living breathers inherent to the FK model do not exist in the 2D SAC with weak background potential. The effect changes scenario of kink-antikink collision with small relative velocity: at weak background potential the collision always results only in intensive phonon radiation while kink-antikink recombination in the FK model results in long-living low-frequency sG breather creation. We found the survival condition for breathers in the 2D SAC on substrate depending on breather frequency and strength of the background potential. The survival condition bears no relation to resonances between breather frequency and frequencies of phonon band—contrary to the case of the FK model.

Controlling Chirality of Entropic Crystals.

PubMed

Damasceno, Pablo F; Karas, Andrew S; Schultz, Benjamin A; Engel, Michael; Glotzer, Sharon C

2015-10-09

Colloidal crystal structures with complexity and diversity rivaling atomic and molecular crystals have been predicted and obtained for hard particles by entropy maximization. However, thus far homochiral colloidal crystals, which are candidates for photonic metamaterials, are absent. Using Monte Carlo simulations we show that chiral polyhedra exhibiting weak directional entropic forces self-assemble either an achiral crystal or a chiral crystal with limited control over the crystal handedness. Building blocks with stronger faceting exhibit higher selectivity and assemble a chiral crystal with handedness uniquely determined by the particle chirality. Tuning the strength of directional entropic forces by means of particle rounding or the use of depletants allows for reconfiguration between achiral and homochiral crystals. We rationalize our findings by quantifying the chirality strength of each particle, both from particle geometry and potential of mean force and torque diagrams.

Crystal structures of (2E)-1-(3-bromo-thio-phen-2-yl)-3-(2-meth-oxy-phen-yl)prop-2-en-1-one and (2E)-1-(3-bromo-thio-phen-2-yl)-3-(3,4-di-meth-oxy-phen-yl)prop-2-en-1-one.

PubMed

Naik, Vasant S; Shettigar, Venkataraya; Berglin, Tyler S; Coburn, Jillian S; Jasinski, Jerry P; Yathirajan, Hemmige S

2015-08-01

In the mol-ecules of the title compounds, (2E)-1-(3-bromo-thio-phen-2-yl)-3-(2-meth-oxy-phen-yl)prop-2-en-1-one, C14H11BrO2S, (I), which crystallizes in the space group P-1 with four independent mol-ecules in the asymmetric unit (Z' = 8), and (2E)-1-(3-bromo-thio-phen-2-yl)-3-(3,4-di-meth-oxy-phen-yl)prop-2-en-1-one, C15H13BrO3S, (II), which crystallizes with Z' = 8 in the space group I2/a, the non-H atoms are nearly coplanar. The mol-ecules of (I) pack with inversion symmetry stacked diagonally along the a-axis direction. Weak C-H⋯Br intra-molecular inter-actions in each of the four mol-ecules in the asymmetric unit are observed. In (II), weak C-H⋯O, bifurcated three-center inter-molecular inter-actions forming dimers along with weak C-H⋯π and π-π stacking inter-actions are observed, linking the mol-ecules into sheets along [001]. A weak C-H⋯Br intra-molecular inter-action is also present. There are no classical hydrogen bonds present in either structure.

Vibrational analysis and Y-aromaticity in bis (N,N‧-diphenyl guanidinium) oxalate crystal: A DFT study

NASA Astrophysics Data System (ADS)

Binoy, J.; James, C.; Hubert Joe, I.; Jayakumar, V. S.

2006-02-01

The compound of therapeutic interest, Bis ( N, N'-diphenyl guanidinium) oxalate, have been crystallized and is subjected to FT IR and Raman spectral studies, along with quantum chemical computations using density functional theory. In the crystal, diphenyl guanidinium ion is found to possess anti anti conformation although syn syn conformer is energetically favored based on the single point energy calculations at B3LYP/6-31G(d) level, which shows the counter ion influence on conformation. The optimized geometry at the same level of theory indicates that guanidinium moiety of diphenyl guanidinium ion is planar, possibly induced by the sp 2 hybridized central carbon atom and the twisting of phenyl ring with respect to guanidinium moiety has been observed. The charge delocalization of the planar oxalate ion predicted by XRD is confirmed by the DFT values of bond lengths. The presence of N-H⋯O intermolecular interactions can be observed in IR spectrum by the broadness of the band in the stretching region and its vibrational spectral consequences can be found as the shifting of band positions for amino group and CO group vibrations. The geometry, vibrational spectra, covalent bond orders and atomic charges of guanidinium ion, diphenyl guanidinium ion and of their corresponding neutral species have been used to investigate the effects of charge delocalization leading to Y-aromaticity. The FT IR and Raman spectra of diphenyl guanidine indicates that phenyl ring modes 8b, 18a, 9b and 6b, active in diphenyl guanidine molecule, are found to be dormant in their ionic species.

Easy methods to study the smart energetic TNT/CL-20 co-crystal.

PubMed

Li, Huarong; Shu, Yuanjie; Gao, Shijie; Chen, Ling; Ma, Qing; Ju, Xuehai

2013-11-01

2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) is a high-energy nitramine explosive with high mechanical sensitivity. 2,4,6-trinitrotoluene (TNT) is insensitive but by no means a high performance explosive. To reveal the significant importance and smart-material functionality of the energetic-energetic co-crystals, the stability, mechanical and explosive properties TNT/CL-20 co-crystal, TNT crystal and CL-20 crystal were studied. Non-hydrogen bonded non-covalent interactions govern the structures of energetic-energetic co-crystals. However, it is very difficult to accurately calculate the non-covalent intermolecular interaction energies. In this paper, the local conformation and the intricate non-covalent interactions were effectively mapped and analyzed from the electron density (ρ) and its derivatives. The results show that the two components TNT and CL-20 are connected mainly by nitro-aromatic interactions, and nitro-nitro interactions. The steric interactions in TNT/CL-20 could not be confronted with the attractive interactions. Moreover, the scatter graph of TNT crystal reveals the reason why TNT is brittle. The detailed electrostatic potential analysis predicted that the detonation velocities (D) and impact sensitivity for the compounds both increase in the sequence of CL-20 > TNT/CL-20 co-crystal > TNT. Additionally, TNT/CL-20 co-crystal has better malleability than its pure components. This demonstrates the capacity and the feasibility of realizing explosive smart materials by co-crystallization, even if strong hydrogen bonding schemes are generally lacking in energetic materials.

Aromatic aldehydes at the active site of aldehyde oxidoreductase from Desulfovibrio gigas: reactivity and molecular details of the enzyme-substrate and enzyme-product interaction.

PubMed

Correia, Hugo D; Marangon, Jacopo; Brondino, Carlos D; Moura, Jose J G; Romão, Maria J; González, Pablo J; Santos-Silva, Teresa

2015-03-01

Desulfovibrio gigas aldehyde oxidoreductase (DgAOR) is a mononuclear molybdenum-containing enzyme from the xanthine oxidase (XO) family, a group of enzymes capable of catalyzing the oxidative hydroxylation of aldehydes and heterocyclic compounds. The kinetic studies reported in this work showed that DgAOR catalyzes the oxidative hydroxylation of aromatic aldehydes, but not heterocyclic compounds. NMR spectroscopy studies using (13)C-labeled benzaldehyde confirmed that DgAOR catalyzes the conversion of aldehydes to the respective carboxylic acids. Steady-state kinetics in solution showed that high concentrations of the aromatic aldehydes produce substrate inhibition and in the case of 3-phenyl propionaldehyde a suicide substrate behavior. Hydroxyl-substituted aromatic aldehydes present none of these behaviors but the kinetic parameters are largely affected by the position of the OH group. High-resolution crystallographic structures obtained from single crystals of active-DgAOR soaked with benzaldehyde showed that the side chains of Phe425 and Tyr535 are important for the stabilization of the substrate in the active site. On the other hand, the X-ray data of DgAOR soaked with trans-cinnamaldehyde showed a cinnamic acid molecule in the substrate channel. The X-ray data of DgAOR soaked with 3-phenyl propionaldehyde showed clearly how high substrate concentrations inactivate the enzyme by binding covalently at the surface of the enzyme and blocking the substrate channel. The different reactivity of DgAOR versus aldehyde oxidase and XO towards aromatic aldehydes and N-heterocyclic compounds is explained on the basis of the present kinetic and structural data.

Additional evidence from x-ray powder diffraction patterns that icosahedral quasi-crystals of intermetallic compounds are twinned cubic crystals

PubMed Central

Pauling, Linus

1988-01-01

Analysis of the measured values of Q for the weak peaks (small maxima, usually considered to be background fluctuations, “noise”) on the x-ray powder diffraction curves for 17 rapidly quenched alloys leads directly to the conclusion that they are formed by an 820-atom or 1012-atom primitive cubic structure that by icosahedral twinning produces the so-called icosahedral quasi-crystals. PMID:16593948

Systematic Approach to Electrostatically Induced 2D Crystallization of Nanoparticles at Liquid Interfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fukuto, M.; Kewalramani, S.; Wang, S.

2011-02-07

We report an experimental demonstration of a strategy for inducing two-dimensional (2D) crystallization of charged nanoparticles on oppositely charged fluid interfaces. This strategy aims to maximize the interfacial adsorption of nanoparticles, and hence their lateral packing density, by utilizing a combination of weakly charged particles and a high surface charge density on the planar interface. In order to test this approach, we investigated the assembly of cowpea mosaic virus (CPMV) on positively charged lipid monolayers at the aqueous solution surface, by means of in situ X-ray scattering measurements at the liquid-vapor interface. The assembly was studied as a function ofmore » the solution pH, which was used to vary the charge on CPMV, and of the mole fraction of the cationic lipid in the binary lipid monolayer, which set the interface charge density. The 2D crystallization of CPMV occurred in a narrow pH range just above the particle's isoelectric point, where the particle charge was weakly negative, and only when the cationic-lipid fraction in the monolayer exceeded a threshold. The observed 2D crystals exhibited nearly the same packing density as the densest lattice plane within the known 3D crystals of CPMV. The above electrostatic approach of maximizing interfacial adsorption may provide an efficient route to the crystallization of nanoparticles at aqueous interfaces.« less

The anomalous 3. 43 and 3. 53 micron emission features toward HD 97048 and Elias 1 - C-C vibrational modes of polycyclic aromatic hydrocarbons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schutte, W.A.; Tielens, A.G.G.M.; Allamandola, L.J.

1990-09-01

The 5-8 micron spectra obtained toward the two protostellar sources, HD 97048 and Elias 1 exhibit strong anomalous emission features at 3.43 and 3.53 microns. Combining these results with earlier data established that the emission in the general IR features is extended on at least a 20-arcsec scale. In view of the high energy density in the emission zone, as well as the apparent correspondence of the anomalous 3.43 and 3.53 micron features with weak emission shoulders associated with the general family of IR emission bands, an explanation for these observations in terms of C-C overtones and combination tones ofmore » large or dehydrogenated polycyclic aromatic hydrocarbons is judged to be provisionally suitable. 62 refs.« less

1-Nitro-4-(4-nitro-phen-oxy)benzene: a second monoclinic polymorph.

PubMed

Naz, Mehwish; Akhter, Zareen; McKee, Vickie; Nadeem, Arif

2013-11-06

In the title compound, C12H8N2O5, the aromatic rings are inclined to one another by 56.14 (7)°. The nitro groups are inclined by to the benzene rings to which they are attached by 3.86 (17) and 9.65 (15)°. In the crystal, mol-ecules are linked by C-H⋯O hydrogen bonds, forming a three-dimensional structure. The title compound is a new monoclinic polymorph, crystallizing in space group P21/c. The first polymorph crystallized in space group C2/c and the mol-ecule possesses twofold rotation symmetry. Two low-temperature structures of this polymorph (150 K and 100 K, respectively) have been reported [Meciarova et al. (2004). Private Communication (refcode IXOGAD). CCDC, Cambridge, England, and Dey & Desiraju (2005). Chem. Commun. pp. 2486-2488].

Room Temperature Curing Polymers

DTIC Science & Technology

1977-05-01

diglycidyl esters are low melting solids, they are easily purified by recrystallization . Both diglycidyl adipate and sebacate were prepared in 88...aromatic amine Shell Z (a eutectic mixture of methylene dianiline and m-phenylene- diamine). The Shell Z cured resins had apparent Tg’s near...cooled to 0oC. The white crystals which formed were recrystallized three times from methanol-water (9:1) to yield 248 g (88%) EEW = 125 (Theory 115

Patterns of Cognitive Strengths and Weaknesses and Relationships to Math Errors

ERIC Educational Resources Information Center

Koriakin, Taylor; White, Erica; Breaux, Kristina C.; DeBiase, Emily; O'Brien, Rebecca; Howell, Meiko; Costa, Michael; Liu, Xiaochen; Pan, Xingyu; Courville, Troy

2017-01-01

This study investigated cognitive patterns of strengths and weaknesses (PSW) and their relationship to patterns of math errors on the Kaufman Test of Educational Achievement (KTEA-3). Participants, ages 5 to 18, were selected from the KTEA-3 standardization sample if they met one of two PSW profiles: high crystallized ability (Gc) paired with low…

DOE Office of Scientific and Technical Information (OSTI.GOV)

Patel, J. R.

We synthesized hexagonal-disc-shaped MgB{sub 2} single crystals under high-pressure conditions and analyzed the microstructure and pinning properties. The lattice constants and the Laue pattern of the crystals from X-ray micro-diffraction showed the crystal symmetry of MgB{sub 2}. A thorough crystallographic mapping within a single crystal showed that the edge and c-axis of hexagonal-disc shape exactly matched the (10-10) and the (0001) directions of the MgB{sub 2} phase. Thus, these well-shaped single crystals may be the best candidates for studying the direction dependences of the physical properties. The magnetization curve and the magnetic hysteresis for these single crystals showed the existencemore » of a wide reversible region and weak pinning properties, which supported our single crystals being very clean.« less

Biochemical and chemical characterization of phenylglyoxal bis(guanylhydrazone), an aromatic analogue of mitoguazone.

PubMed

Elo, H; Koskinen, M; Mutikainen, I; Tilus, P; Lampio, A; Keso, L; Vainio, A; Joutsjoki, V; Alli, K; Yliniva, A

1996-10-01

Since little has been known about the properties of aromatic analogues of the antineoplastic agent methylglyoxal bis(guanylhydrazone) (MGBG), an investigation was performed on phenylglyoxal bis(guanylhydrazone) (PhGBG). PhGBG competitively inhibited yeast adenosylmethionine decarboxylase (AdoMetDC) with a Ki of 65 microM. As compared to MGBG (Ki 0.23 microM), PhGBG is a much weaker inhibitor, being even weaker than the unsubstituted congener glyoxal bis(guanylhydrazone) (GBG, Ki 18 microM). PhGBG inhibited porcine kidney diamine oxidase (DAO) non-competitively, being a more potent inhibitor (Ki 0.12 microM) than GBG (Ki 0.17 microM) or MGBG (Ki 0.33 microM). Thus, PhGBG has an unfavourably high ratio of Ki(AdoMetDC)/Ki(DAO) for potential use for selectively inhibiting polyamine biosynthesis. This does not exclude the possibility that PhGBG or other aromatic congeners might have therapeutic value since the corresponding ratio of the antileukaemic congeners GBG and MGBG is also high as compared to many aliphatic non-antileukaemic analogues. The pKa1 and pKa2 values of PhGBG dication were found to be 6.39 +/- 0.02 and 8.64 +/- 0.02 respectively, their difference being distinctly larger than in the case of GBG or its C-alkylated analogues. This may result from decreased stability of the dication form, caused by the resonance effect or possibly by the inductive effect of the phenyl group. The species distribution of PhGBG (proportion of free base 5.5%, predominant species the monocation) at 37 degrees C resembles that of GBG and MGBG but is clearly different from that of non-antileukaemic C-alkylated analogues. These similarities suggest that PhGBG and its derivatives may be worth antitumour screening. Depending on the conditions used in the crystallization, three different types of crystals of PhGBG sulphate were obtained. Crystallography indicated that, in two of the types, the crystal consisted exclusively of the anti-anti isomer, i.e. the same isomer as has been observed in the case of GBG and its C-alkylated congeners. One crystal type, however, consisted of a different geometrical isomer (anti-syn), suggesting that PhGBG may isomerize more easily than its aliphatic analogues. Previous concepts on the isomerism of GBG and C-alkylated bis(guanylhydrazones) thus cannot be generalized to aromatic congeners. A theory based on resonance, inductive and hyperconjugative effects and electron transfers is presented that is capable of explaining the formation of the two geometrical isomers of PhGBG that were experimentally observed. A similar theory, based on hyperconjugation of C-F bonds, is presented that is capable of explaining the previous finding of the formation of the anti-syn isomer of trifluoromethylglyoxal bis(guanylhydrazone) (CF3GBG). Like that of CF3GBG, the anti-syn isomer of the PhGBG dication is stabilized by an internal hydrogen bond. The lack of structural rigidity may affect the biological properties of PhGBG, e.g. its ability to inhibit AdoMetDC.

Crystal structure of 1-(3-chloro-phen-yl)piperazin-1-ium picrate-picric acid (2/1).

PubMed

Kavitha, Channappa N; Jasinski, Jerry P; Kaur, Manpreet; Anderson, Brian J; Yathirajan, H S

2014-11-01

The title salt {systematic name: bis-[1-(3-chloro-phen-yl)piperazinium 2,4,6-tri-nitro-phenolate]-picric acid (2/1)}, 2C10H14ClN2 (+)·2C6H5N3O7 (-)·C6H6N3O7, crystallized with two independent 1-(3-chloro-phen-yl)piperazinium cations, two picrate anions and a picric acid mol-ecule in the asymmetric unit. The six-membered piperazine ring in each cation adopts a slightly distorted chair conformation and contains a protonated N atom. In the picric acid mol-ecule, the mean planes of the nitro groups in the ortho-, meta-, and para-positions are twisted from the benzene ring by 31.5 (3), 7.7 (1), and 3.8 (2)°, respectively. In the anions, the dihedral angles between the benzene ring and the ortho-, meta-, and para-nitro groups are 36.7 (1), 5.0 (6), 4.8 (2)°, and 34.4 (9), 15.3 (8), 4.5 (1)°, respectively. The nitro group in one anion is disordered and was modeled with two sites for one O atom with an occupancy ratio of 0.627 (7):0.373 (7). In the crystal, the picric acid mol-ecule inter-acts with the picrate anion through a trifurcated O-H⋯O four-centre hydrogen bond involving an intra-molecular O-H⋯O hydrogen bond and a weak C-H⋯O inter-action. Weak inter-molecular C-H⋯O inter-actions are responsible for the formation of cation-anion-cation trimers resulting in a chain along [010]. In addition, weak C-H⋯Cl and weak π-π inter-actions [centroid-centroid distances of 3.532 (3), 3.756 (4) and 3.705 (3) Å] are observed and contribute to the stability of the crystal packing.

Control of optical properties of YAG crystals by thermal annealing

NASA Astrophysics Data System (ADS)

Tkachenko, S.; Arhipov, P.; Gerasymov, I.; Kurtsev, D.; Vasyukov, S.; Nesterkina, V.; Shiran, N.; Mateichenko, P.; Sidletskiy, O.

2018-02-01

Optical properties of YAG crystals grown and annealed under different atmosphere conditions have been compared. Simultaneously we have registered the surface composition of crystals and content of basic admixtures in the crystals grown under the reducing conditions. Unlike YAG grown under weakly oxidizing conditions in Ir crucibles and bleached under oxidizing annealing, YAGMo crystals grown in Mo crucibles under reducing Ar + CO atmosphere can be bleached by both oxidizing and reducing thermal annealing. The bleaching of YAGMo is not reversed by further annealing under any available conditions. Mechanisms of this phenomenon have been discussed, including a possible role of admixtures in elimination of color centers in YAG grown under the reducing conditions.

Crystal structure and vibrational spectra of piperazinium bis(4-hydroxybenzenesulphonate) molecular-ionic crystal

NASA Astrophysics Data System (ADS)

Marchewka, M. K.; Pietraszko, A.

2008-02-01

The piperazinium bis(4-hydroxybenzenesulphonate) crystallizes from water solution at room temperature in P2 1/ c space group of monoclinic system. The crystals are built up of doubly protonated piperazinium cations and ionized 4-hydroxybenzenesulphonate anions that interact through weak hydrogen bonds of O-H⋯O and N-H⋯O type. Mutual orientation of anions is determined by non-conventional hydrogen bonds of C-H⋯π type. Room temperature powder FT IR and FT Raman measurements were carried out. The vibrational spectra are in full agreement with the structure obtained from X-ray crystallography. The big single crystals of the title salt can be grown.

Charge transfer and charge localization in extended radical cations: Investigation of model molecules for peptides

NASA Astrophysics Data System (ADS)

Weinkauf, Rainer; Lehrer, Florian

1998-12-01

Molecules consisting of a flexible tail and an aromatic chromophore are used as model systems to understand the situation of a single chromophore in a small peptide. Their S0-S1 resonant multiphoton ionization (REMPI) spectra show, that in neutral molecules the tail-chromophore interaction is weak and electronic excitation is localized at the chromophore. For molecules, where the ionization energy of the tail is considerable higher than that of the chromophore, by high resolution REMPI photoelectron spectroscopy we find the charge to be localized on the aromatic chromophore. This scheme also in suitable peptides allows local ionization at the aromatic chromophore. An estimate for various charge positions in peptide chains, however, shows, that for most of the amino acids electron hole positions in the nitrogen and oxygen "lone pair" orbitals of the peptide bond are nearly degenerate. REMPI photoelectron spectra of phenylethylamine, which as a model system contains such two degenerate charge positions, show small energetic shift of the ionization energy but strong geometry changes upon electron removal. This result is interpreted as direct ionization into a mixed charge delocalized state. Consequences for the charge transfer mechanism in peptides are discussed.

Determining the relative strengths of aromatic and aliphatic C-H⋅⋅⋅X hydrogen bonds in imidazolium ionic liquids through measurement of H/D isotope effects on 19 F nuclear shielding.

PubMed

Bottini, Gualberto; Moyna, Guillermo

2018-02-01

The relative strengths of aromatic and aliphatic C-H⋅⋅⋅X hydrogen bonds in imidazolium ionic liquids were investigated through measurement of H/D isotope effects on the 19 F nuclear shielding of deuterated isotopologues of 1-n-butyl-3-methylimidazolium hexafluorophosphate and tetrafluoroborate ([C 4 mim]PF 6 and [C 4 mim]BF 4 ). Δ 19 F(H,D) values ranging from 9.7 to 49.7 ppb were observed for [C 4 mim]PF 6 isotopologues, while for the [C 4 mim]BF 4 series these went from 26.2 to 83.8 ppb. Our findings indicate that the interactions between the fluorinated anions and protons on the C-1' and C-1″ position of the N-alkyl sidechains are comparable to, and in some cases stronger than, those involving protons on the aromatic ring, underscoring the role that these weak interionic forces have on the local ordering of imidazolium salts in the liquid state. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Alkyne Benzannulation Reactions for the Synthesis of Novel Aromatic Architectures.

PubMed

Hein, Samuel J; Lehnherr, Dan; Arslan, Hasan; J Uribe-Romo, Fernando; Dichtel, William R

2017-11-21

Aromatic compounds and polymers are integrated into organic field effect transistors, light-emitting diodes, photovoltaic devices, and redox-flow batteries. These compounds and materials feature increasingly complex designs, and substituents influence energy levels, bandgaps, solution conformation, and crystal packing, all of which impact performance. However, many polycyclic aromatic hydrocarbons of interest are difficult to prepare because their substitution patterns lie outside the scope of current synthetic methods, as strategies for functionalizing benzene are often unselective when applied to naphthalene or larger systems. For example, cross-coupling and nucleophilic aromatic substitution reactions rely on prefunctionalized arenes, and even directed metalation methods most often modify positions near Lewis basic sites. Similarly, electrophilic aromatic substitutions access single regioisomers under substrate control. Cycloadditions provide a convergent route to densely functionalized aromatic compounds that compliment the above methods. After surveying cycloaddition reactions that might be used to modify the conjugated backbone of poly(phenylene ethynylene)s, we discovered that the Asao-Yamamoto benzannulation reaction is notably efficient. Although this reaction had been reported a decade earlier, its scope and usefulness for synthesizing complex aromatic systems had been under-recognized. This benzannulation reaction combines substituted 2-(phenylethynyl)benzaldehydes and substituted alkynes to form 2,3-substituted naphthalenes. The reaction tolerates a variety of sterically congested alkynes, making it well-suited for accessing poly- and oligo(ortho-arylene)s and contorted hexabenzocoronenes. In many cases in which asymmetric benzaldehyde and alkyne cycloaddition partners are used, the reaction is regiospecific based on the electronic character of the alkyne substrate. Recognizing these desirable features, we broadened the substrate scope to include silyl- and halogen-substituted alkynes. Through a combined experimental and computational approach, we have elucidated mechanistic insight and key principles that govern the regioselectivity outcome of the benzannulation of structurally diverse alkynes. We have applied these methods to prepare sterically hindered, shape-persistent aromatic systems, heterocyclic aromatic compounds, functionalized 2-aryne precursors, polyheterohalogenated naphthalenes, ortho-arylene foldamers, and graphene nanoribbons. As a result of these new synthetic avenues, aromatic structures with interesting properties were uncovered such as ambipolar charge transport in field effect transistors based on our graphene nanoribbons, conformational aspects of ortho-arylene architectures resulting from intramolecular π-stacking, and modulation of frontier molecular orbitals via protonation of heteroatom containing aromatic systems. Given the availability of many substituted 2-(phenylethynyl)benzaldehydes and the regioselectivity of the benzannulation reaction, naphthalenes can be prepared with control of the substitution pattern at seven of the eight substitutable positions. Researchers in a range of fields are likely to benefit directly from newly accessible molecular and polymeric systems derived from polyfunctionalized naphthalenes.

A first test of the hypothesis of biogenic magnetite-based heterogeneous ice-crystal nucleation in cryopreservation.

PubMed

Kobayashi, Atsuko; Golash, Harry N; Kirschvink, Joseph L

2016-06-01

An outstanding biophysical puzzle is focused on the apparent ability of weak, extremely low-frequency oscillating magnetic fields to enhance cryopreservation of many biological tissues. A recent theory holds that these weak magnetic fields could be inhibiting ice-crystal nucleation on the nanocrystals of biological magnetite (Fe3O4, an inverse cubic spinel) that are present in many plant and animal tissues by causing them to oscillate. In this theory, magnetically-induced mechanical oscillations disrupt the ability of water molecules to nucleate on the surface of the magnetite nanocrystals. However, the ability of the magnetite crystal lattice to serve as a template for heterogeneous ice crystal nucleation is as yet unknown, particularly for particles in the 10-100 nm size range. Here we report that the addition of trace-amounts of finely-dispersed magnetite into ultrapure water samples reduces strongly the incidence of supercooling, as measured in experiments conducted using a controlled freezing apparatus with multiple thermocouples. SQUID magnetometry was used to quantify nanogram levels of magnetite in the water samples. We also report a relationship between the volume change of ice, and the degree of supercooling, that may indicate lower degassing during the crystallization of supercooled water. In addition to supporting the role of ice-crystal nucleation by biogenic magnetite in many tissues, magnetite nanocrystals could provide inexpensive, non-toxic, and non-pathogenic ice nucleating agents needed in a variety of industrial processes, as well as influencing the dynamics of ice crystal nucleation in many natural environments. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

3-Phenyl­pyridinium tetra­chlorido­aurate(III)

PubMed Central

Amani, Vahid; Safari, Nasser; Khavasi, Hamid Reza

2010-01-01

In the title mol­ecular salt, (C11H10N)[AuCl4], the AuIII atom adopts an almost regular square-planar coordination geometry and the dihedral angle between the aromatic rings of the 3-phenyl­pyridinium cation is 23.1 (3)°. In the crystal, the ions inter­act by way of N—H⋯Cl and C—H⋯Cl hydrogen bonds. PMID:21580276

1-(4-Methyl-1-naphth­yl)ethanone

PubMed Central

Hu, Yong-Hong; Zhao, Xiao-Lei; Yang, Wen-Ge; Yao, Jin-Feng; Lu, Xiu-Tao

2008-01-01

In the mol­ecule of the title compound, C13H12O, the two aromatic rings are oriented at a dihedral angle of 2.90 (3)°. An intra­molecular C—H⋯O hydrogen bond results in the formation of a non-planar six-membered ring, which adopts an envelope conformation. In the crystal structure, inter­molecular C—H⋯O hydrogen bonds link the mol­ecules. PMID:21581284

(2E)-3-[4-(Benz-yloxy)phen-yl]-1-(2,6-dichloro-3-fluoro-phen-yl)prop-2-en-1-one.

PubMed

Praveen, Aletti S; Yathirajan, Hemmige S; Gerber, Thomas; van Brecht, Benjamin; Betz, Richard

2012-12-01

In the title compound, C22H15Cl2FO2, a chalcone derivative featuring a threefold-halogenated aromatic substituent, the conformation about the C=C bond is E. In the crystal C-H⋯F and C-H⋯Cl contacts connect the mol-ecules into undulating sheets parallel to (101). In addition, C-H⋯π inter-actions are also present.

Unraveling Complexity in the Solid Form Screening of a Pharmaceutical Salt: Why so Many Forms? Why so Few?

PubMed Central

2017-01-01

The solid form landscape of 5-HT2a antagonist 3-(4-(benzo[d]isoxazole-3-yl)piperazin-1-yl)-2,2-dimethylpropanoic acid hydrochloride (B5HCl) proved difficult to establish. Many crystalline materials were produced by solid form screening, but few forms readily grew high quality crystals to afford a clear picture or understanding of the solid form landscape. Careful control of crystallization conditions, a range of experimental methods, computational modeling of solvate structures, and crystal structure prediction were required to see potential arrangements of the salt in its crystal forms. Structural diversity in the solid form landscape of B5HCl was apparent in the layer structures for the anhydrate polymorphs (Forms I and II), dihydrate and a family of solvates with alcohols. The alcohol solvates, which provided a distinct packing from the neat forms and the dihydrate, form layers with conserved hydrogen bonding between B5HCl and the solvent, as well as stacking of the aromatic rings. The ability of the alcohol hydrocarbon moieties to efficiently pack between the layers accounted for the difficulty in growing some solvate crystals and the inability of other solvates to crystallize altogether. Through a combination of experiment and computation, the crystallization problems, form stability, and desolvation pathways of B5HCl have been rationalized at a molecular level. PMID:29018305

[Microcosmic mechanisms of amorphous indomethacin crystallization and the influence of nano-coating on crystallization].

PubMed

Hui, Ou-Yang; Yi, Tao; Zheng, Qin; Liu, Feng

2011-06-01

Amorphous drugs have higher solubility, better oral bioavailability and are easier to be absorbed than their crystalline counterparts. However, the amorphous drugs, with weak stability, are so easy to crystallize that they will lose the original advantages. Polarization microscope, scanning electron microscope, differential scanning calorimetry, X-ray diffractomer and Raman spectroscopy were used to study the microcosmic crystallization mechanisms of amorphous indometacin and the performance of the drug crystals. The results showed that the growth rate of amorphous indometacin crystals at the free surface was markedly faster than that through the bulk, and that the crystal growth rate decreased observably after spraying an ultrathin melting gold (10 nm) at the free surface of the drug. These results indicated that the high growth rates of amorphous drugs crystals at the free surface were the key to their stability and that an ultrathin coating could be applied to enhance the stability of amorphous drugs.

Microstructure and pinning properties of hexagonal-disc shaped single crystalline MgB2

NASA Astrophysics Data System (ADS)

Jung, C. U.; Kim, J. Y.; Chowdhury, P.; Kim, Kijoon H.; Lee, Sung-Ik; Koh, D. S.; Tamura, N.; Caldwell, W. A.; Patel, J. R.

2002-11-01

We synthesized hexagonal-disc-shaped MgB2 single crystals under high-pressure conditions and analyzed the microstructure and pinning properties. The lattice constants and the Laue pattern of the crystals from x-ray micro-diffraction showed the crystal symmetry of MgB2. A thorough crystallographic mapping within a single crystal showed that the edge and c axis of hexagonal-disc shape exactly matched the [101¯0] and the [0001] directions of the MgB2 phase. Thus, these well-shaped single crystals may be the best candidates for studying the direction dependences of the physical properties. The magnetization curve and the magnetic hysteresis curve for these single crystals showed the existence of a wide reversible region and weak pinning properties, which supported our single crystals being very clean.

Direction-dependent secondary bonds and their stepwise melting in a uracil-based molecular crystal studied by infrared spectroscopy and theoretical modeling

NASA Astrophysics Data System (ADS)

Szekrényes, Zsolt; Nagy, Péter R.; Tarczay, György; Maggini, Laura; Bonifazi, Davide; Kamarás, Katalin

2018-01-01

Three types of supramolecular interactions are identified in the three crystallographic directions in crystals of 1,4-bis[(1-hexylurac-6-yl) ethynyl]benzene, a uracil-based molecule with a linear backbone. These three interactions, characterized by their strongest component, are: intermolecular double H-bonds along the molecular axis, London dispersion interaction of hexyl chains connecting these linear assemblies, and π - π stacking of the aromatic rings perpendicular to the molecular planes. On heating, two transitions happen, disordering of hexyl chains at 473 K, followed by H-bond melting at 534 K. The nature of the bonds and transitions was established by matrix-isolation and temperature-dependent infrared spectroscopy and supported by theoretical computations.

A Deuterium NMR Study of Bent-Core Liquid Crystals. 1; Synthesis and Characterization of Deuterium-Labeled Oxadiazole-Containing Liquid Crystals

NASA Technical Reports Server (NTRS)

Dingemans, Theo J.; Madsen, Louis A.; Samulski, Edward T.; Bushnell, Dennis M. (Technical Monitor)

2002-01-01

We have synthesized two deuterated boomerang-shaped liquid crystals based on 2,5-bis(4-hydroxyphenyl)-1,3,4-oxadiazole (ODBP). Deuterium was introduced in the rigid 2,5-diphenyl-1,3,4-oxadiazole core and in the aromatic ring of the terminal 4-dodecyloxyphenyl moiety using standard acid catalyzed deuterium exchange conditions. Both compounds, ([4,4'(1,3,4-oxadiazole-2,5-diyl-d4)] di-4-dodecyloxybenzoate: ODBP-d4-Ph-O-C12) and ([4,4'(1,3,4-oxadiazole-2,5-diyl)] di-4-dodecyloxy-benzoate-d4; ODBP-Ph-d4-O-C12) were investigated by nuclear magnetic resonance, optical microscopy and differential scanning calorimetry. The optical textures and thermal behavior of both compounds were found to be identical to the non-deuterated analog [4,4(1,3,4-oxadiazole-2,5-diyl)] di-4-dodecyloxybenzoate (ODBP-Ph-O-C12) which we reported earlier. These compounds exhibit behavior indicative of a biaxial nematic liquid crystal phase, which we hope to confirm using deuterium NMR spectroscopy in the next phase of this study.

Calcite crystal growth inhibition by humic substances with emphasis on hydrophobic acids from the Florida Everglades

USGS Publications Warehouse

Hoch, A.R.; Reddy, M.M.; Aiken, G.R.

2000-01-01

The crystallization of calcium carbonate minerals plays an integral role in the water chemistry of terrestrial ecosystems. Humic substances, which are ubiquitous in natural waters, have been shown to reduce or inhibit calcite crystal growth in experiments. The purpose of this study is to quantify and understand the kinetic effects of hydrophobic organic acids isolated from the Florida Everglades and a fulvic acid from Lake Fryxell, Antarctica, on the crystal growth of calcite (CaCO3). Highly reproducible calcite growth experiments were performed in a sealed reactor at constant pH, temperature, supersaturation (?? = 4.5), P(CO2) (10-3.5atm), and ionic strength (0.1 M) with various concentrations of organic acids. Higher plant-derived aquatic hydrophobic acids from the Everglades were more effective growth inhibitors than microbially derived fulvic acid from Lake Fryxell. Organic acid aromaticity correlated strongly with growth inhibition. Molecular weight and heteroatom content correlated well with growth inhibition, whereas carboxyl content and aliphatic nature did not. Copyright (C) 1999 Elsevier Science Ltd.

Centrohexaindane: six benzene rings mutually fixed in three dimensions - solid-state structure and six-fold nitration.

PubMed

Kuck, Dietmar; Linke, Jens; Teichmann, Lisa Christin; Barth, Dieter; Tellenbröker, Jörg; Gestmann, Detlef; Neumann, Beate; Stammler, Hans-Georg; Bögge, Hartmut

2016-04-28

The solid-state molecular structure of centrohexaindane (), a unique hydrocarbon comprising six benzene rings clamped to each other in three dimensions around a neopentane core, and the molecular packing in crystals of ·CHCl3 are reported. The molecular Td-symmetry and the Cartesian orientation of the six indane wings of in the solid state have been confirmed. The course and limitation of electrophilic aromatic substitution of are demonstrated for the case of nitration. Based on nitration experiments of a lower congener of , tribenzotriquinacene , the six-fold nitrofunctionalisation of has been achieved in excellent yield, giving four constitutional isomers, two nonsymmetrical ( and ) and two C3-symmetrical ones ( and ), all of which contain one single nitro group in each of the six benzene rings. The relative yields of the four isomers (∼3 : 1 : 1 : 3) point to a random electrophilic attack of the electrophiles at the twelve formally equivalent outer positions of the aromatic periphery of , suggesting electronic independence of its six aromatic π-electron systems. In turn, the pronounced conformational rigidity of the centrohexacyclic framework of enables the unequivocal structural identification of the isomeric hexanitrocentrohexaindanes by (1)H NMR spectroscopy.

Crystal structure of 2-amino-pyridinium 6-chloro-nicotinate.

PubMed

Jasmine, N Jeeva; Rajam, A; Muthiah, P Thomas; Stanley, N; Razak, I Abdul; Rosli, M Mustaqim

2015-09-01

In the title salt, C5H7N(+)·C6H3ClNO(-), the 2-amino-pyri-din-ium cation inter-acts with the carboxyl-ate group of the 6-chloro-nicotinate anion through a pair of independent N-H⋯O hydrogen bonds, forming an R 2 (2)(8) ring motif. In the crystal, these dimeric units are connected further via N-H⋯O hydrogen bonds, forming chains along [001]. In addition, weak C-H⋯N and C-H⋯O hydrogen bonds, together with weak π-π inter-actions, with centroid-centroid distances of 3.6560 (5) and 3.6295 (5) Å, connect the chains, forming a two-dimensional network parallel to (100).

Broadband Microwave Spectroscopy as a Tool to Study Intermolecular Interactions in the Diphenyl Ether - Water System

NASA Astrophysics Data System (ADS)

Fatima, Mariyam; Perez, Cristobal; Schnell, Melanie

2017-06-01

Many biological processes, such as chemical recognition and protein folding, are mainly controlled by the interplay of hydrogen bonds and dispersive forces. This interplay also occurs between organic molecules and solvent water molecules. Broadband rotational spectroscopy studies of weakly bound complexes are able to accurately reveal the structures and internal dynamics of molecular clusters isolated in the gas phase. Amongst them, water clusters with organic molecules are of particular interest. In this work, we investigate the interplay between different types of weak intermolecular interactions and how it controls the preferred interaction sites of aromatic ethers, where dispersive interactions may play a significant role. We present our results on diphenyl ether (C_{12}H_{10}O, 1,1'-Oxydibenzene) complexed with up to three molecules of water. Diphenyl ether is a flexible molecule, and it offers two competing binding sites for water: the ether oxygen and the aromatic π system. In order to determine the structure of the diphenyl ether-water complexes, we targeted transitions in the 2-8 GHz range using broadband rotational spectroscopy. We identify two isomers with one water, one with two water, and one with three water molecules. Further analysis from isotopic substitution measurements provided accurate structural information. The preferred interactions, as well as the observed structural changes induced upon complexation, will be presented and discussed.

Mutagenicity assessment of aerosols in emissions from domestic combustion processes.

PubMed

Canha, Nuno; Lopes, Isabel; Vicente, Estela Domingos; Vicente, Ana M; Bandowe, Benjamin A Musa; Almeida, Susana Marta; Alves, Célia A

2016-06-01

Domestic biofuel combustion is one of the major sources of regional and local air pollution, mainly regarding particulate matter and organic compounds, during winter periods. Mutagenic and carcinogenic activity potentials of the ambient particulate matter have been associated with the fraction of polycyclic aromatic hydrocarbons (PAH) and their oxygenated (OPAH) and nitrogenated (NPAH) derivatives. This study aimed at assessing the mutagenicity potential of the fraction of this polycyclic aromatic compound in particles (PM10) from domestic combustion by using the Ames assays with Salmonella typhimurium TA98 and TA100. Seven biofuels, including four types of pellets and three agro-fuels (olive pit, almond shell and shell of pine nuts), were tested in an automatic pellet stove, and two types of wood (Pinus pinaster, maritime pine, and Eucalyptus globulus, eucalypt) were burned in a traditional wood stove. For this latter appliance, two combustion phases-devolatilisation and flaming/smouldering-were characterised separately. A direct-acting mutagenic effect for the devolatilisation phase of pine combustion and for both phases of eucalypt combustion was found. Almond shell revealed a weak direct-acting mutagenic effect, while one type of pellets, made of recycled wastes, and pine (devolatilisation) presented a cytotoxic effect towards strain TA100. Compared to the manually fired appliance, the automatic pellet stove promoted lower polyaromatic mutagenic emissions. For this device, only two of the studied biofuels presented a weak mutagenic or cytotoxic potential.

Coexistence of Weak Ferromagnetism and Ferroelectricity in the High Pressure LiNbO3-Type Phase of FeTiO3

NASA Astrophysics Data System (ADS)

Varga, T.; Kumar, A.; Vlahos, E.; Denev, S.; Park, M.; Hong, S.; Sanehira, T.; Wang, Y.; Fennie, C. J.; Streiffer, S. K.; Ke, X.; Schiffer, P.; Gopalan, V.; Mitchell, J. F.

2009-07-01

We report the magnetic and electrical characteristics of polycrystalline FeTiO3 synthesized at high pressure that is isostructural with acentric LiNbO3 (LBO). Piezoresponse force microscopy, optical second harmonic generation, and magnetometry demonstrate ferroelectricity at and below room temperature and weak ferromagnetism below ˜120K. These results validate symmetry-based criteria and first-principles calculations of the coexistence of ferroelectricity and weak ferromagnetism in a series of transition metal titanates crystallizing in the LBO structure.

Coexistence of weak ferromagnetism and ferroelectricity in the high pressure LiNbO3-type phase of FeTiO3.

PubMed

Varga, T; Kumar, A; Vlahos, E; Denev, S; Park, M; Hong, S; Sanehira, T; Wang, Y; Fennie, C J; Streiffer, S K; Ke, X; Schiffer, P; Gopalan, V; Mitchell, J F

2009-07-24

We report the magnetic and electrical characteristics of polycrystalline FeTiO_{3} synthesized at high pressure that is isostructural with acentric LiNbO_{3} (LBO). Piezoresponse force microscopy, optical second harmonic generation, and magnetometry demonstrate ferroelectricity at and below room temperature and weak ferromagnetism below approximately 120 K. These results validate symmetry-based criteria and first-principles calculations of the coexistence of ferroelectricity and weak ferromagnetism in a series of transition metal titanates crystallizing in the LBO structure.

Spatial variations of the 3 micron emission features within UV-excited nebulae - Photochemical evolution of interstellar polycyclic aromatic hydrocarbons

NASA Technical Reports Server (NTRS)

Geballe, T. R.; Tielens, A. G. G. M.; Allamandola, L. J.; Moorhouse, A.; Brand, P. W. J. L.

1989-01-01

Spectra at 3 microns have been obtained at several positions in the Orion Bar region and in the nebula surrounding HD 44179. Weak emission features at 3.40, 3.46, 3.51, and 3.57 microns are prominent in the Orion Bar region. The 3.40- and 3.51-micron features increase in intensity relative to the dominant 3.29-micron feature. The spectrum obtained in the Red Rectangle region 5 arcsecs north of HD 44179 are similar to those in the Orion Bar, with a weak, broad 3.40-micron feature at the position of HD 44179. The spatial behavior of the weak emission features is explained in terms of hot bands of the CH stretch and overtones, and combination bands of other fundamental vibrations in simple PAHs. Based on the susceptibility of PAHs to destruction by the far UV fields in both regions, PAH sizes are estimated at 20-50 carbon atoms.

Thermal conductivity of tungsten: Effects of plasma-related structural defects from molecular-dynamics simulations

NASA Astrophysics Data System (ADS)

Hu, Lin; Wirth, Brian D.; Maroudas, Dimitrios

2017-08-01

We report results on the lattice thermal conductivities of tungsten single crystals containing nanoscale-sized pores or voids and helium (He) nanobubbles as a function of void/bubble size and gas pressure in the He bubbles based on molecular-dynamics simulations. For reference, we calculated lattice thermal conductivities of perfect tungsten single crystals along different crystallographic directions at room temperature and found them to be about 10% of the overall thermal conductivity of tungsten with a weak dependence on the heat flux direction. The presence of nanoscale voids in the crystal causes a significant reduction in its lattice thermal conductivity, which decreases with increasing void size. Filling the voids with He to form He nanobubbles and increasing the bubble pressure leads to further significant reduction of the tungsten lattice thermal conductivity, down to ˜20% of that of the perfect crystal. The anisotropy in heat conduction remains weak for tungsten single crystals containing nanoscale-sized voids and He nanobubbles throughout the pressure range examined. Analysis of the pressure and atomic displacement fields in the crystalline region that surrounds the He nanobubbles reveals that the significant reduction of tungsten lattice thermal conductivity in this region is due to phonon scattering from the nanobubbles, as well as lattice deformation around the nanobubbles and formation of lattice imperfections at higher bubble pressure.

Phase behavior and crystal structure of 3-(1-naphthyloxy)- and 3-(4-indolyloxy)-propane-1,2-diol, synthetic precursors of chiral drugs propranolol and pindolol

NASA Astrophysics Data System (ADS)

Bredikhin, Alexander A.; Gubaidullin, Aidar T.; Bredikhina, Zemfira A.; Fayzullin, Robert R.; Samigullina, Aida I.; Zakharychev, Dmitry V.

2013-08-01

Valuable precursors of popular chiral drugs propranolol and pindolol, 3-(1-naphthyloxy)-propane-1,2-diol 3 and 3-(4-indolyloxy)-propane-1,2-diol 4 were investigated by IR spectroscopy, DSC, and X-ray diffraction methods. Both compounds, crystallizing from enantiopure feed material, form "guaifenesin-like" crystal packing in which the classic H-bonded bilayers, framed in both sides by hydrophobic fragments of the molecules, acts as the basic crystal-forming motif. Diol 4 prone to spontaneous resolution and conserves its packing pattern crystallizing from racemate. Under the same conditions, diol 3 forms weakly stable solid racemic compound. Some reasons for such a behavior are identified and discussed.

Adherence of urease-induced crystals to rat bladder epithelium.

PubMed

Grenabo, L; Hedelin, H; Pettersson, S

1988-01-01

Apart from urine supersaturation with respect to struvite and calcium phosphate caused by urease-producing microorganisms, retention of formed crystals in the urinary tract is necessary for the formation of infection stones. This study was performed to investigate the role of the mucous coat lining the urothelium in the adhesion of urease-induced crystals. Removal of this glycosaminoglycan-containing layer from rat bladders increased the adherence of struvite and calcium phosphate crystals 5-6 times compared to that in intact rat bladders. Heparin completely restored the antiadherence capacity while chondroitin sulphate had a very weak restorative effect and human urine had no restorative effect. These findings support the view that the mucous coat is of importance in preventing retention of urease-induced crystals.

Crystal Structure and Substrate Specificity Modification of Acetyl Xylan Esterase from Aspergillus luchuensis.

PubMed

Komiya, Dai; Hori, Akane; Ishida, Takuya; Igarashi, Kiyohiko; Samejima, Masahiro; Koseki, Takuya; Fushinobu, Shinya

2017-10-15

Acetyl xylan esterase (AXE) catalyzes the hydrolysis of the acetyl bonds present in plant cell wall polysaccharides. Here, we determined the crystal structure of AXE from Aspergillus luchuensis ( Al AXEA), providing the three-dimensional structure of an enzyme in the Esterase_phb family. Al AXEA shares its core α/β-hydrolase fold structure with esterases in other families, but it has an extended central β-sheet at both its ends and an extra loop. Structural comparison with a ferulic acid esterase (FAE) from Aspergillus niger indicated that Al AXEA has a conserved catalytic machinery: a catalytic triad (Ser119, His259, and Asp202) and an oxyanion hole (Cys40 and Ser120). Near the catalytic triad of A lAXEA, two aromatic residues (Tyr39 and Trp160) form small pockets at both sides. Homology models of fungal FAEs in the same Esterase_phb family have wide pockets at the corresponding sites because they have residues with smaller side chains (Pro, Ser, and Gly). Mutants with site-directed mutations at Tyr39 showed a substrate specificity similar to that of the wild-type enzyme, whereas those with mutations at Trp160 acquired an expanded substrate specificity. Interestingly, the Trp160 mutants acquired weak but significant type B-like FAE activity. Moreover, the engineered enzymes exhibited ferulic acid-releasing activity from wheat arabinoxylan. IMPORTANCE Hemicelluloses in the plant cell wall are often decorated by acetyl and ferulic acid groups. Therefore, complete and efficient degradation of plant polysaccharides requires the enzymes for cleaving the side chains of the polymer. Since the Esterase_phb family contains a wide array of fungal FAEs and AXEs from fungi and bacteria, our study will provide a structural basis for the molecular mechanism of these industrially relevant enzymes in biopolymer degradation. The structure of the Esterase_phb family also provides information for bacterial polyhydroxyalkanoate depolymerases that are involved in biodegradation of thermoplastic polymers. Copyright © 2017 American Society for Microbiology.

Engineered Multifunctional Nanophotonic Materials for Ultrafast Optical Switching

DTIC Science & Technology

2012-11-02

and Co3 + placed at tetrahedral and octahedral sites, respectively. Single -layer thin films of Co3O4 nanoparticles have large optical nonlinearity and...the first two methodologies in systems having weakly resonant structures, including 3-D and/or 1-D photonic crystal structures (i.e. nonlinear Bragg...Nonlinear optical transmission of lead phthalocyanine-doped nematic liquid crystal composites for multiscale nonlinear switching from nanosecond to

Growth of PBI 2 single crystals from stoichiometric and Pb excess melts

NASA Astrophysics Data System (ADS)

Hayashi, T.; Kinpara, M.; Wang, J. F.; Mimura, K.; Isshiki, M.

2008-01-01

We have successfully grown high-purity and -quality PbI 2 single crystals by the vertical Bridgman method. The rocking curves of four-crystal X-ray diffraction (XRD) show 120 arcsec in full-width at half-maximum (FWHM). The photoluminescence (PL) spectra at 7.8 K show the resolved intensive exciton emission line and the weak DAP emission band. The deep-level emissions are not observed. The measurement of the electrical and radiographic properties show that Leadiodide (PbI 2) single crystal has a resistivity of 5×10 10 Ω cm and imager lag is 8 s, respectively. In order to improve the controllability of crystal growth, PbI 2 single crystals were also grown from a lead (Pb) excess PbI 2 source. The experimental results show very good reproducibility. In addition, the growth models of crystal are proposed, and the growth mechanism is discussed.

Weak coupling of pseudoacoustic phonons and magnon dynamics in the incommensurate spin-ladder compound S r 14 C u 24 O 41

DOE PAGES

Chen, Xi; Bansal, Dipanshu; Sullivan, Sean; ...

2016-10-21

Intriguing lattice dynamics have been predicted for aperiodic crystals that contain incommensurate substructures. Here we report inelastic neutron scattering measurements of phonon and magnon dispersions in Sr 14Cu 24O 41, which contains incommensurate one-dimensional (1D) chain and two-dimensional (2D) ladder substructures. Two distinct pseudoacoustic phonon modes, corresponding to the sliding motion of one sublattice against the other, are observed for atomic motions polarized along the incommensurate axis. In the long wavelength limit, it is found that the sliding mode shows a remarkably small energy gap of 1.7–1.9 meV, indicating very weak interactions between the two incommensurate sublattices. The measurements alsomore » reveal a gapped and steep linear magnon dispersion of the ladder sublattice. The high group velocity of this magnon branch and weak coupling with acoustic and pseudoacoustic phonons can explain the large magnon thermal conductivity in Sr 14Cu 24O 41 crystals. In addition, the magnon specific heat is determined from the measured total specific heat and phonon density of states and exhibits a Schottky anomaly due to gapped magnon modes of the spin chains. Furthermore, these findings offer new insights into the phonon and magnon dynamics and thermal transport properties of incommensurate magnetic crystals that contain low-dimensional substructures.« less

X-ray Crystallographic Structure of Thermophilic Rhodopsin

PubMed Central

Tsukamoto, Takashi; Mizutani, Kenji; Hasegawa, Taisuke; Takahashi, Megumi; Honda, Naoya; Hashimoto, Naoki; Shimono, Kazumi; Yamashita, Keitaro; Yamamoto, Masaki; Miyauchi, Seiji; Takagi, Shin; Hayashi, Shigehiko; Murata, Takeshi; Sudo, Yuki

2016-01-01

Thermophilic rhodopsin (TR) is a photoreceptor protein with an extremely high thermal stability and the first characterized light-driven electrogenic proton pump derived from the extreme thermophile Thermus thermophilus JL-18. In this study, we confirmed its high thermal stability compared with other microbial rhodopsins and also report the potential availability of TR for optogenetics as a light-induced neural silencer. The x-ray crystal structure of TR revealed that its overall structure is quite similar to that of xanthorhodopsin, including the presence of a putative binding site for a carotenoid antenna; but several distinct structural characteristics of TR, including a decreased surface charge and a larger number of hydrophobic residues and aromatic-aromatic interactions, were also clarified. Based on the crystal structure, the structural changes of TR upon thermal stimulation were investigated by molecular dynamics simulations. The simulations revealed the presence of a thermally induced structural substate in which an increase of hydrophobic interactions in the extracellular domain, the movement of extracellular domains, the formation of a hydrogen bond, and the tilting of transmembrane helices were observed. From the computational and mutational analysis, we propose that an extracellular LPGG motif between helices F and G plays an important role in the thermal stability, acting as a “thermal sensor.” These findings will be valuable for understanding retinal proteins with regard to high protein stability and high optogenetic performance. PMID:27129243

A second triclinic polymorph of azimsulfuron

PubMed Central

Kwon, Eunjin; Kim, Jineun; Park, Hyunjin; Kim, Tae Ho

2016-01-01

The title compound, C13H16N10O5S (systematic name: 1-(4,6-di­meth­oxypyrimidin-2-yl)-3-{[1-methyl-4-(2-methyl-2H-tetra­zol-5-yl)pyrazol-5-yl]sulfonyl}urea), is a second triclinic polymorph of this crystal [for the other, see: Jeon et al., (2015 ▸). Acta Cryst. E71, o470–o471]. There are two mol­ecules, A and B, in the asymmetric unit; the dihedral angles between the pyrazole ring and the tetra­zole and di­meth­oxy­pyrimidine ring planes are 72.84 (10) and 37.24 (14)°, respectively (mol­ecule A) and 84.38 (9) and 26.09 (15)°, respectively (mol­ecule B). Each mol­ecule features an intra­molecular N—H⋯N hydrogen bond. In the crystal, aromatic π–π stacking inter­actions [centroid–centroid separations = 3.9871 (16), 3.4487 (14) and 3.5455 (16) Å] link the mol­ecules into [001] chains. In addition, N—H⋯N, N—H⋯O, C—H⋯O and C—H⋯N hydrogen bonds occur, forming a three-dimensional architecture. We propose that the dimorphism results from differences in conformations and packing owing to different inter­molecular inter­actions, especially aromatic π–π stacking. PMID:27746943

DOE Office of Scientific and Technical Information (OSTI.GOV)

Helmich, Kate E.; Pereira, Jose Henrique; Gall, Daniel L.

Here, lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bonds. Although lignin is a potential source of valuable aromatic chemicals, its recalcitrance to chemical or biological digestion presents major obstacles to both the production of second-generation biofuels and the generation of valuable coproducts from lignin's monoaromatic units. Degradation of lignin has been relatively well characterized in fungi, but it is less well understood in bacteria. A catabolic pathway for the enzymatic breakdown of aromatic oligomers linked via β-aryl ether bonds typically found in lignin has been reported in the bacterium Sphingobium sp. SYK-6. Here, wemore » present x-ray crystal structures and biochemical characterization of the glutathione-dependent β-etherases, LigE and LigF, from this pathway. The crystal structures show that both enzymes belong to the canonical two-domain fold and glutathione binding site architecture of the glutathione S-transferase family. Mutagenesis of the conserved active site serine in both LigE and LigF shows that, whereas the enzymatic activity is reduced, this amino acid side chain is not absolutely essential for catalysis. The results include descriptions of cofactor binding sites, substrate binding sites, and catalytic mechanisms. Because β-aryl ether bonds account for 50–70% of all interunit linkages in lignin, understanding the mechanism of enzymatic β-aryl ether cleavage has significant potential for informing ongoing studies on the valorization of lignin.« less

Roles of bond orientational ordering in glass transition and crystallization.

PubMed

Tanaka, Hajime

2011-07-20

It is widely believed that crystallization in three dimensions is primarily controlled by positional ordering, and not by bond orientational ordering. In other words, bond orientational ordering is usually considered to be merely a consequence of positional ordering and thus has often been ignored. This one-order-parameter (density) description may be reasonable when we consider an equilibrium liquid-solid transition, but may not be enough to describe a metastable state and the kinetics of the transition. Here we propose that bond orientational ordering can play a key role in (i) crystallization, (ii) the ordering to quasi-crystal and (iii) vitrification, which occurs under rather weak frustration against crystallization. In a metastable supercooled state before crystallization, a system generally tends to have bond orientational order at least locally as a result of a constraint of dense packing. For a system interacting with hard-core repulsions, the constraint is intrinsically of geometrical origin and thus the basic physics is the same as nematic ordering of rod-like particles upon densification. Furthermore, positional ordering is easily destroyed even by weak frustration such as polydispersity and anisotropic interactions which favour a symmetry not consistent with that of the equilibrium crystal. Thus we may say that vitrification can be achieved by disturbing and prohibiting long-range positional ordering. Even in such a situation, bond orientational ordering still survives, accompanying its critical-like fluctuations, which are the origin of dynamic heterogeneity for this case. This scenario naturally explains both the absence of positional order and the development of bond orientational order upon cooling in a supercooled state. Although our argument is speculative in nature, we emphasize that this physical picture can coherently explain crystallization, vitrification, quasi-crystallization and their relationship in a natural manner. For a strongly frustrated system, even bond orientational order can be destroyed. Even in such a case there may still appear a structural signature of dense packing, which is linked to slow dynamics.

Data Mining for New Two- and One-Dimensional Weakly Bonded Solids and Lattice-Commensurate Heterostructures.

PubMed

Cheon, Gowoon; Duerloo, Karel-Alexander N; Sendek, Austin D; Porter, Chase; Chen, Yuan; Reed, Evan J

2017-03-08

Layered materials held together by weak interactions including van der Waals forces, such as graphite, have attracted interest for both technological applications and fundamental physics in their layered form and as an isolated single-layer. Only a few dozen single-layer van der Waals solids have been subject to considerable research focus, although there are likely to be many more that could have superior properties. To identify a broad spectrum of layered materials, we present a novel data mining algorithm that determines the dimensionality of weakly bonded subcomponents based on the atomic positions of bulk, three-dimensional crystal structures. By applying this algorithm to the Materials Project database of over 50,000 inorganic crystals, we identify 1173 two-dimensional layered materials and 487 materials that consist of weakly bonded one-dimensional molecular chains. This is an order of magnitude increase in the number of identified materials with most materials not known as two- or one-dimensional materials. Moreover, we discover 98 weakly bonded heterostructures of two-dimensional and one-dimensional subcomponents that are found within bulk materials, opening new possibilities for much-studied assembly of van der Waals heterostructures. Chemical families of materials, band gaps, and point groups for the materials identified in this work are presented. Point group and piezoelectricity in layered materials are also evaluated in single-layer forms. Three hundred and twenty-five of these materials are expected to have piezoelectric monolayers with a variety of forms of the piezoelectric tensor. This work significantly extends the scope of potential low-dimensional weakly bonded solids to be investigated.

(±)-Pestalachloride D, an antibacterial racemate of chlorinated benzophenone derivative from a soft coral-derived fungus Pestalotiopsis sp.

PubMed

Wei, Mei-Yan; Li, Dan; Shao, Chang-Lun; Deng, Dong-Sheng; Wang, Chang-Yun

2013-03-28

A new antibacterial chlorinated benzophenone derivative, (±)-pestalachloride D (1), along with a related analog, (±)-pestalachloride C (2), was recently isolated from the marine-derived fungus Pestalotiopsis sp. isolated from a soft coral Sarcophyton sp. collected from Yongxing Island in the South China Sea. Both chiral HPLC analysis and single-crystal X-ray data indicated that 1 is a racemic mixture. Interestingly, 1 did not exhibit any effect in the zebrafish embryo teratogenicity assay, while 2 led to abnormal growth. The potential impact on zebrafish embryo growth is discussed based on their crystal structures. The main difference of crystal structures between 1 and 2 is that the six-member non-aromatic ring (O4, C10, C9, C8, C2', and C3') in 1 exhibits a distorted chair conformation, while 2 shows a distorted boat conformation. Moreover, compounds 1 and 2 both exhibited moderate antibacterial activity.

Molecular complexes of alprazolam with carboxylic acids, boric acid, boronic acids, and phenols. Evaluation of supramolecular heterosynthons mediated by a triazole ring.

PubMed

Varughese, Sunil; Azim, Yasser; Desiraju, Gautam R

2010-09-01

A series of molecular complexes, both co-crystals and salts, of a triazole drug-alprazolam-with carboxylic acids, boric acid, boronic acids, and phenols have been analyzed with respect to heterosynthons present in the crystal structures. In all cases, the triazole ring behaves as an efficient hydrogen bond acceptor with the acidic coformers. The hydrogen bond patterns exhibited with aromatic carboxylic acids were found to depend on the nature and position of the substituents. Being a strong acid, 2,6-dihydroxybenzoic acid forms a salt with alprazolam. With aliphatic dicarboxylic acids alprazolam forms hydrates and the water molecules play a central role in synthon formation and crystal packing. The triazole ring makes two distinct heterosynthons in the molecular complex with boric acid. Boronic acids and phenols form consistent hydrogen bond patterns, and these are seemingly independent of the substitutional effects. Boronic acids form noncentrosymmetric cyclic synthons, while phenols form O--H...N hydrogen bonds with the triazole ring.

Crystal Structure and Antitumor Activity of the Novel Zwitterionic Complex of tri-n-Butyltin(IV) with 2-Thiobarbituric Acid

PubMed Central

Balas, Vasilios I.; Hadjikakou, Sotiris K.; Hadjiliadis, Nick; Kourkoumelis, Nikolaos; Light, Mark E.; Hursthouse, Mike; Metsios, Apostolos K.; Karkabounas, Spyros

2008-01-01

A novel tri-n-butyl(IV) derivative of 2-thiobarbituric acid (HTBA) of formula [(n-Bu)3Sn(TBA) H2O] (1) has been synthesized and characterized by elemental analysis and 119Sn-NMR and FT-IR spectroscopic techniques. The crystal structure of complex 1 has been determined by single crystal X-ray diffraction analysis at 120(2) K. The geometry around Sn(IV) is trigonal bipyramidal. Three n-butyl groups and one oxygen atom from a deprotonated 2-thiobarbituric ligand are bonded to the metal center. The geometry is completed with one oxygen from a water molecule. Compound 1 exhibits potent, in vitro, cytotoxicity against sarcoma cancer cells (mesenchymal tissue) from the Wistar rat, polycyclic aromatic hydrocarbons (PAH, benzo[a]pyrene) carcinogenesis. In addition, the inhibition caused by 1, in the rate of lipoxygenase (LOX) catalyzed oxidation reaction of linoleic acid to hyperoxolinoleic acid, has been also kinetically and theoretically studied. The results are compared to that of cisplatin. PMID:18401456

The First Mammalian Aldehyde Oxidase Crystal Structure

PubMed Central

Coelho, Catarina; Mahro, Martin; Trincão, José; Carvalho, Alexandra T. P.; Ramos, Maria João; Terao, Mineko; Garattini, Enrico; Leimkühler, Silke; Romão, Maria João

2012-01-01

Aldehyde oxidases (AOXs) are homodimeric proteins belonging to the xanthine oxidase family of molybdenum-containing enzymes. Each 150-kDa monomer contains a FAD redox cofactor, two spectroscopically distinct [2Fe-2S] clusters, and a molybdenum cofactor located within the protein active site. AOXs are characterized by broad range substrate specificity, oxidizing different aldehydes and aromatic N-heterocycles. Despite increasing recognition of its role in the metabolism of drugs and xenobiotics, the physiological function of the protein is still largely unknown. We have crystallized and solved the crystal structure of mouse liver aldehyde oxidase 3 to 2.9 Å. This is the first mammalian AOX whose structure has been solved. The structure provides important insights into the protein active center and further evidence on the catalytic differences characterizing AOX and xanthine oxidoreductase. The mouse liver aldehyde oxidase 3 three-dimensional structure combined with kinetic, mutagenesis data, molecular docking, and molecular dynamics studies make a decisive contribution to understand the molecular basis of its rather broad substrate specificity. PMID:23019336

Crystal structure of octane-1,8-diaminium 4,4′-(diazene-1,2-di­yl)dibenzoate monohydrate

PubMed Central

Elkin, Igor; Christopherson, Jan-Constantin; Borchers, Tristan H.; Barrett, Christopher J.

2018-01-01

The title salt, C8H22N2 2+·C14H8N2O4 2−·H2O, represents a pseudo-polymer ionic material, resulting from the self-organizing behavior of 4,4′-azinodibenzoate dianions and doubly protonated, 1,8-diaminium-octane cations in aqueous solution. The asymmetric unit consists of two halves of octane 1,8-diaminium cations (the complete cations are both generated by crystallographic inversion symmetry), a 4,4′-azinodibenzoate anion [dihedral angle between the aromatic rings = 10.22 (4)°] and a water mol­ecule of crystallization. One of the cations is in a fully extended linear conformation while the second one has a terminal C—C—C—N gauche conformation. In the crystal, the cations, anions and water mol­ecules are linked into a three-dimensional network via a complex pattern of charge-assisted N—H⋯O and O—H⋯O hydrogen bonds. PMID:29850100

(±)-Pestalachloride D, an Antibacterial Racemate of Chlorinated Benzophenone Derivative from a Soft Coral-Derived Fungus Pestalotiopsis sp

PubMed Central

Wei, Mei-Yan; Li, Dan; Shao, Chang-Lun; Deng, Dong-Sheng; Wang, Chang-Yun

2013-01-01

A new antibacterial chlorinated benzophenone derivative, (±)-pestalachloride D (1), along with a related analog, (±)-pestalachloride C (2), was recently isolated from the marine-derived fungus Pestalotiopsis sp. isolated from a soft coral Sarcophyton sp. collected from Yongxing Island in the South China Sea. Both chiral HPLC analysis and single-crystal X-ray data indicated that 1 is a racemic mixture. Interestingly, 1 did not exhibit any effect in the zebrafish embryo teratogenicity assay, while 2 led to abnormal growth. The potential impact on zebrafish embryo growth is discussed based on their crystal structures. The main difference of crystal structures between 1 and 2 is that the six-member non-aromatic ring (O4, C10, C9, C8, C2′, and C3′) in 1 exhibits a distorted chair conformation, while 2 shows a distorted boat conformation. Moreover, compounds 1 and 2 both exhibited moderate antibacterial activity. PMID:23538869

Crystal Structures of the Novel Cytosolic 5′-Nucleotidase IIIB Explain Its Preference for m7GMP

PubMed Central

Monecke, Thomas; Buschmann, Juliane; Neumann, Piotr; Wahle, Elmar; Ficner, Ralf

2014-01-01

5′-nucleotidases catalyze the hydrolytic dephosphorylation of nucleoside monophosphates. As catabolic enzymes they contribute significantly to the regulation of cellular nucleotide levels; misregulation of nucleotide metabolism and nucleotidase deficiencies are associated with a number of diseases. The seven human 5′-nucleotidases differ with respect to substrate specificity and cellular localization. Recently, the novel cytosolic 5′-nucleotidase III-like protein, or cN-IIIB, has been characterized in human and Drosophila. cN-IIIB exhibits a strong substrate preference for the modified nucleotide 7-methylguanosine monophosphate but the structural reason for this preference was unknown. Here, we present crystal structures of cN-IIIB from Drosophila melanogaster bound to the reaction products 7-methylguanosine or cytidine. The structural data reveal that the cytosine- and 7-methylguanine moieties of the products are stacked between two aromatic residues in a coplanar but off-centered position. 7-methylguanosine is specifically bound through π-π interactions and distinguished from unmodified guanosine by additional cation-π coulomb interactions between the aromatic side chains and the positively charged 7-methylguanine. Notably, the base is further stabilized by T-shaped edge-to-face stacking of an additional tryptophan packing perpendicularly against the purine ring and forming, together with the other aromates, an aromatic slot. The structural data in combination with site-directed mutagenesis experiments reveal the molecular basis for the broad substrate specificity of cN-IIIB but also explain the substrate preference for 7-methylguanosine monophosphate. Analyzing the substrate specificities of cN-IIIB and the main pyrimidine 5′-nucleotidase cN-IIIA by mutagenesis studies, we show that cN-IIIA dephosphorylates the purine m7GMP as well, hence redefining its substrate spectrum. Docking calculations with cN-IIIA and m7GMP as well as biochemical data reveal that Asn69 does not generally exclude the turnover of purine substrates thus correcting previous suggestions. PMID:24603684

1-[6-(1H-Indol-1-yl)pyridin-2-yl]-1H-indole-3-carbaldehyde.

PubMed

Ramathilagam, C; Umarani, P R; Venkatesan, N; Rajakumar, P; Gunasekaran, B; Manivannan, V

2014-02-01

In the title compound, C22H15N3O, the dihedral angle between the two indole units is 33.72 (3)°. The mol-ecular structure features a weak intra-molecular C-H⋯N inter-action. In the crystal, weak C-H⋯O and C-H⋯π inter-actions, forming a two-dimensional network parallel to the bc plane.

Crystal structure of (1-eth­oxy­ethyl­idene)di­methyl­aza­nium tetra­phenyl­borate

PubMed Central

Tiritiris, Ioannis; Saur, Stefan; Kantlehner, Willi

2015-01-01

In the cation of the title salt, C6H14NO+·C24H20B−, the C—N bond lengths are 1.297 (2), 1.464 (2) and 1.468 (2) Å, indicating double- and single-bond character, respectively. The C—O bond length of 1.309 (2) Å shows double-bond character, pointing towards charge delocalization within the NCO plane of the iminium ion. In the crystal, C—H⋯π inter­actions between the iminium H atoms and the phenyl C atoms of the anion are present. The phenyl rings form aromatic pockets, in which the iminium ions are embedded. PMID:26870564

High transparent shape memory gel

NASA Astrophysics Data System (ADS)

Gong, Jin; Arai, Masanori; Kabir, M. H.; Makino, Masato; Furukawa, Hidemitsu

2014-03-01

Gels are a new material having three-dimensional network structures of macromolecules. They possess excellent properties as swellability, high permeability and biocompatibility, and have been applied in various fields of daily life, food, medicine, architecture, and chemistry. In this study, we tried to prepare new multi-functional and high-strength gels by using Meso-Decoration (Meso-Deco), one new method of structure design at intermediate mesoscale. High-performance rigid-rod aromatic polymorphic crystals, and the functional groups of thermoreversible Diels-Alder reaction were introduced into soft gels as crosslinkable pendent chains. The functionalization and strengthening of gels can be realized by meso-decorating the gels' structure using high-performance polymorphic crystals and thermoreversible pendent chains. New gels with good mechanical properties, novel optical properties and thermal properties are expected to be developed.

Meso-decorated self-healing gels: network structure and properties

NASA Astrophysics Data System (ADS)

Gong, Jin; Sawamura, Kensuke; Igarashi, Susumu; Furukawa, Hidemitsu

2013-04-01

Gels are a new material having three-dimensional network structures of macromolecules. They possess excellent properties as swellability, high permeability and biocompatibility, and have been applied in various fields of daily life, food, medicine, architecture, and chemistry. In this study, we tried to prepare new multi-functional and high-strength gels by using Meso-Decoration (Meso-Deco), one new method of structure design at intermediate mesoscale. High-performance rigid-rod aromatic polymorphic crystals, and the functional groups of thermoreversible Diels-Alder reaction were introduced into soft gels as crosslinkable pendent chains. The functionalization and strengthening of gels can be realized by meso-decorating the gels' structure using high-performance polymorphic crystals and thermoreversible pendent chains. New gels with good mechanical properties, novel optical properties and thermal properties are expected to be developed.

Crystal Field in Rare-Earth Complexes: From Electrostatics to Bonding.

PubMed

Alessandri, Riccardo; Zulfikri, Habiburrahman; Autschbach, Jochen; Bolvin, Hélène

2018-04-11

The flexibility of first-principles (ab initio) calculations with the SO-CASSCF (complete active space self-consistent field theory with a treatment of the spin-orbit (SO) coupling by state interaction) method is used to quantify the electrostatic and covalent contributions to crystal field parameters. Two types of systems are chosen for illustration: 1) The ionic and experimentally well-characterized PrCl 3 crystal; this study permits a revisitation of the partition of contributions proposed in the early days of crystal field theory; and 2) a series of sandwich molecules [Ln(η n -C n H n ) 2 ] q , with Ln=Dy, Ho, Er, and Tm and n=5, 6, and 8, in which the interaction between Ln III and the aromatic ligands is more difficult to describe within an electrostatic approach. It is shown that a model with three layers of charges reproduces the electrostatic field generated by the ligands and that the covalency plays a qualitative role. The one-electron character of crystal field theory is discussed and shown to be valuable, although it is not completely quantitative. This permits a reduction of the many-electron problem to a discussion of the energy of the seven 4f orbitals. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Elasticity and Strength of Biomacromolecular Crystals: Lysozyme

NASA Technical Reports Server (NTRS)

Holmes, A. M.; Witherow, W. K.; Chen, L. Q.; Chernov, A. A.

2003-01-01

The static Young modulus, E = 0.1 to 0.5 GPa, the crystal critical strength (sigma(sub c)) and its ratio to E,sigma(sub c)/E is approximately 10(exp 3), were measured for the first time for non cross-linked lysozyme crystals in solution. By using a triple point bending apparatus, we also demonstrated that the crystals were purely elastic. Softness of protein crystals built of hard macromolecules (26 GPa for lysozyme) is explained by the large size of the macromolecules as compared to the range of intermolecular forces and by the weakness of intermolecular bonds as compared to the peptide bond strength. The relatively large reported dynamic elastic moduli (approximately 8 GPa) from resonance light scattering should come from averaging over the moduli of intracrystalline water and intra- and intermolecular bonding.

Crystal Structures of New Ammonium 5-Aminotetrazolates

PubMed Central

Lampl, Martin; Salchner, Robert; Laus, Gerhard; Braun, Doris E.; Kahlenberg, Volker; Wurst, Klaus; Fuhrmann, Gerda; Schottenberger, Herwig; Huppertz, Hubert

2015-01-01

The crystal structures of three salts of anionic 5-aminotetrazole are described. The tetramethylammonium salt (P1‒) forms hydrogen-bonded ribbons of anions which accept weak C–H⋯N contacts from the cations. The cystamine salt (C2/c) shows wave-shaped ribbons of anions linked by hydrogen bonds to screw-shaped dications. The tetramethylguanidine salt (P21/c) exhibits layers of anions hydrogen-bonded to the cations. PMID:26753100

Phononic crystals of spherical particles: A tight binding approach

NASA Astrophysics Data System (ADS)

Mattarelli, M.; Secchi, M.; Montagna, M.

2013-11-01

The vibrational dynamics of a fcc phononic crystal of spheres is studied and compared with that of a single free sphere, modelled either by a continuous homogeneous medium or by a finite cluster of atoms. For weak interaction among the spheres, the vibrational dynamics of the phononic crystal is described by shallow bands, with low degree of dispersion, corresponding to the acoustic spheroidal and torsional modes of the single sphere. The phonon displacements are therefore related to the vibrations of a sphere, as the electron wave functions in a crystal are related to the atomic wave functions in a tight binding model. Important dispersion is found for the two lowest phonon bands, which correspond to zero frequency free translation and rotation of a free sphere. Brillouin scattering spectra are calculated at some values of the exchanged wavevectors of the light, and compared with those of a single sphere. With weak interaction between particles, given the high acoustic impedance mismatch in dry systems, the density of phonon states consist of sharp bands separated by large gaps, which can be well accounted for by a single particle model. Based on the width of the frequency gaps, tunable with the particle size, and on the small number of dispersive acoustic phonons, such systems may provide excellent materials for application as sound or heat filters.

Dissipating Step Bunches during Crystallization under Transport Control

NASA Technical Reports Server (NTRS)

Lin, Hong; Yau, S.-T.; Vekilov, Peter, G.

2003-01-01

In studies of crystal formation by the generation and spreading of layers, equidistant step trains are considered unstable---bunches and other spatiotemporal patterns of the growth steps are viewed as ubiquitous. We provide an example to the opposite. We monitor the spatiotemporal dynamics of steps and the resulting step patterns during crystallization of the proteins ferritin and apoferritin using the atomic force microscope. The variations in step velocity and density are not correlated, indicating the lack of a long-range attraction between the steps. We show that (i) because of its coupling to bulk transport, nucleation of new layers is chaotic and occurs at the facet edges, where the interfacial supersaturation is higher; (ii) step bunches self-organize via the competition for supply from the solution; and, (iii) bunches of weakly interacting steps decay as they move along the face. Tests by numerical modeling support the conclusions about the mechanisms underlying our observations. The results from these systems suggest that during crystallization controlled by transport, with weakly or noninteracting growth steps, the stable kinetic state of the surface is an equidistant step train, and step bunches only arise during nucleation of new layers. Since nucleation only occurs at a few sites on the surface, the surface morphology may be controllably patterned or smoothened by locally controlling nucleation.

Liquid-Crystal Thermosets, a New Generation of High-Performance Liquid-Crystal Polymers

NASA Technical Reports Server (NTRS)

Dingemans, Theo; Weiser, Erik; Hou, Tan; Jensen, Brian; St. Clair, Terry

2004-01-01

One of the major challenges for NASA's next-generation reusable-launch-vehicle (RLV) program is the design of a cryogenic lightweight composite fuel tank. Potential matrix resin systems need to exhibit a low coefficient of thermal expansion (CTE), good mechanical strength, and excellent barrier properties at cryogenic temperatures under load. In addition, the resin system needs to be processable by a variety of non-autoclavable techniques, such as vacuum-bag curing, resin-transfer molding (RTM), vacuum-assisted resin-transfer molding (VaRTM), resin-film infusion (RFI), pultrusion, and advanced tow placement (ATP). To meet these requirements, the Advanced Materials and Processing Branch (AMPB) at NASA Langley Research Center developed a new family of wholly aromatic liquid-crystal oligomers that can be processed and thermally cross-linked while maintaining their liquid-crystal order. All the monomers were polymerized in the presence of a cross-linkable unit by use of an environmentally benign melt-condensation technique. This method does not require hazardous solvents, and the only side product is acetic acid. The final product can be obtained as a powder or granulate and has an infinite shelf life. The obtained oligomers melt into a nematic phase and do not exhibit isotropization temperatures greater than the temperatures of decomposition (Ti > T(sub dec)). Three aromatic formulations were designed and tested and included esters, ester-amides, and ester-imides. One of the major advantages of this invention, named LaRC-LCR or Langley Research Center-Liquid Crystal Resin, is the ability to control a variety of resin characteristics, such as melting temperature, viscosity, and the cross-link density of the final part. Depending on the formulation, oligomers can be prepared with melt viscosities in the range of 10-10,000 poise (100 rad/s), which can easily be melt-processed using a variety of composite-processing techniques. This capability provides NASA with custom-made matrix resins that meet the required processing conditions for the fabrication of textile composites. Once the resin is in place, the temperature is raised to 375 C and the oligomers are cross-linked into a high-glass-transition-temperature (Tg) nematic network without releasing volatiles. The mechanical properties of the fully crosslinked, composite articles are comparable to typical composites based on commercially available epoxy resins.

Crystal structure of 1-(3-chloro­phen­yl)piperazin-1-ium picrate–picric acid (2/1)

PubMed Central

Kavitha, Channappa N.; Jasinski, Jerry P.; Kaur, Manpreet; Anderson, Brian J.; Yathirajan, H. S.

2014-01-01

The title salt {systematic name: bis­[1-(3-chloro­phen­yl)piperazinium 2,4,6-tri­nitro­phenolate]–picric acid (2/1)}, 2C10H14ClN2 +·2C6H5N3O7 −·C6H6N3O7, crystallized with two independent 1-(3-chloro­phen­yl)piperazinium cations, two picrate anions and a picric acid mol­ecule in the asymmetric unit. The six-membered piperazine ring in each cation adopts a slightly distorted chair conformation and contains a protonated N atom. In the picric acid mol­ecule, the mean planes of the nitro groups in the ortho-, meta-, and para-positions are twisted from the benzene ring by 31.5 (3), 7.7 (1), and 3.8 (2)°, respectively. In the anions, the dihedral angles between the benzene ring and the ortho-, meta-, and para-nitro groups are 36.7 (1), 5.0 (6), 4.8 (2)°, and 34.4 (9), 15.3 (8), 4.5 (1)°, respectively. The nitro group in one anion is disordered and was modeled with two sites for one O atom with an occupancy ratio of 0.627 (7):0.373 (7). In the crystal, the picric acid mol­ecule inter­acts with the picrate anion through a trifurcated O—H⋯O four-centre hydrogen bond involving an intra­molecular O—H⋯O hydrogen bond and a weak C—H⋯O inter­action. Weak inter­molecular C—H⋯O inter­actions are responsible for the formation of cation–anion–cation trimers resulting in a chain along [010]. In addition, weak C—H⋯Cl and weak π–π inter­actions [centroid–centroid distances of 3.532 (3), 3.756 (4) and 3.705 (3) Å] are observed and contribute to the stability of the crystal packing. PMID:25484834

4-Nitro­benzyl 2-bromo­acetate

PubMed Central

Zhu, Kai; Liu, Hui; Wang, Yan-Hua; Han, Ping-Fang; Wei, Ping

2009-01-01

In the mol­ecule of the title compound, C9H8BrNO4, the acetate group is close to planar [maximum deviation = 0.042 (3) Å] and is oriented at a dihedral angle of 73.24 (3)° with respect to the aromatic ring. In the crystal structure, inter­molecular C—H⋯O inter­actions link the mol­ecules into a three-dimensional network, forming R 2 2(10) ring motifs. PMID:21582813

3-(2,4-Dichloro­anilino)iso­benzo­furan-1(3H)-one1

PubMed Central

Odabaşoğlu, Mustafa; Büyükgüngör, Orhan

2008-01-01

In the mol­ecule of the title compound, C14H9Cl2NO2, the essentially planar phthalide group is oriented at a dihedral angle of 63.23 (5)° with respect to the substituted aromatic ring. In the crystal structure, inter­molecular C—H⋯O and N—H⋯O hydrogen bonds link the mol­ecules, generating R 4 4(21) ring motifs to form a three-dimensional network. PMID:21202144

Magnetic anisotropy in nickel complexes as determined by combined magnetic susceptibility/magnetization/theoretical studies

NASA Astrophysics Data System (ADS)

Mašlejová, Anna; Boča, Roman; Dlháň, L.'ubor; Herchel, Radovan

2004-05-01

The zero-field splitting in nickel(II) complexes was modeled by considering all relevant operators (electron repulsion, crystal-field, spin-orbit coupling, orbital-Zeeman, and spin-Zeeman) in the complete basis set spanned by d n-atomic terms. D-values between weak and strong crystal field limits were evaluated from the crystal-field multiplets as well as using the spin Hamiltonian formalism. Importance of the anisotropic orbital reduction factors is discussed and exemplified by D/hc=-22 cm-1 as subtracted from magnetic data for [Ni(imidazole) 4(acetate) 2] complex.

Investigation of the geometrical barrier in Bi-2212 using the magneto-optical technique

NASA Astrophysics Data System (ADS)

Lin, Z. W.; Gu, G. D.; Russell, G. J.

2000-08-01

It has been found that the penetration of vortices into a weak pinning crystal is governed by a geometrical barrier and they form a dome-shaped flux profile across the crystal. Using the powerful magneto-optical technique, we investigated this geometrical barrier in a high-purity Bi2Sr2CaCu2O8+x single-crystal platelet. Our results show that over the temperature range 20-70 K the dome-shaped profile is observed. Also, the influences of the edge shape and the roughness on the geometrical barrier are discussed.

Optical characteristics of novel bulk and nanoengineered laser host materials

NASA Astrophysics Data System (ADS)

Prasad, Narasimha S.; Sova, Stacey; Kelly, Lisa; Bevan, Talon; Arnold, Bradley; Cooper, Christopher; Choa, Fow-Sen; Singh, N. B.

2018-02-01

The hexagonal apatite single crystals have been investigated for their applications as laser host materials. Czochralksi and flux growth methods have been utilized to obtain single crystals. For low temperature processing (<100 0C), several techniques for crystal growth have been developed. The hexagonal apatite structure (space group P63/m) is characteristic of several compounds, some of which have extremely interesting and useful properties as laser hosts and bone materials. Calcium lanthanum silicate (Nd-doped) and lanthanum aluminate material systems were studied in detail. Nanoengineered calcium and lanthanum based silicates were synthesized by a solution method and their optical and morphological characteristics were compared with Czochralski grown bulk hydroxyapatite single crystals. Materials were evaluated by absorbance, fluorescence and Raman characteristics. Neodymium, iron and chromium doped crystals grown by a solution method showed weak but similar optical properties to that of Czochralski grown single crystals.

Crystal growth and electrical properties of CuFeO 2 single crystals

NASA Astrophysics Data System (ADS)

Dordor, P.; Chaminade, J. P.; Wichainchai, A.; Marquestaut, E.; Doumerc, J. P.; Pouchard, M.; Hagenmuller, P.; Ammar, A.

1988-07-01

Delafossite-type CuFeO 2 single crystals have been prepared by a flux method: crystals obtained in a Cu crucible with LiBO 2 as flux are n-type whereas those prepared in a Pt crucible with a Cu 2O flux are p-type. Electrical measurements have revealed that n-type crystals exhibit weak anisotropic conductivities with large activation energies and small mobilities (r.t. values perpendicular and parallel to the c-axis: μ⊥ = 5 × 10 -5 and μ‖ = 10 -7 cm -2 V -1 sec -1). p-type crystals, less anisotropic, are characterized by low activation energies and higher mobilities ( μ⊥ = 34 and μ‖ = 8.9 cm 2 V -1 sec -1). A two -conduction-band model is proposed to account for the difference observed between the energy gap value deduced from photoelectrochemical measurements and the activation energy of the electrical conductivity in the intrinsic domain.

How aromatic compounds block DNA binding of HcaR catabolite regulator

DOE PAGES

Kim, Youngchang; Joachimiak, Grazyna; Bigelow, Lance; ...

2016-04-25

Bacterial catabolism of aromatic compounds from various sources including phenylpropanoids and flavonoids that are abundant in soil plays an important role in the recycling of carbon in the ecosystem. We have determined the crystal structures of apo-HcaR from Acinetobacter sp. ADP1, a MarR/SlyA transcription factor, in complexes with hydroxycinnamates and a specific DNA operator. The protein regulates the expression of the hca catabolic operon in Acinetobacter and related bacterial strains, allowing utilization of hydroxycinnamates as sole sources of carbon. HcaR binds multiple ligands, and as a result the transcription of genes encoding several catabolic enzymes is increased. The 1.9-2.4 Åmore » resolution structures presented here explain how HcaR recognizes four ligands (ferulate, 3,4-dihydroxybenzoate, p-coumarate, and vanillin) using the same binding site. The ligand promiscuity appears to be an adaptation to match a broad specificity of hydroxycinnamate catabolic enzymes while responding to toxic thioester intermediates. Structures of apo-HcaR and in complex with a specific DNA hca operator when combined with binding studies of hydroxycinnamates show how aromatic ligands render HcaR unproductive in recognizing a specific DNA target. Furthermore, the current study contributes to a better understanding of the hca catabolic operon regulation mechanism by the transcription factor HcaR.« less

The dark and bright sides of an enzyme: a three dimensional structure of the N-terminal domain of Zophobas morio luciferase-like enzyme, inferences on the biological function and origin of oxygenase/luciferase activity.

PubMed

Prado, R A; Santos, C R; Kato, D I; Murakami, M T; Viviani, V R

2016-05-11

Beetle luciferases, the enzymes responsible for bioluminescence, are special cases of CoA-ligases which have acquired a novel oxygenase activity, offering elegant models to investigate the structural origin of novel catalytic functions in enzymes. What the original function of their ancestors was, and how the new oxygenase function emerged leading to bioluminescence remains unclear. To address these questions, we solved the crystal structure of a recently cloned Malpighian luciferase-like enzyme of unknown function from Zophobas morio mealworms, which displays weak luminescence with ATP and the xenobiotic firefly d-luciferin. The three dimensional structure of the N-terminal domain showed the expected general fold of CoA-ligases, with a unique carboxylic substrate binding pocket, permitting the binding and CoA-thioesterification activity with a broad range of carboxylic substrates, including short-, medium-chain and aromatic acids, indicating a generalist function consistent with a xenobiotic-ligase. The thioesterification activity with l-luciferin, but not with the d-enantiomer, confirms that the oxygenase activity emerged from a stereoselective impediment of the thioesterification reaction with the latter, favoring the alternative chemiluminescence oxidative reaction. The structure and site-directed mutagenesis support the involvement of the main-chain amide carbonyl of the invariant glycine G323 as the catalytic base for luciferin C4 proton abstraction during the oxygenase activity in this enzyme and in beetle luciferases (G343).

Reactivity of lithium n-butyl amidinates towards group 14 metal(II) chlorides providing series of hetero- and homoleptic tetrylenes.

PubMed

Chlupatý, Tomáš; Padělková, Zdeňka; Lyčka, Antonín; Brus, Jiří; Růžička, Aleš

2012-04-28

The new class of homo- and heteroleptic n-butyl-N,N'-disubstituted amidinato group 14 metal(II) complexes were prepared by salt elimination from starting lithium amidinates and metal(II) chlorides both in stoichiometric ratio 2:1 and 1:1, respectively. The target amidinates contain less bulky isopropyl or cyclohexyl as well as a sterically demanding aromatic substituent. Desired 1:1 Pb(II) complexes are not accessible by the described procedure. Ligand transfer from Pb to Sn is taking place if homoleptic Pb(II) compounds are reacted with SnCl(2). Prepared tetrylenes were characterized by (1)H, (13)C, (119)Sn and (207)Pb NMR spectroscopy in C(6)D(6) or THF-d(8). X-Ray diffraction studies of one heteroleptic Ge(II) monomeric where the coordination polyhedron of the three coordinated germanium atoms is a trigonal pyramid, two different dimeric structures of heteroleptic Sn(II) complexes, one amidine hydroiodide byproduct and the oxidation product of the heteroleptic chloro Sn(II) amidinate as a tetranuclear species with two Sn(IV) and two Sn(II) atoms in central Sn(2)O(2) planar ring were performed on appropriate single crystals. The dimer of one of the heteroleptic stannylenes reveals a new type of monomeric units connection, weak Sn-Cl contact and an interaction of the tin atom with delocalized N-C(C)-N system of the amidinato ligand of the second molecule. This journal is © The Royal Society of Chemistry 2012

Reversible and Selective Encapsulation of Dextromethorphan and β-Estradiol Using an Asymmetric Molecular Capsule Assembled via the Weak-Link Approach.

PubMed

Mendez-Arroyo, Jose; d'Aquino, Andrea I; Chinen, Alyssa B; Manraj, Yashin D; Mirkin, Chad A

2017-02-01

An allosterically regulated, asymmetric receptor featuring a binding cavity large enough to accommodate three-dimensional pharmaceutical guest molecules as opposed to planar, rigid aromatics, was synthesized via the Weak-Link Approach. This architecture is capable of switching between an expanded, flexible "open" configuration and a collapsed, rigid "closed" one. The structure of the molecular receptor can be completely modulated in situ through the use of simple ionic effectors, which reversibly control the coordination state of the Pt(II) metal hinges to open and close the molecular receptor. The substantial change in binding cavity size and electrostatic charge between the two configurations is used to explore the capture and release of two guest molecules, dextromethorphan and β-estradiol, which are widely found as pollutants in groundwater.

Using the DFT-D method to describe dispersion interactions in systems of weakly-bonded Xe-aromatic molecules

NASA Astrophysics Data System (ADS)

Andriichenko, N. N.; Ermilov, A. Yu.

2013-08-01

The optimum version of the DFT-D class of methods (BHHLYP-D2, 6-31G*) is chosen to describe binding in a Xe-phenol system with the aim of subsequent KM/MM calculations for complex Xe-containing protein systems. It is shown that the stability of the Xe-phenol system is due to weak dispersion interactions not described in conventional approaches using the density functional. The MP2 approach using the (aug)-cc-pVTZ basis and Stuttgart pseudopotential, which yield the best reproduction of the characteristics of a Xe2 xenon dimer, is chosen as the reference standard. It is noted that the 2010 DFT-D3 methods underestimate the binding energy by a factor of nearly three, while DFT methods without dispersion corrections do not reproduce the stability of Xe2 and Xe-phenol systems. It is found that in the best version of calculations, BHHLYP-D2, the binding energy in Xe-phenol complex is estimated to be 2.7 kcal/mol versus the 3.1 kcal/mol found using the comparative approach. It is concluded that BHHLYP-D2 adequately reproduces the difference between the two conformers of the Xe-phenol complex and trend toward an increase in binding energy in the series of aromatic amino acids (phenylalanine, tyrosine, and tryptophan). DFT-D can also indicate the existence of excess conformers that are missing in systems according to more precise descriptions (MP2/(aug)-cc-pVTZ).

Controlling Chirality of Entropic Crystals

NASA Astrophysics Data System (ADS)

Damasceno, Pablo; Karas, Andrew; Schultz, Benjamin; Engel, Michael; Glotzer, Sharon

Colloidal crystal structures with complexity and diversity rivaling atomic and molecular crystals have been predicted and obtained for hard particles by entropy maximization. However, thus far homochiral colloidal crystals, which are candidates for photonic metamaterials, are absent. Using Monte Carlo simulations we show that chiral polyhedra exhibiting weak directional entropic forces self-assemble either an achiral crystal or a chiral crystal with limited control over the crystal handedness. Building blocks with stronger faceting exhibit higher selectivity and assemble a chiral crystal with handedness uniquely determined by the particle chirality. Tuning the strength of directional entropic forces by means of particle rounding or the use of depletants allows for reconfiguration between achiral and homochiral crystals. We rationalize our findings by quantifying the chirality strength of each particle, both from particle geometry and potential of mean force and torque diagrams. Work supported by the National Science Foundation, Division of Materials Research Award No. DMR 1120923, U.S. Army Research Office under Grant Award No. W911NF-10-1-0518, and also by the DOD/ASD (R&E) under Award No. N00244-09-1-0062.

Solute boundary layer on a rotating crystal

NASA Astrophysics Data System (ADS)

Povinelli, Michelle L.; Korpela, Seppo A.; Chait, Arnon

1994-11-01

A perturbation analysis has been carried out for the solutal boundary layer next to a rotating crystal. Our aim is to extend the classical results of Burton, Prim and Slicher [1] in order to obtain higher order terms in asymptotic expansions for the concentration field and boundary-layer thickness. Expressions for the effective segregation coefficient are directly obtained from the concentration solution in the two limits that correspond to weak and strong rotation.

Surface chemistry of aromatic reactants on Pt- and Mo-modified Pt catalysts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Robinson, Allison M.; Mark, Lesli; Rasmussen, Mathew J.

Supported catalysts containing an oxophilic metal such as Mo and a noble metal such as Pt have shown promising activity and selectivity for deoxygenation of biomass-derived compounds. Here, we report that PtMo catalysts also promote hydrogenolysis of the model compound benzyl alcohol, while decarbonylation is most prevalent over unmodified Pt. A combination of single crystal surface science studies, density functional theory (DFT) calculations, and vapor phase upgrading experiments using supported catalysts was carried out to better understand the mechanism by which Mo promotes deoxygenation. Molybdenum was deposited in submonolayer quantities on a Pt(111) surface and reduced at high temperature. Temperature-programmedmore » desorption (TPD) experiments using benzyl alcohol as a reactant showed greatly enhanced yields of the deoxygenation product toluene at moderate Mo coverages. To understand how the interaction of the aromatic group with the surface influenced this reactivity, we investigated the adsorption of toluene as a probe molecule. We found that the addition of Mo to Pt(111) resulted in a significant decrease in toluene decomposition. DFT calculations indicated that this decrease was consistent with decreased aromatic adsorption strengths that accompany incorporation of Mo into the Pt subsurface. The weaker aromatic-surface interaction on Pt/Mo surfaces led to a tilted adsorption geometry for benzyl alcohol, which presumably promotes hydrogenolysis to produce toluene instead of decarbonylation to produce benzene and CO. Alumina-supported Pt and PtMo catalysts were also tested for benzyl alcohol deoxygenation. PtMo catalysts had a higher rate of toluene production and lower rates of benzene and benzaldehyde production. Additionally, when benzaldehyde was used as the reactant to measure decarbonylation activity the mass-normalized rate of benzene production was 2.5 times higher on Pt than PtMo. Altogether, the results of TPD, DFT, and supported catalyst experiments suggest that subsurface Mo sites weaken the binding of aromatic rings on PtMo surfaces; the weakened aromatic-surface interaction is correlated with an improvement in selectivity to C-O bond scission.« less

Surface chemistry of aromatic reactants on Pt- and Mo-modified Pt catalysts

DOE PAGES

Robinson, Allison M.; Mark, Lesli; Rasmussen, Mathew J.; ...

2016-11-01

Supported catalysts containing an oxophilic metal such as Mo and a noble metal such as Pt have shown promising activity and selectivity for deoxygenation of biomass-derived compounds. Here, we report that PtMo catalysts also promote hydrogenolysis of the model compound benzyl alcohol, while decarbonylation is most prevalent over unmodified Pt. A combination of single crystal surface science studies, density functional theory (DFT) calculations, and vapor phase upgrading experiments using supported catalysts was carried out to better understand the mechanism by which Mo promotes deoxygenation. Molybdenum was deposited in submonolayer quantities on a Pt(111) surface and reduced at high temperature. Temperature-programmedmore » desorption (TPD) experiments using benzyl alcohol as a reactant showed greatly enhanced yields of the deoxygenation product toluene at moderate Mo coverages. To understand how the interaction of the aromatic group with the surface influenced this reactivity, we investigated the adsorption of toluene as a probe molecule. We found that the addition of Mo to Pt(111) resulted in a significant decrease in toluene decomposition. DFT calculations indicated that this decrease was consistent with decreased aromatic adsorption strengths that accompany incorporation of Mo into the Pt subsurface. The weaker aromatic-surface interaction on Pt/Mo surfaces led to a tilted adsorption geometry for benzyl alcohol, which presumably promotes hydrogenolysis to produce toluene instead of decarbonylation to produce benzene and CO. Alumina-supported Pt and PtMo catalysts were also tested for benzyl alcohol deoxygenation. PtMo catalysts had a higher rate of toluene production and lower rates of benzene and benzaldehyde production. Additionally, when benzaldehyde was used as the reactant to measure decarbonylation activity the mass-normalized rate of benzene production was 2.5 times higher on Pt than PtMo. Altogether, the results of TPD, DFT, and supported catalyst experiments suggest that subsurface Mo sites weaken the binding of aromatic rings on PtMo surfaces; the weakened aromatic-surface interaction is correlated with an improvement in selectivity to C-O bond scission.« less

Hydrocarbons on Phoebe, Iapetus, and Hyperion: Quantitative Analysis

NASA Technical Reports Server (NTRS)

Cruikshank, Dale P.; MoreauDalleOre, Cristina; Pendleton, Yvonne J.; Clark, Roger Nelson

2012-01-01

We present a quantitative analysis of the hydrocarbon spectral bands measured on three of Saturn's satellites, Phoebe, Iaperus, and Hyperion. These bands, measured with the Cassini Visible-Infrared Mapping Spectrometer on close fly-by's of these satellites, are the C-H stretching modes of aromatic hydrocarbons at approximately 3.28 micrometers (approximately 3050 per centimeter), and the are four blended bands of aliphatic -CH2- and -CH3 in the range approximately 3.36-3.52 micrometers (approximately 2980- 2840 per centimeter) bably indicating the presence of polycyclic aromatic hydrocarbons (PAH), is unusually strong in comparison to the aliphatic bands, resulting in a unique signarure among Solar System bodies measured so far, and as such offers a means of comparison among the three satellites. The ratio of the C-H bands in aromatic molecules to those in aliphatic molecules in the surface materials of Phoebe, NAro:NAliph approximately 24; for Hyperion the value is approximately 12, while laperus shows an intermediate value. In view of the trend of the evolution (dehydrogenation by heat and radiation) of aliphatic complexes toward more compact molecules and eventually to aromatics, the relative abundances of aliphatic -CH2- and -CH3- is an indication of the lengths of the molecular chain structures, hence the degree of modification of the original material. We derive CH2:CH3 approximately 2.2 in the spectrum of low-albedo material on laperus; this value is the same within measurement errors to the ratio in the diffuse interstellar medium. The similarity in the spectral signatures of the three satellites, plus the apparent weak trend of aromatic/aliphatic abundance from Phoebe to Hyperion, is consistent with, and effectively confirms that the source of the hydrocarbon-bearing material is Phoebe, and that the appearance of that material on the other two satellites arises from the deposition of the inward-spiraling dust that populates the Phoebe ring.

Intra- versus intermolecular electron transfer in radical nucleophilic aromatic substitution of dihalo(hetero)arenes – a tool for estimating π-conjugation in aromatic systems† †Electronic supplementary information (ESI) available: Experimental details and procedures, 1H and 13C NMR data, GC traces and mass spectra. CCDC 1526301 and 1526302. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc00100b Click here for additional data file. Click here for additional data file.

PubMed Central

Janhsen, B.; Daniliuc, C. G.

2017-01-01

In this paper, the application of the double radical nucleophilic aromatic substitution (SRN1) in various dihalogenated, mostly diiodinated, π-conjugated systems as a tool for qualitatively estimating their π-conjugation is described. This approach uses electron delocalisation as a measure of π-conjugation. Electron injection into the π-system is achieved via reaction of an intermediate aryl radical, itself generated from a dihalogenated π-system via SET-reduction of the C–I bond and subsequent reaction with a thiolate anion. The generated arene radical anion can then further react with the second aryl-halogen moiety within the π-system via an intramolecular electron transfer process. The efficiency of this intramolecular electron transfer is related to the π-conjugation of the radical anion. If the π-conjugation within the aromatic unit is weak, the arene radical anion reacts via an intermolecular ET with the starting dihalide. The intramolecular ET process delivers a product of a double SRN1 substitution whereas the intermolecular ET pathway provides a product of a mono- SRN1 substitution. By simple product analysis of mono- versus double substitution, π-conjugation can be qualitatively evaluated. This mechanistic tool is applied to various dihalogenated π-conjugated systems and the results are discussed within the context of π-conjugation. The conjugation mode within the π-system and the length of the aromatic system are varied, and the effect of relative positioning of the two halides within small π-systems is also addressed. PMID:28580099

Growth and characterization of Na2Mo2O7 crystal scintillators for rare event searches

NASA Astrophysics Data System (ADS)

Pandey, Indra Raj; Kim, H. J.; Kim, Y. D.

2017-12-01

Disodium dimolybdate (Na2Mo2O7) crystals were grown using the Czochralski technique. The thermal characteristics of the compound were analyzed using thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC) measurements. The crystal structure of the grown sample was confirmed using X-ray diffraction (XRD). Luminescence properties were measured at room and low temperatures, using a light emitting diode (LED) source. Very weak luminescence was observed at room temperature; however, the luminescence intensity was enhanced at low temperatures. The crystal's transmittance spectrum was measured for estimating its optical quality and energy band gap. The grown crystal exhibited a luminescence light yield of 55% compared with CaMoO4 crystals at 10 K, when excited by a 280-nm-wavelength LED source, but does not have the drawbacks of radioactive Ca isotopes. These results suggest that at cryogenic temperatures, Na2Mo2O7 crystal scintillators are promising for the detection of dark matter and neutrinoless double beta decay of 100Mo.

Atomic density functional and diagram of structures in the phase field crystal model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ankudinov, V. E., E-mail: vladimir@ankudinov.org; Galenko, P. K.; Kropotin, N. V.

2016-02-15

The phase field crystal model provides a continual description of the atomic density over the diffusion time of reactions. We consider a homogeneous structure (liquid) and a perfect periodic crystal, which are constructed from the one-mode approximation of the phase field crystal model. A diagram of 2D structures is constructed from the analytic solutions of the model using atomic density functionals. The diagram predicts equilibrium atomic configurations for transitions from the metastable state and includes the domains of existence of homogeneous, triangular, and striped structures corresponding to a liquid, a body-centered cubic crystal, and a longitudinal cross section of cylindricalmore » tubes. The method developed here is employed for constructing the diagram for the homogeneous liquid phase and the body-centered iron lattice. The expression for the free energy is derived analytically from density functional theory. The specific features of approximating the phase field crystal model are compared with the approximations and conclusions of the weak crystallization and 2D melting theories.« less

Powder diffraction and crystal structure prediction identify four new coumarin polymorphs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shtukenberg, Alexander G.; Zhu, Qiang; Carter, Damien J.

Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms and X-ray powder diffraction. With five crystal structures, coumarin has become one of the few rigid molecules showing extensive polymorphism at ambient conditions. We demonstrate the crucial role of advanced electronic structure calculations including many-body dispersion effects for accurate ranking of the stability of coumarin polymorphs and themore » need to account for anharmonic vibrational contributions to their free energy. As such, coumarin is a model system for studying weak intermolecular interactions, crystallization mechanisms, and kinetic effects.« less

Mechanochemical synthesis of N-salicylidene­aniline: thermosalient effect of polymorphic crystals

PubMed Central

Mittapalli, Sudhir; Sravanakumar Perumalla, D.

2017-01-01

Polymorphs of the dichloro derivative of N-salicylideneaniline exhibit mechanical responses such as jumping (Forms I and III) and exploding (Form II) in its three polymorphs. The molecules are connected via the amide N—H⋯O dimer synthon and C—Cl⋯O halogen bond in the three crystal structures. A fourth high-temperature Form IV was confirmed by variable-temperature single-crystal X-ray diffraction at 180°C. The behaviour of jumping exhibited by the polymorphic crystals of Forms I and III is due to the layered sheet morphology and the transmission of thermal stress in a single direction, compared with the corrugated sheet structure of Form II such that heat dissipation is more isotropic causing blasting. The role of weak C—Cl⋯O interactions in the thermal response of molecular crystals is discussed. PMID:28512571

Powder diffraction and crystal structure prediction identify four new coumarin polymorphs

DOE PAGES

Shtukenberg, Alexander G.; Zhu, Qiang; Carter, Damien J.; ...

2017-05-15

Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms and X-ray powder diffraction. With five crystal structures, coumarin has become one of the few rigid molecules showing extensive polymorphism at ambient conditions. We demonstrate the crucial role of advanced electronic structure calculations including many-body dispersion effects for accurate ranking of the stability of coumarin polymorphs and themore » need to account for anharmonic vibrational contributions to their free energy. As such, coumarin is a model system for studying weak intermolecular interactions, crystallization mechanisms, and kinetic effects.« less

Crystal structure of 1-methyl-3-([2,2-dimethyl-4,6-dioxo-1,3-dioxane-5-ylidene]methyl)urea

DOE Office of Scientific and Technical Information (OSTI.GOV)

Habibi, A., E-mail: habibi@khu.ac.ir; Ghorbani, H. S.; Bruno, G.

2013-12-15

The crystal structure of 1-Methyl-3-([2,2-dimethyl-4,6-dioxo-1,3-dioxane-5-ylidene]methyl)urea (C{sub 9}H{sub 12}N{sub 2}O{sub 5}) has been determined by single crystal X-ray diffraction analysis. The crystals are monoclinic, a = 5.3179(2), b = 18.6394(6), c =10.8124(3) Å, β = 100.015(2)°, Z = 4, sp. gr. P2{sub 1}/c, R = 0.0381 for 2537 reflections with I > 2σ(I). Except for C(CH{sub 3}){sub 2} group, the molecule is planar. The structure is stabilized by inter- and intramolecular N-H...O hydrogen bonds and weak C-H...O interactions.

Anion-π Catalysis of Enolate Chemistry: Rigidified Leonard Turns as a General Motif to Run Reactions on Aromatic Surfaces.

PubMed

Cotelle, Yoann; Benz, Sebastian; Avestro, Alyssa-Jennifer; Ward, Thomas R; Sakai, Naomi; Matile, Stefan

2016-03-18

To integrate anion-π, cation-π, and ion pair-π interactions in catalysis, the fundamental challenge is to run reactions reliably on aromatic surfaces. Addressing a specific question concerning enolate addition to nitroolefins, this study elaborates on Leonard turns to tackle this problem in a general manner. Increasingly refined turns are constructed to position malonate half thioesters as close as possible on π-acidic surfaces. The resulting preorganization of reactive intermediates is shown to support the disfavored addition to enolate acceptors to an absolutely unexpected extent. This decisive impact on anion-π catalysis increases with the rigidity of the turns. The new, rigidified Leonard turns are most effective with weak anion-π interactions, whereas stronger interactions do not require such ideal substrate positioning to operate well. The stunning simplicity of the motif and its surprisingly strong relevance for function should render the introduced approach generally useful. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hydrogenated Polycyclic Aromatic Hydrocarbons and the 2940 and 2850 Wavenumber (3.40 and 3.51 micron) Infrared Emission Features

NASA Technical Reports Server (NTRS)

Bernstein, Max P.; Sandford, Scott A.; Allamadola, Louis J.

1996-01-01

The 3150-2700/cm (3.17-3.70 micron) range of the spectra of a number of Ar-matrix-isolated PAHs containing excess H atoms (H(sub n)-PAHS) are presented. This region covers features produced by aromatic and aliphatic C-H stretching vibrations as well as overtone and combination bands involving lower lying fundamentals. The aliphatic C-H stretches in molecules of this type having low to modest excess H coverage provide excellent fits to a number of the weak emission features superposed on the plateau between 3080 and 2700/cm (3.25 and 3.7 micron) in the spectra of many planetary nebulae, reflection nebulae, and H II regions. Higher H coverage is implied for a few objects. We compare these results in context with the other suggested identifications of the emission features in the 2950-2700/cm (3.39-3.70 micron) region and briefly discuss their astrophysical implications.

Self-assembled electrical materials from contorted aromatics

NASA Astrophysics Data System (ADS)

Xiao, Shengxiong

This thesis describes the design, synthesis, self-assembly and electrical properties of new types of contorted polycyclic aromatic hydrocarbons. These topologically interesting contorted aromatics show promising transistor characteristics as new building blocks for organic field-effect transistors (OFETs) at different length scales. In chapter 2, a class of pentacenes that are substituted along their long edges with aromatic rings were synthesized. Their solid-state assemblies were studied by X-ray crystallography. Their performance as thin film transistors (TFTs) and single crystal field effect transistors (SCFETs) were systematically evaluated. A structure-property relationship between these highly phenylated pentacenes was found. Chapter 3 explores the new concept of whether a non-planar aromatic core could yield efficacious electronic materials, as the ultimate success in the organic electronics will require a holistic approach to creating new building blocks. Synthesis, functionalization and assembly of a new type of contorted hexabenzocoronene (HBC) whose aromatic core is heavily distorted away from planarity due to the steric congestion around its proximal carbons were discussed. Structural studies by X-ray crystallography showed that these HBC molecules stack into columnar structures in the solid state, which are ideal for conduction. Chapter 4 describes that microscale liquid crystalline thin film OFETs of tetradodecyloxy HBC showed the best transistor properties of all discotic columnar materials. Chapter 5 details the fabrication and characterization of nanoscale single crystalline fiber OFETs of octadodecyloxyl HBC. In Chapter 6 we show that a molecular scale monolayer of HBC acid chlorides could be self-assembled on SiO2 insulating layer and could be organized laterally between the ends of 2 nm carbon nanotube gaps to form high quality FETs that act as environmental and chemical sensors. Chapter 7 details the enforced one-dimensional photoconductivity studies of core-cladding HBCs in thin films. Physical properties, such as charge generation, separation/recombination, and transport in HBCs liquid crystalline thin films were discussed. Chapter 8 describes the synthesis and electrical properties of the second generation of contorted aromatics octabenzocircumbiphenyl (OBC). The significant finding about OBCs is that they can be reversibly protonated with Bronsted acids. The significance of those results is that the conductance of the semiconductive thin film could be controlled and attenuated by doping with acid, which can lead to switchable electronics. Chapter 9 presents our studies of extending the HBC synthetic strategies to the formation of other curved aromatics using "wet chemistry". First a series of nonplanar polycyclic aromatic hydrocarbons was made starting from the olefination of pentacenequinone. Then we utilize chemical reactivity, X-ray crystallography, and DFT calculations to explore three types of olefins of increasing structural complexity. Chapter 10 discusses the transformation of HBCs into bowl-shaped molecules on ruthenium metal surfaces. Surface chemistry studies using scanning tunneling microscopy (STM), reflectance absorbance infrared spectroscopy (RAIRS), and temperature-programmed desorption (TPD) characterization methods, referred to as "dry chemistry", showed the formation of an aromatic hemisphere, which is the end cap of a (6,6) arm-chair single-walled carbon nanotube.

Enhanced intersystem crossing in core-twisted aromatics† †Electronic supplementary information (ESI) available: Includes details of the synthesis, structural information for all of the compounds (NMR, elemental analysis and mass spectra) and experimental details for the photophysical studies. CCDC 1402604 and 1402605. For ESI and crystallographic data in CIF or other electronic formats see DOI: 10.1039/c6sc05126j Click here for additional data file. Click here for additional data file.

PubMed Central

Nagarajan, Kalaivanan; Mallia, Ajith R.; Muraleedharan, Keerthi

2017-01-01

We describe the design, bottom-up synthesis and X-ray single crystal structure of systematically twisted aromatics 1c and 2d for efficient intersystem crossing. Steric congestion at the cove region creates a nonplanar geometry that induces a significant yield of triplet excited states in the electron-poor core-twisted aromatics 1c and 2d. A systematic increase in the number of twisted regions in 1c and 2d results in a concomitant enhancement in the rate and yield of intersystem crossing, monitored using femtosecond and nanosecond transient absorption spectroscopy. Time-resolved absorption spectroscopic measurements display enhanced triplet quantum yields (Φ T = 10 ± 1% for 1c and Φ T = 30 ± 2% for 2d) in the twisted aromatics when compared to a negligible Φ T (<1%) in the planar analog 3c. Twist-induced spin–orbit coupling via activated out-of-plane C–H/C 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 C vibrations can facilitate the formation of triplet excited states in twisted aromatics 1c and 2d, in contrast to the negligible intersystem crossing in the planar analog 3c. The ease of synthesis, high solubility, access to triplet excited states and strong electron affinity make such imide functionalized core-twisted aromatics desirable materials for organic electronics such as solar cells. PMID:28694952

X-ray Crystallographic Structure of Thermophilic Rhodopsin: IMPLICATIONS FOR HIGH THERMAL STABILITY AND OPTOGENETIC FUNCTION.

PubMed

Tsukamoto, Takashi; Mizutani, Kenji; Hasegawa, Taisuke; Takahashi, Megumi; Honda, Naoya; Hashimoto, Naoki; Shimono, Kazumi; Yamashita, Keitaro; Yamamoto, Masaki; Miyauchi, Seiji; Takagi, Shin; Hayashi, Shigehiko; Murata, Takeshi; Sudo, Yuki

2016-06-03

Thermophilic rhodopsin (TR) is a photoreceptor protein with an extremely high thermal stability and the first characterized light-driven electrogenic proton pump derived from the extreme thermophile Thermus thermophilus JL-18. In this study, we confirmed its high thermal stability compared with other microbial rhodopsins and also report the potential availability of TR for optogenetics as a light-induced neural silencer. The x-ray crystal structure of TR revealed that its overall structure is quite similar to that of xanthorhodopsin, including the presence of a putative binding site for a carotenoid antenna; but several distinct structural characteristics of TR, including a decreased surface charge and a larger number of hydrophobic residues and aromatic-aromatic interactions, were also clarified. Based on the crystal structure, the structural changes of TR upon thermal stimulation were investigated by molecular dynamics simulations. The simulations revealed the presence of a thermally induced structural substate in which an increase of hydrophobic interactions in the extracellular domain, the movement of extracellular domains, the formation of a hydrogen bond, and the tilting of transmembrane helices were observed. From the computational and mutational analysis, we propose that an extracellular LPGG motif between helices F and G plays an important role in the thermal stability, acting as a "thermal sensor." These findings will be valuable for understanding retinal proteins with regard to high protein stability and high optogenetic performance. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Does the number of nitrogen atoms have an influence on the conducting properties of diphenylazines? A DFT insight

NASA Astrophysics Data System (ADS)

Moral, Mónica; Granadino-Roldán, José Manuel; Garzón, Andrés; García, Gregorio; Fernández-Gómez, Manuel

2011-01-01

The present study reports on the variation of some structural and electronic properties related to the electron conductivity for the series of diphenylazines represented by the formula Ph sbnd (C 2+nN 4-nH n) sbnd Ph, n = 0 - 4. Properties such as planarity, aromaticity, HOMO → LUMO excitation energy, electron affinity, LUMO level energy, reorganization energy and electron coupling between neighboring molecules in the crystal were analyzed from a theoretical perspective as a function of the number of nitrogen atoms in the molecular structure. As a result, the planarity, aromaticity and electron affinity increase with the number of N atoms in the central ring while the HOMO → LUMO excitation energy and LUMO levels diminish. It is worth noting that up to n = 3, the frontier orbitals appear delocalized throughout the whole system while for n = 4 the localized character of the LUMO might explain the increase in the reorganization energy and thus the higher difficulty to delocalize the excess of negative charge. Electron coupling between neighboring molecules was also estimated on the basis of the energy splitting in dimer method and the reported crystal structures for some of the studied molecules. Accordingly, the highest | t12| value was obtained for Ph 2T N3 (0.06 eV) while Ph 2Tz should be the most advantageous candidate of the series in terms of electron injection.

Biochemical and structural characterization of recombinant short-chain NAD(H)-dependent dehydrogenase/reductase from Sulfolobus acidocaldarius highly enantioselective on diaryl diketone benzil.

PubMed

Pennacchio, Angela; Sannino, Vincenzo; Sorrentino, Giosuè; Rossi, Mosè; Raia, Carlo A; Esposito, Luciana

2013-05-01

The gene encoding a novel alcohol dehydrogenase that belongs to the short-chain dehydrogenases/reductases superfamily was identified in the aerobic thermoacidophilic crenarchaeon Sulfolobus acidocaldarius strain DSM 639. The saadh2 gene was heterologously overexpressed in Escherichia coli, and the resulting protein (SaADH2) was purified to homogeneity and both biochemically and structurally characterized. The crystal structure of the SaADH2 NADH-bound form reveals that the enzyme is a tetramer consisting of identical 27,024-Da subunits, each composed of 255 amino acids. The enzyme has remarkable thermophilicity and thermal stability, displaying activity at temperatures up to 80 °C and a 30-min half-inactivation temperature of ∼88 °C. It also shows good tolerance to common organic solvents and a strict requirement for NAD(H) as the coenzyme. SaADH2 displays a preference for the reduction of alicyclic, bicyclic and aromatic ketones and α-ketoesters, but is poorly active on aliphatic, cyclic and aromatic alcohols, showing no activity on aldehydes. Interestingly, the enzyme catalyses the asymmetric reduction of benzil to (R)-benzoin with both excellent conversion (98 %) and optical purity (98 %) by way of an efficient in situ NADH-recycling system involving a second thermophilic ADH. The crystal structure of the binary complex SaADH2-NADH, determined at 1.75 Å resolution, reveals details of the active site providing hints on the structural basis of the enzyme enantioselectivity.

Structural basis of stereospecificity in the bacterial enzymatic cleavage of β-aryl ether bonds in lignin

DOE PAGES

Helmich, Kate E.; Pereira, Jose Henrique; Gall, Daniel L.; ...

2015-12-04

Here, lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bonds. Although lignin is a potential source of valuable aromatic chemicals, its recalcitrance to chemical or biological digestion presents major obstacles to both the production of second-generation biofuels and the generation of valuable coproducts from lignin's monoaromatic units. Degradation of lignin has been relatively well characterized in fungi, but it is less well understood in bacteria. A catabolic pathway for the enzymatic breakdown of aromatic oligomers linked via β-aryl ether bonds typically found in lignin has been reported in the bacterium Sphingobium sp. SYK-6. Here, wemore » present x-ray crystal structures and biochemical characterization of the glutathione-dependent β-etherases, LigE and LigF, from this pathway. The crystal structures show that both enzymes belong to the canonical two-domain fold and glutathione binding site architecture of the glutathione S-transferase family. Mutagenesis of the conserved active site serine in both LigE and LigF shows that, whereas the enzymatic activity is reduced, this amino acid side chain is not absolutely essential for catalysis. The results include descriptions of cofactor binding sites, substrate binding sites, and catalytic mechanisms. Because β-aryl ether bonds account for 50–70% of all interunit linkages in lignin, understanding the mechanism of enzymatic β-aryl ether cleavage has significant potential for informing ongoing studies on the valorization of lignin.« less

In Investments, Reason Rules the Road.

ERIC Educational Resources Information Center

Griswold, John S., Jr.

2001-01-01

Suggests that college governing board investment committees should respond to the current economic and terrorism-related crisis by using SWOT analysis (strengths, weaknesses, opportunities, threats) to examine factors that can crystallize money-management decision points. (EV)

Crystal structure and spectral properties of vitamin K3 based nitrobenzo[a]phenoxazines

NASA Astrophysics Data System (ADS)

Chadar, Dattatray; Chakravarty, Debamitra; Lande, Dipali N.; Gejji, Shridhar P.; Sahoo, Suprabha; Salunke-Gawali, Sunita

2017-12-01

Benzo[a]phenoxazines are the planar polycyclic fluorescent compounds, find a variety of applications in biological sciences and are of growing interest. In the present work we synthesized heterocyclic aromatic fluorescent benzo[a]phenoxazines namely, 6-methyl-9-nitro-5H-benzo[a]phenoxazin-5-one (1) and 6-methyl-10-nitro-5H-benzo[a]phenoxazin-5-one (2) which are characterized in terms of the 1H and 13C chemical shifts from 2D gHSQCAD NMR experiments. Single crystal X-ray experiments revealed both 1 and 2 possess the Csbnd H⋯O interactions. Moreover the π•••π stacking interactions between planar polycycles have been noticed only in 1. The structural and vibrational spectral inferences obtained from experiments are corroborated through the ωB97xD based density functional theory.

Piperidinium bis­(2-oxidobenzoato-κ2 O 1,O 2)borate

PubMed Central

Tang, Zhi-Hua; Huang, Chaojun

2009-01-01

The asymmetric unit of the title compound, C5H12N+·C14H8BO6 − or [C5H12N][BO4(C7H4O)2], contains two piperidinium cations and two bis­(salicylato)borate anions. The coordination geometries around the B atoms are distorted tetra­hedral. In the two mol­ecules, the aromatic rings are oriented at dihedral angles of 76.27 (3) and 83.86 (3)°. The rings containing B atoms have twist-boat conformations, while the two cations adopt chair conformations. In the crystal, the component species are linked by N—H⋯O hydrogen bonds. In the crystal structure, intra- and inter­molecular N—H⋯O hydrogen bonds link the mol­ecules. PMID:21581628

Separation and concentration of lower alcohols from dilute aqueous solutions

DOEpatents

Moore, Raymond H.; Eakin, David E.; Baker, Eddie G.; Hallen, Richard T.

1991-01-01

A process for producing, from a dilute aqueous solution of a lower (C.sub.1 -C.sub.5) alcohol, a concentrated liquid solution of the alcohol in an aromatic organic solvent is disclosed. Most of the water is removed from the dilute aqueous solution of alcohol by chilling sufficiently to form ice crystals. Simultaneously, the remaining liquid is extracted at substantially the same low temperature with a liquid organic solvent that is substantially immiscible in aqueous liquids and has an affinity for the alcohol at that temperature, causing the alcohol to transfer to the organic phase. After separating the organic liquid from the ice crystals, the organic liquid can be distilled to enrich the concentration of alcohol therein. Ethanol so separated from water and concentrated in an organic solvent such as toluene is useful as an anti-knock additive for gasoline.

Synthesis, Urease Inhibition, Antioxidant, Antibacterial, and Molecular Docking Studies of 1,3,4-Oxadiazole Derivatives

PubMed Central

Hanif, Muhammad; Shoaib, Khurram; Saleem, Muhammad; Hasan Rama, Nasim; Zaib, Sumera; Iqbal, Jamshed

2012-01-01

A series of eighteen 1,3,4-oxadiazole derivatives have been synthesized by treating aromatic acid hydrazides with carbon disulfide in ethanolic potassium hydroxide yielding potassium salts of 1,3,4-oxadiazoles. Upon neutralization with 1 N hydrochloric acid yielded crude crystals of 1,3,4-oxadiazoles, which were purified by recrystallization in boiling methanol. The synthesized 1,3,4-oxadiazoles derivatives were evaluated in vitro for their urease inhibitory activities, most of the investigated compounds were potent inhibitors of Jack bean urease. The molecular docking studies were performed by docking them into the crystal structure of Jack bean urease to observe the mode of interaction of synthesized compounds. The synthesized compounds were also tested for antibacterial and antioxidant activities and some derivatives exhibited very promising results. PMID:22934191

2-Ferrocenyl-3-meth­oxy-6-methyl­pyridine

PubMed Central

Xu, Chen; Hao, Xin-Qi; Liu, Fang; Wu, Xiu-Juan; Song, Mao-Ping

2009-01-01

In the title compound, [Fe(C5H5)(C12H12NO)], the dihedral angle between the pyridyl and substituted cyclo­penta­dienyl rings is 23.58 (3)°. The crystal structure is characterized by weak inter­molecular C—H⋯N hydrogen-bonding contacts, leading to the formation of chains running parallel to the n-glide planes. A weak inter­molecular C—H⋯π contact is also present. PMID:21583761

7-Meth­oxy­indan-1-one

PubMed Central

Chang, Yuan Jay; Chen, Kew-Yu

2012-01-01

In the title compound, C10H10O2, the 1-indanone unit is essentially planar (r.m.s. deviation = 0.028 Å). In the crystal, molecules are linked via C—H⋯O hydrogen bonds, forming layers lying parallel to the ab plane. This two-dimensional structure is stabilized by a weak C—H⋯π inter­action. A second weak C—H⋯π inter­action links the layers, forming a three-dimensional structure. PMID:23284398

Metal-Free Functionalization of N,N-Dialkylanilines via Temporary Oxidation to N,N-Dialkylaniline N-Oxides and Group Transfer

PubMed Central

2015-01-01

A simple set of protocols for the controlled elaboration of anilines is reported allowing access to a diverse array of aminophenols, aminoarylsulfonates, alkylated anilines, and aminoanilines in 29–95% yield in a single laboratory operation from easily isolable, bench-stable N,N-dialkylaniline N-oxides. The introduction of new C–O, C–C, and C–N bonds on the aromatic ring is made possible by a temporary increase in oxidation level and excision of a weak N–O bond. PMID:24992642

Energy profile of maltooligosaccharide permeation through maltoporin as derived from the structure and from a statistical analysis of saccharide-protein interactions.

PubMed Central

Meyer, J. E.; Schulz, G. E.

1997-01-01

The crystal structure of the maltodextrin-specific porin from Salmonella typhimurium ligated with a maltotrioside at the pore eyelet is known at 2.4 A resolution. The three glucose units assume a conformation close to the natural amylose helix. The pore eyelet fits exactly the cross-section of a maltooligosaccharide chain and thus functions as a constraining orifice. The oligomer permeates the membrane by screwing along the amylose helix through this orifice. Because each glucose glides along the given helix, its interactions can be sampled at any point along the pathway. The interactions are mostly hydrogen bonds, but also contacts to aromatic rings at one side of the pore. We have derived the energy profile of a gliding maltooligosaccharide by following formation and breakage of hydrogen bonds and by assessing the saccharide-aromatics interactions from a statistical analysis of saccharide binding sites in proteins. The resulting profile indicates smooth permeation despite extensive hydrogen bonding at the orifice. PMID:9144780

In-crystal reaction cycle of a toluene-bound diiron hydroxylase

NASA Astrophysics Data System (ADS)

Acheson, Justin F.; Bailey, Lucas J.; Brunold, Thomas C.; Fox, Brian G.

2017-03-01

Electrophilic aromatic substitution is one of the most important and recognizable classes of organic chemical transformation. Enzymes create the strong electrophiles that are needed for these highly energetic reactions by using O2, electrons, and metals or other cofactors. Although the nature of the oxidants that carry out electrophilic aromatic substitution has been deduced from many approaches, it has been difficult to determine their structures. Here we show the structure of a diiron hydroxylase intermediate formed during a reaction with toluene. Density functional theory geometry optimizations of an active site model reveal that the intermediate is an arylperoxo Fe2+/Fe3+ species with delocalized aryl radical character. The structure suggests that a carboxylate ligand of the diiron centre may trigger homolytic cleavage of the O-O bond by transferring a proton from a metal-bound water. Our work provides the spatial and electronic constraints needed to propose a comprehensive mechanism for diiron enzyme arene hydroxylation that accounts for many prior experimental results.

Cocrystal Structures of Primed Side-Extending α-Ketoamide Inhibitors Reveal Novel Calpain-Inhibitor Aromatic Interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qian,J.; Cuerrier, D.; Davies, P.

Calpains are intracellular cysteine proteases that catalyze the cleavage of target proteins in response to Ca2+ signaling. When Ca2+ homeostasis is disrupted, calpain overactivation causes unregulated proteolysis, which can contribute to diseases such as postischemic injury and cataract formation. Potent calpain inhibitors exist, but of these many cross-react with other cysteine proteases and will need modification to specifically target calpain. Here, we present crystal structures of rat calpain 1 protease core ({mu}I-II) bound to two a-ketoamide-based calpain inhibitors containing adenyl and piperazyl primed-side extensions. An unexpected aromatic-stacking interaction is observed between the primed-side adenine moiety and the Trp298 side chain.more » This interaction increased the potency of the inhibitor toward {mu}I-II and heterodimeric m-calpain. Moreover, stacking orients the adenine such that it can be used as a scaffold for designing novel primed-side address regions, which could be incorporated into future inhibitors to enhance their calpain specificity.« less

Structure and biocatalytic scope of thermophilic flavin-dependent halogenase and flavin reductase enzymes.

PubMed

Menon, Binuraj R K; Latham, Jonathan; Dunstan, Mark S; Brandenburger, Eileen; Klemstein, Ulrike; Leys, David; Karthikeyan, Chinnan; Greaney, Michael F; Shepherd, Sarah A; Micklefield, Jason

2016-10-04

Flavin-dependent halogenase (Fl-Hal) enzymes have been shown to halogenate a range of synthetic as well as natural aromatic compounds. The exquisite regioselectively of Fl-Hal enzymes can provide halogenated building blocks which are inaccessible using standard halogenation chemistries. Consequently, Fl-Hal are potentially useful biocatalysts for the chemoenzymatic synthesis of pharmaceuticals and other valuable products, which are derived from haloaromatic precursors. However, the application of Fl-Hal enzymes, in vitro, has been hampered by their poor catalytic activity and lack of stability. To overcome these issues, we identified a thermophilic tryptophan halogenase (Th-Hal), which has significantly improved catalytic activity and stability, compared with other Fl-Hal characterised to date. When used in combination with a thermostable flavin reductase, Th-Hal can efficiently halogenate a number of aromatic substrates. X-ray crystal structures of Th-Hal, and the reductase partner (Th-Fre), provide insights into the factors that contribute to enzyme stability, which could guide the discovery and engineering of more robust and productive halogenase biocatalysts.

The effect of humic acids on biodegradation of polycyclic aromatic hydrocarbons depends on the exposure regime.

PubMed

Tejeda-Agredano, Maria-Carmen; Mayer, Philipp; Ortega-Calvo, Jose-Julio

2014-01-01

Binding of polycyclic aromatic hydrocarbons (PAHs) to dissolved organic matter (DOM) can reduce the freely dissolved concentration, increase apparent solubility or enhance diffusive mass transfer. To study the effects of DOM on biodegradation, we used phenanthrene and pyrene as model PAHs, soil humic acids as model DOM and a soil Mycobacterium strain as a representative degrader organism. Humic acids enhanced the biodegradation of pyrene when present as solid crystals but not when initially dissolved or provided by partitioning from a polymer. Synchronous fluorescence spectrophotometry, scintillation counting and a microscale diffusion technique were applied in order to determine the kinetics of dissolution and diffusive mass transfer of pyrene. We suggest that humic acids can enhance or inhibit biodegradation as a result of the balance of two opposite effects, namely, solubilization of the chemicals on the one hand and inhibition of cell adhesion to the pollutant source on the other. Copyright © 2013 Elsevier Ltd. All rights reserved.

Hot spot generation in energetic materials created by long-wavelength infrared radiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Ming-Wei; You, Sizhu; Suslick, Kenneth S.

Hot spots produced by long-wavelength infrared (LWIR) radiation in an energetic material, crystalline RDX (1,3,5-trinitroperhydro-1,3,5-triazine), were studied by thermal-imaging microscopy. The LWIR source was a CO{sub 2} laser operating in the 28-30 THz range. Hot spot generation was studied using relatively low intensity (∼100 W cm{sup −2}), long-duration (450 ms) LWIR pulses. The hot spots could be produced repeatedly in individual RDX crystals, to investigate the fundamental mechanisms of hot spot generation by LWIR, since the peak hot-spot temperatures were kept to ∼30 K above ambient. Hot spots were generated preferentially beneath RDX crystal planes making oblique angles with the LWIR beam. Surprisingly,more » hot spots were more prominent when the LWIR wavelength was tuned to be weakly absorbed (absorption depth ∼30 μm) than when the LWIR wavelength was strongly absorbed (absorption depth ∼5 μm). This unexpected effect was explained using a model that accounts for LWIR refraction and RDX thermal conduction. The weakly absorbed LWIR is slightly focused underneath the oblique crystal planes, and it penetrates the RDX crystals more deeply, increasing the likelihood of irradiating RDX defect inclusions that are able to strongly absorb or internally focus the LWIR beam.« less

Two-dimensional crystals: managing light for optoelectronics.

PubMed

Eda, Goki; Maier, Stefan A

2013-07-23

Semiconducting two-dimensional (2D) crystals such as MoS2 and WSe2 exhibit unusual optical properties that can be exploited for novel optoelectronics ranging from flexible photovoltaic cells to harmonic generation and electro-optical modulation devices. Rapid progress of the field, particularly in the growth area, is beginning to enable ways to implement 2D crystals into devices with tailored functionalities. For practical device performance, a key challenge is to maximize light-matter interactions in the material, which is inherently weak due to its atomically thin nature. Light management around the 2D layers with the use of plasmonic nanostructures can provide a compelling solution.

Crystal structures, in-silico study and anti-microbial potential of synthetic monocarbonyl curcuminoids

NASA Astrophysics Data System (ADS)

Ud Din, Zia; Serrano, N. F. G.; Ademi, Kastriot; Sousa, C. P.; Deflon, Victor Marcelo; Maia, Pedro Ivo da Silva; Rodrigues-Filho, Edson

2017-09-01

In this work the screening of 20 unsymmetrical chalcone and curcuminoids analogues in regard of their antimicrobial properties was conducted. Electron donating groups in the aromatic rings in the chalcone and curcuminoid derivatives produced higher antimicrobial effect. Compounds 1, 9 and 15 exhibited good activity against Escherichia coli and Staphylococcus aureus. These compounds were further evaluated against nine micro-organisms of pathological interest. Pharmmaper was used for target fishing of compounds against important bacterial targets. Molecular Docking helped to verify the results of these compounds against the selected bacterial target D-alanyl-D-alanine carboxypeptidase (PDB ID: 1PW1). The crystal structure of ligand and docked conformers in the active site of 1PW1 were analyzed. As a result structure-activity relationships are proposed. Structures of compounds 14 and 16 were obtained through single crystals X-ray diffraction studies. Compound 14 crystallizes in monoclinic space group P21/c with unit cell dimensions a = 13.1293(3) Å, b = 17.5364(4) Å, c = 15.1433(3) Å, β = 95.6440(10), V = 3469.70(13) Å3 and Z = 8. Compound 16 crystallizes in triclinic space group Pī with unit cell dimensions a = 6.8226(4) Å, b = 7.2256(4) Å, c = 18.1235(12) Å, β = 87.322(4), V = 850.57(9) Å3 and Z = 2.

Infrared spectroscopy of hydrated polycyclic aromatic hydrocarbon cations: naphthalene+-water.

PubMed

Chatterjee, Kuntal; Dopfer, Otto

2017-12-13

Polycyclic aromatic hydrocarbons (PAHs) are suggested to occur in interstellar media and ice grains. It is important to characterize hydrated PAHs and their cations to explore their stability in interstellar and biological media. Herein, the infrared photodissociation (IRPD) spectrum of the naphthalene + -H 2 O radical cation (Np + -H 2 O) recorded in the O-H and C-H stretch range is analysed by dispersion-corrected density functional theory calculations at the B3LYP-D3/aug-cc-pVTZ level to determine its structure and intermolecular bonding. Monohydration of Np + in its 2 A u ground electronic state leads to the formation of a bifurcated CHO ionic hydrogen bond (H-bond), in which the lone pairs of H 2 O bind to two adjacent CH proton donors of the two aromatic rings. The frequency-dependent branching ratios observed for IRPD of cold Np + -H 2 O-Ar clusters allows the estimation of the dissociation energy of Np + -H 2 O as D 0 ∼ 2800 ± 300 cm -1 . The monohydration motif of Np + differs qualitatively from that of the benzene cation in both structure and binding energy, indicating the strong influence of the multiple aromatic rings on the hydration of PAH + cations. This difference is rationalized by natural bond orbital analysis of the ionic H-bond motif. Comparison with neutral Np-H 2 O reveals the large change in structure and bond strength of the hydrated PAHs upon ionization. While neutral Np-H 2 O is stabilized by weak π H-bonds (OHπ, π-stacking), strong cation-dipole forces favour a planar bifurcated CHO ionic H-bond in Np + -H 2 O.

Soliton-like defects in nematic liquid crystal thin layers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chuvyrov, A. N.; Krekhov, A. P.; Lebedev, Yu. A., E-mail: lebedev@anrb.ru

The nonsingular soliton-like defects in plane nematic liquid crystal (NLC) layers and spherical NLC drops are experimentally detected and studied when the interaction of NLC molecules with a bounding surface is varied. The dynamics and the annihilation of nonsingular defects of opposite signs on a plane surface are investigated. Periodic transformations of the soliton-like defects in NLC drops in an electric field are detected. The theory of elasticity is used to show that the surface energy taken into account in the total free energy of NLC in the case of weak anchoring leads to the possibility of nonsingular solutions ofmore » a director equilibrium equation. The calculated pictures of director distribution in a plane NLC layer and in a spherical NLC drop characterized by weak surface anchoring agree well with the results of polarized light optical observations.« less

Crystallization-induced emission enhancement: A novel fluorescent Au-Ag bimetallic nanocluster with precise atomic structure

PubMed Central

Chen, Tao; Yang, Sha; Chai, Jinsong; Song, Yongbo; Fan, Jiqiang; Rao, Bo; Sheng, Hongting; Yu, Haizhu; Zhu, Manzhou

2017-01-01

We report the first noble metal nanocluster with a formula of Au4Ag13(DPPM)3(SR)9 exhibiting crystallization-induced emission enhancement (CIEE), where DPPM denotes bis(diphenylphosphino)methane and HSR denotes 2,5-dimethylbenzenethiol. The precise atomic structure is determined by x-ray crystallography. The crystalline state of Au4Ag13 shows strong luminescence at 695 nm, in striking contrast to the weak emission of the amorphous state and hardly any emission in solution phase. The structural analysis and the density functional theory calculations imply that the compact C–H⋯π interactions significantly restrict the intramolecular rotations and vibrations and thus considerably enhance the radiative transitions in the crystalline state. Because the noncovalent interactions can be easily modulated via varying the chemical environments, the CIEE phenomenon might represent a general strategy to amplify the fluorescence from weakly (or even non-) emissive nanoclusters. PMID:28835926

Weak interactions involving organic fluorine: analysis of structural motifs in Flunazirine and Haloperidol

NASA Astrophysics Data System (ADS)

Prasanna, M. D.; Row, T. N. Guru

2001-05-01

The crystal structure of Flunazirine, an anticonvulsant drug, is analyzed in terms of intermolecular interactions involving fluorine. The structure displays motifs formed by only weak interactions C-H⋯F and C-H⋯π. The motifs thus generated show cavities, which could serve as hosts for complexation. The structure of Flunazirine displays cavities formed by C-H⋯F and C-H⋯π interactions. Haloperidol, an antipsychotic drug, shows F⋯F interactions in the crystalline lattice in lieu of Cl⋯Cl interactions. However, strong O-H⋯N interactions dominate packing. The salient features of the two structures in terms of intermolecular interactions reveal, even though organic fluorine has lower tendency to engage in hydrogen bonding and F⋯F interactions, these interactions could play a significant role in the design of molecular assemblies via crystal engineering.

Superdiffusive transport and energy localization in disordered granular crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martinez, Alejandro J.; Kevrekidis, Panagiotis G.; Porter, Mason A.

We study the spreading of initially localized excitations in one-dimensional disordered granular crystals. We thereby investigate localization phenomena in strongly nonlinear systems, which we demonstrate to be fundamentally different from localization in linear and weakly nonlinear systems. We conduct a thorough comparison of wave dynamics in chains with three different types of disorder: an uncorrelated (Anderson-like) disorder and two types of correlated disorders (which are produced by random dimer arrangements), and for two families of initial conditions: displacement perturbations and velocity perturbations. We find for strongly precompressed (i.e., weakly nonlinear) chains that the dynamics strongly depends on the initial condition.more » Furthermore, for displacement perturbations, the long-time asymptotic behavior of the second moment m ~2 has oscillations that depend on the type of disorder, with a complex trend that is markedly different from a power law and which is particularly evident for an Anderson-like disorder.« less

2-(Naphthalen-1-yl)-4-(naphthalen-1-yl­methyl­idene)-1,3-oxazol-5(4H)-one

PubMed Central

Gündoğdu, Cevher; Alp, Serap; Ergün, Yavuz; Tercan, Barış; Hökelek, Tuncer

2011-01-01

In the title compound, C24H15NO2, the oxazole ring is oriented at dihedral angles of 10.09 (4) and 6.04 (4)° with respect to the mean planes of the naphthalene ring systems, while the two naphthalene ring systems make a dihedral angle of 4.32 (3)°. Intra­molecular C—H⋯N hydrogen bonds link the oxazole N atom to the naphthalene ring systems. In the crystal, inter­molecular weak C—H⋯O hydrogen bonds link the mol­ecules into centrosymmetric dimers. π–π contacts between the oxazole and naphthalene rings and between the naphthalene ring systems [centroid–centroid distances = 3.5947 (9) and 3.7981 (9) Å] may further stabilize the crystal structure. Three weak C—H⋯π inter­actions also occur. PMID:21754548

Superdiffusive transport and energy localization in disordered granular crystals

DOE PAGES

Martinez, Alejandro J.; Kevrekidis, Panagiotis G.; Porter, Mason A.

2016-02-12

We study the spreading of initially localized excitations in one-dimensional disordered granular crystals. We thereby investigate localization phenomena in strongly nonlinear systems, which we demonstrate to be fundamentally different from localization in linear and weakly nonlinear systems. We conduct a thorough comparison of wave dynamics in chains with three different types of disorder: an uncorrelated (Anderson-like) disorder and two types of correlated disorders (which are produced by random dimer arrangements), and for two families of initial conditions: displacement perturbations and velocity perturbations. We find for strongly precompressed (i.e., weakly nonlinear) chains that the dynamics strongly depends on the initial condition.more » Furthermore, for displacement perturbations, the long-time asymptotic behavior of the second moment m ~2 has oscillations that depend on the type of disorder, with a complex trend that is markedly different from a power law and which is particularly evident for an Anderson-like disorder.« less

Crystal and molecular structure of eight organic acid-base adducts from 2-methylquinoline and different acids

NASA Astrophysics Data System (ADS)

Zhang, Jing; Jin, Shouwen; Tao, Lin; Liu, Bin; Wang, Daqi

2014-08-01

Eight supramolecular complexes with 2-methylquinoline and acidic components as 4-aminobenzoic acid, 2-aminobenzoic acid, salicylic acid, 5-chlorosalicylic acid, 3,5-dinitrosalicylic acid, malic acid, sebacic acid, and 1,5-naphthalenedisulfonic acid were synthesized and characterized by X-ray crystallography, IR, mp, and elemental analysis. All of the complexes are organic salts except compound 2. All supramolecular architectures of 1-8 involve extensive classical hydrogen bonds as well as other noncovalent interactions. The results presented herein indicate that the strength and directionality of the classical hydrogen bonds (ionic or neutral) between acidic components and 2-methylquinoline are sufficient to bring about the formation of binary organic acid-base adducts. The role of weak and strong noncovalent interactions in the crystal packing is ascertained. These weak interactions combined, the complexes 1-8 displayed 2D-3D framework structure.

The tropolone-isobutylamine complex: a hydrogen-bonded troponoid without dominant π-π interactions.

PubMed

Vealey, Zachary N; Mercado, Brandon Q; Vaccaro, Patrick H

2016-10-01

Tropolone long has served as a model system for unraveling the ubiquitous phenomena of proton transfer and hydrogen bonding. This molecule, which juxtaposes ketonic, hydroxylic, and aromatic functionalities in a framework of minimal complexity, also has provided a versatile platform for investigating the synergism among competing intermolecular forces, including those generated by hydrogen bonding and aryl coupling. Small members of the troponoid family typically produce crystals that are stabilized strongly by pervasive π-π, C-H...π, or ion-π interactions. The organic salt (TrOH·iBA) formed by a facile proton-transfer reaction between tropolone (TrOH) and isobutylamine (iBA), namely isobutylammonium 7-oxocyclohepta-1,3,5-trien-1-olate, C 4 H 12 N + ·C 7 H 5 O 2 - , has been investigated by X-ray crystallography, with complementary quantum-chemical and statistical-database analyses serving to elucidate the nature of attendant intermolecular interactions and their synergistic effects upon lattice-packing phenomena. The crystal structure deduced from low-temperature diffraction measurements displays extensive hydrogen-bonding networks, yet shows little evidence of the aryl forces (viz. π-π, C-H...π, and ion-π interactions) that typically dominate this class of compounds. Density functional calculations performed with and without the imposition of periodic boundary conditions (the latter entailing isolated subunits) documented the specificity and directionality of noncovalent interactions occurring between the proton-donating and proton-accepting sites of TrOH and iBA, as well as the absence of aromatic coupling mediated by the seven-membered ring of TrOH. A statistical comparison of the structural parameters extracted for key hydrogen-bond linkages to those reported for 44 previously known crystals that support similar binding motifs revealed TrOH·iBA to possess the shortest donor-acceptor distances of any troponoid-based complex, combined with unambiguous signatures of enhanced proton-delocalization processes that putatively stabilize the corresponding crystalline lattice and facilitate its surprisingly rapid formation under ambient conditions.

Exploring 3D structural influences of aliphatic and aromatic chemicals on α-cyclodextrin binding.

PubMed

Linden, Lukas; Goss, Kai-Uwe; Endo, Satoshi

2016-04-15

Binding of solutes to macromolecules is often influenced by steric effects caused by the 3D structures of both binding partners. In this study, the 1:1 α-cyclodextrin (αCD) binding constants (Ka1) for 70 organic chemicals were determined to explore the solute-structural effects on the αCD binding. Ka1 was measured using a three-part partitioning system with either a headspace or a passive sampler serving as the reference phase. The Ka1 values ranged from 1.08 to 4.97 log units. The results show that longer linear aliphatic chemicals form more stable complexes than shorter ones, and that the position of the functional group has a strong influence on Ka1, even stronger than the type of the functional group. Comparison of linear and variously branched aliphatic chemicals indicates that having a sterically unhindered alkyl chain is favorable for binding. These results suggest that only one alkyl chain can enter the binding cavity. Relatively small aromatic chemicals such as 1,3-dichlorobenzene bind to αCD well, while larger ones like tetrachlorobenzene and 3-ring aromatic chemicals show only a weak interaction with αCD, which can be explained by cavity exclusion. The findings of this study help interpret cyclodextrin binding data and facilitate the understanding of binding processes to macromolecules. Copyright © 2016 Elsevier Inc. All rights reserved.

Complexation facilitated reduction of aromatic N-oxides by aqueous Fe(II)-tiron complex: reaction kinetics and mechanisms.

PubMed

Chen, Yiling; Zhang, Huichun

2013-10-01

Rapid reduction of carbadox (CDX), olaquindox and several other aromatic N-oxides were investigated in aqueous solution containing Fe(II) and tiron. Consistent with previous work, the 1:2 Fe(II)-tiron complex, FeL2(6-), is the dominant reactive species as its concentration linearly correlates with the observed rate constant kobs under various conditions. The N-oxides without any side chains were much less reactive, suggesting direct reduction of the N-oxides is slow. UV-vis spectra suggest FeL2(6-) likely forms 5- or 7-membered rings with CDX and olaquindox through the N and O atoms on the side chain. The formed inner-sphere complexes significantly facilitated electron transfer from FeL2(6-) to the N-oxides. Reduction products of the N-oxides were identified by HPLC/QToF-MS to be the deoxygenated analogs. QSAR analysis indicated neither the first electron transfer nor N-O bond cleavage is the rate-limiting step. Calculations of the atomic spin densities of the anionic N-oxides confirmed the extensive delocalization between the aromatic ring and the side chain, suggesting complex formation can significantly affect the reduction kinetics. Our results suggest the complexation facilitated N-oxide reduction by Fe(II)-tiron involves a free radical mechanism, and the subsequent deoxygenation might also benefit from the weak complexation of Fe(II) with the N-oxide O atom.

Silica-Based, Hyper-Crosslinked Acid Stable Stationary Phases for High Performance Liquid Chromatography

PubMed Central

Zhang, Yu; Luo, Hao; Carr, Peter W.

2011-01-01

A new family of Hyper-Crosslinked (HC) phases has been recently introduced for use under very aggressive acid conditions including those encountered in ultra-fast, high temperature Two-Dimensional Liquid Chromatography (2DLC). This type of stationary phase showed significantly enhanced acid and thermal stability compared to the most acid stable, commercial RPLC phases. In addition, the use of “orthogonal” chemistry to make surface-confined polymer networks ensures good reproducibility and high efficiency. One of the most interesting features of the HC phases is the ability to derivatize the surface aromatic groups with various functional groups. This led to the development of a family of hyper-crosslinked phases possessing a wide variety of chromatographic selectivities by attaching hydrophobic (e.g. –C8), ionizable (e.g. -COOH, -SO3H), aromatic (e.g. –toluene) or polar (e.g. -OH) species to the aromatic polymer network. HC reversed phases with various degrees of hydrophobicity and mixed-mode HC phases with added strong and weak cation exchange sites have been synthesized, characterized and applied. These silica-based acid-stable HC phases, with their attractive chromatographic properties, should be very useful in the separations of bases or biological analytes in acidic media, especially at elevated temperatures. This work reviews the prior research on HC phases and introduces a novel HC phase made by alternative chemistry. PMID:21906745

Crystal structures of substrate-free and retinoic acid-bound cyanobacterial cytochrome P450 CYP120A1.

PubMed

Kühnel, Karin; Ke, Na; Cryle, Max J; Sligar, Stephen G; Schuler, Mary A; Schlichting, Ilme

2008-06-24

The crystal structures of substrate-free and all-trans-retinoic acid-bound CYP120A1 from Synechocystis sp. PCC 6803 were determined at 2.4 and 2.1 A resolution, respectively, representing the first structural characterization of a cyanobacterial P450. Features of CYP120A1 not observed in other P450 structures include an aromatic ladder flanking the channel leading to the active site and a triple-glycine motif within SRS5. Using spectroscopic methods, CYP120A1 is shown to bind 13-cis-retinoic acid, 9-cis-retinoic acid, and retinal with high affinity and dissociation constants of less than 1 microM. Metabolism of retinoic acid by CYP120A1 suggests that CYP120A1 hydroxylates a variety of retinoid derivatives in vivo. On the basis of the retinoic acid-bound CYP120A1 crystal structure, we propose that either carbon 2 or the methyl groups (C16 or C17) of the beta-ionone ring are modified by CYP120A1.

Self-assembly of chiral (1R,2S)-ephedrine and (1S,2S)-pseudoephedrine into low-dimensional aluminophosphate materials driven by their amphiphilic nature.

PubMed

Bernardo-Maestro, Beatriz; Garrido-Martín, Elisa; López-Arbeloa, Fernando; Pérez-Pariente, Joaquín; Gómez-Hortigüela, Luis

2018-03-28

In an attempt to promote the crystallization of chiral inorganic frameworks, we explore the ability of chiral (1R,2S)-ephedrine and its diastereoisomer (1S,2S)-pseudoephedrine to act as organic building blocks for the crystallization of hybrid organo-inorganic aluminophosphate frameworks in the presence of fluoride. These molecules were selected because of their particular molecular asymmetric structure, which enables a rich supramolecular chemistry and a potential chiral recognition phenomenon during crystallization. Up to four new low-dimensional materials have been produced, wherein the organic molecules form an organic bilayer in-between the inorganic networks. We analyze by molecular simulations the trend of these chiral molecules to form these types of framework, which is directly related to their amphiphilic nature that triggers a strong self-assembly through hydrophobic interactions between aromatic rings and hydrophilic interactions with the fluoro-aluminophosphate inorganic units. Such a self-assembly process is strongly dependent on the concentration of the organic molecules.

Influence of biopolymers on the solubility of branched-chain amino acids and stability of their solutions.

PubMed

Hong, Chi Rac; Lee, Gyu Whan; Paik, Hyun-Dong; Chang, Pahn-Shick; Choi, Seung Jun

2018-01-15

This study confirmed the possibility of biopolymer-type stabilizers to increase the saturation concentration of branched-chain amino acids by preventing their crystallization/precipitation. Although microfluidization increased the initial solubility, it failed to increase the saturation concentration of the branched-chain amino acids. The saturation concentration of the branched-chain amino acids increased from 3.81% to 4.42% and 4.85% after the incorporation of food hydrocolloids and proteins, respectively. However, the branched-chain amino acids:stabilizer ratio did not affect the solubility. In the case of food hydrocolloid-based solutions, crystal formation and growth of branched-chain amino acids occurred during storage, resulting in the precipitation of branched-chain amino acid crystals. However, food proteins effectively increased the stability of the solubilized branched-chain amino acids. The improved solubility and stability of the solubilized branched-chain amino acids could be attributed to interactions between the functional groups (carboxyl, amine, sulfate, aliphatic, aromatic, etc.) of the stabilizer and the branched-chain amino acid molecules. Copyright © 2017 Elsevier Ltd. All rights reserved.

The strength of a calcified tissue depends in part on the molecular structure and organization of its constituent mineral crystals in their organic matrix

NASA Technical Reports Server (NTRS)

Landis, W. J.

1995-01-01

High-voltage electron-microscopic tomographic (3D) studies of the ultrastructural interaction between mineral and organic matrix in a variety of calcified tissues reveal different crystal structural and organizational features in association with their respective organic matrices. In brittle or weak pathologic or ectopic calcifications, including examples of osteogenesis imperfecta, calciphylaxis, calcergy, and dermatomyositis, hydroxyapatite crystals occur in various sizes and shapes and are oriented and aligned with respect to collagen in a manner which is distinct from that found in normal calcified tissues. A model of collagen-mineral interaction is proposed which may account for the observed crystal structures and organization. The results indicate that the ultimate strength, support, and other mechanical properties provided by a calcified tissue are dependent in part upon the molecular structure and arrangement of its constituent mineral crystals within their organic matrix.

Conformational dimorphism of isochroman-1-ones in the solid state

NASA Astrophysics Data System (ADS)

Babjaková, Eva; Hanulíková, Barbora; Dastychová, Lenka; Kuřitka, Ivo; Nečas, Marek; Vícha, Robert

2014-12-01

Isochroman-1-one derivatives, which are relatives of coumarins, display a broad spectrum of biological activity; therefore, these derivatives attract the attention of chemists. A series of new isochroman-1-ones were prepared by the reaction of benzyl-derived Grignard reagents with acyl chlorides. All of the prepared compounds were characterized using single-crystal X-ray diffraction as well as FT-IR, NMR and MS techniques. Single crystal X-ray diffraction analysis revealed that the isochromanones can adopt two distinct conformations in the solid state. For one of the compounds, two polymorphs with unique forms crystallized separately under different temperatures. The packing of all of the examined crystals is stabilized via weak intramolecular C-H⋯π and/or C-H⋯O interactions. Although the closed conformer was predominantly found in the actual crystals, the open conformer is thermochemically more stable for all of the examined compounds according to DFT calculations.

Highly Efficient and Simple Route to Synthesize N-(4-Acetylphenyl)-4-chlorobenzenesulfonamide and Its Crystal Structure

NASA Astrophysics Data System (ADS)

Kobkeatthawin, T.; Chantrapromma, S.; Chidan Kumar, C. S.; Fun, H.-K.

2017-12-01

The one-pot synthesis of N-(4-acetylphenyl)-4-chlorobenzenesulfonamide under base conditions is carried out. The present method offers several advantages such as excellent yields, short reaction times and high purity. The chemical structure was elucidated using 1H-NMR, FT-IR and UV-Vis spectroscopy. The crystal structure of the substance was determined by single crystal X-ray structure analysis. The molecule is in a V-shape. The two substituted benzene rings make the dihedral angle of 84.31(9)°. In the crystal packing, the molecules are linked by N-H···O and C-H···O hydrogen bonds into double chains along the b-axis. The crystal is further stabilized by weak C-H···O, C-Cl···π and π···π interactions.

Data on crystal organization in the structure of the Fab fragment from the NIST reference antibody, RM 8671.

PubMed

Gallagher, D T; Karageorgos, I; Hudgens, J W; Galvin, C V

2018-02-01

The reported data describe the crystallization, crystal packing, structure determination and twinning of the unliganded Fab (antigen-binding fragment) from the NISTmAb (standard reference material 8671). The raw atomic coordinates are available as Protein Data Bank structure 5K8A and biological aspects are described in the article, (Karageorgos et al., 2017) [1]. Crystal data show that the packing is unique, and show the basis for the crystal's twinned growth. Twinning is a common and often serious problem in protein structure determination by x-ray crystallography [2]. In the present case the twinning is due to a small deviation (about 0.3 nm) from 4-fold symmetry in the primary intermolecular interface. The deviation produces pseudosymmetry, generating slightly different conformations of the protein, and alternating strong and weak forms of key packing interfaces throughout the lattice.

The strength of a calcified tissue depends in part on the molecular structure and organization of its constituent mineral crystals in their organic matrix.

PubMed

Landis, W J

1995-05-01

High-voltage electron-microscopic tomographic (3D) studies of the ultrastructural interaction between mineral and organic matrix in a variety of calcified tissues reveal different crystal structural and organizational features in association with their respective organic matrices. In brittle or weak pathologic or ectopic calcifications, including examples of osteogenesis imperfecta, calciphylaxis, calcergy, and dermatomyositis, hydroxyapatite crystals occur in various sizes and shapes and are oriented and aligned with respect to collagen in a manner which is distinct from that found in normal calcified tissues. A model of collagen-mineral interaction is proposed which may account for the observed crystal structures and organization. The results indicate that the ultimate strength, support, and other mechanical properties provided by a calcified tissue are dependent in part upon the molecular structure and arrangement of its constituent mineral crystals within their organic matrix.

The transformation of magnetite to hematite and its influence on the rheology of iron oxide rock

NASA Astrophysics Data System (ADS)

Lagoeiro, Leonardo; Barbosa, Paola; Goncalves, Fabio; Rodrigues, Carlos

2013-04-01

Phase transformation is an important process for strain localization after the initiation of ductile shear zones. In polyphase aggregates one important aspect to consider is likely to be the interconnectivity of weak phase after the transformation of the load-bearing framework grains. However the physical processes involved in that transition is not well understood, partially because the microstructures of the initial weakening are generally obliterated by subsequent deformation. Iron oxide-quartz rocks from paleoproterozoic Iron Formations in southern Brazil preserve microstructures that allow a good insight into the evolution of the deformation mechanisms and fabrics during the transition from a load-bearing framework (magnetite) to an interconnected weak phase (hematite). We conducted microstructural and textural analyses of aggregates of magnetite and hematite combining observations in an optical microscope and measurements in the electron back-scatter diffraction (EBSD). The samples were cut parallel to the mineral lineation (the X-axis) and perpendicular to the foliation. Our goal was to understand the evolution of fabric and texture of the iron oxide aggregates caused by the change in deformation behavior resulting from the phase transformation. The studied samples consist mainly of aggregates of magnetite and hematite in a varied proportions. Samples that preserve the early microstructures consist in aggregate of magnetite grains of varied sizes. The grains are partially transformed to hematite along {111} planes but no foliation is observed in the samples. Basically the samples consist of grains of irregular shapes and a weak or absent crystallographic preferred orientation. The newly transformed hematite crystals share the (0001) planes and directions <11-20> with planes {111} and directions <110> of magnetite grains. Other samples present relicts of initial magnetite grains surrounded by a matrix of tabular to platy hematite crystals. The matrix show a preferred orientation of hematite grains. Close to the magnetite, hematite crystals show crystallographic relationship similar to those observed inside the magnetite crystals showing a good match in crystallographic planes and directions. However away from the magnetite crystals hematite of the matrix tend to show a more independent crystallographic orientation with respect to the magnetite grains. The poles to the basal planes of hematite distributed in a small circle centered around the Z-axis and the crystallographic directions <11-20> spread in a wide angle along the foliation plane. In samples where no crystal of magnetite grains is observed only platy hematite with a strong shape preferred orientation occur. Their basal planes show a strong concentration around the foliation pole contrasting to the more dispersed distribution around the Z-axis found in the samples with magnetite relicts.The directions <11-20> also distributed along the foliation planes in platy hematite samples but with a narrower angles than those of samples with magnetite relicts. The progressive transformation of magnetite to hematite led to a change in the iron formation rock fabrics from an isotropic distribution of a load-supporting magnetite to an interconnected weak platy hematite forming a strongly anisotropic fabric. The hard magnetite behaves in a brittle manner with a very limited operation of slip along the main crystallographic planes. The microfracturing creates an easy path for oxidation and transformation of magnetite. The newly formed hematite grains behave in a ductile manner and form a matrix of strongly oriented crystals. The deformation mechanisms change from the microfracturing of the harder magnetite phase to a crystal plastic deformation of the softer hematite platy grains through slip along their basal planes.

Magnetic susceptibility and AMS of the Bushveld alkaline granites, South Africa

NASA Astrophysics Data System (ADS)

Ferré, Eric C.; Wilson, Jeff; Gleizes, Gérard

1999-06-01

The Bushveld Complex in South Africa includes one of the world's largest anorogenic alkaline granite intrusions (66,000 km 2). The granite forms a composite laccolith, of 350 × 250 km in area and about 2 km in thickness, which was emplaced at about 5 km depth into sediments overlying the Kaapvaal craton, at 2054 Ma. The Bushveld granite and its roof-rocks have long been mined for Sn, W and F. The Bushveld granites have high magnetic susceptibilities ( Km from 1000 to 4000 μSI), and a quantitative model is presented, suggesting that susceptibility fabrics are primarily carried by ferromagnetic minerals. The measured AMS foliations coincide with observed subhorizontal mineral lineations and compositional layering. Magnetic lineation trends vary considerably within the horizontal plane. The existence of a weak planar fabric and, an almost absent linear component may reflect (a) laccolithic emplacement by roof uplift, causing flattening magmatic fabrics, or (b) emplacement of largely crystal-free magma crystallizing in-situ and developing horizontal compositional layering from thermal chemical diffusion fronts and gravity-driven mechanisms. Weak magnétic fabrics, like those identified in the Bushveld granites require specific sampling schemes and procedures, in addition to rigorous constraint of magnetic mineralogy and crystallization sequence.

Selecting the spin crossover profile with controlled crystallization of mononuclear Fe(iii) polymorphs.

PubMed

Vicente, Ana I; Ferreira, Liliana P; Carvalho, Maria de Deus; Rodrigues, Vítor H N; Dîrtu, Marinela M; Garcia, Yann; Calhorda, Maria José; Martinho, Paulo N

2018-05-08

Two polymorphic species of the [Fe(5-Br-salEen)2]ClO4 compound were obtained, each of them being selectively recovered after evaporation of the solvent at a controlled rate. While polymorph 1a is formed during slow evaporation, fast evaporation favors polymorph 1b. The importance of the evaporation rate was recognized after detailed studies of the reaction temperature, solvent evaporation rate and crystallization temperature effects. The complex in the new polymorphic form 1a showed an abrupt spin crossover at 172 K with a small 1 K hysteresis window and over a narrow 10 K range. 57Fe Mössbauer spectroscopy and differential scanning calorimetry, complemented by X-ray studies for both the high-spin and low-spin forms, were used to further characterize the new polymorphic phase 1a. Both polymorphs are based on the same Fe(iii) complex cation hydrogen bonded to the perchlorate anion. These units are loosely bound in the crystals via weak interactions. In the new polymorph 1a, the hydrogen bonds are stronger, while the weak hydrogen and halogen bonds, as well as π-π stacking, create a cooperative network, not present in 1b, responsible for the spin transition profile.

Coexistence of ultra-long spin relaxation time and coherent charge transport in organic single-crystal semiconductors

NASA Astrophysics Data System (ADS)

Tsurumi, Junto; Matsui, Hiroyuki; Kubo, Takayoshi; Häusermann, Roger; Mitsui, Chikahiko; Okamoto, Toshihiro; Watanabe, Shun; Takeya, Jun

2017-10-01

Coherent charge transport can occur in organic semiconductor crystals thanks to the highly periodic electrostatic potential--despite the weak van der Waals bonds. And as spin-orbit coupling is usually weak in organic materials, robust spin transport is expected, which is essential if they are to be exploited for spintronic applications. In such systems, momentum relaxation occurs via scattering events, which enables an intrinsic mobility to be defined for band-like charge transport, which is >10 cm2 V-1 s-1. In contrast, there are relatively few experimental studies of the intrinsic spin relaxation for organic band-transport systems. Here, we demonstrate that the intrinsic spin relaxation in organic semiconductors is also caused by scattering events, with much less frequency than the momentum relaxation. Magnetotransport measurements and electron spin resonance spectroscopy consistently show a linear relationship between the two relaxation times over a wide temperature range, clearly manifesting the Elliott-Yafet type of spin relaxation mechanism. The coexistence of an ultra-long spin lifetime of milliseconds and the coherent band-like transport, resulting in a micrometre-scale spin diffusion length, constitutes a key step towards realizing spintronic devices based on organic single crystals.

Separate spatial Holographic-Hamiltonian soliton pairs and solitons interaction in an unbiased series photorefractive crystal circuit.

PubMed

Cai, Xin; Liu, Jinsong; Wang, Shenglie

2009-02-16

This paper presents calculations for an idea in photorefractive spatial soliton, namely, a dissipative holographic soliton and a Hamiltonian soliton in one dimension form in an unbiased series photorefractive crystal circuit consisting of two photorefractive crystals of which at least one must be photovoltaic. The two solitons are known collectively as a separate Holographic-Hamiltonian spatial soliton pair and there are two types: dark-dark and bright-dark if only one crystal of the circuit is photovoltaic. The numerical results show that the Hamiltonian soliton in a soliton pair can affect the holographic one by the light-induced current whereas the effect of the holographic soliton on the Hamiltonian soliton is too weak to be ignored, i.e., the holographic soliton cannot affect the Hamiltonian one.

Flexible ferroelectric organic crystals

DOE PAGES

Owczarek, Magdalena; Hujsak, Karl A.; Ferris, Daniel P.; ...

2016-10-13

Flexible organic materials possessing useful electrical properties, such as ferroelectricity, are of crucial importance in the engineering of electronic devices. But, until now, only ferroelectric polymers have intrinsically met this flexibility requirement, leaving small-molecule organic ferroelectrics with room for improvement. Since both flexibility and ferroelectricity are rare properties on their own, combining them in one crystalline organic material is challenging. We report that trisubstituted haloimidazoles not only display ferroelectricity and piezoelectricity-the properties that originate from their non-centrosymmetric crystal lattice-but also lend their crystalline mechanical properties to fine-tuning in a controllable manner by disrupting the weak halogen bonds between the molecules.more » This element of control makes it possible to deliver another unique and highly desirable property, namely crystal flexibility. Moreover, the electrical properties are maintained in the flexible crystals.« less

Hirshfeld surface analyses and crystal structures of supramolecular self-assembly thiourea derivatives directed by non-covalent interactions

NASA Astrophysics Data System (ADS)

Gumus, Ilkay; Solmaz, Ummuhan; Binzet, Gun; Keskin, Ebru; Arslan, Birdal; Arslan, Hakan

2018-04-01

The novel N-(bis(3,5-dimethoxybenzyl)carbamothioyl)-4-R-benzamide (R: H, Cl, CH3 and OCH3) compounds have been synthesized and characterized by FT-IR, 1H NMR and 13C NMR spectroscopy. Their crystal structures were also determined by single-crystal X-ray diffraction studies. Hirshfeld surfaces analysis and their associated two dimensional fingerprint plots of compounds were used as theoretical approach to assess driving force for crystal structure formation via the intermolecular interactions in the crystal lattices of synthesized compounds. The study of X-ray single crystal diffraction and Hirshfeld surfaces analysis of the prepared compounds shows that hydrogen bonding and other weaker interactions such as Nsbnd H⋯S, weak Csbnd H⋯S, Csbnd H⋯O, Csbnd H⋯N and Csbnd H···π intermolecular interactions and π-π stacking, among molecules of synthesized compounds participate in a cooperative way to stabilize the supramolecular structures.

Observation of a quadrupole interaction for cubic imperfections exhibiting a dynamic Jahn-Teller effect.

NASA Technical Reports Server (NTRS)

Herrington, J. R.; Estle, T. L.; Boatner, L. A.

1972-01-01

The observation and interpretation of weak EPR transitions, identified as 'forbidden' transitions, establish the existence of a new type of quadrupole interaction for cubic-symmetry imperfections. This interaction is simply a consequence of the ground-vibronic-state degeneracy. The signs as well as the magnitudes of the quadrupole-coupling coefficients are determined experimentally. These data agree well with the predictions of crystal field theory modified to account for a weak-to-moderate vibronic interaction (i.e., a dynamic Jahn-Teller effect).

The Eckhaus and the Benjamin-Feir instability near a weakly inverted bifurcation

NASA Technical Reports Server (NTRS)

Brand, Helmut R.; Deissler, Robert J.

1991-01-01

We investigate how the criteria for two prototype instabilities in one dimensional pattern forming systems, namely for the Eckhaus instability and for the Benjamin-Feir instability, change as one goes from a continuous bifurcation, to a spatially periodic or spatially and/or time periodic state, to the corresponding weakly inverted, i.e., hysteretic, cases. We also give the generalization to two dimensional patterns in systems with anisotropy as they arise from hydrodynamic instabilities in nematic liquid crystals.

Metamagnetism and weak ferromagnetism in nickel (II) oxalate crystals

NASA Astrophysics Data System (ADS)

Romero-Tela, E.; Mendoza, M. E.; Escudero, R.

2012-05-01

Microcrystals of orthorhombic nickel (II) oxalate dihydrate were synthesized through a precipitation reaction of aqueous solutions of nickel chloride and oxalic acid. Magnetic susceptibility exhibits a sharp peak at 3.3 K and a broad rounded maximum near 43 K. We associated the lower maximum with a metamagnetic transition that occurs when the magnetic field is about ≥ 3.5 T. The maximum at 43 K is typical of 1D antiferromagnets, whereas weak ferromagnetism behavior was observed in the range of 3.3-43 K.

Eckhaus and Benjamin-Feir instabilities near a weakly inverted bifurcation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brand, H.R.; Deissler, R.J.

1992-03-15

We investigate how the criteria for two prototype instabilities in one-dimensional pattern-forming systems, namely for the Eckhaus instability and for the Benjamin-Feir instability, change as one goes from a continuous bifurcation to a spatially periodic or spatially and/or time-periodic state to the corresponding weakly inverted, i.e., hysteretic, cases. We also give the generalization to two-dimensional patterns in systems with anisotropy as they arise, for example, for hydrodynamic instabilities in nematic liquid crystals.

2-[2-(3-Chloro­phen­yl)hydrazinyl­idene]-1,3-diphenyl­propane-1,3-dione

PubMed Central

Bustos, Carlos; Alvarez-Thon, Luis; Cárcamo, Juan-Guillermo; Ibañez, Andrés; Sánchez, Christian

2011-01-01

The mol­ecular structure of the title compound, C21H15ClN2O2, features one strong intra­molecular N—H⋯O resonance-assisted hydrogen bond (RAHB). In the crystal, mol­ecules form inversion-related dimers via pairs of weak inter­molecular N—H⋯O contacts. These dimers are further stabilized via three weak C—H⋯O contacts, developing the three-dimensional structure. PMID:21754825

[4-(All­yloxy)phen­yl](phen­yl)methanone

PubMed Central

D’Vries, Richard F.; Grande, Carlos D.; Chaur, Manuel N.; Ellena, Javier A.; Advincula, Rigoberto C.

2014-01-01

The structure of the title compound, C16H14O2, features a dihedral angle of 54.4 (3)° between the aromatic rings. The allyl group is rotated by 37.4 (4)° relative to the adjacent benzene ring. The crystal packing is characterized by numerous C—H⋯O and C—H⋯π inter­actions. Most of these inter­actions occur in layers along (011). The layers are linked by C—H⋯π inter­actions along [100], forming a three-dimensional network. PMID:25161593

2-Nitro­benzyl 2-chloro­acetate

PubMed Central

Zhu, Kai; Liu, Hui; Wang, Yan-Hua; Han, Ping-Fang; Wei, Ping

2009-01-01

In the mol­ecule of the title compound, C9H8ClNO4, an intra­molecular C—H⋯O inter­action results in the formation of a near-planar (r.m.s. deviation 0.002 Å) five-membered ring, which is oriented at a dihedral angle of 4.07 (4)° with respect to the adjacent aromatic ring. In the crystal structure, inter­molecular C—H⋯O inter­actions link the mol­ecules into a two-dimensional network. PMID:21577790

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Jongbok; Li, Huanbin; Kalin, Alexander J.

Well-defined, fused-ring aromatic oligomers represent promising candidates for the fundamental understanding and application of advanced carbon-rich materials, though bottom-up synthesis and structure–property correlation of these compounds remain challenging. In this work, an efficient synthetic route was employed to construct extended benzo[k]tetraphene-derived oligomers with up to 13 fused rings. The molecular and electronic structures of these compounds were clearly elucidated. Precise correlation of molecular sizes and crystallization dynamics was established, thus demonstrating the pivotal balance between intermolecular interaction and molecular mobility for optimized processing of highly ordered solids of these extended conjugated molecules.

2,6-Bis[1-(2-isopropyl­phenyl­imino)­ethyl]­pyridine

PubMed Central

Agrifoglio, Giuseppe; Reyes, Julian; Atencio, Reinaldo; Briceño, Alexander

2008-01-01

The title compound, C27H31N3, has E substitution at each imine double bond where the two N atoms adopt a trans–trans relationship. The benzene rings are twisted out of the mean plane of the pyridine ring; the mean planes of the aromatic groups are rotated by 63.0 (1) and 72.58 (8)°. The crystal structure is sustained mainly by C—H⋯π and hydro­phobic methyl–methyl inter­actions. PMID:21200845

(2E)-1-(2,6-Dichloro-3-fluoro-phen-yl)-3-phenyl-prop-2-en-1-one.

PubMed

Praveen, Aletti S; Yathirajan, Hemmige S; Narayana, Badiadka; Gerber, Thomas; Hosten, Eric; Betz, Richard

2012-04-01

In the title compound, C(15)H(9)Cl(2)FO, the F atom shows positional disorder over two positions, with site-occupancy factors of 0.747 (4) and 0.253 (4). The dihedral angle between the rings is 86.37 (10)°. In the crystal, C-H⋯O contacts connect the mol-ecules into chains along the c axis. The shortest inter-centroid distance between two aromatic systems is 3.6686 (12) Å and is apparent between the halogenated rings.

Roles of aromatic side chains and template effects of the hydrophobic cavity of a self-assembled peptide nanoarchitecture for anisotropic growth of gold nanocrystals.

PubMed

Tomizaki, Kin-ya; Kishioka, Kohei; Kobayashi, Hiroki; Kobayashi, Akitsugu; Yamada, Naoki; Kataoka, Shunsuke; Imai, Takahito; Kasuno, Megumi

2015-11-15

Gold nanocrystals are promising as catalysts and for use in sensing/imaging systems, photonic/plasmonic devices, electronics, drug delivery systems, and for photothermal therapy due to their unique physical, chemical, and biocompatible properties. The use of various organic templates allows control of the size, shape, structure, surface modification and topology of gold nanocrystals; in particular, currently the synthesis of gold nanorods requires a cytotoxic surfactant to control morphology. To control the shape of gold nanocrystals, we previously demonstrated the de novo design and synthesis of a β-sheet-forming nonapeptide (RU006: Ac-AIAKAXKIA-NH2, X=L-2-naphthylalanine, Nal) and the fabrication of gold nanocrystals by mixing RU006 and HAuCl4 in water. The reaction afforded ultrathin gold nanoribbons 50-100 nm wide, several nanometers high, and microns long. To understand the mechanism underlying gold nanoribbon formation by the RU006 system, we here report (i) the effects of replacement of the Nal aromatic side chain in the RU006 sequence with other aromatic moieties, (ii) the electrochemical properties of aromatic side chains in the de novo designed template peptides to estimate the redox potential and number of electrons participating in the gold crystallization process, and (iii) the stoichiometry of the RU006 system for gold nanoribbon synthesis. Interestingly, RU006 bearing a naphthalene moiety (oxidation peak potential of 1.50 V vs Ag/Ag(+)) and an analog [Ant(6)]-RU006 bearing a bulky anthracene moiety (oxidation peak potential of 1.05 V vs Ag/Ag(+)) allowed the growth of anisotropic (ribbon-like) and isotropic (round) gold nanocrystals, respectively. This trend in morphology of gold nanocrystals was attributed to spatially-arranged hydrophobic cavities sufficiently large to accommodate the gold precursor and to allow directed crystal growth driven by cross-linking reactions among the naphthalene rings. Support for this mechanism was obtained by decreasing the mole fraction of [Ant(6)]-RU006 against the total concentration of [Ant(6)]-RU006 and [Phe(6)]-RU006: absorption spectra similar to that for RU006 were obtained. Differences in the redox properties of the anthracene and naphthalene moieties scarcely affected morphology. We propose that construction of an appropriate hydrophobic cavity is important for templating gold nanocrystal architectures by peptide self-assembly. This mechanism would be applicable for developing simple, low toxicity, mild synthetic methods for constructing metallic nanomaterials for therapeutic use. Copyright © 2015 Elsevier Ltd. All rights reserved.

Structure of aryl O -demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kohler, Amanda C.; Mills, Matthew J. L.; Adams, Paul D.

Some strains of soil and marine bacteria have evolved intricate metabolic pathways for using environmentally derived aromatics as a carbon source. Many of these metabolic pathways go through intermediates such as vanillate, 3-O-methylgallate, and syringate. Demethylation of these compounds is essential for downstream aryl modification, ring opening, and subsequent assimilation of these compounds into the tricarboxylic acid (TCA) cycle, and, correspondingly, there are a variety of associated aryl demethylase systems that vary in complexity. Intriguingly, only a basic understanding of the least complex system, the tetrahydrofolate-dependent aryl demethylase LigM from Sphingomonas paucimobilis, a bacterial strain that metabolizes lignin-derived aromatics, wasmore » previously available. LigM-catalyzed demethylation enables further modification and rin g opening of the single-ring aromatics vanillate and 3-Omethylgallate, which are common byproducts of biofuel production. We characterize aryl O-demethylation by LigM and report its 1.81-Å crystal structure, revealing a unique demethylase fold and a canonical folate-binding domain. Structural homology and geometry optimization calculations enabled the identification of LigM's tetrahydrofolate-binding site and protein-folate interactions. Computationally guided mutagenesis and kinetic analyses allowed the identification of the enzyme's aryl-binding site location and determination of its unique, catalytic tyrosine-dependent reaction mechanism. This work defines LigM as a distinct demethylase, both structurally and functionally, and provides insight into demethylation and its reaction requirements. Our results afford the mechanistic details required for efficient utilization of LigM as a tool for aryl O-demethylation and as a component of synthetic biology efforts to valorize previously underused aromatic compounds.« less

Structure of aryl O -demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism

DOE PAGES

Kohler, Amanda C.; Mills, Matthew J. L.; Adams, Paul D.; ...

2017-04-03

Some strains of soil and marine bacteria have evolved intricate metabolic pathways for using environmentally derived aromatics as a carbon source. Many of these metabolic pathways go through intermediates such as vanillate, 3-O-methylgallate, and syringate. Demethylation of these compounds is essential for downstream aryl modification, ring opening, and subsequent assimilation of these compounds into the tricarboxylic acid (TCA) cycle, and, correspondingly, there are a variety of associated aryl demethylase systems that vary in complexity. Intriguingly, only a basic understanding of the least complex system, the tetrahydrofolate-dependent aryl demethylase LigM from Sphingomonas paucimobilis, a bacterial strain that metabolizes lignin-derived aromatics, wasmore » previously available. LigM-catalyzed demethylation enables further modification and rin g opening of the single-ring aromatics vanillate and 3-Omethylgallate, which are common byproducts of biofuel production. We characterize aryl O-demethylation by LigM and report its 1.81-Å crystal structure, revealing a unique demethylase fold and a canonical folate-binding domain. Structural homology and geometry optimization calculations enabled the identification of LigM's tetrahydrofolate-binding site and protein-folate interactions. Computationally guided mutagenesis and kinetic analyses allowed the identification of the enzyme's aryl-binding site location and determination of its unique, catalytic tyrosine-dependent reaction mechanism. This work defines LigM as a distinct demethylase, both structurally and functionally, and provides insight into demethylation and its reaction requirements. Our results afford the mechanistic details required for efficient utilization of LigM as a tool for aryl O-demethylation and as a component of synthetic biology efforts to valorize previously underused aromatic compounds.« less

Understanding of assembly phenomena by aromatic-aromatic interactions: benzene dimer and the substituted systems.

PubMed

Lee, Eun Cheol; Kim, Dongwook; Jurecka, Petr; Tarakeshwar, P; Hobza, Pavel; Kim, Kwang S

2007-05-10

Interactions involving aromatic rings are important in molecular/biomolecular assembly and engineering. As a consequence, there have been a number of investigations on dimers involving benzene or other substituted pi systems. In this Feature Article, we examine the relevance of the magnitudes of their attractive and repulsive interaction energy components in governing the geometries of several pi-pi systems. The geometries and the associated binding energies were evaluated at the complete basis set (CBS) limit of coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] using a least biased scheme for the given data set. The results for the benzene dimer indicate that the floppy T-shaped structure (center-to-center distance: 4.96 A, with an axial benzene off-centered above the facial benzene) is isoenergetic in zero-point-energy (ZPE) corrected binding energy (D0) to the displaced-stacked structure (vertical interplanar distance: 3.54 A). However, the T-shaped structure is likely to be slightly more stable (D0 approximately equal to 2.4-2.5 kcal/mol) if quadruple excitations are included in the coupled cluster calculations. The presence of substituents on the aromatic ring, irrespective of their electron withdrawing or donating nature, leads to an increase in the binding energy, and the displaced-stacked conformations are more stabilized than the T-shaped conformers. This explains the wide prevalence of displaced stacked structures in organic crystals. Despite that the dispersion energy is dominating, the substituent as well as the conformational effects are correlated to the electrostatic interaction. This electrostatic origin implies that the substituent effect would be reduced in polar solution, but important in apolar media, in particular, for assembling processes.

Extending Halogen-based Medicinal Chemistry to Proteins

PubMed Central

El Hage, Krystel; Pandyarajan, Vijay; Phillips, Nelson B.; Smith, Brian J.; Menting, John G.; Whittaker, Jonathan; Lawrence, Michael C.; Meuwly, Markus; Weiss, Michael A.

2016-01-01

Insulin, a protein critical for metabolic homeostasis, provides a classical model for protein design with application to human health. Recent efforts to improve its pharmaceutical formulation demonstrated that iodination of a conserved tyrosine (TyrB26) enhances key properties of a rapid-acting clinical analog. Moreover, the broad utility of halogens in medicinal chemistry has motivated the use of hybrid quantum- and molecular-mechanical methods to study proteins. Here, we (i) undertook quantitative atomistic simulations of 3-[iodo-TyrB26]insulin to predict its structural features, and (ii) tested these predictions by X-ray crystallography. Using an electrostatic model of the modified aromatic ring based on quantum chemistry, the calculations suggested that the analog, as a dimer and hexamer, exhibits subtle differences in aromatic-aromatic interactions at the dimer interface. Aromatic rings (TyrB16, PheB24, PheB25, 3-I-TyrB26, and their symmetry-related mates) at this interface adjust to enable packing of the hydrophobic iodine atoms within the core of each monomer. Strikingly, these features were observed in the crystal structure of a 3-[iodo-TyrB26]insulin analog (determined as an R6 zinc hexamer). Given that residues B24–B30 detach from the core on receptor binding, the environment of 3-I-TyrB26 in a receptor complex must differ from that in the free hormone. Based on the recent structure of a “micro-receptor” complex, we predict that 3-I-TyrB26 engages the receptor via directional halogen bonding and halogen-directed hydrogen bonding as follows: favorable electrostatic interactions exploiting, respectively, the halogen's electron-deficient σ-hole and electronegative equatorial band. Inspired by quantum chemistry and molecular dynamics, such “halogen engineering” promises to extend principles of medicinal chemistry to proteins. PMID:27875310

Disorder-induced losses in photonic crystal waveguides with line defects.

PubMed

Gerace, Dario; Andreani, Lucio Claudio

2004-08-15

A numerical analysis of extrinsic diffraction losses in two-dimensional photonic crystal slabs with line defects is reported. To model disorder, a Gaussian distribution of hole radii in the triangular lattice of airholes is assumed. The extrinsic losses below the light line increase quadratically with the disorder parameter, decrease slightly with increasing core thickness, and depend weakly on the hole radius. For typical values of the disorder parameter the calculated loss values of guided modes below the light line compare favorably with available experimental results.

Depressed scattering across grain boundaries in single crystal graphene

NASA Astrophysics Data System (ADS)

Chen, Jiao; Jin, Zhi; Ma, Peng; Wang, Hong; Wang, Haomin; Shi, Jingyuan; Peng, Songang; Liu, Xinyu; Ye, Tianchun

2012-10-01

We investigated the electrical and quantum properties of single-crystal graphene (SCG) synthesized by chemical vapor deposition (CVD). Quantum Hall effect and Shubnikov de Hass oscillation, a distinguishing feature of a 2-dimensional electronic material system, were observed during the low temperature transport measurements. Decreased scattering from grain boundaries in SCG was proven through extracting information from weak localization theory. Our results facilitate understanding the electrical properties of SCG grown by CVD and its applications in high speed transistor and quantum devices.

Pyridine-substituted thiazolylphenol derivatives: Synthesis, modeling studies, aromatase inhibition, and antiproliferative activity evaluation.

PubMed

Ertas, Merve; Sahin, Zafer; Berk, Barkin; Yurttas, Leyla; Biltekin, Sevde N; Demirayak, Seref

2018-04-01

Drugs used in breast cancer treatments target the suppression of estrogen biosynthesis. During this suppression, the main goal is to inhibit the aromatase enzyme that is responsible for the cyclization and structuring of estrogens either with steroid or non-steroidal-type inhibitors. Non-steroidal derivatives generally have a planar aromatic structure attached to the triazole ring system in their structures, which inhibits hydroxylation reactions during aromatization by coordinating the heme group. Bioisosteric replacement of the triazole ring system and development of aromatic/cyclic structures of the side chain can increase the selectivity for aromatase enzyme inhibition. In this study, pyridine-substituted thiazolylphenol derivatives, which are non-steroidal triazole bioisosteres, were synthesized using the Hantzsch method, and physical analysis and structural determination studies were performed. The IC 50 values of the compounds were determined by a fluorescence-based aromatase inhibition assay. Then, their antiproliferative activities on the MCF7 and HEK 293 cell lines were evaluated with the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Furthermore, the crystal structure of human placental aromatase was subjected to a series of docking experiments to identify the possible interactions between the most active structure and the active site. Lastly, an in silico technique was performed to analyze and predict the drug-likeness, molecular and ADME properties of the synthesized molecules. © 2018 Deutsche Pharmazeutische Gesellschaft.

Three novel lanthanide metal-organic frameworks (Ln-MOFs) constructed by unsymmetrical aromatic dicarboxylatic tectonics: synthesis, crystal structures and luminescent properties.

PubMed

Wu, Ya-Pan; Li, Dong-Sheng; Xia, Wei; Guo, Sha-Sha; Dong, Wen-Wen

2014-09-11

Three novel Ln(III)-based coordination polymers, {[Ln2 (2,4-bpda)3 (H2O)x]·yH2O}n (Ln = La (III) (1), x = 2, y = 0, Ce (III) (2), Pr (III) (3), x = 4, y = 1) (2,4-H2bpda = benzophenone-2,4-dicarboxylic acid) have been prepared via a solvothermal method and characterized by elemental analysis, IR, and single-crystal X-ray diffraction techniques. Complex 1 exhibits a 3D complicated framework with a new 2-nodal (3,7)-connected (42·5) (44·51·66·8) topology. Complexes 2 and 3 are isomorphous, and feature a 3D 4-connected (65·8)-CdSO4 network. Moreover, solid-state properties such as thermal stabilities and luminescent properties of 1 and 2 were also investigated. Complex 1 crystallized in a monoclinic space group P21/c with a = 14.800 (3), b = 14.500 (3), c = 18.800 (4) Å, β = 91.00 (3), V = 4033.9 (14) Å3 and Z = 4. Complex 2 crystallized in a monoclinic space group Cc with a = 13.5432 (4), b = 12.9981 (4), c = 25.7567 (11) Å, β = 104.028 (4), V = 1374.16 (7) Å3 and Z = 4.

Expression, purification, crystallization and initial crystallographic characterization of the p-hydroxybenzoate hydroxylase from Corynebacterium glutamicum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kwon, Soo-Young; Kang, Beom Sik; Kim, Ghyung-Hwa

2007-11-01

PHBH from Corynebacterium glutamicum was crystallized using the hanging-drop vapour-diffusion method in the presence of NaH{sub 2}PO{sub 4} and K{sub 2}HPO{sub 4} as precipitants. X-ray diffraction data were collected to a maximum resolution of 2.5 Å on a synchrotron beamline. p-Hydroxybenzoate hydroxylase (PHBH) is an FAD-dependent monooxygenase that catalyzes the hydroxylation of p-hydroxybenzoate (pOHB) to 3,4-dihydroxybenzoate in an NADPH-dependent reaction and plays an important role in the biodegradation of aromatic compounds. PHBH from Corynebacterium glutamicum was crystallized using the hanging-drop vapour-diffusion method in the presence of NaH{sub 2}PO{sub 4} and K{sub 2}HPO{sub 4} as precipitants. X-ray diffraction data were collectedmore » to a maximum resolution of 2.5 Å on a synchrotron beamline. The crystal belongs to the hexagonal space group P6{sub 3}22, with unit-cell parameters a = b = 94.72, c = 359.68 Å, γ = 120°. The asymmetric unit contains two molecules, corresponding to a packing density of 2.65 Å{sup 3} Da{sup −1}. The structure was solved by molecular replacement. Structure refinement is in progress.« less

The application of crystal soaking technique to study the effect of zinc and cresol on insulinotropin crystals grown from a saline solution.

PubMed

Kim, Y; Haren, A M

1995-11-01

The purpose of this study is to investigate the effect of zinc and cresol on the structure of insulinotropin crystals. Insulinotropin crystals grown from a saline solution were treated with zinc and/or m-cresol using a crystal soaking technique. The effects of these additives on the crystal structure were investigated with powder X-ray diffraction, photomicrography, and differential scanning calorimetry. The molecular interaction between insulinotropin and m-trifluorocresol in solution was also studied by 19F NMR: The data suggest that the original crystals grown from a saline solution have relatively weak lattice forces. After the addition of m-cresol to the suspension of the insulinotropin crystals, the crystals were immediately rendered amorphous. The m-cresol molecules which diffused into the crystals through solvent channels may have disturbed the lattice interactions that maintain the integrity of the crystal. In contrast, the zinc added to the suspension stabilized the crystal lattice so that the subsequent addition of m-cresol did not alter the integrity of the crystals. A marked increase in melting point (206 degrees versus 184 degrees) and heat of fusion (24.6 J/g versus 1.4 J/g) of the crystals was observed after the treatment with zinc. The solubility of the zinc treated crystals in a pH 7.1 phosphate buffered saline was 1/20 of that of the original crystals. When the insulinotropin crystals were treated with the additives using a crystal soaking method, the crystals underwent structural changes. Zinc stabilized the crystal lattice, and reduced the solubility of the peptide.

New investigations of the guanine trichloro cuprate(II) complex crystal

NASA Astrophysics Data System (ADS)

Fabijanić, Ivana; Matković-Čalogović, Dubravka; Pilepić, Viktor; Ivanišević, Irena; Mohaček-Grošev, Vlasta; Sanković, Krešimir

2017-01-01

Crystals of the guanine trichloro cuprate(II) complex, (HGua)2[Cu2Cl6]·2H2O (HGua = protonated guanine), were prepared and analysed by spectroscopic (IR, Raman) and computational methods. A new single-crystal X-ray diffraction analysis was conducted to obtain data with lower standard uncertainties than those in the previously published structure. Raman and IR spectroscopy and quantum-mechanical analysis gave us new insight into the vibrational states of the (HGua)2[Cu2Cl6]·2H2O crystal. The vibrational spectra of the crystal were assigned by performing a normal coordinate analysis for a free dimer with a centre of inversion as the only symmetry element. The stretching vibration observed at 279 cm-1 in the infrared spectrum corresponds to the N-Cu bond. The noncovalent interaction (NCI) plots and quantum theory of atoms in molecules (QTAIM) analysis of the electron density obtained from periodic DFT calculations elucidated the interactions that exist within the crystal structure. Closed-shell ionic attractions, as well as weak and medium strength hydrogen bonds, prevailed in the crystal packing.

Tunable Fano resonance using weak-value amplification with asymmetric spectral response as a natural pointer

NASA Astrophysics Data System (ADS)

Singh, Ankit K.; Ray, Subir K.; Chandel, Shubham; Pal, Semanti; Gupta, Angad; Mitra, P.; Ghosh, N.

2018-05-01

Weak measurement enables faithful amplification and high-precision measurement of small physical parameters and is under intensive investigation as an effective tool in metrology and for addressing foundational questions in quantum mechanics. Here we demonstrate weak-value amplification using the asymmetric spectral response of Fano resonance as the pointer arising naturally in precisely designed metamaterials, namely, waveguided plasmonic crystals. The weak coupling between the polarization degree of freedom and the spectral response of Fano resonance arises due to a tiny shift in the asymmetric spectral response between two orthogonal linear polarizations. By choosing the preselected and postselected polarization states to be nearly mutually orthogonal, we observe both real and imaginary weak-value amplifications manifested as a spectacular shift of the Fano-resonance peak and narrowing (or broadening) of the resonance linewidth, respectively. The remarkable control and tunability of Fano resonance in a single device enabled by weak-value amplification may enhance active Fano-resonance-based applications in the nano-optical domain. In general, weak measurements using Fano-type spectral response broadens the domain of applicability of weak measurements using natural spectral line shapes as a pointer in a wide range of physical systems.

Low- and high-spin iron (II) complexes studied by effective crystal field method combined with molecular mechanics.

PubMed

Darkhovskii, M B; Pletnev, I V; Tchougréeff, A L

2003-11-15

A computational method targeted to Werner-type complexes is developed on the basis of quantum mechanical effective Hamiltonian crystal field (EHCF) methodology (previously proposed for describing electronic structure of transition metal complexes) combined with the Gillespie-Kepert version of molecular mechanics (MM). It is a special version of the hybrid quantum/MM approach. The MM part is responsible for representing the whole molecule, including ligand atoms and metal ion coordination sphere, but leaving out the effects of the d-shell. The quantum mechanical EHCF part is limited to the metal ion d-shell. The method reproduces with reasonable accuracy geometry and spin states of the Fe(II) complexes with monodentate and polydentate aromatic ligands with nitrogen donor atoms. In this setting a single set of MM parameters set is shown to be sufficient for handling all spin states of the complexes under consideration. Copyright 2003 Wiley Periodicals, Inc.

Crystal structure of (E)-N′-{[(1R,3R)-3-isopropyl-1-methyl-2-oxo­cyclo­pent­yl]methyl­idene}-4-methyl­benzene­sulfono­hydrazide

PubMed Central

Tymann, David; Dragon, Dina Christina; Golz, Christopher; Preut, Hans; Strohmann, Carsten; Hiersemann, Martin

2015-01-01

The title compound, C17H24N2O3S, was synthesized in order to determine the relative configuration of the corresponding β-keto aldehyde. In the U-shaped mol­ecule, the five-membered ring approximates an envelope with the methyl­ene atom adjacent to the quaternary C atom being the flap. The dihedral angles between the four nearly coplanar atoms of the five-membered ring and the flap and the aromatic ring are 38.8 (4) and 22.9 (2)°, respectively. The bond angles around the S atom are in the range 104.11 (16)–119.95 (16)°. In the crystal, mol­ecules are linked via N—H⋯O by hydrogen bonds, forming a chain along the a-axis direction. PMID:25878892

Thermodynamic study of (anthracene + benzo[a]pyrene) solid mixtures

PubMed Central

Rice, James W.; Suuberg, Eric M.

2010-01-01

To characterize better the thermodynamic behavior of a binary polycyclic aromatic hydrocarbon mixture, thermochemical and vapor pressure experiments were used to examine the phase behavior of the {anthracene (1) + benzo[a]pyrene (2)} system. A solid-liquid phase diagram was mapped for the mixture. A eutectic point occurs at x1 = 0.26. The eutectic mixture is an amorphous solid that lacks organized crystal structure and melts between T = (414 and 420) K. For mixtures that contain 0.10 < x1 < 0.90, the enthalpy of fusion is dominated by that of the eutectic. Solid-vapor equilibrium studies show that mixtures of anthracene and benzo[a]pyrene at x1 < 0.10 sublime at the vapor pressure of pure benzo[a]pyrene. These results suggest that the solid-vapor equilibrium of benzo[a]pyrene is not significantly influenced by moderate levels of anthracene in the crystal structure. PMID:20814451

Thermodynamic study on competitive solubilization of cholesterol and beta-sitosterol in bile salt micelles.

PubMed

Matsuoka, Keisuke; Hirosawa, Takashi; Honda, Chikako; Endo, Kazutoyo; Moroi, Yoshikiyo; Shibata, Osamu

2007-07-01

Differences in the preferential solubilization of cholesterol and competitive solubilizates (beta-sitosterol and aromatic compounds) in bile salt micelles was systematically studied by changing the molar ratio of cholesterol to competitive solubilizates. The cholesterol solubility in a mixed binary system (cholesterol and beta-sitosterol) was almost half that of the cholesterol alone system, regardless of the excess beta-sitosterol quantity added. On the other hand, the mutual solubilities of cholesterol and pyrene were not inhibited by their presence in binary mixed crystals. Finally, the cholesterol solubility was measured by changing the alkyl chain length of n-alkylbenzenes. When tetradecylbenzene was added to the bile solution, the cholesterol solubility decreased slightly and was below the original cholesterol solubility. Based on Gibbs energy change (DeltaG degrees ) for solubilization, chemicals that inhibit cholesterol solubility in their combined crystal systems showed a larger negative DeltaG degrees value than cholesterol alone.

4,4′-[Ethylenebis(nitrilomethylidyne)]dibenzonitrile

PubMed Central

Kia, Reza; Fun, Hoong-Kun; Kargar, Hadi

2009-01-01

The mol­ecule of the title Schiff base compound, C18H14N4, lies across a crystallographic inversion centre and adopts an E configuration with respect to the azomethine (C=N) bonds. The imino groups are coplanar with the aromatic rings with a maximum deviation of 0.1574 (12) Å for the N atom. Within the mol­ecule, the planar units are parallel, but extend in opposite directions from the dimethyl­ene bridge. In the crystal structure, pairs of inter­molecular C—H⋯N hydrogen bonds link neighbouring mol­ecules into centrosymmetric dimers with R 2 2(10) ring motifs. An inter­esting feature of the crystal structure is the short inter­molecular C⋯C inter­action with a distance of 3.3821 (13) Å, which is shorter than the sum of the van der Waals radius of a carbon atom. PMID:21582425

N,N′-Bis(3-chloro-2-fluoro­benzyl­idene)ethane-1,2-diamine

PubMed Central

Fun, Hoong-Kun; Kia, Reza

2008-01-01

The mol­ecule of the title centrosymmetric Schiff base compound, C16H12Cl2F2N2, adopts an E configuration with respect to the azomethine C=N bond. The imino groups are coplanar with the aromatic rings. Within the mol­ecule, the planar units are parallel, but extend in opposite directions from the dimethyl­ene bridge. An inter­esting feature of the crystal structure is the short inter­molecular Cl⋯F [3.1747 (5) Å] inter­actions, which are shorter than the sum of the van der Waals radii of these atoms. These inter­actions link neighbouring mol­ecules along the b axis. The crystal structure is further stabilized by π–π inter­actions, with a centroid–centroid distance of 3.5244 (4) Å. PMID:21201124

Nano-structured noble metal catalysts based on hexametallate architecture for the reforming of hydrocarbon fuels

DOEpatents

Gardner, Todd H.

2015-09-15

Nano-structured noble metal catalysts based on hexametallate lattices, of a spinel block type, and which are resistant to carbon deposition and metal sulfide formation are provided. The catalysts are designed for the reforming of hydrocarbon fuels to synthesis gas. The hexametallate lattices are doped with noble metals (Au, Pt, Rh, Ru) which are atomically dispersed as isolated sites throughout the lattice and take the place of hexametallate metal ions such as Cr, Ga, In, and/or Nb. Mirror cations in the crystal lattice are selected from alkali metals, alkaline earth metals, and the lanthanide metals, so as to reduce the acidity of the catalyst crystal lattice and enhance the desorption of carbon deposit forming moieties such as aromatics. The catalysts can be used at temperatures as high as 1000.degree. C. and pressures up to 30 atmospheres. A method for producing these catalysts and applications of their use also is provided.

Investigation of non-covalent and hydrogen bonding interactions on the formation of crystalline networks and supramolecular synthons of a series of α-aminophosphonates: Crystallography and DFT studies

NASA Astrophysics Data System (ADS)

Mirzaei, Masoud; Eshghi, Hossein; Akhlaghi Bagherjeri, Fateme; Mirzaei, Mahdi; Farhadipour, Abolghasem

2018-07-01

α-Aminophosphonates have been rarely explored in the field of crystal engineering. These organic molecules are capable of forming reliable and reproducible supramolecular synthons through non-covalent interactions that can be employed for designing high dimensional supramolecular architectures. Here, we systematically study the influence of conventional and unconventional hydrogen bonding interactions on the formation of these synthons and stability of the crystal packing. The theoretical studies were employed to further confirm the presence of these synthons by comparing the stabilization energies of the dimers and monomers. The dependence of the stability of NH⋯O hydrogen bonds to the aromatic substituents were investigated using NBO analysis. The most stable compound was determined by comparing the HOMO-LUMO energy gap of all compounds and compared with NBO analysis.

Prediction of weak topological insulators in layered semiconductors.

PubMed

Yan, Binghai; Müchler, Lukas; Felser, Claudia

2012-09-14

We report the discovery of weak topological insulators by ab initio calculations in a honeycomb lattice. We propose a structure with an odd number of layers in the primitive unit cell as a prerequisite for forming weak topological insulators. Here, the single-layered KHgSb is the most suitable candidate for its large bulk energy gap of 0.24 eV. Its side surface hosts metallic surface states, forming two anisotropic Dirac cones. Although the stacking of even-layered structures leads to trivial insulators, the structures can host a quantum spin Hall layer with a large bulk gap, if an additional single layer exists as a stacking fault in the crystal. The reported honeycomb compounds can serve as prototypes to aid in the finding of new weak topological insulators in layered small-gap semiconductors.

Enrofloxacinium citrate monohydrate: Preparation, crystal structure, thermal stability and IR-characterization

NASA Astrophysics Data System (ADS)

Golovnev, Nicolay N.; Vasiliev, Alexander D.; Kirik, Sergei D.

2012-08-01

Enrofloxacinium citrate monohydrate (I), CHFNO3+·CHO7-·HO, [C19H22FN3O3 - enrofloxacin, EnrH] has been crystallized from the mutual solution of citric acid and enrofloxacin in ambient conditions. The colorless crystals have been investigated using X-ray single crystal and powder techniques, and characterized by differential scanning calorimetry, thermogravimetry and infrared spectroscopy. The obtained compound can be considered as a salt with enrofloxacinium in the role of a cation and citrate as an anion. The ions ratio equals to 1:1. The compound crystallizes in the triclinic lattice with a = 9.0489(8) Å, b = 9.6531(8) Å, c = 14.913(1) Å, α = 98.813(1)°, β = 92.029(1)°, γ = 91.013(1)°, Z = 2, V = 1286.1(2) Å3, S.G. P1¯. The crystal structure determination reveals the importance of inter- and intramolecular interactions in the crystal formation. The EnrH2+ and HCit molecular ions are packed in alternating layers with water molecules inserted into the citrate layers. A citrate ion in the layer is linked via H-bondings with two adjacent ones and three water molecules. Enrofloxacinium cations are packaged by means of a benched mode and every cation is linked by three intermolecular thymus type H-bondings with nitrogens of adjacent cations and by two links with the oxygen of the citrate ions. The infrared spectra gave the evidence of H-bonding formation in the obtained salt. The π-stacking interactions are observed between the aromatic cycles of the adjacent cations which are located in an antiparallel style in a layer.

On interaction of P-waves with one-dimensional photonic crystal consisting of weak conducting matter and transparent dielectric layers

NASA Astrophysics Data System (ADS)

Yushkanov, A. A.; Zverev, N. V.

2018-03-01

An influence of quantum and spatial dispersion properties of the non-degenerate electron plasma on the interaction of electromagnetic P-waves with one-dimensional photonic crystal consisting of conductor with low carrier electron density and transparent dielectric matter, is studied numerically. It is shown that at the frequencies of order of the plasma frequency and at small widths of the conducting and dielectric layers of the photonic crystal, optical coefficients in the quantum non-degenerate plasma approach differ from the coefficients in the classical electron gas approach. And also, at these frequencies one observes a temperature dependence of the optical coefficients.

Crystal structure determination of new antimitotic agent bis(p-fluorobenzyl)trisulfide.

PubMed

An, Haoyun; Hu, Xiurong; Gu, Jianming; Chen, Linshen; Xu, Weiming; Mo, Xiaopeng; Xu, Wanhong; Wang, Xiaobo; Xu, Xiao

2008-01-01

The purpose of this research was to investigate the physical characteristics and crystalline structure of bis(p-fluorobenzyl)trisulfide, a new anti-tumor agent. Methods used included X-ray single crystal diffraction, X-ray powder diffraction (XRPD), Fourier-transform infrared (FT-IR) spectroscopy, differential scanning calorimetric (DSC) and thermogravimetric (TG) analyses. The findings obtained with X-ray single crystal diffraction showed that a monoclinic unit cell was a = 12.266(1) A, b = 4.7757(4) A, c = 25.510(1) A, beta = 104.25(1) degrees ; cell volume = 1,448.4(2) A(3), Z = 4, and space group C2/c. The XRPD studies of the four crystalline samples, obtained by recrystallization from four different solvents, indicated that they had the same diffraction patterns. The diffraction pattern stimulated from the crystal structure data is in excellent agreement with the experimental results. In addition, the identical FT-IR spectra of the four crystalline samples revealed absorption bands corresponding to S-S and C-S stretching as well as the characteristic aromatic substitution. Five percent weight loss at 163.3 degrees C was observed when TG was used to study the decomposition process in the temperature range of 20-200 degrees C. DSC also allowed for the determination of onset temperatures at 60.4(1)-60.7(3) degrees C and peak temperatures at 62.1(3)-62.4(3) degrees C for the four crystalline samples studied. The results verified that the single crystal structure shared the same crystal form with the four crystalline samples investigated.

Au36(SPh)24 nanomolecules: X-ray crystal structure, optical spectroscopy, electrochemistry, and theoretical analysis.

PubMed

Nimmala, Praneeth Reddy; Knoppe, Stefan; Jupally, Vijay Reddy; Delcamp, Jared H; Aikens, Christine M; Dass, Amala

2014-12-11

The physicochemical properties of gold:thiolate nanomolecules depend on their crystal structure and the capping ligands. The effects of protecting ligands on the crystal structure of the nanomolecules are of high interest in this area of research. Here we report the crystal structure of an all aromatic thiophenolate-capped Au36(SPh)24 nanomolecule, which has a face-centered cubic (fcc) core similar to other nanomolecules such as Au36(SPh-tBu)24 and Au36(SC5H9)24 with the same number of gold atoms and ligands. The results support the idea that a stable core remains intact even when the capping ligand is varied. We also correct our earlier assignment of "Au36(SPh)23" which was determined based on MALDI mass spectrometry which is more prone to fragmentation than ESI mass spectrometry. We show that ESI mass spectrometry gives the correct assignment of Au36(SPh)24, supporting the X-ray crystal structure. The electronic structure of the title compound was computed at different levels of theory (PBE, LDA, and LB94) using the coordinates extracted from the single crystal X-ray diffraction data. The optical and electrochemical properties were determined from experimental data using UV-vis spectroscopy, cyclic voltammetry, and differential pulse voltammetry. Au36(SPh)24 shows a broad electrochemical gap near 2 V, a desirable optical gap of ∼1.75 eV for dye-sensitized solar cell applications, as well as appropriately positioned electrochemical potentials for many electrocatalytic reactions.

Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR

PubMed Central

Fenwick, R. Bryn; van den Bedem, Henry; Fraser, James S.; Wright, Peter E.

2014-01-01

Detailed descriptions of atomic coordinates and motions are required for an understanding of protein dynamics and their relation to molecular recognition, catalytic function, and allostery. Historically, NMR relaxation measurements have played a dominant role in the determination of the amplitudes and timescales (picosecond–nanosecond) of bond vector fluctuations, whereas high-resolution X-ray diffraction experiments can reveal the presence of and provide atomic coordinates for multiple, weakly populated substates in the protein conformational ensemble. Here we report a hybrid NMR and X-ray crystallography analysis that provides a more complete dynamic picture and a more quantitative description of the timescale and amplitude of fluctuations in atomic coordinates than is obtainable from the individual methods alone. Order parameters (S2) were calculated from single-conformer and multiconformer models fitted to room temperature and cryogenic X-ray diffraction data for dihydrofolate reductase. Backbone and side-chain order parameters derived from NMR relaxation experiments are in excellent agreement with those calculated from the room-temperature single-conformer and multiconformer models, showing that the picosecond timescale motions observed in solution occur also in the crystalline state. These motions are quenched in the crystal at cryogenic temperatures. The combination of NMR and X-ray crystallography in iterative refinement promises to provide an atomic resolution description of the alternate conformational substates that are sampled through picosecond to nanosecond timescale fluctuations of the protein structure. The method also provides insights into the structural heterogeneity of nonmethyl side chains, aromatic residues, and ligands, which are less commonly analyzed by NMR relaxation measurements. PMID:24474795

Smart drugs: green shuttle or real drug?

PubMed

Cornara, L; Borghesi, B; Canali, C; Andrenacci, M; Basso, M; Federici, S; Labra, M

2013-11-01

We have combined morphological, molecular, and chemical techniques in order to identify the plant and chemical composition of some last-generation smart drugs, present on the market under the following names: Jungle Mistic Incense, B-52, Blendz, and Kratom 10x. Micromorphological analyses of botanical fragments allowed identification of epidermal cells, stomata, trichomes, starch, crystals, and pollen. DNA barcoding was carried out by the plastidial gene rbcL and the spacer trnH-psbA as universal markers. The combination of morphological and molecular data revealed a mixture of plants from different families, including aromatic species, viz., Lamiaceae and Turneraceae. GC-MS and LC-MS analyses on ethanol or methanol extracts showed the presence of synthetic cannabinoids, including JWH-250 in Jungle, JWH-122 in B-52, and JWH-073 and JWH-018 in Blendz. In Kratom 10x, only the indole alkaloid mitragynine was detected. All the identified synthetic cannabinoids, apart from mitragynine, are under the restriction of law in Italy (TU 309/90). Synthetic cannabinoid crystals were also identified by scanning electron microscopy and energy dispersive X-ray spectroscopy, which also detected other foreign organic chemicals, probably preservatives or antimycotics. In Kratom only leaf fragments from Mitragyna speciosa, containing the alkaloid mitragynine, were found. In the remaining products, aromatic plant species have mainly the role of hiding synthetic cannabinoids, thus acting as a "green shuttle" rather than as real drugs. Such a multidisciplinary approach is proposed as a method for the identification of herbal blends of uncertain composition, which are widely marketed in "headshops" and on the Internet, and represent a serious hazard to public health.

Preparation and evaluation of silica-UIO-66 composite as liquid chromatographic stationary phase for fast and efficient separation.

PubMed

Yan, Zhiming; Zheng, Jiangnan; Chen, Jinfeng; Tong, Ping; Lu, Minghua; Lin, Zian; Zhang, Lan

2014-10-31

A silica-UIO-66 composite was fabricated by a simple hydrothermal method and then applied as liquid chromatographic stationary phase for fast and efficient separation. X-ray diffraction patterns showed the presence of UIO-66 crystals in the silica-UIO-66 composites; while scanning electron microscope (SEM) images revealed that silica-UIO-66 composites were a homogeneous mixture of silica bead and UIO-66 crystals. A variety of substituted aromatics, chlorobenzene compounds and polycyclic aromatic hydrocarbons (PAHs) were used to evaluate the retention properties of the silica-UIO-66 composite packed column. Under the optimized conditions, baseline separation of ethylbenzene (EB) and styrene was obtained with high resolution and short retention time. In addition, the silica-UIO-66 composite packed column also showed some advantages in separation of positional isomers, with which baseline separation of EB and xylene, chlorotoluene and dichlorobenzene isomers was achieved. Moreover, the retention mechanisms of these compounds were also discussed in detail. The relative standard deviations (RSDs) for the separation of EB and xylene, chlorotoluene and dichlorobenzene isomers, as well as EB and styrene were 0.42-0.9%, 1.0-1.9%, 0.75-2.0%, and 0.9-2.1% for the retention time, peak area, peak height, and half peak width, respectively. The column efficiencies for EB, p-chlorotoluene, p-dichlorobenzene and styrene were 8780, 9060, 9990 and 5130 plates/m. The successful applications suggested high potentials of silica-MOFs composite as stationary phase for fast and efficient liquid chromatography separation. Copyright © 2014 Elsevier B.V. All rights reserved.

Superconductivity and valence state in layered single-crystal HfAs1.67Te0.12

NASA Astrophysics Data System (ADS)

Peng, Jian; Yu, Jia; Zhang, Shuai; Chen, Genfu

2018-01-01

We report a detailed study on single crystals of HfAs1.67Te0.12 within a PbFCl-type layered structure. The single crystals of the title compound were successfully grown using a chemical transport reaction. The temperature dependence of electrical resistivity ρ (T), AC magnetic susceptibility {χ }{AC}(T) and specific heat C(T) show a bulk superconductivity with transition temperature T c = 1.67 K. The jump of C/T at T c is comparable to the traditional BCS weak-coupling model. A full H-T phase diagram is established using the results of ρ (T,H) and C(T) under fields, suggesting a rather weak anisotropy [({H}c2\\parallel {ab}(0)/{H}c2\\parallel c(0)] of 1.8 in orbital limit dominated three-dimension-like superconducting system. The mixed-valence states of Hf and As observed in the binding energy from x-ray photoelectron spectroscopy are consistent with the single-crystal x-ray diffraction analysis, indicating that the As-Te disorder prefers to occur in the [HfAs] layer and a large amount of vacancies are present in tetragonal As layer. As compared to HfAs1.7Se0.2 (T c = 0.52 K), a positive-like vacancy effect on T c has been confirmed in HfAs1.67Te0.12. The analysis of the Hall coefficient implies that the hole-type carriers dominate the transport properties, which is in good agreement with the hole pockets at Fermi surface obtained in a band structure calculation. The detailed study of single-crystal HfAs1.67Te0.12 provides a possible candidate to discuss the non-magnetic Kondo effect.

Crystal structure and hydrogen-bonding patterns in 5-fluoro-cytosinium picrate.

PubMed

Mohana, Marimuthu; Thomas Muthiah, Packianathan; McMillen, Colin D

2017-03-01

In the crystal structure of the title compound, 5-fluoro-cytosinium picrate, C 4 H 5 FN 3 O + ·C 6 H 2 N 3 O 7 - , one N heteroatom of the 5-fluoro-cytosine (5FC) ring is protonated. The 5FC ring forms a dihedral angle of 19.97 (11)° with the ring of the picrate (PA - ) anion. In the crystal, the 5FC + cation inter-acts with the PA - anion through three-centre N-H⋯O hydrogen bonds, forming two conjoined rings having R 2 1 (6) and R 1 2 (6) motifs, and is extended by N-H⋯O hydrogen bonds and C-H⋯O inter-actions into a two-dimensional sheet structure lying parallel to (001). Also present in the crystal structure are weak C-F⋯π inter-actions.

Analyses at High Spatial Resolution of Organic Molecules in Extraterrestrial Samples: Two-Step Laser Mass Spectrometry: Search for Polycyclic Aromatic Hydrocarbons in Antarctic Meteorite and Micrometeorite Samples

NASA Technical Reports Server (NTRS)

Zare, Richard N.

1998-01-01

Perhaps the best way to summarize the past three-year grant period is to cite the publications and present a brief synopsis of each: 1. "Indigenous Polycyclic Aromatic Hydrocarbon Molecules in Circumstellar Graphite Grains." Bulk C-12/C-13 isotope ratios observed in some graphite grains extracted from primitive meteorites point strongly to a circumstellar origin. By applying our technique of microprobe two-step laser desorption laser ionization mass spectrometry ((mu)L(sup 2)MS) to individual circumstellar graphite grains we have measured the C-12/C-13 isotope ratio of various polycyclic aromatic hydrocarbons (PAHS) found in these grains. 2. "Deuterium Enrichments in Cluster IDPS," Large enrichments in the D/H isotope ratios in IDPs likely arise from the preservation of presolar molecules. 3. "Evidence for thermalization of surface-disorder molecules at heating rates of 10(exp 8) K/s". A careful study of the ((mu)L(sup 2)MS) of aniline-d(sub 7) from a single-crystal surface (0001) of sapphire (al2O3) shows that all measured properties are consistent with a thermal mechanism for desorption. 4. "Search for past life on Mars; possible relic biogenic activity in Martian meteorite ALH 84001. The authors examined the Martian meteorite ALH 84001 and found several lines of evidence compatible with existence of past primitive (single-cell) life on early Mars. 5. "Microprobe two-step laser mass spectrometry as an analytical tool for meteorite samples". THis paper presents a comprehensive review of (mu)L(sup 2)MS and how this technique can be applied to meteoritic samples. 6. "Indigenous polycyclic aromatic hydrocarbons in circumstellar graphite grains from primitive meteorites". The C-12/C-13 isotope ratios were measured for PAHs in a total of 89 spherical graphite grains. 7. "Observation of indigenous polycyclic aromatic hydrocarbons in "Giant" carbonaceous antarctic micrometeorites." The (mu)L(sup 2)MS method was used to establish the nature and distribution of PAHs in fragments of fifteen (approx. 200 microns) carbonaceous antarctic micrometeorites (AMMs). 8. "Evidence for the extraterrestrial origin of polycyclic aromatic hydrocarbons in the Martian meteorite ALH 84001" We have undertaken additional contamination studies of ALH 84001.

Influence of molecular electronic properties on the IR spectra of dimeric hydrogen bond systems: polarized spectra of 2-hydroxybenzothiazole and 2-mercaptobenzothiazole crystals

NASA Astrophysics Data System (ADS)

Flakus, Henryk T.; Miros, Artur; Jones, Peter G.

2002-01-01

We have studied the polarized IR spectra of the hydrogen-bonded molecular crystals of 2-hydroxybenzothiazole (HBT) and 2-mercaptobenzothiazole (MBT). The crystal structure of 2-hydroxybenzothiazole was determined by X-ray diffraction. The polarized spectra of the crystals were measured, in the frequency ranges of the νN-H and νN-D bands, at room temperature, and at 77 K. In both systems an extremely strong H/D isotopic effect in the spectra was observed, involving reduction of the well-developed νN-H band fine structure to a single prominent νN-D line only. The two νN-H bands were also shown to exhibit almost identical properties, band shapes, temperature and dichroic properties included. The spectra were quantitatively reconstituted, along with the strong isotopic effect, when calculated using the 'strong-coupling' theory, assuming the centrosymmetric dimers of HBT or MBT to be the structural units responsible for the crystalline spectral properties. The similarity of the spectra of the two crystalline systems was considered to be a result of longer-distance couplings between the proton vibrations in the dimers, via the aromatic ring electrons. When investigating the 'residual' νN-H band shapes for crystals isotopically diluted by deuterium, we observed some 'self-organization' effects in the spectra, indicating the energetically favored presence of two identical hydrogen isotopes in each hydrogen bond dimer.

Nonlinear optical and electroabsorption spectra of polydiacetylene crystals and films

NASA Astrophysics Data System (ADS)

Mukhopadhyay, D.; Soos, Z. G.

1996-01-01

Vibronic structure of nonlinear optical (NLO) coefficients is developed within the Condon approximation, displaced harmonic oscillators, and crude adiabatic states. The displacements of backbone modes of conjugated polymers are taken from vibrational data on the ground and 1B excited state. NLO resonances are modeled by three excitations and transition moments taken from Pariser-Parr-Pople (PPP) theory and optimized to polydiacetylene (PDA) spectra in crystals and films, with blue-shifted 1B exciton. The joint analysis of third-harmonic-generation, two-photon absorption, and nondegenerate four-wave-mixing spectra of PDA crystals and films shows weak two-photon absorption to 2A below 1B, leading to overlapping resonances in the THG spectrum, strong two-photon absorption to an nA state some 35% above 1B, and weak Raman resonances in nondegenerate FWM spectra. The full π-π* spectrum contributes to Stark shifts and field-induced transitions, as shown by PPP results for PDA oligomers. The Stark shift dominates high-resolution electroabsorption (EA) spectra of PDA crystals below 10 K. The close correspondence between EA and the first-derivative I'(ω) of the linear absorption above the 1B exciton in PDA crystals provides an experimental separation of vibrational and electronic contributions that limits any even-parity state in this 0.5 eV interval. An oscillator-strength sum rule is applied to the convergence of PDA oligomers with increasing length, N, and the crystal oscillator strengths are obtained without adjustable parameters. The sum rule for the 1B exciton implies large transition moments to higher-energy Ag states, whose locations in recent models are contrasted to PPP results. Joint analysis of NLO and EA spectra clarifies when a few electronic excitations are sufficient, distinguishes between vibrational and electronic contributions, and supports similar π-electron interactions in conjugated molecules and polymers.

Graphene-ZIF8 composite material as stationary phase for high-resolution gas chromatographic separations of aliphatic and aromatic isomers.

PubMed

Yang, Xiaohong; Li, Changxia; Qi, Meiling; Qu, Liangti

2016-08-19

This work presents the separation performance of graphene-ZIF8 (G-Z) composite material as stationary phase for capillary gas chromatography (GC). The G-Z stationary phase achieved high column efficiency of 5000 plates/m determined by n-dodecane (k=1.22) at 120°C and showed weakly polar nature. Importantly, it exhibited high selectivity and resolving capability for branched alkane isomers and aromatic positional isomers, showing clear advantages over the reported neat graphene and ZIF8. In addition, it attained high resolution for geometric cis-/trans-isomers. The G-Z column exhibited good column thermal stability up to 300°C and column repeatability with RSD values of retention times in the range of 0.01-0.19% for intra-day, 0.05-0.88% for inter-day and 0.66-5.6% for between-column, respectively, Moreover, the G-Z column was employed for the determination of minor impurity isomers in real reagent samples, which demonstrates its promising potential in GC applications. Copyright © 2016 Elsevier B.V. All rights reserved.

1H NMR based metabolic profiling of eleven Algerian aromatic plants and evaluation of their antioxidant and cytotoxic properties.

PubMed

Brahmi, Nabila; Scognamiglio, Monica; Pacifico, Severina; Mekhoukhe, Aida; Madani, Khodir; Fiorentino, Antonio; Monaco, Pietro

2015-10-01

Eleven Algerian medicinal and aromatic plants (Aloysia triphylla, Apium graveolens, Coriandrum sativum, Laurus nobilis, Lavandula officinalis, Marrubium vulgare, Mentha spicata, Inula viscosa, Petroselinum crispum, Salvia officinalis, and Thymus vulgaris) were selected and their hydroalcoholic extracts were screened for their antiradical and antioxidant properties in cell-free systems. In order to identify the main metabolites constituting the extracts, 1 H NMR-based metabolic profiling was applied. Data obtained emphasized the antiradical properties of T. vulgaris, M. spicata and L. nobilis extracts (RACI 1.37, 0.97 and 0.93, respectively), whereas parsley was the less active as antioxidant (RACI -1.26). When the cytotoxic effects of low and antioxidant doses of each extract were evaluated towards SK-N-BE(2)C neuronal and HepG2 hepatic cell lines, it was observed that all the extracts weakly affected the metabolic redox activity of the tested cell lines. Overall, data strongly plead in favor of the use of these plants as potential food additives in replacement of synthetic compounds. Copyright © 2015 Elsevier Ltd. All rights reserved.

Crystal structure of (E)-4-hy-droxy-N'-(3-meth-oxy-benzyl-idene)benzohydrazide.

PubMed

Chantrapromma, Suchada; Prachumrat, Patcharawadee; Ruanwas, Pumsak; Boonnak, Nawong; Kassim, Mohammad B

2016-09-01

The title compound, C 15 H 14 N 2 O 3 , crystallizes with two independent mol-ecules ( A and B ) in the asymmetric unit that differ in the orientation of the 3-meth-oxy-phenyl group with respect to the methyl-idenebenzohydrazide unit. The dihedral angles between the two benzene rings are 24.02 (10) and 29.30 (9)° in mol-ecules A and B , respectively. In mol-ecule A , the meth-oxy group is twisted slightly relative to its bound benzene ring, with a C meth-yl -O-C-C torsion angle of 14.2 (3)°, whereas it is almost co-planar in mol-ecule B , where the corresponding angle is -2.4 (3)°. In the crystal, the mol-ecules are linked by N-H⋯O, O-H⋯N and O-H⋯O hydrogen bonds, as well as by weak C-H⋯O inter-actions, forming sheets parallel to the bc plane. The N-H⋯O hydrogen bond and weak C-H⋯O inter-action link different mol-ecules ( A ⋯ B ) whereas both O-H⋯N and O-H⋯O hydrogen bonds link like mol-ecules ( A ⋯ A ) and ( B ⋯ B ). Pairs of inversion-related B mol-ecules are stacked approximately along the a axis by π-π inter-actions in which the distance between the centroids of the 3-meth-oxy-phenyl rings is 3.5388 (12) Å. The B mol-ecules also participate in weak C-H⋯π inter-actions between the 4-hy-droxy-phenyl and the 3-meth-oxy-phenyl rings.

Quantitative and qualitative characterization of zigzag spatiotemporal chaos in a system of amplitude equations for nematic electroconvection.

PubMed

Oprea, Iuliana; Triandaf, Ioana; Dangelmayr, Gerhard; Schwartz, Ira B

2007-06-01

It has been suggested by experimentalists that a weakly nonlinear analysis of the recently introduced equations of motion for the nematic electroconvection by M. Treiber and L. Kramer [Phys. Rev. E 58, 1973 (1998)] has the potential to reproduce the dynamics of the zigzag-type extended spatiotemporal chaos and localized solutions observed near onset in experiments [M. Dennin, D. S. Cannell, and G. Ahlers, Phys. Rev. E 57, 638 (1998); J. T. Gleeson (private communication)]. In this paper, we study a complex spatiotemporal pattern, identified as spatiotemporal chaos, that bifurcates at the onset from a spatially uniform solution of a system of globally coupled complex Ginzburg-Landau equations governing the weakly nonlinear evolution of four traveling wave envelopes. The Ginzburg-Landau system can be derived directly from the weak electrolyte model for electroconvection in nematic liquid crystals when the primary instability is a Hopf bifurcation to oblique traveling rolls. The chaotic nature of the pattern and the resemblance to the observed experimental spatiotemporal chaos in the electroconvection of nematic liquid crystals are confirmed through a combination of techniques including the Karhunen-Loeve decomposition, time-series analysis of the amplitudes of the dominant modes, statistical descriptions, and normal form theory, showing good agreement between theory and experiments.

A weak electric field-assisted ultrafast electrical switching dynamics in In3SbTe2 phase-change memory devices

NASA Astrophysics Data System (ADS)

Pandey, Shivendra Kumar; Manivannan, Anbarasu

2017-07-01

Prefixing a weak electric field (incubation) might enhance the crystallization speed via pre-structural ordering and thereby achieving faster programming of phase change memory (PCM) devices. We employed a weak electric field, equivalent to a constant small voltage (that is incubation voltage, Vi of 0.3 V) to the applied voltage pulse, VA (main pulse) for a systematic understanding of voltage-dependent rapid threshold switching characteristics and crystallization (set) process of In3SbTe2 (IST) PCM devices. Our experimental results on incubation-assisted switching elucidate strikingly one order faster threshold switching, with an extremely small delay time, td of 300 ps, as compared with no incubation voltage (Vi = 0 V) for the same VA. Also, the voltage dependent characteristics of incubation-assisted switching dynamics confirm that the initiation of threshold switching occurs at a lower voltage of 0.82 times of VA. Furthermore, we demonstrate an incubation assisted ultrafast set process of IST device for a low VA of 1.7 V (˜18 % lesser compared to without incubation) within a short pulse-width of 1.5 ns (full width half maximum, FWHM). These findings of ultrafast switching, yet low power set process would immensely be helpful towards designing high speed PCM devices with low power operation.

Universal dissymmetry and the origin of biomolecular chirality.

PubMed

Mason, S F

1987-01-01

Handed systems are distributed over four general domains. These span the fundamental particles, the molecular enantiomers, the crystal enantiomorphs, and the spiral galaxies. The characterisation of the molecular enantiomers followed from the identification of the crystal enantiomorphs and revealed a chiral homogeneity in the biomolecules of the organic world. The origin of the homogeneity has been variously ascribed to a universal dissymmetric force, from Pasteur, or to a chance choice of the initial enantiomer perpetuated by the stereoselection of diastereomer production with recycling, from Fischer's "key and lock" hypothesis. The classical chiral fields identified by Curie require a particular time or location on the Earth's surface for a determinate molecular enantioselection, as do the weak charged current agencies of the non-classical weak interaction. The weak neutral current of the electroweak interaction provides a constant and uniform chiral agency which favours both the L-series of amino acids and polypeptides and the parent aldotriose of the D-series of sugars. The enantiomeric bias of the electroweak interaction is small at the molecular level: it may become significant either as a trigger-perturbation guiding the transition from a metastable autocatalytic racemic process to one of the two constituent enantiomeric reaction channels, or by cumulative amplification in a large chirally-homogeneous aggregate of enantiomer units.

Bis(tetra­phenyl­phospho­nium) tetra­chlorido­cobaltate(II)

PubMed Central

Ouahida, Zeghouan; Hadjadj, Nasreddine; Guenifa, Fatiha; Bendjeddou, Lamia; Merazig, Hocine

2014-01-01

The title compound, (C24H20P)2[CoCl4], was prepared under hydro­thermal conditions. In the crystal, the tetra­phenyl­phospho­nium cations are linked by pairs of weak C—H⋯π inter­actions into supra­molecular dimers; the CoII cations lie on twofold rotation axes and the tetra­hedral [CoCl4]2− anions are linked with the tetra­phenyl­phospho­nium cations via weak C—H⋯Cl hydrogen bonds. PMID:24940211

(Z)-3-(1-Chloro-prop-1-en-yl)-2-methyl-1-phenyl-sulfonyl-1H-indole.

PubMed

Umadevi, M; Saravanan, V; Yamuna, R; Mohanakrishnan, A K; Chakkaravarthi, G

2013-11-16

In the title compound, C18H16ClNO2S, the indole ring system forms a dihedral angle of 75.07 (8)° with the phenyl ring. The mol-ecular structure is stabilized by a weak intra-molecular C-H⋯O hydrogen bond. In the crystal, mol-ecules are linked by weak C-H⋯O hydrogen bonds, forming a chain along [10-1]. C-H⋯π inter-actions are also observed, leading to a three-dimensional network.

Shubnikov-de Haas oscillations in bulk ZrT e5 single crystals: Evidence for a weak topological insulator

NASA Astrophysics Data System (ADS)

Lv, Yang-Yang; Zhang, Bin-Bin; Li, Xiao; Zhang, Kai-Wen; Li, Xiang-Bing; Yao, Shu-Hua; Chen, Y. B.; Zhou, Jian; Zhang, Shan-Tao; Lu, Ming-Hui; Li, Shao-Chun; Chen, Yan-Feng

2018-03-01

The study of ZrT e5 crystals is revived because of the recent theoretical prediction of topological phase in bulk ZrT e5 . However, the current conclusions for the topological character of bulk ZrT e5 are quite contradictory. To resolve this puzzle, we here identify the Berry phase on both b - and c planes of high-quality ZrT e5 crystals by the Shubnikov-de-Hass (SdH) oscillation under tilted magnetic field at 2 K. The angle-dependent SdH oscillation frequency, both on b - and c planes of ZrT e5 , demonstrates the two-dimensional feature. However, phase analysis of SdH verifies that a nontrivial π-Berry phase is observed in the c -plane SdH oscillation, but not in the b -plane one. Compared to bulk Fermi surface predicted by the first-principle calculation, the two-dimensional-like behavior of SdH oscillation measured at b plane comes from the bulk electron. Based on these analyses, it is suggested that bulk ZrT e5 at low temperature (˜2 K) belongs to a weak topological insulator, rather than Dirac semimetal or strong topological insulator as reported previously.

Identification of N-ethylmethylamine as a novel scaffold for inhibitors of soluble epoxide hydrolase by crystallographic fragment screening.

PubMed

Amano, Yasushi; Tanabe, Eiki; Yamaguchi, Tomohiko

2015-05-15

Soluble epoxide hydrolase (sEH) is a potential target for the treatment of inflammation and hypertension. X-ray crystallographic fragment screening was used to identify fragment hits and their binding modes. Eight fragment hits were identified via soaking of sEH crystals with fragment cocktails, and the co-crystal structures of these hits were determined via individual soaking. Based on the binding mode, N-ethylmethylamine was identified as a promising scaffold that forms hydrogen bonds with the catalytic residues of sEH, Asp335, Tyr383, and Tyr466. Compounds containing this scaffold were selected from an in-house chemical library and assayed. Although the starting fragment had a weak inhibitory activity (IC50: 800μM), we identified potent inhibitors including 2-({[2-(adamantan-1-yl)ethyl]amino}methyl)phenol exhibiting the highest inhibitory activity (IC50: 0.51μM). This corresponded to a more than 1500-fold increase in inhibitory activity compared to the starting fragment. Co-crystal structures of the hit compounds demonstrate that the binding of N-ethylmethylamine to catalytic residues is similar to that of the starting fragment. We therefore consider crystallographic fragment screening to be appropriate for the identification of weak but promising fragment hits. Copyright © 2015 Elsevier Ltd. All rights reserved.

Novel Cholinesterase Inhibitors Based on O-Aromatic N,N-Disubstituted Carbamates and Thiocarbamates.

PubMed

Krátký, Martin; Štěpánková, Šárka; Vorčáková, Katarína; Švarcová, Markéta; Vinšová, Jarmila

2016-02-11

Based on the presence of carbamoyl moiety, twenty salicylanilide N,N-disubstituted (thio)carbamates were investigated using Ellman's method for their ability to inhibit acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). O-Aromatic (thio)carbamates exhibited weak to moderate inhibition of both cholinesterases with IC50 values within the range of 1.60 to 311.0 µM. IC50 values for BChE were mostly lower than those obtained for AChE; four derivatives showed distinct selectivity for BChE. All of the (thio)carbamates produced a stronger inhibition of AChE than rivastigmine, and five of them inhibited BChE more effectively than both established drugs rivastigmine and galantamine. In general, 5-chloro-2-hydroxy-N-[4-(trifluoromethyl)-phenyl]benzamide, 2-hydroxy-N-phenylbenzamide as well as N-methyl-N-phenyl carbamate derivatives led to the more potent inhibition. O-{4-Chloro-2-[(4-chlorophenyl)carbamoyl]phenyl} dimethylcarbamothioate was identified as the most effective AChE inhibitor (IC50 = 38.98 µM), while 2-(phenylcarbamoyl)phenyl diphenylcarbamate produced the lowest IC50 value for BChE (1.60 µM). Results from molecular docking studies suggest that carbamate compounds, especially N,N-diphenyl substituted representatives with considerable portion of aromatic moieties may work as non-covalent inhibitors displaying many interactions at peripheral anionic sites of both enzymes. Mild cytotoxicity for HepG2 cells and consequent satisfactory calculated selectivity indexes qualify several derivatives for further optimization.

Structure of CPV17 polyhedrin determined by the improved analysis of serial femtosecond crystallographic data

DOE PAGES

Ginn, Helen M.; Messerschmidt, Marc; Ji, Xiaoyun; ...

2015-03-09

The X-ray free-electron laser (XFEL) allows the analysis of small weakly diffracting protein crystals, but has required very many crystals to obtain good data. Here we use an XFEL to determine the room temperature atomic structure for the smallest cytoplasmic polyhedrosis virus polyhedra yet characterized, which we failed to solve at a synchrotron. These protein microcrystals, roughly a micron across, accrue within infected cells. We use a new physical model for XFEL diffraction, which better estimates the experimental signal, delivering a high-resolution XFEL structure (1.75 Å), using fewer crystals than previously required for this resolution. The crystal lattice and proteinmore » core are conserved compared with a polyhedrin with less than 10% sequence identity. We explain how the conserved biological phenotype, the crystal lattice, is maintained in the face of extreme environmental challenge and massive evolutionary divergence. Our improved methods should open up more challenging biological samples to XFEL analysis.« less

Cubic-to-tetragonal structural phase transition in Rb1-xCsxCaF3 solid solutions: Thermal expansion and EPR studies

NASA Astrophysics Data System (ADS)

Lahoz, F.; Villacampa, B.; Alcalá, R.; Marquina, C.; Ibarra, M. R.

1997-04-01

The influence of crystal mixing on the structural phase transitions in Rb1-xCsxCaF3 (0=0.44. This transition shows a weak first-order component in the x=0 and 0.1 samples, which is progressively smeared out for x>0.1, indicating a spatial distribution of the critical temperature in those crystals with high ionic substitution rate. In RbCaF3 , another structural phase transition was observed at 20 K with a thermal hysteresis between 20 and 40 K. This transition has not been found in any of the mixed crystals.

Isogyres - Manifestation of Spin-orbit interaction in uniaxial crystal: A closed-fringe Fourier analysis of conoscopic interference

NASA Astrophysics Data System (ADS)

Samlan, C. T.; Naik, Dinesh N.; Viswanathan, Nirmal K.

2016-09-01

Discovered in 1813, the conoscopic interference pattern observed due to light propagating through a crystal, kept between crossed polarizers, shows isochromates and isogyres, respectively containing information about the dynamic and geometric phase acquired by the beam. We propose and demonstrate a closed-fringe Fourier analysis method to disentangle the isogyres from the isochromates, leading us to the azimuthally varying geometric phase and its manifestation as isogyres. This azimuthally varying geometric phase is shown to be the underlying mechanism for the spin-to-orbital angular momentum conversion observed in a diverging optical field propagating through a z-cut uniaxial crystal. We extend the formalism to study the optical activity mediated uniaxial-to-biaxial transformation due to a weak transverse electric field applied across the crystal. Closely associated with the phase and polarization singularities of the optical field, the formalism enables us to understand crystal optics in a new way, paving the way to anticipate several emerging phenomena.

Isogyres - Manifestation of Spin-orbit interaction in uniaxial crystal: A closed-fringe Fourier analysis of conoscopic interference.

PubMed

Samlan, C T; Naik, Dinesh N; Viswanathan, Nirmal K

2016-09-14

Discovered in 1813, the conoscopic interference pattern observed due to light propagating through a crystal, kept between crossed polarizers, shows isochromates and isogyres, respectively containing information about the dynamic and geometric phase acquired by the beam. We propose and demonstrate a closed-fringe Fourier analysis method to disentangle the isogyres from the isochromates, leading us to the azimuthally varying geometric phase and its manifestation as isogyres. This azimuthally varying geometric phase is shown to be the underlying mechanism for the spin-to-orbital angular momentum conversion observed in a diverging optical field propagating through a z-cut uniaxial crystal. We extend the formalism to study the optical activity mediated uniaxial-to-biaxial transformation due to a weak transverse electric field applied across the crystal. Closely associated with the phase and polarization singularities of the optical field, the formalism enables us to understand crystal optics in a new way, paving the way to anticipate several emerging phenomena.

2-Phenyl-4,5-di-2-pyridyl-1H-imidazole

PubMed Central

Felsmann, Marika; Schindler, Diana; Weber, Edwin

2010-01-01

In the title compound, C19H14N4, which was crystallized from dimethyl sulfoxide, the arene and heterocyclic rings of the lophine analogue framework differ only slightly from coplanarity (dihedral angles range from 8.8 to 20.2°), and intramolecular N—H⋯N and C—H⋯N interactions help to establish the conformation. The crystal packing features a number of weak C—H⋯N, N—H⋯N hydrogen-bond type contacts, and C—H⋯π interactions, leading to the formation of a herringbone structure. PMID:21580039

Trisphenalenyl-based neutral radical molecular conductor.

PubMed

Pal, Sushanta K; Itkis, Mikhail E; Tham, Fook S; Reed, Robert W; Oakley, Richard T; Haddon, Robert C

2008-03-26

We report the preparation, crystallization, and solid-state characterization of the first member of a new family of tris(1,9-disubstituted phenalenyl)silicon neutral radicals. In the solid state, the radical packs as weak partial pi-dimers with intermolecular carbon...carbon contacts that fall at the van der Waals atomic separation. Magnetic susceptibility measurements indicate approximately 0.7 Curie spins per molecule from room temperature down to 50 K, below which antiferromagnetic coupling becomes apparent; the compound has a room-temperature single-crystal conductivity of sigmaRT = 2.4 x 10(-6) S cm(-1).

Enhancement of temporal contrast of high-power laser pulses in an anisotropic medium with cubic nonlinearity

NASA Astrophysics Data System (ADS)

Kuz'mina, M. S.; Khazanov, E. A.

2015-05-01

We consider the methods for enhancing the temporal contrast of super-high-power laser pulses, based on the conversion of radiation polarisation in a medium with cubic nonlinearity. For a medium with weak birefringence and isotropic nonlinearity, we propose a new scheme to enhance the temporal contrast. For a medium with anisotropic nonlinearity, the efficiency of the temporal contrast optimisation is shown to depend not only on the spatial orientation of the crystal and B-integral, but also on the type of the crystal lattice symmetry.

Crystal structure of [Eu(CyMe4-BTBP)2κ2O,O'-(NO3)](NO3)2·n-C8H17OH and its structure in 1-octanol solution.

PubMed

Lundberg, Daniel; Persson, Ingmar; Ekberg, Christian

2013-03-21

The structure of the [Eu(CyMe(4)-BTBP)(2)(NO(3))(n)]((3-n)+) complex in 1-octanol solution and solid state has been determined by EXAFS and X-ray crystallography. The crystal structure shows that 1-octanol binds only to the europium(III)-coordinated BTBP molecules through weak van der Waals forces, making it the first indication of the role of the extraction solvent.

Crystal structure of fenclorim.

PubMed

Kwon, Eunjin; Kim, Jineun; Kang, Gihaeng; Kim, Tae Ho

2015-10-01

In the title compound, C10H6Cl2N2 (systematic name: 4,6-di-chloro-2-phenyl-pyrimidine), which is used commercially as the herbicide safener, fenclorim, the dihedral angle between the di-chloro-pyrimidyl and phenyl rings is 9.45 (10)°. In the crystal, C-H⋯N hydrogen bonds link adjacent mol-ecules, forming chains along the c-axis direction. In addition, weak inter-molecular C-Cl⋯π [3.6185 (10) Å] and π-π [3.8796 (11) Å] inter-actions are present, forming a three-dimensional network.

Magnetic assembly of nonmagnetic particles into photonic crystal structures.

PubMed

He, Le; Hu, Yongxing; Kim, Hyoki; Ge, Jianping; Kwon, Sunghoon; Yin, Yadong

2010-11-10

We report the rapid formation of photonic crystal structures by assembly of uniform nonmagnetic colloidal particles in ferrofluids using external magnetic fields. Magnetic manipulation of nonmagnetic particles with size down to a few hundred nanometers, suitable building blocks for producing photonic crystals with band gaps located in the visible regime, has been difficult due to their weak magnetic dipole moment. Increasing the dipole moment of magnetic holes has been limited by the instability of ferrofluids toward aggregation at high concentration or under strong magnetic field. By taking advantage of the superior stability of highly surface-charged magnetite nanocrystal-based ferrofluids, in this paper we have been able to successfully assemble 185 nm nonmagnetic polymer beads into photonic crystal structures, from 1D chains to 3D assemblies as determined by the interplay of magnetic dipole force and packing force. In a strong magnetic field with large field gradient, 3D photonic crystals with high reflectance (83%) in the visible range can be rapidly produced within several minutes, making this general strategy promising for fast creation of large-area photonic crystals using nonmagnetic particles as building blocks.

A new crystal form of a hyperthermophilic endocellulase

PubMed Central

Kataoka, Misumi; Ishikawa, Kazuhiko

2014-01-01

The hyperthermophilic glycoside hydrolase family endocellulase 12 from the archaeon Pyrococcus furiosus (EGPf; Gene ID PF0854; EC 3.2.1.4) catalyzes the hydrolytic cleavage of the β-1,4-glucosidic linkage in β-glucan in lignocellulose biomass. A crystal of EGPf was previously prepared at pH 9.0 and its structure was determined at an atomic resolution of 1.07 Å. This article reports the crystallization of EGPf at the more physiologically relevant pH of 5.5. Structure determination showed that this new crystal form has the symmetry of space group C2. Two molecules of the enzyme are observed in the asymmetric unit. Crystal packing is weak at pH 5.5 owing to two flexible interfaces between symmetry-related molecules. Comparison of the EGPf structures obtained at pH 9.0 and pH 5.5 reveals a significant conformational difference at the active centre and in the surface loops. The interfaces in the vicinity of the flexible surface loops impact the quality of the EGPf crystal. PMID:25005081

Synthesis, characterization, and application of two Al(OR(F))3 Lewis superacids.

PubMed

Kraft, Anne; Trapp, Nils; Himmel, Daniel; Böhrer, Hannes; Schlüter, Peter; Scherer, Harald; Krossing, Ingo

2012-07-23

We report herein the synthesis and full characterization of the donor-free Lewis superacids Al(OR(F))(3) with OR(F) = OC(CF(3))(3) (1) and OC(C(5)F(10))C(6)F(5) (2), the stabilization of 1 as adducts with the very weak Lewis bases PhF, 1,2-F(2)C(6)H(4), and SO(2), as well as the internal C-F activation pathway of 1 leading to Al(2)(F)(OR(F))(5) (4) and trimeric [FAl(OR(F))(2)](3) (5, OR(F) = OC(CF(3))(3)). Insights have been gained from NMR studies, single-crystal structure determinations, and DFT calculations. The usefulness of these Lewis acids for halide abstractions has been demonstrated by reactions with trityl chloride (NMR; crystal structures). The trityl salts allow the introduction of new, heteroleptic weakly coordinating [Cl-Al(OR(F))(3)](-) anions, for example, by hydride or alkyl abstraction reactions. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

On Spectral Invariance of Single Scattering Albedo for Water Droplets and Ice Crystals at Weakly Absorbing Wavelengths

NASA Technical Reports Server (NTRS)

Marshak, Alexander; Knyazikhin, Yuri; Chiu, J. Christine; Wiscombe, Warren J.

2012-01-01

The single scattering albedo omega(sub O lambda) in atmospheric radiative transfer is the ratio of the scattering coefficient to the extinction coefficient. For cloud water droplets both the scattering and absorption coefficients, thus the single scattering albedo, are functions of wavelength lambda and droplet size r. This note shows that for water droplets at weakly absorbing wavelengths, the ratio omega(sub O lambda)(r)/omega(sub O lambda)(r (sub O)) of two single scattering albedo spectra is a linear function of omega(sub O lambda)(r). The slope and intercept of the linear function are wavelength independent and sum to unity. This relationship allows for a representation of any single scattering albedo spectrum omega(sub O lambda)(r) via one known spectrum omega(sub O lambda)(r (sub O)). We provide a simple physical explanation of the discovered relationship. Similar linear relationships were found for the single scattering albedo spectra of non-spherical ice crystals.

Novel Isoniazid cocrystals with aromatic carboxylic acids: Crystal engineering, spectroscopy and thermochemical investigations

NASA Astrophysics Data System (ADS)

Diniz, Luan F.; Souza, Matheus S.; Carvalho, Paulo S.; da Silva, Cecilia C. P.; D'Vries, Richard F.; Ellena, Javier

2018-02-01

Four novel cocrystals of the anti-tuberculosis drug Isoniazid (INH), including two polymorphs, with the aromatic carboxylic acids p-nitrobenzoic (PNBA), p-cyanobenzoic (PCNBA) and p-aminobenzoic (PABA) were rationally designed and synthesized by solvent evaporation. Aiming to explore the possible supramolecular synthons of this API, these cocrystals were fully characterized by X-ray diffraction (SCXRD, PXRD), spectroscopic (FT-IR) and thermal (TGA, DSC, HSM) techniques. The cocrystal formation was found to be mainly driven by the synthons formed by the pyridine and hydrazide moieties. In both INH-PABA polymorphs, the COOH acid groups are H-bonded to pyridine and hydrazide groups giving rise to the acid⋯pyridine and acid⋯hydrazide heterosynthons. In INH-PNBA and INH-PCNBA cocrystals these acid groups are only related to the pyridine moiety. In addition to the structural study, supramolecular and Hirshfeld surface analysis were also performed based on the structural data. The cocrystals were identified from the FT-IR spectra and their thermal behaviors were studied by a combination of DSC, TGA and HSM techniques.

Two new luminescent Zn(II) compounds constructed from guanazole and aromatic polycarboxylate ligands

NASA Astrophysics Data System (ADS)

Zhao, Haixiang; Dong, Yanli; Liu, Haiping

2016-02-01

Two new Zn(II) compounds, namely [(CH3)2NH2]2n[Zn3(bpt)2(datrz)2]n (1) and [(CH3)2NH2)]n[Zn2(bptc)(datrz)]n·n(H2O) (2) (H3bpt = biphenyl-3,4‧,5-tricarboxylic acid, H4bptc = biphenyl-3,3‧,5,5‧-tetracarboxylic acid, Hdatrz = 3,5-diamino-1,2,4-triazole), have been obtained by the self-assemble reactions of Zn(NO3)2, 3,5-diamino-1,2,4-triazole, aromatic polycarboxylate ligands under solvothermal conditions. Single crystal X-ray structural analyses reveal that both compounds display three-dimensional (3D) frameworks. Compound 1 features a trinodal (3, 4, 6)-connected topological network with the point symbol of {4.62}2{4.64.8}{46.64.85}. Compound 2 displays a binodal (4, 6)-connected topological network with the point symbol of {32.62.72}{34.42.64.75}. In addition, the thermal stabilities and luminescent properties of compounds 1 and 2 were also investigated in the solid state at room temperature.

Synthesis of dicyclopenta[a,e]pentalenes via a molybdenum carbonyl mediated tandem allenic Pauson-Khand reaction and the X-ray crystal structure of a planar dicyclopenta[a,e]pentalene.

PubMed

Cao, Hui; Van Ornum, Scott G; Deschamps, Jeffery; Flippen-Anderson, Judith; Laib, Frank; Cook, James M

2005-01-26

Two 14 pi cross-linked annulenes which belong to the family of dicyclopenta[a,e]pentalenes have been synthesized, 14 pi bis enol triflate ester 27 and the 3,7-diisopropylsilyl substituted 14 pi dicyclopenta[a,e]pentalene 30. The new allenic tandem Pauson-Khand reaction mediated by Mo(CO)(6) was employed as the key process to construct the core of the tetracycles. The two linear dicyclopenta[a,e]pentalenes 27 and 30 underwent significant electronic delocalization, perhaps even aromaticity, as revealed by the X-ray structure of 27. The tetracyclic rings in 27 assumed a flat geometry (Figure 4); the bond lengths of the tetracycle in 27 also fit well into the criteria for aromatic compounds. A comparison of the NMR and UV spectra of both 27 and 30 demonstrated that they both exhibited similar electronic properties, therefore, the purple colored 14 pi cross linked annulene 30 is planar as well as delocalized.

3-Chloro-4-fluoro­anilinium picrate

PubMed Central

Sarojini, Balladka K.; Narayana, Badiadka; Yathirajan, Hemmige S.; Gerber, Thomas; van Brecht, Benjamin; Betz, Richard

2013-01-01

In the title picrate salt of a dihalogenated aniline derivative, C6H6ClF+·C6H2N3O7 −, the intra­cyclic C—C—C angles in the picrate anion cover a broad range [111.95 (12)–125.38 (13)°], while those in the aromatic cation span a much narrower range [118.25 (14)–122.33 (13)°]. In the crystal, classical N—H⋯O hydrogen bonds, as well as C—H⋯O contacts, connect the ions into layers parallel to (001). PMID:23424519

N-[4-Cyano-3-(trifluoro­meth­yl)phen­yl]-2-eth­oxy­benzamide

PubMed Central

Naveen, S.; Basappa; Manjunath, H. R.; Sridhar, M. A.; Shashidhara Prasad, J.; Rangappa, K. S.

2010-01-01

In the title compound, C17H13F3N2O2, the two aromatic rings are essentially coplanar, forming a dihedral angle of 2.78 (12)°. The non-H atoms of the eth­oxy group are coplanar with the attached ring [maximum deviation = 0.271 (3) Å]. An intra­molecular N—H⋯O hydrogen bond occurs. In the crystal structure, mol­ecules are linked by inter­molecular C—H⋯N and C—H⋯F hydrogen bonds. PMID:21587782

N,N′-Bis(3,5-dichloro­benzyl­idene)­ethane-1,2-diamine

PubMed Central

Fun, Hoong-Kun; Kia, Reza

2008-01-01

The mol­ecule of the title Schiff base compound, C16H12Cl4N2, lies across an inversion centre and adopts an E configuration with respect to the azomethine C=N bond. The imine groups are coplanar with the aromatic rings. Within the mol­ecule, the planar units are parallel but extend in opposite directions from the dimethyl­ene bridge. In the crystal structure, mol­ecules are linked together by inter­molecular C—H⋯Cl hydrogen bonds along the a axis. PMID:21580993

2,3-Dimethyl-6-nitro-2H-indazole

PubMed Central

Chen, Yan; Fang, Zheng; Wei, Ping

2009-01-01

In the mol­ecule of the title compound, C9H9N3O2, the indazole ring system is almost planar [maximum deviation = 0.019 (3) Å for the C atom bearing the nitro group]. In the crystal structure, inter­molecular C—H⋯O inter­actions link the mol­ecules into centrosymmetric dimers, forming R 2 2(18) ring motifs. Aromatic π–π contacts between indazole rings [centroid–centroid distances = 3.632 (1) and 3.705 (1) Å] may further stabilize the structure. PMID:21583483

Arctigenin: a lignan from Arctium lappa.

PubMed

Gao, Haiyan; Li, Guanglei; Zhang, Junhe; Zeng, Jie

2008-07-19

The title compound {systematic name: (3R-trans)-4-[(3,4-dimethoxy-phen-yl)meth-yl]-3-[(4-hydr-oxy-3-methoxy-phen-yl)meth-yl]-4,5-dihydrofuran-2(3H)-one}, C(21)H(24)O(6), has a dibenz-yl-butyrolactone skeleton. The two aromatic rings are inclined at a dihedral angle of 68.75 (7)° with respect to each other. The lactone ring adopts an envelope conformation. A series of O-H⋯O and C-H⋯O hydrogen bonds contribute to the stabilization of the crystal packing. The absolute configuration was assigned on the basis of the published literature.

(Carbonato-κO,O')bis-(1,10-phenan-throline-κN,N')cobalt(III) nitrate monohydrate.

PubMed

Andaç, Omer; Yolcu, Zuhal; Büyükgüngör, Orhan

2009-12-12

The crystal structure of the title compound, [Co(CO(3))(C(12)H(8)N(2))(2)]NO(3)·H(2)O, consists of Co(III) complex cations, nitrate anions and uncoordinated water mol-ecules. The Co(III) cation is chelated by a carbonate anion and two phenanthroline ligands in a distorted octa-hedral coordination geometry. A three-dimensional supra-molecular structure is formed by O-H⋯O and C-H⋯O hydrogen bonding, C-H⋯π and aromatic π-π stacking [centroid-centroid distance = 3.995 (1)Å] inter-actions.

Glassy phases and driven response of the phase-field-crystal model with random pinning.

PubMed

Granato, E; Ramos, J A P; Achim, C V; Lehikoinen, J; Ying, S C; Ala-Nissila, T; Elder, K R

2011-09-01

We study the structural correlations and the nonlinear response to a driving force of a two-dimensional phase-field-crystal model with random pinning. The model provides an effective continuous description of lattice systems in the presence of disordered external pinning centers, allowing for both elastic and plastic deformations. We find that the phase-field crystal with disorder assumes an amorphous glassy ground state, with only short-ranged positional and orientational correlations, even in the limit of weak disorder. Under increasing driving force, the pinned amorphous-glass phase evolves into a moving plastic-flow phase and then, finally, a moving smectic phase. The transverse response of the moving smectic phase shows a vanishing transverse critical force for increasing system sizes.

Chiral lyotropic chromonic liquid crystals composed of disodium cromoglycate doped with water-soluble chiral additives.

PubMed

Shirai, Tatsuya; Shuai, Min; Nakamura, Keita; Yamaguchi, Akihiro; Naka, Yumiko; Sasaki, Takeo; Clark, Noel A; Le, Khoa V

2018-02-28

We investigated the pitches of cholesteric liquid crystals prepared by mixing disodium cromoglycate (DSCG) in water with 5 different water-soluble chiral additives. The measurements are based on the Grandjean-Cano wedge cell method. Overall, the twisting effect is weak, and the shortest pitch of 2.9 ± 0.2 μm is obtained using trans-4-hydroxy-l-proline, by which the cholesteric sample is iridescent at certain viewing angles. Freeze-fracture transmission electron microscopy (FFTEM) was also performed for the first time on both the nematic and cholesteric phases, revealing that stacked chromonic aggregates are very long, up to a few hundred nm, which explains why cholesteric chromonic liquid crystals hardly have pitches in the visible wavelength region.

Thermal expansion and elastic anisotropy in single crystal Al2O3 and SiC reinforcements

NASA Technical Reports Server (NTRS)

Salem, Jonathan A.; Li, Zhuang; Bradt, Richard C.

1994-01-01

In single crystal form, SiC and Al2O3 are attractive reinforcing components for high temperature composites. In this study, the axial coefficients of thermal expansion and single crystal elastic constants of SiC and Al2O3 were used to determine their coefficients of thermal expansion and Young's moduli as a function of crystallographic orientation and temperature. SiC and Al2O3 exhibit a strong variation of Young's modulus with orientation; however, their moduli and anisotropies are weak functions of temperature below 1000 C. The coefficients of thermal expansion exhibit significant temperature dependence, and that of the non-cubic Al2O3 is also a function of crystallographic orientation.

Band splitting in Cd3As2 measured by magnetotransport

NASA Astrophysics Data System (ADS)

Desrat, W.; Krishtopenko, S. S.; Piot, B. A.; Orlita, M.; Consejo, C.; Ruffenach, S.; Knap, W.; Nateprov, A.; Arushanov, E.; Teppe, F.

2018-06-01

Magnetotransport measurements have been performed on (112)-oriented bulk Cd3As2 samples with in situ rotation at low temperature. The frequency analysis of the Shubnikov-de Haas oscillations reveals two weakly separated frequencies arising from two Fermi ellipsoids. The angle dependence of these frequencies is fitted by an analytical expression that we derived for any magnetic field orientation. It is based on an 8 ×8 k .p model which includes the spin-orbit coupling, the crystal field splitting due to tetragonal distortion, and the additional band splitting occurring in noncentrosymmetric crystals. This band splitting is evaluated to a finite value of 30 meV, demonstrating the absence of inversion symmetry in our Cd3As2 crystal.

All-optical switch based on doped graphene quantum dots in a defect layer of a one-dimensional photonic crystal.

PubMed

Sahrai, Mostafa; Abbasabadi, Majid

2018-01-20

We discuss the light pulse propagation in a one-dimensional photonic crystal doped by graphene quantum dots in a defect layer. The graphene quantum dots behave as a three-level quantum system and are driven by three coherent laser fields. It is shown that the group velocity of the transmitted and reflected pulses can be switched from subluminal to superluminal light propagation by adjusting the relative phase of the applied fields. Furthermore, it is found that by proper choice of the phase difference between applied fields, the weak probe field amplification is achieved through a one-dimensional photonic crystal. In this way, the result is simultaneous subluminal transmission and reflection.

Crystallization and dynamical arrest of attractive hard spheres.

PubMed

Babu, Sujin; Gimel, Jean-Christophe; Nicolai, Taco

2009-02-14

Crystallization of hard spheres interacting with a square well potential was investigated by numerical simulations using so-called Brownian cluster dynamics. The phase diagram was determined over a broad range of volume fractions. The crystallization rate was studied as a function of the interaction strength expressed in terms of the second virial coefficient. For volume fractions below about 0.3 the rate was found to increase abruptly with increasing attraction at the binodal of the metastable liquid-liquid phase separation. The rate increased until a maximum was reached after which it decreased with a power law dependence on the second virial coefficient. Above a critical percolation concentration, a transient system spanning network of connected particles was formed. Crystals were formed initially as part of the network, but eventually crystallization led to the breakup of the network. The lifetime of the transient gels increased very rapidly over a small range of interaction energies. Weak attraction destabilized the so-called repulsive crystals formed in pure hard sphere systems and shifted the coexistence line to higher volume fractions. Stronger attraction led to the formation of a denser, so-called attractive, crystalline phase. Nucleation of attractive crystals in the repulsive crystalline phase was observed close to the transition.

Field-controllable Spin-Hall Effect of Light in Optical Crystals: A Conoscopic Mueller Matrix Analysis.

PubMed

Samlan, C T; Viswanathan, Nirmal K

2018-01-31

Electric-field applied perpendicular to the direction of propagation of paraxial beam through an optical crystal dynamically modifies the spin-orbit interaction (SOI), leading to the demonstration of controllable spin-Hall effect of light (SHEL). The electro- and piezo-optic effects of the crystal modifies the radially symmetric spatial variation in the fast-axis orientation of the crystal, resulting in a complex pattern with different topologies due to the symmetry-breaking effect of the applied field. This introduces spatially-varying Pancharatnam-Berry type geometric phase on to the paraxial beam of light, leading to the observation of SHEL in addition to the spin-to-vortex conversion. A wave-vector resolved conoscopic Mueller matrix measurement and analysis provides a first glimpse of the SHEL in the biaxial crystal, identified via the appearance of weak circular birefringence. The emergence of field-controllable fast-axis orientation of the crystal and the resulting SHEL provides a new degree of freedom for affecting and controlling the spin and orbital angular momentum of photons to unravel the rich underlying physics of optical crystals and aid in the development of active photonic spin-Hall devices.

Theory of the intermediate stage of crystal growth with applications to insulin crystallization

NASA Astrophysics Data System (ADS)

Barlow, D. A.

2017-07-01

A theory for the intermediate stage of crystal growth, where two defining equations one for population continuity and another for mass-balance, is used to study the kinetics of the supersaturation decay, the homogeneous nucleation rate, the linear growth rate and the final distribution of crystal sizes for the crystallization of bovine and porcine insulin from solution. The cited experimental reports suggest that the crystal linear growth rate is directly proportional to the square of the insulin concentration in solution for bovine insulin and to the cube of concentration for porcine. In a previous work, it was shown that the above mentioned system could be solved for the case where the growth rate is directly proportional to the normalized supersaturation. Here a more general solution is presented valid for cases where the growth rate is directly proportional to the normalized supersaturation raised to the power of any positive integer. The resulting expressions for the time dependent normalized supersaturation and crystal size distribution are compared with experimental reports for insulin crystallization. An approximation for the maximum crystal size at the end of the intermediate stage is derived. The results suggest that the largest crystal size in the distribution at the end of the intermediate stage is maximized when nucleation is restricted to be only homogeneous. Further, the largest size in the final distribution depends only weakly upon the initial supersaturation.

A class of mild surfactants that keep integral membrane proteins water-soluble for functional studies and crystallization

PubMed Central

Hovers, Jens; Potschies, Meike; Polidori, Ange; Pucci, Bernard; Raynal, Simon; Bonneté, Françoise; Serrano-Vega, Maria J.; Tate, Christopher G.; Picot, Daniel; Pierre, Yves; Popot, Jean-Luc; Nehmé, Rony; Bidet, Michel; Mus-Veteau, Isabelle; Bußkamp, Holger; Jung, Karl-Heinz; Marx, Andreas; Timmins, Peter A.; Welte, Wolfram

2013-01-01

Mixed protein-surfactant micelles are used for in vitro studies and 3D crystallization when solutions of pure, monodisperse integral membrane proteins are required. However, many membrane proteins undergo inactivation when transferred from the biomembrane into micelles of conventional surfactants with alkyl chains as hydrophobic moieties. Here we describe the development of surfactants with rigid, saturated or aromatic hydrocarbon groups as hydrophobic parts. Their stabilizing properties are demonstrated with three different integral membrane proteins. The temperature at which 50% of the binding sites for specific ligands are lost is used as a measure of stability and dodecyl-β-D-maltoside (“C12-b-M”) as a reference for conventional surfactants. One surfactant increased the stability of two different G protein-coupled receptors by approximately 10°C compared to C12-b-M. Another surfactant yielded a stabilization of the human Patched protein receptor by 13°C. In addition, one of the surfactants was successfully used to stabilize and crystallize the cytochrome b6f complex from Chlamydomonas reinhardtii. The structure was solved to the same resolution as previously reported in C12-b-M. PMID:21314479

Crystal structure of (E)-1-[4-({4-[(4-meth­oxy­benzyl­idene)amino]­phen­yl}sulfan­yl)phen­yl]ethan-1-one

PubMed Central

Hebbachi, Rabihe; Djedouani, Amel; Kadri, Soumia; Mousser, Hénia; Mousser, Abdelhamid

2015-01-01

The title Schiff base compound, C22H19NO2S, crystallized with two independent mol­ecules (A and B) in the asymmetric unit. Both mol­ecules have an E conformation about the C=N bond. The two mol­ecules differ in the orientation of the aromatic rings with respect to each other. The outer 4-meth­oxy­benzene ring is inclined to the central benzene ring and the outer 4-acetyl­benzene ring by 1.80 (19) and 63.73 (19)°, respectively, in mol­ecule A, and by 6.72 (18) and 68.53 (19)°, respectively, in mol­ecule B. The two outer benzene rings are inclined to one another by 63.77 (18) and 63.19 (18)° in mol­ecules A and B, respectively. In the crystal, the individual mol­ecules stack in columns along [010], and are linked by a number of C—H⋯π inter­actions, forming slabs lying parallel to (001). PMID:25878856

Properties of magnetized Coulomb crystals of ions with polarizable electron background

NASA Astrophysics Data System (ADS)

Kozhberov, A. A.

2018-06-01

We have studied phonon and thermodynamic properties of a body-centered cubic (bcc) Coulomb crystal of ions with weakly polarized electron background in a uniform magnetic field B. At B = 0, the difference between phonon moments calculated using the Thomas-Fermi (TF) and random phase approximations is always less than 1% and for description of phonon properties of a crystal, TF formalism was used. This formalism was successfully applied to investigate thermodynamic properties of magnetized Coulomb crystals. It was shown that the influence of the polarization of the electron background is significant only at κ TF a > 0.1 and T ≪ T p ( 1 + h2 ) - 1 / 2 , where κTF is the Thomas-Fermi wavenumber, a is the ion sphere radius, T p ≡ ℏ ω p is the ion plasma temperature, h ≡ ω B / ω p , ωB is the ion cyclotron frequency, and ωp is the ion plasma frequency.

Crystal structure of 3-(adamantan-1-yl)-4-(4-chloro-phen-yl)-1H-1,2,4-triazole-5(4H)-thione.

PubMed

Al-Wabli, Reem I; El-Emam, Ali A; Alroqi, Obaid S; Chidan Kumar, C S; Fun, Hoong-Kun

2015-02-01

The title compound, C18H20ClN3S, is a functionalized triazoline-3-thione derivative. The benzene ring is almost perpendic-ular to the planar 1,2,4-triazole ring [maximum deviation = 0.007 (1) Å] with a dihedral angle of 89.61 (5)° between them and there is an adamantane substituent at the 3-position of the triazole-thione ring. In the crystal, N-H⋯S hydrogen-bonding inter-actions link the mol-ecules into chains extending along the c-axis direction. The crystal packing is further stabilized by weak C-H⋯π inter-actions that link adjacent chains into a two-dimensional structure in the bc plane. The crystal studied was an inversion twin with a 0.50 (3):0.50 (3) domain ratio.

Crystal structure and hydrogen-bonding patterns in 5-fluoro­cytosinium picrate

PubMed Central

Mohana, Marimuthu; Thomas Muthiah, Packianathan; McMillen, Colin D.

2017-01-01

In the crystal structure of the title compound, 5-fluoro­cytosinium picrate, C4H5FN3O+·C6H2N3O7 −, one N heteroatom of the 5-fluoro­cytosine (5FC) ring is protonated. The 5FC ring forms a dihedral angle of 19.97 (11)° with the ring of the picrate (PA−) anion. In the crystal, the 5FC+ cation inter­acts with the PA− anion through three-centre N—H⋯O hydrogen bonds, forming two conjoined rings having R 2 1(6) and R 1 2(6) motifs, and is extended by N—H⋯O hydrogen bonds and C—H⋯O inter­actions into a two-dimensional sheet structure lying parallel to (001). Also present in the crystal structure are weak C—F⋯π inter­actions. PMID:28316809

Mechanisms of the passage of dark currents through Cd(Zn)Te semi-insulating crystals

NASA Astrophysics Data System (ADS)

Sklyarchuk, V.; Fochuk, P.; Rarenko, I.; Zakharuk, Z.; Sklyarchuk, O.; Nykoniuk, Ye.; Rybka, A.; Kutny, V.; Bolotnikov, A. E.; James, R. B.

2014-09-01

We investigated the passage of dark currents through semi-insulating crystals of Cd(Zn)Te with weak n-type conductivity that are used widely as detectors of ionizing radiation. The crystals were grown from a tellurium solution melt at 800 оС by the zone-melting method, in which a polycrystalline rod in a quartz ampoule was moved through a zone heater at a rate of 2 mm per day. The synthesis of the rod was carried out at ~1150 оС. We determined the important electro-physical parameters of this semiconductor, using techniques based on a parallel study of the temperature dependence of current-voltage characteristics in both the ohmic and the space-charge-limited current regions. We established in these crystals the relationship between the energy levels and the concentrations of deep-level impurity states, responsible for dark conductivity and their usefulness as detectors.

Using Magnetic Field Gradients to Simulate Variable Gravity in Fluids and Materials Experiments

NASA Technical Reports Server (NTRS)

Ramachandran, Narayanan

2006-01-01

Fluid flow due to a gravitational field is caused by sedimentation, thermal buoyancy, or solutal buoyancy induced convection. During crystal growth, for example, these flows are undesirable and can lead to crystal imperfections. While crystallization in microgravity can approach diffusion limited growth conditions (no convection), terrestrially strong magnetic fields can be used to control fluid flow and sedimentation effects. In this work, a theory is presented on the stability of solutal convection of a magnetized fluid(weak1y paramagnetic) in the presence of a magnetic field. The requirements for stability are developed and compared to experiments performed within the bore of a superconducting magnet. The theoretical predictions are in good agreement with the experiments. Extension of the technique can also be applied to study artificial gravity requirements for long duration exploration missions. Discussion of this application with preliminary experiments and application of the technique to crystal growth will be provided.

Frequency and Thermal Behavior of Acoustic Absorption in ɛ-GaSe Crystals

NASA Astrophysics Data System (ADS)

Dzhafarova, S. Z.

2018-04-01

The paper presents results of measuring acoustic absorption in ɛ-GaSe crystals. The absorption of a longitudinal wave which propagates normal to the crystal layers, quadratically depends on frequency. However, it does not depend on temperature, i.e. it displays an Akhiezer behavior although its absolute value considerably exceeds the expected. The analysis of the frequency and thermal behavior of absorption of piezoelectric waves propagating along the layers, includes the deduction of contribution made by the interaction between waves and charge carriers. This analysis shows the linear dependence between the lattice absorption of these waves and the frequency. The linear frequency and weak temperature dependences of the acoustic absorption characterize the additional ultra-Akhiezer absorption in glasses. In our case, it can be caused by various polytypes forming in GaSe crystals which differ merely in a mutual arrangement of layers.

Tailoring the structures and photonic properties of low-dimensional organic materials by crystal engineering.

PubMed

Li, Qing; Jin, Wang; Chu, Manman; Zhang, Wei; Gu, Jianmin; Shahid, Bilal; Chen, Aibing; Yu, Yifeng; Qiao, Shanlin; Zhao, Yong Sheng

2018-03-08

Low-dimensional organic materials have given rise to tremendous interest in optoelectronic applications, owing to their controllable photonic properties. However, the controlled-synthesis approaches for organic nano-/micro-architectures are very difficult to attain, because the weak interaction (van der Waals force) between the organic molecules cannot dominate the kinetic process of crystal growth. We report a simple method, which involves selective adhesion to the organic crystal plane by hydrogen-bonding interaction for modulating the crystal growth process, which leads either to the self-assembly of one organic molecule into two-dimensional (2D) microsheets with an obvious asymmetric light propagation or one-dimensional (1D) microrods with low propagation loss. The method of tailoring the structures and photonic properties for fabricating different micro-structures would provide enlightenment for the development of tailor-made mini-sized devices for photonic integrated circuits.

n→π* Non-Covalent Interaction is Weak but Strong in Action

NASA Astrophysics Data System (ADS)

Singh, Santosh Kumar; Das, Aloke

2017-06-01

n→π* interaction is a newly discovered non-covalent interaction which involves delocalization of lone pair (n) electrons of an electronegative atom into π* orbital of a carbonyl group or an aromatic ring. It is widely observed in materials, biomolecules (protein, DNA, RNA), amino acids, neurotransmitter and drugs. However, due to its weak strength and counterintuitive nature its existence is debatable. Such weak interactions are often masked by solvent effects in condense phase or physiological conditions thereby, making it difficult to prove the presence of such weak interactions. Therefore, we have used isolated gas phase spectroscopy in combination with quantum chemical calculations to study n→π* interaction in several molecules where, our molecular systems are free from solvent effects or any external forces. Herein I will be discussing two of the molecular systems (phenyl formate and salicin) where, we have observed the significance of n→π* interaction in determining the conformational specificity of the molecules. We have proved the existence of n→π* interaction for the first time through IR spectroscopy by probing the carbonyl stretching frequency of phenyl formate. Our study is further pursued on a drug named salicin where, we have observed that its conformational preferences is ruled by n→π* interaction even though a strong hydrogen bonding interaction is present in the molecule. Our results show that n→π* interaction, in spite of its weak strength, should not be overlooked as it existence can play an important role in governing the structures of molecules like other strong non-covalent interactions do.

Chemical Composition, Antibacterial, Antibiofilm and Synergistic Properties of Essential Oils from Eucalyptus globulus Labill. and Seven Mediterranean Aromatic Plants.

PubMed

Vieira, Maria; Bessa, Lucinda J; Martins, M Rosário; Arantes, Sílvia; Teixeira, António P S; Mendes, Ângelo; Martins da Costa, Paulo; Belo, Anabela D F

2017-06-01

Essential oils (EOs) from Eucalyptus globulus Labill. ssp. globulus and from Mediterranean autochthonous aromatic plants - Thymus mastichina L., Mentha pulegium L., Rosmarinus officinalis L., Calamintha nepeta (L.) Savi ssp. nepeta, Cistus ladanifer L., Foeniculum vulgare L., Dittrichia viscosa (L.) Greuter ssp. viscosa - were extracted by hydrodistillation and characterized by GC-FID and NMR spectroscopy. EOs were evaluated for antimicrobial properties against several bacterial strains, using diverse methods, namely, the agar disc-diffusion method, the microdilution method, the crystal violet assay and the Live/Dead staining for assessment of biofilm formation. Potential synergy was assessed by a checkerboard method. EOs of R. officinalis and C. ladanifer showed a predominance in monoterpene hydrocarbons (> 60%); EOs of C. nepeta, M. pulegium, T. mastichina, E. globulus and F. vulgare were rich in oxygenated monoterpenes (62 - 96%) whereas EO of D. viscosa was mainly composed of oxygenated sesquiterpenes (54%). All EOs showed antimicrobial activity; M. pulegium and E. globulus generally had the strongest antimicrobial activity. EO of C. nepeta was the most promising in hampering the biofilm formation. The combinations D. viscosa/C. nepeta and E. globulus/T. mastichina were synergistic against Staphylococcus aureus. These results support the notion that EOs from the aromatic plants herein reported should be further explored as potential pharmaceuticals and/or food preservatives. © 2017 Wiley-VHCA AG, Zurich, Switzerland.

Studies on non-steroidal inhibitors of aromatase enzyme; 4-(aryl/heteroaryl)-2-(pyrimidin-2-yl)thiazole derivatives.

PubMed

Sahin, Zafer; Ertas, Merve; Berk, Barkın; Biltekin, Sevde Nur; Yurttas, Leyla; Demirayak, Seref

2018-05-01

Steroidal and non-steroidal aromatase inhibitors target the suppression of estrogen biosynthesis in the treatment of breast cancer. Researchers have increasingly focused on developing non-steroidal derivatives for their potential clinical use avoiding steroidal side-effects. Non-steroidal derivatives generally have planar aromatic structures attached to the azole ring system. One part of this ring system comprises functional groups that inhibit aromatization through the coordination of the haem group of the aromatase enzyme. Replacement of the triazole ring system and development of aromatic/cyclic structures of the side chain can increase selectivity over aromatase enzyme inhibition. In this study, 4-(aryl/heteroaryl)-2-(pyrimidin-2-yl)thiazole derivatives were synthesized and physical analyses and structural determination studies were performed. The IC 50 values were determined by a fluorescence-based aromatase inhibition assay and compound 1 (4-(2-hydroxyphenyl)-2-(pyrimidine-2-yl)thiazole) were found potent inhibitor of enzyme (IC 50 :0.42 nM). Then, their antiproliferative activity over MCF-7 and HEK-293 cell lines was evaluated using a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Compounds 1, 7, 8, 13, 15, 18, 21 were active against MCF-7 breast cancer cells. Lastly, a series of docking experiments were undertaken to analyze the crystal structure of human placental aromatase and identify the possible interactions between the most active structure and the active site. Copyright © 2018 Elsevier Ltd. All rights reserved.

An Aromatic Cap Seals the Substrate Binding Site in an ECF-Type S Subunit for Riboflavin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karpowich, Nathan K.; Song, Jinmei; Wang, Da-Neng

2016-06-13

ECF transporters are a family of active membrane transporters for essential micronutrients, such as vitamins and trace metals. Found exclusively in archaea and bacteria, these transporters are composed of four subunits: an integral membrane substrate-binding subunit (EcfS), a transmembrane coupling subunit (EcfT), and two ATP-binding cassette ATPases (EcfA and EcfA'). We have characterized the structural basis of substrate binding by the EcfS subunit for riboflavin from Thermotoga maritima, TmRibU. TmRibU binds riboflavin with high affinity, and the protein–substrate complex is exceptionally stable in solution. The crystal structure of riboflavin-bound TmRibU reveals an electronegative binding pocket at the extracellular surface inmore » which the substrate is completely buried. Analysis of the intermolecular contacts indicates that nearly every available substrate hydrogen bond is satisfied. A conserved aromatic residue at the extracellular end of TM5, Tyr130, caps the binding site to generate a substrate-bound, occluded state, and non-conservative mutation of Tyr130 reduces the stability of this conformation. Using a novel fluorescence binding assay, we find that an aromatic residue at this position is essential for high-affinity substrate binding. Comparison with other S subunit structures suggests that TM5 and Loop5-6 contain a dynamic, conserved motif that plays a key role in gating substrate entry and release by S subunits of ECF transporters.« less

Synthesis and Structural Data of Tetrabenzo[8]circulene

PubMed Central

Miller, Robert W.; Duncan, Alexandra K.; Schneebeli, Severin T.; Gray, Danielle L.; Whalley, Adam C.

2015-01-01

In 1976, the first attempted synthesis of the saddle-shaped molecule [8]circulene was reported. The next 37 years produced no advancement towards the construction of this complicated molecule. Remarkably, however, over the last six months a flurry of progress has been made with two groups reporting independent and strikingly different strategies for the synthesis of [8]circulene derivatives. Herein, we present a third synthetic method in which we target tetrabenzo[8]circulene. Our approach employs a Diels-Alder reaction and a palladium-catalyzed arylation reaction as the key steps. Despite calculations describing the instability of [8]circulene, coupled with the reported instability of synthesized derivatives of the parent molecule, the addition of four fused benzenoid rings around the periphery of the molecule provides a highly stable structure. This increased stability over the parent [8]circulene was predicted using Clar’s theory of aromatic sextets and is a result of the compound becoming fully benzenoid upon incorporation of these additional rings. The synthesized compound exhibits remarkable stability under ambient conditions – even at elevated temperatures – with no signs of decomposition over several months. The solid-state structure of this compound is significantly twisted compared to the calculated structure primarily as a result of crystal packing forces in the solid state. Despite this contortion from the lowest energy structure, a range of structural data is presented confirming the presence of localized aromaticity in this large polycyclic aromatic hydrocarbon. PMID:24615957

Tunable recognition of the steroid α-face by adjacent π-electron density

PubMed Central

Friščić, T.; Lancaster, R. W.; Fábián, L.; Karamertzanis, P. G.

2010-01-01

We report a previously unknown recognition motif between the α-face of the steroid hydrocarbon backbone and π-electron-rich aromatic substrates. Our study is based on a systematic and comparative analysis of the solid-state complexation of four steroids with 24 aromatic molecules. By using the solid state as a medium for complexation, we circumvent solubility and solvent competition problems that are inherent to the liquid phase. Characterization is performed using powder and single crystal X-ray diffraction, infrared solid-state spectroscopy and is complemented by a comprehensive cocrystal structure prediction methodology that surpasses earlier computational approaches in terms of realism and complexity. Our combined experimental and theoretical approach reveals that the α⋯π stacking is of electrostatic origin and is highly dependent on the steroid backbone’s unsaturated and conjugated character. We demonstrate that the α⋯π stacking interaction can drive the assembly of molecules, in particular progesterone, into solid-state complexes without the need for additional strong interactions. It results in a marked difference in the solid-state complexation propensities of different steroids with aromatic molecules, suggesting a strong dependence of the steroid-binding affinity and even physicochemical properties on the steroid’s A-ring structure. Hence, the hydrocarbon part of the steroid is a potentially important variable in structure-activity relationships for establishing the binding and signaling properties of steroids, and in the manufacture of pharmaceutical cocrystals. PMID:20624985

The first mammalian aldehyde oxidase crystal structure: insights into substrate specificity.

PubMed

Coelho, Catarina; Mahro, Martin; Trincão, José; Carvalho, Alexandra T P; Ramos, Maria João; Terao, Mineko; Garattini, Enrico; Leimkühler, Silke; Romão, Maria João

2012-11-23

Aldehyde oxidases have pharmacological relevance, and AOX3 is the major drug-metabolizing enzyme in rodents. The crystal structure of mouse AOX3 with kinetics and molecular docking studies provides insights into its enzymatic characteristics. Differences in substrate and inhibitor specificities can be rationalized by comparing the AOX3 and xanthine oxidase structures. The first aldehyde oxidase structure represents a major advance for drug design and mechanistic studies. Aldehyde oxidases (AOXs) are homodimeric proteins belonging to the xanthine oxidase family of molybdenum-containing enzymes. Each 150-kDa monomer contains a FAD redox cofactor, two spectroscopically distinct [2Fe-2S] clusters, and a molybdenum cofactor located within the protein active site. AOXs are characterized by broad range substrate specificity, oxidizing different aldehydes and aromatic N-heterocycles. Despite increasing recognition of its role in the metabolism of drugs and xenobiotics, the physiological function of the protein is still largely unknown. We have crystallized and solved the crystal structure of mouse liver aldehyde oxidase 3 to 2.9 Å. This is the first mammalian AOX whose structure has been solved. The structure provides important insights into the protein active center and further evidence on the catalytic differences characterizing AOX and xanthine oxidoreductase. The mouse liver aldehyde oxidase 3 three-dimensional structure combined with kinetic, mutagenesis data, molecular docking, and molecular dynamics studies make a decisive contribution to understand the molecular basis of its rather broad substrate specificity.

Crystal structure, conformation, vibration and optical band gap analysis of bis[ rac-propranolol nitrate

NASA Astrophysics Data System (ADS)

Franklin, S.; Balasubramanian, T.; Nehru, K.; Kim, Youngmee

2009-06-01

The crystal structure of the title rac-propranolol salt, CHNO2+·NO3-, consists of two protonated propranolol residues and nitrate anions. Three virtually flat fragments, characteristics of most of the β-adrenolytics with oxy-methylene bridge are present in both the cations (A and B). The plane of the propranolol chain is twisted with respect to the plane of the aromatic ring in both the cations. Present study investigates the conformation and hydrogen bonding interactions, which play an important role in biological functions. A gauche conformation is observed for the oxo-methylene bridge of cation A, while a trans conformation prevails in cation B. These conformations are found in majority of β-blockers. Presence of twenty intermolecular hydrogen bonds mediating through the anions stabilizes the crystal packing. Vibration analysis and earlier theoretical predictions complement the structure analysed. From the UV-Vis spectral analysis for the crystal, the optical band gap is found to be Eg = 5.12 eV, where as the chloride salt has Eg = 3.81 eV. The increase in the band gap may be attributed by the increase in the number of intermolecular hydrogen bonds. Good optical transmittance in the entire visible region and the direct band gap property suggest that it is a suitable candidate for optical applications in UV region.

Probing phenylalanine/adenine pi-stacking interactions in protein complexes with explicitly correlated and CCSD(T) computations.

PubMed

Copeland, Kari L; Anderson, Julie A; Farley, Adam R; Cox, James R; Tschumper, Gregory S

2008-11-13

To examine the effects of pi-stacking interactions between aromatic amino acid side chains and adenine bearing ligands in crystalline protein structures, 26 toluene/(N9-methyl)adenine model configurations have been constructed from protein/ligand crystal structures. Full geometry optimizations with the MP2 method cause the 26 crystal structures to collapse to six unique structures. The complete basis set (CBS) limit of the CCSD(T) interaction energies has been determined for all 32 structures by combining explicitly correlated MP2-R12 computations with a correction for higher-order correlation effects from CCSD(T) calculations. The CCSD(T) CBS limit interaction energies of the 26 crystal structures range from -3.19 to -6.77 kcal mol (-1) and average -5.01 kcal mol (-1). The CCSD(T) CBS limit interaction energies of the optimized complexes increase by roughly 1.5 kcal mol (-1) on average to -6.54 kcal mol (-1) (ranging from -5.93 to -7.05 kcal mol (-1)). Corrections for higher-order correlation effects are extremely important for both sets of structures and are responsible for the modest increase in the interaction energy after optimization. The MP2 method overbinds the crystal structures by 2.31 kcal mol (-1) on average compared to 4.50 kcal mol (-1) for the optimized structures.

Polycyclic Aromatic Hydrocarbon Emission Toward the Galactic Bulge

NASA Astrophysics Data System (ADS)

Shannon, M. J.; Peeters, E.; Cami, J.; Blommaert, J. A. D. L.

2018-03-01

We examine polycyclic aromatic hydrocarbon (PAH), dust, and atomic/molecular emission toward the Galactic bulge using Spitzer Space Telescope observations of four fields: C32, C35, OGLE, and NGC 6522. These fields are approximately centered on (l, b) = (0.°0, 1.°0), (0.°0, ‑1.°0), (0.°4, ‑2.°4), and (1.°0, ‑3.°8), respectively. Far-infrared photometric observations complement the Spitzer/IRS spectroscopic data and are used to construct spectral energy distributions. We find that the dust and PAH emission are exceptionally similar between C32 and C35 overall, in part explained due to their locations—they reside on or near boundaries of a 7 Myr old Galactic outflow event and are partly shock-heated. Within the C32 and C35 fields, we identify a region of elevated Hα emission that is coincident with elevated fine-structure and [O IV] line emission and weak PAH feature strengths. We are likely tracing a transition zone of the outflow into the nascent environment. PAH abundances in these fields are slightly depressed relative to typical ISM values. In the OGLE and NGC 6522 fields, we observe weak features on a continuum dominated by zodiacal dust. SED fitting indicates that thermal dust grains in C32 and C35 have temperatures comparable to those of diffuse, high-latitude cirrus clouds. Little variability is detected in the PAH properties between C32 and C35, indicating that a stable population of PAHs dominates the overall spectral appearance. In fact, their PAH features are exceptionally similar to that of the M82 superwind, emphasizing that we are probing a local Galactic wind environment.

Effect of mineral surface properties (alumina, kaolinite) on the sorptive fractionation mechanisms of soil fulvic acids: Molecular-scale ESI-MS studies

NASA Astrophysics Data System (ADS)

Fleury, Guillaume; Del Nero, Mirella; Barillon, Rémi

2017-01-01

We addressed the effects of mineral surface properties (kaolinite versus Al-oxide) on the sorption-driven fractionation of a soil fulvic acid (FA) at acidic pH, mainly by means of ESI(-)-FTMS analysis of initial and supernatant solutions of FA sorption batch experiments. The MS data provided clear molecular-scale evidence of distinct mechanisms and molecular parameters controlling the FA fractionation upon its sorption on clay and oxide surfaces, respectively. Identification of sorbing and not-sorbing FA compounds in kaolinite-solution systems revealed a weak fractionation among members of sbnd CO2 series of aliphatics or not-condensed aromatics (NCAs) at pH 3.8, and almost no sorption of poorly-oxygenated polycyclic aromatic compounds (PACs) and NCAs. This first molecular-scale description of a FA fractionation in a clay-solution system suggests that H-bonding with low affinity sites (aluminol/silanol) on the basal planes of the clay particles is the main mechanism of sorption. Due to the predominance of such weak and poorly-selective mechanism, the sorption of aliphatic and NCA molecules bearing oxygenated functionalities was prevented at pH 5, due to dissolved Al competing successfully for their coordination. In contrast, a strong FA fractionation was observed onto alumina, with a preferential retention of PACs and highly-oxygenated aliphatics and NCAs. The major part of the poorly oxygenated aliphatics was left in solution. The sorption degree of NCAs and aliphatics was strongly correlated with molecular acidity. For PACs and poorly-oxygenated NCAs, the sorption was driven by reactions of surface ligand exchange (for the most oxygenated compounds) or by hydrophobic interactions (for the least oxygenated compounds).

Self-organized chiral colloidal crystals of Brownian square crosses.

PubMed

Zhao, Kun; Mason, Thomas G

2014-04-16

We study aqueous Brownian dispersions of microscale, hard, monodisperse platelets, shaped as achiral square crosses, in two dimensions (2D). When slowly concentrated while experiencing thermal excitations, the crosses self-organize into fluctuating 2D colloidal crystals. As the particle area fraction φA is raised, an achiral rhombic crystal phase forms at φA ≈ 0.52. Above φA ≈ 0.56, the rhombic crystal gives way to a square crystal phase that exhibits long-range chiral symmetry breaking (CSB) via a crystal-crystal phase transition; the observed chirality in a particular square crystallite has either a positive or a negative enantiomeric sense. By contrast to triangles and rhombs, which exhibit weak CSB as a result of total entropy maximization, square crosses display robust long-range CSB that is primarily dictated by how they tile space at high densities. We measure the thermal distribution of orientation angles γ of the crosses' arms relative to the diagonal bisector of the local square crystal lattice as a function of φA, and the average measured γ (φA) agrees with a re-scaled model involving efficient packing of rotated cross shapes. Our findings imply that a variety of hard achiral shapes can be designed to form equilibrium chiral phases by considering their tiling at high densities.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bury, Charles S.; Carmichael, Ian; Garman, Elspeth F.

During macromolecular X-ray crystallography experiments, protein crystals held at 100 K have been widely reported to exhibit reproducible bond scission events at doses on the order of several MGy. With the objective to mitigate the impact of radiation damage events on valid structure determination, it is essential to correctly understand the radiation chemistry mechanisms at play. OH-cleavage from tyrosine residues is regularly cited as amongst the most available damage pathways in protein crystals at 100 K, despite a lack of widespread reports of this phenomenon in protein crystal radiation damage studies. Furthermore, no clear mechanism for phenolic C—O bond cleavagemore » in tyrosine has been reported, with the tyrosyl radical known to be relatively robust and long-lived in both aqueous solutions and the solid state. Here, the initial findings of Tyr –OH group damage in a myrosinase protein crystal have been reviewed. Consistent with that study, at increasing doses, clear electron density loss was detectable local to Tyr –OH groups. A systematic investigation performed on a range of protein crystal damage series deposited in the Protein Data Bank has established that Tyr –OH electron density loss is not generally a dominant damage pathway in protein crystals at 100 K. Full Tyr aromatic ring displacement is here proposed to account for instances of observable Tyr –OH electron density loss, with the original myrosinase data shown to be consistent with such a damage model. Also presented are systematic analysis of the effects of other environmental factors, including solvent accessibility and proximity to disulfide bonds or hydrogen bond interactions. Residues in known active sites showed enhanced sensitivity to radiation-induced disordering, as has previously been reported.« less

OH cleavage from tyrosine: debunking a myth

DOE PAGES

Bury, Charles S.; Carmichael, Ian; Garman, Elspeth F.

2017-01-01

During macromolecular X-ray crystallography experiments, protein crystals held at 100 K have been widely reported to exhibit reproducible bond scission events at doses on the order of several MGy. With the objective to mitigate the impact of radiation damage events on valid structure determination, it is essential to correctly understand the radiation chemistry mechanisms at play. OH-cleavage from tyrosine residues is regularly cited as amongst the most available damage pathways in protein crystals at 100 K, despite a lack of widespread reports of this phenomenon in protein crystal radiation damage studies. Furthermore, no clear mechanism for phenolic C—O bond cleavagemore » in tyrosine has been reported, with the tyrosyl radical known to be relatively robust and long-lived in both aqueous solutions and the solid state. Here, the initial findings of Tyr –OH group damage in a myrosinase protein crystal have been reviewed. Consistent with that study, at increasing doses, clear electron density loss was detectable local to Tyr –OH groups. A systematic investigation performed on a range of protein crystal damage series deposited in the Protein Data Bank has established that Tyr –OH electron density loss is not generally a dominant damage pathway in protein crystals at 100 K. Full Tyr aromatic ring displacement is here proposed to account for instances of observable Tyr –OH electron density loss, with the original myrosinase data shown to be consistent with such a damage model. Also presented are systematic analysis of the effects of other environmental factors, including solvent accessibility and proximity to disulfide bonds or hydrogen bond interactions. Residues in known active sites showed enhanced sensitivity to radiation-induced disordering, as has previously been reported.« less

Identification of potential fish carcinogens in sediment from Hamilton Harbour, Ontario, Canada

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balch, G.C.; Metcalfe, C.D.; Huestis, S.Y.

1995-01-01

A carcinogenicity- and mutagenicity-directed fractionation approach was used to identify the carcinogenic compounds in contaminated sediments that are putatively responsible for the high prevalence of tumors in bottom-dwelling fish from Hamilton Harbour, Ontario. Mutagenic activity was detected with Ames tester strains (TA98, TA100) in relatively nonpolar fractions of sediment extract containing PAHs and nitrogen-containing aromatic compounds (NCACs). These fractions were also carcinogenic in an in vivo carcinogenicity bioassay with rainbow trout (Oncorhynchus mykiss). When a more polar extract fraction was tested for mutagenicity and carcinogenicity, weak mutagenic activity was detected with an O-acetyltransferase-enriched Ames tester strain (YG1024), and weak carcinogenicmore » activity was detected in the rainbow trout assay. These data indicate that PAHs in contaminated Hamilton Harbour sediments are potent fish carcinogens, but it is also evident that other organic compounds in the sediment, such as NCACs and nitroarenes, may contribute to carcinogenicity.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Azadi, Sam, E-mail: s.azadi@ucl.ac.uk; Cohen, R. E.

We report an accurate study of interactions between benzene molecules using variational quantum Monte Carlo (VMC) and diffusion quantum Monte Carlo (DMC) methods. We compare these results with density functional theory using different van der Waals functionals. In our quantum Monte Carlo (QMC) calculations, we use accurate correlated trial wave functions including three-body Jastrow factors and backflow transformations. We consider two benzene molecules in the parallel displaced geometry, and find that by highly optimizing the wave function and introducing more dynamical correlation into the wave function, we compute the weak chemical binding energy between aromatic rings accurately. We find optimalmore » VMC and DMC binding energies of −2.3(4) and −2.7(3) kcal/mol, respectively. The best estimate of the coupled-cluster theory through perturbative triplets/complete basis set limit is −2.65(2) kcal/mol [Miliordos et al., J. Phys. Chem. A 118, 7568 (2014)]. Our results indicate that QMC methods give chemical accuracy for weakly bound van der Waals molecular interactions, comparable to results from the best quantum chemistry methods.« less

Effect of surface viscosity, anchoring energy, and cell gap on the response time of nematic liquid crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Souza, R.F. de; Yang, D.-Ke; Lenzi, E.K.

2014-07-15

An analytical expression for the relaxation time of a nematic liquid crystal is obtained for the first time by considering the influence of surface viscosity, anchoring energy strength and cell gap, validated numerically by using the so-called relaxation method. This general equation for the molecular response time (τ{sub 0}) was derived for a vertical aligned cell and by solving an eigenvalue equation coming from the usual balance of torque equation in the Derzhanskii and Petrov formulation, recovering the usual equations in the appropriate limit. The results show that τ∼d{sup b}, where b=2 is observed only for strongly anchored cells, whilemore » for moderate to weak anchored cells, the exponent lies between 1 and 2, depending on both, surface viscosity and anchoring strength. We found that the surface viscosity is important when calculating the response time, specially for thin cells, critical for liquid crystal devices. The surface viscosity’s effect on the optical response time with pretilt is also explored. Our results bring new insights about the role of surface viscosity and its effects in applied physics. - Highlights: • The relaxation of nematic liquid crystals is calculated by taking the surface viscosity into account. • An analytical expression for the relaxation time depending on surface viscosity, anchoring strength and cell gap is obtained. • The results are numerically verified. • Surface viscosity is crucial for thin and weak anchored cells. • The effect on optical time and pretilt angle is also studied.« less

Laboratory studies on the uptake of aromatic hydrocarbons by ice crystals during vapor depositional crystal growth

NASA Astrophysics Data System (ADS)

Fries, Elke; Starokozhev, Elena; Haunold, Werner; Jaeschke, Wolfgang; Mitra, Subir K.; Borrmann, Stephan; Schmidt, Martin U.

Uptake of aromatic hydrocarbons (AH) by ice crystals during vapor deposit growth was investigated in a walk-in cold chamber at temperatures of 242, 251, and 260 K, respectively. Ice crystals were grown from ambient air in the presence of gaseous AH namely: benzene (C 6H 6), toluene (methylbenzene, C 7H 8), the C 8H 10 isomers ethylbenzene, o-, m-, p-xylene (dimethylbenzenes), the C 9H 12 isomers n-propylbenzene, 4-ethyltoluene, 1,3,5-trimethylbenzene (1,3,5-TMB), 1,2,4-trimethylbenzene (1,2,4-TMB), 1,2,3-trimethylbenzene (1,2,3-TMB), and the C 10H 14 compound tert.-butylbenzene. Gas-phase concentrations calculated at 295 K were 10.3-20.8 μg m -3. Uptake of AH was detected by analyzing vapor deposited ice with a very sensitive method composed of solid-phase micro-extraction (SPME), followed by gas chromatography/mass spectrometry (GC/MS). Ice crystal size was lower than 1 cm. At water vapor extents of 5.8, 6.0 and 8.1 g m -3, ice crystal shape changed with decreasing temperatures from a column at a temperature of 260 K, to a plate at 251 K, and to a dendrite at 242 K. Experimentally observed ice growth rates were between 3.3 and 13.3×10 -3 g s -1 m -2 and decreased at lower temperatures and lower value of water vapor concentration. Predicted growth rates were mostly slightly higher. Benzene, toluene, ethylbenzene, and xylenes (BTEX) were not detected in ice above their detection limits (DLs) of 25 pg g ice-1 (toluene, ethylbenzene, xylenes) and 125 pg g ice-1 (benzene) over the entire temperature range. Median concentrations of n-propylbenzene, 4-ethyltoluene, 1,3,5-TMB, tert.-butylbenzene, 1,2,4-TMB, and 1,2,3-TMB were between 4 and 176 pg g ice-1 at gas concentrations of 10.3-10.7 μg m -3 calculated at 295 K. Uptake coefficients ( K) defined as the product of concentration of AH in ice and density of ice related to the product of their concentration in the gas phase and ice mass varied between 0.40 and 10.23. K increased with decreasing temperatures. Values of Gibbs energy (Δ G) were between -4.5 and 2.4 kJ mol -1 and decreased as temperatures were lowered. From the uptake experiments, the uptake enthalpy (Δ H) could be determined between -70.6 and -33.9 kJ mol -1. The uptake entropy (Δ S) was between -281.3 and -126.8 J mol -1 K -1. Values of Δ H and Δ S were rather similar for 4-ethlytoluene, 1,3,5-TMB and tert.-butylbenzene, whereas 1,2,3-TMB showed much higher values.

Impact of Heterogeneity and Lattice Bond Strength on DNA Triangle Crystal Growth.

PubMed

Stahl, Evi; Praetorius, Florian; de Oliveira Mann, Carina C; Hopfner, Karl-Peter; Dietz, Hendrik

2016-09-07

One key goal of DNA nanotechnology is the bottom-up construction of macroscopic crystalline materials. Beyond applications in fields such as photonics or plasmonics, DNA-based crystal matrices could possibly facilitate the diffraction-based structural analysis of guest molecules. Seeman and co-workers reported in 2009 the first designed crystal matrices based on a 38 kDa DNA triangle that was composed of seven chains. The crystal lattice was stabilized, unprecedentedly, by Watson-Crick base pairing. However, 3D crystallization of larger designed DNA objects that include more chains such as DNA origami remains an unsolved problem. Larger objects would offer more degrees of freedom and design options with respect to tailoring lattice geometry and for positioning other objects within a crystal lattice. The greater rigidity of multilayer DNA origami could also positively influence the diffractive properties of crystals composed of such particles. Here, we rationally explore the role of heterogeneity and Watson-Crick interaction strengths in crystal growth using 40 variants of the original DNA triangle as model multichain objects. Crystal growth of the triangle was remarkably robust despite massive chemical, geometrical, and thermodynamical sample heterogeneity that we introduced, but the crystal growth sensitively depended on the sequences of base pairs next to the Watson-Crick sticky ends of the triangle. Our results point to weak lattice interactions and high concentrations as decisive factors for achieving productive crystallization, while sample heterogeneity and impurities played a minor role.

One step Pd(0)-catalyzed synthesis, X-ray analysis, and photophysical properties of cyclopent[hi]aceanthrylene: fullerene-like properties in a nonalternant cyclopentafused aromatic hydrocarbon.

PubMed

Dang, Hung; Levitus, Marcia; Garcia-Garibay, Miguel A

2002-01-09

A simple procedure for the synthesis of cyclopentafused polycyclic aromatic hydrocarbons (CP-PAH) with Pd(PPh(3))(2)Cl(2) catalyst has been applied to the one-pot palladium(0)-catalyzed coupling of 9,10-dibromoanthracene (1) with 2-methyl-3-butyn-2-ol. Reactions carried out in refluxing benzene in the presence of CuSO(4)/Al(2)O(3) yielded 9,10-dialkynylanthracene 2a, alkynyl aceanthrylene 2b, and 2,7-disubstituted cyclopent[hi]aceanthrylene 2c in 13%, 23%, and 19% purified yields, respectively, with total conversions of 80-90%. Sealed tube reactions without copper at 110 degrees C improved the yield of 2c up to >75%. Single-crystal X-ray analyses of 2a and 2c reveal a three-dimensional hydrogen bonding network, producing a unique crystal packing. The packing structure of 2b is dominated by pi-pi stacking interactions between two aceanthrylene molecules. CP-PAHs 2b and 2c have potentially interesting fullerene-like photophysics. While the UV-vis and fluorescence spectra of 2a (Phi(F) = 0.87) show the characteristic vibronic structure of anthracene, the UV-vis spectra of ruby-red aceanthrylene 2b and greenish-black cyclopent[hi]aceanthrylene 2c extend well into the visible range. Isomers 2b and 2c showed no detectable fluorescence emission. Unlike fullerenes, compounds 2b and 2c are poor singlet oxygen sensitizers with measured (1)O(2) quantum yields of 0.02 and 0.06, respectively. As expected from a simple Hückel analysis, 2c has relatively low two-electron reduction potentials as determined by cyclic voltammetry.

Substituent Effects on the Self-Assembly/Coassembly and Hydrogelation of Phenylalanine Derivatives.

PubMed

Liyanage, Wathsala; Nilsson, Bradley L

2016-01-26

Supramolecular hydrogels derived from the self-assembly of organic molecules have been exploited for applications ranging from drug delivery to tissue engineering. The relationship between the structure of the assembly motif and the emergent properties of the resulting materials is often poorly understood, impeding rational approaches for the creation of next-generation materials. Aromatic π-π interactions play a significant role in the self-assembly of many supramolecular hydrogelators, but the exact nature of these interactions lacks definition. Conventional models that describe π-π interactions rely on quadrupolar electrostatic interactions between neighboring aryl groups in the π-system. However, recent experimental and computational studies reveal the potential importance of local dipolar interactions between elements of neighboring aromatic rings in stabilizing π-π interactions. Herein, we examine the nature of π-π interactions in the self- and coassembly of Fmoc-Phe-derived hydrogelators by systematically varying the electron-donating or electron-withdrawing nature of the side chain benzyl substituents and correlating these effects to the emergent assembly and gelation properties of the systems. These studies indicate a significant role for stabilizing dipolar interactions between neighboring benzyl groups in the assembled materials. Additional evidence for specific dipolar interactions is provided by high-resolution crystal structures obtained from dynamic transition of gel fibrils to crystals for several of the self-assembled/coassembled Fmoc-Phe derivatives. In addition to electronic effects, steric properties also have a significant effect on the interaction between neighboring benzyl groups in these assembled systems. These findings provide significant insight into the structure-function relationship for Fmoc-Phe-derived hydrogelators and give cues for the design of next-generation materials with desired emergent properties.

Chemical Modification of a Dehydratase Enzyme Involved in Bacterial Virulence by an Ammonium Derivative: Evidence of its Active Site Covalent Adduct.

PubMed

González-Bello, Concepción; Tizón, Lorena; Lence, Emilio; Otero, José M; van Raaij, Mark J; Martinez-Guitian, Marta; Beceiro, Alejandro; Thompson, Paul; Hawkins, Alastair R

2015-07-29

The first example of an ammonium derivative that causes a specific modification of the active site of type I dehydroquinase (DHQ1), a dehydratase enzyme that is a promising target for antivirulence drug discovery, is described. The resolution at 1.35 Å of the crystal structure of DHQ1 from Salmonella typhi chemically modified by this ammonium derivative revealed that the ligand is covalently attached to the essential Lys170 through the formation of an amine. The detection by mass spectroscopy of the reaction intermediates, in conjunction with the results of molecular dynamics simulations, allowed us to explain the inhibition mechanism and the experimentally observed differences between S. typhi and Staphylococcus aureus enzymes. The results presented here reveal that the replacement of Phe225 in St-DHQ1 by Tyr214 in Sa-DHQ1 and its hydrogen bonding interaction with the conserved water molecule observed in several crystal structures protects the amino adduct against further dehydration/aromatization reactions. In contrast, for the St-DHQ1 enzyme, the carboxylate group of Asp114, with the assistance of this water molecule, would trigger the formation of a Schiff base that can undergo further dehydration reactions until full aromatization of the cyclohexane ring is achieved. Moreover, in vitro antivirulence studies showed that the reported compound is able to reduce the ability of Salmonella Enteritidis to kill A459 respiratory cells. These studies have identified a good scaffold for the design of irreversible inhibitors that can be used as drugs and has opened up new opportunities for the development of novel antivirulence agents by targeting the DHQ1 enzyme.

An Inserted α/β Subdomain Shapes the Catalytic Pocket of Lactobacillus johnsonii Cinnamoyl Esterase

PubMed Central

Vu, Clara; Xu, Xiaohui; Cui, Hong; Molloy, Sara; Savchenko, Alexei; Yakunin, Alexander; Gonzalez, Claudio F.

2011-01-01

Background Microbial enzymes produced in the gastrointestinal tract are primarily responsible for the release and biochemical transformation of absorbable bioactive monophenols. In the present work we described the crystal structure of LJ0536, a serine cinnamoyl esterase produced by the probiotic bacterium Lactobacillus johnsonii N6.2. Methodology/Principal Findings We crystallized LJ0536 in the apo form and in three substrate-bound complexes. The structure showed a canonical α/β fold characteristic of esterases, and the enzyme is dimeric. Two classical serine esterase motifs (GlyXSerXGly) can be recognized from the amino acid sequence, and the structure revealed that the catalytic triad of the enzyme is formed by Ser106, His225, and Asp197, while the other motif is non-functional. In all substrate-bound complexes, the aromatic acyl group of the ester compound was bound in the deepest part of the catalytic pocket. The binding pocket also contained an unoccupied area that could accommodate larger ligands. The structure revealed a prominent inserted α/β subdomain of 54 amino acids, from which multiple contacts to the aromatic acyl groups of the substrates are made. Inserts of this size are seen in other esterases, but the secondary structure topology of this subdomain of LJ0536 is unique to this enzyme and its closest homolog (Est1E) in the Protein Databank. Conclusions The binding mechanism characterized (involving the inserted α/β subdomain) clearly differentiates LJ0536 from enzymes with similar activity of a fungal origin. The structural features herein described together with the activity profile of LJ0536 suggest that this enzyme should be clustered in a new group of bacterial cinnamoyl esterases. PMID:21876742

An inserted α/β subdomain shapes the catalytic pocket of Lactobacillus johnsonii cinnamoyl esterase.

PubMed

Lai, Kin-Kwan; Stogios, Peter J; Vu, Clara; Xu, Xiaohui; Cui, Hong; Molloy, Sara; Savchenko, Alexei; Yakunin, Alexander; Gonzalez, Claudio F

2011-01-01

Microbial enzymes produced in the gastrointestinal tract are primarily responsible for the release and biochemical transformation of absorbable bioactive monophenols. In the present work we described the crystal structure of LJ0536, a serine cinnamoyl esterase produced by the probiotic bacterium Lactobacillus johnsonii N6.2. We crystallized LJ0536 in the apo form and in three substrate-bound complexes. The structure showed a canonical α/β fold characteristic of esterases, and the enzyme is dimeric. Two classical serine esterase motifs (GlyXSerXGly) can be recognized from the amino acid sequence, and the structure revealed that the catalytic triad of the enzyme is formed by Ser(106), His(225), and Asp(197), while the other motif is non-functional. In all substrate-bound complexes, the aromatic acyl group of the ester compound was bound in the deepest part of the catalytic pocket. The binding pocket also contained an unoccupied area that could accommodate larger ligands. The structure revealed a prominent inserted α/β subdomain of 54 amino acids, from which multiple contacts to the aromatic acyl groups of the substrates are made. Inserts of this size are seen in other esterases, but the secondary structure topology of this subdomain of LJ0536 is unique to this enzyme and its closest homolog (Est1E) in the Protein Databank. The binding mechanism characterized (involving the inserted α/β subdomain) clearly differentiates LJ0536 from enzymes with similar activity of a fungal origin. The structural features herein described together with the activity profile of LJ0536 suggest that this enzyme should be clustered in a new group of bacterial cinnamoyl esterases.

Learning Activity Package, Physical Science. LAP Numbers 5, 6, and 7.

ERIC Educational Resources Information Center

Williams, G. J.

These three units of the Learning Activity Packages (LAPs) for individualized instruction in physical science cover the physical and chemical properties of water, dehydration of crystals, solutions, acidity, strong and weak bases, neutral properties of salts, amorphous forms of carbon, hydrocarbons, and petroleum products. Each unit contains a…

Diethyl [(4-bromo­phen­yl)(5-chloro-2-hydroxy­anilino)meth­yl]phospho­nate

PubMed Central

Babu, V. H. H. Surendra; Krishnaiah, M.; Prasad, G. Syam; C. Suresh Reddy; Kant, Rajni

2009-01-01

In the title compound, C17H20BrClNO4P, inter­molecular C—H⋯O and N—H⋯O hydrogen bonds form centrosymmetric R 2 2(10) dimers linked through O—H⋯O inter­molecular hydrogen bonds, which form centrosymmetric R 2 2(16) dimers. All these hydrogen bonds form chains along [010]. In addition, the crystal structure is stabilized by weak C—H⋯Br hydrogen bonds. The very weak intramolecular N—H⋯O interaction forms a five-membered ring. PMID:21578446

ZT 0.1 Electron-Carrying Polymer Thermoelectric Composites with In Situ SnCl 2 Microstructure Growth (Open Access)

DTIC Science & Technology

2015-05-08

derivatives as potential dopants , [ 21 ] achieving elec- trical conductivities of nearly 0.01 S cm −1 and PF of 0.6 W m −1 K −2 . Segalman and co-workers...Weinheim cobalt (III) acetylacetonate (Co(acac) 3 )) to show more broadly that weakly doping microstructured inclusions can act synergis- tically with...P3 ) and PBTTT-C14 ( P4 ). The weak dopant Co(acac) 3 will form large crystals readily in p-type polymers such as P3 and P4 . S > 2000 µV K

High temperature polymers - A review of novel thermally stable hexafluoroisopropylidene-containing polymers

NASA Technical Reports Server (NTRS)

Kane, K. M.; Cassidy, P. E.; Tullos, G. L.; Reynolds, D. W.

1990-01-01

The synthesis and properties to date of several novel HFIP-containing polymers and copolymers are presented. Thermal analyses of polyether ketones (PEK), aromatic polyesters, and polymers from a novel 18F-diacid were performed on a thermal analyzer. All three polymer types exhibited enhanced solubility, thermal stability, and low dielectric constants that are predicted for polymers containing the HFIP moiety. The moderate thermal stability observed in the polymers derived from the 18F-diacid is attributed to the oxidatively weak methylene linkage between the HFIP groups and the phenyl rings. PEKs and polyarylates show potential as high emissivity coatings under conditions where atomic oxygen is present.

5-Amino-3-methyl-1-phenyl-1H-pyrazole-4-carbaldehyde hemihydrate: a polarized electronic structure within hydrogen-bonded sheets of R(10)(8)(34) rings.

PubMed

Quiroga, Jairo; Trilleras, Jorge; Cobo, Justo; Glidewell, Christopher

2010-01-01

In the title compound, C(11)H(11)N(3)O.0.5H(2)O, the water molecule lies across a twofold rotation axis in the space group Pbcn. The bond distances in the organic component provide evidence for polarization of the electronic structure. The molecular components are linked into puckered sheets of R(10)(8)(34) rings by a combination of O-H...N and N-H...O hydrogen bonds; adjacent sheets are weakly linked by an aromatic pi-pi stacking interaction. Comparisons are made with some fused-ring analogues.

Extending Halogen-based Medicinal Chemistry to Proteins: IODO-INSULIN AS A CASE STUDY.

PubMed

El Hage, Krystel; Pandyarajan, Vijay; Phillips, Nelson B; Smith, Brian J; Menting, John G; Whittaker, Jonathan; Lawrence, Michael C; Meuwly, Markus; Weiss, Michael A

2016-12-30

Insulin, a protein critical for metabolic homeostasis, provides a classical model for protein design with application to human health. Recent efforts to improve its pharmaceutical formulation demonstrated that iodination of a conserved tyrosine (Tyr B26 ) enhances key properties of a rapid-acting clinical analog. Moreover, the broad utility of halogens in medicinal chemistry has motivated the use of hybrid quantum- and molecular-mechanical methods to study proteins. Here, we (i) undertook quantitative atomistic simulations of 3-[iodo-Tyr B26 ]insulin to predict its structural features, and (ii) tested these predictions by X-ray crystallography. Using an electrostatic model of the modified aromatic ring based on quantum chemistry, the calculations suggested that the analog, as a dimer and hexamer, exhibits subtle differences in aromatic-aromatic interactions at the dimer interface. Aromatic rings (Tyr B16 , Phe B24 , Phe B25 , 3-I-Tyr B26 , and their symmetry-related mates) at this interface adjust to enable packing of the hydrophobic iodine atoms within the core of each monomer. Strikingly, these features were observed in the crystal structure of a 3-[iodo-Tyr B26 ]insulin analog (determined as an R 6 zinc hexamer). Given that residues B24-B30 detach from the core on receptor binding, the environment of 3-I-Tyr B26 in a receptor complex must differ from that in the free hormone. Based on the recent structure of a "micro-receptor" complex, we predict that 3-I-Tyr B26 engages the receptor via directional halogen bonding and halogen-directed hydrogen bonding as follows: favorable electrostatic interactions exploiting, respectively, the halogen's electron-deficient σ-hole and electronegative equatorial band. Inspired by quantum chemistry and molecular dynamics, such "halogen engineering" promises to extend principles of medicinal chemistry to proteins. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Models of Mass Transport During Microgravity Crystal Growth of Alloyed Semiconductors in a Magnetic Field

NASA Technical Reports Server (NTRS)

Ma, Nancy

2003-01-01

Alloyed semiconductor crystals, such as germanium-silicon (GeSi) and various II-VI alloyed crystals, are extremely important for optoelectronic devices. Currently, high-quality crystals of GeSi and of II-VI alloys can be grown by epitaxial processes, but the time required to grow a certain amount of single crystal is roughly 1,000 times longer than the time required for Bridgman growth from a melt. Recent rapid advances in optoelectronics have led to a great demand for more and larger crystals with fewer dislocations and other microdefects and with more uniform and controllable compositions. Currently, alloyed crystals grown by bulk methods have unacceptable levels of segregation in the composition of the crystal. Alloyed crystals are being grown by the Bridgman process in space in order to develop successful bulk-growth methods, with the hope that the technology will be equally successful on earth. Unfortunately some crystals grown in space still have unacceptable segregation, for example, due to residual accelerations. The application of a weak magnetic field during crystal growth in space may eliminate the undesirable segregation. Understanding and improving the bulk growth of alloyed semiconductors in microgravity is critically important. The purpose of this grant to to develop models of the unsteady species transport during the bulk growth of alloyed semiconductor crystals in the presence of a magnetic field in microgravity. The research supports experiments being conducted in the High Magnetic Field Solidification Facility at Marshall Space Flight Center (MSFC) and future experiments on the International Space Station.

Time Crystal Behavior of Excited Eigenstates

NASA Astrophysics Data System (ADS)

Syrwid, Andrzej; Zakrzewski, Jakub; Sacha, Krzysztof

2017-12-01

In analogy to spontaneous breaking of continuous space translation symmetry in the process of space crystal formation, it was proposed that spontaneous breaking of continuous time translation symmetry could lead to time crystal formation. In other words, a time-independent system prepared in the energy ground state is expected to reveal periodic motion under infinitely weak perturbation. In the case of the system proposed originally by Wilczek, spontaneous breaking of time translation symmetry cannot be observed if one starts with the ground state. We point out that the symmetry breaking can take place if the system is prepared in an excited eigenstate. The latter can be realized experimentally in ultracold atomic gases. We simulate the process of the spontaneous symmetry breaking due to measurements of particle positions and analyze the lifetime of the resulting symmetry broken state.

Time Crystal Behavior of Excited Eigenstates.

PubMed

Syrwid, Andrzej; Zakrzewski, Jakub; Sacha, Krzysztof

2017-12-22

In analogy to spontaneous breaking of continuous space translation symmetry in the process of space crystal formation, it was proposed that spontaneous breaking of continuous time translation symmetry could lead to time crystal formation. In other words, a time-independent system prepared in the energy ground state is expected to reveal periodic motion under infinitely weak perturbation. In the case of the system proposed originally by Wilczek, spontaneous breaking of time translation symmetry cannot be observed if one starts with the ground state. We point out that the symmetry breaking can take place if the system is prepared in an excited eigenstate. The latter can be realized experimentally in ultracold atomic gases. We simulate the process of the spontaneous symmetry breaking due to measurements of particle positions and analyze the lifetime of the resulting symmetry broken state.

Rise and fall of ferromagnetism in O-irradiated Al{sub 2}O{sub 3} single crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Qiang; China Spallation Neutron Source, Institute of High Energy Physics, Chinese Academy of Sciences, Dongguan 523803; Xu, Juping

2015-06-21

In dilute magnetic semiconductors studies, sapphire was usually used as non-magnetic substrate for films. We observed weak ferromagnetic component in Al{sub 2}O{sub 3} single crystal substrate, and excluded the possibility of ferromagnetic contaminations carefully by inductively coupled plasma mass spectrometry and X-ray photoelectron spectroscopy. The ferromagnetism rise and fall during the process of annealing-oxygen irradiation-annealing of the sapphire. The ferromagnetic changes are consistent with Al-vacancy related defects detected by positron annihilation spectroscopy. With first-principle calculations, we confirm that Al-vacancy can introduce magnetic moment for 3 μB in Al{sub 2}O{sub 3} crystal and form stable V{sub Al}-V{sub Al} ferromagnetic coupling at roommore » temperature.« less

Laminar mixing in a small floating zone

NASA Technical Reports Server (NTRS)

Harriott, George M.

1987-01-01

The relationship between the flow and solute fields during steady mass transfer of a dilute component is analyzed for multi-cellular rotating flows in the floating zone process of semiconductor growth. When the recirculating flows are weak in relation to the rate of crystal growth, a closed-form solution clearly shows the link between the convection pattern in the melt and the solute distribution across the surface of the growing solid. In the limit of strong convection, finite element calculations demonstrate the tendency of the composition to become uniform over the majority of the melt. The solute segregation in the product crystal is greatest when the recirculating motion is comparable to the rate of crystal growth, and points to the danger in attempting to grow compositionally uniform materials from a nearly convectionless melt.

Crystal structure and functional characterization of SF216 from Shigella flexneri.

PubMed

Kim, Ha-Neul; Seok, Seung-Hyeon; Lee, Yoo-Sup; Won, Hyung-Sik; Seo, Min-Duk

2017-11-01

Shigella flexneri is a Gram-negative anaerobic bacterium that causes highly infectious bacterial dysentery in humans. Here, we solved the crystal structure of SF216, a hypothetical protein from the S. flexneri 5a strain M90T, at 1.7 Å resolution. The crystal structure of SF216 represents a homotrimer stabilized by intersubunit interactions and ion-mediated electrostatic interactions. Each subunit consists of three β-strands and five α-helices with the β-β-β-α-α-α-α-α topology. Based on the structural information, we also demonstrate that SF216 shows weak ribonuclease activity by a fluorescence quenching assay. Furthermore, we identify potential druggable pockets (putative hot spots) on the surface of the SF216 structure by computational mapping. © 2017 Federation of European Biochemical Societies.

Guiding, bending, and splitting of coupled defect surface modes in a surface-wave photonic crystal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Zhen; Gao, Fei; Zhang, Baile, E-mail: blzhang@ntu.edu.sg

2016-01-25

We experimentally demonstrate a type of waveguiding mechanism for coupled surface-wave defect modes in a surface-wave photonic crystal. Unlike conventional spoof surface plasmon waveguides, waveguiding of coupled surface-wave defect modes is achieved through weak coupling between tightly localized defect cavities in an otherwise gapped surface-wave photonic crystal, as a classical wave analogue of tight-binding electronic wavefunctions in solid state lattices. Wave patterns associated with the high transmission of coupled defect surface modes are directly mapped with a near-field microwave scanning probe for various structures including a straight waveguide, a sharp corner, and a T-shaped splitter. These results may find usemore » in the design of integrated surface-wave devices with suppressed crosstalk.« less

Crystal structure of N′-[(E)-(1S,3R)-(3-isopropyl-1-methyl-2-oxo­cyclo­pent­yl)methyl­idene]-4-methyl­benzene­sulfono­hydrazide

PubMed Central

Tymann, David; Dragon, Dina Christina; Golz, Christopher; Preut, Hans; Strohmann, Carsten; Hiersemann, Martin

2015-01-01

The title compound, C17H24N2O3S, was synthesized in order to determine the relative configuration of the corresponding β-keto aldehyde. In the U-shaped mol­ecule, the five-membered ring approximates an envelope, with the methyl­ene C atom adjacent to the quaternary C atom being the flap, and the methyl and isopropyl substituents lying to the same side of the ring. The dihedral angles between the four nearly coplanar atoms of the five-membered ring and the flap and the aromatic ring are 35.74 (15) and 55.72 (9)°, respectively. The bond angles around the S atom are in the range from 103.26 (12) to 120.65 (14)°. In the crystal, mol­ecules are linked via N—H⋯O hydrogen bonds, forming a chain along the a axis. PMID:26870519

Annealing of aromatic polyimide precursors

NASA Technical Reports Server (NTRS)

Wakelyn, N. T.

1975-01-01

A study has been made of the thermal behavior of polyimide precursors: an isomeric pair of crystals of the complex formed by p-phenylenediamine with the separated isomers of the di-isopropyl ester of pyromellitic acid. Specimens of this material were isothermally annealed in the temperature range 120 C to 170 C for periods of time up to 1 week. Although this temperature range is well below that customarily used for imidizations, the working hypothesis was that it would be more likely that a polymer embodying at least part of the precursor structure could be formed if the molecular motion was minimized to that actually required for the formation of the imide linkage. The progress of the annealing was followed by: infrared spectroscopy, differential thermal analysis, powder X-ray diffraction, and thermal gravimetric analysis. Single crystal X-ray analysis of the meta monomer yields a structure of chains of alternating acid and base and suggests that this monomer is amenable to polymerization with a minimum of geometrical disruption.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuz'mina, L. G.; Fedorova, O. A.; Andryukhina, E. N.

A comparative study of the molecular geometry and crystal packing of crown-containing styryl heterocycles and their dimethoxy substituted analogues is performed. It is established that all the compounds exhibit an identical type of distortions of the geometry of the central styryl fragment. These are the localization of the {pi}-electron density at the ethylene bond and the bond alternation in a half of the phenyl ring due to the conjugation of lone electron pairs of the oxygen substituents with the chromophore system of the molecule. A comparative analysis of the crystal packings of the compounds reveals extended separate hydrophilic and hydrophobicmore » regions. The hydrophilic regions are built of crown ether fragments, and the hydrophobic regions consist of {pi}-conjugated and aromatic molecular fragments. The hydrophobic regions are characterized by a wide variety of packing motifs, among which stacking packing is absent. For two compounds, the formation of sandwich dimers that are preorganized to enter into the photochemical [2 + 2]cycloaddition reaction is observed.« less

Deducing chemical structure from crystallographically determined atomic coordinates

PubMed Central

Bruno, Ian J.; Shields, Gregory P.; Taylor, Robin

2011-01-01

An improved algorithm has been developed for assigning chemical structures to incoming entries to the Cambridge Structural Database, using only the information available in the deposited CIF. Steps in the algorithm include detection of bonds, selection of polymer unit, resolution of disorder, and assignment of bond types and formal charges. The chief difficulty is posed by the large number of metallo-organic crystal structures that must be processed, given our aspiration that assigned chemical structures should accurately reflect properties such as the oxidation states of metals and redox-active ligands, metal coordination numbers and hapticities, and the aromaticity or otherwise of metal ligands. Other complications arise from disorder, especially when it is symmetry imposed or modelled with the SQUEEZE algorithm. Each assigned structure is accompanied by an estimate of reliability and, where necessary, diagnostic information indicating probable points of error. Although the algorithm was written to aid building of the Cambridge Structural Database, it has the potential to develop into a general-purpose tool for adding chemical information to newly determined crystal structures. PMID:21775812

Electrical Properties of Reactive Liquid Crystal Semiconductors

NASA Astrophysics Data System (ADS)

McCulloch, Iain; Coelle, Michael; Genevicius, Kristijonas; Hamilton, Rick; Heckmeier, Michael; Heeney, Martin; Kreouzis, Theo; Shkunov, Maxim; Zhang, Weimin

2008-01-01

Fabrication of display products by low cost printing technologies such as ink jet, gravure offset lithography and flexography requires solution processable semiconductors for the backplane electronics. The products will typically be of lower performance than polysilicon transistors, but comparable to amorphous silicon. A range of prototypes are under development, including rollable electrophoretic displays, active matrix liquid crystal displays (AMLCD's), and flexible organic light-emitting diode (OLED) displays. Organic semiconductors that offer both electrical performance and stability with respect to storage and operation under ambient conditions are required. This work describes the initial evaluation of reactive mesogen semiconductors, which can polymerise within mesophase temperatures, “freezing in” the order in crosslinked domains. These crosslinked domains offer mechanical stability and are inert to solvent exposure in further processing steps. Reactive mesogens containing conjugated aromatic cores, designed to facilitate charge transport and provide good oxidative stability, were prepared and their liquid crystalline properties evaluated. Both time-of-flight and field effect transistor devices were prepared and their electrical characterisation reported.

Structural analysis and antimicrobial activity of 2[1H]-pyrimidinethione/selenone derivatives

NASA Astrophysics Data System (ADS)

Żesławska, Ewa; Korona-Głowniak, Izabela; Szczesio, Małgorzata; Olczak, Andrzej; Żylewska, Alicja; Tejchman, Waldemar; Malm, Anna

2017-08-01

Four new crystal structures of sulfur and selenium analogues of 2[1H]-pyrimidinone derivatives were determined with the use of X-ray diffraction method. The molecular geometry and intermolecular interactions of the investigated molecules were analyzed in order to find the structural features and geometrical parameters, which can be responsible for antimicrobial activities. The influence of chalcogen substituents (sulfur and selenium) on the crystal packing was also studied. The main differences in the molecular structures exist in mutual arrangement of two aromatic rings. The intermolecular interactions in all investigated compounds are similar. Furthermore, the in vitro antibacterial and antifungal activities for these compounds were evaluated. Preliminary investigations have identified two highly potent antibacterial compounds containing selenium atom, which display selectivity towards staphylococci and micrococci. This selectivity was not observed for a control compound used as a drug, namely vancomycin. These compounds possess also good antifungal activity. This is the first report of biological activities of 2[1H]-pyrimidineselenone derivatives.

Interaction of dyes CD–1 and SD–1 with the surface of oligodimethysiloxane

NASA Astrophysics Data System (ADS)

Chausov, D. N.

2018-03-01

We carried out the modeling orientation of the dyes CD–1 and SD–1 relative to the surface of oligodimethysiloxane using the atom–atom potentials method. We have discovered the dependence of the interaction energy in dyes molecules on the angles which characterizes their orientation relative to the surface of the oligodimethysiloxane crystal. It was found out that the obtained energy value of interaction with the surface can explain weak adhesive qualities of the dyes and the orientation type relative to the surface. We identified the break– loose force for the dyes on the oligodimethysiloxane crystal surface.

Effect of temperature on the formation of creep substructure in sodium chloride single crystals

NASA Technical Reports Server (NTRS)

Raj, Sai V.; Pharr, George M.

1992-01-01

The effect of temperature on the substructure morphology and the cell and subgrain size was investigated experimentally in NaCl single crystals under creep in the temperature range 573-873 K. It is found that the effect of temperature on the cell and subgrain sizes is weak in comparison with the effect of stress. However, there was a qualitative change in the substructure morphology with temperature, with the cells and subgrains better defined at higher temperatures. The volume fraction of the cell boundaries decreased with increasing temperature, thereby indicating a refinement of the microstructure at higher temperatures.

Emission polarization control in semiconductor quantum dots coupled to a photonic crystal microcavity.

PubMed

Gallardo, E; Martínez, L J; Nowak, A K; van der Meulen, H P; Calleja, J M; Tejedor, C; Prieto, I; Granados, D; Taboada, A G; García, J M; Postigo, P A

2010-06-07

We study the optical emission of single semiconductor quantum dots weakly coupled to a photonic-crystal micro-cavity. The linearly polarized emission of a selected quantum dot changes continuously its polarization angle, from nearly perpendicular to the cavity mode polarization at large detuning, to parallel at zero detuning, and reversing sign for negative detuning. The linear polarization rotation is qualitatively interpreted in terms of the detuning dependent mixing of the quantum dot and cavity states. The present result is relevant to achieve continuous control of the linear polarization in single photon emitters.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chao, Tzu-Ling; Yang, Chen-I., E-mail: ciyang@thu.edu.tw

The preparations and properties of three new homochiral three-dimensional (3D) coordination polymers, [M(D-cam)(pyz)(H{sub 2}O){sub 2}]{sub n} (M=Co (1) and Ni (2); D-H{sub 2}cam=(+) D-camphoric acid; pyz=pyrazine) and [Mn{sub 2}(D-cam){sub 2}(H{sub 2}O){sub 2}] (3), under solvothermal conditions is described. Single-crystal X-ray diffraction analyses revealed that all of compounds are homochiral 3D structure. 1 and 2 are isostructural and crystallize in the trigonal space group P3{sub 2}21, while 3 crystallizes in monoclinic space group P2{sub 1}. The structure of 1 and 2 consists of metal-D-cam helical chains which are pillared with pyrazine ligands into a 3D framework structure and 3 features amore » 3D homochiral framework involving one-dimensional manganese-carboxylate chains that are aligned parallel to the b axis. Magnetic susceptibility data of all compounds were collected. The findings indicate that μ{sub 2}-pyrazine dominate weak antiferromagnetic coupling within 1 and 2, while 3 exhibits antiferromagnetic behavior through the carboxylate groups of D-cam ligand. -- Graphical abstract: The preparations and properties of three new homochiral three-dimensional (3D) coordination polymers, [M(D-cam)(pyz)(H{sub 2}O){sub 2}]{sub n} (M=Co (1) and Ni (2); D-H{sub 2}cam=(+) D-camphoric acid; pyz=pyrazine) and [Mn{sub 2}(D-cam){sub 2}(H{sub 2}O){sub 2}] (3), under solvothermal conditions is described. Single-crystal X-ray diffraction analyses revealed that all of compounds are homochiral 3D structure. 1 and 2 are isostructural and crystallize in the trigonal space group P3{sub 2}21, while 3 crystallizes in monoclinic space group P2{sub 1}. The structure of 1 and 2 consists of metal-D-cam helical chains which are pillared with pyrazine ligands into a 3D framework structure and 3 features a 3D homochiral framework involving one-dimensional manganese-carboxylate chains that are aligned parallel to the b axis. Magnetic susceptibility data of all compounds were collected. The findings indicate that μ{sub 2}-pyrazine dominate weak antiferromagnetic coupling within 1 and 2, while 3 exhibits antiferromagnetic behavior through the carboxylate groups of D-cam ligand. Highlights: • Three homochiral 3D coordination polymers were synthesized. • 1 and 2 are 3D structure with metal-D-cam helical chains pillared by pyrazine. • 3 shows a 3D homochiral framework involving 1D manganese-carboxylate chains. • Magnetic data analysis indicates that 1–3 exhibit weak antiferromagnetic coupling.« less

DNA Nanotubes for NMR Structure Determination of Membrane Proteins

PubMed Central

Bellot, Gaëtan; McClintock, Mark A.; Chou, James J; Shih, William M.

2013-01-01

Structure determination of integral membrane proteins by solution NMR represents one of the most important challenges of structural biology. A Residual-Dipolar-Coupling-based refinement approach can be used to solve the structure of membrane proteins up to 40 kDa in size, however, a weak-alignment medium that is detergent-resistant is required. Previously, availability of media suitable for weak alignment of membrane proteins was severely limited. We describe here a protocol for robust, large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into dilute liquid crystals for application as weak-alignment media in solution NMR structure determination of membrane proteins in detergent micelles. The DNA nanotubes are heterodimers of 400nm-long six-helix bundles each self-assembled from a M13-based p7308 scaffold strand and >170 short oligonucleotide staple strands. Compatibility with proteins bearing considerable positive charge as well as modulation of molecular alignment, towards collection of linearly independent restraints, can be introduced by reducing the negative charge of DNA nanotubes via counter ions and small DNA binding molecules. This detergent-resistant liquid-crystal media offers a number of properties conducive for membrane protein alignment, including high-yield production, thermal stability, buffer compatibility, and structural programmability. Production of sufficient nanotubes for 4–5 NMR experiments can be completed in one week by a single individual. PMID:23518667

DNA nanotubes for NMR structure determination of membrane proteins.

PubMed

Bellot, Gaëtan; McClintock, Mark A; Chou, James J; Shih, William M

2013-04-01

Finding a way to determine the structures of integral membrane proteins using solution nuclear magnetic resonance (NMR) spectroscopy has proved to be challenging. A residual-dipolar-coupling-based refinement approach can be used to resolve the structure of membrane proteins up to 40 kDa in size, but to do this you need a weak-alignment medium that is detergent-resistant and it has thus far been difficult to obtain such a medium suitable for weak alignment of membrane proteins. We describe here a protocol for robust, large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into dilute liquid crystals for application as weak-alignment media in solution NMR structure determination of membrane proteins in detergent micelles. The DNA nanotubes are heterodimers of 400-nm-long six-helix bundles, each self-assembled from a M13-based p7308 scaffold strand and >170 short oligonucleotide staple strands. Compatibility with proteins bearing considerable positive charge as well as modulation of molecular alignment, toward collection of linearly independent restraints, can be introduced by reducing the negative charge of DNA nanotubes using counter ions and small DNA-binding molecules. This detergent-resistant liquid-crystal medium offers a number of properties conducive for membrane protein alignment, including high-yield production, thermal stability, buffer compatibility and structural programmability. Production of sufficient nanotubes for four or five NMR experiments can be completed in 1 week by a single individual.

Structure of the GH1 domain of guanylate kinase-associated protein from Rattus norvegicus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tong, Junsen; Yang, Huiseon; Eom, Soo Hyun

2014-09-12

Graphical abstract: - Highlights: • The crystal structure of GKAP homology domain 1 (GH1) was determined. • GKAP GH1 is a three-helix bundle connected by short flexible loops. • The predicted helix α4 associates weakly with the helix α3, suggesting dynamic nature of the GH1 domain. - Abstract: Guanylate-kinase-associated protein (GKAP) is a scaffolding protein that links NMDA receptor-PSD-95 to Shank–Homer complexes by protein–protein interactions at the synaptic junction. GKAP family proteins are characterized by the presence of a C-terminal conserved GKAP homology domain 1 (GH1) of unknown structure and function. In this study, crystal structure of the GH1 domainmore » of GKAP from Rattus norvegicus was determined in fusion with an N-terminal maltose-binding protein at 2.0 Å resolution. The structure of GKAP GH1 displays a three-helix bundle connected by short flexible loops. The predicted helix α4 which was not visible in the crystal structure associates weakly with the helix α3 suggesting dynamic nature of the GH1 domain. The strict conservation of GH1 domain across GKAP family members and the lack of a catalytic active site required for enzyme activity imply that the GH1 domain might serve as a protein–protein interaction module for the synaptic protein clustering.« less

Persistent magnetism in silver-doped BaF e 2 A s 2 crystals

DOE PAGES

Li, Li; Cao, Huibo; Parker, David S.; ...

2016-10-12

Here, we investigate the thermodynamic and transport properties of silver-substituted BaF e 2 A s 2 (122) crystals up to ~ 4.5 % . Similar to other transition-metal substitutions in 122, Ag diminishes the antiferromagnetic ( T N ) and structural ( T S ) transition temperatures, but unlike other electron-doped 122s, T N and T S coincide without splitting. Though magnetism drops precipitously to T N = 84 K at doping x = 0.029 , it only weakly changes above this x , settling at T N = 80 K at x = 0.045 . Compared to this persistentmore » magnetism in Ag-122, doping other group 11 elements of either Cu or Au in 122 diminished T N and induced superconductivity near T c = 2 K at x = 0.044 or 0.031, respectively. Ag-122 crystals show reflective surfaces with surprising thicker cross sections for x ≥ 0.019 , the appearance that is in contrast to the typical thin stacked layered feature seen in all other flux-grown x-122 and lower Ag-122. We found that this physical trait may be a manifest of intrinsic weak changes in c lattice and T N . Our theoretical calculations suggest that Ag doping produces strong electronic scattering and yet a relatively small disruption of the magnetic state, both of which preclude superconductivity in this system.« less

Direct Photolithography on Molecular Crystals for High Performance Organic Optoelectronic Devices.

PubMed

Yao, Yifan; Zhang, Lei; Leydecker, Tim; Samorì, Paolo

2018-05-23

Organic crystals are generated via the bottom-up self-assembly of molecular building blocks which are held together through weak noncovalent interactions. Although they revealed extraordinary charge transport characteristics, their labile nature represents a major drawback toward their integration in optoelectronic devices when the use of sophisticated patterning techniques is required. Here we have devised a radically new method to enable the use of photolithography directly on molecular crystals, with a spatial resolution below 300 nm, thereby allowing the precise wiring up of multiple crystals on demand. Two archetypal organic crystals, i.e., p-type 2,7-diphenyl[1]benzothieno[3,2- b][1]benzothiophene (Dph-BTBT) nanoflakes and n-type N, N'-dioctyl-3,4,9,10-perylenedicarboximide (PTCDI-C8) nanowires, have been exploited as active materials to realize high-performance top-contact organic field-effect transistors (OFETs), inverter and p-n heterojunction photovoltaic devices supported on plastic substrate. The compatibility of our direct photolithography technique with organic molecular crystals is key for exploiting the full potential of organic electronics for sophisticated large-area devices and logic circuitries, thus paving the way toward novel applications in plastic (opto)electronics.

Role of the Strength of Drug-Polymer Interactions on the Molecular Mobility and Crystallization Inhibition in Ketoconazole Solid Dispersions.

PubMed

Mistry, Pinal; Mohapatra, Sarat; Gopinath, Tata; Vogt, Frederick G; Suryanarayanan, Raj

2015-09-08

The effects of specific drug-polymer interactions (ionic or hydrogen-bonding) on the molecular mobility of model amorphous solid dispersions (ASDs) were investigated. ASDs of ketoconazole (KTZ), a weakly basic drug, with each of poly(acrylic acid) (PAA), poly(2-hydroxyethyl methacrylate) (PHEMA), and polyvinylpyrrolidone (PVP) were prepared. Drug-polymer interactions in the ASDs were evaluated by infrared and solid-state NMR, the molecular mobility quantified by dielectric spectroscopy, and crystallization onset monitored by differential scanning calorimetry (DSC) and variable temperature X-ray diffractometry (VTXRD). KTZ likely exhibited ionic interactions with PAA, hydrogen-bonding with PHEMA, and weaker dipole-dipole interactions with PVP. On the basis of dielectric spectroscopy, the α-relaxation times of the ASDs followed the order: PAA > PHEMA > PVP. In addition, the presence of ionic interactions also translated to a dramatic and disproportionate decrease in mobility as a function of polymer concentration. On the basis of both DSC and VTXRD, an increase in strength of interaction translated to higher crystallization onset temperature and a decrease in extent of crystallization. Stronger drug-polymer interactions, by reducing the molecular mobility, can potentially delay the crystallization onset temperature as well as crystallization extent.