X-ray studies on crystalline complexes involving amino acids and peptides. XXV. Structures of DL-proline hemisuccinic acid and glycyl-L-histidinium semisuccinate monohydrate and a comparative study of amino-acid and peptide complexes of succinic acid

DL-Proline hemisuccinic acid, C5H9NO2.1/2C4H6O4, M(r) = 174.2, P2(1/c) a = 5.254 (1), b = 17.480 (1), c = 10.230 (i) angstrom, beta = 119.60 (6)-degrees Z = 4, D(m) = 1.41 (4), D(x) = 1.42 g cm-3, R = 0.045 for 973 observed reflections. Glycyl-L-histidinium semisuccinate monohydrate, C8H13N4O3+.C4H5O4-.H2O, M(r) = 348.4, P2(1), a = 4.864 (1), b = 17.071 (2), c = 9.397 (1) angstrom, beta = 90.58-degrees, Z = 2, D(m) = 1.45 (1), D(x) = 1.48 g cm-3, R = 0.027 for 1610 observed reflections. Normal amino-acid and dipeptide aggregation patterns are preserved in the structures in spite of the presence of succinic acid/semisuccinate ions. In both the structures, the amino-acid/dipeptide layers stack in such a way that the succinic acid molecules/semisuccinate ions are enclosed in voids created during stacking. Substantial variability in the ionization state and the stoichiometry is observed in amino-acid and peptide complexes of succinic acid. Succinic acid molecules and succinate ions appear to prefer a planar centro-symmetric conformation with the two carboxyl (carboxylate) groups trans with respect to the central C=C bond. Considerable variation is seen in the departure from and modification of normal amino-acid aggregation patterns produced by the presence of succinic acid. Some of the complexes can be described as inclusion compounds with the amino acid/dipeptide as the 'host' and succinic acid/semisuccinate/succinate as the 'guest'. The effects of change in chirality, though very substantial, are not the same in different pairs of complexes involving DL and L isomers of the same amino acid.

Crystal structures of fluorinated aryl biscarbonates and a biscarbamate: a counterpoise between weak intermolecular interactions and molecular symmetry

Conformational features and supramolecular structural organization in three aryl biscarbonates and an aryl biscarbamate with rigid acetylenic unit providing variable spacer lengths have been probed to gain insights into the packing features associated with molecular symmetry and the intermolecular interactions involving `organic' fluorine. Four structures but-2-yne-1,4-diyl bis(2,3,4,5,6-pentafluorophenylcarbonate), 1; but-2-yne-1,4-diyl bis(4-fluorophenylcarbonate), 2; but-2-yne-1,4-diyl bis(2,3,4,5,6-pentafluorophenylcarbamate), 3 and hexa-2,4-diyne-1,6-diyl bis(2,3,4,5,6-pentafluorophenylcarbonate), 4 have been analyzed in this context. Compound 1 adopts a non-centrosymmetric ``twisted'' (syn) conformation, whereas 2, 3 and 4 acquire a centrosymmetric ``extended'' (anti) conformation. Weak intermolecular interactions and in particular those involving fluorine are found to dictate this conformational variation in the crystal structure of 1. A single-crystal neutron diffraction study at 90 K was performed on 1 to obtain further insights into these interactions involving `organic' fluorine.

Liquid-Liquid Interphase (Biphasic) as the Reaction Medium in the Assembly of a Hierarchy of Structures of 4,4 `-Azodibenzoic Acid with Zinc and Cadmium

The compounds Zn(C12H8N2)](2)C12N2H8(COO)(2)](2)center dot(C6H12O)center dot(H2O), I, Zn(C12H8N2)]C12N2H8(COO)(2)], II, Cd(C12H8N2)(H2O)]C12N2H8(COO)(2)]center dot(H2O), III, Zn(C10N2H8)]C12N2H8(COO)(2)]center dot 0.5(C10N2H8), IV, Cd(C12N2H8(COO)(2)center dot H2O], V, and Zn-3(mu(2)-O)(mu(3)-O)(3)]C12N2H8(COO)(2)], VI, have been synthesized by using a biphasic approach (I, III, V, VI) or regular hydrothermal method (II, IV). The compounds exhibit one (I and II), two (In), and three dimensionally (IV, V, VI) extended structures. The flexible azodibenzoate ligand gives rise to a 3-fold interpenetration (IV) when the synthesis was carried out using normal hydrothermal methods. The biphasic approach forms structures without any interpenetrations, especially in the three-dimensional structures of V and VI. Formation of Cd2O2 dimers in V and extended M-O(H)-M two-dimensional layers in VI suggests the subtle structural control achieved by the biphasic method. Transformation studies indicate that it is possible to transform I to II. Lewis acid catalytic studies have been performed to evaluate the role of the coordination environment in such reactions. All the compounds have been characterized by a variety of techniques that includes powder X-ray diffraction, infrared, thermogravitric analysis, UV-vis, photoluminescence studies.

Influence of acetyl and bromine substitutions on stacking. Crystal and molecular structures of 8-bromo-2',3',5'-triacetyl adenosine and 8-bromo 2',3',5'-triacetyl guanosine

The three dimensional structures of 8-bromo 2',3',5' triacetyl adenosine (8-Br Tri A) and 8-bromo 2',3',5'-triacetyl guanosine (8-Br Tri G) have been determined by single crystal X-ray diffraction methods to study the combined effect of bromine and acetyl substitutions on molecular conformation and interactions. The ribose puckers differ from those found in unbrominated Tri A and Tri G and unacetylated 8-Br A and 8-Br G analogues

Reactions of palladium chloride with amino spirocyclic cyclotriphosphazenes: Isolation and Crystal Structures of Novel Mono- and Bimetallic Complexes Formed by the Hydrolysis of a .lambda.5-Diazaphospholane Ring

The reaction of the amino spirocyclic cyclotriphosphazene N3P3(NMe2)4(NHCH2CH2CH2NH) (2) with palladium chloride gives the stable chelate complex [PdCl2.2] (4). An X-ray crystallographic study reveals that one of the nitrogen atoms of the diaminoalkane moiety and an adjacent phosphazene ring nitrogen atom are bonded to the metal. An analogous reaction with the phosphazene N3P3(NMe2)4(NHCH2CH2NH) (1) gives initially a similar complex which undergoes facile hydrolysis to give the novel monometallic and bimetallic complexes [PdCl2.HN3P3(O)(NMe2)4(NHCH2CH2NH2)] (5) and [PdCl{N3P3(NMe2)4(NCH2CH2NH2)}]2(O) (6), which have been structurally characterized; in the former, an (oxophosphazadienyl)ethylenediamine is chelated to the metal whereas, in the latter, an oxobridged bis(cyclotriphosphazene) acts as a hexadentate nitrogen donor ligand in its dianionic form. Crystal data for 4 : a = 14.137(1) angstrom, b = 8.3332(5) angstrom, c = 19.205(2) angstrom, beta = 96.108(7)degrees, P2(1)/c, Z = 4, R = 0.027 with 3090 reflections (F > 5sigma(F)). Crystal data for 5 : a = 8.368(2) angstrom, b = 16.841(4) A, c = 16.092(5) angstrom, beta = 98.31(2)degrees, P2(1)/n, Z = 4, R = 0.049 with 3519 reflections (F > 5sigma(F)). Crystal data for 6 : a = 22.455(6) angstrom, b = 14.882(3) angstrom, c = 13.026(5) angstrom, 6 = 98.55(2)degrees, C2/c, Z = 4, R = 0.038 with 3023 reflections (F > 5sigma(F)).

Inherent structures of phase-separating binary mixtures: Nucleation, spinodal decomposition, and pattern formation

An energy landscape view of phase separation and nonideality in binary mixtures is developed by exploring their potential energy landscape (PEL) as functions of temperature and composition. We employ molecular dynamics simulations to study a model that promotes structure breaking in the solute-solvent parent binary liquid, at low temperatures. The PEL of the system captures the potential energy distribution of the inherent structures (IS) of the system and is obtained by removing the kinetic energy (including that of intermolecular vibrations). The broader distribution of the inherent structure energy for structure breaking liquid than that of the structure making liquid demonstrates the larger role of entropy in stabilizing the parent liquid of the structure breaking type of binary mixtures. At high temperature, although the parent structure of the structure breaking binary mixture is homogenous, the corresponding inherent structure is found to be always phase separated, with a density pattern that exhibits marked correlation with the energy of its inherent structure. Over a broad range of intermediate inherent structure energy, bicontinuous phase separation prevails with interpenetrating stripes as signatures of spinodal decomposition. At low inherent structure energy, the structure is largely phase separated with one interface where as at high inherent structure energy we find nucleation type growth. Interestingly, at low temperature, the average inherent structure energy (< EIS >) exhibits a drop with temperature which signals the onset of crystallization in one of the phases while the other remains in the liquid state. The nonideal composition dependence of viscosity is anticorrelated with average inherent structure energy.

Synthesis, properties and crystal structures of diastereomeric areneruthenium(II) chiral Schiff-base complexes

Diastereomers (SRu,Sc)-1a and (RRu,Sc)-1b, in a ratio of 85: 15 and formulated as [Ru(η-MeC6H4Pri-p)Cl(L*)], have been prepared by treating [{Ru(η-MeC6H4Pri-p)Cl2}2] with the sodium salt of (S)-α-methylbenzylsalicylaldimine (HL*) in tetrahydrofuran at –70 °C. The reaction of 1(1a+1b) with AgClO4 in acetone followed by an addition of PPh3 or 4-methylpyridine (4Me-py) leads to the formation of adducts [Ru(η-MeC6H4Pri-p)(PPh3)(L*)]ClO42[(SRu,Sc)2a, (FRu,Sc)2b] and [Ru(η-MeC6H4Pri-p)(4Me-py)(L*)]ClO43[(SRu,Sc)3a, (RRu,Sc)3b] in the diastereomeric ratios (SRu,Sc) : (RRu,Sc) of 2 : 98 and 76 : 24, respectively. Complex 1 crystallises with equal numbers of 1a and 1b molecules in an asymmetric unit of monoclinic space group P21 with a= 10.854(1), b= 17.090(1), c= 12.808(4)Å, β= 110.51(1)°, and Z= 4. The structure was refined to R= 0.0552 and R′= 0.0530 with 2893 reflections having I[gt-or-equal] 1.5σ(I). The absolute configurations of the chiral centres in the optically pure single crystal of the PPh3 adduct have been obtained from an X-ray study. Crystals of formulation [Ru(η-MeC6H4Pri-p)-(PPh3)(L*)]2[ClO4][PF6]·1.5 CHCl3, obtained in presence of both ClO4 and PF6 anions, belong to the non-centric triclinic space group P1 with a= 10.852(2), b= 14.028(1), c= 15.950(2)Å, α= 91.51(1), β= 105.97(1), γ= 106.11(1)°, and Z= 2. The final residuals were R= 0.0713, R′= 0.0752 with 7283 reflections having I[gt-or-equal] 2.5σ(I). The crystal structures of 1a,1b, and the PPh3 adduct (2b,2b′) consist of a ruthenium(II) centre bonded to a η-p-cymene, a bidentate chelating Schiff base, and a unidentate ligand (Cl or PPh3). The chirooptical properties of the complexes have been studied using 1H NMR and CD spectral data. The presence of a low-energy barrier for the intermediate involved in these reactions, showing both retention as well as inversion of the metal configuration, is discussed.

The structures of bacteriorhodopsin with different retinal-Schiff base orientations--computer modeling and energy minimization studies

Bacteriorhodopsin has been the subject of intense study in order to understand its photochemical function. The recent atomic model proposed by Henderson and coworkers based on electron cryo-microscopic studies has helped in understanding many of the structural and functional aspects of bacteriorhodopsin. However, the accuracy of the positions of the side chains is not very high since the model is based on low-resolution data. In this study, we have minimized the energy of this structure of bacteriorhodopsin and analyzed various types of interactions such as - intrahelical and interhelical hydrogen bonds and retinal environment. In order to understand the photochemical action, it is necessary to obtain information on the structures adopted at the intermediate states. In this direction, we have generated some intermediate structures taking into account certain experimental data, by computer modeling studies. Various isomers of retinal with 13-cis and/or 15-cis conformations and all possible staggered orientations of Lys-216 side chain were generated. The resultant structures were examined for the distance between Lys-216-schiff base nitrogen and the carboxylate oxygen atoms of Asp-96 - a residue which is known to reprotonate the schiff base at later stages of photocycle. Some of the structures were selected on the basis of suitable retinal orientation and the stability of these structures were tested by energy minimization studies. Further, the minimized structures are analyzed for the hydrogen bond interactions and retinal environment and the results are compared with those of the minimized rest state structure. The importance of functional groups in stabilizing the structure of bacteriorhodopsin and in participating dynamically during the photocycle have been discussed.

Diphenylantimony(V) oxo/chloro carboxylates and phosphinates: crystal structures of {SbPh2Cl[O2P(C6H11)2]}2O and [SbPh2(O2CPh)2]2O

Reaction of SbPh(2)Cl(3) (1 mol) with the silver salt of dicyclohexylphosphinic acid (2 mol) afforded {SbPh(2)Cl[O2P(C6H11)(2)]}O-2 1, a similar reaction with AgO2P(C8H15)(2) gave a product formulated as {SbPh(2)Cl[O2P(C8H15)(2)]}O-2 2. Similar reactions with silver carboxylates (1:3 stoichiometry) led to the crystalline derivatives [SbPh(2)(O(2)CR)(2)]O-2 (R = Ph 3, CHPh(2) 4, 2,4,6-Me(3)C(6)H(2) 5, 2-MeC(6)H(4) 6 or 4-MeC(6)H(4) 7), whereas the 1:2 reaction afforded crystalline SbPh(2)Cl(O(2)CR)(2) (R = Ph 8, 2-MeC(6)H(4) 9 or 4-MeC(6)H(4) 10). Interconversion of the previously known compounds [SbPh(2)(O(2)CMe)(2)]O and Sb(4)Ph(8)O(6) . 3MeCO(2)H was achieved and established by H-1 NMR spectroscopy. Compounds 1 and 3 were further characterized by X-ray diffraction; the antimony in 1 is six-co-ordinated with bridging phosphinates whereas in 3 it is seven-co-ordinated with chelating benzoates. Short Sb-O (oxo) distances (1.923 Angstrom) and near linearity at the bridging ox

Hydrogen-Bond-Directed Nonlinear-Optical Organic Materials - Evidence For The Control Of 2nd-Harmonic Generation Activities From The X-Ray Crystal-Structures Of The Complexes Of L-Tartaric Acid With M-Anisidine and P-Toluidine

Several substituted anilines were converted to binary salts with L-tartaric acid. Second harmonic generation (SHG) activities of these salts were determined. The crystal packing in two structures, (i) m-anisidinium-L-tartrate monohydrate (i) and (ii) p-toluidinium-L-tartrate (2), studied using X-ray diffraction demonstrates that extensive hydrogen bonding steers the components into a framework which has a direct bearing on the SHG activity

Novel Metastable Structures of WO3, MoO3 and W1-xMoxO3 Obtained by the Deintercalation of Layered Amine Adducts

Deintercalation of amines from the layered amine adducts of WO3, MoO3 and W1-xMoxO3 has been employed as a soft chemical route to produce unusual metastable structures of the oxides. After the adducts of WO3, MoO3 and W1-xMoxO3 (x = 0.25, 0.5, 0.75) with amines such as triethylamine (TEA), pyridine, n-butylamine and n-octylamine had been characterized, deintercalation was carried out thermally as well as by acid leaching. Thermal deintercalation yielded novel metastable structures of WO3 and MoO3 that were significantly different from the stable forms, which contain distorted metal-oxygen octahedra. Thus, ReO3-type cubic WO3 was obtained by the thermal deintercalation of WO3 . 0.5 TEA. Acid leaching of the amines gave metastable phases of WO3, MoO3 and W1-xMoxO3, which were different from those obtained thermally. All the metastable phases transformed to the corresponding stable forms at higher temperatures.

Local environmental structures of Mo in the superionic conducting glass (AgI)(0.6)(Ag2MoO4)(0.4) by anomalous X-ray scattering

The anomalous X-ray scattering (AXS) method using Mo K absorption edges has been employed for obtaining the local structural information of superionic conducting glass having the composition (AgI)(0.6)(Ag2MoO4)(0.4). The possible atomic arrangements in the near-neighbor region of this glass were estimated by coupling the results with the least-squares variational analysis so as to reproduce the differential intensity profile for Mo as well as the ordinary scattering profile. The coordination number of oxygen around Mo is found to be about 4 at the distance of 0.180 mn. This implies that the most probable structural entity in the glass is the MoO4 tetrahedral unit which has been proposed based on infrared spectroscopy. The value of the coordination number of I- around Ag+ is estimated as 4.4 at 0.287 nm, suggesting an arrangement similar to that of crystalline or molten AgI.

Micellar structures of dimeric surfactants with phosphate head groups and wettable spacers: A small-angle neutron scattering study

Dimeric or gemini surfactants consist of two hydrophobic chains and two hydrophilic head groups covalently connected by a hydrophobic or hydrophilic spacer. This paper reports the small-angle neutron scattering (SANS) measurements from aqueous micellar solutions of two different recently developed types of dimeric surfactants: (i) bis-anionic C16H33PO4--(CH2)(m)-PO4-C16H33,2Na(+) dimeric surfactants composed of phosphate head groups and a hydrophobic polymethylene spacer, referred to as 16-m-16,2Na(+), for spacer lengths m = 2, 4, 6, and 10, (ii) bis-cationic C16H33N+(CH3)(2)-CH2-(CH2-O-CH2)(p)-CH2-N+ (CH3)(2)C16H33,2Br(-) dimeric surfactants composed of dimethylammonium head groups and a wettable polyethylene oxide spacer, referred to as 16-CH2-p-CH2-16,2Br(-), for spacer lengths p = 1 - 3. The micellar structures of these surfactants are compared with the earlier studied bis-cationic C16H33N+ (CH3)(2)-(CH2)(m)-N+ (CH3)(2)C16H33,2Br(-) dimeric surfactants composed of dimethylammonium head groups and a hydrophobic polymethylene spacer, referred to as 16-m-16,2Br(-). It is found that 16-m-16,2Na(+), similar to 16-m-16,2Br(-), form various micellar structures depending on the spacer length. Micelles an disklike for rn = 2, rodlike for m = 4, and prolate ellipsoidal fur m = 6 and 10. The micelles of 16-CH2-p-CH2-16,2Br(-) are prolate ellipsoidal for all the values of p = 1 - 3. It is also found that micelles of 16-m-16,2Na(+) and 16-CH2-p-CH2-16,2Br(-) are large in comparison to those of 16-in-16,2Br(-) for similar spacer lengths. This is connected with the fact that both in 16-m-16,2Na(+) and 16-CH2-p-CH2-16,2Br(-), the head group or the spacer is more hydrated as compared to that in the 16-m-16,2Br(-). An increase in the hydration of the spacer or the head group increases the screening of the Coulomb repulsion between the charged head groups. This effect has been found to be more pronounced in the dimeric surfactants having wettable spacers. [S1063-651X(99)00303-7].