Conformational analysis 29: Preparation and1H and13C NMR,FTIR, MS,and crystallographic conformational and configurational study of 3-Oxo-1,3-oxathiane and its monomethyl derivatives

3-Oxo-1,3-oxathiane (1) and its monomethyl derivatives were prepared by oxidation of the corresponding 1,3-oxathianes. The structural analysis was carried out by¹H and¹³C NMR, FTIR, and mass spectrometry. At 298 K compound1 was a 1 1 (at 173 K a 3 1) mixture of the SO(ax) and SO(eq) chair forms. The major oxidation products of methyl 1,3-oxathianes attained exclusively the SO(ax), Me(eq) chair forms except that of the 5-methyl derivative, which consisted of 7% of the SO(eq), Me(ax) chair conformation in CDCl₃ solution. The minor products of oxidation existed in anancomeric SO(eq), Me(eq) chair conformations. The oxidation of 2-methyl- 1,3-oxathiane, however, led to 3,3-dioxo derivative (6) in addition to thetrans [SO(eq)] monoxide. The crystal structures of6 andtrans-3-oxo-5-methyl-1,3-oxathiane were solved by X-ray diffractometry.     

One methylene too far: The solid state structure of the para-sulfonatomethylcalix[4]arene

We report here, the first crystallographic structure of the new water soluble calixarene, para-sulfonatomethylcalix[4]arene. Anchoring a methylene group between the aromatic core of the calixarene and sulfonate groups extended the hydrophobic cavity but led to a more flexible macromolecule allowing formation of hydrogen bonds between vicinal sulfonate groups, causing the groups to point towards the cavity and effectively close it, with S  S distances of 9.7 Å × 7.9 Å. The packing motif consists of bilayers of para-sulfonatomethylcalix[4]arene along both the a and b axis.     

Synthesis of a biphenyl library for studies of hydrogen bonding in the solid state

A biphenyl library incorporating amide and sulfonamide groups has been synthesised via microwave-mediated Suzuki-Miyaura couplings. Many derivatives were crystallised from dichloromethane/methanol and analysed by single crystal X-ray diffraction. An interesting structure was obtained for N-(4′-methylbiphenyl-4-yl)acetamide with Z′=6 and hydrogen-bonding networks of the type N-H^…O in the unit cell.     

Inclusion complexes of the natural product gossypol. Clathrate type inclusion complexes of gossypol with carbonyl group containing guests

The crystal structures of 2:1 inclusion complexes of gossypol with methyl propionate (GPMEP) and ethyl acetoacetate (GPEAA) have been determined by X-ray structure analysis. The crystals of GPMEP, C₃₀H₃₀O₈l/2 C₄H₈O₂, are monoclinic, space groupC2/c,a=11.079(3),b = 30.724(7), c = 16.515(5) Å, = 90.46(2)°,V = 5621(3) Å,Z = 8,D _x = 1.33 g cm^–3. The structure has been refined to the finalR value of 0.059 for 1899 observed reflections. The crystals of GPEAA, C₃₀H₃₀O₈l/2 C₆H₁₀O₃, are monoclinic, space groupC2/c,a=11.095(2),b=30.604(9),c = 16.955(5) Å, = 88.27(2)°,V = 5754(3) Å,Z = 8,D _x = 1.35 g cm^–3. The structure has been refined to the finalR value of 0.056 for 2502 observed reflections.In contrast to previously investigated inclusion complexes of gossypol the host molecules do not form centrosymmetric dimersvia hydrogen bonds. In the crystal structures the racemic gossypol is separated into enantiomers forming alternating bimolecular layers. Nearly perpendicular to these chiral bilayers run elongated cavities enclosed on each side by layers of opposite chirality. The surface of these layers is hydrophobic, the polar groups are hidden inside the layer. Guest molecules which are hydrogen bonded to the host are included in cylindrically shaped cavities. Possible hydrogen bonds between host and guest are analysed for this isostructural class of complexes.     

Morphologies of branched-chain pyrogallol[4]arenes in the solid state

A suite of branched-chain pyrogallol[4]arene (Pg) macrocycles, most of which show activity in bilayer membranes, has been prepared and studied by X-ray crystallography. The little-known branched side-chain Pgs include 2-propyl, 2-butyl, 2-pentyl, 3-pentyl, 3-heptyl, 4-heptyl, 5-nonyl and cyclohexyl. The Pgs form self-assembled structures having bilayer, capsule or, in one case, a nanotube morphology. The nanotube structure observed for C-(di-n-ethyl)pyrogallol[4]arene was confirmed by X-ray structure analysis and by transmission and scanning electron microscopies.     

Conformational analysis of new 14-membered ring diketal dilactam macrocycles: molecular mechanics, liquid and solid state NMR studies

A conformational study of new diversely substituted 14-membered diketal dilactam macrocycles was conducted by NMR spectroscopy in liquid and solid states, molecular mechanics calculations and, for one compound, a previous X-ray analysis. The results obtained by the different techniques show that the conformations depend closely on whether the molecules are chiral or achiral and on the stereochemistry of the ketal OMe groups. In achiral compounds, the most stable conformation of each compound has, in both the liquid and solid states, the two NH-CO links positioned perpendicular to the macrocycle plane, lending to the trans-7,7′-OMe macrocycles 6b and 7b a rectangular [3434]-type structure. In contrast, in chiral compounds, the most stable conformations are not the same in the liquid and solid phases. In the liquid state the conformations are set by the presence of one or two N₄-H?O_1′, N_4′-H?O₁ intramolecular hydrogen bonds that position the amide group parallel to the macrocycle plane, whereas in the solid state the amide moieties again adopt a perpendicular position which can be stabilized, when the 3-R substituent is not too bulky, by intermolecular N-H?OC bonds between parallel sheets, and exceptionally, in the cis-7,7′-OMe-3,3′-Ph compound 1c, by a π-π stacking effect between the phenyl groups.     

Molecular structure of decamethylgermanocene in the solid state

The low temperature X-ray structure analysis of decamethylgermanocene reveals two independent molecules in the unit cell, both of which have a bent sandwich structure with angles between the planes of the two C₅Me₅ rings of 31.26(0.09)° and 31.55(0.10)°, respectively. The perpendicular germanium to ring distances are 220 pm, corresponding to Ge-C bond lengths ranging from 240 to 266 pm.     

Inclusion complexes of the natural product gossypol. Crystal structures of gossypol complexes with benzene and chloroform as guests

The crystal structures of the lattice inclusion complexes of gossypol with benzene and chloroform have been determined by X-ray structure analysis. The crystals of (C₃₀H₃₀O₈)₂ · C₆H₆ (GPBNZ) are triclinic, space groupPI,a = 11.241(3),b = 14.986(4),c = 17.380(4) Å, = 98.89(2), = 99.86(2), = 98.91(2)°,V = 2800(2) ų,Z = 2,D _x = 1.32 g cm^–3, (CuK ) = 7.35 cm^–1. The structure has been refined to a finalR value of 0.050 for 6146 observed reflections. The crystals of C₃₀H₃₀O₈·CHCl₃ (GPCLF) are monoclinic, space groupC2/c,a = 28.464(4),b = 8.948(1),c = 26.480(4) Å, = 108.93(2)°,V = 6380(2) ų,Z = 8,D _x = 1.33 g cm^–3, (CuK) = 30.42 cm^–1. The structure has been refined to a finalR value of 0.100 for 1980 observed reflections.GPCLF forms an intercalate-type structure and GPBNZ a clathrate-type structure. There are, however, some similarities in the packing mode of the host molecules in these two structures. On a basis of comparison of the crystal packing of GPCLF and GPBNZ one can postulate that in the desorption process of the intercalate-type GPCLF complex an intermediate clathrate structure of the GPBNZ-type should be formed.     

Inclusion complexes of the natural product gossypol. Strong influence of the guest on the host structure in channel-type isostructural inclusion complexes of gossypol

The crystal structures of 1 : 1 inclusion complexes of gossypol with tetrahydrofuran (GPTHF), cyclohexanone (GPCHN) and butanal (GPBTA) have been determined by X-ray structure analysis. The crystals of GPTHF are triclinic, space group P,a = 10.788(2),b = 10.979(3),c = 13,880(2) Å, = 80. 11(2), = 103.87(1), = 77.96(2)°,V = 1517.8(6) ų,Z = 2,R = 0.052 for 2701 observed reflections. The crystals of GPCHN are triclinic, space groups P,a = 10.803(4),b = 11.157(5),c = 15.428(6) Å, = 108.75(3), = 106.93(3), = 103.34(3)°,V = 1573(1) ų,Z = 2,R = 0.071 for 1879 observed reflections. The crystals of GPBTA are triclinic, space group P,a = 10.190(2),b = 11.335(1),c = 14.665(2) Å, = 73.04(1), = 103.74(1), = 81.07(1)°,V = 1529.9(5) ų,Z = 2,R = 0.068 for 2964 observed reflections. Crystal data for another 13 isostructural inclusion complexes are given.[/p]In this isostructural group of complexes guest molecules are accommodated in channels and are hydrogen bonded to the host molecules via an 0(1)-H....O(1) hydrogen bond. The molecular association changes significantly with the shape and size of the guest component. In GPTHF centrosymmetric dimers of gossypol formedvia O(5)-H...O(3) hydrogen bonds are associated in columns via a weak O(4)-H...O(8) hydrogen bond. In GPCHN the latter bond disappears as the distance O(4)-O(8) is increased to 3.73 Å. In GPBTA the O(5)-H...O(3) bond is replaced by three centre hydrogen bonds O(5)-H...O(2) and O(3)-H...O(5), and a centrosymmetric dimer of a new type is formed. These dimers are further connected by two weak hydrogen bonds to form columns. The butanal molecule interacts with the host structure via two hydrogen bonds. This indicates that a guest component can activate or deactivate different functional groups of the host in channel inclusion complexes of gossypol for hydrogen bond formation.     

Two conformers in the solid state for a novel organotin(IV) complex of a phosphoramidate: Syntheses, spectroscopic study and crystal structures of several new organotin(IV) complexes of N-benzoylphosphoric triamides

Several novel organotin(IV) complexes with formula SnCl₂(CH₃)₂(X)₂, X = C₆H₅C(O)NHP(O)(NC₄H₈)₂ (1), C₆H₅C(O)NHP(O)(NC₅H₁₀)₂ (2), C₆H₅C(O)NHP(O)[N(CH₃)(C₆H₁₁)]₂ (3), C₆H₅C(O)NHP(O)[NH-C(CH₃)₃]₂ (4) were synthesized and characterized by ¹H, ¹³C, ³¹P NMR, IR spectroscopy and elemental analysis. The structures have been determined for each of the four compounds. Compound 1 exists in the form of two symmetrically independent molecules in the crystalline state due to differences in their similar torsion angles. In all of the four structures there are intramolecular -Sn-Cl?H-N- hydrogen bonds, in addition to weak C-H?O and C-H?Cl hydrogen bonds. Both ¹H and ¹³C NMR spectra show the coupling of ^119/117Sn nuclei with methyl proton and carbon atoms. The δ(³¹P) of these complexes are in upfields with respect to their corresponding reported ligands. The spectroscopic and structural properties of these complexes were compared with those corresponding ligands.     

Molecular mechanics-assisted crystal engineering of solid state photoreactions: application to the Yang photocyclization of α-1-norbornylacetophenone derivatives

Based on molecular mechanics, Yang photocyclization of α-1-norbornylacetophenone derivatives in the crystalline state was engineered through methylation adjacent to the carbonyl group, thus changing the conformation in the crystal and leading to enhanced diastereo- and enantioselectivity.     

The Impact of pH on Catalytically Critical Protein Conformational Changes: The Case of the Urease,a Nickel Enzyme

Urease uses a cluster of two Ni^II ions to activate a water molecule for urea hydrolysis. The key to this unsurpassed enzyme is a change in the conformation of a flexible structural motif, the mobile flap, which must be able to move from an open to a closed conformation to stabilize the chelating interaction of urea with the Ni^II cluster. This conformational change brings the imidazole side chain functionality of a critical histidine residue, αHis323, in close proximity to the site that holds the transition state structure of the reaction, facilitating its evolution to the products. Herein, we describe the influence of the solution pH in modulating the conformation of the mobile flap. High-resolution crystal structures of urease inhibited in the presence of N-(n-butyl)phosphoric triamide (NBPTO) at pH 6.5 and pH 7.5 are described and compared to the analogous structure obtained at pH 7.0. The kinetics of urease in the absence and presence of NBPTO are investigated by a calorimetric assay in the pH 6.0–8.0 range. The results indicate that pH modulates the protonation state of αHis323, which was revealed to have pK_a=6.6, and consequently the conformation of the mobile flap. Two additional residues (αAsp224 and αArg339) are shown to be key factors for the conformational change. The role of pH in modulating the catalysis of urea hydrolysis is clarified through the molecular and structural details of the interplay between protein conformation and solution acidity in the paradigmatic case of a metalloenzyme.     

Chemical bonding in metalaheterocumulene complexes: II Demonstration of a temperature dependant conformational disorder of the methyl groups in [(CO)5CrNCN(C2H5)2]

During the determination of the crystal structure of [(CO)₅CrNCN(C₂H₅)₂] by neutron diffraction, a remarkable te temperature-dependance of the intensity of three reference reflections between 100 and 300 K was accidentally observed. In order to try to understand the nature of this phenomenon, the behaviour of this compound as a function of the temperature has been studied by differential calorimetry, and by power and single crystal X-ray diffraction methods. These experiments show neither a phase transition nor a crystal space group modification. The experimental results, supported by a simplified model, suggest a rotational disorder of the methyl groups near room temperature.     

Ionic conduction in the solid state

Solid state ionic conductors are important from an industrial viewpoint. A variety of such conductors have been found. In order to understand the reasons for high ionic conductivity in these solids, there have been a number of experimental, theoretical and computational studies in the literature. We provide here a survey of these investigations with focus on what is known and elaborate on issues that still remain unresolved. Conductivity depends on a number of factors such as presence of interstitial sites, ion size, temperature, crystal structure etc. We discuss the recent results from atomistic computer simulations on the dependence of conductivity in NASICONs as a function of composition, temperature, phase change and cation among others. A new potential for modelling of NASICON structure that has been proposed is also discussed. Dedicated to Prof J Gopalakrishnan on his 62nd birthday.     

Conformational isomerism of 1,2-bis(imidazol-1′-yl)ethane in five-coordination polymers: Influence of metal ions and m-isophthalate ligands bearing different substituents

Four novel coordination polymers, {[Zn(gauche-bime)(bdc)] · 0.5H₂O}_n (1), {[Zn(anti-bime)(HO-bdc)] · 2.5H₂O}_n (2), [Cu(gauche-bime)_0.5(anti-bime)_0.5(O₂N-bdc)]_n (4) and [Ni₂(gauche-bime)(anti-bime)(O₂N-bdc)₂(H₂O)₂]_n (5) were successfully prepared by the solvothermal reactions of 1,2-bis(imidazol-1′-yl)ethane (bime), m-isophthalic acid (H₂bdc) or its two derivatives (HO-H₂bdc = 5-hydroxyisophthalic acid, O₂N-H₂bdc = 5-nitroisophthalic acid) with different metal ions. Interestingly, bime in the four complexes exhibit different conformations owing to the synergetic influence of coexistent neutral (–H), electron-donating (–OH) or electron-withdrawing (–NO₂) groups of the dicarboxylate ligands and different metal ions. In 1 and 2, only one conformation of bime (gauche in 1 and anti in 2) is displayed, while the mixed conformations of bime (gauche:anti = 1:1) are observed in 4 and 5. At the same time, one previously reported compound {[Zn(anti-bime)(O₂N-bdc)] · H₂O}_n (3) as a comparable substance in the research system was also mentioned, in which the anti-conformation of bime was observed.     

The first naphthodiazaphosphorinane in the solid phase; syntheses, spectroscopic studies and X-ray crystallography of some new 1,3,2-diheterophosphorus compounds

New heterocyclic compounds of diazaphosphorinanes, diazaphospholes, and oxazaphospholes were synthesized and characterized by ¹H, ¹³C, ³¹P, NMR, IR spectroscopy, and CHN elemental analysis. The 3D structure of compound (5) was determined by X-ray crystallography. Since benzo- or naphthodiazaphospholes/diazaphosphorinanes containing aromatic rings are usually unstable in the solution state, their single crystal structures are rarely reported and, to the best of our knowledge, this structure is the first occasion of naphthodiazaphosphorinanes obtained here. It is noticeable that the P=O and C=O bonds are closer to syn than anti configuration and the P=O bond is placed in a pseudo-equatorial position. This structure produced a 3D polymeric chain via strong hydrogen bonds and electrostatic short contacts. Due to the ring strain of five-membered rings, for all diazaphospholes great ² J(PNH_endocyclic) coupling constants (about 18.0 Hz), as well as high ^2,3 J(P,C) coupling constants for the aromatic carbon atoms connected to the five-membered ring (about 14.5, 13.5 Hz, respectively) were measured. Replacement of one NH group in a diazaphosphole ring by an oxygen atom caused exceedingly decreased ring strain and hence highly diminished ² J(PNH_endocyclic) coupling constant. Furthermore, ³¹P NMR spectra of oxazaphospholes, like the spectra of diazaphosphorinanes, indicated highly shielded phosphorus atoms relative to those of their diazaphospholes analogs. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Hydrogen bonds in the crystal packings of mesalazine and mesalazine hydrochloride

The crystal structures of pharmaceutical product mesalazine (marketed also under different proprietary names as Salofalk, Asacol, Asacolitin, and Claversal) and its hydrochloride are reported. In the crystal mesalazine is in zwitterion form as 5-ammoniosalicylate (1) whereas mesalazine hydrochloride crystallizes in an ionized form as 5-ammoniosalicylium chloride (2). Compound 1 (C₇H₇O₃N) crystallizes in the monoclinic space group P2₁/n with a = 3.769(1) Å, b = 7.353(2) Å, c = 23.475(5) Å, β = 94.38(2)°, V = 648.7(8) ų, Z = 4, D_c = 1.568 g cm⁻³ and μ(MoK) = 1.2 cm⁻¹. Compound 2 (C₇H₈O₃NCl) crystallizes in the triclinic space group P with a = 4.4839(2) Å, b = 5.7936(2) Å, c = 15.6819(5) Å, = 81.329(3)°, β = 88.026(3)°, γ = 79.317(4)°, V = 395.74(3) ų, Z = 2, D_c = 1.591 g cm⁻³ and μ(CuK) = 40.8 cm⁻¹. The crystal structures were solved by direct methods and refined to R = 0.041 for 1 and 0.028 for 2, using 607 and 1374 observed reflections, respectively. The configuration of both molecules, with the ortho hydroxyl to a carboxyl group, favours the intramolecular hydrogen bonds. Very complex systems of intermolecular hydrogen bonds were observed in both crystal packings. They are discussed in terms of graph-set notation. The mesalazine crystal structure is characterized by two-dimensional network of hydrogen bonds in the ab plane. The crystal structure pattern of mesalazine hydrochloride is a three-dimensional network significantly supported by N⁺---HCl⁻ interactions.     

Rigid ground state structure of 1,2-dihydro-3H-benz[e]inden-3-one deformed in the lowest electronic triplet state

The X-ray diffraction of crystalline 1,2-dihydro-3H-benz[e]inden-3-one (DHBI) reveals that the molecular geometry is fully planar in the electronic ground state. Glassy solutions of naphthaldehyde, 2-acetonaphthone and methyl 2-naphthoate in the mixtures methylcyclohexane/iso-pentane (MIP) and methanol/ethanol (ME) are phosphorescent. DHBI in ME shows phosphorescence, but in MIP it is non-phosphorescent. The phosphorescence spectra of these compounds and of naphthalene have a strong resemblance. This is in accordance with a molecular distortion in the lowest triplet state, which decouples the π electron systems of the carbonyl group and the naphthyl group. The absence of phosphorescence of DHBI in MIP, indicates a geometry of the triplet state, having a non-planar naphthalene ring, when the molecule is in the non-hydrogen bonded form.     

Inclusion complexes of the natural product gossypol. Crystal structure of the 2:1 complex of gossypol withm-Xylene

The crystal structure of a 2: 1 inclusion complex of gossypol withm-xylene has been determined by X-ray structure analysis. The crystals of C₃₀H₃₀O₈·0.5C₈ H₁₀ are triclinic, space groupPl^–,a = 8.478(1),b = 14.087(2),c = 14.411(2) Å, = 115,39(1), = 75.11(1), = 86.80(1)°,V = 1475.2(4) ų,Z = 2,D _x = 1.29 g cm^–3,T = 295 K, (CuK ) = 7.01 cm^–1. The structure has been solved by direct methods and refined to the finalR value of 0.079 for 3910 observed reflections. The gossypol molecules are linked by intermolecular hydrogen bonds and form bimolecular layers parallel to the ab plane. Disorderedm-xylene molecules occupy cavities between these layers. All polar groups of the gossypol molecule are packed in the interior of the bilayer while non-polar groups are directed outwards. An analysis of the crystal packing of other inclusion complexes of gossypol shows that such bilayers are formed in four complexes and three of those structures are generically related to each other.Deceased.     

Inclusion complexes of the natural product gossypol. Crystal structure of the 2:1 complex of gossypol with amyl acrylate

The crystal structure of the 2: 1 inclusion complex of gossypol with amyl acrylate has been determined by X-ray structure analysis. The crystals of (C₃₀H₃₀O₈)₂C₈H₁₄O₂ are triclinic, space group P ,a = 14.425(2),b = 15.519(1),c = 16.409(2) Å, =97.89(1), = 117.80(1), =67.01(1)° (reduced cell:a = 14.425(2),b = 15.519(2),c = 16.017(2)Å, = 92.19(1), = 115.01(l), =67.01(1)°],V = 2986.7(5) ų,Z = 2,D _x = 1.31 g cm^–3, (CuK ) = 7.40 cm^–1,T = 292 K. The structure has been solved by direct methods and refined to the final R value of 0.059 for 5155 observed reflections. The gossypol molecules bonded via several hydrogen bonds form centrosymmetric tetramers. The two independent gossypol molecules, A and B, are related within the tetramer by a local noncrystallographic 2-fold axis. The host molecules in the crystal form cavities in which two guest molecules are placed. The ester molecule interacts via a pair of C-...H-O hydrogen bonds with two gossypol molecules of the same chirality and belonging to the same tetramer unit. The amyloxy group of the ester molecule shows a very large thermal motion. It adopts a non-extended conformation in which it can be fitted into the cavity formed by the host molecules.