Hydrogen-bonded layered structures in two bis(tert-butyldimethylsilyloxy)-substituted cyclic diol derivatives.

2,6-Bis(tert-butyldimethylsilyloxy)-9-oxabicyclo[3.3.1]nonane-3,7-diol, C(20)H(42)O(5)Si(2), (I), and 4,8-bis(tert-butyldimethylsilyloxy)-2,6-dioxatricyclo[3.3.1(3,7)]decane-1,3-diol, C(20)H(40)O(6)Si(2), (II), form layered structures that differ in the way the molecules are connected within each layer. The endocyclic O atom common to both structures plays an active role in the hydrogen-bonding network, whereas the second oxygen bridge in (II) does not participate in any interaction. This work reports the first structural analysis of two bis(tert-butyldimethylsilyloxy)-substituted cyclic diol derivatives and provides insight into the influence of small changes in the molecular structure on the supramolecular aggregation. The unbalanced hydrogen-bond acceptor/donor ratio, greater in (II) than in (I), does not result in the inclusion of water molecules in the structure.

A case of concomitant polymorphism and spontaneous resolution: the tetragonal phase of 5-hydroxymethyl-7,7,N-trimethyl-6-oxabicyclo[3.2.1]octane-1-carboxamide.

The title compound, C(12)H(21)NO(3), crystallizes in two polymorphic forms, viz. the tetragonal form described here and the monoclinic form described previously [Foces-Foces, López-Rodríguez, Pérez, Martín & Pérez-Hernández (2007). Cryst. Growth Des. 7, 905-911]. The differences in the conformations of the hydroxymethyl and methylaminocarbonyl substituents have important consequences in the hydrogen-bond interaction motifs and, therefore, in the packing arrangements. These forms are concomitant polymorphs with melting points differing by 3 K.

Supramolecular aggregation of two hydroxycarboxylic acid derivatives.

The crystal structures of 7,7-dicyclobutyl-5-hydroxymethyl-6-oxabicyclo[3.2.1]octane-1-carboxylic acid, C17H26O4, (I), and 1-(hydroxymethyl)-7-oxaspiro[bicyclo[3.2.1]octane-6,1'-cyclopentane]-5-carboxylic acid, C13H20O4, (II), determined at 170 K, show that the conformation of the hydroxymethyl group (anti or gauche) affects the dimensionality (one- or two-dimensional) of the supramolecular structures via O-H...O hydrogen bonds. In (I), the carboxyl and hydroxymethyl groups interact with themselves, forming a one-dimensional step-ladder, while in (II), a two-dimensional structure is made up of carboxylic acid centrosymmetric R(2)2(8) dimers connected by hydroxyl-to-ether contacts.

Hydrogen-bonding patterns of two dihydroxylactone derivatives.

In the hydrogen-bonding networks of 8-hydroxy-5-hydroxymethyl-3,6-dioxatricyclo[6.3.1.0(1.5)]dodecan-2-one and 5,7-bis(hydroxymethyl)-3,6-dioxatricyclo[5.3.1.0(1.5)]undecan-2-one, both C11H16O5, layers and double strands, respectively, lead to the formation of chains connected by hydroxy-to-hydroxy contacts, where the hydroxymethyl group, present in both structures, acts as a donor. The secondary structures differ in the hydrogen bonding of these chains via the second hydroxy group, which is involved in hydroxy-to-carbonyl and hydroxy-to-hydroxy bonds, respectively.

Tubular hydrogen-bonded networks sustained by water molecules.

The design concept of functional solids relies on controlling the topology of crystal packing through exploitation of weak intermolecular forces. In the context of cyclic aggregates, the ability to anticipate the consequences of ring constituents and their stereochemistries on ring conformation is vitally important since even an apparently slight structural change effected on molecules can dramatically alter the crystal structure. We have found that solid-state structures formed by hydroxy acids with a general structure (+/-)-1 depend on steric interactions. Thus, with the exception of molecules 1b and 1e, compounds (+/-)-1a-(+/-)-1m, which possess bulky and conformationally rigid substituents, aggregate by forming tapes and sheets by alternating (+) and (-) subunits held together through carboxylic acid-to-alcohol hydrogen bonds. Homologue (+/-)-1n, with conformationally flexible substituents which allow conformational deformation, gives, by incorporation of molecules of water, an efficient hexagonal assembly which extends to the third dimension to form tubular H-bonding networks. Each puckered channel can be described as interconnected closely packed hexagons in chairlike conformations. The ethyl groups presented in (+/-)-1n gave the volume required to lock the inner hexagonal wall into a rigid structure. Attempts to obtain cyclic aggregates using small substituents, compounds (+/-)-1o-(+/-)-1q, failed. The observed supramolecular assemblies of the anhydrous compounds can be classified into one-dimensional strands and two-dimensional sheets, while three-dimensional networks are present only in the hydrated molecules (1b, 1e, and 1n). The crystal structure of the anhydrous (+/-)-1n compound confirms the important role played by water molecules in the formation of tubular structures.

A solid-state NMR, X-ray diffraction, and ab initio computational study of hydrogen-bond structure and dynamics of pyrazole-4-carboxylic acid chains.

Using high-resolution solid-state (15)N CMAS NMR, X-ray crystallography, and ab initio calculations, we have studied the structure of solid pyrazole-4-carboxylic acid (1). The crystal structure was determined at 295 and 150 K. Molecules of 1 are located on a two-fold axis, implying proton disorder of the NH and OH groups; no phase transition was observed between these two temperatures. The compound forms quasi-linear ribbons in which the molecules are linked by cyclic hydrogen bonds between pyrazole and carboxylic acid groups with disordered hydrogen-bonded protons. Crystallography is unable to decide whether the disorder is dynamic or static. NMR shows that this disorder is dynamic, that is, consisting of very fast degenerate double proton transfers between two rapidly interconverting O-H.N and O.H-N hydrogen bridges. However, at low temperature, NMR shows a proton disorder-order transition where the protons are preferentially localized on given nitrogen and oxygen atoms. An amorphous phase exhibiting proton order is observed when the compound is precipitated rapidly. In this case, the defects are annealed by moderate heating. Ab initio calculations performed on oligomers of 1 show that the O-H.N hydrogen bridge is about 0.064 A shorter and less bent ( approximately 171 degrees ) than the O.H-N hydrogen bridge ( approximately 150 degrees ). For an isolated ribbon, this result leads to structures with localized protons, either to a cycle with about 200 molecules, or to a quasi-linear ribbon involving an undulated structure, or to a combination of both motifs. Only the undulated structure is compatible with the linear ribbon observed by X-ray crystallography, where the fast proton transfer in the high-temperature phase is assisted by the motions of the undulated chain. A disordered structure is assigned to the amorphous phase, which exhibits the combination of the curved and the undulated motifs.

Three 1,6-anhydro-beta-D-glycopyranose derivatives.

Two of the title compounds, 1,6-anhydro-2,3-O-(S)-benzylidene-beta-D-mannopyranose, C(13)H(14)O(5), (I), and 1,6-anhydro-4-O-benzyl-beta-D-mannopyranose, C(13)H(16)O(5), (II), are derived from beta-D-mannopyranose, while the third, 1,6-anhydro-3,4-O-(S)-benzylidene-beta-D-galactopyranose, C(13)H(14)O(5), (III), is derived from beta-D-galactopyranose. In the crystal packing, each hydroxyl group is involved in O-H.O hydrogen bonds, where the acceptor group is the other hydroxyl group in (II), or the endocyclic O atoms of the dioxolane [in (I)], anhydro [in (II)] or pyranose [in (III)] rings. Differences in the crystal packing arise from the contrasting O--H...O hydrogen-bonding environments.

Supramolecular structure of 1H-pyrazoles in the solid state: a crystallographic and ab initio study.

The secondary structure of 1H-unsubstituted pyrazole derivatives bearing only one hydrogen donor group and one or more acceptor groups has been analyzed in terms of some descriptors representing the substituents at C3 and C5. The substituent at C4 appears to affect mainly the tertiary or quaternary structure of these compounds. The proposed semi-quantitative model, which explains most hydrogen-bonded motifs as a combination of the effects of substituents at C3 and C5, has also been examined as a function of the steric and polarizability effects of these substituents represented by molar refractivity. The model also applies to other five-membered rings (1,2,4-triazoles, 1,2,4-diazaphospholes and 1,2, 4-diazaarsoles). Furthermore, ab initio calculations at RHF/6-31G* have been performed to discover the relative stability of three of the four hydrogen-bond patterns displayed by several symmetrical pyrazoles (dimers, trimers, tetramers). The fourth motif, catemers, has only been discussed geometrically.

A synthetic hydroxy acid that shows tubular-shaped structure in solid-state and ionophoric activity in phospholipid bilayers

[formula: see text] In this contribution, we describe the ability of compound (+/-)-1b and six molecules of water to form in solid-state hexameric aggregates, which self-assemble to give hollow tubular structures. Single-crystal X-ray analysis shows that these tubes are open-ended, with irregular shape and internal van der Waals pore diameter between 6 and 9 A. In addition, transmembrane sodium transport activity was also assessed for (+/-)-1b using dynamic Na(+)-NMR technique.

Biochemical and physical characterization of parvovirus minute virus of mice virus-like particles.

The VP-2 major capsid protein of the prototype strain of the parvovirus minute virus of mice (MVMp) was expressed, using a baculovirus vector, in Sf9 insect cells. Immunogold electron microscopy of infected Sf9 cells showed VP-2 localized in the nucleus and cytoplasm as is observed in mammalian cells during natural infections. The VP-2 subunits self-assembled into empty parvovirus-like particles (VLPs), which appeared morphologically similar to and immunogenically indistinguishable from native empty MVMp particles, which also contain the minor capsid protein, VP1. Incubations under different pH and temperature conditions showed that the MVMp VLPs and native empty MVMp capsids share comparable stability. Once heated the particles can be similarly and specifically cleaved by trypsin at the VP-2 N-terminal domain. This process mimics the further maturation of the "rat-like" parvovirus virions, following viral DNA encapsidation, indicating that biologically relevant features of the MVMp capsid are maintained in the VLPs. Crystals have been obtained for the MVMp VLPs which were isomorphous to those used for the high-resolution structure determination of virions and native empty particles of the immunosuppressive strain of MVM (MVMi). The VLP crystals diffracted X rays to beyond 3-A resolution and are in space group C2 (a = 448.7, b = 416.6, c = 306.1 A, and beta = 95.9 degrees ). This is the first report of crystals from parvoviral particles produced in a heterologous system diffracting X rays to high resolution, indicating that VP-2 of some parvovirus capsids can self-assemble into ordered T = 1 icosahedral capsids in the absence of other viral and host cell functions.

3(5),4-Dimethyl- and 3,4,5-trimethylpyrazole at 200 K. X-ray crystallography and quantum-chemical analysis.

The crystal and molecular structures of 3(5),4-dimethylpyrazole, C(5)H(8)N(2), (I), and of 3,4,5-trimethylpyrazole, C(6)H(10)N(2), (II), have been determined at 200 K. In (I) the 4,5-dimethylpyrazole tautomer is present in the solid state and the six independent molecules in the asymmetric unit form trimers via NH.N hydrogen bonds related by a pseudo centre of symmetry. The asymmetric unit of (II) contains one and a half molecules: these exhibit NH proton disorder and are hydrogen bonded to each other via their respective NH groups to form chains. Ab initio calculations at HF and B3LYP/6-31G** levels indicate that the 3,4-dimethylpyrazole tautomer is more stable than the 4,5-dimethylpyrazole tautomer by only approximately 0.5 kcal mol(-1) (1 kcal mol(-1) = 4.184 kJ mol(-1)).

Strain Effects in Protonated Carbonyl Compounds. An Experimental and ab Initio Treatment of Acyclic Carboxamides and Ketones.

Strain effects have been quantitatively evaluated for a set of 22 compounds including ketones (R(2)CO), carboxamides (RCONH(2)), and N,N-dimethylcarboxamides (RCONMe(2)), where R = Me, Et, i-Pr, t-Bu, 1-adamantyl (1-Ad), in their neutral and protonated forms. To this end, use was made of the gas-phase proton affinities and standard enthalpies of formation of these compounds in the gas phase, as determined by Fourier transform ion cyclotron resonance mass spectrometry (FT ICR) and thermochemical techniques, respectively. The structures of 1-AdCOMe and (1-Ad)(2)CO were determined by X-ray crystallography. Quantum-mechanical calculations, at levels ranging from AM1 to MP2/6-311+G(d,p)//6-31G(d), were performed on the various neutral and protonated species. Constrained space orbital variation (CSOV) calculations were carried out on selected protonated species to further assess the contributions of the various stabilizing factors. Taking neutral and protonated methyl ketones as references, we constructed isodesmic reactions that provided, seemingly for the first time, quantitative measures of strain in the protonated species. A combination of these data with the results of theoretical calculations (which also included several "computational experiments") lead to a unified, conceptually satisfactory, quantitative description of these effects and their physical link to structural properties of the neutral and protonated species.

The structure and absolute configuration of acetomycin.

C10H14O5, Mr = 214.22, orthorhombic, P2(1)2(1)2(1), a = 14.1084 (6), b = 10.6443 (3), c = 7.1970 (1) A, V = 1080.80 (6) A3, Z = 4, D chi = 1.317 Mg m-3, Cu K alpha, lambda = 1.5418 A, mu = 0.8571 mm-1, F(000) = 456, T = 293 K, R = 0.052 for 816 observed [3 sigma (I)] Friedel pairs. The determined absolute configuration may be described as 3S, 4R, 5R, the five-membered ring having an envelope conformation, with the bulky substituents at cis positions. The bond lengths and angles are in agreement with those of the bromoacetoxy derivative.