Complete Molecule Research Articles

Crystal structure of bis-(4-allyl-2-meth-oxy-phen-yl) terephthalate.

The asymmetric unit of the title compound, C28H26O6, contains one half-mol­ecule, with the complete molecule generated by a crystallographic inversion center. The central terephthalate and meth­oxy­benzene rings are approximately perpendicular, making a dihedral angle of 80.31 (5)°. No specific directional contacts are noted in the crystal packing. The terminal vinyl group is disordered over two orientations with an occupancy ratio of 0.796 (4):0.204 (4).

Crystal structure of the charge-transfer complex 2-(1,2,3,4-tetra-hydro-naph-thal-en-1-yl-idene)hydrazinecarbo-thio-amide-pyrazine-2,3,5,6-tetra-carbo-nitrile (2/1).

The reaction of 2-(1,2,3,4-tetra­hydro­napthalen-1-yl­idene)hydrazinecarbo­thio­amide (TTSC) with pyrazine-2,3,5,6-tetra­carbo­nitrile (tetra­cyano­pyrazine, TCNP) yields the title 2:1 charge-transfer adduct, 2C11H12N3S·C6N8. The complete TCNP mol­ecule is generated by a crystallographic inversion centre and the non-aromatic ring in the TTSC mol­ecule adopts an envelope conformation with a methyl­ene C atom as the flap. In the crystal, the thio­semicarbazone mol­ecules are connected through inversion-related pairs of N—H⋯S inter­actions, building a polymeric chain along the b-axis direction. The TCNP mol­ecules are embedded in the structure, forming TTSC–TCNP–TTSC stacks with the aromatic rings of TTSC and the mol­ecular plane of TCNP in a parallel arrangement [centroid–centroid distance = 3.5558 (14) Å]. Charge-transfer (CT) via π-stacking is indicated by a CT band around 550 cm−1 in the single-crystal absorption spectrum.

Twin Tandem Bicycle Pedal Motion - Using X-rays to Resolve Disorder Thermodynamic Parameters

During our research into polar crystals for organic electronic applications, we synthesized E,E-1-[2-(4-nitrophenyl)ethenyl]-4-[2-(2,4-dimethoxyphenyl)ethenyl]benzene, which has a polar crystal structure (space group Pc) and displays the typical bicycle pedal motion, as studied in detail by Harada and Ogawa [1], in one of its ethenylic links. A van `t Hoff plot of the logarithm of the population ratio versus 1/T, however, showed a kink instead of being a straight line, which led us to conclude that an unusual phase transition was occurring in this material [2]. In the mean time we have crystallized the same material in a second, centrosymmetric polymorph (space group P-1). There, the asymmetric unit consists of two complete molecules, and they display the same kind of bicycle pedal motion, but this time in all four different ethenylic linkers. Every one of these population differences increases with temperature, so that four van `t Hoff plots can be constructed for this structure. Two of these behave normally, the other two display a kink, just like the van `t Hoff plot of the pedaling ethenylic link in the other polymorph of this molecule. This is, to the best of our knowledge, the first instance of a structure where four different dynamic equilibria can be resolved simultaneously, and only the second example in which van `t Hoff plots for the thermodynamics of dynamic disorder are not linear, indicating an unusual type of phase transition linked only to the dynamics of the molecules in the crystal.

Structural insights into archeal-type SAHase from Thermotoga maritima

S-adenosyl-L-homocysteine hydrolase (SAHase) catalyzes the reversible breakdown of S-adenosyl-L-homocysteine (SAH) to adenosine (Ado) and homocysteine (Hcy). SAH is formed in methylation reactions that utilize S-adenosyl-L-methionine (SAM) as a methyl donor. By removing the SAH byproduct, SAHase serves as a regulator of SAM-dependent biological methylation reactions.[1] Thermotoga maritima is a thermophilic bacterium, but its genome carries a number of archeal genes as a consequence of massive gene transfers related to adaptation to the high-temperature environment.[2] sahh is one of many genes of archeal origin found in T. maritima. Crystals of recombinant SAHase from T. maritima in complex with adenosine were obtained by the hanging drop vapor diffusion method. The crystals are monoclinic, space group C2, with a = 120.4, b =105.5, c = 85.5 Å, β=108.80and diffract X-rays to 1.80 Å. The crystal contains two protein molecules in the asymmetric unit. The enzyme is active as a homotetramer with a molecular weight of about 180 kDa. The crystal contains two protomers in the asymmetric unit, which exist in both, open and closed conformations. The complete tetrameric enzyme molecule is generated in the crystal lattice through the operation of the crystallographic twofold axis. In contrast to other SAHase structures, only two subunits contain a tightly bound NAD+ cofactor, however their closed conformations exclude the possibility of substrate binding. The other two subunits are in open conformation and bind adenosine molecule in the cofactor binding site. Herein, lack of the cofactor molecule excludes the possibility of an enzymatic reaction. In contrast to other SAHases, the C-terminal domain from adjacent protomer does not participate in the binding of the NAD+. Results presented here indicate a different structural organization of archeal type SAHases.

Fuzzy electron density fragments in macromolecular quantum chemistry, combinatorial quantum chemistry, functional group analysis, and shape-activity relations.

Conspectus Just as complete molecules have no boundaries and have "fuzzy" electron density clouds approaching zero density exponentially at large distances from the nearest nucleus, a physically justified choice for electron density fragments exhibits similar behavior. Whereas fuzzy electron densities, just as any fuzzy object, such as a thicker cloud on a foggy day, do not lend themselves to easy visualization, one may partially overcome this by using isocontours. Whereas a faithful representation of the complete fuzzy density would need infinitely many such isocontours, nevertheless, by choosing a selected few, one can still obtain a limited pictorial representation. Clearly, such images are of limited value, and one better relies on more complete mathematical representations, using, for example, density matrices of fuzzy fragment densities. A fuzzy density fragmentation can be obtained in an exactly additive way, using the output from any of the common quantum chemical computational techniques, such as Hartree-Fock, MP2, and various density functional approaches. Such "fuzzy" electron density fragments properly represented have proven to be useful in a rather wide range of applications, for example, (a) using them as additive building blocks leading to efficient linear scaling macromolecular quantum chemistry computational techniques, (b) the study of quantum chemical functional groups, (c) using approximate fuzzy fragment information as allowed by the holographic electron density theorem, (d) the study of correlations between local shape and activity, including through-bond and through-space components of interactions between parts of molecules and relations between local molecular shape and substituent effects, (e) using them as tools of density matrix extrapolation in conformational changes, (f) physically valid averaging and statistical distribution of several local electron densities of common stoichiometry, useful in electron density databank mining, for example, in medicinal drug design, and (g) tools for combinatorial quantum chemistry approaches using fuzzy fragment databanks and rapid construction of a large number of approximate electron densities for large sets of related molecules, relevant in theoretical molecular and nanostructure design.

3,12-Dimeth-oxy-5,6,9,10-tetra-hydro-[5]helicene-7,8-dicarbo-nitrile.

The complete molecule of the title compound, C26H20N2O2, is generated by a crystallographic twofold axis. The torsion angle between the terminal and central benzene rings is −32.5 (2)°. The torsion angle along the inner helical rim of the molecule is −18.8 (2)° with each other. The C⋯C distance between the terminal rings is 3.016 (2) Å. In the crystal, weak C—H⋯N hydrogen bonds are observed.

2,3,5,6-Tetra-fluoro-1,4-bis-({[(thio-phen-2-yl)methyl-idene]amino}-meth-yl)benzene.

In the title compound, C18H12F4N2S2, a bis-thio­phenyl Schiff base ligand with a perifluorinated aromatic core, the complete molecule is generated by crystallographic inversion symmetry. The thio­phene and tetra­fluorinated benzene rings are oriented at a dihedral angle of 77.38 (4)°. The crystal structure exhibits C—H⋯F hydrogen bonds, resulting in supra­molecular chains along the c-axis direction.

(3Z)-3-[(Z)-2-(2-Oxoindolin-3-yl-idene)hydrazin-1-yl-idene]indolin-2-one 0.17-hydrate.

In the title compound, C16H10N4O2·0.17H2O, prepared by the one-step condensation reaction of isatin with hydrazine hydrate under microwave irradiation, the complete organic mol­ecule is generated by crystallographic inversion symmetry and therefore exists in an S-trans conformation. In the crystal, mol­ecules are linked by N—H⋯O hydrogen bonds, generating a three-dimensional framework with [001] channels, which are occupied by the disordered water mol­ecules.

2,5-Di-bromo-3,6-dimeth-oxycyclo-hexa-2,5-diene-1,4-dione.

In the structure of the title compound, C8H6Br2O4, the complete mol­ecule is generated by the application of a centre of inversion. The mol­ecule is planar (r.m.s. deviation for all non-H atoms but methyl C = 0.0358 Å), with only the methyl groups being deviated from the plane [by ±0.321 (4) Å]. In the crystal packing, Br⋯O(methoxy) halogen bonds [3.2407 (19) Å] connect molecules into supramolecular layers parallel to (101).

4,4′-{[1,2-Phenylenebis(methylene)]bis(oxy)}dibenzoic acid dimethylformamide disolvate

In the title solvate, C22H18O6·2C3H7NO, the complete dicarboxylic acid molecule is generated by a crystallographic twofold axis, which bisects the central benzene ring and one N,N-di­methyl­formamide solvent mol­ecule. The dihedral angle between the central and pendant benzene rings is 54.53 (5)° while that between the pendant rings is 45.44 (5)°. In the crystal, the acid molecules are linked to the solvent molecules via O—H⋯O and weak C—H⋯O hydrogen bonds. Further weak C—H⋯O inter­actions link adjacent acid mol­ecules into a three-dimensional network.

Bis[4-amino-N-(4-methyl-pyrimidin-2-yl-κN (3))benzene-sulfonamidato-κN](2,2'-bi-pyridine-κ(2) N,N')mercury(II).

The complete mol­ecule of the title complex, [Hg(C11H11N4O2S)2(C10H8N2)], is generated by crystallographic twofold symmetry, with the mercury cation lying on the rotation axis. The mercury coordination polyhedron can be described as tetra­hedral (from the N,N′-bidenate bi­pyridine mol­ecule and the sulfonamide N atoms of the sulfamerazine anions) or as squashed trigonal-prismatic, if two long (> 2.80 Å) Hg—N bonds to pyrimidine N atoms are included. The dihedral angle between the aromatic rings in the anion is 73.3 (2)°. In the crystal, N—H⋯(N,O) and N—H⋯N hydrogen bonds link the mol­ecules into a three-dimensional network.

Redetermination of 1,3,6,8-tetra-aza-tri-cyclo-[4.4.1.1(3,8)]dodeca-ne.

The structure of the title compound, C8H16N4, which consists of four fused seven-membered rings, has been redetermined at 173 K. This redetermination corrects the orientation of two H atoms, which were located at unrealistic positions in the original room-temperature study [Murray-Rust (1974 ▶). J. Chem. Soc. Perkin Trans. 2, pp. 1136–1141]. The complete mol­ecule is generated by -42m symmetry, with one quarter of a mol­ecule [one N atom (site symmetry m), two C atoms (one with site symmetry m and the other with site symmetry 2) and two H atoms] in the asymmetric unit. No directional inter­actions beyond van der Waals contacts are apparent in the crystal structure.

2-[(1H-Benzimidazol-1-yl)meth-yl]phenol benzene hemisolvate.

In the title solvate, C14H12N2O·0.5C6H6, the complete benzene molecule is generated by a crystallographic inversion centre. The dihedral angle between the planes of the benzimidazole moiety and the phenol substituent is 75.28 (3)°. In the crystal, O—H⋯N hydrogen bonds link the mol­ecules into parallel chains propagating along [100]. The mol­ecules are further connected by C—H⋯π inter­actions.

4,4'-({[(Pyridine-2,6-di-yl)bis-(methyl-ene)]bis-(-oxy)}bis-(methyl-ene))dibenzo-nitrile.

The complete title molecule, C23H19N3O2, is generated by a twofold axis passing through the central ring. The two oxymethyl­benzo­nitrile arms are attached at the meta positions of the central pyridine ring. The dihedral angle between the pyridine ring and benzene ring of both arms is 84.55 (6)° while the benzene rings make a dihedral angle of 46.07 (7)°. In the crystal, weak C—H⋯π inter­actions link the molecules sheets parallel to the ac plane.

1,3,5-Tris(4-meth-oxy-phen-yl)-1,3,5-triazinane-2,4,6-trione.

The complete mol­ecule of the title compound, C24H21N3O6, is generated by the application of threefold rotation symmetry about an axis perpendicular to the central ring. The mol­ecule exhibits a propeller-like shape. The dihedral angle between each benzene ring and the heterocyclic ring is 74.0 (1)°. The mol­ecules pack with no specific inter­molecular inter­actions between them. The SQUEEZE procedure in PLATON [Spek (2009 ▶). Acta Cryst. D65, 148–155] was used to model disordered solvent mol­ecules, presumed to be acetone; the calculated unit-cell data do not take into account the presence of these.

Molecular Dynamics Simulations of Lipid-Linked Oligosaccharides in Lipid Bilayers

We have used molecular modeling and simulation to study the structure and dynamics of two lipid-linked oligosaccharides (LLO: eukaryotic Glc3-Man9-GlcNAc2-PP-dolichol and bacterial Glc1-GalNAc5-Bac1-PP-undecaprenol) in membrane bilayers of different composition. The LLOs used in this study consist of an isoprenoid moiety and an oligosaccharide linked by pyrophosphates. Each component has been studied previously as independent components, i.e., oligosaccharide in solution and isoprenoid in bilayer. However, the overall structure and dynamics of the complete LLO molecule in bilayer remain elusive. From our molecular dynamics simulations, different lipid types do not perturb the structure and dynamics of the isoprenoid moiety. The oligosaccharide conformation and dynamics appears to be similar to those measured by NMR in solution, however, preferential interaction between the oligosaccharide and bilayer interface is observed. Such preferential interaction may influence the binding to OST. Finally, the potential binding mode of the oligosaccharide moiety to bacterial OST is examined by molecular docking.

Electron density shape analysis of a family of through-space and through-bond interactions

A family of styrene derivatives has been used to study the effects of through-space and through-bond interactions on the local and global shapes of electron densities of complete molecules and a set of substituents on their central rings. Shape analysis methods which have been used extensively in the past for the study of molecular property-molecular shape correlations have shown that in these molecules a complementary role is played by the through-space and through-bond interactions. For each specific example, the dominance of either one of the two interactions can be identified and interpreted in terms of local shapes and the typical reactivities of the various substituents. Three levels of quantum chemical computational methods have been applied for these structures, including the B3LYP/cc-pVTZ level of density functional methodology, and the essential conclusions are the same for all three levels. The general approach is suggested as a tool for the identification of specific interaction types which are able to modify molecular electron densities. By separately influencing the through-space and through-bond components using polar groups and groups capable of conjugation, some fine-tuning of the overall effects becomes possible. The method described may contribute to an improved understanding and control of molecular properties involving complex interactions with a possible role in the emerging field of molecular design.

Photoisomerization of an Azobenzene on the Bi(111) Surface

Modifying surface-bound molecular switches by adding side groups is an established concept for restoration of functionality which a molecule possesses in solution and which is often quenched upon adsorption. Instead of decoupling the photochromic unit from the substrate, we follow a different approach, namely treating the complete molecule–substrate system. We use photoelectron spectroscopies to determine the energetic positions of the frontier orbitals of di-m-cyanoazobenzene on Bi(111) and to elucidate the isomerization mechanism which is stimulated by a substrate-mediated electron transfer process.

Di-μ-iodido-bis(iodido{methyl 4-[(pyridin-2-ylmethylidene)amino]benzoate-κ2N,N′}cadmium)

The complete binuclear molecule of the title compound, [Cd2I4(C14H12N2O2)2], is generated by the application of a centre of inversion. The Cd—I bond lengths of the central core are close and uniformly longer than the exocyclic Cd—I bond. The coordination sphere of the CdII atom is completed by two N atoms of a chelating methyl 4-[(pyridin-2-yl­methyl­idene)amino]­benzoate ligand, and is based on a square pyramid with the terminal I atom in the apical position. The three-dimensional crystal packing is stabilized by C—H⋯O and C—H⋯π inter­actions, each involving the pyridine ring.

Di-μ-acetato-κ4O:O′-bis[(1,10-phenanthroline-κ2N,N′)(trifluoromethanesulfonato-κO)copper(II)

The complete molecule of the title compound, [Cu2(C2H3O2)2(CF3O3S)2(C12H8N2)2], is completed by the application of a twofold rotation and comprises two CuII ions, each of which is penta­coordinated by two N atoms from a bidentate 1,10-phenanthroline (phen) ligand, two O atoms from acetate ligands and an O atom from a tri­fluoro­methane­sulfonate anion, forming a (4 + 1) distorted square-pyramidal coordination geometry. The CuII ions are connected by two acetate bridges in a syn–syn configuration. The F atoms of the tri­fluoro­methane­sulfonate ligands are disordered, with site-occupation factors of 70 and 30. The molecular structure is stabilized by intra­molecular face-to-face π–π inter­actions with centroid–centroid distances in the range 3.5654 (12)–3.8775(12) Å. The crystal structure is stabilized by C—H⋯O interactions, leading to a three-dimensional lattice structure.