Gel- and Solid-State-Structure of Dialanine and Diphenylalanine Amphiphiles: Importance of C⋅⋅⋅H Interactions in Gelation

To investigate the role of the capping group in the solution and solid-state self-assembly of short peptide amphiphiles, dialanine and diphenylalanine have been linked via the N-terminus to a benzene (phenyl) and 3-naphthyl capping groups using three different methylene linkers; (CH₂)_n, n=0–4 for the benezene and 0, 1 and 2 for the naphthalene capping group. Atomic force microscopy (AFM), oscillatory rheology, circular dichroism (CD), and IR analysis have been employed to understand the properties of these peptide-based hydrogels. Several X-ray structures of these short peptide gelators give useful conformational information regarding packing. A comparison of these solid state structures with their gel state properties yielded greater insights into the process of self-assembly in short peptide gelators, particularly in terms of the important role of C⋅⋅⋅H interactions appear to play in determining if a short aromatic peptide does form a gel or not.     

Short but Weak: The Z-DNA Lone-Pair⋅⋅⋅π Conundrum Challenges Standard Carbon Van der Waals Radii

Current interest in lone-pair⋅⋅⋅π (lp⋅⋅⋅π) interactions is gaining momentum in biochemistry and (supramolecular) chemistry. However, the physicochemical origin of the exceptionally short (ca. 2.8 Å) oxygen-to-nucleobase plane distances observed in prototypical Z-DNA CpG steps remains unclear. High-level quantum mechanical calculations, including SAPT2+3 interaction energy decompositions, demonstrate that lp⋅⋅⋅π contacts do not result from n→π* orbital overlaps but from weak dispersion and electrostatic interactions combined with stereochemical effects imposed by the locally strained structural context. They also suggest that the carbon van der Waals (vdW) radii, originally derived for sp³ carbons, should not be used for smaller sp² carbons attached to electron-withdrawing groups. Using a more adapted carbon vdW radius results in these lp⋅⋅⋅π contacts being no longer of the sub-vdW type. These findings challenge the whole lp⋅⋅⋅π concept that refers to elusive orbital interactions that fail to explain short interatomic contact distances.     

Highly selective adenine recognition by a macrocyclic host molecule employing multiple hydrogen bonding and π-π stacking interactions

A new macrocyclic host, which contains a 2,6-bis(oxazol-2-yl)pyridine unit and a 2,7-dialkoxynaphthalene unit tethered by the appropriate length of alkyl side chains is prepared. This host undergoes highly selective complex formation with an adenine nucleobase, accompanied by a fluorescence response in CHCl₃ by a combination of multiple hydrogen bonding and π-π stacking interactions.     

The modulation of face-face π-π interactions in Lewis acid catalysis

The enantiomeric excess observed for the exo-adduct from the Lewis acid catalysed Diels-Alder reaction between cyclopentadiene and methacrolein can be increased up to 21% by simple modification of the electronics of the aromatic ring in a series of stilbene-derived diol ligands, suggesting that the proposed face-face π-π interaction between the catalyst and the dienophile can be modulated by altering the electron density on the aromatic ring.     

Synthesis and Crystal Structure of N-Benzyl-N＇-（2-pyridyl）urea and Its Mononuclear Cu（Ⅱ） Complex

A new ligand of N-benzyl-N＇-（2-pyridyl）urea L and its self-assembly product with CuCl2, [Cu（Ⅱ）LCl2]∞ 1, have been synthesized and structurally characterized by IR, 1H NMR and single-crystal X-ray diffraction analysis. In the structure of L, the urea groups adopt Z,E conformation to form dimers through intermolecular hydrogen bonds; while in complex 1, it assumes Z,Z conformation to fit for the coordination sphere of the Cu（Ⅱ） ions. The coordinated units are connected through intermolecular N-H...Cl hydrogen bonds to form an extended 2D framework. Finally, a 3D structure is obtained via π-π stacking interactions between pyridyl rings     

Mechanochemical Preparations of Anion Coordinated Architectures Based on 3-Iodoethynylpyridine and 3-Iodoethynylbenzoic Acid

The halogen bond has previously been explored as a versatile tool in crystal engineering and anion coordination chemistry, with mechanochemical synthetic techniques having been shown to provide convenient routes towards cocrystals. In an effort to expand our knowledge on the role of halogen bonding in anion coordination, here we explore a series of cocrystals formed between 3-iodoethynylpyridine and 3-iodoethynylbenzoic acid with halide salts. In total, we report the single-crystal X-ray structures of six new cocrystals prepared by mechanochemical ball milling, with all structures exhibiting C≡C−I⋅⋅⋅X⁻ (X=Cl, Br) halogen bonds. Whereas cocrystals featuring a pyridine group favoured the formation of discrete entities, cocrystals featuring a benzoic acid group yielded an alternation of halogen and hydrogen bonds. The compounds studied herein were further characterized by ¹³C and ³¹P solid-state nuclear magnetic resonance, with the chemical shifts offering a clear and convenient method of identifying the occurrence of halogen bonding, using the crude product obtained directly from the mechanochemical ball milling. Whereas the ³¹P chemical shifts were quickly able to identify the occurrence of cocrystallization, ¹³C solid-state NMR was diagnostic of both the occurrence of halogen bonding and of hydrogen bonding.     

Synthesis and Structure of a Novel Macrocyclic Complex [Cd_2(phen)_4(phth)_2]·4H_2O

1 INTRODUCTION In recent years, extensively attention has been fo- cused on the design and synthesis of d10 metal- based complexes[1, 2]. A series of d10 metal-organic frame- works have been described not only because of their intriguing structures but also due to their ptential ap- plications in photoluminescent fields[3～7]. Although phthalate ligand was successfully used to design and synthesize a wide variety of metal complexes, those containing Cd(II) complex are less considered[8～…     

Synthesis and Structure of a Novel Macrocyclic Complex [Cd2(phen)4(phth)2]·4H2O

A novel complex [Cd2(phen)4(phth)2]·4H2O has been synthesized by the reaction of H2phth(phthalic acid) and phen(1,10-phenanthroline) with Cd(Ⅱ) in ethanol-water solution. X-ray crystal structure analysis shows it crystallizes in triclinic, space group P1 with a = 10.619(3), b =12.560(4), c = 12.651(4) A, α = 98.775(5), β = 109.035(5), γ = 113.576(5)°, C32H24CdN4O6, Mr=672.95, V= 1381.7(7) A3, Rint = 0.0358, Z= 2, Dc= 1.618 g/cm3, μ = 0.845 mm-1, -6 ≤h≤13, -15≤k ≤13, -15≤l≤14, F(000) = 680, S = 1.038, R = 0.0480 and wR = 0.0849 for 3992 observed reflections (I ＞ 2σ(Ⅰ)). Phth bridges Cd(Ⅱ) to form a macrocyclic compound, and a 2D supramolecular motif is formed through hydrogen bonds and π-π interaction.     

Synthesis and Crystal Structure of Diisopropyl Genistein-7-yl Phosphate

Diisopropyl genistein-7-yl phosphate (C21H23O8P, Mr = 434.11) has been synthesized by a facile phosphorylated reaction with genistein and diisopropyl phosphite, and its structure was determined by IR, NMR, HR MS and X-ray single-crystal diffraction. The crystal belongs to monoclinic, space group P21/n, with a = 9.0690(18), b = 9.0412(18), c = 26.544(5), β = 99.44(3)°, V = 2147.0(7) 3, Z = 4, Dc = 1.344 Mg/m3, μ = 0.172 mm-1, F(000) = 912, the final R = 0.0545 and wR = 0.1352. In the crystal structure, the title compound is constructed by both intramolecular (O–H···O=C) and intermolecular (O–H···O=P) hydrogen bonding as well as π-π stacking interaction.     

Metal ion coordination in cobalt formate dihydrate

The structure of cobalt formate dihydrate, Co(HCO₂)₂ · 2H₂O, was determined using single-crystal X-ray diffraction data. The crystals are monoclinic, space groupP2₁/c, with unit-cell dimensionsa=8.680(2),b=7.160(2),c=9.272(2) Å,=97.43(2)°,V=571.4(3) ų Z=4.R _obs=0.038 for 1282 unique reflections withI>3(I). The crystal structure is found to be isomorphous with those of other divalent metal formates. This structure is interesting crystallographically because the Patterson map is homometric with respect to the positions of the heavy atoms. The asymmetric unit consists of two independent cobalt atoms on special positions, two formate ions (HCOO^–), and two water molecules. The two cobalt atoms are each coordinated to six oxygen atoms in an octahedral arrangement. One of the cobalt octahedra contains only oxygen atoms from six formate ions. The second cobalt ion is surrounded by four water molecules and an oxygen atom from each of two formate ions. The two different octahedra are bridged by one of the formate ions and by hydrogen bonds. This network extends in a three-dimensional polymeric manner throughout the crystal structure. Each of the four oxygen atoms in the two independent formate ions forms a hydrogen bond to water and is coordinated to a metal ion. It is found that the metal ions lie in the plane of the formate carboxyl group to which they are coordinated, while molecules to which the formate ion is hydrogen bonded lie more out of this plane.     

Solid-State NMR Study of Phase Separation and Order of Water Molecules and Silanol Groups in Polysiloxane Networks

Homogeneity and structure of organically modified polysiloxane networks prepared by sol-gel co-condensation, as well as location and nature of water molecules and silanol groups were studied by 1D and 2D solid-state NMR. ¹H–²⁹Si and ¹H–¹H interatomic distances were estimated from variable contact-time CP/MAS experiments, ¹H NMR chemical shifts and off-resonance WISE NMR. A structure model of these networks is proposed and discussed. The fraction of proton-inaccessible units Q⁴ in the networks decreases with increasing amounts of dimethylsiloxane (D) and methylsiloxane (T) units. In contrast to systems prepared by co-condensation of tetraethoxysilane (TEOS) with dimethyl(diethoxy)silane (DMDEOS), proton-inaccessible units form essential fraction in networks prepared by co-condensation of TEOS with methyl(triethoxy)silane (MTEOS). The proton-accessible part of the networks with high O/Si ratios is nano-heterogeneous phase, which is composed of water containing Q ⁱ particles separated by copolymer domains. The overall homogeneity and uniformity of binding sites around silanol groups increases by co-condensation TEOS with DMDEOS or MTEOS, while the amount of physisorbed water as well as the hydrogen bond strength decreases, as compared with neat silica gel prepared by polycondensation of TEOS.     

Syntheses and Crystal Structures of Two Coordination Compounds CuLCl（H2O） and Ni（L）2 （HL = 2-Carboxy-1,10-phenanthroline）

Two complexes CuLCl（H2O） 1 and Ni（L）2 2 （HL = 2-carboxy-1,10-phenanthroline） have been synthesized and characterized by single-crystal X-ray crystallography. The structure of 1 has a monoclinic space group P21/n with a = 7.985（2）, b = 16.067（3）, c = 9.694（2） A, β = 98.189（30）°, V= 1231.0（4） A^3, Z = 4, Dc = 1.836 g/cm^3,μ =1.998 mm^-1, F（000） = 684, the final R = 0.0301 and wR = 0.0810. The structure of 2 （C26H14N4NiO10） adopts an orthorhombic system, space group Pbea with a = 9.410（2）, b = 23.2410（5）, c = 23.8680（5） A, V = 5219.9（18） A^3, Z = 8, Mr = 601.12, Dc = 1,530 g/cm^3,μ = 0.809 mm^-1, F（000） = 2448, the final R = 0.0448 and wR = 0.1427. The Cu center of complex 1 exhibits a square pyramidal coordination environment with one oxygen and two nitrogen atoms from deprotonated 2-carboxy-1,10-phenanthroline, one oxygen atom from water and one chloride ion. The Ni center of complex 2 assumes a distorted octahedral coordination geometry consisting of two oxygen atoms and four nitrogen atoms of two deprotonated 2-carboxy-1,10-phenanthroline molecules. Supramolecular assembly has been found via noncovalent bonds, such as hydrogen bonds and π-π stacking interactions.     

Ritter reactions. X. Structure of a new multicyclic amide-benzene inclusion compound

5H-Dibenzo[a, d]cyclohepten-5-ol1 can undergo Ritter reaction with acetonitrile and sulfuric acid to afford either the acetamide derivative2 or the multicyclic amide3 depending on the conditions used. The X-ray structure of the inclusion compound of3 with benzene is reported here and analysed in structural terms. This material [(C₁₉H₁₈N₂O)–(C₆H₆),Cc,a=10.694(5),b=22.843(5),c=9.901(4) Å,=124.02(2)°,Z=4,R=0.054] has molecules of3 linked by –N–HO=C intermolecular hydrogen bonds to form parallel chains alongc. Additional inter-host stabilisation is achieved by face-face interactions involving one of the two benzo rings of3. A hydrogen atom of the other host benzo group participates in an edge-face interaction with the benzene guest molecule to produce the inclusion compound. Benzenebenzene inter-guest interactions provide a further, but minor, contribution to the net stability of the structure. Supplementary Data relating to this article are deposited with the British Library as supplementary publication No. SUP 82189 (10 pages).     

Not Your Usual Bioisostere: Solid State Study of 3D Interactions in Cubanes

Previous studies by Desiraju and co-workers have implicated the acidic hydrogen atoms of cubane as a support network for hydrogen bonding groups. Herein we report a detailed structural analysis of all currently available 1,4-disubstituted cubane structures with an emphasis on how the cubane scaffold interacts in its solid-state environment. In this regard, the interactions between the cubane hydrogen atoms and acids, ester, halogens, ethynyl, nitrogenous groups, and other cubane scaffolds were cataloged. The goal of this study was to investigate the potential of cubane as a substitute for phenyl. This could be achieved by analyzing all contacts that are directed by the cubane hydrogen atoms in the X-ray crystal structures. As a result, we have established several new cubane interaction profiles, such as the catemer formation seen in esters, the preferences of halogen–hydrogen contacts over direct halogen bonding, and the stabilizing effects caused by the cubane hydrogen atoms interacting with ethynyl groups. These interaction profiles can then be used as a guide for designing cubane bioisosteres of known materials and drugs containing phenyl moieties.     

Comparative study on the nonadditivity of methyl group in lithium bonding and hydrogen bonding

Quantum chemical calculations at the second‐order Moeller–Plesset (MP2) level with 6‐311++G(d,p) basis set have been performed on the lithium‐bonded and hydrogen‐bonded systems. The interaction energy, binding distance, bond length, and stretch frequency in these systems have been analyzed to study the nonadditivity of methyl group in the lithium bonding and hydrogen bonding. In the complexes involving with NH₃, the introduction of one methyl group into NH₃ molecule results in an increase of the strength of lithium bonding and hydrogen bonding. The insertion of two methyl groups into NH₃ molecule also leads to an increase of the hydrogen bonding strength but a decrease of the lithium bonding strength relative to that of the first methyl group. The addition of three methyl groups into NH₃ molecule causes the strongest hydrogen bonding and the weakest lithium bonding. Although the presence of methyl group has a different influence on the lithium bonding and hydrogen bonding, a negative nonadditivity of methyl group is found in both interactions. The effect of methyl group on the lithium bonding and hydrogen bonding has also been investigated with the natural bond orbital and atoms in molecule analyses. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Non‐Ideal Behaviour and Solution Interactions in Binary DMSO Solutions

The structure and dynamics of hydrogen‐bonded structures are of significant importance in understanding many binary mixtures. Since self‐diffusion is very sensitive to changes in the molecular weight and shape of the diffusing species, hydrogen‐bonded associated structures in dimethylsulfoxide–methanol (DMSO–MeOH) and DMSO–ethanol (DMSO–EtOH) mixtures are investigated using nuclear magnetic resonance (NMR) diffusion experiments and molecular dynamics (MD) simulations over the entire composition range at 298 K. The self‐diffusion coefficients of DMSO–MeOH and DMSO–EtOH mixtures decrease by up to 15% and 10%, respectively, with DMSO concentration, indicating weaker association as compared to DMSO–water mixtures. The calculated heat of mixing and radial distribution functions reveal that the intermolecular structures of DMSO–MeOH and DMSO–EtOH mixtures do not change on mixing. DMSO–alcohol hydrogen‐bonded dimers are the dominant species in mixtures. Direct comparison of the simulated and experimental data afford greater insights into the structural properties of binary mixtures.     

Synthesis and Crystal Structure of Dichlorobis(1-methylimidazoline-2(3H)-thione-S) Cobalt(II)

The reaction of anhydrous cobalt(II) dichloride with 1-methylimidazoline-2(3H)thione in dichloromethane solution gave the title complex, [Co(C4H6N2S)2Cl2]. X-ray single-crystal analysis revealed that the complex crystallizes in a monoclinic system, space group P21/c, a = 13.9707(10), b = 10.0435(7), c = 10.3910(6) (A), β = 91.181(3)o, V = 1457.70(17) (A)3, Z = 4, C8H12Cl2N4S2Co, Mr = 358.17, Dc = 1.632 g/cm3, μ = 1.813 mm-1, F(000) = 724, the final R = 0.0710 and wR = 0.1224 for 1549 observed reflections with I > 2((I). The Co atom is coordinated by two S atoms from two 1-methylimidazoline-2(3H)-thione ligands and two chloride ions in a slightly distorted tetrahedral geometry. The intramolecular classical hydrogen-bonding interactions involving chloride ions and N-H groups of the heterocyclic thione ligands are observed. The offset π-π stacking interactions between the imidazole rings of adjacent molecules with a face-to-face distance of 3.604 (A) are found in the packing diagram.     

Solid-state and inclusion properties of hydrogen-bonded 1,3-cyclohexanedione cyclamers

During crystallization 1,3-cyclohexanedione self assembles into either hydrogen-bonded chains or hexameric rings depending on the solvent conditions. The hexameric rings, called cyclamers, are the subject of this paper. These unusual structures occlude benzene as a guest molecule. The structural and crystal chemical properties of these host-guest compounds are explored here with the use of crystal growth studies, X-ray powder patterns, and thermal analysis. The crystal structure of the benzene cyclamer of 5-methyl-1,3-cyclohexanedione is reported (hexagonal,a =b = 19.19(2)Å,c = 10.545(9)Å,R3,Z = 18,V = 3362(6)ų; 717 unique reflections,R = 0.062). An analysis of the stereochemical implications of cyclic directionality in these cyclamers is also discussed.Alfred P. Sloan Foundation Fellow, 1989–1991.