Solid-State Conformational Flexibility at Work: Zipping and Unzipping within a Cyclic Peptoid Single Crystal

A peptidomimetic compound undergoes a reversible single-crystal-to-single-crystal transformation upon guest release/uptake with the transformation involving a drastic conformational change. The extensive and reversible alteration in the solid state is connected to the formation of an unprecedented "CH-π zipper" which can reversibly open and close (through the formation of CH-π interactions), thus allowing for guest sensing.

Strong orbital interaction in a weak CH-π hydrogen bonding system

For the first time, the intermolecular orbital interaction between benzene and methane in the benzene-methane complex, a representative of weak interaction system, has been studied by us using ab initio calculations based on different methods and basis sets. Our results demonstrate obvious intermolecular orbital interaction between benzene and methane involving orbital overlaps including both occupied and unoccupied orbitals. Similar to interatomic orbital interaction, the intermolecular interaction of orbitals forms “bonding” and “antibonding” orbitals. In the interaction between occupied orbitals, the total energy of the complex increases because of the occupation of the antibonding orbital. The existence of the CH-π hydrogen bond between benzene and methane causes a decrease in rest energy level, leading to at least −1.51 kcal/mol intermolecular interaction energy. Our finding extends the concept of orbital interaction from the intramolecular to the intermolecular regime and gives a reliable explanation of the deep orbital reformation in the benzene-methane complex.

A theoretical study of weak interactions in phenylenediamine homodimer clusters

Utilizing dispersion-corrected density functional theory (DFT) calculations, we demonstrate the weak intermolecular interactions of phenylenediamine dimer (pdd) clusters, emphasizing the local lowest energy structures and decomposition of interaction energies by natural bond orbital (NBO) and atoms in molecule (AIM) analyses.

Cationic CH⋯π interactions as a function of solvation

The energy of a cationic CH⋯π interaction was measured as a function of solvation using molecular torsion balances.

Aliphatic–aromatic stacking interactions in cyclohexane–benzene are stronger than aromatic–aromatic interaction in the benzene dimer

Stacking interactions between cyclohexane and benzene were studied in crystal structures from the Cambridge Structural Database and by ab initio calculations.

Intramolecular H⋯S interactions in metal di-(isopropyl)dithiocarbamate complexes

Intramolecular C–H⋯S interactions create restricted rotation of groups within di(isopropyl)dithiocarbate complexes.

Comparison of π-hole tetrel bonding with σ-hole halogen bonds in complexes of XCN (X = F, Cl, Br, I) and NH3

In addition to the standard halogen bond formed when NH₃approaches XCN (X = F, Cl, Br, I) along its molecular axis, a perpendicular approach is also possible, toward a π-hole that is present above the X–C bond.

Strong orbital deformation due to CH-π interaction in the benzene-methane complex

The orbital distribution and composition of the benzene-methane complex have been investigated systemically using ab initio calculations for the first time. Surprisingly, we find strong deformation in the HOMO-4 and LUMO+2 induced by CH-π interaction, extending the general view that nonbonding interaction does not cause orbital change of molecules.

Novel C,N-Cyclometalated Benzimidazole Ruthenium(II) and Iridium(III) Complexes as Antitumor and Antiangiogenic Agents: A Structure-Activity Relationship Study

A series of novel C,N-cyclometalated benzimidazole ruthenium(II) and iridium(III) complexes of the types [(η(6)-p-cymene)RuCl(κ(2)-N,C-L)] and [(η(5)-C5Me5)IrCl(κ(2)-N,C-L)] (HL = methyl 1-butyl-2-arylbenzimidazolecarboxylate) with varying substituents (H, Me, F, CF3, MeO, NO2, and Ph) in the R4 position of the phenyl ring of 2-phenylbenzimidazole chelating ligand of the ruthenium (3a-g) and iridium complexes (4a-g) have been prepared. The cytotoxic activity of the new ruthenium(II) and iridium(III) compounds has been evaluated in a panel of cell lines (A2780, A2780cisR, A427, 5637, LCLC, SISO, and HT29) in order to investigate structure-activity relationships. Phenyl substitution at the R4 position shows increased potency in both Ru and Ir complexes (3g and 4g, respectively) as compared to their parent compounds (3a and 4a) in all cell lines. In general, ruthenium complexes are more active than the corresponding iridium complexes. The new ruthenium and iridium compounds increased caspase-3 activity in A2780 cells, as shown for 3a,d and 4a,d. Compound 4g is able to increase the production of ROS in A2780 cells. Furthermore, all the new compounds are able to overcome the cisplatin resistance in A2780cisR cells. In addition, some of the metal complexes effectively inhibit angiogenesis in the human umbilical vein endothelial cell line EA.hy926 at 0.5 μM, the ruthenium derivatives 3g (Ph) and 3d (CF3) being the best performers. QC calculations performed on some ruthenium model complexes showed only moderate or slight electron depletion at the phenyl ring of the C,N-cyclometalated ligand and the chlorine atom on increasing the electron withdrawing effect of the R substituent.

Crystal structure of 1-iodo-3-{[4-(tert-butyl-sulfan-yl)phen-yl]ethyn-yl}azulene

The title compound, C20H19IS, features a 1,3-disubstituted azulene involving an ethynylene elongated 4-(tert-butyl-sulfanyl)-phenyl sidearm and an iodine atom as the substituents. The azulene ring system is almost planar (r.m.s. deviation = 0.012 Å) and subtends a dihedral angle of 35.7 (1)° with the benzene ring. As a result of the inherent dipole character of the azulene core, a supra-molecular π-π dimer [separation between the centroids of the five- and seven-membered rings = 3.7632 (10) Å] with anti-parallel orientated mol-ecules can be observed in the crystal. The packing is consolidated by an unusual I⋯π(acetyl-ene) contact [I⋯Cg = 3.34 Å, C-I⋯Cg = 173.3°], and a very weak C-H⋯π inter-action is also found in the structure, with the azulene five-membered ring as the acceptor.

Synthesis and UV/Vis analysis of amino acid-derived bisurea-type receptors involving anion complexation

Sixteen new bisurea compounds incorporating versatile proteinogenic amino acids as well as nipecotic acid have been synthesized via addition reaction to aryl diisocyanates. The products were analytically characterized and their ability for anion recognition was studied by UV/Vis spectroscopy. In the presence of fluoride, acetate or dihydrogenphosphate ions, hyperchromic and bathochromic peak shifts were determined. By way of contrast, bromide, iodide, or hydrogensulfate ions cause no significant change of absorbance. The special effect of heterocyclic derivatives was explained by molecular modeling calculations. In addition, the crystal structure of the byproduct dimethyl N,N′-(1,4-phenylene)dicarbamate is discussed.

Synthesis of macrocyclic receptors with intrinsic fluorescence featuring quinizarin moieties

An unprecedented class of macrocycles with intrinsic fluorescence consisting of phenolic trimers and quinizarin is developed. Though they are lacking strong hydrogen bonds as observed in calixarenes, the two examples introduced here each adopt a vase-like conformation with all four aromatic units pointing in one direction (syn orientation). This "cone" conformation has been confirmed by NMR spectroscopy, molecular modeling, and X-ray crystallography. The laminar, electron-rich fluorophore as part of the macrocycle allows additional contacts to enclosed guest molecules.

Antiparallel Self-Association of a γ,α-Hybrid Peptide: More Relevance of Weak Interactions

To learn how a preorganized peptide-based molecular template, together with diverse weak non-covalent interactions, leads to an effective self-association, we investigated the conformational characteristics of a simple γ,α-hybrid model peptide, Boc-γ-Abz-Gly-OMe. The single-crystal X-ray diffraction analysis revealed the existence of a fully extended β-strand-like structure stabilized by two non-conventional C-H⋅⋅⋅O=C intramolecular H-bonds. The 2D (1) H NMR ROESY experiment led us to propose that the flat topology of the urethane-γ-Abz-amide moiety is predominantly preserved in a non-polar environment. The self-association of the energetically more favorable antiparallel β-strand-mimic in solid-state engenders an unusual 'flight of stairs' fabricated through face-to-face and edge-to-edge Ar⋅⋅⋅Ar interactions. In conjunction with FT-IR spectroscopic analysis in chloroform, we highlight that conformationally semi-rigid γ-Abz foldamer in appositely designed peptides may encourage unusual β-strand or β-sheet-like self-association and supramolecular organization stabilized via weak attractive forces.

CH-π hydrogen bonds in biological macromolecules

This is a sequel to the previous Perspective "The CH-π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates", which featured in a PCCP themed issue on "Weak Hydrogen Bonds - Strong Effects?": Phys. Chem. Chem. Phys., 2011, 13, 13873-13900. Evidence that weak hydrogen bonds play an enormously important role in chemistry and biochemistry has now accumulated to an extent that the rigid classical concept of hydrogen bonds formulated by Pauling needs to be seriously revised and extended. The concept of a more generalized hydrogen bond definition is indispensable for understanding the folding mechanisms of proteins. The CH-π hydrogen bond, a weak molecular force occurring between a soft acid CH and a soft base π-electron system, among all is one of the most important and plays a functional role in defining the conformation and stability of 3D structures as well as in many molecular recognition events. This concept is also valuable in structure-based drug design efforts. Despite their frequent occurrence in organic molecules and bio-molecules, the importance of CH-π hydrogen bonds is still largely unknown to many chemists and biochemists. Here we present a review that deals with the evidence, nature, characteristics and consequences of the CH-π hydrogen bond in biological macromolecules (proteins, nucleic acids, lipids and polysaccharides). It is hoped that the present Perspective will show the importance of CH-π hydrogen bonds and stimulate interest in the interactions of biological macromolecules, one of the most fascinating fields in bioorganic chemistry. Implication of this concept is enormous and valuable in the scientific community.

Crystal structure of diethyl 2-amino-6-[(thio-phen-3-yl)ethyn-yl]azulene-1,3-di-carboxyl-ate

The title compound, C22H19NO4S, has an almost planar geometry supported by intra-molecular N-H⋯O and C-H⋯O hydrogen bonds. The thio-phene ring is inclined to the azulene ring by 4.85 (16)°, while the eth-oxy-carbonyl groups are inclined to the azulene ring by 7.0 (2) and 5.7 (2)°. In the crystal, mol-ecules are linked by pairs of N-H⋯O hydrogen bonds, forming inversion dimers with an R 2 (2)(12) ring motif. The dimers are linked via C-H⋯π inter-actions, forming sheets parallel to (10-1).

Synthesis and crystal structure of a novel prochiral ketoimine: (E)-acetophenoneO-diphenylphosphoryl oxime

A novel activated prochiral ketoimine, (E)-acetophenoneO-diphenylphosphoryl oxime, C20H18NO2P, with an electron-withdrawing substituent on the imine N atom similar to other prochiral ketoimines, has been synthesized and the X-ray crystal stucture determined. The molecules pack together in the solid stateviaweak intermolecular C—H...O interactions and both face-to-face and edge-to-face π-stacking interactions.

Hydrocarbon binding by proteins: structures of protein binding sites for ≥C10 linear alkanes or long-chain alkyl and alkenyl groups

In order to identify potential de novo enzyme templates for the cleavage of C–C single bonds in long-chain hydrocarbons, we analyzed protein structures that bind substrates containing alkyl and alkenyl functional groups. A survey of ligand-containing protein structures deposited in the Protein Data Bank resulted in 874 entries, consisting of 194 unique ligands that have ≥10 carbons in a linear chain. Fatty acids and phospholipids are the most abundant types of ligands. Hydrophobic amino acids forming α-helical structures frequently line the binding pockets. Occupation of these binding sites was evaluated by calculating both the buried surface area and volume employed by the ligands; these quantities are similar to those computed for drug–protein complexes. Surface complementarity is relatively low due to the nonspecific nature of the interaction between the long-chain hydrocarbons and the hydrophobic amino acids. The selected PDB structures were annotated on the basis of their SCOP and EC identification numbers, which will facilitate design template searches based on structural and functional homologies. Relatively low surface complementarity and ∼55% volume occupancy, also observed in synthetic-host, alkane-guest systems, suggest general principles for the recognition of long-chain linear hydrocarbons.

Effect of substituents in the molecular and supramolecular architectures of 1-ferrocenyl-2-(aryl)thioethanones

Relative positioning of substituents in a molecule is determinant in crystal packing of 1-ferrocenyl-2-(aryl)thioethanone derivatives displaying weak hydrogen bonding ability.