Solid state assembly of cyclic α-peptoids

CrystEngComm ◽  
2014 ◽  
Vol 16 (18) ◽  
pp. 3667-3687 ◽  
Author(s):  
Consiglia Tedesco ◽  
Loredana Erra ◽  
Irene Izzo ◽  
Francesco De Riccardis
Keyword(s):  
Solid State ◽  
Secondary Structure ◽  
Hydrogen Bonds ◽  
Side Chains ◽  
Beta Sheet ◽  
Face To Face

In cyclic alpha-peptoids, inter-annular CH⋯OC hydrogen bonds provide face to face or side by side arrangement of macrocycles mimicking the beta-sheet secondary structure in proteins. Side chains may promote the formation of peptoid nanotubes, acting as pillars among neighbouring macrocycles.

Synthesis, crystallization, X-ray structural characterization and solid-state assembly of a cyclic hexapeptoid with propargyl and methoxyethyl side chains

2017 ◽  
Vol 73 (3) ◽  
pp. 399-412 ◽  
Author(s):  
Consiglia Tedesco ◽  
Eleonora Macedi ◽  
Alessandra Meli ◽  
Giovanni Pierri ◽  
Giorgio Della Sala ◽  
...  
Keyword(s):  
Solid State ◽  
Hydrogen Bonds ◽  
Structural Characterization ◽  
Crystal Form ◽  
Side Chains ◽  
Crystal Forms ◽  
Hydrate Crystal ◽  
The Stability ◽  
Efficient Packing

The synthesis and the structural characterization of a cyclic hexapeptoid with four methoxyethyl and two propargyl side chains have disclosed the presence of a hydrate crystal form [form (I)] and an anhydrous crystal form [form (II)]. The relative amounts of form (I) and form (II) in the as-purified product were determined by Rietveld refinement and depend on the purification procedures. In crystal form (I), peptoid molecules assemble in a columnar arrangement by means of side-chain-to-backbone C=CH...OC hydrogen bonds. In the anhydrous crystal form (II), cyclopeptoid molecules form ribbons by means of backbone-to-backbone CH2...OC hydrogen bonds, thus mimicking β-sheet secondary structures in proteins. In both crystal forms side chains act as joints among the columns or the ribbons and contribute to the stability of the whole solid-state assembly. Water molecules in the hydrate crystal form (I) bridge columns of cyclic peptoid molecules, providing a more efficient packing.

scholarly journals Assembling nanotubes with cyclic peptoids

2014 ◽  
Vol 70 (a1) ◽  
pp. C563-C563
Author(s):  
Consiglia Tedesco ◽  
Irene Izzo ◽  
Francesco De Riccardis ◽  
Gavin Vaughan ◽  
Michela Brunelli ◽  
...  
Keyword(s):  
Solid State ◽  
Hydrogen Bonds ◽  
Biological Activities ◽  
Variable Temperature ◽  
Chemical Properties ◽  
Functional Materials ◽  
Building Blocks ◽  
Amide Proton ◽  
Side Chains ◽  
Peptide Backbone

Cyclic alpha-peptoids hold the attention of both synthetic and supramolecular chemists for their biostability and potential diversity but also for their elegant and intriguing architectures.[1] Peptoids differ from peptides in the side chains, which are shifted by one position along the peptide backbone to the nitrogen atom to give N-substituted oligoglycine. The lack of the amide proton prevents the formation of NH···OC hydrogen bonds and weaker interactions, as CH···OC hydrogen bonds and CH-pi interactions, play a key role. Inter-annular CH···OC hydrogen bonds can provide face to face or side by side arrangement of macrocycles mimicking beta-sheet secondary structure in proteins.[2] In particular, the role of side chains in the solid state assembly of peptoid macrocycles will be discussed to show how they can promote the formation of a peptoid nanotube by acting as pillars, extending vertically with respect to the macrocycle planes. [3] Examples of the solid state assembly of free and metallated cyclic peptoids will be reported to show their extreme versatility as building blocks for designing new materials, with novel chemical properties and defined biological activities. In particular the first crystal structure of a recently synthesized novel cyclic alpha-peptoid, containing open channels with a radius of approximately 7 Å, will be discussed as a case of the successful engineering of cyclopeptoid crystals. In figure it is shown the channel void surface as seen along the a axis (0.0003 au, CrystalExplorer 3.1). The results of recent variable temperature high resolution XRPD measurements performed at ESRF beamline ID31 will be also reported to highlight the unusual thermal stability of this class of compounds and how the mobility of the side chains may be exploited to prepare new functional materials. EU FP7-People- IRSES grant number 319011 is gratefully acknowledged.

Finding a single-molecule receptor for citramalic acid through supramolecular chelation

2015 ◽  
Vol 93 (8) ◽  
pp. 822-825 ◽  
Author(s):  
Christer B. Aakeröy ◽  
Michelle Smith ◽  
John Desper
Keyword(s):  
Hydrogen Bond ◽  
Solid State ◽  
Hydrogen Bonds ◽  
Single Molecule ◽  
Conformational Flexibility ◽  
State Structure ◽  
Hydrogen Bond Acceptor ◽  
Solid State Structure ◽  
Face To Face ◽  
Hydrogen Bond Donors

We have demonstrated that the tritopic hydrogen-bond acceptor 1,3,5-(5,6-dimethylbenzimidazol-1-yl)-2,4,6-trimethylbenzene can act as a perfectly complementary receptor for citramalic acid. The solid-state structure of the cocrystal of the two components show that they form 1:1 pairs where each pair is held together by three near-linear O–H···N hydrogen bonds in a converging manner. The conformational flexibility of both species is apparently no hindrance to the formation of discrete dimeric “cups” wherein each species presents three hydrogen-bond donors/acceptors in a face-to-face orientation.

A 3D Chiral Hydrogen Bond Framework Based on Phenanthrolinium Hydrogen 4,5-Dichlorophthalate: Crystal Structure and Luminescent Properties

2012 ◽  
Vol 67 (1) ◽  
pp. 85-88 ◽  
Author(s):  
Bing An ◽  
Yan Bai ◽  
Fan Yang
Keyword(s):  
Solid State ◽  
Hydrogen Bonds ◽  
Uv Spectroscopy ◽  
Luminescent Properties ◽  
Aromatic Rings ◽  
Intermolecular Hydrogen Bonds ◽  
X Ray ◽  
Face To Face ◽  
X Ray Crystallography ◽  
Intramolecular Hydrogen

A salt with the composition [C12H9N2][C8H3Cl2O4] (1) with 4,5-dichlorophthalic acid and 1,10- phenanthroline (phen) has been synthesized and characterized by IR, UV spectroscopy, elemental analysis, and X-ray crystallography. Compound 1 represents a 3D chiral supramolecular framework containing monohelical chains (21 axis) through multiform C-H· · ·O, O-H· · · O, N-H· · ·N intramolecular hydrogen bonds and C-H· · ·O, N-H· · ·O intermolecular hydrogen bonds. Otherwise, two types of face-to-face π · · ·π interactions between the aromatic rings are found in the solid state. The luminescent properties of compound 1 were investigated in the solid state at room temperature

scholarly journals Characterizing Hydrogen Bonds in Intact RNA from MS2 Bacteriophage Using Solid State Magic Angle Spinning NMR

2021 ◽  
Author(s):  
Orr Simon Lusky ◽  
Moran Meir ◽  
Amir Goldbourt
Keyword(s):  
Hydrogen Bond ◽  
Solid State ◽  
Secondary Structure ◽  
Hydrogen Bonds ◽  
Structure Determination ◽  
Spin Diffusion ◽  
Secondary Structure Prediction ◽  
Magic Angle Spinning ◽  
Magic Angle ◽  
Base Pairs

Ribonucleic acid (RNA) is a polymer with pivotal functions in many biological processes. RNA structure determination is thus a vital step towards understanding its function. The secondary structure of RNA is stabilized by hydrogen bonds formed between nucleotide base pairs and it defines the positions and shapes of functional stem-loops, internal loops, bulges, and other functional and structural elements. In this work we present a methodology for studying large intact RNA molecules using homonuclear 15N solid state nuclear magnetic resonance (NMR) spectroscopy. We show that Proton Driven Spin Diffusion (PDSD) experiments with long mixing times, up to 16s, improved by the incorporation of 1H Radiofrequency Dipolar Recoupling (RFDR) pulses, reveal key hydrogen-bond contacts. In the full-length RNA isolated from MS2 phage, we observed strong and dominant contributions of G-C Watson-Crick base pairs, and beyond these common interactions, we observe a significant contribution of the G-U wobble base pairs. Using the improved technique facilitates characterization of hydrogen-bond types in intact large-scale RNA using solid-state NMR. It can be highly useful to guide secondary structure prediction techniques, and possibly to refine higher resolution structure determination methods.

Synthesis and Solid-State Structure of (4-Hydroxy-3,5-diiodophenyl)phosphine Oxides. Dimeric Motifs with the Assistance of O-H···O=P Hydrogen Bonds

2015 ◽  
Vol 19 (5) ◽  
pp. 469-474 ◽  
Author(s):  
Nicholas Bewick ◽  
Agata Arendt ◽  
Yan Li ◽  
S.awomir Szafert ◽  
Tadeusz Lis ◽  
...  
Keyword(s):  
Solid State ◽  
Hydrogen Bonds ◽  
Phosphine Oxides ◽  
State Structure ◽  
Solid State Structure

Charge-Separated Fmoc-Peptide β-Sheets: Sequence-Secondary Structure Relationship for Arranging Charged Side Chains on Both Sides

2014 ◽  
Vol 3 (11) ◽  
pp. 1182-1188 ◽  
Author(s):  
Toru Nakayama ◽  
Taro Sakuraba ◽  
Shunsuke Tomita ◽  
Akira Kaneko ◽  
Eisuke Takai ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Side Chains ◽  
Structure Relationship ◽  
Β Sheets

scholarly journals Organotin(IV) selenate derivatives – Crystal structure of [{(Ph3Sn)2SeO4} ⋅ CH3OH] n

2021 ◽  
Vol 44 (1) ◽  
pp. 213-217
Author(s):  
Waly Diallo ◽  
Hélène Cattey ◽  
Laurent Plasseraud
Keyword(s):  
Crystal Structure ◽  
Solid State ◽  
Hydrogen Bonds ◽  
Point Of View ◽  
Intermolecular Hydrogen Bonds

Abstract Crystallization of [(Ph3Sn)2SeO4] ⋅ 1.5H2O in methanol leads to the formation of [{(Ph3Sn)2SeO4} ⋅ CH3OH] n (1) which constitutes a new specimen of organotin(IV) selenate derivatives. In the solid state, complex 1 is arranged in polymeric zig-zag chains, composed of alternating Ph3Sn and SeO4 groups. In addition, pendant Ph3Sn ⋅ CH3OH moieties are branched along chains according to a syndiotactic organization and via Sn-O-Se connections. From a supramolecular point of view, intermolecular hydrogen bonds established between the selenate groups (uncoordinated oxygen) and the hydroxyl functions (CH3OH) of the pendant groups link the chains together.

scholarly journals Spectroscopic, X-ray Diffraction and Density Functional Theory Study of Intra- and Intermolecular Hydrogen Bonds in Ortho-(4-tolylsulfonamido)benzamides

Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 926
Author(s):  
Malose J. Mphahlele ◽  
Eugene E. Onwu ◽  
Marole M. Maluleka
Keyword(s):  
Density Functional Theory ◽  
Solid State ◽  
Hydrogen Bonds ◽  
Density Functional ◽  
Tetrahedral Geometry ◽  
Hindered Rotation ◽  
Hydrogen Bond Acceptor ◽  
Functional Theory ◽  
Vis Spectroscopy ◽  
Hydrogen Bonded

The conformations of the title compounds were determined in solution (NMR and UV-Vis spectroscopy) and in the solid state (FT-IR and XRD), complemented with density functional theory (DFT) in the gas phase. The nonequivalence of the amide protons of these compounds due to the hindered rotation of the C(O)–NH2 single bond resulted in two distinct resonances of different chemical shift values in the aromatic region of their 1H-NMR spectra. Intramolecular hydrogen bonding interactions between the carbonyl oxygen and the sulfonamide hydrogen atom were observed in the solution phase and solid state. XRD confirmed the ability of the amide moiety of this class of compounds to function as a hydrogen bond acceptor to form a six-membered hydrogen bonded ring and a donor simultaneously to form intermolecular hydrogen bonded complexes of the type N–H···O=S. The distorted tetrahedral geometry of the sulfur atom resulted in a deviation of the sulfonamide moiety from co-planarity of the anthranilamide scaffold, and this geometry enabled oxygen atoms to form hydrogen bonds in higher dimensions.

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