Self-Assembling l-d-l-Tripeptides Dance the Twist

Synlett ◽  
2020 ◽  
Vol 31 (05) ◽  
pp. 434-438 ◽  
Author(s):  
Maria C. Cringoli ◽  
Ottavia Bellotto ◽  
Rita De Zorzi ◽  
Attilio V. Vargiu ◽  
Silvia Marchesan
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Single Crystal ◽  
Self Assembly ◽  
Building Blocks ◽  
Supramolecular Structures ◽  
X Ray Diffraction ◽  
Supramolecular Materials ◽  
X Ray ◽  
Self Assembling

Minimalistic peptides composed of d- and l-amino acids are attractive building blocks for functional supramolecular materials, including catalysts. d-Amino acids have long been known to promote turn conformations in peptides, yet unexpected twists continue to emerge on their effects on self-assembly. The combination of single-crystal X-ray diffraction and full-atom molecular dynamics have finally unraveled fine details of how l-d-l-tripeptides visit different conformations in solution and establish key interactions in supramolecular structures.

4,4'-Bipyridine-2,2',6,6'-tetracarboxamide. Synthesis and Self-Assembling Properties of the Free Base and the 1 : 1 Silver(I) Triflate Complex

2002 ◽  
Vol 67 (8) ◽  
pp. 1236-1246 ◽  
Author(s):  
Petr Sehnal ◽  
Petr Holý ◽  
Miloš Tichý ◽  
Jiří Závada ◽  
Ivana Císařová
Keyword(s):  
Hydrogen Bonds ◽  
Single Crystal ◽  
Diffraction Analysis ◽  
Self Assembly ◽  
Crystal Packing ◽  
Amide Hydrogen ◽  
Free Base ◽  
X Ray Diffraction ◽  
X Ray ◽  
Self Assembling

Self-assembly of 4,4'-bipyridine-2,2',6,6'-tetracarboxamide and its 1 : 1 silver(I) triflate complex was investigated by single crystal X-ray diffraction analysis. It was found that intermolecular amide-amide hydrogen bonds control the crystal packing of the free base giving rise to infinite zig-zag tapes, whereas an octahedral coordination of the Ag(I) ion with the ligand dominates in the packing of the corresponding complex.

Crystal structures of (S)- and (R,S)-2,2′-bipyridine-3,3′-dicarboxylic acid 1,1′-dioxides and of their barium salts: absolute configuration and molecular distortion enforced by supramolecular self-assembly

1997 ◽  
Vol 212 (3) ◽  
Author(s):  
P. Vojtíšek ◽  
I. Císařová ◽  
J. Podlaha ◽  
Z. Žák ◽  
S. Böhm ◽  
...  
Keyword(s):  
Single Crystal ◽  
Dicarboxylic Acid ◽  
Crystal Structures ◽  
Absolute Configuration ◽  
Self Assembly ◽  
Barium Salt ◽  
X Ray Diffraction ◽  
X Ray

AbstractCrystal structures of the title compounds were determined by single crystal X-ray diffraction. Absolute configuration of the barium salt of (+)-(

scholarly journals Crystal structure of Ag-exchanged levyne intergrown with erionite: Single-crystal X-ray diffraction and Molecular Dynamics simulations

2020 ◽  
Vol 105 (11) ◽  
pp. 1631-1638 ◽  
Author(s):  
Georgia Cametti ◽  
Sergey V. Churakov
Keyword(s):  
Molecular Dynamics ◽  
Single Crystal ◽  
Molecular Dynamics Simulations ◽  
Exchange Process ◽  
Structural Refinement ◽  
X Ray Diffraction ◽  
Threefold Axis ◽  
Space Group ◽  
X Ray ◽  
Dynamics Simulations

Abstract The modification of natural zeolites via ion exchange is an efficient technique used to improve their performances and tune their properties for specific applications. In this study, a natural levyne-Ca intergrown with erionite was fully exchanged by Ag+ and its structure [with idealized chemical composition Ag6(Si,Al)18O36·18H2O] was investigated by combining a theoretical and experimental approach. Single-crystal X-ray diffraction data demonstrated that Ag-levyne maintained the R3m space group, characteristic of the natural levyne. Ag ions distribute over partially occupied sites along the threefold axis and, differently from the pristine material, at the wall of the 8-membered ring window of the lev cavity. The lack of ~30% of Ag ions that could not be located by the structural refinement is ascribed to the strong disorder of the extraframework occupants. The structural results obtained by Molecular Dynamics simulations are in overall agreement with the experimental data and showed that, on average, Ag+ is surrounded by ~2 H2O and 1 framework oxygen at distances between 2.43 and 2.6 Å. Molecular Dynamics trajectories indicate that the occurrence of silver inside the D6R cage depends on the water content: silver occupancy of D6R cages is estimated to be 83, 30, and 0% when the structure contains 3, 2.5, and 2 H2O per Ag ion, respectively. The cation-exchange process, as demonstrated by scanning electron microscopy and energy-dispersive spectroscopy (SEM-EDS) spectrometry, affects the intergrown erionite as well. A structural characterization of the Ag-erionite phase (with dimension <100 μm) was possible by means of a CuKα micro-focus source: structure solution pointed to P63/mmc space group, indicating no change with respect to natural erionite. In agreement with previous studies, K ions in the cancrinite cage could not be exchanged, whereas Ag+ is found in the eri cavity.

Synthesis, Structure and Properties of a Novel Metal-Organic Coordination Polymer, [Zn (NH3)2(BDC)]n

2013 ◽  
Vol 575-576 ◽  
pp. 30-36 ◽  
Author(s):  
Ning Ning Wu ◽  
Can Xiong Guo ◽  
Gui An Wu ◽  
Zhao Cai ◽  
Wan Hong He
Keyword(s):  
Coordination Polymer ◽  
Single Crystal ◽  
Diffraction Analysis ◽  
Self Assembly ◽  
Terephthalic Acid ◽  
Differential Scanning Calorimetric ◽  
X Ray Diffraction ◽  
X Ray ◽  
Acid Ligand ◽  
Metal Organic

A novel one-dimensional metal-organic coordination polymer, [Zn (NH3)2(BDC)]n (BDC=1,4-benzenedicaboxylate), has been synthesized by solvent evaporation method through self-assembly of Zn (II) salts with terephthalic acid ligand in ammonia aqueous solution. Single crystal X-ray diffraction analysis indicated that each Zn (II) was coordinated by two nitrogen donors from two NH3 and two oxygen counter donors from terephthalic acid ligand. The adjacent zigzag chains are arranged in a parallel fashion and linked by interchain hydrogen bonding interaction and π-π stacking interactions into higher-dimensional framework. The compound has also been characterized by CHN elemental analyses, Single crystal X-ray diffraction analysis, powder X-ray diffraction (PXRD) analysis, Fourier transform infrared (FT-IR) spectra, Thermalgravimetric-differential scanning calorimetric (TG-DSC) and Solid-state nuclear magnetic resonance (NMR), etc. Results showed that the framework of compound was stable at the temperature up to 246°C. The desolvated product [Zn (BDC)]n, which was obtained by removal of molecular NH3 from [Zn (NH3)2(BDC)]n, can be transferred to the different skeleton structures through coordinating different small hydrogen-bond-forming molecules.

scholarly journals Hydrogels formed from Fmoc amino acids

CrystEngComm ◽  
2015 ◽  
Vol 17 (42) ◽  
pp. 8047-8057 ◽  
Author(s):  
Emily R. Draper ◽  
Kyle L. Morris ◽  
Marc A. Little ◽  
Jaclyn Raeburn ◽  
Catherine Colquhoun ◽  
...  
Keyword(s):  
Amino Acids ◽  
Molecular Weight ◽  
Single Crystal ◽  
Crystal Structures ◽  
Diffraction Data ◽  
Low Molecular Weight ◽  
X Ray Diffraction ◽  
X Ray ◽  
Single Crystal Structures

A number of Fmoc amino acids can be effective low molecular weight hydrogelators; we compare single crystal structures to fibre X-ray diffraction data.

scholarly journals Ligand and solvent effects in the formation and self-assembly of a metallosupramolecular cage

2017 ◽  
Vol 41 (3) ◽  
pp. 1179-1185 ◽  
Author(s):  
N. N. Adarsh ◽  
Amarnath Chakraborty ◽  
Màrius Tarrés ◽  
Surjendu Dey ◽  
Fernando Novio ◽  
...  
Keyword(s):  
Coordination Polymer ◽  
Single Crystal ◽  
Solvent Effects ◽  
Self Assembly ◽  
X Ray Diffraction ◽  
One Dimensional ◽  
X Ray

A metallosupramolecular cage and a one-dimensional coordination polymer have been synthesized and structurally characterized by single crystal X-ray diffraction.

Single crystal structure and molecular dynamics analysis of a myo-inositol derivative

2000 ◽  
Vol 56 (4) ◽  
pp. 738-743
Author(s):  
Jan Dillen ◽  
Martin W. Bredenkamp ◽  
Mare-Loe Prinsloo
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Single Crystal ◽  
Room Temperature ◽  
Quantitative Agreement ◽  
Dynamics Simulation ◽  
X Ray Diffraction ◽  
Field Methods ◽  
X Ray ◽  
Empirical Force Field

The crystal structure of 5-O-tert-butyldimethylsilyl-3,4-O-carbonyl-1,2-O-cyclohexylidene-2-oxo-3-oxa-4-bornanylcarbonyl-D-myo-inositol has been studied by single-crystal X-ray diffraction at both room temperature and 173 K. At room temperature, the tert-butyldimethylsilyl group exhibits dynamical disorder. A molecular dynamics simulation was used to model the disorder and this indicates that the group librates between two stable conformations in the crystal. Approximate relative energies of the different forms and energy barriers for the transition were obtained by empirical force field methods. Calculations of the thermal motion of the atoms are in good qualitative, but fair to poor quantitative agreement with the X-ray data.

Molecular assembly of 1,3,5-tris(cyanomethyl) and 1,4-bis(cyanomethyl)arenes with silver triflate

2006 ◽  
Vol 78 (4) ◽  
pp. 855-871 ◽  
Author(s):  
Kathleen V. Kilway ◽  
Shiping Deng ◽  
Sean Bowser ◽  
Joseph Mudd ◽  
Laronda Washington ◽  
...  
Keyword(s):  
Single Crystal ◽  
Layered Structure ◽  
Building Blocks ◽  
Molecular Assembly ◽  
Porous Channel ◽  
X Ray Diffraction ◽  
X Ray ◽  
Silver Triflate

Dicyano- and tricyano-substituted aromatic angular building blocks were systematically complexed with silver triflate, and their structures were determined by means of single-crystal X-ray diffraction. The molecular assembly of 1,3,5-tris(cyanomethyl)-2,4,6-triethylbenzene with silver triflate from benzene resulted in a layered structure with distorted square pyramidal silver sites. The structure resulting from the complexation of 1,3,5-tris(cyanomethyl)-2,4,6-trimethylbenzene with silver triflate is dependent on the solvent of crystallization. From benzene or toluene, reaction of 1,3,5-tris(cyanomethyl)-2,4,6-trimethylbenzene with silver triflate yielded a porous, channel-containing, solvated structure, but from acetone the resulting material was a network solid containing no solvent. Complexation of 1,4-bis(cyanomethyl)-2,3,5,6-tetraethylbenzene and 1,4-bis(cyanomethyl)-2,3,5,6-tetramethylbenzene with silver triflate resulted in network solids where the triflate anions were strongly coordinated to the silver.

Bis-, Tris- and Tetrakis(lithiomethyl)germanes: New Building Blocks for Organogermanium Compounds

2004 ◽  
Vol 59 (11-12) ◽  
pp. 1570-1578 ◽  
Author(s):  
Carsten Strohmann ◽  
Eric Wack
Keyword(s):  
Single Crystal ◽  
Bond Cleavage ◽  
Building Blocks ◽  
X Ray Diffraction ◽  
X Ray ◽  
Organogermanium Compounds

Bis(lithiomethyl)germanes, R2Ge(CH2Li)2, tris(lithiomethyl)germanes, RGe(CH2Li)3, and tetrakis( lithiomethyl)germane, Ge(CH2Li)4, were prepared by the reductive C-S bond cleavage with lithium naphthalenide (LiC10H8) or lithium p,p’-di-tert-butylbiphenylide (LiDBB) and characterized by trapping with Bu3SnCl. The bis(lithiomethyl)germanes were used for the synthesis of 1,1-dimethyl-3,3-diphenyl-1-germa-3-silacyclobutane, 1,1-diethyl-3,3-diphenyl-1-germa-3-silacyclobutane, 1,1,3,3-tetraphenyl-1-germa-3-silacyclobutane and 1,1,3,3-tetraphenyl-1,3-digermacyclobutane. The single-crystal X-ray diffraction studies of methyltris(phenylthiomethyl)germane and tetrakis(phenylthiomethyl)germane, starting materials for the corresponding poly(lithiomethyl) germanes, indicate tetrahedrally arranged substituents at the germanium atoms.

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