Conformational properties of oxazoline-amino acids
Abstract Oxazoline-amino acids (Xaa-Ozn) occur in natural peptides of potentially important bioactivity. The conformations of the model compounds: Ac-(S)-Ala-Ozn(4R-Me), Ac-(S)-Ala-Ozn(4S–Me), and (gauche+, gauche−, anti) Ac-(S)-Val-Ozn(4R-Me) were studied at meta-hybrid M06-2X/6–311++G(d,p) method including solvent effect. Boc- l -Ala- l -Ozn-4-COOMe and Boc- l -Val- l -Ozn-4-COOMe were synthesized and studied by FT-IR and NMR-NOE methods. The conformations in crystal state were gathered from the Cambridge Structural Data Base. The main conformational feature of the oxazoline amino acids is the conformation β2 (ϕ,ψ ∼ −161°, −6°), which predominates in weakly polar environment and still is …
On Complex Formation between 5-Fluorouracil and β-Cyclodextrin in Solution and in the Solid State: IR Markers and Detection of Short-Lived Complexes by Diffusion NMR
In this work, the nuclear magnetic resonance (NMR) and IR spectroscopic markers of the complexation between 5-fluorouracil (5-FU) and &beta
Gas-Phase Synthesis of the Elusive Trisilicontetrahydride Species (Si3H4)
The bimolecular gas-phase reaction of ground-state atomic silicon (Si; 3P) with disilane (Si2H6; 1A1g) was explored under single-collision conditions in a crossed molecular beam machine at a collision energy of 21 kJ mol–1. Combined with electronic structure calculations, the results suggest the formation of Si3H4 isomer(s) along with molecular hydrogen via indirect scattering dynamics through Si3H6 collision complex(es) and intersystem crossing from the triplet to the singlet surface. The nonadiabatic reaction dynamics can synthesize the energetically accessible singlet Si3H4 isomers in overall exoergic reaction(s) (−93 ± 21 kJ mol–1). All reasonable reaction products are either cyclic or …
Thiazole–amino acids: influence of thiazole ring on conformational properties of amino acid residues
Abstract Post-translational modified thiazole–amino acid (Xaa–Tzl) residues have been found in macrocyclic peptides (e.g., thiopeptides and cyanobactins), which mostly inhibit protein synthesis in Gram + bacteria. Conformational study of the series of model compounds containing this structural motif with alanine, dehydroalanine, dehydrobutyrine and dehydrophenylalanine were performed using DFT method in various environments. The solid-state crystal structure conformations of thiazole–amino acid residues retrieved from the Cambridge Structural Database were also analysed. The studied structural units tend to adopt the unique semi-extended β2 conformation; which is stabilised mainly by N–H⋯N…
Conformational Properties of Oxazole-Amino Acids: Effect of the Intramolecular N–H···N Hydrogen Bond
Oxazole ring occurs in numerous natural peptides, but conformational properties of the amino acid residue containing the oxazole ring in place of the C-terminal amide bond are poorly recognized. A series of model compounds constituted by the oxazole-amino acids occurring in nature, that is, oxazole-alanine (L-Ala-Ozl), oxazole-dehydroalanine (ΔAla-Ozl), and oxazole-dehydrobutyrine ((Z)-ΔAbu-Ozl), was investigated using theoretical calculations supported by FTIR and NMR spectra and single-crystal X-ray diffraction. It was found that the main feature of the studied oxazole-amino acids is the stable conformation β2 with the torsion angles φ and ψ of -150°, -10° for L-Ala-Ozl, -180°, 0° for ΔAl…
Ir-Catalyzed Cycloaddition of Tribenzocyclyne with Biphenylenes
We demonstrate that Ir-catalyzed C-C bond activation in biphenylenes followed by a reaction with tribenzocyclyne is a suitable method for synthesizing strained and unknown monoadducts with the tetradehydrotetrabenzo[a,c,e,i]cyclododecene scaffold ([12]annulenes). Modification of reaction conditions also furnished [12]annulene products with cis and/or trans double bonds formed by hydrogen transfer. The [9]annulene side product was formed upon the reaction of the benzyl radical with tribenzocyclyne during the Bergman cyclization. All isolated compounds were fully characterized by HRMS, NMR, and X-ray diffraction analysis.
Intra- and intermolecular forces dependent main chain conformations of esters of α,β-dehydroamino acids
Abstract Esters of dehydroamino acids occur in nature. To investigate their conformational properties, the low-temperature structures of Ac-ΔAla-OMe, Ac-ΔVal-OMe, Z-(Z)-ΔAbu-OMe, and Z-(Z)-ΔAbu-NHMe were studied by single-crystal X-ray diffraction. The ΔAla ester prefers the fully extended conformation C5. Both the ΔVal and (Z)-ΔAbu esters assume the conformation β, whereas the amide analogue of the latter prefers the conformation α. For the conformations found, DFT calculations using B3LYP/6-311++G(d,p) with the SCRF-PCM and M062X/6-311++G(d,p) with the SCRF-SMD method were applied to mimicking chloroform and water environment. The tendency of the ΔVal and (Z)-ΔAbu esters towards the confo…
Interaction of 5‐fluorouracil with β‐cyclodextrin: A density functional theory study with dispersion correction
Detailed studies on the stability, interaction, and microstructure of host‐guest complexes in the vacuum of 5‐fluorouracil (5FU) with β‐cyclodextrin (βCD) were performed using B3LYP with the inclusion of Grimme's dispersion correction GD3 term and 6‐31+G(d,p) basis set. Among several studied 1:1 5FU‐βCD complexes, the one placing the keto tautomer of 5FU vertically in the host cavity and forming N‐H···OCD and CO···HOCD hydrogen bonds with hydroxyl groups of the smaller rim of βCD has the highest stability (Eint = −195 kJ/mol). Interestingly, there are no interactions with the inner hydrophobic part of the βCD host cavity. The strength of the intermolecular H‐bonds to the smaller rim of βC…
Conformational preferences and synthesis of isomersZandEof oxazole-dehydrophenylalanine
Dehydrophenylalanine, ΔPhe, is the most commonly studied α,β-dehydroamino acid. In nature, further modifications of the α,β-dehydroamino acids were found, for example, replacement of the C-terminal amide group by oxazole ring. The conformational properties of oxazole-dehydrophenylalanine residue (ΔPhe-Ozl), both isomers Z and E, were investigated. To determine all possible conformations, theoretical calculations were performed using Ac-(Z/E)-ΔPhe-Ozl(4-Me) model compounds at M06-2X/6-31++G(d,p) level of theory. Ac-(Z/E)-ΔPhe-Ozl-4-COOEt compounds were synthesized and the conformational preferences of each isomer, Z and E, were investigated using FTIR and NMR-NOE in solutions of increasing p…
Microscopic Revelation of Charge-Trapping Sites in Polymeric Carbon Nitrides for Enhanced Photocatalytic Activity by Correlating with Chemical and Electronic Structures
The influences of chemical and electronic structures on the photophysical properties of polymeric carbon nitrides (PCNs) photocatalysts, which govern the microscopic mechanisms of the superior photocatalytic activity under visible-light irradiation, have been resolved in this work. Time-resolved photoluminescence and in situ electron paramagnetic resonance measurements indicate that the photoexcited electrons in the fractured PCNs swiftly transfer to the C2p-localized states where the trapped photoelectrons exhibit longer lifetime compared to those in the ordinary PCNs. Moreover, the structure deviation at the carbon (Cb) atoms around the bridging sites of heptazine ring units, where trappe…
Imidazole-amino acids. Conformational switch under tautomer and pH change.
AbstractReplacement of the main chain peptide bond by imidazole ring seems to be a promising tool for the peptide-based drug design, due to the specific prototropic tautomeric as well as amphoteric properties. In this study, we present that both tautomer and pH change can cause a conformational switch of the studied residues of alanine (1–4) and dehydroalanine (5–8) with the C-terminal peptide group replaced by imidazole. The DFT methods are applied and an environment of increasing polarity is simulated. The conformational maps (Ramachandram diagrams) are presented and the stability of possible conformations is discussed. The neutral forms, tautomers τ (1) and π (2), adapt the conformations…
CCDC 1451706: Experimental Crystal Structure Determination
Related Article: Monika Staś, Maciej Bujak, Małgorzata A. Broda, Dawid Siodłak|2016|Biopolymers|106|283|doi:10.1002/bip.22852
CCDC 931328: Experimental Crystal Structure Determination
Related Article: Dawid Siodłak, Maciej Bujak, Monika Staś|2013|J.Mol.Struct.|1047|229|doi:10.1016/j.molstruc.2013.04.078
CCDC 931329: Experimental Crystal Structure Determination
Related Article: Dawid Siodłak, Maciej Bujak, Monika Staś|2013|J.Mol.Struct.|1047|229|doi:10.1016/j.molstruc.2013.04.078
CCDC 931327: Experimental Crystal Structure Determination
Related Article: Dawid Siodłak, Maciej Bujak, Monika Staś|2013|J.Mol.Struct.|1047|229|doi:10.1016/j.molstruc.2013.04.078
CCDC 1451707: Experimental Crystal Structure Determination
Related Article: Monika Staś, Maciej Bujak, Małgorzata A. Broda, Dawid Siodłak|2016|Biopolymers|106|283|doi:10.1002/bip.22852
CCDC 931326: Experimental Crystal Structure Determination
Related Article: Dawid Siodłak, Maciej Bujak, Monika Staś|2013|J.Mol.Struct.|1047|229|doi:10.1016/j.molstruc.2013.04.078