0000000001300139
AUTHOR
Dawid Siodłak
showing 68 related works from this author
α,β-Dehydroamino acids in naturally occurring peptides
2014
α,β-Dehydroamino acids are naturally occurring non-coded amino acids, found primarily in peptides. The review focuses on the type of α,β-dehydroamino acids, the structure of dehydropeptides, the source of their origin and bioactivity. Dehydropeptides are isolated primarily from bacteria and less often from fungi, marine invertebrates or even higher plants. They reveal mainly antibiotic, antifungal, antitumour, and phytotoxic activity. More than 60 different structures were classified, which often cover broad families of peptides. 37 different structural units containing the α,β-dehydroamino acid residues were shown including various side chains, Z and E isomers, and main modifications: meth…
Conformational properties of oxazoline-amino acids
2016
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 …
Conformational studies into N-methylation of alanine diamide models: A quantitative approach
2006
Abstract A systematic theoretical analysis was performed on N -acetyl- l -alanine N ′-methylamide (Ac- l -Ala-NHMe) and the analogues methylated on the N-terminus (Ac- l -(Me)Ala-NHMe), C-terminus (Ac- l -Ala-NMe 2 ), and both N/C-termini (Ac- l -(Me)Ala-NMe 2 ), to evaluate the influence of methylation of the amide group on the conformational properties of the affected residues. The ϕ , ψ potential energy surfaces were calculated at the B3LYP/6-31+G**//HF/3-21G level of theory with inclusion of the solvent (water) effect (SCRF method). The conformers localised were fully optimised at the B3LYP/6-31+G** in vacuo. The accessible areas of the potential energy surfaces; the number of conformer…
The conformational properties of dehydrobutyrine and dehydrovaline: theoretical and solid-state conformational studies
2010
Dehydrobutyrine is the most naturally occurring dehydroamino acid. It is also the simplest dehydroamino acid having the geometrical isomers E/Z. To investigate its conformational properties, a theoretical analysis was performed on N-acetyl-α,β-dehydrobutyrine N′-methylamides, Ac-(E)-ΔAbu-NHMe and Ac-(Z)-ΔAbu-NHMe, as well as the dehydrovaline derivative Ac-ΔVal-NHMe. The ϕ, ψ potential energy surfaces and the localised conformers were calculated at the B3LYP/6-311 + + G(d,p) level of theory both in vacuo and with inclusion of the solvent (chloroform, water) effect (SCRF method). The X-ray crystal structures of Ac-(Z)-ΔAbu-NHMe and Ac-ΔVal-NHMe were determined at 85 and 100 K, respectively. …
Experimental and theoretical NMR studies of interaction between phenylalanine derivative and egg yolk lecithin
2014
The interaction of phenylalanine diamide (Ac-Phe-NHMe) with egg yolk lecithin (EYL) in chloroform was studied by 1H and 13C NMR. Six complexes EYL–Ac-Phe-NHMe, stabilized by N–H···O or/and C–H···O hydrogen bonds, were optimized at M06-2X/6-31G(d,p) level. The assignment of EYL and Ac-Phe-NHMe NMR signals was supported using GIAO (gauge including atomic orbital) NMR calculations at VSXC and B3LYP level of theory combined with STO-3Gmag basis set. Results of our study indicate that the interaction of peptides with lecithin occurs mainly in the polar ‘head’ of the lecithin. Additionally, the most probable lecithin site of H-bond interaction with Ac-Phe-NHMe is the negatively charged oxygen in …
Thecis-transisomerization ofN-methyl-α,β-dehydroamino acids
2012
Dehydroamino acids with the methylated N-terminal peptide group occur in natural small cyclic peptides. The structural analysis was used to investigate the cis-trans isomerization of the N-terminal tertiary amide group of diamides: Ac-(Z)-Δ(Me)Abu-NHMe (1), Ac-(Z)-Δ(Me)Phe-NHMe (2), Ac-(E)-Δ(Me)Phe-NHMe (3), Ac-Δ(Me)Ala-NHMe (4), and Ac-(Me)Ala-NHMe (5). The compounds were analyzed in the solid state by an X-ray crystallography (1-3), and in the solution by FTIR (MeCN and CHCl(3) ) and NMR (DMSO-d6 and CDCl(3) ) methods (1-5). In the solid state, the studied compounds adopt the cis configuration of N-terminal amide. In solution, this configuration also prevails for the dehydroamino acids 1-…
Pyrazole amino acids: hydrogen bonding directed conformations of 3-amino-1H-pyrazole-5-carboxylic acid residue
2017
A series of model compounds containing 3-amino-1H-pyrazole-5-carboxylic acid residue with N-terminal amide/urethane and C-terminal amide/hydrazide/ester groups were investigated by using NMR, Fourier transform infrared, and single-crystal X-ray diffraction methods, additionally supported by theoretical calculations. The studies demonstrate that the most preferred is the extended conformation with torsion angles ϕ and ψ close to ±180°. The studied 1H-pyrazole with N-terminal amide/urethane and C-terminal amide/hydrazide groups solely adopts this energetically favored conformation confirming rigidity of that structural motif. However, when the C-terminal ester group is present, the second con…
Effects of side-chain orientation on the backbone conformation of the dehydrophenylalanine residue. Theoretical and X-ray study.
2011
Two E isomers of α,β-dehydro-phenylalanine, Ac-(E)-ΔPhe-NHMe (1a) and Ac-(E)-ΔPhe-NMe(2) (2a), have been synthesized and their low temperature structures determined by single-crystal X-ray diffraction. A systematic theoretical analysis was performed on these molecules and their Z isomers (1b and 2b). The ϕ,ψ potential energy surfaces were calculated at the MP2/6-31+G(d,p) and B3LYP/6-31+G(d,p) levels in the gas phase and at the B3LYP/6-31+G(d,p) level in the chloroform and water solutions with the SCRF-PCM method. All minima were fully optimized by the MP2 and DFT methods, and their relative stabilities were analyzed in terms of π-conjugation, internal H-bonds, and dipole-dipole interaction…
Biphenyl-4-yl 4-methylbenzenesulfonate
2017
Molecules of the title compound, C19H16O3S, are composed of a biphenyl moiety substituted with a toluene-4-sulfonate group. The dihedral angle between the two coplanar biphenyl rings and the toluene ring is 52.72 (6)°.
The impact of model peptides on structural and dynamic properties of egg yolk lecithin liposomes - experimental and DFT studies.
2015
Electron spin resonance (ESR), 1H-NMR, voltage and resistance experiments were performed to explore structural and dynamic changes of Egg Yolk Lecithin (EYL) bilayer upon addition of model peptides. Two of them are phenylalanine (Phe) derivatives, Ac-Phe-NHMe (1) and Ac-Phe-NMe2 (2), and the third one, Ac-(Z)-ΔPhe-NMe2 (3), is a derivative of (Z)-α,β-dehydrophenylalanine. The ESR results revealed that all compounds reduced the fluidity of liposome's membrane, and the highest activity was observed for compound 2 with N-methylated C-terminal amide bond (Ac-Phe-NMe2). This compound, being the most hydrophobic, penetrates easily through biological membranes. This was also observed in voltage an…
Conformational properties of the residues connected by ester and methylated amide bonds: theoretical and solid state conformational studies
2010
Peptides produced by bacteria and fungi often contain an ester bond in the main chain. Some of them have both an ester and methylated amide bond at the same residue. A broad spectrum of biological activities makes these depsipeptides potential drug precursors. To investigate the conformational properties of such modified residues, a systematic theoretical analysis was performed on N-acetyl-L-alanine N′-methylamide (Ac-Ala-NHMe) and the analogues with the ester bond on the C-terminus (Ac-Ala-OMe), N-terminus (Ac-[psi](COO)-Ala-NHMe) as well as the analogues methylated on the N-terminus (Ac-(Me)Ala-OMe) and C-terminus (Ac-[psi](COO)-Ala-NMe2). The ϕ, ψ potential energy surfaces and the confor…
Conformational properties of N-acetyl-L-alanine N',N'-dimethylamide
2004
Ab initio/DFT analysis of the conformational properties of free Ac-Ala-NMe(2) (N-acetyl-L-alanine-N',N'-dimethylamide) in terms of the N-H.O, N-H.N, C-H.O hydrogen bonds and C(delta+) = O(delta-) dipole attractions was performed. The Ala residue combined with the C-terminal tertiary amide prefers an extended conformation and that characteristic of the (i + 1)th position of the betaVIb turn. These can be easily remodelled into a structure compatible with the (i + 1)th position of the betaII/betaVIa turn. The residue has also the potential to adopt the conformation accommodated at both central positions of the betaIII/betaIII' turn or the (i + 1)th position of the betaI/beta'I turn.
Isostructural Inorganic–Organic Piperazine-1,4-diium Chlorido- and Bromidoantimonate(III) Monohydrates: Octahedral Distortions and Hydrogen Bonds
2020
Halogenidoantimonate(III) monohydrates of the (C4H12N2)[SbX5]·
3,5-Bis(trifluoromethyl)phenyl 4-methylbenzenesulfonate
2017
Molecules of the title compound, C15H10F6O3S, are composed of 3,5-bis(trifluoromethyl)phenyl substituted with a toluene-4-sulfonate group. The dihedral angle between two aromatic moieties is 45.10 (5)°. In the crystal, molecules are connected by weak C—H...O and C—H...F contacts. One of the trifluoromethyl groups is disordered.
The effect of β-methylation on the conformation of α, β-dehydrophenylalanine: a DFT study
2009
Dehydroamino acids are non-coded amino acids that offer unique conformational properties. Dehydrophenylalanine (ΔPhe) is most commonly used to modify bioactive peptides to constrain the topography of the phenyl ring in the side chain, which commonly serves as a pharmacophore. The Ramachandran maps (in the gas phase and in CHCl3 mimicking environments) of ΔPhe analogues with methyl groups at the β position of the side chain as well as at the C-terminal amide were calculated using the B3LYP/6-31 + G** method. Unexpectedly, β-methylation alone results in an increase of conformational freedom of the affected ΔPhe residue. However, further modification by introducing an additional methyl group a…
Titanium and Vanadium Catalysts with 2-Hydroxyphenyloxazoline and Oxazine Ligands for Ethylene-Norbornene (co)Polymerization
2019
A series of titanium and vanadium complexes with oxazoline 2-(4,5-dihydro-1,3-oxazol-2-yl)phenol (L1), 2-(4-methyl-4,5-dihydro-1,3-oxazol-2-yl)phenol (L2), and oxazine 2-(5,6-dihydro-4H-1,3-oxazin-2-yl)phenol (L3) ligands were synthesized, and their structures were determined by NMR and MS methods as (L)2MtCl2. The vanadium complexes were found to be highly active in ethylene (7300 kgPE/(molV·
The conformation cis of N-acetyl-N-methyl-α,β-dehydroalanine N′-methylamide and saturated analogues
2007
A series of three homologous amino acids derivatives: N-acetyl-N-methyl-α,β–dehydroalanine N′-methylamide (1), N-acetyl-N-methyl-L-alanine N′-methylamide (2), and N-acetyl-N-methyl-DL-alanine N′-methylamide have been synthesised. The racemic species undergoes spontaneous separation into L and D-enantiomers. From these two chiral forms, the structure of L-enantiomer (3) was analysed. The molecules of 1 – 3 adopt the cis arrangement of the N-terminal amide bond. The molecular conformations are similar for 1 (φ, ψ = 94.6(1)°, −1.7(1)°) and 3 (φ, ψ = 111.5(1)°, −23.8(1)°), and also 2 (φ, ψ = −114.8(2)°, 29.5(2)°), if inversion through the chiral C2 carbon is considered. They are stabilised by i…
Molecular and crystal structure of Ac-(Z)-ΔAbu-NMe2 and Ac-DL-Abu-NMe2 as compared to those of related molecules
2004
Abstract The molecular and crystal structures of two homologous amino acid derivatives: N-acetyl-α,β-dehydro-butyrine N´,N´-dimethylamide (1) and N-acetyl-DL-butyrine N´,N´-dimethylamide (2), have been determined by X-ray crystallography. Similar solid-state association of both compounds is observed; despite different molecular conformation, they form centrosymmetric dimers linked by the intermolecular N–H…O hydrogen bonds. The conformation of two crystallographically independent molecules of 1 [with torsion angles ϕ, ψ, χ 1 ≈ (–47°, 130°, 3°), respectively] is also characteristic of other related diamides – ΔAla, ΔPhe and ΔLeu – previously studied in the solid state. To analyse whether thi…
Conformational investigation of α,β‐dehydropeptides. XV: N‐acetyl‐α,β‐dehydroamino acid N ′N ′‐dimethylamides: conformational properties from infrare…
2005
The FTIR spectra were analysed in the region of the nu(s)(N-H), AI(C=O) and nu(s)(Calpha=Cbeta) bands for a series of Ac-DeltaXaa-NMe2, where DeltaXaa = DeltaAla, (Z)-DeltaAbu, (Z)-DeltaLeu, (Z)-DeltaPhe and DeltaVal, to determine a predominant solution conformation of these alpha,beta-dehydropeptide-related molecules. Measurements were taken in CCl4, DCM and MeCN solutions. In the same way, spectra of saturated analogues Ac-Xaa-NMe2, where Xaa = Ala, Abu, Leu, Phe and Val, were investigated. To help interpret the spectroscopic results, conformational maps were calculated by the B3LYP/6-31+G** method. Also, the relative energies of all conformers of the dehydro compounds in vacuo as well as…
N-Methyldehydroamino acids promote a configuration cis of N-methylamide bond
2008
Abstract Dehydroamino acids with a methylated N-terminal tertiary amide bond occur in natural small cyclic peptide toxins. To investigate their conformational preferences a systematic theoretical analysis was performed on N ′-methylamides of N -acetyl- N -methyldehydroamino acids (Ac-Δ(Me)Xaa-NHMe, where Xaa = ( Z )-Abu, ( E )-Abu, Val, ( Z )-Phe, and ( E )-Phe) considering the configuration trans and cis of the tertiary amide bond. The ϕ , ψ potential energy surfaces were calculated at the B3LYP/6-31+G ∗∗ //HF/3-21G level with inclusion of the solvent (water) effect (SCRF method). The conformers localised were fully optimised at the B3LYP/6-31+G ∗∗ in vacuo. The accessible areas of the pot…
Conformational investigation of alpha,beta-dehydropeptides. XIII. Conformational properties of N-acetyl-alpha,beta-dehydrovaline N',N'-dimethylamide.
2004
The crystal structure of Ac-DeltaVal-NMe(2) (DeltaVal = alpha,beta-dehydrovaline) was determined by X-ray crystallography. The found angles phi = -60 degrees and psi = 125 degrees correspond exactly to the respective values of the (i + 1)th residue in idealised beta-turn II/VIa. Ab initio/DFT studies revealed that the molecule adopts the angle psi restricted only to about |130 degrees | and very readily attains the angle phi = about -50 degrees. This is in line with its solid-state conformation. Taken together, these data suggest that the DeltaVal residue combined with a C-terminal tertiary amide is a good candidate at the (i + 1)th position in a type II/VIa beta-turn.
Naphthalene-2,6-diyl bis(4-methylbenzenesulfonate)
2018
The complete molecule of the title compound, C24H20O6S2, is generated by a crystallographic inversion centre at the middle of the naphthalene ring system. The dihedral angle between the naphthalene ring system and the pendant benzene ring is 10.23 (6)° and the C—S—O—C torsion angle is −172.05 (10)°. In the crystal, weak C—H...O interactions link the molecules into (10-1) sheets.
Thiazole–amino acids: influence of thiazole ring on conformational properties of amino acid residues
2021
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…
Impact of the ΔPhe configuration on the Boc-Gly-ΔPhe-NHMe conformation: experiment and theory
2019
Conformational propensities of N-t-butoxycarbonyl-glycine-(E/Z)-dehydrophenylalanine N′-methylamides (Boc-Gly-(E/Z)-ΔPhe-NHMe) in chloroform were investigated by NMR and IR techniques. The low-temperature crystal structure of the E isomer was determined by single crystal X-ray diffraction and the experimental data were elaborated by theoretical calculations using DFT (B3LYP, M06-2X) and MP2 approaches. The β-turn tendencies for both isomers were determined in the gas phase and in the presence of solvent. The obtained results reveal that the configuration of ΔPhe residue significantly affects the conformations of the studied dehydropeptides. The tendency to adopt β-turn conformations is sign…
Conformational investigation of α, β‐dehydropeptides. XI. Molecular and crystal structure of Ac‐(Z )‐ΔPhe‐NMe2 as compared to those of related molecu…
2003
A series of three homologous dimethyldiamides Ac-(Z)-ΔPhe-NMe2, Ac-L-Phe-NMe2 and Ac-DL-Phe-NMe2 have been synthesized and their structures determined from single-crystal X-ray diffraction data. To learn more about the conformational preferences of the compounds studied, the fully relaxed ϕ, ψ conformational energy maps on the free molecules of Ac-ΔAla-NMe2 and Ac-(Z)-ΔPhe-NMe2 were obtained with the HF/3-21G method and the calculated minima re-optimized with the DFT/B3LYP/6-31G** method. The crystal state results have been compared with the literature data. The studied dimethyldiamide Ac-ΔXaa-NMe2 combines the double bond in positions α, β and the C-terminal tertiary amide within one molec…
Conformational Properties of Oxazole-Amino Acids: Effect of the Intramolecular N–H···N Hydrogen Bond
2014
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…
Conformational properties of N′,N′-dimethylamides of N-acetyldehydroalanine and N-acetyl-(Z)-dehydrophenylalanine
2001
Conformational preferences of Ac-deltaAla-NMe2 and Ac-(Z)-deltaPhe-NMe2 were studied and compared with those of their monomethyl counterparts as well as with those of their saturated analogues. X-Ray data and energy calculations revealed a highly conservative conformation of the dehydro dimethylamides, which is located in a high-energy region of the Ramachandran map.
Conformational investigation of ?,?-dehydropeptides.N-acetyl-(E)-dehydrophenylalanineN?-methylamide: conformational properties from infrared and theo…
2005
N-Acetyl-(E)-dehydrophenylalanine N'-methylamide [Ac-(E)-DeltaPhe-NHMe], one of a few representative (E)-alpha,beta-dehydroamino acids, was studied by FTIR in dichloromethane and acetonitrile. To support spectroscopic interpretations and to gain some deeper insight into the Ac-(E)-DeltaPhe-NHMe molecule, the Ramachandran potential energy surface was calculated by the B3LYP/6-31G*//HF/3-21G method and the conformers localized were fully optimized at the B3LYP/6-31 + G** level. The spectra and calculations were compared with those of the related molecules Ac-DeltaAla-NHMe and Ac-(Z)-DeltaPhe-NHMe. The title compound assumes two conformational states in equilibrium in dichloromethane solution …
Building molecular models using screw-on bottle caps
2013
Chemical models can be built using screw-on bottle caps. Two identical caps can be joined together by thermal welding to form atoms, and the resulting atoms can be joined together by welding or by hot polymer glue to form molecules. The method is easy, can be applied at every level of chemical education, and gives access to an unlimited number of models at almost no cost. It inspires hands-on activity of pupils and can be used to show the dependence between the three-dimensional structure of molecules and their chemical, physical, and biological features.
Conformational analysis of α,β-dehydropeptide models at the HF and DFT levels
2004
Abstract The Ramachandran potential energy surfaces of N-acetyl-α,β-dehydroamino acid N′-monomethylamides Ac-ΔXaa-NHMe (ΔXaa=ΔAla, (Z)-ΔPhe; 1, 2) and N-acetyl-α,β-dehydroamino acid N′,N′-dimethylamides Ac-ΔXaa-NMe2 (ΔXaa=ΔAla, (Z)-ΔPhe, (Z)-ΔAbu; 3–5) were calculated at the HF/6-31G*//HF/3-21G level. The conformers localised were fully optimised at the DFT/B3LYP/6-31+G** level and their relative stabilities were analysed in terms of both π-conjugation and internal hydrogen bonding. The Ac-ΔXaa-NMe2 molecules reveal the low-energy conformer H/F, φ=−41±4°, ψ=128±4°, which is not too easily accessible for common amino acid residues. This conformer is stabilised by the bifurcated N2–CH3 O1 int…
Titanium and vanadium catalysts with oxazoline ligands for ethylene-norbornene (co)polymerization
2018
A series of catalysts, (Py-ox)TiCl4, (Py-box)TiCl4, (Py-ox)VCl3, (Py-box)VCl3, SIL/(Py-ox)VCl3, SIL/(Py-box)VCl3, with 2-(1,3-oxazolin-2-yl)pyridine (Py-ox) and 2,6-bis(1,3-oxazolin-2-yl)pyridine (Py-box) ligands, silica support modified by 1-[3-(triethoxysilyl)propyl]pyridinium ethylchloroaluminate ionic liquid (SIL), activated by AlEt2Cl, AlEtCl2, and methylaluminoxane (MMAO) were studied in ethylene polymerization and ethylene-norbornene copolymerization. Single-crystal X-ray diffraction is given for both Py-ox and Py-box. The complexation was confirmed by NMR and ESI-MS methods. All complexes were found to be active in ethylene polymerization with better performance of the vanadium cata…
Association of model peptides and dehydropeptides: N-acetyl-l-alanine- and dehydroalanine N′,N′-dimethylamides
2005
Abstract The comparative studies on the association of Ac-ΔAla-NMe 2 and Ac- l -Ala-NMe 2 in carbon tetrachloride were performed by the analysis of their average molecular weight, dipole moments and FTIR spectra. To aid spectroscopic interpretation and gain some deeper insight into the nature of associates, the geometries of the minimum energy of the dimers of Ac-ΔAla-NMe 2 and Ac- l -Ala-NMe 2 were calculated by the B3LYP/6-31+G** method. The average molecular weight in the studied concentration range, for the ΔAla and l -Ala peptide, as determined by the osmometric method, did not exceed 1.5 and 1.2 of the monomeric mass, respectively. Accordingly, the percentage of the monomeric form (α)…
The conformational properties ofα,β-dehydroamino acids with aC-terminal ester group
2011
α,β-Dehydroamino acid esters occur in nature. To investigate their conformational properties, a systematic theoretical analysis was performed on the model molecules Ac-ΔXaa-OMe [ΔXaa = ΔAla, (E)-ΔAbu, (Z)-ΔAbu, ΔVal] at the B3LYP/6-311+ + G(d,p) level in the gas phase as well as in chloroform and water solutions with the self-consistent reaction field-polarisable continuum model method. The Fourier transform IR spectra in CCl(4) and CHCl(3) have been analysed as well as the analogous solid state conformations drawn from The Cambridge Structural Database. The ΔAla residue has a considerable tendency to adopt planar conformations C5 (ϕ, ψ ≈ - 180°, 180°) and β2 (ϕ, ψ ≈ - 180°, 0°), regardless…
Annular Tautomerism of 3(5)-Disubstituted-1H-pyrazoles with Ester and Amide Groups
2019
A series of disubstituted 1H-pyrazoles with methyl (1), amino (2), and nitro (3) groups, as well as ester (a) or amide (b) groups in positions 3 and 5 was synthesized, and annular tautomerism was investigated using X-ray, theoretical calculations, NMR, and FT-IR methods. The X-ray experiment in the crystal state showed for the compounds with methyl (1a, 1b) and amino (2b) groups the tautomer with ester or amide groups at position 3 (tautomer 3), but for those with a nitro group (3b, 4), tautomer 5. Similar results were obtained in solution by NMR NOE experiments in CDCl3, DMSO-d6, and CD3OD solvents. However, tautomer equilibrium was observed for 2b in DMSO. The FT-IR spectra in chloroform …
Conformational properties of N-acetyl-N-methyl-alpha,beta-dehydroalanine N'-methylamide.
2006
The conformational properties of Ac-Delta(Me)Ala-NHMe (N-acetyl-N-methyl-alpha,beta-dehydroalanine N'-methylamide), as the simplest model of N-methyl-alpha,beta-dehydroamino acids, was examined with theoretical methods and in comparison with Ac-DeltaAla-NHMe and Ac-DeltaAla-NMe(2). The N-terminal amide of the Delta(Me)Ala residue easily adopts the configuration cis and the torsion angles phi, psi are highly flexible. The Delta(Me)Ala residue is a conformational flexibilizer as compared to the parent DeltaAla, which is a conformational stiffener. This seems to be the reason why Delta(Me)Ala is found in small natural cyclic peptides, where it ensures the conformational flexibility necessary f…
4-Chloronaphthalen-1-yl 4-methylbenzenesulfonate
2018
In the title compound, C17H13ClO3S, the naphthalene ring system and the benzene ring of the tosylate substituent are inclined to one another by 55.32 (5)°. The crystal structure features weak intermolecular C—H...O hydrogen bonds, one of which forms inversion dimers. Additional C—H...O hydrogen bonds and weak Cl...Cl halogen bonds stack the molecules along the b-axis direction.
3,5-Dimethoxyphenyl 4-methylbenzenesulfonate
2017
Molecules of the title compound, C15H16O5S, are composed of a 3,5-dimethoxyphenyl moiety substituted with a toluene-4-sulfonate group. The dihedral angle between two aromatic rings is 57.23 (4)°. In the crystal, molecules are connected by weak C—H...O hydrogen bonds and S...O van der Waals interactions.
Intra- and intermolecular forces dependent main chain conformations of esters of α,β-dehydroamino acids
2013
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…
Building large molecular models with plastic screw-on bottle caps and sturdy connectors
2016
An improved method of connecting atoms formed with screw-on bottle caps is described. Fishing line (artificial polymer), steel wire, and countersunk bolts with nyloc nuts are proposed as sturdy connectors. Advantages and disadvantages of each method are described. The molecular models are stable while handling, can be built in a relatively short time at low cost, and can be useful at every level of education. The method is an alternative to professional model kits, in particular in construction of large models for long-term usage.
Conformational preferences and synthesis of isomersZandEof oxazole-dehydrophenylalanine
2016
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…
2-(1,3-Oxazolin-2-yl)pyridine and 2,6-bis(1,3-oxazolin-2-yl) pyridine
2018
The data presented in this article are related to research articles “Titanium and vanadium catalysts with oxazoline ligands for ethylene-norbornene (co)polymerization (Ochędzan-Siodłak et al., 2018). For the title compounds, 2-(1,3-oxazolin-2-yl)pyridine (Py-ox) and 2,6-bis(1,3-oxazolin-2-yl)pyridine (Py-box), the single-crystal X-ray diffraction measurement together with NMR, GC, MS, DSC analysis, like also the method of crystallization are presented. Keywords: Ligands, Oxazoline, Pyridine, Conformation, Association
Imidazole-amino acids. Conformational switch under tautomer and pH change.
2022
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…
Naturally Occurring Oxazole Structural Units as Ligands of Vanadium Catalysts for Ethylene-Norbornene (Co)polymerization
2021
1,3-Oxazole and 4,5-dihydro-1,3-oxazole are common structural motifs in naturally occurring peptides. A series of vanadium complexes were synthesized using VCl3(THF)3 and methyl substituted (4,5-dihydro-1,3-oxazol-2-yl)-1,3-oxazoles as ligands and analyzed using NMR and MS methods. The complexes were found to be active catalysts both in ethylene polymerization and ethylene-norbornene copolymerization. The position of methyl substituent in the ligand has considerable impact on the performance of (co)polymerization reaction, as well as on the microstructure, and thus physical properties of the obtained copolymers.
Biphasic ethylene polymerisation using 1-n-alkyl-3-methylimidazolium tetrachloroaluminate ionic liquid as a medium of the Cp2TiCl2 titanocene catalyst
2008
Abstract A systematic analysis was performed on a series of 1- n -alkyl-3-methylimidazolium tetrachloroaluminates (where alkyl = ethyl, butyl, hexyl, and octyl), applied as a medium of the Cp 2 TiCl 2 titanocene catalyst, to evaluate the influence of the physical properties of the ionic liquids on the polymerisation reaction carried out in the biphasic ionic liquid/hexane mode. Two alkylaluminium compounds, AlEtCl 2 and AlEt 2 Cl, were used as activators. The influence of the activator/catalyst molar ratio on the performance of the ethylene polymerisation was determined for each ionic liquid studied. The best results were obtained using 1- n -octyl-3-methylimidazolium tetrachloroaluminate. …
Densities and viscosities of imidazolium and pyridinium chloroaluminate ionic liquids
2013
Abstract The chloroaluminate ionic liquids are used in various types of reactions. However, due to their particular vulnerability on water, their physical properties have not been previously investigated very extensively. The densities and viscosities of series imidazolium and pyridinium chloroaluminate ionic liquids having alkyl (butyl, hexyl, octyl) or aralkyl (benzyl, ethylphenyl) chain at the cation, various effective molar fraction of AlCl 3 (χ AlCl3 = 0.5, 0.65, 0.7), as well as they mixture and mixture with common organic solvents (hexane, toluene) were measured at the temperature range 293.15–343.15 K (20–70 °C). Densities, and particularly viscosities decrease with the increase of…
Conformational investigation of α,β-dehydropeptides. X. Molecular and crystal structure of Ac-ΔAla-NMe2 compared with those of Ac-L-Ala-NMe2, Ac-DL-A…
2002
A series of three homologous dimethyldiamides Ac-DeltaAla-NMe2, Ac-L-Ala-NMe2 and Ac-DL-Ala-NMe2 has been synthesized and the structures of these amides determined from single-crystal X-ray diffraction data. To learn more about the conformational preferences of compounds studied, the fully relaxed (phi-psi) conformational energy maps in vacuo (AM1) of Ac-DeltaAla-NMe2 and Ac-L-Ala-NMe2 were obtained, and the calculated minima reoptimized with the DFT/B3LYP/6-31G** method. The crystal-state results have been compared with the literature data. Ac-DeltaAla-NMe2 and other alpha,beta-dehydroamino acid dimethyldiamides, Ac-DeltaXaa-NMe2 adopt the conservative conformation of the torsion angles ph…
CCDC 1534810: Experimental Crystal Structure Determination
2017
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CCDC 1451706: Experimental Crystal Structure Determination
2016
Related Article: Monika Staś, Maciej Bujak, Małgorzata A. Broda, Dawid Siodłak|2016|Biopolymers|106|283|doi:10.1002/bip.22852
CCDC 1825064: Experimental Crystal Structure Determination
2019
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CCDC 931328: Experimental Crystal Structure Determination
2013
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CCDC 862034: Experimental Crystal Structure Determination
2017
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CCDC 931329: Experimental Crystal Structure Determination
2013
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CCDC 931327: Experimental Crystal Structure Determination
2013
Related Article: Dawid Siodłak, Maciej Bujak, Monika Staś|2013|J.Mol.Struct.|1047|229|doi:10.1016/j.molstruc.2013.04.078
CCDC 862033: Experimental Crystal Structure Determination
2017
Related Article: Dawid Siodłak, Agnieszka Macedowska-Capiga, Małgorzata A. Broda, Anna E. Kozioł, Tadeusz Lis|2012|Biopolymers|98|466|doi:10.1002/bip.22082
CCDC 862035: Experimental Crystal Structure Determination
2017
Related Article: Dawid Siodłak, Agnieszka Macedowska-Capiga, Małgorzata A. Broda, Anna E. Kozioł, Tadeusz Lis|2012|Biopolymers|98|466|doi:10.1002/bip.22082
CCDC 1814248: Experimental Crystal Structure Determination
2019
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CCDC 1451707: Experimental Crystal Structure Determination
2016
Related Article: Monika Staś, Maciej Bujak, Małgorzata A. Broda, Dawid Siodłak|2016|Biopolymers|106|283|doi:10.1002/bip.22852
CCDC 1957876: Experimental Crystal Structure Determination
2020
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CCDC 1825063: Experimental Crystal Structure Determination
2019
Related Article: Anna Kusakiewicz-Dawid, Monika Porada, Błażej Dziuk, Dawid Siodłak|2019|Molecules|24|2632|doi:10.3390/molecules24142632
CCDC 1815355: Experimental Crystal Structure Determination
2018
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CCDC 1580983: Experimental Crystal Structure Determination
2018
Related Article: Wioletta Ochędzan-Siodłak, Anna Bihun-Kisiel, Dawid Siodłak, Anna Poliwoda, Błażej Dziuk|2018|Data in Brief|21|449|doi:10.1016/j.dib.2018.09.129
CCDC 1957879: Experimental Crystal Structure Determination
2020
Related Article: Maciej Bujak, Dawid Siodłak|2020|Molecules|25|1361|doi:10.3390/molecules25061361
CCDC 1957878: Experimental Crystal Structure Determination
2020
Related Article: Maciej Bujak, Dawid Siodłak|2020|Molecules|25|1361|doi:10.3390/molecules25061361
CCDC 1957877: Experimental Crystal Structure Determination
2020
Related Article: Maciej Bujak, Dawid Siodłak|2020|Molecules|25|1361|doi:10.3390/molecules25061361
CCDC 931326: Experimental Crystal Structure Determination
2013
Related Article: Dawid Siodłak, Maciej Bujak, Monika Staś|2013|J.Mol.Struct.|1047|229|doi:10.1016/j.molstruc.2013.04.078
CCDC 1825061: Experimental Crystal Structure Determination
2019
Related Article: Anna Kusakiewicz-Dawid, Monika Porada, Błażej Dziuk, Dawid Siodłak|2019|Molecules|24|2632|doi:10.3390/molecules24142632
CCDC 1844066: Experimental Crystal Structure Determination
2019
Related Article: Anna Kusakiewicz-Dawid, Monika Porada, Błażej Dziuk, Dawid Siodłak|2019|Molecules|24|2632|doi:10.3390/molecules24142632
CCDC 1825062: Experimental Crystal Structure Determination
2019
Related Article: Anna Kusakiewicz-Dawid, Monika Porada, Błażej Dziuk, Dawid Siodłak|2019|Molecules|24|2632|doi:10.3390/molecules24142632