Search results for "hydrogen bonding"
showing 10 items of 290 documents
Binding Modes of Nonspherical Anions to N-Alkylammonium Resorcinarenes in the Solid State
2012
A series of hydrogen bond stabilized N-alkylammonium resorcinarene salts with nitrate, triflate, and picrate as the counteranions were synthesized and characterized with 1H NMR and electrospray ionization (ESI) mass spectrometry. Together with electrostatic interactions, the binding of the anions with several hydrogen bond donor sites proceeds through a complex array of intra- and intermolecular hydrogen bonds, evidenced by single crystal X-ray diffraction analysis. These N-alkyl ammonium resorcinarenes bind the larger nonspherical anions into deformed cavitand-like structures and enforce a transformation of the resorcinarene conformation from almost symmetrical to extremely distorted.
Hydrogen bond-stabilised N-alkylammonium resorcinarene halide cavitands
2010
A family of hydrogen bond-stabilised N-alkylammonium resorcinarene chloride and bromide cavitands were synthesised and characterised with 1H NMR and ESI mass spectrometry. The seven compounds exhibit interestingly either self-inclusion or guest complexation in the solid state evidenced by single crystal X-ray diffraction. The four dimers show self-inclusion of the upper rim propyl chains and consist of two hydrogen-bonded resorcinarene tetracations and six halide anions, while the remaining two halide anions are located in between the dimers linking them via hydrogen bonding. Small solvent molecules such as dichloromethane, methanol, n-butanol or chloroform are complexed into the resorcinar…
Carnosine Inhibits Aβ42Aggregation by Perturbing the H-Bond Network in and around the Central Hydrophobic Cluster
2013
Aggregation of the amyloid-β peptide (Aβ) into fibrillar structures is a hallmark of Alzheimer's disease. Thus, preventing self-assembly of the Aβ peptide is an attractive therapeutic strategy. Here, we used experimental techniques and atomistic simulations to investigate the influence of carnosine, a dipeptide naturally occurring in the brain, on Aβ aggregation. Scanning force microscopy, circular dichroism and thioflavin T fluorescence experiments showed that carnosine does not modify the conformational features of Aβ42 but nonetheless inhibits amyloid growth. Molecular dynamics (MD) simulations indicated that carnosine interacts transiently with monomeric Aβ42 by salt bridges with charge…
Solubility and solvation features of native cyclodextrins in 1-ethyl-3-methylimidazolium acetate
2022
The comprehension of the mechanism entailing efficient solvation of cyclodextrins (CD) by green solvents is of great relevance to boost environmentally sustainable usages of smart supramolecular systems. Here, 1-ethyl-3- methylimidazolium acetate, an ecofriendly ionic liquid (IL), is considered as an excellent solvent for native CDs. This IL efficiently dissolves up to 40 wt.% β- and γ-CD already at ambient temperature and X-ray scattering indicates that CDs do not tend to detrimental flocculation under these drastic concentration conditions. Simu- lation techniques reveal the intimate mechanism of CD solvation by the ionic species: while the strong hydrogen bonding acceptor acetate anion i…
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…
Self-assembled dendrimers with uniform structure
2008
Calix[4]arenes substituted at their wide rim by four aryl urea residues (1) form hydrogen-bonded dimers in apolar solvents. Replacement of one urea residue by an acetamido moiety leads to calix[4]arene derivatives (5) which form hydrogen-bonded tetramers under the same conditions. Both self-assembly processes occur independently. Therefore, molecules have been prepared in which a tetra-urea calix[4]arene and a tri-urea mono acetamide derivative are covalently connected between their narrow rims by a long, mainly aliphatic chain [-O-(CH(2))(n)-C(O)-NH-(CH(2))(m)-O-] (7). In the presence of an equimolar amount of tetra-tosyl urea calix[4]arene () they form dendritic assemblies since the well …
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…
Oleochemical carbonates: A comprehensive characterization of an emerging class of organic compounds
2022
Dialkyl carbonates (DAC) with short-medium alkyl length - oleochemical carbonates – are attracting attention because of their appealing properties, including low viscosity, flammability, toxicity, environ- mental impact and wide range of applications: lubricants, personal care, fuel additives etc. However, not much is known concerning their chemical physical properties and, more importantly, on the nature of microscopic correlations that eventually determine bulk performances. In view of this paucity, we pre- sent a large exploration of a series of chemical physical properties of a set of DACs ranging from dimethyl up to didodecyl carbonate. This study extends previously determined database…
The new 5- or 6-azapyrimidine and cyanuric acid derivatives of L-ascorbic acid bearing the free C-5 hydroxy or C-4 amino group at the ethylenic space…
2011
Abstract We report on the synthesis of the novel types of cytosine and 5-azacytosine (1–9), uracil and 6-azauracil (13–18) and cyanuric acid (19–22) derivatives of l -ascorbic acid, and on their cytostatic activity evaluation in human malignant tumour cell lines vs. their cytotoxic effects on human normal fibroblasts (WI38). The CD spectra analysis revealed that cytosine (5 and 6), uracil (14–16), 6-azauracil (17) and cyanuric acid (21) derivatives of l -ascorbic acid bearing free amino group at ethylenic spacer existed as a racemic mixture of enantiomers, whereas L-ascorbic derivatives containing the C-5 substituted hydroxy group at the ethylenic spacer were obtained in (4R, 5S) enantiomer…
Microscopic interactions between ivermectin and key human and viral proteins involved in SARS-CoV-2 infection
2021
The identification of chemical compounds able to bind specific sites of the human/viral proteins involved in the SARS-CoV-2 infection cycle is a prerequisite to design effective antiviral drugs. Here we conduct a molecular dynamics study with the aim to assess the interactions of ivermectin, an antiparasitic drug with broad-spectrum antiviral activity, with the human Angiotensin-Converting Enzyme 2 (ACE2), the viral 3CLpro and PLpro proteases, and the viral SARS Unique Domain (SUD). The drug/target interactions have been characterized in silico by describing the nature of the non-covalent interactions found and by measuring the extent of their time duration along the MD simulation. Results …