How Strong is Hydrogen Bonding to Amide Nitrogen?

Oxidative Damage of Aliphatic Amino Acid Residues by the Environmental Pollutant NO3·: Impact of Water on the Reactivity

The rate of oxidative damage of aliphatic amino acids and dipeptides by the environmental pollutant nitrate radical (NO₃^·) in an aqueous acidic environment was studied by laser flash photolysis. The reactivity dropped by a factor of about four for amino acid residues with secondary amide bonds and by a factor of up to nearly 20 for amino acid residues with tertiary amide bonds, compared with that in acetonitrile. According to density functional theory studies, the lower reactivity is due to protonation of the amide moiety, whereas in neutral water, hydrogen bonding with the amide should have little impact on the absolute reaction rate compared with that in acetonitrile. This finding can be rationalized by the high reactivity and broad reaction pattern of NO₃^·. Although hydrogen bonding involving the amide group raises the energies associated with some electron transfer processes, alternative low-energy pathways remain available so that the overall reaction rate is barely affected. The undiminished high reactivity of NO₃^· toward aliphatic amino acid residues in a neutral aqueous environment highlights the health-damaging potential of exposure to the combined air pollutants nitrogen dioxide (NO₂^·) and ozone (O₃).

peri-Interactions in 1,8-bis(dimethylamino)naphthalene ortho-ketimine cations facilitate [1,5]-hydride shift: selective synthesis of 1,2,3,4-tetrahydrobenzo[h]quinazolines

Selective heterocyclization leading to 1,2,3,4-tetrahydrobenzo[h]quinazolines from ortho-ketimines of 1,8-bis(dimethylamino)naphthalene (DmanIms) under acid catalysis has been revealed. In contrast to the rather unreactive N,N-dimethylaniline ortho-ketimine, DmanIms readily undergo this transformation without an additional catalyst. This distinction in the reactivity underscores the importance of the second peri-NMe₂ group in DmanIms, which facilitates a [1,5]-hydride shift and the subsequent cyclization. The cascade of peri-interactions emerging between 1-NMe₂ and 8-NMe₂ groups has been identified as a reason for the catalytic effect: (1) the hydrogen bond in the DmanIm dication constrains 1-NMe₂ in the desired position providing proximity of reaction centers, (2) the repulsion of the lone pairs of 8-NMe₂ group and unrelaxed 1-NMe₂ group arising right after deprotonation process reduces the Gibbs free energy of activation (ΔG^‡) for the straight hydride shift, and (3) the electrostatic interaction between 8-NMe₂ and the charged NCH₂⁺ group in the intermediate increases the ΔG^‡ for the reverse hydride shift.

Acid catalysis through N-protonation in undistorted carboxamides: improvement of amide proton sponge acylating ability

Acid catalysis of weakly distorted or undistorted carboxamides in acyl-migration reactions proceeding through N-protonation is the process with low probability in contrast to O-protonation. This circumstance made the experimental study...

Tracking the Amide I and αCOO- Terminal ν(C=O) Raman Bands in a Family of l-Glutamic Acid-Containing Peptide Fragments: A Raman and DFT Study

The E-hook of β-tubulin plays instrumental roles in cytoskeletal regulation and function. The last six C-terminal residues of the βII isotype, a peptide of amino acid sequence EGEDEA, extend from the microtubule surface and have eluded characterization with classic X-ray crystallographic techniques. The band position of the characteristic amide I vibration of small peptide fragments is heavily dependent on the length of the peptide chain, the extent of intramolecular hydrogen bonding, and the overall polarity of the fragment. The dependence of the E residue's amide I ν(C=O) and the αCOO- terminal ν(C=O) bands on the neighboring side chain, the length of the peptide fragment, and the extent of intramolecular hydrogen bonding in the structure are investigated here via the EGEDEA peptide. The hexapeptide is broken down into fragments increasing in size from dipeptides to hexapeptides, including EG, ED, EA, EGE, EDE, DEA, EGED, EDEA, EGEDE, GEDEA, and, finally, EGEDEA, which are investigated with experimental Raman spectroscopy and density functional theory (DFT) computations to model the zwitterionic crystalline solids (in vacuo). The molecular geometries and Boltzmann sum of the simulated Raman spectra for a set of energetic minima corresponding to each peptide fragment are computed with full geometry optimizations and corresponding harmonic vibrational frequency computations at the B3LYP/6-311++G(2df,2pd) level of theory. In absence of the crystal structure, geometry sampling is performed to approximate solid phase behavior. Natural bond order (NBO) analyses are performed on each energetic minimum to quantify the magnitude of the intramolecular hydrogen bonds. The extent of the intramolecular charge transfer is dependent on the overall polarity of the fragment considered, with larger and more polar fragments exhibiting the greatest extent of intramolecular charge transfer. A steady blue shift arises when considering the amide I band position moving linearly from ED to EDE to EDEA to GEDEA and, finally, to EGEDEA. However, little variation is observed in the αCOO- ν(C=O) band position in this family of fragments.

Large Stabilization Effects by Intramolecular Beryllium Bonds in Ortho-Benzene Derivatives

Intramolecular interactions are shown to be key for favoring a given structure in systems with a variety of conformers. In ortho-substituted benzene derivatives including a beryllium moiety, beryllium bonds provide very large stabilizations with respect to non-bound conformers and enthalpy differences above one hundred kJ·mol⁻¹ are found in the most favorable cases, especially if the newly formed rings are five or six-membered heterocycles. These values are in general significantly larger than hydrogen bonds in 1,2-dihidroxybenzene. Conformers stabilized by a beryllium bond exhibit the typical features of this non-covalent interaction, such as the presence of a bond critical point according to the topology of the electron density, positive Laplacian values, significant geometrical distortions and strong interaction energies between the donor and acceptor quantified by using the Natural Bond Orbital approach. An isodesmic reaction scheme is used as a tool to measure the strength of the beryllium bond in these systems in terms of isodesmic energies (analogous to binding energies), interaction energies and deformation energies. This approach shows that a huge amount of energy is spent on deforming the donor–acceptor pairs to form the new rings.

A Spectroscopic Overview of Intramolecular Hydrogen Bonds of NH…O,S,N Type

Intramolecular NH…O,S,N interactions in non-tautomeric systems are reviewed in a broad range of compounds covering a variety of NH donors and hydrogen bond acceptors. ¹H chemical shifts of NH donors are good tools to study intramolecular hydrogen bonding. However in some cases they have to be corrected for ring current effects. Deuterium isotope effects on ¹³C and ¹⁵N chemical shifts and primary isotope effects are usually used to judge the strength of hydrogen bonds. Primary isotope effects are investigated in a new range of magnitudes. Isotope ratios of NH stretching frequencies, νNH/ND, are revisited. Hydrogen bond energies are reviewed and two-bond deuterium isotope effects on ¹³C chemical shifts are investigated as a possible means of estimating hydrogen bond energies.

Intelligent Poly(N-Isopropylmethacrylamide) Hydrogels: Synthesis, Structure Characterization, Stimuli-Responsive Swelling Properties, and Their Radiation Decomposition

Poly(N-isopropylmethacrylamide) (p(NiPMAm)) is one of the lesser known homopolymers that has significant potential for designing new "intelligent" materials. The aims of this work were the synthesis a series of cross-linked p(NiPMAm) hydrogels by the free radical polymerization method and the application of gamma-ray radiation for additional cross-linking. The synthesized p(NiPMAm) hydrogels were structurally characterized by Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM). The amount of unreacted monomers was analyzed using high pressure liquid chromatography (HPLC) to evaluate conversion of monomers into polymers. The swelling behavior was monitored in dependence of pH and temperature changes. The previous aim of gamma-ray radiation was the further the cross-linkage of the obtained hydrogel sample in the gelatinous, paste-like state, but the gamma-ray radiation caused decomposition. After absorbing irradiation doses, they transformed into the liquid phase. The results obtained by the gel permeation chromatography (GPC) method indicated that only oligomers and monomers were present in the irradiated liquid material, without molecules with a higher average molar mass, i.e., that the decomposition of the hydrogels occurred. Additionally, the irradiated liquid material was analyzed using the static headspace gas chromatography mass spectrometry (HSS-GC/MS) and gas chromatography/flame ionization detection (HSS-GC/FID) methods. The presence of unchanged initiator molecule and a dominant amount of four new molecules that were different from homopolymers and the reactant (monomer and cross-linker) were determined.