Where does charge reside in amino acids? The effect of side-chain protonation state on the atomic charges of Asp, Glu, Lys, His and Arg

Poly(ether imide) Film Doped with Protonated Tetra(aniline) Molecules for Efficiently Enhancing the Capacitive Energy Storage Performance

The polymer dielectric spacer plays a key role in the performance of film capacitors. However, currently, commercial polymer dielectric films generally have low relative dielectric constants (<4) and low capacitive energy storage densities (<3 J cm-3). Here, we report the use of protonated tetra(aniline) (TANI) molecules with a length of 1.3 nm to improve the energy storage performance of poly(ether imide) (PEI) films. With only a small content of TANI doping, i.e., 0.7 wt %, both the dielectric constant and energy storage density of PEI film can be significantly improved, while the dielectric loss remains as low as that of pure PEI. A maximum energy density of 9.4 J cm-3 is achieved. To manifest the efficacy of protonated TANI, polyaniline and deprotonated TANI are also prepared and used as dopants in PEI. The PANI filler can also increase the dielectric constant, while the dielectric loss is increased as well. The deprotonated TANI doped in PEI has no influence on both the dielectric constant and energy density, implying that the protonated amino groups of TANI molecules are responsible for the enhanced dielectric constant of the PEI/TANI composite. The correlation between protonation of TANI dopants and dielectric properties is discussed in detail.

On hidden anisotropy of formally charged fragments

The proper and precise reproduction of the molecular electrostatic potential (MEP) is crucial to describe correctly electrostatic interactions in molecular modeling. Most of the classical molecular mechanics force fields for biomolecules and drug-like molecules use the atom-centered point charges to describe MEP. However, it has been systematically pointed out in literature that such an approximation is not always enough, and some groups, like amino group or heavy halogens, require the use of anisotropic model for better description of their MEP. At the same time, the formally charged groups have not been as extensively and systematically studied as their neutral counterparts. In this report, we demonstrate that the anisotropic models for formally charged groups do bring improvements in the reference MEP reproduction, that are comparable in magnitude to those for neutral groups.

One electron less or one proton more: how do they differ?

From the NIST website and the literature, we have collected the Ionisation Energies (IE) of 3,052 and the Proton Affinities (PA) of 1,670 compounds. For 614 of these, both the IE and PA are known; this enables a study of the relationships between these quantities for a wide variety of molecules. From the IE and PA values, the hydrogen atom affinities (HA) of molecular ions M^•+ may also be assessed. The PA may be equated to the heterolytic bond energy of [MH]⁺ and HA to the homolytic bond energy. Plots of PA versus IE for these substances show (in agreement with earlier studies) that, for many families of molecules, the slope of the ensuing line is less negative than -1, i.e. changes in the PA are significantly less than the concomitant opposite changes in IE. At one extreme (high PA, low IE) are the metals, their oxides and hydroxides, which show a slope of close to -1, at the other extreme (low PA, high IE) are the hydrogen halides, methyl halides and noble gases, which show a slope of ca. -0.3; other molecular categories show intermediate behaviour. One consequence of a slope less negative than -1 is that the changes in ionic enthalpies of the protonated species more closely follow the changes in the enthalpies of the neutral molecules compared with changes in the ion enthalpies of the corresponding radical cations. This is consistent with findings from ab initio calculations from the literature that the incoming proton, once attached to the molecule, may retain a significant amount of its charge. These collected data allow a comparison of the thermodynamic stability of protonated molecules in terms of their homolytic or heterolytic bond cleavages. Protonated nitriles are particularly stable by virtue of the very large hydrogen atom affinities of their radical cations.

Conserved Binding Regions Provide the Clue for Peptide-Based Vaccine Development: A Chemical Perspective

Synthetic peptides have become invaluable biomedical research and medicinal chemistry tools for studying functional roles, i.e., binding or proteolytic activity, naturally-occurring regions’ immunogenicity in proteins and developing therapeutic agents and vaccines. Synthetic peptides can mimic protein sites; their structure and function can be easily modulated by specific amino acid replacement. They have major advantages, i.e., they are cheap, easily-produced and chemically stable, lack infectious and secondary adverse reactions and can induce immune responses via T- and B-cell epitopes. Our group has previously shown that using synthetic peptides and adopting a functional approach has led to identifying Plasmodium falciparumconserved regions binding to host cells. Conserved high activity binding peptides’ (cHABPs) physicochemical, structural and immunological characteristics have been taken into account for properly modifying and converting them into highly immunogenic, protection-inducing peptides (mHABPs) in the experimental Aotus monkey model. This article describes stereo–electron and topochemical characteristics regarding major histocompatibility complex (MHC)-mHABP-T-cell receptor (TCR) complex formation. Some mHABPs in this complex inducing long-lasting, protective immunity have been named immune protection-inducing protein structures (IMPIPS), forming the subunit components in chemically synthesized vaccines. This manuscript summarizes this particular field and adds our recent findings concerning intramolecular interactions (H-bonds or π-interactions) enabling proper IMPIPS structure as well as the peripheral flanking residues (PFR) to stabilize the MHCII-IMPIPS-TCR interaction, aimed at inducing long-lasting, protective immunological memory.

Proton affinities and ion enthalpies

Proton affinities of a number of alkyl acetates (CH₃-C(=O)-OR) and of methyl alkanoates (R-C(=O)-OCH₃, R=H, alkyl) have been assembled from the literature or measured using the kinetic method. It was observed that the proton affinities for the isomeric species CH₃-C(=O)-OR and R-C(=O)-OCH₃ are almost identical, an unexpected result as the charge in these protonated ester molecules is largely at the keto carbon atom and so this site should be more sensitive to alkyl substitution. Analysis of the data, including those from lone pair ionisation and core-electron ionisation experiments available from the literature, indicate that after protonation, extensive charge relaxation (or polarisation) takes place (as is also the case, according to the literature, after core-electron ionisation). By contrast, after lone pair ionisation, which results in radical cations, such relaxation processes are relatively less extensive. As a consequence, changes in ion enthalpies of these protonated molecules follow more closely the changes in neutral enthalpies, compared with changes in enthalpies of the corresponding radical cations, formed by electron detachment. Preliminary analyses of published energetic data indicate that the above finding for organic esters may well be another example of a more general phenomenon.

Comprehensive analysis of energy minima of the 20 natural amino acids

Energy minima of the 20 natural amino acids (capped by a peptide bond at both the N and the C termini, CH3-C(═O)-N(H)-(H)Cα(R)-C(═O)-N(H)-CH3), were obtained by ab initio geometry optimization. Starting with a large number of minima, quickly generated by MarvinView, geometry optimization at the HF/6-31G(d,p) level of theory reduced the number of minima, followed by further optimization at the B3LYP/apc-1 and MP2/cc-pVDZ levels, which caused some minima to disappear and some stable minima to migrate on the Ramachandran map. There is a relation between the number of minima and the size and the flexibility of the side chain. The energy minima of the 20 amino acids are mainly located in the regions of βL, γL, δL, and αL of the Ramachandran map. Multipole moments of atoms occurring in the fragment [-NH-Cα-C(═O)-] common to all 20 amino acids were calculated at the three levels of theory mentioned above. The near parallelism in behavior of these moments between levels of theory is beneficial toward estimating moments with the more expensive B3LYP and MP2 methods from data calculated with the cheaper HF method. Finally, we explored the transferability of properties between different amino acids: the bond length and angles of the common fragment [-NH-Cα(HαCβ)-C'(═O)-] in all amino acids except Gly and Pro. All bond lengths are highly transferable between different amino acids, and the standard deviations are small.