Aqueous solvation of polyalanine α-helices with specific water molecules and with the CPCM and SM5.2 aqueous continuum models using density functional theory

Acyl Capping Group Identity Effects on α-Helicity: On the Importance of Amide·Water Hydrogen Bonds to α-Helix Stability

Acyl capping groups stabilize α-helices relative to free N-termini by providing one additional C═Oi···Hi+4-N hydrogen bond. The electronic properties of acyl capping groups might also directly modulate α-helix stability: electron-rich N-terminal acyl groups could stabilize the α-helix by strengthening both i/i + 4 hydrogen bonds and i/i + 1 n → π* interactions. This hypothesis was tested in peptides X-AKAAAAKAAAAKAAGY-NH2, where X = different acyl groups. Surprisingly, the most electron-rich acyl groups (pivaloyl and iso-butyryl) strongly destabilized the α-helix. Moreover, the formyl group induced nearly identical α-helicity to that of the acetyl group, despite being a weaker electron donor for hydrogen bonds and for n → π* interactions. Other acyl groups exhibited intermediate α-helicity. These results indicate that the electronic properties of the acyl carbonyl do not directly determine the α-helicity in peptides in water. In order to understand these effects, DFT calculations were conducted on α-helical peptides. Using implicit solvation, α-helix stability correlated with acyl group electronics, with the pivaloyl group exhibiting closer hydrogen bonds and n → π* interactions, in contrast to the experimental results. However, DFT and MD calculations with explicit water solvation revealed that hydrogen bonding to water was impacted by the sterics of the acyl capping group. Formyl capping groups exhibited the closest water-amide hydrogen bonds, while pivaloyl groups exhibited the longest. In α-helices in the PDB, the highest frequency of close amide-water hydrogen bonds is observed when the N-cap residue is Gly. The combination of experimental and computational results indicates that solvation (hydrogen bonding of water) to the N-terminal amide groups is a central determinant of α-helix stability.

DFT Studies on the Al-Speciation and Its Structure in Aqueous Aluminum Sol Formed by Aluminum Formoacetate

The investigation of the Al-speciation and its structure in aluminum sol at the molecular level plays an important role in knowing the subsequent lager polymer gels. In this work, to study the Al-speciation and its structure in aluminum sol prepared from aluminum formoacetate at the molecule level, density functional theory studies on the chemical behaviors of aluminum formoacetate under neutral and acidic conditions were systematically conducted at the B3LYP/6-311G** level. Due to the different thermodynamic dominance of hydration, hydrolysis, and polymerization, the structure of Al-speciation formed in neutral aqueous solution obviously differed from that formed in acidic solution. The products obtained from aluminum formoacetate in neutral aqueous solution contained more carboxyl groups acted as bridging bidentate ligand but less coordinated water molecules. The addition of H⁺ ion had a great impact on the structure of Al-speciation in aluminum sol prepared by aluminum formoacetate. This work would provide guidance for the understanding of the precursor gels of materials.

Probing the role of electrostatics of polypeptide main-chain in protein folding by perturbing N-terminal residue stereochemistry: DFT study with oligoalanine models

Energetics of folding (ΔH_E→F, in kcal mol⁻¹) from the extended (E) structure to the folded (F) structure for Ia and Ib critically depend on the geometrical relationship between the backbone peptide units of the polypeptide structure.

Interfacial water at the trialanine hydrophilic surface: a DFT electronic structure and bottom-up investigation

A model describing a network of hydrogen bonded water-trialanine has been developed to estimate hydration effects on various conformers of the peptide.

Synthesis and helical structures of poly(ω-alkynamide)s having chiral side chains: effect of solvent on their screw-sense inversion

New ω-alkynamides, (S)-HC≡CCH2CONHCH2CH(CH3)CH2CH3 (1) and (S)-HC≡CCH2CH2CONHCH(CH3)CH2CH2CH2CH2CH3 (2) were synthesized and polymerized with a rhodium catalyst in CHCl3 to obtain cis-stereoregular poly(ω-alkynamide)s (poly(1) and poly(2)). Polarimetric, CD, and IR spectroscopic studies revealed that in solution the polymers adopted predominantly one-handed helical structures stabilized by intramolecular hydrogen bonds between the pendent amide groups. This behavior was similar to that of the corresponding poly(N-alkynylamide) counterparts (poly(3) and poly(4)) reported previously, whereas the helical senses were opposite to each other. The helical structures of the poly(ω-alkynamide)s were stable upon heating similar to those of the poly(N-alkynylamide)s, but the solvent response was completely different. An increase in MeOH content in CHCl3/MeOH resulted in inversion of the predominant screw-sense for poly(1) and poly(2). Conversely, poly(3) was transformed into a random coil, and poly(4) maintained the predominant screw-sense irrespective of MeOH content. The solvent dependence of predominant screw-sense for poly(1) and poly(2) was reasonably explained by molecular orbital studies using the conductor-like screening model (COSMO).

The interactions of phenylalanines in β-sheet-like structures from molecular orbital calculations using density functional theory (DFT), MP2, and CCSD(T) methods

We present density functional theory calculations designed to evaluate the importance of π-stacking interactions to the stability of in-register Phe residues within parallel β-sheets, such as amyloids. We have used a model of a parallel H-bonded tetramer of acetylPheNH2 as a model and both functionals that were specifically designed to incorporate dispersion effects (DFs), as well as, several traditional functionals which have not been so designed. None of the functionals finds a global minimum for the π-stacked conformation, although two of the DFs find this to be a local minimum. The stacked phenyls taken from the optimized geometries calculated for each functional have been evaluated using MP2 and CCSD(T) calculations for comparison. The results suggest that π-stacking does not make an important contribution to the stability of this system and (by implication) to amyloid formation.

Capping parallel β-sheets of acetyl(Ala)6NH2 with an acetyl(Ala)5ProNH2 can arrest the growth of the sheet, suggesting a potential for curtailing amyloid growth. An ONIOM and density functional theory study

We present ONIOM calculations using B3LYP/d95(d,p) as the high level and AM1 as the medium level on parallel β-sheets containing four strands of Ac-AAAAAA-NH2 capped with either Ac-AAPAAA-NH2 or Ac-AAAPAA-NH2. Because Pro can form H-bonds from only one side of the peptide linkage (that containing the C═O H-bond acceptor), only one of the two Pro-containing strands can favorably add to the sheet on each side. Surprisingly, when the sheet is capped with AAPAAA-NH2 at one edge, the interaction between the cap and sheet is slightly more stabilizing than that of another all Ala strand. Breaking down the interaction enthalpies into H-bonding and distortion energies shows the favorable interaction to be due to lower distortion energies in both the strand and the four-stranded sheet. Because another strand would be inhibited for attachment to the other side of the capping (Pro-containing) strand, we suggest the possible use of Pro residues in peptides designed to arrest the growth of many amyloids.

Comparison of some dispersion-corrected and traditional functionals as applied to peptides and conformations of cyclohexane derivatives

We compare the energetic and structural properties of fully optimized α-helical and antiparallel β-sheet polyalanines and the energetic differences between axial and equatorial conformations of three cyclohexane derivatives (methyl, fluoro, and chloro) as calculated using several functionals designed to treat dispersion (B97-D, ωB97x-D, M06, M06L, and M06-2X) with other traditional functionals not specifically parametrized to treat dispersion (B3LYP, X3LYP, and PBE1PBE) and with experimental results. Those functionals developed to treat dispersion significantly overestimate interaction enthalpies of folding for the α-helix and predict unreasonable structures that contain Ramachandran φ and ψ and C = O...N H-bonding angles that are out of the bounds of databases compiled the β-sheets. These structures are consistent with overestimation of the interaction energies. For the cyclohexanes, these functionals overestimate the stabilities of the axial conformation, especially when used with smaller basis sets. Their performance improves when the basis set is improved from D95∗∗ to aug-cc-pVTZ (which would not be possible with systems as large as the peptides).

The folding of acetyl(Ala)28NH2 and acetyl(Ala)40NH2 extended strand peptides into antiparallel β-sheets. A density functional theory study of β-sheets with β-turns

We report ONIOM calculations using B3LYP/D95** and AM1 on β-sheet formation from acetyl(Ala)(N)NH(2) (N = 28 or 40). The sheets contain from one to four β-turns for N = 28 and up to six for N = 40. We have obtained four types of geometrically optimized structures. All contain only β-turns. They differ from each other in the types of β-turns formed. The unsolvated sheets containing two turns are most stable. Aqueous solvation (using the SM5.2 and CPCM methods) reduces the stabilities of the folded structures compared to the extended strands.

Binding selectivity of dibenzo-18-crown-6 for alkali metal cations in aqueous solution: A density functional theory study using a continuum solvation model

Background

Dibenzo-18-crown-6 (DB18C6) exhibits the binding selectivity for alkali metal cations in solution phase. In this study, we investigate the main forces that determine the binding selectivity of DB18C6 for the metal cations in aqueous solution using the density functional theory (DFT) and the conductor-like polarizable continuum model (CPCM).

Results

The bond dissociation free energies (BDFE) of DB18C6 complexes with alkali metal cations (M⁺-DB18C6, M = Li, Na, K, Rb, and Cs) in aqueous solution are calculated at the B3LYP/6-311++G(d,p)//B3LYP/6-31 + G(d) level using the CPCM. It is found that the theoretical BDFE is the largest for K⁺-DB18C6 and decreases as the size of the metal cation gets larger or smaller than that of K⁺, which agrees well with previous experimental results.

Conclusion

The solvation energy of M⁺-DB18C6 in aqueous solution plays a key role in determining the binding selectivity of DB18C6. In particular, the non-electrostatic dispersion interaction between the solute and solvent, which depends strongly on the complex structure, is largely responsible for the different solvation energies of M⁺-DB18C6. This study shows that the implicit solvation model like the CPCM works reasonably well in predicting the binding selectivity of DB18C6 in aqueous solution.

Density functional theory study of β-hairpins in antiparallel β-sheets, a new classification based upon H-bond topology

We present a new classification of β-turns specific to antiparallel β-sheets based upon the topology of H-bond formation. This classification results from ONIOM calculations using B3LYP/D95** density functional theory and AM1 semiempirical calculations as the high and low levels, respectively. We chose acetyl(Ala)(6)NH(2) as a model system as it is the simplest all-alanine system that can form all the H-bonds required for a β-turn in a sheet. Of the 10 different conformations we have found, the most stable structures have C(7) cyclic H-bonds in place of the C(10) interactions specified in the classic definition. Also, the chiralities specified for residues i + 1 and i + 2 in the classic definition disappear when the structures are optimized using our techniques, as the energetic differences among the four diastereomers of each structure are not substantial for 8 of the 10 conformations.