Ab Initio Molecular Dynamics Free-Energy Study of Microhydration Effects on the Neutral–Zwitterion Equilibrium of Phenylalanine

Effects of Carbon Spacer Length on Conformational Transitions and Protein Adsorption of Polyzwitterions

The properties of polyzwitterions are closely linked to their carbon spacer length (CSL) between oppositely charged groups. A thorough understanding of the effect of CSL on the properties of polyzwitterion-functionalized membranes is important for their fouling resistance and separation performances. In this work, polyzwitterion-functionalized membranes with different CSLs are prepared by coupling selective swelling-induced pore generation with zwitterionization, and the investigation is focused on comprehending the molecular mechanisms underlying protein resistance and conformational transitions within polyzwitterions under varying CSLs. The zwitterionized films show an enhancement in the surface negative potential with the increase of CSL, attributed to the negatively charged groups distanced from the positively charged groups. Quartz crystal microbalance with dissipation (QCM-D) demonstrates that zwitterionized films with different CSLs display distinct levels of resistance to protein adsorption. The trimethylamine N-oxide-derived polymer (PTMAO, CSL = 0) zwitterionized film shows the highest resistance compared to the poly(3-[dimethyl(2'-methacryloyloxyethyl] ammonio) ethanesulfonate (PMAES, CSL = 2) zwitterionized film and the poly(sulfobetaine methacrylate) (PSBMA, CSL = 3) zwitterionized film, owing to its electrical neutrality and pronounced hydrophilicity. Moreover, analysis of the anti-polyelectrolyte behaviors reveals that PTMAO does not undergo a significant conformation transition in deionized water and salt solutions, while the conformations of PMAES and PSBMA display to be more salt-dependent as the CSL increases, attributed to their increased polarization and dipole moment. As a result, the permeability of zwitterionized membranes exhibits enhanced salt responsiveness with the increase in CSL. The findings of this study are expected to facilitate the design of adsorption-resistant surfaces desired in diverse fields.

A study of the effects of the polarity of the solvents acetone and cyclohexane on the luminescent properties of tryptophan

The luminescent properties of tryptophan in solvents less polar than water, such as acetone, and non-polar ones, such as cyclohexane, are experimentally studied and compared with theoretical calculations using time-dependent density functional theory (TD-DFT) methods. Since tryptophan may present different configurations and charge distributions, the most stable conformer is analyzed for both solvents, including its neutral and zwitterionic forms. To perform the simulation two clusters are proposed with the Zpt conformer in acetone: [Formula: see text] and [Formula: see text] , and four clusters with the Nag⁺ conformer in cyclohexane: (Trp)₁-(C₆H₁₂), (Trp)₂-(C₆H₁₂), (Trp)₃-(C₆H₁₂) and (Trp)₄-(C₆H₁₂), in order to conveniently emulate the concentration in each solvent by reducing the distance between adjacent tryptophan molecules as the concentration increases, since there is no control over the volume parameter. In each case, the UV-vis absorption is computed and compared with the experimental excitation spectra; the results show a good agreement. This calculation allows a more detailed analysis of the experimental results based on the properties of the molecular orbitals involved in electronic transitions. In the present work, a strong effect of the solvent acetone on tryptophan is observed; for this solvent, a charge transfer from the solute to solvent happens. This behavior does not occur with water (polar solvent) or cyclohexane (non-polar solvent). Finally, experimental spectroscopic data of Trp in cyclohexane are explained through the hydrogen bonds between amino acid molecules present in the fluorescent states. In this case, the theoretical and experimental results are compared and also show good agreement.

Identification of the smallest peptide with a zwitterion as the global minimum: a first-principles study on arginine-containing peptides

Zwitterions are believed to play an important role in determining the structures, properties and functions of peptides and proteins. However, the smallest peptide with a zwitterionic structure as the global minimum in the gas phase is still not yet identified. In this study, an effective step-by-step strategy has been used to characterize the stable conformers of arginine-containing peptides arginylalanine (ArgAla) and arginylserine (ArgSer). Energy calculations at the DSD-PBEP86-D3BJ/aug-cc-pVTZ level and further extrapolation to the complete basis set (CBS) limit have confirmed, for the first time, that ArgSer appears to be a promising candidate as the smallest peptide with a zwitterionic global minimum structure. First-principles simulations have been performed for near-edge X-ray absorption fine-structure (NEXAFS) spectra and X-ray photoelectron spectra (XPS) at C, N and O K-edges, as well as for infrared (IR) spectra of these arginine-containing peptides. Notable spectral differences were found which enable the unambiguous identification of different neutral forms in future experiments. Our study thus provides valuable insights into the structural stability of zwitterions with the increase of molecular size and illustrates the competition between the canonical and zwitterionic isomers.

Systematic Study on Hydrated Arginine: Clear Theoretical Evidence for the Canonical-to-Zwitterionic Structure Transition

Extensive ab initio investigations have been performed to characterize the stable conformers of hydrated arginine (Arg-H₂O). Many new low-energy canonical Arg-H₂O conformers were identified and they are more stable than previous results. The large energy differences (more than 5.00 kcal mol^-1) between the canonical and zwitterionic Arg-H₂O isomers calculated by the composite CBS-QB3 method confirmed the dominance of the zwitterions. The micro effects of corrections of the zero-point energy and the basis set superposition error on the stability of hydrated isomers were carefully examined for the first time. The infrared (IR) spectra were simulated at a recommended temperature and the notable spectral differences enable the unambiguous identification of the different hydrated forms. Further transition state calculations revealed that the canonical Arg-H₂O can be transformed to the zwitterions using the amino group as a bridge. Our study thus shows valuable insights into the hydration of large flexible molecules and provides solid theoretical evidence for the canonical-to-zwitterionic structure transition of hydrated arginine.

Microhydration of Protonated Nα-Acetylhistidine: A Theoretical Approach

Extensive exploration of the potential energy surfaces of protonated Nα-acetylhistidine hydrated by 0-3 molecules of water was performed. The methodology combined hierarchical and genealogical (Darwin family tree) approaches using polarizable AMOEBA force field and M06 functional. It is demonstrated that this mixed approach allows recovering a larger number of conformers than the number recovered by using any one of the two methods alone. Hydration enthalpies of protonated Nα-acetylhistidine and of model compounds have been computed using higher theoretical methods, up to the G4MP2 procedure. Excellent agreement with experiment is observed for successive hydration of methylamonium and imidazolium cations using MP2/6-311++G(2d,2p)//M06/6-311++G(d,p) and G4MP2 methods, thereby validating the theory levels used for hydrated protonated Nα-acetylhistidine. It is found that the first hydration enthalpy of protonated Nα-acetylhistidine is ca. 10 kJ mol(-1) lower than that of imidazolium, a result explained by the local environment of the positively charged imidazolium moiety.

Fragment based electronic structural analysis of l-phenylalanine using calculated ionization spectroscopy and dual space analysis

Fragmentation schemes in phenylalanine revealed using ionization spectroscopy and dual space analysis.

Prediction of Absolute Hydroxyl pKa Values for 3-Hydroxypyridin-4-ones

pKa values have been calculated for a series of 3-hydroxypyridin-4-one (HPO) chelators in aqueous solution using coordination constrained ab initio molecular dynamics (AIMD) in combination with thermodynamic integration. This dynamics-based methodology in which the solvent is treated explicitly at the ab initio level has been compared with more commonly used simple, static, approaches. Comparison with experimental numbers has confirmed that the AIMD-based approach predicts the correct trend in the pKa values and produces the lowest average error (∼0.3 pKa units). The corresponding pKa predictions made via static quantum mechanical calculations overestimate the pKa values by 0.3-7 pKa units, with the extent of error dependent on the choice of thermodynamic cycle employed. The use of simple quantitative structure property relationship methods gives prediction errors of 0.3-1 pKa units, with some values overestimated and some underestimated. Beyond merely calculating pKa values, the AIMD simulations provide valuable additional insight into the atomistic details of the proton transfer mechanism and the solvation structure and dynamics at all stages of the reaction. For all HPOs studied, it is seen that proton transfer takes place along a chain of three H2O molecules, although direct hydrogen bonds are seen to form transiently. Analysis of the solvation structure before and after the proton transfer event using radial pair distribution functions and integrated number densities suggests that the trends in the pKa values correlate with the strength of the hydrogen bond and the average number of solvent molecules in the vicinity of the donor oxygen.