A density functional and quantum Monte Carlo study of glutamic acid in vacuo and in a dielectric continuum medium

DFT analysis of nitrogen isotopic reduction partition function ratios in proton exchange equilibria of glutamic acid species in water and its application to the estimation of nitrogen isotope fractionation

L-Glutamic acid (Glu) plays a pivotal role in amino acid metabolism in living organisms. Theoretical knowledge of how metabolism propagates the nitrogen isotope composition (δ15N) is essential for elucidating the mechanism of amino acid metabolism in vivo. In this paper, to estimate the nitrogen isotope fractionation involving Glu and its protonated/deprotonated species, their nitrogen isotopic reduction partition function ratios (RPFRs) were calculated at the apfd/6-311+G(2d,p) level of theory by the SCRF method. The results show that the RPFR values of the eight possible Glu species at 25 °C are: cation > zwitterion with α-COOH and γ-COO- > zwitterion with α-COO- and γ-COOH > anion with -NH3+ ≫ uncharged molecule > anion with -NH2 and γ-COO- > anion with -NH2 and α-COO- > di-anion. Several correlations between RPFR and bond distances were found. Most importantly, it was found that the shorter the distance of the (C-)N⋯H(-O) hydrogen bond (HB), the greater the RPFR value for that species. This correlation indicates that the tri-coordinate nitrogen atom of the amino group may take on the character of the tetra-coordinate nitrogen atom to some extent by forming a HB of this type. The nitrogen isotope exchange equilibrium between Glu and glycine/serine was evaluated at a typical physiological pH of 7.4. Calculations suggest that the equilibrium constant for the former is an increasing function of temperature from 0 to 100 °C, while the latter is a decreasing function of temperature over the same temperature range.

Better force fields start with better data: A data set of cation dipeptide interactions

We present a data set from a first-principles study of amino-methylated and acetylated (capped) dipeptides of the 20 proteinogenic amino acids - including alternative possible side chain protonation states and their interactions with selected divalent cations (Ca2+, Mg2+ and Ba2+). The data covers 21,909 stationary points on the respective potential-energy surfaces in a wide relative energy range of up to 4 eV (390 kJ/mol). Relevant properties of interest, like partial charges, were derived for the conformers. The motivation was to provide a solid data basis for force field parameterization and further applications like machine learning or benchmarking. In particular the process of creating all this data on the same first-principles footing, i.e. density-functional theory calculations employing the generalized gradient approximation with a van der Waals correction, makes this data suitable for first principles data-driven force field development. To make the data accessible across domain borders and to machines, we formalized the metadata in an ontology.

А theoretical study on ionization of sartans in aqueous media and on interactions with surfactant micelles

The ionization order of sartans in aqueous media and possible way of interactions between their equilibrium forms and surfactant micelles have been theoretically investigated. The examined sartans are ampholytes (irbesartan and losartan) and a diacid (valsartan) with the close values of ionization constants. In order to get a better insight in the overlapped protolytic equilibria of sartans and to predict an affinity of the equilibrium forms interacting with micelles as biomembrane mimetic systems, the theoretical study was performed. Energy calculation of the optimized structures of the equilibrium forms was performed at the B3LYP/6-31G (d,p) level of the Density Functional Theory (DFT). The results of the theoretical study helped to assign the experimentally determined pK_a values to the corresponding ionizable centers and confirmed that in all examined compounds, the higher pK_a values can be attributed to ionization of tetrazole. The molecular descriptor values showed that sartans interact predominantly with the micelle surfaces. The equilibrium forms of ampholytes demonstrate higher affinity to the micelles, as compared to the forms of the diprotic acid. Additionally, it was shown that the uncharged molecular forms of ampholytes are more lipophylic then their zwitterionic forms.

First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids

We present a structural data set of the 20 proteinogenic amino acids and their amino-methylated and acetylated (capped) dipeptides. Different protonation states of the backbone (uncharged and zwitterionic) were considered for the amino acids as well as varied side chain protonation states. Furthermore, we studied amino acids and dipeptides in complex with divalent cations (Ca²⁺, Ba²⁺, Sr²⁺, Cd²⁺, Pb²⁺, and Hg²⁺). The database covers the conformational hierarchies of 280 systems in a wide relative energy range of up to 4 eV (390 kJ/mol), summing up to a total of 45,892 stationary points on the respective potential-energy surfaces. All systems were calculated on equal first-principles footing, applying density-functional theory in the generalized gradient approximation corrected for long-range van der Waals interactions. We show good agreement to available experimental data for gas-phase ion affinities. Our curated data can be utilized, for example, for a wide comparison across chemical space of the building blocks of life, for the parametrization of protein force fields, and for the calculation of reference spectra for biophysical applications.

Conformational analysis of glutamic acid: a density functional approach using implicit continuum solvent model

Amino acids are constituents of proteins and enzymes which take part almost in all metabolic reactions. Glutamic acid, with an ability to form a negatively charged side chain, plays a major role in intra and intermolecular interactions of proteins, peptides, and enzymes. An exhaustive conformational analysis has been performed for all eight possible forms at B3LYP/cc-pVTZ level. All possible neutral, zwitterionic, protonated, and deprotonated forms of glutamic acid structures have been investigated in solution by using polarizable continuum model mimicking water as the solvent. Nine families based on the dihedral angles have been classified for eight glutamic acid forms. The electrostatic effects included in the solvent model usually stabilize the charged forms more. However, the stability of the zwitterionic form has been underestimated due to the lack of hydrogen bonding between the solute and solvent; therefore, it is observed that compact neutral glutamic acid structures are more stable in solution than they are in vacuum. Our calculations have shown that among all eight possible forms, some are not stable in solution and are immediately converted to other more stable forms. Comparison of isoelectronic glutamic acid forms indicated that one of the structures among possible zwitterionic and anionic forms may dominate over the other possible forms. Additional investigations using explicit solvent models are necessary to determine the stability of charged forms of glutamic acid in solution as our results clearly indicate that hydrogen bonding and its type have a major role in the structure and energy of conformers.

Electronic excitations in a dielectric continuum solvent with quantum Monte Carlo: acrolein in water

We investigate here the vertical n → π(*) and π → π(*) transitions of s-trans-acrolein in aqueous solution by means of a polarizable continuum model (PCM) we have developed for the treatment of the solute at the quantum Monte Carlo (QMC) level of the theory. We employ the QMC approach which allows us to work with highly correlated electronic wave functions for both the solute ground and excited states and, to study the vertical transitions in the solvent, adopt the commonly used scheme of considering fast and slow dielectric polarization. To perform calculations in a non-equilibrium solvation regime for the solute excited state, we add a correction to the global dielectric polarization charge density, obtained self consistently with the solute ground-state wave function by assuming a linear-response scheme. For the solvent polarization in the field of the solute in the ground state, we use the static dielectric constant while, for the electronic dielectric polarization, we employ the solvent refractive index evaluated at the same frequency of the photon absorbed by the solute for the transition. This choice is shown to be better than adopting the most commonly used value of refractive index measured in the region of visible radiation. Our QMC calculations show that, for standard cavities, the solvatochromic shifts obtained with the PCM are underestimated, even though of the correct sign, for both transitions of acrolein in water. Only by reducing the size of the cavity to values where more than one electron is escaped to the solvent region, we regain the experimental shift for the n → π(*) case and also improve considerably the shift for the π → π(*) transition.