4-Fluoro-Threonine: From Diastereoselective Synthesis to pH-Dependent Conformational Equilibrium in Aqueous Solution

Abstract

4-Fluoro-threonine, the only fluoro amino acid of natural origin discovered so far, is an interesting target for both synthetic and theoretical investigations. In this work, we lay the foundation for spectroscopic characterization of 4-fluoro-threonine. First, we report a diastereoselective synthetic route, which is suitable to produce synthetic material for experimental characterization. The addition of the commercially available ethyl isocyanoacetate to benzyloxyacetaldehyde led to the corresponding benzyloxy-oxazoline, which was hydrolyzed and transformed into ethyl (4S*,5S*)-5-hydroxymethyl-2-oxo-4-oxazolidinecarboxylate in a few steps. Fluorination with diethylamino sulfur trifluoride (DAST) afforded ethyl (4S*,5S*)-5-fluoromethyl-2-oxo-4-oxazolidinecarboxylate, which was deprotected to give the desired diastereomerically pure 4-fluoro-threonine, in 8–10% overall yield. With the synthetic material in our hands, acid–base titrations have been carried out to determine acid dissociation constants and the isoelectric point, which is the testing ground for the theoretical analysis. We have used machine learning coupled with quantum chemistry at the state-of-the-art to analyze the conformational space of 4-fluoro-threonine, with the aim of gaining insights from the comparison of computational and experimental results. Indeed, we have demonstrated that our approach, which couples a last-generation double-hybrid density functional including empirical dispersion contributions with a model combining explicit first-shell molecules and a polarizable continuum for describing solvent effects, provides results and trends in remarkable agreement with experiments. Finally, the conformational analysis applied to fluoro amino acids represents an interesting study for the effect of fluorine on the stability and population of conformers.

Natural and Synthetic Halogenated Amino Acids—Structural and Bioactive Features in Antimicrobial Peptides and Peptidomimetics

“…Final deprotection to ( 28 ) was achieved via treatment with 6N HCl [ 116 ]. Potenti et al recently reported another synthetic route avoiding the use of Ru(III) [ 117 ]. The preparation of 4-chloro-lysine ( 29 ) has been reported by reacting commercially available lysine hydrochloride with Cl 2 under irradiation with UV light.…”

Bringing Machine‐Learning Enhanced Quantum Chemistry and Microwave Spectroscopy to Conformational Landscape Exploration: the Paradigmatic Case of 4‐Fluoro‐Threonine

“…Therefore, we resorted to a purposely tailored version of the Island Model Evolutionary Algorithm (IMEA [14,27] ), which has proven to be an extremely effective machine-learning algorithm for the structural characterization of several flexible molecules. [10,27] The exploration step employed the GFN2-xTB semi empirical method [13] and led to, in addition to the 21 structures deriving from fluorination of Thr, several additional conformers. This panel of structures, together with all missing staggered conformers with respect to the χ 3 dihedral for each candidate (see Table S2 and Figure S1 of the Supplementary Information, SI), was selected for further refinement.…”

“…[45,46] To probe the a priori description of the conformational landscape of 4FT, a sufficient amount of the racemic diastereoisomer (rac-1; see the inset of Figure 1) was obtained following the recently published route (with further details being given in the SI). [10] Being 4FT a solid compound with a high melting point (182-183 °C), [47] the laser ablation (LA) technique [26] was then employed in combination with a chirped-pulse Fourier-transform Microwave spectrometer (CP-FTMW; details are provided in the SI) [48,49] to record the rotational spectrum of 4FT in the 6.0-14.0 GHz frequency region. In the spectrometer, the gas-phase sample is subjected to supersonic expansion.…”

“…According to Tables 3 and S2 of the SI, the I'gg À g À , IIggg À and IItg À g À conformers of 4FT correlate with I'gg À , IIgg and IItg À of Thr, respectively. [9,10] While the relative stability order remains almost unchanged for I'gg À g À (4FT)/I'gg À (Thr) and IIggg À (4FT)/ IIgg(Thr), the introduction of a fluorine atom greatly stabilizes IItg À g À . In all three conformers, fluorine is involved in additional intra-molecular interactions, but Figure 6 points out that, for the latter conformer, such an interaction is more relevant (in terms of both extension of the electron density regions and strength).…”

Fast exploration of potential energy surfaces with a joint venture of quantum chemistry, evolutionary algorithms and unsupervised learning

“…In particular, we are concerned with the use of metaheuristics in the exploration of the Potential Energy Surfaces (PESs) of flexible molecular systems of medium size (roughly containing less than 100 atoms). In previous contributions [15][16][17] we have proposed and validated the application of one of such algorithms, namely the (λ + µ) Island Model Evolutionary Algorithm (IM-EA hereafter), to the investigation of the conformational landscape of biomolecule building blocks 18 or relatively simple organometallic systems 19 . The present contribu-tion presents a number of relevant improvements to the IM-EA method: (i) in the previous contribution we simply checked the capabilities of the method in exploring PESs of flexible systems with the goal of completeness without an in depth discussion of the importance of various components in the method, which is presented in this manuscript; (ii) we previously limited the exploration to dihedral angles of isolated flexible systems, whereas here we present also a new set of operators based on quaternions 20,21 able to deal with inter-molecular interactions; (iii) we add a number of improvements to the method, with new mutation operators and the Hall of Fame mechanism (see section 2.1) and (iv) introduce effective unsupervised clustering of candidate structures in order to reduce as much as possible the number of expensive quantum chemical (QC) computations; neither the computer code, nor the case studies discussed below were presented before.…”