Observation of Distinct Carboxylic Acid Conformers in Aqueous Solution

Elucidation of the hydration pattern of trifluoroacetic acid in dilute solutions: FTIR and computational study

The atmospheric partitioning of trifluoroacetic acid (TFA) in aerosol is a complex function of the size of suspended water droplets and their pH value. The unraveling of the affinity of TFA towards basic but not acidic conditions may be accomplished by providing an insight into the hydration pattern of undissociated TFA. Owing to rather scarce details on very dilute aqueous solutions of trifluoroacetic acid (TFA), we examined CF3COOD and CF3COONa solutions in D2O in the concentration range 0.001-0.1 mol dm-3 using transmission FTIR spectroscopy and computational methods. Besides detecting the signals originated from undissociated species in both CF3COOD (1787 cm-1 and 1766 cm-1 at c0 = 0.1 mol dm-3) and CF3COONa (1807 cm-1 at c0 = 0.1 mol dm-3) D2O solutions, through computational techniques we identified different TFA hydrates that contribute to the complexity of the spectral appearance. The combination of experimental and computational data suggested the concentration dependence of the predominant hydrogen bonding pattern of TFA. The results obtained in this work should help in understanding the partitioning of TFA into micron-size water droplets in the atmosphere in molecular and structural terms, i.e. the eventual stability of a hydrated complex for a particular TFA conformer.

Retinal photoisomerization versus counterion protonation in light and dark-adapted bacteriorhodopsin and its primary photoproduct

Discovered over 50 years ago, bacteriorhodopsin is the first recognized and most widely studied microbial retinal protein. Serving as a light-activated proton pump, it represents the archetypal ion-pumping system. Here we compare the photochemical dynamics of bacteriorhodopsin light and dark-adapted forms with that of the first metastable photocycle intermediate known as "K". We observe that following thermal double isomerization of retinal in the dark from bio-active all-trans 15-anti to 13-cis, 15-syn, photochemistry proceeds even faster than the ~0.5 ps decay of the former, exhibiting ballistic wave packet curve crossing to the ground state. In contrast, photoexcitation of K containing a 13-cis, 15-anti chromophore leads to markedly multi-exponential excited state decay including much slower stages. QM/MM calculations, aimed to interpret these results, highlight the crucial role of protonation, showing that the classic quadrupole counterion model poorly reproduces spectral data and dynamics. Single protonation of ASP212 rectifies discrepancies and predicts triple ground state structural heterogeneity aligning with experimental observations. These findings prompt a reevaluation of counter ion protonation in bacteriorhodopsin and contribute to the broader understanding of its photochemical dynamics.

Determining the Surface pKa of Perfluorooctanoic Acid

Perfluorooctanoic acid (PFOA) is an environmentally prevalent and persistent organic pollutant with toxic and bioaccumulative properties. Despite the known importance of perfluorinated pollutants in the global environment, molecular-level details of the physicochemical behavior of PFOA on aqueous interfaces remain poorly understood. Here, we utilized two surface-specific techniques, vibrational sum frequency generation spectroscopy (SFG) and surface tensiometry, to investigate the pH-induced structural changes of PFOA and octanoic acid (OA) and determined the apparent pKa at the air-water surface. The SFG spectra and surface activity model were investigated over a wide range of pHs. With the surface tension measurements, the surface pKa values for OA and PFOA are determined to be 3.8 ± 0.1 and 2.2 ± 0.2, respectively. These results could provide insights into improved remediation of PFOAs and may impact climate modeling of perfluorinated alkyl chain molecules.

FTIR spectroscopy and molecular level insight of diluted aqueous solutions of acetic acid

Aqueous solutions of acetic acid (AA) have been intensively explored for decades with a particular attention addressed to the hydrogen bond network generated by COOH group at different concentrations. In majority of studies conducted so far the envelope originated from νCO is decomposed into two bands assigned to differently hydrated monomers: the one presumably to AA···H2O, and another one to AA···(H2O)2. In order to examine if species other than the mentioned monomers produce this spectral signature, we performed computational and FTIR spectroscopic study of AA in aqueous solutions. Dilute solutions of deuterated acetic acid (CD3COOD) in D2O and in C2Cl4 as a reference were prepared (c0 = 0.001, 0.01 and 0.1 mol dm-3) as well as of deuterated sodium acetate (CD3COONa) in D2O. CD3COOD in 0.1 mol dm-3 solution in D2O displays a feature that separated in two signals with maxima at 1706 cm-1 and 1687 cm-1. A combined DFT and molecular dynamics study performed in this work showed the assignation of those spectral bands to be a more complex problem than previously thought, with syn-anti isomerism and hydration contributing to the experimentally observed broad νCO envelope.

Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory

We selected 145 reference organic molecules that include model fragments used in computer-aided drug design. We calculated 158 conformational energies and barriers using force fields, with wide applicability in commercial and free softwares and extensive application on the calculation of conformational energies of organic molecules, e.g. the UFF and DREIDING force fields, the Allinger's force fields MM3-96, MM3-00, MM4-8, the MM2-91 clones MMX and MM+, the MMFF94 force field, MM4, ab initio Hartree-Fock (HF) theory with different basis sets, the standard density functional theory B3LYP, the second-order post-HF MP2 theory and the Domain-based Local Pair Natural Orbital Coupled Cluster DLPNO-CCSD(T) theory, with the latter used for accurate reference values. The data set of the organic molecules includes hydrocarbons, haloalkanes, conjugated compounds, and oxygen-, nitrogen-, phosphorus- and sulphur-containing compounds. We reviewed in detail the conformational aspects of these model organic molecules providing the current understanding of the steric and electronic factors that determine the stability of low energy conformers and the literature including previous experimental observations and calculated findings. While progress on the computer hardware allows the calculations of thousands of conformations for later use in drug design projects, this study is an update from previous classical studies that used, as reference values, experimental ones using a variety of methods and different environments. The lowest mean error against the DLPNO-CCSD(T) reference was calculated for MP2 (0.35 kcal mol-1), followed by B3LYP (0.69 kcal mol-1) and the HF theories (0.81-1.0 kcal mol-1). As regards the force fields, the lowest errors were observed for the Allinger's force fields MM3-00 (1.28 kcal mol-1), ΜΜ3-96 (1.40 kcal mol-1) and the Halgren's MMFF94 force field (1.30 kcal mol-1) and then for the MM2-91 clones MMX (1.77 kcal mol-1) and MM+ (2.01 kcal mol-1) and MM4 (2.05 kcal mol-1). The DREIDING (3.63 kcal mol-1) and UFF (3.77 kcal mol-1) force fields have the lowest performance. These model organic molecules we used are often present as fragments in drug-like molecules. The values calculated using DLPNO-CCSD(T) make up a valuable data set for further comparisons and for improved force field parameterization.

Intramolecular Vibrational Redistribution in Formic Acid and its Deuterated Forms

The intramolecular vibrational relaxation dynamics of formic acid and its deuterated isotopologues is simulated on the full-dimensional potential energy surface of Richter and Carbonnière [F. Richter and P. Carbonnière, J. Chem. Phys. 148, 064303 (2018)] using the Heidelberg MCTDH package. We focus on couplings with the torsion vibrational modes close to the trans- cis isomerisation coordinate from the dynamics of artificially excited vibrational mode overtones. The C-O stretch bright vibrational mode is coupled to the out-of-the plane torsion mode in HCOOH, where this coupling could be exploited for laser-induced trans-to- cis isomerisation. Strong isotopic effects are observed: deuteration of the hydroxyl group, i.e., in HCOOD and DCOOD, destroys the C-O stretch to torsion mode coupling whereas in DCOOH, little to no effect is observed.

Accurate molecular orientation at interfaces determined by multimode polarization-dependent heterodyne-detected sum-frequency generation spectroscopy via multidimensional orientational distribution function

Many essential processes occur at soft interfaces, from chemical reactions on aqueous aerosols in the atmosphere to biochemical recognition and binding at the surface of cell membranes. The spatial arrangement of molecules specifically at these interfaces is crucial for many of such processes. The accurate determination of the interfacial molecular orientation has been challenging due to the low number of molecules at interfaces and the ambiguity of their orientational distribution. Here, we combine phase- and polarization-resolved sum-frequency generation (SFG) spectroscopy to obtain the molecular orientation at the interface. We extend an exponentially decaying orientational distribution to multiple dimensions, which, in conjunction with multiple SFG datasets obtained from the different vibrational modes, allows us to determine the molecular orientation. We apply this new approach to formic acid molecules at the air–water interface. The inferred orientation of formic acid agrees very well with ab initio molecular dynamics data. The phase-resolved SFG multimode analysis scheme using the multidimensional orientational distribution thus provides a universal approach for obtaining the interfacial molecular orientation.

Structural and Thermodynamic Effects on the Kinetics of C-H Oxidation by Multisite Proton-Coupled Electron Transfer in Fluorenyl Benzoates

Our recent experimental and theoretical investigations have shown that fluorene C-H bonds can be activated through a mechanism in which the proton and electron are transferred from the C-H bond to a separate base and oxidant in a concerted, elementary step. This multisite proton-coupled electron transfer (MS-PCET) mechanism for C-H bond activation was shown to be facilitated by shorter proton donor-acceptor distances. With the goal of intentionally modulating this donor-acceptor distance, we have now studied C-H MS-PCET in the 3-methyl-substituted fluorenyl benzoate (2-Flr-3-Me-BzO^-). This derivative was readily oxidized by ferrocenium oxidants by initial C-H MS-PCET, with rate constants that were 6-21 times larger than those for 2-Flr-BzO^- with the same oxidants. Structural comparisons by X-ray crystallography and by computations showed that addition of the 3-methyl group caused the expected steric compression; however, the relevant C···O^- proton donor-acceptor distance was longer, due to a twist of the carboxylate group. The structural changes induced by the 3-Me group increased the basicity of the carboxylate, weakened the C-H bond, and reduced the reorganization energy for C-H bond cleavage. Thus, the rate enhancement for 2-Flr-3-Me-BzO^- was due to effects on the thermochemistry and kinetic barrier, rather than from compression of the C···O^- proton donor-acceptor distance. These results highlight both the challenges of controlling molecules on the 0.1 Å length scale and the variety of parameters that affect PCET rate constants.

Matrix Isolation-Vibrational Circular Dichroism Spectroscopic Study of Conformations and Non-Covalent Interactions of Tetrahydro-2-Furoic Acid

The conformational landscape and aggregation behaviour of tetrahydro-2-furoic acid (THFA) were investigated by using matrix isolation-vibrational circular dichroism (MI-VCD). The well-resolved experimental MI-IR and MI-VCD features in an argon matrix at 10 K allow one to identify two dominant monomeric conformations as trans-THFA where the hydroxyl and carbonyl groups of COOH are at opposite sides, as well as one cis-conformer. At 24 K and 30 K deposition temperatures, the experimental IR and VCD spectral features reveal further growth of the binary THFA aggregates. Systematic conformational searches identified three vastly different binary binding topologies, resulting in a few hundred stable (THFA)₂ conformers. Interestingly, the main binary structures observed correspond to an unusual type of structure which is made of two trans-THFA subunits, in contrast to the usual double H-bonded ring binary structures, identified in a previous solution study. The present work showcases the power of MI-VCD spectroscopy in revealing unusual structures formed in a cold rare gas matrix.

Why Does Dimethyl Carbonate Dissociate Li Salt Better Than Other Linear Carbonates? Critical Role of Polar Conformers

The marked difference in the ionic conductivities of linear carbonate (LC) electrolyte solutions despite their similar viscosities and permittivities is a long-standing puzzle. This study unraveled the critical impact of solvent conformational isomerism on salt dissociation in 0.1-3.0 M LiPF₆ dimethyl carbonate (DMC), ethyl methyl carbonate (EMC), and diethyl carbonate (DEC) solutions using Raman and dielectric relaxation spectroscopies. The extent of salt dissociation in the LC solutions, which decreased in the order DMC > EMC > DEC, is closely related to the fraction of polar cis-trans LC conformers, as this conformer participates in Li ion solvation more readily than the nonpolar cis-cis counterpart. Our first-principles calculations corroborated that the cis-trans conformer facilitates free ion formation more than the cis-cis conformer, and the extent of this effect decreased in the order DMC > EMC > DEC. This study provides an avenue for the design of highly conductive electrolytes by exploiting the conformational isomerism of solvent molecules.

Increasing the weights in the molecular work-out of cis- and trans-formic acid: extension of the vibrational database via deuteration

The higher-energy cis- as well as the global minimum trans-rotamers of the four H/D isotopologues of the formic acid monomer have been examined with Raman jet spectroscopy extending the vibrational gas phase reference database by eleven new cis-band positions for HCOOD, DCOOH, and DCOOD. With these new additions, all O-H/D, C-H/D, and C[double bond, length as m-dash]O stretching as well as the O-D in-plane bending vibrations of these higher-energy rotamers are known in addition to the previously determined C-O stretch and OH torsion of cis-HCOOH. Further, a comparison of the vibrational spectra of all four H/D isotopologues of the globally stable trans-rotamer of formic acid is shown to be very helpful in revealing similarities and differences in these systems, particularly with regard to Fermi resonances. Amongst the most prominent ones is the ν5/2ν9 resonance doublet of trans-HCOOH, for which we provide more insight into a recently suggested label switch of the resonance partners via the comparison of infrared and Raman jet spectra.

Effect of intramolecular hydrogen-bond formation on the molecular conformation of amino acids

The molecular conformation of the carboxyl group can be crucial for its chemical properties and intermolecular interactions, especially in complex molecular environments such as polypeptides. Here, we study the conformational behaviour of the model amino acid N-acetylproline in solution at room temperature with two-dimensional infrared spectroscopy. We find that the carboxyl group of N-acetylproline adopts two distinct conformations, syn- and anti-. In the syn-conformer the O-H group is oriented at  ~60^∘ with respect to the C=O and in the anti-conformer the O-H is anti-parallel to the C=O. In hydrogen-bond accepting solvents such as dimethyl sulfoxide or water, we observe that, similar to simple carboxylic acids, around 20% of the -COOH groups adopt an anti-conformation. However, when N-acetylproline is dissolved in a weakly hydrogen-bond accepting solvent (acetonitrile), we observe the formation of a strong intramolecular hydrogen bond between the carboxyl group in the anti-conformation and the amide group, which stabilizes the anti-conformer, increasing its relative abundance to ~60%.

Peptide Side-COOH Groups Have Two Distinct Conformations under Biorelevant Conditions

The carboxyl (COOH) side chain groups of amino acids, such as aspartic acid, play an important role in biochemical processes, including enzymatic proton transport. In many theoretical studies, it was found that the (bio)chemical reactivity of the carboxyl group strongly depends on the conformation of this group. Interestingly, up to now there has been no experimental investigation of the geometry and the stability of different COOH conformers under biorelevant conditions. Here, we investigate the conformational isomerism of the side chain COOH group of N-acetyl aspartic acid amide using polarization-resolved two-dimensional infrared spectroscopy. We find that the carboxyl group shows two distinct near-planar conformers (syn and anti) when dissolved in water at room temperature. Both conformers are significantly populated in aqueous solution (75 ± 10% and 25 ± 10% for syn and anti, respectively). Molecular dynamics simulations show that the anti conformer interacts more strongly with water molecules than the syn conformer, explaining why this conformer is significantly present in aqueous solution.

Ultrafast Chemical Exchange Dynamics of Hydrogen Bonds Observed via Isonitrile Infrared Sensors: Implications for Biomolecular Studies

Local probes are indispensable to study protein structure and dynamics with site-specificity. The isonitrile functional group is a highly sensitive and H-bonding interaction-specific probe. Isonitriles exhibit large spectral shifts and transition dipole moment changes upon H-bonding while being weakly affected by solvent polarity. These unique properties allow a clear separation of distinct subpopulations of interacting species and an elucidation of their ultrafast dynamics with two-dimensional infrared (2D-IR) spectroscopy. Here, we apply 2D-IR to quantify the picosecond chemical exchange dynamics of solute-solvent complexes forming between isonitrile-derivatized alanine and fluorinated ethanol, where the degree of fluorination controls their H-bond-donating ability. We show that the molecules undergo faster exchange in the presence of more acidic H-bond donors, indicating that the exchange process is primarily dependent on the nature of solvent-solvent interactions. We foresee isonitrile as a highly promising probe for studying of H-bonds dynamics in the active site of enzymes.

Concerted Pair Motion Due to Double Hydrogen Bonding: The Formic Acid Dimer Case

Formic acid dimer as the prototypical doubly hydrogen-bonded gas-phase species is discussed from the perspective of the three translational and the three rotational degrees of freedom which are lost when two formic acid molecules form a stable complex. The experimental characterisation of these strongly hindered translations and rotations is reviewed, as are attempts to describe the associated fundamental vibrations, their combinations, and their thermal shifts by different electronic structure calculations and vibrational models. A remarkable match is confirmed for the combination of a CCSD(T)-level harmonic treatment and an MP2-level anharmonic VPT2 correction. Qualitatively correct thermal shifts of the vibrational spectra can be obtained from classical molecular dynamics in CCSD(T)-quality force fields. A detailed analysis suggests that this agreement between experiment and composite theoretical treatment is not strongly affected by fortuitous error cancellation but fully converged variational treatments of the six pair or intermolecular modes and their overtones and combinations in this model system would be welcome.