Lactic acid in solution: Investigations of lactic acid self-aggregation and hydrogen bonding interactions with water and methanol using vibrational absorption and vibrational circular dichroism spectroscopies

How Molar Mass, Acid Type, and Coagulation Bath Composition Influence Coagulation Kinetics, Mechanical Properties, and Swelling Behavior of Chitosan Filaments: A Full Factorial Approach

In this study, a full multilevel factorial design (21 × 31 × 21) × 2 was conducted to investigate the effects of molar mass of chitosan (CS), the type of acid used for dissolution, and the composition of the coagulation bath on the coagulation, mechanical properties, and swelling of the filaments. The results showed the statistical significance of the factors in the characteristics of these filaments. The coagulation followed Fick's second law of diffusion, with an increase in the chitosan molar mass reducing the coagulation rate, as did the use of acetic acid instead of lactic acid. CS with higher molar mass produced filaments with larger diameters, but without a proportional increase in tensile strength. Swelling was influenced by the acid and composition of the coagulation bath. The interaction of CS with acid and the CS molar mass factor were the terms of greatest statistical significance. Crystallinity was higher for samples dissolved in aqueous solutions of acetic acid and coagulated with ethanol, while lactic acid induced greater structural disorder. Samples coagulated with ethanol presented more homogeneous surfaces, while methanol resulted in rougher filaments. These findings emphasize the critical role of processing conditions in tailoring the properties of CS filaments, providing valuable insights for their optimization for biomedical applications.

Local Interactions in Aqueous Ethanol Solution Revealed by the C=O Stretching Probe

Accurately identifying local interactions such as hydrophilicity and hydrophobicity is of critical importance in regulating the functions of amphiphilic biomolecules, but in situ identification methods for such interactions are still lacking. This study proposes a probe based on carbonyl (C=O) stretching vibration to study the hydrophilic and hydrophobic interactions in amphiphilic alcohol-water systems. A combination of theoretical calculations and Raman spectroscopy experiments is employed to investigate the molecular interactions of ethyl acetate C=O in an ethanol aqueous solution, as well as the reasons behind the splitting of spectral peaks. The results indicate that the spectral peak splitting of the C=O stretching vibration is attributed to ethyl acetate existing in different hydrophilic and hydrophobic environments. Specifically, the two low-wavenumber components arise from the formation of double and single hydrogen bonds between C=O and water or ethanol, respectively, while the high-wavenumber component is attributed to the interaction between C=O and the hydrophobic alkyl group. These findings suggest that the C=O stretching vibration of esters is sensitive to the surrounding hydrophilic and hydrophobic environments, thereby indicating its potential as a useful probe for identifying hydrophilic and hydrophobic interactions.

Vibrational circular dichroism spectra of proline in water at different pH values

Recording VCD spectra of aqueous solution poses a particular challenge as water is a strong infrared absorber. Likewise, the computational analysis of VCD spectra by means of DFT-based spectral calculations requires the consideration of explicit solvent molecules, thus posing an even greater challenge. Several studies suggested that by modeling the solvent environment with a few water molecules in a micro-solvation approach would be sufficient to describe experimental spectra. For example, using proline at different pH values, we herein show that a change in the relative spatial orientation of a single water molecule in five-fold solvated structures strongly affects the computed VCD spectral signatures and that Boltzmann-weighted spectra do not correctly reproduce the experiment. We thus explored an approach based on molecular dynamics and subsequent DFT-calculations, in which we considered 30 water molecules (about 1.5 solvation shells). Once again, it was found that the Boltzmann-weighted spectra obtained on the basis of several hundred structures did not correctly reproduce experimental signatures, and a simple averaging scheme resulted in well-matching spectra with comparable bandwidths. The rationale behind the procedure was that sampling the configurational space of the solvent molecules is as equally important as the conformational sampling of the solute. For conformationally more flexible molecules, it is assumed that a much larger set of structures will have to be computed in order to properly sample the conformational space of both solute and solvent.

Is lactic acid a misunderstood trigger of gout attack for a century?

A gout attack could be viewed as a nucleation event. Many reports have shown that the typical molecular structure of crystallization inhibitors usually contains carboxyl and hydroxyl groups, which could interact with solute molecules through hydrogen bonding, thereby suppressing the nucleation and growth of crystals. Since 1923, l-lactic acid (LA), a molecule with structural features of inhibitors, has been speculated to be a trigger for acute gout because metabolized LA temporarily reduces uric acid excretion and leads to a slow increase in serum uric acid concentration. However, many cases of gout presumably triggered by elevated lactate in a very short period of 4 h are often inexplicable. Here, we present the unexpected result that LA has a significant "opposite effect" on the nucleation and growth of gouty pathological crystals, which is that as the concentration of the additive LA increases, the nucleation and growth of the crystals is suppressed and then facilitated. This approach may help our clarifying the long-standing "misunderstandings" and further understanding the association between metabolized LA and increased risk of gout attacks. Finally, a novel mechanism called "tailed-made occupancy (TMO)" was used to explain the nucleation and crystallization effects of LA on sodium urate monohydrate (MSUM).

Conformational distributions of tetrahydro-2-turoic acid in water at different pH values by their IR and vibrational circular dichroism spectra

Infrared (IR) and vibrational circular dichroism (VCD) spectra of tetrahydro-2-furoic acid (THFA) in aqueous solutions under several different pH conditions were recorded. To interpret the IR and VCD spectra of THFA obtained in highly acidic and basic aqueous solutions, extensive and systematic conformational searches were conducted to acquire the low-energy minima for both the neutral and deprotonated forms of THFA species, as well as their hydrated clusters. This was accomplished by using the conformer-rotamer ensemble sampling tool (CREST) with an implicit solvation model for water. The CREST candidates were further optimized at the B3LYP-D3BJ/def2-TZVP level of theory. The simulated VCD spectra of the neutral THFA conformers in the polarizable continuum model (PCM) of water alone exhibit little agreement with the experimental data under highly acidic conditions. Applying the clusters-in-a-liquid solvation model by considering the monohydrate THFA conformers in the PCM of water, significantly improved agreement with the experimental data. Similarly, the deprotonated THFA species solvated with one to four explicit water molecules in the PCM of water were considered. While the IR and VCD spectra of the deprotonated THFA monohydrate conformers offer the best agreement with the experimental data, other larger hydrated clusters, particularly the dihydrates, also contribute to the spectra. Through the synergistic combined experimental and theoretical approach used in the study, comprehensive conformational distributions of the predominant THFA species across various pH conditions were extracted.

Modelling solute-solvent interactions in VCD spectra analysis with the micro-solvation approach

Vibrational circular dichroism (VCD) spectroscopy has become an important part of the (stereo-)chemists' toolbox as a reliable method for the determination of absolute configurations. Being the chiroptical version of infrared spectroscopy, it has also been recognized as being very sensitive to conformational changes and intermolecular interactions. This sensitivity originates from the fact that the VCD spectra of individual conformers are often more different than their IR spectra, so that changes in conformational distributions or band positions and intensities become more pronounced. What is an advantage for studies focussing on intermolecular interactions can, however, quickly turn into a major obstacle during AC determinations: solute-solvent interactions can have a strong influence on spectral signatures and they must be accurately treated when simulating VCD and IR spectra. In this perspective, we showcase selected examples which exhibit particularly pronounced solvent effects. It is demonstrated that it is typically sufficient to model solute-solvent interactions by placing single solvent molecules near hydrogen bonding sites of the solute and subsequently use the optimized structures for spectra simulations. This micro-solvation approach works reasonably well for medium-sized, not too conformationally flexible molecules. We thus also discuss its limitations and outline the next steps that method development needs to take in order to further improve the workflows for VCD spectra predictions.

Multifunctional Amine Modifiers for Selective Dehydration of Methyl Lactate to Acrylates

Dehydration of methyl lactate to acrylic acid and methyl acrylate was experimentally evaluated over a Na-FAU zeolite catalyst impregnated with multifunctional diamines. 1,2-Bis(4-pyridyl)ethane (12BPE) and 4,4'-trimethylenedipyridine (44TMDP), at a nominal loading of 40 wt % or two molecules per Na-FAU supercage, afforded a dehydration selectivity of 96 ± 3% over 2000 min time on stream. Although 12BPE and 44TMDP have van der Waals diameters approximately 90% of the Na-FAU window opening diameter, both flexible diamines interact with internal active sites of Na-FAU as characterized by infrared spectroscopy. During continuous reaction at 300 °C, the amine loadings in Na-FAU remained constant for 12BPE but decreased as much as 83% for 44TMDP. Tuning the weighted hourly space velocity (WHSV) from 0.9 to 0.2 h^-1 afforded a yield as high as 92% at a selectivity of 96% with 44TMDP impregnated Na-FAU, resulting in the highest yield reported to date.

Chirality Discrimination at Binary Organic|Water Interfaces Monitored by Interfacial Tension Measurements with Preliminary Comparison with Molecular Dynamics Simulations

Chirality discrimination at a binary toluene (organic)/water(aqueous) interface between R- or S-Tol-BINAP (2,2'-Bis(di-p-tolylphosphino)-1,1'-binaphthyl) molecules and the water-soluble serine chiral specie is examined for the first time, using a combination of interfacial tension measurements and molecular dynamic simulations. Experimental interfacial measurements exhibit a clear chirality-controlled difference when a homochiral versus a heterochiral enantiomeric pairs are introduced at the interfaces. The related molecular dynamics simulations support the experimental results and provide further molecular insight of intermolecular interactions at the interfaces. The results indicate that interfacial tension measurements can capture the preferential interactions which exist between different pairs of enantiomers at the binary interfaces, opening up a new way for probing chirality discrimination at liquid-liquid interfaces.

Conformations of Steroid Hormones: Infrared and Vibrational Circular Dichroism Spectroscopy

Steroid hormone molecules may exhibit very different functionalities based on the associated functional groups and their 3D arrangements in space, i.e., absolute configurations and conformations. Infrared (IR) and vibrational circular dichroism (VCD) spectra of four different steroid hormones, namely dehydroepiandrosterone (DHEA), 17α-methyltestosterone (MTTT), (16α,17)-epoxyprogesterone (Epoxy-P4), and dehydroepiandrosterone acetate (AcO-DHEA), were measured in deuterated dimethyl sulfoxide and some also in carbon tetrachloride. Extensive conformational searches were carried out using the recent developed conformer-rotamer ensemble sampling tool (CREST) which also accounts for solvent effects using an implicit solvation model. All the CREST conformational candidates were then reoptimized at the B3LYP-D3BJ/def2-TZVPD with the PCM of solvent. The good agreements between the experimental IR and VCD spectra and the theoretical simulations provide a conclusive information about their conformational distribution and absolute configurations. The experimental and theoretical IR and VCD spectra of AcO-DHEA in the carbonyl and alkene stretching region showed some discrepancies, and the possible causes related to solvent effects, large amplitude motions and levels of theory used in the modelling were explored in detail. As part of the investigation, additional calculations at the B3LYP-D3BJ/6-31++G (2d,p) and B3LYP-D3BJ/cc-pVTZ levels, as well as some 'mixed' calculations with the double-hybrid functional B2PLYP-D3 were also carried out. The results indicate that the double-hybrid functional is important for predicting the correct IR band pattern in the carbonyl and alkene stretching region.

Effects of Organic Acids on the Release of Fruity Esters in Water: An Insight at the Molecular Level

It is well known that organic acids (OAs) could affect the flavour of fruit juices and beverages. However, the molecular mechanism of aroma release is still unclear. In this study, the effects of citric acid (CA), L-(-)-malic acid (MA) and L-lactic acid (LA) on the release of six selected esters and their sensory perception were investigated by means of HS-GC-MS analyses and odour detection threshold determination, respectively. Meanwhile, the density functional theory (DFT) calculation was employed to explore the interaction modes between esters and OAs. HS-GC-MS analyses showed that the concentration and the type of OAs regulated the release of esters. The results were basically consistent with the detection threshold change of those esters. The DFT calculation suggested that the main intermolecular interaction was hydrogen bonds, and several esters could form a ternary ring structure with OAs through hydrogen bonds. The interactions can induce the different release behaviours of esters in OAs water solution. The number of carboxyl functional groups in OAs and the spatial conformation of esters appeared to influence the magnitude of the interaction. The above results demonstrated the mechanism of OAs affecting the release of esters and indicated a possible flavour control way by using different OAs and OA concentrations.

Raman Optical Activity of N-Acetyl-L-Cysteine in water and in methanol: the "clusters-in-a-liquid" model and ab initio molecular dynamics simulations

Raman and Raman Optical Activity (ROA) spectra of N-acetyl-L-cysteine (NALC), a flexible chiral molecule, were measured in water and in methanol to evaluate the solvent effects. Two different solvation approaches, i.e. the DFT based clusters-in-a-liquid solvent model and the ab initio molecular dynamics (AIMD) simulations, were applied to simulate the Raman and ROA spectra. Systematic conformational searches were carried out using a recently developed conformational searching tool, CREST, with the inclusion of polarizable continuum model of water and of methanol. The CREST candidates of NALC and the NALC-solvent complexes were re-optimized and their Raman and ROA simulations were done at the B3LYP-D3BJ/def2-TZVP and the B3LYP-aug-cc-pVDZ//cc-pVTZ levels. Also, AIMD simulations , which includes some anharmonic effects and all intermolecular interactions in solution, were performed. By empirically weighting the computed Raman and ROA spectra of each conformer, good agreements with the experimental data were achieved with both approaches, while AIMD offered some improvements in the carbonyl and in the low wavenumber regions over the static DFT approach. The pros and cons of these two different approaches for accounting the solvent effects on Raman and ROA of this flexible chiral system will also be discussed.

Double Hydrogen Bonding Dimerization Propensity of Aqueous Hydroxy Acids Investigated Using Vibrational Optical Activity

Lactic and malic acids are key substances in a number of biochemical processes in living cells and are also utilized in industry. Vibrational spectroscopy represents an efficient and sensitive way to study their structure and interactions. Since water is the natural environment, proper understanding of their molecular dynamics in aqueous solutions is of critical importance. To this end, we employed Raman spectroscopy and Raman optical activity (ROA) to study the conformation of l-lactic and l-malic acids in water (while varying pH, temperature, and concentration), with special emphasis on their double hydrogen bonding dimerization propensity. Raman and ROA experimental data were supported by extensive theoretical calculations of the vibrational properties and by additional experiments (IR absorption, vibrational circular dichroism, and NMR). Conformational behavior of the acids in water was described by molecular dynamics simulations. Reliability of the results was verified by calculating the vibrational properties of populated conformers and by comparing thus obtained spectral features with the experimental data. Calculations estimated the incidence of H-bonded dimers in water to be low in lactic acid and comparable to monomers in malic acid. The "hybrid" approach presented here reveals limitations of relying on the experimental spectra alone to study dimer formation.

The important role of non-covalent interactions for the vibrational circular dichroism of lactic acid in aqueous solution

We present a computational study of vibrational circular dichroism (VCD) in solutions of (S)-lactic acid, relying on ab initio molecular dynamics (AIMD) and full solvation with bulk water. We discuss the effect of the hydrogen bond network on the aggregation behaviour of the acid: while aggregates of the solute represent conditions encountered in a weakly interacting solvent, the presence of water drastically interferes with the clusters - more strongly than originally anticipated. For both scenarios we computed the VCD spectra by means of nuclear velocity perturbation theory (NVPT). The comparison with experimental data allows us to establish a VCD-structure relationship that includes the solvent network around the chiral solute. We suggest that fundamental modes with strong polarisation such as the carbonyl stretching vibration can borrow VCD from the chirally restructured solvent cage, which extends the common explanatory models of VCD generation in aqueous solution.

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.

Hydrophobic Deep Eutectic Solvents for the Recovery of Bio-Based Chemicals: Solid–Liquid Equilibria and Liquid–Liquid Extraction

The solid–liquid equilibrium (SLE) behavior and liquid–liquid extraction (LLX) abilities of deep eutectic solvents (DESs) containing (a) thymol and L-menthol, and (b) trioctylphosphine oxide (TOPO) and L-menthol were evaluated. The distribution coefficients (KD) were determined for the solutes relevant for two biorefinery cases, including formic acid, levulinic acid, furfural, acetic acid, propionic acid, butyric acid, and L-lactic acid. Overall, for both cases, an increasing KD was observed for both DESs for acids increasing in size and thus hydrophobicity. Furfural, being the most hydrophobic, was seen to extract the highest KD (for DES (a) 14.2 ± 2.2 and (b) 4.1 ± 0.3), and the KD of lactic acid was small, independent of the DESs (DES (a) 0.5 ± 0.07 and DES (b) 0.4 ± 0.05). The KD of the acids for the TOPO and L-menthol DES were in similar ranges as for traditional TOPO-containing composite solvents, while for the thymol/L-menthol DES, in the absence of the Lewis base functionality, a smaller KD was observed. The selectivity of formic acid and levulinic acid separation was different for the two DESs investigated because of the acid–base interaction of the phosphine group. The thymol and L-menthol DES was selective towards levulinic acid (Sij = 9.3 ± 0.10, and the TOPO and L-menthol DES was selective towards FA (Sij = 2.1 ± 0.28).

pH Dependence of T2 for Hyperpolarizable 13C-Labelled Small Molecules Enables Spatially Resolved pH Measurement by Magnetic Resonance Imaging

Hyperpolarized ¹³C magnetic resonance imaging often uses spin-echo-based pulse sequences that are sensitive to the transverse relaxation time T₂. In this context, local T₂-changes might introduce a quantification bias to imaging biomarkers. Here, we investigated the pH dependence of the apparent transverse relaxation time constant (denoted here as T₂) of six ¹³C-labelled molecules. We obtained minimum and maximum T₂ values within pH 1–13 at 14.1 T: [1-¹³C]acetate (T_2,min = 2.1 s; T_2,max = 27.7 s), [1-¹³C]alanine (T_2,min = 0.6 s; T_2,max = 10.6 s), [1,4-¹³C₂]fumarate (T_2,min = 3.0 s; T_2,max = 18.9 s), [1-¹³C]lactate (T_2,min = 0.7 s; T_2,max = 12.6 s), [1-¹³C]pyruvate (T_2,min = 0.1 s; T_2,max = 18.7 s) and ¹³C-urea (T_2,min = 0.1 s; T_2,max = 0.1 s). At 7 T, T₂-variation in the physiological pH range (pH 6.8–7.8) was highest for [1-¹³C]pyruvate (ΔT₂ = 0.95 s/0.1pH) and [1-¹³C]acetate (ΔT₂ = 0.44 s/0.1pH). Concentration, salt concentration, and temperature alterations caused T₂ variations of up to 45.4% for [1-¹³C]acetate and 23.6% for [1-¹³C]pyruvate. For [1-¹³C]acetate, spatially resolved pH measurements using T₂-mapping were demonstrated with 1.6 pH units accuracy in vitro. A strong proton exchange-based pH dependence of T₂ suggests that pH alterations potentially influence signal strength for hyperpolarized ¹³C-acquisitions.

Ambient l-lactic acid crystal polymorphism

The second and third crystalline forms of lactic acid are described, yet along with the known structure, they together fail to reproduce any of the supramolecular aggregates that have long been observed in isotropic media.

Theory and algorithms for chiroptical properties and spectroscopies of aqueous systems

Chiroptical properties and spectroscopies are valuable tools to study chiral molecules and assign absolute configurations. The spectra that result from chiroptical measurements may be very rich and complex, and hide much of their information content. For this reason, the interplay between experiments and calculations is especially useful, provided that all relevant physico-chemical interactions that are present in the experimental sample are accurately modelled. The inherent difficulty associated to the calculation of chiral signals of systems in aqueous solutions requires the development of specific tools, able to account for the peculiarities of water-solute interactions, and especially its ability to form hydrogen bonds. In this perspective we discuss a multiscale approach, which we have developed and challenged to model the most used chiroptical techniques.

pH Dependence of T1 for 13 C-Labelled Small Molecules Commonly Used for Hyperpolarized Magnetic Resonance Imaging

Hyperpolarization is a method to enhance the nuclear magnetic resonance signal by up to five orders of magnitude. However, the hyperpolarized (HP) state is transient and decays with the spin-lattice relaxation time (T₁ ), which is on the order of a few tens of seconds. Here, we analyzed the pH-dependence of T₁ for commonly used HP ¹³ C-labelled small molecules such as acetate, alanine, fumarate, lactate, pyruvate, urea and zymonic acid. For instance, the T₁ of HP pyruvate is about 2.5 fold smaller at acidic pH (25 s, pH 1.7, B₀ =1 T) compared to pH close to physiological conditions (66 s, pH 7.3, B₀ =1 T). Our data shows that increasing hydronium ion concentrations shorten the T₁ of protonated carboxylic acids of most of the analyzed molecules except lactate. Furthermore it suggests that intermolecular hydrogen bonding at low pH can contribute to this T₁ shortening. In addition, enhanced proton exchange and chemical reactions at the pK_a appear to be detrimental for the HP-state.

Aggregation of lactic acid in cold rare-gas matrices and the link to solution: a matrix isolation-vibrational circular dichroism study

Crucial insight into lactic acid self-aggregation in solution is obtained by following its unique VCD spectral features in cold matrices.

An experimental and computational IR and hybrid DFT-D3 study of the conformations ofl-lactic and acrylic acid: new insight into the dehydration mechanism of lactic acid to acrylic acid

Effect of the intra-molecular H-bond ofl-lactic acid on its dehydration mechanism: IR and DFT-D3 study,

Solvation of 2-(hydroxymethyl)-2,5,7,8-tetramethyl-chroman-6-ol revealed by circular dichroism: a case of chromane helicity rule breaking

The primary goal of this work is to clarify why 2-(hydroxymethyl)-2,5,7,8-tetramethyl-chroman-6-ol {(S)-TMChM} deviates from the chromane helicity rule under solvent change. The rule, applicable to determining the absolute configuration of molecules containing the chromane chromophore, binds the sign of the 1Lb Cotton effect (CE) with the helicity of the dihydropyran ring. In case of TMChM, however, this CE exhibits extreme solvent dependence: it is negative in non-coordinating solvents and positive in coordinating ones, irrespective of the helicity of the heterocyclic ring. TD-DFT calculations using PCM and hybrid solvation models were performed to explain origin of this phenomenon. It turned out that the 1Lb CE sign directly depends on the position of the phenolic OH group at carbon atom C6 (OHC6). In the absence of interactions with solvents (as in CCl4 or nC6H14) or when a solvent plays proton donor role (as in CHCl3), the OHC6 lies in the phenyl plane and the 1Lb CE sign follows the P/M helicity rule. In contrast, in proton acceptor solvents, like DMSO, CH3OH or CH3CN, the OHC6 group is deflected from the phenyl plane, and the 1Lb CE sign of individual (S)-TMChM conformers depends on the sector in which the OHC6 is located. Thus, in solution, the 1Lb CE sign is an average over different orientations of the OHC6 group and can be positive (as in DMSO and CH3OH) or negative (as in CH3CN) which means that it does not follow the chromane helicity rule. The impact of OHC6 on the 1Lb CE sign and thus the conclusions for the stereochemistry of chromans are demonstrated here for the first time. Additionally, a comparison of experimental and simulated ECD spectra, supported by VCD data, allowed to determine the geometry of intermolecular clusters formed in different solvents.

Effective computational route towards vibrational optical activity spectra of chiral molecules in aqueous solution

A polarizable QM/MM approach to accurately compute the Vibrational Optical Activity (VOA) spectra of chiral systems is proposed and applied to aqueous solutions of (l)-methyl lactate and (S)-glycidol.

On the aggregation of bilirubinoids in solution as evidenced by VCD and ECD spectroscopy and DFT calculations

Vibrational and electronic circular dichroism (VCD and ECD) spectra of 3 optically active bilirubin analogs with propionic acid groups replaced by (1) 1-(S)-methylpropyl groups, (2) 3-acetoxy-1-(S)-methylpropyl groups, and (3) 1-(S)-2-(R)-dimethyl-2-(methoxycarbonyl)ethyl groups have been recorded at different concentrations in chloroform. The aliphatic chains attached to C-8 and C-12 of the 3 chosen mesobilirubins were modified so as to possess no OH group. The variation of the VCD spectra with concentration is consistent with the formation of dimers at high concentration. Density functional theory and time-dependent density functional theory calculations on monomeric and dimeric forms support such a conclusion. Comparing with previous VCD (ECD) and IR (UV) studies of other mesobilirubin molecules, it is concluded that here, the key feature for aggregation is the missing OH groups on the propionic acid chains. The latter, in synergy with the polar groups of lactam moieties, appear to be involved in intramolecular phenomena and thus favor monomeric forms. Investigation of ECD and UV spectra of the same compounds in mixed DMSO/chloroform solutions provide further clues to the proposed picture.

Double Hydrogen Bonding between Side Chain Carboxyl Groups in Aqueous Solutions of Poly (β-L-Malic Acid): Implication for the Evolutionary Origin of Nucleic Acids

The RNA world hypothesis holds that in the evolutionary events that led to the emergence of life RNA preceded proteins and DNA and is supported by the ability of RNA to act as both a genetic polymer and a catalyst. On the other hand, biosynthesis of nucleic acids requires a large number of enzymes and chemical synthesis of RNA under presumed prebiotic conditions is complicated and requires many sequential steps. These observations suggest that biosynthesis of RNA is the end product of a long evolutionary process. If so, what was the original polymer from which RNA and DNA evolved? In most syntheses of simpler RNA or DNA analogs, the D-ribose phosphate polymer backbone is altered and the purine and pyrimidine bases are retained for hydrogen bonding between complementary base pairs. However, the bases are themselves products of complex biosynthetic pathways and hence they too may have evolved from simpler polymer side chains that had the ability to form hydrogen bonds. We hypothesize that the earliest evolutionary predecessor of nucleic acids was the simple linear polyester, poly (β-D-malic acid), for which the carboxyl side chains could form double hydrogen bonds. In this study, we show that in accord with this hypothesis a closely related polyester, poly (β-L-malic acid), uses carboxyl side chains to form robust intramolecular double hydrogen bonds in moderately acidic solution.

Solvation of a chiral carboxylic acid: effects of hydrogen bonding on the IR and VCD spectra of α-methoxyphenylacetic acid

Taking the title compound as a representative example of a chiral carboxylic acid, we investigate how its VCD spectral pattern is affected by hydrogen bonding of different solvents.

Vibrational optical activity as probe for intermolecular interactions

A detailed VCD spectroscopic analysis of well-selected chiral model systems can give valuable and unprecedented insights into intermolecular interactions such as solvation or reactant–substrate binding in catalysis.

Effective Fully Polarizable QM/MM Approach To Model Vibrational Circular Dichroism Spectra of Systems in Aqueous Solution

We propose a methodology, based on the combination of classical Molecular Dynamics (MD) simulations with a fully polarizable Quantum Mechanical (QM)/Molecular Mechanics (MM)/Polarizable Continuum Model (PCM) Hamiltonian, to calculate Vibrational Circular Dichroism (VCD) spectra of chiral systems in aqueous solution. Polarization effects are included in the MM force field by exploiting an approach based on Fluctuating Charges (FQ). By performing the MD, the description of the solvating environment is enriched by taking into account the dynamical aspects of the solute-solvent interactions. On the other hand, the QM/FQ/PCM calculation of the VCD spectrum ensures an accurate description of the electronic density of the solute and a proper account for the specific interactions in solution. The application of our approach to (R)-methyloxirane and (l)-alanine in aqueous solution gives calculated spectra in remarkable agreement with their experimental counterparts and a substantial improvement with respect to the same spectra calculated with the PCM.

The Clusters-in-a-Liquid Approach for Solvation: New Insights from the Conformer Specific Gas Phase Spectroscopy and Vibrational Optical Activity Spectroscopy

Vibrational optical activity spectroscopies, namely vibrational circular dichroism (VCD) and Raman optical activity (ROA), have been emerged in the past decade as powerful spectroscopic tools for stereochemical information of a wide range of chiral compounds in solution directly. More recently, their applications in unveiling solvent effects, especially those associated with water solvent, have been explored. In this review article, we first select a few examples to demonstrate the unique sensitivity of VCD spectral signatures to both bulk solvent effects and explicit hydrogen-bonding interactions in solution. Second, we discuss the induced solvent chirality, or chiral transfer, VCD spectral features observed in the water bending band region in detail. From these chirality transfer spectral data, the related conformer specific gas phase spectroscopic studies of small chiral hydration clusters, and the associated matrix isolation VCD experiments of hydrogen-bonded complexes in cold rare gas matrices, a general picture of solvation in aqueous solution emerges. In such an aqueous solution, some small chiral hydration clusters, rather than the chiral solutes themselves, are the dominant species and are the ones that contribute mainly to the experimentally observed VCD features. We then review a series of VCD studies of amino acids and their derivatives in aqueous solution under different pHs to emphasize the importance of the inclusion of the bulk solvent effects. These experimental data and the associated theoretical analyses are the foundation for the proposed "clusters-in-a-liquid" approach to account for solvent effects effectively. We present several approaches to identify and build such representative chiral hydration clusters. Recent studies which applied molecular dynamics simulations and the subsequent snapshot averaging approach to generate the ROA, VCD, electronic CD, and optical rotatory dispersion spectra are also reviewed. Challenges associated with the molecular dynamics snapshot approach are discussed and the successes of the seemingly random "ad hoc explicit solvation" reported before are also explained. To further test and improve the "clusters-in-a-liquid" model in practice, future work in terms of conformer specific gas phase spectroscopy of sequential solvation of a chiral solute, matrix isolation VCD measurements of small chiral hydration clusters, and more sophisticated models for the bulk solvent effects would be highly valuable.

Simulation of Raman optical activity of multi-component monosaccharide samples

Determination of the saccharide structure in solution is a laborious process that can be significantly enhanced by chiral optical spectroscopies.

Assignment of absolute stereostructures through quantum mechanics electronic and vibrational circular dichroism calculations

Elucidation of absolute configuration of chiral molecules including structurally complex natural products remains a challenging problem in organic chemistry. A reliable method for assigning the absolute stereostructure is to combine the experimental circular dichroism (CD) techniques such as electronic and vibrational CD (ECD and VCD), with quantum mechanics (QM) ECD and VCD calculations. The traditional QM methods as well as their continuing developments make them more applicable with accuracy. Taking some chiral natural products with diverse conformations as examples, this review describes the basic concepts and new developments of QM approaches for ECD and VCD calculations in solution and solid states.

Raman spectroscopic evidence of low temperature stability of D,L-glycolic and L-(+)-lactic acid crystals

Raman and infrared spectra of polycrystalline D,L-glycolic and L-(+) lactic acid are presented and assigned both by an ab initio calculation of normal modes of free conformers and by self-consistent-charge density-functional-theory computational program DFTB+. Temperature dependent Raman spectra from 295 K to 10 K reveal great stability of crystal lattices, since no soft modes and no band splittings that could be attributed to changes of the number of molecules per unit cell were observed. A semiempirical calculation with GULP program was used to estimate the strength of hydrogen bonds in crystals: in glycolic acid they have energies of -0.337 eV/mol, -0.329 eV/mol, -0.262 eV/mol and -0.242 eV/mol, while in lactic acid two hydrogen bonds have energies of -0.283 eV/mol and -0.202 eV/mol.

The Hypothesis that the Genetic Code Originated in Coupled Synthesis of Proteins and the Evolutionary Predecessors of Nucleic Acids in Primitive Cells

Although analysis of the genetic code has allowed explanations for its evolution to be proposed, little evidence exists in biochemistry and molecular biology to offer an explanation for the origin of the genetic code. In particular, two features of biology make the origin of the genetic code difficult to understand. First, nucleic acids are highly complicated polymers requiring numerous enzymes for biosynthesis. Secondly, proteins have a simple backbone with a set of 20 different amino acid side chains synthesized by a highly complicated ribosomal process in which mRNA sequences are read in triplets. Apparently, both nucleic acid and protein syntheses have extensive evolutionary histories. Supporting these processes is a complex metabolism and at the hub of metabolism are the carboxylic acid cycles. This paper advances the hypothesis that the earliest predecessor of the nucleic acids was a β-linked polyester made from malic acid, a highly conserved metabolite in the carboxylic acid cycles. In the β-linked polyester, the side chains are carboxylic acid groups capable of forming interstrand double hydrogen bonds. Evolution of the nucleic acids involved changes to the backbone and side chain of poly(β-d-malic acid). Conversion of the side chain carboxylic acid into a carboxamide or a longer side chain bearing a carboxamide group, allowed information polymers to form amide pairs between polyester chains. Aminoacylation of the hydroxyl groups of malic acid and its derivatives with simple amino acids such as glycine and alanine allowed coupling of polyester synthesis and protein synthesis. Use of polypeptides containing glycine and l-alanine for activation of two different monomers with either glycine or l-alanine allowed simple coded autocatalytic synthesis of polyesters and polypeptides and established the first genetic code. A primitive cell capable of supporting electron transport, thioester synthesis, reduction reactions, and synthesis of polyesters and polypeptides is proposed. The cell consists of an iron-sulfide particle enclosed by tholin, a heterogeneous organic material that is produced by Miller-Urey type experiments that simulate conditions on the early Earth. As the synthesis of nucleic acids evolved from β-linked polyesters, the singlet coding system for replication evolved into a four nucleotide/four amino acid process (AMP = aspartic acid, GMP = glycine, UMP = valine, CMP = alanine) and then into the triplet ribosomal process that permitted multiple copies of protein to be synthesized independent of replication. This hypothesis reconciles the “genetics first” and “metabolism first” approaches to the origin of life and explains why there are four bases in the genetic alphabet.

Systematic approach to conformational sampling for assigning absolute configuration using vibrational circular dichroism

Systematic methods that speed-up the assignment of absolute configuration using vibrational circular dichrosim (VCD) and simplify its usage will advance this technique into a robust platform technology. Applying VCD to pharmaceutically relevant compounds has been handled in an ad hoc fashion, relying on fragment analysis and technical shortcuts to reduce the computational time required. We leverage a large computational infrastructure to provide adequate conformational exploration which enables an accurate assignment of absolute configuration. We describe a systematic approach for rapid calculation of VCD/IR spectra and comparison with corresponding measured spectra and apply this approach to assign the correct stereochemistry of nine test cases. We suggest moving away from the fragment approach when making VCD assignments. In addition to enabling faster and more reliable VCD assignments of absolute configuration, the ability to rapidly explore conformational space and sample conformations of complex molecules will have applicability in other areas of drug discovery.