The Stability of Hydrogen-Bonded Ion-Pair Complex Unexpectedly Increases with Increasing Solvent Polarity.

The generally observed decrease of the electrostatic energy in the complex with increasing solvent polarity has led to the assumption that the stability of the complexes with ion-pair hydrogen bonds decreases with increasing solvent polarity. Besides, the smaller solvent-accessible surface area (SASA) of the complex in comparison with the isolated subsystems results in a smaller solvation energy of the latter, leading to a destabilization of the complex in the solvent compared to the gas phase. In our study, which combines Nuclear Magnetic Resonance, Infrared Spectroscopy experiments, quantum chemical calculations, and molecular dynamics (MD) simulations, we question the general validity of this statement. We demonstrate that the binding free energy of the ion-pair hydrogen-bonded complex between 2-fluoropropionic acid and n-butylamine (CH3CHFCOO-…NH3But+) increases with increased solvent polarity. This phenomenon is rationalized by a substantial charge transfer between the subsystems that constitute the ion-pair hydrogen-bonded complex. This unexpected finding introduces a new perspective to our understanding of solvation dynamics, emphasizing the interplay between solvent polarity and molecular stability within hydrogen-bonded systems.

Induced Chirality in Canthaxanthin Aggregates Reveals Multiple Levels of Supramolecular Organization.

Carotenoids tend to form supramolecular aggregates via non-covalent interactions where the chirality of individual molecules is amplified to the macroscopic level. We show that this can also be achieved for non-chiral carotenoid monomers interacting with polysaccharides. The chirality induction in canthaxanthin (CAX), caused by heparin (HP) and hyaluronic acid (HA), was monitored by chiroptical spectroscopy. Electronic circular dichroism (ECD) and Raman optical activity (ROA) spectra indicated the presence of multiple carotenoid formations, such as H- and J-type aggregates. This is consistent with molecular dynamics (MD) and density functional theory (DFT) simulations of the supramolecular structures and their spectroscopic response.

Conformations and hydration of halopropionic acids studied by molecular dynamics and Raman optical activity.

Chiral 2-halopropionic acids and their derivatives were synthesized and their properties studied computationally using Raman and Raman optical activity (ROA) spectroscopy. For neat acids present as liquids small amount of water led to significant changes in the spectra, resulting even to flipping of some ROA band signs. We find this interesting for the role water plays in interpretation of vibrational optical activity spectra of biomolecules. Analysis of the results shows that when the water is present, it can change ROA band signs due to the changes in acidobasic equilibrium. Corresponding esters without acidic hydrogens do not exhibit such effects.

What are the minimal folding seeds in proteins? Experimental and theoretical assessment of secondary structure propensities of small peptide fragments.

Certain peptide sequences, some of them as short as amino acid triplets, are significantly overpopulated in specific secondary structure motifs in folded protein structures. For example, 74% of the EAM triplet is found in α-helices, and only 3% occurs in the extended parts of proteins (typically ß-sheets). In contrast, other triplets (such as VIV and IYI) appear almost exclusively in extended parts (79% and 69%, respectively). In order to determine whether such preferences are structurally encoded in a particular peptide fragment or appear only at the level of a complex protein structure, NMR, VCD, and ECD experiments were carried out on selected tripeptides: EAM (denoted as pro-'α-helical' in proteins), KAM(α), ALA(α), DIC(α), EKF(α), IYI(pro-ß-sheet or more generally, pro-extended), and VIV(ß), and the reference α-helical CATWEAMEKCK undecapeptide. The experimental data were in very good agreement with extensive quantum mechanical conformational sampling. Altogether, we clearly showed that the pro-helical vs. pro-extended propensities start to emerge already at the level of tripeptides and can be fully developed at longer sequences. We postulate that certain short peptide sequences can be considered minimal "folding seeds". Admittedly, the inherent secondary structure propensity can be overruled by the large intramolecular interaction energies within the folded and compact protein structures. Still, the correlation of experimental and computational data presented herein suggests that the secondary structure propensity should be considered as one of the key factors that may lead to understanding the underlying physico-chemical principles of protein structure and folding from the first principles.

Molecular Vibrations in Chiral Europium Complexes Revealed by Near-Infrared Raman Optical Activity.

Raman optical activity (ROA) is commonly measured with green light (532 nm) excitation. At this wavelength, however, Raman scattering of europium complexes is masked by circularly polarized luminescence (CPL). This can be avoided using near-infrared (near-IR, 785 nm) laser excitation, as demonstrated here by Raman and ROA spectra of three chiral europium complexes derived from camphor. Since luminescence is strongly suppressed, many vibrational bands can be detected. They carry a wealth of structural information about the ligand and the metal core, and can be interpreted based on density functional theory (DFT) simulations of the spectra. For example, jointly with ROA experimental data, the simulations make it possible to determine absolute configuration of chiral lanthanide compounds in solution.

Combination of Resonance and Non-Resonance Chiral Raman Scattering in a Cobalt(III) Complex.

Resonance Raman optical activity (RROA) spectra with high sensitivity reveal details on molecular structure, chirality, and excited electronic properties. Despite the difficulty of the measurements, the recorded data for the Co(III) complex with S,S-N,N-ethylenediaminedisuccinic acid are of exceptional quality and, coupled with the theory, spectacularly document the molecular behavior in resonance. This includes a huge enhancement of the chiral scattering, contribution of the antisymmetric polarizabilities to the signal, and the Herzberg-Teller effect significantly shaping the spectra. The chiral component is by about one order of magnitude bigger than for an analogous aluminum complex. The band assignment and intensity profile were confirmed by simulations based on density functional and vibronic theories. The resonance was attributed to the S0 →S3 transition, with the strongest signal enhancement of Raman and ROA spectral bands below about 800 cm-1 . For higher wavenumbers, other excited electronic states contribute to the scattering in a less resonant way. RROA spectroscopy thus appears as a unique tool to study the structure and electronic states of absorbing molecules in analytical chemistry, biology, and material science.

Molecular Properties of 3d and 4f Coordination Compounds Deciphered by Raman Optical Activity Spectroscopy.

Molecular properties of coordination compounds can be efficiently studied by vibrational spectroscopy. The scope of Raman spectroscopy has been greatly enhanced by the introduction of Raman optical activity (ROA) sensitive to chirality. The present review describes some of its recent applications to study the coordination compounds. 3d and 4f metal complexes often absorb the excitation light, or exhibit luminescence. Therefore, effects caused in ROA spectra by electronic circular dichroism (ECD) and circularly polarized luminescence (CPL) must be taken into consideration.In 3d metal complexes ECD and circularly-polarized Raman scattering compete with the resonance ROA (RROA) signal. Pure RROA spectrum can thus be obtained by subtracting the so-called ECD-Raman component. CPL is frequently encountered in 4f systems. While it can mask the ROA spectra, it is useful to study molecular structure. These electronic effects can be reduced by using near-infrared excitation although vibrational ROA signal is much weaker compared to the usual green laser excitation scenario. The ROA methodology is thus complex, but capable of providing unique information about the molecules of interests and their interaction with light.

Gold nanoshells with magnetic cores and a urea-based receptor for SERS sensing of fluoride anions: experimental and computational study.

The study demonstrates that a combination of plasmonic nanostructures and artificial receptors can be applied for sensing small molecular species. Gold nanoshells containing magnetic cores are used as the SERS-active substrates, which opens the way for the development of multimodal contrast agents with applicability extended to sensing or for the separation of analytes by magnetic solid-phase extraction. Disubstituted ureas forming hydrogen-bonded complexes with certain anions can be employed as molecular sensors. In this case study, gold nanoshells with silica-coated Mn-Zn ferrite cores were prepared by a multistep procedure. The nanoshells were co-functionalized with an N-(4-mercaptophenyl)-N'-(4-nitrophenyl)urea sensor synthesized directly on the gold surface, and with 4-nitrothiophenol, which is adopted as an internal standard. SERS measurements were carried out with acetonitrile solutions of tetrabutylammonium fluoride (Bu4NF) over a concentration range of 10-10-10-1 mol L-1. The spectral response of the sensor is dependent on the fluoride concentration in the range of 10-5-10-1 mol L-1. To investigate further the SERS mechanism, a model sensor, N-(4-bromophenyl)-N'-(4-nitrophenyl)urea, was synthesized and used in Raman spectroscopy with solutions of Bu4NF, up to a molar ratio of 1 : 20. The spectra and the interactions between the sensors and fluoride anions were also studied by extensive DFT computations.

Rotational circular dichroism of diamagnetic and paramagnetic molecules. A computational study.

Rotational circular dichroism (RCD) has not been observed yet, but it is expected to deliver information about chiral molecules useful in many branches of chemistry. In the past, rather weak RCD intensities were predicted for model diamagnetic molecules and a limited number of rotational transitions. Here, we review quantum-mechanical foundations and simulate entire spectral profiles, including larger molecules, open-shell molecular radicals, and high-momentum rotational bands. Contribution of the electric quadrupolar moment was considered, but it turned out that it does not contribute to field-free RCD. Two conformers of a model dipeptide provided clearly distinct spectra. The dissymmetry Kuhn parameter gK predicted for the diamagnetic molecules even for high-J transitions rarely exceeded 10-5, and the simulated RCD spectra were often biased to one sign. In the radicals, the coupling of the rotational angular momentum with the spin for some transitions raised gK to about 10-2, and the RCD pattern was more conservative. In the resultant spectra, many transitions had negligible intensities due to small populations of the involved states, and a convolution with a spectral function made the typical RCD/absorption ratios about 100-times smaller (gK ∼ 10-4). This is still comparable with values typical for electronic or vibrational circular dichroism, and paramagnetic RCD is thus likely to be measurable relatively easily.

Monitoring Conformation and Protonation States of Glutathione by Raman Optical Activity and Molecular Dynamics.

Glutathione (GSH) is a common antioxidant and its biological activity depends on the conformation and protonation state. We used molecular dynamics, Raman and Raman optical activity (ROA) spectroscopies to investigate GSH structural changes in a broad pH range. Factor analysis of the spectra provided protonation constants (2.05, 3.45, 8.62, 9.41) in good agreement with previously published values. Following the analysis, spectra of differently protonated forms were obtained by extrapolation. The complete deprotonation of the thiol group above pH 11 was clearly visible in the spectra; however, many spectral features did not change much with pH. Experimental spectra at various pH values were decomposed into the simulated ones, which allowed us to study the conformer populations and quality of molecular dynamics (MD). According to this combined ROA/MD analysis conformation of the GSH backbone is affected by the pH changes only in a limited way. The combination of ROA with the computations thus has the potential to improve the MD force field and obtain more accurate populations of the conformer species. The methodology can be used for any molecule, but for a more detailed insight better computational techniques are needed in the future.

Glucagon-like peptide 1 aggregates into low-molecular-weight oligomers off-pathway to fibrillation.

The physical stability of peptide-based drugs is of great interest to the pharmaceutical industry. Glucagon-like peptide 1 (GLP-1) is a 31-amino acid peptide hormone, the analogs of which are frequently used in the treatment of type 2 diabetes. We investigated the physical stability of GLP-1 and its C-terminal amide derivative, GLP-1-Am, both of which aggregate into amyloid fibrils. While off-pathway oligomers have been proposed to explain the unusual aggregation kinetics observed previously for GLP-1 under specific conditions, these oligomers have not been studied in any detail. Such states are important as they may represent potential sources of cytotoxicity and immunogenicity. Here, we identified and isolated stable, low-molecular-weight oligomers of GLP-1 and GLP-1-Am, using size-exclusion chromatography. Under the conditions studied, isolated oligomers were shown to be resistant to fibrillation or dissociation. These oligomers contain between two and five polypeptide chains and they have a highly disordered structure as indicated by a variety of spectroscopic techniques. They are highly stable with respect to time, temperature, or agitation despite their noncovalent character, which was established using liquid chromatography-mass spectrometry and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. These results provide evidence of stable, low-molecular-weight oligomers that are formed by an off-pathway mechanism which competes with amyloid fibril formation.

Molecular dynamics and Raman optical activity spectra reveal nucleotide conformation ratios in solution.

Nucleotide conformational flexibility affects their biological functions. Although the spectroscopy of Raman optical activity (ROA) is well suited to structural analyses in aqueous solutions, the link between the spectral shape and the nucleotide geometry is not fully understood. We recorded the Raman and ROA spectra of model nucleotides (rAMP, rGMP, rCMP, and dTMP) and interpreted them on the basis of molecular dynamics (MD) combined with density functional theory (DFT). The relation between the sugar puckering, base conformation and spectral intensities is discussed. Hydrogen bonds between the sugar's C3' hydroxyl and the phosphate groups were found to be important for the sugar puckering. The simulated spectra correlated well with the experimental data and provided an understanding of the dependence of the spectral shapes on conformational dynamics. Most of the strongest spectral bands could be assigned to vibrational molecular motions. Decomposition of the experimental spectra into calculated subspectra based on arbitrary maps of free energies provided experimental conformer populations, which could be used to verify and improve the MD predictions. The analyses indicate some flaws of common MD force fields, such as being unable to describe the fine conformer distribution. Also the accuracy of conformer populations obtained from the spectroscopic data depends on the simulations, improvement of which is desirable for gaining a more detailed insight in the future. Improvement of the spectroscopic and computational methodology for nucleotides also provides opportunities for its application to larger nucleic acids.

Aggregation-aided SERS: Selective detection of arsenic by surface-enhanced Raman spectroscopy facilitated by colloid cross-linking.

Arsenic of natural or industrial origin often occurs in water and makes it impotable. Due to its high toxicity, very sensitive detection is required. In the present study an ultra-sensitive arsenite (As3+) sensing is reported, based on aggregation-aided surface-enhanced Raman scattering (AA-SERS) of modified silver colloids. SERS intensity of mercapto-compounds attached to the colloidal silver nanoparticles surface is greatly increased in the presence of arsenic. Colloid aggregation is facilitated by cross-linking; a meshwork consisting of arsenic atoms and glutathione bridges is formed, as indicated by UV-Vis absorption spectroscopy, TEM and Raman imaging. The best 2-mercaptopyridine reporter molecule makes it possible to directly detect As3+ at concentrations as low as 0.5 ppb, which is better than achieved by the SERS technique so far.

Unexpected Strengthening of the H-Bond Complexes in a Polar Solvent Due to a More Efficient Solvation of the Complex Compared to Isolated Monomers.

It is generally assumed that hydrogen-bonded complexes are less stable in solvents than in the gas phase and that their stability decreases with increasing solvent polarity. This assumption is based on the size of the area available to the solvent, which is always smaller in the complex compared to the subsystems, thereby reducing the solvation energy. This reduction prevails over the amplification of the electrostatic hydrogen bond by the polar solvent. In this work, we show, using experimental IR spectroscopy and DFT calculations, that there are hydrogen-bonded complexes whose stability becomes greater with increasing solvent polarity. The explanation for this surprising stabilization is based on the analysis of the charge redistribution in the complex leading to increase of its dipole moment and solvation energy. Constrained DFT calculations have shown a dominant role of charge transfer over polarization effects for dipole moment and solvation energy.

Anharmonic Vibrational Raman Optical Activity of Methyloxirane: Theory and Experiment Pushed to the Limits.

Combining Raman scattering and Raman optical activity (ROA) with computer simulations reveals fine structural and physicochemical properties of chiral molecules. Traditionally, the region of interest comprised fundamental transitions within 200-1800 cm-1. Only recently, nonfundamental bands could be observed as well. However, theoretical tools able to match the observed spectral features and thus assist their assignment are rather scarce. In this work, we present an accurate and simple protocol based on a three-quanta anharmonic perturbative approach that is fully fit to interpret the observed signals of methyloxirane within 150-4500 cm-1. An unprecedented agreement even for the low-intensity combination and overtone transitions has been achieved, showing that anharmonic Raman and ROA spectroscopies can be valuable tools to understand vibrations of chiral molecules or to calibrate computational models.

Low-frequency Raman optical activity provides insight into the structure of chiral liquids.

Vibrational frequencies of modes involving intermolecular motions in liquids are relatively small, in the Raman scattering close to the excitation frequency, and the bands may merge into a diverging uninterpretable signal. Raman optical activity (ROA) spectral shapes in this region, however, are structured more and may better reflect the nature of the studied systems. To understand the origin of the signal and its relation to the molecules, ROA spectra of six chiral neat liquids are recorded and analyzed on the basis of molecular dynamics and density functional theory computations. The theory of Raman scattering of liquids is discussed and adapted for modeling based on clusters and periodic boundary conditions. A plain cluster approach is compared to a crystal-like model. The results show that the low-frequency optical activity can be reliably modeled and related to the structure. However, momentary arrangement of molecules leads to large variations of optical activity, and a relatively large number of geometries need to be averaged for accurate simulations. The intermolecular modes are intertwined with intramolecular ones and start to dominate as the frequency goes down. The low-frequency ROA signal thus reflects the chemical composition and coupled with the modeling it provides a welcome means to study the structure and interactions of chiral liquids.

Structure of Zinc and Nickel Histidine Complexes in Solution Revealed by Molecular Dynamics and Raman Optical Activity.

The histidine residue has an exceptional affinity for metals, but solution structure of its complexes are difficult to study. For zinc and nickel complexes, Raman and Raman optical activity (ROA) spectroscopy methods to investigate the link between spectral shapes and the geometry were used. The spectra were recorded and interpreted on the basis of ionic equilibria, molecular dynamics, ab initio molecular dynamics, and density functional theory. For zwitterionic histidine the dominant tautomer was determined by the decomposition of experimental spectra into calculated subspectra. An octahedral structure was found to prevail for the ZnHis2 complex in solution, in contrast to a tetrahedral arrangement in the crystal phase. The solution geometry of NiHis2 is more similar to the octahedral structure found by X-ray. The Raman and ROA structural determinations of metal complexes are dependent on extensive computations, but reveal unique information about the studied systems.

Photochemical synthesis of pink silver and its use for monitoring peptide nitration via surface enhanced Raman spectroscopy (SERS).

Oxidative stress may cause extended tyrosine posttranslational modifications of peptides and proteins. The 3-nitro-L-tyrosine (Nit), which is typically formed, affects protein behavior during neurodegenerative processes, such as Alzheimer's and Parkinson's diseases. Such metabolic products may be conveniently detected at very low concentrations by surface enhanced Raman spectroscopy (SERS). Previously, we have explored the SERS detection of the Nit NO2 bending vibrational bands in a presence of hydrogen chloride (Niederhafner et al., Amino Acids 53:517-532, 2021, ibid). In this article, we describe performance of a new SERS substrate, "pink silver", synthesized photochemically. It provides SERS even without the HCl induction, and the acid further decreases the detection limit about 9 times. Strong SERS bands were observed in the asymmetric (1550-1475 cm-1) and symmetric (1360-1290 cm-1) NO stretching in the NO2 group. The bending vibration was relatively weak, but appeared stronger when HCl was added. The band assignments were supported by density functional theory modeling.

Resolving Resonant Electronic States in Chiral Metal Complexes by Raman Optical Activity Spectroscopy.

Chiral metal complexes exhibit rich photophysical properties and are important for applications ranging from biosensing to photocatalysis. We present a combined experimental and computational approach leading to information about energies and transition moments of excited electronic states, documented on two chiral metal complexes. The experimental protocol for measurement of the resonance Raman optical activity comprises multiple techniques, i.e., absorption, circular dichroism, and polarized and differential Raman scattering. An accurate formula for subtraction of the interfering circular dichroism/polarized Raman scattering effect is given. An analysis of the spectra based on density functional theory calculations unveils the geometric and electronic structures of the molecules. Such insight into molecular electronic states of chromophores may be useful for understanding and tuning photochemical properties of metal-containing complexes, biomolecules, and supramolecules.

The stability of covalent dative bond significantly increases with increasing solvent polarity.

It is generally expected that a solvent has only marginal effect on the stability of a covalent bond. In this work, we present a combined computational and experimental study showing a surprising stabilization of the covalent/dative bond in Me3NBH3 complex with increasing solvent polarity. The results show that for a given complex, its stability correlates with the strength of the bond. Notably, the trends in calculated changes of binding (free) energies, observed with increasing solvent polarity, match the differences in the solvation energies (ΔEsolv) of the complex and isolated fragments. Furthermore, the studies performed on the set of the dative complexes, with different atoms involved in the bond, show a linear correlation between the changes of binding free energies and ΔEsolv. The observed data indicate that the ionic part of the combined ionic-covalent character of the bond is responsible for the stabilizing effects of solvents.