Infrared spectroscopy and structure of photochemically protonated biomolecules in the gas phase: a noradrenaline analogue, lysine and alanyl alanine

Cryogenic Ion Vibrational Spectroscopy of Protonated Valine: Messenger Tag Effects

We report the infrared photodissociation spectrum of tagged protonated valine in the range 1000-1900 cm-1, prepared in a cryogenic ion trap. Comparison of experimental results with calculated infrared spectra based on density functional theory shows that the hydroxyl group of the carboxylic acid functionality and the protonated amine group adopt a trans configuration. Nitrogen and methane molecules were used as messenger tags with optimal tagging temperatures of 30 K for N2 and 60 K for CH4. While the calculated infrared spectra of the tagged ion suggest only a weak influence of the messenger tag on the frequency positions of ValH+, the measured intensities for N2-tagged ValH+ appear strongly suppressed for all but the highest frequency feature at 1773 cm-1. We trace this behavior to the binding energy of the N2 tag, which is significantly higher than that of CH4, based on density functional and coupled cluster calculations and rate estimates for photoinduced unimolecular dissociation from statistical theory.

Alleviation of albumin glycation-induced diabetic cardiomyopathy by L-Arginine: Insights into Nrf-2 signaling

In hyperglycemia, accelerated glycation and oxidative stress give rise to many diabetic complications, such as diabetic cardiomyopathy (DCM). Glycated human serum albumin (GHSA) has disturbed structural integrity and hampered functional capabilities. When GHSA accumulates around cardiac cells, Nrf-2 is dysregulated, aiding oxidative stress. L-Arginine (L-Arg) is prescribed to patients with diabetes and cardiovascular diseases. This research contributes to the mechanistic insights on antiglycation and antioxidant potential of L-Arg in alleviating DCM. HSA was glycated with methylglyoxal in the presence of L-Arg (20-640 mM). Structural and functional modifications of HSA were studied. L-Arg and HSA, GHSA interactions, and thermodynamics were determined by steady-state fluorescence. H9c2 cardiomyocytes were given treatments of GHSA-L-Arg along with the inhibitor of the receptor of AGEs. Cellular antioxidant levels, detoxification enzyme activities were measured. Gene, protein expressions, and immunofluorescence data examined the activation and nuclear translocation of Nrf-2 during glycation and oxidative stress. L-Arg protected HSA from glycation-induced structural and functional modifications. The binding affinity of L-Arg was more towards HSA (104 M-1). L-Arg, specifically at lower concentration (20 mM), upregulated Nrf-2 gene, protein expressions and facilitated its nuclear translocation by activating Nrf-2 signaling. The study concluded that L-Arg can be of therapeutic advantage in glycation-induced DCM and associated oxidative stress.

Protective effect of colchicine on albumin glycation and cellular oxidative stress: Insights into diabetic cardiomyopathy

The present work elucidates the role of colchicine (COL) on albumin glycation and cellular oxidative stress in diabetic cardiomyopathy (DCM). Human serum albumin (HSA) was glycated with methylglyoxal in the presence of COL (2.5, 3.75, and 5 µM), whereas positive and negative control samples were maintained separately. The effects of COL on HSA glycation, structural and functional modifications in glycated HSA were analyzed using different spectroscopical and fluorescence techniques. Increased fructosamine, carbonyl, and pentosidine formation in glycated HSA samples were inhibited in the presence of COL. Structural conformation of HSA and glycated HSA samples was examined by field emission scanning electron microscopy, circular dichroism, Fourier transform infrared, and proton nuclear magnetic resonance analyses, where COL maintained both secondary and tertiary structures of HSA against glycation. Functional marker assays included ABTS•+ radical scavenging and total antioxidant activities, advanced oxidative protein product formation, and turbidimetry, which showed preserved functional properties of glycated HSA in COL-containing samples. Afterward, rat cardiomyoblast (H9c2 cell line) was treated with glycated HSA-COL complex (400 μg/mL) for examining various cellular antioxidants (nitric oxide, catalase, superoxide dismutase, and glutathione) and detoxification enzymes (aldose reductase, glyoxalase I, and II) levels. All three concentrations of COL exhibited effective anti-glycation properties, enhanced cellular antioxidant levels, and detoxification enzyme activities. The report comprehensively analyzes the potential anti-glycation and properties of COL during its initial assessment.

Synthesis, spectral, DFT calculation, antimicrobial, antioxidant, DNA/BSA binding and molecular docking studies of bio-pharmacologically active pyrimidine appended Cu(II) and Zn(II) complexes

A new pyrimidine derivative Schiff base (HL) [HL = 2-((4-amino-6-chloropyrimidin-2-ylimino)methyl)-4-nitrophenol] has been synthesized using 2,6-diamino-4-chloropyrimidine and 5-nitrosalicylaldehyde. Transition metal complexes of Cu(II) and Zn(II) complexes [CuL(OAc)] (1), [ZnL(OAc)] (2) are prepared with HL/metal(II) acetate with molar ratio of 1:1. The Schiff base (HL) and the complexes 1 and 2 are evaluated by UV-Visible, 1H-NMR, FT-IR, EI-MS and ESR spectral techniques. Complexes 1 and 2 are confirmed as square planar geometry. Electrochemical studies of the complexes 1 and 2 are used to analyse the quasi reversible process. Density Functional Theory (DFT) using the B3LYP/6-31++G(d,p) level basis set was used to get the optimised geometry and non-linear optical properties. The complexes 1 and 2 are good antimicrobial agents than Schiff base (HL). The interactions of the HL and complexes 1 and 2 with Calf Thymus (CT) DNA are investigated by electronic absorption methods and viscosity measurements. Various molecular spectroscopy techniques, such as UV absorption and fluorescence, were used to explore the mechanism of interaction between the BSA and the ligand HL and complexes 1 & 2 under physiological settings. Complexes 1 and 2 are act as potential antioxidants than free Schiff base (HL) by DPPH radical scavenging assay. Furthermore, the purpose of the molecular docking studies was to better understand how metal complexes interact with biomolecules (CT-DNA and BSA). From these biological analyses, complex 1 acts as good intercalator with CT DNA & BSA and potent antioxidant with DPPH radical than complex 2.Communicated by Ramaswamy H. Sarma.

Cation-π Interactions between a Noble Metal and a Polyfunctional Aromatic Ligand: Ag+ (benzylamine)

The structure of an isolated Ag+ (benzylamine) complex is investigated by infrared multiple photon dissociation (IRMPD) spectroscopy complemented with quantum chemical calculations of candidate geometries and their vibrational spectra, aiming to ascertain the role of competing cation-N and cation-π interactions potentially offered by the polyfunctional ligand. The IRMPD spectrum has been recorded in the 800-1800 cm-1 fingerprint range using the IR free electron laser beamline coupled with an FT-ICR mass spectrometer at the Centre Laser Infrarouge d'Orsay (CLIO). The resulting IRMPD pattern points toward a chelate coordination (N-Ag+ -π) involving both the amino nitrogen atom and the aromatic π-system of the phenyl ring. The gas-phase reactivity of Ag+ (benzylamine) with a neutral molecular ligand (L) possessing either an amino/aza functionality or an aryl group confirms N- and π-binding affinity and suggests an augmented silver coordination in the product adduct ionAg + ( benzylamine ) ( L ) .

Binding Motifs in the Naked Complexes of Target Amino Acids with an Excerpt of Antitumor Active Biomolecule: An Ion Vibrational Spectroscopy Assay

The structures of proton-bound complexes of 5,7-dimethoxy-4H-chromen-4-one (1) and basic amino acids (AAs), namely, histidine (His) and lysine (Lys), have been examined by means of mass spectrometry coupled with IR ion spectroscopy and quantum chemical calculations. This selection of systems is based on the fact that 1 represents a portion of glabrescione B, a natural small molecule of promising antitumor activity, while His and Lys are protein residues lining the cavity of the alleged receptor binding site. These species are thus a model of the bioactive adduct, although clearly the isolated state of the present study bears little resemblance to the complex biological environment. A common feature of [1+AA+H]⁺ complexes is the presence of a protonated AA bound to neutral 1, in spite of the fact that the gas-phase basicity of 1 is comparable to those of Lys and His. The carbonyl group of 1 acts as a powerful hydrogen-bond acceptor. Within [1+AA+H]⁺ the side-chain substituents (imidazole group for His and terminal amino group for Lys) present comparable basic properties to those of the α-amino group, taking part to a cooperative hydrogen-bond network. Structural assignment, relying on the comparative analysis of the infrared multiple photon dissociation (IRMPD) spectrum and calculated IR spectra for the candidate geometries, derives from an examination over two frequency ranges: 900-1800 and 2900-3700 cm^-1 . Information gained from the latter one proved especially valuable, for example, pointing to the contribution of species characterized by an unperturbed carboxylic OH or imidazole NH stretching mode.

Theoretical investigation on hydrogen bond interaction between adrenaline and hydrogen sulfide

In this study, we elucidated the formation of hydrogen bond between adrenaline (AD) and hydrogen sulfide utilizing computational studies. Six potential complexes were studied including geometrical parameters, energy, vibrational frequency, topological analysis, natural bond orbital (NBO), quantum theory of atoms in molecules (QTAIM), and NMR analysis. Moreover, these calculations were examined through DFT/ωB97XD/6-311G++(d,p) level. It was found that there are no indication on formation on hydrogen bonding between the two catecholic OHs where the one formed between the amino group and the hydroxyl oxygen atom of adrenaline monomer was broken in AS₁ to form two new interactions namely SH^...N and O₁H₁^...S, while it retained in other complexes. Furthermore, the bond became stronger due to cooperativity in AS₃ and AS₆, for the presence of withdrawing effect of the phenyl ring, the H-bonds formed with the side chain oxygen atom. The adrenaline and H₂S interaction was experimentally examined via FT-IR spectrometry and thin layer chromatography for confirmation of our theoretical study. Graphical abstract.

BSA binding and antibacterial studies of newly synthesized 5,6-Dihydroimidazo[2,1-b]thiazole-2-carbaldehyde

A new heterocyclic compound, 5,6-Dihydroimidazo[2,1-b]thiazole-2-carbaldehyde (ITC) was synthesized and its antibacterial activity and also its interaction with bovine serum albumin (BSA) were studied. The structure of the synthesized compound was confirmed by ¹H NMR, ¹³C NMR and IR spectroscopic techniques. The antibacterial activity was carried out by minimum inhibitory concentration (MIC) method. The compound showed a good antibacterial activity. The mechanism of interaction between the BSA and ITC under physiological conditions was investigated by various molecular spectroscopic techniques like, fluorescence, circular dichroism (CD), UV absorption and FT-IR. The interaction between ITC and BSA was followed by studying the quenching of intrinsic fluorescence of BSA upon the addition of ITC at three different temperatures. The binding constant (K), Stern-Volmer quenching constant (K_sv) and number of binding sites were determined. The separation distance between BSA and ITC was evaluated based on the fluorescence resonance energy transfer theory. The conformational changes in BSA upon binding of ITC were also confirmed. The interference of some metal ions on interaction was studies. The displacement studies with site specific markers confirm that the site III was the binding site for ITC on BSA.

Multi-spectroscopic approaches and molecular simulation research of the intermolecular interaction between the angiotensin-converting enzyme inhibitor (ACE inhibitor) benazepril and bovine serum albumin (BSA)

Benazepril, a common ACE inhibitor, widely used in the treatment of arterial hypertension and congestive heart failure. In this study, We evaluated the characteristics of the interaction between benazepril and BSA under the simulated physiological condition (pH7.4) through various spectroscopic and molecular docking methods. Fluorescence and absorption spectroscopy results showed benazepril quenched the intrinsic fluorescence of BSA through a combined dynamic and static quenching mechanism. The number of binding sites (n) and the binding constant (K_b) of benazepril-BSA complex were circa 1 and 6.81×10³M^-1 at 298K, respectively, indicating that the binding affinity between benazepril and BSA was moderate. The displacement experiments confirmed that benazepril binding to the site I of BSA, which was quite in accordance with molecular docking. The values of the Gibbs free energy (ΔG⁰), enthalpic change (ΔH⁰) and entropic change (ΔS⁰) were negative, verifying that van der Waals force and hydrogen bonding interaction played a predominant roles in the process of spontaneous bonding. Furthermore, a slight change of the conformation in BSA upon benazepril interaction was proved through SF, 3-DF and FTIR spectroscopy results.

Molecular Interaction of Hemorrheologic Agent, Pentoxifylline with Bovine Serum Albumin: An Approach to Investigate the Drug Protein Interaction Using multispectroscopic, Voltammetry and Molecular Modelling Techniques

The interaction between pentoxifylline (PTX) and bovine serum albumin (BSA) was studied under physiological condition by spectroscopic, voltammetry and molecular modelling techniques. The results of fluorescence studies revealed that the quenching mechanism of BSA by PTX was a static procedure. Binding constant of PTX-BSA was calculated and its value found to be 8.895 × 104 M−1, which is in close agreement with the results obtained from UV-Visible and voltammetry approach. The negative values of thermodynamic parameters (ΔG, ΔH and ΔS) indicated that van der Waals force and hydrogen bonding play major roles in the interaction of PTX with BSA. Based on Forster’s theory of non-radiation energy transfer, the binding distance (r) between the donor (BSA) and acceptor (PTX) was found to be 5.38 nm (298 K). The results of UV-Visible and circular dichroism (CD) spectroscopy showed that PTX interacts with BSA and induces conformational changes by reducing the α-helix content. The results of the UV-visible and voltammetry studies were further verified by the molecular docking method. Molecular modelling studies revealed possible residues involved in the drug-protein interaction and indicated that PTX binds to Site IIA of BSA.

A conformational study of protonated noradrenaline by UV–UV and IR dip double resonance laser spectroscopy combined with an electrospray and a cold ion trap method

In protonated noradrenaline, 3 folded and 2 extended conformers were identified under the ultra-cold condition.

IR spectrum of the protonated neurotransmitter 2-phenylethylamine: dispersion and anharmonicity of the NH3(+)-π interaction

The structure and dynamics of the highly flexible side chain of (protonated) phenylethylamino neurotransmitters are essential for their function. The geometric, vibrational, and energetic properties of the protonated neutrotransmitter 2-phenylethylamine (H(+)PEA) are characterized in the N-H stretch range by infrared photodissociation (IRPD) spectroscopy of cold ions using rare gas tagging (Rg = Ne and Ar) and anharmonic calculations at the B3LYP-D3/(aug-)cc-pVTZ level including dispersion corrections. A single folded gauche conformer (G) protonated at the basic amino group and stabilized by an intramolecular NH(+)-π interaction is observed. The dispersion-corrected density functional theory calculations reveal the important effects of dispersion on the cation-π interaction and the large vibrational anharmonicity of the NH3(+) group involved in the NH(+)-π hydrogen bond. They allow for assigning overtone and combination bands and explain anomalous intensities observed in previous IR multiple-photon dissociation spectra. Comparison with neutral PEA reveals the large effects of protonation on the geometric and electronic structure.

Competing Insertion and External Binding Motifs in Hydrated Neurotransmitters: Infrared Spectra of Protonated Phenylethylamine Monohydrate

Hydration has a drastic impact on the structure and function of flexible biomolecules, such as aromatic ethylamino neurotransmitters. The structure of monohydrated protonated phenylethylamine (H(+) PEA-H2 O) is investigated by infrared photodissociation (IRPD) spectroscopy of cold cluster ions by using rare-gas (Rg=Ne and Ar) tagging and dispersion-corrected density functional theory calculations at the B3LYP-D3/aug-cc-pVTZ level. Monohydration of this prototypical neurotransmitter gives an insight into the first step of the formation of its solvation shell, especially regarding the competition between intra- and intermolecular interactions. The spectra of Rg-tagged H(+) PEA-H2 O reveal the presence of a stable insertion structure in which the water molecule is located between the positively charged ammonium group and the phenyl ring of H(+) PEA, acting both as a hydrogen bond acceptor (NH(+) ⋅⋅⋅O) and donor (OH⋅⋅⋅π). Two other nearly equivalent isomers, in which water is externally H bonded to one of the free NH groups, are also identified. The balance between insertion and external hydration strongly depends on temperature.

Performance of M06, M06-2X, and M06-HF density functionals for conformationally flexible anionic clusters: M06 functionals perform better than B3LYP for a model system with dispersion and ionic hydrogen-bonding interactions

We present a comparative assessment of the performance of the M06 suite of density functionals (M06, M06-2X, and M06-HF) against an MP2 benchmark for calculating the relative energies and geometric structures of the Cl(-)·arginine and Br(-)·arginine halide ion-amino acid clusters. Additional results are presented for the popular B3LYP density functional. The Cl(-)·arginine and Br(-)·arginine complexes are important prototypes for the phenomenon of anion-induced zwitterion formation. Results are presented for the canonical (noncharge separated) and zwitterionic (charge separated) tautomers of the clusters, as well as the numerous conformational isomers of the clusters. We find that all of the M06 functions perform well in terms of predicting the general trends in the conformer relative energies and identifying the global minimum conformer. This is in contrast to the B3LYP functional, which performed significantly less well for the canonical tautomers of the clusters where dispersion interactions contribute more significantly to the conformer energetics. We find that the M06 functional gave the lowest mean unsigned error for the relative energies of the canonical conformers (2.10 and 2.36 kJ/mol for Br(-)·arginine and Cl(-)·arginine), while M06-2X gave the lowest mean unsigned error for the zwitterionic conformers (0.85 and 1.23 kJ/mol for Br(-)·arginine and Cl(-)·arginine), thus providing insight into the types of physical systems where each of these functionals should perform best.

Vibrational spectroscopy and conformational structure of protonated polyalanine peptides isolated in the gas phase

The conformational structures of protonated polyalanine peptides, Ala(n)H(+), have been investigated in the gas phase for n = 3, 4, 5, and 7 using a combination of resonant-infrared multiphoton dissociation (R-IRMPD) spectroscopy in the NH and OH stretch regions and quantum chemical calculations. Agreement between theoretical IR and experimental R-IRMPD spectral features has enabled the assignment of specific hydrogen-bonded conformational motifs in the short protonated peptides and revealed their conformational evolution under elevated-temperature conditions, as a function of increasing chain length. The shortest peptide, Ala(3)H(+), adopts a mixture of extended and cyclic chain conformations, protonated, respectively, at a backbone carbonyl or the N-terminus. The longer peptides adopt folded, cyclic, and globular charge-solvated conformations protonated at the N-terminus, consistent with previous ion-mobility studies. The longest peptide, Ala(7)H(+), adopts a globular conformation with the N-terminus completely charge-solvated, demonstrating the emergence of "physiologically relevant" intramolecular interactions in the peptide backbone. The computed conformational relative free energies highlight the importance of entropic contributions in these peptides.

Diagnostic NH and OH vibrations for oxazolone and diketopiperazine structures: b2 from protonated triglycine

We present infrared multiple photon dissociation (IRMPD) spectra in the hydrogen stretching region of the simplest b fragment, b(2) from protonated triglycine, contrasted to that of protonated cyclo(Gly-Gly). Both spectra confirm the presence of intense, diagnostic vibrations linked to the site of proton attachment. Protonated cyclo(Gly-Gly) serves as a reference spectrum for the diketopiperazine structure, showing a diagnostic O-H(+) stretch of the protonated carbonyl group at 3585 cm(-1). Conversely, b(2) from protonated triglycine exhibits a strong band at 3345 cm(-1), associated with the N-H stretching mode of the protonated oxazolone ring structure. Other weaker N-H stretches can also be discerned, such as the amino NH(2) and amide NH bands. These results demonstrate the usefulness of the hydrogen stretching region, and hence benchtop optical parametric oscillator/amplifier (OPO/A) set-ups, in making structural assignments of product ions in collision-induced dissociation (CID) of peptides.

Theoretical spectroscopy of floppy peptides at room temperature. A DFTMD perspective: gas and aqueous phase

Theoretical spectroscopy is mandatory for a precise understanding and assignment of experimental spectra recorded at finite temperature. We review here room temperature DFT-based molecular dynamics simulations for the purpose of interpreting finite temperature infrared spectra of peptides of increasing size and complexity, in terms of temperature-dependent conformational dynamics and flexibility, and vibrational anharmonicities (potential energy surface anharmonicities, vibrational mode couplings and dipole anharmonicities). We take examples from our research projects in order to illustrate the main key-points and strengths of dynamical spectra modeling in that context. The calculations are presented in relation to room temperature gas phase IR-MPD experiments and room temperature liquid phase IR absorption experiments. These illustrations of floppy polypeptides have been chosen in order to convey the following ideas: temperature-dependent spectra modeling is pivotal for a precise understanding of gas phase spectra recorded at room temperature, including conformational dynamics and vibrational anharmonicities; harmonic spectroscopy (as commonly performed in the literature) can be misleading and even erroneous for a proper interpretation of spectra recorded at finite temperature; taking into account vibrational anharmonicities is pivotal for a proper interplay between theory and experiments; amide I-III bands are not necessarily the most relevant fingerprints for unraveling the local structures of peptides and more complex systems; liquid phase simulations have unraveled relationships between the zwitterionic properties of the peptide bonds and infrared signatures. The review presents a state-of-the-art account of the domain and offers perspectives and new developments for future still more challenging applications.

Vibrational spectroscopy of bare and solvated ionic complexes of biological relevance

The low density of ions in mass spectrometers generally precludes direct infrared (IR) absorption measurements. The IR spectrum of an ion can nonetheless be obtained by inducing photodissociation of the ion using a high-intensity tunable laser. The emergence of free electron lasers (FELs) and recent breakthroughs in bench-top lasers based on nonlinear optics have now made it possible to routinely record IR spectra of gas-phase ions. As the energy of one IR photon is insufficient to cause dissociation of molecules and strongly bound complexes, two main experimental strategies have been developed to effect photodissociation. In infrared multiple-photon dissociation (IR-MPD) many photons are absorbed resonantly and their energy is stored in the bath of vibrational modes, leading to dissociation. In the "messenger" technique a weakly bound van der Waals atom is detached upon absorption of a single photon. Fundamental, historical, and practical aspects of these methods will be presented. Both of these approaches make use of very different methods of ion preparation and manipulation. While in IR-MPD ions are irradiated in trapping mass spectrometers, the "messenger" technique is generally carried out in molecular beam instruments. The main focus of this review is the application of IR spectroscopy to biologically relevant molecular systems (amino acids, peptides, proteins). Particular issues that will be addressed here include gas-phase zwitterions, the (chemical) structures of peptides and their collision-induced dissociation (CID) products, IR spectra of gas-phase proteins, and the chelation of metal-ligand complexes. Another growing area of research is IR spectroscopy on solvated clusters, which offer a bridge between the gas-phase and solution environments. The development of state-of-the-art computational approaches has gone hand-in-hand with advances in experimental techniques. The main advantage of gas-phase cluster research, as opposed to condensed-phase experiments, is that the systems of interest can be understood in detail and structural effects can be studied in isolation. It will be shown that IR spectroscopy of mass-selected (bio)molecular systems is now well-placed to address specific questions on the individual effect of charge carriers (protons and metal ions), as well as solvent molecules on the overall structure.