Effects of Alkaline Earth Metal Ion Complexation on Amino Acid Zwitterion Stability: Results from Infrared Action Spectroscopy

L-serine combined with carboxymethyl chitosan guides amorphous calcium phosphate to remineralize enamel

The aim of this study is to investigate a robust and stable calcium-phosphorus system to remineralize human early enamel caries lesions with nanocomplexes of carboxymethyl chitosan/L-serine/amorphous calcium phosphate (CMC-Ser-ACP) to develop an effective method for mimicking the amelogenin (AMEL) mineralization pattern through ACP assembly. A CMC-Ser-ACP nanocomplex solution was first synthesized by a chemical precipitation method, and then 1% sodium hypochlorite (NaClO) was added to induce ACP phase formation. The morphologies of the nanocomplexes were characterized by transmission electron microscopy (TEM), and zeta potential analysis and Fourier transform infrared spectroscopy (FTIR) were performed to detect surface charge and functional group changes. The subtle changes of the demineralized enamel models induced by the remineralization effect were observed by scanning electron microscopy (SEM) and X-ray diffraction (XRD). The CMC-Ser-ACP nanocomplex solution could be preserved without any precipitation for 45 days. After the application of NaClO and through the guidance of Ser, ACP nanoparticles transformed into relatively orderly arranged hydroxyapatite (HAP) crystals, generating an aprismatic enamel-like layer closely integrated with the demineralized enamel, which resulted in enhanced mechanical properties for the treatment of early enamel caries lesions. The CMC-Ser-ACP nanocomplex solution is a remineralization system with great solution stability, and when NaClO is added, it can rapidly regenerate an aprismatic enamel-like layer in situ on the demineralized enamel surface. This novel remineralization system has stable chemical properties and can greatly increase the therapeutic effects against early enamel caries.

Infrared Spectra of Beauvericin-Alkaline Earth Metal Ion Complexes─Ion Preference to Physiological Ions

Beauvericin (Bv) is a naturally occurring ionophore that selectively transports ions through cell membranes. However, the intrinsic ion selectivity of Bv for alkaline earth metal ions (M2+) is yet to be established due to inconsistent results from condensed phase experiments. Based on fluorescence quenching rates, Ca2+ appears to be preferred while extraction experiments favor Mg2+. In this study, we apply cold ion trap─infrared spectroscopy to Bv-M2+ coupled with electrospray ionization mass spectrometry. The mass spectrum shows that Bv favors binding to physiologically active ions Mg2+ and Ca2+ although it can form complexes with all four alkaline earth metal ions. Infrared spectroscopy, as measured by the H2 tag technique, reveals that Bv binds Mg2+ and Ca2+ ions by six carbonyl oxygens in the center of its cavity. This observation is supported by theoretical calculations. Other alkaline earth metal ions are bound by three carbonyl groups at the amide face. This difference in configuration is consistent with the binding preferences for the alkaline earth metal ions.

How generic is iodide-tagging photoelectron spectroscopy: An extended investigation on the Gly·X- (Gly = glycine, X = Cl or Br) complexes

We report a joint negative ion photoelectron spectroscopy (NIPES) and quantum chemical computational study on glycine-chloride/bromide complexes (denoted Gly·X-, X = Cl/Br) in close comparison to the previously studied Gly·I- cluster ion. Combining experimental NIPE spectra and theoretical calculations, various Gly·X- complexes were found to adopt the same types of low-lying isomers, albeit with different relative energies. Despite more congested spectral profiles for Gly·Cl- and Gly·Br-, spectral assignments were accomplished with the guidance of the knowledge learned from Gly·I-, where a larger spin-orbit splitting of iodine afforded well-resolved, recognizable spectral peaks. Three canonical plus one zwitterionic isomer for Gly·Cl- and four canonical conformers for Gly·Br- were experimentally identified and characterized in contrast to the five canonical ones observed for Gly·I- under similar experimental conditions. Taken together, this study investigates both genericity and variations in binding patterns for the complexes composed of glycine and various halides, demonstrating that iodide-tagging is an effective spectroscopic means to unravel diverse ion-molecule binding motifs for cluster anions with congested spectral bands by substituting the respective ion with iodide.

Effect of salts on the formation of acrylamide, 5-hydroxymethylfurfural and flavour compounds in a crust-like glucose/wheat flour dough system during heating

Among many strategies known to mitigate acrylamide formation, addition of cations, particularly calcium, is effective and can be used in bakery products. In this study, the effects of NaCl, KCl, CaCl₂, MgCl₂, sodium lactate, calcium lactate, and magnesium lactate on aroma and acrylamide formation were investigated in glucose/wheat flour dough systems during heating. Addition of salts inhibited Maillard reaction in favour of caramelisation, with divalent cations found to be most effective. The impact of salts on acrylamide reduction became less effective with increasing temperature. Most Strecker aldehydes and pyrazines decreased in the presence of salts, however CaCl₂ and calcium lactate increased the concentration of furans, furfurals, and diketones. Calcium lactate also increased some ethyl-substituted pyrazines at high temperatures. Reduction of acrylamide with salts is associated with higher amounts of furan derivatives and decreased amounts of Strecker aldehydes and pyrazines. The mechanisms behind these changes are discussed.

Spectroscopic Investigation of the Metal Coordination of the Aromatic Amino Acids with Zinc and Cadmium

The aromatic amino acids (AAA), phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp), were cationized with ZnCl⁺ and CdCl⁺, and the complexes were evaluated using infrared multiple photon dissociation (IRMPD) action spectroscopy. Specifically, the ZnCl⁺(Phe), CdCl⁺(Phe), ZnCl⁺(Tyr), CdCl⁺(Tyr), and ZnCl⁺(Trp) species were examined because the CdCl⁺(Trp) IRMPD spectrum is available in the literature. Several low-energy conformers for all complexes were found using quantum chemical calculations, and their simulated vibrational spectra were compared to the experimental IRMPD spectra to identify dominant isomers formed. In the case of MCl⁺(Phe) and MCl⁺(Tyr), these comparisons indicated the dominant binding motif is a tridentate structure, where the metal atom coordinates with the backbone amino nitrogen and carbonyl oxygen, as well as the aryl ring. These observations are consistent with the predicted ground states at the B3LYP, B3P86, B3LYP-GD3BJ, and MP2 levels of theory. For the ZnCl⁺(Trp) system, the experimental spectrum indicates a similar binding motif, with the zinc atom coordinating with the backbone nitrogen and carbonyl oxygen and either the pyrrole ring or the benzene ring of the indole side chain. These observations are consistent with the predicted low-lying conformers identified by the aforementioned levels of theory, with the B3LYP and B3P86 levels predicting the metal-pyrrole ring interaction is more favorable than the metal-benzene ring interactions and the opposite at the B3LYP-GD3BJ and MP2 levels.

Infrared multiple-photon dissociation spectroscopy of cationized glycine: effects of alkali metal cation size on gas-phase conformation

The gas-phase structures of cationized glycine (Gly), including complexes with Li⁺, Na⁺, K⁺, Rb⁺, and Cs⁺, are examined using infrared multiple-photon dissociation (IRMPD) spectroscopy utilizing light generated by a free electron laser, in conjunction with ab initio calculations. To identify the structures present in the experimental studies, measured IRMPD spectra are compared to spectra calculated at B3LYP/6-311+G(d,p) for the Li⁺, Na⁺, and K⁺ complexes and at B3LYP/def2TZVP for the Rb⁺ and Cs⁺ complexes. Single-point energy calculations were carried out at the B3LYP, B3P86, and MP2(full) levels using the 6-311+G(2d,2p) basis set for Li⁺, Na⁺, K⁺ and the def2TZVPP basis set for Rb⁺ and Cs⁺. The Li⁺ and Na⁺ complexes are identified as metal cation coordination to the amino nitrogen and carbonyl oxygen, [N,CO]-tt, although Na⁺(Gly) may have contributions from additional structures. The heavier metal cations coordinate to either the carbonyl oxygen, [CO]-cc, or the carbonyl oxygen and hydroxy oxygen, [CO,OH]-cc, with the former apparently preferred for Rb⁺ and Cs⁺ and the latter for K⁺. These two structures reside in a double-well potential and different levels of theory predict very different relative stabilities. Some experimental evidence is provided that MP2(full) theory provides the most accurate relative energies.

IRMPD Spectroscopy of [PC (4:0/4:0) + M]+ (M = H, Na, K) and Corresponding CID Fragment Ions

Glycerophospholipids (GPs) are highly abundant in eukaryotic cells and take part in numerous fundamental physiological processes such as molecular signaling. The GP composition of samples is often analyzed using mass spectrometry (MS), but identification of some structural features, for example, differentiation of stereospecific numbering (sn) isomers by well-established tandem MS (MS²) methods, is challenging. In particular, the formation of 1,3-dioxolane over 1,3-dioxane intermediates proposed to be responsible for the sn-selectivity of these tandem MS strategies has not been validated by spectroscopic methods. In this work, we present infrared multiple photon dissociation (IRMPD) spectra of phosphatidylcholine (PC) ions [PC 4:0/4:0 + H/Na/K]⁺ and [PC 4:0/4:0 + Na/K - 183]⁺ fragments generated by electrospray ionization (ESI)-MS and collision-induced dissociation (CID), respectively. IRMPD spectra of protonated, sodiated, and potassiated PC 4:0/4:0 differ in the phosphate- and ester-related bands, which are increasingly shifted to lower wavenumbers with higher adduct masses. Comparison of calculated and experimental IR spectra indicates the presence of multiple, two and one isomer(s) for [PC 4:0/4:0 + H]⁺, [PC 4:0/4:0 + Na]⁺, and [PC 4:0/4:0 + K]⁺, respectively. Isomers exhibiting pronounced sn-1 ester-ion interactions are computationally predicted to be energetically preferred for all species and are in line with experimental results. IRMPD spectra of [PC 4:0/4:0 + Na/K - 183]⁺ are presented and shed the first light on the fragment ion structures, rationalizing MS-based lipidomics strategies that aim to characterize the sn-isomerism of GPs.

Structural Diversity of Di-Metalized Arginine Evidenced by Infrared Multiple Photon Dissociation (IRMPD) Spectroscopy in the Gas Phase

Although metal cations are prevalent in biological media, the species of multi-metal cationized biomolecules have received little attention so far. Studying these complexes in isolated state is important, since it provides intrinsic information about the interaction among them on the molecular level. Our investigation here demonstrates the unexpected structural diversity of such species generated by a matrix-assisted laser desorption ionization (MALDI) source in the gas phase. The photodissociation spectroscopic and theoretical study reflects that the co-existing isomers of [Arg+Rb+K−H]⁺ can have energies ≥95 kJ/mol higher than that of the most stable one. While the result can be rationalized by the great isomerization energy barrier due to the coordination, it strongly reminds us to pay more attention to their structural diversities for multi-metalized fundamental biological molecules, especially for the ones with the ubiquitous alkali metal ions.

Infrared Multiple-Photon Dissociation Spectra of Sodiated Complexes of the Aliphatic Amino Acids

Sodiated complexes of the aliphatic amino acids, Gly, Ala, Val, Leu, and Ile, were examined with infrared multiple-photon dissociation action spectroscopy utilizing light from a free-electron laser. To identify structures, the experimental spectra were compared to linear spectra calculated at the B3LYP/6-311+G(d,p) level of theory. Relative energetics of all complexes were calculated at B3LYP, B3P86, MP2(full), B3LYP-GD3BJ, and M06-2X levels using a 6-311+G(2d,2p) basis set. Spectral comparison for all complexes indicates that the dominant conformation, [N, CO], binds to the amino nitrogen and carbonyl oxygen. For all complexes except Gly, contributions are observed from [CO₂^-] structures, where the sodium cation binds to both oxygens of the carboxylate group in the zwitterionic form of the amino acid. The semiquantitative distribution between these two structures appears to be best-predicted by the B3LYP and MP2(full) levels of theory, with predictions from the other three levels inconsistent with the experiment.

Observation of Conformational Simplification upon N-Methylation on Amino Acid Iodide Clusters

This Letter reports a counterintuitive observation that methylation of the glycine-iodide cluster leads to fewer conformations and spectroscopic simplicity. Cryogenic "iodide-tagging" negative ion photoelectron spectroscopy (NIPES) is used to probe specific binding sites of three N-methylated glycine derivatives, i.e., N-methylglycine (sarcosine), N,N-dimethylglycine, and N,N,N-trimethylglycine (glycine betaine). NIPES reveals a progressive spectral simplification of the iodide clusters with increasing methylation due to fewer contributing structures. Low energy conformers and tautomers of each cluster are computationally identified, and those observed in the experiments are assigned based on excellent agreement between the NIPE spectra and theoretical simulations. Zwitterionic cluster structures are found to be less stable than their canonical forms and do not contribute to the observed spectra. This work demonstrates the power of iodide-tagging NIPES in probing conformations of amino acid-iodide clusters and provides a molecular level understanding on the effect of methyl substitution on amino acid binding sites.

Alkali and alkaline earth coordination polymers constructed from benzene-1,2,4,5-tetracarboxylic acid and flexible dicarboxylate acid ligands: syntheses, structures and spectroscopic and thermal properties

Two new metal coordination complexes, namely, poly[aqua(μ₆-benzene-1,2,4,5-tetracarboxylic acid-κ⁸O¹:O¹,O²:O^2':O⁴:O⁴,O⁵:O^5')(μ-but-2-enedioato-κ²O¹:O⁴)potassium(I)], [K₂(C₄H₂O₄)(C₁₀H₆O₈)(H₂O)₂]_n or [K₂(fum)(H₄btec)(H₂O)₂]_n, (1), and poly[aqua(μ₈-2,5-dicarboxybenzene-1,4-dicarboxylato-κ¹²O¹:O^1',O²:O²,O^2':O^2':O⁴:O^4',O⁵:O⁵,O^5':O^5')(μ-ethanedioato-κ⁴O¹,O²:O^1',O^2')strontium(II)], [Sr₂(C₂O₄)(C₁₀H₄O₈)(H₂O)₂]_n or [Sr₂(ox)(H₂btec)(H₂O)₂]_n, (2) (H₄btec = benzene-1,2,4,5-tetracarboxylic acid, H₂btec = 2,5-dicarboxybenzene-1,4-dicarboxylate, fum = fumarate and ox = oxalate), have been obtained under hydrothermal conditions by reacting the different alkali and alkaline earth metal salts with H₄btec, fumaric acid (H₂fum) and oxalic acid (H₂ox). Complexes (1) and (2) were structurally characterized by single-crystal X-ray diffraction, IR and UV-Vis spectroscopy, powder X-ray diffraction (PXRD) and thermogravimetic analysis-differential scanning calorimetry (TGA-DSC). Complex (1) displays a two-dimensional (2D) layer with the K⁺ ion in a distorted pentagonal bipyramidal geometry and exhibits a uninodal 6-connected hxl/Shubnikov plane net (3,6) with {3⁶.4⁶.5³} topology. Complex (2) displays a three-dimensional (3D) network structure, in which the Sr²⁺ ion is in a distorted monocapped square antiprism geometry. The framework possess a binodal (5,8)-connected net with the Schläfli symbol {3².4¹⁰.5⁸.6⁴.7⁴}{3².4⁶.5²}₂. The 3D Hirshfeld surfaces and 2D fingerprint plots show that the main interactions are the O...H/H...O intermolecular interactions. Moreover, the thermal decompositions of (1) and (2) in the temperature range 303-1273 K revealed that they both decompose in three steps and transform to the corresponding metal oxide.

Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues

Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.

Probing the conformational landscape and thermochemistry of DNA dinucleotide anions via helium nanodroplet infrared action spectroscopy

Isolation of biomolecules in vacuum facilitates characterization of the intramolecular interactions that determine three-dimensional structure, but experimental quantification of conformer thermochemistry remains challenging. Infrared spectroscopy of molecules trapped in helium nanodroplets is a promising methodology for the measurement of thermochemical parameters. When molecules are captured in a helium nanodroplet, the rate of cooling to an equilibrium temperature of ca. 0.4 K is generally faster than the rate of isomerization, resulting in "shock-freezing" that kinetically traps molecules in local conformational minima. This unique property enables the study of temperature-dependent conformational equilibria via infrared spectroscopy at 0.4 K, thereby avoiding the deleterious effects of spectral broadening at higher temperatures. Herein, we demonstrate the first application of this approach to ionic species by coupling electrospray ionization mass spectrometry (ESI-MS) with helium nanodroplet infrared action spectroscopy to probe the structure and thermochemistry of deprotonated DNA dinucleotides. Dinucleotide anions were generated by ESI, confined in an ion trap at temperatures between 90 and 350 K, and entrained in traversing helium nanodroplets. The infrared action spectra of the entrained ions show a strong dependence on pre-pickup ion temperature, consistent with the preservation of conformer population upon cooling to 0.4 K. Non-negative matrix factorization was utilized to identify component conformer infrared spectra and determine temperature-dependent conformer populations. Relative enthalpies and entropies of conformers were subsequently obtained from a van't Hoff analysis. IR spectra and conformer thermochemistry are compared to results from ion mobility spectrometry (IMS) and electronic structure methods. The implementation of ESI-MS as a source of dopant molecules expands the diversity of molecules accessible for thermochemical measurements, enabling the study of larger, non-volatile species.

Cryogenic "Iodide-Tagging" Photoelectron Spectroscopy: A Sensitive Probe for Specific Binding Sites of Amino Acids

This work showcases cryogenic and temperature-dependent "iodide-tagging" photoelectron spectroscopy to probe specific binding sites of amino acids using the glycine-iodide complex (Gly·I^-) as a case study. Multiple Gly·I^- isomers were generated from ambient electrospray ionization and kinetically isolated in a cryogenic ion trap. These structures were characterized with temperature-dependent "iodide-tagging" negative ion photoelectron spectroscopy (NIPES), where iodide was used as the "messenger" to interpret electronic energetics and structural information of various Gly·I^- isomers. Accompanied by theoretical computations and Franck-Condon simulations, a total of five cluster structures have been identified along with their various binding motifs. This work demonstrates that "iodide-tagging" NIPES is a powerful general means for probing specific binding interactions in biological molecules of interest.

Structure of Proton-Bound Methionine and Tryptophan Dimers in the Gas Phase Investigated with IRMPD Spectroscopy and Quantum Chemical Calculations

The structures of three proton-bound dimers (Met₂H⁺, MetTrpH⁺, and Trp₂H⁺) are investigated in the gas phase with infrared multiple photon disassociation (IRMPD) spectroscopy in combination with quantum chemical calculations. Their IRMPD spectra in the range of 600–1850 cm^–1 are obtained experimentally using an FT-ICR mass spectrometer and the CLIO free electron laser as an IR light source. The most abundant conformers are elucidated by comparing the IRMPD spectra with harmonic frequencies obtained at the B3LYP-GD3BJ/6-311++G** level of theory. Discrepancies between the experimental and theoretical data in the region of 1500–1700 cm^–1 are attributed to the anharmonicity of the amino bending modes. We confirm the result of a previous IRMPD study that the structure of gas-phase Trp₂H⁺ is charge-solvated but find that there are more stable structures than originally reported (Feng, R.; Yin, H.; Kong, X. Rapid Commun. Mass Spectrom.2016, 30, 24–28). In addition, gas-phase Met₂H⁺ and MetTrpH⁺ have been revealed to have charge-solvated structures. For all three dimers, the most stable conformer is found to be of type A. The spectrum of Met₂H⁺, however, cannot be explained without some abundance of type B charge-solvated conformers as well as salt-bridged structures.

Combined Experimental and Theoretical Survey of the Gas-Phase Reactions of Serine-Ca2+ Adducts

The association of Ca²⁺ to serine and the subsequent gas-phase unimolecular reactivity of the [Ca(Ser)]²⁺ (Ser = Serine) adduct was investigated throughout the use of tandem mass spectrometry techniques and B3LYP/6-311+G(3df,2p)//B3LYP/6-311+G(d,p) density functional theory calculations. In a first step, the structure and relative stability of all possible conformers of serine were obtained and analyzed, as well as the most stable [serine-Ca]²⁺ adducts. For the analysis of the different potential energy surfaces associated with the gas-phase unimolecular reactivity of these adducts, only those that differ by less than 100 kJ·mol^-1 from the global minimum were taken into account. In agreement with previous studies, the serine-Ca²⁺ global minimum corresponds to a charge-solvated structure in which Ca is tricoordinated to neutral serine. The major peaks observed in the nanoelectrospray-MS/MS spectrum of [Ca(Ser)]²⁺ adduct correspond to both Coulomb explosions, yielding either CaOH⁺ + [C₃,H₆,N,O₂]⁺ or [C₂,H₄,O,N]⁺ + [Ca(C,H₃,O₂)]⁺, and to the loss of neutrals, namely, CH₂O and H₂O. Our theoretical survey of the energy profile allow us to conclude that, although all the aforementioned fragmentation processes can have their origin at the global minimum, similar fragmentations involving low-lying conformers, both zwitterionic and nonzwitterionic, compete and should be considered to account for the observed reactivity. We have also found that in some specific cases post-transition state dynamics similar to the ones described before in the literature for formamide-Ca²⁺ reactions, may also play a role.

Identification of ion pairs in solution by IR spectroscopy: crucial contributions of gas phase data and simulations

In a context where structure elucidation of ion pairs in solution remains a contemporary challenge, this work explores an original approach where accurate gas phase spectroscopic data are used to refine high level quantum chemistry calculations of ion pairs in solution, resulting in an unprecedented level of accuracy in vibrational frequency prediction. First, gas phase studies focus on a series of isolated contact ion pairs (M⁺, Ph-CH₂-COO^-, with M = Li, Na, K, Rb, Cs) for which conformer-selective IR spectra in the CO₂^- stretch region are recorded. These experiments reveal the interactions at play in isolated contact ion pairs, and provide vibrational frequencies enabling us to assess the accuracy of the theoretical approach used, i.e., mode-dependent scaled harmonic frequency calculations at the RI-B97-D3/dhf-TZVPP level. This level of calculation is then employed on large water clusters embedding either a free acetate ion or its contact or solvent-shared pairs with a sodium cation in order to simulate the individual vibrational spectra of these species in solution. This study shows that the stretching modes of carboxylate are sensitive to both solvent-shared and contact ion pair formation. FTIR spectra of solutions of increasing concentrations indeed reveal several spectral changes consistent with the presence of specific types of solvent-shared and contact ion pairs. By providing relevant guidelines for the interpretation of solution phase IR spectra, this work illustrates the potential of the approach for the elucidation of supramolecular structures in electrolyte solutions.

Gas-phase metal ion chelation investigated with IRMPD spectroscopy: A brief review of Robert Dunbar's contributions

With the passing of Prof. Robert C. Dunbar on 31 October 2017, the field of ion chemistry lost one of its modern heroes. Throughout his career in mass spectrometry, two of his main research interests involved the interaction of trapped ions with electromagnetic radiation and the chelation motifs of metal ions with organic ligands. The focus of his early career was on the fundamental processes that take place in molecules upon ultraviolet and infrared excitation. From 2003 to 2017, his scientific interests shifted to more structural questions, notably to resolving the structures and binding motifs of metal ion chelation complexes by application of infrared photodissociation spectroscopy. These experiments were carried out during numerous visits to the (Free Electron Laser for Infrared eXperiments) (FELIX) facility in the Netherlands and were complemented by extensive theoretical investigations by Rob. As a tribute to our friend, we present in this contribution a brief review of this work.

Relative glycosidic bond stabilities of naturally occurring methylguanosines: 7-methylation is intrinsically activating

The frequency and diversity of posttranscriptional modifications add an additional layer of chemical complexity beyond canonical nucleic acid sequence. Methylations are particularly frequently occurring and often highly conserved throughout the kingdoms of life. However, the intricate functions of these modified nucleic acid constituents are often not fully understood. Systematic foundational research that reduces systems to their minimum constituents may aid in unraveling the complexities of nucleic acid biochemistry. Here, we examine the relative intrinsic N-glycosidic bond stabilities of guanosine and five naturally occurring methylguanosines (O2'-, 1-, 7-, N2,N2-di-, and N2,N2,O2'-trimethylguanosine) probed by energy-resolved collision-induced dissociation tandem mass spectrometry and complemented with quantum chemical calculations. Apparent glycosidic bond stability is generally found to increase with increasing methyl substitution (canonical < mono- < di- < trimethylated). Many biochemical transformations, including base excision repair mechanisms, involve protonation and/or noncovalent interactions to increase nucleobase leaving-group ability. The protonated gas-phase methylguanosines require less activation energy for glycosidic bond cleavage than their sodium cationized forms. However, methylation at the N7 position intrinsically weakens the glycosidic bond of 7-methylguanosine more significantly than subsequent cationization, and thus 7-methylguanosine is suggested to be under perpetually activated conditions. N7 methylation also alters the nucleoside geometric preferences relative to the other systems, including the nucleobase orientation in the neutral form, sugar puckering in the protonated form, and the preferred protonation and sodium cation binding sites. All of the methylated guanosines examined here are predicted to have proton affinities and gas-phase basicities that exceed that of canonical guanosine. Additionally, the proton affinity and gas-phase basicity trends exhibit a roughly inverse correlation with the apparent glycosidic bond stabilities.

Development of SrTiO3 Photocatalysts with Visible Light Response Using Amino Acids as Dopant Sources for the Degradation of Organic Pollutants in Aqueous Systems

N-doped and N,S-co-doped SrTiO3 photocatalysts were prepared using glycine and L-histidine amino acids as nitrogen sources and L-cysteine as nitrogen and sulphur source. The samples were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), N2 porosimetry, UV-Vis diffuse reflectance (DRS) and fluorescence spectroscopy, dynamic light scattering (DLS). Cubic SrTiO3 phase is formed in all samples, with crystal size ranged from 14.2 nm to 35.7 nm. The catalysts’ specific surface area and porosity depend on the amino acid dopant showing micro-mesoporosity for glycine, mesoporosity for histidine and non-porosity for cysteine. The lowest band gap (2.95 eV) was observed for the sample G-N-STO3 prepared with glycine (N:Sr:Ti 3:1:1 molar ratio) which produced also the higher amount of •OH radicals. The photocatalytic activity was tested against the degradation of methylene blue (MB) dye under UV-Vis and visible light irradiation following first-order kinetics.

Infrared Multiple Photon Dissociation Spectroscopy of Cationized Canavanine: Side-Chain Substitution Influences Gas-Phase Zwitterion Formation†

Infrared multiple photon dissociation spectroscopy was performed on protonated and cationized canavanine (Cav), a non-protein amino acid oxy-analog of arginine. Infrared spectra in the XH stretching region (3000 - 4000 cm^-1) were obtained at the Centre Laser Infrarouge d'Orsay (CLIO) facility. Comparison of the experimental infrared spectra with scaled harmonic frequencies at the B3LYP/6-31+G(d,p) level of theory indicates that canavanine is in a canonical neutral form in CavH⁺, CavLi⁺, and CavNa⁺; therefore, these cations are charge-solvated structures. The infrared spectrum of CavK⁺ is consistent with a mixture of Cav in canonical and zwitterionic forms leading to both charge-solvated and salt-bridged cationic structures. The Cav moiety in CavCs⁺ is shown to be zwitterionic, forming a salt-bridged structure for the cation. Infrared spectra in the fingerprint region (1000 - 2000 cm^-1) obtained at the FELIX Laboratory in Nijmegen, Netherlands support these assignments. These results show that that a single oxygen atom substitution in the side chain reduces the stability of the zwitterion compared to that of the protein amino acid arginine (Arg), which has been shown previously to adopt a zwitterionic structure in ArgNa⁺ and ArgK⁺. This difference can be explained in part due to the decreased basicity of Cav (PA = 1001 kJ/mol) as compared to arginine (PA = 1051 kJ/mol), but not entirely, as lysine, which has nearly the same proton affinity as Cav, (~993 kJ/mol) forms only canonical structures with Na⁺, K⁺, and Cs⁺. A major difference between the zwitterionic forms of ArgM⁺ and CavM⁺ is that the protonation site is on the side chain for Arg and on the N-terminus for Cav. This results in systematically weaker salt bridges in the Cav zwitterions. In addition, the presence of another hydrogen-bonding acceptor atom in the side chain contributes to the stability of the canonical structures for the smaller alkali cations.

Competition between salt bridge and non-zwitterionic structures in deprotonated amino acid dimers

The effect of side chain functional groups on salt bridge structures in deprotonated amino acid homodimers is investigated using both infrared multiple photon dissociation spectroscopy between 650 and 1850 cm⁻¹ and theory.

A Database of Transition-Metal-Coordinated Peptide Cross-Sections: Selective Interaction with Specific Amino Acid Residues

Ion mobility mass spectrometry (IMS-MS) techniques were used to generate a database of 2288 collision cross sections of transition-metal-coordinated tryptic peptide ions. This database consists of cross sections for 1253 [Pep + X]²⁺ and 1035 [Pep + X + H]³⁺, where X²⁺ corresponds to Mn²⁺, Co²⁺, Ni²⁺, Cu²⁺, or Zn²⁺. This number of measurements enables the extraction of structural trends for transition-metal-coordinated peptide ions. The range of structures and changes in collision cross sections for X²⁺-coordinated species (compared with protonated species of the same charge state) is similar to Mg²⁺-coordinated species. This suggests that the structures are largely determined by similarities in cation size with differences among the cross section distributions presumably caused by X²⁺ interactions with specific functional groups offered by the residue R-groups or the peptide backbone. Cross section contributions for individual residues upon X²⁺ solvation are assessed with the derivation of intrinsic size parameters (ISPs). The comparison of the [Pep + X]²⁺ ISPs with those previously reported for [Pep + Mg]²⁺ ions displays a lower contribution to the cross section for His, carboxyamidomethylated Cys, and Met, and is consistent with specific metal-residue interactions identified within protein X-ray crystallography databases. Graphical Abstract ᅟ.

Effects of Sodium Chloride, Potassium Chloride, and Calcium Chloride on the Formation of α-Dicarbonyl Compounds and Furfurals and the Development of Browning in Cookies during Baking

Effects of NaCl, KCl, CaCl₂, NaHCO₃, and NH₄HCO₃ on the formation of glucosone, 1-deoxyglucosone, 3-deoxyglucosone, glyoxal, methylglyoxal, diacetyl, 5-hydroxymethyl-2-furfural, and 2-furfural and browning were investigated in cookies. The presence of 1.5% NaCl, 1% KCl, and 1% CaCl₂ on flour basis had no effect on α-dicarbonyl compounds, except 1-deoxyglucosone increased in the presence of KCl and CaCl₂. The increase in 5-hydroxymethyl-2-furfural formation in the presence of NaCl, KCl, and CaCl₂ did not relate to 3-deoxyglucosone formation and pH changes. NaCl, KCl, and CaCl₂ increased browning in cookies. Model reaction systems indicated that NaCl, KCl, and CaCl₂ enhance browning by increasing furfurals in caramelization. NaCl, KCl, and CaCl₂ decreased browning intensity in a heated glucose-glycine system. Use of CaCl₂ in cookies may considerably increase furfurals but not α-dicarbonyl compounds. Sodium reduction can be obtained by replacement with potassium without sacrificing the desired consequences of caramelization in sugar-rich baked goods.

Structure of protonated tryptophan dimer in the gas phase investigated by IRPD spectroscopy and theoretical calculations

RATIONAL

In addition to proton affinity (PA), side chains may also have an effect on the structures of amino acid complex ions in the gas phase. A previous study showed that the most stable isomer of Pro2 H(+) favored a salt-bridged structure. Tryptophan has a PA close to that of proline, but a quite different side chain. Thus, it will be interesting to discover whether the salt-bridged or charge-solvated conformation is energetically more favorable for Trp2 H(+) in the gas phase.

METHODS

The infrared photodissociation (IRPD) spectrum of Trp2 H(+) was obtained using a Fourier transform ion cyclotron resonance mass spectrometer equipped with a tunable OPO laser. The non-covalent cluster ions were generated by electrospray ionization. Structural optimization and frequency calculation of the selected isomers were performed at the M062X/6-311++G(d,p) level.

RESULTS

The experimental IRPD spectrum of Trp2 H(+) was reported in the region of 2700-3750 cm(-1) . Theoretical calculations show that the most stable isomer has a charge-solvated structure. Its energy was found to be 9 kcal/mol lower than that of the most stable salt-bridged isomer. The experimental spectrum is consistent with the predicted spectra of the most stable charge-solvated structures. Temperature effect on the stability of isomers was also evaluated and it was revealed that the contribution from salt-bridged isomers can be neglected at a temperature of 300 K.

CONCLUSIONS

Combining the method of IRPD spectroscopy with theoretical calculations, the structures of Trp2 H(+) were investigated. It is shown that the structures of Trp2 H(+) are dominated by charge-solvated forms. The results also indicate that the side chain may considerably affect the stability of the zwitterionic forms. Copyright © 2016 John Wiley & Sons, Ltd.

Calcium Binding to Amino Acids and Small Glycine Peptides in Aqueous Solution: Toward Peptide Design for Better Calcium Bioavailability

Deprotonation of amino acids as occurs during transfer from stomach to intestines during food digestion was found by comparison of complex formation constants as determined electrochemically for increasing pH to increase calcium binding (i) by a factor of around 6 for the neutral amino acids, (ii) by a factor of around 4 for anions of the acidic amino acids aspartic and glutamic acid, and (iii) by a factor of around 5.5 for basic amino acids. Optimized structures of the 1:1 complexes and ΔHbinding for calcium binding as calculated by density functional theory (DFT) confirmed in all complexes a stronger calcium binding and shorter calcium-oxygen bond length in the deprotonated form. In addition, the stronger calcium binding was also accompanied by a binding site shift from carboxylate binding to chelation by α-amino group and carboxylate oxygen for leucine, aspartate, glutamate, alanine, and asparagine. For binary amino acid mixtures, the calcium-binding constant was close to the predicted geometric mean of the individual amino acid binding constants indicating separate binding of calcium to two amino acids when present together in solution. At high pH, corresponding to conditions for calcium absorption, the binding affinity increased in the order Lys < Arg < Cys < Gln < Gly ∼ Ala < Asn < His < Leu < Glu< Asp. In a series of glycine peptides, calcium-binding affinity was found to increase in the order Gly-Leu ∼ Gly-Gly < Ala-Gly < Gly-His ∼ Gly-Lys-Gly < Glu-Cys-Gly < Gly-Glu, an ordering confirmed by DFT calculations for the dipeptides and which also accounted for large synergistic effects in calcium binding for up to 6 kJ/mol when compared to the corresponding amino acid mixtures.

Gas-Phase Spectroscopic Signatures of Carboxylate-Li(+) Contact Ion Pairs: New Benchmarks For Characterizing Ion Pairing in Solution

The coexistence of several types of ion pairs in solution together with their elusive nature hampers their experimental characterization, which relies in practice on theoretical models resorting to numerous approximations. In this context, a series of isolated contact ion pairs between a lithium cation and phenyl-tagged carboxylate anions of various lengths (Ph-(CH2)n-COO(-), n = 1-3) has been investigated in a conformer-selective manner by IR and UV laser spectroscopy, in conjunction with quantum chemistry calculations. The typical gas-phase IR signature of the bidentate structure formed between the carboxylate moiety and Li(+) has thus been obtained in the CO2(-) stretch region. In addition to the cation-anion interaction, a cation-π interaction occurs simultaneously in the largest system investigated (n = 3). The resulting distorted ion pair structure has been evidenced from both the IR signature of the CO2(-) stretches and the unique vibrationally resolved UV spectroscopy of a phenyl ring interacting with a cation. Such specific spectroscopic signatures of contact ion pairs provide experimental benchmarks, alternative to theoretical predictions, that can assist the assignment of vibrational spectra in solution.

Cationic Noncovalent Interactions: Energetics and Periodic Trends

In this review, noncovalent interactions of ions with neutral molecules are discussed. After defining the scope of the article, which excludes anionic and most protonated systems, methods associated with measuring thermodynamic information for such systems are briefly recounted. An extensive set of tables detailing available thermodynamic information for the noncovalent interactions of metal cations with a host of ligands is provided. Ligands include small molecules (H2, NH3, CO, CS, H2O, CH3CN, and others), organic ligands (O- and N-donors, crown ethers and related molecules, MALDI matrix molecules), π-ligands (alkenes, alkynes, benzene, and substituted benzenes), miscellaneous inorganic ligands, and biological systems (amino acids, peptides, sugars, nucleobases, nucleosides, and nucleotides). Hydration of metalated biological systems is also included along with selected proton-based systems: 18-crown-6 polyether with protonated peptides and base-pairing energies of nucleobases. In all cases, the literature thermochemistry is evaluated and, in many cases, reanchored or adjusted to 0 K bond dissociation energies. Trends in these values are discussed and related to a variety of simple molecular concepts.

Hydrogen bond mediated stabilization of the salt bridge structure for the glycine dimer anion

The formation of a salt bridge in deprotonated glycine dimer anions in a solvent-free environment is investigated using both infrared multiple photon dissociation spectroscopy between 600 and 1800 cm(-1) and theory. The zwitterionic and nonzwitterionic forms of glycine in this complex are computed to be nearly iso-energetic, yet predominantly the zwitterionic form is observed experimentally. The zwitterion stability is attributed to both the Coulombic attraction and the high stabilization from intramolecular hydrogen bonding that drives the energetic cost of proton transfer in a solvent free environment. These results show that there is a fine balance between the stabilities of these two forms of the anion. Elucidating the role of intrinsic factors, such as hydrogen bonding, can lead to a better understanding of the stabilities of salt bridges in the interiors of large proteins or at protein interfaces.

Structures and unimolecular chemistry of M(Pro2-H)+(M = Mg, Ca, Sr, Ba, Mn, Fe, Co, Ni, Cu, Zn) by IRMPD spectroscopy, SORI-CID, and theoretical studies

M(Pro₂-H)⁺complexes were electrosprayed and isolated in an FTICR cell where their unimolecular chemistries and structures were explored using SORI-CID and IRMPD spectroscopy.

An insight into the interaction of L-proline with the transition metal cations Fe(2+), Co(2+), Ni(2+): a gas phase theoretical study

The interaction of Fe(2+), Co(2+), and Ni(2+) with L-proline has been studied. Three modes of interaction have been considered: salt bridged (SB), involving binding in a bi-dentate manner through the carboxylate group of L-proline, charge solvated 1 (CS1) involving carbonyl and hydroxyl oxygen, and charge solvated 2 (CS2) involving carbonyl oxygen and the lone pair of the nitrogen atom. All calculations including geometry optimization, metal ion affinities (MIAs), and frequency calculations of the binding structures of Fe(2+), Co(2+), and Ni(2+) to L-proline were calculated using the hybrid density functional theory (DFT-B3LYP) method. All three cations were found to bind preferentially in a zwitterionic (SB) coordination pattern with the metal ion affinity in the order Ni(2+) ˃ Co(2+) ˃ Fe(2+) in all binding forms. The nature of the binding interaction between metal cations and L-proline was found to be mainly electrostatic. Comparison of the infrared vibrations of the C=O, the N-H and the O-H groups of free L-proline with L-proline-M(2+) in both CS1 and CS2 complex structures indicated a considerable shift to lower frequency during complexation. In order to gain more insight into the nature of the interaction of L-proline with group VIIIB metal ions, comparison of the interaction of L-proline with other cations such as (Li(+), Na(+), K(+), Be(2+), Mg(2+), and Ca(2+)) was made. Graphical Abstract L-proline with the transition metal cations Fe(2+), Co(2+), Ni(2.)

Affinity of Smectite and Divalent Metal Ions (Mg(2+), Ca(2+), Cu(2+)) with L-leucine: An Experimental and Theoretical Approach Relevant to Astrobiology

Earth is the only known planet bestowed with life. Several attempts have been made to explore the pathways of the origin of life on planet Earth. The search for the chemistry which gave rise to life has given answers related to the formation of biomonomers, and their adsorption on solid surfaces has gained much attention for the catalysis and stabilization processes related to the abiotic chemical evolution of the complex molecules of life. In this communication, surface interactions of L-leucine (Leu) on smectite (SMT) group of clay (viz. bentonite and montmorillonite) and their divalent metal ion (Mg(2+), Ca(2+) and Cu(2+)) incorporated on SMT has been studied to find the optimal conditions of time, pH, and concentration at ambient temperature (298 K). The progress of adsorption was followed spectrophotometrically and further characterized by FTIR, SEM/EDS and XRD. Leu, a neutral/non polar amino acid, was found to have more affinity in its zwitterionic form towards Cu(2+)- exchanged SMT and minimal affinity for Mg(2+)- exchanged SMT. The vibrational frequency shifts of -NH3 (+) and -COO(-) favor Van der Waal's forces during the course of surface interaction. Quantum calculations using density functional theory (DFT) have been applied to investigate the absolute value of metal ion affinities of Leu (Leu-M(2+) complex, M = Mg(2+), Ca(2+), Cu(2+)) with the help of their physico-chemical parameters. The hydration effect on the relative stability and geometry of the individual species of Leu-M(2+) × (H2O)n, (n =2 and 4) has also been evaluated within the supermolecule approach. Evidence gathered from investigations of surface interactions, divalent metal ions affinities and hydration effects with biomolecules may be important for better understanding of chemical evolution, the stabilization of biomolecules on solid surfaces and biomolecular-metal interactions. These results may have implications for understanding the origin of life and the preservation of biomarkers.

Adding Calcium to Foods and Effect on Acrylamide

Acrylamide is found in widely consumed heat-treated foods such as fried potato and bakery products. It is formed from asparagine via a Maillard reaction at temperatures higher than 100 °C. The presence of acrylamide has been considered as an important food-related crisis since it is classified as probably carcinogenic to humans. For this reason, acrylamide mitigation in foods becomes an important issue. Calcium salts are used to mitigate acrylamide formation in especially potato and bakery products. Calcium cation restricts asparagine to form a Schiff base during Maillard reaction in the presence of carbonyl compounds. There are several studies indicating the effect of calcium on mitigation of acrylamide both in model and food systems. According to these studies usage of calcium salts is found to be effective in mitigation of acrylamide formation. On the other hand, calcium salts cause increases in sugar dehydration products like 5-hydroxymethyl-2-furfural during heating. High solubility in water, effectiveness in low concentrations without changing sensorial properties and low price of calcium salts make them suitable in industrial applications.

New Synthesis Route of Hydrogel through A Bioinspired Supramolecular Approach: Gelation, Binding Interaction, and in Vitro Dressing

Peptide-based supramolecular hydrogels have been comprehensively investigated in biomaterial applications because of their unique bioactivity, biofunctionality, and biocompatible features. However, the presence of organic building blocks in peptide-based hydrogels often results in low mechanical stability. To expand their practical use and range of applications, it is necessary to develop the tool kit available to prepare bioinspired, peptide-based supramolecular hydrogels with improved mechanical stability. In this paper, we present an innovative electrostatic and cross-linking approach in which naphthyl-Phe-Phe-Cys (NapFFC) oligopeptides are combined with gold nanoparticles (AuNPs) and calcium ions (Ca(2+)) to produce peptide-based supramolecular hydrogels. We further investigate the interactions among NapFFC, AuNPs and Ca(2+) by microscopy. The morphology of the nanofibrous network constructions and the binding forces exhibited from the hydrogel demonstrated that the combination of two mechanisms successfully enhanced the mechanical stability through the formation of a densely entangled fibrous network of peptide multimers that is attributed to the AuNP linkage and Ca(2+)-induced agglomeration. UV-vis spectrophotometry and fluorescence analysis were also used to demonstrate the enhanced stability of the hydrogel under various conditions such as thermal, solvent erosion, pH value and sonication. All results indicate that the presence of AuNPs and Ca(2+) can strengthen the prepared hydrogel by more than doubling the diameter of NapFFC nanofibers, enabling the formation of stronger frameworks and slowing the release of components. Further experiments confirmed that HeLa cells can grow on the bioinspired NapFFC-AuNP hydrogel and exhibit high cell viability and that these cells were killed on contact with a hydrogel containing a drug. Our peptide-based supramolecular hydrogels prepared from the observed electrostatic and cross-linking mechanisn exhibited a significantly improved mechanical stability, making them well suited to use as a drug carrier in hydrogel dressings and as extracellular materials (ECMs) for tissue engineering.

Structure of Protonated Threonine Dimers in the Gas Phase: Salt-Bridged or Charge-Solvated?

For homodimers of amino acids, their salt-bridged structures are gradually stabilized as the proton affinity of the component amino acid increases. Threonine has a proton affinity value located in the middle of the list of 20 natural amino acids. Thus, identifying whether the most stable isomer of protonated threonine dimer (Thr(2)H(+)) has a charge-solvated or salt-bridged structure is important and helpful for understanding the structures of other homodimers. By combining infrared photodissociation (IRPD) spectroscopy and theoretical calculations, the structures of Thr(2)H(+) were investigated. Based on calculations at the M062X/6-311++G(d,p)//M062X/6-311++G(d,p) level, the most stable isomer of Thr(2)H(+) was computed to be a charge-solvated structure, with an energy 3.87 kcal/mol lower than the most stable salt-bridged isomer. The predicted infrared spectrum is in good agreement with the experimental spectrum. To evaluate the temperature effect on the distribution of different isomers, the relative concentrations of the six isomers of Thr(2)H(+) were calculated at different temperatures, according to their partition functions and enthalpies. The results show that the isomers are dominated by charge-solvated structures at a temperature of 300 K.

The protonated and sodiated dimers of proline studied by IRMPD spectroscopy in the N-H and O-H stretching region and computational methods

IRMPD spectroscopy and computational chemistry techniques have been used to determine that the proton- and sodium-bound dimers of proline exist as a mixture of a number of different structures. Simulated annealing computations were found to be helpful in determining the unique structures of the protonated and sodiated dimers, augmenting chemical intuition. The experimental and computational results are consistent with the proton-bound dimer of N-protonated proline bound to zwitterionic proline. There was no spectroscopic evidence in the 3200-3800 cm(-1) region for a canonical structure which is predicted to have a weak N-H stretch at about 3440 cm(-1). A well resolved band at 1733 cm(-1) from a previous spectroscopic study (DOI: 10.1021/ja068715a ) was reassigned from a high energy canonical isomer to the C=O stretch of a lower energy zwitterionic structure. This band is a free carboxylate C=O stretch where protonated proline is hydrogen bonded to the other carboxylate oxygen which is also involved in an intramolecular hydrogen bond. Fifteen structures of the sodium bound proline dimer were computed to be within 10 kJ mol(-1) of Gibbs energy and eight structures were within 5 kJ mol(-1). None of these structures can be ruled out based on the experimental IRMPD spectrum. They all have an N-H stretching band predicted in a position that agrees with the experimental spectrum. However, only structures where one of the proline monomers is in the canonical form and having a free O-H bond can produce the band at ∼3600 cm(-1).

Driven molecular dynamics studies of the shared proton motion in the H5O2+·Ar cluster: the effect of argon tagging and deuteration on vibrational spectra

We report IR spectra of H5O2(+) and H5O2(+)·Ar and their deuterium isotopologues using ab initio molecular dynamics. The trajectories were propagated as microcanonical (NVE) ensembles at energies corresponding to temperatures 50 and 100 K. The potential energy surface is calculated on-the-fly at the MP2/aug-cc-pVDZ level of theory. The calculations show that adding an argon atom to H5O2(+) introduces symmetry breaking in the Zundel core ion, causes blueshift in the shared proton vibration by about 200 cm(-1), and leads to the splitting of the OH stretch vibrations into four bands. Driven molecular dynamics (DMD) method is used to assign the spectrum by coupling the dipole moment to an external electric field oscillating at frequency ω. The broad feature at 1100 cm(-1) in the H5O2(+)·Ar spectrum is ascribed to the large amplitude shared proton vibration coupled with torsion and wag modes. MD MP2 simulations predict the H/D redshift in the shared proton vibration and water bending vibration to be about 280 and 460 cm(-1), respectively, in good agreement with experimental observations.