An Investigation of Protonation Sites and Conformations of Protonated Amino Acids by IRMPD Spectroscopy

The protonation sites and structures of a series of protonated amino acids (Gly, Ala, Pro, Phe, Lys and Ser) are investigated by means of infrared multiple‐photon dissociation (IRMPD) spectroscopy and electronic‐structure calculations. The IRMPD spectra of the protonated species are recorded using the combination of a free‐electron laser (FEL) and an electrospray‐ion‐trap mass spectrometer. The structures of different possible isomers of these protonated species are optimized at the B3LYP/6‐311+G(d, p) level of theory and the IR spectra calculated using the same computational method. For every amino acid studied herein, the current results indicate that a proton is bound to the α‐amino nitrogen, except for lysine, in which the protonation site is the amino nitrogen in the side chain. According to the calculated and experimental IRMPD results, the structures of the protonated amino acids may be assigned unambiguously. For Gly, Ala, and Pro, in each of the most stable isomers the protonated amino group forms an intramolecular hydrogen bond with the adjacent carbonyl oxygen. In the case of Gly, the isomer containing a proton bound to the carbonyl oxygen is theoretically possible. However, it does not exist under the experimental conditions because it has a significantly higher energy (i.e. 26.6 kcal mol^?1) relative to the most stable isomer. For Ser and Phe, the protonated amino group forms two intramolecular hydrogen bonds with both the adjacent carbonyl oxygen and the side‐chain group in each of the most stable isomers. In protonated lysine, the protonated amino group in the side chain forms two hydrogen bonds with the α‐amino nitrogen and the carbonyl oxygen, which is a cyclic structure. Interestingly, for protonated lysine the zwitterionic structure is a local minimum energy isomer, but the experimental spectrum indicates that it does not exist under the experimental conditions. This is consistent with the fact that the zwitterionic isomer is 9.2 kcal mol^?1 higher in free energy at 298 K than the most stable isomer. The carbonyl stretching vibration in the range of 1760–1800 cm^?1 is especially sensitive to the structural change. In addition, IRMPD mechanisms for the protonated amino acids are also investigated.     

Ligation Motifs in Zinc-Bound Sulfonamide Drugs Assayed by IR Ion Spectroscopy

The sulfonamide–zinc ion interaction, performing a key role in various biological contexts, is the focus of the present study, with the aim of elucidating ligation motifs in zinc complexes of sulfa drugs, namely sulfadiazine (SDZ) and sulfathiazole (STZ), in a perturbation-free environment. To this end, an approach is exploited based on mass spectrometry coupled with infrared multiple photon dissociation (IRMPD) spectroscopy backed by quantum chemical calculations. IR spectra of Zn(H₂O+SDZ−H)⁺ and Zn(H₂O+STZ−H)⁺ ions are consistent with a three-coordinate zinc complex, where ZnOH⁺ binds to the uncharged sulfonamide via N(heterocycle) and O(sulfonyl) donor atoms. Alternative prototropic isomers Zn(OH₂)(SDZ−H)⁺ and Zn(OH₂)(STZ−H)⁺ lie 63 and 26 kJ mol⁻¹ higher in free energy, respectively, relative to the ground state Zn(OH)(SDZ)⁺ and Zn(OH)(STZ)⁺ species and do not contribute to any significant extent in the sampled population.     

Breslow Intermediates (Amino Enols) and Their Keto Tautomers: First Gas-Phase Characterization by IR Ion Spectroscopy

Breslow intermediates (BIs) are the crucial nucleophilic amino enol intermediates formed from electrophilic aldehydes in the course of N-heterocyclic carbene (NHC)-catalyzed umpolung reactions. Both in organocatalytic and enzymatic umpolung, the question whether the Breslow intermediate exists as the nucleophilic enol or in the form of its electrophilic keto tautomer is of utmost importance for its reactivity and function. Herein, the preparation of charge-tagged Breslow intermediates/keto tautomers derived from three different types of NHCs (imidazolidin-2-ylidenes, 1,2,4-triazolin-5-ylidenes, thiazolin-2-ylidenes) and aldehydes is reported. An ammonium charge tag is introduced through the aldehyde unit or the NHC. ESI-MS IR ion spectroscopy allowed the unambiguous conclusion that in the gas phase, the imidazolidin-2-ylidene-derived BI indeed exists as a diamino enol, while both 1,2,4-triazolin-5-ylidenes and thiazolin-2-ylidenes give the keto tautomer. This result coincides with the tautomeric states observed for the BIs in solution (NMR) and in the crystalline state (XRD), and is in line with our earlier calculations on the energetics of BI keto–enol equilibria.     

Alkali Metal Complexes of the Dipeptides PheAla and AlaPhe: IRMPD Spectroscopy

Complexes of PheAla and AlaPhe with alkali metal ions Na⁺ and K⁺ are generated by electrospray ionization, isolated in the Fourier‐transform ion cyclotron resonance (FT–ICR) ion trapping mass spectrometer, and investigated by infrared multiple‐photon dissociation (IRMPD) using light from the FELIX free electron laser over the mid‐infrared range from 500 to 1900 cm^?1. Insight into structural features of the complexes is gained by comparing the obtained spectra with predicted spectra and relative free energies obtained from DFT calculations for candidate conformers. Combining spectroscopic and energetic results establishes that the metal ion is always chelated by the amide carbonyl oxygen, whilst the C‐terminal hydroxyl does not complex the metal ion and is in the endo conformation. It is also likely that the aromatic ring of Phe always chelates the metal ion in a cation‐π binding configuration. Along with the amide CO and ring chelation sites, a third Lewis‐basic group almost certainly chelates the metal ion, giving a threefold chelation geometry. This third site may be either the C‐terminal carbonyl oxygen, or the N‐terminal amino nitrogen. From the spectroscopic and computational evidence, a slight preference is given to the carbonyl group, in an RO_aO_t chelation pattern, but coordination by the amino group is almost equally likely (particularly for K⁺PheAla) in an RO_aN_t chelation pattern, and either of these conformations, or a mixture of them, would be consistent with the present evidence. (R represents the π ring site, O_a the amide oxygen, O_t the terminal carbonyl oxygen, and N_t the terminal nitrogen.) The spectroscopic findings are in better agreement with the MPW1PW91 DFT functional calculations of the thermochemistry compared with the B3LYP functional, which seems to underestimate the importance of the cation–π interaction.     

Molecular Complexes of Simple Anions with Electron‐Deficient Arenes: Spectroscopic Evidence for Two Types of Structural Motifs for Anion–Arene Interactions

Anion–π interactions between a π‐acidic aromatic system and an anion are gaining increasing recognition in chemistry and biology. Herein, the binding features of an electron‐deficient aromatic system (1,3,5‐trinitrobenzene (TNB)) and selected anions (OH^?, Br^?, and I^?) are examined in the gas phase by using the combined information derived from collision‐induced dissociation experiments at variable energy, infrared multiple‐photon dissociation spectroscopy, and quantum chemical calculations. We provide spectroscopic evidence for two different structural motifs of anion–arene complexes depending on the nature of the anion. The TNB–OR^? complexes (R=H, or alkyl groups which were studied earlier) adopt an anionic σ‐complex structure whereby RO^? attacks the aromatic ring with covalent bond formation, and develops a tetrahedral ring carbon bound to H and OR. The halide complexes rather conform to a structure in which the TNB moiety is hardly altered, and the halogen is placed on an unsubstituted carbon atom over the periphery of the ring at a C–X distance that is appreciably longer than a typical covalent bond length. The ensuing structural motif, previously characterized in the solid state and named weak σ interaction, is now confirmed by an IR spectroscopic assay in the gas phase, in which the sampled species are unperturbed by crystal packing or solvation effects.     

Gas‐Phase Interactions between Lead(II) Ions and Cytosine: Tandem Mass Spectrometry and Infrared Multiple‐Photon Dissociation Spectroscopy Study

Gas‐phase interactions between Pb²⁺ ions and cytosine (C) were studied by combining tandem mass spectrometry, infrared multiple photon dissociation spectroscopy, and density functional theory (DFT) calculations. Both singly and doubly charged complexes were generated by electrospray. The [Pb(C)?H]⁺ complex was extensively studied, and this study shows that two structures, involving the interaction of the metal with the deprotonated canonical keto‐amino tautomer of cytosine, are generated in the gas phase; the prominent structure is the bidentate form involving both the N1 and O2 electronegative centers. The DFT study also points out a significant charge transfer from the nucleobase to the low‐lying p orbitals of the metal and a strong polarization of the base upon complexation. The various potential energy surfaces explored to account for the fragmentation observed are consistent with the high abundance of the [PbNH₂]⁺ fragment ion.     

Applications of Terahertz Spectroscopy in Biosystems

Terahertz (THz) spectroscopic investigations of condensed‐phase biological samples are reviewed ranging from the simple crystalline forms of amino acids, carbohydrates and polypeptides to the more complex aqueous forms of small proteins, DNA and RNA. Vibrationally resolved studies of crystalline samples have revealed the exquisite sensitivity of THz modes to crystalline order, temperature, conformational form, peptide sequence and local solvate environment and have given unprecedented measures of the binding force constants and anharmonic character of the force fields, properties necessary to improve predictability but not readily obtainable using any other method. These studies have provided benchmark vibrational data on extended periodic structures for direct comparisons with classical (CHARMm) and quantum chemical (density functional theory) theories. For the larger amorphous and/or aqueous phase samples, the THz modes form a continuum‐like absorption that arises because of the full accessibility to conformational space and/or the rapid time scale for inter‐conversion in these environments. Despite severe absorption by liquid water, detailed investigations have uncovered the photo‐ and hydration‐induced conformational flexibility of proteins, the solvent shell depth of the water/biomolecule boundary layers and the solvent reorientation dynamics occurring in these interfacial layers that occur on sub‐picosecond time scales. As such, THz spectroscopy has enhanced and extended the accessibility to intermolecular forces, length‐ and timescales important in biological structure and activity.     

Influence of the Charge State on the Structures and Interactions of Vancomycin Antibiotics with Cell‐Wall Analogue Peptides: Experimental and Theoretical Studies

Charge matters! The charge state significantly influences the conformation and the binding energy between vancomycin antibiotic and bacterial cell‐wall analogue peptides (see figure). Surface‐induced dissociation (SID) studies provide a quantitative comparison between the stabilities of different charge states of the complex.

     

Amino Acid Oxidation: A Combined Study of Cysteine Oxo Forms by IRMPD Spectroscopy and Simulations

The redox activity of cysteine sulfur allows numerous post‐translational protein modifications involved in the oxidative regulation of metabolism, in metal binding, and in signal transduction. A combined approach based on infrared multiple photon dissociation spectroscopy at the Centre Laser Infrarouge d'Orsay (CLIO) free electron laser facility, calculations of IR frequencies, and finite temperature ab initio molecular dynamics simulations has been employed to characterize the gas‐phase structures of deprotonated cysteine sulfenic, sulfinic, and sulfonic acids, [cysSO_x]^? (x=1, 2, 3, representing the number of S‐bound oxygen atoms), which are key intermediates in the redox‐switching chemistry of proteins. The ions show different structural motifs owing to preferential binding of the proton to either the carboxylate or sulfur‐containing group. Due to the decreasing basicity of the sulfenic, sulfinic, and sulfonic terminals, the proton bound to SO^? in [cysSO]^? migrates to the carboxylate in [cysSO₃]^?, whereas it turns out to be shared in [cysSO₂]^?. Evidence is gathered that a mixture of close‐lying low‐energy conformers is sampled for each cysteine oxo form in a Paul ion trap at room temperature.     

Infrared Spectroscopy of Dioxouranium(V) Complexes with Solvent Molecules: Effect of Reduction

UO₂⁺–solvent complexes having the general formula [UO₂(ROH)]⁺ (R=H, CH₃, C₂H₅, and n‐C₃H₇) are formed using electrospray ionization and stored in a Fourier transform ion cyclotron resonance mass spectrometer, where they are isolated by mass‐to‐charge ratio, and then photofragmented using a free‐electron laser scanning through the 10 μm region of the infrared spectrum. Asymmetric O=U=O stretching frequencies (ν₃) are measured over a very small range [from ～953 cm^?1 for H₂O to ～944 cm^?1 for n‐propanol (n‐PrOH)] for all four complexes, indicating that the nature of the alkyl group does not greatly affect the metal centre. The ν₃ values generally decrease with increasing nucleophilicity of the solvent, except for the methanol (MeOH)‐containing complex, which has a measured ν₃ value equal to that of the n‐PrOH‐containing complex. The ν₃ frequency values for these U(V) complexes are about 20 cm^?1 lower than those measured for isoelectronic U(VI) ion‐pair species containing analogous alkoxides. ν₃ values for the U(V) complexes are comparable to those for the anionic [UO₂(NO₃)₃]^? complex, and 40–70 cm^?1 lower than previously reported values for ligated uranyl(VI) dication complexes. The lower frequency is attributed to weakening of the O?U?O bonds by repulsion related to reduction of the U metal centre, which increases electron density in the antibonding π* orbitals of the uranyl moiety. Computational modelling of the ν₃ frequencies using the B3LYP and PBE functionals is in good agreement with the IRMPD measurements, in that the calculated values fall in a very small range and are within a few cm^?1 of measurements. The values generated using the LDA functional are slightly higher and substantially overestimate the trends. Subtleties in the trend in ν₃ frequencies for the H₂O–MeOH–EtOH–n‐PrOH series are not reproduced by the calculations, specifically for the MeOH complex, which has a lower than expected value.     

Two‐Dimensional Infrared Spectroscopy Reveals the Structure of an Evans Auxiliary Derivative and Its SnCl4 Lewis Acid Complex

Determining the structure of reactive intermediates is the key to understanding reaction mechanisms. To access these structures, a method combining structural sensitivity and high time resolution is required. Here ultrafast polarization‐dependent two‐dimensional infrared (P2D‐IR) spectroscopy is shown to be an excellent complement to commonly used methods such as one‐dimensional IR and multidimensional NMR spectroscopy for investigating intermediates. P2D‐IR spectroscopy allows structure determination by measuring the angles between vibrational transition dipole moments. The high time resolution makes P2D‐IR spectroscopy an attractive method for structure determination in the presence of fast exchange and for short‐lived intermediates. The ubiquity of vibrations in molecules ensures broad applicability of the method, particularly in cases in which NMR spectroscopy is challenging due to a low density of active nuclei. Here we illustrate the strengths of P2D‐IR by determining the conformation of a Diels–Alder dienophile that carries the Evans auxiliary and its conformational change induced by the complexation with the Lewis acid SnCl₄, which is a catalyst for stereoselective Diels–Alder reactions. We show that P2D‐IR in combination with DFT computations can discriminate between the various conformers of the free dienophile N‐crotonyloxazolidinone that have been debated before, proving antiperiplanar orientation of the carbonyl groups and s‐cis conformation of the crotonyl moiety. P2D‐IR unequivocally identifies the coordination and conformation in the catalyst–substrate complex with SnCl₄, even in the presence of exchange that is fast on the NMR time scale. It resolves a chelate with the carbonyl orientation flipped to synperiplanar and s‐cis crotonyl configuration as the main species. This work sets the stage for future studies of other catalyst–substrate complexes and intermediates using a combination of P2D‐IR spectroscopy and DFT computations.     

Isomerization of Secondary Phosphirane into Terminal Phosphinidene Complexes: An Analogy between Monovalent Phosphorus and Transition Metals

Secondary phosphirane complexes isomerize above 100 °C to give the corresponding terminal phosphinidene complexes, which can be trapped by alkenes and alkynes. This reaction is a rare instance of the isomerization of a P^III derivative into a P^I derivative. It appears to mimic the reductive elimination of alkanes from transition‐alkylmetal hydrides.     

Towards Atomically Precise Supported Catalysts from Monolayer-Protected Clusters: The Critical Role of the Support

Controlling the size and uniformity of metal clusters with atomic precision is essential for fine-tuning their catalytic properties, however for clusters deposited on supports, such control is challenging. Here, by combining X-ray absorption spectroscopy and density functional theory calculations, it is shown that supports play a crucial role in the evolution of monolayer-protected clusters into catalysts. Based on the acidic nature of the support, cluster-support interactions lead either to fragmentation of the cluster into isolated Au–ligand species or ligand-free metallic Au⁰ clusters. On Lewis acidic supports that bind metals strongly, the latter transformation occurs while preserving the original size of the metal cluster, as demonstrated for various Au_n sizes. These findings underline the role of the support in the design of supported catalysts and represent an important step toward the synthesis of atomically precise supported nanomaterials with tailored physico-chemical properties.     

Toward the complete prediction of the 1H and 13C NMR spectra of complex organic molecules by DFT methods: application to natural substances

The NMR parameters (1H and 13C chemical shifts and coupling constants) for a series of naturally occurring molecules have been calculated mostly with DFT methods, and their spectra compared with available experimental ones. The comparison includes strychnine as a test case, as well as some examples of recently isolated natural products (corianlactone, daphnipaxinin, boletunone B) featuring unusual and/or crowded structures and, in the case of boletunone B, being the subject of a recent revision. Whenever experimental spectra were obtained in polar solvents, the calculation of NMR parameters was also carried out with the Integral Equation-Formalism Polarizable Continuum Model (IEF-PCM) continuum method. The computed results generally show a good agreement with experiment, as judged not only by statistical parameters but also by visual comparison of line spectra. The origin of the remaining discrepancies is attributed to the incomplete modeling of conformational and specific solvent effects.     

Towards an Understanding of Halide Interactions with the Carbonyl-Containing Molecule CH3CHO

The anion photoelectron spectra of Cl⁻⋅⋅⋅CD₃CDO, Cl⁻⋅⋅⋅(CD₃CDO)₂, Br⁻⋅⋅⋅CH₃CHO, and I⁻⋅⋅⋅CH₃CHO are presented with electron stabilisation energies of 0.55, 0.93, 0.48, and 0.40 eV, respectively. Optimised geometries of the singly solvated species featured the halide appended to the CH₃CHO molecule in-line with the electropositive portion of the C=O bond and having binding energies between 45 and 52 kJ mol⁻¹. The doubly solvated Cl⁻⋅⋅⋅(CH₃CHO)₂ species features asymmetric solvation upon the addition of a second CH₃CHO molecule. Theoretical detachment energies were found to be in excellent agreement with experiment, with comparisons drawn between other halide complexes with simple carbonyl molecules.