Understanding of protomers/deprotomers by combining mass spectrometry and computation

Multifunctional compounds may form different prototropic isomers under different conditions, which are known as protomers/deprotomers. In biological systems, these protomer/deprotomer isomers affect the interaction modes and conformational landscape between compounds and enzymes and thus present different biological activities. Study on protomers/deprotomers is essentially the study on the acidity/basicity of each intramolecular functional group and its effect on molecular structure. In recent years, the combination of mass spectrometry (MS) and computational chemistry has been proven to be a powerful and effective means to study prototropic isomers. MS-based technologies are developed to discriminate and characterize protomers/deprotomers to provide structural information and monitor transformations, showing great superiority than other experimental methods. Computational chemistry is used to predict the thermodynamic stability of protomers/deprotomers, provide the simulated MS/MS spectra, infrared spectra, and calculate collision cross-section values. By comparing the theoretical data with the corresponding experimental results, the researchers can not only determine the protomer/deprotomer structure, but also investigate the structure-activity relationship in a given system. This review covers various MS methods and theoretical calculations and their devotion to isomer discrimination, structure identification, conformational transformation, and phase transition investigation of protomers/deprotomers.

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 ion Ag + ( benzylamine ) ( L ) .

Heterogeneous Rotational Dynamics of Imidazolium-Based Organic Ionic Plastic Crystals

Organic ionic plastic crystals (OIPCs) are a unique class of materials that undergo orientational and conformational motions while maintaining a long-range ordered lattice structure. OIPCs have attracted attention because the rotational motions were known to accelerate the diffusion of mobile ions such as lithium ions. However, only a small number of combinations of cations and anions lead to OIPCs because the rotational motion may be restricted by both the molecular structure and the crystal class. In this work, we perform molecular dynamics simulations to study the effects of the molecular structure and the crystal class on the rotational motion and the phase transitions. We investigate four imidazolium-based ionic crystals: (1) 1-methyl-3-methylimidazolium hexafluorophosphate ([MMIM][PF₆]), (2) 1-methyl-3-methylimidazolium chloride ([MMIM][Cl]), (3) monoclinic 1-butyl-3-methylimidazolium chloride ([BMIM][Cl]), and (4) orthorhombic [BMIM][Cl] ionic crystals. We construct initial configurations of OIPCs by employing experimental crystalline structures. Then, we increase the temperature gradually and monitor the density and the radial distribution functions. We estimate the rotational van Hove correlation functions and find that molecules in plastic crystal phases undergo rotational hopping motions and OIPCs exhibit rotational dynamic heterogeneity significantly. The structure of anions and cations affect the phase transition of OIPCs. And the crystal class is also critical to the phase transition of OIPCs because the rotational motion of ions depends on the crystal class.

Structural confirmation and spectroscopic study of a biomolecule: Norepinephrine

The present work deals with the conformational and vibrational spectroscopic study of an important bio-molecule named norepinephrine in gas phase. The FTIR and FTRaman spectrum of norepinephrine in amorphous form were recorded in wavenumber range 4000-400 cm^-1 and 4000-50 cm^-1 respectively. We have investigated twenty-seven stable conformational structures of norepinephrine molecule. All the calculations have been done using Density Functional Theory with exchange functional B3LYP incorporated with the 6-31++G(d, p) basis set. The effect of hydrochloride on different bond lengths, bond angles and dihedral angles in the most stable conformer has also been studied. The total potential energy distribution for both the most stable conformer and the most stable conformer in hydrochloride was performed with the help Normal coordinate analysis method. Most of the calculated vibrational frequencies are in good agreement with the experimental frequencies. The natural bond orbital analysis was also performed to ensure the stability of electronic structures of norepinephrine. To know chemical reactivity of norepinephrine molecule we have calculated the energy gap between HOMO and LUMO orbitals and it has found above 5 eV in all the conformers.

Spectroscopy of Proton Coordination with Ethylenediamine

Protonated ethylenediamine monomer, dimer, and trimer were produced in the gas phase by an electrical discharge/supersonic expansion of argon seeded with ethylenediamine (C₂H₈N₂, en) vapor. Infrared spectra of these ions were measured in the region from 1000 to 4000 cm^-1 using laser photodissociation and argon tagging. Computations at the CBS-QB3 level were performed to explore possible isomers and understand the infrared spectra. The protonated monomer exhibits a gauche conformation and an intramolecular hydrogen bond. Its parallel shared proton vibration occurs as a broad band around 2785 cm^-1, despite the formally equivalent proton affinities of the two amino groups involved, which usually leads to low frequency bands. The barrier to intramolecular proton transfer is 2.2 kcal mol^-1 and does not vanish upon addition of the zero-point energy, unlike the related protonated ammonia dimer. The structure of the dimer is formed by chelation of the monomer's NH₃⁺ group, thereby localizing the excess proton and increasing the frequency of the intramolecular shared proton vibration to 3157 cm^-1. Other highly fluxional dimer structures with facile intermolecular proton transfer and concomitant structural reorganization were computed to lie within 2 kcal mol^-1 of the experimentally observed structure. The spectrum of the trimer is rather diffuse, and a clear assignment is not possible. However, an isomer with an intramolecular proton transfer like that of the monomer is most consistent with the experimental spectrum.

Infrared Multiphoton Dissociation Spectroscopy with Free-Electron Lasers: On the Road from Small Molecules to Biomolecules

Infrared multiphoton dissociation (IRMPD) spectroscopy is commonly used to determine the structure of isolated, mass-selected ions in the gas phase. This method has been widely used since it became available at free-electron laser (FEL) user facilities. Thus, in this Minireview, we examine the use of IRMPD/FEL spectroscopy for investigating ions derived from small molecules, metal complexes, organometallic compounds and biorelevant ions. Furthermore, we outline new applications of IRMPD spectroscopy to study biomolecules.

Cobalt(ii) liquid metal salts for high current density electrodeposition of cobalt

Cobalt-containing liquid metal salts were synthesized and characterized. Reversible thermochromism was observed and the electrodeposition of cobalt layers with different morphologies was investigated.

Cobalt(ii) containing liquid metal salts for electrodeposition of cobalt and electrochemical nanoparticle formation

Cobalt(ii) containing ionic liquids were used as electrolytes for the electrodeposition of cobalt thin films and cobalt nanoparticles.

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.

Conformational study of neutral histamine monomer and their vibrational spectra

Molecular modeling and potential energy scanning of histamine molecule, which is an important neurotransmitter, with respect to the dihedral angle of methylamine side chain have done which prefer three different conformers of histamine monomer. We have calculated molecular structures and vibrational spectra with IR and Raman intensities of these conformers using Density Functional Theory (DFT) with the exchange functional B3LYP incorporated with the basis set 6-31++G(d,p) and Hartree-Fock (HF) with the same basis set. We have also employed normal coordinate analysis (NCA) to scale the theoretical frequencies and to calculate potential energy distributions (PEDs) for the conspicuous assignments. Normal modes assignments of some of the vibrational frequencies of all the three conformers are in good agreement with the earlier reported experimental frequencies of histamine whereas others have modified. The standard deviations between the theoretical and experimental frequencies fall in the region 13-20cm(-1) for the three conformers. NBO analyses of histamine conformers were also performed. The net charge transfers from ethylamine side chain to the imidazole ring. The intensive interactions between bonding and anti-bonding orbitals are found in imidazole ring. The HOMO-LUMO energy gap is nearly 5.50eV.

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.

Infrared spectrum of the cold ortho-fluorinated protonated neurotransmitter 2-phenylethylamine: competition between NH+⋯π and NH+⋯F interactions

IR spectra of cold rare-gas tagged ions reveal the switch of the preferred conformation of the highly flexible side chain of a prototypical protonated neurotransmitter induced by site-specific aromatic fluorination.

Structural motifs of 2-(2-fluoro-phenyl)-ethylamine conformers

Vibronic and vibrational spectra of 2-(2-fluoro-phenyl)-ethylamine (2-FPEA) conformers were measured in a molecular beam by resonant two-photon ionization (R2PI), ultraviolet–ultraviolet hole burning (UV–UV HB) spectroscopy, and ionization-loss stimulated Raman spectroscopy (ILSRS).

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.

Dissociation Pathways of Benzylpyridinium "Thermometer" Ions Depend on the Activation Regime: An IRMPD Spectroscopy Study

The dissociation of benzylpyridinium "thermometer" ions is widely used to calibrate the internal energy of ions produced in mass spectrometry. The fragmentation mechanism is usually believed to yield a benzylium cation, although recent studies suggest the possibility of a rearrangement leading to the tropylium isomer, which would compromise the accuracy of energy calibrations. In this study, we used IRMPD spectroscopy to probe the dissociation pathways of the p-(tert-butyl)benzylpyridinium ion. Our results show that the formation of both benzylium and tropylium products is feasible depending on the activation regime and on the reaction time scale. Varying the trapping delays in the hexapole gives insight into a rearrangement mechanism occurring through consecutive reactions with an isomerization from benzylium to tropylium. Our work provides experimental validations for the established calibration procedure and highlights the adequacy of IRMPD spectroscopy to qualitatively resolve gas-phase rearrangement kinetics.

Competing intramolecular vs. intermolecular hydrogen bonds in solution

A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with intramolecular vs. intermolecular hydrogen bonds for different types of small organic molecules. In their most stable gas-phase structure, an intramolecular hydrogen bond is possible. In a protic solution, the intramolecular hydrogen bond may disrupt in favor of two solute-solvent intermolecular hydrogen bonds. The balance of the increased internal energy and the stabilizing effect of the solute-solvent interactions regulates the new conformer composition in the liquid phase. The review additionally considers the solvent effects on the stability of simple dimeric systems as revealed from molecular dynamics simulations or on the basis of the calculated potential of mean force curves. Finally, studies of the solvent effects on the type of the intermolecular hydrogen bond (neutral or ionic) in acid-base complexes have been surveyed.

Cation-π interactions in protonated phenylalkylamines

Phenylalkylamines of the general formula C6H5(CH2)nNH2 (n = 1-4) have been delivered to the gas phase as protonated species using electrospray ionization. The ions thus formed have been assayed by IRMPD spectroscopy in two different spectroscopic domains, namely, the 600-1800 and the 3000-3500 cm(-1) regions using either an IR free electron laser or a tabletop OPO/OPA laser source. The interpretation of the experimental spectra is aided by density functional theory calculations of candidate species and vibrational frequency analyses. Protonated benzylamine presents a relatively straightforward instance of a single stable conformer, providing a trial case for the adopted approach. Turning to the higher homologues, C6H5(CH2)nNH3(+) (n = 2-4), more conformations become accessible. For each C6H5(CH2)nNH3(+) ion (n = 2-4), the most stable geometry is characterized by cation-π interactions between the positively charged ammonium group and the aromatic π-electronic system, permitted by the folding of the polymethylene chain. The IRMPD spectra of the sampled ions confirm the presence of the folded structures by comparison with the calculated IR spectra of the various possible conformers. An inspection of the NH stretching region is helpful in this regard.

Probing protonation sites of isolated flavins using IR spectroscopy: from lumichrome to the cofactor flavin mononucleotide

Infrared spectra of the isolated protonated flavin molecules lumichrome, lumiflavin, riboflavin (vitamin B2), and the biologically important cofactor flavin mononucleotide are measured in the fingerprint region (600-1850 cm(-1)) by means of IR multiple-photon dissociation (IRMPD) spectroscopy. Using density functional theory calculations, the geometries, relative energies, and linear IR absorption spectra of several low-energy isomers are calculated. Comparison of the calculated IR spectra with the measured IRMPD spectra reveals that the N10 substituent on the isoalloxazine ring influences the protonation site of the flavin. Lumichrome, with a hydrogen substituent, is only stable as the N1-protonated tautomer and protonates at N5 of the pyrazine ring. The presence of the ribityl unit in riboflavin leads to protonation at N1 of the pyrimidinedione moiety, and methyl substitution in lumiflavin stabilizes the tautomer that is protonated at O2. In contrast, flavin mononucleotide exists as both the O2- and N1-protonated tautomers. The frequencies and relative intensities of the two C=O stretch vibrations in protonated flavins serve as reliable indicators for their protonation site.