Table 1 - uploaded by Abdul-Rahman Allouche
Content may be subject to copyright.
Source publication
Mid-infrared spectroscopy coupled with mass spectrometry is an appealing tool for the sequencing and structural elucidation of functional modifications in biopolymers, as it offers direct spectroscopic identification of the functionality where the traditional mass spectrometric approach is insufficient. Whereas the gas phase vibrational spectroscop...
Similar publications
Chinese herbal polysaccharides (CHPs) are natural polymers composed of monosaccharides, which are widely found in Chinese herbs and work as one of the important active ingredients. Its biological activity is attributed to its complex chemical structure with diverse spatial conformations. However, the structural elucidation is the foundation but a b...
Citations
... Another major goal of this study was to simulate the theoretical IR spectrum of DPSO2: to calculate the IR absorption of substance in an exceptionally theoretical manner, based on quantum chemical and statistical analysis, which further can be directly matched with experimentally determined one. It is worthwhile to note that concerning the vibrational analysis of sulfur-organic molecules Barnes et.al have shown that among DFT methods cam-B3LYP, M06-2X, wB97X-D, and PBE0 with 6-311++G(2df,2pd) and triple-zeta Dunning's basis sets predict the harmonic IR spectra in close agreement with the experimental spectrum [13], while most of other popular DFT methods completely fail. Thus, there is an overlap of methods with our study, showing that particular methods provide good results both from geometrical and spectral accuracy considerations. ...
In this work, the conformational and vibrational analysis of dipropyl sulfone in its isolated gaseous state with identification of all stable conformers, their energy and degeneracy, relative population determined by Boltzmann distribution, as well as IR spectra have been performed by density functional theory (DFT) methods. Several DFT methods and basis sets were tested. It was demonstrated that the various local and hybrid DFT functionals such as well-known B3LYP, regardless of the size of basis sets, completely fail in the prediction of correct molecular structures, let alone the IR spectra. It was found that only long-range corrected hybrid density functionals, combined with decently sized basis sets are capable to predict correct values of dihedral angles between non-bonded atomic groups: the most important coordinates in conformational analysis. Thus, wB97XD/6-311++G(2df,2pd) method/basis set combination appears to be the best method for the titled system both in terms of geometry and IR spectra prediction. A detailed analysis of the potential energy surface revealed the existence of 28 distinct conformers with various populations at 298 K, which have significant impact in the simulated IR spectra. The linear scaling equation (LSE) fitting methodology was successfully adopted for the calibration of wavenumbers and achievement of the best match between theoretical and experimental absorption regions of functional groups in sulfones. Moreover, in the construction of the simulated IR spectra, the Lorentzian broadening of each calculated mode with different full widths at half maximum was considered to obtain extinction coefficients, thus more realistic ε(ν) dependency, that is directly comparable with experimental spectra. The authenticity of the results obtained have been verified by comparison with existing experimental literature data on sulfones.
... [82,83] The computed vibrational spectra were plotted using GaussSum v2.2.6 software [84] and scaled with a factor of 0.962. [85] The structural depiction and molecular orbitals were generated by using the GaussView 6.0 visualization program. ...
Photo‐initiated intramolecular charge transfer (ICT) processes play a pivotal role in the excited state reaction dynamics in donor‐bridge‐acceptor systems. The efficacy of such a process can be improved by modifying the extent of π‐conjugation, relative orientation/twists of the donor/acceptor entities and polarity of the environment. Herein, 4‐dimethylamino‐4′‐cyanodiphenylacetylene (DACN‐DPA), a typical donor‐π‐bridge‐acceptor system, was chosen to unravel the role of various internal coordinates that govern the extent of photo‐initiated ICT dynamics. Transient absorption (TA) spectra of DACN‐DPA in n‐hexane exhibit a lifetime of >2 ns indicating the formation of a triplet state while, in acetonitrile, a short time‐constant of ∼2 ps indicates the formation of charge transferred species. Ultrafast Raman loss spectroscopy (URLS) measurements show distinct temporal and spectral dynamics of Raman bands associated with C≡C and C=C stretching vibrations. The appearance of a new band at ∼1492 cm⁻¹ in acetonitrile clearly indicates structural modification during the ultrafast ICT process. Furthermore, these observations are supported by TD‐DFT computations.
... Since sulfonate vibrations are not modelled well using B3LYP with a conventional scaling factor of 0.975, the vibrations involving sulfur were scaled by 1.028 (Figures S9 and S10), based on previous observations for benchmark systems. [13] The lowest-energy structures for NAIs derived from 8 involved through-space stabilization of the pseudo-equatorial C-3 acetyl as observed for precursor 7. Indeed, the B3LYP calculated spectrum of the through-space stabilized structure 8a eq closely reproduces the major diagnostic peaks corresponding to the C=O (1710 cm À 1 ) and C=N + (1610 cm À 1 ) stretch modes (Figure 4B), resulting in an excellent match. In contrast, for conformer 8b eq in which the acetyl group points away from the NAI cationic center, the ester carbonyl stretch is calculated at 1790 cm À 1 and the C=N + stretch is shifted by 30 cm À 1 to 1640 cm À 1 with respect to the global minimum energy conformation 8a eq . ...
... The experimentally observed spectrum contains two distinct bands above 1500 cm À 1 , one indicative of a carbonyl stretch (1820 cm À 1 ), while the feature at 1600 cm À 1 could involve a C=N + stretch or a dioxolenium OÀ C=O + stretch. The two structures most consistent with the experimental spectrum result from acetyl participation before (13) or after rearrangement (15), as their calculated IR spectra reproduce these diagnostic features best. The initially formed NAI 11 and intermediates in the rearrangement, 12 and 14, are not detected on the basis of poor spectral overlap in the region above 1500 cm À 1 (see Figures 6D, 6E and 6F). ...
N‐Acyliminium ions are highly reactive intermediates that are important for creating CC‐bonds adjacent to nitrogen atoms. Here we report the characterization of cyclic N‐acyliminium ions in the gas phase, generated by collision induced dissociation tandem mass spectrometry followed by infrared ion spectroscopy using the FELIX infrared free electron laser. Comparison of DFT calculated spectra with the experimentally observed IR spectra provided valuable insights in the conformations of the N‐acyliminium ions.
... The IR spectra of rubidiated iduronic and glucuronic acid (IdoA and GlcA) were recorded in the 3000e4000 cm À1 region and contain significant differences [48]. In some cases, the use of anharmonic computations is required to model experimental IR spectra, as shown for glucosamine 6-sulfate in the 1000e 2000 cm À1 region [49]. IRMPD spectra of deprotonated IdoA, GlcA, and a hyaluronic acid tetrasaccharide (HA-dp4) were measured in the 3000e4000 cm À1 region. ...
Glycans are intrinsically complex biomolecules that pose particular analytical challenges. Standard workflows for glycan analysis are based on mass spectrometry, often coupled with separation techniques such as liquid chromatography and ion mobility spectrometry. However, this approach does not yield direct structural information and cannot always distinguish between isomers. This gap might be filled in the future by gas-phase infrared spectroscopy, which has emerged as a promising structure-sensitive technique for glycan fingerprinting. This review highlights recent applications of gas-phase infrared spectroscopy for the analysis of synthetic and biological glycans and how they can be integrated into mass spectrometry-based workflows.
... Glucosamine 6-sulfate was later used as a model to test the accuracy of a large number of frequency simulation methods. 536 Methods which are satisfying at higher wavenumbers are shown to fail from 500 and 1700 cm −1 as the anharmonic nature of the sulfates challenges the calculations. The best match between experimental and theoretical spectra from 500 to 1700 cm −1 was obtained using the computationally most demanding method. ...
Cells encode information in the sequence of biopolymers, such as nucleic acids, proteins, and glycans. Although glycans are essential to all living organisms, surprisingly little is known about the “sugar code” and the biological roles of these molecules. The reason glycobiology lags behind its counterparts dealing with nucleic acids and proteins lies in the complexity of carbohydrate structures, which renders their analysis extremely challenging. Building blocks that may differ only in the configuration of a single stereocenter, combined with the vast possibilities to connect monosaccharide units, lead to an immense variety of isomers, which poses a formidable challenge to conventional mass spectrometry. In recent years, however, a combination of innovative ion activation methods, commercialization of ion mobility–mass spectrometry, progress in gas-phase ion spectroscopy, and advances in computational chemistry have led to a revolution in mass spectrometry-based glycan analysis. The present review focuses on the above techniques that expanded the traditional glycomics toolkit and provided spectacular insight into the structure of these fascinating biomolecules. To emphasize the specific challenges associated with them, major classes of mammalian glycans are discussed in separate sections. By doing so, we aim to put the spotlight on the most important element of glycobiology: the glycans themselves.
... The match between computed and experimental spectra is satisfying, yet, anharmonicities challenge the calculations for glycosaminoglycans and extend the computational effort. 42 In addition to gas-phase IR spectroscopy, drift tube ion mobility-mass spectrometry (DTIM-MS) experiments were performed to compare the potential of the method for disaccharide differentiation. The rotationally averaged collision cross section (CCS) reflects the shape of an ion and is an instrument-independent physical property. ...
Glycosaminoglycans (GAGs) are a family of complex carbohydrates vital to all mammalian organisms and involved in numerous biological processes. Chondroitin and dermatan sulfate, an important class of GAGs, are linear macromolecules consisting of disaccharide building blocks of N-acetylgalactosamine and two different uronic acids. The varying degree and the site of sulfation render their characterization challenging. Here, we combine mass spectrometry with cryogenic infrared spectroscopy in the wavenumber range from 1000 to 1800 cm–1. Fingerprint spectra were recorded for a comprehensive set of disaccharides bearing all known motifs of sulfation. In addition, state-of-the-art quantum chemical calculations were performed to aid the understanding of the differences in the experimental fingerprint spectra. The results show that the degree and position of charged sulfate groups define the size of the conformational landscape in the gas phase. The detailed understanding of cryogenic infrared spectroscopy for acidic and often highly sulfated glycans may pave the way to utilize the technique in fragment-based sequencing approaches.
... This value reproduces well the experimental IR spectra of H2SO4 in the low frequencies region and scaling factors >1 are generally used for SO containing species. [88][89][90] Less is known on the infrared spectroscopy of the bisulfate anion HSO4 -, which has been studied mostly in the condensed phase, for example in sulfuric acid solutions 91,92 or thin films, 93 or in strongly bound complexes under cryogenic matrix 61 or gas-phase conditions. 90 Due to the absence of experimental data in isolated conditions, we will use the same scaling factors as for H2SO4. ...
The role of complexation with sulfuric acid on the photo-dissociation of protonated cinchona alkaloids, namely cinchonidine (Cd), quinine (Qn) and quinidine (Qd), is studied by combining laser spectroscopy with quantum chemical calculations. The protonated complexes are structurally characterized in a room-temperature ion trap by means of Infra-Red Multiple Photon dissociation (IRMPD) spectroscopy in the fingerprint and the ν(XH) (X=C, N, O) stretch regions. Comparison with density functional theory calculations including dispersion (DFT-D) unambiguously shows that the complex consists of a doubly protonated cinchona alkaloid strongly bound to a bisulfate HSO4- anion, which bridges the two protonated sites of the cinchona alkaloid. UV excitation of the complex does not induce loss of specific photo fragments, in contrast to the protonated monomer or dimer, for which photo-specific fragments were observed. Indeed the UV-induced fragmentation pattern is identical to that observed in collision-induced dissociation experiments. Analysis of the nature of the first electronic transitions at the second order approximate coupled-cluster level (CC2) explains the difference in behavior of the complex relative to the monomer or dimer towards UV excitation.
... Compagnon et al. proposed the first applications of IR ion spectroscopy to the analysis of positional isomers of sulfated carbohydrates [57][58][59]60 ]. Spectroscopic analysis of sulfated isomers of glucosamine supported by quantum chemistry showed that sulfated 3-O-S and 6-O-S isomers have distinctive IR signatures. ...
... [28] Racaud et al. have reported wavelength-dependent UV photodissociation of heparan disaccharides, [29] and Khanal et al. have reported the IR signatures of a series of GAG disaccharides standards using cryogenic messenger-tagging spectroscopy. [26] In this context, we have conducted in-depth structural analysis of GAG-relevant compounds using a combination of IRMPD spectroscopy and quantum chemistry, including Nacetyl hexosamine, [30] sulfated monosaccharides [31,32], and sulfated disaccharides. [33] We have recently proposed an original strategy based on the combination of MS analysis and ion spectroscopy for carbohydrate sequencing, [34] which was successfully applied to the identification of the hexuronic acid content in a HA tetrasaccharide [35]. ...
We report distinctive spectroscopic fingerprints of the monosaccharide standards GalNAc4S and GalNAc6S by coupling mass spectrometry and ion spectroscopy in the 3-μm range. The disaccharide standards CSA and CSC are used to demonstrate the applicability of a novel approach for the analysis of sulfate position in GalNAc-containing glycosaminoglycans. This approach was then used for the analysis of a sample containing CSA and CSC disaccharides. Finally, we discuss the generalization of the coupling of mass spectrometry with ion spectroscopy for the structural analysis of glycosaminoglycans on a tetrasaccharide from dermatan sulfate source.
... In Table 4, the IR and Raman wavenumbers and intensities, and the calculated vibrational wavenumbers for the optimized geometries are shown together with the proposed vibrational modes assignments. The IR and Raman spectra are presented in Fig. 9. DFT calculations overestimate the vibrational frequencies [43] and a proper scaling factor for CAM-B3LYP equal to 0.958 [44] for IR and 0.985 for Raman were applied to the calculated raw spectra in order to establish a more consistent comparison with the experimental data. The aromatic CH stretching vibrations occurs at frequencies greater than 3000 cm À1 , in the 3075e2911 cm À1 range, while the aromatic CH bending occurs at 994-1000 cm À1 . ...
A comprehensive structural study of the compound (2E)-1-((E)-4-(4-methoxybenzylideneamino) phenyl)-3-(4-methoxyphenyl)prop-2-en-1-one was carried out in this work. Single crystal X-ray diffraction (SCXRD), X-ray powder diffraction (XRPD), NMR, Raman and Infrared spectroscopies, and DFT calculations were performed for characterization of this iminochalcone hybrid. Intermolecular interactions were described by Hirshfeld surface analysis derived from crystal structure. Reactivity and intramolecular charge transfer were investigated using the frontier molecular orbitals and molecular electrostatic potential. In addition, we have calculated the Nonlinear Optical Properties at the CAM-B3LYP/6e311þg(d) level of theory in the presence of different solvents (gas-phase, acetone, chloroform, dichloromethane, dimethyl sulfoxide, ethanol, methanol, and water), being found meaningful NLO parameters for our compound. At last, there is a good agreement between calculated and experimental IR spectrum, allowing the assignment of some of normal vibrational modes of the iminochalcone hybrid.
