Pi-complex structure of gaseous benzene-NO cations assayed by IR multiple photon dissociation spectroscopy

[C(6)H(6)NO](+) ions, in two isomeric forms involved as key intermediates in the aromatic nitrosation reaction, have been produced in the gas phase and analyzed by IR multiple photon dissociation (IRMPD) spectroscopy in the 800-2200 cm(-)(1) fingerprint wavenumber range, exploiting the high fluence and wide tunability of a free electron laser (FEL) source. The IRMPD spectra were compared with the IR absorption spectra calculated for the optimized structures of potential isomers, thus allowing structural information on the absorbing species. [C(6)H(6)NO](+) ions were obtained by two routes, taking advantage of the FEL coupling to two different ion traps. In the first one, an FT-ICR mass spectrometer, a sequence of ion-molecule reactions was allowed to occur, ultimately leading to an NO(+) transfer process to benzene. The so-formed ions displayed IRMPD features characteristic of a [benzene,NO](+) pi-complex structure, including a prominent band at 1963 cm(-)(1), within the range for the N-O bond stretching vibration of NO (1876 cm(-)(1)) and NO(+) (2344 cm(-)(1)). A quite distinct species is formed by electrospray ionization (ESI) of a methanol solution of nitrosobenzene. The ions transferred and stored in a Paul ion trap showed the IRMPD features of substituent protonated nitrosobenzene, the most stable among conceivable [C(6)H(6)NO](+) isomers according to computations. It is noteworthy that IRMPD is successful in allowing a discrimination between isomeric [C(6)H(6)NO](+) species, whereas high-energy collision-induced dissociation fails in this task. The [benzene,NO](+) pi-complex is characterized by IRMPD spectroscopy as an exemplary noncovalent ionic adduct between two important biomolecular moieties.     

Infrared multiple photon dissociation spectroscopy of trapped ions

This tutorial review presents the technique of infrared multiple-photon dissociation (IRMPD) spectroscopy of mass-selected trapped ions. This requires coupling of a tunable infrared laser with mass spectrometry instrumentation. IRMPD spectroscopy has recently blossomed due to the emergence of widely tunable free electron lasers, as well as on-going developments of benchtop lasers. The merits of different trapping approaches in mass spectrometry are discussed in the light of photodissociation experiments. This tutorial discusses current capabilities, as well as limitations of the technique.     

Infrared multiple photon dissociation spectroscopy of potassiated proline

The structure of proline in [proline + K]+ has been investigated in the gas phase using high level DFT and MP2 calculations and infrared photo dissociation spectroscopy with a free electron laser (FELIX). The respective FELIX spectrum of [proline + K]+ matches convincingly the calculated spectra of two structurally closely related and nearly iso-energetic zwitterionic salt bridge (SB) structures. An additional unresolved band at approximately 1725 cm(-1) matching with the characteristic CO stretching mode of charge solvation (CS) structures points toward the presence of a minor population of these conformers of proline in [proline + K]+. However, theory predicts a significant energy gap of 18.9 kJ mol(-1) (B3LYP/6-311++G(2d,2p)) or 15.6 kJ mol(-1) (MP2) between the lowest CS conformer of proline and the clearly favored SB structure.     

Infrared multiple photon dissociation spectroscopy of sodium and potassium chlorate anions

The structures of gas‐phase, metal chlorate anions with the formula [M(ClO₃)₂]^?, M = Na and K, were determined using tandem mass spectrometry and infrared multiple photon dissociation (IRMPD) spectroscopy. Structural assignments for both anions are based on comparisons of the experimental vibrational spectra for the two species with those predicted by density functional theory (DFT) and involve conformations that feature either bidentate or tridentate coordination of the cation by chlorate. Our results strongly suggest that a structure in which both chlorate anions are bidentate ligands is preferred for [Na(ClO₃)₂]^?. However, for [K(ClO₃)₂]^? the best agreement between experimental and theoretical spectra is obtained from a composite of predicted spectra for which the chlorate anions are either both bidentate or both tridentate ligands. In general, we find that the overall accuracy of DFT calculations for prediction of IR spectra is dependent on both functional and basis set, with best agreement achieved using frequencies generated at the B3LYP/6‐311+g(3df) level of theory. Copyright © 2009 John Wiley & Sons, Ltd.     

Vibrational spectra and structures of H2O-NO, HDO-NO, and D2O-NO complexes. An IR matrix isolation and DFT study

The IR spectra of H2O+NO, HDO+NO, and D2O+NO, isolated in solid neon at low temperature have been investigated. Concentration effects and detailed vibrational analysis of deuterated and partially deuterated species allowed identification of three 1:1 HDO-NO species, two 1:1 D2O-NO species, and only one 1:1 H2O-NO complex. From comparison between the experimental spectra and the results of DFT calculations, it appeared that two different types of weakly bound complexes between water and nitric oxide can be formed in a neon matrix. The first species is a 1:1 complex where bonding occurs between water hydrogen and nitric oxide nitrogen, in which OH-N and OD-N intermolecular bonds are engaged. For this complex only DOD-NO, HOD-NO, and DOH-NO isotopic species have been experimentally detected and no IR bands of HOH-NO were observed. This result could be explained by the fact that the dissociation energy of HOH-NO is lower than those of DOD-NO, HOD-NO and DOH-NO. For the second detected 1:1 H2O-NO complex and its isotopic variants, the H2O-NO potential surface was explored systematically at the B3LYP level, but no stable species corresponding to the complex could be calculated. The structure of the second observed 1:1 H2O-NO complex results from columbic attractions between water and nitric oxide and could be stabilized only in matrix, probably by interaction between NO, water and (Ne)n.     

Investigation of proton-acceptor properties of oxide surfaces by IR spectroscopy of hydrogen-bonded complexes

Strength of the basic centers on catalyst surfaces is suggested to be characterized by the IR spectra of adsorbed chloroform. The existence of centers with different proton-acceptor properties on several oxides is shown experimentally.

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Vibrational spectra of small silicon monoxide cluster cations measured by infrared multiple photon dissociation spectroscopy

The first gas-phase infrared spectra of silicon monoxide cations (SiO)(n)(+), n = 3-5, using multiple photon dissociation in the 550-1250 cm(-1) frequency range, are reported. All clusters studied here fragment via loss of a neutral SiO unit. The experimental spectra are compared to simulated linear absorption spectra from calculated low energy isomers for each cluster. This analysis indicates that a "ring" isomer is the primary contributor to the (SiO)(3)(+) spectrum, that the (SiO)(4)(+) spectrum results from two close-lying bicyclic ring isomers, and that the (SiO)(5)(+) spectrum is from a bicyclic ring with a central, fourfold-coordinated Si atom. Experiment and theory indicate that the energies and energetic orderings of (SiO)(n)(+) isomers differ from those for neutral (SiO)(n) clusters.     

多硫化钴CoSx结构与稳定性的密度泛函研究

采用量子化学密度泛函方法计算得到CoSx(x=1~6)6组化合物的同分异构体及CoS2的晶体结构.对其分子结构与稳定性、光谱性质及其晶体结构性质进行了分析讨论.发现CoSx和晶体结构中Co原子均带部分正电荷,S原子均带部分负电荷;Co可与不同比例的S原子形成配位键,并有很强的结合能.随着S原子比例的增加配位键伸长,结合能增大.计算的晶体结构数据很好地与实验测定结构吻合.计算结果可为锂插层研究提供有用的信息.     

A study of gelatin by IR spectroscopy

Samples of freshly prepared soluble, naturally aged soluble, and insoluble gelatins (an accumulation of glue taken from a wooden sculpture of the XVth century) before and after heating at 210°C have been investigated by IR spectroscopy. The IR spectra of the samples before heating consisted of the characteristic spectra of collagen or gelatin although there were differences in the 1380–1460 cm^?1 region of the spectra. After the samples had been heated, the IR spectra of the soluble gelatins differed from those of the unheated samples. The changes in the IR spectra are discussed in connection with the probable structural rearrangements taking place in the natural ageing of gelatin.     

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

The gas phase structures of cationized histidine (His), including complexes with Li(+), Na(+), K(+), Rb(+), and Cs(+), are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light generated by a free electron laser, in conjunction with quantum chemical 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) (Li(+), Na(+), and K(+) complexes) and B3LYP/HW*/6-311+G(d,p) (Rb(+) and Cs(+) complexes) levels of theory, where HW* indicates that the Hay-Wadt effective core potential with additional polarization functions was used on the metals. Single point energy calculations were carried out at the B3LYP, B3P86, and MP2(full) levels using the 6-311+G(2d,2p) basis set. On the basis of these experiments and calculations, the only conformation that reproduces the IRMPD action spectra for the complexes of the smaller alkali metal cations, Li(+)(His) and Na(+)(His), is a charge-solvated, tridentate structure where the metal cation binds to the backbone carbonyl oxygen, backbone amino nitrogen, and nitrogen atom of the imidazole side chain, [CO,N(α),N(1)], in agreement with the predicted ground states of these complexes. Spectra of the larger alkali metal cation complexes, K(+)(His), Rb(+)(His), and Cs(+)(His), have very similar spectral features that are considerably more complex than the IRMPD spectra of Li(+)(His) and Na(+)(His). For these complexes, the bidentate [CO,N(1)] conformer in which the metal cation binds to the backbone carbonyl oxygen and nitrogen atom of the imidazole side chain is a dominant contributor, although features associated with the tridentate [CO,N(α),N(1)] conformer remain, and those for the [COOH] conformer are also clearly present. Theoretical results for Rb(+)(His) and Cs(+)(His) indicate that both [CO,N(1)] and [COOH] conformers are low-energy structures, with different levels of theory predicting different ground conformers.     

CO adsorption on CoMo and NiMo sulfide catalysts: a combined IR and DFT study

Experimental IR spectra of carbon monoxide adsorbed on a series of Mo/Al2O3, CoMo/Al2O3, and NiMo/Al2O3 sulfided catalysts have been compared to ab initio DFT calculations of CO adsorption on CoMo and NiMo model surfaces. This approach allows the main IR features of CO adsorbed on the sulfide phase to be assigned with an uncertainty of 15 cm(-1). On the CoMo system, the band at 2070 cm(-1) is specific of the promotion by Co and is assigned to CO interacting either with a Co atom or with a Mo atom adjacent to a Co atom. On the NiMo system, CO adsorption on Ni centers of the promoted phase leads to a high-wavenumber band at approximately 2120 cm(-1) that strongly overlaps the band at 2110 cm(-1) characteristic of nonpromoted Mo sites. For NiMo and CoMo catalysts, broad shoulders at low wave numbers (below 2060 cm(-1)) are characteristic of Mo centers adjacent to promoter atoms, indicating a partial decoration of the MoS2 edges by the promoter.     

Wavelength and fluence dependences of the IR multiple photon dissociation of CH3NH2 to form ground state NH2 radicals

Ground state NH₂ radicals have been detected by laser excited fluorescence following the collisionless multiple photon dissociation of CH₃NH₂ by a pulsed CO₂ laser. The variation of dissociation yield with IR laser fluence and wavelength are reported for several CO₂ lines overlapping the CH₃NH₂ν₈ band. Dissociation is more efficient at wavelengths corresponding to initial absorption in the P branch of this transition than for excitation in the Q or R branches, with the difference in efficiencies being more pronounced at lower fluences. The mechanism of NH₂ production appears to be direct C-N bond fission.     

Infrared multiple photon dissociation action spectroscopy and computational studies of mass-selected gas-phase fluorescein and 2',7'-dichlorofluorescein ions

Fluorescein (FL) and its derivative 2',7'-dichlorofluoroescein (DCF) are well-known fluorescent dyes used in many biological and biochemical applications. Although extensive studies have been carried out to investigate their chemical and photophysical properties in different solvent media, little is known about their intrinsic behaviors in the gas phase. Here, infrared multiple photon dissociation (IRMPD) action spectra are reported for the three charged prototropic forms of FL and DCF and compared with computed IR spectra from electronic structure calculations. In each case, the measured spectra show good agreement with the calculated spectra of the lowest energy computed conformer. Moreover, the major bands of the monoanion IRMPD spectra show striking similarities to those of the dianions and are quite different from those of the cations. These experimental results clearly indicate that the gaseous monoanions are predominantly deprotonated on the xanthene chromophore, rather than the benzoate deprotonation site favored in solution. Investigations such as this, which provide a better understanding of intrinsic properties of ionic dyes, forms a baseline from which to elucidate solvent effects and will aid the rational design of dyes possessing desirable fluorescence properties.     

Structural characterization by infrared multiple photon dissociation spectroscopy of protonated gas-phase ions obtained by electrospray ionization of cysteine and dopamine

Structural characterization of protonated gas-phase ions of cysteine and dopamine by infrared multiple photon dissociation (IRMPD) spectroscopy using a free electron laser in combination with theory based on DFT calculations reveals the presence of two types of protonated dimer ions in the electrospray mass spectra of the metabolites. In addition to the proton-bound dimer of each species, the covalently bound dimer of cysteine (bound by a disulfide linkage) has been identified. The dimer ion of m/z 241 observed in the electrospray mass spectra of cysteine has been identified as protonated cystine by comparison of the experimental IRMPD spectrum to the IR absorption spectra predicted by theory and the IRMPD spectrum of a standard. Formation of the protonated covalently bound disulfide-linked dimer ions (i.e. protonated cystine) from electrospray of cysteine solution is consistent with the redox properties of cysteine. Both the IRMPD spectra and theory indicate that in protonated cystine the covalent disulfide bond is retained and the proton is involved in intramolecular hydrogen bonding between the amine groups of the two cysteine amino acid units. For cysteine, the protonated covalently bound dimer (m/z 241) dominated the mass spectrum relative to the proton-bound dimer (m/z 243), but this was not the case for dopamine, where the protonated monomer and the proton-bound dimer were both observed as major ions. An extended conformation of the ethylammonium side chain of gas-phase protonated dopamine monomer was verified from the correlation between the predicted IR absorption spectra and the experimental IRMPD spectrum. Dopamine has the same extended ethylamine side chain conformation in the proton-bound dopamine dimer identified in the mass spectra of electrosprayed dopamine. The structure of the proton-bound dimer of dopamine is confirmed by calculations and the presence of an IR band due to the shared proton. The presence of the shared proton in the protonated cystine ion can be inferred from the IRMPD spectrum.

Matrix effects on copper(II)phthalocyanine complexes. A combined continuous wave and pulse EPR and DFT study

The effect of the electron withdrawing or donating character of groups located at the periphery of the phthalocyanine ligand, as well as the influence of polar and nonpolar solvents are of importance for the redox chemistry of metal phthalocyanines. Continuous wave and pulse electron paramagnetic resonance and pulse electron nuclear double resonance spectroscopy at X- and Q-band are applied to investigate the electronic structure of the complexes Cu(II)phthalocyanine (CuPc), copper(II) 2,9,16,23-tetra-tert-butyl-29H,31H-phthalocyanine (CuPc(t)), and copper(II) 1,2,3,4,8,9,10,11,15,16,17,18,22,23,24,25-hexadecafluoro-29H,31H-phthalocyanine (CuPc(F)) in various matrices. Isotope substitutions are used to determine the g values, the copper hyperfine couplings and the hyperfine interactions with the 14N, 1H and 19F nuclei of the macrocycle and the surrounding matrix molecules. Simulations and interpretations of the spectra are shown and discussed, and a qualitative analysis of the data using previous theoretical models is given. Density functional computations facilitate the interpretation of the EPR parameters. The experimental g, copper and nitrogen hyperfine and nuclear quadrupole values are found to be sensitive to changes of the solvent and the structure of the macrocycle. To elucidate the electronic, structural and bonding properties the changes in the g principal values are related to data from UV/Vis spectroscopy and to density functional theory (DFT) computations. The analysis of the EPR data indicates that the in-plane metal-ligand sigma bonding is more covalent for CuPc(t) in toluene than in sulfuric acid. Furthermore, the out-of-plane pi bonding is found to be less covalent in the case of a polar sulfuric acid environment than with nonpolar toluene or H2Pc environment, whereby the covalency of this bonding is increased upon addition of tert-butyl groups. No contribution from in-plane pi bonding is found.     

A 45Sc-NMR and DFT calculation study of crystalline scandium compounds

A series of scandium compounds, namely ScPO₄, ScOF, Li₃Sc(BO₃)₂, and CaSc₂O₄, were prepared according to procedures described in the literature, and then characterised by powder X-ray diffraction and solid-state ⁴⁵Sc-NMR spectroscopy. By computer fitting, the quadrupolar interaction parameters χ and η, as well as the isotropic chemical shifts δ_iso were extracted from the NMR spectra. For comparison and site assignment of ⁴⁵Sc, density functional theory (DFT) calculations of the EFG tensor were carried out with the Castep code. For the compounds with a well-defined formal coordination number (CN), a convincing linear correlation between CN and isotropic chemical shift could be established.     

DFT calculation of benzoazacrown ethers and their complexes with calcium perchlorate

The complexation constants of several azacrown ethers with Ca(ClO₄)₂ were determined and turned out to be the higher, the large the macrocycle. The structures of free ligands and their complexes and the complexation energies were calculated by the DFT method. In the aza-12(15)-crown-4(5) ether complexes with Ca(ClO₄)₂, the metal cations lie outside the averaged plane of heteroatoms of the macrocycle, and the coordination of both counterions is V-like. In the complexes of aza-18-crown-6 ethers, the counterions are in the axial position relatively to the macrocycle in the center of which the Ca²⁺ ion is localized. The complexation energies increase with an increase in the size of the azacrown ether macrocycle. The involvement of the nitrogen atom in binding with the Ca²⁺ ion decreases with the expansion of the macrocycle. Two methods for quantitative estimation of the degree of pre-organization of ligands to complexation were considered: geometric and energetic methods. Benzoaza-15-crown-5 ether is a ligand which is more pre-organized to complexation than N-phenylaza-15-crown-5 ether.