Rajeev Sinha | Manipal Academy of Higher Education (original) (raw)
Papers by Rajeev Sinha
The Journal of Physical Chemistry Letters, 2015
The ion corresponding to protonated sulfurous acid, H3SO3(+), has been successfully delivered int... more The ion corresponding to protonated sulfurous acid, H3SO3(+), has been successfully delivered into the gas phase by electrospray ionization of the solution of a suitable precursor and an in-source fragmentation process. The neutral acid is a highly elusive molecule. However, its gas-phase basicity has been ascertained by means of a kinetic study of proton-transfer reactivity. The structure of the H3SO3(+) sampled ion has been probed by IRMPD spectroscopy in two complementary IR frequency ranges in conjunction with density functional theory calculations and found to conform to a trihydroxosulfonium ion. The characteristic IR signatures may aid in deciphering the presence of this species in extraterrestrial atmospheres.
Nature Chemistry, 2014
2-Aminopurine (2 AP) is a fluorescent isomer of adenine and has a fluorescence lifetime of ~11 ns... more 2-Aminopurine (2 AP) is a fluorescent isomer of adenine and has a fluorescence lifetime of ~11 ns in water. It is widely used in biochemical settings as a site-specific fluorescent probe of DNA and RNA structure and base-flipping and -folding. These assays assume that 2 AP is intrinsically strongly fluorescent. Here, we show this not to be the case, observing that gas-phase, jet-cooled 2-aminopurine and 9-methyl-2-aminopurine have very short fluorescence lifetimes (156 ps and 210 ps, respectively); they are, to all intents and purposes, non-fluorescent. We find that the lifetime of 2-aminopurine increases dramatically when it is part of a hydrate cluster, 2 AP · (H2O)n, where n = 1-3. Not only does it depend on the presence of water molecules, it also depends on the specific hydrogen-bonding site to which they attach and on the number of H2O molecules at that site. We selectively microhydrate 2-aminopurine at its sugar-edge, cis-amino or trans-amino sites and see that its fluorescence lifetime increases by 4, 50 and 95 times (to 14.5 ns), respectively.
The Journal of Physical Chemistry B, 2013
2-Aminopurine (2AP) is an adenine analogue with a high fluorescence quantum yield in water soluti... more 2-Aminopurine (2AP) is an adenine analogue with a high fluorescence quantum yield in water solution, which renders it a useful real-time probe of DNA structure. We report the ultraviolet (UV) and infrared (IR) spectra of size-selected and jet-cooled 9H-2AP·(H2O)n clusters with n = 2 and 3. Mass- and species-specific UV/UV holeburning spectroscopy allows to separate the UV spectra of four cluster isomers in the 31,200–33,000 cm(–1) spectral region with electronic band origins at 31339, 31450, 31891, and 32163 cm(–1). Using IR/UV depletion spectroscopy in combination with B3LYP calculated harmonic vibrational frequencies, the H-bonding topologies of two isomers of the n = 2 and of two isomers of the n = 3 cluster are identified. One n = 2 isomer (denoted 2A) forms a water dimer chain between the N9H and N3 atoms at the sugar-edge site, the other isomer (denoted 2D) binds one H2O at the sugar-edge site and the other at the trans-amino site between the N1 atom and the NH2 group. For 2-aminopurine·(H2O)3, one isomer (denoted 3A) forms an H-bonded water wire at the sugar-edge site, while isomer 3B accommodates two H2O molecules at the sugar-edge and one at the trans-amino site. The approximate second-order coupled cluster (CC2) method predicts the adiabatic S1 ← S0 transitions of 9H-2-aminopurine and six water cluster isomers with n = 1–3 in very good agreement with the experimental 0(0)(0) frequencies, with differences of <0.6%. The stabilization of the S1(ππ*) state of 2-aminopurine by water clusters is highly regiospecific: Isomers with one or two H2O molecules H-bonded in the trans-amino position induce large spectra red shifts, corresponding to 1ππ* state stabilization of 10–12 kJ/mol, while water-wire cluster solvation at the sugar-edge leads to much smaller stabilization. The evolution of the IR spectra of the water-wire clusters with n = 1–3 that are H-bonded to the sugar-edge site is discussed. Qualitatively different regions (denoted I to IV) can be attributed to the different free and H-bonded OH, NH, NH2 and OH···OH water-wire stretch vibrations.
The Journal of Physical Chemistry A, 2012
The infrared (IR) spectra of the supersonic-jet cooled 9H-and 7H-tautomers of 2-aminopurine (2AP)... more The infrared (IR) spectra of the supersonic-jet cooled 9H-and 7H-tautomers of 2-aminopurine (2AP) and of the 9H-2-aminopurine·H 2 O monohydrate clusters have been measured by mass-and species-selective IR-UV double resonance spectroscopy in the 3200−3900 cm −1 region, covering the N−H and O−H stretching vibrations. The spectra are complemented by density functional (B3LYP and PW91) and by second-order Møller−Plesset (MP2) calculations of the electronic energies and vibrational frequencies of the respective 2AP tautomers and clusters. The 9H-and 7H-2-aminopurine tautomers were definitively identified by the shifts of their NH and NH 2 symmetric and asymmetric stretching frequencies and by comparison to the B3LYP/TZVP calculated IR spectra. The H-bond topologies of the two previously observed 9H-2-amino-purine·H 2 O isomers (Sinha. R. K.; et al. J. Phys. Chem. A 2011, 115, 6208) are definitively identified as the "sugar-edge" isomer A and the "trans-amino-bound" isomer B by comparing their IR spectra to the calculated frequencies and IR intensities of the cluster isomers A, B, C, and D, as well as to the IR spectrum of 9H-2AP. The sugar-edge isomer A involves N9−H···OH 2 and HOH···N3 hydrogen bonds and is predicted to be the most stable form. The amino-bound isomer B involves NH 2 ···OH 2 and HOH···N1 hydrogen bonds and is calculated to lie 2.5 kJ/mol above isomer A. The H-bond topology of the "cis-amino-bound" isomer C is symmetrically related to isomer B, with a hydrogen bond to the N3 of the pyrimidine group. However, it is calculated to lie 7 kJ/mol above isomer A and indeed is not observed in the supersonic jet. Isomer D involves a single H-bond to the N7 position, is predicted to be 14 kJ/mol above A and is therefore not observed.
The Journal of Physical Chemistry A, 2011
For understanding the major- and minor-groove hydration patterns of DNAs and RNAs, it is importan... more For understanding the major- and minor-groove hydration patterns of DNAs and RNAs, it is important to understand the local solvation of individual nucleobases at the molecular level. We have investigated the 2-aminopurine·H(2)O monohydrate by two-color resonant two-photon ionization and UV/UV hole-burning spectroscopies, which reveal two isomers, denoted A and B. The electronic spectral shift δν of the S(1) ← S(0) transition relative to bare 9H-2-aminopurine (9H-2AP) is small for isomer A (-70 cm(-1)), while that of isomer B is much larger (δν = -889 cm(-1)). B3LYP geometry optimizations with the TZVP basis set predict four cluster isomers, of which three are doubly H-bonded, with H(2)O acting as an acceptor to a N-H or -NH2 group and as a donor to either of the pyrimidine N sites. The "sugar-edge" isomer A is calculated to be the most stable form with binding energy D(e) = 56.4 kJ/mol. Isomers B and C are H-bonded between the -NH2 group and pyrimidine moieties and are 2.5 and 6.9 kJ/mol less stable, respectively. Time-dependent (TD) B3LYP/TZVP calculations predict the adiabatic energies of the lowest (1)ππ* states of A and B in excellent agreement with the observed 0(0)(0) bands; also, the relative intensities of the A and B origin bands agree well with the calculated S(0) state relative energies. This allows unequivocal identification of the isomers. The R2PI spectra of 9H-2AP and of isomer A exhibit intense low-frequency out-of-plane overtone and combination bands, which is interpreted as a coupling of the optically excited (1)ππ* state to the lower-lying (1)nπ* dark state. In contrast, these overtone and combination bands are much weaker for isomer B, implying that the (1)ππ* state of B is planar and decoupled from the (1)nπ* state. These observations agree with the calculations, which predict the (1)nπ* above the (1)ππ* state for isomer B but below the (1)ππ* for both 9H-2AP and isomer A.
The Journal of Chemical Physics, 2014
The UV spectrum of the adenine analogue 9-methyl-2-aminopurine (9M-2AP) is investigated with one-... more The UV spectrum of the adenine analogue 9-methyl-2-aminopurine (9M-2AP) is investigated with one- and two-color resonant two-photon ionization spectroscopy at 0.3 and 0.05 cm(-1) resolution in a supersonic jet. The electronic origin at 32,252 cm(-1) exhibits methyl torsional subbands that originate from the 0A1'' (l = 0) and 1E(″) (l = ±1) torsional levels. These and further torsional bands that appear up to 00 (0)+230 cm(-1) allow to fit the threefold (V3) barriers of the torsional potentials as |V3''|=50 cm(-1) in the S0 and |V3'|=126 cm(-1) in the S1 state. Using the B3LYP density functional and correlated approximate second-order coupled cluster CC2 methods, the methyl orientation is calculated to be symmetric relative to the 2AP plane in both states, with barriers of V3''=20 cm(-1) and V3'=115 cm(-1). The 00 (0) rotational band contour is 75% in-plane (a/b) polarized, characteristic for a dominantly long-axis (1)ππ(*) excitation. The residual 25% c-axis polarization may indicate coupling of the (1)ππ(*) to the close-lying (1)nπ(*) state, calculated at 4.00 and 4.01 eV with the CC2 method. However, the CC2 calculated (1)nπ oscillator strength is only 6% of that of the (1)ππ(*) transition. The (1)ππ(*) vibronic spectrum is very complex, showing about 40 bands within the lowest 500 cm(-1). The methyl torsion and the low-frequency out-of-plane ν1' and ν2' vibrations are strongly coupled in the (1)ππ(*) state. This gives rise to many torsion-vibration combination bands built on out-of-plane fundamentals, which are without precedence in the (1)ππ(*) spectrum of 9H-2-aminopurine [S. Lobsiger, R. K. Sinha, M. Trachsel, and S. Leutwyler, J. Chem. Phys. 134, 114307 (2011)]. From the Lorentzian broadening needed to fit the 00 (0) contour of 9M-2AP, the (1)ππ(*) lifetime is τ ⩾ 120 ps, reflecting a rapid nonradiative transition.
Inorganic Chemistry, 2011
Model ferric heme nitrosyl complexes, [Fe(TPP)(NO)](+) and [Fe(TPFPP)(NO)](+), where TPP is the d... more Model ferric heme nitrosyl complexes, [Fe(TPP)(NO)](+) and [Fe(TPFPP)(NO)](+), where TPP is the dianion of 5,10,15,20-tetrakis-phenyl-porphyrin and TPFPP is the dianion of 5,10,15,20-tetrakis-pentafluorophenyl-porphyrin, have been obtained as isolated species by the gas phase reaction of NO with [Fe(III)(TPP)](+) and [Fe(III) (TPFPP)](+) ions delivered in the gas phase by electrospray ionization, respectively. The so-formed nitrosyl complexes have been characterized by vibrational spectroscopy also exploiting (15)N-isotope substitution in the NO ligand. The characteristic NO stretching frequency is observed at 1825 and 1859 cm(-1) for [Fe(III)(TPP)(NO)](+) and [Fe(III)(TPFPP)(NO)](+) ions, respectively, providing reference values for genuine five-coordinate Fe(III)(NO) porphyrin complexes differing only for the presence of either phenyl or pentafluorophenyl substituents on the meso positions of the porphyrin ligand. The vibrational assignment is aided by hybrid density functional theory (DFT) calculations of geometry and electronic structure and frequency analysis which clearly support a singlet spin electronic state for both [Fe(TPP)(NO)](+) and [Fe(TPFPP)(NO)](+) complexes. Both TD-DFT and CASSCF calculations suggest that the singlet ground state is best described as Fe(II)(NO(+)) and that the open-shell AFC bonding scheme contribute for a high-energy excited state. The kinetics of the NO addition reaction in the gas phase are faster for [Fe(III)(TPFPP)](+) ions by a relatively small factor, though highly reliable because of a direct comparative evaluation. The study was aimed at gaining vibrational and reactivity data on five-coordinate Fe(III)(NO) porphyrin complexes, typically transient species in solution, ultimately to provide insights into the nature of the Fe(NO) interaction in heme proteins.
Indian Journal of Physics, Mar 1, 2012
Spectroscopic studies on jet cooled 3-methylisoquinoline using fluorescence excitation and disper... more Spectroscopic studies on jet cooled 3-methylisoquinoline using fluorescence excitation and dispersed fluorescence methods were carried out. The effect of methyl substitution on the excited state behavior of isoquinoline is focused. Methyl torsional behavior and the effect on torsional potential of methyl group due to excited states mixing are addressed. The possible explanations of the observed intensity pattern of the torsional transitions in the fluorescence excitation spectrum are also presented.
The Journal of Chemical Physics, 2007
The laser induced fluorescence excitation and single vibronic excitation dispersed fluorescence s... more The laser induced fluorescence excitation and single vibronic excitation dispersed fluorescence spectra have been studied for supersonic jet cooled 1-methyl-2͑1h͒-pyridone. The methyl torsional bands and some low frequency vibrational transitions were assigned for both ground and excited states. The torsional parameters V 3 = 244 cm −1 and V 6 =15 cm −1 for the ground state and V 3 = 164 cm −1 and V 6 =40 cm −1 for the excited state were obtained. To get the insight into the methyl torsional barrier, ab initio calculations were performed and compared with the experimental results. Origin of potential barrier was traced by partitioning the barrier energy into changes in bondantibond interaction, structural, and steric energies accompanying methyl rotation using natural bond orbital analysis. The role of local interactions in ascertaining the barrier potential reveals that its nature cannot be understood without considering the molecular flexing. The hyperconjugation between CH * and ring * observed in lowest unoccupied molecular orbital ͑LUMO͒ stabilizes the methyl group conformer that undergoes a 60°rotation in the excited state with respect to that of the ground state, and it is the change in LUMO that plays important role in the excited state barrier formation.
Analytica Chimica Acta, 2008
In this article, we present a systematic study on IgG and Fab fragment of anti-IgG molecules usin... more In this article, we present a systematic study on IgG and Fab fragment of anti-IgG molecules using fluorescence auto- and cross-correlation spectroscopy to investigate their diffusion characteristics, binding kinetics, and the effect of small organic molecule, urea on their binding. Through our analysis, we found that the diffusion coefficient for IgG and Fab fragment of anti-IgG molecules were 37+/-2 microm2s(-1) and 56+/-2 microm2s(-1), respectively. From the binding kinetics study, the respective forward (k(a)) and backward (k(d)) reaction rates were (5.25+/-0.25)x10(6)M(-1)s(-1) and 0.08+/-0.005 s(-1), respectively and the corresponding dissociation binding constant (K(D)) was 15+/-2 nM. We also found that urea inhibits the binding of these molecules at 4M concentration due to denaturation.
The laser induced fluorescence excitation and single vibronic excitation dispersed fluorescence s... more The laser induced fluorescence excitation and single vibronic excitation dispersed fluorescence spectra have been studied for supersonic jet cooled 1-methyl-2͑1h͒-pyridone. The methyl torsional bands and some low frequency vibrational transitions were assigned for both ground and excited states. The torsional parameters V 3 = 244 cm −1 and V 6 =15 cm −1 for the ground state and V 3 = 164 cm −1 and V 6 =40 cm −1 for the excited state were obtained. To get the insight into the methyl torsional barrier, ab initio calculations were performed and compared with the experimental results. Origin of potential barrier was traced by partitioning the barrier energy into changes in bondantibond interaction, structural, and steric energies accompanying methyl rotation using natural bond orbital analysis. The role of local interactions in ascertaining the barrier potential reveals that its nature cannot be understood without considering the molecular flexing. The hyperconjugation between CH * and ring * observed in lowest unoccupied molecular orbital ͑LUMO͒ stabilizes the methyl group conformer that undergoes a 60°rotation in the excited state with respect to that of the ground state, and it is the change in LUMO that plays important role in the excited state barrier formation.
Dalton Transactions, 2003
... 1,10-phenanthroline and L 3− = 1,3,5-triazine-2,4,6-trithiol). Sanjib Kar, Thomas A. Miller, ... more ... 1,10-phenanthroline and L 3− = 1,3,5-triazine-2,4,6-trithiol). Sanjib Kar, Thomas A. Miller, Soma Chakraborty, Biprajit Sarkar, Biswajit Pradhan, Rajeev K. Sinha, Tapanendu Kundu, Michael D. Ward and Goutam Kumar Lahiri ...
Theoretical Chemistry Accounts, 2008
In this article, we present a systematic study on mono-methylindoles to investigate the electroni... more In this article, we present a systematic study on mono-methylindoles to investigate the electronic origin of the threefold symmetric component (V 3) of the methyl torsional potential barrier in the ground electronic state (S 0). The structures and the torsional potential parameters of these molecules were evaluated from ab initio calculation using Hartree-Fock (HF), second order Mollar Plesset perturbation (MP2) and B3LYP density functional level of theories and Gaussian type basis set 6-31G(d, p). Natural bond orbital (NBO) analysis of these molecules were carried out using B3LYP/6-31G(d, p) level of calculation to understand the formation of the threefold V 3 term arising from the changes of various non-covalent interactions during methyl rotation. Our analysis reveals that the contributions from π orbitals play a dominant role in the barrier height determination in this class of molecules. The threefold term in the barrier arises purely from the interactions non-local to the methyl group in case when the methyl group has two single bonds vicinal to it. On the other hand, it is the local interaction that determines the potential energy barrier when the methyl group has one single bond and one double bond vicinal to it. However, in all these cases, the magnitude of the energy barrier depends on the resonance structure formation in the benzene ring frame upon rotation of the methyl group and, therefore, the energetics of the barrier cannot be understood without considering the molecular flexing during methyl rotation.
... 1,10-phenanthroline and L 3− = 1,3,5-triazine-2,4,6-trithiol). Sanjib Kar, Thomas A. Miller, ... more ... 1,10-phenanthroline and L 3− = 1,3,5-triazine-2,4,6-trithiol). Sanjib Kar, Thomas A. Miller, Soma Chakraborty, Biprajit Sarkar, Biswajit Pradhan, Rajeev K. Sinha, Tapanendu Kundu, Michael D. Ward and Goutam Kumar Lahiri ...
Chemical Physics, 2007
To get the insight into the electronic structure-methyl torsion correlation in nitrogen heterocyc... more To get the insight into the electronic structure-methyl torsion correlation in nitrogen heterocyclic molecules, a comparative study on torsion of the methyl group in 1-methyl-2(1H)pyridone (1MPY), 1-methyl-2(1H)pyridinimine (1MPI), and 3-methyl-2(1H)pyridone (3MPY) was carried out using ab initio calculations. To understand the barrier forming mechanism in the ground state and its consequence on the molecular structure, the ground state torsional potential has been investigated by partitioning the barrier energy using the natural bond orbital (NBO) theoretical framework. The NBO analysis reveals that the delocalization energy is the barrier forming term whereas the Lewis energy is always antibarrier for all these molecules. To get further insight into the effect of local electronic structure on the methyl torsional barrier, the individual bond-antibond interactions and structural energy contributions have been investigated. It was found that when the bond order difference between the vicinal bonds does not change appreciably during the course of methyl rotation, the local electronic interactions with the methyl group do not play any decisive role in barrier formation as observed in the case of 1MPY and 1MPI. In these cases, it is the skeletal relaxation during methyl rotation that plays an important role in determining the barrier. On the other hand, if the bond order change is appreciable as is the case for 3MPY, the local interactions alone suffice to describe the origin of the torsional barrier of the methyl group.
Chemical Physics, 2007
The laser induced fluorescence excitation and dispersed fluorescence spectra of three nitrogen he... more The laser induced fluorescence excitation and dispersed fluorescence spectra of three nitrogen heterocyclic molecules 1-methyl-2͑1H͒pyridone ͑1MPY͒, 1-methyl-2͑1H͒pyridinimine ͑1MPI͒, and 3-methyl-2͑1H͒pyridone ͑3MPY͒ have been studied under supersonic jet cooled condition. The methyl torsional and some low frequency vibrational transitions in the fluorescence excitation spectrum were assigned for 1MPY. These new assignments modify the potential parameters to the methyl torsion reported earlier. Some striking similarities exist between the torsional and vibrational transitions in the fluorescence excitation spectra of 1MPY and 1MPI. Apart from pure torsional transitions, a progression of vibration-torsion combination bands was observed for both these molecules. The excitation spectrum of 3MPY resembles the spectrum of its parent molecule, 2-pyridone. The barrier height of the methyl torsion in the excited state of 3MPY is highest amongst all these molecules, whereas the barrier in 1MPI is higher than that of 1MPY. To get an insight into the methyl torsional barrier for these molecules, results of the ab initio calculations were compared with the experimental results. It was found that the conformation of the methyl group undergoes a 60°rotation in the excited state in all these molecules with respect to their ground state conformation. This phase shift of the excited state potential is attributed to the * -* hyperconjugation between the out-of-plane hydrogen of the methyl group and the molecular frame. It has been inferred that the change in lowest unoccupied molecular orbital energy plays the dominant role in the excited state barrier formation.
Dalton Transactions, 2004
The trinuclear complexes [(L&... more The trinuclear complexes [(L'-'")2RuII)3(mu3-L)](ClO4)3, [1] (ClO4)3-[3](ClO4)3 (L = trianionic form of 1,3,5-triazine-2,4,6-trithiol; N(p)C(5)H(4)N=N(a)-C6H4(R), R = H (L'), m-Me (L"), p-Me (L'")) and the analogous mononuclear complex [(L')2RuII(NC5H4S-)]ClO4 [4] ClO4 were synthesized. Crystal structures of [1](ClO4)3 and [4]ClO4 were determined. [1](3+)-[3](3+) exhibit three successive oxidative couples corresponding to Ru(II)Ru(II)Ru(III)<==>Ru(II)Ru(II)Ru(II); Ru(II)Ru(III)Ru(III)<==>Ru(II)Ru(II)Ru(III); Ru(III)Ru(III)Ru(III)<==>Ru(II)Ru(III)Ru(III) where the mixed valent states are moderately coupled. The complexes display multiple reductions associated with the azo functions of the ancillary ligands (L'-'"). The energy of the Ru(II)-based lowest energy MLCT transitions (533-558 nm) involving the pi* level of azoimine chromophore of L'-'" varies depending on the nuclearity as well as substituents in the ligand framework and follows the order: [1](3+) > [2](3+) > [3](3+) > [4](+). The complexes exhibit reasonably high third-order non-linear optical properties with gamma= (0.90-2.45) [times] 10(-29) esu. The interactions of the trinuclear complexes [((L')2RuII)3(mu3-L)]3+[1]3+, [((bpy)2RuII)3((mu3-L)]3+[5]3+ and [((phen)2RuII)3((mu3)-L)]3+[6]3+(bpy = 2,2'-bipyridine and phen = 1,10-phenanthroline) with the circular and linear forms of p-Bluescript DNA show reduced ethidium bromide fluorescence on gel electrophoresis.
International Journal of Mass Spectrometry, 2011
Dedicated to Professor John R. Eyler in admiration for his contributions to gas-phase ion chemist... more Dedicated to Professor John R. Eyler in admiration for his contributions to gas-phase ion chemistry and FT-ICR mass spectrometry and in appreciation for his scientific mentoring. a b s t r a c t Protonated 3-nitrotyrosine ([nitroTyr + H] + ) has been investigated by collision induced dissociation at variable energy and by IR multiple photon dissociation (IRMPD) spectroscopy in conjunction with quantum chemical calculations. Ultimately, this investigation is aimed at providing a diagnostic signature of protein tyrosine nitration, a post translational modification implied in pathological states. IRMPD spectroscopy of [nitroTyr + H] + ions has been examined in two different spectral regions, namely in the 1000-2000 cm −1 range, using the free electron laser beamline at the CLIO facility, and in the 3200-3700 cm −1 range, using a tabletop laser source. [nitroTyr + H] + ions have been assayed in parallel with intact [Tyr + H] + ions revealing characteristic bands at 1329 and 1540 cm −1 . Mode assignments allowed by density functional theory calculations of the IR spectra of the most stable conformers indicate that these features are associated to vibrations of the nitro group and are endowed with enhanced activity. In the NH/OH stretching region, the remarkable difference between the IRMPD spectra is the strong absorption at 3641 cm −1 of the ring OH stretching of [Tyr + H] + which is absent in the nitrated ion due to a strong hydrogen bond engaging the ring OH and the ortho nitro group. These results suggest that IRMPD spectroscopy and tandem mass spectrometry may afford a selective method for the analysis and characterization of 3-nitrotyrosine, to be possibly extended to 3-nitrotyrosine-containing peptides.
Journal of The American Society for Mass Spectrometry, 2011
Charge-directed fragmentation has been shown to be the prevalent dissociation step for protonated... more Charge-directed fragmentation has been shown to be the prevalent dissociation step for protonated peptides under the low-energy activation (eV) regime. Thus, the determination of the ion structure and, in particular, the characterization of the protonation site(s) of peptides and their fragments is a key approach to substantiate and refine peptide fragmentation mechanisms. Here we report on the characterization of the protonation site of oxazolone b 2 ions formed in collision-induced dissociation (CID) of the doubly protonated tryptic model-peptide YIGSR. In support of earlier work, here we provide complementary IR spectra in the 2800–3800 cm–1 range acquired on a table-top laser system. Combining this tunable laser with a high power CO2 laser to improve spectroscopic sensitivity, well resolved bands are observed, with an excellent correspondence to the IR absorption bands of the ring-protonated oxazolone isomer as predicted by quantum chemical calculations. In particular, it is shown that a band at 3445 cm–1, corresponding to the asymmetric N–H stretch of the (nonprotonated) N-terminal NH2 group, is a distinct vibrational signature of the ring-protonated oxazolone structure.
The Journal of Physical Chemistry Letters, 2015
The ion corresponding to protonated sulfurous acid, H3SO3(+), has been successfully delivered int... more The ion corresponding to protonated sulfurous acid, H3SO3(+), has been successfully delivered into the gas phase by electrospray ionization of the solution of a suitable precursor and an in-source fragmentation process. The neutral acid is a highly elusive molecule. However, its gas-phase basicity has been ascertained by means of a kinetic study of proton-transfer reactivity. The structure of the H3SO3(+) sampled ion has been probed by IRMPD spectroscopy in two complementary IR frequency ranges in conjunction with density functional theory calculations and found to conform to a trihydroxosulfonium ion. The characteristic IR signatures may aid in deciphering the presence of this species in extraterrestrial atmospheres.
Nature Chemistry, 2014
2-Aminopurine (2 AP) is a fluorescent isomer of adenine and has a fluorescence lifetime of ~11 ns... more 2-Aminopurine (2 AP) is a fluorescent isomer of adenine and has a fluorescence lifetime of ~11 ns in water. It is widely used in biochemical settings as a site-specific fluorescent probe of DNA and RNA structure and base-flipping and -folding. These assays assume that 2 AP is intrinsically strongly fluorescent. Here, we show this not to be the case, observing that gas-phase, jet-cooled 2-aminopurine and 9-methyl-2-aminopurine have very short fluorescence lifetimes (156 ps and 210 ps, respectively); they are, to all intents and purposes, non-fluorescent. We find that the lifetime of 2-aminopurine increases dramatically when it is part of a hydrate cluster, 2 AP · (H2O)n, where n = 1-3. Not only does it depend on the presence of water molecules, it also depends on the specific hydrogen-bonding site to which they attach and on the number of H2O molecules at that site. We selectively microhydrate 2-aminopurine at its sugar-edge, cis-amino or trans-amino sites and see that its fluorescence lifetime increases by 4, 50 and 95 times (to 14.5 ns), respectively.
The Journal of Physical Chemistry B, 2013
2-Aminopurine (2AP) is an adenine analogue with a high fluorescence quantum yield in water soluti... more 2-Aminopurine (2AP) is an adenine analogue with a high fluorescence quantum yield in water solution, which renders it a useful real-time probe of DNA structure. We report the ultraviolet (UV) and infrared (IR) spectra of size-selected and jet-cooled 9H-2AP·(H2O)n clusters with n = 2 and 3. Mass- and species-specific UV/UV holeburning spectroscopy allows to separate the UV spectra of four cluster isomers in the 31,200–33,000 cm(–1) spectral region with electronic band origins at 31339, 31450, 31891, and 32163 cm(–1). Using IR/UV depletion spectroscopy in combination with B3LYP calculated harmonic vibrational frequencies, the H-bonding topologies of two isomers of the n = 2 and of two isomers of the n = 3 cluster are identified. One n = 2 isomer (denoted 2A) forms a water dimer chain between the N9H and N3 atoms at the sugar-edge site, the other isomer (denoted 2D) binds one H2O at the sugar-edge site and the other at the trans-amino site between the N1 atom and the NH2 group. For 2-aminopurine·(H2O)3, one isomer (denoted 3A) forms an H-bonded water wire at the sugar-edge site, while isomer 3B accommodates two H2O molecules at the sugar-edge and one at the trans-amino site. The approximate second-order coupled cluster (CC2) method predicts the adiabatic S1 ← S0 transitions of 9H-2-aminopurine and six water cluster isomers with n = 1–3 in very good agreement with the experimental 0(0)(0) frequencies, with differences of <0.6%. The stabilization of the S1(ππ*) state of 2-aminopurine by water clusters is highly regiospecific: Isomers with one or two H2O molecules H-bonded in the trans-amino position induce large spectra red shifts, corresponding to 1ππ* state stabilization of 10–12 kJ/mol, while water-wire cluster solvation at the sugar-edge leads to much smaller stabilization. The evolution of the IR spectra of the water-wire clusters with n = 1–3 that are H-bonded to the sugar-edge site is discussed. Qualitatively different regions (denoted I to IV) can be attributed to the different free and H-bonded OH, NH, NH2 and OH···OH water-wire stretch vibrations.
The Journal of Physical Chemistry A, 2012
The infrared (IR) spectra of the supersonic-jet cooled 9H-and 7H-tautomers of 2-aminopurine (2AP)... more The infrared (IR) spectra of the supersonic-jet cooled 9H-and 7H-tautomers of 2-aminopurine (2AP) and of the 9H-2-aminopurine·H 2 O monohydrate clusters have been measured by mass-and species-selective IR-UV double resonance spectroscopy in the 3200−3900 cm −1 region, covering the N−H and O−H stretching vibrations. The spectra are complemented by density functional (B3LYP and PW91) and by second-order Møller−Plesset (MP2) calculations of the electronic energies and vibrational frequencies of the respective 2AP tautomers and clusters. The 9H-and 7H-2-aminopurine tautomers were definitively identified by the shifts of their NH and NH 2 symmetric and asymmetric stretching frequencies and by comparison to the B3LYP/TZVP calculated IR spectra. The H-bond topologies of the two previously observed 9H-2-amino-purine·H 2 O isomers (Sinha. R. K.; et al. J. Phys. Chem. A 2011, 115, 6208) are definitively identified as the "sugar-edge" isomer A and the "trans-amino-bound" isomer B by comparing their IR spectra to the calculated frequencies and IR intensities of the cluster isomers A, B, C, and D, as well as to the IR spectrum of 9H-2AP. The sugar-edge isomer A involves N9−H···OH 2 and HOH···N3 hydrogen bonds and is predicted to be the most stable form. The amino-bound isomer B involves NH 2 ···OH 2 and HOH···N1 hydrogen bonds and is calculated to lie 2.5 kJ/mol above isomer A. The H-bond topology of the "cis-amino-bound" isomer C is symmetrically related to isomer B, with a hydrogen bond to the N3 of the pyrimidine group. However, it is calculated to lie 7 kJ/mol above isomer A and indeed is not observed in the supersonic jet. Isomer D involves a single H-bond to the N7 position, is predicted to be 14 kJ/mol above A and is therefore not observed.
The Journal of Physical Chemistry A, 2011
For understanding the major- and minor-groove hydration patterns of DNAs and RNAs, it is importan... more For understanding the major- and minor-groove hydration patterns of DNAs and RNAs, it is important to understand the local solvation of individual nucleobases at the molecular level. We have investigated the 2-aminopurine·H(2)O monohydrate by two-color resonant two-photon ionization and UV/UV hole-burning spectroscopies, which reveal two isomers, denoted A and B. The electronic spectral shift δν of the S(1) ← S(0) transition relative to bare 9H-2-aminopurine (9H-2AP) is small for isomer A (-70 cm(-1)), while that of isomer B is much larger (δν = -889 cm(-1)). B3LYP geometry optimizations with the TZVP basis set predict four cluster isomers, of which three are doubly H-bonded, with H(2)O acting as an acceptor to a N-H or -NH2 group and as a donor to either of the pyrimidine N sites. The "sugar-edge" isomer A is calculated to be the most stable form with binding energy D(e) = 56.4 kJ/mol. Isomers B and C are H-bonded between the -NH2 group and pyrimidine moieties and are 2.5 and 6.9 kJ/mol less stable, respectively. Time-dependent (TD) B3LYP/TZVP calculations predict the adiabatic energies of the lowest (1)ππ* states of A and B in excellent agreement with the observed 0(0)(0) bands; also, the relative intensities of the A and B origin bands agree well with the calculated S(0) state relative energies. This allows unequivocal identification of the isomers. The R2PI spectra of 9H-2AP and of isomer A exhibit intense low-frequency out-of-plane overtone and combination bands, which is interpreted as a coupling of the optically excited (1)ππ* state to the lower-lying (1)nπ* dark state. In contrast, these overtone and combination bands are much weaker for isomer B, implying that the (1)ππ* state of B is planar and decoupled from the (1)nπ* state. These observations agree with the calculations, which predict the (1)nπ* above the (1)ππ* state for isomer B but below the (1)ππ* for both 9H-2AP and isomer A.
The Journal of Chemical Physics, 2014
The UV spectrum of the adenine analogue 9-methyl-2-aminopurine (9M-2AP) is investigated with one-... more The UV spectrum of the adenine analogue 9-methyl-2-aminopurine (9M-2AP) is investigated with one- and two-color resonant two-photon ionization spectroscopy at 0.3 and 0.05 cm(-1) resolution in a supersonic jet. The electronic origin at 32,252 cm(-1) exhibits methyl torsional subbands that originate from the 0A1'' (l = 0) and 1E(″) (l = ±1) torsional levels. These and further torsional bands that appear up to 00 (0)+230 cm(-1) allow to fit the threefold (V3) barriers of the torsional potentials as |V3''|=50 cm(-1) in the S0 and |V3'|=126 cm(-1) in the S1 state. Using the B3LYP density functional and correlated approximate second-order coupled cluster CC2 methods, the methyl orientation is calculated to be symmetric relative to the 2AP plane in both states, with barriers of V3''=20 cm(-1) and V3'=115 cm(-1). The 00 (0) rotational band contour is 75% in-plane (a/b) polarized, characteristic for a dominantly long-axis (1)ππ(*) excitation. The residual 25% c-axis polarization may indicate coupling of the (1)ππ(*) to the close-lying (1)nπ(*) state, calculated at 4.00 and 4.01 eV with the CC2 method. However, the CC2 calculated (1)nπ oscillator strength is only 6% of that of the (1)ππ(*) transition. The (1)ππ(*) vibronic spectrum is very complex, showing about 40 bands within the lowest 500 cm(-1). The methyl torsion and the low-frequency out-of-plane ν1' and ν2' vibrations are strongly coupled in the (1)ππ(*) state. This gives rise to many torsion-vibration combination bands built on out-of-plane fundamentals, which are without precedence in the (1)ππ(*) spectrum of 9H-2-aminopurine [S. Lobsiger, R. K. Sinha, M. Trachsel, and S. Leutwyler, J. Chem. Phys. 134, 114307 (2011)]. From the Lorentzian broadening needed to fit the 00 (0) contour of 9M-2AP, the (1)ππ(*) lifetime is τ ⩾ 120 ps, reflecting a rapid nonradiative transition.
Inorganic Chemistry, 2011
Model ferric heme nitrosyl complexes, [Fe(TPP)(NO)](+) and [Fe(TPFPP)(NO)](+), where TPP is the d... more Model ferric heme nitrosyl complexes, [Fe(TPP)(NO)](+) and [Fe(TPFPP)(NO)](+), where TPP is the dianion of 5,10,15,20-tetrakis-phenyl-porphyrin and TPFPP is the dianion of 5,10,15,20-tetrakis-pentafluorophenyl-porphyrin, have been obtained as isolated species by the gas phase reaction of NO with [Fe(III)(TPP)](+) and [Fe(III) (TPFPP)](+) ions delivered in the gas phase by electrospray ionization, respectively. The so-formed nitrosyl complexes have been characterized by vibrational spectroscopy also exploiting (15)N-isotope substitution in the NO ligand. The characteristic NO stretching frequency is observed at 1825 and 1859 cm(-1) for [Fe(III)(TPP)(NO)](+) and [Fe(III)(TPFPP)(NO)](+) ions, respectively, providing reference values for genuine five-coordinate Fe(III)(NO) porphyrin complexes differing only for the presence of either phenyl or pentafluorophenyl substituents on the meso positions of the porphyrin ligand. The vibrational assignment is aided by hybrid density functional theory (DFT) calculations of geometry and electronic structure and frequency analysis which clearly support a singlet spin electronic state for both [Fe(TPP)(NO)](+) and [Fe(TPFPP)(NO)](+) complexes. Both TD-DFT and CASSCF calculations suggest that the singlet ground state is best described as Fe(II)(NO(+)) and that the open-shell AFC bonding scheme contribute for a high-energy excited state. The kinetics of the NO addition reaction in the gas phase are faster for [Fe(III)(TPFPP)](+) ions by a relatively small factor, though highly reliable because of a direct comparative evaluation. The study was aimed at gaining vibrational and reactivity data on five-coordinate Fe(III)(NO) porphyrin complexes, typically transient species in solution, ultimately to provide insights into the nature of the Fe(NO) interaction in heme proteins.
Indian Journal of Physics, Mar 1, 2012
Spectroscopic studies on jet cooled 3-methylisoquinoline using fluorescence excitation and disper... more Spectroscopic studies on jet cooled 3-methylisoquinoline using fluorescence excitation and dispersed fluorescence methods were carried out. The effect of methyl substitution on the excited state behavior of isoquinoline is focused. Methyl torsional behavior and the effect on torsional potential of methyl group due to excited states mixing are addressed. The possible explanations of the observed intensity pattern of the torsional transitions in the fluorescence excitation spectrum are also presented.
The Journal of Chemical Physics, 2007
The laser induced fluorescence excitation and single vibronic excitation dispersed fluorescence s... more The laser induced fluorescence excitation and single vibronic excitation dispersed fluorescence spectra have been studied for supersonic jet cooled 1-methyl-2͑1h͒-pyridone. The methyl torsional bands and some low frequency vibrational transitions were assigned for both ground and excited states. The torsional parameters V 3 = 244 cm −1 and V 6 =15 cm −1 for the ground state and V 3 = 164 cm −1 and V 6 =40 cm −1 for the excited state were obtained. To get the insight into the methyl torsional barrier, ab initio calculations were performed and compared with the experimental results. Origin of potential barrier was traced by partitioning the barrier energy into changes in bondantibond interaction, structural, and steric energies accompanying methyl rotation using natural bond orbital analysis. The role of local interactions in ascertaining the barrier potential reveals that its nature cannot be understood without considering the molecular flexing. The hyperconjugation between CH * and ring * observed in lowest unoccupied molecular orbital ͑LUMO͒ stabilizes the methyl group conformer that undergoes a 60°rotation in the excited state with respect to that of the ground state, and it is the change in LUMO that plays important role in the excited state barrier formation.
Analytica Chimica Acta, 2008
In this article, we present a systematic study on IgG and Fab fragment of anti-IgG molecules usin... more In this article, we present a systematic study on IgG and Fab fragment of anti-IgG molecules using fluorescence auto- and cross-correlation spectroscopy to investigate their diffusion characteristics, binding kinetics, and the effect of small organic molecule, urea on their binding. Through our analysis, we found that the diffusion coefficient for IgG and Fab fragment of anti-IgG molecules were 37+/-2 microm2s(-1) and 56+/-2 microm2s(-1), respectively. From the binding kinetics study, the respective forward (k(a)) and backward (k(d)) reaction rates were (5.25+/-0.25)x10(6)M(-1)s(-1) and 0.08+/-0.005 s(-1), respectively and the corresponding dissociation binding constant (K(D)) was 15+/-2 nM. We also found that urea inhibits the binding of these molecules at 4M concentration due to denaturation.
The laser induced fluorescence excitation and single vibronic excitation dispersed fluorescence s... more The laser induced fluorescence excitation and single vibronic excitation dispersed fluorescence spectra have been studied for supersonic jet cooled 1-methyl-2͑1h͒-pyridone. The methyl torsional bands and some low frequency vibrational transitions were assigned for both ground and excited states. The torsional parameters V 3 = 244 cm −1 and V 6 =15 cm −1 for the ground state and V 3 = 164 cm −1 and V 6 =40 cm −1 for the excited state were obtained. To get the insight into the methyl torsional barrier, ab initio calculations were performed and compared with the experimental results. Origin of potential barrier was traced by partitioning the barrier energy into changes in bondantibond interaction, structural, and steric energies accompanying methyl rotation using natural bond orbital analysis. The role of local interactions in ascertaining the barrier potential reveals that its nature cannot be understood without considering the molecular flexing. The hyperconjugation between CH * and ring * observed in lowest unoccupied molecular orbital ͑LUMO͒ stabilizes the methyl group conformer that undergoes a 60°rotation in the excited state with respect to that of the ground state, and it is the change in LUMO that plays important role in the excited state barrier formation.
Dalton Transactions, 2003
... 1,10-phenanthroline and L 3− = 1,3,5-triazine-2,4,6-trithiol). Sanjib Kar, Thomas A. Miller, ... more ... 1,10-phenanthroline and L 3− = 1,3,5-triazine-2,4,6-trithiol). Sanjib Kar, Thomas A. Miller, Soma Chakraborty, Biprajit Sarkar, Biswajit Pradhan, Rajeev K. Sinha, Tapanendu Kundu, Michael D. Ward and Goutam Kumar Lahiri ...
Theoretical Chemistry Accounts, 2008
In this article, we present a systematic study on mono-methylindoles to investigate the electroni... more In this article, we present a systematic study on mono-methylindoles to investigate the electronic origin of the threefold symmetric component (V 3) of the methyl torsional potential barrier in the ground electronic state (S 0). The structures and the torsional potential parameters of these molecules were evaluated from ab initio calculation using Hartree-Fock (HF), second order Mollar Plesset perturbation (MP2) and B3LYP density functional level of theories and Gaussian type basis set 6-31G(d, p). Natural bond orbital (NBO) analysis of these molecules were carried out using B3LYP/6-31G(d, p) level of calculation to understand the formation of the threefold V 3 term arising from the changes of various non-covalent interactions during methyl rotation. Our analysis reveals that the contributions from π orbitals play a dominant role in the barrier height determination in this class of molecules. The threefold term in the barrier arises purely from the interactions non-local to the methyl group in case when the methyl group has two single bonds vicinal to it. On the other hand, it is the local interaction that determines the potential energy barrier when the methyl group has one single bond and one double bond vicinal to it. However, in all these cases, the magnitude of the energy barrier depends on the resonance structure formation in the benzene ring frame upon rotation of the methyl group and, therefore, the energetics of the barrier cannot be understood without considering the molecular flexing during methyl rotation.
... 1,10-phenanthroline and L 3− = 1,3,5-triazine-2,4,6-trithiol). Sanjib Kar, Thomas A. Miller, ... more ... 1,10-phenanthroline and L 3− = 1,3,5-triazine-2,4,6-trithiol). Sanjib Kar, Thomas A. Miller, Soma Chakraborty, Biprajit Sarkar, Biswajit Pradhan, Rajeev K. Sinha, Tapanendu Kundu, Michael D. Ward and Goutam Kumar Lahiri ...
Chemical Physics, 2007
To get the insight into the electronic structure-methyl torsion correlation in nitrogen heterocyc... more To get the insight into the electronic structure-methyl torsion correlation in nitrogen heterocyclic molecules, a comparative study on torsion of the methyl group in 1-methyl-2(1H)pyridone (1MPY), 1-methyl-2(1H)pyridinimine (1MPI), and 3-methyl-2(1H)pyridone (3MPY) was carried out using ab initio calculations. To understand the barrier forming mechanism in the ground state and its consequence on the molecular structure, the ground state torsional potential has been investigated by partitioning the barrier energy using the natural bond orbital (NBO) theoretical framework. The NBO analysis reveals that the delocalization energy is the barrier forming term whereas the Lewis energy is always antibarrier for all these molecules. To get further insight into the effect of local electronic structure on the methyl torsional barrier, the individual bond-antibond interactions and structural energy contributions have been investigated. It was found that when the bond order difference between the vicinal bonds does not change appreciably during the course of methyl rotation, the local electronic interactions with the methyl group do not play any decisive role in barrier formation as observed in the case of 1MPY and 1MPI. In these cases, it is the skeletal relaxation during methyl rotation that plays an important role in determining the barrier. On the other hand, if the bond order change is appreciable as is the case for 3MPY, the local interactions alone suffice to describe the origin of the torsional barrier of the methyl group.
Chemical Physics, 2007
The laser induced fluorescence excitation and dispersed fluorescence spectra of three nitrogen he... more The laser induced fluorescence excitation and dispersed fluorescence spectra of three nitrogen heterocyclic molecules 1-methyl-2͑1H͒pyridone ͑1MPY͒, 1-methyl-2͑1H͒pyridinimine ͑1MPI͒, and 3-methyl-2͑1H͒pyridone ͑3MPY͒ have been studied under supersonic jet cooled condition. The methyl torsional and some low frequency vibrational transitions in the fluorescence excitation spectrum were assigned for 1MPY. These new assignments modify the potential parameters to the methyl torsion reported earlier. Some striking similarities exist between the torsional and vibrational transitions in the fluorescence excitation spectra of 1MPY and 1MPI. Apart from pure torsional transitions, a progression of vibration-torsion combination bands was observed for both these molecules. The excitation spectrum of 3MPY resembles the spectrum of its parent molecule, 2-pyridone. The barrier height of the methyl torsion in the excited state of 3MPY is highest amongst all these molecules, whereas the barrier in 1MPI is higher than that of 1MPY. To get an insight into the methyl torsional barrier for these molecules, results of the ab initio calculations were compared with the experimental results. It was found that the conformation of the methyl group undergoes a 60°rotation in the excited state in all these molecules with respect to their ground state conformation. This phase shift of the excited state potential is attributed to the * -* hyperconjugation between the out-of-plane hydrogen of the methyl group and the molecular frame. It has been inferred that the change in lowest unoccupied molecular orbital energy plays the dominant role in the excited state barrier formation.
Dalton Transactions, 2004
The trinuclear complexes [(L&... more The trinuclear complexes [(L'-'")2RuII)3(mu3-L)](ClO4)3, [1] (ClO4)3-[3](ClO4)3 (L = trianionic form of 1,3,5-triazine-2,4,6-trithiol; N(p)C(5)H(4)N=N(a)-C6H4(R), R = H (L'), m-Me (L"), p-Me (L'")) and the analogous mononuclear complex [(L')2RuII(NC5H4S-)]ClO4 [4] ClO4 were synthesized. Crystal structures of [1](ClO4)3 and [4]ClO4 were determined. [1](3+)-[3](3+) exhibit three successive oxidative couples corresponding to Ru(II)Ru(II)Ru(III)<==>Ru(II)Ru(II)Ru(II); Ru(II)Ru(III)Ru(III)<==>Ru(II)Ru(II)Ru(III); Ru(III)Ru(III)Ru(III)<==>Ru(II)Ru(III)Ru(III) where the mixed valent states are moderately coupled. The complexes display multiple reductions associated with the azo functions of the ancillary ligands (L'-'"). The energy of the Ru(II)-based lowest energy MLCT transitions (533-558 nm) involving the pi* level of azoimine chromophore of L'-'" varies depending on the nuclearity as well as substituents in the ligand framework and follows the order: [1](3+) > [2](3+) > [3](3+) > [4](+). The complexes exhibit reasonably high third-order non-linear optical properties with gamma= (0.90-2.45) [times] 10(-29) esu. The interactions of the trinuclear complexes [((L')2RuII)3(mu3-L)]3+[1]3+, [((bpy)2RuII)3((mu3-L)]3+[5]3+ and [((phen)2RuII)3((mu3)-L)]3+[6]3+(bpy = 2,2'-bipyridine and phen = 1,10-phenanthroline) with the circular and linear forms of p-Bluescript DNA show reduced ethidium bromide fluorescence on gel electrophoresis.
International Journal of Mass Spectrometry, 2011
Dedicated to Professor John R. Eyler in admiration for his contributions to gas-phase ion chemist... more Dedicated to Professor John R. Eyler in admiration for his contributions to gas-phase ion chemistry and FT-ICR mass spectrometry and in appreciation for his scientific mentoring. a b s t r a c t Protonated 3-nitrotyrosine ([nitroTyr + H] + ) has been investigated by collision induced dissociation at variable energy and by IR multiple photon dissociation (IRMPD) spectroscopy in conjunction with quantum chemical calculations. Ultimately, this investigation is aimed at providing a diagnostic signature of protein tyrosine nitration, a post translational modification implied in pathological states. IRMPD spectroscopy of [nitroTyr + H] + ions has been examined in two different spectral regions, namely in the 1000-2000 cm −1 range, using the free electron laser beamline at the CLIO facility, and in the 3200-3700 cm −1 range, using a tabletop laser source. [nitroTyr + H] + ions have been assayed in parallel with intact [Tyr + H] + ions revealing characteristic bands at 1329 and 1540 cm −1 . Mode assignments allowed by density functional theory calculations of the IR spectra of the most stable conformers indicate that these features are associated to vibrations of the nitro group and are endowed with enhanced activity. In the NH/OH stretching region, the remarkable difference between the IRMPD spectra is the strong absorption at 3641 cm −1 of the ring OH stretching of [Tyr + H] + which is absent in the nitrated ion due to a strong hydrogen bond engaging the ring OH and the ortho nitro group. These results suggest that IRMPD spectroscopy and tandem mass spectrometry may afford a selective method for the analysis and characterization of 3-nitrotyrosine, to be possibly extended to 3-nitrotyrosine-containing peptides.
Journal of The American Society for Mass Spectrometry, 2011
Charge-directed fragmentation has been shown to be the prevalent dissociation step for protonated... more Charge-directed fragmentation has been shown to be the prevalent dissociation step for protonated peptides under the low-energy activation (eV) regime. Thus, the determination of the ion structure and, in particular, the characterization of the protonation site(s) of peptides and their fragments is a key approach to substantiate and refine peptide fragmentation mechanisms. Here we report on the characterization of the protonation site of oxazolone b 2 ions formed in collision-induced dissociation (CID) of the doubly protonated tryptic model-peptide YIGSR. In support of earlier work, here we provide complementary IR spectra in the 2800–3800 cm–1 range acquired on a table-top laser system. Combining this tunable laser with a high power CO2 laser to improve spectroscopic sensitivity, well resolved bands are observed, with an excellent correspondence to the IR absorption bands of the ring-protonated oxazolone isomer as predicted by quantum chemical calculations. In particular, it is shown that a band at 3445 cm–1, corresponding to the asymmetric N–H stretch of the (nonprotonated) N-terminal NH2 group, is a distinct vibrational signature of the ring-protonated oxazolone structure.