Insights from first principles molecular dynamics studies toward infrared multiple-photon and single-photon action spectroscopy: case study of the proton-bound dimethyl ether dimer

We have used finite temperature ab initio molecular dynamics simulations in conjunction with computation of critical quantum nuclear effects to probe the differences between single-photon argon tagged action spectral results and infrared multiple-photon dissociation experiments for a proton bound molecular ion system. We find that the principal difference between the results in these experimental techniques is essentially that of cluster temperature. The multiple-photon dissociation experiments conducted using room temperature ions reflect a larger degree of conformational freedom compared to the colder single-photon argon tagged action spectral results. Our ab initio molecular dynamics simulation techniques accurately capture the effects of conformational sampling, adequately reproduce both spectra, and can be utilized to assign the dynamically averaged finite temperature spectra.     

Resonant infrared multiphoton dissociation spectroscopy of gas-phase protonated peptides. Experiments and Car-Parrinello dynamics at 300 K

The gas-phase structures of protonated peptides are studied by means of resonant infrared multiphoton dissociation spectroscopy (R-IRMPD) performed with a free electron laser. The peptide structures and protonation sites are obtained through comparison between experimental IR spectra and their prediction from quantum chemistry calculations. Two different analyses are conducted. It is first supposed that only well-defined conformations, sufficiently populated according to a Boltzmann distribution, contribute to the observed spectra. On the contrary, DFT-based Car-Parrinello molecular dynamics simulations show that at 300 K protonated peptides no longer possess well-defined structures, but rather dynamically explore the set of conformations considered in the first conventional approach.     

Multiphoton dissociation of C3F6O

Major characteristics of multiphoton absorption and multiphoton dissociation of hexafluoropropene oxide (HFPO) were studied. Spectral relationships of the average number of IR photons absorbed per molecule and the yield of multiphoton dissociation were determined in the range of 1040-985 cm^–1 at different laser fluences. At the laser line 1025.3 cm^–1, the effect of collisions with buffer gases on the HFPO multiphoton absorption and multiphoton dissociation was studied and theq-factor was determined (q = O.6 at= 0.55J cm^–2). Characteristic features of HFPO decomposition under collisional conditions (p _HFPO> 0.1 Torr) were discussed. An anomalous difference in the values for quantum efficiency of multiphoton dissociation for long-wave and short-wave wings of HFPO absorption band was revealed. A procedure for correlating the experimental and theoretical data on the yield of multiphoton dissociation (when theq-factor is unknown) was suggested, and corresponding calculations were performed for the frequency 989.6 cm^–1.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 1927–1932, November, 1994.     

Infrared multiphoton and collision-induced dissociation studies of some gaseous alkylamine ions

Collision-induced dissociation and infrared multiphoton dissociation of ions formed in di- and tri-ethylamine, di- and tri-n-propylamine, and di-isopropylamine were investigated by Fourier-transform ion-cyclotron resonance mass spectrometry. Molecular ions of all amines except di-n-propylamine produced similar fragment ions when subjected to either dissociation technique. The initial fragmentation involved C_αC_β bond cleavage, loss of an alkyl radical, and formation of an immonium ions. Subsequent fragmentations of the immonium ions produced by both dissociation mechanisms involved McLafferty-type rearrangements and loss of alkenes. The molecular ion of di-n-propylamine fragmented by a different mechanism when subjected to infrared irradiation. Protonated molecules of di- and tri-n-propylamine yielded C₃H₆ and an ammonium ion upon infrared multiphoton dissociation, while protonated molecules of the other amines did not dissociate when this technique was applied. In contrast, collision-induced dissociation produced fragmentation for all protonated molecules. Explanation of the different fragmentations observed for the two dissociation techniques is given in terms of a mechanism involving a tight transition state for protonated di- and tri-n-propylamine dissociation.     

Multiphoton dissociation of molecules with low power cw infrared lasers: collisional enhancement of dissociation probabilities

Multiphoton dissociation of C₃F⁺₆ is observed using low intensity cw CO₂ laser radiation. Ion cyclotron resonance (ICR) techniques are used to store ions for irradiation. Ion storage times up to 2 s are used. Multiphoton dissociation is observed at laser intensities below 100 W cm^?2 and at pressures below 10^?5 Torr. Only the lowest energy decomposition of C₃F⁺₆, to give C₂⁺₄ and CF₂, is observed. Multiphoton dissociation probabilities show a sharp wavelength dependence in contrast to typical pulsed laser multiphoton dissociation experiments. The photodissociation spectrum of C₃F⁺₆ is similar to the infrared absorption spectrum of neutral C₃F₆ at both low and high resolution. Collisions between C₃F⁺₆ and unreactive buffer gases (Ar, N₂, SF₆) are seen to enhance multiphoton dissociation, while collisions with C₃F₆ deactive the laser excited species. The results are discussed in terms of mechanisms for slow multiphoton dissociation.     

Investigating the relationship between infrared spectra of shared protons in different chemical environments: a comparison of protonated diglyme and protonated water dimer

The energetics, dynamics, and infrared spectroscopy of the shared proton in different chemical environments is investigated using molecular dynamics simulations. A three-dimensional potential energy surface (PES) suitable for describing proton transfer between an acceptor and a donor oxygen atom is combined with an all-atom force field to carry out reactive molecular dynamics simulations. The construction of the fully dimensional PES is inspired from the established mixed quantum mechanics/molecular mechanics treatment of larger systems. The "morphing potential" method is used to transform the generic PES for proton transfer along an O...H+...O motif into a three-dimensional PES for proton transfer in protonated diglyme. Using molecular dynamics simulations at finite temperature, the gas phase infrared spectra are calculated for both species from the Fourier transform of the dipole moment autocorrelation function. For protonated diglyme the modes involving the H+ motion are strongly mixed with other degrees of freedom. At low temperature, the O...H+...O asymmetric stretching vibration is found at 870 cm-1, whereas for H5O2+ this band is at 724 cm-1. As expected, the vibrational bands of protonated diglyme show no temperature dependence whereas for H5O2+ at T = 100 K the proton transfer mode is found at 830 cm-1, in good agreement with 861 cm-1 from very recent molecular dynamics simulations.     

On the mechanism of the copper-mediated C-S bond formation in the intramolecular disproportionation of imine disulfides

The mechanism of the copper-mediated disproportionation of aromatic imine disulfides to benzothiazoles in the gas phase is investigated by experimental and theoretical methods. Application of infrared multiphoton dissociation and hydrogen/deuterium exchange experiments combined with density functional theory (DFT) calculations of the relevant molecular structures and the associated infrared spectra allows the identification of the observed ionic intermediates. The theoretical investigation of the possible reaction pathways supported by collision-induced dissociation experiments provides a consistent mechanistic picture of the reaction catalyzed by a single copper(I) ion. Activation of the substrate proceeds via homolytic sulfur-sulfur bond cleavage, yielding metal complexes in the formal +3 oxidation state; carbon-sulfur coupling and hydrogen-atom transfer complete the transformation to the products. Exploratory studies demonstrate that in the gas phase, the disproportionation of the imine disulfide can also be mediated by other metal ions via different either homo- or heterolytic mechanisms without involving high-valent intermediates.     

Infrared spectra of homogeneous and heterogeneous proton-bound dimers in the gas phase

Infrared multiphoton dissociation spectra of three homogeneous and two heterogeneous proton-bound dimers were recorded in the gas phase. Comparison of the experimental infrared spectra recorded in the fingerprint region of the proton-bound dimers with spectra predicted by electronic structure calculations shows that all modes which are observed contain motion of the proton oscillating between the two monomers. The O-H-O asymmetric stretch for the homogeneous dimers is shown to occur at around 800 cm-1. As expected, the O-H-O asymmetric stretching modes for the heterogeneous proton-bound dimers are observed to shift to significantly higher energy with respect to those for the homogeneous proton-bound dimers due to the asymmetry of the O-H-O moeity. This shift is shown to be predictable from the difference in proton affinities between the two monomers. Density functional predictions of the infrared spectra based on the harmonic oscillator model are demonstrated to predict the observed spectra of the homogeneous proton-bound dimers with reasonable accuracy. Calculations of the structure and infrared spectrum of protonated diglyme at the B3LYP/6-31+G** level and basis also agree well with an infrared spectrum recorded previously. For both heterogeneous proton-bound dimers, however, the predicted spectra are blue-shifted with respect to experiment.     

Infrared multiphoton excitation: Energy distribution of reacting molecules from overtone excitation studies

A method is offered to estimate quantitatively the energy distribution of molecules reacting after being excited by multiphoton absorption of infrared radiation. The method is based on the comparison of the real time reaction kinetics obtained in the infrared multiphoton experiment with those observed upon excitation of a vibrational overtone. Results obtained for the dissociation of tetramethyldioxetane under low-pressure conditions are used as a demonstration.     

Isomerization and dissociation dynamics of HCN in a picosecond infrared laser field: a full-dimensional classical study

We report a full-dimensional study of the classical dynamics of HCN-->HNC isomerization and of HCN rovibrational dissociation driven by a strong but nonionizing picosecond infrared laser field. The dynamics of the isolated molecule and of the molecule in liquid Ar have both been studied. Our theoretical and numerical results show that when all degrees of freedom are accounted for the field induced molecular dynamics can be totally different from what was found in previous studies, where the HCN molecule is restricted to a plane containing the external field. It is shown that as HCN is driven by an infrared laser field, the rotation of the H atom around the C-N bond provides an important and highly efficient energy absorption mechanism. In the presence of a monochromatic picosecond infrared laser field with an intensity of 10(13) W/cm(2), this energy absorption mechanism generates considerable HCN-->HNC isomerization yield or high rovibrational dissociation yield without molecular preorientation or prealignment. Our study of the field induced isomerization and dissociation dynamics of the same system in liquid Ar shows that the picosecond isomerization dynamics is insignificantly affected by the surrounding atomic liquid whereas the dissociation yield may be greatly suppressed in a high density liquid. The implications of this study for full-dimensional quantum dynamics of multiphoton rovibrational excitation and dissociation of triatomics are briefly discussed.     

The line profiles of single rotational lines of the H 2 B - X(3, 0) band in an intense infrared light field

The first investigation of the lineshape of single rotational lines of the H ₂ B - X(3, 0) band in an intense infrared light field (λ = 1064 nm) at intensities between 10¹⁰ W/cm² and 10¹² W/cm² is reported. The B - X(3, 0) band is excited with low intensity vacuum ultraviolet radiation (λ ≈ 106 nm). B-state excitation is observed by multiphoton ionization and dissociation of H ₂ with H ⁺ as final product. The lineshapes of the B-X(3, 0) band behave differently in both decay channels. This indicates that they branch before the molecule is photoionized. The intensity dependence of the lineshapes seems to show that at certain intensities in the focused infrared light beam the AC-Stark effect induces transient resonances into the multiphoton excitation process starting at the B(v = 3, J) rotational levels. A qualitative analysis of the states which may influence the B(v = 3, J) multiphoton excitation rate is given.     

Fragmentation study of peptides using Fourier transform ion cyclotron resonance with infrared multiphoton dissociation: experiment and simulation

In this study, the fragmentation of gas-phase protonated Angiotensin II is investigated using electrospray ionization (ESI), Fourier-transform ion cyclotron resonance (FT-ICR), and mass spectrometry (MS) with a laser cleavage infrared multiphoton dissociation (IRMPD) technique. The experimental results show that the spectra peaks for the photoproducts are y2/b6- and y7-type ions, corresponding to the cleavage of His-Pro and Asp-Arg in the parent amino acid sequence. The fragmentation of the peptide under collision-free vacuum conditions is modeled using molecular dynamics simulations (MD). The binding energy for the peptide bonds (C'-N bond) of Angiotensin II is estimated from ab initio calculations. The calculations are directed at predicting experimental measurements of the product ions from the photodissociation of the peptide. The product distributions simulated by the MD dissociation trajectories include predominantly y7/b1 and y2/b6 pair ions.     

Time dependence of cn internal energy distribution following ir multiphoton dissociation of vinyl cyanide

Laser-induced fluorescence was used to study the CN radical produced by infrared multiphoton dissociation of vinyl cyanide. The time between the photolysis pulse and observation was varied. CN fragments produced at short times were hotter rotationally than those produced later, even under the collisionless conditions of a molecular beam.     

Infrared fingerprint spectroscopy and theoretical studies of potassium ion tagged amino acids and peptides in the gas phase

Infrared multiple-photon dissociation spectroscopy is effected on the K(+) tagged aromatic amino acids tyrosine and phenylalanine, as well as the K(+) tagged peptides bradykinin fragment 1-5 and [Leu]-enkephalin. The fingerprint (800-1800 cm(-1)) infrared spectra of these species are compared to density-functional theory (DFT) calculated spectra to determine whether the complex is in the charge solvation (CS) or salt bridge (SB) (i.e. zwitterionic) configuration. For the aromatic amino acids the CS structure is favored and the tridentate N/O/ring structure is found to be the preferred binding geometry for K(+). The experimental and theoretical evidence for bradykinin fragment 1-5 tagged with K(+) suggests that the SB structure is favored; the calculations indicate a head-to-tail looped structure stabilized by a salt bridge between the protonated guanidine group and the deprotonated C-terminus, which allows K(+) to sit in a binding pocket with five C=O electrostatic interactions. For K(+) tagged [Leu]-enkephalin the spectroscopic evidence is not as clear. While the calculations clearly favor a CS structure and the observation of a weak carboxylic acid C=O stretching band in the infrared spectrum matches this finding, the prominence of a band at 1600 cm(-1) renders the analysis more ambiguous, and hence the presence of some salt bridge ions cannot be excluded. Another striking feature in the [Leu]-enkephalin spectrum is the high infrared activity of the tyrosine side-chain modes, which can be clearly identified from comparison to the [Tyr + K](+) experimental spectrum, but which is not reproduced by the DFT calculations.     

Vibrational relaxation in simulated two-dimensional infrared spectra of two amide modes in solution

Two-dimensional infrared spectroscopy is capable of following the transfer of vibrational energy between modes in real time. We develop a method to include vibrational relaxation in simulations of two-dimensional infrared spectra at finite temperature. The method takes into account the correlated fluctuations that occur in the frequencies of the vibrational states and in the coupling between them as a result of interaction with the environment. The fluctuations influence the two-dimensional infrared line shape and cause vibrational relaxation during the waiting time, which is included using second-order perturbation theory. The method is demonstrated by applying it to the amide-I and amide-II modes in N-methylacetamide in heavy water. Stochastic information on the fluctuations is obtained from a molecular dynamics trajectory, which is converted to time dependent frequencies and couplings with a map from a density functional calculation. Solvent dynamics with the same frequency as the energy gap between the two amide modes lead to efficient relaxation between amide-I and amide-II on a 560 fs time scale. We show that the cross peak intensity in the two-dimensional infrared spectrum provides a good measure for the vibrational relaxation.     

Computational spectroscopy of carbon monoxide isotopomers in helium clusters

The rotational excitation spectrum, including the vibrational shift of the rotational band, of several CO isotopomers solvated in He clusters has been calculated. Reptation quantum Monte Carlo simulations are used in conjunction with an accurate He-CO potential energy surface, which quantitatively describes the rovibrational spectrum of the binary complex. Our simulations, when compared with number-selective infrared spectra taken for different isotopomers, help discriminate among the alternative assignments proposed for cluster sizes around 15 He atoms. The origin of the vibrational band has a red shift that is nearly linear with the cluster size within the first solvation shell and is almost constant up to the largest cluster studied, well beyond completion of the second solvation shell. A blue upturn at even larger sizes would be needed to attain the nanodroplet limit, as recently estimated from the isotopic dependence of the measured R(0) transitions.     

Real-time multiphoton ionization detection of iodine atoms produced by infrared multiphoton dissociation of perfluoroalkyl iodides

We report the direct detection of iodine atoms following infrared multiphoton dissociation of perfluoroalkyl iodides. The technique, three-photon resonant two-photon ionization, shows great promise as an actinometer for primary dissociation yield in IRMPD.     

Electron detachment dissociation of fluorescently labeled sialylated oligosaccharides

We explored the application of electron detachment dissociation (EDD) and infrared multiphoton dissociation (IRMPD) tandem mass spectrometry to fluorescently labeled sialylated oligosaccharides. Standard sialylated oligosaccharides and a sialylated N-linked glycan released from human transferrin were investigated. EDD yielded extensive glycosidic cleavages and cross-ring cleavages in all cases studied, consistently providing complementary structural information compared with infrared multiphoton dissociation. Neutral losses and satellite ions such as C-2H ions were also observed following EDD. In addition, we examined the influence of different fluorescent labels. The acidic label 2-aminobenzoic acid (2-AA) enhanced signal abundance in negative-ion mode. However, few cross-ring fragments were observed for 2-AA-labeled oligosaccharides. The neutral label 2-aminobenzamide (2-AB) resulted in more cross-ring cleavages compared with 2-AA-labeled species, but not as extensive fragmentation as for native oligosaccharides, likely resulting from altered negative charge locations from introduction of the fluorescent tag.     

Atomistic Simulations of CO Vibrations in Ices Relevant to Astrochemistry

The experimental absorption band of carbon monoxide (CO) in mixed ices has been extensively studied in the past. The astrophysical interest in this band is related to its characteristic shape, which appears to depend on the surrounding ice structure. Herein, molecular dynamics simulations are carried out to analyze the relationship between the structure of the ice and the infrared (IR) spectrum of embedded CO molecules at different concentrations. Instead of conventional force fields, anharmonic potentials are used for the bonded interactions. The electrostatic interactions are more accurately described by means of fluctuating atomic multipole moments (up to quadrupole). The experimentally observed splitting of the CO absorption band (gas phase: 2143 cm^?1) into a blue‐ (2152 cm^?1) and a red‐shifted (2138 cm^?1) signal is also found in the simulations. Complementary atomistic simulations allow us to relate the spectra with the structural features. The distinction between interstitial and substitutional CO molecules as the origin of this splitting is found to be qualitatively correct. However, at increasing CO concentrations, additional effects—such as mutual interactions between CO molecules—become important, and the simplistic picture needs to be revised.     

Infrared study of the bacterial autoinducer N-hexanoyl-homoserine lactone (C6-HSL) in the gas-phase, water, and octanol solutions

The N-hexanoyl-homoserine lactone (C6-HSL) molecule has been investigated by means of infrared multiphoton dissociation (IRMPD) and Fourier-transform infrared spectroscopy (FT-IR) under different conditions in an attempt to mimic biological situations encountered in communication between bacteria for quorum sensing. The protonated molecular ion was studied in the gas-phase that corresponds to a solvent-free situation somewhat analogous to that encountered in the receptor. The simulation of the IRMPD spectrum of the isolated ion was then conducted by means of quantum chemistry calculations in vacuum. In the case of the neutral species, the FT-IR spectra were recorded in D(2)O, mimicking the cytosolic and extracellular media as well as in 1-octanol that is often used for simulation of cell membranes. The interpretation was conducted by considering a C6-HSL molecule in its endo or exo conformation hydrogen-bonded to, respectively, six D(2)O and four 1-octanol molecules. A satisfying agreement with the experimental FT-IR studies conducted in solution at room temperature was obtained as long as a continuum IEFPCM model was added to the explicit solvent environment.