A Computational Analysis of the Collision-Induced Dissociation Mechanisms of the Dipeptide Glycine-Serine Under Mass Spectrometry

Collision-induced dissociation (CID) of peptides using tandem mass spectrometry (MS) has been used to determine the identity of peptides and other large biological molecules. Mass spectrometry (MS) is a useful tool for determining the identity of molecules based on their interaction with electromagnetic fields. If coupled with another method like infrared (IR) vibrational spectroscopy, MS can provide structural information, but in its own right, MS can only provide the mass-to-charge (m/z) ratio of the fragments produced, which may not be enough information to determine the mechanism of the collision-induced dissociation (CID) of the molecule. In this case, theoretical calculations provide a useful companion for MS data and yield clues about the energetics of the dissociation. In this study, negative ion electrospray tandem MS was used to study the CID of the deprotonated dipeptide glycine-serine (Gly-Ser). Though negative ion MS is not as popular a choice as positive ion MS, studies by Bowie et al. show that it yields unique clues about molecular structure which complement positive ion spectroscopy, such as characteristic fragmentations like the loss of formaldehyde from the serine residue.2 The increase in the collision energy in the mass spectrometer alters the flexibility of the dipeptide backbone, enabling isomerizations (reactions not resulting in a fragment loss) and dissociations to take place. The mechanism of the CID of Gly-Ser was studied using two computational methods, B3LYP/6-311+G* and M06-2X/6-311++G**. The main pathway for molecular dissociation was analyzed in 5 conformers in an attempt to verify the initial mechanism proposed by Dr. James Swan after examination of the MS data. The results suggest that the loss of formaldehyde from serine, which Bowie et al. indicates is a characteristic of the presence of serine in a protein residue, is an endothermic reaction that is made possible by the conversion of the translational energy of the ion into internal energy as the ion collides with the inert collision gas. It has also been determined that the M06-2X functional¿s improved description of medium and long-range correlation makes it more effective than the B3LYP functional at finding elusive transition states. M06-2X also more accurately predicts the energy of those transition states than does B3LYP. A second CID mechanism, which passes through intermediates with the same m/z ratio as the main pathway for molecular dissociation, but different structures, including a diketopiperazine intermediate, was also studied. This pathway for molecular dissociation was analyzed with 3 conformers and the M06-2X functional, due to its previously determined effectiveness. The results suggest that the latter pathway, which meets the same intermediate masses as the first mechanism, is lower in overall energy and therefore a more likely pathway of dissociation than the first mechanism.

Vibrational Relaxation of N2O (v2) by Atomic Oxygen Measured by Tunable Diode Laser Absorption Spectroscopy

Through the use of Transient Diode Laser Absorption Spectroscopy (TDLAS), the rate coefficient for the vibrational relaxation of N2O (ν2) by O(3P) at room temperature (32 ºC)) was determined to be (1.51 ± 0.11)x10-12 cm3molecule-1sec-1. A Q-switched, frequency quadrupled (266 nm) Nd:YAG laser pulse was used as the pump for this experiment. This pulse caused the photodissociation of O3 into O2 and O atoms.Excited oxygen (O(1D)) was collisionally quenched to ground state (O(3P)) by Ar and/or Xe. Photodissociation also caused a temperature jump within the system, exciting the ν2 state of N2O molecules. Population in the ν2 state was monitored through a TDLASobservation of a ν3 transition. Data were fit using a Visual Fortran 6.0 Global Fitting program. Analysis of room temperature data taken using only Ar to quench O atoms to the ground state gave the same rate coefficient as analysis of data taken using an Ar/Xe mixture, suggesting Ar alone is a sufficient bath gas. Experimentation was alsoperformed at -27 ºC and -82 ºC for a temperature dependence analysis. A linear regression analysis gave a rate coefficient dependence on temperature of ... for the rate coefficient of the vibrational relaxation of N2O (ν2) by atomic oxygen.

Prediction of Accurate Anharmonic Experimental Vibrational Frequencies for Water Clusters, (H2O)n, n = 2−5

Accurate anharmonic experimental vibrational frequencies for water clusters consisting of 2−5 water molecules have been predicted on the basis of comparing different methods with MP2/aug-cc-pVTZ calculated and experimental anharmonic frequencies. The combination of using HF/6-31G* scaled frequencies for intramolecular modes and anharmonic frequencies for intermolecular modes gives excellent agreement with experiment for the water dimer and trimer and are as good as the expensive anharmonic MP2 calculations. The water trimer, the cyclic Ci and S4 tetramers, and the cyclic pentamer all have unique peaks in the infrared spectrum between 500 and 800 cm-1 and between 3400 and 3700 cm-1. Under the right experimental conditions these different clusters can be uniquely identified using high-resolution IR spectroscopy.

Vibrational spectroscopic monitoring of CO2-O energy transfer: cooling processes in atmospheres of Venus & Mars

The vibrational excitation of CO2 by a fast-moving O atom followed by infrared emission from the vibrationally excited CO2 has been shown to be an important cooling mechanism in the upper atmospheresof Venus, Earth and Mars. We are trying to determine more precisely the efficiency (rate coefficient) of the CO2-O vibrational energy transfer. For experimental ease the reverse reaction is used, i.e. collision of a vibrationally excited CO2 with atomic O, where we are able to convert to the atmospherically relevant reaction via a known equilibrium constant. The goal of this experiment was to measure the magnitudes of rate coefficients for vibrational energy states above the first excited state, a bending mode in CO2. An isotope of CO2, 13CO2, was used for experimental ease. The rate coefficients for given vibrational energy transfers in 13CO2 are not significantly different from 12CO2 at this level of precision. A slow-flowing gas mixture was flowed through a reaction cell: 13CO2 (vibrational specie of interest), O3(atomic O source), and Ar (bath gas). Transient diode laser absorption spectroscopy was used to monitor thechanging absorption of certain vibrational modes of 13CO2 after a UV pulse from a Nd:YAG laser was fired. Ozone absorbed the UV pulse in a process which vibrationally excited 13CO2 and liberated atomic O.Transient absorption signals were obtained by tuning the diode laser frequency to an appropriate ν3 transition and monitoring the population as a function of time following the Nd:YAG pulse. Transient absorption curves were obtained for various O atom concentrations to determine the rate coefficient of interest. Therotational states of the transitions used for detection were difficult to identify, though their short reequilibration timescale made the identification irrelevant for vibrational energy transfer measurements. The rate coefficient for quenching of the (1000) state was found to be (4 ± 8) x 10-12 cm3 s-1 which is the same order of magnitude as the lowest-energy bend-excited mode: (1.8 ± 0.3) x 10-12 cm3 s-1. More data is necessary before it can be certain that the numerical difference between the two is real.

Vibrational Relaxation of 13CO2(v2) by Atomic Oxygen

Carbon dioxide (CO2) has been of recent interest due to the issue of greenhouse cooling in the upper atmosphere by species such as CO2 and NO. In the Earth’s upper atmosphere, between altitudes of 75 and 110 km, a collisional energy exchange occurs between CO2 and atomic oxygen, which promotes a population of ground state CO2 to the bend excited state. The relaxation of CO2 following this excitation is characterized by spontaneous emission of 15-μm. Most of this energy is emitted away from Earth. Due to the low density in the upper atmosphere, most of this energy is not reabsorbed and thus escapes into space, leading to a local cooling effect in the upper atmosphere. To determine the efficiency of the CO2- O atom collisional energy exchange, transient diode laser absorption spectroscopy was used to monitor the population of the first vibrationally excited state, 13CO2(0110) or ν2, as a function of time. The rate coefficient, kO(ν2), for the vibrational relaxation 13CO2 (ν2)-O was determined by fitting laboratory measurements using a home-written linear least squares algorithm. The rate coefficient, kO(ν2), of the vibrational relaxation of 13CO2(ν2), by atomic oxygen at room temperature was determined to be (1.6 ± 0.3 x 10-12 cm3 s-1), which is within the uncertainty of the rate coefficient previously found in this group for 12CO2(ν2) relaxation. The cold temperature kO(ν2) values were determined to be: (2.1 ± 0.8) x 10-12 cm3 s-1 at Tfinal = 274 K, (1.8 ± 0.3) x 10-12 cm3 s-1 at Tfinal = 239 K, (2 ± 1) x 10-12 cm3 s-1 at Tfinal = 208 K, and (1.7 ± 0.3) x 10-12 cm3 s-1 at Tfinal = 186 K. These data did not show a definitive negative temperature dependence comparable to that found for 12CO2 previously.

Vibrational Relaxation of O3(nu2) by O((3)P)

Laboratory measurements of the rate coefficient for quenching of O3(nu2) by ground-state atomic oxygen, kO(nu2), at room temperature are presented. kO(nu2) is currently not well known and is necessary for appropriate nonlocal thermodynamic equilibrium modeling of the upper mesosphere and lower thermosphere. In this work, a 266 nm laser pulse photolyzes a small amount of O3 in a slow-flowing gas mixture of O3, Xe, and Ar. This process simultaneously produces atomic oxygen and increases the temperature of the gas mixture slightly, thereby increasing the population in the O3(nu2) state. Transient diode laser absorption spectroscopy is used to monitor the populations of the O3(nu2) and ground vibrational states as the system re-equilibrates. Relaxation rates are measured over a range of quencher concentrations to extract the rate coefficient of interest. The value of kO(nu2) was determined to be (2.2 0.5) * 10(-12) cm(3) s(-1).