Synchrotron IR spectromicroscopy: chemistry of living cells

Advanced analytical capabilities of synchrotron IR spectromicroscopy meet the demands of modern biological research for studying molecular reactions in individual living cells. (To listen to a podcast about this article, please go to the Analytical Chemistry multimedia page at pubs.acs.org/page/ancham/audio/index.html.).

Improved spatial resolution for reflection mode infrared microscopy

Standard commercial infrared microscopes operating in reflection mode use a mirror to direct the reflected light from the sample to the detector. This mirror blocks about half of the incident light, however, and thus degrades the spatial resolution by reducing the numerical aperture of the objective. Here, we replace the mirror with a 50% beamsplitter to allow full illumination of the objective and retain a way to direct the reflected light to the detector. The improved spatial resolution is demonstrated using two different microscopes capable of diffraction-limited resolution: the first microscope is coupled to a synchrotron source and utilizes a single point detector, whereas the second microscope has a standard blackbody source and uses a focal plane array detector.

Observation of the A1A" state of isocyanogen

The A1A" state of isocyanogen, CNCN, is observed using photofragment fluorescence excitation spectroscopy in a room temperature cell and in a molecular beam. The spectra are highly congested, but progressions that correspond to the Franck-Condon active C-N-C bending vibration in the excited state are evident. Linewidth measurements indicate that the excited state lifetime is <10 ps. These measurements are consistent with previous ab initio calculations, which predicted a bent excited state with a short lifetime due to predissociation. Although we do not believe that we have observed the origin band of the electronic transition, we place an upper limit of 42,523 cm(-1) on the energy of the excited state zero point level.

Beam Action Spectroscopy via Inelastic Scattering

In this article, a new technique we call Beam Action Spectroscopy via Inelastic Scattering (BASIS) is demonstrated. BASIS takes advantage of the sensitivity of rotational state distributions in a supersonic molecular beam to inelastic scattering within the beam. We exploit BASIS to achieve increased sensitivity in two very different types of experiments. In the first, the UV photodissociation spectrum of OClO is recovered by monitoring intensity changes in the pure rotational transition of a spectator molecule (OCS) downstream from the nozzle, revealing a new vibrational structure in the region between 30,000 and 36,000 cm(-1). In the second, the mid-IR vibrational spectrum of acetylene is recorded simply by monitoring a single pure rotational transition of OCS co-expanded with acetylene. The technique may prove particularly fruitful when an excitation process produces product dark states that are not easily probed by conventional spectroscopy.

Comparing reactions of H and Cl with C–H stretch-excited CHD3

We report the methyl radical product state distributions for the reactions of H and Cl with CHD3(nu1 = 1,2) at collision energies of 1.53 and 0.18 eV, respectively. Both reactions demonstrate mode selectivity. The resulting state distributions from the H+CHD3(nu1 = 1,2) reactions are well described by a spectator model. The reactions Cl + CHD3(nu1 = 1,2) exhibit similar behavior, but in some aspects the spectator model breaks down. We attribute this breakdown to enhanced intramolecular vibrational redistribution in the Cl + CHD3(nu1 = 1,2) reactions compared to the H + CHD3(nu1 = 1,2) reactions, caused by the interaction of the slower Cl atom with the vibrationally excited CHD3, which is promoted either by its longer collision duration, its stronger coupling, or both.

H + CD4 Abstraction Reaction Dynamics: Product Energy Partitioning

This paper presents experimental and theoretical studies of the product energy partitioning associated with the H + CD4 (nu = 0) --> HD + CD3 reaction for the collision energy range 0.5-3.0 eV. The theoretical results are based on quasiclassical trajectories from (1) first principles direct dynamics calculations (B3LYP/6-31G), (2) an empirical surface developed by Espinosa-García [J. Chem. Phys. 2002, 116, 10664] (EG), and (3) two semiempirical surfaces (MSINDO and reparametrized MSINDO). We find that most of the energy appears in product translation at energies just above the reactive threshold; however, HD vibration and rotation become quite important at energies above 1 eV, each accounting for over 20% of the available energy above 1.5 eV, according to the B3LYP calculations. The barrier on the B3LYP surface, though being later than that on EG, predicts significantly higher HD vibrational excitation than EG. This deviation is contradictory to what would be expected on the basis of the Polanyi rules and derives from modest differences in the potential energy surfaces. The CD3 internal energy is generally quite low, and we present detailed rotational state distributions which show that the CD3 rotational distribution is largely independent of collision energy in the 0.75-1.95 eV range. The most populated rotational levels are N = 5 and 6 on B3LYP, with most of that excitation being associated with motion about the C2 axes, rather than C3 axis, of the CD3 product, in good agreement with the experimental results. Through our extensive studies in this and previous work concerning the scattering dynamics, we conclude that B3LYP/6-31G provides the best available description of the overall dynamics for the title reaction at relatively high collision energies.

H + CD4 Abstraction Reaction Dynamics: Excitation Function and Angular Distributions

We compare experimental photoloc measurements and quasi-classical trajectory calculations of the integral cross sections, lab-frame speed distributions, and angular distributions associated with the CD3 products of the H + CD4(nu = 0) --> CD3 + HD reaction at collision energies ranging from 0.5 to 3.0 eV. Of the potential energy surfaces (PES) we explored, the direct dynamics calculations using the B3LYP/6-31G** density functional theory PES provide the best agreement with the experimental measurements. This agreement is likely due to the better overall description that B3LYP provides for geometries well removed from the minimum energy path, even though its barrier height is low by approximately 0.2 eV. In contrast to previous theoretical calculations, the angular distributions on this surface show behavior associated with a stripping mechanism, even at collision energies only approximately 0.1 eV above the reaction barrier. Other potential energy surfaces, which include an analytical potential energy surface from Espinosa-García and a direct dynamics calculation based on the MSINDO semiempirical Hamiltonian, are less accurate and predict more rebound dynamics at these energies than is observed. Reparametrization of the MSINDO surface, though yielding better agreement with the experiment, is not sufficient to capture the observed dynamics. The differences between these surfaces are interpreted using an analysis of the opacity functions, where we find that the wider cone of acceptance on the B3LYP surface plays a crucial role in determining the integral cross sections and angular distributions.

Millimeter-wave-detected, millimeter-wave optical polarization spectroscopy

We report a new form of microwave optical double-resonance spectroscopy called millimeter-wave-detected, millimeter-wave optical polarization spectroscopy (mmOPS). In contrast to other forms of polarization spectroscopy, in which the polarization rotation of optical beams is detected, the mmOPS technique is based on the polarization rotation of millimeter waves induced by the anisotropy from optical pumping out of the lower or upper levels of the millimeter wave transition. By monitoring ground-state rotational transitions with the millimeter waves, the mmOPS technique is capable of identifying weak or otherwise difficult-to-observe optical transitions in complex chemical environments, where multiple molecular species or vibrational states can lead to spectral congestion. Once a transition is identified, mmOPS can then be used to record pure rotational transitions in vibrationally and electronically excited states, with the resolution limited only by the radiative decay rate. Here, the sensitivity of this nearly-background-free technique is demonstrated by optically pumping the weak, nominally spin-forbidden CS e (3)Sigma(-)-X (1)Sigma(+) (2-0) and d (3)Delta-X (1)Sigma(+) (6-0) electronic transitions while probing the CS X (1)Sigma(+) (v(")=0,J(")=2-1) rotational transition with millimeter waves. The J(')=2,N(')=2<--J(')=1,N(')=1 pure rotational transition of the CS e (3)Sigma(-) (v(')=2) state is then recorded by optically preparing the J(')=1,N(')=1 level of the e (3)Sigma(-) (v(')=2) state via the J(')=1,N(')=1<--J(")=1 transition of the e (3)Sigma(-)-X (1)Sigma(+) (2-0) band.

Effects of C–H stretch excitation on the H+CH4 reaction

We have investigated the effects of C-H stretching excitation on the H+CH4-->CH3+H2 reaction dynamics using the photo-LOC technique. The CH3 product vibrational state and angular distribution are measured for the reaction of fast H atoms with methane excited in either the antisymmetric stretching fundamental (nu3=1) or first overtone (nu3=2) with a center-of-mass collision energy of Ecoll ranging from 1.52 to 2.20 eV. We find that vibrational excitation of the nu3=1 mode enhances the overall reaction cross section by a factor of 3.0+/-1.5 for Ecoll=1.52 eV, and this enhancement factor is approximately constant over the 1.52-2.20-eV collision energy range. A local-mode description of the CH4 stretching vibration, in which the C-H oscillators are uncoupled, is used to describe the observed state distributions. In this model, the interaction of the incident H atom with either a stretched or an unstretched C-H oscillator determines the vibrational state of the CH3 product. We also compare these results to the similar quantities obtained previously for the Cl+CH4-->CH3+HCl reaction at Ecoll=0.16 eV [Z. H. Kim, H. A. Bechtel, and R. N. Zare, J. Chem. Phys. 117, 3232 (2002); H. A. Bechtel, J. P. Camden, D. J. A. Brown, and R. N. Zare, ibid. 120, 5096 (2004)] in an attempt to elucidate the differences in reactivity for the same initially prepared vibration.

A Reinterpretation of the Mechanism of the Simplest Reaction at an sp3-Hybridized Carbon Atom: H + CD4 → CD3 + HD

A comparison between theory and experiment for the benchmark H + CD4 --> HD + CD3 abstraction reaction yields a reinterpretation of the reaction mechanism and highlights the unexpected contribution of a stripping mechanism. Whereas the best analytic surface fails to reproduce experiment, a first-principles direct-dynamics (on the fly) treatment is in good agreement, showing that the H + CD4 reaction exhibits extreme sensitivity to modest differences in the potential energy surface. We find that bent H-D-C transition state geometries play an important role in the dynamics. A simple model that relates the scattering angle impact parameter and cone of acceptance accounts well for the overall reaction dynamics.

Effect of bending and torsional mode excitation on the reaction Cl+CH4→HCl+CH3

A beam containing CH(4), Cl(2), and He is expanded into a vacuum chamber where CH(4) is prepared via infrared excitation in a combination band consisting of one quantum of excitation each in the bending and torsional modes (nu(2)+nu(4)). The reaction is initiated by fast Cl atoms generated by photolysis of Cl(2) at 355 nm, and the resulting CH(3) and HCl products are detected in a state-specific manner using resonance-enhanced multiphoton ionization (REMPI). By comparing the relative amplitudes of the action spectra of Cl+CH(4)(nu(2)+nu(4)) and Cl+CH(4)(nu(3)) reactions, we determine that the nu(2)+nu(4) mode-driven reaction is at least 15% as reactive as the nu(3) (antisymmetric stretch) mode-driven reaction. The REMPI spectrum of the CH(3) products shows no propensity toward the formation of umbrella bend mode excited methyl radical, CH(3)(nu(2)=1), which is in sharp distinction to the theoretical expectation based on adiabatic correlations between CH(4) and CH(3). The rotational distribution of HCl(v=1) products from the Cl+CH(4)(nu(2)+nu(4)) reaction is hotter than the corresponding distribution from the Cl+CH(4)(nu(3)) reaction, even though the total energies of the two reactions are the same within 4%. An explanation for this enhanced rotational excitation of the HCl product from the Cl+CH(4)(nu(2)+nu(4)) reaction is offered in terms of the projection of the bending motion of the CH(4) reagent onto the rotational motion of the HCl product. The angular distributions of the HCl(nu=0) products from the Cl+CH(4)(nu(2)+nu(4)) reaction are backward scattered, which is in qualitative agreement with theoretical calculation. Overall, nonadiabatic product vibrational correlation and mode specificity of the reaction indicate that either the bending mode or the torsional mode or both modes are strongly coupled to the reaction coordinate.

Comparing the dynamical effects of symmetric and antisymmetric stretch excitation of methane in the Cl+CH4 reaction

The effects of two nearly isoenergetic C-H stretching motions on the gas-phase reaction of atomic chlorine with methane are examined. First, a 1:4:9 mixture of Cl(2), CH(4), and He is coexpanded into a vacuum chamber. Then, either the antisymmetric stretch (nu(3)=3019 cm(-1)) of CH(4) is prepared by direct infrared absorption or the infrared-inactive symmetric stretch (nu(1)=2917 cm(-1)) of CH(4) is prepared by stimulated Raman pumping. Photolysis of Cl(2) at 355 nm generates fast Cl atoms that initiate the reaction with a collision energy of 1290+/-175 cm(-1) (0.16+/-0.02 eV). Finally, the nascent HCl or CH(3) products are detected state-specifically via resonance enhanced multiphoton ionization and separated by mass in a time-of-flight spectrometer. We find that the rovibrational distributions and state-selected differential cross sections of the HCl and CH(3) products from the two vibrationally excited reactions are nearly indistinguishable. Although Yoon et al. [J. Chem. Phys. 119, 9568 (2003)] report that the reactivities of these two different types of vibrational excitation are quite different, the present results indicate that the reactions of symmetric-stretch excited or antisymmetric-stretch excited methane with atomic chlorine follow closely related product pathways. Approximately 37% of the reaction products are formed in HCl(v=1,J) states with little rotational excitation. At low J states these products are sharply forward scattered, but become almost equally forward and backward scattered at higher J states. The remaining reaction products are formed in HCl(v=0,J) and have more rotational excitation. The HCl(v=0,J) products are predominantly back and side scattered. Measurements of the CH(3) products indicate production of a non-negligible amount of umbrella bend excited methyl radicals primarily in coincidence with the HCl(v=0,J) products. The data are consistent with a model in which the impact parameter governs the scattering dynamics.

State-to-state dynamics of the Cl+CH3OH→HCl+CH2OH reaction

Molecular chlorine, methanol, and helium are co-expanded into a vacuum chamber using a custom designed "late-mixing" nozzle. The title reaction is initiated by photolysis of Cl2 at 355 nm, which generates monoenergetic Cl atoms that react with CH3OH at a collision energy of 1960 +/- 170 cm(-1) (0.24 +/- 0.02 eV). Rovibrational state distributions of the nascent HCl products are obtained via 2 + 1 resonance enhanced multiphoton ionization, center-of-mass scattering distributions are measured by the core-extraction technique, and the average internal energy of the CH3OH co-products is deduced by measuring the spatial anisotropy of the HCl products. The majority (84 +/- 7%) of the HCl reaction products are formed in HCl(v = 0) with an average rotational energy of [Erot] = 390 +/- 70 cm(-1). The remaining 16 +/- 7% are formed in HCl(v = 1) and have an average rotational energy of [Erot] = 190 +/- 30 cm(-1). The HCl(v = 1) products are primarily forward scattered, and they are formed in coincidence with CH2OH products that have little internal energy. In contrast, the HCl(v = 0) products are formed in coincidence with CH2OH products that have significant internal energy. These results indicate that two or more different mechanisms are responsible for the dynamics in the Cl + CH3OH reaction. We suggest that (1) the HCl(v = 1) products are formed primarily from collisions at high impact parameter via a stripping mechanism in which the CH2OH co-products act as spectators, and (2) the HCl(v = 0) products are formed from collisions over a wide range of impact parameters, resulting in both a stripping mechanism and a rebound mechanism in which the CH2OH co-products are active participants. In all cases, the reaction of fast Cl atoms with CH3OH is with the hydrogen atoms on the methyl group, not the hydrogen on the hydroxyl group.

Bond and mode selectivity in the reaction of atomic chlorine with vibrationally excited CH2D2

The title reaction is investigated by co-expanding a mixture of Cl2 and CH2D2 into a vacuum chamber and initiating the reaction by photolyzing Cl2 with linearly polarized 355 nm light. Excitation of the first C-H overtone of CH2D2 leads to a preference for hydrogen abstraction over deuterium abstraction by at least a factor of 20, whereas excitation of the first C-D overtone of CH2D2 reverses this preference by at least a factor of 10. Reactions with CH2D2 prepared in a local mode containing two quanta in one C-H oscillator /2000>- or in a local mode containing one quantum each in two C-H oscillators /1100> lead to products with significantly different rotational, vibrational, and angular distributions, although the vibrational energy for each mode is nearly identical. The Cl+CH2D2/2000>- reaction yields methyl radical products primarily in their ground state, whereas the Cl+CH2D2/1100> reaction yields methyl radical products that are C-H stretch excited. The HCl(v=1) rotational distribution from the Cl+CH2D2/2000>- reaction is significantly hotter than the HCl(v=1) rotational distribution from the Cl+CH2D2/1100> reaction, and the HCl(v=1) differential cross-section (DCS) of the Cl+CH2D2/2000>- reaction is more broadly side scattered than the HCl(v=1) DCS of the Cl+CH2D2/1100> reaction. The results can be explained by a simple spectator model and by noting that the /2000>- mode leads to a wider cone of acceptance for the reaction than the /1100> mode. These measurements represent the first example of mode selectivity observed in a differential cross section, and they demonstrate that vibrational excitation can be used to direct the reaction pathway of the Cl+CH2D2 reaction.