Michael Z. Kamrath

Determination of Noncovalent Docking by Infrared Spectroscopy of Cold Gas-Phase Complexes

Ties That Bind Almost by definition, effective catalysts bind their substrates for a very short time—releasing them quickly after helping them react and then moving on to bind new, as yet unreacted, substrates. This property engenders an efficient cycle, but it hinders study of the binding motif. Garand et al. (p. 694, published online 19 January; see the Perspective by Zwier) devised a technique to extract bound complexes from solution and freeze their conformations in cold, gas-phase clusters. Probing these clusters by vibrational spectroscopy in conjunction with theoretical calculations then allowed the sites of hydrogen bonding that hold the complexes together to be pinpointed. Conformationally freezing a weakly bound complex in the gas phase sheds light on its likely binding motifs in solution. Multidentate, noncovalent interactions between small molecules and biopolymer fragments are central to processes ranging from drug action to selective catalysis. We present a versatile and sensitive spectroscopic probe of functional groups engaged in hydrogen bonding in such contexts. This involves measurement of the frequency changes in specific covalent bonds upon complex formation, information drawn from otherwise transient complexes that have been extracted from solution and conformationally frozen near 10 kelvin in gas-phase clusters. Resonances closely associated with individual oscillators are easily identified through site-specific isotopic labeling, as demonstrated by application of the method to an archetypal system involving a synthetic tripeptide known to bind biaryl substrates through tailored hydrogen bonding to catalyze their asymmetric bromination. With such data, calculations readily converge on the plausible operative structures in otherwise computationally prohibitive, high-dimensionality landscapes.

How the Shape of an H-Bonded Network Controls Proton-Coupled Water Activation in HONO Formation

Its the Network Numerous reactions of small molecules and ions in the atmosphere take place in the confines of watery aerosols. Relph et al. (p. 308; see the Perspective by Siefermann and Abel) explored the specific influence of a water clusters geometry on the transformation of solvated nitrosonium (NO+) to nitrous acid (HONO). The reaction involves (O)N–O(H) bond formation with one water molecule, concomitant with proton transfer to additional, surrounding water molecules. Vibrational spectroscopy and theoretical simulations suggest that certain arrangements of the surrounding water network are much more effective than others in accommodating this charge transfer, and thus facilitating the reaction. Vibrational spectroscopy uncovers the role of a surrounding water network in the mediating reaction of a solvated ion. Many chemical reactions in atmospheric aerosols and bulk aqueous environments are influenced by the surrounding solvation shell, but the precise molecular interactions underlying such effects have rarely been elucidated. We exploited recent advances in isomer-specific cluster vibrational spectroscopy to explore the fundamental relation between the hydrogen (H)–bonding arrangement of a set of ion-solvating water molecules and the chemical activity of this ensemble. We find that the extent to which the nitrosonium ion (NO+)and water form nitrous acid (HONO) and a hydrated proton cluster in the critical trihydrate depends sensitively on the geometrical arrangement of the water molecules in the network. Theoretical analysis of these data details the role of the water network in promoting charge delocalization.

Isomer-Specific IR-IR Double Resonance Spectroscopy of D2-Tagged Protonated Dipeptides Prepared in a Cryogenic Ion Trap.

Isomer-specific vibrational predissociation spectra are reported for the gas-phase GlySarH(+) and SarSarH(+) [Gly = glycine; Sar = sarcosine] ions prepared by electrospray ionization and tagged with weakly bound D2 adducts using a cryogenic ion trap. The contributions of individual isomers to the overlapping vibrational band patterns are completely isolated using a pump-probe photochemical hole-burning scheme involving two tunable infrared lasers and two stages of mass selection (hence IR(2)MS(2)). These patterns are then assigned by comparison with harmonic (MP2/6-311+G(d,p)) spectra for various possible conformers. Both systems occur in two conformations based on cis and trans configurations with respect to the amide bond. In addition to the usual single intramolecular hydrogen bond motif between the protonated amine and the nearby amide oxygen atom, cis-SarSarH(+) adopts a previous unreported conformation in which both amino NHs act as H-bond donors. The correlated red shifts in the NH donor and C═O acceptor components of the NH···O═C linkage to the acid group are unambiguously assigned in the double H-bonded conformer.

Vibrational Predissociation Spectrum of the Carbamate Radical Anion, C5H5N-CO2−, Generated by Reaction of Pyridine with (CO2)m−

We report the vibrational predissociation spectrum of C(5)H(5)N-CO(2)(-), a radical anion which is closely related to the key intermediates postulated to control activation of CO(2) in photoelectrocatalysis with pyridine (Py). The anion is prepared by the reaction of Py vapor with (CO(2))(m)(-) clusters carried out in an ionized, supersonic entrainment ion source. Comparison with the results of harmonic frequency calculations establishes that this species is a covalently bound molecular anion derived from the corresponding carbamate, C(5)H(5)N-CO(2)(-) (H(+)). These results confirm the structural assignment inferred in an earlier analysis of the cluster distributions and photoelectron spectra of the mixed Py(m)(CO(2))(n)(-) complexes [J. Chem. Phys. 2000, 113 (2), 596-601]. The spectra of the (CO(2))(m)(-) (m = 5 and 7) clusters are presented for the first time in the lower energy range (1000-2400 cm(-1)), which reveal several of the fundamental modes that had only been characterized previously by their overtones and combination bands. Comparison of these new spectra with those displayed by Py(CO(2))(n)(-) suggests that a small fraction of the Py(CO(2))(n)(-) ions are trapped entrance channel reaction intermediates in which the charge remains localized on the (CO(2))(m)(-) part of the cluster.