Infrared studies of ionic clusters: the influence of Yuan T. Lee.
02 Oct 2006-Journal of Chemical Physics (American Institute of Physics)-Vol. 125, Iss: 13, pp 132302-132302
TL;DR: This paper will focus on the major areas of research initiated by the Yuan T. Lee group and how these studies stimulated and influenced others in what is currently a vibrant and growing field of ionic clusters.
Abstract: Beginning in the mid-1980s, a number of innovative experimental studies on ionic clusters emerged from the laboratory of Yuan T. Lee combining infrared laser spectroscopy and tandem mass spectrometry. Coupled with modern electronic structure calculations, this research explored many facets of ionic clusters including solvation, structure, and dynamics. These efforts spawned a resurgence in gas-phase cluster spectroscopy. This paper will focus on the major areas of research initiated by the Lee group and how these studies stimulated and influenced others in what is currently a vibrant and growing field.
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TL;DR: A comparative assessment of the performance of the M06 suite of density functionals against an MP2 benchmark for calculating the relative energies and geometric structures of the Cl(-)·arginine and Br(-)-amino acid clusters is presented, providing insight into the types of physical systems where each of these functionals should perform best.
Abstract: We present a comparative assessment of the performance of the M06 suite of density functionals (M06, M06-2X, and M06-HF) against an MP2 benchmark for calculating the relative energies and geometric structures of the Cl(-)·arginine and Br(-)·arginine halide ion-amino acid clusters. Additional results are presented for the popular B3LYP density functional. The Cl(-)·arginine and Br(-)·arginine complexes are important prototypes for the phenomenon of anion-induced zwitterion formation. Results are presented for the canonical (noncharge separated) and zwitterionic (charge separated) tautomers of the clusters, as well as the numerous conformational isomers of the clusters. We find that all of the M06 functions perform well in terms of predicting the general trends in the conformer relative energies and identifying the global minimum conformer. This is in contrast to the B3LYP functional, which performed significantly less well for the canonical tautomers of the clusters where dispersion interactions contribute more significantly to the conformer energetics. We find that the M06 functional gave the lowest mean unsigned error for the relative energies of the canonical conformers (2.10 and 2.36 kJ/mol for Br(-)·arginine and Cl(-)·arginine), while M06-2X gave the lowest mean unsigned error for the zwitterionic conformers (0.85 and 1.23 kJ/mol for Br(-)·arginine and Cl(-)·arginine), thus providing insight into the types of physical systems where each of these functionals should perform best.
501 citations
TL;DR: It will be shown that IR spectroscopy of mass-selected (bio)molecular systems is now well-placed to address specific questions on the individual effect of charge carriers (protons and metal ions), as well as solvent molecules on the overall structure.
Abstract: The low density of ions in mass spectrometers generally precludes direct infrared (IR) absorption measurements. The IR spectrum of an ion can nonetheless be obtained by inducing photodissociation of the ion using a high-intensity tunable laser. The emergence of free electron lasers (FELs) and recent breakthroughs in bench-top lasers based on nonlinear optics have now made it possible to routinely record IR spectra of gas-phase ions. As the energy of one IR photon is insufficient to cause dissociation of molecules and strongly bound complexes, two main experimental strategies have been developed to effect photodissociation. In infrared multiple-photon dissociation (IR-MPD) many photons are absorbed resonantly and their energy is stored in the bath of vibrational modes, leading to dissociation. In the "messenger" technique a weakly bound van der Waals atom is detached upon absorption of a single photon. Fundamental, historical, and practical aspects of these methods will be presented. Both of these approaches make use of very different methods of ion preparation and manipulation. While in IR-MPD ions are irradiated in trapping mass spectrometers, the "messenger" technique is generally carried out in molecular beam instruments. The main focus of this review is the application of IR spectroscopy to biologically relevant molecular systems (amino acids, peptides, proteins). Particular issues that will be addressed here include gas-phase zwitterions, the (chemical) structures of peptides and their collision-induced dissociation (CID) products, IR spectra of gas-phase proteins, and the chelation of metal-ligand complexes. Another growing area of research is IR spectroscopy on solvated clusters, which offer a bridge between the gas-phase and solution environments. The development of state-of-the-art computational approaches has gone hand-in-hand with advances in experimental techniques. The main advantage of gas-phase cluster research, as opposed to condensed-phase experiments, is that the systems of interest can be understood in detail and structural effects can be studied in isolation. It will be shown that IR spectroscopy of mass-selected (bio)molecular systems is now well-placed to address specific questions on the individual effect of charge carriers (protons and metal ions), as well as solvent molecules on the overall structure.
395 citations
Cites background from "Infrared studies of ionic clusters:..."
...…co-workers have considered other mixed complexes containing an alkali metal chelated by water molecules and a competitive ligand, such as hexafluorobenzene (Patwari & Lisy, 2003), para-difluorobenzene (Miller & Lisy, 2006a), indole (Miller & Lisy, 2006b) and n-methylacetamide (Miller & Lisy, 2007)....
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...…also surveys recent developments to complement a range of reviews that have appeared on IR spectroscopy of ions over the years (Bieske & Dopfer, 2000; Duncan, 2000, 2003; Oomens et al., 2003, 2006; Dopfer, 2005; Lisy, 2006; Asmis & Sauer, 2007; MacAleese & Maitre, 2007; Polfer & Oomens, 2007)....
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...The profound influence of Lee’s work on gas-phase spectroscopy of clusters has been reviewed recently (Lisy, 2006)....
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TL;DR: The new and exciting techniques of infrared consequence spectroscopy of gaseous ions are reviewed and this review mainly covers the topics with which the author has been directly involved in research: structures of proton-bound dimers, protonated amino acids and DNA bases, amino acid andDNA bases bound to metal ions and, more recently, solvated ionic complexes.
Abstract: In this article, the new and exciting techniques of infrared consequence spectroscopy (sometimes called action spectroscopy) of gaseous ions are reviewed. These techniques include vibrational predissociation spectroscopy and infrared multiple photon dissociation spectroscopy and they typically complement one another in the systems studied and the information gained. In recent years infrared consequence spectroscopy has provided long-awaited direct evidence into the structures of gaseous ions from organometallic species to strong ionic hydrogen bonded structures to large biomolecules. Much is being learned with respect to the structures of ions without their stabilizing solvent which can be used to better understand the effect of solvent on their structures. This review mainly covers the topics with which the author has been directly involved in research: structures of proton-bound dimers, protonated amino acids and DNA bases, amino acid and DNA bases bound to metal ions and, more recently, solvated ionic complexes. It is hoped that this review reveals the impact that infrared consequence spectroscopy has had on the field of gaseous ion chemistry.
197 citations
Cites background from "Infrared studies of ionic clusters:..."
...The closely related but subtly different VPD spectroscopy, aspects of which has also been reviewed recently (Duncan, 2003; Walker, Walters, & Duncan, 2005; Lisy, 2006), will be discussed in conjuction with newer techniques....
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...Gas phase IRMPD studies on Kþ(H2O)m showed that the first solvation shell is full at m¼ 4 but was increased to 8 in Kþ(H2O)1(difluorobenzene)n (Miller & Lisy, 2006)....
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...Studies of alkali metal cation bound dimers (Vaden & Lisy, 2005) and trimers (Vaden & Lisy, 2006) of phenol show that Liþ prefers strong ion–p bonding, that intermolecular hydrogen bonding becomes important for the larger alkali metal ions, and that the relatively tight hydrogen-bonded structures…...
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TL;DR: The performance of infrared (IR) spectroscopy of gas-phase ions in a commercially available 7 T Fourier transform ion cyclotron resonance mass spectrometer has been characterized and a pi-allyl-palladium reactive intermediate involved in the catalytic allylation of amine is studied.
Abstract: The performance of infrared (IR) spectroscopy of gas-phase ions in a commercially available 7 T Fourier transform ion cyclotron resonance mass spectrometer has been characterized. A π-allyl−palladium reactive intermediate, [(π-allyl)Pd(P(C6H5)3)2]+, involved in the catalytic allylation of amine is studied. A solution of this transition metal complex is electrosprayed, and the IR multiple photon dissociation (IRMPD) spectrum of the mass-selected ions is recorded in two spectral ranges. The fingerprint spectrum (650−1550 cm-1) is recorded using the Orsay free-electron laser, and the dependence of the IRMPD efficiency on laser power and irradiation time is characterized. The DFT-calculated IR absorption spectrum of the [(π-allyl)Pd(P(C6H5)3)2]+ complex shows good agreement with the experimental spectrum. The π-interaction between the palladium and the allyl moiety is reflected by the assignment of the IRMPD bands, and the observed allylic CH2 wagging modes appear to form a sensitive probe for the π-interacti...
149 citations
TL;DR: This review focuses on the rich chemistry of hydrated metal ions in the gas phase, covering coordination chemistry, charge separation in multiply charged systems, as well as intracluster and ion-molecule reactions.
Abstract: Studying metal ion solvation, especially hydration, in the gas phase has developed into a field that is dominated by a tight interaction between experiment and theory. Since the studied species carry charge, mass spectrometry is an indispensable tool in all experiments. Whereas gas-phase coordination chemistry and reactions of bare metal ions are reasonably well understood, systems containing a larger number of solvent molecules are still difficult to understand. This review focuses on the rich chemistry of hydrated metal ions in the gas phase, covering coordination chemistry, charge separation in multiply charged systems, as well as intracluster and ion-molecule reactions. Key ideas of metal ion solvation in the gas phase are illustrated with rare-gas solvated metal ions. © 2007 Wiley Periodicals, Inc., Mass Spectrom. Rev.
133 citations
References
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TL;DR: A great deal of direct and circumstantial evidence indicates that cation-π interactions are important in a variety of proteins that bind cationic ligands or substrates.
Abstract: Cations bind to the π face of an aromatic structure through a surprisingly strong, noncovalent force termed the cation-π interaction. The magnitude and generality of the effect have been established by gas-phase measurements and by studies of model receptors in aqueous media. To first order, the interaction can be considered an electrostatic attraction between a positive charge and the quadrupole moment of the aromatic. A great deal of direct and circumstantial evidence indicates that cation-π interactions are important in a variety of proteins that bind cationic ligands or substrates. In this context, the amino acids phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp) can be viewed as polar, yet hydrophobic, residues.
2,443 citations
TL;DR: In this article, the authors used ab initio path integral simulations to address the question that the hydrated proton forms a fluxional defect in the hydrogen-bonded network, with both H9O4+ and H5O2+ occurring only in the sense of "limiting" or "ideal" structures.
Abstract: Explanations for the anomalously high mobility of protons in liquid water began with Grotthuss's idea1, 2 of ‘structural diffusion’ nearly two centuries ago Subsequent explanations have refined this concept by invoking thermal hopping3, 4, proton tunnelling5, 6 or solvation effects7 More recently, two main structural models have emerged for the hydrated proton Eigen8, 9 proposed the formation of an H9O4+ complex in which an H3O+ core is strongly hydrogen-bonded to three H2O molecules Zundel10, 11, meanwhile, supported the notion of an H5O2+ complex in which the proton isshared between two H2O molecules Here we use ab initio path integral12,13,14 simulations to address this question These simulations include time-independent equilibrium thermal and quantum fluctuations of all nuclei, and determine interatomic interactions from the electronic structure We find that the hydrated proton forms a fluxional defect in the hydrogen-bonded network, with both H9O4+ and H5O2+ occurring only in thesense of ‘limiting’ or ‘ideal’ structures The defect can become delocalized over several hydrogen bonds owing to quantum fluctuations Solvent polarization induces a small barrier to proton transfer, which is washed out by zero-point motion The proton can consequently be considered part of a ‘low-barrier hydrogen bond’15, 16, in which tunnelling is negligible and the simplest concepts of transition-state theory do not apply The rate of proton diffusion is determined by thermally induced hydrogen-bond breaking in the second solvation shell
1,559 citations
TL;DR: The solution structures and transport mechanisms of hydrated hydroxide are reported from first-principles computer simulations that explicitly treat quantum and thermal fluctuations of all nuclei and find that the transport mechanism differs significantly from the proton hole picture.
Abstract: Compared to other ions, protons (H+) and hydroxide ions (OH-) exhibit anomalously high mobilities in aqueous solutions1. On a qualitative level, this behaviour has long been explained by ‘structural diffusion’—the continuous interconversion between hydration complexes driven by fluctuations in the solvation shell of the hydrated ions. Detailed investigations have led to a clear understanding of the proton transport mechanism at the molecular level2,3,4,5,6,7,8. In contrast, hydroxide ion mobility in basic solutions has received far less attention2,3,9,10, even though bases and base catalysis play important roles in many organic and biochemical reactions and in the chemical industry. The reason for this may be attributed to the century-old notion11 that a hydrated OH- can be regarded as a water molecule missing a proton, and that the transport mechanism of such a ‘proton hole’ can be inferred from that of an excess proton by simply reversing hydrogen bond polarities11,12,13,14,15,16,17,18. However, recent studies2,3 have identified OH- hydration complexes that bear little structural similarity to proton hydration complexes. Here we report the solution structures and transport mechanisms of hydrated hydroxide, which we obtained from first-principles computer simulations that explicitly treat quantum and thermal fluctuations of all nuclei19,20,21. We find that the transport mechanism, which differs significantly from the proton hole picture, involves an interplay between the previously identified hydration complexes2,3 and is strongly influenced by nuclear quantum effects.
835 citations
TL;DR: This work reports how the vibrational spectrum of protonated water clusters evolves in the size range from 2 to 11 water molecules, revealing the pronounced spectral impact of subtle changes in the hydration environment.
Abstract: The ease with which the pH of water is measured obscures the fact that there is presently no clear molecular description for the hydrated proton. The mid-infrared spectrum of bulk aqueous acid, for example, is too diffuse to establish the roles of the putative Eigen (H 3 O + ) and Zundel (H 5 O 2 + ) ion cores. To expose the local environment of the excess charge, we report how the vibrational spectrum of protonated water clusters evolves in the size range from 2 to 11 water molecules. Signature bands indicating embedded Eigen or Zundel limiting forms are observed in all of the spectra with the exception of the three- and five-membered clusters. These unique species display bands appearing at intermediate energies, reflecting asymmetric solvation of the core ion. Taken together, the data reveal the pronounced spectral impact of subtle changes in the hydration environment.
714 citations