Gas-Phase Spectroscopy of Biomolecular Building BlocksStimulated emission pumping–hole ﬁlling...

ANRV308-PC58-22 ARI 22 February 2007 10:38

Gas-Phase Spectroscopyof BiomolecularBuilding BlocksMattanjah S. de Vries1 and Pavel Hobza2

1Department of Chemistry and Biochemistry, University of California, Santa Barbara,California 93106; email: [email protected] of Organic Chemistry and Biochemistry, Academy of Sciences of the CzechRepublic, 166 10 Prague 6, Czech Republic; email: [email protected]

Annu. Rev. Phys. Chem. 2007. 58:585–612

First published online as a Review in Advanceon December 6, 2006

The Annual Review of Physical Chemistry isonline at http://physchem.annualreviews.org

This article’s doi:10.1146/annurev.physchem.57.032905.104722

Copyright c© 2007 by Annual Reviews.All rights reserved

0066-426X/07/0505-0585$20.00

Key Words

biomolecules, REMPI, computational chemistry, spectral holeburning, jet cooling

AbstractGas-phase spectroscopy lends itself ideally to the study of isolatedmolecules and provides important data for comparison with theory.In recent years, we have seen enormous progress in the study ofbiomolecular building blocks in the gas phase. The motivation forsuch work is threefold: (a) It is important to distinguish betweenintrinsic molecular properties and properties that result from thebiological environment. (b) Gas-phase spectroscopy of clusters pro-vides insights into fundamental interactions and into microsolvation.(c) Gas-phase data support quantum-chemical calculations. This re-view focuses on the current status of (poly)amino acids and DNAbases. Recent results help elucidate structure and hydrogen-bondedinteractions, as well as showcase a successful interplay between the-ory and experiment.

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DFT: density-functionaltheory

1. INTRODUCTION

Research in the past decade has shown considerable progress in the study of biomolec-ular building blocks in the gas phase, which makes it possible to distinguish betweenintrinsic molecular properties and properties resulting from the biological environ-ment. The details of fundamental biochemical characteristics and interactions areoften hidden by macroscopic solvent effects, interactions with other molecules, con-straints imposed by the macromolecular backbone, and averaging. Thus studyingindividual biomolecules, free of the external biological environment, reveals the in-trinsic properties of the most basic biomolecular processes. Detailed processes arefurther elucidated by observing how the intrinsic properties of the isolated moleculeschange with biomolecular interaction and with the sequential addition of single-solvent molecules. For example, isolated DNA bases can form hydrogen-bonded pairsin many arrangements, but study of isolated guanine-cytosine pairs found the Watson-Crick structure to be distinguished by unique photochemistry, and isolated modelpeptides show folding motifs without solvent stabilization in very short sequences.

The study of isolated molecules is the prime domain of gas-phase research, whichalso provides the best data for comparison with theory. Until recently, DNA bases,amino acids, and related molecules could not be studied in the gas phase for practicalreasons. Experimentally, these compounds have low vapor pressures, and theydecompose when heated. Computationally these systems were intractable on a hightheoretical level because of their size and because correlation or dispersion energywould have to be included to properly describe them. Therefore, semiempiricalquantum-chemical methods and even ab initio Hartree-Fock and density-functionaltheory (DFT) methods were of limited use. In both areas, significant progress hasnow been made.

In recent years the problem of transferring biomolecules into the gas phase intacthas largely been solved, making a rich tool chest of gas-phase techniques availablefor the study of these molecules. This review focuses on the spectroscopy of neutralbiomolecular building blocks. Although optical spectroscopy can provide detailedstructural information, it also poses additional practical challenges. High resolutionrequires low internal temperatures; furthermore, densities in the gas phase are usuallyquite low. Therefore, among the most ubiquitous approaches are those that employjet cooling in combination with electronic spectroscopy. The latter allows for thedetection of ions from multiphoton ionization or fluorescence to overcome sensitivitylimitations. Other spectral ranges, such as the infrared (IR), can then be studied bydouble-resonance techniques. We thus mainly devote this review to covering thesetypes of experiments.

Spectroscopy requires computational theory for the interpretation of spectra, butthe increasing size of the molecules studied challenges state-of-the-art computations.New algorithms and force fields need to be developed, which in turn require gas-phaseexperiments for calibration. In fact, simultaneous progress in theory and experimenthas driven the explosive progress in this field.

We mainly distinguish between two types of biomolecular building blocks for thepurpose of this review:

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Conformationallandscape: peptides canadopt a large number ofstructural shapes, orconformations; the lowestenergy structures are themost stable

REMPI:resonance-enhancedmultiphoton ionization

Laser-desorption jetcooling: technique to bringlarge, Fred Childbiomolecules into the gasphase intact, with reducedinternal energy

Spectral hole burning:double-resonancespectroscopy, measuringburn laser transitions by adecreased signal from aprobe laser

1. (Poly)amino acids. For these compounds, the emphasis of gas-phase spec-troscopy is on the study of conformations. Line shifts in combination withhigh-level calculations can help map conformational landscapes. Shape is cru-cial in biology, and the hope is that by recognizing fundamental propensities,it will eventually be possible to add to our understanding of protein folding.

2. Nucleobases. For these compounds the emphasis is on elucidating their pho-tochemistry and their hydrogen (H)-bonding interactions, which shed light onbase-pairing dynamics and on the details of solvation.

Other types of biomolecular building blocks studied in the gas phase include sugars(1), and smaller molecules and their derivatives that constitute the chromophoresof the major building blocks, such as purines and pyrimidines as nucleobase chro-mophores, and indole as an amino-acid chromophore.

2. EXPERIMENTAL TECHNIQUES

2.1. Laser-Desorption Jet Cooling

Following early reports on the laser desorption of large molecules (2, 3), Cable et al. (4)studied the spectroscopy of tryptophan di- and tripeptides by resonance-enhancedmultiphoton ionization (REMPI), as well as by laser-induced fluorescence (LIF),following laser desorption. Li & Lubman (5) demonstrated that for laser-desorbedtyrosine and related structural analogs, electronic spectroscopy can be a sensitiveprobe of small structural changes in related biological compounds. Arrowsmith et al.(6) and Meijer et al. (7) explored the characteristics of the technique.

The process of neutral laser desorption is poorly understood. A few mechanismshave been proposed (8, 9), and only a small number of experiments has been reportedto study the process (10–12). In nonresonant ionization (e.g., at 193 nm or 266 nm),one can control fragmentation by the proper choice of wavelength and laser fluence.Tembreull & Lubman (13) and Grotemeyer et al. (14) have shown that fragmentationcan be controlled by the ionization laser fluence. This control can be used to theadvantage of structural analysis. Higher ionization efficiencies have been obtained byfemtosecond laser pulse excitation, involving quasi-resonant effects (15).

2.2. Spectroscopy

Electronic spectroscopy in molecular beams includes LIF and REMPI (see Figure 1).The latter has the advantage of mass selectivity (16). Isomer distinction is possiblewith double-resonance techniques, which appear schematically in Figure 1. In thesetechniques, also called spectral hole burning (SHB), a burn laser pulse resonantlydepletes the ground state and is followed approximately 100 ns later by a probelaser pulse, which is tuned to a vibronic transition of a single specific isomer. Theresulting decrease in the probe laser signal thus provides isomer-specific (and inthe case of a REMPI probe, also mass-selective) spectroscopy. Ultraviolet-ultraviolet(UV-UV) double resonance allows the deconvolution of a vibronic spectrum in the

www.annualreviews.org • Gas-Phase Biomolecular Spectroscopy 587

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R2PI UV-UV IR-UV LIF

a b c d

S0

S1

IP

Figure 1Schematic representationof spectroscopictechniques described inthe text. IR-UV,infrared-ultraviolet holeburning; LIF,laser-inducedfluorescence; R2P1,resonant two-photonionization; UV-UV,ultraviolet-ultraviolet holeburning.

contributions from different isomers, whereas IR-UV double resonance allows forstructural assignments (17).

The red shifts of the NH-, OH-, C O-stretching vibrations and the blue shiftsof OH and NH in-plane bending vibrations upon hydrogen bonding often allowan unambiguous assignment of H-bonded structures (18, 19). Therefore the wave-length range of 2800–3600 cm−1 provides an excellent structural tool. This rangeis available from table optical parametric oscillator/amplifier systems. Recent exten-sions of tabletop laser systems to include the C O stretch frequency at approximately1800 cm−1 have enhanced this capability (20). Experiments at free-electron laser facil-ities cover lower frequencies (1, 19). Such lower-frequency experiments are in princi-ple more diagnostic for details of side-group conformations and can serve as tests forcomputations that include anharmonic contributions to the potentials. However, theresolution of such lasers is generally limited to approximately 1% of the wavelength.

The isomer selectivity distinguishes molecular-beam spectroscopy from cold-matrix spectroscopy together with the absence of matrix effects. Typical UV res-olutions of the order of a wave number combine with internal temperatures of theorder of 10–20 K (7). The use of pulsed-dye amplifiers provides higher resolutions toallow for rotationally resolved spectra (21). In the near-IR range, optical parametricoscillator devices achieve resolutions on the order of a few wave numbers, whereasfree-electron lasers in the mid-IR typically provide 10% resolution of the frequency.

We briefly describe related techniques that fall outside the scope of this re-view below. Stimulated emission pumping–hole filling spectroscopy and stimulatedemission pumping–induced population-transfer spectroscopy provide insights intoisomerization pathways (22). Microwave spectroscopy can lead to the accurate struc-tural determination of small molecules (23). Helium droplets are unique because ofthe low temperature; among the possible applications is polarization-dependent IRspectroscopy (24). Populations of isomers in helium droplets may differ from thosein supersonic beams because the timescale of cooling is much faster in the former.Another possible difference in the resulting spectroscopy stems from the possibility of


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PES: potential-surface

FES: free-energy surface

Molecular dynamicsquenching (MD/Q):computational simulation,repeatedly heating andcooling a molecule to findits low energy structures

the He environment causing matrix effects. Finally, all results included in this reviewrefer to the spectroscopy of neutral molecules. Limited work exists thus far on theoptical spectroscopy of ions, although many other forms of ion spectroscopy exist,such as ion-drift spectroscopy and unimolecular reactions.

3. THEORY

3.1. Molecular Structure and Geometry

Structure and properties of molecular clusters are mainly determined by noncovalentinteractions. A theoretical description of these interactions is difficult and requires themost accurate methods of computational chemistry available. Two structural motifsdominate biomolecular building blocks and their clusters: H-bonding and stacking.For the latter, London dispersion energy is the main source of stabilization. WhereasH-bonding interactions are well understood, stacking interactions are difficult to treatcomputationally. Figure 2 illustrates a case study for phenylalanine-glycine-glycine(Phe-Gly-Gly) for which double-resonance spectroscopy provides vibrational spectraof four conformations, one of which (Figure 2b) is stabilized by dispersive forces(25). The challenge for theory is to find the lowest-energy conformations, which canbe tested by comparing their vibrational frequencies with the experimental spectra.Figure 2 shows the four calculated conformations and the corresponding comparisonof frequencies. The following sections discuss the computational strategies for dealingwith a conformational phase space of this size, and possibly larger.

3.1.1. Strategy. The aim of theoretical studies is the determination of minimum-energy structures, as well as their populations and properties at experimental condi-tions. Although it is sufficient to merely study the potential-energy surface (PES) fora system at 0 K, a complete description at nonzero temperatures requires extensionto the free-energy surface (FES). The PES and FES differ; for example, the globalminimum at both surfaces might correspond to completely different structures. ThePES of biomolecular clusters is rich and contains a large number of energy minima.Finding the global minimum requires an efficient searching procedure. Moleculardynamics (MD) simulations, together with quenching (MD/Q), can provide a fulldescription of the PES. However, generally MD/Q calculations employ empirical po-tentials, limiting their applicability and accuracy. The empirical potential used shouldbe carefully a priori and a posteriori tested. Inevitably the combination of inaccuratepotentials and high-level MD simulations yields inaccurate results. Therefore, struc-tures obtained with the MD/Q treatment should be reoptimized at a high correlatedab initio level. Subsequently, detailed properties, such as vibrational frequencies, canbe determined for the most stable structures of the PES or FES with a high-levelquantum-chemical treatment.

3.1.2. Structure and geometry. Standard gradient optimization performed at thecorrelated Møller-Plesset second-order perturbation level (MP2) with a basis setof TZ + P quality [e.g., Dunning’s cc-pVTZ (correlation-consistent polarized


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Figure 2Optimized minimum energy structures for phenylalanine-glycine-glycine (Phe-Gly-Gly)(right-hand column). (b–e) Computed frequencies as stick spectra and infrared-ultravioletspectral hole burning (IR-UV SHB) spectra, recorded with the probe laser at the wavelengthsshown by the arrows in corresponding colors in the REMPI spectrum (a).

valence triple-zeta basis set)] generally yields sufficiently accurate results forH-bonded, stacked, T-shaped, and other structures of molecular clusters (26, 27).Further improvement is possible with counterpoise-corrected gradient optimization,which is, however, considerably more time consuming (28, 29). Resulting structuresare close to the experimental ones, and thus may have predictive value in the absence of


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CCSD: coupled clusterwith inclusion of single- anddouble-electron excitations

RI-MP2: resolution ofidentity Møller-Plessetsecond-order perturbation

CBS: complete basis set

experimental data. Moving beyond MP2 to highly correlated ab initio methods, suchas coupled cluster with inclusion of single- and double-electron excitations (CCSD)or even CCSD(T) (including triple-electron excitations), does not yield substantialimprovement and is impractical for larger biomolecular clusters.

The application of the resolution of identity MP2 (RI-MP2) method represents animportant next step, allowing the use of extended basis sets even for large complexeswith more than 24 atoms (the size of a benzene dimer). This method is capable of anaccurate description of H-bonded and stacked DNA base interactions (30). Resultsobtained with the RI-MP2 method differ only marginally from those evaluated withthe exact MP2 method, whereas the time saved is as large as one order of magnitude.

Understanding the interplay between planar H-bonding and vertical stacking isoften important when determining the structure of a biomolecular cluster. Origi-nally it was believed that specific H-bonding interactions are much stronger andcontribute dominantly to the cluster stability. It is now becoming clear, based onadvanced quantum-chemical calculations, that nonspecific stacking interactions aremore important than first expected. H-bonding and stacking interactions affect notonly the stability of biomolecular clusters such as DNA base pairs (31–35) and amino-acid interactions (36, 37)—at the heart of key problems in biochemistry—but theyalso apply to a wide variety of problems in other fields, ranging from gas-phasephysicochemical experiments to condensed-phase experiments and simulations.

Roughly speaking, H-bonding originates in electrostatic interactions and chargetransfer (induction), whereas stacking is a result of London dispersion energy. Hencemethods that are not able to cover the latter energy contribution are of limited usein biomolecular applications.

3.1.3. Stabilization energy. Stabilization energies strongly depend on the theoreti-cal level used, and reliable stabilization energies are only obtainable at high quantum-chemical ab initio levels. This is especially important for comparison of differentstructural types, such as H-bonded versus stacked structures. A reliable stabiliza-tion energy (�E ) follows from the complete basis set (CBS) limit of the CCSD(T)stabilization energy. Direct determination of this energy over an extended range isimpractical, and the energy is thus approximated by the sum of the CBS limit ofthe MP2 stabilization energy (�EMP2

CBS ) and a (�ECCSD(T) − �E MP2) correction termcovering the difference between the MP2 and CCSD(T) stabilization energies (31).The latter term depends much less on the basis-set size and thus requires a rathersmall basis set:

�E = �ECCSD(T)CBS = �EMP2

CBS +(�ECCSD(T)−�EMP2

).

Whereas we can already consider the Hartree-Fock (HF) interaction energy con-verged with respect to the one-electron basis set for relatively small basis sets, theMP2 correlation part of the interaction energy converges to its CBS limit unsatisfac-torily slowly. Therefore, the HF and MP2 energies should be extrapolated separately.Several studies have demonstrated successful extrapolation schemes in the literature,


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including the following equation by Helgaker and coworkers (38):

EHFX = EHF

CBS + Ae−a X and EcorrX = Ecorr

CBS + B X−3,

where EX and ECBS are energies for the basis set with the largest angular momentum Xand for the CBS, respectively, and the α parameter is fitted by the authors. The schemeuses the two-point form: It extrapolates two successive basis-set results. The two-point extrapolation form is preferable as inclusion of additional (lower-quality basisset) points results in extrapolations of lower quality to the fit, especially when using thesmallest basis set (e.g., cc-pVDZ). The authors applied the basis-set superposition-error counterpoise correction and frozen-core approximations throughout this study.They also applied the CBS extrapolation to all calculated energies (dimer, monomersin both monomer- and dimer-centered basis sets, and monomers in vacuo); i.e., bothdeformation and basis-set superposition-error corrections were extrapolated.

So far we have considered only highly correlated wave-function theories. The useof popular DFTs cannot be recommended because they neglect the London dispersionenergy part of the correlation (39–42). At present, the only possible approach is anempirical one in which an empirical dispersion energy augments the DFT energy. Theapproximate self-consistent charge density-functional tight-binding method, which isaugmented by an empirical London dispersion energy, appears promising (43). Themethod yields good estimates of stabilization energies for stacked and H-bondedDNA base pairs and amino-acid pairs. The procedure is fast and can even be used inMD simulations.

3.1.4. Thermodynamic characteristics. MD/Q simulations with kinetic energyhigher than any energy barrier scan the whole PES and localize all the energy minima.With sufficiently long simulations, the population of each structure can be found.Population is directly proportional to the change in free energy, and this approachthus extends the PES to the FES. Entropy always plays an important role, and certaintypes of energy minima are entropically favored. This is the case, for example, forstacked structures that are entropically favored over planar H-bonded structures. TheMD/Q procedure is based on empirical potentials, but it is anharmonic in nature.

Another possibility for generating thermodynamic parameters is a standardstatistical-thermodynamical treatment based on partition functions using the rigid-rotor harmonic-oscillator ideal-gas approximation. In this case, molecular parame-ters, such as rotational constants and vibrational frequencies, are obtained througha quantum-chemical treatment and are thus of higher quality, based on empiricalpotentials only. In addition to entropy, the enthalpy should be also determined. It isconstructed as a sum of the interaction energy, the zero-point vibration energy, andtemperature-dependent enthalpy terms.

3.1.5. Vibrational frequencies. Harmonic vibrational frequencies are computed byanalytical or numerical calculation of second derivatives of the energy. The numericalapproach is more time consuming, as well as less accurate, but it can be performedeven for extended clusters described by large basis sets. The lowest level is formed by


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correlated MP2 calculations using DZ + P basis sets. To match experimental frequen-cies, it is necessary to cover anharmonic effects, and the easiest way to achieve this is byintroducing scaling factors. Satisfactory vibrational frequencies are mostly obtainedwhen using a single-scaling factor based on experimental vibrational frequencies ofthe X-Y stretching coordinate of an isolated monomer. Use of multiple-scaling fac-tors based on various X-Y coordinates should result in even closer agreement withexperimental values.

3.2. Isolated Peptides

Isolated peptides exhibit features similar to those that characterize molecular clusters,and likewise two main structural motifs (H-bonding and stacking) dominate. Thetheoretical description of isolated peptides is therefore similar to that of molecularclusters, and only highly accurate quantum-chemical procedures yield satisfactoryresults in comparison with experiments.

3.2.1. Strategy. The PES of simple peptides is considerably more complicated thanthat of DNA base pairs. Once again, stabilization of these structures is mainly a resultof H-bonding and stacking, which involves delocalized electrons of phenyl groups,peptide bonds, and other units. The choice of empirical potential is difficult, androutinely used potentials such as AMBER or CHARMM are not always suitable.The aim is to select several dozen lowest-energy structures that can later be treatedby reliable correlated ab initio optimization. This treatment is time consuming andtherefore cannot be performed for all structures of a peptide. For example, in the caseof Phe-Gly-Gly tripeptide, more than 1000 energy minima exist. The first screeningmethod should be fast enough to allow MD simulations to be performed, and the useof the approximate self-consistent charge density-functional tight-binding methodcovering the dispersion energy is promising.

4. AMINO ACIDS AND PEPTIDES

4.1. Amino Acids

There are three aromatic amino acids that provide the basic repertoire of chro-mophores for the study of peptides by electronic spectroscopy: phenylalanine (Phe),tyrosine (Tyr), and tryptophan (Trp). Their functional groups contain the respectivechromophores of benzene, phenol, and indole. The spectra of these amino acids areaffected by their molecular environment and therefore can report information onmolecular conformation (44). Several authors have reported studies of derivatives ofthe three basic chromophores, such as tryptamine (45–48).

The conformers of several nonaromatic amino acids such as glycine (Gly), alanine(Ala), valine (Val), and proline (Pro) have been characterized using Fourier-transformmicrowave spectroscopy in a supersonic jet (49, 50). Typical stabilizing interactionsderive from hydrogen bonds involving the acidic proton, the amino group, and partsof the functional group, such π-electrons on an aromatic ring.


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Fourier-transform IR spectroscopy of amino acids has been implemented re-cently by fast thermal heating of the amino-acid solids followed by fast-scan Fourier-transform IR prior to decomposition (51). At the high temperatures of the experiment,no conformer freezing is possible, but a large spectral range from near- to mid-IRis accessible so that the quality of vibrational calculations can be checked. Gly is thebest-investigated amino acid with regard to the anharmonicity of its vibrations, and itcan act as a benchmark when comparing the vibrational spectroscopy of amino acidswith theory (52).

All amino acids investigated in the gas phase exhibit a neutral structure withCOOH and NH2 terminal groups rather than the zwitterionic structure of the solidsand the aqueous phase. Experiments to stabilize the zwitterionic form in the gas phaseby sequentially adding water molecules have thus far been in vain (53, 54).

4.2. (Poly)amino Acids

(Poly)amino acids serve as model systems for the fundamental interactions that governpeptide folding with conformational motifs that are similar to folding motifs. Asshown in Figure 3, we can categorize shapes based on the number of residues betweenhydrogen bonds.

One promising approach is the study of small segments of peptides, representedby very short sequences with capped end groups (55). We describe examples of thesein the next section. In this section, we describe studies of small uncapped (poly)aminoacids. When studying such sequences as a function of increasing length (such as X,X-Gly, and X-Gly-Gly), one finds that the propensity appears to be a reductionof the observed number of conformations with increasing length in spite of thelarger number of possible shapes. For example, the six conformers of Trp reduceto four Trp-Gly and two Trp-Gly-Gly conformers (4). Presumably the increasedlength of the backbone allows the peptides to better lock in the most favorable con-formations with the maximum number of stress-free hydrogen bonds and disper-sion interactions. The most stable conformer of Trp-Gly-Gly, for example, is foldedwith an extended chain of hydrogen bonds, NH(indole)· · ·O C(R)-OH· · ·O C(R)-NH· · ·O C(γ-turn), and a favorable dispersion interaction between the side chain

N

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βL

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131075 CCCC

βα

Figure 3Schematic classification of α-, β-, and γ-turn motifs.


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Table 1 (Poly)amino acids studied bydouble-resonance spectroscopy

Uncapped Reference(s)GW, WG, WGG 4, 18, 19, 116WAGGDASE 19SW 116PW 116PG, PGG 25, 117YA, AY 117LF, PP 56Cyclo PS 57Gramicidin A-D, S 58WGGGY 58FDASV 118Cyclo GY 69

α-, β-, γ-turns: certainturns, involving hydrogenbonding between specificamino-acid intervals andleading to typical foldingmotives

and the aromatic ring system (18). Table 1 lists (poly)amino acids that have beenstudied by double-resonance spectroscopy.

The importance of dispersion poses an extra challenge for the theoretical treat-ment of these structures, as discussed in Section 3 (see Figure 2). Geometrical re-straints may hinder stress-free hydrogen bonds so that dispersion stabilization cancompete favorably. Several tripeptides exhibit γ-turn-type structures, and α-turn-type structures have been observed in pentapeptides. Structures of cyclic and chiraldipeptides have been reported as well (56, 57). There are also reports of results onpeptides of increasing size, including the nine-residue delta-sleep-inducing peptide(19) and 15-residue gramicidins (58). Figure 4 shows IR-UV spectra of three peptidesthat represent different secondary-structural folding patterns, a random-coil Gly se-quence, cyclic gramicidin S that forms internal bonds similar to a β-sheet structure,and gramicidin A with a β-helix structure. These experiments give hope that thefirst steps of peptide folding can be studied in the gas phase in microscopic detail.Entropic effects, however, are probably less important at the ultralow temperaturesof the jet experiments so that the jet temperature has to be varied and microhydratedpeptides have to be studied to elucidate hydrophobic/hydrophilic (entropic) effectsduring peptide folding. No zwitterionic peptides have been observed in the gas phase.

4.3. Protected End Groups

A number of groups have studied amino acids and peptides with so-called protectedend groups (acetylated, methylated, and cyclic). A recent review by Chin et al. (55)provides a detailed account of these studies, so we merely summarize them here.Capped peptides can often be transferred to the gas phase by simple thermal heating.They are cutouts of structural motifs in large peptides in which the end groupsdo not significantly contribute to global folding. γ-turns have been characterized


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Figure 4Infrared-ultraviolet spectral hole burning (IR-UV) spectra of three peptides that representdifferent secondary-structural folding patterns: (a) random-coil glycine sequence,(b) gramicidin A exhibiting a β-helix structure, and (c) cyclic gramicidin S forming internalbonds similar to a β-sheet structure.

by SHB (18, 19, 59–62). These turns and loops do not occur periodically but atwell-defined locations in proteins, and they determine their folding just as α-helicesand β-sheets do.

By the dimerization of stretched conformers of protected amino acids and peptides,researchers have formed β-sheet model systems in the gas phase with intermolecularC O· · ·HN hydrogen bonds (20, 61, 63, 64). These β-sheets can be stabilized bymultipoint connectors such as pyrazole. These studies may support the developmentof optimized drugs against diseases such as Alzheimer’s (64).

4.4. Conformer-Dependent Dynamics

The transition-moment orientation and S1 lifetime of Phe strongly depend onthe conformation of the alanyl side chain (21). The most stable conformer witha COOH → NH2 → π H-bond sequence has a lifetime of 20 ns compared with80–120 ns for the other conformers, revealing an efficient nonradiative-decay path-way (21). The transition-moment orientation of tryptamine drastically dependson vibronic excitation of the respective conformer, indicating a vibration- and


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IC: internal conversion

conformation-dependent coupling of the initially excited 1Lb(S1−) state to othernearby states, possibly the 1La(S2−) state (65).

Sobolewski and coworkers (66) have proposed an internal conversion (IC) mecha-nism via a charge-transfer intermediate state that may govern excited-state dynamicsin many H-bonded biomolecules, including peptides. We discuss this mechanismfurther in Sections 5.1 and 5.2.

Lee et al. (67, 68) measured the ionization energies of Phe using tunable two-color resonant two-photon ionization and found them to be strongly conformationdependent. The most stable conformers change their structure drastically on ioniza-tion because the attractive interaction between the amino hydrogen atom and thephenyl ring turns into a repulsive one (68), which leads to the higher energy of thecation. Similarly, the most stable conformer of cyclic Trp-Gly exhibits a peptide ringto indole ring interaction, leading to a repulsion between the two rings in the cationand a higher ionization energy than that of 3-methylindole (69).

Peptide radical cations can exhibit photo-activated positive-charge migration fromthe initially electronically excited phenyl, tyrosyl, and indole cation to the N terminus,as identified by a positively charged N-terminal fragment (70). The efficiency of thischarge-transfer process depends not only on the number and type of residues betweenthe excited chromophore and the N terminus, but also on the amino-acid or peptideconformation (67, 68, 71, 72).

5. DNA

5.1. Single Bases

Brady et al. (16) reported the first attempt to record the electronic spectroscopy ofDNA bases in the gas phase with the broad spectra for the pyrimidine bases uracil andthymine. Nir et al. (73) demonstrated the first successful experiment to report a well-resolved DNA base spectrum, by recording the discrete electronic spectrum of laser-desorbed, jet-cooled guanine. This was followed by a second purine, adenine (74), andfinally by the pyrimidine cytosine, as well as derivatives of these bases (75). Nir et al.(76) also reported the electronic spectroscopy of the nucleoside guanosine. Two majorissues emerged for these molecules: The spectra are complicated by tautomerism, andtheir photochemistry appears dominated by the properties of the excited electronicstate.

5.1.1. Tautomers. Nucleobases can adopt a number of different tautomeric forms.Tautomerism has been implicated in theories describing mutagenic reactions. Thefour lowest-energy tautomers of the purine bases are the keto and enol forms, whichcan each appear in the N7H and the N9H form. Figure 5 shows an example of thefour lowest-energy tautomers of guanine, all of which have been found in the gas phase(77, 78). Enol and keto tautomers are easily distinguished by IR-UV SHB, thanks tothe characteristic enol-OH stretch at approximately 3600 cm−1. However, becausethe N7H and N9H frequencies are quite similar, some uncertainty remains regardingthe final assignment of these forms. Comparison with the origins of tautomerically


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O

N1

2

3

4

56

7

8

9

N

NNN

Figure 5The four lowest-energy tautomers of guanine.

WC: Watson-Crick

Base pairing: recognitionin DNA relies on thepreferred base-pairformation ofcytosine-guanine andadenine-thymine byhydrogen bonding

blocked species (by methylation) allowed an N7H/N9H assignment (78). Based onthis comparison, the form predicted to have the lowest energy appears to be observedwith less abundance in the molecular beam. In the case of cytosine, the enol-REMPIspectrum is blue-shifted relative to the keto spectrum by a remarkable 5000 cm−1

(75, 79).The existence of keto and enol tautomers of neutral cytosine in the gas phase had

already been identified by anion spectroscopy (80). In the gas phase, the nucleobasesare found in both the keto and enol forms. All nine substituted derivatives of guanine,including the guanosine nucleosides, are observed exclusively in the enol form in thegas phase when using REMPI or LIF for analysis (81). This is intriguing because insolution the nucleosides appear exclusively in the keto form, required for the Watson-Crick (WC) base pairing in DNA. Failure to observe these keto tautomers may bea result of a short excited-state lifetime, as we discuss below. Regarding the othernucleobases, N9-H adenine (82) and diketo-thymine (83) seem to be the dominanttautomers in the gas phase.

5.1.2. Photochemistry. The nucleobases involved in replication have a shortexcited-state lifetime (84). This may provide a mechanism to protect the buildingblocks of life against photochemical damage, by providing a pathway for rapid IC to


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Excited-state lifetime: therelative rates of competingdecay processes determinethe lifetime and the fate ofthe excitation energy

the ground state (85). In this way, the molecule can dispose of excitation energy toits environment in the form of heat, rather than being trapped in a reactive excitedstate, with even possible intersystem crossing to a triplet state. The proposed mecha-nism involves a so-called doorway state with curve crossings or conical intersections,connecting the S1 excited state and the S0 ground state. The nature of this doorwaystate has been the subject of a number of investigations. Broo (85) has proposed thatit might consist of a state with nπ∗ character and that the relative energies of the nπ∗

and ππ∗ transitions are critical in determining the photochemistry. More recent mod-els (86, 87) include mixed nπ∗-/ππ∗-states owing to puckering of the six-memberedring of adenine at the C2-H group. Consistent with this mechanism, 2-aminopurinehas a large fluorescence quantum yield, as opposed to its isomer adenine (88–90).A weak absorption can also be observed for adenine close to that of the dominantspectrum, which can be ascribed to the nπ∗ transition, consistent with this model(74, 82). Sobolewski and coworkers (66, 91) have proposed a doorway state of πσ∗

character, associated with motion along an N-H coordinate; for adenine this wouldbe the N9-H coordinate. Consistent with this mechanism, Hunig et al. (92) directlyobserved N-H photodissociation in adenine at 243-nm photolysis energy via the res-onant ionization of product H atoms arising from N9-H but also to some extent fromthe NH2 group. Zierhut et al. (93) obtained similar results at 239-nm and 266-nmphotolysis energy. Conversely, Kang et al. (94) measured the excited-state lifetimes infemtosecond 267-nm pump-probe experiments and found them to be similar for alladenine derivatives, including 9-methyl adenine. The onset of the πσ∗ state thereforeis probably at approximately 266-nm or even shorter wavelengths, and a contributionto fast IC at 277–273 nm in the region of the sharp vibronic resonances of adenine isimprobable.

The IC pathways of the other nucleobases are less well investigated. They seemto involve C C twisting in cytosine (95), with a low barrier for keto-cytosine and aconsiderable energy gap to the S0 state even at extended twisting for enol-cytosine(96). For 9-methyl guanine, the IC pathway seems to involve a strongly bent aminogroup in position two (97).

5.2. Base Pairs

Cluster formation in a supersonic expansion provides the opportunity to study in-teractions between individual molecules. Purines and pyrimidines have been studiedas base-pair mimics (98). The first reported REMPI spectrum of an actual base-paircluster involved guanine-cytosine (GC) (99). As of this writing, the spectra have beenreported for over 27 base-pair combinations, with REMPI, UV-UV, and IR-UVdouble resonance for most of these (96) (see Table 2).

Anharmonic vibrational frequencies were recently determined for the GC com-plex and compared with gas-phase IR-UV double-resonance spectral data. Har-monic frequencies were obtained at the RI-MP2/cc-pVDZ and RI-MP2/TZVPP(triple-zeta valence double-polarization basis-set) levels, and anharmonic frequen-cies were obtained by the vibrational self-consistent field method based on the im-proved semiempirical parameterized method 3 results. Comparison of the data with


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Table 2 Origins of selected nucleobases and their clusters in cm−1

Bases Origins (cm−1) of different structures Reference(s)G 32,864; 33,269; 33,928; 34,773 73, 77, 121, 1227mG 32,579; 33,080 1219mG 34,630 121A 36,105 74, 89C 31,826 75, 791mC 31,908 965mC 31,269 96Guanosine 34,492 76, 81Adenosine 35,550 1232-aminopurine 32,368 89G-H2O 33,049; 33,218; 33,301 108G-G 33,103; 33,282 125C-C 33,483 124G-C 32,810; 33,314 119, 120A-T 35,064 104, 114GG(H2O) 32,926 126A-A 35,040 127C-1mC 33,419 124C-5mC 32,500; 32,691; 32,916 1245mC-5mC 32,493; 32,691; 32,872 124

Multiple values are for multiple isomers.

experimental results indicates that the average absolute-percentage deviationsfor the method are 2.6% for harmonic RI-MP2/cc-pVDZ, 2.5% for harmonicRI-MP2/TZVPP, and 2.3% for adopted PM3 CC-VSCF (parameterized method3 vibrational self-consistent field). The use of an empirical scaling factor for the abinitio harmonic calculations improves the stretching frequencies but decreases the ac-curacy of the other mode frequencies. The mid-IR region can also provide additionalinformation about sugar conformations in the study of nucleoside clusters (100).

The REMPI spectra show low-frequency H-bond vibrations, as expected for thesix H-bond modes. Those mode frequencies are not diagnostic for structure becausetheir order of magnitude is similar in most cases. Stacked structures are not observed,with the exception of methylated adenine dimers (101). In this case, the derivatizationblocks H-bonding sites of the lowest-energy H-bonded structures.

Possibly the most intriguing finding is that all observed combinations of base pairsso far exhibit sharp REMPI spectra, with the notable exception of the three cases as-signed as WC structures (see Figure 6). In fact, the two non-WC GC structuresfeature sharp REMPI spectra, whereas the WC structures of the same, albeit deriva-tized, base pair are broad. A possible explanation involves a similar model as thatfor the short-lived monomers, namely a coupling with a doorway state that in turncouples with the electronic ground state via conical intersections. Depending on the


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Figure 6Data for isolated guanine-cytosine (GC) base-pair structures. (a) Results for the Watson-Crickstructure. (b,c) The second and third lowest-energy structures, respectively. The secondcolumn shows the infrared-ultraviolet (IR-UV) double-resonance data compared with the abinitio calculations. Lines with an asterisk refer to a mode localized on the guanine moiety.Broad red-shifted peaks are the result of hydrogen bonding. The third column shows theUV-excitation spectra, measured by resonant two-photon ionization (R2PI). The fourthcolumn shows potential energy diagrams from Reference 102.

energetics of the excited states, the transition from the S1 state to the doorway statemay be barrierless, leading to a diffuse spectrum, or may feature a barrier, resultingin a discrete spectrum. The nature of the doorway states may be different from thatof the monomers. Sobolewski and colleagues (102) predict a charge-transfer statethat indeed provides a barrierless transition from S1 and a conical intersection, withS0 only for the WC structure. One intriguing implication is that the structure thatrapidly reconverts to the ground state is more photochemically stable. This may havebeen especially relevant under the conditions of prebiotic chemistry with abundantdeeper UV irradiation than today, before the formation of the atmospheric ozonelayer. Importantly, in solution this particular decay mechanism of DNA competeswith charge transfer along the stacked structure.

Short-lived excited states reduce multiphoton ionization efficiency. Femtosecondexcited states are dark to REMPI with nanosecond laser pulses. Therefore, there may


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Microhydration: solvationby a small number of watermolecules to study solvationdetails

be isomers in the molecular beam that go unobserved by virtue of the mismatch oftimescales of the detection method and excited-state lifetime. Structures that so farhave not been observed, in spite of predicted low energy, include symmetric GGand AA dimers, keto tautomers of H9 substituted guanines, and, as discussed below,various H2O clusters.

The relative stability of clusters is one of the most valuable parameters for com-parison with theory; however, it is also one of the most difficult ones to obtain ex-perimentally. Jet cooling is a nonequilibrium process, and relative abundances ofisomers in a molecular beam are thus not reliable observations for determining ther-modynamic quantities. So far only field ionization measurements have provided someexperimental data on the relative stability of the structures (103).

5.3. Complexes with Water

One appealing feature of molecular-beam spectroscopy is the ability to study mass-selected clusters with water. This so-called microhydration makes it possible to ob-serve the role of the solvent by sequentially adding one water molecule at a time. Kimet al. (104) employed a specially designed thermal-evaporation source to measure theionization potentials of adenine and thymine clusters as a function of the number ofwater molecules. Water also plays an important role in the structure and functionof DNA and RNA. A number of theoretical studies aimed at describing the effects ofwater molecules on the purine nucleobases (105–107). Because of the relative diffi-culty of bringing the nucleobases into the gas phase and clustering them with water,few experimental studies examine the effects of microscopic water on the structureof the bases (106, 108). Kim and colleagues (109, 110) concluded that electronicallyexcited clusters of the adenine monomer with water dissociate within 200 fs as a resultof vibronic coupling with a repulsive state of n-π∗ character. He et al. (111) examinedthe effects of water molecules on the S1 lifetimes of the pyrimidine bases and con-cluded that the presence of water molecules could increase the IC rate to the groundstate through an intermediate dark state. Chin et al. (106) observed just one structure,an enol-amino tautomer, for 9-methylguanine monohydrate under jet-cooled condi-tions, although calculations predict a keto structure to be close in energy, just 0.45kcal mol−1 higher than the enol tautomer. Crews et al. (108) found three structuresfor guanine monohydrate, including both enol and keto forms.

Theoretical calculations show that for the adenine-thymine base pair, the presenceof two water molecules suffices to stabilize a stacked structure more than a H-bondedstructure (112, 113). The enhanced stabilization results from the water molecules sur-rounding the base pair and creating a bridge between the bases. Calculations predictthat for GG base pairs, approximately 20% of the structures stack on addition of twowater molecules (112). Additional water further stabilizes stacking structures, and onthe addition of a fourth water molecule, 90% of the structures are predicted to bestacked. Sivanesan et al. (114) predict that five to six water molecules preferentiallystabilize stacked GC pairs. Microhydration also can stabilize specific tautomers (107).IR-UV resonance spectra by Abo-Riziq et al. (115) on microhydrated GG pairs sug-gest that a single H2O molecule suffices to stabilize one specific base-pair structure,


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relative to one that in the absence of solvent is close in energy. Two water moleculesdo not suffice to lead to observable populations of a stacked GG structure.

6. OUTLOOK

In the past five years, researchers have made accelerated progress in the gas-phasespectroscopy of biomolecular building blocks. This progress has been driven in partby the confluence of improved capabilities in studying molecules of increasing sizein both experiment and theory. In this lucky circumstance, gas-phase experimentaldata serve as benchmarks for computational algorithms and force fields, whereascomputational results help interpret and guide experiments. As a result, an increasingnumber of research groups has entered this field, and significant further progressmay be expected in years to come. Challenges include the following: (a) increasingthe size of the molecules studied, (b) expanding the studies of larger water clusters toserve as a bridge with the solution state, and (c) studies of the dynamics of isolatedsystems, such as charge transfer, proton transfer, and isomerization. Fast excited-statedynamics may necessitate studies at subpicosecond timescales.

SUMMARY POINTS

1. The study of isolated biomolecules provides insights into intrinsic proper-ties that are otherwise masked by elements of the biological environment,such as solvent and macromolecular structure. Gas-phase experiments, to-gether with quantum calculations, reveal details of structure, interactions,and dynamics at the molecular level.

2. Theoretical treatment of biomolecular building blocks of increasing size re-quires the development of new computational strategies. Among the specialchallenges are large conformational landscapes and the role of dispersiveforces.

3. Hydrogen bonding and dispersive forces are the two major motifs stabilizingbiomolecular structure. An example is the combination of base pairing andstacking in DNA.

4. Exploration of the conformational landscape of (poly)amino acids showselements of folding motives in peptides.

5. Clusters of DNA bases reveal the unique hydrogen bonding that plays a rolein base pairing.

6. Ultrafast excited-state dynamics in biomolecules provides photochemicalstability.

7. The study of clusters with water provides insight into microhydration, re-vealing details of solvation.


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ACKNOWLEDGMENTS

This material is based on work supported by the National Science Foundation undergrant CHE-0244341 and by the Donors of the American Chemical Society PetroleumResearch Fund. This work was supported by grants 2003/05/0009, A400550510, andLC512 from the Grant Agency of the Czech Republic, Grant Agency of the Academyof Sciences of the Czech Republic, and MSMT of the Czech Republic.

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29. Simon S, Duran M, Dannenberg JJ. 1996. How does basis set superpositionerror change the potential surfaces for hydrogen bonded dimers? J. Chem. Phys.105:11024–31

30. Jurecka P, Nachtigall P, Hobza P. 2001. RI-MP2 calculations with extendedbasis sets: a promising tool for study of H-bonded and stacked DNA base pairs.Phys. Chem. Chem. Phys. 3:4578–82

31. Jurecka P, Hobza P. 2003. True stabilization energies for the opti-mal planar hydrogen-bonded and stacked structures of guanine· · ·cytosine,adenine· · ·thymine, and their 9- and 1-methyl derivatives: complete basis setcalculations at the MP2 and CCSD(T) levels and comparison with experiment.J. Am. Chem. Soc. 125:15608–13

32. Cızek M, Horacek J, Sergenton AC, Popovic DB, Allan M, et al. 2001. Inelasticlow-energy electron collisions with the HBr and DBr molecules: experimentand theory. Phys. Rev. A 63:062710

33. Tsuzuki S, Honda K, Uchimaru T, Mikami M, Tanabe K. 2002. The interactionof benzene with chloro- and fluoromethanes: effects of halogenation on CH/πinteraction. J. Phys. Chem. A 106:4423–28

34. Tsuzuki S, Honda K, Uchimaru T, Mikami M, Tanabe K. 1999. High-levelab initio calculations of interaction energies of C2H4-CH4 and C2H6-CH4dimers: a model study of CH/π interaction. J. Phys. Chem. A 103:8265–71

35. Tsuzuki S, Honda K, Uchimaru T, Mikami M, Tanabe K. 2000. The magnitudeof the CH/π interaction between benzene and some model hydrocarbons. J. Am.Chem. Soc. 122:3746–53

36. Vondrasek J, Bendova L, Klusak V, Hobza P. 2005. Unexpectedly strong energystabilization inside the hydrophobic core of small protein rubredoxin mediatedby aromatic residues: correlated ab initio quantum chemical calculations. J. Am.Chem. Soc. 127:2615–19

37. Sponer J, Hobza P. 2000. Interaction energies of hydrogen-bonded formamidedimer, formamidine dimer, and selected DNA base pairs obtained with largebasis sets of atomic orbitals. J. Phys. Chem. A 104:4592–97

38. Halkier A, Helgaker T, Jorgensen P, Klopper W, Koch H, et al. 1998. Basis-setconvergence in correlated calculations on Ne, N2, and H2O. Chem. Phys. Lett.286:243–52

39. Hobza P, Sponer J. 1999. Structure, energetics, and dynamics of the nucleicacid base pairs: nonempirical ab initio calculations. Chem. Rev. 99:3247–76

40. Kristyan S, Pulay P. 1994. Can (semi)local density-functional theory accountfor the London dispersion forces? Chem. Phys. Lett. 229:175–80

41. Meijer EJ, Sprik M. 1996. A density-functional study of the intermolecularinteractions of benzene. J. Chem. Phys. 105:8684–89

42. Kurita N, Sekino H. 2003. Ab initio and DFT studies for accurate description ofvan der Waals interaction between rare-gas atoms. Int. J. Quant. Chem. 91:355–62

43. Elstner M, Hobza P, Frauenheim T, Suhai S, Kaxiras E. 2001. Hydrogen bond-ing and stacking interactions of nucleic acid base pairs: a density-functional-theory based treatment. J. Chem. Phys. 114:5149–55


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44. Explorescomputational landscapes.

44. Snoek LC, Robertson EG, Kroemer RT, Simons JP. 2000. Conforma-tional landscapes in amino acids: infrared and UV ion-dip spectroscopyof phenylalanine in the gas phase. Chem. Phys. Lett. 321:49–56

45. Park YD, Rizzo TR, Peteanu LA, Levy DH. 1986. Electronic spectroscopy oftryptophan analogs in supersonic jets: 3-indole acetic acid, 3-indole propionicacid, tryptamine, and N-acetyl tryptophan ethyl ester. J. Chem. Phys. 84:6539–49

46. Carney JR, Zwier TS. 1999. Infrared and UV spectroscopy of water-containingclusters of indole, 1-methylindole, and 3-methylindole. J. Phys. Chem. A103:9943–57

47. Connell LL, Corcoran TC, Joireman PW, Felker PM. 1990. Conformationalanalysis of jet-cooled tryptophan analogs by rotational coherence spectroscopy.Chem. Phys. Lett. 166:510–16

48. Martinez SJ III, Alfano JC, Levy DH. 1991. The electronic spectroscopy oftyrosine and phenylalanine analogs in a supersonic jet: acidic analogs. J. Mol.Spectrosc. 145:100–11

49. Lesarri A, Mata S, Cocinero EJ, Blanco S, Lopez JC, Alonso JL. 2002. Thestructure of neutral proline. Angew. Chem. Int. Ed. Engl. 41:4673–76

50. McGlone SJ, Elmes PS, Brown RD, Godfrey PD. 1999. Molecular structure ofa conformer of glycine by microwave spectroscopy. J. Mol. Struct. 486:225–38

51. Linder R, Nispel M, Haber T, Kleinermanns K. 2005. Gas phase FTIR-spectraof natural amino acids. Chem. Phys. Lett. 409:260–64

52. Chaban GM, Jung JO, Gerber RB. 2000. Anharmonic vibrational spectroscopyof glycine: testing of ab initio and empirical potentials. J. Phys. Chem. A104:10035–44

53. Snoek LC, Kroemer RT, Simons JP. 2002. A spectroscopic and computationalexploration of tryptophan water cluster structures in the gas phase. Phys. Chem.Chem. Phys. 4:2130–39

54. Carcabal P, Kroemer RT, Snoek LC, Simons JP, Bakker JM, et al. 2004. Hy-drated complexes of tryptophan: ion dip infrared spectroscopy in the ‘molecularfingerprint’ region, 100–2000 cm−1. Phys. Chem. Chem. Phys. 6:4546–52

55. Chin W, Piuzzi F, Dimicoli I, Mons M. 2006. Probing the competition be-tween secondary structures and local preferences in gas phase isolated peptidebackbones. Phys. Chem. Chem. Phys. 8:1033–48

56. Abo-Riziq AG, Bushnell JE, Crews B, Callahan MP, Grace L, de Vries MS.2005. Discrimination between diastereoisomeric dipeptides by IR-UV doubleresonance spectroscopy and ab initio calculations. Int. J. Quant. Chem. 105:437–45

57. Abo-Riziq AG, Crews B, Bushnell JE, Callahan MP, de Vries MS. 2005. Con-formational analysis of cyclo(Phe-Ser) by UV-UV and IR-UV double resonancespectroscopy and ab initio calculations. Mol. Phys. 103:1491–95

58. Presents a gas-phasestudy of 15 amino-acidpeptides.

58. Abo-Riziq A, Crews BO, Callahan MP, Grace L, de Vries MS. 2006.Spectroscopy of isolated gramicidin peptides. Angew. Chem. Int. Ed. Engl.118:5290–93


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59. Explores gas-phasestructure and foldingmotives.

59. Chin W, Mons M, Dognon JP, Piuzzi F, Tardivel B, Dimicoli I. 2004.Competition between local conformational preferences and secondarystructures in gas-phase model tripeptides as revealed by laser spec-troscopy and theoretical chemistry. Phys. Chem. Chem. Phys. 6:2700–9

60. Chin W, Compagnon I, Dognon JP, Canuel C, Piuzzi F, et al. 2005. Spectro-scopic evidence for gas-phase formation of successive β-turns in a three-residuepeptide chain. J. Am. Chem. Soc. 127:1388–89

61. Gerhards M, Unterberg C, Gerlach A, Jansen A. 2004. β-sheet model systemsin the gas phase: structures and vibrations of Ac-Phe-NHMe and its dimer(Ac-Phe-NHMe)2. Phys. Chem. Chem. Phys. 6:2682–90

62. Dian BC, Florio GM, Clarkson JR, Longarte A, Zwier TS. 2004. Infrared-induced conformational isomerization and vibrational relaxation dynamics inmelatonin and 5-methoxy-N-acetyl tryptophan methyl amide. J. Chem. Phys.120:9033–46

63. Unterberg C, Gerlach A, Schrader T, Gerhards M. 2003. Structure of theprotected dipeptide Ac-Val-Phe-OMe in the gas phase: towards a β-sheet modelsystem. J. Chem. Phys. 118:8296–300

64. Unterberg C, Gerlach A, Schrader T, Gerhards M. 2002. Clusters of a protectedamino acid with pyrazole derivatives: β-sheet model systems in the gas phase.Eur. Phys. J. D 20:543–50

65. Schmitt M, Vu C, Ratzer C, Kleinermanns K. 2005. Structural selectionby microsolvation: conformational locking of tryptamine. J. Am. Chem. Soc.127:10356–64

66. Sobolewski AL, Domcke W, Dedonder-Lardeux C, Jouvet C. 2002. Excited-state hydrogen detachment and hydrogen transfer driven by repulsive 1πσ∗

states: a new paradigm for nonradiative decay in aromatic biomolecules. Phys.Chem. Chem. Phys. 4:1093–200

67. Lee KT, Sung J, Lee KJ, Park YD, Kim SK. 2002. Conformation-dependentionization energies of l-phenylalanine. Angew. Chem. Int. Ed. Engl. 41:4114–17

68. Lee KT, Sung JH, Lee KJ, Kim SK, Park YD. 2003. Conformation-dependentionization of l-phenylalanine: structures and energetics of cationic conformers.Chem. Phys. Lett. 368:262–68

69. Wiedemann S, Metsala A, Nolting D, Weinkauf R. 2004. The dipeptidecyclic(glycyltryptophanyl) in the gas phase: a concerted action of density func-tional calculations, S-0-S-1 two-photon ionization, spectral UV/UV hole burn-ing and laser photoelectron spectroscopy. Phys. Chem. Chem. Phys. 6:2641–49

70. Weinkauf R, Schanen P, Metsala A, Schlag EW, Burgle M, Kessler H. 1996.Highly efficient charge transfer in peptide cations in the gas phase: thresholdeffects and mechanism. J. Phys. Chem. 100:18567–85

71. Crews B, Abo-Riziq AG, Grace L, de Vries M. 2004. Charge transfer in con-formationally selected small peptides. Abstr. Pap. Am. Chem. Soc. 227:U323

72. Weinkauf R, Schanen P, Yang D, Sonkara S, Schlag EW. 1995. Elementaryprocesses in peptides: electron mobility and dissociations in peptide cations inthe gas phase. J. Phys. Chem. 99:11255–65


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73. Nir E, Grace LI, Brauer B, de Vries MS. 1999. REMPI spectroscopy of jetcooled guanine. J. Am. Chem. Soc. 121:4896–97

74. Kim NJ, Jeong G, Kim YS, Sung J, Kim SK, Park YD. 2000. Resonant two-photon ionization and laser induced fluorescence spectroscopy of jet-cooledadenine. J. Chem. Phys. 113:10051–55

75. Nir E, Muller M, Grace LI, de Vries MS. 2002. REMPI spectroscopy of cyto-sine. Chem. Phys. Lett. 355:59–64

76. Nir E, Imhof P, Kleinermanns K, de Vries MS. 2000. REMPI spectroscopy oflaser desorbed guanosines. J. Am. Chem. Soc. 122:8091–92

77. Nir E, Janzen C, Imhof P, Kleinermanns K, de Vries MS. 2001. Guanine tau-tomerism revealed by UV-UV and IR-UV hole burning spectroscopy. J. Chem.Phys. 115:4604–11

78. Chin W, Mons M, Dimicoli I, Piuzzi F, Tardivel B, Elhanine M. 2002. Tautomercontributions to the near UV spectrum of guanine: towards a refined picturefor the spectroscopy of purine molecules. Eur. Phys. J. D 20:347–55

79. Nir E, Hunig I, Kleinermanns K, de Vries MS. 2003. The nucleobase cytosineand the cytosine dimer investigated by double resonance laser spectroscopy andab initio calculations. Phys. Chem. Chem. Phys. 5:4780–85

80. Schiedt J, Weinkauf R, Neumark DM, Schlag EW. 1998. Anion spectroscopyof uracil, thymine and the amino-oxo and amino-hydroxy tautomers of cytosineand their water clusters. Chem. Phys. 239:511–24

81. Nir E, Hunig I, Kleinermanns K, de Vries MS. 2004. Conformers of guanosinesand their vibrations in the electronic ground and excited states, as revealed bydouble-resonance spectroscopy and ab initio calculations. Chemphyschem 5:131–37

82. Plutzer C, Kleinermanns K. 2002. Tautomers and electronic states of jet-cooledadenine investigated by double resonance spectroscopy. Phys. Chem. Chem. Phys.4:4877–82

83. Plutzer C, Hunig I, Kleinermanns K, Nir E, de Vries MS. 2003. Pairing ofisolated nucleobases: double resonance laser spectroscopy of adenine-thymine.Chemphyschem 4:838–42

84. Explores theexcited-state dynamics ofDNA in solution.

84. Crespo-Hernandez CE, Cohen B, Hare PM, Kohler B. 2004. Ultrafastexcited-state dynamics in nucleic acids. Chem. Rev. 104:1977–2019

85. Broo A. 1998. A theoretical investigation of the physical reason for the very dif-ferent luminescence properties of the two isomers adenine and 2-aminopurine.J. Phys. Chem. A 102:526–31

86. Marian CM. 2005. A new pathway for the rapid decay of electronically excitedadenine. J. Chem. Phys. 122:104314

87. Perun S, Sobolewski AL, Domcke W. 2005. Ab initio studies on the radiationlessdecay mechanisms of the lowest excited singlet states of 9H-adenine. J. Am.Chem. Soc. 127:6257–65

88. Seefeld KA, Plutzer C, Lowenich D, Haber T, Linder R, et al. 2005. Tautomersand electronic states of jet-cooled 2-aminopurine investigated by double reso-nance spectroscopy and theory. Phys. Chem. Chem. Phys. 7:3021–26

89. Nir E, Kleinermanns K, Grace L, de Vries MS. 2001. On the photochemistryof purine nucleobases. J. Phys. Chem. A 105:5106–10


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90. Plutzer C, Nir E, de Vries MS, Kleinermanns K. 2001. IR-UV double-resonancespectroscopy of the nucleobase adenine. Phys. Chem. Chem. Phys. 3:5466–69

91. Sobolewski AL, Domcke W. 2002. On the mechanism of nonradiative decay ofDNA bases: ab initio and TDDFT results for the excited states of 9H-adenine.Eur. Phys. J. D 20:369–74

92. Hunig I, Plutzer C, Seefeld KA, Lowenich D, Nispel M, Kleinermanns K.2004. Photostability of isolated and paired nucleobases: N-H dissociation ofadenine and hydrogen transfer in its base pairs examined by laser spectroscopy.Chemphyschem 5:1427–31

93. Zierhut M, Roth W, Fischer I. 2004. Dynamics of H-atom loss in adenine. Phys.Chem. Chem. Phys. 6:5178–83

94. Kang H, Jung B, Kim SK. 2003. Mechanism for ultrafast internal conversionof adenine. J. Chem. Phys. 118:6717–19

95. Tomic K, Tatchen J, Marian C. 2005. Quantum chemical investigation of theelectronic spectra of the keto, enol, and keto-imine tautomers of cytosine. J.Phys. Chem. A 109:8410–18

96. Nir E, Plutzer C, Kleinermanns K, de Vries M. 2002. Properties of isolatedDNA bases, base pairs and nucleosides examined by laser spectroscopy. Eur.Phys. J. D 20:317–29

97. Langer H, Doltsinis NL. 2004. Nonradiative decay of photoexcited methylatedguanine. Phys. Chem. Chem. Phys. 6:2742–48

98. Borst DR, Roscioli JR, Pratt DW, Florio GM, Zwier TS, et al. 2002. Hydrogenbonding and tunneling in the 2-pyridone·2-hydroxypyridine dimer: effect ofelectronic excitation. Chem. Phys. 283:341–54

99. Nir E, Kleinermanns K, de Vries MS. 2000. Pairing of isolated nucleic-acidbases in the absence of the DNA backbone. Nature 408:949–51

100. Bakker JM, Compagnon I, Meijer G, von Helden G, Kabelac M, et al. 2004. Themid-IR absorption spectrum of gas-phase clusters of the nucleobases guanineand cytosine. Phys. Chem. Chem. Phys. 6:2810–15

101. Kabelac M, Plutzer C, Kleinermanns K, Hobza P. 2004. Isomer selective IR ex-periments and correlated ab initio quantum chemical calculations support planarH-bonded structure of the 7-methyl adenine· · ·adenine and stacked structure ofthe 9-methyl adenine· · ·adenine base pairs. Phys. Chem. Chem. Phys. 6:2781–85

102. Exploresexcited-state dynamics inbiomolecules.

102. Sobolewski AL, Domcke W, Hattig C. 2005. Tautomeric selectivity of theexcited-state lifetime of guanine/cytosine base pairs: the role of electron-driven proton-transfer processes. Proc. Natl. Acad. Sci. USA 102:17903–6

103. Yanson IK, Teplitsky AB, Sukhodub LF. 1979. Molecular interactions in nucleicacids. Biopolymers 18:1149–70

104. Kim SK, Lee W, Herschbach DH. 1996. Cluster beam chemistry: hydrationof nucleic acid bases; ionization potentials of hydrated adenine and thymine. J.Phys. Chem. 100:7933–37

105. Forde G, Flood A, Salter L, Hill G, Gorb L, Leszczynski J. 2003. Theoreticalab initio study of the effects of methylation on structure and stability of G:CWatson-Crick base pair. J. Biomol. Struct. Dyn. 20:811–17


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106. Chin W, Mons M, Piuzzi F, Tardivel B, Dimicoli I, et al. 2004. Gas phaserotamers of the nucleobase 9-methylguanine enol and its monohydrate: opticalspectroscopy and quantum mechanical calculations. J. Phys. Chem. A 108:8237–43

107. Hanus M, Ryjacek F, Kabelac M, Kubar T, Bogdan TV, et al. 2003. Correlatedab initio study of nucleic acid bases and their tautomers in the gas phase, ina microhydrated environment and in aqueous solution. Guanine: surprisingstabilization of rare tautomers in aqueous solution. J. Am. Chem. Soc. 125:7678–88

108. Crews B, Abo-Riziq A, Grace L, Callahan M, Kabelac M, et al. 2005. IR-UVdouble resonance spectroscopy of guanine-H2O clusters. Phys. Chem. Chem.Phys. 7:3015–20

109. Kang H, Lee KT, Kim SK. 2002. Femtosecond real time dynamics of hydro-gen bond dissociation in photoexcited adenine-water clusters. Chem. Phys. Lett.359:213–19

110. Kim NJ, Kang H, Jeong G, Kim YS, Lee KT, Kim SK. 2000. Anomalousfragmentation of hydrated clusters of DNA base adenine in UV photoionization.J. Phys. Chem. A 104:6552–57

111. He YG, Wu CY, Kong W. 2004. Photophysics of methyl-substituted uracilsand thymines and their water complexes in the gas phase. J. Phys. Chem. A108:943–49

112. Kabelac M, Hobza P. 2001. At nonzero temperatures, stacked structures ofmethylated nucleic acid base pairs and microhydrated nonmethylated nucleicacid base pairs are favored over planar hydrogen-bonded structures: a moleculardynamics simulations study. Chem. A Eur. J. 7:2067–74

113. Kabelac M, Ryjacek F, Hobza P. 2000. Already two water molecules changeplanar H-bonded structures of the adenine· · ·thymine base pair to the stackedones: a molecular dynamics simulations study. Phys. Chem. Chem. Phys. 2:4906–9

114. Sivanesan D, Sumathi I, Welsh WJ. 2003. Comparative studies between hy-drated hydrogen bonded and stacked DNA base pair. Chem. Phys. Lett. 367:351–60

115. Abo-Riziq A, Crews B, Grace L, de Vries MS. 2005. Microhydration of guaninebase pairs. J. Am. Chem. Soc. 127:2374–75

116. Hunig I, Seefeld KA, Kleinermanns K. 2003. REMPI and UV-UV double res-onance spectroscopy of tryptophan ethylester and the dipeptides tryptophan-serine, glycine-tryptophan and proline-tryptophan. Chem. Phys. Lett. 369:173–79

117. Cohen R, Nir E, Grace LI, Brauer B, de Vries MS. 2000. Resonance-enhancedmultiphoton ionization spectroscopy of dipetides. J. Phys. Chem. A 104:6351–55

118. Abo-Riziq A, Bushnell JE, Crews BO, Callahan MP, Grace L, de Vries MS.2006. Gas phase spectroscopy of the penta-peptide FDASV. Submitted

119. Nir E, Janzen C, Imhof P, Kleinermanns K, de Vries MS. 2002. Pairing of thenucleobases guanine and cytosine in the gas phase studied by IR-UV double-resonance spectroscopy and ab initio calculations. Phys. Chem. Chem. Phys.4:732–39


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120. Abo-Riziq A, Grace L, Nir E, Kabelac M, Hobza P, de Vries MS. 2005. Photo-chemical selectivity in guanine-cytosine base-pair structures. Proc. Natl. Acad.Sci. USA 102:20–23

121. Mons M, Dimicoli I, Piuzzi F, Tardivel B, Elhanine M. 2002. Tautomerism ofthe DNA base guanine and its methylated derivatives as studied by gas-phaseinfrared and UV spectroscopy. J. Phys. Chem. A 106:5088–94

122. Piuzzi F, Mons M, Dimicoli I, Tardivel B, Zhao Q. 2001. Ultraviolet spec-troscopy and tautomerism of the DNA base guanine and its hydrate formed ina supersonic jet. Chem. Phys. 270:205–14

123. Nir E, de Vries MS. 2002. Fragmentation of laser-desorbed 9-substitutedadenines. Int. J. Mass Spectrom. 219:133–38

124. Nir E, Hunig I, Kleinermanns K, de Vries MS. 2003. The nucleobase cytosineand the cytosine dimer investigated by double resonance laser spectroscopy andab initio calculations. Phys. Chem. Chem. Phys. 5:4780–85

125. Nir E, Janzen C, Imhof P, Kleinermanns K, de Vries MS. 2002. Pairing ofthe nucleobase guanine studied by IR-UV double-resonance spectroscopy andab initio calculations. Phys. Chem. Chem. Phys. 4:740–50

126. Abo-Riziq A, Crews B, Grace L, de Vries MS. 2005. Microhydration of guaninebase pairs. J. Am. Chem. Soc. 127:2374–75

127. Plutzer C, Hunig I, Kleinermanns K. 2003. Pairing of the nucleobase adeninestudied by IR-UV double-resonance spectroscopy and ab initio calculations.Phys. Chem. Chem. Phys. 5:1158–63


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AR308-FM ARI 23 February 2007 13:44

Annual Review ofPhysical Chemistry

Volume 58, 2007Contents

FrontispieceC. Bradley Moore � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �xvi

A Spectroscopist’s View of Energy States, Energy Transfers, andChemical ReactionsC. Bradley Moore � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 1

Stochastic Simulation of Chemical KineticsDaniel T. Gillespie � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 35

Protein-Folding Dynamics: Overview of Molecular SimulationTechniquesHarold A. Scheraga, Mey Khalili, and Adam Liwo � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 57

Density-Functional Theory for Complex FluidsJianzhong Wu and Zhidong Li � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 85

Phosphorylation Energy Hypothesis: Open Chemical Systems andTheir Biological FunctionsHong Qian � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �113

Theoretical Studies of Photoinduced Electron Transfer inDye-Sensitized TiO2

Walter R. Duncan and Oleg V. Prezhdo � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �143

Nanoscale Fracture MechanicsSteven L. Mielke, Ted Belytschko, and George C. Schatz � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �185

Modeling Self-Assembly and Phase Behavior inComplex MixturesAnna C. Balazs � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �211

Theory of Structural Glasses and Supercooled LiquidsVassiliy Lubchenko and Peter G. Wolynes � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �235

Localized Surface Plasmon Resonance Spectroscopy and SensingKatherine A. Willets and Richard P. Van Duyne � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �267

Copper and the Prion Protein: Methods, Structures, Function,and DiseaseGlenn L. Millhauser � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �299

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AR308-FM ARI 23 February 2007 13:44

Aging of Organic Aerosol: Bridging the Gap Between Laboratory andField StudiesYinon Rudich, Neil M. Donahue, and Thomas F. Mentel � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �321

Molecular Motion at Soft and Hard Interfaces: From PhospholipidBilayers to Polymers and LubricantsSung Chul Bae and Steve Granick � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �353

Molecular Architectonic on Metal SurfacesJohannes V. Barth � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �375

Highly Fluorescent Noble-Metal Quantum DotsJie Zheng, Philip R. Nicovich, and Robert M. Dickson � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �409

State-to-State Dynamics of Elementary Bimolecular ReactionsXueming Yang � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �433

Femtosecond Stimulated Raman SpectroscopyPhilipp Kukura, David W. McCamant, and Richard A. Mathies � � � � � � � � � � � � � � � � � � � � �461

Single-Molecule Probing of Adsorption and Diffusion on SilicaSurfacesMary J. Wirth and Michael A. Legg � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �489

Intermolecular Interactions in Biomolecular Systems Examined byMass SpectrometryThomas Wyttenbach and Michael T. Bowers � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �511

Measurement of Single-Molecule ConductanceFang Chen, Joshua Hihath, Zhifeng Huang, Xiulan Li, and N.J. Tao � � � � � � � � � � � � � � �535

Structure and Dynamics of Conjugated Polymers in Liquid CrystallineSolventsP.F. Barbara, W.-S. Chang, S. Link, G.D. Scholes, and Arun Yethiraj � � � � � � � � � � � � � � �565

Gas-Phase Spectroscopy of Biomolecular Building BlocksMattanjah S. de Vries and Pavel Hobza � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �585

Isomerization Through Conical IntersectionsBenjamin G. Levine and Todd J. Martínez � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �613

Spectral and Dynamical Properties of Multiexcitons in SemiconductorNanocrystalsVictor I. Klimov � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �635

Molecular Motors: A Theorist’s PerspectiveAnatoly B. Kolomeisky and Michael E. Fisher � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �675

Bending Mechanics and Molecular Organization in BiologicalMembranesJay T. Groves � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �697

Exciton Photophysics of Carbon NanotubesMildred S. Dresselhaus, Gene Dresselhaus, Riichiro Saito, and Ado Jorio � � � � � � � � � � � �719

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Gas-Phase Spectroscopy of Biomolecular Building BlocksStimulated emission pumping–hole ﬁlling...

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