Letter pubs.acs.org/JPCL
Capping Motif for Peptide Helix Formation Aleksandra V. Zabuga and Thomas R. Rizzo* Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland S Supporting Information *
ABSTRACT: It is known that a C-terminal lysine stabilizes helix formation in polyalanine peptides that have seven or more residues. Using a combination of cold ion spectroscopy and DFT calculations, we demonstrate that even a three-residue peptide, Ac-Phe-Ala-LysH+, adopts a structure in which the lysine side chain forms three hydrogen bonds with backbone carbonyls, reproducing the capping motif of larger polyalanine helices. This is confirmed by comparison with Ac-Phe-(Ala)5LysH+, which forms a 310 helix containing the same structural feature. In both molecules, we identified the vibrational bands of the N- and C-terminal amide NH stretches, which lack strong hydrogen bonds with carbonyls and consequently appear in a characteristic region above 3400 cm−1. A similar pattern is also present in the even longer peptide Ac-Phe-(Ala)10-LysH+, illustrating the generality of this capping motif. The two longer peptides contain additional, characteristic amide NH stretch bands below 3400 cm−1, which form the core of the helix.
H
temperature octopole. A packet of ions is then released from the octopole and sent to a 22-pole ion trap maintained at 4 K, where the ions cool to ∼10 K in collisions with helium. We then pass laser beams through the trap and obtain information on the structure of these cold ions using variants of photofragment spectroscopy. The photofragments are released from the trap, mass-selected with the second quadrupole, and detected. The cycle is repeated at 10 Hz. We first perform UV photofragment spectroscopy to measure an electronic spectrum of the cold, protonated peptides, by counting the number of phenylalanine side-chain loss fragments as a function of excitation wavelength. This spectrum allows us to address single conformations of the molecules in our ion trap by fixing the UV laser wavenumber on the different features in the electronic spectrum and recording their infrared spectra. We perform both IR−UV and UV−IR double resonance spectroscopy to record infrared spectra of the ground and first electronically excited state of AcPhe-Ala-LysH+, respectively. When the IR OPO excites the protonated peptides 150 ns before the UV laser, we record ground-state spectra as a depletion in the UV-induced phenylalanine side-chain loss fragmentation yield while scanning the IR OPO.8 When the IR OPO probes a single conformation of a UV-excited peptide 5 ns after the UV laser pulse, we record conformer-specific infrared spectra of molecules in the S1 state by detecting the increase of the same fragment as a function of the IR OPO wavenumber.9 We identified two major conformers in the UV photofragmentation spectrum of Ac-Phe-Ala-LysH+ (Figure S1,
elices are one of the most common secondary structures of proteins. The amino acid alanine has one of the highest helix formation propensities, and alanine-based polypeptides have been widely studied to understand protein folding. Jarrold and co-workers reported that introduction of the lysine amino acid at the C-terminus of a capped polyalanine chain with at least seven residues results in a highly stable gasphase helix,1−3 and theoretical studies have confirmed this.4 However, the key structures that stabilize helix formation may already be present in smaller peptides.5 For example, using IR− UV spectroscopy, Mons and co-workers studied the conformational preferences of neutral alanine tripeptides Ac-(Ala)3-NH2, where one of the alanines was substituted with phenylalanine.6 They observed signs of a 310 helical structure for some conformations.6 Stearns et al. identified the four most stable conformations of a protonated seven amino acid peptide AcPhe-(Ala)5-LysH+ in the gas phase and demonstrated that they all contain a 310 helix.5 We show in this report that the charged lysine amino acid at the C-terminus forms the same capping structure in a three amino acid peptide as it does in larger polyalanines. Using a combination of gas-phase spectroscopy and DFT calculations, we have identified the most stable conformations of the tripeptide Ac-Phe-Ala-LysH+ and demonstrated that it has similar interactions as those observed at both ends of the longer helical peptide Ac-Phe-(Ala)5LysH+.5 One clear spectroscopic consequence of this is the characteristic pattern of the “free” amide NH stretch bands at either end of the helix. Our experimental setup is described elsewhere.7 Briefly, we introduce Ac-Phe-Ala-LysH+ into the gas phase via nanoelectrospray from a 0.2 mM solution in 50:50:0.1 water/ methanol/acetic acid. The first quadrupole selects parent ions of a specific mass, which are then trapped in a room© 2015 American Chemical Society
Received: February 25, 2015 Accepted: April 8, 2015 Published: April 8, 2015 1504
DOI: 10.1021/acs.jpclett.5b00407 J. Phys. Chem. Lett. 2015, 6, 1504−1508
Letter
The Journal of Physical Chemistry Letters Supporting Information), which we labeled as A and B. Figure 1a and c presents the ground-state infrared spectra of both
In the electronically excited state, the phenylalanine NH stretch (3415 cm−1 in conformer A and 3365 cm−1 in conformer B) is red-shifted 29 cm−1 from its position in the ground state for conformer A and 39 cm−1 for conformer B (see pink lines in Figure 1). The stronger effect of the electronic excitation on the frequency of the phenylalanine NH in conformer B led us to consider also a stronger interaction of the phenylalanine NH with the π cloud of the phenyl ring. Moreover, in the electronically excited state of conformer A, the band at around 3451 cm−1 (Figure 1b) is red-shifted ∼5 cm−1 from its position in the ground-state spectrum (Figure 1a), whereas in conformer B, the corresponding vibrational band is not affected by the electronic excitation (Figure 1c,d). The electronic excitation of the aromatic chromophore results in the perturbation of the modes involving atoms in the closest proximity to the expanded π cloud, implying that the bond associated with the vibrational band at ∼3451 cm−1 is closer to the aromatic ring in conformer A than in conformer B. By performing a preliminary conformational search with the MMFF9411,12 force field in the Conflex program,13 we found 60 conformations within the energy window of 1 kcal/mol. Reoptimization of the 40 lowest-energy structures at the DFT B3LYP14−16/6-31+G** level of theory in Gaussian 0917 resulted in the increase of the energy variation between conformations up to 15 kcal/mol. The two lowest-energy structures with an energy difference of 0.8 kcal/mol (IB3LYP and IIB3LYP), shown in Figure 2, exhibit hydrogen bonds between the NH3+ group of the lysine side chain and the three carbonyls and differ mainly by the rotation of the phenylalanine side chain. Another favorable interaction that one might expect to observe in this molecule is a cation−π interaction between the charged side chain of lysine and an aromatic side chain of phenylalanine, as observed in the H+-Ala-Tyr dipeptide.18 Cation−π interactions are common in proteins and often occur between cationic side chains of basic amino acids and the side chains of aromatic amino acids, influencing the three-dimensional structure.19,20 While our conformational search using the force field revealed a few conformations of Ac-Phe-Ala-LysH+ in which the NH3+ group of lysine interacts with the π system of the aromatic side chain, after reoptimization at the DFT B3LYP/6-31+G** level of theory, those conformations appeared at least 12.8 kcal/mol higher in energy than the most stable calculated conformer IB3LYP (Figure 2). This is consistent with our observation that the band origin of conformers A and B in the electronic spectrum of Ac-PheAla-LysH+ is only slightly shifted from that of protonated phenylalanine,21 indicating that the π cloud of the phenylalanine aromatic ring is probably not involved in a strong interaction with NH3+ in either conformer (Figure S1, Supporting Information). As shown in Figure 3, the pattern of NH stretch vibrations in the experimental spectrum of conformers A (a) and B (b) of Ac-Phe-Ala-LysH+ appears reminiscent of the vibrational bands for the terminal NH’s in conformers A (c) and B (d) of the helical, seven-amino-acid peptide Ac-Phe-(Ala)5-LysH+.5 The phenylalanine NH appears more red-shifted in the ground-state infrared spectrum in conformer B than in conformer A in both molecules. This difference between the infrared spectra of two conformers of Ac-Phe-Ala-LysH+, which is the only significant one, can result from the different orientation of the phenylalanine side chain, similar to what Stearns et al. observed in conformers A and B of the helical molecule Ac-Phe-(Ala)5-
Figure 1. S0 ground state vs the S1 electronic state infrared spectra of conformer A (a,b) and B (c,d) of Ac-Phe-Ala-LysH+. Black traces correspond to Ac-15Phe-Ala-LysH+, where 15Phe is 15N isotopically substituted phenylalanine. The UV laser excites the band origin of conformer A (37484.0 cm−1) or conformer B (37532.2 cm−1). The pink dashed lines show the position of the phenylalanine NH stretch. The black stars correspond to phenylalanine combination bands with a low-frequency mode.10
conformers in the NH stretch and the amide I regions. The assignment of the phenylalanine NH stretch is determined by 15 N isotopic substitution on the phenylalanine residue, as demonstrated by black traces. Upon 15N isotopic substitution, the phenylalanine NH stretch shifts ∼8 cm−1 to the red (from 3444 to 3436 cm−1 in conformer A and from 3404 to 3396 cm−1 in conformer B). The other transitions at ∼3417 and ∼3452 cm−1 correspond to lysine/alanine NH stretches. In the amide I region, the transitions at around 1670, 1700, and 1790 cm−1 are mainly due to CO stretch vibrations, and the spectroscopic transitions at 1600 and 1630 cm−1 are most probably caused by vibrations of the NH3+ lysine group or other NH bending modes. The most intense infrared band at 1700 cm−1 in the spectrum of conformer A seems to consist of two overlapping vibrations that separate in conformer B (1695 and 1705 cm−1), suggesting that one of the COs in conformer B has a weaker hydrogen bond. The ground-state infrared spectra for conformers A and B thus differ primarily by the position of the phenylalanine NH stretch and the one CO stretch. Figure 1b and d presents the infrared spectra of the S1 electronic state of conformers A and B, recorded as a gain in the photofragmentation yield when the IR OPO is scanned 5 ns after the UV excitation.9 As above, the position of the phenylalanine NH stretch is determined with 15N isotopic substitution (black traces in Figure 1b,d). Curiously, in the infrared spectrum of conformer A, three infrared bands shift 8 cm−1 upon isotopic substitution (Figure 1b), which means that all of them are associated with the phenylalanine NH. We have assigned these additional bands to the combination bands that involve one quantum of phenylalanine NH stretch and up to two quanta of a low-frequency vibration of ∼14 cm−1.10 1505
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the phenylalanine and the lysine NH stretches in the calculated vibrational spectra of structures IB3LYP and IIB3LYP (Figure 3c,d) are too low compared with the experiment (Figure 2a,b). The observation that the structures and measured vibrational fingerprints are similar between the three- and seven-aminoacid molecules while the calculated spectra are different suggested that we have to find a proper level of theory to describe the experimental results. While the B3LYP functional with a 6-31+G** basis set described well the geometries and the frequencies of different conformers of the seven-amino-acid helical peptide Ac-Phe(Ala)5-LysH+,5 in our case, it seems to underestimate the weak van der Waals and dispersion interactions. Hohenstein et al. showed that the empirical exchange−correlation functionals, M05-2X and M06-2X, better describe noncovalent interactions than traditional density functionals without dispersion.22 Rothlisberger and Rizzo validated with experimental data that the M05-2X functional correctly describes the energetics and vibrational frequencies of gas-phase bare and microsolvated tryptophan and gas-phase doubly protonated gramicidin S.23,24 Zwier and co-workers also confirmed the excellent reproduction of vibrational frequencies and infrared intensities using this level of theory for various α-peptides, α/β-peptides, and γpeptides.25 To test our predictions that the deficiency of the calculated vibrational spectra of Ac-Phe-Ala-Lys-H+ arises from the underestimated role of dispersion in our previous calculations, we reoptimized the geometries of IB3LYP and IIB3LYP at the M052X26,27/6-31G** level of theory with tight convergence criteria and an ultrafine grid and then computed the vibrational frequencies using the same method (Figure 2e,f). The main difference between the structures optimized with the B3LYP functional and those reoptimized with the M05-2X functional is the CαCβCγ dihedral angle of the phenylalanine side chain (Figure 2). In structure IM052X, this angle is 111.5°, while in structure IB3LYP, this angle is 113.2°. Such a position of the chromophore results in a stronger NH−π interaction of the phenylalanine NH with the aromatic ring in conformer IM052X than in conformer IB3LYP, which causes the red shift of the phenylalanine NH stretch. In conformer IIM052X, on the other hand, this type of interaction is weaker than that in IIB3LYP, resulting in a higher-frequency phenylalanine NH stretch. The simulated vibrational spectra of structures IM052X and IIM052X better describe the experimental spectra of conformers B and A of Ac-Phe-Ala-LysH+, respectively (Figure 2e,f). However, the theoretical lysine NH stretch frequency is still too low compared with the experiment, which might be due to a different isomeric form of the lysine side chain. Having found a functional that describes well the dispersion interaction between the phenylalanine NH and the aromatic ring, we performed a more extensive Monte Carlo conformational search using the optimized potentials for liquid simulations (OPLS) force field28,29 with the improved parametrization for proteins.30 After geometry optimization of the 60 lowest-energy structures in Gaussian 0917 using M052X26,27/6-31G**, the lowest-energy structures were those that we predicted. These geometries were reoptimized again at the M05-2X/6-31++G** level with tight convergence criteria and an ultrafine grid, and their vibrational frequencies were calculated at the same level of theory. The resulting vibrational spectra are presented in Figure 4 along with the corresponding structures. Conformer A has the lowest energy at this level of theory, and conformer B is 0.43 kcal/mol higher in energy, in
Figure 2. Experimental ground-state infrared spectra of conformers A (green) and B (blue) of Ac-Phe-Ala-LysH+ in comparison with the calculated spectra of the corresponding structures IB3LYP, IIB3LYP, IM052X, and IIM052X. Structures IB3LYP and IIB3LYP are calculated using the B3LYP functional. Structures IM052X and IIM052X were calculated by geometry reoptimization of IB3LYP and IIB3LYP with the M05-2X functional. The harmonic frequencies were calculated for IB3LYP and IIB3LYP structures using the B3LYP/6-31+G** level of theory and for IM052X and IIM052X structures using the M05-2X/6-31G** level of theory. The scale factors in the amide I region are 0.987 and 0.946, and those in the NH stretch region are 0.952 and 0.932 for the geometries optimized with B3LYP and M05-2X, respectively.
LysH+ (Figure 3).5 In conformer A of Ac-Phe-Ala-LysH+, the phenylalanine side chain is located just under the alanine and the phenylalanine NH’s, and in conformer B, it turns away from the alanine NH, forming a hydrogen bond between the π cloud and the phenylalanine NH. By analogy with the larger molecule, and also taking into account the spectra of the electronically excited state (Figure 1b,d), we attribute the infrared band at around 3451 cm−1 in the ground state of conformers A and B of Ac-Phe-Ala-LysH+ to the alanine NH stretch. We thus assign the remaining infrared transition at 3417 cm−1 to the lysine NH stretch. With this comparison in mind, we can confine our search to two conformations that differ by the rotation of the phenylalanine ring around the Cα−Cβ bond and in which the lysine side chain is not involved in a cation−π interaction. The structures IB3LYP and IIB3LYP seem to fulfill those criteria. However, the calculated vibrational spectrum in the NH stretch region does not exhibit any significant difference between these structures (Figure 2c,d). We would expect the phenylalanine NH stretch vibration to be further red-shifted in the calculated spectrum of IB3LYP compared with that of IIB3LYP due to a stronger NH−π interaction. In addition, the wavenumbers of 1506
DOI: 10.1021/acs.jpclett.5b00407 J. Phys. Chem. Lett. 2015, 6, 1504−1508
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Figure 3. Ground-state infrared spectra of conformers A (a) and B (b) of Ac-Phe-Ala-Lys-H+ compared to the ground-state infrared spectra of conformers A (c) and B (d) of Ac-Phe-(Ala)5-Lys-H+.5 We highlight in green the NH region with similar positions of spectroscopic bands in the two molecules. The corresponding structures of conformers A and B of Ac-Phe-(Ala)5-Lys-H+ are presented to the right (modified from ref 5).
Figure 4. Experimental ground-state infrared spectra of conformers A (a) and B (c) of Ac-Phe-Ala-LysH+ in comparison with the calculated spectra (using M05-2X/6-31++G** level of theory) of the corresponding structures A (b) and B (d). We use a scale factor of 0.937 and 0.959 in the amide I and NH stretch regions, respectively. The labels Lys, Phe, and Ala correspond to the lysine, the phenylalanine, and the alanine NH stretches, and the label COAc stands for the acetyl group CO stretch. The calculated structures with their relative zero-point corrected energies (in kcal/mol) are presented to the right.
bonding interactions. The similarities between the structure of this simple tripeptide and the longer polyalanine helix are reflected in the region of the infrared spectrum above 3400 cm−1 corresponding to the N- and C-terminal amides. To demonstrate the robustness of this spectroscopic fingerprint, we also compare the spectra of both molecules to that of an even longer peptide, Ac-Phe-(Ala)10-LysH+ in Figure S2 (Supporting Information),5 and find a similar pattern. Thus, both the ammonium interaction with the carbonyls, which stabilizes the helix, and the spectroscopic fingerprint of the ends of the helix seem to be already present in the small tripeptide.
accordance with conformer A giving rise to more abundant peaks in the electronic spectrum (Figure S1, Supporting Information). The structures of conformers A and B differ by the rotation of the aromatic chromophore around the Cα−Cβ bond. In conformer B, the phenylalanine NH forms a slightly stronger hydrogen bond with the π cloud of the phenyl ring than in conformer A, similar to what Stearns et al. observed in the two most prominent conformations of the helical peptide Ac-Phe-(Ala)5-LysH+.5 Peptide folding is guided to a large extent by hydrogen bonding and dispersion interactions.31 We have identified two structures of Ac-Phe-Ala-LysH+, in both of which the ammonium side chain of lysine prefers to form hydrogen bonds with the three backbone carbonyls rather than interact with the π cloud of the aromatic ring. By analogy with the two conformers of the helical peptide Ac-Phe-(Ala)5-LysH+,5 these structures represent the capping motif for helix formation. The role of the lysine is to stabilize the helix by blocking the ability of backbone carbonyls from participating in other hydrogen
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ASSOCIATED CONTENT
S Supporting Information *
UV photofragmentation spectrum of Ac-Phe-Ala-Lys-H+; comparison between the infrared spectra of Ac-Phe-AlaLysH+, Ac-Phe-(Ala)5-LysH+, and Ac-Phe-(Ala)10-LysH+; and complete ref 17. This material is available free of charge via the Internet at http://pubs.acs.org. 1507
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(19) Gallivan, J. P.; Dougherty, D. A. Cation−π Interactions in Structural Biology. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9459−9464. (20) Dougherty, D. A. Cation−π Interactions in Chemistry and Biology: A New View of Benzene, Phe, Tyr, and Trp. Science 1996, 271, 163−168. (21) Stearns, J. A.; Mercier, S.; Seaiby, C.; Guidi, M.; Boyarkin, O. V.; Rizzo, T. R. Conformation-Specific Spectroscopy and Photodissociation of Cold, Protonated Tyrosine and Phenylalanine. J. Am. Chem. Soc. 2007, 129, 11814−11820. (22) Hohenstein, E. G.; Chill, S. T.; Sherrill, C. D. Assessment of the Performance of the M05-2X and M06-2X Exchange−Correlation Functionals for Noncovalent Interactions in Biomolecules. J. Chem. Theory Comput. 2008, 4, 1996−2000. (23) Doemer, M.; Guglielmi, M.; Athri, P.; Nagornova, N. S.; Rizzo, T. R.; Boyarkin, O. V.; Tavernelli, I.; Rothlisberger, U. Assessing the Performance of Computational Methods for the Prediction of the Ground State Structure of a Cyclic Decapeptide. Int. J. Quantum Chem. 2013, 113, 808−814. (24) Nagornova, N. S.; Guglielmi, M.; Doemer, M.; Tavernelli, I.; Rothlisberger, U.; Rizzo, T. R.; Boyarkin, O. V. Cold-Ion Spectroscopy Reveals the Intrinsic Structure of a Decapeptide. Angew. Chem., Int. Ed. 2011, 50, 5383−5386. (25) Buchanan, E. G.; James, W. H.; Choi, S. H.; Guo, L.; Gellman, S. H.; Müller, C. W.; Zwier, T. S. Single-Conformation Infrared Spectra of Model Peptides in the Amide I and Amide II Regions: ExperimentBased Determination of Local Mode Frequencies and Inter-Mode Coupling. J. Chem. Phys. 2012, 137, 094301. (26) Zhao, Y.; Schultz, N. E.; Truhlar, D. G. Exchange−Correlation Functional with Broad Accuracy for Metallic and Nonmetallic Compounds, Kinetics, and Noncovalent Interactions. J. Chem. Phys. 2005, 123, 161103. (27) Zhao, Y.; Schultz, N. E.; Truhlar, D. G. Design of Density Functionals by Combining the Method of Constraint Satisfaction with Parametrization for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions. J. Chem. Theory Comput. 2006, 2, 364−382. (28) Jorgensen, W. L.; Maxwell, D. S.; TiradoRives, J. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. J. Am. Chem. Soc. 1996, 118, 11225−11236. (29) Kaminski, G.; Duffy, E. M.; Matsui, T.; Jorgensen, W. L. Free Energies of Hydration and Pure Liquid Properties of Hydrocarbons from the OPLS All-Atom Model. J. Phys. Chem. 1994, 98, 13077− 13082. (30) Kaminski, G. A.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. L. Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides. J. Phys. Chem. B 2001, 105, 6474−6487. (31) Berg, J. M.; Tymoczko, J. L.; Stryer, L. Biochemistry, 5th ed.; W.H. Freeman: New York, 2002; p 1100.
AUTHOR INFORMATION
Corresponding Author
*E-mail: thomas.rizzo@epfl.ch. Notes
The authors declare no competing financial interest.
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ACKNOWLEDGMENTS We thank Marta Andreia Da Silva Perez and Yoshiya Inokuchi for their advice about the calculations, and we thank Ecole Polytechnique Fédérale de Lausanne and the Swiss National Science Foundation (through Grant 200020_152804) for their generous support of this work.
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REFERENCES
(1) Jarrold, M. F. Helices and Sheets in Vacuo. Phys. Chem. Chem. Phys. 2007, 9, 1659−1671. (2) Hudgins, R. R.; Jarrold, M. F. Helix Formation in Unsolvated Alanine-Based Peptides: Helical Monomers and Helical Dimers. J. Am. Chem. Soc. 1999, 121, 3494−3501. (3) Hudgins, R. R.; Ratner, M. A.; Jarrold, M. F. Design of Helices that are Stable in Vacuo. J. Am. Chem. Soc. 1998, 120, 12974−12975. (4) Ponomarev, S. Y.; Sa, Q.; Kaminski, G. A. Effects of Lysine Substitution on Stability of Polyalanine α Helix. J. Chem. Theory Comput. 2012, 8, 4691−4706. (5) Stearns, J. A.; Seaiby, C.; Boyarkin, O. V.; Rizzo, T. R. Spectroscopy and Conformational Preferences of Gas-Phase Helices. Phys. Chem. Chem. Phys. 2009, 11, 125−132. (6) Chin, W.; Piuzzi, F.; Dognon, J.-P.; Dimicoli, I.; Tardivel, B.; Mons, M. Gas Phase Formation of a 310-Helix in a Three-Residue Peptide Chain: Role of Side Chain−Backbone Interactions as Evidenced by IR−UV Double Resonance Experiments. J. Am. Chem. Soc. 2005, 127, 11900−11901. (7) Svendsen, A.; Lorenz, U. J.; Boyarkin, O. V.; Rizzo, T. R. A New Tandem Mass Spectrometer for Photofragment Spectroscopy of Cold, Gas-Phase Molecular Ions. Rev. Sci. Instrum. 2010, 81, 073107. (8) Nagornova, N. S.; Rizzo, T. R.; Boyarkin, O. V. Exploring the Mechanism of IR−UV Double-Resonance for Quantitative Spectroscopy of Protonated Polypeptides and Proteins. Angew. Chem., Int. Ed. 2013, 52, 6002−6005. (9) Zabuga, A. V.; Kamrath, M. Z.; Boyarkin, O. V.; Rizzo, T. R. Fragmentation Mechanism of UV-Excited Peptides in the Gas Phase. J. Chem. Phys. 2014, 141, 154309. (10) Zabuga, A. Dynamics of UV-Excited, Protonated Peptides in the Gas Phase. PhD Thesis, EPFL, Lausanne, 2014. (11) Halgren, T. A. Merck Molecular Force Field. I. Basis, Form, Scope, Parameterization, and Performance of MMFF94. J. Comput. Chem. 1996, 17, 490−519. (12) Halgren, T. A. MMFF VII. Characterization of MMFF94, MMFF94s, and Other Widely Available Force Fields for Conformational Energies and for Intermolecular-Interaction Energies and Geometries. J. Comput. Chem. 1999, 20, 730−748. (13) CONFLEX, version 7; CONFLEX Corporation: Japan, 2012. (14) Becke, A. D. Density-Functional Exchange-Energy Approximation with Correct Asymptotic Behavior. Phys. Rev. A 1988, 38, 3098−3100. (15) Becke, A. D. Density-Functional Thermochemistry. III. The Role of Exact Exchange. J. Chem. Phys. 1993, 98, 5648−5652. (16) Lee, C. T.; Yang, W. T.; Parr, R. G. Development of the Colle− Salvetti Correlation-Energy Formula into a Functional of the Electron Density. Phys. Rev. B 1988, 37, 785−789. (17) Frisch, M. J.; et al. Gaussian 09, revision B.01; Gaussian, Inc.: Wallingford, CT, 2009. (18) Stearns, J. A.; Guidi, M.; Boyarkin, O. V.; Rizzo, T. R. Conformation-Specific Infrared and Ultraviolet Spectroscopy of Tyrosine-Based Protonated Dipeptides. J. Chem. Phys. 2007, 127, 154322. 1508
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