[show abstract][hide abstract] ABSTRACT: Ab initio calculations of the six-dimensional intermolecular potential have shown the benzene dimer to be an asymmetric top molecule at equilibrium with one benzene moiety forming the "stem" and the other a "tilted cap" in a T-shaped structure. Internal rotation of the cap about its C6 axis is essentially free; the barriers for cap tilting and for internal rotation of the stem about its C6 axis are hindered by successively higher barriers. In previous work we have validated these theoretical results using Fourier transform microwave spectroscopy in conjunction with dynamics calculations. We have also measured the Stark effect, and despite the fact that the equilibrium structure is that of an asymmetric top, the assigned transitions involving K = 0 exhibit a second-order Stark effect whereas those involving K = 1 exhibit a first-order Stark effect. This is typical for a symmetric-top molecule, but anomalous for an asymmetric-top molecule. We use symmetry arguments to explain how this asymmetric-top molecule can have a first-order Stark effect in certain states that have excitation of cap internal rotation. Cap internal rotation is essentially the twisting of the monomers relative to each other about the intermolecular axis, and such torsional motion occurs in other asymmetric top dimers such as benzene-CO and benzene-H2O. These latter dimers will also have levels that exhibit a first-order Stark effect, which we can explain using our symmetry arguments.
The Journal of Physical Chemistry A 10/2013; · 2.77 Impact Factor
[show abstract][hide abstract] ABSTRACT: Specific interactions between cations and proteins have a strong impact on peptide and protein structure. Herein, we shed light on the nature of the underlying interactions, especially regarding effects on the polyamide backbone structure. This was done by comparing the conformational ensembles of model peptides in isolation and in the presence of either Li(+) or Na(+) by using state-of-the-art density-functional theory (including van der Waals effects) and gas-phase infrared spectroscopy. These monovalent cations have a drastic effect on the local backbone conformation of turn-forming peptides, by disruption of the hydrogen-bonding networks, thus resulting in severe distortion of the backbone conformations. In fact, Li(+) and Na(+) can even have different conformational effects on the same peptide. We also assess the predictive power of current approximate density functionals for peptide-cation systems and compare to results with those of established protein force fields as well as high-level quantum chemistry calculations (CCSD(T)).
[show abstract][hide abstract] ABSTRACT: We report a combined theoretical and microwave spectroscopy study of the internal dynamics of the benzene dimer, a benchmark system for dispersion forces. Although the extensive ab initio calculations and experimental work on the equilibrium geometry of this dimer have converged to a tilted T-shaped structure, the rich internal dynamics due to low barriers for internal rotation have remained largely unexplored. We present new microwave spectroscopy data for both the normal (C6H6)2 and partially deuterated (C6D6)(C6H6) dimers. The splitting patterns obtained for both species are unraveled and understood using a reduced-dimensionality theoretical approach. The hindered sixfold rotation of the stem can explain the observed characteristic 1 : 2 : 1 tunneling splitting pattern, but only the concerted stem rotation and tilt tunneling motion, accompanied by overall rotation of the dimer, yield the correct magnitude of the splittings and their strong dependence on the dimer angular momentum J that is essential to explain the experimental data. Also the surprising observation that the splittings are reduced by 30% for the mixed (C6D6)(C)(C6H6)(S) dimer in which only the cap (C) in the T-shaped structure is deuterated, while the rotating stem (S) monomer is the same as in the homodimer, is understood using this approach. Stark shift measurements allowed us to determine the dipole moment of the benzene dimer, μ = 0.58 ± 0.051 D. The assumption that this dipole moment is the vector sum of the dipole moments induced in the monomers by the electric field of the quadrupole on the other monomer yields a calculated value of μ = 0.63 D. Furthermore, the observed Stark behavior is typical for a symmetric top, another confirmation of our analysis.
Physical Chemistry Chemical Physics 05/2013; · 3.83 Impact Factor
[show abstract][hide abstract] ABSTRACT: The benzene dimer, an important prototype for studying noncovalent interactions, exhibits characteristic splitting patterns in its rotational spectrum, which for a long time were not understood. A new theoretical model reveals their origin: a concerted internal motion involving sixfold hindered rotation tunneling of the molecule forming the stem of the T-shaped structure and tilt tunneling of the cap.
Angewandte Chemie International Edition 04/2013; · 13.73 Impact Factor
[show abstract][hide abstract] ABSTRACT: There is ongoing debate on the extent to which protein structure is retained after transfer into the gas phase. Here using ion mobility mass spectrometry, we investigate the impact of side-chain backbone interactions on the structure of gas-phase protein ions by non-covalent attachment of crown ethers (CE). Our results indicate that in the absence of solvent, secondary interactions between charged lysine side chains and backbone carbonyls can significantly influence the structure of a protein. Once the charged residues are capped with CEs, certain charge states of the protein are found to undergo a significant structural compaction.
Journal of the American Chemical Society 01/2013; · 10.68 Impact Factor
[show abstract][hide abstract] ABSTRACT: We report on a method by which mass/charge selected ions are picked up from a linear ion trap by liquid helium droplets. The size distributions of the doped droplets are measured via acceleration experiments. Depending on the source temperature, droplet sizes ranging from tens of thousands to several million helium atoms are obtained. Droplets doped with hemin, an iron containing porphyrin molecule, in the charge state +1 are then investigated using laser spectroscopy. It is observed that excitation with UV/VIS light can lead to ejection of the ion from the droplet. For doped droplets with a median size of ∼150 000 helium atoms, the absorption of two photons at 380 nm is needed for ejection to become efficient. When droplets become smaller, the ejection efficiency is observed to strongly increase. Monitoring the ejection yield as a function of excitation wavelength can be used to obtain the optical spectrum of hemin(+). Compared to the spectrum of free gas-phase hemin(+) at room temperature, the here obtained spectrum is slightly narrower and shifted to the blue.
Physical Chemistry Chemical Physics 08/2012; 14(38):13370-7. · 3.83 Impact Factor
[show abstract][hide abstract] ABSTRACT: An experimental approach is presented that allows for the incorporation of large mass-to-charge ratio selected ions in liquid helium droplets. It is demonstrated that droplets can be efficiently doped with a mass-to-charge ratio selected amino acid as well as with the much bigger m ≈ 12,000 amu protein cytochrome C in selected charge states. The sizes of the ion-doped droplets are determined via electrostatic deflection. Under the experimental conditions employed, the observed droplet sizes are very large and range, depending on the incorporated ion, from 10¹⁰ helium atoms for protonated phenylalanine to 10¹² helium atoms for cytochrome C. As a possible explanation, a simple model based on the size and internal energy dependence of the pickup efficiency is given.
[show abstract][hide abstract] ABSTRACT: An improved intermolecular potential surface for the benzene dimer is constructed from interaction energies computed by symmetry-adapted perturbation theory, SAPT(DFT), with the inclusion of third-order contributions. Twelve characteristic points on the surface have been investigated also using the coupled-cluster method with single, double, and perturbative triple excitations, CCSD(T), and triple-zeta quality basis sets with midbond functions. The SAPT and CCSD(T) results are in close agreement and provide the best representation of these points to date. The potential was used in calculations of vibration-rotation-tunneling (VRT) levels of the dimer by a method appropriate for large amplitude intermolecular motions and tunneling between multiple equivalent minima in the potential. The resulting VRT levels were analyzed with the use of the permutation-inversion full cluster tunneling (FCT) group G(576) and a chain of subgroups that starts from the molecular symmetry group C(s)(M) of the rigid dimer at its equilibrium C(s) geometry and leads to G(576) if all possible intermolecular tunneling mechanisms are feasible. Further information was extracted from the calculated wave functions. It was found, in agreement with the experimental data, that for all of the 54 G(576) symmetry species (with different nuclear spin statistical weights) the lower VRT states have a tilted T-shape (TT) structure; states with the parallel-displaced structure are higher in energy than the ground state of A symmetry by at least 30 cm(-1). The dissociation energy D(0) equals 870 cm(-1), while the depth D(e) of the TT minimum in the potential is 975 cm(-1). Hindered rotation of the cap in the TT structure and tilt tunneling lead to level splittings on the order of 1 cm(-1). Also intermolecular vibrations with excitation energies starting at a few cm(-1) were identified. A further small, but probably significant, level splitting was assigned to cap turnover, although in scans of the potential surface we could not find a plausible 'reaction path' for this process. Rotational constants were extracted from energy levels calculated for total angular momentum J = 0 and 1, and from expectation values of the inertia tensor. Although the end-over-end rotational constant B + C agrees well with the measured microwave spectra, there is disagreement with the measurements concerning the (a)symmetric rotor character of the benzene dimer. It is concluded from calculations for the 54 nuclear spin species that the microwave spectrum should show overlapping contributions from many different species. Another interesting conclusion regards the role of the quantum number K, for a prolate near-symmetric rotor the projection of the total angular momentum on the prolate axis. For the benzene dimer, K has a substantial effect on the energy levels associated with the intermolecular motions of the complex.
Physical Chemistry Chemical Physics 08/2010; 12(29):8219-40. · 3.83 Impact Factor
[show abstract][hide abstract] ABSTRACT: Cationic iron-oxide clusters of several sizes and stoichiometries have been synthesized and studied isolated in the gas phase. Vibrational spectra of the clusters have been measured using resonant IR-induced dissociation of FenOm+2+→FenOm++O2 in the 250–1250 cm−1 range. Density-functional theory was used to investigate the geometry and spin configuration of the representative Fe4O60/+ cluster. Its lowest-energy state was found to be an almost tetrahedral cagelike structure with a ferrimagnetic arrangement of spins, resulting in total cluster spin of S=5 for the neutral cluster. These results were confirmed for Fe4O6+ by the comparison of the calculated infrared spectrum to the experimentally obtained one.
[show abstract][hide abstract] ABSTRACT: An improved intermolecular potential surface for the benzene dimer has been constructed from interaction energies computed by symmetry-adapted perturbation theory with the inclusion of third-order contributions. The potential was used in calculations of vibration-rotation-tunneling levels of the dimer by a method appropriate for large amplitude intermolecular motions and tunneling between multiple equivalent minima in the potential. The resulting levels were analyzed using the permutation-inversion full cluster tunneling group G576 and a chain of subgroups that starts from the molecular symmetry group C_s(M) of the rigid dimer at its equilibrium C_s geometry and leads to G576 if all possible intermolecular tunneling mechanisms are feasible.
[show abstract][hide abstract] ABSTRACT: The polyalanine-based peptide series Ac-Ala_n-LysH+ (n=5-20) is a prime example that a secondary structure motif which is well-known from the solution phase (here: helices) can be formed in vacuo. We here revisit this conclusion for n=5,10,15, using density-functional theory (van der Waals corrected generalized gradient approximation), and gas-phase infrared vibrational spectroscopy. For the longer molecules (n=10,15) \alpha-helical models provide good qualitative agreement (theory vs. experiment) already in the harmonic approximation. For n=5, the lowest energy conformer is not a simple helix, but competes closely with \alpha-helical motifs at 300K. Close agreement between infrared spectra from experiment and ab initio molecular dynamics (including anharmonic effects) supports our findings. Comment: 4 pages, 4 figures, Submitted to JPC Letters
[show abstract][hide abstract] ABSTRACT: Mid-infrared (IR) hole burning spectra of the model tripeptide Z-Aib-Pro-NHMe (Z = benzyloxycarbonyl) in gas phase and its micro-clusters with one and two methanol molecules are presented. To establish a relation between experimental spectra and the underlying conformations, calculations at the DFT [B3LYP/6-311++G(d,p)] level of theory are performed. In particular, the intra-peptide and the peptide-methanol hydrogen bonds can be identified from spectral shifts in the amide I, II, and III regions. While the unsolvated tripeptide as well as its one-methanol cluster prefer a gamma-turn structure, a beta-turn structure is found for the two-methanol cluster, in agreement with previous condensed phase studies. Comparison of measured and simulated spectra reveals that the favorable methanol binding sites are at the head and tail parts of the tripeptide. The interconversions between gamma-turn and beta-turn structures are governed by potential barriers below 10 kJ mol(-1) inside one of the low energy basins of the potential energy surface.
Physical Chemistry Chemical Physics 04/2010; 12(14):3415-25. · 3.83 Impact Factor
[show abstract][hide abstract] ABSTRACT: Well defined secondary structure motifs (e.g., helices) in polypeptides can be systematically studied in vacuo, offering a unique ``clean room" condition to quantify the stabilizing intramolecular interactions. Here we address theoretically the structure of alanine polypeptides Ac-Alan-LysH^+ (n=5,10,15), for which gas-phase helical structure was indicated in experiment . Using van der Waals (vdW) corrected  Density Functional Theory (DFT), we present vibrational spectra and compare to room temperature multiple photon IR spectroscopy data obtained at the FELIX free electron laser. For the longer molecules (n=10,15) alpha-helical models provide good qualitative agreement (theory vs. experiment) already in the harmonic approximation. For Ac-Ala5LysH^+, the predicted lowest energy conformer (``g-1'') in vdW corrected DFT (PBE, B3LYP, revPBE) is not a simple helix. However, the harmonic free energy suggests that g-1 and the lowest-energy alpha-helical conformers are energetically close at 300 K, and thus might all coexist in experiment. Consistently, their calculated vibrational spectra agree with experiment, but only if anharmonic effects are included by explicit molecular dynamics simulations.  R. Hudgins et al., JACS 120, 12974 (1998)  A. Tkatchenko, M. Scheffler, PRL 102, 073005 (2009)
[show abstract][hide abstract] ABSTRACT: In the condensed phase, the peptide gramicidin S is often considered as a model system for a beta-sheet structure. Here, we investigate gramicidin S free of any influences of the environment by measuring the mid-IR spectra of doubly protonated (deuterated) gramicidin S in the gas phase. In the amide I (i.e., C=O stretch) region, the spectra show a broad split peak between 1580 and 1720 cm(-1). To deduce structural information, the conformational space has been searched using molecular dynamics methods and several structural candidates have been further investigated at the density functional level. The calculations show the importance of the interactions of the charged side-chains with the backbone, which is responsible for the lower frequency part of the amide I peak. When this interaction is inhibited via complexation with two 18-crown-6 molecules, the amide I peak narrows and shows two maxima at 1653 and 1680 cm(-1). A comparison to calculations shows that for this complexed ion, four C=O groups are in an antiparallel beta-sheet arrangement. Surprisingly, an analysis of the calculated spectra shows that these beta-sheet C=O groups give rise to the vibrations near 1680 cm(-1). This is in sharp contrast to expectations based on values for the condensed phase, where resonances of beta-sheet sections are thought to occur near 1630 cm(-1). The difference between those values might be caused by interactions with the environment, as the condensed phase value is mostly deduced for beta-sheet sections that are embedded in larger proteins, that interact strongly with solvent or that are part of partially aggregated species.
Journal of the American Chemical Society 02/2010; 132(6):2085-93. · 10.68 Impact Factor
[show abstract][hide abstract] ABSTRACT: The sequential absorption of multiple infrared (IR) photons by isolated gas-phase species can lead to their dissociation and/or ionization. Using the newly constructed "Free-Electron Laser for IntraCavity Experiments" (FELICE) beam line at the FELIX facility, neutral C(60) molecules have been exposed to an extremely high number (approximately 10(23)) of photons/cm(2) for a total time duration of up to 5 micros. At wavelengths around 20 microm, resonant with allowed IR transitions of C(60), ionization and extensive fragmentation of the fullerenes are observed. The resulting photofragment distributions are attributed to absorption in fragmentation products formed once C(60) is excited to internal energies at which fragmentation or ionization takes place within the duration of the laser pulse. The high IR intensities available combined with the large interaction volume permit spatially resolved detection of the ions inside the laser beam, thereby disentangling the contributions from different IR intensities. The use of spatial imaging reveals intensity dependent mass distributions that are substantially narrower than what has been observed previously, indicating rather narrow energy distributions. A simple rate-equation modeling of the excitation process supports the experimental observations.
The Journal of chemical physics 02/2010; 132(7):074305. · 3.09 Impact Factor
[show abstract][hide abstract] ABSTRACT: No solution for the zwitterion: An acid- and base-containing pentapeptide was designed to explore the possibility of zwitterion formation in the gas phase, in the absence of a net charge. Internal proton transfer between peptide side chains in vacuo gave a zwitterion (highlighted in yellow; the canonical form is highlighted in blue), which was identified by gas-phase IR spectroscopy.
Angewandte Chemie International Edition 02/2010; 49(13):2332-5. · 13.73 Impact Factor
[show abstract][hide abstract] ABSTRACT: Cationic iron-oxide clusters of several sizes and stoichiometries have been synthesized and studied isolated in the gas phase. Vibrational spectra of the clusters have been measured using resonant IR-induced dissociation of FenO m+2+ → FenOm+ + O2 in the 250 – 1250 cm−1 range. Density-functional theory was used to investigate the geometry and spin configuration of the representative Fe4O60/+ cluster. Its lowest-energy state was found to be an almost tetrahedral cagelike structure with a ferrimagnetic arrangement of spins, resulting in total cluster spin of S=5 for the neutral cluster. These results were confirmed for Fe4O6+ by the comparison of the calculated infrared spectrum to the experimentally obtained one.