Chantal Pfaffen

Strong N-H pi Hydrogen Bonding in Amide-Benzene Interactions

Among the weak intermolecular interactions found in proteins, the amide N--H...pi interaction has been widely observed but remains poorly characterized as an individual interaction. We have investigated the isolated supersonic-jet-cooled dimer of the cis-amide and nucleobase analogue 2-pyridone (2PY) with benzene and benzene-d6. Both MP2 and SCS-MP2 geometry optimizations yield a T-shaped structure with a N--H...pi hydrogen bond to the benzene ring and the C=O group above, but far from the C--H bonds of benzene. The CCSD(T) calculated binding energy at the optimum geometry is De = 25.2 kJ/mol (dissociation energy D0 = 21.6 kJ/mol), corresponding to the H-bond strength of the water dimer or of N--H...O hydrogen bonds. The T-shaped geometry is supported by the infrared-ultraviolet depletion spectra of 2PY x benzene: The N--H stretch vibrational frequency is lowered by 56 cm(-1), and the C=O stretch vibration is lowered by 10 cm(-1), relative to those of bare 2PY, indicating a strong N--H...pi interaction and a weak interaction of the C=O group. The benzene C--H infrared stretches exhibit very small shifts (approximately 2 cm(-1)) relative to benzene, signaling the absence of interactions with the benzene C--H groups. The infrared spectral shifts are consistent with a strong nonconventional pi hydrogen bond and a T-shaped structure for 2PY x benzene. Symmetry-adapted perturbation theory calculations show that the N--H...pi interaction is by far the dominant stabilization factor.

Large-amplitude vibrations of an N-H center dot center dot center dot pi hydrogen bonded cis-amide-benzene complex

The ground-state N-H...pi interaction of 2-pyridone.benzene (2PY.Bz) has been studied by infrared-UV depletion spectroscopy of the supersonic-jet cooled complex [P. Ottiger et al., J. Phys. Chem. B (2009) 113, 2937]. Here, we investigate the large-amplitude vibrations of 2PY.Bz and its d(1)-2PY and benzene-d(6) isotopologues in the S(1) state, using two-color resonant two-photon ionization and UV-holeburning spectroscopies, complemented by RI-CC2 and SCS-RI-CC2 calculations of the S(1) state. The latter predict a tilted T-shaped structure with an N-H...pi hydrogen bond to the benzene ring, similar to the S(0) state. The binding energy is predicted to increase by 1.5 kJ mol(-1) upon S(1)<--S(0) excitation, in close agreement with the experimental value of 1.2 kJ mol(-1). The vibronic band structure up to 60 cm(-1) above the 0 band is dominated by large-amplitude delta tilting excitations, reflecting a change in the tilt angle of the T-shaped complex. The S(0) and S(1) state delta potentials were fitted to experiment, yielding a single minimum in the S(0) state and a double-minimum S(1) potential with delta(min) = +/-13 degrees. The second large-amplitude vibration is the theta twisting or benzene internal-rotation mode. Due to the C(6) symmetry of the benzene moiety the S(0) and S(1) state theta potentials are sixfold symmetric. Analysis of the theta band structure reveals that the S(0) and S(1)theta potentials are mutually aligned and that the internal rotation barriers are V(6)(S(0)) < 0.2 kJ mol(-1) and V(6)(S(1)) = 0.10(1) kJ mol(-1), in close agreement with the calculations. Weaker excitations of the totally symmetric intermolecular vibrations chi (shear), omega (bend) and sigma (stretch) vibrations are also observed. The 2PY intramolecular nu(1) overtone, corresponding to an 2PY amide out-of-plane twist distortion, lies approximately 30% higher than in bare 2PY, reflecting the hindrance of this motion by the strong N-H...pi interaction.

Structure and intermolecular vibrations of perylene·trans-1,2-dichloroethene, a weak charge-transfer complex.

The vibronic spectra of strong charge-transfer complexes are often congested or diffuse and therefore difficult to analyze. We present the spectra of the π-stacked complex perylene trans-1,2-dichloroethene, which is in the limit of weak charge transfer, the electronic excitation remaining largely confined to the perylene moiety. The complex is formed in a supersonic jet, and its S0 ↔ S1 spectra are investigated by two-color resonant two-photon ionization (2C-R2PI) and fluorescence spectroscopies. Under optimized conditions, vibrationally cold (T(vib) ≈ 9 K) and well resolved spectra are obtained. These are dominated by vibrational progressions in the “hindered-rotation” Rc intermolecular vibration with very low frequencies of 11 (S0) and 13 cm(–1) (S1). The intermolecular Tz stretch and the Ra and Rb bend vibrations are also observed. The normally symmetry-forbidden intramolecular 1a(u) “twisting” vibration of perylene also appears, showing that the π- stacking interaction deforms the perylene moiety, lowering its local symmetry from D2h to D2. We calculate the structure and vibrations of this complex using six different density functional theory (DFT) methods (CAM-B3LYP, BH&HLYP, B97-D3, ωB97X-D, M06, and M06-2X) and compare the results to those calculated by correlated wave function methods (SCS-MP2 and SCS-CC2). The structures and vibrational frequencies predicted with the CAM-B3LYP and BH&HLYP methods disagree with the other calculations and with experiment. The other four DFT and the ab initio methods all predict a π-stacked “centered” structure with nearly coplanar perylene and dichloroethene moieties and intermolecular binding energies of D(e) = −20.8 to −26.1 kJ/mol. The 000 band of the S0 → S1 transition is red-shifted by δν = −301 cm(–1) relative to that of perylene, implying that the D(e) increases by 3.6 kJ/mol or 15% upon electronic excitation. The intermolecular vibrational frequencies are assigned to the calculated Rc, Tz, Ra, and Rb vibrations by comparing to the observed/calculated frequencies and S0 ↔ S1 Franck–Condon factors. Of the three TD-DFT methods tested, the hybrid-meta-GGA functional M06-2X shows the best agreement with the experimental electronic transition energies, spectral shifts, and vibronic spectra, closely followed by the ωB97X-D functional, while the M06 functional gives inferior results.

Modeling the Histidine–Phenylalanine Interaction: The NH···π Hydrogen Bond of Imidazole·Benzene

NH···π hydrogen bonds occur frequently between the amino acid side groups in proteins and peptides. Data-mining studies of protein crystals find that ∼80% of the T-shaped histidine···aromatic contacts are CH···π, and only ∼20% are NH···π interactions. We investigated the infrared (IR) and ultraviolet (UV) spectra of the supersonic-jet-cooled imidazole·benzene (Im·Bz) complex as a model for the NH···π interaction between histidine and phenylalanine. Ground- and excited-state dispersion-corrected density functional calculations and correlated methods (SCS-MP2 and SCS-CC2) predict that Im·Bz has a Cs-symmetric T-shaped minimum-energy structure with an NH···π hydrogen bond to the Bz ring; the NH bond is tilted 12° away from the Bz C6 axis. IR depletion spectra support the T-shaped geometry: The NH stretch vibrational fundamental is red shifted by -73 cm(-1) relative to that of bare imidazole at 3518 cm(-1), indicating a moderately strong NH···π interaction. While the S0(A1g) → S1(B2u) origin of benzene at 38 086 cm(–1) is forbidden in the gas phase, Im·Bz exhibits a moderately intense S0 → S1 origin, which appears via the D(6h) → Cs symmetry lowering of Bz by its interaction with imidazole. The NH···π ground-state hydrogen bond is strong, De=22.7 kJ/mol (1899 cm–1). The combination of gas-phase UV and IR spectra confirms the theoretical predictions that the optimum Im·Bz geometry is T shaped and NH···π hydrogen bonded. We find no experimental evidence for a CH···π hydrogen-bonded ground-state isomer of Im·Bz. The optimum NH···π geometry of the Im·Bz complex is very different from the majority of the histidine·aromatic contact geometries found in protein database analyses, implying that the CH···π contacts observed in these searches do not arise from favorable binding interactions but merely from protein side-chain folding and crystal-packing constraints. The UV and IR spectra of the imidazole·(benzene)2 cluster are observed via fragmentation into the Im·Bz+ mass channel. The spectra of Im·Bz and Im·Bz2 are cleanly separable by IR hole burning. The UV spectrum of Im·Bz2 exhibits two 000 bands corresponding to the S0 → S1 excitations of the two inequivalent benzenes, which are symmetrically shifted by -86/+88 cm(-1) relative to the 000 band of benzene