Probing Solvation Dynamics around Aromatic and Biological Molecules at the Single-Molecular Level

Editorial of the PCCP themed issue on "Physical Chemistry for Life Sciences"

This themed issue features high quality and original research on the theme of Physical Chemistry for Life Sciences.

Infrared photodissociation spectroscopy of cold cationic trimethylamine complexes

Infrared spectroscopic studies reveal the general trends in the stepwise growth motif of trimethylamine (TMA)_n⁺ complexes.

Infrared spectroscopy of gas phase alpha hydroxy carboxylic acid homo and hetero dimers

New gas phase infrared spectroscopy is reported for an aromatic alpha hydroxy carboxylic acid homo dimer of 9-hydroxy-9-fluorene carboxylic acid (9HFCA)₂, and the hetero dimer of 9HFCA with glycolic acid.

Sequential microhydration of cationic 5-hydroxyindole (5HI+): infrared photodissociation spectra of 5HI+–Wn clusters (W = H2O, n ≤ 4)

The hydrogen-bonding properties of the acidic OH and NH groups of the 5-hydroxyindole cation are probed by infrared spectroscopy and DFT calculations of its microhydrated clusters.

Structure and Dynamics in Formamide-(H2O)3: A Water Pentamer Analogue

Water self-association dominates the formation of microsolvated molecular clusters which may give rise to complex structures resembling those of pure water clusters. We present a rotational study of the complex formamide-(H₂O)₃ formed in a supersonic jet and several monosubstituted isotopologues. Formamide and water molecules form a four-body sequential cycle through N-H···O, O-H···O, and O-H···O═C hydrogen bonds, resulting in a chiral structure with a nonplanar skeleton that can be overlapped to that of water pentamer. The analysis of the ¹⁴N-nucleus quadrupole coupling effects shows the depletion of the electron density of the N atom lone pair with respect to the bare formamide that affects the amide group C-N and C═O distances. The study of the observed tunneling doublets shows that formamide-(H₂O)₃ follows a path to invert its structure driven by the flipping of water subunits and passing through successive nonplanar configurations, a motion reminiscent of the pseudorotation of water pentamer.

The Structure of Diphenyl Ether-Methanol in the Electronically Excited and Ionic Ground States: A Combined IR/UV Spectroscopic and Theoretical Study

Diphenyl ether offers competing docking sites for methanol: the ether oxygen acts as a common hydrogen-bond acceptor and the π system of each phenyl ring allows for OH-π interactions driven by electrostatic, induction, and dispersion forces. Based on investigations in the electronic ground state (S₀ ), we present a detailed study of the electronically excited state (S₁ ) and the ionic ground state (D₀ ), in which an impact on the structural preference is expected compared with the S₀ state. Dispersion forces in the electronically excited state were analyzed by comparing the computed binding energies at the coupled-cluster-singles (CCS) and approximate coupled-cluster-singles-doubles levels of theory (CC2 approximation). By applying UV/IR/UV spectroscopy, we found a more strongly bound OH-π structure in the S₁ state compared with the S₀ state, in agreement with spin-component-scaled CC2 calculations. A structural rearrangement into a non-hydrogen-bonded structure takes places upon ionization in the D₀ state, which was revealed by using IR photodissociation spectroscopy and confirmed by theory.

Infrared spectroscopy of O˙- and OH- in water clusters: evidence for fast interconversion between O˙- and OH˙OH. Phys Chem Chem Phys 2017;19:25346-25351. [PMID: 28891582 PMCID: PMC7100789 DOI: 10.1039/c7cp04577h]

We present infrared multiple photon dissociation (IRMPD) spectra of (H2O)nO˙- and (H2O)nOH- cluster ensembles for n[combining macron] ≈ 8 and 47 in the range of 2400-4000 cm-1. Both hydrated ions exhibit the same spectral features, in good agreement with theoretical calculations. Decomposition of the calculated spectra shows that bands originating from H2OO˙- and H2OOH- interactions span almost the whole spectral region of interest. Experimentally, evaporation of OH˙ is observed to a small extent, which requires interconversion of (H2O)nO˙- into (H2O)n-1OH˙OH-, with subsequent H2O evaporation preferred over OH˙ evaporation. The modeling shows that (H2O)nO˙- and (H2O)n-1OH˙OH- cannot be distinguished by IRMPD spectroscopy.

Structural features of monohydrated 2-(4-fluorophenyl)ethylamine: a combined spectroscopic and computational study

A jet-cooled singly hydrated 2-(4-fluorophenyl)ethylamine (4-FPEA-H₂O) cluster has been studied by ionization-loss stimulated Raman spectroscopy of the 4-FPEA photofragment and density functional calculations of the parent. Comparison of the measured spectrum of the photofragment to computed scaled harmonic Raman spectra of different conformers of the 4-FPEA-H₂O cluster, at the M06-2X/6-311++G(d,p) level of theory, allowed determination of the calculated spectrum that best fits the experimental one. The correlation between them was further supported by the stability of the cluster, as revealed from the calculated energies of the fully optimized geometries of the possible different clusters in the ground electronic state. The corresponding structure consists of a water molecule, which is hydrogen-bonded to the nitrogen lone pair of the folded ethylamino side chain in the most stable gauche conformer of 4-FPEA. The presence of the hydrogen bond and other bonding and non-bonding interactions was also tested by atoms in molecules and noncovalent interaction analyses. The former approach showed no critical points in electron density, while the latter revealed regional topologies of reduced density gradients, indicating the formation of this hydrogen-bond and other attractive and repulsive interactions. The monohydration of 4-FPEA provides an insight into the intra- and inter-molecular interactions that play a role in stabilizing the cluster.

Quantum Mechanics Approach to Hydration Energies and Structures of Alanine and Dialanine

A systematic approach to the phenomena related to hydration of biomolecules is reported at the state of the art of electronic-structure methods. Large-scale CCSD(T), MP4-SDQ, MP2, and DFT(M06-2X) calculations for some hydrated complexes of alanine and dialanine (Ala⋅13 H₂ O, Ala₂ H⁺ ⋅18 H₂ O, and Ala₂ ⋅18 H₂ O) are compared with experimental data and other elaborate modeling to assess the reliability of a simple bottom-up approach. The inclusion of a minimal number of water molecules for microhydration of the polar groups together with the polarizable continuum model is sufficient to reproduce the relative bulk thermodynamic functions of the considered biomolecules. These quantities depend on the adopted electronic-structure method, which should be chosen with great care. Nevertheless, the computationally feasible MP2 and M06-2X functionals with the aug-cc-pVTZ basis set satisfactorily reproduce values derived by high-level CCSD(T) and MP4-SDQ methods, and thus they are suitable for future developments of more elaborate and hence more biochemically significant peptides.

Microsolvation of the pyrrole cation (Py+) with nonpolar and polar ligands: infrared spectra of Py+–Ln with L = Ar, N2, and H2O (n ≤ 3)

IR spectra and dispersion-corrected density functional calculations of pyrrole cluster ions with Ar, N₂, and H₂O reveal the competition between H-bonding and π-stacking motifs of this prototypical heterocyclic aromatic cation in a hydrophobic and hydrophilic solvent.

Quantitative probing of subtle interactions among H-bonds in alpha hydroxy carboxylic acid complexes

The alpha OH stretching frequency may be affected upon complexing with water and formic acid.

A structural study on the excimer state of an isolated benzene dimer using infrared spectroscopy in the skeletal vibration region

IR spectroscopy on an isolated benzene excimer reveals that both the electronic and vibrational excitations are in resonance.

Deciphering environment effects in peptide bond solvation dynamics by experiment and theory

Probing solvation dynamics at the molecular level: different water migration pathways around a peptide bond.

Infrared spectroscopy of hydrated polycyclic aromatic hydrocarbon cations: naphthalene+–water

The combination of infrared spectroscopy and quantum chemical calculations unravels the salient properties of the bifurcated CH⋯O ionic hydrogen bond typical for the PAH⁺–H₂O interaction.

Photoionization-induced π ↔ H site switching dynamics in phenol+–Rg (Rg = Ar, Kr) dimers probed by picosecond time-resolved infrared spectroscopy

Picosecond time-resolved infrared spectroscopy of phenol–rare gas dimer cations reveal delocalization of a wavepacket of the single rare gas atom above and below phenol in around 100 ps.