Theoretical Study on the Size Dependence of Ground-State Proton Transfer in 1‑Naphthol–Ammonia Clusters

The geometries of 1-naphthol–(ammonia)_<i>n</i> (1-NpOH–(NH₃)_<i>n</i>) (<i>n</i> = 6–9) clusters have been calculated by using the density functional theory (DFT) to investigate ground-state proton transfer (GSPT). For <i>n</i> ≤ 7 clusters, the most stable isomer is a non-proton-transferred (non-PT) structure, and isomers within 1.4 kcal/mol unstable from it were also non-PT structures. For <i>n</i> = 8 and 9, the most stable isomer is also a non-PT structure; however, the second stable isomer is the PT structure, of which the relative energy is within 0.5 kcal/mol. We therefore concluded that the threshold size of GSPT is <i>n</i> = 8 under the conventional experimental condition. It is also found that the minimal distance between the π-ring and the solvent moiety is a good indicator of the PT reaction. This suggests that the solvation of the π-ring is important to trigger the PT reaction

Stepwise Microhydration of Aromatic Amide Cations: Formation of Water Solvation Network Revealed by Infrared Spectra of Formanilide⁺–(H₂O)_<i>n</i> Clusters (<i>n</i> ≤ 5)

Hydration of peptides and proteins has a strong impact on their structure and function. Infrared photodissociation spectra (IRPD) of size-selected clusters of the formanilide cation, FA⁺–(H₂O)_<i>n</i> (<i>n</i> = 1–5), are analyzed by density functional theory calculations at the ωB97X-D/aug-cc-pVTZ level to determine the sequential microhydration of this prototypical aromatic amide cation. IRPD spectra are recorded in the hydride stretch and fingerprint ranges to probe the preferred interaction motifs and the cluster growth. IRPD spectra of cold Ar-tagged clusters, FA⁺–(H₂O)_<i>n</i>–Ar, reveal the important effects of temperature and entropy on the observed hydration motifs. At low temperature, the energetically most stable isomers are prominent, while at higher temperature less stable but more flexible isomers become increasingly populated because of entropy. In the most stable structures, the H₂O ligands form a hydrogen-bonded solvent network attached to the acidic NH proton of the amide, which is stabilized by large cooperative effects arising from the excess positive charge. In larger clusters, hydration bridges the gap between the NH and CO groups (<i>n</i> ≥ 4) solvating the amide group rather than the more positively charged phenyl ring. Comparison with neutral FA–(H₂O)_<i>n</i> clusters reveals the strong impact of ionization on the acidity of the NH proton, the strength and topology of the interaction potential, and the structure of the hydration shell

Theoretical Study on the Size Dependence of Excited State Proton Transfer in 1‑Naphthol–Ammonia Clusters

The geometries and energetics of the ground and lower-lying singlet excited states S₀, L_a, and L_b of 1-naphthol (NpOH)–(NH₃)_<i>n</i> (<i>n</i> = 0–5) clusters have been computed using density functional theory (DFT) and time-dependent density functional theory (TD-DFT) methods. Cluster size dependence of the excited state proton transfer (ESPT) reaction was investigated by the vertical transitions from the geometries that can be populated in the molecular beam experiments. For the <i>n</i> = 3 and 4 clusters, the proton-transferred geometries cannot be accessible without significant geometrical rearrangement from the initially populated isomers. For the <i>n</i> = 5 clusters, the proton-transferred structure is found in the L_a excited state of the isomer that can be populated in the beam. Thus, ESPT is possible by the optically prepared L_b state via internal conversion to L_a. We concluded that the threshold cluster size of ESPT is <i>n</i> = 5 under the experimental condition with low excess energy

Cation-Size-Dependent Conformational Locking of Glutamic Acid by Alkali Ions: Infrared Photodissociation Spectroscopy of Cryogenic Ions

Consolidated knowledge of conformation and stability of amino acids and their clusters is required to understand their biochemical recognition. Often, alkali ions interact with amino acids and proteins. Herein, infrared photodissociation (IRPD) spectra of cryogenic metalated glutamic acid ions (GluM⁺, M = Li–Cs) are systematically analyzed in the isomer-specific fingerprint and XH stretch ranges (1100–1900, 2600–3600 cm^–1) to provide a direct measure for cation-size-dependent conformational locking. GluM⁺ ions are generated by electrospray ionization and cooled down to 15 K in a cryogenic quadrupole ion trap. The assignment of the IRPD spectra is supported by density functional theory calculations at the dispersion-corrected B3LYP-D3/aug-cc-pVTZ level. In the global minimum of GluM⁺, the flexibility of Glu is strongly reduced by the formation of rigid ionic CO···M⁺···OC metal bridges, corresponding to charge solvation. The M⁺ binding energy decreases monotonically with increasing cation size from <i>D</i>₀ = 314 to 119 kJ/mol for Li–Cs. Whereas for Li and Na only the global minimum of GluM⁺ is observed, for K–Cs at least three isomers exist at cryogenic temperature. The IRPD spectra of cold GluM⁺ ions are compared to IR multiple-photon dissociation spectra measured at room temperature. Furthermore, we elucidate the differences of the impact of protonation and metalation on the structure and conformational locking of Glu

Anharmonic Vibrational Analyses of Pentapeptide Conformations Explored with Enhanced Sampling Simulations

An accurate theoretical prediction of the vibrational spectrum of polypeptides remains to be a challenge due to (1) their conformational flexibility and (2) non-negligible anharmonic effects. The former makes the search for conformers that contribute to the spectrum difficult, and the latter requires an expensive, quantum mechanical calculation for both electrons and vibrations. Here, we propose a new theoretical approach, which implements an enhanced conformational sampling by the replica-exchange molecular dynamics method, a structural clustering to identify distinct conformations, and a vibrational structure calculation by the second-order vibrational quasi-degenerate perturbation theory (VQDPT2). A systematic mode-selection scheme is developed to reduce the cost of VQDPT2 and the generation of a potential energy surface by the electronic structure calculation. The proposed method is applied to a pentapeptide, SIVSF-NH₂, for which the infrared spectrum has recently been measured in the gas phase with high resolution in the OH and NH stretching region. The theoretical spectrum of the lowest energy conformer is obtained with a mean absolute deviation of 11.2 cm^–1 from the experimental spectrum. Furthermore, the NH stretching frequencies of the five lowest energy conformers are found to be consistent with the literature values measured for small peptides with a similar secondary structure. Therefore, the proposed method is a promising way to analyze the vibrational spectrum of polypeptides

Infrared Spectra of Beauvericin-Alkaline Earth Metal Ion ComplexesIon Preference to Physiological Ions

Beauvericin (Bv) is a naturally occurring ionophore that selectively transports ions through cell membranes. However, the intrinsic ion selectivity of Bv for alkaline earth metal ions (M2+) is yet to be established due to inconsistent results from condensed phase experiments. Based on fluorescence quenching rates, Ca2+ appears to be preferred while extraction experiments favor Mg2+. In this study, we apply cold ion trapinfrared spectroscopy to Bv-M2+ coupled with electrospray ionization mass spectrometry. The mass spectrum shows that Bv favors binding to physiologically active ions Mg2+ and Ca2+ although it can form complexes with all four alkaline earth metal ions. Infrared spectroscopy, as measured by the H2 tag technique, reveals that Bv binds Mg2+ and Ca2+ ions by six carbonyl oxygens in the center of its cavity. This observation is supported by theoretical calculations. Other alkaline earth metal ions are bound by three carbonyl groups at the amide face. This difference in configuration is consistent with the binding preferences for the alkaline earth metal ions

Affinity of Nicotinoids to a Model Nicotinic Acetylcholine Receptor (nAChR) Binding Pocket in the Human Brain

The binding affinity of nicotinoids to the binding residues of the α4β2 variant of the nicotinic acetylcholine receptor (nAChR) was identified as a strong predictor of the nicotinoid’s addictive character. Using ab initio calculations for model binding pockets of increasing size composed of 3, 6, and 14 amino acids (3AA, 6AA, and 14AA) that are derived from the crystal structure, the differences in binding affinity of 6 nicotinoids, namely, nicotine (NIC), nornicotine (NOR), anabasine (ANB), anatabine (ANT), myosmine (MYO), and cotinine (COT) were correlated to their previously reported doses required for increases in intracranial self-stimulation (ICSS) thresholds, a metric for their addictive function. By employing the many-body decomposition, the differences in the binding affinities of the various nicotinoids could be attributed mainly to the proton exchange energy between the pyridine and non-pyridine rings of the nicotinoids and the interactions between them and a handful of proximal amino acids, namely Trp156, Trpβ57, Tyr100, and Tyr204. Interactions between the guest nicotinoid and the amino acids of the binding pocket were found to be mainly classical in nature, except for those between the nicotinoid and Trp156. The larger pockets were found to model binding structures more accurately and predicted the addictive character of all nicotinoids, while smaller models, which are more computationally feasible, would only predict the addictive character of nicotinoids that are similar to nicotine. The present study identifies the binding affinity of the guest nicotinoid to the host binding pocket as a strong descriptor of the nicotinoid’s addiction potential, and as such it can be employed as a fast-screening technique for the potential addiction of nicotine analogs

Structure of Gas Phase Monohydrated Nicotine: Implications for Nicotine’s Native Structure in the Acetylcholine Binding Protein

We report a joint experimental–theoretical study of the never reported before structure and infrared spectra of gas phase monohydrated nicotine (NIC) and nornicotine (NOR) and use them to assign their protonation sites. NIC’s biological activity is strongly affected by its protonation site, namely, the pyrrolidine (Pyrro-NICH+, anticipated active form) and pyridine (Pyri-NICH+) forms; however, these have yet to be directly experimentally determined in either the nicotinic acetylcholine receptor (nAChR, no water present) or the acetylcholine-binding protein (AChBP, a single water molecule is present) but can only be inferred to be Pyrro-NICH+ from the intermolecular distance to the neighboring residues (i.e., tryptophan). Our temperature-controlled double ion trap infrared spectroscopic experiments assisted by the collisional stripping method and high-level theoretical calculations yield the protonation ratio of Pyri:Pyrro = 8:2 at 240 K for the gas phase NICH+···(H2O) complex, which resembles the molecular cluster present in the AChBP. Therefore, a single water molecule in the gas phase enhances this ratio in NICH+ relative to the 3:2 for the nonhydrated gas phase NICH+ in a trend that contrasts with the almost exclusive presence of Pyrro-NICH+ in aqueous solution. In contrast, the Pyri-NORH+ protomer is exclusively observed, a fact that may correlate with its weaker biological activity

Switching of Protonation Sites in Hydrated Nicotine via a Grotthuss Mechanism

The switching of the protonation sites in hydrated nicotine, probed by experimental infrared (IR) spectroscopy and theoretical ab initio calculations, is facilitated via a Grotthuss instead of a bimolecular proton transfer (vehicle) mechanism at the experimental temperature (T = 130 K) as unambiguously confirmed by experiments with deuterated water. In contrast, the bimolecular vehicle mechanism is preferred at higher temperatures (T = 300 K) as determined by theory. The Grotthuss mechanism for the concerted proton transfer results in the production of nicotine’s bioactive and addictive pyrrolidine-protonated (Pyrro-H+) protomer with just 5 water molecules. Theoretical analysis suggests that the concerted proton transfer occurs via hydrogen-bonded bridges consisting of a 3 water molecule “core” that connects the pyridine protonated (Pyri-H+) with the pyrrolidine-protonated (Pyrro-H+) protomers. Additional water molecules attached as acceptors to the hydrogen-bonded “core” bridge result in lowering the reaction barrier of the concerted proton transfer down to less than 6 kcal/mol, which is consistent with the experimental observations

Absorption Spectra and Photochemical Reactions in a Unique Photoactive Protein, Middle Rhodopsin MR

Photoactive proteins with cognate chromophores are widespread in organisms, and function as light-energy converters or receptors for light-signal transduction. Rhodopsins, which have retinal (vitamin A aldehyde) as their chromophore within their seven transmembrane α-helices, are classified into two groups, microbial (type-1) and animal (type-2) rhodopsins. In general, light absorption by type-1 or type-2 rhodopsins triggers a <i>trans</i>–<i>cis</i> or <i>cis</i>–<i>trans</i> isomerization of the retinal, respectively, initiating their photochemical reactions. Recently, we found a new microbial rhodopsin (middle rhodopsin, MR), binding three types of retinal isomers in its original state: all-<i>trans</i>, 13-<i>cis</i>, and 11-<i>cis</i>. Here, we identified the absolute absorption spectra of MR by a combination of high performance liquid chromatography (HPLC) and UV–vis spectroscopy under varying light conditions. The absorption maxima of MR with all-<i>trans</i>, 13-<i>cis</i>, or 11-<i>cis</i> retinal are located at 485, 479, and 495 nm, respectively. Their photocycles were analyzed by time-resolved laser spectroscopy using various laser wavelengths. In conclusion, we propose that the photocycles of MR are MR­(<i>trans</i>) → MR_K:lifetime = 93 μs → MR_M:lifetime = 12 ms → MR, MR­(13-<i>cis</i>) → MR_O‑like:lifetime = 5.1 ms → MR, and MR­(11-<i>cis</i>) → MR_K‑like:lifetime = 8.2 μs → MR, respectively. Thus, we demonstrate that a single photoactive protein drives three independent photochemical reactions