Para-Aminobenzoic acid (PABA) is a benchmark molecule to study solvent-induced proton site switching. Protonation of the carboxy and amino groups of PABA generates O- and N-protomers of PABAH+, respectively. Ion mobility mass spectrometry (IMS) and infrared photodissociation (IRPD) studies have claimed that the O-protomer most stable in the gas phase is converted to the N-protomer most stable in solution upon hydration with six water molecules in the gas-phase cluster. However, the threshold size has remained ambiguous because the arrival time distributions in the IMS experiments exhibit multiple peaks. On the other hand, IRPD spectroscopy could not detect the N-protomer for smaller hydrated clusters because of broad background due to annealing required to reduce kinetic trapping. Herein, we report the threshold size for O → N protomer switching without ambiguity using IR spectroscopy in a double ion trap spectrometer from 1300 to 1800 cm-1. The pure O-protomer is prepared by electrospray, and size-specific hydrated clusters are formed in a reaction ion trap. The resulting clusters are transferred into a second cryogenic ion trap and the distribution of O- and N-protomers is determined by mid-IR spectroscopy without broadening. The threshold to promote O → N protomer switching is indeed five water molecules. It is smaller than the value reported previously, and as a result, its pentahydrated structure does not support the Grotthuss mechanism proposed previously. The extent of O → N proton transfer is evaluated by collision-assisted stripping IR spectroscopy, and the N-protomer population increases with the number of water molecules. This result is consistent with the dominant population of the N-protomer in aqueous solution.

pdf/hydration-induced-protomer-switching-in-p-aminobenzoic-acid-286kep5a.pdf

Hydration-induced protomer switching in p-aminobenzoic acid studied by cold double ion trap infrared spectroscopy.

Investigation of crystal structures, spectral (FT-IR and NMR) analysis, DFT, and molecular docking studies of novel piperazine derivatives as antineurotic drugs

This work investigates the motion of a non-relativistic charged particle in the spacetime of a global monopole. We introduce the Schrödinger equation to describe the particle's motion with two interactions by considering the Kratzer and the screened modified Kratzer potential. The problem's eigenfunctions and eigenvalues are obtained by deriving and solving the radial equation. The effective potential encompasses both the Kratzer and electrostatic self-interaction potential and leads to bound states solutions. The energy spectrum is investigated, particularly emphasizing its dependence on the system's physical parameters. The screened modified Kratzer potential, and the screened self-interaction potential reveal an important role in influencing both the effective potential and the energy spectrum. Additionally, it also accommodates the existence of bound states. All these behaviors are illustrated with graphs and discussed in detail. 

Exact and approximate bound state solutions of the Schrödinger equation with a class of Kratzer-type potentials in the global monopole spacetime

Understanding of protomers/deprotomers by combining mass spectrometry and computation

Harmonic bond force constants and bond lengths are shown to generally obey the simple relationships, ke=ζ2Re−3 (hydrides) and ke=10ζ1/2Re−4 (all other bond types), where ζ is the reduced nuclear charge and Re is the equilibrium bond length. Equally simple power-law relationships are found for higher-order bond force constants. Although not spectroscopically accurate, these models are nonetheless of significant heuristic value for identifying strongly multireference states of diatomic molecules (including electronically coupled excited states ill-suited for inclusion in laser-cooling schemes), rationalizing the observed trends in vibrational frequencies for diatomics and/or local mode oscillators within molecules or complexes and estimating and/or validating covalent bonding parameters within molecular mechanics force fields. Particular advantages of our approach over other bond length-strength scaling relationships proposed in the literature include its simplicity and generality and its appropriate asymptotic behavior. Notably, the relationships derived in this work can be used to predict harmonic and higher-order force constant bonds between any pair of atoms in the Periodic Table (including transition metals and lanthanides) without requiring row- or column-dependent parameterization, to accuracies commensurate with conventional force field transferability errors. We therefore anticipate that they will expedite force field development for metal-containing complexes and materials, which are structurally well-characterized but challenging to parameterize ab initio.

Simple, near-universal relationships between bond lengths, strengths, and anharmonicities

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.

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

A Generalized Morse Potential (GMP) is an extension of the Morse Potential (MP) with an additional exponential term and an additional parameter that compensate for MP's erroneous behavior in the long range part of the interaction potential. Because of the additional term and parameter, the vibrational levels of the GMP cannot be solved analytically, unlike the case for the MP. We present several numerical approaches for solving the vibrational problem of the GMP based on Galerkin methods, namely, the Laguerre Polynomial Method (LPM), the Symmetrized LPM, and the Polynomial Expansion Method (PEM), and apply them to the vibrational levels of the homonuclear diatomic molecules B2, O2, and F2, for which high level theoretical near full configuration interaction (CI) electronic ground state potential energy surfaces and experimentally measured vibrational levels have been reported. Overall, the LPM produces vibrational states for the GMP that are converged to within spectroscopic accuracy of 0.01 cm-1 in between 1 and 2 orders of magnitude faster and with much fewer basis functions/grid points than the Colbert-Miller Discrete Variable Representation (CN-DVR) method for the three homonuclear diatomic molecules examined in this study. A Python library that fits and solves the GMP and similar potentials can be downloaded from https://gitlab.com/gds001uw/generalized-morse-solver.

https://aip.scitation.org/doi/pdf/10.1063/5.0103433

Vibrational levels of a generalized Morse potential.

We rely on a total of 23 (cluster size, 8 structural, and 14 connectivity) descriptors to investigate structural patterns and connectivity motifs associated with water cluster aggregation. In addition to the cluster size n (number of molecules), the 8 structural descriptors can be further categorized into (i) one-body (intramolecular): covalent OH bond length (rOH) and HOH bond angle (θHOH), (ii) two-body: OO distance (rOO), OHO angle (θOHO), and HOOX dihedral angle (ϕHOOX), where X lies on the bisector of the HOH angle, (iii) three-body: OOO angle (θOOO), and (iv) many-body: modified tetrahedral order parameter (q) to account for two-, three-, four-, five-coordinated molecules (qm, m = 2, 3, 4, 5) and radius of gyration (Rg). The 14 connectivity descriptors are all many-body in nature and consist of the AD, AAD, ADD, AADD, AAAD, AAADD adjacencies [number of hydrogen bonds accepted (A) and donated (D) by each water molecule], Wiener index, Average Shortest Path Length, hydrogen bond saturation (% HB), and number of non-short-circuited three-membered cycles, four-membered cycles, five-membered cycles, six-membered cycles, and seven-membered cycles. We mined a previously reported database of 4 948 959 water cluster minima for (H2O)n, n = 3-25 to analyze the evolution and correlation of these descriptors for the clusters within 5 kcal/mol of the putative minima. It was found that rOH and % HB correlated strongly with cluster size n, which was identified as the strongest predictor of energetic stability. Marked changes in the adjacencies and cycle count were observed, lending insight into changes in the hydrogen bond network upon aggregation. A Principal Component Analysis (PCA) was employed to identify descriptor dependencies and group clusters into specific structural patterns across different cluster sizes. The results of this study inform our understanding of how water clusters evolve in size and what appropriate descriptors of their structural and connectivity patterns are with respect to system size, stability, and similarity. The approach described in this study is general and can be easily extended to other hydrogen-bonded systems.

Descriptors of water aggregation.

A scale quantifying the strength of intramolecular hydrogen bonds from ir spectroscopy

The Nicotine-Tryptophan Dimer: Probing the Principal Interaction of Nicotine with the Nicotinic Acetylcholine Receptor (nAChR), the Binding Pocket in the Human Brain.

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