Mechanisms of Double Proton Transfer. Theory and Applications

Systematic analysis of electronic barrier heights and widths for concerted proton transfer in cyclic hydrogen bonded clusters: (HF)n, (HCl)n and (H2O)n where n = 3, 4, 5

The MP2 and CCSD(T) methods are paired with correlation consistent basis sets as large as aug-cc-pVQZ to optimize the structures of the cyclic minima for (HF)n, (HCl)n and (H2O)n where n = 3-5, as well as the corresponding transition states (TSs) for concerted proton transfer (CPT). MP2 and CCSD(T) harmonic vibrational frequencies confirm the nature of each minimum and TS. Both conventional and explicitly correlated CCSD(T) computations are employed to assess the electronic dissociation energies and barrier heights for CPT near the complete basis (CBS) limit for all 9 clusters. Results for (HF)n are consistent with prior studies identifying Cnh and Dnh point group symmetry for the minima and TSs, respectively. Our computations also confirm that CPT proceeds through Cs TS structures for the C1 minima of (H2O)3 and (H2O)5, whereas the process goes through a TS with D2d symmetry for the S4 global minimum of (H2O)4. This work corroborates earlier findings that the minima for (HCl)3, (HCl)4 and (HCl)5 have C3h, S4 and C1 point group symmetry, respectively, and that the Cnh structures are not minima for n = 4 and 5. Moreover, our computations show the TSs for CPT in (HCl)3, (HCl)4 and (HCl)5 have D3h, D2d, and C2 point group symmetry, respectively. At the CCSD(T) CBS limit, (HF)4 and (HF)5 have the smallest electronic barrier heights for CPT (≈15 kcal mol-1 for both), followed by the HF trimer (≈21 kcal mol-1). The barriers are appreciably higher for the other clusters (around 27 kcal mol-1 for (H2O)4 and (HCl)3; roughly 30 kcal mol-1 for (H2O)3, (H2O)5 and (HCl)4; up to 38 kcal mol-1 for (HCl)5). At the CBS limit, MP2 significantly underestimates the CCSD(T) barrier heights (e.g., by ca. 2, 4 and 7 kcal mol-1 for the pentamers of HF, H2O and HCl, respectively), whereas CCSD overestimates these barriers by roughly the same magnitude. Scaling the barrier heights and dissociation energies by the number of fragments in the cluster reveals strong linear relationships between the two quantities and with the magnitudes of the imaginary vibrational frequency for the TSs.

Synthesis of 3,3'-dihydroxy-2,2'-diindan-1,1'-dione derivatives for tautomeric organic semiconductors exhibiting intramolecular double proton transfer

To investigate potential applications of the 3,3'-dihydroxy-2,2'-biindan-1,1'-dione (BIT) structure as an organic semiconductor with intramolecular hydrogen bonds, a new synthetic route under mild conditions is developed based on the addition reaction of 1,3-dione to ninhydrin and the subsequent hydrogenation of the hydroxyl group. This route affords several new BIT derivatives, including asymmetrically substituted structures that are difficult to access by conventional high-temperature synthesis. The BIT derivatives exhibit rapid tautomerization by intramolecular double proton transfer in solution. The tautomerizations are also observed in the solid state by variable temperature measurements of X-ray diffractometry and magic angle spinning 13C solid-state NMR. Possible interplay between the double proton transfer and the charge transport is suggested by quantum chemical calculations. The monoalkylated BIT derivative with a lamellar packing structure suitable for lateral charge transport in films shows a hole mobility of up to 0.012 cm2 V-1 s-1 with a weak temperature dependence in an organic field effect transistor.

Reducing the Cost of Neural Network Potential Generation for Reactive Molecular Systems

Although machine learning potentials have recently had a substantial impact on molecular simulations, the construction of a robust training set can still become a limiting factor, especially due to the requirement of a reference ab initio simulation that covers all the relevant geometries of the system. Recognizing that this can be prohibitive for certain systems, we develop the method of transition tube sampling that mitigates the computational cost of training set and model generation. In this approach, we generate classical or quantum thermal geometries around a transition path describing a conformational change or a chemical reaction using only a sparse set of local normal mode expansions along this path and select from these geometries by an active learning protocol. This yields a training set with geometries that characterize the whole transition without the need for a costly reference trajectory. The performance of the method is evaluated on different molecular systems with the complexity of the potential energy landscape increasing from a single minimum to a double proton-transfer reaction with high barriers. Our results show that the method leads to training sets that give rise to models applicable in classical and path integral simulations alike that are on par with those based directly on ab initio calculations while providing the computational speedup we have come to expect from machine learning potentials.

Metastable Charged Dimers in Organometallic Species: A Look into Hydrogen Bonding between Metallocene Derivatives

Multiply charged complexes bound by noncovalent interactions have been previously described in the literature, although they were mostly focused on organic and main group inorganic systems. In this work, we show that similar complexes can also be found for organometallic systems containing transition metals and deepen in the reasons behind the existence of these species. We have studied the structures, binding energies, and dissociation profiles in the gas phase of a series of charged hydrogen-bonded dimers of metallocene (Ru, Co, Rh, and Mn) derivatives isoelectronic with the ferrocene dimer. Our results indicate that the carboxylic acid-containing dimers are more strongly bonded and present larger barriers to dissociation than the amide ones and that the cationic complexes tend to be more stable than the anionic ones. Additionally, we describe for the first time the symmetric proton transfer that can occur while in the metastable phase. Finally, we use a density-based energy decomposition analysis to shine light on the nature of the interaction between the dimers.

A Structure-Based Gaussian Expansion for Quantum Reaction Dynamics in Molecules: Application to Hydrogen Tunneling in Malonaldehyde

We developed an approximate method for quantum reaction dynamics simulations, namely, a structure-based Gaussian (SBG) expansion approach, where SBG bases for the expansion of the wave function Ψ, expressed by a product of single-atom Cartesian Gaussians centered at the positions of respective nuclei, are mainly placed around critical structures on reaction pathways such as on the intrinsic reaction coordinate (IRC) through a transition state. In the present approach, the "pseudo-lattice points" at which SBGs are deployed are selected in a perturbative manner so as to make moderate the expansion length. We first applied the SBG idea to a two-dimensional quadruple-well model and obtained accurate tunneling splitting values between the lowest four states. We then applied it to hydrogen tunneling in malonaldehyde and achieved a tunneling splitting of 27.1 cm^-1 with only 875 SBGs at the MP2/6-31G(d,p) level of theory, in good agreement with 25 cm^-1 by the more elaborate multiconfiguration time-dependent Hartree method. Reasonable results were also obtained for singly and doubly deuterated malonaldehyde. We analyzed the tunneling states by utilizing expansion coefficients of individual SBGs and found that 40-45% of the SBGs in Ψ are nonplanar structures and SBGs away from the IRC contribute a little to hydrogen transfer.

Searching for correlations between geometric and spectroscopic parameters of intramolecular hydrogen bonds in porphyrin-like macrocycles

Chemical bond lengths and angles are characteristic structural parameters of a molecule. Similarly, the frequencies of the vibrational modes and the NMR chemical shifts are unique "chemical fingerprints" specific to a compound. These are the basic parameters describing newly obtained compounds and enabling their identification. Intramolecular hydrogen bonding significantly influences the physicochemical properties of macrocyclic compounds with a porphyrin-like structure. This work presents the verification for correlations between geometric and spectroscopic parameters related to hydrogen bonds in this type of macrocyclic compounds. In particular, such relationships were investigated for a large group of porphyrin, porphycene, and dibenzotetraaza[14]annulene derivatives and a group of other macrocycles with similar structure. A very strong linear correlation was found only between the vibrational frequencies of the NH groups involved in a hydrogen bond and the length of this bond, which applied to all macrocyclic compounds of this type. Several other relationships were found between spectroscopic (IR, Raman, NMR) and geometric (X-ray) parameters, highlighting differences and similarities between different families of macrocycles. Apart from providing a better understanding of the nature of hydrogen bonds and their characteristics in porphyrin-like macrocyclic compounds, these relationships will facilitate the identification of new macrocycles and the extrapolation of their spectroscopic properties.

Non-Covalent Forces in Naphthazarin-Cooperativity or Competition in the Light of Theoretical Approaches

Non-covalent interactions responsible for molecular features and self-assembly in Naphthazarin C polymorph were investigated on the basis of diverse theoretical approaches: Density Functional Theory (DFT), Diffusion Quantum Monte Carlo (DQMC), Symmetry-Adapted Perturbation Theory (SAPT) and Car-Parrinello Molecular Dynamics (CPMD). The proton reaction paths in the intramolecular hydrogen bridges were studied. Two potential energy minima were found indicating that the proton transfer phenomena occur in the electronic ground state. Diffusion Quantum Monte Carlo (DQMC) and other levels of theory including Coupled Cluster (CC) employment enabled an accurate inspection of Potential Energy Surface (PES) and revealed the energy barrier for the proton transfer. The structure and reactivity evolution associated with the proton transfer were investigated using Harmonic Oscillator Model of Aromaticity - HOMA index, Fukui functions and Atoms In Molecules (AIM) theory. The energy partitioning in the studied dimers was carried out based on Symmetry-Adapted Perturbation Theory (SAPT) indicating that dispersive forces are dominant in the structure stabilization. The CPMD simulations were performed at 60 K and 300 K in vacuo and in the crystalline phase. The temperature influence on the bridged protons dynamics was studied and showed that the proton transfer phenomena were not observed at 60 K, but the frequent events were noticed at 300 K in both studied phases. The spectroscopic signatures derived from the CPMD were computed using Fourier transformation of autocorrelation function of atomic velocity for the whole molecule and bridged protons. The computed gas-phase IR spectra showed two regions with OH absorption that covers frequencies from 2500 cm−1 to 2800 cm−1 at 60 K and from 2350 cm−1 to 3250 cm−1 at 300 K for both bridged protons. In comparison, the solid state computed IR spectra revealed the environmental influence on the vibrational features. For each of them absorption regions were found between 2700–3100 cm−1 and 2400–2850 cm−1 at 60 K and 2300–3300 cm−1 and 2300–3200 cm−1 at 300 K respectively. Therefore, the CPMD study results indicated that there is a cooperation of intramolecular hydrogen bonds in Naphthazarin molecule.

The Role of Proton Transfer on Mutations

Hydrogen bonds play a critical role in nucleobase studies as they encode genes, map protein structures, provide stability to the base pairs, and are involved in spontaneous and induced mutations. Proton transfer mechanism is a critical phenomenon that is related to the acid-base characteristics of the nucleobases in Watson-Crick base pairs. The energetic and dynamical behavior of the proton can be depicted from these characteristics and their adjustment to the water molecules or the surrounding ions. Further, new pathways open up in which protonated nucleobases are generated by proton transfer from the ionized water molecules and elimination of a hydroxyl radical in this review, the analysis will be focused on understanding the mechanism of untargeted mutations in canonical, wobble, Hoogsteen pairs, and mutagenic tautomers through the non-covalent interactions. Further, rare tautomer formation through the single proton transfer (SPT) and the double proton transfer (DPT), quantum tunneling in nucleobases, radiation-induced bystander effects, role of water in proton transfer (PT) reactions, PT in anticancer drugs-DNA interaction, displacement and oriental polarization, possible models for mutations in DNA, genome instability, and role of proton transfer using kinetic parameters for RNA will be discussed.

Spectroscopy and Tautomerization Studies of Porphycenes

Tautomerization in porphycenes, constitutional isomers of porphyrins, is strongly entangled with spectral and photophysical parameters. The intramolecular double hydrogen transfer occurring in the ground and electronically excited states leads to uncommon spectroscopic characteristics, such as depolarized emission, viscosity-dependent radiationless depopulation, and vibrational-mode-specific tunneling splittings. This review starts with documentation of the electronic spectra of porphycenes: Absorption and magnetic circular dichroism are discussed, together with their analysis based on the perimeter model. Next, photophysical characteristics are presented, setting the stage for the final part, which discusses the developments in research on tautomerism. Porphycenes have been studied in different experimental regimes: molecules in condensed phases, isolated in supersonic jets and helium nanodroplets, and, recently also on the level of single molecules investigated by optical and scanning probe microscopies. Because of the rich and detailed information obtained from these diverse investigations, porphycenes emerge as very good models for studying the complex, multidimensional phenomena involved in the process of intramolecular double hydrogen transfer.

Kinetics of Coupled Double Proton and Deuteron Transfer in Hydrogen-Bonded Ribbons of Crystalline Pyrazole-4-carboxylic Acid

The proton tautomerism of pyrazole-4-carboxylic acid (PCA) has been studied by a combination of 15N CPMAS and 2H NMR spectroscopy and relaxometry. Down to 250 K, PCA forms a hydrogen bonded ribbon where adjacent carboxylic and pyrazole groups are linked by an OH···N and an O···HN hydrogen bond, forming either the tautomeric state A or B. Down to about 250 K, the tautomerism is fast on the NMR timescale and degenerate, corresponding to a phase exhibiting dynamic proton disorder. At lower temperatures, a transition to an ordered phase is observed with localized protons, assigned to an all-syn conformation adopting the sequence of tautomeric states ..ABABA.. The longitudinal 15N relaxation times T 1 of PCA-15N2 have been measured at 9.12 MHz (2.1 T). Because of the low field, a chemical shift anisotropy mechanism could be neglected, and the data were analyzed in terms of a dipolar 1H-15N relaxation mechanism, yielding the rate constants k HH. The rate constants k HD and k DD were obtained from the measurement and analysis of the 2H T 1 values of PCA-15N1-d0.9 and PCA-15N1-d0.1 measured at 46.03 MHz. Within the margin of error, no kinetic isotope effects could be detected, in contrast to previous results reported for the very fast tautomerism of solid benzoic acid dimers and the much slower tautomerism of solid 3,5-diphenyl-4-brompyrazole (DPBrP) dimers. The Arrhenius curves of all three systems were simulated using the Bell–Limbach tunneling model. Evidence for a major heavy atom motion for the tautomerism of PCA is obtained, associated with small angle reorientation of PCA molecules around the molecular axis. The observed proton order-disorder transition and the mechanism of the observed rate process are discussed in terms of a coupling of adjacent tautomeric states.