Single Protonation Research Articles

Photoredox-Catalyzed Markovnikov Hydroamination of Alkenes with Azoles.

A visible-light induced intermolecular hydroamination of alkenes with azoles is reported, delivering pharmaceutically valuable N-benzyl azoles in high yields with excellent Markovnikov selectivity. Mechanistic studies suggest that the process is initiated by the energy transfer of the excited photocatalyst with alkenes, followed by the single electron reduction, protonation, and subsequent single electron oxidation to afford the key alkyl carbocation intermediate. This protocol exhibits advantages of broad functional group tolerance, excellent atom economy, high efficiency, and mild reaction conditions.

Silyl Radical as an Isocyanide Transfer Agent for Giese-Type Reactions Involving Aliphatic Amines.

Herein we report silyl radicals serve as isocyanide transfer agents for Giese-type reaction from aliphatic amines and electron-deficient olefins. α-Primary, α-secondary, and sterically encumbered α-tertiary primary amines could be easily converted into isocyanides for coupling with electron-deficient olefins by employing latent silyl radicals under visible light irradiation. Notably, the abstraction of silane-mediated isocyanide not only enables voltage-independent activation of strong C-N bonds but also represents a mechanistic alternative Giese-type reaction in which single electron reduction and protonation processes are replaced by direct hydrogen atom transfer. This transformation occurs under photoinduced catalyst-free conditions and exhibits excellent functional group compatibility and mild reaction conditions.

Retinal photoisomerization versus counterion protonation in light and dark-adapted bacteriorhodopsin and its primary photoproduct

Discovered over 50 years ago, bacteriorhodopsin is the first recognized and most widely studied microbial retinal protein. Serving as a light-activated proton pump, it represents the archetypal ion-pumping system. Here we compare the photochemical dynamics of bacteriorhodopsin light and dark-adapted forms with that of the first metastable photocycle intermediate known as “K”. We observe that following thermal double isomerization of retinal in the dark from bio-active all-trans 15-anti to 13-cis, 15-syn, photochemistry proceeds even faster than the ~0.5 ps decay of the former, exhibiting ballistic wave packet curve crossing to the ground state. In contrast, photoexcitation of K containing a 13-cis, 15-anti chromophore leads to markedly multi-exponential excited state decay including much slower stages. QM/MM calculations, aimed to interpret these results, highlight the crucial role of protonation, showing that the classic quadrupole counterion model poorly reproduces spectral data and dynamics. Single protonation of ASP212 rectifies discrepancies and predicts triple ground state structural heterogeneity aligning with experimental observations. These findings prompt a reevaluation of counter ion protonation in bacteriorhodopsin and contribute to the broader understanding of its photochemical dynamics.

Modeling pH-Dependent Biomolecular Photochemistry.

The tuning mechanism of pH can be extremely challenging to model computationally in complex biological systems, especially with respect to the photochemical properties. This article reports a protocol aimed at modeling pH-dependent photodynamics using a combination of constant-pH molecular dynamics and semiclassical nonadiabatic molecular dynamics simulations. With retinal photoisomerization in Anabaena sensory rhodopsin (ASR) as a testbed, we show that our protocol produces pH-dependent photochemical properties, such as the isomerization quantum yield or decay rates. We decompose our results into single-titrated residue contributions, identifying some key tuning amino acids. Additionally, we assess the validity of the single protonation state picture to represent the system at a given pH and propose the most populated protein charge state as a compromise between cost and accuracy.

Automatic Rhodopsin Modeling with Multiple Protonation Microstates.

Automatic Rhodopsin Modeling (ARM) is a simulation protocol providing QM/MM models of rhodopsins capable of reproducing experimental electronic absorption and emission trends. Currently, ARM is restricted to a single protonation microstate for each rhodopsin model. Herein, we incorporate an extension of the minimal electrostatic model (MEM) into the ARM protocol to account for all relevant protonation microstates at a given pH. The new ARM+MEM protocol determines the most important microstates contributing to the description of the absorption spectrum. As a test case, we have applied this methodology to simulate the pH-dependent absorption spectrum of a toy model, showing that the single-microstate picture breaks down at certain pH values. Subsequently, we applied ARM+MEM toAnabaenasensory rhodopsin, confirming an improved description of its absorption spectrum when the titration of several key residues is considered.

Single protonation of the reduced quinone in respiratory complex I drives four-proton pumping.

Complex I is a key proton-pumping enzyme in bacterial and mitochondrial respiratory electron transport chains. Using quantum chemistry and electrostatic calculations, we have examined the pKa of the reduced quinone QH-/QH2 in the catalytic cavity of complex I. We find that pKa (QH-/QH2) is very high, above 20. This means that the energy of a single protonation reaction of the doubly reduced quinone (i.e. the reduced semiquinone QH-) is sufficient to drive four protons across the membrane with a potential of 180 mV. Based on these calculations, we propose a possible scheme of redox-linked proton pumping by complex I. The model explains how the energy of the protonation reaction can be divided equally among four pumping units of the pump, and how a single proton can drive translocation of four additional protons in multiple pumping blocks.

A Computational Study of the Dissociation of CaS Nanoclusters in the Extracellular Fluid of Cancer Cells: the Effect of pH in the Structure and Stability of Protonated CaS Nanoclusters

The acidic pH found in the extracellular fluid of many cancer tumors is an important difference from the slightly basic pH found in the corresponding benign cells. Contrary to common anti‐cancer drugs that have significant side effects in healthy cells, calcium sulfide (CaS) nanoclusters have shown to induce apoptosis selectively in human lung, skin, and breast cancer cell lines in vitro. We hypothesize that CaS nanostructures selectively dissociate in the characteristic acidic extracellular environments of cancer cells into free Ca2+ ions and sulfides such as H2S, HS‐ and S2‐, which can be proved via bench and computational experiments. Theoretical calculations at the DFT/B3LYP/DGVZVP level of theory of bare and protonated (CaS)n clusters (n = 1 to 4) were performed to address this hypothesis using the Gaussian 16W and GaussView 6.0.16 programs by varying the number of protons in a CaS cluster to assess cluster stability and reaction pathways in both acidic and neutral media. The total cluster energy decreases with the number of monomer units (n) in the (CaS)n clusters. The CaS monomer and dimer are more stable in water than in their corresponding standard state by about 336kJ/mol and 390kJ/mol, respectively. A single protonation of a sulfur atom in the solvated monomer results in an increase in the Ca‐S bond length from 2.55Å to 2.73Å, indicative of increasing drive to dissociate. It requires protonation of a sulfur atom by two hydrogen atoms to dissociate the cluster into free Ca2+ and H2S. Water facilitates the dissociation of the clusters when the sulfur atom is bonded by two protons. The products of the reaction of the solvated (CaSH2)2+ is more stable than the corresponding gas phase cluster ion by a significant 1479 kJ/mole. These results are consistent with the dissociation of CaS clusters to free Ca2+ and H2S in acidic media like the one found in the extracellular fluid of malignant tumors. Ca2+ ions are known to cause cell damage in cytosolic concentrations higher than 500nM. The biochemistry of H2S is still under study by several groups worldwide but it is generally accepted that it can be genotoxic and induce apoptosis. Therefore, CaS nanoclusters are promising drugs to selectively inhibit malignant tumor growth with little impact on benign tissue. The results are discussed in terms of the basic requirements of a (CaS)n‐based formulation for cancer treatment.

Enhancing magnetic coupling through protonation of benzylideneaniline-bridged diradicals and comparison with stilbene- and azobenzene-based diradicals.

Taking nitroxide radicals as spin sources, we explore the intramolecular magnetic coupling interactions of the trans- and cis-forms of benzylideneaniline (BA)-bridged diradicals, in which the central -CH[double bond, length as m-dash]N- unit can undergo single protonation to convert to its protonated counterpart or vice versa. The calculated results for these two pairs of diradicals (protonated versus unprotonated trans and cis forms) verify that the signs of their magnetic coupling constants J do not change, but the magnitudes significantly increase after protonation. In the structure, the better conjugation of the protonated trans diradical and two reduced CCNC and CCCN torsion angles of the protonated cis one make for a more efficient spin transport, promoting the spin polarization, thus leading to larger spin couplings. In terms of mechanism, the proton-induced magnetic enhancement should be attributed to strong participation of the coupler BA through its lowest unoccupied molecular orbital (LUMO) with a lower energy level after protonation, and the small HOMO-LUMO (HOMO: highest occupied molecular orbital) gap of the coupler BA through protonation is crucial in explaining such remarkable spin-coupling enhancement. Furthermore, different linking modes of the radical groups to the couplers are also considered to confirm our conclusions. In addition, we also make a comparison of the magnetic coupling strengths among their isoelectronic analogues of BA-, AB- and stilbene-bridged nitroxide diradicals before or after protonation, and find a linear correlation among them. It should be noted that the magnetic behaviors of all these diradicals obey the spin alternation rule and singly occupied molecular orbital (SOMO) effect. This work provides helpful information for the rational design of promising magnetic molecular switches.

A new grand-canonical potential for the thermodynamic description of the reactions in solutions with constant pH

This review emphasizes the necessity to perform additional Legendre transformation of the free energy for a correct thermodynamic description of reactions in the environment with constant pH. The power of this new thermodynamic potential (Gibbs-Alberty free energy ΔGA0) is demonstrated on three examples. First example, a DFT-based study of interaction of cisplatin with glycine, demonstrates the grand canonical character of the potential, which is manifested by the fact that ΔGA0 energy is not dependent on a concrete form of molecules (protonated or deprotonated) used for energy evaluation. This independence on concrete molecular form strongly contradicts to the standard quantum–mechanical approach where only a single protonation state is used to represent each molecule. Second example, the reaction of hydroxo form of cisplatin with methionine which exhibits quite interesting pH dependency, demonstrates that it is possible to predict metal coordination sites of the amino acid based on proton (hydronium) concentration in solution: in neutral environment the metal binds to thio-group, in basic solutions to amino-group of the amino acid, and in acidic solutions to carboxyl group. This prediction is in the remarkable agreement with the pH-dependent migration of the coordination site observed experimentally in Reedijk laboratory. The final example is the combination of the approach with QM/MM MD simulations of the interaction of (hydrated) mercury cation with thymine. In this reaction, ΔGA0 changes from endergonic to exergonic when the pH passes from acidic to basic values.

A theoretical investigation on the structures of (NH3)·(H2SO4)·(H2O)0‐14 clusters

AbstractTernary clusters (NH3)·(H2SO4)·(H2O)n have been widely studied. However, the structures and binding energies of relatively larger cluster (n > 6) remain unclear, which hinders the study of other interesting properties. Ternary clusters of (NH3)·(H2SO4)·(H2O)n, n = 0‐14, were investigated using MD simulations and quantum chemical calculations. For n = 1, a proton was transferred from H2SO4 to NH3. For n = 10, both protons of H2SO4 were transferred to NH3 and H2O, respectively. The NH4+ and HSO4− formed a contact ion‐pair [NH4+‐HSO4−] for n = 1‐6 and a solvent separated ion‐pair [NH4+‐H2O‐HSO4−] for n = 7‐9. Therefore, we observed two obvious transitions from neutral to single protonation (from H2SO4 to NH3) to double protonation (from H2SO4 to NH3 and H2O) with increasing n. In general, the structures with single protonation and solvated ion‐pair were higher in entropy than those with double protonation and contact ion‐pair of single protonation and were thus preferred at higher temperature. As a result, the inversion between single and double protonated clusters was postponed until n = 12 according to the average binding Gibbs free energy at the normal condition. These results can serve as a good start point for studies of the other properties of these clusters and as a model for the solvation of the [H2SO4‐NH3] complex in bulk water.

Approach to the Mechanism of Hydrogen Evolution Electrocatalyzed by a Model Co Clathrochelate: A Theoretical Study by Density Functional Theory.

The hydrogen evolution reaction (HER) has attracted much attention within the scientific community because of increasing demands of modern society for clean and renewable energy sources. Molecular complexes of 3d-transition metals, such as cobalt, hold potential to replace platinum for the HER in acidic media. Among these, cage complexes such as tris-glyoximate metal clathrochelates, have demonstrated promising catalytic properties towards the HER. However, it is not clear whether the catalytic activity of this molecule stems from metal-centered activation of H+ , due to a low oxidation state of the metal stabilized by the surrounding organic cage, or if it is the organic cage playing a further cooperative role in bringing protons together. Herein, we report on a density functional theory study of two possible mechanisms for the HER catalyzed by a model Co clathrochelate. To assess the putative ligand involvement in the mechanism, several combinations of single and double protonation sites were investigated. The structural and energetic analysis of relevant intermediates suggests that the electrocatalytic mechanism is not based on the cooperation between the ligand and the metal. Instead, it is mainly due to the activation of H+ by the Co metallocenter. Our calculations further suggest that the last step in the mechanism is a proton coupled electron transfer step.

One‐Pot Synthesis of Contracted and Expanded Porphyrins with meso‐CF3 Groups

AbstractCorrole and sapphyrin with the smallest meso‐substituents reported so far were prepared in a one‐pot synthesis that relies on a non‐aldehydic precursor for introducing CF3 groups. The substantial amounts of products obtained by this facile pathway allowed for the full characterization of 5,10,15‐tris(trifluoromethyl)corrole, the access to a variety of stable chelates thereof and investigations that disclose the unique structural and chemical properties induced by the CF3 substituents. The novel 5,10,15,20‐tetra(trifluoromethyl)sapphyrin undergoes only single protonation, which according to its crystal structure is stabilized by favorable non‐bonding F/H interaction between the meso‐CF3 and the inverted pyrrolic NH.

One-Pot Synthesis of Contracted and Expanded Porphyrins with meso-CF3 Groups.

Corrole and sapphyrin with the smallest meso-substituents reported so far were prepared in a one-pot synthesis that relies on a non-aldehydic precursor for introducing CF3 groups. The substantial amounts of products obtained by this facile pathway allowed for the full characterization of 5,10,15-tris(trifluoromethyl)corrole, the access to a variety of stable chelates thereof and investigations that disclose the unique structural and chemical properties induced by the CF3 substituents. The novel 5,10,15,20-tetra(trifluoromethyl)sapphyrin undergoes only single protonation, which according to its crystal structure is stabilized by favorable non-bonding F/H interaction between the meso-CF3 and the inverted pyrrolic NH.

Protonation-Enhanced Antiferromagnetic Couplings in Azobenzene-Bridged Diradicals

Proton-induced magnetic enhancement in an organic diradical is an appealing phenomenon. Here, taking two nitroxide groups as spin sources, we predict the magnetic properties of the trans and cis forms of azobenzene (AB)-bridged diradicals in which the central −N═N– unit can undergo single protonation to convert to its protonated counterpart or vice versa. The calculated results for these two pairs of diradicals (protonated versus unprotonated trans and cis forms) indicate that the signs of their magnetic coupling constants J do not change, but the magnitudes remarkably increase after protonation from −716.4 to −1787.1 cm–1 for the trans form and from −388.1 to −1227.9 cm–1 for the cis form, respectively. Such noticeable magnetic enhancements induced by protonation are mainly attributed to the strong mediating role of the coupler AB between two radical groups through its lowest unoccupied molecular orbital (LUMO) with a lower energy level after protonation. The planar structure for the protonated trans dir...

Conjugation of chlorins with spermine enhances phototoxicity to cancer cells in vitro

Photodynamic therapy (PDT) is one of the most promising methods of specific cancer treatment. However, commercially available photosensitizers (PSs) show significant drawbacks, such as side toxicity, low penetration ability, low blood solubility, low tumor selectivity etc. In addition, as was shown previously, a conjugation of polyamines with several toxic agents led to an increased toxicity to cancer cells. Here, we synthesized conjugates of two chlorine photosensitizers, purpurin 18 and pheophorbide a, with spermine in natural and Boc-protected form. Using specialized software, we calculated octanol-water partition coefficients for single protonation state (logP) of single PSs and PS/spermine conjugates. We found that the addition of spermine to chlorine PSs shifted the logP towards higher hydrophilicity in comparison to logP of single chlorines. In vitro studies on several cancer cells indicated that conjugation of purpurin 18 with spermine increased its retention in cancer cells. Using various concentrations of this conjugate, we found that lower concentrations (under 0.2μM) of purpurin 18/spermine conjugate launched apoptosis in HeLa cells. This combined with its high phototoxicity makes the purpurin 18/spermine conjugate a promising photosensitizer for PDT. Obtained results might serve as a basis for further studies of this potential third-generation PS on mammalian models in vivo.

Protonation of ninhydrin and indan-1,2,3-trione revisited: A combined theoretical and experimental study

The literature data on protonation of indan-1,2,3-trione and ninhydrin (indantrione hydrate) in acidic media are inconsistent, formation of dications at pH 3 and very low extent of protonation in superacid CF3SO3H were claimed. Our combined theoretical (DFT, MP2, CCSD) and experimental (NMR) study has shown that indantrione undergoes single protonation in CF3SO3H resulting in monocation formation. In more strong superacid FSO3H-SbF5 dication is formed, but, contrary to the literary data, trication is not formed even in this superacid. Significant dependence of 13C NMR chemical shifts of indantrione on media acidity allows using this compound as a convenient indicator of acidity in a broad range, from H0 −3 to −25.

Arsenic Adsorption on Lanthanum-Impregnated Activated Alumina: Spectroscopic and DFT Study.

Rare earth-modified adsorbents (REMAs) have been widely used to remove oxyanion pollutants from water, including arsenic (As). However, the molecular-level structural information and reactions at the liquid/solid interface are still murky, which limits the design of applicable REMAs. Herein, a lanthanum-impregnated activated alumina (LAA) was synthesized as a representative REMA, and its As uptake mechanisms were explored using multiple complementary characterization techniques. Our adsorption experiments showed that LAA exhibited 2-3 times higher As adsorption capacity than AA. In contrast to the bidentate configuration formed on most metal oxide surfaces, our EXAFS and DFT results suggest that As(III) and As(V) form monodentate surface complexes on LAA through As-O-La coordinative bonding. In situ flow cell ATR-FTIR observed a strong dependence of As-O peak positions on pH, which could be interpreted as the change in the fractions of As(V) surface complexes with zero- to double-protonation on LAA, AA, and LaOOH. As(V) on LAA existed as singly and doubly protonated surface species, and the pKa of transition from double to single protonation (∼5.8) was lower than that for its soluble counterpart (6.97). The surface reaction and structural configuration were incorporated in a CD-MUSIC model to satisfactorily predict macroscopic As adsorption behaviors. The insights gained from the molecular-level reactions shed light on the design and application of REMAs in environmental remediation for As and its structural analogues.

Computational scheme for pH-dependent binding free energy calculation with explicit solvent.

We present a computational scheme to compute the pH-dependence of binding free energy with explicit solvent. Despite the importance of pH, the effect of pH has been generally neglected in binding free energy calculations because of a lack of accurate methods to model it. To address this limitation, we use a constant-pH methodology to obtain a true ensemble of multiple protonation states of a titratable system at a given pH and analyze the ensemble using the Bennett acceptance ratio (BAR) method. The constant pH method is based on the combination of enveloping distribution sampling (EDS) with the Hamiltonian replica exchange method (HREM), which yields an accurate semi-grand canonical ensemble of a titratable system. By considering the free energy change of constraining multiple protonation states to a single state or releasing a single protonation state to multiple states, the pH dependent binding free energy profile can be obtained. We perform benchmark simulations of a host-guest system: cucurbit[7]uril (CB[7]) and benzimidazole (BZ). BZ experiences a large pKa shift upon complex formation. The pH-dependent binding free energy profiles of the benchmark system are obtained with three different long-range interaction calculation schemes: a cutoff, the particle mesh Ewald (PME), and the isotropic periodic sum (IPS) method. Our scheme captures the pH-dependent behavior of binding free energy successfully. Absolute binding free energy values obtained with the PME and IPS methods are consistent, while cutoff method results are off by 2 kcal mol(-1) . We also discuss the characteristics of three long-range interaction calculation methods for constant-pH simulations.

Molecular Spectral Analysis and Ab Initio Calculations of bis(3-aminopyridinium) Tetrachlorocuprate (II), 3-Ammoniumpyridinium Tetrachlorocuprate (II), and bis(3-aminopyridinium) Hexachlorodicuprate (II)

The aromatic character, distortion, and stabilization as a result of single and double protonation of 3-aminopyridine like three different complex salts were studied by infrared-, ultraviolet spectral analysis, proton nuclear magnetic resonance, and quantum chemical ab initio calculations. Linear-dichroic infrared spectroscopy was applied for identification of the infrared bands. The correlation structure-spectroscopic properties of the model systems are determined: bis(3-aminopyridinium) tetrachlorocuprate (II) salt, where the ring nitrogen atom participates in protonation; 3-ammoniumpyridinium tetrachlorocuprate (II) salt, where both nitrogen atoms are protonated; and a complex with copper (II) bis(3-aminopyridinium) hexachlorodicuprate (II), where the metal ion is coordinated through amino group.

The use of chromium(III) to supercharge peptides by protonation at low basicity sites.

The addition of chromium(III) nitrate to solutions of peptides with seven or more residues greatly increases the formation of doubly protonated peptides, [M + 2H](2+), by electrospray ionization. The test compound heptaalanine has only one highly basic site (the N-terminal amino group) and undergoes almost exclusive single protonation using standard solvents. When Cr(III) is added to the solution, abundant [M + 2H](2+) forms, which involves protonation of the peptide backbone or the C-terminus. Salts of Al(III), Mn(II), Fe(III), Fe(II), Cu(II), Zn (II), Rh(III), La(III), Ce(IV), and Eu(III) were also studied. Although several metal ions slightly enhance protonation, Cr(III) has by far the greatest ability to generate [M + 2H](2+). Cr(III) does not supercharge peptide methyl esters, which suggests that the mechanism involves interaction of Cr(III) with a carboxylic acid group. Other factors may include the high acidity of hexa-aquochromium(III) and the resistance of Cr(III) to reduction. Nitrate salts enhance protonation more than chloride salts and a molar ratio of 10:1 Cr(III):peptide produces the most intense [M + 2H](2+). Cr(III) also supercharges numerous other small peptides, including highly acidic species. For basic peptides, Cr(III) increases the charge state (2+ versus 1+) and causes the number of peptide molecules being protonated to double or triple. Chromium(III) does not supercharge the proteins cytochrome c and myoglobin. The ability of Cr(III) to enhance [M + 2H](2+) intensity may prove useful in tandem mass spectrometry because of the resulting overall increase in signal-to-noise ratio, the fact that [M + 2H](2+) generally dissociate more readily than [M + H](+), and the ability to produce [M + 2H](2+) precursors for electron-based dissociation techniques.