Protic Environments Research Articles

Calculation of the geometry, absorption spectrum, and first hyperpolarizability of 4,5-dicyanoimidazole derivatives in solution. A multiscale ASEC-FEG study.

We investigate the effects of solvents on the geometry, absorption spectrum, and first hyperpolarizability of six push-pull molecules, each containing a 4,5-dicyanoimidazole group as an electron acceptor and a N,N-dimethylamino group as an electron donor, with systematically extended π-conjugated systems. Geometry optimizations in dichloromethane, methanol, water, and formamide under normal thermodynamic conditions were performed using the average solvent electrostatic configuration-free energy gradient method, which employs a discrete solvent model. The conformational structure of molecules is moderately affected by the environment, with the π-conjugated system becoming more planar in protic solvents. Solvent effects on the first hyperpolarizability result in marked increases that are in line with the red shifts of the absorption spectrum. The hyperpolarizability of smaller molecules within the set may be significantly influenced by the effects of geometry relaxation in highly polar protic solvents. The results illustrate the role of hydrogen bonds in the structure and electronic properties of push-pull molecules in protic environments. For smaller molecules, hydrogen bonds significantly contribute to enhancing the hyperpolarizability, but the effect of these specific interactions becomes less significant with the length of the π-conjugated system.

Total Synthesis and Structural Plasticity of Kratom Pseudoindoxyl Metabolites.

Mitragynine pseudoindoxyl, a kratom metabolite, has attracted increasing attention due to its favorable side effect profile as compared to conventional opioids. Herein, we describe the first enantioselective and scalable total synthesis of this natural product and its epimeric congener, speciogynine pseudoindoxyl. The characteristic spiro-5-5-6-tricyclic system of these alkaloids was formed through a protecting-group-free cascade relay process in which oxidized tryptamine and secologanin analogues were used. Furthermore, we discovered that mitragynine pseudoindoxyl acts not as a single molecular entity but as a dynamic ensemble of stereoisomers in protic environments; thus, it exhibits structural plasticity in biological systems. Accordingly, these synthetic, structural, and biological studies provide a basis for the planned design of mitragynine pseudoindoxyl analogues, which can guide the development of next-generation analgesics.

Total Synthesis and Structural Plasticity of Kratom Pseudoindoxyl Metabolites**

AbstractMitragynine pseudoindoxyl, a kratom metabolite, has attracted increasing attention due to its favorable side effect profile as compared to conventional opioids. Herein, we describe the first enantioselective and scalable total synthesis of this natural product and its epimeric congener, speciogynine pseudoindoxyl. The characteristic spiro‐5‐5‐6‐tricyclic system of these alkaloids was formed through a protecting‐group‐free cascade relay process in which oxidized tryptamine and secologanin analogues were used. Furthermore, we discovered that mitragynine pseudoindoxyl acts not as a single molecular entity but as a dynamic ensemble of stereoisomers in protic environments; thus, it exhibits structural plasticity in biological systems. Accordingly, these synthetic, structural, and biological studies provide a basis for the planned design of mitragynine pseudoindoxyl analogues, which can guide the development of next‐generation analgesics.

Protein protic and aprotic interactions systematically mapped via IR spectroscopy and polarizable molecular dynamics.

Nitrile vibrational frequencies can readily report on the environmental electric field except in hydrogen bonding (H-bonding) environments, where factors other than the field contribute to frequency shifts; these environments are very commonly found in proteins, among other forms of condensed phase matter, so an alternative observable for unambiguous field determination is desirable. We previously showed that the nitrile's transition dipole moment (TDM) – and therefore peak area – experiences a new vibrational Stark effect that linearly correlates with the field in all environments, unlike frequencies. As a proof-of-concept, we demonstrated this relationship using nitrile probes in solvents and applied it to four variants of photoactive yellow protein (PYP) with nitrile-containing ortho-cyanophenylalanine residues introduced via amber suppression (JACS, 144, 7562-7567 (2022)). Eight further PYP mutants were constructed from one variant to modify the H-bonding/electric fields experienced by the nitrile probe. IR spectroscopy yielded four consistent IR lineshapes, interpreted as environmental phenotypes, which included mixtures of protic and aprotic environments. TDM-based electric fields were assessed, and high-resolution crystal structures were obtained to further interpretation of the spectroscopic data. The structures showed that either the mutated residue or newly accessible waters around the nitrile serve as the H-bond donor(s) and could explain the environmental phenotypes on a qualitative level. For a more quantitative assessment, we performed molecular dynamics (MD) on PYPs with polarizable AMOEBA force fields: a strong correlation is found between average electric fields from simulation and experimental TDM analysis, further establishing that the field-TDM relationship extends to complex protein environments. Also, characterizations of the nitrile environment (average structure, H-bond donor identities, etc.) correlated well with environmental phenotype, implying that polarizable force fields realistically model local protein interactions.

Combined experimental and computational studies on the photophysical properties of systematically substituted polypyridyl based ligands on a benzene core

• Investigated dendritic systems show interesting solvent modulated photophysics; • Inter-chromophoric interaction is present in highly substituted systems; • Theoretical calculation results support the experimental observations; • Strongly modulated photochemistry of L1 and L2 in lower DMSO fraction; • Can lead to design new antenna systems with bipyridyl chromophores on benzene core. Photophysical behavior of ligands containing systematically substituted 2,2′-dipyridylamine (DPyA) chromophores on a benzene core was studied by steady-state and time resolved fluorescence experiments in combination with density functional theory (DFT) calculations. All the investigated derivatives show significant solvent modulated photophysical properties. The redshift along with the broadening in fluorescence spectra in polar protic environments could be explained by the formation of extensive solvent hydrogen bonding network with the investigated compounds. On the other hand, extremely low fluorescence yield in aqueous medium is mostly due to the significant drop in radiative deactivation pathway. In addition to the polarity outcome, the contribution of specific interactions like solvent hydrogen bond formation towards the spectral properties were examined by multi-parametric linear regression analysis using Kamlet-Taft (KT) and Catalán formalisms. While the mono and di-substituted systems ( L1 and L2 , respectively) show almost similar excited state deactivation parameters, additional interchromophoric interaction is predicted in the tri-substituted derivative ( L3 ). The experimental results were verified with TDDFT studies on isolated as well as micro-solvated ligand-water complexes.

Free-Energy Landscape of the SN2 Reaction CH3Br + Cl- → CH3Cl + Br- in Different Liquid Environments.

This work describes in detail the reaction path of the well-known SN2 reaction CH3Br + Cl- → CH3Cl + Br-, whose reaction rate has a huge variation with the solvent in the gas phase and in protic and aprotic liquid environments. We employed the ASEC-FEG method to optimize for minima (reactants and products) and saddle points (transition states) in the in-solution free-energy hypersurface. The method takes atomistic details of the solvent into account. A polarizable continuum model (PCM) has also been employed for comparison. The most perceptive structural changes are noted in aqueous solution by using the ASEC-FEG approach. The activation energies in all solvents, estimated by means of free-energy perturbation calculations, are in good agreement with the experimental data. The total solute-solvent hydrogen bonds play an important role in the increased barrier height observed in water and are therefore crucial to explain the huge decrease in the kinetic constant. It is also found that the hydration shell around the ions breaks itself spontaneously to accommodate the molecule, thus forming minimum energy complexes.

Nitrile Infrared Intensities Characterize Electric Fields and Hydrogen Bonding in Protic, Aprotic, and Protein Environments.

Nitriles are widely used vibrational probes; however, the interpretation of their IR frequencies is complicated by hydrogen bonding (H-bonding) in protic environments. We report a new vibrational Stark effect (VSE) that correlates the electric field projected on the -C≡N bond to the transition dipole moment and, by extension, the nitrile peak area or integrated intensity. This linear VSE applies to both H-bonding and non-H-bonding interactions. It can therefore be generally applied to determine electric fields in all environments. Additionally, it allows for semiempirical extraction of the H-bonding contribution to the blueshift of the nitrile frequency. Nitriles were incorporated at H-bonding and non-H-bonding protein sites using amber suppression, and each nitrile variant was structurally characterized at high resolution. We exploited the combined information available from variations in frequency and integrated intensity and demonstrate that nitriles are a generally useful probe for electric fields.

Cyclic Thiosulfonates for Thiol-Mediated Uptake: Cascade Exchangers, Transporters, Inhibitors.

Thiol-mediated uptake is emerging as a powerful method to penetrate cells. Cyclic oligochalcogenides (COCs) have been identified as privileged scaffolds to enable and inhibit thiol-mediated uptake because they can act as dynamic covalent cascade exchangers, i.e., every exchange produces a new, covalently tethered exchanger. In this study, our focus is on the essentially unexplored COCs of higher oxidation levels. Quantitative characterization of the underlying dynamic covalent exchange cascades reveals that the initial ring opening of cyclic thiosulfonates (CTOs) proceeds at a high speed even at a low pH. The released sulfinates exchange with disulfides in aprotic but much less in protic environments. Hydrophobic domains were thus introduced to direct CTOs into hydrophobic pockets to enhance their reactivity. Equipped with such directing groups, fluorescently labeled CTOs entered the cytosol of living cells more efficiently than the popular asparagusic acid. Added as competitive agents, CTOs inhibit the uptake of various COC transporters and SARS-CoV-2 lentivectors. Orthogonal trends found with different transporters support the existence of multiple cellular partners to account for the diverse expressions of thiol-mediated uptake. Dominant self-inhibition and high activity of dimers imply selective and synergistic exchange in hydrophobic pockets as distinguishing characteristics of thiol-mediated uptake with CTOs. The best CTO dimers with hydrophobic directing groups inhibit the cellular entry of SARS-CoV-2 lentivectors with an IC50 significantly lower than the previous best CTO, below the 10 μM threshold and better than ebselen. Taken together, these results identify CTOs as an intriguing motif for use in cytosolic delivery, as inhibitors of lentivector entry, and for the evolution of dynamic covalent networks in the broadest sense, with reactivity-based selectivity of cascade exchange emerging as a distinguishing characteristic that deserves further attention.

Hydrogen Bond-Enhanced Nanoaggregation and Antisolvatochromic Fluorescence for Protein-Recognition by Si-Coumarins.

Silicon-substituted coumarin (SiC) was established as a substantial family of both intramolecular and intermolecular hydrogen bond (H-bond) enhanced fluorescent probes for sensitively tracking proteins in vivo through the assemble and disassemble of its nanoaggregates. The intramolecular H-bond in SiC has led to significant aggregation, antisolvatochromism, and strong fluorescence with bathochromically shifted spectra into far-red or near-infrared (NIR) regions in polar, protic environments. Without further furnishing with organic linkers, the compact skeleton of SiC bearing H-bond has ensured sensitively and selectively sensing the targeting proteins with the protic reaction pockets through efficient disassemble of the aggregates. In the existence of strong intermolecular H-bonds with the target protein pocket, SiC resolved as high as >250-fold fluorescence enhancement. Selectively tracking proteins, including human serum albumin, human carbonic anhydrase (hCAII), avidin, SNAP-tag protein, and translocator protein, has confirmed SiC a versatile skeleton for sensitively monitoring proteins in complicated biological systems.

Nitrile IR intensities directly measure electric fields in protic and non-protic environments

Nitriles are useful vibrational probes; the interpretation of their frequencies, however, is complicated by hydrogen bonding in protic environments. Here we observed a vibrational Stark effect (VSE) which correlates electric field to transition dipole moment (and, by extension, the nitrile peak area) instead of to frequency. This VSE governs the transition dipole moment for the CO stretch in acetophenone and the CN stretch in benzonitrile, with studies performed in bulk-phase solvents. While modest for the acetophenone carbonyl CO, the VSE for the benzonitrile nitrile CN is dramatic, and a >300% increase in absolute peak area from hexanes to water.

Abiotic reduction of ketones with silanes catalysed by carbonic anhydrase through an enzymatic zinc hydride.

Enzymatic reactions through mononuclear metal hydrides are unknown in nature, despite the prevalence of such intermediates in the reactions of synthetic transition-metal catalysts. If metalloenzymes would react through abiotic intermediates like these, then the scope of enzyme-catalyzed reactions would expand. Here we show that zinc-containing carbonic anhydrase enzymes catalyze hydride transfers from silanes to ketones with high enantioselectivity and report mechanistic data providing strong evidence that the process involves a mononuclear zinc hydride. This work shows that abiotic silanes can act as reducing equivalents in an enzyme-catalyzed process and that monomeric hydrides of electropositive metals, which are typically unstable in protic environments, can be catalytic intermediates in enzymatic processes. Overall, this work bridges a gap between the types of transformations in molecular catalysis and biocatalysis.

Impact of Heteroatom Substitution on Dual-State Emissive Rigidified 2-(2'-hydroxyphenyl)benzazole Dyes: Towards Ultra-Bright ESIPT Fluorophores*.

2-(2'-Hydroxyphenyl)benzazole (HBX) fluorophores are well-known excited-state intramolecular proton transfer (ESIPT) emitters largely studied for their synthetic versatility, photostability, strong solid-state fluorescence and ability to engineer dual emission, thus paving the way to applications as white emitters, ratiometric sensors, and cryptographic dyes. However, they are heavily quenched in solution, due to efficient non-radiative pathways taking place as a consequence of the proton transfer in the excited-state. In this contribution, the nature of the heteroring constitutive of these rigidified HBX dyes was modified and we demonstrate that this simple structural modification triggers major optical changes in terms of emission color, dual emission engineering, and importantly, fluorescent quantum yield. Investigation of the photophysical properties in solution and in the solid state of a series of ethynyl-TIPS extended HBX fluorophores, along with ab initio calculations demonstrate the very promising abilities of these dyes to act as bright dual-state emitters, in both solution (even in protic environments) and solid state.

Reversible Spatial Control in Aqueous Media by Visible Light: A Thioindigo Photoswitch that is Soluble and Operates Efficiently in Water.

Aiming to extend the scope of indigoid photoswitches to polar protic environments, we have synthesized a sulfonated thioindigo derivative highly soluble in water. Studies by UV/Vis absorption, fluorescence, and NMR spectroscopy indicate that, despite aggregation effects at micromolar concentrations, the novel dye offers satisfactory performance in aqueous solution in the absence of solvation aides. Enrichment of the metastable cis isomer by irradiation may exceed 65 % and its half-life at room temperature may exceed several hours. Degradation after 20 yellow and blue light irradiation cycles within 2 hours is less than 2 %. Performance can be expected to further improve in future molecular designs if the tendency towards self-association is further reduced. Crucially, photoisomerization of indigoids is not necessarily inhibited by water and, thus, the superior spatial control offered by this class of molecular switches may be of great benefit also in biological systems.

Photophysics of a Ruthenium Complex with a π-Extended Dipyridophenazine Ligand for DNA Quadruplex Labeling.

The light-switch mechanism of the complex [Ru(bpy)2(Br-dpqp)](PF6)2 (1, bpy = 2,2'-bipyridine, Br-dpqp = 12-bromo-14-ethoxydipyrido[3,2- a:2',3'- c]quinolino[3,2- h]phenazine), i.e., a light-up probe for the selective labeling of G-quadruplexes, is investigated by time-resolved transient absorption and emission spectroscopy. We show that, in contrast to the prototypical light-switch complex [Ru(bpy)2(dppz)](PF6)2 (2, dppz = dipyrido[3,2- a:2',3'- c]phenazine), a 3ππ* state localized on the π-extended ligand is the state determining the excited-state properties in both protic and aprotic environments. In aprotic environments, emission originates from a bright 3MLCTphen state, which is thermally accessible from the 3ππ* state at ambient temperature. In the presence of water, i.e., in environments resembling in cellulo situations, the thermally accessible 3MLCT state is altered and becomes close in energy to the 3ππ* state, which induces a rapid excited-state deactivation of the 3ππ* state and a comparably weak emission.

Conformational dynamics of 4-formylaminoantipyrine based on NMR and theoretical calculations

We investigated the metamizole metabolite 4-formylaminoantipyrine (4-FAA) by 1H dynamic nuclear magnetic resonance. 4-FAA exhibits a carbon-nitrogen partial double bond that rotates slowly enough, on a resonance time scale, to provide the simultaneous spectra of two rotamers. We examined various solvents in an attempt to understand how protic and aprotic environments influence the anti and syn rotamer equilibriums. Moreover, we compared experimental data and theoretical calculations to evaluate the thermodynamic parameters of the rotational process.

Determination of the ground- and excited-state dipole moments of bromocresol purple in protic and aprotic solvents

Although it has been widely recognized that hydrogen bonds play a significant role in the photophysics of molecules, this phenomenon has rarely been applied to the solvatochromic method for determination of dipole moments. The difference in the dipole moment between the ground and excited state was determined in protic and aprotic solvents using both the Lippert–Mataga equation and the Bilot–Kawski equation for bromocresol purple, a molecule capable of hydrogen-bond donation and acceptance. The dipole change in protic environments was determined to be 15.2±1.0D for the Lippert–Mataga method and 9.2±1.0D for the Bilot–Kawski method, while the change in aprotic environments was 10.4±1.0D and 6.7±1.0D, respectively. Both methods highlighted the importance of hydrogen bonding in stabilizing increased charge-separation of the excited state, allowing for larger changes in dipole moments in protic environments. This study further validates a simple, rational modification to the commonly used methods that allows access to dipole-moment data on dyes with hydrogen-bonding capabilities through solvatochromic experiments.

Photophysics of Flavin Derivatives Absorbing in the Blue-Green Region: Thioflavins As Potential Cofactors of Photoswitches

The purpose of this study was to find flavin derivatives with absorption maxima in the blue-green region of the visible spectrum that might be used as alternative cofactors in blue-light photoreceptors. To this end, the vertical absorption spectra of eight lumiflavin-related compounds were calculated by means of quantum chemical methods. The compounds differ from lumiflavin by the subsitution of an S atom for an O atom at the 2- and/or 4-positions of the isoalloxazine core, the substitution of an N atom for a CH group in the 6- and/or 9-positions, or an extension of the π system at the 7- and 8-positions. For the three most promising compounds, 2-thio-lumiflavin, 4-thio-lumiflavin, and 2,4-dithio-lumiflavin, the quantum chemical investigations were extended to include geometry relaxations in the excited states, rates for spin-forbidden transitions and an estimate of spectral shifts brought about by polar protic environments. We find these thiocarbonyl compounds to have very promising excited-state properties. They absorb in the blue-green wavelength regime around 500 nm, i.e., substantially red-shifted with respect to lumiflavin that is the cofactor of natural blue-light photoreceptors. Their triplet quantum yields are predicted to be close to unity while their triplet lifetimes are long enough to enable bimolecular photochemical reactions. The combination of these properties makes the thioflavins potentially suitable candidates as cofactors in biomimetic photoswitches.

Reliable Quantum Chemical Prediction of the Localized/Delocalized Character of Organic Mixed-Valence Radical Anions. From Continuum Solvent Models to Direct-COSMO-RS.

A recently proposed quantum-chemical protocol for the description of the character of organic mixed-valence (MV) compounds, close from both sides to the localized/delocalized borderline, is evaluated and extended for a series of dinitroaryl radical anions 1-6. A combination of global hybrid functionals with exact-exchange admixtures of 35% (BLYP35) or 42% (BMK) with appropriate solvent modeling allows an essentially quantitative treatment of, for example, structural symmetry-breaking in Robin/Day class II systems, thermal electron transfer (ET) barriers, and intervalence charge-transfer (IV-CT) excitation energies, while covering also the delocalized class III cases. Global hybrid functionals with lower exact-exchange admixtures (e.g., B3LYP, M05, or M06) provide a too delocalized description, while functionals with higher exact-exchange admixtures (M05-2X, M06-2X) provide a too localized one. The B2PLYP double hybrid gives reasonable structures but far too small barriers in class II cases. The CAM-B3LYP range hybrid gives somewhat too high ET barriers and IV-CT energies, while the range hybrids ωB97X and LC-BLYP clearly exhibit too much exact exchange. Continuum solvent models describe the situation well in most aprotic solvents studied. The transition of 1,4-dinitrobenzene anion 1 from a class III behavior in aprotic solvents to a class II behavior in alcohols is not recovered by continuum solvent models. In contrast, it is treated faithfully by the novel direct conductor-like screening model for real solvents (D-COSMO-RS). The D-COSMO-RS approach, the TURBOMOLE implementation of which is reported, also describes accurately the increased ET barriers of class II systems 2 and 3 in alcohols as compared to aprotic solvents and can distinguish at least qualitatively between different aprotic solvents with identical or similar dielectric constants. The dominant role of the solvent environment for the ET character of these MV radical anions is emphasized, as in contrast to some previous computational suggestions essentially all of the present systems have delocalized class III character in the gas phase. The present approach allows accurate estimates from the gas phase to aprotic and protic solvent environments, without the need for explicit ab initio molecular dynamics simulations, and without artificial constraints.

Structure and Function of Quinones in Biological Solar Energy Transduction: A Differential Pulse Voltammetry, EPR, and Hyperfine Sublevel Correlation (HYSCORE) Spectroscopy Study of Model Benzoquinones

Quinones are widely used electron transport cofactors in photosynthetic reaction centers. Previous studies have suggested that the structure of the quinone cofactors and the protein interactions or "smart" matrix effects from the surrounding environment govern the redox potential and hence the function of quinones in photosynthesis. In the present study, a series of 1,4-benzoquinone models are examined via differential pulse voltammetry to provide relative redox potentials. In parallel, CW and pulsed EPR methods are used to directly determine the electronic properties of each benzoquinone in aprotic and protic environments. The shifts in the redox potential of the quinones are found to be dependent on the nature of the substituent group and the number of substituent groups on the quinone molecule. Further, we establish a direct correlation between the nature of the substituent group and the change in electronic properties of the benzosemiquinone by analysis of the isotropic and anisotropic components of the electron-nuclear hyperfine interactions observed by CW and pulsed EPR studies, respectively. Examination of an extensive library of model quinones in both aprotic and protic solvents indicates that hydrogen-bonding interactions consistently accentuate the effects of the substituent groups of the benzoquinones. This study provides direct support for the tuning and control of quinone cofactors in biological solar energy transduction through interactions with the surrounding protein matrix.

Intramolecular Hydrogen Bonding in ortho-Substituted Arylamide Oligomers: A Computational and Experimental Study of ortho-Fluoro- and ortho-Chloro-N-methylbenzamides

As a part of our systematic study of foldamer structural elements, we analyze and quantify the conformational behavior of two model compounds based on a frequently used class of aromatic oligoamide building blocks. Combining computational and NMR approaches, we investigate ortho-fluoro- and ortho-chloro-N-methylbenzamide. Our results indicate that the -F substituent in an ortho position can be used to fine-tune the rigidity of the oligomer backbone. It provides a measurably attenuated but still considerably strong hydrogen bond (H-bond) to the peptide group proton when compared to the -OCH3 substituent in the same position. On the other hand, the ortho-Cl substituent does not impose significant restrictions on the flexibility of the backbone. Its effect on the final shape of an oligomer is likely governed by its size rather than by noncovalent intramolecular interactions. Furthermore, the effect of solvent on the conformational preferences of these building blocks has been quantified. The number of intramolecularly H-bonded conformations decreases significantly when going from nonprotic to protic environments. This study will facilitate rational design of novel arylamide foldamers.