pH Dependence of HSF1 trimerization is shaped by intramolecular interactions

Heat shock factor 1 (HSF1) primarily regulates various cellular stress responses. Previous studies have shown that low pH within the physiological range directly activates HSF1 function in vitro. However, the detailed molecular mechanisms remain unclear. This study proposes a molecular mechanism based on the trimerization behavior of HSF1 at different pH values. Extensive mutagenesis of human and goldfish HSF1 revealed that the optimal pH for trimerization depended on the identity of residue 103. In particular, when residue 103 was occupied by tyrosine, a significant increase in the optimal pH was observed, regardless of the rest of the sequence. This behavior can be explained by the protonation state of the neighboring histidine residues, His101 and His110. Residue 103 plays a key role in trimerization by forming disulfide or non-covalent bonds with Cys36. If tyrosine resides at residue 103 in an acidic environment, its electrostatic interactions with positively charged histidine residues prevent effective trimerization. His101 and His110 are neutralized at a higher pH, which releases Tyr103 to interact with Cys36 and drives the effective trimerization of HSF1. This study showed that the protonation state of a histidine residue can regulate the intramolecular interactions, which consequently leads to a drastic change in the oligomerization behavior of the entire protein.

Enhancement of intrinsic guanine fluorescence by protonation in DNA of various structures

Understanding the diversity of DNA structure and functions in biology requires tools to study this biomolecule selectively and thoroughly. Fluorescence methods are powerful technique for non-invasive research. Due to the low quantum yield, the intrinsic fluorescence of nucleotides has not been considered for use in the detection and differentiation of nucleic acid bases. Here, we have studied the influence of protonation of nucleotides on their fluorescence properties. We show that protonation of ATP and GTP leads to enhanced intrinsic fluorescence. Fluorescence enhancement at acidic pH has been observed for double-stranded DNA and single-stranded oligonucleotides. The formation of G4 secondary structures apparently protected certain nucleotides from protonation, resulting in less pronounced fluorescence enhancement. Furthermore, acid-induced depurination under protonation was less noticeable in G4 structures than in double-stranded and single-stranded DNA. We show that changes in the intrinsic fluorescence of guanine can be used as a sensitive sensor for changes in the structure of the DNA and for the protonation of specific nucleotides.

Nanographene with a Nitrogen-Doped Cavity

Nitrogen-doped cavities are pervasive in graphenic materials, and represent key sites for catalytic and electrochemical activity. However, their structures are generally heterogeneous. In this study, we present the synthesis of a well-defined molecular cutout of graphene featuring N-doped cavity. The graphitization of a macrocyclic pyridinic precursor was achieved through photochemical cyclodehydrochlorination. In comparison to its counterpart with pyridinic nitrogen at the edges, the pyridinic nitrogen atoms in this nanographene cavity exhibit significantly reduced basicity and selective binding to Ag+ ion. Analysis of the protonation and coordination equilibria revealed that the tri-N-doped cavity binds three protons, but only one Ag+ ion. These distinct protonation and coordination behaviors clearly illustrate the space confinement effect imparted by the cavities.

Favoring CO Intermediate Stabilization and Protonation by Crown Ether for CO2 Electromethanation in Acidic Media

The large-scale deployment of CO2 electroreduction is hampered by deficient carbon utilization in neutral and alkaline electrolytes due to CO2 loss into (bi)carbonates. Switching to acidic media mitigates carbonation, but suffers from low product selectivity because of hydrogen evolution. Here we report a crown ether decoration strategy on a Cu catalyst to enhance carbon utilization and selectivity of CO2 methanation under acidic conditions. Macrocyclic 18-Crown-6 is found to enrich potassium cations near the Cu electrode surface, simultaneously enhancing the interfacial electric field to stabilize the *CO intermediate and accelerate water dissociation to boost *CO protonation. Remarkably, the mixture of 18-Crown-6 and Cu nanoparticles affords a CH4 Faradaic efficiency of 51.2 % and a single pass carbon efficiency of 43.0 % toward CO2 electroreduction in electrolyte with pH=2. This study provides a facile strategy to promote CH4 selectivity and carbon utilization by modifying Cu catalysts with supramolecules.

Extraction of Rh(III) from hydrochloric acid by protonated NTAamide(C6) and analogous compounds and understanding of extraction equilibria by using UV spectroscopy and DFT calculations

Extraction of Rh from hydrochloric acid is conducted using NTAamide(C6) (N,N,N´,N´,N´´,N´´-hexahexyl-nitrilotriacetamide) and other related compounds. We use the ion-pair extraction of anionic species of Rh-chloride and protonated extractant. Rh ions exist as Rh(Cl)n(H2O)6-n (n ≤ 5) and the tertiary nitrogen atom in an extractant are protonated to produce a quaternary amine in acidic condition. The D(Rh) values are changeable because the Rh-Cl-H2O complex forms from + 3 to - 2 valency. Rh-chloride ion with a peak of spectrum at 504 nm can be extracted effectively, where RhCl4(H2O)- and RhCl5(H2O)2- exist from Density functional theory calculation and UV spectrum. The maximum distribution ratio (D) of Rh(III) is 16, and 85 mM Rh can be extracted from 1 M HCl dissolving 96 mM, due to less third phase formation. Approximate 80% of Rh can be stripped by the water-soluble reagents having the activities of neutralization and solvation. The figure for the Graphical Index saved in the JPEG, PNG or TIFF format at 300 dpi should be pasted with the size adjusted to the frame below (5 cm long and 8 cm wide).

Extended Light Absorption and Improved Charge Separation by Protonation of the Organic Ligand in a Bismuth Based Metal-Organic Framework

In this work, we report a new method to extend the light absorption and improve the photocatalytic activity of metal-organic frameworks (MOFs) with nitrogen-containing ligand, namely the protonation of nitrogen. Specifically, a protonated Bi-based MOF synthesized by a hydrothermal method (Bi-MMTAA-H, MMTAA= 2-mercapto-4-methyl-5-thiazoleacetic acid) displays a wider visible light absorption than Bi-MMTAA-R with the same single-crystal structure but synthesized by a reflux method. The red-shifted light absorption was confirmed to be caused by the protonation of nitrogen in the thiazolyl ring in MMTAA. Moreover, this protonation also facilitates the charge separation and transfer and improves the photocatalytic activity of selective oxidation of α-terpinene to p-cymene. Our results provide a new idea for nitrogen-containing Bi-based MOFs to extend the light absorption and improve the photocatalytic performance.

N-Protonation as a Switch of the Twisted Excited States with ππ* or nπ* Character and Correlation with the π-electrons Characteristic of Rotatable Bonds

N-protonation for numerous fluorophores is widely known as an efficient switch for the fluorescence turn-on/off in acidic conditions, which has been applied in various scenarios that involve pH monitoring. Yet the universal mechanism for fluorescence regulation through N-protonation is still elusive. Herein, we systematically investigated the excited state deactivation processes for a series of nitrogen-containing fluorescent probes through theoretical approaches. We concluded two types of mechanisms for the complex fluorescent phenomena by N-protonation: one is through the regulation for the transition to a ππ* twisted intramolecular charge transfer (TICT) state; the other one applies for the case when nonradiative decay pathway is predominant by a dark nπ* state, which is also accompanied by an evident structural twisting and can be regarded as another kind of TICT state. More generally, we found that the formation of the TICT state is closely related to the conjugated π-electrons on the single bond that links the acceptor and donor part of fluorophores, which provides a simple strategy for evaluating the occurrence of the TICT process. We anticipate that the current contributions can bring novel insights for the rational design of functional fluorophores that involve TICT process in the excited states.

Cryo-EM structure of a eukaryotic zinc transporter at a low pH suggests its Zn2+-releasing mechanism

Zinc transporter 8 (ZnT8) is mainly expressed in pancreatic islet β cells and is responsible for H⁺-coupled uptake (antiport) of Zn²⁺ into the lumen of insulin secretory granules. Structures of human ZnT8 and its prokaryotic homolog YiiP have provided structural basis for constructing a plausible transport cycle for Zn²⁺. However, the mechanistic role that protons play in the transport process remains unclear. Here we present a lumen-facing cryo-EM structure of ZnT8 from Xenopus tropicalis (xtZnT8) in the presence of Zn²⁺ at a luminal pH (5.5). Compared to a Zn²⁺-bound xtZnT8 structure at a cytosolic pH (7.5), the low-pH structure displays an empty transmembrane Zn²⁺-binding site with a disrupted coordination geometry. Combined with a Zn²⁺-binding assay our data suggest that protons may disrupt Zn²⁺ coordination at the transmembrane Zn²⁺-binding site in the lumen-facing state, thus facilitating Zn²⁺ release from ZnT8 into the lumen.

Proton-Induced Spin State Switching in an FeIII Complex

Reversible proton-induced spin state switching of an Fe^III complex in solution is observed at room temperature. A reversible magnetic response was detected in the complex, [Fe^III (sal₂ 323)]ClO₄ (1), using Evans' method ¹ H NMR spectroscopy which indicated cumulative switching from low-spin to high-spin upon addition of one and two equivalents of acid. Infrared spectroscopy suggests a coordination-induced spin state switching (CISSS) effect, whereby protonation displaces the metal-phenoxo donors. The analogous complex, [Fe^III (4-NEt₂ -sal₂ 323)]ClO₄ (2), with a diethylamino group on the ligand, was used to combine the magnetic change with a colorimetric response. Comparison of the protonation responses of 1 and 2 reveals that the magnetic switching is caused by perturbation of the immediate coordination sphere of the complex. These complexes constitute a new class of analyte sensor which operate by magneto-modulation, and in the case of 2, also yield a colorimetric response.

Enhancement of Visible-Light-Driven Hydrogen Evolution Activity of 2D π-Conjugated Bipyridine-Based Covalent Organic Frameworks via Post-Protonation

Photocatalytic hydrogen (H₂ ) evolution represents a promising and sustainable technology. Covalent organic frameworks (COFs)-based photocatalysts have received growing attention. A 2D fully conjugated ethylene-linked COF (BTT-BPy-COF) was fabricated with a dedicated designed active site. The introduced bipyridine sites enable a facile post-protonation strategy to fine-tune the actives sites, which results in a largely improved charge-separation efficiency and increased hydrophilicity in the pore channels synergically. After modulating the degree of protonation, the optimal BTT-BPy-PCOF exhibits a remarkable H₂ evolution rate of 15.8 mmol g^-1  h^-1 under visible light, which surpasses the biphenyl-based COF 6 times. By using different types of acids, the post-protonation is proved to be a potential universal strategy for promoting photocatalytic H₂ evolution. This strategy would provide important guidance for the design of highly efficient organic semiconductor photocatalysts.

On-off-on Control of Molecular Inversion Symmetry via Multi-stage Protonation: Elucidating Vibronic Laporte Rule

The Laporte rule dictates that one- and two-photon absorption spectra of inversion-symmetric molecules should display alternatively forbidden electronic transitions; however, for organic fluorophores, drawing clear distinction between the symmetric- and non-inversion symmetric two-photon spectra is often obscured due to prevalent vibronic interactions. We take advantage of consecutive single- and double-protonation to break and then reconstitute inversion symmetry in a nominally symmetric diketopyrrolopyrrole, causing large changes in two-photon absorption. By performing detailed one- and two-photon titration experiments, with supporting quantum-chemical model calculations, we explain how certain low-frequency vibrational modes may lead to apparent deviations from the strict Laporte rule. As a result, the system may be indeed considered as an on-off-on inversion symmetry switch, opening new avenues for two-photon sensing applications.

A novel route to enhance the dissolution of apatite: Structural incorporation of hydrogen phosphate

Potential use of hydroxyapatite nanoparticles (HANPs) [Ca₁₀(PO₄)₆(OH)₂] as slow P-release fertilizer (SRF) has recently attracted wider attention. However, commercially available HANP (with Ca/P ratio = 1.667) is the least soluble calcium phosphate and thus limits its full potential as an SRF in agronomic applications. In this research, we sought to enhance the dissolution rate of HANPs by enriching hydrogen phosphate (HPO₄^2-) species in the phosphate (PO₄^3-) structural sites. Seven different types of pure crystalline HANPs were synthesized at a range of Ca/P ratio from 1.46 (at pH 6.0) to 2.10 (at pH 12.0). Complementary results from FTIR and solid-state ³¹P MAS NMR spectroscopies showed that HPO₄^2- species is most abundant in HANPs crystallized at pH 6.0 and gradually depleted at higher pH products. The rate of depletion of HPO₄^2- species is proportional to the increase in carbonate incorporation into the HANP lattice, which preferentially forms B-type carbonated HANPs. The enhanced dissolution rate of HANPs due to hydrogen phosphate incorporation was tested using a flow-through macro-dialysis system that limits the partial transition of HANPs to other solid phases, which otherwise interfere with dissolution. The results show that the dissolution rate of HANPs increased with decreasing pH of synthesis and was highest in HANPs at pH 6.0. The dissolution rate differed by ten times between HANPs synthesized at pH 7.0 and 10.0. Overall, the atom-efficient synthetic route developed and the ability to tune the dissolution rate of HANPs are significant steps forward in improving the P-release efficiency of a potent SRF and is expected to contribute to efforts toward enhancing agricultural sustainability.

Protonated cross-linkable nanocomposite coatings with outstanding underwater superoleophobic and anti-viscous oil-fouling properties for crude oil/water separation

Superhydrophilic/underwater superoleophobic coatings that effectively prevent viscous oil contamination have been of considerable interest for the great potential in oil spill remediation and oilfield wastewater treatment. In the present work, a protonated cross-linkable nanocomposite coating with robust underwater superoleophobicity and intensified hydration capability is proposed through the synthesis of active polymeric nanocomplex (PNC), cross-linking reaction between PNC and hydrophilic chitosan (CS), and final protonation to further improve water affinity. Benefiting from the hierarchical structure and strong hydration capability induced by electrostatic interactions and hydrogen bondings, the nanocomposite coating coated textile exhibits excellent superhydrophilicity (within 0.28 s with water contact angle reaching 0°), underwater superoleophobicity (underwater crude oil contact angle at 160°), and ultralow oil adhesion even to highly viscous silicone oil. Moreover, the nanocomposite coating presents a robust chemical resistance, mechanical tolerance, and storage stability. Simultaneously, the nanocomposite coating adapts well to various porous substrates (e.g., stainless steel mesh and Ni sponge) with great anti-oil-fouling and self-cleaning performances. Importantly, the coating coated textile is successfully applied in crude oil/water separation with excellent efficiency and repeatability. The findings conceivably stand out as a new methodology to fabricate superhydrophilic/underwater superoleophobic materials with outstanding anti-viscous oil-fouling property for practically treating oily wastewater.

2D-2D lattice engineering route for intimately coupled nanohybrids of layered double hydroxide and potassium hexaniobate: Chemiresistive SO2 sensor

2D-2D lattice engineering route is used to synthesize intimately coupled nanohybrids of layered double hydroxide (LDH) and potassium hexaniobate. The 2D-2D lattice engineering route is based on the electrostatically derived self-assembly of delaminated zinc-chromium-layered double hydroxide (ZC-LDH) nanosheets and potassium hexaniobate (HNb) nanosheets (ZCNb nanohybrids). The 2D-2D lattice-engineered ZCNb nanohybrids display expanded surface area, mesoporous anchored nanosheets network morphology, and intimate coupling between nanosheets. The 2D-2D lattice engineered ZCNb nanohybrids are used for the low temperature operated gas sensor. The ZCNb nanohybrids display outstanding selectivity for the SO₂, with the high response of 61.5% compared to pristine ZC-LDH (28.08%) and potassium niobate (8%) at 150 °C. Moreover, ZCNb sensors demonstrate superior response and recovery periods of 6 and 167 s at 150 °C, respectively. This result underscores the exceptional functionality of the ZCNb nanohybrids as efficient SO₂ sensors. Moreover, these findings vividly demonstrate that the 2D-2D lattice-engineered ZCNb nanohybrids are quite effective not only in improving the gas sensor activity but also in developing of new type of intimately coupled mesoporous LDH-metal-oxide based hybrid materials.

Enhancement of E. coli inactivation by photosensitized erythrosine-based solar disinfection under weakly acidic conditions

Cost-effective disinfection technology is urgently needed in poor rural areas. Erythrosine (ERY)-based solar disinfection (SODIS) provides a promising solution because of its effective inactivation of viruses and gram-positive bacteria at low cost. However, the poor gram-negative bacteria (G^-, e.g., Escherichia coli) inactivation of photosensitized ERY inhibits its application. Herein, for the first time, the protonation of ERY was found to greatly enhance its G^- inactivation, and 99.99999% (7.0 log) of E. coli were completely inactivated within only 30 s using 2.5 mg/L ERY under 200 mW/cm² visible light irradiation. The inactivation rate constant (k) reached 17.5 min^-1 at pH 4.0, which was 4730 times higher than that at pH 7.0. At a lower pH, more severe cell wall and genomic DNA damage was observed. A linear correlation between k and monoanionic ERY (HE^-) content was obtained, indicating that HE^- rather than dianionic ERY (E^2-) participated in the inactivation at pH 5.0-7.0, which was further explained by the higher production of reactive oxygen species and bacterial adsorption of HE^- than E^2-. Both ¹O₂ and O₂^-• dominated bacterial inactivation, contributing 56.8% and 43.2%, respectively. O₂^-• but not ¹O₂ caused ERY photobleaching. OH• was not involved in either inactivation or photobleaching. Humic acid and salts (NaCl, Na₂SO₄, CaCl₂, and MgCl₂) slightly inhibited inactivation, while NaHCO₃ accelerated inactivation. Complete inactivation (99.9999%) of E. coli was achieved within ∼30 min at pH 5.0 in ERY-based SODIS with good adaptation to various water matrices and weather (sunny or partly cloudy). This work will help to promote the application of ERY-based disinfection especially for SODIS in poor rural areas.

Metalloceneincorporated Hybrid Singly N-Methyl N-Confused Calixphyrins: Synthesis, Characterization, Protonation and Deprotonation Studies

Rational design and isolation of two hitherto unknown highly stable single conformer of ferrocene incorporated meso-aryl substituted singly N-methyl N-confused-calixphyrins have been achieved in quantitative yields. The solid-state crystal structure reveals the obvious trans-geometry for the meso-protons with the possibility for both the macrocycles to exist either racemic or enantiomer forms. However, thorough solution-state spectroscopic characterization strongly concludes the experimental isolation of a single isomer for both the macrocycles. The drastic modification of UV-vis spectral patterns upon imine pyrrole N protonation and amine pyrrole NH deprotonation of both the calixphyrins could pave way for these macrocycles to act as opto-electronic materials. The conformational preorganization and protonation and deprotonation induced conformational reorganization have been extensively studied by solution state spectroscopic techniques, solid state X-ray crystal structure and in depth DFT level theoretical calculations.

Specific interactions between the alkaline protease of P. aeruginosa and its natural peptide inhibitor: ab initio molecular simulations

Alkaline protease aeruginolysin (APR) is an important virulence factor in the evasion of the immune system by Pseudomonas aeruginosa (P. aeruginosa). The P. aeruginosa genome also encodes the highly potent and specific APR peptide inhibitor (APRin). However, the structural reason for the significant inhibition has not been revealed. Using ab initio molecular simulations, we here investigated the specific interactions between APR and APRin to elucidate which amino acid residues of APRin and APR contribute strongest to the inhibition. Since APR has a Zn²⁺ ion at the ligand-binding site and histidine and glutamic acid residues are coordinated with Zn²⁺, it is essential to precisely describe these coordination bonds to elucidate the specific interactions between APR and APRin. Therefore, we employed the ab initio fragment molecular orbital method to investigate the specific interactions at an electronic level. The results revealed that Ser1 and Ser2 at the N-terminus of APRin significantly contribute to the binding between APRin and APR. In particular, Ser1 binds strongly to Zn²⁺ as well as to the sidechains of His176(Hid), His180(Hid), and His186(Hid) in APR. This is the main reason for the strong interaction between APR and APRin. The results also elucidated significant contributions of the positively charged Arg83 and Arg90 residues of APRin to the binding with APR. These findings may provide information useful for the design of novel small agents as potent APR inhibitors.

Protonation tuned dipolar order mediated 1H→13C cross-polarization for dissolution-dynamic nuclear polarization experiments

A strategy of dipolar order mediated nuclear spin polarization transfer has recently been combined with dissolution-dynamic nuclear polarization (dDNP) and improved by employing optimized shaped radiofrequency pulses and suitable molecular modifications. In the context of dDNP experiments, this offers a promising means of transferring polarization from high-gamma ¹H spins to insensitive ¹³C spins with lower peak power and lower energy compared with state-of-the-art cross-polarization schemes. The role of local molecular groups and the glassing matrix protonation level are both postulated to play a key role in the polarization transfer pathway via an intermediary reservoir of dipolar spin order. To gain appreciation of the mechanisms involved in the dipolar order mediated polarization transfer under dDNP conditions, we investigate herein the influence of the pivotal characteristics of the sample makeup: (i) revising the protonation level for the constituents of the DNP glass; and (ii) utilizing deuterated molecular derivatives. Experimental demonstrations are presented for the case of [1-¹³C]sodium acetate. We find that the proton sample molarity has a large impact on both the optimal parameters and the performance of the dipolar order mediated cross-polarization sequence, with the ¹³C signal build-up time drastically shortened in the case of high solvent protonation levels. In the case of a deuterated molecular derivative, we observe that the nearby ²H substituted methyl group is deleterious to the ¹H→¹³C transfer phenomenon (particularly at low levels of sample protonation). Overall, increased solvent protonation makes the dipolar order governed polarization transfer significantly faster and more efficient. This study sheds light on the influential sample formulation traits which govern the dipolar order-controlled transfer of polarization and indicates that the polarization transfer efficiencies of deuterated molecules can be boosted and reach high performances simply by adequate solvent protonation.

Influence of pH on radical reactions between kynurenic acid and amino acids tryptophan and tyrosine. Part II. Amino acids within the protein globule of lysozyme

An acidosis, a decrease of pH within a living tissue, may alter yields of radical reactions if participating radicals undergo partial or complete protonation. One of photosensitizers found in the human eye lens, kynurenic acid (KNA^-), possesses pKa 5.5 for its radical form that is close to physiological pH 6.89 for a healthy lens. In this work we studied the influence of pH on mechanisms and products of photoinduced radical reactions between KNA^- and amino acids tryptophan (Trp) and tyrosine (Tyr) within a globule of model protein, Hen White Egg Lysozyme (HEWL). Our results show that the rate constant of back electron transfer from kynurenyl to HEWL^• radicals with the restoration of initial reagents - the major decay pathway for these radicals - does not change in the pH 3-7. The quantum yield of HEWL degradation is also pH independent, however a shift of pH from 7 to 5 completely changes the outcome of photoinduced damage to HEWL from intermolecular cross-linking to oxygenation. HPLC-MS analysis has shown that four of six Trp and all Tyr residues of HEWL are modified in different extents at all pH, but the lowering of pH from 7 to 5 significantly changes the direction of main photodamage from Trp⁶² to Trp¹⁰⁸ located at the entrance and bottom of enzymatic center, respectively. A decrease of intermolecular cross-links via Trp⁶² is followed by an increase in quantities of intramolecular cross-links Tyr²⁰-Tyr²³ and Tyr²³-Tyr⁵³. The obtained results point out the competence of cross-linking and oxygenation reactions for Trp and Tyr radicals within a protein globule and significant increase of oxygenation to the total damage of protein in the case of cross-linking deceleration by coulombic repulsion of positively charged protein globules.

Protonation of the oxo-bridged heme/copper assemblies: Modeling the oxidized state of the cytochrome c oxidase active site

In this study on model compounds for the resting oxidized state of the iron‑copper binuclear center in cytochrome c oxidase (CcO), we describe the synthesis of a new μ-oxo-heme/Cu complex, [(TPP)Fe^III-O-Cu^II(tmpa)][B(C₆F₅)₄] (2) {TPP: tetraphenyl porphyrinate(2-); TMPA: tris(2-pyridylmethylamine)}, as well as two protonation events for three μ-oxo-heme/Cu complexes with varying peripheral substituents on the heme site. The addition of increasing amounts of strong acid to these μ-oxo-heme/Cu systems successively led to the generation of the corresponding μ-hydroxo, μ-aquo, and the dissociated complexes. The heme/Cu assemblies bridged through a water ligand are reported here for the first time and the ¹H NMR and ¹⁹F NMR spectral properties are consistent with antiferromagnetically coupled high-spin iron(III) and copper(II) centers. By titration using a series of protonated amines, the pK_a values for the corresponding μ-hydroxo-heme/Cu species (i.e., the first protonation event) have been reported and compared with the pK_a ranges previously estimated for related systems. These synthetic systems may represent structural models for the oxidized Fe^III-X-Cu^II resting state, or turnover intermediates and can be employed to clarify the nature of proton/electron transfer events in CcO. SYNOPSIS: The resting oxidized state of the cytochrome c oxidase active site contains an Fe_a3-OH_x-Cu_B moiety. Here, we investigated two successive protonation events, for a series of μ-oxo-heme/Cu assemblies and reported the pK_a values for the first protonation event. The μ-aquo-heme/Cu complexes described here are the first examples of such systems.

Influence of pH on radical reactions between kynurenic acid and amino acids tryptophan and tyrosine. Part I. Amino acids in free state

In the human eye lens the endogenous chromophores of UV-A light (315-400 nm) are able to sensitize radical reactions leading to protein modifications during normal aging and the cataract progression. Kynurenic acid (KNA^-) is the most photochemically active dye of the human eye lens reported to date with pK_a(KNAH₂^•) 5.5 for its radical form. Cataract is thought to develop under oxidative stress which could be accompanied by acidosis, an acidification of the intracellular environment. Protonation of kynurenyl radicals at mildly acidic conditions may change the outcome of radical reactions leading to additional damage to proteins. In this work we investigated the influence of pH on the degradation of initial reagents and the formation of products in photoinduced radical reactions between KNA^- and amino acids tryptophan (Trp) and tyrosine (Tyr) in free states. Our results have shown that pH variation has minor influence on kinetics of reagent decay and accumulation of products in reactions between tyrosyl and kynurenic acid radicals. However in the case of Trp a two-fold decrease of the reagent degradation without visible changes in the composition of formed products was observed with pH decrease from 7 to 3. Time-resolved measurements have shown similar acidification-induced two-fold acceleration of decay of kynurenyl and tryptophanyl radicals via Back Electron Transfer (BET) with the restoration of initial reagents. Experiments with tryptophan derivatives with different pK_a values for their radical forms point out the protonation of tryptophanyl radical as the driving force for BET acceleration at low pH. Our results demonstrate that the protonation of kynurenyl radical does not change its reactivity towards amino acids radicals but the total yield of radical photodamage decreases with the protonation of tryptophanyl radicals. It could be expected that radical induced damage to proteins will depend on the pK_a of tryptophanyl radicals within a protein globule.

pK a Calculations in Membrane Proteins from Molecular Dynamics Simulations

The conformational changes of membrane proteins are crucial to their function and usually lead to fluctuations in the electrostatic environment of the protein surface. A very effective way to quantify these changes is by calculating the pK _a values of the protein's titratable residues, which can be regarded as electrostatic probes. To achieve this, we need to take advantage of the fast and reliable pK _a calculators developed for globular proteins and adapt them to include the explicit effects of membranes. Here, we provide a detailed linear response approximation protocol that uses our own software (PypKa) to calculate reliable pK _a values from short MD simulations of membrane proteins.

Mononuclear nickel(II) dithiolate complexes with chelating diphosphines: Insight into protonation and electrochemical proton reduction

Inspired by the metal active sites of [FeFe]- and [NiFe]‑hydrogenases, a series of mononuclear Ni(II) ethanedithiolate complexes [{(Ph₂PCH₂)₂×}Ni(SCH₂CH₂S)] (X = NCH₂C₅H₄N-p (2a), NCH₂C₆H₅ (2b), NCH₂CHMe₂ (2c), and CH₂ (2d)) with chelating diphosphines were readily synthesized through the room-temperature treatments of mononuclear Ni(II) dichlorides [{(Ph₂PCH₂)₂×}NiCl₂] (1a-1d) with ethanedithiol (HSCH₂CH₂SH) in the presence of triethylamine (Et₃N) as acid-binding agent. All the as-prepared complexes 1a-1d and 2a-2d are fully characterized through elemental analysis, nuclear magnetic resonance (NMR) spectrum, and by X-ray crystallography for 1b, 2a-2d. To further explore proton-trapping behaviors of this type of mononuclear Ni(II) complexes for catalytic hydrogen (H₂) evolution, the protonation and electrochemical proton reduction of 2a-2c with aminodiphosphines (labeled PCNCP = (Ph₂PCH₂)₂NR) and reference analogue 2d with nitrogen-free diphosphine (dppp = (Ph₂PCH₂)₂CH₂) are studied and compared under trifluoroacetic acid (TFA) as a proton source. Interestingly, the treatments of 2a-2d with excess TFA resulted in the unexpected formation of dinuclear Ni(II)-Ni(II) dication complexes [{(Ph₂PCH₂)₂×}₂Ni₂(μ-SCH₂CH₂S)](CF₃CO₂)₂ (3a-3d) and mononuclear Ni(II) N-protonated complexes [{(Ph₂PCH₂)₂N(H)R}Ni(SCH₂CH₂S)](CF₃CO₂) (4a-4c), which has been well supported by high-resolution electrospray ionization mass spectroscopy (HRESI-MS), NMR (³¹P, ¹H) as well as fourier transform infrared spectroscopy (FT-IR) techniques, and especially by X-ray crystallography for 3d. Additionally, the electrochemical properties of 2a-2d are investigated in the absence and presence of strong acid (TFA) by using cyclic voltammetry (CV), showing that the complete protonation of 2a-2d gave rise to dinuclear Ni₂S₂ species 3a-3d for electrocatalytic proton reduction to H₂.

Single-strand DNA-nanorod conjugates - tunable anisotropic colloids for on-demand self-assembly

Directed self-assembly uses different stimuli to initiate and control the interaction between nanocrystals. Protonation at reduced pH represents a convenient stimulus for initiating self-assembly. Prior work has focused on protonation-induced hydrogen bonding between peptide or amino acid functionalized nanocrystals for reversible cycling between dispersed and aggregated states. Here, we discuss a fundamentally different approach, in which changes in pH modify the nonspecific interparticle interaction between Au nanorods conjugated with single-stranded (ss) DNA. While electrostatic repulsion stabilizes dispersed suspensions at neutral pH, protonation in acidic solution modifies the DNA corona, turning the interaction between the rods attractive and triggering their self-assembly. Analysis of in-situ electron microscopy of ssDNA-Au nanorods in solution is consistent with a van der Waals attraction of charge-neutral monomers at acidic pH. The results demonstrate ssDNA-conjugated anisotropic nanostructures as versatile building blocks with stimuli-programmable interactions for on-demand self-assembly.

Quantum-refinement studies of the bidentate ligand of V‑nitrogenase and the protonation state of CO-inhibited Mo‑nitrogenase

Nitrogenase is the only enzyme that can cleave the triple bond in N₂, making nitrogen available to plants (although the enzyme itself is strictly microbial). It has been studied extensively with both experimental and computational methods, but many details of the reaction mechanism are still unclear. X-ray crystallography is the main source of structural information for biomacromolecules, but it has problems to discern hydrogen atoms or to distinguish between elements with the same number of electrons. These problems can sometimes be alleviated by introducing quantum chemical calculations in the refinement, providing information about the ideal structure (in the same way as the empirical restraints used in standard crystallographic refinement) and comparing different interpretations of the structure with normal crystallographic and quantum mechanical quality measures. We have performed such quantum-refinement calculations to address two important issues for nitrogenase. First, we show that the bidentate ligand of the active-site FeV cluster in V‑nitrogenase is carbonate, rather than bicarbonate or nitrate. Second, we study the CO-inhibited structure of Mo‑nitrogenase. CO binds to a reduced and protonated state of the enzyme by replacing one of the sulfide ions (S2B) in the active-site FeMo cluster. We examined if it is possible to deduce from the crystal structure the location of the protons. Our results indicates that the crystal structure is best modelled as fully deprotonated.

The assembly of silica species with alkylamines: Mechanism of wastewater-free synthesis and the application of gel as a catalyst

Silica species generated by the hydrolysis and condensation of tetraethyl orthosilicate (TEOS) could assemble with alkylamines to form silica gel. Herein, it was evidenced that part of the added amines, including butylamine (BA), octylamine (OA) or dodecylamine (DA), was protonated in the mixture of water and ethanol. Therefore, besides the hydrogen bonding between neutral silica species and the micelles composed of the non-protonated amines (Tanev and Pinnavaia, 1995), there existed strong electrostatic attraction between negatively charged silica species and the micelles composed of the protonated amines. This coexisting assembly mechanism could explain why the uncalcined BA- and OA-gels were millimeter-sized small blocks with large porosities and synthesized without waste water emission, while the uncalcined DA-gel was almost non-porous and formed via precipitation from its reaction medium. The uncalcined BA gel was proved to be efficient as a solid basic catalyst, replacing the commonly used ammonia solution which is easily volatilized and has a pungent smell, for the hydrolysis and condensation of TEOS to prepare silica microspheres.

Aquaporins with lactate/lactic acid permeability at physiological pH conditions

The spectrum of putative and experimentally shown permeants of cellular water and solute channels of the ubiquitous aquaporin family is still increasing. Virtually all AQP substrates, e.g. water, glycerol, urea, hydrogen peroxide, or carbon dioxide, are permanently neutral small molecule compounds. Several reports, however, describe aquaporins that exhibit lactate permeability. Lactate in aqueous solution undergoes a pH-dependent protonation equilibrium with neutral lactic acid, which likely represents the actual substrate form passing the aquaporin channel. Certain aquaporins, however, appear to be better geared for lactate/lactic acid permeability even at low proton availability. Here, we discuss the structural properties of such aquaporins and compare them to the microbial protein family of the formate-nitrite (lactate) transporters that assume the aquaporin fold despite unrelated protein sequences.

A novel near-infrared fluorescent probe with large stokes shifts for sensing extreme acidity and its application in bioimaging

In this work, we reported a novel near-infrared (NIR) fluorescent probe RQNN with large Stokes shift (98 nm) for monitoring pH under extremely acidic conditions. For the preparation of this probe, a 1,4-diethylpiperazine moiety was introduced in rhodamine scaffold to tune the electron-donating character, and an o-phenylenediamine was introduced in spironolactone to provide larger steric hindrance. The deprotonated-protonated equilibrium between RQNN, RQNN-H⁺ and RQNN-H⁺⁺ were evaluated in different pH by absorption and emission spectra. As expected, RQNN exhibited lower pk_a values (pk_a1 = 4.83, pk_a2 = 2.99), indicating that the probe can be used in extremely acidic pH. Moreover, RQNN possessed highly selective response to H⁺ over essential metal ions and biologically related redox molecules, high photo-stability, rapid response time, and excellent reversibility. Importantly, the probe had excellent cell membrane permeability and was further applied successfully to monitor pH fluctuations in live cells.

Comparison of the properties of standard soil and aquatic fulvic and humic acids based on the data of differential absorbance and fluorescence spectroscopy

This study compared effects of pH, ionic strength and complexation with Mg²⁺ on the chromophores and fluorophores of aquatic and terrestrial NOM exemplified by the standard isolates Suwannee River fulvic and humic acid (SRFA and SRHA) and Pahokee Peat fulvic and humic acids (PPFA and PPHA) provided by the International Humic Substance Society (IHSS). The intensity of the differential spectra of the NOM isolates increased monotonically with pH. These spectra comprised contributions of similar chromophore systems associated with the carboxylic and phenolic moieties. The intensity of SRFA and PPFA fluorescence changed non-monotonically vs. pH indicating that the deprotonation of the phenolic fluorophores decreased their emission yields. Examination of the effects of pH on the slopes of the log-transformed absorbance of NOM showed that the influence of deprotonation on the conformations of PPFA and PPHA molecules was less prominent than those for SRFA but not dissimilar to those of SRHA. Changes of the differential spectra and spectral slopes showed that Mg²⁺/PPFA and Mg²⁺/PPHA complexation was more effected by electrostatic interactions while the involvement of phenolic groups was notable for SRFA. The observed trends highlight similarities and differences in the properties of the chromophores and fluorophores in the standard isolates of soil and aquatic NOM. These results necessitate further systematic comparison of the properties of NOM isolates and those of unaltered NOM.

Preparation of C3N5 nanosheets with enhanced performance in photocatalytic methylene blue (MB) degradation and H2-evolution from water splitting

Ultrathin C₃N₅ nanosheets with enhanced photocatalytic methylene blue (MB) degradation and H₂-evolution performance were prepared from thermal treatment of 3-amino-1,2,4-triazole (3-AT) and NH₄Cl followed with a protonate procedure. The characterization results revealed that the protonating process could contribute to the exfoliation of C₃N₅ with large surface area, the effective charge transfer capability and the modified band structure. The as-prepared C₃N₅ nanosheets exhibited enhanced properties in photocatalytic reactions such as MB photodegradation and H₂-evolution from water splitting. This study offered a feasible route to prepare highly-efficient two-dimensional photocatalyst, which could be applied potentially for implementation in wide range of energy generation and environmental applications.

Formulation of anomerization and protonation in d-glucosamine, based on 1H NMR

The major anomer of non-protonated neutral d-glucosamine GlcN⁰ is the β-form, while the α-anomer is dominant for protonated cationic glucosamine GlcNH⁺. The present work confirmed correlation between the anomerization and the protonation by simultaneous determination of signal intensity and chemical shift in pD-variation ¹H NMR, and formulated the equilibrium constants between subspecies α-GlcN⁰, β-GlcN⁰, α-GlcND⁺, and β-GlcND⁺ to interpret the correlation. The individual anomerization constants, K_an = [βGlcN]/[αGlcN] and K_anD = [βGlcND⁺]/[αGlcND⁺], are linked to each other through the relation K_Dα∙K_anD = K_Dβ∙K_an with the deuteration constants K_Dα and K_Dβ of the anomers. The anomer populations are stimulated by OD^- and D⁺ ions in the dose-response form. The acidic deuteron in α-GlcND⁺ is populated mostly at the nitrogen atom, whereas the population in β-GlcND⁺ is comparable at nitrogen and anomeric oxygen; this difference is consistent with the basicity of the nitrogen and the anomerization process of glucosamine.

Low-molecular-weight organic acids enable biochar to immobilize nitrate

Batch experiments were conducted using two biochar materials produced from different feedstocks to examine the behavior of solution-borne nitrate in the presence and absence of three model low-molecular weight organic acids (LMWOAs). The results showed that the biochar materials alone were not able to remove the solution-borne nitrate. LMWOAs caused protonation of the biochar surfaces and consequently enabled the biochar materials to adsorb nitrate from the solution. Different types of LMWOA had different capacities to immobilize solution-borne nitrate. Over 80% of the solution-borne nitrate could be removed within 72 h in the presence of citric acid or malic acid. By comparison, removal rate of nitrate was lower in the presence of oxalic acid, possibly due to competition of oxalate ion with nitrate for the available adsorption sites on the biochar surfaces. Nitrate adsorption onto the MSP700 biochar in the presence of all three-LMWOAs followed first order and second order kinetics, suggesting that the immobilization of nitrate involved complex interplay of physisorption and chemisorption. Nitrate adsorption onto RH700 biochar in citric and malic acid treatment systems followed second order kinetics. In the presence of oxalic acid for both biochar materials, nitrate adsorption showed perfect correlation R² = 1 for both models.

IMAGINE: The neutron protein crystallography beamline at the high flux isotope reactor

IMAGINE is a high intensity, quasi-Laue neutron crystallography beamline developed at the 85MW High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory (ORNL). This state-of-the-art facility for neutron-diffraction enables neutron protein structures to be determined at or near atomic resolutions from crystals with volumes of <1mm³ and unit cell edges of <150Å. The beamline features include elliptical focusing mirrors that deliver neutrons into a 2.0×3.2mm² focal spot at the sample position, and variable short and long wavelength cutoff optics that provide automated exchange between multiple wavelength configurations. The beamline is equipped with a single-axis goniometer, neutron-sensitive cylindrical image plate detector and room temperature and cryogenic sample environments. This article describes the beamline components, the diffractometer and the data collection and data analysis protocols that are used, and outlines the protein deuteration, crystallization and conventional crystallography capabilities that are available to users at ORNL's neutron facilities. We also present examples of the scientific questions being addressed at this beamline and highlight important findings in enzyme chemistry that have been made possible by IMAGINE.

Construction of electrochemical sensing interface towards Cd(II) based on activated g-C3N4 nanosheets: considering the effects of exfoliation and protonation treatment

There is an urgent need to construct highly selective low-cost sensors for fast detection of toxic metal ions such as cadmium. When compared with 3D bulk materials, 2D layered materials after activation treatments show superior performances for electrochemical metal ion detection. The bulk graphitic carbon nitride (hereafter b-g-C₃N₄) was prepared by thermal polymerization with urea as a precursor; it was then activated through ultrasonic liquid exfoliation and protonation which resulted in successful fabrication of activated ultrathin g-C₃N₄ nanosheets (hereafter a-g-C₃N₄). The a-g-C₃N₄-modified glassy carbon electrode demonstrates excellent electrochemical performances for Cd²⁺ detection with 22.668 μA/μM sensitivity and 3.9 nM LOD (S/N = 3) due to high specific surface area and active sites created on the 2D layered structure. The chemical interference of Pb²⁺, Cu²⁺, and Hg²⁺ on Cd²⁺ detection was minimal. We have also measured Cd²⁺ in natural water and rice samples using the newly developed a-g-C₃N₄-modified electrode with high spike recoveries. Our results demonstrate the potential applications of newly developed a-g-C₃N₄-modified electrode for rapid detection of toxic metal ions in different sample matrixes. Graphical Abstract The activated g-C₃N₄ nanosheets (a-g-C₃N₄) were synthesized and used to construct electrochemical sensors with high sensitivity and anti-interference performance.

Hydrogen bonding and protonation effects in amino acids' anthraquinone derivatives - Spectroscopic and electrochemical studies

Six novel amino acid chromophores were synthesized and their spectroscopic, acid-base, and electrochemical properties are discussed in this work. In studied compounds, selected amino acid residues (l-Aspartic acid, l-Glutamic acid, l-Glutamine, l-Histidine, l-Lysine, l-Arginine) are attached to the 1-(piperazine) 9,10-anthraquinone skeleton via the amide bond between the carboxyl group of amino acid and nitrogen atom of the piperazine ring. All derivatives have been characterized using a variety of spectroscopic techniques (mass spectrometry, 1HNMR, UV-Vis, IR spectroscopy), acid-base (electrochemical and UV-Vis) titrations, and cyclic voltammetry methods. Basing on observed experimental effects, supported by quantum chemical simulations, the structure-properties links were established. They are indicative of the specific interactions within and/or in-between amino acid side groups, which are prone to form both, intra- and intermolecular hydrogen bonds as well as electrostatic interactions with the anthraquinone system.

Identification of a pH sensor in Influenza hemagglutinin using X-ray crystallography

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X-ray crystallography identifies a conserved histidine, HA1-H38, that changes side chain conformation at low pH.

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We attribute the observed conformational change to cation-cation repulsion between protonated HA1-H18 and HA1-H38.

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We suggest that the HA1-H18 and HA1-H38 pair plays a role in the pathway toward the postfusion conformation of HA.

Hemagglutnin (HA) mediates entry of influenza virus through a series of conformational changes triggered by the low pH of the endosome. The residue or combination of residues acting as pH sensors has not yet been fully elucidated. In this work, we assay pH effects on the structure of H5 HA by soaking HA crystallized at pH 6.5 in a series of buffers with lower pH, mimicking the conditions of the endosome. We find that HA1-H38, which is conserved in Group 1 HA, undergoes a striking change in side chain conformation, which we attribute to its protonation and cation-cation repulsion with conserved HA1-H18. This work suggests that x-ray crystallography can be applied for studying small-scale pH-induced conformational changes providing valuable information on the location of pH sensors in HA. Importantly, the observed change in HA1-H38 conformation is further evidence that the pH-induced conformational changes of HA are the result of a series of protonation events to conserved and non-conserved pH sensors.

Structural and Energetic Effects of O2'-Ribose Methylation of Protonated Pyrimidine Nucleosides

The 2'-substituents distinguish DNA from RNA nucleosides. 2'-O-methylation occurs naturally in RNA and plays important roles in biological processes. Such 2'-modifications may alter the hydrogen-bonding interactions of the nucleoside and thus may affect the conformations of the nucleoside in an RNA chain. Structures of the protonated 2'-O-methylated pyrimidine nucleosides were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy, assisted by electronic structure calculations. The glycosidic bond stabilities of the protonated 2'-O-methylated pyrimidine nucleosides, [Nuom+H]⁺, were also examined and compared to their DNA and RNA nucleoside analogues via energy-resolved collision-induced dissociation (ER-CID). The preferred sites of protonation of the 2'-O-methylated pyrimidine nucleosides parallel their canonical DNA and RNA nucleoside analogues, [dNuo+H]⁺ and [Nuo+H]⁺, yet their nucleobase orientation and sugar puckering differ. The glycosidic bond stabilities of the protonated pyrimidine nucleosides follow the order: [dNuo+H]⁺ < [Nuo+H]⁺ < [Nuom+H]⁺. The slightly altered structures help explain the stabilization induced by 2'-O-methylation of the pyrimidine nucleosides.

Leaving Group Effects in a Series of Electrosprayed CcHhN1 Anthracene Derivatives

We investigate the gas-phase structures and fragmentation pathways of model compounds of anthracene derivatives of the general formula C_cH_hN₁ utilizing tandem mass spectrometry and computational methods. We vary the substituent alkyl chain length, composition, and degree of branching. We find substantial experimental and theoretical differences between the linear and branched congeners in terms of fragmentation thresholds, available pathways, and distribution of products. Our calculations predict that the linear substituents initially isomerize to form lower energy branched isomers prior to loss of the alkyl substituents as alkenes. The rate-determining chemistry underlying these related processes is dominated by the ability to stabilize the alkene loss transition structures. This task is more effectively undertaken by branched substituents. Consequently, analyte lability systematically increased with degree of branching (linear < secondary < tertiary). The resulting anthracen-9-ylmethaniminium ion generated from these alkene loss reactions undergoes rate-limiting proton transfer to enable expulsion of either hydrogen cyanide or CNH. The combination of the differences in primary fragmentation thresholds and degree of radical-based fragmentation processes provide a potential means of distinguishing compounds that contain branched alkyl chain substituents from those with linear ones.

Structural Properties of Gas-Phase Molybdenum Oxide Clusters [Mo4O13]2-, [HMo4O13]-, and [CH3Mo4O13]- Studied by Collision-Induced Dissociation

Molybdenum oxide-based catalysts are widely used for the ammoxidation of toluene, methanation of CO, or hydrodeoxygenation. As a first step towards a gas-phase model system, we investigate here structural properties of mass-selected [Mo₄O₁₃]^2-, [HMo₄O₁₃]^-, and [CH₃Mo₄O₁₃]^- by a combination of collision-induced dissociation (CID) experiments and quantum chemical calculations. According to calculations, the common structural motif is an eight-membered ring composed of four MoO₂ units and four O atoms. The 13th O atom is located above the center of the ring and connects two to four Mo centers. For [Mo₄O₁₃]^2- and [HMo₄O₁₃]^-, dissociation requires opening or rearrangement of the ring structure, which is quite facile for the doubly charged [Mo₄O₁₃]^2-, but energetically more demanding for [HMo₄O₁₃]^-. In the latter case, the hydrogen atom is found to stay preferentially with the negatively charged fragments [HMo₂O₇]^- or [HMoO₄]^-. The doubly charged species [Mo₄O₁₃]^2- loses one MoO₃ unit at low energies while Coulomb explosion into the complementary fragments [Mo₂O₆]^- and [Mo₂O₇]^- dominates at elevated collision energies. [CH₃Mo₄O₁₃]^- affords rearrangements of the methyl group with low barriers, preferentially eliminating formaldehyde, while the ring structure remains intact. [CH₃Mo₄O₁₃]^- also reacts efficiently with water, leading to methanol or formaldehyde elimination.

Impact of Sodium Cationization on Gas-Phase Conformations of DNA and RNA Cytidine Mononucleotides

Gas-phase conformations of the sodium-cationized forms of the 2'-deoxycytidine and cytidine mononucleotides, [pdCyd+Na]⁺ and [pCyd+Na]⁺, are examined by infrared multiple photon dissociation action spectroscopy. Complimentary electronic structure calculations at the B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) level of theory provide candidate conformations and their respective predicted IR spectra for comparison across the IR fingerprint and hydrogen-stretching regions. Comparisons of the predicted IR spectra and the measured infrared multiple photon dissociation action spectra provide insight into the impact of sodium cationization on intrinsic mononucleotide structure. Further, comparison of present results with those reported for the sodium-cationized cytidine nucleoside analogues elucidates the impact of the phosphate moiety on gas-phase structure. Across the neutral, protonated, and sodium-cationized cytidine mononucleotides, a preference for stabilization of the phosphate moiety and nucleobase orientation is observed, although the details of this stabilization differ with the state of cationization. Several low-energy conformations of [pdCyd+Na]⁺ and [pCyd+Na]⁺ involving several different orientations of the phosphate moiety and sugar puckering modes are observed experimentally.

A new perylene-based fluorescent pH chemosensor for strongly acidic condition

A highly selective and sensitive pH chemosensor N,N-bis[(2-thiophene)-ethyl]-3,4,9,10-perylene tetracarboxylic diimide (TEPTD) was designed and synthesized through Schiff-base condensation reaction. It exhibited large Stokes shifts, good water solubility, excellent selectivity and outstanding photo-stability. The pK_a of the probe was 3.0, which indicated that it could be used in highly acid conditions. With the addition of H⁺, the fluorescence intensity increased gradually. The sensing mechanisms involved photo-induced electron transfer, protonation and deprotonation, which were confirmed by ¹H NMR titration experiment with trifluoroacetic acid. The probe can be used as a convenient probe to distinguish acidic from neutral or alkaline solutions by "naked-eye".

Theoretical and experimental study on the effects of pH and surfactant on the internal charge transfer process in distyrylnaphthalene-based conjugated oligoelectrolytes

In this study we have investigated the effects of pH and surfactant on the internal charge transfer (ICT) process in the DSNN derivative, DSNN-NMe⁺₃ (4,4'-bis(4'-(N,N-bis(6″-(N,N,N-trimethylammonium)hexyl)amino)-styryl) naphthalene tetraiodide) with the aim to show that environmentally-induced changes in the degree of ICT process determine the spectral response of the DSNN chromophore. Obtained results showed that DSNN chromophore exhibits evident changes in linear optical properties (absorption/emission wavelengths, quantum yield) upon protonation. These changes are a manifestation of the attenuation of the internal charge transfer processes, which accompanies binding of proton to the nitrogen atoms of the dialkylamino groups at the termini of DSNN chromophore. The results obtained in this study clearly demonstrated the sensitivity of the ICT process in DSNN upon protonation, which, together with the affinity of DSNN towards biological and artificial membranes, may open new perspectives for its utility in fluorescence-based sensing. Moreover, the studied compound showed substantial surfactochromic effects in the ionic and non-ionic surfactant solutions, which indicate the formation of various self-organized DSNN-surfactant aggregates. The structure of these aggregates is determined by the type of specific intermolecular interactions between the chromophore and surfactant molecules. The knowledge of the nature of these interactions may be substantial in the future development of DSNN-based sensing platforms with suitable optical properties.

Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules

Small-molecule protonation can promote or discourage protein binding by altering hydrogen-bond, electrostatic, and van-der-Waals interactions. To improve virtual-screen pose and affinity predictions, researchers must account for all major small-molecule ionization states. But existing programs for calculating these states have notable limitations such as high cost, restrictive licenses, slow execution times, and poor modularity. Here, we present dimorphite-DL 1.0, a fast, accurate, accessible, and modular open-source program for enumerating small-molecule ionization states. Dimorphite-DL uses a straightforward empirical algorithm that leverages substructure searching and draws on a database of experimentally characterized ionizable molecules. We have tested dimorphite-DL using several versions of Python and RDKit on all major operating systems. We release it under the terms of the Apache License, Version 2.0. A copy is available free of charge from http://durrantlab.com/dimorphite-dl/.

Fluorescence regional integration and differential fluorescence spectroscopy for analysis of structural characteristics and proton binding properties of fulvic acid sub-fractions

Structural characteristics and proton binding properties of sub-fractions (FA₃-FA₁₃) of fulvic acid (FA), eluted stepwise by pyrophosphate buffer were examined by use of fluorescence titration combined with fluorescence regional integration (FRI) and differential fluorescence spectroscopy (DFS). Humic-like (H-L) and fulvic-like (F-L) materials, which accounted for more than 80% of fluorescence response, were dominant in five sub-fractions of FA. Based on FRI analysis, except the response of F-L materials in FA₉ and FA₁₃, maximum changes in percent fluorescence response were less than 10% as pH was increased from 2.5 to 11.5. Contents of carboxylic and phenolic groups were compared for fluorescence peaks of FA sub-fractions based on pH-dependent fluorescence derived from DFS. Static quenching was the dominant mechanism for binding of protons by FA sub-fractions. Dissociation constants (pKa) were calculated by use of results of DFS and the modified Stern-Volmer relationship. The pK_a of H-L, F-L, tryptophan-like and tyrosine-like materials of FA sub-fractions exhibited ranges of 3.17-4.06, 3.12-3.97, 4.14-4.45 and 4.25-4.76, respectively, for acidic pHs. At basic pHs, values of pKa for corresponding materials were in ranges of 9.71-10.24, 9.62-10.99, 9.67-10.31 and 9.33-10.28, respectively. At acidic pH, protein-like (P-L) materials had greater affinities for protons than did either H-L or F-L materials. The di-carboxylic and phenolic groups were likely predominant sites of protonation for both H-L and F-L materials at both acidic and basic pHs. Amino acid groups were significant factors during proton binding to protein-like materials of FA sub-fractions at basic pH.

Degradation mechanisms of carbamazepine by δ-MnO2: Role of protonation of degradation intermediates

Carbamazepine (CBZ), a widely used antiepileptic drug, is refractory to biological wastewater treatment. Rapid removal of CBZ is possible using synthetic manganese oxide (δ-MnO₂) but the removal mechanisms require further investigation. In this study, CBZ degradation by δ-MnO₂ was carried out at different pH to further explore the degradation mechanisms. Results show that CBZ degradation by δ-MnO₂ was highly pH dependent, and rapid degradation occurred when pH <2.8. Based on the density functional theory calculations, increasing [H⁺] not only increased the reactivity of δ-MnO₂, but also enhanced the secondary reactions of the intermediates. During the degradation process, protonation of CBZ degradation intermediates, instead of CBZ, played an important role. The overall kinetics of CBZ degradation was then described by the retarded first-order model. The initial rate (r_init) in the model between pH 2.0 and 6.2 was determined to be r_init = (2.41 ± 0.51) × 10^-3[CBZ]^1.21[MnO₂]^1.07[H⁺]^1.41. This is the first report revealing that protonation of intermediates from CBZ degradation can improve the CBZ oxidation by δ-MnO2. The pathways of CBZ degradation by δ-MnO₂ were also proposed. The results of this study provide a new insight into the processing mechanism.

Concurrent reduction-adsorption of chromium using m-phenylenediamine-modified magnetic chitosan: kinetics, isotherm, and mechanism

Magnetic chitosan particles (MCS) were chemically grafted by m-phenylenediamine (mPD) forming a distinctive shell layer with abundant nitrogenous functional groups and used as an adsorbent for the effective removal of Cr(VI) from aqueous solution. By interaction among functional groups in the facile oxidative polymerization process, the grafting of mPD and its polymers on MCS surface was innovatively realized. Through Fourier-transformed infrared spectroscopy, energy dispersive spectrometer, X-ray photoelectron spectroscopy, etc., the chemical properties of MCS before and after modification were characterized and the concurrent reduction-adsorption mechanism in Cr(VI) adsorption by mPD-MCS was carefully analyzed. The maximal Cr(VI) removal performance of mPD-MCS reached 227.27 mg/g, which was significantly better than that of the original MCS. The analysis indicated that Cr(VI) could be efficiently reduced to Cr(III) and the removal of Cr(VI) and Cr(III) was through adsorption and chelation simultaneously by mPD-MCS. Results also indicated that the concurrent reduction-adsorption was enhanced by protonation of nitrogenous functional groups under low pH. The obtained results suggest that mPD-MCS has a good potential in removal and detoxication of Cr(VI) from aqueous solutions.

Positive effect of strong acidity on the twist of Aβ42 fibrils and the counteraction of Aβ42 N-terminus

pH is a crucial factor in terms of affecting the aggregation and morphology of β-Amyloid and hence a focus of study. In this study, structural and mechanical properties of a series of models (5, 6, …, 30 layer) of one-fold Aβ₄₂ fibrils at pH 1.5, 3.0 and 7.5, have been computed by using all-atom molecular dynamics simulations. 12, 14, and 15 layers are established to be the smallest realistic models for Aβ₄₂ fibrils at pH 1.5, 3.0 and 7.5, with twist angles of 0.40°, 0.34°, 0.31° respectively, disclosing the favorable effect of strong acidity on fibril twist. However, these angles are all lower than that (0.48°) determined for the truncated Aβ_17-42 fibril at pH 7.5, indicating that the disordered N-terminal depresses greatly the fibril twist and the lower pH disfavors the depression. Three commonly used indices to measure the fibril properties, namely number of H-bonds, interstrand distance and β-sheet content have imperceptible changes with the pH alternation, therefore changes in fibril twist can be taken as a probe to monitor fibril properties. By contrast, N-terminus is determined not only to inhibit the U-shaped fibril twist by hampering the stagger between β1 and β2 strands, but also to play a vital carrier role in feeling solution (i.e., pH, salt) changes. These results can help design the nextgeneration of amyloid materials for state-of-the-art bio-nano-med applications by changing the solution pH or modifying chain length.

Water-soluble polyol-methanofullerenes as mitochondria-targeted antioxidants: Mechanism of action

The mechanism of an antioxidant action of water-soluble polyol - methanofullerenes C₆₀[C₉H₁₀O₄(OH)₄]₆ and C₆₀[C₁₃H₁₈O₄(OH)₄]₆ as the mild uncouplers of an oxidative phosphorylation and respiration is postulated. According to this mechanism, hydroxyl group of methanofullerenols can be protonated under excess of protons in the intermembrane space of hyperpolarized mitochondria. Protonation of fullerene derivatives is confirmed by the decrease in their negative Zeta potential in the pH below 5.4. Heavily protonated methanofullerenols become positively charged and move into the mitochondrial matrix. As a consequence, the proton gradient is dissipated, which causes a decrease in mitochondrial transmembrane potential (ΔΨ_m) and reduction in ROS production.

Refining Protein Penetration into the Lipid Bilayer Using Fluorescence Quenching and Molecular Dynamics Simulations: The Case of Diphtheria Toxin Translocation Domain

Dynamic disorder of the lipid bilayer presents a challenge for establishing structure-function relationships in membranous systems. The resulting structural heterogeneity is especially evident for peripheral and spontaneously inserting membrane proteins, which are not constrained by the well-defined transmembrane topology and exert their action in the context of intimate interaction with lipids. Here, we propose a concerted approach combining depth-dependent fluorescence quenching with Molecular Dynamics simulation to decipher dynamic interactions of membrane proteins with the lipid bilayers. We apply this approach to characterize membrane-mediated action of the diphtheria toxin translocation domain. First, we use a combination of the steady-state and time-resolved fluorescence spectroscopy to characterize bilayer penetration of the NBD probe selectively attached to different sites of the protein into membranes containing lipid-attached nitroxyl quenching groups. The constructed quenching profiles are analyzed with the Distribution Analysis methodology allowing for accurate determination of transverse distribution of the probe. The results obtained for 12 NBD-labeled single-Cys mutants are consistent with the so-called Open-Channel topology model. The experimentally determined quenching profiles for labeling sites corresponding to L350, N373, and P378 were used as initial constraints for positioning TH8-9 hairpin into the lipid bilayer for Molecular Dynamics simulation. Finally, we used alchemical free energy calculations to characterize protonation of E362 in soluble translocation domain and membrane-inserted conformation of its TH8-9 fragment. Our results indicate that membrane partitioning of the neutral E362 is more favorable energetically (by ~ 6 kcal/mol), but causes stronger perturbation of the bilayer, than the charged E362.

Role of proton balance in formation of self-assembled chitosan nanoparticles

Researchers have explored the ability of chitosan to form nanoparticles, to suit varying applications, ranging from wound-healing to gene delivery. Ionic gelation is a widely used method for formulating chitosan nanoparticles, where self-assembly plays a crucial role. This self-assembly is initially promoted by hydrophilic-hydrophobic parity amongst individual chitosan residues, along with electrostatic and Van der Waals interactions with the cross-linker. However, until now the intrinsic ability of chitosan to self-assemble is not widely studied; hence, we investigate the self-assembly of chitosan, based on proton balance between its protonated and deprotonated residues, to promote facile nanoparticle synthesis. This is one of the first reports that highlights subtle but critical influence of proton balance in the chitosan polymer on the formation of chitosan nanoparticles.