Proton Positions Research Articles

New insights into the oxidation process from neutron and X-ray crystal structures of an O2-sensitive [NiFe]-hydrogenase.

[NiFe]-hydrogenase from Desulfovibrio vulgaris Miyazaki F is an O2-sensitive enzyme that is inactivated in the presence of O2 but the oxidized enzyme can recover its catalytic activity by reacting with H2 under anaerobic conditions. Here, we report the first neutron structure of [NiFe]-hydrogenase in its oxidized state, determined at a resolution of 2.20 Å. This resolution allowed us to reinvestigate the structure of the oxidized active site and to observe the positions of protons in several short hydrogen bonds. X-ray anomalous scattering data revealed that a part of the Ni ion is dissociated from the active site Ni-Fe complex and forms a new square-planar Ni complex, accompanied by rearrangement of the coordinated thiolate ligands. One of the thiolate Sγ atoms is oxidized to a sulfenate anion but remains attached to the Ni ion, which was evaluated by quantum chemical calculations. These results suggest that the square-planar complex can be generated by the attack of reactive oxygen species derived from O2, as distinct from one-electron oxidation leading to a conventional oxidized form of the Ni-Fe complex. Another major finding of this neutron structure analysis is that the Cys17S thiolate Sγ atom coordinating to the proximal Fe-S cluster forms an unusual hydrogen bond with the main-chain amide N atom of Gly19S with a distance of 3.25 Å, where the amide proton appears to be delocalized between the donor and acceptor atoms. This observation provides insight into the contribution of the coordinated thiolate ligands to the redox reaction of the Fe-S cluster.

Observation of proton-transfer-coupled spin transition by single-crystal neutron-diffraction measurement.

The application of single-crystal neutron diffraction (SCND) to observe proton-transfer phenomena in crystalline compounds exhibiting unusual protonation states or proton dynamics has garnered significant research interest in recent years. However, proton tautomerism, which results in different protonation states before and after proton transfer, has never been observed using the SCND technique. Thus, to observe the proton tautomerism phenomenon by SCND measurements, we developed an iron(II) complex that forms a large crystal and exhibits a proton-transfer-coupled spin transition (PCST). The presence of the two types of proton tautomers was determined by conventional analysis of the proton position by X-ray crystallography, infrared spectroscopy, and density functional theory calculations. Finally, our results confirmed that proton tautomerism was successfully observed for the first time using variable-temperature SCND measurements.

Interplay of Hydration and Protonation Dynamics in the K-Channel of Cytochrome c Oxidase.

Cytochrome c oxidase is a membrane protein of the respiratory chain that consumes protons and molecular oxygen to produce water and uses the resulting energy to pump protons across the membrane. Our molecular dynamics simulations with an excess proton located at different positions in one of the proton-conducting channels, the K-channel, show a clear dependence of the number of water molecules inside the channel on the proton position. A higher hydration level facilitates the formation of hydrogen-bonded chains along which proton transfer can occur. However, a sufficiently high hydration level for such proton transport is observed only when the excess proton is located above S365, i.e., the lower third of the channel. From the channel entrance up to this point, proton transport is via water molecules as proton carriers. These hydronium ions move with their surrounding water molecules, up to K362, filling and widening the channel. The conformation of K362 depends on its own protonation state and on the hydration level, suggesting its role to be proton transport from a hydronium ion at the height of K362 to the upper part of the channel via a conformational change. The protonation-dependent conformational dynamics of E101 at the bottom of the channel renders proton transfer via E101 unlikely. Instead, its role is rather that of an amplifier of H96's proton affinity, suggesting H96 as the initial proton acceptor.

The structures of eleven (4-phen-yl)piperazinium salts containing organic anions.

Eleven (4-phen-yl)piperazinium salts containing organic anions have been prepared and structurally characterized, namely, 4-phenyl-piperazin-1-ium 4-fluoro-benzoate monohydrate, C10H15N2 +·C7H4FO2 -·H2O, 1; 4-phenyl-piperazin-1-ium 4-bromo-benzoate monohydrate, C10H15N2 +·C7H4BrO2 -·H2O, 3; 4-phenyl-piperazin-1-ium 4-iodo-benzoate, C10H15N2 +·C7H4IO2 -, 4; 4-phenyl-piperazin-1-ium 4-nitro-benzoate, C10H15N2 +·C7H4NO4 -, 5; 4-phenyl-piperazin-1-ium 3,5-di-nitro-salicylate, C10H15N2 +·C7H3N2O7 -, 6; 4-phenyl-piperazin-1-ium 3,5-di-nitro-benzoate, C10H15N2 +·C7H3N2O6 -, 7; 4-phenyl-piperazin-1-ium picrate, C10H15N2 +·C6H2N3O7 -, 8; 4-phenyl-piperazin-1-ium benzoate monohydrate, C10H15N2 +·C7H5O2 -·H2O, 9; 4-phenyl-piperazin-1-ium p-toluene-sulfonate, C10H15N2 +·C7H7O3S-, 10; 4-phenyl-piperazin-1-ium tartarate monohydrate, C10H15N2 +·C4H5O6 -·H2O, 11; and 4-phenyl-piperazin-1-ium fumarate, C10H15N2 +·C4H3O4 -, 12. Compounds 1 and 3-12 are all 1:1 salts with the acid proton transferred to the phenyl-piperaizine basic N atom (the secondary amine) with the exception of 3 where there is disorder in the proton position with it being 68% attached to the base and 32% attached to the acid. Of the structures with similar stoichiometries only 3 and 9 are isomorphous. The 4-phenyl substituent in all cases occupies an equatorial position except for 12 where it is in an axial position. The crystal chosen for structure 7 was refined as a non-merohedral twin. There is disorder in 5, 6, 10 and 11. For both 5 and 6, a nitro group is disordered and was modeled with two equivalent orientations with occupancies of 0.62 (3)/0.38 (3) and 0.690 (11)/0.310 (11), respectively. For 6, 10 and 11, this disorder is associated with the phenyl ring of the phenyl-piperazinium cation with occupancies of 0.687 (10)/0.313 (10), 0.51 (7)/0.49 (7) and 0.611 (13)/389 (13), respectively. For all salts, the packing is dominated by the N-H⋯O hydrogen bonds formed by the cation and anion. In addition, several structures contain C-H⋯π (1, 3, 4, 8, 9, 10, and 12) and aromatic π-π stacking inter-actions (6 and 8) and one structure (5) contains a -NO2⋯π inter-action. For all structures, the Hirshfeld surface fingerprint plots show the expected prominent spikes as a result of the N-H⋯O and O-H⋯O hydrogen bonds.

A coarse-grained approach to NMR-data-assisted modeling of protein structures.

The ESCASA algorithm for analytical estimation of proton positions from coarse-grained geometry developed in our recent work has been implemented in modeling protein structures with the highly coarse-grained UNRES model of polypeptide chains (two sites per residue) and nuclear magnetic resonance (NMR) data. A penalty function with the shape of intersecting gorges was applied to treat ambiguous distance restraints, which automatically selects consistent restraints. Hamiltonian replica exchange molecular dynamics was used to carry out the conformational search. The method was tested with both unambiguous and ambiguous restraints producing good-quality models with GDT_TS from 7.4units higher to 14.4units lower than those obtained with the CYANA or MELD software for protein-structure determination from NMR data at the all-atom resolution. The method can thus be applied in modeling the structures of flexible proteins, for which extensive conformational search enabled by coarse-graining is more important than high modeling accuracy.

The effect of hydrostatic compression on the crystal structure of glycinium phosphite

The crystal structure of glycinium phosphite (GPI) was studied in the pressure range from ambient to 6.5 GPa at 293 K using single-crystal X-ray diffraction. The changes in the unit-cell volume and parameters were continuous and anisotropic. The major compression was observed normal to the direction of the spontaneous polarization that occurs in this structure during a ferroelectric phase transition on cooling, whereas the structural compression along the b axis coinciding with the 21 axis was almost zero. The effect of pressure on the hydrogen bonds linking the H2PO3 tetrahedra into zigzag chains along the c axis was different from that on the hydrogen bonds connecting the glycinium cations with the H2PO3 tetrahedra in the (b × c) plane. The discontinuous changes in the geometries of selected hydrogen bonds at about 1.21 GPa may be evidence of a phase transition, e.g. into an ordered ferroelectric phase (with ordered positions of protons). The anisotropy of compression of GPI in the ferroelectric state (at 0 K) was studied using DFT calculations taking into account dispersive van der Waals interactions. The calculations predicted negative linear compressibility along the b axis.

Ultrafast opto-protonics in a hydrogen-bonded π-molecular ferroelectric crystal

We investigated the ultrafast photo-response of a ferroelectric co-crystal of Hdppz–Hca composed of protonated 2,3-di (2-pyridinyl)pyrazine (Hdppz) and deprotonated chloranilic acid (Hca). Whereas the intermolecular proton transfer triggers the ferroelectricity in Hdppz–Hca, the majority of the large spontaneous polarization has a quantum mechanical origin from the highly polarizable π-electron system. In this study, we prepared a carrier-envelope phase-stable mid-infrared pulse tuned to the proton vibration of this system and investigated the time dependence of the subsequent change in the second harmonic generation (SHG) yield. By exciting the proton vibration, the relative change in SHG yield increased by about 100%, and the enhancement was only observed within the duration of the applied electric field. The huge enhancement and ultrafast response of the SHG, which is not seen in usual ferroelectrics, is attributed to the fact that the photoexcitation dynamically changes the stable position of protons and π-electrons, resulting in an ultrafast increase in the value of χ(2) of Hdppz–Hca. The phenomena observed here indicate a new property of this system as a quantum material with nonlinearity and can be regarded as opto-protonics in proton-mediated ferroelectrics.

Proton transfer in La2-xCaxZr2O7-δ pyrochlores: Reasons for limited water uptake and high grain boundary conductivity

Proton-conducting electrolytes based on zirconates with a pyrochlore-like structure are known for their excellent thermal and chemical stability, low grain boundaries (GB) resistance, and low contribution of electronic conductivity. However, the values of proton conductivity seem to be undermined by insufficient incorporation of protons into the structure. The current study aims to identify the causes of these barriers from standpoints of crystal and defect structure, water uptake, and proton transfer. The thermogravimetric analysis (TGA) results show limited water uptake, which is ∼60% of the theoretical value. We show that several oxygen vacancies are not involved in the hydration, due to a significant structural nonequivalence of oxygen sites in the pyrochlore. Additionally, the proton positions themselves are energetically nonequivalent due to the different electrostatic repulsion energy of protons from the nearest cations, which ultimately leads to a weak proton transfer in the bulk of the material. At the same time, we observe the segregation of Ca on the grain boundaries without any impurity formation. This leads to the high apparent GB conductivity according to electrochemical impedance spectroscopy. These findings suggest that the proton conductivity of pyrochlore-like zirconates could be improved by tailoring their GBs instead of perfecting bulk properties.

Irregular particle morphology and membrane rupture facilitate ion gradients in the lumen of phagosomes

Localized fluxes, production, and/or degradation coupled to limited diffusion are well known to result in stable spatial concentration gradients of biomolecules in the cell. In this study, we demonstrate that this also holds true for small ions, since we found that the close membrane apposition between the membrane of a phagosome and the surface of the cargo particle it encloses, together with localized membrane rupture, suffice for stable gradients of protons and iron cations within the lumen of the phagosome. Our data show that, in phagosomes containing hexapod-shaped silica colloid particles, the phagosomal membrane is ruptured at the positions of the tips of the rods, but not at other positions. This results in the confined leakage at these positions of protons and iron from the lumen of the phagosome into the cytosol. In contrast, acidification and iron accumulation still occur at the positions of the phagosomes nearer to the cores of the particles. Our study strengthens the concept that coupling metabolic and signaling reaction cascades can be spatially confined by localized limited diffusion.

Revisiting the concept of peptide bond planarity in an iron-sulfur protein by neutron structure analysis.

The planarity of the peptide bond is important for the stability and structure formation of proteins. However, substantial distortion of peptide bonds has been reported in several high-resolution structures and computational analyses. To investigate the peptide bond planarity, including hydrogen atoms, we report a 1.2-Å resolution neutron structure of the oxidized form of high-potential iron-sulfur protein. This high-resolution neutron structure shows that the nucleus positions of the amide protons deviate from the peptide plane and shift toward the acceptors. The planarity of the H─N─C═O plane depends strongly on the pyramidalization of the nitrogen atom. Moreover, the orientation of the amide proton of Cys75 is different in the reduced and oxidized states, possibly because of the electron storage capacity of the iron-sulfur cluster.

Comparative accuracy and resolution assessment of two prototype proton computed tomography scanners.

Improving the accuracy of relative stopping power (RSP) in proton therapy may allow reducing range margins. Proton computed tomography (pCT) has been shown to provide state-of-the-art RSP accuracy estimation, and various scanner prototypes have recently been built. The different approaches used in scanner design are expected to impact spatial resolution and RSPaccuracy. The goal of this study was to perform the first direct comparison, in terms of spatial resolution and RSP accuracy, of two pCT prototype scanners installed at the same facility and by using the same image reconstructionalgorithm. A phantom containing cylindrical inserts of known RSP was scanned at the phase-II pCT prototype of the U.S. pCT collaboration and at the commercially oriented ProtonVDA scanner. Following distance-driven binning filtered backprojection reconstruction, the radial edge spread function of high-density inserts was used to estimate the spatial resolution. RSP accuracy was evaluated by the mean absolute percent error (MAPE) over the inserts. No direct imaging dose estimation was possible, which prevented a comparison of the two scanners in terms of RSPnoise. In terms of RSP accuracy, both scanners achieved the same MAPE of 0.72% when excluding the porous sinus insert from the evaluation. The ProtonVDA scanner reached a better overall MAPE when all inserts and the body of the phantom were accounted for (0.81%), compared to the phase-II scanner (1.14%). The spatial resolution with the phase-II scanner was found to be 0.61lp/mm, while for the ProtonVDA scanner somewhat lower at 0.46lp/mm. The comparison between two prototype pCT scanners operated in the same clinical facility showed that they both fulfill the requirement of an RSP accuracy of about 1%. Their spatial resolution performance reflects the different design choices of either a scanner with full tracking capabilities (phase-II) or of a more compact tracker system, which only provides the positions of protons but not their directions (ProtonVDA).

Revealing Intra- and Intermolecular Interactions Determining Physico-Chemical Features of Selected Quinolone Carboxylic Acid Derivatives.

The intra- and intermolecular interactions of selected quinolone carboxylic acid derivatives were studied in monomers, dimers and crystals. The investigated compounds are well-recognized as medicines or as bases for further studies in drug design. We employed density functional theory (DFT) in its classical formulation to develop gas-phase and solvent reaction field (PCM) models describing geometric, energetic and electronic structure parameters for monomers and dimers. The electronic structure was investigated based on the atoms in molecules (AIM) and natural bond orbital (NBO) theories. Special attention was devoted to the intramolecular hydrogen bonds (HB) present in the investigated compounds. The characterization of energy components was performed using symmetry-adapted perturbation theory (SAPT). Finally, the time-evolution methods of Car–Parrinello molecular dynamics (CPMD) and path integral molecular dynamics (PIMD) were employed to describe the hydrogen bond dynamics as well as the spectroscopic signatures. The vibrational features of the O-H stretching were studied using Fourier transformation of the autocorrelation function of atomic velocity. The inclusion of quantum nuclear effects provided an accurate depiction of the bridged proton delocalization. The CPMD and PIMD simulations were carried out in the gas and crystalline phases. It was found that the polar environment enhances the strength of the intramolecular hydrogen bonds. The SAPT analysis revealed that the dispersive forces are decisive factors in the intermolecular interactions. In the electronic ground state, the proton-transfer phenomena are not favourable. The CPMD results showed generally that the bridged proton is localized at the donor side, with possible proton-sharing events in the solid-phase simulation of stronger hydrogen bridges. However, the PIMD enabled the quantitative estimation of the quantum effects inclusion—the proton position was moved towards the bridge midpoint, but no qualitative changes were detected. It was found that the interatomic distance between the donor and acceptor atoms was shortened and that the bridged proton was strongly delocalized.

Rationalising the regioselectivity of substituted phenols from the FERMO concept: stereoelectronic effects on protonation and functionalization

ABSTRACT The relative extent of protonation in oxygen and carbon atoms and the position of protonation in carbons depend on several factors. We seek to locate the frontier molecular orbitals involved in the protonation reactions of substituted phenols using the FERMO concept through the MOLPROJ software, to compare the computational results with experimental NMR data obtained in the literature. We evaluate computationally the stereo-electronic effects that govern reactions of aromatic electrophilic substitution using an experimental study as an example. The MOLPROJ returned a percentage of correct answers of approximately 86% in the protonation sites. The experimental results on the protonation sites were rationalised in terms of stereoelectronic effects.

Inside out Approach to Rotator State in Hydrogen-Bonded System-Experimental and Theoretical Cross-Examination in n-Octanol.

The experimental and theoretical description of premelting behavior is one of the most challenging tasks in contemporary material science. In this paper, n-octanol was studied using a multi-method approach to investigate it at macroscopic and molecular levels. The experimental infrared (IR) spectra were collected in the solid state and liquid phase at temperature range from C to −15 C to detect temperature-related indicators of pretransitional phenomena. Next, the nonlinear dielectric effect (NDE) was measured at various temperatures (from −30 C to −15 C) to provide insight into macroscopic effects of premelting. As a result, a two-step mechanism of premelting in n-octanol was established based on experimental data. It was postulated that it consists of a rotator state formation followed by the surface premelting. In order to shed light onto molecular-level processes, classical molecular dynamics (MD) was performed to investigate the time evolution of the changes in metric parameters as a function of simulation temperature. The applied protocol enabled simulations in the solid state as well as in the liquid (the collapse of the ordered crystal structure). The exact molecular motions contributing to the rotator state formation were obtained, revealing an enabling of the rotational freedom of the terminal parts of the chains. The Car–Parrinello molecular dynamics (CPMD) was applied to support and interpret experimental spectroscopic findings. The vibrational properties of the stretching of OH within the intermolecular hydrogen bond were studied using Fourier transformation of the autocorrelation function of both dipole moments and atomic velocity. Finally, path integral molecular dynamics (PIMD) was carried out to analyze the quantum effect’s influence on the bridged proton position in the hydrogen bridge. On the basis of the combined experimental and theoretical conclusions, a novel mechanism of the bridged protons dynamics has been postulated—the interlamellar hydrogen bonding pattern, resulting in an additional OH stretching band, visible in the solid-state experimental IR spectra.

Structural Insights Into Tautomeric Dynamics in Nucleic Acids and in Antiviral Nucleoside Analogs.

DNA (2′-deoxyribonucleic acid) and RNA (ribonucleic acid) play diverse functional roles in biology and disease. Despite being comprised primarily of only four cognate nucleobases, nucleic acids can adopt complex three-dimensional structures, and RNA in particular, can catalyze biochemical reactions to regulate a wide variety of biological processes. Such chemical versatility is due in part to the phenomenon of nucleobase tautomerism, whereby the bases can adopt multiple, yet distinct isomeric forms, known as tautomers. For nucleobases, tautomers refer to structural isomers that differ from one another by the position of protons. By altering the position of protons on nucleobases, many of which play critical roles for hydrogen bonding and base pairing interactions, tautomerism has profound effects on the biochemical processes involving nucleic acids. For example, the transient formation of minor tautomers during replication could generate spontaneous mutations. These mutations could arise from the stabilization of mismatches, in the active site of polymerases, in conformations involving minor tautomers that are indistinguishable from canonical base pairs. In this review, we discuss the evidence for tautomerism in DNA, and its consequences to the fidelity of DNA replication. Also reviewed are RNA systems, such as the riboswitches and self-cleaving ribozymes, in which tautomerism plays a functional role in ligand recognition and catalysis, respectively. We also discuss tautomeric nucleoside analogs that are efficacious as antiviral drug candidates such as molnupiravir for coronaviruses and KP1212 for HIV. The antiviral efficacy of these analogs is due, in part, to their ability to exist in multiple tautomeric forms and induce mutations in the replicating viral genomes. From a technical standpoint, minor tautomers of nucleobases are challenging to identify directly because they are rare and interconvert on a fast, millisecond to nanosecond, time scale. Nevertheless, many approaches including biochemical, structural, computational and spectroscopic methods have been developed to study tautomeric dynamics in RNA and DNA systems, and in antiviral nucleoside analogs. An overview of these methods and their applications is included here.

Molecular origins of Epoxy-Amine/Iron oxide interphase formation

HypothesisInterphase properties in composites, adhesives and protective coatings can be predicted on the basis of interfacial interactions between polymeric precursor molecules and the inorganic surface during network formation. The strength of molecular interactions is expected to determine local segmental mobility (polymer glass transition temperature, Tg) and cure degree. ExperimentsConventional analysis techniques and atomic force microscopy coupled with infrared (AFM-IR) are applied to nanocomposite specimens to precisely characterise the epoxy-amine/iron oxide interphase, whilst molecular dynamics simulations are applied to identify the molecular interactions underpinning its formation. FindingsAttenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy and high-resolution AFM-IR mapping confirm the presence of nanoscale under-cured interphase regions. Interfacial segregation of the molecular triethylenetetraamine (TETA) cross-linker results in an excess of epoxy functionality near synthetic hematite, (Fe2O3) magnetite (Fe3O4) and goethite (Fe(O)OH) particle surfaces. This occurs independently of the variable surface binding energies, as a result of entropic segregation during the cure. Thermal analysis and molecular dynamics simulations demonstrate that restricted segmental motion is imparted by strong interfacial binding between surface Fe sites in goethite, where the position of surface hydroxyl protons enables synergistic hydrogen bonding and electrostatic binding to Fe atoms at specific sites. This provides a strong driving force for molecular orientation resulting in significantly raised Tg values for the goethite composite samples.

Experimental and theoretical evaluation of a novel organic proton transfer crystal p-Toluidinium 5‑chloro-2-hydroxybenzoate for third order nonlinear optical applications

In the present work, novel organic p-Toluidinium 5‑chloro-2-hydroxybenzoate (PT5C) single crystal was grown by slow evaporation solution growth method using ethanol as solvent at room temperature. The lattice parameters and crystal system of PT5C were analyzed by single crystal (SCXRD) X-ray diffraction studies. The crystalline nature and phase purity were identified by powder X-ray diffraction (PXRD) analysis. FT-IR and 1H NMR felicitate to identify the various vibrational and the occurrence of various proton positions in the grown crystal respectively. The cut-off wavelength and bandgap energy value were analyzed by the UV–Vis study. The TG/DSC establishes the thermal nature of the PT5C crystal. The microhardness test was performed to estimate the mechanical nature and third-order nonlinear optical characteristics of PT5C were analyzed by the Z-scan technique. Density functional theory (DFT) computations were performed with the B3LYP method /6–311++G (d,p) basis set. The optimized geometry, Frontier molecular orbital (FMO) analysis, Mulliken population analysis, electrostatic potential (ESP), and natural bond orbital (NBO) analysis were computed.

Crystal structures and high-temperature and high-pressure vibrational spectra of synthetic fluorine-bearing brucites

Abstract Brucite [Mg(OH)2] has been extensively studied as a simple yet important analog for studying physical and chemical properties of hydrous minerals, and fluorine substitution (OH– = F–) is common in hydrous minerals since the radius of F– is similar to that of O2−. We synthesized two F-bearing brucite samples, Mg(OH)1.78F0.22 and Mg(OH)1.16F0.84, at 9.5 GPa and 1373 K. Single-crystal X-ray diffraction measurements indicate that both phases still crystallize in the space group of P3m1, and fluorine substitution significantly reduces the unit-cell volume, axial lengths, and averaged Mg-O(F) bond lengths. The averaged O···H distances get slightly shortened, and the H-O-H angles become smaller due to the fluorine effect. Additional IR-active OH-stretching bands are observed at 3660, 3644, and 3513 cm−1 for the F-bearing samples, besides the original one at 3695 cm−1. In situ high-temperature and high-pressure Raman and Fourier transform infrared (FTIR) spectra were collected on the F-bearing brucite samples, and comparisons were made with the natural one with 0.7 mol% F–. The temperature dependence [(∂vi/∂T)P] of the OH-stretching modes is inversely correlated to the vibrational frequencies from 3500 to 3700 cm−1, whereas (∂vi/∂P)T is in positive correlation with vi. In addition, the dehydration temperatures of the F-bearing brucites are 100–150 K higher than that for the F-free sample at ambient pressure. By creating new proton positions in lower energies, fluorine substitution stabilizes hydrous minerals (like brucite) to higher temperatures and significantly affects their thermodynamic properties, which has significant implications in mineral physical and geochemical studies.

The Relationship between Enzyme Conformational Change, Proton Transfer, and Phosphoryl Transfer in β-Phosphoglucomutase

Molecular details for the timing and role of proton transfer in phosphoryl transfer reactions are poorly understood. Here, we have combined QM models, experimental NMR measurements, and X-ray structures to establish that the transition of an archetypal phosphoryl transfer enzyme, βPGM, from a very closed near-attack conformation to a fully closed transition state analogue (TSA) conformation triggers both partial proton transfer from the general acid–base residue to the leaving group oxygen and partial dissociation of the transferring phosphoryl group from the leaving group oxygen. Proton transfer continues but is not completed throughout the reaction path of the phosphoryl transfer with the enzyme in the TSA conformation. Moreover, using interacting quantum atoms (IQA) and relative energy gradient (REG) analysis approaches, we observed that the change in the position of the proton and the corresponding increased electrostatic repulsion between the proton and the phosphorus atom provide a stimulus for phosphoryl transfer in tandem with a reduction in the negative charge density on the leaving group oxygen atom. The agreement between solution-phase 19F NMR measurements and equivalent QM models of βPGMWT and βPGMD10N TSA complexes confirms the protonation state of G6P in the two variants, validating the employed QM models. Furthermore, QM model predictions of an AlF4 distortion in response to the proton position are confirmed using high resolution X-ray crystal structures, not only providing additional validation to the QM models but also further establishing metal fluorides as highly sensitive experimental predictors of active-site charge density distributions.

Crystal and Magnetic Structures of Monoclinic FeOHSO4.

The crystal and magnetic structures and properties of the monoclinic form of the iron hydroxysulfate FeOHSO4 were investigated by magnetometry and neutron powder diffraction. The space group C2/c was confirmed, and the proton position was located close to that predicted by ab initio calculations. The collinear antiferromagnetic k(0,0,0) structure forming below the Néel temperature TN ∼ 125 K is described by the C2'/c' (No. 15.89) magnetic space group, with the moments along the b axis. Overall, FeOHSO4 is isostructural to FeSO4F in terms of both the crystal and magnetic structures.