Initial Proton Transfer Research Articles

The energetics of the primary proton transfer in bacteriorhodopsin revisited: It is a sequential light-induced charge separation after all

The light-induced proton transport in bacteriorhodopsin has been considered as a model for other light-induced proton pumps. However, the exact nature of this process is still unclear. For example, it is not entirely clear what the driving force of the initial proton transfer is and, in particular, whether it reflects electrostatic forces or other effects. The present work simulates the primary proton transfer (PT) by a specialized combination of the EVB and the QCFF/PI methods. This combination allows us to obtain sufficient sampling and a quantitative free energy profile for the PT at different protein configurations. The calculated profiles provide new insight about energetics of the primary PT and its coupling to the protein conformational changes. Our finding confirms the tentative analysis of an earlier work (A. Warshel, Conversion of light energy to electrostatic energy in the proton pump of Halobacterium halobium, Photochem. Photobiol. 30 (1979) 285–290) and determines that the overall PT process is driven by the energetics of the charge separation between the Schiff base and its counterion Asp85. Apparently, the light-induced relaxation of the steric energy of the chromophore leads to an increase in the ion-pair distance, and this drives the PT process. Our use of the linear response approximation allows us to estimate the change in the protein conformational energy and provides the first computational description of the coupling between the protein structural changes and the PT process. It is also found that the PT is not driven by twist-modulated changes of the Schiff base's p K a, changes in the hydrogen bond directionality, or other non-electrostatic effects. Overall, based on a consistent use of structural information as the starting point for converging free energy calculations, we conclude that the primary event should be described as a light-induced formation of an unstable ground state, whose relaxation leads to charge separation and to the destabilization of the ion-pair state. This provides the driving force for the subsequent PT steps.

Ultrafast Proton Transfer of Pyranine in a Supramolecular Assembly: PEO−PPO−PEO Triblock Copolymer and CTAC

Excited-state proton transfer (ESPT) of pyranine (8-hydroxypyrene-1,3,6-trisulfonate, HPTS) is studied in a polymer-surfactant aggregate using femtosecond emission spectroscopy. The polymer-surfactant aggregate is a supramolecular assembly consisting of a triblock copolymer (PEO)(20)-(PPO)(70)-(PEO)(20) (P123) and a cationic surfactant, cetyltrimethylammonium chloride (CTAC). ESPT of the protonated species (HA) in HPTS leads to the formation of A(-). The dynamics of ESPT may be followed from the decay of the HA emission (at approximately 440 nm) and rise of the A(-) emission (at approximately 550 nm). Both steady-state and time-resolved studies suggest that ESPT of HPTS in P123-CTAC aggregate is much slower than that in bulk water, in P123 micelle, or in CTAC micelle. The ratio of the steady-state emission intensities (HA/A(-)) in P123-CTAC aggregate is 2.2. This ratio is approximately 50, 12, and 2 times higher than that respectively in water, in P123 micelle, and in CTAC micelle. Retardation of ESPT causes an increase in the rise time of the A(-) emission of HPTS. In P123-CTAC aggregate, A(-) displays three rise times: 30, 250, and 2400 ps. These rise times are longer than those in CTAC micelle (23, 250, and 1800 ps), in bulk water (0.3, 3, and 90 ps), and in P123 micelle (15 and 750 ps). The rate constants for initial proton transfer, recombination, and dissociation of the ion pair are estimated using a simple kinetic scheme. The slow fluorescence anisotropy decay of HPTS in P123-CTAC aggregate is analyzed in terms of the wobbling-in-cone model.

A Quantum Mechanical Investigation of Possible Mechanisms for the Nucleotidyl Transfer Reaction Catalyzed by DNA Polymerase β

Several quantum mechanical (QM) and hybrid quantum/molecular mechanical (QM/MM) studies have been employed recently to analyze the nucleotidyl transfer reaction in DNA polymerase beta (pol beta). Our examination reveals strong dependence of the reported mechanism on the initial molecular model. Thus, we explore here several model systems by QM methods to investigate pol beta's possible pathway variations. Although our most favorable pathway involves a direct proton transfer from O3'(primer) to O2alpha(Palpha), we also discuss other initial proton-transfer steps--to an adjacent water, to triphosphate, or to aspartic units--and the stabilizing effect of crystallographic water molecules in the active site. Our favored reaction route has an energetically undemanding initial step of less than 1.0 kcal/mol (at the B3LYP/6-31G(d,p) level), and involves a slight rearrangement in the geometry of the active site. This is followed by two major steps: (1) direct proton transfer from O3'(primer) to O2alpha(Palpha) leading to the formation of a pentavalent, trigonal bipyramidal Palpha center, via an associative mechanism, at a cost of about 28 kcal/mol, and (2) breakage of the triphosphate unit (exothermic process, approximately 22 kcal/mol) that results in the full transfer of the nucleotide to the DNA and the formation of pyrophosphate. These energy values are expected to be lower in the physical system when full protein effects are incorporated. We also discuss variations from this dominant pathway, and their impact on the overall repair process. Our calculated barrier for the chemical reaction clearly indicates that chemistry is rate-limiting overall for correct nucleotide insertion in pol beta, in accord with other studies. Protonation studies on relevant intermediates suggest that, although protonation at a single aspartic residue may occur, the addition of a second proton to the system significantly disturbs the active site. We conclude that the active site rearrangement step necessary to attain a reaction-competent geometry is essential and closely related to the "pre-chemistry" avenue described recently as a key step in the overall kinetic cycle of DNA polymerases. Thus, our work emphasizes the many possible ways for DNA polymerase beta's chemical reaction to occur, determined by the active site environment and initial models.

A Water-Mediated and Substrate-Assisted Catalytic Mechanism forSulfolobus solfataricusDNA Polymerase IV

DNA polymerases are enzymes responsible for the synthesis of DNA from nucleotides. Understanding their molecular fundamentals is a prerequisite for elucidating their aberrant activities in diseases such as cancer. Here we have carried out ab initio quantum mechanical/molecular mechanical (QM/MM) studies on the nucleotidyl-transfer reaction catalyzed by the lesion-bypass DNA polymerase IV (Dpo4) from Sulfolobus solfataricus, with template guanine and Watson-Crick paired dCTP as the nascent base pair. The results suggested a novel water-mediated and substrate-assisted (WMSA) mechanism: the initial proton transfer to the alpha-phosphate of the substrate via a bridging crystal water molecule is the rate-limiting step, the nucleotidyl-transfer step is associative with a metastable pentacovalent phosphorane intermediate, and the pyrophosphate leaving is facilitated by a highly coordinated proton relay mechanism through mediation of water which neutralizes the evolving negative charge. The conserved carboxylates, which retain their liganding to the two Mg2+ ions during the reaction process, are found to be essential in stabilizing transition states. This WMSA mechanism takes specific advantage of the unique structural features of this low-fidelity lesion-bypass Y-family polymerase, which has a more spacious and solvent-exposed active site than replicative and repair polymerases.

Collision induced dissociation of deprotonated glycolic acid

Glycolic acid has been recently found to be a contaminant in a drinking water sample from Canada. An in-depth study was conducted to establish a mechanism of the unique fragmentation patterns of deprotonated glycolic acid by using ion trap and Q-TOF tandem mass spectrometry. Tandem mass spectrometry information from analysis of isotopically labeled ( 13C and D) glycolic acids revealed two general dissociation pathways of glycolate. Major fragmentation patterns, initiated by nucleophilic attack of a negatively charged carboxylic oxygen on the α-carbon, proceed through an α-lactone intermediate ion and result in formation of glyoxalate, hydroxymethanolate, formate, and hydroxyl anions. The hydroxyl anion was detected as a species solvated by a molecule of water or methanol. Minor dissociation patterns originate from the initial proton transfer from the α-carbon to a negatively charged oxygen of the carboxylic group and lead to formation of hydroxymethanolate and hydrated hydroxyl ion. Proposed mechanisms of all fragmentation patterns of glycolate are presented in detail. Postulated gas phase dissociation reactions are described in terms of charge redistribution following collisional excitation. This approach has facilitated elucidation of the unique fragmentation pathways of glycolate and provided explanation for significant differences observed in dissociation of structurally similar hydroxycarboxylic acids.

Regulation of DNA repair fidelity by molecular checkpoints: "gates" in DNA polymerase beta's substrate selection.

With an increasing number of structural, kinetic, and modeling studies of diverse DNA polymerases in various contexts, a complex dynamical view of how atomic motions might define molecular "gates" or checkpoints that contribute to polymerase specificity and efficiency is emerging. Such atomic-level information can offer insights into rate-limiting conformational and chemical steps to help piece together mechanistic views of polymerases in action. With recent advances, modeling and dynamics simulations, subject to the well-appreciated limitations, can access transition states and transient intermediates along a reaction pathway, both conformational and chemical, and such information can help bridge the gap between experimentally determined equilibrium structures and mechanistic enzymology data. Focusing on DNA polymerase beta (pol beta), we present an emerging view of the geometric, energetic, and dynamic selection criteria governing insertion rate and fidelity mechanisms of DNA polymerases, as gleaned from various computational studies and based on the large body of existing kinetic and structural data. The landscape of nucleotide insertion for pol beta includes conformational changes, prechemistry, and chemistry "avenues", each with a unique deterministic or stochastic pathway that includes checkpoints for selective control of nucleotide insertion efficiency. For both correct and incorrect incoming nucleotides, pol beta's conformational rearrangements before chemistry include a cascade of slow and subtle side chain rearrangements, followed by active site adjustments to overcome higher chemical barriers, which include critical ion-polymerase geometries; this latter notion of a prechemistry avenue fits well with recent structural and NMR data. The chemical step involves an associative mechanism with several possibilities for the initial proton transfer and for the interaction among the active site residues and bridging water molecules. The conformational and chemical events and associated barriers define checkpoints that control enzymatic efficiency and fidelity. Understanding the nature of such active site rearrangements can facilitate interpretation of existing data and stimulate new experiments that aim to probe enzyme features that contribute to fidelity discrimination across various polymerases via such geometric, dynamic, and energetic selection criteria.

Influence of the Membrane Potential on the Protonation of Bacteriorhodopsin: Insights from Electrostatic Calculations into the Regulation of Proton Pumping

Proton binding and release are elementary steps for the transfer of protons within proteins, which is a process that is crucial in biochemical catalysis and biological energy transduction. Local electric fields in proteins affect the proton binding energy compared to aqueous solution. In membrane proteins, also the membrane potential affects the local electrostatics and can thus be crucial for protein function. In this paper, we introduce a procedure to calculate the protonation probability of titratable sites of a membrane protein in the presence of a membrane potential. In the framework of continuum electrostatics, we use a modified Poisson-Boltzmann equation to include the influence of the membrane potential. Our method considers that in a transmembrane protein each titratable site is accessible for protons from only one side of the membrane depending on the hydrogen bond pattern of the protein. We show that the protonation of sites receiving their protons from different sides of the membrane is differently influenced by the membrane potential. In addition, the effect of the membrane potential is combined with the effect of the pH gradient resulting from proton pumping. Our method is applied to bacteriorhodopsin, a light-activated proton pump. We find that the proton pumping of this protein might be regulated by Asp115, a conserved residue for which no function has been identified yet. According to our calculations, the interaction of Asp115 with Asp85 leads to the protonation of the latter if the pH gradient or the membrane potential becomes too large. Since Asp85 is the primary proton acceptor in the photocycle, bacteriorhodopsin molecules in which Asp85 is protonated cannot pump protons. Furthermore, we estimate how the membrane potential affects the energetics of the individual proton-transfer reactions of the photocycle. Most reactions, except the initial proton transfer from the Schiff base to Asp85, are influenced. Our calculations give new insights into the mechanism with which bacteriorhodopsin senses the membrane potential and the pH gradient and how the proton pumping is regulated by these parameters.

Concerted proton-electron transfer in the oxidation of hydrogen-bonded phenols.

Three phenols with pendant, hydrogen-bonded bases (HOAr-B) have been oxidized in MeCN with various one-electron oxidants. The bases are a primary amine (-CPh(2)NH(2)), an imidazole, and a pyridine. The product of chemical and quasi-reversible electrochemical oxidations in each case is the phenoxyl radical in which the phenolic proton has transferred to the base, (*)OAr-BH(+), a proton-coupled electron transfer (PCET) process. The redox potentials for these oxidations are lower than for other phenols, predominately from the driving force for proton movement. One-electron oxidation of the phenols occurs by a concerted proton-electron transfer (CPET) mechanism, based on thermochemical arguments, isotope effects, and DeltaDeltaG(++)/DeltaDeltaG degrees . The data rule out stepwise paths involving initial electron transfer to form the phenol radical cations [(*)(+)HOAr-B] or initial proton transfer to give the zwitterions [(-)OAr-BH(+)]. The rate constant for heterogeneous electron transfer from HOAr-NH(2) to a platinum electrode has been derived from electrochemical measurements. For oxidations of HOAr-NH(2), the dependence of the solution rate constants on driving force, on temperature, and on the nature of the oxidant, and the correspondence between the homogeneous and heterogeneous rate constants, are all consistent with the application of adiabatic Marcus theory. The CPET reorganization energies, lambda = 23-56 kcal mol(-)(1), are large in comparison with those for electron transfer reactions of aromatic compounds. The reactions are not highly non-adiabatic, based on minimum values of H(rp) derived from the temperature dependence of the rate constants. These are among the first detailed analyses of CPET reactions where the proton and electron move to different sites.

A Kinetic Study of the Reaction between N,N‐Dimethyl‐p‐toluidine and its Electrogenerated Radical Cation in a Room Temperature Ionic Liquid

The reaction between N,N-dimethyl-p-toluidine (DMT) and the radical cation generated through its one-electron oxidation has been studied electrochemically in the room temperature ionic liquid N-methyl-N-butylpyrrolidinium bis(trifluoromethylsulfonyl)imide, [Py14][NTf2]. Kinetic information obtained as linear sweep and cyclic voltammetry collected at 5 microm, 10 microm and 0.3 mm diameter platinum disk electrodes over a range of initial substrate concentrations and scan rates spanning five orders of magnitude was complemented by chronoamperometric measurements designed to probe the rate of diffusion. At the fastest scan rates the homogeneous reactions following the initial electron transfer were effectively out-run, facilitating an assessment of the electrode kinetics using DIGISIM and a validated Nicholson's method. Through digital simulation the voltammetry was then shown to be consistent with a mechanism established for the same reaction in acetonitrile, involving dimerisation of the DMT radicals following an initial and rate-determining proton transfer step. After careful consideration of all parameters, a bimolecular rate constant of (3.4 +/- 1.1) x 10(2) dm3 mol(-1) s(-1) was deduced by fitting the data. This was compared to the equivalent value for acetonitrile and, in light of this, the implications on the viability of ionic liquids for use as alternative mainstream solvents briefly assessed.

Models for Proton-coupled Electron Transfer in Photosystem II

The coupling of proton and electron transfers is a key part of the chemistry of photosynthesis. The oxidative side of photosystem II (PS II) in particular seems to involve a number of proton-coupled electron transfer (PCET) steps in the S-state transitions. This mini-review presents an overview of recent studies of PCET model systems in the authors' laboratory. PCET is defined as a chemical reaction involving concerted transfer of one electron and one proton. These are thus distinguished from stepwise pathways involving initial electron transfer (ET) or initial proton transfer (PT). Hydrogen atom transfer (HAT) reactions are one class of PCET, in which H(+) and e (-) are transferred from one reagent to another: AH + B --> A + BH, roughly along the same path. Rate constants for many HAT reactions are found to be well predicted by the thermochemistry of hydrogen transfer and by Marcus Theory. This includes organic HAT reactions and reactions of iron-tris(alpha-diimine) and manganese-(mu-oxo) complexes. In PS II, HAT has been proposed as the mechanism by which the tyrosine Z radical (Y(Z)*) oxidizes the manganese cluster (the oxygen evolving complex, OEC). Another class of PCET reactions involves transfer of H(+) and e (-) in different directions, for instance when the proton and electron acceptors are different reagents, as in AH-B + C(+) --> A-HB(+) + C. The oxidation of Y(Z) by the chlorophyll P680 + has been suggested to occur by this mechanism. Models for this process - the oxidation of phenols with a pendent base - are described. The oxidation of the OEC by Y(Z)* could also occur by this second class of PCET reactions, involving an Mn-O-H fragment of the OEC. Initial attempts to model such a process using ruthenium-aquo complexes are described.

Initial driving force for proton transfer in Nafion

We explore the initial driving force for proton transfer in Nafion using ab initio density functional calculations. We confirm that the direct and indirect proton transfer mechanisms are possible based on the previously suggested mechanisms. The initial proton transfer involves a water molecule (H 2O) and a subsequent hydronium ion (H 3O +) via the hydrogen bonding between the aqueous media and the – SO 3 - groups of the Nafion side chains to reorganize and energetically stabilize the side chains. The proton transfer is favorably assisted via the H 2O molecule between the two – SO 3 - groups involving the internal conversion between covalent and hydrogen O–H bonds.

Excited state proton transfer of pyranine in a γ-cyclodextrin cavity

Excited state proton transfer of pyranine (8-hydroxypyrene-1,3,6-trisulfonate, HPTS) in γ-cyclodextrin (γ-CD) is studied using picosecond and femtosecond fluorescence spectroscopy. It is shown that confinement of pyranine in γ-CD cavity accelerates recombination of the geminate ion pair and slows down the initial proton transfer step and the dissociation of the geminate ion pair. This results in enhanced emission from the protonated species.

Neighbouring group processes in the deamination of protonated phenylalanine derivatives

The gas-phase fragmentation of protonated phenylalanine and a series of its derivatives (tyrosine, 4-methylphenylalanine, 4-aminophenylalanine, 4-methoxyphenylalanine, 4-tert-butylphenylalanine, 4-fluorophenylalanine, 4-chlorophenylalanine, 4-bromophenylalanine, 4-iodophenylalanine, 4-cyanophenylalanine, 4-nitrophenylalanine, 3-fluorophenylalanine, and 3,4-dichlorophenylalanine) were examined using a combination of low energy CID in a quadrupole ion trap mass spectrometer as well as DFT calculations and RRKM modelling. In particular, the relationship between the electron-donating ability of the substituent and the competitive losses of H2O + CO and NH3 were explored through the application of the Hammett equation. It was found that electron-donating substituents promote the loss of NH3, while electron-withdrawing substituents suppress the loss of NH3 and favour the H2O + CO loss fragmentation channel instead. These observations are consistent with a neighbouring group pathway operating for the loss of NH3. Molecular orbital calculation (at the B3LYP/6-31+G(d,p) level of theory) were also performed for a range of derivatives to compare the relative transition state energy barriers for three competing mechanisms: (i) the combined loss of H2O + CO, which is triggered by an initial intramolecular proton transfer from the ammonium group to hydroxyl OH, followed by the combined loss of H2O and CO to form an immonium ion; (ii) loss of NH3 via an aryl assisted neighbouring group pathway to yield a phenonium ion; (iii) loss of NH3 via a 1,2-hydride migration process, which results in the formation of a benzyl cation. The relative energy barriers for H2O + CO loss remain nearly constant, while that for both NH3 pathways increase as the substituent moves from electron-donating to electron-withdrawing. The relative transition state energy for loss of NH3 via the aryl assisted neighbouring group pathway is always lower than that of the 1,2-hydride migration process. RRKM modelling of the DFT predicted barrier heights suggest that the rate constants for H2O + CO loss are insensitive to the substituent on the ring, while the NH3 loss channels are greatly affected by the substituent. These theoretical results are consistent with the experimental observation of the relative yields of the competing fragmentation channels. Finally, comparisons with published gas phase and condensed phase studies on related systems are made.

One-electron oxidation of a hydrogen-bonded phenol occurs by concerted proton-coupled electron transfer.

The hydrogen-bonded phenol 2-(aminodiphenylmethyl)-4,6-di-tert-butylphenol (HOAr-NH2) was prepared and oxidized in MeCN by a series of one-electron oxidants. The product is the phenoxyl radical in which the phenolic proton has transferred to the amine, *OAr-NH3+. The reaction of HOAr-NH2 and tris(p-tolyl)aminium ([N(tol)3]*+) to give *OAr-NH3+ + N(tol)3 has Keq = 2.0 +/- 0.5, follows second-order kinetics with k = (1.1 +/- 0.2) x 105 M-1 s-1 (DeltaG = 11 kcal mol-1), and has a primary isotope effect kH/kD = 2.4 +/- 0.4. Oxidation of HOAr-NH2 with [N(C6H4Br)3]*+ is faster, with k congruent with 4 x 107 M-1 s-1. The isotope effect, thermochemical arguments, and the dependence of the rate on driving force (DeltaDeltaG/DeltaDeltaG degrees = 0.53) all indicate that electron transfer from HOAr-NH2 must occur concerted with intramolecular proton transfer from the phenol to the amine (proton-coupled electron transfer, PCET). The data rule out stepwise paths that involve initial electron transfer to form the phenol radical cation *+HOAr-NH2 or that involve initial proton transfer to give the zwitterion -OAr-NH3+. The dependence of the electron-transfer rate constants on driving force can be fit with the adiabatic Marcus equation, yielding a large intrinsic barrier: lambda = 34 kcal mol-1 for reactions of HOAr-NH2 with NAr3*+.

Synthesis and Protonation Chemistry of (dfepe)Pt(η2-alkyne) Complexes

An extension of prior protonolysis studies of platinum-carbon bonds to in situ generated Pt-C(sp 2 ) bonds is reported. A series of (dfepe)Pt(η 2 -RC≡CR') complexes (R = Me, R' = H; R = tert-butyl, R' = H; R = Me 3 Si, R' = Me; R = Ph, R' = Me; R = R' = Me; R = R' = Ph) have been prepared by treatment of [(dfepe)Pt(μ-H)] 2 with the corresponding alkyne in order to examine the addition of Bronsted acids to form the alkenyl complexes (dfepe)Pt(C(R')= C(H)R)(X). In the case where RC≡CR' = propyne, a small (5%) amount of the propyne-bridged dimer [(dfepe)Pt]2(μ-η 2 :η 2 -MeC≡CH) was also formed which could be prepared in pure form by the thermolysis of (dfepe)Pt(η 2 -HC≡CMe) (1) at 90 °C. Dissolution of 1 in FSO 3 H at -80 °C produced the double-proton-transfer propene adduct [(dfepe)Pt(η 2 -H 2 C=C(H)Me)-(X)] + , without evidence for a propenyl Pt(II) intermediate. In contrast, dissolution of 1 in FSO 3 D at -80 °C cleanly produced the fully deuterated propenyl complex (dfepe)Pt(C(D)= C(D)CD 3 )(OSO 2 F), which was characterized by 3 1 P and 1 3 C NMR. The direct observation of this initial proton-transfer intermediate in deuterated acid is ascribed to an unusually large kinetic isotope effect for the second proton-transfer step.

Transmission coefficient calculation for proton transfer in triosephosphate isomerase based on the reaction path potential method.

A global potential energy surface has been constructed through interpolation of our recently developed reaction path potential for chemical reactions in enzymes which is derived from combined ab initio quantum mechanical and molecular mechanical calculations. It has been implemented for the activated molecular dynamics simulations of the initial proton transfer reaction catalyzed by triosephosphate isomerase. To examine the dynamical effects on the rate constants of the enzymatic reaction, the classical transmission coefficient kappa(t) is evaluated to be 0.47 with the reactive flux approach, demonstrating considerable deviations from transition state theory. In addition, the fluctuations of protein environments have small effects on the barrier recrossing, and the transmission coefficient kappa(t) strongly depends on the fluctuations of atoms near the active site of the enzyme.

Structure elucidation of unsaturated fatty acids after vicinal hydroxylation of the double bonds by negative electrospray ionisation low-energy tandem mass spectrometry.

A method for determining the positions of double bonds in unsaturated fatty acids by use of negative electrospray ionisation low-energy tandem mass spectrometry is described. First, a vicinal hydroxylation of the double bonds of mono- and poly-unsaturated fatty acids was performed. Low-energy collision activation dissociation of the deprotonated molecules produced structurally informative ions formed by a-cleavages relative to the hydroxyl groups. Abundant fragment ions that confirmed the positions of all hydroxyl groups, and thus the positions of the double bonds in the native fatty acids, were observed in the spectra of derivatised mono-, di-, and tri-unsaturated fatty acids. Two types of ions were observed, called [alpha'(n)](-) and [alpha(n)](-). The letter n indicates the positions of the hydroxyl groups. The structurally diagnostic ions [alpha'(n)](-) were produced by cleavages distal to the hydroxyl-groups with the charge retained on the carboxylate. [alpha'(n)](-) ions originating from all hydroxyl-groups were observed in the spectra of modified mono-, di-, and tri-unsaturated fatty acids. Initial proton transfer of a hydroxyl proton to the carboxylate with subsequent cleavages proximal to the hydroxyl groups, relative to the carboxylate, resulted in the two structurally diagnostic [alpha(n)](-) ions. In hydroxylated fatty acids having two or more double bonds in their native structure, [alpha(n)](-) ions originating only from the two final hydroxyl-groups were observed. The formation of all ions of [alpha'(n)](-) and [alpha(n)](-) type can be rationalised by a six-membered transition state. Hydroxylated deprotonated tetra-, penta-, and hexa-unsaturated fatty acids also produced [alpha'(n)](-) ions indicating the positions of most of the hydroxyl-groups, whereas the [alpha(n)](-) ions were observed as described above. The method described offers a simple approach to the determination of the positions of double bonds in unsaturated fatty acids, and is an alternative to utilising di-lithiated fatty acids. The method should also be applicable when fatty acids are constituents of more complex molecules such as phospholipids.

Consequences of structural and biophysical studies for the molecular mechanism of photosynthetic oxygen evolution: functional roles for calcium and bicarbonate

Possible chemical mechanisms for catalyzing O2 evolution from water in natural photosynthesis are summarized, based on the atomic and electronic structures of the inorganic core as revealed by spectroscopic and X-ray diffraction experiments and insights gained from inorganic complexes that achieve O–O bond formation. The thermodynamic and kinetic requirements for this multi-step reaction are reexamined, including the coupling of the individual electron-proton steps (PCET) and the O–O bond formation step. The four oxygen atoms at the corners of the proposed hetero-cubical Mn3CaO4 core (3 μ3-oxos and one μ4-oxo) can be distinguished by the number and types of chemical bonds to Ca2+ and Mn (geometries and orbital hybridization). Two of these μ3-oxos, postulated as substrates, are located at unique sites indicative of sp2 + pπ hybridized orbitals. Both proposed substrate oxos are strongly hydrogen-bonded to different protein carboxylate residues, which are postulated as the initial proton transfer sites. Ca2+ is weakly bonded to these substrate oxos via non-directional ionic bonds that are postulated to provide stereochemical flexibility for the homolytic formation of the O–O bond. A previously postulated heterolytic pathway involving an electrophilic oxo and nucleophilic hydroxide species is reevaluated. We extend this mechanism by postulating roles for (bi)carbonate either in proton transfer or delivering the nucleophile for O2 formation.

Optimal alignment for enzymatic proton transfer: structure of the Michaelis complex of triosephosphate isomerase at 1.2-A resolution.

In enzyme catalysis, where exquisitely positioned functionality is the sine qua non, atomic coordinates for a Michaelis complex can provide powerful insights into activation of the substrate. We focus here on the initial proton transfer of the isomerization reaction catalyzed by triosephosphate isomerase and present the crystal structure of its Michaelis complex with the substrate dihydroxyacetone phosphate at near-atomic resolution. The active site is highly compact, with unusually short and bifurcated hydrogen bonds for both catalytic Glu-165 and His-95 residues. The carboxylate oxygen of the catalytic base Glu-165 is positioned in an unprecedented close interaction with the ketone and the alpha-hydroxy carbons of the substrate (C em leader O approximately 3.0 A), which is optimal for the proton transfer involving these centers. The electrophile that polarizes the substrate, His-95, has close contacts to the substrate's O1 and O2 (N em leader O < or = 3.0 and 2.6 A, respectively). The substrate is conformationally relaxed in the Michaelis complex: the phosphate group is out of the plane of the ketone group, and the hydroxy and ketone oxygen atoms are not in the cisoid configuration. The epsilon ammonium group of the electrophilic Lys-12 is within hydrogen-bonding distance of the substrate's ketone oxygen, the bridging oxygen, and a terminal phosphate's oxygen, suggesting a role for this residue in both catalysis and in controlling the flexibility of active-site loop.

Oxidation and electronic state dependence of proton transfer in the enzymatic cycle of cytochrome P450eryF

Hydrogen bond networks, consisting of hydrogen bonded waters anchored by polar/acidic amino acid sidechains, are often present in the vicinity of the oxygen binding clefts of P450s. Density functional and quantum dynamics calculations of a O 2 binding cleft network model of cytochrome P450eryF(CYP107A1) indicate that such structural motifs facilitate ultrafast proton transfer from network waters to the dioxygen of the reduced oxyferrous species via a multiple proton translocation mechanism with barriers of 7–10 kcal/mol on its doublet ground state, and that the energies of the proton transfer reactant and constrained proton transfer products have an electronic and oxidation state dependence [J. Am. Chem. Soc. 124 (2002) 1430]. In the present study, the origin of the oxidation state dependence is shown to have its roots in differential proton affinities while the electronic state dependence of the reduced oxyferrous heme has its origins in subtle differences in network topologies near the transition state of the initial proton transfer event. Relaxed potential surface scans and unconstrained proton transfer product optimizations indicate that the proton transfer product in both the singlet oxyferrous heme and the reduced oxyferrous heme species in a quartet state are not viable stable (bound) states relative to the reactant form. While the proton affinity of H 3O + is sufficient for it to protonate both the oxyferrous and the reduced oxyferrous heme species, hydrogen bond network stabilized water is only capable of protonating the reduced oxyferrous form. This interpretation is substantiated by study of the NO bound reduced ferrous heme of P450nor, which is isoelectronic with the oxyferrous heme and has a similar proton affinity. Density functional calculations on a more extensive O 2 binding cleft model support the multiple proton translocation mechanism of transfer but indicates that the significant negative charge density on the bound dioxygen of the reduced oxyferrous heme species, in its doublet ground state, polarizes the associated hydrogen bond network sufficiently so as to result in short, strong, low-barrier hydrogen bonds. The computed O–H–O bond distances are less than 2.55 Å and have a near degeneracy of the proton transfer reactant and initial (sudden) proton transfer products. These low-barrier hydrogen bond features, in addition to the finding of a (zero point uncorrected) barrier of 1.3 kcal/mol, indicate that proton transfer from water to the distal oxygen should be rapid, facile and may not require large curvature tunneling as originally suggested by use of a smaller model. An initial assessment of protonation of the reduced oxyferrous heme distal oxygen by a model of 6-deoxyerythronolide B (6-DEB) indicates it to be low barrier (3.8 kcal/mol) and exothermic (−2.9 kcal/mol). The combined results indicate the plausibility of simultaneous diprotonation of the distal oxygen of the reduced oxyferrous heme, leading to O–O bond scission, using the combined water network and 6-DEB substrate protonation agents.