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The Journal of Physical Chemistry. A Feb 2010An explicit application of isodesmic reaction (a proton exchange between the studied and structurally similar reference molecule), where the free energy change of the...
Density functional theory and isodesmic reaction based prediction of four stepwise protonation constants, as log KH(n), for nitrilotriacetic acid. The importance of a kind and protonated form of a reference molecule used.
An explicit application of isodesmic reaction (a proton exchange between the studied and structurally similar reference molecule), where the free energy change of the protonation reaction in water was obtained using the free energies in solution from a single continuum model, was used to predict stepwise protonation constants of nitrilotriacetic acid. Calculations were performed at the RB3LYP/6-311+G(d,p) level of theory in conjunction with the PCM-UA0 solvation model. Five reference molecules were investigated. It has been established that one must pay special attention to structural similarities between the studied and reference molecules and selection of a protonated form of the reference molecule. The protonation reactions in which the studied and reference molecule are involved in must be (if possible) of the same order; e.g., the first (or generally nth) protonation reaction of the reference molecule must be used to compute the first (or nth) protonation constant of the studied molecule. The lowest energy conformer must always be used. The first, second, third, and fourth computed protonation constants differed, on average, from experimental values by 3.3, 0.8, 0.2, and 0.2 log units, respectively. It appears that the charge on the reference molecule has more decisive influence on the accuracy of computed protonation constants than its structural differences when compared with the studied molecule. Results reported can be used as a guide in constructing isodesmic reactions useful for the theoretical prediction of protonation constants by use of methodology described in this work.
Topics: Computer Simulation; Crystallography, X-Ray; Models, Molecular; Nitrilotriacetic Acid; Protons; Quantum Theory; Solvents
PubMed: 20063850
DOI: 10.1021/jp9092964 -
Organic Letters Apr 2006[reaction: see text] Asymmetric protonation of lithium enolates was examined using commercially available amino acid derivatives as chiral proton sources. Among the...
[reaction: see text] Asymmetric protonation of lithium enolates was examined using commercially available amino acid derivatives as chiral proton sources. Among the amino acid derivatives tested, Nbeta-l-aspartyl-l-phenylalanine methyl ester was found to cause significant asymmetric induction in the protonation of lithium enolates. The enantiomeric excess (up to 88% ee) of the products obtained in the presence of a catalytic amount of the chiral proton source was higher than those obtained in the stoichiometric reaction.
Topics: Amino Acids; Aspartame; Catalysis; Lithium; Molecular Structure; Protons; Stereoisomerism
PubMed: 16597150
DOI: 10.1021/ol0603007 -
Proceedings of the National Academy of... Oct 2015Glycoside hydrolase (GH) enzymes apply acid/base chemistry to catalyze the decomposition of complex carbohydrates. These ubiquitous enzymes accept protons from solvent...
Glycoside hydrolase (GH) enzymes apply acid/base chemistry to catalyze the decomposition of complex carbohydrates. These ubiquitous enzymes accept protons from solvent and donate them to substrates at close to neutral pH by modulating the pKa values of key side chains during catalysis. However, it is not known how the catalytic acid residue acquires a proton and transfers it efficiently to the substrate. To better understand GH chemistry, we used macromolecular neutron crystallography to directly determine protonation and ionization states of the active site residues of a family 11 GH at multiple pD (pD=pH+0.4) values. The general acid glutamate (Glu) cycles between two conformations, upward and downward, but is protonated only in the downward orientation. We performed continuum electrostatics calculations to estimate the pKa values of the catalytic Glu residues in both the apo- and substrate-bound states of the enzyme. The calculated pKa of the Glu increases substantially when the side chain moves down. The energy barrier required to rotate the catalytic Glu residue back to the upward conformation, where it can protonate the glycosidic oxygen of the substrate, is 4.3 kcal/mol according to free energy simulations. These findings shed light on the initial stage of the glycoside hydrolysis reaction in which molecular motion enables the general acid catalyst to obtain a proton from the bulk solvent and deliver it to the glycosidic oxygen.
Topics: Biocatalysis; Carbohydrate Conformation; Catalytic Domain; Crystallography, X-Ray; Fungal Proteins; Glutamic Acid; Glycoside Hydrolases; Glycosides; Hydrogen Bonding; Hydrogen-Ion Concentration; Hydrolysis; Models, Chemical; Models, Molecular; Neutrons; Protein Binding; Protein Structure, Tertiary; Protons; Static Electricity; Substrate Specificity; Temperature; Trichoderma
PubMed: 26392527
DOI: 10.1073/pnas.1504986112 -
Biochimica Et Biophysica Acta Dec 1987The laser-induced proton pulse (Gutman, M. (1986) Methods Enzymol. 127, 522-538) was used for transient protonation of one side of a black lipid membrane. The charging...
The laser-induced proton pulse (Gutman, M. (1986) Methods Enzymol. 127, 522-538) was used for transient protonation of one side of a black lipid membrane. The charging of the membrane drives an electric (voltage or current) signal selectively representing the fast proton exchange at the membrane/electrolyte interface. The sensitivity of the electric signal to the presence of buffer indicates that proton transfer is measured, not some dyes or membrane photoelectric artifact. The same event can be visualized in an analogous system consisting of a pH indicator adsorbed to neutral detergent-phospholipid mixed micelles. The time-resolved light absorption transient is equivalent to the electrically determined transient charging of the membrane surface. The sensitivity of the current measurement exceeds the spectrophotometric method by 6-8 orders of magnitudes. As little as 10(-18) mol of H+ reacting with 0.75 mm2 of the membrane surface can be monitored in a time-resolved observation. Both types of observed transients were accurately reconstructed by the numerical solution of coupled, non-linear, differential equations describing the system. The rate constants of the various proton transfer reactions were calculated and found to be of diffusion controlled reactions. There is no evidence for any barrier at the interface which either prevents protons from reaching the membrane, or keeps proton on the interface. The electric measurements can be applied for monitoring proton transfer kinetics of complex biomembrane preparations.
Topics: Hydrogen-Ion Concentration; Indicators and Reagents; Lasers; Membrane Lipids; Membrane Potentials; Membranes, Artificial; Protons; Spectrophotometry
PubMed: 2825785
DOI: 10.1016/0005-2736(87)90468-8 -
Inorganic Chemistry Mar 2013Reduction and protonation of Mo(IV) imido complexes with diphosphine coligands constitutes the second part of the Chatt cycle for biomimetic reduction of N2 to ammonia....
Reduction and protonation of Mo(IV) imido complexes with diphosphine coligands constitutes the second part of the Chatt cycle for biomimetic reduction of N2 to ammonia. In order to obtain insights into the corresponding elementary reactions we synthesized the Mo(IV) ethylimido complex [Mo(CH3CN)(NEt)(depe)2](OTf)2 (2-MeCN) from the Mo(IV)-NNH2 precursor [Mo(NNH2)(OTf)(depe)2](OTf) (1). As shown by UV-vis and NMR spectroscopy, exchange of the acetonitrile ligand with one of the counterions in THF results in formation of the so far unknown complex [Mo(OTf)(NEt)(depe)2](OTf) (2-OTf). 2-MeCN and 2-OTf are studied by spectroscopy and X-ray crystallography in conjunction with DFT calculations. Furthermore, both complexes are investigated by cyclic voltammetry and spectroelectrochemistry. The complex 2-OTf undergoes a two-electron reduction in THF associated with loss of the trans ligand triflate. In contrast, 2-MeCN in acetonitrile is reduced to an unprecedented Mo(III) alkylnitrene complex [Mo(NEt)(CH3CN)(depe)2]OTf (5) which abstracts a proton from the parent Mo(IV) compound 2-MeCN, forming the Mo(III) ethylamido complex 5H and a Mo(II) azavinylidene complex 6. Compound 5 is also protonated to the Mo(III) ethylamido complex 5H in the presence of externally added acid and further reduced to the Mo(II) ethylamido complex 7. The results of this study provide further support to a central reaction paradigm of the Schrock and Chatt cycles: double reductions (and double protonations) lead to high-energy intermediates, and therefore, every single reduction has to be followed by a single protonation (and vice versa). Only in this way the biomimetic conversion of dinitrogen to ammonia proceeds on a minimum-energy pathway.
Topics: Acetonitriles; Ammonia; Imides; Ligands; Models, Molecular; Molybdenum; Nitrogen; Organometallic Compounds; Oxidation-Reduction; Phosphines; Protons; Quantum Theory
PubMed: 23398558
DOI: 10.1021/ic301828e -
Proton-detected solid-state NMR spectroscopy at aliphatic sites: application to crystalline systems.Accounts of Chemical Research Sep 2013When applied to biomolecules, solid-state NMR suffers from low sensitivity and resolution. The major obstacle to applying proton detection in the solid state is the... (Review)
Review
When applied to biomolecules, solid-state NMR suffers from low sensitivity and resolution. The major obstacle to applying proton detection in the solid state is the proton dipolar network, and deuteration can help avoid this problem. In the past, researchers had primarily focused on the investigation of exchangeable protons in these systems. In this Account, we review NMR spectroscopic strategies that allow researchers to observe aliphatic non-exchangeable proton resonances in proteins with high sensitivity and resolution. Our labeling scheme is based on u-[(2)H,(13)C]-glucose and 5-25% H2O (95-75% D2O) in the M9 bacterial growth medium, known as RAP (reduced adjoining protonation). We highlight spectroscopic approaches for obtaining resonance assignments, a prerequisite for any study of structure and dynamics of a protein by NMR spectroscopy. Because of the dilution of the proton spin system in the solid state, solution-state NMR (1)HCC(1)H type strategies cannot easily be transferred to these experiments. Instead, we needed to pursue ((1)H)CC(1)H, CC(1)H, (1)HCC or ((2)H)CC(1)H type experiments. In protonated samples, we obtained distance restraints for structure calculations from samples grown in bacteria in media containing [1,3]-(13)C-glycerol, [2]-(13)C-glycerol, or selectively enriched glucose to dilute the (13)C spin system. In RAP-labeled samples, we obtained a similar dilution effect by randomly introducing protons into an otherwise deuterated matrix. This isotopic labeling scheme allows us to measure the long-range contacts among aliphatic protons, which can then serve as restraints for the three-dimensional structure calculation of a protein. Due to the high gyromagnetic ratio of protons, longer range contacts are more easily accessible for these nuclei than for carbon nuclei in homologous experiments. Finally, the RAP labeling scheme allows access to dynamic parameters, such as longitudinal relaxation times T1, and order parameters S(2) for backbone and side chain carbon resonances. We expect that these measurements will open up new opportunities to obtain a more detailed description of protein backbone and side chain dynamics.
Topics: Crystallography, X-Ray; Magnetic Resonance Spectroscopy; Protein Structure, Tertiary; Proteins; Protons
PubMed: 23745638
DOI: 10.1021/ar400063y -
The Journal of Physical Chemistry. B Apr 2012By employing computationally intensive molecular dynamics simulations using hybrid quantum-mechanical/molecular-mechanical approach, we analyze here the kinetic and...
By employing computationally intensive molecular dynamics simulations using hybrid quantum-mechanical/molecular-mechanical approach, we analyze here the kinetic and thermodynamic stabilities of various active site protonation states of a fully solvated class C β-lactamase. We report the detailed mechanism of proton transfer between catalytically important active site residues and the associated free energy barriers. In the apoenzyme, significant structural changes are associated with the proton transfer, and the orientations of active site residues are distinctly different for various protonation states. Among several propositions on the protonation state of the apoprotein, we find that the one with Tyr150 deprotonated and both Lys67 and Lys315 residues being protonated is the most stable one, both thermodynamically and kinetically. However, the equilibrium structure at room temperature is a dynamic one, with Lys315Hζ delocalized between Tyr150Oη and Lys315Nζ. Of great importance, the kinetic and thermodynamic stability of protonation states are significantly affected on noncovalently complexing with cephalothin, an antibiotic molecule. The equilibrium structure of the enzyme-substrate (precovalent) complex has a dynamic protonation state where a proton shuttles frequently between the Tyr150Oη and Lys67Nζ. We examine here the genesis of the manifold change in stability at the molecular level. The importance of our observations toward understanding the reactivity of the enzyme is discussed and experimental observations are rationalized.
Topics: Catalytic Domain; Kinetics; Molecular Dynamics Simulation; Molecular Structure; Protons; Thermodynamics; beta-Lactamases
PubMed: 22480335
DOI: 10.1021/jp212186q -
Molecules (Basel, Switzerland) Feb 2020Protonated rare gas clusters have previously been shown to display markably different structures than their pure, cationic counterparts. Here we have performed high...
Protonated rare gas clusters have previously been shown to display markably different structures than their pure, cationic counterparts. Here we have performed high resolution mass spectrometry measurements of protonated and pristine clusters of He containing up to 50 atoms. We identify notable differences between the magic numbers present in the two types of clusters, but in contrast to heavier rare gas clusters, neither the protonated nor pure clusters exhibit signs of icosahedral symmetries. These findings are discussed in light of results from heavier rare gases and previous theoretical work on protonated helium.
Topics: Cations; Helium; Mass Spectrometry; Protons
PubMed: 32120989
DOI: 10.3390/molecules25051066 -
The Journal of Chemical Physics Aug 2022Acid ionization constants (pK's) of titratable amino acid side chains have received a large amount of experimental and theoretical attention. In many situations,...
Acid ionization constants (pK's) of titratable amino acid side chains have received a large amount of experimental and theoretical attention. In many situations, however, the rates of protonation and deprotonation, k and k, may also be important, for example, in understanding the mechanism of action of proton channels or membrane proteins that couple proton transport to other processes. Protonation and deprotonation involve the making and breaking of covalent bonds, which cannot be studied by classical force fields. However, environment effects on the rates should be captured by such methods. Here, we present an approach for estimating deprotonation rates based on Warshel's extension of Marcus's theory of electron transfer, with input from molecular simulations. The missing bond dissociation energy is represented by a constant term determined by fitting the pK value in solution. The statistics of the energy gap between protonated and deprotonated states is used to compute free energy curves of the two states and, thus, free energy barriers, from which the rate can be deduced. The method is applied to Glu, Asp, and His in bulk solution and select membrane proteins: the M2 proton channel, bacteriorhodopsin, and cytochrome c oxidase.
Topics: Amino Acids; Aspartic Acid; Bacteriorhodopsins; Hydrogen-Ion Concentration; Kinetics; Protons
PubMed: 36050014
DOI: 10.1063/5.0101960 -
Organic & Biomolecular Chemistry Dec 2010Protonation of gossypol Schiff bases (S1 and S2), possessing different numbers of basic N-atoms, was studied using potentiometric, spectroscopic, ESI MS and PM5 methods....
Protonation of gossypol Schiff bases (S1 and S2), possessing different numbers of basic N-atoms, was studied using potentiometric, spectroscopic, ESI MS and PM5 methods. Titration of S1 and S2 with HClO(4), monitored by the FT-IR and (1)H NMR, indicated that the change from the enamine-enamine into the protonated imine-imine tautomeric form occurs at different Schiff base-H(+) ratio. The FT-IR and PM5 results show that for S1 the first protonation step occurs at Schiff base moiety whereas for S2 it is realised at N-atom of the morpholine. The formation of N(+)-HO hydrogen bond between morpholine moieties within S2 contributes to high pK(a(ACN)) = 22.65.
Topics: Gossypol; Hydrogen Bonding; Models, Molecular; Molecular Structure; Protons; Schiff Bases
PubMed: 20959900
DOI: 10.1039/c0ob00288g