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Journal of Colloid and Interface Science Aug 2003The aim of the present study is to compare available surface titration curves of kaolinite, to explain the differences between them, and to constrain their... (Comparative Study)
Comparative Study
The aim of the present study is to compare available surface titration curves of kaolinite, to explain the differences between them, and to constrain their interpretation based on predictions of surface protonation that emerged from dissolution experiments. Comparison of six surface titration curves obtained at 25 degrees C reveals significant discrepancies, both in the shape of the curves and in the pH of the point of zero net proton charge (pH(PZNPC)). Based on an analysis of the different sites available for adsorption on kaolinite surfaces we conclude that different kaolinite samples are expected to have similar pH(PZNPC). Therefore, the major reason for the differences in the observed surface protonation is related to the different ways in which the pH(PZNPC) was determined. To compare the titration curves, some of the curves were recalculated so that the proton surface concentrations of all the titration curves would be zero around pH 5. As a result, we obtained a good agreement between the titration curves. A prediction of the molar fraction of protonated sites was retrieved from modeling of kaolinite dissolution reaction and was compared to the protonation data obtained from surface titration. The model successfully predicts the surface protonation data of most of the surface titrations.
Topics: Hydrogen-Ion Concentration; Kaolin; Kinetics; Protons; Solubility; Surface Properties
PubMed: 12885520
DOI: 10.1016/s0021-9797(03)00298-4 -
Journal of Computer-aided Molecular... May 2020The pK is the standard measure used to describe the aqueous proton affinity of a compound, indicating the proton concentration (pH) at which two protonation states (e.g....
The pK is the standard measure used to describe the aqueous proton affinity of a compound, indicating the proton concentration (pH) at which two protonation states (e.g. A and AH) have equal free energy. However, compounds can have additional protonation states (e.g. AH), and may assume multiple tautomeric forms, with the protons in different positions (microstates). Macroscopic pKs give the pH where the molecule changes its total number of protons, while microscopic pKs identify the tautomeric states involved. As tautomers have the same number of protons, the free energy difference between them and their relative probability is pH independent so there is no pK connecting them. The question arises: What is the best way to describe protonation equilibria of a complex molecule in any pH range? Knowing the number of protons and the relative free energy of all microstates at a single pH, ∆G°, provides all the information needed to determine the free energy, and thus the probability of each microstate at each pH. Microstate probabilities as a function of pH generate titration curves that highlight the low energy, observable microstates, which can then be compared with experiment. A network description connecting microstates as nodes makes it straightforward to test thermodynamic consistency of microstate free energies. The utility of this analysis is illustrated by a description of one molecule from the SAMPL6 Blind pK Prediction Challenge. Analysis of microstate ∆G°s also makes a more compact way to archive and compare the pH dependent behavior of compounds with multiple protonatable sites.
Topics: Entropy; Hydrogen-Ion Concentration; Models, Chemical; Protons; Thermodynamics; Water
PubMed: 32052350
DOI: 10.1007/s10822-020-00280-7 -
The Journal of Chemical Physics Aug 2005The protonation of N2 bound to the active center of nitrogenase has been investigated using state-of-the-art density-functional theory calculations. Dinitrogen in the...
The protonation of N2 bound to the active center of nitrogenase has been investigated using state-of-the-art density-functional theory calculations. Dinitrogen in the bridging mode is activated by forming two bonds to Fe sites, which results in a reduction of the energy for the first hydrogen transfer by 123 kJ/mol. The axial binding mode with open sulfur bridge is less reactive by 30 kJ/mol and the energetic ordering of the axial and bridged binding modes is reversed in favor of the bridging dinitrogen during the first protonation. Protonation of the central ligand is thermodynamically favorable but kinetically hindered. If the central ligand is protonated, the proton is transferred to dinitrogen following the second protonation. Protonation of dinitrogen at the Mo site does not lead to low-energy intermediates.
Topics: Binding Sites; Chemistry, Physical; Histidine; Hydrogen Bonding; Imidazoles; Kinetics; Ligands; Models, Chemical; Models, Molecular; Molecular Conformation; Molybdoferredoxin; Nitrogen; Nitrogenase; Protons; Thermodynamics
PubMed: 16229569
DOI: 10.1063/1.2008227 -
Journal of Mass Spectrometry : JMS Jan 1997Gas-phase protonation of pyridine with CH3NH3+, NH4+, t-C4H9+, H3O+ and CH5+ under thermal conditions was studied by variable-time neutralization-reionization mass...
Gas-phase protonation of pyridine with CH3NH3+, NH4+, t-C4H9+, H3O+ and CH5+ under thermal conditions was studied by variable-time neutralization-reionization mass spectrometry and ab initio calculations. N-Protonation was found to occur exclusively for CH3NH3+ through H3O+ and predominantly for CH5+. The calculated MP2/6-311G(2d,p) energies gave the proton affinities of N, C-2, C-3 and C-4 in pyridine as 924, 658, 686 and 637 kJ mol-1, respectively, which were in good agreement with previous experimental and theoretical results. Vertical neutralization of the N-protonated isomer (1H+) was accompanied by moderate Franck-Condon effects that deposited 20-21 kJ mol-1 in the 1H-pyridinium radicals (1H) formed. 1H was calculated by UMP2/6-311G(2d,p) and B3LYP/6-311G(2d,p) to be a bound species in its ground electronic state. A substantial fraction of stable 1H was detected in the spectra, which depended on the precursor ion internal energy. Deuterium labeling showed a specific loss of the N-bound hydrogen or deuterium in the radicals. The specificity increased with increasing internal energy in the radicals and decreasing contribution of ion dissociations following reionization. Variable-time measurements established specific loss of the N-bound deuterium also in dissociating low-energy 1D. Loss of hydrogen from 1H+ cations following reionization was highly endothermic and was accompanied by rearrangements that partially scrambled the ring hydrogens.
Topics: Chemical Phenomena; Chemistry; Gases; Mass Spectrometry; Molecular Structure; Protons; Pyridines
PubMed: 9008868
DOI: 10.1002/(SICI)1096-9888(199701)32:1<55::AID-JMS447>3.0.CO;2-M -
Chemical Reviews May 2022Proton detection developed in the last 20 years as the method of choice to study biomolecules in the solid state. In perdeuterated proteins, proton dipolar interactions... (Review)
Review
Proton detection developed in the last 20 years as the method of choice to study biomolecules in the solid state. In perdeuterated proteins, proton dipolar interactions are strongly attenuated, which allows yielding of high-resolution proton spectra. Perdeuteration and backsubstitution of exchangeable protons is essential if samples are rotated with MAS rotation frequencies below 60 kHz. Protonated samples can be investigated directly without spin dilution using proton detection methods in case the MAS frequency exceeds 110 kHz. This review summarizes labeling strategies and the spectroscopic methods to perform experiments that yield assignments, quantitative information on structure, and dynamics using perdeuterated samples. Techniques for solvent suppression, H/D exchange, and deuterium spectroscopy are discussed. Finally, experimental and theoretical results that allow estimation of the sensitivity of proton detected experiments as a function of the MAS frequency and the external field in a perdeuterated environment are compiled.
Topics: Magnetic Resonance Imaging; Magnetic Resonance Spectroscopy; Nuclear Magnetic Resonance, Biomolecular; Proteins; Protons
PubMed: 34870415
DOI: 10.1021/acs.chemrev.1c00681 -
The Journal of Physical Chemistry. B Apr 2012Cluster expansion techniques are used to obtain microconstants and microenthalpies of protonation reactions. The approach relies on the analysis of macroscopic...
Cluster expansion techniques are used to obtain microconstants and microenthalpies of protonation reactions. The approach relies on the analysis of macroscopic protonation constants and protonation enthalpies within a homologous series. Various linear aliphatic polyamines are considered, including 3,4-tri (spermidine), 3,4,3-tet (spermine), and 2,2,2,2-pent. Besides the full resolution of the microscopic protonation equilibria, one obtains information on the temperature dependence of the microstate probabilities. We find that the concentrations of the dominant microspecies increase with increasing temperature. Due to the large negative protonation enthalpies that are typical for amines, higher temperatures generally favor the less protonated species.
Topics: Protons; Spermidine; Spermine; Temperature; Thermodynamics
PubMed: 22380971
DOI: 10.1021/jp301164f -
Journal of Physics. Condensed Matter :... Jan 2016In 1804, Theodore von Grotthuss proposed a mechanism for proton (H(+)) transport between water molecules that involves the exchange of a covalent bond between H and O... (Review)
Review
In 1804, Theodore von Grotthuss proposed a mechanism for proton (H(+)) transport between water molecules that involves the exchange of a covalent bond between H and O with a hydrogen bond. This mechanism also supports the transport of OH(-) as a proton hole and is essential in explaining proton transport in intramembrane proton channels. Inspired by the Grotthuss mechanism and its similarity to electron and hole transport in semiconductors, we have developed semiconductor type devices that are able to control and monitor a current of H(+) as well as OH(-) in hydrated biopolymers. In this topical review, we revisit these devices that include protonic diodes, complementary, transistors, memories and transducers as well as a phenomenological description of their behavior that is analogous to electronic semiconductor devices.
Topics: Biopolymers; Hydrogen Bonding; Protons; Semiconductors; Water
PubMed: 26657711
DOI: 10.1088/0953-8984/28/2/023001 -
Physical Chemistry Chemical Physics :... Oct 2015The best determination of the most stable protonation site in aromatic molecules relies nowadays on the IR spectroscopy and ab initio calculations. It appears that these...
The best determination of the most stable protonation site in aromatic molecules relies nowadays on the IR spectroscopy and ab initio calculations. It appears that these methods are not necessarily unambiguous and cannot always be safely employed. We present in this paper an example showing that electronic spectroscopy of cold ions complemented with ab initio calculations gives clear results on the protonation site. In the example given on the aminophenol isomers (in ortho, meta and para positions), the protonation site is assigned from the electronic spectroscopy and in particular we show that for the meta isomer the proton is not on the amino group as observed for the other isomers. It shows also that the protonation site is not conserved in the electrospray evaporation-ionization process.
Topics: Aminophenols; Isomerism; Models, Molecular; Photoelectron Spectroscopy; Protons
PubMed: 25790330
DOI: 10.1039/c5cp01122a -
Acta Crystallographica. Section D,... Feb 2017There are more H atoms than any other type of atom in an X-ray crystal structure of a protein-ligand complex, but as H atoms only have one electron they diffract X-rays...
There are more H atoms than any other type of atom in an X-ray crystal structure of a protein-ligand complex, but as H atoms only have one electron they diffract X-rays weakly and are `hard to see'. The positions of many H atoms can be inferred by our chemical knowledge, and such H atoms can be added with confidence in `riding positions'. For some chemical groups, however, there is more ambiguity over the possible hydrogen placements, for example hydroxyls and groups that can exist in multiple protonation states or tautomeric forms. This ambiguity is far from rare, since about 25% of drugs have more than one tautomeric form. This paper focuses on the most common, `prototropic', tautomers, which are isomers that readily interconvert by the exchange of an H atom accompanied by the switch of a single and an adjacent double bond. Hydrogen-exchange rates and different protonation states of compounds (e.g. buffers) are also briefly discussed. The difference in heavy (non-H) atom positions between two tautomers can be small, and careful refinement of all possible tautomers may single out the likely bound ligand tautomer. Experimental methods to determine H-atom positions, such as neutron crystallography, are often technically challenging. Therefore, chemical knowledge and computational approaches are frequently used in conjugation with experimental data to deduce the bound tautomer state. Proton movement is a key feature of many enzymatic reactions, so understanding the orchestration of hydrogen/proton motion is of critical importance to biological chemistry. For example, structural studies have suggested that, just as a chemist may use heat, some enzymes use directional movement to protonate specific O atoms on phosphates to catalyse phosphotransferase reactions. To inhibit `wriggly' enzymes that use movement to effect catalysis, it may be advantageous to have inhibitors that can maintain favourable contacts by adopting different tautomers as the enzyme `wriggles'.
Topics: Crystallization; Crystallography, X-Ray; DNA; DNA Topoisomerases, Type II; Hydrogen; Isomerism; Ligands; Models, Molecular; Protein Conformation; Proteins; Protons; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Small Molecule Libraries
PubMed: 28177309
DOI: 10.1107/S2059798316020283 -
Journal of the American Society For... Sep 2012Tautomerization induced by protonation of halouracils may increase their efficacy as anti-cancer drugs by altering their reactivity and hydrogen bonding characteristics,...
Tautomerization induced by protonation of halouracils may increase their efficacy as anti-cancer drugs by altering their reactivity and hydrogen bonding characteristics, potentially inducing errors during DNA and RNA replication. The gas-phase structures of protonated complexes of five halouracils, including 5-fluorouracil, 5-chlorouracil, 5-bromouracil, 5-iodouracil, and 6-chlorouracil are examined via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical electronic structure calculations. IRMPD action spectra were measured for each complex in the IR fingerprint region extending from ~1000 to 1900 cm(-1) using the free electron laser (FELIX). Correlations are made between the measured IRMPD action spectra and the linear IR spectra for the stable low-energy tautomeric conformations computed at the B3LYP/6-311+G(2d,2p)//B3LYP/6-31G* level of theory. Absence of an intense band(s) in the IRMPD spectrum arising from the carbonyl stretch(es) that are expected to appear near 1825 cm(-1) provides evidence that protonation induces tautomerization and preferentially stabilizes alternative, noncanonical tautomers of these halouracils where both keto functionalities are converted to hydroxyl groups upon binding of a proton. The weak, but measurable absorption, which does occur for these systems near 1835 cm(-1) suggests that in addition to the ground-state conformer, very minor populations of excited, low-energy conformers that contain keto functionalities are also present in these experiments.
Topics: Hydrocarbons, Halogenated; Isomerism; Mass Spectrometry; Photochemical Processes; Protons; Spectrophotometry, Infrared; Thermodynamics; Uracil
PubMed: 22821195
DOI: 10.1007/s13361-012-0434-7