scholarly journals pH-controlled hydrogen-bonding (Short Communication)

1974 ◽  
Vol 143 (3) ◽  
pp. 775-777 ◽  
Author(s):  
John L. Wood
Keyword(s):  
Hydrogen Bonding ◽  
Dissociation Constant ◽  
Small Proportion ◽  
Association Constant ◽  
Short Communication ◽  
Dibasic Acid ◽  
Ph Dependence ◽  
Ph Values ◽  
Conjugate Acid ◽  
Total Base

The pH-dependence of the degree of hydrogen-bonding between a base and its conjugate acid is considered. When only a small proportion of the total base is complexed, the amount complexed is proportional to (1+coshp)−1 where p=2.303 (pKa–pH), pKa being the dissociation constant of the conjugate acid. This represents sharp pH-dependence. As the proportion complexed increases, the curve broadens, eventually becoming flat-topped, with more than half the base complexed over the range of pH values pKa±logKC, approximately. (K is the complex association constant and C is the formal base concentration, including all forms.) There are similarities to the extent of mono-protonation of a dibasic acid.

pH Effects in trypsin catalysis

1969 ◽  
Vol 47 (21) ◽  
pp. 4021-4029 ◽  
Author(s):  
H. P. Kasserra ◽  
K. J. Laidler
Keyword(s):  
Complex Formation ◽  
Ph Dependence ◽  
Specific Rotation ◽  
Ph Effects ◽  
Ph Values ◽  
A Value ◽  
Available Information ◽  
Hydrolysis Of ◽  
Substrate Concentrations ◽  
Covalent Complex

A kinetic study has been made of the trypsin-catalyzed hydrolysis of N-benzoyl-L-alanine methyl ester, at pH values ranging from 6 to 10. The substrate concentrations varied from 1.7 × 10−3 to 4.3 × 10−2 M. From the rates were calculated, at each pH, values of [Formula: see text] (corresponding to [Formula: see text]), [Formula: see text] (corresponding to [Formula: see text]) and [Formula: see text] The specific levorotation of trypsin was measured and found to vary with pH in the pH region 5–11, the change in specific rotation following the ionization of a single group with pK(app) of 9.4. At pH 11 the specific rotation of trypsin, its zymogen, and its phosphorylated derivative were approximately the same, suggesting similar conformations for all three forms of the protein.The kinetic results on the acid side were very similar to those obtained by other investigators for chymotrypsin; they imply that there is a group of [Formula: see text] in the free enzyme, presumably the imidazole function of a histidine residue, and that this group is involved in acylation and deacylation, which can only occur if it is unprotonated. The behavior on the basic side was found to be different from that with chymotrypsin revealing a decrease in [Formula: see text] at high pH corresponding to a value of [Formula: see text] whereas [Formula: see text] showed sigmoid pH-dependence. An interpretation of these results that is consistent with all available information is that a group of [Formula: see text] (presumably the —NH3+ function of the terminal isoleucine) controls the conformation and thereby the activity of the enzyme at different stages of complex formation. In contrast to chymotrypsin, the pK of this ionizing group appears to be generally lowered by covalent complex formation between trypsin and its substrates.

scholarly journals Effects of pH on aquatic biodegradation processes

2009 ◽  
Vol 6 (1) ◽  
pp. 491-514 ◽  
Author(s):  
R. F. Krachler ◽  
R. Krachler ◽  
A. Stojanovic ◽  
B. Wielander ◽  
A. Herzig
Keyword(s):  
Organic Matter ◽  
Lake Water ◽  
Decomposition Rate ◽  
Degradation Mechanism ◽  
Ph Dependence ◽  
Degradation Process ◽  
Plant Litter ◽  
Lake Basin ◽  
Causal Connection ◽  
Ph Values

Abstract. To date, little is known about the pH-stimulated mineralization of organic matter in aquatic environments. In this study, we investigated biodegradation processes in alkaline waters. Study site is a large shallow soda lake in Central Europe (Neusiedler See/Ferto). The decomposition rate of plant litter was measured as a function of pH by incubating air-saturated lake-water samples in contact with Phragmites litter (leaves) from the littoral vegetation. All samples showed high decomposition rates (up to 32% mass loss within 35 days) and a characteristic two-step degradation mechanism. During the degradation process, the solid plant litter was dissolved forming humic colloids. Subsequently, the humic colloids were mineralized to CO2 in the water column. The decomposition rate was linearly related to pH. Increasing pH values accelerated significantly the leaching of humic colloids as well as the final degradation process. The observed two-step mechanism controls the wetland/lake/air carbon fluxes, since large quantities of humic colloids are currently produced in the reed belt, exported through wind-driven circulations and incorporated into the open lake foodweb. At present, the lake is rapidly shrinking due to peat deposition in the littoral zone, whereas it has been resistant to silting-up processes for thousands of years. In order to investigate the cause of this abrupt change, the chemical composition of the lake-water was measured during 1995–2007. A thorough analysis of these data revealed that major lake-water discharges through the lake's artificial outlet channel led to a decline in salinity and alkalinity. According to our estimates, the lake's original salinity and alkalinity was 70–90% higher compared to the present conditions, with the consequence of substantially lower pH values in the present lake. The observed pH dependence of reed litter biodegradation rates points to a causal connection between low pH values and accumulation of peat in the lake basin. Our results suggest that the pH stimulated remineralisation of organic matter plays a major role in maintaining the long-term integrity of saline lake/wetland systems.

scholarly journals Site-selective Protonation of the One-electron Reduced Cofactor in [FeFe]-Hydrogenase

2020 ◽  
Author(s):  
Konstantin Laun ◽  
Iuliia Baranova ◽  
Jifu Duan ◽  
Leonie Kertess ◽  
Florian Wittkamp ◽  
...  
Keyword(s):  
Proton Transfer ◽  
Active Site ◽  
Catalytic Mechanism ◽  
Ph Dependence ◽  
H2 Evolution ◽  
Proton Reduction ◽  
Ph Values ◽  
Site Selective ◽  
H2 Oxidation ◽  
Diiron Site

Hydrogenases are microbial redox enzymes that catalyze H2 oxidation and proton reduction (H2 evolution). While all hydrogenases show high oxidation activities, the majority of [FeFe]-hydrogenases are excellent H2 evolution catalysts as well. Their active site cofactor comprises a [4Fe-4S] cluster covalently linked to a diiron site equipped with carbon monoxide and cyanide ligands that facilitate catalysis at low overpotential. Distinct proton transfer pathways connect the active site niche with the solvent, resulting in a non-trivial dependence of hydrogen turnover and bulk pH. To analyze the catalytic mechanism of [FeFe]-hydrogenase, we employ in situ infrared spectroscopy and infrared spectro-electrochemistry. Titrating the pH under H2 oxidation or H2 evolution conditions reveals the influence of site-selective protonation on the equilibrium of reduced cofactor states. Governed by pKa differences across the active site niche and proton transfer pathways, we find that individual electrons are stabilized either at the [4Fe-4S] cluster (alkaline pH values) or at the diiron site (acidic pH values). This observation is discussed in the context of the natural pH dependence of hydrogen turnover as catalyzed by [FeFe]-hydrogenase.<br>

scholarly journals Mechanism of d-fructose isomerization by Arthrobacterd-xylose isomerase

1992 ◽  
Vol 283 (1) ◽  
pp. 223-233 ◽  
Author(s):  
M Rangarajan ◽  
B S Hartley
Keyword(s):  
Ring Opening ◽  
Ph Dependence ◽  
Xylose Isomerase ◽  
Competitive Inhibitor ◽  
Apparent Dissociation Constant ◽  
Ph Values ◽  
Rate Limiting Step ◽  
Competitive Inhibitors ◽  
Rate Limiting ◽  
Very High

The mechanism of D-fructose isomerization by Arthrobacter D-xylose isomerase suggested from X-ray-crystallographic studies was tested by detailed kinetic analysis of the enzyme with various metal ions at different pH values and temperatures. At D-fructose concentrations used in commercial processes Mg2+ is the best activator with an apparent dissociation constant of 63 microM; Co2+ and Mn2+ bind more strongly (apparent Kd 20 microM and 10 microM respectively) but give less activity (45% and 8% respectively). Ca2+ is a strict competitive inhibitor versus Mg2+ (Ki 3 microM) or Co2+ (Ki 105 microM). The kinetics show a compulsory order of binding; Co2+ binds first to Site 2 and then to Site 1; then D-fructose binds at Site 1. At normal concentrations Mg2+ binds at Site 1, then D-fructose and then Mg2+ at Site 2. At very high Mg2+ concentrations (greater than 10 mM) the order is Mg2+ at Site 1, Mg2+ at Site 2, then D-fructose. The turnover rate (kcat.) is controlled by ionization of a residue with apparent pKa at 30 degrees C of 6.0 +/- 0.07 (Mg2+) or 5.3 +/- 0.08 (Co2+) and delta H = 23.5 kJ/mol. This appears to be His-219, which is co-ordinated to M[2]; protonation destroys isomerization by displacing M[2]; Co2+ binds more strongly at Site 2 than Mg2+, so competes more strongly against H+. The inhibition constant (Ki) for the two competitive inhibitors 5-thio-alpha-D-glucopyranose and D-sorbitol is invariant with pH, but Km(app.) in the Mg[1]-enzyme is controlled by ionization of a group with pKa 6.8 +/- 0.07 and delta H = 27 kJ/mol, which appears to be His-53. This shows that Km(app.) is a complex constant that includes the rate of the ring-opening step catalysed by His-53, which explains the pH-dependence. In the Mg[1]Mg[2]-enzyme or Co[1]Co[2]-enzyme, the pKa is lower (6.2 +/- 0.1 or 5.6 +/- 0.08) because of the extra adjacent cation. Hence the results fit the previously proposed pathway, but show that the mechanisms differ for Mg2+ and Co2+ and that the rate-limiting step is isomerization and not ring-opening as previously postulated.

scholarly journals Experimental Sensing and DFT Mechanism of Zn(II) Complex for Highly Sensitive and Selective Detection of Acetone

Crystals ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 324
Author(s):  
Mohd. Muddassir ◽  
Mohammad Usman ◽  
Abdullah Alarifi ◽  
Mohd. Afzal ◽  
Khulud Abdullah Alshali ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Energy Barrier ◽  
Association Constant ◽  
Theoretical Calculations ◽  
Selective Detection ◽  
Acetone Molecule ◽  
Hydrogen Bonding Interactions ◽  
Highly Sensitive ◽  
Perchlorate Complex ◽  
Selective Sensor

In the present work, a new Zn(II) perchlorate complex with 2,2’–bipyridyl of formulation {[Zn(bipy)2(H2O)](ClO4)2} (1) was obtained and well analyzed. This chemosensor was evaluated as a selective sensor for acetone among the several different organic solvents(CH3OH, EtOH, i–PrOH, i–BuOH, CHCl3, CH2Cl2, CCl4, C6H6, C7H8, C8H10, C2H3N, C3H7NO, C4H8O2, C3H6O3) in a fluorescence turn–off response in accordance with theoretical calculations. Sensing experiments were performed at ambient temperature which shows the acetone molecule distinctly reduces transfer of energy barrier to complex 1 and hence, produces remarkable luminescent quenching. Also, the weak intermolecular hydrogen–bonding interactions thanks to the presence of various hydrogen bonding donors and acceptors, exist between ligand molecules, which were broken during fluorescence, resulting in quenching. The stoichiometry ratio and association constant were evaluated using Benesi–Hildebrand relation giving 1:1 stoichiometry between complex 1 and acetone. Additionally, DFT results can also explicate the significant response on complex 1 upon addition of acetone. This work is vital in a new loom for the detection of acetone and other ketones.

Chromatographic Determination of Thermodynamic Acid Dissociation Constants of Tetracycline Antibiotics and Their Epimers

2019 ◽  
Vol 57 (8) ◽  
pp. 745-750
Author(s):  
İlkay Konçe ◽  
Ebru Çubuk Demiralay ◽  
Hülya Yılmaz Ortak
Keyword(s):  
Experimental Data ◽  
Dissociation Constant ◽  
Binary Mixtures ◽  
Dissociation Constants ◽  
Reversed Phase ◽  
Acid Dissociation ◽  
Acid Dissociation Constant ◽  
Chromatography Method ◽  
Ph Values

Abstract The presented study describes the development of reversed-phase liquid chromatography method using a core-shell particle column with a pentafluorophenyl stationary phase for the dissociation constant (pKa) determination of the tetracycline group antibiotics (tetracycline, oxytetracycline, chlortetracycline) and their epimers (4-epitetracycline, 4-epioxytetracycline, 4-epichlortetracycline). The pH values were measured in the acetonitrile (ACN)–water binary mixtures, used as mobile phases, instead of in water and take into account the effect of the activity coefficients. Thermodynamic acid dissociation constant (pKa1) values of studied antibiotics and their epimers were calculated using retention factor (k) at different mobile phase pH values in studied binary mixtures with ACN percentages of 20, 25, 30 and 35% (v/v). Experimental data were analyzed by using an Origin 7.0 program to fit experimental data to the nonlinear expression derived. From calculated pKa1 values, the aqueous pKa values of studied compounds were calculated by different approaches and these values were compared.

scholarly journals The interplay of electrostatic fields and binding interactions determining catalytic-site reactivity in actinidin. A possible origin of differences in the behaviour of actinidin and papain

1989 ◽  
Vol 259 (2) ◽  
pp. 443-452 ◽  
Author(s):  
D Kowlessur ◽  
M O'Driscoll ◽  
C M Topham ◽  
W Templeton ◽  
E W Thomas ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Ligand Binding ◽  
Transition State ◽  
Rate Constant ◽  
Ph Dependence ◽  
Order Rate Constant ◽  
Catalytic Site ◽  
Binding Interactions ◽  
Electrostatic Fields ◽  
Transition State Geometry

1. The pH-dependence of the second-order rate constant (k) for the reaction of actinidin (EC 3.4.22.14) with 2-(N'-acetyl-L-phenylalanylamino)ethyl 2'-pyridyl disulphide was determined and the contributions to k of various hydronic states were evaluated. 2. The data were used to assess the consequences for transition-state geometry of providing P2/S2 hydrophobic contacts in addition to hydrogen-bonding opportunities in the S1-S2 intersubsite region. 3. The P2/S2 contacts (a) substantially improve enzyme-ligand binding, (b) greatly enhance the contribution to reactivity of the hydronic state bounded by pKa 3 (the pKa characteristic of the formation of catalytic-site-S-/-ImH+ state) and pKa 5 (a relatively minor contributor in reactions that lack the P2/S2 contacts), such that the major rate optimum occurs at pH 4 instead of at pH 2.8-2.9, and (c) reveal the kinetic influence of a pKa approx. 6.3 not hitherto observed in reactions of actinidin. 4. Possibilities for the interplay of electrostatic effects and binding interactions in both actinidin and papain (EC 3.4.22.2) are discussed.

scholarly journals The effects of calcium ions and pH on bovine prothrombin fragment 1. Intrinsic fluroescence studies

1979 ◽  
Vol 177 (3) ◽  
pp. 879-886 ◽  
Author(s):  
M E Scott ◽  
K A Koehler ◽  
R G Hiskey
Keyword(s):  
Ph Dependence ◽  
Tight Binding ◽  
Ph Titration ◽  
Prothrombin Fragment ◽  
Ph Values ◽  
Titration Curves ◽  
Or Groups ◽  
Effects Of Ph ◽  
Induced Changes ◽  
Apparent Association

The effects of pH and Ca2+ on the intrinsic fluorescence of bovine prothrombin fragment 1 were investigated to deduce the nature of protein functional groups involved in Ca2+ binding to fragment 1. From pH values of 9 to 3, increasing the H3O+ concentration results in quenching of the fluorescence of fragment 1. Reversible pH-titration curves are obtained which appear to consist of two regions. From pH 4 to pH6.5 a broad titration curve is obtained, whereas from pH6.5 to 9 a more pronounced titration behaviour is evidenced by a group or groups on fragment 1 with an apparent pKa of approx. 7.5. In contrast, the apparent association constant for Ca2+ and fragment 1 shows a sharp pH-dependence in the region between pH7 and 8 with tighter Ca2+ binding at higher pH values. A PKa of approx. 7.5 can be estimated for the group or groups on fragment 1 linked to the tight binding of Ca2+. Both H3O+ and Ca2+ result in blue-shifts in the wave-lengths of fragment-1 emission. These results are interpreted in terms of H+ - and Ca2+ - induced changes in the conformation of fragment 1 as a result of surface-charge neutralization.

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