Oops, It should be: [H3O+]/[OH-]= 50/50 Kw = [H3O+][OH-],
pH = pKa +log ([OH-]/[H2O]) H3O+ concentration of pure water is 10^-7 mol/L total H+ = 55.5M * 10^-7 = 5.55* 10^-6 mole. Is this right? Regards, Kevin On Tue, Feb 7, 2012 at 12:13 PM, Zachary Wood <z...@bmb.uga.edu> wrote: > Hi Kevin, > > Hate to point this out, but under pH 7.0, the protonation state of water is > not 50:50, and it is not a good acid. The H30+ concentration of pure water > is 10^-7 Molar. In pure water (assuming 55.5 M) only 1:555,000,000 water > molecules is in the protonated, charged state (H3O+). This is why when an > enzyme uses water in its mechanism as a nucleophile, base, or acid, there is > usually an acid/base catalyst or metal that protonates or deprotonates the > water to 'activate it'. > > > Best regards, > > Z > > > *********************************************** > Zachary A. Wood, Ph.D. > Assistant Professor > Department of Biochemistry & Molecular Biology > University of Georgia > Life Sciences Building, Rm A426B > 120 Green Street > Athens, GA 30602-7229 > Office: 706-583-0304 > Lab: 706-583-0303 > FAX: 706-542-1738 > *********************************************** > > > > > > > On Feb 7, 2012, at 11:22 AM, Kevin Jin wrote: > >> As we know, the pKa of water is 15.7. Under pH 7.0, its protonation >> should be 50/50. >> In this case, we may need to consider water in two formats: >> >> H2O vs. H3O+ >> >> When we say water as acid, it usually stands for H3O+ in chemistry. In >> chemical equation, H+ represents H3O+. >> >> In enzyme catalysis, water as a general acid sounds reasonable under >> pH 7.0. In some famous paper, water has been concluded as the general >> base (pKa 15.7) to deprotonate an alpha hydrogen (pKa ~ 22) or a >> hydrogen from a sp3 hybridized carbon (pKa ~36). This logic may need >> to be reconsidered. >> . >> Recently, I have read papers for pKa perturbation. I am also >> interested in the general base of Asp and Glu in enzyme catalysis. >> >> >> I will be very happy to read your paper in the future. >> >> Regards, >> >> Kevin Jin >> >> On Tue, Feb 7, 2012 at 3:48 AM, Deepak Oswal <deepos...@gmail.com> wrote: >>> Dear colleagues, >>> >>> We have solved the crystal structure of a human enzyme. The pKa of a >>> catalytically critical aspartic acid has increased to 6.44. It is hydrogen >>> bonded (2.8 Angstroms) to a water molecule that is supposed to donate a >>> proton during the catalysis. Can anybody help me a) interpret the >>> significance of this increase in pKa of the aspartic acid from 3.8 to 6.44 >>> in context with the catalysis? Is this advantageous or detrimental? b) How >>> is pKa related to an amino acids’ ability to force a water molecule to >>> donate a proton? c) At pH 7.4, the aspartic acid would be de-protonated >>> irrespective of whether the pKa is 3.8 or 6.44; isn’t that true? d) Have >>> similar increase in pKa values observed for aspartic acids before? I would >>> be grateful if anybody could explain or comment on the above queries. >>> >>> Deepak Oswal >> >
