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Figure 1. O·O hydrogen bonds follow a linear relationship with donor
and acceptor ΔpKa (ΔpKa = pKa
Donor −pKa
Acceptor). (A) As the donor/
acceptor ΔpKa increases from 0.0 (green) to 8.2 (red), the O·O
hydrogen bond distance also increases (see footnote c). Lengths are
reported from small molecule neutron diffraction st... | ./PDFs_Hbond_collagen/Hbondpaper_1.pdf | {'format': 'PDF 1.3', 'title': 'Hydrogen Bonds: Simple after All?', 'author': 'Daniel Herschlag and Margaux M. Pinney', 'subject': 'Biochemistry 2018.57:3338-3352', 'keywords': '', 'creator': 'Arbortext Advanced Print Publisher 10.0.1465/W Unicode', 'producer': 'Acrobat Distiller 8.1.0 (Windows); modified using iText 4... | ||
Figure 2. 1H chemical shifts have a strong inverse correlation with
hydrogen bond O·O distances. (A) As the hydrogen bond shortens,
the 1H chemical shift of the hydrogen-bonded proton increases. This
increase in chemical shift is due to deshielding of the hydrogen-
bonded proton, which arises from the lengthening of th... | ./PDFs_Hbond_collagen/Hbondpaper_1.pdf | {'format': 'PDF 1.3', 'title': 'Hydrogen Bonds: Simple after All?', 'author': 'Daniel Herschlag and Margaux M. Pinney', 'subject': 'Biochemistry 2018.57:3338-3352', 'keywords': '', 'creator': 'Arbortext Advanced Print Publisher 10.0.1465/W Unicode', 'producer': 'Acrobat Distiller 8.1.0 (Windows); modified using iText 4... | ||
Figure 3. Substituted salicylates have the same hydrogen bond lengths in nonpolar solvents and water.26 (A) Substituted salicylates used by Sigala et
al. and their donor and acceptor ΔpKa values. (B) 1H NMR spectra of substituted salicylates in chloroform, acetone, and water at 4 °C. (C) 1H
chemical shifts and estimate... | ./PDFs_Hbond_collagen/Hbondpaper_1.pdf | {'format': 'PDF 1.3', 'title': 'Hydrogen Bonds: Simple after All?', 'author': 'Daniel Herschlag and Margaux M. Pinney', 'subject': 'Biochemistry 2018.57:3338-3352', 'keywords': '', 'creator': 'Arbortext Advanced Print Publisher 10.0.1465/W Unicode', 'producer': 'Acrobat Distiller 8.1.0 (Windows); modified using iText 4... | ||
Figure 4. Hydrogen bond distances derived from 1H NMR of small molecules follow a linear relationship with donor/acceptor ΔpKa for (A) O·O,
(B) N·O, and (C) N·N hydrogen bonds. Hydrogen bond lengths were estimated from 1H chemical shifts of the hydrogen-bonded proton using the
empirical correlation function from Figure... | ./PDFs_Hbond_collagen/Hbondpaper_1.pdf | {'format': 'PDF 1.3', 'title': 'Hydrogen Bonds: Simple after All?', 'author': 'Daniel Herschlag and Margaux M. Pinney', 'subject': 'Biochemistry 2018.57:3338-3352', 'keywords': '', 'creator': 'Arbortext Advanced Print Publisher 10.0.1465/W Unicode', 'producer': 'Acrobat Distiller 8.1.0 (Windows); modified using iText 4... | ||
Figure 6. Linear relationship between hydrogen bond distance and
ΔpKa that accounts for 86, 74, and 69% of the observed difference in
hydrogen bond lengths for O·O, N·O, and N·N hydrogen bonds,
respectively (R2 = 0.86, 0.74, and 0.69 for panels A−C, respectively).
However, there remains variation that is beyond experime... | ./PDFs_Hbond_collagen/Hbondpaper_1.pdf | {'format': 'PDF 1.3', 'title': 'Hydrogen Bonds: Simple after All?', 'author': 'Daniel Herschlag and Margaux M. Pinney', 'subject': 'Biochemistry 2018.57:3338-3352', 'keywords': '', 'creator': 'Arbortext Advanced Print Publisher 10.0.1465/W Unicode', 'producer': 'Acrobat Distiller 8.1.0 (Windows); modified using iText 4... | ||
Figure 5. Hydrogen bond distances derived from 1H NMR and ultra-high-resolution (≤1.0 Å) X-ray crystal structures of proteins (cyan points) also
follow a linear relationship with donor and acceptor ΔpKa for (A) O·O, (B) N·O, and (C) N·N hydrogen bonds. Dark and light gray points are for
small molecule hydrogen bonds fr... | ./PDFs_Hbond_collagen/Hbondpaper_1.pdf | {'format': 'PDF 1.3', 'title': 'Hydrogen Bonds: Simple after All?', 'author': 'Daniel Herschlag and Margaux M. Pinney', 'subject': 'Biochemistry 2018.57:3338-3352', 'keywords': '', 'creator': 'Arbortext Advanced Print Publisher 10.0.1465/W Unicode', 'producer': 'Acrobat Distiller 8.1.0 (Windows); modified using iText 4... | ||
Figure 8. Intramolecular hydrogen bonds are generally shorter than intermolecular hydrogen bonds of similar ΔpKa.18 (A−C) Comparison of
intermolecular (black) and intramolecular (red) (A) O·O, (B) N·O, and (C) N·N hydrogen bond lengths from small molecule neutron diffraction
structures.
| ./PDFs_Hbond_collagen/Hbondpaper_1.pdf | {'format': 'PDF 1.3', 'title': 'Hydrogen Bonds: Simple after All?', 'author': 'Daniel Herschlag and Margaux M. Pinney', 'subject': 'Biochemistry 2018.57:3338-3352', 'keywords': '', 'creator': 'Arbortext Advanced Print Publisher 10.0.1465/W Unicode', 'producer': 'Acrobat Distiller 8.1.0 (Windows); modified using iText 4... | ||
Figure 7. Common coupling relationship observed between oxyanion hole hydrogen bonds in pKSI, tKSI, and PYP. (A) Hydrogen bond networks
in the active sites of two variants of ketosteroid isomerase (KSI) and photoactive yellow protein (PYP). Perturbations made to each residue are
shown in parentheses. (B) Coupled change... | ./PDFs_Hbond_collagen/Hbondpaper_1.pdf | {'format': 'PDF 1.3', 'title': 'Hydrogen Bonds: Simple after All?', 'author': 'Daniel Herschlag and Margaux M. Pinney', 'subject': 'Biochemistry 2018.57:3338-3352', 'keywords': '', 'creator': 'Arbortext Advanced Print Publisher 10.0.1465/W Unicode', 'producer': 'Acrobat Distiller 8.1.0 (Windows); modified using iText 4... | ||
Figure 10. Crystal structures of pKSI D40N bound to 2,6-
difluorophenolate (pKa = 7.1; orange; Protein Data Bank entry
2INX) and phenolate (pKa = 10.0; blue; Protein Data Bank entry
2PZV). (A) Overlay of pKSI·2,6-difluorophenolate (orange) and
pKSI·phenolate (blue) structures. (B) Side view of the overlay in panel
A high... | ./PDFs_Hbond_collagen/Hbondpaper_1.pdf | {'format': 'PDF 1.3', 'title': 'Hydrogen Bonds: Simple after All?', 'author': 'Daniel Herschlag and Margaux M. Pinney', 'subject': 'Biochemistry 2018.57:3338-3352', 'keywords': '', 'creator': 'Arbortext Advanced Print Publisher 10.0.1465/W Unicode', 'producer': 'Acrobat Distiller 8.1.0 (Windows); modified using iText 4... | ||
Figure 9. Intermolecular hydrogen bonds have angles of ∼180°,
whereas intramolecular hydrogen bonds of similar lengths generally
have bent hydrogen bonds. (A) Intermolecular and intramolecular O−
H·O hydrogen bond lengths and angles from selected small molecule
neutron diffraction structures (CSD IDs are UROXAL01, SUCAB... | ./PDFs_Hbond_collagen/Hbondpaper_1.pdf | {'format': 'PDF 1.3', 'title': 'Hydrogen Bonds: Simple after All?', 'author': 'Daniel Herschlag and Margaux M. Pinney', 'subject': 'Biochemistry 2018.57:3338-3352', 'keywords': '', 'creator': 'Arbortext Advanced Print Publisher 10.0.1465/W Unicode', 'producer': 'Acrobat Distiller 8.1.0 (Windows); modified using iText 4... | ||
Figure 12. Thermodynamic framework for dissecting hydrogen bond energetics in different environments. Equilibria for hydrogen bond formation
(ΔGf
HB, horizontal lines) are depicted in water (front, blue) and a nonpolar solvent (back, tan) for a ground state (top line, ΔGf,GS
HB ) and a transition
state (bottom line, ΔGf... | ./PDFs_Hbond_collagen/Hbondpaper_1.pdf | {'format': 'PDF 1.3', 'title': 'Hydrogen Bonds: Simple after All?', 'author': 'Daniel Herschlag and Margaux M. Pinney', 'subject': 'Biochemistry 2018.57:3338-3352', 'keywords': '', 'creator': 'Arbortext Advanced Print Publisher 10.0.1465/W Unicode', 'producer': 'Acrobat Distiller 8.1.0 (Windows); modified using iText 4... | ||
Figure 11. Hydrogen bond formation (ΔGHB) between an acid [A
(blue) or A′ (red)] and a base [B (blue) or B′ (red)], where ΔGHB′
(red) is more favorable than ΔGHB (blue).
| ./PDFs_Hbond_collagen/Hbondpaper_1.pdf | {'format': 'PDF 1.3', 'title': 'Hydrogen Bonds: Simple after All?', 'author': 'Daniel Herschlag and Margaux M. Pinney', 'subject': 'Biochemistry 2018.57:3338-3352', 'keywords': '', 'creator': 'Arbortext Advanced Print Publisher 10.0.1465/W Unicode', 'producer': 'Acrobat Distiller 8.1.0 (Windows); modified using iText 4... |
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