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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 structures (CSD IDs
of NAHMAL01 and SUCACBO3 for green and red, respectively). (B)
O·O hydrogen bonds in small molecule neutron diffraction structures.
Reproduced from ref 26. Copyright 2015 American Chemical Society.
| ./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 4.2.0 by 1T3XT', 'creationDate': "D:20180611144746-04'00'", 'modDate': "D:20240406031325-07'00'", 'trapped': '', 'encryption': None} | ||
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 the covalent O−
H bond that accompanies shorter O·O (rO·O) and H·O (rO·H)
distances, as has been widely discussed.27,69,115,116 (B) Correlation of
O·O hydrogen bond distances from X-ray crystal structures of diverse
small molecules with 1H chemical shifts from solid-state NMR of the
same compound. Panel B is reproduced from ref 117. Copyright 1999
John Wiley & Sons, Inc. Data are from ref 118. The empirical fit of the
data in panel B (black line) has been used extensively in the literature
to estimate hydrogen bond lengths from chemical shift data.117−125
| ./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 4.2.0 by 1T3XT', 'creationDate': "D:20180611144746-04'00'", 'modDate': "D:20240406031325-07'00'", 'trapped': '', 'encryption': None} | ||
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 estimated hydrogen bond lengths vs ΔpKa (slopes = 0.8−1.0 ppm/pKa unit; R2 = 0.82−0.92 and 0.027−0.032 Å/pKa unit; R2 =
0.82−0.93). (D) 1H NMR spectra for the hydrogen-bonded proton of 2-hydroxyphenylacetate in chloroform and in a 10% water/90% acetone
mixture. (E) One-dimensional potential energy curve for displacement of the hydrogen-bonded proton between the donor and acceptor oxygen
atoms of the water−hydroxide dimer. Calculations were performed at the B3LYP level using the 6-311++G(d,p) basis set. Panels B−E are
reproduced from ref 26. Copyright 2015 American Chemical Society.
| ./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 4.2.0 by 1T3XT', 'creationDate': "D:20180611144746-04'00'", 'modDate': "D:20240406031325-07'00'", 'trapped': '', 'encryption': None} | ||
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 2A for O·O hydrogen bonds.117 N·O and N·N hydrogen bonds from small molecule crystal structures in
the Cambridge Structural Database are, on average, 0.13 and 0.30 Å longer than O·O hydrogen bonds, respectively, reflecting the larger van der
Waals radius of nitrogen (S. Alvarez, personal communication; see also footnote g). To account for this difference, N·O and N·N hydrogen bond
distances predicted from 1H NMR chemical shifts were uniformly corrected by the factors mentioned above, consistent with a previous analysis from
ref 126 of N·O hydrogen bonds (see also Text S3 in ref 50). This correction does not influence the scale of the length vs ΔpKa relationship and thus
does not change the conclusions herein. The origin of the steeper relationship between O·O hydrogen bond lengths and ΔpKa from 1H NMR
remains to be determined. One factor that may contribute to this difference is potential inaccuracies in converting 1H NMR chemical shifts to
hydrogen bond lengths due to the scatter in the empirical relationship in Figure 2B. Values are reported in Tables S1−S5 and Table S1 of ref 26.
Slopes are reported in Table 1.
| ./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 4.2.0 by 1T3XT', 'creationDate': "D:20180611144746-04'00'", 'modDate': "D:20240406031325-07'00'", 'trapped': '', 'encryption': None} | ||
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 experimental error in
neutron diffraction structures.48,49 In neutron diffraction structures of
3,5-dinitrosailcylate, the intramolecular hydrogen bond length varies
on the order of 0.1 Å (A, green) despite standard uncertainties of these
structures of 0.001−0.010 Å.50
| ./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 4.2.0 by 1T3XT', 'creationDate': "D:20180611144746-04'00'", 'modDate': "D:20240406031325-07'00'", 'trapped': '', 'encryption': None} | ||
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 from neutron diffraction and 1H NMR, respectively. Hydrogen bond lengths from 1H NMR were, again, estimated
using the empirical correlation function from Figure 2B, and lengths of N·O and N·N hydrogen bonds derived from this relationship were corrected
by 0.13 and 0.30 Å, respectively, as in Figure 4. Values are reported in Tables S6 and S7. Slopes are reported in Table 1.
| ./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 4.2.0 by 1T3XT', 'creationDate': "D:20180611144746-04'00'", 'modDate': "D:20240406031325-07'00'", 'trapped': '', 'encryption': None} | ||
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 4.2.0 by 1T3XT', 'creationDate': "D:20180611144746-04'00'", 'modDate': "D:20240406031325-07'00'", 'trapped': '', 'encryption': None} | ||
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 changes in oxyanion hole hydrogen bond lengths follow a single correlation line with a slope of −0.30 ± 0.03.
The “1° H-Bond” is the oxyanion hole hydrogen bond most directly affected by the perturbation (e.g., the Asp103·phenolate hydrogen bond for an
Asp103Asn mutation in pKSI), and the “2° H-Bond” is the other oxyanion hole hydrogen bond (in this example the Tyr16·phenolate). N·O
hydrogen bonds from small molecule crystal structures in the Cambridge Structural Database are, on average, 0.13 Å longer than O·O hydrogen
bonds, reflecting the larger van der Waals radius of nitrogen (S. Alvarez, personal communication). To account for this, distances for N·O hydrogen
bonds were corrected by 0.13 Å for direct comparison to O·O distances. This correction does not alter the interpretation of these results. Data are
from ref 50.
| ./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 4.2.0 by 1T3XT', 'creationDate': "D:20180611144746-04'00'", 'modDate': "D:20240406031325-07'00'", 'trapped': '', 'encryption': None} | ||
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 highlighting the ∼15° rotation of 2,6-difluorophenolate relative to
the phenolate ligand.54 This reorientation is consistent with repulsion
that is partially relieved by the rotation. The 2,6-difluorophenolate
hydrogen bond is longer than that for phenolates of the same pKa (not
shown).54
| ./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 4.2.0 by 1T3XT', 'creationDate': "D:20180611144746-04'00'", 'modDate': "D:20240406031325-07'00'", 'trapped': '', 'encryption': None} | ||
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, SUCAB03,
LIHPAL01-02, and DHNAPH17, from top right). (B) O·O hydrogen
bond lengths vs O−H·O angles for inter- and intramolecular hydrogen
bonds from small molecule neutron diffraction structures collected in
ref 27. Slopes in panel B are −133°/Å and −28°/Å for intra- and
intermolecular hydrogen bonds, respectively.
| ./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 4.2.0 by 1T3XT', 'creationDate': "D:20180611144746-04'00'", 'modDate': "D:20240406031325-07'00'", 'trapped': '', 'encryption': None} | ||
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,TS
HB ). Equilibria for transfer between water and a nonpolar solvent (ΔEnvironment) are depicted for non-hydrogen-bonded
(left) and hydrogen-bonded (right) ground state (ΔGGS,−HB
Tx
and ΔGGS,+HB
Tx
, top line) and transition state (ΔGTS,−HB
Tx
and ΔGTS,+HB
Tx
, bottom line)
species. Finally, a schematic reaction from ground state to transition state (vertical “Reaction” coordinate) is depicted in water (front) or a nonpolar
solvent (back) without (ΔGW,−HB
⧧
and ΔGNP,−HB
⧧
, left) and with (ΔGW,+HB
⧧
and ΔGNP,+HB
⧧
, right) hydrogen bond formation.
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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).
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