FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W1551351981> ?p ?o ?g. }

• W1551351981 endingPage "9837" @default.
• W1551351981 startingPage "9832" @default.
• W1551351981 abstract "Although the peptide CαH group has historically not been thought to form hydrogen bonds within proteins, ab initio quantum calculations show it to be a potent proton donor. Its binding energy to a water molecule lies in the range between 1.9 and 2.5 kcal/mol for nonpolar and polar amino acids; the hydrogen bond (H-bond) involving the charged lysine residue is even stronger than a conventional OH··O interaction. The preferred H-bond lengths are quite uniform, about 3.32 Å. Formation of each interaction results in a downfield shift of the bridging hydrogen's chemical shift and a blue shift in the CαH stretching frequency, potential diagnostics of the presence of such an H-bond within a protein. Although the peptide CαH group has historically not been thought to form hydrogen bonds within proteins, ab initio quantum calculations show it to be a potent proton donor. Its binding energy to a water molecule lies in the range between 1.9 and 2.5 kcal/mol for nonpolar and polar amino acids; the hydrogen bond (H-bond) involving the charged lysine residue is even stronger than a conventional OH··O interaction. The preferred H-bond lengths are quite uniform, about 3.32 Å. Formation of each interaction results in a downfield shift of the bridging hydrogen's chemical shift and a blue shift in the CαH stretching frequency, potential diagnostics of the presence of such an H-bond within a protein. hydrogen bond and hydrogen bonding, respectively Whereas conventional hydrogen bonds that involve electronegative atoms like oxygen and nitrogen have been thoroughly studied over the decades since their first introduction into the literature and are presently well understood (1Jeffrey G.A. Saenger W. Hydrogen Bonding in Biological Structures. Springer-Verlag, Berlin1991Crossref Google Scholar, 2Smith, D. A. (ed) (1994) Am. Chem. Soc. Symp. Ser. 569, 82-219Google Scholar, 3Scheiner S. Hydrogen Bonding: A Theoretical Perspective. Oxford University Press, New York1997: 52-290Google Scholar), the same cannot be said for the CH··O interaction, which is only now gaining wide acceptance as a genuine hydrogen bond (H-bond)1 (4Wahl M.C. Sundaralingam M. Trends Biochem. Sci. 1997; 22: 97-102Abstract Full Text PDF PubMed Scopus (327) Google Scholar, 5Desiraju G.R. Steiner T. The Weak Hydrogen Bond in Structural Chemistry and Biology. Oxford University Press, New York1999: 29-121Google Scholar). Although normally weaker than its conventional OH··O cousin, the CH··O interaction is thought to be crucial in a large number of molecular complexes and crystal structures (6Meadows E.S. De Wall S.L. Barbour L.J. Fronczek F.R. Kim M.-S. Gokel G.W. J. Am. Chem. Soc. 2000; 122: 3325-3335Crossref Scopus (70) Google Scholar, 7Steiner T. J. Phys. Chem. A. 2000; 104: 433-435Crossref Scopus (34) Google Scholar, 8Kuduva S.S. Craig D.C. Nangia A. Desiraju G.R. J. Am. Chem. Soc. 1999; 121: 1936-1944Crossref Scopus (253) Google Scholar, 9Harakas G. Vu T. Knobler C.B. Hawthorne M.F. J. Am. Chem. Soc. 1998; 120: 6405-6406Crossref Scopus (61) Google Scholar, 10Desiraju G.R. Science. 1997; 278: 404-405Crossref Scopus (206) Google Scholar). Indeed, the CH··O bond has been deemed so important as to foster the recommendation that the many crystal refinement programs that treat nonbonded C··O separations as repulsive ought to be revised (4Wahl M.C. Sundaralingam M. Trends Biochem. Sci. 1997; 22: 97-102Abstract Full Text PDF PubMed Scopus (327) Google Scholar, 11Desiraju G.R. Acc. Chem. Res. 1996; 29: 441-449Crossref PubMed Scopus (1794) Google Scholar, 12Auffinger P. Westhof E. J. Mol. Biol. 1997; 274: 54-63Crossref PubMed Scopus (142) Google Scholar). This being the case, it would be surprising indeed if the CH··O bond were any less important in biological systems. In fact, after some early proposals of CH··O contacts (13Sussman J.L. Seeman N.C., S.-H., K. Berman H.M. J. Mol. Biol. 1972; 66: 403-421Crossref PubMed Scopus (169) Google Scholar, 14Rubin J. Brennan T. Sundaralingam M. Biochemistry. 1972; 11: 3112-3128Crossref PubMed Scopus (151) Google Scholar, 15Saenger W. Angew. Chem. Int. Ed. Engl. 1973; 12: 591-601Crossref PubMed Scopus (146) Google Scholar), they were positively identified in components like sugars (16Taylor R. Kennard O. J. Am. Chem. Soc. 1982; 104: 5063-5070Crossref Scopus (2087) Google Scholar). They are now known to be prevalent in larger systems such as carbohydrates (17Steiner T. Saenger W. J. Am. Chem. Soc. 1992; 114: 10146-10154Crossref Scopus (333) Google Scholar) and nucleic acids (18Leonard G.A. McAuley-Hecht K. Brown T. Hunter W.N. Acta Crystallogr. D. 1995; 51: 136-139Crossref PubMed Scopus (108) Google Scholar, 19Biswas R. Sundaralingam M. J. Mol. Biol. 1997; 270: 511-519Crossref PubMed Scopus (44) Google Scholar, 20Brandl M. Lindauer K. Meyer M. Sühnel J. Theor. Chem. Acc. 1999; 101: 103-113Crossref Scopus (68) Google Scholar), where these interactions can be prime determinants for base pairing specificity (21Wahl M.C. Rao S.T. Sundaralingam M. Nat. Struct. Biol. 1996; 3: 24-31Crossref PubMed Scopus (105) Google Scholar) or general folding motifs (22Berger I. Egli M. Rich A. Proc. Natl. Acad. Sci. U. S. A. 1996; 93: 12116-12121Crossref PubMed Scopus (158) Google Scholar). The CH··O bond also plays an important role in the interactions of nucleic acids with proteins (23Mandel-Gutfreund Y. Margalit H. Jernigan R.L. Zhurkin V.B. J. Mol. Biol. 1998; 277: 1129-1140Crossref PubMed Scopus (161) Google Scholar, 24Gray N.S. Wodicka L. Thunnissen A.W.H. Norman T.C. Kwon S. Espinoza F.H. Morgan D.O. Barnes G. LeClerc S. Meijer L. Kim S.-H. Lockhart D.J. Schultz P.G. Science. 1998; 281: 533-538Crossref PubMed Scopus (846) Google Scholar) and drug binding (25Glusker J.P. Acta Crystallogr. D. 1995; 51: 418-427Crossref PubMed Google Scholar, 26Pascard C. Acta Crystallogr. D. 1995; 51: 407-417Crossref PubMed Google Scholar, 27Takahara P.M. Frederick C.A. Lippard S.J. J. Am. Chem. Soc. 1996; 118: 12309-12321Crossref Scopus (407) Google Scholar). There is an increasing body of evidence that CH··O contacts occur with some regularity in proteins as well. It was noted some time ago that the crystal structures of various amino acids contain these interactions (28Jeffrey G.A. Maluszynska H. Int. J. Biol. Macromol. 1982; 4: 173-185Crossref Scopus (147) Google Scholar), but their importance to larger protein segments such as α-glycine (29Berkovitch-Yellin Z. Leiserowitz L. Acta Crystallogr. B. 1984; 40: 159-165Crossref Scopus (295) Google Scholar) has been revealed as well. Other groups that appear to be involved in CH··O H-bonding include the aryl groups of aromatic residues like phenylalanine (30Thomas K.T. Smith G.M. Thomas T.B. Feldmann R.J. Proc. Natl. Acad. Sci. U. S. A. 1982; 79: 4843-4847Crossref PubMed Scopus (165) Google Scholar), the CδH of proline (31Chakrabarti P. Chakrabarti S. J. Mol. Biol. 1998; 284: 867-873Crossref PubMed Scopus (170) Google Scholar), the CH groups of histidine (32Derewenda Z.S. Derewenda U. Kobos P.M. J. Mol. Biol. 1994; 241: 83-93Crossref PubMed Scopus (203) Google Scholar, 33Ash E.L. Sudmeier J.L. Day R.M. Vincent M. Torchilin E.V. Haddad K.C. Bradshaw E.M. Sanford D.G. Bachovchin W.W. Proc. Natl. Acad. Sci. U. S. A. 2000; 97: 10371-10376Crossref PubMed Scopus (129) Google Scholar), and the lysine CεH and valine Cγ2H groups (34Steiner T. Saenger W. J. Am. Chem. Soc. 1993; 115: 4540-4547Crossref Scopus (284) Google Scholar). By far the most prevalent CH group in proteins involves the Cα of each amino acid residue, so its possible involvement in H-bonds is of profound consequence. Even if individually weak, the sheer number of such CαH··O H-bonds could exert an enormous influence upon the structure and function of a protein (4Wahl M.C. Sundaralingam M. Trends Biochem. Sci. 1997; 22: 97-102Abstract Full Text PDF PubMed Scopus (327) Google Scholar, 35Musah R.A. Jensen G.M. Rosenfeld R.J. McRee D.E. Goodin D.B. Bunte S.W. J. Am. Chem. Soc. 1997; 119: 9083-9084Crossref Scopus (105) Google Scholar). Perhaps the earliest direct evidence that the CαH group might in fact participate in H-bonds derives from a neutron diffraction study of amino acid crystals (28Jeffrey G.A. Maluszynska H. Int. J. Biol. Macromol. 1982; 4: 173-185Crossref Scopus (147) Google Scholar), which found geometric indicators of as many as 16 different CαH··O H-bonds. This idea was later confirmed in a wide variety of proteins (36Derewenda Z.S. Lee L. Derewenda U. J. Mol. Biol. 1995; 252: 248-262Crossref PubMed Scopus (500) Google Scholar), including the collagen triple helix (37Bella J. Berman H.M. J. Mol. Biol. 1996; 264: 734-742Crossref PubMed Scopus (198) Google Scholar), and in β-sheets (38Fabiola G.F. Krishnaswamy S. Nagarajan V. Pattabhi V. Acta Crystallogr. D. 1997; 53: 316-320Crossref PubMed Scopus (148) Google Scholar), where the CH··O bonds are thought to confer additional stability. Despite the finding of numerous CαH··O contacts in proteins, major questions remain about their importance. While providing a wealth of information about geometries, the numerous crystal structures on which most current knowledge about the CαH··O interaction is based are silent on the energetic aspects. In short, “nothing is known experimentally about the strength of these interactions” (35Musah R.A. Jensen G.M. Rosenfeld R.J. McRee D.E. Goodin D.B. Bunte S.W. J. Am. Chem. Soc. 1997; 119: 9083-9084Crossref Scopus (105) Google Scholar). Yet it is the strength of this binding that is of most importance in understanding the possible role that the CαH··O H-bond may play in the folding and function of proteins. It is here that one can profitably turn to ab initio quantum calculations, a particular strength of which is the assessment of interaction energies between various entities. In the case of the general CH··O interaction, there have been a number of relevant calculations (see Ref. 39Scheiner, S., Advances in Molecular Structure Research, Hargittai, M., Hargittai, I., 6, 2000, 159, 207, JAI Press, Stamford, CT.Google Scholar for a summary). It has been learned for example that the interaction energy of a small prototype, the methane-water pair, is 0.5 ± 0.1 kcal/mol (40Novoa J.J. Tarron B. Whangbo M.-H. Williams J.M. J. Chem. Phys. 1991; 95: 5179-5186Crossref Scopus (91) Google Scholar, 41Szczesniak M.M. Chalasinski G. Cybulski S.M. Cieplak P. J. Chem. Phys. 1993; 98: 3078-3089Crossref Scopus (104) Google Scholar, 42Rovira M.C. Novoa J.J. Whangbo M.-H. Williams J.M. Chem. Phys. 1995; 200: 319-335Crossref Scopus (68) Google Scholar, 43Novoa J.J. Planas M. Rovira M.C. Chem. Phys. Lett. 1996; 251: 33-46Crossref Scopus (88) Google Scholar). This value is increased systematically by roughly 1 kcal/mol as each hydrogen atom of methane is replaced by electronegative atoms like fluorine or chlorine, which make the CH a progressively stronger proton donor (44Alkorta I. Maluendes S. J. Phys. Chem. 1995; 99: 6457-6460Crossref Scopus (72) Google Scholar, 45Novoa J.J. Mota F. Chem. Phys. Lett. 1997; 266: 23-30Crossref Scopus (57) Google Scholar, 46Hobza P. Spirko V. Selzle H.L. Schlag E.W. J. Phys. Chem. A. 1998; 102: 2501-2504Crossref Scopus (341) Google Scholar, 47Cubero E. Orozco M. Luque F.J. Chem. Phys. Lett. 1999; 310: 445-450Crossref Scopus (67) Google Scholar, 48Alkorta I. Rozas I. Elguero J. J. Fluor. Chem. 2000; 101: 233-238Crossref Scopus (73) Google Scholar). This enhancement is not limited to simple atoms like fluorine or chlorine but occurs as well when the CH is adjacent to larger electronegative groups as in the context of a carboxylic acid or amide (49Turi L. Dannenberg J.J. J. Phys. Chem. 1993; 97: 12197-12204Crossref Scopus (145) Google Scholar, 50Neuheuser T. Hess B.A. Reutel C. Weber E. J. Phys. Chem. 1994; 98: 6459-6467Crossref Scopus (115) Google Scholar, 51Kim K. Friesner R.A. J. Am. Chem. Soc. 1997; 119: 12952-12961Crossref Scopus (69) Google Scholar, 52Vargas R. Garza J. Dixon D.A. Hay B.P. J. Am. Chem. Soc. 2000; 122: 4750-4755Crossref Scopus (399) Google Scholar, 53Sponer J. Hobza P. J. Phys. Chem. A. 2000; 104: 4592-4597Crossref Scopus (110) Google Scholar). Since the CαH group of each amino acid residue in a protein is directly adjacent to a pair of electronegative groups (the N and C ends of two amide groups), it is logical to presume that its ability to form an H-bond is comparable with that of a small molecule like CH2F2. Since recent calculations (54Gu Y. Kar T. Scheiner S. J. Am. Chem. Soc. 1999; 121: 9411-9422Crossref Scopus (920) Google Scholar) have demonstrated that the latter molecule does form a true H-bond, which, under certain circumstances, can be of a strength similar to a conventional OH··O interaction, an explicit examination of the H-bonding abilities of the CαH group of real amino acid residues is warranted. Reported here for the first time are the binding strengths calculated for the CαH group of a number of representative amino acids, with a common oxygen acceptor. The results indicate the comparative H-bond energy of each. In addition, supplementary IR and NMR spectroscopic information are computed so as to aid in the identification of such bonds in an experimental setting. Ab initio calculations were carried out with the GAUSSIAN 98 program using the 6–31+G** basis set (55Frisch M.J. Trucks G.W. Schlegel H.B. Scuseria G.E. Robb M.A. Cheeseman J.R. Zakrzewski V.G. Montgomery J.A. Stratmann R.E. Burant J.C. Dapprich S. Millam J.M. Daniels A.D. Kudin K.N. Strain M.C. Farkas O. Tomasi J. Barone V. Cossi M. Cammi R. Mennucci B. Pomelli C. Adamo C. Clifford S. Ochterski J. Petersson G.A. Ayala P.Y. Cui Q. Morokuma K. Malick D.K. Rabuck A.D. Raghavachari K. Foresman J.B. Cioslowski J. Ortiz J.V. Stefanov B.B. Liu G. Liashenko A. Piskorz P. Komaromi I. Gomperts R. Martin R.L. Fox D.J. Keith T. Al-Laham M.A. Peng C.Y. Nanayakkara A. Gonzalez C. Challacombe M. Gill P.M.W. Johnson B. Chen W. Wong M.W. Andres J.L. Gonzalez C. Head-Gordon M. Replogle E.S. Pople J.A. GAUSSIAN 98. Gaussian, Inc., Pittsburgh, PA1998Google Scholar). Electron correlation was included by second-order Møller-Plesset perturbation theory (MP2), which has been shown to compare favorably with more advanced schemes for related systems (53Sponer J. Hobza P. J. Phys. Chem. A. 2000; 104: 4592-4597Crossref Scopus (110) Google Scholar, 56Rivelino R. Canuto S. Chem. Phys. Lett. 2000; 322: 207-212Crossref Scopus (31) Google Scholar, 57Hartmann M. Radom L. J. Phys. Chem. A. 2000; 104: 968-973Crossref Scopus (47) Google Scholar). NMR chemical shift tensors were evaluated by the gauge-independent atomic orbital (58Wolinski K. Hilton J.F. Pulay P. J. Am. Chem. Soc. 1990; 112: 8251Crossref Scopus (5967) Google Scholar) method. The binding energies are computed as the difference in total energy between the complex on one hand and the sum of the isolated, optimized monomers on the other; basis set superposition error is removed by the counterpoise procedure (59Boys S.F. Bernardi F. Mol. Phys. 1970; 19: 553-566Crossref Scopus (19446) Google Scholar). Gly, Ala, and Val are taken as representative of the nonpolar amino acids. Ser and Cys contain the polar OH and SH groups, respectively. As examples of charged residues, the Lys+ cation and the Asp− anion were considered. All amino acids were considered in their NH2CHRCOOH nonzwitterion state so as to better model their neutral condition within a protein. Water was taken as the proton acceptor in each complex. Geometries were fully optimized; the sole restriction was that a θ(CH··O) angle of 180° was maintained in the complex to prevent the formation of complicating secondary interactions. The interaction energies of each of the various amino acids with water as the proton acceptor are reported as ΔE in the first column of data in TableI, under the convention that a negative ΔE corresponds to a favorable binding energy. The first row illustrates data for the water dimer, as a classic paradigm of an OH··O hydrogen bond, for which the electronic contribution to the binding energy is 4.51 kcal/mol at this level of theory. (This value compares quite favorably with quantities predicted at higher levels (60Scheiner S. Annu. Rev. Phys. Chem. 1994; 45: 23-56Crossref PubMed Scopus (173) Google Scholar).) Replacement of the OH of the water donor by a CH group is expected to weaken the H-bond considerably. This supposition is correct in that even after the addition of two electronegative fluorine atoms to enhance its acidity, proton donor F2HCH binds to the water acceptor by only 2.53 kcal/mol, about half the value for the water dimer (54Gu Y. Kar T. Scheiner S. J. Am. Chem. Soc. 1999; 121: 9411-9422Crossref Scopus (920) Google Scholar), as reported in the next row of Table I.Table IMP2/6–31+G** calculated properties of interaction of various proton donors with waterProton donorΔE1-aInteraction energy (negative of binding energy) including counterpoise correction.R(C–O)Δr(CH)1-bChange in CH (OH for water) bond length, in mÅ, resulting from formation of complex.Δv 1-cShift in stretching frequency of CH bond (OH for water).I/I01-dRatio between intensity of CH stretch in complex versus isolated monomer.Δςiso 1-eChange in isotropic shift of bridging proton resulting from the formation of complex.Δςan 1-fChange in anisotropic shift of bridging proton resulting from the formation of complex.kcal/molÅmÅcm−1ppmppmHOH−4.512.927+4.8−311.9−2.6010.86F2HCH−2.533.336−2.4260.2−1.276.07Gly, R = H−2.503.343−1.0144.4−1.355.91Ala, R = CH3−2.103.339−3.1511.7−1.446.76Val, CH(CH3)2−2.003.346−0.3560.3−1.516.67Ser, CH2OH−2.303.315−1.2226.4−1.717.46Cys, CH2SH−1.903.310−2.6511.0−1.617.67Lys+, (CH2)4NH3+−4.923.315−2.16 1-gCalculated at SCF level.1.0 1-gCalculated at SCF level.−1.70 1-gCalculated at SCF level.6.71 1-gCalculated at SCF level.Asp−, CH2COO−+1.433.330−4.6700.2−1.526.68All amino acids form a CαH–O interaction.1-a Interaction energy (negative of binding energy) including counterpoise correction.1-b Change in CH (OH for water) bond length, in mÅ, resulting from formation of complex.1-c Shift in stretching frequency of CH bond (OH for water).1-d Ratio between intensity of CH stretch in complex versus isolated monomer.1-e Change in isotropic shift of bridging proton resulting from the formation of complex.1-f Change in anisotropic shift of bridging proton resulting from the formation of complex.1-g Calculated at SCF level. Open table in a new tab All amino acids form a CαH–O interaction. The replacement of the two fluorine atoms by the COOH and NH2 groups, respectively, results in the NH2CH2COOH amino acid glycine. Since the two substituent groups are rather electronegative, much as the two fluorine atoms, one might anticipate only a minor perturbation upon the binding energy in the complex with water. In fact, inspection of Table Iconfirms this expectation in that glycine and F2HCH have nearly identical H-bond energies. The remainder of Table I focuses upon the changes conferred by replacement of glycine by each of several other amino acids. Substitution of one hydrogen atom by methyl yields the alanine residue and a reduction of the interaction energy by 0.4 kcal/mol. Enlargement of the methyl group of alanine to the isopropyl group of valine reduces the binding energy by another 0.1 kcal/mol. It is logical to presume that the slightly larger aliphatic side chains of Leu and Ile would be similar to the result for Val, and that the binding energies of this series of amino acids, containing simple alkyl side chains, lie in the range between 2.0 and 2.5 kcal/mol. The serine residue contains the polar hydroxyl group in its CH2OH side chain. Nonetheless, its calculated H-bond energy of 2.3 kcal/mol falls right within the range of the nonpolar residues. In a more highly refined way of looking at the data, the replacement of one hydrogen atom of the Ala methyl group by the more electronegative OH enhances the H-bond energy by some 0.2 kcal/mol. In contrast, the CH2SH sulfhydryl side chain of the Cys residue reduces the binding energy of Ala by 0.2 kcal/mol. In summary, the H-bond energies of the above amino acids, including aliphatic side chains, polar CH2OH, and less polar CH2SH, are all quite similar to one another, in the 1.9–2.5 kcal/mol range. Moving on to the charged residues, we first consider the cationic lysine residue with its (CH2)4NH3+ side chain. It is logical to expect the positive charge to make the CαH group a more powerful proton donor, enhancing its H-bond to water, as occurs with conventional H-bonds. This expectation is verified in the case of the Lys+ residue, with a binding energy of 4.9 kcal/mol, about double that of the neutral residues, although the -NH3+ group bearing the formal charge is several bonds removed from the site of H-bonding. In fact, this particular CH··O H-bond is slightly stronger than the conventional OH··O of the water dimer. Turning now to aspartate, the upper curve of Fig.1 illustrates the potential for the interaction between the aspartate residue (R=CH2COO−) and a water molecule. It may be first noted that this curve contains a minimum at a R(C··O) separation of about 3.33 Å. A stretch of this H-bond by as much as 2 or 3 Å acts against an attractive force pulling the two groups together. However, once the separation has reached 5 or 6 Å and the energy has risen to 2.5 kcal/mol above the minimum, the force changes from attractive to repulsive, acting to push the groups even further apart. This long range repulsion is understandable on the basis of the electrostatic repulsion between the aspartate anion and the negative end of the water molecule's dipole moment. In one respect, this interaction represents a H-bond of about 2.5 kcal/mol, since that is the energy required to overcome the barrier in the potential. (One must be cautious about the definition of the H-bond energy in such a case, since Table I reveals that the complex is higher in energy than the two separated monomers by 1.4 kcal/mol.) The situation is less complex in the cases of the other amino acids where the potentials have no maximum. The behavior of the complex between Ala and water, illustrated by the lower curve in Fig. 1, is a case in point, where the H-bond energy is defined simply as the energy of the minimum, relative to infinite separation. In conclusion, there appears to be an attractive interaction that prevents the separation of the aspartate residue from water, despite their long range repulsive interaction. It is intriguing, but undoubtedly coincidental, that the height of this barrier is very close in magnitude to the H-bond energies of the neutral amino acids. The second column of Table Ilists the equilibrium distances between the proton donor atom and the oxygen of the water acceptor, the intrinsically preferred H-bond length. This quantity is generally correlated with ΔE, with stronger H-bonds associated with a shorter length. It is therefore interesting to find that this H-bond distance is rather uniform in all CH··O H-bonds, covering a rather narrow range between 3.31 and 3.35 Å. This range agrees quite well with the H-bond length of 3.35 Å measured by neutron diffraction for the interaction between a CαH group and a water molecule (61Steiner T. J. Chem. Soc. Perkin Trans. 1995; II: 1315-1319Crossref Google Scholar), as well as the average Cα··O distance of 3.31 Å in parallel β-sheets (38Fabiola G.F. Krishnaswamy S. Nagarajan V. Pattabhi V. Acta Crystallogr. D. 1997; 53: 316-320Crossref PubMed Scopus (148) Google Scholar). The H-bond length is nearly constant, about 3.34 Å, for F2HCH as well as for the three aliphatic amino acids Gly, Ala, and Val. It shortens slightly to 3.31 Å for the Ser and Cys residues. Despite the stronger binding of the Lys+ residue, its H-bond length of 3.32 Å is in the same range as the other complexes, as is the separation (3.33 Å) for the anionic Asp−. The effect of the formation of the CH··O H-bond upon the CH bond length is reported in the third column of Table I (in mÅ). The first row illustrates the 5-mÅ stretch in the water dimer, a stretch that is characteristic of conventional OH··O bonds. This elongation behavior contrasts markedly with the contractions that occur in the CH··O H-bonds of all amino acids as well as F2HCH. This seemingly opposite behavior, observed in a number of CH··O bonds (46Hobza P. Spirko V. Selzle H.L. Schlag E.W. J. Phys. Chem. A. 1998; 102: 2501-2504Crossref Scopus (341) Google Scholar, 62Giribet C.G. Vizioli C.V. Ruiz de Azua C. Contreras R.H. Dannenberg J.J. Masunov A. J. Chem. Soc. Faraday Trans. 1996; 92: 3029-3033Crossref Scopus (48) Google Scholar, 63Yoshida H. Harada T. Murase T. Ohno K. Matsuura H. J. Phys. Chem. A. 1997; 101: 1731-1737Crossref Scopus (51) Google Scholar, 64Wu D.Y. Ren Y. Wang X. Tian A.M. Wong N.B. Li W.-K. J. Mol. Struct. (Theochem). 1999; 459: 171-176Crossref Scopus (10) Google Scholar, 65Hobza P. Havlas Z. Chem. Phys. Lett. 1999; 303: 447-452Crossref Scopus (200) Google Scholar, 66Cubero E. Orozco M. Hobza P. Luque F.J. J. Phys. Chem. A. 1999; 103: 6394-6401Crossref Scopus (228) Google Scholar, 67Karger N. Amorim da Costa A.M. Ribeiro-Claro J.A. J. Phys. Chem. A. 1999; 103: 8672-8677Crossref Scopus (74) Google Scholar), has nevertheless been demonstrated to be consistent with the characterization of the CH··O interaction as a true H-bond (54Gu Y. Kar T. Scheiner S. J. Am. Chem. Soc. 1999; 121: 9411-9422Crossref Scopus (920) Google Scholar). There is no clear pattern concerning the magnitude of this contraction. For example, Gly and Val elicit very small contractions, while a much larger one occurs in the similar Ala. The positive charge of the Lys+ residue does not appear to unduly raise the magnitude of this bond shortening. The largest contraction of all is associated with the aspartate anion, although its complex with water might be considered the weakest of all those considered. At any rate, the consistency of the negative values in all cases supports the idea that the CαH bond is shortened, albeit by a small amount, in all amino acid H-bonds, as occurs in a variety of other CH··O interactions. Associated with the OH bond stretch of a conventional H-bond is a red shift of its vibrational frequency. As listed in the first row of TableI, this shift amounts to −31 cm−1 for the water dimer. The positive signs of the remaining entries in the fourth column of Table I indicate that the amino acid CH bonds all shift in the opposite direction, to the blue. These positive shifts correlate with the CH bond contractions and are in fact consistent with a number of experimental observations involving CH··O bonds over the years (68Pinchas S. Anal. Chem. 1955; 27: 2-6Crossref Scopus (74) Google Scholar, 69Pinchas S. J. Phys. Chem. 1963; 67: 1862-1865Crossref Scopus (47) Google Scholar, 70Sammes M.P. Harlow R.L. J. Chem. Soc. Perkin Trans. 1976; II: 1130-1135Crossref Scopus (22) Google Scholar, 71Satonaka H. Abe K. Hirota M. Bull. Chem. Soc. Jpn. 1988; 61: 2031-2037Crossref Google Scholar, 72Adcock J.L. Zhang H. J. Org. Chem. 1995; 60: 1999-2002Crossref Scopus (27) Google Scholar, 73Mizuno K. Ochi T. Shindo Y. J. Chem. Phys. 1998; 109: 9502-9507Crossref Scopus (126) Google Scholar, 74Hobza P. Spirko V. Havlas Z. Buchhold K. Reimann B. Barth H.-D. Brutschy B. Chem. Phys. Lett. 1999; 299: 180-186Crossref Scopus (271) Google Scholar). Also consonant with previous findings, the magnitudes of these shifts are variable and, like the contractions of the CH bond, do not fit a simple pattern, although there is a trend for larger blue shifts to be associated with a greater amount of bond contraction. The largest shift of 70 cm−1 is associated with the aspartate anion. As mentioned above, these opposing patterns in the OH and CH covalent bond behavior are not entirely unexpected, having been observed on a number of occasions. There is now some reason to believe that the CH bond contraction/blue shift commonly occurs when the C atom is bonded to four other atoms, i.e. sp3 hybridization, as in the amino acids, but that the sp hybridization of the alkyne CH is associated with the stretch and red shift typical of conventional H-bonds (39Scheiner, S., Advances in Molecular Structure Research, Hargittai, M., Hargittai, I., 6, 2000, 159, 207, JAI Press, Stamford, CT.Google Scholar). The magnitude of blue shifts calculated here is consistent with prior work dealing with CH··O bonds (67Karger N. Amorim da Costa A.M. Ribeiro-Claro J.A. J. Phys. Chem. A. 1999; 103: 8672-8677Crossref Scopus (74) Google Scholar, 75Bedell B.L. Goldfarb L. Mysak E.R. Samet C. Maynard A. J. Phys. Chem. A. 1999; 103: 4572-4579Crossref Scopus (22) Google Scholar). In any event, these blue shifts ought to serve as a marker of the presence of a CαH··O H-bond in proteins. The next column of Table I reports the effect of H-bond formation upon the calculated intensity of each CH bond stretching frequency. The water dimer undergoes a characteristic enhancement, with the band 1.9 times stronger in the complex than in the isolated water monomer. There is little obvious pattern within the CH··O complexes, in that some bands are intensified (value greater than 1) while others behave in the opposite fashion. Hence, while a blue shift in frequency can be taken as a clear indication of the formation of a CH··O bond, it might be misleading to use the intensity as an indicator. Nuclear magnetic resonance frequencies have been used to good effect to monitor the presence of hydrogen bonds (76Wishart D.S. Sykes B.D. Richards F.M. J. Mol. Biol. 1991; 222: 311-333Crossref PubMed Scopus (1790) Google Scholar). The calculated values of the shifts of the bridging hydrogen are reported in the last two columns of Table I, relative to the isolated monomers. The isotropic shift is listed first, followed by the anisotropic value. Probably the most well recognized NMR diagn" @default.
• W1551351981 created "2016-06-24" @default.
• W1551351981 creator A5000575202 @default.
• W1551351981 creator A5036812068 @default.
• W1551351981 creator A5085422555 @default.
• W1551351981 date "2001-03-01" @default.
• W1551351981 modified "2023-10-16" @default.
• W1551351981 title "Strength of the CαH··O Hydrogen Bond of Amino Acid Residues" @default.
• W1551351981 cites W1865582112 @default.
• W1551351981 cites W1964277385 @default.
• W1551351981 cites W1965451259 @default.
• W1551351981 cites W1968075152 @default.
• W1551351981 cites W1969421741 @default.
• W1551351981 cites W1970310587 @default.
• W1551351981 cites W1973260055 @default.
• W1551351981 cites W1973382304 @default.
• W1551351981 cites W1975840975 @default.
• W1551351981 cites W1977730605 @default.
• W1551351981 cites W1982769333 @default.
• W1551351981 cites W1983271674 @default.
• W1551351981 cites W1984289353 @default.
• W1551351981 cites W1985465446 @default.
• W1551351981 cites W1986418242 @default.
• W1551351981 cites W1988445101 @default.
• W1551351981 cites W1989178532 @default.
• W1551351981 cites W1989377944 @default.
• W1551351981 cites W1990275895 @default.
• W1551351981 cites W1991309986 @default.
• W1551351981 cites W1993514782 @default.
• W1551351981 cites W1995675132 @default.
• W1551351981 cites W1996901439 @default.
• W1551351981 cites W2004826474 @default.
• W1551351981 cites W2005006476 @default.
• W1551351981 cites W2008379660 @default.
• W1551351981 cites W2009487455 @default.
• W1551351981 cites W2011673894 @default.
• W1551351981 cites W2011830733 @default.
• W1551351981 cites W2012068802 @default.
• W1551351981 cites W2014053367 @default.
• W1551351981 cites W2025286459 @default.
• W1551351981 cites W2029081636 @default.
• W1551351981 cites W2030643546 @default.
• W1551351981 cites W2031618329 @default.
• W1551351981 cites W2032997316 @default.
• W1551351981 cites W2037813720 @default.
• W1551351981 cites W2037875211 @default.
• W1551351981 cites W2039461296 @default.
• W1551351981 cites W2039735251 @default.
• W1551351981 cites W2043759893 @default.
• W1551351981 cites W2044125074 @default.
• W1551351981 cites W2045950270 @default.
• W1551351981 cites W2047244384 @default.
• W1551351981 cites W2051617312 @default.
• W1551351981 cites W2054164390 @default.
• W1551351981 cites W2055714796 @default.
• W1551351981 cites W2056651981 @default.
• W1551351981 cites W2057224549 @default.
• W1551351981 cites W2062282649 @default.
• W1551351981 cites W2064246675 @default.
• W1551351981 cites W2065126106 @default.
• W1551351981 cites W2072413554 @default.
• W1551351981 cites W2073312936 @default.
• W1551351981 cites W2073512708 @default.
• W1551351981 cites W2073687211 @default.
• W1551351981 cites W2074581038 @default.
• W1551351981 cites W2076904919 @default.
• W1551351981 cites W2080046078 @default.
• W1551351981 cites W2080972330 @default.
• W1551351981 cites W2086743209 @default.
• W1551351981 cites W2090250026 @default.
• W1551351981 cites W2091244182 @default.
• W1551351981 cites W2091316615 @default.
• W1551351981 cites W2093657900 @default.
• W1551351981 cites W2093713382 @default.
• W1551351981 cites W2097981550 @default.
• W1551351981 cites W2100314081 @default.
• W1551351981 cites W2107146401 @default.
• W1551351981 cites W2132218204 @default.
• W1551351981 cites W2138870170 @default.
• W1551351981 cites W2146000663 @default.
• W1551351981 cites W2148941593 @default.
• W1551351981 cites W2154918056 @default.
• W1551351981 cites W2162901683 @default.
• W1551351981 cites W2327855492 @default.
• W1551351981 doi "https://doi.org/10.1074/jbc.m010770200" @default.
• W1551351981 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/11152477" @default.
• W1551351981 hasPublicationYear "2001" @default.
• W1551351981 type Work @default.
• W1551351981 sameAs 1551351981 @default.
• W1551351981 citedByCount "270" @default.
• W1551351981 countsByYear W15513519812012 @default.
• W1551351981 countsByYear W15513519812013 @default.
• W1551351981 countsByYear W15513519812014 @default.
• W1551351981 countsByYear W15513519812015 @default.
• W1551351981 countsByYear W15513519812016 @default.
• W1551351981 countsByYear W15513519812017 @default.
• W1551351981 countsByYear W15513519812018 @default.
• W1551351981 countsByYear W15513519812019 @default.

• next