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Samanta AK, Banerjee P, Bandyopadhyay B, Pandey P, Chakraborty T. Antagonistic Interplay Between an Intermolecular CH···O and an Intramolecular OH···O Hydrogen Bond in a 1:1 Complex Between 1,2-Cyclohexanedione and Chloroform: A Combined Matrix Isolation Infrared and Quantum Chemistry Study. J Phys Chem A 2017; 121:6012-6020. [PMID: 28737917 DOI: 10.1021/acs.jpca.7b05615] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Matrix isolation infrared spectra of a weak C-H···O hydrogen-bonded complex between the keto-enol form of 1,2-cyclohexanedione (HCHD) and chloroform have been measured. The spectra reveal that the intramolecular O-H···O H-bond of HCHD is weakened as a result of complex formation, manifesting in prominent blue shift (∼23 cm-1) of the νO-H band and red shifts (∼7 cm-1) of νC═O bands of the acceptor (HCHD). The νC-H band of donor CHCl3 undergoes a large red shift of ∼33 cm-1. Very similar spectral effects are also observed for formation of the complex in CCl4 solution at room temperature. Our analysis reveals that out of several possible iso-energetic conformational forms of the complex, the one involving antagonistic interplay between the two hydrogen bonds (intermolecular C-H···O and intramolecular O-H···O) is preferred. The combined experimental and calculated data presented here suggest that in condensed media, conformational preferences are guided by directional hyperconjugative charge transfer interactions at the C-H···O hydrogen bonding site of the complex.
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Affiliation(s)
- Amit Kumar Samanta
- Center for Free-Electron Laser Science (CFEL) , Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Pujarini Banerjee
- Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
| | - Biman Bandyopadhyay
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, J. L. N. Marg , Jaipur, India
| | | | - Tapas Chakraborty
- Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
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2
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Bhattacherjee A, Wategaonkar S. Role of the C(2)–H Hydrogen Bond Donor in Gas-Phase Microsolvation of Imidazole Derivatives with ROH (R = CH3, C2H5). J Phys Chem A 2017; 121:4283-4295. [DOI: 10.1021/acs.jpca.7b03329] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aditi Bhattacherjee
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
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3
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Bhattacherjee A, Wategaonkar S. Water bridges anchored by a C–H⋯O hydrogen bond: the role of weak interactions in molecular solvation. Phys Chem Chem Phys 2016; 18:27745-27749. [DOI: 10.1039/c6cp05469b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogen-bonded water bridges are re-directed from a polar NH bond to a weakly activated C(2)–H bond upon N-methylation. Infrared spectra, supported by ab initio calculations, provide direct evidence of the role of the C(2)–H donor in the solvation of the imidazole ring.
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Affiliation(s)
- Aditi Bhattacherjee
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Mumbai 400 005
- India
| | - Sanjay Wategaonkar
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Mumbai 400 005
- India
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4
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Bhattacherjee A, Wategaonkar S. Conformational preferences of monohydrated clusters of imidazole derivatives revisited. Phys Chem Chem Phys 2015; 17:20080-92. [DOI: 10.1039/c5cp02422f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
IR-UV double resonance spectroscopy was used to identify the conformers of monohydrated benzimidazole andN-methylbenzimidazole in a supersonic jet. A new OH–N bound conformer relevant to histidine containing proteins was discovered. The long standing differences in the literature about the relative energies and abundance of the monohydrated imidazole derivatives have also been resolved.
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Affiliation(s)
- Aditi Bhattacherjee
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Mumbai 400 005
- India
| | - Sanjay Wategaonkar
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Mumbai 400 005
- India
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5
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Kossack W, Adrjanowicz K, Tarnacka M, Kiprop Kipnusu W, Dulski M, Mapesa EU, Kaminski K, Pawlus S, Paluch M, Kremer F. Glassy dynamics and physical aging in fucose saccharides as studied by infrared- and broadband dielectric spectroscopy. Phys Chem Chem Phys 2013; 15:20641-50. [DOI: 10.1039/c3cp52551a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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6
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Zischang J, Lee JJ, Suhm MA. Communication: Where does the first water molecule go in imidazole? J Chem Phys 2012; 135:061102. [PMID: 21842918 DOI: 10.1063/1.3624841] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Supersonic jet FTIR spectroscopy supplemented by (18)O substitution shows unambiguously that water prefers to act as an O-H···N hydrogen bond donor towards imidazole, instead of acting as a N-H···O acceptor. Previous matrix isolation, helium droplet, and aromatic substitution experiments had remained ambiguous, as are standard quantum chemical calculations. The finding is supported by a study of the analogous methanol complexes and by higher level quantum chemical calculations.
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Affiliation(s)
- Julia Zischang
- Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Tammannstr. 6, 37077 Göttingen, Germany
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7
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Leavens FMV, Churchill CDM, Wang S, Wetmore SD. Evaluating how discrete water molecules affect protein-DNA π-π and π(+)-π stacking and T-shaped interactions: the case of histidine-adenine dimers. J Phys Chem B 2011; 115:10990-1003. [PMID: 21809837 DOI: 10.1021/jp205424z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Changes in the magnitude of (M06-2X/6-31+G(d,p)) π-π stacking and T-shaped (nucleobase-edge and amino acid-edge) interactions between (neutral or protonated) histidine (His) and adenine (A) dimers upon microsolvation with up to four discrete water molecules were determined. A variety of histidine-water interactions were considered including conventional (N-H···O, N···H-O, C-H···O) hydrogen bonding and nonconventional (X-H···π (neutral His) or lone-pair···π (protonated His)) contacts. Overall, the effects of discrete His-H(2)O interactions on the neutral histidine-adenine π-π contacts are negligible (<3 kJ mol(-1) or 15%) regardless of the type of water binding, the number of water molecules bound, or the His-A dimer (stacked or (amino acid- or nucleobase-edge) T-shaped) configuration. This suggests that previously reported gas-phase binding strengths for a variety of neutral amino acid-nucleobase dimers are likely relevant for a wide variety of (microsolvated) environments. In contrast, the presence of water decreases the histidine-adenine π(+)-π interaction by up to 15 kJ mol(-1) (or 30%) for all water binding modes and orientations, as well as different stacked and T-shaped His(+)-A dimers. Regardless of the larger effect of discrete histidine-water interactions on the magnitude of the π(+)-π compared with π-π interactions, the π(+)-π binding strengths remain substantially larger than the corresponding π-π contacts. These findings emphasize the distinct nature of π(+)-π and π-π interactions and suggest that π(+)-π contacts can provide significant stabilization in biological systems relative to π-π contacts under many different environmental conditions.
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Affiliation(s)
- Fern M V Leavens
- Department of Chemistry & Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4
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8
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Ramírez J, Brelot L, Osinska I, Stadler AM. CH…O hydrogen bond in the crystal structure of a pyrazine-based ligand and determination of the amplitude of the ligand conformational change induced by Cu(II) coordination. J Mol Struct 2009. [DOI: 10.1016/j.molstruc.2009.05.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Mukhopadhyay A, Mukherjee M, Pandey P, Samanta AK, Bandyopadhyay B, Chakraborty T. Blue Shifting C−H···O Hydrogen Bonded Complexes between Chloroform and Small Cyclic Ketones: Ring-Size Effects on Stability and Spectral Shifts. J Phys Chem A 2009; 113:3078-87. [DOI: 10.1021/jp900473w] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anamika Mukhopadhyay
- Department of Physical Chemistry and Raman Center for Atomic Molecular and Optical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Moitrayee Mukherjee
- Department of Physical Chemistry and Raman Center for Atomic Molecular and Optical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Prasenjit Pandey
- Department of Physical Chemistry and Raman Center for Atomic Molecular and Optical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Amit K. Samanta
- Department of Physical Chemistry and Raman Center for Atomic Molecular and Optical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Biman Bandyopadhyay
- Department of Physical Chemistry and Raman Center for Atomic Molecular and Optical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Tapas Chakraborty
- Department of Physical Chemistry and Raman Center for Atomic Molecular and Optical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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10
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Li FF, Gao X, Zheng M. Why [6,6]- and 1,2-Benzal-3-N-4-O-Cyclic Phenylimidate C60 Undergo Electrochemically Induced Retro-Addition Reactions while 1,4-Dibenzyl-2,3-Cyclic Phenylimidate C60 Does Not? C−H···X (X = N, O) Intramolecular Interactions in Organofullerenes. J Org Chem 2008; 74:82-7. [DOI: 10.1021/jo801769q] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fang-Fang Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Graduate School of Chinese Academy of Sciences, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, Jilin 130022, China
| | - Xiang Gao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Graduate School of Chinese Academy of Sciences, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, Jilin 130022, China
| | - Min Zheng
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Graduate School of Chinese Academy of Sciences, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, Jilin 130022, China
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11
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Niebel C, Lokshin V, Sigalov M, Krief P, Khodorkovsky V. Intra- and Intermolecular C(sp2)-H···O Hydrogen Bonds in a Series of Isobenzofuranone Derivatives: Manifestation and Energetics. European J Org Chem 2008. [DOI: 10.1002/ejoc.200800357] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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12
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Clark J, English AM, Hansen JC, Francisco JS. Computational Study on the Existence of Organic Peroxy Radical-Water Complexes (RO2·H2O). J Phys Chem A 2008; 112:1587-95. [DOI: 10.1021/jp077266d] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jared Clark
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602
| | - Alecia M. English
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602
| | - Jaron C. Hansen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602
| | - Joseph S. Francisco
- Department of Chemistry and Department of Earth and Atmospheric Sciences, Purdue University, West Lafayette, Indiana 47907
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13
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Venkataramana G, Sankararaman S. Synthesis and Spectroscopic Investigation of Aggregation through Cooperative π−π and C−H···O Interactions in a Novel Pyrene Octaaldehyde Derivative. Org Lett 2006; 8:2739-42. [PMID: 16774245 DOI: 10.1021/ol060767h] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] Synthesis of a pyrene octaaldehyde derivative and its aggregation through pi-pi and C-H...O interactions in solution and in the solid state probed by fluorescence emission and other spectroscopic methods are reported. The effect of solvent, concentration, and temperature on the aggregation is investigated.
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14
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Ding S, Hong YW, Chen CY, Chang NC. One and two dimensional 1H and 13C high resolution NMR investigation of lariat ethers and their alkali metal ionic complexes: a more tangible evidence for the presence of less common C-H***O hydrogen bonds. Biophys Chem 2006; 121:75-83. [PMID: 16455180 DOI: 10.1016/j.bpc.2006.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2005] [Revised: 01/05/2006] [Accepted: 01/05/2006] [Indexed: 11/18/2022]
Abstract
The possible existence of less common hydrogen bonds in three lariat ethers and their alkali-metal ionic complexes have been investigated with one- and two-dimensional (1D and 2D) proton and carbon-13 high resolution liquid state NMR spectroscopy. The occurrence of hydrogen-bonding induced by the addition of metal ions has been identified with the observation of indirect dipolar coupling between the coupling partners involved in the hydrogen-bonding. The addition of metal ions, moreover, causes appreciable change of chemical shift of several protons and carbons. The chemical shift change depends on the ion radius, larger ions causing smaller change. Moreover, the change of chemical shift is in coincidence with the occurrence of hydrogen-bonding. The values of the coupling constants have been obtained for each of these hydrogen bonds and were used for evaluating the hydrogen-bond strength. An intriguing and surprising observation is that a C-H***O hydrogen bond identified in solution by this work was not found in the previous study with X-ray diffraction or other methods.
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Affiliation(s)
- Shangwu Ding
- Department of Chemistry and Center for Nanoscience and Nanotechnology, National Sun Yat-Sen University, 70 Lien-Hai Road, Kaohsiung, Taiwan 80424, Republic of China.
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15
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Andrei HS, Solcà N, Dopfer O. Microhydration of Protonated Biomolecular Building Blocks: IR Spectra of Protonated Imidazole-Watern Complexes. Chemphyschem 2006; 7:107-10. [PMID: 16317795 DOI: 10.1002/cphc.200500432] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Horia-Sorin Andrei
- Institut für Physikalische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
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16
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Pierce AC, Sandretto KL, Bemis GW. Kinase inhibitors and the case for CH...O hydrogen bonds in protein-ligand binding. Proteins 2002; 49:567-76. [PMID: 12402365 DOI: 10.1002/prot.10259] [Citation(s) in RCA: 177] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Although the hydrogen bond is known to be an important mediator of intermolecular interactions, there has yet to be an analysis of the role of CH...O hydrogen bonds in protein-ligand complexes. In this work, we present evidence for such nonstandard hydrogen bonds from a survey of aromatic ligands in 184 kinase crystal structures and 358 high-resolution structures from the Protein Data Bank. CH groups adjacent to the positively charged nitrogen of nicotinamide exhibit geometric preferences strongly suggestive of hydrogen bonding interactions, as do heterocyclic CH groups in kinase ligands, while other aromatic CH groups do not exhibit these characteristics. Ab initio calculations reveal a considerable range of CH...O hydrogen bonding potentials among different aromatic ring systems, with nicotinamide and heterocycles preferred in kinase inhibitors showing particularly favorable interactions. These results provide compelling evidence for the existence of CH...O hydrogen bonds in protein-ligand interactions, as well as information on the relative strength of various aromatic CH donors. Such knowledge will be of considerable value in protein modeling, ligand design, and structure-activity analysis.
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Affiliation(s)
- Albert C Pierce
- Vertex Pharmaceuticals, Cambridge, Massachusetts 02139, USA.
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17
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Scheiner S, Kar T, Pattanayak J. Comparison of various types of hydrogen bonds involving aromatic amino acids. J Am Chem Soc 2002; 124:13257-64. [PMID: 12405854 DOI: 10.1021/ja027200q] [Citation(s) in RCA: 265] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ab initio calculations are used to compare the abilities of the aromatic groups of the Phe, Tyr, Trp, and His amino acids (modeled respectively by benzene, phenol, indole, and imidazole) to form H-bonds of three different types. Strongest of all are the conventional H-bonds (e.g., OH..O and OH..N). His forms the strongest such H-bond, followed by Tyr, and then by Trp. Whereas OH..phi bonds formed by the approach of a proton donor to the pi electron cloud above the aromatic system are somewhat weaker, they nonetheless represent an important class of stabilizing interactions. The strengths of H-bonds in this category follow the trend Trp > His > Tyr approximately Phe. CH.O interactions are weaker still, and only those involving His and Trp are strong enough to make significant contributions to protein structure. A protonated residue such as HisH(+) makes for a very powerful proton donor, such that even its CH..O H-bonds are stronger than the conventional H-bonds formed by neutral groups.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry & Biochemistry, Utah State University, Logan, Utah 84322-0300, USA
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18
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Abstract
For the first time, a statistical potential has been developed to quantitatively describe the CH.O hydrogen bonding interaction at the protein-protein interface. The calculated energies of the CH.O pair interaction show a favorable valley at approximately 3.3 A, exhibiting a feature typical of an H-bond and similar to the ab initio quantum calculation result (Scheiner, S., Kar, T., and Gu, Y. (2001) J. Biol. Chem. 276, 9832-9837). The potentials have been applied to a set of 469 protein-protein complexes to calculate the contribution of different types of interactions to each protein complex: the average energy contribution of a conventional H-bond is approximately 30%; that of a CH.O H-bond is 17%; and that of a hydrophobic interaction is 50%. In some protein-protein complexes, the contribution of the CH.O H-bond can reach as high as approximately 40-50%, indicating the importance of the CH.O H-bond at the protein interface. At the interfaces of these complexes, C(alpha)H.O H-bonds frequently occur between adjacent strands in both parallel and antiparallel orientations, having the obvious structural motif of bifurcated H-bonds. Our study suggests that the weak CH.O H-bond makes an important contribution to the association and stability of protein complexes and needs more attention in protein-protein interaction studies.
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Affiliation(s)
- Lin Jiang
- State Key Laboratory for Structural Chemistry of Stable and Unstable Species, the Institute of Physical Chemistry, Department of Chemical Biology, College of Chemistry, and the Center for Theoretical Biology, Peking University, Beijing 100871, China
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Kitova EN, Bundle DR, Klassen JS. Evidence for the preservation of specific intermolecular interactions in gaseous protein-oligosaccharide complexes. J Am Chem Soc 2002; 124:9340-1. [PMID: 12167006 DOI: 10.1021/ja025908z] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Arrhenius parameters, obtained with the blackbody infrared radiative dissociation technique, are reported for the dissociation of a series of gaseous protonated complexes composed of mutants of a single chain variable fragment (scFv) of the monoclonal antibody Se155-4 and three trisaccharide ligands. Hydrogen bonding between a ligand and a particular amino acid residue is identified from a comparison of activation energies measured for the complex of the unmodified scFv and the corresponding mutant. It is shown that the specific hydrogen bond between His(101H) and Man C-4 OH is preserved in the gaseous complex.
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Affiliation(s)
- Elena N Kitova
- Department of Chemistry, University of Alberta, Edmonton, Canada T6G 2G2
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20
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Kitova EN, Bundle DR, Klassen JS. Thermal dissociation of protein-oligosaccharide complexes in the gas phase: mapping the intrinsic intermolecular interactions. J Am Chem Soc 2002; 124:5902-13. [PMID: 12010066 DOI: 10.1021/ja017213o] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Blackbody infrared radiative dissociation (BIRD) and functional group replacement are used to map the location and strength of hydrogen bonds between an antibody single chain fragment (scFv) and its natural trisaccharide receptor, alpha-D-Galp (1-->2)[alpha-D-Abep (1-->3)]alpha-D-Manp1-->OMe (1), in the gaseous, multiply protonated complex. Arrhenius activation parameters (E(a) and A) are reported for the loss of 1 and a series of monodeoxy trisaccharide congeners (5-8 identical with tri) from the (scFv + tri + 10H)(+10) complex. The energetic contribution of the specific oligosaccharide OH groups to the stability of the (scFv + 1 + 10H)(+10) complex is determined from the differences in E(a) measured for the trisaccharide analogues and 1 (55.2 kcal/mol). A decrease of 6 to 11 kcal/mol in E(a), measured for the monodeoxy trisaccharides, indicates that the deleted OH groups interact strongly with the scFv and that they account for a majority of the stabilizing intermolecular interactions. A partial map of the hydrogen bond donor/acceptor groups of 1 and the strength of the interactions is presented for the protonated +10 complex. A comparison of the gas-phase map with the crystal structure indicates that significant structural differences exist. The hydroxyl groups located outside of the binding pocket, and exposed to solvent in solution, participate in new protein-oligosaccharide hydrogen bonds in the gas phase. The decrease in kinetic and energetic stability of the (scFv + 2 + nH)(n)()(+) complex with increasing charge-state is attributed to conformational differences in the binding region induced by electrostatic repulsion. The similarity in the Arrhenius parameters for the +9 and +10 charge states suggests that repulsion effects on the structure of the binding region are negligible below +11.
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Affiliation(s)
- Elena N Kitova
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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21
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Mentré P, Hui Bon Hoa G. Effects of high hydrostatic pressures on living cells: a consequence of the properties of macromolecules and macromolecule-associated water. INTERNATIONAL REVIEW OF CYTOLOGY 2001; 201:1-84. [PMID: 11057830 DOI: 10.1016/s0074-7696(01)01001-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Sixty percent of the Earth's biomass is found in the sea, at depths greater than 1000 m, i.e., at hydrostatic pressures higher than 100 atm. Still more surprising is the fact that living cells can reversibly withstand pressure shifts of 1000 atm. One explanation lies in the properties of cellular water. Water forms a very thin film around macromolecules, with a heterogeneous structure that is an image of the heterogeneity of the macromolecular surface. The density of water in contact with macromolecules reflects the physical properties of their different domains. Therefore, any macromolecular shape variations involving the reorganization of water and concomitant density changes are sensitive to pressure (Le Chatelier's principle). Most of the pressure-induced changes to macromolecules are reversible up to 2000 atm. Both the effects of pressure shifts on living cells and the characteristics of pressure-adapted species are opening new perspectives on fundamental problems such as regulation and adaptation.
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Affiliation(s)
- P Mentré
- Station INRA 806, Institut de Biologie Physico-Chimique, Paris, France
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22
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Gu Y, Kar T, Scheiner S. Comparison of the CH⋯N and CH⋯O interactions involving substituted alkanes. J Mol Struct 2000. [DOI: 10.1016/s0022-2860(00)00455-5] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Scheiner S, Gu Y, Kar T. Evaluation of the H-bonding properties of CH⋯O interactions based upon NMR spectra. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s0166-1280(00)00375-4] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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24
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Meyer M, Steinke T, Brandl M, S�hnel J. Density functional study of guanine and uracil quartets and of guanine quartet/metal ion complexes. J Comput Chem 2000. [DOI: 10.1002/1096-987x(20010115)22:1<109::aid-jcc11>3.0.co;2-5] [Citation(s) in RCA: 112] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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25
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Gu Y, Kar T, Scheiner S. Fundamental Properties of the CH···O Interaction: Is It a True Hydrogen Bond? J Am Chem Soc 1999. [DOI: 10.1021/ja991795g] [Citation(s) in RCA: 810] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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Meyer M, Wohlfahrt G, Knäblein J, Schomburg D. Aspects of the mechanism of catalysis of glucose oxidase: a docking, molecular mechanics and quantum chemical study. J Comput Aided Mol Des 1998; 12:425-40. [PMID: 9834905 DOI: 10.1023/a:1008020124326] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The complex structure of glucose oxidase (GOX) with the substrate glucose was determined using a docking algorithm and subsequent molecular dynamics simulations. Semiempirical quantum chemical calculations were used to investigate the role of the enzyme and FAD co-enzyme in the catalytic oxidation of glucose. On the basis of a small active site model, substrate binding residues were determined and heats of formation were computed for the enzyme substrate complex and different potential products of the reductive half reaction. The influence of the protein environment on the active site model was estimated with a point charge model using a mixed QM/MM method. Solvent effects were estimated with a continuum model. Possible modes of action are presented in relation to experimental data and discussed with respect to related enzymes. The calculations indicate that the redox reaction of GOX differs from the corresponding reaction of free flavins as a consequence of the protein environment. One of the active site histidines is involved in substrate binding and stabilization of potential intermediates, whereas the second histidine is a proton acceptor. The former one, being conserved in a series of oxidoreductases, is also involved in the stabilization of a C4a-hydroperoxy dihydroflavin in the course of the oxidative half reaction.
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Affiliation(s)
- M Meyer
- Institut für Molekulare Biotechnologie (IMB), Jena, Germany
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Mandel-Gutfreund Y, Margalit H, Jernigan RL, Zhurkin VB. A role for CH...O interactions in protein-DNA recognition. J Mol Biol 1998; 277:1129-40. [PMID: 9571027 DOI: 10.1006/jmbi.1998.1660] [Citation(s) in RCA: 152] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The concept of CH...O hydrogen bonds has recently gained much interest, with a number of reports indicating the significance of these non-classical hydrogen bonds in stabilizing nucleic acid and protein structures. Here, we analyze the CH...O interactions in the protein-DNA interface, based on 43 crystal structures of protein-DNA complexes. Surprisingly, we find that the number of close intermolecular CH...O contacts involving the thymine methyl group and position C5 of cytosine is comparable to the number of protein-DNA hydrogen bonds involving nitrogen and oxygen atoms as donors and acceptors. A comprehensive analysis of the geometries of these close contacts shows that they are similar to other CH...O interactions found in proteins and small molecules, as well as to classical NH...O hydrogen bonds. Thus, we suggest that C5 of cytosine and C5-Met of thymine form relatively weak CH...O hydrogen bonds with Asp, Asn, Glu, Gln, Ser, and Thr, contributing to the specificity of recognition. Including these interactions, in addition to the classical protein-DNA hydrogen bonds, enables the extraction of simple structural principles for amino acid-base recognition consistent with electrostatic considerations.
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Affiliation(s)
- Y Mandel-Gutfreund
- Department of Molecular Genetics and Biotechnology, The Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel
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