메뉴 건너뛰기




Volumn 169, Issue 1, 2008, Pages 8-18

Evidence for a Grotthuss-like mechanism in the formation of the rhamnose alkoxy radical based on periodic DFT calculations

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA LEVO RHAMNOSE; HYDROXYL GROUP; HYDROXYL RADICAL; MONOSACCHARIDE; PROTON; RHAMNOSE; UNCLASSIFIED DRUG; WATER; ALCOHOL DERIVATIVE; ALKOXY RADICAL; OXYGEN;

EID: 39049089015     PISSN: 00337587     EISSN: None     Source Type: Journal    
DOI: 10.1667/RR1039.1     Document Type: Article
Times cited : (18)

References (43)
  • 1
    • 0030980402 scopus 로고    scopus 로고
    • Where are the sugar radicals in irradiated DNA?
    • D. M. Close, Where are the sugar radicals in irradiated DNA? Radiat. Res. 147, 663-673 (1997).
    • (1997) Radiat. Res , vol.147 , pp. 663-673
    • Close, D.M.1
  • 2
    • 19444383778 scopus 로고    scopus 로고
    • Sugar radicals in DNA: Isolation of neutral radicals in gamma-irradiated DNA by hole and electron scavenging
    • L. I. Shukla, R. Pazdro, D. Becker and M. D. Sevilla, Sugar radicals in DNA: Isolation of neutral radicals in gamma-irradiated DNA by hole and electron scavenging. Radiat. Res. 163, 591-602 (2005).
    • (2005) Radiat. Res , vol.163 , pp. 591-602
    • Shukla, L.I.1    Pazdro, R.2    Becker, D.3    Sevilla, M.D.4
  • 3
    • 26944440558 scopus 로고    scopus 로고
    • UVA-visible photo-excitation of guanine radical cations produces sugar radicals in DNA and model structures
    • A. Adhikary, A. Y. S. Malkhasian, S. Collins, J. Koppen, D. Becker and M. D. Sevilla, UVA-visible photo-excitation of guanine radical cations produces sugar radicals in DNA and model structures. Nucleic Acids Res. 33, 5553-5564 (2005).
    • (2005) Nucleic Acids Res , vol.33 , pp. 5553-5564
    • Adhikary, A.1    Malkhasian, A.Y.S.2    Collins, S.3    Koppen, J.4    Becker, D.5    Sevilla, M.D.6
  • 4
    • 33645547868 scopus 로고    scopus 로고
    • C5′- and C3′-sugar radicals produced via photo-excitation of one-electron oxidized adenine in 2′-deoxyadenonsine and its derivatives
    • A. Adhikary, D. Becker, S. Collins, J. Koppen and M. D. Sevilla, C5′- and C3′-sugar radicals produced via photo-excitation of one-electron oxidized adenine in 2′-deoxyadenonsine and its derivatives. Nucleic Acids Res. 34, 1501-1511 (2006).
    • (2006) Nucleic Acids Res , vol.34 , pp. 1501-1511
    • Adhikary, A.1    Becker, D.2    Collins, S.3    Koppen, J.4    Sevilla, M.D.5
  • 5
    • 36749110225 scopus 로고
    • Radiation effects in X-irradiated hydroxy compounds
    • E. E. Budzinski, W. R. Potter and H. C. Box, Radiation effects in X-irradiated hydroxy compounds. J. Chem. Phys. 72, 972-975 (1980).
    • (1980) J. Chem. Phys , vol.72 , pp. 972-975
    • Budzinski, E.E.1    Potter, W.R.2    Box, H.C.3
  • 6
    • 0025218580 scopus 로고
    • Studies of electrons trapped in X-irradiated rhamnose crystals
    • H. C. Box, E. E. Budzinski and H. G. Freund, Studies of electrons trapped in X-irradiated rhamnose crystals. Radiat. Res. 121, 262-266 (1990).
    • (1990) Radiat. Res , vol.121 , pp. 262-266
    • Box, H.C.1    Budzinski, E.E.2    Freund, H.G.3
  • 7
    • 2642630525 scopus 로고
    • Primary reactions of localized electrons in rhamnose crystals studied by pulse-radiolysis and ESR spectroscopy
    • P. O. Samskog, A. Lund, G. Nilsson and M. C. R. Symons, Primary reactions of localized electrons in rhamnose crystals studied by pulse-radiolysis and ESR spectroscopy. J. Chem. Phys. 73, 4862-4866 (1980).
    • (1980) J. Chem. Phys , vol.73 , pp. 4862-4866
    • Samskog, P.O.1    Lund, A.2    Nilsson, G.3    Symons, M.C.R.4
  • 8
    • 2642601901 scopus 로고
    • Geometric model of trapped electrons in X-ray-irradiated single-crystals of rhamnose
    • P. O. Samskog, L. D. Kispert and A. Lund, Geometric model of trapped electrons in X-ray-irradiated single-crystals of rhamnose. J. Chem. Phys. 79, 635-638 (1983).
    • (1983) J. Chem. Phys , vol.79 , pp. 635-638
    • Samskog, P.O.1    Kispert, L.D.2    Lund, A.3
  • 9
    • 33745790604 scopus 로고
    • The alkoxy radical RCHO formed in irradiated single crystals of rhamnose
    • P. O. Samskog and A. Lund, The alkoxy radical RCHO formed in irradiated single crystals of rhamnose. Chem. Phys. Lett. 75, 525-527 (1980).
    • (1980) Chem. Phys. Lett , vol.75 , pp. 525-527
    • Samskog, P.O.1    Lund, A.2
  • 10
    • 33745772898 scopus 로고
    • Alkoxy radicals - delta-proton hyperfine couplings
    • E. E. Budzinski and H. C. Box, Alkoxy radicals - delta-proton hyperfine couplings. J. Chem. Phys. 82, 3487-3490 (1985).
    • (1985) J. Chem. Phys , vol.82 , pp. 3487-3490
    • Budzinski, E.E.1    Box, H.C.2
  • 11
    • 0026332626 scopus 로고
    • Electron trapping and reactions in rhamnose by ESR and ENDOR
    • E. Sagstuen, M. Lindgren and A. Lund, Electron trapping and reactions in rhamnose by ESR and ENDOR. Radiat. Res. 128, 235-242 (1991).
    • (1991) Radiat. Res , vol.128 , pp. 235-242
    • Sagstuen, E.1    Lindgren, M.2    Lund, A.3
  • 12
    • 33745767792 scopus 로고    scopus 로고
    • Study of rhamnose radicals in the solid state adopting a density functional theory cluster approach
    • E. Pauwels, V. Van Speybroeck and M. Waroquier, Study of rhamnose radicals in the solid state adopting a density functional theory cluster approach. J. Phys. Chem. A 110, 6504-6513 (2006).
    • (2006) J. Phys. Chem. A , vol.110 , pp. 6504-6513
    • Pauwels, E.1    Van Speybroeck, V.2    Waroquier, M.3
  • 13
    • 0001064332 scopus 로고
    • Neutron-diffraction refinement of crystal structure of alpha-1-rhamnose monohydrate
    • S. Takagi and G. A. Jeffrey, Neutron-diffraction refinement of crystal structure of alpha-1-rhamnose monohydrate. Acta Cryst. B 34, 2551-2555 (1978).
    • (1978) Acta Cryst. B , vol.34 , pp. 2551-2555
    • Takagi, S.1    Jeffrey, G.A.2
  • 14
    • 39749104937 scopus 로고    scopus 로고
    • CPMD V3.11. ©IBM Corp. 1996-2006, ©MPI für Festkörperforschung Stuttgart 1997-2001.
    • CPMD V3.11. ©IBM Corp. 1996-2006, ©MPI für Festkörperforschung Stuttgart 1997-2001.
  • 15
    • 5944261746 scopus 로고
    • Density-functional approximation for the correlation energy of the inhomogeneous electron gas
    • J. P. Perdew, Density-functional approximation for the correlation energy of the inhomogeneous electron gas. Phys. Rev. B 33, 8822-8824 (1986).
    • (1986) Phys. Rev. B , vol.33 , pp. 8822-8824
    • Perdew, J.P.1
  • 16
    • 77956779984 scopus 로고
    • Density-functional thermochemistry 1: The effect of the exchange-only gradient correction
    • A. D. Becke, Density-functional thermochemistry 1: the effect of the exchange-only gradient correction. J. Chem. Phys. 96, 2155-2160 (1992).
    • (1992) J. Chem. Phys , vol.96 , pp. 2155-2160
    • Becke, A.D.1
  • 17
    • 20544463457 scopus 로고
    • Soft self-consistent pseudopotentials in a generalized eigenvalue formalism
    • D. Vanderbilt, Soft self-consistent pseudopotentials in a generalized eigenvalue formalism. Phys. Rev. B 41, 7892-7895 (1990).
    • (1990) Phys. Rev. B , vol.41 , pp. 7892-7895
    • Vanderbilt, D.1
  • 19
    • 33845265639 scopus 로고    scopus 로고
    • First-principles calculations of hyperfine parameters with the Gaussian and augmented-plane-wave method: Application to radicals embedded in a crystalline environment
    • R. Declerck, E. Pauwels, V. Van Speybroeck and M. Waroquier, First-principles calculations of hyperfine parameters with the Gaussian and augmented-plane-wave method: Application to radicals embedded in a crystalline environment. Phys. Rev. B 74, 245103 (2006).
    • (2006) Phys. Rev. B , vol.74 , pp. 245103
    • Declerck, R.1    Pauwels, E.2    Van Speybroeck, V.3    Waroquier, M.4
  • 20
    • 11444250501 scopus 로고    scopus 로고
    • Evaluation of different model space approaches based on DFT to examine the EPR parameters of a radiation-induced radical in solid-state alpha glycine
    • E. Pauwels, V. Van Speybroeck and M. Waroquier, Evaluation of different model space approaches based on DFT to examine the EPR parameters of a radiation-induced radical in solid-state alpha glycine. J. Phys. Chem. A 108, 11321-11332 (2004).
    • (2004) J. Phys. Chem. A , vol.108 , pp. 11321-11332
    • Pauwels, E.1    Van Speybroeck, V.2    Waroquier, M.3
  • 21
    • 33644906103 scopus 로고    scopus 로고
    • Comparing DFT cluster calculations with magnetic resonance experiments
    • Radiation-induced radicals in alpha-D-glucose
    • E. Pauwels, V. Van Speybroeck and M. Waroquier, Radiation-induced radicals in alpha-D-glucose: Comparing DFT cluster calculations with magnetic resonance experiments. Spectrochim. Acta A 63, 795-801 (2006).
    • (2006) Spectrochim. Acta A , vol.63 , pp. 795-801
    • Pauwels, E.1    Van Speybroeck, V.2    Waroquier, M.3
  • 22
    • 39749167228 scopus 로고    scopus 로고
    • M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven, K. N. Kudin and J. A. Pople, Gaussian 03, Revision B.03. Gaussian, Inc., Wallingford, CT, 2004.
    • M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven, K. N. Kudin and J. A. Pople, Gaussian 03, Revision B.03. Gaussian, Inc., Wallingford, CT, 2004.
  • 23
    • 11144255959 scopus 로고    scopus 로고
    • Density-functional thermochemistry 4: A new dynamical correlation functional and implications for exact-exchange mixing
    • A. D. Becke, Density-functional thermochemistry 4: a new dynamical correlation functional and implications for exact-exchange mixing. J. Chem. Phys. 104, 1040-1046 (1996).
    • (1996) J. Chem. Phys , vol.104 , pp. 1040-1046
    • Becke, A.D.1
  • 24
    • 26844534384 scopus 로고
    • Self-consistent molecular-orbital methods 20: Basis set for correlated wave-functions
    • R. Krishnan, J. S. Binkley, R. Seeger and J. A. Pople, Self-consistent molecular-orbital methods 20: basis set for correlated wave-functions. J. Chem. Phys. 72, 650-654 (1980).
    • (1980) J. Chem. Phys , vol.72 , pp. 650-654
    • Krishnan, R.1    Binkley, J.S.2    Seeger, R.3    Pople, J.A.4
  • 25
    • 0141509423 scopus 로고
    • Contracted Gaussian-basis sets for molecular calculations 1: 2nd row atoms, z = 11-18
    • A. D. McLean and G. S. Chandler, Contracted Gaussian-basis sets for molecular calculations 1: 2nd row atoms, z = 11-18. J. Chem. Phys. 72, 5639-5648 (1980).
    • (1980) J. Chem. Phys , vol.72 , pp. 5639-5648
    • McLean, A.D.1    Chandler, G.S.2
  • 26
    • 2442617487 scopus 로고
    • Self-consistent molecular-orbital methods 21: Small split-valence basis sets for 1st-row elements
    • J. S. Binkley, J. A. Pople and W. J. Hehre, Self-consistent molecular-orbital methods 21: small split-valence basis sets for 1st-row elements. J. Am. Chem. Soc. 102, 939-947 (1980).
    • (1980) J. Am. Chem. Soc , vol.102 , pp. 939-947
    • Binkley, J.S.1    Pople, J.A.2    Hehre, W.J.3
  • 27
    • 33845555195 scopus 로고
    • Self-consistent molecular-orbital methods 22: Small split-valence basis sets for 2nd-row elements
    • M. S. Gordon, J. S. Binkley, J. A. Pople, W. J. Pietro and W. J. Hehre, Self-consistent molecular-orbital methods 22: small split-valence basis sets for 2nd-row elements J. Am. Chem. Soc. 104, 2797-2803 (1982).
    • (1982) J. Am. Chem. Soc , vol.104 , pp. 2797-2803
    • Gordon, M.S.1    Binkley, J.S.2    Pople, J.A.3    Pietro, W.J.4    Hehre, W.J.5
  • 28
    • 33645072745 scopus 로고    scopus 로고
    • First-principles calculation of the EPR g tensor in extended periodic systems
    • R. Declerck, V. Van Speybroeck and M. Waroquier, First-principles calculation of the EPR g tensor in extended periodic systems. Phys. Rev. B 73, 115113 (2006).
    • (2006) Phys. Rev. B , vol.73 , pp. 115113
    • Declerck, R.1    Van Speybroeck, V.2    Waroquier, M.3
  • 29
    • 4243553426 scopus 로고
    • Density-functional exchange-energy approximation with correct asymptotic behavior
    • A. D. Becke, Density-functional exchange-energy approximation with correct asymptotic behavior. Phys. Rev. A 38, 3098-3100 (1988).
    • (1988) Phys. Rev. A , vol.38 , pp. 3098-3100
    • Becke, A.D.1
  • 30
    • 0345491105 scopus 로고
    • Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
    • C. T. Lee, W. T. Yang and R. G. Parr, Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B 37, 785-789 (1988).
    • (1988) Phys. Rev. B , vol.37 , pp. 785-789
    • Lee, C.T.1    Yang, W.T.2    Parr, R.G.3
  • 31
    • 0000160164 scopus 로고    scopus 로고
    • Separable dual-space Gaussian pseudopotentials
    • S. Goedecker, M. Teter and J. Hutter, Separable dual-space Gaussian pseudopotentials. Phys. Rev. B 54, 1703-1710 (1996).
    • (1996) Phys. Rev. B , vol.54 , pp. 1703-1710
    • Goedecker, S.1    Teter, M.2    Hutter, J.3
  • 32
    • 0002036605 scopus 로고
    • Mémoire sur la décomposition de l'eau et des corps qu'elle tient en dissolution à l'aide de l'électricité galvanique.
    • C. J. T. de Grotthuss, Mémoire sur la décomposition de l'eau et des corps qu'elle tient en dissolution à l'aide de l'électricité galvanique. Ann. Chim. 58, 54-74 (1806).
    • (1806) Ann. Chim , vol.58 , pp. 54-74
    • de Grotthuss, C.J.T.1
  • 33
    • 33748897143 scopus 로고    scopus 로고
    • C. J. T. de Grotthuss, Memoir on the decomposition of water and of the bodies that it holds in solution by means of galvanic electricity. Biochim. Biophys. Acta 1757, 871-875 (2006). [English translation by R. Pomès]
    • C. J. T. de Grotthuss, Memoir on the decomposition of water and of the bodies that it holds in solution by means of galvanic electricity. Biochim. Biophys. Acta 1757, 871-875 (2006). [English translation by R. Pomès]
  • 34
    • 11744384413 scopus 로고
    • The Grotthuss mechanism
    • N. Agmon, The Grotthuss mechanism. Chem. Phys. Lett. 244, 456-462 (1995).
    • (1995) Chem. Phys. Lett , vol.244 , pp. 456-462
    • Agmon, N.1
  • 35
    • 33748889129 scopus 로고    scopus 로고
    • Special issue on proton transfer in biological systems - Preface
    • P. Adelröth, Special issue on proton transfer in biological systems - Preface. Biochim. Biophys. Acta 1757, 867-870 (2006).
    • (2006) Biochim. Biophys. Acta , vol.1757 , pp. 867-870
    • Adelröth, P.1
  • 36
    • 0028020369 scopus 로고
    • The influence of packing on free radical yields in crystalline nucleic acids - the pyrimidine bases
    • W. A. Bernhard, J. Barnes, K. R. Mercer and N. Mroczka, The influence of packing on free radical yields in crystalline nucleic acids - the pyrimidine bases. Radiat. Res. 140, 199-214 (1994).
    • (1994) Radiat. Res , vol.140 , pp. 199-214
    • Bernhard, W.A.1    Barnes, J.2    Mercer, K.R.3    Mroczka, N.4
  • 37
    • 0031973837 scopus 로고    scopus 로고
    • Electron spin resonance and electron nuclear double resonance study of X-irradiated deoxyadenosine: Proton transfer behavior of primary ionic radicals
    • W. H. Nelson, E. Sagstuen, E. O. Hole and D. M. Close, Electron spin resonance and electron nuclear double resonance study of X-irradiated deoxyadenosine: Proton transfer behavior of primary ionic radicals. Radiat. Res. 149, 75-86 (1998).
    • (1998) Radiat. Res , vol.149 , pp. 75-86
    • Nelson, W.H.1    Sagstuen, E.2    Hole, E.O.3    Close, D.M.4
  • 38
    • 0034300984 scopus 로고    scopus 로고
    • Experimental and theoretical investigation of the mechanism of radiation-induced radical formation in hydrogen-bonded cocrystals of 1-methylcytosine and 5-fluorouracil
    • D. M. Close, L. A. Eriksson, E. O. Hole, E. Sagstuen and W. H. Nelson, Experimental and theoretical investigation of the mechanism of radiation-induced radical formation in hydrogen-bonded cocrystals of 1-methylcytosine and 5-fluorouracil. J. Phys. Chem. B 104, 9343-9350 (2000).
    • (2000) J. Phys. Chem. B , vol.104 , pp. 9343-9350
    • Close, D.M.1    Eriksson, L.A.2    Hole, E.O.3    Sagstuen, E.4    Nelson, W.H.5
  • 39
    • 0000276418 scopus 로고
    • Structure, magnetic properties and reactivities of open-shell species from density functional and self-consistent hybrid methods
    • D. P. Chong, Ed, pp, World Scientific, Singapore
    • V. Barone, Structure, magnetic properties and reactivities of open-shell species from density functional and self-consistent hybrid methods. In Recent Advances in Density Functional Methods, Part I (D. P. Chong, Ed.), pp. 287-334. World Scientific, Singapore, 1995.
    • (1995) Recent Advances in Density Functional Methods, Part I , pp. 287-334
    • Barone, V.1
  • 40
    • 33749043747 scopus 로고    scopus 로고
    • Et tu, Grotthuss! and other unfinished stories
    • S. Cukierman, Et tu, Grotthuss! and other unfinished stories. Biochim. Biophys. Acta 1757, 876-885 (2006).
    • (2006) Biochim. Biophys. Acta , vol.1757 , pp. 876-885
    • Cukierman, S.1
  • 41
    • 0036225143 scopus 로고    scopus 로고
    • + conduction in the single-file water chain of the gramicidin channel
    • + conduction in the single-file water chain of the gramicidin channel. Biophys. J. 82, 2304-2316 (2002).
    • (2002) Biophys. J , vol.82 , pp. 2304-2316
    • Pomès, R.1    Roux, B.2
  • 42
    • 0031862465 scopus 로고    scopus 로고
    • + conduction along hydrogen-bonded chains of water molecules
    • + conduction along hydrogen-bonded chains of water molecules. Biophys. J. 75, 33-40 (1998).
    • (1998) Biophys. J , vol.75 , pp. 33-40
    • Pomès, R.1    Roux, B.2
  • 43
    • 0001300510 scopus 로고
    • A variation of the alkoxy radical
    • H. C. Box and E. E. Budzinski, A variation of the alkoxy radical. J. Chem. Phys. 79, 4142-4145 (1983).
    • (1983) J. Chem. Phys , vol.79 , pp. 4142-4145
    • Box, H.C.1    Budzinski, E.E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.