水环境下羧基与氨基间为单氢键的α-Ala旋光异构及羟自由基和氢氧根的作用
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摘要
采用密度泛函理论的B3LYP方法、微扰理论的MP2方法和自洽反应场(SCRF)理论的SMD模型方法,研究了水环境下羧基与氨基间为单氢键的α-Ala旋光异构及羟自由基和氢氧根作用的反应。研究发现:α-Ala的旋光异构可在a和b两个通道实现,a通道为羧基顺反异构后,水分子簇作媒介质子以氨基为桥从α碳的一侧向另一侧迁移;b通道为水分子簇作媒介,质子从α碳向氨基氮的迁移与羧基顺反异构协同进行。在a通道,羟自由基水分子簇可致α-Ala损伤。势能面计算表明:水环境下,在a通道3个水分子簇作氢迁移媒介,决速步能垒为113.37 kJ·mol~(-1),氢氧根水分子簇的催化使该能垒降到64.45 kJ·mol~(-1);在b通道2个水分子簇作氢迁移媒介,决速步能垒为135.00 kJ·mol~(-1)。羟自由基水分子簇致α-Ala损伤的能垒在水分子抽氢和羟自由基抽氢时分别为24.47和80.60 kJ·mol~(-1)。
The title reaction is studied by using the B3 LYP method of density functional theory,the MP2 method of perturbation theory and the SMD model method based on self-consistent reaction field(SCRF) theory.The research shows that there are two channels a and b in the optical isomer reaction of α-Ala.In channel a,the proton is transferred from the side of the α-carbon to the other side with the amino as the bridge after the carboxyl anti-isomeric using water clusters as medium,and hydroxyl radicals of water clusters can damage the α-Ala.In channel b,the transfer of proton from chiral carbon to amino groups is coordinated with the anti-isomerism of carboxyl groups with water clusters as medium.The potential energy surface calculation shows that the energy barrier of rate-limiting step is 113.37 kJ·mol~(-1)with three water molecule clusters as hydrogen transfer agents in channel a,while the hydroxyl groups reduce the barrier to 64.45 kJ·mol~(-1)in water liquid environment.In channel b,the energy barrier of rate-limiting step is 135.00 kJ·mol~(-1)with two water molecule clusters as hydrogen transfer agents.The energy barrier of hydrogen abstraction reaction which damage the α-Ala molecules is 24.47 kJ·mol~(-1)by water molecules and 80.60 kJ·mol~(-1)by hydroxyl radicals,relatively.
The title reaction is studied by using the B3 LYP method of density functional theory,the MP2 method of perturbation theory and the SMD model method based on self-consistent reaction field(SCRF) theory.The research shows that there are two channels a and b in the optical isomer reaction of α-Ala.In channel a,the proton is transferred from the side of the α-carbon to the other side with the amino as the bridge after the carboxyl anti-isomeric using water clusters as medium,and hydroxyl radicals of water clusters can damage the α-Ala.In channel b,the transfer of proton from chiral carbon to amino groups is coordinated with the anti-isomerism of carboxyl groups with water clusters as medium.The potential energy surface calculation shows that the energy barrier of rate-limiting step is 113.37 kJ·mol~(-1)with three water molecule clusters as hydrogen transfer agents in channel a,while the hydroxyl groups reduce the barrier to 64.45 kJ·mol~(-1)in water liquid environment.In channel b,the energy barrier of rate-limiting step is 135.00 kJ·mol~(-1)with two water molecule clusters as hydrogen transfer agents.The energy barrier of hydrogen abstraction reaction which damage the α-Ala molecules is 24.47 kJ·mol~(-1)by water molecules and 80.60 kJ·mol~(-1)by hydroxyl radicals,relatively.
引文
[1]FISHER G H,D'ANIELLO A,VETERE A,et al Free D-aspartate and D-alanine in normal and Alzheimer brain[J].Brain Research Bulletin,1991,26(6):983-985.DOI:10.1016/0361-9230(91)90266-M
[2]THOMPSON R J,BOUWER H G,PORTNOY DA,et al.Pathogenicity and immunogenicity of a listeria monocytogenes strain that requires D-alanine for growth[J].Infection and Immunity,1998,66(8):3552-3561.DOI:10.1021/jp9803135
[3]TAJKHORSHID E,JALKANEN K J,SUHAI S.Structure and vibrational spectra of the zwitterion l-Alanine in the presence of explicit water molecules:A density functional analysis[J].Journal of Physical Chemistry B,1998,102(30):5899-5913.
[4]STEPANIAN S G,REVA I D,RADCHENKO ED,et al.Conformational behavior ofα-Alanine matrixisolation infrared and theoretical DFT and ab initio study[J].Journal of Physical Chemistry A,1998,102(24):4623-4629.DOI:10.1021/jp973479z
[5]WANG W Q,LIU Y N,GONG Y,et al.Chiral molecules parity breaking:The research on D and Lalanine variable temperature neutron structure[J].Acta Physico-Chimica Sinica,2004,20(11):1345-1351.
[6]王佐成,刘凤阁,吕洋,等.孤立条件下α-丙氨酸分子手性转变机制的密度泛函理论[J].吉林大学学报(理学版),2014,52(4):825-830.DOI:10.13413/j.cnki.jdxblxb.2014.04.38WANG Z C,LIU F G,LYU Y,et al.Chiral transformaition mechanism ofα-Alanine under isolated condition by density functional theory[J].Journal of Jilin University(Science Edition),2014,52(4):825-830.DOI:10.13413/j.cnki.jdxblxb.2014.04.38
[7]王佐成,赵衍辉,梅泽民,等.α-Ala分子旋光异构反应通道及水分子作用的理论研究[J].浙江大学学报(理学版).2015,42(2):189-197.DOI:10.3785/j.issn.1008-9497.2015.02.013WANG Z C,ZHAO Y H,MEI Z M,et al.Theoretical research on the chiral transformation pathway ofα-alanine and effect of water molecules[J].Journal of Zhejiang University(Science Edition),2015,42(2):189-197.DOI:10.3785/j.issn.1008-9497.2015.02.013
[8]王佐成,佟华,梅泽民,等.水环境下α-丙氨酸分子手性的转变机制[J].吉林大学学报(理学版),2015,53(1):134-141.DOI:10.13413/j.cnki.jdxblxb.2015.01.29WANG Z C,TONG H,MEI Z M,et al.α-Alanine molecule chiral shift mechanism in water[J].Journal of Jilin University(Science Edition),2015,53(1):134-141.DOI:10.13413/j.cnki.jdxblxb.2015.01.29
[9]WANG Z C,LIU Y F,YAN H Y,et al.Theoretical investigations of the chiral transition ofα?Amino acid confined in various sized armchair Boron-Nitride nanotubes[J].The Journal of Physical Chemistry A,2017,121(8):1833-1840.DOI:10.1021/acs.jpca.7b00079
[10]田子德,高峰,杨晓翠,等.具有氨基和羧基间单氢键的α-Ala分子旋光异构机理及水和羟自由基的作用[J].复旦学报(自然科学版),2018,57(4):517-527.DOI:0427-7104(2018)04-0517-10TIAN Z D,GAO Feng,YANG X C,et al.Mechanism of optical isomerism ofα-Ala molecules with hydrogen bonds between amino and carboxyl groups and roles of water and hydroxyl radicals[J].Journal of FuDan University(Natural Science),2018,57(4):517-527.DOI:0427-7104(2018)04-0517-10
[11]黄志坚.氨基酸的构型和性质研究[D].北京:中国科学技术大学,2006.DOI:10.7666/d.y1078078HUANG Z J.Structures and Properties of the Amino Acids[D].Beijing:University of Science and Technology of China,2006.DOI:10.7666/d.y1078078
[12]BECKE A D.Density-functional thermochemistry.III.The role of exact exchange[J].Journal of Chemical Physics,1993,98(7):5648-5652.DOI:10.1063/1.464913
[13]GARRETT B C,TRUHLAR D G.Criterion of minimum state density in the transition state theory of bimolecular reactions[J].The Journal of Chemical Physics,1979,70(4):1593-1598.DOI:10.1063/1.437698
[14]BINKLEY J S,POPLE J A.Moeller-Plesset theory for atomic ground state energies[J].International Journal of Quantum Chemistry,1975,9(2):229-236.DOI:10.1002/qua.560090204
[15]MARENICH A V,CRAMER C J,TRUHLAR DG,et al.Universal slovation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions[J].Journal of Physical Chemistry B,2009,113(18):6378-6396.DOI:10.1021/jp810292n
[16]GONZALEZ C,SCHLEGEL H.Reaction path following in mass-weighted internal coordinates[J].Journal of Physical Chemistry,1990,94(14):5523-5527.DOI:10.1021/j100377a021
[17]FRISCH M J,TRUCKS G W,SCHLEGEL H B,et al.Gaussian 09.Revision E.01[CP].Pittsburgh U SA:Gaussian,Inc,Wallingford CT,2013.
[18]GORB L,LESZCZYNSKI J.Intramolecular proton transfer in mono and dihydrated tautomers of Guanine:An ab initio post Hartree-fock study[J].Journal of the American Chemical Society,1998,120(20):5024-5032.DOI:10.1021/ja972017w
[2]THOMPSON R J,BOUWER H G,PORTNOY DA,et al.Pathogenicity and immunogenicity of a listeria monocytogenes strain that requires D-alanine for growth[J].Infection and Immunity,1998,66(8):3552-3561.DOI:10.1021/jp9803135
[3]TAJKHORSHID E,JALKANEN K J,SUHAI S.Structure and vibrational spectra of the zwitterion l-Alanine in the presence of explicit water molecules:A density functional analysis[J].Journal of Physical Chemistry B,1998,102(30):5899-5913.
[4]STEPANIAN S G,REVA I D,RADCHENKO ED,et al.Conformational behavior ofα-Alanine matrixisolation infrared and theoretical DFT and ab initio study[J].Journal of Physical Chemistry A,1998,102(24):4623-4629.DOI:10.1021/jp973479z
[5]WANG W Q,LIU Y N,GONG Y,et al.Chiral molecules parity breaking:The research on D and Lalanine variable temperature neutron structure[J].Acta Physico-Chimica Sinica,2004,20(11):1345-1351.
[6]王佐成,刘凤阁,吕洋,等.孤立条件下α-丙氨酸分子手性转变机制的密度泛函理论[J].吉林大学学报(理学版),2014,52(4):825-830.DOI:10.13413/j.cnki.jdxblxb.2014.04.38WANG Z C,LIU F G,LYU Y,et al.Chiral transformaition mechanism ofα-Alanine under isolated condition by density functional theory[J].Journal of Jilin University(Science Edition),2014,52(4):825-830.DOI:10.13413/j.cnki.jdxblxb.2014.04.38
[7]王佐成,赵衍辉,梅泽民,等.α-Ala分子旋光异构反应通道及水分子作用的理论研究[J].浙江大学学报(理学版).2015,42(2):189-197.DOI:10.3785/j.issn.1008-9497.2015.02.013WANG Z C,ZHAO Y H,MEI Z M,et al.Theoretical research on the chiral transformation pathway ofα-alanine and effect of water molecules[J].Journal of Zhejiang University(Science Edition),2015,42(2):189-197.DOI:10.3785/j.issn.1008-9497.2015.02.013
[8]王佐成,佟华,梅泽民,等.水环境下α-丙氨酸分子手性的转变机制[J].吉林大学学报(理学版),2015,53(1):134-141.DOI:10.13413/j.cnki.jdxblxb.2015.01.29WANG Z C,TONG H,MEI Z M,et al.α-Alanine molecule chiral shift mechanism in water[J].Journal of Jilin University(Science Edition),2015,53(1):134-141.DOI:10.13413/j.cnki.jdxblxb.2015.01.29
[9]WANG Z C,LIU Y F,YAN H Y,et al.Theoretical investigations of the chiral transition ofα?Amino acid confined in various sized armchair Boron-Nitride nanotubes[J].The Journal of Physical Chemistry A,2017,121(8):1833-1840.DOI:10.1021/acs.jpca.7b00079
[10]田子德,高峰,杨晓翠,等.具有氨基和羧基间单氢键的α-Ala分子旋光异构机理及水和羟自由基的作用[J].复旦学报(自然科学版),2018,57(4):517-527.DOI:0427-7104(2018)04-0517-10TIAN Z D,GAO Feng,YANG X C,et al.Mechanism of optical isomerism ofα-Ala molecules with hydrogen bonds between amino and carboxyl groups and roles of water and hydroxyl radicals[J].Journal of FuDan University(Natural Science),2018,57(4):517-527.DOI:0427-7104(2018)04-0517-10
[11]黄志坚.氨基酸的构型和性质研究[D].北京:中国科学技术大学,2006.DOI:10.7666/d.y1078078HUANG Z J.Structures and Properties of the Amino Acids[D].Beijing:University of Science and Technology of China,2006.DOI:10.7666/d.y1078078
[12]BECKE A D.Density-functional thermochemistry.III.The role of exact exchange[J].Journal of Chemical Physics,1993,98(7):5648-5652.DOI:10.1063/1.464913
[13]GARRETT B C,TRUHLAR D G.Criterion of minimum state density in the transition state theory of bimolecular reactions[J].The Journal of Chemical Physics,1979,70(4):1593-1598.DOI:10.1063/1.437698
[14]BINKLEY J S,POPLE J A.Moeller-Plesset theory for atomic ground state energies[J].International Journal of Quantum Chemistry,1975,9(2):229-236.DOI:10.1002/qua.560090204
[15]MARENICH A V,CRAMER C J,TRUHLAR DG,et al.Universal slovation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions[J].Journal of Physical Chemistry B,2009,113(18):6378-6396.DOI:10.1021/jp810292n
[16]GONZALEZ C,SCHLEGEL H.Reaction path following in mass-weighted internal coordinates[J].Journal of Physical Chemistry,1990,94(14):5523-5527.DOI:10.1021/j100377a021
[17]FRISCH M J,TRUCKS G W,SCHLEGEL H B,et al.Gaussian 09.Revision E.01[CP].Pittsburgh U SA:Gaussian,Inc,Wallingford CT,2013.
[18]GORB L,LESZCZYNSKI J.Intramolecular proton transfer in mono and dihydrated tautomers of Guanine:An ab initio post Hartree-fock study[J].Journal of the American Chemical Society,1998,120(20):5024-5032.DOI:10.1021/ja972017w