水液相环境下α-丙氨酸分子的旋光异构及氢氧根和羟基自由基的作用
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摘要
在MP2/6-311++G(3df,2pd)//B3LYP/6-31+G(d,p)水平,采用自洽反应场(SCRF)理论的SMD模型研究了水液相环境下具有氨基和羧基间双氢键的α-丙氨酸(α-Ala)分子的旋光异构。研究发现:α-Ala的旋光异构有a、b和c三个反应通道,分别是质子以羰基氧、羧基及氨基为桥从手性碳的一侧迁移到另一侧。势能面计算结果显示:2个水分子簇的催化及溶剂效应的作用下,三个反应通道的决速步骤能垒分别为154.96、171.79和123.98kJ·mol~(-1),反应通道c为优势通道;3个水分子簇作氢迁移媒介时,反应通道c的决速步骤能垒降至109.61kJ·mol~(-1)。氢氧根水分子团簇的催化使该能垒降至61.83kJ·mol~(-1)。羟基自由基水分子簇致α-Ala损伤有水分子拔氢和羟基自由基拔氢两种机理,反应能垒分别为23.84、80.34kJ·mol~(-1)。结果表明:水液相环境下,α-Ala分子可缓慢地发生旋光异构,氢氧根水分子簇的催化可使α-Ala分子较快地旋光异构,羟基自由基水分子簇可使α-Ala分子迅速损伤。
In water liquid phase environment,optical isomerization ofα-alanine(α-Ala)with dihydrogen bond between amino and carboxyl groups was researched by using solvation model density(SMD)model based on self-consistent reaction field(SCRF)theory in MP2/6-311++G(3df,2pd)//B3LYP/6-31+G(d,p)level.The study shows that there are three channels a,b and c in the optical isomerization reaction ofα-Ala,where protons are transferred from one side to the other of the chiral C with carbonyl oxygen,carboxyl and amino groups as a bridge,respectively.Calculations of potential energy surface show that energy barriers of the rate-determining step of three reaction channels a,b and c are154.96,171.79 and 123.98kJ·mol~(-1) respectively with the help of two water molecules clusters catalyst and solvent effect,and channel c is the dominant reaction.In addition,the energy barrier of the step-determining of dominant reaction channel c is reduced to 109.61kJ·mol~(-1) with three water molecule clusters as hydrogen transfer agents,and the catalysis of the hydroxyl ion water clusters can reduce the barrier to 61.83kJ·mol~(-1).There are two mechanisms forα-Ala damage induced by hydroxyl radical water clusters:one is H-atom abstraction of water molecules,and the otheris H-atom abstraction of hydroxyl radicals,and the corresponding reaction energy barriers are 23.84 and 80.34kJ·mol~(-1),respectively.The results show thatα-Ala molecules in water liquid phase environment take place optical isomerization slowly,the presence of hydroxyl ion water clusters causes the faster optical isomerization ofα-Ala molecules,and the presence of hydroxyl radical water clusters causes damage toα-Ala molecule rapidly.
In water liquid phase environment,optical isomerization ofα-alanine(α-Ala)with dihydrogen bond between amino and carboxyl groups was researched by using solvation model density(SMD)model based on self-consistent reaction field(SCRF)theory in MP2/6-311++G(3df,2pd)//B3LYP/6-31+G(d,p)level.The study shows that there are three channels a,b and c in the optical isomerization reaction ofα-Ala,where protons are transferred from one side to the other of the chiral C with carbonyl oxygen,carboxyl and amino groups as a bridge,respectively.Calculations of potential energy surface show that energy barriers of the rate-determining step of three reaction channels a,b and c are154.96,171.79 and 123.98kJ·mol~(-1) respectively with the help of two water molecules clusters catalyst and solvent effect,and channel c is the dominant reaction.In addition,the energy barrier of the step-determining of dominant reaction channel c is reduced to 109.61kJ·mol~(-1) with three water molecule clusters as hydrogen transfer agents,and the catalysis of the hydroxyl ion water clusters can reduce the barrier to 61.83kJ·mol~(-1).There are two mechanisms forα-Ala damage induced by hydroxyl radical water clusters:one is H-atom abstraction of water molecules,and the otheris H-atom abstraction of hydroxyl radicals,and the corresponding reaction energy barriers are 23.84 and 80.34kJ·mol~(-1),respectively.The results show thatα-Ala molecules in water liquid phase environment take place optical isomerization slowly,the presence of hydroxyl ion water clusters causes the faster optical isomerization ofα-Ala molecules,and the presence of hydroxyl radical water clusters causes damage toα-Ala molecule rapidly.
引文
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[2] THOMPSON R J,BOUWER H G,PORTNOY D A,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.
[3] EMADEDDIN T,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].The Journal of Physical Chemistry B,1998,102(30):5899-5913.DOI:10.1021/jp9803135.
[4] STEPANIAN S G,REVA I D,RADCHENKO E D,et al.Conformational behavior ofα-alanine matrix-isolation infrared and theoretical DFT and ab initio study[J].The Journal of Physical Chemistry A,1998,102(24):4623-4629.DOI:10.1021/jp973479z.
[5]王文清,刘轶男,龚?.手性分子中的宇称破缺:D-和L-丙氨酸的变温中子结构研究[J].物理化学学报,2004,20(11):1345-1351.WANG W Q,LIU Y N,GONG Y,et al.Chiral molecules parity breaking:The research on D-and L-alanine variable temperature neutron structure[J].Acta PhysicoChimica Sinica,2004,20(11):1345-1351(Ch).
[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.2014.04.38.WANG Z C,LIU F G,LY,et al.Chiral transformation 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(Ch).
[7]王佐成,高峰,赵衍辉,等.α-丙氨酸分子手性转变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.1008-9497.2015.02.013.WANG Z C,GAO F,ZHAO Y H,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(Ch).
[8]王佐成,佟华,王丽萍,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.2015.01.29.WANG Z C,TONG H,WANG L P,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(Ch).
[9]李忠华,佟华,杨晓翠,等.基于氨基作H转移桥梁单体α-丙氨酸的手性转变机理[J].复旦学报(自然科学版),2015,54(5):642-647.DOI:0427-7104(2015)05-0642-06.LI Z H,TONG H,YANG X C,et al.The chiral transition mechanism of monomerα-Alanine based on amino as H transfer bridge[J].Journal of Fudan University(Natural Sciences),2015,54(5):102-108.DOI:0427-7104(2015)05-0642-06(Ch).
[10]王彦全,王佐成,闫红彦,等.水环境下基于氨基作氢迁移桥梁α-丙氨酸的手性转变机制[J].中山大学学报(自然科学版),2016,55(5):57-65.DOI:10.1347/j.cnki.acta.snus.2016.05.011.WANG Y Q,WANG Z C,YAN H Y,et al.Chiral transition mechanism ofα-lalanine molecule under the water environment based on anmino used as hydrogen transfer bridges[J].Acta Scientiarum Naturalium Universitatis Sunyatseni,2016,55(5):57-65.DOI:10.1347/j.cnki.acta.snus.2016.05.011(Ch).
[11]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.
[12]DEZWART L L,MEERMAN J H N,COMMANDEUR J N M,et al.Biomarkers of free radical damage:Applications in experimental animals and in humans[J].Free Radical Biology and Medicine,1999,26(1-2):202-226.DOI:10.1016/S0891-5849(98)00196-8.
[13]黄志坚.氨基酸的构型和性质研究[D].合肥:中国科学技术大学,2006:11.HUANG Z J.Structures and Properties of the Amino Acids[D].Hefei:University of Science and Technology of China,2006:11(Ch).
[14]MARENICH A V,CRAMER C J,TRUHLAR D G.Universal solvation 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.
[15]BECKE A D.Density-functional thermochemistry.Ⅲ.The role of exact exchange[J].Chemistry Physics,1993,98(7):5648-5652.doi.org/10.1063/1.464913.
[16]BINKLEY J S,POPLE J A.Moelle-plesset theory for atomic ground state energies[J].International Journal of Quantum Chemistry,1975,9(2):229-236.DOI:10.1002/qua.560090204.
[17]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.
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[19]FRISCH M J,TRUCKS G W,SCHLEGEL H B,et al.Gaussian 09.Revision E.01[CP].Pittsburgh:Gaussian Inc,2013.
[20]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.