氧化受損甘氨酸分子內(nèi)質(zhì)子遷移的機(jī)理

孟祥軍,石 瑾,楊笑春,賈俊芳,楊 靜(唐山師范學(xué)院化學(xué)系,河北唐山063000)

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氧化受損甘氨酸分子內(nèi)質(zhì)子遷移的機(jī)理

孟祥軍*,石 瑾,楊笑春,賈俊芳,楊 靜
(唐山師范學(xué)院化學(xué)系,河北唐山063000)

摘要:采用M06,B3LYP和CCSD方法,在6-31++G(**)基組水平研究了氧化受損甘氨酸分子的構(gòu)象異構(gòu)化機(jī)理,探討了甘氨酸氧化受損后的性質(zhì)變化和溶劑化效應(yīng).找到7個(gè)甘氨酸陽離子穩(wěn)定構(gòu)型和9個(gè)過渡態(tài),發(fā)現(xiàn)甘氨酸陽離子構(gòu)象異構(gòu)化過程存在質(zhì)子遷移反應(yīng),質(zhì)子從羧基遷移到氨基的能壘為15.2 kJ/mol,從α-C遷移到羰基O的能壘為138.6 kJ/ mol;最穩(wěn)定甘氨酸構(gòu)象失去一個(gè)電子的垂直電離勢為878.0 kJ/mol;N5原子失電子最多(超過0.4),其他各原子失去電荷不多(均低于0.1);電荷變化導(dǎo)致遷移質(zhì)子所在化學(xué)鍵顯著被削弱.溶劑化效應(yīng)能顯著增高質(zhì)子遷移反應(yīng)能壘.

關(guān)鍵詞:氧化損傷;甘氨酸陽離子;質(zhì)子遷移;反應(yīng)機(jī)理;量子化學(xué)

氨基酸是重要的生命物質(zhì),參與眾多生理過程;氨基酸分子結(jié)構(gòu)和性質(zhì)的研究[1-2]是深入探討其在生化反應(yīng)中變化情況的基石,也是理解復(fù)雜生物分子(如多肽和蛋白質(zhì)等)結(jié)構(gòu)和功能的基礎(chǔ).近年來蛋白質(zhì)氧化損傷現(xiàn)象成為自由基生物學(xué)研究的熱點(diǎn)之一[3],人們發(fā)現(xiàn)許多病理過程中酶的失活都與肽鏈上氨基酸的氧化受損有關(guān)[4].

甘氨酸(glycine)在20種天然氨基酸中結(jié)構(gòu)最簡單,所以它是實(shí)驗(yàn)和理論研究的首選測試對象.對于甘氨酸構(gòu)象和穩(wěn)定性的認(rèn)識已經(jīng)比較清晰:量子化學(xué)理論研究[5-10]得到8種甘氨酸分子穩(wěn)定構(gòu)象,電子衍射技術(shù)[11]、基質(zhì)隔離紅外光譜技術(shù)[12]、振動(dòng)拉曼光譜技術(shù)[13]實(shí)驗(yàn)觀測得到3種穩(wěn)定構(gòu)象;理論結(jié)果和實(shí)驗(yàn)結(jié)果存在的差異也得到了合理的解釋[14].氧化受損產(chǎn)生的甘氨酸自由基的結(jié)構(gòu)、性質(zhì)和解離過程也有較多文獻(xiàn)報(bào)道[15-19],然而有關(guān)甘氨酸陽離子結(jié)構(gòu)和性質(zhì)的文獻(xiàn)比較缺乏.2000年Rodríguez-Santiago等采用B3LYP和BHLYP等理論方法研究了4種甘氨酸陽離子構(gòu)象,并發(fā)現(xiàn)分子內(nèi)能夠發(fā)生質(zhì)子遷移反應(yīng)[20]; 2005年Simon等采用B3LYP/6-31++G(d,p)方法研究了甘氨酸陽離子最穩(wěn)定構(gòu)象的裂解產(chǎn)物[21];2012 年Lee采用B3LYP/6-31++G**方法研究了丙氨酸陽離子分子內(nèi)質(zhì)子遷移反應(yīng)機(jī)理[22].

通過比較甘氨酸和甘氨酸陽離子的相關(guān)文獻(xiàn),我們認(rèn)識到:1)甘氨酸陽離子構(gòu)象的研究尚不全面;2)甘氨酸陽離子構(gòu)象間的異構(gòu)化機(jī)理不清楚; 3)氧化對甘氨酸結(jié)構(gòu)和性質(zhì)的影響仍不清楚;4)缺乏溶劑化效應(yīng)方面的認(rèn)識.本文針對上述問題,采用量子化學(xué)理論方法系統(tǒng)地研究了甘氨酸陽離子構(gòu)象間的異構(gòu)化機(jī)理.

1 計(jì)算方法

本文采用B3LYP/6-31+ +G**方法和M06/6-31++G**方法[23]對甘氨酸陽離子結(jié)構(gòu)進(jìn)行全梯度優(yōu)化.找出穩(wěn)定態(tài)構(gòu)象后,采用QST2方法尋找構(gòu)象間轉(zhuǎn)化的過渡態(tài)結(jié)構(gòu).再對各構(gòu)象進(jìn)行振動(dòng)頻率計(jì)算,對過渡態(tài)進(jìn)行反應(yīng)內(nèi)稟坐標(biāo)(IRC)計(jì)算來驗(yàn)證各結(jié)構(gòu)的正確性.然后對M06/6-31++G**方法下的各構(gòu)象采用CCSD/6-31++G**方法計(jì)算單點(diǎn)能,并對能量進(jìn)行了零點(diǎn)能(ZPE)校正;采用相對能ΔE(ΔE =E-Emin,其中Emin是最穩(wěn)定構(gòu)象的能量)表示各構(gòu)象的能量大小.最后采用極化連續(xù)介質(zhì)(PCM)模型計(jì)算了CCSD∥M06/6-31++G**方法下的溶劑化效應(yīng).所有計(jì)算任務(wù)均使用Gaussian 09程序完成.

2 結(jié)果與討論

2.1穩(wěn)定構(gòu)象

本文找到7種甘氨酸陽離子穩(wěn)定構(gòu)象,示于圖1.構(gòu)象間轉(zhuǎn)化的過渡態(tài)有9個(gè),過渡態(tài)的名稱由對應(yīng)的反應(yīng)物和產(chǎn)物名稱組合得到.為了便于討論構(gòu)象轉(zhuǎn)化機(jī)理,先統(tǒng)一不同構(gòu)象中相應(yīng)原子的編號(見圖1中的構(gòu)象Ⅰ),再將這些構(gòu)象按照轉(zhuǎn)化途徑進(jìn)行排列.

各構(gòu)象能量數(shù)據(jù)(ΔE、異構(gòu)化正反應(yīng)的活化能Ea和逆反應(yīng)活化能Ea')列于表1,其中υ1和υ2分別是M06/6-31++G**方法下的第一和第二振動(dòng)頻率,υ1為正表明構(gòu)象是穩(wěn)定態(tài),υ1為負(fù)而υ2為正則表明構(gòu)象是過渡態(tài).在CCSD/6-31++G**方法下,構(gòu)象穩(wěn)定性順序?yàn)棰?Ⅰ>Ⅱ>Ⅲ>Ⅳ>Ⅴ>Ⅵ,ΔE分別為0,80.3,94.3,103.6,124.4,141.3,147.0 kJ/mol,最穩(wěn)定構(gòu)象Ⅶ為二醇形式.

在過渡態(tài)中:Ⅰ-Ⅲ由相應(yīng)構(gòu)象旋轉(zhuǎn)C1—N5鍵得到,CCSD/6-31++G**方法下ΔE為104.1 kJ/mol,構(gòu)象Ⅰ轉(zhuǎn)化為Ⅲ的Ea為23.8 kJ/mol,Ea'為0.4 kJ/ mol;Ⅱ-Ⅲ和Ⅴ-Ⅵ都對應(yīng)于C1—C2鍵的旋轉(zhuǎn),ΔE不超過11.8 kJ/mol;Ⅱ-Ⅵ和Ⅲ-Ⅴ是C2—O4鍵旋轉(zhuǎn)的過渡態(tài),Ea分別為63.5和49.2 kJ/mol,Ea'分別為10.8和11.5 kJ/mol;Ⅳ-Ⅵ是質(zhì)子從羧基遷移到氨基的過渡態(tài),Ea和Ea'分別為37.8和15.2 kJ/mol;Ⅰ-Ⅱ和Ⅲ-Ⅱ是質(zhì)子在2個(gè)羧基O原子間的遷移,ΔE高于170.5 kJ/mol;Ⅱ-Ⅶ是α-H遷移到羰基O的過渡態(tài),Ea為138.6 kJ/mol.

圖1　甘氨酸陽離子的構(gòu)象及轉(zhuǎn)化途徑Fig.1 The stable conformers of glycine cations and the isomerization reaction paths

2.2構(gòu)象轉(zhuǎn)化機(jī)理

甘氨酸陽離子構(gòu)象間轉(zhuǎn)化的途徑和能級變化示于圖2.2個(gè)羧基O原子間質(zhì)子遷移的ΔE高于170.5 kJ/mol,反應(yīng)難以發(fā)生;構(gòu)象Ⅶ是α-H遷移的產(chǎn)物, ΔE達(dá)162.6 kJ/mol,該反應(yīng)也難以發(fā)生;而質(zhì)子從羧基遷移到氨基變?yōu)榧嫘噪x子Ⅳ的ΔE只有15.2 kJ/mol,該反應(yīng)容易發(fā)生.因此我們重點(diǎn)介紹由構(gòu)象Ⅰ轉(zhuǎn)變?yōu)榧嫘噪x子Ⅳ的機(jī)理,轉(zhuǎn)化途徑為:Ⅰ?Ⅰ-Ⅲ?Ⅲ?Ⅲ-Ⅴ?Ⅴ?Ⅴ-Ⅵ?Ⅵ?Ⅳ-Ⅵ?Ⅳ.

表1　構(gòu)象的振動(dòng)頻率和能量數(shù)據(jù)Tab.1 The vibration frequency variations and energy data of each conformer

圖2　CCSD∥M06/6-31++G(d,p)方法下的甘氨酸陽離子構(gòu)象轉(zhuǎn)化能級圖Fig.2 The energy level diagram of isomerization reaction of glycine cations by CCSD∥M06/6-31++G(d,p)

構(gòu)象Ⅰ經(jīng)C1—N5鍵的旋轉(zhuǎn)變?yōu)檫^渡態(tài)Ⅰ-Ⅲ(二面角Φ(H7—N5—C1—C2)由180.0°變?yōu)?18.0°),能量升高23.8 kJ/mol;C1—N5鍵繼續(xù)旋轉(zhuǎn)(Φ(H7—N5—C1—C2)變?yōu)?7.2°),得到構(gòu)象Ⅲ,能量降低0.4 kJ/mol.

構(gòu)象Ⅲ經(jīng)C2—O4鍵的旋轉(zhuǎn)變?yōu)檫^渡態(tài)Ⅲ-Ⅴ(Φ(H6—O4—C2—C1)由-179.3°變?yōu)?86.8°),能量升高49.2 kJ/mol;C2—O4鍵繼續(xù)旋轉(zhuǎn)(Φ(H6—O4—C2—C1)變?yōu)?3.6°),得到構(gòu)象Ⅴ,能量降低11.5 kJ/mol.

構(gòu)象Ⅴ經(jīng)C1—C2鍵的旋轉(zhuǎn)變?yōu)檫^渡態(tài)Ⅴ-Ⅵ(Φ(N5—C1—C2—O4)由148.3°變?yōu)?2.4°),能量升高7.6 kJ/mol;C1—C2鍵繼續(xù)旋轉(zhuǎn)(Φ(N5—C1—C2—O4)變?yōu)?°),得到構(gòu)象Ⅵ,能量降低2.0 kJ/mol.

構(gòu)象Ⅵ經(jīng)質(zhì)子遷移變?yōu)闃?gòu)象Ⅳ.構(gòu)象Ⅵ中H6質(zhì)子距離O4原子97.4 pm,距離N5原子230.6 pm. H6質(zhì)子遠(yuǎn)離O4原子,距離N5原子130.2 pm時(shí)(此時(shí)距離O4原子122.8 pm),得到過渡態(tài)Ⅳ-Ⅵ,能量升高15.3 kJ/mol;H6質(zhì)子繼續(xù)靠近N5原子到104.8 pm時(shí)(此時(shí)距離O4原子188.8 pm),得到構(gòu)象Ⅳ,能量降低37.9 kJ/mol.

2.3甘氨酸氧化受損后的性質(zhì)變化

按照垂直電離的概念,圖3中甘氨酸最穩(wěn)定3種構(gòu)象G1、G2和G3(能量數(shù)據(jù)見表1)經(jīng)垂直電離相應(yīng)地得到甘氨酸陽離子Ⅲ、Ⅱ和Ⅰ.G3→Ⅰ、G2→Ⅱ和G1→Ⅲ的垂直電離勢分別為849.2,862.4和878.0 kJ/mol,G1異構(gòu)化為G3的能壘為6.9 kJ/mol,所以甘氨酸陽離子Ⅰ比最穩(wěn)定甘氨酸分子G1的能量高856.1 kJ/mol.

甘氨酸失去一個(gè)電子變?yōu)殛栯x子,從表2中甘氨酸各位點(diǎn)ΔQ數(shù)據(jù)可知:N5原子失電荷最多,超過0.41;除C1原子外,其他原子電荷均有缺失,但是幅度較小,不超過0.1;C1原子電荷有增有減,變化不大,低于0.08.從ΔR(O4—H6)和Δυ(O4—H6)數(shù)據(jù)可知:氧化損傷導(dǎo)致遷移質(zhì)子所在化學(xué)鍵(O4和H6原子間的化學(xué)鍵)的鍵長增加0.5 pm以上,導(dǎo)致該鍵振動(dòng)的紅移超過64.1 cm-1,遷移質(zhì)子所在化學(xué)鍵被削弱,可見氧化損傷有利于甘氨酸羧基H遷移到氨基上.

圖3　CCSD∥M06/6-31++G(d,p)方法計(jì)算的甘氨酸構(gòu)象轉(zhuǎn)化途徑Fig.3 Conformational isomerization paths of glycine calculated with the CCSD∥M06/6-31++G(d,p)

表2　氧化損傷后甘氨酸中各位點(diǎn)的電荷、鍵長和振動(dòng)頻率的變化值(ΔQ、ΔR(O4—H6)和Δυ(O4—H6))Tab.2 The differences of charge,bond length and vibration frequency after oxidation of glycine

2.4甘氨酸陽離子異構(gòu)化的溶劑化效應(yīng)

采用PCM模型,在CCSD∥M06/6-31++G**方法下考查甘氨酸陽離子異構(gòu)化的水溶劑化效應(yīng).考慮水溶劑的作用后,圖1中大部分構(gòu)象的結(jié)構(gòu)并未發(fā)生明顯變化(如PCM模型下的[Ⅰ]與氣相模型的Ⅰ結(jié)構(gòu)相近),圖1仍可作為構(gòu)象異構(gòu)化途徑和機(jī)理的參照.溶劑化效應(yīng)引起的主要結(jié)構(gòu)變化如下:1)構(gòu)象Ⅲ經(jīng)全優(yōu)化后氨基發(fā)生旋轉(zhuǎn)(氨基H最終與分子骨架共面),得到的穩(wěn)定構(gòu)象[Ⅲ]與[Ⅰ]結(jié)構(gòu)相同(二者區(qū)別是H7和H8位置互換),[Ⅲ]與[Ⅰ]轉(zhuǎn)化的過渡態(tài)是[Ⅰ-Ⅲ](結(jié)構(gòu)與Ⅰ-Ⅲ相近);2)Ⅰ-Ⅱ和Ⅲ-Ⅱ收斂為同一過渡態(tài)[Ⅰ-Ⅱ](結(jié)構(gòu)與Ⅰ-Ⅱ相近);3)Ⅲ、Ⅲ-Ⅴ和Ⅴ3個(gè)構(gòu)象的氨基旋轉(zhuǎn)至與分子骨架共面,對應(yīng)變?yōu)閇Ⅲ]、[Ⅲ-Ⅴ]和[Ⅴ].

表3列出了PCM模型下各構(gòu)象的能量數(shù)據(jù).依據(jù)CCSD∥M06/6-31++G**方法,各構(gòu)象的穩(wěn)定性次序?yàn)閇Ⅶ]>[Ⅰ]=[Ⅲ]>[Ⅱ]>[Ⅴ]>[Ⅵ]>[Ⅳ], ΔE分別為0,71.9,71.9,81.5,90.2,122.1,129.7 kJ/mol,可見最穩(wěn)定構(gòu)象還是二醇形式的[Ⅶ],但是溶劑化效應(yīng)使構(gòu)象[Ⅳ]的相對穩(wěn)定性變差;此外,溶劑化效應(yīng)顯著地增高了質(zhì)子遷移反應(yīng)的能壘,如構(gòu)象[Ⅳ-Ⅵ]反應(yīng)能壘增高54.0 kJ/mol(即表3中ΔE值91.8 kJ/mol與表1中對應(yīng)的Ea值37.8 kJ/mol之差,下同),[Ⅰ-Ⅱ]和[Ⅱ-Ⅶ]的反應(yīng)能壘分別增高34.9和77.1 kJ/mol.

3 結(jié) 論

本文采用M06/6-31++G**方法和B3LYP/6-31 ++G**方法研究了甘氨酸陽離子構(gòu)象異構(gòu)化反應(yīng)機(jī)理,并探討了甘氨酸氧化受損后的性質(zhì)變化和溶劑化效應(yīng),得到如下結(jié)論:

1)甘氨酸陽離子穩(wěn)定構(gòu)象有7個(gè),甘氨酸陽離子構(gòu)象異構(gòu)化過程存在質(zhì)子遷移反應(yīng),質(zhì)子從羧基遷移到氨基的能壘為15.3 kJ/mol,質(zhì)子從α-H遷移到羰基O的能壘為138.6 kJ/mol;

2)最穩(wěn)定甘氨酸構(gòu)象變?yōu)楦拾彼彡栯x子的垂直電離能為878.0 kJ/mol;

3)甘氨酸失去一個(gè)電子變?yōu)殛栯x子,N5原子失電子最多(超過0.4),其他各原子失去的電荷不多(均低于0.1),變?yōu)殛栯x子后利于質(zhì)子從羧基遷移到氨基;

4)溶劑化效應(yīng)顯著增高了質(zhì)子遷移反應(yīng)能壘.

表3　PCM模型下各構(gòu)象的振動(dòng)頻率和能量數(shù)據(jù)Tab.3 The vibration frequency variations and energy data of each conformer by PCM model

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Intramolecular Proton-transfer Mechanism of Oxidized Glycine Molecule

MENG Xiangjun*,SHI Jin,YANG Xiaochun,JIA Junfang,YANG Jing
(Department of Chemistry,Tangshan Normal University,Tangshan 063000,China)

Abstract:M06,B3LYP and CCSD methods were applied at the 6-31++G(**)basis set level to investigate the isomerization mechanism of glycine cations.In addition,property differences caused by oxidation and solvation effect were discussed.7 stable minimums and 9 transition states of glycine cations were obtained.It is found that the carboxyl proton can transfer to amino by stepping over a 15.2 kJ/mol energy barrier during the isomerization reactions,andα-H can transfer to carbonyl O over a 138.6 kJ/mol energy barrier.Vertical ionization potential of the most stable glycine conformation is 878.0 kJ/mol.More than 0.4 charge was lost on N5 atom in ionization process,while on other atoms less than 0.1 charge was lost.The charge variation is conducive to the reaction of proton transfer,while solvation effect greatly increases the energy barriers of proton transfer reactions.

Key words:oxidation damage;glycine cation;proton-transfer;reaction mechanism;quantum chemistry

*通信作者:xjmeng_1974@126.com

基金項(xiàng)目:河北省高等學(xué)?？茖W(xué)技術(shù)研究青年基金(QN2014312);唐山師范學(xué)院科學(xué)研究重點(diǎn)項(xiàng)目(2015B04)

收稿日期:2015-05-28 錄用日期:2015-08-29

doi:10.6043/j.issn.0438-0479.2016.02.004

中圖分類號:O 641

文獻(xiàn)標(biāo)志碼:A

文章編號:0438-0479(2016)02-0168-06

引文格式:孟祥軍,石瑾,楊笑春,等.氧化受損甘氨酸分子內(nèi)質(zhì)子遷移的機(jī)理[J].廈門大學(xué)學(xué)報(bào)(自然科學(xué)版),2016,55(2): 168-173.

Citation:MENG X J,SHI J,YANG X C,et al.Intramolecular proton-transfer mechanism of oxidized glycine molecule[J]. Journal of Xiamen University(Natural Science),2016,55(2):168-173.(in Chinese)