与DNA空穴迁移有关的负解离能态相关性质研究
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摘要
长程的DNA空穴迁移是现在研究的一个热点话题。单电子氧化的DNA形成的空穴能够通过π堆积效应沿着DNA链迁移,由于鸟嘌呤的电离势在四个碱基中最小,氧化破坏的位置一般在鸟嘌呤碱基上。氧化破坏的鸟嘌呤被认为是突变和致癌作用的来源,能够导致疾病和老化。一般来说,碱基的序列、堆积以及水或者氧对空穴的接近被认为是显著的影响空穴俘获的位置和有效性的主要因素,但是由于DNA双螺旋中大沟与小沟的存在,DNA周围的生物环境中的一些其它因素也能够影响和调控DNA空穴迁移。本文首次发现了三螺旋Cp·G(?)C(·和(?)分别表示Watson-Crick氢键和Hoogsteen氢键)第三链上质子化的胞嘧啶Cp、渗透到DNA大小沟中的金属抗衡离子以及带正电荷的氨基酸残基这些不同外界因素在影响DNA迁移中出现的一种反常的负解离能现象,进而探讨了与负解离能现象相关的一些性质以及影响负解离能现象的一些因素如质子转移、水化效应、溶剂化效应等,从而为理解相关领域的能量的储存和转移机制提供定性和定量的信息。取得了一些有意义的研究成果,具体如下：
1.三螺旋DNA空穴迁移中发现的负解离能现象：我们在研究三螺旋Cp·G(?)C空穴迁移过程中首次发现了一种新颖的负解离能现象。从头算计算显示了氢键的一种反常的能量学现象。三螺旋空穴迁移的实验表明,这种氢键是空穴在三螺旋Cp·G(?)C位置上停留时产生的。这种能量学现象能够解释在三螺旋Cp·G(?)C位置上虽然较少但确实存在的氧化可能性。空穴俘获能够很大程度上使得一个三螺旋Cp·G(?)C单元的稳定性降低,从而导致了一种意想不到的具有负解离能的解离通道。由于势垒的阻碍,化合物不会自动解离,从而能够暂时稳定存在。这种解离通道是由静电排斥和氢键吸引力这两种相互作用之间的平衡决定的。上述两种相互作用是在构成氢键的两个相应的分子片之间产生的,并且这两种对立的相互作用随着氢键的距离增大它们衰减的程度不一样。这种三螺旋Cp·G(?)C单元可以看作DNA分子线上的高能连接点,同时还能够通过它不寻常的能量学现象来调控空穴在这个位置上分布或者通过这个位置的迁移。本文提供了有用的信息,这些信息可以用来理解一种未知类型的复杂的分子间相互作用,一种新颖的高能氢键。同时这种现象也可以用来进一步解释一些隐藏的转移特性以及在相应领域能量储存和转移机制。
2.金属离子调控DNA空穴迁移过程中发现的负解离能现象：本章首次发现了渗透到DNA大小沟中的金属离子在调控DNA空穴迁移过程中出现的一种反常的负解离能现象。我们用密度泛函的理论方法研究了化合物Na+GC和其空穴俘获的衍生物[Na+GC]+的电子及能量学特性。其中,化合物Na+GC表示钠离子在DNA大沟方向中结合到鸟嘌呤碱基上N7和06位置上形成的化合物。钠离子从化合物Na+GC中解离时它的解离能是正的。和这种正常的情况所不同的是,对于俘获空穴之后的化合物[Na+GC]+,势能面的探测显示出一种不同寻常的能量学现象。空穴俘获能够非常显著地使Na+-N7/O6键的解离能从正值(63.09kcal/mol)减少到负值(-14.80kcal/mol),这表明空穴俘获会导致化合物中Na+···N7/O6化学键的不稳定。但是频率分析证明了这种俘获空穴之后的化合物[Na+GC]+仍然是稳定的,并没有自动地沿着Na+···N7/O6化学键的方向解离。这种出人意料的负解离能现象表明化合物Na+GC在俘获空穴之后会处于一种特殊的亚稳定状态,并且俘获空穴的过程中在Na+···N7/O6化学键的区域储存了大约16kcal/mol的能量。键的临界点的电子密度以及它的拉普拉斯算符数值的拓扑特性表明这种新颖的能量学现象主要起源于空穴俘获导致在两个由储能键(Na+···N7/O6化学键)结合的两个单体之间增加的静电排斥相互作用。空穴俘获导致的从鸟嘌呤到胞嘧啶之间的质子转移会使得负解离能现象覆盖整个Na+…N7/O6化学键和Watson-Crick氢键区域。钠离子结合到小沟并且空穴在此处俘获时,我们也能观察到类似的负解离能现象。空穴俘获之后的化合物水合之后能够对负解离能产生不同的影响,这主要取决于水分子结合到化合物上的位置。气相中的负解离能的数值在不同溶液中会随着介电常数的增加而减少。
3.氨基酸残基调控过程DNA空穴迁移中发现的负解离能现象：虽然渗透到DNA大小沟中的金属离子能够调控DNA空穴迁移,但是能够金属离子渗透到沟中的情况并不是普遍存在的。在生物体中,DNA是和周围的蛋白质紧密结合在一起的。通过研究蛋白质中带正电荷的氨基酸残基对DNA空穴迁移的调控作用,我们首次发现了一种潜在的负解离能现象,为理解蛋白质在DNA空穴迁移中所起的作用提供了一个新的角度。我们使用密度泛函的理论计算方法在B3LYP/6-311++G**的理论水平上优化得到了带正电荷的精氨酸基团(ArgH+)、赖氨酸基团(LysH+)和组氨酸基团残基(HisH+)分别在DNA的大小沟位置上与单电子氧化的Watson-Crick型碱基对Guanine-Cytosine发生相互作用的化合物,并选取其中最稳定的六种化合物进行了研究。我们在研究这些化合物势能面的时候首次发现了一种新颖的负解离能现象。当带正电荷的氨基酸基团与单电子氧化的GC碱基对之间的氢键断裂时,解离能是负的。这表明化合物的能量要比两个单体的能量之和高,化合物处于一种高能状态。我们考察了这些化合物的分子轨道,静电势,自旋密度并对化合物中的所有氢键进行了AIM (atom in molecular)成键分析。根据AIM的分析结果,我们把这种负解离能现象的本质归结为氢键连接的两个单体(带正电荷的氨基酸残基和单电子氧化的GC)之间产生的静电排斥作用。在单电子氧化的情况下,上述六种化合物容易发生从鸟嘌呤到胞嘧啶的单质子转移反应,质子转移的产物中Watson-Crick (WC)氢键的解离能也变成了负值。此外,我们还研究了解离能与电离势二者之间的关系,Y+从化合物Y+GC中分离时的负解离能会使得化合物的电离势数值大大增加。
4.构造储能键：负解离能现象是我们首次发现的一种特殊的能量学现象。这种解离能是负值的化学键我们称之为储能键。在氨基酸与多阳离子的化合物、氧化的GC碱基对与质子化的胞嘧啶、金属离子以及带正电荷的氨基酸残基的化合物中都发现了这种反常的能量学现象。我们把这些体系中负解离能现象所具有的共同本质归结为静电排斥相互作用。我们设计了一些碱基类似物来探究构造储能键的条件以及影响负解离能大小的一些外在因素,得到了下面一些结论。构造具有负解离能的储能键的必要条件是储能键连接的两个单体必须带有同种电荷,这样两个单体之间才能够产生静电排斥相互作用。含有储能键的化合物水化时,随着水分子数目从1个增加到4个,负解离能的数值是不断增大的。具有不同性质,在不同位置的取代基团对负解离能的大小的影响是不一样的,吸电子基团会使得负解离能的数值变大,而供电子基团会使得负解离能的数值减小。此外,我们还发现储能键的键长是储存能量大小的一个标志。在储能键存在的情况下,其键长越大,负解离能的数值越大。
Recently, extensive attention has been paid to long-distance radical cation migration in DNA. The radical cation (hole) formed by one-electron oxidation of DNA can migrate to remote guanines through DNAπ-stack, causing damage selectively at a guanine cluster. Damaged guanines have been believed to be sources of mutagenesis and carcinogenesis which can result in disease and aging. Although base sequences, base stacking, and accessibility of water and/or oxygen to the hole are the principle factors which can significantly affect the site and efficiency of hole trapping, some other factors in the biological environment around DNA can also modulate hole migration due to the presence of major/minor groove of DNA. In the present paper an unusual phenomenon of negative dissociation energy was first discovered in the process of duplex DNA hole transfer affected by some external factors, such as protonated cytosine in the triplex DNA CP·G(?)C, metal ion penetration into the major/minor grooves of DNA and the positively charged amino acid residues. The related properties of negative dissociation energy state and some factors which can affect this phenomenon such as proton transfer, hydrate effect and solvent effect were explored. The exploration of this novel phenomenon can offer some qualitative or quantitative understanding about the energy conversion/transfer mechanisms in the related fields. Some significant progresses have been made, which can be described as follows.
1. Negative dissociation energy phenomenon discovered in triplex DNA hole transfer:Ab initio calculations reveal an unknown energetic phenomenon for H-bonds in the hole-trapping triplex CP·G(?)C motif observed experimentally in hole migration which can explain the lower but really available oxidization possibility in CP·G(?)C site. Hole-trapping can considerably destabilize the CP·G(?)C unit and lead to an unexpected barrier-hindered channel with a negative dissociation energy. This channel is governed by a balance between electrostatic repulsion and H-bonding attraction in the two associated moieties and different attenuations of two opposite interactions with respect to the H-bond distance. This CP·G(?)C unit can be viewed as a high-energy node in a DNA wire which modulates migration of a hole into or through it via its unusual energetics. It provides useful information for understanding of an unknown type of the complicated intermolecular interactions, a novel type of "high-energy" bond, and can be applied further to interpret the hidden transport properties and the energy conversion/transfer mechanisms in the related fields.
2. Negative dissociation energy phenomenon discovered in duplex DNA hole transfer gated by metal counterion:In the present paper, we investigated the electronic and energetic properties of Na+GC, where sodium ion (Na+) binds to guanine (G) base at the N7 and 06 sites in the major groove, and its hole-trapped derivative [Na+GC]+ by using density functional theory calculations. Different from the normal dissociation of Na+GC which has positive dissociation energies, potential energy surface exploration on the hole-trapped Na+GC reveals an unusual energetics phenomenon that hole-trapping can reduce significantly the dissociation energy of the Na+...N7/O6 bond from positive to negative values (63.09 vs-14.80 kcal/mol), implying that hole-trapping destabilizes the Na+...N7/O6 bond in Na+GC. But frequency analysis verifies that this hole-trapped complex [Na+GC]+is still stable and does not spontaneously dissociate along its Na+...N7/O6 bond vector. This unexpected negative dissociation energy phenomenon indicates that a Na+GC complex could become metastable upon hole-trapping, and thus can reserve some energy (～16kcal/mol) in its Na+...N7/O6 bond zone. The topological properties of the electron densities and its Laplacian values at the bond critical points indicate that this energetics phenomenon mainly origins from additional electrostatic repulsion between two moieties linked via the energy-reserved bond (Na+...N7/O6 bond) due to the hole-trapping. Proton transfer from guanine to cytosine induced by hole-trapping can develop the negative dissociation energy phenomenon over both the Na+...N7/O6 and WC H-bond zones. Similar phenomenon can be observed for the case of the Na+ binding at the minor groove when hole-trapping. Hydration of the hole-trapped complexes may yield different effects on the negative dissociation energies, depending on the binding sites for water molecules. The negative dissociation energy in gas phase decreases with the increase of dielectric constants in the different solvents.
3. Negative dissociation energy phenomenon discovered in duplex DNA hole transfer regulated by positive charged amino acid residues:The optimized geometries of complexes formed by the positively charged amino acid residues Y+ (Y+= ArgH+, LysH+ and HisH+) with one-electron oxidized guanine-cytosine (G+C) base pair in the major/minor groove were obtained at the level of B3LYP/6-311++G** and six of them were selected to explore the interaction between two monomers Y+and G+C. The groups of NH and NH2 in the amino acid residues can interact with N7 and O6 atoms of guanine base via one or two hydrogen bonds. From the exploration of potential energy surfaces (PESs) of these complexes, a novel phenomenon of negative dissociation energy was first discovered. That is, the dissociation energy is negative when the hydrogen bonds between the amino acid residues and one-electron oxidized GC base pair were broken, implicating that the energy of complex is larger than sum of energies of two monomers. But frequency calculation indicated that all these complexes are global minimum in their corresponding PESs. Obviously, this is a special phenomenon which is different from general combination. To explore these complexes at the state of high energy, the molecular orbital, electrostatic potential, spin density and the character of critical points of hydrogen bonds were considered. Base on the analysis of atom in molecular (AIM), the nature of negative dissociation energy is attributed to the electrostatic repulsion between two monomers Y+and G+C. The proton transfer reaction from guanine to cytosine can occur easily upon hole-trapping. The dissociation energy of Watson-Crick hydrogen bonds becomes negative in the product of proton transfer. In addition, the relation of dissociation energy and ionization potential (IP) in the complex Y+GC was also explored. The ionization potential of complex Y+GC has great increase when the dissociation energy is negative in the separation of Y+ from the complex Y+GC.
4. Construct energy-reserved bond:The phenomenon of negative dissociation energy is an unusual energetic phenomenon which was first discovered by our group. The chemical bond which has negative dissociation energy is taken as energy-reserved bond. This unusual energetic phenomenon appears not only in the complex in which the amino acid is binding with two positive ions but also the complexes in which one-electron oxidized guanine-cytosine (GC) base pair interacts with protonated cytosine (Cp), metal cations and positively charged amino acid residues. We attribute the nature of this phenomenon of negative dissociation energy to electrostatic repulsion between two monomers which were linked by energy-reserved bond. A series of model moleculars similar to base or base pair were designed to explore how to construct this energy-reserved bond and the external factors which can affect the value of negative dissociation energy were considered. The prerequisite to construct energy-reserved bond is that two monomers linked by energy-reserved bond are with same charge. The value of negative dissociation energy increases as the increase of number of water molecular. The effect of substituent group with different character on the value of negative dissociation energy is different. The value of negative dissociation energy increases in the substitute of electron withdrawing group and decreases in the electron-donating groups. In addition, we also found that the value of negative dissociation energy increases as the increase of bond length of energy-reserved bond.
1.三螺旋DNA空穴迁移中发现的负解离能现象：我们在研究三螺旋Cp·G(?)C空穴迁移过程中首次发现了一种新颖的负解离能现象。从头算计算显示了氢键的一种反常的能量学现象。三螺旋空穴迁移的实验表明,这种氢键是空穴在三螺旋Cp·G(?)C位置上停留时产生的。这种能量学现象能够解释在三螺旋Cp·G(?)C位置上虽然较少但确实存在的氧化可能性。空穴俘获能够很大程度上使得一个三螺旋Cp·G(?)C单元的稳定性降低,从而导致了一种意想不到的具有负解离能的解离通道。由于势垒的阻碍,化合物不会自动解离,从而能够暂时稳定存在。这种解离通道是由静电排斥和氢键吸引力这两种相互作用之间的平衡决定的。上述两种相互作用是在构成氢键的两个相应的分子片之间产生的,并且这两种对立的相互作用随着氢键的距离增大它们衰减的程度不一样。这种三螺旋Cp·G(?)C单元可以看作DNA分子线上的高能连接点,同时还能够通过它不寻常的能量学现象来调控空穴在这个位置上分布或者通过这个位置的迁移。本文提供了有用的信息,这些信息可以用来理解一种未知类型的复杂的分子间相互作用,一种新颖的高能氢键。同时这种现象也可以用来进一步解释一些隐藏的转移特性以及在相应领域能量储存和转移机制。
2.金属离子调控DNA空穴迁移过程中发现的负解离能现象：本章首次发现了渗透到DNA大小沟中的金属离子在调控DNA空穴迁移过程中出现的一种反常的负解离能现象。我们用密度泛函的理论方法研究了化合物Na+GC和其空穴俘获的衍生物[Na+GC]+的电子及能量学特性。其中,化合物Na+GC表示钠离子在DNA大沟方向中结合到鸟嘌呤碱基上N7和06位置上形成的化合物。钠离子从化合物Na+GC中解离时它的解离能是正的。和这种正常的情况所不同的是,对于俘获空穴之后的化合物[Na+GC]+,势能面的探测显示出一种不同寻常的能量学现象。空穴俘获能够非常显著地使Na+-N7/O6键的解离能从正值(63.09kcal/mol)减少到负值(-14.80kcal/mol),这表明空穴俘获会导致化合物中Na+···N7/O6化学键的不稳定。但是频率分析证明了这种俘获空穴之后的化合物[Na+GC]+仍然是稳定的,并没有自动地沿着Na+···N7/O6化学键的方向解离。这种出人意料的负解离能现象表明化合物Na+GC在俘获空穴之后会处于一种特殊的亚稳定状态,并且俘获空穴的过程中在Na+···N7/O6化学键的区域储存了大约16kcal/mol的能量。键的临界点的电子密度以及它的拉普拉斯算符数值的拓扑特性表明这种新颖的能量学现象主要起源于空穴俘获导致在两个由储能键(Na+···N7/O6化学键)结合的两个单体之间增加的静电排斥相互作用。空穴俘获导致的从鸟嘌呤到胞嘧啶之间的质子转移会使得负解离能现象覆盖整个Na+…N7/O6化学键和Watson-Crick氢键区域。钠离子结合到小沟并且空穴在此处俘获时,我们也能观察到类似的负解离能现象。空穴俘获之后的化合物水合之后能够对负解离能产生不同的影响,这主要取决于水分子结合到化合物上的位置。气相中的负解离能的数值在不同溶液中会随着介电常数的增加而减少。
3.氨基酸残基调控过程DNA空穴迁移中发现的负解离能现象：虽然渗透到DNA大小沟中的金属离子能够调控DNA空穴迁移,但是能够金属离子渗透到沟中的情况并不是普遍存在的。在生物体中,DNA是和周围的蛋白质紧密结合在一起的。通过研究蛋白质中带正电荷的氨基酸残基对DNA空穴迁移的调控作用,我们首次发现了一种潜在的负解离能现象,为理解蛋白质在DNA空穴迁移中所起的作用提供了一个新的角度。我们使用密度泛函的理论计算方法在B3LYP/6-311++G**的理论水平上优化得到了带正电荷的精氨酸基团(ArgH+)、赖氨酸基团(LysH+)和组氨酸基团残基(HisH+)分别在DNA的大小沟位置上与单电子氧化的Watson-Crick型碱基对Guanine-Cytosine发生相互作用的化合物,并选取其中最稳定的六种化合物进行了研究。我们在研究这些化合物势能面的时候首次发现了一种新颖的负解离能现象。当带正电荷的氨基酸基团与单电子氧化的GC碱基对之间的氢键断裂时,解离能是负的。这表明化合物的能量要比两个单体的能量之和高,化合物处于一种高能状态。我们考察了这些化合物的分子轨道,静电势,自旋密度并对化合物中的所有氢键进行了AIM (atom in molecular)成键分析。根据AIM的分析结果,我们把这种负解离能现象的本质归结为氢键连接的两个单体(带正电荷的氨基酸残基和单电子氧化的GC)之间产生的静电排斥作用。在单电子氧化的情况下,上述六种化合物容易发生从鸟嘌呤到胞嘧啶的单质子转移反应,质子转移的产物中Watson-Crick (WC)氢键的解离能也变成了负值。此外,我们还研究了解离能与电离势二者之间的关系,Y+从化合物Y+GC中分离时的负解离能会使得化合物的电离势数值大大增加。
4.构造储能键：负解离能现象是我们首次发现的一种特殊的能量学现象。这种解离能是负值的化学键我们称之为储能键。在氨基酸与多阳离子的化合物、氧化的GC碱基对与质子化的胞嘧啶、金属离子以及带正电荷的氨基酸残基的化合物中都发现了这种反常的能量学现象。我们把这些体系中负解离能现象所具有的共同本质归结为静电排斥相互作用。我们设计了一些碱基类似物来探究构造储能键的条件以及影响负解离能大小的一些外在因素,得到了下面一些结论。构造具有负解离能的储能键的必要条件是储能键连接的两个单体必须带有同种电荷,这样两个单体之间才能够产生静电排斥相互作用。含有储能键的化合物水化时,随着水分子数目从1个增加到4个,负解离能的数值是不断增大的。具有不同性质,在不同位置的取代基团对负解离能的大小的影响是不一样的,吸电子基团会使得负解离能的数值变大,而供电子基团会使得负解离能的数值减小。此外,我们还发现储能键的键长是储存能量大小的一个标志。在储能键存在的情况下,其键长越大,负解离能的数值越大。
Recently, extensive attention has been paid to long-distance radical cation migration in DNA. The radical cation (hole) formed by one-electron oxidation of DNA can migrate to remote guanines through DNAπ-stack, causing damage selectively at a guanine cluster. Damaged guanines have been believed to be sources of mutagenesis and carcinogenesis which can result in disease and aging. Although base sequences, base stacking, and accessibility of water and/or oxygen to the hole are the principle factors which can significantly affect the site and efficiency of hole trapping, some other factors in the biological environment around DNA can also modulate hole migration due to the presence of major/minor groove of DNA. In the present paper an unusual phenomenon of negative dissociation energy was first discovered in the process of duplex DNA hole transfer affected by some external factors, such as protonated cytosine in the triplex DNA CP·G(?)C, metal ion penetration into the major/minor grooves of DNA and the positively charged amino acid residues. The related properties of negative dissociation energy state and some factors which can affect this phenomenon such as proton transfer, hydrate effect and solvent effect were explored. The exploration of this novel phenomenon can offer some qualitative or quantitative understanding about the energy conversion/transfer mechanisms in the related fields. Some significant progresses have been made, which can be described as follows.
1. Negative dissociation energy phenomenon discovered in triplex DNA hole transfer:Ab initio calculations reveal an unknown energetic phenomenon for H-bonds in the hole-trapping triplex CP·G(?)C motif observed experimentally in hole migration which can explain the lower but really available oxidization possibility in CP·G(?)C site. Hole-trapping can considerably destabilize the CP·G(?)C unit and lead to an unexpected barrier-hindered channel with a negative dissociation energy. This channel is governed by a balance between electrostatic repulsion and H-bonding attraction in the two associated moieties and different attenuations of two opposite interactions with respect to the H-bond distance. This CP·G(?)C unit can be viewed as a high-energy node in a DNA wire which modulates migration of a hole into or through it via its unusual energetics. It provides useful information for understanding of an unknown type of the complicated intermolecular interactions, a novel type of "high-energy" bond, and can be applied further to interpret the hidden transport properties and the energy conversion/transfer mechanisms in the related fields.
2. Negative dissociation energy phenomenon discovered in duplex DNA hole transfer gated by metal counterion:In the present paper, we investigated the electronic and energetic properties of Na+GC, where sodium ion (Na+) binds to guanine (G) base at the N7 and 06 sites in the major groove, and its hole-trapped derivative [Na+GC]+ by using density functional theory calculations. Different from the normal dissociation of Na+GC which has positive dissociation energies, potential energy surface exploration on the hole-trapped Na+GC reveals an unusual energetics phenomenon that hole-trapping can reduce significantly the dissociation energy of the Na+...N7/O6 bond from positive to negative values (63.09 vs-14.80 kcal/mol), implying that hole-trapping destabilizes the Na+...N7/O6 bond in Na+GC. But frequency analysis verifies that this hole-trapped complex [Na+GC]+is still stable and does not spontaneously dissociate along its Na+...N7/O6 bond vector. This unexpected negative dissociation energy phenomenon indicates that a Na+GC complex could become metastable upon hole-trapping, and thus can reserve some energy (～16kcal/mol) in its Na+...N7/O6 bond zone. The topological properties of the electron densities and its Laplacian values at the bond critical points indicate that this energetics phenomenon mainly origins from additional electrostatic repulsion between two moieties linked via the energy-reserved bond (Na+...N7/O6 bond) due to the hole-trapping. Proton transfer from guanine to cytosine induced by hole-trapping can develop the negative dissociation energy phenomenon over both the Na+...N7/O6 and WC H-bond zones. Similar phenomenon can be observed for the case of the Na+ binding at the minor groove when hole-trapping. Hydration of the hole-trapped complexes may yield different effects on the negative dissociation energies, depending on the binding sites for water molecules. The negative dissociation energy in gas phase decreases with the increase of dielectric constants in the different solvents.
3. Negative dissociation energy phenomenon discovered in duplex DNA hole transfer regulated by positive charged amino acid residues:The optimized geometries of complexes formed by the positively charged amino acid residues Y+ (Y+= ArgH+, LysH+ and HisH+) with one-electron oxidized guanine-cytosine (G+C) base pair in the major/minor groove were obtained at the level of B3LYP/6-311++G** and six of them were selected to explore the interaction between two monomers Y+and G+C. The groups of NH and NH2 in the amino acid residues can interact with N7 and O6 atoms of guanine base via one or two hydrogen bonds. From the exploration of potential energy surfaces (PESs) of these complexes, a novel phenomenon of negative dissociation energy was first discovered. That is, the dissociation energy is negative when the hydrogen bonds between the amino acid residues and one-electron oxidized GC base pair were broken, implicating that the energy of complex is larger than sum of energies of two monomers. But frequency calculation indicated that all these complexes are global minimum in their corresponding PESs. Obviously, this is a special phenomenon which is different from general combination. To explore these complexes at the state of high energy, the molecular orbital, electrostatic potential, spin density and the character of critical points of hydrogen bonds were considered. Base on the analysis of atom in molecular (AIM), the nature of negative dissociation energy is attributed to the electrostatic repulsion between two monomers Y+and G+C. The proton transfer reaction from guanine to cytosine can occur easily upon hole-trapping. The dissociation energy of Watson-Crick hydrogen bonds becomes negative in the product of proton transfer. In addition, the relation of dissociation energy and ionization potential (IP) in the complex Y+GC was also explored. The ionization potential of complex Y+GC has great increase when the dissociation energy is negative in the separation of Y+ from the complex Y+GC.
4. Construct energy-reserved bond:The phenomenon of negative dissociation energy is an unusual energetic phenomenon which was first discovered by our group. The chemical bond which has negative dissociation energy is taken as energy-reserved bond. This unusual energetic phenomenon appears not only in the complex in which the amino acid is binding with two positive ions but also the complexes in which one-electron oxidized guanine-cytosine (GC) base pair interacts with protonated cytosine (Cp), metal cations and positively charged amino acid residues. We attribute the nature of this phenomenon of negative dissociation energy to electrostatic repulsion between two monomers which were linked by energy-reserved bond. A series of model moleculars similar to base or base pair were designed to explore how to construct this energy-reserved bond and the external factors which can affect the value of negative dissociation energy were considered. The prerequisite to construct energy-reserved bond is that two monomers linked by energy-reserved bond are with same charge. The value of negative dissociation energy increases as the increase of number of water molecular. The effect of substituent group with different character on the value of negative dissociation energy is different. The value of negative dissociation energy increases in the substitute of electron withdrawing group and decreases in the electron-donating groups. In addition, we also found that the value of negative dissociation energy increases as the increase of bond length of energy-reserved bond.
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