取代法计算多肽中N-H...O=C分子内氢键键能
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摘要
氢键在生命过程中起着非常重要的作用,是化学和生物中最常见的名词之一。氢键分为分子间氢键和分子内氢键。在理论上,分子间氢键可以利用超分子方法计算其能量。但超分子方法不能用来计算分子内氢键键能。现在,已有几种方法用来计算一些特殊体系中的分子内氢键键能,例如cis-trans方法、ortho-para方法和isodesmic reaction方法。但这些方法都不能应用于计算多肽和蛋白质体系中的N-H…O=C分子内氢键键能。
本论文的主要研究任务是设计一种能够计算多肽和蛋白质体系中N-H…O=C分子内氢键键能的新方法(本论文中称为取代法)。在说明取代法的合理性后应用此方法计算α-和β-多肽结构中不同类型的N-H…O=C分子内氢键键能。论文主要内容分为如下几个方面:
(1)设计一种计算多肽体系中N-H…O=C分子内氢键键能的新方法。我们用CH2基团取代多肽构象中形成N-H…O=C分子内氢键的NH基团,因此称此新方法为取代法。对一些特殊体系,使用取代法,cis-trans方法和超分子方法计算了氢键键能,取代法计算得到的氢键键能与cis-trans方法、超分子方法的计算结果相符。
(2)计算α-多肽和β-多肽中N-H…O=C分子内氢键键能。详细分析了6个α-多肽构象和14个β-多肽构象中N-H…O=C分子内氢键结构特点。应用取代法估算了这20个α-和β-多肽构象中不同类型的N-H…O=C分子内氢键键能。计算结果与这些构象中N-H…O=C分子内氢键结构特点一致。本文的计算结果对深入研究α-和β-多肽构象的空间结构和稳定性有重要参考价值。
(3)估算C-H…O=C分子内氢键键能。为了进一步完善我们所设计的取代法,需要估算C-H…O=C分子内氢键键能。我们从每一个含有C-H…O=C分子内氢键的结构中提取一个乙酰氨和丙醛二聚体,利用超分子方法计算C-H…O=C分子间氢键键能。同时我们也计算了C-H…O=C氢键键能在N-H…O=C分子内氢键键能中所占的比例。
The hydrogen bond plays a very vital role in many life processes and is one of the most frequently used terms in chemistry and biology. Hydrogen bonds can be separated into two categories: intermolecular hydrogen bond and intramolecular hydrogen bond. Theoretically, intermolecular interactions are usually investigated through a supermolecular approach. However, such an approach cannot be used to evaluate the intramolecular interactions. At present, some theoretical procedures were proposed to investigate the energies of intramolecular hydrogen bonds for special systems, such as cis-trans method, ortho-para method, and isodesmic reaction method. None of them is suitable to predict the intramolecular N-H…O=C hydrogen bonding energies for peptides.
In this paper, a method was proposed to evaluate the intramolecular N-H…O=C hydrogen bonding energies for peptides. The reasonability of the substitution method was explained. And then different kinds of intramolecular N-H…O=C hydrogen bonding energies for peptides were evaluated by the substitution method. The main content of this paper are as follows:
(1) A new method was proposed for predicting the intramolecular N-H…O=C hydrogen bonding energies for peptides. In this method CH2 group was used to substitute the NH group involved in the intramolecular N-H…O=C hydrogen bond, so the new method proposed in this paper was named as substitution method. The intramolecular hydrogen bonding energies for some special systems were evaluated by means of the substitution method, cis-trans method, and supermolecular approach. The intramolecular hydrogen bonding energies predicted by the substitution method agree well with the values obtained by the cis-trans method and the supermolecular approach.
(2) Evaluating the intramolecular N-H…O=C hydrogen bonding energies forα- andβ-peptides. The structural features of the intramolecular hydrogen bonds for the sixα-peptide conformers and the fourteenβ-peptide conformers were analyzed detailed. The hydrogen bonding energies for the twentyα- andβ-peptide conformers were evaluated by the substitution method. The results showed that the intramolecular hydrogen bonding energies obtained by the substitution method were in agreement with the structural features of the intramolecular hydrogen bonds. The values obtained in this paper are helpful for deeply understanding the structure and stability of theα- andβ-peptide conformers.
(3) Predicting the intramolecular C-H…O=C hydrogen bonding energies. In order to perfect the substitution method proposed by us, the intramolecular C-H…O=C hydrogen bonding energies should be predicted. An acetamide and propaldehyde dimer was extracted from the each optimal structure containing the intramolecular C-H…O=C hydrogen bonding. The supermolecular approach was then used to predict the C-H…O=C intermolecular hydrogen bonding energies. At the same time, the proportions of the C-H…O=C hydrogen bonding energies in the N-H…O=C hydrogen bonding energies were also calculated.
本论文的主要研究任务是设计一种能够计算多肽和蛋白质体系中N-H…O=C分子内氢键键能的新方法(本论文中称为取代法)。在说明取代法的合理性后应用此方法计算α-和β-多肽结构中不同类型的N-H…O=C分子内氢键键能。论文主要内容分为如下几个方面:
(1)设计一种计算多肽体系中N-H…O=C分子内氢键键能的新方法。我们用CH2基团取代多肽构象中形成N-H…O=C分子内氢键的NH基团,因此称此新方法为取代法。对一些特殊体系,使用取代法,cis-trans方法和超分子方法计算了氢键键能,取代法计算得到的氢键键能与cis-trans方法、超分子方法的计算结果相符。
(2)计算α-多肽和β-多肽中N-H…O=C分子内氢键键能。详细分析了6个α-多肽构象和14个β-多肽构象中N-H…O=C分子内氢键结构特点。应用取代法估算了这20个α-和β-多肽构象中不同类型的N-H…O=C分子内氢键键能。计算结果与这些构象中N-H…O=C分子内氢键结构特点一致。本文的计算结果对深入研究α-和β-多肽构象的空间结构和稳定性有重要参考价值。
(3)估算C-H…O=C分子内氢键键能。为了进一步完善我们所设计的取代法,需要估算C-H…O=C分子内氢键键能。我们从每一个含有C-H…O=C分子内氢键的结构中提取一个乙酰氨和丙醛二聚体,利用超分子方法计算C-H…O=C分子间氢键键能。同时我们也计算了C-H…O=C氢键键能在N-H…O=C分子内氢键键能中所占的比例。
The hydrogen bond plays a very vital role in many life processes and is one of the most frequently used terms in chemistry and biology. Hydrogen bonds can be separated into two categories: intermolecular hydrogen bond and intramolecular hydrogen bond. Theoretically, intermolecular interactions are usually investigated through a supermolecular approach. However, such an approach cannot be used to evaluate the intramolecular interactions. At present, some theoretical procedures were proposed to investigate the energies of intramolecular hydrogen bonds for special systems, such as cis-trans method, ortho-para method, and isodesmic reaction method. None of them is suitable to predict the intramolecular N-H…O=C hydrogen bonding energies for peptides.
In this paper, a method was proposed to evaluate the intramolecular N-H…O=C hydrogen bonding energies for peptides. The reasonability of the substitution method was explained. And then different kinds of intramolecular N-H…O=C hydrogen bonding energies for peptides were evaluated by the substitution method. The main content of this paper are as follows:
(1) A new method was proposed for predicting the intramolecular N-H…O=C hydrogen bonding energies for peptides. In this method CH2 group was used to substitute the NH group involved in the intramolecular N-H…O=C hydrogen bond, so the new method proposed in this paper was named as substitution method. The intramolecular hydrogen bonding energies for some special systems were evaluated by means of the substitution method, cis-trans method, and supermolecular approach. The intramolecular hydrogen bonding energies predicted by the substitution method agree well with the values obtained by the cis-trans method and the supermolecular approach.
(2) Evaluating the intramolecular N-H…O=C hydrogen bonding energies forα- andβ-peptides. The structural features of the intramolecular hydrogen bonds for the sixα-peptide conformers and the fourteenβ-peptide conformers were analyzed detailed. The hydrogen bonding energies for the twentyα- andβ-peptide conformers were evaluated by the substitution method. The results showed that the intramolecular hydrogen bonding energies obtained by the substitution method were in agreement with the structural features of the intramolecular hydrogen bonds. The values obtained in this paper are helpful for deeply understanding the structure and stability of theα- andβ-peptide conformers.
(3) Predicting the intramolecular C-H…O=C hydrogen bonding energies. In order to perfect the substitution method proposed by us, the intramolecular C-H…O=C hydrogen bonding energies should be predicted. An acetamide and propaldehyde dimer was extracted from the each optimal structure containing the intramolecular C-H…O=C hydrogen bonding. The supermolecular approach was then used to predict the C-H…O=C intermolecular hydrogen bonding energies. At the same time, the proportions of the C-H…O=C hydrogen bonding energies in the N-H…O=C hydrogen bonding energies were also calculated.
引文
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