背景:本文考虑了几种氨基酸及其二肽的结构和偶极矩的特征,这些氨基酸及其二肽在基于它们的肽纳米管的形成中起着重要作用。考虑了它们的手性特征(左L和右D)和氨基酸的α-螺旋构象的影响。特别是,带有芳香环的氨基酸,如苯丙氨酸(Phe/F),和支链氨基酸(BCAAs)-亮氨酸(Leu/L)和异亮氨酸(Ile/I)-以及相应的二肽(二苯丙氨酸(FF),二亮氨酸(LL),和二异亮氨酸(II))。这些二肽结构和肽纳米管(PNTs)的主要特征和性质,基于它们,使用计算分子建模和量子化学半经验计算进行了研究。他们的极地,压电,并对光电特性和特征进行了详细的研究。偶极矩和极化的计算结果,以及压电系数和带隙宽度,对于不同类型的螺旋肽纳米管。给出了各种纳米管的手性指数的计算值,取决于初始二肽的手性-随着分子结构的层次变得更加复杂,获得的结果与手性类型的变化规律一致。估计了纳米管内腔中水分子对其物理性质的影响。提出并讨论了通过各种计算方法将这些计算结果与可用的实验数据进行比较。
方法:这项工作中对所有研究的纳米结构进行分子建模的主要工具是HyperChem8.01软件包。这里使用的主要方法是Hartree-Fock(HF)自洽场(SCF),在受限的Hartree-Fock(RHF)和非受限的Hartree-Fock(UHF)近似中具有各种量子化学半经验方法(AM1,PM3,RM1)。在这项工作中,使用Polak-Ribeire算法(共轭梯度法)进行了分子系统的优化及其最佳几何结构的搜索,它在最小总能量点确定优化的几何形状。对于这种优化的结构,偶极矩D和电子能级(如EHOMO和ELUMO),以及带隙Eg=ELUMO-EHOMO,然后计算。对于每个优化的分子结构,使用也在HyperChem软件包中实施的QSAR程序计算体积.
BACKGROUND: The paper considers the features of the structure and dipole moments of several amino acids and their dipeptides which play an important role in the formation of the peptide nanotubes based on them. The influence of the features of their
chirality (left L and right D) and the alpha-helix conformations of amino acids are taken into account. In particular, amino acids with aromatic rings, such as phenylalanine (Phe/F), and branched-chain amino acids (BCAAs)-leucine (Leu/L) and isoleucine (Ile/I)-as well as corresponding dipeptides (diphenylalanine (FF), dileucine (LL), and diisoleucine (II)) are considered. The main features and properties of these dipeptide structures and peptide nanotubes (PNTs), based on them, are investigated using computational molecular modeling and quantum-chemical semi-empirical calculations. Their polar, piezoelectric, and photoelectronic properties and features are studied in detail. The results of calculations of dipole moments and polarization, as well as piezoelectric coefficients and band gap width, for different types of helical peptide nanotubes are presented. The calculated values of the
chirality indices of various nanotubes are given, depending on the
chirality of the initial dipeptides-the results obtained are consistent with the law of changes in the type of
chirality as the hierarchy of molecular structures becomes more complex. The influence of water molecules in the internal cavity of nanotubes on their physical properties is estimated. A comparison of the results of these calculations by various computational methods with the available experimental data is presented and discussed.
METHODS: The main tool for molecular modeling of all studied nanostructures in this work was the HyperChem 8.01 software package. The main approach used here is the Hartree-Fock (HF) self-consistent field (SCF) with various quantum-chemical semi-empirical methods (AM1, PM3, RM1) in the restricted Hartree-Fock (RHF) and in the unrestricted Hartree-Fock (UHF) approximations. Optimization of molecular systems and the search for their optimal geometry is carried out in this work using the Polak-Ribeire algorithm (conjugate gradient method), which determines the optimized geometry at the point of their minimum total energy. For such optimized structures, dipole moments D and electronic energy levels (such as EHOMO and ELUMO), as well as the band gap Eg = ELUMO - EHOMO, were then calculated. For each optimized molecular structure, the volume was calculated using the QSAR program implemented also in the HyperChem software package.