基于密度泛函理论方法的核酸碱基拉曼光谱研究

核酸碱基是核酸的重要组成部分,而拉曼光谱是研究分子结构的一种重要技术,利用拉曼光谱对核酸碱基分子进行研究对于研究核酸大分子的结构变化,以及核酸分子与小分子之间的作用具有重要的意义.本研究以表征核酸碱基的拉曼光谱为目的,利用密度泛函理论(density functional theory,DFT)的方法优化腺嘌呤、鸟嘌呤、胞嘧啶、胸腺嘧啶和尿嘧啶的分子结构,对这5种核酸碱基的分子内化学键振动进行了量化计算并获得了理论拉曼光谱结果.利用计算结果对实验获得的碱基的固体拉曼光谱进行了表征,并且结合前人的研究结果对每种碱基的一些重要特征拉曼谱峰进行了细致的阐释,为进一步利用拉曼光谱研究核酸分子的结构信息奠定了理论基础.     

基于密度泛函叶绿素a分子活性的量子化学计算

在液相环境下,根据量子化学密度泛函(DFT)的B3LYP泛函在6-31G基组水平的计算结果,从叶绿素a分子的光谱特性、特征基团对前线轨道能量贡献率、激发态、Mulliken电荷分布等量化参数分析比较了其各特征基团的生物活性及吸收波长。结果表明:叶绿素a分子中的5个活性基团中,C(33)、O(34)所组成的酮羰基活性最强,卟啉环的活性次之,C(36)位置上的酯羰基和C(13)位置上的酯羰基及共轭碳碳双键的活性较弱;在发生HOMO→LUMO跃迁后,卟啉环转移的电荷变化总量为0.00012。而酮羰基得到的电荷变化,总量为-0.00062。     

一类泛函微分方程的多重正周期解(英文)

联合运用Krasnoselskii不动点定理和Avery-Henderson不动点定理研究一类泛函微分方程的多重正周期解的存在性,获得了存在多重正周期解的充分条件.     

基于自稀疏理论的杉木人工林密度指标研究

量化林分密度是精准林业实现的基础。选择合适的林分密度指标用于杉木人工林的模拟和预测研究。基于同一套数据构建3个林分密度指标,根据这些指标的理论分析和动态变化规律进行选优。理论上,Reneike林分密度指数(SDI)和Curtis相对密度(RD)可互相转换,SDI可作为Nilson密度(SD)指标的特例;杉木人工林分的实证结果表明,SD指标的动态变化规律优于传统的SDI和RD密度,更能反映林分的生长规律;而且具有与立地质量不相关的比较优势。Nilson密度指标可用来模拟和预测杉木人工林的生长和收获。     

棕色田鼠种群繁殖特征及密度制约调节(英)

1992年～1994年在河南灵宝市郊黄土高源农作区春夏秋逐月捕获并解剖棕色田鼠1757只（雌性961只,雄性796只）,总性比为1．2073。全年都有繁殖鼠出现,但怀孕率、胎仔数、性比、繁殖指数有明显的季节变化,年间也有一定的差异。不同年龄组的性比、怀孕率、胎仔数、繁殖指数、睾丸下降率不同。种群密度对繁殖特征有明显的调节作用。高密度年份的棕色田鼠的性比、怀孕率和繁殖指数低于低密度年份。高密度区种群的繁殖强度受到抑制,雌鼠怀孕率、睾丸下降率低于低密度种群。     

具有比率依赖和密度制约的周期捕食-被捕食系统的一致持久性(英文)

系统的讨论了具有比率依赖和密度制约的周期捕食-被捕食系统的持久性问题,不仅得到了系统一致持久的充分条件,还得到了必要条件,并且持久性条件在模型中得到验证.     

卵跳小蜂Ooencyrtus nezarae Ishii对豆缘蝽和豆璧蝽卵的选择性和密度反应(英文)

本文研究了卵跳小蜂对豆缘蝽 (R .clavatusThunberg)和豆璧蝽 (P .hybneriGmelin)卵的选择性和密度反应。在自由选择试验中 ,两种豆蝽卵中羽化的卵跳小蜂在不同的卵密度和比例中均选择豆缘蝽 ;而在非选择性试验中 ,从豆璧蝽中羽化的卵跳小蜂同时选择豆缘蝽和豆璧蝽卵 ,寄生率较高 ;然而 ,从豆缘蝽卵羽化的卵跳小蜂对豆璧蝽卵的寄生率非常低。嗅觉试验表明 ,从豆缘蝽卵上释放的气味对卵跳小蜂的搜寻和寄生行为影响很大。卵跳小蜂寄生的卵数量随着豆缘蝽和豆璧蝽卵密度的增加而提高 ;然而 ,卵跳小蜂对豆璧蝽的寄生率随着卵的密度增加而降低 ,尤其是从豆缘蝽卵中羽化的寄生蜂。研究还表明 ,卵跳小蜂在大田中对豆缘蝽卵的寄生存在着空间或时间上的障碍。     

基于区间值模糊集理论的顺势疗法药物选择(英文)

利用区间值模糊集理论,将Sanchez的医疗诊断方法应用到了顺势疗法的药物选择中.文章中讨论了两类区间值模糊关系和选择指数,并给出了一种新的利用软情报学的方法.     

五指山黑桫椤(Alsophila podophylla)种群特征与森林立木密度和土壤的关系

研究了五指山黑桫椤(Alsophila podophylla)种群密度、高度和胸径等基本特征及种群与立木密度和土壤因子的关系.结果表明:山地雨林和低地雨林黑桫椤平均密度及立木平均密度各自差异极显著,黑桫椤平均高度和平均胸径各自差异不显著.低地雨林黑桫椤平均密度(0.12 ind·m-2)是山地雨林(0.06 ind·m-2)的2倍,后者的立木平均密度(0.467 ind·m-2)是前者(0.343 ind·m-2)的1.4倍,在一定海拔范围内,随海拔升高,黑桫椤种群密度逐渐减少,立木平均密度增大.山地雨林黑桫椤平均密度与平均高度正相关,黑桫椤种群趋于稳定;低地雨林中两者负相关,黑桫椤种群呈增长型,其相关关系都可用二项式方程拟合.山地雨林黑桫椤平均密度与立木平均密度负相关,低地雨林中两者正相关,相关关系可用一元线性方程拟合.山地雨林与低地雨林比较,土壤有机质、全氮、水含量和pH总体上表现为增大趋势,而全磷和全钾含量总体上表现为下降趋势;黑桫椤种群平均密度、高度和胸径与土壤pH、全磷含量和全钾含量关系密切,各自可用二元线性回归方程拟合;3个土壤因子对黑桫椤的作用大小是全钾含量＞pH＞全磷含量.可以根据以上模型指导黑桫椤保护、繁殖和栽培研究.     

磷限制下大型海藻与微藻间资源竞争理论的实验验证(英文)

用一次性培养法结合Monod方程测得海洋微藻_亚心型扁藻 (Tetraselmissubcordiformis (Wile)Hazen)与大型海藻_孔石莼 (UlvapertusaKjellm .)磷限制下的生长动力参数。孔石莼具有较低的半饱和生长常数及最大生长率 ,其分别为 0 .0 16 μmol/L和 0 .16d-1,而亚心型扁藻的半饱和生长常数和最大生长率分别是 0 .0 2 1μmol/L和 0 .83d-1。两种藻类间的营养竞争实验采用半连续培养法在磷限制条件下进行 ,实验过程中 ,分别对两者施予相同或不同的去除率 ,使两者享有相同或不同的资源需求值R 。由Monod方程所作的竞争预测与实验观察结果的比较显示 :仅在两种藻类间的资源需求值R 差异显著 (t检验 ,P <0 .0 1)时 ,Monod方程才能对竞争结果作出较为准确的预测 ;在两种藻类享有相同的资源需求值R 时 ,亚心型扁藻在竞争中取代孔石莼。Monod模型仅能部分预测大型海藻与海洋微藻间的竞争结果。     

Configuration of wobble base pairs having pyrimidines as anticodon wobble bases: significance for codon degeneracy

Degeneracy of the genetic code was attributed by Crick to imprecise hydrogen-bonded base-pairing at the wobble position during codon–anticodon pairing. The Crick wobble rules define but do not explain the RNA base pair combinations allowed at this position. We select six pyrimidine bases functioning as anticodon wobble bases (AWBs) to study their H-bonded pairing properties with the four major RNA bases using density functional theory at the B3LYP/6-31G(d,p) level. This is done to assess the extent to which the configuration of a solitary RNA wobble base pair may in itself determine specificity and degeneracy of the genetic code by allowing or disallowing the given base pair during codon–anticodon pairing. Calculated values of select configuration markers for the base pairs screen well between allowed and disallowed base pairs for most cases examined here, where the base pair width emerges as an important factor. A few allowed wobble pairs invoke the involvement of RNA nucleoside conformation, as well as involvement of the exocyclic substituent in H-bonding. This study, however, cannot explain the disallowed status of the Ura?Gua wobble pair on the basis of configuration alone. Explanation of the allowed status of the V?Ura pair requires further study on the mediatory role of water molecules. Apart from these two cases, these computational results are sufficient, on the basis of base pair configuration alone, to account for the specificity and degeneracy of the genetic code for all known cases of codon–anticodon pairing which involve the pyrimidine AWBs studied here.     

Hydrogen bonds in galactopyranoside and glucopyranoside: a density functional theory study

Density functional theory calculations on two glycosides, namely, n-octyl-β-D-glucopyranoside (C₈O-β-Glc) and n-octyl-β-D-galactopyranoside (C₈O-β-Gal) were performed for geometry optimization at the B3LYP/6-31G level. Both molecules are stereoisomers (epimers) differing only in the orientation of the hydroxyl group at the C4 position. Thus it is interesting to investigate electronically the effect of the direction (axial/equatorial) of the hydroxyl group at the C4 position. The structure parameters of X-H???Y intramolecular hydrogen bonds were analyzed, while the nature of these bonds and the intramolecular interactions were considered using the atoms in molecules (AIM) approach. Natural bond orbital analysis (NBO) was used to determine bond orders, charge and lone pair electrons on each atom and effective non-bonding interactions. We have also reported electronic energy and dipole moment in gas and solution phases. Further, the electronic properties such as the highest occupied molecular orbital, lowest unoccupied molecular orbital, ionization energy, electron affinity, electronic chemical potential, chemical hardness, softness and electrophilicity index, are also presented here for both C₈O-β-Glc and C₈O-β-Gal. These results show that, while C₈O-β-Glc possess– only one hydrogen bond, C₈O-β-Gal has two intramolecular hydrogen bonds, which further confirms the anomalous stability of the latter in self-assembly phenomena.     

Interactions of anticancer drugs with usual and mismatch base pairs - density functional theory studies

The antitumor activity of a drug is associated with its molecular properties as well as its interactions with target molecules. The molecular structures of usual, mismatch base pairs and their drug (Hydroxyurea and 5-Fluorouracil) interacting complexes were studied using density functional theory methods. The two and three-body interaction energies have been used to analyze the influence of a drug on the stability of base pairs. The sharing of electron density between the interacting molecules is shown through electron density difference maps. The Atoms in Molecules theory and Natural Bond Orbital analysis have been performed to study the hydrogen bonds in the drug interacting complexes.     

Silver(I)-mediated Hoogsteen-type base pairs

Metal-mediated Hoogsteen-type base pairs are useful for the construction of DNA duplexes containing contiguous stretches of metal ions along the helical axis. To fine-tune the stability of such base pairs and the selectivity toward different metal ions, the availability of a selection of artificial nucleobases is highly desirable. In this study, we follow a theoretical approach utilizing dispersion-corrected density functional methods to evaluate a variety of artificial nucleobases as candidates for metal-mediated Hoogsteen-type base pairs. We focus on silver(I)-mediated Hoogsteen- and reverse Hoogsteen-type base pairs formed between 1-deaza- and 1,3-dideazapurine-derived nucleobases, respectively, and cytosine. Apart from two coordinative bonds, these base pairs are stabilized by a hydrogen bond. We elucidate the impact of different substituents at the C6 position and the presence or absence of an endocyclic N3 nitrogen atom on the overall stability of a base pair and concomitantly on the strength of the hydrogen and coordinative bonds. All artificial base pairs investigated in this study are less stable than the experimentally established benchmark base pair C–Ag⁺–G. The base pair formed from 1,3-dideaza-6-methoxypurine is isoenergetic to the experimentally observed C–Ag⁺–C base pair. This makes 1,3-dideaza-6-methoxypurine a promising candidate for the use as an artificial nucleobase in DNA.     

Numerical simulations of Raman spectra of guanine-cytosine Watson-Crick and protonated Hoogsteen base pairs

Large changes in the Raman spectra of calf thymus DNA are observed upon lowering the pH. In order to gain a better insight into these effects, several simulations of the Raman spectra of the guanine-cytosine (GC) Watson-Crick and Hoogsteen base pairs are performed. By comparing the Raman bands of GC base pairs in calf thymus DNA at high and low pH with the theoretical simulations of GC base pairs, it is found that the intensity changes in the theoretical bands located between 400 and 1000 cm(-1) are small compared to the experimental ones. The behavior of the cytosine band at 1257 cm(-1) upon lowering the pH is not reproduced in the GC theoretical spectra. The bands located above 1300 cm(-1) in the theoretical spectra display intensity changes that are similar to those found for GC base pairs in calf thymus DNA spectra.     

A density functional theory parameterised neural network model of zirconia

We have developed a Behler–Parrinello Neural Network (BPNN) that can be employed to calculate energies and forces of zirconia bulk structures with oxygen vacancies with similar accuracy as that of the density functional theory (DFT) calculations that were used to train the BPNN. In this work, we have trained the BPNN potential with a reference set of 2178 DFT calculations and validated it against a dataset of untrained data. We have shown that the bulk structural parameters, equation of states, oxygen vacancy formation energies and diffusion barriers predicted by the BPNN potential are in good agreement with the reference DFT data. The transferability of the BPNN potential has also been benchmarked with the prediction of structures that were not included in the reference set. The evaluation time of the BPNN is orders of magnitude less than corresponding DFT calculations, although the training process of the BPNN potential requires non-negligible amount of computational resources to prepare the dataset. The computational efficiency of the NN enabled it to be used in molecular dynamics simulations of the temperature-dependent diffusion of an oxygen vacancy and the corresponding diffusion activation energy.     

Probing the nature of hydrogen bonds in DNA base pairs

Energy decomposition analyses based on the block-localized wave-function (BLW-ED) method are conducted to explore the nature of the hydrogen bonds in DNA base pairs in terms of deformation, Heitler–London, polarization, electron-transfer and dispersion-energy terms, where the Heitler–London energy term is composed of electrostatic and Pauli-exchange interactions. A modest electron-transfer effect is found in the Watson–Crick adenine–thymine (AT), guanine–cytosine (GC) and Hoogsteen adenine-thymine (H-AT) pairs, confirming the weak covalence in the hydrogen bonds. The electrostatic attraction and polarization effects account for most of the binding energies, particularly in the GC pair. Both theoretical and experimental data show that the GC pair has a binding energy (−25.4 kcal mol⁻¹ at the MP2/6-31G** level) twice that of the AT (−12.4 kcal mol⁻¹) and H-AT (−12.8 kcal mol⁻¹) pairs, compared with three conventional N-H···O(N) hydrogen bonds in the GC pair and two in the AT or H-AT pair. Although the remarkably strong binding between the guanine and cytosine bases benefits from the opposite orientations of the dipole moments in these two bases assisted by the π-electron delocalization from the amine groups to the carbonyl groups, model calculations demonstrate that π-resonance has very limited influence on the covalence of the hydrogen bonds. Thus, the often adopted terminology “resonance-assisted hydrogen bonding (RHAB)” may be replaced with “resonance-assisted binding” which highlights the electrostatic rather than electron-transfer nature of the enhanced stabilization, as hydrogen bonds are usually regarded as weak covalent bonds. Figure Electron density difference (EDD) maps for the GC pair: a shows the polarization effect (isodensity 1.2×10⁻³ a.u.); b shows the charge transfer effect (isodensity 2×10⁻⁴ a.u.) Dedicated to Professor Paul von Ragué Schleyer on the occasion of his 75th birthday     

Conformational preferences of 1,4,7-trithiacyclononane: a molecular mechanics and density functional theory study

Conformational preferences of 1,4,7-trithiacyclononane were studied using a highly efficient sampling technique based on local nonstochastic deformations and the MM2(91) force field. The results show that conformers that the molecule adopts in the crystal state were found to be low-energy conformers (LECs) within 5 kcal mol(-1) of the global minimum. A conformation with C1 symmetry was the global minimum and the C3 and C2 conformations were calculated to be 0.03 and 1.78 kcal mol(-1) higher in energy, respectively. The structures were further minimized using Density Functional Theory (DFT) calculations with two different functionals. The C2 and the C1 conformations were found to be LECs with the C3 conformation more than 4.0 kcal mol(-1) above the global minimum. The relative energies and structural ordering obtained using the BP86 functional are in agreement with the previously reported relative energies calculated using second-order Moller-Plesset (MP2) ab initio calculations. With the energy ordering being dependent on the molecular mechanics force field used, the approach of MM-->DFT (searching exhaustively the available conformational space at the MM level followed by generating the energy ordering through DFT calculations) appears to be appropriate for thiacrown ethers.     

Probing the effect of nitro groups in nitramine based energetic molecules: a DFT and charge density study

The structure, electron density distribution, energetic and electrostatic properties of simple nitramine based energetic TMA, DMNA, MDA and TNA molecules were determined using density functional theory (B3LYP) with the 6-311G^** and aug-cc-pVDZ basis sets coupled with Bader's theory of atoms in molecules. In the NO₂ group substituted molecules, the N–N bond distance increases with the increase of NO₂ groups, whereas in C–N bonds, this effect is relatively less, and the distances are almost equal. The topological analysis of electron density reveals that the electron density ρ_bcp(r) of C–N and N–N bonds are significantly decreasing with the increase of NO₂ groups in the nitramine molecules. The Laplacian of electron density ▽²ρ_bcp(r) of N–NO₂ bonds [DMNA: ? 16.7 eÅ^? 5, MDA: ? 12.8 eÅ^? 5 and TNA: ? 7.9 eÅ^? 5] of the molecules are relatively less negative, and the values also decrease with the increase of NO₂ groups; this implies that the charge concentration decreases with the increase of NO₂ groups, which leads to weakening the N–N bonds of the molecules. The isosurface of molecular electrostatic potential displays high electronegative regions around the NO₂ groups. The oxygen balance OB₁₀₀ of the molecules increases as the number of NO₂ group increases in the molecules, in which, the TNA molecule having maximum OB₁₀₀ value [+7.89]. The band gap, heat of detonation, bond dissociation energy and charge imbalance are predominantly depends on the number of NO₂ group present in the molecule. The charge imbalance parameter (ν) has been calculated for all molecules, which reveals that TNA is a highly sensitive molecule, the corresponding ν value is 0.047.