【作者】 张玉芬；

【导师】 赵显； 慕宇光；

【作者基本信息】 山东大学 ， 材料学， 2009， 博士

【摘要】 1.立方尖晶石结构Ⅳ（B）氮化物的物理性质的第一原理研究高温亚稳态的立方尖晶石结构的氮化硅（γ-Si₃N₄）和其他氮化物的发现为人们提供了一类新型的固态材料,因其卓越的机械,电子和热性能吸引了实验和理论方面的广泛的研究.根据第一性原理的计算,尖晶石结构的氮化硅和氮化碳被预测为具有宽的直接带隙的半导体材料,其电光性能可与GaN相媲美。在这些包含有四配位和八配位的阳离子的二元结构中,有人建议,第三种元素的引入可以显著提高材料的性能,特别是难熔性和电子性质。众所周知,在GaN中掺杂极低浓度的P/As元素可以对其电子性质产生深刻的影响。因此可以推测,在γ-A₃N₄（A=C,Si,Ge,Sn,Ti等）掺杂低浓度P/As元素或者第三种元素B（B=C,Ge,Ti等）（表示为γ-A₃N₄:P/As,B）有可能显著地改变材料的电子结构与物理性能,从而导致新的应用。因此,及时研究这些体系的电子结构及其性能是非常有必要的。根据第一性原理的计算,γ-Si₃N₄和γ-Ge₃N₄被预测为具有较大的体模量（B₀）的新型超硬材料。众所周知,在实际应用中,关键的步骤是如何在较低的压力下合成γ-Si₃N₄。根据推测在γ-Si₃N₄引入具有较大离子半径的Ge原子可以诱导产生内部压力从而可以在较低压力下稳定γ-Si₃N₄。因此可以推测,在γ-Si₃N₄掺杂Ge原子有可能显著地改变材料的电子结构与物理性能,从而对六方（β）相到立方尖晶石相（β-to-γ）相变产生深刻的影响。因此,及时研究这些掺杂的γ-Si₃N₄体系的电子结构及其压力诱导的β-to-γ相变是非常有必要的。在本文中,我们进行了基于密度泛函理论的第一性原理的计算,研究Si₃N₄-Ge₃N₄体系的压力诱导相变。这对于探索合理的低压合成γ-Si₃N₄的途径是非常有意义的。基于DFT理论的CASTEP 4.1软件包完成的第一原理电子结构的计算,确定了研究体系的稳定性与电子性质。采用Vanderbilt超软赝势,结合PerdewBurke Ernzerhof广义梯度近似（GGA-PBE）交换关联势,模拟我们的研究体系。选择Monkhorst-Pack方案设置k点网格用于研究体系Brillouin区的积分计算计算,以上的设置取得了良好的收敛性。根据Broyden-Fletcher-Goldfarb-Shanno（BFGS）方法,在特定空间群下的几何优化允许晶胞参数和内部坐标协调变化。密度泛函理论（DFT）方法已成功地应用于预测Ⅳ（B）-氮化物晶体结构和性质。在本文中,我们进行了基于DFT理论的第一性原理的计算,研究掺杂的γ-A₃N₄（A=C,Si,Ge,Sn等）体系的电子性质以及Si₃N₄-Ge₃N₄体系的压力诱导相变。通过这些计算,希望可以提供更多的关于尖晶石结构的Ⅳ（B）-氮化物的结构和性能之间的关系。通过研究得到了以下结论:1.在γ-Si₃N₄结构中四配位阳离子的位置,当硅原子被碳原子所取代,同时用极少量的磷取代氮（1.56%）,材料的带隙可以被调整;当C/Si=～0.27材料会发生绝缘体到金属的转变。从态密度图中可以观察到价带顶端的能量明显地上升,这源于P 3p轨道的贡献。2.在γ-Si₃N₄中,当晶体中少量的四配位的硅原子被碳原子所取代,同时用少量的砷原子取代氮原子,晶体结构的带隙可以被调整;当C/Si=～0.063,As/N=～0.047材料会发生绝缘体到金属的转变。从态密度图中可以观察到价带顶端的能量明显地上升,这源于As 4p轨道的贡献。3.在γ-Sn₃N₄结构中四配位阳离子的位置,当极少量的锡被锗所取代,同时用极少量的磷取代氮,材料的带隙可以被调整;当Ge/Sn=～2.08%,P/N=～1.56%材料会发生绝缘体到金属的转变。从态密度图中可以观察到价带顶端的能量明显地上升,这源于P 3p轨道的贡献.另外,由于Ge4s-P3p轨道的混合,使得导带底移向较低的能量状态。4.在γ-Ge₃N₄结构中四配位阳离子的位置,当极少量的硅被碳所取代,同时用少量的Ti取代八配位的Ge,材料的带隙可以被调整;当Ti/Ge=～0.08,材料会发生绝缘体到金属的转变。从态密度图中可以观察到导带底的能量明显地上移,这源于Ti 3d轨道的贡献。由于Ge4s-Ti3d轨道在导带底的混合,使得导带移向较低的能量状态。5.通过第一性原理赝势的计算,可以预测,在Si₃N₄结构中,当硅被锗所取代,材料的β-to-γ相变会在较低的压力下发生;随着四配位Ge的增加,β-to-γP_t迅速地减小。这种减小主要源于四配位的Si原子被Ge所取代而导致的γ相的稳定性的增加,以及Ge原子的引入所导致的β相的堆积结构更加紧密。2.用REMD方法研究:RNA GCAA发夹结构的构象转变发夹结构是RNA折叠过程的基本结构单元,包含一个由配对碱基形成的干结构和一个由未配对核苷酸序列形成的环结构。其最明显的特性是用以扭转RNA骨架的方向。由于空间位阻的存在,最小的发夹结构是3个核苷酸形成的环结构。但是由4个核苷酸形成的环结构,命名为tetraloops,被发现是最常见的发卡结构。在四个碱基序列的tetraloop中,GNRA（N为任何核苷酸和R是嘌呤）tetraloop具有良好的结构与稳定性。探讨RNA的结构特点的最有力的工具是晶体学和核磁共振测量。这些结构生物学工具通常提供一个明确的结构或有限变化的结构体系。随着新的技术的开发,RNA分子的动力学的特性吸引人们的关注。例如,¹³C核磁共振碳弛豫测量发现tetraloops的环区域存在着大量的动力学波动。RNA的动力学的特性,或结构异质性也可以用荧光光谱的方法得到解决。例如,对2-aminopurine取代的GAAA tetraloop的荧光检测温度跳转弛豫分析,其结果表明在环结构中存在一个以上的有不同碱基堆积方式的构象。通过对2-aminopurine和7-deazaguanine共同取代的GNRA tetraloops的研究,另一研究小组采用飞秒荧光光谱研究了环构象的异质性。他们的发现不仅证实了先前的观测结果,还提供了更多的特定位置的荧光衰减数据和更详细的tetraloop动力学的多重构象模型。分子动力学模拟是探讨RNA tetraloops构象变化的另一个有力的工具;例如,用自由能微扰的方法研究碱基替代对GCAA tetraloop稳定性的影响,大部分理论研究是针对短的RNA环的折叠╱伸展的动力学。模拟研究所解决的共同特点是证明环构象的多样性和折叠自由能的分层性。然而,关于局部能量最小的天然稳定结构（the native-structure local minimum）附近的构象的动力学的详细分析以及直接与现有的荧光实验数据相比较的模拟研究是非常有限。本文中采用副本交换的MD方法（REMD）方法在确定溶剂的溶液中,从原子的角度详细地研究了在最小能量的稳定结构附近的RNA tetraloop的结构转变机制。为了直接与实验数据相比较,对环碱基的替代堆叠模式进行监测。该REMD模拟可以克服传统的MD的采样的局限性,在REMD模拟中,多个复制体系在不同温度下的并行模拟,并且允许相邻的体系以一定的间隔发生交换。因此,REMD方法可以大大提高取样的准确性。这项技术已成功地用于模拟发夹的环结构。REMD的关键部分是设置不同温度的复制体系之间的构象的交换率。这种算法有助于克服大的能垒并允许在较大的构象空间进行取样。同时,它保持了结构的连续的变化。结合扩展的clustering分析方法,充裕的tetraloop的结构转变信息被检测。由此产生的构造演化图能够与现有的实验数据进行直接比较,这也证实了目前的理论模型的预测能力。本文中进行了在确定溶剂的溶液中120 ns REMD模拟计算,探索多种构象共存的5′-GGGCGCAAGCCU-3′的RNA GCAA tetraloop发夹结构。采用广泛的聚类分析的方法,得到RNA GCAA发夹结构的动力学构象转变图,很好地符合最近超快荧光光谱实验测量的结果,这证明了RNA GCAA tetraloop动力学的性质。此外,还揭示了以前没有预测到的新的过渡结构类型。同时,预测折叠自由能的变化主要与发夹结构的干部分的变化相关,而与环部分联系较少。通过REMD模拟广泛的聚类分析的方法,可以得出以下的结论。1.证明了RNA GCAA tetraloop动力学的性质。此外,还揭示了以前没有预测到的新的过渡结构类型。同时,预测折叠自由能的变化主要与发夹结构的干部分的变化相关,而与环部分联系较少。2.揭示了RNA GCAA tetraloop的多态折叠机制,包括折叠,中间和展开态,很好地符合了以前的RNA模拟结果。从自由能表面和代表性的结构可以得出一些关于RNA GCAA tetraloop折叠/展开机制的结论。3.根据我们的模拟结果和聚类分析,构造一个动态的GCAA tetraloop结构转变图,很好符合了荧光测量方法得到的结构转变模型。对于主要结构转变途径的可能的解释进行了讨论。这里提出的GCAA tetraloop结构转变图将加深对GNRA tetraloop的动力学转变机制的理解。更多还原

【Abstract】 1.Density functional study on physical properties of of spinelⅣ（B） nitrideThe discovery of spinel silicon nitride（γ-Si₃N₄） with high temperature metastability and the other spinel nitrides provides a new class of solid-state materials which have attracted many experimental and theoretical investigations for its outstanding mechanical,electronic,and thermal properties,γ-Si₃N₄,as well as spinel carbon nitride,was predicted to be a wide-band-gap semiconductor by first-principles calculations,whose electro-optic properties are comparable to those of GaN.In these binary structures,containing cations on both tetrahedral and octahedral sites,it has been suggested that incorporation of a third element can enhance the properties of the structure especially refractory and electronic properties.It is also well known that very low concentrations of substitutional P or As in GaN have a profound effect on the electronic properties.So it can be speculated that incorporation of low concentrations of As/P impurity or a third element B inγ-A₃N₄（A,B=C,Si,Ge,Sn, Ti...）（denoted asγ-A₃N₄:As/P,B） could induce a different electronic structure with drastically altered physical properties that may lead to new applications.It is therefore timely to investigate the electronic structure of these nitrides systems.By first-principles calculations,γ-Si₃N₄ was predicted to be a new super hard material,with quite a large bulk modulus.It is well to known that the real challenge for the realistic applications is how to synthesizeγ-Si₃N₄ at a lower pressure.Ching et al has suggested that including Ge inγ-Si₃N₄ can induce internal pressure to stabilize the spinel phase at a lower pressure.So it can be speculated that replacing Si by Ge in Si₃N₄ could induce a different electronic structure that may lead to a profound effect on theβ-to-γphase transition.It is therefore timely to investigate the electronic structure and phase transition of these ternary systems.In this paper,we carried out first-principles calculations based on DFT to investigate the the pressure-induced hexagonal beta phase（P6₃/m） to cubic spinel phase（Fd₃/m） transition in silicon germanium nitride systems at zero temperature in order to search for reasonable synthesis route.We hope that such calculations could provide more insights into the relation between the structure and the properties for silicon nitride. The method of density functional theory（DFT） has been successfully used in predicting crystal structures and properties of group-Ⅳnitrides.In this paper,we carried out first-principles calculations based on DFT to investigate the electronic properties ofγ-A₃N₄:As/P,B and theβ-to-γphase transition in Si₃N₄-Ge₃N₄.We hope that such calculations could provide more insights into the relation between the structure and the properties for silicon nitride.The first-principles electronic structure calculations based on DFT within CASTEP 4.1 code were carried out to determine the stability and electronic properties of these systems.The Vanderbilt ultrasoft pseudopotential with generalized gradient approximation due to Perdew Burke Ernzerhof（GGA-PBE） for exchange-correlation effects was used to model our systems.A Monkhorst-Pack grid was used for integration over the irreducible part of the Brillouin zone of these nitrides system. Good convergence was achieved with these above parameter setting.To explore the electronic properties of these solid solutions,we employed supercell with the starting configurations suggested in Ref.Ching et al（Phys.Rev.B 61）.We substituted Si atoms by Ge（or C,Sn and Ti） in silicon nitrides to model substitutional Ge Ge（or C, Sn and Ti） neutral impurity(Ge atoms on the Si sites,donated Ge_Si).Within the Broyden-Fletcher-Goldfarb-Shanno（BFGS） scheme,geometry optimization was performed under preselected space group allowing both cell parameter and internal coordinates relaxation.From the above study,some conclusions can be drawn.1.When Si is substituted with C at tet sites inγ-Si₃N₄:P,the band-gap can be adjusted,and an insulator-to-metal transition will occur at the C to Si ratio of 0.27. The pronounced change of the pressure dependence of band-gap variation inγ-Si₃N₄:P indicates that adding of P can greatly change the nature of band structure. From the DOS spectra,it is observed that the TDOS increases at the valence band maximum,which originates from the contribution of 3p orbitals of P.2.When very low concentrations of Si is replaced by C at the tetrahedral sites, together with the doping of substitutional As impurity in spinel silicon nitride,the band-gap can be adjusted,and an insulator-to-metal transition will occur at the C/Si ratio～0.063 and As/N ratio～0.047.From the DOS spectra,it is clearly observed that the TDOS increases at the valence band maximum,while the conduction band shift to lower energy with increasing As.3.It is predicted that when low concentrations of Sn is substituted with Ge at oct sites,together with the doping of substitutional P impurity inγ-Sn₃N₄,the band-gap can be adjusted,and an insulator-to-metal transition will occur at the Ge/Sn ratio=～2.08%and P/N ratio=～l.56%.From the DOS spectra,it is observed that the TDOS increases at the valence band maximum,which originates from the contribution of 3p orbitals of P.It is also found the conduction band shift to lower energy with increasing Ge,due to the Ge4s-P3p mixing.4.It is predicted that when Ge is substituted with Ti at oct sites in undoped and C-dopedγ-Ge₃N₄,the band-gap can be adjusted,and an insulator-to-metal transition will occur at the Ti to Ge ratio of 0.13 for C-dopedγ-Ge₃N₄,the ratio of 0.17 for undoped system.From the DOS spectra,it is observed that the conduction band shifts to the lower energy with a concomitant reduction in E_g,which originates from the contribution of 3d orbitals of Ti.5.It is predicted that when Si is replaced by Ge in silicon nitride,theβ-to-γphase transitions will occur at a lower pressure.As Ge increases,a large P_t reduction is observed.It is clear to find that including Ge in Si₃N₄ will stabilize the spinel phase and make a more closed-packed beta phase.2.Conformational transitions of a RNA GCAA tetraloop explored by replica-exchange molecular dynamics simulationHairpins are elementary structural units responsible for RNA folding.Hairpin loop contains a base-paired stem structure and a loop sequence with unpaired nucleotides. Its most obvious property is to function as a "bender" to reverse the direction of backbone.Due to the steric hindrance there exists a minimum of three nucleotides to make a loop structure.However loops with four nucleotides,named as tetraloops,are found to be much populated.Among the four base tetraloop motif,the family of GNRA（N is any nucleotide and R is a purine） tetraloop is well structured with unusual stability.The most powerful tools to explore the structure features of RNA tetraloops are crystallography and nuclear magnetic resonance measurements.These structure biological tools usually provide a well-defined structure or a structural ensemble with limited fluctuations.With the newly developed techniques the dynamical features of RNA molecules are attracting attentions.For example,NMR ¹³C relaxation measurements discovered substantial dynamic fluctuations in the loop region of several tetraloops.The dynamical properties,or structural heterogeneity of RNA loop can also be resolved by fluorescence spectroscopy.For instances,a GAAA tetraloop which was substituted with 2-aminopurine residues and followed by fluorescence-detected temperature-jump relaxation analysis,was demonstrated existence of more than a single conformation state with different base stacking patterns in the loop.By incorporating both 2-aminopurine and 7-deazaguanine residues into similar GNRA tetraloops another group studied the heterogeneity of loop conformation by femtosecond time-resolved fluorescence.What they found not only confirmed the previous observation,with more position-specific fluorescence decay data a more detailed dynamic multi-conformation model for the tetraloop was proposed.Molecular dynamics simulations are another powerful tool to explore the conformational dynamics of RNA tetraloops.Most of the theoretical studies were targeted at the folding/unfolding dynamics of short RNA loops.The common features resolved by the modeling studies affirmed the hierarchical properties of folding free energy landscapes and general heterogeneity of loop conformation.However detailed analysis of the conformational dynamics near the native-structure local minimum and direct comparison with available fluorescence experimental data are scarce.In this report the structural transition mechanism of RNA tetraloop near the native-structure minimum at atomic detail was interrogated by a replica exchange molecular dynamics（REMD） simulation in explicit solvent for a GCAA RNA tetraloop.In order to directly compare with experimental data the alternative stacking patterns of loop residues were monitored.The REMD simulation can overcome the sampling limitations of standard MD methods.During REMD simulation,several replicas of a system are simulated at different temperatures in parallel,allowing for exchanges between neighboring replicas at frequent intervals.So,the REMD simulation can significantly enhance the conformational sampling.This technique has been successfully used for the simulations of hairpin loop structure.The key component in replica exchange simulations is the exchange of configurations between different replicas/temperatures by rescaling the velocities.Such algorithm helps to overcome large energy barriers and allows large conformational space to be sampled. Meanwhile it maintains the continuous transformation of structures.Together with extensive clustering analysis the ample structural transition information of the tetraloop was detected.The resultant structural evolution map was able to directly compare with available experimental data which confirms the predictive power of current theoretical model.A 120 ns replica-exchange molecular dynamics simulation in explicit solvent is performed to probe the conformational transitions in 5’-GGGCGCAAGCCU-3’ RNA GCAA tetraloop.The ample structural transition information of the loop is detected on the basis of extensive clustering analysis.The resultant loop structural transition map nicely agrees with the recent ultrafast fluorescence measurement,which confirms the dynamical properties of this tetraloop.Moreover,a new transition pattern that was not disclosed previously is predicted.Meanwhile,the folding free energy landscapes were characterized:the global folding dynamics is coupled mainly with the stem rather than the loop part.From the calculation,some conclusions can be drawn.1.The dynamical properties of RNA GCAA tetraloop were confirmed;a new transition pattern that was not disclosed previously was predicted.2.An obvious multiple-state（including folded,intermediate and unfolded states） folding landscape of the RNA GCAA tetraloop is disclosed which is in good agreement with the previous RNA simulations.From the free energy surfaces and the representative structures some conclusions about the folding/unfolding of RNA GCAA tetraloop can be drawn.3.On the basis of the results of our simulation and cluster analysis,a dynamic structure transition map for the GCAA tetraloop is constructed,which is well consistent with the model from fluorescence measurements.The possible examinations for the major transitions pathways are discussed.The structure transition map of the GCAA tetraloop presented here should lead a further understanding of the dynamic transition mechanism of the GNRA tetraloop family.更多还原