Gamma-Ⅳ（B）氮化物的物理性质以及RNA GCAA发夹结构的理论研究
|
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-Si_3N_4)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-A_3N_4(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-A_3N_4: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-Si_3N_4和γ-Ge_3N_4被预测为具有较大的体模量(B_0)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-Si_3N_4。根据推测在γ-Si_3N_4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-Si_3N_4。因此可以推测,在γ-Si_3N_4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-Si_3N_4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Si_3N_4-Ge_3N_4体系的压力诱导相变。这对于探索合理的低压合成γ-Si_3N_4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-A_3N_4(A=C,Si,Ge,Sn等)体系的电子性质以及Si_3N_4-Ge_3N_4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-Si_3N_4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-Si_3N_4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-Sn_3N_4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-Ge_3N_4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Si_3N_4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,~(13)C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。
1.Density functional study on physical properties of of spinelⅣ(B) nitride
The discovery of spinel silicon nitride(γ-Si_3N_4) 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-Si_3N_4,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-A_3N_4(A,B=C,Si,Ge,Sn, Ti...)(denoted asγ-A_3N_4: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-Si_3N_4 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-Si_3N_4 at a lower pressure.Ching et al has suggested that including Ge inγ-Si_3N_4 can induce internal pressure to stabilize the spinel phase at a lower pressure.So it can be speculated that replacing Si by Ge in Si_3N_4 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(P6_3/m) to cubic spinel phase(Fd_3/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-A_3N_4:As/P,B and theβ-to-γphase transition in Si_3N_4-Ge_3N_4.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-Si_3N_4: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-Si_3N_4: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-Sn_3N_4,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-Ge_3N_4,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-Ge_3N_4,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 Si_3N_4 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 simulation
Hairpins 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 ~(13)C 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.
高温亚稳态的立方尖晶石结构的氮化硅(γ-Si_3N_4)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-A_3N_4(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-A_3N_4: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-Si_3N_4和γ-Ge_3N_4被预测为具有较大的体模量(B_0)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-Si_3N_4。根据推测在γ-Si_3N_4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-Si_3N_4。因此可以推测,在γ-Si_3N_4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-Si_3N_4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Si_3N_4-Ge_3N_4体系的压力诱导相变。这对于探索合理的低压合成γ-Si_3N_4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-A_3N_4(A=C,Si,Ge,Sn等)体系的电子性质以及Si_3N_4-Ge_3N_4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-Si_3N_4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-Si_3N_4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-Sn_3N_4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-Ge_3N_4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Si_3N_4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,~(13)C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。
1.Density functional study on physical properties of of spinelⅣ(B) nitride
The discovery of spinel silicon nitride(γ-Si_3N_4) 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-Si_3N_4,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-A_3N_4(A,B=C,Si,Ge,Sn, Ti...)(denoted asγ-A_3N_4: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-Si_3N_4 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-Si_3N_4 at a lower pressure.Ching et al has suggested that including Ge inγ-Si_3N_4 can induce internal pressure to stabilize the spinel phase at a lower pressure.So it can be speculated that replacing Si by Ge in Si_3N_4 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(P6_3/m) to cubic spinel phase(Fd_3/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-A_3N_4:As/P,B and theβ-to-γphase transition in Si_3N_4-Ge_3N_4.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-Si_3N_4: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-Si_3N_4: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-Sn_3N_4,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-Ge_3N_4,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-Ge_3N_4,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 Si_3N_4 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 simulation
Hairpins 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 ~(13)C 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.
引文
[1]Liu M L.Calculation of bulk moduli diamond and zinc-blends solids[J].Cohen,Phys.Rev.B,1985(32):7988-7991.
[2]Liu A Y,Cohen M L.Prediction of new low compressibility solid[J].Science,1989,24(5):841-842.
[3]Liu Amy Y,Cohen Marvin L.Structural properties and electronic structure of low compressibility materials:β-Si3N4 and hypothetical β-C3N4[J].Phys.Rev.B,1990,41(15):723-734.
[4]唐翠霞,唐敬友,寇自力,刘雨生,贺红亮.立方氮化硅的研究进展[J].材料导报,2007,21(9).
[1]M D Segall,Philip J D Lindan,M J Probert,C J Pickard,P J Hasnip,S J Clark and M C Payne.First-principles simulation:ideas,illustrations and the CASTEP code,J.Phys.:Condens.Matter,2002,14,2717-2744
[2]Dreizler R M,Gross E K U.Density Functional Theory[M].Berlin:Springer-Vertag,1990.
[3]P.Hohenberg,W.Kohn,Inhomogeneous Electron Gas[J].Phys.Rev.,1964,136:B864-871.
[4]Kohn W,Sham L J.Self-Consistent Equations Including Exchange and Correlation Effects[J].Phys Rev,1965,140:1133-1138.
[5]Slater J C,A Simplification of the Hartree-Fock Method,Phys.Rev.1951,81,385-390.
[6]Perdew TP,Zunger A.Self-interaction correction to density-functional approximations for many-electron systems[J].Phys Rev B,1981,23:5048-5079.
[7]Jones R O,Gunnarsson O.The density functional formalism,its applications and prospects[J].Rev Mod Phys,1989,61:689-746.
[8]Beeke A D.Density-functional exchange-energy approximation with correct asymptotic behavior[J].Phys Rcv A,1988,38:3098-3100.
[9]Langreth C,Perdew J P.Analysis of the gradient approximation and a generalization that works[J].Pllys Rev B,1980,21:5469-5493.
[10]Perdew J P,Burke K.Generalized gradient approximation made simple[J].Phys Rev Lett,1996,77:3865-3868.
[11]Kohn W,Meir Y D E.Van der waals energies in density functional theory[J].Phys Rev Lett,1998,80:4153-4156
[12]文玉华,朱如曾,周富信,等.分子动力学模拟的主要技术[J].力学进展,2003,33(1):65-73.
[13]申海兰,赵靖松.分子动力学模拟方法概述[J].装备制造技术,2007,10:29-30.
[14]崔守鑫,胡海泉,肖效光,黄海军.分子动力学模拟基本原理和主要技术[J].聊城大学学报,2005,18(1):30-34.
[15]樊康旗,贾建援.经典分子动力学模拟的主要技术[J].微纳电子技术,2005,42(3):133-137.
[1]A.Zerr,G.Miehe,G.Serghiou,M.Schwarz,E.Kroke,R.Riedel,H.Fueβ,P.Kroll,and R.Boehler,"Synthesis of cubic silicon nitfide "[J].Nature(London)400(1999),340-342.
[2]M.Schwarz,G.Miehe,A.Zerr,E.Kroke,B.Poe,H.Fuess and R.Riedel."Spinel-Si3N4:Multi-Anvil Press Synthesis and Structural Refinement".Adv.Mater.12(2000),883-887.
[3]E.Soignard,M.Somayazulu,J.J.Dong,O.F.Sankey and P.F.McMillan."High pressure-high temperature synthesis and elasticity of the cubic nitride spinel γ-Si_3N_4",J.Phys.Condens.Matter 13(2001),557-563.
[4]T.Sekine,"Shock synthesis of cubic silicon nitride"[J].J.Am.Ceram.Soc.,85(2002),113-116.
[5](2 Serghiou,G.Miehe,O.Tschauner,A.Zerr,and R.Boehler,"Synthesis of a cubic Ge3N4 phase at high pressures and temperatures"[J],J.Chem.Phys.111(1999),4659-4662.
[6]K.Leinenweber,M.O'Keeffe,M.S.Somayazulu,H.Hubert,P.F.McMillan,G.H.Wolf,"Synthesis and Structure Refinement of the Spinel,γ-Ge_3N_4.Chem.Eur.J.,5(1999),3076-3078.
[7]N.Scotti,W.Kockelmann,J.Senker,S.TraBel,H.Jacobs,Z.Anorg.Allg."Sn_3N_4,a tin(Ⅳ) nitride-Syntheses and the first crystal structure determination of a binary tin-nitrogen compound".Chem.,625(1999),1435-1439.
[8]E.Soignard,P.F.McMillan,and K.Leinenweber,"Solid Solutions and Ternary Compound Formation among Ge3Na-Si3N4 Nit'fide Spinels Synthesized at High Pressure and High Temperature".Chem.Mater.16(2004),5344-5349.
[9]T.Sekine and T.Mitsuhashi."High-temperature metastability of cubic spinel Si_3N_4".Appl.Phys.Lett.79(2001),2719-2721.
[10]S.-D.Mo,L.Ouyang,W.Y.Ching,I.Tanaka,Y.Komyama,and R.Riedel,"Interesting Physical Properties of the New Spinel Phase of Si3N4 and C3N4",Phys.Rev.Lett.83(1999),5046-5049.
[11]J.Dong,J.Deslippe,O.F.Sankey,E.Soignard,and P.F.McMillan,"Theoretical study of the ternary spinel nitride system Si3N4-Ge3N4".Phys.Rev.B 67(2003),094104-1-7.
[12]W.Y.Ching,S.-D.Mo,I.Tanaka,and M.Yoshiya,"Prediction of spinel structure and properties of single and double nitrides".Phys.Rev.B 63(2001),064102-1-4.
[13]W.Y.Ching,S.-D.Mo,L.Ouyang,I.Tanaka,and M.Yoshiya,"Prediction of the new spinel phase of Ti3N4 and SiTi2N4 and the metal-insulator transition".Phys.Rev.B 61(2000),10609-10614.
[14]J.J.Dong,O.F.Sankey,S.K.Deb,G.Wolf and P.F.McMillan."Theoretical study of β-Ge3N4 and its high-pressure spinel γ,phase".Phys.Rev.B 61(2000),11979-11992.
[15]W.Y.Ching,S.-D.Mo,L.Oyuang,"Electronic and optical properties of the cubic spinel phase ofc-Si3N4,c-Ge_3N_4,c-SiGe_2N_4,and c-GeSi_2N_4",Phys.Rev.B 63(2001),245110-245117.
[16]J.E.Lowther."High-pressure phases and structural bonding of Ge3N4",Phys.Rev.B 62(2000),5-8.
[17]W.Y.Ching,S.D.Mo,L.Ouyan,P.Rulis,I.Tanaka and M.Yoshiya,"Theoretical prediction of the structure and properties of cubic spinel nitrides",J.Am.Ceram.Soc.85(2002),75-80.
[18]W.Y.Ching and P.Rulis,"Ab-initio calculation of the electronic and spectroscopic properties of spinel γ-Sn3N4",Phys.Rev.B 73(2006),045202-1-9.
[19]F.Oba,K.Tatsumi,I.Tanaka and H.Adachi,"Effective Doping in Cubic Si3N4and Ge3N4:A First-Principles Study",J.Amer.Ceram.Soc.85(2002),97-100.
[20]P.Kroll."Pathways to metastable nitride structures",J.Solid State Chem.,176(2003),530-537.
[21]Y.F.Zhang,X.Zhao,X.F.Cheng,and Y.G.Mu,"Density functional study on electronic properties of P-doped spinel silicon carbon nitride",J.Solid State Chem.[J],2008,181:2113-2116.
[22]A.Zerr,R.Riedel,T.Sekine,J.E.Lowther,W.Y.Ching,I.Tanaka,"Recent Advances in New Hard High-Pressure Nitrides".Adv.Mat.,18(2006),2933-2948.
[23]Y.C.Zhou and Z.M.Sun,"Electronic structure of the layered compound Ti3GeC2".J.Appl.Phys.,86(1999),1430-1432.
[24]M.Y.Lv,Z.W.Chen,and R.P.Liu,"Ab initio study of electronic properties in polymorphs of compound Ti3SiC2 and Ti3GeC2",Mater.lett.60(2006),538-540.
[25]J.I.Pankove and J.A.Hutchby,"Photoluminescence of ion-implanted GaN".J.Appl.Phys.47(1976),5387-5390.
[26]L.Bellaiche,S.-H.Wei,and A.Zunger,"Band gaps of GaPN and GaAsN alloys",Appl.Phys.Lett.70(1997),3558-3560.
[27]J.B.Li and L.W.Wang,"Energy levels of isoelectronic impurities by large scale LDA calculations",Phys.Rev.B 67(2003),033102-1-4.
[28]W.Kohn and L.J.Sham,"Self-Consistent Equations Including Exchange and Correlation Effects",Phys.Rev.140(1965),A1133-A1138.
[29]M.C.Payne,M.P.Teter,D.C.Allan,T.A.Arias,and J.D.Joannopoulos,"Iterative minimization techniques for ab initio total-energy calculations:molecular dynamics and conjugate gradients",Rev.Mod.Phys.64(1992),1045-1097.
[30]D.Vanderbilt,"Soft self-consistent pseudopotentials in a generalized eigenvalue formalism",Phys.Rev.B 41(1990),7892-7895.
[31]J.P.Perdew,K.Burke,and M.Ernzerhof,"Generalized Gradient Approximation Made Simple",Phys.Rev.Lett.77(1996),3865-3868.
[32]H.J.Monkhorst and J.D.Pack,"Special points for Brillouin-zone integrations",Phys.Rev.B 13(1976),5188-5192.
[33]E.Polak,Computational Methods in Optimization(Academic,New York,1971),p.56.
[34]Zerr A et al 2002 Acta Crystallogr.A 58 C47
[35]S Leitch,A Moewes,L Ouyang,W YChing and T Sekine,"Properties of non-equivalent sites and bandgap of spinel-phase silicon nitride",J.Phys.:Condens.Matter,16(2004),6469-6476.
[36]J.J.Lagowski,Modern Inorganic Chemistry,Marcel Dekker,New York(1973).
[37] W. Y. Ching, L. Ouyang, and J. D. Gale. "Full ab initio geometry optimization of all known crystalline phases of Si3N4". Phys. Rev. B 61 (2000), 8696-8700.
[38] GC. Liu, Z.W. Lu, M. Klein, "Pressure-induced phase transformations in AlAs: Comparison between ab initio theory and experiment". Phys. Rev. B 51 (1995), 5678-5681.
[39] E. D. Jones, N. A. Modine, A. A. Allerman, S. R. Kurtz, A. F. Wright, S. T. Tozer, and X. Wei, "Band structure of In_xGa_(1-x)As_(1-y)N_y alloys and effects of pressure", Phys. Rev. B 60 (1999), 4430-4433.
[40] M. Xua, Y.C. Dinga, G. Xionga, W.J. Zhua, and H.L. He, Physica B, 2008,403, 2515-2520.
1.Cheong,C.J.,Varani,G.and Tinoco,I.(1990) SOLUTION STRUCTURE OF AN UNUSUALLY STABLE RNA HAIRPIN,5'GGAC(UUCG)GUCC.Nature,346,680-682.
2.Uhlenbeck,O.C.(1990) NUCLEIC-ACID STRUCTURE-TETRALOOPS AND RNA FOLDING Nature,346,613-614.
3.Wolters,J.(1992) The nature of preferred hairpin structures in 16S-like rRNA variable regions.Nucleic Acids Research,20,1843-1850.
4.Uhlenbeck,O.C.(1990) Tetraloops and RNA folding.Nature,346,613-614
5.Heus,H.A.and Pardi,A.(1991) STRUCTURAL FEATURES THAT GIVE RISE TO THE UNUSUAL STABILITY OF RNA HAIRPINS CONTAINING GNRA LOOPS.Science,253,191-194.
6.Jucker,F.M.,Heus,H.A.,Yip,P.F.,Moors,E.H.M.and Pardi,A.(1996) A network of heterogeneous hydrogen bonds in GNRA tetraloops.Journal of Molecular Biology,264,968-980.
7.Care,J.H.,Gooding,A.R.,Podell,E.,Zhou,K.H.,Golden,B.L.,Kundrot,C.E.,Cech,T.R.and Doudna,J.A.(1996) Crystal structure of a group I ribozyme domain:Principles of RNA packing.Science,273,1678-1685.
8.Kalurachchi,K.and Nikonowicz,E.P.(1998) NMR structure determination of the binding site for ribosomal protein S8 from Escherichia coli 16 S rRNA.Journal of Molecular Biology,280,639-654.
9.H.A.Heus,a.A.P.(1991) Structural Features that Give Rise to the Unusual Stability of RNA Hairpins Containing GNRA Loops.Science,253,191-194
10.Zhang,Q.and A1-Hashimi,H.M.(2008) Extending the NMR spatial resolution limit for RNA by motional couplings.Nat Meth,5,243-245.
11.Hodak,J.H.,Fiore,J.L.,Nesbitt,D.J.,Downey,C.D.and Pardi,A.(2005)Docking kinetics and equilibrium of a GAAA tetra loop-receptor motif probed by single-molecule FRET.Proc.Natl.Acad.Sci.U.S.A.,102,10505-10510.
12.Furtig,B.,Richter,C.,Wohnert,J.and Schwalbe,H.(2003) NMR spectroscopy o fRNA.Chembiochem,4,936-962.
13.Legault,P.,Hoogstraten,C.G.,Metlitzky,E.and Pardi,A.(1998) Order,dynamics and metal-binding in the lead-dependent ribozyme.Journal of Molecular Biology,284,325-335.
14.Hoogstraten,C.G.,Wank,J.R.and Pardi,A.(2000) Active site dynamics in the lead-dependent ribozyme.Biochemistry,39,9951-9958.
15.Trantirek,L.,Caha,E.,Kaderavek,P.and Fiala,R.(2007) NMR C-13-relaxation study of base and sugar dynamics in GCAA RNA hairpin tetraloop.J..Biomol.Struct.Dyn.,25,243-252.
16.Menger,M.,Eckstein,F.and Porschke,D.(2000) Dynamics of the RNA Hairpin GNRA Tetraloop.Biochemistry,39,4500-4507.
17.Rist,M.J.and Marino,J.P.(2002) Fluorescent nucleotide base analogs as probes of nucleic acid structure,dynamics and interactions.Current Organic Chemistry,6,775-793.
18.Zhao,L.and Xia,T.B.(2007) Direct revelation of multiple conformations in RNA by femtosecond dynamics.Journal of the American Chemical Society,129,4118-4119.
19.Sorin,E.J.,Engelhardt,M.A.,Herschlag,D.and Pande,V.S.(2002) RNA simulations:Probing hairpin unfolding and the dynamics of a GNRA tetraloop.Journal of Molecular Biology,317,493-506.
20.Nivon,L.G.and Shakhnovich,E.I.(2004) All-atom Monte Carlo simulation of GCAA RNA folding.Journal of Molecular Biology,344,29-45.
21.Koplin,J.,Mu,Y.,Richter,C.,Schwalbe,H.and Stock,G.(2005) Structure and Dynamics of an RNA Tetraloop:A Joint Molecular Dynamics and NMR Study.Structure,13,1255-1267.
22.Hyeon,C.and Thirumalai,D.(2006) Forced-Unfolding and Force-Quench Refolding of RNA Hairpins.Biophysical Journal,90,3410-3427.
23.Ma,H.,Proctor,D.J.,Kierzek,E.,Kierzek,R.,Bevilacqua,P.C.and Gruebele,M.(2006) Exploring the Energy Landscape of a Small RNA Hairpin.Journal of the American Chemical Society,128,1523-1530.
24.Kannan,S.and Zacharias,M.(2007) Folding of a DNA hairpin loop structure in explicit solvent using replica-exchange molecular dynamics Simulations.Biophysical Journal,93,3218-3228.
25.McDowell,S.E.,Spackova,N.,Sponer,J.and Walter,N.G.(2007) Molecular dynamics simulations of RNA:An in silico single molecule approach.Biopolymers,85,169-184.
26.Nystrom,B.and Nilsson,L.(2007) Molecular dynamics study of intrinsic stability in six RNA terminal loop motifs.Journal of Biomolecular Structure and Dynamics,24,525-535.
27.Zhuang,L.,Jaeger,L.and Shea,J.-E.(2007) Probing the structural hierarchy and energy landscape of an RNA T-loop hairpin.Nucleic Acids Research 35,6995-7002
28.Garcia,A.E.and Paschek,D.(2008) Simulation of the Pressure and Temperature Folding/Unfolding Equilibrium of a Small RNA Hairpin.Journal of the American Chemical Society,130,815-817.
29.Villa,A.,Widjajakusuma,E.and Stock,G.(2008) Molecular Dynamics Simulation of the Structure,Dynamics,and Thermostability of the RNA Hairpins uCACGg and cUUCGg.Journal of Physical Chemistry B,112,134-142.
30.Mitsutake,A.,Sugita,Y.and Okamoto,Y.(2001) Generalized-ensemble algorithms for molecular simulations of biopolymers.Biopolymers,60,96-123.
31.Sanbonmatsu,K.Y.and Garcia,A.E.(2002) Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics.Proteins-Structure Function and Genetics,46,225-234.
32.Zhou,R.H.(2004) Exploring the protein folding free energy landscape:coupling replica exchange method with P3ME/RESPA algorithm.Journal of Molecular Graphics & Modelling,22,451-463.
33.Mu,Y.,Nordenskiold,L.and Tam,J.P.(2006) Folding,Misfolding,and Amyloid Protofibril Formation of WW Domain FBP28.Biophysical Journal 90,3983-3992
34.Sanbonmatsu K.Y.,A.E.Ga.(2002) Structure of Met-Enkephalin in Explicit Aqueous Solution Using Replica Exchange Molecular Dynamics.Structure,Function,and Genetics,46,225-234
35.Zhang,J.,Qin,M.and Wang,W.(2006) Folding mechanism of beta-hairpins studied by replica exchange molecular simulations.Proteins-Structure Function and Bioinformatics,62,672-685.
36.Berendsen,H.J.C.,Vanderspoel,D.and Vandrunen,R.(1995) GROMACS-A MESSAGE-PASSING PARALLEL MOLECULAR-DYNAMICS IMPLEMENTATION.Computer Physics Communications,91,43-56.
37.Cheatham,T.E.,Cieplak,P.and Kollman,P.A.(1999) A modified version of the Cornell et al.force field with improved sugar pucker phases and helical repeat. Journal of Biomolecular Structure & Dynamics, 16, 845-862.
38. Hess, B., Bekker, H., Berendsen, H.J.C. and Fraaije, J. (1997) LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18,1463-1472.
39. Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W. and Klein, M.L. (1983) Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79, 926-935.
40. Daura, X., Gademann, K., Jaun, B., Seebach, D., van Gunsteren, W.F. and Mark, A.E. (1999) Peptide folding: When simulation meets experiment. Angewandte Chemie-International Edition, 38, 236-240.
41. Lavery, R. and Sklenar, H. (1988) THE DEFINITION OF GENERALIZED HELICOIDAL PARAMETERS AND OF AXIS CURVATURE FOR IRREGULAR NUCLEIC-ACIDS. Journal of Biomolecular Structure & Dynamics, 6, 63-91.
42. Garcia, A.E. and Paschek, D. (2008) Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin. Journal of the American Chemical Society, 130, 815-+.
43. Davis, J.H., Tonelli, M., Scott, L.G., Jaeger, L., Williamson, J.R. and Butcher, S.E. (2005) RNA helical packing in solution: NMR structure of a 30 kDa GAAA tetraloop-receptor complex. Journal of Molecular Biology, 351, 371-382.
44. Klosterman, P.S., Hendrix, D.K., Tamura, M., Holbrook, S.R. and Brenner, S.E. (2004) Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns. Nucleic Acids Research, 32, 2342-2352.
45. Pley, H.W., Flaherty, K.M. and McKay, D.B. (1994) MODEL FOR AN RNA TERTIARY INTERACTION FRONT THE STRUCTURE OF AN INTERMOLECULAR COMPLEX BETWEEN A GAAA TETRALOOP AND AN RNA HELIX. Nature, 372, 111 -113.
46. Mao, H.Y., White, S.A. and Williamson, J.R. (1999) A novel loop-loop recognition motif in the yeast ribosomal protein L30 autoregulatory RNA complex. Nature Structural Biology, 6, 1139-1147.
47. Battiste, J.L., Mao, H.Y., Rao, N.S., Tan, R.Y., Muhandiram, D.R., Kay, L.E., Frankel, A.D. and Williamson, J.R. (1996) alpha helix-RNA major groove recognition in an HIV-1 Rev peptide RRE RNA complex. Science, 273, 1547-1551.
48.Baugh,C.,Grate,D.and Wilson,C.(2000) 2.8 angstrom crystal structure of the malachite green aptamer.Journal of Molecular Biology,301,117-128.
49.Nikulin,A.,Serganov,A.,Ennifar,E.,Tishchenko,S.,Nevskaya,N.,Shepard,W.,Portier,C.,Garber,M.,Ehresmann,B.,Ehresmann,C.et al.(2000) Crystal structure of the S 15-rRNA complex.Nature Structural Biology,7,273-277.
50.Stoldt,M.,Wohnert,J.,Ohlenschlager,O.,Gorlach,M.and Brown,L.R.(1999)The NMR structure of the 5S rRNA E-domain-protein L25 complex shows preformed and induced recognition.Embo Journal,18,6508-6521.
51.Butcher,S.E.,Dieckmann,T.and Feigon,J.(1997) Solution structure ofa GAAA tetraloop receptor RNA.Embo Journal,16,7490-7499.
52.Rowsell,S.,Stonehouse,N.J.,Convery,M.A.,Adams,C.J.,Ellington,A.D.,Hirao,I.,Peabody,D.S.,Stockley,P.G.and Phillips,S.E.V.(1998) Crystal structures of a series of RNA aptamers complexed to the same protein target.Nature Structural Biology,5,970-975.
53.Kerwood,D.J.and Borer,P.N.(1996) Structure refinement for a 24-nucleotide RNA hairpin.Magnetic Resonance in Chemistry,34,S136-S146.
54.Smith,J.S.and Nikonowicz,E.P.(2000) Phosphorothioate substitution can substantially alter RNA conformation.Biochemistry,39,5642-5652.
55.Leulliot,N.,Baumruk,V.,Abdelkafi,M.,Turpin,P.Y.,Namane,A.,Gouyette,C.,Huynh-Dinh,T.and Ghomi,M.(1999) Unusual nucleotide conformations in GNRA and UNCG type tetraloop hairpins:evidence from Raman markers assignments.Nucleic Acids Research,27,1398-1404.
56.Saenger,W.(1984).Springer-Vedag,New York.
57.Perez,A.,Marchan,I.,Svozil,D.,Sponer,J.,Cheatham,T.E.,III,Laughton,C.A.and Orozco,M.(2007) Refinement of the AMBER Force Field for Nucleic Acids:Improving the Description of {alpha}/{gamma} Conformers.Biophysical Journal,92,3817-3829.
[2]Liu A Y,Cohen M L.Prediction of new low compressibility solid[J].Science,1989,24(5):841-842.
[3]Liu Amy Y,Cohen Marvin L.Structural properties and electronic structure of low compressibility materials:β-Si3N4 and hypothetical β-C3N4[J].Phys.Rev.B,1990,41(15):723-734.
[4]唐翠霞,唐敬友,寇自力,刘雨生,贺红亮.立方氮化硅的研究进展[J].材料导报,2007,21(9).
[1]M D Segall,Philip J D Lindan,M J Probert,C J Pickard,P J Hasnip,S J Clark and M C Payne.First-principles simulation:ideas,illustrations and the CASTEP code,J.Phys.:Condens.Matter,2002,14,2717-2744
[2]Dreizler R M,Gross E K U.Density Functional Theory[M].Berlin:Springer-Vertag,1990.
[3]P.Hohenberg,W.Kohn,Inhomogeneous Electron Gas[J].Phys.Rev.,1964,136:B864-871.
[4]Kohn W,Sham L J.Self-Consistent Equations Including Exchange and Correlation Effects[J].Phys Rev,1965,140:1133-1138.
[5]Slater J C,A Simplification of the Hartree-Fock Method,Phys.Rev.1951,81,385-390.
[6]Perdew TP,Zunger A.Self-interaction correction to density-functional approximations for many-electron systems[J].Phys Rev B,1981,23:5048-5079.
[7]Jones R O,Gunnarsson O.The density functional formalism,its applications and prospects[J].Rev Mod Phys,1989,61:689-746.
[8]Beeke A D.Density-functional exchange-energy approximation with correct asymptotic behavior[J].Phys Rcv A,1988,38:3098-3100.
[9]Langreth C,Perdew J P.Analysis of the gradient approximation and a generalization that works[J].Pllys Rev B,1980,21:5469-5493.
[10]Perdew J P,Burke K.Generalized gradient approximation made simple[J].Phys Rev Lett,1996,77:3865-3868.
[11]Kohn W,Meir Y D E.Van der waals energies in density functional theory[J].Phys Rev Lett,1998,80:4153-4156
[12]文玉华,朱如曾,周富信,等.分子动力学模拟的主要技术[J].力学进展,2003,33(1):65-73.
[13]申海兰,赵靖松.分子动力学模拟方法概述[J].装备制造技术,2007,10:29-30.
[14]崔守鑫,胡海泉,肖效光,黄海军.分子动力学模拟基本原理和主要技术[J].聊城大学学报,2005,18(1):30-34.
[15]樊康旗,贾建援.经典分子动力学模拟的主要技术[J].微纳电子技术,2005,42(3):133-137.
[1]A.Zerr,G.Miehe,G.Serghiou,M.Schwarz,E.Kroke,R.Riedel,H.Fueβ,P.Kroll,and R.Boehler,"Synthesis of cubic silicon nitfide "[J].Nature(London)400(1999),340-342.
[2]M.Schwarz,G.Miehe,A.Zerr,E.Kroke,B.Poe,H.Fuess and R.Riedel."Spinel-Si3N4:Multi-Anvil Press Synthesis and Structural Refinement".Adv.Mater.12(2000),883-887.
[3]E.Soignard,M.Somayazulu,J.J.Dong,O.F.Sankey and P.F.McMillan."High pressure-high temperature synthesis and elasticity of the cubic nitride spinel γ-Si_3N_4",J.Phys.Condens.Matter 13(2001),557-563.
[4]T.Sekine,"Shock synthesis of cubic silicon nitride"[J].J.Am.Ceram.Soc.,85(2002),113-116.
[5](2 Serghiou,G.Miehe,O.Tschauner,A.Zerr,and R.Boehler,"Synthesis of a cubic Ge3N4 phase at high pressures and temperatures"[J],J.Chem.Phys.111(1999),4659-4662.
[6]K.Leinenweber,M.O'Keeffe,M.S.Somayazulu,H.Hubert,P.F.McMillan,G.H.Wolf,"Synthesis and Structure Refinement of the Spinel,γ-Ge_3N_4.Chem.Eur.J.,5(1999),3076-3078.
[7]N.Scotti,W.Kockelmann,J.Senker,S.TraBel,H.Jacobs,Z.Anorg.Allg."Sn_3N_4,a tin(Ⅳ) nitride-Syntheses and the first crystal structure determination of a binary tin-nitrogen compound".Chem.,625(1999),1435-1439.
[8]E.Soignard,P.F.McMillan,and K.Leinenweber,"Solid Solutions and Ternary Compound Formation among Ge3Na-Si3N4 Nit'fide Spinels Synthesized at High Pressure and High Temperature".Chem.Mater.16(2004),5344-5349.
[9]T.Sekine and T.Mitsuhashi."High-temperature metastability of cubic spinel Si_3N_4".Appl.Phys.Lett.79(2001),2719-2721.
[10]S.-D.Mo,L.Ouyang,W.Y.Ching,I.Tanaka,Y.Komyama,and R.Riedel,"Interesting Physical Properties of the New Spinel Phase of Si3N4 and C3N4",Phys.Rev.Lett.83(1999),5046-5049.
[11]J.Dong,J.Deslippe,O.F.Sankey,E.Soignard,and P.F.McMillan,"Theoretical study of the ternary spinel nitride system Si3N4-Ge3N4".Phys.Rev.B 67(2003),094104-1-7.
[12]W.Y.Ching,S.-D.Mo,I.Tanaka,and M.Yoshiya,"Prediction of spinel structure and properties of single and double nitrides".Phys.Rev.B 63(2001),064102-1-4.
[13]W.Y.Ching,S.-D.Mo,L.Ouyang,I.Tanaka,and M.Yoshiya,"Prediction of the new spinel phase of Ti3N4 and SiTi2N4 and the metal-insulator transition".Phys.Rev.B 61(2000),10609-10614.
[14]J.J.Dong,O.F.Sankey,S.K.Deb,G.Wolf and P.F.McMillan."Theoretical study of β-Ge3N4 and its high-pressure spinel γ,phase".Phys.Rev.B 61(2000),11979-11992.
[15]W.Y.Ching,S.-D.Mo,L.Oyuang,"Electronic and optical properties of the cubic spinel phase ofc-Si3N4,c-Ge_3N_4,c-SiGe_2N_4,and c-GeSi_2N_4",Phys.Rev.B 63(2001),245110-245117.
[16]J.E.Lowther."High-pressure phases and structural bonding of Ge3N4",Phys.Rev.B 62(2000),5-8.
[17]W.Y.Ching,S.D.Mo,L.Ouyan,P.Rulis,I.Tanaka and M.Yoshiya,"Theoretical prediction of the structure and properties of cubic spinel nitrides",J.Am.Ceram.Soc.85(2002),75-80.
[18]W.Y.Ching and P.Rulis,"Ab-initio calculation of the electronic and spectroscopic properties of spinel γ-Sn3N4",Phys.Rev.B 73(2006),045202-1-9.
[19]F.Oba,K.Tatsumi,I.Tanaka and H.Adachi,"Effective Doping in Cubic Si3N4and Ge3N4:A First-Principles Study",J.Amer.Ceram.Soc.85(2002),97-100.
[20]P.Kroll."Pathways to metastable nitride structures",J.Solid State Chem.,176(2003),530-537.
[21]Y.F.Zhang,X.Zhao,X.F.Cheng,and Y.G.Mu,"Density functional study on electronic properties of P-doped spinel silicon carbon nitride",J.Solid State Chem.[J],2008,181:2113-2116.
[22]A.Zerr,R.Riedel,T.Sekine,J.E.Lowther,W.Y.Ching,I.Tanaka,"Recent Advances in New Hard High-Pressure Nitrides".Adv.Mat.,18(2006),2933-2948.
[23]Y.C.Zhou and Z.M.Sun,"Electronic structure of the layered compound Ti3GeC2".J.Appl.Phys.,86(1999),1430-1432.
[24]M.Y.Lv,Z.W.Chen,and R.P.Liu,"Ab initio study of electronic properties in polymorphs of compound Ti3SiC2 and Ti3GeC2",Mater.lett.60(2006),538-540.
[25]J.I.Pankove and J.A.Hutchby,"Photoluminescence of ion-implanted GaN".J.Appl.Phys.47(1976),5387-5390.
[26]L.Bellaiche,S.-H.Wei,and A.Zunger,"Band gaps of GaPN and GaAsN alloys",Appl.Phys.Lett.70(1997),3558-3560.
[27]J.B.Li and L.W.Wang,"Energy levels of isoelectronic impurities by large scale LDA calculations",Phys.Rev.B 67(2003),033102-1-4.
[28]W.Kohn and L.J.Sham,"Self-Consistent Equations Including Exchange and Correlation Effects",Phys.Rev.140(1965),A1133-A1138.
[29]M.C.Payne,M.P.Teter,D.C.Allan,T.A.Arias,and J.D.Joannopoulos,"Iterative minimization techniques for ab initio total-energy calculations:molecular dynamics and conjugate gradients",Rev.Mod.Phys.64(1992),1045-1097.
[30]D.Vanderbilt,"Soft self-consistent pseudopotentials in a generalized eigenvalue formalism",Phys.Rev.B 41(1990),7892-7895.
[31]J.P.Perdew,K.Burke,and M.Ernzerhof,"Generalized Gradient Approximation Made Simple",Phys.Rev.Lett.77(1996),3865-3868.
[32]H.J.Monkhorst and J.D.Pack,"Special points for Brillouin-zone integrations",Phys.Rev.B 13(1976),5188-5192.
[33]E.Polak,Computational Methods in Optimization(Academic,New York,1971),p.56.
[34]Zerr A et al 2002 Acta Crystallogr.A 58 C47
[35]S Leitch,A Moewes,L Ouyang,W YChing and T Sekine,"Properties of non-equivalent sites and bandgap of spinel-phase silicon nitride",J.Phys.:Condens.Matter,16(2004),6469-6476.
[36]J.J.Lagowski,Modern Inorganic Chemistry,Marcel Dekker,New York(1973).
[37] W. Y. Ching, L. Ouyang, and J. D. Gale. "Full ab initio geometry optimization of all known crystalline phases of Si3N4". Phys. Rev. B 61 (2000), 8696-8700.
[38] GC. Liu, Z.W. Lu, M. Klein, "Pressure-induced phase transformations in AlAs: Comparison between ab initio theory and experiment". Phys. Rev. B 51 (1995), 5678-5681.
[39] E. D. Jones, N. A. Modine, A. A. Allerman, S. R. Kurtz, A. F. Wright, S. T. Tozer, and X. Wei, "Band structure of In_xGa_(1-x)As_(1-y)N_y alloys and effects of pressure", Phys. Rev. B 60 (1999), 4430-4433.
[40] M. Xua, Y.C. Dinga, G. Xionga, W.J. Zhua, and H.L. He, Physica B, 2008,403, 2515-2520.
1.Cheong,C.J.,Varani,G.and Tinoco,I.(1990) SOLUTION STRUCTURE OF AN UNUSUALLY STABLE RNA HAIRPIN,5'GGAC(UUCG)GUCC.Nature,346,680-682.
2.Uhlenbeck,O.C.(1990) NUCLEIC-ACID STRUCTURE-TETRALOOPS AND RNA FOLDING Nature,346,613-614.
3.Wolters,J.(1992) The nature of preferred hairpin structures in 16S-like rRNA variable regions.Nucleic Acids Research,20,1843-1850.
4.Uhlenbeck,O.C.(1990) Tetraloops and RNA folding.Nature,346,613-614
5.Heus,H.A.and Pardi,A.(1991) STRUCTURAL FEATURES THAT GIVE RISE TO THE UNUSUAL STABILITY OF RNA HAIRPINS CONTAINING GNRA LOOPS.Science,253,191-194.
6.Jucker,F.M.,Heus,H.A.,Yip,P.F.,Moors,E.H.M.and Pardi,A.(1996) A network of heterogeneous hydrogen bonds in GNRA tetraloops.Journal of Molecular Biology,264,968-980.
7.Care,J.H.,Gooding,A.R.,Podell,E.,Zhou,K.H.,Golden,B.L.,Kundrot,C.E.,Cech,T.R.and Doudna,J.A.(1996) Crystal structure of a group I ribozyme domain:Principles of RNA packing.Science,273,1678-1685.
8.Kalurachchi,K.and Nikonowicz,E.P.(1998) NMR structure determination of the binding site for ribosomal protein S8 from Escherichia coli 16 S rRNA.Journal of Molecular Biology,280,639-654.
9.H.A.Heus,a.A.P.(1991) Structural Features that Give Rise to the Unusual Stability of RNA Hairpins Containing GNRA Loops.Science,253,191-194
10.Zhang,Q.and A1-Hashimi,H.M.(2008) Extending the NMR spatial resolution limit for RNA by motional couplings.Nat Meth,5,243-245.
11.Hodak,J.H.,Fiore,J.L.,Nesbitt,D.J.,Downey,C.D.and Pardi,A.(2005)Docking kinetics and equilibrium of a GAAA tetra loop-receptor motif probed by single-molecule FRET.Proc.Natl.Acad.Sci.U.S.A.,102,10505-10510.
12.Furtig,B.,Richter,C.,Wohnert,J.and Schwalbe,H.(2003) NMR spectroscopy o fRNA.Chembiochem,4,936-962.
13.Legault,P.,Hoogstraten,C.G.,Metlitzky,E.and Pardi,A.(1998) Order,dynamics and metal-binding in the lead-dependent ribozyme.Journal of Molecular Biology,284,325-335.
14.Hoogstraten,C.G.,Wank,J.R.and Pardi,A.(2000) Active site dynamics in the lead-dependent ribozyme.Biochemistry,39,9951-9958.
15.Trantirek,L.,Caha,E.,Kaderavek,P.and Fiala,R.(2007) NMR C-13-relaxation study of base and sugar dynamics in GCAA RNA hairpin tetraloop.J..Biomol.Struct.Dyn.,25,243-252.
16.Menger,M.,Eckstein,F.and Porschke,D.(2000) Dynamics of the RNA Hairpin GNRA Tetraloop.Biochemistry,39,4500-4507.
17.Rist,M.J.and Marino,J.P.(2002) Fluorescent nucleotide base analogs as probes of nucleic acid structure,dynamics and interactions.Current Organic Chemistry,6,775-793.
18.Zhao,L.and Xia,T.B.(2007) Direct revelation of multiple conformations in RNA by femtosecond dynamics.Journal of the American Chemical Society,129,4118-4119.
19.Sorin,E.J.,Engelhardt,M.A.,Herschlag,D.and Pande,V.S.(2002) RNA simulations:Probing hairpin unfolding and the dynamics of a GNRA tetraloop.Journal of Molecular Biology,317,493-506.
20.Nivon,L.G.and Shakhnovich,E.I.(2004) All-atom Monte Carlo simulation of GCAA RNA folding.Journal of Molecular Biology,344,29-45.
21.Koplin,J.,Mu,Y.,Richter,C.,Schwalbe,H.and Stock,G.(2005) Structure and Dynamics of an RNA Tetraloop:A Joint Molecular Dynamics and NMR Study.Structure,13,1255-1267.
22.Hyeon,C.and Thirumalai,D.(2006) Forced-Unfolding and Force-Quench Refolding of RNA Hairpins.Biophysical Journal,90,3410-3427.
23.Ma,H.,Proctor,D.J.,Kierzek,E.,Kierzek,R.,Bevilacqua,P.C.and Gruebele,M.(2006) Exploring the Energy Landscape of a Small RNA Hairpin.Journal of the American Chemical Society,128,1523-1530.
24.Kannan,S.and Zacharias,M.(2007) Folding of a DNA hairpin loop structure in explicit solvent using replica-exchange molecular dynamics Simulations.Biophysical Journal,93,3218-3228.
25.McDowell,S.E.,Spackova,N.,Sponer,J.and Walter,N.G.(2007) Molecular dynamics simulations of RNA:An in silico single molecule approach.Biopolymers,85,169-184.
26.Nystrom,B.and Nilsson,L.(2007) Molecular dynamics study of intrinsic stability in six RNA terminal loop motifs.Journal of Biomolecular Structure and Dynamics,24,525-535.
27.Zhuang,L.,Jaeger,L.and Shea,J.-E.(2007) Probing the structural hierarchy and energy landscape of an RNA T-loop hairpin.Nucleic Acids Research 35,6995-7002
28.Garcia,A.E.and Paschek,D.(2008) Simulation of the Pressure and Temperature Folding/Unfolding Equilibrium of a Small RNA Hairpin.Journal of the American Chemical Society,130,815-817.
29.Villa,A.,Widjajakusuma,E.and Stock,G.(2008) Molecular Dynamics Simulation of the Structure,Dynamics,and Thermostability of the RNA Hairpins uCACGg and cUUCGg.Journal of Physical Chemistry B,112,134-142.
30.Mitsutake,A.,Sugita,Y.and Okamoto,Y.(2001) Generalized-ensemble algorithms for molecular simulations of biopolymers.Biopolymers,60,96-123.
31.Sanbonmatsu,K.Y.and Garcia,A.E.(2002) Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics.Proteins-Structure Function and Genetics,46,225-234.
32.Zhou,R.H.(2004) Exploring the protein folding free energy landscape:coupling replica exchange method with P3ME/RESPA algorithm.Journal of Molecular Graphics & Modelling,22,451-463.
33.Mu,Y.,Nordenskiold,L.and Tam,J.P.(2006) Folding,Misfolding,and Amyloid Protofibril Formation of WW Domain FBP28.Biophysical Journal 90,3983-3992
34.Sanbonmatsu K.Y.,A.E.Ga.(2002) Structure of Met-Enkephalin in Explicit Aqueous Solution Using Replica Exchange Molecular Dynamics.Structure,Function,and Genetics,46,225-234
35.Zhang,J.,Qin,M.and Wang,W.(2006) Folding mechanism of beta-hairpins studied by replica exchange molecular simulations.Proteins-Structure Function and Bioinformatics,62,672-685.
36.Berendsen,H.J.C.,Vanderspoel,D.and Vandrunen,R.(1995) GROMACS-A MESSAGE-PASSING PARALLEL MOLECULAR-DYNAMICS IMPLEMENTATION.Computer Physics Communications,91,43-56.
37.Cheatham,T.E.,Cieplak,P.and Kollman,P.A.(1999) A modified version of the Cornell et al.force field with improved sugar pucker phases and helical repeat. Journal of Biomolecular Structure & Dynamics, 16, 845-862.
38. Hess, B., Bekker, H., Berendsen, H.J.C. and Fraaije, J. (1997) LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18,1463-1472.
39. Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W. and Klein, M.L. (1983) Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79, 926-935.
40. Daura, X., Gademann, K., Jaun, B., Seebach, D., van Gunsteren, W.F. and Mark, A.E. (1999) Peptide folding: When simulation meets experiment. Angewandte Chemie-International Edition, 38, 236-240.
41. Lavery, R. and Sklenar, H. (1988) THE DEFINITION OF GENERALIZED HELICOIDAL PARAMETERS AND OF AXIS CURVATURE FOR IRREGULAR NUCLEIC-ACIDS. Journal of Biomolecular Structure & Dynamics, 6, 63-91.
42. Garcia, A.E. and Paschek, D. (2008) Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin. Journal of the American Chemical Society, 130, 815-+.
43. Davis, J.H., Tonelli, M., Scott, L.G., Jaeger, L., Williamson, J.R. and Butcher, S.E. (2005) RNA helical packing in solution: NMR structure of a 30 kDa GAAA tetraloop-receptor complex. Journal of Molecular Biology, 351, 371-382.
44. Klosterman, P.S., Hendrix, D.K., Tamura, M., Holbrook, S.R. and Brenner, S.E. (2004) Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns. Nucleic Acids Research, 32, 2342-2352.
45. Pley, H.W., Flaherty, K.M. and McKay, D.B. (1994) MODEL FOR AN RNA TERTIARY INTERACTION FRONT THE STRUCTURE OF AN INTERMOLECULAR COMPLEX BETWEEN A GAAA TETRALOOP AND AN RNA HELIX. Nature, 372, 111 -113.
46. Mao, H.Y., White, S.A. and Williamson, J.R. (1999) A novel loop-loop recognition motif in the yeast ribosomal protein L30 autoregulatory RNA complex. Nature Structural Biology, 6, 1139-1147.
47. Battiste, J.L., Mao, H.Y., Rao, N.S., Tan, R.Y., Muhandiram, D.R., Kay, L.E., Frankel, A.D. and Williamson, J.R. (1996) alpha helix-RNA major groove recognition in an HIV-1 Rev peptide RRE RNA complex. Science, 273, 1547-1551.
48.Baugh,C.,Grate,D.and Wilson,C.(2000) 2.8 angstrom crystal structure of the malachite green aptamer.Journal of Molecular Biology,301,117-128.
49.Nikulin,A.,Serganov,A.,Ennifar,E.,Tishchenko,S.,Nevskaya,N.,Shepard,W.,Portier,C.,Garber,M.,Ehresmann,B.,Ehresmann,C.et al.(2000) Crystal structure of the S 15-rRNA complex.Nature Structural Biology,7,273-277.
50.Stoldt,M.,Wohnert,J.,Ohlenschlager,O.,Gorlach,M.and Brown,L.R.(1999)The NMR structure of the 5S rRNA E-domain-protein L25 complex shows preformed and induced recognition.Embo Journal,18,6508-6521.
51.Butcher,S.E.,Dieckmann,T.and Feigon,J.(1997) Solution structure ofa GAAA tetraloop receptor RNA.Embo Journal,16,7490-7499.
52.Rowsell,S.,Stonehouse,N.J.,Convery,M.A.,Adams,C.J.,Ellington,A.D.,Hirao,I.,Peabody,D.S.,Stockley,P.G.and Phillips,S.E.V.(1998) Crystal structures of a series of RNA aptamers complexed to the same protein target.Nature Structural Biology,5,970-975.
53.Kerwood,D.J.and Borer,P.N.(1996) Structure refinement for a 24-nucleotide RNA hairpin.Magnetic Resonance in Chemistry,34,S136-S146.
54.Smith,J.S.and Nikonowicz,E.P.(2000) Phosphorothioate substitution can substantially alter RNA conformation.Biochemistry,39,5642-5652.
55.Leulliot,N.,Baumruk,V.,Abdelkafi,M.,Turpin,P.Y.,Namane,A.,Gouyette,C.,Huynh-Dinh,T.and Ghomi,M.(1999) Unusual nucleotide conformations in GNRA and UNCG type tetraloop hairpins:evidence from Raman markers assignments.Nucleic Acids Research,27,1398-1404.
56.Saenger,W.(1984).Springer-Vedag,New York.
57.Perez,A.,Marchan,I.,Svozil,D.,Sponer,J.,Cheatham,T.E.,III,Laughton,C.A.and Orozco,M.(2007) Refinement of the AMBER Force Field for Nucleic Acids:Improving the Description of {alpha}/{gamma} Conformers.Biophysical Journal,92,3817-3829.