Theoretical Study On Both Physical Properties Of Spinel Ⅳ(B) Nitride And RNA GCAA Tetraloop

1.Density functional study on physical properties of of spinelâ…£(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-â…£nitrides.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.