分子动力学模拟是研究包括RNA在内的生物大分子结构和功能的重要方法,但常规的显式溶剂模拟耗时较长,影响了其进一步应用。隐式溶剂模型通过用连续模型代替溶剂分子,能大大加速模拟速度,因此提高模拟效率。然而,现有的隐式溶剂模型都不...分子动力学模拟是研究包括RNA在内的生物大分子结构和功能的重要方法,但常规的显式溶剂模拟耗时较长,影响了其进一步应用。隐式溶剂模型通过用连续模型代替溶剂分子,能大大加速模拟速度,因此提高模拟效率。然而,现有的隐式溶剂模型都不能很好地描述核酸分子,尤其是RNA。在之前的研究中(已接收),我们提出了一个新的隐式溶剂模型,并分别测试了A型RNA双螺旋、28S r RNA和t RNA等多个系统,验证了该模型可以更好地计算隐式溶剂下的静电相互作用。由于上述系统均以稳定的结构作为起始,因此没有采集到大的构象变化。在本文中,我们将采用B型RNA双螺旋(B-RNA)作为测试系统来验证该模型是否能正确地采集到大尺度的构象转变过程。初步结果表明,在我们的模型下,B-RNA不仅能够正确地采集A型RNA双链构象,而且其搜索速度也比相应的显式模型快。展开更多
目的通过一组单线性梯度洗脱实验获取线性溶剂强度模型的参数值,为色谱图的预测提供所必须的参数值。方法首先,在实验中固定流动相组成的起始和结束值,通过改变梯度洗脱的时间,从而改变梯度的斜率(B)。测定溶质在这些梯度条件下的保留时...目的通过一组单线性梯度洗脱实验获取线性溶剂强度模型的参数值,为色谱图的预测提供所必须的参数值。方法首先,在实验中固定流动相组成的起始和结束值,通过改变梯度洗脱的时间,从而改变梯度的斜率(B)。测定溶质在这些梯度条件下的保留时间,计算其流出色谱柱时所对应的流动相组成(φR)。然后,将描述φR与B之间关系的数学公式对实验数据进行非线性拟合,从而获取线性溶剂强度模型的参数值。拟合基于Levenberg-Marquardt算法,通过Excel中的Visual Basic for Applications(VBA)语言编程实现。结果计算机程序的可靠性通过实验进行验证。以12种芳环化合物为分离的对象,以C18柱为固定相,含1%乙酸的甲醇-水溶液为流动相,应用所编写的程序对单线性梯度洗脱实验数据进行处理,获取溶剂强度模型的参数值。然后,根据所得到的参数值预测多线性梯度洗脱条件下的色谱图,得到的理论色谱图与实验色谱图吻合。结论所建立的方法可快速准确地获取线性溶剂强度模型的参数值,具有良好的实用价值。展开更多
在化工、能源、环境、食品和药物等工业设计过程中,真实混合物的可靠溶解度数据非常重要,不仅能丰富相平衡数据库,还能指导工艺设备设计和产品质量控制。本文介绍了烃-水体系相互溶解度的模型化研究,包括状态方程法、活度系数法和经验...在化工、能源、环境、食品和药物等工业设计过程中,真实混合物的可靠溶解度数据非常重要,不仅能丰富相平衡数据库,还能指导工艺设备设计和产品质量控制。本文介绍了烃-水体系相互溶解度的模型化研究,包括状态方程法、活度系数法和经验关联式,以及近年来发展起来的真实溶剂似导体屏蔽模型法(conductor-like screening model for real solvents,COSMO-RS)。状态方程法和活度系数法主要是通过选择非对称的混合规则以及引进描述水分子极性作用的参数,来改善对烃-水体系相互溶解度的计算精度。经验关联式主要是对实验数据的拟合,每种烃的参数不同。COSMO-RS模型根据密度泛函理论(即建立极化电荷密度的简单经验式)计算单个分子嵌入虚拟导体产生的作用,通过准确描述界面统计相互作用获得体系的热力学性质。因此,该方法对各种体系具有普适性。分析表明,COSMO-RS模型对烃-水体系相互溶解度的预测值与实验值吻合良好,可以补充某些难以通过实验获得的烃-水体系互溶度数据。最后总结和展望了烃-水体系相互溶解度模型化的未来发展方向。展开更多
Molecular structures of fourteen xanthine tautomers were calculated by using the B3LYP/6-311G**method both in the gas and aqueous phases with full geometry optimization.The Onsager solvation model was employed for aqu...Molecular structures of fourteen xanthine tautomers were calculated by using the B3LYP/6-311G**method both in the gas and aqueous phases with full geometry optimization.The Onsager solvation model was employed for aqueous solution calculations.The structures,total energy,standard enthalpy,standard entropy and standard free energy were obtained.The calculations showed that xanthine existing as the diketo form is the predominant isomer in the gas and aqueous phases.The dioxo-N（7）（H）isomer is more stable than the dioxo-N（9）（H）isomer in the gas and aqueous phases.The results are in good agreement with available experimental results.The entropy effect on the Gibbs free energy of xanthine base is very small and there is little significance for the tautomeric equilibria of the base.The enthalpic term is dominant in the determinatio of tautomeric equilibria.The free energy of solvation is well correlated with the dipole moments of xanthine tautomers.Additionally,origins of the solvent effects were examined by analyzing the changes of the dipole moments due to the change of a solvent polarity.展开更多
In order to explore the effect mechanism of solvent on the synthesis of the metal organic framework materials, the microscopic interaction between solvent and framework and the effects of N,N-dimethyl-formamide(DMF) o...In order to explore the effect mechanism of solvent on the synthesis of the metal organic framework materials, the microscopic interaction between solvent and framework and the effects of N,N-dimethyl-formamide(DMF) or N-methyl- 2-pyrrolidone(NMP) on solvothermal synthesis of [Zn4O(BDC)3]8 were investigated through a combined DFT and experimental study. XRD and SEM showed that the absorbability of NMP in the pore of [Zn4O(BDC)3]8 was weaker than that of DMF. The thermal decomposition temperature of [Zn4O(BDC)3]8 synthesized in DMF was higher than that in NMP according to TG and FT-IR. In addition, the nitrogen sorption isotherms indicated that NMP improved gas sorption property of [Zn4O(BDC)3]8. The COSMO optimized calculations indicated that the total energy of Zn4O(BDC)3 in NMP was higher than that in DMF, and compared with non-solvent system, the charge of zinc atoms decreased and the charge value was the smallest in NMP. Furthermore, the interaction of DMF, NMP or DEF in [Zn4O(BDC)3]8 crystal model was calculated by DFT method. The results suggested that NMP should be easier to be removed from pore of materials than DMF from the point of view of energy state. It can be concluded that NMP was a favorable solvent to synthesize [Zn4O(BDC)3]8 and the microscopic mechanism was that the binding force between Zn4O(BDC)3 and NMP molecule was weaker than DMF.展开更多
文摘分子动力学模拟是研究包括RNA在内的生物大分子结构和功能的重要方法,但常规的显式溶剂模拟耗时较长,影响了其进一步应用。隐式溶剂模型通过用连续模型代替溶剂分子,能大大加速模拟速度,因此提高模拟效率。然而,现有的隐式溶剂模型都不能很好地描述核酸分子,尤其是RNA。在之前的研究中(已接收),我们提出了一个新的隐式溶剂模型,并分别测试了A型RNA双螺旋、28S r RNA和t RNA等多个系统,验证了该模型可以更好地计算隐式溶剂下的静电相互作用。由于上述系统均以稳定的结构作为起始,因此没有采集到大的构象变化。在本文中,我们将采用B型RNA双螺旋(B-RNA)作为测试系统来验证该模型是否能正确地采集到大尺度的构象转变过程。初步结果表明,在我们的模型下,B-RNA不仅能够正确地采集A型RNA双链构象,而且其搜索速度也比相应的显式模型快。
文摘目的通过一组单线性梯度洗脱实验获取线性溶剂强度模型的参数值,为色谱图的预测提供所必须的参数值。方法首先,在实验中固定流动相组成的起始和结束值,通过改变梯度洗脱的时间,从而改变梯度的斜率(B)。测定溶质在这些梯度条件下的保留时间,计算其流出色谱柱时所对应的流动相组成(φR)。然后,将描述φR与B之间关系的数学公式对实验数据进行非线性拟合,从而获取线性溶剂强度模型的参数值。拟合基于Levenberg-Marquardt算法,通过Excel中的Visual Basic for Applications(VBA)语言编程实现。结果计算机程序的可靠性通过实验进行验证。以12种芳环化合物为分离的对象,以C18柱为固定相,含1%乙酸的甲醇-水溶液为流动相,应用所编写的程序对单线性梯度洗脱实验数据进行处理,获取溶剂强度模型的参数值。然后,根据所得到的参数值预测多线性梯度洗脱条件下的色谱图,得到的理论色谱图与实验色谱图吻合。结论所建立的方法可快速准确地获取线性溶剂强度模型的参数值,具有良好的实用价值。
文摘在化工、能源、环境、食品和药物等工业设计过程中,真实混合物的可靠溶解度数据非常重要,不仅能丰富相平衡数据库,还能指导工艺设备设计和产品质量控制。本文介绍了烃-水体系相互溶解度的模型化研究,包括状态方程法、活度系数法和经验关联式,以及近年来发展起来的真实溶剂似导体屏蔽模型法(conductor-like screening model for real solvents,COSMO-RS)。状态方程法和活度系数法主要是通过选择非对称的混合规则以及引进描述水分子极性作用的参数,来改善对烃-水体系相互溶解度的计算精度。经验关联式主要是对实验数据的拟合,每种烃的参数不同。COSMO-RS模型根据密度泛函理论(即建立极化电荷密度的简单经验式)计算单个分子嵌入虚拟导体产生的作用,通过准确描述界面统计相互作用获得体系的热力学性质。因此,该方法对各种体系具有普适性。分析表明,COSMO-RS模型对烃-水体系相互溶解度的预测值与实验值吻合良好,可以补充某些难以通过实验获得的烃-水体系互溶度数据。最后总结和展望了烃-水体系相互溶解度模型化的未来发展方向。
文摘Molecular structures of fourteen xanthine tautomers were calculated by using the B3LYP/6-311G**method both in the gas and aqueous phases with full geometry optimization.The Onsager solvation model was employed for aqueous solution calculations.The structures,total energy,standard enthalpy,standard entropy and standard free energy were obtained.The calculations showed that xanthine existing as the diketo form is the predominant isomer in the gas and aqueous phases.The dioxo-N（7）（H）isomer is more stable than the dioxo-N（9）（H）isomer in the gas and aqueous phases.The results are in good agreement with available experimental results.The entropy effect on the Gibbs free energy of xanthine base is very small and there is little significance for the tautomeric equilibria of the base.The enthalpic term is dominant in the determinatio of tautomeric equilibria.The free energy of solvation is well correlated with the dipole moments of xanthine tautomers.Additionally,origins of the solvent effects were examined by analyzing the changes of the dipole moments due to the change of a solvent polarity.
基金Project(51104185)supported by the National Natural Science Foundation of ChinaProject(2010QZZD003)supported by the Key Project of Central South University of Fundamental Research Funds for the Central Universities of China
文摘In order to explore the effect mechanism of solvent on the synthesis of the metal organic framework materials, the microscopic interaction between solvent and framework and the effects of N,N-dimethyl-formamide(DMF) or N-methyl- 2-pyrrolidone(NMP) on solvothermal synthesis of [Zn4O(BDC)3]8 were investigated through a combined DFT and experimental study. XRD and SEM showed that the absorbability of NMP in the pore of [Zn4O(BDC)3]8 was weaker than that of DMF. The thermal decomposition temperature of [Zn4O(BDC)3]8 synthesized in DMF was higher than that in NMP according to TG and FT-IR. In addition, the nitrogen sorption isotherms indicated that NMP improved gas sorption property of [Zn4O(BDC)3]8. The COSMO optimized calculations indicated that the total energy of Zn4O(BDC)3 in NMP was higher than that in DMF, and compared with non-solvent system, the charge of zinc atoms decreased and the charge value was the smallest in NMP. Furthermore, the interaction of DMF, NMP or DEF in [Zn4O(BDC)3]8 crystal model was calculated by DFT method. The results suggested that NMP should be easier to be removed from pore of materials than DMF from the point of view of energy state. It can be concluded that NMP was a favorable solvent to synthesize [Zn4O(BDC)3]8 and the microscopic mechanism was that the binding force between Zn4O(BDC)3 and NMP molecule was weaker than DMF.
基金supported by the National Key Research and Development Program of China(2018YFA0208600)the National Science Foundation of China(21773032,21972023,21533001,22022301,91545107,91745201)。
