We used ABEEMon（atom-bond electronegativity equalization method） polarizable force field（ABEEMσπ PFF） method combined with QM and molecular dynamics-free energy perturbation（MD-FEP） methods to investigatethe f...We used ABEEMon（atom-bond electronegativity equalization method） polarizable force field（ABEEMσπ PFF） method combined with QM and molecular dynamics-free energy perturbation（MD-FEP） methods to investigatethe function of water molecules in hydrolysis process of ImH[trans-Ru（Im）2Cl4]（ICR）. The activation free energiesobtained via MD-FEP calculation are in fair agreement with the experimental data. In addition, QM/MM（ABEEM）rationally describes the charge distributions and the electrostatic interaction between molecules. ABEEMσπ fluctua-ting charge model has the following good characteristics： （1） not only atomic charge regions but also σ,π bond andlone pair charge regions are explicitly represented for a molecule; （2） the region charges are geometry dependent andcalculated from time to time in the dynamic simulation without any iterative procedure so that its performance istime-saving compared with the Drude model and induced dipole model.展开更多
Modeling structural and thermodynamic prop- erties of nucleic acids has long been a challenge in the development of force fields. Polarizable force fields are a new generation of potential functions to take charge red...Modeling structural and thermodynamic prop- erties of nucleic acids has long been a challenge in the development of force fields. Polarizable force fields are a new generation of potential functions to take charge redistribution and induced dipole into account, and have been proved to be reliable to model small molecules, polypeptides and proteins, but their use on nucleic acids is still rather limited. In this article, the interactions between nucleic acids and a small molecule or ion were modeled by AMOEBAbio09, a modern polarizable force field, and conventional non-polarizable AMBER99sb and CHARMM36 force fields. The resulting intermolecular interaction energies were compared with those calculated by ab initio quantum mechanics methods. Although the test is not sufficient to prove the reliability of the polarizable force field, the results at least validate its capability in modeling energetics of static configurations, which is one basic component in force field parameterization.展开更多
The microscopic mechanisms of ion hydration and ion selectivity in biomolecular systems are long-standing research topics, in which the difficulty is how to reasonably and accurately describe the ion-water and ion-bio...The microscopic mechanisms of ion hydration and ion selectivity in biomolecular systems are long-standing research topics, in which the difficulty is how to reasonably and accurately describe the ion-water and ion-biomolecule interactions. This paper summarizes the development and applications of the atom-bond electronegativity equalization fluctuating charge force field model, ABEEM/MM, in the investigations of ion hydration, metalloproteins and ion-DNA bases systems. Based on high-level quantum chemistry calculations, the parameters were optimized and the molecular potential functions were constructed and applied to studies of structures, activities, energetics, and thermodynamic and kinetic properties of these ion-containing sys- tems. The results show that the performance of ABEEM]MM is generally better than that of the common force fields, and its accuracy can reach or approach that of the hlgh-level ab initio MP2 method. These studies provide a solid basis for further investigations of ion selectivity in biomolecular systems, the structures and properties of metalloproteins and other related ion-containing systems.展开更多
文摘We used ABEEMon（atom-bond electronegativity equalization method） polarizable force field（ABEEMσπ PFF） method combined with QM and molecular dynamics-free energy perturbation（MD-FEP） methods to investigatethe function of water molecules in hydrolysis process of ImH[trans-Ru（Im）2Cl4]（ICR）. The activation free energiesobtained via MD-FEP calculation are in fair agreement with the experimental data. In addition, QM/MM（ABEEM）rationally describes the charge distributions and the electrostatic interaction between molecules. ABEEMσπ fluctua-ting charge model has the following good characteristics： （1） not only atomic charge regions but also σ,π bond andlone pair charge regions are explicitly represented for a molecule; （2） the region charges are geometry dependent andcalculated from time to time in the dynamic simulation without any iterative procedure so that its performance istime-saving compared with the Drude model and induced dipole model.
基金This work was financially supported by the National Natural Science Foundation of China （Grant Nos. 21573217, 31370714, and 91430110）.
文摘Modeling structural and thermodynamic prop- erties of nucleic acids has long been a challenge in the development of force fields. Polarizable force fields are a new generation of potential functions to take charge redistribution and induced dipole into account, and have been proved to be reliable to model small molecules, polypeptides and proteins, but their use on nucleic acids is still rather limited. In this article, the interactions between nucleic acids and a small molecule or ion were modeled by AMOEBAbio09, a modern polarizable force field, and conventional non-polarizable AMBER99sb and CHARMM36 force fields. The resulting intermolecular interaction energies were compared with those calculated by ab initio quantum mechanics methods. Although the test is not sufficient to prove the reliability of the polarizable force field, the results at least validate its capability in modeling energetics of static configurations, which is one basic component in force field parameterization.
基金supported by the National Natural Science Foundation of China(21133005 and 20703022)
文摘The microscopic mechanisms of ion hydration and ion selectivity in biomolecular systems are long-standing research topics, in which the difficulty is how to reasonably and accurately describe the ion-water and ion-biomolecule interactions. This paper summarizes the development and applications of the atom-bond electronegativity equalization fluctuating charge force field model, ABEEM/MM, in the investigations of ion hydration, metalloproteins and ion-DNA bases systems. Based on high-level quantum chemistry calculations, the parameters were optimized and the molecular potential functions were constructed and applied to studies of structures, activities, energetics, and thermodynamic and kinetic properties of these ion-containing sys- tems. The results show that the performance of ABEEM]MM is generally better than that of the common force fields, and its accuracy can reach or approach that of the hlgh-level ab initio MP2 method. These studies provide a solid basis for further investigations of ion selectivity in biomolecular systems, the structures and properties of metalloproteins and other related ion-containing systems.
