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
By utilizing the classical turning point of the electron movement, we have defined and computed the mo-lecular intrinsic characteristic contour (MICC) via the com-bination of the ab initio quantum chemistry computatio...By utilizing the classical turning point of the electron movement, we have defined and computed the mo-lecular intrinsic characteristic contour (MICC) via the com-bination of the ab initio quantum chemistry computational method with the ionization potential measured by photo-electron spectroscopy experiment. In this paper, we calcu-lated the MICCs of several small organic molecules contain-ing oxygen atom for the first time. The three-dimensional pictures have been drawn, by performing a large number of calculations. The analysis on some characterized cross-sec-tions of the MICC can provide atomic spatial changing information in the process of forming a molecule.展开更多
Constrained molecular dynamics simulations have been used to investigate the LiCl and NaCl ionic association in water in terms of atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/M...Constrained molecular dynamics simulations have been used to investigate the LiCl and NaCl ionic association in water in terms of atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM). The simulations make use of the seven-site fluctuating charge and flexible ABEEM-7P water model, based on which an ion-water interaction potential has been constructed. The mean force and the potential of mean force for LiCl and NaCl in water, the charge distributions, as well as the structural and dynamical properties of contact ion pair dissociation have been investigated. The results are reasonable and informative. For LiCl ion pair in water, the solvent-separated ion pair configurations are more stable than contact ion pair configurations. The calculated PMF for NaCl in water indicates that contact ion pair and solvent-separated ion pair configurations are of comparable stability.展开更多
The potential acting on an electron within a molecule (PAEM) is formulated, and then calculated using the ab initio MELD program plus a separate calculation program in the RHF molecular orbital theory, finally the thr...The potential acting on an electron within a molecule (PAEM) is formulated, and then calculated using the ab initio MELD program plus a separate calculation program in the RHF molecular orbital theory, finally the three-dimensional graphs of the potentials have been drawn. We have systematically investigated this kind of the potentials for a series of the diatomic molecules, such as HF, HCl, HBr, LiF, LiCl, and so on. The three-dimensional graph can clearly display the variation of the potential felt by an electron within a molecule and get a deeper understanding of the electronic motion and chemical bonding within a molecule.展开更多
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.
文摘By utilizing the classical turning point of the electron movement, we have defined and computed the mo-lecular intrinsic characteristic contour (MICC) via the com-bination of the ab initio quantum chemistry computational method with the ionization potential measured by photo-electron spectroscopy experiment. In this paper, we calcu-lated the MICCs of several small organic molecules contain-ing oxygen atom for the first time. The three-dimensional pictures have been drawn, by performing a large number of calculations. The analysis on some characterized cross-sec-tions of the MICC can provide atomic spatial changing information in the process of forming a molecule.
基金Supported by the National Natural Science Foundation of China (Grant Nos. 20633050 and 20703022)
文摘Constrained molecular dynamics simulations have been used to investigate the LiCl and NaCl ionic association in water in terms of atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM). The simulations make use of the seven-site fluctuating charge and flexible ABEEM-7P water model, based on which an ion-water interaction potential has been constructed. The mean force and the potential of mean force for LiCl and NaCl in water, the charge distributions, as well as the structural and dynamical properties of contact ion pair dissociation have been investigated. The results are reasonable and informative. For LiCl ion pair in water, the solvent-separated ion pair configurations are more stable than contact ion pair configurations. The calculated PMF for NaCl in water indicates that contact ion pair and solvent-separated ion pair configurations are of comparable stability.
基金This work was supported by the National Natural Science Foundation of China (Grant No. 20073018).
文摘The potential acting on an electron within a molecule (PAEM) is formulated, and then calculated using the ab initio MELD program plus a separate calculation program in the RHF molecular orbital theory, finally the three-dimensional graphs of the potentials have been drawn. We have systematically investigated this kind of the potentials for a series of the diatomic molecules, such as HF, HCl, HBr, LiF, LiCl, and so on. The three-dimensional graph can clearly display the variation of the potential felt by an electron within a molecule and get a deeper understanding of the electronic motion and chemical bonding within a molecule.
