A fluctuating charge interaction potential function for alanine-water was constructed in the spirit of newly developed ABEEMax/MM（atom-bond electronegativity equalization method at the azc level fused into molecular ...A fluctuating charge interaction potential function for alanine-water was constructed in the spirit of newly developed ABEEMax/MM（atom-bond electronegativity equalization method at the azc level fused into molecular mechanics）. The properties of gaseous neutral alanine-（H20）n（n=l--7） clusters were systematically investigated by quantum mechanics（QM） and the constructed ABEEMax/MM potential, such as conformations, hydrogen bonds （H-bonds）, interaction energies, charge distributions, and so on. The results of ABEEM^rrc/MM model are in fair agreement with those of QM and available experimental data. For isolated alanine, compared with those of experi- mental structure, the average absolute deviations（AAD） of bond length and bond angle are 0.002 nm and 1.4~, re- spectively. For alanine-water clusters, the AAD of interaction energies and H-bond lengths are only 3.77 kJ/mol and 0.012 nm, respectively, compared to the results of MP2/aug-cc-pVDZ//MP2/6-31 I＋G＊＊ method. The ABEEMa charges fluctuate with the changing conformation of the system, and can accurately and reasonably reflect the inter- polarization between water and alanine. The presented alanine-water potential function may provide a basis for fur- ther simulations on related aqueous solutions ofbiomolecules.展开更多
Molecular dynamics simulation on BPTI (biovine pancreatic trypsin inhibitor) aqueous solution has been performed for the first time in terms of the atom-bond electronegativity equalization method fused with molecular ...Molecular dynamics simulation on BPTI (biovine pancreatic trypsin inhibitor) aqueous solution has been performed for the first time in terms of the atom-bond electronegativity equalization method fused with molecular mechanics (ABEEM/MM). The simulated parameters including ABEEM parameters and force field parameters have been tested. Some structural properties including root-mean-square deviations of atomic coordinates and radial distribution functions were studied by ABEEM/MM fluctuating charge method. The results demonstrate that this model can obtain reasonable structural properties compared with experimental crystal data. The radial distribution functions indicate that ABEEM/MM method can well embody the electrostatic polarizations between protein molecule and its surrounding solvent waters.展开更多
基金Supported by the National Natural Science Foundation of China（Nos.21133005, 20703022 and 21011120087） and the Project of Educational Bureau of Liaoning Province, China（No.2009T057）.
文摘A fluctuating charge interaction potential function for alanine-water was constructed in the spirit of newly developed ABEEMax/MM（atom-bond electronegativity equalization method at the azc level fused into molecular mechanics）. The properties of gaseous neutral alanine-（H20）n（n=l--7） clusters were systematically investigated by quantum mechanics（QM） and the constructed ABEEMax/MM potential, such as conformations, hydrogen bonds （H-bonds）, interaction energies, charge distributions, and so on. The results of ABEEM^rrc/MM model are in fair agreement with those of QM and available experimental data. For isolated alanine, compared with those of experi- mental structure, the average absolute deviations（AAD） of bond length and bond angle are 0.002 nm and 1.4~, re- spectively. For alanine-water clusters, the AAD of interaction energies and H-bond lengths are only 3.77 kJ/mol and 0.012 nm, respectively, compared to the results of MP2/aug-cc-pVDZ//MP2/6-31 I＋G＊＊ method. The ABEEMa charges fluctuate with the changing conformation of the system, and can accurately and reasonably reflect the inter- polarization between water and alanine. The presented alanine-water potential function may provide a basis for fur- ther simulations on related aqueous solutions ofbiomolecules.
基金the National Natural Science Foundation of China (Grant Nos. 20633050 and 20403007)
文摘Molecular dynamics simulation on BPTI (biovine pancreatic trypsin inhibitor) aqueous solution has been performed for the first time in terms of the atom-bond electronegativity equalization method fused with molecular mechanics (ABEEM/MM). The simulated parameters including ABEEM parameters and force field parameters have been tested. Some structural properties including root-mean-square deviations of atomic coordinates and radial distribution functions were studied by ABEEM/MM fluctuating charge method. The results demonstrate that this model can obtain reasonable structural properties compared with experimental crystal data. The radial distribution functions indicate that ABEEM/MM method can well embody the electrostatic polarizations between protein molecule and its surrounding solvent waters.
