Myoglobin has important biological functions in storing and transporting small diatomic molecules in human body. Two possible orientations of carbon monoxide （CO） in the heme distal pocket （named as BI and B2 state...Myoglobin has important biological functions in storing and transporting small diatomic molecules in human body. Two possible orientations of carbon monoxide （CO） in the heme distal pocket （named as BI and B2 states） of myoglobin have been experimentally indicated. In this study, ab initio quantum mechanics/molecular mechanics （QM/MM） molecular dynamics simulation of CO in myoglobin was carried out to investigate the two possible B states. Our results demonstrate that the B1 and B2 states correspond to Fe... CO （with carbon atom closer to iron center of heme） and Fe... OC （with oxygen atom closer to Fe）, by comparing with the experimental infrared spectrum. QM electrostatic polarization effect on CO brought from the protein and solvent environment is the main driving force, which anchors CO in two distinctive orientations and hinders its rotation. The calculated vibrational frequency shift between the state B1 and B2 is 13.1 cm-1, which is in good agreement with experimental value of 11.5 cm-1. This study also shows that the electric field produced by the solvent plays an important role in assisting protein functions by exerting directional electric field at the active site of the protein, From residue-based electric field decomposition, several residues were found to have most contributions to the total electric field at the CO center, including a few charged residues and three adjacent uncharged polar residues （namely, HIS64, ILE107, and PHE43）. This study provides new physical insights on rational design of enzyme with higher electric field at the active site.展开更多
In this paper, the effective pyroelectric coefficient and polarization offset of the compositionally step-like graded multilayer ferroelectric structures have been studied by use of the first-principles approach. It i...In this paper, the effective pyroelectric coefficient and polarization offset of the compositionally step-like graded multilayer ferroelectric structures have been studied by use of the first-principles approach. It is exhibited that the dielectric gradient has a nontrivial influence on the effective pyroelectric coefficient, but has a little influence on the polarization offset; and the polarization gradient plays an important role in the abnormal hysteresis loop phenomenon of the co.mpositionally step-like graded ferroelectric structures. Moreover, the origin of the polarization offset is explored,which can be attributed to the polarization gradient in the compositionally step-like graded structure.展开更多
The knowledge of the hyperpolarizabilities of atoms and ions is helpful for the analysis of the high order effects of the frequency shifts in precision spectroscopy experiments. Liu et al. [Phys. Rev. Lett. 114, 2230...The knowledge of the hyperpolarizabilities of atoms and ions is helpful for the analysis of the high order effects of the frequency shifts in precision spectroscopy experiments. Liu et al. [Phys. Rev. Lett. 114, 223001 （2015）] proposed to establish all-optical trapped ion clocks using laser at the magic wavelength for clock transition. To evaluate the high-order frequency shifts in this new scheme of optical clocks, hyperpolarizabilities are needed, but absent. Using the finite field method based on the B-spline basis set and model potentials, we calculated the electric-field-dependent energy shifts of the ground and low-lying excited states in Be＋, Mg＋, and Ca＋ in the field strength range of 0.0-6×10-5 a.u.. The scalar and tensor polarizabilities （α0, α2） and hyperpolarizabilities （Y0,Y2, 74） were deduced. The results of the hyperpolarizabilities for Be＋ showed good agreement with the values in literature, implying that the present method can be applied for the effective estimation of the atomic hyperpolarizabilities, which are rarely reported but needed in experiments. The feasibility of optical trapping of Ca＋ is discussed, and the contributions of hyperpolarizabilities to the transition frequency shift for Ca＋ in the optical dipole trap are estimated using quasi-electrostatic approximation.展开更多
文摘Myoglobin has important biological functions in storing and transporting small diatomic molecules in human body. Two possible orientations of carbon monoxide （CO） in the heme distal pocket （named as BI and B2 states） of myoglobin have been experimentally indicated. In this study, ab initio quantum mechanics/molecular mechanics （QM/MM） molecular dynamics simulation of CO in myoglobin was carried out to investigate the two possible B states. Our results demonstrate that the B1 and B2 states correspond to Fe... CO （with carbon atom closer to iron center of heme） and Fe... OC （with oxygen atom closer to Fe）, by comparing with the experimental infrared spectrum. QM electrostatic polarization effect on CO brought from the protein and solvent environment is the main driving force, which anchors CO in two distinctive orientations and hinders its rotation. The calculated vibrational frequency shift between the state B1 and B2 is 13.1 cm-1, which is in good agreement with experimental value of 11.5 cm-1. This study also shows that the electric field produced by the solvent plays an important role in assisting protein functions by exerting directional electric field at the active site of the protein, From residue-based electric field decomposition, several residues were found to have most contributions to the total electric field at the CO center, including a few charged residues and three adjacent uncharged polar residues （namely, HIS64, ILE107, and PHE43）. This study provides new physical insights on rational design of enzyme with higher electric field at the active site.
文摘In this paper, the effective pyroelectric coefficient and polarization offset of the compositionally step-like graded multilayer ferroelectric structures have been studied by use of the first-principles approach. It is exhibited that the dielectric gradient has a nontrivial influence on the effective pyroelectric coefficient, but has a little influence on the polarization offset; and the polarization gradient plays an important role in the abnormal hysteresis loop phenomenon of the co.mpositionally step-like graded ferroelectric structures. Moreover, the origin of the polarization offset is explored,which can be attributed to the polarization gradient in the compositionally step-like graded structure.
基金supported by the National Natural Science Foundation of China (Grant No. 91536102)the National Basic Research Program of China (Grant No. 2012CB821305)
文摘The knowledge of the hyperpolarizabilities of atoms and ions is helpful for the analysis of the high order effects of the frequency shifts in precision spectroscopy experiments. Liu et al. [Phys. Rev. Lett. 114, 223001 （2015）] proposed to establish all-optical trapped ion clocks using laser at the magic wavelength for clock transition. To evaluate the high-order frequency shifts in this new scheme of optical clocks, hyperpolarizabilities are needed, but absent. Using the finite field method based on the B-spline basis set and model potentials, we calculated the electric-field-dependent energy shifts of the ground and low-lying excited states in Be＋, Mg＋, and Ca＋ in the field strength range of 0.0-6×10-5 a.u.. The scalar and tensor polarizabilities （α0, α2） and hyperpolarizabilities （Y0,Y2, 74） were deduced. The results of the hyperpolarizabilities for Be＋ showed good agreement with the values in literature, implying that the present method can be applied for the effective estimation of the atomic hyperpolarizabilities, which are rarely reported but needed in experiments. The feasibility of optical trapping of Ca＋ is discussed, and the contributions of hyperpolarizabilities to the transition frequency shift for Ca＋ in the optical dipole trap are estimated using quasi-electrostatic approximation.
