The hydrogen bonding character between the BF4- and glycine was theoretically studied at the level of B3LYP/6-31＋G^＊, single point energies were performed at the level of B3LYP/6-311＋＋G^＊＊. The relevant geometri...The hydrogen bonding character between the BF4- and glycine was theoretically studied at the level of B3LYP/6-31＋G^＊, single point energies were performed at the level of B3LYP/6-311＋＋G^＊＊. The relevant geometrical characteristics, energy properties, as well as the characters of the intramolecular hydrogen bonds have been studied. Atoms in molecule theory topological analysis indicated the （3,-1） critical points for hydrogen bonds. In addition, the electron density and Laplacian were in the range suggested for the hydrogen bonds. Especially, the changes of atomic charge, hydrogen upon hydrogen bonds formation dipole moment, enegry as well as volume of the were systemitically discussed.展开更多
The structure and stability of the compounds MRg^(+)and MRg F(Rg=Ar,Kr,and Xe;M=Co,Rh,and Ir)were investigated using the B3 LYP,MP2,MP4(SDQ)and CCSD(T)methods.We reported the geometry,vibrational frequencies and therm...The structure and stability of the compounds MRg^(+)and MRg F(Rg=Ar,Kr,and Xe;M=Co,Rh,and Ir)were investigated using the B3 LYP,MP2,MP4(SDQ)and CCSD(T)methods.We reported the geometry,vibrational frequencies and thermodynamics properties of these compounds.A series of theoretical methods on the basis of wavefunction analysis,including natural bond orbitals,atoms in molecules,electron localization function,and energy decomposition analysis,were performed to explore bonding nature of the M-Rg and Rg-F bonds.These bonds are mainly noncovalent,the metal weakly interacts with Rg in MRg^(+),but their interaction is much stronger in MRg F.The neutral molecule MRg F can be well described by the Lewis structure[MRg]^(+)F^(-).展开更多
Reduced point charge models of amino acids are used to model Ubiquitin （PDB： 1UBQ）. They are designed （i） from local ex- tremum positions in charge density （CD） distribution functions built from the Poisson equ...Reduced point charge models of amino acids are used to model Ubiquitin （PDB： 1UBQ）. They are designed （i） from local ex- tremum positions in charge density （CD） distribution functions built from the Poisson equation applied to smoothed molecular electrostatic potential functions, or （ii） from local maximum positions in promolecular electron density distribution （ED） func- tions. Charge values are fitted versus all-atom Amber99 molecular electrostatic potentials. The program GROMACS is used to generate molecular dynamics trajectories of the protein, under various implementation schemes, solvation, and temperature conditions. Point charges that are not located on atoms are considered as virtual sites with a null mass and radius. The results illustrate that secondary structure is best preserved with the CD-based model at low temperatures and in vacuum. This indi- cates that local potential energy wells are consistent with the all-atom model. However, at room temperature, the structure is best conserved when point charges are forced to be located on atoms, due to a better description of the Coulomb l-4 energy terms. The ED-based model, generated at a lower resolution, led to the largest discrepancies versus the all-atom case. The CD-based model allows the formation of protein-water H-bonds with geometrical properties similar to the all-atom ones. Con- trarily, intra-molecular H-bonds are not well described. Structural, thermodynamical, and dynamical properties of proteins modelled with reduced point charge models are also significantly affected by the choice of the solvent force field.展开更多
文摘The hydrogen bonding character between the BF4- and glycine was theoretically studied at the level of B3LYP/6-31＋G^＊, single point energies were performed at the level of B3LYP/6-311＋＋G^＊＊. The relevant geometrical characteristics, energy properties, as well as the characters of the intramolecular hydrogen bonds have been studied. Atoms in molecule theory topological analysis indicated the （3,-1） critical points for hydrogen bonds. In addition, the electron density and Laplacian were in the range suggested for the hydrogen bonds. Especially, the changes of atomic charge, hydrogen upon hydrogen bonds formation dipole moment, enegry as well as volume of the were systemitically discussed.
文摘The structure and stability of the compounds MRg^(+)and MRg F(Rg=Ar,Kr,and Xe;M=Co,Rh,and Ir)were investigated using the B3 LYP,MP2,MP4(SDQ)and CCSD(T)methods.We reported the geometry,vibrational frequencies and thermodynamics properties of these compounds.A series of theoretical methods on the basis of wavefunction analysis,including natural bond orbitals,atoms in molecules,electron localization function,and energy decomposition analysis,were performed to explore bonding nature of the M-Rg and Rg-F bonds.These bonds are mainly noncovalent,the metal weakly interacts with Rg in MRg^(+),but their interaction is much stronger in MRg F.The neutral molecule MRg F can be well described by the Lewis structure[MRg]^(+)F^(-).
文摘Reduced point charge models of amino acids are used to model Ubiquitin （PDB： 1UBQ）. They are designed （i） from local ex- tremum positions in charge density （CD） distribution functions built from the Poisson equation applied to smoothed molecular electrostatic potential functions, or （ii） from local maximum positions in promolecular electron density distribution （ED） func- tions. Charge values are fitted versus all-atom Amber99 molecular electrostatic potentials. The program GROMACS is used to generate molecular dynamics trajectories of the protein, under various implementation schemes, solvation, and temperature conditions. Point charges that are not located on atoms are considered as virtual sites with a null mass and radius. The results illustrate that secondary structure is best preserved with the CD-based model at low temperatures and in vacuum. This indi- cates that local potential energy wells are consistent with the all-atom model. However, at room temperature, the structure is best conserved when point charges are forced to be located on atoms, due to a better description of the Coulomb l-4 energy terms. The ED-based model, generated at a lower resolution, led to the largest discrepancies versus the all-atom case. The CD-based model allows the formation of protein-water H-bonds with geometrical properties similar to the all-atom ones. Con- trarily, intra-molecular H-bonds are not well described. Structural, thermodynamical, and dynamical properties of proteins modelled with reduced point charge models are also significantly affected by the choice of the solvent force field.
