Under the method of density functional theory, the geometry structures, values of energy and population analysis of the combo of crown tetraalanylpeptide (C4-AIa) with ions (Xn) are calculated, based on the founda...Under the method of density functional theory, the geometry structures, values of energy and population analysis of the combo of crown tetraalanylpeptide (C4-AIa) with ions (Xn) are calculated, based on the foundation of former studies. It was found that the coronary structure changed little whether in C4-Ala or C4-Ala-Xn, and the electrons transferred between C4-Ala and Xn at the mean time. There were coordinate bonds between Xn+ and the nitrogen from -NH-, hydrogen bonds between Xa and the hydrogen from -NH-, and they became weaker when the radii of ions turned larger. Besides, the values of the single point bonding energy fluctuated gradually as a shape of saddle, but cations and anions located in opposite directions of the center of coronary structure when reach minimum, respectively.展开更多
Inhibition of the enzyme COMT (catechol-O-methyltransferase) is an important approach in the treatment of Parkinson's disease. A series of potent catechols for COMT may give insight to develop new ways of antiparki...Inhibition of the enzyme COMT (catechol-O-methyltransferase) is an important approach in the treatment of Parkinson's disease. A series of potent catechols for COMT may give insight to develop new ways of antiparkinson drug. COMT inhibitors represent a new class of antiparkinson drugs, when they are coadministered with levodopa. Our goal of research is to study the inhibition of catechol-O-methyltransferase by molecular modeling methods. Different molecular modeling tools are used to perform this work (molecular mechanics, molecular dynamics and molecular docking (molegro virtnaldocker)). The results obtained from this work, into which the inhibition of catechol-O-methyltransferase by molecular modeling methods was elucidated, allow us to conclude that different catechols presents a more optimised inhibition of catechol-O-methyltransferase. The results suggest reducing the severity of Parkinson's disease.展开更多
The production of chemicals from biomass is a very challenging process due to its diverse chemical composition. Lignin, cellulose and hemicellulose are the three main biopolymers of wood biomass, with cell walls &pla...The production of chemicals from biomass is a very challenging process due to its diverse chemical composition. Lignin, cellulose and hemicellulose are the three main biopolymers of wood biomass, with cell walls &plant origin. Lignin has been chosen for the present studies due to its range of different linkages and structures. The present work involved a computational study of the most dominant lignin dimers and their vibrational structures, based on the Density Functional Theory method. Full geometry optimization of the compartments used the StoBe code with cluster model and non-local functional (RPBE) approach. The calculations of the vibrational frequencies were performed with harmonic approximations as well as an anharmonicity fit in the Morse potential function, as implemented in the StoBe code. In the case oflignin, the calculations included three different precursors based on: coumaryl alcohol, coniferyl alcohol and sinapyl alcohol. To represent the cellulose and hemicellulose derivatives, selected aldopentoses and aldohexoses (arabinose, xylose, glucose, galactose, and mannose) were considered. Presented here are the theoretical investigations for a variety of biomass derived compounds, to give the possibility of obtaining a theoretical VBD (Vibrations Basis Database) for experimental spectra interpretation. Such a database could be further used in the preliminary composition assessment of biomass derived substrates, which will be discussed here in more detail.展开更多
Geometry optimization at the B3LYP/6-31++G* level of theory has been undertaken on clusters containing L-Met (L-methionine) or L-Cys (L-cysteine) surrounded by eight water molecules. The comparison of the struc...Geometry optimization at the B3LYP/6-31++G* level of theory has been undertaken on clusters containing L-Met (L-methionine) or L-Cys (L-cysteine) surrounded by eight water molecules. The comparison of the structural parameters of L-Met and L-Cys with X-ray experimental values is in good agreement within 4.8%. This result shows that the privileged positions of water molecules and the possible hydrogen bonding network formed around the backbone of both AAs (amino acids) are adequate. Subsequent calculations of the harmonic vibrational modes followed by a post-processing treatment enable us to assign the vibrational modes of L-Met and L-Cys surrounded explicitly by eight water molecules. The frequencies of the assigned modes are in good agreement with available IR (infra red) and Raman values within 5%.展开更多
Crown peptide is a kind of special conformation found on the homodetic cyclopeptide, regular array about the main chain containing imido groups, and the monolithic conformation presents coronary analogy to crown ether...Crown peptide is a kind of special conformation found on the homodetic cyclopeptide, regular array about the main chain containing imido groups, and the monolithic conformation presents coronary analogy to crown ether. There are high symmetrical ionophores belonging to Cn point group. The channels or apertures can form easily for recognizing certain ion or molecular, and also the function of intending dual-recognition and the ability for transporting as ionophores can be possessed. Under the method of density functional theory, the geometry structures, values energy and population analysis of the combo of crown tetraalanylpeptide (C4-Ala) with NO3- and SO4/2- are calculated, based on the foundation of former studies. Compared with the structure of C4-AIa without NO3- and SO4/2- it is found that the coronary shape changes little in the complex of C4-Ala-YOm/n-, and the electrons transfer between C4-AIa and YOm/n- at the mean time. There are hydrogen bond between oxygen of YOm/n- and the hydrogen from imine groups of C4-AIa, and they become weaker when the average charge density lessens.展开更多
文摘Under the method of density functional theory, the geometry structures, values of energy and population analysis of the combo of crown tetraalanylpeptide (C4-AIa) with ions (Xn) are calculated, based on the foundation of former studies. It was found that the coronary structure changed little whether in C4-Ala or C4-Ala-Xn, and the electrons transferred between C4-Ala and Xn at the mean time. There were coordinate bonds between Xn+ and the nitrogen from -NH-, hydrogen bonds between Xa and the hydrogen from -NH-, and they became weaker when the radii of ions turned larger. Besides, the values of the single point bonding energy fluctuated gradually as a shape of saddle, but cations and anions located in opposite directions of the center of coronary structure when reach minimum, respectively.
文摘Inhibition of the enzyme COMT (catechol-O-methyltransferase) is an important approach in the treatment of Parkinson's disease. A series of potent catechols for COMT may give insight to develop new ways of antiparkinson drug. COMT inhibitors represent a new class of antiparkinson drugs, when they are coadministered with levodopa. Our goal of research is to study the inhibition of catechol-O-methyltransferase by molecular modeling methods. Different molecular modeling tools are used to perform this work (molecular mechanics, molecular dynamics and molecular docking (molegro virtnaldocker)). The results obtained from this work, into which the inhibition of catechol-O-methyltransferase by molecular modeling methods was elucidated, allow us to conclude that different catechols presents a more optimised inhibition of catechol-O-methyltransferase. The results suggest reducing the severity of Parkinson's disease.
文摘The production of chemicals from biomass is a very challenging process due to its diverse chemical composition. Lignin, cellulose and hemicellulose are the three main biopolymers of wood biomass, with cell walls &plant origin. Lignin has been chosen for the present studies due to its range of different linkages and structures. The present work involved a computational study of the most dominant lignin dimers and their vibrational structures, based on the Density Functional Theory method. Full geometry optimization of the compartments used the StoBe code with cluster model and non-local functional (RPBE) approach. The calculations of the vibrational frequencies were performed with harmonic approximations as well as an anharmonicity fit in the Morse potential function, as implemented in the StoBe code. In the case oflignin, the calculations included three different precursors based on: coumaryl alcohol, coniferyl alcohol and sinapyl alcohol. To represent the cellulose and hemicellulose derivatives, selected aldopentoses and aldohexoses (arabinose, xylose, glucose, galactose, and mannose) were considered. Presented here are the theoretical investigations for a variety of biomass derived compounds, to give the possibility of obtaining a theoretical VBD (Vibrations Basis Database) for experimental spectra interpretation. Such a database could be further used in the preliminary composition assessment of biomass derived substrates, which will be discussed here in more detail.
文摘Geometry optimization at the B3LYP/6-31++G* level of theory has been undertaken on clusters containing L-Met (L-methionine) or L-Cys (L-cysteine) surrounded by eight water molecules. The comparison of the structural parameters of L-Met and L-Cys with X-ray experimental values is in good agreement within 4.8%. This result shows that the privileged positions of water molecules and the possible hydrogen bonding network formed around the backbone of both AAs (amino acids) are adequate. Subsequent calculations of the harmonic vibrational modes followed by a post-processing treatment enable us to assign the vibrational modes of L-Met and L-Cys surrounded explicitly by eight water molecules. The frequencies of the assigned modes are in good agreement with available IR (infra red) and Raman values within 5%.
文摘Crown peptide is a kind of special conformation found on the homodetic cyclopeptide, regular array about the main chain containing imido groups, and the monolithic conformation presents coronary analogy to crown ether. There are high symmetrical ionophores belonging to Cn point group. The channels or apertures can form easily for recognizing certain ion or molecular, and also the function of intending dual-recognition and the ability for transporting as ionophores can be possessed. Under the method of density functional theory, the geometry structures, values energy and population analysis of the combo of crown tetraalanylpeptide (C4-Ala) with NO3- and SO4/2- are calculated, based on the foundation of former studies. Compared with the structure of C4-AIa without NO3- and SO4/2- it is found that the coronary shape changes little in the complex of C4-Ala-YOm/n-, and the electrons transfer between C4-AIa and YOm/n- at the mean time. There are hydrogen bond between oxygen of YOm/n- and the hydrogen from imine groups of C4-AIa, and they become weaker when the average charge density lessens.