The alcoholysis mechanism of 1,2-thiazetidine-1,1-dioxide with methanol, in which the relatively stable product is sulfonate ester, has been investigated by quantum chemical method. Our calculations indicate the react...The alcoholysis mechanism of 1,2-thiazetidine-1,1-dioxide with methanol, in which the relatively stable product is sulfonate ester, has been investigated by quantum chemical method. Our calculations indicate the reaction for alcoholysis of 1,2-thiazetidine-1,1-dioxide proceeds via two possible mechanisms: concerted and stepwise. In the stepwise mechanism, two possible reaction pathways can be followed while only one possible reaction pathway can be followed in the concerted mechanism.展开更多
In this paper, we evaluate semiempirical methods (AM1, PM3, and ZINDO), HF and DFT (B3LYP) in different basis sets to determine which method best describes the sign and magnitude of the geometrical parameters of artem...In this paper, we evaluate semiempirical methods (AM1, PM3, and ZINDO), HF and DFT (B3LYP) in different basis sets to determine which method best describes the sign and magnitude of the geometrical parameters of artemisinin in the region of the endoperoxide ring compared to crystallographic data. We also classify these methods using statistical analysis. The results of PCA were based on three main components, explaining 98.0539% of the total variance, for the geometrical parameters C3O13, O1O2C3, O13C12C12a, and O2C3O13C12. The DFT method (B3LYP) corresponded well with the experimental data in the hierarchical cluster analysis (HCA). The experimental and theoretical angles were analyzed by simple linear regression, and statistical parameters (correlation coefficients, significance, and predictability) were evaluated to determine the accuracy of the calculations. The statistical analysis exhibited a good correlation and high predictive power for the DFT (B3LYP) method in the 6-31G** basis set.展开更多
Molecular mechanics, molecular dynamics and semi empirical quantum chemical method have been used to study the geometric and electronic structures of six phosphonate ester as rare earth extractants. The results show ...Molecular mechanics, molecular dynamics and semi empirical quantum chemical method have been used to study the geometric and electronic structures of six phosphonate ester as rare earth extractants. The results show that the phosphorus atom exhibits sp 3 hybridization. The structures of the extractants are determined by the repulsion of the hydrocarbon groups. In the extractants that have two 2 ethyl hexyl groups, one 2 ethyl hexyl extends straight, and the other extends twistily. When the number of oxygen atom decreases, the negative charge of the phosphoryl oxygen atom increases, but the negative charge of oxygen atom and the positive charge of hydrogen of the hydroxyl group decreases, and the energies of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital(LUMO) increase. The energies of the occupied frontier orbitals are close to each other.展开更多
Quantum chemical parameters of 10 amino acids with D- and L-configurations were firstly calculated with semi-empirical AM1 method. Furthermore, the relationship between molecular structures of D-, L-amino acids and t...Quantum chemical parameters of 10 amino acids with D- and L-configurations were firstly calculated with semi-empirical AM1 method. Furthermore, the relationship between molecular structures of D-, L-amino acids and their sweetness were observed. The results show that upon different configurations of amino acids, the sweetness is relative with their formation heat, dipole moment, energy gap of frontier orbital and other parameters. The formation heats of the same amino acids possessing D- and L-configurations are different except glycine. The algebraic value of D-amino acid is generally larger than that of corresponding L-configuration with only one except of tyrosine. The dipole moment of D-amino acid is generally larger than that of corresponding L-amino acid except tyrosine and lysine. The lowest unoccupied orbital energy （ELUMO） of D-amino acid is higher than that of corresponding L-configuration except phenylalanine. △E of D-amino acid is larger than that of L-amino acid except histidine, phenylalanine and lysine. The larger gap will have advantage for its matching with frontier orbital energy of human protein acceptor, which strengthens the interaction between D-amino acid and sweet taste acceptor. Besides, the changing rules of these parameters are generally identical.展开更多
The interaction of molecular iodine with virus DNA nucleotide is studied by ab initio RHF/3-21G** method. Formation of the nucleoprotein complex of the HIV DNA, molecular iodine and the HIV-1 integrase co-factor is co...The interaction of molecular iodine with virus DNA nucleotide is studied by ab initio RHF/3-21G** method. Formation of the nucleoprotein complex of the HIV DNA, molecular iodine and the HIV-1 integrase co-factor is considered to cause the inhibition action of the integrase enzyme. Experimental data on the anti-HIV effect of the molecular iodine complex compounds and the results of calculations suggest that molecular iodine contained in iodine polymer complexes may be considered as a compound inhibiting the catalytic center of the integrase enzyme. Unlike the known integrase inhibitors, molecular iodine also changes the virus DNA structure and produces the N-I bond in the purine bases of adenosine and guanosine nucleotides.展开更多
The electronic structures of the species Ni(DMG)_2, (Ni(DMG)_2)^- and (Ni(DMG)_2)_(2-) have been studied by INDO quantum chemical method. The results have clearly shown that in the first stage of the electroreduction ...The electronic structures of the species Ni(DMG)_2, (Ni(DMG)_2)^- and (Ni(DMG)_2)_(2-) have been studied by INDO quantum chemical method. The results have clearly shown that in the first stage of the electroreduction of Ni(DMG)_2, one electron interacts with the d orbitals on the nickel atom, while in the further stage the second electron interacts with the p orbitals on the nitrogen atoms. It conforms with our electrochemical experimental studies which showed that not only Ni(Ⅱ) is reduced but also DMG is catalytically reduced during the reduction of Ni(DMG)_2.展开更多
The central importance of quantum chemistry is to obtain solutions of the Schr?dinger equation for the accurate determination of the properties of atomic and molecular systems that occurred from the calculation of wav...The central importance of quantum chemistry is to obtain solutions of the Schr?dinger equation for the accurate determination of the properties of atomic and molecular systems that occurred from the calculation of wave functions accurate for many diatomic and polyatomic molecules, using Self Consistent Field method (SCF). The application of quantum chemical methods in the study and planning of bioactive compounds has become a common practice nowadays. From the point of view of planning it is important to note, when it comes to the use of molecular modeling, a collective term that refers to methods and theoretical modeling and computational techniques to mimic the behavior of molecules, not intend to reach a bioactive molecule simply through the use of computer programs. The choice of method for energy minimization depends on factors related to the size of the molecule, parameters of availability, stored data and computational resources. Molecular models generated by the computer are the result of mathematical equations that estimate the positions and properties of the electrons and nuclei, the calculations exploit experimentally, the characteristics of a structure, providing a new perspective on the molecule. In this work we show that studies of Highest Occupied Molecular Orbital Energy (HOMO), Low Unoccupied Molecular Orbital Energy (LUMO) and Map of molecular electrostatic potential (MEP) using Hatree-Fock method with different basis sets (HF/3-21G*, HF/3-21G**, HF/6-31G, HF/6-31G*, HF/6-31G** and HF/6-311G), that are of great importance in modern chemistry, biochemistry, molecular biology, and other fields of knowledge of health sciences. In order to obtain a significant correlation, it is essential that the descriptors are used appropriately. Thus, the quantum chemical calculations are an attractive source of new molecular descriptors that can, in principle, express all the geometrical and electronic properties of molecules and their interactions with biological receptor.展开更多
Quantum-chemical calculation methods have been used to examine an influence of tautomeric equilibrium [Azo Hydrazo] on a structure of 1:2 chromium metal complex dyes called Gryfalan Navy Blue RL (CI 15 707, Acid...Quantum-chemical calculation methods have been used to examine an influence of tautomeric equilibrium [Azo Hydrazo] on a structure of 1:2 chromium metal complex dyes called Gryfalan Navy Blue RL (CI 15 707, Acid Blue 193) and Gryfalan Black RL (Acid Black 194). Chromatographic analysis indicates that synthesis yields a mixture of several dyes with different shades. Studies conducted to date have suggested that such dye complexes can constitute Drew-Pfitzner or Pfeiffer-Schetty structural isomers [1]. It is a know fact, that o-hydroxy-azo dyes exist in equilibrium of tautomeric azo and hydrazone forms. We decided to examine, whether color properties of examined metal-complex dyes can be influenced also by an azo-hydrazone equilibrium and what kind of influence on it has sulphonic groups present in molecules. Calculation and optimization of the geometrical structure were performed using the AM1 methods for monoazoo-hydroxy-azo dyesand ZINDO/1 for 1:2 chromium metal complex dyes. It was stated that monoazo dyes can create complexes in both forms: azo and hydrazone, because energy differences between each form of the metal complex dye are so small, that the monoazo dye can, in practice, create complexes in both the azo and the hydrazone form, with energy differences not exceeding about 4 - 11 kcal/mol. It is calculated that spatial structure changes with an angle of about 90° between two molecules of the dye, and angles of 10° - 20° between the naphthalene moieties. Similar electron density on the hydroxyl and ketone groups suggests that the mixture contains a dominant share of the azo form. The presence of an ionised sulphonic group was also found to affect on the tautomer equilibrium.展开更多
The geometric configurations of binuclear Zinc( complex Zn2[(n-Bu)2NCSS]4 and the ligand Na[(n-Bu)2 NCSS] have been optimized by B3LYP quantum chemical method. The electronic structures have been performed by density ...The geometric configurations of binuclear Zinc( complex Zn2[(n-Bu)2NCSS]4 and the ligand Na[(n-Bu)2 NCSS] have been optimized by B3LYP quantum chemical method. The electronic structures have been performed by density functional theory at B3LYP/6-31G* level. The electronic spectrums of the complex and ligand were calculated by ZINDO/S-CIS method. It is indicated from the calculation that: (1) The coordination effect of bridging ligand is bigger than that of chelating one, and the bridging ligands also translate more charge to Zn than the chelating one. (2) The calculated results about electronic spectrums are similarly to experimental measurement, and farther explain that absorption band at λ=267 nm of complex is assigned to two n → π* transitions :one arising from the bridging ligands and the another mainly arising from the chelating ligands;but absorption band at λ=236 nm of complex is assigned to π → π* transition which the electron mainly translates from the bridging ligands to the chelating ligands. (3) By consideration of delocalization and polar effects in coordination, the charge transfer from ligand to metal decreases the π-π and p-π conjugation effects in the chromophore group NCS2 and to increase the energy needed for the π → π* and n → π* transitions, and results in the absorption bands shifting towards the short wavelength direction.展开更多
文摘The alcoholysis mechanism of 1,2-thiazetidine-1,1-dioxide with methanol, in which the relatively stable product is sulfonate ester, has been investigated by quantum chemical method. Our calculations indicate the reaction for alcoholysis of 1,2-thiazetidine-1,1-dioxide proceeds via two possible mechanisms: concerted and stepwise. In the stepwise mechanism, two possible reaction pathways can be followed while only one possible reaction pathway can be followed in the concerted mechanism.
文摘In this paper, we evaluate semiempirical methods (AM1, PM3, and ZINDO), HF and DFT (B3LYP) in different basis sets to determine which method best describes the sign and magnitude of the geometrical parameters of artemisinin in the region of the endoperoxide ring compared to crystallographic data. We also classify these methods using statistical analysis. The results of PCA were based on three main components, explaining 98.0539% of the total variance, for the geometrical parameters C3O13, O1O2C3, O13C12C12a, and O2C3O13C12. The DFT method (B3LYP) corresponded well with the experimental data in the hierarchical cluster analysis (HCA). The experimental and theoretical angles were analyzed by simple linear regression, and statistical parameters (correlation coefficients, significance, and predictability) were evaluated to determine the accuracy of the calculations. The statistical analysis exhibited a good correlation and high predictive power for the DFT (B3LYP) method in the 6-31G** basis set.
文摘Molecular mechanics, molecular dynamics and semi empirical quantum chemical method have been used to study the geometric and electronic structures of six phosphonate ester as rare earth extractants. The results show that the phosphorus atom exhibits sp 3 hybridization. The structures of the extractants are determined by the repulsion of the hydrocarbon groups. In the extractants that have two 2 ethyl hexyl groups, one 2 ethyl hexyl extends straight, and the other extends twistily. When the number of oxygen atom decreases, the negative charge of the phosphoryl oxygen atom increases, but the negative charge of oxygen atom and the positive charge of hydrogen of the hydroxyl group decreases, and the energies of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital(LUMO) increase. The energies of the occupied frontier orbitals are close to each other.
文摘Quantum chemical parameters of 10 amino acids with D- and L-configurations were firstly calculated with semi-empirical AM1 method. Furthermore, the relationship between molecular structures of D-, L-amino acids and their sweetness were observed. The results show that upon different configurations of amino acids, the sweetness is relative with their formation heat, dipole moment, energy gap of frontier orbital and other parameters. The formation heats of the same amino acids possessing D- and L-configurations are different except glycine. The algebraic value of D-amino acid is generally larger than that of corresponding L-configuration with only one except of tyrosine. The dipole moment of D-amino acid is generally larger than that of corresponding L-amino acid except tyrosine and lysine. The lowest unoccupied orbital energy （ELUMO） of D-amino acid is higher than that of corresponding L-configuration except phenylalanine. △E of D-amino acid is larger than that of L-amino acid except histidine, phenylalanine and lysine. The larger gap will have advantage for its matching with frontier orbital energy of human protein acceptor, which strengthens the interaction between D-amino acid and sweet taste acceptor. Besides, the changing rules of these parameters are generally identical.
文摘The interaction of molecular iodine with virus DNA nucleotide is studied by ab initio RHF/3-21G** method. Formation of the nucleoprotein complex of the HIV DNA, molecular iodine and the HIV-1 integrase co-factor is considered to cause the inhibition action of the integrase enzyme. Experimental data on the anti-HIV effect of the molecular iodine complex compounds and the results of calculations suggest that molecular iodine contained in iodine polymer complexes may be considered as a compound inhibiting the catalytic center of the integrase enzyme. Unlike the known integrase inhibitors, molecular iodine also changes the virus DNA structure and produces the N-I bond in the purine bases of adenosine and guanosine nucleotides.
基金Project supported by the National Natural Science Foundstion of China.
文摘The electronic structures of the species Ni(DMG)_2, (Ni(DMG)_2)^- and (Ni(DMG)_2)_(2-) have been studied by INDO quantum chemical method. The results have clearly shown that in the first stage of the electroreduction of Ni(DMG)_2, one electron interacts with the d orbitals on the nickel atom, while in the further stage the second electron interacts with the p orbitals on the nitrogen atoms. It conforms with our electrochemical experimental studies which showed that not only Ni(Ⅱ) is reduced but also DMG is catalytically reduced during the reduction of Ni(DMG)_2.
文摘The central importance of quantum chemistry is to obtain solutions of the Schr?dinger equation for the accurate determination of the properties of atomic and molecular systems that occurred from the calculation of wave functions accurate for many diatomic and polyatomic molecules, using Self Consistent Field method (SCF). The application of quantum chemical methods in the study and planning of bioactive compounds has become a common practice nowadays. From the point of view of planning it is important to note, when it comes to the use of molecular modeling, a collective term that refers to methods and theoretical modeling and computational techniques to mimic the behavior of molecules, not intend to reach a bioactive molecule simply through the use of computer programs. The choice of method for energy minimization depends on factors related to the size of the molecule, parameters of availability, stored data and computational resources. Molecular models generated by the computer are the result of mathematical equations that estimate the positions and properties of the electrons and nuclei, the calculations exploit experimentally, the characteristics of a structure, providing a new perspective on the molecule. In this work we show that studies of Highest Occupied Molecular Orbital Energy (HOMO), Low Unoccupied Molecular Orbital Energy (LUMO) and Map of molecular electrostatic potential (MEP) using Hatree-Fock method with different basis sets (HF/3-21G*, HF/3-21G**, HF/6-31G, HF/6-31G*, HF/6-31G** and HF/6-311G), that are of great importance in modern chemistry, biochemistry, molecular biology, and other fields of knowledge of health sciences. In order to obtain a significant correlation, it is essential that the descriptors are used appropriately. Thus, the quantum chemical calculations are an attractive source of new molecular descriptors that can, in principle, express all the geometrical and electronic properties of molecules and their interactions with biological receptor.
文摘Quantum-chemical calculation methods have been used to examine an influence of tautomeric equilibrium [Azo Hydrazo] on a structure of 1:2 chromium metal complex dyes called Gryfalan Navy Blue RL (CI 15 707, Acid Blue 193) and Gryfalan Black RL (Acid Black 194). Chromatographic analysis indicates that synthesis yields a mixture of several dyes with different shades. Studies conducted to date have suggested that such dye complexes can constitute Drew-Pfitzner or Pfeiffer-Schetty structural isomers [1]. It is a know fact, that o-hydroxy-azo dyes exist in equilibrium of tautomeric azo and hydrazone forms. We decided to examine, whether color properties of examined metal-complex dyes can be influenced also by an azo-hydrazone equilibrium and what kind of influence on it has sulphonic groups present in molecules. Calculation and optimization of the geometrical structure were performed using the AM1 methods for monoazoo-hydroxy-azo dyesand ZINDO/1 for 1:2 chromium metal complex dyes. It was stated that monoazo dyes can create complexes in both forms: azo and hydrazone, because energy differences between each form of the metal complex dye are so small, that the monoazo dye can, in practice, create complexes in both the azo and the hydrazone form, with energy differences not exceeding about 4 - 11 kcal/mol. It is calculated that spatial structure changes with an angle of about 90° between two molecules of the dye, and angles of 10° - 20° between the naphthalene moieties. Similar electron density on the hydroxyl and ketone groups suggests that the mixture contains a dominant share of the azo form. The presence of an ionised sulphonic group was also found to affect on the tautomer equilibrium.
文摘The geometric configurations of binuclear Zinc( complex Zn2[(n-Bu)2NCSS]4 and the ligand Na[(n-Bu)2 NCSS] have been optimized by B3LYP quantum chemical method. The electronic structures have been performed by density functional theory at B3LYP/6-31G* level. The electronic spectrums of the complex and ligand were calculated by ZINDO/S-CIS method. It is indicated from the calculation that: (1) The coordination effect of bridging ligand is bigger than that of chelating one, and the bridging ligands also translate more charge to Zn than the chelating one. (2) The calculated results about electronic spectrums are similarly to experimental measurement, and farther explain that absorption band at λ=267 nm of complex is assigned to two n → π* transitions :one arising from the bridging ligands and the another mainly arising from the chelating ligands;but absorption band at λ=236 nm of complex is assigned to π → π* transition which the electron mainly translates from the bridging ligands to the chelating ligands. (3) By consideration of delocalization and polar effects in coordination, the charge transfer from ligand to metal decreases the π-π and p-π conjugation effects in the chromophore group NCS2 and to increase the energy needed for the π → π* and n → π* transitions, and results in the absorption bands shifting towards the short wavelength direction.
