Theoretical calculations were carried out using the DFT/B3LYP/6-31+G(d) methodology in an attempt to predict the preferred interaction site of a polyfunctional heterocyclic base 3-methyl-4- pyrimidone molecule with a ...Theoretical calculations were carried out using the DFT/B3LYP/6-31+G(d) methodology in an attempt to predict the preferred interaction site of a polyfunctional heterocyclic base 3-methyl-4- pyrimidone molecule with a series of proton donors of different acidic strength, i.e. water, methanol, phenol, 1-naphtol, 2,4,5 trichlorophenol, pentachlorophenol, picric acid and hydrogen chlordide. Computed H-bond interaction energies (ΔEc), internuclear and intermolecular distances r(O…H) and r(O…O), infrared frequency shifts Δv(C=O) and (Δv(OH) are proved to be reliable parameters for predicting the preferred interaction site of 3-methyl-4-pyrimidone. These computational data suggest that the O-H…O=C complex is preferred with water, methanol, phenol, 1-naphtol, 2,4,5 trichlorophenol and pentachlorophenol. However, for H-bonding with stronger acids such as picric acid or hydrochloric acid, the computational data suggest that the H-bonding occurs at the N1 ring atom of 3-methyl-4-pyrimidone. In the O-H…O=C com- plex, where the H-bond at the carbonyl O-atom can be oriented “anti” (Ha) and “syn” (Hb) with respect to the N3 atom, the same computational data suggest a higher stability of the “anti-O” compared to the “syn-O” orientation.展开更多
Benzothiazole (BTH) and its derivatives are organic molecules with biologic actions. Because of their many applications, they are produced on a massive scale and used in a number of environmental compartments. Their d...Benzothiazole (BTH) and its derivatives are organic molecules with biologic actions. Because of their many applications, they are produced on a massive scale and used in a number of environmental compartments. Their discharge into water produces environmental problems, exposing our environment to public health problems. A solution that can contribute to their deterioration is becoming a necessity. For this reason, a conceptual analysis of the reactivity of benzothiazole and four of its compounds was undertaken in order to investigate certain aspects of their biodegradability. A theoretical investigations of the compounds studied were conducted in the gas and water phases with the most widely used density functional theory method, Becke-3-Parameter-Lee-Yang-Parr (B3LYP) with 6-31G+ (d, p) basis. Reactivity study calculated global indices of reactivity revealed that 2-SCH3_BTH is the most reactive. Dipole moment values analysis reveals that 2-NH2_BTH is the most soluble in water, while the lipophilicity shows that 2-NH2_BTH is the most hydrophilic compound. Thermodynamic parameters values reflect that reactions are respectively exothermic and spontaneous. By analyzing an Electrostatic Molecular Potential (EMP) map, researchers can pinpoint reactive sites on a molecule and anticipate its reactivity. This assessment is further enhanced by incorporating global and local reactivity descriptors. Additionally, an exploration of frontier molecular orbitals offers valuable insights into the molecule’s charge transfer characteristics. Moreover, a combined examination of internal and external molecular interactions unveils hyperconjugative interactions arising from charge delocalization, as elucidated through natural bond orbital (NBO) analysis.展开更多
For the uracil-BX3 （X = F, Cl） systems, geometries and binding energies have been calculated by using the Lee-Young-Parr correlation functionals （B3LYP） method of density functional theory （DFT） and the second-o...For the uracil-BX3 （X = F, Cl） systems, geometries and binding energies have been calculated by using the Lee-Young-Parr correlation functionals （B3LYP） method of density functional theory （DFT） and the second-order Moller-Plesset （MP2） method of ab initio at the 6- 311 ＋G^＊ or 6-311 ＋＋G^＊ basis set. Four isomers were found for each system, and then the single-point energy evaluations were performed using the larger basis sets of （6-311 ＋G（2df, p） and aug-cc-pVDZ with DFF method. In the most stable isomer of uracil-BF3 or uracil-BCl3, the boron atom of BX3 （X = F, Cl） connects to the carbonyl oxygen O7 of uracil with a stabilization energy of -46.56 or -31.10 kJ/mol at the B3LYP/6-31 1＋G^＊ level （BSSE corrected）. The analyses for combining interaction between BX3 and uracil with the atom-in-molecule theory （AIM） and natural bond orbital method （NBO） have been performed. The results indicate that all isomers were formed with σ-p type interactions between uracil and BX3, in which the carbonyl oxygen offers its lone pair electrons to the empty p orbital of boron atom and the concomitances of charge transfer from uracil to BX3 occur. Moreover, there exists one or two hydrogen bonds in most isomers of uracil-BX3 system and these hydrogen bonds contribute to the stability of the complex systems. Frequency analysis suggests that the stretching vibration of BX3 undergoes a red shift in complexes. Uracil-BF3 complex is more stable than uracil-BCl3 although the distance of B-O is shorter in the latter. Besides, the conversion mechanisms between different isomers of uracil-BF3 have been obtained.展开更多
The ammonia adsorption on the GaN (0001) surface has been investigated by using DFT/B3LYP method combined with the cluster model approach. The dissociative adsorp- tion of NH2 and H is found thermodynamically favored ...The ammonia adsorption on the GaN (0001) surface has been investigated by using DFT/B3LYP method combined with the cluster model approach. The dissociative adsorp- tion of NH2 and H is found thermodynamically favored relative to the molecular NH3 adsorption by decreasing the total energy of 0.95 eV. The adsorption geometries of the molecular and dis- sociative NH3 are given in detail, among which the molecular NH3 bonds to the surface Ga with its lone electronic pair, and the N atom of NH2 adspecies forms the four-fold coordinated N by bridging two surface Ga atoms.展开更多
Geometry optimization and subsequent harmonic vibration calculations of prior synthesized （E）-3-（4-fluorophenyl）-N-[4-（phenyl-amino） quinazoline-7-yl] acrylamide were carried out by DFT/B3LYP method with both 6-...Geometry optimization and subsequent harmonic vibration calculations of prior synthesized （E）-3-（4-fluorophenyl）-N-[4-（phenyl-amino） quinazoline-7-yl] acrylamide were carried out by DFT/B3LYP method with both 6-31G and 6-311G basis sets.The Infrared （IR） spectrum of the title compound was recorded in the field of 400-4000 cm 1 and then assigned.The correlation analyses between the scaled theoretical vibration frequencies and the experimental ones indicate that there exist good linearity relationships since the correlation coefficients R 2 are larger than 0.999.The intramolecular interactions existed in the title molecule were confirmed by the Atoms in molecules （AIM） method,and their influences on the absorption frequency were also investigated.展开更多
The potential energy profile of the reaction between the atomic oxygen radical anion and acetonitrile has been mapped at the G3MP2B3 level of theory. Geometries of the reactants, products, intermediate complexes, and ...The potential energy profile of the reaction between the atomic oxygen radical anion and acetonitrile has been mapped at the G3MP2B3 level of theory. Geometries of the reactants, products, intermediate complexes, and transition states involved in this reaction have been optimized at the （U）B3LYP/6-31＋G（d,p） level, and then their accurate relative energies have been improved using the G3MP2B3 method. The potential energy profile is confirmed via intrinsic reaction coordinate calculations of transition states. Four possible production channels are examined respectively, as H＋ transfer, H-atom transfer, H2＋ transfer, and bi- molecular nucleophilic substitution （SN2） reaction pathways. Based on present calculations, the H2＋ transfer reaction is major among these four channels, which agrees with previous experimental conclusions.展开更多
1,2-Benzothiazine derivatives methyl 3-methoxy-4-oxo-3,4-dihydro-2H-benzo[e] [1,2]thiazine-3-carboxylate 1,1-dioxide（1） and methyl 2-ethyl-3-hydroxy-4-oxo-3,4-dihydro-2Hbenzo[e][1,2]thiazine-3-carboxylate 1,1-dioxid...1,2-Benzothiazine derivatives methyl 3-methoxy-4-oxo-3,4-dihydro-2H-benzo[e] [1,2]thiazine-3-carboxylate 1,1-dioxide（1） and methyl 2-ethyl-3-hydroxy-4-oxo-3,4-dihydro-2Hbenzo[e][1,2]thiazine-3-carboxylate 1,1-dioxide（2） were synthesized, and characterized by spectroscopic techniques; 1H-NMR and infrared（IR） spectroscopy. Crystals of 1 and 2 were grown by slow evaporation of methanol and ethyl acetate, respectively and their crystal structures were investigated by single-crystal X-ray diffraction analysis. Geometric properties were calculated by the B3 LYP method of density functional theory（DFT） at the 6-31G＋（d） basis set to compare with the experimental data. Simulated properties were found in strong agreement with the experimental ones. Intermolecular forces have also been modeled in order to investigate the strength of packing and strong hydrogen bonding was observed in both compounds 1 and 2. Electronic properties such as Ionization Potential（IP）, Electron Affinities（EA） and coefficients of the highest occupied molecular orbital（HOMO） and the lowest unoccupied molecular orbital（LUMO） of com- pounds 1 and 2 were simulated for the first time.展开更多
The SCR reaction mechanism of NO with C3H6catalyzed by CuO was studied by the method of Density Functional Theory(DFT)at the B3LYP/LanL2DZ levels.The optimized geometries of the stationary points on the potential surf...The SCR reaction mechanism of NO with C3H6catalyzed by CuO was studied by the method of Density Functional Theory(DFT)at the B3LYP/LanL2DZ levels.The optimized geometries of the stationary points on the potential surface were obtained and the transition state was confirmed by IRC and vibration analysis.The activation energy was calculated being 34.26 kJ/mol.It was shown that propylene reacted firstly with Cu forming intermediate,and then nitrogen monoxide immediately reacted with the intermediate to be reduced.It was proved to be a direct interaction 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
文摘Theoretical calculations were carried out using the DFT/B3LYP/6-31+G(d) methodology in an attempt to predict the preferred interaction site of a polyfunctional heterocyclic base 3-methyl-4- pyrimidone molecule with a series of proton donors of different acidic strength, i.e. water, methanol, phenol, 1-naphtol, 2,4,5 trichlorophenol, pentachlorophenol, picric acid and hydrogen chlordide. Computed H-bond interaction energies (ΔEc), internuclear and intermolecular distances r(O…H) and r(O…O), infrared frequency shifts Δv(C=O) and (Δv(OH) are proved to be reliable parameters for predicting the preferred interaction site of 3-methyl-4-pyrimidone. These computational data suggest that the O-H…O=C complex is preferred with water, methanol, phenol, 1-naphtol, 2,4,5 trichlorophenol and pentachlorophenol. However, for H-bonding with stronger acids such as picric acid or hydrochloric acid, the computational data suggest that the H-bonding occurs at the N1 ring atom of 3-methyl-4-pyrimidone. In the O-H…O=C com- plex, where the H-bond at the carbonyl O-atom can be oriented “anti” (Ha) and “syn” (Hb) with respect to the N3 atom, the same computational data suggest a higher stability of the “anti-O” compared to the “syn-O” orientation.
文摘Benzothiazole (BTH) and its derivatives are organic molecules with biologic actions. Because of their many applications, they are produced on a massive scale and used in a number of environmental compartments. Their discharge into water produces environmental problems, exposing our environment to public health problems. A solution that can contribute to their deterioration is becoming a necessity. For this reason, a conceptual analysis of the reactivity of benzothiazole and four of its compounds was undertaken in order to investigate certain aspects of their biodegradability. A theoretical investigations of the compounds studied were conducted in the gas and water phases with the most widely used density functional theory method, Becke-3-Parameter-Lee-Yang-Parr (B3LYP) with 6-31G+ (d, p) basis. Reactivity study calculated global indices of reactivity revealed that 2-SCH3_BTH is the most reactive. Dipole moment values analysis reveals that 2-NH2_BTH is the most soluble in water, while the lipophilicity shows that 2-NH2_BTH is the most hydrophilic compound. Thermodynamic parameters values reflect that reactions are respectively exothermic and spontaneous. By analyzing an Electrostatic Molecular Potential (EMP) map, researchers can pinpoint reactive sites on a molecule and anticipate its reactivity. This assessment is further enhanced by incorporating global and local reactivity descriptors. Additionally, an exploration of frontier molecular orbitals offers valuable insights into the molecule’s charge transfer characteristics. Moreover, a combined examination of internal and external molecular interactions unveils hyperconjugative interactions arising from charge delocalization, as elucidated through natural bond orbital (NBO) analysis.
基金This work was supported by the National Natural Science Foundation of China (No. 20171031)
文摘For the uracil-BX3 （X = F, Cl） systems, geometries and binding energies have been calculated by using the Lee-Young-Parr correlation functionals （B3LYP） method of density functional theory （DFT） and the second-order Moller-Plesset （MP2） method of ab initio at the 6- 311 ＋G^＊ or 6-311 ＋＋G^＊ basis set. Four isomers were found for each system, and then the single-point energy evaluations were performed using the larger basis sets of （6-311 ＋G（2df, p） and aug-cc-pVDZ with DFF method. In the most stable isomer of uracil-BF3 or uracil-BCl3, the boron atom of BX3 （X = F, Cl） connects to the carbonyl oxygen O7 of uracil with a stabilization energy of -46.56 or -31.10 kJ/mol at the B3LYP/6-31 1＋G^＊ level （BSSE corrected）. The analyses for combining interaction between BX3 and uracil with the atom-in-molecule theory （AIM） and natural bond orbital method （NBO） have been performed. The results indicate that all isomers were formed with σ-p type interactions between uracil and BX3, in which the carbonyl oxygen offers its lone pair electrons to the empty p orbital of boron atom and the concomitances of charge transfer from uracil to BX3 occur. Moreover, there exists one or two hydrogen bonds in most isomers of uracil-BX3 system and these hydrogen bonds contribute to the stability of the complex systems. Frequency analysis suggests that the stretching vibration of BX3 undergoes a red shift in complexes. Uracil-BF3 complex is more stable than uracil-BCl3 although the distance of B-O is shorter in the latter. Besides, the conversion mechanisms between different isomers of uracil-BF3 have been obtained.
基金Supported by the National Natural Science Foundation of China (202730313)
文摘The ammonia adsorption on the GaN (0001) surface has been investigated by using DFT/B3LYP method combined with the cluster model approach. The dissociative adsorp- tion of NH2 and H is found thermodynamically favored relative to the molecular NH3 adsorption by decreasing the total energy of 0.95 eV. The adsorption geometries of the molecular and dis- sociative NH3 are given in detail, among which the molecular NH3 bonds to the surface Ga with its lone electronic pair, and the N atom of NH2 adspecies forms the four-fold coordinated N by bridging two surface Ga atoms.
文摘Geometry optimization and subsequent harmonic vibration calculations of prior synthesized （E）-3-（4-fluorophenyl）-N-[4-（phenyl-amino） quinazoline-7-yl] acrylamide were carried out by DFT/B3LYP method with both 6-31G and 6-311G basis sets.The Infrared （IR） spectrum of the title compound was recorded in the field of 400-4000 cm 1 and then assigned.The correlation analyses between the scaled theoretical vibration frequencies and the experimental ones indicate that there exist good linearity relationships since the correlation coefficients R 2 are larger than 0.999.The intramolecular interactions existed in the title molecule were confirmed by the Atoms in molecules （AIM） method,and their influences on the absorption frequency were also investigated.
文摘The potential energy profile of the reaction between the atomic oxygen radical anion and acetonitrile has been mapped at the G3MP2B3 level of theory. Geometries of the reactants, products, intermediate complexes, and transition states involved in this reaction have been optimized at the （U）B3LYP/6-31＋G（d,p） level, and then their accurate relative energies have been improved using the G3MP2B3 method. The potential energy profile is confirmed via intrinsic reaction coordinate calculations of transition states. Four possible production channels are examined respectively, as H＋ transfer, H-atom transfer, H2＋ transfer, and bi- molecular nucleophilic substitution （SN2） reaction pathways. Based on present calculations, the H2＋ transfer reaction is major among these four channels, which agrees with previous experimental conclusions.
基金funded by the Saudi Basic Industries Corporation(SABIC) and the Deanship of Scientific Research(DSR),King Abdulaziz University,Jeddah,under grant no.(MS/15/396/1434)
文摘1,2-Benzothiazine derivatives methyl 3-methoxy-4-oxo-3,4-dihydro-2H-benzo[e] [1,2]thiazine-3-carboxylate 1,1-dioxide（1） and methyl 2-ethyl-3-hydroxy-4-oxo-3,4-dihydro-2Hbenzo[e][1,2]thiazine-3-carboxylate 1,1-dioxide（2） were synthesized, and characterized by spectroscopic techniques; 1H-NMR and infrared（IR） spectroscopy. Crystals of 1 and 2 were grown by slow evaporation of methanol and ethyl acetate, respectively and their crystal structures were investigated by single-crystal X-ray diffraction analysis. Geometric properties were calculated by the B3 LYP method of density functional theory（DFT） at the 6-31G＋（d） basis set to compare with the experimental data. Simulated properties were found in strong agreement with the experimental ones. Intermolecular forces have also been modeled in order to investigate the strength of packing and strong hydrogen bonding was observed in both compounds 1 and 2. Electronic properties such as Ionization Potential（IP）, Electron Affinities（EA） and coefficients of the highest occupied molecular orbital（HOMO） and the lowest unoccupied molecular orbital（LUMO） of com- pounds 1 and 2 were simulated for the first time.
基金Sponsored by the Education Department of Heilongjiang Province(Grant No.11511117).
文摘The SCR reaction mechanism of NO with C3H6catalyzed by CuO was studied by the method of Density Functional Theory(DFT)at the B3LYP/LanL2DZ levels.The optimized geometries of the stationary points on the potential surface were obtained and the transition state was confirmed by IRC and vibration analysis.The activation energy was calculated being 34.26 kJ/mol.It was shown that propylene reacted firstly with Cu forming intermediate,and then nitrogen monoxide immediately reacted with the intermediate to be reduced.It was proved to be a direct interaction 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.
