Using molecular mechanics method,values of the heat of formation (HF) of different conformations,of perylenequinonoid photosensitizes hypocrellin A (HA) and hypocrellin B (HB) were calculated and the variance of HF af...Using molecular mechanics method,values of the heat of formation (HF) of different conformations,of perylenequinonoid photosensitizes hypocrellin A (HA) and hypocrellin B (HB) were calculated and the variance of HF after phenolic protons' dissociation were calculated as well The following was found:(i) The HF values of lour conformational isomers of HA and HB are similar to each other,so the four isomcrs can transform to each other room temperature,(ii) There exists the difference between the ability of dissociation of phenolic protons of HA and that of HB,the former is higher than the latter (iii) There exist two intramolecular hydrogen bonds in HA and HB The bond energy is approximately 8 kJ/mol and the energy of conformation Ⅰ is lower than that of conformationⅡ The bond energy of HA is lower than that of HB.(iv) There exists a low energy snot when phenolic hydroxyl bond twists 180° from the position where hydrogen bond is formed,which suggests that this kind of conformation probably exists,(v) The phenolic hydrogen of HBMC forms hydrogen bond with the neighbouring nitrogen,which is its striticture basis of possessing photosensitizing activity.展开更多
The phase sensitive NOESY spectrum of oridonin was treated using Full Relaxation Matrix Analysis(FRMA) approach, and the cross relaxation rates of proton pairs were obtained by diagonalizing the NOE matrix of oridonin...The phase sensitive NOESY spectrum of oridonin was treated using Full Relaxation Matrix Analysis(FRMA) approach, and the cross relaxation rates of proton pairs were obtained by diagonalizing the NOE matrix of oridonin. The inter proton distances were calculated according to 1/r6 ij ∝σij. The three-dimensional structure of oridonin in solution was calculated by the combination of WUPH, WUPH-S method with molecular mechanics minimization on the basis of NMR experiment.展开更多
A bistable[2]rotaxane with a conformation-adaptive macrocycle bearing a 9,14-diphenyl-9,14-dihydrodibenzo[a,c]phenazine(DPAC)unit was synthesized,which could be utilized to optical probe the molecular shuttling motion...A bistable[2]rotaxane with a conformation-adaptive macrocycle bearing a 9,14-diphenyl-9,14-dihydrodibenzo[a,c]phenazine(DPAC)unit was synthesized,which could be utilized to optical probe the molecular shuttling motion of the functionalized rotaxane system.The UV-vis,^(1) H NMR and PL spectroscopic data clearly demonstrated that the DPAC ring was interlocked onto the thread and the fluorescence intensity of the DPAC unit in the macrocycle was effectively regulated by the location change of the macrocycle along the thread under acid/base stimulation,which was attributed to the modulation of the intramolecular photo-induced electron transfer between the DPAC unit and the methyltriazole(MTA)unit.This bistable rotaxane system containing a conformation-adaptive fluorophore unit in the macrocycle moiety opens an alternative way to design functional bistable mechanically interlocked molecules.展开更多
Transthyretin（TTR）, as a tetrameric protein, functions as a neuroprotector. The native TTR homotetramer dissociates into dimers and monomers. Dimers and monomers self-assemble into amyloid fibrils, and this process ...Transthyretin（TTR）, as a tetrameric protein, functions as a neuroprotector. The native TTR homotetramer dissociates into dimers and monomers. Dimers and monomers self-assemble into amyloid fibrils, and this process can lead to some diseases. Native TTR homotetramer is a widely accepted model for TTR amyloid formation. In this study, simulations using molecular dynamics（MD） and steered MD（SMD） were performed to explore the mechanisms for glabridin（Glab）, a specific inhibitor for TTR binding, for V30A mutant and wild-type（WT） TTR. MD simulation results indicate that, compared with Glab binding to WT and V30A mutant, the WT TTR could lead to the collapse of β-strands from Ser52 to His56 at chain A. This phenomenon facilitated the easy dissociation of chains A and C. Calculations of the binding free energy between the two chains showed that the V30A-Glab TTR complex displayed a lower binding energy than other systems（WT TTR and WT-Glab TTR）. Then, SMD simulation was performed to ex- plore the unbinding pathway for Glab through the WT and V30A mutant TTR. The results show that Lysl 5（chain A） produced a hydrogen bond with Glab at the force peak via the WT TTR tunnel. Meanwhile, in the V30A TTR mutant, the hydrogen bond between Lysl 5（chain A） and Glab was broken at the force peak. This condition was beneficial for Glab to be taken off from the protein. Our theoretical results will be useful in designing a new specific inhibitor of TTR protein to control the TTR homotetramer dissociation.展开更多
The compound trifluoroiodomethane can be activated to react with the electron donor, 1,4-dilithiotetraphenyl butadiene, by means of electron transfer catalysis (ETC). The structure of the product, 1,3-difluorotetraphe...The compound trifluoroiodomethane can be activated to react with the electron donor, 1,4-dilithiotetraphenyl butadiene, by means of electron transfer catalysis (ETC). The structure of the product, 1,3-difluorotetraphenyl, benzene (1), was determined by MS, NMR, and X-ray single crystal diffraction. The conformations of compound 1 and its derivatives were analysized by molecular mechanics.展开更多
There is a growing interest in the study of structures and properties of biomolecules in gas phase. Applications of force fields are highly desirable for the computational efficiency of the gas phase study. To help th...There is a growing interest in the study of structures and properties of biomolecules in gas phase. Applications of force fields are highly desirable for the computational efficiency of the gas phase study. To help the selection of force fields, the performances of five repre- sentative force fields for gaseous neutral, protonated, deprotonated and capped amino acids are systematically examined and compared. The tested properties include relative conforma- tional energies, energy differences between cis and trans structures, the number and strength of predicted hydrogen bonds, and the quality of the optimized structures. The results of BHandHLYP/6-311＋＋G（d,p） are used as the references. GROMOS53A6 and ENCADS are found to perform poorly for gaseous biomoleeules, while the performance of AMBER99SB, CHARMM27 and OPLSAA/L are comparable when applicable. Considering the general availability of the force field parameters, CHARMM27 is the most recommended, followed by OPLSAA/L, for the study of biomolecules in gas phase展开更多
基金Project supported by the National Natural Science Foundation of China
文摘Using molecular mechanics method,values of the heat of formation (HF) of different conformations,of perylenequinonoid photosensitizes hypocrellin A (HA) and hypocrellin B (HB) were calculated and the variance of HF after phenolic protons' dissociation were calculated as well The following was found:(i) The HF values of lour conformational isomers of HA and HB are similar to each other,so the four isomcrs can transform to each other room temperature,(ii) There exists the difference between the ability of dissociation of phenolic protons of HA and that of HB,the former is higher than the latter (iii) There exist two intramolecular hydrogen bonds in HA and HB The bond energy is approximately 8 kJ/mol and the energy of conformation Ⅰ is lower than that of conformationⅡ The bond energy of HA is lower than that of HB.(iv) There exists a low energy snot when phenolic hydroxyl bond twists 180° from the position where hydrogen bond is formed,which suggests that this kind of conformation probably exists,(v) The phenolic hydrogen of HBMC forms hydrogen bond with the neighbouring nitrogen,which is its striticture basis of possessing photosensitizing activity.
基金Supported by the National Natural Science Foundation of China
文摘The phase sensitive NOESY spectrum of oridonin was treated using Full Relaxation Matrix Analysis(FRMA) approach, and the cross relaxation rates of proton pairs were obtained by diagonalizing the NOE matrix of oridonin. The inter proton distances were calculated according to 1/r6 ij ∝σij. The three-dimensional structure of oridonin in solution was calculated by the combination of WUPH, WUPH-S method with molecular mechanics minimization on the basis of NMR experiment.
基金supported by the National Natural Science Foundation of China(Nos.22025503,21790361 and 21871084)Shanghai Municipal Science and Technology Major Project(No.2018SHZDZX03)+3 种基金the Fundamental Research Funds for the Central Universitiesthe Program of Introducing Talents of Discipline to Universities(No.B16017)the Shanghai Science and Technology Committee(No.17520750100)funding from China Postdoctoral Science Foundation funded project(No.J100–5R-20130)。
文摘A bistable[2]rotaxane with a conformation-adaptive macrocycle bearing a 9,14-diphenyl-9,14-dihydrodibenzo[a,c]phenazine(DPAC)unit was synthesized,which could be utilized to optical probe the molecular shuttling motion of the functionalized rotaxane system.The UV-vis,^(1) H NMR and PL spectroscopic data clearly demonstrated that the DPAC ring was interlocked onto the thread and the fluorescence intensity of the DPAC unit in the macrocycle was effectively regulated by the location change of the macrocycle along the thread under acid/base stimulation,which was attributed to the modulation of the intramolecular photo-induced electron transfer between the DPAC unit and the methyltriazole(MTA)unit.This bistable rotaxane system containing a conformation-adaptive fluorophore unit in the macrocycle moiety opens an alternative way to design functional bistable mechanically interlocked molecules.
基金Supported by the Major Scientific Research Projects of Jilin Province, China（No.20140203025NY） and the Natural Science Foundation of Jilin Province, China（No. 3B812C201465）.
文摘Transthyretin（TTR）, as a tetrameric protein, functions as a neuroprotector. The native TTR homotetramer dissociates into dimers and monomers. Dimers and monomers self-assemble into amyloid fibrils, and this process can lead to some diseases. Native TTR homotetramer is a widely accepted model for TTR amyloid formation. In this study, simulations using molecular dynamics（MD） and steered MD（SMD） were performed to explore the mechanisms for glabridin（Glab）, a specific inhibitor for TTR binding, for V30A mutant and wild-type（WT） TTR. MD simulation results indicate that, compared with Glab binding to WT and V30A mutant, the WT TTR could lead to the collapse of β-strands from Ser52 to His56 at chain A. This phenomenon facilitated the easy dissociation of chains A and C. Calculations of the binding free energy between the two chains showed that the V30A-Glab TTR complex displayed a lower binding energy than other systems（WT TTR and WT-Glab TTR）. Then, SMD simulation was performed to ex- plore the unbinding pathway for Glab through the WT and V30A mutant TTR. The results show that Lysl 5（chain A） produced a hydrogen bond with Glab at the force peak via the WT TTR tunnel. Meanwhile, in the V30A TTR mutant, the hydrogen bond between Lysl 5（chain A） and Glab was broken at the force peak. This condition was beneficial for Glab to be taken off from the protein. Our theoretical results will be useful in designing a new specific inhibitor of TTR protein to control the TTR homotetramer dissociation.
基金Project supported by the National Natural Science Foundation of China.
文摘The compound trifluoroiodomethane can be activated to react with the electron donor, 1,4-dilithiotetraphenyl butadiene, by means of electron transfer catalysis (ETC). The structure of the product, 1,3-difluorotetraphenyl, benzene (1), was determined by MS, NMR, and X-ray single crystal diffraction. The conformations of compound 1 and its derivatives were analysized by molecular mechanics.
文摘There is a growing interest in the study of structures and properties of biomolecules in gas phase. Applications of force fields are highly desirable for the computational efficiency of the gas phase study. To help the selection of force fields, the performances of five repre- sentative force fields for gaseous neutral, protonated, deprotonated and capped amino acids are systematically examined and compared. The tested properties include relative conforma- tional energies, energy differences between cis and trans structures, the number and strength of predicted hydrogen bonds, and the quality of the optimized structures. The results of BHandHLYP/6-311＋＋G（d,p） are used as the references. GROMOS53A6 and ENCADS are found to perform poorly for gaseous biomoleeules, while the performance of AMBER99SB, CHARMM27 and OPLSAA/L are comparable when applicable. Considering the general availability of the force field parameters, CHARMM27 is the most recommended, followed by OPLSAA/L, for the study of biomolecules in gas phase
