Pub Date : 2018-06-01DOI: 10.4208/jams.101518.112818a
Wentao Sun
{"title":"An potential energy surface for the O + O2 reaction using neutral network approach","authors":"Wentao Sun","doi":"10.4208/jams.101518.112818a","DOIUrl":"https://doi.org/10.4208/jams.101518.112818a","url":null,"abstract":"","PeriodicalId":15131,"journal":{"name":"Journal of Atomic and Molecular Sciences","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82708192","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-06-01DOI: 10.4208/jams.030618.051518a
Dapeng Yang
At the B3LYP/6-311+G(d, p)/IEFPCM (in dichloromethane) theory level, the N-H-based excited-state intramolecular proton transfer (N-H-based ESIPT) process of 2-(2’-aminophenyl)benzothiazole (PBT-NH2) and its three derivatives 2-(2’-methylaminophenyl)benzothiazole(PBT-NHMe), 2-(2’acetylaminophenyl)benzothiazole (PBT-NHAc) and 2-(2’-tosylaminophenyl) benzothiazole (PBT-NHTs) have been explored by the time-dependent density functional theory (TD-DFT) method. Our calculated hydrogen bond lengths and angles sufficiently confirm that the intramolecular hydrogen bonds N1-H•••N2 formed at the S0 states of the four compounds should be significantly strengthened in the S1 state, which are further supported by the results obtained based on the analyses of infrared spectra shifts. The scanned potential energy curves reveal that the energy barriers of the first singlet excited state of the four titled compounds along the ESIPT reactions are predicted at 8.74, 8.98, 6.72 and 1.69 kcal/mol, respectively, suggesting that the inclusion of a strong electron-withdrawing tosyl (Ts) group can remarkably facilitate the occurrence of the ESIPT reaction, while the involvement of an electron-donating methyl group has slight opposite effect on the ESIPT process of the amino-type hydrogen-bonding system.
{"title":"Modulating N-H-based excited-state intramolecular proton transfer by different electron-donating/withdrawing substituents in 2-(2’-aminophenyl)benzothiazole compounds","authors":"Dapeng Yang","doi":"10.4208/jams.030618.051518a","DOIUrl":"https://doi.org/10.4208/jams.030618.051518a","url":null,"abstract":"At the B3LYP/6-311+G(d, p)/IEFPCM (in dichloromethane) theory level, the N-H-based excited-state intramolecular proton transfer (N-H-based ESIPT) process of 2-(2’-aminophenyl)benzothiazole (PBT-NH2) and its three derivatives 2-(2’-methylaminophenyl)benzothiazole(PBT-NHMe), 2-(2’acetylaminophenyl)benzothiazole (PBT-NHAc) and 2-(2’-tosylaminophenyl) benzothiazole (PBT-NHTs) have been explored by the time-dependent density functional theory (TD-DFT) method. Our calculated hydrogen bond lengths and angles sufficiently confirm that the intramolecular hydrogen bonds N1-H•••N2 formed at the S0 states of the four compounds should be significantly strengthened in the S1 state, which are further supported by the results obtained based on the analyses of infrared spectra shifts. The scanned potential energy curves reveal that the energy barriers of the first singlet excited state of the four titled compounds along the ESIPT reactions are predicted at 8.74, 8.98, 6.72 and 1.69 kcal/mol, respectively, suggesting that the inclusion of a strong electron-withdrawing tosyl (Ts) group can remarkably facilitate the occurrence of the ESIPT reaction, while the involvement of an electron-donating methyl group has slight opposite effect on the ESIPT process of the amino-type hydrogen-bonding system.","PeriodicalId":15131,"journal":{"name":"Journal of Atomic and Molecular Sciences","volume":"68 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81681030","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-06-01DOI: 10.4208/jams.100718.111518a
Jiang Yanliu
A balance between the local excitation (LE) and charge-transfer (CT) transitions is an important issue of a density functional. In this work, we compare the performance between the global hybrid functional M062X and long-range separated functional CAM-B3LYP when they calculate the absorption energies of visible light photoswitches hemithioindigo (HTI) Z1, Z2, Z4, Z5 and Z7. The electronic excitations of HTI Z1 and Z2 are mixtures of LE and CT transitions. CAM-B3LYP succeeds to predict the same absorption energy sequence of the five compounds as the experimental results while M062X predicts a wrong sequence of HTI Z1 and Z2. Another global hybrid functional M06 is also employed for a comparison. Finally, we suggest CAMB3LYP rather than M062X when dealing with mixed electronic transtions.
{"title":"Outperformance of CAM-B3LYP than M062X density functional in mixed transition of local excitation and charge transfer","authors":"Jiang Yanliu","doi":"10.4208/jams.100718.111518a","DOIUrl":"https://doi.org/10.4208/jams.100718.111518a","url":null,"abstract":"A balance between the local excitation (LE) and charge-transfer (CT) transitions is an important issue of a density functional. In this work, we compare the performance between the global hybrid functional M062X and long-range separated functional CAM-B3LYP when they calculate the absorption energies of visible light photoswitches hemithioindigo (HTI) Z1, Z2, Z4, Z5 and Z7. The electronic excitations of HTI Z1 and Z2 are mixtures of LE and CT transitions. CAM-B3LYP succeeds to predict the same absorption energy sequence of the five compounds as the experimental results while M062X predicts a wrong sequence of HTI Z1 and Z2. Another global hybrid functional M06 is also employed for a comparison. Finally, we suggest CAMB3LYP rather than M062X when dealing with mixed electronic transtions.","PeriodicalId":15131,"journal":{"name":"Journal of Atomic and Molecular Sciences","volume":"5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84204024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-06-01DOI: 10.4208/JAMS.011818.042318A
Jia Li
{"title":"Theoretical elaboration about excited state behaviors and fluoride anion sensor mechanism for 2-{[2-(2-Hydroxy-phenyl)-1H-benzoimidazo-5-yl]-phenyl-methylene} malononitrile","authors":"Jia Li","doi":"10.4208/JAMS.011818.042318A","DOIUrl":"https://doi.org/10.4208/JAMS.011818.042318A","url":null,"abstract":"","PeriodicalId":15131,"journal":{"name":"Journal of Atomic and Molecular Sciences","volume":"87 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88619934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-06-01DOI: 10.4208/jams.042518.081318a
Qiaoli Zhang
Two N-H type excited state intramolecular proton transfer (ESIPT) systems (i.e., 2-amino-3-(2’benzoxazolyl)quinoline (ABO) and 2-amino-3-(2’-benzothiazolyl)-quinoline (ABT)) have been investigated. Adopting DFT and TDDFT methods coupling with B3LYP functional and TZVP basis set, our simulations about ABO and ABT molecules have successfully reappeared experimental results, based on which the rationality of our calculations is confirmed. Using Atoms in Molecules (AIM) analytical method, we firstly explore the interactions about chemical bond and verify the formation of hydrogen bond N-H•••N for ABO and ABT in the S0 state. Investigating the primary geometrical parameters involved in N-H•••N, we find it should be strengthened in the S1 state. Upon photoexcitation, charge transfer phenomenon is found via frontier molecular orbitals (MOs), and charge redistribution provides the tendency of ESIPT reaction for ABO and ABT. According to our constructed potential energy curves of both S0 and S1 states for ABO and ABT using two kinds of methods (i.e., the elongation of N-H single bond and the weakening of H•••N hydrogen bond), we clarify the ESIPT mechanisms and explain the recovery of four-level reaction cycle. Our searching transition state (TS) structures and simulated intrinsic reaction coordinate (IRC) path further confirm the ESIPT reaction.
{"title":"Theoretical insights into the excited state hydrogen bond and ESIPT reaction for 2-amino-3-(2’-benzoxazolyl)quinoline and 2-amino-3-(2’-benzothiazolyl)-quinoline","authors":"Qiaoli Zhang","doi":"10.4208/jams.042518.081318a","DOIUrl":"https://doi.org/10.4208/jams.042518.081318a","url":null,"abstract":"Two N-H type excited state intramolecular proton transfer (ESIPT) systems (i.e., 2-amino-3-(2’benzoxazolyl)quinoline (ABO) and 2-amino-3-(2’-benzothiazolyl)-quinoline (ABT)) have been investigated. Adopting DFT and TDDFT methods coupling with B3LYP functional and TZVP basis set, our simulations about ABO and ABT molecules have successfully reappeared experimental results, based on which the rationality of our calculations is confirmed. Using Atoms in Molecules (AIM) analytical method, we firstly explore the interactions about chemical bond and verify the formation of hydrogen bond N-H•••N for ABO and ABT in the S0 state. Investigating the primary geometrical parameters involved in N-H•••N, we find it should be strengthened in the S1 state. Upon photoexcitation, charge transfer phenomenon is found via frontier molecular orbitals (MOs), and charge redistribution provides the tendency of ESIPT reaction for ABO and ABT. According to our constructed potential energy curves of both S0 and S1 states for ABO and ABT using two kinds of methods (i.e., the elongation of N-H single bond and the weakening of H•••N hydrogen bond), we clarify the ESIPT mechanisms and explain the recovery of four-level reaction cycle. Our searching transition state (TS) structures and simulated intrinsic reaction coordinate (IRC) path further confirm the ESIPT reaction.","PeriodicalId":15131,"journal":{"name":"Journal of Atomic and Molecular Sciences","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85016948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In present work, we investigated the surface-enhanced raman scattering(SERS) of 4,4’-bipyridine on Graphene surface with a quasi-analytical approach based on density functional perturbation theory(DFPT). Three different configurations were considered to simulate the adsorption structures on the Graphene surface. The interaction between 4,4’-bipyridine molecule and Graphene surface depends on the adsorption structure, which also results in the distinct spectroscopy. The relationship between the configurations and SERS spectroscopy were interpreted. We also performed the experimental SERS spectroscopy of 4,4’bipyridine molecule on Graphene. Comparing with the experimental SERS spectroscopy, the landscape of 4,4’-bipyridine on Graphene has been revealed.
{"title":"Theoretical and experimental study of surface-enhanced raman scattering of 4,4'-bipyridine molecule on graphene","authors":"Yong Ma, Sheng-Yu Wang, Zhen Li, Wei Hu, Shouzhen Jiang, Xiu-Neng Song, Chuan-Kui Wang","doi":"10.4208/jams.112317.122817a","DOIUrl":"https://doi.org/10.4208/jams.112317.122817a","url":null,"abstract":"In present work, we investigated the surface-enhanced raman scattering(SERS) of 4,4’-bipyridine on Graphene surface with a quasi-analytical approach based on density functional perturbation theory(DFPT). Three different configurations were considered to simulate the adsorption structures on the Graphene surface. The interaction between 4,4’-bipyridine molecule and Graphene surface depends on the adsorption structure, which also results in the distinct spectroscopy. The relationship between the configurations and SERS spectroscopy were interpreted. We also performed the experimental SERS spectroscopy of 4,4’bipyridine molecule on Graphene. Comparing with the experimental SERS spectroscopy, the landscape of 4,4’-bipyridine on Graphene has been revealed.","PeriodicalId":15131,"journal":{"name":"Journal of Atomic and Molecular Sciences","volume":"165 1","pages":"127-130"},"PeriodicalIF":0.0,"publicationDate":"2018-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75705659","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-02-01DOI: 10.4208/jams.102817.121817a
Qi Wu, Kunlun Wu, Qingtain Meng
It is necessary to fully understand the interaction between the cell penetration peptide and the different types of phospholipid membranes. In this research the interaction between R9 antibacterial peptide and asymmetric phospholipid is studied by using the method of coarse-grained dynamic simulation. The investigation shows that when there is only one R9 antibacterial peptide in the system, it is hard to penetrate through the phospholipid membrane spontaneously. When the concentration of the antibacterial peptide reaches a certain value, with the help of the enhanced electrostatic interactions and the cooperative effect, the peptides will pass through the phospholipid bilayer and reach the inside of the cell. Increasing the concentration of antimicrobial peptides is helpful to improve the penetration rate of the peptides. Our results can provide some theoretical guidance for drug delivery in the biological system.
{"title":"Influences of cell-penetrating peptide concentration on the penetration of phospholipid membrane","authors":"Qi Wu, Kunlun Wu, Qingtain Meng","doi":"10.4208/jams.102817.121817a","DOIUrl":"https://doi.org/10.4208/jams.102817.121817a","url":null,"abstract":"It is necessary to fully understand the interaction between the cell penetration peptide and the different types of phospholipid membranes. In this research the interaction between R9 antibacterial peptide and asymmetric phospholipid is studied by using the method of coarse-grained dynamic simulation. The investigation shows that when there is only one R9 antibacterial peptide in the system, it is hard to penetrate through the phospholipid membrane spontaneously. When the concentration of the antibacterial peptide reaches a certain value, with the help of the enhanced electrostatic interactions and the cooperative effect, the peptides will pass through the phospholipid bilayer and reach the inside of the cell. Increasing the concentration of antimicrobial peptides is helpful to improve the penetration rate of the peptides. Our results can provide some theoretical guidance for drug delivery in the biological system.","PeriodicalId":15131,"journal":{"name":"Journal of Atomic and Molecular Sciences","volume":"3 1","pages":"141-145"},"PeriodicalIF":0.0,"publicationDate":"2018-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90631639","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract. Properties of methanol molecules adsorbed on graphene are studied theoretically and various adsorption geometrical structures, density of states as well as the optical properties are obtained by means of first-principles calculations. Electronic characteristics and optical properties of graphene are sensitive to the molecule adsorptions. It is found that band gap appears when the methanol molecules are adsorbed. The dielectric function, refractive index, extinction coefficient, absorption coefficient and the reflectivity are changed. In the case of one methanol molecule adsorption, the peaks for the imaginary of the dielectric function and the adsorption coefficient shift to the high energy region, and new peaks appear in the visible range. The maximum value of extinction coefficient rises, and new peaks appear in the visible range when two methanol molecules are adsorbed.
{"title":"Electronic and optical properties of graphene adsorbed with methanol molecules: first-principles calculations","authors":"Xiuwen Zhao, Mengyao Liu, Xiaotian Zhang, Yufeng Li, Xiaobo Yuan, J. Ren","doi":"10.4208/jams.112217.122917a","DOIUrl":"https://doi.org/10.4208/jams.112217.122917a","url":null,"abstract":"Abstract. Properties of methanol molecules adsorbed on graphene are studied theoretically and various adsorption geometrical structures, density of states as well as the optical properties are obtained by means of first-principles calculations. Electronic characteristics and optical properties of graphene are sensitive to the molecule adsorptions. It is found that band gap appears when the methanol molecules are adsorbed. The dielectric function, refractive index, extinction coefficient, absorption coefficient and the reflectivity are changed. In the case of one methanol molecule adsorption, the peaks for the imaginary of the dielectric function and the adsorption coefficient shift to the high energy region, and new peaks appear in the visible range. The maximum value of extinction coefficient rises, and new peaks appear in the visible range when two methanol molecules are adsorbed.","PeriodicalId":15131,"journal":{"name":"Journal of Atomic and Molecular Sciences","volume":"1 1","pages":"131-135"},"PeriodicalIF":0.0,"publicationDate":"2018-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90233556","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-02-01DOI: 10.4208/JAMS.110217.121717A
Jun Bi, Ran Liu, Huan Fu, Feng Sun, Zong-Liang Li
Due to the small size, single-molecule device may be sensitive to the ambient molecules. Thus, it is significant for fabricating single-molecule sensors to understand the influence of ambient molecule on molecular device. Based on the ab initio calculations combined with non-equilibrium Green's function method, the adsorption effects of H2O, CO2 and NO2 molecule on the pyrene-1,8-dithiol molecular junctions are studied systematically. The numerical results show that, the influence of H2O or CO2 molecule on the pyrene-1,8-dithiol molecular junction is very slight when they are adsorbed on the pyrene-1,8-dithiol molecules, which attributes to the closed-shell ground states of these two molecules. Different from H2O and CO2 molecule, being a radical, NO2 molecule shows obvious influence on the electronic transport of pyrene1,8-dithiol molecular junctions. The system with NO2 adsorbate is more conductive in the positive and lower negative bias regime than those of the other two molecular systems, which is due to the evident coupling between the states of NO2 molecule and pyrene-1,8-dithiol molecule.
{"title":"Ambient molecule effects on the electronic transport of pyrene-1,8-dithiol molecular junction","authors":"Jun Bi, Ran Liu, Huan Fu, Feng Sun, Zong-Liang Li","doi":"10.4208/JAMS.110217.121717A","DOIUrl":"https://doi.org/10.4208/JAMS.110217.121717A","url":null,"abstract":"Due to the small size, single-molecule device may be sensitive to the ambient molecules. Thus, it is significant for fabricating single-molecule sensors to understand the influence of ambient molecule on molecular device. Based on the ab initio calculations combined with non-equilibrium Green's function method, the adsorption effects of H2O, CO2 and NO2 molecule on the pyrene-1,8-dithiol molecular junctions are studied systematically. The numerical results show that, the influence of H2O or CO2 molecule on the pyrene-1,8-dithiol molecular junction is very slight when they are adsorbed on the pyrene-1,8-dithiol molecules, which attributes to the closed-shell ground states of these two molecules. Different from H2O and CO2 molecule, being a radical, NO2 molecule shows obvious influence on the electronic transport of pyrene1,8-dithiol molecular junctions. The system with NO2 adsorbate is more conductive in the positive and lower negative bias regime than those of the other two molecular systems, which is due to the evident coupling between the states of NO2 molecule and pyrene-1,8-dithiol molecule.","PeriodicalId":15131,"journal":{"name":"Journal of Atomic and Molecular Sciences","volume":"137 1","pages":"122-126"},"PeriodicalIF":0.0,"publicationDate":"2018-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79806599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-02-01DOI: 10.4208/jams.110417.121517a
Fangfang Yan, Xinguo Liu, Shaolong Zhang, J. Su, Qinggang Zhang, Jianzhong Chen
Adipocyte fatty-acid binding protein (A-FABP) is abundantly expressed in macrophage and adipocyte, and it is a potential target for the treatment of atherosclerosis and metabolic disease. In this work, binding differences of two inhibitors ACD and TDZ to A-FABP were studied by using principal component (PC) analysis, molecular mechanics generalized Born surface area (MM-GBSA) and solvated interaction energy (SIE) methods. The results show that the binding of inhibitor TDZ to A-FABP is stronger than that of ACD to AFABP. The calculation of residue-based free energy decomposition and dynamics analysis of hydrogen bonds suggest that hydrophobic interactions and hydrogen bonding interactions play important roles in the structural stability of A-FABP. The information obtained from this work will provide a useful clue for design of effective drugs targeting A-FABP.
脂肪细胞脂肪酸结合蛋白(fatty-acid binding protein, a - fabp)在巨噬细胞和脂肪细胞中大量表达，是治疗动脉粥样硬化和代谢性疾病的潜在靶点。本文采用主成分分析(PC)、分子力学广义Born表面积(MM-GBSA)和溶剂化相互作用能(SIE)等方法研究了两种抑制剂ACD和TDZ与A-FABP的结合差异。结果表明，抑制剂TDZ与A-FABP的结合强于ACD与AFABP的结合。残基自由能分解计算和氢键动力学分析表明，疏水相互作用和氢键相互作用对A-FABP的结构稳定性起重要作用。本研究结果将为设计靶向a - fabp的有效药物提供有益的线索。
{"title":"Binding difference of inhibitors ACD and TDZ to A-FABP revealed by molecular dynamics simulations","authors":"Fangfang Yan, Xinguo Liu, Shaolong Zhang, J. Su, Qinggang Zhang, Jianzhong Chen","doi":"10.4208/jams.110417.121517a","DOIUrl":"https://doi.org/10.4208/jams.110417.121517a","url":null,"abstract":"Adipocyte fatty-acid binding protein (A-FABP) is abundantly expressed in macrophage and adipocyte, and it is a potential target for the treatment of atherosclerosis and metabolic disease. In this work, binding differences of two inhibitors ACD and TDZ to A-FABP were studied by using principal component (PC) analysis, molecular mechanics generalized Born surface area (MM-GBSA) and solvated interaction energy (SIE) methods. The results show that the binding of inhibitor TDZ to A-FABP is stronger than that of ACD to AFABP. The calculation of residue-based free energy decomposition and dynamics analysis of hydrogen bonds suggest that hydrophobic interactions and hydrogen bonding interactions play important roles in the structural stability of A-FABP. The information obtained from this work will provide a useful clue for design of effective drugs targeting A-FABP.","PeriodicalId":15131,"journal":{"name":"Journal of Atomic and Molecular Sciences","volume":"40 1","pages":"97-104"},"PeriodicalIF":0.0,"publicationDate":"2018-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90521291","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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