Modeling Dynamic Conformations of Organic Molecules: Alkyne Carotenoids in Solution
文献类型：期刊论文
| 作者 | Streckaite, Simona; Macernis, Mindaugas; Li, Fei3; Trskova, Eliska Kuthanova4,5; Litvin, Radek4,6; Yang, Chunhong3; Pascal, Andrew A.; Valkunas, Leonas2; Robert, Bruno; Llansola-Portoles, Manuel J. |
| 刊名 | JOURNAL OF PHYSICAL CHEMISTRY A
 |
| 出版日期 | 2020 |
| 卷号 | 124期号:14页码:2792-2801 |
| ISSN号 | 1089-5639 |
| DOI | 10.1021/acs.jpca.9b11536 |
| 文献子类 | Article |
| 英文摘要 | Calculating the spectroscopic properties of complex conjugated organic molecules in their relaxed state is far from simple. An additional complexity arises for flexible molecules in solution, where the rotational energy barriers are low enough so that nonminimum conformations may become dynamically populated. These metastable conformations quickly relax during the minimization procedures preliminary to density functional theory calculations, and so accounting for their contribution to the experimentally observed properties is problematic. We describe a strategy for stabilizing these nonminimum conformations in silico, allowing their properties to be calculated. Diadinoxanthin and alloxanthin present atypical vibrational properties in solution, indicating the presence of several conformations. Performing energy calculations in vacuo and polarizable continuum model calculations in different solvents, we found three different conformations with values for the delta dihedral angle of the end ring ca. 0, 180, and 90 degrees with respect to the plane of the conjugated chain. The latter conformation, a nonglobal minimum, is not stable during the minimization necessary for modeling its spectroscopic properties. To circumvent this classical problem, we used a Car-Parinello MD supermolecular approach, in which diadinoxanthin was solvated by water molecules so that metastable conformations were stabilized by hydrogen-bonding interactions. We progressively removed the number of solvating waters to find the minimum required for this stabilization. This strategy represents the first modeling of a carotenoid in a distorted conformation and provides an accurate interpretation of the experimental data. |
| 学科主题 | Chemistry, Physical ; Physics, Atomic, Molecular & Chemical |
| 出版地 | WASHINGTON |
| 电子版国际标准刊号 | 1520-5215 |
| WOS关键词 | DENSITY-FUNCTIONAL THEORY ; LIGHT-HARVESTING COMPLEX ; RESONANCE RAMAN-SPECTRA ; CIS-TRANS ISOMERS ; BETA-CAROTENE ; PHOTOSYNTHETIC BACTERIA ; REACTION CENTERS ; SPHAEROIDES G1C ; CONFIGURATIONS ; ABSORPTION |
| WOS研究方向 | Chemistry ; Physics |
| 语种 | 英语 |
| WOS记录号 | WOS:000526394300008 |
| 出版者 | AMER CHEMICAL SOC |
| 资助机构 | ERC funding agency (PHOTPROT project) ; French Infrastructure for Integrated Structural Biology (FRISBI) [ANR-10-INBS-05] ; European UnionEuropean Commission [675006 (SE2B)] ; Gilibert project [S-LZ-19-3] ; Czech Science FoundationGrant Agency of the Czech Republic [1911494S, 31-19-28323X] ; Czech Ministry of Education, Youth and SportMinistry of Education, Youth & Sports - Czech Republic [RVO:60077344, MSMT LO1416] |
| 源URL | [http://ir.ibcas.ac.cn/handle/2S10CLM1/21805]  |
| 专题 | 中科院光生物学重点实验室 |
| 作者单位 | 1.Ctr Phys Sci & Technol, Mol Cpds Phys Dept, LT-10257 Vilnius, Lithuania 2.Vilnius Univ, Fac Phys, Inst Chem Phys, LT-10222 Vilnius, Lithuania 3.Streckaite, Simona; Li, Fei; Pascal, Andrew A.; Robert, Bruno; Llansola-Portoles, Manuel J.] Univ Paris Saclay, CEA, CNRS, I2BC, F-91198 Gif Sur Yvette, France 4.Chinese Acad Sci, Inst Bot, Key Lab Photobiol, Beijing 100093, Peoples R China 5.Univ South Bohemia, Fac Sci, Ceske Budejovice 37005, Czech Republic 6.Acad Sci Czech Republ, Inst Microbiol, Trebon 37981, Czech Republic 7.Czech Acad Sci, Biol Ctr, Ceske Budejovice 37005, Czech Republic |
| 推荐引用方式 GB/T 7714 | Streckaite, Simona,Macernis, Mindaugas,Li, Fei,et al. Modeling Dynamic Conformations of Organic Molecules: Alkyne Carotenoids in Solution[J]. JOURNAL OF PHYSICAL CHEMISTRY A,2020,124(14):2792-2801. |
| APA | Streckaite, Simona.,Macernis, Mindaugas.,Li, Fei.,Trskova, Eliska Kuthanova.,Litvin, Radek.,...&Llansola-Portoles, Manuel J..(2020).Modeling Dynamic Conformations of Organic Molecules: Alkyne Carotenoids in Solution.JOURNAL OF PHYSICAL CHEMISTRY A,124(14),2792-2801. |
| MLA | Streckaite, Simona,et al."Modeling Dynamic Conformations of Organic Molecules: Alkyne Carotenoids in Solution".JOURNAL OF PHYSICAL CHEMISTRY A 124.14(2020):2792-2801. |
入库方式： OAI收割
来源：植物研究所
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