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Modeling Dynamic Conformations of Organic Molecules: Alkyne Carotenoids in Solution
Streckaite, Simona; Macernis, Mindaugas; Li, Fei3; Trskova, Eliska Kuthanova4,5; Litvin, Radek4,6; Yang, Chunhong3; Pascal, Andrew A.; Valkunas, Leonas1; Robert, Bruno; Llansola-Portoles, Manuel J.
2020
发表期刊JOURNAL OF PHYSICAL CHEMISTRY A
ISSN1089-5639
卷号124期号:14页码:2792-2801
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.
学科领域Chemistry, Physical ; Physics, Atomic, Molecular & Chemical
DOI10.1021/acs.jpca.9b11536
收录类别SCI
语种英语
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
WOS记录号WOS:000526394300008
出版者AMER CHEMICAL SOC
文献子类Article
出版地WASHINGTON
EISSN1520-5215
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]
作者邮箱leonas.valkunas@ff.vu.lt ; BrunoROBERT@cea.fr ; manuel.llansola@i2bc.paris-saclay.fr
作品OA属性Green Published, hybrid, Green Submitted
引用统计
被引频次:3[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符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.Vilnius Univ, Fac Phys, Inst Chem Phys, LT-10222 Vilnius, Lithuania
2.Ctr Phys Sci & Technol, Mol Cpds Phys Dept, LT-10257 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
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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.
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