Influence of valine enantiomer configuration on the molecular dynamics simulation of their separation by β-cyclodextrin

Alvira, E.

doi:10.1016/j.cplett.2017.04.062

Cited by 10 publications

(13 citation statements)

References 22 publications

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“…For instance, complexation of molecules such as puerarin and daidzin were elucidated with MD simulations and the conformational changes on the CD molecule upon complexation (Zhang, Feng, Li, & Tan, 2010). The interest in using computational approach to study the molecular mechanism of CD complexation is growing in the food field (Alvira, 2017;Oda & Kuroda, 2016;Zhao et al, 2018).…”

Section: Simulation Proceduresmentioning

confidence: 99%

“…The interactions between various molecules not only contribute to the stability and equilibrium of food systems, but also have a large influence in the formation of colloidal systems such as casein micelles and inclusion complexes (Alvira, 2017;Fourtaka, Christoforides, Mentzafos, & Bethanis, 2018;Mehranfar et al, 2013). The use of MD simulations has provided a small scale perspective to understand mechanisms of those interactions, as well as the effects of processing conditions on those molecules.…”

Section: Simulations To Evaluate the Dynamic Behaviors Of Componenmentioning

confidence: 99%

See 1 more Smart Citation

Molecular Dynamics Simulation for Mechanism Elucidation of Food Processing and Safety: State of the Art

Chen

Huang

Miao

et al. 2018

Comp Rev Food Sci Food Safe

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Molecular dynamics (MD) simulation is a useful technique to study the interaction between molecules and how they are affected by various processes and processing conditions. This review summarizes the application of MD simulations in food processing and safety, with an emphasis on the effects that emerging nonthermal technologies (for example, high hydrostatic pressure, pulsed electric field) have on the molecular and structural characteristics of foods and biomaterials. The advances and potential projection of MD simulations in the science and engineering aspects of food materials are discussed and focused on research work conducted to study the effects of emerging technologies on food components. It is expected by showing key case studies that it will stir novel developments as a valuable tool to study the effects of emerging food technologies on biomaterials. This review is useful to food researchers and the food industry, as well as researchers and practitioners working on flavor and nutraceutical encapsulations, dietary carbohydrate product developments, modified starches, protein engineering, and other novel food applications.

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Section: Simulation Proceduresmentioning

confidence: 99%

Section: Simulations To Evaluate the Dynamic Behaviors Of Componenmentioning

confidence: 99%

Molecular Dynamics Simulation for Mechanism Elucidation of Food Processing and Safety: State of the Art

Chen

Huang

Miao

et al. 2018

Comp Rev Food Sci Food Safe

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“…However, the initial disposition of enantiomers in the trajectories cannot be the same because they are mirror images and, although there is no single method to select them, it is a question insufficiently dealt with in MD simulations. In our previous studies with amino acids, we tested different models to calculate the initial dispositions of enantiomers based on energetic, numerical or geometrical criteria (Alvira, 2017b ). The method applied in the present study minimizes the differences in the van der Waals energy and average atomic distances between the enantiomers, as we already adopted in our more recent research with Ile (Alvira, 2019 ).…”

Section: Methodsmentioning

confidence: 99%

Molecular Simulation of the Separation of Some Amino Acid Enantiomers by β-Cyclodextrin in Gas-Phase

Alvira

2020

Front. Chem.

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The complexes formed by β-cyclodextrin and some amino acids (alanine, valine, leucine, and isoleucine) in vacuo are studied by molecular mechanics and dynamics simulations. These methods have been improved with respect to our previous studies with amino acids, regarding the determination of molecular structures or initial enantiomer dispositions in the molecular dynamics trajectories. The greatest contribution to the interaction energy is from the van der Waals term, although the discrimination between enantiomers is due mainly to the electrostatic contribution. The lowest energy structures of the complexes obtained from molecular mechanics are inclusion complexes in which the carboxylic end of amino acids is pointing toward the narrow (D-) or wide rim (L-) of β-cyclodextrin. The position probability density provided by molecular dynamics also confirms inclusion complex formation, because the guests spend most time inside the cavity of β-cyclodextrin along its axis, with the carboxylic end pointing toward the narrow rim. The L-amino acids are the first eluted enantiomers in all cases and chiral discrimination increases with the size of guests, except leucine, which has the lowest capacity to discriminate. During the simulation, Ala and Val remain in weakly enantioselective regions, while Leu and Ile stay in zones with great chiral selectivity.

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“…Current trends in molecular modelling applied to the study of CDs have been recently reviewed with a specific focus on drug delivery matrixes and intelligent nanodevices such as CD‐based molecular motors. Moreover, in the last years Alvira performed a deep investigation on MD simulation approaches to model amino acid enantiodiscrimination by using α‐, β‐, γCDs and a series of CD derivatives . Several studies have been performed concerning the conformational sampling of native CDs.…”

Section: Cyclodextrinsmentioning

confidence: 99%

Recent studies of docking and molecular dynamics simulation for liquid‐phase enantioseparations

et al. 2019

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Liquid‐phase enantioseparations have been fruitfully applied in several fields of science. Various applications along with technical and theoretical advancements contributed to increase significantly the knowledge in this area. Nowadays, chromatographic techniques, in particular HPLC on chiral stationary phase, are considered as mature technologies. In the last thirty years, CE has been also recognized as one of the most versatile technique for analytical scale separation of enantiomers. Despite the huge number of papers published in these fields, understanding mechanistic details of the stereoselective interaction between selector and selectand is still an open issue, in particular for high‐molecular weight chiral selectors like polysaccharide derivatives. With the ever growing improvement of computer facilities, hardware and software, computational techniques have become a basic tool in enantioseparation science. In this field, molecular docking and dynamics simulations proved to be extremely adaptable to model and visualize at molecular level the spatial proximity of interacting molecules in order to predict retention, selectivity, enantiomer elution order, and profile noncovalent interaction patterns underlying the recognition process. On this basis, topics and trends in using docking and molecular dynamics as theoretical complement of experimental LC and CE chiral separations are described herein. The basic concepts of these computational strategies and seminal studies performed over time are presented, with a specific focus on literature published between 2015 and November 2018. A systematic compilation of all published literature has not been attempted.

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Influence of valine enantiomer configuration on the molecular dynamics simulation of their separation by β-cyclodextrin

Cited by 10 publications

References 22 publications

Molecular Dynamics Simulation for Mechanism Elucidation of Food Processing and Safety: State of the Art

Molecular Dynamics Simulation for Mechanism Elucidation of Food Processing and Safety: State of the Art

Molecular Simulation of the Separation of Some Amino Acid Enantiomers by β-Cyclodextrin in Gas-Phase

Recent studies of docking and molecular dynamics simulation for liquid‐phase enantioseparations

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