scholarly journals Unexpected Trends in the Hydrophobicity of Fluorinated Amino Acids Reflect Competing Changes in Polarity and Conformation

2018 ◽  
Author(s):  
João R. Robalo ◽  
Ana Vila Verde
Keyword(s):  
Amino Acids ◽  
Free Energy ◽  
Side Chain ◽  
Side Chains ◽  
Hydration Free Energy ◽  
Crossover Point ◽  
Fluorinated Amino Acids ◽  
Road Map ◽  
Alkyl Side Chains ◽  
The Impact

<div><div><div><p>Fluorination can dramatically improve the thermal and proteolytic stability of proteins and their enzymatic activity. Key to the impact of fluorination on protein properties is the hydrophobicity of fluorinated amino acids. We use molecular dynamics simulations, together with a new fixed-charge, atomistic force field, to quantify the changes in hydration free energy for amino acids with alkyl side chains and with 1 to 6 –CH to –CF side chain substitutions. Fluorination changes the hydration free energy by 1.5 to +2 kcal mol<sup>-</sup>1, but the number of fluorines is a poor predictor of hydrophobicity. Changes in hydration free energy reflect two main contributions: i) fluorination alters side chain-water interactions; we identify a crossover point from hydrophilic to hydrophobic fluoromethyl groups which may be used to estimate the hydrophobicity of fluorinated alkyl side-chains; ii) fluorination alters the number of backbone-water hydrogen bonds via changes in the relative side chain-backbone conformation. Our results offer a road map to mechanistically understand how fluorination alters hydrophobicity of (bio)polymers.</p></div></div></div>

scholarly journals Unexpected Trends in the Hydrophobicity of Fluorinated Amino Acids Reflect Competing Changes in Polarity and Conformation

2018 ◽  
Author(s):  
João R. Robalo ◽  
Ana Vila Verde
Keyword(s):  
Amino Acids ◽  
Free Energy ◽  
Side Chain ◽  
Side Chains ◽  
Hydration Free Energy ◽  
Crossover Point ◽  
Fluorinated Amino Acids ◽  
Road Map ◽  
Alkyl Side Chains ◽  
The Impact

<div><div><div><p>Fluorination can dramatically improve the thermal and proteolytic stability of proteins and their enzymatic activity. Key to the impact of fluorination on protein properties is the hydrophobicity of fluorinated amino acids. We use molecular dynamics simulations, together with a new fixed-charge, atomistic force field, to quantify the changes in hydration free energy for amino acids with alkyl side chains and with 1 to 6 –CH to –CF side chain substitutions. Fluorination changes the hydration free energy by 1.5 to +2 kcal mol<sup>-</sup>1, but the number of fluorines is a poor predictor of hydrophobicity. Changes in hydration free energy reflect two main contributions: i) fluorination alters side chain-water interactions; we identify a crossover point from hydrophilic to hydrophobic fluoromethyl groups which may be used to estimate the hydrophobicity of fluorinated alkyl side-chains; ii) fluorination alters the number of backbone-water hydrogen bonds via changes in the relative side chain-backbone conformation. Our results offer a road map to mechanistically understand how fluorination alters hydrophobicity of (bio)polymers.</p></div></div></div>

scholarly journals Unexpected trends in the hydrophobicity of fluorinated amino acids reflect competing changes in polarity and conformation

2019 ◽  
Vol 21 (4) ◽  
pp. 2029-2038 ◽  
Author(s):  
João R. Robalo ◽  
Ana Vila Verde
Keyword(s):  
Amino Acids ◽  
Free Energy ◽  
Analytical Model ◽  
Molecular Simulations ◽  
Hydration Free Energy ◽  
Fluorinated Amino Acids

The hydration free energy of fluorinated amino acids is calculated with molecular simulations and explained with an analytical model.

scholarly journals Synthesis of New Derivatives of BEDT-TTF: Installation of Alkyl, Ethynyl, and Metal-Binding Side Chains and Formation of Tris(BEDT-TTF) Systems

2021 ◽  
Vol 7 (8) ◽  
pp. 110
Author(s):  
Songjie Yang ◽  
Matteo Zecchini ◽  
Andrew Brooks ◽  
Sara Krivickas ◽  
Desiree Dalligos ◽  
...  
Keyword(s):  
Metal Binding ◽  
Tricarboxylic Acid ◽  
Metal Salts ◽  
Side Chain ◽  
Side Chains ◽  
Ethynyl Group ◽  
X Ray ◽  
Transition Metal Salts ◽  
Alkyl Side Chains ◽  
Derivatives Of

The syntheses of new BEDT-TTF derivatives are described. These comprise BEDT-TTF with one ethynyl group (HC≡C-), with two (n-heptyl) or four (n-butyl) alkyl side chains, with two trans acetal (-CH(OMe)2) groups, with two trans aminomethyl (-CH2NH2) groups, and with an iminodiacetate (-CH2N(CH2CO2−)2 side chain. Three transition metal salts have been prepared from the latter donor, and their magnetic properties are reported. Three tris-donor systems are reported bearing three BEDT-TTF derivatives with ester links to a core derived from benzene-1,3,5-tricarboxylic acid. The stereochemistry and molecular structure of the donors are discussed. X-ray crystal structures of two BEDT-TTF donors are reported: one with two CH(OMe)2 groups and with one a -CH2N(CH2CO2Me)2 side chain.

scholarly journals Free Energy Landscape and Rate Estimation of the Aromatic Ring Flips in Basic Pancreatic Trypsin Inhibitor Using Metadynamics

2021 ◽  
Author(s):  
Pär Söderhjelm ◽  
Mandar Kulkarni
Keyword(s):  
Free Energy ◽  
Trypsin Inhibitor ◽  
Side Chain ◽  
Side Chains ◽  
Aromatic Residues ◽  
Basic Pancreatic Trypsin Inhibitor ◽  
Pancreatic Trypsin Inhibitor ◽  
Energy Surfaces ◽  
Aromatic Side Chains

Aromatic side-chains (phenylalanine and tyrosine) of a protein flip by 180° around the Cβ-Cγ axis (χ2 dihedral of side-chain) producing two symmetry-equivalent states. The ring-flip dynamics act as an NMR probe to understand local conformational fluctuations. Ring-flips are categorized as slow (ms onwards) or fast (ns to near ms) based on timescales accessible to NMR experiments. In this study, we investigated the ability of the infrequent metadynamics approach to discriminate between slow and fast ring-flips for eight individual aromatic side-chains (F4, Y10, Y21, F22, Y23, F33, Y35, F45) of basic pancreatic trypsin inhibitor (BPTI). Well-tempered metadynamics simulations were performed to observe ring-flipping free energy surfaces for all eight aromatic residues. The results indicate that χ2 as a standalone collective variable (CV) is not sufficient to classify fast and slow ring-flips. Most of the residues needed χ1 (N−Cχα) as a complementary CV, indicating the importance of librational motions in ring-flips. Multiple pathways and mechanisms were observed for residues F4, Y10, and F22. Recrossing events are observed for residues F22 and F33, indicating a possible role of friction effects in the ring-flipping. The results demonstrate the successful application of the metadynamics based approach to estimate ring-flip rates of aromatic residues in BPTI and identify certain limitations of the approach.

scholarly journals Controlled steric selectivity in molecular doping towards closest-packed supramolecular conductors

2020 ◽  
Vol 1 (1) ◽  
Author(s):  
Shinya Kohno ◽  
Yu Yamashita ◽  
Naotaka Kasuya ◽  
Tsubasa Mikie ◽  
Itaru Osaka ◽  
...  
Keyword(s):  
Conjugated Polymers ◽  
Steric Effects ◽  
Side Chain ◽  
Side Chains ◽  
Void Space ◽  
Alkyl Side Chains ◽  
Recent Developments ◽  
High Carrier ◽  
Molecular Doping ◽  
Steric Selectivity

Abstract Recent developments in molecular doping technologies allow extremely high carrier densities in polymeric semiconductors, exhibiting great diversity because of the unique size, conformation, and steric effect of molecular dopants. However, it is controversial how steric effects can limit the doping efficiency and to what extent dopants can be accommodated in polymers. Here, we employ two distinct conjugated polymers with different alkyl side-chain densities, where polymers are doped via anion-change, allowing greater variation in the incorporation of molecular dopants having different electrostatic potentials and shapes. We characterize the doping efficiency with regard to steric effects, considering the unique void space in the conjugated polymers. Our study reveals that doping efficiency of polymers with sparse alkyl side-chains is significantly greater than that with dense side-chains. A closest-packed supramolecule is realized with a particular combination of a sparse polymer and a large dopant, giving rise to high conductivity, air stability, and remarkably high work function. This work provides a critical insight into overcoming steric effects in molecular doping.

n-Alkylresorcinol Occurrence in Mercurialis perennis L. (Euphorbiaceae)

2010 ◽  
Vol 65 (3-4) ◽  
pp. 174-179 ◽  
Author(s):  
Peter Lorenz ◽  
Matthias Knödler ◽  
Julia Bertrams ◽  
Melanie Berger ◽  
Ulrich Meyer ◽  
...  
Keyword(s):  
Side Chain ◽  
Side Chains ◽  
Alkyl Side Chain ◽  
Alkyl Side Chains ◽  
Chain Lengths ◽  
New View

Investigation of the dichloromethane extracts from herbal and root parts of Mercurialis perennis L. afforded a mixture of 11 homologous n-alkylresorcinols (ARs) with saturated odd-numbered alkyl side chains (C15:0-C27:0). In addition to three predominant ARs (C19:0, C21:0 and C23:0), a number of minor ARs were identified by use of LC-MS/MS and GC-MS techniques. Among the compounds detected, four uncommon ARs with evennumbered alkyl side chain lengths were also determined. The overall AR concentration in herbal parts was 7 to 9 times higher compared to that of the roots. The results presented may open a new view on the phytochemistry and pharmacognosy of M. perennis and other members of the Euphorbiaceae family.

Synthesis ofβ-Peptides withβ-Helices from New C-Linked Carbo-β-Amino Acids: Study on the Impact of Carbohydrate Side Chains

2009 ◽  
Vol 4 (1) ◽  
pp. 181-193 ◽  
Author(s):  
Gangavaram V. M. Sharma ◽  
Kota Sudhakar Rao ◽  
Rapolu Ravi ◽  
Kongari Narsimulu ◽  
Pendem Nagendar ◽  
...  
Keyword(s):  
Amino Acids ◽  
Side Chains ◽  
The Impact

Low band gap conjugated polymers combining siloxane-terminated side chains and alkyl side chains: side-chain engineering achieving a large active layer processing window for PCE > 10% in polymer solar cells

2017 ◽  
Vol 5 (33) ◽  
pp. 17619-17631 ◽  
Author(s):  
Xuncheng Liu ◽  
Li Nian ◽  
Ke Gao ◽  
Lianjie Zhang ◽  
Lechi Qing ◽  
...  
Keyword(s):  
Conjugated Polymers ◽  
Active Layer ◽  
Polymer Solar Cells ◽  
Hole Transport ◽  
Random Copolymers ◽  
Side Chain ◽  
Active Layer Thickness ◽  
Side Chains ◽  
Alkyl Side Chains ◽  
Thickness Tolerance

Side-chain random copolymers show high 3-D hole transport and offer excellent active layer thickness tolerance.

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