Molecular dynamics simulation for the crystal structure of synthetic sugar-based bolaamphiphiles

Mikami, Masato; Matsuzaki, Tomokazu; Masuda, Mitsutoshi; Shimizu, Toshimi; Tanabe, K.

doi:10.1016/s0927-0256(98)00118-9

Cited by 6 publications

(7 citation statements)

References 19 publications

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“…Molecular Dynamics Simulation. We have performed a molecular dynamics simulation for the 2(10) and 1(11) crystals to clarify the conformational change . The following dynamics simulation results are in good agreement with the molecular structures in crystal.…”

Section: Discussionmentioning

confidence: 56%

“…To clarify the intermolecular interactions involved, we calculated the intermolecular potential energy for dimers of 2(10) and 1(11) with displacement of the relative arrangement of the mass center from the equilibrium position along a , b , and c axes. The energetics indicated a strong intermolecular interaction between the sugar headgroups . The intermolecular interaction for 2 ( 10 ) and 1 ( 11 ) could be broken down into hydrogen-bonding (HB, −5.7 and −10.4 kJ mol -1 for 2(10) and 1(11) , respectively), electrostatic (ES, −10.4 and −16.9 kJ mol -1 ), and van der Waals (vdW, −11.6 and −10.6 kJ mol -1 ) components .…”

Section: Discussionmentioning

confidence: 98%

“…Thus, we found that a conformational change of the oligomethylene spacer from an all- trans to a gauche -including conformation when the dumbbell-shaped bolaamphiphiles with hydrogen-bonded headgroups self-assemble to form stable layered assemblies. The oligomethylene chain conformation of 2(10) and 1(11) in the crystal lattice could be modeled using a molecular dynamics simulation of the self-assembly . An extended oligomethylene chain of 2(10) generated as an initial structure 10 transformed dynamically into a gauche -including conformation within 100 ps at 100 K and 0.1 MPa.…”

Section: Discussionmentioning

confidence: 99%

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Conformational and Thermal Phase Behavior of Oligomethylene Chains Constrained by Carbohydrate Hydrogen-Bond Networks

2000

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The oligomethylene spacer conformation and phase transition behavior of a series of N,N′-bis(β- 14, 16, 18, and 20] in a self-assembled solid state has been investigated using DSC, XRD, light microscopy, and FT-IR measurements. Both the chain conformation and thermal behavior of the assemblies have been used to classify them into three categories, short (6 e n e 8, and n ) 10), medium (n ) 9, and 11 e n e 13), and long chain (14 e n e 20). Thus, the bolaamphiphiles with a short-chain spacer self-assembled in water to form a gauche-including monolayered self-assembly, while the medium-and long-chain homologues formed monolayered assemblies with an all-trans oligomethylene conformation. The short-and long-chain bolaamphiphiles also exhibited a polymorphism on heating which proceeded with retention of the gauche chain conformation, with the long-chain homologues transforming from the K1 crystalline phase to the K2 crystalline phase (keeping an all-trans conformation) and eventually into the K3 crystalline phase with a gauche-including spacer. In addition, the long-chain, 1(n), and mediumchain, 1(13), bolaamphiphiles formed a thermotropic mesophase (smectic A).

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Section: Discussionmentioning

confidence: 56%

Section: Discussionmentioning

confidence: 98%

Section: Discussionmentioning

confidence: 99%

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Conformational and Thermal Phase Behavior of Oligomethylene Chains Constrained by Carbohydrate Hydrogen-Bond Networks

2000

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“…64 Higher level energy minimization and molecular dynamics calculations have also been used to model the primary structure of gels. In this way, possible modes of aggregation for gelators of both aqueous 31,36,94 and organic solvents 83,[95][96][97][98] have been identified.…”

Section: Modelingmentioning

confidence: 99%

Water Gelation by Small Organic Molecules

2004

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“…[35][36][37][38][39][40] Both atomistic and coarse-grained MD approaches have been used with peptide amphiphiles, including PbAs. [41,42] In a study conducted by Tekin, United atom MD simulations of cylindrical nanofibers made from the peptide amphiphile C12-VVAGERGD showed the self-assembly and stability of various layered fibers. [43] Atomistic MD simulations of glycolipid-based carboxylic bolaamphiphiles, known as sophorolipids, showed self-assembly into large vesicles with varying arrangements of bolaamphiphile heads and tails.…”

Section: Introductionmentioning

confidence: 99%

Investigation of Self‐Assembly of Symmetric and Asymmetric Peptide Bolaamphiphiles by COSMO‐RS and Atomistic Simulations and Their Interactions with POPC Bilayers

Lebedenko

Banerjee

2021

Macro Theory & Simulations

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In this work, eight new peptide bolaamphiphiles (PbAs) are designed containing polar (serine or threonine) and nonpolar amino acid head groups (tryptophan or tyrosine) connected by varying aliphatic carbon chains of different lengths and saturation. The physicochemical properties of the bolaamphiphiles are examined by COSMO-RS to determine sigma profiles, potential, and sigma surfaces. Self-assembly is studied using atomistic molecular dynamic simulations under protonated and deprotonated conditions. To mimic physiological conditions, simulations are also carried out in the presence of sodium chloride and the impact of salt on the self-assembly process is also studied. In general, hydrophobic PbAs are found to form higher-order supramolecular structures while PbAs connected by shorter chains or hydrophilic head groups form globular, more compact structures. Self-assembly is more favorable when the PbAs are protonated. Membrane interactions are then studied using MD simulations and the results indicate that the hydrophobic PbAs interact more favorably with the POPC membrane surfaces. These simulations provide insights about the intricate interactions and properties of the PbAs and shed light on the ability to form fine-tuned structures at the nanoscale. This study may lead to the development of novel PbAs for potential applications in a wide variety of biological applications.

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Molecular dynamics simulation for the crystal structure of synthetic sugar-based bolaamphiphiles

Cited by 6 publications

References 19 publications

Conformational and Thermal Phase Behavior of Oligomethylene Chains Constrained by Carbohydrate Hydrogen-Bond Networks

Conformational and Thermal Phase Behavior of Oligomethylene Chains Constrained by Carbohydrate Hydrogen-Bond Networks

Water Gelation by Small Organic Molecules

Investigation of Self‐Assembly of Symmetric and Asymmetric Peptide Bolaamphiphiles by COSMO‐RS and Atomistic Simulations and Their Interactions with POPC Bilayers

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