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Ab Initio Molecular Dynamics Simulations of Aqueous LiTFSI Solutions─Structure, Hydrogen Bonding, and IR Spectra.

ABSTRACT: Simulations of Density Functional Theory-based ab initio molecular dynamics (AIMD) have been performed for a series of aqueous lithium bis(trifluoromethylsulfonyl)imide (LiTFSI) solutions with concentrations ranging from salt-in-water to water-in-salt systems. Analysis of the structure of electrolytes has revealed a preference of Li⁺ cations to interact with water molecules. In concentrated LiTFSI solutions, water molecules form small associates. The total number of hydrogen bonds (HBs) in the system decreases with salt concentrations, with bonds to water acceptors being only partially replaced by interactions with TFSI anions. Infrared (IR) spectra in the region of the O-H stretching frequency calculated from AIMD trajectories are in good agreement with experimental data. Statistics of oscillations of individual O-H bonds have shown correlations between vibrational frequencies and the structure of HBs formed by water. The changes in the IR spectrum have been related to the varying contributions of different local environments of the water molecules. The abundances of the three spectral components calculated from the simulations agree well with the decomposition of the experimental IR spectra reported in the literature.

SUBMITTER: Wrobel P

PROVIDER: S-EPMC10839825 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature

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Ab Initio Molecular Dynamics Simulations of Aqueous LiTFSI Solutions─Structure, Hydrogen Bonding, and IR Spectra.

Wróbel Piotr P Kubisiak Piotr P Eilmes Andrzej A

The journal of physical chemistry. B 20240118 4

Simulations of Density Functional Theory-based ab initio molecular dynamics (AIMD) have been performed for a series of aqueous lithium bis(trifluoromethylsulfonyl)imide (LiTFSI) solutions with concentrations ranging from salt-in-water to water-in-salt systems. Analysis of the structure of electrolytes has revealed a preference of Li<sup>+</sup> cations to interact with water molecules. In concentrated LiTFSI solutions, water molecules form small associates. The total number of hydrogen bonds (HB ...[more]

PMID: 38235720

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Project description:BackgroundPredicting 3-dimensional protein structures from amino-acid sequences is an important unsolved problem in computational structural biology. The problem becomes relatively easier if close homologous proteins have been solved, as high-resolution models can be built by aligning target sequences to the solved homologous structures. However, for sequences without similar folds in the Protein Data Bank (PDB) library, the models have to be predicted from scratch. Progress in the ab initio structure modeling is slow. The aim of this study was to extend the TASSER (threading/assembly/refinement) method for the ab initio modeling and examine systemically its ability to fold small single-domain proteins.ResultsWe developed I-TASSER by iteratively implementing the TASSER method, which is used in the folding test of three benchmarks of small proteins. First, data on 16 small proteins (< 90 residues) were used to generate I-TASSER models, which had an average Calpha-root mean square deviation (RMSD) of 3.8A, with 6 of them having a Calpha-RMSD < 2.5A. The overall result was comparable with the all-atomic ROSETTA simulation, but the central processing unit (CPU) time by I-TASSER was much shorter (150 CPU days vs. 5 CPU hours). Second, data on 20 small proteins (< 120 residues) were used. I-TASSER folded four of them with a Calpha-RMSD < 2.5A. The average Calpha-RMSD of the I-TASSER models was 3.9A, whereas it was 5.9A using TOUCHSTONE-II software. Finally, 20 non-homologous small proteins (< 120 residues) were taken from the PDB library. An average Calpha-RMSD of 3.9A was obtained for the third benchmark, with seven cases having a Calpha-RMSD < 2.5A.ConclusionOur simulation results show that I-TASSER can consistently predict the correct folds and sometimes high-resolution models for small single-domain proteins. Compared with other ab initio modeling methods such as ROSETTA and TOUCHSTONE II, the average performance of I-TASSER is either much better or is similar within a lower computational time. These data, together with the significant performance of automated I-TASSER server (the Zhang-Server) in the 'free modeling' section of the recent Critical Assessment of Structure Prediction (CASP)7 experiment, demonstrate new progresses in automated ab initio model generation. The I-TASSER server is freely available for academic users http://zhang.bioinformatics.ku.edu/I-TASSER.

Dataset Information

Ab Initio Molecular Dynamics Simulations of Aqueous LiTFSI Solutions─Structure, Hydrogen Bonding, and IR Spectra.

Publications

Ab Initio Molecular Dynamics Simulations of Aqueous LiTFSI Solutions─Structure, Hydrogen Bonding, and IR Spectra.

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