Preparative electrochromatography of proteins in various types of porous media

Tellez, Carlos M.; Cole, Kenneth D.

doi:10.1002/(sici)1522-2683(20000301)21:5<1001::aid-elps1001>3.0.co;2-3

Cited by 21 publications

(2 citation statements)

References 36 publications

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“…Accurate prediction of diffusion coefficients and associated mass transport is important for understanding many phenomena, including transport in intercellular media, , protein aggregation, molecular processing, and for the validation of molecular mechanics force fields. In addition, molecular diffusion can be a limiting factor in the rates of chemical reactions, so an accurate description of diffusion is key for predicting reaction yields.…”

Section: Introductionmentioning

confidence: 99%

Effective Fragment Potential-Based Molecular Dynamics Studies of Diffusion in Acetone and Hexane

et al. 2021

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To facilitate more reliable descriptions of transport properties in liquids, molecular dynamics (MD) simulations are performed based on the effective fragment potential (EFP) method derived from first-principles quantum mechanics (in contrast to MD based upon empirically fitted potentials). The EFP method describes molecular interactions in terms of Coulomb, polarization/induction, dispersion, exchange-repulsion, and charge-transfer interactions. The EFP MD simulations described in this paper, performed on hexane and acetone, are able to track the mean-square displacement of molecules for sufficient time to reliably extract translational diffusion coefficients. The results reported here are in reasonable agreement with experiment.

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Section: Introductionmentioning

confidence: 99%

Effective Fragment Potential-Based Molecular Dynamics Studies of Diffusion in Acetone and Hexane

et al. 2021

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“…Development of reliable methods of predicting diffusion coefficients for proteins and other macromolecules is of great interest as diffusion is involved in a number of biochemical processes, such as protein aggregation [2] and transportation in intercellular media. [3,4] Molecular dynamics (MD) simulation is an essential technique to study a variety of molecular properties including molecular diffusion. It can study diffusion process not only in atomic details but also under a thermodynamic condition that is unreachable by experiments.…”

Section: Introductionmentioning

confidence: 99%

Application of molecular dynamics simulations in molecular property prediction II: Diffusion coefficient

2011

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In this work, we have evaluated how well the General AMBER force field (GAFF) performs in studying the dynamic properties of liquids. Diffusion coefficients (D) have been predicted for 17 solvents, 5 organic compounds in aqueous solutions, 4 proteins in aqueous solutions, and 9 organic compounds in non-aqueous solutions. An efficient sampling strategy has been proposed and tested in the calculation of the diffusion coefficients of solutes in solutions. There are two major findings of this study. First of all, the diffusion coefficients of organic solutes in aqueous solution can be well predicted: the average unsigned error (AUE) and the root-mean-square error (RMSE) are 0.137 and 0.171 ×10−5 cm−2s−1, respectively. Second, although the absolute values of D cannot be predicted, good correlations have been achieved for 8 organic solvents with experimental data (R2 = 0.784), 4 proteins in aqueous solutions (R2 = 0.996) and 9 organic compounds in non-aqueous solutions (R2 = 0.834). The temperature dependent behaviors of three solvents, namely, TIP3P water, dimethyl sulfoxide (DMSO) and cyclohexane have been studied. The major MD settings, such as the sizes of simulation boxes and with/without wrapping the coordinates of MD snapshots into the primary simulation boxes have been explored. We have concluded that our sampling strategy that averaging the mean square displacement (MSD) collected in multiple short-MD simulations is efficient in predicting diffusion coefficients of solutes at infinite dilution.

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