The critical helping hand of water: theory shows the way to obtain elusive, granular information about kinetic asymmetry driven systems

Kinetic asymmetry is crucial in chemical systems where the selective synthesis of one product over another, or the acceleration of specific reaction(s) is necessary. However, obtaining precise information with current experimental methods about the behavior of such systems as a function of time, substrate concentration and other relevant factors, is not possible. Computational chemistry provides a powerful means to address this problem. The current study unveils a two-pronged computational approach: (i) full quantum chemical studies with density functional theory (DFT), followed by (ii) stochastic simulations with a validated Gillespie algorithm (GA) (using representative model systems where necessary), to study the behavior of a kinetic asymmetry driven unidirectional molecular motor (1-phenylpyrrole2,2'-dicarboxylic acid) (<i>Nature</i>, 2022, <b>604</b> (7904), 80-85). Our approach allows us to understand what is really taking place in the system, underlining the crucial role played by water molecules in facilitating the rotation of the motor. It is seen that water lubricates the motion by increasing the rotation rate constant of the final step by, remarkably, more than ten orders of magnitude! These insights further serve to explain the efficient rotation of the very recently reported gel-embedded molecular motor (<i>Nature</i>, 2025, <b>637</b> (8046), 594-600), providing an upper limit for the allowed rotation barrier in such systems, and thus also casts light into the functioning of bio-molecular motors. The current work therefore provides a template for carefully and properly studying a wide variety of important, kinetic asymmetry driven systems in the future.

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Publication Details

Journal
Chemical Science
Published
2025-01-01
DOI
https://doi.org/10.1039/d5sc03256c
Primary Topic
Advanced Thermodynamics and Statistical Mechanics
Type
article
Field-Weighted Citation Impact
0.00

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article

The critical helping hand of water: theory shows the way to obtain elusive, granular information about kinetic asymmetry driven systems

Kumar Vanka, Priyam Bajpai, Shrivatsa Thulasiram
Chemical Science
Advanced Thermodynamics and Statistical Mechanics
article

The critical helping hand of water: theory shows the way to obtain elusive, granular information about kinetic asymmetry driven systems

Kumar Vanka, Priyam Bajpai, Shrivatsa Thulasiram
article en

Abstract

Kinetic asymmetry is crucial in chemical systems where the selective synthesis of one product over another, or the acceleration of specific reaction(s) is necessary. However, obtaining precise information with current experimental methods about the behavior of such systems as a function of time, substrate concentration and other relevant factors, is not possible. Computational chemistry provides a powerful means to address this problem. The current study unveils a two-pronged computational approach: (i) full quantum chemical studies with density functional theory (DFT), followed by (ii) stochastic simulations with a validated Gillespie algorithm (GA) (using representative model systems where necessary), to study the behavior of a kinetic asymmetry driven unidirectional molecular motor (1-phenylpyrrole2,2'-dicarboxylic acid) (<i>Nature</i>, 2022, <b>604</b> (7904), 80-85). Our approach allows us to understand what is really taking place in the system, underlining the crucial role played by water molecules in facilitating the rotation of the motor. It is seen that water lubricates the motion by increasing the rotation rate constant of the final step by, remarkably, more than ten orders of magnitude! These insights further serve to explain the efficient rotation of the very recently reported gel-embedded molecular motor (<i>Nature</i>, 2025, <b>637</b> (8046), 594-600), providing an upper limit for the allowed rotation barrier in such systems, and thus also casts light into the functioning of bio-molecular motors. The current work therefore provides a template for carefully and properly studying a wide variety of important, kinetic asymmetry driven systems in the future.

Chemical ScienceVol. 16(33)
Indian Institute of Science Education and Research Pune (IN), National Chemical Laboratory (IN), Academy of Scientific and Innovative Research (IN)
Department of Science and Technology, Ministry of Science and Technology, India, Indian Institute of Science Education and Research Pune, Indian Institute of Science Education and Research Mohali, Science and Engineering Research Board
Openalex Percentile: Top 86%
Advanced Thermodynamics and Statistical Mechanics
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