Ion-Pairing Propensity in Guanidinium Salts Dictates Their Protein (De)stabilization Behavior DOI

Ria Saha,

Subhadip Chakraborty, Krishnendu Sinha

et al.

The Journal of Physical Chemistry Letters, Journal Year: 2024, Volume and Issue: 15(41), P. 10341 - 10348

Published: Oct. 7, 2024

Since the proposition of Hofmeister series, guanidinium (Gdm) salts hold a special mention in protein science owing to their contrasting effect on protein(s) depending counteranion(s). For example, while GdmCl is known act as potential denaturant, Gdm2SO4 offers minimal structure. Despite fact that theoretical studies reckon formation ion-pairing be responsible for such behavior, experimental validation this hypothesis still sparse. In study, we combine electrochemical impedance spectroscopy (EIS) and THz underline model amide molecule N-methylacetamide (NMA). Molecular dynamics (MD) simulation predict forms heteroion pairing water, which inhibits Gdm+ ions approach NMA molecules, case GdmCl, directly interact with NMA. The findings ion hydration, specifically detailed analysis ion–water rattling mode, appears frequency domain, unambiguously endorse hypothesis. Our study establishes propensity Gdm dictates (de)stabilization proteins.

Language: Английский

MBX: A many-body energy and force calculator for data-driven many-body simulations DOI Open Access
Marc Riera, Chris Knight, Ethan F. Bull-Vulpe

et al.

The Journal of Chemical Physics, Journal Year: 2023, Volume and Issue: 159(5)

Published: Aug. 1, 2023

Many-Body eXpansion (MBX) is a C++ library that implements many-body potential energy functions (PEFs) within the "many-body energy" (MB-nrg) formalism. MB-nrg PEFs integrate an underlying polarizable model with explicit machine-learned representations of interactions to achieve chemical accuracy from gas condensed phases. MBX can be employed either as stand-alone package or energy/force engine integrated generic software for molecular dynamics and Monte Carlo simulations. parallelized internally using Open Multi-Processing utilize Message Passing Interface when available in interfaced simulation software. enables classical quantum simulations PEFs, well hybrid combine conventional force fields diverse systems ranging small gas-phase clusters aqueous solutions fluids biomolecular metal-organic frameworks.

Language: Английский

Citations

38
Many-body interactions and deep neural network potentials for water DOI Creative Commons
Yaoguang Zhai,

Richa Rashmi,

Etienne Palos

et al.

The Journal of Chemical Physics, Journal Year: 2024, Volume and Issue: 160(14)

Published: April 8, 2024

We present a detailed assessment of deep neural network potentials developed within the Deep Potential Molecular Dynamics (DeePMD) framework and trained on MB-pol data-driven many-body potential energy function. Specific focus is directed at ability DeePMD-based to correctly reproduce accuracy across various water systems. Analyses bulk interfacial properties as well interactions characteristic elucidate inherent limitations in transferability predictive potentials. These can be traced back an incomplete implementation "nearsightedness electronic matter" principle, which may common throughout machine learning that do not include proper representation self-consistently determined long-range electric fields. findings provide further support for "short-blanket dilemma" faced by potentials, highlighting challenges achieving balance between computational efficiency rigorous, physics-based water. Finally, we believe our study contributes ongoing discourse development application models simulating systems, offering insights could guide future improvements field.

Language: Английский

Citations

11
Current Status of the MB-pol Data-Driven Many-Body Potential for Predictive Simulations of Water Across Different Phases DOI
Etienne Palos, Ethan F. Bull-Vulpe, Xuanyu Zhu

et al.

Journal of Chemical Theory and Computation, Journal Year: 2024, Volume and Issue: 20(21), P. 9269 - 9289

Published: Oct. 14, 2024

Developing a molecular-level understanding of the properties water is central to numerous scientific and technological applications. However, accurately modeling through computer simulations has been significant challenge due complex nature hydrogen-bonding network that molecules form under different thermodynamic conditions. This complexity led over five decades research many attempts. The introduction MB-pol data-driven many-body potential energy function marked advancement toward universal molecular model capable predicting structural, thermodynamic, dynamical, spectroscopic across all phases. By integrating physics-based (i.e., machine-learned) components, which correctly capture delicate balance among interactions, achieves chemical accuracy, enabling realistic water, from gas-phase clusters liquid ice. In this review, we present comprehensive overview formalism adopted by MB-pol, highlight main results predictions made with date, discuss prospects for future extensions potentials generic reactive systems.

Language: Английский

Citations

6
The Near-Sightedness of Many-Body Interactions in Anharmonic Vibrational Couplings DOI
R. Spencer, Asylbek A. Zhanserkeev, Emily L. Yang

et al.

Journal of the American Chemical Society, Journal Year: 2024, Volume and Issue: 146(22), P. 15376 - 15392

Published: May 21, 2024

Couplings between vibrational motions are driven by electronic interactions, and these couplings carry special significance in energy transfer, multidimensional spectroscopy experiments, simulations of spectra. In this investigation, the many-body contributions to analyzed computationally context clathrate-like alkali metal cation hydrates, including Cs+(H2O)20, Rb+(H2O)20, K+(H2O)20, using both analytic quantum-chemistry potential surfaces. Although harmonic spectra one-dimensional anharmonic depend strongly on mode-pair were, perhaps surprisingly, found be dominated one-body effects, even cases low-frequency modes that involved motion multiple water molecules. The origin effect was traced mainly geometric distortion within monomers cancellation effects differential couplings, also shown agnostic identity ion. These outcomes provide new understanding suggest possibility improved computational methods for simulation infrared Raman

Language: Английский

Citations

4
MBX V1.2: Accelerating Data-Driven Many-Body Molecular Dynamics Simulations DOI
Shreya Gupta, Ethan F. Bull-Vulpe, Henry Agnew

et al.

Journal of Chemical Theory and Computation, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 14, 2025

The MBX software provides an advanced platform for molecular dynamics simulations, leveraging state-of-the-art MB-pol and MB-nrg data-driven many-body potential energy functions. Developed over the past decade, these functions integrate physics-based machine-learned terms trained on electronic structure data calculated at "gold standard" coupled-cluster level of theory. Recent advancements in have focused optimizing its performance, resulting release v1.2. While inherently nature ensures high accuracy, it poses computational challenges. v1.2 addresses challenges with significant performance improvements, including enhanced parallelism that fully harnesses power modern multicore CPUs. These enable simulations nanosecond time scales condensed-phase systems, significantly expanding scope high-accuracy, predictive complex systems powered by

Language: Английский

Citations

0
Assessing the environmental influence on ‘local-monomer’ vibrational spectra via many-body potentials DOI
Alexandria G. Watrous,

Ryan P. Steele

Molecular Physics, Journal Year: 2025, Volume and Issue: unknown

Published: April 29, 2025

Language: Английский

Citations

0
Ion-Pairing Propensity in Guanidinium Salts Dictates Their Protein (De)stabilization Behavior DOI

Ria Saha,

Subhadip Chakraborty, Krishnendu Sinha

et al.

The Journal of Physical Chemistry Letters, Journal Year: 2024, Volume and Issue: 15(41), P. 10341 - 10348

Published: Oct. 7, 2024

Since the proposition of Hofmeister series, guanidinium (Gdm) salts hold a special mention in protein science owing to their contrasting effect on protein(s) depending counteranion(s). For example, while GdmCl is known act as potential denaturant, Gdm2SO4 offers minimal structure. Despite fact that theoretical studies reckon formation ion-pairing be responsible for such behavior, experimental validation this hypothesis still sparse. In study, we combine electrochemical impedance spectroscopy (EIS) and THz underline model amide molecule N-methylacetamide (NMA). Molecular dynamics (MD) simulation predict forms heteroion pairing water, which inhibits Gdm+ ions approach NMA molecules, case GdmCl, directly interact with NMA. The findings ion hydration, specifically detailed analysis ion–water rattling mode, appears frequency domain, unambiguously endorse hypothesis. Our study establishes propensity Gdm dictates (de)stabilization proteins.

Language: Английский

Citations

0