Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters via Ab Initio Molecular Dynamics Simulations To Accurately Model Glycosaminoglycan Electrostatic Interactions DOI Creative Commons
Miguel Riopedre-Fernández, Vojtěch Košt́ál, Tomáš Martínek

и другие.

Journal of Chemical Information and Modeling, Год журнала: 2024, Номер 64(18), С. 7122 - 7134

Опубликована: Сен. 9, 2024

Glycosaminoglycans (GAGs) are negatively charged polysaccharides found on cell surfaces, where they regulate transport pathways of foreign molecules toward the cell. The structural and functional diversity GAGs is largely attributed to varied sulfation patterns along polymer chains, which makes understanding their molecular recognition mechanisms crucial. Molecular dynamics (MD) simulations, thanks unmatched microscopic resolution, have potential be a reference tool for exploring responsible biologically relevant interactions. However, capability force fields used in biosimulations accurately capture sulfation-specific interactions not well established, partly due intrinsic properties that pose challenges most experimental techniques. In this work, we evaluate performance sulfated by studying ion pairing Ca

Язык: Английский

Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field DOI Creative Commons
Ricky Nencini, Carmelo Tempra, Denys Biriukov

и другие.

Journal of Chemical Theory and Computation, Год журнала: 2024, Номер 20(17), С. 7546 - 7559

Опубликована: Авг. 26, 2024

prosECCo75 is an optimized force field effectively incorporating electronic polarization via charge scaling. It aims to enhance the accuracy of nominally nonpolarizable molecular dynamics simulations for interactions in biologically relevant systems involving water, ions, proteins, lipids, and saccharides. Recognizing inherent limitations fields precisely modeling electrostatic essential various biological processes, we mitigate these shortcomings by accounting polarizability a physically rigorous mean-field way that does not add computational costs. With this scaling (both integer partial) charges within CHARMM36 framework, addresses overbinding artifacts. This improves agreement with experimental ion binding data across broad spectrum systems─lipid membranes, proteins (including peptides amino acids), saccharides─without compromising their biomolecular structures. thus emerges as computationally efficient tool providing enhanced broader applicability simulating complex interplay between ions biomolecules, pivotal improving our understanding many processes.

Язык: Английский

Процитировано

14
Accuracy limit of non-polarizable four-point water models: TIP4P/2005 vs OPC. Should water models reproduce the experimental dielectric constant? DOI
L. F. Sedano, S. Blazquez, Carlos Vega

и другие.

The Journal of Chemical Physics, Год журнала: 2024, Номер 161(4)

Опубликована: Июль 24, 2024

The last generation of four center non-polarizable models water can be divided into two groups: those reproducing the dielectric constant water, as OPC, and significantly underestimating its value, TIP4P/2005. To evaluate global performance OPC TIP4P/2005, we shall follow test proposed by Vega Abascal in 2011 evaluating about 40 properties to fairly address this comparison. liquid–vapor liquid–solid equilibria are computed, well heat capacities, isothermal compressibilities, surface tensions, densities different ice polymorphs, density maximum, equations state at high pressures, transport properties. General aspects phase diagram considered comparing ratios temperatures (namely, temperature maximum density, melting hexagonal ice, critical temperature). final scores 7.2 for TIP4P/2005 6.3 OPC. results work strongly suggest that have reached limit what achieved with attempt reproduce experimental deteriorates force field. reason is depends on surfaces (potential energy dipole moment surfaces), whereas absence an electric field, all determined simply from just one (the potential surface). consequences choice model modeling electrolytes also discussed.

Язык: Английский

Процитировано

8
Theoretically grounded approaches to account for polarization effects in fixed-charge force fields DOI
Miguel Jorge

The Journal of Chemical Physics, Год журнала: 2024, Номер 161(18)

Опубликована: Ноя. 8, 2024

Non-polarizable, or fixed-charge, force fields are the workhorses of most molecular simulation studies. They attempt to describe potential energy surface (PES) system by including polarization effects in an implicit way. This has historically been done a rather empirical and ad hoc manner. Recent theoretical treatments polarization, however, offer promise for getting out fixed-charge judicious choice parameters (most significantly net charge dipole moment model) application post facto corrections. Perspective describes these theories, namely "halfway-charge" theory dynamics electronic continuum theory, shows that they lead qualitatively (and often, quantitatively) similar predictions. Moreover, can be reconciled into unified approach construct field development workflow yield non-polarizable models with charge/dipole values provide optimal description PES. Several applications this reviewed, avenues future research proposed.

Язык: Английский

Процитировано

4
Self-Assembled Oligomers Facilitate Amino Acid-Driven CO2 Capture at the Air–Aqueous Interface DOI
Nitesh Kumar, Vyacheslav S. Bryantsev

The Journal of Physical Chemistry B, Год журнала: 2025, Номер unknown

Опубликована: Янв. 29, 2025

Direct air capture of CO2 using amino acid absorbents, such as glycine or sarcosine, is constrained by the relatively slow mass transfer through air-aqueous interface. Our recent study showed a marked improvement in introducing CO2-permeable oligo-dimethylsiloxane (ODMS-MIM+) oligomers with cationic (imidazolium, MIM+) headgroups. In this work, we have employed all-atom molecular dynamics simulations combination subensemble analysis network theory to provide detailed picture behavior and glycinate anions (Gly-) at ODMS-MIM+ decorated interfaces. We show that head groups surfactants enhance concentration lifetime Gly- interfacial region, while ODMS tails promote physisorption region. Together, these two factors increase effective region contact probability interactions between compared pure The fundamental insights gained work establish essential foundations for developing hybrid systems oligomer-decorated interfaces maximize overall rates.

Язык: Английский

Процитировано

0
Transport properties of CaCl2 are determined by the balance of ion-ion and ion-water interactions as revealed by molecular dynamics simulations DOI Creative Commons

Salman Shabbir,

Dezső Boda, Zoltán Ható

и другие.

Journal of Molecular Liquids, Год журнала: 2025, Номер unknown, С. 127308 - 127308

Опубликована: Март 1, 2025

Язык: Английский

Процитировано

0
Experimental evidence of quantum Drude oscillator behavior in liquids revealed with probabilistic iterative Boltzmann inversion DOI
B. Shanks, Harry W. Sullivan, Pavel Jungwirth

и другие.

The Journal of Chemical Physics, Год журнала: 2025, Номер 162(16)

Опубликована: Апрель 22, 2025

The first experimental evidence of quantum Drude oscillator behavior in liquids is uncovered using probabilistic machine learning-augmented iterative Boltzmann inversion applied to noble gas radial distribution functions. Furthermore, classical force fields for gases are shown be reduced a single parameter through simple empirical relations linked atomic dipole polarizability. These findings highlight how neutron scattering data can inspire innovative field design and offer insight into interatomic forces advance molecular simulations.

Язык: Английский

Процитировано

0
Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field DOI Creative Commons
Ricky Nencini, Carmelo Tempra, Denys Biriukov

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 3, 2024

prosECCo75 is an optimized force field effectively incorporating electronic polarization via charge scaling. It aims to enhance the accuracy of nominally nonpolarizable molecular dynamics (MD) simulations for interactions in biologically relevant systems involving water, ions, proteins, lipids, and saccharides. Recognizing inherent limitations fields precisely modeling electrostatic essential various biological processes, we mitigate these shortcomings by accounting polarizability a physical rigorous mean-field way that does not add computational costs. With this scaling (both integer partial) charges within CHARMM36 framework, addresses overbinding artifacts. This improves agreement with experimental ion binding data across broad spectrum - lipid membranes, proteins (including peptides amino acids), saccharides without compromising their biomolecular structures. thus emerges as computationally efficient tool providing enhanced broader applicability simulating complex interplay between ions biomolecules, pivotal improving our understanding many processes.

Язык: Английский

Процитировано

2
Beyond the Debye–Hückel limit: Toward a general theory for concentrated electrolytes DOI Creative Commons
Mohammadhasan Dinpajooh, Nadia N. Intan, Timothy T. Duignan

и другие.

The Journal of Chemical Physics, Год журнала: 2024, Номер 161(23)

Опубликована: Дек. 16, 2024

The phenomenon of underscreening in concentrated electrolyte solutions leads to a larger decay length the charge-charge correlation than prediction Debye-Hückel (DH) theory and has found resurgence both theoretical experimental interest chemical physics community. To systematically understand investigate this electrolytes requires describe correlations beyond DH theory. We review theories that can transition from limit concentrations where charge dominate, giving rise associated Kirkwood Transitions (KTs). In perspective, we provide conceptual approach formulation exploits competition between molecular-informed short-range (SR) long-range interactions. demonstrate all deviations for real be expressed through single function ΣQ determined theoretically numerically. Importantly, directly related details SR interactions and, therefore, used as tool how differences representations interaction influence collective effects. precise form inferred Gaussian field number densities. resulting is validated by experiment accurately screening bulk electrolytes. predictions lengths appear less ∼1 nm at above KTs.

Язык: Английский

Процитировано

2
Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters via Ab Initio Molecular Dynamics Simulations To Accurately Model Glycosaminoglycan Electrostatic Interactions DOI Creative Commons
Miguel Riopedre-Fernández, Vojtěch Košt́ál, Tomáš Martínek

и другие.

Journal of Chemical Information and Modeling, Год журнала: 2024, Номер 64(18), С. 7122 - 7134

Опубликована: Сен. 9, 2024

Glycosaminoglycans (GAGs) are negatively charged polysaccharides found on cell surfaces, where they regulate transport pathways of foreign molecules toward the cell. The structural and functional diversity GAGs is largely attributed to varied sulfation patterns along polymer chains, which makes understanding their molecular recognition mechanisms crucial. Molecular dynamics (MD) simulations, thanks unmatched microscopic resolution, have potential be a reference tool for exploring responsible biologically relevant interactions. However, capability force fields used in biosimulations accurately capture sulfation-specific interactions not well established, partly due intrinsic properties that pose challenges most experimental techniques. In this work, we evaluate performance sulfated by studying ion pairing Ca

Язык: Английский

Процитировано

1