Common Cations Are Not Polarizable: Effects of Dispersion Correction on Hydration Structures from Ab Initio Molecular Dynamics

Košťál, Vojtěch; Mason, Philip E.; Martinez‐Seara, Hector; Jungwirth, Pavel

doi:10.1021/acs.jpclett.3c00856

Cited by 11 publications

(18 citation statements)

References 37 publications

(63 reference statements)

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“…94 Drawing from our data as well as a topic-focused "conversation" with ChatGPT (provided in the Supporting Information), we suggest some initial ways 12−14 It is also the acknowledged use of ChatGPT in some recent research articles. 15,16 (3) Execution and Revision of AI-Generated Protocols. AI has great potential for helping to develop lab protocols, but as described above, it gives experimental details that often do not fit a given real-life lab.…”

Section: Incorporation Of Generative Aimentioning

confidence: 99%

“…2−9 Some authors are using and acknowledging ChatGPT for manuscript text generation and/or improvement (Figure 1). 15,16 As per the guidelines of this Journal, 17 we acknowledge our use of ChatGPT for a conversation about its implementation in classrooms. Conversely, use of AI tools is not allowed for some academic applications; for example, as of June 2023, the NIH forbids the use of AI for peer review, citing a lack of confidentiality.…”

Section: ■ Introductionmentioning

confidence: 99%

“…Based on these data, we offer our own perspectives and considerations on the fit of generative AI in the chemistry curriculum. We offer some possible mitigation approaches for 15 (left) and second 16 (right) articles ever to cite ChatGPT use for language improvement within the ACS family of journals. those seeking to discourage student use as well as some suggestions for how to incorporate ChatGPT into laboratory writing assignments.…”

Section: ■ Introductionmentioning

confidence: 99%

“…Figure1. Acknowledgments sections from the first15 (left) and second16 (right) articles ever to cite ChatGPT use for language improvement within the ACS family of journals.…”

mentioning

confidence: 99%

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An Analysis of AI-Generated Laboratory Reports across the Chemistry Curriculum and Student Perceptions of ChatGPT

West,

Franz,

Hein

et al. 2023

J. Chem. Educ.

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AI technologies are rapidly pervading many areas of our world. AI-driven text generators such as ChatGPT are at the forefront of this due to their simplicity and accessibility. Their influence on higher education is already being observed, and perceptions among faculty and students vary widely. We have undertaken a cross-curriculum study of ChatGPT’s ability to generate laboratory reports. AI-generated reports from general, organic, analytical, physical, inorganic, and biochemistry courses were graded as if they were student reports and analyzed for grade distributions and common strengths and weaknesses. To further gauge ChatGPT’s current impact, we surveyed all students in our Spring 2023 laboratory courses regarding their awareness and use of ChatGPT. We have also laid out suggestions, guidance, and considerations for instructors who wish to prohibit ChatGPT use by their students as well as for those who wish to begin incorporating this new, powerful tool into their teaching.

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Section: Incorporation Of Generative Aimentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

“…Figure1. Acknowledgments sections from the first15 (left) and second16 (right) articles ever to cite ChatGPT use for language improvement within the ACS family of journals.…”

mentioning

confidence: 99%

See 2 more Smart Citations

An Analysis of AI-Generated Laboratory Reports across the Chemistry Curriculum and Student Perceptions of ChatGPT

West,

Franz,

Hein

et al. 2023

J. Chem. Educ.

View full text Add to dashboard Cite

show abstract

“…Electronic structure was calculated at each MD step by the revPBE-D3 − generalized gradient approximation (GGA) density functional. The pairwise D3 correction was employed while disabled specifically for all the pairs involving cations . The orbitals were expanded into the TZV2P Gaussian basis set, density into plane-wave basis with a 600 Ry energy cutoff, and the core electrons were represented by the Goedecker–Teter–Hutter (GTH) pseudopotentials .…”

Section: Computational Detailsmentioning

confidence: 99%

Nonaqueous Ion Pairing Exemplifies the Case for Including Electronic Polarization in Molecular Dynamics Simulations

Kostal,

Jungwirth,

Martinez-Seara

2023

J. Phys. Chem. Lett.

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The inclusion of electronic polarization is of crucial importance in molecular simulations of systems containing charged moieties. When neglected, as often done in force field simulations, charge–charge interactions in solution may become severely overestimated, leading to unrealistically strong bindings of ions to biomolecules. The electronic continuum correction introduces electronic polarization in a mean-field way via scaling of charges by the reciprocal of the square root of the high-frequency dielectric constant of the solvent environment. Here, we use ab initio molecular dynamics simulations to quantify the effect of electronic polarization on pairs of like-charged ions in a model nonaqueous environment where electronic polarization is the only dielectric response. Our findings confirm the conceptual validity of this approach, underlining its applicability to complex aqueous biomolecular systems. Simultaneously, the results presented here justify the potential employment of weaker charge scaling factors in force field development.

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Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters via Ab Initio Molecular Dynamics Simulations To Accurately Model Glycosaminoglycan Electrostatic Interactions

Riopedre-Fernandez,

Kostal,

Martinek

et al. 2024

J. Chem. Inf. Model.

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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 of GAGs is largely attributed to varied sulfation patterns along the polymer chains, which makes understanding their molecular recognition mechanisms crucial. Molecular dynamics (MD) simulations, thanks to their unmatched microscopic resolution, have the potential to be a reference tool for exploring the patterns responsible for biologically relevant interactions. However, the capability of molecular dynamics force fields used in biosimulations to accurately capture sulfation-specific interactions is not well established, partly due to the intrinsic properties of GAGs that pose challenges for most experimental techniques. In this work, we evaluate the performance of molecular dynamics force fields for sulfated GAGs by studying ion pairing of Ca 2+ to sulfated moieties— N -methylsulfamate and methylsulfate—that resemble N- and O-sulfation found in GAGs, respectively. We tested available nonpolarizable (CHARMM36 and GLYCAM06) and explicitly polarizable (Drude and AMOEBA) force fields, and derived new implicitly polarizable models through charge scaling (prosECCo75 and GLYCAM-ECC75) that are consistent with our developed “charge-scaling” framework. The calcium–sulfamate/sulfate interaction free energy profiles obtained with the tested force fields were compared against reference ab initio molecular dynamics (AIMD) simulations, which serve as a robust alternative to experiments. AIMD simulations indicate that the preferential Ca 2+ binding mode to sulfated GAG groups is solvent-shared pairing. Only our scaled-charge models agree satisfactorily with the AIMD data, while all other force fields exhibit poorer agreement, sometimes even qualitatively. Surprisingly, even explicitly polarizable force fields display a notable disagreement with the AIMD data, likely attributed to difficulties in their optimization and possible inherent limitations in depicting high-charge-density ion interactions accurately. Finally, the underperforming force fields lead to unrealistic aggregation of sulfated saccharides, which qualitatively disagrees with our understanding of the soft glycocalyx environment. Our results highlight the importance of accurately treating electronic polarization in MD simulations of sulfated GAGs and caution against over-reliance on currently available models without thorough validation and optimization.

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Common Cations Are Not Polarizable: Effects of Dispersion Correction on Hydration Structures from Ab Initio Molecular Dynamics

Cited by 11 publications

References 37 publications

An Analysis of AI-Generated Laboratory Reports across the Chemistry Curriculum and Student Perceptions of ChatGPT

An Analysis of AI-Generated Laboratory Reports across the Chemistry Curriculum and Student Perceptions of ChatGPT

Nonaqueous Ion Pairing Exemplifies the Case for Including Electronic Polarization in Molecular Dynamics Simulations

Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters via Ab Initio Molecular Dynamics Simulations To Accurately Model Glycosaminoglycan Electrostatic Interactions

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