Student or educator? Sign up with your school email and get 6 months of Pro free.
CoChat
Sign Up
Cited by 785

The DOI matches its Crossref record; 76 of the 76 references it cites were found in a registry or an index.

Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent

Open access
Li, Pengfei, Roberts, Benjamin P., Chakravorty, Dhruva K., Merz, Kenneth M.·2013·Journal of Chemical Theory and Computation
DOI 10.1021/ct400146w
Open this paper in CoChat — free account

Abstract

Metal ions play significant roles in biological systems. Accurate molecular dynamics (MD) simulations on these systems require a validated set of parameters. Although there are more detailed ways to model metal ions, the nonbonded model, which employs a 12–6 Lennard-Jones (LJ) term plus an electrostatic potential, is still widely used in MD simulations today due to its simple form. However, LJ parameters have limited transferability due to different combining rules, various water models, and diverse simulation methods. Recently, simulations employing a Particle Mesh Ewald (PME) treatment for long-range electrostatics have become more and more popular owing to their speed and accuracy. In the present work, we have systematically designed LJ parameters for 24 +2 metal (M(II)) cations to reproduce different experimental properties appropriate for the Lorentz–Berthelot combining rules and PME simulations. We began by testing the transferability of currently available M(II) ion LJ parameters. The results showed that there are differences between simulations employing Ewald summation with other simulation methods and that it was necessary to design new parameters specific for PME based simulations. Employing the thermodynamic integration (TI) method and performing periodic boundary MD simulations employing PME, allowed for a systematic investigation of the LJ parameter space. Hydration free energies (HFEs), the ion–oxygen distance in the first solvation shell (IOD), and coordination numbers (CNs) were obtained for various combinations of the parameters of the LJ potential for four widely used water models (TIP3P, SPC/E, TIP4P, and TIP4P EW ). Results showed that the three simulated properties were highly correlated. Meanwhile, M(II) ions with the same parameters in different water models produce remarkably different HFEs but similar structural properties. It is difficult to reproduce various experimental values simultaneously because the nonbonded model underestimates the interaction between the metal ions and water molecules at short-range. Moreover, the extent of underestimation increases successively for the TIP3P, SPC/E, TIP4P EW, and TIP4P water models. Nonetheless, we fitted a curve to describe the relationship between ε (the well depth) and radius ( R min /2) from experimental data on noble gases to facilitate the generation of the best possible compromise models. Hence, by targeting different experimental values, we developed three sets of parameters for M(II) cations for three different water models (TIP3P, SPC/E, and TIP4P EW ). These parameters we feel represent the best possible compromise that can be achieved using the nonbonded model for the ions in combination with simple water models. From a computational uncertainty analysis we estimate that the uncertainty in our computed HFEs is on the order of ±1 kcal/mol. Further improvements will require more advanced nonbonded models likely with inclusion of polarization.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1021/ct400146w

Cites

76 of 76 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Research works printed but not linked: 15

  1. Chakravorty D. K., 2011, J. Am. Chem. Soc., 133, 19330, 10.1021/ja208662z · doi:10.1021/ja208662z
  2. Chakravorty D., 2013, J. Biomol. NMR, 1
  3. Ponomarev S. Y., 2011, J. Phys. Chem. B, 115, 10079, 10.1021/jp2051933 · doi:10.1021/jp2051933
  4. Mancini G., 2008, J. Phys. Chem. B, 112, 4694, 10.1021/jp074545s · doi:10.1021/jp074545s
  5. Migliorati V., 2011, Inorg. Chem., 50, 8509, 10.1021/ic201100q · doi:10.1021/ic201100q
  6. Migliorati V., 2011, J. Phys. Chem. A, 115, 4798, 10.1021/jp201060y · doi:10.1021/jp201060y
  7. Marrone T. J., 1994, J. Phys. Chem., 98, 8256, 10.1021/j100084a050 · doi:10.1021/j100084a050
  8. Mitchell M. J., 1991, J. Comput. Chem., 12, 271, 10.1002/jcc.540120218 · doi:10.1002/jcc.540120218
  9. Mezei M., 1987, J. Chem. Phys., 86, 7084, 10.1063/1.452357 · doi:10.1063/1.452357
  10. Yang J., 2007, J. Comput. Phys., 221, 799, 10.1016/j.jcp.2006.06.039 · doi:10.1016/j.jcp.2006.06.039
  11. Liu W., 2008, Comput. Phys. Commun., 179, 634, 10.1016/j.cpc.2008.05.008 · doi:10.1016/j.cpc.2008.05.008
  12. Liu W., 2007, High Performance Computing, 4873, 185
  13. Miyanaga T., 1988, Chem. Lett., 17, 1073, 10.1246/cl.1988.1073 · doi:10.1246/cl.1988.1073
  14. Radëtìsig A., 1985, Reference Data on Atoms, Molecules, and Ions
  15. Stokes R., 1964, J. Am. Chem. Soc., 86, 979, 10.1021/ja01060a002 · doi:10.1021/ja01060a002

Cited by

See all 785

Metadata

Authors
Li, P., Roberts, B. P., Chakravorty, D. K., & Merz, K. M.
Venue
Journal of Chemical Theory and Computation
Publisher
American Chemical Society (ACS)
Published
2013-05-23
Volume
9
Issue
6
Pages
2733-2748
ISSN
  • 1549-9618 (ISSN-L)
  • 1549-9626
DOI
10.1021/ct400146w
OpenAlex
W1979401635
Cited by
785
References
76
FWCI
15.47
Type
journal article
Language
en
Open access
green

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.