Skip to content
DraconiticResearch
Search Sources API
203,234 studies31 sourcesUpdated 44 min ago
PreprintCC BYChemRxiv

Atomic Decomposition and Mapping of Solute Thermodynamics

  • Joe Cruz
  • Samrat Lohar
  • Helmut Carter
  • Steven Ramsey1,2
  • Daniel R. Roe3,4
  • Michael K. Gilson5,6
  • Tom Kurtzman1,2
6 affiliations
  1. 1Department of Chemistry, Lehman College4
  2. 2City University of New York
  3. 3National Heart, Lung, and Blood Institute
  4. 4National Institutes of Health
  5. 5Skaggs School of Pharmacy and Pharmaceutical Sciences
  6. 6University of California San Diego
Open at sourcePDFDOICite

Abstract

Here we present theory, methods, and software that decomposes the free energy of a solvated solute into its energetic and entropic contributions and maps these quantities to solute atoms. Because the mapping is atomic, contributions can be summed over any set of atoms of interest, giving thermodynamic values for ligand functional groups, protein backbone and side chains, individual residues, or an entire binding site. Software implementing the energy decomposition is integrated into cpptraj in AmberTools and software introduced and described here. We illustrate the approach by atomistically mapping the energetic and entropic contributions of ligand 735 and of the binding-site residues of PPAR-α.

Related

  1. Universal mapping of the structural space by 20 NMR-verifiable C,H,O-atomic units
    Norbert Hertkorn, Siyu Li, Sepehr Shakeri Yekta +7
    ChemRxivPreprintLicence not statedPhysical chemistryChemRxiv
  2. SCO ATLAS: Mapping Spin-Crossover Thermodynamics across Experimentally Grounded Fe(II)N6 Complexes
    Sergi Vela
    ChemRxivPreprintCC BYFull textMaterials & polymersChemRxiv
  3. Atomic-Scale Mapping of an Emergent Interfacial Two-Dimensional Electron Gas at Anatase/LaAlO3
    Michael Oberaigner, Manuel Ederer, Sandeep K. Chaluvadi +5
    Nano LettersPeer-reviewedCC BY 4.0Full textMaterials & polymersPMC
  4. Relating solute interactions to interfacial properties
    Varun Mandalaparthy, Benjamin M. Curlee, William G. Noid
    arXivPreprintCC BY 4.0Full textPhysical chemistryCondensed matterarXiv
  5. Sequential replica exchange with solute tempering for atomistic modeling of supramolecular polymer structures
    Hadi H. Arefi, Takeshi Yamamoto
    arXivPreprintarXiv licenceFull textPhysical chemistryCondensed matterarXiv

Cite

BibTeXRIS
BibTeX
@misc{cruz2026atomic,
  title = {{Atomic Decomposition and Mapping of Solute Thermodynamics}},
  author = {Joe Cruz and Samrat Lohar and Helmut Carter and Steven Ramsey and Daniel R. Roe and Michael K. Gilson and Tom Kurtzman},
  howpublished = {ChemRxiv},
  year = {2026},
  month = aug,
  doi = {10.26434/chemrxiv.15008034/v1},
  url = {https://chemrxiv.org/doi/full/10.26434/chemrxiv.15008034/v1},
  note = {CC BY},
}
RIS
TY  - UNPB
TI  - Atomic Decomposition and Mapping of Solute Thermodynamics
AU  - Joe Cruz
AU  - Samrat Lohar
AU  - Helmut Carter
AU  - Steven Ramsey
AU  - Daniel R. Roe
AU  - Michael K. Gilson
AU  - Tom Kurtzman
PY  - 2026
DA  - 2026/08/30
PB  - ChemRxiv
DO  - 10.26434/chemrxiv.15008034/v1
UR  - https://chemrxiv.org/doi/full/10.26434/chemrxiv.15008034/v1
AB  - Here we present theory, methods, and software that decomposes the free energy of a solvated solute into its energetic and entropic contributions and maps these quantities to solute atoms. Because the mapping is atomic, contributions can be summed over any set of atoms of interest, giving thermodynamic values for ligand functional groups, protein backbone and side chains, individual residues, or an entire binding site. Software implementing the energy decomposition is integrated into cpptraj in AmberTools and software introduced and described here. We illustrate the approach by atomistically mapping the energetic and entropic contributions of ligand 735 and of the binding-site residues of PPAR-α.
ER  -