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PreprintCC BYChemRxiv

GMAP: A General Purpose Hamiltonian Mapping Program for Computational Spectroscopy

  • Kim E. van Adrichem1
  • Tim Zuidema1
  • Stephanie Gonzalez-Migoni1
  • Gijsbert A. H. ten Hoven1
  • Kai Zhong1
  • Mónica K. Espinoza Cangahuala1
  • Mia L. Falatko1
  • Markuss G. Ķēniņš1,2
  • Tsjerk A. Wassenaar3,4
  • Thomas L. C. Jansen1
4 affiliations
  1. 1Zernike Institute for Advanced Materials, AG Groningen, Nijenborgh 3, Netherlands, 9747
  2. 2Department of Mathematics, Rämistrasse 101, Zürich, Switzerland, CH-8092
  3. 3Groningen Biomolecular Sciences and Biotechnology institute, University of Groningen, Nijenborgh 7, AG Groningen, Netherlands, 9747
  4. 4Knowledge Center Biobased Economy, Zernikeplein 11, AS Groningen, Netherlands, 9747
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Abstract

Vibrational and electronic spectra provide useful information about structure, dynamics, and function in the condensed phase. Electrostatic mappings have proved to be powerful tools for predicting and interpreting both vibrational and electronic spectra. Numerous special purpose programs exist; however, a general purpose framework is still missing. In this paper, we present a new general purpose mapping program for bridging the gap between structural and dynamical information obtained in molecular dynamics simulations and programs for calculating spectroscopic observables. It comes with a number of preexisting maps to, for example, predict the amide I vibrational spectrum of proteins or to model the electronic Qy band of strongly coupled chlorophyll molecules in photosynthetic systems. The program applying mappings connecting structural or electrostatic properties with excitation frequencies, transition dipoles, and couplings is designed so that the user can easily adapt existing maps or add new maps for desired chromophores.

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Cite

BibTeXRIS
BibTeX
@misc{adrichem2026gmap,
  title = {{GMAP: A General Purpose Hamiltonian Mapping Program for Computational Spectroscopy}},
  author = {Kim E. van Adrichem and Tim Zuidema and Stephanie Gonzalez-Migoni and Gijsbert A. H. ten Hoven and Kai Zhong and Mónica K. Espinoza Cangahuala and Mia L. Falatko and Markuss G. Ķēniņš and Tsjerk A. Wassenaar and Thomas L. C. Jansen},
  howpublished = {ChemRxiv},
  year = {2026},
  month = oct,
  doi = {10.26434/chemrxiv.15010172/v1},
  url = {https://chemrxiv.org/doi/full/10.26434/chemrxiv.15010172/v1},
  note = {CC BY},
}
RIS
TY  - UNPB
TI  - GMAP: A General Purpose Hamiltonian Mapping Program for Computational Spectroscopy
AU  - Kim E. van Adrichem
AU  - Tim Zuidema
AU  - Stephanie Gonzalez-Migoni
AU  - Gijsbert A. H. ten Hoven
AU  - Kai Zhong
AU  - Mónica K. Espinoza Cangahuala
AU  - Mia L. Falatko
AU  - Markuss G. Ķēniņš
AU  - Tsjerk A. Wassenaar
AU  - Thomas L. C. Jansen
PY  - 2026
DA  - 2026/10/09
PB  - ChemRxiv
DO  - 10.26434/chemrxiv.15010172/v1
UR  - https://chemrxiv.org/doi/full/10.26434/chemrxiv.15010172/v1
AB  - Vibrational and electronic spectra provide useful information about structure, dynamics, and function in the condensed phase. Electrostatic mappings have proved to be powerful tools for predicting and interpreting both vibrational and electronic spectra. Numerous special purpose programs exist; however, a general purpose framework is still missing. In this paper, we present a new general purpose mapping program for bridging the gap between structural and dynamical information obtained in molecular dynamics simulations and programs for calculating spectroscopic observables. It comes with a number of preexisting maps to, for example, predict the amide I vibrational spectrum of proteins or to model the electronic Qy band of strongly coupled chlorophyll molecules in photosynthetic systems. The program applying mappings connecting structural or electrostatic properties with excitation frequencies, transition dipoles, and couplings is designed so that the user can easily adapt existing maps or add new maps for desired chromophores.
ER  -