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Molecular Modeling in Pharmaceutical Sciences

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pharmacology".

Deadline for manuscript submissions: 20 June 2026 | Viewed by 449

Special Issue Editor


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Guest Editor
Department of Organic Chemistry and Pharmaceutical Technology, Wroclaw Medical University, Borowska 211 A, 50-556 Wroclaw, Poland
Interests: antioxidants; antisense oligonucleotides; photodynamic therapy; senotherapeutics; molecular modeling; computer aided drug design
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Special Issue Information

Dear Colleagues,

Molecular modeling is a powerful tool in chemistry that enables the exploration and understanding of chemical and biochemical processes at the atomistic level. Its application in pharmacy is broad and impactful, ranging from elucidating mechanisms of drug action to predicting interactions of bioactive molecules with biological targets. This Special Issue aims to highlight advances in molecular modeling techniques—including quantum mechanics, molecular dynamics, and hybrid approaches—applied to pharmaceutically relevant compounds. Topics of interest include, but are not limited to, mechanistic studies of drug action at the molecular level; the simulation of interactions with proteins, membranes, nucleic acids, or other biomolecules; the modeling of synthetic or natural bioactive compounds; and structure-based drug design and activity prediction for novel or known compounds. Submissions may involve either newly synthesized compounds or theoretical predictions of pharmacological activity. We welcome original research articles and short communications that offer novel insights or methodological advances in this area.

Dr. Maciej Spiegel
Guest Editor

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Keywords

  • molecular modeling
  • computer-aided drug design
  • molecular docking
  • drug discovery
  • quantum chemistry
  • molecular dynamics simulations
  • virtual screening
  • computational pharmacology
  • pharmacy
  • in silico methods

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Published Papers (1 paper)

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Research

26 pages, 2519 KB  
Article
Two–Photon Absorption Properties and Structure–Property Relationships of Natural 9,10–Anthraquinones: A Curated RI–CC2 Dataset
by Maciej Spiegel
Int. J. Mol. Sci. 2026, 27(1), 87; https://doi.org/10.3390/ijms27010087 - 21 Dec 2025
Viewed by 221
Abstract
This work provides the first systematic survey of the two–photon properties of 97 natural 9,10–anthraquinones from plants and fungi. A comprehensive computational dataset of two–photon absorption properties calculated using RI–CC2/aug–cc–pVDZ is presented. Single degenerate photon energies required for two–photon excitation span 491.6–1007.9 nm [...] Read more.
This work provides the first systematic survey of the two–photon properties of 97 natural 9,10–anthraquinones from plants and fungi. A comprehensive computational dataset of two–photon absorption properties calculated using RI–CC2/aug–cc–pVDZ is presented. Single degenerate photon energies required for two–photon excitation span 491.6–1007.9 nm across the five lowest singlet states, with all S0→S1 transitions falling within the biological therapeutic window. Remarkably, S3 state exhibits systematically enhanced TPA efficiency, with 60% of compounds surpassing 1 GM and achieving a mean cross–section of 29.9 GM–substantially higher than S1 (mean: 7.5 GM). Three compounds demonstrate exceptional performance: cynodontin (73.6 GM, S2), dermocybin (68.7 GM, S4), and morindone (50.7 GM, S3). Orbital analysis reveals that these excitations possess high configurational purity and diagnostics validating the single–reference treatment. The observed spatial separation between hole and particle NTOs, combined with extreme transition dipole anisotropy along the molecular long axis, indicates dipolar charge–transfer enhancement. Comprehensive structure–property analysis establishes that strategic modification may maximise TPA cross–sections. Comparison with aqueous–phase calculations for three compounds reveals non–systematic solvent–induced redistributions of TPA activity across excited states, indicating that gas–phase outcomes serve primarily as internal benchmarks and intrinsic descriptors of structure–property relationships rather than quantitative predictors of photoactivity. Full article
(This article belongs to the Special Issue Molecular Modeling in Pharmaceutical Sciences)
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