We present a versatile new code released for open community use, the nonadiabatic excited state molecular dynamics (NEXMD) package. This software aims to simulate nonadiabatic excited state molecular dynamics using several semiempirical Hamiltonian models. To model such dynamics of a molecular system, the NEXMD uses the fewest-switches surface hopping algorithm, where the probability of transition from one state to another depends on the strength of the derivative nonadiabatic coupling. In addition, there are a number of algorithmic improvements such as empirical decoherence corrections and tracking trivial crossings of electronic states. While the primary intent behind the NEXMD was to simulate nonadiabatic molecular dynamics, the code can also perform geometry optimizations, adiabatic excited state dynamics, and single-point calculations all in vacuum or in a simulated solvent. In this report, first, we lay out the basic theoretical framework underlying the code. Then we present the code's structure and workflow. To demonstrate the functionality of NEXMD in detail, we analyze the photoexcited dynamics of a polyphenylene ethynylene dendrimer (PPE, CH) in vacuum and in a continuum solvent. Furthermore, the PPE molecule example serves to highlight the utility of the helper script to form a streamlined workflow. This script, provided with the package, can both set up NEXMD calculations and analyze the results, including, but not limited to, collecting populations, generating an average optical spectrum, and restarting unfinished calculations.
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http://dx.doi.org/10.1021/acs.jctc.0c00248 | DOI Listing |
Inorg Chem
January 2025
Department of Chemistry University of Tennessee, Knoxville, Tennessee 37996-1600, United States.
A series of 2-pyridone[α]-fused BOPHYs - were prepared via a two-step procedure involving the preparation of enamine, followed by an intramolecular heterocyclization reaction. In addition to being fully conjugated with the BOPHY core pyridone fragment, BOPHYs and have a pyridine group connected to the BOPHY core via one- or two -CH- groups. New BOPHYs were characterized by spectroscopy as well as X-ray diffraction.
View Article and Find Full Text PDFSmall
January 2025
Department of Materials Science and State Key Laboratory of Molecular Engineering of Polymers, Academy for Engineering and Technology, Fudan University, Shanghai, 200433, P. R. China.
The transient receptor potential (TRP) channel is a key sensor for diverse cellular stimuli, regulating the excitability of primary nociceptive neurons. Sensitization of the TRP channel can heighten pain sensitivity to innocuous or mildly noxious stimuli. Here, reversible modulation of TRP channels is achieved by controlling both the light-induced photoelectrochemical reaction to induce neuronal depolarization, and antioxidants for neuronal protection.
View Article and Find Full Text PDFChem Asian J
January 2025
Birla Institute of Technology & Science Pilani - Hyderabad Campus, Chemistry, Jawaharnagar, Shamirpet Mandal, 500078, Hyderabad, INDIA.
Despite significant advancements in the structural flexibility and functional diversity of fluorescent molecular sensors, the chromophores often require complex synthetic processes and are typically designed to perform only a specific function. Herein, we have demonstrated the unique features of fluorophores based on a fused coumarin-indole scaffold, which are synthetically available via a one-step reaction. Four fluorophores (ICH, ICEst, ICOMe, and ICNMe2) with varying substituents were synthesized and characterized.
View Article and Find Full Text PDFJ Comput Chem
January 2025
Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia, USA.
The energies and geometries of the lowest lying singlet and triplet states of the four diradicals formed by removing two H atoms from thiophene have been characterized. We utilized the highly correlated, multireference methods configuration interaction with single and double excitations with and without the Pople correction for size-extensivity (MR-CISD+Q and MR-CISD) and averaged quadratic coupled cluster theory (MR-AQCC). CAS (8,7) and CAS (10,8) active spaces involving σ, σ*, π, and π* orbitals were employed along with the cc-pVDZ and cc-pVTZ basis sets.
View Article and Find Full Text PDFPhys Chem Chem Phys
January 2025
Departamento de Química Física y Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, Valladolid, Spain.
This article reports a theoretical study on the halogen exchange reactions YX + CHO → Y + XCHO (with Y = F, Cl, Br; X = Cl, Br, I) carried out at a high level of accuracy using coupled-cluster based methodologies including CCSD(T)-F12, CCSD(T)/CBS and CCSDT(Q). Most of the reactions are exothermic at room temperature, with the exception of the reactions FI + CHO → F + ICHO and ClI + CHO → Cl + ICHO. Exothermicity follows two concurrent trends established by the strength of the bonds being cleaved and formed: Y = F < Cl < Br (X-Y bond strength) and X = Cl > Br > I (C-X bond strength).
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