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1. The impact of stacking and phonon environment on energy transfer in organic chromophores: computational insights

   https://doi.org/10.1039/D3TC00479A  

   Mukazhanova, Aliya; Negrin-Yuvero, Hassiel; Freixas, Victor M.; Tretiak, Sergei; Fernandez-Alberti, Sebastian; Sharifzadeh, Sahar (April 2023, Journal of Materials Chemistry C)

   Energy transfer in organic materials is extensively studied due to many applications in optoelectronics. The electronic and vibrational relaxations within molecular assemblies can be influenced by stacking arrangements or additions of a backbone that unites them. Here, we present the computational study of the photoexcitation dynamics of a perylene diimide monomer, and face-to-face stacked dimer and trimer. By using non-adiabatic excited-state molecular dynamics simulations, we show that the non-radiative relaxation is accelerated with the number of stacked molecules. This effect is explained by differences in the energy splitting between states that impacts their corresponding nonadiabatic couplings. Additionally, our analysis of the vibronic dynamics reveals that the passage through the different conical intersections that participate in the relaxation of the stacked systems, activate a positive feedback mechanism. This effect involves a narrow set of vibrational normal modes that accelerate the process by increasing the efficiency of its vibronic dynamics. In contrast, an addition of a biologically inspired backbone slows down the relaxation rate due to its participation in the vibronic dynamics of the molecular stacking arrangements. Our results suggest the stacking arrangements and common backbones as strategies to modulate the efficiency of electronic and vibrational relaxation of diimide-based systems and other molecular aggregates. 

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2. Role of charge transfer states into the formation of cyclobutane pyrimidine dimers in DNA

   https://doi.org/10.1039/C8FD00184G  

   Lee, Wook; Matsika, Spiridoula (July 2019, Faraday Discussions)

   Photoinduced charge transfer between neighboring bases plays an important role in DNA. One of its important effects is shown in its ability to affect the photochemical yields of the formation of cyclobutane pyrimidine dimer (CPD) products between adjacent pyrimidine bases. In this work we examine how the energies of charge transfer states depend on the sequences of oligonucleotides using a hybrid quantum and molecular mechanics (QM/MM) methodology combined with the algebraic diagrammatic construction through a second order electronic structure method for excited states. Specifically, we examine 10 sequences with guanine being on the 5′ or 3′ position of two pyrimidine bases. The results show that the energies of charge transfer states are affected by the nature of the donor acceptor pair, by the distance between them, and by other electrostatic effects created by the surrounding environment. 

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3. Computing L- and M-edge spectra using the DFT/CIS method with spin–orbit coupling

   https://doi.org/10.1039/D5CP01656H  

   Mandal, Aniket; Herbert, John M (July 2025, Physical Chemistry Chemical Physics)

   Modeling L-edge spectra at X-ray wavelengths requires consideration of spin–orbit splitting of the 2p orbitals. We introduce a low-cost tool to compute core-level spectra that combines a spin–orbit mean-field description of the Breit–Pauli Hamiltonian with nonrelativistic excited states computed using the semi-empirical density-functional theory configuration-interaction singles (DFT/CIS) method, within the state-interaction approach. Our version of DFT/CIS was introduced recently for K-edge spectra and includes a semi-empirical correction to the core orbital energies, significantly reducing ad hoc shifts that are typically required when time-dependent (TD-)DFT is applied to core-level excitations. In combination with the core/valence separation approximation and spin–orbit couplings, the DFT/CIS method affords semiquantitative L-edge spectra at CIS cost. Spin–orbit coupling has a qualitative effect on the spectra, as demonstrated for a variety of 3d transition metal systems and main-group compounds. The use of different active orbital spaces helps to facilitate spectral assignments. We find that spin–orbit splitting has a negligible effect on M-edge spectra for 3d transition metal species. 

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4. Structure of an anti-PEG antibody reveals an open ring that captures highly flexible PEG polymers

   https://doi.org/10.1038/s42004-020-00369-y  

   Huckaby, Justin T.; Jacobs, Tim M.; Li, Zhongbo; Perna, Robert J.; Wang, Anting; Nicely, Nathan I.; Lai, Samuel K. (September 2020, Communications Chemistry)

   Abstract Polyethylene glycol (PEG) is a polymer routinely used to modify biologics and nanoparticles to prolong blood circulation and reduce immunogenicity of the underlying therapeutic. However, several PEGylated therapeutics induce the development of anti-PEG antibodies (APA), leading to reduced efficacy and increased adverse events. Given the highly flexible structure of PEG, how APA specifically bind PEG remains poorly understood. Here, we report a crystal structure illustrating the structural properties and conformation of the APA 6-3 Fab bound to the backbone of PEG. The structure reveals an open ring-like sub-structure in the Fab paratope, whereby PEG backbone is captured and then stabilized via Van der Waals interactions along the interior and exterior of the ring paratope surface. Our finding illustrates a strategy by which antibodies can bind highly flexible repeated structures that lack fixed conformations, such as polymers. This also substantially advances our understanding of the humoral immune response generated against PEG. 

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5. Polariton spectra under the collective coupling regime. II. 2D non-linear spectra

   https://doi.org/10.1063/5.0249705  

   Mondal, M Elious; Vamivakas, A Nickolas; Cundiff, Steven T; Krauss, Todd D; Huo, Pengfei (February 2025, The Journal of Chemical Physics)

   In our previous work [Mondal et al., J. Chem. Phys. 162, 014114 (2025)], we developed several efficient computational approaches to simulate exciton–polariton dynamics described by the Holstein–Tavis–Cummings (HTC) Hamiltonian under the collective coupling regime. Here, we incorporated these strategies into the previously developed Lindblad-partially linearized density matrix (L-PLDM) approach for simulating 2D electronic spectroscopy (2DES) of exciton–polariton under the collective coupling regime. In particular, we apply the efficient quantum dynamics propagation scheme developed in Paper I to both the forward and the backward propagations in the PLDM and develop an efficient importance sampling scheme and graphics processing unit vectorization scheme that allow us to reduce the computational costs from O(K2)O(T3) to O(K)O(T0) for the 2DES simulation, where K is the number of states and T is the number of time steps of propagation. We further simulated the 2DES for an HTC Hamiltonian under the collective coupling regime and analyzed the signal from both rephasing and non-rephasing contributions of the ground state bleaching, excited state emission, and stimulated emission pathways. 

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