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1. Quasiclassical sampling and Wigner sampling of initial vibrational coordinates and momenta for polyatomic molecules in Monte Carlo molecular dynamics simulations

   https://doi.org/10.1080/00268976.2025.2483436  

   Shu, Yinan; Zhou, Jian-Ge; Truhlar, Donald G (October 2025, Molecular Physics)

   In a quasiclassical trajectory simulation, the vibrational modes are initialised with quantised vibrational energies, but vibrational phases are sampled by Monte Carlo. This requires an algorithm to assign coordinates and momenta to the various atoms. In this work, we present two methods for implementing this for nonrotating polyatomic molecules, namely, fixed-energy vibrational-state-selected initial conditions and thermal initial conditions. We also present a method for initiating classical trajectories with a ground-state Wigner distribution. These vibrational treatments are sufficient to initialise trajectories for unimolecular processes, and we also show how they can be applied to simulate bimolecular collision processes. The treatments of unimolecular and bimolecular collision processes are available in two Python codes called wigner_state_selected.py and bimolecular_collision.py, respectively, which will generate initial condition files that are recognisable by the SHARC and SHARC-MN computer programs for dynamics calculations. Both codes are available as standalone programs, as well as being included in SHARC-MN, and they will be included in future versions of SHARC. The methods implemented in these codes are mostly also available in the ANT computer program, and those that are not available in ANT will be incorporated in future versions of ANT. 

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2. Extracting molecular responses from ultrafast charge dynamics at material interfaces

   https://doi.org/10.1039/d0tc01819h  

   Wang, Chenglai; Li, Yingmin; Xiong, Wei (September 2020, Journal of Materials Chemistry C)

   null (Ed.)

   We introduce a new data analysis method, which can be applied to transient vibrational sum-frequency generation spectroscopy to reveal hidden molecular dynamics of charge transfer at molecular heterojunction interfaces. After validating the method, we used it to extract molecular dynamics at organic semiconductor/metal interfaces, which was otherwise dominated by electronic dynamics. Such an ability can advance the understanding of the roles of molecules in interfacial charge transfer dynamics. 

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3. Development of a universal method for vibrational analysis of the terminal alkyne C≡C stretch

   https://doi.org/10.1063/5.0185580  

   Streu, Kristina; Hunsberger, Sara; Patel, Jeanette; Wan, Xiang; Daly, Jr., Clyde_A (February 2024, The Journal of Chemical Physics)

   The terminal alkyne C≡C stretch has a large Raman scattering cross section in the “silent” region for biomolecules. This has led to many Raman tag and probe studies using this moiety to study biomolecular systems. A computational investigation of these systems is vital to aid in the interpretation of these results. In this work, we develop a method for computing terminal alkyne vibrational frequencies and isotropic transition polarizabilities that can easily and accurately be applied to any terminal alkyne molecule. We apply the discrete variable representation method to a localized version of the C≡C stretch normal mode. The errors of (1) vibrational localization to the terminal alkyne moiety, (2) anharmonic normal mode isolation, and (3) discretization of the Born–Oppenheimer potential energy surface are quantified and found to be generally small and cancel each other. This results in a method with low error compared to other anharmonic vibrational methods like second-order vibrational perturbation theory and to experiments. Several density functionals are tested using the method, and TPSS-D3, an inexpensive nonempirical density functional with dispersion corrections, is found to perform surprisingly well. Diffuse basis functions are found to be important for the accuracy of computed frequencies. Finally, the computation of vibrational properties like isotropic transition polarizabilities and the universality of the localized normal mode for terminal alkynes are demonstrated. 

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4. Predicting the formation of fractionally doped perovskite oxides by a function-confined machine learning method

   https://doi.org/10.1038/s43246-022-00269-9  

   Zhai, Ximei; Ding, Fei; Zhao, Zeyu; Santomauro, Aaron; Luo, Feng; Tong, Jianhua (December 2022, Communications Materials)

   Abstract Fractionally doped perovskites oxides (FDPOs) have demonstrated ubiquitous applications such as energy conversion, storage and harvesting, catalysis, sensor, superconductor, ferroelectric, piezoelectric, magnetic, and luminescence. Hence, an accurate, cost-effective, and easy-to-use methodology to discover new compositions is much needed. Here, we developed a function-confined machine learning methodology to discover new FDPOs with high prediction accuracy from limited experimental data. By focusing on a specific application, namely solar thermochemical hydrogen production, we collected 632 training data and defined 21 desirable features. Our gradient boosting classifier model achieved a high prediction accuracy of 95.4% and a high F1 score of 0.921. Furthermore, when verified on additional 36 experimental data from existing literature, the model showed a prediction accuracy of 94.4%. With the help of this machine learning approach, we identified and synthesized 11 new FDPO compositions, 7 of which are relevant for solar thermochemical hydrogen production. We believe this confined machine learning methodology can be used to discover, from limited data, FDPOs with other specific application purposes. 

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5. DFT-based calculation of vibrational sum frequency generation spectral features of crystalline β-sheets in silk: Polarization and azimuth angle dependences

   https://doi.org/10.1063/5.0236676  

   Ryu, Jihyeong; Chen, Sibing; Choi, Juseok; Chen, Xing; Kim, Seong H (December 2024, The Journal of Chemical Physics)

   Sum frequency generation (SFG) necessitates both noncentrosymmetry and coherence over multiple length scales. These requirements make vibrational SFG spectroscopy capable of probing structural information of noncentrosymmetric organic crystals interspersed in polymeric matrices and their three-dimensional spatial distributions within the matrices without spectral interferences from the amorphous components. However, this analysis is not as straightforward as simple vibrational spectroscopy or scattering experiments; it requires knowing the molecular hyperpolarizability of SFG-active vibrational modes and their interplay within the coherence length. This study demonstrates how density function theory (DFT) calculations can be used to construct the molecular hyperpolarizability of a model system and combine it with the SFG theory to predict the polarization and azimuth angle dependences of SFG intensities. A model system with short peptide chains mimicking β-sheet domains in Bombyx mori silk was chosen. SFG signals of the amide-I, II, III, and A bands and one of the CH deformation modes were simulated and compared with the experimental results and the predictions from the group theory. The SFG features of amide-I and A bands of antiparallel β-sheet could be explained with DFT-based theoretical calculations. Although vibrational coupling with neighboring groups breaks the symmetry of the D2 point group, the group theory approach and DFT calculations gave similar results for the amide-I mode. The DFT calculation results for amide-II did not match with experimental data, which suggested vibrational coupling within a larger crystalline domain may dominate the SFG spectral features of these modes. This methodology can be applied to the structural analysis of other biopolymers. 

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