Article
Chemistry, Physical
Tsuyoshi Yamaguchi, Norio Yoshida
Summary: In this study, the theory of solvation structure in an electronically polarizable solvent is extended to dynamics by combining with time-dependent density functional theory. Test calculations on model charge-transfer systems in water show that electronic polarizability slightly retards solvation dynamics, attributed to the decrease in the curvature of the nonequilibrium free energy profile. Solvent relaxation is found to be bimodal, with faster and slower modes assigned to reorientational and translational modes, respectively.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Materials Science, Multidisciplinary
Xueying Lu, Yongxu Hu, Huapeng Liu, Jiannan Qi, Xiaosong Chen, Yajing Sun, Wenping Hu
Summary: Purely organic fluorescence emitters with ultrahigh exciton utilization, such as thermally-activated delayed fluorescence (TADF) materials, are pursued as the cornerstone of the new-generation organic light-emitting diodes (OLEDs). However, most TADF emitters suffer from the dilemma of the aggregation-caused fluorescence quenching effects, severely limiting their applications. Excitingly, the recently proposed aggregation-induced delayed fluorescence (AIDF) strategy holds the potential to tackle this problem thoroughly. Here, the recently reported AIDF emitters CP-BP-PXZ and its halogenated counterparts, 3-CCP-BP-PXZ and 3-BCP-BP-PXZ, are investigated with a united theoretical and experimental insight. Based on first-principles calculations combined with the polarizable continuum model (PCM) and the quantum mechanics/molecular mechanics (QM/MM) model, the photophysical mechanisms of these novel materials are proposed. It is found that both reverse intersystem crossing (RISC) and the subsequent radiative transition of CP-BP-PXZ are promoted via aggregation, owing to the increased effective RISC channels and boosted oscillator strength. Meanwhile, the unfavorable internal conversion rate is greatly slumped, ascribed to the suppressed Duschinsky rotation effect (DRE). The unique heavy-atom effect is disclosed in 3-CCP-BP-PXZ and 3-BCP-BP-PXZ that the halogens act as steric blockers in crystal, rather than spin-orbit coupling enhancers. It is hoped that this work can shed new light on the designation of high-efficient solid-state fluorescence emitters.
ADVANCED OPTICAL MATERIALS
(2022)
Review
Pharmacology & Pharmacy
Naike Ye, Zekai Yang, Yuchen Liu
Summary: This article reviews the recent advances in using density functional theory (DFT) in molecular modeling studies of COVID-19 pharmaceuticals. It provides an overview of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) drugs and targets, introduces the basic principles and application methods of DFT, discusses different approaches of applying DFT, and highlights important factors to consider when incorporating DFT in future drug modeling research.
DRUG DISCOVERY TODAY
(2022)
Article
Chemistry, Multidisciplinary
J. Eeckhoudt, T. Bettens, P. Geerlings, R. Cammi, B. Chen, M. Alonso, F. De Proft
Summary: High pressure chemistry offers possibilities for controlling chemical reactivity, developing new materials, and fine-tuning chemical properties. However, the focus has primarily been on volume changes and thermodynamics, neglecting the electronic effects at the molecular scale. This study combines the DFT framework with the XP-PCM method to analyze the effects of high pressure on chemical properties. The results reveal the relationship between pressure and various properties, such as ionization potential, electron affinity, electronegativity, chemical hardness, softness, and electron density. The findings provide insights into the periodic trends and correlations between these properties under pressure.
Article
Chemistry, Medicinal
Dongbo Zhao, Shubin Liu, Dahua Chen
Summary: Using density functional theory (DFT) and the information-theoretic approach (ITA) to evaluate the energetics and properties of biopolymers is still an ongoing task. This study reveals that the exchange-correlation effect is the primary factor influencing the molecular stability of base pairs, while the electrostatic potential and steric effect play secondary roles. Additionally, simple density-based ITA functions show good relationships with molecular polarizabilities.
Article
Chemistry, Physical
Roshan Khatri, Barry D. Dunietz
Summary: A polarization consistent framework is employed for the study of solvation energies. The results show that dielectric screening significantly affects DFT-PCM and HF-PCM solvation energies, with screened solvation energies being smaller compared to unscreened values. These findings contribute to improving the accuracy of DFT-PCM calculations of solvation energy.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Joshua A. Rackers, Roseane R. Silva, Zhi Wang, Jay W. Ponder
Summary: A new empirical potential, the HIPPO force field, has been developed for efficient molecular dynamics simulation of water, balancing a wide range of water properties across different conditions. This model explicitly correlates water structure, dynamics, and thermodynamics with ab initio energy decomposition, offering comparable accuracy to previous polarizable atomic multipole force fields. The HIPPO water model can serve as a cornerstone for developing similarly detailed physics-based models for other molecular species.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Computer Science, Artificial Intelligence
Serbulent Unsal, Heval Atas, Muammer Albayrak, Kemal Turhan, Aybar C. Acar, Tunca Dogan
Summary: This Analysis compares the performances and advantages of recent deep learning approaches in protein prediction tasks and finds that they show promising results in extracting complex sequence-structure-function relationships.
NATURE MACHINE INTELLIGENCE
(2022)
Article
Chemistry, Physical
Zehua Chen, Yang Yang
Summary: This study develops a new approach (CNEO-MD) to accurately and efficiently incorporate nuclear quantum effects into classical molecular dynamics (MD) simulations by combining constrained nuclear-electronic orbital (CNEO) theory with classical MD. It provides a theoretical foundation for CNEO-MD by developing an alternative formulation of the equations of motion for MD. The results show that this new MD approach is significantly more accurate than the conventional way of performing classical MD and generally outperforms centroid MD and ring-polymer MD in describing vibrations in model systems.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Polymer Science
Yu-Che Chen, Yan-Cheng Lin, Chih-Cheng Kuo, Mitsuru Ueda, Wen-Chang Chen
Summary: This study comprehensively investigated the relationship between the chemical structures and dielectric properties of polyimides (PIs) with low dielectric constant (Dk) and dissipation factor (Df). By utilizing density functional theory simulation, the limitations of the additive group contribution method were addressed. The study established a confident correlation of Dk and Df values with the structure parameters of PIs, shedding light on the design of insulating materials at high frequencies.
Article
Biochemistry & Molecular Biology
Dongbo Zhao, Xin He, Paul W. Ayers, Shubin Liu
Summary: Accurately and efficiently determining the polarizabilities of excited states is a challenge in both experimental and computational studies. This research demonstrates that density-based functions can be used to predict excited-state polarizabilities and verifies their correlation and predictability through experiments.
Article
Materials Science, Multidisciplinary
M. Mirnezhad, R. Ansari, S. R. Falahatgar, P. Aghdasi
Summary: In this study, quantum and molecular mechanics were used to investigate the quantum effects of fine scaling on the buckling strength of multi-walled carbon nanotubes under axial loading. The results showed that changes in structure size have significant effects on buckling strength, and the critical buckling strain of multi-walled carbon nanotubes with different chiralities falls within the range of zigzag and armchair nanotubes.
APPLIED PHYSICS A-MATERIALS SCIENCE & PROCESSING
(2021)
Article
Environmental Sciences
Zexi Hou, Yanwei Li, Mingna Zheng, Xinning Liu, Qingzhu Zhang, Wenxing Wang
Summary: Recently, the activation mechanism and possible metabolites of heterocyclic PAHs catalyzed by human CYP1A1 have been explored using high level QM/MM calculations. Electrophilic addition was determined as the rate-determining step, followed by possible reactions including epoxidation, NIH shift, and proton shuttle. The main metabolites (hydroxylated carbazoles) were estimated to be more toxic than carbazole.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Review
Biochemistry & Molecular Biology
Samira Mahmoudi, Mehrdad Mohammadpour Dehkordi, Mohammad Hossein Asgarshamsi
Summary: This article compares the antioxidant activity of compounds using density functional theory, finding that antioxidants with higher aromaticity have more stable radicals. The solvent model can impact the antioxidant mechanism, suggesting that it should be considered in pharmacological evaluations.
JOURNAL OF MOLECULAR MODELING
(2021)
Article
Chemistry, Physical
Raphael Robidas, Claude Y. Legault
Summary: This study investigates the applications of molecular iodine in organic synthesis and the challenges in choosing computational methods for this element. The results demonstrate the importance of using triple-zeta basis sets for obtaining quality results and indicate that post hoc corrections are overall detrimental to the research.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
(2023)