Review
Physics, Multidisciplinary
Niclas Westerberg, Robert Bennett
Summary: Our experience of the world is mainly determined by the interactions between light and matter, which are described by the quantum electrodynamics. However, solving the equations of quantum electrodynamics for real systems is often impractical, leading to the use of approximations and idealizations. This review provides an overview of these approximations and idealizations, focusing on the use of external boundary conditions as a control method. It also discusses recent advances in the design and optimization of light-matter interactions and explores the interface between quantum light and matter in chemistry and quantum chemistry.
PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Derek S. Wang, Susanne F. Yelin, Johannes Flick
Summary: This study demonstrates how to tune the optical properties of defects in solid-state materials via the formation of defect polaritons in an optical cavity from first principles. It shows significant polaritonic splitting and absorption intensity enhancement, potentially overcoming phonon-limited single-photon emission from defect centers. These findings are expected to inspire experimental investigations of strong light-matter coupling between defect centers and cavity photons for applications in quantum technologies.
Article
Multidisciplinary Sciences
Alex M. Ganose, Junsoo Park, Alireza Faghaninia, Rachel Woods-Robinson, Kristin A. Persson, Anubhav Jain
Summary: The authors developed a computationally efficient method for calculating carrier scattering rates of semiconductors, which shows similar accuracy to state-of-the-art methods but at a much lower computational cost. This approach enables high-throughput computational workflows for accurate screening of carrier mobilities, lifetimes, and thermoelectric power.
NATURE COMMUNICATIONS
(2021)
Article
Physics, Multidisciplinary
Fangzhou Zhao, Mark E. Turiansky, Audrius Alkauskas, Chris G. Van de Walle
Summary: Trap-assisted Auger-Meitner recombination is highlighted as a dominant nonradiative process in wide-band-gap materials, and a first-principles methodology is presented to determine the rates of this process in semiconductors or insulators due to defects or impurities.
PHYSICAL REVIEW LETTERS
(2023)
Article
Materials Science, Multidisciplinary
L. Pizzagalli
Summary: Research on the compression of C-60 reveals three regimes: elastic deformation, stochastic carbon bond breakings, and irreversible deformation. Additionally, a correlation between the electronic gap and compression orientation is discovered.
DIAMOND AND RELATED MATERIALS
(2022)
Article
Multidisciplinary Sciences
Mohammad Bagheri, Hannu-Pekka Komsa
Summary: Raman spectroscopy is a widely-used non-destructive method for characterizing materials and determining their atomic structure and chemical composition. This study presents an optimized workflow for efficiently calculating Raman spectra using existing material databases. The workflow was validated by comparing the calculated spectra with experimental results, and high-throughput calculations were performed for a large number of materials from various classes, resulting in a comprehensive database of Raman spectra that agree well with experiments.
Article
Chemistry, Physical
Huan Tran, Aubrey Toland, Kellie Stellmach, McKinley K. Paul, Will Gutekunst, Rampi Ramprasad
Summary: This study developed a first-principles computational scheme for accurately calculating the enthalpy of ring-opening polymerization (Delta H-ROP). The scheme demonstrated a smaller root-mean-square error compared to conventional approaches when validated on a diverse benchmark set. This development opens up new pathways for building a high-quality database of Delta H-ROP and accelerating the design of depolymerizable polymers.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Huan Tran, Aubrey Toland, Kellie Stellmach, McKinley K. Paul, Will Gutekunst, Rampi Ramprasad
Summary: Researchers have developed a first-principles computational scheme to calculate Delta H-ROP for polymer systems, achieving a root-mean-square error of 7 kJ/mol on a benchmark set of 42 ROP polymers. This development paves the way for building a high-quality database of Delta H-ROP for predictive machine-learning models and accelerating the design of depolymerizable polymers.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Materials Science, Multidisciplinary
Matthew Heine, Olle Hellman, David Broido
Summary: The study highlights the opposition between magnetic and lattice thermal disorders in Fe, with their interactions being influenced by temperature. At certain temperatures, the magnetic interactions show little temperature dependence, while at other temperatures, there is a sharp decrease, reflecting the complexity of spin-lattice coupling.
Article
Chemistry, Multidisciplinary
Xin Wang, Xiaoyue Zhang, Liwei Liu, Tielei Song, Zhifeng Liu, Xin Cui
Summary: Due to the similarity in valence electron structures, boron nitride can form various polymorphs with different frameworks, similar to carbon. In this study, three new low-density porous BN polymorphs, named Cub-B16N16, Tet-B16N16, and Ort-B16N16, were established using a hollow cage-like B16N16 cluster as building blocks. Density functional theory (DFT) calculations showed that these porous structures were energetically, dynamically, thermally, and mechanically stable, even more stable than some known phases. The results also demonstrated the mechanical anisotropy and semiconductor nature of these new phases.
Article
Materials Science, Ceramics
V. I. Ivashchenko, P. E. A. Turchi, R. Shevchenko, Leonid Gorb, Jerzy Leszczynski
Summary: First-principles molecular dynamics simulations were used to generate samples of amorphous a-AlB2, a-AlBC, and a-AlBN alloys, which exhibited boron clustering and different structural characteristics. The phonon spectra of the amorphous samples displayed broad bands, while the alloys varied in hardness, ideal tensile strength, Debye temperature, and fracture toughness. Predictions suggest that crystalline AlB2 is closer to a brittle material, while the amorphous alloys are expected to exhibit ductile behavior and semiconductor properties with a mobility gap in a certain range.
JOURNAL OF NON-CRYSTALLINE SOLIDS
(2022)
Article
Chemistry, Physical
Tianlun Allan Huang, Marios Zacharias, D. Kirk Lewis, Feliciano Giustino, Sahar Sharifzadeh
Summary: Exciton-phonon interactions in monolayer germanium selenide lead to the renormalization of the optical gap, with the strongest coupling to optical phonons at around 100 cm(-1). The interaction between excitons and phonons is similar in monolayer and bulk GeSe. Overall, the combination of many-body perturbation theory and special displacements offers a new approach to study electron-phonon couplings and band gap renormalization in excitonic spectra.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Physical
FengLu Cui, Xu Jin, Jun Xia, He Liu, HengAn Wu, FengChao Wang
Summary: Understanding the mechanisms of oil/brine/rock interactions at the nanoscale is crucial for enhancing oil recovery techniques in shale oil exploration. This study comprehensively analyzed the interaction and destruction of hydrated ion bridges (HIB) and water bridges (WB) using first-principles calculations. The results showed that ions, especially divalent ions, increased the oil/rock interaction strength. The study also visualized hydrogen bonds and van der Waals interactions, providing a better understanding of the interaction and destruction of HIB and WB connections. These findings offer valuable insights into oil/brine/rock interfacial interactions and theoretical support for efficient oil extraction.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Chemistry, Physical
Hui Wang, Bin Li, Xiaoting Wang, Fu Yin, Qiaoyu Wei, Xudong Wang, Yuxiang Ni, Hongyan Wang
Summary: Research on the square chalcogen interaction of 2ChMIDLINE HORIZONTAL ELLIPSIS2N (Ch = S, Se, Te) has been widely explored recently. Crystal Structure Database search identified various square chalcogen structures with 2ChMIDLINE HORIZONTAL ELLIPSIS2N interactions. This study constructed a model for square chalcogen bonds using dimers of 2,1,3-benzothiadiazole (C6N2H4S), 2,1,3-benzoselenadiazole (C6N2H4Se), and 2,1,3-benzotelluradiazole (C6N2H4Te) from CSD, and investigated their adsorption behavior on Ag(110) surfaces using first principles. The results indicate that the strength of the 2ChMIDLINE HORIZONTAL ELLIPSIS2N square chalcogen bond follows the order of S < Se < Te.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Multidisciplinary Sciences
Rahul Nikhar, Krzysztof Szalewicz
Summary: Developing theoretical frameworks for predicting new polymorphs is valuable. This study presents an ab initio based force-field approach that significantly speeds up crystal structure prediction compared to fully ab initio schemes. The authors have developed an inexpensive and reliable method for molecular crystal structure predictions. The method starts from a two-dimensional graph of the crystal's monomers and utilizes quantum mechanical calculations to develop an accurate force field for crystal prediction. The robustness of this method has been demonstrated by successfully finding the experimental crystal within the top 20 predicted polymorphs for each molecule investigated.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Medicinal
Lauren Nelson, Sofia Bariami, Chris Ringrose, Joshua T. Horton, Vadiraj Kurdekar, Antonia S. J. S. Mey, Julien Michel, Daniel J. Cole
Summary: The QUBE force-field approach has been developed for deriving potential energy function parameters for modeling protein-ligand binding, validated in Monte Carlo simulations, and successfully implemented in the SOMD and GROMACS software packages. It is shown that the availability of QUBE in a modern simulation package that utilizes GPU acceleration will facilitate high-throughput alchemical free-energy calculations.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Chemistry, Physical
Josh D. Littlefair, Daniel J. Cole, Thomas J. Penfold
Summary: This study uses simple approximations to improve the accuracy of density functionals, while simultaneously investigating the impact of energy and density errors in CuCl and related complexes; the results show that simple metrics can reveal the relative contributions of energy errors from approximate density and exchange-correlation functionals.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
(2021)
Article
Chemistry, Physical
Lupeng Yang, Joshua T. Horton, Michael C. Payne, Thomas J. Penfold, Daniel J. Cole
Summary: This study demonstrates that parameters tailored for thermally activated delayed fluorescence (TADF) emitters used in organic light-emitting diodes (OLEDs) can be easily derived from a small number of quantum mechanics calculations using the QUBEKit software, improving the overall accuracy of these simulations.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Multidisciplinary Sciences
Diana Zatreanu, Helen M. R. Robinson, Omar Alkhatib, Marie Boursier, Harry Finch, Lerin Geo, Diego Grande, Vera Grinkevich, Robert A. Heald, Sophie Langdon, Jayesh Majithiya, Claire McWhirter, Niall M. B. Martin, Shaun Moore, Joana Neves, Eeson Rajendra, Marco Ranzani, Theresia Schaedler, Martin Stockley, Kimberley Wiggins, Rachel Brough, Sandhya Sridhar, Aditi Gulati, Nan Shao, Luned M. Badder, Daniela Novo, Eleanor G. Knight, Rebecca Marlow, Syed Haider, Elsa Callen, Graeme Hewitt, Joost Schimmel, Remko Prevo, Christina Alli, Amanda Ferdinand, Cameron Bell, Peter Blencowe, Chris Bot, Mathew Calder, Mark Charles, Jayne Curry, Tennyson Ekwuru, Katherine Ewings, Wojciech Krajewski, Ellen MacDonald, Hollie McCarron, Leon Pang, Chris Pedder, Laurent Rigoreau, Martin Swarbrick, Ed Wheatley, Simon Willis, Ai Ching Wong, Andre Nussenzweig, Marcel Tijsterman, Andrew Tutt, Simon J. Boulton, Geoff S. Higgins, Stephen J. Pettitt, Graeme C. M. Smith, Christopher J. Lord
Summary: The study identifies small molecule inhibitors targeting Pol theta polymerase activity that induce BRCA1/2 synthetic lethality, enhance PARP inhibitor effects, and address PARP inhibitor resistance caused by defects in the 53BP1/Shieldin pathway.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
David Peter Kovacs, Cas van der Oord, Jiri Kucera, Alice E. A. Allen, Daniel J. Cole, Christoph Ortner, Gabor Csanyi
Summary: The ACE framework can be used to build fast and accurate linear force fields with form reminiscent of traditional molecular mechanics force fields, reaching the accuracy typical of machine learning methods. ACE not only demonstrates superior accuracy and speed on benchmark datasets, but also outperforms empirical force fields in more important tasks.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Multidisciplinary
Mateusz K. Bieniek, Ben Cree, Rachael Pirie, Joshua T. Horton, Natalie J. Tatum, Daniel J. Cole
Summary: This study introduces a workflow for free energy calculations that can build congeneric series of ligands in protein binding pockets and predict their binding energies. The workflow demonstrates its effectiveness by constructing and scoring binding poses for various ligand series bound to different protein targets.
COMMUNICATIONS CHEMISTRY
(2022)
Article
Oncology
Gonzalo Rodriguez-Berriguete, Marco Ranzani, Remko Prevo, Rathi Puliyadi, Nicole Machado, Hannah R. Bolland, Val Millar, Daniel Ebner, Marie Boursier, Aurora Cerutti, Alessandro Cicconi, Alessandro Galbiati, Diego Grande, Vera Grinkevich, Jayesh B. Majithiya, Desiree Piscitello, Eeson Rajendra, Martin L. Stockley, Simon J. Boulton, Ester M. Hammond, Robert A. Heald, Graeme C. M. Smith, Helen M. R. Robinson, Geoff S. Higgins
Summary: This study evaluates the feasibility of targeting DNA polymerase theta (Pol theta) with novel small-molecule inhibitors to enhance the efficacy of radiotherapy. The results demonstrate that these inhibitors effectively radiosensitize tumor cells without affecting normal cells. Mechanistically, the inhibition of Pol theta impairs DNA damage repair, particularly in replicating cells. Additionally, these inhibitors can overcome hypoxia-induced radioresistance. In vivo experiments show that the combination of Pol theta inhibition with fractionated radiation is well-tolerated and significantly reduces tumor growth.
CLINICAL CANCER RESEARCH
(2023)
Article
Chemistry, Medicinal
Joshua T. Horton, Simon Boothroyd, Jeffrey Wagner, Joshua A. Mitchell, Trevor Gokey, David L. Dotson, Pavan Kumar Behara, Venkata Krishnan Ramaswamy, Mark Mackey, John D. Chodera, Jamshed Anwar, David L. Mobley, Daniel J. Cole
Summary: The development of accurate transferable force fields is essential for maximizing the potential of atomistic modeling in studying biological processes. This study presents software packages for fitting torsion parameters to quantum mechanical reference data, and demonstrates significant improvements in accuracy by using bespoke force fields.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Physical
Miguel Jorge, Maria Cecilia Barrera, Andrew W. Milne, Chris Ringrose, Daniel J. Cole
Summary: In classical nonpolarizable models, the correct degree of polarization for fixed-charge models to achieve the best balance of interactions and describe the energy surface of a liquid phase has been a fundamental question. Two independent approaches, QUBE and PolCA, provide consistent answers that the model's dipole moment should be approximately halfway between the gas and liquid phases. However, the estimation of the reference liquid-phase dipole requires considering both mean-field and local contributions to polarization, as continuum dielectric models are inadequate for this purpose.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Simon Boothroyd, Pavan Kumar Behara, Owen C. Madin, David F. Hahn, Hyesu Jang, Vytautas Gapsys, Jeffrey R. Wagner, Joshua T. Horton, David L. Dotson, Matthew W. Thompson, Jessica Maat, Trevor Gokey, Lee-Ping Wang, Daniel J. Cole, Michael K. Gilson, John D. Chodera, Christopher I. Bayly, Michael R. Shirts, David L. Mobley
Summary: We introduce the OpenFF 2.0.0 small molecule force field Sage, an improved version of Parsley. It features improved LJ parameters and fitting to a larger database of quantum chemical calculations. Force field benchmarks show improved performance and estimation of physical properties. Complete data and training results are available at https://github.com/openforcefield/openff-sage.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Finlay Clark, Graeme Robb, Daniel J. Cole, Julien Michel
Summary: Alchemical absolute binding free energy calculations are increasingly important in drug discovery. Multiple distance restraints between anchor points in the receptor and ligand provide a framework without inherent instabilities and can improve convergence. However, calculating the free energy of releasing these restraints is challenging. This study proposes a method to rigorously calculate the free energies of binding with multiple distance restraints by imposing intramolecular restraints on the anchor points.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Meeting Abstract
Biophysics
Chapin E. Cavender, Pavan K. Behara, Simon Boothroyd, David L. Dotson, Joshua T. Horton, Joshua A. Mitchell, Ivan Pulido, Matthew W. Thompson, Jeffrey Wagner, Lily Wang, John D. Chodera, Daniel J. Cole, David L. Mobley, Michael R. Shirts, Michael K. Gilson
BIOPHYSICAL JOURNAL
(2023)
Meeting Abstract
Biophysics
Lily Wang, Simon Boothroyd, Joshua T. Horton, Matthew W. Thompson, Michael R. Shirts, Daniel J. Cole, John D. Chodera, David L. Mobley
BIOPHYSICAL JOURNAL
(2023)
Article
Chemistry, Medicinal
Martin L. Stockley, Amanda Ferdinand, Giovanni Benedetti, Peter Blencowe, Susan M. Boyd, Mat Calder, Mark D. Charles, Lucy V. Edwardes, Tennyson Ekwuru, Harry Finch, Alessandro Galbiati, Lerin Geo, Diego Grande, Vera Grinkevich, Nicholas D. Holliday, Wojciech W. Krajewski, Ellen MacDonald, Jayesh B. Majithiya, Hollie McCarron, Claire L. McWhirter, Viral Patel, Chris Pedder, Eason Rajendra, Macro Ranzani, Laurent J. M. Rigoreau, Helen M. R. Robinson, Theresia Schaedler, Julija Sirina, Graeme C. M. Smith, Martin E. Swarbrick, Andrew P. Turnbull, Simon Willis, Robert A. Heald
Summary: This article describes the discovery and characterization of selective small molecule probes for human DNA polymerase theta (Pol0), a key enzyme involved in microhomology-mediated DNA repair. The crystallographic data provides insight into the unique mechanism of inhibition of these compounds, which could be valuable for the treatment of BRCA deficient and other DNA repair pathway defective cancers.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Chris Ringrose, Joshua T. Horton, Lee-Ping Wang, Daniel J. Cole
Summary: This study proposes the use of quantum mechanics to inform molecular mechanics parameter derivation in order to reduce the number of parameters that require fitting to experiment and increase the pace of force field development. The authors design and train a collection of 15 new protocols for small, organic molecule force field derivation, and test their accuracy against experimental liquid properties. The best performing model has only seven fitting parameters, yet achieves high accuracy compared to experiment in liquid densities and heats of vaporisation.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)