Article
Multidisciplinary Sciences
Hong-Guang Duan, Ajay Jha, Lipeng Chen, Vandana Tiwari, Richard J. Cogdell, Khuram Ashraf, Valentyn I. Prokhorenko, Michael Thorwart, R. J. Dwanye Miller
Summary: Scientists have discovered that electronic coherence in light harvesting can be prolonged at extremely low temperatures, increasing the stability of the process against fragile quantum effects.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Physical
Linyu Yan, Chu Li, Meng Li, Shuqi Mu, Kebin Shi, Qihuang Gong, Yan Li
Summary: This study experimentally verifies the ultrafast coherent energy transport among chlorophyll molecules inside the FMO complex and uncovers its dynamic process. The high similarities between experimental and theoretical results demonstrate precise control of the photonic lattices. These findings contribute to a deeper understanding of the mechanism and have significant applications in artificial light energy transport.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Chemistry, Physical
Ellen Mulvihill, Kristina M. Lenn, Xing Gao, Alexander Schubert, Barry D. Dunietz, Eitan Geva
Summary: The M-GQME approach captures the effect of nuclear degrees of freedom on the time evolution of the electronic density matrix through a memory kernel superoperator, providing accurate results in predicting energy transfer dynamics in complex molecular systems.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Zhubin Hu, Zengkui Liu, Xiang Sun
Summary: The heterogeneous protein environment in the FMO complex of green sulfur bacteria affects excitation energy transfer. A more realistic model shows slower energy transfer dynamics than the traditional model. Larger reorganization energy, heterogeneity in spectral densities, and low-frequency modes facilitate energy dissipation.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Quantum Science & Technology
Zixuan Hu, Kade Head-Marsden, David A. Mazziotti, Prineha Narang, Sabre Kais
Summary: This paper introduces the research on using quantum algorithms to simulate complex physical processes and demonstrates the simulation of the dynamics of the FMO complex using a quantum algorithm. The study shows that quantum methods have a query complexity advantage in addressing open quantum dynamics.
Article
Chemistry, Physical
Yongbin Kim, Zach Mitchell, Jack Lawrence, Dmitry Morozov, Sergei Savikhin, Lyudmila V. Slipchenko
Summary: Multiscale molecular modeling is used to predict the optical absorption and circular dichroism spectra of two single-point mutants of the Fenna-Matthews-Olson photosynthetic pigment-protein complex. The modeling approach combines classical molecular dynamics simulations, structural refinement of photosynthetic pigments, and calculations of their excited states in a polarizable protein environment. The modeling demonstrates that a single-point mutation can induce long-range effects on the protein structure and that extensive structural changes near a pigment do not necessarily lead to significant changes in the electronic properties of that pigment.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Xuan Leng, Peng Lei, Wen-zhao Zhang
Summary: The absorption and two-dimensional rephasing spectra of the Fenna-Matthews-Olson (FMO) complex at 77K were simulated using hierarchical equations of motion method. Three cases of vibrational coupling were studied in the FMO complex model, showing that the vibrational mode significantly weakens the intensity of the absorption peak of high-energy electronic transitions. It was also observed that long-lived quantum beatings originate from vibration, while short-lived electronic coherence still exists. Furthermore, the speed-up of rephasing dynamics by electronic resonance mode is not directly proportional to the coupling strength, and the low-energy electronic-vibrational resonance dimer exhibits a greater speed-up.
Article
Chemistry, Physical
XueYan Cui, YiJing Yan, JianHua Wei
Summary: This study investigates the impact of pigment-protein coupling on the dynamics of photosynthetic energy transport in chromophoric complexes, revealing that the heterogeneous local protein environment affects the excitation energy transfer process and leads to asymmetric excitation oscillation timescales at different pigment sites. The results suggest that the interaction between excited chromophores and their environment plays a critical role in coherent energy-transfer processes, with quantum dynamical simulations showing sustained oscillations of coherent excitation on a long timescale.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Physical
Zhe Huai, Zhengqing Tong, Ye Mei, Yan Mo
Summary: This study investigated the spectral differences between Fenna-Matthews-Olson proteins from C. tepidum and P. aestuarii mutants, revealing that a single-point mutation near BChl 6 can significantly affect the absorption spectrum and excitonic structures of neighboring pigments. The results are consistent with previous experiments and indicate the critical role of protein scaffold in modulating optical properties.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Biochemistry & Molecular Biology
Francisco Delgado, Marco Enriquez
Summary: Fenna-Mathews-Olson complexes play a role in the photosynthetic process of Sulfur Green Bacteria, exhibiting quantum features such as multipartite entanglement and apparent tunnelling. A multidisciplinary approach involving experimental biology, spectroscopy, physics, and math modelling is required to study these aspects. The Hierarchical Equations of Motion are used to solve the open quantum system problem and a new measure of multipartite entanglement is employed. The study provides new insights into FMO multipartite entanglement and tracks the dynamical evolution of the initial state.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Maxim F. Gelin, Raffaele Borrelli
Summary: A fully quantum, numerically accurate wave function-based approach for calculating third-order spectroscopic signals of polyatomic molecules and molecular aggregates at finite temperature has been developed. The approach, based on Thermo Field Dynamics (TFD) representation and tensor-train (TT) machinery, efficiently simulates the quantum evolution of systems with many degrees of freedom. The developed approach has been applied to calculate time- and frequency-resolved fluorescence spectra of the Fenna-Matthews-Olson (FMO) antenna complex at room temperature, considering various factors such as finite resolution, orientational averaging, and static disorder.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Proceedings Paper
Quantum Science & Technology
B. Gonzalez-Soria, F. Delgado
Summary: The high efficiency of excitation energy transfer in the Fenna-Matthews-Olson light-harvesting complex in green sulfur bacteria is determined by its array of bacteriochlorophylls, which are central to the photosynthetic process of these bacteria and controversially associated with long-lived coherence. This study investigates the temperature effects on entanglement and coherence in bacteriochlorophyll excitation energy transfer within the Fenna-Matthews-Olson complex, considering the latest arrangement of 8 bacteriochlorophylls. The Hierarchical Equations of Motion method is used to analyze the system evolution and obtain the global and semi-local entanglement, as well as coherence in the system.
INTERNATIONAL CONFERENCE ON QUANTUM PHENOMENA, QUANTUM CONTROL AND QUANTUM OPTICS, QUANTUM FEST 2021
(2023)
Article
Nanoscience & Nanotechnology
Denis G. Baranov, Christian Schafer, Maxim V. Gorkunov
Summary: Coupling between light and material excitations generates a variety of optical phenomena. Polaritons, as eigenstates of a coupled system, exhibit properties of both photons and electrons, and offer new ways for controlling electronic transport and chemical kinetics. In chiral quantum emitters, which have nonzero electric and magnetic dipole moments, there is potential for novel effects in strong light-matter coupling. This emerging field at the intersection of nanophotonics, quantum optics, and chemistry is still in its early stages, but holds great promise for future research.
Article
Materials Science, Multidisciplinary
Lauren Blanc, Christopher J. Bartel, Haegyeom Kim, Yaosen Tian, Hyunchul Kim, Akira Miura, Gerbrand Ceder, Linda F. Nazar
Summary: Although theoretical computations predicted that MgxCr(2)S(4) could be a suitable cathode candidate, experimental attempts have shown that the Cr3+/4+ redox couple is inaccessible within this structure, preventing reversible (de)intercalation of Mg2+ and leading to dissolution of the active material during charging.
ACS MATERIALS LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Alexander S. Frolov, Carolien Callaert, Maria Batuk, Joke Hadermann, Andrey A. Volykhov, Anna P. Sirotina, Matteo Amati, Luca Gregoratti, Lada Yashina
Summary: This study investigates the reaction between the GeTe (111) surface with molecular oxygen, focusing on crystals with sole inversion domains. The reaction kinetics and structure of the oxide layer are evaluated, revealing nanoscale phase separation of GeO2 and Te, which is unusual for semiconductors.
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
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
Sofia Goia, Matthew A. P. Turner, Jack M. Woolley, Michael D. Horbury, Alexandra J. Borrill, Joshua J. Tully, Samuel J. Cobb, Michael Staniforth, Nicholas D. M. Hine, Adam Burriss, Julie Macpherson, Ben R. Robinson, Vasilios G. Stavros
Summary: The study introduces a TA-SEC approach using BDD mesh electrodes to investigate early-stage photoinduced dynamics of reactive species. By electrochemically generating intermediates, the relaxation mechanisms of AQS and AH(2)QS are unravelled in the first 2.5 ns following UV absorption.
Article
Materials Science, Multidisciplinary
S. J. Magorrian, A. J. Graham, N. Yeung, F. Ferreira, P. Nguyen, A. Barinov, V. Fal'ko, N. R. Wilson, N. D. M. Hine
Summary: In this work, the relative alignment and hybridization of bands in van der Waals heterostructures of transition metal dichalcogenides (TMDs) and hexagonal boron nitride (hBN) are studied. By comparing density functional calculations with experimental angle-resolved photoemission spectroscopy (ARPES) results, the hybridization between TMD and hBN valence states and its effects on band crossings are explored.
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
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, 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)
Article
Chemistry, Physical
Natercia d N. Rodrigues, Jack M. Woolley, Konstantina M. Krokidi, Maria A. Tesa-Serrate, Matthew A. P. Turner, Nicholas D. M. Hine, Vasilios G. Stavros
Summary: This study evaluates the relaxation pathways of two derivatives of methyl anthranilate in solution and finds their sensitivity to solvent polarity and hydrogen bonding character. Common computational methods may not adequately model the observed spectroscopic data due to an inability to account for explicit solvent interactions, suggesting a challenge for computational chemistry.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Materials Science, Multidisciplinary
Siow Mean Loh, Xue Xia, Neil R. Wilson, Nicholas D. M. Hine
Summary: The study investigates the electronic properties of monolayer transition metal dichalcogenide materials with aliovalent doping, using Nb-doped WS2 as an example. Electronic structure calculations and conductivity calculations on realistic models show that a high level of anisotropy can be expected in properties, including conductivity. Predictions suggest in-plane conductivity anisotropy as high as 5:1, the highest observed in any TMDC system in the [Mo,W][S,Se](2) class.
Article
Materials Science, Multidisciplinary
Xue Xia, Siow Mean Loh, Jacob Viner, Natalie C. Teutsch, Abigail J. Graham, Viktor Kandyba, Alexei Barinov, Ana M. Sanchez, David C. Smith, Nicholas D. M. Hine, Neil R. Wilson
Summary: The study investigates the atomic and electronic structure of Mo(1-x)WxS2 alloys, showing that alloying is an important tool for controlling the electronic structure of MX2 for spintronic and valleytronic applications. The results also demonstrate the retention of spin-valley locking in monolayer Mo0.5W0.5S2 despite the predicted reduction of spin-orbit splitting at intermediate compositions.
JOURNAL OF PHYSICS-MATERIALS
(2021)