المؤلفون: Boothroyd, Simon, Behara, Pavan Kumar, Madin, Owen C., Hahn, David F., Jang, Hyesu, Gapsys, Vytautas, Wagner, Jeffrey R., Horton, Joshua T., Dotson, David L., Thompson, Matthew W., Maat, Jessica, Gokey, Trevor, Wang, Lee-Ping, Cole, Daniel J., Gilson, Michael K., Chodera, John D., Bayly, Christopher I., Shirts, Michael R., Mobley, David L.

المساهمون: Division of Chemistry, UK Research and Innovation, American Chemical Society Petroleum Research Fund, National Institute of General Medical Sciences, Open Molecular Software Foundation, Open Force Field Consortium

المصدر: Journal of Chemical Theory and Computation ; volume 19, issue 11, page 3251-3275 ; ISSN 1549-9618 1549-9626

الإتاحة: https://doi.org/10.1021/acs.jctc.3c00039Test

المؤلفون: Ringrose, Chris, Horton, Joshua T., Wang, Lee-Ping, Cole, Daniel J.

المساهمون: UK Research and Innovation, Engineering and Physical Sciences Research Council, Newcastle University

المصدر: Physical Chemistry Chemical Physics ; volume 24, issue 28, page 17014-17027 ; ISSN 1463-9076 1463-9084

الوصف: Use of quantum mechanics to inform molecular mechanics force field derivation is used to speed up the design process. We design and train 15 new protocols for force field derivation, and test their accuracy against experimental liquid properties.

الإتاحة: https://doi.org/10.1039/d2cp02864fTest
http://pubs.rsc.org/en/content/articlepdf/2022/CP/D2CP02864FTest

المؤلفون: Smith, Daniel G. A., Lolinco, Annabelle T., Glick, Zachary L., Lee, Jiyoung, Alenaizan, Asem, Barnes, Taylor A., Borca, Carlos H., Di Remigio, Roberto, Dotson, David L., Ehlert, Sebastian, Heide, Alexander G., Herbst, Michael F., Hermann, Jan, Hicks, Colton B., Horton, Joshua T., Hurtado, Adrian G., Kraus, Peter, Kruse, Holger, Lee, Sebastian J. R., Misiewicz, Jonathon P., Naden, Levi N., Ramezanghorbani, Farhad, Scheurer, Maximilian, Schriber, Jeffrey B., Simmonett, Andrew C., Steinmetzer, Johannes, Wagner, Jeffrey R., Ward, Logan, Welborn, Matthew, Altarawy, Doaa, Anwar, Jamshed, Chodera, John D., Dreuw, Andreas, Kulik, Heather J., Liu, Fang, Martinez, Todd J., Matthews, Devin A., Schaefer, Henry F., III, Sponer, Jiri, Turney, Justin M., Wang, Lee-Ping, De Silva, Nuwan, King, Rollin A., Stanton, John F., Gordon, Mark S., Windus, Theresa L., Sherrill, C. David, Burns, Lori A.

المصدر: Journal of Chemical Physics. 155(20)

الوصف: Community efforts in the computational molecular sciences (CMS) are evolving toward modular, open, and interoperable interfaces that work with existing community codes to provide more functionality and composability than could be achieved with a single program. The Quantum Chemistry Common Driver and Databases (QCDB) project provides such capability through an application programming interface (API) that facilitates interoperability across multiple quantum chemistry software packages. In tandem with the Molecular Sciences Software Institute and their Quantum Chemistry Archive ecosystem, the unique functionalities of several CMS programs are integrated, including CFOUR, GAMESS, NWChem, OpenMM, Psi4, Qcore, TeraChem, and Turbomole, to provide common computational functions, i.e., energy, gradient, and Hessian computations as well as molecular properties such as atomic charges and vibrational frequency analysis. Both standard users and power users benefit from adopting these APIs as they lower the language barrier of input styles and enable a standard layout of variables and data. These designs allow end-to-end interoperable programming of complex computations and provide best practices options by default.

وصف الملف: print

الوصول الحر: https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-462360Test
https://doi.org/10.1063/5.0059356Test

المؤلفون: Xu, Zhongxing, Federman, S. R., Jackson, William M., Ng, Cheuk-Yiu, Wang, Lee-Ping, Crabtree, Kyle N.

المصدر: Journal of Chemical Physics; 7/14/2022, Vol. 157 Issue 2, p1-15, 15p

مصطلحات موضوعية: EXCITED states, POTENTIAL energy, SERIES expansion (Mathematics)

مصطلحات جغرافية: LEIDEN (Netherlands)

مستخلص: Photodissociation is one of the main destruction pathways for dicarbon (C2) in astronomical environments, such as diffuse interstellar clouds, yet the accuracy of modern astrochemical models is limited by a lack of accurate photodissociation cross sections in the vacuum ultraviolet range. C2 features a strong predissociative F 1 Π u − X 1 Σ g + electronic transition near 130 nm originally measured in 1969; however, no experimental studies of this transition have been carried out since, and theoretical studies of the F¹Πu state are limited. In this work, potential energy curves of excited electronic states of C2 are calculated with the aim of describing the predissociative nature of the F¹Πu state and providing new ab initio photodissociation cross sections for astrochemical applications. Accurate electronic calculations of 56 singlet, triplet, and quintet states are carried out at the DW-SA-CASSCF/MRCI+Q level of theory with a CAS(8,12) active space and the aug-cc-pV5Z basis set augmented with additional diffuse functions. Photodissociation cross sections arising from the vibronic ground state to the F¹Πu state are calculated by a coupled-channel model. The total integrated cross section through the F¹Πuv = 0 and v = 1 bands is 1.198 × 10⁻¹³ cm² cm⁻¹, giving rise to a photodissociation rate of 5.02 × 10⁻¹⁰ s⁻¹ under the standard interstellar radiation field, much larger than the rate in the Leiden photodissociation database. In addition, we report a new 2 1 Σ u + state that should be detectable via a strong 2 1 Σ u + − X 1 Σ g + band around 116 nm. [ABSTRACT FROM AUTHOR]

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المؤلفون: Setiadi, Jeffry, Boothroyd, Simon, Slochower, David R., Dotson, David L., Thompson, Matthew W., Wagner, Jeffrey R., Wang, Lee-Ping, Gilson, Michael K.

المصدر: Journal of Chemical Theory & Computation; 1/9/2024, Vol. 20 Issue 1, p239-252, 14p

المؤلفون: Caceres Delpiano, Javier, Wang, Lee-Ping, Essex, Jonathan W.

الوصف: Atomistic models provide a detailed representation of molecular systems, but are sometimes inadequate for simulations of large systems over long timescales. Coarse-grained models enable accelerated simulations by reducing the number of degrees of freedom, at the cost of reduced accuracy. New optimisation processes to parameterise these models could improve their quality and range of applicability. We present an automated approach for the optimisation of coarse-grained force fields, by reproducing free energy data derived from atomistic molecular simulations. To illustrate the approach, we implemented hydration free energy gradients as a new target for force field optimisation in ForceBalance and applied it successfully to optimise the un-charged side-chains and the protein backbone in the SIRAH protein coarse-grain force field. The optimised parameters closely rejproduced hydration free energies of atomistic models and gave improved agreement with experiment

وصف الملف: text

العلاقة: https://eprints.soton.ac.uk/452038/1/D0CP05041E.pdfTest; https://eprints.soton.ac.uk/452038/2/d0cp05041e_1_.pdfTest; Caceres Delpiano, Javier, Wang, Lee-Ping and Essex, Jonathan W. (2021) The automated optimisation of a coarse-grained force field using free energy data. Physical Chemistry Chemical Physics, 23 (43), 24842-24851. (doi:10.1039/D0CP05041E ).

الإتاحة: https://doi.org/10.1039/D0CP05041ETest
https://eprints.soton.ac.uk/452038Test/
https://eprints.soton.ac.uk/452038/1/D0CP05041E.pdfTest
https://eprints.soton.ac.uk/452038/2/d0cp05041e_1_.pdfTest

المؤلفون: LiWang, Andy, Porter, Lauren L., Wang, Lee‐Ping

المصدر: Biopolymers ; volume 112, issue 10 ; ISSN 0006-3525 1097-0282

الإتاحة: https://doi.org/10.1002/bip.23478Test

المؤلفون: Caceres-Delpiano, Javier, Wang, Lee-Ping, Essex, Jonathan W.

المساهمون: National Institutes of Health

المصدر: Physical Chemistry Chemical Physics ; volume 23, issue 43, page 24842-24851 ; ISSN 1463-9076 1463-9084

الوصف: New parameterisation processes for coarse-grained models can improve their quality and range of applicability. We present an automated approach for the optimisation of a coarse-grained protein force field using free energy gradients as a new target.

الإتاحة: https://doi.org/10.1039/d0cp05041eTest
http://pubs.rsc.org/en/content/articlepdf/2021/CP/D0CP05041ETest

المؤلفون: LiWang, Patricia J., Wang, Lee-Ping, LiWang, Andy

المساهمون: US Army Research Office

المصدر: Trends in Biochemical Sciences ; volume 46, issue 6, page 433-434 ; ISSN 0968-0004

مصطلحات موضوعية: Molecular Biology, Biochemistry

الإتاحة: https://doi.org/10.1016/j.tibs.2021.03.003Test
https://api.elsevier.com/content/article/PII:S0968000421000487?httpAccept=text/xmlTest
https://api.elsevier.com/content/article/PII:S0968000421000487?httpAccept=text/plainTest

المؤلفون: Borges, Ricardo M., Colby, Sean M., Das, Susanta, Edison, Arthur S., Fiehn, Oliver, Kind, Tobias, Lee, Jesi, Merrill, Amy T., Merz, Kenneth M., Metz, Thomas O., Nunez, Jamie R., Tantillo, Dean J., Wang, Lee-Ping, Wang, Shunyang, Renslow, Ryan S.

المساهمون: National Institute of Environmental Health Sciences

المصدر: Chemical Reviews ; volume 121, issue 10, page 5633-5670 ; ISSN 0009-2665 1520-6890

الإتاحة: https://doi.org/10.1021/acs.chemrev.0c00901Test