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Yang Y, Jin Q, Yin S. Development of an anisotropic polarizable model for the all-atom AMOEBA force field. Phys Chem Chem Phys 2024; 26:22900-22911. [PMID: 39169824 DOI: 10.1039/d4cp01568a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
For planar and rigid π-conjugated molecular systems, electrostatic and inductive interactions are pivotal in governing molecular packing structures and electron polarization energies. These electrostatic interactions typically exhibit an anisotropic nature within π-conjugated systems. In this study, we utilize the atoms in molecules (AIM) theory in conjunction with linear response theory to decompose molecular polarizability into distributed atomic polarizability tensors. On the basis of atomic polarizability tensors, we extended an anisotropic polarizable model into the AMOEBA polarizable force field. Both anisotropic and isotropic polarizable models in combination with various density functional theory (DFT)-derived atomic multipoles were applied to optimize the experimental crystals of naphthalene and anthracene. Furthermore, these two types of electrostatic models, coupled with the evolutionary algorithm USPEX program, are utilized to predict the crystal structures of oligoacenes. Our findings demonstrate that the anisotropic polarizable model exhibits superior performance in crystal refinement and crystal structure prediction. This enriched anisotropic polarizable model is seamlessly integrated into the AMOEBA polarizable force field and readily applicable within our modified Tinker program.
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Affiliation(s)
- Yanyan Yang
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an City 710119, People's Republic of China.
| | - Qianqian Jin
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an City 710119, People's Republic of China.
| | - Shiwei Yin
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an City 710119, People's Republic of China.
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2
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Wang L, Behara PK, Thompson MW, Gokey T, Wang Y, Wagner JR, Cole DJ, Gilson MK, Shirts MR, Mobley DL. The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling. J Phys Chem B 2024; 128:7043-7067. [PMID: 38989715 DOI: 10.1021/acs.jpcb.4c01558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Force fields are a key component of physics-based molecular modeling, describing the energies and forces in a molecular system as a function of the positions of the atoms and molecules involved. Here, we provide a review and scientific status report on the work of the Open Force Field (OpenFF) Initiative, which focuses on the science, infrastructure and data required to build the next generation of biomolecular force fields. We introduce the OpenFF Initiative and the related OpenFF Consortium, describe its approach to force field development and software, and discuss accomplishments to date as well as future plans. OpenFF releases both software and data under open and permissive licensing agreements to enable rapid application, validation, extension, and modification of its force fields and software tools. We discuss lessons learned to date in this new approach to force field development. We also highlight ways that other force field researchers can get involved, as well as some recent successes of outside researchers taking advantage of OpenFF tools and data.
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Affiliation(s)
- Lily Wang
- Open Force Field, Open Molecular Software Foundation, Davis, California 95616, United States
| | - Pavan Kumar Behara
- Center for Neurotherapeutics, University of California, Irvine, California 92697, United States
| | - Matthew W Thompson
- Open Force Field, Open Molecular Software Foundation, Davis, California 95616, United States
| | - Trevor Gokey
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Yuanqing Wang
- Simons Center for Computational Physical Chemistry and Center for Data Science, New York, New York 10004, United States
| | - Jeffrey R Wagner
- Open Force Field, Open Molecular Software Foundation, Davis, California 95616, United States
| | - Daniel J Cole
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California at San Diego, La Jolla, California 92093, United States
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80305, United States
| | - David L Mobley
- Department of Chemistry, University of California, Irvine, California 92697, United States
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
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3
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Berger E, Niemelä J, Lampela O, Juffer AH, Komsa HP. Raman Spectra of Amino Acids and Peptides from Machine Learning Polarizabilities. J Chem Inf Model 2024; 64:4601-4612. [PMID: 38829726 DOI: 10.1021/acs.jcim.4c00077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Raman spectroscopy is an important tool in the study of vibrational properties and composition of molecules, peptides, and even proteins. Raman spectra can be simulated based on the change of the electronic polarizability with vibrations, which can nowadays be efficiently obtained via machine learning models trained on first-principles data. However, the transferability of the models trained on small molecules to larger structures is unclear, and direct training on large structures is prohibitively expensive. In this work, we first train two machine learning models to predict the polarizabilities of all 20 amino acids. Both models are carefully benchmarked and compared to density functional theory (DFT) calculations, with the neural network method being found to offer better transferability. By combination of machine learning models with classical force field molecular dynamics, Raman spectra of all amino acids are also obtained and investigated, showing good agreement with experiments. The models are further extended to small peptides. We find that adding structures containing peptide bonds to the training set greatly improves predictions, even for peptides not included in training sets.
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Affiliation(s)
- Ethan Berger
- Microelectronics Research Unit, Faculty of Information Technology and Electrical Engineering, University of Oulu, P.O. Box 4500, Oulu FIN-90014, Finland
| | - Juha Niemelä
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FIN-90014, Finland
| | - Outi Lampela
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FIN-90014, Finland
| | - André H Juffer
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FIN-90014, Finland
| | - Hannu-Pekka Komsa
- Microelectronics Research Unit, Faculty of Information Technology and Electrical Engineering, University of Oulu, P.O. Box 4500, Oulu FIN-90014, Finland
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4
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Gao Y, Wang J, Sun M, Jing Y, Chen L, Liang Z, Yang Y, Zhang C, Yao J, Wang X. Tandem Catalysts Enabling Efficient C-N Coupling toward the Electrosynthesis of Urea. Angew Chem Int Ed Engl 2024; 63:e202402215. [PMID: 38581164 DOI: 10.1002/anie.202402215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/21/2024] [Accepted: 04/02/2024] [Indexed: 04/08/2024]
Abstract
The development of a methodology for synthesizing value-added urea (CO(NH2)2) via a renewable electricity-driven C-N coupling reaction under mild conditions is highly anticipated. However, the complex catalytic active sites that act on the carbon and nitrogen species make the reaction mechanism unclear, resulting in a low efficiency of C-N coupling from the co-reduction of carbon dioxide (CO2) and nitrate (NO3 -). Herein, we propose a novel tandem catalyst of Mo-PCN-222(Co), in which the Mo sites serve to facilitate nitrate reduction to the *NH2 intermediate, while the Co sites enhance CO2 reduction to carbonic oxide (CO), thus synergistically promoting C-N coupling. The synthesized Mo-PCN-222(Co) catalyst exhibited a noteworthy urea yield rate of 844.11 mg h-1 g-1, alongside a corresponding Faradaic efficiency of 33.90 % at -0.4 V vs. reversible hydrogen electrode (RHE). By combining in situ spectroscopic techniques with density functional theory calculations, we demonstrate that efficient C-N coupling is attributed to a tandem system in which the *NH2 and *CO intermediates produced by the Mo and Co active sites of Mo-PCN-222(Co) stabilize the formation of the *CONH2 intermediate. This study provides an effective avenue for the design and synthesis of tandem catalysts for electrocatalytic urea synthesis.
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Affiliation(s)
- Yuhang Gao
- Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, P. R. China
- University of Chinese Academy of Sciences, 100049, Beijing, P. R. China
| | - Jingnan Wang
- Molecular Plus and Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, 300072, Tianjin, P. R. China
| | - Menglong Sun
- Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, P. R. China
- University of Chinese Academy of Sciences, 100049, Beijing, P. R. China
| | - Yuan Jing
- Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, P. R. China
- University of Chinese Academy of Sciences, 100049, Beijing, P. R. China
| | - Lili Chen
- Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, P. R. China
- University of Chinese Academy of Sciences, 100049, Beijing, P. R. China
| | - Zhiqin Liang
- Key Laboratory of Luminescence and Optical Information, Ministry of Education, School of Physical Science and Engineering, Beijing Jiaotong University, 100044, Beijing, P. R. China
- Tangshan Research Institute of Beijing Jiaotong University, 063000, Tangshan, P. R. China
| | - Yijun Yang
- Key Laboratory of Luminescence and Optical Information, Ministry of Education, School of Physical Science and Engineering, Beijing Jiaotong University, 100044, Beijing, P. R. China
- Tangshan Research Institute of Beijing Jiaotong University, 063000, Tangshan, P. R. China
| | - Chuang Zhang
- Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, P. R. China
- University of Chinese Academy of Sciences, 100049, Beijing, P. R. China
| | - Jiannian Yao
- Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, P. R. China
- University of Chinese Academy of Sciences, 100049, Beijing, P. R. China
| | - Xi Wang
- Key Laboratory of Luminescence and Optical Information, Ministry of Education, School of Physical Science and Engineering, Beijing Jiaotong University, 100044, Beijing, P. R. China
- Tangshan Research Institute of Beijing Jiaotong University, 063000, Tangshan, P. R. China
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5
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Zhao S, Cieplak P, Duan Y, Luo R. Assessment of Amino Acid Electrostatic Parametrizations of the Polarizable Gaussian Multipole Model. J Chem Theory Comput 2024; 20:2098-2110. [PMID: 38394331 PMCID: PMC11060985 DOI: 10.1021/acs.jctc.3c01347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Accurate parametrization of amino acids is pivotal for the development of reliable force fields for molecular modeling of biomolecules such as proteins. This study aims to assess amino acid electrostatic parametrizations with the polarizable Gaussian Multipole (pGM) model by evaluating the performance of the pGM-perm (with atomic permanent dipoles) and pGM-ind (without atomic permanent dipoles) variants compared to the traditional RESP model. The 100-conf-combterm fitting strategy on tetrapeptides was adopted, in which (1) all peptide bond atoms (-CO-NH-) share identical set of parameters and (2) the total charges of the two terminal N-acetyl (ACE) and N-methylamide (NME) groups were set to neutral. The accuracy and transferability of electrostatic parameters across peptides with varying lengths and real-world examples were examined. The results demonstrate the enhanced performance of the pGM-perm model in accurately representing the electrostatic properties of amino acids. This insight underscores the potential of the pGM-perm model and the 100-conf-combterm strategy for the future development of the pGM force field.
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Affiliation(s)
- Shiji Zhao
- Nurix Therapeutics, Inc., 1700 Owens St. Suite 205, San Francisco, CA 94158, USA
| | - Piotr Cieplak
- SBP Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yong Duan
- UC Davis Genome Center and Department of Biomedical Engineering, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine. Irvine, California 92697, United States
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6
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Saraceno P, Sláma V, Cupellini L. First-principles simulation of excitation energy transfer and transient absorption spectroscopy in the CP29 light-harvesting complex. J Chem Phys 2023; 159:184112. [PMID: 37962444 DOI: 10.1063/5.0170295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
The dynamics of delocalized excitons in light-harvesting complexes (LHCs) can be investigated using different experimental techniques, and transient absorption (TA) spectroscopy is one of the most valuable methods for this purpose. A careful interpretation of TA spectra is essential for the clarification of excitation energy transfer (EET) processes occurring during light-harvesting. However, even in the simplest LHCs, a physical model is needed to interpret transient spectra as the number of EET processes occurring at the same time is very large to be disentangled from measurements alone. Physical EET models are commonly built by fittings of the microscopic exciton Hamiltonians and exciton-vibrational parameters, an approach that can lead to biases. Here, we present a first-principles strategy to simulate EET and transient absorption spectra in LHCs, combining molecular dynamics and accurate multiscale quantum chemical calculations to obtain an independent estimate of the excitonic structure of the complex. The microscopic parameters thus obtained are then used in EET simulations to obtain the population dynamics and the related spectroscopic signature. We apply this approach to the CP29 minor antenna complex of plants for which we follow the EET dynamics and transient spectra after excitation in the chlorophyll b region. Our calculations reproduce all the main features observed in the transient absorption spectra and provide independent insight on the excited-state dynamics of CP29. The approach presented here lays the groundwork for the accurate simulation of EET and unbiased interpretation of transient spectra in multichromophoric systems.
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Affiliation(s)
- Piermarco Saraceno
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Vladislav Sláma
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
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7
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Ozaydin B, Curutchet C. Unraveling the role of thermal fluctuations on the exciton structure of the cryptophyte PC612 and PC645 photosynthetic antenna complexes. Front Mol Biosci 2023; 10:1268278. [PMID: 37790875 PMCID: PMC10544999 DOI: 10.3389/fmolb.2023.1268278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 08/30/2023] [Indexed: 10/05/2023] Open
Abstract
Protein scaffolds play a crucial role in tuning the light harvesting properties of photosynthetic pigment-protein complexes, influencing pigment-protein and pigment-pigment excitonic interactions. Here, we investigate the influence of thermal dynamic effects on the protein tuning mechanisms of phycocyanin PC645 and PC612 antenna complexes of cryptophyte algae, featuring closed or open quaternary structures. We employ a dual molecular dynamics (MD) strategy that combines extensive classical MD simulations with multiple short Born-Oppenheimer quantum/molecular mechanical (QM/MM) simulations to accurately account for both static and dynamic disorder effects. Additionally, we compare the results with an alternative protocol based on multiple QM/MM geometry optimizations of the pigments. Subsequently, we employ polarizable QM/MM calculations using time-dependent density functional theory (TD-DFT) to compute the excited states, and we adopt the full cumulant expansion (FCE) formalism to describe the absorption and circular dichroism spectra. Our findings indicate that thermal effects have only minor impacts on the energy ladder in PC612, despite its remarkable flexibility owing to an open quaternary structure. In striking contrast, thermal effects significantly influence the properties of PC645 due to the absence of a hydrogen bond controlling the twist of ring D in PCB β82 bilins, as well as the larger impact of fluctuations on the excited states of MBV pigments, which possess a higher conjugation length compared to other bilin types. Overall, the dual MD protocol combined with the FCE formalism yields excellent spectral properties for PC612 and PC645, and the resultant excitonic Hamiltonians pave the way for future investigations concerning the implications of open and closed quaternary structures on phycocyanin light harvesting properties.
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Affiliation(s)
- Beste Ozaydin
- Departament de Farmàcia i Tecnologia Farmacèutica, i Fisicoquímica, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona (UB), Barcelona, Spain
- Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona (UB), Barcelona, Spain
| | - Carles Curutchet
- Departament de Farmàcia i Tecnologia Farmacèutica, i Fisicoquímica, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona (UB), Barcelona, Spain
- Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona (UB), Barcelona, Spain
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8
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Mulvey D, Jordan KD. Application of a Fluctuating Charge Polarization Model to Large Polyaromatic Hydrocarbons and Graphene Nanoflakes. J Phys Chem Lett 2023; 14:7869-7875. [PMID: 37639228 PMCID: PMC10494230 DOI: 10.1021/acs.jpclett.3c02013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 08/21/2023] [Indexed: 08/29/2023]
Abstract
We present a polarization model incorporating coupled fluctuating charges and point inducible dipoles that is able to accurately describe the dipole polarizabilities of small hydrocarbons and, for sufficiently large graphene nanoflakes, reproduce the classical image potential of an infinite conducting sheet. When our fluctuating charge model is applied to the hexagonal carbon nanoflake C60000 we attain excellent agreement with the image potential and induced charge distribution of a conducting sheet. With the inclusion of inducible dipole terms, the model predicts an image plane of zim = 1.3334 a0, which falls in line with prior estimates for graphene. We consider the case of two charges placed on opposite sides of C60000 and find that the fluctuating charge model reproduces classical electrostatics once again. By testing opposing and similar signs of the external charges, we conclude that an atomically thin molecule or extended system does not fully screen their interaction.
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Affiliation(s)
- Devin
M. Mulvey
- Department of Chemistry, University
of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Kenneth D. Jordan
- Department of Chemistry, University
of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
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9
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Cupellini L, Qian P, Nguyen-Phan TC, Gardiner AT, Cogdell RJ. Quantum chemical elucidation of a sevenfold symmetric bacterial antenna complex. PHOTOSYNTHESIS RESEARCH 2023; 156:75-87. [PMID: 35672557 PMCID: PMC10070313 DOI: 10.1007/s11120-022-00925-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
The light-harvesting complex 2 (LH2) of purple bacteria is one of the most studied photosynthetic antenna complexes. Its symmetric structure and ring-like bacteriochlorophyll arrangement make it an ideal system for theoreticians and spectroscopists. LH2 complexes from most bacterial species are thought to have eightfold or ninefold symmetry, but recently a sevenfold symmetric LH2 structure from the bacterium Mch. purpuratum was solved by Cryo-Electron microscopy. This LH2 also possesses unique near-infrared absorption and circular dichroism (CD) spectral properties. Here we use an atomistic strategy to elucidate the spectral properties of Mch. purpuratum LH2 and understand the differences with the most commonly studied LH2 from Rbl. acidophilus. Our strategy exploits a combination of molecular dynamics simulations, multiscale polarizable quantum mechanics/molecular mechanics calculations, and lineshape simulations. Our calculations reveal that the spectral properties of LH2 complexes are tuned by site energies and exciton couplings, which in turn depend on the structural fluctuations of the bacteriochlorophylls. Our strategy proves effective in reproducing the absorption and CD spectra of the two LH2 complexes, and in uncovering the origin of their differences. This work proves that it is possible to obtain insight into the spectral tuning strategies of purple bacteria by quantitatively simulating the spectral properties of their antenna complexes.
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Affiliation(s)
- Lorenzo Cupellini
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124, Pisa, Italy.
| | - Pu Qian
- Materials and Structure Analysis, Thermofisher Scientific, Achtseweg Nordic 5, 5651 GTC, Eindhoven, The Netherlands
| | - Tu C Nguyen-Phan
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Alastair T Gardiner
- Laboratory of Anoxygenic Phototrophs, Centre Algatech, Novohradská 237 - Opatovický mlýn, 379 01, Třeboň, Czech Republic
| | - Richard J Cogdell
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, UK
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10
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Feng C, Xi J, Zhang Y, Jiang B, Zhou Y. Accurate and Interpretable Dipole Interaction Model-Based Machine Learning for Molecular Polarizability. J Chem Theory Comput 2023; 19:1207-1217. [PMID: 36753749 DOI: 10.1021/acs.jctc.2c01094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Polarizabilities play significant roles in describing dispersive and inductive interactions of the atom and molecular systems. However, an accurate prediction of molecular polarizabilities from first principles is computationally prohibitive. Although physical models or statistical machine learning models have been proposed, either a lack of accurate description of local chemical environments or demanding a large number of samples for training has limited their practical applications. In this study, we combine a physically inspired dipole interaction model and an accurate neural network method for predicting the polarizability tensors of molecules. With the local chemical environment precisely described and the requirement of rotational covariance naturally fulfilled, this hybrid model is proven to give an accurate molecular polarizability prediction, essentially reducing the number of training samples. The atomic polarizabilities are physically interpretable and transferable to larger molecules unseen in the training set. This promising method may find its wide range of applications, such as spectroscopic simulations and the construction of polarizable force fields.
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Affiliation(s)
- Chaoqiang Feng
- Anhui Key Laboratory of Optoelectric Materials Science and Technology, Department of Physics, Anhui Normal University, Wuhu, Anhui 241000, China.,Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jin Xi
- Anhui Key Laboratory of Optoelectric Materials Science and Technology, Department of Physics, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Yaolong Zhang
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Bin Jiang
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemical Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yong Zhou
- Anhui Key Laboratory of Optoelectric Materials Science and Technology, Department of Physics, Anhui Normal University, Wuhu, Anhui 241000, China
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11
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Solovyova IV, Yang S, Starovoytov ON. Molecular dynamics simulation studies of 1,3-dimethyl imidazolium nitrate ionic liquid with water. J Chem Phys 2023; 158:084505. [PMID: 36859108 DOI: 10.1063/5.0134465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The fundamental understanding of intermolecular interactions of ionic liquids (ILs) with water is essential in predicting IL-water thermodynamic properties. In this study, intermolecular or noncovalent interactions were studied for 1,3-dimethyl imidazolium [DMIM]+ cation and nitrate [NO3]- anion with water, employing quantum mechanics and molecular dynamics simulations. Molecular dynamics simulations were performed using a revised multipolar polarizable force field. The effect of water on ionic liquids was evaluated in terms of thermodynamic and dynamic properties. Thermodynamic properties included liquid densities ρ, excess molar volumes ΔVE, and liquid structures gr. Dynamic properties included self-diffusion coefficients D of mixture constituents as a function of water concentration. The density of ionic liquid-water mixtures monotonically decrease with increasing concentration of water. A negative excess volume was obtained for low and high water concentrations, demonstrating strong intermolecular interactions of water with ionic liquid components. Liquid structures of ionic liquid-water mixtures revealed a tendency for anions to interact with cations at shorter intermolecular distances when the water concentration is increased. Diffusion rates were found to increase for all mixture components with increase in the fraction of water. A significant change in the diffusion rate was found at ∼0.3 weight fraction of water. However, the water self-diffusion coefficient was dominant at all concentrations. The ratio of water/anion and anion/cation self-diffusion coefficients was found to decrease linearly with increasing concentration of water molecules.
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Affiliation(s)
- Iana V Solovyova
- Institute of Engineering Science, Ural Branch of the Russian Academy of Sciences, Yekaterinburg 620049, Russia
| | - Shizhong Yang
- Southern University and A&M College, Department of Computer Science, Baton Rouge, Louisiana 70807, USA
| | - Oleg N Starovoytov
- Southern University and A&M College, Department of Computer Science, Baton Rouge, Louisiana 70807, USA
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12
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Zhao S, Cieplak P, Duan Y, Luo R. Transferability of the Electrostatic Parameters of the Polarizable Gaussian Multipole Model. J Chem Theory Comput 2023; 19:924-941. [PMID: 36696564 PMCID: PMC10152989 DOI: 10.1021/acs.jctc.2c01048] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Accuracy and transferability are the two highly desirable properties of molecular mechanical force fields. Compared with the extensively used point-charge additive force fields that apply fixed atom-centered point partial charges to model electrostatic interactions, polarizable force fields are thought to have the advantage of modeling the atomic polarization effects. Previous works have demonstrated the accuracy of the recently developed polarizable Gaussian multipole (pGM) models. In this work, we assessed the transferability of the electrostatic parameters of the pGM models with (pGM-perm) and without (pGM-ind) atomic permanent dipoles in terms of reproducing the electrostatic potentials surrounding molecules/oligomers absent from electrostatic parameterizations. Encouragingly, both the pGM-perm and pGM-ind models show significantly improved transferability than the additive model in the tests (1) from water monomer to water oligomer clusters; (2) across different conformations of amino acid dipeptides and tetrapeptides; (3) from amino acid tetrapeptides to longer polypeptides; and (4) from nucleobase monomers to Watson-Crick base pair dimers and tetramers. Furthermore, we demonstrated that the double-conformation fittings using amino acid tetrapeptides in the αR and β conformations can result in good transferability not only across different tetrapeptide conformations but also from tetrapeptides to polypeptides with lengths ranging from 1 to 20 repetitive residues for both the pGM-ind and pGM-perm models. In addition, the observation that the pGM-ind model has significantly better accuracy and transferability than the point-charge additive model, even though they have an identical number of parameters, strongly suggest the importance of intramolecular polarization effects. In summary, this and previous works together show that the pGM models possess both accuracy and transferability, which are expected to serve as foundations for the development of next-generation polarizable force fields for modeling various polarization-sensitive biological systems and processes.
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Affiliation(s)
- Shiji Zhao
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Piotr Cieplak
- SBP Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yong Duan
- UC Davis Genome Center and Department of Biomedical Engineering, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States
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13
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Cignoni E, Cupellini L, Mennucci B. Machine Learning Exciton Hamiltonians in Light-Harvesting Complexes. J Chem Theory Comput 2023; 19:965-977. [PMID: 36701385 PMCID: PMC9933434 DOI: 10.1021/acs.jctc.2c01044] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Indexed: 01/27/2023]
Abstract
We propose a machine learning (ML)-based strategy for an inexpensive calculation of excitonic properties of light-harvesting complexes (LHCs). The strategy uses classical molecular dynamics simulations of LHCs in their natural environment in combination with ML prediction of the excitonic Hamiltonian of the embedded aggregate of pigments. The proposed ML model can reproduce the effects of geometrical fluctuations together with those due to electrostatic and polarization interactions between the pigments and the protein. The training is performed on the chlorophylls of the major LHC of plants, but we demonstrate that the model is able to extrapolate well beyond the initial training set. Moreover, the accuracy in predicting the effects of the environment is tested on the simulation of the small changes observed in the absorption spectra of the wild-type and a mutant of a minor LHC.
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Affiliation(s)
- Edoardo Cignoni
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124Pisa, Italy
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14
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Ignatov SK, Masunov AE. Unexpected polarization properties of sub-nanosized magnesium clusters. RSC Adv 2023; 13:4065-4076. [PMID: 36756583 PMCID: PMC9890678 DOI: 10.1039/d2ra08086a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 01/20/2023] [Indexed: 01/29/2023] Open
Abstract
The isotropic electrostatic polarizability (IEP) of sub-nanosized magnesium clusters Mg2-Mg32 was studied in an extensive set comprising 1237 structurally unique isomers. These isomers were found in the course of the global search for the potential energy surface minima of the magnesium clusters at the BP86/6-31G(d) level. The calculation of the polarizability at the same DFT level reveals an unexpected property of the IEP: the linear correlation between the polarizability of the most favorable isomers (and only them) and the cluster nuclearity n. Moreover, for each n, the most stable cluster isomer demonstrates nearly minimal IEP value among all found isomers of a given nuclearity. Surprisingly, these observed features are independent of the cluster structures which are quite different. We hypothesize that the energetic favorability of a cluster structure is related to their low polarizability. Apparently, the atoms forming the cluster tend to arrange themselves in such a way as to provide the most compact distribution of the cluster electron density. A possible explanation of the observed trends, their significance for cluster structure prediction, and the practical applications are discussed.
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Affiliation(s)
- Stanislav K Ignatov
- Lobachevsky State University of Nizhny Novgorod Nizhny Novgorod 603950 Russia
| | - Artëm E Masunov
- NanoScience Technology Center, University of Central Florida Orlando Florida 32826 USA
- School of Modeling, Simulations and Training, University of Central Florida Orlando Florida 32826 USA
- South Ural State University (National Research University) Chelyabinsk Russia
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15
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Zhao S, Wei H, Cieplak P, Duan Y, Luo R. Accurate Reproduction of Quantum Mechanical Many-Body Interactions in Peptide Main-Chain Hydrogen-Bonding Oligomers by the Polarizable Gaussian Multipole Model. J Chem Theory Comput 2022; 18:6172-6188. [PMID: 36094401 PMCID: PMC10152986 DOI: 10.1021/acs.jctc.2c00710] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A key advantage of polarizable force fields is their ability to model the atomic polarization effects that play key roles in the atomic many-body interactions. In this work, we assessed the accuracy of the recently developed polarizable Gaussian Multipole (pGM) models in reproducing quantum mechanical (QM) interaction energies, many-body interaction energies, as well as the nonadditive and additive contributions to the many-body interactions for peptide main-chain hydrogen-bonding conformers, using glycine dipeptide oligomers as the model systems. Two types of pGM models were considered, including that with (pGM-perm) and without (pGM-ind) permanent atomic dipoles. The performances of the pGM models were compared with several widely used force fields, including two polarizable (Amoeba13 and ff12pol) and three additive (ff19SB, ff15ipq, and ff03) force fields. Encouragingly, the pGM models outperform all other force fields in terms of reproducing QM interaction energies, many-body interaction energies, as well as the nonadditive and additive contributions to the many-body interactions, as measured by the root-mean-square errors (RMSEs) and mean absolute errors (MAEs). Furthermore, we tested the robustness of the pGM models against polarizability parameterization errors by employing alternative polarizabilities that are either scaled or obtained from other force fields. The results show that the pGM models with alternative polarizabilities exhibit improved accuracy in reproducing QM many-body interaction energies as well as the nonadditive and additive contributions compared with other polarizable force fields, suggesting that the pGM models are robust against the errors in polarizability parameterizations. This work shows that the pGM models are capable of accurately modeling polarization effects and have the potential to serve as templates for developing next-generation polarizable force fields for modeling various biological systems.
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Affiliation(s)
- Shiji Zhao
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Haixin Wei
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Piotr Cieplak
- SBP Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yong Duan
- UC Davis Genome Center and Department of Biomedical Engineering, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States
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16
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Liu M, Yan T. A Unified Approach to Derive Atomic Partial Charges and Polarizabilities of Ionic Liquids. J Chem Theory Comput 2022; 18:4342-4353. [PMID: 35700352 DOI: 10.1021/acs.jctc.1c01273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We propose a unified approach to fit simultaneously a set of atomic partial charges and polarizabilities of the polarizable model against the ab initio electrostatic potential (ESP) and polarizability. The polarizable model is represented with interactive atomic dipoles with distance-dependent attenuation. For the polarizable model employed in this study, the internal electric field on the polarization sites is fully turned on, and thus allows self-induced dipoles, which persist even for an isolated molecule/ion. By such treatment, the contribution of ESP stems not only from the partial charges but also from the self-induced dipoles, and the atomic partial charges and polarizabilities can be fitted simultaneously against ESP in a unified manner. The fitting with 1-ethyl-3-methylimidazolium (EMIM+) and nitrate (NO3-), a prototypical organic cation and inorganic anion, respectively, that can form ionic liquid, demonstrates that allowance of the self-induced dipoles gives much better fitness. Moreover, test on the total dipole of an EMIM+/NO3- ion pair shows that the agreement with the ab initio dipole is also much improved for the polarizable model, which highlights the importance of the polarization effects of ionic liquids.
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Affiliation(s)
- Menglin Liu
- Institute of New Energy Material Chemistry, School of Materials Science and Engineering, Nankai University, Tianjin 300350, P. R. China
| | - Tianying Yan
- Institute of New Energy Material Chemistry, School of Materials Science and Engineering, Nankai University, Tianjin 300350, P. R. China
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17
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Cignoni E, Cupellini L, Mennucci B. A fast method for electronic couplings in embedded multichromophoric systems. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:304004. [PMID: 35552268 DOI: 10.1088/1361-648x/ac6f3c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Electronic couplings are key to understanding exciton delocalization and transport in natural and artificial light harvesting processes. We develop a method to compute couplings in multichromophoric aggregates embedded in complex environments without running expensive quantum chemical calculations. We use a transition charge approximation to represent the quantum mechanical transition densities of the chromophores and an atomistic and polarizable classical model to describe the environment atoms. We extend our framework to estimate transition charges directly from the chromophore geometry, i.e., bypassing completely the quantum mechanical calculations using a regression approach. The method allows to rapidly compute accurate couplings for a large number of geometries along molecular dynamics trajectories.
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Affiliation(s)
- Edoardo Cignoni
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124, Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124, Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124, Pisa, Italy
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18
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Zhao S, Wei H, Cieplak P, Duan Y, Luo R. PyRESP: A Program for Electrostatic Parameterizations of Additive and Induced Dipole Polarizable Force Fields. J Chem Theory Comput 2022; 18:3654-3670. [PMID: 35537209 DOI: 10.1021/acs.jctc.2c00230] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular modeling at the atomic level has been applied in a wide range of biological systems. The widely adopted additive force fields typically use fixed atom-centered partial charges to model electrostatic interactions. However, the additive force fields cannot accurately model polarization effects, leading to unrealistic simulations in polarization-sensitive processes. Numerous efforts have been invested in developing induced dipole-based polarizable force fields. Whether additive atomic charge models or polarizable induced dipole models are used, proper parameterization of the electrostatic term plays a key role in the force field developments. In this work, we present a Python program called PyRESP for performing atomic multipole parameterizations by reproducing ab initio electrostatic potential (ESP) around molecules. PyRESP provides parameterization schemes for several electrostatic models, including the RESP model with atomic charges for the additive force fields and the RESP-ind and RESP-perm models with additional induced and permanent dipole moments for the polarizable force fields. PyRESP is a flexible and user-friendly program that can accommodate various needs during force field parameterizations for molecular modeling of any organic molecules.
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Affiliation(s)
- Shiji Zhao
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Haixin Wei
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Piotr Cieplak
- SBP Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yong Duan
- UC Davis Genome Center and Department of Biomedical Engineering, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States
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19
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Kumar A, Pandey P, Chatterjee P, MacKerell AD. Deep Neural Network Model to Predict the Electrostatic Parameters in the Polarizable Classical Drude Oscillator Force Field. J Chem Theory Comput 2022; 18:1711-1725. [PMID: 35148088 PMCID: PMC8904317 DOI: 10.1021/acs.jctc.1c01166] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The Drude polarizable force field (FF) captures electronic polarization effects via auxiliary Drude particles that are attached to non-hydrogen atoms, distinguishing it from commonly used additive FFs that rely on fixed charges. The Drude FF currently includes parameters for biomolecules such as proteins, nucleic acids, lipids, and carbohydrates and small-molecule representative of those classes of molecules as well as a range of atomic ions. Extension of the Drude FF to novel small druglike molecules is challenging as it requires the assignment of partial charges, atomic polarizabilities, and Thole scaling factors. In the present article, deep neural network (DNN) models are trained on quantum mechanical (QM)-based partial charges and atomic polarizabilities along with Thole scale factors trained to target QM molecular dipole moments and polarizabilities. Training of the DNN model used a collection of 39 421 molecules with molecular weights up to 200 Da and containing H, C, N, O, P, S, F, Cl, Br, or I atoms. The DNN model utilizes bond connectivity, including 1,2, 1,3, 1,4, and 1,5 terms and distances of Drude FF atom types as the feature vector to build the model, allowing it to capture both local and nonlocal effects in the molecules. Novel methods have been developed to determine restrained electrostatic potential (RESP) charges on atoms and external points representing lone pairs and to determine Thole scale factors, which have no QM analogue. A penalty scheme is devised as a performance predictor of the trained model. Validation studies show that these DNN models can precisely predict molecular dipole and polarizabilities of Food and Drug Administration (FDA)-approved drugs compared to reference MP2 calculations. The availability of the DNN model allowing for the rapid estimation of the Drude electrostatic parameters will facilitate its applicability to a wider range of molecular species.
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Affiliation(s)
- Anmol Kumar
- School of Pharmacy, University of Maryland, Baltimore, 20 Penn Street, HSFII, Baltimore, Maryland 21201, United States
| | - Poonam Pandey
- School of Pharmacy, University of Maryland, Baltimore, 20 Penn Street, HSFII, Baltimore, Maryland 21201, United States
| | - Payal Chatterjee
- School of Pharmacy, University of Maryland, Baltimore, 20 Penn Street, HSFII, Baltimore, Maryland 21201, United States
| | - Alexander D MacKerell
- School of Pharmacy, University of Maryland, Baltimore, 20 Penn Street, HSFII, Baltimore, Maryland 21201, United States
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20
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Anti-glioblastoma effects of phenolic variants of benzoylphenoxyacetamide (BPA) with high potential for blood brain barrier penetration. Sci Rep 2022; 12:3384. [PMID: 35232976 PMCID: PMC8888627 DOI: 10.1038/s41598-022-07247-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/14/2022] [Indexed: 12/13/2022] Open
Abstract
Glioblastomas are the most aggressive brain tumors for which therapeutic options are limited. Current therapies against glioblastoma include surgical resection, followed by radiotherapy plus concomitant treatment and maintenance with temozolomide (TMZ), however, these standard therapies are often ineffective, and average survival time for glioblastoma patients is between 12 and 18 months. We have previously reported a strong anti-glioblastoma activity of several metabolic compounds, which were synthetized based compounds, which were synthetized based on the chemical structure of a common lipid-lowering drug, fenofibrate, and share a general molecular skeleton of benzoylphenoxyacetamide (BPA). Extensive computational analyses of phenol and naphthol moieties added to the BPA skeleton were performed in this study with the objective of selecting new BPA variants for subsequent compound preparation and anti-glioblastoma testing. Initially, 81 structural variations were considered and their physical properties such as solubility (logS), blood–brain partitioning (logBB), and probability of entering the CNS calculated by the Central Nervous System—Multiparameter Optimization (MPO-CNS) algorithm were evaluated. From this initial list, 18 compounds were further evaluated for anti-glioblastoma activity in vitro. Nine compounds demonstrated desirable glioblastoma cell toxicity in cell culture, and two of them, HR51, and HR59 demonstrated significantly improved capability of crossing the model blood–brain-barrier (BBB) composed of endothelial cells, astrocytes and pericytes.
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21
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Structure of the stress-related LHCSR1 complex determined by an integrated computational strategy. Commun Biol 2022; 5:145. [PMID: 35177775 PMCID: PMC8854571 DOI: 10.1038/s42003-022-03083-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/25/2022] [Indexed: 11/08/2022] Open
Abstract
Light-harvesting complexes (LHCs) are pigment-protein complexes whose main function is to capture sunlight and transfer the energy to reaction centers of photosystems. In response to varying light conditions, LH complexes also play photoregulation and photoprotection roles. In algae and mosses, a sub-family of LHCs, light-harvesting complex stress-related (LHCSR), is responsible for photoprotective quenching. Despite their functional and evolutionary importance, no direct structural information on LHCSRs is available that can explain their unique properties. In this work, we propose a structural model of LHCSR1 from the moss P. patens, obtained through an integrated computational strategy that combines homology modeling, molecular dynamics, and multiscale quantum chemical calculations. The model is validated by reproducing the spectral properties of LHCSR1. Our model reveals the structural specificity of LHCSR1, as compared with the CP29 LH complex, and poses the basis for understanding photoprotective quenching in mosses. The structure of the moss P. patens light-harvesting complex stress-related 1 (LHCSR1) is determined using a multi-scale computational approach for investigations of its photoprotective function.
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22
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Abstract
Thole-style mutual induction models for molecular polarization have been adopted by several popular polarizable force fields (FFs) for their simplicity and transferability. The atomic polarizability parameters of these models are typically derived by fitting to ab initio or/and experimental molecular polarizabilities. In this work, we improve upon Thole polarizability parameters by employing both high-level quantum mechanics molecular polarizabilities and electrostatic potential (ESP) responses on three-dimensional grids. Our results indicate that the two approaches to derive atomic polarizability parameters are both effective, while the ESP approaches can also capture the polarization for the atoms with lone pair electrons. The resulting polarizability parameters have been validated on a set of over 7200 molecules covering the most common elements found in organic molecules (C, H, O, N, P, S, F, Cl, Br, and I). These parameters have also been tested on the experimentally measured molecular polarizabilities of 422 molecules. The final set of parameters derived in this work show notable improvement over the current AMOEBA set. The result is a highly transferable, expanded set of atomic polarizabilities defined by the local chemical environment in the form of SMARTS patterns. These parameters can be used directly in molecular mechanics polarizable potential energy functions such as AMOEBA, AMOEBA+, and other Thole-style models.
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Affiliation(s)
| | | | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
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23
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Machine-learning-based many-body energy analysis of argon clusters: Fit for size? Chem Phys 2022. [DOI: 10.1016/j.chemphys.2021.111347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Kim JY, Kim KB, Lee BM. Validation of Quantitative Structure-Activity Relationship (QSAR) and Quantitative Structure-Property Relationship (QSPR) approaches as alternatives to skin sensitization risk assessment. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2021; 84:945-959. [PMID: 34338166 DOI: 10.1080/15287394.2021.1956660] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The aim of this study was conducted to validate the physicochemical properties of a total of 362 chemicals [305 skin sensitizers (212 in the previous study + 93 additional new chemicals), 57 non-skin sensitizers (38 in the previous study + 19 additional new chemicals)] for skin sensitization risk assessment using quantitative structure-activity relationship (QSAR)/quantitative structure-property relationship (QSPR) approaches. The average melting point (MP), surface tension (ST), and density (DS) of the 305 skin sensitizers and 57 non-sensitizers were used to determine the cutoff values distinguishing positive and negative sensitization, and correlation coefficients were employed to derive effective 3-fold concentration (EC3 (%)) values. QSAR models were also utilized to assess skin sensitization. The sensitivity, specificity, and accuracy were 80, 15, and 70%, respectively, for the Toxtree QSAR model; 88, 46, and 81%, respectively, for Vega; and 56, 61, and 56%, respectively, for Danish EPA QSAR. Surprisingly, the sensitivity, specificity, and accuracy were 60, 80, and 64%, respectively, when MP, ST, and DS (MP+ST+DS) were used in this study. Further, MP+ST+DS exhibited a sensitivity of 77%, specificity 57%, and accuracy 73% when the derived EC3 values were classified into local lymph node assay (LLNA) skin sensitizer and non-sensitizer categories. Thus, MP, ST, and DS may prove useful in predicting EC3 values as not only an alternative approach to animal testing but also for skin sensitization risk assessment.
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Affiliation(s)
- Ji Yun Kim
- Division of Toxicology, College of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi-do, South Korea
| | - Kyu-Bong Kim
- College of Pharmacy, Dankook University Dandae-ro, Cheonan, Chungnam, South Korea
| | - Byung-Mu Lee
- Division of Toxicology, College of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi-do, South Korea
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25
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Zauchner MG, Dal Forno S, Cśanyi G, Horsfield A, Lischner J. Predicting polarizabilities of silicon clusters using local chemical environments. MACHINE LEARNING: SCIENCE AND TECHNOLOGY 2021. [DOI: 10.1088/2632-2153/ac2cfe] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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26
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Introducing the effective polarizable bond (EPB) model in DNA simulations. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.139160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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27
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Hashem S, Macaluso V, Nottoli M, Lipparini F, Cupellini L, Mennucci B. From crystallographic data to the solution structure of photoreceptors: the case of the AppA BLUF domain. Chem Sci 2021; 12:13331-13342. [PMID: 34777752 PMCID: PMC8528011 DOI: 10.1039/d1sc03000k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/01/2021] [Indexed: 12/28/2022] Open
Abstract
Photoreceptor proteins bind a chromophore, which, upon light absorption, modifies its geometry or its interactions with the protein, finally inducing the structural change needed to switch the protein from an inactive to an active or signaling state. In the Blue Light-Using Flavin (BLUF) family of photoreceptors, the chromophore is a flavin and the changes have been connected with a rearrangement of the hydrogen bond network around it on the basis of spectroscopic changes measured for the dark-to-light conversion. However, the exact conformational change triggered by the photoexcitation is still elusive mainly because a clear consensus on the identity not only of the light activated state but also of the dark one has not been achieved. Here, we present an integrated investigation that combines microsecond MD simulations starting from the two conflicting crystal structures available for the AppA BLUF domain with calculations of NMR, IR and UV-Vis spectra using a polarizable QM/MM approach. Thanks to such a combined analysis of the three different spectroscopic responses, a robust characterization of the structure of the dark state in solution is given together with the uncovering of important flaws of the most popular molecular mechanisms present in the literature for the dark-to-light activation.
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Affiliation(s)
- Shaima Hashem
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Veronica Macaluso
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
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28
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Bin Faheem A, Kim JY, Bae SE, Lee KK. Efficient parameterization of intermolecular force fields for molecular dynamics simulations via genetic algorithms. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116579] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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29
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Hayakawa D, Watanabe Y, Gouda H. Unpolarizable molecular model describing electron distribution for treating halogen bonds. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138824] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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30
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Wei H, Qi R, Wang J, Cieplak P, Duan Y, Luo R. Efficient formulation of polarizable Gaussian multipole electrostatics for biomolecular simulations. J Chem Phys 2021; 153:114116. [PMID: 32962395 DOI: 10.1063/5.0019560] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Molecular dynamics simulations of biomolecules have been widely adopted in biomedical studies. As classical point-charge models continue to be used in routine biomolecular applications, there have been growing demands on developing polarizable force fields for handling more complicated biomolecular processes. Here, we focus on a recently proposed polarizable Gaussian Multipole (pGM) model for biomolecular simulations. A key benefit of pGM is its screening of all short-range electrostatic interactions in a physically consistent manner, which is critical for stable charge-fitting and is needed to reproduce molecular anisotropy. Another advantage of pGM is that each atom's multipoles are represented by a single Gaussian function or its derivatives, allowing for more efficient electrostatics than other Gaussian-based models. In this study, we present an efficient formulation for the pGM model defined with respect to a local frame formed with a set of covalent basis vectors. The covalent basis vectors are chosen to be along each atom's covalent bonding directions. The new local frame can better accommodate the fact that permanent dipoles are primarily aligned along covalent bonds due to the differences in electronegativity of bonded atoms. It also allows molecular flexibility during molecular simulations and facilitates an efficient formulation of analytical electrostatic forces without explicit torque computation. Subsequent numerical tests show that analytical atomic forces agree excellently with numerical finite-difference forces for the tested system. Finally, the new pGM electrostatics algorithm is interfaced with the particle mesh Ewald (PME) implementation in Amber for molecular simulations under the periodic boundary conditions. To validate the overall pGM/PME electrostatics, we conducted an NVE simulation for a small water box of 512 water molecules. Our results show that to achieve energy conservation in the polarizable model, it is important to ensure enough accuracy on both PME and induction iteration. It is hoped that the reformulated pGM model will facilitate the development of future force fields based on the pGM electrostatics for applications in biomolecular systems and processes where polarization plays crucial roles.
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Affiliation(s)
- Haixin Wei
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California, Irvine, Irvine, California 92697, USA
| | - Ruxi Qi
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California, Irvine, Irvine, California 92697, USA
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Piotr Cieplak
- SBP Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Yong Duan
- UC Davis Genome Center and Department of Biomedical Engineering, University of California, Davis, One Shields Avenue, Davis, California 95616, USA
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California, Irvine, Irvine, California 92697, USA
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31
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King E, Qi R, Li H, Luo R, Aitchison E. Estimating the Roles of Protonation and Electronic Polarization in Absolute Binding Affinity Simulations. J Chem Theory Comput 2021; 17:2541-2555. [PMID: 33764050 DOI: 10.1021/acs.jctc.0c01305] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Accurate prediction of binding free energies is critical to streamlining the drug development and protein design process. With the advent of GPU acceleration, absolute alchemical methods, which simulate the removal of ligand electrostatics and van der Waals interactions with the protein, have become routinely accessible and provide a physically rigorous approach that enables full consideration of flexibility and solvent interaction. However, standard explicit solvent simulations are unable to model protonation or electronic polarization changes upon ligand transfer from water to the protein interior, leading to inaccurate prediction of binding affinities for charged molecules. Here, we perform extensive simulation totaling ∼540 μs to benchmark the impact of modeling conditions on predictive accuracy for absolute alchemical simulations. Binding to urokinase plasminogen activator (UPA), a protein frequently overexpressed in metastatic tumors, is evaluated for a set of 10 inhibitors with extended flexibility, highly charged character, and titratable properties. We demonstrate that the alchemical simulations can be adapted to utilize the MBAR/PBSA method to improve the accuracy upon incorporating electronic polarization, highlighting the importance of polarization in alchemical simulations of binding affinities. Comparison of binding energy prediction at various protonation states indicates that proper electrostatic setup is also crucial in binding affinity prediction of charged systems, prompting us to propose an alternative binding mode with protonated ligand phenol and Hid-46 at the binding site, a testable hypothesis for future experimental validation.
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Affiliation(s)
| | - Ruxi Qi
- Cryo-EM Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
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32
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Cardoso
Ramos F, Cupellini L, Mennucci B. Computational Investigation of Structural and Spectroscopic Properties of LOV-Based Proteins with Improved Fluorescence. J Phys Chem B 2021; 125:1768-1777. [PMID: 33566620 PMCID: PMC7917436 DOI: 10.1021/acs.jpcb.0c10834] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/27/2021] [Indexed: 01/22/2023]
Abstract
Flavin-based fluorescent proteins are a class of fluorescent reporters derived from light, oxygen, and voltage (LOV) sensing proteins. Through mutagenesis, natural LOV proteins have been engineered to obtain improved fluorescence properties. In this study, we combined extended classical Molecular Dynamics simulations and multiscale Quantum Mechanics/Molecular Mechanics methods to clarify the relationship between structural and dynamic changes induced by specific mutations and the spectroscopic response. To reach this goal we compared two LOV variants, one obtained by the single mutation needed to photochemically inactivate the natural system, and the other (iLOV) obtained through additional mutations and characterized by a significantly improved fluorescence. Our simulations confirmed the "flipping and crowding" effect induced in iLOV by the additional mutations and revealed its mechanism of action. We also showed that these mutations, and the resulting differences in the composition and flexibility of the binding pockets, are not reflected in significant shifts of the excitation and emission energies, in agreement with the similarity of the spectra measured for the two systems. However, a small but consistent reduction was found in the Stokes shift of iLOV, suggesting a reduction of the intermolecular reorganization experienced by the chromophore after excitation, which could slow down its internal conversion to the ground state and improve the fluorescence.
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Affiliation(s)
- Felipe Cardoso
Ramos
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, Via G. Moruzzi 13, Pisa, I-56124, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, Via G. Moruzzi 13, Pisa, I-56124, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, Via G. Moruzzi 13, Pisa, I-56124, Italy
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33
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Zhao S, Schaub AJ, Tsai SC, Luo R. Development of a Pantetheine Force Field Library for Molecular Modeling. J Chem Inf Model 2021; 61:856-868. [PMID: 33534558 PMCID: PMC8266206 DOI: 10.1021/acs.jcim.0c01384] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pantetheine is ubiquitous in nature in various forms of pantetheine-containing ligands (PCLs), including coenzyme A and phosphopantetheine. Lack of scalable force field libraries for PCLs has hampered the computational studies of biological macromolecules containing PCLs. We describe here the development of the first generation Pantetheine Force Field (PFF) library that is compatible with Amber force fields; parameterized using Gasteiger, AM1-BCC, or RESP charging methods combined with gaff2 and ff14SB parameter sets. In addition, a "plug-and-play" strategy was employed to enable the systematic charging of computationally expensive molecules sharing common substructural motifs. The validation studies performed on the PFF library showed promising performance where molecular dynamics (MD) simulations results were compared with experimental data of three representative systems. The PFF library represents the first force field library capable of modeling systems containing PCLs in silico and will aid in various applications including protein engineering and drug discovery.
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Affiliation(s)
- Shiji Zhao
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697, United States
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, California 92697, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, United States
| | - Andrew J Schaub
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697, United States
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, California 92697, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, United States
| | - Shiou-Chuan Tsai
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697, United States
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, United States
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697, United States
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, California 92697, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States
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34
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Mu J, Liu H, Zhang J, Luo R, Chen HF. Recent Force Field Strategies for Intrinsically Disordered Proteins. J Chem Inf Model 2021; 61:1037-1047. [PMID: 33591749 PMCID: PMC8256680 DOI: 10.1021/acs.jcim.0c01175] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Intrinsically disordered proteins (IDPs) are widely distributed across eukaryotic cells, playing important roles in molecular recognition, molecular assembly, post-translational modification, and other biological processes. IDPs are also associated with many diseases such as cancers, cardiovascular diseases, and neurodegenerative diseases. Due to their structural flexibility, conventional experimental methods cannot reliably capture their heterogeneous structures. Molecular dynamics simulation becomes an important complementary tool to quantify IDP structures. This review covers recent force field strategies proposed for more accurate molecular dynamics simulations of IDPs. The strategies include adjusting dihedral parameters, adding grid-based energy correction map (CMAP) parameters, refining protein-water interactions, and others. Different force fields were found to perform well on specific observables of specific IDPs but also are limited in reproducing all available experimental observables consistently for all tested IDPs. We conclude the review with perspective areas for improvements for future force fields for IDPs.
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Affiliation(s)
- Junxi Mu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hao Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jian Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai 20025, China
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical and Molecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, California 92697-3900, United States
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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35
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Sláma V, Cupellini L, Mennucci B. Exciton properties and optical spectra of light harvesting complex II from a fully atomistic description. Phys Chem Chem Phys 2020; 22:16783-16795. [PMID: 32662461 DOI: 10.1039/d0cp02492a] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We present a fully atomistic simulation of linear optical spectra (absorption, fluorescence and circular dichroism) of the Light Harvesting Complex II (LHCII) trimer using a hybrid approach, which couples a quantum chemical description of the chlorophylls with a classical model for the protein and the external environment (membrane and water). The classical model uses a polarizable Molecular Mechanics force field, thus allowing mutual polarization effects in the calculations of the excitonic properties. The investigation is performed both on the crystal structure and on structures generated by a μs long classical molecular dynamics simulation of the complex within a solvated membrane. The results show that this integrated approach not only provides a good description of the excitonic properties and optical spectra without the need for additional refinements of the excitonic parameters, but it also allows an atomistic investigation of the relative importance of electronic, structural and environment effects in determining the optical spectra.
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Affiliation(s)
- Vladislav Sláma
- Department of Chemistry and Industrial Chemistry, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy.
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36
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Duan G, Ji C, Zhang JZH. Developing an effective polarizable bond method for small molecules with application to optimized molecular docking. RSC Adv 2020; 10:15530-15540. [PMID: 35495446 PMCID: PMC9052371 DOI: 10.1039/d0ra01483d] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 03/31/2020] [Indexed: 12/20/2022] Open
Abstract
Electrostatic interaction plays an essential role in protein-ligand binding. Due to the polarization effect, electrostatic interactions are largely impacted by their local environments. However, traditional force fields use fixed point charge-charge interactions to describe electrostatic interactions but is unable to include the polarization effect. The lack of the polarization effect in the force field representation can result in substantial error in biomolecular studies, such as molecular dynamics and molecular docking. Docking programs usually employ traditional force fields to estimate the binding energy between a ligand and a protein for pose selection or scoring. The intermolecular interaction energy mainly consists of van der Waals and electrostatic interaction in the force field representation. In the current study, we developed an Effective Polarizable Bond (EPB) method for small organic molecules and applied this EPB method to optimize protein-ligand docking in computational tests for a variety of protein-ligand systems. We tested the method on a set of 38 cocrystallized structures taken from the Protein Data Bank (PDB) and found that the maximum error was reduced from 7.98 Å to 2.03 Å when using EPB Dock, providing strong evidence that the use of EPB charges is important. We found that our optimized docking approach with EPB charges could improve the docking performance, sometimes dramatically, and the maximum error was reduced from 12.88 Å to 1.57 Å in Optimized Docking (in the case of 1fqx). The average RMSD decreased from 2.83 Å to 1.85 Å. Further investigations showed that the use of the EBP method could enhance intermolecular hydrogen bonding, which is a major contributing factor to improved docking performance. Developed tools for the calculation of the polarized ligand charge from a protein-ligand complex structure with the EPB method are freely available on GitHub (https://github.com/Xundrug/EPB).
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Affiliation(s)
- Guanfu Duan
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China
| | - Changge Ji
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 China
| | - John Z H Zhang
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 China
- Department of Chemistry, New York University NY NY 10003 USA
- Collaborative Innovation Center of Extreme Optics, Shanxi University Taiyuan Shanxi 030006 China
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37
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Identification of Novel Chemical Entities for Adenosine Receptor Type 2A Using Molecular Modeling Approaches. Molecules 2020; 25:molecules25051245. [PMID: 32164183 PMCID: PMC7179438 DOI: 10.3390/molecules25051245] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/01/2020] [Accepted: 03/06/2020] [Indexed: 12/20/2022] Open
Abstract
Adenosine Receptor Type 2A (A2AAR) plays a role in important processes, such as anti-inflammatory ones. In this way, the present work aimed to search for compounds by pharmacophore-based virtual screening. The pharmacokinetic/toxicological profiles of the compounds, as well as a robust QSAR, predicted the binding modes via molecular docking. Finally, we used molecular dynamics to investigate the stability of interactions from ligand-A2AAR. For the search for A2AAR agonists, the UK-432097 and a set of 20 compounds available in the BindingDB database were studied. These compounds were used to generate pharmacophore models. Molecular properties were used for construction of the QSAR model by multiple linear regression for the prediction of biological activity. The best pharmacophore model was used by searching for commercial compounds in databases and the resulting compounds from the pharmacophore-based virtual screening were applied to the QSAR. Two compounds had promising activity due to their satisfactory pharmacokinetic/toxicological profiles and predictions via QSAR (Diverset 10002403 pEC50 = 7.54407; ZINC04257548 pEC50 = 7.38310). Moreover, they had satisfactory docking and molecular dynamics results compared to those obtained for Regadenoson (Lexiscan®), used as the positive control. These compounds can be used in biological assays (in vitro and in vivo) in order to confirm the potential activity agonist to A2AAR.
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38
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Caricato M. Coupled cluster theory in the condensed phase within the singles‐T density scheme for the environment response. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Marco Caricato
- Department of Chemistry University of Kansas Lawrence Kansas
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39
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Reinholdt P, Kjellgren ER, Steinmann C, Olsen JMH. Cost-Effective Potential for Accurate Polarizable Embedding Calculations in Protein Environments. J Chem Theory Comput 2020; 16:1162-1174. [PMID: 31855427 DOI: 10.1021/acs.jctc.9b00616] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The fragment-based polarizable embedding (PE) model combined with an appropriate electronic structure method constitutes a highly efficient and accurate multiscale approach for computing spectroscopic properties of a central moiety including effects from its molecular environment through an embedding potential. There is, however, a comparatively high computational overhead associated with the computation of the embedding potential, which is derived from first-principles calculations on individual fragments of the environment. To reduce the computational cost associated with the calculation of embedding potential parameters, we developed a set of amino acid-specific transferable parameters tailored for large-scale PE-based calculations that include proteins. The amino acid-based parameters are obtained by simultaneously fitting to a set of reference electric potentials based on structures derived from a backbone-dependent rotamer library. The developed cost-effective polarizable protein potential (CP3) consists of atom-centered charges and isotropic dipole-dipole polarizabilities of the standard amino acids. In terms of reproduction of electric potentials, the CP3 is shown to perform consistently and with acceptable accuracy across both small tripeptide test systems and larger proteins. We show, through applications on realistic protein systems, that acceptable accuracy can be obtained by using a pure CP3 representation of the protein environment, thus altogether omitting the cost associated with the calculation of embedding potential parameters. High accuracy comparable to that of the full fragment-based approach can be achieved through a mixed description where the CP3 is used only to describe amino acids beyond a threshold distance from the central quantum part.
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Affiliation(s)
- Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , Campusvej 55 , DK-5230 Odense M , Denmark
| | - Erik Rosendahl Kjellgren
- Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , Campusvej 55 , DK-5230 Odense M , Denmark
| | - Casper Steinmann
- Department of Chemistry and Bioscience , Aalborg University , Fredrik Bajers Vej 7H , DK-9220 Aalborg , Denmark
| | - Jógvan Magnus Haugaard Olsen
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry , UiT The Arctic University of Norway , Tromsø N-9037 , Norway
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40
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Exploring anticancer activity of structurally modified benzylphenoxyacetamide (BPA); I: Synthesis strategies and computational analyses of substituted BPA variants with high anti-glioblastoma potential. Sci Rep 2019; 9:17021. [PMID: 31745126 PMCID: PMC6864087 DOI: 10.1038/s41598-019-53207-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/21/2019] [Indexed: 12/12/2022] Open
Abstract
Structural variations of the benzylphenoxyacetamide (BPA) molecular skeleton were explored as a viable starting point for designing new anti-glioblastoma drug candidates. Hand-to-hand computational evaluation, chemical modifications, and cell viability testing were performed to explore the importance of some of the structural properties in order to generate, retain, and improve desired anti-glioblastoma characteristics. It was demonstrated that several structural features are required to retain the anti-glioblastoma activity, including a carbonyl group of the benzophenone moiety, as well as 4′-chloro and 2,2-dimethy substituents. In addition, the structure of the amide moiety can be modified in such a way that desirable anti-glioblastoma and physical properties can be improved. Via these structural modifications, more than 50 compounds were prepared and tested for anti-glioblastoma activity. Four compounds were identified (HR28, HR32, HR37, and HR46) that in addition to HR40 (PP1) from our previous study, have been determined to have desirable physical and biological properties. These include high glioblastoma cytotoxicity at low μM concentrations, improved water solubility, and the ability to penetrate the blood brain barrier (BBB), which indicate a potential for becoming a new class of anti-glioblastoma drugs.
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41
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Cardoso Ramos F, Nottoli M, Cupellini L, Mennucci B. The molecular mechanisms of light adaption in light-harvesting complexes of purple bacteria revealed by a multiscale modeling. Chem Sci 2019; 10:9650-9662. [PMID: 32055335 PMCID: PMC6988754 DOI: 10.1039/c9sc02886b] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/23/2019] [Indexed: 12/27/2022] Open
Abstract
The light-harvesting in photosynthetic purple bacteria can be tuned in response to the light conditions during cell growth. One of the used strategies is to change the energy of the excitons in the major fight-harvesting complex, commonly known as LH2. In the present study we report the first systematic investigation of the microscopic origin of the exciton tuning using three complexes, namely the common (high-light) and the low-light forms of LH2 from Rps. acidophila plus a third complex analogous to the PucD complex from Rps. palustris. The study is based on the combination of classical molecular dynamics of each complex in a lipid membrane and excitonic calculations based on a multiscale quantum mechanics/molecular mechanics approach including a polarizable embedding. From the comparative analysis, it comes out that the mechanisms that govern the adaptation of the complex to different light conditions use the different H-bonding environment around the bacteriochlorophyll pigments to dynamically control both internal and inter-pigment degrees of freedom. While the former have a large effect on the site energies, the latter significantly change the electronic couplings, but only the combination of the two effects can fully reproduce the tuning of the final excitons and explain the observed spectroscopic differences.
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Affiliation(s)
- Felipe Cardoso Ramos
- Dipartimento di Chimica e Chimica Industriale , Università di Pisa , Via G. Moruzzi 13 , 56124 Pisa , Italy .
| | - Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale , Università di Pisa , Via G. Moruzzi 13 , 56124 Pisa , Italy .
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale , Università di Pisa , Via G. Moruzzi 13 , 56124 Pisa , Italy .
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale , Università di Pisa , Via G. Moruzzi 13 , 56124 Pisa , Italy .
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42
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Duan G, Ji C, Zhang JZH. A force consistent method for electrostatic energy calculation in fluctuating charge model. J Chem Phys 2019; 151:094105. [PMID: 31492061 DOI: 10.1063/1.5118224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A practical approach to include the polarization effect in a molecular force field is the fluctuating charge method in which atomic charges vary as the configuration of the molecular system changes. However, the use of the Coulomb formula to evaluate energy in a fluctuating charge method is theoretically inconsistent with the forces given by the fluctuating method. In this work, we propose a force-consistent method to correctly calculate electrostatic energies of molecular systems using a fluctuating charge model (Effective Polarizable Bond or EPB). In this protocol, the electrostatic energy is obtained by numerical interaction of the atomic forces along the MD trajectory, rather than using the default Coulomb formula in the EPB model. Test study on the benchmark Barnase-Barstar protein-protein interaction system demonstrates that although the total electrostatic energy of the system shows little deviation due to the averaging effect, specific residue-residue electrostatic interaction energy is affected and the level of the effect depends on the charges of the interacting residues with charged residues showing pronounced differences in calculated energies between using the current protocol and the standard Coulomb formula. It is recommended that the proposed numerical interaction method should be preferred in the calculation of electrostatic energy in fluctuating charge models used in molecular dynamics simulations.
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Affiliation(s)
- Guanfu Duan
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Changge Ji
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - John Z H Zhang
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
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43
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Ren S, Lipparini F, Mennucci B, Caricato M. Coupled Cluster Theory with Induced Dipole Polarizable Embedding for Ground and Excited States. J Chem Theory Comput 2019; 15:4485-4496. [PMID: 31265278 DOI: 10.1021/acs.jctc.9b00468] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this work, we present the theory and implementation of the coupled cluster single and double excitations (CCSD) method combined with a classical polarizable molecular mechanics force field (MMPol) based on the induced dipole model. The method is developed to compute electronic excitation energies within the state specific (SS) and linear response (LR) formalisms for the interaction of the quantum mechanical and classical regions. Furthermore, we consider an approximate expression of the correlation energy, originally developed for CCSD with implicit solvation models, where the interaction term is linear in the coupled cluster density. This approximation allows us to include the explicit contribution of the environment to the CC equations without increasing the computational effort. The test calculations on microsolvated systems, where the CCSD/MMPol method is compared to full CCSD calculations, demonstrates the reliability of this computational protocol for all interaction schemes (errors < 2%). We also show that it is important to include induced dipoles on all atom centers of the classical region and that too diffuse functions in the basis set may be problematic due to too strong interaction with the environment.
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Affiliation(s)
- Sijin Ren
- Department of Chemistry , University of Kansas , 1567 Irving Hill Road , Lawrence , Kansas 66044 , United States
| | - Filippo Lipparini
- Department of Chemistry , Università di Pisa , Via Giuseppe Moruzzi , 13 56124 Pisa , Italy
| | - Benedetta Mennucci
- Department of Chemistry , Università di Pisa , Via Giuseppe Moruzzi , 13 56124 Pisa , Italy
| | - Marco Caricato
- Department of Chemistry , University of Kansas , 1567 Irving Hill Road , Lawrence , Kansas 66044 , United States
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44
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Corbella M, Cupellini L, Lipparini F, Scholes GD, Curutchet C. Spectral Variability in Phycocyanin Cryptophyte Antenna Complexes is Controlled by Changes in the α‐Polypeptide Chains. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Marina Corbella
- Department of Pharmacy and Pharmaceutical Technology and Physical Chemistry and Institute of Theoretical and Computational Chemistry (IQTC-UB), Faculty of Pharmacy and Food SciencesUniversity of Barcelona Av. Joan XXIII s/n 08028 Barcelona Spain
- Department of ChemistryUppsala University BMC Box 576 Uppsala S-751 23 Sweden
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica IndustrialeUniversity of Pisa Via Risorgimento 35 56126 Pisa Italy
- Institute for Research in Biomedicine (IRB Barcelona)The Barcelona Institute of Science and Technology Baldiri Reixac 10 08028 Barcelona Spain
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica IndustrialeUniversity of Pisa Via Risorgimento 35 56126 Pisa Italy
| | - Gregory D. Scholes
- Department of ChemistryPrinceton University Washington Road, Princeton New Jersey 08544 United States
| | - Carles Curutchet
- Department of Pharmacy and Pharmaceutical Technology and Physical Chemistry and Institute of Theoretical and Computational Chemistry (IQTC-UB), Faculty of Pharmacy and Food SciencesUniversity of Barcelona Av. Joan XXIII s/n 08028 Barcelona Spain
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Manz TA, Chen T, Cole DJ, Limas NG, Fiszbein B. New scaling relations to compute atom-in-material polarizabilities and dispersion coefficients: part 1. Theory and accuracy. RSC Adv 2019; 9:19297-19324. [PMID: 35519408 PMCID: PMC9064874 DOI: 10.1039/c9ra03003d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/03/2019] [Indexed: 11/21/2022] Open
Abstract
Polarizabilities and London dispersion forces are important to many chemical processes. Force fields for classical atomistic simulations can be constructed using atom-in-material polarizabilities and C n (n = 6, 8, 9, 10…) dispersion coefficients. This article addresses the key question of how to efficiently assign these parameters to constituent atoms in a material so that properties of the whole material are better reproduced. We develop a new set of scaling laws and computational algorithms (called MCLF) to do this in an accurate and computationally efficient manner across diverse material types. We introduce a conduction limit upper bound and m-scaling to describe the different behaviors of surface and buried atoms. We validate MCLF by comparing results to high-level benchmarks for isolated neutral and charged atoms, diverse diatomic molecules, various polyatomic molecules (e.g., polyacenes, fullerenes, and small organic and inorganic molecules), and dense solids (including metallic, covalent, and ionic). We also present results for the HIV reverse transcriptase enzyme complexed with an inhibitor molecule. MCLF provides the non-directionally screened polarizabilities required to construct force fields, the directionally-screened static polarizability tensor components and eigenvalues, and environmentally screened C6 coefficients. Overall, MCLF has improved accuracy compared to the TS-SCS method. For TS-SCS, we compared charge partitioning methods and show DDEC6 partitioning yields more accurate results than Hirshfeld partitioning. MCLF also gives approximations for C8, C9, and C10 dispersion coefficients and quantum Drude oscillator parameters. This method should find widespread applications to parameterize classical force fields and density functional theory (DFT) + dispersion methods.
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Affiliation(s)
- Thomas A Manz
- Department of Chemical & Materials Engineering, New Mexico State University Las Cruces New Mexico 88003-8001 USA
| | - Taoyi Chen
- Department of Chemical & Materials Engineering, New Mexico State University Las Cruces New Mexico 88003-8001 USA
| | - Daniel J Cole
- School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne NE1 7RU UK
| | - Nidia Gabaldon Limas
- Department of Chemical & Materials Engineering, New Mexico State University Las Cruces New Mexico 88003-8001 USA
| | - Benjamin Fiszbein
- Department of Chemical & Materials Engineering, New Mexico State University Las Cruces New Mexico 88003-8001 USA
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DelloStritto M, Klein ML, Borguet E. Bond-Dependent Thole Model for Polarizability and Spectroscopy. J Phys Chem A 2019; 123:5378-5387. [DOI: 10.1021/acs.jpca.8b12011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Waibel C, Gross J. Polarizable Transferable Anisotropic United-Atom Force Field Based on the Mie Potential for Phase Equilibria: Ethers, n-Alkanes, and Nitrogen. J Chem Theory Comput 2019; 15:2561-2573. [DOI: 10.1021/acs.jctc.8b01238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christian Waibel
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
| | - Joachim Gross
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
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Wang J, Cieplak P, Luo R, Duan Y. Development of Polarizable Gaussian Model for Molecular Mechanical Calculations I: Atomic Polarizability Parameterization To Reproduce ab Initio Anisotropy. J Chem Theory Comput 2019; 15:1146-1158. [PMID: 30645118 PMCID: PMC7197406 DOI: 10.1021/acs.jctc.8b00603] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A set of atomic polarizability parameters for a new polarizable Gaussian model (pGM) has been developed with the goal to accurately reproduce the polarizability anisotropy, taking advantage of its ability to attenuate all short-range electrostatic interactions, by fitting the ab initio molecular polarizability tensors ( A pq) calculated at the B3LYP/aug-cc-pVTZ level. For comparison, we also rederived the parameters for three Thole models in which the 1-2 (bonded), 1-3 (separated by two bonds), and 1-4 (separated by three bonds) interactions are fully included. The average percent errors (APEs) of molecular polarizability tensors for 4842 molecules or dimers are 2.98, 3.76, 3.28, and 3.82% for the pGM, Thole linear, Thole exponential, and Thole Amoeba models, respectively, with atom-type independent, universal screening factors (USF). The APEs are reduced further to 2.30, 2.69, 2.25, and 2.48% for the four corresponding polarizable models with atom-type dependent, variable screening factors (VSF). It is encouraging that the pGM with variable screening factors achieved APEs of 1.83 for 1155 amino acid analogs, dipeptides, and tetrapeptides, 1.39 for 28 nucleic acid bases, 0.708 for 1464 water clusters, and 1.99 for 85 dimers of water and biological building blocks. Compared to the new set of models, the APEs of the old Thole models that were fitted to isotropic molecular polarizabilities are 8.7% for set A (without the 1-2 and 1-3 interactions) and 6.3% for set D (with the 1-2 and 1-3 interactions) models, respectively. MPAD, a metric of molecular polarization anisotropy difference based on the diagonal terms of molecular polarizability tensors was defined and applied to assess the polarizable models in reproducing the ab initio molecular polarization anisotropy. The MPADs are 3.71, 4.70, 4.11, and 4.77% for the pGM, Thole linear, Thole exponential, and Thole Amoeba USF models, respectively. The APEs are reduced further to 2.85, 3.58, 2.90, and 3.15% for the four corresponding VSF models. Thus, the new pGM and Thole models notably improve molecular polarization anisotropy. Since pGM attenuates all short-range electrostatic interactions, its application is expected to improve stability in charge fitting, energy, and force calculations and the accuracy of multibody polarization.
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Affiliation(s)
- Junmei Wang
- Department of Pharmaceutical Sciences , University of Pittsburgh , 3501 Terrace Street , Pittsburgh , Pennsylvania 15261 , United States
| | - Piotr Cieplak
- SBP Medical Discovery Institute , 10901 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering , University of California, Irvine , Irvine , California 92697 , United States
| | - Yong Duan
- UC Davis Genome Center and Department of Biomedical Engineering , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
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Abstract
We review recent work on property decomposition techniques using quantum chemical methods and discuss some topical applications in terms of quantum mechanics-molecular mechanics calculations and the constructing of properties of large molecules and clusters. Starting out from the so-called LoProp decomposition scheme [Gagliardi et al., J. Chem. Phys., 2004, 121, 4994] for extracting atomic and inter-atomic contributions to molecular properties we show how this method can be generalized to localized frequency-dependent polarizabilities, to localized hyperpolarizabilities and to localized dispersion coefficients. Some applications of the generalized decomposition technique are reviewed - calculations of frequency-dependent polarizabilities, Rayleigh scattering of large clusters, and calculations of hyperpolarizabilities of proteins.
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Affiliation(s)
- Hans Ågren
- KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Theoretical Chemistry and Biology, SE-106 91 Stockholm, Sweden.
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Liu H, Jenkins AJ, Wildman A, Frisch MJ, Lipparini F, Mennucci B, Li X. Time-Dependent Complete Active Space Embedded in a Polarizable Force Field. J Chem Theory Comput 2019; 15:1633-1641. [DOI: 10.1021/acs.jctc.8b01152] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Hongbin Liu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Andrew J. Jenkins
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Andrew Wildman
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Michael J. Frisch
- Gaussian Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, United States
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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