1
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Devereux M, Boittier ED, Meuwly M. Systematic improvement of empirical energy functions in the era of machine learning. J Comput Chem 2024; 45:1899-1913. [PMID: 38695412 DOI: 10.1002/jcc.27367] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/13/2024] [Accepted: 02/21/2024] [Indexed: 07/05/2024]
Abstract
The impact of targeted replacement of individual terms in empirical force fields is quantitatively assessed for pure water, dichloromethane (CH 2 Cl 2 ), and solvated K + and Cl - ions. For the electrostatic interactions, point charges (PCs) and machine learning (ML)-based minimally distributed charges (MDCM) fitted to the molecular electrostatic potential are evaluated together with electrostatics based on the Coulomb integral. The impact of explicitly including second-order terms is investigated by adding a fragment molecular orbital (FMO)-derived polarization energy to an existing force field, in this case CHARMM. It is demonstrated that anisotropic electrostatics reduce the RMSE for water (by 1.4 kcal/mol), CH 2 Cl 2 (by 0.8 kcal/mol) and for solvated Cl - clusters (by 0.4 kcal/mol). An additional polarization term can be neglected for CH 2 Cl 2 but further improves the models for pure water (by ∼ 1.0 kcal/mol) and hydrated Cl - (by 0.4 kcal/mol), and is key for solvated K + , reducing the RMSE by 2.3 kcal/mol. A 12-6 Lennard-Jones functional form performs satisfactorily with PC and MDCM electrostatics, but is not appropriate for descriptions that account for the electrostatic penetration energy. The importance of many-body contributions is assessed by comparing a strictly 2-body approach with self-consistent reference data. Two-body interactions suffice for CH 2 Cl 2 whereas water and solvated K + and Cl - ions require explicit many-body corrections. Finally, a many-body-corrected dimer potential energy surface exceeds the accuracy attained using a conventional empirical force field, potentially reaching that of an FMO calculation. The present work systematically quantifies which terms improve the performance of an existing force field and what reference data to use for parametrizing these terms in a tractable fashion for ML fitting of pure and heterogeneous systems.
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Affiliation(s)
- Mike Devereux
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Eric D Boittier
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Basel, Switzerland
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2
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Evangelista FA, Li C, Verma P, Hannon KP, Schriber JB, Zhang T, Cai C, Wang S, He N, Stair NH, Huang M, Huang R, Misiewicz JP, Li S, Marin K, Zhao Z, Burns LA. Forte: A suite of advanced multireference quantum chemistry methods. J Chem Phys 2024; 161:062502. [PMID: 39132791 DOI: 10.1063/5.0216512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 06/24/2024] [Indexed: 08/13/2024] Open
Abstract
Forte is an open-source library specialized in multireference electronic structure theories for molecular systems and the rapid prototyping of new methods. This paper gives an overview of the capabilities of Forte, its software architecture, and examples of applications enabled by the methods it implements.
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Affiliation(s)
- Francesco A Evangelista
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Chenyang Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Prakash Verma
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Kevin P Hannon
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Jeffrey B Schriber
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
- Department of Chemistry and Biochemistry, Iona University, New Rochelle, New York 10801, USA
| | - Tianyuan Zhang
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Chenxi Cai
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Shuhe Wang
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Nan He
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Nicholas H Stair
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Meng Huang
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Renke Huang
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Jonathon P Misiewicz
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Shuhang Li
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Kevin Marin
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Zijun Zhao
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Lori A Burns
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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3
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Kukk E, Niskanen J, Travnikova O, Berholts M, Kooser K, Peng D, Ismail I, Piancastelli MN, Püttner R, Hergerhahn U, Simon M. Orientational anisotropy due to molecular field splitting in sulfur 2p photoemission from CS 2 and SF 6 - theoretical treatment and application to photoelectron recoil. Phys Chem Chem Phys 2024. [PMID: 39101747 DOI: 10.1039/d4cp01463d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
Photoelectron recoil strongly modifies the high kinetic energy photoemission spectra from atoms and molecules as well as from surface structures. In most cases studied so far, photoemission from atomic-like inner-shell or core orbitals has been assumed to be isotropic in the molecular frame of reference. However, in the presence of molecular field splitting of p or d orbitals, this assumption is not justified per se. We present a general theoretical treatment, linking the orientational distribution of gas-phase molecules to the electron emission and detection in a certain direction in the laboratory frame. The approach is then applied to the S 2p photoemission from a linear molecule such as CS2 and we investigate, how the predicted orientational anisotropies due to molecular field splitting affect the photoelectron recoil excitations. Lastly, experimental S 2p high-kinetic-energy photoelectron spectra of SF6 and CS2 are analyzed using the modeled recoil lineshapes representing the anisotropy-affected recoil effects.
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Affiliation(s)
- Edwin Kukk
- Department of Physics and Astronomy, University of Turku, FI-20014 Turku, Finland.
| | - Johannes Niskanen
- Department of Physics and Astronomy, University of Turku, FI-20014 Turku, Finland.
| | - Oksana Travnikova
- Sorbonne Université, CNRS, UMR 7614, Laboratoire de Chimie Physique-Matière et Rayonnement, F-75005 Paris, France
| | - Marta Berholts
- Institute of Physics, University of Tartu, W. Ostwaldi 1, EE-50411 Tartu, Estonia
| | - Kuno Kooser
- Institute of Physics, University of Tartu, W. Ostwaldi 1, EE-50411 Tartu, Estonia
| | - Dawei Peng
- Sorbonne Université, CNRS, UMR 7614, Laboratoire de Chimie Physique-Matière et Rayonnement, F-75005 Paris, France
| | - Iyas Ismail
- Sorbonne Université, CNRS, UMR 7614, Laboratoire de Chimie Physique-Matière et Rayonnement, F-75005 Paris, France
| | - Maria Novella Piancastelli
- Sorbonne Université, CNRS, UMR 7614, Laboratoire de Chimie Physique-Matière et Rayonnement, F-75005 Paris, France
| | - Ralph Püttner
- Fachbereich Physik, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Uwe Hergerhahn
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Marc Simon
- Sorbonne Université, CNRS, UMR 7614, Laboratoire de Chimie Physique-Matière et Rayonnement, F-75005 Paris, France
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4
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Ugur E, Said AA, Dally P, Zhang S, Petoukhoff CE, Rosas-Villalva D, Zhumagali S, Yildirim BK, Razzaq A, Sarwade S, Yazmaciyan A, Baran D, Laquai F, Deger C, Yavuz I, Allen TG, Aydin E, De Wolf S. Enhanced cation interaction in perovskites for efficient tandem solar cells with silicon. Science 2024; 385:533-538. [PMID: 39088622 DOI: 10.1126/science.adp1621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 06/20/2024] [Indexed: 08/03/2024]
Abstract
To achieve the full potential of monolithic perovskite/silicon tandem solar cells, crystal defects and film inhomogeneities in the perovskite top cell must be minimized. We discuss the use of methylenediammonium dichloride as an additive to the perovskite precursor solution, resulting in the incorporation of in situ-formed tetrahydrotriazinium (THTZ-H+) into the perovskite lattice upon film crystallization. The cyclic nature of the THTZ-H+ cation enables a strong interaction with the lead octahedra of the perovskite lattice through the formation of hydrogen bonds with iodide in multiple directions. This structure improves the device power conversion efficiency (PCE) and phase stability of 1.68 electron volts perovskites under prolonged light and heat exposure under 1-sun illumination at 85°C. Monolithic perovskite/silicon tandems incorporating THTZ-H+ in the perovskite photo absorber reached a 33.7% independently certified PCE for a device area of 1 square centimeter.
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Affiliation(s)
- Esma Ugur
- King Abdullah University of Science and Technology (KAUST), KAUST Solar Center (KSC), Physical Sciences and Engineering Division (PSE), Material Science and Engineering Program (MSE), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Ahmed Ali Said
- King Abdullah University of Science and Technology (KAUST), KAUST Solar Center (KSC), Physical Sciences and Engineering Division (PSE), Material Science and Engineering Program (MSE), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Pia Dally
- King Abdullah University of Science and Technology (KAUST), KAUST Solar Center (KSC), Physical Sciences and Engineering Division (PSE), Material Science and Engineering Program (MSE), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Shanshan Zhang
- King Abdullah University of Science and Technology (KAUST), KAUST Solar Center (KSC), Physical Sciences and Engineering Division (PSE), Material Science and Engineering Program (MSE), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Christopher E Petoukhoff
- King Abdullah University of Science and Technology (KAUST), KAUST Solar Center (KSC), Physical Sciences and Engineering Division (PSE), Material Science and Engineering Program (MSE), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Diego Rosas-Villalva
- King Abdullah University of Science and Technology (KAUST), KAUST Solar Center (KSC), Physical Sciences and Engineering Division (PSE), Material Science and Engineering Program (MSE), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Shynggys Zhumagali
- King Abdullah University of Science and Technology (KAUST), KAUST Solar Center (KSC), Physical Sciences and Engineering Division (PSE), Material Science and Engineering Program (MSE), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Bumin K Yildirim
- King Abdullah University of Science and Technology (KAUST), KAUST Solar Center (KSC), Physical Sciences and Engineering Division (PSE), Material Science and Engineering Program (MSE), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Arsalan Razzaq
- King Abdullah University of Science and Technology (KAUST), KAUST Solar Center (KSC), Physical Sciences and Engineering Division (PSE), Material Science and Engineering Program (MSE), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Shruti Sarwade
- King Abdullah University of Science and Technology (KAUST), KAUST Solar Center (KSC), Physical Sciences and Engineering Division (PSE), Material Science and Engineering Program (MSE), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Aren Yazmaciyan
- King Abdullah University of Science and Technology (KAUST), KAUST Solar Center (KSC), Physical Sciences and Engineering Division (PSE), Material Science and Engineering Program (MSE), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Derya Baran
- King Abdullah University of Science and Technology (KAUST), KAUST Solar Center (KSC), Physical Sciences and Engineering Division (PSE), Material Science and Engineering Program (MSE), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Frédéric Laquai
- King Abdullah University of Science and Technology (KAUST), KAUST Solar Center (KSC), Physical Sciences and Engineering Division (PSE), Material Science and Engineering Program (MSE), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Caner Deger
- Department of Physics, Marmara University, Istanbul, Türkiye
| | - Ilhan Yavuz
- Department of Physics, Marmara University, Istanbul, Türkiye
| | - Thomas G Allen
- King Abdullah University of Science and Technology (KAUST), KAUST Solar Center (KSC), Physical Sciences and Engineering Division (PSE), Material Science and Engineering Program (MSE), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Erkan Aydin
- King Abdullah University of Science and Technology (KAUST), KAUST Solar Center (KSC), Physical Sciences and Engineering Division (PSE), Material Science and Engineering Program (MSE), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Stefaan De Wolf
- King Abdullah University of Science and Technology (KAUST), KAUST Solar Center (KSC), Physical Sciences and Engineering Division (PSE), Material Science and Engineering Program (MSE), Thuwal, 23955-6900, Kingdom of Saudi Arabia
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5
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Prinsa, Saha S, Bulbul MZH, Ozeki Y, Alamri MA, Kawsar SMA. Flavonoids as potential KRAS inhibitors: DFT, molecular docking, molecular dynamics simulation and ADMET analyses. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2024; 26:955-992. [PMID: 38647682 DOI: 10.1080/10286020.2024.2343821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/11/2024] [Indexed: 04/25/2024]
Abstract
KRAS mutations linked with cancer. Flavonoids were docked against KRAS G12C and G12D receptors. Abyssinone III, alpha naphthoflavone, beta naphthoflavone, abyssinone I, abyssinone II and beta naphthoflavone, genistin, daidzin showed good docking scores against KRAS G12C and G12D receptors, respectively. The MD simulation data revealed that Rg, RMSD, RMSF, and SASA values were within acceptable limits. Alpha and beta naphthoflavone showed good binding energies with KRAS G12C and G12D receptors. DFT and MEP analysis highlighted the nucleophilic and electrophilic zones of best-docked flavonoids. A novel avenue for the control of KRAS G12C and G12D mutations is made possible by flavonoids.
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Affiliation(s)
- Prinsa
- Department of Pharmaceutical Chemistry, Siddhartha Institute of Pharmacy, Near IT-Park, Dehradun, Uttarakhand, India
| | - Supriyo Saha
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, Uttarakhand, India
| | - Md Zahidul Haque Bulbul
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
| | - Yasuhiro Ozeki
- Graduate School of Nanobio Sciences, Yokohama City University, Yokohama, Japan
| | - Mubarak A Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Sarkar M A Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
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6
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Paciotti R, Re N, Storchi L. Combining the Fragment Molecular Orbital and GRID Approaches for the Prediction of Ligand-Metalloenzyme Binding Affinity: The Case Study of hCA II Inhibitors. Molecules 2024; 29:3600. [PMID: 39125005 PMCID: PMC11313991 DOI: 10.3390/molecules29153600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 07/18/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Polarization and charge-transfer interactions play an important role in ligand-receptor complexes containing metals, and only quantum mechanics methods can adequately describe their contribution to the binding energy. In this work, we selected a set of benzenesulfonamide ligands of human Carbonic Anhydrase II (hCA II)-an important druggable target containing a Zn2+ ion in the active site-as a case study to predict the binding free energy in metalloprotein-ligand complexes and designed specialized computational methods that combine the ab initio fragment molecular orbital (FMO) method and GRID approach. To reproduce the experimental binding free energy in these systems, we adopted a machine-learning approach, here named formula generator (FG), considering different FMO energy terms, the hydrophobic interaction energy (computed by GRID) and logP. The main advantage of the FG approach is that it can find nonlinear relations between the energy terms used to predict the binding free energy, explicitly showing their mathematical relation. This work showed the effectiveness of the FG approach, and therefore, it might represent an important tool for the development of new scoring functions. Indeed, our scoring function showed a high correlation with the experimental binding free energy (R2 = 0.76-0.95, RMSE = 0.34-0.18), revealing a nonlinear relation between energy terms and highlighting the relevant role played by hydrophobic contacts. These results, along with the FMO characterization of ligand-receptor interactions, represent important information to support the design of new and potent hCA II inhibitors.
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Affiliation(s)
- Roberto Paciotti
- Department of Pharmacy, Università “G. D’Annunzio” Di Chieti-Pescara, 66100 Chieti, Italy; (N.R.); (L.S.)
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7
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Del Angel Cruz D, Ferreras KN, Harville T, Schoendorff G, Gordon MS. Analysis of bonding motifs in unusual molecules I: planar hexacoordinated carbon atoms. Phys Chem Chem Phys 2024. [PMID: 39078376 DOI: 10.1039/d4cp01800a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
The bonding structures of CO3Li3+ and CS3Li3+ are studied by means of oriented quasi-atomic orbitals (QUAOs) to assess the possibility of these molecules being planar hexacoordinated carbon (phC) systems. CH3Li and CO32- are employed as reference molecules. It is found that the introduction of Li+ ions into the molecular environment of carbonate has a greater effect on the orbital structure of the O atoms than it does on the C atom. Partial charges computed from QUAO populations imply repulsion between the positively charged C and Li atoms in CO3Li3+. Upon the transition from CO3Li3+ to CS3Li3+, the analysis reveals that the substitution of O atoms by S atoms inverts the polarity of the carbon-chalcogen σ bond. This is linked to the difference in s- and p-fractions of the QUAOs of C and S, as element electronegativities do not explain the observed polarity of the CSσ bond. Partial charges indicate that the larger electron population on the C atom in CS3Li3+ makes C-Li attraction possible. Upon comparison with the C-Li bond in methyllithium, it is found that the C-Li covalent interactions in CO3Li3+ and CS3Li3+ have about 14% and 6% of the strength of the C-Li covalent interaction in CH3Li, respectively. Consequently, it is concluded that only CS3Li3+ may be considered to be a phC system.
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Affiliation(s)
- Daniel Del Angel Cruz
- Department of Chemistry and Ames National Laboratory, Iowa State University, Ames, Iowa, 50011, USA.
| | - Katherine N Ferreras
- Department of Chemistry and Ames National Laboratory, Iowa State University, Ames, Iowa, 50011, USA.
| | - Taylor Harville
- Department of Chemistry and Ames National Laboratory, Iowa State University, Ames, Iowa, 50011, USA.
| | - George Schoendorff
- Department of Chemistry, University of South Dakota, Vermillion, South Dakota, 57069, USA
| | - Mark S Gordon
- Department of Chemistry and Ames National Laboratory, Iowa State University, Ames, Iowa, 50011, USA.
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8
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Manna A, Jangid B, Pant R, Dutta AK. Efficient State-Specific Natural Orbital Based Equation of Motion Coupled Cluster Method for Core-Ionization Energies: Theory, Implementation, and Benchmark. J Chem Theory Comput 2024. [PMID: 39073757 DOI: 10.1021/acs.jctc.4c00546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
We have implemented a reduced-cost partial triples correction scheme to the equation of motion coupled cluster method for core-ionization energy based on state-specific natural orbitals. The second-order Algebraic Diagrammatic Construction (ADC) method is used to generate the state-specific natural orbital, which provides quicker convergence of the core-IP value with respect to the size of the virtual space than that observed in standard MP2-based natural orbitals. The error due to truncation of the virtual orbital can be reduced by using a perturbative correction. The accuracy of the method can be controlled by a single threshold, and there is a black box to use. The inclusion of the partial triples correction in the natural orbital based EOM-CCSD method greatly improves the agreement of the results with the experiment. The efficiency of the present implementation is demonstrated by calculating the core-ionization energy of a molecule containing 60 atoms and more than 2000 basis functions.
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Affiliation(s)
- Amrita Manna
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Bhavnesh Jangid
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Rakesh Pant
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Achintya Kumar Dutta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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9
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Yuwono SH, Li RR, Zhang T, Surjuse KA, Valeev EF, Li X, Eugene DePrince A. Relativistic Coupled Cluster with Completely Renormalized and Perturbative Triples Corrections. J Phys Chem A 2024. [PMID: 39074123 DOI: 10.1021/acs.jpca.4c02583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
We have implemented noniterative triples corrections to the energy from coupled-cluster with single and double excitations (CCSD) within the 1-electron exact two-component (1eX2C) relativistic framework. The effectiveness of both the CCSD(T) and the completely renormalized (CR) CC(2,3) approaches are demonstrated by performing all-electron computations of the potential energy curves and spectroscopic constants of copper, silver, and gold dimers in their ground electronic states. Spin-orbit coupling effects captured via the 1eX2C framework are shown to be crucial for recovering the correct shape of the potential energy curves, and the correlation effects due to triples in these systems change the dissociation energies by about 0.1-0.2 eV or about 4-7%. We also demonstrate that relativistic effects and basis set size and contraction scheme are significantly more important in Au2 than in Ag2 or Cu2.
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Affiliation(s)
- Stephen H Yuwono
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Run R Li
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Tianyuan Zhang
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | | | - Edward F Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - A Eugene DePrince
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
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10
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Berquist E, Dumi A, Upadhyay S, Abarbanel OD, Cho M, Gaur S, Cano Gil VH, Hutchison GR, Lee OS, Rosen AS, Schamnad S, Schneider FSS, Steinmann C, Stolyarchuk M, Vandezande JE, Zak W, Langner KM. cclib 2.0: An updated architecture for interoperable computational chemistry. J Chem Phys 2024; 161:042501. [PMID: 39051837 DOI: 10.1063/5.0216778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 07/01/2024] [Indexed: 07/27/2024] Open
Abstract
Interoperability in computational chemistry is elusive, impeded by the independent development of software packages and idiosyncratic nature of their output files. The cclib library was introduced in 2006 as an attempt to improve this situation by providing a consistent interface to the results of various quantum chemistry programs. The shared API across programs enabled by cclib has allowed users to focus on results as opposed to output and to combine data from multiple programs or develop generic downstream tools. Initial development, however, did not anticipate the rapid progress of computational capabilities, novel methods, and new programs; nor did it foresee the growing need for customizability. Here, we recount this history and present cclib 2, focused on extensibility and modularity. We also introduce recent design pivots-the formalization of cclib's intermediate data representation as a tree-based structure, a new combinator-based parser organization, and parsed chemical properties as extensible objects.
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Affiliation(s)
- Eric Berquist
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Amanda Dumi
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Shiv Upadhyay
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Omri D Abarbanel
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA
| | - Minsik Cho
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA
| | - Sagar Gaur
- MarkovML 23, Geary St. Suite 600, San Francisco, California 94108, USA
- International Institute of Information Technology, Prof. CR Rao Road Gachibowli, Hyderabad 500032, Telangana, India
| | | | - Geoffrey R Hutchison
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA
| | - Oliver S Lee
- Organic Semiconductor Centre, EaStCHEM School of Chemistry, University of St Andrews, St. Andrews KY16 9ST, United Kingdom
- Organic Semiconductor Centre, SUPA School of Physics and Astronomy, University of St Andrews, St. Andrews KY16 9SS, United Kingdom
| | - Andrew S Rosen
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
- Department of Materials Science and Engineering, University of California, Berkeley, California 94720, USA
| | | | | | - Casper Steinmann
- Department of Chemistry and Bioscience, Aalborg University, DK-9230 Aalborg, Denmark
| | | | | | - Weronika Zak
- Department of Computer Science, Loughborough University, Epinal Way, Loughborough, Leicestershire LE11 3TU, United Kingdom
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11
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Einsele R, Mitrić R. Nonadiabatic Exciton Dynamics and Energy Gradients in the Framework of FMO-LC-TDDFTB. J Chem Theory Comput 2024. [PMID: 39051619 DOI: 10.1021/acs.jctc.4c00539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
We introduce a novel methodology for simulating the excited-state dynamics of extensive molecular aggregates in the framework of the long-range corrected time-dependent density-functional tight-binding fragment molecular orbital method (FMO-LC-TDDFTB) combined with the mean-field Ehrenfest method. The electronic structure of the system is described in a quasi-diabatic basis composed of locally excited and charge-transfer states of all fragments. In order to carry out nonadiabatic molecular dynamics simulations, we derive and implement the excited-state gradients of the locally excited and charge-transfer states. Subsequently, the accuracy of the analytical excited-state gradients is evaluated. The applicability to the simulation of exciton transport in organic semiconductors is illustrated on a large cluster of anthracene molecules. Additionally, nonadiabatic molecular dynamics simulations of a model system of benzothieno-benzothiophene molecules highlight the method's utility in studying charge-transfer dynamics in organic materials. Our new methodology will facilitate the investigation of excitonic transfer in extensive biological systems, nanomaterials, and other complex molecular systems consisting of thousands of atoms.
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Affiliation(s)
- Richard Einsele
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität, Würzburg 97074, Germany
| | - Roland Mitrić
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität, Würzburg 97074, Germany
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12
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Deshpande VV, Chauhan V, Bandyopadhyay D, Anoop A, Bhattacharyya S. Structure of small yttrium monoxide clusters, chemical bonding, and photoionization: threshold photoionization and density functional theory investigations. Phys Chem Chem Phys 2024; 26:20123-20133. [PMID: 39011880 DOI: 10.1039/d4cp02351j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
The photoionization (PI) spectra of small gas-phase yttrium monoxide clusters, YnO (n = 1-8), are investigated, and the adiabatic ionization energies are determined. The stable structures are obtained from density functional theory (DFT) calculations. The ground state structures are further confirmed by the CCSD(T) method. The PI spectra are calculated for these stable structures and are compared with the experimental PI spectra. The ground-state structures of the neutral and cation clusters are experimentally assigned with confidence on the basis of a favourable agreement between the experimental and calculated PI spectra. New structures are proposed for Y2O, Y6O, and Y8O compared to the previous literature. Y2O is a linear molecule in the ground state that was previously proposed as a C2v bent molecule. The YnO clusters become 3-dimensional from n ≥ 3. The O atom stays outside, bridging a triangular face of yttrium clusters. Chemical bonding between the yttrium and oxygen atoms is mostly ionic. The excess charge on the oxygen atom is around 1.4e-, transferred from the yttrium atoms bonded with it. Yttrium atoms are mostly covalently bonded. However, for the bigger clusters, free charges of both polarities appear on yttrium atoms that are not bonded with oxygen, indicating ionic interactions. Frontier orbitals consist of mainly delocalized 4d electrons with some 5s contributions, forming Y-Y bonding interactions, but with little contribution and zero contribution from the oxygen orbitals, regardless of the cluster size. The lost electron of YnO+ mostly comes from the 5s orbitals of all Y atoms in the cluster up to size n = 4, and then from 4d-5s hybrid orbitals from n ≥ 5, with the d contribution increasing with size. This is contrary to the previous view in the literature that photoionization occurs from a localized 4d orbital.
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Affiliation(s)
- Varun Vinayak Deshpande
- Atomic & Molecular Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085, India.
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400 094, India
| | - Vaibhav Chauhan
- Atomic & Molecular Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085, India.
| | - Debashis Bandyopadhyay
- Physics Department, Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India
| | - Anakuthil Anoop
- School of Digital Sciences, Kerala University of Digital Science, Innovation, and Technology, Digital University Kerala, Technopark Phase IV, Pallipuram, Thiruvananthapuram, Kerala - 695317, India
| | - Soumen Bhattacharyya
- Atomic & Molecular Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085, India.
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400 094, India
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13
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Martynov AI, Belov AS, Nevolin VK. Using non-adiabatic excitation transfer for signal transmission between molecular logic gates. NANOSCALE 2024. [PMID: 39037702 DOI: 10.1039/d4nr01206b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Molecular logic gates (MLGs) are molecules which perform logic operations. They can potentially be used as building blocks for nano-sized computational devices. However, their physical and functional integration is a difficult task which remains to be solved. The problem lies in the field of signal exchange between the gates within the system. We propose using non-adiabatic excitation transfer between the gates to address this problem while absorption and fluorescence are left to communicate with external devices. Excitation transfer was studied using the modified Bixon-Jortner-Plotnikov theory with the example of the 3H-thioxanthene-TTF-dibenzo-BODIPY covalently linked triad. Several designs of the molecule were studied in a vacuum and cyclohexane. It was found that the molecular logic system has to be planar and rigid to isolate radiative interfaces from other gates. Functioning of these gates is based on dark πσ*-states in contrast to bright ππ*-states of radiative interfaces. There are no fundamental differences between ππ* → πσ* and ππ* → ππ* transitions for cases when an exciton hops from one gate to another. The rates of such transitions depend only on an energy gap between states and the distance between gates. The circuit is highly sensitive to the choice of solvent which could rearrange its state structure thereby altering its behavior. According to the obtained results, non-adiabatic transfer can be considered as one of the possible ways for transmitting a signal between MLGs.
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Affiliation(s)
- A I Martynov
- National Research University of Electronic Technology, 1 Shokin Square, Zelenograd, Moscow, Russia.
| | - A S Belov
- Department of Chemistry, Lomonosov Moscow State University, 1-3 Leninskie gory, Moscow, Russia
| | - V K Nevolin
- National Research University of Electronic Technology, 1 Shokin Square, Zelenograd, Moscow, Russia.
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14
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Zhang L, Shen Z, Zeng Y, Li X, Zhang X. Insight into the Metal-Involving Chalcogen Bond in the Pd II/Pt II-Based Complexes: Comparison with the Conventional Chalcogen Bond. J Phys Chem A 2024; 128:5567-5577. [PMID: 39003760 DOI: 10.1021/acs.jpca.4c02723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The metal-involving Ch···M chalcogen bond and the conventional Ch···O chalcogen bond between ChX2 (Ch = Se, Te; X = CCH, CN) acting as a Lewis acid and M(acac)2 (M = Pd, Pt; Hacac = acetylacetone) acting as a Lewis base were studied by density functional theory calculations. It has been observed that the nucleophilicity of the PtII complexes is higher than that of the corresponding PdII complexes. As a result, the PtII complexes tend to exhibit a more negative interaction energy and larger orbital interaction. The strength of the chalcogen bond increases with the increase of the chalcogen atom and the electronegativity of the substituent on the Lewis acid and vice versa. The metal-involving chalcogen bond shows a typical weak closed-shell noncovalent interaction in the (HCC)2Ch···M(acac)2 complexes, while it exhibits a partially covalent nature in the (NC)2Ch···M(acac)2 complexes. The conventional Ch···O chalcogen bond displays the character of a weak noncovalent interaction, and its strength is generally weaker than that of metal-involving Ch···M interactions. It could be argued that the metal-involving chalcogen bond is primarily determined by the correlation term, whereas the conventional chalcogen bond is mainly governed by the electrostatic interaction.
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Affiliation(s)
- Lili Zhang
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang 050024, China
| | - Zixuan Shen
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang 050024, China
| | - Yanli Zeng
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang 050024, China
- Hebei Key Laboratory of Inorganic Nano-materials, Hebei Normal University, Shijiazhuang 050024, China
| | - Xiaoyan Li
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang 050024, China
- Hebei Key Laboratory of Inorganic Nano-materials, Hebei Normal University, Shijiazhuang 050024, China
| | - Xueying Zhang
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang 050024, China
- Hebei Key Laboratory of Inorganic Nano-materials, Hebei Normal University, Shijiazhuang 050024, China
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15
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Miller H, Wallace JQ, Li H, Li XZ, de Bettencourt-Dias A, Kievit FM. Sensitization of Europium Oxide Nanoparticles Enhances Signal-to-Noise over Autofluorescence with Time-Gated Luminescence Detection. ACS OMEGA 2024; 9:31093-31104. [PMID: 39035920 PMCID: PMC11256319 DOI: 10.1021/acsomega.4c04457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 05/24/2024] [Accepted: 06/14/2024] [Indexed: 07/23/2024]
Abstract
Clinical translation of nanoparticle-based therapeutics has been limited, and a lack of preclinical delivery characterization is partly to blame, limiting our understanding of the mechanisms of failure. The improvement of the preclinical delivery assessment requires nanoparticles with higher detectability. This work focused on the exploration of several aromatic carboxylic ligands (terephthalic acid, quinaldic acid, and kynurenic acid) for the sensitization of europium oxide nanoparticles with a long emission lifetime to overcome cellular autofluorescence, a key confounder of detection in luminescence-based bioimaging. A facile one-pot synthesis and ligand exchange process generated and sensitized ultrasmall Eu2O3 cores. As reflected in the emission spectra and lifetimes, ligand binding yielded unique coordination environments around Eu3+. Then, the efficacy of sensitization was tested against the autofluorescence provided by tissue lysate. Normal (simultaneous excite-read) measurements showed integrated signal improvements over autofluorescence of 2.2-, 3.9-, and 14.0-fold for EuTA, EuQA, and EuKA, respectively. In time-gated mode, the improvements over autofluorescence were more dramatic with fold differences of 75-, 89-, and 108-fold for EuTA, EuQA, and EuKA, respectively. The investigation of novel sensitizers expands the breadth of the field of sensitized lanthanide oxide nanoparticles, and the signal enhancement observed with sensitization and time-gating supports the utility of the generated samples for future bioimaging applications.
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Affiliation(s)
- Hunter
A. Miller
- Department
of Biological Systems Engineering, University
of Nebraska-Lincoln, Lincoln, Nebraska 68583, United States
| | - Jessica Q. Wallace
- Department
of Chemistry, University of Nevada, Reno, Reno, Nevada 89557, United States
| | - Hui Li
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Xing-Zhong Li
- Nebraska
Center for Materials and Nanoscience, University
of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | | | - Forrest M. Kievit
- Department
of Biological Systems Engineering, University
of Nebraska-Lincoln, Lincoln, Nebraska 68583, United States
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16
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Hagiwara Y, Takanabe A, Asahi T, Koshima H. Photo-triggered Phase Transition of Crystals and Photoactuation. Chemistry 2024; 30:e202401590. [PMID: 38749912 DOI: 10.1002/chem.202401590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Indexed: 06/27/2024]
Abstract
Photo-triggered phase transition is a new type of phase transition in which a photochromic crystal with a thermal phase transition transforms into an identical high-temperature phase in a temperature region lower than the thermal phase transition temperature upon light irradiation. Here, we report a second crystal that exhibits a photo-triggered phase transition, thereby demonstrating that the photo-triggered phase transition is a general phenomenon that occurs in crystals. When the chiral salicylidenephenylethylamine crystal was irradiated with ultraviolet (UV) light, the photo-triggered phase transition occurred in the temperature range -30 to -10 °C. The photo-triggered phase transition is induced by local stress due to trans-keto molecules produced by photoisomerization near the irradiated surface. Crystal cantilevers exhibited stepwise bending by the combination of the photo-triggered phase transition and photoisomerization. Alternate irradiation with UV and visible light achieved locomotion of single crystals driven by repeated stepwise bending. Finally, a detailed comparison of photo-triggered and non-photo-triggered phase transition crystals revealed that a sufficient molecular conformation change in affordable crystal voids, smooth photoisomerization, and most likely a chiral molecular arrangement are required for inducing the photo-triggered phase transition.
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Affiliation(s)
- Yuki Hagiwara
- Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Akifumi Takanabe
- Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Toru Asahi
- Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
- Research Organization for Nano & Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
| | - Hideko Koshima
- Research Organization for Nano & Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
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17
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Ferrer M, Alkorta I, Elguero J, Barrios-Llacuachaqui JR, Tiznado W, Oliva-Enrich JM. Striking Borane Planarization in the Thermal Rearrangement (η 5-C 5H 5)Fe(η 3-B 5H 10)→(η 5-C 5H 5)Fe(η 5-B 5H 10). Chemistry 2024; 30:e202401536. [PMID: 38712946 DOI: 10.1002/chem.202401536] [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: 04/19/2024] [Revised: 05/06/2024] [Accepted: 05/06/2024] [Indexed: 05/08/2024]
Abstract
In 1977 Weiss and Grimes, by means of mass spectrometry and 1H and 11B NMR spectroscopy, proposed two structures (I and II) for the ferraborane (η5-C5H5)Fe(B5H10), isoelectronic with ferrocene. In this work, by means of high-level quantum-chemical computations, we confirm the experimental structures of the two isomers with their corresponding energies, and assign the reported 1H and 11B NMR chemical shifts. A striking result from this study is the planarization (3D→2D) of the B5H10 - ligand - an unknown isolated anion, isoelectronic with aromatic cyclopentadienyl anion C5H5 - - when attached to the (η5-C5H5)Fe+ moiety, thus resulting in a more stable ferraborane isomer II.
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Affiliation(s)
- Maxime Ferrer
- Instituto de Química Médica (CSIC), 28006, Madrid, Spain
- PhD Program in Theoretical Chemistry and Computational Modelling, Doctoral School, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Ibon Alkorta
- Instituto de Química Médica (CSIC), 28006, Madrid, Spain
| | - José Elguero
- Instituto de Química Médica (CSIC), 28006, Madrid, Spain
| | - Julio R Barrios-Llacuachaqui
- Centro de Química Teórica & Computacional (CQT&C), Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andrés Bello, República 275, Santiago, Chile
- Programa de Doctorado en Fisicoquímica Molecular, Facultad de Ciencias Exactas, Universidad Andrés Bello, Av. República 275, 8370146, Santiago, Chile
| | - William Tiznado
- Centro de Química Teórica & Computacional (CQT&C), Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andrés Bello, República 275, Santiago, Chile
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18
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Fedorov DG. The Peptide Bond: Resonance Increases Bond Order and Complicates Fragmentation. Chemphyschem 2024; 25:e202400170. [PMID: 38749916 DOI: 10.1002/cphc.202400170] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/15/2024] [Indexed: 06/28/2024]
Abstract
The enhancement of the peptide bond order by a resonance in the lone pair of N and the π-bond of CO is analyzed. A decomposition of the bond order in terms of localized molecular orbitals is developed and applied to the peptide bond. A combination of two rotations of hybrid orbitals is proposed to improve the boundary treatment in the fragment molecular orbital method. The developed approach is applied to peptide bonds, and it is found crucial to retain the π orbital in the variational space of both fragments across the boundary. The interaction energies between conventional amino acid residues in Trp-cage (1L2Y) are discussed.
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Affiliation(s)
- Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan
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19
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Goodlett SM, Kitzmiller NL, Turney JM, Schaefer HF. MolSym: A Python package for handling symmetry in molecular quantum chemistry. J Chem Phys 2024; 161:024107. [PMID: 38984965 DOI: 10.1063/5.0216738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/20/2024] [Indexed: 07/11/2024] Open
Abstract
A consideration of the point group symmetry of molecules is often advantageous from a computational efficiency standpoint and sometimes necessary for the correct treatment of chemical physics problems. Many modern electronic structure software packages include a treatment of symmetry, but these are sometimes incomplete or unusable outside of that program's environment. Therefore, we have developed the MolSym package for handling molecular symmetry and its associated functionalities to provide a platform for including symmetry in the implementation and development of other methods. Features include point group detection, molecule symmetrization, arbitrary generation of symmetry element sets and character tables, and symmetry adapted linear combinations of real spherical harmonic basis functions, Cartesian displacement coordinates, and internal coordinates. We present some of the advantages of using molecular symmetry as achieved by MolSym, particularly with respect to Hartree-Fock theory, and the reduction of finite difference displacements in gradient/Hessian computations. This package is designed to be easily integrated into other software development efforts and may be extended to further symmetry applications.
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Affiliation(s)
- Stephen M Goodlett
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Nathaniel L Kitzmiller
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Justin M Turney
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
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20
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Nogueira-Júnior V, Sousa FRN, da S M Rebouças C, Braz HLB, Dos S Morais MLG, Goes P, de C Brito GA, Jorge RJB, Barbosa FG, Mafezoli J, Silva-Filho CJA, de O Capistrano AL, Bezerra MM, de C Leitão RF. Exploring the osteogenic potential of semisynthetic triterpenes from Combretum leprosum: An in vitro and in silico study. In Vitro Cell Dev Biol Anim 2024:10.1007/s11626-024-00928-w. [PMID: 38992216 DOI: 10.1007/s11626-024-00928-w] [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: 11/14/2023] [Accepted: 05/13/2024] [Indexed: 07/13/2024]
Abstract
Combretum leprosum Mart. is a plant of the Combretaceae family, widely distributed in the Northeast region of Brazil, popularly used as an anti-inflammatory agent, and rich in triterpenes. This study evaluated in vitro and in silico potential osteogenic of two semisynthetic triterpenes (CL-P2 and CL-P2A) obtained from the pentacyclic triterpene 3β,6β,16β-trihydroxylup-20(29)-ene (CL-1) isolated from C. leprosum. Assays were carried out in cultured murine osteoblasts (OFCOL II), first investigating the possible toxicity of the compounds on these cells through viability assays (MTT). Cell proliferation and activation were investigated by immunohistochemical evaluation of Ki-67, bone alkaline phosphatase (ALP) activity, and mineralization test by Von Kossa. Molecular docking analysis was performed to predict the binding affinity of CL-P2 and CL-P2A to target proteins involved in the regulation of osteogenesis, including: bone morphogenetic protein 2 (BMP-2), proteins related to Wingless-related integration (WNT) pathway (Low-density lipoprotein receptor-related protein 6-LRP6 and sclerostin-SOST), and receptor activator of nuclear factor (NF)-kB-ligand (RANK-L). Next, Western Blot and immunofluorescence investigated BMP-2, WNT, RANK-L, and OPG protein expressions in cultured murine osteoblasts (OFCOL II). None of the CL-P2 and CL-P2A concentrations were toxic to osteoblasts. Increased cell proliferation, ALP activity, and bone mineralization were observed. Molecular docking assays demonstrated interactions with BMP-2, LRP6, SOST, and RANK-L/OPG. There was observed increased expression of BMP-2, WNT, and RANK-L/OPG proteins. These results suggest, for the first time, the osteogenic potential of CL-P2 and CL-P2A.
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Affiliation(s)
- Valdo Nogueira-Júnior
- Postgraduate Program in Morphofunctional Sciences, Department of Morphology, School of Medicine, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Fátima Regina N Sousa
- Department of Morphology, Medical School, Federal University of Piaui, Picos, Piauí, Brazil
| | - Conceição da S M Rebouças
- Postgraduate Program in Morphofunctional Sciences, Department of Morphology, School of Medicine, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Helyson L B Braz
- Postgraduate Program in Morphofunctional Sciences, Department of Morphology, School of Medicine, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Maria Luana G Dos S Morais
- Postgraduate Program in Morphofunctional Sciences, Department of Morphology, School of Medicine, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Paula Goes
- Postgraduate Program in Morphofunctional Sciences, Department of Morphology, School of Medicine, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Gerly Anne de C Brito
- Postgraduate Program in Morphofunctional Sciences, Department of Morphology, School of Medicine, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Roberta Jeane B Jorge
- Postgraduate Program in Morphofunctional Sciences, Department of Morphology, School of Medicine, Federal University of Ceará, Fortaleza, Ceará, Brazil
- Department of Physiology and Pharmacology, School of Medicine, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Francisco Geraldo Barbosa
- Department of Organic and Inorganic Chemistry, Science Centre, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Jair Mafezoli
- Department of Organic and Inorganic Chemistry, Science Centre, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Carlos José A Silva-Filho
- Department of Organic and Inorganic Chemistry, Science Centre, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - André Luiz de O Capistrano
- Department of Organic and Inorganic Chemistry, Science Centre, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Mirna M Bezerra
- Postgraduate Program in Health Sciences, School of Medicine, Federal University of Ceará, Sobral, Ceará, Brazil.
| | - Renata F de C Leitão
- Postgraduate Program in Morphofunctional Sciences, Department of Morphology, School of Medicine, Federal University of Ceará, Fortaleza, Ceará, Brazil
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21
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Fedorov DG. Partition analysis of dipole moments in solution applied to functional groups in polypeptide motifs. Phys Chem Chem Phys 2024; 26:18614-18628. [PMID: 38919134 DOI: 10.1039/d4cp01654h] [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: 06/27/2024]
Abstract
A partition analysis based on segments is developed for density functional theory defining solute dipole moments of functional groups, and the corresponding induced solvent dipoles representing solvent screening. The accuracy of dipoles from the fragment molecular orbital method is evaluated in comparison to unfragmented values. The analysis is applied to evaluate dipole moments of side chains, amino and carbonyl groups in common polypeptide motifs, α-helixes, β-turns, and random coils in solution. The membrane domain of the ATP synthase (1B9U) is analyzed, revealing the effect of the bend splitting of the α-helix into two pieces.
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Affiliation(s)
- Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan.
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22
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Ferreras KN, Gordon MS. A Merger of the Spin-Flip ORMAS Approach and the MC-PDFT Method. J Chem Theory Comput 2024; 20:5487-5496. [PMID: 38916956 DOI: 10.1021/acs.jctc.4c00322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
The SF-ORMAS-PDFT (spin-flip occupation restricted multiple active space-pair density functional theory) approach combines the SF-ORMAS-CI method with the MC-PDFT method to treat both static and dynamic correlation in multiconfigurational systems. The static correlation description is generated via the spin-flip approach, which uses a high-spin single reference determinant to treat excited states with multiconfigurational characters. The on-top pair density functional theory uses a translation scheme applied to GGA density functionals. The SF-ORMAS-PDFT scheme has also been combined with virtual valence orbitals (VVO), a well-defined subspace of the virtual molecular orbitals, giving rise to significant speedups relative to the use of the full virtual space. The accuracy of the SF-ORMAS-PDFT method is tested by calculating 65 vertical excitation energies of 12 small- and medium-sized organic molecules. The SF-ORMAS-PDFT vertical excitation energies calculated with VVOs are comparable to those calculated with the full virtual space. The SF-ORMAS-PDFT/6-31G(d) level of theory predicts the rotational barrier of ethylene to be 65.5 and 65.9 kcal/mol, with full virtual space and VVOs, respectively. These predicted barrier heights compare well with the experimental value of 65 kcal/mol.
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Affiliation(s)
- Katherine N Ferreras
- Department of Chemistry, Iowa State University and Ames National Laboratory, Ames, Iowa 50011, United States
| | - Mark S Gordon
- Department of Chemistry, Iowa State University and Ames National Laboratory, Ames, Iowa 50011, United States
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23
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Hu L, Sarwono YP, Ding Y, He F, Zhang RQ. An improved DIIS method using a versatile residual matrix to accelerate SCF starting from a crude guess. J Comput Chem 2024. [PMID: 38979915 DOI: 10.1002/jcc.27463] [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: 02/19/2024] [Revised: 05/30/2024] [Accepted: 06/24/2024] [Indexed: 07/10/2024]
Abstract
The minimization of the commutator of the Fock and density matrices as the error matrix in the direct inversion of the iterative subspace (CDIIS) developed by Pulay is a powerful self-consistent field (SCF) acceleration technique for the construction of optimum Fock matrix, if initiated with a fair initial guess. In this work, we present an alternative minimized error matrix to the commutator in the CDIIS, namely the residual or the gradient of the energy-functional for a Slater determinant subject to the orthonormality constraints among orbitals, representing the search for a newly improved Fock matrix in the direction of the residual in the direct inversion of the iterative subspace (RDIIS). Implemented in the computational chemistry package GAMESS, the RDIIS is compared with the standard CDIIS and the second order SCF orbital optimization (SOSCF) for tested molecules started with a crude guess. As a result, the RDIIS stably and efficiently performs the SCF convergence acceleration. Furthermore, the RDIIS is considerably independent on the subspace size with the concentrated linear coefficients accounting proportionally for the Fock matrices close to the current iteration.
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Affiliation(s)
- Linping Hu
- Shenzhen JL Computational Science and Applied Research Institute, Shenzhen, China
| | - Yanoar Pribadi Sarwono
- Shenzhen JL Computational Science and Applied Research Institute, Shenzhen, China
- Research Center for Quantum Physics, National Research and Innovation Agency (BRIN), South Tangerang, Indonesia
| | - Yonglong Ding
- Beijing Computational Science Research Center, Beijing, China
| | - Fang He
- Shenzhen JL Computational Science and Applied Research Institute, Shenzhen, China
| | - Rui-Qin Zhang
- Shenzhen JL Computational Science and Applied Research Institute, Shenzhen, China
- Beijing Computational Science Research Center, Beijing, China
- Department of Physics, City University of Hong Kong, Hong Kong SAR, China
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24
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Fedorov DG. Use of caps in the auxiliary basis set formulation of the fragment molecular orbital method. J Comput Chem 2024; 45:1540-1551. [PMID: 38490813 DOI: 10.1002/jcc.27345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/19/2024] [Accepted: 02/29/2024] [Indexed: 03/17/2024]
Abstract
An auxiliary polarization formulation of the fragment molecular orbital (FMO) method is developed, combining a basis set correction computed for capped isolated fragments with a polarization obtained from uncapped fragments. For a set of organic and inorganic test systems, it is shown that the total energy and atomic charges are accurately reproduced with respect to full unfragmented calculations. It is demonstrated that the method is accurate for computing electronic excited states. The developed approach is applied to rank the isomers of chignolin from experimental NMR data (PDB: 1UAO) according to their relative energy. Contributions of polarization and basis set effects to pair interactions between fragments are elucidated.
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Affiliation(s)
- Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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25
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Wojciechowski M, Czapinska H, Krwawicz J, Rafalski D, Bochtler M. Cytosine analogues as DNA methyltransferase substrates. Nucleic Acids Res 2024:gkae568. [PMID: 38966999 DOI: 10.1093/nar/gkae568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 05/23/2024] [Accepted: 06/20/2024] [Indexed: 07/06/2024] Open
Abstract
DNA methyltransferases are drug targets for myelodysplastic syndrome (MDS), chronic myelomonocytic leukemia (CMML), acute myelogenous leukemia (AML) and possibly β-hemoglobinopathies. We characterize the interaction of nucleoside analogues in DNA with a prokaryotic CpG-specific DNA methyltransferase (M.MpeI) as a model for mammalian DNMT1 methyltransferases. We tested DNA containing 5-hydroxymethylcytosine (5hmC), 5-hydroxycytosine (5OHC), 5-methyl-2-pyrimidinone (in the ribosylated form known as 5-methylzebularine, 5mZ), 5,6-dihydro-5-azacytosine (dhaC), 5-fluorocytosine (5FC), 5-chlorocytosine (5ClC), 5-bromocytosine (5BrC) and 5-iodocytosine (5IC). Covalent complex formation was by far most efficient for 5FC. Non-covalent complexes were most abundant for dhaC and 5mZ. Surprisingly, we observed methylation of 5IC and 5BrC, and to a lesser extent 5ClC and 5FC, in the presence, but not the absence of small molecule thiol nucleophiles. For 5IC and 5BrC, we demonstrated by mass spectrometry that the reactions were due to methyltransferase driven dehalogenation, followed by methylation. Crystal structures of M.MpeI-DNA complexes capture the 'in' conformation of the active site loop for analogues with small or rotatable (5mZ) 5-substituents and its 'out' form for bulky 5-substituents. Since very similar 'in' and 'out' loop conformations were also observed for DNMT1, it is likely that our conclusions generalize to other DNA methyltransferases.
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Affiliation(s)
- Marek Wojciechowski
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Plant Breeding and Acclimatization Institute - National Research Institute, 05-870 Radzikow, Poland
| | - Honorata Czapinska
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Joanna Krwawicz
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Dominik Rafalski
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Matthias Bochtler
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
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26
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Mittal K, Pham AV, Davis AG, Richardson AD, De Hoe C, Dean RT, Baird V, McDonald AR, Frantz DK. Intramolecular Diels-Alder Reaction of a Biphenyl Group in a Strained meta-Quaterphenylene Acetylene. J Org Chem 2024; 89:9620-9626. [PMID: 36701431 PMCID: PMC11232012 DOI: 10.1021/acs.joc.2c02280] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Indexed: 01/27/2023]
Abstract
At elevated temperatures, a strained, cyclic meta-quaterphenylene acetylene undergoes an intramolecular cyclization reaction to form benz[e]indeno[1,2,3-hi]acephenanthrylene. This reaction represents an example of a Diels-Alder reaction at the 2-, 1-, 1'-, and 2'-positions of a biphenyl derivative, a region analogous to the bay regions of perylene and other periacenes. The reaction proceeds cleanly with high conversion. Kinetics studies of a methylated derivative reveal that the ΔG‡ for the reaction is ∼40-41 kcal/mol, and computational models predict a similar value of Grel for the transition state of a concerted [4 + 2]-cycloaddition.
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Affiliation(s)
- Komal Mittal
- Department of Chemistry and Biochemistry, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Ashley V Pham
- Department of Chemistry and Biochemistry, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Amanda G Davis
- Department of Chemistry and Biochemistry, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Abigail D Richardson
- Department of Chemistry and Biochemistry, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Clement De Hoe
- Department of Chemistry and Biochemistry, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Ryan T Dean
- Department of Chemistry and Biochemistry, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Vi Baird
- Department of Chemistry and Biochemistry, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Ashley Ringer McDonald
- Department of Chemistry and Biochemistry, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Derik K Frantz
- Department of Chemistry and Biochemistry, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
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27
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Silva MO, da Costa RF, Bettega MHF. Elastic and Electronically Inelastic Cross Sections for the Scattering of Electrons by Pyrrole. J Phys Chem A 2024; 128:5128-5137. [PMID: 38860841 PMCID: PMC11229005 DOI: 10.1021/acs.jpca.4c02719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/12/2024]
Abstract
Integral and differential cross sections for elastic and electronically inelastic electron scattering from the pyrrole molecule are reported. The cross section calculations employed the Schwinger multichannel method with norm-conserving pseudopotentials. The collision dynamics was described according to a model in which up to 209 energetically accessible channels were treated as open. In the elastic channel, calculations carried out in the interval of energies from 0 to 50 eV revealed the presence of four resonances with peaks located at 2.56 eV (π1*), 3.82 eV (π2*), 4.70 eV (σNH*), and between 8.30 and 9.50 eV (σ*) positions which are in good agreement with previous assignments. Moreover, the role of the multichannel coupling effects in obtaining accurate cross sections was evaluated by comparing the present results with theoretical results recently reported in the literature and early measurements performed for elastic electron collisions with furan. Electronic excitation cross sections involving the transitions from ground state to the 13B2, 13A1, 11A2, and 11A1 excited states of pyrrole driven by electron impact are presented for energies from thresholds up to 50 eV and, whenever possible, critically compared with the data available in the literature.
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Affiliation(s)
- Murilo O. Silva
- Instituto
Federal do Paraná, Campus Avançado Goioerê, Rodovia Luiz Dechiche, s/no, 87360-000 Goioerê, Paraná, Brazil
- Departamento
de Física, Universidade Federal do
Paraná, Caixa
Postal 19044, 81531-980 Curitiba, Paraná, Brazil
- Centro
de Ciências Naturais e Humanas, Universidade
Federal do ABC, 09210-580 Santo André, São Paulo, Brazil
| | - Romarly F. da Costa
- Centro
de Ciências Naturais e Humanas, Universidade
Federal do ABC, 09210-580 Santo André, São Paulo, Brazil
| | - Márcio H. F. Bettega
- Departamento
de Física, Universidade Federal do
Paraná, Caixa
Postal 19044, 81531-980 Curitiba, Paraná, Brazil
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28
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Metya S, Roy S, Mandal S, Huang QR, Kuo JL, Das A. Modulation of the strength of weak S-H⋯O hydrogen-bond: Spectroscopic study of the complexes of 2-flurothiophenol with methanol and ethanol. J Chem Phys 2024; 160:224302. [PMID: 38856058 DOI: 10.1063/5.0208086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 05/27/2024] [Indexed: 06/11/2024] Open
Abstract
Spectroscopic exploration of sulfur-centered hydrogen bonding involving a thiol group (S-H) as the hydrogen bond donor is scarce in the literature. Herein, we have investigated 1:1 complexes of 2-fluorothiophenol (2-FTP) with methanol (MeOH) and ethanol (EtOH) in the gas phase to examine the physical characteristics and strength of the S-H⋯O hydrogen bond. Structures, conformations, and the strength of the S-H⋯O interaction are investigated by measuring the electronic and Infrared (IR) spectra of the two complexes employing resonant two-photon ionization, UV-UV hole-burning, and IR-UV double resonance spectroscopic techniques combined with quantum chemical calculations. Three conformers of 2-FTP⋯MeOH and two conformers of 2-FTP⋯EtOH have been detected in the experiment. A comparison of the IR spectra obtained from the experiment with those of the low-energy conformers of 2-FTP⋯MeOH and 2-FTP⋯EtOH predicted from the theory confirms that all the observed conformers of the two complexes are primarily S-H⋯O hydrogen bonded. The IR red-shifts found in the S-H stretching frequencies in 2-FTP⋯MeOH and 2-FTP⋯EtOH concerning that in 2-FTP are ∼76 and ∼88 cm-1, respectively, which are much larger than that was reported earlier in the 2-FTP⋯H2O complex (30 cm-1). The strength and physical nature of different noncovalent interactions, including the S-H⋯O hydrogen bond existing in the complexes, are further analyzed using natural bond orbital analysis, quantum theory of atoms in molecules, and localized molecular orbital-energy decomposition analysis. The current investigation reveals that the S-H⋯O hydrogen bond can be strengthened by judicial choices of the hydrogen bond acceptors of higher proton affinities.
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Affiliation(s)
- Surajit Metya
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Supravat Roy
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Sourav Mandal
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Qian-Rui Huang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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29
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Kumar R, Ghosh A, Vaval N. Relaxation of the 2a1 ionized water dimer: An interplay of intermolecular Coulombic decay (ICD) and proton transfer processes. J Chem Phys 2024; 160:214302. [PMID: 38832734 DOI: 10.1063/5.0199888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/16/2024] [Indexed: 06/05/2024] Open
Abstract
This article investigates the relaxation dynamics of the ionized 2a1 state of a water molecule within a water dimer. The study was motivated by findings from two previous pieces of research that focused on the relaxation behaviors of the inner-valence ionized water dimer. The present study discloses an observation indicating that water dimers display specific fragmentation patterns following inner-valence ionization, depending on the position of the vacancy. Vacancies were created in the 2a1 state of the proton-donating water molecule (PDWM) and proton-accepting water molecule (PAWM). Utilizing Born-Oppenheimer molecular dynamics simulations, the propagation of the 2a1 ionized state was carried out for both scenarios. The results revealed proton transfer occurred when the vacancy resided in the PDWM, accompanied by the closing of decay channels for O-H bond distance (RO-H) > 1.187 Å (matching Richter et al.'s findings). Conversely, when vacancy was on PAWM, we observed no closing of decay channels (aligning with Jahnke et al.'s findings). This difference translates to distinct fragmentation pathways. In PDWM cases, 2a1 state ionization leads to H3O+ -OH• formation. In contrast, PAWM vacancies result in decay pathways leading to H2O+-H2O+ products.
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Affiliation(s)
- Ravi Kumar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Aryya Ghosh
- Department of Chemistry, Ashoka University, Sonipat, Haryana 131029, India
| | - Nayana Vaval
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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30
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Fukumoto Y, Suzuki N, Hara R, Tanaka YK, Ogra Y. Development of a Biosafety Level 1 Cellular Assay for Identifying Small-Molecule Antivirals Targeting the Main Protease of SARS-CoV-2: Evaluation of Cellular Activity of GC376, Boceprevir, Carmofur, Ebselen, and Selenoneine. Int J Mol Sci 2024; 25:5767. [PMID: 38891954 PMCID: PMC11172239 DOI: 10.3390/ijms25115767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/13/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
While research has identified several inhibitors of the main protease (Mpro) of SARS-CoV-2, a significant portion of these compounds exhibit reduced activity in the presence of reducing agents, raising concerns about their effectiveness in vivo. Furthermore, the conventional biosafety level 3 (BSL-3) for cellular assays using viral particles poses a limitation for the widespread evaluation of Mpro inhibitor efficacy in a cell-based assay. Here, we established a BSL-1 compatible cellular assay to evaluate the in vivo potential of Mpro inhibitors. This assay utilizes mammalian cells expressing a tagged Mpro construct containing N-terminal glutathione S-transferase (GST) and C-terminal hemagglutinin (HA) tags and monitors Mpro autodigestion. Using this method, GC376 and boceprevir effectively inhibited Mpro autodigestion, suggesting their potential in vivo activity. Conversely, carmofur and ebselen did not exhibit significant inhibitory effects in this assay. We further investigated the inhibitory potential of selenoneine on Mpro using this approach. Computational analyses of binding energies suggest that noncovalent interactions play a critical role in facilitating the covalent modification of the C145 residue, leading to Mpro inhibition. Our method is straightforward, cost-effective, and readily applicable in standard laboratories, making it accessible to researchers with varying levels of expertise in infectious diseases.
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Grants
- 19K07079 Ministry of Education, Culture, Sports, Science and Technology
- 21H04920 Ministry of Education, Culture, Sports, Science and Technology
- 19H05772 Ministry of Education, Culture, Sports, Science and Technology
- 22K05345 Ministry of Education, Culture, Sports, Science and Technology
- 24K09793 Ministry of Education, Culture, Sports, Science and Technology
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Affiliation(s)
- Yasunori Fukumoto
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan; (N.S.); (Y.-k.T.); (Y.O.)
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31
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Fatima M, Siddiqui WA, Choudhary MI, Ashraf A, Niaz S, Raza MA, Alam SM, Ashfaq M, Tahir MN, Dahlous KA. Synthesis of dimeric 1,2-benzothiazine 1,1-dioxide scaffolds: molecular structures, Hirshfeld surface analysis, DFT and enzyme inhibition studies. RSC Adv 2024; 14:16935-16944. [PMID: 38808235 PMCID: PMC11130764 DOI: 10.1039/d4ra02009j] [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: 03/15/2024] [Accepted: 05/20/2024] [Indexed: 05/30/2024] Open
Abstract
1,2-Benzothiazines are bioactive compounds with diverse pharmacological properties. We report here the synthesis of a series of dimers containing 1,2-benzothiazine scaffolds as potential pharmacophores. The characterization of compounds was done using analytical techniques such as FT-IR, 1H NMR, and elemental analyses. The molecular structures of the compounds (5-8) were confirmed by X-ray crystallography. The molecular interactions in compounds (5-8) were determined by Hirshfeld Surface Analysis (HSA). Density functional theory (DFT) investigations were carried out to calculate vibrational properties, NMR behaviour, dipole moments, molecular electrostatic potential (MEP), frontier molecular orbital (FMO), natural bonding orbital (NBO) analysis and global reactivity descriptors. The global reactivity descriptors indicated the charge transfer reactions and stabilized as follows: 8 > 7 > 6 > 5. In FMO analysis a substantial HOMO-LUMO gap, ranging from 4.43 to 5.12 eV, with high LUMO values was observed for all compounds, while the highest value for linear polarizability was found in compound 8. The in vitro and in silico studies confirm that compound 8 is more active toward AChE and BChE enzymes.
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Affiliation(s)
- Muqudis Fatima
- Institute of Chemistry, University of Sargodha Sargodha 40100 Pakistan
| | | | - Muhammad Iqbal Choudhary
- International Center for Chemical and Biological Sciences, H. E. J Research Institute of Chemistry, University of Karachi Karachi Pakistan
| | - Adnan Ashraf
- Department of Chemistry, The University of Lahore Lahore Pakistan
| | - Shanawer Niaz
- Department of Physics, Thal University Bhakkar Bhakkar 30000 Pakistan
| | | | - Seikh Mafiz Alam
- Department of Chemistry, Aliah University New Town Kolkata 700 156 India
| | - Muhammad Ashfaq
- Department of Physics, University of Sargodha Sargodha-40100 Pakistan
| | | | - Kholood Ahmed Dahlous
- Department of Chemistry, College of Science, King Saud University P. O. Box 2455 Riyadh 11451 Saudi Arabia
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32
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Capone M, Romanelli M, Castaldo D, Parolin G, Bello A, Gil G, Vanzan M. A Vision for the Future of Multiscale Modeling. ACS PHYSICAL CHEMISTRY AU 2024; 4:202-225. [PMID: 38800726 PMCID: PMC11117712 DOI: 10.1021/acsphyschemau.3c00080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 05/29/2024]
Abstract
The rise of modern computer science enabled physical chemistry to make enormous progresses in understanding and harnessing natural and artificial phenomena. Nevertheless, despite the advances achieved over past decades, computational resources are still insufficient to thoroughly simulate extended systems from first principles. Indeed, countless biological, catalytic and photophysical processes require ab initio treatments to be properly described, but the breadth of length and time scales involved makes it practically unfeasible. A way to address these issues is to couple theories and algorithms working at different scales by dividing the system into domains treated at different levels of approximation, ranging from quantum mechanics to classical molecular dynamics, even including continuum electrodynamics. This approach is known as multiscale modeling and its use over the past 60 years has led to remarkable results. Considering the rapid advances in theory, algorithm design, and computing power, we believe multiscale modeling will massively grow into a dominant research methodology in the forthcoming years. Hereby we describe the main approaches developed within its realm, highlighting their achievements and current drawbacks, eventually proposing a plausible direction for future developments considering also the emergence of new computational techniques such as machine learning and quantum computing. We then discuss how advanced multiscale modeling methods could be exploited to address critical scientific challenges, focusing on the simulation of complex light-harvesting processes, such as natural photosynthesis. While doing so, we suggest a cutting-edge computational paradigm consisting in performing simultaneous multiscale calculations on a system allowing the various domains, treated with appropriate accuracy, to move and extend while they properly interact with each other. Although this vision is very ambitious, we believe the quick development of computer science will lead to both massive improvements and widespread use of these techniques, resulting in enormous progresses in physical chemistry and, eventually, in our society.
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Affiliation(s)
- Matteo Capone
- Department
of Physical and Chemical Sciences, University
of L’Aquila, L’Aquila 67010, Italy
| | - Marco Romanelli
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Davide Castaldo
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Giovanni Parolin
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Alessandro Bello
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
- Department
of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Gabriel Gil
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
- Instituto
de Cibernética, Matemática y Física (ICIMAF), La Habana 10400, Cuba
| | - Mirko Vanzan
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
- Department
of Physics, University of Milano, Milano 20133, Italy
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33
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Skrzyński G, Musial M. An Intruder-Free Fock Space Coupled-Cluster Study of the Potential Energy Curves of LiMg + within the (2,0) Sector. Molecules 2024; 29:2364. [PMID: 38792225 PMCID: PMC11124300 DOI: 10.3390/molecules29102364] [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: 04/18/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
The potential energy curves (PECs) and spectroscopic constants of the ground and excited states of a LiMg+ molecular cation were investigated. We obtained accurate results for the fifteen lowest-lying states of the LiMg+ cation using the Intermediate Hamiltonian Fock Space Multireference Coupled Cluster (IH-FS-CC) method applied to the (2,0) sector. Relativistic corrections were accounted for using the third-order Douglas-Kroll method. In each instance, smooth PECs were successfully computed across the entire range of interatomic distances from equilibrium to the dissociation limit. The results are in good accordance with previous studies of this molecular cation. Notably, this study marks the first application of IH-FS-CC in investigating a mixed alkali and alkaline earth molecular cation, proving its usability in determining accurate PECs of such diatomics and their spectroscopic constants.
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Affiliation(s)
- Grzegorz Skrzyński
- Institute of Chemistry, University of Silesia in Katowice, Szkolna 9, 40-006 Katowice, Poland
| | - Monika Musial
- Institute of Chemistry, University of Silesia in Katowice, Szkolna 9, 40-006 Katowice, Poland
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34
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Filatov M, Mironov V, Kraka E. Unraveling the effect of aromaticity for the dynamics of excited states of single benzene fluorophores. J Comput Chem 2024; 45:1033-1045. [PMID: 38216513 DOI: 10.1002/jcc.27304] [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: 09/29/2023] [Revised: 11/23/2023] [Accepted: 12/23/2023] [Indexed: 01/14/2024]
Abstract
The photophysical properties of a series of recently synthesized single benzene fluorophores were investigated using ensemble density functional theory calculations. The energetic stability of the ground and excited state species were counterposed against the aromaticity index derived from local vibrational modes. It was found that the large Stokes shift of the fluorophores (up to ca. 5800 cm - 1 ) originates from the effect of electron donating and electron withdrawing substituents rather than π -delocalization and related (anti-)aromaticity. On the basis of nonadiabatic molecular dynamics simulations, the absence of fluorescence from one of the regioisomers was explained by the occurrence of easily accessible S 1 /S 0 conical intersections below the vertical excitation energy level. It is demonstrated in the manuscript that the analysis of local mode force constants and the related aromaticity index represent a useful tool for the characterization of π -delocalization effects in π -conjugated compounds.
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Affiliation(s)
- Michael Filatov
- Center for Multidimensional Carbon Materials, Institute for Basic Science (IBS), Ulsan, Republic of Korea
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, Texas, USA
| | | | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, Texas, USA
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35
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Xu J, Hao J, Bu C, Meng Y, Xiao H, Zhang M, Li C. XMECP: Reaching State-of-the-Art MECP Optimization in Multiscale Complex Systems. J Chem Theory Comput 2024; 20:3590-3600. [PMID: 38651739 DOI: 10.1021/acs.jctc.4c00033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
The Python-based program, XMECP, is developed for realizing robust, efficient, and state-of-the-art minimum energy crossing point (MECP) optimization in multiscale complex systems. This article introduces the basic capabilities of the XMECP program by theoretically investigating the MECP mechanism of several example systems including (1) the photosensitization mechanism of benzophenone, (2) photoinduced proton-coupled electron transfer in the cytosine-guanine base pair in DNA, (3) the spin-flip process in oxygen activation catalyzed by an iron-containing 2-oxoglutarate-dependent oxygenase (Fe/2OGX), and (4) the photochemical pathway of flavoprotein adjusted by the intensity of an external electric field. MECPs related to multistate reaction and multistate reactivity in large-scale complex biochemical systems can be well-treated by workflows suggested by the XMECP program. The branching plane updating the MECP optimization algorithm is strongly recommended as it provides derivative coupling vector (DCV) with explicit calculation and can equivalently evaluate contributions from non-QM residues to DCV, which can be nonadiabatic coupling or spin-orbit coupling in different cases. In the discussed QM/MM examples, we also found that the influence on the QM region by DCV can occur through noncovalent interactions and decay with distance. In the example of DNA base pairs, the nonadiabatic coupling occurs across the π-π stacking structure formed in the double-helix system. In contrast to general intuition, in the example of Fe/2OGX, the central ferrous and oxygen part contribute little to the spin-orbit coupling; however, a nearby arginine residue, which is treated by molecular mechanics in the QM/MM method, contributes significantly via two hydrogen bonds formed with α-ketoglutarate (α-KG). This indicates that the arginine residue plays a significant role in oxygen activation, driving the initial triplet state toward the productive quintet state, which is more than the previous knowledge that the arginine residue can bind α-KG at the reaction site by hydrogen bonds.
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Affiliation(s)
- Jiawei Xu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jian Hao
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Caijie Bu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou 350117, Fujian, P. R. China
| | - Yajie Meng
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Han Xiao
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
| | - Minyi Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
| | - Chunsen Li
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen University, Xiamen 361005, Fujian, P. R. China
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Meng F, Liu J, Cao Z, Yu J, Steurer B, Yang Y, Wang Y, Cai X, Zhang M, Ren F, Aliper A, Ding X, Zhavoronkov A. Discovery of macrocyclic CDK2/4/6 inhibitors with improved potency and DMPK properties through a highly efficient macrocyclic drug design platform. Bioorg Chem 2024; 146:107285. [PMID: 38547721 DOI: 10.1016/j.bioorg.2024.107285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/07/2024] [Accepted: 03/12/2024] [Indexed: 04/13/2024]
Abstract
Cyclin-dependent kinases (CDKs) are critical cell cycle regulators that are often overexpressed in tumors, making them promising targets for anti-cancer therapies. Despite substantial advancements in optimizing the selectivity and drug-like properties of CDK inhibitors, safety of multi-target inhibitors remains a significant challenge. Macrocyclization is a promising drug discovery strategy to improve the pharmacological properties of existing compounds. Here we report the development of a macrocyclization platform that enabled the highly efficient discovery of a novel, macrocyclic CDK2/4/6 inhibitor from an acyclic precursor (NUV422). Using dihedral angle scan and structure-based, computer-aided drug design to select an optimal ring-closing site and linker length for the macrocycle, we identified compound 8 as a potent new CDK2/4/6 inhibitor with optimized cellular potency and safety profile compared to NUV422. Our platform leverages both experimentally-solved as well as generative chemistry-derived macrocyclic structures and can be deployed to streamline the design of macrocyclic new drugs from acyclic starting compounds, yielding macrocyclic compounds with enhanced potency and improved drug-like properties.
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Affiliation(s)
- Fanye Meng
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Jinxin Liu
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Zhongying Cao
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Jiaojiao Yu
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Barbara Steurer
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong
| | - Yilin Yang
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Yazhou Wang
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Xin Cai
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Man Zhang
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Feng Ren
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Alex Aliper
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong
| | - Xiao Ding
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China.
| | - Alex Zhavoronkov
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China; Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong; Insilico Medicine AI Limited, Masdar City, Abu Dhabi 145748, United Arab Emirates.
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37
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Petrusevich EF, Reis H, Ośmiałowski B, Jacquemin D, Luis JM, Zaleśny R. One- and two-photon absorption spectra of organoboron complexes: vibronic and environmental effects. Phys Chem Chem Phys 2024; 26:13239-13250. [PMID: 38634828 DOI: 10.1039/d4cp01089b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
We synthesized a series of four parent aza-β-ketoiminate organoboron complexes and performed spectroscopic studies using both experimental and computational techniques. We studied how benzannulation influences the vibronic structure of the UV/Vis absorption bands with a focus on the bright lowest-energy π → π* electronic excitation. Theoretical simulations, accounting for inhomogeneous broadening effects using different embedding schemes, allowed gaining in-depth insights into the observed differences in band shapes induced by structural modifications. We observed huge variations in the distributions of vibronic transitions depending on the position of benzannulation. By and large, the harmonic approximation combined with the adiabatic hessian model delivers qualitatively correct band shapes for the one-photon absorption spectra, except in one case. We also assessed the importance of non-Condon effects (accounted for by the linear term in Herzberg-Teller expansion of the dipole moment) for S0 → S1 band shapes. It turned out that non-Condon contributions have no effect on the band shape in one-photon absorption spectra. In contrast, these effects significantly change the Franck-Condon band shapes of the two-photon absorption spectra. For one of the studied organoboron complexes we also performed a preliminary exploration of mechanical anharmonicity, resulting in an increase of the intensity of the 0-0 transition, which improves the agreement with the experimental data compared to the harmonic model.
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Affiliation(s)
- Elizaveta F Petrusevich
- Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
- Institute of Computational Chemistry and Catalysis and Department of Chemistry, University of Girona, Campus de Montilivi, 17003, Girona, Catalonia, Spain.
| | - Heribert Reis
- Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), Vassileos Constantinou Ave 48th, 116 35 Athens, Greece
| | - Borys Ośmiałowski
- Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100 Toruń, Poland
| | - Denis Jacquemin
- Nantes Université, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
- Institut Universitaire de France (IUF), F-75005 Paris, France
| | - Josep M Luis
- Institute of Computational Chemistry and Catalysis and Department of Chemistry, University of Girona, Campus de Montilivi, 17003, Girona, Catalonia, Spain.
| | - Robert Zaleśny
- Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
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Escayola S, Jimenez-Izal E, Matito E, Ugalde JM, Grande-Aztatzi R, Mercero JM. Unveiling the quantum secrets of triel metal triangles: a tale of stability, aromaticity, and relativistic effects. Phys Chem Chem Phys 2024; 26:12619-12627. [PMID: 38597590 DOI: 10.1039/d4cp00484a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Low lying electronic states of Al3-, Ga3-, In3-, and Tl3- have been characterized using high level multiconfigurational quasi degenerate perturbation theory on the multiconfigurational self-consistent field. Among these species, the singlet states emerge as the predominant energy minima, displaying remarkable stability. However, within the Tl3- series, our investigation leads to the identification of the high-spin , as the most stable spin state, a result corroborated by previous experimental detection via photoelectron spectroscopy. Similarly, we have also identified the singlet state of In3- as the signal detected previously experimentally. By applying Mandado's rules and an array of aromaticity indicators, it is conclusively demonstrated that both the singlet and quintet states exhibit multiple-fold aromaticity, while the triplets exhibit conflicting aromaticity. Furthermore, this investigation highlights the significant impact of relativistic effects, as they enhance the stability of the state relative to its singlet counterpart. These findings shed new light on the electronic structures and properties of these ions, offering valuable insights into their chemical behavior and potential applications.
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Affiliation(s)
- Sílvia Escayola
- Institute of Computational Chemistry and Catalysis and Department of Chemistry, University of Girona, C/M. Aurèlia Capmany, 69, 17003 Girona, Catalonia, Spain
- Donostia International Physics Center (DIPC), 20018 Donostia, Euskadi, Spain.
| | - Elisa Jimenez-Izal
- Donostia International Physics Center (DIPC), 20018 Donostia, Euskadi, Spain.
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), P.K. 1072, 20080 Donostia, Euskadi, Spain
| | - Eduard Matito
- Donostia International Physics Center (DIPC), 20018 Donostia, Euskadi, Spain.
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Euskadi, Spain
| | - Jesus M Ugalde
- Donostia International Physics Center (DIPC), 20018 Donostia, Euskadi, Spain.
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), P.K. 1072, 20080 Donostia, Euskadi, Spain
| | - Rafael Grande-Aztatzi
- Donostia International Physics Center (DIPC), 20018 Donostia, Euskadi, Spain.
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Av. Eugenio Garza Sada 2501, 64849 Monterrey, Nuevo León, Mexico
| | - Jose M Mercero
- Donostia International Physics Center (DIPC), 20018 Donostia, Euskadi, Spain.
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), P.K. 1072, 20080 Donostia, Euskadi, Spain
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Bai T, Li H. Revealing the Mechanism of Alcohol Dehydroxylation and C-C Bond Formation through Concerted Catalysis by Ir/Cu Bimetallic Complexes. J Org Chem 2024; 89:5363-5370. [PMID: 38593184 DOI: 10.1021/acs.joc.3c02740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
The density functional theory (DFT) was employed to theoretically investigate the reaction mechanism of alcohol deoxygenation/trifluoromethylation. The substrate alcohol (R1) forms a complex (INT3) by binding with benzoxazole salts (NHCs). Under the influence of the photocatalyst ([IrIII]*) and quinuclidine, the C-H bond in INT3 is activated through either electron transfer-proton transfer (ETPT) or hydrogen atom transfer (HAT) mechanisms, resulting in the cleavage of C-O bonds and generation of deoxyalkyl radicals. The distribution of high-valent and low-valent states in the catalytic cycle of [Ir]-complexes is governed by the redox potential mechanism. Investigation was conducted on the source of hydrogen atom transfer reagents in the HAT reaction process under both optimal and nonoptimal conditions. The results demonstrate distinct reactivity among various radicals involved in the Cu-mediated radical capture process. Further investigations into INT3 activation modes, cycling facilitated by [Ir]-complexes, and understanding the role played by [Cu]-complexes in this reaction system provide a valuable theoretical foundation for comprehending and enhancing Ir/Cu bimetallic cooperative catalysis in alcohol deoxygenation/trifluoromethylation reactions. This provides anticipated theoretical support for future designs of more efficient and rational alcohol deoxygenation reactions.
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Affiliation(s)
- Taiming Bai
- Key Laboratory of Chemical Engineering and Technology, State Ethnic Affairs Commission, North Minzu University, 750021 Yinchuan, China
- Ningxia Key Laboratory of Solar Chemical Conversion Technology, North Minzu University, 750021 Yinchuan, China
| | - Hui Li
- Key Laboratory of Chemical Engineering and Technology, State Ethnic Affairs Commission, North Minzu University, 750021 Yinchuan, China
- Ningxia Key Laboratory of Solar Chemical Conversion Technology, North Minzu University, 750021 Yinchuan, China
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40
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Bursik B, Eller J, Gross J. Predicting Solvation Free Energies from the Minnesota Solvation Database Using Classical Density Functional Theory Based on the PC-SAFT Equation of State. J Phys Chem B 2024; 128:3677-3688. [PMID: 38579126 DOI: 10.1021/acs.jpcb.3c07447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024]
Abstract
We critically assess the capabilities of classical density functional theory (DFT) based on the perturbed-chain statistical associating fluid theory (PC-SAFT) equation of state to predict the solvation free energies of small molecules in various hydrocarbon solvents. We compare DFT results with experimental data from the Minnesota solvation database and utilize statistical methods to analyze the accuracy of our approach, as well as its weaknesses. The mean absolute error of the solvation free energies is 3.7 kJ mol-1 for n-alkane solvents, ranging from pentane to hexadecane, with 473 solute-solvent systems. For solvents consisting of cyclic hydrocarbons (cyclohexane, benzene, toluene, and ethylbenzene) with 245 solute-solvent systems, we report a slightly larger mean absolute error of 4.2 kJ mol-1. We identify three possible sources of errors: (i) the neglect of solute-solvent and solvent-solvent Coulomb interactions, which limits the applicability of PC-SAFT DFT to nonpolar and weakly polar molecules; (ii) the solute's Lennard-Jones parameters supplied by the general AMBER force field, which are not parametrized toward solvation free energies; and (iii) the application of the Lorentz-Berthelot combining rules to the dispersive interactions between a segment of the PC-SAFT solvent and a Lennard-Jones interaction site of the solute. The approach is more accurate than standard implementations of phenomenological models in common chemistry software packages, which exhibit mean absolute errors larger than 9.12 kJ mol-1, even though newer phenomenological models achieve a mean absolute error of about 2 kJ mol-1. PC-SAFT DFT is more computationally efficient than state of the art explicit molecular simulations in combination with free energy perturbation methods. It is predictive with respect to solvation free energies, i.e., the input for the model is the (element-specific) molecular force field, the solute configuration from molecular dynamics simulations, and the (substance-specific) PC-SAFT parameters. The PC-SAFT parametrization uses pure-component data and does not require experimental solvation free energies. The PC-SAFT equation of state, without applying a DFT formalism, can also be used to calculate solvation free energies, provided that the PC-SAFT parameters for the solute are available. A large number of substances was recently parametrized by members of our group (Esper, T.; Bauer, G.; Rehner, P.; Gross, J. Ind. Eng. Chem. Res. 2023, 62), which enables a comparison to the DFT approach for 103 substances. Accurate results are obtained from the PC-SAFT equation of state with an MAE below 2.51 kJ mol-1. The DFT approach does not require PC-SAFT parameters for the solute and can be applied to all solutes that can be represented by the molecular force field.
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Affiliation(s)
- Benjamin Bursik
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Stuttgart 70569, Germany
| | - Johannes Eller
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Stuttgart 70569, Germany
| | - Joachim Gross
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Stuttgart 70569, Germany
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Zhao RR, Wu JH, Tong LW, Li JY, Lu YS, Shao JW. Multifunctional metal-coordinated Co-assembled carrier-free nanoplatform based on dual-drugs for ferroptosis-mediated cocktail therapy of hepatocellular carcinoma growth and metastasis. J Colloid Interface Sci 2024; 660:257-276. [PMID: 38244494 DOI: 10.1016/j.jcis.2024.01.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 01/22/2024]
Abstract
The heterogeneity of hepatocellular carcinoma (HCC) and the complexity of the tumor microenvironment (TME) pose challenges to efficient drug delivery and the antitumor efficacy of combined or synergistic therapies. Herein, a metal-coordinated carrier-free nanodrug (named as USFe3+ LA NPs) was developed for ferroptosis-mediated multimodal synergistic anti-HCC. Natural product ursolic acid (UA) was incorporated to enhance the sensitivity of tumor cells to sorafenib (SRF). Surface decoration of cell penetration peptide and epithelial cell adhesion molecule aptamer facilitated the uptake of USFe3+ LA NPs by HepG2 cells. Meanwhile, Fe3+ ions could react with intracellular hydrogen peroxide, generating toxic hydroxyl radical (·OH) for chemodynamical therapy (CDT) and amplified ferroptosis by cystine/glutamate antiporter system (System Xc-), which promoted the consumption of glutathione (GSH) and inhibited the expression of glutathione peroxidase 4 (GPX4). Notably, these all-in-one nanodrugs could inhibit tumor metastasis and induced immunogenic cell death (ICD). Last but not least, the nanodrugs demonstrated favorable biocompatibility, augmenting the immune response against the programmed death-ligand 1 (PD-L1) by increasing cytotoxic T cell infiltration. In vivo studies revealed significant suppression of tumor growth and distant metastasis. Overall, our work introduced a novel strategy for applications of metal-coordinated co-assembled carrier-free nano-delivery system in HCC combination therapy, especially in the realms of cancer metastasis prevention and immunotherapy.
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Affiliation(s)
- Rui-Rui Zhao
- Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Ju-Hong Wu
- National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Ling-Wu Tong
- Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Jin-Yu Li
- National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Yu-Sheng Lu
- Fujian-Taiwan-Hongkong-Macao Science and Technology Cooperation Base of Intelligent Pharmaceutics, College of Materials and Chemical Engineering, Minjiang University, Fuzhou, Fujian 350108, China
| | - Jing-Wei Shao
- Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, College of Chemistry, Fuzhou University, Fuzhou 350108, China; Fujian-Taiwan-Hongkong-Macao Science and Technology Cooperation Base of Intelligent Pharmaceutics, College of Materials and Chemical Engineering, Minjiang University, Fuzhou, Fujian 350108, China.
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42
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Barrena-Espés D, Munárriz J, Martín Pendás Á. How electrons still guard the space: Electron number distribution functions based on QTAIM∩ELF intersections. J Chem Phys 2024; 160:144106. [PMID: 38591678 DOI: 10.1063/5.0199318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/24/2024] [Indexed: 04/10/2024] Open
Abstract
Despite the importance of the one-particle picture provided by the orbital paradigm, a rigorous understanding of the spatial distribution of electrons in molecules is still of paramount importance to chemistry. Considerable progress has been made following the introduction of topological approaches, capable of partitioning space into chemically meaningful regions. They usually provide atomic partitions, for example, through the attraction basins of the electron density in the quantum theory of atoms in molecules (QTAIM) or electron-pair decompositions, as in the case of the electron localization function (ELF). In both cases, the so-called electron distribution functions (EDFs) provide a rich statistical description of the electron distribution in these spatial domains. Here, we take the EDF concept to a new fine-grained limit by calculating EDFs in the QTAIM ∩ ELF intersection domains. As shown in AHn systems based on main group elements, as well as in the CO, NO, and BeO molecules, this approach provides an exquisitely detailed picture of the electron distribution in molecules, allowing for an insightful combination of the distribution of electrons between Lewis entities (such as bonds and lone pairs) and atoms at the same time. Besides mean-field calculations, we also explore the impact of electron correlation through Hartree-Fock (HF), density functional theory (DFT) (B3LYP), and CASSCF calculations.
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Affiliation(s)
- Daniel Barrena-Espés
- Departamento de Química Física y Analítica, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Julen Munárriz
- Departamento de Química Física and Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Ángel Martín Pendás
- Departamento de Química Física y Analítica, Universidad de Oviedo, 33006 Oviedo, Spain
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Rihon J, Mattelaer CA, Montalvão RW, Froeyen M, Pinheiro VB, Lescrinier E. Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline. Nucleic Acids Res 2024; 52:2836-2847. [PMID: 38412249 PMCID: PMC11014352 DOI: 10.1093/nar/gkae135] [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] [Received: 09/22/2023] [Accepted: 02/19/2024] [Indexed: 02/29/2024] Open
Abstract
The field of synthetic nucleic acids with novel backbone structures [xenobiotic nucleic acids (XNAs)] has flourished due to the increased importance of XNA antisense oligonucleotides and aptamers in medicine, as well as the development of XNA processing enzymes and new XNA genetic materials. Molecular modeling on XNA structures can accelerate rational design in the field of XNAs as it contributes in understanding and predicting how changes in the sugar-phosphate backbone impact on the complementation properties of the nucleic acids. To support the development of novel XNA polymers, we present a first-in-class open-source program (Ducque) to build duplexes of nucleic acid analogs with customizable chemistry. A detailed procedure is described to extend the Ducque library with new user-defined XNA fragments using quantum mechanics (QM) and to generate QM-based force field parameters for molecular dynamics simulations within standard packages such as AMBER. The tool was used within a molecular modeling workflow to accurately reproduce a selection of experimental structures for nucleic acid duplexes with ribose-based as well as non-ribose-based nucleosides. Additionally, it was challenged to build duplexes of morpholino nucleic acids bound to complementary RNA sequences.
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Affiliation(s)
- Jérôme Rihon
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, Box 1030, B-3000 Leuven, Belgium
| | - Charles-Alexandre Mattelaer
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, Box 1030, B-3000 Leuven, Belgium
- Quantum Chemistry and Physical Chemistry, Celestijnenlaan 200f, Box 2404, B-3001, Leuven, Belgium
| | - Rinaldo Wander Montalvão
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, Box 1030, B-3000 Leuven, Belgium
- Gain Therapeutics sucursal en España, Barcelona Science Park, Baldiri Reixac 4-10, 08028 Barcelona, Spain
| | - Mathy Froeyen
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, Box 1030, B-3000 Leuven, Belgium
| | - Vitor Bernardes Pinheiro
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, Box 1030, B-3000 Leuven, Belgium
| | - Eveline Lescrinier
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, Box 1030, B-3000 Leuven, Belgium
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Aligholizadeh D, Johnson M, Hondrogiannis E, Devadas MS. Detection with NO Modification: (N═O)-Au Interactions for Instantaneous Label-Free Detection of N-Nitrosodiphenylamine. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:7405-7411. [PMID: 38551809 DOI: 10.1021/acs.langmuir.3c03739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Increasing concerns have been raised about dangerous, yet nearly undetectable levels of nitrosamines in foods, medications, and drinking water. Their ubiquitous presence and carcinogenicity necessitates a method of sensitive and selective detection of these potent toxins. While the detection of two major nitrosamines─N-nitrosodimethylamine and N-nitrosodiethylamine─has seen success, low detection limits are scarcer for the other members of this class. One member, N-nitrosodiphenylamine (NDPhA), has had little progress not only in its detection in low quantities but also in its detection at all. NDPhA has unique difficulty in its identification due to its aromaticity, making it far more problematic to distinguish in the common GC-MS or LC-MS/MS methods used for nitrosamine sensing. Despite this detection barrier, it has been listed among the top 6 carcinogenic nitrosamines by the Food and Drug Administration as of 2023. Due to its evasive nature, a unique methodology must be applied to facilitate its sensitive identification. Herein, we describe the use of surface-enhanced Raman spectroscopy for the first account of liquid-phase detection of NDPhA using cysteamine-functionalized gold nanostars and a portable Raman spectrometer. Our methodology requires no chemical modification to the nitrosated structure as well as the usage of two well-understood biocompatible materials: cysteamine and gold nanoparticles.
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Affiliation(s)
| | - Mansoor Johnson
- Department of Chemistry, Towson University, Towson, Maryland 21252, United States
| | - Ellen Hondrogiannis
- Department of Chemistry, Towson University, Towson, Maryland 21252, United States
| | - Mary Sajini Devadas
- Department of Chemistry, Towson University, Towson, Maryland 21252, United States
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Tuckman H, Neuscamman E. Aufbau Suppressed Coupled Cluster Theory for Electronically Excited States. J Chem Theory Comput 2024; 20:2761-2773. [PMID: 38502102 DOI: 10.1021/acs.jctc.3c01285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
We introduce an approach to improve single-reference coupled cluster theory in settings where the Aufbau determinant is absent from or plays only a small role in the true wave function. Using a de-excitation operator that can be efficiently hidden within a similarity transform, we create a coupled cluster wave function in which de-excitations work to suppress the Aufbau determinant and produce wave functions dominated by other determinants. Thanks to an invertible and fully exponential form, the approach is systematically improvable, size consistent, size extensive, and, interestingly, size intensive in a granular way that should make the adoption of some ground state techniques, such as local correlation, relatively straightforward. In this initial study, we apply the general formalism to create a state-specific method for orbital-relaxed, singly excited states. We find that this approach matches the accuracy of similar-cost equation-of-motion methods in valence excitations while offering improved accuracy for charge transfer states. We also find the approach to be more accurate than excited-state-specific perturbation theory in both types of states.
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Affiliation(s)
- Harrison Tuckman
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Eric Neuscamman
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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46
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Baykov SV, Katlenok EA, Baykova SO, Semenov AV, Bokach NA, Boyarskiy VP. Conformation-Associated C··· dz2-Pt II Tetrel Bonding: The Case of Cyclometallated Platinum(II) Complex with 4-Cyanopyridyl Urea Ligand. Int J Mol Sci 2024; 25:4052. [PMID: 38612862 PMCID: PMC11012616 DOI: 10.3390/ijms25074052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/30/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
The nucleophilic addition of 3-(4-cyanopyridin-2-yl)-1,1-dimethylurea (1) to cis-[Pt(CNXyl)2Cl2] (2) gave a new cyclometallated compound 3. It was characterized by NMR spectroscopy (1H, 13C, 195Pt) and high-resolution mass spectrometry, as well as crystallized to obtain two crystalline forms (3 and 3·2MeCN), whose structures were determined by X-ray diffraction. In the crystalline structure of 3, two conformers (3A and 3B) were identified, while the structure 3·2MeCN had only one conformer 3A. The conformers differed by orientation of the N,N-dimethylcarbamoyl moiety relative to the metallacycle plane. In both crystals 3 and 3·2MeCN, the molecules of the Pt(II) complex are associated into supramolecular dimers, either {3A}2 or {3B}2, via stacking interactions between the planes of two metal centers, which are additionally supported by hydrogen bonding. The theoretical consideration, utilizing a number of computational approaches, demonstrates that the C···dz2(Pt) interaction makes a significant contribution in the total stacking forces in the geometrically optimized dimer [3A]2 and reveals the dz2(Pt)→π*(PyCN) charge transfer (CT). The presence of such CT process allowed for marking the C···Pt contact as a new example of a rare studied phenomenon, namely, tetrel bonding, in which the metal site acts as a Lewis base (an acceptor of noncovalent interaction).
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Affiliation(s)
- Sergey V. Baykov
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., Saint Petersburg 199034, Russia; (E.A.K.); (A.V.S.); (V.P.B.)
| | | | | | | | - Nadezhda A. Bokach
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., Saint Petersburg 199034, Russia; (E.A.K.); (A.V.S.); (V.P.B.)
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Croney K, McCarty J. Exploring Product Release from Yeast Cytosine Deaminase with Metadynamics. J Phys Chem B 2024; 128:3102-3112. [PMID: 38516924 PMCID: PMC11000218 DOI: 10.1021/acs.jpcb.3c07972] [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] [Received: 12/05/2023] [Revised: 02/26/2024] [Accepted: 02/29/2024] [Indexed: 03/23/2024]
Abstract
The yeast cytosine deaminase (yCD) enzyme/5-fluorocytosine prodrug system is a promising candidate for targeted chemotherapeutics. After conversion of the prodrug into the toxic chemotherapeutic drug, 5-fluorouracil (5-FU), the slow product release from the enzyme limits the overall catalytic efficiency of the enzyme/prodrug system. Here, we present a computational study of the product release of the anticancer drug, 5-FU, from yCD using metadynamics. We present a comparison of the 5-FU drug to the natural enzyme product, uracil. We use volume-based metadynamics to compute the free energy landscape for product release and show a modest binding affinity for the product to the enzyme, consistent with experiments. Next, we use infrequent metadynamics to estimate the unbiased release rate from Kramers time-dependent rate theory and find a favorable comparison to experiment with a slower rate of product release for the 5-FU system. Our work demonstrates how adaptive sampling methods can be used to study the protein-ligand unbinding process for engineering enzyme/prodrug systems and gives insights into the molecular mechanism of product release for the yCD/5-FU system.
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Affiliation(s)
- Kayla
A. Croney
- Department of Chemistry, Western
Washington University, Bellingham, Washington 98225, United States
| | - James McCarty
- Department of Chemistry, Western
Washington University, Bellingham, Washington 98225, United States
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48
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Mendonça SC, Gomes BA, Campos MF, da Fonseca TS, Esteves MEA, Andriolo BV, Cheohen CFDAR, Constant LEC, da Silva Costa S, Calil PT, Tucci AR, de Oliveira TKF, Rosa ADS, Ferreira VNDS, Lima JNH, Miranda MD, da Costa LJ, da Silva ML, Scotti MT, Allonso D, Leitão GG, Leitão SG. Myrtucommulones and Related Acylphloroglucinols from Myrtaceae as a Promising Source of Multitarget SARS-CoV-2 Cycle Inhibitors. Pharmaceuticals (Basel) 2024; 17:436. [PMID: 38675398 PMCID: PMC11054083 DOI: 10.3390/ph17040436] [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: 03/11/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
The LABEXTRACT plant extract bank, featuring diverse members of the Myrtaceae family from Brazilian hot spot regions, provides a promising avenue for bioprospection. Given the pivotal roles of the Spike protein and 3CLpro and PLpro proteases in SARS-CoV-2 infection, this study delves into the correlations between the Myrtaceae species from the Atlantic Forest and these targets, as well as an antiviral activity through both in vitro and in silico analyses. The results uncovered notable inhibitory effects, with Eugenia prasina and E. mosenii standing out, while E. mosenii proved to be multitarget, presenting inhibition values above 72% in the three targets analyzed. All extracts inhibited viral replication in Calu-3 cells (EC50 was lower than 8.3 µg·mL-1). Chemometric analyses, through LC-MS/MS, encompassing prediction models and molecular networking, identified potential active compounds, such as myrtucommulones, described in the literature for their antiviral activity. Docking analyses showed that one undescribed myrtucommulone (m/z 841 [M - H]-) had a higher fitness score when interacting with the targets of this study, including ACE2, Spike, PLpro and 3CLpro of SARS-CoV-2. Also, the study concludes that Myrtaceae extracts, particularly from E. mosenii and E. prasina, exhibit promising inhibitory effects against crucial stages in SARS-CoV-2 infection. Compounds like myrtucommulones emerge as potential anti-SARS-CoV-2 agents, warranting further exploration.
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Affiliation(s)
- Simony Carvalho Mendonça
- Departamento de Produtos Naturais e Alimentos, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil; (S.C.M.); (B.A.G.); (M.F.C.)
| | - Brendo Araujo Gomes
- Departamento de Produtos Naturais e Alimentos, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil; (S.C.M.); (B.A.G.); (M.F.C.)
- Programa de Pós-Graduação em Biotecnologia Vegetal e Bioprocessos, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
| | - Mariana Freire Campos
- Departamento de Produtos Naturais e Alimentos, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil; (S.C.M.); (B.A.G.); (M.F.C.)
- Programa de Pós-Graduação em Biotecnologia Vegetal e Bioprocessos, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
| | - Thamirys Silva da Fonseca
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil;
| | - Maria Eduarda Alves Esteves
- Programa de Pós-Graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.A.E.); (M.L.d.S.)
| | - Bruce Veiga Andriolo
- Programa de Pós-Graduação em Biotecnologia, Instituto Nacional de Metrologia, Qualidade e Tecnologia, Duque de Caxias 25250-020, RJ, Brazil;
| | - Caio Felipe de Araujo Ribas Cheohen
- Programa de Pós-Graduação Multicêntrico em Ciências Fisiológicas, Centro de Ciências da Saúde, Instituto de Biodiversidade e Sustentabilidade NUPEM, Universidade Federal do Rio de Janeiro, Macaé 27965-045, RJ, Brazil;
| | - Larissa Esteves Carvalho Constant
- Programa de Pós-Graduação em Ciências Biológicas, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, RJ, Brazil; (L.E.C.C.); (S.d.S.C.); (D.A.)
| | - Stephany da Silva Costa
- Programa de Pós-Graduação em Ciências Biológicas, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, RJ, Brazil; (L.E.C.C.); (S.d.S.C.); (D.A.)
| | - Pedro Telles Calil
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, RJ, Brazil; (P.T.C.); (L.J.d.C.)
| | - Amanda Resende Tucci
- Laboratory of Morphology and Viral Morphogenesis, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (T.K.F.d.O.); (A.d.S.R.); (V.N.d.S.F.); (J.N.H.L.); (M.D.M.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Thamara Kelcya Fonseca de Oliveira
- Laboratory of Morphology and Viral Morphogenesis, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (T.K.F.d.O.); (A.d.S.R.); (V.N.d.S.F.); (J.N.H.L.); (M.D.M.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Alice dos Santos Rosa
- Laboratory of Morphology and Viral Morphogenesis, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (T.K.F.d.O.); (A.d.S.R.); (V.N.d.S.F.); (J.N.H.L.); (M.D.M.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Vivian Neuza dos Santos Ferreira
- Laboratory of Morphology and Viral Morphogenesis, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (T.K.F.d.O.); (A.d.S.R.); (V.N.d.S.F.); (J.N.H.L.); (M.D.M.)
| | - Julia Nilo Henrique Lima
- Laboratory of Morphology and Viral Morphogenesis, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (T.K.F.d.O.); (A.d.S.R.); (V.N.d.S.F.); (J.N.H.L.); (M.D.M.)
| | - Milene Dias Miranda
- Laboratory of Morphology and Viral Morphogenesis, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (T.K.F.d.O.); (A.d.S.R.); (V.N.d.S.F.); (J.N.H.L.); (M.D.M.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Luciana Jesus da Costa
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, RJ, Brazil; (P.T.C.); (L.J.d.C.)
| | - Manuela Leal da Silva
- Programa de Pós-Graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.A.E.); (M.L.d.S.)
- Programa de Pós-Graduação em Biotecnologia, Instituto Nacional de Metrologia, Qualidade e Tecnologia, Duque de Caxias 25250-020, RJ, Brazil;
- Programa de Pós-Graduação Multicêntrico em Ciências Fisiológicas, Centro de Ciências da Saúde, Instituto de Biodiversidade e Sustentabilidade NUPEM, Universidade Federal do Rio de Janeiro, Macaé 27965-045, RJ, Brazil;
| | - Marcus Tullius Scotti
- Departamento de Química, Universidade Federal da Paraíba, João Pessoa 58033-455, PB, Brazil;
| | - Diego Allonso
- Programa de Pós-Graduação em Ciências Biológicas, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, RJ, Brazil; (L.E.C.C.); (S.d.S.C.); (D.A.)
- Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
| | - Gilda Guimarães Leitão
- Instituto de Pesquisas de Produtos Naturais, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
| | - Suzana Guimarães Leitão
- Departamento de Produtos Naturais e Alimentos, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil; (S.C.M.); (B.A.G.); (M.F.C.)
- Programa de Pós-Graduação em Biotecnologia Vegetal e Bioprocessos, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil;
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49
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Sattasathuchana T, Xu P, Bertoni C, Kim YL, Leang SS, Pham BQ, Gordon MS. The Effective Fragment Molecular Orbital Method: Achieving High Scalability and Accuracy for Large Systems. J Chem Theory Comput 2024; 20:2445-2461. [PMID: 38450638 DOI: 10.1021/acs.jctc.3c01309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
The effective fragment molecular orbital (EFMO) method has been developed to predict the total energy of a very large molecular system accurately (with respect to the underlying quantum mechanical method) and efficiently by taking advantage of the locality of strong chemical interactions and employing a two-level hierarchical parallelism. The accuracy of the EFMO method is partly attributed to the accurate and robust intermolecular interaction prediction between distant fragments, in particular, the many-body polarization and dispersion effects, which require the generation of static and dynamic polarizability tensors by solving the coupled perturbed Hartree-Fock (CPHF) and time-dependent HF (TDHF) equations, respectively. Solving the CPHF and TDHF equations is the main EFMO computational bottleneck due to the inefficient (serial) and I/O-intensive implementation of the CPHF and TDHF solvers. In this work, the efficiency and scalability of the EFMO method are significantly improved with a new CPU memory-based implementation for solving the CPHF and TDHF equations that are parallelized by either message passing interface (MPI) or hybrid MPI/OpenMP. The accuracy of the EFMO method is demonstrated for both covalently bonded systems and noncovalently bound molecular clusters by systematically examining the effects of basis sets and a key distance-related cutoff parameter, Rcut. Rcut determines whether a fragment pair (dimer) is treated by the chosen ab initio method or calculated using the effective fragment potential (EFP) method (separated dimers). Decreasing the value of Rcut increases the number of separated (EFP) dimers, thereby decreasing the computational effort. It is demonstrated that excellent accuracy (<1 kcal/mol error per fragment) can be achieved when using a sufficiently large basis set with diffuse functions coupled with a small Rcut value. With the new parallel implementation, the total EFMO wall time is substantially reduced, especially with a high number of MPI ranks. Given a sufficient workload, nearly ideal strong scaling is achieved for the CPHF and TDHF parts of the calculation. For the first time, EFMO calculations with the inclusion of long-range polarization and dispersion interactions on a hydrated mesoporous silica nanoparticle with explicit water solvent molecules (more than 15k atoms) are achieved on a massively parallel supercomputer using nearly 1000 physical nodes. In addition, EFMO calculations on the carbinolamine formation step of an amine-catalyzed aldol reaction at the nanoscale with explicit solvent effects are presented.
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Affiliation(s)
- Tosaporn Sattasathuchana
- Department of Chemistry, Iowa State University and Ames National Laboratory, Ames, Iowa 50011, United States
| | - Peng Xu
- Department of Chemistry, Iowa State University and Ames National Laboratory, Ames, Iowa 50011, United States
| | - Colleen Bertoni
- Argonne Leadership Computing Facility, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Yu Lim Kim
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Sarom S Leang
- EP Analytics, Inc., 9909 Mira Mesa Blvd Ste. 230, San Diego, California 92131, United States
| | - Buu Q Pham
- Department of Chemistry, Iowa State University and Ames National Laboratory, Ames, Iowa 50011, United States
| | - Mark S Gordon
- Department of Chemistry, Iowa State University and Ames National Laboratory, Ames, Iowa 50011, United States
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50
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Rana M, Ghosh A. Full Dynamical and Ab Initio Investigation of the Electron Transfer-Mediated Decay Mechanism of He + in the Presence of Heavier Alkali Dimers. J Phys Chem A 2024; 128:1973-1983. [PMID: 38447163 DOI: 10.1021/acs.jpca.3c07115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
We have studied the electron transfer-mediated decay (ETMD) process for the 1s ionized state of the He atom in the presence of a heavier alkali homonuclear dimer (Na2, K2, and Rb2) as well as heteronuclear dimer (LiNa, NaK, and KRb). In our computation, we have considered all the alkali dimers being in the singlet electronic ground state. The electron transfer from the alkali dimer to He (1s-1) leads to the emission of another electron from the alkali dimer into the continuum. We have investigated the impact of the distance of the He atom from the center of mass of the alkali dimer on the ETMD decay width. We also performed the Born-Oppenheimer molecular dynamics simulation to understand the impact of nuclear dynamics on the ETMD process.
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Affiliation(s)
- Meenakshi Rana
- Department of Chemistry, Ashoka University, Sonipat, Haryana 131029, India
| | - Aryya Ghosh
- Department of Chemistry, Ashoka University, Sonipat, Haryana 131029, India
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