51
|
Zhang ZP, Wang SH, Shang YL, Liu JH, Luo SN. Theoretical Study on Ethylamine Dissociation Reactions Using VRC-VTST and SS-QRRK Methods. J Phys Chem A 2024; 128:2191-2199. [PMID: 38456900 DOI: 10.1021/acs.jpca.3c08373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
Barrierless bond dissociation reactions play an important role in fuel combustion. In this work, the pressure-dependent dissociation rate constants of ethylamine (EA) are accurately determined using variable-reaction-coordinate variational transition-state theory combined with the system-specific quantum Rice-Ramsperger-Kassel method. Before the kinetics calculations, the performances of four density functional theory methods in describing the bond dissociation of EA are evaluated against the benchmark method, FIC-MRCISD(T)+Q/cc-pVTZ, and the MN15-L/cc-pVTZ method is the best choice. By comparison of the Gibbs free energies and the rate constants for the bond dissociation reactions of EA, ethanol, and propane, the influence of functional groups on the reaction kinetics is discussed. The kinetics calculations show that the dissociation rate constants of EA are sensitive to pressure at low pressures and high temperatures, and the dominant channel is the reaction that yields C2H5 and NH2 radicals. A literature combustion model of EA is updated with our calculations, and the satisfactory agreement between the model predictions and reported ignition delay times of EA suggests the reliability of our calculations.
Collapse
Affiliation(s)
- Z P Zhang
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu, Sichuan 610031, P. R. China
- Dynamic Materials Data Science Center, Southwest Jiaotong University, Chengdu, Sichuan 610031, P. R. China
| | - S H Wang
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu, Sichuan 610031, P. R. China
- Dynamic Materials Data Science Center, Southwest Jiaotong University, Chengdu, Sichuan 610031, P. R. China
| | - Y L Shang
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu, Sichuan 610031, P. R. China
- Energy Research Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong 250014, P. R. China
- The Peac Institute of Multiscale Sciences, Chengdu, Sichuan 610027, P. R. China
- Dynamic Materials Data Science Center, Southwest Jiaotong University, Chengdu, Sichuan 610031, P. R. China
| | - J H Liu
- Chengdu JiangDe Technology Co., Ltd, Chengdu, Sichuan 610100, P. R. China
| | - S N Luo
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu, Sichuan 610031, P. R. China
- Dynamic Materials Data Science Center, Southwest Jiaotong University, Chengdu, Sichuan 610031, P. R. China
| |
Collapse
|
52
|
Gun'ko VM, Turov VV. Interfacial Phenomena in Nanostructured Systems with Various Materials. Chemphyschem 2024; 25:e202300622. [PMID: 38259051 DOI: 10.1002/cphc.202300622] [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: 08/31/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 01/24/2024]
Abstract
Interfacial phenomena linked to the behavior of bound water, organic solvents (co-sorbates, dispersion media), hydrogen, methane, acids/bases, and salts bound to various silicas, polymers, and carbon materials were analyzed vs. temperature and concentrations using 1 H NMR spectroscopy, differential scanning calorimetry (DSC) and other methods. The material characteristics were studied using microscopy, infrared spectroscopy (IR), small angle X-ray scattering (SAXS), and nitrogen adsorption. Confined space effects (CSE) result in enhanced freezing point depression (FPD) and stronger diminution of solvent activity and colligative properties of liquid mixtures in narrower pores. Short hydrophobic functionalities (≡Si-CH3 , =Si(CH3 )2 ) at a silica surface and the presence of nanopores result in differentiation of bound water into weakly (WAW, δH =0.2-2.0 ppm) and strongly (SAW, δH =4-6 ppm) associated waters of smaller solvent activity in smaller clusters located in narrower pores and unfrozen below a bulk freezing point. These effects are enhanced in hydrophobic dispersion media. Hydrophobic liquids could displace bound water into narrower pores inaccessible for their molecules larger than water and/or into broader pores to reduce contact area between immiscible liquids. The observed phenomena depend on sorbent/sorbate kinds and play an important role on practical applications of various sorbents.
Collapse
Affiliation(s)
- Volodymyr M Gun'ko
- Chuiko Institute of Surface Chemistry of National Academy of Sciences of Ukraine, 17 General Naumov Street, Kyiv, 03164, Ukraine
| | - Volodymyr V Turov
- Chuiko Institute of Surface Chemistry of National Academy of Sciences of Ukraine, 17 General Naumov Street, Kyiv, 03164, Ukraine
| |
Collapse
|
53
|
Cornwell Z, Enders JJ, Harrison AW, Murray C. Temperature-Dependent Kinetics of the Reactions of the Criegee Intermediate CH 2OO with Hydroxyketones. J Phys Chem A 2024; 128:1880-1891. [PMID: 38428028 PMCID: PMC10945482 DOI: 10.1021/acs.jpca.4c00156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 03/03/2024]
Abstract
Though there is a growing body of literature on the kinetics of CIs with simple carbonyls, CI reactions with functionalized carbonyls such as hydroxyketones remain unexplored. In this work, the temperature-dependent kinetics of the reactions of CH2OO with two hydroxyketones, hydroxyacetone (AcOH) and 4-hydroxy-2-butanone (4H2B), have been studied using a laser flash photolysis transient absorption spectroscopy technique and complementary quantum chemistry calculations. Bimolecular rate constants were determined from CH2OO loss rates observed under pseudo-first-order conditions across the temperature range 275-335 K. Arrhenius plots were linear and yielded T-dependent bimolecular rate constants: kAcOH(T) = (4.3 ± 1.7) × 10-15 exp[(1630 ± 120)/T] and k4H2B(T) = (3.5 ± 2.6) × 10-15 exp[(1700 ± 200)/T]. Both reactions show negative temperature dependences and overall very similar rate constants. Stationary points on the reaction energy surfaces were characterized using the composite CBS-QB3 method. Transition states were identified for both 1,3-dipolar cycloaddition reactions across the carbonyl and 1,2-insertion/addition at the hydroxyl group. The free-energy barriers for the latter reaction pathways are higher by ∼4-5 kcal mol-1, and their contributions are presumed to be negligible for both AcOH and 4H2B. The cycloaddition reactions are highly exothermic and form cyclic secondary ozonides that are the typical primary products of Criegee intermediate reactions with carbonyl compounds. The reactivity of the hydroxyketones toward CH2OO appears to be similar to that of acetaldehyde, which can be rationalized by consideration of the energies of the frontier molecular orbitals involved in the cycloaddition. The CH2OO + hydroxyketone reactions are likely too slow to be of significance in the atmosphere, except at very low temperatures.
Collapse
Affiliation(s)
- Zachary
A. Cornwell
- Department
of Chemistry, University of California,
Irvine, Irvine, California 92697, United States
| | - Jonas J. Enders
- Department
of Chemistry, University of California,
Irvine, Irvine, California 92697, United States
| | - Aaron W. Harrison
- Department
of Chemistry, Austin College, Sherman, Texas 75090, United States
| | - Craig Murray
- Department
of Chemistry, University of California,
Irvine, Irvine, California 92697, United States
| |
Collapse
|
54
|
Tolbin AY, Savelyev MS, Vasilevsky PN, Gerasimenko AY. Conditions for the efficiency of optical limiting based on experiment and quantum chemical calculations. Phys Chem Chem Phys 2024; 26:8965-8972. [PMID: 38436498 DOI: 10.1039/d4cp00055b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
The development of suitable protection against laser radiation has proven challenging due to the lack of predictive models. The purpose of this article is to exclude the existing drawback by creating a universal strategy based on correlations between experimental and theoretical data characterizing the nonlinear optical properties of absorbers, for which a series of low-symmetry penta(chloro)cyclotriphosphazene-substituted monophthalocyanines was chosen. To search for correlations on a small series of dyes, we used the advanced algorithm CORRELATO, which has been proven to construct even the most unusual relationships demonstrated in our previous works. Due to the reducing symmetry of molecules, large values of the nonlinear absorption coefficient (more than 3000 cm GW-1) and, as a result, wide dynamic ranges (up to 630) with a high degree of attenuation of nanosecond laser radiation (10-20 times) were achieved. The use of the finite-field DFT method has allowed the calculation of dipole moments, polarizabilities and hyperpolarizabilities. The numerical data obtained during the calculations were used in correlations of theory vs. experiment to derive mathematical expressions (inequalities) to assess the effectiveness of absorbers in limiting the power of laser radiation.
Collapse
Affiliation(s)
- Alexander Yu Tolbin
- FSBIS Institute of Physiologically Active Compounds of the Russian Academy of Sciences, Russian Academy of Sciences, 1, Severny proezd, Chernogolovka, 142432, Moscow Region, Russian Federation.
| | - Mikhail S Savelyev
- National Research University of Electronic Technology Institute of Biomedical Systems, Zelenograd, 124498, Moscow, Russian Federation
- Institute for Bionic Technologies and Engineering, Sechenov University, 2, Bolshaya Pirogovskaya st., Moscow, 119991, Russian Federation
| | - Pavel N Vasilevsky
- National Research University of Electronic Technology Institute of Biomedical Systems, Zelenograd, 124498, Moscow, Russian Federation
| | - Alexander Yu Gerasimenko
- National Research University of Electronic Technology Institute of Biomedical Systems, Zelenograd, 124498, Moscow, Russian Federation
- Institute for Bionic Technologies and Engineering, Sechenov University, 2, Bolshaya Pirogovskaya st., Moscow, 119991, Russian Federation
| |
Collapse
|
55
|
Yoshida Y, Mizukami W, Yoshida N. Solvent Distribution Effects on Quantum Chemical Calculations with Quantum Computers. J Chem Theory Comput 2024; 20:1962-1971. [PMID: 38377035 DOI: 10.1021/acs.jctc.3c01189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
We present a combination of three-dimensional reference interaction site model self-consistent field (3D-RISM-SCF) theory and the variational quantum eigensolver (VQE) to consider the solvent distribution effects within the framework of quantum-classical hybrid computing. The present method, 3D-RISM-VQE, does not include any statistical errors from the solvent configuration sampling owing to the analytical treatment of the statistical solvent distribution. We apply 3D-RISM-VQE to compute the spatial distribution functions of solvent water around a water molecule, the potential and Helmholtz energy curves of NaCl, and to analyze the Helmholtz energy component and related properties of H2O and NH4+. Moreover, we utilize 3D-RISM-VQE to analyze the extent to which solvent effects alter the efficiency of quantum calculations compared with calculations in the gas phase using the L1-norms of molecular electronic Hamiltonians. Our results demonstrate that the efficiency of quantum chemical calculations on a quantum computer in solution is virtually the same as that in the gas phase.
Collapse
Affiliation(s)
- Yuichiro Yoshida
- Center for Quantum Information and Quantum Biology, Osaka University, 1-2 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Wataru Mizukami
- Center for Quantum Information and Quantum Biology, Osaka University, 1-2 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Norio Yoshida
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishiku, Fukuoka 819-0395, Japan
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ward, Nagoya 464-8601, Japan
| |
Collapse
|
56
|
Silva MO, Moreira GM, Rosado J, Blanco F, García G, Bettega MHF, da Costa RF. Elastic and electronically inelastic scattering of electrons by the pyrazine molecule. Phys Chem Chem Phys 2024; 26:7276-7286. [PMID: 37987761 DOI: 10.1039/d3cp04619b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
We report on elastic and electronically inelastic integral and differential cross sections as well as ionization and total cross sections for electron collisions with the pyrazine molecule. The Schwinger multichannel method is applied in calculations carried out according to the minimal orbital basis for single configuration interactions strategy from the 1-channel up to 139-channels close-coupling level of approximation. With these calculations we have obtained integral and differential cross sections as well as excitation functions for elastic electron scattering and, also, integral and differential cross sections for electronic excitation from the ground state to the 3B1u, 3B2u, 3B3u, 1B1u, 1B2u and 1B3u excited states of pyrazine by electron impact. By summing the total ionization cross section obtained by means of the binary-encounter-Bethe model to these elastic and electronically inelastic contributions, we provided an estimate for the total cross section describing the electron-pyrazine interaction process. The independent atom model with the screening-corrected additivity rule plus interference terms method was also used in the present study to determine elastic integral and differential as well as ionization and total cross sections for electron collisions from pyrazine. The present results were, whenever possible, critically compared to the experimental and theoretical data available in the literature. In general, the overall agreement between the present results and the experiment is quite encouraging.
Collapse
Affiliation(s)
- Murilo O Silva
- Departamento de Física, Universidade Federal do Paraná, Caixa Postal 19044, 81531-980 Curitiba, Paraná, Brazil
| | - Giseli M Moreira
- Departamento de Física, Universidade Estadual do Centro-Oeste, 85040-167 Guarapuava, Paraná, Brazil
| | - Jaime Rosado
- Departamento de Estructura de la Materia, Física Térmica y Electrónica e IPARCOS, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Francisco Blanco
- Departamento de Estructura de la Materia, Física Térmica y Electrónica e IPARCOS, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Gustavo García
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
| | - Márcio H F Bettega
- Departamento de Física, Universidade Federal do Paraná, Caixa Postal 19044, 81531-980 Curitiba, Paraná, Brazil
| | - Romarly F da Costa
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, 09210-580 Santo André, São Paulo, Brazil.
| |
Collapse
|
57
|
Vysotskiy VP, Filippi C, Ryde U. Scalar Relativistic All-Electron and Pseudopotential Ab Initio Study of a Minimal Nitrogenase [Fe(SH) 4H] - Model Employing Coupled-Cluster and Auxiliary-Field Quantum Monte Carlo Many-Body Methods. J Phys Chem A 2024; 128:1358-1374. [PMID: 38324717 PMCID: PMC10895656 DOI: 10.1021/acs.jpca.3c05808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 02/09/2024]
Abstract
Nitrogenase is the only enzyme that can cleave the triple bond in N2, making nitrogen available to organisms. The detailed mechanism of this enzyme is currently not known, and computational studies are complicated by the fact that different density functional theory (DFT) methods give very different energetic results for calculations involving nitrogenase models. Recently, we designed a [Fe(SH)4H]- model with the fifth proton binding either to Fe or S to mimic different possible protonation states of the nitrogenase active site. We showed that the energy difference between these two isomers (ΔE) is hard to estimate with quantum-mechanical methods. Based on nonrelativistic single-reference coupled-cluster (CC) calculations, we estimated that the ΔE is 101 kJ/mol. In this study, we demonstrate that scalar relativistic effects play an important role and significantly affect ΔE. Our best revised single-reference CC estimates for ΔE are 85-91 kJ/mol, including energy corrections to account for contributions beyond triples, core-valence correlation, and basis-set incompleteness error. Among coupled-cluster approaches with approximate triples, the canonical CCSD(T) exhibits the largest error for this problem. Complementary to CC, we also used phaseless auxiliary-field quantum Monte Carlo calculations (ph-AFQMC). We show that with a Hartree-Fock (HF) trial wave function, ph-AFQMC reproduces the CC results within 5 ± 1 kJ/mol. With multi-Slater-determinant (MSD) trials, the results are 82-84 ± 2 kJ/mol, indicating that multireference effects may be rather modest. Among the DFT methods tested, τ-HCTH, r2SCAN with 10-13% HF exchange with and without dispersion, and O3LYP/O3LYP-D4, and B3LYP*/B3LYP*-D4 generally perform the best. The r2SCAN12 (with 12% HF exchange) functional mimics both the best reference MSD ph-AFQMC and CC ΔE results within 2 kJ/mol.
Collapse
Affiliation(s)
- Victor P. Vysotskiy
- Department
of Computational Chemistry, Lund University,
Chemical Centre, SE-221 00 Lund, Sweden
| | - Claudia Filippi
- MESA+
Institute for Nanotechnology, University
of Twente, P.O. Box 217, Enschede 7500 AE, Netherlands
| | - Ulf Ryde
- Department
of Computational Chemistry, Lund University,
Chemical Centre, SE-221 00 Lund, Sweden
| |
Collapse
|
58
|
Kaur J, Almujibah H, Alam MM, Singh A, Saxena A, Verma DK, Berdimurodov E. Electrochemical and DFT Studies of the Pistacia Integerrima Gall Extract: An Eco-friendly Approach towards the Corrosion of Steel in Acidic Medium. ACS OMEGA 2024; 9:7643-7657. [PMID: 38405447 PMCID: PMC10882615 DOI: 10.1021/acsomega.3c06824] [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: 09/08/2023] [Revised: 12/30/2023] [Accepted: 01/22/2024] [Indexed: 02/27/2024]
Abstract
A novel application of the Pistacia integerrima gall extract as an environmentally friendly corrosion inhibitor is reported in this study. The major phytochemicals present in the gall extract, namely pistagremic acid, β-sitosterol, pistiphloroglucinyl ether, pistaciaphenyl ester, naringenin, and 5,7-dihydroxy-2-(4-hydroxyphenyl)-2,3-dihydrochromen-4-one, play key roles in its anticorrosive behavior on steel in aggressive media. Several approaches were used to study the corrosion prevention activity of steel in 1 M H2SO4, including weight loss analysis, scanning electron microscopy (SEM), electrochemical impedance spectroscopy (EIS), potentiodynamic polarization (PDP), and density functional theory (DFT). At 2000 mg L-1, the highest efficiency of 92.19% was observed in 1 M H2SO4. An SEM study was conducted to validate the surface coverage of the metal surface. DFT studies revealed several nucleophilic regions present in the phytochemicals of the inhibitor, which supported the favorable nucleophilicity. Corrosion studies have not been performed on this sample. Phytochemicals make it an effective corrosion inhibitor, and its extraction process utilizes distilled water, making it better than other inhibitors. It has been proven that the obtained values of ΔEInhDFT for pistiphloroglucinyl, pistaciaphenyl ether, and naringenin organic compounds were very low, confirming the high reactivity of these corrosion inhibitors. The order of the values of ΔEInhDFT is as follows: pistaciaphenyl ether > pistiphloroglucinyl ether > naringenin organic compound; this suggests that pistaciaphenyl ether is more reactive than the other compounds. In this study, P. integerrima gall extract emerges as a novel and highly effective corrosion resistance agent in 1 M H2SO4, chosen for its relevance to acid pickling and cleaning processes.
Collapse
Affiliation(s)
- Jasdeep Kaur
- Department
of Chemistry, Chandigarh University Mohali, NH-05, Ludhiana - Chandigarh State
Highway, Sahibzada Ajit Singh Nagar, Punjab 140413, India
| | - Hamad Almujibah
- Department
of Civil Engineering, College of Engineering, Taif University, P.O. Box 11099, Taif City 21974, Saudi Arabia
| | - Mohammad Mahtab Alam
- Department
of Basic Medical Sciences, College of Applied Medical Science, King Khalid University, Abha 61421, Saudi Arabia
| | - Abha Singh
- Department
of Basic Sciences, College of Science and Theoretical Studies, Dammam-branch, Saudi Electronic University, Riyadh 11673, Saudi Arabia
| | - Akhil Saxena
- Department
of Chemistry, Chandigarh University Mohali, NH-05, Ludhiana - Chandigarh State
Highway, Sahibzada Ajit Singh Nagar, Punjab 140413, India
| | - Dakeshwar Kumar Verma
- Department
of Chemistry, Government Digvijay Autonomous
Postgraduate College, Rajnandgaon Chhattisgarh, 491441, India
| | - Elyor Berdimurodov
- New Uzbekistan
University, Mustaqillik
ave. 54, Tashkent 100007, Uzbekistan
- Medical
School, Central Asian University, Tashkent 111221, Uzbekistan
- Faculty
of Chemistry, National University of Uzbekistan, Tashkent 100034, Uzbekistan
| |
Collapse
|
59
|
Fedorov DG. Analysis of Site Energies and Excitonic Couplings: The Role of Symmetry and Polarization. J Phys Chem A 2024; 128:1154-1162. [PMID: 38302431 DOI: 10.1021/acs.jpca.3c06293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
An excitonic coupling model is developed based on an equation-of-motion coupled cluster combined with the fragment molecular orbital method. The effects of polarization and excitonic coupling on the splitting of quasi-degenerate levels in systems containing multiple chromophores are elucidated on dimers of formaldehyde, water, formic acid, hydrogen fluoride, and carbon monoxide. It is shown that the level structure is mainly determined by the mutual polarization of chromophores and to a lesser extent by the excitonic coupling. The role of symmetry in excitonic coupling in dimers is discussed. The excitonic coupling between all residues in the photoactive yellow protein (PDB: 2PHY) is analyzed.
Collapse
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
| |
Collapse
|
60
|
Barati F, Hosseini F, Vafaee R, Sabouri Z, Ghadam P, Arab SS, Shadfar N, Piroozmand F. In silico approaches to investigate enzyme immobilization: a comprehensive systematic review. Phys Chem Chem Phys 2024; 26:5744-5761. [PMID: 38294035 DOI: 10.1039/d3cp03989g] [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: 02/01/2024]
Abstract
Enzymes are popular catalysts with many applications, especially in industry. Biocatalyst usage on a large scale is facing some limitations, such as low operational stability, low recyclability, and high enzyme cost. Enzyme immobilization is a beneficial strategy to solve these problems. Bioinformatics tools can often correctly predict immobilization outcomes, resulting in a cost-effective experimental phase with the least time consumed. This study provides an overview of in silico methods predicting immobilization processes via a comprehensive systematic review of published articles till 11 December 2022. It also mentions the strengths and weaknesses of the processes and explains the computational analyses in each method that are required for immobilization assessment. In this regard, Web of Science and Scopus databases were screened to gain relevant publications. After screening the gathered documents (n = 3873), 60 articles were selected for the review. The selected papers have applied in silico procedures including only molecular dynamics (MD) simulations (n = 20), parallel tempering Monte Carlo (PTMC) and MD simulations (n = 3), MD and docking (n = 1), density functional theory (DFT) and MD (n = 1), only docking (n = 11), metal ion binding site prediction (MIB) server and docking (n = 2), docking and DFT (n = 1), docking and analysis of enzyme surfaces (n = 1), only DFT (n = 1), only MIB server (n = 2), analysis of an enzyme structure and surface (n = 12), rational design of immobilized derivatives (RDID) software (n = 3), and dissipative particle dynamics (DPD; n = 2). In most included studies (n = 51), enzyme immobilization was investigated experimentally in addition to in silico evaluation.
Collapse
Affiliation(s)
- Farzaneh Barati
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Fakhrisadat Hosseini
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Rayeheh Vafaee
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Zahra Sabouri
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran
| | - Parinaz Ghadam
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Najmeh Shadfar
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Firoozeh Piroozmand
- Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| |
Collapse
|
61
|
Imamura K, Yokogawa D, Sato H. Recent developments and applications of reference interaction site model self-consistent field with constrained spatial electron density (RISM-SCF-cSED): A hybrid model of quantum chemistry and integral equation theory of molecular liquids. J Chem Phys 2024; 160:050901. [PMID: 38341702 DOI: 10.1063/5.0190116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/04/2024] [Indexed: 02/13/2024] Open
Abstract
The significance of solvent effects in electronic structure calculations has long been noted, and various methods have been developed to consider this effect. The reference interaction site model self-consistent field with constrained spatial electron density (RISM-SCF-cSED) is a hybrid model that combines the integral equation theory of molecular liquids with quantum chemistry. This method can consider the statistically convergent solvent distribution at a significantly lower cost than molecular dynamics simulations. Because the RISM theory explicitly considers the solvent structure, it performs well for systems where hydrogen bonds are formed between the solute and solvent molecules, which is a challenge for continuum solvent models. Taking advantage of being founded on the variational principle, theoretical developments have been made in calculating various properties and incorporating electron correlation effects. In this review, we organize the theoretical aspects of RISM-SCF-cSED and its distinctions from other hybrid methods involving integral equation theories. Furthermore, we carefully present its progress in terms of theoretical developments and recent applications.
Collapse
Affiliation(s)
- Kosuke Imamura
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Daisuke Yokogawa
- Graduate School of Arts and Science, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| |
Collapse
|
62
|
Hegedüsová L, Blaise N, Pašteka LF, Budzák Š, Medveď M, Filo J, Mravec B, Slavov C, Wachtveitl J, Grabarz AM, Cigáň M. Enhancing the Potential of Fused Heterocycle-Based Triarylhydrazone Photoswitches. Chemistry 2024; 30:e202303509. [PMID: 38212244 DOI: 10.1002/chem.202303509] [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: 10/24/2023] [Indexed: 01/13/2024]
Abstract
Triarylhydrazones represent an attractive class of photochromic compounds offering many interesting features including high molar absorptivity, good addressability, and extraordinary thermal stability. In addition, unlike most other hydrazone-based photoswitches, they effectively absorb light above 365 nm. However, previously prepared triaryhydrazones suffer from low quantum yields of the Z→E photoisomerization. Here, we have designed a new subclass of naphthoyl-benzothiazole hydrazones that balance the most beneficial features of previously reported naphthoyl-quinoline and benzoyl-pyridine triarylhydrazones. These preserve the attractive absorption characteristics, exhibit higher thermal stability of the metastable form than the former and enhance the rate of the Z→E photoisomerization compared to the later, as a result of the weakening of the intramolecular hydrogen bonding between the hydrazone hydrogen and the benzothiazole moiety. Introducing the benzothiazole motif extends the tunability of the photochromic behaviour of hydrazone-based switches.
Collapse
Affiliation(s)
- Lea Hegedüsová
- Department of Organic Chemistry, Faculty of Natural Sciences, Comenius University, Bratislava, 84215, Slovakia
| | - Nadine Blaise
- Institute of Physical and Theoretical Chemistry, Faculty of Biochemistry, Chemistry, Pharmacy, Goethe University, Frankfurt am Main, 60438, Germany
| | - Lukáš F Pašteka
- Van Swinderen Institute for Particle Physics and Gravity, University of Groningen, Groningen, 9747AG, The Netherlands
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Bratislava, 84215, Slovakia
| | - Šimon Budzák
- Department of Chemistry, Faculty of Natural Sciences, Matej Bel University, Banská Bystrica, 97400, Slovakia
| | - Miroslav Medveď
- Department of Chemistry, Faculty of Natural Sciences, Matej Bel University, Banská Bystrica, 97400, Slovakia
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, 77900, Czechia
| | - Juraj Filo
- Department of Organic Chemistry, Faculty of Natural Sciences, Comenius University, Bratislava, 84215, Slovakia
| | - Bernard Mravec
- Department of Organic Chemistry, Faculty of Natural Sciences, Comenius University, Bratislava, 84215, Slovakia
| | - Chavdar Slavov
- Department of Chemistry, University of South Florida, Tampa, FL 33620, Florida, US
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Faculty of Biochemistry, Chemistry, Pharmacy, Goethe University, Frankfurt am Main, 60438, Germany
| | - Anna M Grabarz
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Bratislava, 84215, Slovakia
- Institute of Advanced Materials, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, 50370, Poland
| | - Marek Cigáň
- Department of Organic Chemistry, Faculty of Natural Sciences, Comenius University, Bratislava, 84215, Slovakia
| |
Collapse
|
63
|
Barends TRM, Gorel A, Bhattacharyya S, Schirò G, Bacellar C, Cirelli C, Colletier JP, Foucar L, Grünbein ML, Hartmann E, Hilpert M, Holton JM, Johnson PJM, Kloos M, Knopp G, Marekha B, Nass K, Nass Kovacs G, Ozerov D, Stricker M, Weik M, Doak RB, Shoeman RL, Milne CJ, Huix-Rotllant M, Cammarata M, Schlichting I. Influence of pump laser fluence on ultrafast myoglobin structural dynamics. Nature 2024; 626:905-911. [PMID: 38355794 PMCID: PMC10881388 DOI: 10.1038/s41586-024-07032-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/04/2024] [Indexed: 02/16/2024]
Abstract
High-intensity femtosecond pulses from an X-ray free-electron laser enable pump-probe experiments for the investigation of electronic and nuclear changes during light-induced reactions. On timescales ranging from femtoseconds to milliseconds and for a variety of biological systems, time-resolved serial femtosecond crystallography (TR-SFX) has provided detailed structural data for light-induced isomerization, breakage or formation of chemical bonds and electron transfer1,2. However, all ultrafast TR-SFX studies to date have employed such high pump laser energies that nominally several photons were absorbed per chromophore3-17. As multiphoton absorption may force the protein response into non-physiological pathways, it is of great concern18,19 whether this experimental approach20 allows valid conclusions to be drawn vis-à-vis biologically relevant single-photon-induced reactions18,19. Here we describe ultrafast pump-probe SFX experiments on the photodissociation of carboxymyoglobin, showing that different pump laser fluences yield markedly different results. In particular, the dynamics of structural changes and observed indicators of the mechanistically important coherent oscillations of the Fe-CO bond distance (predicted by recent quantum wavepacket dynamics21) are seen to depend strongly on pump laser energy, in line with quantum chemical analysis. Our results confirm both the feasibility and necessity of performing ultrafast TR-SFX pump-probe experiments in the linear photoexcitation regime. We consider this to be a starting point for reassessing both the design and the interpretation of ultrafast TR-SFX pump-probe experiments20 such that mechanistically relevant insight emerges.
Collapse
Affiliation(s)
| | - Alexander Gorel
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | | | - Giorgio Schirò
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | | | | | | | - Lutz Foucar
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | | | | | - Mario Hilpert
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | - James M Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | | | | | - Bogdan Marekha
- ENSL, CNRS, Laboratoire de Chimie UMR 5182, Lyon, France
| | - Karol Nass
- Paul Scherrer Institute, Villigen, Switzerland
| | | | | | | | - Martin Weik
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - R Bruce Doak
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | | | | | | | | | | |
Collapse
|
64
|
Fukumoto Y, Kyono R, Shibukawa Y, Tanaka YK, Suzuki N, Ogra Y. Differential molecular mechanisms of substrate recognition by selenium methyltransferases, INMT and TPMT, in selenium detoxification and excretion. J Biol Chem 2024; 300:105599. [PMID: 38159853 PMCID: PMC10844679 DOI: 10.1016/j.jbc.2023.105599] [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: 09/15/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024] Open
Abstract
It is known that the recommended dietary allowance of selenium (Se) is dangerously close to its tolerable upper intake level. Se is detoxified and excreted in urine as trimethylselenonium ion (TMSe) when the amount ingested exceeds the nutritional level. Recently, we demonstrated that the production of TMSe requires two methyltransferases: thiopurine S-methyltransferase (TPMT) and indolethylamine N-methyltransferase (INMT). In this study, we investigated the substrate recognition mechanisms of INMT and TPMT in the Se-methylation reaction. Examination of the Se-methyltransferase activities of two paralogs of INMT, namely, nicotinamide N-methyltransferase and phenylethanolamine N-methyltransferase, revealed that only INMT exhibited Se-methyltransferase activity. Consistently, molecular dynamics simulations demonstrated that dimethylselenide was preferentially associated with the active center of INMT. Using the fragment molecular orbital method, we identified hydrophobic residues involved in the binding of dimethylselenide to the active center of INMT. The INMT-L164R mutation resulted in a deficiency in Se- and N-methyltransferase activities. Similarly, TPMT-R152, which occupies the same position as INMT-L164, played a crucial role in the Se-methyltransferase activity of TPMT. Our findings suggest that TPMT recognizes negatively charged substrates, whereas INMT recognizes electrically neutral substrates in the hydrophobic active center embedded within the protein. These observations explain the sequential requirement of the two methyltransferases in producing TMSe.
Collapse
Affiliation(s)
- Yasunori Fukumoto
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan.
| | - Rin Kyono
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Yuka Shibukawa
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Yu-Ki Tanaka
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Noriyuki Suzuki
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Yasumitsu Ogra
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| |
Collapse
|
65
|
Slipchenko LV. Detangling Solvatochromic Effects by the Effective Fragment Potential Method. J Phys Chem A 2024; 128:656-669. [PMID: 38193780 DOI: 10.1021/acs.jpca.3c06194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Understanding molecular interactions in complex systems opens avenues for the efficient design of new materials with target properties. Energy decomposition methods provide a means to obtain a detailed picture of intermolecular interactions. This work introduces a molecular modeling approach for decomposing the solvatochromic shifts of the electronic excited states into the contributions of the individual molecular fragments of the environment surrounding the chromophore. The developed approach is implemented for the QM/EFP (quantum mechanics/effective fragment potential) model that provides a rigorous first-principles-based description of the electronic states of the chromophores in complex polarizable environments. On the example of two model systems, water pentamer and hydrated uracil, we show how the decomposition of the solvatochromic shifts into the contributions of individual solvent water molecules provides a detailed picture of the intermolecular interactions in the ground and excited states of these systems. The analysis also demonstrates the nonadditivity of solute-solvent interactions and the significant contribution of solute polarization to the total values of solvatochromic shifts.
Collapse
Affiliation(s)
- Lyudmila V Slipchenko
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47906, United States
| |
Collapse
|
66
|
Ren X, Zou J, Zhang H, Li W, Li S. Block-Correlated Coupled Cluster Theory with up to Four-Pair Correlation for Accurate Static Correlation of Strongly Correlated Systems. J Phys Chem Lett 2024; 15:693-700. [PMID: 38207241 DOI: 10.1021/acs.jpclett.3c03373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
A block-correlated coupled cluster method with up to four-pair correlation based on the generalized valence bond wave function (GVB-BCCC4) is first implemented, which offers an alternative method for electronic structure calculations of strongly correlated systems. We developed some techniques to derive a set of compact and cost-effective equations for GVB-BCCC4, which include the definition of n-block (n = 1-4) Hamiltonian matrices, the combination of excitation operators, and the definition of independent amplitudes. We then applied the GVB-BCCC4 method to investigate several potential energy surfaces of strongly correlated systems with singlet ground states. Our calculations demonstrate that the GVB-BCCC4 method can provide nearly exact static correlation energies as the density matrix renormalization group method (on the basis of the same GVB orbitals). This work highlights the significance of four-pair correlation in quantitative descriptions of static correlation energy for strongly correlated systems.
Collapse
Affiliation(s)
- Xiaochuan Ren
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, People's Republic of China
| | - Jingxiang Zou
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, People's Republic of China
| | - Haodong Zhang
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, People's Republic of China
| | - Wei Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, People's Republic of China
| | - Shuhua Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, People's Republic of China
| |
Collapse
|
67
|
Takashima C, Nakai H. Range Separation Method for Density Functional Theory Based on Two-Electron Infinite-Order Two-Component Hamiltonian. J Chem Theory Comput 2024; 20:738-751. [PMID: 38193820 DOI: 10.1021/acs.jctc.3c01102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
The range separation method for density functional theory (DFT) was extended to a two-component relativistic theory based on the unitary transformation of one- and two-electron operators and a density operator. In the framework of the spin-free infinite-order two-component Hamiltonian, we implemented several types of two-electron integrals of range-separated two-electron interactions arising from the unitary transformation. Numerical assessments were performed using long-range-corrected (LC)-DFT, which utilizes the range separation of an exchange functional. The present method successfully reproduced the reference values obtained by the four-component LC-DFT calculations when the whole unitary transformations of one-electron, full-range, and range-separated two-electron operators and a density operator were considered. An efficient scheme for the unitary transformation, which is termed the local unitary transformation (LUT), was also applied to the range-separated two-electron term and other operators. The LUT method reduced the computational costs of the LC-DFT calculations significantly without any loss of accuracy.
Collapse
Affiliation(s)
- Chinami Takashima
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| |
Collapse
|
68
|
Abdeen O, Ismael M, Abdou A. Boiling, critical, and freezing temperatures in light of molecular descriptors: correlation and causation. Phys Chem Chem Phys 2024; 26:2426-2439. [PMID: 38168700 DOI: 10.1039/d3cp04788a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
In the pursuit of tracking some physicochemical properties of fluids down to the molecular level, ab initio molecular surface analyses were performed on 169 molecules. This included electrostatic potential (EP), average local ionization energy (ALIE), and electron localization function (ELF) mapped onto an electron density isosurface value of 0.001 au. Using stepwise linear regression (SLR) analysis, it was found that besides the well-studied EP, ALIE and ELF played important roles in determining the normal boiling and freezing points and critical temperatures of fluids. Apparently, the ALIE and ELF were relevant to the attractive polarization forces and repulsive Pauli forces, respectively, between molecules. To further demonstrate and rationalize this assumption, a localized molecular orbital energy decomposition analysis (LMO-EDA) was carried out. In the LMO-EDA analysis, the complexes of the helium atom, He, and ClCl, ClBr, ClI, OCO, OCS, OCSe, and CO/OC molecules were investigated, where the helium atom faced different molecular sites in each molecule. Fortunately, the results showed that lower the ALIE value on a molecular site, the stronger (i.e., more attractive) the polarization interaction energy. The results also indicated that higher the ELF value on a molecular site, the stronger (i.e., more repulsive) the Pauli interaction. The work is aimed to present novel molecular-based rationales to physical chemists, chemical engineers, and materials scientists.
Collapse
Affiliation(s)
- Ossama Abdeen
- Chemistry Department, Faculty of Science, Sohag University, Sohag, 82524, Egypt.
| | - Mohamed Ismael
- Chemistry Department, Faculty of Science, Sohag University, Sohag, 82524, Egypt.
| | - Aly Abdou
- Chemistry Department, Faculty of Science, Sohag University, Sohag, 82524, Egypt.
| |
Collapse
|
69
|
Xu P, Leonard SL, O'Brien W, Gordon MS. R -8 Dispersion Interaction: Derivation and Application to the Effective Fragment Potential Method. J Phys Chem A 2024; 128:292-327. [PMID: 38150458 DOI: 10.1021/acs.jpca.3c05115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
The anisotropic and isotropic R-8 dispersion contributions (disp8) are derived and implemented within the framework of the effective fragment potential (EFP) method formulated with imaginary frequency-dependent Cartesian polarizability tensors distributed at the centroids of the localized molecular orbitals (LMOs). Two forms of damping functions, intermolecular overlap-based and Tang-Toennies, are extended for disp8. To obtain LMO polarizability tensors centered at LMO centroids, an origin-shifting transformation is derived and implemented for the dipole-octopole polarizability tensor and the quadrupole-quadrupole polarizability tensor. The analytic gradient is derived and implemented for the isotropic disp8 contribution. Relative to the previously implemented empirical EFP disp8 energy, the isotropic disp8 component of the interaction energy improves the overall agreement of the EFP dispersion energies with the symmetry-adapted perturbation theory (SAPT) benchmarks, reducing the mean absolute errors (MAEs) and mean absolute percentage errors for most of the databases examined in this work. While the anisotropic disp8 can further enhance the accuracy of the EFP dispersion energy and yield smaller MAEs, significantly overbound dispersion energies are predicted by the anisotropic disp8 when the maximum element in the intermolecular overlap matrix is greater than 0.1, possibly due to the breakdown of the approximations made in the EFP dispersion derivation at a short range. For potential energy scan databases, the newly developed EFP dispersion model with isotropic disp8 yields the overall correct curvature and good agreement with SAPT benchmarks around equilibrium and longer but overestimates the dispersion interactions at a short range. While the overlap-based dispersion-damping functions produce better MAEs than Tang-Toennies damping functions, further improvement is needed to better screen the large attractive dispersion energies at a short range (overlap >0.1).
Collapse
Affiliation(s)
- Peng Xu
- Department of Chemistry, Iowa State University and Ames National Laboratory, Ames, Iowa 50014, United States
| | - Samuel L Leonard
- Department of Chemistry, Iowa State University and Ames National Laboratory, Ames, Iowa 50014, United States
| | - William O'Brien
- Science Undergraduate Research Internship (SULI): Department of Energy, Ames National Laboratory, Iowa State University, Ames, Iowa50011-3020, United States
| | - Mark S Gordon
- Department of Chemistry, Iowa State University and Ames National Laboratory, Ames, Iowa 50014, United States
| |
Collapse
|
70
|
Afify ND, Sweatman MB. Solvent-mediated modification of thermodynamics and kinetics of monoethanolamine regeneration reaction in amine-stripping carbon capture: Computational chemistry study. J Chem Phys 2024; 160:014501. [PMID: 38165096 DOI: 10.1063/5.0169382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/22/2023] [Indexed: 01/03/2024] Open
Abstract
A major limitation of amine-based post-combustion carbon capture technology is the necessity to regenerate amines at high temperatures, which dramatically increases operating costs. This paper concludes the effect of solvent choice as a possible route to modify the thermodynamics and kinetics characterizing the involved amine regeneration reactions and discusses whether these modifications can be economically beneficial. We report experimentally benchmarked computational chemistry calculations of monoethanolamine regeneration reactions employing aqueous and non-aqueous solvents with a wide range of dielectric constants. Unlike previous studies, our improved computational chemistry framework could accurately reproduce the right experimental activation energy of zwitterion formation. From the thermodynamics and kinetics of the predicted reactions, the use of non-aqueous solvents with small dielectric constants led to reductions in regeneration Gibbs free energies, activation barriers, and enthalpy changes. This can reduce energy consumption and give an opportunity to run desorption columns at relatively lower temperatures, thus offering the possibility of relying on low-grade waste heat as an energy input.
Collapse
Affiliation(s)
- N D Afify
- Institute for Materials and Processes, School of Engineering, The University of Edinburgh, Edinburgh EH9 3FB, United Kingdom
| | - M B Sweatman
- Institute for Materials and Processes, School of Engineering, The University of Edinburgh, Edinburgh EH9 3FB, United Kingdom
| |
Collapse
|
71
|
Stepin EA, Sushko ES, Vnukova NG, Churilov GN, Rogova AV, Tomilin FN, Kudryasheva NS. Effects of Endohedral Gd-Containing Fullerenols with a Different Number of Oxygen Substituents on Bacterial Bioluminescence. Int J Mol Sci 2024; 25:708. [PMID: 38255785 PMCID: PMC10815327 DOI: 10.3390/ijms25020708] [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: 11/09/2023] [Revised: 12/28/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
Gadolinium (Gd)-containing fullerenols are perspective agents for magnetic resonance imaging and cancer research. They combine the unique paramagnetic properties of Gd with solubility in water, low toxicity and antiradical activity of fullerenols. We compared the bioeffects of two Gd-containing fullerenols with a different number of oxygen groups-20 and 42: Gd@C82O20H14 and Gd@C82O42H32. The bioluminescent bacteria-based assay was applied to monitor the toxicity of fullerenols, bioluminescence was applied as a signal physiological parameter, and bacterial enzyme-based assay was used to evaluate the fullerenol effects on enzymatic intracellular processes. Chemiluminescence luminol assay was applied to monitor the content of reactive oxygen species (ROS) in bacterial and enzymatic media. It was shown that Gd@C82O42H32 and Gd@C82O20H14 inhibited bacterial bioluminescence at >10-1 and >10-2 gL-1, respectively, revealing a lower toxicity of Gd@C82O42H32. Low-concentration (10-3-10-1 gL-1) bacterial bioluminescence activation by Gd@C82O42H32 was observed, while this activation was not found under exposure to Gd@C82O20H14. Additional carboxyl groups in the structure of Gd@C82O42H32 were determined by infrared spectroscopy and confirmed by quantum chemical calculations. The groups were supposed to endow Gd@C82O42H32 with higher penetration ability through the cellular membrane, activation ability, lower toxicity, balancing of the ROS content in the bacterial suspensions, and lower aggregation in aqueous media.
Collapse
Affiliation(s)
- Evsei A. Stepin
- Biophysics Department, School of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia; (E.A.S.); (E.S.S.)
| | - Ekaterina S. Sushko
- Biophysics Department, School of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia; (E.A.S.); (E.S.S.)
- Institute of Biophysics SB RAS, FRC KSC SB RAS, 660036 Krasnoyarsk, Russia
- Institute of Physics SB RAS, FRC KSC SB RAS, 660036 Krasnoyarsk, Russia; (N.G.V.); (G.N.C.); (F.N.T.)
| | - Natalia G. Vnukova
- Institute of Physics SB RAS, FRC KSC SB RAS, 660036 Krasnoyarsk, Russia; (N.G.V.); (G.N.C.); (F.N.T.)
- Department of Solid State Physics and Nanotechnology, School of Engineering Physics and Radioelectronics, Siberian Federal University, 660074 Krasnoyarsk, Russia
| | - Grigoriy N. Churilov
- Institute of Physics SB RAS, FRC KSC SB RAS, 660036 Krasnoyarsk, Russia; (N.G.V.); (G.N.C.); (F.N.T.)
- Department of Solid State Physics and Nanotechnology, School of Engineering Physics and Radioelectronics, Siberian Federal University, 660074 Krasnoyarsk, Russia
| | - Anastasia V. Rogova
- Department of Physical and Inorganic Chemistry, School of Non-Ferrous Metals and Materials Science, Siberian Federal University, 660025 Krasnoyarsk, Russia;
- Laboratory for Digital Controlled Drugs and Theranostics, FRC KSC SB RAS, 660036 Krasnoyarsk, Russia
| | - Felix N. Tomilin
- Institute of Physics SB RAS, FRC KSC SB RAS, 660036 Krasnoyarsk, Russia; (N.G.V.); (G.N.C.); (F.N.T.)
- Department of Physical and Inorganic Chemistry, School of Non-Ferrous Metals and Materials Science, Siberian Federal University, 660025 Krasnoyarsk, Russia;
- Laboratory for Digital Controlled Drugs and Theranostics, FRC KSC SB RAS, 660036 Krasnoyarsk, Russia
| | - Nadezhda S. Kudryasheva
- Biophysics Department, School of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia; (E.A.S.); (E.S.S.)
- Institute of Biophysics SB RAS, FRC KSC SB RAS, 660036 Krasnoyarsk, Russia
| |
Collapse
|
72
|
Sun Q, Biswas A, Lyumkis D, Levy R, Deng N. Elucidating the Molecular Determinants of the Binding Modes of a Third-Generation HIV-1 Integrase Strand Transfer Inhibitor: The Importance of Side Chain and Solvent Reorganization. Viruses 2024; 16:76. [PMID: 38257776 PMCID: PMC11154245 DOI: 10.3390/v16010076] [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: 11/25/2023] [Revised: 12/21/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
The first- and second-generation clinically used HIV-1 integrase (IN) strand transfer inhibitors (INSTIs) are key components of antiretroviral therapy (ART), which work by blocking the integration step in the HIV-1 replication cycle that is catalyzed by a nucleoprotein assembly called an intasome. However, resistance to even the latest clinically used INSTIs is beginning to emerge. Developmental third-generation INSTIs, based on naphthyridine scaffolds, are promising candidates to combat drug-resistant viral variants. Among these novel INSTIs, compound 4f exhibits two distinct conformations when binding with intasomes from HIV-1 and the closely related prototype foamy virus (PFV) despite the high structural similarity of their INSTI binding pockets. The molecular mechanism and the key active site residues responsible for these differing binding modes in closely related intasomes remain elusive. To unravel the molecular determinants governing the two distinct binding modes, we applied a novel molecular dynamics-based free energy method that utilizes alchemical pathways to overcome the sampling challenges associated with transitioning between the two bound conformations of ligand 4f within the crowded environments of the INSTI binding pockets in these intasomes. The calculated conformational free energies successfully recapitulate the experimentally observed binding mode preferences in the two viral intasomes. Analysis of the simulated structures suggests that the observed binding mode preferences are caused by amino acid residue differences in both the front and the central catalytic sub-pocket of the INSTI binding site in HIV-1 and PFV. Additional free energy calculations on mutants of HIV-1 and PFV revealed that while both sub-pockets contribute to binding mode selection, the central sub-pocket plays a more important role. These results highlight the importance of both side chain and solvent reorganization, as well as the conformational entropy in determining the ligand binding mode, and will help inform the development of more effective INSTIs for combatting drug-resistant viral variants.
Collapse
Affiliation(s)
- Qinfang Sun
- Center for Biophysics and Computational Biology and Department of Chemistry, Temple University, Philadelphia, PA 19122, USA; (Q.S.); (R.L.)
| | - Avik Biswas
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; (A.B.); (D.L.)
- Department of Physics, University of California San Diego, La Jolla, CA 92093, USA
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; (A.B.); (D.L.)
- Graduate Schools for Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Ronald Levy
- Center for Biophysics and Computational Biology and Department of Chemistry, Temple University, Philadelphia, PA 19122, USA; (Q.S.); (R.L.)
| | - Nanjie Deng
- Department of Chemistry and Physical Sciences, Pace University, New York, NY 10038, USA
| |
Collapse
|
73
|
Nakamura T, Dangi BB, Wu L, Zhang Y, Schoendorff G, Gordon MS, Yang DS. Spin-orbit coupling of electrons on separate lanthanide atoms of Pr2O2 and its singly charged cation. J Chem Phys 2023; 159:244303. [PMID: 38131482 DOI: 10.1063/5.0185579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
Although it plays a critical role in the photophysics and catalysis of lanthanides, spin-orbit coupling of electrons on individual lanthanide atoms in small clusters is not well understood. The major objective of this work is to probe such coupling of the praseodymium (Pr) 4f and 6s electrons in Pr2O2 and Pr2O2+. The approach combines mass-analyzed threshold ionization spectroscopy and spin-orbit multiconfiguration second-order quasi-degenerate perturbation theory. The energies of six ionization transitions are precisely measured; the adiabatic ionization energy of the neutral cluster is 38 045 (5) cm-1. Most of the electronic states involved in these transitions are identified as spin-orbit coupled states consisting of two or more electron spins. The electron configurations of these states are 4f46s2 for the neutral cluster and 4f46s for the singly charged cation, both in planar rhombus-type structures. The spin-orbit splitting due to the coupling of the electrons on the separate Pr atoms is on the order of hundreds of wavenumbers.
Collapse
Affiliation(s)
- Taiji Nakamura
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011-3111, USA
- Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Beni B Dangi
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
| | - Lu Wu
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
| | - Yuchen Zhang
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
| | - George Schoendorff
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011-3111, USA
- Propellants Branch, Rocket Propulsion Division, Aerospace Systems Directorate, Air Force Research Laboratory, AFRL/RQRP, Edwards Air Force Base, California 93524, USA
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011-3111, USA
| | - Dong-Sheng Yang
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
| |
Collapse
|
74
|
Costa GJ, Egbemhenghe A, Liang R. Computational Characterization of the Reactivity of Compound I in Unspecific Peroxygenases. J Phys Chem B 2023; 127:10987-10999. [PMID: 38096487 DOI: 10.1021/acs.jpcb.3c06311] [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: 12/29/2023]
Abstract
Unspecific peroxygenases (UPOs) are emerging as promising biocatalysts for selective oxyfunctionalization of unactivated C-H bonds. However, their potential in large-scale synthesis is currently constrained by suboptimal chemical selectivity. Improving the selectivity of UPOs requires a deep understanding of the molecular basis of their catalysis. Recent molecular simulations have sought to unravel UPO's selectivity and inform their design principles. However, most of these studies focused on substrate-binding poses. Few researchers have investigated how the reactivity of CpdI, the principal oxidizing intermediate in the catalytic cycle, influences selectivity in a realistic protein environment. Moreover, the influence of protein electrostatics on the reaction kinetics of CpdI has also been largely overlooked. To bridge this gap, we used multiscale simulations to interpret the regio- and enantioselective hydroxylation of the n-heptane substrate catalyzed by Agrocybe aegerita UPO (AaeUPO). We comprehensively characterized the energetics and kinetics of the hydrogen atom-transfer (HAT) step, initiated by CpdI, and the subsequent oxygen rebound step forming the product. Notably, our approach involved both free energy and potential energy evaluations in a quantum mechanics/molecular mechanics (QM/MM) setting, mitigating the dependence of results on the choice of initial conditions. These calculations illuminate the thermodynamics and kinetics of the HAT and oxygen rebound steps. Our findings highlight that both the conformational selection and the distinct chemical reactivity of different substrate hydrogen atoms together dictate the regio- and enantio-selectivity. Building on our previous study of CpdI's formation in AaeUPO, our results indicate that the HAT step is the rate-limiting step in the overall catalytic cycle. The subsequent oxygen rebound step is swift and retains the selectivity determined by the HAT step. We also pinpointed several polar and charged amino acid residues whose electrostatic potentials considerably influence the reaction barrier of the HAT step. Notably, the Glu196 residue is pivotal for both the CpdI's formation and participation in the HAT step. Our research offers in-depth insights into the catalytic cycle of AaeUPO, which will be instrumental in the rational design of UPOs with enhanced properties.
Collapse
Affiliation(s)
- Gustavo J Costa
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Abel Egbemhenghe
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Ruibin Liang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| |
Collapse
|
75
|
Urbina AS, Slipchenko LV, Ben-Amotz D. Quantifying the Nearly Random Microheterogeneity of Aqueous tert-Butyl Alcohol Solutions Using Vibrational Spectroscopy. J Phys Chem Lett 2023; 14:11376-11383. [PMID: 38078837 DOI: 10.1021/acs.jpclett.3c02603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
The microheterogeneous structure of aqueous tert-butyl alcohol (TBA) solutions is quantified by combining experimental, simulations, and theoretical results. Experimental Raman multivariate curve resolution (Raman-MCR) C-H frequency shift measurements are compared with predictions obtained using combined quantum mechanical and effective fragment potential (QM/EFP) calculations, as well as with molecular dynamics (MD), random mixture (RM), and finite lattice (FL) predictions. The results indicate that the microheterogeneous aggregation in aqueous TBA solutions is slightly less than that predicted by MD simulations performed using either CHARMM generalized force field (CGenFF) or optimized parameters for liquid simulations all atom (OPLS-AA) force fields but slightly more than that in a self-avoiding RM of TBA-like molecules. The results imply that the onset of microheterogeneity in aqueous solutions occurs when solute contact free energies are about an order of magnitude smaller than thermal fluctuations, thus suggesting a fundamental bound of relevance to biological self-assembly.
Collapse
Affiliation(s)
- Andres S Urbina
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Lyudmila V Slipchenko
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Dor Ben-Amotz
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| |
Collapse
|
76
|
Mortera-Carbonell AJ, Francisco E, Martín Pendás Á, Hernández-Trujillo J. The Ehrenfest force field: A perspective based on electron density functions. J Chem Phys 2023; 159:234110. [PMID: 38108480 DOI: 10.1063/5.0177631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/24/2023] [Indexed: 12/19/2023] Open
Abstract
The topology of the Ehrenfest force field (EhF) is investigated as a tool for describing local interactions in molecules and intermolecular complexes. The EhF is obtained by integrating the electronic force operator over the coordinates of all but one electron, which requires knowledge of both the electron density and the reduced pair density. For stationary states, the EhF can also be obtained as minus the divergence of the kinetic stress tensor, although this approach leads to well-documented erroneous asymptotic behavior at large distances from the nuclei. It is shown that these pathologies disappear using the electron density functions and that the EhF thus obtained displays the correct behavior in real space, with no spurious critical points or attractors. Therefore, its critical points can be unambiguously obtained and classified. Test cases, including strained molecules, isomerization reactions, and intermolecular interactions, were analyzed. Various chemically relevant facts are highlighted: for example, non-nuclear attractors are generally absent, potential hydrogen-hydrogen interactions are detected in crowded systems, and a bifurcation mechanism is observed in the isomerization of HCN. Moreover, the EhF atomic basins are less charged than those of the electron density. Although integration of the EhF over regions of real space can also be performed to yield the corresponding atomic forces, several numerical drawbacks still need to be solved if electron density functions are to be used for that purpose. Overall, the results obtained support the Ehrenfest force field as a reliable descriptor for the definition of atomic basins and molecular structure.
Collapse
Affiliation(s)
- Aldo J Mortera-Carbonell
- Departamento de Física y Química Teórica, Facultad de Química, UNAM, Ciudad de México 04510, Mexico
| | - Evelio Francisco
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Ángel Martín Pendás
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Jesús Hernández-Trujillo
- Departamento de Física y Química Teórica, Facultad de Química, UNAM, Ciudad de México 04510, Mexico
| |
Collapse
|
77
|
Li H, Bai T. Theoretical study of copper hydride complexes catalyzing terminal alkyne hydroalkylation for C(sp 2)-C(sp 3) bond formation. Dalton Trans 2023; 53:153-161. [PMID: 38018369 DOI: 10.1039/d3dt03514j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
This study applies Density Functional Theory (DFT) to theoretically investigate the reaction mechanism of a copper complex catalyst facilitating the reaction between a terminal alkyne and α-bromo amide, enabling the formation of E-alkenes through C(sp2)-C(sp3) coupling. Initially, the study explores the reaction mechanism, identifying the predominant reaction pathway and the rate-determining step. Next, we discuss the addition reaction mode of copper hydride with terminal alkynes, determining the causes of regional and stereoselectivity. Subsequently, the reaction mechanism between the alkenyl copper intermediate and α-bromo amide is examined, including the discussion of alkyl fragment activation and introduction methods. Furthermore, the role of NHC ligands in catalyzing the single electron transfer process for C-Br bond activation is investigated. Finally, we analyze and discuss the reasons for the high energy barrier of the non-radical pathway. These investigations not only deepen our understanding of the reaction mechanisms of terminal alkynes and α-bromo amide catalyzed by copper but also provide valuable guidance for the future design of more efficient catalysts and reaction conditions.
Collapse
Affiliation(s)
- Hui Li
- Key Laboratory of Chemical Engineering and Technology, State Ethnic Affairs Commission, North Minzu University, Yinchuan, China.
- Ningxia Key Laboratory of Solar Chemical Conversion Technology, North Minzu University, Yinchuan, China
| | - Taiming Bai
- Key Laboratory of Chemical Engineering and Technology, State Ethnic Affairs Commission, North Minzu University, Yinchuan, China.
- Ningxia Key Laboratory of Solar Chemical Conversion Technology, North Minzu University, Yinchuan, China
| |
Collapse
|
78
|
Omelchenko AN, Okotrub KA, Surovtsev NV. Raman spectroscopy of yeast cells cultured on a deuterated substrate. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 303:123262. [PMID: 37607454 DOI: 10.1016/j.saa.2023.123262] [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: 02/05/2023] [Revised: 06/13/2023] [Accepted: 08/13/2023] [Indexed: 08/24/2023]
Abstract
Raman spectroscopy of cells cultured in a deuterated substrate is a promising approach to the characterization of mass transfer and enzymatic reactions in living cells. Here, we studied the potential of this approach using the example of yeast cells cultured under aerobic and anaerobic conditions. In our experiments, unadapted to D2O Saccharomyces cerevisiae were cultured in a medium with different concentrations of deuterium oxide and deuterated glucose. It has been shown that the addition of even 10% heavy water leads to a general decrease in the amount of lipids in cells. In the Raman spectra of cells cultured at high concentrations of D2O, additional peaks are found, which are associated with the deuteration of entire chemical groups. We observed a similar effect in the ethanol synthesized by yeast fermentation, the deuteration of which also depends on the concentration of D2O. The results on the characterization of cell deuteration turned out to be in qualitative agreement with the known estimate that aerobic metabolism is 15 times more active than ethanol fermentation. The results of our work determine new limitations and prospects for further application and development of the Raman method of spectroscopy of deuterium tags.
Collapse
Affiliation(s)
- Anastasia N Omelchenko
- Novosibirsk State University, Novosibirsk, 630090, Russia; Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Konstantin A Okotrub
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk 630090, Russia.
| | - Nikolay V Surovtsev
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk 630090, Russia
| |
Collapse
|
79
|
Paciotti R, Marrone A. A computational insight on the aromatic amino acids conjugation with [Cp*Rh(H 2O) 3] 2+ by using the meta-dynamics/FMO3 approach. J Mol Model 2023; 30:4. [PMID: 38082186 PMCID: PMC10713709 DOI: 10.1007/s00894-023-05794-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023]
Abstract
CONTEXT Rh(III) complexes demonstrated to exert promising pharmacological effects with potential applications as anti-cancer, anti-bacterial, and antimicrobial agents. One important Rh(III)-ligand is the pentamethylcyclopentadienyl (Cp*) group forming in water the [Cp*Rh(H2O)3]2+ complex. Among of its attractive chemical properties is the ability to react specifically with Tyr amino acid side chain of G-protein-coupled receptor (GPCR) peptides by means of highly chemoselective bioconjugation reaction, at room temperature and at pH 5-6. In this computational work, in order to deepen the mechanism of this chemoselective conjugation, we study the ligand exchange reaction between [Cp*Rh(H2O)3]2+ and three small molecules, namely p-cresol, 3-methylimidazole, and toluene, selected as mimetic of aromatic side chains of tyrosine (Tyr), tryptophan (Trp) and phenylalanine (Phe), respectively. Our outcomes suggest that the high selectivity for Tyr side chain might be related to OH group able to affect both thermodynamic and kinetic of ligand exchange reaction, due to its ability to act as both H bond acceptor and donor. These mechanistic aspects can be used to design new metal drugs containing the [Cp*Rh]2+ scaffold targeting specifically Tyr residues involved in biological/pathological processes such as phosphorylation by means of Tyr-kinase enzyme and protein-protein interactions. METHODS The geometry of three encounter complexes and product adducts were optimized at the B3LYP//CPCM/ωB97X-D level of theory, adopting the 6-311+G(d,p) basis set for all non-metal atoms and the LANL2DZ pseudopotential for the Rh atom. Meta-dynamics RMSD (MTD(RMSD)) calculations at GFN2-xTB level of theory were performed in NVT conditions at 298.15 K to investigate the bioconjugation reactions (simulation time: 100 ps; integration step 2.0; implicit solvent model: GBSA). The MTD(RMSD) simulation was performed in two replicates for each encounter complex. Final representative subsets of 100 structures for each run were gained with a sampling rate of 1 ps and analyzed by performing single point calculations using the FMO3 method at RI-MP2/6-311G//PCM[1] level of theory, adopting the MCP-TZP core potential for Rh atom.
Collapse
Affiliation(s)
- Roberto Paciotti
- Department of Pharmacy, Università "G. D'Annunzio" Di Chieti-Pescara, I-66100, Chieti, Italy.
| | - Alessandro Marrone
- Department of Pharmacy, Università "G. D'Annunzio" Di Chieti-Pescara, I-66100, Chieti, Italy
| |
Collapse
|
80
|
Tran AL, Guidez EB, Lin H. Adaptive-Partitioning Multilayer Dynamics Simulations: 2. Implementations of the Permuted and Interpolated Adaptive-Partitioning Gradients. J Phys Chem A 2023; 127:10320-10333. [PMID: 38058156 PMCID: PMC10712430 DOI: 10.1021/acs.jpca.3c05600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/06/2023] [Accepted: 10/17/2023] [Indexed: 12/08/2023]
Abstract
Recently, an adaptive-partitioning multilayer Q1/Q2/MM method was proposed, where Q1 and Q2 denote, respectively, two distinct quantum-mechanical levels of theory and MM, the molecular-mechanical force fields. Such a multilayer model resembles the ONIOM (our own N-layered integrated molecular orbital and molecular mechanics) model by Morokuma and co-workers, but it is distinguished by on-the-fly reclassifying atoms to be Q1, Q2, or MM in dynamics simulations. To smoothly blend the levels of descriptions of the atoms, buffer zones are introduced between adjacent layers, and the energy is smoothly interpolated. In particular, the Q1/Q2 interaction energy was expressed in two different formalisms: permuted and interpolated adaptive-partitioning (PAP and IAP), respectively. While the PAP energy is based on a weighted many-body expansion, the IAP energy is derived via alchemical quantum calculations with interpolated Fock and overlap matrices. In this article, we examine in-depth the irregularities in the IAP energy near the boundary between the buffer and Q2 zones, which were found prominent in some calculations. These irregularities are due to basis-set linear dependencies, which can be effectively suppressed using a cutoff for the weighted atomic orbital coefficients. Furthermore, we derived and implemented the gradients for both PAP and IAP. Test calculations on a series of water cluster models show perfectly smooth gradients in PAP, while a minor discontinuity occurs in IAP gradients at the buffer/Q2 boundary. The energy and gradient discontinuities in IAP become smaller when moving the buffer/Q2 boundary further away from the Q1 center and when increasing the size of the basis sets used. Overall, those discontinuities are controllable, and possible ways to further diminish them are discussed.
Collapse
Affiliation(s)
- Anh L. Tran
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, United States
| | - Emilie B. Guidez
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, United States
| | - Hai Lin
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, United States
| |
Collapse
|
81
|
Li W, Wang Y, Ni Z, Li S. Cluster-in-Molecule Local Correlation Method for Dispersion Interactions in Large Systems and Periodic Systems. Acc Chem Res 2023; 56:3462-3474. [PMID: 37991873 DOI: 10.1021/acs.accounts.3c00538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
ConspectusThe noncovalent interactions, including dispersion interactions, control the structures and stabilities of complex chemical systems, including host-guest complexes and the adsorption process of molecules on the solid surfaces. The density functional theory (DFT) with empirical dispersion correction is now the working horse in many areas of applications. Post-Hartree-Fock (post-HF) methods have been well recognized to provide more accurate descriptions in a systematic way. However, traditional post-HF methods are mainly limited to small- or medium-sized systems, and their applications to periodic condensed phase systems are still very limited due to their expensive computational costs.To extend post-HF calculations to large molecules, the cluster-in-molecule (CIM) local correlation approach has been established, allowing highly accurate electron correlation calculations that are routinely available for very large systems. In the CIM approach, the electron correlation energy of a large molecule could be obtained from electron correlation calculations on a series of clusters, each of which contains a subset of occupied and virtual localized molecular orbitals. The CIM method could be massively and efficiently parallelized on general computer clusters. The CIM method has been implemented at various electron correlation levels, including second-order Mo̷ller-Plesset perturbation theory (MP2), coupled cluster singles and doubles (CCSD), CCSD with perturbative triples correction [CCSD(T)], etc. The CIM-MP2 energy gradient algorithm was developed and applied to the geometry optimizations of large systems. The CIM method has also been extended to condensed-phase systems under periodic boundary conditions (PBC-CIM). For periodic systems, the correlation energy per unit cell could be evaluated with correlation energy contributions from a series of clusters that are built with localized Wannier functions.CIM-based electron correlation calculations have been employed to investigate a number of chemical problems in which the dispersion interaction is important. CIM-based post-HF methods including CIM domain-based local pair natural orbital (DLPNO) CCSD(T) are applied to compute the relative or binding energies of biological systems or supramolecular complexes, the reaction barrier in a relatively complex chemical reaction. The CIM-MP2 method is used to obtain the optimized geometry of large systems. CIM-based post-HF calculations have also been used to compute the cohesive energies of molecular crystals and adsorption energies of molecules on the solid surfaces. The CIM and its PBC variant are expected to become a powerful theoretical tool for accurate calculations of the energies and structures for a broad range of large systems and condensed-phase systems with significant dispersion interactions.
Collapse
Affiliation(s)
- Wei Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Yuqi Wang
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Zhigang Ni
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, People's Republic of China
| | - Shuhua Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| |
Collapse
|
82
|
Dugarte-Dugarte AJ, Toro RA, van de Streek J, Henao JA, Fitch AN, Dejoie C, Delgado JM, Díaz de Delgado G. Hydrogen bonding patterns and C-H...π interactions in the structure of the antiparkinsonian drug (R)-rasagiline mesylate determined using laboratory and synchrotron X-ray powder diffraction data. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2023; 79:462-472. [PMID: 37820013 PMCID: PMC10833353 DOI: 10.1107/s2052520623007758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/06/2023] [Indexed: 10/13/2023]
Abstract
The structure of (R)-rasagiline mesylate [(R)-RasH+·Mes-], an active pharmaceutical ingredient used to treat Parkinson's disease, is presented. The structure was determined from laboratory and synchrotron powder diffraction data, refined using the Rietveld method, and validated and optimized using dispersion-corrected DFT calculations. The unit-cell parameters obtained in both experiments are in good agreement and the refinement with both datasets converged to good agreement factors. The final parameters obtained from laboratory data were a = 5.4905 (8), b = 6.536 (2), c = 38.953 (3) Å, V = 1398.0 (4) Å3 and from synchrotron powder data were a = 5.487530 (10) Å, b = 6.528939 (12) Å, c = 38.94313 (9) Å, V = 1395.245 (5) Å3 with Z = 4 and space group P212121. Preferred orientation was properly accounted for using the synchrotron radiation data, leading to a March-Dollase parameter of 1.140 (1) instead of the 0.642 (1) value obtained from laboratory data. In the structure, (R)-RasH+ moieties form layers parallel to the ab plane connected by mesylate ions through N-H...O and C-H...O hydrogen bonds. These layers stack along the c axis and are further connected by C-H...π interactions. Hirshfeld surface analysis and fingerprint plot calculations indicate that the main interactions are: H...H (50.9%), H...C/C...H (27.1%) and H...O/O...H (21.1%).
Collapse
Affiliation(s)
- Analio J. Dugarte-Dugarte
- Laboratorio de Cristalografía-LNDRX, Departamento de Química, Facultad de Ciencias, Universidad de Los Andes, Mérida, 5101, Venezuela
| | - Robert A. Toro
- Grupo de Investigación en Química Estructural (GIQUE), Escuela de Química, Facultad de Ciencias, Universidad Industrial de Santander, Bucaramanga, Colombia
| | | | - José Antonio Henao
- Grupo de Investigación en Química Estructural (GIQUE), Escuela de Química, Facultad de Ciencias, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Andrew N. Fitch
- European Synchrotron Radiation Facility (ESRF), 71 Avenue des Martyrs, CS40220, Grenoble, Cedex 9 38043, France
| | - Catherine Dejoie
- European Synchrotron Radiation Facility (ESRF), 71 Avenue des Martyrs, CS40220, Grenoble, Cedex 9 38043, France
| | - José Miguel Delgado
- Laboratorio de Cristalografía-LNDRX, Departamento de Química, Facultad de Ciencias, Universidad de Los Andes, Mérida, 5101, Venezuela
| | - Graciela Díaz de Delgado
- Laboratorio de Cristalografía-LNDRX, Departamento de Química, Facultad de Ciencias, Universidad de Los Andes, Mérida, 5101, Venezuela
| |
Collapse
|
83
|
Ditte M, Barborini M, Medrano Sandonas L, Tkatchenko A. Molecules in Environments: Toward Systematic Quantum Embedding of Electrons and Drude Oscillators. PHYSICAL REVIEW LETTERS 2023; 131:228001. [PMID: 38101380 DOI: 10.1103/physrevlett.131.228001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/26/2023] [Accepted: 10/20/2023] [Indexed: 12/17/2023]
Abstract
We develop a quantum embedding method that enables accurate and efficient treatment of interactions between molecules and an environment, while explicitly including many-body correlations. The molecule is composed of classical nuclei and quantum electrons, whereas the environment is modeled via charged quantum harmonic oscillators. We construct a general Hamiltonian and introduce a variational Ansatz for the correlated ground state of the fully interacting molecule-environment system. This wave function is optimized via the variational Monte Carlo method and the ground state energy is subsequently estimated through the diffusion Monte Carlo method. The proposed scheme allows an explicit many-body treatment of electrostatic, polarization, and dispersion interactions between the molecule and the environment. We study solvation energies and excitation energies of benzene derivatives, obtaining excellent agreement with explicit ab initio calculations and experiments.
Collapse
Affiliation(s)
- Matej Ditte
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Matteo Barborini
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Leonardo Medrano Sandonas
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| |
Collapse
|
84
|
Paciotti R, Marrone A, Coletti C, Re N. Improving the accuracy of the FMO binding affinity prediction of ligand-receptor complexes containing metals. J Comput Aided Mol Des 2023; 37:707-719. [PMID: 37743428 PMCID: PMC10618332 DOI: 10.1007/s10822-023-00532-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/07/2023] [Indexed: 09/26/2023]
Abstract
Polarization and charge transfer strongly characterize the ligand-receptor interaction when metal atoms are present, as for the Au(I)-biscarbene/DNA G-quadruplex complexes. In a previous work (J Comput Aided Mol Des2022, 36, 851-866) we used the ab initio FMO2 method at the RI-MP2/6-31G* level of theory with the PCM [1] solvation approach to calculate the binding energy (ΔEFMO) of two Au(I)-biscarbene derivatives, [Au(9-methylcaffein-8-ylidene)2]+ and [Au(1,3-dimethylbenzimidazole-2-ylidene)2]+, able to interact with DNA G-quadruplex motif. We found that ΔEFMO and ligand-receptor pair interaction energies (EINT) show very large negative values making the direct comparison with experimental data difficult and related this issue to the overestimation of the embedded charge transfer energy between fragments containing metal atoms. In this work, to improve the accuracy of the FMO method for predicting the binding affinity of metal-based ligands interacting with DNA G-quadruplex (Gq), we assess the effect of the following computational features: (i) the electron correlation, considering the Hartree-Fock (HF) and a post-HF method, namely RI-MP2; (ii) the two (FMO2) and three-body (FMO3) approaches; (iii) the basis set size (polarization functions and double-ζ vs. triple-ζ) and (iv) the embedding electrostatic potential (ESP). Moreover, the partial screening method was systematically adopted to simulate the solvent screening effect for each calculation. We found that the use of the ESP computed using the screened point charges for all atoms (ESP-SPTC) has a critical impact on the accuracy of both ΔEFMO and EINT, eliminating the overestimation of charge transfer energy and leading to energy values with magnitude comparable with typical experimental binding energies. With this computational approach, EINT values describe the binding efficiency of metal-based binders to DNA Gq more accurately than ΔEFMO. Therefore, to study the binding process of metal containing systems with the FMO method, the adoption of partial screening solvent method combined with ESP-SPCT should be considered. This computational protocol is suggested for FMO calculations on biological systems containing metals, especially when the adoption of the default ESP treatment leads to questionable results.
Collapse
Affiliation(s)
- R Paciotti
- Department of Pharmacy, Università "G. D'Annunzio" Di Chieti-Pescara, Chieti, Italy.
| | - A Marrone
- Department of Pharmacy, Università "G. D'Annunzio" Di Chieti-Pescara, Chieti, Italy
| | - C Coletti
- Department of Pharmacy, Università "G. D'Annunzio" Di Chieti-Pescara, Chieti, Italy
| | - N Re
- Department of Pharmacy, Università "G. D'Annunzio" Di Chieti-Pescara, Chieti, Italy
| |
Collapse
|
85
|
Witoszka K, Matalińska J, Misicka A, Lipiński PFJ. Moving out of CF 3 -Land: Synthesis, Receptor Affinity, and in silico Studies of NK1 Receptor Ligands Containing a Pentafluorosulfanyl (SF 5 ) Group. ChemMedChem 2023; 18:e202300315. [PMID: 37821725 DOI: 10.1002/cmdc.202300315] [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: 06/17/2023] [Revised: 09/23/2023] [Accepted: 10/11/2023] [Indexed: 10/13/2023]
Abstract
The NK1 receptor (NK1R) is a molecular target for both approved and experimental drugs intended for a variety of conditions, including emesis, pain, and cancers. While contemplating modifications to the typical NK1R pharmacophore, we wondered whether the CF3 groups common for many NK1R ligands, could be replaced with some other moiety. Our attention was drawn by the SF5 group, and so we designed, synthesized, and tested ten novel SF5 -containing compounds for NK1R affinity. All analogues exhibit detectable NK1R binding, with the best of them, compound 5 a, (3-bromo-5-(pentafluoro-λ6 -sulfanyl)benzyl acetyl-L-tryptophanate) binding only slightly worse (IC50 =34.3 nM) than the approved NK1R-targeting drug, aprepitant (IC50 =27.7 nM). Molecular docking provided structural explanation of SAR. According to our analysis, the SF5 group in our compounds occupies a position similar to that of one of the CF3 groups of aprepitant as found in the crystal structure. Additionally, we checked whether the docking scoring function or energies derived from Fragment Molecular Orbital quantum chemical calculations may be helpful in explaining and predicting the experimental receptor affinities for our analogues. Both these methods produce moderately good results. Overall, this is the first demonstration of the utility of the SF5 group in the design of NK1R ligands.
Collapse
Affiliation(s)
- Katarzyna Witoszka
- Department of Neuropeptides, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawińskiego 5, 02-106, Warsaw, Poland
| | - Joanna Matalińska
- Department of Neuropeptides, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawińskiego 5, 02-106, Warsaw, Poland
| | - Aleksandra Misicka
- Department of Neuropeptides, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawińskiego 5, 02-106, Warsaw, Poland
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Piotr F J Lipiński
- Department of Neuropeptides, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawińskiego 5, 02-106, Warsaw, Poland
| |
Collapse
|
86
|
Alías-Rodríguez M, Bonfrate S, Park W, Ferré N, Choi CH, Huix-Rotllant M. Solvent Effects and pH Dependence of the X-ray Absorption Spectra of Proline from Electrostatic Embedding Quantum Mechanics/Molecular Mechanics and Mixed-Reference Spin-Flip Time-dependent Density-Functional Theory. J Phys Chem A 2023. [PMID: 38019644 DOI: 10.1021/acs.jpca.3c05070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
The accurate description of solvent effects on X-ray absorption spectra (XAS) is fundamental for comparing the simulated spectra with experiments in solution. Currently, few protocols exist that can efficiently reproduce the effects of the solute/solvent interactions on XAS. Here, we develop an efficient and accurate theoretical protocol for simulating the solvent effects on XAS. The protocol combines electrostatic embedding QM/MM based on electrostatic potential fitted operators for describing the solute/solvent interactions and mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) for simulating accurate XAS spectra. To demonstrate the capabilities of our protocol, we compute the X-ray absorption of neutral proline in the gas phase and ionic proline in water in all relevant K-edges, showing excellent agreement with experiments. We show that states represented by core to π* transitions are almost unaffected by the interaction with water, whereas the core to σ* transitions are more impacted by the fluctuation of proline structure and the electrostatic interaction with the solvent. Finally, we reconstruct the pH-dependent XAS of proline in solution, determining that the N K-edge can be used to distinguish its three protonation states.
Collapse
Affiliation(s)
| | | | - Woojin Park
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Nicolas Ferré
- Aix-Marseille Univ, CNRS, ICR, Marseille 13013, France
| | - Cheol Ho Choi
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | | |
Collapse
|
87
|
Peyton BG, Stewart ZJ, Weidman JD, Wilson AK. Tailoring light-induced charge transfer and intersystem crossing in FeCO using time-dependent spin-orbit configuration interaction. J Chem Phys 2023; 159:204108. [PMID: 38014783 DOI: 10.1063/5.0173529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/02/2023] [Indexed: 11/29/2023] Open
Abstract
Real-time (RT) electronic structure methods provide a natural framework for describing light-matter interactions in arbitrary time-dependent electromagnetic fields (EMF). Optically induced excited state transitions are of particular interest, which require tuned EMF to drive population transfer to and from the specific state(s) of interest. Intersystem crossing, or spin-flip, may be driven through shaped EMF or laser pulses. These transitions can result in long-lived "spin-trapped" excited states, which are especially useful for materials requiring charge separation or protracted excited state lifetimes. Time-dependent configuration interaction (TDCI) is unique among RT methods in that it may be implemented in a basis of eigenstates, allowing for rapid propagation of the time-dependent Schrödinger equation. The recent spin-orbit TDCI (TD-SOCI) enables a real-time description of spin-flip dynamics in an arbitrary EMF and, therefore, provides an ideal framework for rational pulse design. The present study explores the mechanism of multiple spin-flip pathways for a model transition metal complex, FeCO, using shaped pulses designed to drive controlled intersystem crossing and charge transfer. These results show that extremely tunable excited state dynamics can be achieved by considering the dipole transition matrix elements between the states of interest.
Collapse
Affiliation(s)
- Benjamin G Peyton
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Zachary J Stewart
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Jared D Weidman
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Angela K Wilson
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| |
Collapse
|
88
|
Yang EL, Talbot JJ, Spencer RJ, Steele RP. Pitfalls in the n-mode representation of vibrational potentials. J Chem Phys 2023; 159:204104. [PMID: 38010326 DOI: 10.1063/5.0176612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/19/2023] [Indexed: 11/29/2023] Open
Abstract
Simulations of anharmonic vibrational motion rely on computationally expedient representations of the governing potential energy surface. The n-mode representation (n-MR)-effectively a many-body expansion in the space of molecular vibrations-is a general and efficient approach that is often used for this purpose in vibrational self-consistent field (VSCF) calculations and correlated analogues thereof. In the present analysis, a lack of convergence in many VSCF calculations is shown to originate from negative and unbound potentials at truncated orders of the n-MR expansion. For cases of strong anharmonic coupling between modes, the n-MR can both dip below the true global minimum of the potential surface and lead to effective single-mode potentials in VSCF that do not correspond to bound vibrational problems, even for bound total potentials. The present analysis serves mainly as a pathology report of this issue. Furthermore, this insight into the origin of VSCF non-convergence provides a simple, albeit ad hoc, route to correct the problem by "painting in" the full representation of groups of modes that exhibit these negative potentials at little additional computational cost. Somewhat surprisingly, this approach also reasonably approximates the results of the next-higher n-MR order and identifies groups of modes with particularly strong coupling. The method is shown to identify and correct problematic triples of modes-and restore SCF convergence-in two-mode representations of challenging test systems, including the water dimer and trimer, as well as protonated tropine.
Collapse
Affiliation(s)
- Emily L Yang
- Department of Chemistry, The University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, USA
- Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112, USA
| | - Justin J Talbot
- Department of Chemistry, University of California-Berkeley, 420 Latimer Hall, Berkeley, California 94720, USA
| | - Ryan J Spencer
- Department of Chemistry, The University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, USA
- Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112, USA
| | - Ryan P Steele
- Department of Chemistry, The University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, USA
- Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112, USA
| |
Collapse
|
89
|
Li Z, Mizuno M, Ejiri T, Hayashi S, Kandori H, Mizutani Y. Unique Vibrational Characteristics and Structures of the Photoexcited Retinal Chromophore in Ion-Pumping Rhodopsins. J Phys Chem B 2023; 127:9873-9886. [PMID: 37940604 DOI: 10.1021/acs.jpcb.3c02146] [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: 11/10/2023]
Abstract
Photoisomerization of an all-trans-retinal chromophore triggers ion transport in microbial ion-pumping rhodopsins. Understanding chromophore structures in the electronically excited (S1) state provides insights into the structural evolution on the potential energy surface of the photoexcited state. In this study, we examined the structure of the S1-state chromophore in Natronomonas pharaonis halorhodopsin (NpHR), a chloride ion-pumping rhodopsin, using time-resolved resonance Raman spectroscopy. The spectral patterns of the S1-state chromophore were completely different from those of the ground-state chromophore, resulting from unique vibrational characteristics and the structure of the S1 state. Mode assignments were based on a combination of deuteration shifts of the Raman bands and hybrid quantum mechanics-molecular mechanics calculations. The present observations suggest a weakened bond alternation in the π conjugation system. A strong hydrogen-out-of-plane bending band was observed in the Raman spectra of the S1-state chromophore in NpHR, indicating a twisted polyene structure. Similar frequency shifts for the C═N/C═C and C-C stretching modes of the S1-state chromophore in NpHR were observed in the Raman spectra of sodium ion-pumping and proton-pumping rhodopsins, suggesting that these unique features are common to the S1 states of ion-pumping rhodopsins.
Collapse
Affiliation(s)
- Zixuan Li
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Osaka, Toyonaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Osaka, Toyonaka 560-0043, Japan
| | - Tomo Ejiri
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Osaka, Toyonaka 560-0043, Japan
| |
Collapse
|
90
|
Guidez EB. Quasi-atomic orbital analysis of halogen bonding interactions. J Chem Phys 2023; 159:194307. [PMID: 37987522 DOI: 10.1063/5.0174171] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
A quasi-atomic orbital analysis of the halogen bonded NH3⋯XF complexes (X = F, Cl, Br, and I) is performed to gain insight into the electronic properties associated with these σ-hole interactions. It is shown that significant sharing of electrons between the nitrogen lone pair of the ammonia molecule and the XF molecule occurs, resulting in a weakening of the X-F bond. In addition, the N-X bond shows increasing covalent character as the size of the halogen atom X increases. While the Mulliken outer complex NH3⋯XF appears to be overall the main species, the strength of the covalent interaction of the N-X bond becomes increasingly similar to that of the N-X bond in the [NH3X]+ cation as the size of X increases.
Collapse
Affiliation(s)
- Emilie B Guidez
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, USA
| |
Collapse
|
91
|
Trowbridge L, Averkiev B, Sues PE. Electrocatalytic Hydrogen Evolution using a Nickel-based Calixpyrrole Complex: Controlling the Secondary Coordination Sphere on an Electrode Surface. Chemistry 2023; 29:e202301920. [PMID: 37665793 PMCID: PMC10842979 DOI: 10.1002/chem.202301920] [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: 06/16/2023] [Revised: 08/31/2023] [Accepted: 09/04/2023] [Indexed: 09/06/2023]
Abstract
Incorporating design elements from homogeneous catalysts to construct well defined active sites on electrode surfaces is a promising approach for developing next generation electrocatalysts for energy conversion reactions. Furthermore, if functionalities that control the electrode microenvironment could be integrated into these active sites it would be particularly appealing. In this context, a square planar nickel calixpyrrole complex, Ni(DPMDA) (DPMDA=2,2'-((diphenylmethylene)bis(1H-pyrrole-5,2-diyl))bis(methaneylylidene))bis(azaneylylidene))dianiline) with pendant amine groups is reported that forms a heterogeneous hydrogen evolution catalyst using anilinium tetrafluoroborate as the proton source. The supported Ni(DPMDA) catalyst was surprisingly stable and displayed fast reaction kinetics with turnover frequencies (TOF) up to 25,900 s-1 or 366,000 s-1 cm-2 . Kinetic isotope effect (KIE) studies revealed a KIE of 5.7, and this data, combined with Tafel slope analysis, suggested that a proton-coupled electron transfer (PCET) process involving the pendant amine groups was rate-limiting. While evidence of an outer-sphere reduction of the Ni(DPMDA) catalyst was observed, it is hypothesized that the control over the secondary coordination sphere provided by the pendant amines facilitated such high TOFs and enabled the PCET mechanism. The results reported herein provide insight into heterogeneous catalyst design and approaches for controlling the secondary coordination sphere on electrode surfaces.
Collapse
Affiliation(s)
- Logan Trowbridge
- Department of Chemistry, Kansas State University, 1212 Mid-Campus Drive North, Manhattan, Kansas, 66503, USA
| | - Boris Averkiev
- Department of Chemistry, Kansas State University, 1212 Mid-Campus Drive North, Manhattan, Kansas, 66503, USA
| | - Peter E Sues
- Department of Chemistry, Kansas State University, 1212 Mid-Campus Drive North, Manhattan, Kansas, 66503, USA
| |
Collapse
|
92
|
Skrzyński G, Musial M. Benchmark Study of the Electronic States of the LiRb Molecule: Ab Initio Calculations with the Fock Space Coupled Cluster Approach. Molecules 2023; 28:7645. [PMID: 38005367 PMCID: PMC10675596 DOI: 10.3390/molecules28227645] [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: 09/06/2023] [Revised: 10/27/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Accurate potential energy curves (PECs) are determined for the twenty-two electronic states of LiRb. In contrast to previous studies, the applied approach relies on the first principle calculations involving correlation among all electrons. The current methodology is founded on the multireference coupled cluster (CC) scheme constructed within the Fock space (FS) formalism, specifically for the (2,0) sector. The FS methodology is established within the framework of the intermediate Hamiltonian formalism and offers an intruder-free, efficient computational scheme. This method has a distinctive feature that, when applied to the doubly ionized system, provides the characteristics of the neutral case. This proves especially beneficial when investigating PECs in situations where a closed-shell molecule dissociates into open-shell fragments, yet its double positive ion forms closed-shell species. In every instance, we successfully computed continuous PECs spanning the entire range of interatomic distances, from the equilibrium to the dissociation limit. Moreover, the spectroscopic characteristic of various electronic states is presented, including relativistic effects. Relativistic corrections included at the third-order Douglas-Kroll level have a non-negligible effect on the accuracy of the determined spectroscopic constants.
Collapse
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
| |
Collapse
|
93
|
Kim S, Conrad JA, Tow GM, Maginn EJ, Boatz JA, Gordon MS. Intermolecular interactions in clusters of ethylammonium nitrate and 1-amino-1,2,3-triazole. Phys Chem Chem Phys 2023; 25:30428-30457. [PMID: 37917371 DOI: 10.1039/d3cp02407e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
The intermolecular interaction energies, including hydrogen bonds (H-bonds), of clusters of the ionic liquid ethylammonium nitrate (EAN) and 1-amino-1,2,3-triazole (1-AT) based deep eutectic propellants (DeEP) are examined. 1-AT is introduced as a neutral hydrogen bond donor (HBD) to EAN in order to form a eutectic mixture. The effective fragment potential (EFP) is used to examine the bonding interactions in the DeEP clusters. The resolution of the Identity (RI) approximated second order Møller-Plesset perturbation theory (RI-MP2) and coupled cluster theory (RI-CCSD(T)) are used to validate the EFP results. The EFP method predicts that there are significant polarization and charge transfer effects in the EAN:1-AT complexes, along with Coulombic, dispersion and exchange repulsion interactions. The EFP interaction energies are in good agreement with the RI-MP2 and RI-CCSD(T) results. The quasi-atomic orbital (QUAO) bonding and kinetic bond order (KBO) analyses are additionally used to develop a conceptual and semi-quantitative understanding of the H-bonding interactions as a function of the size of the system. The QUAO and KBO analyses suggest that the H-bonds in the examined clusters follow the characteristic hydrogen bonding three-center four electron interactions. The strongest H-bonding interactions between the (EAN)1:(1-AT)n and (EAN)2:(1-AT)n (n = 1-5) complexes are observed internally within EAN; that is, between the ethylammonium cation [EA]+ and the nitrate anion ([NO3]-). The weakest H-bonding interactions occur between [NO3]- and 1-AT. Consequently, the average strengths of the H-bonds within a given (EAN)x:(1-AT)n complex decrease as more 1-AT molecules are introduced into the EAN monomer and EAN dimer. The QUAO bonding analysis suggests that 1-AT in (EAN)x:(1-AT)n can act as both a HBD and a hydrogen bond acceptor simultaneously. It is observed that two 1-AT molecules can form H-bonds to each other. Although the KBOs that correspond to H-bonding interactions in [EA]+:1-AT, [NO3]-:1-AT and between two 1-AT molecules are weaker than the H-bonds in EAN, those weak H-bond networks with 1-AT could be important to form a stable DeEP.
Collapse
Affiliation(s)
- Shinae Kim
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, IA 50011, USA.
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94550, USA
| | - Justin A Conrad
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, IA 50011, USA.
| | - Garrett M Tow
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Edward J Maginn
- Department of Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Jerry A Boatz
- Aerospace Systems Directorate, Air Force Research Laboratory, Edwards Air Force Base, California 93524, USA
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, IA 50011, USA.
| |
Collapse
|
94
|
Moi D, Bonanni D, Belluti S, Linciano P, Citarella A, Franchini S, Sorbi C, Imbriano C, Pinzi L, Rastelli G. Discovery of potent pyrrolo-pyrimidine and purine HDAC inhibitors for the treatment of advanced prostate cancer. Eur J Med Chem 2023; 260:115730. [PMID: 37633202 DOI: 10.1016/j.ejmech.2023.115730] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/01/2023] [Accepted: 08/14/2023] [Indexed: 08/28/2023]
Abstract
The development of drugs for the treatment of advanced prostate cancer (PCA) remains a challenging task. In this study we have designed, synthesized and tested twenty-nine novel HDAC inhibitors based on three different zinc binding groups (trifluoromethyloxadiazole, hydroxamic acid, and 2-mercaptoacetamide). These warheads were conveniently tethered to variously substituted phenyl linkers and decorated with differently substituted pyrrolo-pyrimidine and purine cap groups. Remarkably, most of the compounds showed nanomolar inhibitory activity against HDAC6. To provide structural insights into the Structure-Activity Relationships (SAR) of the investigated compounds, docking of representative inhibitors and molecular dynamics of HDAC6-inhibitor complexes were performed. Compounds of the trifluoromethyloxadiazole and hydroxamic acid series exhibited promising anti-proliferative activities, HDAC6 targeting in PCA cells, and in vitro tumor selectivity. Representative compounds of the two series were tested for solubility, cell permeability and metabolic stability, demonstrating favorable in vitro drug-like properties. The more interesting compounds were subjected to migration assays, which revealed that compound 13 and, to a lesser extent, compound 15 inhibited the invasive behaviour of androgen-sensitive and -insensitive advanced prostate cancer cells. Compound 13 was profiled against all HDACs and found to inhibit all members of class II HDACs (except for HDAC10) and to be selective with respect to class I and class IV HDACs. Overall, compound 13 combines potent inhibitory activity and class II selectivity with favorable drug-like properties, an excellent anti-proliferative activity and marked anti-migration properties on PCA cells, making it an excellent lead candidate for further optimization.
Collapse
Affiliation(s)
- Davide Moi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Davide Bonanni
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Silvia Belluti
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Pasquale Linciano
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Andrea Citarella
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Silvia Franchini
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Claudia Sorbi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Carol Imbriano
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Luca Pinzi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy.
| | - Giulio Rastelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy.
| |
Collapse
|
95
|
Sugisaki K. Projective Measurement-Based Quantum Phase Difference Estimation Algorithm for the Direct Computation of Eigenenergy Differences on a Quantum Computer. J Chem Theory Comput 2023; 19:7617-7625. [PMID: 37874368 PMCID: PMC10653105 DOI: 10.1021/acs.jctc.3c00784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Indexed: 10/25/2023]
Abstract
Quantum computers are capable of calculating the energy difference of two electronic states using the quantum phase difference estimation (QPDE) algorithm. The Bayesian inference-based implementations for the QPDE have been reported so far, but in this approach, the quality of the calculated energy difference depends on the input wave functions being used. Here, we report the inverse quantum Fourier transformation-based QPDE with Na of ancillary qubits, which allows us to compute the difference of eigenenergies based on the single-shot projective measurement. As proof-of-concept demonstrations, we report numerical experiments for the singlet-triplet energy difference of the hydrogen molecule and the vertical excitation energies of halogen-substituted methylenes (CHF, CHCl, CF2, CFCl, and CCl2) and formaldehyde (HCHO).
Collapse
Affiliation(s)
- Kenji Sugisaki
- Graduate
School of Science and Technology, Keio University, 7-1 Shinkawasaki, Saiwai-ku, Kawasaki, Kanagawa 212-0032, Japan
- Quantum
Computing Center, Keio University, 3-14-1 Hiyoshi,
Kohoku-ku Yokohama, Kanagawa 223-8522, Japan
- Centre
for Quantum Engineering, Research and Education
TCG Centres for Research and Education in Science and Technology, Sector V, Salt Lake, Kolkata 700091, India
| |
Collapse
|
96
|
Komarov K, Park W, Lee S, Huix-Rotllant M, Choi CH. Doubly Tuned Exchange-Correlation Functionals for Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory. J Chem Theory Comput 2023; 19:7671-7684. [PMID: 37844129 DOI: 10.1021/acs.jctc.3c00884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
It is demonstrated that significant accuracy improvements in MRSF-TDDFT can be achieved by introducing two different exchange-correlation (XC) functionals for the reference Kohn-Sham DFT and the response part of the calculations, respectively. Accordingly, two new XC functionals of doubly tuned Coulomb attenuated method-vertical excitation energy (DTCAM-VEE) and DTCAM-AEE were developed on the basis of the "adaptive exact exchange (AEE)" concept in the framework of the Coulomb-attenuating XC functionals. The values by DTCAM-VEE are in excellent agreement with those of Thiel's set [mean absolute errors (MAEs) and the interquartile range (IQR) values of 0.218 and 0.327 eV, respectively]. On the other hand, DTCAM-AEE faithfully reproduced the qualitative aspects of conical intersections (CIs) of trans-butadiene and thymine and the nonadiabatic molecular dynamics (NAMD) simulations on thymine. The latter functional also remarkably exhibited the exact 1/R asymptotic behavior of the charge-transfer state of an ethylene-tetrafluoroethylene dimer and the accurate potential energy surfaces (PESs) along the two torsional angles of retinal protonated Schiff base model with six double bonds (rPSB6). Overall, DTCAM-AEE generally performs well, as its MAE (0.237) and IQR (0.41 eV) are much improved as compared to BH&HLYP. The current idea can also be applied to other XC functionals as well as other variants of linear response theories, opening a new way of developing XC functionals.
Collapse
Affiliation(s)
- Konstantin Komarov
- Center for Quantum Dynamics, Pohang University of Science and Technology, Pohang 37673, South Korea
| | - Woojin Park
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Seunghoon Lee
- Department of Chemistry, Seoul National University, Seoul, 151-747, South Korea
| | | | - Cheol Ho Choi
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| |
Collapse
|
97
|
Datta D, Gordon MS. Accelerating Coupled-Cluster Calculations with GPUs: An Implementation of the Density-Fitted CCSD(T) Approach for Heterogeneous Computing Architectures Using OpenMP Directives. J Chem Theory Comput 2023; 19:7640-7657. [PMID: 37878756 DOI: 10.1021/acs.jctc.3c00876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
An algorithm is presented for the coupled-cluster singles, doubles, and perturbative triples correction [CCSD(T)] method based on the density fitting or the resolution-of-the-identity (RI) approximation for performing calculations on heterogeneous computing platforms composed of multicore CPUs and graphics processing units (GPUs). The directive-based approach to GPU offloading offered by the OpenMP application programming interface has been employed to adapt the most compute-intensive terms in the RI-CCSD amplitude equations with computational costs scaling as O ( N O 2 N V 4 ) , O ( N O 3 N V 3 ) , and O ( N O 4 N V 2 ) (where NO and NV denote the numbers of correlated occupied and virtual orbitals, respectively) and the perturbative triples correction to execute on GPU architectures. The pertinent tensor contractions are performed using an accelerated math library such as cuBLAS or hipBLAS. Optimal strategies are discussed for splitting large data arrays into tiles to fit them into the relatively small memory space of the GPUs, while also minimizing the low-bandwidth CPU-GPU data transfers. The performance of the hybrid CPU-GPU RI-CCSD(T) code is demonstrated on pre-exascale supercomputers composed of heterogeneous nodes equipped with NVIDIA Tesla V100 and A100 GPUs and on the world's first exascale supercomputer named "Frontier", the nodes of which consist of AMD MI250X GPUs. Speedups within the range 4-8× relative to the recently reported CPU-only algorithm are obtained for the GPU-offloaded terms in the RI-CCSD amplitude equations. Applications to polycyclic aromatic hydrocarbons containing 16-66 carbon atoms demonstrate that the acceleration of the hybrid CPU-GPU code for the perturbative triples correction relative to the CPU-only code increases with the molecule size, attaining a speedup of 5.7× for the largest circumovalene molecule (C66H20). The GPU-offloaded code enables the computation of the perturbative triples correction for the C60 molecule using the cc-pVDZ/aug-cc-pVTZ-RI basis sets in 7 min on Frontier when using 12,288 AMD GPUs with a parallel efficiency of 83.1%.
Collapse
Affiliation(s)
- Dipayan Datta
- Department of Chemistry and Ames Laboratory, Iowa State University, 2416 Pammel Drive, Ames, Iowa 50011-2416, United States
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, 2416 Pammel Drive, Ames, Iowa 50011-2416, United States
| |
Collapse
|
98
|
Fedorov DG. Site-Specific Ionization Potentials and Electron Affinities in Large Molecular Systems at Coupled Cluster Level. J Phys Chem A 2023; 127:9357-9364. [PMID: 37782030 DOI: 10.1021/acs.jpca.3c04847] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
A many-body expansion of ionization potentials and electron affinities is developed based on a combination of the fragment molecular orbital method and equation-of-motion coupled-cluster (EOM-CC). In addition to site-specific values, obtained as one-body properties, pair and triple corrections are added to account for nonlocal EOM-CC contributions of the molecular environment of a chromophore. The developed method is applied to carboxylic acids, alkyl cations, a protein ubiquitin (Protein Data Bank ID 1UBQ), and a nano ribbon of white graphene elucidating the effect of environment on ionization potential and electron affinity.
Collapse
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
| |
Collapse
|
99
|
Tanabe M, Sakate R, Nakabayashi J, Tsumura K, Ohira S, Iwato K, Kimura T. A novel in silico scaffold-hopping method for drug repositioning in rare and intractable diseases. Sci Rep 2023; 13:19358. [PMID: 37938624 PMCID: PMC10632405 DOI: 10.1038/s41598-023-46648-1] [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: 06/16/2023] [Accepted: 11/03/2023] [Indexed: 11/09/2023] Open
Abstract
In the field of rare and intractable diseases, new drug development is difficult and drug repositioning (DR) is a key method to improve this situation. In this study, we present a new method for finding DR candidates utilizing virtual screening, which integrates amino acid interaction mapping into scaffold-hopping (AI-AAM). At first, we used a spleen associated tyrosine kinase inhibitor as a reference to evaluate the technique, and succeeded in scaffold-hopping maintaining the pharmacological activity. Then we applied this method to five drugs and obtained 144 compounds with diverse structures. Among these, 31 compounds were known to target the same proteins as their reference compounds and 113 compounds were known to target different proteins. We found that AI-AAM dominantly selected functionally similar compounds; thus, these selected compounds may represent improved alternatives to their reference compounds. Moreover, the latter compounds were presumed to bind to the targets of their references as well. This new "compound-target" information provided DR candidates that could be utilized for future drug development.
Collapse
Affiliation(s)
- Mao Tanabe
- Laboratory of Rare Disease Information and Resource Library, Center for Intractable Diseases and ImmunoGenomics Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Osaka, Japan
| | - Ryuichi Sakate
- Laboratory of Rare Disease Information and Resource Library, Center for Intractable Diseases and ImmunoGenomics Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Osaka, Japan
| | - Jun Nakabayashi
- Analysis Technology Center, FUJIFILM Corporation, 210 Nakanuma, Minami-ashigara, Kanagawa, Japan
| | - Kyosuke Tsumura
- Analysis Technology Center, FUJIFILM Corporation, 210 Nakanuma, Minami-ashigara, Kanagawa, Japan
| | - Shino Ohira
- Analysis Technology Center, FUJIFILM Corporation, 210 Nakanuma, Minami-ashigara, Kanagawa, Japan
| | - Kaoru Iwato
- Analysis Technology Center, FUJIFILM Corporation, 210 Nakanuma, Minami-ashigara, Kanagawa, Japan
| | - Tomonori Kimura
- Reverse Translational Research Project, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki-City, Osaka, Japan.
- KAGAMI Project, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Ibaraki, Osaka, Japan.
- Department of Nephrology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan.
| |
Collapse
|
100
|
Gan H, Jiang Q, Ma Y. A theoretical study on π-stacking and ferromagnetism of the perylene diimide radical anion dimer and tetramer. Phys Chem Chem Phys 2023; 25:30005-30013. [PMID: 37905461 DOI: 10.1039/d3cp02496b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Ferromagnetism is rare in pure organic materials. Recently, the perylene diimide radical anion (PDI-) salt prepared through solvothermal reduction by hydrazine hydrate has shown room-temperature ferromagnetism in our work [Jiang et al., Adv. Mater., 2022, 34, 2108103]. Based on this, herein we conduct a theoretical study based on density functional theory (DFT) to reveal the stacked geometries between two NH4PDI monomers for low-spin (LS) and high-spin (HS) states and their magnetic exchange interactions (JAB) using Yamaguchi's approximate spin projection. It is observed that the pancake-bonded dimer of NH4PDI is the most stable pimer compared to others on both LS and HS potential energy surfaces. A transition of magnetic properties from strong antiferromagnetic (-1333.9 cm-1) to moderate ferromagnetic (67.0 cm-1) appears after increasing the interplanar distance between monomers and their relative rotation angle to access the HS state. According to energy decomposition analysis, the enhanced hydrogen bond formation and decrease of Pauli repulsion is able to counteract the decrease of attraction induced by electron correlation after accessing the HS state. Stacking patterns of exchange-coupled chain consisting of the NH4PDI tetramer are obtained for the HS state after geometry optimization of the structure constructed by two most stable HS pimers. The exchange interactions (51.8 cm-1, 381.2 cm-1 and 53.2 cm-1) between adjacent NH4PDI monomers are ferromagnetic in the HS state, which is in accordance with the experimentally observed room-temperature ferromagnetism.
Collapse
Affiliation(s)
- Hanlin Gan
- State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou 510640, China.
| | - Qinglin Jiang
- State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou 510640, China.
| | - Yuguang Ma
- State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou 510640, China.
- Guangdong Provincial Key Laboratory of Luminescence from Molecular Aggregates, South China University of Technology, Guangzhou 510640, China
| |
Collapse
|