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Peyton BG, Wang Z, Crawford TD. Reduced Scaling Real-Time Coupled Cluster Theory. J Phys Chem A 2023; 127:8486-8499. [PMID: 37782945 DOI: 10.1021/acs.jpca.3c05151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Real-time coupled cluster (CC) methods have several advantages over their frequency-domain counterparts, namely, response and equation of motion CC theories. Broadband spectra, strong fields, and pulse manipulation allow for the simulation of complex spectroscopies that are unreachable using frequency-domain approaches. Due to the high-order polynomial scaling, the required numerical time propagation of the CC residual expressions is a computationally demanding process. This scaling may be reduced by local correlation schemes, which aim to reduce the size of the (virtual) orbital space by truncation according to user-defined parameters. We present the first application of local correlation to real-time CC. As in previous studies of locally correlated frequency-domain CC, traditional local correlation schemes are of limited utility for field-dependent properties; however, a perturbation-aware scheme proves promising. A detailed analysis of the amplitude dynamics suggests that the main challenge is a strong time dependence of the wave function sparsity.
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Affiliation(s)
- Benjamin G Peyton
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Zhe Wang
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - T Daniel Crawford
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
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2
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Parsons T, Balduf T, Caricato M. On the choice of coordinate origin in length gauge optical rotation calculations. Chirality 2023; 35:708-717. [PMID: 37137811 DOI: 10.1002/chir.23575] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 04/11/2023] [Indexed: 05/05/2023]
Abstract
In this work, we explore the issue of origin dependence in optical rotation (OR) calculations in the length dipole gauge (LG) using standard approximate methods belonging to density functional theory (DFT) and coupled cluster (CC) theory. We use the origin-invariant LG approach, LG(OI), that we recently proposed as reference for the calculations, and we study whether a proper choice of coordinate origin and molecular orientation can be made such that diagonal elements of the LG-OR tensor match those of the LG(OI) tensor. Using a numerical search algorithm, we show that multiple spatial orientations can be found where the LG and LG(OI) results match. However, a simple analytical procedure provides a spatial orientation where the origin of the coordinate system is close to the center of mass of the molecule. At the same time, we also show that putting the origin at the center of mass is not an ideal choice for every molecule (relative errors in the OR up to 70% can be obtained in out test set). Finally, we show that the choice of coordinate origin based on the analytical procedure is transferable across different methods and it is superior to putting the origin in the center of mass or center of nuclear charge. This is important because the LG(OI) approach is trivial to implement for DFT, but not necessarily for nonvariational methods in the CC family. Therefore, one can determine an optimal coordinate origin at DFT level and use it for standard LG-CC response calculations.
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Affiliation(s)
- Taylor Parsons
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - Ty Balduf
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - Marco Caricato
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
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3
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Le TH, Dang PH, Nguyen HX, Do TNV, Nguyen NT, Nguyen MTT. Strebluses E-H, four new stilbene-like derivatives from the stems of Streblus ilicifolius. RSC Adv 2022; 13:570-574. [PMID: 36605660 PMCID: PMC9773016 DOI: 10.1039/d2ra07294g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Following bioactivity-guided isolation, four new stilbene-like derivatives, named Strebluses E-H, were isolated from the EtOAc-soluble fraction of the stems of Streblus ilicifolius (Moraceae). Their chemical structures were elucidated based on NMR spectroscopic data interpretation and optical rotation calculation. Streblus E possesses potent tyrosinase inhibitory activity with an IC50 value of 0.1 μM. Oxy-tyrosinase has two bound Cu2+ ions and a peroxide group in the binding site, which has a role in the catalytic oxidation. Thus, a docking study of Streblus E with oxy-tyrosinase was performed to analyze the ligand-protein interactions. With in silico modelling, the S value and the ligand-protein interactions suggested that Streblus E showed lower binding affinity for oxy-tyrosinase than that of Streblus C.
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Affiliation(s)
- Tho Huu Le
- Faculty of Chemistry, University of ScienceHo Chi Minh City72711Vietnam,Vietnam National UniversityHo Chi Minh City71300Vietnam,Research Lab for Drug Discovery and Development, University of ScienceHo Chi Minh City72711Vietnam
| | - Phu Hoang Dang
- Faculty of Chemistry, University of ScienceHo Chi Minh City72711Vietnam,Vietnam National UniversityHo Chi Minh City71300Vietnam,Research Lab for Drug Discovery and Development, University of ScienceHo Chi Minh City72711Vietnam
| | - Hai Xuan Nguyen
- Faculty of Chemistry, University of ScienceHo Chi Minh City72711Vietnam,Vietnam National UniversityHo Chi Minh City71300Vietnam,Research Lab for Drug Discovery and Development, University of ScienceHo Chi Minh City72711Vietnam
| | - Truong Nhat Van Do
- Faculty of Chemistry, University of ScienceHo Chi Minh City72711Vietnam,Vietnam National UniversityHo Chi Minh City71300Vietnam,Research Lab for Drug Discovery and Development, University of ScienceHo Chi Minh City72711Vietnam
| | - Nhan Trung Nguyen
- Faculty of Chemistry, University of ScienceHo Chi Minh City72711Vietnam,Vietnam National UniversityHo Chi Minh City71300Vietnam,Research Lab for Drug Discovery and Development, University of ScienceHo Chi Minh City72711Vietnam
| | - Mai Thanh Thi Nguyen
- Faculty of Chemistry, University of ScienceHo Chi Minh City72711Vietnam,Vietnam National UniversityHo Chi Minh City71300Vietnam,Research Lab for Drug Discovery and Development, University of ScienceHo Chi Minh City72711Vietnam
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Dang PH, Nguyen HX, Le TH, Van Do TN, Nguyen MTT, Nguyen NT. A New abeo-Icetexane-Type Diterpenoid from the Stem Barks of Taxus wallichiana. Chem Biodivers 2022; 19:e202200520. [PMID: 36380709 DOI: 10.1002/cbdv.202200520] [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: 05/26/2022] [Accepted: 11/15/2022] [Indexed: 11/17/2022]
Abstract
From a CH2 Cl2 -soluble fraction of the stem barks of Taxus wallichiana, one new abeo-icetexane-type diterpenoid, taxamairin I (1), was isolated. Its absolute configuration was elucidated based on spectroscopic interpretation and time-dependent density functional theory (TD-DFT) calculation of optical rotation. In addition, the plausible biosynthesis pathway for the formation of the new abeo-icetexane-type diterpenoid was proposed. Taxamairin I (1), at a concentration of 100 μM, did not show cytotoxicity against Hep3B human liver cancer cell lines.
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Affiliation(s)
- Phu Hoang Dang
- Faculty of Chemistry, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
- Research Lab for Drug Discovery and Development, University of Science, Ho Chi Minh City, Vietnam
| | - Hai Xuan Nguyen
- Faculty of Chemistry, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
- Research Lab for Drug Discovery and Development, University of Science, Ho Chi Minh City, Vietnam
| | - Tho Huu Le
- Faculty of Chemistry, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
- Research Lab for Drug Discovery and Development, University of Science, Ho Chi Minh City, Vietnam
| | - Truong Nhat Van Do
- Faculty of Chemistry, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
- Research Lab for Drug Discovery and Development, University of Science, Ho Chi Minh City, Vietnam
| | - Mai Thanh Thi Nguyen
- Faculty of Chemistry, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
- Research Lab for Drug Discovery and Development, University of Science, Ho Chi Minh City, Vietnam
- Cancer Research Laboratory, University of Science, Ho Chi Minh City, Vietnam
| | - Nhan Trung Nguyen
- Faculty of Chemistry, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
- Research Lab for Drug Discovery and Development, University of Science, Ho Chi Minh City, Vietnam
- Cancer Research Laboratory, University of Science, Ho Chi Minh City, Vietnam
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de Albuquerque Barros G, Henrique Morgon N. Finding reliable methodology for optical rotation and correct predictions of (s)-methyloxirane and (1R,5R)-β-pinene. Chirality 2022; 34:1197-1208. [PMID: 35670135 DOI: 10.1002/chir.23479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 12/25/2022]
Abstract
Theoretical calculations of optical rotation (OR), although important to predict absolute configurations (ACs) and corroborate experiments, require efficient methodology able to reproduce enantiomer specificity and real OR values. Also, troublesome molecules are recurring in the literature, such as (S)-methyloxirane and (1R,5R)-β-pinene. This study evaluates DFT functionals B3LYP, CAM-B3LYP, ωB97X-D, M06-2X, and PBE0 considering basis sets aug-cc-pVDZ, aug-cc-pVTZ, 6-311++G(2d,p), and 6-311++G(3df,2p) in OR prediction of 42 rigid organic molecules assessing cases with wrong enantiomeric determination comparing to available experimental data at wavelengths 355, 589, and 633 nm. Functionals CAM-B3LYP and ωB97X-D with aug-cc-pVTZ are indicated here to reproduce experimental values more accurately considering fewer number of wrong AC predictions, normalized RMSD values below 0.70, and a good approximation to experimental values in hierarchical cluster analysis. Methyloxirane AC was reproduced in CAM-B3LYP and PBE0, with [ α ] 355 = 6 . 94 $$ {\left[\alpha \right]}_{355}=6.94 $$ for CAM-B3LYP/aug-cc-pVTZ close to experimental value [ α ] 355 = 7 . 49 ± 0 . 30 $$ {\left[\alpha \right]}_{355}=7.49\pm 0.30 $$ . Good results were found for AC of β-pinene in M06-2X, CAM-B3LYP, and ωB97X-D while the latter in 6-311++G(3df,2p) obtained OR values of [ α ] 589 = 3 . 44 $$ {\left[\alpha \right]}_{589}=3.44 $$ and [ α ] 689 = 4 . 20 $$ {\left[\alpha \right]}_{689}=4.20 $$ close to experimental values [ α ] 589 = 2 . 8 $$ {\left[\alpha \right]}_{589}=2.8 $$ and [ α ] 689 = 4 . 66 ± 0 . 60 $$ {\left[\alpha \right]}_{689}=4.66\pm 0.60 $$ . The two molecules aforementioned are, for the first time, reported to give valid theoretical OR values in such simple methodologies. OR calculations were all performed after geometry optimization at the same level of theory, and analysis of different functional combinations for each step in β-pinene showed it can interfere with AC prediction even in rigid molecules.
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Affiliation(s)
| | - Nelson Henrique Morgon
- Department of Physical Chemistry, Institute of Chemistry, Campinas State University, Campinas, Brazil
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Morgante P, Ludowieg HD, Autschbach J. Comparative Study of Vibrational Raman Optical Activity with Different Time-Dependent Density Functional Approximations: The VROA36 Database. J Phys Chem A 2022; 126:2909-2927. [PMID: 35512708 DOI: 10.1021/acs.jpca.2c00951] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A new database, VROA36, is introduced to investigate the performance of computational approaches for vibrational Raman optical activity (VROA) calculations. The database is composed of 36 molecules with known experimental VROA spectra. It includes 93 conformers. Normal modes calculated with B3LYP-D3(BJ)/def2-TZVP are used to compute the VROA spectra with four functionals, B3LYP-D3(BJ), ωB97X-D, M11, and optimally tuned LC-PBE, as well as several basis sets. SimROA indices and frequency scaling factors are used to compare calculated spectra with each other and with experimental data. The four functionals perform equally well independently of the basis set and usually achieve good agreement with the experimental data. For molecules in near- or at-resonance conditions, the inclusion of a complex (damped) linear response approach is important to obtain physically meaningful VROA intensities. The use of any of the tested functional approximations with the def2-SVPD Gaussian-type basis set, or a basis of similar flexibility, can be recommended for efficient and reliable theoretical VROA studies.
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Affiliation(s)
- Pierpaolo Morgante
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
| | - Herbert D Ludowieg
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
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Parsons T, Balduf T, Cheeseman JR, Caricato M. Basis Set Dependence of Optical Rotation Calculations with Different Choices of Gauge. J Phys Chem A 2022; 126:1861-1870. [PMID: 35271772 DOI: 10.1021/acs.jpca.2c00201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, the basis set dependence of optical rotation (OR) calculations is examined for various choices of gauge/level of theory. The OR is calculated for a set of 50 molecules using B3LYP and CAM-B3LYP and 17 molecules using coupled cluster with single and double excitations (CCSD). The calculations employ the correlation-consistent basis sets, aug-cc-pVζZ with ζ = D, T, Q. An inverse-power extrapolation formula is then utilized to obtain OR values at the complete basis set (CBS) limit. We investigate the basis set convergence for these methods and three choices of gauge: length gauge (with gauge-including atomic orbitals, LG(GIAOs), for DFT), the origin-invariant length gauge [LG(OI)], and the modified velocity gauge (MVG). The results show that all methods converge smoothly to the CBS limit and that the LG(OI) approach has a slightly faster convergence rate than the other choices of gauge. While the DFT methods reach gauge invariance at the CBS limit, CCSD does not. The significant difference between the MVG and LG(OI) results at the CBS limit, 26%, indicates that CCSD is not quite at convergence in the description of electron correlation for this property. On the other hand, gauge invariance at the CBS limit for DFT does not lead to the same OR values for the two density functionals, which is also due to electron correlation incompleteness. A limited comparison to gas-phase experimental OR values for the DFT methods shows that CAM-B3LYP seems more accurate than B3LYP. Overall, this study shows that the LG(OI) approach with the aug-cc-pVTZ basis set for DFT, and with the CBS(DT) extrapolation for CCSD, provides a good cost/accuracy balance.
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Affiliation(s)
- Taylor Parsons
- Department of Chemistry, University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
| | - Ty Balduf
- Department of Chemistry, University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
| | - James R Cheeseman
- Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, United States
| | - Marco Caricato
- Department of Chemistry, University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
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Tyrosinase Inhibitors from the Stems of Streblus Ilicifolius. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:5561176. [PMID: 34306141 PMCID: PMC8266447 DOI: 10.1155/2021/5561176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/25/2021] [Indexed: 01/31/2023]
Abstract
Two new stilbene derivatives, named strebluses C and D, were isolated from the EtOAc-soluble fraction of the stems of Streblus ilicifolius (Moraceae). Its absolute configuration was elucidated based on NMR spectroscopic data interpretation and optical rotation calculation. Streblus C possesses strong tyrosinase inhibitory activity with an IC50 value of 0.01 μM. Docking studies of 1 and 2 with oxy-tyrosinase were carried out to analyze their interactions. The analysis of the docked poses confirmed that 1 showed better binding affinity for oxy-tyrosinase than that of 2.
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Galeano Carrano RS, Provasi PF, Ferraro MB, Alkorta I, Elguero J, Sauer SPA. A Density Functional Theory Study of Optical Rotation in Some Aziridine and Oxirane Derivatives. Chemphyschem 2021; 22:764-774. [PMID: 33528071 DOI: 10.1002/cphc.202001010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/01/2021] [Indexed: 12/25/2022]
Abstract
We present time-dependent density functional theory (TDDFT) calculations of the electronic optical rotation (ORP) for seven oxirane and two aziridine derivatives in the gas phase and in solution and compare the results with the available experimental values. For seven of the studied molecules it is the first time that their optical rotation was studied theoretically and we have therefore investigated the influence of several settings in the TDDFT calculations on the results. This includes the choice of the one-electron basis set, the exchange-correlation functional or the particular polarizable continuum model (PCM). We can confirm that polarized quadruple zeta basis sets augmented with diffuse functions are necessary for converged results and find that the aug-pc-3 basis set is a viable alternative to the frequently employed aug-cc-pVQZ basis set. Based on our study, we cannot recommend the generalized gradient functional KT3 for calculations of the ORP in these compounds, whereas the hybrid functional PBE0 gives results quite similar to the long-range correct CAM-B3LYP functional. Finally, we observe large differences in the solvent effects predicted by the integral equation formalism of PCM and the SMD variant of PCM. For the majority of solute/solvent combinations in this study, we find that the SMD model in combination with the PBE0 functional and the aug-pc-3 basis set gives the best agreement with the experimental values.
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Affiliation(s)
- Ramiro S Galeano Carrano
- Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Argentina
| | - Patricio F Provasi
- Department of Physics, IMIT, Northeastern University, CONICET, Corrientes, Argentina
| | - Marta B Ferraro
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IFIBA, CONICET, Buenos Aires, Argentina
| | - Ibon Alkorta
- Instituto de Química Médica (C.S.I.C.), Madrid, Spain
| | - José Elguero
- Instituto de Química Médica (C.S.I.C.), Madrid, Spain
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
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Mamede R, de-Almeida BS, Chen M, Zhang Q, Aires-de-Sousa J. Machine Learning Classification of One-Chiral-Center Organic Molecules According to Optical Rotation. J Chem Inf Model 2020; 61:67-75. [PMID: 33350814 DOI: 10.1021/acs.jcim.0c00876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, machine learning algorithms were investigated for the classification of organic molecules with one carbon chiral center according to the sign of optical rotation. Diverse heterogeneous data sets comprising up to 13,080 compounds and their corresponding optical rotation were retrieved from Reaxys and processed independently for three solvents: dichloromethane, chloroform, and methanol. The molecular structures were represented by chiral descriptors based on the physicochemical and topological properties of ligands attached to the chiral center. The sign of optical rotation was predicted by random forests (RF) and artificial neural networks for independent test sets with an accuracy of up to 75% for dichloromethane, 82% for chloroform, and 82% for methanol. RF probabilities and the availability of structures in the training set with the same spheres of atom types around the chiral center defined applicability domains in which the accuracy is higher.
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Affiliation(s)
- Rafael Mamede
- LAQV and REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica 2829-516, Portugal
| | - Bruno Simões de-Almeida
- LAQV and REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica 2829-516, Portugal
| | - Mengyao Chen
- Henan Engineering Research Center of Industrial Circulating Water Treatment, Henan Joint International Research Laboratory of Environmental Pollution Control Materials, Henan University, Kaifeng 475004, PR China
| | - Qingyou Zhang
- Henan Engineering Research Center of Industrial Circulating Water Treatment, Henan Joint International Research Laboratory of Environmental Pollution Control Materials, Henan University, Kaifeng 475004, PR China
| | - Joao Aires-de-Sousa
- LAQV and REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica 2829-516, Portugal
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