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Liu XM, Xia QY, Ju XH. Theoretical study on optimizing dipeptidomimetic isocyanonaphthalene chemosensor and the fluorescence mechanism for detecting Hg 2. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 322:124835. [PMID: 39024787 DOI: 10.1016/j.saa.2024.124835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/10/2024] [Accepted: 07/13/2024] [Indexed: 07/20/2024]
Abstract
The excited (S1) state charge distribution characteristics and fluorescence mechanism of fluorescence probes benzyl (6-cyano-2-naphthoyl)-L-valinate (NPI) and benzyl (6-amino-2-naphthoyl)-L-valinate (NPA) have been discussed using density functional theory (DFT) and time-dependent density functional theory (TD-DFT). Further analysis by constructing a torsional potential energy curve (PEC) shows that a well-defined minimum energy conformation is observed when the C-C single bond between the valine benzyl ester and naphthalene ring in NPI rotates. For NPA, the most stable conformation is the naphthalene ring conformation with dihedral angle N2C1C2C3 of -30.60°, whose total energy is 0.17 kcal/mol lower than that of the second most stable conformer. The frontier molecular orbitals (FMOs) demonstrate that NPI exhibits a low degree of charge coupling, and the oscillator intensity is close to zero, indicating that it is not conducive to luminescence. However, in the S1 state, the oscillator strength of NPA is 1.2044, which is a bright state, resulting in the strong emitting. Additionally, fluorescence imaging is favored as a visual observation technique, and Stokes shift is an important physical parameter to measure fluorescence. According to the idea that changing the number and position of functional groups can affect the photophysical properties of fluorescent dyes, o-NPDI, p-NPDI and m-NPDI dyes were newly designed and o-NPDA, p-NPDA, m-NPDA produced after recognition of Hg2+. The spectral performance results show that the newly designed fluorescent dye (p-NPDA) can not only emit in the near infrared region after recognizing Hg2+, but also has a large Stokes shift (236 nm). This indirectly reflects that para-substitution is more conducive to Stokes shift, and has become one of the strategies for fluorescent dye design.
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Affiliation(s)
- Xiu-Min Liu
- Key Laboratory of Soft Chemistry and Functional Materials of MOE, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, PR China
| | - Qi-Ying Xia
- School of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, PR China.
| | - Xue-Hai Ju
- Key Laboratory of Soft Chemistry and Functional Materials of MOE, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, PR China.
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2
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Mu H, Yang M, Wang S, Zhang Y, Guan X, Li H, Jin G. Concerning for the solvent-polarity-dependent conformational equilibrium and ESIPT mechanism in Pz3HC system: A novel insight. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 317:124412. [PMID: 38733913 DOI: 10.1016/j.saa.2024.124412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/17/2024] [Accepted: 05/05/2024] [Indexed: 05/13/2024]
Abstract
In this report, we propose a new insight into the interaction between the solvent-polarity-dependent conformational equilibrium and excited state intramolecular proton transfer (ESIPT) behavior of Pz3HC system in four different polar solvents (polarity order: ACN > THF > TOL > CYC). Using quantum chemistry method, we first announce a coexistence mechanism between Pz3HC-1 and Pz3HC-3 in the ground state in four solvents based on the Boltzmann distribution. In particular, Pz3HC-1 is the principal configuration in non-polar solvent, but Pz3HC-3 is the principal configuration in polar solvent. In addition, the simulated fluorescence spectra interprets the negative solvatochromism effect of Pz3HC-1 and Pz3HC-3 in four solvents. The evidence from intramolecular hydrogen bonding (IHB) parameters and electronic perspective collectively confirms the light-induced IHB enhancement and intramolecular charge transfer (ICT) properties in Pz3HC-1 and Pz3HC-3, which raises the likelihood of the ESIPT process. Combining the calculation of potential energy curve (PEC) and intrinsic reaction coordinate (IRC), we demonstrate that the ESIPT ease of Pz3HC-1 in different polar solvents obeys the order of CYC > TOL > THF > ACN, while the order of ESIPT ease in Pz3HC-3 is opposite. Notably, the ESIPT process of Pz3HC-3 in CYC solvent is accompanied by the twisted intramolecular charge transfer (TICT) process. In addition, we also reveal that the enol* and keto* fluorescence peaks of Pz3HC-3 in CYC solvent are quenched by ISC and TICT process, respectively. Our work not only provides a satisfactory explanation of the novel dynamics mechanism for Pz3HC system, but also brings light to the design and application of new sensing molecules in the future.
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Affiliation(s)
- Hongyan Mu
- Jilin Key Laboratory of Solid-State Laser Technology and Application, School of Physics, Changchun University of Science and Technology, Changchun 130022, China
| | - Min Yang
- Jilin Key Laboratory of Solid-State Laser Technology and Application, School of Physics, Changchun University of Science and Technology, Changchun 130022, China
| | - Siqi Wang
- Jilin Key Laboratory of Solid-State Laser Technology and Application, School of Physics, Changchun University of Science and Technology, Changchun 130022, China
| | - Yifu Zhang
- Jilin Key Laboratory of Solid-State Laser Technology and Application, School of Physics, Changchun University of Science and Technology, Changchun 130022, China
| | - Xiaotong Guan
- Jilin Key Laboratory of Solid-State Laser Technology and Application, School of Physics, Changchun University of Science and Technology, Changchun 130022, China
| | - Hui Li
- Jilin Key Laboratory of Solid-State Laser Technology and Application, School of Physics, Changchun University of Science and Technology, Changchun 130022, China.
| | - Guangyong Jin
- Jilin Key Laboratory of Solid-State Laser Technology and Application, School of Physics, Changchun University of Science and Technology, Changchun 130022, China.
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Shi T, Wang Z, Aldossary A, Liu Y, Li XS, Head-Gordon M. Local Second Order Mo̷ller-Plesset Theory with a Single Threshold Using Orthogonal Virtual Orbitals: A Distributed Memory Implementation. J Chem Theory Comput 2024. [PMID: 39221855 DOI: 10.1021/acs.jctc.4c01016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
In order to alleviate the computational burden associated with superlinear compute scalings with molecular size in electron correlation methods, researchers have developed local correlation methods that wisely treat relatively small contributions as zeros but still yield accurate energy approximation. Such local correlation techniques can also be combined with parallel computing resources to obtain further efficiency and scalability. This work focuses on the distributed memory parallel implementation of a local correlation method for second order Mo̷ller-Plesset (MP2) theory. This method also only has a single threshold to control the dropping of terms and accuracy of different computing kernels in the algorithm. The process partitioning strategy and distributed parallel implementation with the message passing interface (MPI) are discussed. In particular, the algorithm relies on a fixed sparsity pattern matrix multiplication and a corresponding distributed conjugate gradient solver, which exhibits almost linear scaling in both strong and weak scaling analyses. Numerical experiments on a range of molecules, including linear chains and molecules with 2 and 3-dimensional characters, are reported. For example, with only 32 MPI ranks, this MP2 implementation can calculate the correlation energy of vancomycin in def2-TZVP basis within 0.003% accuracy (10-6.5 threshold) in half an hour, where the same problem is unfeasible to solve with sequential or pure shared memory implementations.
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Affiliation(s)
- Tianyi Shi
- Applied Mathematics and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Zhenling Wang
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | | | - Yang Liu
- Applied Mathematics and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Xiaoye S Li
- Applied Mathematics and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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4
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Benoune RA, Dems MA, Boulcina R, Bensouici C, Robert A, Harakat D, Debache A. Synthesis, biological evaluation, theoretical calculations, QSAR and molecular docking studies of novel arylaminonaphthols as potent antioxidants and BChE inhibitors. Bioorg Chem 2024; 150:107598. [PMID: 38959645 DOI: 10.1016/j.bioorg.2024.107598] [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: 03/31/2024] [Revised: 06/12/2024] [Accepted: 06/17/2024] [Indexed: 07/05/2024]
Abstract
A completely green protocol was developed for the synthesis of a series of arylaminonaphthol derivatives in the presence of N-ethylethanolamine (NEEA) as a catalyst under ultrasonic irradiation and solventless conditions. The major assets of this methodology were the use of non-toxic organic medium, available catalyst, mild reaction condition, and good to excellent yield of desired products. All of the synthesized products were screened for their in vitro antioxidant activity using DPPH, ABTS, and Ferric-phenanthroline assays and it was found that most of them are potent antioxidant agents. Also, their butyrylcholinesterase inhibitory activity has been investigated in vitro. All tested compounds exhibited potential inhibitory activity toward BuChE when compared to standard reference drug galantamine, however, compounds 4r, 4u, 4 g and 4x gave higher butyrylcholinesterase inhibitory with IC50 values of 14.78 ± 0.65 µM, 16.18 ± 0.50 µM, 20.00 ± 0.50 µM, and 20.28 ± 0.08 µM respectively. On the other hand, we employed density functional theory (DFT), calculations to analyze molecular geometry and global reactivity descriptors, and MESP analysis to predict electrophilic and nucleophilic attacks. A quantitative structure-activity relationship (QSAR) investigation was conducted on the antioxidant and butyrylcholinesterase properties of 25 arylaminonaphthol derivatives, resulting in robust and satisfactory models. To evaluate their anti-Alzheimer's activity, compounds 4 g, 4q, 4r, 4u, and 4x underwent docking simulations at the active site of the acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), revealing why these compounds displayed superior activity, consistent with the biological findings.
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Affiliation(s)
- Racha Amira Benoune
- Laboratory of Synthesis of Molecules with Biological Interest, Faculty of Exact Sciences, Mentouri - Constantine 1 University, 25000 Constantine, Algeria
| | | | - Raouf Boulcina
- Laboratory of Synthesis of Molecules with Biological Interest, Faculty of Exact Sciences, Mentouri - Constantine 1 University, 25000 Constantine, Algeria; Department of Engineering Process, Faculty of Technology, Mostefa Benboulaïd-Batna 2 University, 5000 Batna, Algeria.
| | | | - Anthony Robert
- Reims Champagne-Ardenne University, CNRS UMR 7312, ICMR, URCATech, 51100 Reims, France
| | - Dominique Harakat
- Reims Champagne-Ardenne University, CNRS UMR 7312, ICMR, URCATech, 51100 Reims, France
| | - Abdelmadjid Debache
- Laboratory of Synthesis of Molecules with Biological Interest, Faculty of Exact Sciences, Mentouri - Constantine 1 University, 25000 Constantine, Algeria
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5
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Zhang W, Ding S, Zhang J, Cheng Z, Wu Z. A 2D low-buckled hexagonal honeycomb Weyl-point spin-gapless semiconductor family with the quantum anomalous Hall effect. NANOSCALE 2024. [PMID: 39189678 DOI: 10.1039/d4nr00120f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
Spin-gapless semiconductors (SGSs), serving as superior alternatives to half-metals, open up new avenues in spintronics. Specifically, Weyl-point SGSs (WPSGSs) with ideal Weyl points at the Fermi energy level represent an optimal amalgamation of spintronics and topological physics. Moreover, considering spin-orbital coupling (SOC), most two-dimensional (2D) WPSGSs undergo transformation into half Chern insulators (HCIs) with the emergence of the quantum anomalous Hall effect (QAHE). The 2D I-II-V half-Heusler compounds, constituting a broad family of narrow-bandgap semiconductors with low-buckled hexagonal honeycomb crystal structures akin to silicene, aptly function as SGSs and serve as nontrivial topological parent materials. Through first-principles calculations, we propose that the Li12X10Cr2Y12 (X = Mg, Zn, Cd; Y = P, As) monolayers, derived by substituting certain X atoms in the LiXY (X = Mg, Zn, Cd; Y = P, As) monolayers of I-II-V half-Heusler compounds with Cr atoms, emerge as potential candidates for ideal 2D WPSGSs. These monolayers exhibit stable thermodynamic properties and 100% spin polarization. With SOC taken into account, the Li12X10Cr2Y12 monolayers transition into HCIs with a Chern number of +1, giving rise to the QAHE. These intriguing findings lay the groundwork for a promising material platform for the development of low-power spintronic and topological microelectronic devices.
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Affiliation(s)
- Weihua Zhang
- School of Physics and Electronic Engineering, Chongqing Normal University, Chongqing 401331, China.
| | - Shoubing Ding
- School of Physics and Electronic Engineering, Chongqing Normal University, Chongqing 401331, China.
| | - Jie Zhang
- School of Physics and Electronic Engineering, Chongqing Normal University, Chongqing 401331, China.
| | - Zhenxiang Cheng
- Institute for Superconducting and Electronic Materials (ISEM), University of Wollongong, Wollongong 2500, Australia.
| | - Zhimin Wu
- School of Physics and Electronic Engineering, Chongqing Normal University, Chongqing 401331, China.
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6
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Moradi S, Tomann R, Hendrix J, Head-Gordon M, Stein CJ. Spin parameter optimization for spin-polarized extended tight-binding methods. J Comput Chem 2024. [PMID: 39175165 DOI: 10.1002/jcc.27482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 07/24/2024] [Accepted: 07/30/2024] [Indexed: 08/24/2024]
Abstract
We present an optimization strategy for atom-specific spin-polarization constants within the spin-polarized GFN2-xTB framework, aiming to enhance the accuracy of molecular simulations. We compare a sequential and global optimization of spin parameters for hydrogen, carbon, nitrogen, oxygen, and fluorine. Sensitivity analysis using Sobol indices guides the identification of the most influential parameters for a given reference dataset, allowing for a nuanced understanding of their impact on diverse molecular properties. In the case of the W4-11 dataset, substantial error reduction was achieved, demonstrating the potential of the optimization. Transferability of the optimized spin-polarization constants over different properties, however, is limited, as we demonstrate by applying the optimized parameters on a set of singlet-triplet gaps in carbenes. Further studies on ionization potentials and electron affinities highlight some inherent limitations of current extended tight-binding methods that can not be resolved by simple parameter optimization. We conclude that the significantly improved accuracy strongly encourages the present re-optimization of the spin-polarization constants, whereas the limited transferability motivates a property-specific optimization strategy.
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Affiliation(s)
- Siyavash Moradi
- Department of Chemistry, Technical University of Munich, TUM School of Natural Sciences and Catalysis Research Center, Garching, Germany
| | - Rebecca Tomann
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California, USA
| | - Josie Hendrix
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California, USA
| | - Martin Head-Gordon
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California, USA
| | - Christopher J Stein
- Department of Chemistry, Technical University of Munich, TUM School of Natural Sciences and Catalysis Research Center, Garching, Germany
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7
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Ayub AR, Akram W, Yaqoob U, Salba, Maqsood N, Rafiq S, Nabat KY, Anwer A, Somaily HH, Alansari A, Iqbal J. Optoelectronic analysis of designed semi-circular shaped thiophene-based bridged Y-series NFAs for organic solar cell applications. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 324:125022. [PMID: 39186876 DOI: 10.1016/j.saa.2024.125022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/29/2024] [Accepted: 08/20/2024] [Indexed: 08/28/2024]
Abstract
The highly adaptable optoelectronic and morphological properties of non-fullerene acceptors (NFAs) have made them a prominent research topic in the organic solar cell (OSC) field. This work describes the design of new molecules and investigates the potential optoelectronic aspects of remodified Y-series NFAs endowing with five new semi-circular shaped derivatives (BTPB1-BTPB5) based on the DFT-based quantum simulations. The designed molecules possess higher-lying LUMO energy levels with narrowed bandgaps and excellent coherence between the acceptor and core via inserted bridges. The molecules demonstrate a significant red shift and a wide-ranging absorption spectrum extending from 400 nm to 1500 nm, with the most extensive absorption occurring in the near-infrared (NIR) region. Effective π-π stacking and drastically lower binding energy certify facile charge dissociation and transmission rate. Thiophene-based bridge modification decreased reorganization energy by 47 % which results in facile charge transmission and high current density. Theoretically, simulated PCE is achieved as high as 31.49 % owing to the higher-lying LUMOs. The results demonstrate the value of designing systems and exploring new possibilities for developing effective Y-series NFAs-based high-performance organic solar cells.
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Affiliation(s)
- Ali Raza Ayub
- Key Laboratory of Clusters Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, PR China
| | - Waqas Akram
- Department of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan
| | - Umer Yaqoob
- Department of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan
| | - Salba
- Department of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan
| | - Nimra Maqsood
- University of Science and Technology of China, No. 96 Jinzhai Road, Hefei, 23002 Anhui, PR China
| | - Sidra Rafiq
- Department of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan
| | - Karim Youssef Nabat
- Key Laboratory of Clusters Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, PR China
| | - Arslan Anwer
- Department of Chemistry, University of Education, Lahore, Punjab 54770, Pakistan
| | - H H Somaily
- Department of Physics, Faculty of Science, King Khalid University, P.O. Box 9004, Abha, Saudi Arabia
| | - Abdulkarim Alansari
- Mechanical Engineering Department, College of Engineering, Northern Border University, Arar, Saudi Arabia
| | - Javed Iqbal
- Department of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan.
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8
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Song M, Alavi A, Li Manni G. Permutation symmetry in spin-adapted many-body wave functions. Faraday Discuss 2024. [PMID: 39158096 DOI: 10.1039/d4fd00061g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
In the domain of exchange-coupled polynuclear transition-metal (PNTM) clusters, local emergent symmetries exist which can be exploited to greatly increase the sparsity of the configuration interaction (CI) eigensolutions of such systems. Sparsity of the CI secular problem is revealed by exploring the site permutation space within spin-adapted many-body bases, and highly compressed wave functions may arise by finding optimal site orderings. However, the factorial cost of searching through the permutation space remains a bottleneck for clusters with a large number of metal centers. In this work, we explore ways to reduce the factorial scaling, by combining permutation and point group symmetry arguments, and using commutation relations between cumulative partial spin and the Hamiltonian operators, . Certain site orderings lead to commuting operators, from which more sparse wave functions arise. Two graphical strategies will be discussed, one to rapidly evaluate the commutators of interest, and one in the form of a tree search algorithm to predict how many and which distinct site permutations are to be analyzed, eliminating redundancies in the permutation space. Particularly interesting is the case of the singlet spin states for which an additional reversal symmetry can be utilized to further reduce the number of distinct site permutations.
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Affiliation(s)
- Maru Song
- Electronic Structure Theory Department, Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany.
| | - Ali Alavi
- Electronic Structure Theory Department, Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany.
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Giovanni Li Manni
- Electronic Structure Theory Department, Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany.
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9
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Opi MH, Ahmed T, Swarna MR, Piya AA, Shamim SUD. Assessment of the drug delivery potential of graphene, boron nitride and their in-plane doped structures for hydroxyurea anti-cancer drug via DFT study. NANOSCALE ADVANCES 2024:d4na00428k. [PMID: 39148501 PMCID: PMC11322902 DOI: 10.1039/d4na00428k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 07/30/2024] [Indexed: 08/17/2024]
Abstract
Globally, cancer is the most common cause of mortality among all deadly diseases. As a result, a nanotechnology-based drug delivery system is used to improve the efficacy of cancer treatment, which provides an improved therapeutic index and delivers multiple drugs directly to the tumor site. In the present work, DFT calculations were employed to investigate the surface adsorption of a hydroxyurea (HU) anticancer drug on pristine graphene (GP), boron nitride (B24N24), and doped GP by replacing some of its carbon atoms with boron (B) and nitrogen (N) atoms to form C30B9N9, C16B16N16, and C6B21N21 nanosheets. In gas media, HU is adsorbed on these C30B9N9, C16B16N16, C6B21N21, and B24N24 nanosheets with adsorption energies of -0.70, -3.03, -2.47, and -1.96 eV, respectively. Alternatively, in water solvent media, the adsorption energies of C30B9N9, C16B16N16, C6B21N21, and B24N24 are -0.82, -0.29, -0.15, and -0.26 eV, respectively. The energy gaps of the nanosheets were found to be 0.288, 0.174, 0.14, and 4.562 eV before adsorption, respectively. After the adsorption of HU on the proposed nanosheets, the energy gap was reduced to 0.15 eV for C16B16N16. According to the DOS spectra, noticeable peaks appeared in the Fermi level after the adsorption of HU on the nanosheets, which indicates the reduction of the energy gap. Quantum molecular analysis predicted that the chemical potential, electrophilicity index, and nucleophilicity index of C16B16N16 increased, whereas global hardness decreased, indicating high reactivity. Therefore, it can be concluded that among the proposed nanosheets, C16B16N16 would be an appropriate carrier for the HU drug.
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Affiliation(s)
- Mehedi Hasan Opi
- Department of Physics, Mawlana Bhashani Science and Technology University Tangail Bangladesh
| | - Tanvir Ahmed
- Department of Physics, Mawlana Bhashani Science and Technology University Tangail Bangladesh
| | - Mithila Roy Swarna
- Department of Physics, Mawlana Bhashani Science and Technology University Tangail Bangladesh
| | - Afiya Akter Piya
- Department of Physics, Mawlana Bhashani Science and Technology University Tangail Bangladesh
| | - Siraj Ud Daula Shamim
- Department of Physics, Mawlana Bhashani Science and Technology University Tangail Bangladesh
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10
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Voss J. Machine learning for accuracy in density functional approximations. J Comput Chem 2024; 45:1829-1845. [PMID: 38668453 DOI: 10.1002/jcc.27366] [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: 10/30/2023] [Revised: 02/16/2024] [Accepted: 03/25/2024] [Indexed: 07/21/2024]
Abstract
Machine learning techniques have found their way into computational chemistry as indispensable tools to accelerate atomistic simulations and materials design. In addition, machine learning approaches hold the potential to boost the predictive power of computationally efficient electronic structure methods, such as density functional theory, to chemical accuracy and to correct for fundamental errors in density functional approaches. Here, recent progress in applying machine learning to improve the accuracy of density functional and related approximations is reviewed. Promises and challenges in devising machine learning models transferable between different chemistries and materials classes are discussed with the help of examples applying promising models to systems far outside their training sets.
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Affiliation(s)
- Johannes Voss
- SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, Menlo Park, California, USA
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11
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Keivanloo M, Sandoghchi M, Mohammadizadeh MR, Khazaei M. Study on superconductivity in Nb 2 SC and Nb 2 AsC MAX phases at various pressures. Sci Rep 2024; 14:17516. [PMID: 39080294 PMCID: PMC11289396 DOI: 10.1038/s41598-024-66909-x] [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: 06/09/2024] [Accepted: 07/05/2024] [Indexed: 08/02/2024] Open
Abstract
Nb 2 SC and Nb 2 AsC are among the identified superconducting MAX phases, both exhibiting a transition temperature T c lower than 10 K. These compounds appear to belong to the conventional class of superconductors. By calculating the electron-phonon couplings of these materials, we have found that the predicted transition temperatures are approximately 6 K for Nb 2 SC and 2 K for Nb 2 AsC, closely matching the experimental findings. However, when subjected to pressure or strain, Nb 2 SC and Nb 2 AsC exhibit contrasting behaviors. While the transition temperature of Nb 2 SC can be doubled by applying pressure up to 50 GPa, the transition temperature of Nb 2 AsC significantly decreases under the same pressure. On the other hand, in the case of Nb 2 AsC, a uniaxial tensile strain of approximately 2% along the c direction can enhance the compound's transition temperature by about 40%. These results show that with the right pressure or strain, it is possible to increase superconducting transition temperature in the Nb 2 AC compounds.
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Affiliation(s)
- Mohammad Keivanloo
- Department of Physics, University of Tehran, North Kargar Ave, Tehran, 14395-547, Iran
| | - Mohammad Sandoghchi
- Department of Physics, University of Tehran, North Kargar Ave, Tehran, 14395-547, Iran.
| | - Mohammad Reza Mohammadizadeh
- Department of Physics, University of Tehran, North Kargar Ave, Tehran, 14395-547, Iran
- Superconductivity Research Laboratory (SRL), Department of Physics, University of Tehran, North Kargar Ave., Tehran, 14395-547, Iran
| | - Mohammad Khazaei
- Department of Physics, University of Tehran, North Kargar Ave, Tehran, 14395-547, Iran.
- School of Nano Science, Institute for Research in Fundamental Sciences (IPM), Tehran, 19395-5531, Iran.
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12
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Joyner NA, Romeu JGF, Kent B, Dixon DA. The electronic structure of diatomic nickel oxide. Phys Chem Chem Phys 2024; 26:19646-19657. [PMID: 38957895 DOI: 10.1039/d4cp01796j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
The nature of the Ni-O bond is relevant to catalytic and environmental applications. The vibrational frequency and electronic structure of NiO were calculated using CASSCF, icMRCI+Q, CCSD(T), and DFT. CASSCF predicted a quintet state (5Σ-) ground state for the equilibrium bond distance with a state crossing at 1.65 Å, where the triplet (3Σ-) state becomes of lower energy. These states arise from the 3d8(3F)4s2 (3F) and 3d9(2D)4s1 (3D) configurations of Ni. The icMRCI+Q method predicts a triplet (3Σ-) ground state and does not predict a state crossing with the quintet. This state has significant ionic character with the 2pz of O bonding with the 4s/3dz2 of the Ni to form a σ bond. The NiO frequency at the icMRCI+Q level of 835.0 cm-1 is in excellent agreement with experiment; the value of re is 1.5992 Å at this computational level. CCSD(T) predicts ωe = 888.80 cm-1 when extrapolated to the complete basis set limit. Frequencies predicted using CCSD(T) deviate from experiment consistent with the calculations showing large multireference character. A wide array of density functionals were benchmarked. Of the 43 functionals tested, the ones that gave the best prediction of the frequency are ωB97XD, CAM-B3LYP, and τ-HCTH with respective values of 831.8, 838.3, and 837.4 cm-1 respectively. The bond dissociation energy (BDE) of NiO is predicted to be 352.4 kJ mol-1 at the Feller-Peterson-Dixon (FPD) level in good agreement with one of the experimental values. The calculated BDEs at the DFT level are sensitive to the choice of functional and atomic asymptote. Sixteen functionals predicted the BDE within 20 kJ mol-1 of the FPD value.
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Affiliation(s)
- Nickolas A Joyner
- The University of Alabama, Department of Chemistry and Biochemistry, Shelby Hall, Tuscaloosa AL, 35487-0336, USA.
| | - João Gabriel Farias Romeu
- The University of Alabama, Department of Chemistry and Biochemistry, Shelby Hall, Tuscaloosa AL, 35487-0336, USA.
| | - Brian Kent
- The University of Alabama, Department of Chemistry and Biochemistry, Shelby Hall, Tuscaloosa AL, 35487-0336, USA.
| | - David A Dixon
- The University of Alabama, Department of Chemistry and Biochemistry, Shelby Hall, Tuscaloosa AL, 35487-0336, USA.
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Ding YM, Yan L, Wu Y, Zhou L. Exciton-Driven and Layer-Independent Linear and Nonlinear Optical Properties in NbOCl 2. J Phys Chem Lett 2024; 15:7191-7198. [PMID: 38968446 DOI: 10.1021/acs.jpclett.4c01677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2024]
Abstract
We investigate the electronic structure and linear and nonlinear [second-harmonic generation (SHG)] spectra of the NbOCl2 monolayer, bilayer, and bulk by using a real-time first-principles approach based on many-body theory. First, the interlayer couplings between NbOCl2 layers are very weak, due to the relatively large interlayer distance, saturation of the p orbital of Cl atoms, and high degree of localization of charge density around the Nb atom for both the lowest conduction band and the highest valence band. Second, the quasiparticle gaps and exciton binding energy for the three systems show layer-dependent features and decrease with an increase in layer thickness. Most importantly, the linear and SHG spectra of the NbOCl2 monolayer, bilayer, and bulk are dominated by strong excitonic resonances and exhibit layer-independent features due to the weak interlayer couplings. Our findings demonstrate that excitonic effects should be included in studying the optical properties of not only two-dimensional materials but also layered bulk materials with weak interlayer couplings.
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Affiliation(s)
- Yi-Min Ding
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou 313001, China
| | - Luo Yan
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou 313001, China
- School of Physics, State Key Laboratory of Electronic Thin Films and Integrated Devices, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Yu Wu
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou 313001, China
| | - Liujiang Zhou
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou 313001, China
- School of Physics, State Key Laboratory of Electronic Thin Films and Integrated Devices, University of Electronic Science and Technology of China, Chengdu 611731, China
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14
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Dos Santos GA, Gomes JVT, da Silva ACP, Dos Santos JL, Bello ML, Santos BAMC. Computer-aided drug design supporting sunscreen research: a showcase study using previously synthesized hybrid UV filter-antioxidant compounds. J Mol Model 2024; 30:255. [PMID: 38970658 DOI: 10.1007/s00894-024-06056-2] [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: 03/17/2024] [Accepted: 06/28/2024] [Indexed: 07/08/2024]
Abstract
CONTEXT Although quantum mechanical calculations have proven effective in accurately predicting UV absorption and assessing the antioxidant potential of compounds, the utilization of computer-aided drug design (CADD) to support sustainable synthesis research of new sunscreen active ingredients remains an area with limited exploration. Furthermore, there are ongoing concerns about the safety and effectiveness of existing sunscreens. Therefore, it remains crucial to investigate photoprotection mechanisms and develop enhanced strategies for mitigating the harmful effects of UVR exposure, improving both the safety and efficacy of sunscreen products. A previous study conducted synthesis research on eight novel hybrid compounds (I-VIII) for use in sunscreen products by molecular hybridization of trans-resveratrol (RESV), avobenzone (AVO), and octinoxate (OMC). Herein, time-dependent density functional theory (TD-DFT) calculations performed in the gas phase on the isolated hybrid compounds (I-VIII) proved to reproduce the experimental UV absorption. Resveratrol-avobenzone structure-based hybrids (I-IV) present absorption maxima in the UVB range with slight differences between them, while resveratrol-OMC structure-based hybrids (V-VIII) showed main absorption in the UVA range. Among RESV-OMC hybrids, compounds V and VI exhibited higher UV absorption intensity, and compound VIII stood out for its broad-spectrum coverage in our simulations. Furthermore, both in silico and in vitro analyses revealed that compounds VII and VIII exhibited the highest antioxidant activity, with compound I emerging as the most reactive antioxidant within RESV-AVO hybrids. The study suggests a preference for the hydrogen atom transfer (HAT) mechanism over single-electron transfer followed by proton transfer (SET-PT) in the gas phase. With a strong focus on sustainability, this approach reduces costs and minimizes effluent production in synthesis research, promoting the eco-friendly development of new sunscreen active ingredients. METHODS The SPARTAN'20 program was utilized for the geometry optimization and energy calculations of all compounds. Conformer distribution analysis was performed using the Merck molecular force field 94 (MMFF94), and geometry optimization was carried out using the parametric method 6 (PM6) followed by density functional theory (DFT/B3LYP/6-31G(d)). The antioxidant behavior of the hybrid compounds (I-VIII) was determined using the highest occupied molecular orbital (εHOMO) and the lowest unoccupied molecular orbital (εLUMO) energies, as well as the bond dissociation enthalpy (BDE), ionization potential (IP), and proton dissociation enthalpy (PDE) values, all calculated at the same level of structural optimization. TD-DFT study is carried out to calculate the excitation energy using the B3LYP functional with the 6-31G(d) basis set. The calculated transitions were convoluted with a Gaussian profile using the Gabedit program.
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Affiliation(s)
- Gustavo Alencar Dos Santos
- Laboratório de Planejamento Farmacêutico e Simulação Computacional (LaPFarSC), Faculdade de Farmácia, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - João Victor Teixeira Gomes
- Laboratório de Planejamento Farmacêutico e Simulação Computacional (LaPFarSC), Faculdade de Farmácia, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Anne Cherem Peixoto da Silva
- Laboratório de Planejamento Farmacêutico e Simulação Computacional (LaPFarSC), Faculdade de Farmácia, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Jean Leandro Dos Santos
- Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista (UNESP), Câmpus Araraquara, Araraquara, SP, Brazil
| | - Murilo Lamim Bello
- Laboratório de Planejamento Farmacêutico e Simulação Computacional (LaPFarSC), Faculdade de Farmácia, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Bianca Aloise Maneira Corrêa Santos
- Laboratório de Planejamento Farmacêutico e Simulação Computacional (LaPFarSC), Faculdade de Farmácia, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil.
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15
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Kontkanen OV, Hukka TI, Rantala TT. Electronic structures of three anchors of triphenylamine on a p-type nickel oxide(100) surface: density functional theory with periodic models. Phys Chem Chem Phys 2024; 26:17588-17598. [PMID: 38863304 DOI: 10.1039/d4cp01313a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
In this paper, we investigate the electronic structures of triphenylamine molecules with three different anchoring groups (pyridinyl, carboxyl, and phenyl-1,2-diol) before and after attachment with a p-type semiconductor, nickel oxide (100), surface. To understand the charge transfer characteristics of these structures commonly used in dyes of the dye-sensitized solar cells (DSSC), we use periodic models to study their configurations with density functional theory (DFT). We find that carboxyl and phenyl-1,2-diol anchors adsorb more strongly compared to pyridinyl anchor on NiO(100). Stronger binding is reflected as a bigger dipole moment and a more viable charge transfer from the anchors to NiO(100). Furthermore, the alignment of electronic levels favors charge transfer only for pyridinyl and phenyl-1,2-diol anchors. Despite its weaker binding on the NiO(100) surface, pyridinyl is a more promising anchoring group for transferring charge to NiO, as it does not create trap states.
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Affiliation(s)
- Outi V Kontkanen
- Chemistry and Advanced Materials, Materials Science and Environmental Engineering, Faculty of Engineering and Natural Sciences, Tampere University, P.O. Box 541, FI-33014, Finland.
| | - Terttu I Hukka
- Chemistry and Advanced Materials, Materials Science and Environmental Engineering, Faculty of Engineering and Natural Sciences, Tampere University, P.O. Box 541, FI-33014, Finland.
| | - Tapio T Rantala
- Department of Physics, Tampere University, P.O. Box 692, FI-33014, Finland
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16
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Benavides M, Granda E. Au⋅⋅⋅H-X (X=N or C) Intramolecular Interactions in Gold (I)-NHC Carbene Complexes with Potential Anticancer Properties: A Quantum Mechanical Study with Two Basis Sets. ChemistryOpen 2024:e202400140. [PMID: 38924317 DOI: 10.1002/open.202400140] [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: 05/06/2024] [Revised: 05/14/2024] [Indexed: 06/28/2024] Open
Abstract
Three cationic Gold(I)-NHC complexes with potential anticancer properties were studied using DFT with B3LYP functional in combination with two basis sets, LanL2DZ and SDD. Obtained equilibrium geometries and computed IR spectra were found in excellent agreement with previously reported x-ray structures and experimental IR spectral data. NBO population analysis showed gold(I) has a charge deficiency of 0.26-0.30 e. All three complex cations are polar, with dipole moment values ranging from 6.8 to 7.4 Debye. Regardless of some structural differences in their co-ligands, all three complex cations have remarkably similar HOMO-LUMO energy gaps, with values ranging from 5.2 to 5.4 eV, confirming they are chemically stable and that they share an almost identical stability. Long-range intramolecular interactions Au ⋅⋅⋅H-X (X=N or C) in all three cationic complexes were identified. Both basis sets employed in this study were found equally effective in producing reliable results.
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Affiliation(s)
- Maria Benavides
- Department of Natural Sciences, University of Houston-Downtown, One Main Street, Houston, Texas, 77002
| | - Elizabeth Granda
- Department of Natural Sciences, University of Houston-Downtown, One Main Street, Houston, Texas, 77002
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17
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Shafiq N, Arshad M, Ali A, Rida F, Mohany M, Arshad U, Umar M, Milošević M. Integrated computational modeling and in-silico validation of flavonoids-Alliuocide G and Alliuocide A as therapeutic agents for their multi-target potential: Combination of molecular docking, MM-GBSA, ADMET and DFT analysis. SOUTH AFRICAN JOURNAL OF BOTANY 2024; 169:276-300. [DOI: 10.1016/j.sajb.2024.04.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2024]
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18
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Phipps CA, Zirilli CD, Duff BG, Erickson JD, Karki S, Okolocha C, Mashuta MS, Buchanan RM, Grapperhaus CA. Enhancing CO 2 Capture via Metal-Ligand Cooperativity: Tuning Ligand Basicity and Zn(II) Lewis Acidity. Inorg Chem 2024; 63:9992-10000. [PMID: 38742312 DOI: 10.1021/acs.inorgchem.4c01159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
A series of thiosemicarbazonato-hydrazinatopyridine zinc(II) complexes were evaluated as direct air CO2 capture agents. The complexes sequester CO2 in a methanol solution as a metal-coordinated methylcarbonate. The reaction is reversible upon sparging of solutions with an inert gas (N2 or Ar). The capture process involves metal-ligand cooperativity with the noncoordinating nitrogen of the hydrazinatopyridine functional group serving as a Brønsted-Lowry base and the zinc acting as a Lewis acid. In this study, the pendent amine of the thiosemicarbazonato group was varied to include 4-phenyl (ZnL5), 4-(trifluoromethyl)phenyl (ZnL6), 4-cyanophenyl (ZnL7), 4-tolyl (ZnL8), and 4-naphthyl (ZnL9). Hyperconjugation between the pendent group and the ligand core resulted in modulation of the metal ion acidity, as quantified by ligand exchange equilibrium constants (K3 = 193-511) and ligand basicity (pKa,MeOH = 11.09-11.94). Variations in electronic structure that decreased ligand basicity were more than offset by increases in Lewis acidity. The equilibrium constant (K1) for CO2 capture varied from 46300 to 73700. Overall, the value of K1 was directly related to the relative Lewis acidity of the complexes (K3). Notably, there was an overall inverse relationship between K1 and the ligand basicity. The results provide insights into ligand design to further improve CO2 capture.
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Affiliation(s)
- Christine A Phipps
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, Kentucky 40292, United States
| | - Calian D Zirilli
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, Kentucky 40292, United States
| | - Bailee G Duff
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, Kentucky 40292, United States
| | - Jeremy D Erickson
- Institute for Integrated Catalysis, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Sanjit Karki
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, Kentucky 40292, United States
| | - Chekwube Okolocha
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, Kentucky 40292, United States
| | - Mark S Mashuta
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, Kentucky 40292, United States
| | - Robert M Buchanan
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, Kentucky 40292, United States
| | - Craig A Grapperhaus
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, Kentucky 40292, United States
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19
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Tao J, Liu T. s valence electrons in cations of metal oxides serving as descriptors for electron and hole polarons. Phys Chem Chem Phys 2024; 26:14705-14712. [PMID: 38716579 DOI: 10.1039/d4cp00195h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
In some metal oxides, an excess electron can give rise to the formation of a small polaron localized on a single site. However, there are still some metal oxides that exhibit the formation of a large polaron. The underlying mechanism behind this phenomenon remains unclear. In this study, we investigate polaron formation in metal oxides favorable for polaron formation using different functionals and through a review of the literature. Our findings indicate that the s valence electrons in cations could serve as a descriptor to classify the polarons in materials. In metal oxides with cations having ns (n ⩾ 5) valence electrons, excess charges trend to localize on several sites or form a two-dimensional shape, and even a large polaron, as these s electrons are delocalized in nature and have a large effect on p or d state polarons. The delocalized nature of ns (n ⩽ 4) valence electrons in cations is relatively small and does not affect the localization condition of p or d state polarons. Therefore, the excess charges in these metal oxides with ns (n ⩽ 4) valence electrons prefer to form a small polaron localizing on a single site. This work unveils the impact of the s valence in cations on polaron formation and provides a fundamental understanding of various types of polarons in metal oxides.
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Affiliation(s)
- Junyan Tao
- National & Local Joint Engineering Research Center for Applied Technology of Hybrid Nanomaterials, Henan University, Kaifeng, 475004, China.
| | - Taifeng Liu
- National & Local Joint Engineering Research Center for Applied Technology of Hybrid Nanomaterials, Henan University, Kaifeng, 475004, China.
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20
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Sarkar S, Tiwari RK, Samanta D, Guchhait T, Sañudo EC, Rajaraman G, Rath SP. Unusual Stabilisation of Remarkably Bent Tetra-Cationic Tetra-radical Intermolecular Fe(III) μ-Oxo Tetranuclear Complexes. Angew Chem Int Ed Engl 2024; 63:e202402344. [PMID: 38478415 DOI: 10.1002/anie.202402344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Indexed: 04/24/2024]
Abstract
A hitherto unknown series of air stable, π-conjugated, remarkably bent tetra-cation tetra-radical intermolecular Fe(III) μ-oxo tetranuclear complex, isolated from the dication diradical diiron(III) porphyrin dimers, has been synthesised and spectroscopically characterised along with single crystal X-ray structure determination of two such molecules. These species facilitate long-range charge/radical delocalisation through the bridge across the entire tetranuclear unit manifesting an unusually intense NIR band. Assorted spin states of Fe(III) centres are stabilised within these unique tetranuclear frameworks: terminal six-coordinate iron centres stabilise the admixed intermediate spin states while the central five-coordinate iron centres stabilise the high-spin states. Variable temperature magnetic susceptibility measurements indicated strong antiferromagnetic coupling for the Fe(III)-O-Fe(III) unit while the exchange interactions between the Fe centres and the porphyrin π-cation radicals are weaker as supported both by magnetic data and DFT calculations. The nature of orbital overlap between the SOMOs of Fe(III) and π* orbital of the porphyrin was found to rationalise the observed exchange coupling, establishing such a complex magnetic exchange in this tetranuclear model with a significant bioinorganic relevance.
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Affiliation(s)
- Sabyasachi Sarkar
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Rupesh Kumar Tiwari
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Deepannita Samanta
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Tapas Guchhait
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - E Carolina Sañudo
- Secció de Química Inorgànica, Department de Química Inorgànica i Orgànica, Facultat de Química, Universitat de Barcelona, C/Martí i Franqués 1-11, 08028, Barcelona, Spain
- Institut de Nanociència i Nanotecnologia, IN2UB, Universitat de Barcelona, C/Martí i Franqués 1-11, 08028, Barcelona, Spain
| | - Gopalan Rajaraman
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Sankar Prasad Rath
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
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21
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de Souza BB, Meegoda J. Insights into PFAS environmental fate through computational chemistry: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171738. [PMID: 38494023 DOI: 10.1016/j.scitotenv.2024.171738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 02/28/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are widely used chemicals that exhibit exceptional chemical and thermal stability. However, their resistance to degradation has led to their widespread environmental contamination. PFAS also negatively affect the environment and other organisms, highlighting the need for effective remediation methods to mitigate their presence and prevent further contamination. Computational chemistry methods, such as Density Functional Theory (DFT) and Molecular Dynamics (MD) offer valuable tools for studying PFAS and simulating their interactions with other molecules. This review explores how computational chemistry methods contribute to understanding and tackling PFAS in the environment. PFAS have been extensively studied using DFT and MD, each method offering unique advantages and computational limitations. MD simulates large macromolecules systems however it lacks the ability model chemical reactions, while DFT provides molecular insights however at a high computational cost. The integration of DFT with MD shows promise in predicting PFAS behavior in different environments. This work summarizes reported studies on PFAS compounds, focusing on adsorption, destruction, and bioaccumulation, highlighting contributions of computational methods while discussing the need for continued research. The findings emphasize the importance of computational chemistry in addressing PFAS contamination, guiding risk assessments, and informing future research and innovations in this field.
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Affiliation(s)
- Bruno Bezerra de Souza
- John A. Reif, Jr. Department of Civil and Environmental Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Jay Meegoda
- John A. Reif, Jr. Department of Civil and Environmental Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA.
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22
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Santis GD, Okura Y, Hirata K, Ishiuchi SI, Fujii M, Xantheas SS. Affinity of Nicotinoids to a Model Nicotinic Acetylcholine Receptor (nAChR) Binding Pocket in the Human Brain. J Phys Chem B 2024; 128:4577-4589. [PMID: 38696590 DOI: 10.1021/acs.jpcb.3c07919] [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: 05/04/2024]
Abstract
The binding affinity of nicotinoids to the binding residues of the α4β2 variant of the nicotinic acetylcholine receptor (nAChR) was identified as a strong predictor of the nicotinoid's addictive character. Using ab initio calculations for model binding pockets of increasing size composed of 3, 6, and 14 amino acids (3AA, 6AA, and 14AA) that are derived from the crystal structure, the differences in binding affinity of 6 nicotinoids, namely, nicotine (NIC), nornicotine (NOR), anabasine (ANB), anatabine (ANT), myosmine (MYO), and cotinine (COT) were correlated to their previously reported doses required for increases in intracranial self-stimulation (ICSS) thresholds, a metric for their addictive function. By employing the many-body decomposition, the differences in the binding affinities of the various nicotinoids could be attributed mainly to the proton exchange energy between the pyridine and non-pyridine rings of the nicotinoids and the interactions between them and a handful of proximal amino acids, namely Trp156, Trpβ57, Tyr100, and Tyr204. Interactions between the guest nicotinoid and the amino acids of the binding pocket were found to be mainly classical in nature, except for those between the nicotinoid and Trp156. The larger pockets were found to model binding structures more accurately and predicted the addictive character of all nicotinoids, while smaller models, which are more computationally feasible, would only predict the addictive character of nicotinoids that are similar to nicotine. The present study identifies the binding affinity of the guest nicotinoid to the host binding pocket as a strong descriptor of the nicotinoid's addiction potential, and as such it can be employed as a fast-screening technique for the potential addiction of nicotine analogs.
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Affiliation(s)
- Garrett D Santis
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Yuika Okura
- Department of Chemistry, School of Science, Tokyo Intitute of Technology; 2-12-1 4259 Ookayama, Meguro-ku, Tokyo 152855, Japan
| | - Keisuke Hirata
- Department of Chemistry, School of Science, Tokyo Intitute of Technology; 2-12-1 4259 Ookayama, Meguro-ku, Tokyo 152855, Japan
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Shun-Ichi Ishiuchi
- Department of Chemistry, School of Science, Tokyo Intitute of Technology; 2-12-1 4259 Ookayama, Meguro-ku, Tokyo 152855, Japan
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Masaaki Fujii
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
- Research and Development Initiative, Chuo University, Tokyo 112-8551, Japan
| | - Sotiris S Xantheas
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, MS K1-83, P.O. Box 999, Richland, Washington 99352, United States
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23
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Cartier NG, Giesbertz KJH. Exploiting the Hessian for a Better Convergence of the SCF-RDMFT Procedure. J Chem Theory Comput 2024; 20:3669-3682. [PMID: 38668734 PMCID: PMC11099978 DOI: 10.1021/acs.jctc.4c00118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 05/15/2024]
Abstract
One-body reduced density matrix functional theory provides an alternative to density functional theory, which is able to treat static correlation while keeping a relatively low computation scaling. Its disadvantageous cost comes mainly from a slow convergence of the self-consistent energy optimization. To improve on that problem, we propose in this work the use of the Hessian of the energy, including the coupling term. We show that using the exact Hessian is very effective at reducing the number of iterations. However, since the exact Hessian is too expensive to use in practice, we propose an approximation based on an inexpensive exact part and BFGS updates.
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Affiliation(s)
- Nicolas G. Cartier
- Department of Chemistry & Pharmaceutical
Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS),
Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Klaas J. H. Giesbertz
- Department of Chemistry & Pharmaceutical
Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS),
Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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Ding YM, Huo Y, Fang G, Yan L, Wu Y, Zhou L. Two-dimensional half-metals MSi 2N 4 (M = Al, Ga, In, Tl) with intrinsic p-type ferromagnetism and ultrawide bandgaps. Phys Chem Chem Phys 2024; 26:13327-13334. [PMID: 38639877 DOI: 10.1039/d3cp05940e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Intrinsic half-metallic nanomaterials with 100% spin polarization are highly demanded for next-generation spintronic devices. Here, by using first-principles calculations, we have designed a class of new two-dimensional (2D) p-type half-metals, MSi2N4 (M = Al, Ga, In and Tl), which show high mechanical, thermal and dynamic stabilities. MSi2N4 not only have ultrawide electronic bandgaps for spin-up channels in the range of 4.05 to 6.82 eV but also have large half-metallic gaps in the range of 0.75 to 1.47 eV, which are large enough to prevent the spin-flip transition. The calculated magnetic moment is 1 μB per cell, resulting from polarized N1-px/py orbitals. Moreover, MSi2N4 possess robust long-range ferromagnetic orderings with Curie temperatures in the range of 35-140 K, originating from the interplay of N1-M-N1 superexchange interactions. Furthermore, spin dependent electronic transport calculations reveal 100% spin polarization. Our results highlight new promising 2D ferromagnetic half-metals toward future spintronic applications.
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Affiliation(s)
- Yi-Min Ding
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou 313001, China.
| | - Yiqi Huo
- School of Physics, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Gaojing Fang
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou 313001, China.
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Luo Yan
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou 313001, China.
- School of Physics, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yu Wu
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou 313001, China.
| | - Liujiang Zhou
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou 313001, China.
- School of Physics, University of Electronic Science and Technology of China, Chengdu 610054, China
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25
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Chen J, Huang H, Gong W, Chen Y, Dong R, Ren L, Qiu T. Fine-Tuning Electron-Donor Capability in the Basic Anion of Poly(ionic liquid) Frameworks for Revolutionizing Catalytic Synthesis of Ethyl Methyl Carbonate with Both Ultrahigh Catalytic Activity and Selectivity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:9233-9243. [PMID: 38623907 DOI: 10.1021/acs.langmuir.4c00650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Ethyl methyl carbonate (EMC) is a crucial solvent extensively utilized in lithium-ion battery electrolytes; the transesterification of dimethyl carbonate (DMC) with ethanol is a pivotal reaction for EMC production. However, this reaction faces challenges due to the trade-off between catalytic activity and selectivity from the basic catalysts. In this issue, we report an innovative strategy through fine-tuning the electron-donor capability of the basic phenolate anion ([PhO]) in a novel poly(ionic liquid) (PIL) framework, as synthesized via an alkylation reaction between 1,3,5-tris(bromomethyl)benzene, biphenyldiimidazole, and N,N'-carbonyldiimidazole (CDI) to trigger targeted basicity that can directionally catalyze the transesterification of DMC with ethanol, so as to achieve both ultrahigh catalytic activity and selectivity toward EMC. By varying the substituent groups with electron-withdrawing and electron-donating effects on the phenolate anion, the PILs show expected changes in the catalytic performance, following well with the trend of charge density on these substituted phenolate anions. The optimized catalyst [CPIL-CDI][MeOPhO], induced by p-methoxyphenolate anions, allows an extraordinary EMC yield of 72.19% and an EMC selectivity of 91.48% under mild conditions without any process intensifications, suppressing all of the reported catalysts reported to date. Outcomes and approaches shown in this work have the potential to expedite the systematic design of cations and anions within PILs for industrial-scale EMC production through environmentally friendly transesterification processes.
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Affiliation(s)
- Jie Chen
- Engineering Research Center of Reactive Distillation, Fujian Province University, College of Chemical Engineering, Fuzhou University, Fuzhou 350108, Fujian, China
- Qingyuan Innovation Laboratory, Quanzhou 362801, Fujian, China
| | - Huiyao Huang
- Engineering Research Center of Reactive Distillation, Fujian Province University, College of Chemical Engineering, Fuzhou University, Fuzhou 350108, Fujian, China
- Qingyuan Innovation Laboratory, Quanzhou 362801, Fujian, China
| | - Wangquan Gong
- Engineering Research Center of Reactive Distillation, Fujian Province University, College of Chemical Engineering, Fuzhou University, Fuzhou 350108, Fujian, China
| | - Yi Chen
- Engineering Research Center of Reactive Distillation, Fujian Province University, College of Chemical Engineering, Fuzhou University, Fuzhou 350108, Fujian, China
| | - Rong Dong
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou 350108, Fujian, China
| | - Limei Ren
- Department of Chemical Engineering, Shijiazhuang University, Hebei 050035, China
| | - Ting Qiu
- Engineering Research Center of Reactive Distillation, Fujian Province University, College of Chemical Engineering, Fuzhou University, Fuzhou 350108, Fujian, China
- Qingyuan Innovation Laboratory, Quanzhou 362801, Fujian, China
- Fuzhou University International Joint Laboratory of Thermochemical Conversion of Biomass, Fuzhou University, Fuzhou 350108, Fujian, China
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26
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Zhuang H, Shi W, Zhao G, Li Y. Regulating and controlling the stepwise ESDPT channel of BP(OH) 2DCEt 2 using the strategy of solvent polarity and external electric field. Phys Chem Chem Phys 2024; 26:12016-12026. [PMID: 38576357 DOI: 10.1039/d4cp00989d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Excited state double proton transfer (ESDPT) has attracted great scientific interest because of its excellent luminescent properties. However, the complex process of ESDPT has plagued theoretical and experimental scientists for a long time and has become a hot issue. In this work, the ESDPT process of 2,2'-bipyridine-3,3'-diol-5,5'-dicarboxylic acid ethyl ester (BP(OH)2DCEt2) is systematically studied and the regulation of the ESDPT process is further realized. The potential energy curves indicate that BP(OH)2DCEt2 shows the characteristics of stepwise ESDPT in different polar solvents. The increase in solvent polarity will be beneficial to the stepwise ESDPT reaction. Regrettably, it is not possible to distinguish the specific stepwise transfer path of the BP(OH)2DCEt2 molecule due to the symmetry of the potential energy surface along the diagonal. On this basis, we proposed a method to control and regulate the stepwise ESDPT path using an external electric field. The results show that the increase of external electric field intensity is favorable to stepwise ESDPT. It is interesting to note that applying an external electric field in a specific direction will effectively distinguish stepwise ESDPT reaction paths. Therefore, this work not only helps to understand the mechanism of ESDPT, but also contributes to regulation and design of new luminescent materials with excellent luminescent properties.
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Affiliation(s)
- Hongbin Zhuang
- School of Physics, Liaoning University, Shenyang 110036, P. R. China.
| | - Wei Shi
- School of Physics, Liaoning University, Shenyang 110036, P. R. China.
| | - Guijie Zhao
- School of Physics, Liaoning University, Shenyang 110036, P. R. China.
| | - Yongqing Li
- School of Physics, Liaoning University, Shenyang 110036, P. R. China.
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27
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Waddar B, Gandi S, Parne SR, Chari VR, Prasanth GR. Investigation of second-order NLO properties of novel 1,3,4-oxadiazole derivatives: a DFT study. J Mol Model 2024; 30:118. [PMID: 38561544 DOI: 10.1007/s00894-024-05910-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/20/2024] [Indexed: 04/04/2024]
Abstract
CONTEXT In this study, we have developed four new chromophores (TM1-TM4) and performed quantum chemical calculations to explore their nonlinear optical properties. Our focus was on understanding the impact of electron-donating substituents on 1,3,4-oxadiazole derivative chromophores. The natural bond orbital analysis confirmed the interactions between donors and acceptors as well as provided insights into intramolecular charge transfer. We also estimated dipole moment, linear polarizability molecular electrostatic potential, UV-visible spectra, and first hyperpolarizability. Our results revealed that TM1 with a strong and stable electron-donating group exhibited high first hyperpolarizability (β) 293,679.0178 × 10-34 esu. Additionally, TM1 exhibited a dipolar moment (μ) of 5.66 Debye and polarizability (α) of 110.62 × 10-24 esu when measured in dimethyl sulfoxide (DMSO) solvent. Furthermore, in a benzene solvent, TM1 showed a low energy band gap of 5.33 eV by using the ωB97XD functional with a 6-311 + + G(d, p) basis set. Moreover, our study of intramolecular charge transfers highlighted N, N dimethyl triphenylamine and carbazole as major electron-donating groups among the four 1,3,4-oxadiazole derivative chromophores. This research illustrates the potential applications of these organic molecules in photonics due to their versatile nature. METHODS The molecules were individually optimized using different functionals, including APFD, B3LYP, CAM B3LYP, and ωB97XD combined with the 6-311 + + G (d, p) basis set in Gaussian 16 software. These methods encompass long-range functionals such as APFD and B3LYP, along with long-range corrected functionals like CAM B3LYP and ωB97XD. The employed functionals of APFD, B3LYP, CAM B3LYP, and ωB97XD with the 6-311 + + G (d,p) basis set were used to extract various properties such as geometrical structures, dipole moment, molecular electrostatic potential, and first hyperpolarizability through precise density functional theory (DFT). Additionally, TD-DFT was utilized for obtaining UV-visible spectra. All studies have been conducted in both gas and solvent phases.
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Affiliation(s)
- Balachandar Waddar
- Department of Applied Sciences, National Institute of Technology Goa, Kottamoll Plateau, Cuncolim, Goa, 403703, India
| | - Suman Gandi
- Department of Applied Sciences, National Institute of Technology Goa, Kottamoll Plateau, Cuncolim, Goa, 403703, India
| | - Saidi Reddy Parne
- Department of Applied Sciences, National Institute of Technology Goa, Kottamoll Plateau, Cuncolim, Goa, 403703, India.
| | - Vishnu Rama Chari
- School of Chemical Sciences, Goa University, Taleigao Plateau, Goa, 403206, India
| | - Gurusiddappa R Prasanth
- Department of Electronics & Communication Engineering, National Institute of Technology Goa, Kottamoll Plateau, Cuncolim, Goa, 403703, India
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28
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Sun S, Zhang Y, Shi X, Sun W, Felser C, Li W, Li G. From Charge to Spin: An In-Depth Exploration of Electron Transfer in Energy Electrocatalysis. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2312524. [PMID: 38482969 DOI: 10.1002/adma.202312524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/24/2024] [Indexed: 05/01/2024]
Abstract
Catalytic materials play crucial roles in various energy-related processes, ranging from large-scale chemical production to advancements in renewable energy technologies. Despite a century of dedicated research, major enduring challenges associated with enhancing catalyst efficiency and durability, particularly in green energy-related electrochemical reactions, remain. Focusing only on either the crystal structure or electronic structure of a catalyst is deemed insufficient to break the linear scaling relationship (LSR), which is the golden rule for the design of advanced catalysts. The discourse in this review intricately outlines the essence of heterogeneous catalysis reactions by highlighting the vital roles played by electron properties. The physical and electrochemical properties of electron charge and spin that govern catalysis efficiencies are analyzed. Emphasis is placed on the pronounced influence of external fields in perturbing the LSR, underscoring the vital role that electron spin plays in advancing high-performance catalyst design. The review culminates by proffering insights into the potential applications of spin catalysis, concluding with a discussion of extant challenges and inherent limitations.
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Affiliation(s)
- Shubin Sun
- CAS Key Laboratory of Magnetic Materials and Devices, and Zhejiang Province Key Laboratory of Magnetic Materials and Application Technology, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315201, China
- State Key Laboratory Breeding Base of Green Chemistry-Synthesis Technology Key Laboratory of Green Chemistry-Synthesis Technology of Zhejiang Province, College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yudi Zhang
- CAS Key Laboratory of Magnetic Materials and Devices, and Zhejiang Province Key Laboratory of Magnetic Materials and Application Technology, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315201, China
- College of Material Sciences and Opto-Electronic Technology, University of Chinese Academy of Sciences, 19 A Yuquan Rd, Shijingshan District, Beijing, 100049, China
| | - Xin Shi
- CAS Key Laboratory of Magnetic Materials and Devices, and Zhejiang Province Key Laboratory of Magnetic Materials and Application Technology, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315201, China
- School of Materials Science and Chemical Engineering, Ningbo University, 818 A Fenghua Rd, Jiangbei District, Ningbo, 315211, China
| | - Wen Sun
- CAS Key Laboratory of Magnetic Materials and Devices, and Zhejiang Province Key Laboratory of Magnetic Materials and Application Technology, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315201, China
- College of Material Sciences and Opto-Electronic Technology, University of Chinese Academy of Sciences, 19 A Yuquan Rd, Shijingshan District, Beijing, 100049, China
| | - Claudia Felser
- Topological Quantum Chemistry, Max Planck Institute for Chemical Physics of Solids, Nöthnitzer Strasse 40, 01187, Dresden, Germany
| | - Wei Li
- CAS Key Laboratory of Magnetic Materials and Devices, and Zhejiang Province Key Laboratory of Magnetic Materials and Application Technology, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315201, China
- CISRI & NIMTE Joint Innovation Center for Rare Earth Permanent Magnets, Chinese Academy of Sciences, Ningbo Institute of Material Technology and Engineering, Ningbo, 315201, China
| | - Guowei Li
- CAS Key Laboratory of Magnetic Materials and Devices, and Zhejiang Province Key Laboratory of Magnetic Materials and Application Technology, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315201, China
- College of Material Sciences and Opto-Electronic Technology, University of Chinese Academy of Sciences, 19 A Yuquan Rd, Shijingshan District, Beijing, 100049, China
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29
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Ma X, Jin X, Bai H, Ma L, Li X, Fang X, Chen W, She M. Visual detection of water content in liquor with near-infrared fluorescence sensor assisted by smartphone. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 308:123791. [PMID: 38134656 DOI: 10.1016/j.saa.2023.123791] [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: 10/12/2023] [Revised: 12/11/2023] [Accepted: 12/16/2023] [Indexed: 12/24/2023]
Abstract
Water content was an essential indicator in organic solvents, and it was necessary to develop a facile, cheap and readily available tool for the real-time, specifical and sensitive detection of water content. In this work, two novel D-π-A type near-infrared fluorescence sensors (DCM-1 and DCM-2) were designed and synthesized for the detection of trace water in organic solvents. DCM-1 and DCM-2 with solvent-dependent effects and large Stokes shift (>120 nm) showed good linear "intensity-to-content" relationships in four commonly-used organic solvents, and accomplished the ultra-fast and high-accuracy detection of the trace water in organic solvents. More importantly, a portable, fast, and accurate smartphone-assisted visual assay was designed for visual quantitative detection of the water content in organic solvents with a detection limit as low as 1.028 % v/v (e.g. in ethanol) and a wide detection range (0-60 % v/v). The smartphone-based visual assay was further applied to estimate the water content in disinfection alcohol and commercial liquor, which furnished a new strategy and broad prospects to achieve the accurate onsite detection of water content.
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Affiliation(s)
- Xuehao Ma
- Engineering Research Center of Light Stabilizers for Polymer Materials, Universities of Shaanxi Province, School of Materials and Chemical Engineering, Xi'an Technological University, Xi'an 710021, PR China
| | - Xilang Jin
- Engineering Research Center of Light Stabilizers for Polymer Materials, Universities of Shaanxi Province, School of Materials and Chemical Engineering, Xi'an Technological University, Xi'an 710021, PR China.
| | - Haiyan Bai
- Engineering Research Center of Light Stabilizers for Polymer Materials, Universities of Shaanxi Province, School of Materials and Chemical Engineering, Xi'an Technological University, Xi'an 710021, PR China
| | - Liyuan Ma
- Engineering Research Center of Light Stabilizers for Polymer Materials, Universities of Shaanxi Province, School of Materials and Chemical Engineering, Xi'an Technological University, Xi'an 710021, PR China
| | - Xiao Li
- Engineering Research Center of Light Stabilizers for Polymer Materials, Universities of Shaanxi Province, School of Materials and Chemical Engineering, Xi'an Technological University, Xi'an 710021, PR China
| | - Xingliang Fang
- Engineering Research Center of Light Stabilizers for Polymer Materials, Universities of Shaanxi Province, School of Materials and Chemical Engineering, Xi'an Technological University, Xi'an 710021, PR China
| | - Weixing Chen
- Engineering Research Center of Light Stabilizers for Polymer Materials, Universities of Shaanxi Province, School of Materials and Chemical Engineering, Xi'an Technological University, Xi'an 710021, PR China
| | - Mengyao She
- Ministry of Education Key Laboratory of Resource Biology and Modern Biotechnology in Western China, The College of Life Sciences, Northwest University, Xi'an, Shaanxi Province 710069, PR China.
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30
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Benítez FJ, Gutiérrez-Oliva S, Herrera B, Toro-Labbé A. Basis Electronic Activity of Molecular Systems. A Theory of Bond Reactivity. J Phys Chem A 2024. [PMID: 38437616 DOI: 10.1021/acs.jpca.4c00359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
In this paper, we present a new finding, the basis electronic activity (BEA) of molecular systems; it corresponds to the significant, although nonreactive, vibrationally induced electronic activity that takes place in any molecular system. Although the molecule's BEA is composed of an equal number of local contributions as the vibrational degrees of freedom, our results indicate that only stretching modes contribute to it. To account for this electronic activity, a new descriptor, the bond electronic flux (BEF), is introduced. The BEF combined with the force constant of the potential well hosting the electronic activity gives rise to the effective bond reactivity index (EBR), which turns out to be the first density functional theory-based descriptor that simultaneously accounts for structural and electronic effects. Besides quantifying the bond reactivity, EBR provides a basis to compare the reactivities of bonds inserted in different chemical environments and paves the way for the exertion of selective control to enhance or inhibit their reactivities. The new concepts formulated in this paper and the associated computational tools are illustrated with characterization of the BEA of a set of representative molecules. In all cases, the BEFs follow the same linear pattern, whose slopes indicate the intensity of the electronic activity and quantify the reactivity of chemical bonds.
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Affiliation(s)
- Francisca J Benítez
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avda. Vicuña Mackenna 4860 Macul, Santiago 7820436, Chile
| | - Soledad Gutiérrez-Oliva
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avda. Vicuña Mackenna 4860 Macul, Santiago 7820436, Chile
| | - Bárbara Herrera
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avda. Vicuña Mackenna 4860 Macul, Santiago 7820436, Chile
| | - Alejandro Toro-Labbé
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avda. Vicuña Mackenna 4860 Macul, Santiago 7820436, Chile
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31
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Il'in AV, Anisimova KS, Bogdanov AV, Shulaeva MP, Pozdeev OK, Babaeva OB, Voloshina AD, Serov NY, Bukharov MS, Islamov DR. α-Umpolung/Michael Addition/Quaternization Tandem Reaction to provide α-Imido-β-phosphonium Propanoates with Broad Spectrum of Biological Activity. Chem Biodivers 2024; 21:e202302022. [PMID: 38298091 DOI: 10.1002/cbdv.202302022] [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: 12/14/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/02/2024]
Abstract
This paper has been supported by the Kazan Federal University Strategic Academic Leadership Program ('PRIORITY-2030'). HRMS data were obtained in the CSF-SAC FRC KSC RAS by support of the State Assignment of the Federal Research Center "Kazan Scientific Center", Russian Academy of Sciences. A.D.V, conducted studies of anticancer activity with financial support form the government assignment for FRC Kazan Scientific Center of RAS.
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Affiliation(s)
- Anton V Il'in
- A. M. Butlerov Institute of Chemistry, Kazan Federal University, 29 Kremlevskaya St., Kazan, 420008, Russian Federation
| | - Kristina S Anisimova
- A. M. Butlerov Institute of Chemistry, Kazan Federal University, 29 Kremlevskaya St., Kazan, 420008, Russian Federation
| | - Andrei V Bogdanov
- A. M. Butlerov Institute of Chemistry, Kazan Federal University, 29 Kremlevskaya St., Kazan, 420008, Russian Federation
| | - Marina P Shulaeva
- Microbiology Department, Kazan State Medical Academy, Butlerova str. 3b, 420012, Kazan, Russian Federation
| | - Oskar K Pozdeev
- Microbiology Department, Kazan State Medical Academy, Butlerova str. 3b, 420012, Kazan, Russian Federation
| | - Olga B Babaeva
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov St., 8, Kazan, 420088, Russian Federation
| | - Alexandra D Voloshina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov St., 8, Kazan, 420088, Russian Federation
| | - Nikita Yu Serov
- A. M. Butlerov Institute of Chemistry, Kazan Federal University, 29 Kremlevskaya St., Kazan, 420008, Russian Federation
| | - Mikhail S Bukharov
- A. M. Butlerov Institute of Chemistry, Kazan Federal University, 29 Kremlevskaya St., Kazan, 420008, Russian Federation
| | - Daut R Islamov
- A. M. Butlerov Institute of Chemistry, Kazan Federal University, 29 Kremlevskaya St., Kazan, 420008, Russian Federation
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32
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Hasan AMM, Susan MABH. Synergism in carbon nanotubes and carbon-dots: counter electrode of a high-performance dye-sensitized solar cell. RSC Adv 2024; 14:7616-7630. [PMID: 38440284 PMCID: PMC10911412 DOI: 10.1039/d4ra00601a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 02/27/2024] [Indexed: 03/06/2024] Open
Abstract
Dye-sensitized solar cells (DSSCs) play a crucial role in the realm of renewable energy technology by converting solar energy into electrical energy in an efficient and cost-effective way. In the pursuit of improving the photoconversion efficiency (PCE) of DSSCs, this work aims at fabricating a new counter electrode (CE) using a binary composite of heteroatom-doped carbon dots (C-dots) and functionalized multi-walled carbon nanotubes (o-MWCNTs). We demonstrate that this binary composite exhibits superior performance to pristine o-MWCNTs, resulting in a remarkable enhancement in the PCE. The PCE of the o-MWCNT/C-dots composite was measured at an impressive 4.28%, significantly outperforming the pristine o-MWCNT electrode, which yielded an efficiency of 2.24%. The enhanced performance of the o-MWCNT/C-dots composite can be attributed to the synergistic effects of heteroatom-doped C-dots since their binding to the o-MWCNTs by activated oxygenic surface functional groups increases the surface area from 218 to 253 m2 g-1. This enhanced surface area results from the reduction of π-π stacking interactions of the individual tubes and production of a new hollow channel in the structure that provides an ideal scaffold for I2 adsorption and electron transfer. We demonstrate the role of C-dots on MWCNT's property modulation toward higher PCE by density functional theory (DFT) calculation and electrochemical analysis. Electron-excess N and S doped C-dots exhibit strong catalytic activity, allowing for rapid electron transfer processes in the CE-electrolyte surface via the donor acceptor mechanism, whereas electron-deficient B doped C-dots undermine the cell performance by forming a charge recombination trap at the CE surface. The synthesized composite has higher redox reversibility up to 100 CV cycles and chemical stability, studied by the post-performance material characterization. The findings offer a promising avenue for the development of high-performance DSSCs, which will help to promote sustainable and renewable energy technologies.
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Affiliation(s)
| | - Md Abu Bin Hasan Susan
- Department of Chemistry, University of Dhaka Dhaka-1000 Bangladesh
- Dhaka University Nanotechnology Center (DUNC), University of Dhaka Dhaka-1000 Bangladesh
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33
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Li R, Zhou C, Singh A, Pei Y, Henkelman G, Li L. Local-environment-guided selection of atomic structures for the development of machine-learning potentials. J Chem Phys 2024; 160:074109. [PMID: 38380745 DOI: 10.1063/5.0187892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/26/2024] [Indexed: 02/22/2024] Open
Abstract
Machine learning potentials (MLPs) have attracted significant attention in computational chemistry and materials science due to their high accuracy and computational efficiency. The proper selection of atomic structures is crucial for developing reliable MLPs. Insufficient or redundant atomic structures can impede the training process and potentially result in a poor quality MLP. Here, we propose a local-environment-guided screening algorithm for efficient dataset selection in MLP development. The algorithm utilizes a local environment bank to store unique local environments of atoms. The dissimilarity between a particular local environment and those stored in the bank is evaluated using the Euclidean distance. A new structure is selected only if its local environment is significantly different from those already present in the bank. Consequently, the bank is then updated with all the new local environments found in the selected structure. To demonstrate the effectiveness of our algorithm, we applied it to select structures for a Ge system and a Pd13H2 particle system. The algorithm reduced the training data size by around 80% for both without compromising the performance of the MLP models. We verified that the results were independent of the selection and ordering of the initial structures. We also compared the performance of our method with the farthest point sampling algorithm, and the results show that our algorithm is superior in both robustness and computational efficiency. Furthermore, the generated local environment bank can be continuously updated and can potentially serve as a growing database of feature local environments, aiding in efficient dataset maintenance for constructing accurate MLPs.
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Affiliation(s)
- Renzhe Li
- Shenzhen Key Laboratory of Micro/Nano-Porous Functional Materials (SKLPM), Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, People's Republic of China
- College of Chemistry, Xiangtan University, Xiangtan 411105, Hunan Province, People's Republic of China
| | - Chuan Zhou
- Shenzhen Key Laboratory of Micro/Nano-Porous Functional Materials (SKLPM), Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, People's Republic of China
| | - Akksay Singh
- Shenzhen Key Laboratory of Micro/Nano-Porous Functional Materials (SKLPM), Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, People's Republic of China
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, USA
- Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Yong Pei
- College of Chemistry, Xiangtan University, Xiangtan 411105, Hunan Province, People's Republic of China
| | - Graeme Henkelman
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, USA
- Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Lei Li
- Shenzhen Key Laboratory of Micro/Nano-Porous Functional Materials (SKLPM), Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, People's Republic of China
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34
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DeLuca M, Sensale S, Lin PA, Arya G. Prediction and Control in DNA Nanotechnology. ACS APPLIED BIO MATERIALS 2024; 7:626-645. [PMID: 36880799 DOI: 10.1021/acsabm.2c01045] [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] [Indexed: 03/08/2023]
Abstract
DNA nanotechnology is a rapidly developing field that uses DNA as a building material for nanoscale structures. Key to the field's development has been the ability to accurately describe the behavior of DNA nanostructures using simulations and other modeling techniques. In this Review, we present various aspects of prediction and control in DNA nanotechnology, including the various scales of molecular simulation, statistical mechanics, kinetic modeling, continuum mechanics, and other prediction methods. We also address the current uses of artificial intelligence and machine learning in DNA nanotechnology. We discuss how experiments and modeling are synergistically combined to provide control over device behavior, allowing scientists to design molecular structures and dynamic devices with confidence that they will function as intended. Finally, we identify processes and scenarios where DNA nanotechnology lacks sufficient prediction ability and suggest possible solutions to these weak areas.
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Affiliation(s)
- Marcello DeLuca
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Sebastian Sensale
- Department of Physics, Cleveland State University, Cleveland, Ohio 44115, United States
| | - Po-An Lin
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Gaurav Arya
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
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35
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Parveen S, Shehzadi S, Shafiq N, Rashid M, Naz S, Mehmood T, Riaz R, S Almaary K, Nafidi HA, Bourhia M. A discovery of potent kaempferol derivatives as multi-target medicines against diabetes as well as bacterial infections: an in silico approach. J Biomol Struct Dyn 2024:1-23. [PMID: 38334277 DOI: 10.1080/07391102.2024.2308773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/14/2024] [Indexed: 02/10/2024]
Abstract
Flavonoids demonstrate beneficial effects on human health because flavonoids contain important biological properties. Kaempferol is a flavonol, type of flavonoid found in eatable plants and in plants usually employed in ancient drugs (Moringa oleifera, Tilia spp., fern genus spp. and gingko etc.). Some medicinal studies have shown that the use of foods full of kaempferol decreases the risk of many (cancer, vascular) diseases. All the data of 50 kaempferol derivatives were collected from PubChem database. Through Schrödinger software, 3D-QSAR study was performed for 50 compounds by using method of field base. Conformer of kaempferol derivatives was docked against anti-diabetic, anti-microbial co-crystal structures and protein. To monitor the best anti-diabetic and antibacterial agent, particular kaempferol derivatives were downloaded from PubChem database. Virtual screening by molecular docking provided four lead compounds with four different proteins. These hit compounds were found to be potent inhibitor for diabetic enzymes alpha-amylase and DPP IV and had the potential to suppress DNA gyrase and dihydrofolate reductase synthesis. Molecular dynamic simulation of docked complexes evaluates the value of root mean square fluctuation by iMOD server. Kaempferol 3-O-alpha-L-(2, 3-di-Z-p-coumaroyl) rhamnoside (42) compound used as anti-diabetic and kaempferol 3-O-gentiobioside (3) as antibacterial with good results can be used for drug discovery.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shagufta Parveen
- Synthetic and Natural Product Drug Discovery Laboratory, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Saman Shehzadi
- Synthetic and Natural Product Drug Discovery Laboratory, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Nusrat Shafiq
- Synthetic and Natural Product Drug Discovery Laboratory, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Maryam Rashid
- Synthetic and Natural Product Drug Discovery Laboratory, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Sadaf Naz
- Department of Chemistry, The University of Lahore, Lahore, Pakistan
| | - Tahir Mehmood
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, Punjab, Pakistan
| | - Rabia Riaz
- Synthetic and Natural Product Drug Discovery Laboratory, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Khalid S Almaary
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Hiba-Allah Nafidi
- Department of Food Science, Faculty of Agricultural and Food Sciences, Laval University, Quebec, QC, Canada
| | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Laayoune, Morocco
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36
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Okura Y, Santis GD, Hirata K, Melissas VS, Ishiuchi SI, Fujii M, Xantheas SS. Switching of Protonation Sites in Hydrated Nicotine via a Grotthuss Mechanism. J Am Chem Soc 2024; 146:3023-3030. [PMID: 38261007 DOI: 10.1021/jacs.3c08922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The switching of the protonation sites in hydrated nicotine, probed by experimental infrared (IR) spectroscopy and theoretical ab initio calculations, is facilitated via a Grotthuss instead of a bimolecular proton transfer (vehicle) mechanism at the experimental temperature (T = 130 K) as unambiguously confirmed by experiments with deuterated water. In contrast, the bimolecular vehicle mechanism is preferred at higher temperatures (T = 300 K) as determined by theory. The Grotthuss mechanism for the concerted proton transfer results in the production of nicotine's bioactive and addictive pyrrolidine-protonated (Pyrro-H+) protomer with just 5 water molecules. Theoretical analysis suggests that the concerted proton transfer occurs via hydrogen-bonded bridges consisting of a 3 water molecule "core" that connects the pyridine protonated (Pyri-H+) with the pyrrolidine-protonated (Pyrro-H+) protomers. Additional water molecules attached as acceptors to the hydrogen-bonded "core" bridge result in lowering the reaction barrier of the concerted proton transfer down to less than 6 kcal/mol, which is consistent with the experimental observations.
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Affiliation(s)
- Yuika Okura
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 4259 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Garrett D Santis
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Keisuke Hirata
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 4259 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | | | - Shun-Ichi Ishiuchi
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 4259 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Masaaki Fujii
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Sotiris S Xantheas
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, United States
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Tan Z, Deng H, Ou H, Wu X, Liao Z, Ou H. Interfacial quantum chemical characterization of aromatic organic matter adsorption on oxidized microplastic surfaces. CHEMOSPHERE 2024; 350:141132. [PMID: 38184084 DOI: 10.1016/j.chemosphere.2024.141132] [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: 09/08/2023] [Revised: 12/13/2023] [Accepted: 01/03/2024] [Indexed: 01/08/2024]
Abstract
Examining the adsorption efficiency of individual contaminants on microplastics (MPs) is resource-intensive and time-consuming. To address this challenge, combined laboratory adsorption experiments with model simulations were performed to investigate the adsorption capacities and mechanisms of MPs before and after aging. Our adsorption experiments revealed that aged polyethylene (PE) and polyvinyl chloride (PVC) MPs exhibited increased adsorption capacity for benzene, phenol, and naphthalene. Additionally, density functional theory (DFT) simulations provided insights into changes in adsorption sites, adsorption energy, and charge density on MPs. The π bond of the benzene ring emerged as a pivotal factor in the adsorption process, with van der Waals forces exerting dominant influence. For instance, the adsorption energy of benzene on pristine PE was -0.01879 eV. When oxidized groups, such as hydroxyl, carbonyl, and carboxyl, on the surface of aged PE became the adsorption sites, the adsorption energy increased to -0.06976, -0.04781, and -0.04903 eV, respectively. Regions with unoxidized functional groups also exhibited higher adsorption energies than pristine PE. These results indicated that aged PE had a stronger affinity for benzene compared to pristine PE, enhancing its adsorption. Charge density difference and energy density of states corroborated this observation, revealing larger π-bond charge accumulation areas for benzene on aged PE, suggesting stronger dipole interactions and enhanced adsorption. Similar trends were observed for phenol and naphthalene. In summary, the DFT calculations aligned with the adsorption experiment findings, confirming the effectiveness of simulation methods in predicting changes in the adsorption performance of aged MPs.
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Affiliation(s)
- Zongyi Tan
- Guangdong Key Laboratory of Environmental Pollution and Health, Center for Environmental Microplastics Studies, School of Environment, Jinan University, Guangzhou 511443, China; Key Laboratory of Philosophy and Social Science in Guangdong Province of Community of Life for Man and Nature, Jinan University, Guangzhou 511443, China
| | - Haiyang Deng
- CECEP Construction Engineering Design Institute Limited Company, Chengdu 610052, China
| | - Huali Ou
- Guangdong Key Laboratory of Environmental Pollution and Health, Center for Environmental Microplastics Studies, School of Environment, Jinan University, Guangzhou 511443, China; Key Laboratory of Philosophy and Social Science in Guangdong Province of Community of Life for Man and Nature, Jinan University, Guangzhou 511443, China
| | - Xinni Wu
- Guangdong Key Laboratory of Environmental Pollution and Health, Center for Environmental Microplastics Studies, School of Environment, Jinan University, Guangzhou 511443, China
| | - Zhianqi Liao
- Guangdong Key Laboratory of Environmental Pollution and Health, Center for Environmental Microplastics Studies, School of Environment, Jinan University, Guangzhou 511443, China
| | - Huase Ou
- Guangdong Key Laboratory of Environmental Pollution and Health, Center for Environmental Microplastics Studies, School of Environment, Jinan University, Guangzhou 511443, China; Key Laboratory of Philosophy and Social Science in Guangdong Province of Community of Life for Man and Nature, Jinan University, Guangzhou 511443, China.
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38
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Ayers PW. Energy is not a convex function of particle number for r-k interparticle potentials with k > log34. J Chem Phys 2024; 160:044110. [PMID: 38275194 DOI: 10.1063/5.0179137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/11/2023] [Indexed: 01/27/2024] Open
Abstract
The energy of a many-particle system is not convex with respect to particle number for r-k interparticle repulsion potentials if k > log34 ≈ 1.262. With such potentials, some finite electronic systems have ionization potentials that are less than the electron affinity: they have negative band gap (chemical hardness). Although the energy may be a convex function of the number of electrons (for which k = 1), it suggests that finding an analytic proof of convexity will be very difficult. The bound on k is postulated to be tight. An apparent signature of non-convex behavior is that the Dyson orbital corresponding to the lowest-energy mode of electron attachment has a vanishingly small amplitude.
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Affiliation(s)
- Paul W Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
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39
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Zhai Z, Zhang B, Wang Y, Liu G. Fine-tuned local coordination environment of Pt-N in nanocarbons for efficient propane dehydrogenation. Phys Chem Chem Phys 2024; 26:3263-3273. [PMID: 38196379 DOI: 10.1039/d3cp04215d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Based on the disturbance of electronic density, nitrogen-doped nanocarbons show promising properties to anchor metal clusters. However, precisely regulating the coordination mode between N species and the active site remains challenging. Herein, we rationally designed three N types (graphitic N, pyridinic N and pyrrolic N) in nanocarbons to anchor Pt clusters for the benchmark propane dehydrogenation. The specific activity of the pyridinic-N-doped catalyst was 147.54 molC3H6 molPt-1 h-1 at 550 °C, which was 1.3 times higher than those of graphitic- and pyrrolic-N-doped catalysts. Unlike the regular tetrahedron Pt cluster in the graphitic-N catalyst or the distorted three-layered Pt cluster in the pyrrolic-N catalyst, the Pt cluster in the pyridinic-N catalyst was an inverted tetrahedron, which increased the contact degree without geometric repulsion towards C-H bond scission. The geometric parameters of detached H and C atoms in the methylene group for the pyridinic N catalyst was decreased to strengthen the C-H bond scission. After CH3CHCH3* adsorption, the Bader charge of the Pt active site also became highly positive, which tailored the d-band center closer to the Fermi level and provided more vacant orbitals for C-H bond breakage. Therefore, pyridinic N in nanocarbons is promising to anchor small-sized Pt for alkane dehydrogenation in terms of geometric and electronic effects.
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Affiliation(s)
- Ziwei Zhai
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Bofeng Zhang
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Yutong Wang
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Guozhu Liu
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, China
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40
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Yuan LD, Li SS, Luo JW. Direct bandgap emission from strain-doped germanium. Nat Commun 2024; 15:618. [PMID: 38242877 PMCID: PMC10799082 DOI: 10.1038/s41467-024-44916-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 01/04/2024] [Indexed: 01/21/2024] Open
Abstract
Germanium (Ge) is an attractive material for Silicon (Si) compatible optoelectronics, but the nature of its indirect bandgap renders it an inefficient light emitter. Drawing inspiration from the significant expansion of Ge volume upon lithiation as a Lithium (Li) ion battery anode, here, we propose incorporating Li atoms into the Ge to cause lattice expansion to achieve the desired tensile strain for a transition from an indirect to a direct bandgap. Our first-principles calculations show that a minimal amount of 3 at.% Li can convert Ge from an indirect to a direct bandgap to possess a dipole transition matrix element comparable to that of typical direct bandgap semiconductors. To enhance compatibility with Si Complementary-Metal-Oxide-Semiconductors (CMOS) technology, we additionally suggest implanting noble gas atoms instead of Li atoms. We also demonstrate the tunability of the direct-bandgap emission wavelength through the manipulation of dopant concentration, enabling coverage of the mid-infrared to far-infrared spectrum. This Ge-based light-emitting approach presents exciting prospects for surpassing the physical limitations of Si technology in the field of photonics and calls for experimental proof-of-concept studies.
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Affiliation(s)
- Lin-Ding Yuan
- State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, 100083, China
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Shu-Shen Li
- State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, 100083, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun-Wei Luo
- State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, 100083, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China.
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41
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Rubiales-Martínez A, Martínez J, Mera-Jiménez E, Pérez-Flores J, Téllez-Isaías G, Miranda Ruvalcaba R, Hernández-Rodríguez M, Mancilla Percino T, Macías Pérez ME, Nicolás-Vázquez MI. Design of Two New Sulfur Derivatives of Perezone: In Silico Study Simulation Targeting PARP-1 and In Vitro Study Validation Using Cancer Cell Lines. Int J Mol Sci 2024; 25:868. [PMID: 38255943 PMCID: PMC10815500 DOI: 10.3390/ijms25020868] [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: 12/14/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Poly-ADP-Ribose Polymerase (PARP-1) is an overexpressed enzyme in several carcinomas; consequently, the design of PARP-1 inhibitors has acquired special attention. Hence, in the present study, three compounds (8-10) were produced through a Michael addition protocol, using phenylmethanethiol, 5-fluoro-2-mercaptobenzyl alcohol, and 4-mercaptophenylacetic acid, respectively, as nucleophiles and perezone as the substrate, expecting them to be convenient candidates that inhibit PARP-1. It is convenient to note that in the first stage of the whole study, the molecular dynamics (MD) simulations and the quantum chemistry studies of four secondary metabolites, i.e., perezone (1), perezone angelate (2), hydroxyperezone (3), and hydroxyperezone monoangelate (4), were performed, to investigate their interactions in the active site of PARP-1. Complementarily, a docking study of a set of eleven sulfur derivatives of perezone (5-15) was projected to explore novel compounds, with remarkable affinity to PARP-1. The molecules 8-10 provided the most adequate results; therefore, they were evaluated in vitro to determine their activity towards PARP-1, with 9 having the best IC50 (0.317 µM) value. Additionally, theoretical calculations were carried out using the density functional theory (DFT) with the hybrid method B3LYP with a set of base functions 6-311++G(d,p), and the reactivity properties were compared between the natural derivatives of perezone and the three synthesized compounds, and the obtained results exhibited that 9 has the best properties to bind with PARP-1. Finally, it is important to mention that 9 displays significant inhibitory activity against MDA-MB-231 and MCF-7 cells, i.e., 145.01 and 83.17 µM, respectively.
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Affiliation(s)
- Alejandro Rubiales-Martínez
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán Campo 1, Universidad Nacional Autónoma de México, Avenida 1o de Mayo s/n, Colonia Santa María las Torres, Cuautitlán Izcalli 54740, Mexico; (A.R.-M.); (J.M.); (R.M.R.)
| | - Joel Martínez
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán Campo 1, Universidad Nacional Autónoma de México, Avenida 1o de Mayo s/n, Colonia Santa María las Torres, Cuautitlán Izcalli 54740, Mexico; (A.R.-M.); (J.M.); (R.M.R.)
| | - Elvia Mera-Jiménez
- Laboratorio de Cultivo Celular, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Ciudad de México 11340, Mexico; (E.M.-J.); (M.H.-R.)
| | - Javier Pérez-Flores
- Laboratorio de Espectrometría de Masas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Alcaldía Coyoacán, Ciudad de México 04510, Mexico;
| | | | - René Miranda Ruvalcaba
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán Campo 1, Universidad Nacional Autónoma de México, Avenida 1o de Mayo s/n, Colonia Santa María las Torres, Cuautitlán Izcalli 54740, Mexico; (A.R.-M.); (J.M.); (R.M.R.)
| | - Maricarmen Hernández-Rodríguez
- Laboratorio de Cultivo Celular, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Ciudad de México 11340, Mexico; (E.M.-J.); (M.H.-R.)
| | - Teresa Mancilla Percino
- Chemistry Department, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Alcaldía Gustavo A. Madero, Ciudad de México 07000, Mexico
| | - Martha Edith Macías Pérez
- Laboratorio de Cultivo Celular, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Ciudad de México 11340, Mexico; (E.M.-J.); (M.H.-R.)
| | - María Inés Nicolás-Vázquez
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán Campo 1, Universidad Nacional Autónoma de México, Avenida 1o de Mayo s/n, Colonia Santa María las Torres, Cuautitlán Izcalli 54740, Mexico; (A.R.-M.); (J.M.); (R.M.R.)
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Riaz R, Parveen S, Rashid M, Shafiq N. Combined Experimental and Theoretical Insights: Spectroscopic and Molecular Investigation of Polyphenols from Fagonia indica via DFT, UV-vis, and FT-IR Approaches. ACS OMEGA 2024; 9:730-740. [PMID: 38222607 PMCID: PMC10785638 DOI: 10.1021/acsomega.3c06544] [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: 08/31/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 01/16/2024]
Abstract
This review deals with computational study of polyphenolic compounds of medicinal importance and interest for drug development. Herein, four polyphenolic compounds comprising catechol (1), caffeic acid (II), gallic acid (III), and pyrogallol (IV) have been isolated from a medicinal specie, Fagonia indica, by applying silica gel column chromatography. These compounds were identified by using gas chromatography-mass spectrometry (GC-MS) analysis and confirmed by geometric computational analysis. According to computational results, caffeic acid has shown the highest biological activation due to higher chemical softness, electronegativity (χ (eV) = -648.644), and electrostatic potential value (-8.424 × 10-2 to +8.424 × 10-2), while smaller values of chemical potential (-0.269), ELUMO (-0.080), and energy gap (ΔE = 0.149). The Mulliken atomic charges were calculated by using DFT/B3LYP with basis set 6-311G for the determination of active sites. The oxygen atom of catechol showed highest nucleophilic characteristic with a more negative charge (08 = -0.695), and pyrogallol indicated a strong electrophilic center at C14 = 0.415 with a higher positive charge. Moreover, UV-visible absorption spectra and a detailed study of vibrational frequencies for all phenolic compounds by employing the DFT approach with 3-21G, 6-31G, and 6-311G basis sets at the ground-state level showed the great agreement with experimental results. ANOVA has been applied to validate the theoretical data. Results suggest that compounds I-IV are suitable in diverse fields.
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Affiliation(s)
- Rabia Riaz
- Department of Chemistry, Government College Women University Faisalabad 38000, Pakistan
| | - Shagufta Parveen
- Department of Chemistry, Government College Women University Faisalabad 38000, Pakistan
| | - Maryam Rashid
- Department of Chemistry, Government College Women University Faisalabad 38000, Pakistan
| | - Nusrat Shafiq
- Department of Chemistry, Government College Women University Faisalabad 38000, Pakistan
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43
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Lee H, Kwon S, Min J, Jin SM, Hwang JH, Lee E, Lee WB, Park MJ. Thermodynamically stable plumber's nightmare structures in block copolymers. Science 2024; 383:70-76. [PMID: 38175890 DOI: 10.1126/science.adh0483] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 11/08/2023] [Indexed: 01/06/2024]
Abstract
Block copolymer self-assembly affords diverse nanostructures, spanning from spheres and cylinders to networks, offering meticulous control over properties and functionalities at the nanoscale. However, creating thermodynamically stable network structures with high packing frustration remains a challenge. In this study, we report a methodology to access diverse network structures such as gyroid, diamond, and primitive phases from diblock copolymers using end group and linker chemistry. The stability of the medial packing of polymer chain ends (plumber's nightmare structure) over skeletal aggregation (gyroid) is attributed to the interplay between the strength of the end-end interactions and the initial shape of the curvature. Our study establishes an approach to develop tailored network structures from block copolymers, providing an important platform for using block copolymers in nanotechnology applications.
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Affiliation(s)
- Hojun Lee
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Sangwoo Kwon
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul 08826, Republic of Korea
| | - Jaemin Min
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Seon-Mi Jin
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Jun Ho Hwang
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Eunji Lee
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Won Bo Lee
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul 08826, Republic of Korea
| | - Moon Jeong Park
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
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44
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Basceken S. Theoretical insight into the regioselective formation of pyrazolo[1,4]-oxazepine and -oxazines. J Mol Graph Model 2024; 126:108643. [PMID: 37806144 DOI: 10.1016/j.jmgm.2023.108643] [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: 08/09/2023] [Revised: 09/17/2023] [Accepted: 09/27/2023] [Indexed: 10/10/2023]
Abstract
AuCl-, AuCl3-, or AuClPEt3-catalyzed formation mechanisms of pyrazolo[1,4]oxazepines and the NaH-promoted mechanism of pyrazolo[1,4]oxazines were investigated computationally. The structural properties of the reactants were studied in various solvents and with different functionals. The hybrid functionals B3LYP, M06, M06-2X, PBEPBE, and wB97X-D in density functional theory were used to determine and discuss the energetics of the compounds. The electronic properties of groups (R = H or R ≠ H) attached to the alkyne moiety played an essential role in the corresponding 7-endo-dig cyclization or 6-exo-dig cyclization in the presence of a gold catalyst. The regioselectivities of the products were investigated, and the natural bond orbitals of the reactants were determined. Furthermore, a gold-catalyzed alternative mechanism is suggested for synthesizing pyrazolo[1,4]oxazines using a terminal alkyne (R = H) moiety as substrate.
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Affiliation(s)
- Sinan Basceken
- Department of Chemistry, Hitit University, 19030, Corum, Turkey.
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45
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Constantin LA, Jana S, Śmiga S, Della Sala F. Adiabatic connection interaction strength interpolation method made accurate for the uniform electron gas. J Chem Phys 2023; 159:244111. [PMID: 38149733 DOI: 10.1063/5.0178800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023] Open
Abstract
The adiabatic connection interaction strength interpolation (ISI)-like method provides a high-level expression for the correlation energy, being, in principle, exact not only in the weak-interaction limit, where it recovers the second-order Görling-Levy perturbation term, but also in the strong-interaction limit that is described by the strictly correlated electron approach. In this work, we construct a genISI functional made accurate for the uniform electron gas, a solid-state physics paradigm that is a very difficult test for ISI-like correlation functionals. We assess the genISI functional for various jellium spheres with the number of electrons Z ≤ 912 and for the non-relativistic noble atoms with Z ≤ 290. For the jellium clusters, the genISI is remarkably accurate, while for the noble atoms, it shows a good performance, similar to other ISI-like methods. Then, the genISI functional can open the path using the ISI-like method in solid-state calculations.
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Affiliation(s)
- Lucian A Constantin
- Institute for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy
| | - Subrata Jana
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovoth 76100, Israel
| | - Szymon Śmiga
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, ul. Grudziądzka 5, 87-100 Toruń, Poland
| | - Fabio Della Sala
- Institute for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy
- Center for Biomolecular Nanotechnologies, Istituto Italiano di Tecnologia, Via Barsanti 14, 73010 Arnesano (LE), Italy
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Patel HC, Patel MS, Parekh JN, Chudasama DD, Dalwadi P, Kunjadiya A, Bhatt V, Modi KM, Patel CN, Ram KR. In silico and in vitro evaluation of newly synthesized pyrazolo-pyridine fused tetrazolo-pyrimidines derivatives as potential anticancer and antimicrobial agents. J Biomol Struct Dyn 2023:1-24. [PMID: 38146736 DOI: 10.1080/07391102.2023.2298731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/18/2023] [Indexed: 12/27/2023]
Abstract
Diversely functionalized pyrazolo-pyridine fused tetrazolo-pyrimidines 10aa-am and 10ba-bn were successfully synthesized via a catalyst-free synthetic protocol with moderate to very good yields. The compounds were evaluated for cytotoxicity against MCF-7 and HEK-293 cells using MTT assay. Among the tested compounds, 10ab (IC50- 23.83 µM) and 10ah (IC50- 23.30 µM) demonstrated the highest potency against MCF-7 cells, while 10bc (IC50- 14.46 µM) and 10bh (IC50- 2.53 µM) exhibited excellent cytotoxicity against HEK-293 cells. Additionally, antibacterial screening was performed against three Gram-negative bacteria (E. coli, P. aeruginosa, and S. enterica) and three Gram-positive bacteria (S. aureus, B. megaterium, and B. subtilis) using broth dilution method, while antifungal activity was assessed against three fungal strains (A. niger, Penicillium, and S. cerevisiae) using agar well diffusion method. In antimicrobial screening, the majority of the compounds demonstrated significant antibacterial efficacy compared to antifungal activity. We also conducted comprehensive computational studies, including DFT calculations, molecular docking and dynamics, and drug-likeness assessments. In the DFT study, compounds 10ac and 10bc displayed stable conformations, indicating their potential for higher therapeutic activity. Molecular docking analyses revealed compelling interactions, with compound 10ah demonstrating docking score -7.42 kcal/mol against catalytical domain PARP1 (PDB ID: 7KK4) and 10bh exhibiting a best docking score -10.77 kcal/mol against human corticotropin-releasing factor receptor 1 (PDB ID: 4Z9G). A 100 ns molecular dynamics (MD) simulation study of compounds 10ah and 10bh revealed the stable conformation and binding energy in a stimulating environment. In drug-likeness assessments, both the compounds 10ah and 10bh adhere all the established guidelines.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Harsh C Patel
- Department of Chemistry, Sardar Patel University, Vallabh Vidyanagar, Gujarat, India
| | - Manan S Patel
- Department of Chemistry, Sardar Patel University, Vallabh Vidyanagar, Gujarat, India
| | - Jaydeepkumar N Parekh
- Department of Chemistry, Sardar Patel University, Vallabh Vidyanagar, Gujarat, India
| | | | - Priyanka Dalwadi
- Department of Applied and Interdisciplinary Sciences (IICISST), Sardar Patel University, Vallabh Vidyanagar, Gujarat, India
| | - Anju Kunjadiya
- Department of Applied and Interdisciplinary Sciences (IICISST), Sardar Patel University, Vallabh Vidyanagar, Gujarat, India
| | - Vaibhav Bhatt
- School of Applied Sciences and Technology, Gujarat Technological University, Ahmedabad, Gujarat, India
| | - Krunal M Modi
- Department of Humanity and Science, School of Engineering, Indrashil University, Mehsana, Gujarat, India
| | - Chirag N Patel
- Biotechnology Research Center, Technology Innovation Institute, Abu Dhabi, United Arab Emirates
- Department of Botany, Bioinformatics, and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Kesur R Ram
- Department of Chemistry, Sardar Patel University, Vallabh Vidyanagar, Gujarat, India
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Joyner NA, Lee ZR, Dixon DA. Binding of SO 3 to Group 4 Transition Metal Oxide Nanoclusters. J Phys Chem A 2023; 127:9541-9549. [PMID: 37934079 DOI: 10.1021/acs.jpca.3c06389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Transition metal oxide (TMO) clusters are being studied for their ability to absorb acid gases generated by energy production processes. The interaction of SO3, a byproduct of common industrial processes, with group 4 metal (Ti, Zr, and Hf) oxide nanoclusters, has been predicted using electronic structure methods. The calculations were done at the density functional theory (DFT) and correlated molecular orbital coupled cluster singles and doubles CCSD(T) theory levels. There is a reasonable agreement between the DFT/ωB97x-D energies with the CCSD(T) results. SO3 is predicted to strongly chemisorb to these clusters, as do NO2 and CO2. For SO3, these chemisorption processes favor binding to TMO clusters as SO42- sulfate in both the terminal and bridging configurations. It is predicted that SO3 fully extracts the bridging oxygen from the TMO lattice to form bridging SO42-. This is favorable because of the lower S-O bond dissociation energy of SO3, whereas other acid gases add across the bridging oxygen because of their higher A-O bond dissociation energy. SO3 is capable of physisorption as long as an exposed metal center is present in the lattice. If a metal center has a terminal oxo-group, then SO3 will prefer the SO42- configuration. An approximately linear relationship exists between the physisorption energy and proton affinity for rows 2 and 3 elements.
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Affiliation(s)
- Nickolas A Joyner
- Department of Chemistry and Biochemistry, The University of Alabama, Shelby Hall, Tuscaloosa, Alabama 35487-0336, United States
| | - Zachary R Lee
- Department of Chemistry and Biochemistry, The University of Alabama, Shelby Hall, Tuscaloosa, Alabama 35487-0336, United States
| | - David A Dixon
- Department of Chemistry and Biochemistry, The University of Alabama, Shelby Hall, Tuscaloosa, Alabama 35487-0336, United States
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Tatarin SV, Meshcheriakova EA, Kozyukhin SA, Emets VV, Bezzubov SI. Rational design of efficient photosensitizers based on cyclometalated iridium(III) complexes with 2-arylbenzimidazole and aromatic 1,3-diketone ligands. Dalton Trans 2023; 52:16261-16275. [PMID: 37855226 DOI: 10.1039/d3dt02789a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
A judicious selection of substituents in cyclometalating 2-arylbenzimidazoles and an ancillary aromatic 1,3-diketone enabled the creation of heteroleptic iridium(III) complexes demonstrating strong light absorption up to 500 nm (ε ≈ 10 000-12 000 M-1 cm-1). The complexes, which were studied by various spectroscopic techniques, single-crystal X-ray diffraction and cyclic voltammetry, displayed tunable absorption maxima depending on the nature of substituents and their positions. The experimental study was corroborated by quantum chemical calculations, which showed an increased contribution of intraligand charge transfer transitions to the visible light absorption in the case of complexes containing electron-withdrawing substituents in the ligands. Despite being of high intensity, some of these transitions are responsible for the formation of the excited states located at large distances from the 'anchoring' fragment incorporated in the ancillary ligand. In turn, incorporation of electron-donating substituents at the para-position to the Ir-C bonds increases the number of excited states located on the ancillary ligand. The destabilization of the HOMO, which is caused by the increase in the electron-donating ability of the substituents in the metalated rings, translated into negative shifts of the Ir4+/Ir3+ redox potential, affecting, in some cases, the degree of electrochemical reversibility of the complexes. Several complexes having strong light-harvesting characteristics and undergoing reversible oxidation in the appropriate potential range were used for coating the TiO2 photoanodes, which reached an efficiency of 2.15% upon irradiation with the standard AM 1.5 spectrum.
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Affiliation(s)
- Sergei V Tatarin
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii pr. 31, Moscow 119991, Russia.
| | - Elizaveta A Meshcheriakova
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii pr. 31, Moscow 119991, Russia.
- Lomonosov Moscow State University, Lenin's Hills, 1-3, Moscow, 119991, Russia
| | - Sergey A Kozyukhin
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii pr. 31, Moscow 119991, Russia.
| | - Victor V Emets
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninskii pr. 31, Moscow 119071, Russia
| | - Stanislav I Bezzubov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii pr. 31, Moscow 119991, Russia.
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Wang Z, Aldossary A, Shi T, Liu Y, Li XS, Head-Gordon M. Local Second-Order Møller-Plesset Theory with a Single Threshold Using Orthogonal Virtual Orbitals: Theory, Implementation, and Assessment. J Chem Theory Comput 2023; 19:7577-7591. [PMID: 37877899 DOI: 10.1021/acs.jctc.3c00744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
It has long been clear that electron correlation methods exhibit unphysical compute scalings with molecular size, which has motivated the development of local correlation methods to discard effectively zero contributions in a controlled way to yield an approximate correlation energy. The ideal local correlation method should have a single numerical threshold that controls the dropping of terms with the ability to have that threshold set small enough so that the correlation energy is reproduced to enough significant figures such that the result is chemically identical. This work reports such a method for the second-order Møller-Plesset (MP2) theory. The theory, implementation, and testing of this local MP2 theory are reported. Thresholds ranging from 10-5 to 10-8 and basis sets ranging from split valence plus polarization through to quadruple-ζ are assessed for local MP2 calculations on a range of molecules, including linear chains and molecules with two- and three-dimensional character. The implementation is shared memory parallel via OpenMP and yields roughly 50% parallel efficiency with 16 cores for a large job. Considerable efforts were made to minimize memory demands, which increased as thresholds were tightened. A variety of relative energy calculations are presented as a function of threshold to provide some guidance to users on how to obtain adequate precision at a low compute cost. It is particularly clear that derivative properties require tighter thresholds in order to achieve an adequate precision.
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Affiliation(s)
- Zhenling Wang
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Abdulrahman Aldossary
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Tianyi Shi
- Applied Mathematics and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Yang Liu
- Applied Mathematics and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Xiaoye S Li
- Applied Mathematics and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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50
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Patel H, Dabhi VA, Vora AM. Investigating Electronic, Optical, Thermodynamic, and Thermoelectric Properties of SrO and SrO 2 Phases: A Density Functional Theory Approach. ACS OMEGA 2023; 8:43008-43023. [PMID: 38024681 PMCID: PMC10652381 DOI: 10.1021/acsomega.3c06221] [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: 08/22/2023] [Revised: 10/15/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023]
Abstract
The significance of strontium oxide (SrO) and strontium peroxide (SrO2) is currently being investigated as one of the countless potential uses for green energy. However, few studies have examined the distinctive properties of several phases of SrO and SrO2. In order to fill this research gap, we have conducted a study on their various properties through "density functional theory (DFT)" under ideal conditions. This includes the study of electronic, optical, thermodynamic, and thermoelectric properties of the above-mentioned materials. For this study, the "Quantum Espresso" tool in DFT using Perdew-Burke-Ernzerhof-generalized-gradient approximation (PBE-GGA) as the exchange-correlation functional and "Optimized Norm-Conserving Vanderbilt (ONCV)" as the pseudopotential has been used. The face-centered cubic (FCC), body-centered cubic (BCC), hexagonal-1, and hexagonal-2 phases of SrO and the tetragonal and orthorhombic phases of SrO2 have been selected for the aforesaid study, for which some structural information has already been available. During this study, the energy band gap as an electronic property; the dielectric constant, refractive index, absorption coefficient, reflectivity, and energy loss function as optical properties; entropy, heat capacity, Debye temperature, and Debye sound velocity as thermodynamic properties; and the Seebeck coefficient, thermal conductivity, electrical conductivity, and figure of merit as thermoelectric properties have been investigated. In addition, phonon dispersion curves and formation energies have been used to confirm the dynamical stability and thermodynamic stability, respectively, for all of the materials mentioned above. The curve showed that the FCC, hexagonal-1, and hexagonal-2 phases of "SrO" are dynamically stable. These materials have good optoelectronic properties and can be used in ultraviolet sensors due to their intermediate band gap and highest material response in the ultraviolet range. In terms of thermoelectric property, the maximum value of "figure of merit" for the above material has been achieved up to 0.5. Satisfactory agreement has been found between the current findings and the known theoretical and experimental findings.
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Affiliation(s)
- Hiren
S. Patel
- Department of Physics, University
School of Sciences, Gujarat University, Navrangpura, Ahmedabad 380 009, Gujarat, India
| | - Vishnu A. Dabhi
- Department of Physics, University
School of Sciences, Gujarat University, Navrangpura, Ahmedabad 380 009, Gujarat, India
| | - Aditya M. Vora
- Department of Physics, University
School of Sciences, Gujarat University, Navrangpura, Ahmedabad 380 009, Gujarat, India
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