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Xiao F, Lei D, Liu C, Li Y, Ren W, Li J, Li D, Zu B, Dou X. Coherent Modulation of the Aggregation Behavior and Intramolecular Charge Transfer in Small Molecule Probes for Sensitive and Long-term Nerve Agent Monitoring. Angew Chem Int Ed Engl 2024; 63:e202400453. [PMID: 38323751 DOI: 10.1002/anie.202400453] [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: 01/08/2024] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 02/08/2024]
Abstract
Aggregation-induced emission (AIE) shows promising performance in chemical sensing relying on the change of the emission behavior of the probe molecule monomers to the aggregated product. However, whether the response contrast could be further boosted by utilizing the emission property of the aggregated probe and the aggregated product remains a big challenge. Here, an exciting AIE probe regulation strategy was proposed by coherently modulating the aggregation behavior and the intramolecular charge transfer (ICT) property of the probes and thus an aggregated-to-aggregated colorimetric-fluorescent dual-mode detection was achieved. The blue emissive film obtained with the optimal AIE probe has been proven to be effective to recognize the vapor of nerve agent analog DCP in air by emitting a sharp green fluorescence. In addition, a porous polymer-based wet sensing chip loaded with the probe enables the immediate response to DCP vapor with a limit of detection (LOD) of 1.7 ppb, and it was further integrated into a wearable watch device for long-term monitoring of DCP vapor up to two weeks. We expect the present probe design strategy would greatly deepen the AIE-based science and provide new insights for long-term monitoring sensors toward trace hazardous substances.
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Affiliation(s)
- Fangfang Xiao
- Xinjiang Key Laboratory of Trace Chemicals Sensing, Xinjiang Technical Institute of Physics & Chemistry, Chinese Academy of Sciences, Urumqi, 830000, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Da Lei
- Xinjiang Key Laboratory of Trace Chemicals Sensing, Xinjiang Technical Institute of Physics & Chemistry, Chinese Academy of Sciences, Urumqi, 830000, China
| | - Chaogan Liu
- Xinjiang Key Laboratory of Trace Chemicals Sensing, Xinjiang Technical Institute of Physics & Chemistry, Chinese Academy of Sciences, Urumqi, 830000, China
| | - Yushu Li
- Xinjiang Key Laboratory of Trace Chemicals Sensing, Xinjiang Technical Institute of Physics & Chemistry, Chinese Academy of Sciences, Urumqi, 830000, China
| | - Wenfei Ren
- Xinjiang Key Laboratory of Trace Chemicals Sensing, Xinjiang Technical Institute of Physics & Chemistry, Chinese Academy of Sciences, Urumqi, 830000, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiguang Li
- Xinjiang Key Laboratory of Trace Chemicals Sensing, Xinjiang Technical Institute of Physics & Chemistry, Chinese Academy of Sciences, Urumqi, 830000, China
| | - Dezhong Li
- Xinjiang Key Laboratory of Trace Chemicals Sensing, Xinjiang Technical Institute of Physics & Chemistry, Chinese Academy of Sciences, Urumqi, 830000, China
| | - Baiyi Zu
- Xinjiang Key Laboratory of Trace Chemicals Sensing, Xinjiang Technical Institute of Physics & Chemistry, Chinese Academy of Sciences, Urumqi, 830000, China
| | - Xincun Dou
- Xinjiang Key Laboratory of Trace Chemicals Sensing, Xinjiang Technical Institute of Physics & Chemistry, Chinese Academy of Sciences, Urumqi, 830000, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
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2
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Masoumifeshani E, Korona T. AROFRAG─A Systematic Approach for Fragmentation of Aromatic Molecules. J Chem Theory Comput 2024. [PMID: 38252847 DOI: 10.1021/acs.jctc.3c00875] [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
We present a new systematic fragmentation scheme of polycyclic aromatic hydrocarbons (PAHs), including fullerenes and nanotubes, based on an idea to treat a sextet ring as a single unbreakable unit so that the basic unit of aromaticity remains preserved upon fragmentation. In the approach, denoted as AROFRAG (from aromatic fragmentation), a set of predefined elementary subsystems, such as naphthalene and biphenyl in the first model and larger PAHs in the second and third models, is generated with appropriate weights with the aim of reproducing the structure of the original molecule. The energies of the molecules are approximated as weighted sums of the energies of these subsystems. For symmetric cases, e.g., fullerenes, the point-group symmetry is preserved during the decomposition. The AROFRAG is used in conjunction with the molecule-in-molecule (MIM) technique to obtain an accurate description of the electronic energies. The new approach has been applied for selected graphene structures and fullerene doped with boron and nitrogen atoms, for which isomerization energies were calculated, as well as for several nanotubes and regular fullerene molecules. The combination of the third AROFRAG model and the MIM approach leads to the reproduction of electronic energies with a few milli-hartree accuracy at a fraction of the computational cost of the original method.
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Affiliation(s)
- Emran Masoumifeshani
- Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warsaw, Poland
| | - Tatiana Korona
- Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warsaw, Poland
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3
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Chen WK, Fang WH, Cui G. Extending multi-layer energy-based fragment method for excited-state calculations of large covalently bonded fragment systems. J Chem Phys 2023; 158:044110. [PMID: 36725521 DOI: 10.1063/5.0129458] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Recently, we developed a low-scaling Multi-Layer Energy-Based Fragment (MLEBF) method for accurate excited-state calculations and nonadiabatic dynamics simulations of nonbonded fragment systems. In this work, we extend the MLEBF method to treat covalently bonded fragment ones. The main idea is cutting a target system into many fragments according to chemical properties. Fragments with dangling bonds are first saturated by chemical groups; then, saturated fragments, together with the original fragments without dangling bonds, are grouped into different layers. The accurate total energy expression is formulated with the many-body energy expansion theory, in combination with the inclusion-exclusion principle that is used to delete the contribution of chemical groups introduced to saturate dangling bonds. Specifically, in a two-layer MLEBF model, the photochemically active and inert layers are calculated with high-level and efficient electronic structure methods, respectively. Intralayer and interlayer energies can be truncated at the two- or three-body interaction level. Subsequently, through several systems, including neutral and charged covalently bonded fragment systems, we demonstrate that MLEBF can provide accurate ground- and excited-state energies and gradients. Finally, we realize the structure, conical intersection, and path optimizations by combining our MLEBF program with commercial and free packages, e.g., ASE and SciPy. These developments make MLEBF a practical and reliable tool for studying complex photochemical and photophysical processes of large nonbonded and bonded fragment systems.
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Affiliation(s)
- Wen-Kai Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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4
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Liu J, He X. Recent advances in quantum fragmentation approaches to complex molecular and condensed‐phase systems. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy China Pharmaceutical University Nanjing China
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering East China Normal University Shanghai China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering East China Normal University Shanghai China
- New York University‐East China Normal University Center for Computational Chemistry New York University Shanghai Shanghai China
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5
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Fluorescence-based monitoring of the pressure-induced aggregation microenvironment evolution for an AIEgen under multiple excitation channels. Nat Commun 2022; 13:5234. [PMID: 36068224 PMCID: PMC9448794 DOI: 10.1038/s41467-022-32968-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 08/25/2022] [Indexed: 11/09/2022] Open
Abstract
The development of organic solid-state luminescent materials, especially those sensitive to aggregation microenvironment, is critical for their applications in devices such as pressure-sensitive elements, sensors, and photoelectric devices. However, it still faces certain challenges and a deep understanding of the corresponding internal mechanisms is required. Here, we put forward an unconventional strategy to explore the pressure-induced evolution of the aggregation microenvironment, involving changes in molecular conformation, stacking mode, and intermolecular interaction, by monitoring the emission under multiple excitation channels based on a luminogen with aggregation-induced emission characteristics of di(p-methoxylphenyl)dibenzofulvene. Under three excitation wavelengths, the distinct emission behaviors have been interestingly observed to reveal the pressure-induced structural evolution, well consistent with the results from ultraviolet-visible absorption, high-pressure angle-dispersive X-ray diffraction, and infrared studies, which have rarely been reported before. This finding provides important insights into the design of organic solid luminescent materials and greatly promotes the development of stimulus-responsive luminescent materials.
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6
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Wang K, Xie Z, Luo Z, Ma H. Low-Scaling Excited State Calculation Using the Block Interaction Product State. J Phys Chem Lett 2022; 13:462-470. [PMID: 35015548 DOI: 10.1021/acs.jpclett.1c03445] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We develop an automatic and efficient scheme for the accurate construction of the bases for excitonic models, which can enable "black-box" excited state structure calculations for large molecular systems. These new and optimized bases, which are named the block interaction product state (BIPS), can be expressed as the direct products of the local states for each chromophore. Each chromophore's local states are selected by diagonalization of its reduced density matrix, which is obtained by quantum chemical calculation of the small subsystem composed of the chromophore and its nearest neighbors. We implemented the BIPS framework with fragment-based calculations considering two- and three-body interactions. Test calculations for eight different molecular aggregates demonstrate that this framework provides an accurate description of not only the excitation energies but also the first-order wave function properties (dipole moment and transition dipole moment) of the low-lying excited states at a low-scaling computational cost.
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Affiliation(s)
- Ke Wang
- School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University, Nanjing 210023, China
| | - Zhaoxuan Xie
- School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University, Nanjing 210023, China
| | - Zhen Luo
- School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University, Nanjing 210023, China
| | - Haibo Ma
- School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University, Nanjing 210023, China
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7
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Shen C, Wang X, He X. Fragment-Based Quantum Mechanical Calculation of Excited-State Properties of Fluorescent RNAs. Front Chem 2022; 9:801062. [PMID: 35004616 PMCID: PMC8727457 DOI: 10.3389/fchem.2021.801062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Fluorescent RNA aptamers have been successfully applied to track and tag RNA in a biological system. However, it is still challenging to predict the excited-state properties of the RNA aptamer–fluorophore complex with the traditional electronic structure methods due to expensive computational costs. In this study, an accurate and efficient fragmentation quantum mechanical (QM) approach of the electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) scheme was applied for calculations of excited-state properties of the RNA aptamer–fluorophore complex. In this method, the excited-state properties were first calculated with one-body fragment quantum mechanics/molecular mechanics (QM/MM) calculation (the excited-state properties of the fluorophore) and then corrected with a series of two-body fragment QM calculations for accounting for the QM effects from the RNA on the excited-state properties of the fluorophore. The performance of the EE-GMFCC on prediction of the absolute excitation energies, the corresponding transition electric dipole moment (TEDM), and atomic forces at both the TD-HF and TD-DFT levels was tested using the Mango-II RNA aptamer system as a model system. The results demonstrate that the calculated excited-state properties by EE-GMFCC are in excellent agreement with the traditional full-system time-dependent ab initio calculations. Moreover, the EE-GMFCC method is capable of providing an accurate prediction of the relative conformational excited-state energies for different configurations of the Mango-II RNA aptamer system extracted from the molecular dynamics (MD) simulations. The fragmentation method further provides a straightforward approach to decompose the excitation energy contribution per ribonucleotide around the fluorophore and then reveals the influence of the local chemical environment on the fluorophore. The applications of EE-GMFCC in calculations of excitation energies for other RNA aptamer–fluorophore complexes demonstrate that the EE-GMFCC method is a general approach for accurate and efficient calculations of excited-state properties of fluorescent RNAs.
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Affiliation(s)
- Chenfei Shen
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Xianwei Wang
- College of Science, Zhejiang University of Technology, Hangzhou, China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.,New York University-East China Normal University Center for Computational Chemistry at New York University Shanghai, Shanghai, China
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8
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Li W, Ma H, Li S, Ma J. Computational and data driven molecular material design assisted by low scaling quantum mechanics calculations and machine learning. Chem Sci 2021; 12:14987-15006. [PMID: 34909141 PMCID: PMC8612375 DOI: 10.1039/d1sc02574k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/12/2021] [Indexed: 12/11/2022] Open
Abstract
Electronic structure methods based on quantum mechanics (QM) are widely employed in the computational predictions of the molecular properties and optoelectronic properties of molecular materials. The computational costs of these QM methods, ranging from density functional theory (DFT) or time-dependent DFT (TDDFT) to wave-function theory (WFT), usually increase sharply with the system size, causing the curse of dimensionality and hindering the QM calculations for large sized systems such as long polymer oligomers and complex molecular aggregates. In such cases, in recent years low scaling QM methods and machine learning (ML) techniques have been adopted to reduce the computational costs and thus assist computational and data driven molecular material design. In this review, we illustrated low scaling ground-state and excited-state QM approaches and their applications to long oligomers, self-assembled supramolecular complexes, stimuli-responsive materials, mechanically interlocked molecules, and excited state processes in molecular aggregates. Variable electrostatic parameters were also introduced in the modified force fields with the polarization model. On the basis of QM computational or experimental datasets, several ML algorithms, including explainable models, deep learning, and on-line learning methods, have been employed to predict the molecular energies, forces, electronic structure properties, and optical or electrical properties of materials. It can be conceived that low scaling algorithms with periodic boundary conditions are expected to be further applicable to functional materials, perhaps in combination with machine learning to fast predict the lattice energy, crystal structures, and spectroscopic properties of periodic functional materials.
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Affiliation(s)
- Wei Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Haibo Ma
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
- Jiangsu Key Laboratory of Advanced Organic Materials, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University Nanjing 210023 China
| | - Shuhua Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Jing Ma
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
- Jiangsu Key Laboratory of Advanced Organic Materials, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University Nanjing 210023 China
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9
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Hisama K, Orimoto Y, Pomogaeva A, Nakatani K, Aoki Y. Ab initio multi-level layered elongation method and its application to local interaction analysis between DNA bulge and ligand molecules. J Chem Phys 2021; 155:044110. [PMID: 34340364 DOI: 10.1063/5.0050096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A multi-level layered elongation method was developed for efficiently analyzing the electronic states of local structures in large bio/nano-systems at the full ab initio level of theory. The original elongation method developed during the last three decades in our group has focused on the system in one direction from one terminal to the other terminal to sequentially construct the electronic states of a polymer, called a theoretical synthesis of polymers. In this study, an important region termed the central (C) part is targeted in a large polymer and the remainder are terminal (T) parts. The electronic structures along with polymer elongation are calculated repeatedly from both end T parts to the C central part at the same time. The important C part is treated with large basis sets (high level) and the other regions are treated with small basis sets (low level) in the ab initio theoretical framework. The electronic structures besides the C part can be reused for other systems with different structures at the C part, which renders the method computationally efficient. This multi-level layered elongation method was applied to the investigation on DNA single bulge recognition of small molecules (ligands). The reliability and validity of our approach were examined in comparison with the results obtained by direct calculations using a conventional quantum chemical method for the entire system. Furthermore, stabilization energies by the formation of the complex of bulge DNA and a ligand were estimated with basis set superposition error corrections incorporated into the elongation method.
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Affiliation(s)
- Keisuke Hisama
- Department of Interdisciplinary Engineering Sciences, Chemistry and Materials Science, Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
| | - Yuuichi Orimoto
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
| | - Anna Pomogaeva
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Yuriko Aoki
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
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10
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Ozaki Y, Beć KB, Morisawa Y, Yamamoto S, Tanabe I, Huck CW, Hofer TS. Advances, challenges and perspectives of quantum chemical approaches in molecular spectroscopy of the condensed phase. Chem Soc Rev 2021; 50:10917-10954. [PMID: 34382961 DOI: 10.1039/d0cs01602k] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The purpose of this review is to demonstrate advances, challenges and perspectives of quantum chemical approaches in molecular spectroscopy of the condensed phase. Molecular spectroscopy, particularly vibrational spectroscopy and electronic spectroscopy, has been used extensively for a wide range of areas of chemical sciences and materials science as well as nano- and biosciences because it provides valuable information about structure, functions, and reactions of molecules. In the meantime, quantum chemical approaches play crucial roles in the spectral analysis. They also yield important knowledge about molecular and electronic structures as well as electronic transitions. The combination of spectroscopic approaches and quantum chemical calculations is a powerful tool for science, in general. Thus, our article, which treats various spectroscopy and quantum chemical approaches, should have strong implications in the wider scientific community. This review covers a wide area of molecular spectroscopy from far-ultraviolet (FUV, 120-200 nm) to far-infrared (FIR, 400-10 cm-1)/terahertz and Raman spectroscopy. As quantum chemical approaches, we introduce several anharmonic approaches such as vibrational self-consistent field (VSCF) and the combination of periodic harmonic calculations with anharmonic corrections based on finite models, grid-based techniques like the Numerov approach, the Cartesian coordinate tensor transfer (CCT) method, Symmetry-Adapted Cluster Configuration-Interaction (SAC-CI), and the ZINDO (Semi-empirical calculations at Zerner's Intermediate Neglect of Differential Overlap). One can use anharmonic approaches and grid-based approaches for both infrared (IR) and near-infrared (NIR) spectroscopy, while CCT methods are employed for Raman, Raman optical activity (ROA), FIR/terahertz and low-frequency Raman spectroscopy. Therefore, this review overviews cross relations between molecular spectroscopy and quantum chemical approaches, and provides various kinds of close-reality advanced spectral simulation for condensed phases.
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Affiliation(s)
- Yukihiro Ozaki
- School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan. and Toyota Physical and Chemical Research Institute, Yokomichi, Nagakute, Aichi 480-1192, Japan
| | - Krzysztof B Beć
- Institute of Analytical Chemistry and Radiochemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Yusuke Morisawa
- Department of Chemistry, School of Science and Engineering, Kindai University, Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Shigeki Yamamoto
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Ichiro Tanabe
- Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Christian W Huck
- Institute of Analytical Chemistry and Radiochemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Thomas S Hofer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A6020 Innsbruck, Austria
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11
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Shen C, Jin X, Glover WJ, He X. Accurate Prediction of Absorption Spectral Shifts of Proteorhodopsin Using a Fragment-Based Quantum Mechanical Method. Molecules 2021; 26:4486. [PMID: 34361639 PMCID: PMC8347797 DOI: 10.3390/molecules26154486] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 11/17/2022] Open
Abstract
Many experiments have been carried out to display different colors of Proteorhodopsin (PR) and its mutants, but the mechanism of color tuning of PR was not fully elucidated. In this study, we applied the Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps (EE-GMFCC) method to the prediction of excitation energies of PRs. Excitation energies of 10 variants of Blue Proteorhodopsin (BPR-PR105Q) in residue 105GLN were calculated with the EE-GMFCC method at the TD-B3LYP/6-31G* level. The calculated results show good correlation with the experimental values of absorption wavelengths, although the experimental wavelength range among these systems is less than 50 nm. The ensemble-averaged electric fields along the polyene chain of retinal correlated well with EE-GMFCC calculated excitation energies for these 10 PRs, suggesting that electrostatic interactions from nearby residues are responsible for the color tuning. We also utilized the GMFCC method to decompose the excitation energy contribution per residue surrounding the chromophore. Our results show that residues ASP97 and ASP227 have the largest contribution to the absorption spectral shift of PR among the nearby residues of retinal. This work demonstrates that the EE-GMFCC method can be applied to accurately predict the absorption spectral shifts for biomacromolecules.
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Affiliation(s)
- Chenfei Shen
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China; (C.S.); (X.J.)
| | - Xinsheng Jin
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China; (C.S.); (X.J.)
| | - William J. Glover
- NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China;
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China; (C.S.); (X.J.)
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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12
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Han Y, Wang Z, Wei Z, Liu J, Li J. Machine learning builds full-QM precision protein force fields in seconds. Brief Bioinform 2021; 22:6279287. [PMID: 34017993 DOI: 10.1093/bib/bbab158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/29/2021] [Accepted: 04/04/2021] [Indexed: 11/14/2022] Open
Abstract
Full-quantum mechanics (QM) calculations are extraordinarily precise but difficult to apply to large systems, such as biomolecules. Motivated by the massive demand for efficient calculations for large systems at the full-QM level and by the significant advances in machine learning, we have designed a neural network-based two-body molecular fractionation with conjugate caps (NN-TMFCC) approach to accelerate the energy and atomic force calculations of proteins. The results show very high precision for the proposed NN potential energy surface models of residue-based fragments, with energy root-mean-squared errors (RMSEs) less than 1.0 kcal/mol and force RMSEs less than 1.3 kcal/mol/Å for both training and testing sets. The proposed NN-TMFCC method calculates the energies and atomic forces of 15 representative proteins with full-QM precision in 10-100 s, which is thousands of times faster than the full-QM calculations. The computational complexity of the NN-TMFCC method is independent of the protein size and only depends on the number of residue species, which makes this method particularly suitable for rapid prediction of large systems with tens of thousands or even hundreds of thousands of times acceleration. This highly precise and efficient NN-TMFCC approach exhibits considerable potential for performing energy and force calculations, structure predictions and molecular dynamics simulations of proteins with full-QM precision.
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Affiliation(s)
| | | | - Zhiyun Wei
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jinyun Liu
- Key Laboratory of Functional Molecular Solids of Ministry of Education, Anhui Normal University, China
| | - Jinjin Li
- Key Laboratory for Thin Film and Microfabrication of Ministry of Education, Department of Micro/Nano Electronics, Shanghai Jiao Tong University, China
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13
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Zhang Q, Cao Z. Packing Effect on Light Emission of Naphthyridine-Based Luminophor: Insights from Quantum Mechanics and Quantum Mechanics/Molecular Mechanics Calculations. J Phys Chem B 2021; 125:3005-3013. [PMID: 33721999 DOI: 10.1021/acs.jpcb.1c01557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Luminescent properties of the naphthyridine-based luminophor, 2,7-di(9,9-dimethylacridin-10(9H)-yl)-1,8-naphthyridine (DMAC-ND), have been explored by using quantum mechanics and quantum mechanics/molecular mechanics calculations. Based on different packing models for DMAC-ND monomer in tetrahydrofuran (THF) solution and its crystal and amorphous aggregated states, the morphology dependence of light absorption and emission has been explored. Calculations reveal that the intersystem crossing rates (kisc) from S1 to T1 are comparable with their corresponding non-radiative decay rates (knr) from S1 to S0 in crystal and amorphous phases, while the kisc value in THF solution is 6 orders of magnitude smaller than its corresponding knr, suggesting that effective intersystem crossing (ISC) may occur only in the aggregated configurations. The predicted reverse intersystem crossing rates (krisc) are also comparable with their corresponding non-radiative decay rates from T1 to S0, and there would be an effective upconversion process in the aggregated state. The predicted krisc values show notable morphology and temperature dependences, and the aggregation and the increase in temperature can facilitate the reverse intersystem crossing process. Based on the independent gradient model and energy decomposition analysis, combined with the estimation of the Huang-Rhys factors, such remarkable packing effects on the luminescent properties of DMAC-ND can be ascribed into the strong intermolecular interactions and the restriction of low-frequency vibrations in the crystal and amorphous phases.
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Affiliation(s)
- Qing Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, People's Republic of China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, People's Republic of China
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14
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Li W, Gu Q, Wang X, Zhang D, Wang Y, He X, Wang W, Yang H. AIE‐Active Chiral [3]Rotaxanes with Switchable Circularly Polarized Luminescence. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100934] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Wei‐Jian Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes & Chang-Kung Chuang Institute School of Chemistry and Molecular Engineering East China Normal University 3663 N. Zhongshan Road Shanghai 200062 P. R. China
| | - Qingyi Gu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development School of Chemistry and Molecular Engineering East China Normal University 3663 N. Zhongshan Road Shanghai 200062 P. R. China
| | - Xu‐Qing Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes & Chang-Kung Chuang Institute School of Chemistry and Molecular Engineering East China Normal University 3663 N. Zhongshan Road Shanghai 200062 P. R. China
| | - Dan‐Yang Zhang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes & Chang-Kung Chuang Institute School of Chemistry and Molecular Engineering East China Normal University 3663 N. Zhongshan Road Shanghai 200062 P. R. China
| | - Yu‐Te Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes & Chang-Kung Chuang Institute School of Chemistry and Molecular Engineering East China Normal University 3663 N. Zhongshan Road Shanghai 200062 P. R. China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development School of Chemistry and Molecular Engineering East China Normal University 3663 N. Zhongshan Road Shanghai 200062 P. R. China
| | - Wei Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes & Chang-Kung Chuang Institute School of Chemistry and Molecular Engineering East China Normal University 3663 N. Zhongshan Road Shanghai 200062 P. R. China
| | - Hai‐Bo Yang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes & Chang-Kung Chuang Institute School of Chemistry and Molecular Engineering East China Normal University 3663 N. Zhongshan Road Shanghai 200062 P. R. China
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15
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Li W, Gu Q, Wang X, Zhang D, Wang Y, He X, Wang W, Yang H. AIE‐Active Chiral [3]Rotaxanes with Switchable Circularly Polarized Luminescence. Angew Chem Int Ed Engl 2021; 60:9507-9515. [DOI: 10.1002/anie.202100934] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/07/2021] [Indexed: 12/16/2022]
Affiliation(s)
- Wei‐Jian Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes & Chang-Kung Chuang Institute School of Chemistry and Molecular Engineering East China Normal University 3663 N. Zhongshan Road Shanghai 200062 P. R. China
| | - Qingyi Gu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development School of Chemistry and Molecular Engineering East China Normal University 3663 N. Zhongshan Road Shanghai 200062 P. R. China
| | - Xu‐Qing Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes & Chang-Kung Chuang Institute School of Chemistry and Molecular Engineering East China Normal University 3663 N. Zhongshan Road Shanghai 200062 P. R. China
| | - Dan‐Yang Zhang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes & Chang-Kung Chuang Institute School of Chemistry and Molecular Engineering East China Normal University 3663 N. Zhongshan Road Shanghai 200062 P. R. China
| | - Yu‐Te Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes & Chang-Kung Chuang Institute School of Chemistry and Molecular Engineering East China Normal University 3663 N. Zhongshan Road Shanghai 200062 P. R. China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development School of Chemistry and Molecular Engineering East China Normal University 3663 N. Zhongshan Road Shanghai 200062 P. R. China
| | - Wei Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes & Chang-Kung Chuang Institute School of Chemistry and Molecular Engineering East China Normal University 3663 N. Zhongshan Road Shanghai 200062 P. R. China
| | - Hai‐Bo Yang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes & Chang-Kung Chuang Institute School of Chemistry and Molecular Engineering East China Normal University 3663 N. Zhongshan Road Shanghai 200062 P. R. China
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16
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Zhang J, Zhang H, Lam JWY, Tang BZ. Restriction of Intramolecular Motion(RIM): Investigating AIE Mechanism from Experimental and Theoretical Studies. Chem Res Chin Univ 2021. [DOI: 10.1007/s40242-021-0381-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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17
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Chen WK, Zhang Y, Jiang B, Fang WH, Cui G. Efficient Construction of Excited-State Hessian Matrices with Machine Learning Accelerated Multilayer Energy-Based Fragment Method. J Phys Chem A 2020; 124:5684-5695. [DOI: 10.1021/acs.jpca.0c04117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Wen-Kai Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yaolong Zhang
- Hefei National Laboratory for Physical Science at the Microscale, Department of Chemical Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Bin Jiang
- Hefei National Laboratory for Physical Science at the Microscale, Department of Chemical Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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