1
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Morgunov A, Tran HK, Meitei OR, Chien YC, Van Voorhis T. MP2-Based Composite Extrapolation Schemes Can Predict Core-Ionization Energies for First-Row Elements with Coupled-Cluster Level Accuracy. J Phys Chem A 2024; 128:6989-6998. [PMID: 39121455 DOI: 10.1021/acs.jpca.4c01606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2024]
Abstract
X-ray photoelectron spectroscopy (XPS) measures core-electron binding energies (CEBEs) to reveal element-specific insights into the chemical environment and bonding. Accurate theoretical CEBE prediction aids XPS interpretation but requires proper modeling of orbital relaxation and electron correlation upon core-ionization. This work systematically investigates basis set selection for extrapolation to the complete basis set limit of CEBEs from ΔMP2 and ΔCC energies across 94 K-edges in diverse organic molecules. We demonstrate that an alternative composite scheme using ΔMP2 in a large basis corrected by ΔCC-ΔMP2 difference in a small basis can quantitatively recover optimally extrapolated ΔCC CEBEs within 0.02 eV. Unlike ΔCC, MP2 calculations do not suffer from convergence issues and are computationally cheaper, and thus, the composite ΔMP2/ΔCC scheme balances accuracy and cost, overcoming limitations of solely using either method. We conclude by providing a comprehensive analysis of the choice of small and large basis sets for the composite schemes and provide practical recommendations for highly accurate (within 0.10-0.15 eV MAE) ab initio prediction of XPS data.
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Affiliation(s)
- Anton Morgunov
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Henry K Tran
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Oinam Romesh Meitei
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yu-Che Chien
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Troy Van Voorhis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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2
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Jaime-Adán E, Germán-Acacio JM, Páez-Franco JC, Lara VH, Reyes-Marquez V, Morales-Morales D. Exploring the persistence of the fluorinated thiolate 2,3,5,6-S(C 6F 4H-4) motif to establish π F-π F stacking in metal complexes: a crystal engineering perspective. Dalton Trans 2024. [PMID: 39171661 DOI: 10.1039/d4dt01978d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
π-π stacking interactions are versatile because they are involved in many processes, such as protein folding, DNA stacking, and drug recognition. However, from the point of view of crystal engineering, there is an incipient knowledge of its exploitation. A comparison of these interactions with hydrogen bonds shows a huge difference in their employment as a reliable non-covalent interaction. And different reasons can be listed to explain why hydrogen bonding can be considered a more robust interaction than π-π stacking. For instance, hydrogen bonds encompass a wide energy range (25-40 kJ mol-1). From this, these interactions can be classified as strong, moderate, and weak. Hence, the first two can be considered highly to moderately directional to be exploited in crystal engineering. This aspect is relevant for them to be used in a relatively reliably way in this area of supramolecular chemistry. On the other hand, in the case of π-π stacking, the energy range is 0-10 kJ mol-1, thus implying that hydrogen bonds or any other energetically more robust contact would predominate in the competition for establishing packing interactions in a given arrangement. In this sense, if stacking is pretended to be exploited from the point of view of crystal engineering, one of the points that must be ensured is that this interaction will be the one energetically predominant. However, although there are other factors to consider, it seems that energetics is the dominant one. In this line, our research group has obtained and studied many single-crystalline structures of coordination and organometallic compounds containing fluorinated thiolates. This being particularly true in the case of the thiolate 2,3,5,6-S(C6F4H-4) bound to different metals, where it has been observed that they preferentially tend to establish πF-πF stacking interactions, results that have been reported in several papers. Thus, from this perspective, we have explored, using ConQuest (CCDC) a number of structures to observe how feasible is to find stacking in coordination and organometallic compounds containing the thiolate 2,3,5,6-S(C6F4H-4).
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Affiliation(s)
- Everardo Jaime-Adán
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Ciudad de México, C. P. 04510, Mexico.
| | - Juan Manuel Germán-Acacio
- Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México-CIC, Instituto Nacional de Ciencias Médicas y Nutrición SZ, C. P.14000, Ciudad de México, Mexico.
| | - José Carlos Páez-Franco
- Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México-CIC, Instituto Nacional de Ciencias Médicas y Nutrición SZ, C. P.14000, Ciudad de México, Mexico.
| | - Victor H Lara
- Universidad Autonoma Metropolitana, Iztapalapa, Av. San Rafael Atlixco No. 186, Col. Vicentina, 09340 Ciudad de México, Mexico
| | - Viviana Reyes-Marquez
- Departamento de Ciencias Químico-Biológicas, Universidad de Sonora, Luis Encinas y Rosales s/n, Hermosillo C.P. 83000, Sonora, Mexico
| | - David Morales-Morales
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Ciudad de México, C. P. 04510, Mexico.
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3
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Guo X, Jiang Y, Xie D, Zhou Y. Computational investigation on the binding modes of PET polymer to PETase. J Biomol Struct Dyn 2024; 42:6842-6849. [PMID: 37505088 DOI: 10.1080/07391102.2023.2240893] [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: 04/10/2023] [Accepted: 07/08/2023] [Indexed: 07/29/2023]
Abstract
Poly(ethylene terephthalate) (PET) has been widely utilized in daily life, but its non-degradability has induced severe environmental and health problems. Recently, PETase, which has been isolated from bacterium Ideonella sakaiensisis, was reported to have the highest PET degradation activity and specificity under room temperature, but no crystal structure for PET in complex with PETase has been reported. To provide deep insight into the binding mode of PET polymer on PETase and the binding interactions, we employed molecular docking and molecular dynamics simulations to study the substrate binding at the atomic level. Different PET oligomers have been studied with chain lengths varying from 2 to 8. In addition, the binding energies and hot-spot residues were analyzed to gain better insights into the binding mechanism by MM/GBSA approach. The PET oligomers adopt stable and reactive conformations in a shallow cleft on a flat surface of PETase. The binding cleft can only accommodate four moieties, and others beyond the region will be stabilized by the π-stacking interactions with Trp156 at the terephthalic acid terminal. Our studies provide a clear picture of how the binding mode of PET polymer and its interactions with PETase change with the chain length. Those studies would provide useful information for the rational design of catalytically more efficient PETase variants toward plastic degradation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xuehui Guo
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Yiming Jiang
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Daiqian Xie
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Yanzi Zhou
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
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4
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Al-Ansi AY, Al-Shawesh GH, Ru X, Lin Z. Quantum Mechanics-Based Fast and Reliable Prediction of Binding Pose Structures. J Phys Chem B 2024; 128:6059-6070. [PMID: 38875526 DOI: 10.1021/acs.jpcb.4c02596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
Abstract
Predicting the binding poses of docking with an accurate estimation of binding energies is highly important but very challenging in computational drug design. A quantum mechanics (QM) calculation-based docking approach considering multiple conformations and orientations of the ligand is introduced here to tackle the problem. This QM docking consists of three steps: generating an ensemble of binding poses with a conventional docking simulation, computing the binding energies with self-consistent charge density functional theory tightly binding with dispersion correction (DFTB-D) to selecting the 10 top binding modes, and optimizing the selected binding mode structures using the ONIOM(DFTB:PM7) technique to determine the binding poses. The ONIOM(DFTB-D:PM6) docking approach is tested on 121 ligand-receptor biocomplexes with the crystal structures obtained from the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB). The result shows that the new method is highly satisfactory for the accurate prediction of the binding poses. The new docking method should be beneficial to structure-based drug design.
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Affiliation(s)
- Amar Y Al-Ansi
- Department of Physics, University of Science and Technology of China, Hefei 230026, China
- Department of Physics, Sana'a University, Sana'a, Yemen
- Hangzhou Nain Biotech Co. Ltd., Hangzhou 310015, China
| | - Gamal H Al-Shawesh
- Department of Physics, University of Science and Technology of China, Hefei 230026, China
| | - Xiao Ru
- Department of Physics, University of Science and Technology of China, Hefei 230026, China
- Hefei National Laboratory, University of Science and Technology of China, Hefei 230088, China
| | - Zijing Lin
- Department of Physics, University of Science and Technology of China, Hefei 230026, China
- Hefei National Laboratory, University of Science and Technology of China, Hefei 230088, China
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5
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He Z, Zhang Z, Ding J, Gao W, Li M, Chen C. Managing Pb-Related Imperfections via Rationally Designed Aniline Derivative with Bilateral Cyano and Acetyl Groups as Lewis Base for High-Efficiency Perovskite Solar Cells Exceeding 24. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2404334. [PMID: 38864215 DOI: 10.1002/smll.202404334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Indexed: 06/13/2024]
Abstract
Pb-related imperfections (surface or halide vacancy induced uncoordinated Pb2+, Pb-I antisite, and Pb2+ vacancy defects) of the ionic crystal perovskite film seriously restrict the photovoltaic performance of perovskite solar cells (PSCs). Here, an aniline derivative N-(4-cyanophenyl)acetamide (CAL) is rationally designed, incorporating bilateral functional sites of cyano and acetyl groups, acting as Lewis base molecule for managing the Pb-related imperfections in perovskite surface through post-treatment. Theoretical calculation and experimental verification together proved the reduced defect density, improved crystallinity, and inhibited ion migration in the CAL-modified perovskite. Precisely, cyano as a side group and acetyl as another side group can both coordinate with Pb2+ for its low electrostatic potential energy. Further, the aniline core and the π-π conjugate structure in the benzene ring of the ligand tend to form a dimer to improve the mobility for carrier transportation and collection. The strategy demonstrates a champion PCE of 24.35% for the air-processed PSCs with over 1200 hours of maximum power point tracking (MPPT) stability. This study presents a comprehensive approach to overcoming the current Pb-related imperfections induced limitations in PSCs, paving the way for their integration into mainstream solar technologies.
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Affiliation(s)
- Zijie He
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Zuolin Zhang
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Jike Ding
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Wenhuan Gao
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Mengjia Li
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Cong Chen
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, School of Materials Science and Engineering, Hebei University of Technology, Tianjin, 300401, China
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6
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Wu X, Hartmann P, Berne D, De Bruyn M, Cuminet F, Wang Z, Zechner JM, Boese AD, Placet V, Caillol S, Barta K. Closed-loop recyclability of a biomass-derived epoxy-amine thermoset by methanolysis. Science 2024; 384:eadj9989. [PMID: 38603486 DOI: 10.1126/science.adj9989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/16/2024] [Indexed: 04/13/2024]
Abstract
Epoxy resin thermosets (ERTs) are an important class of polymeric materials. However, owing to their highly cross-linked nature, they suffer from poor recyclability, which contributes to an unacceptable level of environmental pollution. There is a clear need for the design of inherently recyclable ERTs that are based on renewable resources. We present the synthesis and closed-loop recycling of a fully lignocellulose-derivable epoxy resin (DGF/MBCA), prepared from dimethyl ester of 2,5-furandicarboxylic acid (DMFD), 4,4'-methylenebis(cyclohexylamine) (MBCA), and glycidol, which displays excellent thermomechanical properties (a glass transition temperature of 170°C, and a storage modulus at 25°C of 1.2 gigapascals). Notably, the material undergoes methanolysis in the absence of any catalyst, regenerating 90% of the original DMFD. The diamine MBCA and glycidol can subsequently be reformed by acetolysis. Application and recycling of DGF/MBCA in glass and plant fiber composites are demonstrated.
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Affiliation(s)
- Xianyuan Wu
- Stratingh Institute for Chemistry, University of Groningen, 9747AG Groningen, Netherlands
- Institute of Chemistry, Organic and Bioorganic Chemistry, University of Graz, 8010 Graz, Austria
| | - Peter Hartmann
- Institute of Chemistry, Organic and Bioorganic Chemistry, University of Graz, 8010 Graz, Austria
| | - Dimitri Berne
- ICGM, Univ Montpellier, CNRS, ENSCM, 34000 Montpellier, France
| | - Mario De Bruyn
- Institute of Chemistry, Organic and Bioorganic Chemistry, University of Graz, 8010 Graz, Austria
| | - Florian Cuminet
- ICGM, Univ Montpellier, CNRS, ENSCM, 34000 Montpellier, France
| | - Zhiwen Wang
- Institute of Chemistry, Organic and Bioorganic Chemistry, University of Graz, 8010 Graz, Austria
| | | | - Adrian Daniel Boese
- Institute of Chemistry, Organic and Bioorganic Chemistry, University of Graz, 8010 Graz, Austria
| | - Vincent Placet
- Université de Franche-Comté, CNRS, institut FEMTO-ST, 2500 Besançon, France
| | - Sylvain Caillol
- ICGM, Univ Montpellier, CNRS, ENSCM, 34000 Montpellier, France
| | - Katalin Barta
- Institute of Chemistry, Organic and Bioorganic Chemistry, University of Graz, 8010 Graz, Austria
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7
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Ge K, Shao H, Raymundo-Piñero E, Taberna PL, Simon P. Cation desolvation-induced capacitance enhancement in reduced graphene oxide (rGO). Nat Commun 2024; 15:1935. [PMID: 38431624 PMCID: PMC10908864 DOI: 10.1038/s41467-024-46280-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/15/2024] [Indexed: 03/05/2024] Open
Abstract
Understanding the local electrochemical processes is of key importance for efficient energy storage applications, including electrochemical double layer capacitors. In this work, we studied the charge storage mechanism of a model material - reduced graphene oxide (rGO) - in aqueous electrolyte using the combination of cavity micro-electrode, operando electrochemical quartz crystal microbalance (EQCM) and operando electrochemical dilatometry (ECD) tools. We evidence two regions with different charge storage mechanisms, depending on the cation-carbon interaction. Notably, under high cathodic polarization (region II), we report an important capacitance increase in Zn2+ containing electrolyte with minimum volume expansion, which is associated with Zn2+ desolvation resulting from strong electrostatic Zn2+-rGO interactions. These results highlight the significant role of ion-electrode interaction strength and cation desolvation in modulating the charging mechanisms, offering potential pathways for optimized capacitive energy storage. As a broader perspective, understanding confined electrochemical systems and the coupling between chemical, electrochemical and transport processes in confinement may open tremendous opportunities for energy, catalysis or water treatment applications in the future.
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Affiliation(s)
- Kangkang Ge
- Université Paul Sabatier, CIRIMAT UMR CNRS 5085, 118 Route de Narbonne, 31062, Toulouse, France
| | - Hui Shao
- i-Lab, CAS Center for Excellence in Nanoscience, Suzhou Institute of Nano-Tech and Nano-Bionics (SINANO), Chinese Academy of Sciences (CAS), Suzhou, 215123, China
| | - Encarnacion Raymundo-Piñero
- Réseau sur le Stockage Electrochimique de l'Energie (RS2E), FR CNRS 3459, Amiens, France
- Université Orléans, CNRS, CEMHTI UPR3079, Orléans, France
| | - Pierre-Louis Taberna
- Université Paul Sabatier, CIRIMAT UMR CNRS 5085, 118 Route de Narbonne, 31062, Toulouse, France.
- Réseau sur le Stockage Electrochimique de l'Energie (RS2E), FR CNRS 3459, Amiens, France.
| | - Patrice Simon
- Université Paul Sabatier, CIRIMAT UMR CNRS 5085, 118 Route de Narbonne, 31062, Toulouse, France.
- Réseau sur le Stockage Electrochimique de l'Energie (RS2E), FR CNRS 3459, Amiens, France.
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8
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Wang Z, Li Y, Sun M. The effect of weak π-π interactions on single-molecule electron transport properties of the tetraphenylethene molecule and its derivatives: a first-principles study. Phys Chem Chem Phys 2024; 26:1067-1076. [PMID: 38095244 DOI: 10.1039/d3cp04593e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Intramolecular π-π interactions are a significant research focus in fields such as chemistry, biology, and materials science. Different configurations of benzene-benzene moieties within a molecule can affect the magnitude of their π-π interactions, consequently influencing the electronic transport capabilities of the molecule. In this study, we designed three π-conjugated molecules, TPEM, TPEEM, and TEEPM, based on tetraphenylethene (TPE). These three molecules exhibit three distinct π-conjugated structures: linear cis-π-conjugation, linear trans-π-conjugation, and cross-π-conjugation. Thereinto, TPEM and TPEEM molecules share the same TPE core, with identical π-π interaction distances, while the TEEPM molecule has acetylene groups between the TPE units, thereby increasing the π-π interaction distances between the benzene moieties. Using density functional theory calculations combined with non-equilibrium Green's function (DFT+NEGF), our results reveal that the conductance order of different π-conjugated structures in TPEM and TPEEM molecules is as follows: cis > cross ≈ trans. Through analysis of transmission spectra, transmission pathways, and the innermost π orbitals, we find that in TPEM and TPEEM molecules, the cis- and cross-π-conjugated structures exhibit π-π interactions between benzene moieties and provide special through-space electron transport pathways, enhancing their electronic transport capabilities in coordination with the bonded molecular framework, whereas their trans-conjugated structures only allow electron transport along the molecular backbone. In contrast, in TEEPM molecule, due to the absence of π-π interactions, the conductance of different π-conjugated structures is primarily determined by the molecular backbone and follows the order: trans > cis > cross. These findings provide a theoretical basis for designing single-molecule electronic devices with multiple electron channels based on intramolecular π-π interactions.
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Affiliation(s)
- Zhiye Wang
- Department of Materials and Metallurgy, Wuhan University of Science and Technology, 430081, Wuhan, China.
| | - Yunchuan Li
- Department of Materials and Metallurgy, Wuhan University of Science and Technology, 430081, Wuhan, China.
| | - Mingjun Sun
- Department of Materials and Metallurgy, Wuhan University of Science and Technology, 430081, Wuhan, China.
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9
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Afshinpour M, Smith LA, Chakravarty S. AQcalc: A web server that identifies weak molecular interactions in protein structures. Protein Sci 2023; 32:e4762. [PMID: 37596782 PMCID: PMC10503417 DOI: 10.1002/pro.4762] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/25/2023] [Accepted: 08/15/2023] [Indexed: 08/20/2023]
Abstract
Weak molecular interactions play an important role in protein structure and function. Computational tools that identify weak molecular interactions are, therefore, valuable for the study of proteins. Here, we present AQcalc, a web server (https://aqcalcbiocomputing.com/) that can be used to identify anion-quadrupole (AQ) interactions, which are weak interactions involving aromatic residue (Trp, Tyr, and Phe) ring edges and anions (Asp, Glu, and phosphate ion) both within proteins and at their interfaces (protein-protein, protein-nucleic acids, and protein-lipid bilayer). AQcalc identifies AQ interactions as well as clusters involving AQ, cation-π, and salt bridges, among others. Utilizing AQcalc we analyzed weak interactions in protein models, even in the absence of experimental structures, to understand the contributions of weak interactions to deleterious structural changes, including those associated with oncogenic and germline disease variants. We identified several deleterious variants with disrupted AQ interactions (comparable in frequency to cation-π disruptions). Amyloid fibrils utilize AQ to bury anions at frequencies that far exceed those observed for globular proteins. AQ interactions were detected three and five times more frequently than the hydrogen-bonded AQ (HBAQ) in fibril structures and protein-lipid bilayer interfaces, respectively. By contrast, AQ and HBAQ interactions were detected with similar frequencies in globular proteins. Collectively, these findings suggest AQcalc will be effective in facilitating fine structural analysis. As other web utilities designed to identify protein residue interaction networks do not report AQ interactions, wide use of AQcalc will enrich our understanding of residue interaction networks and facilitate hypothesis testing by identifying and experimentally characterizing these comparably weak but important interactions.
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Affiliation(s)
- Maral Afshinpour
- Department of Chemistry & BiochemistrySouth Dakota State UniversityBrookingsSouth DakotaUSA
| | - Logan A. Smith
- Department of Chemistry & BiochemistrySouth Dakota State UniversityBrookingsSouth DakotaUSA
| | - Suvobrata Chakravarty
- Department of Chemistry & BiochemistrySouth Dakota State UniversityBrookingsSouth DakotaUSA
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10
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Kokkin DL, Reilly NJ, Ivanov M, Rathore R, Reid SA. Excitonic Coupling in Fluorene-Based Bichromophoric Systems: Vibrational Quenching and the Transition from Weak to Intermediate Coupling. J Phys Chem A 2023; 127:7198-7204. [PMID: 37594308 DOI: 10.1021/acs.jpca.3c03511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Excimeric systems (i.e., excited dimers) have well served as model compounds for the study of the delocalization of electronic energy over weakly interacting chromophores. However, there remain relatively few isolated systems in which such interactions can be studied experimentally at a level to afford detailed comparisons with theory. In this Article, we examine a series of covalently and noncovalently linked dimers of fluorene, as a model aromatic chromophore, where the formation of excimers requires a π-stacked, cofacial orientation at van der Waals contact. Building upon a series of seminal prior studies that examined vibronic quenching of the excitation interaction in van der Waals dimers, the key question that we sought to address here is whether a single quenching factor could reproduce experimental excitonic splittings across a series of covalently and noncovalently linked bichromophoric systems built from the same chromophore. In comparing experimentally measured excitonic splittings with calculated static splittings using time-dependent density functional methods, we find that all systems save one fall on a line with a slope of 0.080(8), reflecting a vibrational quenching of roughly 1 order of magnitude. The outlier, which shows a significantly reduced quenching factor, represents a cyclophane-linked system where the fluorene moieties are constrained in a cofacial arrangement. We argue that this system evidences the transition from the weak to intermediate coupling regime.
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Affiliation(s)
- Damian L Kokkin
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Neil J Reilly
- Department of Chemistry, University of Massachusetts-Boston, Boston, Massachusetts 02125, United States
| | - Maxim Ivanov
- Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, California 91320, United States
| | | | - Scott A Reid
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
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11
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Trinh PB, Schäfer AI. Adsorption of glyphosate and metabolite aminomethylphosphonic acid (AMPA) from water by polymer-based spherical activated carbon (PBSAC). JOURNAL OF HAZARDOUS MATERIALS 2023; 454:131211. [PMID: 37121034 DOI: 10.1016/j.jhazmat.2023.131211] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/06/2023] [Accepted: 03/13/2023] [Indexed: 05/19/2023]
Abstract
Glyphosate (GLY) is the most commonly used herbicide worldwide, and aminomethylphosphonic acid (AMPA) is its main metabolite. Their occurrence in ground and surface waters causes diseases in humans, while complex physico-chemical properties hinder detection and effective removal. Polymer-based spherical activated carbon (PBSAC) can adsorb many micropollutants efficiently and, hence, overcome the shortfalls of conventional treatment methods. The static adsorption of a mixture of GLY and AMPA by PBSAC was investigated with varying PBSAC properties and relevant solution chemistry. The results show that PBSAC can remove 95% GLY and 57% AMPA from an initial concentration of 1 µg/L at pH 8.2. PBSAC properties (size, activation level, and surface charge) have a strong influence on herbicide removal, where surface area plays a key role. Low to neutral pH favors non-charge interactions and results in good adsorption, while higher temperatures equally enhance GLY/AMPA adsorption by PBSAC. The work demonstrated the effective removal of GLY to meet the European guideline concentration (0.1 µg/L), while AMPA could not be removed to the required level.
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Affiliation(s)
- Phuong Bich Trinh
- Institute for Advanced Membrane Technology (IAMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Andrea Iris Schäfer
- Institute for Advanced Membrane Technology (IAMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
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12
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Yamaguchi T, Taborosi A, Sakai C, Akao K, Mori S, Kohzuma T. Systematic elucidation of the second coordination sphere effect on the structure and properties of a blue copper protein, pseudoazurin. J Inorg Biochem 2023; 246:112292. [PMID: 37354604 DOI: 10.1016/j.jinorgbio.2023.112292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023]
Abstract
The rational structural and computational studies of a blue copper protein, pseudoazurin (PAz), and its Met16X (X = Phe, Leu, Val, Ile) variants gave clear functional meanings of the noncovalent interaction (NCI) through the second coordination sphere. The high-resolution X-ray crystal structures of Met16X PAz demonstrated that the active site geometry is significantly affected by the substitution of Met16, which is located within the NCI distance from the His81 imidazole ring at the copper active site. The computational chemistry calculations based on the crystal structure analyses confirmed that the NCI of S-π/CH-π (wild-type), π-π (Met16Phe), double CH-π (Met16Leu), and single CH-π (Met16Val and Met16Ile). The estimated interaction energies for the NCI demonstrated that the fine-tuning of the protein stability and Cu site properties form the second coordination sphere of PAz.
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Affiliation(s)
- Takahide Yamaguchi
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan; Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1, Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Attila Taborosi
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan; Research Initiative for Supra-Materials, Faculty of Engineering, Shinshu University, 4-17-1, Wakasato, Nagano, Nagano 380-8553, Japan
| | - Chihiro Sakai
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Kohei Akao
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Seiji Mori
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan; Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1, Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Takamitsu Kohzuma
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan; Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1, Shirakata, Tokai, Ibaraki 319-1106, Japan.
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13
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R A C Lima CF, Mague JT, Du Y, Pascal RA, Santos LMNBF. How great is the stabilization of crowded polyphenylbiphenyls by London dispersion? Phys Chem Chem Phys 2023; 25:13359-13375. [PMID: 37145056 DOI: 10.1039/d2cp05085d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Decaphenylbiphenyl (1) and 2,2',4,4',6,6'-hexaphenylbiphenyl (2) are bulky molecules expected to be greatly destabilized by steric crowding. Herein, through a combined experimental and computational approach, we evaluate the molecular energetics of crowded biphenyls. This is complemented by the study of phase equilibria for 1 and 2. Compound 1 shows a rich phase behavior, displaying an unusual interconversion between two polymorphs. Surprisingly, the polymorph with distorted molecules of C1 symmetry is found to have the highest melting point and to be the one that is preferentially formed. The thermodynamic results also indicate that the polymorph displaying the more regular D2 molecular geometry has larger heat capacity and is probably the more stable at lower temperatures. The melting and sublimation data clearly reveal the weakening of cohesive forces in crowded biphenyls due to the lower molecular surface area. The experimental quantification of the intramolecular interactions in 1 and 2 indicated, using homodesmotic reactions, a molecular stabilization of about 30 kJ mol-1. We attribute the origin of this stabilization in both compounds to the existence of two parallel-displaced π⋯π interactions between the ortho-phenyl substituents on each side of the central biphenyl. Computational calculations with dispersion-corrected DFT methods underestimate the stabilization in 1, unless the steric crowding is well balanced in a homodesmotic scheme. This work demonstrates that London dispersion forces are important in crowded aromatic systems, making these molecules considerably more stable than previously thought.
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Affiliation(s)
- Carlos F R A C Lima
- CIQUP, Institute of Molecular Sciences (IMS), Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, rua do Campo Alegre s/n, 4169-007 Porto, Portugal.
| | - Joel T Mague
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA
| | - Yuchen Du
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA
| | - Robert A Pascal
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA
| | - Luís M N B F Santos
- CIQUP, Institute of Molecular Sciences (IMS), Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, rua do Campo Alegre s/n, 4169-007 Porto, Portugal.
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14
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Chen Z, Yang J, Huang D, Wang S, Jiang K, Sun W, Chen Z, Cao Z, Ren Y, Wang Q, Liu H, Zhang X, Sun X. Adsorption behavior of aniline pollutant on polystyrene microplastics. CHEMOSPHERE 2023; 323:138187. [PMID: 36806808 DOI: 10.1016/j.chemosphere.2023.138187] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Microplastic contamination is ubiquitous in aquatic environments. As global plastic production increases, the abundance of microplastic contaminants released into the environment has also continued to soar. The hydrophobic surfaces of plastic particles can adsorb a variety of chemical pollutants, and could therefore facilitate toxin accumulation through the food chain. In this study, the adsorption behavior of aniline, a priority environmental pollutant from industrial production, on the surface of polystyrene microplastics (mPS) was investigated. The results showed that the maximum adsorption capacity of mPS was 0.060 mg/g. Adsorption equilibrium was reached after 24 h, and the pseudo-second-order model was employed to explain the adsorption kinetics of aniline on the mPS particles. The Freundlich models could describe the adsorption isotherms. The potential adsorption mechanisms may include π-π interactions and hydrophobic interactions. pH, ionic strength, and ambient temperature of the solution played important roles in the adsorption process.
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Affiliation(s)
- Zhenyu Chen
- School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, 453007, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Garo-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Jinchan Yang
- School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, 453007, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Garo-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Duanyi Huang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Garo-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China; College of Environmental Science and Engineering, Hunan University, Changsha, 410082, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, China
| | - Shuni Wang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Garo-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China; Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, China
| | - Kai Jiang
- School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, 453007, China
| | - Weimin Sun
- School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, 453007, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Garo-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Zhihua Chen
- School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, 453007, China
| | - Zhiguo Cao
- School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, 453007, China
| | - Youhua Ren
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Garo-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China; College of Food Science and Technology, Hunan Agricultural University, Changsha, 410128, China
| | - Qi Wang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Garo-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Huaqing Liu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Garo-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Xin Zhang
- School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, 453007, China.
| | - Xiaoxu Sun
- School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, 453007, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Garo-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.
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15
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Kumawat RL, Sherrill CD. High-Order Quantum-Mechanical Analysis of Hydrogen Bonding in Hachimoji and Natural DNA Base Pairs. J Chem Inf Model 2023; 63:3150-3157. [PMID: 37125692 DOI: 10.1021/acs.jcim.3c00428] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
High-order quantum chemistry is applied to hydrogen-bonded natural DNA nucleobase pairs [adenine:thymine (A:T) and guanine:cytosine (G:C)] and non-natural Hachimoji nucleobase pairs [isoguanine:1-methylcytosine (B:S) and 2-aminoimidazo[1,2a][1,3,5]triazin-4(1H)-one:6-amino-5-nitropyridin-2-one (P:Z)] to see how the intermolecular interaction energies and their energetic components (electrostatics, exchange-repulsion, induction/polarization, and London dispersion interactions) vary among the base pairs. We examined the Hoogsteen (HG) geometries in addition to the traditional Watson-Crick (WC) geometries. Coupled-cluster theory through perturbative triples [CCSD(T)] extrapolated to the complete basis set (CBS) limit and high-order symmetry-adapted perturbation theory (SAPT) at the SAPT2+(3)(CCD)δMP2/aug-cc-pVTZ level are used to estimate highly accurate noncovalent interaction energies. Electrostatic interactions are the most attractive component of the interaction energies, but the sum of induction/polarization and London dispersion is nearly as large, for all base pairs and geometries considered. Interestingly, the non-natural Hachimoji base pairs interact more strongly than the corresponding natural base pairs, by -21.8 (B:S) and -0.3 (P:Z) kcal mol-1 in the WC geometries, according to CCSD(T)/CBS. This is consistent with the H-bond distances being generally shorter in the non-natural base pairs. The natural base pairs are energetically more stabilized in their Hoogsteen geometries than in their WC geometries. The Hoogsteen geometry makes the A:T base pair slightly more stable, by -0.8 kcal mol-1, and it greatly stabilizes the G:C+ base pair, by -15.3 kcal mol-1. The G:C+ stabilization is mainly due to the fact that C has typically added a proton when found in Hoogsteen geometries. By contrast, Hoogsteen geometries are substantially less favorable than WC geometries for non-natural Hachimoji base pairs, by 17.3 (B:S) and 13.8 (P:Z) kcal mol-1.
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Affiliation(s)
- Rameshwar L Kumawat
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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16
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Palmisano VF, Faraji S, Nogueira JJ. Effect of stacking interactions on charge transfer states in photoswitches interacting with ion channels. Phys Chem Chem Phys 2023; 25:8331-8335. [PMID: 36883995 PMCID: PMC10696555 DOI: 10.1039/d2cp05678j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/24/2023] [Indexed: 03/06/2023]
Abstract
The activity of ion channels can be reversibly photo-controlled via the binding of molecular photoswitches, often based on an azobenzene scaffold. Those azobenzene derivatives interact with aromatic residues of the protein via stacking interactions. In the present work, the effect of face-to-face and t-shaped stacking interactions on the excited state electronic structure of azobenzene and p-diaminoazobenzene integrated into the NaV1.4 channel is computationally investigated. The formation of a charge transfer state, caused by electron transfer from the protein to the photoswitches, is observed. This state is strongly red shifted when the interaction takes place in a face-to-face orientation and electron donating groups are present on the aromatic ring of the amino acids. The low-energy charge transfer state can interfere with the photoisomerization process after excitation to the bright state by leading to the formation of radical species.
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Affiliation(s)
- Vito F Palmisano
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
- Theoretical Chemistry Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.
| | - Shirin Faraji
- Theoretical Chemistry Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.
| | - Juan J Nogueira
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
- Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, Madrid 28049, Spain
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17
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Poirot A, Vanucci-Bacqué C, Delavaux-Nicot B, Meslien C, Saffon-Merceron N, Serpentini CL, Bedos-Belval F, Benoist E, Fery-Forgues S. Using a diphenyl-bi-(1,2,4-triazole) tricarbonylrhenium(I) complex with intramolecular π-π stacking interaction for efficient solid-state luminescence enhancement. Dalton Trans 2023; 52:5453-5465. [PMID: 36880588 DOI: 10.1039/d2dt03573a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Since intramolecular π-π stacking interactions can modify the geometry, crystal packing mode, or even the electronic properties of transition metal complexes, they are also likely to influence the solid-state luminescence properties. Following this concept, a new tricarbonylrhenium(I) complex (Re-BPTA) was designed, based on a simple symmetrical 5,5'-dimethyl-4,4'-diphenyl-3,3'-bi-(1,2,4-triazole) organic ligand. The complex was prepared in good yield using a three-step procedure. The crystallographic study revealed that both phenyl rings are located on the same side of the molecule, and twisted by 71° and 62°, respectively, with respect to the bi-(1,2,4-triazole) unit. They overlap significantly, although they are slipped parallel to each other to minimize the intramolecular interaction energy. The π-π stacking interaction was also revealed by 1H NMR spectroscopy, in good agreement with the results of theoretical calculations. In organic solutions, a peculiar electrochemical signature was observed compared to closely-related pyridyl-triazole (pyta)-based complexes. With regard to the optical properties, the stiffness of the Re-BPTA complex led to the stabilization of the 3MLCT state, and thus to an enhancement of the red phosphorescence emission compared to the more flexible pyta complexes. However, an increased sensitivity to quenching by oxygen appeared. In the microcrystalline phase, the Re-BPTA complex showed strong photoluminescence (PL) emission in the green-yellow wavelength range (λPL = 548 nm, ΦPL = 0.52, 〈τPL〉 = 713 ns), and thus a dramatic solid-state luminescence enhancement (SLE) effect. These attractive emission properties can be attributed to the fact that the molecule undergoes little distortion between the ground state and the triplet excited state, as well as to a favorable intermolecular arrangement that minimizes detrimental interactions in the crystal lattice. The aggregation-induced phosphorescence emission (AIPE) effect was clear, with a 7-fold increase in emission intensity at 546 nm, although the aggregates formed in aqueous medium were much less emissive than the native microcrystalline powder. In this work, the rigidity of the Re-BPTA complex is reinforced by the intramolecular π-π stacking interaction of the phenyl rings. This original concept provides a rhenium tricarbonyl compound with very good SLE properties, and could be used more widely to successfully develop this area of research.
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Affiliation(s)
- Alexandre Poirot
- SPCMIB, CNRS UMR 5068, Université de Toulouse III Paul Sabatier, 118 route de Narbonne, 31062 Toulouse cedex 9, France.
| | - Corinne Vanucci-Bacqué
- SPCMIB, CNRS UMR 5068, Université de Toulouse III Paul Sabatier, 118 route de Narbonne, 31062 Toulouse cedex 9, France.
| | - Béatrice Delavaux-Nicot
- Laboratoire de Chimie de Coordination, CNRS (UPR 8241), Université de Toulouse (UPS, INPT), 205 route de Narbonne, 31077 Toulouse Cedex 4, France
| | - Clarisse Meslien
- SPCMIB, CNRS UMR 5068, Université de Toulouse III Paul Sabatier, 118 route de Narbonne, 31062 Toulouse cedex 9, France.
| | - Nathalie Saffon-Merceron
- Service Diffraction des Rayons X, Institut de Chimie de Toulouse, ICT- UAR 2599, Université de Toulouse III Paul Sabatier, 118 route de Narbonne, 31062 Toulouse cedex 9, France
| | - Charles-Louis Serpentini
- Laboratoire IMRCP, CNRS UMR 5623, Université de Toulouse III Paul Sabatier, 118 route de Narbonne, 31062 Toulouse cedex 9, France
| | - Florence Bedos-Belval
- SPCMIB, CNRS UMR 5068, Université de Toulouse III Paul Sabatier, 118 route de Narbonne, 31062 Toulouse cedex 9, France.
| | - Eric Benoist
- SPCMIB, CNRS UMR 5068, Université de Toulouse III Paul Sabatier, 118 route de Narbonne, 31062 Toulouse cedex 9, France.
| | - Suzanne Fery-Forgues
- SPCMIB, CNRS UMR 5068, Université de Toulouse III Paul Sabatier, 118 route de Narbonne, 31062 Toulouse cedex 9, France.
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18
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Mitani T, Tsurumaki E, Toyota S. Structures and Supramolecular Properties of Inclusion Complexes of Anthracene-Triptycene Nanocages with Fullerene Guests and Their Dynamic Motion as Molecular Gyroscopes. Chemistry 2023; 29:e202203462. [PMID: 36460616 DOI: 10.1002/chem.202203462] [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: 11/08/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/04/2022]
Abstract
Three derivatives of macrocyclic cage compounds consisting of diarylanthracene and triptycene units were synthesized. These nanocages formed host-guest complexes with C60 and other fullerene guests as confirmed by 1 H NMR and fluorescence spectroscopy. The association constant of the mesityl and 2,4,6-tributoxyphenyl derivatives with C60 was determined to be 2.2 × 104 L mol-1 , which was larger than that of the pentafluorophenyl derivative. Direct experimental evidence of the complexation was obtained by X-ray diffraction analysis: the guest C60 molecule was included in the cavity via multipoint CH⋅⋅⋅π interactions. Dynamic disorders of the included C60 molecule in variable-temperature X-ray analysis indicated uniaxial motion, such as gyroscopic motion. The unique dynamic behavior of the spherical C60 rotor anchored by the cage stator via CH⋅⋅⋅π interactions in the crystal, as well as substituent effects on the association properties, are discussed with the aid of DFT calculations.
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Affiliation(s)
- Takuji Mitani
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Eiji Tsurumaki
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Shinji Toyota
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
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19
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Tutov A, Chen X, Werner RA, Mühlig S, Zimmermann T, Nose N, Koshino K, Lapa C, Decker M, Higuchi T. Rationalizing the Binding Modes of PET Radiotracers Targeting the Norepinephrine Transporter. Pharmaceutics 2023; 15:pharmaceutics15020690. [PMID: 36840011 PMCID: PMC9963373 DOI: 10.3390/pharmaceutics15020690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/09/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
PURPOSE A new PET radiotracer 18F-AF78 showing great potential for clinical application has been reported recently. It belongs to a new generation of phenethylguanidine-based norepinephrine transporter (NET)-targeting radiotracers. Although many efforts have been made to develop NET inhibitors as antidepressants, systemic investigations of the structure-activity relationships (SARs) of NET-targeting radiotracers have rarely been performed. METHODS Without changing the phenethylguanidine pharmacophore and 3-fluoropropyl moiety that is crucial for easy labeling, six new analogs of 18F-AF78 with different meta-substituents on the benzene-ring were synthesized and evaluated in a competitive cellular uptake assay and in in vivo animal experiments in rats. Computational modeling of these tracers was established to quantitatively rationalize the interaction between the radiotracers and NET. RESULTS Using non-radiolabeled reference compounds, a competitive cellular uptake assay showed a decrease in NET-transporting affinity from meta-fluorine to iodine (0.42 and 6.51 µM, respectively), with meta-OH being the least active (22.67 µM). Furthermore, in vivo animal studies with radioisotopes showed that heart-to-blood ratios agreed with the cellular experiments, with AF78(F) exhibiting the highest cardiac uptake. This result correlates positively with the electronegativity rather than the atomic radius of the meta-substituent. Computational modeling studies revealed a crucial influence of halogen substituents on the radiotracer-NET interaction, whereby a T-shaped π-π stacking interaction between the benzene-ring of the tracer and the amino acid residues surrounding the NET binding site made major contributions to the different affinities, in accordance with the pharmacological data. CONCLUSION The SARs were characterized by in vitro and in vivo evaluation, and computational modeling quantitatively rationalized the interaction between radiotracers and the NET binding site. These findings pave the way for further evaluation in different species and underline the potential of AF78(F) for clinical application, e.g., cardiac innervation imaging or molecular imaging of neuroendocrine tumors.
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Affiliation(s)
- Anna Tutov
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy and Food Chemistry, University of Würzburg, D-97074 Würzburg, Germany
| | - Xinyu Chen
- Nuclear Medicine, Faculty of Medicine, University of Augsburg, D-86156 Augsburg, Germany
- Department of Nuclear Medicine and Comprehensive Heart Failure Center, University Hospital Würzburg, D-97080 Würzburg, Germany
| | - Rudolf A. Werner
- Department of Nuclear Medicine and Comprehensive Heart Failure Center, University Hospital Würzburg, D-97080 Würzburg, Germany
- Division of Nuclear Medicine, The Russell H Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Saskia Mühlig
- Department of Nuclear Medicine and Comprehensive Heart Failure Center, University Hospital Würzburg, D-97080 Würzburg, Germany
| | - Thomas Zimmermann
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy and Food Chemistry, University of Würzburg, D-97074 Würzburg, Germany
| | - Naoko Nose
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-0082, Japan
| | - Kazuhiro Koshino
- Department of Systems and Informatics, Hokkaido Information University, Ebetsu 069-0832, Japan
| | - Constantin Lapa
- Nuclear Medicine, Faculty of Medicine, University of Augsburg, D-86156 Augsburg, Germany
| | - Michael Decker
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy and Food Chemistry, University of Würzburg, D-97074 Würzburg, Germany
- Correspondence: (M.D.); (T.H.); Tel.: +49-(931)-201-35455 (T.H.)
| | - Takahiro Higuchi
- Department of Nuclear Medicine and Comprehensive Heart Failure Center, University Hospital Würzburg, D-97080 Würzburg, Germany
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-0082, Japan
- Correspondence: (M.D.); (T.H.); Tel.: +49-(931)-201-35455 (T.H.)
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20
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Jayadev NK, Ferino-Pérez A, Matz F, Krylov AI, Jagau TC. The Auger spectrum of benzene. J Chem Phys 2023; 158:064109. [PMID: 36792526 DOI: 10.1063/5.0138674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We present an ab initio computational study of the Auger electron spectrum of benzene. Auger electron spectroscopy exploits the Auger-Meitner effect, and although it is established as an analytic technique, the theoretical modeling of molecular Auger spectra from first principles remains challenging. Here, we use coupled-cluster theory and equation-of-motion coupled-cluster theory combined with two approaches to describe the decaying nature of core-ionized states: (i) Feshbach-Fano resonance theory and (ii) the method of complex basis functions. The spectra computed with these two approaches are in excellent agreement with each other and also agree well with experimental Auger spectra of benzene. The Auger spectrum of benzene features two well-resolved peaks at Auger electron energies above 260 eV, which correspond to final states with two electrons removed from the 1e1g and 3e2g highest occupied molecular orbitals. At lower Auger electron energies, the spectrum is less well resolved, and the peaks comprise multiple final states of the benzene dication. In line with theoretical considerations, singlet decay channels contribute more to the total Auger intensity than the corresponding triplet decay channels.
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Affiliation(s)
- Nayanthara K Jayadev
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Florian Matz
- Department of Chemistry, KU Leuven, B-3001 Leuven, Belgium
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Thomas-C Jagau
- Department of Chemistry, KU Leuven, B-3001 Leuven, Belgium
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21
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Yu Y, Lv B, Wu J, Chen W. Mussel-Based Biomimetic Strategies in Musculoskeletal Disorder Treatment: From Synthesis Principles to Diverse Applications. Int J Nanomedicine 2023; 18:455-472. [PMID: 36718191 PMCID: PMC9884062 DOI: 10.2147/ijn.s386635] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/03/2022] [Indexed: 01/26/2023] Open
Abstract
Musculoskeletal disorders are the second leading cause of disability worldwide, posing a huge global burden to the public sanitation system. Currently, tissue engineering-based approaches act as effective strategies, which are, however, challenging in limited application scenarios. Mussel-based biomimetic materials, exhibit numerous unique properties such as intense adhesion, biocompatibility, moisture resistance, and injectability, to name only a few, and have attracted extensive research interest. In particular, featuring state-of-the-art properties, mussel-inspired biomaterials have been widely explored in innumerable musculoskeletal disorder treatments including osteochondral defects, osteosarcoma, osteoarthritis, ligament rupture, and osteoporosis. Nevertheless, a comprehensive and timely discussion of their applications in musculoskeletal disorders is insufficient. In this review, we emphasize on (1) the main categories and characteristics of mussel foot proteins and their fundamental mechanisms for the spectacular adhesion in mussels; (2) the diverse synthetic methods and modification of various polymers; and (3) the emerging applications of mussel-biomimetic materials, the future perspectives, and challenges, especially in the area of musculoskeletal disorder. We envision that this review will provide a unique and insightful perspective to improve the development of a new generation of mussel biomimetic strategies.
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Affiliation(s)
- Yajie Yu
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China,Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People’s Republic of China,Hubei Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, People’s Republic of China
| | - Bin Lv
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Juntao Wu
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Wei Chen
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People’s Republic of China,Hubei Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, People’s Republic of China,Correspondence: Wei Chen, Email
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22
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El Harrar T, Gohlke H. Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions. J Chem Inf Model 2023; 63:281-298. [PMID: 36520535 DOI: 10.1021/acs.jcim.2c01123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The interactions of amino acid side-chains confer diverse energetic contributions and physical properties to a protein's stability and function. Various computational tools estimate the effect of changing a given amino acid on the protein's stability based on parametrized (free) energy functions. When parametrized for the prediction of protein stability in water, such energy functions can lead to suboptimal results for other solvents, such as ionic liquids (IL), aqueous ionic liquids (aIL), or salt solutions. However, to our knowledge, no comprehensive data are available describing the energetic effects of aIL on intramolecular protein interactions. Here, we present the most comprehensive set of potential of mean force (PMF) profiles of pairwise protein-residue interactions to date, covering 50 relevant interactions in water, the two biotechnologically relevant aIL [BMIM/Cl] and [BMIM/TfO], and [Na/Cl]. These results are based on a cumulated simulation time of >1 ms. aIL and salt ions can weaken, but also strengthen, specific residue interactions by more than 3 kcal mol-1, depending on the residue pair, residue-residue configuration, participating ions, and concentration, necessitating considering such interactions specifically. These changes originate from a complex interplay of competitive or cooperative noncovalent ion-residue interactions, changes in solvent structural dynamics, or unspecific charge screening effects and occur at the contact distance but also at larger, solvent-separated distances. This data provide explanations at the atomistic and energetic levels for complex IL effects on protein stability and should help improve the prediction accuracies of computational tools that estimate protein stability based on (free) energy functions.
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Affiliation(s)
- Till El Harrar
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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23
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Borosky GL, Laali KK. A DFT Computational and Synthetic Study of New Curcuminoidpropargyl Adducts with Pseudo‐Cofacial Aryl Rings. ChemistrySelect 2022. [DOI: 10.1002/slct.202203127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Gabriela L. Borosky
- INFIQC CONICET and Departamento de Química Teórica y Computacional Facultad de Ciencias Químicas Universidad Nacional de Córdoba, Ciudad Universitaria Córdoba 5000 Argentina
| | - Kenneth K. Laali
- Department of Chemistry University of North Florida, 1 UNF Drive Jacksonville Florida 32224 USA
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24
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Monajjemi M, Mollaamin F, Najaflou N, Sakhaeinia H. Physical Chemistry Study of Graphite Liquid Exfoliation through (π–π) Interaction by (n)-Annulene. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2022. [DOI: 10.1134/s0036024422100247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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25
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Yamada M, Kurihara Y, Koizumi M, Tsuji K, Maeda Y, Suzuki M. Understanding the Nature and Strength of Noncovalent Face‐to‐Face Arene–Fullerene Interactions. Angew Chem Int Ed Engl 2022; 61:e202212279. [DOI: 10.1002/anie.202212279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Michio Yamada
- Department of Chemistry Tokyo Gakugei University Nukuikitamachi 4-1-1, Koganei Tokyo 184-8501 Japan
| | - Yukiyo Kurihara
- Department of Chemistry Tokyo Gakugei University Nukuikitamachi 4-1-1, Koganei Tokyo 184-8501 Japan
| | - Masaaki Koizumi
- Department of Chemistry Tokyo Gakugei University Nukuikitamachi 4-1-1, Koganei Tokyo 184-8501 Japan
| | - Kasumi Tsuji
- Department of Chemistry Tokyo Gakugei University Nukuikitamachi 4-1-1, Koganei Tokyo 184-8501 Japan
| | - Yutaka Maeda
- Department of Chemistry Tokyo Gakugei University Nukuikitamachi 4-1-1, Koganei Tokyo 184-8501 Japan
| | - Mitsuaki Suzuki
- Department of Chemistry Josai University Sakado Saitama 350-0295 Japan
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26
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Krishnan A, Diaz‐Andres A, Sudhakaran KP, John AT, Hariharan M, Casanova D. Deciphering the Role of (Anti)Aromaticity in Cofacial Excimers of Linear Acenes. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Akhilesh Krishnan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram Thiruvananthapuram Kerala India
| | | | - Keerthy P. Sudhakaran
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram Thiruvananthapuram Kerala India
| | - Athira T. John
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram Thiruvananthapuram Kerala India
| | - Mahesh Hariharan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram Thiruvananthapuram Kerala India
| | - David Casanova
- Donostia International Physics Center (DIPC) Donostia Euskadi Spain
- IKERBASQUE, Basque Foundation for Science Bilbao Euskadi Spain
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27
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Yamada M, Kurihara Y, Koizumi M, Tsuji K, Maeda Y, Suzuki M. Understanding the Nature and Strength of Noncovalent Face‐to‐Face Arene–Fullerene Interactions. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202212279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Michio Yamada
- Tokyo Gakugei University Department of Chemistry 4-1-1 Nukuikitamachi 184-8501 Koganei, Tokyo JAPAN
| | - Yukiyo Kurihara
- Tokyo Gakugei University: Tokyo Gakugei Daigaku Department of Chemistry JAPAN
| | - Masaaki Koizumi
- Tokyo Gakugei University: Tokyo Gakugei Daigaku Department of Chemistry JAPAN
| | - Kasumi Tsuji
- Tokyo Gakugei University: Tokyo Gakugei Daigaku Department of Chemistry JAPAN
| | - Yutaka Maeda
- Tokyo Gakugei University: Tokyo Gakugei Daigaku Department of Chemistry JAPAN
| | - Mitsuaki Suzuki
- Josai University: Josai Daigaku Department of Chemistry JAPAN
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28
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Paik D, Lee H, Kim H, Choi JM. Thermodynamics of π–π Interactions of Benzene and Phenol in Water. Int J Mol Sci 2022; 23:ijms23179811. [PMID: 36077201 PMCID: PMC9456204 DOI: 10.3390/ijms23179811] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
The π–π interaction is a major driving force that stabilizes protein assemblies during protein folding. Recent studies have additionally demonstrated its involvement in the liquid–liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs). As the participating residues in IDPs are exposed to water, π–π interactions for LLPS must be modeled in water, as opposed to the interactions that are often established at the hydrophobic domains of folded proteins. Thus, we investigated the association of free energies of benzene and phenol dimers in water by integrating van der Waals (vdW)-corrected density functional theory (DFT) and DFT in classical explicit solvents (DFT-CES). By comparing the vdW-corrected DFT and DFT-CES results with high-level wavefunction calculations and experimental solvation free energies, respectively, we established the quantitative credibility of these approaches, enabling a reliable prediction of the benzene and phenol dimer association free energies in water. We discovered that solvation influences dimer association free energies, but not significantly when no direct hydrogen-bond-type interaction exists between two monomeric units, which can be explained by the enthalpy–entropy compensation. Our comprehensive computational study of the solvation effect on π–π interactions in water could help us understand the molecular-level driving mechanism underlying the IDP phase behaviors.
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Affiliation(s)
- Dooam Paik
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Hankyul Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Hyungjun Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
- Correspondence: (H.K.); (J.-M.C.)
| | - Jeong-Mo Choi
- Department of Chemistry, Pusan National University, Busan 46241, Korea
- Correspondence: (H.K.); (J.-M.C.)
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29
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Feng A, Zhou Y, Al-Shebami MAY, Chen L, Pan Z, Xu W, Zhao S, Zeng B, Xiao Z, Yang Y, Hong W. σ-σ Stacked supramolecular junctions. Nat Chem 2022; 14:1158-1164. [PMID: 35902741 DOI: 10.1038/s41557-022-01003-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 06/20/2022] [Indexed: 11/09/2022]
Abstract
Intermolecular charge transport plays an essential role in organic electronic materials and biological systems. To date, experimental investigations of intermolecular charge transport in molecular materials and electronic devices have been restricted to conjugated systems in which π-π stacking interactions are involved. Herein we demonstrate that the σ-σ stacking interactions between neighbouring non-conjugated molecules offer an efficient pathway for charge transport through supramolecular junctions. The conductance of σ-σ stacked molecular junctions formed between two non-conjugated cyclohexanethiol or single-anchored adamantane molecules is comparable to that of π-π stacked molecular junctions formed between π-conjugated benzene rings. The current-voltage characteristics and flicker noise analysis demonstrate the existence of stacked molecular junctions formed between the electrode pairs and exhibit the characteristics of through-space charge transport. Density functional theory calculations combined with the non-equilibrium Green's function method reveal that efficient charge transport occurs between two molecules configured with σ-σ stacking interactions.
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Affiliation(s)
- Anni Feng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, China
| | - Yu Zhou
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, China
| | - Mohammed A Y Al-Shebami
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, China
| | - Lichuan Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, China
| | - Zhichao Pan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, China
| | - Wei Xu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, China
| | - Shiqiang Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, China
| | - Biaofeng Zeng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, China
| | - Zongyuan Xiao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, China
| | - Yang Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, China.
| | - Wenjing Hong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) & Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, China.
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30
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Barcza B, Szirmai ÁB, Szántó KJ, Tajti A, Szalay PG. Comparison of approximate intermolecular potentials for ab initio fragment calculations on medium sized N-heterocycles. J Comput Chem 2022; 43:1079-1093. [PMID: 35478353 PMCID: PMC9321956 DOI: 10.1002/jcc.26866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/26/2022] [Accepted: 03/29/2022] [Indexed: 01/15/2023]
Abstract
The ground state intermolecular potential of bimolecular complexes of N-heterocycles is analyzed for the impact of individual terms in the interaction energy as provided by various, conceptually different theories. Novel combinations with several formulations of the electrostatic, Pauli repulsion, and dispersion contributions are tested at both short- and long-distance sides of the potential energy surface, for various alignments of the pyrrole dimer as well as the cytosine-uracil complex. The integration of a DFT/CCSD density embedding scheme, with dispersion terms from the effective fragment potential (EFP) method is found to provide good agreement with a reference CCSD(T) potential overall; simultaneously, a quantum mechanics/molecular mechanics approach using CHELPG atomic point charges for the electrostatic interaction, augmented by EFP dispersion and Pauli repulsion, comes also close to the reference result. Both schemes have the advantage of not relying on predefined force fields; rather, the interaction parameters can be determined for the system under study, thus being excellent candidates for ab initio modeling.
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Affiliation(s)
- Bónis Barcza
- Institute of Chemistry, Laboratory of Theoretical ChemistryELTE Eötvös Loránd UniversityBudapestHungary
| | - Ádám B. Szirmai
- Institute of Chemistry, Laboratory of Theoretical ChemistryELTE Eötvös Loránd UniversityBudapestHungary
| | - Katalin J. Szántó
- Institute of Chemistry, Laboratory of Theoretical ChemistryELTE Eötvös Loránd UniversityBudapestHungary
| | - Attila Tajti
- Institute of Chemistry, Laboratory of Theoretical ChemistryELTE Eötvös Loránd UniversityBudapestHungary
| | - Péter G. Szalay
- Institute of Chemistry, Laboratory of Theoretical ChemistryELTE Eötvös Loránd UniversityBudapestHungary
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31
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Taghavi A, Riveros I, Wales DJ, Yildirim I. Evaluating Geometric Definitions of Stacking for RNA Dinucleoside Monophosphates Using Molecular Mechanics Calculations. J Chem Theory Comput 2022; 18:3637-3653. [PMID: 35652685 DOI: 10.1021/acs.jctc.2c00178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNA modulation via small molecules is a novel approach in pharmacotherapies, where the determination of the structural properties of RNA motifs is considered a promising way to develop drugs capable of targeting RNA structures to control diseases. However, due to the complexity and dynamic nature of RNA molecules, the determination of RNA structures using experimental approaches is not always feasible, and computational models employing force fields can provide important insight. The quality of the force field will determine how well the predictions are compared to experimental observables. Stacking in nucleic acids is one such structural property, originating mainly from London dispersion forces, which are quantum mechanical and are included in molecular mechanics force fields through nonbonded interactions. Geometric descriptions are utilized to decide if two residues are stacked and hence to calculate the stacking free energies for RNA dinucleoside monophosphates (DNMPs) through statistical mechanics for comparison with experimental thermodynamics data. Here, we benchmark four different stacking definitions using molecular dynamics (MD) trajectories for 16 RNA DNMPs produced by two different force fields (RNA-IL and ff99OL3) and show that our stacking definition better correlates with the experimental thermodynamics data. While predictions within an accuracy of 0.2 kcal/mol at 300 K were observed in RNA CC, CU, UC, AG, GA, and GG, stacked states of purine-pyrimidine and pyrimidine-purine DNMPs, respectively, were typically underpredicted and overpredicted. Additionally, population distributions of RNA UU DNMPs were poorly predicted by both force fields, implying a requirement for further force field revisions. We further discuss the differences predicted by each RNA force field. Finally, we show that discrete path sampling (DPS) calculations can provide valuable information and complement the MD simulations. We propose the use of experimental thermodynamics data for RNA DNMPs as benchmarks for testing RNA force fields.
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Affiliation(s)
- Amirhossein Taghavi
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458, United States.,Department of Chemistry, Scripps Research Institute Florida, Jupiter, Florida 33458, United States
| | - Ivan Riveros
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458, United States
| | - David J Wales
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Ilyas Yildirim
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458, United States
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32
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Sirianni DA, Zhu X, Sitkoff DF, Cheney DL, Sherrill CD. The influence of a solvent environment on direct non-covalent interactions between two molecules: A symmetry-adapted perturbation theory study of polarization tuning of π-π interactions by water. J Chem Phys 2022; 156:194306. [PMID: 35597646 DOI: 10.1063/5.0087302] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
High-level quantum chemical computations have provided significant insight into the fundamental physical nature of non-covalent interactions. These studies have focused primarily on gas-phase computations of small van der Waals dimers; however, these interactions frequently take place in complex chemical environments, such as proteins, solutions, or solids. To better understand how the chemical environment affects non-covalent interactions, we have undertaken a quantum chemical study of π-π interactions in an aqueous solution, as exemplified by T-shaped benzene dimers surrounded by 28 or 50 explicit water molecules. We report interaction energies (IEs) using second-order Møller-Plesset perturbation theory, and we apply the intramolecular and functional-group partitioning extensions of symmetry-adapted perturbation theory (ISAPT and F-SAPT, respectively) to analyze how the solvent molecules tune the π-π interactions of the solute. For complexes containing neutral monomers, even 50 explicit waters (constituting a first and partial second solvation shell) change total SAPT IEs between the two solute molecules by only tenths of a kcal mol-1, while significant changes of up to 3 kcal mol-1 of the electrostatic component are seen for the cationic pyridinium-benzene dimer. This difference between charged and neutral solutes is attributed to large non-additive three-body interactions within solvated ion-containing complexes. Overall, except for charged solutes, our quantum computations indicate that nearby solvent molecules cause very little "tuning" of the direct solute-solute interactions. This indicates that differences in binding energies between the gas phase and solution phase are primarily indirect effects of the competition between solute-solute and solute-solvent interactions.
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Affiliation(s)
- Dominic A Sirianni
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Xiao Zhu
- Molecular Structure and Design, Bristol Myers Squibb Company, P.O. Box 5400, Princeton, New Jersey 08543, USA
| | - Doree F Sitkoff
- Molecular Structure and Design, Bristol Myers Squibb Company, P.O. Box 5400, Princeton, New Jersey 08543, USA
| | - Daniel L Cheney
- Molecular Structure and Design, Bristol Myers Squibb Company, P.O. Box 5400, Princeton, New Jersey 08543, USA
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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33
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Novel Thermostable Heparinase Based on the Genome of Bacteroides Isolated from Human Gut Microbiota. Foods 2022; 11:foods11101462. [PMID: 35627031 PMCID: PMC9141863 DOI: 10.3390/foods11101462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 05/16/2022] [Accepted: 05/16/2022] [Indexed: 02/01/2023] Open
Abstract
Among the nutrients available to the human gut microbiota, the complex carbohydrates and glycosaminoglycans are important sources of carbon for some of the species of human gut microbiota. Glycosaminoglycan (heparin) from the host is a highly preferred carbohydrate for Bacteroides. To explore how gut microbiota can effectively use heparin as a carbon source for growth, we conducted a screening of the Carbohydrate-Active enzymes (CAZymes) database for lytic enzymes of the PL13 family and Research Center of Food Biotechnology at School of Food Science and Technology of Jiangnan University database of Bacteroides to identify novel glycosaminoglycan-degrading bacterial strains. Four Bacteroides species (Bacteroides eggerthii, Bacteroides clarus, Bacteroides nordii, and Bacteroides finegoldii) that degraded heparin were selected for further studies. Analysis of the polysaccharide utilization sites of the four strains revealed that all of them harbored enzyme encoding genes of the PL13 family. Functional analysis revealed the activity of CAZymes in a medium containing heparin as the sole carbon source, suggesting their potential to degrade heparin and support growth. The four enzymes were heterologous expressed, and their enzymatic properties, kinetics, and thermal stability were determined. The lytic enzyme of B. nordii had high enzymatic activity and thermal stability. The features that cause this high thermal stability were elucidated based on an examination of the three-dimensional structure of the protein. Our findings provide an important theoretical basis for the application of glycosaminoglycans and glycosaminoglycan-degrading enzymes in the medical and biotechnology industries, and an important scientific basis for precision nutrition and medical intervention studies using gut microbiota or enzymes as targets.
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34
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Intramolecular resonance-assisted hydrogen bonds: Insights from symmetry adapted perturbation theory. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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35
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Gayathri V, Sheyara RTB, Devassy N, Samanta D. Investigating the degradation of
PET
utilizing
NHC
‐based catalysts and effective reuse of the degradation product as an additive with polyurethane adhesive material. J Appl Polym Sci 2022. [DOI: 10.1002/app.52474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Varnakumar Gayathri
- Polymer Science & Technology Department CSIR‐Central Leather Research Institute, Adyar Chennai India
- Academy of Scientific and Innovative Research Ghaziabad Uttar Pradesh India
| | - R. Tata Birla Sheyara
- Polymer Science & Technology Department CSIR‐Central Leather Research Institute, Adyar Chennai India
| | - Neenu Devassy
- Polymer Science & Technology Department CSIR‐Central Leather Research Institute, Adyar Chennai India
| | - Debasis Samanta
- Polymer Science & Technology Department CSIR‐Central Leather Research Institute, Adyar Chennai India
- Academy of Scientific and Innovative Research Ghaziabad Uttar Pradesh India
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36
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Lin J, Wang F, Tian J, Zhang J, Wang Y, Sun W. Theoretical and experimental investigations of the enantioselective epoxidation of olefins catalyzed by manganese complexes. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.08.092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Xiao LY, Zhang LX, Kang YN, Yin YY, Yuan ZY, Ma T, Li LX, Luo CY, Liu Y, He YM, Bie LJ. Single‐Crystal‐to‐Single‐Crystal (SCSC) Transformation of a Binuclear Cadmium (II) Complex to a Discrete Mononuclear Cadmium (II) Complex. Z Anorg Allg Chem 2022. [DOI: 10.1002/zaac.202100159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Le-Xi Zhang
- Tianjin University of Technology School of Materials Science and Engineering 391 Binshui Xidao, Xiqing District 300384 Tianjin CHINA
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Ultrafast energy transfer between π-stacked aromatic rings upon inner-valence ionization. Nat Chem 2022; 14:232-238. [PMID: 34931045 DOI: 10.1038/s41557-021-00838-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 10/18/2021] [Indexed: 11/08/2022]
Abstract
Non-covalently bound aromatic systems are ubiquitous and govern the physicochemical properties of various organic materials. They are important to many phenomena of biological and technological relevance, such as protein folding, base-pair stacking in nucleic acids, molecular recognition and self-assembly, DNA-drug interactions, crystal engineering and organic electronics. Nevertheless, their molecular dynamics and chemical reactivity, particularly in electronic excited states, are not fully understood. Here, we observe intermolecular Coulombic decay in benzene dimers, (C6H6)2-the simplest prototypes of noncovalent π-π interactions between aromatic systems. Intermolecular Coulombic decay is initiated by a carbon 2s vacancy state produced by electron-impact ionization and proceeds through ultrafast energy transfer between the benzene molecules. As a result, the dimer relaxes with the emission of a further low-energy electron (<10 eV) and a pair of C6H6+ cations undergoing Coulomb explosion. Coincident fragment-ion and electron momentum spectroscopy, accompanied by ab initio calculations, enables us to elucidate the dynamical details of this ultrafast relaxation process.
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Wakchaure PD, Ganguly B. Unraveling the Role of π-Stacking Interactions in Ligand Binding to the Thiamine Pyrophosphate Riboswitch with High-level Quantum Chemical Calculations and Docking Study. J Phys Chem B 2022; 126:1076-1084. [PMID: 35089046 DOI: 10.1021/acs.jpcb.1c08587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The thiamine pyrophosphate (TPP) riboswitch has emerged as the new target for designing new ligands for antibiotic purpose. Binding of the natural ligand TPP to the TPP riboswitch causes downregulation of the genes responsible for its biosynthesis. We have reported the role of π-stacking energy contributions to ligand binding with a TPP riboswitch. In conjunction with the docking study, the higher-level quantum chemical calculations performed with the wB97XD and Def2TZVPP basis set in the aqueous phase revealed that the optimum ring size is crucial to attain the effective binding efficiency of ligands with a TPP riboswitch. The π-stacking energy contributions observed for the ligands studied are largely similar; however, the cases studied with higher π-stacking energies with larger rings have a weaker ability to displace the radiolabeled thiamine from the riboswitch. The EDA and NCI analyses suggest the role of larger dispersive interactions in stabilizing the π-stacking rings. The contribution from hydrogen-bonding interactions of the hydrogen-bond donor groups on the A ring augments the binding affinity of the ligand. This study sheds light on various factors that contribute to the design of new ligands for efficient binding with a TPP riboswitch and inhibition of gene expression.
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Affiliation(s)
- Padmaja D Wakchaure
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, Gujarat, India.,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh 201 002, India
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, Gujarat, India.,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh 201 002, India
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41
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Mahanta H, Paul AK. Dynamical Behavior of Aromatic Trimer Complexes in Unimolecular Dissociation Reaction at High Temperatures. Case Studies on C 6H 6-C 6F 6-C 6H 6 and C 6H 6 Trimer Complexes. J Phys Chem A 2022; 126:259-271. [PMID: 34994202 DOI: 10.1021/acs.jpca.1c09073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The intramolecular vibrational energy redistribution (IVR) dynamics during unimolecular dissociation of aromatic trimers at high temperatures is the primary interest of this study. Chemical dynamics simulations are performed for the unimolecular dissociation of benzene-hexafluorobenzene-benzene (Bz-HFB-Bz) and benzene trimer (Bz-trimer) complexes at a temperature range of 1000-2000 K. Partial dissociation of both the complexes is observed, which leads to a dimer and a monomer in the dynamics. However, the probability of such dissociation was found much lower in the case of the Bz-trimer, which further decreases with the increase of temperature. The rate of partial dissociation of Bz-HFB-Bz is faster at 1500, 1800, and 2000 K, whereas the rate of complete dissociation of the Bz-trimer is significantly faster than Bz-HFB-Bz at all temperatures. This is just the opposite of the corresponding dimer's dissociation, where benzene-hexafluorobenzene (Bz-HFB) dissociates at a faster rate than the benzene dimer (Bz-dimer). Thus, the dissociation dynamics of the trimer is different than that of the dimer. Simulations with excited intramolecular and intermolecular modes of the trimer complexes reveal that energy flows from intermolecular to intramolecular modes of Bz-HFB-Bz more freely than the Bz-trimer, and the dissociation process becomes slower for the former. Calculated activation energies for both types of dynamics are much lower than the corresponding binding energies, which may be due to the anharmonicity. The Arrhenius equation with an anharmonic correction factor is considered to recalculate the activation energy and pre-exponential factor.
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Affiliation(s)
- Himashree Mahanta
- Department of Chemistry, National Institute of Technology Meghalaya, Shillong 793003, Meghalaya, India
| | - Amit Kumar Paul
- Department of Chemistry, National Institute of Technology Meghalaya, Shillong 793003, Meghalaya, India
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42
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Li X, Spada L, Alessandrini S, Zheng Y, Lengsfeld KG, Grabow J, Feng G, Puzzarini C, Barone V. Stacked but not Stuck: Unveiling the Role of π→π* Interactions with the Help of the Benzofuran-Formaldehyde Complex. Angew Chem Int Ed Engl 2022; 61:e202113737. [PMID: 34697878 PMCID: PMC9298890 DOI: 10.1002/anie.202113737] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Indexed: 12/14/2022]
Abstract
The 1:1 benzofuran-formaldehyde complex has been chosen as model system for analyzing π→π* interactions in supramolecular organizations involving heteroaromatic rings and carbonyl groups. A joint "rotational spectroscopy-quantum chemistry" strategy unveiled the dominant role of π→π* interactions in tuning the intermolecular interactions of such adduct. The exploration of the intermolecular potential energy surface led to the identification of 14 low-energy minima, with 4 stacked isomers being more stable than those linked by hydrogen bond or lone-pair→π interactions. All energy minima are separated by loose transition states, thus suggesting an effective relaxation to the global minimum under the experimental conditions. This expectation has been confirmed by the experimental detection of only one species, which was unambiguously assigned owing to the computation of accurate spectroscopic parameters and the characterization of 11 isotopologues. The large number of isotopic species opened the way to the determination of the first semi-experimental equilibrium structure for a molecular complex of such a dimension.
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Affiliation(s)
- Xiaolong Li
- School of Chemistry and Chemical EngineeringChongqing UniversityDaxuecheng South Rd. 55Chongqing401331China
| | - Lorenzo Spada
- Scuola Normale SuperiorePiazza dei Cavalieri 756126PisaItaly
| | - Silvia Alessandrini
- Scuola Normale SuperiorePiazza dei Cavalieri 756126PisaItaly
- Dipartimento di Chimica “Giacomo Ciamician”University of BolognaVia F. Selmi 240126BolognaItaly
| | - Yang Zheng
- School of Chemistry and Chemical EngineeringChongqing UniversityDaxuecheng South Rd. 55Chongqing401331China
| | - Kevin Gregor Lengsfeld
- Institut für Physikalische Chemie and ElektrochemieGottfried Wilhelm Leibniz Universität HannoverCallinstrasse 3A30167HannoverGermany
| | - Jens‐Uwe Grabow
- Institut für Physikalische Chemie and ElektrochemieGottfried Wilhelm Leibniz Universität HannoverCallinstrasse 3A30167HannoverGermany
| | - Gang Feng
- School of Chemistry and Chemical EngineeringChongqing UniversityDaxuecheng South Rd. 55Chongqing401331China
| | - Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”University of BolognaVia F. Selmi 240126BolognaItaly
| | - Vincenzo Barone
- Scuola Normale SuperiorePiazza dei Cavalieri 756126PisaItaly
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Li X, Spada L, Alessandrini S, Zheng Y, Lengsfeld KG, Grabow J, Feng G, Puzzarini C, Barone V. Gestapelt, nicht geklebt: Enthüllung der π→π*‐Wechselwirkung mithilfe des Benzofuran‐Formaldehyd‐Komplexes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xiaolong Li
- School of Chemistry and Chemical Engineering Chongqing University Daxuecheng South Rd. 55 Chongqing 401331 China
| | - Lorenzo Spada
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italien
| | - Silvia Alessandrini
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italien
- Dipartimento di Chimica “Giacomo Ciamician” Università di Bologna Via F. Selmi 2 40126 Bologna Italien
| | - Yang Zheng
- School of Chemistry and Chemical Engineering Chongqing University Daxuecheng South Rd. 55 Chongqing 401331 China
| | - Kevin Gregor Lengsfeld
- Institut für Physikalische Chemie und Elektrochemie Gottfried Wilhelm Leibniz Universität Hannover Callinstraße 3A 30167 Hannover Deutschland
| | - Jens‐Uwe Grabow
- Institut für Physikalische Chemie und Elektrochemie Gottfried Wilhelm Leibniz Universität Hannover Callinstraße 3A 30167 Hannover Deutschland
| | - Gang Feng
- School of Chemistry and Chemical Engineering Chongqing University Daxuecheng South Rd. 55 Chongqing 401331 China
| | - Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician” Università di Bologna Via F. Selmi 2 40126 Bologna Italien
| | - Vincenzo Barone
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italien
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Al-Noaimi M, Awwadi FF, Mansi IA, Sawwan M, Abu-Irmaileh B, Dege N. Polymorphism, spectroscopic, DFT and anticancer activity of a palladium(II) complex with a thiophenyl azoimine-quinoline SNN’N” ligand. Polyhedron 2022. [DOI: 10.1016/j.poly.2021.115541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Teixeira Campos P, Machado Rodrigues G, Pereira Afonso L, Uecker Krüger V, Siqueira da Silva RM, Milani MA. Energetic and Topological Supramolecular Study and Nucleation Proposal of Halogenated Aryl Amides. CrystEngComm 2022. [DOI: 10.1039/d2ce00049k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A supramolecular study of 12 halogenated aryl amides (F, Cl, Br, I) in the ortho, meta, or para positions was realized. From mono crystal X-ray diffraction data and theoretical calculations...
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Igarashi M, Nozawa T, Matsumoto T, Yagihashi F, Kikuchi T, Sato K. Parallel-stacked aromatic molecules in hydrogen-bonded inorganic frameworks. Nat Commun 2021; 12:7025. [PMID: 34893610 PMCID: PMC8664825 DOI: 10.1038/s41467-021-27324-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 11/11/2021] [Indexed: 12/02/2022] Open
Abstract
By precisely constructing molecules and assembling these into well-defined supramolecular structures, novel physical properties and functionalities can be realized, and new areas of the chemical space can be accessed. In both materials science and biology, a deeper understanding of the properties and exploitation of the reversible character of weak bonds and interactions, such as hydrogen bonds and π–π interactions, is anticipated to lead to the development of materials with novel properties and functionalities. We apply the hydrogen-bonded organic frameworks (HOFs) strategy to inorganic materials science using the cubic octamer of orthosilicic acid, [Si8O12][OH]8, as a building block, and find that various types of hydrogen-bonded inorganic frameworks (HIFs). We succeed in parallel π-stacking pure benzene, thiophene, selenophene, p-benzoquinone, thiophene·p-benzoquinone, and benzene·p-benzoquinone polymers infinitely. These polymers interact via their π-systems by taking advantage of the flexible pores of the three-dimensional nano-honeycomb HIFs, which consist of periodic wide and narrow segments. Hydrogen-bonded inorganic frameworks are porous structures that may lead to novel materials with unprecedented properties and functionalities. Here the authors report the solid-state structures of orthosilicic acid-based hydrogen-bonded inorganic frameworks that can encapsulate small unsaturated cyclic molecules such as benzene, which are found stacked in parallel.
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Affiliation(s)
- Masayasu Igarashi
- Interdisciplinary Research Center for Catalytic Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, 305-8565, Japan.
| | - Takeshi Nozawa
- Interdisciplinary Research Center for Catalytic Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, 305-8565, Japan
| | - Tomohiro Matsumoto
- Interdisciplinary Research Center for Catalytic Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, 305-8565, Japan
| | - Fujio Yagihashi
- Interdisciplinary Research Center for Catalytic Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, 305-8565, Japan
| | - Takashi Kikuchi
- Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima-shi, Tokyo, 196-8666, Japan
| | - Kazuhiko Sato
- Interdisciplinary Research Center for Catalytic Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, 305-8565, Japan.
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Malloum A, Conradie J. Structures, binding energies and non-covalent interactions of furan clusters. J Mol Graph Model 2021; 111:108102. [PMID: 34915345 DOI: 10.1016/j.jmgm.2021.108102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 12/20/2022]
Abstract
Understanding of the furan solvent is subjected to the knowledge of the structures of the furan clusters and interactions taking place therein. Although, furan clusters can be very important to determine the dynamics and the properties of the furan solvent, there has been only a few investigations reported on furan dimer. In this work, we have explored the potential energy surfaces (PESs) of the furan clusters using two incremental levels of theory. Structures have been initially generated using classical molecular dynamics followed by full optimization at the MP2/aug-cc-pVDZ level of theory. The results show that the most stable structure of the furan dimer has a stacking configuration while that of the trimer has a cyclic configuration. We have noted that the structures of the furan tetramer have no definite configurations. In addition, we have performed a quantum theory of atoms in molecule (QTAIM) analysis to identify all possible non-covalent interactions of the furan clusters. The results show that six different types of non-covalent interactions can be identified in furan clusters. We have noted that the CH⋯C and CH⋯O hydrogen bondings are the strongest non-covalent interactions while the H⋯H bonding interaction is found to be the weakest. Furthermore, we have assessed the performance of ten DFT functionals in calculating the binding energies of the furan clusters. The ten DFT functionals (M05, M05-2X, M06, M06-2X, M08HX, PBE0, ωB97XD, PW6B95D3, APFD and MN15) have been benchmarked to DLPNO-CCSD(T)/CBS. The functionals M05-2X and M06 are recommended for further affordable investigations of the furan clusters.
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Affiliation(s)
- Alhadji Malloum
- Department of Chemistry, University of the Free State, PO BOX 339, Bloemfontein, 9300, South Africa; Department of Physics, Faculty of Science, University of Maroua, PO BOX 46, Maroua, Cameroon.
| | - Jeanet Conradie
- Department of Chemistry, University of the Free State, PO BOX 339, Bloemfontein, 9300, South Africa; Department of Chemistry, UiT - The Arctic University of Norway, N-9037 Tromsø, Norway
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48
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Lebedenko CG, Banerjee IA. Investigation of Self‐Assembly of Symmetric and Asymmetric Peptide Bolaamphiphiles by COSMO‐RS and Atomistic Simulations and Their Interactions with POPC Bilayers. MACROMOL THEOR SIMUL 2021. [DOI: 10.1002/mats.202100066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Ipsita A. Banerjee
- Department of Chemistry Fordham University 441 East Fordham Road Bronx NY 10458 USA
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Sparrow ZM, Ernst BG, Joo PT, Lao KU, DiStasio RA. NENCI-2021. I. A large benchmark database of non-equilibrium non-covalent interactions emphasizing close intermolecular contacts. J Chem Phys 2021; 155:184303. [PMID: 34773949 DOI: 10.1063/5.0068862] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we present NENCI-2021, a benchmark database of ∼8000 Non-Equilibirum Non-Covalent Interaction energies for a large and diverse selection of intermolecular complexes of biological and chemical relevance. To meet the growing demand for large and high-quality quantum mechanical data in the chemical sciences, NENCI-2021 starts with the 101 molecular dimers in the widely used S66 and S101 databases and extends the scope of these works by (i) including 40 cation-π and anion-π complexes, a fundamentally important class of non-covalent interactions that are found throughout nature and pose a substantial challenge to theory, and (ii) systematically sampling all 141 intermolecular potential energy surfaces (PESs) by simultaneously varying the intermolecular distance and intermolecular angle in each dimer. Designed with an emphasis on close contacts, the complexes in NENCI-2021 were generated by sampling seven intermolecular distances along each PES (ranging from 0.7× to 1.1× the equilibrium separation) and nine intermolecular angles per distance (five for each ion-π complex), yielding an extensive database of 7763 benchmark intermolecular interaction energies (Eint) obtained at the coupled-cluster with singles, doubles, and perturbative triples/complete basis set [CCSD(T)/CBS] level of theory. The Eint values in NENCI-2021 span a total of 225.3 kcal/mol, ranging from -38.5 to +186.8 kcal/mol, with a mean (median) Eint value of -1.06 kcal/mol (-2.39 kcal/mol). In addition, a wide range of intermolecular atom-pair distances are also present in NENCI-2021, where close intermolecular contacts involving atoms that are located within the so-called van der Waals envelope are prevalent-these interactions, in particular, pose an enormous challenge for molecular modeling and are observed in many important chemical and biological systems. A detailed symmetry-adapted perturbation theory (SAPT)-based energy decomposition analysis also confirms the diverse and comprehensive nature of the intermolecular binding motifs present in NENCI-2021, which now includes a significant number of primarily induction-bound dimers (e.g., cation-π complexes). NENCI-2021 thus spans all regions of the SAPT ternary diagram, thereby warranting a new four-category classification scheme that includes complexes primarily bound by electrostatics (3499), induction (700), dispersion (1372), or mixtures thereof (2192). A critical error analysis performed on a representative set of intermolecular complexes in NENCI-2021 demonstrates that the Eint values provided herein have an average error of ±0.1 kcal/mol, even for complexes with strongly repulsive Eint values, and maximum errors of ±0.2-0.3 kcal/mol (i.e., ∼±1.0 kJ/mol) for the most challenging cases. For these reasons, we expect that NENCI-2021 will play an important role in the testing, training, and development of next-generation classical and polarizable force fields, density functional theory approximations, wavefunction theory methods, and machine learning based intra- and inter-molecular potentials.
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Affiliation(s)
- Zachary M Sparrow
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Brian G Ernst
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Paul T Joo
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Ka Un Lao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Robert A DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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50
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Ultrafast selective adsorption of pretreatment inhibitors from lignocellulosic hydrolysate with metal-organic frameworks: Performance and adsorption mechanisms. Sep Purif Technol 2021. [DOI: 10.1016/j.seppur.2021.119183] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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