1
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Fu C, Du K, Xue J, Xin H, Zhang J, Li H. Mechanisms of acid generation from ionic photoacid generators for extreme ultraviolet and electron beam lithography. Phys Chem Chem Phys 2024; 26:18547-18556. [PMID: 38805008 DOI: 10.1039/d4cp01814a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Photoacid generators (PAGs) are important components of chemically amplified resists. The properties of PAGs directly affect the sensitivity of photoresists, line edge roughness, and resolution. Understanding the photoacid generation process in extreme ultraviolet (EUV) and electron beam (EB) lithography is helpful for photoresist design. However, the microscopic mechanisms remain largely unclear and the large variety in the molecular structure of PAGs presents a challenge to overcome. In this work, we investigate the microscopic processes of photoacid production of ionic PAGs for EUV and EB lithography. The PAG dissociation pathway is found to depend on the molecular structure and conformations. The processes of photoacid production and by-product generation are also revealed. The results contribute to a better understanding of the photochemical reactions in EUV and EB lithography, providing insights into the molecular design of novel PAGs and photoresists.
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Affiliation(s)
- Chengbin Fu
- School of Microelectronics, Shanghai University, Shanghai 201800, China.
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, China
| | - Kun Du
- School of Microelectronics, Shanghai University, Shanghai 201800, China.
| | - Jie Xue
- School of Microelectronics, Shanghai University, Shanghai 201800, China.
| | - Hanshen Xin
- School of Microelectronics, Shanghai University, Shanghai 201800, China.
| | - Jianhua Zhang
- School of Microelectronics, Shanghai University, Shanghai 201800, China.
| | - Haoyuan Li
- School of Microelectronics, Shanghai University, Shanghai 201800, China.
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, China
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2
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Guo B, Xue Q, Zhang Z, Zhai J, Wang C, Zhao Y, Zhang J. Atomic Insight into the Enzymatic Selectivity of Acetyltransferase for Endogenous Polyamines. Chemphyschem 2024:e202400412. [PMID: 38772911 DOI: 10.1002/cphc.202400412] [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: 04/23/2024] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 05/23/2024]
Abstract
The N1-Spermidine/spermine acetyltransferase (SSAT) serves as the rate-limiting enzyme in the polyamine metabolism pathway, specifically catalyzing the acetylation of spermidine, spermine, and other specific polyamines. The source of its enzymatic selectivity remains elusive. Here, we used quantum mechanics and molecular mechanics simulations combined with various technologies to explore the enzymatic mechanism of SSAT for endogenous polyamines from an atomic perspective. The static binding and chemical transformation were considered. The binding affinity was identified to be dependent on protonated state of polyamine. The order of the binding affinity for Spm, Spd, and Put is consistent with the experimental results, which is also verified by the dynamic separation of polyamine and SSAT. Hydrogen bond interactions and salt bridges contribute most, and the common hot residues were identified. In addition, the transfer of acetyl and proton between polyamine and AcCoA was discovered to follow a concert mechanism, and thermodynamic properties are responsible for the catalytic efficiency of SSAT. This work may be helpful for development of polyamine derivatives based on catalysis to regulate polyamine metabolism.
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Affiliation(s)
- Baolin Guo
- Henan Key Laboratory of Natural Medicine Innovation and Transformation, State Key Laboratory of Antiviral Drugs, Henan University, Kaifeng, 475001, China
| | - Qian Xue
- Henan Key Laboratory of Natural Medicine Innovation and Transformation, State Key Laboratory of Antiviral Drugs, Henan University, Kaifeng, 475001, China
| | - Zhiyang Zhang
- Henan Key Laboratory of Natural Medicine Innovation and Transformation, State Key Laboratory of Antiviral Drugs, Henan University, Kaifeng, 475001, China
| | - Jihang Zhai
- Henan Key Laboratory of Natural Medicine Innovation and Transformation, State Key Laboratory of Antiviral Drugs, Henan University, Kaifeng, 475001, China
| | - Chaojie Wang
- Henan Key Laboratory of Natural Medicine Innovation and Transformation, State Key Laboratory of Antiviral Drugs, Henan University, Kaifeng, 475001, China
| | - Yuan Zhao
- Henan Key Laboratory of Natural Medicine Innovation and Transformation, State Key Laboratory of Antiviral Drugs, Henan University, Kaifeng, 475001, China
| | - Jie Zhang
- Henan Key Laboratory of Natural Medicine Innovation and Transformation, State Key Laboratory of Antiviral Drugs, Henan University, Kaifeng, 475001, China
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3
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Mó O, Montero-Campillo MM, Yáñez M, Alkorta I, Elguero J. A Holistic View of the Interactions between Electron-Deficient Systems: Clustering of Beryllium and Magnesium Hydrides and Halides. Molecules 2023; 28:7507. [PMID: 38005228 PMCID: PMC10673300 DOI: 10.3390/molecules28227507] [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: 10/03/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
In the search for common bonding patterns in pure and mixed clusters of beryllium and magnesium derivatives, the most stable dimers and trimers involving BeX2 and MgX2 (X = H, F, Cl) have been studied in the gas phase using B3LYP and M06-2X DFT methods and the G4 ab initio composite procedure. To obtain some insight into their structure, stability, and bonding characteristics, we have used two different energy decomposition formalisms, namely MBIE and LMO-EDA, in parallel with the analysis of the electron density with the help of QTAIM, ELF, NCIPLOT, and AdNDP approaches. Some interesting differences are already observed in the dimers, where the stability sequence observed for the hydrides differs entirely from that of the fluorides and chlorides. Trimers also show some peculiarities associated with the presence of compact trigonal cyclic structures that compete in stability with the more conventional hexagonal and linear forms. As observed for dimers, the stability of the trimers changes significantly from hydrides to fluorides or chlorides. Although some of these clusters were previously explored in the literature, the novelty of this work is to provide a holistic approach to the entire series of compounds by using chemical bonding tools, allowing us to understand the stability trends in detail and providing insights for a significant number of new, unexplored structures.
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Affiliation(s)
- Otilia Mó
- Departamento de Química, Módulo 13, Facultad de Ciencias, and Institute of Advanced Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain; (O.M.); (M.Y.)
| | - M. Merced Montero-Campillo
- Departamento de Química, Módulo 13, Facultad de Ciencias, and Institute of Advanced Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain; (O.M.); (M.Y.)
| | - Manuel Yáñez
- Departamento de Química, Módulo 13, Facultad de Ciencias, and Institute of Advanced Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain; (O.M.); (M.Y.)
| | - Ibon Alkorta
- Instituto de Química Médica, IQM-CSIC, Juan de la Cierva, 3, 28006 Madrid, Spain;
| | - José Elguero
- Instituto de Química Médica, IQM-CSIC, Juan de la Cierva, 3, 28006 Madrid, Spain;
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4
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Liao Q, Xie P, Wang Z. Enantiodetermining processes in the synthesis of alanine, serine, and isovaline. Phys Chem Chem Phys 2023; 25:28829-28834. [PMID: 37853775 DOI: 10.1039/d3cp03212d] [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: 10/20/2023]
Abstract
In this study, quantum chemical calculations were used to explore the synthesis of three chiral α-amino acids, specifically alanine, serine, and isovaline, from reactants found in interstellar space. Our focus is on the crucial step in the synthesis pathway that determines the chirality of the amino acids. The results indicate that in the case of alanine, the determination of enantiomer is primarily influenced by the direction of the collision of molecules or functional groups, which leads to the formation of a chirality center in a crucial intermediate. However, contrary to chemical expectations, the enantiodetermining/enantioselection step for serine and isovaline synthesis occurs prior to the creation of a chirality center.
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Affiliation(s)
- Qingli Liao
- School of Physical Science and Technology, Guangxi University, Nanning 530004, China.
| | - Peng Xie
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Zhao Wang
- School of Physical Science and Technology, Guangxi University, Nanning 530004, China.
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5
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Coufal R, Vohlídal J. Pyrazinyl and pyridinyl bis-azomethines formation: an experimental and computational study. Sci Rep 2023; 13:17383. [PMID: 37833405 PMCID: PMC10575867 DOI: 10.1038/s41598-023-44585-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023] Open
Abstract
Formation of bis-azomethines from hydrazine and heterocyclic aromatic carbaldehydes, namely pyridine-2-carbaldehyde and pyrazine-2-carbaldehyde, is studied using density functional theory. The theoretical investigation is correlated with experimental results obtained by means of NMR spectroscopy. The presence of bis-hemiaminal intermediates is evidenced by NMR spectra while surprisingly stable hemiaminal intermediate was isolated experimentally. Water, methanol and acetic acid were outlined to play a crucial role as active catalysts of elementary steps of the reaction mechanisms. The possible reaction sequences, i.e. addition-dehydration-addition-dehydration or addition-addition-dehydration-dehydration are investigated and discussed. Also, alternative mechanistic path via ionic mechanism was proposed for the formation of hemiaminals.
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Affiliation(s)
- Radek Coufal
- Department of Science and Research, Faculty of Health Studies, Technical University of Liberec, Studentská 1402/2, 461 17, Liberec 1, Czech Republic.
| | - Jiří Vohlídal
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8/2030, 128 40, Prague 2, Czech Republic
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6
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Coufal R, Tošner Z, Drahoňovský D, Vohlídal J. Hemiacetal-based dynamic systems: a new mechanistic insight. Org Biomol Chem 2023; 21:6956-6968. [PMID: 37581612 DOI: 10.1039/d3ob00668a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
The formation of hemiacetals from pyrazine trifluoromethylketone as a model receptor and four simple alcohols was studied by using quantum chemical calculations and NMR spectroscopy. Free energy profiles for four types of mechanistic pathways were calculated and discussed with respect to kinetic and thermodynamic measurements. We show that hemiacetal formation is facilitated by an assisted proton transfer process via a pseudo eight-membered transition state which brings the theory and experiment into close agreement. Also, a newly proposed mechanistic pathway for hemiacetal formation via a five-membered transition state leading to zwitterionic intermediates is discussed. Direct proton transfer in a pseudo four-membered transition state can be ruled out due to the high energy of transition states with respect to other mechanistic pathways. We also show that in the case of hemiacetals, water and alcohol molecules cannot account sufficiently for the H-transfer process via six-membered transition states.
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Affiliation(s)
- Radek Coufal
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8/2030, 128 40 Prague 2, Czech Republic.
- Department of Science and Research, Faculty of Health Studies, Technical University of Liberec, Studentská 1402/2, 461 17 Liberec 1, Czech Republic
| | - Zdeněk Tošner
- NMR Laboratory, Faculty of Science, Charles University, Hlavova 8/2030, 128 40 Prague 2, Czech Republic
| | - Dušan Drahoňovský
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8/2030, 128 40 Prague 2, Czech Republic
| | - Jiří Vohlídal
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8/2030, 128 40 Prague 2, Czech Republic.
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7
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Mó O, Montero-Campillo MM, Yáñez M, Alkorta I, Elguero J. Dispersion, Rehybridization, and Pentacoordination: Keys to Understand Clustering of Boron and Aluminum Hydrides and Halides. J Phys Chem A 2023. [PMID: 37418427 PMCID: PMC10364081 DOI: 10.1021/acs.jpca.3c02747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
The structure, stability, and bonding characteristics of dimers and trimers involving BX3 and AlX3 (X = H, F, Cl) in the gas phase, many of them explored for the first time, were investigated using different DFT (B3LYP, B3LYP/D3BJ, and M06-2X) and ab initio (MP2 and G4) methods together with different energy decomposition formalisms, namely, many-body interaction-energy and localized molecular orbital energy decomposition analysis. The electron density of the clusters investigated was analyzed with QTAIM, electron localization function, NCIPLOT, and adaptive natural density partitioning approaches. Our results for triel hydride dimers and Al2X6 (X = F, Cl) clusters are in good agreement with previous studies in the literature, but in contrast with the general accepted idea that B2F6 and B2Cl6 do not exist, we have found that they are predicted to be weakly bound systems if dispersion interactions are conveniently accounted for in the theoretical schemes used. Dispersion interactions are also dominant in both homo- and heterotrimers involving boron halide monomers. Surprisingly, B3F9 and B3Cl9 C3v cyclic trimers, in spite of exhibiting rather strong B-X (X = F, Cl) interactions, were found to be unstable with respect to the isolated monomers due to the high energetic cost of the rehybridization of the B atom, which is larger than the two- and three-body stabilization contributions when the cyclic is formed. Another important feature is the enhanced stability of both homo- and heterotrimers in which Al is the central atom because Al is systematically pentacoordinated, whereas this is not the case when the central atom is B, which is only tri- or tetra-coordinated.
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Affiliation(s)
- Otilia Mó
- Departamento de Química, Módulo 13, Facultad de Ciencias, and Institute of Advanced Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - M Merced Montero-Campillo
- Departamento de Química, Módulo 13, Facultad de Ciencias, and Institute of Advanced Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Manuel Yáñez
- Departamento de Química, Módulo 13, Facultad de Ciencias, and Institute of Advanced Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Ibon Alkorta
- Instituto de Química Médica, IQM-CSIC, Juan de la Cierva, 3, 28006 Madrid, Spain
| | - José Elguero
- Instituto de Química Médica, IQM-CSIC, Juan de la Cierva, 3, 28006 Madrid, Spain
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8
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Charvati E, Sun H. Potential Energy Surfaces Sampled in Cremer-Pople Coordinates and Represented by Common Force Field Functionals for Small Cyclic Molecules. J Phys Chem A 2023; 127:2646-2663. [PMID: 36893434 DOI: 10.1021/acs.jpca.3c00095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
The complex conformations of the cyclic moieties impact the physical and chemical properties of molecules. In this work, we chose 22 molecules of four-, five-, and six-membered rings and performed a thorough conformational sampling using Cremer-Pople coordinates. With consideration of symmetries, we obtained a total of 1504 conformational structures for four-membered, 5576 for five-membered, and 13509 for six-membered rings. All well-known and many less well-known conformers for each molecule were identified. We represented the potential energy surfaces (PESs) by fitting the data to common analytical force field (FF) functional forms. We found that the general features of PESs can be described by the essential FF functional forms; however, the accuracy of representation can be improved remarkably by including the torsion-bond and torsion-angle coupling terms. The best fit yields R-squared (R2) values close to 1.0 and mean absolute errors in energy less than 0.3 kcal/mol.
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Affiliation(s)
- Evangelia Charvati
- School of Chemistry and Chemical Engineering, Materials Genome Initiative Center, and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huai Sun
- School of Chemistry and Chemical Engineering, Materials Genome Initiative Center, and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
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9
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Yadav S, Bhunia S, Kumar R, Seth R, Singh A. Designing Excess Electron Compounds by Substituting Alkali Metals to a Small and Versatile Tetracyclic Framework: A Theoretical Perspective. ACS OMEGA 2023; 8:7978-7988. [PMID: 36872966 PMCID: PMC9979228 DOI: 10.1021/acsomega.2c07743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Organic compound-based nonlinear optical (NLO) materials have sparked a lot of attention due to their multitude of applications and shorter optical response times than those of inorganic NLO materials. In the present investigation, we designed exo-exo-tetracyclo[6.2.1.13,6.02,7]dodecane (TCD) derivatives, which were obtained by replacing H atoms of methylene bridge carbon with alkali metals (Li, Na, and K). It was observed that upon the substitution of alkali metals at bridging CH2 carbon, absorption within the visible region occurred. Moving from 1 to 7 derivatives, the maximum absorption wavelength of the complexes exhibited a red shift. The designed molecules showed a high degree of intramolecular charge transfer (ICT) and excess electrons in nature, which were responsible for rapid optical response time and significant large molecular (hyper)polarizability. Calculated trends also inferred that the crucial transition energy decreased in order that also played a key role in the higher nonlinear optical response. Furthermore, to examine the effect of the structure/property relationship on the nonlinear optical properties of these investigated compounds (1-7), we calculated the density of state (DOS), transition density matrix (TDM), and frontier molecular orbitals (FMOs). The largest first static hyperpolarizability (βtot) of TCD derivative 7 was 72059 au, which was 43 times greater than that of the prototype p-nitroaniline (βtot = 1675 au).
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Affiliation(s)
- Santosh
Kumar Yadav
- Department
of Chemistry, Prof. Rajendra Singh (Rajju Bhaiya) Institute of Physical
Sciences for Study and Research, V.B.S.
Purvanchal University, Jaunpur 222003, India
| | - Snehasis Bhunia
- Department
of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Rd., Taipei 10617, Taiwan (R.O.C.)
| | - Rajneesh Kumar
- Department
of Chemistry, Prof. Rajendra Singh (Rajju Bhaiya) Institute of Physical
Sciences for Study and Research, V.B.S.
Purvanchal University, Jaunpur 222003, India
| | - Ritu Seth
- Department
of Chemistry, Prof. Rajendra Singh (Rajju Bhaiya) Institute of Physical
Sciences for Study and Research, V.B.S.
Purvanchal University, Jaunpur 222003, India
| | - Ajeet Singh
- Department
of Chemistry, Prof. Rajendra Singh (Rajju Bhaiya) Institute of Physical
Sciences for Study and Research, V.B.S.
Purvanchal University, Jaunpur 222003, India
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10
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Zhong W, Zhao M, Zhao J, Wang F, Gao Z, Bian H. Exploring the kinetics and mechanism of C2F5C(O)CF(CF3)2 reaction with hydrogen radical. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.140130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Wang Y, Zeng X, Shu S. Theoretical study on the degradation mechanism of propranolol in aqueous solution initiated by hydroxyl and sulfate radicals. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113924] [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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12
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Bursch M, Mewes J, Hansen A, Grimme S. Best-Practice DFT Protocols for Basic Molecular Computational Chemistry. Angew Chem Int Ed Engl 2022; 61:e202205735. [PMID: 36103607 PMCID: PMC9826355 DOI: 10.1002/anie.202205735] [Citation(s) in RCA: 137] [Impact Index Per Article: 68.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Indexed: 01/11/2023]
Abstract
Nowadays, many chemical investigations are supported by routine calculations of molecular structures, reaction energies, barrier heights, and spectroscopic properties. The lion's share of these quantum-chemical calculations applies density functional theory (DFT) evaluated in atomic-orbital basis sets. This work provides best-practice guidance on the numerous methodological and technical aspects of DFT calculations in three parts: Firstly, we set the stage and introduce a step-by-step decision tree to choose a computational protocol that models the experiment as closely as possible. Secondly, we present a recommendation matrix to guide the choice of functional and basis set depending on the task at hand. A particular focus is on achieving an optimal balance between accuracy, robustness, and efficiency through multi-level approaches. Finally, we discuss selected representative examples to illustrate the recommended protocols and the effect of methodological choices.
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Affiliation(s)
- Markus Bursch
- Max-Planck-Institut für KohlenforschungKaiser-Wilhelm-Platz 145470Mülheim an der RuhrGermany
| | - Jan‐Michael Mewes
- Mulliken Center for Theoretical ChemistryInstitut für Physikalische und Theoretische ChemieUniversität BonnBeringstraße 453115BonnGermany
| | - Andreas Hansen
- Mulliken Center for Theoretical ChemistryInstitut für Physikalische und Theoretische ChemieUniversität BonnBeringstraße 453115BonnGermany
| | - Stefan Grimme
- Mulliken Center for Theoretical ChemistryInstitut für Physikalische und Theoretische ChemieUniversität BonnBeringstraße 453115BonnGermany
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13
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Bursch M, Mewes J, Hansen A, Grimme S. Best‐Practice DFT Protocols for Basic Molecular Computational Chemistry**. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Markus Bursch
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
| | - Jan‐Michael Mewes
- Mulliken Center for Theoretical Chemistry Institut für Physikalische und Theoretische Chemie Universität Bonn Beringstraße 4 53115 Bonn Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry Institut für Physikalische und Theoretische Chemie Universität Bonn Beringstraße 4 53115 Bonn Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry Institut für Physikalische und Theoretische Chemie Universität Bonn Beringstraße 4 53115 Bonn Germany
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14
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Costa AM, Castro-Alvarez A, Vilarrasa J, Fillot D. Computational Comparison of the Stability of Iminium Ions and Salts from Enals and Pyrrolidine Derivatives (Aminocatalysts). European J Org Chem 2022. [DOI: 10.1002/ejoc.202200627] [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)
- Anna M. Costa
- Universitat de Barcelona Facultat de Química: Universitat de Barcelona Facultat de Quimica Organic Chemistry Section Av. Diagonal 645 08028 Barcelona SPAIN
| | - Alejandro Castro-Alvarez
- Universidad de la Frontera Facultad de Medicina Ciencias Preclínicas Av. Alemania 0458 4810296 Temuco CHILE
| | - Jaume Vilarrasa
- Universitat de Barcelona Organic Chemistry Section, Fac. Quimica Av. Diagonal 645 08028 Barcelona SPAIN
| | - Daniel Fillot
- Universidad de Barcelona Facultad de Química: Universitat de Barcelona Facultat de Quimica Organic Chemistry Section (Dep. Quim. Inorg. i Org.) Diagonal 645 08028 Barcelona SPAIN
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15
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Costa AM, Cascales V, Castro-Alvarez A, Vilarrasa J. Computational Study of the Stability of Pyrrolidine-Derived Iminium Ions: Exchange Equilibria between Iminium Ions and Carbonyl Compounds. ACS OMEGA 2022; 7:18247-18258. [PMID: 35694469 PMCID: PMC9178767 DOI: 10.1021/acsomega.1c07020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
The tendency of carbonyl compounds to form iminium ions by reaction with pyrrolidine or chiral pyrrolidine derivatives (in other words, the relative stability to hydrolysis of these iminium ions) has been computationally examined, mainly using the M06-2X/6-311+G(d,p) method. We have thus obtained the equilibrium positions for R-CH=O + CH2=CH-CH=N+R2* → R-CH=N+R2* + CH2=CH-CH=O reactions and for related exchanges. In these exchanges, there is a transfer of a secondary amine between two carbonyl compounds. Their relative energies may be used to predict which iminium species can be predominantly formed when two or more carbonyl groups are present in a reaction medium. In the catalytic Michael additions of nucleophiles to iminium ions arising from conjugated enals, dienals, and trienals, if the formation of the new Nu-C bond is favorable, the chances of amino-catalyzed reactions to efficiently proceed, with high conversions, depend on the calculated energy values for these exchange equilibria, where the iminium tetrafluoroborates of the adducts (final iminium intermediates) must be more prone to hydrolysis than the initial iminium tetrafluoroborates. The density functional theory (DFT) calculations indicate that the MacMillan catalysts and related oxazolidinones are especially suitable in this regard.
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16
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Chen S, Zhong Y, Fan W, Xiang J, Wang G, Zhou Q, Wang J, Geng Y, Sun R, Zhang Z, Piao Y, Wang J, Zhuo J, Cong H, Jiang H, Ling J, Li Z, Yang D, Yao X, Xu X, Zhou Z, Tang J, Shen Y. Enhanced tumour penetration and prolonged circulation in blood of polyzwitterion-drug conjugates with cell-membrane affinity. Nat Biomed Eng 2021; 5:1019-1037. [PMID: 33859387 DOI: 10.1038/s41551-021-00701-4] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 02/16/2021] [Indexed: 02/01/2023]
Abstract
Effective anticancer nanomedicines need to exhibit prolonged circulation in blood, to extravasate and accumulate in tumours, and to be taken up by tumour cells. These contrasting criteria for persistent circulation and cell-membrane affinity have often led to complex nanoparticle designs with hampered clinical translatability. Here, we show that conjugates of small-molecule anticancer drugs with the polyzwitterion poly(2-(N-oxide-N,N-diethylamino)ethyl methacrylate) have long blood-circulation half-lives and bind reversibly to cell membranes, owing to the negligible interaction of the polyzwitterion with proteins and its weak interaction with phospholipids. Adsorption of the polyzwitterion-drug conjugates to tumour endothelial cells and then to cancer cells favoured their transcytosis-mediated extravasation into tumour interstitium and infiltration into tumours, and led to the eradication of large tumours and patient-derived tumour xenografts in mice. The simplicity and potency of the polyzwitterion-drug conjugates should facilitate the design of translational anticancer nanomedicines.
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Affiliation(s)
- Siqin Chen
- Zhejiang Key Laboratory of Smart BioMaterials and Center for Bionanoengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Yin Zhong
- Zhejiang Key Laboratory of Smart BioMaterials and Center for Bionanoengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Wufa Fan
- Zhejiang Key Laboratory of Smart BioMaterials and Center for Bionanoengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China.,Department of Polymer Science and Engineering, Peking University, Beijing, China
| | - Jiajia Xiang
- Zhejiang Key Laboratory of Smart BioMaterials and Center for Bionanoengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Guowei Wang
- Zhejiang Key Laboratory of Smart BioMaterials and Center for Bionanoengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Quan Zhou
- Zhejiang Key Laboratory of Smart BioMaterials and Center for Bionanoengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Jinqiang Wang
- Zhejiang Key Laboratory of Smart BioMaterials and Center for Bionanoengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Yu Geng
- Zhejiang Key Laboratory of Smart BioMaterials and Center for Bionanoengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Rui Sun
- Zhejiang Key Laboratory of Smart BioMaterials and Center for Bionanoengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Zhen Zhang
- Zhejiang Key Laboratory of Smart BioMaterials and Center for Bionanoengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Ying Piao
- Zhejiang Key Laboratory of Smart BioMaterials and Center for Bionanoengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Jianguo Wang
- Department of Surgery, First Affiliated Hospital of School of Medicine, Zhejiang University, Hangzhou, China
| | - Jianyong Zhuo
- Department of Surgery, First Affiliated Hospital of School of Medicine, Zhejiang University, Hangzhou, China
| | - Hailin Cong
- Institute of Biomedical Materials and Engineering, College of Materials Science and Engineering, Qingdao University, Qingdao, China
| | - Haiping Jiang
- Department of Medical Oncology, The First Affiliated Hospital of School of Medicine, Zhejiang University, Hangzhou, China
| | - Jun Ling
- Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
| | - Zichen Li
- Department of Polymer Science and Engineering, Peking University, Beijing, China
| | - Dingding Yang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xin Yao
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiao Xu
- Department of Surgery, First Affiliated Hospital of School of Medicine, Zhejiang University, Hangzhou, China
| | - Zhuxian Zhou
- Zhejiang Key Laboratory of Smart BioMaterials and Center for Bionanoengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Jianbin Tang
- Zhejiang Key Laboratory of Smart BioMaterials and Center for Bionanoengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Youqing Shen
- Zhejiang Key Laboratory of Smart BioMaterials and Center for Bionanoengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China. .,Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China. .,Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China.
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17
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Costa AM, Bosch L, Petit E, Vilarrasa J. Computational Study of the Addition of Methanethiol to 40+ Michael Acceptors as a Model for the Bioconjugation of Cysteines. J Org Chem 2021; 86:7107-7118. [PMID: 33914532 PMCID: PMC8631706 DOI: 10.1021/acs.joc.1c00349] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Indexed: 12/17/2022]
Abstract
A long series of Michael acceptors are studied computationally as potential alternatives to the maleimides that are used in most antibody-drug conjugates to link Cys of mAbs with cytotoxic drugs. The products of the reaction of methanethiol (CH3SH/MeSH, as a simple model of Cys) with N-methylated ethynesulfonamide, 2-ethynylpyridinium ion, propynamide, and methyl ethynephosphonamidate (that is, with HC≡C-EWG) are predicted by the M06-2X/6-311+G(d,p) method to be thermodynamically more stable, in relation to their precursors, than that of MeSH with N-methylmaleimide and, in general, with H2C═CH-EWG; calculations with AcCysOMe and tBuSH are also included. However, for the addition of the anion (MeS-), which is the reactive species, the order changes and N-methylated 2-vinylpyridinium ion, 2,3-butadienamide, and maleimide may give more easily the anionic adducts than several activated triple bonds; moreover, the calculated ΔG⧧ values increase following the order HC≡C-SO2NHMe, N-methylmaleimide, HC≡C-PO(OMe)NHMe, and HC≡C-CONHMe. In other words, MeS- is predicted to react more rapidly with maleimides than with ethynephosphonamidates and with propynamides, in agreement with the experimental results. New mechanistic details are disclosed regarding the advantageous use of some amides, especially of ethynesulfonamides, which, however, are more prone to double additions and exchange reactions.
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Affiliation(s)
- Anna M. Costa
- Organic
Chemistry Section,
Facultat de Química, Universitat
de Barcelona, Diagonal 645, Barcelona 08028, Catalonia, Spain
| | - Lluís Bosch
- Organic
Chemistry Section,
Facultat de Química, Universitat
de Barcelona, Diagonal 645, Barcelona 08028, Catalonia, Spain
| | - Elena Petit
- Organic
Chemistry Section,
Facultat de Química, Universitat
de Barcelona, Diagonal 645, Barcelona 08028, Catalonia, Spain
| | - Jaume Vilarrasa
- Organic
Chemistry Section,
Facultat de Química, Universitat
de Barcelona, Diagonal 645, Barcelona 08028, Catalonia, Spain
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18
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Benzene-1,3-diol derivatives as the inhibitors of butyrylcholinesterase: An emergent target of Alzheimer’s disease. JOURNAL OF THE SERBIAN CHEMICAL SOCIETY 2021. [DOI: 10.2298/jsc210416073d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Molecular docking is a powerful and significant approach for the identification of lead molecules on the basis of virtual screening. With it a large number of compounds can be tested and based on the scoring function and ranking, the conclusion can be made about how the selected compounds can inhibit the targeted protein/receptor. Considering the importance of selective inhibitors of cholinesterase in the treatment of Alzheimer disease, this research is focused on the determination of the mechanism of binding interactions of few benzene-1,3-diol derivatives within the active site of both acetyl-choline-sterase (AChE) and butyrylcholinesterase (BChE). All the selective ligands were found to have a greater binding affinity with the BChE when compared to that of AChE, by an average value of ~?28.4 and ~?12.5 kJ/mol, respectively. The results suggested that the identified inhibitors can be used as the lead com-pounds for the development of novel inhibitors of the targeted enzymes against some specific diseases, thus opening the possibility of new therapeutic strategies.
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19
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Ciou JM, Zhu HF, Chang CW, Chen JY, Lin YF. Physical organic studies and dynamic covalent chemistry of picolyl heterocyclic amino aminals. RSC Adv 2020; 10:40421-40427. [PMID: 35520848 PMCID: PMC9057465 DOI: 10.1039/d0ra08527h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 10/30/2020] [Indexed: 12/03/2022] Open
Abstract
A dynamic covalent system of the picolyl heterocyclic amino aminals has been studied. The aminals are characterized as a metastable species and easily switch to other forms via external stimuli. The solvent, temperature, acid-base and substituent effects have been examined to evaluate the dynamic covalent system. The results reveal that a more polar solvent, a lower temperature, basic conditions and an electron-withdrawing moiety contribute to the stabilities of aminals. The existence of the n → π* interaction between acetonitrile and the C[double bond, length as m-dash]N moiety makes the N-pyrimidyl imine (4c and 4d) yield higher in CD3CN. In a similar fashion, all aminals tend to convert to the corresponding hemiaminal ethers in a methanol environment. According to these findings, we successfully synthesized the following species: (a) N-2-picolylpyrimidin-2-amine 6c obtained by reduction using acetonitrile as the specific solvent; (b) a picolyl aromatic amino aminal 3e prepared from 2-pyridinecarboxaldehyde and the electron withdrawing 2-methoxy-5-nitroaniline.
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Affiliation(s)
- Ji-Ming Ciou
- Department of Fragrance and Cosmetic Science, Kaohsiung Medical University 100 Shi-Chuan 1st Rd., San-Ming Dist. Kaohsiung 80708 Taiwan
| | - Hong-Feng Zhu
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University Kaohsiung 80708 Taiwan
| | - Chia-Wen Chang
- Department of Fragrance and Cosmetic Science, Kaohsiung Medical University 100 Shi-Chuan 1st Rd., San-Ming Dist. Kaohsiung 80708 Taiwan
| | - Jing-Yun Chen
- Department of Fragrance and Cosmetic Science, Kaohsiung Medical University 100 Shi-Chuan 1st Rd., San-Ming Dist. Kaohsiung 80708 Taiwan
| | - Ya-Fan Lin
- Department of Fragrance and Cosmetic Science, Kaohsiung Medical University 100 Shi-Chuan 1st Rd., San-Ming Dist. Kaohsiung 80708 Taiwan
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University Kaohsiung 80708 Taiwan
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20
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Castro-Alvarez A, Carneros H, Calafat J, Costa AM, Marco C, Vilarrasa J. NMR and Computational Studies on the Reactions of Enamines with Nitroalkenes That May Pass through Cyclobutanes. ACS OMEGA 2019; 4:18167-18194. [PMID: 31720519 PMCID: PMC6844152 DOI: 10.1021/acsomega.9b02074] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
The addition of aldehyde enamines to nitroalkenes affords cyclobutanes in all solvents, with all of the pyrrolidine and proline derivatives tested by us and with all of the substrates we have examined. Depending on the temperature, concentration of water, solvent polarity, and other factors, the opening and hydrolysis of such a four-membered ring may take place rapidly or last for several days, producing the final Michael-like adducts (4-nitrobutanals). Thirteen new cyclobutanes have now been characterized by NMR spectroscopy. As could be expected, s-trans-enamine conformers give rise to all-trans-(4S)-4-nitrocyclobutylpyrrolidines, while s-cis-enamine conformers afford all-trans-(4R)-4-nitrocyclobutylpyrrolidines. These four-membered rings can isomerize to adduct enamines, which should be hydrolyzed via their iminium ions. MP2 and M06-2X calculations predict that one iminium ion is more stable than the other iminium species, so that protonation of the adduct enamines can be quite stereoselective; in the presence of water, the so-called syn adducts (e.g., OCH-*CHR-*CHPh-CH2NO2, with R and Ph syn) eventually become the major products. Why one syn adduct is obtained with aldehydes, whereas cyclic ketones (the predicted ring-fused cyclobutanes of which isomerize to their enamines more easily) produce the other syn adduct, is also explained by means of molecular orbital calculations. Nitro-Michael reactions of aldehyde enamines that "stop" at the nitrocyclobutane stage and final enamine stage do not work catalytically, as known, but those of cyclic ketone enamines that do not work stop at the final enamine stage (if their hydrolysis to the corresponding nitroethylketones is less favorable than expected). These and other facts are accounted for, and the proposals of the groups led by Seebach and Hayashi, Blackmond, and Pihko and Papai are reconciled.
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21
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Nie B, Li R, Wu Y, Yuan X, Zhang W. Theoretical Calculation of the Thermodynamic Properties of 20 Amino Acid Ionic Liquids. J Phys Chem B 2018; 122:10548-10557. [PMID: 30359517 DOI: 10.1021/acs.jpcb.8b06813] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The thermodynamic properties of gas-phase amino acid ionic liquids (AAILs) containing 20 amino acids ([AA]-) and 1-ethyl-3-methylimidazolium ([Emim]+) are studied using a combination of the ab initio method, molecular dynamics simulations, Born-Haber (BH) cycle analysis, and isodesmic reactions. The M06-2X/TZVP method is used to explore the structure and dissociation enthalpies of [Emim][AA] by considering dispersion interaction, and the MP2/Aug-cc-pVTZ method is used to correct these enthalpies. The vaporization enthalpies of all 20 AAILs are calculated by molecular dynamics simulations, and the gas-phase formation enthalpies (Δf H) of the 20 [AA]- anions and [Emim]+ cation are calculated by the density functional theory/M06-2X method and isodesmic reaction approaches. To obtain the Δf H of the AAILs, interconnections in the corresponding BH cycles are evaluated. A systematic study of the 20 [Emim][AA] ion pairs provides some initial factors contributing to the thermodynamic properties of AAILs: including length of the alkyl chain, interatomic electronic effects, steric repulsion from the cyclic group, and H-bonds formed by functional groups. Generally speaking, the results of this work provide insights into the structure-property relationships of not only ILs but also any ionic or molecular substance.
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22
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Pandey J, Prajapati P, Srivastava A, Tandon P, Sinha K, Ayala AP, Bansal AK. Spectroscopic and molecular structure (monomeric and dimeric model) investigation of Febuxostat: A combined experimental and theoretical study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 203:1-12. [PMID: 29852375 DOI: 10.1016/j.saa.2018.05.074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 05/20/2018] [Indexed: 06/08/2023]
Abstract
Febuxostat (FXT) is a urate-lowering drug and xanthine oxidase inhibitor which is used for the treatment of hyperuricemia and gout caused by increased levels of uric acid in the blood (hyperuricemia). The present study aims to provide deeper knowledge of the structural, vibrational spectroscopic and physiochemical properties of FXT based on monomeric and dimeric model with the aid of combination of experimental and computational methods. The conformational analysis of form Q has been done to predict the possible structure of unknown form A. Vibrational spectra of form A and Q has been compared to get an idea of hydrogen bonding interactions of form A. A computational study of FXT has been executed at different level (B3LYP, M06-2X, WB97XD) of theory and 6-31 G (d, p) basis set for dimeric model to elucidate the nature of intermolecular hydrogen bond. The red shift observed in the stretching modes of OH, CO groups and blue shift in stretching mode of CN group in experimental as well as in theoretical spectra explains the involvement of these groups in intermolecular hydrogen bonding. NBO analysis shows that change in electron density (ED) in the lone pair orbital to σ* antibonding orbital (LP1 (N39) → σ* (O3-H38)) with maximum value of E(2) energy confirms the presence of hydrogen bond (N39⋯H38-O3) leading to dimer formation. Study of topological parameters was executed for dimer using Bader's atoms in molecules (AIM) theory predicting the partially covalent nature of hydrogen bonds present in the molecule. The study of molecular electrostatic potential surface (MEPS) map ascertains that the CO, CN group are prone to electrophilic attack and OH group is active towards nucleophilic attack. The lower energy band gap and higher value of softness of dimeric model of FXT indicates its more reactivity, polarisability than monomeric model. The local reactivity descriptors predict the order of reactive sites towards electrophilic, nucleophilic and radical attack. An investigation made to determine the ligand protein interaction of FXT through docking with different molecular targets reveals the inhibitive as well as antibacterial nature of FXT.
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Affiliation(s)
- Jaya Pandey
- Department of Physics, University of Lucknow, Lucknow 226007, India
| | - Preeti Prajapati
- Department of Physics, University of Lucknow, Lucknow 226007, India
| | | | - Poonam Tandon
- Department of Physics, University of Lucknow, Lucknow 226007, India.
| | - Kirti Sinha
- Department of Physics, University of Lucknow, Lucknow 226007, India
| | - Alejandro P Ayala
- Departamento de Fisica, Universidade Federal do Ceará, C.P. 6030, 60.455-900 Fortaleza, CE, Brazil
| | - Arvind K Bansal
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Sector-67, S.A.S. Nagar, Punjab 160062, India
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23
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Exploring the effect of confinement on water clusters in carbon nanotubes. J Mol Model 2017; 23:133. [PMID: 28341994 DOI: 10.1007/s00894-017-3299-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 02/27/2017] [Indexed: 10/19/2022]
Abstract
Using armchair-type single-walled carbon nanotubes (SWCNTs) of different sizes as model compounds for lignite, the effect of water molecule confinement on the water-holding capacity of lignite pores was investigated. Results indicated that the water-holding capacity of pores with diameters of <10 nm was eight times larger than that of pores with diameters of 100 nm. The configuration of the cluster of water molecules in each SWCNT and the binding energy between each SWCNT and the water molecules within it were calculated by means of density functional theory using a hybrid functional: M06-2X/6-311+G**, 6-31G*. The results prove that the configurations of the water molecules in the SWCNTs are very different to their configuration in the unconfined state. In vacuum, the cluster of three water molecules adopted a trimer configuration, while they presented a linear configuration in the 6.78 Å SWCNT. Similarly, in vacuum, the cluster of five water molecules formed a five-membered ring, while they favored a linear configuration in the 6.78 Å SWCNT, a zigzag configuration in the 8.14 Å SWCNT, and a trimer + 1 + 1 configuration (i.e., a trimer plus two isolated water molecules) in the 9.49 Å, 10.85 Å, and 13.75 Å SWCNTs. There was found to be a degree of competition between the coupling energy of the water molecules with the SWCNT and the hydrogen bonding among the water molecules. When the diameter of the SWCNT was >1 nm, the hydrogen bonding among the water molecules dominated, while the coupling energy of the water molecules with the SWCNT amounted to only 30-40% of the total interaction energy of the water molecules. Graphical Abstract Computed equilibrium structures of five water molecules confined in SWCNTs with diameters of 6.78 Å, 8.14 Å, 9.49 Å, 10.85 Å, and 13.75 Å, and in vacuum.
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24
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Chen J, Guo W, Xia Y. Computational Revisit to the β-Carbon Elimination Step in Rh(III)-Catalyzed C–H Activation/Cycloaddition Reactions of N-Phenoxyacetamide and Cyclopropenes. J Org Chem 2016; 81:2635-8. [DOI: 10.1021/acs.joc.6b00003] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Jiajia Chen
- College of Chemistry and
Materials Engineering, Wenzhou University, Wenzhou 325035, P. R. China
| | - Wei Guo
- College of Chemistry and
Materials Engineering, Wenzhou University, Wenzhou 325035, P. R. China
| | - Yuanzhi Xia
- College of Chemistry and
Materials Engineering, Wenzhou University, Wenzhou 325035, P. R. China
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25
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Grimblat N, Sarotti AM, Kaufman TS, Simonetti SO. A theoretical study of the Duff reaction: insights into its selectivity. Org Biomol Chem 2016; 14:10496-10501. [DOI: 10.1039/c6ob01887d] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The selectivity-determining step of the Duff ortho-formylation was studied using DFT calculations; a hydrogen bond establishes the position where the formylation will take place.
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Affiliation(s)
- Nicolás Grimblat
- Instituto de Química Rosario (IQUIR
- CONICET-UNR)
- Facultad de Ciencias Bioquímicas y Farmacéuticas
- Universidad Nacional de Rosario
- Rosario (2000)
| | - Ariel M. Sarotti
- Instituto de Química Rosario (IQUIR
- CONICET-UNR)
- Facultad de Ciencias Bioquímicas y Farmacéuticas
- Universidad Nacional de Rosario
- Rosario (2000)
| | - Teodoro S. Kaufman
- Instituto de Química Rosario (IQUIR
- CONICET-UNR)
- Facultad de Ciencias Bioquímicas y Farmacéuticas
- Universidad Nacional de Rosario
- Rosario (2000)
| | - Sebastian O. Simonetti
- Instituto de Química Rosario (IQUIR
- CONICET-UNR)
- Facultad de Ciencias Bioquímicas y Farmacéuticas
- Universidad Nacional de Rosario
- Rosario (2000)
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