1
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Luo Z, Liao M, Li W, Zhao S, Tang K, Zheng P, Chi YR, Zhang X, Wu X. Ionic Hydrogen Bond-Assisted Catalytic Construction of Nitrogen Stereogenic Center via Formal Desymmetrization of Remote Diols. Angew Chem Int Ed Engl 2024; 63:e202404979. [PMID: 38745374 DOI: 10.1002/anie.202404979] [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: 03/13/2024] [Revised: 04/23/2024] [Accepted: 05/14/2024] [Indexed: 05/16/2024]
Abstract
The control of noncarbon stereogenic centers is of profound importance owing to their enormous interest in bioactive compounds and chiral catalyst or ligand design for enantioselective synthesis. Despite various elegant approaches have been achieved for construction of S-, P-, Si- and B-stereocenters over the past decades, the catalyst-controlled strategies to govern the formation of N-stereogenic compounds have garnered less attention. Here, we disclose the first organocatalytic approach for efficient access to a wide range of nitrogen-stereogenic compounds through a desymmetrization approach. Intriguingly, the pro-chiral remote diols, which are previously not well addressed with enantiocontrol, are well differentiated by potent chiral carbene-bound acyl azolium intermediates. Preliminary studies shed insights on the critical importance of the ionic hydrogen bond (IHB) formed between the dimer aggregate of diols to afford the chiral N-oxide products that feature a tetrahedral nitrogen as the sole stereogenic element with good yields and excellent enantioselectivities. Notably, the chiral N-oxide products could offer an attractive strategy for chiral ligand design and discovery of potential antibacterial agrochemicals.
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Grants
- National Natural Science Fund for Excellent Young Scientists Fund Program (Overseas)-YQHW
- the starting grant of Guizhou University [(2022)47)]
- National Natural Science Foundation of China (21732002, 22061007, 22071036, and 22207022)
- Frontiers Science Center for Asymmetric Synthesis and Medicinal Molecules
- Department of Education, Science and Technology Department of Guizhou Province [Qiankehe-jichu-ZK[2022]zhongdian024]
- Program of Introducing Talents of Discipline to Universities of China (111 Program, D20023) at Guizhou University
- Singapore National Research Foundation under its NRF Investigatorship (NRF-NRFI2016-06) and Competitive Research Program (NRF-CRP22-2019-0002)
- Ministry of Education, Singapore, under its MOE AcRF Tier 1 Award (RG7/20, RG70/21), MOE AcRF Tier 2 (MOE2019-T2-2-117)
- a Chair Professorship Grant, and Nanyang Technological University
- (2022)47 starting grant of Guizhou University
- 21732002 National Natural Science Foundation of China
- 22061007 National Natural Science Foundation of China
- 22071036 National Natural Science Foundation of China
- 22207022 National Natural Science Foundation of China
- Qiankehe-jichu-ZK[2022]zhongdian024 Department of Education, Science and Technology Department of Guizhou Province
- Qiankehejichu-ZK[2024]yiban030 Department of Education, Science and Technology Department of Guizhou Province
- NRF-NRFI2016-06 Singapore National Research Foundation under its NRF Investigatorship and Competitive Research Program
- NRF-CRP22-2019-0002 Singapore National Research Foundation under its NRF Investigatorship and Competitive Research Program
- RG7/20, RG70/21 Ministry of Education, Singapore, under its MOE AcRF Tier 1 Award, MOE AcRF Tier 2
- MOE2019-T2-2-117 Ministry of Education, Singapore, under its MOE AcRF Tier 1 Award, MOE AcRF Tier 2
- Chair Professorship Grant, and Nanyang Technological University
- C210812008 Agency for Science, Technology and Research (A*STAR) under its Career Development Fund
- M22K3c0091 Manufacturing, TradeConnectivity (MTC) Young Individual Research Grants.
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Affiliation(s)
- Zhongfu Luo
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang, 550025, China
| | - Minghong Liao
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang, 550025, China
| | - Wei Li
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang, 550025, China
| | - Sha Zhao
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang, 550025, China
| | - Kun Tang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang, 550025, China
| | - Pengcheng Zheng
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang, 550025, China
| | - Yonggui Robin Chi
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang, 550025, China
- School of Chemistry, Chemical Engineering, and Biotechnology, Nanyang Technological University, Singapore, 637371, Singapore
| | - Xinglong Zhang
- Institute of High Performance Computing (IHPC), A*STAR, Singapore, 138632, Singapore
| | - Xingxing Wu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang, 550025, China
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2
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Mizuide A, Fujii A. Hydrogen bond network structures of protonated dimethylamine clusters H +(DMA) n ( n = 3-7). Phys Chem Chem Phys 2024; 26:19418-19432. [PMID: 38973623 DOI: 10.1039/d4cp01931h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Infrared spectroscopy of protonated dimethylamine clusters, H+(DMA)n, (n = 3-7), and their Ar-tagged clusters was performed in the NH and CH stretching vibrational region to explore their hydrogen bond network structures. A stable isomer search and vibrational spectral simulations of the clusters were also carried out to support the interpretations of the observed spectra. Weakly hydrogen-bonded NH stretching vibrational bands, which are characteristic of cyclic structures of small-sized protonated clusters, are observed in the spectra of the Ar-tagged clusters of n ≥ 5, while only linear chain type structures are suggested for the Ar-tagged clusters of n = 3-4 and the bare clusters of all the sizes. These results demonstrate that the size and temperature dependence of the hydrogen bond network structures of the protonated dimethylamine clusters is analogous to that of protonated monohydric alcohol clusters.
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Affiliation(s)
- Atsuya Mizuide
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Asuka Fujii
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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3
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Raczyńska ED, Gal JF, Maria PC. Strong Bases and beyond: The Prominent Contribution of Neutral Push-Pull Organic Molecules towards Superbases in the Gas Phase. Int J Mol Sci 2024; 25:5591. [PMID: 38891779 PMCID: PMC11172071 DOI: 10.3390/ijms25115591] [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: 04/24/2024] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
In this review, the principles of gas-phase proton basicity measurements and theoretical calculations are recalled as a reminder of how the basicity PA/GB scale, based on Brønsted-Lowry theory, was constructed in the gas-phase (PA-proton affinity and/or GB-gas-phase basicity in the enthalpy and Gibbs energy scale, respectively). The origins of exceptionally strong gas-phase basicity of some organic nitrogen bases containing N-sp3 (amines), N-sp2 (imines, amidines, guanidines, polyguanides, phosphazenes), and N-sp (nitriles) are rationalized. In particular, the role of push-pull nitrogen bases in the development of the gas-phase basicity in the superbasicity region is emphasized. Some reasons for the difficulties in measurements for poly-functional nitrogen bases are highlighted. Various structural phenomena being in relation with gas-phase acid-base equilibria that should be considered in quantum-chemical calculations of PA/GB parameters are discussed. The preparation methods for strong organic push-pull bases containing a N-sp2 site of protonation are briefly reviewed. Finally, recent trends in research on neutral organic superbases, leaning toward catalytic and other remarkable applications, are underlined.
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Affiliation(s)
- Ewa Daniela Raczyńska
- Department of Chemistry, Warsaw University of Life Sciences (SGGW), ul. Nowoursynowska 159c, 02-776 Warsaw, Poland
| | - Jean-François Gal
- Institut de Chimie de Nice, UMR 7272, Université Côte d’Azur, Parc Valrose, 06108 Nice, France;
| | - Pierre-Charles Maria
- Institut de Chimie de Nice, UMR 7272, Université Côte d’Azur, Parc Valrose, 06108 Nice, France;
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4
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Zhang B, Burchill L, Altalhi WAO, Ma HZ, O'Hair RAJ. A fixed-charge model of the N-protomer of 4-aminobenzoic acid to facilitate the study of the unimolecular and bimolecular chemistry of its "neutral" carboxylic acid group. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024; 38:e9681. [PMID: 38355884 DOI: 10.1002/rcm.9681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/24/2023] [Accepted: 11/25/2023] [Indexed: 02/16/2024]
Abstract
RATIONALE There are a growing number of examples of protomers formed via electrospray ionization (ESI) that do not fragment under mobile proton conditions, giving rise to distinct tandem mass spectra. To model the N-protomer of 4-aminobenzoic acid, here we study the gas-phase unimolecular and bimolecular chemistry of the 4-(carboxyphenyl)trimethylammonium ion. METHODS 4-(Carboxyphenyl)trimethylammonium iodide was synthesized, purified via recrystallization and transferred to the gas phase via ESI. 4-(Carboxyphenyl)trimethylammonium ion, 7, was mass selected and subjected to collision-induced dissociation and ion-molecule reactions in a linear ion trap mass spectrometer. RESULTS The major fragmentation channel for the fixed-charge cation 7 is methyl radical loss, whereas loss of trimethylamine and CO2 represents minor pathways. The free carboxylic acid functional group of 7 is unreactive toward a number of neutral reagents (methanol, acetone, acetonitrile, and N,N'-diisopropylcarbodiimide). 7 reacts very slowly with trimethylborate via addition-elimination, consistent with density functional theory (DFT) calculations that show this reaction is slightly endothermic. The deuterated cation 7(D) undergoes slow D/H exchange with ethanol, and DFT calculations reveal that a flip-flop mechanism operates. CONCLUSIONS The free carboxylic group of 7 is not very reactive toward neutral reagents in the gas phase.
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Affiliation(s)
- Beiang Zhang
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Laura Burchill
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Weam A O Altalhi
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
- Department of Chemistry, Prince Sattam Bin Abdulaziz University, Hotat Bani Tamim, Saudi Arabia
| | - Howard Z Ma
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Richard A J O'Hair
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
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5
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Martínez-Haya B, Avilés-Moreno JR, Gámez F, Martens J, Oomens J, Berden G. Correlated proton dynamics in hydrogen bonding networks: the benchmark case of 3-hydroxyglutaric acid. Phys Chem Chem Phys 2023; 26:198-208. [PMID: 38053486 DOI: 10.1039/d3cp04514e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Proton and hydrogen-bonded networks sustain a broad range of structural and charge transfer processes in supramolecular materials. The modelling of proton dynamics is however challenging and demands insights from prototypical benchmark systems. The intramolecular H-bonding networks induced by either protonation or deprotonation of 3-hydroxyglutaric acid provide intriguing case studies of correlated proton dynamics. The vibrational signatures associated with the fluxional proton bonding and its coupling with the hydroxyglutaric backbone are investigated here with infrared action ion spectroscopy experiments and Born-Oppenheimer molecular dynamics (BOMD) computations. Despite the formally similar symmetry of protonated and deprotonated hydroxyglutaric acid, the relative proton affinities of the oxygen centers of the carboxylic and carboxylate groups with respect to that of the central hydroxyl group lead to distinct proton dynamics. In the protonated acid, a tautomeric arrangement of the type HOCO·[HOH]+·OCOH is preferred with the proton binding tighter to the central hydroxyl moiety and the electronic density being shared between the two nearly symmetric H-bonds with the carboxylic end groups. In the deprotonated acid, the asymmetric [OCO]-·HO·HOCO configuration is more stable, with a stronger H-bonding on the bare carboxylate end. Both systems display active backbone dynamics and concerted Grothuss-like proton motions, leading to diffuse band structures in their vibrational spectra. These features are accurately reproduced by the BOMD computations.
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Affiliation(s)
- Bruno Martínez-Haya
- Center for Nanoscience and Sustainable Technologies (CNATS), Universidad Pablo de Olavide, E-41013 Seville, Spain.
| | - Juan Ramón Avilés-Moreno
- Department of Applied Physical Chemistry, Universidad Autónoma de Madrid, E-28049, Madrid, Spain
| | - Francisco Gámez
- Departamento de Química Física, Universidad Complutense, E-28040 Madrid, Spain
| | - Jonathan Martens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Jos Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Giel Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
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6
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Kato T, Fujii A. Experimental confirmation of the Badger-Bauer rule in the protonated methanol clusters: weak hydrogen bond formation as a measure of terminal OH acidity in hydrogen bond networks. Phys Chem Chem Phys 2023; 25:30188-30192. [PMID: 37920966 DOI: 10.1039/d3cp04644c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
We report a linear correlation between the OH stretch frequency shift of the protonated methanol cluster, H+(MeOH)n, upon the π-hydrogen bond formation with benzene and the enthalpy change in clustering of H+(MeOH)n to H+(MeOH)n+1. This result suggests a new method to explore hydrogen bond strength in hydrogen bond networks.
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Affiliation(s)
- Takeru Kato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Asuka Fujii
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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7
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Luo C, Wang X, Liu Y, Cai J, Lu X, Cai Y. Like-Charge PISA: Polymerization-Induced Like-Charge Electrostatic Self-Assembly. ACS Macro Lett 2023; 12:1045-1051. [PMID: 37440526 DOI: 10.1021/acsmacrolett.3c00372] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
We report the use of l-aspartic acid chiral ionic hydrogen bonds to drive liquid-liquid phase separation (LLPS) and precision two-dimensional electrostatic self-assembly in photo-RAFT aqueous polymerization-induced self-assembly (photo-PISA). Homopolymerization can yield salt-resistant, 3 nm ultrafine fibril-structured 5 nm ultrathin lamellae via LLPS, a left-to-right-handed chirality transition, and a droplets-to-lamellae transition. Like-charge block copolymerization leads to supercharged yet identical fibril-structured ultrathin lamellae, also, via LLPS, the left-to-right chirality transition and the droplets-to-lamellae transition. Ultrafine structures maintain intactness upon the seeded polymerization of the oppositely charged monomer. This work demonstrates that amino acid chiral ionic hydrogen bonds are powerful for the precision synthesis of salt-resistant ultrathin membrane nanomaterials.
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Affiliation(s)
- Caihui Luo
- State-Local Joint Engineering Laboratory for Novel Functional Polymer Materials, Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Xiyu Wang
- State-Local Joint Engineering Laboratory for Novel Functional Polymer Materials, Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Yuanyuan Liu
- State-Local Joint Engineering Laboratory for Novel Functional Polymer Materials, Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Jie Cai
- State-Local Joint Engineering Laboratory for Novel Functional Polymer Materials, Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Xinhua Lu
- State-Local Joint Engineering Laboratory for Novel Functional Polymer Materials, Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Yuanli Cai
- State-Local Joint Engineering Laboratory for Novel Functional Polymer Materials, Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
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8
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Pahlavan F, Ghasemi H, Yazdani H, Fini EH. Soil amended with Algal Biochar Reduces Mobility of deicing salt contaminants in the environment: An atomistic insight. CHEMOSPHERE 2023; 323:138172. [PMID: 36804634 DOI: 10.1016/j.chemosphere.2023.138172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Soil-based filter media in green infrastructure buffers only a minor portion of deicing salt in surface water, allowing most of that to infiltrate into groundwater, thus negatively impacting drinking water and the aquatic ecosystem. The capacity of the filter medium to adsorb and fixate sodium (Na+) and chloride (Cl-) ions has been shown to improve by biochar amendment. The extent of improvement, however, depends on the type and density of functional groups on the biochar surface. Here, we use density functional theory (DFT) and molecular dynamics (MD) simulations to show the merits of biochar grafted by nitrogenous functional groups to adsorb Cl-. Our group has shown that such functional groups are abundant in biochar made from protein-rich algae feedstock. DFT is used to model algal biochar surface and its possible interactions with Cl- through two possible mechanisms: direct adsorption and cation (Na+)-bridging. Our DFT calculations reveal strong adsorption of Cl- to the biochar surface through hydrogen bonding and electrostatic attractions between the ions and active sites on biochar. MD results indicate the efficacy of algal biochar in delaying chloride diffusion. This study demonstrates the potential of amending soils with algal biochar as a dual-targeting strategy to sequestrate carbon and prevent deicing salt contaminants from leaching into water bodies.
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Affiliation(s)
- Farideh Pahlavan
- School of Sustainable Engineering and the Built Environment, Ira A. Fulton Schools of Engineering, Arizona State University, 660 S. College Avenue, Tempe, AZ 85287-3005, USA
| | - Hamid Ghasemi
- School of Sustainable Engineering and the Built Environment, Ira A. Fulton Schools of Engineering, Arizona State University, 660 S. College Avenue, Tempe, AZ 85287-3005, USA
| | - Hessam Yazdani
- Department of Civil and Environmental Engineering, University of Missouri , W1024 Lafferre Hall, MO 65211, Columbia
| | - Elham H Fini
- School of Sustainable Engineering and the Built Environment, Ira A. Fulton Schools of Engineering, Arizona State University, 660 S. College Avenue, Tempe, AZ 85287-3005, USA.
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9
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Liebman JF. Paradigms and paradoxes: stabilization, destabilization and resonance energy of α-diketones, dienes and derived radical ions. Struct Chem 2023. [DOI: 10.1007/s11224-023-02155-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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10
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Martínez-Haya B, Avilés-Moreno JR, Gámez F, Martens J, Oomens J, Berden G. A Dynamic Proton Bond: MH +·H 2O ⇌ M·H 3O + Interconversion in Loosely Coordinated Environments. J Phys Chem Lett 2023; 14:1294-1300. [PMID: 36723385 PMCID: PMC9923742 DOI: 10.1021/acs.jpclett.2c03832] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
The interaction of organic molecules with oxonium cations within their solvation shell may lead to the emergence of dynamic supramolecular structures with recurrently changing host-guest chemical identity. We illustrate this phenomenon in benchmark proton-bonded complexes of water with polyether macrocyles. Despite the smaller proton affinity of water versus the ether group, water in fact retains the proton in the form of H3O+, with increasing stability as the coordination number increases. Hindrance in many-fold coordination induces dynamic reversible (ether)·H3O+ ⇌ (etherH+)·H2O interconversion. We perform infrared action ion spectroscopy over a broad spectral range to expose the vibrational signatures of the loose proton bonding in these systems. Remarkably, characteristic bands for the two limiting proton bonding configurations are observed in the experimental vibrational spectra, superimposed onto diffuse bands associated with proton delocalization. These features cannot be described by static equilibrium structures but are accurately modeled within the framework of ab initio molecular dynamics.
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Affiliation(s)
- Bruno Martínez-Haya
- Department
of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, 41013 Seville, Spain
| | | | - Francisco Gámez
- Departamento
de Química Física, Universidad Complutense, 28040 Madrid, Spain
| | - Jonathan Martens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Jos Oomens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Giel Berden
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
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11
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Properties of Gaseous Deprotonated L-Cysteine S-Sulfate Anion [cysS-SO 3] -: Intramolecular H-Bond Network, Electron Affinity, Chemically Active Site, and Vibrational Fingerprints. Int J Mol Sci 2023; 24:ijms24021682. [PMID: 36675196 PMCID: PMC9862062 DOI: 10.3390/ijms24021682] [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: 12/03/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
L-cysteine S-sulfate, Cys-SSO3H, and their derivatives play essential roles in biological chemistry and pharmaceutical synthesis, yet their intrinsic molecular properties have not been studied to date. In this contribution, the deprotonated anion [cysS-SO3]- was introduced in the gas phase by electrospray and characterized by size-selected, cryogenic, negative ion photoelectron spectroscopy. The electron affinity of the [cysS-SO3]• radical was determined to be 4.95 ± 0.10 eV. In combination with theoretical calculations, it was found that the most stable structure of [cysS-SO3]- (S1) is stabilized via three intramolecular hydrogen bonds (HBs); i.e., one O-H⋯⋯N between the -COOH and -NH2 groups, and two N-H⋯⋯O HBs between -NH2 and -SO3, in which the amino group serves as both HB acceptor and donor. In addition, a nearly iso-energetic conformer (S2) with the formation of an O-H⋯⋯N-H⋯⋯O-S chain-type binding motif competes with S1 in the source. The most reactive site of the molecule susceptible for electrophilic attacks is the linkage S atom. Theoretically predicted infrared spectra indicate that O-H and N-H stretching modes are the fingerprint region (2800 to 3600 cm-1) to distinguish different isomers. The obtained information lays out a foundation to better understand the transformation and structure-reactivity correlation of Cys-SSO3H in biologic settings.
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12
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SADOON AM. Theoretical Investigation of the Structures and Energetics of (MX)-Ethanol Complexes in the Gas Phase. JOURNAL OF THE TURKISH CHEMICAL SOCIETY, SECTION A: CHEMISTRY 2022. [DOI: 10.18596/jotcsa.1146250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The structures and energy of alkali halide salt (MX) complexes with ethanol have been investigated in this work. The core of this study is to explore the effect of ion size on the interactions between solvent and solute. LiF and KBr as monovalent salts with different sizes of inion and cation have been chosen to explore this difference in addition to various physical properties. Three complexes of each LiF and KBr with ethanol taking the formula MX(CH3CH2OH)n (n=1-3), were studied. Ab-initio calculations have been performed to optimize the chemical structures of these complexes and explore the possible structures, isomers, and their corresponding IR spectra using Density functional theory (DFT/ B3LYP). 6-311G** were chosen as basis sets for these calculations. The geometry evaluations, energy searches, vibrational frequency calculations, and each complex's binding energy were also theoretically extracted in this study. The minimum energy structures were calculated, and different isomers were found. The presence of Ionic hydrogen bonds (IHBs) was observed and proposed to be the main binding between the MX salt and ethanol. Also, the infrared vibrational bands in the OH stretching region were recorded for the minimum structures, and the determined red-shift was at about 400 cm-1. In addition, the binding energy calculations found a gradual rise in the BE value with every additional ethanol molecule added to MX salt.
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13
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van Walree CA. Intramolecular Hydrogen Bonding in DIBMA Model Compounds. MACROMOL THEOR SIMUL 2022. [DOI: 10.1002/mats.202200042] [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)
- Cornelis A. van Walree
- Membrane Biochemistry and Biophysics Utrecht University Padualaan 8 Utrecht 3584 CH Netherlands
- University College Utrecht Campusplein 1 Utrecht 3584 ED the Netherlands
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14
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Xiong W, Wang X, Liu Y, Luo C, Lu X, Cai Y. Polymerization-Induced Electrostatic Self-Assembly Governed by Guanidinium Ionic Hydrogen Bonds. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c01323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Weixing Xiong
- State-Local Joint Engineering Laboratory for Novel Functional Polymer Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Xiyu Wang
- State-Local Joint Engineering Laboratory for Novel Functional Polymer Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Yuanyuan Liu
- State-Local Joint Engineering Laboratory for Novel Functional Polymer Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Caihui Luo
- State-Local Joint Engineering Laboratory for Novel Functional Polymer Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Xinhua Lu
- State-Local Joint Engineering Laboratory for Novel Functional Polymer Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Yuanli Cai
- State-Local Joint Engineering Laboratory for Novel Functional Polymer Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
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15
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Christensen ZA, Pearcy AC, Mason KA, El-Shall MS. Gas-Phase External Solvation of Protonated Benzonitrile by Eight Methanol Molecules. J Phys Chem A 2022; 126:5160-5166. [PMID: 35917155 DOI: 10.1021/acs.jpca.2c03715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The gas-phase sequential association of methanol onto protonated benzonitrile (C6H5CNH+) and the proton-bound dimer (C6H5CN)2H+ have been examined experimentally by equilibrium thermochemical measurements and computationally by density functional theory (DFT). The bonding enthalpy (ΔH°) for the association of methanol with protonated benzonitrile (25.2 kcal mol-1) reflects the strong electrostatic interaction provided by the formation of an ionic hydrogen bond in the C6H5CNH+OHCH3 cluster in excellent agreement with a DFT-calculated binding energy of 24.9 kcal mol-1. The sequential bonding enthalpy within the (C6H5CN)H+(OHCH3)n clusters decreases from 25.2 to 10.6 kcal mol-1 for the eighth solvation step (n = 8), which remains more than 25% above the enthalpy of vaporization of liquid methanol (8.4 kcal mol-1). The nonbulk convergence of ΔH°n-1,n with eight solvent molecules is attributed to the external solvation of a benzonitrile molecule by an extended hydrogen bonding network of protonated methanol clusters H+(CH3OH)n. In the external solvation of protonated benzonitrile by methanol, the proton resides on the methanol subcluster and the neutral benzonitrile molecule remains outside and bonded to the surface of the protonated methanol cluster. The bonding enthalpy of methanol to the proton-bound benzonitrile dimer (C6H5CN)H+(NCC6H5) is measured to be 18.0 kcal mol-1, in good agreement with a DFT-calculated value of 17.1 kcal mol-1, which reflects the association of the proton with the lower proton affinity methanol molecule, thus forming a highly stable structure of protonated methanol terminated by two ionic hydrogen bonds to the two benzonitrile molecules. The external solvation of benzonitrile by methanol ices in space allows benzonitrile to remain on the ice grain surface rather than being isolated inside the ice. This could provide accessibility for reactions with incoming ions and molecules or for photochemical processes by UV irradiation, leading to the formation of complex organics on the surface of ice grains.
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Affiliation(s)
- Zachary A Christensen
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | - Adam C Pearcy
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | - Kyle A Mason
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | - M Samy El-Shall
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
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16
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Mason KA, Pearcy AC, Christensen ZA, Attah IK, Meot-Ner Mautner M, El-Shall MS. Water-Assisted Proton Transfer in the Sequential Hydration of Benzonitrile Radical Cation C 6H 5CN •+(H 2O) n: Transition to Hydrated Distonic Cation •C 6H 4CNH +(H 2O) n with n ≥ 4. J Am Chem Soc 2022; 144:9684-9694. [PMID: 35609235 DOI: 10.1021/jacs.2c01143] [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 stepwise hydration of the benzonitrile•+ radical cation with one-seven H2O molecules was investigated experimentally and computationally with density functional theory in C6H5CN•+(H2O)n clusters. The stepwise binding energies (ΔHn-1,n°) were determined by equilibrium measurements for C6H5CN•+(H2O) and for •C6H4CNH+(H2O)n with n = 5, 6, and 7 to be 8.8 and 11.3, 11.0, and 10.0 kcal/mol, respectively. The populations of n = 2 and 3 of the C6H5CN•+(H2O)n clusters were observed only in trace abundance due to fast depletion processes leading to the formation of the hydrated distonic cations •C6H4CNH+(H2O)n with n = 4-7. The observed transition occurs between conventional radical cations hydrated on the ring in C6H5CN•+(H2O)n clusters with n = 1-3 and the protonated radical •C6H4CNH+ (distonic ion) formed by a proton transfer to the CN nitrogen and ionic hydrogen bonding to water molecules in •C6H4CNH+(H2O)n clusters with n = 4-7. The measured binding energy of the hydrated ion C6H5CN•+(H2O) (8.8 kcal/mol) is similar to that of the hydrated benzene radical cation (8.5 kcal/mol) that involves a relatively weak CHδ+···O hydrogen bonding interaction. Also, the measured binding energies of the •C6H4CNH+(H2O)n clusters with n = 5-7 are similar to those of the protonated benzonitrile (methanol)n clusters [C6H5CNH+(CH3OH)n, n = 5-7] that involve CNH+···O ionic hydrogen bonds. The proton shift from the para-•C ring carbon to the nitrogen of the benzonitrile radical cation is endothermic without solvent but thermoneutral for n = 1 and exothermic for n = 2-4 in C6H5CN•+(H2O)n clusters to form the distonic •C6H4CN···H+(OH2)n clusters. The distonic clusters •C6H4CN···H+(OH2)n constitute a new class of structures in radical ion/solvent clusters.
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Affiliation(s)
- Kyle A Mason
- Department of Chemistry, Virginia Commonwealth University, Richmond 23284-2006 Virginia, United States
| | - Adam C Pearcy
- Department of Chemistry, Virginia Commonwealth University, Richmond 23284-2006 Virginia, United States
| | - Zachary A Christensen
- Department of Chemistry, Virginia Commonwealth University, Richmond 23284-2006 Virginia, United States
| | - Isaac K Attah
- Department of Chemistry, Virginia Commonwealth University, Richmond 23284-2006 Virginia, United States
| | - Michael Meot-Ner Mautner
- Department of Chemistry, Virginia Commonwealth University, Richmond 23284-2006 Virginia, United States
| | - M Samy El-Shall
- Department of Chemistry, Virginia Commonwealth University, Richmond 23284-2006 Virginia, United States
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17
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Ultrafast proton-coupled isomerization in the phototransformation of phytochrome. Nat Chem 2022; 14:823-830. [PMID: 35577919 PMCID: PMC9252900 DOI: 10.1038/s41557-022-00944-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 04/01/2022] [Indexed: 11/08/2022]
Abstract
The biological function of phytochromes is triggered by an ultrafast photoisomerization of the tetrapyrrole chromophore biliverdin between two rings denoted C and D. The mechanism by which this process induces extended structural changes of the protein is unclear. Here we report ultrafast proton-coupled photoisomerization upon excitation of the parent state (Pfr) of bacteriophytochrome Agp2. Transient deprotonation of the chromophore's pyrrole ring D or ring C into a hydrogen-bonded water cluster, revealed by a broad continuum infrared band, is triggered by electronic excitation, coherent oscillations and the sudden electric-field change in the excited state. Subsequently, a dominant fraction of the excited population relaxes back to the Pfr state, while ~35% follows the forward reaction to the photoproduct. A combination of quantum mechanics/molecular mechanics calculations and ultrafast visible and infrared spectroscopies demonstrates how proton-coupled dynamics in the excited state of Pfr leads to a restructured hydrogen-bond environment of early Lumi-F, which is interpreted as a trigger for downstream protein structural changes.
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18
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Godfrey RC, Jones HE, Green NJ, Lawrence AL. Unified total synthesis of the brevianamide alkaloids enabled by chemical investigations into their biosynthesis. Chem Sci 2022; 13:1313-1322. [PMID: 35222915 PMCID: PMC8809396 DOI: 10.1039/d1sc05801k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/27/2021] [Indexed: 01/08/2023] Open
Abstract
The bicyclo[2.2.2]diazaoctane alkaloids are a vast group of natural products which have been the focus of attention from the scientific community for several decades. This interest stems from their broad range of biological activities, their diverse biosynthetic origins, and their topologically complex structures, which combined make them enticing targets for chemical synthesis. In this article, full details of our synthetic studies into the chemical feasibility of a proposed network of biosynthetic pathways towards the brevianamide family of bicyclo[2.2.2]diazaoctane alkaloids are disclosed. Insights into issues of reactivity and selectivity in the biosynthesis of these structures have aided the development of a unified biomimetic synthetic strategy, which has resulted in the total synthesis of all known bicyclo[2.2.2]diazaoctane brevianamides and the anticipation of an as-yet-undiscovered congener.
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Affiliation(s)
- Robert C Godfrey
- EaStCHEM School of Chemistry, University of Edinburgh Joseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Helen E Jones
- EaStCHEM School of Chemistry, University of Edinburgh Joseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Nicholas J Green
- EaStCHEM School of Chemistry, University of Edinburgh Joseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Andrew L Lawrence
- EaStCHEM School of Chemistry, University of Edinburgh Joseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
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19
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Kato T, Fujii A. How many methanol molecules effectively solvate an excess proton in the gas phase? Infrared spectroscopy of H +(methanol) n-benzene clusters. Phys Chem Chem Phys 2021; 24:163-171. [PMID: 34878469 DOI: 10.1039/d1cp04689f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
An excess proton in a hydrogen-bonded system enhances the strength of hydrogen bonds of the surrounding molecules. The extent of this influence can be a measure of the number of molecules effectively solvating the excess proton. Such extent in methanol has been discussed by the observation of the π-hydrogen-bonded OH stretch bands of the terminal sites of protonated methanol clusters, H+(methanol)n, in benzene solutions, and it has been concluded that ∼8 molecules effectively solvate the excess proton (Stoyanov et al., Chem. Eur. J. 2008, 14, 3596-3604). In the present study, we performed infrared spectroscopy of H+(methanol)n-benzene clusters in the gas phase. The cluster size and hydrogen-bonded network structure are identified by the tandem mass spectrometric technique and the comparison of the observed infrared spectra with density functional theory calculations. Though changes of the preferred hydrogen bond network type occur with the increase of cluster size in the gas phase clusters, the observed size dependence of the π-hydrogen bonded OH frequency agrees well with that in the benzene solutions. This means that the observations in both the gas and condensed phases catch the same physical essence of the excess proton solvation by methanol.
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Affiliation(s)
- Takeru Kato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Asuka Fujii
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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20
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Darii E, Gimbert Y, Alves S, Damont A, Perret A, Woods AS, Fenaille F, Tabet JC. First Direct Evidence of Interpartner Hydride/Deuteride Exchanges for Stored Sodiated Arginine/Fructose-6-phosphate Complex Anions within Salt-Solvated Structures. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1424-1440. [PMID: 33929837 DOI: 10.1021/jasms.1c00040] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Mass spectrometric investigations of noncovalent binding between low molecular weight compounds revealed the existence of gas-phase (GP) noncovalent complex (NCC) ions involving zwitterionic structures. ESI MS is used to prove the formation of stable sodiated NCC anions between fructose (F6P) and arginine (R) moieties. Theoretical calculations indicate a folded solvated salt (i.e., sodiated carboxylate interacting with phosphate) rather than a charge-solvated form. Under standard CID conditions, [(F6P+R-H+Na)-H]- competitively forms two major product ions (PIs) through partner splitting [(R-H+Na) loss] and charge-induced cross-ring cleavage while preserving the noncovalent interactions (noncovalent product ions (NCPIs)). MS/MS experiments combined with in-solution proton/deuteron exchanges (HDXs) demonstrated an unexpected labeling of PIs, i.e., a correlated D-enrichment/D-depletion. An increase in activation time up to 3000 ms favors such processes when limited to two H/D exchanges. These results are rationalized by interpartner hydride/deuteride exchanges (⟨HDX⟩) through stepwise isomerization/dissociation of sodiated NCC-d11 anions. In addition, the D-enrichment/D-depletion discrepancy is further explained by back HDX with residual water in LTQ (selective for the isotopologue NCPIs as shown by PI relaxation experiments). Each isotopologue leads to only one back HDX unlike multiple HDXs generally observed in GP. This behavior shows that NCPIs are zwitterions with charges solvated by a single water molecule, thus generating a back HDX through a relay mechanism, which quenches the charges and prevents further back HDX. By estimating back HDX impact on D-depletion, the interpartner ⟨HDX⟩ complementarity was thus illustrated. This is the first description of interpartner ⟨HDX⟩ and selective back HDX validating salt-solvated structures.
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Affiliation(s)
- Ekaterina Darii
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Yves Gimbert
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Grenoble Alpes, 38058 Grenoble, France
- Sorbonne Université, Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), F-75005 Paris, France
| | - Sandra Alves
- Sorbonne Université, Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), F-75005 Paris, France
| | - Annelaure Damont
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - Alain Perret
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Amina S Woods
- NIDA IRP, NIH Structural Biology Unit Cellular Neurobiology Branch, 333 Cassell Drive, Baltimore, Maryland 21224, United States
- The Johns Hopkins University School of Medicine, Pharmacology and Molecular Sciences, Baltimore, Maryland 21205, United States
| | - François Fenaille
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - Jean-Claude Tabet
- Sorbonne Université, Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), F-75005 Paris, France
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
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21
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Ultrafast proton release reaction and primary photochemistry of phycocyanobilin in solution observed with fs-time-resolved mid-IR and UV/Vis spectroscopy. Photochem Photobiol Sci 2021; 20:715-732. [PMID: 34002345 DOI: 10.1007/s43630-021-00045-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/16/2021] [Indexed: 12/27/2022]
Abstract
Deactivation processes of photoexcited (λex = 580 nm) phycocyanobilin (PCB) in methanol were investigated by means of UV/Vis and mid-IR femtosecond (fs) transient absorption (TA) as well as static fluorescence spectroscopy, supported by density-functional-theory calculations of three relevant ground state conformers, PCBA, PCBB and PCBC, their relative electronic state energies and normal mode vibrational analysis. UV/Vis fs-TA reveals time constants of 2.0, 18 and 67 ps, describing decay of PCBB*, of PCBA* and thermal re-equilibration of PCBA, PCBB and PCBC, respectively, in line with the model by Dietzek et al. (Chem Phys Lett 515:163, 2011) and predecessors. Significant substantiation and extension of this model is achieved first via mid-IR fs-TA, i.e. identification of molecular structures and their dynamics, with time constants of 2.6, 21 and 40 ps, respectively. Second, transient IR continuum absorption (CA) is observed in the region above 1755 cm-1 (CA1) and between 1550 and 1450 cm-1 (CA2), indicative for the IR absorption of highly polarizable protons in hydrogen bonding networks (X-H…Y). This allows to characterize chromophore protonation/deprotonation processes, associated with the electronic and structural dynamics, on a molecular level. The PCB photocycle is suggested to be closed via a long living (> 1 ns), PCBC-like (i.e. deprotonated), fluorescent species.
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22
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Comparisons of NH…O and OH…O hydrogen bonds in various ethanolammonium–based protic ionic liquids. Struct Chem 2021. [DOI: 10.1007/s11224-021-01792-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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23
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Bessam S, Reguig FH, Krallafa AM, Martínez-Haya B. Dynamics of coordination of H 3O + and NH 4+ in crown ether cavities. Phys Chem Chem Phys 2021; 23:8633-8640. [PMID: 33876024 DOI: 10.1039/d1cp00575h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Crown ethers stand out for their ability to form inclusion complexes with metal cations and positively charged molecular moieties. Hydronium and ammonium interact strongly with crown ethers and potentially modulate their ionophoric activity in protic solvents and physiological environments commonly involved in (bio)technological applications. In this work, Born-Oppenheimer molecular dynamics (BOMD) computations are employed to gain insights into the coordination arrangements of H3O+ and NH4+ in the complexes with the native crown ethers 15-crown-5 (15c5) and 18-crown-6 (18c6). Both cations display dynamic changes in coordination inside the cavities of the crown ethers. On the one hand, hydronium explores different coordination arrangements, through rotation around its C3 axis in the 15c5 complex, and through breathing motions, involving rapid inversions of the O atom along the C3 axis in the 18c6 complex. On the other hand, ammonium undergoes a facile rotation in three dimensional space, leading to frequent changes in the NH bonds involved in the coordination with the crown ether. The reduced host-guest symmetry matching of the 15c5 macrocycle enhances the reorientation dynamics and, in the case of H3O+, it promotes short H-bonding distances yielding events of proton transfer to the crown ether. The infrared vibrational spectra predicted by the BOMD computations within this dynamic framework reproduce with remarkable accuracy the action spectra of the isolated complexes obtained in previous infrared laser spectroscopy experiments. The experimentally observed band positions and broadening can then be rationalized in terms of orientational diffusion of the cations, changes in the coordinating H-bonding pairs sustaining the complex and eventual proton bridge formation.
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Affiliation(s)
- S Bessam
- LCPM Laboratory, Faculty of Sciences, Chemistry Department, University of Oran 1, Ahmed BenBella, Oran, Algeria
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24
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Ogata K, Chang CH, Ishihama Y. Effect of Phosphorylation on the Collision Cross Sections of Peptide Ions in Ion Mobility Spectrometry. Mass Spectrom (Tokyo) 2021; 10:A0093. [PMID: 33552826 PMCID: PMC7843839 DOI: 10.5702/massspectrometry.a0093] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/09/2020] [Indexed: 11/23/2022] Open
Abstract
The insertion of ion mobility spectrometry (IMS) between LC and MS can improve peptide identification in both proteomics and phosphoproteomics by providing structural information that is complementary to LC and MS, because IMS separates ions on the basis of differences in their shapes and charge states. However, it is necessary to know how phosphate groups affect the peptide collision cross sections (CCS) in order to accurately predict phosphopeptide CCS values and to maximize the usefulness of IMS. In this work, we systematically characterized the CCS values of 4,433 pairs of mono-phosphopeptide and corresponding unphosphorylated peptide ions using trapped ion mobility spectrometry (TIMS). Nearly one-third of the mono-phosphopeptide ions evaluated here showed smaller CCS values than their unphosphorylated counterparts, even though phosphorylation results in a mass increase of 80 Da. Significant changes of CCS upon phosphorylation occurred mainly in structurally extended peptides with large numbers of basic groups, possibly reflecting intramolecular interactions between phosphate and basic groups.
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Affiliation(s)
- Kosuke Ogata
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606–8501, Japan
| | - Chih-Hsiang Chang
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606–8501, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606–8501, Japan
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25
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Chen X, Zhao J, Dong M, Yang N, Wang J, Zhang Y, Liu K, Tong X. Pd(0)-Catalyzed Asymmetric Carbohalogenation: H-Bonding-Driven C(sp3)–Halogen Reductive Elimination under Mild Conditions. J Am Chem Soc 2021; 143:1924-1931. [DOI: 10.1021/jacs.0c10797] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Xin Chen
- Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, School of Petrochemical Engineering, Changzhou University, 1 Gehu Road, Changzhou 213164, China
| | - Jixiao Zhao
- Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, School of Petrochemical Engineering, Changzhou University, 1 Gehu Road, Changzhou 213164, China
| | - Ming Dong
- Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, School of Petrochemical Engineering, Changzhou University, 1 Gehu Road, Changzhou 213164, China
| | - Ninglei Yang
- Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, School of Petrochemical Engineering, Changzhou University, 1 Gehu Road, Changzhou 213164, China
| | - Jiaoyang Wang
- Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, School of Petrochemical Engineering, Changzhou University, 1 Gehu Road, Changzhou 213164, China
| | - Yueqi Zhang
- Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, School of Petrochemical Engineering, Changzhou University, 1 Gehu Road, Changzhou 213164, China
| | - Kun Liu
- College of Chemistry, Tianjin Normal University, 393 Binshui West Road, Tianjin 300387, China
| | - Xiaofeng Tong
- Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, School of Petrochemical Engineering, Changzhou University, 1 Gehu Road, Changzhou 213164, China
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26
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Dereka B, Yu Q, Lewis NHC, Carpenter WB, Bowman JM, Tokmakoff A. Crossover from hydrogen to chemical bonding. Science 2021; 371:160-164. [DOI: 10.1126/science.abe1951] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/20/2020] [Indexed: 11/02/2022]
Affiliation(s)
- Bogdan Dereka
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Qi Yu
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, GA 30322, USA
| | - Nicholas H. C. Lewis
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637, USA
| | - William B. Carpenter
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Joel M. Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, GA 30322, USA
| | - Andrei Tokmakoff
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637, USA
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27
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Shmukler L, Fedorova I, Fadeeva YA, Safonova L. The physicochemical properties and structure of alkylammonium protic ionic liquids of RnH4-nNX (n = 1–3) family. A mini–review. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114350] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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28
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Lin CY, Boxer SG. Unusual Spectroscopic and Electric Field Sensitivity of Chromophores with Short Hydrogen Bonds: GFP and PYP as Model Systems. J Phys Chem B 2020; 124:9513-9525. [DOI: 10.1021/acs.jpcb.0c07730] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Chi-Yun Lin
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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29
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Ren J, Zhang XY, Kong XL. Structure of protonated heterodimer of proline and phenylalanine: Revealed by infrared multiphoton dissociation spectroscopy and theoretical calculations. CHINESE J CHEM PHYS 2020. [DOI: 10.1063/1674-0068/cjcp2006089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Juan Ren
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xian-yi Zhang
- School of Physics and Electronic Information, Anhui Normal University, Anhui Normal University, Wuhu 241000, China
| | - Xiang-lei Kong
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
- Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
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30
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Fedorova IV, Safonova LP. Ion Pair Structures and Hydrogen Bonding in R nNH 4-n Alkylammonium Ionic Liquids with Hydrogen Sulfate and Mesylate Anions by DFT Computations. J Phys Chem A 2020; 124:3170-3179. [PMID: 32243166 DOI: 10.1021/acs.jpca.0c01282] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Density function theory calculations are employed to study the interaction of amines bearing different numbers of alkyl substituents of different sizes on the nitrogen atom with sulfuric and methanesulfonic acids. The proton affinities of the studied amines are calculated, and it is shown that the higher the value is, the more probable is its protonation. The most stable structures of the ion pairs resulting from the acid-base interaction are obtained and characterized. The geometric parameters of the ion pairs and the characteristics derived from the NBO and QTAIM analysis show that there are hydrogen bonding interactions between the cation and the anion. The hydrogen bonding character of the ion pairs and the strength of the interaction between the ions strongly depend on the nature of the cation itself. The interaction between the ions in the ion pairs weakens with the increase in the cation size. The trend of change in the structural parameters of the H-bonds and energetic characteristics in the cation series for the studied ion pairs is not dependent on the nature of the anion.
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Affiliation(s)
- Irina V Fedorova
- G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 1 Akademicheskaya Street, Ivanovo 153045, Russia
| | - Lyubov P Safonova
- G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 1 Akademicheskaya Street, Ivanovo 153045, Russia
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31
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Chen L, Fu C, Li Z, Zhu T, Chen X, Gao C, Wang T, Pang W, Liu C. A new strategy for sensing cyanide ions by cyanide-induced nucleophilic substitution of hydrogen in nitro-controlled electron-deficient fluorophores. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.151656] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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32
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Ahmed M, Kostko O. From atoms to aerosols: probing clusters and nanoparticles with synchrotron based mass spectrometry and X-ray spectroscopy. Phys Chem Chem Phys 2020; 22:2713-2737. [DOI: 10.1039/c9cp05802h] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Synchrotron radiation provides insight into spectroscopy and dynamics in clusters and nanoparticles.
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Affiliation(s)
- Musahid Ahmed
- Chemical Sciences Division
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
| | - Oleg Kostko
- Chemical Sciences Division
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
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33
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Zhang L, Yue X, Li N, Shi H, Zhang J, Zhang Z, Dang F. One-step maltose-functionalization of magnetic nanoparticles based on self-assembled oligopeptides for selective enrichment of glycopeptides. Anal Chim Acta 2019; 1088:63-71. [DOI: 10.1016/j.aca.2019.08.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/14/2019] [Accepted: 08/19/2019] [Indexed: 01/19/2023]
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34
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Khodja W, Collière V, Kahn ML, Roques N, Sutter JP. Controlled Growth of Ag Nanocrystals in a H-Bonded Open Framework. Chemistry 2019; 25:13705-13708. [PMID: 31448835 DOI: 10.1002/chem.201903684] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Indexed: 01/07/2023]
Abstract
A procedure that enabled rational access to the first example of hybrid material made of NPs grown within a H-bonded framework is reported. To avoid competitive reactions with the framework units, the metal precursor was chemically trapped in the porous structure and subsequently photo-reduced to afford the hybrid material Ag@SPA-2, which consists of Ag NPs of nanometric sizes (<15 nm) homogeneously distributed in the crystals of the host material. In a subsequent step, taking advantage of the porous matrix the silver NPs have been transformed in situ to Ag2 S NP by simple infiltration of H2 S. The supramolecular network is shown to play an important role in stabilizing the inorganic nanomaterials and thus in controlling their growth.
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Affiliation(s)
- Walid Khodja
- Laboratoire de Chime de Coordination, CNRS, Université de Toulouse, 205 route de Narbonne, 31077, Toulouse, France
| | - Vincent Collière
- Laboratoire de Chime de Coordination, CNRS, Université de Toulouse, 205 route de Narbonne, 31077, Toulouse, France
| | - Myrtil L Kahn
- Laboratoire de Chime de Coordination, CNRS, Université de Toulouse, 205 route de Narbonne, 31077, Toulouse, France
| | - Nans Roques
- Laboratoire de Chime de Coordination, CNRS, Université de Toulouse, 205 route de Narbonne, 31077, Toulouse, France
| | - Jean-Pascal Sutter
- Laboratoire de Chime de Coordination, CNRS, Université de Toulouse, 205 route de Narbonne, 31077, Toulouse, France
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35
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Cheisson T, Jian J, Su J, Eaton TM, Gau MR, Carroll PJ, Batista ER, Yang P, Gibson JK, Schelter EJ. Halide anion discrimination by a tripodal hydroxylamine ligand in gas and condensed phases. Phys Chem Chem Phys 2019; 21:19868-19878. [PMID: 31475264 DOI: 10.1039/c9cp03764k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Electrospray ionization of solutions containing a tripodal hydroxylamine ligand, H3TriNOx ([((2-tBuNOH)C6H4CH2)3N]) denoted as L, and a hydrogen halide HX: HCl, HBr and/or HI, yielded gas-phase anion complexes [L(X)]- and [L(HX2)]-. Collision induced dissociation (CID) of mixed-halide complexes, [L(HXaXb)]-, indicated highest affinity for I- and lowest for Cl-. Structures and energetics computed by density functional theory are in accord with the CID results, and indicate that the gas-phase binding preference is a manifestation of differing stabilities of the HX molecules. A high halide affinity of [L(H)]+ in solution was also demonstrated, though with a highest preference for Cl- and lowest for I-, the opposite observation of, but not in conflict with, what is observed in gas phase. The results suggest a connection between gas- and condensed-phase chemistry and computational approaches, and shed light on the aggregation and anion recognition properties of hydroxylamine receptors.
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Affiliation(s)
- Thibault Cheisson
- P. Roy and Diana T. Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 S 34th St., Philadelphia, PA 19104, USA.
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36
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Endo T, Matsuda Y, Moriyama S, Fujii A. Infrared Spectroscopic Study on Trimethyl Amine Radical Cation: Correlation between Proton-Donating Ability and Structural Deformation. J Phys Chem A 2019; 123:5945-5950. [DOI: 10.1021/acs.jpca.9b01261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tomoya Endo
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8578, Miyagi, Japan
| | - Yoshiyuki Matsuda
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8578, Miyagi, Japan
| | - Shohei Moriyama
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8578, Miyagi, Japan
| | - Asuka Fujii
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8578, Miyagi, Japan
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37
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Pike SJ, Lavagnini E, Varley LM, Cook JL, Hunter CA. H-Bond donor parameters for cations. Chem Sci 2019; 10:5943-5951. [PMID: 31360400 PMCID: PMC6566073 DOI: 10.1039/c9sc00721k] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/01/2019] [Indexed: 11/21/2022] Open
Abstract
UV/Vis absorption and NMR spectroscopy titrations have been used to investigate the formation of complexes between cations and neutral H-bond acceptors in organic solvents. Complexes formed by two different H-bond acceptors with fifteen different cations were studied in acetone and in acetonitrile. The effects of water and ion pairing with the counter-anion were found to be negligible in the two polar solvents employed for this study. The data were used to determine self-consistent H-bond donor parameters (α) for a series of organic and inorganic cations; guanidinium, primary, tertiary and quaternary ammonium, imidazolium, methylpyridinium, lithium, sodium, potassium, rubidium and caesium. The results demonstrate the transferability of α parameters for cations between different solvents and different H-bond acceptor partners, allowing reliable prediction of cation recognition properties in different environments. Lithium and protonated nitrogen cations form the most stable complexes, but the α parameter is only 5.0, which is similar to the neutral H-bond donor 3-trifluoromethyl,4-nitrophenol (α = 5.1). Quaternary ammonium is the weakest H-bond donor investigated with an α value of 2.7, which is comparable to an alcohol. The α parameters for alkali metal cations decrease down the group from 5.0 (Li+) to 3.5 (Cs+).
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Affiliation(s)
- Sarah J Pike
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - Ennio Lavagnini
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - Lisa M Varley
- Department of Chemistry , University of Sheffield , Sheffield , S3 7HF , UK
| | - Joanne L Cook
- Unilever R&D Port Sunlight , Quarry Road East , Bebington , Wirral CH63 3JW , UK
| | - Christopher A Hunter
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
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38
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Liu G. Tuning the Properties of Charged Polymers at the Solid/Liquid Interface with Ions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:3232-3247. [PMID: 29806944 DOI: 10.1021/acs.langmuir.8b01158] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In conventional theories, where ions are treated as point charges, the properties of charged polymers can be tuned using ions via the ionic strength. However, this article will show that the properties of charged polymers at the solid/liquid interface, including charged polymer brushes and polyelectrolyte multilayers, can be tuned by ions beyond ionic strength effects. Ion specificity, multivalency, ionic hydrogen bonding, and ionic hydrophobicity/hydrophilicity are used to tune a range of properties of charged polymers at the solid/liquid interface such as hydration, conformation, stiffness, surface wettability, lubricity, adhesion, and protein adsorption. The ionic effects demonstrated here greatly broaden our understanding of the use of ions to tune the interfacial properties of charged polymers. It is anticipated that these ionic effects can be further expanded by incorporating new types of important ion-charged polymer interactions and can also be extended to neutral polymer systems.
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Affiliation(s)
- Guangming Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics , University of Science and Technology of China , Hefei , P. R. China 230026
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39
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Pearcy AC, Mason KA, El-Shall MS. Ionic Hydrogen and Halogen Bonding in the Gas Phase Association of Acetonitrile and Acetone with Halogenated Benzene Cations. J Phys Chem A 2019; 123:1363-1371. [PMID: 30452257 DOI: 10.1021/acs.jpca.8b09094] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report on the gas phase association of the small polar and aprotic solvent molecules acetonitrile (CH3CN) and acetone (CH3COCH3) with the halogenated benzene radical cations (C6H5X•+, X = F, Cl, Br, and I) using the mass-selected ion mobility technique and density functional theory calculations. The association energies (-Δ H°) of CH3CN (CH3COCH3) with C6H5F•+ and C6H5I•+ are similar [13.0 (13.3) and 13.2 (14.1) kcal/mol, respectively] but higher than those of CH3CN (CH3COCH3) with C6H5Cl•+ and C6H5Br•+ [10.5 (11.5) and 10.9 (10.6) kcal/mol, respectively]. However, the electrostatic potentials of the lowest energy structures of C6H5Br•+(CH3CN) and C6H5Br•+(CH3COCH3) or C6H5I•+(CH3CN) and C6H5I•+(CH3COCH3) complexes clearly show the formation of the ionic halogen bonds (IXBs) C-Brδ+- -NCCH3 and C-Brδ+- -OC(CH3)2 or C-Iδ+- -NCCH3 and C-Iδ+- -OC(CH3)2 driven by positively charged σ-holes on the external sides of the C-Br and C-I bond axes of the bromobenzene and iodobenzene radical cations, respectively. For the C6H5F•+(CH3CN) complex, the dominant interaction involves a T-shaped structure between the N atom of CH3CN and the C atom of the C-F bond of C6H5F•+. The structure of the C6H5Cl•+(CH3CN) complex shows the formation of unconventional ionic hydrogen bonds (uIHBs) between the N atom of CH3CN and the C-H bonds of the C6H5Cl•+ cation. Similar results are obtained for the association of acetone with the halogenated benzene radical cations. The formation of IXBs of the iodobenzene cation with acetonitrile or acetone involves a significant entropy loss (-Δ S° = 25-27 cal /(mol K)) resulting from the formation of more ordered and highly directional structures between the nitrogen or oxygen lone pair of electrons of acetonitrile or acetone, respectively, and the electropositive region around the iodine atom of the iodobenzene cation. In comparison, for the association of acetonitrile or acetone with the fluorobenzene, chlorobenzene, and bromobenzene cations, -Δ S° = 16-23 cal/(mol K), consistent with the formation of less ordered structures and loose interactions. The lowest energy structures of the C6H5Br•+(CH3COCH3)2 and C6H5I•+(CH3COCH3)2 clusters show a novel combination of ionic halogen bonding and hydrogen bonding where the oxygen atom of one acetone molecule forms the halogen bond while the oxygen atom of the second acetone molecule becomes the hydrogen acceptor from the methyl group of the first acetone molecule.
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Affiliation(s)
- Adam C Pearcy
- Department of Chemistry , Virginia Commonwealth University , Richmond , Virginia 23284-2006 , United States
| | - Kyle A Mason
- Department of Chemistry , Virginia Commonwealth University , Richmond , Virginia 23284-2006 , United States
| | - M Samy El-Shall
- Department of Chemistry , Virginia Commonwealth University , Richmond , Virginia 23284-2006 , United States
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40
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Wollschläger JM, Schalley CA. Ion Mobility Mass Spectrometric Investigation on the Photoisomerization of a 4,4’‐Diamidoazobenzene Model. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201800251] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Jan M. Wollschläger
- Institut für Chemie und Biochemie der Freien Universität Berlin Takustr 3 14195 Berlin Germany
| | - Christoph A. Schalley
- Institut für Chemie und Biochemie der Freien Universität Berlin Takustr 3 14195 Berlin Germany
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41
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Vušurović J, Breuker K. Relative Strength of Noncovalent Interactions and Covalent Backbone Bonds in Gaseous RNA-Peptide Complexes. Anal Chem 2019; 91:1659-1664. [PMID: 30614682 PMCID: PMC6335609 DOI: 10.1021/acs.analchem.8b05387] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Interactions of ribonucleic acids (RNA) with basic ligands such as proteins or aminoglycosides play a key role in fundamental biological processes. Native top-down mass spectrometry (MS) has recently been extended to binding site mapping of RNA-ligand interactions by collisionally activated dissociation, without the need for laborious sample preparation procedures. The technique relies on the preservation of noncovalent interactions at energies that are sufficiently high to cause RNA backbone cleavage. In this study, we address the question of how many and what types of noncovalent interactions allow for binding site mapping by top-down MS. We show that proton transfer from protonated ligand to deprotonated RNA within salt bridges initiates loss of the ligand, but that proton transfer becomes energetically unfavorable in the presence of additional hydrogen bonds such that the noncovalent interactions remain stronger than the covalent RNA backbone bonds.
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Affiliation(s)
- Jovana Vušurović
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI) , Universität Innsbruck , Innrain 80-82 , 6020 Innsbruck , Austria
| | - Kathrin Breuker
- Institut für Organische Chemie and Center for Molecular Biosciences Innsbruck (CMBI) , Universität Innsbruck , Innrain 80-82 , 6020 Innsbruck , Austria
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42
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Fedorova IV, Safonova LP. Ab Initio Investigation of the Interionic Interactions in Triethylammonium-Based Protic Ionic Liquids: The Role of Anions in the Formation of Ion Pair and Hydrogen Bonded Structure. J Phys Chem A 2018; 123:293-300. [DOI: 10.1021/acs.jpca.8b10906] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Irina V. Fedorova
- G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 1 Akademicheskaya Street, Ivanovo 153045, Russia
| | - Lyubov P. Safonova
- G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 1 Akademicheskaya Street, Ivanovo 153045, Russia
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43
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Zhao H, Liu C, Yang D, Wan X, Shang R, Quan P, Fang L. Molecular mechanism of ion-pair releasing from acrylic pressure sensitive adhesive containing carboxyl group: Roles of doubly ionic hydrogen bond in the controlled release process of bisoprolol ion-pair. J Control Release 2018; 289:146-157. [DOI: 10.1016/j.jconrel.2018.09.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 08/31/2018] [Accepted: 09/26/2018] [Indexed: 12/31/2022]
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44
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Sugawara N, Hsu PJ, Fujii A, Kuo JL. Competition between hydrogen bonds and van der Waals forces in intermolecular structure formation of protonated branched-chain alcohol clusters. Phys Chem Chem Phys 2018; 20:25482-25494. [PMID: 30276413 DOI: 10.1039/c8cp05222k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To investigate the influence of bulky alkyl groups on hydrogen-bonded (H-bonded) network structures of alcohols, infrared (IR) spectra of protonated clusters of 2-propanol (2-PrOH) and tert-butyl alcohol (t-BuOH) were observed in the OH and CH stretch regions. In addition, by varying the tag species, the temperature dependence profile of the isomer population of H+(t-BuOH)n was revealed. An extensive search for stable isomers was performed using dispersion-corrected density functional theory methods, and temperature-dependent IR spectral simulations were done on the basis of the harmonic superposition approximation. The computational results qualitatively agreed with the observed size and temperature dependence of the H-bonded network structures of these protonated bulky alcohol clusters. However, the difficulty in the quantitative evaluation of dispersion was also demonstrated. It was shown that H+(2-PrOH)n (n = 4-7) have essentially the same network structures as the protonated normal alcohol clusters studied so far. On the other hand, H+(t-BuOH)n (n = 4-8) showed a clear preference for the smaller-membered ring structures, that is very different from the preference of the protonated normal alcohol clusters. The origin of the different structure preferences was discussed in terms of the steric effect and dispersion.
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Affiliation(s)
- Natsuko Sugawara
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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45
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Bouchoux G. Gas phase basicities of polyfunctional molecules. Part 6: Cyanides and isocyanides. MASS SPECTROMETRY REVIEWS 2018; 37:533-564. [PMID: 28621817 DOI: 10.1002/mas.21538] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/15/2017] [Indexed: 05/26/2023]
Abstract
This paper gathers structural and thermochemical informations related to the gas-phase basicity of molecules containing cyanides (nitriles) and isocyanides (isonitriles) functional groups. It constitutes the sixth part of a general review devoted to gas-phase basicities of polyfunctional compounds. A large corpus of cyanides and isocyanides molecules is examined under seven major chapters. In the first one, a rapid overview of the definitions and methods leading to gas-phase basicity, GB, proton affinity, PA, and protonation entropy, Δp S°, is given. In the same chapter, several aspects of the gas phase chemistry of protonated cyanides and isocyanides are also presented. Chapters II-VI detail the protonation energetics of aliphatic, unsaturated, and heteroatom substituted (halogens, O, S, N, P) cyanides. A seventh chapter is devoted to isocyanides. Experimental data available in the literature (120 references) were reevaluated according to the presently adopted basicity scale that is the NIST database anchored to PA(NH3 ) = 853.6 kJ/mol and GB (NH3 ) = 819 kJ/mol. In this latter source, however, several erroneous values have been identified which were corrected in the present review. Structural and energetic information given by G4MP2 quantum chemistry computations on ca. 60 typical systems are presented. The present review includes the GB, PA, and Δp S° values of ca. 110 cyanides and isocyanides, and, for selected examples, is completed by a set of computed heats of formation (Δf H°) at 0 and 298 K.
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Affiliation(s)
- Guy Bouchoux
- Département de Chimie, Laboratoire de Chimie Moléculaire, UMR CNRS 9168, Ecole Polytechnique, Palaiseau, France
- Université Paris-Sud XI, ICMO, Orsay, France
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46
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Avilés-Moreno JR, Berden G, Oomens J, Martínez-Haya B. Intra-cavity proton bonding and anharmonicity in the anionophore cyclen. Phys Chem Chem Phys 2018; 20:8968-8975. [PMID: 29557457 DOI: 10.1039/c8cp00660a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Proton bonding drives the supramolecular chemistry of a broad range of materials with polar moieties. Proton delocalization and electronic charge redistribution have a profound impact on the structure of proton-bound molecular frameworks, and pose fundamental challenges to quantum chemical modelling. This study provides insights into the structural and spectral signatures of the intramolecular proton bond formed in a benchmark polyazamacrocycle anionophore (cyclen, 1,4,7,10-tetraazacyclododecane). Infrared action spectroscopy is employed to characterize the macrocycle, isolated in protonated form. In its most stable configuration, protonated cyclen adopts an open arrangement of Cs symmetry with a particularly strong NHδ+N bond across the cavity. The quantum chemical analysis of the infrared spectrum reveals intrinsic difficulties for the accurate description of the vibrational modes of the system. The reconciliation of the computational predictions with experiment demands a careful anharmonic treatment of the proton motion, which exposes the limitations of current methods. Best results are obtained with the incorporation of anharmonicity only to the fundamental modes directly related to motions of the proton. However, the full anharmonic treatment of the system fails to describe correctly the vibrations related to the macrocycle backbone. The results should serve as motivation for new developments in the modelling of proton bonded systems.
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Affiliation(s)
- Juan Ramón Avilés-Moreno
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, E-41013 Seville, Spain.
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Bruno Martínez-Haya
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, E-41013 Seville, Spain.
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47
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Weinhold F. Theoretical Prediction of Robust Second-Row Oxyanion Clusters in the Metastable Domain of Antielectrostatic Hydrogen Bonding. Inorg Chem 2018; 57:2035-2044. [PMID: 29381336 DOI: 10.1021/acs.inorgchem.7b02943] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We provide ab initio and density functional theory evidence for a family of surprisingly robust like-charged clusters of common HSO4- and H2PO4- oxyanions, ranging up to tetramers of net charge 4-. Our results support other recent theoretical and experimental evidence for "antielectrostatic" hydrogen-bonded (AEHB) species that challenge conventional electrostatic conceptions and force-field modeling of closed-shell ion interactions. We provide structural and energetic descriptors of the predicted kinetic well-depths (in the range 3-10 kcal/mol) and barrier widths (in the range 2-4 Å) for simple AEHB dimers, including evidence of extremely strong hydrogen bonding in the fluoride-bisulfate dianion. For more complex polyanionic species, we employ natural-bond-orbital-based descriptors to characterize the electronic features of the cooperative hydrogen-bonding network that are able to successfully defy Coulomb explosion. The computational results suggest a variety of kinetically stable AEHB species that may be suitable for experimental detection as long-lived gas-phase species or structural units of condensed phases, despite the imposing electrostatic barriers that oppose their formation under ambient conditions.
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Affiliation(s)
- Frank Weinhold
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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48
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Fujii A, Sugawara N, Hsu PJ, Shimamori T, Li YC, Hamashima T, Kuo JL. Hydrogen bond network structures of protonated short-chain alcohol clusters. Phys Chem Chem Phys 2018; 20:14971-14991. [DOI: 10.1039/c7cp08072g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protonated alcohol clusters enable extraction of the physical essence of the nature of hydrogen bond networks.
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Affiliation(s)
- Asuka Fujii
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Natsuko Sugawara
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Takuto Shimamori
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Ying-Cheng Li
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Toru Hamashima
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
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49
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Heiles S, Berden G, Oomens J, Williams ER. Competition between salt bridge and non-zwitterionic structures in deprotonated amino acid dimers. Phys Chem Chem Phys 2018; 20:15641-15652. [DOI: 10.1039/c8cp01458b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The effect of side chain functional groups on salt bridge structures in deprotonated amino acid homodimers is investigated using both infrared multiple photon dissociation spectroscopy between 650 and 1850 cm−1 and theory.
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Affiliation(s)
- Sven Heiles
- Department of Chemistry
- University of California
- Berkeley
- USA
- Institute of Inorganic and Analytical Chemistry
| | - Giel Berden
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
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50
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Umezono S, Okuno T. Systematic study of intermolecular C–X⋯O S (X = Cl, Br, I) halogen bonds in (E)-10-(1,2-dihalovinyl)-10H-phenothiazine 5,5-dioxides. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.06.135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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