1
|
Jóźwiak K, Jezierska A, Panek JJ, Kochel A, Łydżba-Kopczyńska B, Filarowski A. Very Strong Hydrogen Bond in Nitrophthalic Cocrystals. Molecules 2024; 29:3565. [PMID: 39124970 PMCID: PMC11314142 DOI: 10.3390/molecules29153565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2024] [Revised: 07/22/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024] Open
Abstract
This work presents the studies of a very strong hydrogen bond (VSHB) in biologically active phthalic acids. Research on VSHB comes topical due to its participation in many biological processes. The studies cover the modelling of intermolecular interactions and phthalic acids with 2,4,6-collidine and N,N-dimethyl-4-pyridinamine complexes with aim to obtain a VSHB. The four synthesized complexes were studied by experimental X-ray, IR, and Raman methods, as well as theoretical Car-Parrinello Molecular Dynamics (CP-MD) and Density Functional Theory (DFT) simulations. By variation of the steric repulsion and basicity of the complex' components, a very short intramolecular hydrogen bond was achieved. The potential energy curves calculated by the DFT method were characterized by a low barrier (0.7 and 0.9 kcal/mol) on proton transfer in the OHN intermolecular hydrogen bond for 3-nitrophthalic acid with either 2,4,6-collidine or N,N-dimethyl-4-pyridinamine cocrystals. Moreover, the CP-MD simulations exposed very strong bridging proton dynamics in the intermolecular hydrogen bonds. The accomplished crystallographic and spectroscopic studies indicate that the OHO intramolecular hydrogen bond in 4-nitrophthalic cocrystals is VSHB. The influence of a strong steric effect on the geometry of the studied cocrystals and the stretching vibration bands of the carboxyl and carboxylate groups was elaborated.
Collapse
Affiliation(s)
| | | | | | | | | | - Aleksander Filarowski
- Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie Str., 50-383 Wrocław, Poland; (K.J.); (A.J.); (J.J.P.); (A.K.); (B.Ł.-K.)
| |
Collapse
|
2
|
Tupikina EY, Sigalov MV, Alkhuder O, Tolstoy PM. Charge Relay Without Proton Transfer: Coupling of Two Short Hydrogen Bonds via Imidazole in Models of Catalytic Triad of Serine Protease Active Site. Chemphyschem 2024; 25:e202300970. [PMID: 38563616 DOI: 10.1002/cphc.202300970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/01/2024] [Accepted: 03/27/2024] [Indexed: 04/04/2024]
Abstract
A homologous series of 20 substituted alcohol-imidazole-acetate model complexes imitating the charge relay system in Ser-His-Asp catalytic triad of serine proteases is considered quantum-chemically. We show qualitatively that the geometries of alcohol-imidazole and imidazole-acetate short hydrogen bonds are strongly coupled via the central imidazole and such complexes are capable of effectively relaying the charge from acetate to alcohol moiety upon relatively small concerted proton displacements. We hypothesize an alternative catalytic mechanism of serine proteases that does not require two complete proton transfers or hydrogen bond breakage between Ser and His residues.
Collapse
Affiliation(s)
- Elena Yu Tupikina
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - Mark V Sigalov
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Omar Alkhuder
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - Peter M Tolstoy
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| |
Collapse
|
3
|
Shitov DA, Krutin DV, Tupikina EY. Mutual influence of non-covalent interactions formed by imidazole: A systematic quantum-chemical study. J Comput Chem 2024; 45:1046-1060. [PMID: 38216334 DOI: 10.1002/jcc.27309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/14/2024]
Abstract
Imidazole is a five-membered heterocycle that is part of a number of biologically important molecules such as the amino acid histidine and the hormone histamine. Imidazole has a unique ability to participate in a variety of non-covalent interactions involving the NH group, the pyridine-like nitrogen atom or the π-system. For many biologically active compounds containing the imidazole moiety, its participation in formation of hydrogen bond NH⋯O/N and following proton transfer is the key step of mechanism of their action. In this work a systematic study of the mutual influence of various paired combinations of non-covalent interactions (e.g., hydrogen bonds and π-interactions) involving the imidazole moiety was performed by means of quantum chemistry (PW6B95-GD3/def2-QZVPD) for a series of model systems constructed based on analysis of available x-ray data. It is shown that for considered complexes formation of additional non-covalent interactions can only enhance the proton-donating ability of imidazole. At the same time, its proton-accepting ability can be both enhanced and weakened, depending on what additional interactions are added to a given system. The mutual influence of non-covalent interactions involving imidazole can be classified as weak geometric and strong energetic cooperativity-a small change in the length of non-covalent interaction formed by imidazole can strongly influence its strength. The latter can be used to develop methods for controlling the rate and selectivity of chemical reactions involving the imidazole fragment in larger systems. It is shown that the strong mutual influence of non-covalent interactions involving imidazole is due to the unique ability of the imidazole ring to effectively redistribute electron density in non-covalently bound systems with its participation.
Collapse
Affiliation(s)
- Daniil A Shitov
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - Danil V Krutin
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - Elena Yu Tupikina
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| |
Collapse
|
4
|
Chhetri A, Karthick K, Karmakar A, Kundu S, Mitra J. Melamine-Based Hydrogen-bonded Systems as Organoelectrocatalysts for Water Oxidation Reaction. CHEMSUSCHEM 2023; 16:e202300220. [PMID: 36852710 DOI: 10.1002/cssc.202300220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 02/22/2023] [Indexed: 06/10/2023]
Abstract
Applications of small organic molecules and hydrogen-bonded aggregates, instead of traditional transition-metal-based electrocatalysts, are gaining momentum for addressing the issue of low-cost generation of H2 to power a sustainable environment. Such systems offer the possibility to integrate desired functional moieties with predictive structural repetition for modulating their properties. Despite these advantages, hydrogen-bonded organic systems have largely remained unexplored, especially as electrocatalysts. Melamine and adipic acid-based hydrogen-bonded organic ionic (BMA) and co-crystal systems developed under varying temperatures are explored as electrocatalysts for water oxidation reaction (WOR). These systems are easily modifiable with precisely designed molecular architecture and judiciously positioned nitrogen atoms. Combined effect of charge-assisted hydrogen bonding stabilizes the ionic BMA system under corrosive alkaline conditions and augments its remarkable electrocatalytic WOR activity, achieving a current density of 10 mA cm-2 at an overpotential of 387 mV and Faradaic efficiency ∼94.5 %. The enhanced electrocatalytic ability of BMA is attributed to its hydrophilic nature, unique molecular composition with complementary hydrogen-bonded motifs and a high density of positively charged nitrogen atoms on the surface, that facilitates electrostatic interactions and accelerate charge and mass transport processes culminating in a turnover frequency of ∼0.024 s-1 . This work validates the potential of hydrogen-bonded molecular organo-electrocatalysts towards WOR.
Collapse
Affiliation(s)
- Ashis Chhetri
- Inorganic Materials & Catalysis Division, CSIR-Central Salt & Marine Chemicals Research Institute, Gijubhai Badheka Marg, 364002, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research (AcSIR), AcSIR Headquarters, CSIR-HRDC Campus, Sector-19, Kamla Nehru Nagar, 201002, Ghaziabad, U.P., India
- Centre for Advanced Materials & Industrial Chemistry, RMIT University, 3000, Melbourne, VIC, Australia
| | - Kannimuthu Karthick
- Academy of Scientific and Innovative Research (AcSIR), AcSIR Headquarters, CSIR-HRDC Campus, Sector-19, Kamla Nehru Nagar, 201002, Ghaziabad, U.P., India
- Electrochemical Process Engineering (EPE) Division, CSIR-CECRI, 630003, Karaikudi, Tamil Nadu, India
| | - Arun Karmakar
- Academy of Scientific and Innovative Research (AcSIR), AcSIR Headquarters, CSIR-HRDC Campus, Sector-19, Kamla Nehru Nagar, 201002, Ghaziabad, U.P., India
- Electrochemical Process Engineering (EPE) Division, CSIR-CECRI, 630003, Karaikudi, Tamil Nadu, India
| | - Subrata Kundu
- Academy of Scientific and Innovative Research (AcSIR), AcSIR Headquarters, CSIR-HRDC Campus, Sector-19, Kamla Nehru Nagar, 201002, Ghaziabad, U.P., India
- Electrochemical Process Engineering (EPE) Division, CSIR-CECRI, 630003, Karaikudi, Tamil Nadu, India
| | - Joyee Mitra
- Inorganic Materials & Catalysis Division, CSIR-Central Salt & Marine Chemicals Research Institute, Gijubhai Badheka Marg, 364002, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research (AcSIR), AcSIR Headquarters, CSIR-HRDC Campus, Sector-19, Kamla Nehru Nagar, 201002, Ghaziabad, U.P., India
| |
Collapse
|
5
|
Li B, Zhang Y, Wang J, Yan B, Liang J, Dong Y, Zhou Q. Fast and Reversibly Humidity-Responsive Fluorescence Based on AIEgen Proton Transfer. ACS APPLIED MATERIALS & INTERFACES 2022; 14:49119-49127. [PMID: 36256864 DOI: 10.1021/acsami.2c13652] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The construction of humidity-responsive fluorescent materials with reversibility, specificity, and sensitivity is of great importance for the development of information encryption, fluorescence patterning, and sensors. Nevertheless, to date, the application of these materials has been limited by their slow response rate and nonspecificity. Herein, a humidity-responsive fluorescence system was designed and assembled to achieve a rapid, reversible, and specific moisture response. The system comprised tetra-(4-pyridylphenyl)ethylene (TPE-4Py) as a fluorescent proton acceptor with an aggregation-induced emission (AIE) effect and poly(acrylic acid) (PAA) as a proton donor with an efficient moisture-capturing ability. The fluorescence color and intensity rapidly changed with increasing relative humidity (RH) because of TPE-4Py protonation, and TPE-4Py deprotonation resulted in recovery of the original fluorescence color in low-humidity environments. The proton transfer between the pyridyl group in TPE-4Py and the carboxyl group in PAA was reversible and chemically stable, and the humidity-responsive fluorescence system showed a high response/recovery speed, an obvious color change, good reversibility, and an outstanding specific moisture response. Because of these advantages, diverse applications of this humidity-responsive fluorescence system in transient fluorescent patterning and the encryption of information were also developed and demonstrated.
Collapse
Affiliation(s)
- Botian Li
- College of New Energy and Materials, China University of Petroleum, Beijing 102249, China
| | - Yichi Zhang
- College of New Energy and Materials, China University of Petroleum, Beijing 102249, China
| | - Jian Wang
- College of New Energy and Materials, China University of Petroleum, Beijing 102249, China
| | - Bo Yan
- College of New Energy and Materials, China University of Petroleum, Beijing 102249, China
| | - Jundang Liang
- College of New Energy and Materials, China University of Petroleum, Beijing 102249, China
| | - Yuping Dong
- Beijing Key Laboratory of Construction Tailorable Advanced Functional Materials and Green Applications, School of Materials Science and Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Qiong Zhou
- College of New Energy and Materials, China University of Petroleum, Beijing 102249, China
| |
Collapse
|
6
|
Joerg F, Schröder C. Polarizable molecular dynamics simulations on the conductivity of pure 1-methylimidazolium acetate systems. Phys Chem Chem Phys 2022; 24:15245-15254. [PMID: 35703101 DOI: 10.1039/d2cp01501c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The protic ionic liquid 1-methylimidazolium acetate is in equilibrium with its neutral species 1-methylimidazole and acetic acid. Although several experimental data indicate that the equilibrium favors the neutral species, the system exhibits a significant conductivity. We developed a polarizable force field to describe the ionic liquid accurately and applied it to several mixtures of the neutral and charged species. In addition to comparing single values, such as density, diffusion coefficients, and conductivity, with experimental data, the complete frequency-dependent dielectric spectrum ranging from several MHz to THz can be used to determine the equilibrium composition of the reaction mentioned above.
Collapse
Affiliation(s)
- Florian Joerg
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstr. 17, A-1090 Vienna, Austria. .,University of Vienna, Vienna Doctoral School in Chemistry (DoSChem), Währingerstr. 42, A-1090 Vienna, Austria
| | - Christian Schröder
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstr. 17, A-1090 Vienna, Austria.
| |
Collapse
|
7
|
Yang J, Li Y, Qiu Q, Wang R, Yan W, Yu Y, Niu L, Pei H, Wei H, Ouyang L, Ye H, Xu D, Wei Y, Chen Q, Chen L. Small Molecules Promote Selective Denaturation and Degradation of Tubulin Heterodimers through a Low-Barrier Hydrogen Bond. J Med Chem 2022; 65:9159-9173. [PMID: 35762925 DOI: 10.1021/acs.jmedchem.2c00379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Here, we report a novel mechanism to selectively degrade target proteins. 3-(3-Phenoxybenzyl)amino-β-carboline (PAC), a tubulin inhibitor, promotes selective degradation of αβ-tubulin heterodimers. Biochemical studies have revealed that PAC specifically denatures tubulin, making it prone to aggregation that predisposes it to ubiquitinylation and then degradation. The degradation is mediated by a single hydrogen bond formed between the pyridine nitrogen of PAC and βGlu198, which is identified as a low-barrier hydrogen bond (LBHB). In contrast, another two tubulin inhibitors that only form normal hydrogen bonds with βGlu198 exhibit no degradation effect. Thus, the LBHB accounts for the degradation. We then screened for compounds capable of forming an LBHB with βGlu198 and demonstrated that BML284, a Wnt signaling activator, also promotes tubulin heterodimer degradation through the LBHB. Our study provided a unique example of LBHB function and identified a novel approach to obtain tubulin degraders.
Collapse
Affiliation(s)
- Jianhong Yang
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Yong Li
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Qiang Qiu
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Ruihan Wang
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Wei Yan
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Yamei Yu
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Lu Niu
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Heying Pei
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Haoche Wei
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Liang Ouyang
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Haoyu Ye
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yuquan Wei
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Qiang Chen
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Lijuan Chen
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| |
Collapse
|
8
|
Absorption wavelength along chromophore low-barrier hydrogen bonds. iScience 2022; 25:104247. [PMID: 35521532 PMCID: PMC9062252 DOI: 10.1016/j.isci.2022.104247] [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: 08/17/2021] [Revised: 03/18/2022] [Accepted: 04/07/2022] [Indexed: 11/22/2022] Open
Abstract
In low-barrier hydrogen bonds (H-bonds), the pKa values for the H-bond donor and acceptor moieties are nearly equal, whereas the redox potential values depend on the H+ position. Spectroscopic details of low-barrier H-bonds remain unclear. Here, we report the absorption wavelength along low-barrier H-bonds in protein environments, using a quantum mechanical/molecular mechanical approach. Low-barrier H-bonds form between Glu46 and p-coumaric acid (pCA) in the intermediate pRCW state of photoactive yellow protein and between Asp116 and the retinal Schiff base in the intermediate M-state of the sodium-pumping rhodopsin KR2. The H+ displacement of only ∼0.4 Å, which does not easily occur without low-barrier H-bonds, is responsible for the ∼50 nm-shift in the absorption wavelength. This may be a basis of how photoreceptor proteins have evolved to proceed photocycles using abundant protons. The low-barrier H-bond formation is a prerequisite for proton transfer How the absorption wavelength changes as H+ moves is an open question The H+ displacement of ∼0.4 Å leads to the absorption wavelength shift of ∼50 nm The localization of the molecular orbitals plays a key role in the wavelength shift
Collapse
|
9
|
Jacobi R, Joerg F, Steinhauser O, Schröder C. Emulating proton transfer reactions in the pseudo-protic ionic liquid 1-methylimidazolium acetate. Phys Chem Chem Phys 2022; 24:9277-9285. [PMID: 35403653 PMCID: PMC9020328 DOI: 10.1039/d2cp00643j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Proton transfer reactions can enhance conductivity in protic ionic liquids. However, several proton reactions are possible in a multicomponent system of charged and neutral species, resulting in a complex reaction network. Probabilities and equilibrium concentrations of the involved species are modeled by the combination of reducible Markov chains and quantum-mechanical calculations. Proton transfer reactions can enhance conductivity in protic ionic liquids.![]()
Collapse
Affiliation(s)
- Richard Jacobi
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria.,Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Straße 42, 1090 Vienna, Austria
| | - Florian Joerg
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Straße 42, 1090 Vienna, Austria.,Department of Computational Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria.
| | - Othmar Steinhauser
- Department of Computational Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria.
| | - Christian Schröder
- Department of Computational Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria.
| |
Collapse
|
10
|
Štoček JR, Socha O, Císařová I, Slanina T, Dračínský M. Importance of Nuclear Quantum Effects for Molecular Cocrystals with Short Hydrogen Bonds. J Am Chem Soc 2022; 144:7111-7116. [PMID: 35394771 DOI: 10.1021/jacs.1c10885] [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
Many efforts have been recently devoted to the design and investigation of multicomponent pharmaceutical solids, such as salts and cocrystals. The experimental distinction between these solid forms is often challenging. Here, we show that the transformation of a salt into a cocrystal with a short hydrogen bond does not occur as a sharp phase transition but rather a smooth shift of the positional probability of the hydrogen atoms. A combination of solid-state NMR spectroscopy, X-ray diffraction, and diffuse reflectance measurements with density functional theory calculations that include nuclear quantum effects (NQEs) provides evidence of temperature-induced hydrogen atom shift in cocrystals with short hydrogen bonds. We demonstrate that for the predictions of the salt/cocrystal solid forms with short H-bonds, the computations have to include NQEs (particularly hydrogen nuclei delocalization) and temperature effects.
Collapse
Affiliation(s)
- Jakub Radek Štoček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 160 00, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, Prague 2 12840, Czech Republic
| | - Ondřej Socha
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 160 00, Czech Republic
| | - Ivana Císařová
- Department of Inorganic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, Prague 2 12840, Czech Republic
| | - Tomáš Slanina
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 160 00, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 160 00, Czech Republic
| |
Collapse
|
11
|
Kostin MA, Pylaeva S, Tolstoy P. Phosphine oxides as NMR and IR spectroscopic probes for geometry and energy of PO···H–A hydrogen bonds. Phys Chem Chem Phys 2022; 24:7121-7133. [DOI: 10.1039/d1cp05939d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work we evaluate the possibility to use the NMR and IR spectral properties of P=O group to estimate the geometry and strength of hydrogen bonds which it forms...
Collapse
|
12
|
Alkorta I, Elguero J. The SN2 reaction and its relationship with the Walden inversion, the Finkelstein and Menshutkin reactions together with theoretical calculations for the Finkelstein reaction. Struct Chem 2021. [DOI: 10.1007/s11224-021-01805-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractThis communication gives an overview of the relationships between four reactions that although related were not always perceived as such: SN2, Walden, Finkelstein, and Menshutkin. Binary interactions (SN2 & Walden, SN2 & Menshutkin, SN2 & Finkelstein, Walden & Menshutkin, Walden & Finkelstein, Menshutkin & Finkelstein) were reported. Carbon, silicon, nitrogen, and phosphorus as central atoms and fluorides, chlorides, bromides, and iodides as lateral atoms were considered. Theoretical calculations provide Gibbs free energies that were analyzed with linear models to obtain the halide contributions. The M06-2x DFT computational method and the 6-311++G(d,p) basis set have been used for all atoms except for iodine where the effective core potential def2-TZVP basis set was used. Concerning the central atom pairs, carbon/silicon vs. nitrogen/phosphorus, we reported here for the first time that the effect of valence expansion was known for Si but not for P. Concerning the lateral halogen atoms, some empirical models including the interaction between F and I as entering and leaving groups explain the Gibbs free energies.
Collapse
|
13
|
Giba IS, Mulloyarova VV, Denisov GS, Tolstoy PM. Sensitivity of 31 P NMR chemical shifts to hydrogen bond geometry and molecular conformation for complexes of phosphinic acids with pyridines. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:465-477. [PMID: 33332667 DOI: 10.1002/mrc.5123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 12/10/2020] [Accepted: 12/14/2020] [Indexed: 06/12/2023]
Abstract
The results of the quantum-chemical investigation of a series of hydrogen-bonded 1:1 acid-base complexes formed by model phosphinic acids, Me2 POOH, and PhHPOOH, are reported. A series of substituted pyridines (pKa range from 0.5 to 10) was chosen as proton acceptors. Gradual changes of isotropic 31 P nuclear magnetic resonance (NMR) chemical shift, δP, were correlated with the bridging proton position in the intermolecular OHN hydrogen bond, namely, r (OH) distance; the proposed correlation could easily be extended to other phosphinic acids as well. For complexes with pyridine and 2,4,6-trimethylpyridine, we have investigated in more detail several factors influencing the δP values: (1) the proton transfer within the OHN hydrogen bond; (2) the rotation of the pyridine ring around the hydrogen bond axis (associated with the formation/breakage of additional weak PO···H-C hydrogen bond); and (3) the rotation of the phenyl substituent in phenylphosphinic acid around the P-C axis. All these factors appeared to be of similar magnitude, thus masking their individual contributions that have to be independently estimated for a reliable spectral interpretation.
Collapse
Affiliation(s)
- Ivan S Giba
- Institute of Chemistry, St. Petersburg State University, Saint Petersburg, Russia
- Department of Physics, St. Petersburg State University, Saint Petersburg, Russia
| | | | - Gleb S Denisov
- Department of Physics, St. Petersburg State University, Saint Petersburg, Russia
| | - Peter M Tolstoy
- Institute of Chemistry, St. Petersburg State University, Saint Petersburg, Russia
| |
Collapse
|
14
|
Raynal M, Li Y, Troufflard C, Przybylski C, Gontard G, Maistriaux T, Idé J, Lazzaroni R, Bouteiller L, Brocorens P. Experimental and computational diagnosis of the fluxional nature of a benzene-1,3,5-tricarboxamide-based hydrogen-bonded dimer. Phys Chem Chem Phys 2021; 23:5207-5221. [PMID: 33625418 DOI: 10.1039/d0cp06128j] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Precise characterization of the hydrogen bond network present in discrete self-assemblies of benzene-1,3,5-tricarboxamide monomers derived from amino-esters (ester BTAs) is crucial for the construction of elaborated functional co-assemblies. For all ester BTA dimeric structures previously reported, ester carbonyls in the side chain acted as hydrogen bond acceptors, yielding well-defined dimers stabilized by six hydrogen bonds. The ester BTA monomer derived from glycine (BTA Gly) shows a markedly different self-assembly behaviour. We report herein a combined experimental and computational investigation aimed at determining the nature of the dimeric species formed by BTA Gly. Two distinct dimeric structures were characterized by single-crystal X-ray diffraction measurements. Likewise, a range of spectroscopic and scattering techniques as well as molecular modelling were employed to diagnose the nature of dynamic dimeric structures in toluene. Our results unambiguously establish that both ester and amide carbonyls are involved in the hydrogen bond network of the discrete dimeric species formed by BTA Gly. The participation of roughly 4.5 ester carbonyls and 1.5 amide carbonyls per dimer as determined by FT-IR spectroscopy implies that several conformations coexist in solution. Moreover, NMR analysis and modelling data reveal rapid interconversion between these different conformers leading to a symmetric structure on the NMR timescale. Rapid hydrogen bond shuffling between conformers having three (three), two (four), one (five) and zero (six) amide carbonyl groups (ester carbonyl groups, respectively) as hydrogen bond acceptors is proposed to explain the magnetic equivalence of the amide N-H on the NMR timescale. When compared to other ester BTA derivatives in which only ester carbonyls act as hydrogen bond acceptors, the fluxional behaviour of the hydrogen-bonded dimers of BTA Gly likely originates from a larger range of energetically favorable conformations accessible through rotation of the BTA side chains.
Collapse
Affiliation(s)
- M Raynal
- Sorbonne Université, CNRS, IPCM, UMR 8232, 4 Place Jussieu, 75252 Paris Cedex 05, France.
| | - Y Li
- Sorbonne Université, CNRS, IPCM, UMR 8232, 4 Place Jussieu, 75252 Paris Cedex 05, France.
| | - C Troufflard
- Sorbonne Université, CNRS, IPCM, UMR 8232, 4 Place Jussieu, 75252 Paris Cedex 05, France.
| | - C Przybylski
- Sorbonne Université, CNRS, IPCM, UMR 8232, 4 Place Jussieu, 75252 Paris Cedex 05, France.
| | - G Gontard
- Sorbonne Université, CNRS, IPCM, UMR 8232, 4 Place Jussieu, 75252 Paris Cedex 05, France.
| | - T Maistriaux
- Service de Chimie des Matériaux Nouveaux, Institut de Recherche sur les Matériaux, Université de Mons, Place du Parc, 20, B-7000, Mons, Belgium.
| | - J Idé
- Service de Chimie des Matériaux Nouveaux, Institut de Recherche sur les Matériaux, Université de Mons, Place du Parc, 20, B-7000, Mons, Belgium.
| | - R Lazzaroni
- Service de Chimie des Matériaux Nouveaux, Institut de Recherche sur les Matériaux, Université de Mons, Place du Parc, 20, B-7000, Mons, Belgium.
| | - L Bouteiller
- Sorbonne Université, CNRS, IPCM, UMR 8232, 4 Place Jussieu, 75252 Paris Cedex 05, France.
| | - P Brocorens
- Service de Chimie des Matériaux Nouveaux, Institut de Recherche sur les Matériaux, Université de Mons, Place du Parc, 20, B-7000, Mons, Belgium.
| |
Collapse
|
15
|
Dreier C, Prädel L, Ehrhard AA, Wagner M, Hunger J. Association Equilibria of Organo-Phosphoric Acids with Imines from a Combined Dielectric and Nuclear Magnetic Resonance Spectroscopy Approach. Anal Chem 2021; 93:3914-3921. [PMID: 33600142 PMCID: PMC7931174 DOI: 10.1021/acs.analchem.0c04669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 02/08/2021] [Indexed: 11/29/2022]
Abstract
Aggregates formed between organo-phosphoric acids and imine bases in aprotic solvents are the reactive intermediates in Brønsted acid organo-catalysis. Due to the strong hydrogen-bonding interaction of the acids in solution, multiple homo- and heteroaggregates are formed with profound effects on catalytic activity. Yet, due to the similar binding motifs-hydrogen-bonds-it is challenging to experimentally quantify the abundance of these aggregates in solution. Here we demonstrate that a combination of nuclear magnetic resonance (NMR) and dielectric relaxation spectroscopy (DRS) allows for accurate speciation of these aggregates in solution. We show that only by using the observables of both experiments heteroaggregates can be discriminated with simultaneously taking homoaggregation into account. Comparison of the association of diphenyl phosphoric acid and quinaldine or phenylquinaline in chloroform, dichloromethane, or tetrahydrofuran suggests that the basicity of the base largely determines the association of one acid and one base molecule to form an ion-pair. We find the ion-pair formation constants to be highest in chloroform, slightly lower in dichloromethane and lowest in tetrahydrofuran, which indicates that the hydrogen-bonding ability of the solvent also alters ion-pairing equilibria. We find evidence for the formation of multimers, consisting of one imine base and multiple diphenyl phosphoric acid molecules for both bases in all three solvents. This subsequent association of an acid to an ion-pair is however little affected by the nature of the base or the solvent. As such our findings provide routes to enhance the overall fraction of these multimers in solution, which have been reported to open new catalytic pathways.
Collapse
Affiliation(s)
- Christian Dreier
- Max
Planck Institute for Polymer Research, Department for Molecular Spectroscopy, Ackermannweg 10, 55128 Mainz, Germany
| | - Leon Prädel
- Max
Planck Institute for Polymer Research, Department for Molecular Spectroscopy, Ackermannweg 10, 55128 Mainz, Germany
| | - Amelie A. Ehrhard
- Max
Planck Institute for Polymer Research, Department for Molecular Spectroscopy, Ackermannweg 10, 55128 Mainz, Germany
| | - Manfred Wagner
- Max
Planck Institute for Polymer Research, Department for Molecular Spectroscopy, Ackermannweg 10, 55128 Mainz, Germany
| | - Johannes Hunger
- Max
Planck Institute for Polymer Research, Department for Molecular Spectroscopy, Ackermannweg 10, 55128 Mainz, Germany
| |
Collapse
|
16
|
Notti A, Pisagatti I, Nastasi F, Patanè S, Parisi MF, Gattuso G. Stimuli-Responsive Internally Ion-Paired Supramolecular Polymer Based on a Bis-pillar[5]arene Dicarboxylic Acid Monomer. J Org Chem 2020; 86:1676-1684. [PMID: 33369427 PMCID: PMC7871325 DOI: 10.1021/acs.joc.0c02501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
A novel
bis-pillar[5]arene dicarboxylic acid self-assembles in
the presence of 1,12-diaminododecane to yield overall neutral, internally
ion-paired supramolecular polymers. Their aggregation, binding mode,
and morphology can be tuned by external stimuli such as solvent polarity,
concentration, and base treatment.
Collapse
Affiliation(s)
- Anna Notti
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Ilenia Pisagatti
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Francesco Nastasi
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Salvatore Patanè
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Melchiorre F Parisi
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Giuseppe Gattuso
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| |
Collapse
|
17
|
Malm C, Prädel LA, Marekha BA, Grechko M, Hunger J. Composition-Dependent Hydrogen-Bonding Motifs and Dynamics in Brønsted Acid-Base Mixtures. J Phys Chem B 2020; 124:7229-7238. [PMID: 32701282 PMCID: PMC7443859 DOI: 10.1021/acs.jpcb.0c04714] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
In
recent years the interaction of organophosphates and imines,
which is at the core of Brønsted acid organocatalysis, has been
established to be based on strong ionic hydrogen bonds. Yet, besides
the formation of homodimers consisting of two acid molecules and heterodimers
consisting of one acid and one base, also multimeric molecular aggregates
are formed in solution. These multimeric aggregates consist of one
base and several acid molecules. The details of the intermolecular
bonding in such aggregates, however, have remained elusive. To characterize
composition-dependent bonding and bonding dynamics in these aggregates,
we use linear and nonlinear infrared (IR) spectroscopy at varying
molar ratios of diphenyl phosphoric acid and quinaldine. We identify
the individual aggregate species, giving rise to the structured, strong,
and very broad infrared absorptions, which span more than 1000 cm–1. Linear infrared spectra and density functional theory
calculations of the proton transfer potential show that doubly ionic
intermolecular hydrogen bonds between the acid and the base lead to
absorptions which peak at ∼2040 cm–1. The
contribution of singly ionic hydrogen bonds between an acid anion
and an acid molecule is observed at higher frequencies. As common
to such strong hydrogen bonds, ultrafast IR spectroscopy reveals rapid,
∼ 100 fs, dissipation of energy from the proton transfer coordinate.
Yet, the full dissipation of the excess energy occurs on a ∼0.8–1.1
ps time scale, which becomes longer when multimers dominate. Our results
thus demonstrate the coupling and collectivity of the hydrogen bonds
within these complexes, which enable efficient energy transfer.
Collapse
Affiliation(s)
- Christian Malm
- Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Leon A Prädel
- Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Bogdan A Marekha
- Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Maksim Grechko
- Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Johannes Hunger
- Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| |
Collapse
|
18
|
Kaczmarek-Kędziera A. Gas Phase Computational Study of Diclofenac Adsorption on Chitosan Materials. Molecules 2020; 25:molecules25112549. [PMID: 32486148 PMCID: PMC7321203 DOI: 10.3390/molecules25112549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/23/2020] [Accepted: 05/27/2020] [Indexed: 02/07/2023] Open
Abstract
Environmental pollution with non-steroidal anti-inflammatory drugs and their metabolites exposes living organisms on their long-lasting, damaging influence. Hence, the ways of non-steroidal anti-inflammatory drugs (NSAIDs) removal from soils and wastewater is sought for. Among the potential adsorbents, biopolymers are employed for their good availability, biodegradability and low costs. The first available theoretical modeling study of the interactions of diclofenac with models of pristine chitosan and its modified chains is presented here. Supermolecular interaction energy in chitosan:drug complexes is compared with the the mutual attraction of the chitosan dimers. Supermolecular interaction energy for the chitosan-diclofenac complexes is significantly lower than the mutual interaction between two chitosan chains, suggesting that the diclofenac molecule will encounter problems when penetrating into the chitosan material. However, its surface adsorption is feasible due to a large number of hydrogen bond donors and acceptors both in biopolymer and in diclofenac. Modification of chitosan material introducing long-distanced amino groups significantly influences the intramolecular interactions within a single polymer chain, thus blocking the access of diclofenac to the biopolymer backbone. The strongest attraction between two chitosan chains with two long-distanced amino groups can exceed 120 kcal/mol, while the modified chitosan:diclofenac interaction remains of the order of 20 to 40 kcal/mol.
Collapse
Affiliation(s)
- Anna Kaczmarek-Kędziera
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland
| |
Collapse
|
19
|
Brehm M, Thomas M, Gehrke S, Kirchner B. TRAVIS—A free analyzer for trajectories from molecular simulation. J Chem Phys 2020; 152:164105. [DOI: 10.1063/5.0005078] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- M. Brehm
- Institut für Chemie, Martin-Luther-Universität Halle–Wittenberg, von-Danckelmann-Platz 4, D-06120 Halle (Saale), Germany
| | - M. Thomas
- Institut für Chemie, Martin-Luther-Universität Halle–Wittenberg, von-Danckelmann-Platz 4, D-06120 Halle (Saale), Germany
| | - S. Gehrke
- Mulliken Center for Theoretical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Beringstr. 4+6, D-53115 Bonn, Germany
| | - B. Kirchner
- Mulliken Center for Theoretical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Beringstr. 4+6, D-53115 Bonn, Germany
| |
Collapse
|
20
|
Shenderovich IG, Denisov GS. Adduct under Field-A Qualitative Approach to Account for Solvent Effect on Hydrogen Bonding. Molecules 2020; 25:molecules25030436. [PMID: 31973045 PMCID: PMC7037398 DOI: 10.3390/molecules25030436] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 01/17/2020] [Accepted: 01/20/2020] [Indexed: 02/08/2023] Open
Abstract
The location of a mobile proton in acid-base complexes in aprotic solvents can be predicted using a simplified Adduct under Field (AuF) approach, where solute–solvent effects on the geometry of hydrogen bond are simulated using a fictitious external electric field. The parameters of the field have been estimated using experimental data on acid-base complexes in CDF3/CDClF2. With some limitations, they can be applied to the chemically similar CHCl3 and CH2Cl2. The obtained data indicate that the solute–solvent effects are critically important regardless of the type of complexes. The temperature dependences of the strength and fluctuation rate of the field explain the behavior of experimentally measured parameters.
Collapse
Affiliation(s)
- Ilya G. Shenderovich
- Institute of Organic Chemistry, University of Regensburg, Universitaetstrasse 31, 93053 Regensburg, Germany
- Correspondence: ; Tel.:+49-941-9434027
| | - Gleb S. Denisov
- Department of Physics, Saint-Petersburg State University, 198504 Saint-Petersburg, Russia;
| |
Collapse
|
21
|
Crosslinking ionic oligomers as conformable precursors to calcium carbonate. Nature 2019; 574:394-398. [PMID: 31619792 DOI: 10.1038/s41586-019-1645-x] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 08/01/2019] [Indexed: 11/08/2022]
Abstract
Inorganic materials have essential roles in society, including in building construction, optical devices, mechanical engineering and as biomaterials1-4. However, the manufacture of inorganic materials is limited by classical crystallization5, which often produces powders rather than monoliths with continuous structures. Several precursors that enable non-classical crystallization-such as pre-nucleation clusters6-8, dense liquid droplets9,10, polymer-induced liquid precursor phases11-13 and nanoparticles14-have been proposed to improve the construction of inorganic materials, but the large-scale application of these precursors in monolith preparations is limited by availability and by practical considerations. Inspired by the processability of polymeric materials that can be manufactured by crosslinking monomers or oligomers15, here we demonstrate the construction of continuously structured inorganic materials by crosslinking ionic oligomers. Using calcium carbonate as a model, we obtain a large quantity of its oligomers (CaCO3)n with controllable molecular weights, in which triethylamine acts as a capping agent to stabilize the oligomers. The removal of triethylamine initiates crosslinking of the (CaCO3)n oligomers, and thus the rapid construction of pure monolithic calcium carbonate and even single crystals with a continuous internal structure. The fluid-like behaviour of the oligomer precursor enables it to be readily processed or moulded into shapes, even for materials with structural complexity and variable morphologies. The material construction strategy that we introduce here arises from a fusion of classic inorganic and polymer chemistry, and uses the same cross-linking process for the manufacture the materials.
Collapse
|
22
|
Giba IS, Mulloyarova VV, Denisov GS, Tolstoy PM. Influence of Hydrogen Bonds in 1:1 Complexes of Phosphinic Acids with Substituted Pyridines on 1H and 31P NMR Chemical Shifts. J Phys Chem A 2019; 123:2252-2260. [PMID: 30807160 DOI: 10.1021/acs.jpca.9b00625] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two series of 1:1 complexes with strong OHN hydrogen bonds formed by dimethylphosphinic and phenylphosphinic acids with 10 substituted pyridines were studied experimentally by liquid state NMR spectroscopy at 100 K in solution in a low-freezing polar aprotic solvent mixture CDF3/CDClF2. The hydrogen bond geometries were estimated using previously established correlations linking 1H NMR chemical shifts of bridging protons with the O···H and H···N interatomic distances. A new correlation is proposed allowing one to estimate the interatomic distance within the OHN bridge from the displacement of 31P NMR signal upon complexation. We show that the values of 31P NMR chemical shifts are affected by an additional CH···O hydrogen bond formed between the P═O group of the acid and ortho-CH proton of the substituted pyridines. Breaking of this bond in the case of 2,6-disubstituted bases shifts the 31P NMR signal by ca. 1.5 ppm to the high field.
Collapse
Affiliation(s)
- Ivan S Giba
- Institute of Chemistry , St. Petersburg State University , Universitetskij pr. 26 , 198504 St. Petersburg , Russia.,Department of Physics , St. Petersburg State University , Ulyanovskaya 1 , 198504 St. Petersburg , Russia
| | - Valeria V Mulloyarova
- Institute of Chemistry , St. Petersburg State University , Universitetskij pr. 26 , 198504 St. Petersburg , Russia
| | - Gleb S Denisov
- Department of Physics , St. Petersburg State University , Ulyanovskaya 1 , 198504 St. Petersburg , Russia
| | - Peter M Tolstoy
- Institute of Chemistry , St. Petersburg State University , Universitetskij pr. 26 , 198504 St. Petersburg , Russia
| |
Collapse
|
23
|
Shenderovich IG. Simplified calculation approaches designed to reproduce the geometry of hydrogen bonds in molecular complexes in aprotic solvents. J Chem Phys 2018; 148:124313. [PMID: 29604820 DOI: 10.1063/1.5011163] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The impact of the environment onto the geometry of hydrogen bonds can be critically important for the properties of the questioned molecular system. The paper reports on the design of calculation approaches capable to simulate the effect of aprotic polar solvents on the geometric and NMR parameters of intermolecular hydrogen bonds. A hydrogen fluoride and pyridine complex has been used as the main model system because the experimental estimates of these parameters are available for it. Specifically, F-H, F⋯N, and H-N distances, the values of 15N NMR shift, and spin-spin coupling constants 1J(19F1H), 1hJ(1H15N), and 2hJ(19F15N) have been analyzed. Calculation approaches based on the gas-phase and the Polarizable Continuum Model (PCM) approximations and their combinations with geometric constraints and additional noncovalent interactions have been probed. The main result of this work is that the effect of an aprotic polar solvent on the geometry of a proton-donor⋯H⋯proton-acceptor complex cannot be reproduced under the PCM approximation if no correction for solvent-solute interactions is made. These interactions can be implicitly accounted for using a simple computational protocol.
Collapse
Affiliation(s)
- Ilya G Shenderovich
- Institute of Organic Chemistry, University of Regensburg, Universitaetstrasse 31, 93053 Regensburg, Germany
| |
Collapse
|
24
|
Xu HL, Li QZ, Scheiner S. Effect of Magnesium Bond on the Competition Between Hydrogen and Halogen Bonds and the Induction of Proton and Halogen Transfer. Chemphyschem 2018; 19:1456-1464. [PMID: 29544030 DOI: 10.1002/cphc.201800102] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Indexed: 01/18/2023]
Abstract
HOX (X=Cl, Br, I, and At) can engage in either a H-bond (HB) or halogen bond (XB) with a base-like HCN, NH3 , and imidazole. Although the former is energetically preferred for X=Cl and Br, it is the XB that is more stable for At, with I showing little preference. MgY2 forms a Mg-bond with the O atom of HOX, which grows stronger in the order X=Cl<Br<I<At and Y=F<Cl<Br. When all three molecules are combined, both the Mg and the H/X bonds are cooperatively strengthened to a large degree. Rather than causing a reversal in the HB/XB competition, the Mg-bond acts primarily to amplify the natural preference within the dimer. The Mg-bond induces a certain degree of transfer from O to N of the bridging atom in the H/X bond. Comparison is also made with the effects of a Be-bond.
Collapse
Affiliation(s)
- Hui-Li Xu
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
| | - Qing-Zhong Li
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, 84322-0300, USA
| |
Collapse
|
25
|
Zhang J, Wei Y, Li W, Cheng J, Li Q. Triel-hydride triel bond between ZX3
(Z = B and Al; X = H and Me) and THMe3
(T = Si, Ge and Sn). Appl Organomet Chem 2018. [DOI: 10.1002/aoc.4367] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Jingru Zhang
- Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering; Yantai University; Yantai 264005 People's Republic of China
| | - Yuanxin Wei
- Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering; Yantai University; Yantai 264005 People's Republic of China
| | - Wenzuo Li
- Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering; Yantai University; Yantai 264005 People's Republic of China
| | - Jianbo Cheng
- Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering; Yantai University; Yantai 264005 People's Republic of China
| | - Qingzhong Li
- Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering; Yantai University; Yantai 264005 People's Republic of China
| |
Collapse
|
26
|
Van Hoozen BL, Petersen PB. Vibrational tug-of-war: The pKAdependence of the broad vibrational features of strongly hydrogen-bonded carboxylic acids. J Chem Phys 2018; 148:134309. [PMID: 29626887 DOI: 10.1063/1.5026675] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Brian L. Van Hoozen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Poul B. Petersen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| |
Collapse
|
27
|
Levina E, Penkov NV, Rodionova NN, Tarasov SA, Barykina DV, Vener MV. Hydration of the Carboxylate Group in Anti-Inflammatory Drugs: ATR-IR and Computational Studies of Aqueous Solution of Sodium Diclofenac. ACS OMEGA 2018; 3:302-313. [PMID: 30023777 PMCID: PMC6044930 DOI: 10.1021/acsomega.7b01034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 12/27/2017] [Indexed: 05/12/2023]
Abstract
Diclofenac (active ingredient of Voltaren) has a significant, multifaceted role in medicine, pharmacy, and biochemistry. Its physical properties and impact on biomolecular structures still attract essential scientific interest. However, its interaction with water has not been described yet at the molecular level. In the present study, we shed light on the interaction between the steric hindrance (the intramolecular N-H···O bond, etc.) carboxylate group (-CO2-) with water. Aqueous solution of sodium declofenac is investigated using attenuated total reflection-infrared (ATR-IR) and computational approaches, i.e., classical molecular dynamics (MD) simulations and density functional theory (DFT). Our coupled classical MD simulations, DFT calculations, and ATR-IR spectroscopy results indicated that the -CO2- group of the diclofenac anion undergoes strong specific interactions with the water molecules. The combined experimental and theoretical techniques provide significant insights into the spectroscopic manifestation of these interactions and the structure of the hydration shell of the -CO2- group. Moreover, the developed methodology for the theoretical analysis of the ATR-IR spectrum could serve as a template for the future IR/Raman studies of the strong interaction between the steric hindrance -CO2- group of bioactive molecules with the water molecules in dilute aqueous solutions.
Collapse
Affiliation(s)
- Elena
O. Levina
- Department
of Molecular and Chemical Physics, Moscow
Institute of Physics and Technology, 7 Institutskiy per., 141700 Dolgoprudny, Russia
| | - Nikita V. Penkov
- Department
of Methods of Optical and Spectral Analysis, Institute of Cell Biophysics, Russian Academy of Sciences, 3 Institutskaya Street, 142292 Pushchino, Russia
| | - Natalia N. Rodionova
- OOO
“NPF” Materia Medica Holding, 47-1 Trifonovskaya Street, 129272 Moscow, Russia
| | - Sergey A. Tarasov
- OOO
“NPF” Materia Medica Holding, 47-1 Trifonovskaya Street, 129272 Moscow, Russia
| | - Daria V. Barykina
- OOO
“NPF” Materia Medica Holding, 47-1 Trifonovskaya Street, 129272 Moscow, Russia
| | - Mikhail V. Vener
- Department
of Quantum Chemistry, Mendeleev University
of Chemical Technology, 9 Miusskaya Square, 125047 Moscow, Russia
- E-mail:
| |
Collapse
|
28
|
Malm C, Kim H, Wagner M, Hunger J. Complexity in Acid-Base Titrations: Multimer Formation Between Phosphoric Acids and Imines. Chemistry 2017; 23:10853-10860. [PMID: 28597513 PMCID: PMC5582606 DOI: 10.1002/chem.201701576] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Indexed: 11/08/2022]
Abstract
Solutions of Brønsted acids with bases in aprotic solvents are not only common model systems to study the fundamentals of proton transfer pathways but are also highly relevant to Brønsted acid catalysis. Despite their importance the light nature of the proton makes characterization of acid-base aggregates challenging. Here, we track such acid-base interactions over a broad range of relative compositions between diphenyl phosphoric acid and the base quinaldine in dichloromethane, by using a combination of dielectric relaxation and NMR spectroscopy. In contrast to what one would expect for an acid-base titration, we find strong deviations from quantitative proton transfer from the acid to the base. Even for an excess of the base, multimers consisting of one base and at least two acid molecules are formed, in addition to the occurrence of proton transfer from the acid to the base and simultaneous formation of ion pairs. For equimolar mixtures such multimers constitute about one third of all intermolecular aggregates. Quantitative analysis of our results shows that the acid-base association constant is only around six times larger than that for the acid binding to an acid-base dimer, that is, to an already protonated base. Our findings have implications for the interpretation of previous studies of reactive intermediates in organocatalysis and provide a rationale for previously observed nonlinear effects in phosphoric acid catalysis.
Collapse
Affiliation(s)
- Christian Malm
- Department of Molecular SpectroscopyMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Heejae Kim
- Department of Molecular SpectroscopyMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Manfred Wagner
- Department of Molecular SpectroscopyMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Johannes Hunger
- Department of Molecular SpectroscopyMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| |
Collapse
|
29
|
Pylaeva SA, Elgabarty H, Sebastiani D, Tolstoy PM. Symmetry and dynamics of FHF− anion in vacuum, in CD2Cl2 and in CCl4. Ab initio MD study of fluctuating solvent–solute hydrogen and halogen bonds. Phys Chem Chem Phys 2017; 19:26107-26120. [DOI: 10.1039/c7cp04493c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Asymmetric solvation of FHF− by halogen- and hydrogen-bonding solvents breaks the symmetry of the anion.
Collapse
Affiliation(s)
- S. A. Pylaeva
- Institute of Chemistry, Martin-Luther Universität Halle-Wittenberg
- Germany
| | - H. Elgabarty
- Institute of Chemistry, Martin-Luther Universität Halle-Wittenberg
- Germany
| | - D. Sebastiani
- Institute of Chemistry, Martin-Luther Universität Halle-Wittenberg
- Germany
| | - P. M. Tolstoy
- Center for Magnetic Resonance, St. Petersburg State University
- Russia
| |
Collapse
|