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Seo D, Seong S, Kim H, Oh HS, Lee JH, Kim H, Kim YO, Maeda S, Chikami S, Hayashi T, Noh J. Molecular Self-Assembly and Adsorption Structure of 2,2'-Dipyrimidyl Disulfides on Au(111) Surfaces. Molecules 2024; 29:846. [PMID: 38398598 PMCID: PMC10892263 DOI: 10.3390/molecules29040846] [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: 01/22/2024] [Revised: 02/08/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
The effects of solution concentration and pH on the formation and surface structure of 2-pyrimidinethiolate (2PymS) self-assembled monolayers (SAMs) on Au(111) via the adsorption of 2,2'-dipyrimidyl disulfide (DPymDS) were examined using scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS). STM observations revealed that the formation and structural order of 2PymS SAMs were markedly influenced by the solution concentration and pH. 2PymS SAMs formed in a 0.01 mM ethanol solution were mainly composed of a more uniform and ordered phase compared with those formed in 0.001 mM or 1 mM solutions. SAMs formed in a 0.01 mM solution at pH 2 were composed of a fully disordered phase with many irregular and bright aggregates, whereas SAMs formed at pH 7 had small ordered domains and many bright islands. As the solution pH increased from pH 7 to pH 12, the surface morphology of 2PymS SAMs remarkably changed from small ordered domains to large ordered domains, which can be described as a (4√2 × 3)R51° packing structure. XPS measurements clearly showed that the adsorption of DPymDS on Au(111) resulted in the formation of 2PymS (thiolate) SAMs via the cleavage of the disulfide (S-S) bond in DPymDS, and most N atoms in the pyrimidine rings existed in the deprotonated form. The results herein will provide a new insight into the molecular self-assembly behaviors and adsorption structures of DPymDS molecules on Au(111) depending on solution concentration and pH.
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Affiliation(s)
- Dongjin Seo
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea; (D.S.); (S.S.); (H.K.); (H.S.O.); (J.H.L.); (H.K.); (Y.O.K.)
| | - Sicheon Seong
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea; (D.S.); (S.S.); (H.K.); (H.S.O.); (J.H.L.); (H.K.); (Y.O.K.)
| | - Haeri Kim
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea; (D.S.); (S.S.); (H.K.); (H.S.O.); (J.H.L.); (H.K.); (Y.O.K.)
| | - Hyun Su Oh
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea; (D.S.); (S.S.); (H.K.); (H.S.O.); (J.H.L.); (H.K.); (Y.O.K.)
| | - Jun Hyeong Lee
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea; (D.S.); (S.S.); (H.K.); (H.S.O.); (J.H.L.); (H.K.); (Y.O.K.)
| | - Hongki Kim
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea; (D.S.); (S.S.); (H.K.); (H.S.O.); (J.H.L.); (H.K.); (Y.O.K.)
| | - Yeon O Kim
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea; (D.S.); (S.S.); (H.K.); (H.S.O.); (J.H.L.); (H.K.); (Y.O.K.)
| | - Shoichi Maeda
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan; (S.M.); (S.C.)
| | - Shunta Chikami
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan; (S.M.); (S.C.)
| | - Tomohiro Hayashi
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan; (S.M.); (S.C.)
| | - Jaegeun Noh
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea; (D.S.); (S.S.); (H.K.); (H.S.O.); (J.H.L.); (H.K.); (Y.O.K.)
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan; (S.M.); (S.C.)
- Research Institute for Convergence of Basic Science, Hanyang University, Seoul 04763, Republic of Korea
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Singh M, Baruah JB. Combinations of Tautomeric Forms and Neutral-Cationic Forms in the Cocrystals of Sulfamethazine with Carboxylic Acids. ACS OMEGA 2019; 4:11609-11620. [PMID: 31460268 PMCID: PMC6682086 DOI: 10.1021/acsomega.9b01437] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 06/24/2019] [Indexed: 05/15/2023]
Abstract
The cocrystals of sulfamethazine with different acids, namely, 2-mercaptophenylcarboxylic acid, 2,6-pyridinedicarboxylic acid, 4-(4-hydroxyphenylazo)phenylcarboxylic acid, 3-(4-hydroxyphenyl)propanoic acid, and 4-(phenyl)phenylcarboxylic acid, are studied here. Each has distinct notable supramolecular features. The pyrimidin-2-amine unit of the sulfamethazine provided unique examples of cocrystals in which amidine and imidine forms or neutral and protonated forms of sulfamethazine are observed in 2:2 ratios. Hence, this study provides avenues to explore cocrystals with tautomeric forms together in a cocrystal and also neutral and protonated cocrystal partners as apparent multicomponents in cocrystals. Among the cocrystals, three of them have the amidine form of the sulfamethazine in respective self-assembly. The cocrystal of 2-mercapto-phenylcarboxylic acid with sulfamethazine has the amidine form and it has the distinction of having S-H···π interactions. The cocrystal of sulfamethazine with 2,6-pyridinecarboxylic acid is a rare example of a 1:1 cocrystal of sulfmethazine with dicarboxylic acid. It has methanol molecules as a solvent of crystallization. Sulfamethazine forms a hydrated cocrystal with 4-(4-hydroxyphenylazo)-phenylcarboxylic acid that has conventional R 2 2(8) synthons of amidine hydrogen-bonding with carboxylic acid. The phenolic part of the acid component is anchored to the water molecule and provides a robust self-assembly. The hydrated cocrystal of sulfamethazine with 3-(4-hydroxyphenyl)propanoic acid (2:2 cocrystal) has two independent molecules of sulfamethazine, one in amidine form and the other in imidine form. It has two neutral carboxylic acids anchored through complementary hydrogen bonds and also has two water molecules of crystallization. The cocrystal of sulfamethazine with 4-(phenyl)phenylcarboxylic acid is also a 2:2 cocrystal. It is a di-hydrate, which has a neutral and protonated form of sulfamethazine. The neutral form is hydrogen-bonded to a neutral carboxylic acid, whereas the protonated form is charge-assisted hydrogen-bonded to the corresponding carboxylate anion.
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Affiliation(s)
- Munendra
Pal Singh
- Department of Chemistry, Indian
Institute of Technology Guwahati, Guwahati 781 039 Assam, India
| | - Jubaraj B. Baruah
- Department of Chemistry, Indian
Institute of Technology Guwahati, Guwahati 781 039 Assam, India
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Liu X, Wei X, Zhou H, Meng S, Zhao Y, Xue J, Zheng X. UV and Resonance Raman Spectroscopic and Theoretical Studies on the Solvent-Dependent Ground and Excited-State Thione → Thiol Tautomerization of 4,6-Dimethyl-2-mercaptopyrimidine (DMMP). J Phys Chem A 2018; 122:5710-5720. [PMID: 29889517 DOI: 10.1021/acs.jpca.8b04525] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The vibrational spectra of 4,6-dimethyl-2-mercaptopyrimidine (DMMP) in acetonitrile, methanol, and water were assigned by resonance Raman spectroscopy through a combination of Fourier-transform infrared spectroscopy (FT-IR), FT-Raman UV-vis spectroscopy, and density functional theoretical (DFT) calculations. The FT-Raman spectra show that the neat solid DMMP is formed as a dimer due to intermolecular hydrogen bonding. In methanol and water, however, the majority of the Raman spectra were assigned to the vibrational modes of DMMP(solvent) n ( n = 1-4) clusters containing NH···O hydrogen bonds. The intermolecular NH···O hydrogen bond interactions, which are key constituents of the stable DMMP thione structure, revealed significant structural differences in acetonitrile, methanol, and water. In addition, UV-induced hydrogen transfer isomeric reactions between the thione and thiol forms of DMMP were detected in water and acetonitrile. DFT calculations indicate that the observed thione → thiol tautomerization should occur easily in lower excited states in acetonitrile and water.
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Abd El-Fatah NA, Darweesh AF, Mohamed AA, Abdelhamid IA, Elwahy AH. Experimental and theoretical study on the regioselective bis- and polyalkylation of 2-mercaptonicotinonitrile and 2-mercaptopyrimidine-5-carbonitrile derivatives. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.01.047] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Experimental and theoretical investigations on the tautomerism of 1-phenyl-2-thiobarbituric acid and its methylation reaction. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2012.12.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Owczarzak AM, Kourkoumelis N, Hadjikakou SK, Kubicki M. The impact of the anion size on the crystal packing in 2-mercaptopyrimidine halides; isostructurality and polymorphism. CrystEngComm 2013. [DOI: 10.1039/c3ce40240a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Freeman F, Lau DJ, Patel AR, Pavia PR, Willey JD. Substituent Effects on Singlet−Triplet Gaps and Mechanisms of 1,2-Rearrangements of 1,3-Oxazol-2-ylidenes to 1,3-Oxazoles. J Phys Chem A 2008; 112:8775-84. [DOI: 10.1021/jp8030286] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fillmore Freeman
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025
| | - Desirae J. Lau
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025
| | - Atitkumar R. Patel
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025
| | - Paulo R. Pavia
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025
| | - Justin D. Willey
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025
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de Greef TFA, Ligthart GBWL, Lutz M, Spek AL, Meijer EW, Sijbesma RP. The Mechanism of Ureido-Pyrimidinone:2,7-Diamido-Naphthyridine Complexation and the Presence of Kinetically Controlled Pathways in Multicomponent Hydrogen-Bonded Systems. J Am Chem Soc 2008; 130:5479-86. [DOI: 10.1021/ja709971y] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tom F. A. de Greef
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Bijvoet Center for Biomolecular Research, Crystal and Structural Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - G. B. W. L. Ligthart
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Bijvoet Center for Biomolecular Research, Crystal and Structural Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Martin Lutz
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Bijvoet Center for Biomolecular Research, Crystal and Structural Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Anthony L. Spek
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Bijvoet Center for Biomolecular Research, Crystal and Structural Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - E. W. Meijer
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Bijvoet Center for Biomolecular Research, Crystal and Structural Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Rint P. Sijbesma
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Bijvoet Center for Biomolecular Research, Crystal and Structural Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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Freeman F, Po HN, Ho TS, Wang X. Electrochemical Oxidation of 2-Pyrimidinethiols and Theoretical Study of Their Dimers, Disulfides, Sulfenyl Radicals, and Tautomers. J Phys Chem A 2008; 112:1643-55. [DOI: 10.1021/jp076545y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fillmore Freeman
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025
| | - Henry N. Po
- Department of Chemistry and Biochemistry, California State University, Long Beach, Long Beach, California 90840
| | - Thach S. Ho
- Department of Chemistry and Biochemistry, California State University, Long Beach, Long Beach, California 90840
| | - Ximeng Wang
- Department of Chemistry and Biochemistry, California State University, Long Beach, Long Beach, California 90840
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Greer EM, Aebisher D, Greer A, Bentley R. Computational studies of the tropone natural products, thiotropocin, tropodithietic acid, and troposulfenin. Significance of thiocarbonyl-enol tautomerism. J Org Chem 2007; 73:280-3. [PMID: 18062698 DOI: 10.1021/jo7018416] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Computations provide insight to the stability and isomeric possibilities of thiotropocin, tropodithietic acid, and troposulfenin. Thiotropocin and tropodithietic acid contain a flat 7-membered ring and delocalized pi-bonds similar to those of tropylium ion (C(7)H(7)(+)). Troposulfenin is far less stable; it contains a puckered tropone ring and localized bonds similar to 1,3,5-cycloheptatriene. A facile 1,5-hydrogen shift suggests that thiotropocin and tropodithietic acid exist as a pair of interconverting tautomers. Loss of an acidic proton from these three tautomers produces the same conjugate base structure.
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Affiliation(s)
- Edyta M Greer
- Department of Chemistry and Graduate Center & The City University of New York, Brooklyn College, Brooklyn, New York 11210, USA
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Trujillo C, Mó O, Yáñez M. A theoretical study of hydration effects on the prototropic tautomerism of selenouracils. Org Biomol Chem 2007; 5:3092-9. [PMID: 17878967 DOI: 10.1039/b708045j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The prototropic tautomerism of 2-, 4-selenouracil and 2,4-diselenouracil has been studied using density functional theory (DFT) methods, at the B3LYP/6-311 + G(3df,2p)//B3LYP/6-31G(d,p) level. The relative stability order of selenouracil tautomers does not resemble that of uracil tautomers, but it is similar to that of thiouracils, even though the energy gaps between the different tautomers of selenouracils are smaller than for thiouracils. The tautomerism activation barriers are high enough as to conclude that only the oxo-selenone or the diselenone structures should be found in the gas phase. The specific interaction with one water molecule reduces these barriers by a half, but still the oxo-selenone form is always the most stable tautomer. The addition of a second water molecule has a relatively small effect, as well as bulk effects, evaluated by means of a continuum-polarized model. For isolated 2- and 4-selenouracils, the more favorable tautomerization process corresponds to a hydrogen transfer towards the selenium atom, the activation barriers for transfer towards the oxygen atom being much higher. This situation changes when specific and bulk effects are included, and the latter process becomes the more favorable one. For 2,4-diselenouracil the more favorable tautomerization, in the gas phase, corresponds to the H shift from N1 to the Se atom at C2, while solvation effects favor the transfer from N3 to the Se atom at C4.
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Affiliation(s)
- Cristina Trujillo
- Departamento de Química, C-9, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
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