1
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Gao Y, Xu S, Qiao J, Wang C, Wang K, Sun J, Liu L, Li L, Liang M, Hu K. AZIN2 is associated with apoptosis of germ cells in undescended testis. Cells Dev 2024; 179:203925. [PMID: 38797332 DOI: 10.1016/j.cdev.2024.203925] [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: 07/26/2023] [Revised: 04/24/2024] [Accepted: 05/03/2024] [Indexed: 05/29/2024]
Abstract
Undescended testis (UDT), known as cryptorchidism (CRY), is a common congenital disorder in which one or both testicles do not descend normally into the scrotum. A unilateral UDT model was established by inducing UDT in mice through surgery. The results showed that the testis in the UDT model group was abnormal; the lumen of the seminiferous tubule was atrophic; apoptosis, necrosis and shedding were observed in many of the germ cells; the level of sex hormones was abnormal; and mature sperm was reduced. Subsequently, transcriptome sequencing was conducted on the testicular tissue of UDT model mice. Through analysis and verification of differential genes, AZIN2 was identified as playing a key role in the decline in male fertility caused by cryptorchidism. AZIN2 expression and spermine content was down-regulated in the testis of the UDT group. We then used a combination of hypoxanthine and xanthine to create a GC-1 cell damage model. In this model, AZIN2 expression and spermine content was down-regulated. When si-Azin2 transfected GC-1 cells, cell viability and proliferation were decreased. However, in the GC-1 cell damage model transfected with Azin2 over-expressed plasmid, AZIN2 expression and spermine content was up-regulated, reversing the cell damage caused by hypoxanthine and xanthine, and restoring the proliferation ability of GC-1 cells. These results indicate that in UDT, down-regulated AZIN2 expression is a factor in testicular damage. This discussion of the connection between AZIN2 and germ cells has important clinical significance as it provides an important reference for the diagnosis and treatment of cryptorchidism.
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Affiliation(s)
- Yuanyuan Gao
- School of Life Science, Bengbu Medical University, Bengbu, Anhui, People's Republic of China
| | - Shumin Xu
- School of Life Science, Bengbu Medical University, Bengbu, Anhui, People's Republic of China
| | - Jiajun Qiao
- School of Life Science, Bengbu Medical University, Bengbu, Anhui, People's Republic of China
| | - Chen Wang
- School of Life Science, Bengbu Medical University, Bengbu, Anhui, People's Republic of China
| | - Kaixian Wang
- School of Life Science, Bengbu Medical University, Bengbu, Anhui, People's Republic of China
| | - Junpei Sun
- First Affiliated Hospital, Bengbu Medical University, Bengbu, Anhui, People's Republic of China
| | - Lei Liu
- First Affiliated Hospital, Bengbu Medical University, Bengbu, Anhui, People's Republic of China
| | - Leina Li
- School of Life Science, Bengbu Medical University, Bengbu, Anhui, People's Republic of China
| | - Meng Liang
- School of Life Science, Bengbu Medical University, Bengbu, Anhui, People's Republic of China.
| | - Ke Hu
- School of Life Science, Bengbu Medical University, Bengbu, Anhui, People's Republic of China.
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2
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Osifová Z, Socha O, Mužíková Čechová L, Šála M, Janeba Z, Dračínský M. Hydrogen‐Bonding Interactions of Methylated Adenine Derivatives. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Zuzana Osifová
- Institute of Organic Chemistry and Biochemistry ASCR Flemingovo nám. 2 16000 Prague Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University Hlavova 2030 Prague 128 00 Czech Republic
| | - Ondřej Socha
- Institute of Organic Chemistry and Biochemistry ASCR Flemingovo nám. 2 16000 Prague Czech Republic
| | - Lucie Mužíková Čechová
- Institute of Organic Chemistry and Biochemistry ASCR Flemingovo nám. 2 16000 Prague Czech Republic
| | - Michal Šála
- Institute of Organic Chemistry and Biochemistry ASCR Flemingovo nám. 2 16000 Prague Czech Republic
| | - Zlatko Janeba
- Institute of Organic Chemistry and Biochemistry ASCR Flemingovo nám. 2 16000 Prague Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry ASCR Flemingovo nám. 2 16000 Prague Czech Republic
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3
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Rozenberg M, Fausto R, Reva I. Variable temperature FTIR spectra of polycrystalline purine nucleobases and estimating strengths of individual hydrogen bonds. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 251:119323. [PMID: 33508682 DOI: 10.1016/j.saa.2020.119323] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/19/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
In the first part of this work, we report the FTIR spectra of pure NH and isotopically substituted ND (10-15% D and 80-90% D) polycrystalline hypoxanthine, xanthine, adenine and guanine recorded in the 400-4000 cm-1 range, as a function of temperature (10-300 K). We provide assignments of the stretching and out-of-plane bending amine (NH2) and imine (NH) bands to the distinct H-bonds present in the crystal, based on the temperature sensitivity and isotopic exchange behavior. Empirical correlations between spectral and thermodynamic or structural parameters enabled us to estimate the energies and lengths of H-bonds in the studied nucleobase crystals and to correlate them with literature data. The empirical H-bonding energies are compared with H-bonding and stacking energies computed for hypoxanthine. In the second part, strategies for using the empirical correlations together with information extracted from quantum mechanical data (in particular from the Bader's quantum theory of atoms in molecules, QTAIM) for the evaluation of hydrogen bonding properties are discussed, and their advantages and drawbacks pointed out. The justification for a cooperative use of quantum-mechanical calculations with empirical spectra-energy correlations is discussed.
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Affiliation(s)
- M Rozenberg
- The Hebrew University of Jerusalem, Department of Inorganic and Analytical Chemistry, Jerusalem, Givat Ram 91904, Israel.
| | - R Fausto
- University of Coimbra, CQC, Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - I Reva
- University of Coimbra, CQC, Department of Chemistry, 3004-535 Coimbra, Portugal; University of Coimbra, CIEPQPF, Department of Chemical Engineering, 3030-790 Coimbra, Portugal.
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4
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Wu B, Liu Y, Chen F, Li J, Yu Y, Zhou Y, Li L, Xiao J, Ma Y. Investigation on the formation mechanism of twinned crystals of hypoxanthine-doped beta-phase anhydrous guanine microplatelets. CrystEngComm 2021. [DOI: 10.1039/d1ce00148e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Herein, hypoxanthine-doped β phase anhydrous guanine (I-doped β-AG) twinned crystals with varying hypoxanthine contents were obtained in formamide. The occlusion of hypoxanthine in β-AG might be a key factor for formation of twinned β-AG crystals.
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Affiliation(s)
- Bianbian Wu
- MOE Key Laboratory of Cluster Science
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing
- China
| | - Yanan Liu
- MOE Key Laboratory of Cluster Science
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing
- China
| | - Fenghua Chen
- MOE Key Laboratory of Cluster Science
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing
- China
| | - Jiangfeng Li
- MOE Key Laboratory of Cluster Science
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing
- China
| | - Yue Yu
- College of Chemistry
- Peking University
- Beijing
- China
| | - Yinglin Zhou
- College of Chemistry
- Peking University
- Beijing
- China
| | - Ling Li
- Department of Mechanical Engineering
- Virginia Polytechnic Institute and State University
- Blacksburg
- 24061 USA
| | - Jie Xiao
- Department of Highly Sensitive X-ray Spectroscopy
- Helmholtz-Zentrum Berlin für Materialien und Energie
- Berlin
- Germany
| | - Yurong Ma
- MOE Key Laboratory of Cluster Science
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing
- China
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5
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Abedini F, Omidyan R, Salehi M. Theoretical insights on nonradiative deactivation mechanisms of protonated xanthine. J Photochem Photobiol A Chem 2019. [DOI: 10.1016/j.jphotochem.2019.112067] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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6
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Vallejo Narváez WE, Jiménez EI, Romero-Montalvo E, Sauza-de la Vega A, Quiroz-García B, Hernández-Rodríguez M, Rocha-Rinza T. Acidity and basicity interplay in amide and imide self-association. Chem Sci 2018; 9:4402-4413. [PMID: 29896381 PMCID: PMC5956980 DOI: 10.1039/c8sc01020j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 04/05/2018] [Indexed: 12/23/2022] Open
Abstract
Simple acid–base properties explain the differences in amide and imide dimerisation, and represent an alternative to the secondary interactions hypothesis.
Amides dimerise more strongly than imides despite their lower acidity. Such an unexpected result has been rationalised in terms of the Jorgensen Secondary Interactions Hypothesis (JSIH) that involves the spectator (C
Created by potrace 1.16, written by Peter Selinger 2001-2019
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OS) and H-bonded (C
Created by potrace 1.16, written by Peter Selinger 2001-2019
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OHB) carbonyl groups in imides. Notwithstanding the considerable body of experimental and theoretical evidence supporting the JSIH, there are some computational studies which suggest that there might be other relevant intermolecular interactions than those considered in this model. We conjectured that the spectator carbonyl moieties could disrupt the resonance-assisted hydrogen bonds in imide dimers, but our results showed that this was not the case. Intrigued by this phenomenon, we studied the self-association of a set of amides and imides via1H-NMR, 1H-DOSY experiments, DFT calculations, QTAIM topological analyses of the electron density and IQA partitions of the electronic energy. These analyses revealed that there are indeed repulsions of the type OS···OHB in accordance with the JSIH but our data also indicate that the C
Created by potrace 1.16, written by Peter Selinger 2001-2019
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OS group has an overall attraction with the interacting molecule. Instead, we found correlations between self-association strength and simple Brønsted–Lowry acid/base properties, namely, N–H acidities and C
Created by potrace 1.16, written by Peter Selinger 2001-2019
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O basicities. The results in CDCl3 and CCl4 indicate that imides dimerise less strongly than structurally related amides because of the lower basicity of their carbonyl fragments, a frequently overlooked aspect in the study of H-bonding. Overall, the model proposed herein could provide important insights in diverse areas of supramolecular chemistry such as the study of multiple hydrogen-bonded adducts which involve amide or imide functional groups.
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Affiliation(s)
- Wilmer E Vallejo Narváez
- Institute of Chemistry , National Autonomous University of Mexico , Ciudad Universitaria , Circuito Exterior, Del. Coyoacán , Mexico City , 04510 , Mexico . ;
| | - Eddy I Jiménez
- Institute of Chemistry , National Autonomous University of Mexico , Ciudad Universitaria , Circuito Exterior, Del. Coyoacán , Mexico City , 04510 , Mexico . ;
| | - Eduardo Romero-Montalvo
- Institute of Chemistry , National Autonomous University of Mexico , Ciudad Universitaria , Circuito Exterior, Del. Coyoacán , Mexico City , 04510 , Mexico . ;
| | - Arturo Sauza-de la Vega
- Institute of Chemistry , National Autonomous University of Mexico , Ciudad Universitaria , Circuito Exterior, Del. Coyoacán , Mexico City , 04510 , Mexico . ;
| | - Beatriz Quiroz-García
- Institute of Chemistry , National Autonomous University of Mexico , Ciudad Universitaria , Circuito Exterior, Del. Coyoacán , Mexico City , 04510 , Mexico . ;
| | - Marcos Hernández-Rodríguez
- Institute of Chemistry , National Autonomous University of Mexico , Ciudad Universitaria , Circuito Exterior, Del. Coyoacán , Mexico City , 04510 , Mexico . ;
| | - Tomás Rocha-Rinza
- Institute of Chemistry , National Autonomous University of Mexico , Ciudad Universitaria , Circuito Exterior, Del. Coyoacán , Mexico City , 04510 , Mexico . ;
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7
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Brovarets’ OO, Zhurakivsky RO, Hovorun DM. A QM/QTAIM microstructural analysis of the tautomerisationviathe DPT of the hypoxanthine·adenine nucleobase pair. Mol Phys 2014. [DOI: 10.1080/00268976.2013.877170] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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8
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Brovarets’ OO, Hovorun DM. Prototropic tautomerism and basic molecular principles of hypoxanthine mutagenicity: an exhaustive quantum-chemical analysis. J Biomol Struct Dyn 2013; 31:913-36. [PMID: 22962845 DOI: 10.1080/07391102.2012.715041] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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9
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Brovarets’ OO, Zhurakivsky RO, Hovorun DM. The physico-chemical mechanism of the tautomerisation via the DPT of the long Hyp∗·Hyp Watson–Crick base pair containing rare tautomer: A QM and QTAIM detailed look. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.05.067] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Röttger K, Sönnichsen FD, Temps F. Ultrafast electronic deactivation dynamics of the inosine dimer--a model case for H-bonded purine bases. Photochem Photobiol Sci 2013; 12:1466-73. [PMID: 23788062 DOI: 10.1039/c3pp50093d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The structural properties and ultrafast electronic deactivation dynamics of the inosine dimer in CHCl3 have been investigated by two-dimensional (1)H NMR and static FTIR spectroscopy and by femtosecond time-resolved transient absorption spectroscopy, respectively. The (1)H NMR and IR spectra show the formation of a well-defined, symmetric dimer with an association equilibrium constant of KI·I = 690 ± 100 M(-1). The excited-state dynamics after photoexcitation at λpump = 260 nm monitored by ultrafast absorption spectroscopy show great similarity with those of the monomer inosine in an aqueous solution and are governed by a decay time of τ = 90 ± 10 fs, which is one of the shortest electronic lifetimes of all nucleobases and nucleobase dimers studied so far. On the basis of these observations, the inosine dimer is expected to follow a similar relaxation pathway as the monomer, involving an out-of-plane deformation of the six-membered ring. The importance of the C(2) position for the electronic deactivation of hypoxanthine and guanine is discussed. The obtained well-determined structure and straightforward dynamics qualify the inosine dimer as an excellent reference case for more complicated systems such as the G·G dimer and the G·C and A·T Watson-Crick pairs.
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Affiliation(s)
- Katharina Röttger
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
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11
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Basílio Janke EM, Weisz K. A TT Dinucleotide with a Nonionic Silyl Backbone: Impact on Conformation and H-Bond Mediated Base Pairing as Studied by Low-Temperature NMR. Z PHYS CHEM 2013. [DOI: 10.1524/zpch.2013.0382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
A TSiT dinucleotide linked through a nonionic diisopropylsilyl backbone has been synthesized and studied for its self-association through base–base recognition together with a free thymidine nucleoside. To characterize hydrogen-bonded associates in more detail, NMR measurements were performed in a freonic solvent at temperatures as low as 113 K in the slow hydrogen bond exchange regime. For the thymidine, TT base pairs with both the 2- and 4-carbonyl engaged in hydrogen bonds to the imino proton were observed. Whereas hydrogen bonds to the O4 acceptor are stronger as evidenced by a more deshielded proton in the hydrogen bridge when compared to hydrogen bonds to the O2 acceptor, the latter is nevertheless slightly favored over O4 in the H-bond formation of TT base pairs. The diisopropylsilyl linkage of the TSiT dinucleotide has no significant impact on the geometry and strength of formed NH–O2 and NH–O4 hydrogen bonds indicating, that the silyl backbone does not compromise the alignment of bases and does not pose any restrictions to the cyclic hydrogen bond formation between thymidines of the two strands. However, NMR results point to an exclusive formation of TSiT duplexes with an antiparallel strand orientation.
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12
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Basílio Janke EM, Weisz K. Low-Temperature NMR Studies on the Geometry of Base Pairs Involving 5-Substituted Uracil Derivatives. J Phys Chem B 2013; 117:4853-9. [DOI: 10.1021/jp400348x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Eline M. Basílio Janke
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Straße 4,
D-17487 Greifswald, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Straße 4,
D-17487 Greifswald, Germany
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13
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Villabona-Monsalve JP, Noria R, Matsika S, Peón J. On the Accessibility to Conical Intersections in Purines: Hypoxanthine and its Singly Protonated and Deprotonated Forms. J Am Chem Soc 2012; 134:7820-9. [DOI: 10.1021/ja300546x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Juan. P. Villabona-Monsalve
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria,
México, 04510,
D.F., México
| | - Raquel Noria
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria,
México, 04510,
D.F., México
| | - Spiridoula Matsika
- Department
of Chemistry, Temple University, 13th and
Norris Streets, Philadelphia
Pennsylvania 19122, United States
| | - Jorge Peón
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria,
México, 04510,
D.F., México
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14
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Ośmiałowski B, Kolehmainen E, Kowalska M. 2-Acylamino-6-pyridones: Breaking of an Intramolecular Hydrogen Bond by Self-association and Complexation with Double and Triple Hydrogen Bonding Counterparts. Uncommon Steric Effect on Intermolecular Interactions. J Org Chem 2012; 77:1653-62. [DOI: 10.1021/jo201800u] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Borys Ośmiałowski
- Faculty of Chemical Technology
and Engineering, University of Technology and Life Sciences, Seminaryjna 3, PL-85-326 Bydgoszcz, Poland
| | - Erkki Kolehmainen
- Department of Chemistry, University of Jyväskylä, P.O. Box 35,
FI-40014 Finland
| | - Magdalena Kowalska
- Faculty of Chemical Technology
and Engineering, University of Technology and Life Sciences, Seminaryjna 3, PL-85-326 Bydgoszcz, Poland
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15
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Janke EMB, Riechert-Krause F, Weisz K. Low-temperature NMR studies on inosine wobble base pairs. J Phys Chem B 2011; 115:8569-74. [PMID: 21644523 DOI: 10.1021/jp200840j] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Base pairs formed by the inosine nucleoside (I) play an important role in many physiological processes as well as in various DNA technologies. Relative stabilities and favored base pair geometries of free inosine wobble base pairs in aprotic solvents have been determined through (1)H NMR measurements at room temperature and at very low temperatures in a freonic solvent. As indicated by its significantly deshielded imino proton, the Watson-Crick-type I·C base pair forms a remarkably strong NHN hydrogen bond. For the thermodynamically less stable I·A wobble base pair, two configurations of similar population coexist at 133 K in the slow hydrogen bond exchange regime, namely a Watson-Crick(I)-Watson-Crick(A) geometry and a Watson-Crick(I)-Hoogsteen(A) geometry. I·U base pairs are stabilized by two rather weak hydrogen bonds and are significantly disfavored over inosine self-associates in a low-temperature Freon solution.
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16
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Engels B, Schmidt TC, Gatti C, Schirmeister T, Fink RF. Challenging Problems in Charge Density Determination: Polar Bonds and Influence of the Environment. ELECTRON DENSITY AND CHEMICAL BONDING II 2011. [DOI: 10.1007/430_2010_36] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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17
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Xiao Z, Weisz K. Base-base recognition of nonionic dinucleotide analogues in an apolar environment studied by low-temperature NMR spectroscopy. J Am Chem Soc 2010; 132:3862-9. [PMID: 20180555 DOI: 10.1021/ja910220s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Two self-complementary dinucleotide analogues T(Si)A and A(Si)T with a nonionic diisopropylsilyl-modified backbone were synthesized, and their association in a nonaqueous aprotic environment was studied by NMR spectroscopy. Using a CDClF(2)/CDF(3) solvent mixture, measurements at temperatures as low as 113 K allowed the observation and structural characterization of individual complexes in the slow exchange regime. The A(Si)T analogue associates to exclusively form a dinucleotide antiparallel duplex with regular Watson-Crick base pairing, but both A and T nucleosides exhibit a predominant C3'-endo sugar pucker reminiscent of an A-type conformation. In contrast to A(Si)T, the T(Si)A dinucleotide is found to exhibit significant variability and flexibility. Thus, different secondary structures with weaker hydrogen bonds for all T(Si)A structures are observed at low temperatures. Although a B-like Watson-Crick antiparallel dinucleotide duplex with a preferred C2'-endo sugar pucker largely predominates at temperatures above 153 K, two additional species, namely a dinucleotide Hoogsteen duplex with a syn glycosidic torsion angle of the adenosine nucleoside and a presumably intramolecularly folded structure, are increasingly populated upon further cooling. By adding typical DNA intercalators like anthracene or benz[c]acridine derivatives to the A(Si)T dinucleotide duplex in the aprotic solvent environment, no binding of the polycyclic aromatic molecules can be detected even at lower temperatures. Obviously, van der Waals and stacking interactions are insufficient to compensate for the other unfavorable contributions to the overall free energy of binding, and only in the presence of additional hydrophobic effects in an aqueous environment does binding occur.
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Affiliation(s)
- Zhou Xiao
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Str. 4, D-17489 Greifswald, Germany
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18
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Schlund S, Basílio Janke EM, Weisz K, Engels B. Predicting the tautomeric equilibrium of acetylacetone in solution. I. The right answer for the wrong reason? J Comput Chem 2010; 31:665-70. [PMID: 19557765 DOI: 10.1002/jcc.21354] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This study investigates how the various components (method, basis set, and treatment of solvent effects) of a theoretical approach influence the relative energies between keto and enol forms of acetylacetone, which is an important model system to study the solvent effects on chemical equilibria from experiment and theory. The computations show that the most popular density functional theory (DFT) approaches, such as B3LYP overestimate the stability of the enol form with respect to the keto form by approximately 10 kJ mol(-1), whereas the very promising SCS-MP2 approach is underestimating it. MP2 calculations indicate that in particular the basis set size is crucial. The Dunning Huzinaga double zeta basis (D95z(d,p)) used in previous studies overestimates the stability of the keto form considerably as does the popular split-valence plus polarization (SVP) basis. Bulk properties of the solvent included by continuum approaches strongly stabilize the keto form, but they are not sufficient to reproduce the reversal in stabilities measured by low-temperature nuclear magnetic resonance experiments in freonic solvents. Enthalpic and entropic effects further stabilize the keto form, however, the reversal is only obtained if also molecular effects are taken into account. Such molecular effects seem to influence only the energy difference between the keto and the enol forms. Trends arising due to variation in the dielectric constant of the solvent result from bulk properties of the solvent, i.e., are already nicely described by continuum approaches. As such this study delivers a deep insight into the abilities of various approaches to describe solvent effects on chemical equilibria.
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Affiliation(s)
- Sebastian Schlund
- Institute for Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
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19
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Sun X, Lee JK. Stability of DNA Duplexes Containing Hypoxanthine (Inosine): Gas versus Solution Phase and Biological Implications. J Org Chem 2010; 75:1848-54. [DOI: 10.1021/jo9023683] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Xuejun Sun
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901
| | - Jeehiun K. Lee
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901
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20
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Paasche A, Arnone M, Fink RF, Schirmeister T, Engels B. Origin of the reactivity differences of substituted aziridines: CN vs CC bond breakages. J Org Chem 2009; 74:5244-9. [PMID: 19719251 DOI: 10.1021/jo900505q] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Aziridines are broadly used as starting materials for various chemical syntheses, and the underlying reactions (CN vs CC bond breaking accompanied by an attack of a nucleophile or a dipolarophile) are strongly influenced by the substitution pattern. The present study investigates reaction courses of possible ring-opening reactions accompanied by the attack of a nucleophile for different substitution patterns of the aziridine. Information is obtained through the computation of the underlying potential energy surfaces and reaction paths. The results provide insight into the mechanisms of different ring-opening reactions and explain how the kinetics and thermodynamics of the reaction are influenced by substituents. This allows predicting substitution patterns that steer the reaction course to either CN or CC bond cleavage.
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Affiliation(s)
- Alexander Paasche
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, Würzburg D-97074, Germany
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21
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Janke EMB, Schlund S, Paasche A, Engels B, Dede R, Hussain I, Langer P, Rettig M, Weisz K. Tautomeric equilibria of 3-formylacetylacetone: low-temperature NMR spectroscopy and ab initio calculations. J Org Chem 2009; 74:4878-81. [PMID: 19485345 DOI: 10.1021/jo9004475] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Keto-enol tautomerization of 3-formylacetylacetone has been studied by NMR spectroscopy, ab initio, and DFT calculations in the gas phase and continuum solvation. By employing very low temperatures in a freonic solvent, tautomeric and conformational equilibria in the slow exchange regime were analyzed in detail. The beta-tricarbonyl compound always adopts a structure with an enolized keto group irrespective of an increasing dielectric constant of the solvent when lowering the temperature of the Freon mixture. This experimentally observed tautomeric distribution of 3-formylacetylacetone is correctly reproduced by continuum solvated DFT calculations.
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Affiliation(s)
- Eline M. Basílio Janke
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Sebastian Schlund
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Alexander Paasche
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Bernd Engels
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Rüdiger Dede
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Ibrar Hussain
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Peter Langer
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Michael Rettig
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Klaus Weisz
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
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22
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Mladenovic M, Arnone M, Fink RF, Engels B. Environmental effects on charge densities of biologically active molecules: do molecule crystal environments indeed approximate protein surroundings? J Phys Chem B 2009; 113:5072-82. [PMID: 19320453 DOI: 10.1021/jp809537v] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the present paper, we investigate whether crystal and enzyme environments influence the electron density (ED) of active compounds in a similar manner. This supposition is essential for high-resolution X-ray studies, which use the EDs obtained from crystals of the pure active compound as approximations for the ED of the active compound in its complex with the target enzyme. The EDs of such complexes determine the molecular recognition process between the targeted enzyme and active compound and are, hence, extremely useful tools for rational drug design. The approximation of such EDs by data obtained from crystals of the pure active compound is needed since high-resolution X-ray experiments of the target-ligand complexes are still extremely demanding. Quantum mechanical/molecular mechanical (QM/MM) and pure QM calculations are employed to determine the EDs of two inhibitors, the reversible trans-4-(aminomethyl)cyclohexane-1-carboxylic acid (AMCHA) and the irreversible E64c in four different environments (the enzyme-inhibitor complex, crystals of the pure compounds, a continuum solvation model, and the gas phase). Our investigation shows that the environment inside of the crystal of the pure active compound generally influences the ED of an active compound in a very similar way as the enzyme surrounding in the complex between the active compound and target enzyme. However, this does not hold any more if the geometrical arrangement of the inhibitor in the enzyme differs significantly from that in the crystal. While EDs computed for gas-phase environments deviate strongly from those in crystal and protein surroundings, polar solvent environments provide rather similar electron distributions. Thus, such continuum solvation models are very well suited to compute density databases which are to be employed for the determination of the ED of macromolecules.
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Affiliation(s)
- Milena Mladenovic
- Institut fur Organische Chemie, Universitat Wurzburg, Am Hubland, D-97074 Wurzburg, Germany
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23
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Buback V, Mladenovic M, Engels B, Schirmeister T. Rational Design of Improved Aziridine-Based Inhibitors of Cysteine Proteases. J Phys Chem B 2009; 113:5282-9. [DOI: 10.1021/jp810549n] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Verena Buback
- Institut für Pharmazie and Lebensmittelchemie, Institut für Organische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Milena Mladenovic
- Institut für Pharmazie and Lebensmittelchemie, Institut für Organische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Bernd Engels
- Institut für Pharmazie and Lebensmittelchemie, Institut für Organische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Tanja Schirmeister
- Institut für Pharmazie and Lebensmittelchemie, Institut für Organische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
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24
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Bartl T, Zacharová Z, Sečkářová P, Kolehmainen E, Marek R. NMR Quantification of Tautomeric Populations in Biogenic Purine Bases. European J Org Chem 2009. [DOI: 10.1002/ejoc.200801016] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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25
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Mladenovic M, Ansorg K, Fink RF, Thiel W, Schirmeister T, Engels B. Atomistic insights into the inhibition of cysteine proteases: first QM/MM calculations clarifying the stereoselectivity of epoxide-based inhibitors. J Phys Chem B 2008; 112:11798-808. [PMID: 18712902 DOI: 10.1021/jp803895f] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Due to their important role in many diseases, cysteine proteases represent new promising drug targets. An important class of cysteine-protease inhibitors is derived from the naturally occurring compound E64, possessing an epoxysuccinyl moiety as warhead. Experimental studies show stereoselectivity concerning the inhibition potency, e.g., a trans-configured epoxide ring is essential for inhibition, and furthermore, in most cases, the ( S, S)-configured inhibitors have a higher inhibition potency than their ( R, R)-counterparts. However, the underlying effects are not fully understood. In this work, such effects are investigated by classical molecular dynamics simulations and combined quantum mechanics/molecular modeling (QM/MM) calculations for the E64c-cathepsin B complex. Our computations reveal that the hydrogen bonding network between the enzyme and the E64c (or its derivatives) determines the stereoselectivity of the subsequent ring opening reaction by governing the distance between the attacking thiolate and the attacked C2 atom of the epoxide ring. For the ( S, S)-configuration, a strong network can be realized which enables a close contact between the reacting centers, so that the irreversible step becomes very efficient. The ( R, S)-configuration ( cis-configuration) can only form networks in which the two reacting centers are so far away from each other that the irreversible step can hardly happen. The ( R, R)-configuration is in between, less optimal than the ( S, S)-configuration but much better than the ( R, S)-configuration. Exceptions where the ( R, R)-configurations shows higher potency than the ( S, S) ones are also explained.
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Affiliation(s)
- Milena Mladenovic
- Institut fur Organische Chemie, Universitat Wurzburg, Am Hubland, Wurzburg, Germany
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26
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Mladenovic M, Fink RF, Thiel W, Schirmeister T, Engels B. On the origin of the stabilization of the zwitterionic resting state of cysteine proteases: a theoretical study. J Am Chem Soc 2008; 130:8696-705. [PMID: 18557615 DOI: 10.1021/ja711043x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Papain-like cysteine proteases are ubiquitous proteolytic enzymes. The protonated His199/deprotonated Cys29 ion pair (cathepsin B numbering) in the active site is essential for their proper functioning. The presence of this ion pair stands in contrast to the corresponding intrinsic residue p K a values, indicating a strong influence of the enzyme environment. In the present work we show by molecular dynamics simulations on quantum mechanical/molecular mechanical (QM/MM) potentials that the ion pair is stabilized by a complex hydrogen bond network which comprises several amino acids situated in the active site of the enzyme and 2-4 water molecules. QM/MM reaction path computations for the proton transfer from His199 to the thiolate of the Cys29 moiety indicate that the ion pair is about 32-36 kJ mol (-1) more stable than the neutral form if the whole hydrogen bonding network is active. Without any hydrogen bonding network the ion pair is predicted to be significantly less stable than the neutral form. QM/MM charge deletion analysis and QM model calculations are used to quantify the stabilizing effect of the active-site residues and the L1 helix in favor of the zwitterionic form. The active-site water molecules contribute about 30 kJ mol (-1) to the overall stabilization. Disruption of the hydrogen bonding network upon substrate binding is expected to enhance the nucleophilic reactivity of the thiolate.
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Affiliation(s)
- Milena Mladenovic
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
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27
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Mladenovic M, Junold K, Fink RF, Thiel W, Schirmeister T, Engels B. Atomistic insights into the inhibition of cysteine proteases: first QM/MM calculations clarifying the regiospecificity and the inhibition potency of epoxide- and aziridine-based inhibitors. J Phys Chem B 2008; 112:5458-69. [PMID: 18393547 DOI: 10.1021/jp711287c] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Epoxides and aziridines are important building blocks for inhibitors of cysteine proteases which are promising drug targets for many diseases. In spite of the large amount of experimental data concerning inhibition potency, structure-activity relationships, and structural arrangements of enzyme-inhibitor complexes, little is known about the basic principles which connect the substitution pattern with the resulting activities. To shed some light on this issue which is essential for the rational design of improved compounds, we have studied the inhibition processes theoretically for various inhibitors using quantum mechanical/molecular mechanical hybrid approaches and classical molecular dynamics simulations. The careful analysis of the computational results allows insight into the interactions which govern the regio- and stereospecificity of the interactions. Known structure-activity relationships are rationalized in terms of the same interactions that determine the measured pH dependencies. Inconsistencies in existing X-ray structures are resolved through comparison with the computed structures, which leads to a reassessment of the factors that control the inhibition potency. Similarities and differences in the mode of action of epoxide- and aziridine-based inhibitors are elucidated. Finally the small reaction barriers computed for the irreversible step in E64 analogues call into question the commonly accepted two-step model of inhibition since the second, irreversible step is predicted to be so fast that suitably oriented enzyme-inhibitor complexes will react rather than dissociate and equilibrate.
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Affiliation(s)
- Milena Mladenovic
- Institut für Organische Chemie, and Institut für Pharmazie und Lebensmittelchemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
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28
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Spickermann C, Felder T, Schalley C, Kirchner B. How Can Rotaxanes Be Modified by Varying Functional Groups at the Axle?—A Combined Theoretical and Experimental Analysis of Thermochemistry and Electronic Effects. Chemistry 2008; 14:1216-27. [DOI: 10.1002/chem.200700479] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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29
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Rutledge LR, Wheaton CA, Wetmore SD. A computational characterization of the hydrogen-bonding and stacking interactions of hypoxanthine. Phys Chem Chem Phys 2007; 9:497-509. [PMID: 17216066 DOI: 10.1039/b606388h] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The hydrogen-bonding and stacking interactions of hypoxanthine, a potential universal nucleobase, were calculated using a variety of methodologies (CCSD(T), MP2, B3LYP, PWB6K, AMBER). All methods predict that the hydrogen-bonding interaction in the hypoxanthine-cytosine pair is approximately 25 kJ mol(-1) stronger than that in the other dimers. Although the calculations support suggestions from experiments that hypoxanthine preferentially binds with cytosine, the trend in the calculated hydrogen-bond strengths for the remaining natural nucleobases do not show a strong correlation with the experimentally predicted binding preferences. However, our calculations suggest that the stacking interactions of hypoxanthine are similar in magnitude to the hydrogen-bonding interactions at all levels of theory (with the exception of B3LYP, which incorrectly predicts stacked dimers to be unstable). Therefore, stacking interactions should also be considered when analyzing the stability of DNA helices containing hypoxanthine and the use of larger models that account for both hydrogen-bonding and stacking within DNA duplexes will likely result in better agreement with experimental observations. For the majority of the dimers, PWB6K and AMBER provide reasonable binding strengths at reduced computational costs, and therefore will be useful techniques for considering larger models.
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Affiliation(s)
- Lesley R Rutledge
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick, Canada E4L 1G8
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Schlund S, Müller R, Grassmann C, Engels B. Conformational analysis of arginine in gas phase—A strategy for scanning the potential energy surface effectively. J Comput Chem 2007; 29:407-15. [PMID: 17631648 DOI: 10.1002/jcc.20798] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The determination of all possible low-lying energy conformers of flexible molecules is of fundamental interest for various applications. It necessitates a reliable conformational search that is able to detect all important minimum structures and calculates the energies on an adequate level of theory. This work presents a strategy to identify low-energy conformers using arginine as an example by means of a force-field based conformational search in combination with high-level geometry optimizations (RI-MP2/TZVPP+). The methods used for various stages in the conformational search strategy are shown and various pitfalls are discussed. We can show that electronic energies calculated on a DFT level of theory with standard exchange-correlation functionals strongly underestimate the intramolecular stabilization resulting from stacked orientations of the guanidine and carbonyl moiety of arginine due to the deficiency of DFT to describe dispersion effects. In this case by usage of electron correlation methods, low energy conformers comprising stacked arrangements that are counterintuitive become favorable.
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Affiliation(s)
- Sebastian Schlund
- Institute for Organic Chemistry, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
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31
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Schlund S, Schmuck C, Engels B. “Knock-Out” Analogues as a Tool to Quantify Supramolecular Processes: A Theoretical Study of Molecular Interactions in Guanidiniocarbonyl Pyrrole Carboxylate Dimers. J Am Chem Soc 2005; 127:11115-24. [PMID: 16076219 DOI: 10.1021/ja052536w] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It was recently shown experimentally that 5-(guanidiniocarbonyl)-1H-pyrrole-2-carboxylate 1, a self-complementary zwitterion, dimerizes even in water with an unprecedented high association constant of K = 170 M(-1) (J. Am. Chem. Soc. 2003, 125, 452-459). To get an insight into the importance of the various noncovalent binding interactions and of their interplay (electrostatic interactions, hydrogen binding, cooperative effects), we employ density functional theory to study the stability of several "knock-out" analogues in which single hydrogen bonds within these multiple point binding motif are switched off by replacing N-H hydrogen-donor groups with either methylene groups or an oxygen ether bridge. The influence of a highly polar solvent on the dimer stabilities is also examined. These calculations reproduce the experimental data for zwitterion 1. A comparison of 1 with the arginine dimer shows that the energy contents of the monomers also significantly influence the dimer stabilities. The analysis of the various "knock-out" analogues reveals as a main conclusion that simple models either based just on hydrogen-bond counting or on the assumption that the charge interaction by itself is the main and dominant factor fail to explain the stability of such self-assembled dimers. Our computations show that the hydrogen-bond network, the electrostatic attraction, and also their mutual interactions are responsible for the high stability of zwitterion 1.
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Affiliation(s)
- Sebastian Schlund
- University of Wuerzburg, Institute for Organic Chemistry, Am Hubland, 97074 Wuerzburg, Germany
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