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Lachance-Brais C, Hennecker CD, Alenaizan A, Luo X, Toader V, Taing M, Sherrill CD, Mittermaier AK, Sleiman HF. Tuning DNA Supramolecular Polymers by the Addition of Small, Functionalized Nucleobase Mimics. J Am Chem Soc 2021; 143:19824-19833. [PMID: 34783562 DOI: 10.1021/jacs.1c08972] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nucleobase mimicking small molecules able to reconfigure DNA are a recently discovered strategy that promises to extend the structural and functional diversity of nucleic acids. However, only simple, unfunctionalized molecules such as cyanuric acid and melamine have so far been used in this approach. In this work, we show that the addition of substituted cyanuric acid molecules can successfully program polyadenine strands to assemble into supramolecular fibers. Unlike conventional DNA nanostructure functionalization, which typically end-labels DNA strands, our approach incorporates functional groups into DNA with high density using small molecules and results in new DNA triple helices coated with alkylamine or alcohol units that grow into micrometer-long fibers. We find that small changes in the small molecule functional group can result in large structural and energetic variation in the overall assembly. A combination of circular dichroism, atomic force microscopy, molecular dynamics simulations, and a new thermodynamic method, transient equilibrium mapping, elucidated the molecular factors behind these large changes. In particular, we identify substantial DNA sugar and phosphate group deformations to accommodate a hydrogen bond between the phosphate and the small-molecule functional groups, as well as a critical chain length of the functional group which switches this interaction from intra- to interfiber. These parameters allow the controlled formation of hierarchical, hybrid DNA assemblies simply through the addition and variation of small, functionalized molecules.
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Affiliation(s)
| | - Christopher D Hennecker
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Asem Alenaizan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332-0400, United States
| | - Xin Luo
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Violeta Toader
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Monica Taing
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - C David Sherrill
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332-0400, United States
| | - Anthony K Mittermaier
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
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2
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Oelgemöller M, Hoffmann N. Studies in organic and physical photochemistry - an interdisciplinary approach. Org Biomol Chem 2016; 14:7392-442. [PMID: 27381273 DOI: 10.1039/c6ob00842a] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Traditionally, organic photochemistry when applied to synthesis strongly interacts with physical chemistry. The aim of this review is to illustrate this very fruitful interdisciplinary approach and cooperation. A profound understanding of the photochemical reactivity and reaction mechanisms is particularly helpful for optimization and application of these reactions. Some typical reactions and particular aspects are reported such as the Norrish-Type II reaction and the Yang cyclization and related transformations, the [2 + 2] photocycloadditions, particularly the Paternò-Büchi reaction, photochemical electron transfer induced transformations, different kinds of catalytic reactions such as photoredox catalysis for organic synthesis and photooxygenation are discussed. Particular aspects such as the structure and reactivity of aryl cations, photochemical reactions in the crystalline state, chiral memory, different mechanisms of hydrogen transfer in photochemical reactions or fundamental aspects of stereoselectivity are discussed. Photochemical reactions are also investigated in the context of chemical engineering. Particularly, continuous flow reactors are of interest. Novel reactor systems are developed and modeling of photochemical transformations and different reactors play a key role in such studies. This research domain builds a bridge between fundamental studies of organic photochemical reactions and their industrial application.
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Affiliation(s)
- Michael Oelgemöller
- James Cook University, College of Science and Engineering, Townsville, QLD 4811, Australia.
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3
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Nguyen CN, Young TK, Gilson MK. Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril. J Chem Phys 2012; 137:044101. [PMID: 22852591 DOI: 10.1063/1.4733951] [Citation(s) in RCA: 236] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The displacement of perturbed water upon binding is believed to play a critical role in the thermodynamics of biomolecular recognition, but it is nontrivial to unambiguously define and answer questions about this process. We address this issue by introducing grid inhomogeneous solvation theory (GIST), which discretizes the equations of inhomogeneous solvation theory (IST) onto a three-dimensional grid situated in the region of interest around a solute molecule or complex. Snapshots from explicit solvent simulations are used to estimate localized solvation entropies, energies, and free energies associated with the grid boxes, or voxels, and properly summing these thermodynamic quantities over voxels yields information about hydration thermodynamics. GIST thus provides a smoothly varying representation of water properties as a function of position, rather than focusing on hydration sites where solvent is present at high density. It therefore accounts for full or partial displacement of water from sites that are highly occupied by water, as well as for partly occupied and water-depleted regions around the solute. GIST can also provide a well-defined estimate of the solvation free energy and therefore enables a rigorous end-states analysis of binding. For example, one may not only use a first GIST calculation to project the thermodynamic consequences of displacing water from the surface of a receptor by a ligand, but also account, in a second GIST calculation, for the thermodynamics of subsequent solvent reorganization around the bound complex. In the present study, a first GIST analysis of the molecular host cucurbit[7]uril is found to yield a rich picture of hydration structure and thermodynamics in and around this miniature receptor. One of the most striking results is the observation of a toroidal region of high water density at the center of the host's nonpolar cavity. Despite its high density, the water in this toroidal region is disfavored energetically and entropically, and hence may contribute to the known ability of this small receptor to bind guest molecules with unusually high affinities. Interestingly, the toroidal region of high water density persists even when all partial charges of the receptor are set to zero. Thus, localized regions of high solvent density can be generated in a binding site without strong, attractive solute-solvent interactions.
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Affiliation(s)
- Crystal N Nguyen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0736, USA
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Borovkov VV, Hembury GA, Inoue Y. Enthalpy-entropy compensation upon syn-anti conformational switching of bis-porphyrins by amines and alcohols. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424603000434] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Upon interaction with amine and alcohol guests, Zn - Zn and Zn -2 H ethane-bridged bis-porphyrin hosts undergo dramatic conformational switching from a syn to an anti form. The thermodynamic parameters obtained exhibit excellent linear enthalpy-entropy correlations, which are distinctly different for amines and alcohols but essentially independent of the host structure. Analyses of the compensation plots reveal a more rigid complex structure and more extensive desolvation upon complexation with amines than for alcohols, which may be ascribed to the different nucleophilicity, binding strength, solvation and geometry.
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Affiliation(s)
- Victor V. Borovkov
- Entropy Control Project, ICORP, JST, 4-6-3 Kamishinden, Toyonaka-shi, Osaka 560-0085, Japan
| | - Guy A. Hembury
- Entropy Control Project, ICORP, JST, 4-6-3 Kamishinden, Toyonaka-shi, Osaka 560-0085, Japan
| | - Yoshihisa Inoue
- Entropy Control Project, ICORP, JST, 4-6-3 Kamishinden, Toyonaka-shi, Osaka 560-0085, Japan
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6
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Masson E, Ling X, Joseph R, Kyeremeh-Mensah L, Lu X. Cucurbituril chemistry: a tale of supramolecular success. RSC Adv 2012. [DOI: 10.1039/c1ra00768h] [Citation(s) in RCA: 768] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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7
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Kitamura M, Nishimoto H, Aoki K, Tsukamoto M, Aoki S. Molecular recognition of inositol 1,4,5-trisphosphate and model compounds in aqueous solution by ditopic Zn(2+) complexes containing chiral linkers. Inorg Chem 2010; 49:5316-27. [PMID: 20420391 DOI: 10.1021/ic1004038] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report on molecular recognition of inositol 1,4,5-trisphosphate (Ins(1,4,5)P(3)), an important intracellular second messenger, and some related model compounds, cyclohexanediol bisphosphate derivatives (CDP(2)), by ditopic Zn(2+) complexes containing chiral linkers ((S,S)- and (R,R)-11) in aqueous solution at physiological pH. A crystal structure analysis of (S,S)-11 indicated that the distance between two Zn(2+) ions (6.8 A) is suitable for accommodating two phosphate groups at the 4- and 5-positions of Ins(1,4,5)P(3) and two phosphate groups of trans-1,2-CDP(2). (1)H NMR, (31)P NMR, potentiometric pH, and isothermal calorimetric titration data indicate that (S,S)-11 forms 1:1 complexes with (S,S)- and (R,R)-1,2-CDP(2) at pH 7.4 and 25 degrees C. The apparent 1:1 complexation constants (log K(app)) for (S,S)-11-(S,S)-1,2-CDP(2) and (S,S)-11-(R,R)-1,2-CDP(2) (K(app) = [(S,S)-11-1,2-CDP(2) complex]/[(S,S)-11][1,2-CDP(2)] (M(-1))) were determined to be 7.6 +/- 0.1 and 7.3 +/- 0.1, respectively, demonstrating that both enantiomers of 11 bind to chiral trans-1,2-CDP(2) to almost the same extent. The log K(app) value of 6.3 was obtained for a 1:1 complex of (S,S)-11 with cis-1,3-CDP(2), while a small amount of 2:1 (S,S)-11-cis-1,3-CDP(2) was detected, as evidenced by electrospray ionization mass spectrometry (ESI-MS). In contrast, 11 formed several complexes with trans-1,4-CDP(2). On the basis of isothermal titration calorimetry data for (S,S)- and (R,R)-11 with Ins(1,4,5)P(3), it was concluded that 11 forms a 2:1 complex with Ins(1,4,5)P(3), in which the first molecule of 11 binds to the 4- and 5-phosphates of Ins(1,4,5)P(3) and the second molecule of 11 binds to the 1- and 5-phosphates.
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Affiliation(s)
- Masanori Kitamura
- Faculty of Pharmaceutical Sciences, Tokyo University of Science,2641 Yamazaki, Noda 278-8510, Japan
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8
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Matsumura K, Mori T, Inoue Y. Solvent and Temperature Effects on Diastereodifferentiating Paternó−Büchi Reaction of Chiral Alkyl Cyanobenzoates with Diphenylethene upon Direct versus Charge-Transfer Excitation. J Org Chem 2010; 75:5461-9. [DOI: 10.1021/jo101332x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Kazuyuki Matsumura
- Department of Applied Chemistry, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan
| | - Tadashi Mori
- Department of Applied Chemistry, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan
| | - Yoshihisa Inoue
- Department of Applied Chemistry, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan
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9
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Moghaddam S, Inoue Y, Gilson MK. Host-guest complexes with protein-ligand-like affinities: computational analysis and design. J Am Chem Soc 2009; 131:4012-21. [PMID: 19133781 DOI: 10.1021/ja808175m] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
It has recently been discovered that guests combining a nonpolar core with cationic substituents bind cucurbit[7]uril (CB[7]) in water with ultrahigh affinities. The present study uses the Mining Minima algorithm to study the physics of these extraordinary associations and to computationally test a new series of CB[7] ligands designed to bind with similarly high affinity. The calculations reproduce key experimental observations regarding the affinities of ferrocene-based guests with CB[7] and beta-cyclodextrin and provide a coherent view of the roles of electrostatics and configurational entropy as determinants of affinity in these systems. The newly designed series of compounds is based on a bicyclo[2.2.2]octane core, which is similar in size and polarity to the ferrocene core of the existing series. Mining Minima predicts that these new compounds will, like the ferrocenes, bind CB[7] with extremely high affinities.
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Affiliation(s)
- Sarvin Moghaddam
- Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA
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10
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Imai H, Misawa K, Munakata H, Uemori Y. Water-soluble zinc porphyrins as artificial receptors for amino acids. Chem Pharm Bull (Tokyo) 2008; 56:1470-2. [PMID: 18827393 DOI: 10.1248/cpb.56.1470] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The binding of amino acids to water-soluble zinc porphyrins in basic aqueous solution was spectrophotometrically analyzed. The amino acids were bound to the porphyrins through the coordination of the N atom with the central zinc ion. Additional attractions arise due to Coulomb interactions between the -COO(-) anion of the amino acids and the -N(CH(3))(3)(+) cation of the porphyrin substituents and due to hydrophobic interactions between the porphyrin plane and the hydrophobic substituents of the amino acids. These attractions could be explained based on the binding data. The compensatory relationships of DeltaS and DeltaH were also discussed.
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Affiliation(s)
- Hiroyasu Imai
- Faculty of Pharmaceutical Sciences, Hokuriku University, Kanazawa, Japan.
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11
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You CC, Agasti S, Rotello V. Isomeric Control of Protein Recognition with Amino Acid- and Dipeptide-Functionalized Gold Nanoparticles. Chemistry 2007; 14:143-50. [DOI: 10.1002/chem.200701234] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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12
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De M, You CC, Srivastava S, Rotello VM. Biomimetic Interactions of Proteins with Functionalized Nanoparticles: A Thermodynamic Study. J Am Chem Soc 2007; 129:10747-53. [PMID: 17672456 DOI: 10.1021/ja071642q] [Citation(s) in RCA: 232] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Gold nanoparticles (NPs) functionalized with L-amino acid-terminated monolayers provide an effective platform for the recognition of protein surfaces. Isothermal titration calorimetry (ITC) was used to quantify the binding thermodynamics of these functional NPs with alpha-chymotrypsin (ChT), histone, and cytochrome c (CytC). The enthalpy and entropy changes for the complex formation depend upon the nanoparticle structure and the surface characteristics of the proteins, e.g., distributions of charged and hydrophobic residues on the surface. Enthalpy-entropy compensation studies on these NP-protein systems indicate an excellent linear correlation between DeltaH and TDeltaS with a slope (alpha) of 1.07 and an intercept (TDeltaS0) of 35.2 kJ mol(-1). This behavior is closer to those of native protein-protein systems (alpha = 0.92 and TDeltaS0 = 41.1 kJ mol(-1)) than other protein-ligand and synthetic host-guest systems.
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Affiliation(s)
- Mrinmoy De
- Department of Chemistry, University of Massachusetts, 710 North Pleasant Street, Amherst, Massachusetts 01003, USA
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13
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Inclusion Complex Formation of Thiacalix[4]arene and Xe in Aqueous Solution Studied by Hyperpolarized 129Xe NMR. J INCL PHENOM MACRO 2006. [DOI: 10.1007/s10847-006-9130-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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14
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Liu Y, Li S, Bai XP, Wada T, Inoue Y. Complexation Thermodynamics of p-tert-Butylcalix[4]arene Derivatives with Light Lanthanoid Nitrates in Acetonitrile. Supramol Chem 2006. [DOI: 10.1080/10610270108028299] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Yu Liu
- a Department of Chemistry , Nankai University , Tianjin, 300071, China
| | - Shang Li
- a Department of Chemistry , Nankai University , Tianjin, 300071, China
| | - Xiao-Peng Bai
- a Department of Chemistry , Nankai University , Tianjin, 300071, China
| | - Takehiko Wada
- c Department of Molecular Chemistry , Osaka University , 2-1 Yamadaoka, Suita, 565-0871, Japan
| | - Yoshihisa Inoue
- b Inoue Photochirogenesis Project , ERATO, JST , 4-6-3 Kamishinden, Toyonaka, 565-0085, Japan
- c Department of Molecular Chemistry , Osaka University , 2-1 Yamadaoka, Suita, 565-0871, Japan
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15
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Kitamatsu M, Shigeyasu M, Saitoh M, Sisido M. Configurational preference of pyrrolidine-based oxy-peptide nucleic acids as hybridization counterparts with DNA and RNA. Biopolymers 2006; 84:267-73. [PMID: 16130130 DOI: 10.1002/bip.20364] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A new series of oxy-peptide nucleic acids (pyrrolidine-based oxy-peptide nucleic acids = POPNAs) of four different stereoisomeric forms (cis-L, cis-D, trans-L, trans-D) have been synthesized. To find a favorable stereoisomer of POPNA for hybridization with DNA or RNA, thermodynamic parameters and conformations of the hybrids between the four stereoisomers with 9 adenine bases [po(A(9))s] and dT(9) or rU(9) were investigated from ultraviolet (UV) melting curves and circular dichroism (CD) spectra. The cis-L-po(A(9)) formed the most stable hybrid with dT(9), because of the smallest entropy loss, despite the smallest enthalpy gain. In contrast, trans-L-po(A(9)) formed the most stable hybrid with rU(9), because of the largest enthalpy gain, despite the largest entropy loss. The hybrid stability of trans-L-po(A(9)) with rU(9) was significantly improved as compared with a previous version of oxy-peptide nucleic acid (OPNA) that lacks the pyrrolidine ring.
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Affiliation(s)
- Mizuki Kitamatsu
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Japan
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16
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Egan TJ. Interactions of quinoline antimalarials with hematin in solution. J Inorg Biochem 2006; 100:916-26. [PMID: 16384600 DOI: 10.1016/j.jinorgbio.2005.11.005] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2005] [Revised: 11/02/2005] [Accepted: 11/06/2005] [Indexed: 11/26/2022]
Abstract
Quinoline antimalarial drugs such as chloroquine and related compounds are believed to act by targeting ferriprotoporphyrin IX (Fe(III)PPIX) in the form of hematin (H(2)O/HO-Fe(III)PPIX), its mu-oxo dimer ([Fe(III)PPIX](2)O) or crystalline beta-hematin ([Fe(III)PPIX](2)) in the malaria parasite. Fe(III)PPIX is formed when the parasite digests host hemoglobin during its intraerythrocytic blood stage. This has led to a number of studies on the interaction of Fe(III)PPIX with quinoline antimalarials and related compounds. This article reviews the spectroscopy, thermodynamics and structures of Fe(III)PPIX-quinoline complexes in solution.
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Affiliation(s)
- Timothy J Egan
- Department of Chemistry, University of Cape Town, Private Bag, Rondebosch 7701, South Africa.
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Thirumoorthy K, Nandi N. Comparison of the Intermolecular Energy Surfaces of Amino Acids: Orientation-Dependent Chiral Discrimination. J Phys Chem B 2006; 110:8840-9. [PMID: 16640443 DOI: 10.1021/jp055295n] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the present work, we compare the intermolecular energy surfaces of the alanine molecule in its neutral and zwitterionic state using ab initio theory (HF/6-311++G) as a function of mutual orientation. Starting from the optimized structures of the nonbonded homochiral (l-l) and heterochiral (d-l) pairs of molecules, the energy surfaces are studied with rigid geometry by varying the distance and orientation. The potential energy surfaces of the l-l and d-l pairs are found to be dissimilar and reflect the underlying chirality of the homochiral pair and racemic nature of the heterochiral pair. The intermolecular energy surface of the l-l pair is more favorable than the corresponding energy surface of the d-l pair. The study, for the first time, reveals clear homochiral preference without use of parameters, which was unobserved in previous detailed simulations but predicted by theory. The electrostatic interaction further augments the chiral discrimination. The basis set superposition error (BSSE) corrected results show enhanced discrimination. Use of higher-level Møller-Plesset perturbation theory (MP2) and further BSSE correction do not change the conclusions made at the Hartree-Fock (HF) level. The major conclusions based on HF and MP2 level calculations remain unaltered when the calculations of the potential energy surfaces for the neutral and zwitterionic pairs are repeated using the density functional theory (DFT) (B3LYP/6-311++G). The observed orientation dependence has significance in the biological chiral recognition as well as peptide synthesis at the peptidyl transferase center where the amino terminal and peptidyl terminal undergo mutual rotatory motion.
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Affiliation(s)
- Krishnan Thirumoorthy
- Chemistry Department, Birla Institute of Technology and Science, Pilani, Rajasthan 333031, India
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Imai H, Munakata H, Uemori Y, Sakura N. Chiral Recognition of Amino Acids and Dipeptides by a Water-Soluble Zinc Porphyrin. Inorg Chem 2004; 43:1211-3. [PMID: 14966952 DOI: 10.1021/ic0302837] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A chiral water-soluble zinc porphyrin was optically resolved on a chiral HPLC column, and the binding of chiral amino acids and peptides to each of the enantiomers was examined spectrophotometrically in basic aqueous solution. The binding data apparently indicated that the zinc porphyrin has chiral selectivity for amino acids and dipeptides. This was reasonably explained in terms of the triple cooperation of coordination, Coulomb, and steric interactions of the chiral amino carboxylates with the porphyrin. A compensatory relationship among the thermodynamic parameters for chiral recognition was also shown.
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Affiliation(s)
- Hiroyasu Imai
- Faculty of Pharmaceutical Sciences, Hokuriku University, 3-Ho Kanagawa-machi, Kanazawa 920-1181, Japan.
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Egan TJ, Ncokazi KK. Effects of solvent composition and ionic strength on the interaction of quinoline antimalarials with ferriprotoporphyrin IX. J Inorg Biochem 2004; 98:144-52. [PMID: 14659643 DOI: 10.1016/j.jinorgbio.2003.09.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Enthalpy-entropy compensation in the interaction of quinoline antimalarials with ferriprotoporphyrin IX (Fe(III)PPIX) in 40% aqueous dimethyl sulfoxide (DMSO) has been compared with that in pure aqueous solution. The data indicate that the degree of desolvation and loss of conformational freedom is virtually identical in both systems. Taken together with previous findings showing that the molar free energies of association of these drugs with Fe(III)PPIX in both solvent systems are very similar, this suggests that the recognition site on the metalloporphyrin is comparable in both cases. This is despite the fact that Fe(III)PPIX exists as a dimer in aqueous solution, but is monomeric in 40% DMSO. Free energies of association of chloroquine, quinine and quinidine with Fe(III)PPIX are largely insensitive to the concentration of sodium perchlorate in 40% DMSO. This demonstrates that electrostatic interactions play only a minor role in the overall stability of these complexes under these conditions. Increasing DMSO concentration greatly weakens the interactions of chloroquine, amodiaquine, quinine, quinidine and 9-epiquinine with Fe(III)PPIX. This suggests that hydrophobic interaction plays a major role in the stability of these complexes. Further investigation of chloroquine has revealed that the free energy of association with Fe(III)PPIX also weakens as a function of decreasing solvent polarity in pure organic solvents. However, the free energies of association are weaker in the mixed aqueous solvent than in pure organic solvents. This indicates that dispersion and electrostatic interactions are relatively strong in the non-aqueous environment. The results demonstrate that any successful model of antimalarial drug-Fe(III)PPIX interactions will need to take both solvation and electrostatic factors into account.
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Affiliation(s)
- Timothy J Egan
- Department of Chemistry, University of Cape Town, Private Bag, Rondebosch 7701, South Africa.
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Rekharsky MV, Inoue Y. Solvent and guest isotope effects on complexation thermodynamics of alpha-, beta-, and 6-amino-6-deoxy-beta-cyclodextrins. J Am Chem Soc 2002; 124:12361-71. [PMID: 12371880 DOI: 10.1021/ja027031+] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The stability constant (K), standard free energy (DeltaG degrees ), enthalpy (DeltaH degrees ), and entropy changes (TDeltaS degrees ) for the complexation of native alpha- and beta-cyclodextrins (CDs) and 6-amino-6-deoxy-beta-CD with more than 30 neutral, positively, and negatively charged guests, including seven fully or partially deuterated guests, have been determined in phosphate buffer solutions (pH/pD 6.9) of hydrogen oxide (H(2)O) or deuterium oxide (D(2)O) at 298.15 K by titration microcalorimetry. Upon complexation with these native and modified CDs, both nondeuterated and deuterated guests examined consistently exhibited higher affinities (by 5-20%) in D(2)O than in H(2)O. The quantitative affinity enhancement in D(2)O versus H(2)O directly correlates with the size and strength of the hydration shell around the charged/hydrophilic group of the guest. For that reason, negatively/positively charged guests, possessing a relatively large and strong hydration shell, afford smaller K(H2O)/K(D2O) ratios than those for neutral guests with a smaller and weaker hydration shell. Deuterated guests showed lower affinities (by 5-15%) than the relevant nondeuterated guests in both H(2)O and D(2)O, which is most likely ascribed to the lower ability of the C-D bond to produce induced dipoles and thus the reduced intracavity van der Waals interactions. The excellent enthalpy-entropy correlation obtained can be taken as evidence for the very limited conformational changes upon transfer of CD complexes from H(2)O to D(2)O.
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Affiliation(s)
- Mikhail V Rekharsky
- Entropy Control Project, ICORP, JST, 4-6-3 Kamishinden, Toyonaka 560-0085, Japan
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Hefter G, Marcus Y, Waghorne WE. Enthalpies and entropies of transfer of electrolytes and ions from water to mixed aqueous organic solvents. Chem Rev 2002; 102:2773-836. [PMID: 12175268 DOI: 10.1021/cr010031s] [Citation(s) in RCA: 128] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Glenn Hefter
- Department of Chemistry, University College, Belfield, Dublin 4, Ireland.
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22
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Rekharsky MV, Inoue Y. Complexation and chiral recognition thermodynamics of 6-amino-6-deoxy-beta-cyclodextrin with anionic, cationic, and neutral chiral guests: counterbalance between van der Waals and coulombic interactions. J Am Chem Soc 2002; 124:813-26. [PMID: 11817957 DOI: 10.1021/ja010889z] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The stability constant (K), standard free energy (Delta G degrees), enthalpy (Delta H degrees), and entropy changes (T Delta S degrees) for the complexation of 6-amino-6-deoxy-beta-cyclodextrin with more than 50 negatively or positively charged as well as neutral guests, including 22 enantiomer pairs, have been determined in aqueous phosphate buffer (pH 6.9) at 298.15 K by titration microcalorimetry. The thermodynamic parameters obtained in this study and the relevant data for native beta-cyclodextrin indicate that the complexation and chiral discrimination behavior of the cationic host with charged guests are governed by the critical counterbalance between the electrostatic interactions of the charged groups in host and guest and the conventional intracavity interactions of the hydrophobic moiety of guest, such as hydrophobic, van der Waals, solvation/desolvation, and hydrogen-bonding interactions.
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Affiliation(s)
- Mikhail V Rekharsky
- Inoue Photochirogenesis Project, ERATO, JST, 4-6-3 Kamishinden, Toyonaka 560-0085, Japan
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Liu L, Yang C, Guo QX. Enthalpy–Entropy Compensation of Cyclodextrin Complexation with Different Classes of Substrates. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2001. [DOI: 10.1246/bcsj.74.2311] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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24
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Flood KG, Reynolds ER, Snow NH. Characterization of inclusion complexes of betamethasone-related steroids with cyclodextrins using high-performance liquid chromatography. J Chromatogr A 2000; 903:49-65. [PMID: 11153955 DOI: 10.1016/s0021-9673(00)00867-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
HPLC was used to study the inclusion complexes formed between various beta- and gamma-cyclodextrins and a series of corticosteroids related to betamethasone. Apparent association constants were measured in acetonitrile-water for a set of 13 steroids. An increase in the stability of the steroid-cyclodextrin complex is observed at lower concentrations of acetonitrile. The effects of the nature of the halide at the 9-position, the location of a double bond within the C-ring, substitution at the 9- and 11-positions, and modification of the D-ring of the steroid backbone were studied. The 11- and 17-positions were found to be critically involved in the inclusion process. Larger apparent association constants were obtained with gamma-cyclodextrin (gamma-CD) than with beta-cyclodextrin (beta-CD) due to the increased diameter of the gamma-CD cavity. Van't Hoff plots were constructed to examine the thermodynamic properties of the inclusion process. Plots constructed using retention factors were found to be nonlinear when gamma-CD was present in the mobile phase. This is due to an increase in the strength of the inclusion complex as temperature decreases. Plots constructed using apparent association constants were linear, indicating that the mechanism of inclusion does not change over the range of temperatures studied (10 to 80 degrees C). Enthalpy-entropy compensation was observed for 11 of the 13 steroids studied. The usefulness of cyclodextrins to achieve the separation of steroids in HPLC is discussed and a practical application for the analysis of a steroid and three potential impurities is described.
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Affiliation(s)
- K G Flood
- Seton Hall University, Department of Chemistry, South Orange, NJ 07079, USA
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Schönherr H, Beulen MWJ, Bügler J, Huskens J, van Veggel FCJM, Reinhoudt DN, Vancso GJ. Individual Supramolecular Host−Guest Interactions Studied by Dynamic Single Molecule Force Spectroscopy. J Am Chem Soc 2000. [DOI: 10.1021/ja994040i] [Citation(s) in RCA: 143] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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Inoue Y, Ikeda H, Kaneda M, Sumimura T, Everitt SRL, Wada T. Entropy-Controlled Asymmetric Photochemistry: Switching of Product Chirality by Solvent. J Am Chem Soc 2000. [DOI: 10.1021/ja993542t] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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27
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Singh SK, Nilsson S. Thermodynamics of Interaction between Some Cellulose Ethers and SDS by Titration Microcalorimetry. J Colloid Interface Sci 1999; 213:133-151. [PMID: 10191016 DOI: 10.1006/jcis.1999.6122] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The interaction between certain nonionic cellulose ethers (ethyl hydroxyethyl cellulose and hydroxypropyl methyl cellulose) and sodium dodecyl sulphate (SDS) has been investigated using isothermal titration microcalorimetry at temperatures between 25-50 degrees C. The observed heat flow curves have been interpreted in terms of a plausible mechanism of the interaction of the substituent groups with SDS monomers and clusters. The data have been related to changes occuring in the system at the macro- and microscopic levels with the addition of surfactants and with temperature. The process consists predominantly of polymer-surfactant interactions initially and surfactant-surfactant interactions at the later stages. A phenomenological model of the cooperative interaction (adsorption) process has been derived, and earlier published equilibrium binding data have been used to recover binding constants and Gibbs energy changes for this process. The adsorption enthalpies and entropies have been recovered along with the heat capacity change. The enthalpic cost of confining the nonpolar regions of the polymers in surfactant clusters is high, but the entropy gain from release of hydration shell water molecules as well as increased freedom of movement of these nonpolar regions in the clusters gives the process a strong entropic driving force. The process is entropy-driven initially and converts to being both enthalpy and entropy-driven at high SDS concentrations. An enthalpy-entropy compensation behavior is seen. Strongly negative heat capacity changes have been obtained resulting from the transfer of nonpolar groups from aqueous into nonpolar environments, as well as a reduction of conformational domains that the chains can populate. Changes in these two components cause the heat capacity change to become less negative at the higher binding levels. The system can be classified as exhibiting nonclassical hydrophobic binding at the later stages of binding. Copyright 1999 Academic Press.
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Affiliation(s)
- SK Singh
- Department of Pharmaceutics, Pharmacia & Upjohn AB, Uppsala, S-751 82, Sweden
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Singh SK, Nilsson S. Thermodynamics of Interaction between Some Cellulose Ethers and SDS by Titration Microcalorimetry. J Colloid Interface Sci 1999; 213:152-159. [PMID: 10191017 DOI: 10.1006/jcis.1999.6121] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A titration calorimetric study of the interaction between nonionic cellulose ethers and ionic surfactant (SDS) has been extended to a larger number of polymers to explore the effect of variation of polymer hydrophobicity on the energetics of the process. "Hydrophobicity" as used here is an overall effect of the nature, degree, and number of substituents and is characterized by the cloud point and (aqueous) surface tension lowering abilities of the polymer. A direct correlation is found between the extent of "hydrophobicity" and the endo-enthalpic peak in the initial SDS concentration region of interaction. However, the overall mechanism of interaction is similar for all the polymers, being dominated by polymer-surfactant interactions initially and converting into a surfactant-surfactant interaction process at higher SDS concentrations. The importance of polymer characteristics thus becomes weaker at the later stages of the process. Differences between the polymers is also reduced by an increase of temperature, leading to a near overlap of observed enthalpy curves at 40 degrees C. The energetics of interaction are also mirrored by the isothermal surfactant binding curves and the changes in macroscopic and microviscosity of the system. Copyright 1999 Academic Press.
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Affiliation(s)
- SK Singh
- Department of Pharmaceutics, Pharmacia & Upjohn AB, S-751 82 Uppsala, Sweden
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Liu Y, Dong SP, Inoue Y, Wada T. Complexation Thermodynamics of Selenacrown Ether: Origin of High Silver(I) Selectivity of 1,5,14,18-Tetraselena-8,11,21,24-tetraoxacyclohexacosane. JOURNAL OF CHEMICAL RESEARCH 1999. [DOI: 10.1177/174751989902300419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The thermodynamic parameters and relative cation selectivity for complexation of some alkali and heavy metal cations with 1,5,14,18-tetraselena-8,11,21,24-tetraoxacyclohexacosane (selena-26-crown-8) are investigated for the first time by titration calorimetry in water–acetonitrile (1:24 v/v) at 25 °C to show the contrasting complexation thermodynamic behaviour between Ag+ and alkali or Tl+ and a very high Ag+ selectivity, originating from the exclusive contribution of the enthalpy term probably owing to the partially covalent interaction between Ag+ and Se donor.
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Affiliation(s)
- Yu Liu
- Department of Chemistry, Nankai University, Tianjin 300071, China
| | - Shu-Ping Dong
- Department of Chemistry, Nankai University, Tianjin 300071, China
| | - Yoshihisa Inoue
- Department of Molecular Chemistry, Faculty of Engineering, Osaka University, Yamadaoka, Suita 565, Japan
| | - Takehiko Wada
- Department of Molecular Chemistry, Faculty of Engineering, Osaka University, Yamadaoka, Suita 565, Japan
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Inoue Y, Matsushima E, Wada T. Pressure and Temperature Control of Product Chirality in Asymmetric Photochemistry. Enantiodifferentiating Photoisomerization of Cyclooctene Sensitized by Chiral Benzenepolycarboxylates. J Am Chem Soc 1998. [DOI: 10.1021/ja981929a] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yoshihisa Inoue
- Contribution from the Inoue Photochirogenesis Project, ERATO, JST, 4-6-3 Kamishinden, Toyonaka 565-0085, Japan, and Department of Molecular Chemistry, Faculty of Engineering, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan
| | - Eiji Matsushima
- Contribution from the Inoue Photochirogenesis Project, ERATO, JST, 4-6-3 Kamishinden, Toyonaka 565-0085, Japan, and Department of Molecular Chemistry, Faculty of Engineering, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan
| | - Takehiko Wada
- Contribution from the Inoue Photochirogenesis Project, ERATO, JST, 4-6-3 Kamishinden, Toyonaka 565-0085, Japan, and Department of Molecular Chemistry, Faculty of Engineering, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan
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Affiliation(s)
- Mikhail V. Rekharsky
- Inoue Photochirogenesis Project, ERATO, JST, 4-6-3 Kamishinden, Toyonaka 565-0085, Japan, and Department of Molecular Chemistry, Faculty of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
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