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Hassan A, Dinadayalane TC, Grabowski SJ, Leszczynski J. Structural, energetic, spectroscopic and QTAIM analyses of cation–π interactions involving mono- and bi-cyclic ring fused benzene systems. Phys Chem Chem Phys 2013; 15:20839-56. [PMID: 24196371 DOI: 10.1039/c3cp53927j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Ayorinde Hassan
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, 1400 J.R. Lynch Street, P.O. Box 17910, Jackson, MS 39217, USA.
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Trabuco LG, Harrison CB, Schreiner E, Schulten K. Recognition of the regulatory nascent chain TnaC by the ribosome. Structure 2010; 18:627-37. [PMID: 20462496 DOI: 10.1016/j.str.2010.02.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 02/03/2010] [Accepted: 02/06/2010] [Indexed: 10/19/2022]
Abstract
Regulatory nascent chains interact with the ribosomal exit tunnel and modulate their own translation. To characterize nascent chain recognition by the ribosome at the atomic level, extensive molecular dynamics simulations of TnaC, the leader peptide of the tryptophanase operon, inside the exit tunnel were performed for an aggregate time of 2.1 mus. The simulations, complemented by quantum chemistry calculations, suggest that the critical TnaC residue W12 is recognized by the ribosome via a cation-pi interaction, whereas TnaC's D16 forms salt bridges with ribosomal proteins. The simulations also show that TnaC-mediated translational arrest does not involve a swinging of ribosomal protein L22, as previously proposed. Furthermore, bioinformatic analyses and simulations suggest nascent chain elements that may prevent translational arrest in various organisms. Altogether, the current study unveils atomic-detail interactions that explain the role of elements of TnaC and the ribosome essential for translational arrest.
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Affiliation(s)
- Leonardo G Trabuco
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Rezabal E, Marino T, Mercero JM, Russo N, Ugalde JM. Complexation of AlIII by Aromatic Amino Acids in the Gas Phase. Inorg Chem 2007; 46:6413-9. [PMID: 17608416 DOI: 10.1021/ic7004776] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The coordination properties of three natural aromatic amino acids (AAAs)-phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp)-to AlIII are studied in this work, devoting special attention to the role of the aromatic side chain. A comparison with aluminum(III)-alanine complexes is also presented. The polarizability arising from the ring has been seen to be a key factor in the stability of the complexes, with the order being Trp-AlIII > Tyr-AlIII > Phe-AlIII, starting from the most stable one. Cation-pi interactions between the metal and the aromatic ring are present in the lowest energy conformers, especially for Trp, which seems to be very well suited for these kinds of interactions, occurring with both the six- and five-membered rings of the indole side chain. The most stable coordination mode for the three AAAs is found to be tricoordinated with the N and O of the backbone chain and the aromatic ring, as was found theoretically and experimentally for other metals.
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Affiliation(s)
- E Rezabal
- Kimika Fakultatea, Euskal Herriko Unibertsitatea and Donostia International Physics Center, PK 1072, 20080 Donostia, Euskadi, Spain.
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Ruan C, Yang Z, Rodgers MT. Influence of the d orbital occupation on the nature and strength of copper cation–π interactions: threshold collision-induced dissociation and theoretical studies. Phys Chem Chem Phys 2007; 9:5902-18. [DOI: 10.1039/b709820k] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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6
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Bhowmik R, Katti KS, Katti D. Molecular dynamics simulation of hydroxyapatite–polyacrylic acid interfaces. POLYMER 2007. [DOI: 10.1016/j.polymer.2006.11.015] [Citation(s) in RCA: 150] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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7
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Rimola A, Rodríguez-Santiago L, Sodupe M. Cation−π Interactions and Oxidative Effects on Cu+ and Cu2+ Binding to Phe, Tyr, Trp, and His Amino Acids in the Gas Phase. Insights from First-Principles Calculations. J Phys Chem B 2006; 110:24189-99. [PMID: 17125391 DOI: 10.1021/jp064957l] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The coordination properties of the four natural aromatic amino acids (AA(arom) = Phe, Tyr, Trp, and His) to Cu+ and Cu2+ have been exhaustively studied by means of ab initio calculations. For Cu+-Phe, Cu+-Tyr and Cu+-Trp, the two charge solvated tridentate N/O/ring and bidentate N/ring structures, with the metal cation interacting with the pi system of the ring, were found to be the lowest ones, relative DeltaG(298K) energies being less than 0.5 kcal/mol. The Cu+-His ground-state structure has the metal cation interacting with the NH2 group and the imidazole N. For these low-lying structures vibrational features are also discussed. Unlike Cu+ complexes, the ground-state structure of Cu2+-Phe, Cu2+-Tyr, and Cu2+-Trp does not present cation-pi interactions due to the oxidation of the aromatic ring induced by the metal cation. The ground-state structure of Cu2+-His does not present oxidation of the amino acid, the coordination to Cu2+ being tridentate with the oxygen of the carbonyl group, the nitrogen of the amine, and the N of the imidazole. Other less stable isomers, however, show oxidation of His, particularly of the imidazole ring, which can induce spontaneous proton-transfer reactions from the NH of the imidazole to the NH2 of the backbone. Finally, the computed binding energies for Cu+-AA(arom) and Cu2+-AA(arom) systems have been computed, the order found for the single charged systems being Cu+-His > Cu+-Trp > Cu+-Tyr > Cu+-Phe, in very good agreement with the experimental data.
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Affiliation(s)
- Albert Rimola
- Departament de Química, Universitat Autonoma de Barcelona, Bellaterra 08193, Spain
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Hassanali AA, Li T, Zhong D, Singer SJ. A Molecular Dynamics Study of Lys-Trp-Lys: Structure and Dynamics in Solution Following Photoexcitation. J Phys Chem B 2006; 110:10497-508. [PMID: 16722759 DOI: 10.1021/jp0601926] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report studies of the structure and dynamics of a tripeptide Lys-Trp-Lys (KWK) in aqueous solution following photoexcitation by molecular dynamics simulations. For ground-state KWK, we observe three stable conformations with free energy differences of less than 5.2 kJ/mol. Each conformer is stabilized by a pi-cation interaction between one of three protonated amino groups and the indole moiety. For the excited state of tryptophan in KWK, the simulated molecular dynamics of the three isomers are similar, all in good agreement with recent femtosecond experiments (J. Phys. Chem. B 2005, 109, 16901). Specifically, we observe: (1) the fluorescence anisotropy is dominated by a single-exponential component and decays in approximately 130 ps, (2) the total dynamic Stokes shift reaches approximately 2700 cm(-1), and (3) the excited state relaxation dynamics occurs on several time scales ranging from femtoseconds to tens of picoseconds. The relaxation dynamics involve rapid initial response of neighboring water, followed by local motions of flexible peptide chains. These processes drive global restructuring of the tripeptide on a rather flat energy surface, inducing slower dynamics evident in both the water and protein contributions to the stabilization energy of the photoexcited chromophore. The water and protein dynamics are strongly correlated. On a still longer time scale, we observe isomerization of two excited state conformers to the other most stable one, an analogue for evolution of trajectories along the funnel on the rugged free energy landscape to the final "native" state. Our studies suggest new experiments to detect this unique dynamics.
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Affiliation(s)
- Ali A Hassanali
- Biophysics Program, Ohio State University, Columbus, Ohio 43210, USA
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Coletti C, Re N. Theoretical Study of Alkali Cation−Benzene Complexes: Potential Energy Surfaces and Binding Energies with Improved Results for Rubidium and Cesium. J Phys Chem A 2006; 110:6563-70. [PMID: 16706415 DOI: 10.1021/jp060771a] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
High level ab initio quantum chemical calculations have been carried out on the binding of alkali metal to benzene with special attention to heavier metals for which the agreement between the most recent theoretical investigations and the experimental bond dissociation energies (BDEs) is not very good. We performed BSSE-corrected geometry optimizations employing the MP2 level of theory with large basis sets and a modified Stuttgart RSC 1997 basis set for rubidium and cesium and carried out single point energy calculations at the MP4 level, obtaining, also for the latter metals, BDE values in good agreement with the experimental results. Furthermore, in view of the development of empirical correction terms to force fields to describe cation-pi interactions, we evaluated the potential energy surface along the benzene symmetry axis and discussed the role of the BSSE correction on the accuracy of our results.
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Affiliation(s)
- Cecilia Coletti
- Dipartimento di Scienze del Farmaco, Università G. d'Annunzio, Via dei Vestini 31, 66100 Chieti, Italy
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10
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Alonso JL, Echenique P. A physically meaningful method for the comparison of potential energy functions. J Comput Chem 2006; 27:238-52. [PMID: 16331642 DOI: 10.1002/jcc.20337] [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: 11/10/2022]
Abstract
In the study of the conformational behavior of complex systems, such as proteins, several related statistical measures are commonly used to compare two different potential energy functions. Among them, the Pearson's correlation coefficient r has no units and allows only semiquantitative statements to be made. Those that do have units of energy and whose value may be compared to a physically relevant scale, such as the root-mean-square deviation (RMSD), the mean error of the energies (ER), the standard deviation of the error (SDER) or the mean absolute error (AER), overestimate the distance between potentials. Moreover, their precise statistical meaning is far from clear. In this article, a new measure of the distance between potential energy functions is defined that overcomes the aforementioned difficulties. In addition, its precise physical meaning is discussed, the important issue of its additivity is investigated, and some possible applications are proposed. Finally, two of these applications are illustrated with practical examples: the study of the van der Waals energy, as implemented in CHARMM, in the Trp-Cage protein (PDB code 1L2Y) and the comparison of different levels of the theory in the ab initio study of the Ramachandran map of the model peptide HCO-L-Ala-NH2.
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Affiliation(s)
- José Luis Alonso
- Instituto de Biocomputación y Física de los Sistemas Complejos (BIFI), EdificioCervantes, Corona de Aragón 42, 50009 Zaragoza, Spain
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Ruan C, Yang Z, Hallowita N, Rodgers MT. Cation−π Interactions with a Model for the Side Chain of Tryptophan: Structures and Absolute Binding Energies of Alkali Metal Cation−Indole Complexes†. J Phys Chem A 2005; 109:11539-50. [PMID: 16354046 DOI: 10.1021/jp053830d] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Threshold collision-induced dissociation techniques are employed to determine bond dissociation energies (BDEs) of mono- and bis-complexes of alkali metal cations, Li+, Na+, K+, Rb+, and Cs+, with indole, C8H7N. The primary and lowest energy dissociation pathway in all cases is endothermic loss of an intact indole ligand. Sequential loss of a second indole ligand is observed at elevated energies for the bis-complexes. Density functional theory calculations at the B3LYP/6-31G level of theory are used to determine the structures, vibrational frequencies, and rotational constants of these complexes. Theoretical BDEs are determined from single point energy calculations at the MP2(full)/6-311+G(2d,2p) level using the B3LYP/6-31G* geometries. The agreement between theory and experiment is very good for all complexes except Li+ (C8H7N), where theory underestimates the strength of the binding. The trends in the BDEs of these alkali metal cation-indole complexes are compared with the analogous benzene and naphthalene complexes to examine the influence of the extended pi network and heteroatom on the strength of the cation-pi interaction. The Na+ and K+ binding affinities of benzene, phenol, and indole are also compared to those of the aromatic amino acids, phenylalanine, tyrosine, and tryptophan to elucidate the factors that contribute to the binding in complexes to the aromatic amino acids. The nature of the binding and trends in the BDEs of cation-pi complexes between alkali metal cations and benzene, phenol, and indole are examined to help understand nature's preference for engaging tryptophan over phenylalanine and tyrosine in cation-pi interactions in biological systems.
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Affiliation(s)
- Chunhai Ruan
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
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12
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Xu Y, Shen J, Zhu W, Luo X, Chen K, Jiang H. Influence of the Water Molecule on Cation−π Interaction: Ab Initio Second Order Møller−Plesset Perturbation Theory (MP2) Calculations. J Phys Chem B 2005; 109:5945-9. [PMID: 16851648 DOI: 10.1021/jp044568w] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The influence of introducing water molecules into a cation-pi complex on the interaction between the cation and the pi system was investigated using the MP2/6-311++G method to explore how a cation-pi complex changes in terms of both its geometry and its binding strength during the hydration. The calculation on the methylammonium-benzene complex showed that the cation-pi interaction is weakened by introducing H(2)O molecules into the system. For example, the optimized interaction distance between the cation and the benzene becomes longer and longer, the transferred charge between them becomes less and less, and the cation-pi binding strength becomes weaker and weaker as the water molecule is introduced one by one. Furthermore, the introduction of the third water molecule leads to a dramatic change in both the complex geometry and the binding energy, resulting in the destruction of the cation-pi interaction. The decomposition on the binding energy shows that the influence is mostly brought out through the electrostatic and induction interactions. This study also demonstrated that the basis set superposition error, thermal energy, and zero-point vibrational energy are significant and needed to be corrected for accurately predicting the binding strength in a hydrated cation-pi complex at the MP2/6-311++G level. Therefore, the results are helpful to better understand the role of water molecules in some biological processes involving cation-pi interactions.
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Affiliation(s)
- Yechun Xu
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, People's Republic of China
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Lensink MF, Christiaens B, Vandekerckhove J, Prochiantz A, Rosseneu M. Penetratin-membrane association: W48/R52/W56 shield the peptide from the aqueous phase. Biophys J 2004; 88:939-52. [PMID: 15542560 PMCID: PMC1305166 DOI: 10.1529/biophysj.104.052787] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Using molecular dynamics simulations, we studied the mode of association of the cell-penetrating peptide penetratin with both a neutral and a charged bilayer. The results show that the initial peptide-lipid association is a fast process driven by electrostatic interactions. The homogeneous distribution of positively charged residues along the axis of the helical peptide, and especially residues K46, R53, and K57, contribute to the association of the peptide with lipids. The bilayer enhances the stability of the penetratin helix. Oriented parallel to the lipid-water interface, the subsequent insertion of the peptide through the bilayer headgroups is significantly slower. The presence of negatively charged lipids considerably enhances peptide binding. Lateral side-chain motion creates an opening for the helix into the hydrophobic core of the membrane. The peptide aromatic residues form a pi-stacking cluster through W48/R52/W56 and F49/R53, protecting the peptide from the water phase. Interaction with the penetratin peptide has only limited effect on the overall membrane structure, as it affects mainly the conformation of the lipids which interact directly with the peptide. Charge matching locally increases the concentration of negatively charged lipids, lateral lipid diffusion locally decreases. Lipid disorder increases, through decreased order parameters of the lipids interacting with the penetratin side chains. Penetratin molecules at the membrane surface do not seem to aggregate.
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Affiliation(s)
- M F Lensink
- Department of Lipoprotein Chemistry, Faculty of Medicine and Health Sciences, Ghent, Belgium.
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Ruan C, Rodgers MT. Cation−π Interactions: Structures and Energetics of Complexation of Na+ and K+ with the Aromatic Amino Acids, Phenylalanine, Tyrosine, and Tryptophan. J Am Chem Soc 2004; 126:14600-10. [PMID: 15521780 DOI: 10.1021/ja048297e] [Citation(s) in RCA: 163] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Threshold collision-induced dissociation of M(+)(AAA) with Xe is studied using guided ion beam tandem mass spectrometry. M(+) include the alkali metal ions Na(+) and K(+). The three aromatic amino acids are examined, AAA = phenylalanine, tyrosine, or tryptophan. In all cases, endothermic loss of the intact aromatic amino acid is the dominant reaction pathway. The threshold regions of the cross sections are interpreted to extract 0 and 298 K bond dissociation energies for the M(+)-AAA complexes after accounting for the effects of multiple ion-neutral collisions, internal energy of the reactant ions, and dissociation lifetimes. Density functional theory calculations at the B3LYP/6-31G level of theory are used to determine the structures of the neutral aromatic amino acids and their complexes to Na(+) and K(+) and to provide molecular constants required for the thermochemical analysis of the experimental data. Theoretical bond dissociation energies are determined from single-point energy calculations at the B3LYP/6-311++G(3df,3pd) level using the B3LYP/6-31G geometries. Good agreement between theory and experiment is found for all systems. The present results are compared to earlier studies of these systems performed via kinetic and equilibrium methods. The present results are also compared to the analogous Na(+) and K(+) complexes to glycine, benzene, phenol, and indole to elucidate the relative contributions that each of the functional components of these aromatic amino acids make to the overall binding in these complexes.
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Affiliation(s)
- Chunhai Ruan
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
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Validation of the Applicability of Force Fields to Reproduce Ab Initio Noncovalent Interactions Involving Aromatic Groups. ADVANCES IN QUANTUM CHEMISTRY 2004. [DOI: 10.1016/s0065-3276(04)47005-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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16
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Macias AT, Norton JE, Evanseck JD. Impact of multiple cation-pi interactions upon calix[4]arene substrate binding and specificity. J Am Chem Soc 2003; 125:2351-60. [PMID: 12590565 DOI: 10.1021/ja0285971] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cation-pi interaction influence on the conformation and binding of calix[4]arenes to alkali-metal cations has been studied using a dehydroxylated model. The model allows for the separation of cooperative cation-pi and electrostatic forces commonly found in the binding motifs found in calixarene complexes. Starting from the four well-known calix[4]arene conformations, six conformers for this dehydroxylated model (cone, partial cone, flattened cone, chair, 1,2-alternate, and 1,3-alternate) have been characterized by geometry optimization and frequency analysis using the Becke three-parameter exchange functional with the nonlocal correlation functional of Lee, Yang, and Parr and the 6-31G(d) basis set. Without the stabilization provided by the hydroxyl hydrogen bonds in calix[4]arene, neither the cone nor the 1,2-alternate conformation is computed to be a ground-state structure. The partial cone, flattened cone, chair, and 1,3-alternate conformers have been identified as ground-state structures in a vacuum, with the partial cone and the 1,3-alternate as the lowest energy minima in the aromatic model. The C(4)(v)() cone conformation is found to be a transition structure separating the flattened cone (C(2)(v)()) conformers. The energetic and structural preferences of the calix[4]arene model change dramatically when it is bound to Li(+), Na(+), and K(+). The number of pi-faces, the positioning of these pi-faces with respect to the cations, and the nature of the cation were studied as factors in the binding strength. A detailed study of the distances and angles between the aromatic ring centroids and the cations reveals the energetic advantages of multiple weak cation-pi interactions. The geometries are often far from the optimal cation-pi interaction in which the cation approaches in a perpendicular path the aromatic ring center, where the quadrupole moment is strongest. The results reveal that multiple weaker nonoptimal cation-pi interactions contribute significantly to the overall binding strength. This theoretical analysis underscores the importance of neighboring aromatic faces and provides new insight into the significance of cation-pi binding, not only for calix[4]arenes, but also for other supramolecular and biological systems.
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Affiliation(s)
- Alba T Macias
- Center for Computational Sciences, Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282-1530, USA
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Amunugama R, Rodgers MT. The Influence of Substituents on Cation−π Interactions. 4. Absolute Binding Energies of Alkali Metal Cation−Phenol Complexes Determined by Threshold Collision-Induced Dissociation and Theoretical Studies,. J Phys Chem A 2002. [DOI: 10.1021/jp0211584] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R. Amunugama
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - M. T. Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
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Amunugama R, Rodgers MT. Influence of Substituents on Cation−π Interactions. 2. Absolute Binding Energies of Alkali Metal Cation−Fluorobenzene Complexes Determined by Threshold Collision-Induced Dissociation and Theoretical Studies. J Phys Chem A 2002. [DOI: 10.1021/jp020459a] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R. Amunugama
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - M. T. Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
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Amunugama R, Rodgers MT. Influence of Substituents on Cation−π Interactions. 1. Absolute Binding Energies of Alkali Metal Cation−Toluene Complexes Determined by Threshold Collision-Induced Dissociation and Theoretical Studies. J Phys Chem A 2002. [DOI: 10.1021/jp014307b] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- R. Amunugama
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - M. T. Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
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21
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Gokel GW, Barbour LJ, De Wall SL, Meadows ES. Macrocyclic polyethers as probes to assess and understand alkali metal cation-π interactions. Coord Chem Rev 2001. [DOI: 10.1016/s0010-8545(01)00380-0] [Citation(s) in RCA: 131] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Gapeev A, Dunbar RC. Cation-pi interactions and the gas-phase thermochemistry of the Na(+)/phenylalanine complex. J Am Chem Soc 2001; 123:8360-5. [PMID: 11516285 DOI: 10.1021/ja010351t] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The complex of Na(+) with phenylalanine (Phe) is a prototype for the participation of cation-pi interactions in metal-ion binding to biological molecules. A recent comparison of this complex with the Na(+)/alanine (Na(+)/Ala) counterpart suggested only a small contribution of the phenyl ring interaction to binding, casting doubt on the extent of the cation-pi effect. The present work reexamines this thermochemistry using ligand-exchange equilibrium measurements in the Fourier transform ion cyclotron resonance (FT-ICR) ion trapping mass spectrometer. An increment of 7 +/- 2 kcal mol(-1) was found in the Ala/Phe comparison of binding enthalpies, confirming the importance of cation-pi binding enhancement in the Phe case. Absolute Na(+) binding enthalpies of 38 +/- 2 and 45 +/- 2 kcal mol(-1) were assigned for Ala and Phe, respectively, using pyridine as the thermochemical reference ligand. All of these results were supported by quantum calculations using both density functional and Hartree-Fock/MP2 methods, improved in several respects over previous calculations. Alanine methyl ester (AlaMe) was also observed, and found to have an Na(+) ion affinity larger by 2.3 kcal mol(-1) than Ala. New, lower energy conformations of neutral Phe were discovered in the computations.
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Affiliation(s)
- A Gapeev
- Chemistry Department, Case Western Reserve University, Cleveland, OH 44106, USA
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23
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Felder C, Jiang HL, Zhu WL, Chen KX, Silman I, Botti SA, Sussman JL. Quantum/Classical Mechanical Comparison of Cation−π Interactions between Tetramethylammonium and Benzene. J Phys Chem A 2001. [DOI: 10.1021/jp002933n] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Clifford Felder
- Department of Structural Biology and Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, Center for Drug Discovery and Design & Design and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, People's Republic of China, and Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651
| | - Hua-Liang Jiang
- Department of Structural Biology and Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, Center for Drug Discovery and Design & Design and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, People's Republic of China, and Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651
| | - Wei-Liang Zhu
- Department of Structural Biology and Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, Center for Drug Discovery and Design & Design and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, People's Republic of China, and Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651
| | - Kai-Xian Chen
- Department of Structural Biology and Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, Center for Drug Discovery and Design & Design and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, People's Republic of China, and Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651
| | - Israel Silman
- Department of Structural Biology and Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, Center for Drug Discovery and Design & Design and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, People's Republic of China, and Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651
| | - Simone A. Botti
- Department of Structural Biology and Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, Center for Drug Discovery and Design & Design and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, People's Republic of China, and Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651
| | - Joel L. Sussman
- Department of Structural Biology and Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, Center for Drug Discovery and Design & Design and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, People's Republic of China, and Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651
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Kim KS, Tarakeshwar P, Lee JY. Molecular Clusters of pi-Systems: Theoretical Studies of Structures, Spectra, and Origin of Interaction Energies. Chem Rev 2000; 100:4145-86. [PMID: 11749343 DOI: 10.1021/cr990051i] [Citation(s) in RCA: 917] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- K S Kim
- National Creative Research Initiative Center for Superfunctional Materials, Department of Chemistry, Division of Molecular and Life Sciences, Pohang University of Science and Technology, San 31, Hyojadong, Pohang 790-784, Korea
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Barbour LJ, De Wall SL, Meadows ES, Gokel GW. Experimental Evidence for Alkali-Metal Ion Cation−π Interactions Using Bibracchial Lariat Ether Complexes. Ind Eng Chem Res 2000. [DOI: 10.1021/ie990780o] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Leonard J. Barbour
- Bioorganic Chemistry Program and Department of Molecular Biology & Pharmacology, Washington University School of Medicine, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, Missouri 63110, and Department of Chemistry, University of Missouri, 601 S. College Avenue, Columbia, Missouri 65211
| | - Stephen L. De Wall
- Bioorganic Chemistry Program and Department of Molecular Biology & Pharmacology, Washington University School of Medicine, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, Missouri 63110, and Department of Chemistry, University of Missouri, 601 S. College Avenue, Columbia, Missouri 65211
| | - Eric S. Meadows
- Bioorganic Chemistry Program and Department of Molecular Biology & Pharmacology, Washington University School of Medicine, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, Missouri 63110, and Department of Chemistry, University of Missouri, 601 S. College Avenue, Columbia, Missouri 65211
| | - George W. Gokel
- Bioorganic Chemistry Program and Department of Molecular Biology & Pharmacology, Washington University School of Medicine, 660 S. Euclid Avenue, Campus Box 8103, St. Louis, Missouri 63110, and Department of Chemistry, University of Missouri, 601 S. College Avenue, Columbia, Missouri 65211
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Abstract
Cation-pi interactions in protein structures are identified and evaluated by using an energy-based criterion for selecting significant sidechain pairs. Cation-pi interactions are found to be common among structures in the Protein Data Bank, and it is clearly demonstrated that, when a cationic sidechain (Lys or Arg) is near an aromatic sidechain (Phe, Tyr, or Trp), the geometry is biased toward one that would experience a favorable cation-pi interaction. The sidechain of Arg is more likely than that of Lys to be in a cation-pi interaction. Among the aromatics, a strong bias toward Trp is clear, such that over one-fourth of all tryptophans in the data bank experience an energetically significant cation-pi interaction.
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Affiliation(s)
- J P Gallivan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Ryzhov V, Dunbar RC. Interactions of Phenol and Indole with Metal Ions in the Gas Phase: Models For Tyr and Trp Side-Chain Binding. J Am Chem Soc 1999. [DOI: 10.1021/ja983272z] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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