1
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Janicki TD, Van Vleet MJ, Schmidt JR. Development and Implementation of Atomically Anisotropic First-Principles Force Fields: A Benzene Case Study. J Phys Chem A 2023; 127:1736-1749. [PMID: 36780209 DOI: 10.1021/acs.jpca.2c07244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
π-interactions are an important motif in chemical and biochemical systems. However, due to their anisotropic electron densities and complex balance of intermolecular interactions, aromatic molecules represent an ongoing challenge for accurate and transferable force field development. Historically, ab initio force fields for aromatics have not exhibited good accuracy with respect to bulk properties or have only been used to study gas-phase dimers. Using benzene as a proof of concept, herein we show how our own ab initio MASTIFF force field incorporates an atomically anisotropic description of intermolecular interactions to yield an accurate and robust model for aromatic interactions irrespective of phase. Compared to existing models, the MASTIFF benzene force field not only is accurate for liquid phase properties but also offers transferability to the gas and solid phases. Additionally, we introduce a computationally efficient OpenMM plugin which enables customizable anisotropic intermolecular functional forms and which can be generically used in any MD simulation where a model for nonspherical atomic features is required. Overall, our results demonstrate the importance of atomic-level anisotropy in enabling next-generation ab initio force field development.
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Affiliation(s)
- Tesia D Janicki
- Department of Chemistry, University of Wisconsin─Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Mary J Van Vleet
- Department of Chemistry and Biochemistry, Spelman College, 350 Spelman Ln SW, Atlanta, Georgia 30314, United States
| | - J R Schmidt
- Department of Chemistry, University of Wisconsin─Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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2
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Thioglycolic acid oxidation by N, N'-phenylenebis(salicylideneiminato)manganese(III) in DMSO/H2O: Effects of sodium dodecylsulfate and cetyltrimethylammonium bromide. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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3
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Ali M, Song X, Ding D, Wang Q, Zhang Z, Tang Z. Bioremediation of PAHs and heavy metals co-contaminated soils: Challenges and enhancement strategies. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 295:118686. [PMID: 34920044 DOI: 10.1016/j.envpol.2021.118686] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/20/2021] [Accepted: 12/12/2021] [Indexed: 06/14/2023]
Abstract
Systemic studies on the bioremediation of co-contaminated PAHs and heavy metals are lacking, and this paper provides an in-depth review on the topic. The released sources and transport of co-contaminated PAHs and heavy metals, including their co-occurrence through formation of cation-π interactions and their adsorption in soil are examined. Moreover, it is investigated that co-contamination of PAHs and heavy metals can drive a synergistic positive influence on bioremediation through enhanced secretion of extracellular polymeric substances (EPSs), production of biosynthetic genes, organic acid and enzymatic proliferation. However, PAHs molecular structure, PAHs-heavy metals bioavailability and their interactive cytotoxic effects on microorganisms can exert a challenging influence on the bioremediation under co-contaminated conditions. The fluctuations in bioavailability for microorganisms are associated with soil properties, chemical coordinative interactions, and biological activities under the co-contaminated PAHs-heavy metals conditions. The interactive cytotoxicity caused by the emergence of co-contaminants includes microbial cell disruption, denaturation of DNA and protein structure, and deregulation of antioxidant biological molecules. Finally, this paper presents the emerging strategies to overcome the bioavailability problems and recommends the use of biostimulation and bioaugmentation along with the microbial immobilization for enhanced bioremediation of PAHs-heavy metals co-contaminated sites. Better knowledge of the bioremediation potential is imperative to improve the use of these approaches for the sustainable and cost-effective remediation of PAHs and heavy metals co-contamination in the near future.
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Affiliation(s)
- Mukhtiar Ali
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Song
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Da Ding
- Nanjing Institute of Environmental Science, Ministry of Ecology and Environment of the People's Republic of China, Nanjing, 210042, China
| | - Qing Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Zhuanxia Zhang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiwen Tang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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4
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H2O2 modified-hydrochar derived from paper waste sludge for enriched surface functional groups and promoted adsorption to ammonium. J Taiwan Inst Chem Eng 2021. [DOI: 10.1016/j.jtice.2021.06.057] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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5
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Alirezapour F, Khanmohammadi A. Theoretical study on the interaction of phenylalaninal with group
IA
(Li
+
, Na
+
, K
+
) and
IIA
(Be
2+
, Mg
2+
, Ca
2+
) metal cations. J CHIN CHEM SOC-TAIP 2021. [DOI: 10.1002/jccs.202000383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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6
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Heydari Z, Rashidi-Ranjbar P. Synthesis and photophysical properties of a new carbazole-based acidochromic molecular switch. J Photochem Photobiol A Chem 2019. [DOI: 10.1016/j.jphotochem.2019.03.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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7
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Kim I, Lee Y, Kim SD. Cytotoxicity induced by the mixture components of nickel and poly aromatic hydrocarbons. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2019; 41:391-400. [PMID: 29934778 DOI: 10.1007/s10653-018-0139-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 03/12/2018] [Indexed: 06/08/2023]
Abstract
Although particulate matter (PM) is composed of various chemicals, investigations regarding the toxicity that results from mixing the substances in PM are insufficient. In this study, the effects of low levels of three PAHs (benz[a]anthracene, benzo[a]pyrene, and dibenz[a,h]anthracene) on Ni toxicity were investigated to assess the combined effect of Ni-PAHs on the environment. We compared the difference in cell mortality and total glutathione (tGSH) reduction between single Ni and Ni-PAHs co-exposure using A549 (human alveolar carcinoma). In addition, we measured the change in Ni solubility in chloroform that was triggered by PAHs to confirm the existence of cation-π interactions between Ni and PAHs. In the single Ni exposure, the dose-response curve of cell mortality and tGSH reduction were very similar, indicating that cell death was mediated by the oxidative stress. However, 10 μM PAHs induced a depleted tGSH reduction compared to single Ni without a change in cell mortality. The solubility of Ni in chloroform was greatly enhanced by the addition of benz[a]anthracene, which demonstrates the cation-π interactions between Ni and PAHs. Ni-PAH complexes can change the toxicity mechanisms of Ni from oxidative stress to others due to the reduction of Ni2+ bioavailability and the accumulation of Ni-PAH complexes on cell membranes. The abundant PAHs contained in PM have strong potential to interact with metals, which can affect the toxicity of the metal. Therefore, the mixture toxicity and interactions between diverse metals and PAHs in PM should be investigated in the future.
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Affiliation(s)
- Injeong Kim
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, South Korea
| | - Yeseul Lee
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, South Korea
| | - Sang Don Kim
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, South Korea.
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8
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Wang Y, Luo X, Zhang L, Zhang S, Zhang L. A reversible, colorimetric, pH-responsive indole-based hydrogel and its application in urea detection. RSC Adv 2019; 9:24299-24304. [PMID: 35527878 PMCID: PMC9069612 DOI: 10.1039/c9ra03815a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 07/27/2019] [Indexed: 11/21/2022] Open
Abstract
A new type of pH-responsive indole-based (4-HINF) hydrogel, fabricated by a sol–gel method, was utilized as a platform for colorimetric detection of urea in aqueous solution. The colorimetric sensor was established by virtue of the synergistic effect of cation–π interaction and hydrogen bonding with good regenerative ability. The results exhibited linear response in the range of 0–10 mM with a limit of detection of 10 μM. The prepared 4-HINF hydrogel possessed high selectivity to pH change under complicated environments ensuring further applications in environmental and bio-systems. A new type of pH-responsive indole-based (4-HINF) hydrogel, fabricated by a sol–gel method, was utilized as a platform for colorimetric detection of urea in aqueous solution.![]()
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Affiliation(s)
- Yan Wang
- Research Center of Laser Fusion
- China Academy of Engineering Physicals
- Mianyang
- P. R. China
| | - Xuan Luo
- Research Center of Laser Fusion
- China Academy of Engineering Physicals
- Mianyang
- P. R. China
| | - Longfei Zhang
- Research Center of Laser Fusion
- China Academy of Engineering Physicals
- Mianyang
- P. R. China
| | - Shuai Zhang
- Research Center of Laser Fusion
- China Academy of Engineering Physicals
- Mianyang
- P. R. China
| | - Lin Zhang
- Research Center of Laser Fusion
- China Academy of Engineering Physicals
- Mianyang
- P. R. China
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9
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Juszczak LJ, Eisenberg AS. The Color of Cation-π Interactions: Subtleties of Amine-Tryptophan Interaction Energetics Allow for Radical-like Visible Absorbance and Fluorescence. J Am Chem Soc 2017; 139:8302-8311. [PMID: 28537725 DOI: 10.1021/jacs.7b03442] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Several peptides and a protein with an inter- or intramolecular cation-π interaction between tryptophan (Trp) and an amine cation are shown to absorb and fluoresce in the visible region of the spectrum. Titration of indole with sodium hydroxide or ammonium hydroxide yields an increasing visible fluorescence as well. Visible absorption and multipeaked fluorescence excitation spectra correlate with experimental absorption spectra and the vibrational modes of calculated absorption spectra for the neutral Trp radical. The radical character of the cation-indole interaction is predicted to stem from the electrostatic dislocation of indole highest occupied molecular orbital (HOMO) charge density toward the cation with a subsequent electronic transition from the HOMO-2 to the HOMO. Because this is a vertical transition, fluorescence is possible. Hydrogen bonding at the indole amine most likely stabilizes the radical-like state. These results provide new spectroscopic tools for the investigation of cation-π interactions in numerous biological systems, among them, proteins and their myriad ligands, and show that one, or at most, two, point mutations with natural amino acids are all that is required to impart visible fluorescence to proteins.
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Affiliation(s)
- Laura J Juszczak
- Chemistry Department, Brooklyn College, The City University of New York , New York, New York 11210, United States.,PhD programs in Chemistry and Biochemistry, The Graduate Center, The City University of New York , New York, New York 10016, United States
| | - Azaria S Eisenberg
- Chemistry Department, Brooklyn College, The City University of New York , New York, New York 11210, United States
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10
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Carrazana-García JA, Cabaleiro-Lago EM, Rodríguez-Otero J. A theoretical study of complexes formed between cations and curved aromatic systems: electrostatics does not always control cation–π interaction. Phys Chem Chem Phys 2017; 19:10543-10553. [DOI: 10.1039/c7cp01491k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cation–π interactions in curved aromatic systems are not controlled by electrostatics; induction and dispersion dominate in most cases studied.
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Affiliation(s)
- Jorge A. Carrazana-García
- Departamento de Química Física
- Facultade de Ciencias
- Universidade de Santiago de Compostela
- Campus de Lugo
- Avenida Alfonso X El Sabio s/n
| | - Enrique M. Cabaleiro-Lago
- Departamento de Química Física
- Facultade de Ciencias
- Universidade de Santiago de Compostela
- Campus de Lugo
- Avenida Alfonso X El Sabio s/n
| | - Jesús Rodríguez-Otero
- Centro de investigación en Química Biolóxica e Materiais Moleculares
- CIQUS
- Universidade de Santiago de Compostela
- Rúa Jenaro de la Fuente s/n
- Santiago de Compostela
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11
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Dawoud JN. Substitution effects on interaction forces in Na+·C4H4O complexes. Computational study. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.06.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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12
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Dehez F, Ángyán JG, Gutiérrez IS, Luque FJ, Schulten K, Chipot C. Modeling Induction Phenomena in Intermolecular Interactions with an Ab Initio Force Field. J Chem Theory Comput 2015; 3:1914-26. [PMID: 26636194 DOI: 10.1021/ct700156a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
One possible road toward the development of a polarizable potential energy function relies on the use of distributed polarizabilities derived from the induction energy mapped around the molecule. Whereas such polarizable models are expected to reproduce the signature induction energy with an appreciable accuracy, it is far from clear whether they will perform equally well in the context of intermolecular interactions. To address this issue, while pursuing the ultimate goal of a "plug-and-play"-like approach, polarizability models determined quantum mechanically and consisting of atomic isotropic dipole plus charge-flow polarizabilities were combined with the classical, nonpolarizable Charmm force field. Performance of the models was probed in the challenging test cases of cation-π binding and the association of a divalent calcium ion with water, where induction effects are envisioned to be considerable. Since brute force comparison of the binding energies estimated from the polarizable and the classical Charmm potential energy functions is not justified, the individual electrostatic and induction contributions of the force field were confronted to the corresponding terms of a symmetry-adapted perturbation theory (SAPT) expansion carried out with the 6-311++G(d,p) basis set. While the quantum-mechanical and the molecular-mechanical electrostatic and damped induction contributions agree reasonably well, overall reproduction of the binding energies is plagued by an underestimated repulsion that underlines the necessity of de novo parametrization of the classical 6-12 form of the van der Waals potential. Based on the SAPT expansion, new Lennard-Jones parameters were optimized, which, combined with the remainder of the polarizable force field, yield an improved reproduction of the target binding energies.
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Affiliation(s)
- François Dehez
- Equipe de dynamique des assemblages membranaires, UMR 7565 and Equipe de modélisation quantique et cristallographique, LCM3B, UMR 7036, Nancy Université, BP 239, 54506 Vandœuvre-lès-Nancy Cedex, France, Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avgda, Diagonal 643, Barcelona 08028, Spain, and Theoretical and Computational Biophysics Group, Beckman Institute, University of Illinois at Urbana [Formula: see text] Champaign, Urbana, Illinois 61801
| | - János G Ángyán
- Equipe de dynamique des assemblages membranaires, UMR 7565 and Equipe de modélisation quantique et cristallographique, LCM3B, UMR 7036, Nancy Université, BP 239, 54506 Vandœuvre-lès-Nancy Cedex, France, Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avgda, Diagonal 643, Barcelona 08028, Spain, and Theoretical and Computational Biophysics Group, Beckman Institute, University of Illinois at Urbana [Formula: see text] Champaign, Urbana, Illinois 61801
| | - Ignacio Soteras Gutiérrez
- Equipe de dynamique des assemblages membranaires, UMR 7565 and Equipe de modélisation quantique et cristallographique, LCM3B, UMR 7036, Nancy Université, BP 239, 54506 Vandœuvre-lès-Nancy Cedex, France, Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avgda, Diagonal 643, Barcelona 08028, Spain, and Theoretical and Computational Biophysics Group, Beckman Institute, University of Illinois at Urbana [Formula: see text] Champaign, Urbana, Illinois 61801
| | - F Javier Luque
- Equipe de dynamique des assemblages membranaires, UMR 7565 and Equipe de modélisation quantique et cristallographique, LCM3B, UMR 7036, Nancy Université, BP 239, 54506 Vandœuvre-lès-Nancy Cedex, France, Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avgda, Diagonal 643, Barcelona 08028, Spain, and Theoretical and Computational Biophysics Group, Beckman Institute, University of Illinois at Urbana [Formula: see text] Champaign, Urbana, Illinois 61801
| | - Klaus Schulten
- Equipe de dynamique des assemblages membranaires, UMR 7565 and Equipe de modélisation quantique et cristallographique, LCM3B, UMR 7036, Nancy Université, BP 239, 54506 Vandœuvre-lès-Nancy Cedex, France, Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avgda, Diagonal 643, Barcelona 08028, Spain, and Theoretical and Computational Biophysics Group, Beckman Institute, University of Illinois at Urbana [Formula: see text] Champaign, Urbana, Illinois 61801
| | - Christophe Chipot
- Equipe de dynamique des assemblages membranaires, UMR 7565 and Equipe de modélisation quantique et cristallographique, LCM3B, UMR 7036, Nancy Université, BP 239, 54506 Vandœuvre-lès-Nancy Cedex, France, Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avgda, Diagonal 643, Barcelona 08028, Spain, and Theoretical and Computational Biophysics Group, Beckman Institute, University of Illinois at Urbana [Formula: see text] Champaign, Urbana, Illinois 61801
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13
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Abstract
The interactions of aromatic groups have been identified as playing a crucial role in many systems of interest. Unfortunately, conventional atom-centered force fields provide only an approximate representation of these molecules owing to their failure to consider the quadrupole moment arising from the π electrons. In this paper the structure of liquid benzene, the prototypical aromatic system, is investigated using a novel approach to Monte Carlo simulation, parametrized against experimental thermodynamic data, which incorporates an explicit representation of the aromatic π electrons. In contrast to previous simulations of liquid benzene it is found that a perpendicular arrangement of benzene molecules is preferred to a parallel arrangement. This result is in good agreement with experimental data.
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Affiliation(s)
- Christopher M Baker
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, U.K. OX1 3QZ, and Unilever Centre for Molecular Informatics, The University Chemical Laboratory, Lensfield Road, Cambridge, U.K. CB2 1EW
| | - Guy H Grant
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, U.K. OX1 3QZ, and Unilever Centre for Molecular Informatics, The University Chemical Laboratory, Lensfield Road, Cambridge, U.K. CB2 1EW
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14
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Truncated structures used in search for new lead compounds and in a retrospective analysis of thienopyrimidine-based EGFR inhibitors. Eur J Med Chem 2015; 94:175-94. [DOI: 10.1016/j.ejmech.2015.03.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 02/28/2015] [Accepted: 03/02/2015] [Indexed: 12/15/2022]
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15
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Phipps MJS, Fox T, Tautermann CS, Skylaris CK. Energy decomposition analysis approaches and their evaluation on prototypical protein–drug interaction patterns. Chem Soc Rev 2015; 44:3177-211. [DOI: 10.1039/c4cs00375f] [Citation(s) in RCA: 226] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The partitioning of the interaction energy into chemical components such as electrostatics, polarization, and charge transfer is possible with energy decomposition analysis approaches. We review and evaluate these for biomolecular applications.
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Affiliation(s)
| | - Thomas Fox
- Lead Identification and Optimization Support
- Boehringer Ingelheim Pharma GmbH & Co. KG
- 88397 Biberach
- Germany
| | - Christofer S. Tautermann
- Lead Identification and Optimization Support
- Boehringer Ingelheim Pharma GmbH & Co. KG
- 88397 Biberach
- Germany
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16
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Molecular structure and bonding character of mono and divalent metal cations (Li+, Na+, K+, Be2+, Mg2+, and Ca2+) with substituted benzene derivatives: AIM, NBO, and NMR analyses. Struct Chem 2014. [DOI: 10.1007/s11224-014-0405-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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Ansorg K, Tafipolsky M, Engels B. Cation−π Interactions: Accurate Intermolecular Potential from Symmetry-Adapted Perturbation Theory. J Phys Chem B 2013; 117:10093-102. [DOI: 10.1021/jp403578r] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kay Ansorg
- Institut
für Physikalische und Theoretische
Chemie, Universität Würzburg, Campus Hubland Nord, Emil-Fischer-Strasse 42, D-97074 Würzburg,
Germany
| | - Maxim Tafipolsky
- Institut
für Physikalische und Theoretische
Chemie, Universität Würzburg, Campus Hubland Nord, Emil-Fischer-Strasse 42, D-97074 Würzburg,
Germany
| | - Bernd Engels
- Institut
für Physikalische und Theoretische
Chemie, Universität Würzburg, Campus Hubland Nord, Emil-Fischer-Strasse 42, D-97074 Würzburg,
Germany
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18
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Mahadevi AS, Sastry GN. Cation-π interaction: its role and relevance in chemistry, biology, and material science. Chem Rev 2012; 113:2100-38. [PMID: 23145968 DOI: 10.1021/cr300222d] [Citation(s) in RCA: 728] [Impact Index Per Article: 60.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- A Subha Mahadevi
- Molecular Modeling Group, CSIR-Indian Institute of Chemical Technology Tarnaka, Hyderabad 500 607, Andhra Pradesh, India
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19
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Varadwaj A, Varadwaj PR. Can a Single Molecule of Water be Completely Isolated Within the Subnano-Space Inside the Fullerene C60Cage? A Quantum Chemical Prospective. Chemistry 2012; 18:15345-60. [DOI: 10.1002/chem.201200969] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Indexed: 11/11/2022]
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20
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Cation–π vs. π–π interactions: Complexes of 2-pyridinylguanidinium derivatives and aromatic systems. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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Bauzá A, Quiñonero D, Deyà PM, Frontera A. Theoretical ab initio study of lone pair and anion–π interactions in fluorinated tropolones. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.05.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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22
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23
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Bouchoux G. Gas phase basicities of polyfunctional molecules. Part 3: Amino acids. MASS SPECTROMETRY REVIEWS 2012; 31:391-435. [PMID: 22611554 DOI: 10.1002/mas.20349] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The present article is the third part of a general overview of the gas-phase protonation thermochemistry of polyfunctional molecules (first part: Mass Spectrom. Rev., 2007, 26:775-835, second part: Mass Spectrom. Rev., 2011, in press). This review is devoted to the 20 proteinogenic amino acids and is divided in two parts. In the first one, the experimental data obtained during the last 30 years using the equilibrium, thermokinetic and kinetic methods are presented. A general re-assignment of the values originating from these various experiments has been done on the basis of the commonly accepted Hunter & Lias 1998 gas-phase basicity scale in order to provide an homogeneous set of data. In the second part, theoretical investigations on gaseous neutral and protonated amino acids are reviewed. Conformational landscapes of both types of species were examined in order to provide theoretical protonation thermochemistry based on the truly identified most stable conformers. Proton affinities computed at the presently highest levels of theory (i.e. composite methods such as Gn procedures) are presented. Estimates of thermochemical parameters calculated using a Boltzmann distribution of conformers at 298K are also included. Finally, comparison between experiment and theory is discussed and a set of evaluated proton affinities, gas-phase basicities and protonation entropies is proposed.
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Affiliation(s)
- Guy Bouchoux
- Département de Chimie, Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique, 91120 Palaiseau, France.
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Philip V, Harris J, Adams R, Nguyen D, Spiers J, Baudry J, Howell EE, Hinde RJ. A survey of aspartate-phenylalanine and glutamate-phenylalanine interactions in the protein data bank: searching for anion-π pairs. Biochemistry 2011; 50:2939-50. [PMID: 21366334 DOI: 10.1021/bi200066k] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein structures are stabilized using noncovalent interactions. In addition to the traditional noncovalent interactions, newer types of interactions are thought to be present in proteins. One such interaction, an anion-π pair, in which the positively charged edge of an aromatic ring interacts with an anion, forming a favorable anion-quadrupole interaction, has been previously proposed [Jackson, M. R., et al. (2007) J. Phys. Chem. B111, 8242-8249]. To study the role of anion-π interactions in stabilizing protein structure, we analyzed pairwise interactions between phenylalanine (Phe) and the anionic amino acids, aspartate (Asp) and glutamate (Glu). Particular emphasis was focused on identification of Phe-Asp or -Glu pairs separated by less than 7 Å in the high-resolution, nonredundant Protein Data Bank. Simplifying Phe to benzene and Asp or Glu to formate molecules facilitated in silico analysis of the pairs. Kitaura-Morokuma energy calculations were performed on roughly 19000 benzene-formate pairs and the resulting energies analyzed as a function of distance and angle. Edgewise interactions typically produced strongly stabilizing interaction energies (-2 to -7.3 kcal/mol), while interactions involving the ring face resulted in weakly stabilizing to repulsive interaction energies. The strongest, most stabilizing interactions were identified as preferentially occurring in buried residues. Anion-π pairs are found throughout protein structures, in helices as well as β strands. Numerous pairs also had nearby cation-π interactions as well as potential π-π stacking. While more than 1000 structures did not contain an anion-π pair, the 3134 remaining structures contained approximately 2.6 anion-π pairs per protein, suggesting it is a reasonably common motif that could contribute to the overall structural stability of a protein.
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Affiliation(s)
- Vivek Philip
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, United States
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Cerutti DS, Freddolino PL, Duke RE, Case DA. Simulations of a protein crystal with a high resolution X-ray structure: evaluation of force fields and water models. J Phys Chem B 2011; 114:12811-24. [PMID: 20860388 DOI: 10.1021/jp105813j] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We use classical molecular dynamics and 16 combinations of force fields and water models to simulate a protein crystal observed by room-temperature X-ray diffraction. The high resolution of the diffraction data (0.96 Å) and the simplicity of the crystallization solution (nearly pure water) make it possible to attribute any inconsistencies between the crystal structure and our simulations to artifacts of the models rather than inadequate representation of the crystal environment or uncertainty in the experiment. All simulations were extended for 100 ns of production dynamics, permitting some long-time scale artifacts of each model to emerge. The most noticeable effect of these artifacts is a model-dependent drift in the unit cell dimensions, which can become as large as 5% in certain force fields; the underlying cause is the replacement of native crystallographic contacts with non-native ones, which can occur with heterogeneity (loss of crystallographic symmetry) in simulations with some force fields. We find that the AMBER FF99SB force field maintains a lattice structure nearest that seen in the X-ray data, and produces the most realistic atomic fluctuations (by comparison to crystallographic B-factors) of all the models tested. We find that the choice of water model has a minor effect in comparison to the choice of protein model. We also identify a number of artifacts that occur throughout all of the simulations: excessive formation of hydrogen bonds or salt bridges between polar groups and loss of hydrophobic interactions. This study is intended as a foundation for future work that will identify individual parameters in each molecular model that can be modified to improve their representations of protein structure and thermodynamics.
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Affiliation(s)
- David S Cerutti
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers, the State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854-8066, USA.
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Baker CM, Lopes PEM, Zhu X, Roux B, MacKerell AD. Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field. J Chem Theory Comput 2010; 6:1181-1198. [PMID: 20401166 PMCID: PMC2853947 DOI: 10.1021/ct9005773] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Lennard-Jones (LJ) parameters for a variety of model compounds have previously been optimized within the CHARMM Drude polarizable force field to reproduce accurately pure liquid phase thermodynamic properties as well as additional target data. While the polarizable force field resulting from this optimization procedure has been shown to satisfactorily reproduce a wide range of experimental reference data across numerous series of small molecules, a slight but systematic overestimate of the hydration free energies has also been noted. Here, the reproduction of experimental hydration free energies is greatly improved by the introduction of pair-specific LJ parameters between solute heavy atoms and water oxygen atoms that override the standard LJ parameters obtained from combining rules. The changes are small and a systematic protocol is developed for the optimization of pair-specific LJ parameters and applied to the development of pair-specific LJ parameters for alkanes, alcohols and ethers. The resulting parameters not only yield hydration free energies in good agreement with experimental values, but also provide a framework upon which other pair-specific LJ parameters can be added as new compounds are parametrized within the CHARMM Drude polarizable force field. Detailed analysis of the contributions to the hydration free energies reveals that the dispersion interaction is the main source of the systematic errors in the hydration free energies. This information suggests that the systematic error may result from problems with the LJ combining rules and is combined with analysis of the pair-specific LJ parameters obtained in this work to identify a preliminary improved combining rule.
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Keiluweit M, Kleber M. Molecular-level interactions in soils and sediments: the role of aromatic pi-systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2009; 43:3421-3429. [PMID: 19544834 DOI: 10.1021/es8033044] [Citation(s) in RCA: 284] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
This review intends to deepen our understanding of mechanisms by which molecules with aromatic moieties attach to organic and mineral components of terrestrial environments. We present published evidence for the existence of specific, sorptive interactions of aromatic moieties with environmental sorbents. We find that aromatic pi-systems within organic compounds have the capacity to adsorb to minerals and organic soil and sediment components such as natural organic matter (NOM) and fire-derived black carbon (BC) through specific sorptive forces other than hydrophobic interactions. Polar interactions of aromatic pi-donor and -acceptor compounds show adsorption energies between 4 and 167 kJ mol(-1). Bonding strengths of cation-pi interactions and pi-pi electron donor-acceptor (EDA) interactions appear to be larger than H bonding strengths and comparable to inner- and outer-sphere complex formation. We conclude that, in analogy to polar and ionizable functional groups, components with aromatic pi-donor and -acceptor systems equip organic molecules with a substantial sorptive potential. This observation has important implications for the fate and transport of aromatic contaminants. The resulting sorptive interactions might also play a yet-overlooked functional role in the complex chain of processes which preserve NOM against decomposition.
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Affiliation(s)
- Marco Keiluweit
- Department of Crop and Soil Science, Soils Division, Oregon State University, Corvallis, Oregon 97331, USA.
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Bouchoux G, Bourcier S, Blanc V, Desaphy S. Gas Phase Protonation Thermochemistry of Phenylalanine and Tyrosine. J Phys Chem B 2009; 113:5549-62. [DOI: 10.1021/jp810240v] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guy Bouchoux
- Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique, CNRS, 91128 Palaiseau, France
| | - Sophie Bourcier
- Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique, CNRS, 91128 Palaiseau, France
| | - Virginie Blanc
- Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique, CNRS, 91128 Palaiseau, France
| | - Sylvain Desaphy
- Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique, CNRS, 91128 Palaiseau, France
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Bhayana B, Wilcox CS. A Minimal Protein Folding Model To Measure Hydrophobic and CH–π Effects on Interactions between Nonpolar Surfaces in Water. Angew Chem Int Ed Engl 2007; 46:6833-6. [PMID: 17676565 DOI: 10.1002/anie.200700932] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Brijesh Bhayana
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
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Bhayana B, Wilcox C. A Minimal Protein Folding Model To Measure Hydrophobic and CH–π Effects on Interactions between Nonpolar Surfaces in Water. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200700932] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Ghoufi A, Archirel P, Morel JP, Morel-Desrosiers N, Boutin A, Malfreyt P. Methodology for the Calculation of the Potential of Mean Force for a Cation–π Complex in Water. Chemphyschem 2007; 8:1648-56. [PMID: 17583904 DOI: 10.1002/cphc.200700197] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We report potential of mean force (PMF) calculations on the interaction between the p-sulfonatocalix[4]arene and a monovalent cation (Cs(+)). It has been recently shown from microcalorimetry and (133)Cs NMR experiments that the association with Cs(+) is governed by favourable cation-pi interactions and is characterized by the insertion of the cation into the cavity of the macrocycle. We show that the PMF calculation based upon a classical model is not able to reproduce both the thermodynamic properties of association and the insertion of the cation. In order to take into account the different contributions of the cation-pi interactions, we develop a new methodology consisting of changing the standard PMF by an additional contribution resulting from quantum calculations. The calculated thermodynamic properties of association are thus in line with the microcalorimetry and (133)Cs NMR experiments and the structure of the complex at the Gibbs free-energy minimum shows the insertion of the cation into the cavity of the calixarene.
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Affiliation(s)
- Aziz Ghoufi
- Laboratoire de Thermodynamique des Solutions et des Polymères, UMR CNRS 6003, Université Blaise Pascal, 63177 Aubière Cedex, France
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Baker CM, Grant GH. The effect of solvation on biomolecular conformation: 2-amino-1-phenylethanol. J Phys Chem B 2007; 111:9940-54. [PMID: 17672488 DOI: 10.1021/jp071059w] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Small molecule neurotransmitters form one the most important classes of pharmaceutical molecules. While the behavior of these molecules in their neutral forms in the gas phase is well understood, their behavior in more biologically relevant scenarios (protonated and in aqueous solution) has received comparatively little attention. Here we address this problem by using molecular mechanics simulations to build up a detailed picture of the conformational behavior of 2-amino-1-phenylethanol, a noradrenaline analogue, in aqueous solution in both its neutral and protonated forms. For the sake of comparison, equivalent simulations are also performed on the gas-phase molecules and gas-phase hydrated clusters. These calculations reveal the important role that water has to play in determining the conformational preferences and dynamic behavior of the molecules. Water molecules are found to bridge between the various functional groups within the molecule, significantly affecting their relative stabilities in comparison to the gas-phase values. The reorganization of these solvation structures also provides a mechanism for conformational interconversion. The role of the solvent in mediating interactions between the various functional groups within the molecule suggests that in noradrenaline the catechol groups will be able to interact, albeit indirectly, with the other functional groups, thereby influencing the behavior of the molecule.
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Affiliation(s)
- Christopher M Baker
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, The University of Oxford, South Parks Road, Oxford, United Kingdom OX1 3QZ
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Jackson MR, Beahm R, Duvvuru S, Narasimhan C, Wu J, Wang HN, Philip VM, Hinde RJ, Howell EE. A Preference for Edgewise Interactions between Aromatic Rings and Carboxylate Anions: The Biological Relevance of Anion−Quadrupole Interactions. J Phys Chem B 2007; 111:8242-9. [PMID: 17580852 DOI: 10.1021/jp0661995] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Noncovalent interactions are quite important in biological structure-function relationships. To study the pairwise interaction of aromatic amino acids (phenylalanine, tyrosine, tryptophan) with anionic amino acids (aspartic and glutamic acids), small molecule mimics (benzene, phenol or indole interacting with formate) were used at the MP2 level of theory. The overall energy associated with an anion-quadrupole interaction is substantial (-9.5 kcal/mol for a benzene-formate planar dimer at van der Waals contact distance), indicating the electropositive ring edge of an aromatic group can interact with an anion. Deconvolution of the long-range coplanar interaction energy into fractional contributions from charge-quadrupole interactions, higher-order electrostatic interactions, and polarization terms was achieved. The charge-quadrupole term contributes between 30 to 45% of the total MP2 benzene-formate interaction; most of the rest of the interaction arises from polarization contributions. Additional studies of the Protein Data Bank (PDB Select) show that nearly planar aromatic-anionic amino acid pairs occur more often than expected from a random angular distribution, while axial aromatic-anionic pairs occur less often than expected; this demonstrates the biological relevance of the anion-quadrupole interaction. While water may mitigate the strength of these interactions, they may be numerous in a typical protein structure, so their cumulative effect could be substantial.
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Affiliation(s)
- Michael R Jackson
- Department of Biochemistry, Cellular, and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, USA
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34
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Macleod NA, Simons JP. Infrared photodissociation spectroscopy of protonated neurotransmitters in the gas phase. Mol Phys 2007. [DOI: 10.1080/00268970701194285] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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35
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Macleod‡ NA, Simons JP. Infrared photodissociation spectroscopy of protonated neurotransmitters in the gas phase – ARTICLE WITHDRAWN. Mol Phys 2006. [DOI: 10.1080/00268970601110340] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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36
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Pratuangdejkul J, Jaudon P, Ducrocq C, Nosoongnoen W, Guerin GA, Conti M, Loric S, Launay JM, Manivet P. Cation-π Interactions in Serotonin: Conformational, Electronic Distribution, and Energy Decomposition Analysis. J Chem Theory Comput 2006; 2:746-60. [DOI: 10.1021/ct0600316] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jaturong Pratuangdejkul
- Service de Biochimie et de Biologie Moléculaire, IFR 139, Hôpital Lariboisière, 2, rue Ambroise Paré, 75475 Paris Cedex 10, France, E.A. 3621, Laboratoire de Biologie Cellulaire, UFR des Sciences Pharmaceutiques et Biologiques, 4 Avenue de l'Observatoire, 75270 Paris, Cedex 06, France, I.C.M.M.O. Laboratoire de Chimie Structurale Organique, Université Paris-Sud, Bat. 410, 91405 Orsay, Cedex, France, Institut de Chimie des Substances Naturelles, CNRS, F-91198 Gif-sur-Yvette, France, BioQuanta Corp., 2850
| | - Pascale Jaudon
- Service de Biochimie et de Biologie Moléculaire, IFR 139, Hôpital Lariboisière, 2, rue Ambroise Paré, 75475 Paris Cedex 10, France, E.A. 3621, Laboratoire de Biologie Cellulaire, UFR des Sciences Pharmaceutiques et Biologiques, 4 Avenue de l'Observatoire, 75270 Paris, Cedex 06, France, I.C.M.M.O. Laboratoire de Chimie Structurale Organique, Université Paris-Sud, Bat. 410, 91405 Orsay, Cedex, France, Institut de Chimie des Substances Naturelles, CNRS, F-91198 Gif-sur-Yvette, France, BioQuanta Corp., 2850
| | - Claire Ducrocq
- Service de Biochimie et de Biologie Moléculaire, IFR 139, Hôpital Lariboisière, 2, rue Ambroise Paré, 75475 Paris Cedex 10, France, E.A. 3621, Laboratoire de Biologie Cellulaire, UFR des Sciences Pharmaceutiques et Biologiques, 4 Avenue de l'Observatoire, 75270 Paris, Cedex 06, France, I.C.M.M.O. Laboratoire de Chimie Structurale Organique, Université Paris-Sud, Bat. 410, 91405 Orsay, Cedex, France, Institut de Chimie des Substances Naturelles, CNRS, F-91198 Gif-sur-Yvette, France, BioQuanta Corp., 2850
| | - Wichit Nosoongnoen
- Service de Biochimie et de Biologie Moléculaire, IFR 139, Hôpital Lariboisière, 2, rue Ambroise Paré, 75475 Paris Cedex 10, France, E.A. 3621, Laboratoire de Biologie Cellulaire, UFR des Sciences Pharmaceutiques et Biologiques, 4 Avenue de l'Observatoire, 75270 Paris, Cedex 06, France, I.C.M.M.O. Laboratoire de Chimie Structurale Organique, Université Paris-Sud, Bat. 410, 91405 Orsay, Cedex, France, Institut de Chimie des Substances Naturelles, CNRS, F-91198 Gif-sur-Yvette, France, BioQuanta Corp., 2850
| | - Georges-Alexandre Guerin
- Service de Biochimie et de Biologie Moléculaire, IFR 139, Hôpital Lariboisière, 2, rue Ambroise Paré, 75475 Paris Cedex 10, France, E.A. 3621, Laboratoire de Biologie Cellulaire, UFR des Sciences Pharmaceutiques et Biologiques, 4 Avenue de l'Observatoire, 75270 Paris, Cedex 06, France, I.C.M.M.O. Laboratoire de Chimie Structurale Organique, Université Paris-Sud, Bat. 410, 91405 Orsay, Cedex, France, Institut de Chimie des Substances Naturelles, CNRS, F-91198 Gif-sur-Yvette, France, BioQuanta Corp., 2850
| | - Marc Conti
- Service de Biochimie et de Biologie Moléculaire, IFR 139, Hôpital Lariboisière, 2, rue Ambroise Paré, 75475 Paris Cedex 10, France, E.A. 3621, Laboratoire de Biologie Cellulaire, UFR des Sciences Pharmaceutiques et Biologiques, 4 Avenue de l'Observatoire, 75270 Paris, Cedex 06, France, I.C.M.M.O. Laboratoire de Chimie Structurale Organique, Université Paris-Sud, Bat. 410, 91405 Orsay, Cedex, France, Institut de Chimie des Substances Naturelles, CNRS, F-91198 Gif-sur-Yvette, France, BioQuanta Corp., 2850
| | - Sylvain Loric
- Service de Biochimie et de Biologie Moléculaire, IFR 139, Hôpital Lariboisière, 2, rue Ambroise Paré, 75475 Paris Cedex 10, France, E.A. 3621, Laboratoire de Biologie Cellulaire, UFR des Sciences Pharmaceutiques et Biologiques, 4 Avenue de l'Observatoire, 75270 Paris, Cedex 06, France, I.C.M.M.O. Laboratoire de Chimie Structurale Organique, Université Paris-Sud, Bat. 410, 91405 Orsay, Cedex, France, Institut de Chimie des Substances Naturelles, CNRS, F-91198 Gif-sur-Yvette, France, BioQuanta Corp., 2850
| | - Jean-Marie Launay
- Service de Biochimie et de Biologie Moléculaire, IFR 139, Hôpital Lariboisière, 2, rue Ambroise Paré, 75475 Paris Cedex 10, France, E.A. 3621, Laboratoire de Biologie Cellulaire, UFR des Sciences Pharmaceutiques et Biologiques, 4 Avenue de l'Observatoire, 75270 Paris, Cedex 06, France, I.C.M.M.O. Laboratoire de Chimie Structurale Organique, Université Paris-Sud, Bat. 410, 91405 Orsay, Cedex, France, Institut de Chimie des Substances Naturelles, CNRS, F-91198 Gif-sur-Yvette, France, BioQuanta Corp., 2850
| | - Philippe Manivet
- Service de Biochimie et de Biologie Moléculaire, IFR 139, Hôpital Lariboisière, 2, rue Ambroise Paré, 75475 Paris Cedex 10, France, E.A. 3621, Laboratoire de Biologie Cellulaire, UFR des Sciences Pharmaceutiques et Biologiques, 4 Avenue de l'Observatoire, 75270 Paris, Cedex 06, France, I.C.M.M.O. Laboratoire de Chimie Structurale Organique, Université Paris-Sud, Bat. 410, 91405 Orsay, Cedex, France, Institut de Chimie des Substances Naturelles, CNRS, F-91198 Gif-sur-Yvette, France, BioQuanta Corp., 2850
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Morera E, Nalli M, Mollica A, Paglialunga Paradisi M, Aschi M, Gavuzzo E, Mazza F, Lucente G. Peptides containing 4-amino-1,2-dithiolane-4-carboxylic acid (Adt): conformation of Boc-Adt-Adt-NHMe and NH...S interactions. J Pept Sci 2005; 11:104-12. [PMID: 15635640 DOI: 10.1002/psc.602] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To study the conformational preferences induced by the insertion of the 4-amino-1,2-dithiolane-4-carboxylic acid (Adt) residue into a peptide backbone, the achiral N-protected dipeptide methylamide Boc-Adt-Adt-NHMe (1) was synthesized and its crystal state and solution conformation studied and compared with that exhibited by its carba-analogue Boc-Ac5c-Ac5c-NHMe containing two residues of 1-aminocyclopentane-1-carboxylic acid (Ac5c). Compound 1 in the crystal adopts a type-III beta-turn conformation and an analogous structure is that preferred in chloroform solution as established by 1H-NMR and NOE information. In the crystal packing three different Adt rings form a cavity and the involved sulphur atoms give rise to unusual multiple interactions with one NH group. The chemical nature of these intermolecular and intramolecular main-chain...side-chain NH...S interactions are discussed in terms of quantum chemical calculations.
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Affiliation(s)
- Enrico Morera
- Dipartimento di Studi Farmaceutici, Università di Roma La Sapienza and Istituto di Chimica Biomolecolare, Sezione di Roma, CNR, 00185 Roma, Italy
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Laali KK, Hupertz S, Temu AG, Galembeck SE. Electrospray mass spectrometric and DFT study of substituent effects in Ag+ complexation to polycyclic aromatic hydrocarbons (PAHs). Org Biomol Chem 2005; 3:2319-26. [PMID: 16010367 DOI: 10.1039/b503084f] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Complexation of Ag(i) cation to a series of substituted anthracenes (AN), phenanthrenes (PH), pyrenes (PY) and cyclopenta[a]phenanthrenes (CPaPH) was studied in competitive experiments by allowing PAHs to react in pairs with AgOTf. The resulting complexes were examined by electrospray mass spectrometry (ES-MS) to determine relative abundances of the corresponding monomeric and dimeric complexes. Based on this data a sequence of complexation ability rankings was derived for each group. Among the substituents examined, a -COMe group when placed at the meso position in AN and PH, or at the C-1 in PY is most effective in Ag(+) complexation, whereas an -NO(2) group is least efficient. Methyl groups at the meso positions are better than in the terminal rings. For the CPaPH series, bay region substitution (methyl and alkoxy) have limited effect as does carbonyl substitution in the annelated CP ring. In the PY series, a -COPh or a -CH(Me)OH group at C-1 is as efficient as -COMe. Based on extensive potential energy searches, four types of complexation modes were identified by B3LYP/LANL2DZ calculations involving Ag(+) complexation to -NO(2) oxygens, to -COMe or to -OH and a peri-carbon, to just one ring carbon, or by bridging two ring carbons. Among these modes, the first two are most favorable. The energetic preferences were rationalized with charge decomposition analysis (CDA). Effect of Ag(+) complexation on relative aromaticity in various rings was examined by NICS (nucleus independent chemical shift) in two representative cases. Structures and energies of the acetyl pyrene-Ag(+)-pyrene hetero-dimer and acetyl pyrene-Ag(+)-acetyl pyrene homo-dimer complexes were determined with the same model. These complexes have sandwich structures.
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Affiliation(s)
- Kenneth K Laali
- Department of Chemistry, Kent State University, Kent, OH 44242, USA.
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Garau C, Frontera A, Quiñonero D, Ballester P, Costa A, Deyà PM. Cation-π versus anion-π interactions: a comparative ab initio study based on energetic, electron charge density and aromatic features. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.05.049] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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40
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Cafeo G, Garozzo D, Kohnke FH, Pappalardo S, Parisi MF, Pistone Nascone R, Williams DJ. From calixfurans to heterocyclophanes containing isopyrazole units. Tetrahedron 2004. [DOI: 10.1016/j.tet.2003.12.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Kim D, Hu S, Tarakeshwar P, Kim KS, Lisy JM. Cation−π Interactions: A Theoretical Investigation of the Interaction of Metallic and Organic Cations with Alkenes, Arenes, and Heteroarenes. J Phys Chem A 2003. [DOI: 10.1021/jp0224214] [Citation(s) in RCA: 213] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dongwook 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
| | - Shaowen Hu
- 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
| | - P. Tarakeshwar
- 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
| | - Kwang 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
| | - James M. Lisy
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
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