1
|
Averdunk C, Hanke K, Schatz D, Wegner HA. Molecular Wind-Up Meter for the Quantification of London Dispersion Interactions. Acc Chem Res 2024; 57:257-266. [PMID: 38131644 DOI: 10.1021/acs.accounts.3c00616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
ConspectusThe experimental quantification of interactions on the molecular level provides the necessary basis for the design of functional materials and chemical processes. The interplay of multiple parameters and the small quantity of individual interactions pose a special challenge for such endeavors. The common method is the use of molecular balances, which can exist in two different states. Thereby, a stabilizing interaction can occur in one of the states, favoring its formation and thus affecting the thermodynamic equilibrium of the system. One challenge is determining the change in this equilibrium since various analytical methods could not be applied to fast-changing equilibria. A new and promising method for quantifying molecular interactions is the use of Molecular Wind-up Meters (MWM) in which the change in kinetics, rather than the effect on thermodynamics, is investigated. An MWM is transformed with an energy input (e.g. irradiation) into a metastable state. Then, the rate of thermal transformation back to the ground state is measured. The strength of interactions present in the metastable state controls the kinetics of the back reactions, allowing direct correlation. The advantage of this approach lies in the high sensitivity (energy differences can be larger by 1 order of magnitude) and, in general, allows the use of a broader range of solvents and analytical methods. An Azobenzene-based MWM has been established as a powerful tool to quantify London dispersion interactions. London dispersion (LD) represents the attractive part of the van der Waals potential. Although neglected in the past due to its weak character, it has been shown that the influence of LD on the structure, stability, and reactivity of matter can be decisive. Especially in larger molecules, its energy contribution increases overproportionately with the number of atoms, which has sparked increasing interest in the use of so-called dispersion energy donors (DED) as a new structural element. Application of the azobenzene-based MWM not only allowed the differentiation of bulkiness, but also systematically addressed the influence of the length of n-alkyl chains. Additionally, the solvent influence on LD was studied. Based on the azobenzene MWM, an increment system has been proposed, allowing a rough estimate of the effect of a specific DED.
Collapse
Affiliation(s)
- Conrad Averdunk
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
- Center of Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| | - Kai Hanke
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
- Center of Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| | - Dominic Schatz
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
- Center of Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| | - Hermann A Wegner
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
- Center of Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| |
Collapse
|
2
|
Wang XD, Zhu J, Wang DX. Intermolecular n→π* Interactions in Supramolecular Chemistry and Catalysis. Chempluschem 2023; 88:e202300288. [PMID: 37609956 DOI: 10.1002/cplu.202300288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 08/24/2023]
Abstract
The n→π* interactions describing attractive force between lone pairs (lps) of nucleophile and carbonyl or polarized unsaturated bonds have recently attracted growing attentions in various disciplines. So far, such non-covalent driving force are mainly concentrated to intramolecular systems. Intermolecular n→π* interactions in principle could produce fascinated supramolecular systems or facilitate organic reactions, however, they remain largely underexplored due to the very weak energy of individual interaction. This review attempts to give an overview of the challenging intermolecular n→π* interactions, much efforts emphasize the supramolecular systems, catalytic processes and spectroscopic measurements.
Collapse
Affiliation(s)
- Xu-Dong Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jun Zhu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De-Xian Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
3
|
Adhav V, Saikrishnan K. The Realm of Unconventional Noncovalent Interactions in Proteins: Their Significance in Structure and Function. ACS OMEGA 2023; 8:22268-22284. [PMID: 37396257 PMCID: PMC10308531 DOI: 10.1021/acsomega.3c00205] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023]
Abstract
Proteins and their assemblies are fundamental for living cells to function. Their complex three-dimensional architecture and its stability are attributed to the combined effect of various noncovalent interactions. It is critical to scrutinize these noncovalent interactions to understand their role in the energy landscape in folding, catalysis, and molecular recognition. This Review presents a comprehensive summary of unconventional noncovalent interactions, beyond conventional hydrogen bonds and hydrophobic interactions, which have gained prominence over the past decade. The noncovalent interactions discussed include low-barrier hydrogen bonds, C5 hydrogen bonds, C-H···π interactions, sulfur-mediated hydrogen bonds, n → π* interactions, London dispersion interactions, halogen bonds, chalcogen bonds, and tetrel bonds. This Review focuses on their chemical nature, interaction strength, and geometrical parameters obtained from X-ray crystallography, spectroscopy, bioinformatics, and computational chemistry. Also highlighted are their occurrence in proteins or their complexes and recent advances made toward understanding their role in biomolecular structure and function. Probing the chemical diversity of these interactions, we determined that the variable frequency of occurrence in proteins and the ability to synergize with one another are important not only for ab initio structure prediction but also to design proteins with new functionalities. A better understanding of these interactions will promote their utilization in designing and engineering ligands with potential therapeutic value.
Collapse
|
4
|
Livingstone K, Siebold K, Meyer S, Martín-Heras V, Daniliuc CG, Gilmour R. Skeletal Ring Contractions via I(I)/I(III) Catalysis: Stereoselective Synthesis of cis-α,α-Difluorocyclopropanes. ACS Catal 2022; 12:14507-14516. [PMID: 36504915 PMCID: PMC9724094 DOI: 10.1021/acscatal.2c04511] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/17/2022] [Indexed: 11/12/2022]
Abstract
The clinical success of α,α-difluorocyclopropanes, combined with limitations in the existing synthesis portfolio, inspired the development of an operationally simple, organocatalysis-based strategy to access cis-configured derivatives with high levels of stereoselectivity (up to >20:1 cis:trans). Leveraging an I(I)/I(III)-catalysis platform in the presence of an inexpensive HF source, it has been possible to exploit disubstituted bicyclobutanes (BCBs) as masked cyclobutene equivalents for this purpose. In situ generation of this strained alkene, enabled by Brønsted acid activation, facilitates an unprecedented 4 → 3 fluorinative ring contraction, to furnish cis-α,α-difluorinated cyclopropanes in a highly stereoselective manner (up to 88% yield). Mechanistic studies are disclosed together with conformational analysis (X-ray crystallography and NMR) to validate cis-α,α-difluorocyclopropanes as isosteres of the 1,4-dicarbonyl moiety. Given the importance of this unit in biology and the foundational no → π* interactions that manifest themselves in this conformation (e.g., collagen), it is envisaged that the title motif will find application in focused molecular design.
Collapse
|
5
|
Meredith NY, Borsley S, Smolyar IV, Nichol GS, Baker CM, Ling KB, Cockroft SL. Dissecting Solvent Effects on Hydrogen Bonding. Angew Chem Int Ed Engl 2022; 61:e202206604. [PMID: 35608961 PMCID: PMC9400978 DOI: 10.1002/anie.202206604] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Indexed: 12/26/2022]
Abstract
The experimental isolation of H‐bond energetics from the typically dominant influence of the solvent remains challenging. Here we use synthetic molecular balances to quantify amine/amide H‐bonds in competitive solvents. Over 200 conformational free energy differences were determined using 24 H‐bonding balances in 9 solvents spanning a wide polarity range. The correlations between experimental interaction energies and gas‐phase computed energies exhibited wild solvent‐dependent variation. However, excellent correlations were found between the same computed energies and the experimental data following empirical dissection of solvent effects using Hunter's α/β solvation model. In addition to facilitating the direct comparison of experimental and computational data, changes in the fitted donor and acceptor constants reveal the energetics of secondary local interactions such as competing H‐bonds.
Collapse
Affiliation(s)
- Nicole Y Meredith
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Stefan Borsley
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Ivan V Smolyar
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Gary S Nichol
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Christopher M Baker
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK
| | - Kenneth B Ling
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK
| | - Scott L Cockroft
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
| |
Collapse
|
6
|
Meredith NY, Borsley S, Smolyar IV, Nichol GS, Baker CM, Ling KB, Cockroft SL. Dissecting Solvent Effects on Hydrogen Bonding. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Nicole Y. Meredith
- EaStCHEM School of Chemistry University of Edinburgh Joseph Black Building, David Brewster Road Edinburgh EH9 3FJ UK
| | - Stefan Borsley
- EaStCHEM School of Chemistry University of Edinburgh Joseph Black Building, David Brewster Road Edinburgh EH9 3FJ UK
| | - Ivan V. Smolyar
- EaStCHEM School of Chemistry University of Edinburgh Joseph Black Building, David Brewster Road Edinburgh EH9 3FJ UK
| | - Gary S. Nichol
- EaStCHEM School of Chemistry University of Edinburgh Joseph Black Building, David Brewster Road Edinburgh EH9 3FJ UK
| | - Christopher M. Baker
- Syngenta Jealott's Hill International Research Centre Bracknell, Berkshire RG42 6EY UK
| | - Kenneth B. Ling
- Syngenta Jealott's Hill International Research Centre Bracknell, Berkshire RG42 6EY UK
| | - Scott L. Cockroft
- EaStCHEM School of Chemistry University of Edinburgh Joseph Black Building, David Brewster Road Edinburgh EH9 3FJ UK
| |
Collapse
|
7
|
O‧‧‧C═O interaction, its occurrence and implications for protein structure and folding. Proteins 2022; 90:1159-1169. [DOI: 10.1002/prot.26298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/21/2021] [Accepted: 01/04/2022] [Indexed: 11/07/2022]
|
8
|
Neveselý T, Molloy JJ, McLaughlin C, Brüss L, Daniliuc CG, Gilmour R. Leveraging the n→π* Interaction in Alkene Isomerization by Selective Energy Transfer Catalysis. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Tomáš Neveselý
- Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Corrensstrasse 36 48149 Münster Germany
| | - John J. Molloy
- Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Corrensstrasse 36 48149 Münster Germany
- Current address: Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Germany
| | - Calum McLaughlin
- Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Corrensstrasse 36 48149 Münster Germany
| | - Linda Brüss
- Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Corrensstrasse 36 48149 Münster Germany
| | - Constantin G. Daniliuc
- Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Corrensstrasse 36 48149 Münster Germany
| | - Ryan Gilmour
- Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Corrensstrasse 36 48149 Münster Germany
| |
Collapse
|
9
|
Neveselý T, Molloy JJ, McLaughlin C, Brüss L, Daniliuc CG, Gilmour R. Leveraging the n→π* Interaction in Alkene Isomerization by Selective Energy Transfer Catalysis. Angew Chem Int Ed Engl 2021; 61:e202113600. [PMID: 34748684 PMCID: PMC9299456 DOI: 10.1002/anie.202113600] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Indexed: 11/09/2022]
Abstract
Examples of geometric alkene isomerization in nature are often limited to the net exergonic direction (ΔG°<0), with the antipodal net endergonic processes (ΔG°>0) comparatively under‐represented. Inspired by the expansiveness of the maleate to fumarate (Z→E) isomerization in biochemistry, we investigated the inverse E→Z variant to validate nO→πC=O* interactions as a driving force for contra‐thermodynamic isomerization. A general protocol involving selective energy transfer catalysis with inexpensive thioxanthone as a sensitizer (λmax=402 nm) is disclosed. Whilst in the enzymatic process nO→πC=O* interactions commonly manifest themselves in the substrate, these same interactions are shown to underpin directionality in the antipodal reaction by shortening the product alkene chromophore. The process was validated with diverse fumarate derivatives (>30 examples, up to Z:E>99:1), including the first examples of tetrasubstituted alkenes, and the involvement of nO→πC=O* interactions was confirmed by X‐ray crystallography.
Collapse
Affiliation(s)
- Tomáš Neveselý
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 36, 48149, Münster, Germany
| | - John J Molloy
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 36, 48149, Münster, Germany.,Current address: Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Calum McLaughlin
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 36, 48149, Münster, Germany
| | - Linda Brüss
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 36, 48149, Münster, Germany
| | - Constantin G Daniliuc
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 36, 48149, Münster, Germany
| | - Ryan Gilmour
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 36, 48149, Münster, Germany
| |
Collapse
|
10
|
Vik EC, Li P, Madukwe DO, Karki I, Tibbetts GS, Shimizu KD. Analysis of the Orbital and Electrostatic Contributions to the Lone Pair-Aromatic Interaction Using Molecular Rotors. Org Lett 2021; 23:8179-8182. [PMID: 34670094 DOI: 10.1021/acs.orglett.1c02878] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The attractive interaction between carbonyl oxygens and the π-face of aromatic surfaces was studied using N-phenylimide molecular rotors. The C═O···Ar interactions could stabilize the transition states but were half the strength of comparable C═O···C═O interactions. The C═O···Ar interaction had a significant electrostatic component but only a small orbital delocalization component.
Collapse
Affiliation(s)
- Erik C Vik
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ping Li
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Daniel O Madukwe
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ishwor Karki
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Gabriel S Tibbetts
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ken D Shimizu
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| |
Collapse
|
11
|
Tykwinski RR, Nierengarten JF. François Diederich’s legacy. Chem 2021. [DOI: 10.1016/j.chempr.2021.04.003] [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]
|
12
|
Sahariah B, Sarma BK. Spectroscopic evidence of n → π* interactions involving carbonyl groups. Phys Chem Chem Phys 2021; 22:26669-26681. [PMID: 33226050 DOI: 10.1039/d0cp03557b] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
n → π* has emerged as an important noncovalent interaction that can affect the conformations of both small- and macromolecules including peptides and proteins. Carbonyl-carbonyl (COCO) n → π* interactions involving CO groups are well studied. Recent studies have shown that the COCO n → π* interactions are the most abundant secondary interactions in proteins with a frequency of 33 interactions per 100 residues and, among the various secondary interactions, n → π* interactions are expected to provide the highest enthalpic contributions to the conformational stability of globular proteins. However, n → π* interactions are relatively weak and provide an average stabilization of about 0.25 kcal mol-1 per interaction in proteins. The strongest n → π* interaction could be as strong as a moderate hydrogen bond. Therefore, it is challenging to detect and quantify these weak interactions, especially in solution in the presence of perturbation from other intermolecular interactions. Accordingly, spectroscopic investigations that can provide direct evidence of n → π* interaction are limited, and the majority of papers published in this area have relied on X-ray crystallography and/or theoretical calculations to establish the presence of this interaction. The aim of this perspective is to discuss the studies where a spectroscopic signature in support of n → π* interaction was observed. As the "n → π* interaction" is a relatively new terminology, there remains the possibility of there being earlier studies where spectroscopic evidence for n → π* interactions was obtained but it was not discussed in light of the n → π* terminology. We noticed several such studies and, as can be expected, these studies were often overlooked in the discussion of n → π* interactions in the recent literature. In this perspective, we have also discussed these studies and provided computational support for the presence of n → π* interaction.
Collapse
Affiliation(s)
- Biswajit Sahariah
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India.
| | | |
Collapse
|
13
|
Sala V, Cnudde SJ, Murabito A, Massarotti A, Hirsch E, Ghigo A. Therapeutic peptides for the treatment of cystic fibrosis: Challenges and perspectives. Eur J Med Chem 2021; 213:113191. [PMID: 33493828 DOI: 10.1016/j.ejmech.2021.113191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 12/21/2020] [Accepted: 01/08/2021] [Indexed: 02/07/2023]
Abstract
Cystic fibrosis (CF) is the most common amongst rare genetic diseases, affecting more than 70.000 people worldwide. CF is characterized by a dysfunctional chloride channel, termed cystic fibrosis conductance regulator (CFTR), which leads to the production of a thick and viscous mucus layer that clogs the lungs of CF patients and traps pathogens, leading to chronic infections and inflammation and, ultimately, lung damage. In recent years, the use of peptides for the treatment of respiratory diseases, including CF, has gained growing interest. Therapeutic peptides for CF include antimicrobial peptides, inhibitors of proteases, and modulators of ion channels, among others. Peptides display unique features that make them appealing candidates for clinical translation, like specificity of action, high efficacy, and low toxicity. Nevertheless, the intrinsic properties of peptides, together with the need of delivering these compounds locally, e.g. by inhalation, raise a number of concerns in the development of peptide therapeutics for CF lung disease. In this review, we discuss the challenges related to the use of peptides for the treatment of CF lung disease through inhalation, which include retention within mucus, proteolysis, immunogenicity and aggregation. Strategies for overcoming major shortcomings of peptide therapeutics will be presented, together with recent developments in peptide design and optimization, including computational analysis and high-throughput screening.
Collapse
Affiliation(s)
- Valentina Sala
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Torino, Via Nizza 52, 10126, Torino, Italy
| | - Sophie Julie Cnudde
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Torino, Via Nizza 52, 10126, Torino, Italy
| | - Alessandra Murabito
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Torino, Via Nizza 52, 10126, Torino, Italy
| | - Alberto Massarotti
- Department of Pharmaceutical Science, University of Piemonte Orientale "A. Avogadro", Largo Donegani 2, 28100, Novara, Italy
| | - Emilio Hirsch
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Torino, Via Nizza 52, 10126, Torino, Italy; Kither Biotech S.r.l., Via Nizza 52, 10126, Torino, Italy
| | - Alessandra Ghigo
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Torino, Via Nizza 52, 10126, Torino, Italy; Kither Biotech S.r.l., Via Nizza 52, 10126, Torino, Italy.
| |
Collapse
|
14
|
Elmi A, Cockroft SL. Quantifying Interactions and Solvent Effects Using Molecular Balances and Model Complexes. Acc Chem Res 2021; 54:92-103. [PMID: 33315374 DOI: 10.1021/acs.accounts.0c00545] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Where the basic units of molecular chemistry are the bonds within molecules, supramolecular chemistry is based on the interactions that occur between molecules. Understanding the "how" and "why" of the processes that govern molecular self-assembly remains an open challenge to the supramolecular community. While many interactions are readily examined in silico through electronic structure calculations, such insights may not be directly applicable to experimentalists. The practical limitations of computationally accounting for solvation is perhaps the largest bottleneck in this regard, with implicit solvation models failing to comprehensively account for the specific nature of solvent effects and explicit models incurring a prohibitively high computational cost. Since molecular recognition processes usually occur in solution, insight into the nature and effect of solvation is imperative not only for understanding these phenomena but also for the rational design of systems that exploit them.Molecular balances and supramolecular complexes have emerged as useful tools for the experimental dissection of the physicochemical basis of various noncovalent interactions, but they have historically been underexploited as a platform for the evaluation of solvent effects. Contrasting with large biological complexes, smaller synthetic model systems enable combined experimental and computational analyses, often facilitating theoretical analyses that can work in concert with experiment.Our research has focused on the development of supramolecular systems to evaluate the role of solvents in molecular recognition, and further characterize the underlying mechanisms by which molecules associate. In particular, the use of molecular balances has provided a framework to measure the magnitude of solvent effects and to examine the accuracy of solvent models. Such approaches have revealed how solvation can modulate the electronic landscape of a molecule and how competitive solvation and solvent cohesion can provide thermodynamic driving forces for association. Moreover, the use of simple model systems facilitates the interrogation and further dissection of the physicochemical origins of molecular recognition. This tandem experimental/computational approach has married less common computational techniques, like symmetry adapted perturbation theory (SAPT) and natural bonding orbital (NBO) analysis, with experimental observations to elucidate the influence of effects that are difficult to resolve experimentally (e.g., London dispersion and electron delocalization).
Collapse
Affiliation(s)
- Alex Elmi
- EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
| | - Scott L. Cockroft
- EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
| |
Collapse
|
15
|
Dittrich J, Kather M, Holzberger A, Pich A, Gohlke H. Cumulative Submillisecond All-Atom Simulations of the Temperature-Induced Coil-to-Globule Transition of Poly(N-vinylcaprolactam) in Aqueous Solution. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c01896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Jonas Dittrich
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Michael Kather
- DWI-Leibniz-Institute for Interactive Materials, RWTH Aachen University, 52056 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany
| | - Anna Holzberger
- DWI-Leibniz-Institute for Interactive Materials, RWTH Aachen University, 52056 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany
| | - Andrij Pich
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, 52425 Jülich, Germany
- DWI-Leibniz-Institute for Interactive Materials, RWTH Aachen University, 52056 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, 52425 Jülich, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| |
Collapse
|
16
|
Abstract
The fundamental underpinnings of noncovalent bonds are presented, focusing on the σ-hole interactions that are closely related to the H-bond. Different means of assessing their strength and the factors that control it are discussed. The establishment of a noncovalent bond is monitored as the two subunits are brought together, allowing the electrostatic, charge redistribution, and other effects to slowly take hold. Methods are discussed that permit prediction as to which site an approaching nucleophile will be drawn, and the maximum number of bonds around a central atom in its normal or hypervalent states is assessed. The manner in which a pair of anions can be held together despite an overall Coulombic repulsion is explained. The possibility that first-row atoms can participate in such bonds is discussed, along with the introduction of a tetrel analog of the dihydrogen bond.
Collapse
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA
| |
Collapse
|
17
|
Burns RJ, Mati IK, Muchowska KB, Adam C, Cockroft SL. Quantifying Through-Space Substituent Effects. Angew Chem Int Ed Engl 2020; 59:16717-16724. [PMID: 32542910 PMCID: PMC7540488 DOI: 10.1002/anie.202006943] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Indexed: 01/12/2023]
Abstract
The description of substituents as electron donating or withdrawing leads to a perceived dominance of through-bond influences. The situation is compounded by the challenge of separating through-bond and through-space contributions. Here, we probe the experimental significance of through-space substituent effects in molecular interactions and reaction kinetics. Conformational equilibrium constants were transposed onto the Hammett substituent constant scale revealing dominant through-space substituent effects that cannot be described in classic terms. For example, NO2 groups positioned over a biaryl bond exhibited similar influences as resonant electron donors. Meanwhile, the electro-enhancing influence of OMe/OH groups could be switched off or inverted by conformational twisting. 267 conformational equilibrium constants measured across eleven solvents were found to be better predictors of reaction kinetics than calculated electrostatic potentials, suggesting utility in other contexts and for benchmarking theoretical solvation models.
Collapse
Affiliation(s)
- Rebecca J. Burns
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Ioulia K. Mati
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Kamila B. Muchowska
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Catherine Adam
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Scott L. Cockroft
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| |
Collapse
|
18
|
Yamada M, Narita H, Maeda Y. A Fullerene‐Based Molecular Torsion Balance for Investigating Noncovalent Interactions at the C
60
Surface. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Michio Yamada
- Department of Chemistry Tokyo Gakugei University Nukuikitamachi 4-1-1 Koganei Tokyo 184-8501 Japan
| | - Haruna Narita
- Department of Chemistry Tokyo Gakugei University Nukuikitamachi 4-1-1 Koganei Tokyo 184-8501 Japan
| | - Yutaka Maeda
- Department of Chemistry Tokyo Gakugei University Nukuikitamachi 4-1-1 Koganei Tokyo 184-8501 Japan
| |
Collapse
|
19
|
Yamada M, Narita H, Maeda Y. A Fullerene-Based Molecular Torsion Balance for Investigating Noncovalent Interactions at the C 60 Surface. Angew Chem Int Ed Engl 2020; 59:16133-16140. [PMID: 32458522 DOI: 10.1002/anie.202005888] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Indexed: 12/12/2022]
Abstract
To investigate the nature and strength of noncovalent interactions at the fullerene surface, molecular torsion balances consisting of C60 and organic moieties connected through a biphenyl linkage were synthesized. NMR and computational studies show that the unimolecular system remains in equilibrium between well-defined folded and unfolded conformers owing to restricted rotation around the biphenyl C-C bond. The energy differences between the two conformers depend on the substituents and is ascribed to differences in the intramolecular noncovalent interactions between the organic moieties and the fullerene surface. Fullerenes favor interacting with the π-faces of benzenes bearing electron-donating substituents. The correlation between the folding free energies and corresponding Hammett constants of the substituents in the arene-containing torsion balances reflects the contributions of the electrostatic interactions and dispersion force to face-to-face arene-fullerene interactions.
Collapse
Affiliation(s)
- Michio Yamada
- Department of Chemistry, Tokyo Gakugei University, Nukuikitamachi 4-1-1, Koganei, Tokyo, 184-8501, Japan
| | - Haruna Narita
- Department of Chemistry, Tokyo Gakugei University, Nukuikitamachi 4-1-1, Koganei, Tokyo, 184-8501, Japan
| | - Yutaka Maeda
- Department of Chemistry, Tokyo Gakugei University, Nukuikitamachi 4-1-1, Koganei, Tokyo, 184-8501, Japan
| |
Collapse
|
20
|
Muchowska KB, Pascoe DJ, Borsley S, Smolyar IV, Mati IK, Adam C, Nichol GS, Ling KB, Cockroft SL. Reconciling Electrostatic and n→π* Orbital Contributions in Carbonyl Interactions. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005739] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Kamila B. Muchowska
- EaStCHEM School of Chemistry The University of Edinburgh Joseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Dominic J. Pascoe
- EaStCHEM School of Chemistry The University of Edinburgh Joseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Stefan Borsley
- EaStCHEM School of Chemistry The University of Edinburgh Joseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Ivan V. Smolyar
- EaStCHEM School of Chemistry The University of Edinburgh Joseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Ioulia K. Mati
- EaStCHEM School of Chemistry The University of Edinburgh Joseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Catherine Adam
- EaStCHEM School of Chemistry The University of Edinburgh Joseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Gary S. Nichol
- EaStCHEM School of Chemistry The University of Edinburgh Joseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Kenneth B. Ling
- Syngenta Jealott's Hill International Research Centre Bracknell Berkshire RG42 6EY UK
| | - Scott L. Cockroft
- EaStCHEM School of Chemistry The University of Edinburgh Joseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| |
Collapse
|
21
|
Muchowska KB, Pascoe DJ, Borsley S, Smolyar IV, Mati IK, Adam C, Nichol GS, Ling KB, Cockroft SL. Reconciling Electrostatic and n→π* Orbital Contributions in Carbonyl Interactions. Angew Chem Int Ed Engl 2020; 59:14602-14608. [PMID: 32485046 PMCID: PMC7496118 DOI: 10.1002/anie.202005739] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/29/2020] [Indexed: 12/16/2022]
Abstract
Interactions between carbonyl groups are prevalent in protein structures. Earlier investigations identified dominant electrostatic dipolar interactions, while others implicated lone pair n→π* orbital delocalisation. Here these observations are reconciled. A combined experimental and computational approach confirmed the dominance of electrostatic interactions in a new series of synthetic molecular balances, while also highlighting the distance-dependent observation of inductive polarisation manifested by n→π* orbital delocalisation. Computational fiSAPT energy decomposition and natural bonding orbital analyses correlated with experimental data to reveal the contexts in which short-range inductive polarisation augment electrostatic dipolar interactions. Thus, we provide a framework for reconciling the context dependency of the dominance of electrostatic interactions and the occurrence of n→π* orbital delocalisation in C=O⋅⋅⋅C=O interactions.
Collapse
Affiliation(s)
- Kamila B. Muchowska
- EaStCHEM School of ChemistryThe University of EdinburghJoseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Dominic J. Pascoe
- EaStCHEM School of ChemistryThe University of EdinburghJoseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Stefan Borsley
- EaStCHEM School of ChemistryThe University of EdinburghJoseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Ivan V. Smolyar
- EaStCHEM School of ChemistryThe University of EdinburghJoseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Ioulia K. Mati
- EaStCHEM School of ChemistryThe University of EdinburghJoseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Catherine Adam
- EaStCHEM School of ChemistryThe University of EdinburghJoseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Gary S. Nichol
- EaStCHEM School of ChemistryThe University of EdinburghJoseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Kenneth B. Ling
- SyngentaJealott's Hill International Research CentreBracknellBerkshireRG42 6EYUK
| | - Scott L. Cockroft
- EaStCHEM School of ChemistryThe University of EdinburghJoseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| |
Collapse
|
22
|
Burns RJ, Mati IK, Muchowska KB, Adam C, Cockroft SL. Quantifying Through‐Space Substituent Effects. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Rebecca J. Burns
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Ioulia K. Mati
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Kamila B. Muchowska
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Catherine Adam
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Scott L. Cockroft
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| |
Collapse
|
23
|
Abstract
In this review, we provide a consistent description of noncovalent interactions, covering most groups of the Periodic Table. Different types of bonds are discussed using their trivial names. Moreover, the new name “Spodium bonds” is proposed for group 12 since noncovalent interactions involving this group of elements as electron acceptors have not yet been named. Excluding hydrogen bonds, the following noncovalent interactions will be discussed: alkali, alkaline earth, regium, spodium, triel, tetrel, pnictogen, chalcogen, halogen, and aerogen, which almost covers the Periodic Table entirely. Other interactions, such as orthogonal interactions and π-π stacking, will also be considered. Research and applications of σ-hole and π-hole interactions involving the p-block element is growing exponentially. The important applications include supramolecular chemistry, crystal engineering, catalysis, enzymatic chemistry molecular machines, membrane ion transport, etc. Despite the fact that this review is not intended to be comprehensive, a number of representative works for each type of interaction is provided. The possibility of modeling the dissociation energies of the complexes using different models (HSAB, ECW, Alkorta-Legon) was analyzed. Finally, the extension of Cahn-Ingold-Prelog priority rules to noncovalent is proposed.
Collapse
|
24
|
Rani J, Ashim, Ahamed JI, Adhikari D, Natarajan P, Venugopalan P, Patra R. Nature of fluorine interactions in ‘wheel and axle’ topology based hexa-coordinated Sn( iv)-porphyrins: an experimental and theoretical analysis. CrystEngComm 2020. [DOI: 10.1039/d0ce00333f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The experimental and theoretical investigations on Sn(iv)-tetrapyridylporphyrins demonstrate that ‘Gulliver effect’ has to be taken into consideration in explaining the genesis of F-based intermolecular interactions.
Collapse
Affiliation(s)
- Jyoti Rani
- Department of Chemistry and Centre for Advanced Studies in Chemistry
- Panjab University
- Chandigarh-160014
- India
| | - Ashim
- Department of Chemistry and Centre for Advanced Studies in Chemistry
- Panjab University
- Chandigarh-160014
- India
| | - J. Irshad Ahamed
- Amity Institute of Click Chemistry Research and Studies
- Amity University
- Noida
- India
| | - Debashis Adhikari
- Department of Chemical Sciences
- Indian Institute of Science Education and Research (IISER) Mohali
- S. A. S. Nagar
- India
| | - Palani Natarajan
- Department of Chemistry and Centre for Advanced Studies in Chemistry
- Panjab University
- Chandigarh-160014
- India
| | - Paloth Venugopalan
- Department of Chemistry and Centre for Advanced Studies in Chemistry
- Panjab University
- Chandigarh-160014
- India
| | - Ranjan Patra
- Department of Chemistry and Centre for Advanced Studies in Chemistry
- Panjab University
- Chandigarh-160014
- India
- Amity Institute of Click Chemistry Research and Studies
| |
Collapse
|
25
|
Deka JKR, Sahariah B, Baruah K, Bar AK, Sarma BK. Conformational control of N-methyl-N,N′-diacylhydrazines by noncovalent carbon bonding in solution. Chem Commun (Camb) 2020; 56:4874-4877. [DOI: 10.1039/d0cc00943a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Unusual N(amide)⋯C–X noncovalent carbon bonding interactions stabilize the trans–cis (t–c) amide bond rotamers of N-methyl-N,N′-diacylhydrazines over the expected trans–trans (t–t) rotamers in solution.
Collapse
Affiliation(s)
| | - Biswajit Sahariah
- Department of Chemistry
- School of Natural Sciences
- Shiv Nadar University
- Dadri
- India
| | - Kalpita Baruah
- Department of Chemistry
- School of Natural Sciences
- Shiv Nadar University
- Dadri
- India
| | - Arun Kumar Bar
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER) Tirupati
- Tirupati 517507
- India
| | - Bani Kanta Sarma
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
- Bangalore 560064
- India
| |
Collapse
|
26
|
Hubbs AF, Kreiss K, Cummings KJ, Fluharty KL, O'Connell R, Cole A, Dodd TM, Clingerman SM, Flesher JR, Lee R, Pagel S, Battelli LA, Cumpston A, Jackson M, Kashon M, Orandle MS, Fedan JS, Sriram K. Flavorings-Related Lung Disease: A Brief Review and New Mechanistic Data. Toxicol Pathol 2019; 47:1012-1026. [PMID: 31645208 DOI: 10.1177/0192623319879906] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Flavorings-related lung disease is a potentially disabling and sometimes fatal lung disease of workers making or using flavorings. First identified almost 20 years ago in microwave popcorn workers exposed to butter-flavoring vapors, flavorings-related lung disease remains a concern today. In some cases, workers develop bronchiolitis obliterans, a severe form of fixed airways disease. Affected workers have been reported in microwave popcorn, flavorings, and coffee production workplaces. Volatile α-dicarbonyl compounds, particularly diacetyl (2,3-butanedione) and 2,3-pentanedione, are implicated in the etiology. Published studies on diacetyl and 2,3-pentanedione document their ability to cause airway epithelial necrosis, damage biological molecules, and perturb protein homeostasis. With chronic exposure in rats, they produce airway fibrosis resembling bronchiolitis obliterans. To add to this knowledge, we recently evaluated airway toxicity of the 3-carbon α-dicarbonyl compound, methylglyoxal. Methylglyoxal inhalation causes epithelial necrosis at even lower concentrations than diacetyl. In addition, we investigated airway toxicity of mixtures of diacetyl, acetoin, and acetic acid, common volatiles in butter flavoring. At ratios comparable to workplace scenarios, the mixtures or diacetyl alone, but not acetic acid or acetoin, cause airway epithelial necrosis. These new findings add to existing data to implicate α-dicarbonyl compounds in airway injury and flavorings-related lung disease.
Collapse
Affiliation(s)
- Ann F Hubbs
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Kathleen Kreiss
- Respiratory Health Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Kristin J Cummings
- Respiratory Health Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Kara L Fluharty
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Ryan O'Connell
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA.,West Virginia University, Morgantown, WV, USA. Cummings is now with California Department of Public Health, Richmond, CA, USA. O'Connell is now with Department of Biochemistry, West Virginia, University, Morgantown, WV, USA. Flesher is now with Department of Biology, West Virginia University, Morgantown, WV, USA. Cole is now with Department of Pediatrics-Hematology/Oncology, University of Colorado School of Medicine, Aurora, CO, USA. Kreiss (retired) is in Sitka, AK, USA
| | - Allison Cole
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA.,Respiratory Health Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Tiana M Dodd
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Sidney M Clingerman
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA.,West Virginia University, Morgantown, WV, USA. Cummings is now with California Department of Public Health, Richmond, CA, USA. O'Connell is now with Department of Biochemistry, West Virginia, University, Morgantown, WV, USA. Flesher is now with Department of Biology, West Virginia University, Morgantown, WV, USA. Cole is now with Department of Pediatrics-Hematology/Oncology, University of Colorado School of Medicine, Aurora, CO, USA. Kreiss (retired) is in Sitka, AK, USA
| | - Jordan R Flesher
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA.,West Virginia University, Morgantown, WV, USA. Cummings is now with California Department of Public Health, Richmond, CA, USA. O'Connell is now with Department of Biochemistry, West Virginia, University, Morgantown, WV, USA. Flesher is now with Department of Biology, West Virginia University, Morgantown, WV, USA. Cole is now with Department of Pediatrics-Hematology/Oncology, University of Colorado School of Medicine, Aurora, CO, USA. Kreiss (retired) is in Sitka, AK, USA
| | - Rebecca Lee
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA.,West Virginia University, Morgantown, WV, USA. Cummings is now with California Department of Public Health, Richmond, CA, USA. O'Connell is now with Department of Biochemistry, West Virginia, University, Morgantown, WV, USA. Flesher is now with Department of Biology, West Virginia University, Morgantown, WV, USA. Cole is now with Department of Pediatrics-Hematology/Oncology, University of Colorado School of Medicine, Aurora, CO, USA. Kreiss (retired) is in Sitka, AK, USA
| | - Samantha Pagel
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA.,West Virginia University, Morgantown, WV, USA. Cummings is now with California Department of Public Health, Richmond, CA, USA. O'Connell is now with Department of Biochemistry, West Virginia, University, Morgantown, WV, USA. Flesher is now with Department of Biology, West Virginia University, Morgantown, WV, USA. Cole is now with Department of Pediatrics-Hematology/Oncology, University of Colorado School of Medicine, Aurora, CO, USA. Kreiss (retired) is in Sitka, AK, USA
| | - Lori A Battelli
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Amy Cumpston
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Mark Jackson
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Michael Kashon
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Marlene S Orandle
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Jeffrey S Fedan
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Krishnan Sriram
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| |
Collapse
|
27
|
Jarvis A, Ouvry G. Essential ingredients for rational drug design. Bioorg Med Chem Lett 2019; 29:126674. [PMID: 31521476 DOI: 10.1016/j.bmcl.2019.126674] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/03/2019] [Accepted: 09/04/2019] [Indexed: 01/09/2023]
Abstract
This short review focuses on three aspects of rational drug design that we consider of utmost importance: the conformation of small molecules in solid form, the conformation of small molecules in solution and lesser studied interactions in protein-ligand complexes. Using examples from recent literature, we will illustrate these different aspects and how they have contributed to the discovery of potent modulators.
Collapse
Affiliation(s)
- Ashley Jarvis
- Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Gilles Ouvry
- Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom.
| |
Collapse
|
28
|
Abstract
A complete inventory of the forces governing protein folding is critical for productive protein modeling, including structure prediction and de novo design, as well as understanding protein misfolding diseases of clinical significance. The dominant contributors to protein folding include the hydrophobic effect and conventional hydrogen bonding, along with Coulombic and van der Waals interactions. Over the past few decades, important additional contributors have been identified, including C-H···O hydrogen bonding, n→π* interactions, C5 hydrogen bonding, chalcogen bonding, and interactions involving aromatic rings (cation-π, X-H···π, π-π, anion-π, and sulfur-arene). These secondary contributions fall into two general classes: (1) weak but abundant interactions of the protein main chain and (2) strong but less frequent interactions involving protein side chains. Though interactions with high individual energies play important roles in specifying nonlocal molecular contacts and ligand binding, we estimate that weak but abundant interactions are likely to make greater overall contributions to protein folding, particularly at the level of secondary structure. Further research is likely to illuminate additional roles of these noncanonical interactions and could also reveal contributions yet unknown.
Collapse
Affiliation(s)
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
29
|
Xu Z, Li Y. Triel bonds in RZH 2···NH 3: hybridization, solvation, and substitution. J Mol Model 2019; 25:219. [PMID: 31300929 DOI: 10.1007/s00894-019-4089-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/04/2019] [Indexed: 12/19/2022]
Abstract
The influence of hybridization, substitution, and solvation on the triel bond has been investigated in the complexes of RZH2···NH3 (Z = B and Al). The magnitude of the π-hole on the triel atom is related to the nature of the Z atom and the hybridization of R. CH3BH2 has the largest π-hole among RBH2, while for RAlH2 the largest π-hole is found in CH≡CAlH2. The interaction energy is partly inconsistent with the magnitude of the π-hole on the triel atom and the orbital interaction from the N lone pair of NH3 into the empty p orbital of the triel atom. The strongest B···N triel bond is found in CH≡CBH2···NH3, while the weakest Al···N triel bond is in CH3AlH2···NH3. The strength of the triel bond is increased in solvents, and its enhancement is prominent with the increase of solvent polarity. Solvents also change the nature of the Al···N triel bond from an electrostatic interaction to a partially covalent one. The F substituent in the triel donor strengthens the triel bond, depending on the substitution position and number. Graphical Abstract The π-hole triel bonded complexes between RZH2 (Z =B and Al) and NH3 have been investigated. We focused on the effects of hybridization, solvent, and substitution on the strength and nature of π-hole triel bond.
Collapse
Affiliation(s)
- Zhefeng Xu
- Department of Chemical Engineering, Inner Mongolia Vocational College of Chemical Engineering, Hohhot, 010070, People's Republic of China
| | - Yan Li
- Department of Chemical Engineering, Inner Mongolia Vocational College of Chemical Engineering, Hohhot, 010070, People's Republic of China.
| |
Collapse
|
30
|
Trujillo C, Flood A, Sánchez-Sanz G, Twamley B, Rozas I. Planarity or Nonplanarity: Modulating Guanidine Derivatives as α2-Adrenoceptors Ligands. J Chem Inf Model 2019; 59:2479-2486. [DOI: 10.1021/acs.jcim.9b00140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Cristina Trujillo
- School of Chemistry, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Aoife Flood
- School of Chemistry, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Goar Sánchez-Sanz
- Irish Centre
of
High-End Computing, Grand Canal Quay, Dublin 2, Ireland
| | - Brendan Twamley
- School of Chemistry, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Isabel Rozas
- School of Chemistry, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| |
Collapse
|
31
|
Fayzullin RR, Shteingolts SA, Lodochnikova OA, Mamedova VL, Korshin DE, Mamedov VA. Intermolecular head-to-head interaction of carbonyl groups in bicyclic hydrogen-bonded synthon based on β-hydroxy ketones. CrystEngComm 2019. [DOI: 10.1039/c8ce02132e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, we report a counterintuitive carbonyl–carbonyl interaction explored for crystalline (2RS,3RS)-1-aryl-2-bromo-3-hydroxy-3-(2-nitrophenyl)-propan-1-ones.
Collapse
Affiliation(s)
- Robert R. Fayzullin
- Arbuzov Institute of Organic and Physical Chemistry
- FRC Kazan Scientific Center of Russian Academy of Sciences
- Kazan 420088
- Russian Federation
| | - Sergey A. Shteingolts
- Arbuzov Institute of Organic and Physical Chemistry
- FRC Kazan Scientific Center of Russian Academy of Sciences
- Kazan 420088
- Russian Federation
| | - Olga A. Lodochnikova
- Arbuzov Institute of Organic and Physical Chemistry
- FRC Kazan Scientific Center of Russian Academy of Sciences
- Kazan 420088
- Russian Federation
| | - Vera L. Mamedova
- Arbuzov Institute of Organic and Physical Chemistry
- FRC Kazan Scientific Center of Russian Academy of Sciences
- Kazan 420088
- Russian Federation
| | - Dmitry E. Korshin
- Arbuzov Institute of Organic and Physical Chemistry
- FRC Kazan Scientific Center of Russian Academy of Sciences
- Kazan 420088
- Russian Federation
| | - Vakhid A. Mamedov
- Arbuzov Institute of Organic and Physical Chemistry
- FRC Kazan Scientific Center of Russian Academy of Sciences
- Kazan 420088
- Russian Federation
| |
Collapse
|
32
|
Sahariah B, Sarma BK. Relative orientation of the carbonyl groups determines the nature of orbital interactions in carbonyl-carbonyl short contacts. Chem Sci 2018; 10:909-917. [PMID: 30774885 PMCID: PMC6346288 DOI: 10.1039/c8sc04221g] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 10/27/2018] [Indexed: 12/13/2022] Open
Abstract
Carbonyl-carbonyl (CO···CO) interactions are emerging noncovalent interactions found in many small molecules, polyesters, peptides and proteins. However, little is known about the effect of the relative orientation of the two carbonyl groups on the nature of these interactions. Herein, we first show that simple homodimers of acetone and formaldehyde can serve as models to understand the effect of relative orientations of the two carbonyl groups on the nature of CO···CO interactions. Further, from a comprehensive statistical analysis of molecules having inter- or intramolecular CO···CO interactions, we show that the molecules can be broadly categorized into six different structural motifs (I-VI). The analysis of pyramidality of the acceptor carbon atoms in these motifs and natural bond orbital (NBO) analysis suggest that the relative orientation of the two interacting carbonyl groups determines whether the orbital interaction between the two carbonyl groups would be n → π* or π → π* or a combination of both.
Collapse
Affiliation(s)
- Biswajit Sahariah
- Department of Chemistry , School of Natural Sciences , Shiv Nadar University , Dadri , Uttar Pradesh-201314 , India .
| | - Bani Kanta Sarma
- Department of Chemistry , School of Natural Sciences , Shiv Nadar University , Dadri , Uttar Pradesh-201314 , India .
| |
Collapse
|
33
|
Sun X, Li M, Sun M, Li X, Xi BJ, Wu Y, Yao J, Zhan Z, Bai X, Xi N. Studies on structural requirements for atropisomerism in N -phenyl γ-lactams. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.04.090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
34
|
Sarma R, Wong KY, Lynch GC, Pettitt BM. Peptide Solubility Limits: Backbone and Side-Chain Interactions. J Phys Chem B 2018; 122:3528-3539. [PMID: 29384681 PMCID: PMC5909690 DOI: 10.1021/acs.jpcb.7b10734] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We calculate the solubility limit of pentapeptides in water by simulating the phase separation in an oversaturated aqueous solution. The solubility limit order followed by our model peptides (GGRGG > GGDGG > GGGGG > GGVGG > GGQGG > GGNGG > GGFGG) is found to be the same as that reported for amino acid monomers from experiment (R > D > G > V > Q > N > F). Investigation of dynamical properties of peptides shows that the higher the solubility of a peptide is, the lower the time spent by the peptide in the aggregated cluster is. We also demonstrate that fluctuations in conformation and hydration number of peptide in monomeric form are correlated with the solubility of the peptide. We considered energetic mechanisms and dynamical properties of interbackbone CO-CO and CO···HN interactions. Our results confirm that CO-CO interactions more than the interbackbone H-bonds are important in peptide self-assembly and association. Further, we find that the stability of H-bonded peptide pairs arises mainly from coexisting CO-CO and CO···HN interactions.
Collapse
Affiliation(s)
- Rahul Sarma
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-0304, United States
| | - Ka-Yiu Wong
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-0304, United States
| | - Gillian C. Lynch
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-0304, United States
| | - B. Montgomery Pettitt
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-0304, United States
| |
Collapse
|
35
|
Trupp L, Laurella SL, Tettamanzi MC, Barja BC, Bruttomesso AC. Long-range anisotropic effects in a V–shaped Tröger's base diformanilide: Conformational study by NMR assignment and DFT calculations. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.11.092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
36
|
Shukla R, Chopra D. Characterization of the short OC⋯OC π-hole tetrel bond in the solid state. CrystEngComm 2018. [DOI: 10.1039/c8ce00697k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An in-depth structure database investigation and experimental charge density analysis of the OC⋯OC π-hole tetrel bonds.
Collapse
Affiliation(s)
- Rahul Shukla
- Crystallography and Crystal Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal
- 462066 India
| | - Deepak Chopra
- Crystallography and Crystal Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal
- 462066 India
| |
Collapse
|
37
|
Claramunt RM, Santa María D, Alkorta I, Elguero J. The Structure ofN-phenyl-pyrazoles and Indazoles: Mononitro, Dinitro, and Trinitro Derivatives. J Heterocycl Chem 2017. [DOI: 10.1002/jhet.3026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Rosa M. Claramunt
- Departamento de Química Orgánica y Bio-Orgánica, Facultad de Ciencias; UNED; Paseo Senda del Rey, 9 28040 Madrid Spain
| | - Dolores Santa María
- Departamento de Química Orgánica y Bio-Orgánica, Facultad de Ciencias; UNED; Paseo Senda del Rey, 9 28040 Madrid Spain
| | - Ibon Alkorta
- Instituto de Química Médica, Centro de Química Orgánica “Manuel Lora-Tamayo”; CSIC; Juan de la Cierva, 3 28006 Madrid Spain
| | - José Elguero
- Instituto de Química Médica, Centro de Química Orgánica “Manuel Lora-Tamayo”; CSIC; Juan de la Cierva, 3 28006 Madrid Spain
| |
Collapse
|
38
|
Pascoe DJ, Ling KB, Cockroft SL. The Origin of Chalcogen-Bonding Interactions. J Am Chem Soc 2017; 139:15160-15167. [PMID: 28985065 DOI: 10.1021/jacs.7b08511] [Citation(s) in RCA: 333] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Favorable molecular interactions between group 16 elements have been implicated in catalysis, biological processes, and materials and medicinal chemistry. Such interactions have since become known as chalcogen bonds by analogy to hydrogen and halogen bonds. Although the prevalence and applications of chalcogen-bonding interactions continues to develop, debate still surrounds the energetic significance and physicochemical origins of this class of σ-hole interaction. Here, synthetic molecular balances were used to perform a quantitative experimental investigation of chalcogen-bonding interactions. Over 160 experimental conformational free energies were measured in 13 different solvents to examine the energetics of O···S, O···Se, S···S, O···HC, and S···HC contacts and the associated substituent and solvent effects. The strongest chalcogen-bonding interactions were found to be at least as strong as conventional H-bonds, but unlike H-bonds, surprisingly independent of the solvent. The independence of the conformational free energies on solvent polarity, polarizability, and H-bonding characteristics showed that electrostatic, solvophobic, and van der Waals dispersion forces did not account for the observed experimental trends. Instead, a quantitative relationship between the experimental conformational free energies and computed molecular orbital energies was consistent with the chalcogen-bonding interactions being dominated by n → σ* orbital delocalization between a lone pair (n) of a (thio)amide donor and the antibonding σ* orbital of an acceptor thiophene or selenophene. Interestingly, stabilization was manifested through the same acceptor molecular orbital irrespective of whether a direct chalcogen···chalcogen or chalcogen···H-C contact was made. Our results underline the importance of often-overlooked orbital delocalization effects in conformational control and molecular recognition phenomena.
Collapse
Affiliation(s)
- Dominic J Pascoe
- EaStCHEM School of Chemistry, University of Edinburgh , Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Kenneth B Ling
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, U.K
| | - Scott L Cockroft
- EaStCHEM School of Chemistry, University of Edinburgh , Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
| |
Collapse
|
39
|
Cieplak AS. Protein folding, misfolding and aggregation: The importance of two-electron stabilizing interactions. PLoS One 2017; 12:e0180905. [PMID: 28922400 PMCID: PMC5603215 DOI: 10.1371/journal.pone.0180905] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 06/22/2017] [Indexed: 12/17/2022] Open
Abstract
Proteins associated with neurodegenerative diseases are highly pleiomorphic and may adopt an all-α-helical fold in one environment, assemble into all-β-sheet or collapse into a coil in another, and rapidly polymerize in yet another one via divergent aggregation pathways that yield broad diversity of aggregates’ morphology. A thorough understanding of this behaviour may be necessary to develop a treatment for Alzheimer’s and related disorders. Unfortunately, our present comprehension of folding and misfolding is limited for want of a physicochemical theory of protein secondary and tertiary structure. Here we demonstrate that electronic configuration and hyperconjugation of the peptide amide bonds ought to be taken into account to advance such a theory. To capture the effect of polarization of peptide linkages on conformational and H-bonding propensity of the polypeptide backbone, we introduce a function of shielding tensors of the Cα atoms. Carrying no information about side chain-side chain interactions, this function nonetheless identifies basic features of the secondary and tertiary structure, establishes sequence correlates of the metamorphic and pH-driven equilibria, relates binding affinities and folding rate constants to secondary structure preferences, and manifests common patterns of backbone density distribution in amyloidogenic regions of Alzheimer’s amyloid β and tau, Parkinson’s α-synuclein and prions. Based on those findings, a split-intein like mechanism of molecular recognition is proposed to underlie dimerization of Aβ, tau, αS and PrPC, and divergent pathways for subsequent association of dimers are outlined; a related mechanism is proposed to underlie formation of PrPSc fibrils. The model does account for: (i) structural features of paranuclei, off-pathway oligomers, non-fibrillar aggregates and fibrils; (ii) effects of incubation conditions, point mutations, isoform lengths, small-molecule assembly modulators and chirality of solid-liquid interface on the rate and morphology of aggregation; (iii) fibril-surface catalysis of secondary nucleation; and (iv) self-propagation of infectious strains of mammalian prions.
Collapse
Affiliation(s)
- Andrzej Stanisław Cieplak
- Department of Chemistry, Bilkent University, Ankara, Turkey
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
40
|
Rahim A, Saha P, Jha KK, Sukumar N, Sarma BK. Reciprocal carbonyl-carbonyl interactions in small molecules and proteins. Nat Commun 2017; 8:78. [PMID: 28724906 PMCID: PMC5517579 DOI: 10.1038/s41467-017-00081-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 05/31/2017] [Indexed: 01/29/2023] Open
Abstract
Carbonyl-carbonyl n→π* interactions where a lone pair (n) of the oxygen atom of a carbonyl group is delocalized over the π* orbital of a nearby carbonyl group have attracted a lot of attention in recent years due to their ability to affect the 3D structure of small molecules, polyesters, peptides, and proteins. In this paper, we report the discovery of a "reciprocal" carbonyl-carbonyl interaction with substantial back and forth n→π* and π→π* electron delocalization between neighboring carbonyl groups. We have carried out experimental studies, analyses of crystallographic databases and theoretical calculations to show the presence of this interaction in both small molecules and proteins. In proteins, these interactions are primarily found in polyproline II (PPII) helices. As PPII are the most abundant secondary structures in unfolded proteins, we propose that these local interactions may have implications in protein folding.Carbonyl-carbonyl π* non covalent interactions affect the structure and stability of small molecules and proteins. Here, the authors carry out experimental studies, analyses of crystallographic databases and theoretical calculations to describe an additional type of carbonyl-carbonyl interaction.
Collapse
Affiliation(s)
- Abdur Rahim
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh, 201314, India
| | - Pinaki Saha
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh, 201314, India
| | - Kunal Kumar Jha
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh, 201314, India
| | - Nagamani Sukumar
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh, 201314, India
| | - Bani Kanta Sarma
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh, 201314, India.
| |
Collapse
|
41
|
Affiliation(s)
- Gennaro Pescitelli
- Dipartimento Di Chimica E Chimica Industriale; Università Di Pisa; Pisa Italy
| | - Lorenzo Di Bari
- Dipartimento Di Chimica E Chimica Industriale; Università Di Pisa; Pisa Italy
| |
Collapse
|
42
|
Riwar LJ, Trapp N, Kuhn B, Diederich F. Substituent Effects in Parallel-Displaced π-π Stacking Interactions: Distance Matters. Angew Chem Int Ed Engl 2017; 56:11252-11257. [DOI: 10.1002/anie.201703744] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Indexed: 01/10/2023]
Affiliation(s)
- Leslie-Joana Riwar
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Nils Trapp
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Bernd Kuhn
- F. Hoffmann-La Roche Ltd., Pharma Research and Early Development (pRED), Therapeutic Modalities; Roche Innovation Center Basel; Grenzacherstrasse 124 4070 Basel Switzerland
| | - François Diederich
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| |
Collapse
|
43
|
Riwar LJ, Trapp N, Kuhn B, Diederich F. Substituenteneffekte auf Stapelwechselwirkungen parallel verschobener π-Systeme: der Abstand ist entscheidend. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703744] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Leslie-Joana Riwar
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Schweiz
| | - Nils Trapp
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Schweiz
| | - Bernd Kuhn
- F. Hoffmann-La Roche Ltd., Pharma Research and Early Development (pRED), Therapeutic Modalities; Roche Innovation Center Basel; Grenzacherstrasse 124 4070 Basel Schweiz
| | - François Diederich
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Schweiz
| |
Collapse
|
44
|
Sun H, Horatscheck A, Martos V, Bartetzko M, Uhrig U, Lentz D, Schmieder P, Nazaré M. Direct Experimental Evidence for Halogen-Aryl π Interactions in Solution from Molecular Torsion Balances. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700520] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Han Sun
- Departments of Chemical Biology and Structural Biology; Leibniz-Institut fϋr Molekulare Pharmakologie (FMP); Campus Berlin-Buch; Robert-Roessle-Strasse 10 13125 Berlin Germany
| | - André Horatscheck
- Departments of Chemical Biology and Structural Biology; Leibniz-Institut fϋr Molekulare Pharmakologie (FMP); Campus Berlin-Buch; Robert-Roessle-Strasse 10 13125 Berlin Germany
- Drug Discovery and Development Centre (H3D); Department of Chemistry; University of Cape Town; Rondebosch 7701 South Africa
| | - Vera Martos
- Departments of Chemical Biology and Structural Biology; Leibniz-Institut fϋr Molekulare Pharmakologie (FMP); Campus Berlin-Buch; Robert-Roessle-Strasse 10 13125 Berlin Germany
| | - Max Bartetzko
- Departments of Chemical Biology and Structural Biology; Leibniz-Institut fϋr Molekulare Pharmakologie (FMP); Campus Berlin-Buch; Robert-Roessle-Strasse 10 13125 Berlin Germany
- Max-Planck-Institut für Kolloid- und Grenzflächenforschung; Am Mühlenberg 1 14476 Potsdam Germany
| | - Ulrike Uhrig
- European Molecular Biology Laboratory (EMBL); Chemical Biology Core Facility; Meyerhofstrasse 1 69117 Heidelberg Germany
| | - Dieter Lentz
- Institut für Chemie und Biochemie; Anorganische Chemie; Freie Universität Berlin; Fabeckstrasse 34-36 14195 Berlin Germany
| | - Peter Schmieder
- Departments of Chemical Biology and Structural Biology; Leibniz-Institut fϋr Molekulare Pharmakologie (FMP); Campus Berlin-Buch; Robert-Roessle-Strasse 10 13125 Berlin Germany
| | - Marc Nazaré
- Departments of Chemical Biology and Structural Biology; Leibniz-Institut fϋr Molekulare Pharmakologie (FMP); Campus Berlin-Buch; Robert-Roessle-Strasse 10 13125 Berlin Germany
| |
Collapse
|
45
|
Sun H, Horatscheck A, Martos V, Bartetzko M, Uhrig U, Lentz D, Schmieder P, Nazaré M. Direct Experimental Evidence for Halogen-Aryl π Interactions in Solution from Molecular Torsion Balances. Angew Chem Int Ed Engl 2017; 56:6454-6458. [PMID: 28452102 DOI: 10.1002/anie.201700520] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Indexed: 12/24/2022]
Abstract
We dissected halogen-aryl π interactions experimentally using a bicyclic N-arylimide based molecular torsion balances system, which is based on the influence of the non-bonded interaction on the equilibria between folded and unfolded states. Through comparison of balances modulated by higher halogens with fluorine balances, we determined the magnitude of the halogen-aryl π interactions in our unimolecular systems to be larger than -5.0 kJ mol-1 , which is comparable with the magnitude estimated in the biomolecular systems. Our study provides direct experimental evidence of halogen-aryl π interactions in solution, which until now have only been revealed in the solid state and evaluated theoretically by quantum-mechanical calculations.
Collapse
Affiliation(s)
- Han Sun
- Departments of Chemical Biology and Structural Biology, Leibniz-Institut fϋr Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Roessle-Strasse 10, 13125, Berlin, Germany
| | - André Horatscheck
- Departments of Chemical Biology and Structural Biology, Leibniz-Institut fϋr Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Roessle-Strasse 10, 13125, Berlin, Germany.,Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa
| | - Vera Martos
- Departments of Chemical Biology and Structural Biology, Leibniz-Institut fϋr Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Roessle-Strasse 10, 13125, Berlin, Germany
| | - Max Bartetzko
- Departments of Chemical Biology and Structural Biology, Leibniz-Institut fϋr Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Roessle-Strasse 10, 13125, Berlin, Germany.,Max-Planck-Institut für Kolloid- und Grenzflächenforschung, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Ulrike Uhrig
- European Molecular Biology Laboratory (EMBL), Chemical Biology Core Facility, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Dieter Lentz
- Institut für Chemie und Biochemie, Anorganische Chemie, Freie Universität Berlin, Fabeckstrasse 34-36, 14195, Berlin, Germany
| | - Peter Schmieder
- Departments of Chemical Biology and Structural Biology, Leibniz-Institut fϋr Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Roessle-Strasse 10, 13125, Berlin, Germany
| | - Marc Nazaré
- Departments of Chemical Biology and Structural Biology, Leibniz-Institut fϋr Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Roessle-Strasse 10, 13125, Berlin, Germany
| |
Collapse
|
46
|
Luccarelli J, Jones IM, Thompson S, Hamilton AD. Unpicking the determinants of amide NH⋯OC hydrogen bond strength with diphenylacetylene molecular balances. Org Biomol Chem 2017; 15:9156-9163. [DOI: 10.1039/c7ob02026k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The stereoelectronic properties affecting hydrogen bond strength are investigated with a series of diphenylacetylene-based molecular balances.
Collapse
Affiliation(s)
| | - Ian M. Jones
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
- Department of Chemistry
| | - Sam Thompson
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
- Chemistry
| | - Andrew D. Hamilton
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
- Department of Chemistry
| |
Collapse
|
47
|
Harrowfield JM, Ling I, Skelton BW, Sobolev AN, White AH. Structural Systematics for Lanthanide(III) Systems: Interactions of the Achiral Hexamminecobalt(III) Cation with Tris(dipicolinato)lanthanate(III) Anions. Aust J Chem 2017. [DOI: 10.1071/ch16584] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Extended structural studies, largely determinations at ~150 K, of the family of hydrates of [Co(NH3)6][Ln(dipic)3] (Ln = La–Lu, and Y; dipic = dipicolinate = pyridine-2,6-dicarboxylate) have provided detailed evidence of the nature of the interactions between the formally achiral cation and the chiral anions. They also provide a reference point for consideration of related systems incorporating chiral cations with and without the capacity to act as H-bond donors.
Collapse
|
48
|
Harrowfield JM, Kim Y, Skelton BW, Sobolev AN, White AH. Chiral discrimination in solid-state interactions of cobalt(iii)–polyamine complex cations with tris-(dipicolinato)lanthanate(iii) anions. CrystEngComm 2017. [DOI: 10.1039/c6ce02573k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
49
|
Bis(cyclic carbonate) based on d-mannitol, d-sorbitol and di(trimethylolpropane) in the synthesis of non-isocyanate poly(carbonate-urethane)s. Eur Polym J 2016. [DOI: 10.1016/j.eurpolymj.2016.04.021] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
50
|
von Krbek LKS, Achazi AJ, Solleder M, Weber M, Paulus B, Schalley CA. Allosteric and Chelate Cooperativity in Divalent Crown Ether/Ammonium Complexes with Strong Binding Enhancement. Chemistry 2016; 22:15475-15484. [DOI: 10.1002/chem.201603098] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Larissa K. S. von Krbek
- Institut für Chemie und Biochemie; Organische Chemie; Freie Universität Berlin; Takustr. 3 14195 Berlin Germany
| | - Andreas J. Achazi
- Institut für Chemie und Biochemie; Organische Chemie; Freie Universität Berlin; Takustr. 3 14195 Berlin Germany
| | - Marthe Solleder
- Zuse Institute Berlin (ZIB); Takustr. 7 14195 Berlin Germany
| | - Marcus Weber
- Zuse Institute Berlin (ZIB); Takustr. 7 14195 Berlin Germany
| | - Beate Paulus
- Institut für Chemie und Biochemie; Organische Chemie; Freie Universität Berlin; Takustr. 3 14195 Berlin Germany
| | - Christoph A. Schalley
- Institut für Chemie und Biochemie; Organische Chemie; Freie Universität Berlin; Takustr. 3 14195 Berlin Germany
| |
Collapse
|