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Panwaria P, Das A. N···C═O n → π* Interaction: Gas-Phase Electronic and Vibrational Spectroscopy Combined with Quantum Chemistry Calculations. J Phys Chem A 2024; 128:4685-4693. [PMID: 38814588 DOI: 10.1021/acs.jpca.4c02181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Herein, we have used gas-phase electronic and vibrational spectroscopic techniques for the first time to study the N···C═O n → π* interaction in ethyl 2-(2-(dimethylamino) phenyl) acetate (NMe2-Ph-EA). We have measured the electronic spectra of NMe2-Ph-EA in the mass channels of its two distinct fragments of m/z = 15 and 192 using a resonant two-photon ionization technique as there was extensive photofragmentation of NMe2-Ph-EA. Identical electronic spectra obtained in the mass channels of both fragments confirm the dissociation of NMe2-Ph-EA in the ionic state, and hence, the electronic spectrum of the fragment represents that of NMe2-Ph-EA only. UV-UV hole-burning spectroscopy proved the presence of a single conformer of NMe2-Ph-EA in the experiment. Detailed quantum chemistry calculations reveal the existence of a N···C═O n → π* interaction in all six low-energy conformers of NMe2-Ph-EA. A comparison of the IR spectrum of NMe2-Ph-EA acquired from the gas-phase experiment with those obtained from theoretical calculations indicates that the experimentally observed conformer has a N···C═O n → π* interaction. The present finding might be further valuable in drug design and their recognition based on the N···C═O n → π* interaction.
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Affiliation(s)
- Prakash Panwaria
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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2
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Byerly-Duke J, O'Brien EA, Wall BJ, VanVeller B. Thioimidates provide general access to thioamide, amidine, and imidazolone peptide-bond isosteres. Methods Enzymol 2024; 698:27-55. [PMID: 38886036 DOI: 10.1016/bs.mie.2024.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Thioamides, amidines, and heterocycles are three classes of modifications that can act as peptide-bond isosteres to alter the peptide backbone. Thioimidate protecting groups can address many of the problematic synthetic issues surrounding installation of these groups. Historically, amidines have received little attention in peptides due to limitations in methods to access them. The first robust and general procedure for the introduction of amidines into peptide backbones exploits the utility of thioimidate protecting groups as a means to side-step reactivity that ultimately renders existing methods unsuitable for the installation of amidines along the main-chain of peptides. Further, amidines formed on-resin can be reacted to form (4H)-imidazolone heteorcycles which have recently been shown to act as cis-amide isosteres. General methods for heterocyclic installation capable of geometrically restricting peptide conformation are also under-developed. This work is significant because it describes a generally applicable and divergent approach to access unexplored peptide designs and architectures.
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Affiliation(s)
- Jacob Byerly-Duke
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | - Emily A O'Brien
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | - Brendan J Wall
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | - Brett VanVeller
- Department of Chemistry, Iowa State University, Ames, IA, United States.
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3
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Byerly-Duke J, VanVeller B. Thioimidate Solutions to Thioamide Problems during Thionopeptide Deprotection. Org Lett 2024; 26:1452-1457. [PMID: 38341867 PMCID: PMC11031844 DOI: 10.1021/acs.orglett.4c00035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2024]
Abstract
Thioamides have structural and chemical similarity to peptide bonds, offering valuable insights when probing peptide backbone interactions, but are prone to side reactions during solid-phase peptide synthesis (SPPS). Thioimidates have been demonstrated to be effective protecting groups for thioamides during peptide elongation. We further demonstrate how thioimidates can assist thioamides through the most yield-crippling step of thionopeptide deprotection, allowing for the first isolation of an important benchmark α-helical peptide that had previously eluded synthesis and isolation.
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Affiliation(s)
- Jacob Byerly-Duke
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Brett VanVeller
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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4
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Madubuike H, Ferry N. Enhanced Activity and Stability of an Acetyl Xylan Esterase in Hydrophilic Alcohols through Site-Directed Mutagenesis. Molecules 2023; 28:7393. [PMID: 37959811 PMCID: PMC10647838 DOI: 10.3390/molecules28217393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/29/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023] Open
Abstract
Current demands for the development of suitable biocatalysts showing high process performance is stimulated by the need to replace current chemical synthesis with cleaner alternatives. A drawback to the use of biocatalysts for unique applications is their low performance in industrial conditions. Hence, enzymes with improved performance are needed to achieve innovative and sustainable biocatalysis. In this study, we report the improved performance of an engineered acetyl xylan esterase (BaAXE) in a hydrophilic organic solvent. The structure of BaAXE was partitioned into a substrate-binding region and a solvent-affecting region. Using a rational design approach, charged residues were introduced at protein surfaces in the solvent-affecting region. Two sites present in the solvent-affecting region, A12D and Q143E, were selected for site-directed mutagenesis, which generated the mutants MUT12, MUT143 and MUT12-143. The mutants MUT12 and MUT143 reported lower Km (0.29 mM and 0.27 mM, respectively) compared to the wildtype (0.41 mM). The performance of the mutants in organic solvents was assessed after enzyme incubation in various strengths of alcohols. The mutants showed improved activity and stability compared to the wild type in low strengths of ethanol and methanol. However, the activity of MUT143 was lost in 40% methanol while MUT12 and MUT12-143 retained over 70% residual activity in this environment. Computational analysis links the improved performance of MUT12 and MUT12-143 to novel intermolecular interactions that are absent in MUT143. This work supports the rationale for protein engineering to augment the characteristics of wild-type proteins and provides more insight into the role of charged residues in conferring stability.
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Affiliation(s)
- Henry Madubuike
- School of Science Engineering and Environment, University of Salford, Manchester M5 4WT, UK
| | - Natalie Ferry
- School of Science Engineering and Environment, University of Salford, Manchester M5 4WT, UK
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5
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Wang H, Caminati W, Li M, Chen J, Tian X, Grabow JU, Gou Q. n → π* Interaction Enabling Transient Inversion of Chirality. J Phys Chem Lett 2023; 14:8874-8879. [PMID: 37756497 DOI: 10.1021/acs.jpclett.3c02264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
This study reports the observation and characterization of two isomers of the acrolein dimer by using high-resolution rotational spectroscopy in pulsed jets. The first isomer is stabilized by two hydrogen bonds, adopting a planar configuration, and is energetically favored over the second isomer, which exhibits a dominant n → π* interaction in a nearly orthogonal arrangement. Surprisingly, the n → π* interaction was revealed to enable a concerted tunneling motion of two moieties along the carbonyl group. This motion leads to the inversion of transient chirality associated with the exchange of donor-acceptor roles, as revealed by the spectral feature of quadruplets. Inversion of transient chirality is a fundamental phenomenon in quantum mechanics and commonly observed for only inversional motions of protons. It is the first discovery, to the best of our knowledge, that such heavy moieties can also undergo chirality inversion.
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Affiliation(s)
- Hao Wang
- Department of Chemistry School of Chemistry and Chemical Engineering, Chongqing University, No. 55 Daxuecheng South Road Shapingba, Chongqing 401331, China
| | - Walther Caminati
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, Via Selmi 2, Bologna I-40126, Italy
| | - Meng Li
- Institut für Physikalische Chemie & Elektrochemie, Leibniz Universität Hannover, 30167 Hannover, Germany
| | - Junhua Chen
- School of Pharmacy, Guizhou Medical University, Guiyang 550025, Guizhou, China
| | - Xiao Tian
- Department of Chemistry School of Chemistry and Chemical Engineering, Chongqing University, No. 55 Daxuecheng South Road Shapingba, Chongqing 401331, China
| | - Jens-Uwe Grabow
- Institut für Physikalische Chemie & Elektrochemie, Leibniz Universität Hannover, 30167 Hannover, Germany
| | - Qian Gou
- Department of Chemistry School of Chemistry and Chemical Engineering, Chongqing University, No. 55 Daxuecheng South Road Shapingba, Chongqing 401331, China
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6
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Li X, Hu L, Lu G, Wang Y. Carbon-Bonding Metal Catalysis (CBMC): A Supramolecular Complex Directs Structural-Isomer Selection in Gold-Catalyzed Reactions. J Am Chem Soc 2023; 145:21554-21561. [PMID: 37668596 DOI: 10.1021/jacs.3c07551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Carbon is a primary element to constitute organic molecules, while metal catalysis is a basic tool in organic synthesis. The establishment of a link between the ubiquitous carbon bonding and metal catalysis is thus a fundamentally important problem. However, there is yet no experimental example to introduce the role of carbon bonding in a metal catalysis process. Herein, we merged the topics of carbon bonding and metal catalysis together and demonstrated that a supramolecular carbon-bonding metal complex can not only give rise to catalytic activity but, more remarkably, direct structural-isomer selection events in gold-catalyzed reactions. The experimental results unveil the fact that the imposing of weak carbon-bonding interactions on a gold complex can alter the carbene as well as the Lewis acid property of these catalysts. These results illustrate a non-negligible role of weak carbon-bonding interactions in the modulation of metal catalysis. As such, carbon-bonding metal catalysis is suggested to be used as a routine tool not only in the development of reactions but more frequently in analyzing reaction processes in metal catalysis.
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Affiliation(s)
- Xinxin Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, Shandong University, Jinan 250100, P. R. China
| | - Lingfei Hu
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, Shandong University, Jinan 250100, P. R. China
| | - Gang Lu
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, Shandong University, Jinan 250100, P. R. China
| | - Yao Wang
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, Shandong University, Jinan 250100, P. R. China
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7
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Panwaria P, Das A. Modulation of n → π* Interaction in the Complexes of p-Substituted Pyridines with Aldehydes: A Theoretical Study. J Phys Chem A 2023. [PMID: 37463490 DOI: 10.1021/acs.jpca.3c03103] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
n → π* interaction is analogous to the hydrogen bond in terms of the delocalization of the electron density between the two orbitals. Studies on the intermolecular complexes stabilized by the n → π* interaction are scarce in the literature. Herein, we have studied intermolecular N···C═O n → π* interactions in the complexes of p-substituted pyridines (p-R-Py) with formaldehyde (HCHO), formyl chloride (HCOCl), and acetaldehyde (CH3CHO) using quantum chemistry calculations. We have shown that the strength of the n → π* interaction can be modulated by varying the electronic substituents at the donor and acceptor sites in the complexes. Variation of the substituents at the para position of the pyridine ring from the electron-withdrawing groups (EWGs) to the electron-donating groups (EDGs) results in a systematic increase in the strength of the n → π* interaction. The strength of this interaction is also modulated by tuning the electron density toward the carbonyl bond by substituting the hydrogen atom of HCHO with the methyl and chloro groups. The modulation of this interaction due to the electronic substitutions at the n → π* donor and acceptor sites in the complexes is monitored by probing the relevant geometrical parameters, binding energies, C═O frequency redshift, NBO energies, and electron density for this interaction derived from QTAIM and NCI index analyses. Energy decomposition analysis reveals that the electrostatic interaction dominates the binding energies of these complexes, while the charge transfer interaction, which is representative of the n → π* interaction, also has a significant contribution to these.
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Affiliation(s)
- Prakash Panwaria
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra 411008, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra 411008, India
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8
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Panwaria P, Das A. Effect of Substituents on the Intramolecular n→π* Interaction in 3-[2-(Dimethylamino) phenyl] propanal: A Computational Study. J Phys Chem A 2023; 127:3339-3346. [PMID: 37036493 DOI: 10.1021/acs.jpca.2c08641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
n→π* non-covalent interaction (NCI) and hydrogen bond have similarity in terms of delocalization of the electron density between the two orbitals involved in the interaction. Hydrogen bond (X-H···Y) involves delocalization of the lone pair electrons (n) on the Y atom into the σ* orbital of the X-H bond. In contrast, the n→π* interaction deals with delocalizing the lone pair electrons (n) on the N, O, or S atom into the π* orbital of a C═O group or aromatic ring. Herein, we have shown a resemblance of this weak n→π* interaction with the relatively stronger hydrogen bond in terms of folding the side chains in flexible molecules. This work reports the study of folding of the flexible side-chain in 3-[2-(dimethylamino) phenyl] propanal (DMAPhP) through a N···C═O n→π* interaction using various computational approaches such as NBO, QTAIM, and NCI analyses. The folding of the molecule by the n→π* interaction observed in this study is found to be similar to that present in the secondary structures of peptides or proteins through hydrogen bonding interactions. Interestingly, the stabilization of the global minimum conformer of DMAPhP by the n→π* interaction demonstrates the importance of this NCI in providing conformational preferences in molecular systems. Another important finding of this study is that the theoretical redshift obtained in the C═O stretching frequency of the most stable conformer of the DMAPhP is contributed mostly by the n→π* interaction as the C═O group is not involved in hyperconjugation with any neighboring heteroatom, which is a common phenomenon in any ester or amide. We have also demonstrated here that the strength of the intramolecular n→π* interaction can be modulated by varying the electronic substituents at the para position of the donor group involved in the interaction.
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Affiliation(s)
- Prakash Panwaria
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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9
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Kojasoy V, Tantillo DJ. Importance of Noncovalent Interactions Involving Sulfur Atoms in Thiopeptide Antibiotics─Glycothiohexide α and Nocathiacin I. J Phys Chem A 2023; 127:2081-2090. [PMID: 36855831 DOI: 10.1021/acs.jpca.2c07600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Noncovalent interactions involving sulfur atoms play essential roles in protein structure and function by significantly contributing to protein stability, folding, and biological activity. Sulfur is a highly polarizable atom that can participate in many types of noncovalent interactions including hydrogen bonding, sulfur-π interactions, and S-lone pair interactions, but the impact of these sulfur-based interactions on molecular recognition and drug design is still often underappreciated. Here, we examine, using quantum chemical calculations, the roles of sulfur-based noncovalent interactions in complex naturally occurring molecules representative of thiopeptide antibiotics: glycothiohexide α and its close structural analogue nocathiacin I. While donor-acceptor orbital interactions make only very small contributions, electrostatic and dispersion contributions are predicted to be significant in many cases. In pursuit of understanding the magnitudes and nature of these noncovalent interactions, we made potential structural modifications that could significantly expand the chemical space of effective thiopeptide antibiotics.
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Affiliation(s)
- Volga Kojasoy
- Department of Chemistry, University of California─Davis, Davis, California 95616, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California─Davis, Davis, California 95616, United States
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10
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Baishya T, Gomila RM, Frontera A, Barcelo-Oliver M, Verma AK, Bhattacharyya MK. Enclathration of Mn(II)(H2O)6 guests and unusual Cu⋯O bonding contacts in supramolecular assemblies of Mn(II) Co-crystal hydrate and Cu(II) Pyridinedicarboxylate: Antiproliferative evaluation and theoretical studies. Polyhedron 2023. [DOI: 10.1016/j.poly.2022.116243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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11
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Kojasoy V, Tantillo DJ. Impacts of noncovalent interactions involving sulfur atoms on protein stability, structure, folding, and bioactivity. Org Biomol Chem 2022; 21:11-23. [PMID: 36345987 DOI: 10.1039/d2ob01602h] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This review discusses the various types of noncovalent interactions in which sulfur atoms participate and their effects on protein stability, structure, folding and bioactivity. Current approaches and recommendations for modelling these noncovalent interactions (in terms of both geometries and interaction energies) are highlighted.
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Affiliation(s)
- Volga Kojasoy
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, CA, 95616, USA.
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, CA, 95616, USA.
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12
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Panwaria P, Juanes M, Mishra KK, Saragi R, Borish K, Usabiaga I, Camiruaga A, Fernández JA, Lesarri A, Das A. Microhydration of Phenyl Formate: Gas-Phase Laser Spectroscopy, Microwave Spectroscopy, and Quantum Chemistry Calculations. Chemphyschem 2022; 23:e202200330. [PMID: 35984348 DOI: 10.1002/cphc.202200330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/17/2022] [Indexed: 01/04/2023]
Abstract
Herein, we have investigated the structure of phenyl formate⋅⋅⋅water (PhOF⋅⋅⋅H2 O) dimer and various non-covalent interactions present there using gas-phase laser spectroscopy and microwave spectroscopy combined with quantum chemistry calculations. Two conformers of PhOF⋅⋅⋅H2 O (C1 and T1), built on the two cis/trans conformers of the bare molecule, have been observed in the experiment. In cis-PhOF, there is an nCO → π A r * ${{{\rm \pi }}_{{\rm A}{\rm r}}^{{\rm {^\ast}}}}$ interaction between the lone-pair orbital of the carbonyl oxygen atom and the π* orbital of the phenyl ring, which persists in the monohydrated C1 conformer of PhOF⋅⋅⋅H2 O according to the NBO and NCI analyses. On the other hand, this interaction is absent in the trans-PhOF conformer as the C=O group is away from the phenyl ring. The C1 conformer is primarily stabilized by an interplay between O-H⋅⋅⋅O=C hydrogen bond and O-H⋅⋅⋅π interactions, while the stability of the T1 conformer is primarily governed by the O-H⋅⋅⋅O=C hydrogen bond. The most important finding of the present work is that the conformational preference of the PhOF monomer is retained in its monohydrated complex.
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Affiliation(s)
- Prakash Panwaria
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Marcos Juanes
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias-I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén, 7, 47011, Valladolid, Spain
| | - Kamal K Mishra
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India.,Present address: Department of Chemistry, University of Kentucky, Lexington, Kentucky, 40503, USA
| | - Rizalina Saragi
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias-I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén, 7, 47011, Valladolid, Spain
| | - Kshetrimayum Borish
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Imanol Usabiaga
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Ander Camiruaga
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - José A Fernández
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias-I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén, 7, 47011, Valladolid, Spain
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
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Purushotham M, Paul B, Govindachar DM, Singh AK, Periyasamy G, Peter SC. Ortho-halogen effects: n→π* interactions, halogen bonding, and deciphering chiral attributes in N-aryl glycine peptoid foldamers. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Zondlo NJ. Solvation stabilizes intercarbonyl n→π* interactions and polyproline II helix. Phys Chem Chem Phys 2022; 24:13571-13586. [PMID: 35635541 DOI: 10.1039/d2cp00857b] [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
n→π* interactions between consecutive carbonyls stabilize the α-helix and polyproline II helix (PPII) conformations in proteins. n→π* interactions have been suggested to provide significant conformational biases to the disordered states of proteins. To understand the roles of solvation on the strength of n→π* interactions, computational investigations were conducted on a model n→π* interaction, the twisted-parallel-offset formaldehyde dimer, as a function of explicit solvation of the donor and acceptor carbonyls, using water and HF. In addition, the effects of urea, thiourea, guanidinium, and monovalent cations on n→π* interaction strength were examined. Solvation of the acceptor carbonyl significantly strengthens the n→π* interaction, while solvation of the donor carbonyl only modestly weakens the n→π* interaction. The n→π* interaction strength was maximized with two solvent molecules on the acceptor carbonyl. Urea stabilized the n→π* interaction via simultaneous engagement of both oxygen lone pairs on the acceptor carbonyl. Solvent effects were further investigated in the model peptides Ac-Pro-NMe2, Ac-Ala-NMe2, and Ac-Pro2-NMe2. Solvent effects in peptides were similar to those in the formaldehyde dimer, with solvation of the acceptor carbonyl increasing n→π* interaction strength and resulting in more compact conformations, in both the proline endo and exo ring puckers, as well as a reduction in the energy difference between these ring puckers. Carbonyl solvation leads to an energetic preference for PPII over both the α-helix and β/extended conformations, consistent with experimental data that protic solvents and protein denaturants both promote PPII. Solvation of the acceptor carbonyl weakens the intraresidue C5 hydrogen bond that stabilizes the β conformation.
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Affiliation(s)
- Neal J Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
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15
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Patarroyo MA, Patarroyo ME, Pabón L, Alba MP, Bermudez A, Rugeles MT, Díaz-Arevalo D, Zapata-Builes W, Zapata MI, Reyes C, Suarez CF, Agudelo W, López C, Aza-Conde J, Melo M, Escamilla L, Oviedo J, Guzmán F, Silva Y, Forero M, Flórez-Álvarez L, Aguilar-Jimenez W, Moreno-Vranich A, Garry J, Avendaño C. SM-COLSARSPROT: Highly Immunogenic Supramutational Synthetic Peptides Covering the World's Population. Front Immunol 2022; 13:859905. [PMID: 35693819 PMCID: PMC9175637 DOI: 10.3389/fimmu.2022.859905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/19/2022] [Indexed: 12/02/2022] Open
Abstract
Fifty ~20-amino acid (aa)-long peptides were selected from functionally relevant SARS-CoV-2 S, M, and E proteins for trial B-21 and another 53 common ones, plus some new ones derived from the virus' main genetic variants for complementary trial C-21. Peptide selection was based on tremendous SARS-CoV-2 genetic variability for analysing them concerning vast human immunogenetic polymorphism for developing the first supramutational, Colombian SARS-protection (SM-COLSARSPROT), peptide mixture. Specific physicochemical rules were followed, i.e., aa predilection for polyproline type II left-handed (PPIIL) formation, replacing β-branched, aromatic aa, short-chain backbone H-bond-forming residues, π-π interactions (n→π* and π-CH), aa interaction with π systems, and molecular fragments able to interact with them, disrupting PPIIL propensity formation. All these modified structures had PPIIL formation propensity to enable target peptide interaction with human leukocyte antigen-DRβ1* (HLA-DRβ1*) molecules to mediate antigen presentation and induce an appropriate immune response. Such modified peptides were designed for human use; however, they induced high antibody titres against S, M, and E parental mutant peptides and neutralising antibodies when suitably modified and chemically synthesised for immunising 61 major histocompatibility complex class II (MHCII) DNA genotyped Aotus monkeys (matched with their corresponding HLA-DRβ1* molecules), predicted to cover 77.5% to 83.1% of the world's population. Such chemically synthesised peptide mixture represents an extremely pure, stable, reliable, and cheap vaccine for COVID-19 pandemic control, providing a new approach for a logical, rational, and soundly established methodology for other vaccine development.
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Affiliation(s)
- Manuel A. Patarroyo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Manuel E. Patarroyo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Laura Pabón
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Martha P. Alba
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Adriana Bermudez
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - María Teresa Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Diana Díaz-Arevalo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Wildeman Zapata-Builes
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - María Isabel Zapata
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - César Reyes
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Carlos F. Suarez
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - William Agudelo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Carolina López
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Jorge Aza-Conde
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Miguel Melo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Luis Escamilla
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Jairo Oviedo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Fanny Guzmán
- Núcleo de Biotecnología, Pontificia U. Católica de Valparaíso, Valparaíso, Chile
| | - Yolanda Silva
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Martha Forero
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Lizdany Flórez-Álvarez
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Wbeimar Aguilar-Jimenez
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Armando Moreno-Vranich
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Jason Garry
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Catalina Avendaño
- Facultad de Ciencias Agropecualrias, Universidad de Ciencias Aplicadas y Ambientales (UDCA), Bogotá, Colombia
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16
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Chen J, Wang H, Zheng Y, Zhang X, Xu X, Gou Q. Sp 2- and sp 3-C⋯O tetrel bonds in the 3-oxetanone homodimer. Phys Chem Chem Phys 2022; 24:8992-8998. [PMID: 35380142 DOI: 10.1039/d2cp00703g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The structures and non-covalent interactions at play in the 3-oxetanone homodimer have been investigated using a pulsed jet Fourier transform microwave spectrometer supplemented with quantum chemical calculations. Two isomers were identified in the pulsed jet. With the analyses of non-covalent intermolecular interactions including the quantum theory of atoms, Johnson's non-covalent interactions and natural bond orbital, the observed global minimum is stabilized by a combination of one sp2-C⋯O tetrel bond and a network of multiple C-H⋯O weak hydrogen bonds. The second isomer is characterized by carbonyl-carbonyl interactions, with the formation of one sp2- and one sp3-C⋯O tetrel bond. The conformational population of the two observed isomers in the supersonic expansion was estimated to be NCE1/NCC1 ≈ 7/5.
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Affiliation(s)
- Junhua Chen
- School of Pharmacy, Guizhou Medical University, Guiyang 550000, Guizhou, China.,Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China.
| | - Hao Wang
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China.
| | - Yang Zheng
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China.
| | - Xinyue Zhang
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China.
| | - Xuefang Xu
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China.
| | - Qian Gou
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China. .,Chongqing Key Laboratory of Theoretical and Computational Chemistry, Daxuecheng South Rd. 55, 401331, Chongqing, China
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17
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Das A, Sharma P, Gomila RM, Frontera A, Verma AK, Sarma B, Bhattacharyya MK. Synthesis, structural topologies and anticancer evaluation of phenanthroline-based 2,6-pyridinedicarboxylato Cu(II) and Ni(II) compounds. Polyhedron 2022. [DOI: 10.1016/j.poly.2021.115632] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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18
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Rees GJ, Pitak MB, Lari A, Day SP, Yates JR, Gierth P, Barnsley K, Smith ME, Coles SJ, Hanna JV, Wallis JD. Mapping of N−C Bond Formation from a Series of Crystalline Peri‐Substituted Naphthalenes by Charge Density and Solid‐State NMR Methodologies. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202111100] [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)
- Gregory J. Rees
- Department of Physics University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
- Department of Materials University of Oxford Parks Rd Oxford OX1 3PH UK
| | - Mateusz B. Pitak
- School of Chemistry University of Southampton Highfield Southampton SO17 1BJ UK
| | - Alberth Lari
- School of Science and Technology Nottingham Trent University Clifton Lane Nottingham NG11 8NS UK
| | - Stephen P. Day
- Department of Physics University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Jonathan R. Yates
- Department of Materials University of Oxford Parks Rd Oxford OX1 3PH UK
| | | | - Kristian Barnsley
- Department of Physics University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Mark E. Smith
- Vice-Chancellor's Office University of Southampton Highfield Southampton SO17 1BJ UK
| | - Simon J. Coles
- School of Chemistry University of Southampton Highfield Southampton SO17 1BJ UK
| | - John V. Hanna
- Department of Physics University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - John D. Wallis
- School of Science and Technology Nottingham Trent University Clifton Lane Nottingham NG11 8NS UK
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19
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Rees GJ, Pitak MB, Lari A, Day SP, Yates JR, Gierth P, Barnsley K, Smith ME, Coles SJ, Hanna JV, Wallis JD. Mapping of N-C Bond Formation from a Series of Crystalline Peri-Substituted Naphthalenes by Charge Density and Solid-State NMR Methodologies. Angew Chem Int Ed Engl 2021; 60:23878-23884. [PMID: 34464506 PMCID: PMC8596510 DOI: 10.1002/anie.202111100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Indexed: 11/21/2022]
Abstract
A combination of charge density studies and solid state nuclear magnetic resonance (NMR) 1 JNC coupling measurements supported by periodic density functional theory (DFT) calculations is used to characterise the transition from an n-π* interaction to bond formation between a nucleophilic nitrogen atom and an electrophilic sp2 carbon atom in a series of crystalline peri-substituted naphthalenes. As the N⋅⋅⋅C distance reduces there is a sharp decrease in the Laplacian derived from increasing charge density between the two groups at ca. N⋅⋅⋅C = 1.8 Å, with the periodic DFT calculations predicting, and heteronuclear spin-echo NMR measurements confirming, the 1 JNC couplings of ≈3-6 Hz for long C-N bonds (1.60-1.65 Å), and 1 JNC couplings of <1 Hz for N⋅⋅⋅C >2.1 Å.
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Affiliation(s)
- Gregory J. Rees
- Department of PhysicsUniversity of WarwickGibbet Hill RoadCoventryCV4 7ALUK
- Department of MaterialsUniversity of OxfordParks RdOxfordOX1 3PHUK
| | - Mateusz B. Pitak
- School of ChemistryUniversity of SouthamptonHighfieldSouthamptonSO17 1BJUK
| | - Alberth Lari
- School of Science and TechnologyNottingham Trent UniversityClifton LaneNottinghamNG11 8NSUK
| | - Stephen P. Day
- Department of PhysicsUniversity of WarwickGibbet Hill RoadCoventryCV4 7ALUK
| | | | | | - Kristian Barnsley
- Department of PhysicsUniversity of WarwickGibbet Hill RoadCoventryCV4 7ALUK
| | - Mark E. Smith
- Vice-Chancellor's OfficeUniversity of SouthamptonHighfieldSouthamptonSO17 1BJUK
| | - Simon J. Coles
- School of ChemistryUniversity of SouthamptonHighfieldSouthamptonSO17 1BJUK
| | - John V. Hanna
- Department of PhysicsUniversity of WarwickGibbet Hill RoadCoventryCV4 7ALUK
| | - John D. Wallis
- School of Science and TechnologyNottingham Trent UniversityClifton LaneNottinghamNG11 8NSUK
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20
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Wang W, Li X, Zhou PP, Wang Y. Catalysis with Supramolecular Carbon-Bonding Interactions. Angew Chem Int Ed Engl 2021; 60:22717-22721. [PMID: 34352156 DOI: 10.1002/anie.202108973] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/02/2021] [Indexed: 12/14/2022]
Abstract
Herein, we describe a new catalysis platform, supramolecular carbon-bonding catalysis, which exploits the highly directional weak interactions between carbon centers of catalysts and electron donors to drive chemical reactions. To demonstrate this catalysis approach, we discovered a class of cyclopropane derivatives incorporated with carbonyl, ester and cyano groups as catalysts which showed general catalysis capability in different types of benchmark reactions. Among these typical examples, a challenging tail-to-head terpene cyclization can be achieved by supramolecular carbon-bonding catalysis. The co-crystal structures of catalyst and electron donors, comparison experiments, and titrations support a catalysis mode of carbon-bonding activation of Lewis basic reactants.
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Affiliation(s)
- Wei Wang
- School of Chemistry and Chemical Engineering, Key Laboratory of the Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan, 250100, China
| | - Xinxin Li
- School of Chemistry and Chemical Engineering, Key Laboratory of the Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan, 250100, China
| | - Pan-Pan Zhou
- Key Laboratory of Advanced Catalysis of Gansu Province, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Yao Wang
- School of Chemistry and Chemical Engineering, Key Laboratory of the Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan, 250100, China.,State Key Laboratory of Crystal Materials, Shandong University, Jinan, 250100, China
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21
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Wang W, Li X, Zhou P, Wang Y. Catalysis with Supramolecular Carbon‐Bonding Interactions. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108973] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Wei Wang
- School of Chemistry and Chemical Engineering Key Laboratory of the Colloid and Interface Chemistry Ministry of Education, Shandong University Jinan 250100 China
| | - Xinxin Li
- School of Chemistry and Chemical Engineering Key Laboratory of the Colloid and Interface Chemistry Ministry of Education, Shandong University Jinan 250100 China
| | - Pan‐Pan Zhou
- Key Laboratory of Advanced Catalysis of Gansu Province College of Chemistry and Chemical Engineering Lanzhou University Lanzhou 730000 China
| | - Yao Wang
- School of Chemistry and Chemical Engineering Key Laboratory of the Colloid and Interface Chemistry Ministry of Education, Shandong University Jinan 250100 China
- State Key Laboratory of Crystal Materials Shandong University Jinan 250100 China
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22
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Rincón D, Doerr M, Daza MC. Hydrogen Bonds and n → π* Interactions in the Acetylation of Propranolol Catalyzed by Candida antarctica Lipase B: A QTAIM Study. ACS OMEGA 2021; 6:20992-21004. [PMID: 34423207 PMCID: PMC8375099 DOI: 10.1021/acsomega.1c02559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Enzyme-substrate interactions play a crucial role in enzymatic catalysis. Quantum theory of atoms in molecules (QTAIM) calculations are extremely useful in computational studies of these interactions because they provide very detailed information about the strengths and types of molecular interactions. QTAIM also provides information about the intramolecular changes that occur in the catalytic reaction. Here, we analyze the enzyme-substrate interactions and the topological properties of the electron density in the enantioselective step of the acylation of (R,S)-propranolol, an aminoalcohol with therapeutic applications, catalyzed by Candida antarctica lipase B. Eight reaction paths (four for each enantiomer) are investigated and the energies, atomic charges, hydrogen bonds, and n → π* interactions of propranolol, the catalytic triad (composed of D187, H224, and S105), and the oxyanion hole are analyzed. It is found that D187 acts as an electron density reservoir for H224, and H224 acts as an electron density reservoir for the active site of the protein. It releases electron density when the tetrahedral intermediate is formed from the Michaelis complex and receives it when the enzyme-product complex is formed. Hydrogen bonds can be grouped into noncovalent and covalent hydrogen bonds. The latter are stronger and more important for the reaction than the former. We also found weak n → π* interactions, which are characterized by QTAIM and the natural bond orbital (NBO) analysis.
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23
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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.
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Affiliation(s)
- Biswajit Sahariah
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India.
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24
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Daicho K, Ozawa Y, Sugimoto K, Abe M. A pyrazine‐bridged trimer of oxo‐centered triruthenium–carbonyl clusters and the supramolecular assembly built from multiple noncovalent contacts. J CHIN CHEM SOC-TAIP 2020. [DOI: 10.1002/jccs.202000491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Keita Daicho
- Graduate School of Material Science University of Hyogo Ako‐gun Japan
| | - Yoshiki Ozawa
- Graduate School of Material Science University of Hyogo Ako‐gun Japan
| | - Kunihisa Sugimoto
- Diffraction & Scattering Division, Japan Synchrotron Radiation Research Institute (JASRI) Sayo‐gun Japan
| | - Masaaki Abe
- Graduate School of Material Science University of Hyogo Ako‐gun Japan
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25
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Kilgore HR, Olsson CR, D’Angelo KA, Movassaghi M, Raines RT. n→π* Interactions Modulate the Disulfide Reduction Potential of Epidithiodiketopiperazines. J Am Chem Soc 2020; 142:15107-15115. [PMID: 32701272 PMCID: PMC7484275 DOI: 10.1021/jacs.0c06477] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Epithiodiketopiperazines (ETPs) are a structurally complex class of fungal natural products with potent anticancer activity. In ETPs, the diketopiperazine ring is spanned by a disulfide bond that is constrained in a high-energy eclipsed conformation. We employed computational, synthetic, and spectroscopic methods to investigate the physicochemical attributes of this atypical disulfide bond. We find that the disulfide bond is stabilized by two n→π* interactions, each with large energies (3-5 kcal/mol). The n→π* interactions in ETPs make disulfide reduction much more difficult, endowing stability in physiological environments in a manner that could impact their biological activity. These data reveal a previously unappreciated means to stabilize a disulfide bond and highlight the utility of the n→π* interaction in molecular design.
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Affiliation(s)
| | | | - Kyan A. D’Angelo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mohammad Movassaghi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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26
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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
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27
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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.
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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
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28
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Talaikis M, Strazdaitė S, Žiaunys M, Niaura G. Far-Off Resonance: Multiwavelength Raman Spectroscopy Probing Amide Bands of Amyloid-β-(37-42) Peptide. Molecules 2020; 25:E3556. [PMID: 32759766 PMCID: PMC7435454 DOI: 10.3390/molecules25153556] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/24/2020] [Accepted: 08/02/2020] [Indexed: 01/22/2023] Open
Abstract
Several neurodegenerative diseases, like Alzheimer's and Parkinson's are linked with protein aggregation into amyloid fibrils. Conformational changes of native protein into the β-sheet structure are associated with a significant change in the vibrational spectrum. This is especially true for amide bands which are inherently sensitive to the secondary structure of a protein. Raman amide bands are greatly intensified under resonance conditions, in the UV spectral range, allowing for the selective probing of the peptide backbone. In this work, we examine parallel β-sheet forming GGVVIA, the C-terminus segment of amyloid-β peptide, using UV-Vis, FTIR, and multiwavelength Raman spectroscopy. We find that amide bands are enhanced far from the expected UV range, i.e., at 442 nm. A reasonable two-fold relative intensity increase is observed for amide II mode (normalized according to the δCH2/δCH3 vibration) while comparing 442 and 633 nm excitations; an increase in relative intensity of other amide bands was also visible. The observed relative intensification of amide II, amide S, and amide III modes in the Raman spectrum recorded at 442 nm comparing with longer wavelength (633/785/830 nm) excited spectra allows unambiguous identification of amide bands in the complex Raman spectra of peptides and proteins containing the β-sheet structure.
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Affiliation(s)
- Martynas Talaikis
- Department of Bioelectrochemistry and Biospectroscopy, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekis Ave. 7, LT-10257 Vilnius, Lithuania;
| | - Simona Strazdaitė
- Department of Organic Chemistry, Center for Physical Sciences and Technology (FTMC), Saulėtekis Ave. 3, LT-10257 Vilnius, Lithuania;
| | - Mantas Žiaunys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekis Ave. 7, LT-10257 Vilnius, Lithuania;
| | - Gediminas Niaura
- Department of Organic Chemistry, Center for Physical Sciences and Technology (FTMC), Saulėtekis Ave. 3, LT-10257 Vilnius, Lithuania;
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29
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Heywood VL, Alford TPJ, Roeleveld JJ, Lekanne Deprez SJ, Verhoofstad A, van der Vlugt JI, Domingos SR, Schnell M, Davis AP, Mooibroek TJ. Observations of tetrel bonding between sp 3-carbon and THF. Chem Sci 2020; 11:5289-5293. [PMID: 34122986 PMCID: PMC8159407 DOI: 10.1039/d0sc01559h] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/05/2020] [Indexed: 12/15/2022] Open
Abstract
We report the direct observation of tetrel bonding interactions between sp3-carbons of the supramolecular synthon 3,3-dimethyl-tetracyanocyclopropane (1) and tetrahydrofuran in the gas and crystalline phase. The intermolecular contact is established via σ-holes and is driven mainly by electrostatic forces. The complex manifests distinct binding geometries when captured in the crystalline phase and in the gas phase. We elucidate these binding trends using complementary gas phase quantum chemical calculations and find a total binding energy of -11.2 kcal mol-1 for the adduct. Our observations pave the way for novel strategies to engineer sp3-C centred non-covalent bonding schemes for supramolecular chemistry.
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Affiliation(s)
- Victoria L Heywood
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Thomas P J Alford
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Julius J Roeleveld
- van 't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - Siebe J Lekanne Deprez
- van 't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - Abraham Verhoofstad
- van 't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - Jarl Ivar van der Vlugt
- van 't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
- Institute of Chemistry, Carl von Ossietzky University Oldenburg Carl-von-Ossietzky-Straße 9-11 D-12629 Oldenburg Germany
| | - Sérgio R Domingos
- Deutsches Elektronen-Synchrotron (DESY) Notkestraße 85 22607 Hamburg Germany
| | - Melanie Schnell
- Deutsches Elektronen-Synchrotron (DESY) Notkestraße 85 22607 Hamburg Germany
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel Max-Eyth-Str. 1 24118 Kiel Germany
| | - Anthony P Davis
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Tiddo J Mooibroek
- van 't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
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30
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Urmey AR, Zondlo NJ. Structural preferences of cysteine sulfinic acid: The sulfinate engages in multiple local interactions with the peptide backbone. Free Radic Biol Med 2020; 148:96-107. [PMID: 31883974 DOI: 10.1016/j.freeradbiomed.2019.12.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 02/06/2023]
Abstract
Cysteine sulfinic acid (Cys-SO2-) is a non-enzymatic oxidative post-translational modification (PTM) that has been identified in hundreds of proteins. However, the effects of cysteine sulfination are in most cases poorly understood. Cys-SO2- is structurally distinctive, with long sulfur-carbon and sulfur-oxygen bonds, and with tetrahedral geometry around sulfur due to its lone pair. Cys-SO2- thus has a unique range of potential interactions with the protein backbone which could facilitate protein structural changes. Herein, the structural effects of cysteine oxidation to the sulfinic acid were investigated in model peptides and folded proteins using NMR spectroscopy, circular dichroism, bioinformatics, and computational studies. In the PDB, Cys-SO2- shows a greater preference for α-helix than Cys. In addition, Cys-SO2- is more commonly found in structures with φ > 0, including in multiple types of β-turn. Sulfinate oxygens engage in hydrogen bonds with adjacent (i or i + 1) amide hydrogens. Over half of sulfinates have at least one hydrogen bond with an adjacent amide, and several structures have hydrogen bonds with both adjacent amides. Alternately, sulfur or either oxygen can act as an electron donor for n→π* interactions with the backbone carbonyl of the same residue, as indicated by frequent S⋯CO or O⋯CO distances below the sums of their van der Waals radii in protein structures. In peptides, Cys-SO2- favored α-helical structure at the N-terminus, consistent with helix dipole effects and backbone hydrogen bonds with the sulfinate promoting α-helix. Cys-SO2- has only modestly greater polyproline II helix propensity than Cys-SH, likely due to competition from multiple side chain-backbone interactions. Cys-SO2- stabilizes the i+1 position of a β-turn relative to Cys-SH. Within proteins, the range of side chain-main chain interactions available to Cys-SO2- compared to Cys-SH provides a basis for potential changes in protein structure and function due to cysteine oxidation to the sulfinic acid.
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Affiliation(s)
- Andrew R Urmey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States
| | - Neal J Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States.
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31
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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.
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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
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32
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Kia R. Non-covalent sulfoxide⋯(nitrosyl group) interactions involving coordinated nitrosyl in a Ru( ii) nitrosyl complex with an α-diimine ligand: structural and computational studies. CrystEngComm 2020. [DOI: 10.1039/d0ce01063d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Inspection of the X-ray structure of the newly prepared Ru–nitrosyl complex bearing an α-diimine ligand revealed for the first time the π-hole interaction involving the coordinated nitrosyl group with DMSO.
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Affiliation(s)
- Reza Kia
- Chemistry Department
- Sharif University of Technology
- Tehran
- Iran
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33
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Rees GJ, Day SP, Barnsley KE, Iuga D, Yates JR, Wallis JD, Hanna JV. Measuring multiple 17O–13C J-couplings in naphthalaldehydic acid: a combined solid state NMR and density functional theory approach. Phys Chem Chem Phys 2020; 22:3400-3413. [DOI: 10.1039/c9cp03977e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combined multinuclear solid-state NMR and a density functional theory computational approach, with SIMPSON simulations, is evaluated to determine the four heteronuclear 1J(13C,17O) couplings in naphthalaldehydic acid.
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Affiliation(s)
| | | | | | - Dinu Iuga
- Department of Physics
- University of Warwick
- Coventry
- UK
| | | | - John D. Wallis
- School of Science and Technology
- Nottingham Trent University
- Nottingham
- UK
| | - John V. Hanna
- Department of Physics
- University of Warwick
- Coventry
- UK
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34
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Bristow JC, Naftalin I, Cliff SVA, Yang S, Carravetta M, Heinmaa I, Stern R, Wallis JD. Modelling of an aza-Michael reaction from crystalline naphthalene derivatives containing peri–peri interactions: very long N–C bonds? CrystEngComm 2020. [DOI: 10.1039/d0ce01137a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A correlation between N–C bond formation and CC bond breaking is constructed from the structures of a family of peri-naphthalenes with a second set of peri substituents.
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Affiliation(s)
- Jonathan C. Bristow
- School of Science and Technology
- Nottingham Trent University
- Nottingham NG11 8NS
- UK
| | - Isaac Naftalin
- School of Science and Technology
- Nottingham Trent University
- Nottingham NG11 8NS
- UK
| | - Stacey V. A. Cliff
- School of Science and Technology
- Nottingham Trent University
- Nottingham NG11 8NS
- UK
| | - Songjie Yang
- School of Science and Technology
- Nottingham Trent University
- Nottingham NG11 8NS
- UK
| | | | - Ivo Heinmaa
- Laboratory of Chemical Physics
- National Institute of Chemical Physics and Biophysics
- Tallinn
- Estonia
| | - Raivo Stern
- Laboratory of Chemical Physics
- National Institute of Chemical Physics and Biophysics
- Tallinn
- Estonia
| | - John D. Wallis
- School of Science and Technology
- Nottingham Trent University
- Nottingham NG11 8NS
- UK
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35
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Vik EC, Li P, Pellechia PJ, Shimizu KD. Transition-State Stabilization by n→π* Interactions Measured Using Molecular Rotors. J Am Chem Soc 2019; 141:16579-16583. [DOI: 10.1021/jacs.9b08542] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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
| | - Perry J. Pellechia
- 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
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36
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Harris T, Chenoweth DM. Sterics and Stereoelectronics in Aza-Glycine: Impact of Aza-Glycine Preorganization in Triple Helical Collagen. J Am Chem Soc 2019; 141:18021-18029. [DOI: 10.1021/jacs.9b05524] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Trevor Harris
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - David M. Chenoweth
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
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37
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Intermolecular Non-Covalent Carbon-Bonding Interactions with Methyl Groups: A CSD, PDB and DFT Study. Molecules 2019; 24:molecules24183370. [PMID: 31527496 PMCID: PMC6767229 DOI: 10.3390/molecules24183370] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 09/05/2019] [Accepted: 09/12/2019] [Indexed: 01/15/2023] Open
Abstract
A systematic evaluation of the CSD and the PDB in conjunction with DFT calculations reveal that non-covalent Carbon-bonding interactions with X-CH3 can be weakly directional in the solid state (P ≤ 1.5) when X = N or O. This is comparable to very weak CH hydrogen bonding interactions and is in line with the weak interaction energies calculated (≤ -1.5 kcal·mol-1) of typical charge neutral adducts such as [Me3N-CH3···OH2] (2a). The interaction energy is enhanced to ≤-5 kcal·mol-1 when X is more electron withdrawing such as in [O2N-CH3··O=Cdme] (20b) and to ≤18 kcal·mol-1 in cationic species like [Me3O+-CH3···OH2]+ (8a).
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38
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Singh SK, Panwaria P, Mishra KK, Das A. Steric as well as n→π* Interaction Controls the Conformational Preferences of Phenyl Acetate: Gas‐phase Spectroscopy and Quantum Chemical Calculations. Chem Asian J 2019; 14:4705-4711. [DOI: 10.1002/asia.201901158] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/03/2019] [Indexed: 01/26/2023]
Affiliation(s)
- Santosh K. Singh
- Department of ChemistryIndian Institute of Science Education and Research (IISER) Pune Dr. Homi Bhabha Road Pashan, Pune- 411008 India
- Current Address: Department of ChemistryUniversity of Hawaii, Manoa Honolulu Hawaii 96822 USA
| | - Prakash Panwaria
- Department of ChemistryIndian Institute of Science Education and Research (IISER) Pune Dr. Homi Bhabha Road Pashan, Pune- 411008 India
| | - Kamal K. Mishra
- Department of ChemistryIndian Institute of Science Education and Research (IISER) Pune Dr. Homi Bhabha Road Pashan, Pune- 411008 India
| | - Aloke Das
- Department of ChemistryIndian Institute of Science Education and Research (IISER) Pune Dr. Homi Bhabha Road Pashan, Pune- 411008 India
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39
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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.
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Affiliation(s)
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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40
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Aliev AE, Motherwell WB. Some Recent Advances in the Design and Use of Molecular Balances for the Experimental Quantification of Intramolecular Noncovalent Interactions of π Systems. Chemistry 2019; 25:10516-10530. [DOI: 10.1002/chem.201900854] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 05/09/2019] [Indexed: 02/03/2023]
Affiliation(s)
- Abil E. Aliev
- Department of ChemistryUniversity College London 20 Gordon Street London WC1H 0AJ UK
| | - William B. Motherwell
- Department of ChemistryUniversity College London 20 Gordon Street London WC1H 0AJ UK
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41
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Sandoval-Lira J, Solano-Altamirano JM, Cortezano-Arellano O, Cruz-Gregorio S, Meza-León RL, Hernández-Pérez JM, Sartillo-Piscil F. Can an n (O) → π* Interaction Provide Thermodynamic Stability to Naturally Occurring Cephalosporolides? J Org Chem 2019; 84:2126-2132. [PMID: 30649874 DOI: 10.1021/acs.joc.8b03116] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The stereocontrolled synthesis of naturally occurring products containing a 5,5-spiroketal molecular structure represents a major synthetic problem. Moreover, in a previous work, the stereocontrolled synthesis of cephalosporolide E (ceph E), which presumably was obtained from its epimer congener (ceph F) through an acid-mediated equilibration process, was reported. Consequently, we performed a theoretical investigation to provide relevant information regarding the title question, and it was found that the higher thermodynamic stability of ceph E, relative to ceph F, is caused by an n → π* interaction between a lone electron pair of the oxygen atom of the spiroketal ring (nO) and the antibonding orbital of the carbonyl group (π*C=O). Although similar stereoelectronic interactions have been disclosed in other molecular structures, its presence in ceph E, and very likely in other related naturally occurring products, represents a novel nonanomeric stabilizing effect that should be introduced into the chemical literature.
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Affiliation(s)
- Jacinto Sandoval-Lira
- Centro de Investigación de la Facultad de Ciencias Químicas , Benemérita Universidad Autónoma de Puebla (BUAP) , 14 Sur Esq. San Claudio, Col. San Manuel , 72570 Puebla , México.,Centro Conjunto de Investigación en Química Sustentable UAEM-UNAM , Personal de la UNAM , Carretera Km. 14.5, Unidad San Cayetano, Toluca - Atlacomulco , 50200 Toluca de Lerdo , México
| | - Juan M Solano-Altamirano
- Centro de Investigación de la Facultad de Ciencias Químicas , Benemérita Universidad Autónoma de Puebla (BUAP) , 14 Sur Esq. San Claudio, Col. San Manuel , 72570 Puebla , México
| | - Omar Cortezano-Arellano
- Centro de Investigación de la Facultad de Ciencias Químicas , Benemérita Universidad Autónoma de Puebla (BUAP) , 14 Sur Esq. San Claudio, Col. San Manuel , 72570 Puebla , México
| | - Silvano Cruz-Gregorio
- Centro de Investigación de la Facultad de Ciencias Químicas , Benemérita Universidad Autónoma de Puebla (BUAP) , 14 Sur Esq. San Claudio, Col. San Manuel , 72570 Puebla , México
| | | | - Julio M Hernández-Pérez
- Centro de Investigación de la Facultad de Ciencias Químicas , Benemérita Universidad Autónoma de Puebla (BUAP) , 14 Sur Esq. San Claudio, Col. San Manuel , 72570 Puebla , México
| | - Fernando Sartillo-Piscil
- Centro de Investigación de la Facultad de Ciencias Químicas , Benemérita Universidad Autónoma de Puebla (BUAP) , 14 Sur Esq. San Claudio, Col. San Manuel , 72570 Puebla , México
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42
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Etzkorn FA, Ware RI, Pester AM, Troya D. Conformational Analysis of n→π* Interactions in Collagen Triple Helix Models. J Phys Chem B 2019; 123:496-503. [PMID: 30525631 DOI: 10.1021/acs.jpcb.8b08384] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ab initio calculations of three models of collagen at positions Pro-Pro-Gly (1), Pro-Gly-Pro (2), and Gly-Pro-Pro (3) were performed to assess the conformational variation of n→π* contributions to the stability of the collagen triple helix. Full conformational analyses by relaxed potential-energy scans of the Ψ dihedral angle of the central residue in models 1, 2, and 3 revealed the presence of several n→π* interactions. In model 2, with Gly as the central residue, both the Φ and Ψ dihedral angles of Gly were scanned. Most minima of each model contained one or two n→π* interactions, with pyramidalization at the π* carbon. We also observed pyramidalization at the n→π* donor amide nitrogens. Minima with hydrogen-bond or non-native n→π* interactions compete with the collagen stabilizing n→π* interactions. The collagen-like n→ re-π* conformation was found as the global minimum only in model 3. The global minimum of 1 had a 5-membered ring hydrogen bond with an additional weak n→ si-π* interaction. The global minimum of 2 was in the extended conformation. We predict that the n→π* interactions found in native collagen, while individually small, cumulatively contribute to the stability of the triple helix conformation of collagen.
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Affiliation(s)
- Felicia A Etzkorn
- Department of Chemistry , Virginia Tech , Blacksburg Virginia 24061 , United States
| | - Rachel I Ware
- Department of Chemistry , Virginia Tech , Blacksburg Virginia 24061 , United States
| | - Amanda M Pester
- Department of Chemistry , Virginia Tech , Blacksburg Virginia 24061 , United States
| | - Diego Troya
- Department of Chemistry , Virginia Tech , Blacksburg Virginia 24061 , United States
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43
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León I, Alonso ER, Cabezas C, Mata S, Alonso JL. Unveiling the n→π* interactions in dipeptides. Commun Chem 2019. [DOI: 10.1038/s42004-018-0103-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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44
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Franconetti A, Frontera A, Mooibroek TJ. Intramolecular π–hole interactions with nitro aromatics. CrystEngComm 2019. [DOI: 10.1039/c9ce01015g] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A thorough CSD evaluation and DFT calculations reveal that intramolecular ElR⋯NO2 π-hole interactions can stabilize conformers of nitro aromatics by up to 2–3 kcal mol−1 when ElR and N separated by ≥4 bonds.
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Affiliation(s)
| | - Antonio Frontera
- Department of Chemistry
- Universitat de les Illes Balears
- 07122 Palma
- Spain
| | - Tiddo J. Mooibroek
- van't Hoff Institute for Molecular Sciences
- Universiteit van Amsterdam
- 1098 XH Amsterdam
- The Netherlands
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45
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Bristow JC, Addicoat MA, Wallis JD. O(−)⋯C interactions and bond formation in 1-naphtholate anions with peri-located electrophilic carbon centres. CrystEngComm 2019. [DOI: 10.1039/c8ce01872c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
n–π* interactions between naphtholate O anions and carbonyl groups are determined to be shorter than in corresponding naphthols by X-ray crystallography, and lead to cyclisations with long O–C bonds when the carbonyl group is replaced by a strongly electron deficient alkene.
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Affiliation(s)
- Jonathan C. Bristow
- School of Science and Technology
- Nottingham Trent University
- Nottingham NG11 8NS
- UK
| | - Matthew A. Addicoat
- School of Science and Technology
- Nottingham Trent University
- Nottingham NG11 8NS
- UK
| | - John D. Wallis
- School of Science and Technology
- Nottingham Trent University
- Nottingham NG11 8NS
- UK
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46
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Dutta N, Dutta Chowdhury S, Lahiri A. Probing the functional conformations of an atypical proline-rich fusion peptide. Phys Chem Chem Phys 2019; 21:20727-20742. [DOI: 10.1039/c9cp02216c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Simulations confirm a propensity for extended and solvent exposed conformations of the p15 fusion peptide capable of membrane targeting.
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Affiliation(s)
- Nivedita Dutta
- Department of Biophysics
- Molecular Biology and Bioinformatics
- University of Calcutta
- Kolkata 700009
- India
| | - Saikat Dutta Chowdhury
- Department of Biophysics
- Molecular Biology and Bioinformatics
- University of Calcutta
- Kolkata 700009
- India
| | - Ansuman Lahiri
- Department of Biophysics
- Molecular Biology and Bioinformatics
- University of Calcutta
- Kolkata 700009
- India
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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.
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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 .
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Rahim A, Sahariah B, Sarma BK. N, N'-Di(acylamino)-2,5-diketopiperazines: Strategic Incorporation of Reciprocal n → π* Interactions in a Druglike Scaffold. Org Lett 2018; 20:5743-5746. [PMID: 30156856 DOI: 10.1021/acs.orglett.8b02449] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The incorporation of the recently discovered reciprocal n → π* interactions in 2,5-diketopiperazines (DKPs) is reported to design a novel N, N'-di(acylamino)-2,5-diketopiperazine (daa-DKP) scaffold. The design, synthesis, and structural features of daa-DKPs and the effect of reciprocal n → π* interactions in their structural rigidity is discussed.
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Affiliation(s)
- Abdur Rahim
- Department of Chemistry, School of Natural Sciences , Shiv Nadar University , Dadri , Uttar Pradesh 201314 , India
| | - 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
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Singh SK, Joshi PR, Shaw RA, Hill JG, Das A. Interplay between hydrogen bonding and n→π* interaction in an analgesic drug salicin. Phys Chem Chem Phys 2018; 20:18361-18373. [PMID: 29942975 DOI: 10.1039/c8cp00655e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The competition and cooperation between weak intermolecular interactions are important in determining the conformational preferences of molecules. Understanding the relative strengths of these effects in the context of potential drug candidates is therefore essential. We use a combination of gas-phase spectroscopy and quantum-chemical calculations to elucidate the nature of such interactions for the analgesic salicin [2-(hydroxymethyl)phenyl β-d-glucopyranoside], an analog of aspirin found in willow bark. Of several possible conformers, only three are observed experimentally, and these are found to correspond with the three lowest energy conformers obtained from density functional theory calculations and simulated Franck-Condon spectra. Natural bond orbital analyses show that these are characterized by a subtle interplay between weak n→π* interaction and conventional strong hydrogen bond, with additional insights into this interaction provided by analysis of quantum theory of atoms in molecules and symmetry-adapted perturbation theory calculations. In contrast, the higher energy conformers, which are not observed experimentally, are mostly stabilized by the hydrogen bond with negligible contribution of n→π* interaction. The n→π* interaction results in a preference for the benzyl alcohol group of salicin to adopt a gauche conformation, a characteristic also found when salicin is bound to the β-glucosidase enzyme. As such, understanding the interplay between these weak interactions has significance in the rationalization of protein structures.
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Affiliation(s)
- Santosh K Singh
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune-411008, Maharashtra, India.
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Echeverría J. Intermolecular Carbonyl···Carbonyl Interactions in Transition-Metal Complexes. Inorg Chem 2018; 57:5429-5437. [PMID: 29664621 DOI: 10.1021/acs.inorgchem.8b00392] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We performed a comprehensive analysis of intermolecular carbonyl-carbonyl interactions in transition-metal complexes. Those interactions can be classified in two main types depending on the organometallic or organic nature of the donor carbonyl: M-CO···CO and R-CO···CO, respectively. By means of a combined structural and computational study we unraveled their geometrical features and strength. Moreover, electronic structure, natural bond orbitals, energy decomposition analysis, and quantum theory of atoms in molecules calculations were performed to try to understand their nature. Remarkably, we discovered that these carbonyl-carbonyl contacts have several features of the n → π* interaction. The charge transfer from an oxygen lone pair to an empty antibonding π orbital of the acceptor carbonyl is also accompanied by an electrostatic Oδ-···Cδ+ interaction. To the best of our knowledge this is the first report of an intermolecular n → π* interaction in metal complexes. These results might be significant, for instance, for the catalytic activation of carbonyl-containing small molecules with metal compounds or in the design of hybrid organic-inorganic materials, metal-organic frameworks, and other extended structures.
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Affiliation(s)
- Jorge Echeverría
- Departament de Química Inorgànica i Orgànica and Institut de Química Teòrica i Computacional IQTC-UB , Universitat de Barcelona , Martí i Franquès 1-11 , 08028 Barcelona , Spain
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