1
|
Kubyshkin V, Rubini M. Proline Analogues. Chem Rev 2024; 124:8130-8232. [PMID: 38941181 DOI: 10.1021/acs.chemrev.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Within the canonical repertoire of the amino acid involved in protein biogenesis, proline plays a unique role as an amino acid presenting a modified backbone rather than a side-chain. Chemical structures that mimic proline but introduce changes into its specific molecular features are defined as proline analogues. This review article summarizes the existing chemical, physicochemical, and biochemical knowledge about this peculiar family of structures. We group proline analogues from the following compounds: substituted prolines, unsaturated and fused structures, ring size homologues, heterocyclic, e.g., pseudoproline, and bridged proline-resembling structures. We overview (1) the occurrence of proline analogues in nature and their chemical synthesis, (2) physicochemical properties including ring conformation and cis/trans amide isomerization, (3) use in commercial drugs such as nirmatrelvir recently approved against COVID-19, (4) peptide and protein synthesis involving proline analogues, (5) specific opportunities created in peptide engineering, and (6) cases of protein engineering with the analogues. The review aims to provide a summary to anyone interested in using proline analogues in systems ranging from specific biochemical setups to complex biological systems.
Collapse
Affiliation(s)
| | - Marina Rubini
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| |
Collapse
|
2
|
Zhu J, Tuo DH, Wang XD, Ao YF, Wang QQ, Wang DX. Anion-Carbonyl Interactions. Org Lett 2024. [PMID: 38975861 DOI: 10.1021/acs.orglett.4c02060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Presented herein is the exploration of a novel non-covalent anion-carbonyl (X-···C═O) interaction using aromatic imides as receptors and halides as lone pair donors. Combined theoretical calculations and experimental methods including 13C NMR, IR, and crystallographic analyses were performed to provide the physical origin and experimental evidence of anion-carbonyl interactions. The EDA analysis (energy decomposition analysis) based on DFT calculation indicates that electrostatic terms are the dominant contributions for the binding energy while electron delocalization also significantly contributes alongside the electrostatic attraction. Orbital interaction (n → π*) involving the delocalization of halide lone pairs on the carbonyl antibonding orbitals was visualized with NBO (Natural Bond Orbital) analysis. 13C NMR and IR spectra demonstrated upfield chemical shifts and red-shift frequency of hosts upon the addition of halides, reflecting the effect of orbital overlap between the halide lone pairs and π* of carbonyl (n → π* contribution). The anion-carbonyl interactions were directly revealed by X-ray structural analysis of anion and benzene triimide complexes.
Collapse
Affiliation(s)
- Jun Zhu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - De-Hui Tuo
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Xu-Dong Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Yu-Fei Ao
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi-Qiang Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - De-Xian Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
3
|
D'Arminio N, Ruggiero V, Pierri G, Marabotti A, Tedesco C. Emerging role of carbonyl-carbonyl interactions in the classification of beta turns. Protein Sci 2024; 33:e4868. [PMID: 38100281 PMCID: PMC10806932 DOI: 10.1002/pro.4868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
Carbonyl-carbonyl interactions in peptides and proteins attracted considerable interest in recent years. Here, we report a survey of carbonyl-carbonyl interactions in cyclic peptides, depsipeptides, peptoids and discuss the relationship between backbone torsion angles and CO∙∙∙CO distances. In general, φ values in the range between -40° and -90° and between 40° and 90° correspond to CO∙∙∙CO distances below 3.22 Å. By extending the analysis of carbonyl-carbonyl interactions in different types of beta turns in proteins, we also highlight the role of direct or reciprocal carbonyl-carbonyl interactions in stabilizing the beta turn conformation for each specific type. We confirmed the new type II beta turn, detected by Dunbrack and coworkers, and named Pa, and detect the presence of a direct carbonyl-carbonyl interaction between the second and third residues of the turn. We also evidenced the existence of another new type II beta turn, named pA (following Dunbrack's notation), which represents the alternative conformation of Pa with opposite φ and ψ values and is characterized by a direct carbonyl-carbonyl interaction between the second and third residues of the turn. Finally, we show that the occurrence of CO∙∙∙CO interactions could be also advocated to explain from a chemical point of view the diversity of turn types.
Collapse
Affiliation(s)
- Nancy D'Arminio
- Department of Chemistry and Biology “A. Zambelli”University of SalernoFiscianoItaly
| | - Valentina Ruggiero
- Department of Chemistry and Biology “A. Zambelli”University of SalernoFiscianoItaly
- Present address:
Department of PharmacyUniversity of SalernoFiscianoItaly
| | - Giovanni Pierri
- Department of Chemistry and Biology “A. Zambelli”University of SalernoFiscianoItaly
| | - Anna Marabotti
- Department of Chemistry and Biology “A. Zambelli”University of SalernoFiscianoItaly
| | - Consiglia Tedesco
- Department of Chemistry and Biology “A. Zambelli”University of SalernoFiscianoItaly
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Wang XD, Zhu J, Wang DX. Intermolecular n→π* Interactions in Supramolecular Chemistry and Catalysis. Chempluschem 2023; 88:e202300288. [PMID: 37609956 DOI: 10.1002/cplu.202300288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 08/24/2023]
Abstract
The n→π* interactions describing attractive force between lone pairs (lps) of nucleophile and carbonyl or polarized unsaturated bonds have recently attracted growing attentions in various disciplines. So far, such non-covalent driving force are mainly concentrated to intramolecular systems. Intermolecular n→π* interactions in principle could produce fascinated supramolecular systems or facilitate organic reactions, however, they remain largely underexplored due to the very weak energy of individual interaction. This review attempts to give an overview of the challenging intermolecular n→π* interactions, much efforts emphasize the supramolecular systems, catalytic processes and spectroscopic measurements.
Collapse
Affiliation(s)
- Xu-Dong Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jun Zhu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De-Xian Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
6
|
Zhu J, Wang XD, Ao YF, Wang QQ, Wang DX. Intermolecular n→π* Interactions Based on a Tailored Multicarbonyl-Containing Macrocycle. Chemistry 2023; 29:e202203485. [PMID: 36445795 DOI: 10.1002/chem.202203485] [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: 11/09/2022] [Revised: 11/24/2022] [Accepted: 11/24/2022] [Indexed: 11/30/2022]
Abstract
Towards unexplored intermolecular n→π* interactions, presented herein are the synthesis, structure, self-assembly and function of a multicarbonyl-containing macrocycle calix[2]arene[2]barbiturate 1. X-ray single crystal diffraction reveals the presence of Cl⋅⋅⋅C=O interactions in CH2 Cl2 ⊂1 host-guest complex and multiple intermolecular C=O⋅⋅⋅C=O interactions between molecules 1 in crystalline state. The intermolecular C=O⋅⋅⋅C=O interactions as attractive driving force led to unprecedented self-assembly of nanotube with diameter around 1.4 nm and inner surface engineered by aromatic rings. SEM and TEM images of the self-assembly of 1 demonstrated temperature-dependent morphologies which allows the observation of spheres at 25 °C and rods at 0 °C, respectively. XRD analysis indicated consistent hexagonal patterns in the self-assembly and single crystal lattice, indicating the nanotubes driven by C=O⋅⋅⋅C=O interactions constitute the basic structural architectures of both aggregates. The nanoscopic tubes (pores) formed in the rodlike single crystal engendering the separation of moving dyes were preliminarily investigated by a single-crystal chromatography and crystal-packed column chromatography.
Collapse
Affiliation(s)
- Jun Zhu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China)
| | - Xu-Dong Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yu-Fei Ao
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China)
| | - Qi-Qiang Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China)
| | - De-Xian Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China)
| |
Collapse
|
7
|
Dutta J, Routray C, Pandey S, Biswal HS. Intermolecular noncovalent interactions with carbon in solution. Chem Sci 2022; 13:14327-14335. [PMID: 36545132 PMCID: PMC9749111 DOI: 10.1039/d2sc05431k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/20/2022] [Indexed: 11/22/2022] Open
Abstract
One of the most familiar carbon-centered noncovalent interactions (NCIs) involving an antibonding π*-orbital situated at the Bürgi-Dunitz angle from the electron donor, mostly lone pairs of electrons, is known as n → π* interactions, and if it involves a σ* orbital in a linear fashion, then it is known as the carbon bond. These NCIs can be intra- or inter-molecular and are usually weak in strength but have a paramount effect on the structure and function of small-molecular crystals and proteins. Surprisingly, the experimental evidence of such interactions in the solution phase is scarce. It is even difficult to determine the interaction energy in the solution. Using NMR spectroscopy aided with molecular dynamics (MD) simulation and high-level quantum mechanical calculations, herein we provide the experimental evidence of intermolecular carbon-centered NCIs in solution. The challenge was to find appropriate heterodimers that could sustain room temperature thermal energy and collisions from the solvent molecules. However, after several trial model compounds, the pyridine-N-oxide:dimethyltetracyanocyclopropane (PNO-DMTCCP) complex was found to be a good candidate for the investigation. NBO analyses show that the PNO:DMTCCP complex is stabilized mainly by intermolecular n → π* interaction when a weaker carbon bond gives extra stability to the complex. From the NMR study, it is observed that the NCIs between DMTCCP and PNO are enthalpy driven with an enthalpy change of -28.12 kJ mol-1 and dimerization energy of ∼-38 kJ mol-1 is comparable to the binding energies of a conventional hydrogen-bonded dimer. This study opens up a new strategy to investigate weak intermolecular interactions such as n → π* interaction and carbon bonds in the solution phase.
Collapse
Affiliation(s)
- Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO - Bhimpur-Padanpur, Via-Jatni, District - Khurda PIN - 752050 Bhubaneswar India +91-674-2494-185, +91-674-2494-186
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Chinmay Routray
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO - Bhimpur-Padanpur, Via-Jatni, District - Khurda PIN - 752050 Bhubaneswar India +91-674-2494-185, +91-674-2494-186
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Shalini Pandey
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO - Bhimpur-Padanpur, Via-Jatni, District - Khurda PIN - 752050 Bhubaneswar India +91-674-2494-185, +91-674-2494-186
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO - Bhimpur-Padanpur, Via-Jatni, District - Khurda PIN - 752050 Bhubaneswar India +91-674-2494-185, +91-674-2494-186
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| |
Collapse
|
8
|
Martínez-Ahumada E, López-Olvera A, Carmona-Monroy P, Díaz-Salazar H, Garduño-Castro MH, Obeso JL, Leyva C, Martínez A, Hernández-Rodríguez M, Solis-Ibarra D, Ibarra IA. SO 2 capture and detection using a Cu(II)-metal-organic polyhedron. Dalton Trans 2022; 51:18368-18372. [PMID: 36268816 DOI: 10.1039/d2dt03096a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The SO2 adsorption-desorption capacity at room temperature and 1 bar of the metal-organic polyhedron MOP-CDC was investigated. In addition, the qualitative solid-state absorption-emission properties of this material (before and after SO2 exposure) were measured and tested, and it demonstrated remarkable capability for SO2 detection. Our results represent the first example of fluorimetric SO2 detection in a MOP.
Collapse
Affiliation(s)
- Eva Martínez-Ahumada
- Laboratorio de Fisicoquímica y Reactividad de Superficies (LaFReS), Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Circuito Exterior s/n, CU, Del Coyoacán, 04510, México D.F., Mexico.
| | - Alfredo López-Olvera
- Laboratorio de Fisicoquímica y Reactividad de Superficies (LaFReS), Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Circuito Exterior s/n, CU, Del Coyoacán, 04510, México D.F., Mexico.
| | - Paulina Carmona-Monroy
- Laboratorio de Fisicoquímica y Reactividad de Superficies (LaFReS), Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Circuito Exterior s/n, CU, Del Coyoacán, 04510, México D.F., Mexico.
| | - Howard Díaz-Salazar
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Del. Coyoacán, C. P. 04510, Cd. Mx., Mexico
| | | | - Juan L Obeso
- Instituto Politécnico Nacional, Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Calz. Legaria 694, Col. Irrigación, Miguel Hidalgo, 11500, CDMX, Mexico
| | - Carolina Leyva
- Instituto Politécnico Nacional, Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Calz. Legaria 694, Col. Irrigación, Miguel Hidalgo, 11500, CDMX, Mexico
| | - Ana Martínez
- Departamento de Materiales de Baja Dimensionalidad, Instituto de Investigaciones en Materiales, and Facultad de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, CU, Del. Coyoacán, Ciudad de México 04510, Mexico
| | - Marcos Hernández-Rodríguez
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Del. Coyoacán, C. P. 04510, Cd. Mx., Mexico
| | - Diego Solis-Ibarra
- Laboratorio de Fisicoquímica y Reactividad de Superficies (LaFReS), Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Circuito Exterior s/n, CU, Del Coyoacán, 04510, México D.F., Mexico.
| | - Ilich A Ibarra
- Laboratorio de Fisicoquímica y Reactividad de Superficies (LaFReS), Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Circuito Exterior s/n, CU, Del Coyoacán, 04510, México D.F., Mexico.
| |
Collapse
|
9
|
Livingstone K, Siebold K, Meyer S, Martín-Heras V, Daniliuc CG, Gilmour R. Skeletal Ring Contractions via I(I)/I(III) Catalysis: Stereoselective Synthesis of cis-α,α-Difluorocyclopropanes. ACS Catal 2022; 12:14507-14516. [PMID: 36504915 PMCID: PMC9724094 DOI: 10.1021/acscatal.2c04511] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/17/2022] [Indexed: 11/12/2022]
Abstract
The clinical success of α,α-difluorocyclopropanes, combined with limitations in the existing synthesis portfolio, inspired the development of an operationally simple, organocatalysis-based strategy to access cis-configured derivatives with high levels of stereoselectivity (up to >20:1 cis:trans). Leveraging an I(I)/I(III)-catalysis platform in the presence of an inexpensive HF source, it has been possible to exploit disubstituted bicyclobutanes (BCBs) as masked cyclobutene equivalents for this purpose. In situ generation of this strained alkene, enabled by Brønsted acid activation, facilitates an unprecedented 4 → 3 fluorinative ring contraction, to furnish cis-α,α-difluorinated cyclopropanes in a highly stereoselective manner (up to 88% yield). Mechanistic studies are disclosed together with conformational analysis (X-ray crystallography and NMR) to validate cis-α,α-difluorocyclopropanes as isosteres of the 1,4-dicarbonyl moiety. Given the importance of this unit in biology and the foundational no → π* interactions that manifest themselves in this conformation (e.g., collagen), it is envisaged that the title motif will find application in focused molecular design.
Collapse
|
10
|
Kumar S, Borish K, Dey S, Nagesh J, Das A. Sequence dependent folding motifs of the secondary structures of Gly-Pro and Pro-Gly containing oligopeptides. Phys Chem Chem Phys 2022; 24:18408-18418. [PMID: 35880873 DOI: 10.1039/d2cp01306a] [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
Folding motifs of the secondary structures of peptides and proteins are primarily based on the hydrogen bonding interactions in the backbone as well as the sequence of the amino acid residues present. For instance, the β-turn structure directed by the Pro-Gly sequence is the key to the β-hairpin structure of peptides/proteins as well as a selective site for the enzymatic hydroxylation of pro-collagen. Herein, we have investigated the sequence dependent folding motifs of end-protected Gly-Pro and Pro-Gly dipeptides using a combination of gas phase laser spectroscopy, quantum chemistry calculations, solution phase IR and NMR spectroscopy and single crystal X-Ray diffraction (XRD). All three observed conformers of the Gly-Pro peptide in the gas phase have been found to have extended β-strand or polyproline-II (PP-II) structures with C5-C7 hydrogen bonding interactions, which correlates well with the structure obtained from solution phase spectroscopy and XRD. On the other hand, we have found that the Pro-Gly peptide has a C10/β-turn structure in the solution phase in contrast to the C7-C7 (i.e. 27-ribbon) structure observed in the gas phase. Although the lowest energy structure in the gas phase is not C10, we find that C7-C7 is an abundantly found structural motif of Pro-Gly containing peptides in the Cambridge Structural Database, indicating that the gas phase conformers are not sampling any unusual forms. We surmise that the role of the solvent could be crucial in dictating the preferential stabilization of the C10 structure in the solution phase. The present investigation provides a comprehensive picture of the folding motifs of the Gly-Pro and Pro-Gly peptides observed in the gas phase and condensed phase weaving a fine interplay of the intrinsic conformational properties, solvation, and crystal packing of the peptides.
Collapse
Affiliation(s)
- Satish Kumar
- Department of Chemistry, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pashan, Pune-411008, India.
| | - Kshetrimayum Borish
- Department of Chemistry, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pashan, Pune-411008, India.
| | - Sanjit Dey
- Department of Chemistry, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pashan, Pune-411008, India.
| | - Jayashree Nagesh
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore-560012, India.
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pashan, Pune-411008, India.
| |
Collapse
|
11
|
Panwaria P, Das A. Understanding the n → π* non-covalent interaction using different experimental and theoretical approaches. Phys Chem Chem Phys 2022; 24:22371-22389. [PMID: 35822956 DOI: 10.1039/d2cp02070j] [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
Herein, a perspective on the recent understanding of weak n → π* interaction obtained using different experimental and theoretical approaches is presented. This interaction is purely an orbital interaction that involves the delocalization of the lone pair electrons (n) on nitrogen, oxygen, and sulfur to the π* orbitals of CO, CN, and aromatic rings. The n → π* interaction has been found to profoundly influence the stabilization of peptides, proteins, drugs, and various small molecules. Although the functional properties of this non-covalent interaction are still quite underestimated, there are recent demonstrations of applying this interaction to the regulation of synthetic chemistry, catalysis, and molecular recognition. However, the identification and quantification of the n → π* interaction remain a demanding task as this interaction is quite weak and based on the electron delocalization between the two orbitals, while hyperconjugation interactions between neighboring atoms and the group involved in the n → π* interaction are simultaneously present. This review provides a comprehensive picture of understanding the n → π* interaction using different experimental approaches such as the X-ray diffraction technique, and electronic, NMR, microwave, and IR spectroscopy, in addition to quantum chemistry calculations. A detailed understanding of the n → π* interaction can help in modulating the strength of this interaction, which will be further helpful in designing efficient drugs, synthetic peptides, peptidomimetics, etc.
Collapse
Affiliation(s)
- Prakash Panwaria
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India.
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India.
| |
Collapse
|
12
|
Chu B, Zhang H, Chen K, Liu B, Yu QL, Zhang CJ, Sun J, Yang Q, Zhang XH, Tang BZ. Aliphatic Polyesters with White-Light Clusteroluminescence. J Am Chem Soc 2022; 144:15286-15294. [PMID: 35796412 DOI: 10.1021/jacs.2c05948] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Single-molecule white-light emission (SMWLE) has many advantages in practical applications; however, the fabrication of SMWLE from nonconjugated luminescent polymers, namely, clusteroluminogens (CLgens), is still a big challenge. Herein, the first example of linear nonconjugated polyesters with SMWLE is reported. Twenty-four kinds of nonconjugated aliphatic polyesters with tunable clusteroluminescence (CL) colors and efficiency were synthesized by the copolymerization of six epoxides and four anhydrides. Experimental and calculation results prove that, at the primary structure level, the balance of structural flexibility and rigidity via adjusting the side-chain length significantly enhances the efficiency of CL without wavelength change. However, altering the chemical structures of the monomer from succinic anhydride to trans-maleic anhydride (MA), cis-MA, and citraconic anhydride (CA), secondary structures of these polyesters change from helix to straight and folding sheet accompanied by gradually red-shifted CL from 460 to 570 nm due to the increase in through-space n-π* interactions, as demonstrated by the computational and experimental results. Then, pure SMWLE with CIE coordination (0.30, 0.32) based on overlapped short-wavelength and long-wavelength CL is achieved in CA-based polyesters. This work not only provides further insights into the emission mechanism of CL but also provides a new strategy to manipulate the properties of CL by regulating the hierarchical structures of CLgens.
Collapse
Affiliation(s)
- Bo Chu
- State Key Laboratory of Motor Vehicle Biofuel Technology, International Research Center for X Polymers, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Haoke Zhang
- State Key Laboratory of Motor Vehicle Biofuel Technology, International Research Center for X Polymers, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China.,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311215, China.,Guangdong Provincial Key Laboratory of Luminescence from Molecular Aggregates, South China University of Technology, Guangzhou 510640, China
| | - Kailuo Chen
- State Key Laboratory of Motor Vehicle Biofuel Technology, International Research Center for X Polymers, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Bin Liu
- School of Energy and Power Engineering, North University of China, Taiyuan 030051, P. R. China
| | - Qing-Lei Yu
- State Key Laboratory of Motor Vehicle Biofuel Technology, International Research Center for X Polymers, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Cheng-Jian Zhang
- State Key Laboratory of Motor Vehicle Biofuel Technology, International Research Center for X Polymers, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Jingzhi Sun
- State Key Laboratory of Motor Vehicle Biofuel Technology, International Research Center for X Polymers, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Qing Yang
- State Key Laboratory of Silicon Materials, Zhejiang University, Hangzhou 310027, China
| | - Xing-Hong Zhang
- State Key Laboratory of Motor Vehicle Biofuel Technology, International Research Center for X Polymers, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Ben Zhong Tang
- Shenzhen Institute of Aggregate Science and Technology, School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen 518172, China
| |
Collapse
|
13
|
Buschmann P, Lengsfeld KG, Djahandideh J, Grabow JU. From rotational resolved spectra to an extended increment system of planar moments allowing ad-hoc conformational identification – Exemplification by the broadband microwave spectrum of α-hydroxyisobutyric acid. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131805] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
14
|
Sanz-Novo M, León I, Alonso ER, Alonso JL. Unleashing the shape of L-DOPA at last. Phys Chem Chem Phys 2021; 24:3546-3554. [PMID: 34908061 DOI: 10.1039/d1cp05066d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Herein, we report the first rotational study of neutral L-DOPA, an extensively used supramolecular synthon and an amino acid precursor of the neurotransmitters dopamine, norepinephrine (noradrenaline), and epinephrine (adrenaline) using broadband and narrowband Fourier transform microwave spectroscopies coupled with a laser ablation vaporization system. The spectroscopic parameters derived from the analysis of the rotational spectrum conclusively identify the existence of four distinct conformers of L-DOPA in the supersonic jet, further rejecting the previously reported catechol ring-induced conformational restriction. The analysis of the 14N nuclear quadrupole coupling hyperfine structure further revealed the orientation of the N-bearing functional group, proving the existence of stabilizing N-H⋯π interactions for the observed structures.
Collapse
Affiliation(s)
- Miguel Sanz-Novo
- Espectroscopía Molecular (GEM), Edificio Quifima Laboratorios de Espectroscopía y Bioespectroscopía Unidad Asociada CSIC, Parque Científico Uva Universidad de Valladolid, Paseo de Belén 5, Valladolid 47011, Spain.
| | - Iker León
- Espectroscopía Molecular (GEM), Edificio Quifima Laboratorios de Espectroscopía y Bioespectroscopía Unidad Asociada CSIC, Parque Científico Uva Universidad de Valladolid, Paseo de Belén 5, Valladolid 47011, Spain.
| | - Elena R Alonso
- Espectroscopía Molecular (GEM), Edificio Quifima Laboratorios de Espectroscopía y Bioespectroscopía Unidad Asociada CSIC, Parque Científico Uva Universidad de Valladolid, Paseo de Belén 5, Valladolid 47011, Spain.
| | - José L Alonso
- Espectroscopía Molecular (GEM), Edificio Quifima Laboratorios de Espectroscopía y Bioespectroscopía Unidad Asociada CSIC, Parque Científico Uva Universidad de Valladolid, Paseo de Belén 5, Valladolid 47011, Spain.
| |
Collapse
|
15
|
Kolesniková L, León I, Alonso ER, Mata S, Alonso JL. An Innovative Approach for the Generation of Species of the Interstellar Medium. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Lucie Kolesniková
- Department of Analytical Chemistry University of Chemistry and Technology Technická 5 16628 Prague 6 Czech Republic
| | - Iker León
- Grupo de Espectroscopia Molecular (GEM) Edificio Quifima Área de Química-Física Laboratorios de Espectroscopia y, Bioespectroscopia Parque Científico UVa Unidad Asociada CSIC Universidad de Valladolid 47011 Valladolid Spain
| | - Elena R. Alonso
- Instituto Biofisika (UPV/EHU, CSIC) University of the Basque Country 48940 Leioa Spain
- Departamento de Química Física Facultad de Ciencia y Tecnología Universidad del País Vasco Barrio Sarriena s/n 48940 Leioa Spain
| | - Santiago Mata
- Grupo de Espectroscopia Molecular (GEM) Edificio Quifima Área de Química-Física Laboratorios de Espectroscopia y, Bioespectroscopia Parque Científico UVa Unidad Asociada CSIC Universidad de Valladolid 47011 Valladolid Spain
| | - Jose Luis Alonso
- Grupo de Espectroscopia Molecular (GEM) Edificio Quifima Área de Química-Física Laboratorios de Espectroscopia y, Bioespectroscopia Parque Científico UVa Unidad Asociada CSIC Universidad de Valladolid 47011 Valladolid Spain
| |
Collapse
|
16
|
Kolesniková L, León I, Alonso ER, Mata S, Alonso JL. An Innovative Approach for the Generation of Species of the Interstellar Medium. Angew Chem Int Ed Engl 2021; 60:24461-24466. [PMID: 34496111 PMCID: PMC8597129 DOI: 10.1002/anie.202110325] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/02/2021] [Indexed: 11/16/2022]
Abstract
The large amount of unstable species in the realm of interstellar chemistry drives an urgent need to develop efficient methods for the in situ generations of molecules that enable their spectroscopic characterizations. Such laboratory experiments are fundamental to decode the molecular universe by matching the interstellar and terrestrial spectra. We propose an approach based on laser ablation of nonvolatile solid organic precursors. The generated chemical species are cooled in a supersonic expansion and probed by high‐resolution microwave spectroscopy. We present a proof of concept through a simultaneous formation of interstellar compounds and the first generation of aminocyanoacetylene using diaminomaleonitrile as a prototypical precursor. With this micro‐laboratory, we open the door to generation of unsuspected species using precursors not typically accessible to traditional techniques such as electric discharge and pyrolysis.
Collapse
Affiliation(s)
- Lucie Kolesniková
- Department of Analytical Chemistry, University of Chemistry and Technology, Technická 5, 16628, Prague 6, Czech Republic
| | - Iker León
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Área de Química-Física, Laboratorios de Espectroscopia y, Bioespectroscopia, Parque Científico UVa, Unidad Asociada CSIC, Universidad de Valladolid, 47011, Valladolid, Spain
| | - Elena R Alonso
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940, Leioa, Spain.,Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Barrio Sarriena s/n, 48940, Leioa, Spain
| | - Santiago Mata
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Área de Química-Física, Laboratorios de Espectroscopia y, Bioespectroscopia, Parque Científico UVa, Unidad Asociada CSIC, Universidad de Valladolid, 47011, Valladolid, Spain
| | - Jose Luis Alonso
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Área de Química-Física, Laboratorios de Espectroscopia y, Bioespectroscopia, Parque Científico UVa, Unidad Asociada CSIC, Universidad de Valladolid, 47011, Valladolid, Spain
| |
Collapse
|
17
|
Alonso ER, León I, Kolesniková L, Mata S, Alonso JL. Unveiling Five Naked Structures of Tartaric Acid. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Elena R. Alonso
- Instituto Biofisika (UPV/EHU, CSIC) University of the Basque Country 48940 Leioa Spain
- Departamento de Química Física Facultad de Ciencia y Tecnología Universidad del País Vasco Barrio Sarriena s/n 48940 Leioa Spain
| | - Iker León
- Grupo de Espectroscopia Molecular (GEM) Edificio Quifima Área de Química-Física Laboratorios de Espectroscopia y Bioespectroscopia Parque Científico UVa Unidad Asociada CSIC Universidad de Valladolid 47011 Valladolid Spain
| | - Lucie Kolesniková
- Department of Analytical Chemistry University of Chemistry and Technology Technická 5 16628 Prague 6 Czech Republic
| | - Santiago Mata
- Grupo de Espectroscopia Molecular (GEM) Edificio Quifima Área de Química-Física Laboratorios de Espectroscopia y Bioespectroscopia Parque Científico UVa Unidad Asociada CSIC Universidad de Valladolid 47011 Valladolid Spain
| | - Jose Luis Alonso
- Grupo de Espectroscopia Molecular (GEM) Edificio Quifima Área de Química-Física Laboratorios de Espectroscopia y Bioespectroscopia Parque Científico UVa Unidad Asociada CSIC Universidad de Valladolid 47011 Valladolid Spain
| |
Collapse
|
18
|
León I, Alonso ER, Mata S, Alonso JL. Shape of Testosterone. J Phys Chem Lett 2021; 12:6983-6987. [PMID: 34283615 PMCID: PMC8327310 DOI: 10.1021/acs.jpclett.1c01743] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
We have successfully characterized the structure of testosterone, one of the essential steroids, through high-resolution rotational spectroscopy. A single conformer has been detected, and a total of 404 transitions have been fitted, allowing a precise determination of the rotational constants. It allowed us to unravel that the isolated structure of testosterone adopts an extended disposition. The results obtained in this work highlight how using laser ablation techniques in combination with Fourier transform microwave techniques allow the study of large biomolecules or common pharmaceuticals. It is an important step toward studying relevant biomolecules and developing new analytical techniques with unprecedented sensitivity and resolution.
Collapse
Affiliation(s)
- Iker León
- Grupo
de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios
de Espectroscopia y Bioespectroscopia, Unidad
Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011 Valladolid, Spain
| | - Elena R. Alonso
- Instituto
Biofisika (UPV/EHU, CSIC), University of
the Basque Country, 48940 Leioa, Spain
- Departamento
de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Santiago Mata
- Grupo
de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios
de Espectroscopia y Bioespectroscopia, Unidad
Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011 Valladolid, Spain
| | - José L. Alonso
- Grupo
de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios
de Espectroscopia y Bioespectroscopia, Unidad
Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011 Valladolid, Spain
| |
Collapse
|
19
|
Alonso ER, León I, Kolesniková L, Mata S, Alonso JL. Unveiling Five Naked Structures of Tartaric Acid. Angew Chem Int Ed Engl 2021; 60:17410-17414. [PMID: 34060688 PMCID: PMC8361959 DOI: 10.1002/anie.202105718] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Indexed: 11/10/2022]
Abstract
The unbiased, naked structures of tartaric acid, one of the most important organic compounds existing in nature and a candidate to be present in the interstellar medium, has been revealed in this work for the first time. Solid samples of its naturally occurring (R,R) enantiomer have been vaporized by laser ablation, expanded in a supersonic jet, and characterized by Fourier transform microwave spectroscopy. In the isolation conditions of the jet, we have discovered up to five different structures stabilized by intramolecular hydrogen-bond networks dominated by O-H⋅⋅⋅O=C and O-H⋅⋅⋅O motifs extended along the entire molecule. These five forms, two with an extended (trans) disposition of the carbon chain and three with a bent (gauche) disposition, can serve as a basis to represent the shape of tartaric acid. This work also reports the first set of spectroscopy data that can be used to detect tartaric acid in the interstellar medium.
Collapse
Affiliation(s)
- Elena R Alonso
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940, Leioa, Spain.,Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Barrio Sarriena s/n, 48940, Leioa, Spain
| | - Iker León
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Área de Química-Física, Laboratorios de Espectroscopia y Bioespectroscopia, Parque Científico UVa, Unidad Asociada CSIC, Universidad de Valladolid, 47011, Valladolid, Spain
| | - Lucie Kolesniková
- Department of Analytical Chemistry, University of Chemistry and Technology, Technická 5, 16628, Prague 6, Czech Republic
| | - Santiago Mata
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Área de Química-Física, Laboratorios de Espectroscopia y Bioespectroscopia, Parque Científico UVa, Unidad Asociada CSIC, Universidad de Valladolid, 47011, Valladolid, Spain
| | - Jose Luis Alonso
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Área de Química-Física, Laboratorios de Espectroscopia y Bioespectroscopia, Parque Científico UVa, Unidad Asociada CSIC, Universidad de Valladolid, 47011, Valladolid, Spain
| |
Collapse
|
20
|
Alonso ER, Fusè M, León I, Puzzarini C, Alonso JL, Barone V. Exploring the Maze of Cycloserine Conformers in the Gas Phase Guided by Microwave Spectroscopy and Quantum Chemistry. J Phys Chem A 2021; 125:2121-2129. [DOI: 10.1021/acs.jpca.1c00455] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elena R. Alonso
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, Leioa, Spain
| | - Marco Fusè
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Iker León
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005 Valladolid, Spain
| | - Cristina Puzzarini
- Dipartimento di “Chimica Giacomo Ciamician”, University of Bologna, via F. Selmi 2, 40126, Bologna, Italy
| | - José L. Alonso
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005 Valladolid, Spain
| | - Vincenzo Barone
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| |
Collapse
|
21
|
Iwaoka M, Yoshida K, Shimosato T. Application of a Distance-Dependent Sigmoidal Dielectric Constant to the REMC/SAAP3D Simulations of Chignolin, Trp-Cage, and the G10q Mutant. Protein J 2020; 39:402-410. [PMID: 33108545 DOI: 10.1007/s10930-020-09936-7] [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] [Accepted: 10/22/2020] [Indexed: 11/26/2022]
Abstract
The replica-exchange Monte Carlo method based on the single amino acid potential (SAAP) force field, i.e., REMC/SAAP3D, was recently developed by our group for the molecular simulation of short peptides. In this study, the method has been improved by applying a distance-dependent dielectric (DDD) constant and extended to the peptides containing D-amino acid (AA) residues. For chignolin (10 AAs), a sigmoidal DDD model reasonably allocated the native-like β-hairpin structure with all-atom root mean square deviation (RMSD) = 2.0 Å as a global energy minimum. The optimal DDD condition was subsequently applied for Trp-cage (20 AAs) and its G10q mutant. The native-like α-rich folded structures with main-chain RMSD = 3.7 and 3.8 Å were obtained as global energy minima for Trp-cage and G10q, respectively. The results suggested that the REMC/SAAP3D method with the sigmoidal DDD model is useful for structural prediction for the short peptides comprised of up to 20 AAs. In addition, the relative contributions of SAAP to the total energy (%SAAP) were evaluated by energetic component analysis. The ratios of %SAAP were about 40 and 20% for chignolin and Trp-cage (or G10q), respectively. It was proposed that SAAP is more important for the secondary structure formation than for the assembly to a higher-order folded structure, in which the attractive van der Waals interaction may play a more important role.
Collapse
Affiliation(s)
- Michio Iwaoka
- Department of Chemistry, School of Science, Tokai University, Kitakaname, Hiratsuka-shi, Kanagawa, 259-1292, Japan.
| | - Koji Yoshida
- Department of Chemistry, School of Science, Tokai University, Kitakaname, Hiratsuka-shi, Kanagawa, 259-1292, Japan
| | - Taku Shimosato
- Department of Chemistry, School of Science, Tokai University, Kitakaname, Hiratsuka-shi, Kanagawa, 259-1292, Japan
| |
Collapse
|
22
|
Kubyshkin V. Polarity effects in 4-fluoro- and 4-(trifluoromethyl)prolines. Beilstein J Org Chem 2020; 16:1837-1852. [PMID: 32765799 PMCID: PMC7385359 DOI: 10.3762/bjoc.16.151] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/06/2020] [Indexed: 12/14/2022] Open
Abstract
Fluorine-containing analogues of proline are valuable tools in engineering and NMR spectroscopic studies of peptides and proteins. Their use relies on the fundamental understanding of the interplay between the substituents and the main chain groups of the amino acid residue. This study aims to showcase the polarity-related effects that arise from the interaction between the functional groups in molecular models. Properties such as conformation, acid-base transition, and amide-bond isomerism were examined for diastereomeric 4-fluoroprolines, 4-(trifluoromethyl)prolines, and 1,1-difluoro-5-azaspiro[2.4]heptane-6-carboxylates. The preferred conformation on the proline ring originated from a preferential axial positioning for a single fluorine atom, and an equatorial positioning for a trifluoromethyl- or a difluoromethylene group. This orientation of the substituents explains the observed trends in the pK a values, lipophilicity, and the kinetics of the amide bond rotation. The study also provides a set of evidences that the transition state of the amide-bond rotation in peptidyl-prolyl favors C4-exo conformation of the pyrrolidine ring.
Collapse
|
23
|
Joyce LA, Schultz DM, Sherer EC, Neill JL, Sonstrom RE, Pate BH. Direct regioisomer analysis of crude reaction mixtures via molecular rotational resonance (MRR) spectroscopy. Chem Sci 2020; 11:6332-6338. [PMID: 32953028 PMCID: PMC7472927 DOI: 10.1039/d0sc01853h] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/30/2020] [Indexed: 01/05/2023] Open
Abstract
Direct analyses of crude reaction mixtures have been carried out using molecular rotational resonance (MRR) spectroscopy. Two examples are presented, a demonstration application in photocatalytic CH-arylation as well as generation of an intermediate in a natural product synthesis. In both cases, the reaction can proceed at more than one site, leading to a mixture of regioisomers that can be challenging to distinguish. MRR structural parameters were calculated for the low lying conformers for the desired compounds, and then compared to the experimental spectra of the crude mixtures to confirm the presence of these species. Next, quantitation was performed by comparing experimentally measured line intensities with simulations based on computed values for the magnitude and direction of the molecular dipole moment of each species. This identification and quantification was performed without sample purification and without isolated standards of the compounds of interest. The values obtained for MRR quantitation were in good agreement with the chromatographic values. Finally, previously unknown impurities were discovered within the photocatalytic CH-arylation work. This paper demonstrates the utility of MRR as a reaction characterization tool to simplify analytical workflows.
Collapse
Affiliation(s)
- Leo A Joyce
- Department of Process Research & Development , Merck & Co., Inc. , Rahway , NJ 07065 , USA .
| | - Danielle M Schultz
- Department of Process Research & Development , Merck & Co., Inc. , Rahway , NJ 07065 , USA .
| | - Edward C Sherer
- Department of Computational and Structural Chemistry , Merck & Co., Inc. , Rahway , NJ 07065 , USA
| | - Justin L Neill
- BrightSpec, Inc. , 770 Harris St., Suite 104b , Charlottesville , VA 22904 , USA .
| | - Reilly E Sonstrom
- Department of Chemistry , University of Virginia , McCormick Road , Charlottesville , VA 22904 , USA
| | - Brooks H Pate
- Department of Chemistry , University of Virginia , McCormick Road , Charlottesville , VA 22904 , USA
| |
Collapse
|
24
|
Gupta S, Singh I, Sharma AK, Kumar P. Ultrashort Peptide Self-Assembly: Front-Runners to Transport Drug and Gene Cargos. Front Bioeng Biotechnol 2020; 8:504. [PMID: 32548101 PMCID: PMC7273840 DOI: 10.3389/fbioe.2020.00504] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/29/2020] [Indexed: 12/18/2022] Open
Abstract
The translational therapies to promote interaction between cell and signal come with stringent eligibility criteria. The chemically defined, hierarchically organized, and simpler yet blessed with robust intermolecular association, the peptides, are privileged to make the cut-off for sensing the cell-signal for biologics delivery and tissue engineering. The signature service and insoluble network formation of the peptide self-assemblies as hydrogels have drawn a spell of research activity among the scientists all around the globe in the past decades. The therapeutic peptide market players are anticipating promising growth opportunities due to the ample technological advancements in this field. The presence of the other organic moieties, enzyme substrates and well-established protecting groups like Fmoc and Boc etc., bring the best of both worlds. Since the large sequences of peptides severely limit the purification and their isolation, this article reviews the account of last 5 years' efforts on novel approaches for formulation and development of single molecule amino acids, ultra-short peptide self-assemblies (di- and tri- peptides only) and their derivatives as drug/gene carriers and tissue-engineering systems.
Collapse
Affiliation(s)
- Seema Gupta
- Chemistry Department, Acharya Narendra Dev College, University of Delhi, New Delhi, India
| | - Indu Singh
- Chemistry Department, Acharya Narendra Dev College, University of Delhi, New Delhi, India
- Nucleic Acids Research Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Ashwani K. Sharma
- Nucleic Acids Research Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Pradeep Kumar
- Nucleic Acids Research Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| |
Collapse
|
25
|
Yang TQ, Peng B, Shan BQ, Zong YX, Jiang JG, Wu P, Zhang K. Origin of the Photoluminescence of Metal Nanoclusters: From Metal-Centered Emission to Ligand-Centered Emission. NANOMATERIALS 2020; 10:nano10020261. [PMID: 32033058 PMCID: PMC7075164 DOI: 10.3390/nano10020261] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/26/2020] [Accepted: 01/29/2020] [Indexed: 12/17/2022]
Abstract
Recently, metal nanoclusters (MNCs) emerged as a new class of luminescent materials and have attracted tremendous interest in the area of luminescence-related applications due to their excellent luminous properties (good photostability, large Stokes shift) and inherent good biocompatibility. However, the origin of photoluminescence (PL) of MNCs is still not fully understood, which has limited their practical application. In this mini-review, focusing on the origin of the photoemission emission of MNCs, we simply review the evolution of luminescent mechanism models of MNCs, from the pure metal-centered quantum confinement mechanics to ligand-centered p band intermediate state (PBIS) model via a transitional ligand-to-metal charge transfer (LMCT or LMMCT) mechanism as a compromise model.
Collapse
Affiliation(s)
| | | | | | | | | | - Peng Wu
- Correspondence: (P.W.); (K.Z.)
| | | |
Collapse
|
26
|
Shida N, Imada Y, Okada Y, Chiba K. Mechanistic Insights on Concentrated Lithium Salt/Nitroalkane Electrolyte Based on Analogy with Fluorinated Alcohols. European J Org Chem 2020. [DOI: 10.1002/ejoc.201901576] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Naoki Shida
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu 183-8509 Tokyo Japan
| | - Yasushi Imada
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu 183-8509 Tokyo Japan
| | - Yohei Okada
- Department of Chemical Engineering; Tokyo University of Agriculture and Technology; 2-24-16 Naka-cho, Koganei 184-8588 Tokyo Japan
| | - Kazuhiro Chiba
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; 3-5-8 Saiwai-cho, Fuchu 183-8509 Tokyo Japan
| |
Collapse
|
27
|
P band intermediate state (PBIS) tailors photoluminescence emission at confined nanoscale interface. Commun Chem 2019. [DOI: 10.1038/s42004-019-0233-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
AbstractThe availability of a range of excited states has endowed low dimensional quantum nanostructures with interesting luminescence properties. However, the origin of photoluminescence emission is still not fully understood, which has limited its practical application. Here we judiciously manipulate the delicate surface ligand interactions at the nanoscale interface of a single metal nanocluster, the superlattice, and mesoporous materials. The resulting interplay of various noncovalent interactions leads to a precise modulation of emission colors and quantum yield. A new p-band state, resulting from the strong overlapping of p orbitals of the heteroatoms (O, N, and S) bearing on the targeting ligands though space interactions, is identified as a dark state to activate the triplet state of the surface aggregated chromophores. The UV-Visible spectra calculated by time-dependent density functional theory (TD-DFT) are in quantitative agreement with the experimental adsorption spectra. The energy level of the p-band center is very sensitive to the local proximity ligand chromophores at heterogeneous interfaces.
Collapse
|
28
|
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
| |
Collapse
|
29
|
Zheng H, Ye H, Yu X, You L. Interplay between n→π* Interactions and Dynamic Covalent Bonds: Quantification and Modulation by Solvent Effects. J Am Chem Soc 2019; 141:8825-8833. [PMID: 31075197 DOI: 10.1021/jacs.9b01006] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Orbital donor-acceptor interactions play critical roles throughout chemistry, and hence, their regulation and functionalization are of great significance. Herein we demonstrate for the first time the investigation of n→π* interactions through the strategy of dynamic covalent chemistry (DCC), and we further showcase its use in the stabilization of imine. The n→π* interaction between donor X and acceptor aldehyde/imine within 2-X-2'-formylbiphenyl derivatives was found to significantly influence the thermodynamics of imine exchange. The orbital interaction was then quantified through imine exchange, the equilibrium of which was successfully correlated with the difference in natural bond orbital stabilization energy of n→π* interactions of aldehyde and its imine. Moreover, the examination of solvent effects provided insights into the distinct feature of the modulation of n→π* interaction with aprotic and protic solvents. The n→π* interaction involving imine was enhanced in protic solvents due to hydrogen bonding with the solvent. This finding further enabled the stabilization of imine in purely aqueous solution. The strategies and results reported should find application in many fields, including molecular recognition, biological labeling, and asymmetric catalysis.
Collapse
Affiliation(s)
- Hao Zheng
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , Fuzhou 350002 , China.,College of Chemistry and Material Science , Fujian Normal University , Fuzhou 350007 China
| | - Hebo Ye
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , Fuzhou 350002 , China.,University of Chinese of Academy of Sciences , Beijing 100049 , China
| | - Xiaoxia Yu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , Fuzhou 350002 , China.,College of Chemistry and Material Science , Fujian Normal University , Fuzhou 350007 China
| | - Lei You
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , Fuzhou 350002 , China.,University of Chinese of Academy of Sciences , Beijing 100049 , China
| |
Collapse
|