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Rai Deka JK, Sahariah B, Sarma BK. Understanding the Cis-Trans Amide Bond Isomerization of N, N'-Diacylhydrazines to Develop Guidelines for A Priori Prediction of Their Most Stable Solution Conformers. J Org Chem 2024; 89:10419-10433. [PMID: 36700530 DOI: 10.1021/acs.joc.2c01891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
N,N'-diacylhydrazines (R1CO-NR3-NR4-COR2) are a class of small molecules with a wide range of applications in chemistry and biology. They are structurally unique in the sense that their two amide groups are connected via a N-N single bond, and as a result, these molecules can exist in eight different isomeric forms. Four of these are amide isomers [trans-trans (t-t), trans-cis (t-c), cis-trans (c-t), and cis-cis (c-c)] arising from C-N bond restricted rotation. In addition, each of these amide isomers can exist in two different isomeric forms due to N-N bond restricted rotation, especially when R3 and R4 groups are relatively bigger. Herein, we have systematically investigated the conformations of 55 N,N'-diacylhydrazines using a combination of solution NMR spectroscopy, X-ray crystallography, and density functional theory calculations. Our data suggest that when the substituents R3 and R4 on the nitrogen atoms are both hydrogens. These molecules prefer twisted trans-trans (t-t) (>90%) geometries (H-N-C═O ∼ 180°), whereas the N-alkylated and N,N'-dialkylated molecules prefer twisted trans-cis (t-c) geometries. Herein, we have analyzed the stabilization of the various isomers of these molecules in light of steric and stereoelectronic effects. We provide a guideline to a priori predict the most stable conformers of the N,N'-diacylhydrazines just by examining their substituents (R1-R4).
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Affiliation(s)
- Jugal Kishore Rai Deka
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore 560064, India
| | - Biswajit Sahariah
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore 560064, India
| | - Bani Kanta Sarma
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore 560064, India
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2
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Li M, Tian X, Du W, Wang X, Lei J, Gao T, Zou S, Xu X, Wang H, Chen J, Gou Q. Decrypting the critical point of internal rotation of formaldehyde: A rotational study of the acrolein-formaldehyde complex. J Chem Phys 2024; 160:234303. [PMID: 38884398 DOI: 10.1063/5.0211674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/31/2024] [Indexed: 06/18/2024] Open
Abstract
The rotational spectrum of an acrolein-formaldehyde complex has been characterized using pulsed jet Fourier transform microwave spectroscopy complemented with quantum chemical calculations. One isomer has been observed in pulsed jets, which is stabilized by a dominant O=C⋯O tetrel bond (n → π* interaction) and a secondary C-H⋯O hydrogen bond. Splittings arising from the internal rotation of formaldehyde around its C2v axis were also observed, from which its V2 barrier was evaluated. It seems that when V2 equals or exceeds 4.61 kJ mol-1, no splitting of the spectral lines of the rotational spectrum was observed. The nature of the non-covalent interactions of the target complex is elucidated through natural bond orbital analysis. These findings contribute to a deeper understanding on the non-covalent interactions within the dimeric complex formed by two aldehydes.
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Affiliation(s)
- Meiyue Li
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China
| | - Xiao Tian
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China
| | - Weiping Du
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China
| | - Xiujuan Wang
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China
| | - Juncheng Lei
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China
| | - Tianyue Gao
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China
| | - Siyu Zou
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China
| | - Xuefang Xu
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China
| | - Hao Wang
- State Key Laboratory of Coal Conversion, Institute of Coal Chemistry, Chinese Academy of Sciences, Taoyuan South Rd. 27, Taiyuan 030001, Shanxi, China
| | - Junhua Chen
- School of Pharmacy, Guizhou Medical University, Guiyang 561113, Guizhou, China
| | - Qian Gou
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China
- School of Chemistry and Chemical Engineering, Chongqing Key Laboratory of Chemical Theory and Mechanism, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China
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3
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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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4
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Zhao W, Gao M, Kong L, Yu S, Zhao C, Chen C. Chirality-Regulated Clusteroluminescence in Polypeptides. Biomacromolecules 2024; 25:1897-1905. [PMID: 38330502 DOI: 10.1021/acs.biomac.3c01328] [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: 02/10/2024]
Abstract
The low emission efficiency of clusteroluminogens restricts their practical applications in the fields of sensors and biological imaging. In this work, the clusteroluminescence of ordered/disordered polypeptides was observed, and the photoluminescence (PL) intensity of polypeptides can be modulated by the chirality of amino acid residues. Polyglutamates with different chiral compositions were synthesized, and the racemic polypeptides exhibited a significantly higher PL intensity than the enantiopure ones. This emission originates from the n-π* transition between C═O groups of polypeptides and is enhanced by clusterization of polypeptides. CD and Fourier transform infrared spectra demonstrated that the enantiopure and racemic polypeptides form α-helix and random coil structures, respectively. The disordered polypeptides can form more chain entanglements and interchain interactions because of their high flexibility, leading to more clusterizations and stronger PL intensity. The rigidity of ordered helical structures restrains the chain entanglements, and the formation of intrachain hydrogen bonds between amide groups of the backbone impairs the interchain interaction between polypeptides, resulting in lower PL intensity. The PL intensity of the polypeptides can also be manipulated by the addition of urea or trifluoroacetic acid. Our study not only elucidates the chirality/order-based structure-property relationship of clusteroluminescence in peptide-based polymers but also offers implications for the rational design of fluorescent peptides/proteins.
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Affiliation(s)
- Wangtao Zhao
- School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Mei Gao
- School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Liufen Kong
- School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Shunfeng Yu
- School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Chuanzhuang Zhao
- School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Chongyi Chen
- School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
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5
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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.
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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
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6
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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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7
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Babu G, Das A, Chakrabarty A, Chowdhury G, Goswami M. Criegee Intermediate-Mediated Oxidation of Dimethyl Disulfide: Effect of Formic Acid and Its Atmospheric Relevance. J Phys Chem A 2023; 127:8415-8426. [PMID: 37782474 DOI: 10.1021/acs.jpca.3c04730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
The oxidation-reduction reactions of disulfides are important in both chemistry and biology. Dimethyl disulfide (DMDS), the smallest reduced sulfur species with a disulfide bond, is emitted in significant quantities from natural sources and contributes to the formation of aerosols and hazardous haze. Although atmospheric removal of DMDS via the reactions with OH or NO3 radicals and photolysis is known, the reactions of DMDS with other atmospheric oxidants are yet to be explored. Herein, using quantum chemical calculations, we explored the reactions of DMDS with CH2OO (formaldehyde oxide) and other methyl-substituted Criegee intermediates. The various reaction pathways evaluated were found to have positive energy barriers. However, in the presence of formic acid, a direct oxygen-transfer pathway leading to the corresponding sulfoxide (CH3SS(O)CH3) was found to proceed through a submerged transition state below the separated reactants. Calculations for the methyl-substituted Criegee intermediates, particularly for anti-CH3CHOO, show a significant increase in the rate of the direct oxygen-transfer reaction when catalyzed by formic acid. The presence of formic acid also alters the mechanism and reduces the enthalpic barrier of a second pathway, forming thioformaldehyde and hydroperoxide without any rate enhancement. Our data indicated that, although Criegee intermediates are unlikely to be an important atmospheric sink of DMDS under normal conditions, in regions rich in DMDS and formic acid, the formic acid-catalyzed Criegee intermediate-mediated oxidation of DMDS via the direct oxygen-transfer pathway could lead to organic sulfur compounds contributing to atmospheric aerosol.
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Affiliation(s)
- Gowtham Babu
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore, TN 632014, India
| | - Arijit Das
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, KA 560012, India
| | - Anindita Chakrabarty
- Department of Life Science, School of Natural Sciences, Shiv Nadar Institution of Eminence Deemed to be University, Delhi-NCR, UP 201314, India
| | | | - Mausumi Goswami
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore, TN 632014, India
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8
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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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9
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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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10
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Adhav V, Saikrishnan K. The Realm of Unconventional Noncovalent Interactions in Proteins: Their Significance in Structure and Function. ACS OMEGA 2023; 8:22268-22284. [PMID: 37396257 PMCID: PMC10308531 DOI: 10.1021/acsomega.3c00205] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023]
Abstract
Proteins and their assemblies are fundamental for living cells to function. Their complex three-dimensional architecture and its stability are attributed to the combined effect of various noncovalent interactions. It is critical to scrutinize these noncovalent interactions to understand their role in the energy landscape in folding, catalysis, and molecular recognition. This Review presents a comprehensive summary of unconventional noncovalent interactions, beyond conventional hydrogen bonds and hydrophobic interactions, which have gained prominence over the past decade. The noncovalent interactions discussed include low-barrier hydrogen bonds, C5 hydrogen bonds, C-H···π interactions, sulfur-mediated hydrogen bonds, n → π* interactions, London dispersion interactions, halogen bonds, chalcogen bonds, and tetrel bonds. This Review focuses on their chemical nature, interaction strength, and geometrical parameters obtained from X-ray crystallography, spectroscopy, bioinformatics, and computational chemistry. Also highlighted are their occurrence in proteins or their complexes and recent advances made toward understanding their role in biomolecular structure and function. Probing the chemical diversity of these interactions, we determined that the variable frequency of occurrence in proteins and the ability to synergize with one another are important not only for ab initio structure prediction but also to design proteins with new functionalities. A better understanding of these interactions will promote their utilization in designing and engineering ligands with potential therapeutic value.
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11
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Yin C, Lu H, Ye H, Feng Z, Zou H, Zhang M, You L. Double n→π* Interactions with One Electron Donor: Structural and Mechanistic Insights. Org Lett 2023; 25:1470-1475. [PMID: 36856609 DOI: 10.1021/acs.orglett.3c00205] [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
Double n→π* interactions between one common electron donor of the carbonyl oxygen and two individual acceptor aldehyde/imine units are presented. The structural and mechanistic insights were revealed through a collection of experimental and computational evidence. The orientation and further energetic dependence of orbital interactions were facilely regulated by the size of cyclic urea scaffolds, the bulkiness of aldehydes/imines, and the flexibility of imine macrocycles.
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Affiliation(s)
- Chaowei Yin
- 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 Academy of Sciences, Beijing 100049, China
| | - Hanwei Lu
- 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 Academy of Sciences, Beijing 100049, 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
| | - Zelin Feng
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Hanxun Zou
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Meilan Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, 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 Academy of Sciences, Beijing 100049, China
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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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13
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Involvement of the -C(O)-CH=CH- linker chain in different π interactions in crystalline chalcones, (2E)-phenyl-C(C=O)-CH=CH-benzene derivatives. Importance of anti-parallel layered motifs in benzyloxy substituted compounds. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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14
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Araszczuk AM, D'Amato A, Schettini R, Costabile C, Della Sala G, Pierri G, Tedesco C, De Riccardis F, Izzo I. Macrocyclic Triazolopeptoids: A Promising Class of Extended Cyclic Peptoids. Org Lett 2022; 24:7752-7756. [PMID: 36223077 DOI: 10.1021/acs.orglett.2c03062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Head-to-tail cyclization of linear oligoamides containing 4-benzylaminomethyl-1H-1,2,3-triazol-1-yl acetic acid monomers afforded a novel class of "extended macrocyclic peptoids". The identification of the conformation in solution for a cyclodimer and the X-ray crystal structure of a cyclic tetraamide are reported.
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Affiliation(s)
- Alicja M Araszczuk
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, Fisciano, SA 84084, Italy
| | - Assunta D'Amato
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, Fisciano, SA 84084, Italy
| | - Rosaria Schettini
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, Fisciano, SA 84084, Italy
| | - Chiara Costabile
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, Fisciano, SA 84084, Italy
| | - Giorgio Della Sala
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, Fisciano, SA 84084, Italy
| | - Giovanni Pierri
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, Fisciano, SA 84084, Italy
| | - Consiglia Tedesco
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, Fisciano, SA 84084, Italy
| | - Francesco De Riccardis
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, Fisciano, SA 84084, Italy
| | - Irene Izzo
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, via Giovanni Paolo II, 132, Fisciano, SA 84084, Italy
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15
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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.
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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.
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16
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Mitra D, Das Mohapatra PK. In silico comparative structural and compositional analysis of glycoproteins of RSV to study the nature of stability and transmissibility of RSV A. SYSTEMS MICROBIOLOGY AND BIOMANUFACTURING 2022; 3:312-327. [PMID: 38013803 PMCID: PMC9135598 DOI: 10.1007/s43393-022-00110-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/07/2022] [Accepted: 05/08/2022] [Indexed: 11/29/2022]
Abstract
The current scenario of COVID-19 makes us to think about the devastating diseases that kill so many people every year. Analysis of viral proteins contributes many things that are utterly useful in the evolution of therapeutic drugs and vaccines. In this study, sequence and structure of fusion glycoproteins and major surface glycoproteins of respiratory syncytial virus (RSV) were analysed to reveal the stability and transmission rate. RSV A has the highest abundance of aromatic residues. The Kyte-Doolittle scale indicates the hydrophilic nature of RSV A protein which leads to the higher transmission rate of this virus. Intra-protein interactions such as carbonyl interactions, cation-pi, and salt bridges were shown to be greater in RSV A compared to RSV B, which might lead to improved stability. This study discovered the presence of a network aromatic-sulphur interaction in viral proteins. Analysis of ligand binding pocket of RSV proteins indicated that drugs are performing better on RSV B than RSV A. It was also shown that increasing the number of tunnels in RSV A proteins boosts catalytic activity. This study will be helpful in drug discovery and vaccine development.
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Affiliation(s)
- Debanjan Mitra
- Department of Microbiology, Raiganj University, Raiganj, WB India
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17
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Bhandary S, Pathigoolla A, Madhusudhanan MC, Sureshan KM. Azide–Alkyne Interactions: A Crucial Attractive Force for Their Preorganization for Topochemical Cycloaddition Reaction. Chemistry 2022; 28:e202200820. [DOI: 10.1002/chem.202200820] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Indexed: 12/17/2022]
Affiliation(s)
- Subhrajyoti Bhandary
- School of Chemistry Indian Institute of Science Education and Research Thiruvananthapuram Kerala 695551 India
| | - Atchutarao Pathigoolla
- School of Chemistry Indian Institute of Science Education and Research Thiruvananthapuram Kerala 695551 India
| | - Mithun C. Madhusudhanan
- School of Chemistry Indian Institute of Science Education and Research Thiruvananthapuram Kerala 695551 India
| | - Kana M. Sureshan
- School of Chemistry Indian Institute of Science Education and Research Thiruvananthapuram Kerala 695551 India
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18
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O‧‧‧C═O interaction, its occurrence and implications for protein structure and folding. Proteins 2022; 90:1159-1169. [DOI: 10.1002/prot.26298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/21/2021] [Accepted: 01/04/2022] [Indexed: 11/07/2022]
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19
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Sampaio-Dias IE, Sousa CAD, Silva-Reis SC, Pinto da Silva L, Garcia-Mera X, Rodriguez-Borges JE. Isolation and Structural Characterization of Stable Carbamic-Carbonic Anhydrides: An Experimental and Computational Study. Org Chem Front 2022. [DOI: 10.1039/d2qo00038e] [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
Carbamic-carbonic anhydrides are elusive species that have been only indirectly detected under controlled conditions. This functional group is transiently formed during the reaction of secondary amines with anhydrides in the...
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20
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Mehreen S, Zia M, Khan A, Hussain J, Ullah S, Anwar MU, Al-Harrasi A, Naseer MM. Phenoxy pendant isatins as potent α-glucosidase inhibitors: reciprocal carbonyl⋯carbonyl interactions, antiparallel π⋯π stacking driven solid state self-assembly and biological evaluation. RSC Adv 2022; 12:20919-20928. [PMID: 35919179 PMCID: PMC9302069 DOI: 10.1039/d2ra03307k] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/02/2022] [Indexed: 11/28/2022] Open
Abstract
Carbonyl–carbonyl (CO⋯CO) interactions are recently explored noncovalent interactions of significant interest owing to their role in the stability of biomacromolecules. Currently, substantial efforts are being made to understand the nature of these interactions. In this study, twelve phenoxy pendant isatins 1–12 have been evaluated for their α-glucosidase inhibitory potential in addition to the analysis of X-ray single crystals of 4 and 9. Both compounds 4 and 9 showed intriguing and unique self-assembled structures. The CO⋯CO and antiparallel displaced π⋯π stacking interactions are mainly involved in the formation of 1D-stair like supramolecular chains of 4 whereas antiparallel π⋯π stacking interactions drive the formation of 1D-columnar stacks of 9. These compounds not only highlight the potential of the isatin moiety in forming strong CO⋯CO and antiparallel π⋯π stacking interactions but also are interesting models to provide considerable insight into the nature of these interactions. The in vitro biological studies revealed that all twelve phenoxy pendant isatins 1–12 are highly potent inhibitors of α-glucosidase enzyme with IC50 values ranging from 5.32 ± 0.17 to 150.13 ± 0.62 μM, showing many fold more potent activity than the standard drug, acarbose (IC50 = 873.34 ± 1.67). Easy access and high α-glucosidase inhibition potential of these phenoxy pendant isatins 1–12 provide an attractive platform for finding more effective medication for controlling postprandial hyperglycemia. Carbonyl–carbonyl (CO⋯CO) interactions are recently explored noncovalent interactions of significant interest owing to their role in the stability of biomacromolecules.![]()
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Affiliation(s)
- Saba Mehreen
- Department of Chemistry, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Mehwash Zia
- Department of Chemistry, Allama Iqbal Open University, Islamabad-44000, Pakistan
| | - Ajmal Khan
- Natural and Medical Sciences Research Centre, University of Nizwa, Birkat Almouz 616, Oman
| | - Javid Hussain
- Department of Biological Sciences & Chemistry, College of Arts and Sciences, University of Nizwa, Nizwa, Oman
| | - Saeed Ullah
- Natural and Medical Sciences Research Centre, University of Nizwa, Birkat Almouz 616, Oman
| | - Muhammad U. Anwar
- Natural and Medical Sciences Research Centre, University of Nizwa, Birkat Almouz 616, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Centre, University of Nizwa, Birkat Almouz 616, Oman
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21
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Divya IS, Kandasamy S, Hasebe S, Sasaki T, Koshima H, Woźniak K, Varughese S. Flexible organic crystals. Understanding the tractable co-existence of elastic and plastic bending. Chem Sci 2022; 13:8989-9003. [PMID: 36091219 PMCID: PMC9365086 DOI: 10.1039/d2sc02969c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/04/2022] [Indexed: 11/25/2022] Open
Abstract
As an emerging class of flexible materials, mechanically bendable molecular crystals are broadly classified as elastic or plastic. Nevertheless, flexible organic crystals with mutually exclusive elastic and plastic traits, with contrasting structural requirements, co-existing under different stress settings are exceptional; hence, it is imperative to establish the concurring factors that beget this rare occurrence. We report a series of halogen-substituted benzil crystals showing elastic bending (within ∼2.45% strain), followed by elastoplastic deformation under ambient conditions. Under higher stress settings, they display exceptional plastic flexibility that one could bend, twist, or even coil around a capillary tube. X-ray diffraction, microscopy, and computational data reveal the microscopic and macroscopic basis for the exciting co-existence of elastic, elastoplastic, and plastic properties in the crystals. The layered molecular arrangement and the weak dispersive interactions sustaining the interlayer region provide considerable tolerance towards breaking and making upon engaging or releasing the external stress; it enables restoring the original state within the elastic strain. Comparative studies with oxalate compounds, wherein the twisted diketo moiety in benzil was replaced with a rigid and coplanar central oxalate moiety, enabled us to understand the effect of the anisotropy factor on the crystal packing induced by the C
Created by potrace 1.16, written by Peter Selinger 2001-2019
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O⋯C tetral interactions. The enhanced anisotropy depreciated the elastic domain, making the oxalate crystals more prone to plastic deformation. Three-point bending experiments and the determined Young's moduli further corroborate the co-existence of the elastic and plastic realm and highlight the critical role of the underlying structural elements that determine the elastic to plastic transformation. The work highlights the possible co-existence of orthogonal mechanical characteristics in molecular crystals and further construed the concurrent role of microscopic and macroscopic elements in attaining this exceptional mechanical trait. Structural and mechanical studies of benzil and oxalate crystals highlight the microscopic and macroscopic basis for the co-existence of orthogonal mechanical traits and the elastic to plastic transformation under different stress settings.![]()
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Affiliation(s)
- Indira S. Divya
- Chemical Science and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | | | - Shodai Hasebe
- Department of Advanced Science and Engineering, Waseda University, Tokyo 162-8480, Japan
| | - Toshiyuki Sasaki
- Graduate School of Nanobioscience, Yokohama City University, Kanagawa 236-0027, Japan
| | - Hideko Koshima
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo 162-0041, Japan
| | - Krzysztof Woźniak
- Crystallochemistry Laboratory, University of Warsaw, Warsaw 02-093, Poland
| | - Sunil Varughese
- Chemical Science and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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22
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Arcoria PJ, Ware RI, Makwana SV, Troya D, Etzkorn FA. Conformational Analysis of Fluoro-, Chloro-, and Proteo-Alkene Gly-Pro and Pro-Pro Isosteres to Mimic Collagen. J Phys Chem B 2021; 126:217-228. [PMID: 34968406 DOI: 10.1021/acs.jpcb.1c09180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Collagen is the most abundant human protein, with the canonical sequence (Gly-Pro-Hyp)n in its triple helix region. Cis-trans isomerization of the Xaa-Pro amide has made two of these amide bonds the target of alkene replacement: the Gly-Pro and the Pro-Hyp positions. The conformations of Gly-Pro and Pro-Pro (as a Pro-Hyp model) fluoro-, chloro-, and proteo-alkene mimic models were investigated computationally to determine whether these alkenes can stabilize the polyproline type II (PPII) conformation of collagen. Second-order Møller-Plesset (MP2) calculations with various basis sets were used to perform the conformational analyses and locate stationary points. The calculation results predict that fluoro- and chloro-alkene mimics of Gly-Pro and Pro-Pro can participate in n→π* donation to stabilize PPII conformations, yet they are poor n→π* acceptors, shifting the global minima away from PPII conformations. For the proteo-alkene mimics, the lack of significant n→π* interactions and unstable PPII-like geometries explains their known destabilization of the triple helix in collagen-like peptides.
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Affiliation(s)
- Paul J Arcoria
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Rachel I Ware
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Sunny V Makwana
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Diego Troya
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Felicia A Etzkorn
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
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23
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Sahariah B, Sarma BK. Deciphering the Backbone Noncovalent Interactions that Stabilize Polyproline II Conformation and Reduce cis Proline Abundance in Polyproline Tracts. J Phys Chem B 2021; 125:13394-13405. [PMID: 34851647 DOI: 10.1021/acs.jpcb.1c07875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proline (Pro) has a higher propensity to adopt cis amide geometry than the other natural amino acids, and a poly-Pro (poly-P) tract can adopt either a polyproline I (PPI, all cis amide) or a polyproline II (PPII, all trans amide) helical conformation. Recent studies have revealed a reduced abundance of cis amide geometry among the inner Pro residues of a poly-P tract. However, the forces that stabilize the polyproline helices and the reason for the higher trans amide propensity of the inner Pro residues of a poly-P tract are poorly understood. Herein, we have studied both Pro and non-Pro PPII helical sequences and identified the backbone noncovalent interactions that are crucial to the higher stability of the trans Pro-amide geometry and the preference for a PPII helical conformation. We show the presence of reciprocal CO···CO interactions that extend over the whole PPII helical region. Interestingly, the CO···CO interactions strengthen with the increase in the PPII helical chain length and the inner CO groups possess stronger CO···CO interactions, which could explain the reduced cis abundance of the inner Pro residues of a poly-P tract. We also identified a much stronger (∼0.9 kcal·mol-1) nO → σ*Cα-Cβ interaction between the N-terminal CO oxygen lone pair and the antibonding orbital (σ*) of their Cα-Cβ bonds. As the nO → σ*Cα-Cβ interaction is possible only in the trans isomers of Pro, this interaction should be crucial for the stabilization of a PPII helix. Finally, an unusual nN(amide) → σ*C-N interaction (∼0.3 kcal·mol-1) was observed between the peptidic nitrogen lone pair (nN) and the antibonding orbital (σ*C-N) of the subsequent C-terminal peptide C-N bond. We propose a cumulative effect of these interactions in the stabilization of a PPII helix.
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Affiliation(s)
- Biswajit Sahariah
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India
| | - Bani Kanta Sarma
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India
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24
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Zhang Y, Chen M, Zhou S, Han H, Zhang M, Qiu H. A carbonylative coupling approach to alkyl stationary phases with variable embedded carbamate groups for high-performance liquid chromatography. J Chromatogr A 2021; 1661:462718. [PMID: 34875517 DOI: 10.1016/j.chroma.2021.462718] [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: 07/13/2021] [Revised: 11/12/2021] [Accepted: 11/26/2021] [Indexed: 12/15/2022]
Abstract
A highly efficient carbonylative coupling method for the preparation of alkyl stationary phases with variable numbers of carbamate groups was established. The effectiveness of such method was verified through elemental analysis, X-ray photoelectron spectroscopy and solid-state 13C nuclear magnetic resonance spectroscopy of three as-synthesized stationary phases bearing different alkyl chains and different numbers of carbamate groups (octadecyl/one carbamate group, C18C; docosyl/three carbamate groups, C22C3; triacontyl/two carbamate groups, C30C2). The comparative evaluation of these stationary phases using a great variety of analytes, including three sets of isomers of alkylbenzenes, two sets of standard mixtures of polycyclic aromatic hydrocarbons (SRM 1647e and 869b), nine polychlorinated biphenyls, fiveteen N-substituted ureas, ten sulfonylureas, five xanthines and some other phytonutrients, revealed their remarkable applicability in reversed-phase liquid chromatography. Notably, the intercalated carbamate groups rendered the resultant stationary phases compatible with 100% aqueous mobile phase. The suppression of silanol activity was positively related to the number of polar groups embedded in the bonded selector, and the smallest peak tailing factor (1.14) for amitriptyline was obtained by C22C3. The molecular shape-related selectivity was found to be more closely related to the length of the selector's aliphatic chain, as supported by the lowest αTBN/BaP value (0.31) by C30C2. These carbamate-embedded alkyl stationary phases constituted another class of polar-embedded stationary phases possessing a single type of functional ligand.
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Affiliation(s)
- Yujie Zhang
- School of Chemistry and Chemical Engineering, Huaiyin Normal University, Huai'an, 223000, China; CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Min Chen
- Jiangsu Hanbon Science & Technology Co., Ltd., Huai'an, 223000, China
| | - Shouyong Zhou
- School of Chemistry and Chemical Engineering, Huaiyin Normal University, Huai'an, 223000, China
| | - Haifeng Han
- Jiangsu Hanbon Science & Technology Co., Ltd., Huai'an, 223000, China; CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Mingliang Zhang
- Jiangsu Hanbon Science & Technology Co., Ltd., Huai'an, 223000, China; CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.
| | - Hongdeng Qiu
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China; College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China.
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25
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Enabling three-dimensional porous architectures via carbonyl functionalization and molecular-specific organic-SERS platforms. Nat Commun 2021; 12:6119. [PMID: 34675208 PMCID: PMC8531383 DOI: 10.1038/s41467-021-26385-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/28/2021] [Indexed: 11/21/2022] Open
Abstract
Molecular engineering via functionalization has been a great tool to tune noncovalent intermolecular interactions. Herein, we demonstrate three-dimensional highly crystalline nanostructured D(C7CO)-BTBT films via carbonyl-functionalization of a fused thienoacene π-system, and strong Raman signal enhancements in Surface-Enhanced Raman Spectroscopy (SERS) are realized. The small molecule could be prepared on the gram scale with a facile synthesis-purification. In the engineered films, polar functionalization induces favorable out-of-plane crystal growth via zigzag motif of dipolar C = O···C = O interactions and hydrogen bonds, and strengthens π-interactions. A unique two-stage film growth behavior is identified with an edge-on-to-face-on molecular orientation transition driven by hydrophobicity. The analysis of the electronic structures and the ratio of the anti-Stokes/Stokes SERS signals suggests that the π-extended/stabilized LUMOs with varied crystalline face-on orientations provide the key properties in the chemical enhancement mechanism. A molecule-specific Raman signal enhancement is also demonstrated on a high-LUMO organic platform. Our results demonstrate a promising guidance towards realizing low-cost SERS-active semiconducting materials, increasing structural versatility of organic-SERS platforms, and advancing molecule-specific sensing via molecular engineering. Nanostructured films of organic semiconductors with low lying LUMO orbitals can enhance Raman signals via a chemical enhancement mechanism but currently the material choice is limited to fluorinated oligothiophenes. Here, the authors investigate the growth of a porous thienoacene film enabled by carbonyls and demonstrate molecular specific organic-SERS platforms.
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26
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Deka JKR, Sahariah B, Sakpal SS, Bar AK, Bagchi S, Sarma BK. Evidence of an n N(amide) → π* Ar Interaction in N-Alkyl- N, N'-diacylhydrazines. Org Lett 2021; 23:7003-7007. [PMID: 33973795 DOI: 10.1021/acs.orglett.1c00834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
1,2-Dibenzoyl-1-tert-butylhydrazine (RH-5849) and related N-alkyl-N,N'-diacylhydrazines are environmentally benign insect growth regulators. Herein, we show that an unusual nN(amide) → π*Ar interaction mediated by a hydrazide amide nitrogen atom plays a crucial role in stabilizing their biologically active trans-cis (t-c) rotameric conformations. We provide NMR and IR spectroscopic evidence for the presence of these interactions, which is also supported by X-ray crystallographic and computational studies.
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Affiliation(s)
- Jugal Kishore Rai Deka
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh 201314, India
| | - Biswajit Sahariah
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India
| | - Sushil S Sakpal
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, Maharashtra, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Arun Kumar Bar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 501507, India
| | - Sayan Bagchi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, Maharashtra, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Bani Kanta Sarma
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India
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27
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de Zwart FJ, Reus B, Laporte AAH, Sinha V, de Bruin B. Metrical Oxidation States of 1,4-Diazadiene-Derived Ligands. Inorg Chem 2021; 60:3274-3281. [PMID: 33587616 PMCID: PMC8023656 DOI: 10.1021/acs.inorgchem.0c03685] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The
conventional method of assigning formal oxidation states (FOSs)
to metals and ligands is an important tool for understanding and predicting
the chemical reactivity, in particular, in catalysis research. For
complexes containing redox-noninnocent ligands, the oxidation state
of the ligand can be ambiguous (i.e., their spectroscopic oxidation
state can differ from the FOS) and thus frustrates the assignment
of the oxidation state of the metal. A quantitative correlation between
the empirical metric data of redox-active
ligands and their oxidation states using a metrical oxidation state
(MOS) model has been developed for catecholate- and amidophenoxide-derived
ligands by Brown. In the present work, we present a MOS model for
1,4-diazabutadiene (DADn) ligands. This
model is based on a similar approach as reported by Brown, correlating
the intra-ligand bond lengths of the DADn moiety in a quantitative manner with the MOS using geometrical information
from X-ray structures in the Cambridge Crystallographic Data Center
(CCDC) database. However, an accurate determination of the MOS of
these ligands turned out to be dependent on the coordination mode
of the DAD2– moiety, which can adopt both a planar
κ2-N2-geometry and a
η4-N2C2 π-coordination mode in (transition) metal complexes
in its doubly reduced, dianionic enediamide oxidation state. A reliable
MOS model was developed taking the intrinsic differences in intra-ligand
bond distances between these coordination modes of the DAD2– ligand into account. Three different models were defined and tested
using different geometric parameters (C=C → M distance,
M–N–C angle, and M–N–C–C torsion
angle) to describe the C=C backbone coordination with the metal
in the η4-N2-C2 π-coordination mode of the DAD2– ligand. Statistical analysis revealed that the C=C →
M distance best describes the η4-N2-C2 coordination mode using
a cutoff value of 2.46 Å for π-coordination. The developed
MOS model was used to validate the oxidation state assignment of elements
not contained within the training set (Sr, Yb, and Ho), thus demonstrating
the applicability of the MOS model to a wide range of complexes. Chromium
complexes with complex electronic structures were also shown to be
accurately described by MOS analysis. Furthermore, it is shown that
a combination of MOS analysis and FOD calculations provides an inexpensive
method to gain insight into the electronic structure of singlet spin
state (S = 0) [M(trop2dad)] transition-metal complexes
showing (potential) singlet biradical character. Assigning oxidation states to metals
and ligands is an important
tool for understanding and predicting the chemical reactivity. For
complexes containing redox-noninnocent ligands, the oxidation state
of the ligand can be ambiguous. We present a metrical oxidation state
model for 1,4-diazabutadiene ligands, correlating the intra-ligand
bond lengths with the oxidation state using information from X-ray
structures. This model accounts for the difference in bond length
distances between the different coordination modes of the fully reduced
ligand.
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Affiliation(s)
- Felix J de Zwart
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Bente Reus
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Annechien A H Laporte
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Vivek Sinha
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Bas de Bruin
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
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28
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Pierri G, Corno M, Macedi E, Voccia M, Tedesco C. Solid-State Conformational Flexibility at Work: Energetic Landscape of a Single Crystal-to-Single Crystal Transformation in a Cyclic Hexapeptoid. CRYSTAL GROWTH & DESIGN 2021; 21:897-907. [PMID: 33584152 PMCID: PMC7877721 DOI: 10.1021/acs.cgd.0c01244] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/05/2021] [Indexed: 05/10/2023]
Abstract
We describe the energetic landscape beyond the solid-state dynamic behavior of a cyclic hexapeptoid decorated with four propargyl and two methoxyethyl side chains, namely, cyclo-(Nme-Npa2)2, Nme = N-(methoxyethyl)glycine, Npa = N-(propargyl)glycine. By increasing the temperature above 40 °C, the acetonitrile solvate form 1A starts to release acetonitrile molecules and undergoes a reversible single crystal-to-single crystal transformation into crystal form 1B with a remarkable conformational change in the macrocycle: two propargyl side chains move by 113° to form an unprecedented "CH-π zipper". Then, upon acetonitrile adsorption, the "CH-π zipper" opens and the crystal form 1B transforms back to 1A. By conformational energy and lattice energy calculations, we demonstrate that the dramatic side-chain movement is a peculiar feature of the solid-state assembly and is determined by a backbone conformational change that leads to stabilizing CH···OC backbone-to-backbone interactions tightening the framework upon acetonitrile release. Weak interactions as CH···OC and CH-π bonds with the guest molecules are able to reverse the transformation, providing the energy contribution to unzip the framework. We believe that the underlined mechanism could be used as a model system to understand how external stimuli (as temperature, humidity, or volatile compounds) could determine conformational changes in the solid state.
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Affiliation(s)
- Giovanni Pierri
- Department
of Chemistry and Biology “A. Zambelli”, University of Salerno, Via Giovanni Paolo II, 84084 Fisciano, SA, Italy
| | - Marta Corno
- Department
of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Center, University of Turin, Via P. Giuria 7, 10125 Turin, Italy
| | - Eleonora Macedi
- Department
of Pure and Applied Science, University
of Urbino “Carlo Bo”, Via della Stazione 4, 61029 Urbino, Italy
| | - Maria Voccia
- Department
of Chemistry and Biology “A. Zambelli”, University of Salerno, Via Giovanni Paolo II, 84084 Fisciano, SA, Italy
| | - Consiglia Tedesco
- Department
of Chemistry and Biology “A. Zambelli”, University of Salerno, Via Giovanni Paolo II, 84084 Fisciano, SA, Italy
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29
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Sauceda HE, Vassilev-Galindo V, Chmiela S, Müller KR, Tkatchenko A. Dynamical strengthening of covalent and non-covalent molecular interactions by nuclear quantum effects at finite temperature. Nat Commun 2021; 12:442. [PMID: 33469007 PMCID: PMC7815839 DOI: 10.1038/s41467-020-20212-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 11/12/2020] [Indexed: 11/08/2022] Open
Abstract
Nuclear quantum effects (NQE) tend to generate delocalized molecular dynamics due to the inclusion of the zero point energy and its coupling with the anharmonicities in interatomic interactions. Here, we present evidence that NQE often enhance electronic interactions and, in turn, can result in dynamical molecular stabilization at finite temperature. The underlying physical mechanism promoted by NQE depends on the particular interaction under consideration. First, the effective reduction of interatomic distances between functional groups within a molecule can enhance the n → π* interaction by increasing the overlap between molecular orbitals or by strengthening electrostatic interactions between neighboring charge densities. Second, NQE can localize methyl rotors by temporarily changing molecular bond orders and leading to the emergence of localized transient rotor states. Third, for noncovalent van der Waals interactions the strengthening comes from the increase of the polarizability given the expanded average interatomic distances induced by NQE. The implications of these boosted interactions include counterintuitive hydroxyl-hydroxyl bonding, hindered methyl rotor dynamics, and molecular stiffening which generates smoother free-energy surfaces. Our findings yield new insights into the versatile role of nuclear quantum fluctuations in molecules and materials.
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Affiliation(s)
- Huziel E Sauceda
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg.
- Machine Learning Group, Technische Universität Berlin, 10587, Berlin, Germany.
- BASLEARN, BASF-TU joint Lab, Technische Universität Berlin, 10587, Berlin, Germany.
| | - Valentin Vassilev-Galindo
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg
| | - Stefan Chmiela
- Machine Learning Group, Technische Universität Berlin, 10587, Berlin, Germany
| | - Klaus-Robert Müller
- Machine Learning Group, Technische Universität Berlin, 10587, Berlin, Germany.
- Department of Artificial Intelligence, Korea University, Anam-dong, Seongbuk-gu, Seoul, 02841, Korea.
- Max Planck Institute for Informatics, Stuhlsatzenhausweg, 66123, Saarbrücken, Germany.
- Google Research, Brain team, Berlin, Germany.
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg.
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30
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Tang WK, Mu X, Li M, Martens J, Berden G, Oomens J, Chu IK, Siu CK. Formation of n → π + interaction facilitating dissociative electron transfer in isolated tyrosine-containing molecular peptide radical cations. Phys Chem Chem Phys 2021; 22:21393-21402. [PMID: 32940309 DOI: 10.1039/d0cp00533a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Long-range electron transfer in proteins can be rationalized as a sequential short-distance electron-hopping processes via amino acid residues having low ionization energy as relay stations. Tyrosine residues can serve as such redox-active intermediates through one-electron oxidation to form a π-radical cation at its phenol side chain. An electron transfer from a vicinal functional group to this π-electron hole completes an elementary step of charge migration. However, transient oxidized/reduced intermediates formed at those relay stations during electron transfer processes have not been observed. In this study, formation of analog reactive intermediates via electron donor-acceptor coupling is observed by using IRMPD action spectroscopy. An elementary charge migration at the molecular level in model tyrosine-containing peptide radical cations [M]˙+ in the gas phase is revealed with its unusual Cα-Cβ bond cleavage at the side chain of the N-terminal residue. This reaction is induced by the radical character of the N-terminal amino group (-NH2˙+) resulting from an n → π+ interaction between the nonbonding electron pair of NH2 (n) and the π-electron hole at the Tyr side chain (π+). The formation of -NH2˙+ is supported by the IRMPD spectrum showing a characteristic NH2 scissor vibration coupled with Tyr side-chain stretches at 1577 cm-1. This n → π+ interaction facilitates a dissociative electron transfer with NH2 as the relay station. The occurrence of this side-chain cleavage may be an indicator of the formation of reactive conformers featuring the n → π+ interaction.
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Affiliation(s)
- Wai Kit Tang
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China.
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31
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Structural basis for voltage-sensor trapping of the cardiac sodium channel by a deathstalker scorpion toxin. Nat Commun 2021; 12:128. [PMID: 33397917 PMCID: PMC7782738 DOI: 10.1038/s41467-020-20078-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 11/10/2020] [Indexed: 01/29/2023] Open
Abstract
Voltage-gated sodium (NaV) channels initiate action potentials in excitable cells, and their function is altered by potent gating-modifier toxins. The α-toxin LqhIII from the deathstalker scorpion inhibits fast inactivation of cardiac NaV1.5 channels with IC50 = 11.4 nM. Here we reveal the structure of LqhIII bound to NaV1.5 at 3.3 Å resolution by cryo-EM. LqhIII anchors on top of voltage-sensing domain IV, wedged between the S1-S2 and S3-S4 linkers, which traps the gating charges of the S4 segment in a unique intermediate-activated state stabilized by four ion-pairs. This conformational change is propagated inward to weaken binding of the fast inactivation gate and favor opening the activation gate. However, these changes do not permit Na+ permeation, revealing why LqhIII slows inactivation of NaV channels but does not open them. Our results provide important insights into the structural basis for gating-modifier toxin binding, voltage-sensor trapping, and fast inactivation of NaV channels.
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32
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Combes GF, Pellay FX, Radman M. [Common cause and mechanism for all pathologies of aging?]. Med Sci (Paris) 2020; 36:1129-1134. [PMID: 33296629 DOI: 10.1051/medsci/2020221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Health is harmony, aging and its diseases (are) functional disharmony at the molecular, cellular and tissue levels. Our observations lead us to think that there seems to be a common cause and a common mechanism for aging and its many and diverse diseases. This common cause is the oxidative damage to particular proteins emerging from a combination of imperfect folding and oxidative stress. This common cause jointly goes with the biological clock common to various age-related diseases, whose the incidence increases exponentially over time and causes 90% of human mortality. Pharmacological interventions on the common cause could avoid and simultaneously attenuate all degenerative and malignant diseases, as it is the natural case of super-centenarians.
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Affiliation(s)
- Guillaume F Combes
- Mediterranean Institute for Life Sciences (MedILS), Meštrovic΄evo šetalište 45, 21000 Split, Croatie - Naos Institute for Life Sciences, 355 rue Pierre-Simon Laplace, 13593 Aix-en-Provence, France - Inserm U1001, Université Paris-Descartes, Faculté de médecine Paris-Descartes, 24 rue du faubourg Saint-Jacques, 75014 Paris, France - Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM-REI), Interdisciplinary Center for Advanced Sciences and Technology (ICAST), Université de Split, Poljička cesta 35, 21000 Split, Croatie
| | - François-Xavier Pellay
- Mediterranean Institute for Life Sciences (MedILS), Meštrovic΄evo šetalište 45, 21000 Split, Croatie - Naos Institute for Life Sciences, 355 rue Pierre-Simon Laplace, 13593 Aix-en-Provence, France
| | - Miroslav Radman
- Mediterranean Institute for Life Sciences (MedILS), Meštrovic΄evo šetalište 45, 21000 Split, Croatie - Naos Institute for Life Sciences, 355 rue Pierre-Simon Laplace, 13593 Aix-en-Provence, France - Inserm U1001, Université Paris-Descartes, Faculté de médecine Paris-Descartes, 24 rue du faubourg Saint-Jacques, 75014 Paris, France - Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM-REI), Interdisciplinary Center for Advanced Sciences and Technology (ICAST), Université de Split, Poljička cesta 35, 21000 Split, Croatie
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33
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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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34
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Intermolecular Interactions in Crystal Structures of Imatinib-Containing Compounds. Int J Mol Sci 2020; 21:ijms21238970. [PMID: 33255944 PMCID: PMC7731260 DOI: 10.3390/ijms21238970] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 02/07/2023] Open
Abstract
Imatinib, one of the most used therapeutic agents to treat leukemia, is an inhibitor that specifically blocks the activity of tyrosine kinases. The molecule of imatinib is flexible and contains several functional groups able to take part in H-bonding and hydrophobic interactions. Analysis of molecular conformations for this drug was carried out using density functional theory calculations of rotation potentials along single bonds and by analyzing crystal structures of imatinib-containing compounds taken from the Cambridge Structural Database and the Protein Data Bank. Rotation along the N-C bond in the region of the amide group was found to be the reason for two relatively stable molecular conformations, an extended and a folded one. The role of various types of intermolecular interactions in stabilization of the particular molecular conformation was studied in terms of (i) the likelihood of H-bond formation, and (ii) their contribution to the Voronoi molecular surface. It is shown that experimentally observed hydrogen bonds are in accord with the likelihood of their formation. The number of H-bonds in ligand-receptor complexes surpasses that in imatinib salts due to the large number of donors and acceptors of H-bonding within the binding pocket of tyrosine kinases. Contribution of hydrophilic intermolecular interactions to the Voronoi molecular surface is similar for both conformations, while π...π stacking is more typical for the folded conformation of imatinib.
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35
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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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36
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Cincinelli R, Musso L, Guglielmi MB, La Porta I, Fucci A, Luca D'Andrea E, Cardile F, Colelli F, Signorino G, Darwiche N, Gervasoni S, Vistoli G, Pisano C, Dallavalle S. Novel adamantyl retinoid-related molecules with POLA1 inhibitory activity. Bioorg Chem 2020; 104:104253. [PMID: 32920362 DOI: 10.1016/j.bioorg.2020.104253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 02/08/2023]
Abstract
Atypical retinoids (AR) or retinoid-related molecules (RRMs) represent a promising class of antitumor compounds. Among AR, E-3-(3'-adamantan-1-yl-4'-hydroxybiphenyl-4-yl)acrylic acid (adarotene), has been extensively investigated. In the present work we report the results of our efforts to develop new adarotene-related atypical retinoids endowed also with POLA1 inhibitory activity. The effects of the synthesized compounds on cell growth were determined on a panel of human and hematological cancer cell lines. The most promising compounds showed antitumor activity against several tumor histotypes and increased cytotoxic activity against an adarotene-resistant cell line, compared to the parent molecule. The antitumor activity of a selected compound was evaluated on HT-29 human colon carcinoma and human mesothelioma (MM487) xenografts. Particularly significant was the in vivo activity of the compound as a single agent compared to adarotene and cisplatin, against pleural mesothelioma MM487. No reduction of mice body weight was observed, thus suggesting a higher tolerability with respect to the parent compound adarotene.
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Affiliation(s)
- Raffaella Cincinelli
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
| | - Loana Musso
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
| | | | | | | | | | | | | | | | - Nadine Darwiche
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Silvia Gervasoni
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, via Mangiagalli 25, Milano 20133, Italy
| | - Giulio Vistoli
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, via Mangiagalli 25, Milano 20133, Italy
| | - Claudio Pisano
- Biogem, Research Institute, Ariano Irpino, Avellino, Italy.
| | - Sabrina Dallavalle
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy.
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37
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Khatri B, Majumder P, Nagesh J, Penmatsa A, Chatterjee J. Increasing protein stability by engineering the n → π* interaction at the β-turn. Chem Sci 2020; 11:9480-9487. [PMID: 34094214 PMCID: PMC8161691 DOI: 10.1039/d0sc03060k] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Abundant n → π* interactions between adjacent backbone carbonyl groups, identified by statistical analysis of protein structures, are predicted to play an important role in dictating the structure of proteins. However, experimentally testing the prediction in proteins has been challenging due to the weak nature of this interaction. By amplifying the strength of the n → π* interaction via amino acid substitution and thioamide incorporation at a solvent exposed β-turn within the GB1 proteins and Pin 1 WW domain, we demonstrate that an n → π* interaction increases the structural stability of proteins by restricting the ϕ torsion angle. Our results also suggest that amino acid side-chain identity and its rotameric conformation play an important and decisive role in dictating the strength of an n → π* interaction. Amino acid residues adopt a right-handed α-helical conformation with increasing strength of the n → π* interaction. We also demonstrate a direct consequence of n → π* interactions on enhancing the structural stability of proteins.![]()
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Affiliation(s)
- Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - Puja Majumder
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - Jayashree Nagesh
- Solid State and Structural Chemistry Unit, Indian Institute of Science Bangalore India
| | - Aravind Penmatsa
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
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38
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Rahim A, Sahariah B, Baruah K, Deka JKR, Sarma BK. Solid-Phase Synthesis of Hybrid 2,5-Diketopiperazines Using Acylhydrazide, Carbazate, Semicarbazide, Amino Acid, and Primary Amine Submonomers. J Org Chem 2020; 85:2927-2937. [PMID: 32000488 DOI: 10.1021/acs.joc.9b02083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the solid-phase synthesis of N,N'-di(acylamino)-2,5-diketopiperazine, an acylhydrazide-based conformationally rigid 2,5-DKP scaffold having exocyclic N-N bonds. We also show that different combinations of acylhydrazides, carbazates, semicarbazides, amino acids, and primary amines can be used to synthesize a highly diverse collection of hybrid DKP molecules via the solid-phase submonomer synthesis route. Finally, we show incorporation of a methyl substituent in one of the carbon atoms of the DKP ring to generate chiral daa- and hybrid-DKPs without compromising the synthetic efficiency.
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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
| | - Kalpita Baruah
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh 201314, India
| | - Jugal Kishore Rai Deka
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh 201314, India
| | - Bani Kanta Sarma
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India
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39
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Chen H, Ye H, Hai Y, Zhang L, You L. n → π* interactions as a versatile tool for controlling dynamic imine chemistry in both organic and aqueous media. Chem Sci 2020; 11:2707-2715. [PMID: 34084329 PMCID: PMC8157614 DOI: 10.1039/c9sc05698j] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 01/31/2020] [Indexed: 11/21/2022] Open
Abstract
The imine bond holds a prominent place in supramolecular chemistry and materials science, and one issue is the stability of imines due to their electrophilic nature. Here we introduced ortho-carboxylate groups into a series of aromatic aldehydes/imines for dictating imine dynamic covalent chemistry (DCC) through n → π* interactions, one class of widespread and yet underused non-covalent interactions. The thermodynamically stabilizing role of carboxylate-aldehyde/imine n → π* interactions in acetonitrile was elucidated by the movement of the imine exchange equilibrium and further supported by crystal analysis. Computational studies provided mechanistic insights for n → π* interactions, the strength of which can surpass that of CH hydrogen bonding and is dependent on the orientation of interacting sites based on natural bond orbital analysis. Moreover, the substituent effect and the combination of recognition sites allowed additional means for modulation. Finally, to show the relevance of our findings ortho-carboxylate containing aldehydes were used to regulate imine formation/exchange in water, and modification of the N-terminus of amino acids and peptides was achieved in a neutral buffer. This work represents the latest example of weak interactions governing DCC and sets the stage for assembly and application studies.
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Affiliation(s)
- Hang Chen
- 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 Academy of Sciences Beijing 100049 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
| | - Yu Hai
- 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 Academy of Sciences Beijing 100049 China
| | - Ling Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences Fuzhou 350002 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 Academy of Sciences Beijing 100049 China
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40
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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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41
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Zhang Z. An X-shaped cyano–carbonyl interaction on the polar surface of (cyanoacetyl)hydrazones. CrystEngComm 2020. [DOI: 10.1039/d0ce00359j] [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
An X-shaped CN⋯CO interaction, which plays a critical role in dictating the molecule conformation and crystal packing patterns, has been found to occur on the polar surface of (cyanoacetyl)hydrazones, and is rationalized by density functional theory calculations.
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Affiliation(s)
- Zhenfeng Zhang
- School of Chemistry and Chemical Engineering
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals
- Henan Key Laboratory of Organic Functional Molecule and Drug Innovation
- Key Laboratory of Green Chemical Media and Reactions
- Ministry of Education
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42
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Unravelling the Importance of H bonds, σ–hole and π–hole-Directed Intermolecular Interactions in Nature. J Indian Inst Sci 2019. [DOI: 10.1007/s41745-019-00144-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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43
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Hubbs AF, Kreiss K, Cummings KJ, Fluharty KL, O'Connell R, Cole A, Dodd TM, Clingerman SM, Flesher JR, Lee R, Pagel S, Battelli LA, Cumpston A, Jackson M, Kashon M, Orandle MS, Fedan JS, Sriram K. Flavorings-Related Lung Disease: A Brief Review and New Mechanistic Data. Toxicol Pathol 2019; 47:1012-1026. [PMID: 31645208 DOI: 10.1177/0192623319879906] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Flavorings-related lung disease is a potentially disabling and sometimes fatal lung disease of workers making or using flavorings. First identified almost 20 years ago in microwave popcorn workers exposed to butter-flavoring vapors, flavorings-related lung disease remains a concern today. In some cases, workers develop bronchiolitis obliterans, a severe form of fixed airways disease. Affected workers have been reported in microwave popcorn, flavorings, and coffee production workplaces. Volatile α-dicarbonyl compounds, particularly diacetyl (2,3-butanedione) and 2,3-pentanedione, are implicated in the etiology. Published studies on diacetyl and 2,3-pentanedione document their ability to cause airway epithelial necrosis, damage biological molecules, and perturb protein homeostasis. With chronic exposure in rats, they produce airway fibrosis resembling bronchiolitis obliterans. To add to this knowledge, we recently evaluated airway toxicity of the 3-carbon α-dicarbonyl compound, methylglyoxal. Methylglyoxal inhalation causes epithelial necrosis at even lower concentrations than diacetyl. In addition, we investigated airway toxicity of mixtures of diacetyl, acetoin, and acetic acid, common volatiles in butter flavoring. At ratios comparable to workplace scenarios, the mixtures or diacetyl alone, but not acetic acid or acetoin, cause airway epithelial necrosis. These new findings add to existing data to implicate α-dicarbonyl compounds in airway injury and flavorings-related lung disease.
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Affiliation(s)
- Ann F Hubbs
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Kathleen Kreiss
- Respiratory Health Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Kristin J Cummings
- Respiratory Health Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Kara L Fluharty
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Ryan O'Connell
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA.,West Virginia University, Morgantown, WV, USA. Cummings is now with California Department of Public Health, Richmond, CA, USA. O'Connell is now with Department of Biochemistry, West Virginia, University, Morgantown, WV, USA. Flesher is now with Department of Biology, West Virginia University, Morgantown, WV, USA. Cole is now with Department of Pediatrics-Hematology/Oncology, University of Colorado School of Medicine, Aurora, CO, USA. Kreiss (retired) is in Sitka, AK, USA
| | - Allison Cole
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA.,Respiratory Health Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Tiana M Dodd
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Sidney M Clingerman
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA.,West Virginia University, Morgantown, WV, USA. Cummings is now with California Department of Public Health, Richmond, CA, USA. O'Connell is now with Department of Biochemistry, West Virginia, University, Morgantown, WV, USA. Flesher is now with Department of Biology, West Virginia University, Morgantown, WV, USA. Cole is now with Department of Pediatrics-Hematology/Oncology, University of Colorado School of Medicine, Aurora, CO, USA. Kreiss (retired) is in Sitka, AK, USA
| | - Jordan R Flesher
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA.,West Virginia University, Morgantown, WV, USA. Cummings is now with California Department of Public Health, Richmond, CA, USA. O'Connell is now with Department of Biochemistry, West Virginia, University, Morgantown, WV, USA. Flesher is now with Department of Biology, West Virginia University, Morgantown, WV, USA. Cole is now with Department of Pediatrics-Hematology/Oncology, University of Colorado School of Medicine, Aurora, CO, USA. Kreiss (retired) is in Sitka, AK, USA
| | - Rebecca Lee
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA.,West Virginia University, Morgantown, WV, USA. Cummings is now with California Department of Public Health, Richmond, CA, USA. O'Connell is now with Department of Biochemistry, West Virginia, University, Morgantown, WV, USA. Flesher is now with Department of Biology, West Virginia University, Morgantown, WV, USA. Cole is now with Department of Pediatrics-Hematology/Oncology, University of Colorado School of Medicine, Aurora, CO, USA. Kreiss (retired) is in Sitka, AK, USA
| | - Samantha Pagel
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA.,West Virginia University, Morgantown, WV, USA. Cummings is now with California Department of Public Health, Richmond, CA, USA. O'Connell is now with Department of Biochemistry, West Virginia, University, Morgantown, WV, USA. Flesher is now with Department of Biology, West Virginia University, Morgantown, WV, USA. Cole is now with Department of Pediatrics-Hematology/Oncology, University of Colorado School of Medicine, Aurora, CO, USA. Kreiss (retired) is in Sitka, AK, USA
| | - Lori A Battelli
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Amy Cumpston
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Mark Jackson
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Michael Kashon
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Marlene S Orandle
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Jeffrey S Fedan
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Krishnan Sriram
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
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44
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Taylor R, Wood PA. A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts. Chem Rev 2019; 119:9427-9477. [PMID: 31244003 DOI: 10.1021/acs.chemrev.9b00155] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The founding in 1965 of what is now called the Cambridge Structural Database (CSD) has reaped dividends in numerous and diverse areas of chemical research. Each of the million or so crystal structures in the database was solved for its own particular reason, but collected together, the structures can be reused to address a multitude of new problems. In this Review, which is focused mainly on the last 10 years, we chronicle the contribution of the CSD to research into molecular geometries, molecular interactions, and molecular assemblies and demonstrate its value in the design of biologically active molecules and the solid forms in which they are delivered. Its potential in other commercially relevant areas is described, including gas storage and delivery, thin films, and (opto)electronics. The CSD also aids the solution of new crystal structures. Because no scientific instrument is without shortcomings, the limitations of CSD research are assessed. We emphasize the importance of maintaining database quality: notwithstanding the arrival of big data and machine learning, it remains perilous to ignore the principle of garbage in, garbage out. Finally, we explain why the CSD must evolve with the world around it to ensure it remains fit for purpose in the years ahead.
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Affiliation(s)
- Robin Taylor
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
| | - Peter A Wood
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
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45
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Wenzell NA, Ganguly HK, Pandey AK, Bhatt MR, Yap GPA, Zondlo NJ. Electronic and Steric Control of n→π* Interactions: Stabilization of the α-Helix Conformation without a Hydrogen Bond. Chembiochem 2019; 20:963-967. [PMID: 30548564 PMCID: PMC6458595 DOI: 10.1002/cbic.201800785] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Indexed: 11/06/2022]
Abstract
The preferred conformations of peptides and proteins are dependent on local interactions that bias the conformational ensemble. The n→π* interaction between consecutive carbonyls promotes compact conformations, including the α-helix and polyproline II helix. In order to further understand the n→π* interaction and to develop methods to promote defined conformational preferences through acyl N-capping motifs, a series of peptides was synthesized in which the electronic and steric properties of the acyl group were modified. Using NMR spectroscopy, van't Hoff analysis of enthalpies, X-ray crystallography, and computational investigations, we observed that more electron-rich donor carbonyls (pivaloyl, iso-butyryl, propionyl) promote stronger n→π* interactions and more compact conformations than acetyl or less electron-rich donor carbonyls (methoxyacetyl, fluoroacetyl, formyl). X-ray crystallography indicates a strong, electronically tunable preference for the α-helix conformation, as observed directly on the φ and ψ torsion angles. Electron-donating acyl groups promote the α-helical conformation, even in the absence of the hydrogen bonding that stabilizes the α-helix. In contrast, electron-withdrawing acyl groups led to more extended conformations. More sterically demanding groups can promote trans amide bonds independent of the electronic effect on n→π* interactions. Chloroacetyl groups additionally promote n→π* interactions through the interaction of the chlorine lone pair with the proximal carbonyl π*. These data provide additional support for an important role of n→π* interactions in the conformational ensemble of disordered or unfolded proteins. Moreover, this work suggests that readily incorporated acyl N-capping motifs that modulate n→π* interactions may be employed rationally to promote conformational biases in peptides, with potential applications in molecular design and medicinal chemistry.
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Affiliation(s)
- Nicole A. Wenzell
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; ,
| | - Himal K. Ganguly
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; ,
| | - Anil K. Pandey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; ,
| | - Megh R. Bhatt
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; ,
| | - Glenn P. A. Yap
- 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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46
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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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47
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Singh SK, More S, Kumar S, Mishra KK, Ganesh KN, Das A. A conformation-specific IR spectroscopic signature for weak CO⋯CO n→π* interaction in capped 4R-hydroxyproline. Phys Chem Chem Phys 2019; 21:4755-4762. [DOI: 10.1039/c8cp07660j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
CO⋯CO n→π*-amide interaction in the monomeric building block of collagen is probed using conformation-specific IR spectroscopy.
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Affiliation(s)
- Santosh K. Singh
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER)
- Pune-411008
- India
| | - Shahaji More
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER)
- Tirupati-517507
- India
| | - Satish Kumar
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER)
- Pune-411008
- India
| | - Kamal K. Mishra
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER)
- Pune-411008
- India
| | - Krishna N. Ganesh
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER)
- Tirupati-517507
- India
| | - Aloke Das
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER)
- Pune-411008
- India
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48
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Fayzullin RR, Shteingolts SA, Lodochnikova OA, Mamedova VL, Korshin DE, Mamedov VA. Intermolecular head-to-head interaction of carbonyl groups in bicyclic hydrogen-bonded synthon based on β-hydroxy ketones. CrystEngComm 2019. [DOI: 10.1039/c8ce02132e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, we report a counterintuitive carbonyl–carbonyl interaction explored for crystalline (2RS,3RS)-1-aryl-2-bromo-3-hydroxy-3-(2-nitrophenyl)-propan-1-ones.
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Affiliation(s)
- Robert R. Fayzullin
- Arbuzov Institute of Organic and Physical Chemistry
- FRC Kazan Scientific Center of Russian Academy of Sciences
- Kazan 420088
- Russian Federation
| | - Sergey A. Shteingolts
- Arbuzov Institute of Organic and Physical Chemistry
- FRC Kazan Scientific Center of Russian Academy of Sciences
- Kazan 420088
- Russian Federation
| | - Olga A. Lodochnikova
- Arbuzov Institute of Organic and Physical Chemistry
- FRC Kazan Scientific Center of Russian Academy of Sciences
- Kazan 420088
- Russian Federation
| | - Vera L. Mamedova
- Arbuzov Institute of Organic and Physical Chemistry
- FRC Kazan Scientific Center of Russian Academy of Sciences
- Kazan 420088
- Russian Federation
| | - Dmitry E. Korshin
- Arbuzov Institute of Organic and Physical Chemistry
- FRC Kazan Scientific Center of Russian Academy of Sciences
- Kazan 420088
- Russian Federation
| | - Vakhid A. Mamedov
- Arbuzov Institute of Organic and Physical Chemistry
- FRC Kazan Scientific Center of Russian Academy of Sciences
- Kazan 420088
- Russian Federation
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49
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Mundlapati VR, Sahoo DK, Bhaumik S, Jena S, Chandrakar A, Biswal HS. Noncovalent Carbon-Bonding Interactions in Proteins. Angew Chem Int Ed Engl 2018; 57:16496-16500. [DOI: 10.1002/anie.201811171] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Indexed: 12/14/2022]
Affiliation(s)
- V. Rao Mundlapati
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Dipak Kumar Sahoo
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Suman Bhaumik
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Subhrakant Jena
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Amol Chandrakar
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- 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
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
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50
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Mundlapati VR, Sahoo DK, Bhaumik S, Jena S, Chandrakar A, Biswal HS. Noncovalent Carbon-Bonding Interactions in Proteins. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201811171] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- V. Rao Mundlapati
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Dipak Kumar Sahoo
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Suman Bhaumik
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Subhrakant Jena
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Amol Chandrakar
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- 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
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
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