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Kumar B, Das T, Das S, Maniukiewicz W, Nesterov DS, Kirillov AM, Das S. Coupling 6-chloro-3-methyluracil with copper: structural features, theoretical analysis, and biofunctional properties. Dalton Trans 2021; 50:13533-13542. [PMID: 34505590 DOI: 10.1039/d1dt02018h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
As nucleobases in RNA and DNA, uracil and 5-methyluracil represent a recognized class of bioactive molecules and versatile ligands for coordination compounds with various biofunctional properties. In this study, 6-chloro-3-methyluracil (Hcmu) was used as an unexplored building block for the self-assembly generation of a new bioactive copper(II) complex, [Cu(cmu)2(H2O)2]·4H2O (1). This compound was isolated as a stable crystalline solid and fully characterized in solution and solid state by a variety of spectroscopic methods (UV-vis, EPR, fluorescence spectroscopy), cyclic voltammetry, X-ray diffraction, and DFT calculations. The structural, topological, H-bonding, and Hirshfeld surface features of 1 were also analyzed in detail. The compound 1 shows a distorted octahedral {CuN2O4} coordination environment with two trans cmu- ligands adopting a bidentate N,O-coordination mode. The monocopper(II) molecular units participate in strong H-bonding interactions with water molecules of crystallization, leading to structural 0D → 3D extension into a 3D H-bonded network with a tfz-d topology. Molecular docking and ADME analysis as well as antibacterial and antioxidant activity studies were performed to assess the bioactivity of 1. In particular, this compound exhibits a prominent antibacterial effect against Gram negative (E. coli, P. aeruginosa) and positive (S. aureus, B. cereus) bacteria. The obtained copper(II) complex also represents the first structurally characterized coordination compound derived from 6-chloro-3-methyluracil, thus introducing this bioactive building block into a family of uracil metal complexes with notable biofunctional properties.
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Affiliation(s)
- Brajesh Kumar
- Department of Chemistry, National Institute of Technology Patna, Ashok Rajpath, Patna 800005, India.
| | - Tushar Das
- Department of Chemistry, National Institute of Technology Patna, Ashok Rajpath, Patna 800005, India.
| | - Subhadeep Das
- Department of Life Science and Biotechnology, Jadavpur University, 188 Raja S.C. Mallick Rd, Kolkata 700032, India
| | - Waldemar Maniukiewicz
- Institute of General and Ecological Chemistry, Lodz University of Technology, Żeromskiego 116, Łódź, Poland
| | - Dmytro S Nesterov
- Centro de Química Estrutural and Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal.
| | - Alexander M Kirillov
- Centro de Química Estrutural and Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal. .,Research Institute of Chemistry, Peoples' Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya st., Moscow, 117198, Russian Federation
| | - Subrata Das
- Department of Chemistry, National Institute of Technology Patna, Ashok Rajpath, Patna 800005, India.
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Jana K, Wakchaure PD, Hussain N, Mukherjee D, Ganguly B. The mechanism of conversion of substituted glycals to chiral acenes via Diels-Alder reaction: a computational study. Org Biomol Chem 2021; 19:6353-6367. [PMID: 34231642 DOI: 10.1039/d1ob00408e] [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
Synthesis of linearly fused aromatic systems using a glycal-based diene with an aryne is a long-standing topic of interest in glycal chemistry. We have examined the mechanistic pathways for the transformation of substituted glycals to chiral fused aromatic cores via Diels-Alder (DA) reaction using the SMDACN-M06-2X/6-31G(d) level of theory. The DA reactions of E (1a) and Z (1a') forms of C-2 alkenyl glycal and an aryl glycal (1b) as a diene were examined with a benzyne intermediate generated as a dienophile. The computational results reveal that 1a and 1b can only be transformed into the fused aromatic cores by the base-catalyzed reaction because a [1,5] sigmatropic hydrogen shift is not feasible. The activation free energy barrier for the base-catalyzed proton abstraction process is 4.2 kcal mol-1 and there is almost no barrier for stereoisomeric 1a DA-complexes. The activation free energy barrier values for stereoisomeric 1b DA-complexes for the base-catalyzed proton abstraction process are 10.8 and 12.4 kcal mol-1. The appropriate orientation of glycal-ring-oxygen and hydrogen at the 5th position of Z (1a') forms of C-2 alkenyl glycal facilitates the [1,5] sigmatropic hydrogen shift; however, the base-catalyzed reaction is energetically more favored than the former case. The rate-determining step for 1a and 1a' is the ring-opening step (18.2 and 19.5 kcal mol-1 for the S-stereoisomer), whereas the DA adduct formation step is the rate-determining step for 1b (16.1 kcal mol-1 for the S-stereoisomer). The structural analysis reveals the formation of the preferred S-stereoisomer over the R-stereoisomer with the respective dienes.
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Affiliation(s)
- Kalyanashis Jana
- CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India. and Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh-201 002, India
| | - Padmaja D Wakchaure
- CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India. and Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh-201 002, India
| | - Nazar Hussain
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh-201 002, India and Natural Product Chemistry Division, Indian Institute of Integrative Medicine (IIIM), Jammu 180001, India
| | - Debaraj Mukherjee
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh-201 002, India and Natural Product Chemistry Division, Indian Institute of Integrative Medicine (IIIM), Jammu 180001, India
| | - Bishwajit Ganguly
- CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India. and Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh-201 002, India
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Su P, Tang Z, Wu W. Generalized Kohn‐Sham energy decomposition analysis and its applications. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1460] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Peifeng Su
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering Xiamen University Xiamen China
| | - Zhen Tang
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering Xiamen University Xiamen China
| | - Wei Wu
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering Xiamen University Xiamen China
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Wang P, Sun J, Yu Z, Han L, Liu T. Theoretical investigation on the palladium-catalyzed diastereoselective oxidative carbocyclization of enallenes assisted by hydroxyl group. J Organomet Chem 2019. [DOI: 10.1016/j.jorganchem.2019.04.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Jana K, Ganguly B. DFT Study To Explore the Importance of Ring Size and Effect of Solvents on the Keto-Enol Tautomerization Process of α- and β-Cyclodiones. ACS OMEGA 2018; 3:8429-8439. [PMID: 31458971 PMCID: PMC6644555 DOI: 10.1021/acsomega.8b01008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/18/2018] [Indexed: 06/01/2023]
Abstract
We have explored the effect of ring size on keto-enol tautomerization of α- and β-cyclodiones using the M062X-SMDaq/6-31+G(d,p)//M062X/6-31+G(d,p) level of theory. The calculated results show that the activation free energy barrier for the keto-enol tautomerization process of α-cyclopropanedione (1) is 54.9 kcal/mol, which is lower compared to that of the other cyclic diketo systems studied here. The four-membered α- and β-cyclobutanedione (2 and 6) do not favor keto-enol tautomerization unlike other studied cyclic systems because of the ring strain developed in the transition-state geometries and their corresponding products. Water-assisted keto-enol tautomerization with one molecule reveals that the free energy activation barriers reduce almost half compared to those for the uncatalyzed systems. The two-water-assisted process is favorable as the activation free energy barriers lowered by ∼10 kcal/mol compared to those of the one-water-assisted process. The ion-pair formation seems to govern the lowering of activation barriers of α- and β-cyclodiones with two water molecules during the keto-enol tautomerization process, which however also overcomes the favorable aromatization in the three-membered ring system. The free energy activation barriers calculated with the M062X-SMDaq/6-31+G(d,p) level predicted that the keto-enol tautomerization process for the α-cyclodiones follows the following trend: 2 > 3 > 4 > 5 > 1. Water-assisted tautomerization of α-cyclodiones also predicted 1-W and 1-2W as the most favored processes; however, 5-W and 5-2W were found to be disfavored in this case. The β-cyclodione systems also showed similar trends as obtained with α-diketone systems. The influence of bulk solvent on the keto-enol tautomerization process favors the formation of the enol form in a more polar solvent medium even under mixed solvent conditions in acetonitrile and hexane at M062X-SMDacetonitrile/6-31+G(d,p) and M062X-SMDhexane/6-31+G(d,p) levels of theory.
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Affiliation(s)
- Kalyanashis Jana
- Computation
and Simulation Unit (Analytical Discipline and Centralized
Instrument Facility) and Academy of Scientific and Innovative Research, CSIR—Central Salt and Marine Chemicals Research
Institute, Bhavnagar 364002, India
| | - Bishwajit Ganguly
- Computation
and Simulation Unit (Analytical Discipline and Centralized
Instrument Facility) and Academy of Scientific and Innovative Research, CSIR—Central Salt and Marine Chemicals Research
Institute, Bhavnagar 364002, India
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Amini SK. Relative Populations of Some Tautomeric Forms of 2'-Deoxyguanosine-5-Fluorouridine Mismatch. J Phys Chem B 2018; 122:4433-4444. [PMID: 29608855 DOI: 10.1021/acs.jpcb.8b00818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The importance of the 2'-deoxyguanosine-uridine mispair as the most occurring mismatch in transcriptional studies of RNAs from DNAs is multiplied when 5-halo-substituted uridine species cause a serious increase in the probability of its occurrence. Many studies relate this higher probability to the existence of possible tautomeric and ionic forms of its constituent bases. According to these statements, relative populations of mismatches between 5-fluorouridine and both keto and enol forms of 2'-deoxyguanosine are computed by using a conformational search. In order to have a complete scan of all of the highly probable conformers in a moderate computational time, an extensive conformational search methodology is employed here, which benefits from the advantages of both the molecular dynamics simulations and quantum mechanics calculations. The population of an enolic tautomer of normal wobble orientation is about 0.057% of that of its keto tautomer, whereas the population of an enolic tautomer of reverse wobble orientation is about 0.0054% of that of its keto tautomer. Totally, the reverse wobble orientation is about six times more populated than the normal wobble orientation. Calculated populations are in good agreement with experimental populations of closely related compounds. The reliability of the applied methodology is certified, in part, by a good agreement obtained between some experimental data and corresponding Boltzmann-weighted average data of most probable conformers such as NMR parameters. The validation of this methodology is certified with high accuracy by applying it on the substituted diuridine pairs, where experimental populations are available. Not only are the calculated populations and NMR parameters of this test in very good agreement with the experimental data, but also they are free of the ambiguities mentioned by experimentalists.
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Affiliation(s)
- Saeed K Amini
- Chemistry and Chemical Engineering Research Center of Iran , Tehran , Iran
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7
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Jana K, Ganguly B. DFT studies on quantum mechanical tunneling in tautomerization of three-membered rings. Phys Chem Chem Phys 2018; 20:28049-28058. [DOI: 10.1039/c8cp03963a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Amino–imino and keto–enol tautomerization processes in three-membered ring systems have been explored to examine the role of quantum mechanical tunneling along with aromaticity. The DFT calculations shed light on the role of aromaticity in tautomerization processes and as perceived this property may not contribute entirely to facilitate the formation of tautomeric forms.
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Affiliation(s)
- Kalyanashis Jana
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility)
- CSIR-Central Salt and Marine Chemicals Research Institute
- Bhavnagar-364002
- India
- Academy of Scientific and Innovative Research
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility)
- CSIR-Central Salt and Marine Chemicals Research Institute
- Bhavnagar-364002
- India
- Academy of Scientific and Innovative Research
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Abstract
Minima of the electric field and positions of K+ and Na+ (zero of the x-coordinate is the center of the cavity).
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Affiliation(s)
- Giovanni Villani
- Istituto di Chimica dei Composti OrganoMetallici
- ICCOM – UOS Pisa
- Area della Ricerca del CNR
- I-56124 Pisa
- Italy
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Agarwal P, Dabi M, More P, Patel K, Jana K, Agarwal PK. Improved Shoot Regeneration, Salinity Tolerance and Reduced Fungal Susceptibility in Transgenic Tobacco Constitutively Expressing PR-10a Gene. FRONTIERS IN PLANT SCIENCE 2016; 7:217. [PMID: 26973666 PMCID: PMC4770195 DOI: 10.3389/fpls.2016.00217] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 02/08/2016] [Indexed: 05/06/2023]
Abstract
Plants in ecosystems are simultaneously exposed to abiotic and biotic stresses, which restrict plant growth and development. The complex responses to these stresses are largely regulated by plant hormones, which in turn, orchestrate the different biochemical and molecular pathways to maneuver stress tolerance. The PR-10 protein family is reported to be involved in defense regulation, stress response and plant growth and development. The JcPR-10a overexpression resulted in increased number of shoot buds in tobacco (Nicotiana tabacum), which could be due to high cytokinin to auxin ratio in the transgenics. The docking analysis shows the binding of three BAP molecules at the active sites of JcPR-10a protein. JcPR-10a transgenics showed enhanced salt tolerance, as was evident by increased germination rate, shoot and root length, relative water content, proline, soluble sugar and amino acid content under salinity. Interestingly, the transgenics also showed enhanced endogenous cytokinin level as compared to WT, which, further increased with salinity. Exposure of gradual salinity resulted in increased stomatal conductance, water use efficiency, photosynthesis rate and reduced transpiration rate. Furthermore, the transgenics also showed enhanced resistance against Macrophomina fungus. Thus, JcPR-10a might be working in co-ordination with cytokinin signaling in mitigating the stress induced damage by regulating different stress signaling pathways, leading to enhanced stress tolerance.
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Affiliation(s)
- Parinita Agarwal
- Division of Wasteland Research, CSIR-Central Salt and Marine Chemicals Research Institute, Council of Scientific & Industrial ResearchBhavnagar, India
| | - Mitali Dabi
- Division of Wasteland Research, CSIR-Central Salt and Marine Chemicals Research Institute, Council of Scientific & Industrial ResearchBhavnagar, India
- Academy of Scientific and Innovative Research, CSIR-Central Salt and Marine Chemicals Research Institute, Council of Scientific and Industrial ResearchBhavnagar, India
| | - Prashant More
- Division of Wasteland Research, CSIR-Central Salt and Marine Chemicals Research Institute, Council of Scientific & Industrial ResearchBhavnagar, India
- Academy of Scientific and Innovative Research, CSIR-Central Salt and Marine Chemicals Research Institute, Council of Scientific and Industrial ResearchBhavnagar, India
| | - Khantika Patel
- Division of Wasteland Research, CSIR-Central Salt and Marine Chemicals Research Institute, Council of Scientific & Industrial ResearchBhavnagar, India
| | - Kalyanashis Jana
- Academy of Scientific and Innovative Research, CSIR-Central Salt and Marine Chemicals Research Institute, Council of Scientific and Industrial ResearchBhavnagar, India
| | - Pradeep K. Agarwal
- Division of Wasteland Research, CSIR-Central Salt and Marine Chemicals Research Institute, Council of Scientific & Industrial ResearchBhavnagar, India
- Academy of Scientific and Innovative Research, CSIR-Central Salt and Marine Chemicals Research Institute, Council of Scientific and Industrial ResearchBhavnagar, India
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Jana K, Ganguly B. In silico studies with substituted adenines to achieve a remarkable stability of mispairs with thymine nucleobase. NEW J CHEM 2016. [DOI: 10.1039/c5nj02311d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The modified adenine and thymine mispair achieves a remarkable stability, which can presumably help the DNA lesions to be less cytotoxic.
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Affiliation(s)
- Kalyanashis Jana
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility)
- CSIR – Central Salt and Marine Chemicals Research Institute
- Bhavnagar – 364002
- India
- Academy of Scientific and Innovative Research
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility)
- CSIR – Central Salt and Marine Chemicals Research Institute
- Bhavnagar – 364002
- India
- Academy of Scientific and Innovative Research
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