1
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Abdelaziz B, Chérif I, Gassoumi B, Patanè S, Ayachi S. Linear and Nonlinear Optical Responses of Nitrobenzofurazan-Sulfide Derivatives: DFT-QTAIM Investigation on Twisted Intramolecular Charge Transfer. J Phys Chem A 2023; 127:9895-9910. [PMID: 37972307 PMCID: PMC10694821 DOI: 10.1021/acs.jpca.3c04277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/07/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023]
Abstract
In this study, we report on the green fluorescence exhibited by nitrobenzofurazan-sulfide derivatives (NBD-Si, i = 1-4). The optical responses of these studied compounds in a polar methanol solvent were simulated by the use of time-dependent density functional theory (TD-DFT) employing the Becke-3-Parameter-Lee-Yang-Parr (B3LYP) functional along with the 6-31G(d,p) basis set. The computed energy and oscillator strength (f) results complement the experimental results. The band gap was calculated as the difference between the lowest unoccupied molecular orbital (LUMO) and the highest occupied molecular orbital (HOMO). Additionally, the density of states (DOS) was computed, providing a comprehensive understanding of the fundamental properties of these materials and further corroborating the experimental data. When the experimental data derived from ultraviolet/visible (UV/visible) and fluorescence spectroscopic techniques and those from simulated spectra are analyzed, the extracted values match up adequately. In addition, the NBD-sulfide compounds exhibit a large Stokes shift up to 85 nm in a polar methanol solvent. They are hypothesized to represent a novel paradigm of excited-state intramolecular charge transfer (ICT). To understand the intrinsic optical properties of NBD-Si materials, an ICT was identified, and its direction within the molecule was evaluated using the ratio of βvect and βtotal, values extracted from the computed nonlinear optical (NLO) properties. Moreover, the reduced density gradient (RDG)-based noncovalent interactions (NCIs) were employed to characterize the strength and type of NBD-Si interactions. Furthermore, noncovalent interactions were identified and categorized using the Quantum Theory of Atoms in Molecules (QTAIM) analysis. Ultimately, the combination of Hirshfeld surface analysis and DFT calculations was utilized to enhance the characterization and rationalization of these NCIs.
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Affiliation(s)
- Balkis Abdelaziz
- Laboratory
of Physico-Chemistry of Materials (LR01ES19), Faculty of Sciences, University of Monastir, Avenue of the Environment, 5019 Monastir, Tunisia
- Department
of Mathematical and Computer Sciences, Physical Sciences and Earth
Sciences, University of Messina, I-98166 Messina, Italy
| | - Imen Chérif
- Laboratory
of Physico-Chemistry of Materials (LR01ES19), Faculty of Sciences, University of Monastir, Avenue of the Environment, 5019 Monastir, Tunisia
| | - Bouzid Gassoumi
- Laboratoire
Interfaces et Matériaux Avancés (LIMA), Faculté
des Sciences, Université de Monastir, Avenue de l’Environnement, 5019 Monastir, Tunisia
| | - Salvatore Patanè
- Department
of Mathematical and Computer Sciences, Physical Sciences and Earth
Sciences, University of Messina, I-98166 Messina, Italy
| | - Sahbi Ayachi
- Laboratory
of Physico-Chemistry of Materials (LR01ES19), Faculty of Sciences, University of Monastir, Avenue of the Environment, 5019 Monastir, Tunisia
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2
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Schweer SM, Gawrilow M, Nejad A, Suhm MA. Formic acid-methanol complexation vs. esterification: elusive pre-reactive species identified by vibrational spectroscopy. Phys Chem Chem Phys 2023; 25:29982-29992. [PMID: 37904580 DOI: 10.1039/d3cp04705a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Vibrational spectra of the mixed dimer and the two mixed trimers of methanol and formic acid as well as some of their isotopologues are presented. Out of the eight expected OH stretching fundamentals of these three pre-reactive hydrogen-bonded complexes, the three modes mainly involving an acid OH group bound to the alcohol appear to be missing in the jet-cooled spectra despite a combination of infrared and Raman probing. A possibility of spectral overlap is discussed in the mixed dimer case, but largely discarded. The missing modes correspond to (fractional) concerted elongation of all engaged OH bonds, promoting synchronous degenerate proton transfer between the molecules. One other trimer mode is very tentatively attributed to a broad spectral feature, whereas all OH bonds contacting carbonyl groups can be unambiguously identified by four relatively narrow infrared absorptions. The spectral features are confirmed by vibrational perturbation theory and deviate in a subtle but systematic way from scaled harmonic predictions which were previously validated for the formic acid complex with a more acidic alcohol. Despite being exothermic and exergonic, ester formation can only be detected in the rarefied gas expansions after extended pre-mixture of the gases, which somewhat contrasts the recent microwave spectroscopic evidence of in situ ester formation and in particular the lack of pre-reactive complex signals.
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Affiliation(s)
- Sophie M Schweer
- Institute of Physical Chemistry, University of Goettingen, Tammannstr. 6, 37077 Goettingen, Germany.
| | - Maxim Gawrilow
- Institute of Physical Chemistry, University of Goettingen, Tammannstr. 6, 37077 Goettingen, Germany.
| | - Arman Nejad
- Institute of Physical Chemistry, University of Goettingen, Tammannstr. 6, 37077 Goettingen, Germany.
| | - Martin A Suhm
- Institute of Physical Chemistry, University of Goettingen, Tammannstr. 6, 37077 Goettingen, Germany.
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3
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Ahmed M, Gupta MK, Ansari A. DFT and TDDFT exploration on the role of pyridyl ligands with copper toward bonding aspects and light harvesting. J Mol Model 2023; 29:358. [PMID: 37919553 DOI: 10.1007/s00894-023-05765-4] [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: 09/25/2023] [Accepted: 10/24/2023] [Indexed: 11/04/2023]
Abstract
CONTEXT Schiff base-containing metal complexes have been the subject of extensive research. In this work, a coordination polymer-derived complex called [Cu(L)] that is solution-stable (L = 2-(2-hydroxybenzylidene-amino)phenol) has been explored theoretically with five different pyridyl-based ligands using DFT/TDDFT in order to understand the structural-functional and electronic transitions of these five complexes. Frontier molecular orbital (FMO) analysis was carried out to assess the reactivity behavior of all five complexes. For the purpose of studying the charge energy distribution over complexes, electrostatic potential maps were also drawn. Furthermore, in order to identify any stabilizing interactions that may be present in the given complexes, an NBO analysis was studied. To learn more about any potential correlations between the properties of these five complexes, a comparative analysis was explored. Our calculations demonstrate that complex 3 having pyridine-4-carboxamide as a ligand has a lower energy gap and a higher negative electrostatic potential which may indicate its higher reactivity and this may be due to the electron withdrawing group (carboxamide). TDDFT results show that the highest light harvesting efficiency (LHE) of all the studied complexes is found in the range of 440-448 nm. Complexes 1, 2, and 4 show the higher light harvesting efficiency as compared to complexes 3 and 5. Our findings are in good accordance with the available experimental data. METHODS All DFT computations were performed using the Gaussian16 with unrestricted B3LYP-D2 functional with the basis sets 6-31G(d,p) for O, N, C, and H while LanL2DZ for Cu. The polarized continuum model (PCM) was used for the solvation. The software GaussView6.1 was utilized for the modeling of initial geometries and the plotting of MEP maps. The NBO6.0 program which is incorporated in Gaussian16 was utilized to investigate the bonding nature and stabilization energies of the complexes. The ORCA program was used to simulate the absorption spectra.
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Affiliation(s)
- Mukhtar Ahmed
- Department of Chemistry, Central University of Haryana, Mahendergarh, Haryana, 123031, India
| | - Manoj Kumar Gupta
- Department of Chemistry, Central University of Haryana, Mahendergarh, Haryana, 123031, India
| | - Azaj Ansari
- Department of Chemistry, Central University of Haryana, Mahendergarh, Haryana, 123031, India.
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4
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Oladipo SD, Zamisa SJ, Badeji AA, Ejalonibu MA, Adeleke AA, Lawal IA, Henni A, Lawal MM. Ni 2+ and Cu 2+ complexes of N-(2,6-dichlorophenyl)-N-mesityl formamidine dithiocarbamate structural and functional properties as CYP3A4 potential substrates. Sci Rep 2023; 13:13414. [PMID: 37591990 PMCID: PMC10435461 DOI: 10.1038/s41598-023-39502-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/26/2023] [Indexed: 08/19/2023] Open
Abstract
Metal compounds continued to attract diverse applications due to their malleability in several capacities. In this study, we present our findings on the crystal structures and functional properties of Ni2+ and Cu2+ complexes of N'-(2,6-dichlorophenyl)-N-mesitylformamidine dithiocarbamate (L) comprising [Ni-(L)2] (1) and [Cu-(L)2] (2) with a four-coordinate metal center. We established the two complex structures through 1H and 13C nuclear magnetic resonance (NMR), elemental, and single-crystal X-ray analysis. The analyses showed that the two complexes are isomorphous, having P21/c as a space group and a unit-cell similarity index (π) of 0.002. The two complexes conform to a distorted square planar geometry around the metal centers. The calculated and experimental data, including bond lengths, angles, and NMR values, are similar. Hirshfeld surface analysis revealed the variational contribution of the different types of intermolecular contacts driven by the crystal lattice of the two solvated complexes. Our knowledge of the potential biological implication of these structures enabled us to probe the compounds as prospective CYP3A4 inhibitors. This approach mimics current trends in pharmaceutical design and biomedicine by incorporating potentially active molecules into various media to predict their biological efficacies. The simulations show appreciable binding of compounds 1 and 2 to CYP3A4 with average interaction energies of -97 and -87 kcal/mol, respectively. The protein attains at least five conformational states in the three studied models using a Gaussian Mixture Model-based clustering and free energy prediction. Electric field analysis shows the crucial residues to substrate binding at the active site, enabling CYP3A4 structure to function prediction. The predicted inhibition with these Ni2+ and Cu2+ complexes indicates that CYP3A4 overexpression in a diseased state like cancer would reduce, thereby increasing the chemotherapeutic compounds' shelf-lives for adsorption. This multidimensional study addresses various aspects of molecular metal electronics, including their application as substrate-mimicking inhibitors. The outcome would enable further research on bio-metal compounds of critical potential.
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Affiliation(s)
- Segun D Oladipo
- Department of Chemical Sciences, Olabisi Onabanjo University, P.M.B 2002, Ago-Iwoye, Nigeria.
- School of Chemistry and Physics, Westville Campus, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa.
| | - Sizwe J Zamisa
- School of Chemistry and Physics, Westville Campus, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa
| | - Abosede A Badeji
- Department of Chemical Sciences, Tai Solarin University of Education, Ogun State, Ijagun, Nigeria
| | - Murtala A Ejalonibu
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa
| | - Adesola A Adeleke
- Department of Chemical Sciences, Olabisi Onabanjo University, P.M.B 2002, Ago-Iwoye, Nigeria
| | - Isiaka A Lawal
- Faculty of Engineering and Applied Science, University of Regina, 3737 Wascana Parkway, Regina, SK, S4S 0A2, Canada
| | - Amr Henni
- Faculty of Engineering and Applied Science, University of Regina, 3737 Wascana Parkway, Regina, SK, S4S 0A2, Canada
| | - Monsurat M Lawal
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa.
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5
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Wigh DS, Tissot M, Pasau P, Goodman JM, Lapkin AA. Quantitative In Silico Prediction of the Rate of Protodeboronation by a Mechanistic Density Functional Theory-Aided Algorithm. J Phys Chem A 2023; 127:2628-2636. [PMID: 36916916 PMCID: PMC10041635 DOI: 10.1021/acs.jpca.2c08250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Computational reaction prediction has become a ubiquitous task in chemistry due to the potential value accurate predictions can bring to chemists. Boronic acids are widely used in industry; however, understanding how to avoid the protodeboronation side reaction remains a challenge. We have developed an algorithm for in silico prediction of the rate of protodeboronation of boronic acids. A general mechanistic model devised through kinetic studies of protodeboronation was found in the literature and forms the foundation on which the algorithm presented in this work is built. Protodeboronation proceeds through 7 distinct pathways, though for any particular boronic acid, only a subset of mechanistic pathways are active. The rate of each active mechanistic pathway is linearly correlated with its characteristic energy difference, which in turn can be determined using Density Functional Theory. We validated the algorithm using leave-one-out cross-validation on a data set of 50 boronic acids and made a further 50 rate predictions on academically and industrially important boronic acids out of sample. We believe this work will provide great assistance to chemists performing reactions that feature boronic acids, such as Suzuki-Miyaura and Chan-Evans-Lam couplings.
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Affiliation(s)
- Daniel S Wigh
- Department of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, U.K
| | | | | | - Jonathan M Goodman
- Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, U.K
| | - Alexei A Lapkin
- Department of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, U.K
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6
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Pengthong P, Bopp PA, Jungsuttiwong S, Nanok T. Mechanistic insights into the self-esterification of lactic acid under neutral and acidic conditions. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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7
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Gummidi L, Kerru N, Adeniyi AA, Dhawan S, Singh P. Comparative experimental and DFT analysis of novel indole tagged [1,3,4]thiadiazolo[3,2-a]pyrimidin-5-one hybrid. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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8
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Monika, Ansari A. Electronic structures and energetic of metal(II)-superoxo species: a DFT exploration. Struct Chem 2022. [DOI: 10.1007/s11224-022-02030-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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9
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Effects of the feeding procedure on the thermal behaviors of autocatalytic esterifications in semibatch processes. J Loss Prev Process Ind 2022. [DOI: 10.1016/j.jlp.2021.104651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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Magwenyane AM, Lawal MM, Amoako DG, Somboro AM, Agoni C, Khan RB, Mhlongo NN, Kumalo HM. Exploring the inhibitory mechanism of resorcinylic isoxazole amine NVP-AUY922 towards the discovery of potential heat shock protein 90 (Hsp90) inhibitors. SCIENTIFIC AFRICAN 2022. [DOI: 10.1016/j.sciaf.2022.e01107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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11
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Schweer SM, Nejad A, Suhm MA. Coupled proton vibrations between two weak acids: the hinge complex between formic acid and trifluoroethanol. Phys Chem Chem Phys 2022; 24:26449-26457. [DOI: 10.1039/d2cp04176f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Raman and FTIR spectra of an acid–alcohol complex show complementary signatures from acidic and alcoholic OH stretching, proving its existence.
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Affiliation(s)
- Sophie M. Schweer
- Institute of Physical Chemistry, University of Goettingen, Tammannstr. 6, 37077 Goettingen, Germany
| | - Arman Nejad
- Institute of Physical Chemistry, University of Goettingen, Tammannstr. 6, 37077 Goettingen, Germany
| | - Martin A. Suhm
- Institute of Physical Chemistry, University of Goettingen, Tammannstr. 6, 37077 Goettingen, Germany
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12
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Yusuf T, Oladipo SD, Zamisa S, Kumalo HM, Lawal IA, Lawal MM, Mabuba N. Design of New Schiff-Base Copper(II) Complexes: Synthesis, Crystal Structures, DFT Study, and Binding Potency toward Cytochrome P450 3A4. ACS OMEGA 2021; 6:13704-13718. [PMID: 34095663 PMCID: PMC8173565 DOI: 10.1021/acsomega.1c00906] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/07/2021] [Indexed: 06/01/2023]
Abstract
We report the synthesis and crystal structures of three new copper(II) Schiff-base complexes. The complexes have been characterized by elemental analysis and Fourier transform infrared (FT-IR) and UV-visible spectroscopies. The X-ray diffraction (XRD) analysis reveals that complexes 1 and 3 crystallize in a monoclinic space group C2/c and 2 in a triclinic space group P1̅, each adopting a square planar geometry around the metal center. We use a density functional theory method to explore the quantum chemical properties of these complexes. The calculation proceeds with the three-dimensional (3D) crystal structure characterization of the complexes in which the calculated IR and UV-vis values are comparable to the experimental results. Charge distribution and molecular orbital analyses enabled quantum chemical property prediction of these complexes. We study the drug-likeness properties and binding potentials of the synthesized complexes. The in silico outcome showed that they could serve as permeability-glycoprotein (P-gp) and different cytochrome P450 substrates. Our calculations showed that the complexes significantly bind to cytochrome P450 3A4.
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Affiliation(s)
- Tunde
L. Yusuf
- Department
of Chemical Sciences, University of Johannesburg, Doornfontein, P.O.
Box 17011, Johannesburg 2028, South Africa
| | - Segun D. Oladipo
- Department
of Chemical Sciences, Olabisi Onabanjo University, P. M. B., 2002 Ago-Iwoye, Nigeria
| | - Sizwe Zamisa
- School
of Chemistry and Physics, University of
KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa
| | - Hezekiel M. Kumalo
- Discipline
of Medical Biochemistry, School of Laboratory Medicine and Medical
Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South
Africa
| | - Isiaka A. Lawal
- Chemistry
Department, Faculty of Applied and Computer Science, Vaal University of Technology, Vanderbijlpark Campus, Boulevard, 1900 Vanderbijlpark, South Africa
| | - Monsurat M. Lawal
- Discipline
of Medical Biochemistry, School of Laboratory Medicine and Medical
Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South
Africa
| | - Nonhlangabezo Mabuba
- Department
of Chemical Sciences, University of Johannesburg, Doornfontein, P.O.
Box 17011, Johannesburg 2028, South Africa
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13
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A Theoretical and Experimental Study on Esterification of Citric Acid with the Primary Alcohols and the Hydroxyl Groups of Cellulose Chain (n = 1-2) in Parched Condition. J CHEM-NY 2020. [DOI: 10.1155/2020/8825456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Esterification of citric acid (CA) with the primary alcohols and the hydroxyl groups of cellulose chain (n = 1-2) in parched condition were investigated by using density functional theory (DFT) method and a two-layer ONIOM approach. Geometry and energy of reactants, products, and transition state (TS) structures were optimized at B3LYP/6-311g (d, p) level and ONIOM (B3LYP/6-311g (d, p):PM3MM) level. The computational results show that the esterification occurs in the two main steps: the first step is the dehydration reaction of CA to form anhydrides of 5-membered ring and 6-membered ring and the second step is the ring opening reaction with the hydroxyl –OH groups to form the ester products. The energy barrier of dehydration reaction step is much higher than that of ring opening reaction step. Effect of substituent R in primary alcohol R-CH2OH (R: CH=CH2, CH2NHCH3, CH2OCH3, CH2Cl) and cellulose chain (1G, 2G) on the reactivity, which has negative inductive effect –I, is significant. The combination of calculation data and experiment data were applied to make findings more rigorous. The activation energy of CA was determined by using differential scanning calorimetry (DSC) and thermal gravimetric (TG) analysis to be
= 47.8 kcal/mol; the experimental data favoured the dehydration reaction step of CA.
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14
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Adeowo FY, Ejalonibu MA, Elrashedy AA, Lawal MM, Kumalo HM. Multi-target approach for Alzheimer's disease treatment: computational biomolecular modeling of cholinesterase enzymes with a novel 4- N-phenylaminoquinoline derivative reveal promising potentials. J Biomol Struct Dyn 2020; 39:3825-3841. [PMID: 33030113 DOI: 10.1080/07391102.2020.1826129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The identification of dual inhibitors targeting the active sites of the cholinesterase enzymes, acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE), have lately surfaced as a multi-approach towards Alzheimer treatment. More recently, a novel series of 4-N-phenylaminoquinolines was synthesized and evaluated against AChE and BuChE in which one of the compounds displayed appreciable inhibition compared to the standard compound, galantamine. To provide a clearer picture of the inhibition mechanism of this potent compound at the molecular level, computational biomolecular modeling was carried out. The investigation was initiated with the exploration of the chemical properties of the identified compound 11 b and reference drug, galantamine. Density functional theory (DFT) calculations reveal some conceptual parameters that provide information on the stability and reactivity of the compounds as potential inhibitors. To unveil the binding mechanism, energetics and enzyme-ligand interactions, molecular dynamics (MD) simulations of six different systems were executed over a period. Calculated binding free energy values are in the same order with experimental IC50 data. Identification of the main residues driving optimum binding of the active compound 11 b to the binding region of both AChE and BuChE showed Trp81 and Trp110 as the most important, respectively. It was proposed that the studied compound could serve as a dual inhibitor for AChE and BuChE, therefore, would potentially be a promising moiety in a multi-target approach for the treatment of Alzheimer's disorder.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fatima Y Adeowo
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Murtala A Ejalonibu
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Ahmed A Elrashedy
- Molecular Bio-computational and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Monsurat M Lawal
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Hezekiel M Kumalo
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
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15
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Zhao MM, Zhang H, Iimura S, Bednarz MS, Song QL, Lim NK, Yan J, Wu W, Dai K, Gu X, Wang Y. Process Development of Sotagliflozin, a Dual Inhibitor of Sodium–Glucose Cotransporter-1/2 for the Treatment of Diabetes. Org Process Res Dev 2020. [DOI: 10.1021/acs.oprd.0c00359] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Matthew M. Zhao
- Chemical Development, Lexicon Pharmaceuticals Incorporation, 110 Allen Road, Basking Ridge, New Jersey 07920, United States
| | - Haiming Zhang
- Chemical Development, Lexicon Pharmaceuticals Incorporation, 110 Allen Road, Basking Ridge, New Jersey 07920, United States
| | - Shinya Iimura
- Chemical Development, Lexicon Pharmaceuticals Incorporation, 110 Allen Road, Basking Ridge, New Jersey 07920, United States
| | - Mark S. Bednarz
- Chemical Development, Lexicon Pharmaceuticals Incorporation, 110 Allen Road, Basking Ridge, New Jersey 07920, United States
| | - Qiu-Ling Song
- Chemical Development, Lexicon Pharmaceuticals Incorporation, 110 Allen Road, Basking Ridge, New Jersey 07920, United States
| | - Ngiap-Kie Lim
- Chemical Development, Lexicon Pharmaceuticals Incorporation, 110 Allen Road, Basking Ridge, New Jersey 07920, United States
| | - Jie Yan
- Chemical Development, Lexicon Pharmaceuticals Incorporation, 110 Allen Road, Basking Ridge, New Jersey 07920, United States
| | - Wenxue Wu
- Chemical Development, Lexicon Pharmaceuticals Incorporation, 110 Allen Road, Basking Ridge, New Jersey 07920, United States
| | - Kuangchu Dai
- Process R&D, WuXi Apptec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Xiaodong Gu
- Process R&D, WuXi Apptec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Youchu Wang
- Process R&D, WuXi Apptec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
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16
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Lawal MM, Sanusi ZK, Govender T, Maguire GE, Honarparvar B, Kruger HG. From Recognition to Reaction Mechanism: An Overview on the Interactions between HIV-1 Protease and its Natural Targets. Curr Med Chem 2020; 27:2514-2549. [DOI: 10.2174/0929867325666181113122900] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 11/04/2018] [Accepted: 11/07/2018] [Indexed: 12/28/2022]
Abstract
Current investigations on the Human Immunodeficiency Virus Protease (HIV-1
PR) as a druggable target towards the treatment of AIDS require an update to facilitate further
development of promising inhibitors with improved inhibitory activities. For the past two
decades, up to 100 scholarly reports appeared annually on the inhibition and catalytic mechanism
of HIV-1 PR. A fundamental literature review on the prerequisite of HIV-1 PR action
leading to the release of the infectious virion is absent. Herein, recent advances (both computationally
and experimentally) on the recognition mode and reaction mechanism of HIV-1 PR
involving its natural targets are provided. This review features more than 80 articles from
reputable journals. Recognition of the natural Gag and Gag-Pol cleavage junctions by this
enzyme and its mutant analogs was first addressed. Thereafter, a comprehensive dissect of
the enzymatic mechanism of HIV-1 PR on its natural polypeptide sequences from literature
was put together. In addition, we highlighted ongoing research topics in which in silico
methods could be harnessed to provide deeper insights into the catalytic mechanism of the
HIV-1 protease in the presence of its natural substrates at the molecular level. Understanding
the recognition and catalytic mechanism of HIV-1 PR leading to the release of an infective
virion, which advertently affects the immune system, will assist in designing mechanismbased
inhibitors with improved bioactivity.
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Affiliation(s)
- Monsurat M. Lawal
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Zainab K. Sanusi
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Thavendran Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Glenn E.M. Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Hendrik G. Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
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Lawal MM, Lawal IA, Klink MJ, Tolufashe GF, Ndagi U, Kumalo HM. Density functional theory study of gold(III)-dithiocarbamate complexes with characteristic anticancer potentials. J Inorg Biochem 2020; 206:111044. [DOI: 10.1016/j.jinorgbio.2020.111044] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/29/2020] [Accepted: 02/13/2020] [Indexed: 01/12/2023]
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18
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Craig AJ, Cording AP, Garden AL, Hawkins BC. Does the Reaction of Cyclopropyl Acid Chlorides and Imines To Form 1,3-Oxazin-4-enone Heterocycles Proceed via a Ketene or an N-Acyl-iminium Mechanism? J Org Chem 2020; 85:5486-5492. [PMID: 32207973 DOI: 10.1021/acs.joc.0c00229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mechanism of the reaction between cyclopropyl acid chlorides and imines to form 1,3-oxazin-4-enones was probed through physical and computational experiments. The data gathered strongly support the reaction proceeding through an N-acyl iminium intermediate mechanism rather than a ketene intermediate mechanism.
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Affiliation(s)
- Alexander J Craig
- Department of Chemistry, University of Otago, Dunedin 9054, New Zealand
| | - Andrew P Cording
- Department of Chemistry, University of Otago, Dunedin 9054, New Zealand
| | - Anna L Garden
- Department of Chemistry, University of Otago, Dunedin 9054, New Zealand
| | - Bill C Hawkins
- Department of Chemistry, University of Otago, Dunedin 9054, New Zealand
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19
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Magwenyane AM, Mhlongo NN, Lawal MM, Amoako DG, Somboro AM, Sosibo SC, Shunmugam L, Khan RB, Kumalo HM. Understanding the Hsp90 N-terminal Dynamics: Structural and Molecular Insights into the Therapeutic Activities of Anticancer Inhibitors Radicicol (RD) and Radicicol Derivative (NVP-YUA922). Molecules 2020; 25:E1785. [PMID: 32295059 PMCID: PMC7221724 DOI: 10.3390/molecules25081785] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/03/2020] [Accepted: 04/08/2020] [Indexed: 11/23/2022] Open
Abstract
Heat shock protein 90 (Hsp90) is a crucial component in carcinogenesis and serves as a molecular chaperone that facilitates protein maturation whilst protecting cells against temperature-induced stress. The function of Hsp90 is highly dependent on adenosine triphosphate (ATP) binding to the N-terminal domain of the protein. Thus, inhibition through displacement of ATP by means of competitive binding with a suitable organic molecule is considered an attractive topic in cancer research. Radicicol (RD) and its derivative, resorcinylic isoxazole amine NVP-AUY922 (NVP), have shown promising pharmacodynamics against Hsp90 activity. To date, the underlying binding mechanism of RD and NVP has not yet been investigated. In this study, we provide a comprehensive understanding of the binding mechanism of RD and NVP, from an atomistic perspective. Density functional theory (DFT) calculations enabled the analyses of the compounds' electronic properties and results obtained proved to be significant in which NVP was predicted to be more favorable with solvation free energy value of -23.3 kcal/mol and highest stability energy of 75.5 kcal/mol for a major atomic delocalization. Molecular dynamic (MD) analysis revealed NVP bound to Hsp90 (NT-NVP) is more stable in comparison to RD (NT-RD). The Hsp90 protein exhibited a greater binding affinity for NT-NVP (-49.4 ± 3.9 kcal/mol) relative to NT-RD (-28.9 ± 4.5 kcal/mol). The key residues influential in this interaction are Gly 97, Asp 93 and Thr 184. These findings provide valuable insights into the Hsp90 dynamics and will serve as a guide for the design of potent novel inhibitors for cancer treatment.
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Affiliation(s)
- Ayanda M. Magwenyane
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.M.M.); (N.N.M.); (M.M.L.); (D.G.A.); (A.M.S.); (L.S.); (R.B.K.)
| | - Ndumiso N. Mhlongo
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.M.M.); (N.N.M.); (M.M.L.); (D.G.A.); (A.M.S.); (L.S.); (R.B.K.)
| | - Monsurat M. Lawal
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.M.M.); (N.N.M.); (M.M.L.); (D.G.A.); (A.M.S.); (L.S.); (R.B.K.)
| | - Daniel G. Amoako
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.M.M.); (N.N.M.); (M.M.L.); (D.G.A.); (A.M.S.); (L.S.); (R.B.K.)
- Biomedical Resource Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Anou M. Somboro
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.M.M.); (N.N.M.); (M.M.L.); (D.G.A.); (A.M.S.); (L.S.); (R.B.K.)
- Biomedical Resource Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Sphelele C. Sosibo
- School of Physical and Chemical Sciences, Department of Chemistry, North West University, Mafikeng Campus, Mmabatho 2790, South Africa;
| | - Letitia Shunmugam
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.M.M.); (N.N.M.); (M.M.L.); (D.G.A.); (A.M.S.); (L.S.); (R.B.K.)
| | - Rene B. Khan
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.M.M.); (N.N.M.); (M.M.L.); (D.G.A.); (A.M.S.); (L.S.); (R.B.K.)
| | - Hezekiel M. Kumalo
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.M.M.); (N.N.M.); (M.M.L.); (D.G.A.); (A.M.S.); (L.S.); (R.B.K.)
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20
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Drug repurposing: Fusidic acid as a potential inhibitor of M. tuberculosis FtsZ polymerization – Insight from DFT calculations, molecular docking and molecular dynamics simulations. Tuberculosis (Edinb) 2020; 121:101920. [DOI: 10.1016/j.tube.2020.101920] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 11/23/2022]
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21
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Lawal IA, Lawal MM, Akpotu SO, Okoro HK, Klink M, Ndungu P. Noncovalent Graphene Oxide Functionalized with Ionic Liquid: Theoretical, Isotherm, Kinetics, and Regeneration Studies on the Adsorption of Pharmaceuticals. Ind Eng Chem Res 2020. [DOI: 10.1021/acs.iecr.9b06634] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Isiaka A. Lawal
- Chemistry Department, Faculty of Applied and Computer Science, Vaal University of Technology, Vanderbijlpark Campus Boulevard, 1900 Vanderbijlpark, South Africa
| | - Monsurat M. Lawal
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Samson O. Akpotu
- Chemistry Department, Faculty of Applied and Computer Science, Vaal University of Technology, Vanderbijlpark Campus Boulevard, 1900 Vanderbijlpark, South Africa
| | - Hussein Kehinde Okoro
- Analytical-Environmental and Material Science Research Group, Department of Industrial Chemistry, Faculty of Physical Sciences, Faculty of Physical Sciences, P.M.B 1515, Ilorin 234000, Nigeria
| | - Michael Klink
- Chemistry Department, Faculty of Applied and Computer Science, Vaal University of Technology, Vanderbijlpark Campus Boulevard, 1900 Vanderbijlpark, South Africa
| | - Patrick Ndungu
- Energy, Sensors, and Multifunctional Nanomaterials Research Group, Department of Applied Chemistry, University of Johannesburg, Doornfontein, 2028 Johannesburg, South Africa
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22
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Sanusi ZK, Lawal MM, Govender T, Baijnath S, Naicker T, Maguire GEM, Honarparvar B, Kruger HG. Concerted hydrolysis mechanism of HIV-1 natural substrate against subtypes B and C-SA PR: insight through molecular dynamics and hybrid QM/MM studies. Phys Chem Chem Phys 2020; 22:2530-2539. [PMID: 31942584 DOI: 10.1039/c9cp05639d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
It is well known that understanding the catalytic mechanism of HIV-1 PR is the rationale on which its inhibitors were developed; therefore, a better understanding of the mechanism of natural substrate hydrolysis is important. Herein, the reaction mechanism of HIV-1 natural substrates with subtypes B and common mutant in South Africa (subtype C-SA) protease were studied through transition state modelling, using a general acid-general base (GA-GB) one-step concerted process. The activation free energies of enzyme-substrate complexes were compared based on their rate of hydrolysis using a two-layered ONIOM (B3LYP/6-31++G(d,p):AMBER) method. We expanded our computational model to obtain a better understanding of the mechanism of hydrolysis as well as how the enzyme recognises or chooses the cleavage site of the scissile bonds. Using this model, a potential substrate-based inhibitor could be developed with better potency. The calculated activation energies of natural substrates in our previous study correlated well with experimental data. A similar trend was observed for the Gag and Gag-Pol natural substrates in the present work for both enzyme complexes except for the PR-RT substrate. Natural bond orbital (NBO) analysis was also applied to determine the extent of charge transfer within the QM part of both enzymes considered and the PR-RT natural substrate. The result of this study shows that the method can be utilized as a dependable computational technique to rationalize lead compounds against specific targets.
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Affiliation(s)
- Zainab K Sanusi
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa.
| | - Monsurat M Lawal
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa.
| | | | - Sooraj Baijnath
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa.
| | - Tricia Naicker
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa.
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa. and School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa.
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa.
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23
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Kerru N, Gummidi L, Bhaskaruni SVHS, Maddila SN, Singh P, Jonnalagadda SB. A comparison between observed and DFT calculations on structure of 5-(4-chlorophenyl)-2-amino-1,3,4-thiadiazole. Sci Rep 2019; 9:19280. [PMID: 31848439 PMCID: PMC6917775 DOI: 10.1038/s41598-019-55793-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 11/30/2019] [Indexed: 01/09/2023] Open
Abstract
The crystal and molecular structure of 5-(4-chlorophenyl)-2-amino-1,3,4-thiadiazole 3 was reported, which was characterized by various spectroscopic techniques (FT-IR, NMR and HRMS) and single-crystal X-ray diffraction. The crystal structure 3 (C8H6ClN3S) crystallized in the orthorhombic space group Pna21 and the unit cell consisted of 8 asymmetric molecules. The unit cell parameters were a = 11.2027(2) Å, b = 7.6705(2) Å, c = 21.2166(6) Å, α = β = γ = 90°, V = 1823.15(8) Å3, Z = 8. In addition, the structural geometry (bond lengths, bond angles, and torsion angles), the electronic properties of mono and dimeric forms of compound 3 were calculated by using the density functional theory (DFT) method at B3LYP level 6-31+ G(d,p), 6-31++ G(d,p) and 6-311+ G(d,p) basis sets in ground state. A good correlation was found (R2 = 0.998) between the observed and theoretical vibrational frequencies. Frontier molecular orbitals (HOMO and LUMO) and Molecular Electrostatic Potential map of the compound was produced by using the optimized structures. The NBO analysis was suggested that the molecular system contains N-H…N hydrogen bonding, strong conjugative interactions and the molecule become more polarized owing to the movement of π-electron cloud from donor to acceptor. The calculated structural and geometrical results were in good rational agreement with the experimental X-ray crystal structure data of 1,3,4-thiadiazol-2-amine, 3. The compound 3 exhibited n→π* UV absorption peak of UV cutoff edge, and great magnitude of the first-order hyperpolarizability was observed. The obtained results suggest that compound 3 could have potential application as NLO material. Therefore, this study provides valuable insight experimentally and theoretically, for designing new chemical entities to meet the demands of specific applications.
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Affiliation(s)
- Nagaraju Kerru
- School of Chemistry & Physics, University of KwaZulu-Natal, Westville Campus, Chiltern Hills, P/Bag X54001, Durban, 4000, South Africa
| | - Lalitha Gummidi
- School of Chemistry & Physics, University of KwaZulu-Natal, Westville Campus, Chiltern Hills, P/Bag X54001, Durban, 4000, South Africa
| | - Sandeep V H S Bhaskaruni
- School of Chemistry & Physics, University of KwaZulu-Natal, Westville Campus, Chiltern Hills, P/Bag X54001, Durban, 4000, South Africa
| | - Surya Narayana Maddila
- School of Chemistry & Physics, University of KwaZulu-Natal, Westville Campus, Chiltern Hills, P/Bag X54001, Durban, 4000, South Africa
| | - Parvesh Singh
- School of Chemistry & Physics, University of KwaZulu-Natal, Westville Campus, Chiltern Hills, P/Bag X54001, Durban, 4000, South Africa
| | - Sreekantha B Jonnalagadda
- School of Chemistry & Physics, University of KwaZulu-Natal, Westville Campus, Chiltern Hills, P/Bag X54001, Durban, 4000, South Africa.
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24
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Umar Ndagi, Lawal MM, Soliman ME. DFT Study of the Structural and Electronic Properties of Selected Organogold(III) Compounds with Characteristic Anticancer Activity. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2019. [DOI: 10.1134/s0036024419080302] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Sanusi ZK, Lawal MM, Govender T, Maguire GEM, Honarparvar B, Kruger HG. Theoretical Model for HIV-1 PR That Accounts for Substrate Recognition and Preferential Cleavage of Natural Substrates. J Phys Chem B 2019; 123:6389-6400. [DOI: 10.1021/acs.jpcb.9b02207] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Zainab K. Sanusi
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Monsurat M. Lawal
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | | | - Glenn E. M. Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
- School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Hendrik G. Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
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26
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Gummidi L, Kerru N, Ibeji CU, Singh P. Crystal structure and DFT studies of (E)-1-(4-fluorophenyl)-3-(1H-indol-1-yl)-4-styrylazetidin-2-one. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.03.053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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27
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Lawal MM, Sanusi ZK, Govender T, Tolufashe GF, Maguire GEM, Honarparvar B, Kruger HG. Unraveling the concerted catalytic mechanism of the human immunodeficiency virus type 1 (HIV-1) protease: a hybrid QM/MM study. Struct Chem 2018. [DOI: 10.1007/s11224-018-1251-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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28
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Ibeji CU, Tolufashe GF, Ntombela T, Govender T, Maguire GEM, Lamichhane G, Kruger HG, Honarparvar B. The catalytic role of water in the binding site of l,d-transpeptidase 2 within acylation mechanism: A QM/MM (ONIOM) modelling. Tuberculosis (Edinb) 2018; 113:222-230. [PMID: 30514506 DOI: 10.1016/j.tube.2018.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/11/2018] [Accepted: 10/14/2018] [Indexed: 01/13/2023]
Abstract
Mycobacterium tuberculosis is the causative agent of Tuberculosis. Formation of 3 → 3 crosslinks in the peptidoglycan layer of M. tuberculosis is catalyzed by l,d-transpeptidases. These enzymes can confer resistance against classical β-lactams that inhibit enzymes that generate 4 → 3 peptidoglycan crosslinks. The focus of this study is to investigate the catalytic role of water molecules in the acylation mechanism of the β-lactam ring within two models; 4- and 6-membered ring systems using two-layered our Own N-layer integrated Molecular Mechanics ONIOM (B3LYP/6-311++G(2d,2p): AMBER) model. The obtained thermochemical parameters revealed that the 6-membered ring model best describes the inhibition mechanism of acylation which indicates the role of water in the preference of 6-membered ring reaction pathway. This finding is in accordance with experimental data for the rate-limiting step of cysteine protease with the same class of inhibitor and binding affinity for both inhibitors. As expected, the ΔG# results also reveal that the 6-membered ring reaction pathway is the most favourable. The electrostatic potential (ESP) and the natural bond orbital analysis (NBO) showed stronger interactions in 6-membered ring transition state (TS-6) mechanism involving water in the active site of the enzyme. This study could be helpful in the development of novel antibiotics against l,d-transpeptidase.
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Affiliation(s)
- Collins U Ibeji
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa; Department of Pure and Industrial Chemistry, Faculty of Physical Sciences, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria
| | - Gideon F Tolufashe
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Thandokuhle Ntombela
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Thavendran Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa; School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Gyanu Lamichhane
- Center for Tuberculosis Research, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa.
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa.
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29
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Applicability of DFT model in reactive distillation. PHYSICAL SCIENCES REVIEWS 2017. [DOI: 10.1515/psr-2017-0144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe density functional theory (DFT) applicability to reactive distillation is discussed. Brief modeling techniques description of distillation and rectification with chemical reaction is provided as a background for quantum method usage description. The equilibrium and nonequilibrium distillation models are described for that purpose. The DFT quantum theory is concisely described. The usage of DFT in the modeling of reactive distillation is described in two parts. One of the fundamental and very important component of distillation modeling is vapor-liquid equilibrium description for which the DFT quantum approach can be used. The representative DFT models, namely COSMO-RS (Conductor like Screening Model for Real Solvents), COSMOSPACE (COSMO Surface Pair Activity Coefficient) and COSMO-SAC (SAC – segment activity coefficient) approaches are described. The second part treats the way in which the chemical reaction is described by means of quantum DFT method. The intrinsic reaction coordinate (IRC) method is described which is used to find minimum energy path of substrates to products transition. The DFT is one of the methods which can be used for that purpose. The literature data examples are provided which proves that IRC method is applicable for chemical reaction kinetics description.
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Desmet GB, D'hooge DR, Sabbe MK, Reyniers MF, Marin GB. Computational Investigation of the Aminolysis of RAFT Macromolecules. J Org Chem 2016; 81:11626-11634. [PMID: 27809531 DOI: 10.1021/acs.joc.6b01844] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work presents a detailed computational study and kinetic analysis of the aminolysis of dithioates, dithiobenzoates, trithiocarbonates, xanthates, and thiocarbamates, which are frequently used as chain-transfer agents for reversible addition-fragmentation chain-transfer (RAFT) polymerization. Rate coefficients were obtained from ab initio calculations, taking into account a diffusional contribution according to the encounter pair model. A kinetic model was constructed and reveals a reaction mechanism of four elementary steps: (i) formation of a zwitterionic intermediate, (ii) formation of a complex intermediate in which an assisting amine molecule takes over the proton from the zwitterionic intermediate, (iii) breakdown of the complex into a neutral tetrahedral intermediate with release of the assisting amine molecule, and (iv) amine-assisted breakdown of the neutral intermediate to the products. Furthermore, a comparative analysis indicates that the alkanedithioates and dithiobenzoates react the fastest, followed, respectively, by xanthates and trithiocarbonates, which react almost equally fast, and dithiocarbamates, which are not reactive at typical experimentally used conditions.
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Affiliation(s)
- Gilles B Desmet
- Laboratory for Chemical Technology and ‡Department of Textiles, Ghent University , Technologiepark 914, 9052 Gent, Belgium
| | - Dagmar R D'hooge
- Laboratory for Chemical Technology and ‡Department of Textiles, Ghent University , Technologiepark 914, 9052 Gent, Belgium
| | - Maarten K Sabbe
- Laboratory for Chemical Technology and ‡Department of Textiles, Ghent University , Technologiepark 914, 9052 Gent, Belgium
| | - Marie-Françoise Reyniers
- Laboratory for Chemical Technology and ‡Department of Textiles, Ghent University , Technologiepark 914, 9052 Gent, Belgium
| | - Guy B Marin
- Laboratory for Chemical Technology and ‡Department of Textiles, Ghent University , Technologiepark 914, 9052 Gent, Belgium
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