Crystal Structure, Hirshfeld Surface Analysis and Computational Studies of Two Benzo [b][1, 4] Diazepine Derivatives
- Odame, Felix, Madanhire, T, Hosten, Eric C, Lobb, Kevin A
- Authors: Odame, Felix , Madanhire, T , Hosten, Eric C , Lobb, Kevin A
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452689 , vital:75162 , xlink:href="https://doi.org/10.1134/S0022476623120041"
- Description: The DFT computational studies, crystal structures and Hirshfeld surface analysis of (E)-4-(2-chlorostyryl)-2,2-dimethyl-2,3-dihydro-1H-benzo[b][1,4]diazepine (1) and (E)-4-(2-(2,2-dimethyl-2,3-dihydro-1H-benzo[b][1,4]diazepin-4-yl)vinyl)phenol (2) have been presented. The compounds crystallized in the monoclinic space group P21/c with 4 molecules in their unit cells each. The experimental and computed bond lengths and bond angles deviated from each other to some extent but also showed good agreement with each other in some cases. Hirshfeld surface analysis of the compounds provided further information about the structural properties of the compounds.
- Full Text:
- Date Issued: 2023
- Authors: Odame, Felix , Madanhire, T , Hosten, Eric C , Lobb, Kevin A
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452689 , vital:75162 , xlink:href="https://doi.org/10.1134/S0022476623120041"
- Description: The DFT computational studies, crystal structures and Hirshfeld surface analysis of (E)-4-(2-chlorostyryl)-2,2-dimethyl-2,3-dihydro-1H-benzo[b][1,4]diazepine (1) and (E)-4-(2-(2,2-dimethyl-2,3-dihydro-1H-benzo[b][1,4]diazepin-4-yl)vinyl)phenol (2) have been presented. The compounds crystallized in the monoclinic space group P21/c with 4 molecules in their unit cells each. The experimental and computed bond lengths and bond angles deviated from each other to some extent but also showed good agreement with each other in some cases. Hirshfeld surface analysis of the compounds provided further information about the structural properties of the compounds.
- Full Text:
- Date Issued: 2023
Unveiling the reactivity of truxillic and truxinic acids (TXAs): deprotonation, anion center dot center dot center dot HO, cation center dot center dot center dot O and cation center dot center dot center dot pi interactions in TXA (0) center dot center dot center dot Y+ and TXA (0) center dot center dot center dot Z (-) complexes (Y= Li, Na, K; Z= F, Cl, Br)
- Isamura, Bienfait K, Patouossa, Issofa, Muya, Jules T, Lobb, Kevin A
- Authors: Isamura, Bienfait K , Patouossa, Issofa , Muya, Jules T , Lobb, Kevin A
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452827 , vital:75173 , xlink:href="https://link.springer.com/content/pdf/10.1007/s11224-022-01965-5.pdf"
- Description: Herein, we report a quantum chemistry investigation of the interaction between µ-truxinic acid, referred to as TXA0 , and Y+ (Y=Li, Na, K) and Z− (Z=F, Cl, Br) ions using M06-2X, B3LYP and 휔 B97XD functionals in conjunction with the 6–31+ +G(d,p), aug-cc-pVDZ(-X2C) and 6–311+ +G (d, p) basis sets. Our computations suggest that Y+ cations can bind to TXA0 through several combinations of cation…O and cation-π interactions, while Z− anions generally establish anion… H–O contacts. Predicted binding energies at the M06-2X/6–311+ +G(d,p) level range between−26.6 and−70.2 kcal/mol for cationic complexes and−20.4 and−62.3 kcal/mol for anionic ones. As such, TXA0 appears as an amphoteric molecule with a slight preference for electrophilic (cation... O) attacks. Furthermore, the most favourable binding site for cations allows for the formation of O…cation…O interactions where the cation is trapped between O37 and O38 atoms of TXA0 . Anions do not behave uniformly towards TXA0 : while the fuoride anion F− induces the deprotonation of TXA0 , Br− and Cl− do not. All of these structural insights are supported by topological calculations in the context of the quantum theory of atoms in molecules (QTAIM). Finally, SAPT0 analyses suggest that TXA0 …Y+ and TXA0 …Z− complexes are mainly stabilized by electrostatic and inductive efects, whose combined contributions account for more than 60 percent of the total interaction energy.
- Full Text:
- Date Issued: 2023
- Authors: Isamura, Bienfait K , Patouossa, Issofa , Muya, Jules T , Lobb, Kevin A
- Date: 2023
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452827 , vital:75173 , xlink:href="https://link.springer.com/content/pdf/10.1007/s11224-022-01965-5.pdf"
- Description: Herein, we report a quantum chemistry investigation of the interaction between µ-truxinic acid, referred to as TXA0 , and Y+ (Y=Li, Na, K) and Z− (Z=F, Cl, Br) ions using M06-2X, B3LYP and 휔 B97XD functionals in conjunction with the 6–31+ +G(d,p), aug-cc-pVDZ(-X2C) and 6–311+ +G (d, p) basis sets. Our computations suggest that Y+ cations can bind to TXA0 through several combinations of cation…O and cation-π interactions, while Z− anions generally establish anion… H–O contacts. Predicted binding energies at the M06-2X/6–311+ +G(d,p) level range between−26.6 and−70.2 kcal/mol for cationic complexes and−20.4 and−62.3 kcal/mol for anionic ones. As such, TXA0 appears as an amphoteric molecule with a slight preference for electrophilic (cation... O) attacks. Furthermore, the most favourable binding site for cations allows for the formation of O…cation…O interactions where the cation is trapped between O37 and O38 atoms of TXA0 . Anions do not behave uniformly towards TXA0 : while the fuoride anion F− induces the deprotonation of TXA0 , Br− and Cl− do not. All of these structural insights are supported by topological calculations in the context of the quantum theory of atoms in molecules (QTAIM). Finally, SAPT0 analyses suggest that TXA0 …Y+ and TXA0 …Z− complexes are mainly stabilized by electrostatic and inductive efects, whose combined contributions account for more than 60 percent of the total interaction energy.
- Full Text:
- Date Issued: 2023
A multiscale ONIOM study of the buckminsterfullerene (C60) Diels–Alder reaction: from model design to reaction path analysis
- Isamura, Bienfait K, Lobb, Kevin A
- Authors: Isamura, Bienfait K , Lobb, Kevin A
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452517 , vital:75140 , xlink:href=" https://link.springer.com/article/10.1007/s00894-022-05319-0"
- Description: The hybrid ONIOM (Our own N-layered Integrated molecular Orbital and molecular Mechanics) formalism is employed to investigate the Diels–Alder reaction of the buckminsterfullerene C60. Our computa-tions suggest that the ONIOM2(M06-2X/6-31G(d): SVWN/STO3G) mod-el, enclosing both the diene and the pyracyclene fragment of C60 in the higher-layer, provides a reasonable trade-of between accuracy and computational cost as it comes to predicting reaction energetics. Moreover, the frontier molecular orbital (FMO) theory and activation strain model (ASM) are jointly relied on to rationalize the efect of –OH and –CN substituents on the activation barrier of this reaction. Finally, reaction paths are scrutinized to get insight into the various forces un-derpinning the process of cycloadduct formation.
- Full Text:
- Date Issued: 2022
- Authors: Isamura, Bienfait K , Lobb, Kevin A
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/452517 , vital:75140 , xlink:href=" https://link.springer.com/article/10.1007/s00894-022-05319-0"
- Description: The hybrid ONIOM (Our own N-layered Integrated molecular Orbital and molecular Mechanics) formalism is employed to investigate the Diels–Alder reaction of the buckminsterfullerene C60. Our computa-tions suggest that the ONIOM2(M06-2X/6-31G(d): SVWN/STO3G) mod-el, enclosing both the diene and the pyracyclene fragment of C60 in the higher-layer, provides a reasonable trade-of between accuracy and computational cost as it comes to predicting reaction energetics. Moreover, the frontier molecular orbital (FMO) theory and activation strain model (ASM) are jointly relied on to rationalize the efect of –OH and –CN substituents on the activation barrier of this reaction. Finally, reaction paths are scrutinized to get insight into the various forces un-derpinning the process of cycloadduct formation.
- Full Text:
- Date Issued: 2022
Solvent promoted tautomerism in thione-containing tetraazatricyclics: evidence from 1H NMR spectroscopy and transition state studies
- Odame, Felix, Tshentu, Zenixole R, Lobb, Kevin A
- Authors: Odame, Felix , Tshentu, Zenixole R , Lobb, Kevin A
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/453198 , vital:75230 , xlink:href="https://link.springer.com/article/10.1007/s00894-022-05204-w"
- Description: Tautomerism in the nitro substituted thione-containing traazatricyclics has been investigated. Evidence from 1 H NMR indicating the existence of the tautomers has been augmented with computational studies providing evidence of the stability or otherwise of these tautomers. The role of water and DMSO in the formation of the tautomers has been explained. The role of the nitro group in assisting in the formation of the tautomers has been discussed.
- Full Text:
- Date Issued: 2022
- Authors: Odame, Felix , Tshentu, Zenixole R , Lobb, Kevin A
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/453198 , vital:75230 , xlink:href="https://link.springer.com/article/10.1007/s00894-022-05204-w"
- Description: Tautomerism in the nitro substituted thione-containing traazatricyclics has been investigated. Evidence from 1 H NMR indicating the existence of the tautomers has been augmented with computational studies providing evidence of the stability or otherwise of these tautomers. The role of water and DMSO in the formation of the tautomers has been explained. The role of the nitro group in assisting in the formation of the tautomers has been discussed.
- Full Text:
- Date Issued: 2022
SANCDB: an update on South African natural compounds and their readily available analogs
- Diallo, Bakary N, Glenister, Michael, Musyoka, Thommas M, Lobb, Kevin A, Taştan Bishop, Özlem
- Authors: Diallo, Bakary N , Glenister, Michael , Musyoka, Thommas M , Lobb, Kevin A , Taştan Bishop, Özlem
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/451154 , vital:75023 , xlink:href="https://doi.org/10.1186/s13321-021-00514-2"
- Description: The dimeric dihydropyrimidine dehydrogenase (DPD), metalloenzyme, an adjunct anti-cancer drug target, contains highly specialized 4 × Fe2+4S2−4 clusters per chain. These clusters facilitate the catalysis of the rate-limiting step in the pyrimidine degradation pathway through a harmonized electron transfer cascade that triggers a redox catabolic reaction. In the process, the bulk of the administered 5-fluorouracil (5-FU) cancer drug is inactivated, while a small proportion is activated to nucleic acid antimetabolites. The occurrence of missense mutations in DPD protein within the general population, including those of African descent, has adverse toxicity effects due to altered 5-FU metabolism. Thus, deciphering mutation effects on protein structure and function is vital, especially for precision medicine purposes. We previously proposed combining molecular dynamics (MD) and dynamic residue network (DRN) analysis to decipher the molecular mechanisms of missense mutations in other proteins. However, the presence of Fe2+4S2−4 clusters in DPD poses a challenge for such in silico studies. The existing AMBER force field parameters cannot accurately describe the Fe2+ center coordination exhibited by this enzyme. Therefore, this study aimed to derive AMBER force field parameters for DPD enzyme Fe2+ centers, using the original Seminario method and the collation features Visual Force Field Derivation Toolkit as a supportive approach. All-atom MD simulations were performed to validate the results. Both approaches generated similar force field parameters, which accurately described the human DPD protein Fe2+4S2−4 cluster architecture. This information is crucial and opens new avenues for in silico cancer pharmacogenomics and drug discovery related research on 5-FU drug efficacy and toxicity issues.
- Full Text:
- Date Issued: 2021
- Authors: Diallo, Bakary N , Glenister, Michael , Musyoka, Thommas M , Lobb, Kevin A , Taştan Bishop, Özlem
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/451154 , vital:75023 , xlink:href="https://doi.org/10.1186/s13321-021-00514-2"
- Description: The dimeric dihydropyrimidine dehydrogenase (DPD), metalloenzyme, an adjunct anti-cancer drug target, contains highly specialized 4 × Fe2+4S2−4 clusters per chain. These clusters facilitate the catalysis of the rate-limiting step in the pyrimidine degradation pathway through a harmonized electron transfer cascade that triggers a redox catabolic reaction. In the process, the bulk of the administered 5-fluorouracil (5-FU) cancer drug is inactivated, while a small proportion is activated to nucleic acid antimetabolites. The occurrence of missense mutations in DPD protein within the general population, including those of African descent, has adverse toxicity effects due to altered 5-FU metabolism. Thus, deciphering mutation effects on protein structure and function is vital, especially for precision medicine purposes. We previously proposed combining molecular dynamics (MD) and dynamic residue network (DRN) analysis to decipher the molecular mechanisms of missense mutations in other proteins. However, the presence of Fe2+4S2−4 clusters in DPD poses a challenge for such in silico studies. The existing AMBER force field parameters cannot accurately describe the Fe2+ center coordination exhibited by this enzyme. Therefore, this study aimed to derive AMBER force field parameters for DPD enzyme Fe2+ centers, using the original Seminario method and the collation features Visual Force Field Derivation Toolkit as a supportive approach. All-atom MD simulations were performed to validate the results. Both approaches generated similar force field parameters, which accurately described the human DPD protein Fe2+4S2−4 cluster architecture. This information is crucial and opens new avenues for in silico cancer pharmacogenomics and drug discovery related research on 5-FU drug efficacy and toxicity issues.
- Full Text:
- Date Issued: 2021
Synthesis, characterization, computational studies and DPPH scavenging activity of some triazatetracyclic derivatives
- Odame, Felix, Hosten, Eric C, Betz, Richard, Krause, Jason, Frost, Carminita L, Lobb, Kevin A, Tshentu, Zenixole R
- Authors: Odame, Felix , Hosten, Eric C , Betz, Richard , Krause, Jason , Frost, Carminita L , Lobb, Kevin A , Tshentu, Zenixole R
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/451186 , vital:75026 , xlink:href="https://doi.org/10.1007/s13738-021-02158-3"
- Description: Some dihydrobenzo[4,5]imidazo[1,2-c]quinazolines have been synthesized from aldehydes and ketones, using the ketones as both reagents and solvents and tetrahydrofuran (THF) as the solvent for the aldehydes, to yield the triazatetracyclics. The compounds have been characterized with spectroscopy and microanalysis. The crystal structures of 9,9-dimethyl-8,10,17- triazatetracyclo[8.7.02,7.011,16]heptadeca-1(17),2,4,6,11(16),12,14-heptaene (I), 9-butyl-9-methyl-8,10,17-triazatetracyclo[8.7.0.02 , 7 .011,16]heptadeca-(17),2,4,6,11(16),12,14-heptaene (III) and 9-phenyl-8,10,17-triazatetracyclo[8.7.0 02 7.011,16] heptadeca-1(17),2,4,6,11(16),12,14-heptaene (VIII) have been discussed. The computed NMR, IR, molecular electrostatic potential and frontier molecular orbitals of compounds I, III and VIII have been discussed. The M06 functional gave most of its values closest to the experimental values for the bond lengths and bond angles of compounds I and III. For compound VIII, none of the functionals gave values for bond lengths and bond angles that were consistent with the experimental values, but M06 gave values closest to experimental values. The 1,1-diphenyl-2-picrylhydrazyl (DPPH) scavenging activity of the triazatetracyclics showed that compound I exhibits signifcant DPPH scavenging activity with an IC50 of 56.18 µM compared to 2.37 µM for ascorbic acid.
- Full Text:
- Date Issued: 2021
- Authors: Odame, Felix , Hosten, Eric C , Betz, Richard , Krause, Jason , Frost, Carminita L , Lobb, Kevin A , Tshentu, Zenixole R
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/451186 , vital:75026 , xlink:href="https://doi.org/10.1007/s13738-021-02158-3"
- Description: Some dihydrobenzo[4,5]imidazo[1,2-c]quinazolines have been synthesized from aldehydes and ketones, using the ketones as both reagents and solvents and tetrahydrofuran (THF) as the solvent for the aldehydes, to yield the triazatetracyclics. The compounds have been characterized with spectroscopy and microanalysis. The crystal structures of 9,9-dimethyl-8,10,17- triazatetracyclo[8.7.02,7.011,16]heptadeca-1(17),2,4,6,11(16),12,14-heptaene (I), 9-butyl-9-methyl-8,10,17-triazatetracyclo[8.7.0.02 , 7 .011,16]heptadeca-(17),2,4,6,11(16),12,14-heptaene (III) and 9-phenyl-8,10,17-triazatetracyclo[8.7.0 02 7.011,16] heptadeca-1(17),2,4,6,11(16),12,14-heptaene (VIII) have been discussed. The computed NMR, IR, molecular electrostatic potential and frontier molecular orbitals of compounds I, III and VIII have been discussed. The M06 functional gave most of its values closest to the experimental values for the bond lengths and bond angles of compounds I and III. For compound VIII, none of the functionals gave values for bond lengths and bond angles that were consistent with the experimental values, but M06 gave values closest to experimental values. The 1,1-diphenyl-2-picrylhydrazyl (DPPH) scavenging activity of the triazatetracyclics showed that compound I exhibits signifcant DPPH scavenging activity with an IC50 of 56.18 µM compared to 2.37 µM for ascorbic acid.
- Full Text:
- Date Issued: 2021
Characterization and computational studies of 2-(benzamido) thiazol-5-yl benzoate
- Odame, Felix, Hosten, Eric C, Betz, Richard, Lobb, Kevin A, Tshentu, Zenixole R
- Authors: Odame, Felix , Hosten, Eric C , Betz, Richard , Lobb, Kevin A , Tshentu, Zenixole R
- Date: 2019
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/447003 , vital:74576 , xlink:href="https://doi.org/10.1134/S0022476619010190"
- Description: Thiazoles have shown a broad range of biological activities and are found in many potent biologically active molecules such as Sulfathiazol (antimicrobial drug), Ritonavir (antiretroviral drug), Abafungin (antifungal drug), and Tiazofurin (antineoplastic drug) [1]. They have exhibited some degree of plant growth regulatory and antifungal activities [2], whilst some thiazoles have shown anti-infective [3] as well as antibacterial activities [4]. The regio-controlled synthesis of 2,5-disubstituted and 2,4,5-trisubstituted thiazoles from ethyl-2-bromo-5-chloro-4-thiazolecarboxylates using sequential palladium-catalyzed coupling reactions has been reported [5]. An efficient general method for the preparation of 2,4-di- and trisubsituted thiazoles is via P–TsOH. H2O-Catalyzed cyclization of trisubstituted propargylic alcohols with thioamides has been accomplished with moderate to excellent product yields under mild and standard conditions [6]. In the presence of triethylamine, (Z)-(2-acetoxyl-1-alkenyl) phenyl-λ3 iodanes reacts with thioureas or thioamides in methanol to afford 2,4- disubstituted thiazoles in good yields. The reaction is thought to proceed by the generation of highly reactive α-λ3 iodanyl ketones through ester exchange of the β-acetoxy group with liberation of methyl acetate, followed by nucleophilic substitutions with thioureas or thioamides [7].
- Full Text:
- Date Issued: 2019
- Authors: Odame, Felix , Hosten, Eric C , Betz, Richard , Lobb, Kevin A , Tshentu, Zenixole R
- Date: 2019
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/447003 , vital:74576 , xlink:href="https://doi.org/10.1134/S0022476619010190"
- Description: Thiazoles have shown a broad range of biological activities and are found in many potent biologically active molecules such as Sulfathiazol (antimicrobial drug), Ritonavir (antiretroviral drug), Abafungin (antifungal drug), and Tiazofurin (antineoplastic drug) [1]. They have exhibited some degree of plant growth regulatory and antifungal activities [2], whilst some thiazoles have shown anti-infective [3] as well as antibacterial activities [4]. The regio-controlled synthesis of 2,5-disubstituted and 2,4,5-trisubstituted thiazoles from ethyl-2-bromo-5-chloro-4-thiazolecarboxylates using sequential palladium-catalyzed coupling reactions has been reported [5]. An efficient general method for the preparation of 2,4-di- and trisubsituted thiazoles is via P–TsOH. H2O-Catalyzed cyclization of trisubstituted propargylic alcohols with thioamides has been accomplished with moderate to excellent product yields under mild and standard conditions [6]. In the presence of triethylamine, (Z)-(2-acetoxyl-1-alkenyl) phenyl-λ3 iodanes reacts with thioureas or thioamides in methanol to afford 2,4- disubstituted thiazoles in good yields. The reaction is thought to proceed by the generation of highly reactive α-λ3 iodanyl ketones through ester exchange of the β-acetoxy group with liberation of methyl acetate, followed by nucleophilic substitutions with thioureas or thioamides [7].
- Full Text:
- Date Issued: 2019
Characterization and computational studies of a co-crystal of 2-aminobenzimidazole and 2-[(benzoylcarbamothioyl) amino] propanoic acid
- Odame, Felix, Hosten, Eric C, Betz, Richard, Lobb, Kevin A, Tshentu, Zenixole R
- Authors: Odame, Felix , Hosten, Eric C , Betz, Richard , Lobb, Kevin A , Tshentu, Zenixole R
- Date: 2018
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/447030 , vital:74578 , xlink:href="https://doi.org/10.1134/S0022476618050268"
- Description: A novel co-crystal of 2-aminobenzimidazole and 2-[(benzoylcarbamothioyl)amino] propanoic acid is synthesized and characterized by spectroscopy, elemental analysis, GC-MS, and single crystal XRD. A computation of the structures involved in the formation of the co-crystal are carried out and their contribution to reactivity is explained.
- Full Text:
- Date Issued: 2018
- Authors: Odame, Felix , Hosten, Eric C , Betz, Richard , Lobb, Kevin A , Tshentu, Zenixole R
- Date: 2018
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/447030 , vital:74578 , xlink:href="https://doi.org/10.1134/S0022476618050268"
- Description: A novel co-crystal of 2-aminobenzimidazole and 2-[(benzoylcarbamothioyl)amino] propanoic acid is synthesized and characterized by spectroscopy, elemental analysis, GC-MS, and single crystal XRD. A computation of the structures involved in the formation of the co-crystal are carried out and their contribution to reactivity is explained.
- Full Text:
- Date Issued: 2018
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