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
AMADAR: a python-based package for large scale prediction of Diels–Alder transition state geometries and IRC 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/10962/453143 , vital:75226 , xlink:href="https://link.springer.com/article/10.1186/s13321-022-00618-3"
- Description: Predicting transition state geometries is one of the most challenging tasks in computational chemistry, which often requires expert-based knowledge and permanent human intervention. This short communication reports technical details and preliminary results of a python-based tool (AMADAR) designed to generate any Diels–Alder (DA) transition state geometry (TS) and analyze determined IRC paths in a (quasi-)automated fashion, given the product SMILES. Two modules of the package are devoted to performing, from IRC paths, reaction force analyses (RFA) and atomic (fragment) decompositions of the reaction force F and reaction force constant κ. The performance of the protocol has been assessed using a dataset of 2000 DA cycloadducts retrieved from the ZINC database. The sequential location of the corresponding TSs was achieved with a success rate of 95%. RFA plots confrmed the reaction force constant κ to be a good indicator of the (non)synchronicity of the associated DA reactions. Moreover, the atomic decomposition of κ allows for the rationalization of the (a)synchronicity of each DA reaction in terms of contributions stemming from pairs of interacting atoms. The source code of the AMADAR tool is available on GitHub [CMCDD/AMADAR(github. com)] and can be used directly with minor customizations, mostly regarding the local working environment of the user.
- 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/10962/453143 , vital:75226 , xlink:href="https://link.springer.com/article/10.1186/s13321-022-00618-3"
- Description: Predicting transition state geometries is one of the most challenging tasks in computational chemistry, which often requires expert-based knowledge and permanent human intervention. This short communication reports technical details and preliminary results of a python-based tool (AMADAR) designed to generate any Diels–Alder (DA) transition state geometry (TS) and analyze determined IRC paths in a (quasi-)automated fashion, given the product SMILES. Two modules of the package are devoted to performing, from IRC paths, reaction force analyses (RFA) and atomic (fragment) decompositions of the reaction force F and reaction force constant κ. The performance of the protocol has been assessed using a dataset of 2000 DA cycloadducts retrieved from the ZINC database. The sequential location of the corresponding TSs was achieved with a success rate of 95%. RFA plots confrmed the reaction force constant κ to be a good indicator of the (non)synchronicity of the associated DA reactions. Moreover, the atomic decomposition of κ allows for the rationalization of the (a)synchronicity of each DA reaction in terms of contributions stemming from pairs of interacting atoms. The source code of the AMADAR tool is available on GitHub [CMCDD/AMADAR(github. com)] and can be used directly with minor customizations, mostly regarding the local working environment of the user.
- Full Text:
- Date Issued: 2022
Regioselectivity, chemical bonding and physical nature of the interaction between imidazole and XAHs (X= H, F, Cl, Br, CH3, and A= S, Se, Te)
- Isamura, Bienfait K, Lobb, Kevin A, Muya, Jules T
- Authors: Isamura, Bienfait K , Lobb, Kevin A , Muya, Jules T
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/453183 , vital:75229 , xlink:href="https://doi.org/10.1080/00268976.2022.2026511"
- Description: Theambidentreactivityofsmall-sizedXAHs(X=H,F,Cl,Br,CH3,andA=S,Se,Te)moleculestowardsthe imidazole molecule (IMZ) has been investigated using wave function (MP2) and Density Func-tional Theory (B3LYP, B3LYP-D3). Molecular electrostatic potentials (MEPs) and frontier molecularorbitals of monomers are computed to rationalise the regioselectivity of IMZ towards XAHs. Thechemical bonding of each complex is described in the framework of the quantum theory of atomsin molecules (QTAIM) and natural bond orbital (NBO) paradigms. The symmetry-adapted pertur-bation theory (SAPT) is employed to assess the physical nature of the interactions. Our findingssuggest that XAHs mainly bind to IMZ through H-bonding and chalcogen-bonding interactionsof weak to moderate strength, with binding energies ranging from−3.1 to−17.6 kcal/mol at theMP2/aug-cc-pVDZ(-PP) level. Topological QTAIM descriptors reveal all H-bonds between IMZ andXAHs to be purely noncovalent contacts, while chalcogen bonds of halogenated XAHs (X=F, Cl, Br) show a partial covalent character. SAPT2 calculations indicate that both H-bonded and chalcogen-bonded complexes are mainly stabilised by electrostatic interactions. Insights drawn from this studyare expected to constitute the bedrock for further investigations about noncovalent interactionbetween middle to big-sized chalcogen-containing molecules and imidazole derivatives.
- Full Text:
- Date Issued: 2022
- Authors: Isamura, Bienfait K , Lobb, Kevin A , Muya, Jules T
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/453183 , vital:75229 , xlink:href="https://doi.org/10.1080/00268976.2022.2026511"
- Description: Theambidentreactivityofsmall-sizedXAHs(X=H,F,Cl,Br,CH3,andA=S,Se,Te)moleculestowardsthe imidazole molecule (IMZ) has been investigated using wave function (MP2) and Density Func-tional Theory (B3LYP, B3LYP-D3). Molecular electrostatic potentials (MEPs) and frontier molecularorbitals of monomers are computed to rationalise the regioselectivity of IMZ towards XAHs. Thechemical bonding of each complex is described in the framework of the quantum theory of atomsin molecules (QTAIM) and natural bond orbital (NBO) paradigms. The symmetry-adapted pertur-bation theory (SAPT) is employed to assess the physical nature of the interactions. Our findingssuggest that XAHs mainly bind to IMZ through H-bonding and chalcogen-bonding interactionsof weak to moderate strength, with binding energies ranging from−3.1 to−17.6 kcal/mol at theMP2/aug-cc-pVDZ(-PP) level. Topological QTAIM descriptors reveal all H-bonds between IMZ andXAHs to be purely noncovalent contacts, while chalcogen bonds of halogenated XAHs (X=F, Cl, Br) show a partial covalent character. SAPT2 calculations indicate that both H-bonded and chalcogen-bonded complexes are mainly stabilised by electrostatic interactions. Insights drawn from this studyare expected to constitute the bedrock for further investigations about noncovalent interactionbetween middle to big-sized chalcogen-containing molecules and imidazole derivatives.
- Full Text:
- Date Issued: 2022
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