{"title":"Rigidity Analysis of Hydride Tunneling-Ready States From Secondary Kinetic Isotope Effects and Hammett Correlations: Relating to the Temperature Dependence of Kinetic Isotope Effects","authors":"Mingxuan Bai, Grishma Singh, Yun Lu","doi":"10.1002/poc.70002","DOIUrl":"https://doi.org/10.1002/poc.70002","url":null,"abstract":"<div>\u0000 \u0000 <p>Recent study on the effects of enzyme mutations on the primary kinetic isotope effects (1° KIEs) of H-tunneling reactions revealed that a more rigid system results in a weaker temperature dependence of KIEs, indicated by a smaller isotopic activation energy difference (∆<i>E</i><sub>a</sub> = <i>E</i><sub>aD</sub> − <i>E</i><sub>aH</sub>). In literature, a more rigid system has been defined by the presence of shorter, more densely populated hydrogen donor-acceptor distances (DADs) in both the productive reactant complexes (PRCs) and the tunneling-ready states (TRSs). Studying the relationship between DAD<sub>PRC</sub>/DAD<sub>TRS</sub> and ∆<i>E</i><sub>a</sub> can help validate existing H-tunneling models or guide the development of new theories. In a previous publication, we employed Hammett correlations on hydride acceptors (NAD<sup>+</sup> analogues) to propose TRS electronic structures for qualitative analysis of DAD<sub>TRS</sub> order. In this paper, we selected a pair of such systems and used secondary (2°) KIEs on the hydride donor (NADH analogue) to obtain quantitative DAD<sub>TRS</sub> information at the molecular level. TRS structures were computed, and the corresponding 2° KIEs were calculated and fitted to the observed values to extract DAD<sub>TRS</sub> data. PRC structures were also computed. The DAD<sub>PRC</sub>/DAD<sub>TRS</sub> information aligns with the rigidity order derived from Hammett correlation analysis, and the correlation between DAD<sub>PRC</sub>/DAD<sub>TRS</sub> and ∆<i>E</i><sub>a</sub> is consistent with observations in enzyme systems.</p>\u0000 </div>","PeriodicalId":16829,"journal":{"name":"Journal of Physical Organic Chemistry","volume":"38 3","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143120013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jason D. Josephson, John Paul Pezacki, Masaya Nakajima
{"title":"Machine Learning Enabling the Prediction of Activation Energies of SPAAC","authors":"Jason D. Josephson, John Paul Pezacki, Masaya Nakajima","doi":"10.1002/poc.4679","DOIUrl":"https://doi.org/10.1002/poc.4679","url":null,"abstract":"<div>\u0000 \u0000 <p>This study leverages machine learning to predict the activation energies of strain-promoted azide-alkyne cycloaddition (SPAAC) reactions. Using DFT calculations, 631 sets of bond angles and Mulliken charges from two acyclic alkynes were collected. Multiple machine learning models were trained on these data, achieving high accuracy (<i>R</i><sup>2</sup> > 0.95). Both bond angle and charge were crucial for reliable predictions. The models successfully predicted activation energies for SPAAC reactions with unseen cycloalkynes, within certain limitations.</p>\u0000 </div>","PeriodicalId":16829,"journal":{"name":"Journal of Physical Organic Chemistry","volume":"38 2","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143115962","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Theoretical Study on ESIPT for NHBQ-NO2 and NHBQ-NH2: A DFT/TDDFT Study","authors":"Wen Zeng, Wenlong Shao, Jinfeng Zhao, Jiahe Chen","doi":"10.1002/poc.4680","DOIUrl":"https://doi.org/10.1002/poc.4680","url":null,"abstract":"<div>\u0000 \u0000 <p>Inspired by distinguished characteristics of novel optical materials, there has been significant research interest in organic molecules that present excited-state intramolecular proton transfer (ESIPT) properties. Given the vital effects of substituent effect on molecular designs, in this study, we focus on probing into excited state behaviors of NHBQ-NO<sub>2</sub> (i.e., submitted by strong electron-withdrawing group -NO<sub>2</sub>) and NHBQ-NH<sub>2</sub> (i.e., submitted by strong electron-donating group -NH<sub>2</sub>). Exploring hydrogen bonding effects via photoexcitation, we verify the impact of substituent effect (-NO<sub>2</sub> and -NH<sub>2</sub>) on interactions involving photo-induced hydrogen bonding effects, redistribution of charges, and associated phenomena related to ESIPT reaction. By comparing and quantifying the barriers for reactions in relative excited state, our results indicate electron-donating substituent -NH<sub>2</sub> enhances the ESIPT reaction for NHBQ fluorophore.</p>\u0000 </div>","PeriodicalId":16829,"journal":{"name":"Journal of Physical Organic Chemistry","volume":"38 2","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143111475","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Simplice Koudjina, Vipin Kumar, Anuj Tripathi, Guy Yacole Sylvain Atohoun, Joachim Djimon Gbenou, Prabhakar Chetti
{"title":"Mechanistic Multiscale Simulations and Charge Transport Properties of Amorphous and Crystalline α-NPD Molecular Conformations: Insights From Molecule to Material Level","authors":"Simplice Koudjina, Vipin Kumar, Anuj Tripathi, Guy Yacole Sylvain Atohoun, Joachim Djimon Gbenou, Prabhakar Chetti","doi":"10.1002/poc.4677","DOIUrl":"https://doi.org/10.1002/poc.4677","url":null,"abstract":"<div>\u0000 \u0000 <p>The optoelectronic and charge transfer integral properties of N,N′-di(1-naphthyl)-N,N′-diphenyl-4,4′-diamine (α-NPD) organic light-emitting diode (OLED) in amorphous and crystalline structures is studied based on the Marcus–Levitch–Jortner theory and quantum chemistry calculations. The charge transfer integral simulations have been investigated through hole-hopping regime from molecule-to-molecule in dimers molecules and are determined by <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mtext>HOMO</mtext>\u0000 <mo>→</mo>\u0000 <mtext>LUMO</mtext>\u0000 </mrow>\u0000 <annotation>$$ mathrm{HOMO}to mathrm{LUMO} $$</annotation>\u0000 </semantics></math> frontier molecular orbitals (FMOs) for hole and electron transport. Quantum approaches with TD/DFT and DFT have been used to describe the most relevant electronic transitions of α-NPD, which present <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>π</mi>\u0000 <mo>→</mo>\u0000 <msup>\u0000 <mi>π</mi>\u0000 <mo>*</mo>\u0000 </msup>\u0000 </mrow>\u0000 <annotation>$$ pi to {pi}^{ast } $$</annotation>\u0000 </semantics></math> character in harmony with the solvent states. Furthermore, the obtained results reveal that geometric deformations have been relied to naphthalene form and benzene rings in α-NPD structures, and the charge transfer integral in amorphous state shows <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mi>t</mi>\u0000 <mtext>hole</mtext>\u0000 </msub>\u0000 <mo>=</mo>\u0000 <mn>4.46</mn>\u0000 <mspace></mspace>\u0000 <mi>meV</mi>\u0000 </mrow>\u0000 <annotation>$$ {t}_{mathrm{hole}}=4.46 mathrm{meV} $$</annotation>\u0000 </semantics></math> and <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mi>t</mi>\u0000 <mtext>elec</mtext>\u0000 </msub>\u0000 <mo>=</mo>\u0000 <mn>3.18</mn>\u0000 <mspace></mspace>\u0000 <mi>meV</mi>\u0000 </mrow>\u0000 <annotation>$$ {t}_{mathrm{elec}}=3.18 mathrm{meV} $$</annotation>\u0000 </semantics></math>, and in the crystalline state, it shows <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mi>t</mi>\u0000 <mtext>hole</mtext>\u0000 </msub>\u0000 <mo>=</mo>\u0000 <mn>4.25</mn>\u0000 <mspace></mspace>\u0000 <mi>meV</mi>\u0000 </mrow>\u0000 <annotation>$$ {t}_{mathrm{hole}}=4.25 mathrm{meV} $$</annotation>\u0000 </semantics></math> and <span></sp","PeriodicalId":16829,"journal":{"name":"Journal of Physical Organic Chemistry","volume":"38 2","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143110773","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Solvent-Assisted Prototopic Switching of Norharmane Along Hydrogen-Bonded Network: Assessing the Precise Length of Network","authors":"Suvendu Paul, Nilanjan Dey","doi":"10.1002/poc.4678","DOIUrl":"https://doi.org/10.1002/poc.4678","url":null,"abstract":"<div>\u0000 \u0000 <p>In this article, the proton transfer dynamics along a stable norharmane•(H<sub>2</sub>O)<sub>n</sub> (<i>n</i> = 2–4) hydrogen-bonded cluster on conversion from the neutral to cationic form of norharmane (<b>NHM</b>) in water medium was demonstrated experimentally and theoretically. The distinct absorption and emission bands of different prototropic forms of <b>NHM</b> are well-known in the literature. Initially, the conversion from neutral to cationic form of <b>NHM</b> on moving from a polar aprotic (acetonitrile) to a polar protic (water) solvent was ensured by steady-state absorption and fluorescence studies. The analysis of IR spectra and steady-state anisotropy data of <b>NHM</b> confirmed the possibility of the formation of a hydrogen-bonded network in the presence of water. The length of the network was explored and assumed by extensive Density Functional Theory (DFT) calculations. Then, by time-dependent density functional theory (TD-DFT), the excited state proton transfer (ESPT) pathway was established interrogating the <b>NHM</b>-water cluster with different numbers of water molecules. The theoretical analysis assured that the <b>NHM</b>•(H<sub>2</sub>O)<sub>2</sub> cluster was incapable of maintaining the stable hydrogen bonding wire in the course of the ESPT mechanism. Rather, <b>NHM</b>•(H<sub>2</sub>O)<sub>3</sub> and <b>NHM</b>•(H<sub>2</sub>O)<sub>4</sub> clusters were simultaneously involved in operating the ESPT mechanism. The <b>NHM</b>•(H<sub>2</sub>O)<sub>4</sub> cluster was more feasible to carry out the proton transfer than the <b>NHM</b>•(H<sub>2</sub>O)<sub>3</sub> cluster. To the best of our knowledge, this was possibly the first theoretical evidence behind the conversion from neutral to cationic form of <b>NHM</b> via the formation of a hydrogen-bonded network.</p>\u0000 </div>","PeriodicalId":16829,"journal":{"name":"Journal of Physical Organic Chemistry","volume":"38 2","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143119148","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kaitlyn Morrill, Jason D. Josephson, Didier A. Bilodeau, Baha Altamimi, Masaya Nakajima, John Paul Pezacki
{"title":"Bioorthogonal Reactions of Oxadiazinones With Strained trans-Cyclooctenes","authors":"Kaitlyn Morrill, Jason D. Josephson, Didier A. Bilodeau, Baha Altamimi, Masaya Nakajima, John Paul Pezacki","doi":"10.1002/poc.4674","DOIUrl":"https://doi.org/10.1002/poc.4674","url":null,"abstract":"<div>\u0000 \u0000 <p>We report quantitative details of addition reactions of a strained <i>trans</i>-cyclooctene with a series of oxadiazinones, analogues of the bioorthogonally fruitful tetrazines. Both experimental and computational studies of these ligations reveal their sensitivity to differing electronic character of oxadiazinone substituents. Achieving rate constants up to 9.5 L mol<sup>−1</sup> s<sup>−1</sup>, oxadiazinones demonstrate untapped potential for bioorthogonal applications.</p>\u0000 </div>","PeriodicalId":16829,"journal":{"name":"Journal of Physical Organic Chemistry","volume":"38 2","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/poc.4674","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143117879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Counter-Anion-Dependent Optical Properties of Cationic N22-Methylated Chlorophyll-a Derivatives","authors":"Riko Ataka, Yuichi Kitagawa, Hitoshi Tamiaki","doi":"10.1002/poc.4676","DOIUrl":"https://doi.org/10.1002/poc.4676","url":null,"abstract":"<p>Methyl N22-methylpyropheophorbides-<i>a</i> with chloride or hexafluorophosphate were prepared by chemically modifying chlorophyll-<i>a</i>. The resulting product composed of cationic <i>N</i>-methylated chlorin and chloride anion exhibited visible absorption and fluorescence emission maxima in chloroform at longer wavelengths than those with hexafluorophosphate. Both the absorption and emission spectra of the former were hypsochromically shifted by change of the solvent from chloroform to methanol to give almost the same corresponding spectra of the latter independent of solvents. The apparent counter-anion dependency in chloroform and the specific solvent dependency in the <i>N</i>-methyl-chlorin with chloride are ascribable to the weak solvation of a hard chloride anion over soft hexafluorophosphate in chloroform and strong electrostatic interaction of the cationic chlorin with a chloride anion over hexafluorophosphate in chloroform as well as well solvation of both the anions in methanol. In addition, less emission of <i>N</i>-methyl-chlorin with chloride in chloroform would be due to partial fluorescence quenching based on the heavy atom effect of the adjacent chloride anion.</p>","PeriodicalId":16829,"journal":{"name":"Journal of Physical Organic Chemistry","volume":"38 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/poc.4676","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142868402","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Competition of C–F, C–S, and S–F Bond Activation in SF5CF3 Using N-Heterocyclic Olefins Derivatives: A Computational Study","authors":"Xingyu Xu, Xiaoming Xie","doi":"10.1002/poc.4675","DOIUrl":"https://doi.org/10.1002/poc.4675","url":null,"abstract":"<div>\u0000 \u0000 <p>SF<sub>5</sub>CF<sub>3</sub>, commonly recognized as a potent greenhouse gas, has recently emerged as a valuable source of fluoride functional groups. Despite its traditional role, recent studies have highlighted its potential applications beyond its environmental implications. However, investigations into its reactivity remain limited, particularly regarding the activation of its constituent bonds. In this study, we conducted a comprehensive computational analysis to elucidate the competition among C–F, C–S, and S–F bond activations within SF<sub>5</sub>CF<sub>3</sub> utilizing <i>N</i>-heterocyclic olefin derivatives. Our investigations shed light on the underlying mechanisms of bond activation, revealing a preference for the activation of the S–F bond in SF<sub>5</sub>CF<sub>3</sub> by both NHOs and mNHOs. Specifically, we observed a Gibbs free energy barrier (Δ<i>G</i><sup>≠</sup>) ranging from 24.90 to 25.77 kcal/mol in the case of mNHOs, indicating a favorable energetics for this process.</p>\u0000 </div>","PeriodicalId":16829,"journal":{"name":"Journal of Physical Organic Chemistry","volume":"38 2","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143119682","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Computational Studies of the Optoelectronic and Charge Transport Properties of Porphyrin and Corrole-Based Molecules","authors":"Angat Dhiman, C. N. Ramachandran","doi":"10.1002/poc.4673","DOIUrl":"https://doi.org/10.1002/poc.4673","url":null,"abstract":"<div>\u0000 \u0000 <p>The structural, optoelectronic and charge transport properties of porphyrin and its analogues are investigated using the density functional theoretical methods. Most of the above molecules absorb in visible region with high light harvesting efficiency. The small energy gap between the frontier molecular orbitals (FMOs) suggests that porphyrin and its derivatives can be used in organic semiconductors. Electronic properties such as ionization potential, electron affinity, reorganization energy and the charge transfer integral are calculated to obtain their charge transport properties. It is revealed that porphyrin, porphyrazine and phthalocyanine act as hole transporters, whereas corrole and corrolazine act as electron transporters.</p>\u0000 </div>","PeriodicalId":16829,"journal":{"name":"Journal of Physical Organic Chemistry","volume":"38 2","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143117174","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
C. Rajalakshmi, G. Krishnaveni, Binuja Varghese, Anandhu Gopan, Vibin Ipe Thomas
{"title":"Unveiling the Novel Mechanistic Insights and Role of Base in Zn-Catalyzed Csp–Csp2 Cross-Coupling Reaction","authors":"C. Rajalakshmi, G. Krishnaveni, Binuja Varghese, Anandhu Gopan, Vibin Ipe Thomas","doi":"10.1002/poc.4671","DOIUrl":"https://doi.org/10.1002/poc.4671","url":null,"abstract":"<div>\u0000 \u0000 <p>A detailed mechanistic investigation of the Zn (II)-catalyzed Csp–Csp<sup>2</sup> (Sonogashira-type) cross-coupling reaction is reported herein, using the Density Functional Theory method. The present study unveiled an unconventional non-redox mechanism for Zn-catalyzed cross-coupling reaction, where the oxidation state of Zn remains intact throughout the catalytic cycle. Our study further revealed the significant role of the base in controlling the feasibility of cross-coupling reactions that are catalyzed by electron-deficient metal centers. Our study indicates that K<sub>3</sub>PO<sub>4</sub> acts as an ancillary ligand (Lewis base) for the electron-deficient Zn (II) catalytic center rather than as a proton abstractor for the nucleophilic coupling partner (phenylacetylene) in this reaction. The active catalyst was identified to be a four-coordinate bis-DMEDA Zn (II) complex. The mechanism proceeds via the initial activation of the nucleophilic coupling partner (phenylacetylene), followed by the electrophilic coupling partner (organic halide) activation liberating the cross-coupled product by a concerted nucleophilic substitution pathway. The turn-over limiting step was identified to be the activation of the electrophilic coupling partner. The activation barrier obtained for the reaction, 31.0 kcal/mol concords well with experimental temperature requirements (125°C). The coordination by base is found to stabilize the rate-determining intermediates and transition states involved in the reaction. The mechanistic insights gained from this study could aid in the rational design and development of sustainable cross-coupling reactions using zinc as the catalyst.</p>\u0000 </div>","PeriodicalId":16829,"journal":{"name":"Journal of Physical Organic Chemistry","volume":"38 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142868158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}