The Journal of Physical Chemistry A最新文献_第8页

Quantum Chemical Calculations of the Nonenzymatic Bicarbonate Ion-Catalyzed Lactamization of Ornithine Residues to Identify the Components of Primitive Proteins.

IF 2.7 2区化学

The Journal of Physical Chemistry A Pub Date : 2025-03-13 Epub Date: 2025-02-26 DOI: 10.1021/acs.jpca.4c07299

Ayato Mizuno, Tomoki Nakayoshi, Eiji Kurimoto, Koichi Kato, Akifumi Oda

{"title":"Quantum Chemical Calculations of the Nonenzymatic Bicarbonate Ion-Catalyzed Lactamization of Ornithine Residues to Identify the Components of Primitive Proteins.","authors":"Ayato Mizuno, Tomoki Nakayoshi, Eiji Kurimoto, Koichi Kato, Akifumi Oda","doi":"10.1021/acs.jpca.4c07299","DOIUrl":"10.1021/acs.jpca.4c07299","url":null,"abstract":"Ornithine (Orn) is biochemically significant amino acid and has a structure similar to lysine, yet a noncanonical amino acid. When Orn is incorporated into a peptide chain, irreversible nonenzymatic C-terminal peptide cleavage and lactamization occur, inhibiting the synthesis of a peptide chain. The Orn reactivity is high, and likely to proceed even in the absence of enzymes. Nonenzymatic reactions could proceed with prebiotic catalysts that existed on the primitive Earth and may have played a crucial role in the origin of proteins. However, the mechanisms of these reactions have not been studied in great detail. In this study, quantum chemical calculations of these reactions were performed using the model compound Ac-Orn-NMe (Ac = acetyl, NMe = methylamino). Two reaction stages were considered: cyclization and C-terminal cleavage. Because the gem-hydroxylamine intermediate structure is diastereomeric, reaction pathways involving both R- and S-configured intermediates were investigated. The activation barriers for the Orn lactamization involving R- and S-intermediates with bicarbonate ions as a catalyst were estimated to be 82.4 and 76.6 kJ mol-1, respectively. Thus, the Orn lactamization can proceed easily compared to lysine. The high reactivity of Orn may be the reason for the exclusion of Orn from the Magic 20.","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2387-2395"},"PeriodicalIF":2.7,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143497525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Theoretical Study of Spectroscopy and Photodynamics of Decatetraene as a Representative Dimethylated Polyene.

IF 2.7 2区化学

The Journal of Physical Chemistry A Pub Date : 2025-03-13 Epub Date: 2025-02-27 DOI: 10.1021/acs.jpca.4c08185

Anjan Chattopadhyay, Maximilian F S J Menger, Dilawar Singh Sisodiya, Horst Köppel

{"title":"Theoretical Study of Spectroscopy and Photodynamics of Decatetraene as a Representative Dimethylated Polyene.","authors":"Anjan Chattopadhyay, Maximilian F S J Menger, Dilawar Singh Sisodiya, Horst Köppel","doi":"10.1021/acs.jpca.4c08185","DOIUrl":"10.1021/acs.jpca.4c08185","url":null,"abstract":"The photodynamics and UV spectroscopy of decatetraene following excitation to the bright 1Bu state are studied theoretically, based on ab initio computations of the underlying potential energy (PE) surfaces. Both photophysical and photochemical aspects are investigated. The former involves smaller amplitude displacements, and - in addition to determining multidimensional PE surfaces - also a quantal treatment of the ensuing nuclear dynamics. The inclusion of the 1Bu-2Ag vibronic interaction allows to compute the vibrational structure of the 1Ag-1Bu UV spectral band and the femtosecond 1Bu-2Ag internal conversion (population transfer). The results are compared with analogous features of octatetraene and octatriene. The photochemical aspects involving larger-amplitude displacements are investigated from a quantum-chemical point of view, focusing on the stationary points and the seams of conical intersections that are involved. A comparison of decatetraene with octatetraene reveals the contrasting features of their 2Ag and 1Bu state minima, where the latter is more stable in the dimethylated system. The small barrier connecting these two states lies between 0.06 and 0.11 eV. The nonradiative decay channels originating from these minima are characterized by comparatively higher barriers in decatetraene and influence the outcome of the radiative processes in a different manner in comparison to that of octatetraene.","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2442-2453"},"PeriodicalIF":2.7,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143522126","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

DFT-Assisted Microkinetic Study of Transfer Hydrogenation over Homogeneous and Immobilized Cp*Ir Complexes.

IF 2.7 2区化学

The Journal of Physical Chemistry A Pub Date : 2025-03-13 Epub Date: 2025-03-02 DOI: 10.1021/acs.jpca.4c08718

Ivan Mitrichev, A John Blacker, Michael Chapman, Yuji Kawakami, Mikhail Vasilev, Gert Goltz, Anna Podobedova, Antonia Borissova, Eleonora Koltsova

{"title":"DFT-Assisted Microkinetic Study of Transfer Hydrogenation over Homogeneous and Immobilized Cp*Ir Complexes.","authors":"Ivan Mitrichev, A John Blacker, Michael Chapman, Yuji Kawakami, Mikhail Vasilev, Gert Goltz, Anna Podobedova, Antonia Borissova, Eleonora Koltsova","doi":"10.1021/acs.jpca.4c08718","DOIUrl":"10.1021/acs.jpca.4c08718","url":null,"abstract":"DFT calculations were done to investigate the kinetic mechanism of benzaldehyde transfer hydrogenation using [Cp*IrCl2]2 complexes in isopropyl alcohol in the presence of potassium tert-butoxide. Predicted energy barriers provide evidence that the inner-sphere (IS) mechanism (effective barrier 53.0 kJ/mol) is favored over the outer-sphere (OS) and Meerwein-Pondorf-Verley (MPV) mechanisms. Reaction kinetics was studied using both homogeneous and immobilized Cp*Ir complexes as catalysts. A mathematical model was developed to simulate the transfer hydrogenation of benzaldehyde on these catalysts, accounting for possible mass transfer limitations for the immobilized catalyst. A microkinetic model was constructed using both our density functional theory calculations and fitting of the kinetic parameters of catalyst activation and deactivation reactions. The simulation results predict that only about a quarter of Ir immobilized complexes are involved in the reaction, and this is the main reason for the observed higher activity of the homogeneous catalyst. The activity of the immobilized catalyst was found to be related to the hydride species concentration, which is a function of the base concentration. The results suggest that the amount of base has a drastic effect on the immobilized catalyst activity.","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2548-2557"},"PeriodicalIF":2.7,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143536194","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Breaking Down Polychlorinated Biphenyls and Aryl Chlorides: A Computational Study of Thermal-, Pressure-, and Shear-Induced Decomposition.

IF 2.7 2区化学

The Journal of Physical Chemistry A Pub Date : 2025-03-13 Epub Date: 2025-02-27 DOI: 10.1021/acs.jpca.4c08086

L Pisarova, O A Loboda, I Minami, S J Eder

{"title":"Breaking Down Polychlorinated Biphenyls and Aryl Chlorides: A Computational Study of Thermal-, Pressure-, and Shear-Induced Decomposition.","authors":"L Pisarova, O A Loboda, I Minami, S J Eder","doi":"10.1021/acs.jpca.4c08086","DOIUrl":"10.1021/acs.jpca.4c08086","url":null,"abstract":"Reactive molecular dynamics (MD) simulations were used to study the decomposition of aryl chlorides, including polychlorinated biphenyls (PCBs), under varying conditions. Using the ReaxFF force field, which models bond breaking and formation, the study focused on PCB 77 (3,3',4,4'-tetrachlorobiphenyl) and compared it to safer alternatives: 1,2-dichlorobenzene (DCB) and 3,4-dichlorotoluene (DCT). Density functional theory (DFT) calculations validated decomposition pathways and enthalpies of C-Cl bond homolytic cleavage, revealing a multistep radical mechanism. Analysis showed that the decomposition rate and product distribution were sensitive to temperature and Cl-binding positions, emphasizing the complexity of PCB breakdown. Decomposition products were analyzed to understand the efficiency and safety of current remediation processes, such as incineration, which can produce hazardous byproducts like dioxins if poorly managed. The results suggested DCT as a promising candidate for further investigation in laboratory experiments due to its decomposition pathways and relevance to PCB analogues. This study advances knowledge of PCB degradation mechanisms, informing safer, sustainable remediation strategies, and highlighting the risks of pyrolysis-based approaches.","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2568-2583"},"PeriodicalIF":2.7,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912490/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143522115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Infrared Spectroscopy of Radical Cation Clusters (NH₃)₂⁺ and (NH₃)₃^.

IF 2.7 2区化学

The Journal of Physical Chemistry A Pub Date : 2025-03-13 Epub Date: 2025-02-26 DOI: 10.1021/acs.jpca.4c08362

Amandeep Singh, Arisa Iguchi, Tom C Bernaards, Zane Golpariani, Kenta Mizuse, Asuka Fujii, Hajime Tanuma, Toshiyuki Azuma, Susumu Kuma, Andrey Vilesov

{"title":"Infrared Spectroscopy of Radical Cation Clusters (NH3)2+ and (NH3)3.","authors":"Amandeep Singh, Arisa Iguchi, Tom C Bernaards, Zane Golpariani, Kenta Mizuse, Asuka Fujii, Hajime Tanuma, Toshiyuki Azuma, Susumu Kuma, Andrey Vilesov","doi":"10.1021/acs.jpca.4c08362","DOIUrl":"10.1021/acs.jpca.4c08362","url":null,"abstract":"The ionization of protic molecules such as H2O and NH3 in the condensed phase initiates ion-molecule reactions, which remain poorly understood. Studies of the structure and reactivity of small ionic clusters in molecular beams have yielded a wealth of information on protonated clusters. However, unprotonated radical cation clusters have a low concentration in a typical experiment and thus remain challenging. Here we report the infrared spectra of the (NH3)2+ and (NH3)3+ radical cations solvated in helium nanodroplets. Radical cation clusters often have several isomers with different ionic cores, including proton-transferred and hemibonded structures. Infrared spectra of the cations obtained in this work indicate that the formation of the ammonia dimer ((NH3)2+) and trimer ((NH3)3+) cations yields the proton-transferred structures, which correspond to the respective global minima of the calculated structures. Spectral assignments are corroborated by density functional theory calculations. The spectra also indicate that the NH4+ and NH3 moieties within the clusters undergo internal rotation with rotational constants close to those in the gas phase.","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2472-2481"},"PeriodicalIF":2.7,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Overview on Building Blocks and Applications of Efficient and Robust Extended Tight Binding.

IF 2.7 2区化学

The Journal of Physical Chemistry A Pub Date : 2025-03-13 Epub Date: 2025-02-27 DOI: 10.1021/acs.jpca.4c08263

Abylay Katbashev, Marcel Stahn, Thomas Rose, Vahideh Alizadeh, Marvin Friede, Christoph Plett, Pit Steinbach, Sebastian Ehlert

{"title":"Overview on Building Blocks and Applications of Efficient and Robust Extended Tight Binding.","authors":"Abylay Katbashev, Marcel Stahn, Thomas Rose, Vahideh Alizadeh, Marvin Friede, Christoph Plett, Pit Steinbach, Sebastian Ehlert","doi":"10.1021/acs.jpca.4c08263","DOIUrl":"10.1021/acs.jpca.4c08263","url":null,"abstract":"The extended tight binding (xTB) family of methods opened many new possibilities in the field of computational chemistry. Within just 5 years, the GFN2-xTB parametrization for all elements up to Z = 86 enabled more than a thousand applications, which were previously not feasible with other electronic structure methods. The xTB methods provide a robust and efficient way to apply quantum mechanics-based approaches for obtaining molecular geometries, computing free energy corrections or describing noncovalent interactions and found applicability for many more targets. A crucial contribution to the success of the xTB methods is the availability within many simulation packages and frameworks, supported by the open source development of its program library and packages. We present a comprehensive summary of the applications and capabilities of xTB methods in different fields of chemistry. Moreover, we consider the main software packages for xTB calculations, covering their current ecosystem, novel features, and usage by the scientific community.","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2667-2682"},"PeriodicalIF":2.7,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514123","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

AtomDB: A Python Library and Database for Atomic and Promolecular Properties.

IF 2.7 2区化学

The Journal of Physical Chemistry A Pub Date : 2025-03-13 Epub Date: 2025-02-28 DOI: 10.1021/acs.jpca.4c07353

Gabriela Sánchez Díaz, Michelle Richer, Marco Martínez González, Maximilian van Zyl, Leila Pujal, Alireza Tehrani, Julianna Bianchi, Valerii Chuiko, Jannis Erhard, Fanwang Meng, Paul W Ayers, Farnaz Heidar-Zadeh

{"title":"AtomDB: A Python Library and Database for Atomic and Promolecular Properties.","authors":"Gabriela Sánchez Díaz, Michelle Richer, Marco Martínez González, Maximilian van Zyl, Leila Pujal, Alireza Tehrani, Julianna Bianchi, Valerii Chuiko, Jannis Erhard, Fanwang Meng, Paul W Ayers, Farnaz Heidar-Zadeh","doi":"10.1021/acs.jpca.4c07353","DOIUrl":"10.1021/acs.jpca.4c07353","url":null,"abstract":"AtomDB is a free and open-source Python library for accessing and manipulating neutral and charged atomic species and their promolecular properties. It serves as a computational toolset, operating on an accompanying \"extended periodic table\" database, with experimental and computational data covering atomic species with a wide range of charges and multiplicities. AtomDB includes facilities for computing promolecules: local promolecular properties, constructed from the corresponding atomic densities, and scalar promolecular properties, computed from the corresponding scalar atomic properties, both taking into account whether properties are extensive or intensive. AtomDB is designed to be easy to use, extend, and maintain: it follows best practices for modern software development, including comprehensive documentation, extensive testing, continuous integration/delivery protocols, and package management. This article is the official release note for the AtomDB library.","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2598-2611"},"PeriodicalIF":2.7,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143530934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Electron Attachment to Nitric Oxide (NO) Controversy.

IF 2.7 2区化学

The Journal of Physical Chemistry A Pub Date : 2025-03-13 Epub Date: 2025-02-28 DOI: 10.1021/acs.jpca.4c07675

Ana I Lozano, Juan C Oller, Paulo Limão-Vieira, Gustavo García

引用次数: 0

Negative-Ion Formation upon Soft X-ray Photoexcitation of 2-Propanol.

IF 2.7 2区化学

The Journal of Physical Chemistry A Pub Date : 2025-03-13 Epub Date: 2025-02-27 DOI: 10.1021/acs.jpca.4c08226

Antti Kivimäki, Eetu Pelimanni, Kirill Chernenko, Abdul Rahman Abid, Christian Stråhlman

引用次数: 0

Mechanism and Origins of Regio- and Stereoselectivities of NHC-Catalyzed Dearomative Annulation of Benzoazoles and Cinnamaldehydes from DFT.

IF 2.7 2区化学

The Journal of Physical Chemistry A Pub Date : 2025-03-13 Epub Date: 2025-03-05 DOI: 10.1021/acs.jpca.4c08373

Yan Li, Yanlong Kang, Junjie Xiao, Zhiqiang Zhang

{"title":"Mechanism and Origins of Regio- and Stereoselectivities of NHC-Catalyzed Dearomative Annulation of Benzoazoles and Cinnamaldehydes from DFT.","authors":"Yan Li, Yanlong Kang, Junjie Xiao, Zhiqiang Zhang","doi":"10.1021/acs.jpca.4c08373","DOIUrl":"10.1021/acs.jpca.4c08373","url":null,"abstract":"A theoretical study on the mechanism, regioselectivity, and enantioselectivity of NHC-catalyzed dearomatizing annulation of benzoxazoles with enals has been conducted using density functional theory calculations. Our calculated results indicate that the favored mechanism occurs through eight reaction steps: initial binding of the NHC to enals, followed by formation of the Breslow intermediate via proton transfer. Subsequent oxidation generates the α,β-unsaturated acylazolium intermediate, which can undergo Michael addition with benzoxazoles. Sequential protonation/deprotonation/cyclization produces the six-membered cyclic intermediate that undergoes catalyst elimination, leading to the final product. DABCO·H+ was found to play important roles in proton transfer and cyclization. Without DABCO·H+, the energy barrier up to 44.2 kcal/mol for step 2 is too high to be accessible. With DABCO·H+, the corresponding value is lowered to 18.6 kcal/mol. The energy barrier for cyclization can be lowered by 7.4 kcal/mol by using DABCO·H+. The Michael addition step determines both the enantioselectivity and the regioselectivity. According to NCI analysis, the enantioselectivity is controlled by the strong interactions (such as C-H···O, C-H···N, and π···π) between the α,β-unsaturated acylazolium intermediate and benzoxazoles. We also discuss the solvent and substituent effects on the enantioselectivity and the role of the NHC. The mechanistic insights obtained in the present study would help improving current reaction systems or designing new synthetic routes.","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2482-2492"},"PeriodicalIF":2.7,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143555358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0