The Journal of Physical Chemistry A最新文献_第9页

Importance of Charge Balance for the Embedding of Zwitterionic Solutes in the Fragment Molecular Orbital Method.

IF 2.7 2区化学

The Journal of Physical Chemistry A Pub Date : 2024-12-12 DOI: 10.1021/acs.jpca.4c07218

Dmitri G Fedorov

引用次数: 0

A DFT Study on the NHC-Catalyzed Reaction of Enals with Aminoacrylates: Mechanism, Regioselectivity, and Stereoselectivity. 关于烯醛与氨基丙烯酸酯的 NHC 催化反应的 DFT 研究：机理、区域选择性和立体选择性。

IF 2.7 2区化学

The Journal of Physical Chemistry A Pub Date : 2024-12-12 Epub Date: 2024-11-27 DOI: 10.1021/acs.jpca.4c06435

Yan Li, Junjie Xiao, Yanlong Kang, Zhiqiang Zhang

{"title":"A DFT Study on the NHC-Catalyzed Reaction of Enals with Aminoacrylates: Mechanism, Regioselectivity, and Stereoselectivity.","authors":"Yan Li, Junjie Xiao, Yanlong Kang, Zhiqiang Zhang","doi":"10.1021/acs.jpca.4c06435","DOIUrl":"10.1021/acs.jpca.4c06435","url":null,"abstract":"DFT (M06-2X) calculations were used to study the NHC-catalyzed [3 + 3] cycloaddition of enals with aminoacrylates. The catalytic cycle begins with the binding of the NHC to enal. Subsequent intramolecular proton transfer generates the Breslow intermediate. This intermediate undergoes an oxidative reaction, leading to the formation of an acyl azolium intermediate, which further reacts with the other substrate aminoacrylate via a new C-C bond formation. This step determines the stereoselectivity of the current reaction, and re-face addition mode leading to the formation of the intermediate with an S-configuration is predominant. Afterward, sequential protonation, deprotonation, and cyclization form the six-membered cyclic intermediate, which upon elimination of the NHC affords the final cycloaddition product dihydropyridinone. The computed enantiomeric excess (99.1% ee) is in very good agreement with the experimentally reported value (99% ee). The origin of enantioselectivity is traced to the stronger LP···π interactions between the acyl azolium intermediate and aminoacrylate in the favored S-congurational transition state.","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"10544-10554"},"PeriodicalIF":2.7,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142737816","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

DNA Hybridization Kinetics Observed at the Single-Molecule Level Using Graphene Near-Field Effects.

IF 2.7 2区化学

The Journal of Physical Chemistry A Pub Date : 2024-12-12 Epub Date: 2024-12-02 DOI: 10.1021/acs.jpca.4c05740

Maria M Soares, João Freitas, Tiago Queirós, Agnes Purwidyantri, Pedro Alpuim, Jana B Nieder

{"title":"DNA Hybridization Kinetics Observed at the Single-Molecule Level Using Graphene Near-Field Effects.","authors":"Maria M Soares, João Freitas, Tiago Queirós, Agnes Purwidyantri, Pedro Alpuim, Jana B Nieder","doi":"10.1021/acs.jpca.4c05740","DOIUrl":"10.1021/acs.jpca.4c05740","url":null,"abstract":"We present the development of an advanced sensing platform using a monolayer of graphene functionalized with fluorophore-labeled DNA hairpins to detect the kinetics of single hairpins during the hybridization reaction. The near-field photonic effects of graphene induce a distance-dependent quenching effect on the attached fluorescent labels, resulting in distinct optical signals in response to axial displacements resulting from DNA hybridization. Employing a wide-field Total Internal Reflection Fluorescence (TIRF) optical setup coupled with a sensitive Electron-Multiplying Charge-Coupled Device (EM-CCD) camera, we successfully detected fluorescent signals of individual or a low number of individual DNA hairpins within a low-concentration environment DNA target (tDNA). These signals were used to determine the optical setup's Point Spread Function (PSF) in a novel approach to super-resolution reconstruction. Combining these techniques, the subpixel localization of single hairpin molecules and their respective intensity profiles were extracted, enabling a kinetic assessment of individual DNA hairpins, with estimated unfolding times of approximately 7 s. Observations of kinetic phenomena unveiled intermediate partially hybridized states, extending the time required to unfold the hairpin probes by more than a factor of 2. Furthermore, a developed semiempirical model allowed the conversion of fluorescent signals into fluorophore-graphene distances. At the nanometer scale, we observed a step-like unfolding process characterized by intermittent metastates of unfolding and static periods, which can be attributed to nucleation events in some cases. Our graphene-based sensing platform and optical methodologies can be adopted for further research into the kinetics of different biomolecules under diverse environmental conditions.","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"10689-10696"},"PeriodicalIF":2.7,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142764874","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

Laser-Induced Crystallization of Amino Acids through the Coordinated Effect of Optical Forces and Marangoni Convection.

IF 2.7 2区化学

The Journal of Physical Chemistry A Pub Date : 2024-12-12 DOI: 10.1021/acs.jpca.4c05518

Shao-Feng Liu, Yeqi Wang, Linhan Lin

引用次数: 0

Electron Loss and Dissociation Pathways of a Complex Dicarboxylate Dianion: EDTA².

IF 2.7 2区化学

The Journal of Physical Chemistry A Pub Date : 2024-12-11 DOI: 10.1021/acs.jpca.4c06679

Jemma A Gibbard

引用次数: 0

Theoretical Study on the Spectroscopic Properties and Line Intensities of the O₂⁺ Cation.

IF 2.7 2区化学

The Journal of Physical Chemistry A Pub Date : 2024-12-11 DOI: 10.1021/acs.jpca.4c06839

Hao Chen, Guosen Wang, Xinlu Cheng, Hong Zhang

{"title":"Theoretical Study on the Spectroscopic Properties and Line Intensities of the O2+ Cation.","authors":"Hao Chen, Guosen Wang, Xinlu Cheng, Hong Zhang","doi":"10.1021/acs.jpca.4c06839","DOIUrl":"https://doi.org/10.1021/acs.jpca.4c06839","url":null,"abstract":"O2+ cation, as one of the major gas components in the near space environment, has attracted significant attention due to its spectroscopic properties. In this study, we systematically investigate the spectroscopic properties of the O2+ cation using ab initio methods. The potential energy curves and transition dipole moments of O2+ were obtained using the icMRCI + Q method combined with the ACV5Z-DK basis set. Subsequently, the vibrational and rotational energy levels, as well as the corresponding spectroscopic constants for both ground and excited states, were determined by solving the one-dimensional radial Schrödinger equation. Based on the vibrational and rotational energy levels of bound electronic states, the internal partition function of O2+ was computed over the temperature range of 100-10,000 K. Utilizing the precise potential energy functions, transition dipole moment functions, and internal partition functions, the line intensities for the First Negative Band System (a4Πu-b4Σg-) and the Second Negative Band System (X2Πg-A2Πu) were calculated. For the first negative band system, the spectral line intensity of Δν = 1 is maximized at temperatures ranging from 100 to 7000 K. In the case of the second negative band system, the strongest vibrational band shifts with increasing temperature. We also discuss the impact of temperature on spectral lines; at higher temperatures, a greater number of energy levels are populated, allowing for the observation of more spectral lines. These findings are significant for understanding the spectral behavior of high-temperature nonequilibrium plasmas and their role during spacecraft reentry, providing a theoretical basis for experimental research.","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142811526","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

Early Oxidation Kinetics of N-Dodecane under High-Temperature Conditions.

IF 2.7 2区化学

The Journal of Physical Chemistry A Pub Date : 2024-12-11 DOI: 10.1021/acs.jpca.4c04202

Teng Zhang, Kun Yang, Danyang Liu, Wei Fan, Yao Long, Lang Chen, Jun Chen

{"title":"Early Oxidation Kinetics of N-Dodecane under High-Temperature Conditions.","authors":"Teng Zhang, Kun Yang, Danyang Liu, Wei Fan, Yao Long, Lang Chen, Jun Chen","doi":"10.1021/acs.jpca.4c04202","DOIUrl":"https://doi.org/10.1021/acs.jpca.4c04202","url":null,"abstract":"n-Dodecane(C12H26) is a typical surrogate fuel for aviation kerosene used in high-performance aero engines. The combustion kinetics of n-dodecane at temperatures above the critical point condition is the focus of attention in the aerospace field. In this paper, the first-principles molecular dynamics method is used to study the high-temperature oxidation of C12H26. Before C-C bond dissociation, C12H26 is oxidized to form oxidized C12 species containing multiple C═O, -OH, -O-, and -COOH groups, while releasing a large amount of energy. In addition, before the C-C bond dissociation of each C12H26, there are four main types of reactions: H-abstraction, H-addition, intramolecular H transfer, and O-addition. The H-abstraction and O-addition reactions have the highest frequencies. O2 molecules and H, OH, HO2, and O radicals also play important roles in promoting the oxidation of C12H26. The first investigation of the early oxidation reaction mechanism of C12H26 provides novel insights into the complex oxidation kinetics of long-chain alkanes.","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142811494","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

Assessing Computational Methods to Calculate the Binding Energies of Dimers of Five-Membered Heterocyclic Molecules

IF 2.7 2区化学

The Journal of Physical Chemistry A Pub Date : 2024-12-10 DOI: 10.1021/acs.jpca.4c0540910.1021/acs.jpca.4c05409

Alhadji Malloum*, and , Jeanet Conradie,

{"title":"Assessing Computational Methods to Calculate the Binding Energies of Dimers of Five-Membered Heterocyclic Molecules","authors":"Alhadji Malloum*,  and , Jeanet Conradie, ","doi":"10.1021/acs.jpca.4c0540910.1021/acs.jpca.4c05409","DOIUrl":"https://doi.org/10.1021/acs.jpca.4c05409https://doi.org/10.1021/acs.jpca.4c05409","url":null,"abstract":"Computational electronic structure methods, including ab initio and density functional theory (DFT), have been assessed in calculating the binding energies of 14 five-membered heterocyclic dimers. The configurations were generated using classical molecular dynamics before optimization at the MP2/aug-cc-pVTZ. Benchmark binding energies are calculated at the CCSD(T)/CBS level of theory. Among the ab initio methods, the DLPNO-CCSD(T)/CBS method has the best performance, reproducing CCSD(T)/CBS with a mean absolute deviation (MAD) of 0.17 kcal/mol. In addition, a schematic CCSD(T)/CBS approach perfectly reproduces the canonical CCSD(T)/CBS with a mean absolute error of 0.08 kcal/mol. Regarding DFT functionals, it has been found that counterpoise corrections have negligible effects on the accuracy of the functionals. Furthermore, including the D3 empirical dispersion considerably enhances the accuracy of the DFT functionals. As a result, outstanding performance is noted for the double hybrid functional B2K-PLYP, with a mean absolute error of 0.25 kcal/mol. In addition to the B2K-PLYP double hybrid functional, M05-D3, B97D, M05-2X-D3, M05-2X, M06-HF, M08-HX, M11, TPSSh-D3, and RSX-0DH-D3(BJ) have MAD values lower than 0.5 kcal/mol. These functionals are recommended for further investigations of five-membered heterocyclic clusters.","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":"128 50","pages":"10775–10784 10775–10784"},"PeriodicalIF":2.7,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142850309","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

Reactive Radical Etching of Quartz by Microwave Activated CH4/H2 Plasmas Promotes Gas Phase Nanoparticle Formation

IF 2.7 2区化学

The Journal of Physical Chemistry A Pub Date : 2024-12-10 DOI: 10.1021/acs.jpca.4c0578710.1021/acs.jpca.4c05787

Michael N. R. Ashfold*, Basile F. E. Curchod, Daniel Hollas, Jie Ma and Yuri A. Mankelevich*,

{"title":"Reactive Radical Etching of Quartz by Microwave Activated CH4/H2 Plasmas Promotes Gas Phase Nanoparticle Formation","authors":"Michael N. R. Ashfold*, Basile F. E. Curchod, Daniel Hollas, Jie Ma and Yuri A. Mankelevich*, ","doi":"10.1021/acs.jpca.4c0578710.1021/acs.jpca.4c05787","DOIUrl":"https://doi.org/10.1021/acs.jpca.4c05787https://doi.org/10.1021/acs.jpca.4c05787","url":null,"abstract":"An attenuation of visible probe radiation identified in earlier absorption studies of microwave plasma-activated CH4/H2/Ar gas mixtures is shown to arise from nanoparticles in under-pumped regions on opposing sides of a reactor used for diamond chemical vapor deposition. The present modeling studies highlight (i) ejection of Si-containing species into the gas phase by reactive radical etching of the quartz window through which the microwave radiation enters the reactor, enabled by suitably high window temperatures (TSiO2) and the synergistic action of near-window H atoms and CyHx radicals; (ii) subsequent processing of the ejected material, some of which are transported to and accumulate in stagnation regions in the entrance to the reactor side arms; and (iii) the importance of Si in facilitating homogeneous gas phase nucleation, clustering, and nanoparticle growth in these regions. The observed attenuation, its probe wavelength dependence, and its variations with changes in process conditions can all be rationalized by a combination of absorption and scattering contributions from Si/C/H containing nanoparticles with diameters d in the range of 50–100 nm. Possible implications for Si incorporation in CVD diamond samples are discussed.","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":"128 50","pages":"10884–10905 10884–10905"},"PeriodicalIF":2.7,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jpca.4c05787","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142842143","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

Influence of Noncovalent Interaction on the Nucleophilicity and Electrophilicity of Metal Centers in [MII(S2CNEt2)2] (M = Ni, Pd, Pt)

IF 2.7 2区化学

The Journal of Physical Chemistry A Pub Date : 2024-12-09 DOI: 10.1021/acs.jpca.4c0570610.1021/acs.jpca.4c05706

Zixuan Shen, Xiaoyan Li, Yanli Zeng and Xueying Zhang*,

{"title":"Influence of Noncovalent Interaction on the Nucleophilicity and Electrophilicity of Metal Centers in [MII(S2CNEt2)2] (M = Ni, Pd, Pt)","authors":"Zixuan Shen, Xiaoyan Li, Yanli Zeng and Xueying Zhang*, ","doi":"10.1021/acs.jpca.4c0570610.1021/acs.jpca.4c05706","DOIUrl":"https://doi.org/10.1021/acs.jpca.4c05706https://doi.org/10.1021/acs.jpca.4c05706","url":null,"abstract":"A systematic theoretical study was performed on the electrophilic and nucleophilic properties of Group 10 square-planar metal compounds [MII(S2CNEt2)2] (M = Ni 1, Pd 2, and Pt 3) and their complexes. The nucleophilic metal center and coordinated sulfur atom in [M(S2CNEt2)2] facilitate the formation of metal-involving and conventional noncovalent bonds. The presence a heavier metal center results in a more negative electrostatic potential and a larger nucleophilicity, which in turn leads to the formation of stronger metal-involving noncovalent bonds than those formed by a lighter metal center. The NiII center was observed to display electrophilic–nucleophilic dualism with regard to noncovalent interactions, forming both a metal-involving halogen bond (Ni···I) with iodine chloride (ICl) and a semicoordination bond (Ni···N) with N-bases. The nucleophilicity and electrophilicity of the NiII center are enhanced in the ternary complexes LB···1···XCl (X = H, I; LB = NH3, NHCH2, pyridine) due to the push–pull mechanism. The N···Ni semicoordination bond exerts a push effect on the dz2 orbital of the NiII center, while the Ni···X noncovalent bond provides a symbiotic pull effect on this orbital. Furthermore, the formation of metal-involving noncovalent bonds may enhance the electrophilic ability of the PdII and PtII center, resulting in the formation of stable ternary complexes Py···2/3···XCl (X = H, I), which are characterized by M···N and M···X interactions.","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":"128 50","pages":"10796–10807 10796–10807"},"PeriodicalIF":2.7,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142850283","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