The Journal of Physical Chemistry A最新文献

{"title":"Molecular Properties of Hydroxyamino Acids in Water.","authors":"Roman Boča, Žofia Rádiková, Juraj Štofko, Beata Vranovičová, Cyril Rajnák","doi":"10.1021/acs.jpca.5c00701","DOIUrl":"10.1021/acs.jpca.5c00701","url":null,"abstract":"<p><p>Aliphatic hydroxyamino acids, namely, α-hydroxyglycine, α-hydroxyalanine, serine, threonine, and homoserine, were studied by quantum chemical calculations using two methods in water as a solvent. A hybrid variant of DFT-B3LYP was applied to optimize the geometry of neutral molecules, molecular cations, and anions for the canonical and zwitterionic form of amino acids. In the energy minimum, vibrational analysis was applied, enabling the evaluation of thermodynamic functions (internal energy, enthalpy, entropy, and Gibbs energy) of individual species and absolute oxidation and reduction potentials for redox couples. In the B3LYP preoptimized geometry, the advanced DLPNO-CCSD(T) method was applied to include the major part of the interelectron correlation energy. Calculated molecular descriptors were compared with previously studied molecules by the same method, and the whole set for 17 amino acids was processed by advanced statistical methods such as cluster analysis and principal component analysis. Calculated oxidation potentials correlate with the adiabatic ionization energies along a straight line, and analogously, the calculated reduction potential correlates with the electrophilicity index. The ionization energy in α-amino acids is systematically influenced (reduced) by the functional groups such as hydroxyl, methyl, ethyl, and <i>iso</i>-propyl; it decreases along a series of α-, β-, γ-, and δ-amino acids.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2903-2911"},"PeriodicalIF":2.7,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143655527","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}

{"title":"Surface Formation Pathway of Nitrogen- and Sulfur-Containing Organic Compounds on Ammonium Sulfate.","authors":"Jie Chen, George Wandera Kisimbiri, Ivan Gladich, Nicolas Fauré, Erik S Thomson, Robert Temperton, Zamin A Kanji, Xiangrui Kong","doi":"10.1021/acs.jpca.5c00332","DOIUrl":"10.1021/acs.jpca.5c00332","url":null,"abstract":"<p><p>The formation of nitrogen- and sulfur-containing organic compounds (N-Org and S-Org) is important for atmospheric secondary organic aerosol (SOA) production, thereby influencing air quality and global climate. However, the mechanisms underlying N-Org and S-Org formation on aerosol particle surfaces are poorly understood due to the limited availability of surface-sensitive analytical techniques. This study investigates the surface interactions of glyoxal (GL), a known SOA precursor, with ammonium sulfate (NH₄)₂SO₄, under varying relative humidity (RH) conditions, using ambient-pressure X-ray photoelectron spectroscopy (APXPS), near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, and molecular dynamics (MD) simulations. N-Org species, such as imines, a key intermediate in brown carbon (BrC) formation, are identified on the (NH₄)₂SO₄ surface at low RH (≤13.3%). The formed S-Org species cannot be specified due to the difficulties in distinguishing S-Org from inorganic sulfate in the XPS spectra. Elemental ratios on (NH₄)₂SO₄ surface across the entire probing depth show increased S/O and N/O ratios upon GL exposure, indicating the formation of N-Org and S-Org species. NEXAFS measurements further confirm the surface changes of (NH₄)₂SO₄ associated with the adsorption of GL and water. These findings provide compelling evidence of surface-driven N-Org and S-Org formation pathways, demonstrating that heterogeneous reactions on (NH₄)₂SO₄ particle surfaces could be an active source of atmospheric BrC and SOA.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2922-2931"},"PeriodicalIF":2.7,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956130/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143622889","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}

{"title":"Theoretical Exploration of the Effects of Conjugated Side Chains on the Photoelectric Properties of Y6-Based Nonfullerene Acceptors.","authors":"Xingyu Xie, Zhiyun Chen, Shaohui Zheng","doi":"10.1021/acs.jpca.4c08587","DOIUrl":"10.1021/acs.jpca.4c08587","url":null,"abstract":"<p><p>With the application of nonfullerene acceptors (NFAs) Y6 and its derivatives, the power conversion efficiencies (PCEs) of single-junction organic solar cells (OSCs) have exceeded 20%. Side-chain engineering has proven to be an important strategy for optimizing Y6-based NFAs. However, studies on the incorporation of conjugated side chains into Y6-based NFAs are still rare, and the corresponding underlying mechanisms are still not well understood. In this article, we systematically designed eight molecules based on modifications to the conjugated side chains of two reported Y6-based NFAs, involving alterations of branched alkyl chains at different positions on the thiophene, benzene, bithiophene, and benzene-thiophene moieties that serve as conjugated side chains. Using reliable density functional theory (DFT) and time-dependent DFT calculations, we obtained key photovoltaic parameters such as molecular planarity, dipole moments, electrostatic potential and corresponding fluctuations, frontier molecular orbitals, exciton binding energy (<i>E</i>_b), singlet-triplet energy differences (Δ<i>E</i>_<i>ST</i>), and UV-vis absorption spectra of these newly designed NFAs. The results show that the side conjugated rings and the positions of lateral alkyl chains attached to these rings exert noticeable influences on their photoelectric properties. Notably, compared to the prototype T3EH, 2T2EH, 2T3EH, PT2EH, PT3EH, and P2EH exhibit enhanced absorption (manifesting as increased total oscillator strength) and smaller <i>E</i>_b and Δ<i>E_ST</i> values, hinting at their promising potential as novel NFAs.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2866-2875"},"PeriodicalIF":2.7,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143622890","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}

{"title":"Comprehensive DFTB Parametrization and Its Utilization as a Preoptimizer for Investigating Au-Nanostructures + H₂O Systems.","authors":"Paria Fallahi, Hossein Farrokhpour","doi":"10.1021/acs.jpca.4c07923","DOIUrl":"10.1021/acs.jpca.4c07923","url":null,"abstract":"<p><p>A novel parameterization of a self-consistent charge density functional-based tight-binding scheme (SCC-DFTB) to characterize gold (Au)-water hybrid systems by developing new pair parameters for (Au, O, H-X where X = Au, O, H) using the DFTB module of Material Studio 2020 is introduced. To characterize Au-water systems within the DFTB framework, the derived parameters are systematically compared with DFT-DMOL3 and DFTB-AuOrg (existing library of DFTB) data for Au_n clusters (<i>n</i> = 2, 4, 8, 25, and 34), Au_n mono layer surfaces (<i>n</i> = 7, 19, 25, 37, and 49), Au₅₀ bilayer surface, and Au nanostructures-H₂O complexes. The geometrical, energetic, and electronic characteristics derived from the newly parametrized library (DFTB-AuOH) for the Au clusters align well with both the DFT-DMOL3 and the DFTB-AuOrg results, demonstrating that the stability of the Au clusters is accurately represented by the existing parameters. The structural outcomes derived from the DFTB-AuOH for Au surfaces indicate its substantial capability to optimize extensive gold surfaces in comparison to the DFT-DMOL3 approach, in which, in this case, the DFTB-AuOrg approach identified bent surfaces as the optimized configurations. Furthermore, the structural and energetic achievements determined from the DFTB-AuOH for Au nanostructure complexes with water molecule(s) reveal low-energy configurations and optimized structures with minimal variation when compared to DFT-DMOL3. The linear correlation equations of <i>Y</i> = (-0.044) <i>X</i> - 10.198 and <i>Y</i> = (-0.05) <i>X</i> - 10.538 are applied to the adsorption and interaction energy, respectively, to scale these DFTB-AuOH energies to their corresponding DFT-DMOL3 energies and to investigate all these energies in relation to the gold surface size, thereby confirming these accomplishments and demonstrating their compatibility significantly. The activation energy of water dissociation on Au surfaces is compared through all three approaches, and it also demonstrates significant compatibility as well. Lastly, the study of the molecular dynamics simulations reveals significant variations in the expected dynamic behavior among the DFTB-AuOH, DFT-DMOL3, and DFTB-AuOrg techniques. DFTB-AuOH consistently exhibits variations that more closely align with DFT-DMOL3, albeit of lesser magnitude, in contrast to DFTB-AuOrg, which predicts significantly smaller fluctuations overall.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2835-2853"},"PeriodicalIF":2.7,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143629982","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}

{"title":"Machine Learning Approaches for Developing Potential Surfaces: Applications to OH^-(H₂O)_<i>n</i> (<i>n</i> = 1-3) Complexes.","authors":"Greta M Jacobson, Lixue Cheng, Vignesh C Bhethanabotla, Jiace Sun, Anne B McCoy","doi":"10.1021/acs.jpca.4c08826","DOIUrl":"10.1021/acs.jpca.4c08826","url":null,"abstract":"<p><p>An approach for obtaining high-level <i>ab initio</i> potential surfaces is described. The approach takes advantage of machine learning strategies in a two-step process. In the first, the molecular-orbital based machine learning (MOB-ML) model uses Gaussian process regression to learn the correlation energy at the CCSD(T) level using the molecular orbitals obtained from Hartree-Fock calculations. In this work, the MOB-ML approach is expanded to use orbitals obtained using a smaller basis set, aug-cc-pVDZ, as features for learning the correlation energies at the complete basis set (CBS) limit. This approach is combined with the development of a neural-network potential, where the sampled geometries and energies that provide the training data for the potential are obtained using a diffusion Monte Carlo (DMC) calculation, which was run using the MOB-ML model. Protocols are developed to make full use of the structures that are obtained from the DMC calculation in the training process. These approaches are used to develop potentials for OH^-(H₂O) and H₃O⁺(H₂O), which are used for subsequent DMC calculations. The results of these calculations are compared to those performed using previously reported potentials. Overall, the results of the two sets of DMC calculations are in good agreement for these very floppy molecules. Potentials are also developed for OH^-(H₂O)₂ and OH^-(H₂O)₃, for which there are not available potential surfaces. The results of DMC calculations for these ions are compared to those for the corresponding H₃O⁺(H₂O)₂ and H₃O⁺(H₂O)₃ ions. It is found that the level of delocalization of the shared proton is similar for a hydroxide or hydronium ion bound to the same number of water molecules. This finding is consistent with the experimental observation that these sets of ions have similar spectra.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2958-2972"},"PeriodicalIF":2.7,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143655526","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}

{"title":"Exploring Emission Ratios: Influence of Neighboring Groups on TSAL Core.","authors":"Olaf Morawski, Pawel Gawrys, Marzena Banasiewicz, Cristina A Barboza","doi":"10.1021/acs.jpca.5c01560","DOIUrl":"https://doi.org/10.1021/acs.jpca.5c01560","url":null,"abstract":"<p><p>The photophysics of tris(salicylidenealdimines) (TSALs) has been examined, as they offer the possibility of populating multiple emissive species through the excited-state intramolecular proton transfer (ESIPT) reaction, resulting in broad visible spectrum coverage, a desirable property for white organic light-emitting diodes (wOLEDs). In this contribution, the synthesis and photophysical characterization of a new TSAL derivative, <b>C16</b>, are reported. It displays a distinct emission profile compared to previously studied tris(salicylideneanilines), with an inversion of the ESIPT/LE emission intensity ratio, exhibiting almost exclusively tautomer emission upon excitation in less polar solvents. <i>Ab initio</i> calculations suggest that the absence of emission from the locally excited (LE) state in nonpolar solvents may be related to the competition between two processes: ESIPT and <i>N</i>-pyramidalization of the enaminic nitrogen. Conversely, in polar aprotic solvents, the planar LE conformation is stabilized, and dual emission is observed. In protic solvents, however, the ESIPT reaction is suppressed due to competition with intermolecular hydrogen bonding interactions.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143727099","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}

{"title":"Reaction between Hydrogen Peroxide and Ozone: Possibility of the Formation of H₂O₅.","authors":"Bhabesh Baro, Himanshu Borah, Shankupar Rynjah, Biplab Sarkar","doi":"10.1021/acs.jpca.4c06707","DOIUrl":"10.1021/acs.jpca.4c06707","url":null,"abstract":"<p><p>Gas-phase reaction of ozone and hydrogen peroxide to form water and singlet oxygen, a reactive oxygen species, has been investigated employing density functional theory and ab initio coupled cluster, CCSD(T) methods. The calculated H₂O₂ loss (4.01 × 10^-7 s^-1 at 296 K) has excellent agreement with the experimental observations considering the ozone concentration in the stratosphere and upper troposphere of the order of 10¹³ molecules cm^-3. Notably, a new pathway leading to the formation of H₂O₅ has been observed, which has not been reported in the existing literature until now.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2829-2834"},"PeriodicalIF":2.7,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143655528","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}

{"title":"Binding Energy Calculations of Anthracene and Rhodamine 6G H-Type Dimers: A Comparative Study of DFT and SMD Methods.","authors":"Daniel Doveiko, Karina Kubiak-Ossowska, Yu Chen","doi":"10.1021/acs.jpca.4c07867","DOIUrl":"10.1021/acs.jpca.4c07867","url":null,"abstract":"<p><p>With the ever-growing need to study systems of increased size and complexity, modern density functional theory (DFT) methods often encounter problems arising from the growing computational demands. In this work, we have presented a comprehensive DFT validation of the steered molecular dynamics (SMD) approach in estimating the binding energies of aromatic dimers. By performing DFT calculations on optimized and unoptimized anthracene and rhodamine 6G (R6G) dimers using functionals with progressively enhanced exchange-correlation energy description and comparing the obtained results with SMD-predicted values, it was found that SMD predictions are in good agreement with the results obtained from hybrid DFT calculations. The average binding energies for optimized anthracene dimers were found to be 6.46 kcal/mol using DFT at ωB97X-D4/def2-QZVPP and 7.64 ± 1.61 kcal/mol as predicted by the SMD. For the R6G H-type dimer, the binding energies were 17.48 and 19.02 ± 2.22 kcal/mol, respectively. The study also revealed that due to the lack of explicit terms accounting for electron-electron interactions in MD force fields, the proposed method tends to overbind dimers. It is anticipated that the presented method can be applied to more complex dimers, potentially accelerating the calculations of binding energies. Moreover, this study further validates the accuracy of the CHARMM36 FF.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2946-2957"},"PeriodicalIF":2.7,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956137/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143254152","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}

{"title":"Spontaneous Deprotonation of HO₂^• at Air-Water Interface.","authors":"Philips Kumar Rai, Amit Kumar, Pradeep Kumar","doi":"10.1021/acs.jpca.4c08194","DOIUrl":"10.1021/acs.jpca.4c08194","url":null,"abstract":"<p><p>HO₂^• is a crucial radical in atmospheric chemistry, with applications ranging from HO₂^•/OH^• interconversion to controlling the budget of various trace gases in the atmosphere. It is known that one of the potential sinks for HO₂^• is clouds and aerosols, though the mechanism is not clear to date. In the present study, using Born-Oppenheimer molecular dynamics simulations, we have demonstrated that the dissociation of HO₂^• on the surface of a water droplet, as well as in the bulk phase, is a spontaneous process. In addition, we have computed the Gibbs free energy for the deprotonation of HO₂^• on both the surface and in the bulk, which suggests that deprotonation of HO₂^• on the surface occurs faster compared to the same in the bulk.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2912-2921"},"PeriodicalIF":2.7,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143655530","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}

{"title":"Infrared Spectroscopy of [H₂O-N₂O]⁺-(H₂O)_<i>n</i> (<i>n</i> = 1 and 2): Microhydration Effects on the Hemibond.","authors":"Tatsuki Hosoda, Mizuhiro Kominato, Asuka Fujii","doi":"10.1021/acs.jpca.5c00428","DOIUrl":"10.1021/acs.jpca.5c00428","url":null,"abstract":"<p><p>The hemibond, a nonclassical covalent bond involving three electrons shared between two centers, has attracted considerable attention due to its significance in radiation chemistry. Water radical cation clusters, [H₂O-X]⁺, exhibit two primary bonding motifs: the hemibond and the hydrogen bond. Although hydrogen bond formation typically dominates, recent studies have identified instances of hemibond formation in some systems involving water molecules. This study focuses on the [H₂O-N₂O]⁺ radical cation cluster, a rare system exhibiting hemibond formation. We investigate the stability of this hemibond in [H₂O-N₂O]⁺ against microhydration by employing infrared photodissociation spectroscopy and conducting theoretical calculations on [H₂O-N₂O]⁺-(H₂O)_<i>n</i> (<i>n</i> = 1 and 2). By comparing experimental and simulated spectra, we determined the predominant intermolecular bonding motifs in [H₂O-N₂O]⁺-(H₂O)_<i>n</i> (<i>n</i> = 1 and 2). Our analysis revealed that proton-transferred-type isomers are almost exclusively populated for <i>n</i> = 1 and 2, whereas hemibonded-type isomers are energetically unfavorable. These findings indicate that microhydration disrupts the hemibond and shifts the stable structural motifs.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2896-2902"},"PeriodicalIF":2.7,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143612845","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}