Physical Chemistry Chemical Physics最新文献

{"title":"Atomistic adsorption of PETase onto large-scale PET 3D-models that mimic reality","authors":"Pedro Paiva, Emiliano Ippoliti, Paolo Carloni, Pedro Alexandrino Fernandes, Maria Joao Joao Ramos","doi":"10.1039/d4cp03488k","DOIUrl":"https://doi.org/10.1039/d4cp03488k","url":null,"abstract":"Polyethylene terephthalate (PET) has been widely used in plastic products, leading to massive PET waste accumulation in ecosystems worldwide. The efforts to find greener processes for dealing with post-consumer PET waste led to the discovery of PET-degrading enzymes such as Ideonella sakaiensis PETase (IsPETase). In silico studies have provided valuable contributions to this field, shedding light on the catalytic mechanisms and substrate interactions in many PET hydrolase enzymes. However, most of these studies often rely on short PET oligomers, failing to replicate the catalytic-relevant interactions and the true substrate motions occurring during contact with a PET-degrading enzyme. A comprehensive atomistic study of PET in both its crystalline (cPET) and amorphous (aPET) states, along with the adsorption of a PET-degrading enzyme onto solid PET, would greatly advance our understanding of the mechanisms driving PET biodegradation. In this study, we developed large-scale computational models of cPET, comprising thousands of monomers, and conducted Molecular Dynamics simulations to follow the transformation of cPET into aPET. These models were validated by confrontation with experimentally determined data. We then studied the adsorption of IsPETase on the assembled PET models, discussed the main phenomena that differentiate the two adsorption processes, and explored them from a catalytic perspective. The results and the computational PET models provided herein are envisioned to aid in the development of innovative strategies for PET waste biodegradation.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"12 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142809886","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of Hydrogen Storage in Sandstone Reservoirs using 1H Nuclear Magnetic Resonance Spectroscopy","authors":"Son T. Dang, Sidi Mamoudou, Chandra S. Rai, Tuan A Ho","doi":"10.1039/d4cp04366a","DOIUrl":"https://doi.org/10.1039/d4cp04366a","url":null,"abstract":"Evaluation of hydrogen storage capacity of porous rocks is crucial for underground hydrogen storage. Using 1H Nuclear Magnetic Resonance (NMR) spectroscopy we successfully characterized the hydrogen responses and identified storage mechanisms in Berea sandstone under varying water saturation. The results indicate that the injected hydrogen behaves as a free gas phase and is capable of occupying the empty pore volume regardless of saturation state. No hysteresis was observed during injection and production cycles.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"231 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142809509","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular dynamics as an efficient process to predict 15N chemical shift anisotropy at very high NMR magnetic field","authors":"Maggy HOLOGNE, Po-Chia Chen, François-Xavier Cantrelle, Olivier Walker","doi":"10.1039/d4cp03821e","DOIUrl":"https://doi.org/10.1039/d4cp03821e","url":null,"abstract":"The emergence of very high NMR magnetic fields will certainly encourage the study of larger biological systems with their dynamics and interactions. NMR spin relaxation allows to probe dynamical properties of proteins where the <small>¹⁵</small>N longitudinal (R<small>₁</small>) and transverse (R<small>₂</small>) relaxation rates additional to the <small>¹</small>H-<small>¹⁵</small>N heteronuclear NOE describe the ps-ns time scale. Their analytical representation involves the chemical shift anisotropy (CSA) effect that represents the major contribution at very high magnetic field above 18.8 T. An accurate analysis of the latter parameters in terms of Model Free (MF) requires considering its effect. Until now, a uniform value of -160 ppm for the CSA is widely used to derive the backbone order parameters (S<small>²</small>), giving rise to a large fluctuation of its value at very high magnetic field. Conversely, the use of a site-specific CSA improves the accurate analysis of protein dynamics but requires a cost-effective experimental multi-field approach. In the present paper, we show how the CSA mainly contributes to the relaxation parameters at 28.2 T compared to lower magnetic fields and may bias the determination of S<small>²</small>. We propose to replace the time-consuming measurement of spin relaxation at multiple fields by a combination of molecular dynamics (MD) and the measurement of spin relaxation at one very high magnetic field only. We applied this strategy to three well-folded proteins (ubiquitin, GB3 and ribonuclease H) to show that the determined order parameters are in good agreement with the ones obtained by means of experimental data only.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"89 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142809513","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Further Exploration on the Physicochemical Nature of μ2-Bridge-Relevant Deprotonations via the Elucidation of Four Kinds of Alditol Complexes","authors":"Yi Wu, Linchen Xie, Ye Jiang, Anqi He, Da Li, Limin Yang, Yizhuang Xu, Kexin Liu, Yukihiro Ozaki, Isao Noda","doi":"10.1039/d4cp03612c","DOIUrl":"https://doi.org/10.1039/d4cp03612c","url":null,"abstract":"Single-crystal structures of four alditol complexes are presented. In LuCl<small>₃</small>/galactitol and ScCl<small>₃</small>/<em>myo</em>-inositol complexes, μ<small>₂</small>-bridge-relevant deprotonations were observed. The polarization from two rare earth ions in the μ<small>₂</small>-bridge activates the chemically inert OH and promotes deprotonation. Additionally, mass spectrometry, pH experiments, and quantum chemistry calculations were conducted to enhance our understanding of the μ<small>₂</small>-bridge-relevant deprotonations. A common structural feature of the complexes where μ<small>₂</small>-bridge-relevant deprotonation takes place is that two metal ions and two oxygen atoms in two μ<small>₂</small>-bridges form an M<small>₂</small>O<small>₂</small> cluster. The four atoms in the M<small>₂</small>O<small>₂</small> cluster make up a parallelogram. Such a structure is useful to balance the strong Coulombic repulsions between two M<small>³⁺</small> and between two O<small>^-</small>. In the ScCl<small>₃</small>/<em>myo</em>-inositol complex, the deprotonation exhibits a characteristic of regional/chiral selectivity. Galactitol is a third alditol ligand where μ<small>₂</small>-bridge-relevant deprotonation is observed. The flexible backbone of the galactitol allows the formation of more five-membered chelating rings and six-membered chelating rings, which are used to stabilize the rare earth ions of the μ<small>₂</small>-bridge. The coordination makes the backbone of galactitol deviate from the zigzag conformation. The above results are helpful in the rational design of high-performance catalysts.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"42 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142809512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Frequency and Time Domain 19F ENDOR Spectroscopy: Role of Nuclear Dipolar Couplings to Determine Distance Distributions","authors":"Annemarie Kehl, Lucca Sielaff, Laura Remmel, Maya Lilly Rämisch, Marina Bennati, Andreas Meyer","doi":"10.1039/d4cp04443f","DOIUrl":"https://doi.org/10.1039/d4cp04443f","url":null,"abstract":"<small>¹⁹</small>F electron-nuclear double resonance (ENDOR) spectroscopy is emerging as a method of choice to determine molecular distances in biomolecules in the angstrom to nanometer range. However, line broadening mechanisms in <small>¹⁹</small>F ENDOR spectra can obscure the detected spin-dipolar coupling that encodes the distance information, thus limiting the resolution and accessible distance range. So far, the origin of these mechanisms has not been understood. Here, we employ a combined approach of rational molecular design, frequency and time domain ENDOR methods as well as quantum mechanical spin dynamics simulations to analyze these mechanisms. We present the first application of Fourier transform ENDOR to remove power broadening and measure T<small>_2n</small> of the <small>¹⁹</small>F nucleus. We identify nuclear dipolar couplings between the fluorine and protons up to 14 kHz as a major source of spectral broadening. When removing these interactions by H/D exchange, an unprecedented spectral width of 9 kHz was observed suggesting that, generally, the accessible distance range can be extended. In a spin labeled RNA duplex we were able to predict the spectral ENDOR line width, which in turn enabled to extract a distance distribution. This study represents a first step towards a quantitative determination of distance distributions in biomolecules from <small>¹⁹</small>F ENDOR.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"44 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142815491","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-scale circuit model bridges molecular modeling and experimental measurements of conductive metal-organic framework supercapacitors","authors":"Liang Niu, Zhou Liu, Ding Yu, Volker Presser, Ming Chen, Guang Feng","doi":"10.1039/d4cp02487g","DOIUrl":"https://doi.org/10.1039/d4cp02487g","url":null,"abstract":"The multi-scale model is crucial for combining experiments and simulations to reveal the energy storage mechanism. As novel electrode materials, conductive metal-organic frameworks (c-MOFs) provide an ideal platform for understanding the energy storage process in supercapacitors. However, the prevailing circuit models lack consideration of the distinctive transmission path of c-MOF, which hinders accurate descriptions of c-MOF supercapacitors. By proposing a concept for clarifying the c-MOF electrode to a crystal-matrix electrode according to the crystallinity, we developed a universal multi-scale circuit model considering crystal shape and porosity to describe the impedance and capacitance of c-MOF electrodes. For supercapacitors with c-MOF electrodes and ionic liquid electrolytes, results predicted from the new multi-scale circuit model, based on microscale parameters obtained from molecular dynamics simulations, demonstrate quantitative agreement with experimental data for electrodes with different crystallinities","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"40 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142805074","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhancing the stability and performance of Ni-rich cathode materials through Ta doping: a combined theoretical and experimental study","authors":"Frederike Monsees, Casimir Misiewicz, Mert Dalkilic, Diddo Diddens, Andreas Heuer","doi":"10.1039/d4cp03911d","DOIUrl":"https://doi.org/10.1039/d4cp03911d","url":null,"abstract":"As the demand for high-energy batteries to power electric vehicles continues to grow, Ni-rich cathode materials have emerged as promising candidates due to their high capacity. However, these materials are prone to rapid degradation under increased voltages, posing significant challenges for their long-term stability and safety. In this study, we investigate the effects of tantalum (Ta) doping on the performance and stability of LiNi<small>_0.80</small>Mn<small>_0.1</small>Co<small>_0.1</small>O<small>₂</small> (NMC811) cathode materials. Using a combined theoretical and experimental approach, we employ density functional theory (DFT) and cluster expansion models to analyze the electronic structure and oxygen vacancy formation enthalpy in Ta-doped NMC811. Experimental validation is conducted using cycling and gas measurements <em>via</em> on-line electrochemical mass spectrometry (OEMS) on in-house synthesized cathode active materials. Both theoretical and experimental approaches show an improvement in oxygen binding due to tantalum doping, with the DFT results highlighting the impact of Ni<small>⁴⁺</small> concentration on the proximity of the vacancy. Our results suggest that Ta doping inhibits the formation of oxygen vacancy-induced side phases, reducing cracking and enhancing the longevity and safety of Ni-rich cathodes.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"21 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142805104","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A new carbon allotrope with high carrier mobility and optical absorption","authors":"Zhigang Shao, Guangyu Zhou, Canglong Wang, Lei Yang","doi":"10.1039/d4cp02685c","DOIUrl":"https://doi.org/10.1039/d4cp02685c","url":null,"abstract":"Carbon atom has different bonding modes, which provides the possibility for the existence of multilayer carbon allotropes. Among these bonding modes, the sp<small>³</small> hybrid bonding mode often causes atoms to be noncoplanar. This provides the possibility for the emergence of two-dimensional (2D) multilayer materials. In this work, a new 2D multilayer carbon allotrope named trilaminar buckled T-graphene is proposed. Carbon atoms have sp<small>²</small> and sp<small>³</small> hybridization in this structure. It is nonmagnetic and has an indirect band gap of 1.70 eV. It has mechanical stability and dynamic stability, and formation energy calculations also prove that it is stable. Thermal stability calculations results indicate that it does not change the bonding pattern at 1000 K. It is an elastically soft material with a low value of elastic constants. This structure shows amazing electrical properties, which has a high hole mobility of close to 3071 cm<small>²</small> V<small>⁻¹</small> s<small>⁻¹</small>. Optical property calculations results show that it has an optical gap of 1.70 eV and an ultrahigh absorption in visible and near ultraviolet light. Considering all its properties, this structure has great application potential in high-speed electronic and optoelectronic devices, optical filters, modified substrates, and adsorption sensors.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"119 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142805148","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sulfur-doping effects on the oxygen vacancy formation of LaBO3 (B= Fe, Co, and Ni) perovskites","authors":"Ting Jia, Yinuo Hao, Hua Hao","doi":"10.1039/d4cp03834g","DOIUrl":"https://doi.org/10.1039/d4cp03834g","url":null,"abstract":"Oxygen vacancy (VO) formation in perovskites plays an important role in improving their functional applications. Using density functional theory calculations, we investigated the effect of sulfur (S) doping on the VO formation of LaBO3 (B= Fe, Co, and Ni) perovskites, considering the HS, IS, and LS states of Co ions in LaCoO3 to examine the influence of spin states. Our results show that the weaker electronegativity of S2- relative to O2- leads to a decreased magnetic moment of B atoms directly adjacent to the substituted S and an increase in the electrical conductivity of the insulating systems. The formation energy Ef calculations suggest that S doping is beneficial for the VO formation. In particular, VO is more likely to form at oxygen positions adjacent to the S ion. Moreover, upon S doping, the spin state transition is not a necessary condition to lower the Ef. Instead, the main reason for reducing the Ef of VO is the decreased relaxation energy of the lattice following VO formation. Therefore, we revealed a common mechanism for S-doping promoted VO formation, which could be extended to other perovskites.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"77 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142805139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Wavelength-dependent intersystem crossing dynamics of phenolic carbonyls in wildfire emissions","authors":"Rashid R. Valiev, Theo Kurtén, Greg T. Drozd, Yiheng He, Tate Weltzin, Allen Zhu, Dong Lee, Ellery Moore, Aidan Gee","doi":"10.1039/d4cp03501a","DOIUrl":"https://doi.org/10.1039/d4cp03501a","url":null,"abstract":"Quantum chemical calculations were employed to construct Jablonski diagrams for a series of phenolic carbonyls, including vanillin, iso-vanillin, 4-hydroxybenzaldehyde, syringaldehyde, and coniferyl aldehyde. These molecules can enter the Earth’s atmosphere from forest fire emissions and participate in photochemical reactions within atmospheric water, including cloud and fog droplets and aqueous aerosol particles. This photochemistry alters the composition of light-absorbing organic content, or brown carbon, in droplets and particles through formation and destruction of key chromophores. This study demonstrates that following photon absorption, Phenolic carbonyls efficiently transition to triplet states via the intersystem crossing (ISC) mechanism, with rates ranging from 109 to 1010 s−1. Despite the presence of multiple potential ISC pathways due to several lower-lying triplet states, a single channel is found to dominate. We investigated the dependence of the ISC rate constant (kISC) on the vibrational excitation energy of the singlet excited state (S1) and compared it with the measured photochemical quantum yield (Φloss) as a function of wavelength. Although our model only accounts for intramolecular nonradiative electronic transitions, it successfully captures the overall trends. All the molecules, except coniferyl aldehyde, exhibit saturation in the dependence of kISC and Φloss on photon wavenumber or vibrational excitation energy. In contrast, coniferyl aldehyde displays a single maximum followed by a monotonic decrease as excitation energy increases. This distinct behavior in coniferyl aldehyde may be attributed to the presence of a double-bonded substituent, which enhances π-electron conjugation and reduces the exchange energy and adiabatic energy gap between the S1 state and the target triplet state. For small energy gaps, the classical acceptor modes of the ISC process are less effective, leading to a low effective density of final states. Larger gaps enhance the effective density of states, making the ISC dependence more pronounced. Our calculations show that coniferyl aldehyde has a smaller adiabatic gap (1700 cm−1) compared to the other phenolic carbonyls studied, with similar acceptor modes. The magnitude of the adiabatic gap is identified as the primary factor distinguishing the different ISC dependencies and Φloss.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"19 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142805107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}