The Journal of Physical Chemistry Letters

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ISSN / EISSN : 1948-7185 / 1948-7185
Published by: American Chemical Society (ACS) (10.1021)
Total articles ≅ 11,030
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The Journal of Physical Chemistry Letters pp 6628-6633; doi:10.1021/acs.jpclett.1c01823

Abstract:
Vibrational energies are partitioned into the contributions of molecular parts called segments, for instance, residues in proteins. The fragment molecular orbital method is used to facilitate vibrational calculations of large systems at the DFTB and HF-3c levels. The vibrational analysis is combined with the partitioning of the electronic energy, yielding free-energy contributions of segments to the binding energy, pinpointing hot spots for drug discovery and other studies. The analysis is illustrated on two protein–ligand complexes in solution.
The Journal of Physical Chemistry Letters pp 6634-6638; doi:10.1021/acs.jpclett.1c01073

Abstract:
Vibrational spectroscopy is a powerful tool used to analyze biological and chemical samples. However, in proteins, the most predominant peaks that arise from the backbone amide groups overlap one another, hampering site-specific analyses. Isotope editing has provided a robust, noninvasive approach to overcome this hurdle. In particular, the 1-13C═16O and 1-13C═18O labels that shift the amide I vibrational mode have enabled 1D- and 2D-IR spectroscopy to characterize proteins with excellent site-specific resolution. Herein, we expand the vibrational spectroscopy toolkit appreciably by introducing the 1-13C15N probe at specific locations along the protein backbone. A new, isotopically edited amide II peak is observed clearly in the spectra despite the presence of unlabeled modes arising from the rest of the protein. The experimentally determined shift of −30 cm–1 is reproduced by DFT calculations providing further credence to the mode assignment. Since the amide II mode arises from different elements than the amide I mode, it affords molecular insights that are both distinct and complementary. Moreover, multiple labeling schemes may be used simultaneously, enhancing vibrational spectroscopy’s ability to provide detailed molecular insights.
Hui Peng, Xinxin Wang, Ye Tian, Tiantian Dong, Yonghao Xiao, Tao Huang, Yongchang Guo, ,
The Journal of Physical Chemistry Letters pp 6639-6647; doi:10.1021/acs.jpclett.1c01794

Abstract:
Here, we report (C4H9)4NCuCl2 single crystals with a luminous intensity that remains largely the same after soaking in water for 24 h. (CH9)4NCuCl2 has a new type zero-dimensional framework, in which the isolated [CuCl2]− anions are wrapped by organic (C4H9)4N+ cations. As expected, (C4H9)4NCuCl2 shows a broad emission band at 508 nm with a photoluminescence quantum yield of approximately 82% at room temperature, stemming from self-trapped exciton (STE) emission. Temperature-dependent photoluminescence measurement reveals that there is an energy barrier ΔE (24.0 meV) between the intrinsic state and STE state, which leads to the increase in emission intensity with an increase in temperature (98–278 K), while the emission intensity begins to decrease when the temperature is higher than 278 K due to the effects of both thermal quenching and carrier scattering. Our findings provide a new idea for the design of lead-free anti-water stability metal halide materials.
, Iwona Płowaś-Korus
The Journal of Physical Chemistry Letters pp 6613-6621; doi:10.1021/acs.jpclett.1c01798

Abstract:
We report the vibrational and thermodynamic properties of four known CsPbI3 polymorphs in the framework of the density functional theory. We compare the recently introduced strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) with the local density approximation (LDA). We found that the SCAN, compared to the LDA, could explain discrepancies between theoretical and experimental results. Evaluating the Helmholtz free energy as a function of temperature, we found that within the SCAN (a) all polymorphs had negative formation enthalpies at the room temperature and (b) CsPbI3 underwent the phase transition from the δ- to α-phase at 480 K. This is not true for the LDA. In contrast to the previous reports based on the LDA, we did not find the ferroelectric instability in the phonon spectra of the cubic and tetragonal phases at the meta-GGA level. This result agrees with the lack of observation of the ferroelectricity in CsPbI3.
Mattia Bondanza, ,
The Journal of Physical Chemistry Letters pp 6604-6612; doi:10.1021/acs.jpclett.1c01929

Abstract:
Xanthophylls are a class of oxygen-containing carotenoids, which play a fundamental role in light-harvesting pigment–protein complexes and in many photoresponsive proteins. The complexity of the manifold of the electronic states and the large sensitivity to the environment still prevent a clear and coherent interpretation of their photophysics and photochemistry. In this Letter, we compare cutting-edge ab initio methods (CC3 and DMRG/NEVPT2) with time-dependent DFT and semiempirical CI (SECI) on model keto-carotenoids and show that SECI represents the right compromise between accuracy and computational cost to be applied to real xanthophylls in their biological environment. As an example, we investigate canthaxanthin in the orange carotenoid protein and show that the conical intersections between excited states and excited–ground states are mostly determined by the effective bond length alternation coordinate, which is significantly tuned by the protein through geometrical constraints and electrostatic effects.
, Junbeom Jo, Youngmin Kim, , Changin Kim, Yeeun Kim, Chang Woo Kim, Srinivasan Muniyappan, Sang Jin Lee, Yonggwan Kim, et al.
The Journal of Physical Chemistry Letters pp 6565-6573; doi:10.1021/acs.jpclett.1c01277

Abstract:
Here, we introduce the nanoparticle-aided cryo-electron microscopy sampling (NACS) method to access the conformational distribution of a protein molecule. Two nanogold particles are labeled at two target sites, and the interparticle distance is measured as a structural parameter via cryo-electron microscopy (cryo-EM). The key aspect of NACS is that the projected distance information instead of the global conformational information is extracted from each protein molecule. This is possible because the contrast provided by the nanogold particles is strong enough to provide the projected distance, while the protein itself is invisible due to its low contrast. We successfully demonstrate that various protein conformations, even for small or disordered proteins, which generally cannot be accessed via cryo-EM, can be captured. The demonstrated method with the potential to directly observe the conformational distribution of such systems may open up new possibilities in studying their dynamics at a single-molecule level.
The Journal of Physical Chemistry Letters pp 6596-6603; doi:10.1021/acs.jpclett.1c01617

Abstract:
Two-dimensional materials exhibit properties promising for novel applications. Topologically protected states at their edges can be harnessed for use in quantum devices. We use ab initio simulations to examine properties of edges in 1T′-WTe2 monolayers, known to exhibit topological order, and their interactions with Cu atoms. Comparison of (010)-oriented edges that have the same composition but different terminations shows that, as the number of Cu atoms increases, their thermodynamically preferred arrangement depends on the details of the edge structure. Cu atoms aggregate into a cluster at the most stable edge; while the cluster is nonmagnetic, it spin-polarizes the W atoms along the edge, which removes the topological protection. At the metastable edge, Cu atoms form a chain incorporated into the WTe2 lattice; the topological state is preserved in spite of the dramatic edge restructuring. This suggests that exploiting interactions of metal species with metastable edge terminations can provide a path toward noninvasive interfaces.
, Hang Zhou, Hongsheng Dong, Changrui Shi, , Huiquan Liu, Yongchen Song
The Journal of Physical Chemistry Letters pp 6622-6627; doi:10.1021/acs.jpclett.1c01649

Abstract:
Methane hydrate (MH) makes it possible to store methane using the cheapest and safest solvent: water. However, the sluggish formation kinetics hinders its practical utilization. Recently, the use of nanomaterials has been suggested as a potential solution; however, there is still a lack of high-efficiency kinetic promotors, and the promoting mechanism remains unclear. Herein, we demonstrated that MXene dispersion is promising for the storage of methane via MH with rapid formation kinetics, high storage capacity, and impressive cyclic stability. MXene can significantly shorten the induction time for MH formation. The enhanced kinetics was achieved by providing extra nucleation sites and enhancing thermal conductivity, although the increased surface tension of MXene dispersion could impede the MH formation via limited mass transfer. We confirmed that the concentration-dependent promoting effect of MXene dispersions results from regulating the assembly of water molecules. The insight of this work can apply to develop high-efficiency additives to control the formation kinetics of MH.
Huidong Li, Yucheng Hu, Longfei Li, Yaoming Xie,
The Journal of Physical Chemistry Letters pp 6486-6491; doi:10.1021/acs.jpclett.1c01619

Abstract:
In 2019, Diaz-Urrutia and Ott developed a high-yield method for direct conversion of methane to methanesulfonic acid and proposed a cationic chain reaction mechanism. However, Roytman and Singleton questioned this mechanism, and they favored a free-radical mechanism. In the present paper, we studied both the cationic chain and radical mechanisms and found the radical mechanism is more favorable, since it has a much lower energy barrier. However, the radical mechanism has not considered the effect of ions for the reaction taking place in oleum. Thus, we studied a simple model of a protonated radical mechanism, which further lowers the energy barrier. Although the true mechanism for the CH4 + SO3 reaction could be more complicated in electrolyte solutions, this model should be helpful for the further study of the mechanism of this reaction.
Tianpei Ge, Zhaobo Wei, Xiaoli Zheng, Pengfei Yan,
The Journal of Physical Chemistry Letters pp 6543-6550; doi:10.1021/acs.jpclett.1c01703

Abstract:
Supercritical carbon dioxide (SC CO2) has shown great potential in fabrication of two-dimensional (2D) amorphous nanomaterials with excellent electric and optical properties, while the amorphization mechanism led by SC CO2 is still unclear. In this work, by investigating the amorphization kinetics of MoO3–x nanomaterials in SC CO2, we find two amorphization mechanisms dependent on the SC CO2 pressure. At lower pressure, forming oxygen vacancies is the dominant effect, while at higher pressure, atomic rearrangement is the controlling factor. Furthermore, we demonstrate that amorphization directly affects the optical performance of MoO3–x nanosheets because of the change in coordination, which further indicates the atomic rearrangement during the amorphization process. Therefore, this work reveals the amorphization mechanism led by SC CO2 and builds a link between amorphization and optical performance; it also provides new inspiration for fabrication of amorphous nanomaterials with tunable optical and photocatalytic performance.
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