Journal of Chemical Physics最新文献_第10页

Nonconventional growth characteristics of tin silicon oxide grown by thermal atomic layer deposition using H2O as oxidant. 以水为氧化剂，热原子层沉积法生长锡氧化硅的非常规生长特性。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-08-21 DOI: 10.1063/5.0279669

Sanghun Lee, Namkyu Yoo, Seunggi Seo, Tae Hyun Kim, Seonyeong Park, Jeongwoo Seo, Seung-Min Chung, Hyungjun Kim

{"title":"Nonconventional growth characteristics of tin silicon oxide grown by thermal atomic layer deposition using H2O as oxidant.","authors":"Sanghun Lee, Namkyu Yoo, Seunggi Seo, Tae Hyun Kim, Seonyeong Park, Jeongwoo Seo, Seung-Min Chung, Hyungjun Kim","doi":"10.1063/5.0279669","DOIUrl":"https://doi.org/10.1063/5.0279669","url":null,"abstract":"Atomic layer deposition (ALD) of tin silicon oxide was performed via an ALD supercycle on an amorphous carbon (a-C) layer, which serves as the mandrel in self-aligned double patterning (SADP) techniques. This approach addresses limitations of conventional ALD SiO2 processes using ozone (O3) as the oxidant, which can lead to degradation of a-C mandrel or collapse of the SiO2 spacer itself under aggressive scaling. In this study, tetrakis(dimethylamino)tin (TDMASn) and bis-diethylaminosilane (BDEAS) were used as Sn and Si precursors, respectively, with H2O as the oxidant to avoid damage to the a-C layer. SiO2 was not grown via a single ALD process due to the low reactivity of BDEAS with H2O. Nevertheless, x-ray photoelectron spectroscopy analyses revealed that Si was incorporated into the film grown by the supercycle of ALD SnOx and SiO2. Notably, it is observed that the growth characteristics of tin silicon oxide exhibited a nonlinear dependence on the cycle ratio. Understanding this unexpected behavior is crucial for SADP, as it affects growth per cycle and film characteristics, such as etch rate and surface roughness. Fourier-transform infrared spectroscopy and density functional theory calculations suggest that hydrogen abstraction between TDMASn and Si-H groups enable the growth of tin silicon oxide. Finally, transmission electron microscopy analysis demonstrated that the a-C layer remained undamaged during the ALD process, whereas a few seconds of ozone exposure caused the ashing of the a-C layer.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"163 7","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144873397","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

Reaction dynamics for the [NNO] system from state-resolved and coarse-grained models. 基于状态分解和粗粒度模型的[NNO]系统反应动力学。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-08-21 DOI: 10.1063/5.0284631

Juan Carlos San Vicente Veliz, Sung Min Jo, Jingchun Wang, Raymond J Bemish, Markus Meuwly

{"title":"Reaction dynamics for the [NNO] system from state-resolved and coarse-grained models.","authors":"Juan Carlos San Vicente Veliz, Sung Min Jo, Jingchun Wang, Raymond J Bemish, Markus Meuwly","doi":"10.1063/5.0284631","DOIUrl":"10.1063/5.0284631","url":null,"abstract":"The dynamics for the NO(X2Π) + N(4S) ↔ N2(X1Σg+) + O(3P) reaction was followed in the 3A' electronic state using state-to-state (STS) and Arrhenius-based rates from two different high-level potential energy surfaces represented as a reproducing kernel Hilbert space (RKHS, PESB for \"Basel PES\") and permutationally invariant polynomials (PIPs, PESM for \"Minnesota PES\"). Despite the different number of bound states supported by PESB and PESM, the ignition points from STS and Arrhenius rates are at ∼10-6 s whether or not reverse rates are from assuming microreversibility or explicitly given. Conversion from NO to N2 is incomplete if Arrhenius rates are used, but complete turnover is observed if STS information is used. This is due to non-equilibrium energy flow and state dynamics, which requires a state-based description. Including full dissociation asymptotically leads to the correct 2:1 [N]:[O] concentration with little differences for the species' dynamics depending on the PES used for the STS information. In conclusion, concentration profiles from coarse-grained simulations are consistent over 14 orders of magnitude in time using STS information based on two different high-level PESs.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"163 7","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144873399","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

Discriminant analysis optimizes progress coordinate in weighted ensemble simulations of rare event kinetics. 判别分析优化了罕见事件动力学加权集合模拟的进度坐标。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-08-21 DOI: 10.1063/5.0276623

Praveen Ranganath Prabhakar, Dhiman Ray, Ioan Andricioaei

{"title":"Discriminant analysis optimizes progress coordinate in weighted ensemble simulations of rare event kinetics.","authors":"Praveen Ranganath Prabhakar, Dhiman Ray, Ioan Andricioaei","doi":"10.1063/5.0276623","DOIUrl":"10.1063/5.0276623","url":null,"abstract":"Calculating the kinetics of rare-but-important conformational transitions in complex biomolecules is a significant challenge in computational biophysics. Because of the long timescales needed to observe such processes, regular molecular dynamics simulations are too slow to sample these events by direct integration of the equations of motion. Recently, the weighted ensemble method has gained significant popularity for its ability to compute the rates of conformational transitions in biomolecular systems using unbiased simulations. However, the progress coordinate(s) of the weighted ensemble simulation should be carefully designed to capture the slow degrees of freedom of the system. Here, we demonstrate the application of a machine learning approach, harmonic linear discriminant analysis, which builds a predictive model for class membership, to design progress coordinates for weighted ensemble simulations. We test the accuracy and efficiency of this technique for computing the kinetics of the conformational transition of alanine dipeptide and the unfolding of a small protein. The key advantage of our data-driven approach is its minimal system knowledge requirement, which potentially extends its applicability to more complex and physiologically relevant systems.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"163 7","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144873391","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

The effect of hydration and dynamics on the mass density of single proteins. 水合作用和动力学对单个蛋白质质量密度的影响。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-08-21 DOI: 10.1063/5.0276752

C C W McAllister, L S P Rudden, E H C Bromley, M T Degiacomi

{"title":"The effect of hydration and dynamics on the mass density of single proteins.","authors":"C C W McAllister, L S P Rudden, E H C Bromley, M T Degiacomi","doi":"10.1063/5.0276752","DOIUrl":"10.1063/5.0276752","url":null,"abstract":"The density of a protein molecule is a key property within a variety of experimental techniques. We present a computational method for determining protein mass density that explicitly incorporates hydration effects. Our approach uses molecular dynamics simulations to quantify the volume of solvent excluded by a protein. Applied to a dataset of 260 soluble proteins, this yields an average density of 1.296 ± 0.001 g cm-3, notably lower than the widely cited value of 1.35 g cm-3. Contrary to previous suggestions, we find no correlation between protein density and molecular weight. We instead find correlations with residue composition, particularly with hydrophobic amino acid content. Using these correlations, we train a regressor capable of accurately predicting protein density from sequence-derived features alone. Examining the effect of incorporating water molecules on the measured density, we find that water molecules buried in internal cavities have a negligible effect, whereas those at the surface have a profound impact. Furthermore, by calculating the density of a titin domain and of the Bovine Pancreatic Trypsin over molecular dynamics trajectories, we show that individual proteins can occupy states with close but distinguishable densities. Finally, we analyze the density of water in the vicinity of proteins, showing that the first two hydration shells exhibit higher density than bulk water. When included in cumulative density calculations, these hydration layers contribute to a net increase in local solvent density. Overall, we find that proteins are less dense than previously reported, which is offset by their ability to induce a higher density of water in their vicinity.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"163 7","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144873402","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

HEroBM: A deep equivariant graph neural network for high-fidelity backmapping from coarse-grained to all-atom structures. 用于从粗粒度到全原子结构高保真反向映射的深度等变图神经网络。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-08-21 DOI: 10.1063/5.0280330

Daniele Angioletti, Stefano Raniolo, Vittorio Limongelli

{"title":"HEroBM: A deep equivariant graph neural network for high-fidelity backmapping from coarse-grained to all-atom structures.","authors":"Daniele Angioletti, Stefano Raniolo, Vittorio Limongelli","doi":"10.1063/5.0280330","DOIUrl":"10.1063/5.0280330","url":null,"abstract":"Molecular simulations play a pivotal role in chemistry, biology, and material sciences, enabling the study of complex dynamic properties within systems. Coarse-grained (CG) techniques have emerged as indispensable tools in this domain, facilitating the sampling of large-scale systems and extending simulation timescales by simplifying system representation. However, CG approaches involve a trade-off: they sacrifice atomistic details that may be crucial for understanding the underlying processes. To address this challenge, a recommended strategy is to identify key CG conformations and employ backmapping methods to retrieve atomistic coordinates. Currently, rule-based methods often yield suboptimal geometries and rely on energy relaxation, resulting in less-than-optimal outcomes. In contrast, machine learning techniques offer higher accuracy but may lack transferability between systems or be tied to specific CG mappings. In this study, we present HEroBM, a dynamic and scalable method that utilizes deep equivariant graph neural networks and a hierarchical approach to achieve high-resolution backmapping. HEroBM is capable of handling any type of CG mapping, providing a versatile and efficient protocol for reconstructing atomistic structures with high accuracy. Grounded in local principles, HEroBM spans the entire chemical space and can be applied across systems of varying composition and sizes. We demonstrate the versatility of our framework through a range of biological systems, including a complex real-case scenario. Here, our end-to-end backmapping approach accurately generates atomistic coordinates for a G protein-coupled receptor bound to an organic small molecule within a cholesterol/phospholipid bilayer. The high-fidelity HEroBM backmapping enables researchers to effortlessly transition between CG and all-atom simulations, opening unprecedented avenues for molecular investigations.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"163 7","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144873393","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

Minimized reaction network method for the construction of combustion reaction mechanism: NH3/DME mixed combustion. NH3/二甲醚混合燃烧反应机理的最小化反应网络构建方法。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-08-21 DOI: 10.1063/5.0276807

Wenhan Zhang, Lei Shi, Wenwen Xia, Yufan Du, Li Yao

{"title":"Minimized reaction network method for the construction of combustion reaction mechanism: NH3/DME mixed combustion.","authors":"Wenhan Zhang, Lei Shi, Wenwen Xia, Yufan Du, Li Yao","doi":"10.1063/5.0276807","DOIUrl":"10.1063/5.0276807","url":null,"abstract":"In view of the shortcomings of the previous NH3/DME reaction mechanism, combustion reaction mechanisms of NH3, DME, and NH3/DME were constructed by using the minimized reaction network method under the condition of determining the number of chemical species. The mechanism of the construction had a simple reaction network using reversible reaction form, and the reaction direction was unified in form. The mechanism construction process of NH3, DME, and NH3/DME avoided the mechanism simplification step, which can greatly reduce the number of species and reactions. Finally, the NH3 chemical reaction mechanism containing 18 species and 43 reactions, the DME chemical reaction mechanism containing 34 species and 51 reactions, and the NH3/DME chemical reaction mechanism containing 44 species and 93 reactions were developed. The laminar burning velocity and ignition delay time of NH3, NH3/H2, DME, DME/H2, and NH3/DME combustion under a wide range of initial conditions were validated. The results showed that the errors of laminar burning velocity and ignition delay time compared with the experimental values were within 10% under most initial conditions, which verifies the reliability and practicability of each combustion reaction mechanism.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"163 7","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144873396","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

A model of protein folding with multiple native states: Metamorphicity, intrinsic disorderness, and folding upon binding of proteins. 具有多种天然状态的蛋白质折叠模型：变质性、内在无序性和蛋白质结合时的折叠。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-08-21 DOI: 10.1063/5.0274970

Rohon Mitra, Biman Jana

{"title":"A model of protein folding with multiple native states: Metamorphicity, intrinsic disorderness, and folding upon binding of proteins.","authors":"Rohon Mitra, Biman Jana","doi":"10.1063/5.0274970","DOIUrl":"10.1063/5.0274970","url":null,"abstract":"The sequence-structure-function paradigm in biology states that a protein's amino acid sequence determines its unique folded state structure, which in turn dictates its unique biological function. This classic concept has been severely challenged by the discovery of metamorphic and intrinsically disordered proteins (IDPs). Metamorphic proteins can fold into multiple native structures and perform multiple functions. IDPs, on the contrary, remain unstructured under physiological conditions but can fold to a unique structure upon binding to a target protein and show functionality. Here, we present a statistical mechanical model of protein folding with multiple native states and analyze their folding phase diagrams. While recovering the classic sequence-structure-function paradigm for a single native state, our model shows metamorphicity at a lower number of native states. An expansion of the unfolded region in the phase diagram at a higher number of native states, making the unfolded state the stable state under physiological conditions, indicates the emergence of an IDP-like scenario. Folding upon binding scenario of IDPs has also been demonstrated when an energetic bias is introduced for a specific native state. A regaining of the folded region upon biasing, increasing the folding propensity of the system, with folding toward a specific native state, is shown. Therefore, our model is general enough to reproduce the classic sequence-structure-function, metamorphicity, intrinsic disorderness, and folding upon binding scenarios of proteins.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"163 7","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144873390","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

Interaction strength of carbon dioxide on graphene from periodic quantum diffusion Monte Carlo. 二氧化碳在石墨烯上的相互作用强度的周期性量子扩散蒙特卡罗。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-08-21 DOI: 10.1063/5.0283254

Flaviano Della Pia, Giaan Kler-Young, Andrea Zen, Fabian Berger, Dario Alfè, Angelos Michaelides

引用次数: 0

Detection of the tunneling-rotation transitions of malonaldehyde in the submillimeter-wave region and proton tunneling dynamics. 亚毫米波区域丙二醛隧穿旋转跃迁的探测及质子隧穿动力学。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-08-21 DOI: 10.1063/5.0278646

Keiichi Tanaka, Takeshi Baba, Kensuke Harada, Isamu Morino, Koichi M T Yamada

引用次数: 0

Thermally modulated triplet-triplet annihilation: Deciphering the temperature dependence of upconversion dynamics. 热调制三重态-三重态湮灭：解读上转换动力学的温度依赖性。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2025-08-14 DOI: 10.1063/5.0277862

Jinsong Shao, Yiwei Zhang, Haoran Liu, Doudou Duan, Zhongfa Sun, Zhou Lu, Yaxiong Wei, Xinsheng Xu

{"title":"Thermally modulated triplet-triplet annihilation: Deciphering the temperature dependence of upconversion dynamics.","authors":"Jinsong Shao, Yiwei Zhang, Haoran Liu, Doudou Duan, Zhongfa Sun, Zhou Lu, Yaxiong Wei, Xinsheng Xu","doi":"10.1063/5.0277862","DOIUrl":"https://doi.org/10.1063/5.0277862","url":null,"abstract":"The quantum efficiency ceiling of triplet-triplet annihilation upconversion is intrinsically governed by the spin statistical factor (f), yet the physical origin of its anomalously elevated values (f > 0.6) remains a subject of intense debate. By conducting systematic variable-temperature kinetic studies, integrating time-resolved transient absorption spectroscopy with steady-state fluorescence spectral analysis, we elucidated the temperature-dependent reaction dynamics of the benchmark PtOEP/DPA system to investigate the interaction between f and high-energy excited-state (T2) decay pathways. Notably, the positive temperature dependence of f (rising from 0.575 at 190 K to 0.808 at 280 K) and a small activation energy (Ea = 1.92 kJ/mol) demonstrated the dominance of a direct 3(AA)* → S1 reverse intersystem crossing (RISC) mechanism while excluding the hypothesized 3(AA)* → T2 → S1 cascade. These results not only resolve longstanding debates concerning f-enhancement but also provide a rationale for designing annihilators that exploit low-barrier RISC pathways to circumvent spin-statistical constraints.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"163 6","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144821566","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