ChemRxiv最新文献_第6页

Molecular Determinants of Optical Modulation in ssDNA-Carbon Nanotube Biosensors: Insights from Experimental and Computational Approaches ssDNA-碳纳米管生物传感器中光学调制的分子决定因素：实验和计算方法的启示

ChemRxiv Pub Date : 2024-09-18 DOI: 10.26434/chemrxiv-2024-8k2q2

Abraham, Beyene, Andrew, Krasley, Sayantani, Chakraborty, Lela, Vukovic

{"title":"Molecular Determinants of Optical Modulation in ssDNA-Carbon Nanotube Biosensors: Insights from Experimental and Computational Approaches","authors":"Abraham, Beyene, Andrew, Krasley, Sayantani, Chakraborty, Lela, Vukovic","doi":"10.26434/chemrxiv-2024-8k2q2","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-8k2q2","url":null,"abstract":"Most traditional optical biosensors operate through molecular recognition, where ligand binding causes conformational changes that lead to optical perturbations in the emitting motif. Optical sensors developed from single-strand DNA functionalized single-walled carbon nanotubes (ssDNA-SWCNT) have started to make useful contributions to biological research. However, the mechanisms underlying their function have remained poorly understood. In this study, we used a combination of experimental and computational approaches to show that ligand binding alone is not sufficient for optical modulation in this class of synthetic biosensors. Instead, the optical response that occurs after ligand binding is highly dependent on the chemical properties of the ligands, resembling mechanisms seen in activity-based biosensors. Specifically, we show that in ssDNA-SWCNT catecholamine sensors, the optical response correlates positively with electron density on the aryl motif, even when ligand binding affinities are similar. These findings could serve as a foundation for tuning the performance of existing sensors and guiding the development of new biosensors of this class.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":"64 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142267149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Semi-Analytical Solution for a Lumped Model of a Co-Current Moving Bed Reactor 同流移动床反应器结块模型的半解析解法

ChemRxiv Pub Date : 2024-09-18 DOI: 10.26434/chemrxiv-2024-t30tv

Natan, Padoin, Cíntia, Soares, Sávio , Bertoli, Jesús, Apolinar-Hernández, Carolina, Krebs de Souza, Marcel, Jeferson Gonçalves

引用次数: 0

Simulation of Ultrafast Excited-State Dynamics in Fe(II) Complexes: Assessment of Electronic Structure Descriptions 铁（II）配合物的超快激发态动力学模拟：电子结构描述评估

ChemRxiv Pub Date : 2024-09-18 DOI: 10.26434/chemrxiv-2024-sfn8p

Mátyás, Pápai

{"title":"Simulation of Ultrafast Excited-State Dynamics in Fe(II) Complexes: Assessment of Electronic Structure Descriptions","authors":"Mátyás, Pápai","doi":"10.26434/chemrxiv-2024-sfn8p","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-sfn8p","url":null,"abstract":"The assessment of electronic structure descriptions utilized in the simulation of ultrafast excited-state dynamics of Fe(II) complexes is presented. Herein, we evaluate the performance of the RPBE, OPBE, BLYP, B3LYP, B3LYP*, CAM-B3LYP, and LC-BLYP (time-dependent) density functional theory (DFT/TD-DFT) methods in full-dimensional trajectory surface hopping (TSH) simulations carried out on linear vibronic coupling (LVC) potentials. We exploit the existence of time-resolved X-ray emission spectroscopy (XES) data for the [Fe(bmip)2]2+ and [Fe(terpy)2]2+ prototypes for dynamics between metal-to-ligand charge transfer (MLCT) and metal-centered (MC) states, which serve as a reference to benchmark the calculations (bmip = 2,6-bis(3-methyl-imidazole-1-ylidine)-pyridine, terpy = 2,2’:6’,2''-terpyridine). The results show that the simulated ultrafast population dynamics between MLCT and MC states with various spin multiplicilities (singlet, triplet, quintet) highly depend on the utilized DFT/TD-DFT method with the percentage of exact (Hartree-Fock) exchange being the governing factor. Importantly, B3LYP* is the only DFT/TD-DFT method reproducing all important aspects of the experimentally resolved dynamics for both complexes, signalling an optimal balance in the description of MLCT-MC energetics. This work demonstrates the power of combining TSH/LVC dynamics simulations with time-resolved experimental reference data to benchmark full-dimensional potential energy surfaces.","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142267135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

All-in-one foundational models learning across quantum chemical levels 跨量子化学层次的一体化基础模型学习

ChemRxiv Pub Date : 2024-09-18 DOI: 10.26434/chemrxiv-2024-ng3ws

Pavlo O., Dral, Yuxinxin, Chen

{"title":"All-in-one foundational models learning across quantum chemical levels","authors":"Pavlo O., Dral, Yuxinxin, Chen","doi":"10.26434/chemrxiv-2024-ng3ws","DOIUrl":"https://doi.org/10.26434/chemrxiv-2024-ng3ws","url":null,"abstract":"Machine learning (ML) potentials typically target a single quantum chemical (QC) level while the ML models developed for multi-fidelity learning have not been shown to provide scalable solutions for foundational models. Here we introduce the all-in-one (AIO) ANI model architecture based on multimodal learning which can learn an arbitrary number of QC levels. Our all-in-one learning approach offers a more general and easier-to-use alternative to transfer learning. We use it to train the AIO-ANI-UIP foundational model with the generalization capability comparable to semi-empirical GFN2-xTB and DFT with a double-zeta basis set for organic molecules. We show that the AIO-ANI model can learn across different QC levels ranging from semi-empirical to density functional theory to coupled cluster. We also use AIO models to design the foundational model Δ-AIO-ANI based on Δ-learning with increased accuracy and robustness compared to AIO-ANI-UIP. The code and the foundational models are available at https://github.com/dralgroup/aio-ani; they will be integrated into the universal and updatable AI-enhanced QM (UAIQM) library and made available in the MLatom package so that they can be used online at the XACS cloud computing platform (see https://github.com/dralgroup/mlatom for updates).","PeriodicalId":9813,"journal":{"name":"ChemRxiv","volume":"49 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142267356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Compatibilization of polyolefin blends through acid–base interactions 通过酸碱相互作用实现聚烯烃混合物的相容

ChemRxiv Pub Date : 2024-09-18 DOI: 10.26434/chemrxiv-2024-qhsj9

Yucheng, Yuan, Jiawei, He, Jiangwei, Liu, Ming-Chi, Wang, Tuhin, Ganguly, John, Santoro, Junpeng, Wang, Jeffery, Byers, Jia, Niu, Mingjiang, Zhong, Dunwei, Wang

引用次数: 0

2D TiNBr as photocatalyst for overall water splitting 二维 TiNBr 作为光催化剂用于整体水分离

ChemRxiv Pub Date : 2024-09-18 DOI: 10.26434/chemrxiv-2024-vxdq4

Yatong, Wang, Geert, Brocks, Ceren, Tayran, Süleyman, Er

引用次数: 0

Enhanced Sampling with Sub-optimal Collective Variables: Reconciling Accuracy and Convergence Speed 次优集合变量的增强采样：兼顾精度与收敛速度

ChemRxiv Pub Date : 2024-09-18 DOI: 10.26434/chemrxiv-2024-mfpcn

Dhiman, Ray, Valerio, Rizzi

引用次数: 0

Chemical composition and antibacterial activity of the essential oil of Coreopsis lanceolata leaves 拟南芥叶精油的化学成分和抗菌活性

ChemRxiv Pub Date : 2024-09-18 DOI: 10.26434/chemrxiv-2024-dk7v6

Antônio, Crotti, Richard, Lima, Ana Carla, Colli, Sara, Souza, Milton, Groppo, Carlos, Martins

引用次数: 0

Reversing the Chemoselectivity in Photocatalytic C–F Bond Cleavage Enabled by Zirconocene and Photoredox Catalysis 利用二茂锆和光氧化催化逆转光催化 C-F 键裂解的化学选择性

ChemRxiv Pub Date : 2024-09-18 DOI: 10.26434/chemrxiv-2024-ssj00

Junichiro, Yamaguchi, Haruki, Takimoto, Kazuhiro, Aida, Yoshio, Nishimoto, Daisuke, Yokogawa, Eisuke, Ota

引用次数: 0

Structure-Based Optimization and Biological Evaluation of SARS-CoV-2 3CLpro Covalent Inhibitors 基于结构的 SARS-CoV-2 3CLpro 共价抑制剂优化与生物学评估

ChemRxiv Pub Date : 2024-09-18 DOI: 10.26434/chemrxiv-2024-091mt

Nicolas, Moitessier, Guanyu, Wang, Julia, Stille, Richard, Boulon, Christopher, Hennecker, Xiaocong, Zhang, Nicole, Blaine, Steven, Laplante, Anthony, Mittermaier

引用次数: 0