
Research Square (Research Square), Год журнала: 2025, Номер unknown
Опубликована: Фев. 13, 2025
Язык: Английский
Research Square (Research Square), Год журнала: 2025, Номер unknown
Опубликована: Фев. 13, 2025
Язык: Английский
Chemical Science, Год журнала: 2025, Номер unknown
Опубликована: Янв. 1, 2025
Assessing the performance of modern machine learning force fields across diverse chemical systems to identify their strengths and limitations within TEA Challenge 2023.
Язык: Английский
Процитировано
2Physical Chemistry Chemical Physics, Год журнала: 2024, Номер 26(32), С. 21379 - 21394
Опубликована: Янв. 1, 2024
Efficient dispersion corrections are an indispensable component of modern density functional theory, semi-empirical quantum mechanical, and even force field methods. In this work, we extend the well established D3 D4 London to full actinides series, francium, radium. To keep consistency with existing versions, original parameterization strategy model was only slightly modified. This includes improved reference Hirshfeld atomic partial charges at ωB97M-V/ma-def-TZVP level fit required electronegativity equilibration charge (EEQ) model. context, developed a new actinide data set called AcQM, which covers most common molecular compound space. Furthermore, efficient calculation dynamic polarizabilities that needed construct
Язык: Английский
Процитировано
12Current Opinion in Structural Biology, Год журнала: 2024, Номер 87, С. 102870 - 102870
Опубликована: Июнь 24, 2024
The expansion of the chemical space to tangible libraries containing billions synthesizable molecules opens exciting opportunities for drug discovery, but also challenges power computer-aided design prioritize best candidates. This directly hits quantum mechanics (QM) methods, which provide chemically accurate properties, subject small-sized systems. Preserving accuracy while optimizing computational cost is at heart many efforts develop high-quality, efficient QM-based strategies, reflected in refined algorithms and approaches. QM-tailored physics-based force fields coupling QM with machine learning, conjunction computing performance supercomputing resources, will enhance ability use these methods discovery. challenge formidable, we undoubtedly see impressive advances that define a new era.
Язык: Английский
Процитировано
11Journal of Chemical Theory and Computation, Год журнала: 2025, Номер unknown
Опубликована: Янв. 9, 2025
Our recently developed approach based on the local coupled-cluster with single, double, and perturbative triple excitation [LCCSD(T)] model gives very efficient means to compute ideal-gas enthalpies of formation. The expanded uncertainty (95% confidence) method is about 3 kJ·mol–1 for medium-sized compounds, comparable typical experimental measurements. Larger compounds interest often exhibit many conformations that can significantly differ in intramolecular interactions. Although present capabilities allow processing even a few hundred distinct conformer structures given compound, systems numbers well excess 1000. In this study, we investigate how reduce number expensive LCCSD(T) calculations large ensembles while controlling error approximation. best strategy found was correct results lower-level, surrogate (density functional theory, DFT) systematic manner. It also conformational contribution introduced by mainly driven (bias) rather than random component DFT energy deviation from target. This distinction usually overlooked benchmarking studies. As result work, formation 20 cannabinoid cannabinoid-related were obtained. Comprehensive analysis suggests uncertainties obtained values are below 4 kJ·mol–1.
Язык: Английский
Процитировано
1The Journal of Physical Chemistry Letters, Год журнала: 2025, Номер unknown, С. 1114 - 1125
Опубликована: Янв. 23, 2025
With their narrow-band emission, high quantum yield, and good chemical stability, multiresonance thermally activated delayed fluorescence (MR-TADF) emitters are promising materials for OLED technology. However, accurately modeling key properties, such as the singlet-triplet (ST) energy gap energy, remains challenging. While time-dependent density functional theory (TD-DFT), workhorse of computational science, suffers from fundamental issues, wave function-based coupled-cluster (CC) approaches, like approximate CC second-order (CC2), accurate but suffer cost unfavorable scaling with system size. This work demonstrates that a state-specific ΔDFT approach based on unrestricted Kohn-Sham (ΔUKS) combines best both worlds: diverse benchmark set 35 MR-TADF emitters, ΔUKS performs or better than CC2, recovering experimental ST gaps mean absolute deviation (MAD) 0.03 eV at small fraction CC2. When combined tuned range-separated LC-ωPBE functional, excellent performance extends to energies MR- donor-acceptor TADF even molecules an inverted (INVEST), rendering this jack all trades organic electronics.
Язык: Английский
Процитировано
1Journal of Medicinal Chemistry, Год журнала: 2025, Номер unknown
Опубликована: Янв. 29, 2025
Linker structures are a crucial component of proteolysis-targeting chimeras (PROTACs) and have traditionally been designed based on empirical methods, which presents significant challenges in the development PROTACs. Current optimization strategies typically focus reducing number rotatable bonds linker to limit conformational freedom. However, this approach overlooks complexity target protein degradation process. Retrospective analyses suggest that merely adjusting is insufficient control freedom PROTACs, indicating need for new strategies. By integration computational methods such as molecular dynamics simulations, study investigates role throughout induction process, particularly its impact formation stability ternary complex. This offers potential overcoming limitations traditional strategies, reliance enhancing overall efficiency effectiveness PROTAC design.
Язык: Английский
Процитировано
1The Journal of Physical Chemistry C, Год журнала: 2025, Номер unknown
Опубликована: Фев. 13, 2025
Язык: Английский
Процитировано
1Chemical Reviews, Год журнала: 2025, Номер unknown
Опубликована: Март 10, 2025
In this field guide, we outline empirical and theory-based approaches to characterize the fundamental properties of liquid multivalent-ion battery electrolytes, including (i) structure chemistry, (ii) transport, (iii) electrochemical properties. When detailed molecular-scale understanding multivalent electrolyte behavior is insufficient use examples from well-studied lithium-ion electrolytes. recognition that coupling techniques highly effective, but often nontrivial, also highlight recent characterization efforts uncover a more comprehensive nuanced underlying structures, processes, reactions drive performance system-level behavior. We hope insights these discussions will guide design future studies, accelerate development next-generation batteries through modeling with experiments, help avoid pitfalls ensure reproducibility results.
Язык: Английский
Процитировано
1The Journal of Physical Chemistry B, Год журнала: 2024, Номер 128(13), С. 3145 - 3156
Опубликована: Март 21, 2024
In this study, a three-layered multicenter ONIOM approach is implemented to characterize the naive folding pathway of bovine pancreatic trypsin inhibitor (BPTI). Each layer represents distinct level theory, where initial layer, encompassing entire protein, modeled by general all-atom force-field GFN-FF. An intermediate electronic structure consisting three fragments introduced with state-of-the-art semiempirical tight-binding method GFN2-xTB. Higher accuracy, specifically addressing breaking and formation disulfide bonds, achieved at innermost using composite DFT r2SCAN-3c. Our analysis sheds light on structural stability BPTI, particularly significance interlinking bonds. The accuracy efficiency QM/SQM/MM are benchmarked oxidative cystine. For relative stabilities investigated through calculation free energy contributions for selected intermediates, focusing impact bond. results highlight intricate trade-off between computational cost, demonstrating that provides well-balanced comprehensive solution describe effects in biomolecular systems. We conclude multiscale landscape exploration robust methodology study intriguing biological targets.
Язык: Английский
Процитировано
6RSC Advances, Год журнала: 2024, Номер 14(28), С. 20048 - 20055
Опубликована: Янв. 1, 2024
Reparameterization of GFN1-xTB for atmospheric molecular clusters leads to a massive decrease in energy errors and deviation.
Язык: Английский
Процитировано
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