Structural properties of over 55 small proteins have been determined using both density-based and wave-function-based electronic structure methods in order to assess the ability of ab initio "force fields" to retain the properties described by experimental structures measured with crystallography or nuclear magnetic resonance. The efficiency of the GPU-based quantum chemistry algorithms implemented in our TeraChem program enables us to carry out systematic optimization of ab initio protein structures, which we compare against experimental and molecular mechanics force field references. We show that the quality of the ab initio optimized structures, as judged by conventional protein health metrics, increases with increasing basis set size. On the other hand, there is little evidence for a significant improvement of predicted structures using density functional theory as compared to Hartree-Fock methods. Although occasional pathologies of minimal basis sets are observed, these are easily alleviated with even the smallest double-ζ basis sets.
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http://dx.doi.org/10.1021/jp307741u | DOI Listing |
Angew Chem Int Ed Engl
December 2024
University of Science and Technology of China, Hefei National Research Center for Physical Sciences at Microscale, jinzhai road, hefei, CHINA.
Herein, we first report a photocatalytic OCM using CO2 as a soft oxidant for C2H6 production under mild conditions, where an efficient photocatalyst with unique interface sites is constructed to facilitate CO2 adsorption and activation, while concurrently boosting CH4 dissociation. As a prototype, the Au quantum dots anchored on oxygen-deficient TiO2 nanosheets are fabricated, where the Au-Vo-Ti interface sites for CO2 adsorption and activation are collectively disclosed by in situ Kelvin probe force microscopy, quasi in situ X-ray photoelectron spectroscopy and theoretical calculations. Compared with single metal site, the Au-Vo-Ti interface sites exhibit the lower CO2 adsorption energy and decrease the energy barrier of the *CO2 hydrogenation step from 1.
View Article and Find Full Text PDFNat Comput Sci
December 2024
Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Machine learning plays an important role in quantum chemistry, providing fast-to-evaluate predictive models for various properties of molecules; however, most existing machine learning models for molecular electronic properties use density functional theory (DFT) databases as ground truth in training, and their prediction accuracy cannot surpass that of DFT. In this work we developed a unified machine learning method for electronic structures of organic molecules using the gold-standard CCSD(T) calculations as training data. Tested on hydrocarbon molecules, our model outperforms DFT with several widely used hybrid and double-hybrid functionals in terms of both computational cost and prediction accuracy of various quantum chemical properties.
View Article and Find Full Text PDFPhotochem Photobiol Sci
December 2024
Department of Applied Chemistry for Environment, Graduate School of Urban Environmental Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji-Shi, Tokyo, 192-0397, Japan.
The fluorescence quantum yield of berberine in aqueous solution is significantly smaller than those of organic solution. The time profile of fluorescence intensity of berberine was analyzed by a bi-exponential function, showing that two kinds of states of berberine exist in the solutions. The observed fluorescence lifetime of shorter lifetime species of berberine in water (0.
View Article and Find Full Text PDFMikrochim Acta
December 2024
State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, 214122, China.
A dual-signal aptamer-based assay utilizing colorimetric and fluorescence techniques was developed for the determination of zearalenone (ZEN). The CdTe quantum dots, serving as the fluorescent signal source, were surface-modified onto FeO@SiO and subsequently functionalized with the aptamer. The COF-Au was modified with complementary chain, which possessed peroxide (POD)-like enzyme properties, and could catalyze the peroxidation of 3,3',5,5'-tetramethylbenzidine (TMB) to ox TMB, resulting in the generation of colorimetric signals.
View Article and Find Full Text PDFInorg Chem
December 2024
School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.
The interplay between quantum effects from magnetic frustration, low-dimensionality, spin-orbit coupling, and crystal electric field in rare-earth materials leads to nontrivial ground states with unusual magnetic excitations. Here, we investigate YbTaO, which hosts a buckled square net of Yb ions with = 1/2 moments. The observed Curie-Weiss temperature is about -1 K, implying an antiferromagnetic coupling between the Yb moments.
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