The accurate representation of the structural and dynamical properties of water is essential for simulating the unique behavior of this ubiquitous solvent. Here we assess the current status of describing liquid water using molecular dynamics, with a special focus on the performance of all the later generation Minnesota functionals. Findings are contextualized within the current knowledge on DFT for describing bulk water under ambient conditions and compared to experimental data. We find that, contrary to the prevalent idea that local and semilocal functionals overstructure water and underestimate dynamical properties, M06-L, revM06-L, and M11-L understructure water, while MN12-L and MN15-L overdistance water molecules due to weak cohesive effects. This can be attributed to a weakening of the hydrogen bond network, which leads to dynamical fingerprints that are over fast. While most of the hybrid Minnesota functionals (M06, M08-HX, M08-SO, M11, MN12-SX, and MN15) also yield understructured water, their dynamical properties generally improve over their semilocal counterparts. It emerges that exact exchange is a crucial component for accurately describing hydrogen bonds, which ultimately leads to corrections in both the dynamical and structural properties. However, an excessive amount of exact exchange strengthens hydrogen bonds and causes overstructuring and slow dynamics (M06-HF). As a compromise, M06-2X is the best performing Minnesota functional for water, and its D3 corrected variant shows very good structural agreement. From previous studies considering nuclear quantum effects (NQEs), the hybrid revPBE0-D3, and the rung-5 RPA (RPA@PBE) have been identified as the only two approximations that closely agree with experiments. Our results suggest that the M06-2X(-D3) functionals have the potential to further improve the reproduction of experimental properties when incorporating NQEs through path integral approaches. This work provides further proof that accurate modeling of water interactions requires the inclusion of both exact exchange and balanced (non-local) correlation, highlighting the need for higher rungs on Jacob's ladder to achieve predictive simulations of complex biological systems in aqueous environments.
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http://dx.doi.org/10.1039/d3sc05828j | DOI Listing |
J Phys Chem B
January 2025
UM-DAE Centre for Excellence in Basic Sciences, Kalina Campus of Mumbai University, Santacruz (E), Mumbai 400098, India.
Excited-state proton transfer (ESPT) in organic photoacids is a widely studied phenomenon in which D-luciferin is of special mention, considering the fact that apart from its phenolic OH group, the nitrogen atoms at either of the two thiazole moieties could also participate in hydrogen bonding interactions with a proton-donating solvent during ESPT. As a result, several transient species could appear during the ESPT process. We hereby deploy subpicosecond time-resolved fluorescence upconversion (FLUP) and transient absorption (TA) spectroscopic techniques to understand the detailed photophysics of D-luciferin in water as well as in dimethyl sulfoxide (DMSO) and ethanol.
View Article and Find Full Text PDFInt J Biol Macromol
January 2025
The Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, School of Chemical and Material Engineering, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China. Electronic address:
Cellulose is a renewable biodegradable polymer derived from abundant natural resources. Substituting petroleum-based polymers with cellulose-based bioplastics is an effective way to alleviate environmental issues like resource depletion and white pollution. However, challenges such as poor thermostability, hard to thermoform and water sensitivity seriously hinder the fabrication and use of cellulose-based bioplastics.
View Article and Find Full Text PDFPLoS Genet
January 2025
School of Life Sciences, Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou, China.
A key property of the circadian clock is that it is reset by light to remain synchronized with the day-night cycle. An attractive model to explore light input to the circadian clock in vertebrates is the zebrafish. Circadian clocks in zebrafish peripheral tissues and even zebrafish-derived cell lines are entrainable by direct light exposure thus providing unique insight into the function and evolution of light regulatory pathways.
View Article and Find Full Text PDFHum Mol Genet
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Genom Ltd., Ilica 190, Zagreb 10000, Croatia.
The most severe form of male infertility is idiopathic non-obstructive azoospermia (NOA), a complete sperm absence in the ejaculate. We performed exome sequencing in the Croatian infertile brothers with NOA and found a variant in DMRT1 (Doublesex and mab-3 related transcription factor 1) gene that was further assessed by the EMSA assay and molecular dynamic simulations. We additionally screened for DMRT1 mutations in 1940 infertile men diagnosed with spermatogenic failure, 644 normozoospermic controls, and 105 females with primary ovarian insufficiency (POI) recruited to the GEnetics of Male INfertility Initiative (GEMINI) or Estonian Andrology (ESTAND) cohorts.
View Article and Find Full Text PDFNature
January 2025
Department of Chemistry, The University of Hong Kong, Hong Kong SAR, China.
Mimicking the superstructures and properties of spherical biological encapsulants such as viral capsids and ferritin offers viable pathways to understand their chiral assemblies and functional roles in living systems. However, stereospecific assembly of artificial polyhedra with mechanical properties and guest-binding attributes akin to biological encapsulants remains a formidable challenge. Here we report the stereospecific assembly of dynamic supramolecular snub cubes from 12 helical macrocycles, which are held together by 144 weak C-H hydrogen bonds.
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