Characterizing Interfaces by Voronoi Tessellation

Konstantinovsky, Daniel; Yan, Elsa C. Y.; Hammes‐Schiffer, Sharon

doi:10.1021/acs.jpclett.3c01159

Cited by 4 publications

(5 citation statements)

References 64 publications

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“…This calculated chiral SFG response of water spans the spectral region of ~3100-3750 cm -1 and supports our experimental observation of a redshift upon H2 18 O substitution of vibrational features in this region (Figure 2b, panel iii). We also used the algorithm of Voronoi tessellation 32,42,43…”

Section: Chiral Sfg Is Sensitive To Water In the Dsdna First Hydratio...mentioning

confidence: 99%

“…We define these subpopulations using Voronoi analysis (see Methods). 42 Figure 6 shows the chiral SFG spectra of the first hydration shell, including water molecules in the minor and major grooves, and water molecules hydrating the dsDNA backbone. The average number of water molecules in each subpopulation is indicated beside the molecular models.…”

Section: Chiral Sfg Can Sense Chiral Hydration Structures Around Dsdn...mentioning

confidence: 99%

“…The mean molecular dipole vector was calculated from partial positive charge to partial negative charge on each water molecule, and therefore the arrows point radially outward from the negatively-charged dsDNA. For visualization, representative structures for the first and second hydration shells were selected via Voronoi tessellation (see next section), 42 and the dsDNA geometry was averaged over all frames. Water molecules are depicted as the van der Waals spheres of their oxygen atoms.…”

Section: Analysis Of Water Dipole Orientationmentioning

confidence: 99%

“…Water molecules in the first hydration shell were identified using Voronoi tessellation. 42 Voronoi tessellation defines cells for each atom consisting of the points closer to that atom than to any other atom;…”

Section: Selection Of Water Molecule Subsetsmentioning

confidence: 99%

“…In the second step, these water molecules near the minor groove were removed using Voronoi tessellation. 42 From selection backbone 1…”

Section: Selection Of Water Molecule Subsetsmentioning

confidence: 99%

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Beyond the "Spine of Hydration": Chiral SFG Spectroscopy Detects DNA First Hydration Shell and Base Pair Structures

Perets,

Konstantinovsky,

Santiago

et al. 2024

Preprint

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Experimental methods capable of selectively probing water at the DNA minor groove, major groove, and phosphate backbone are crucial for understanding how hydration influences DNA structure and function. Chiral-selective sum frequency generation spectroscopy (chiral SFG) is unique among vibrational spectroscopies because it can selectively probe water molecules that form chiral hydration structures around biomolecules. However, interpreting chiral SFG spectra is challenging since both water and the biomolecule can produce chiral SFG signals. Here, we combine experiment and computation to establish a theoretical framework for rigorous interpretation of chiral SFG spectra of DNA. We demonstrate that chiral SFG detects the N-H stretch of DNA base pairs and the O-H stretch of water, exclusively probing water molecules in the DNA first hydration shell. Our analysis reveals that DNA transfers chirality to water molecules only within the first hydration shell, so they can be probed by chiral SFG spectroscopy. Beyond the first hydration shell, electric field-induced water structure is symmetric and therefore precludes chiral SFG response. Furthermore, we find that chiral SFG can differentiate chiral subpopulations of first hydration shell water molecules at the minor groove, major groove, and phosphate backbone. Our findings challenge the scientific perspective dominant for more than 40 years that the minor groove “spine of hydration” is the only chiral water structure surrounding the DNA double helix. By identifying the molecular origins of the DNA chiral SFG spectrum, we lay a robust experimental and theoretical foundation for applying chiral SFG to explore the chemical and biological physics of DNA hydration.

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Section: Chiral Sfg Is Sensitive To Water In the Dsdna First Hydratio...mentioning

confidence: 99%

Section: Chiral Sfg Can Sense Chiral Hydration Structures Around Dsdn...mentioning

confidence: 99%

Section: Analysis Of Water Dipole Orientationmentioning

confidence: 99%

Section: Selection Of Water Molecule Subsetsmentioning

confidence: 99%

“…In the second step, these water molecules near the minor groove were removed using Voronoi tessellation. 42 From selection backbone 1…”

Section: Selection Of Water Molecule Subsetsmentioning

confidence: 99%

See 3 more Smart Citations

Beyond the "Spine of Hydration": Chiral SFG Spectroscopy Detects DNA First Hydration Shell and Base Pair Structures

Perets,

Konstantinovsky,

Santiago

et al. 2024

Preprint

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Numerical investigation of thermal damage in rocks under high‐voltage electric pulse

Zhu,

Liu,

Liu

et al. 2024

Contrib. Plasma Phys

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The high‐voltage electric pulse fracturing (HVEPF) technology represents a novel and highly promising approach in rock fracturing. The investigation of thermal damage inflicted upon rocks by high‐voltage electrical pulses under multi‐physical field coupling is of great significance in the development of deep geothermal energy. This study establishes a damage model for rocks under electric fragmentation conditions by integrating electric field, heat transfer field, and solid mechanics field. Based on the developed damage model, the insulating properties, temperature variations, and forms of damage of rocks during electric fracturing are explored. Subsequently, the influence of voltage on rock damage status is investigated. The findings reveal that damage to the rock does not occur immediately after electrical breakdown; rather, it increases with the growth of current and temperature within the breakdown channel. Initial damage occurs at the ends of the breakdown channel, followed closely by damage in the central region of the channel. The predominant form of damage in rocks is tensile failure, with shear failure playing a secondary role, and the volume of damage increases with voltage. These results elucidate the characteristics of rock damage during electric fracturing, providing valuable insights for the engineering application of electric fracturing techniques.

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Interfacial interpretation

Rosu-Finsen

2023

Nat Rev Chem

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Characterizing Interfaces by Voronoi Tessellation

Cited by 4 publications

References 64 publications

Beyond the "Spine of Hydration": Chiral SFG Spectroscopy Detects DNA First Hydration Shell and Base Pair Structures

Beyond the "Spine of Hydration": Chiral SFG Spectroscopy Detects DNA First Hydration Shell and Base Pair Structures

Numerical investigation of thermal damage in rocks under high‐voltage electric pulse

Interfacial interpretation

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