The role of high-density and low-density amorphous ice on biomolecules at cryogenic temperatures: a case study with polyalanine

Eltareb, Ali; López, Gustavo E.; Giovambattista, Nicolás

doi:10.1039/d1cp02734d

Cited by 3 publications

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“…The results of this work should be helpful for our understanding of the nature of amorphous ices, including MDA. In particular, we note that the IA may play a relevant role in important technological applications, such as cryo-electron microscopy (cryoEM) 58 – 60 , cryopreservation techniques 61 – 64 , and x-ray experiments of protein crystals 65 , 66 . While vitrification of water under pressure is not uncommon in cryoEM experiments, experimental/computational studies characterizing the properties of amorphous ices generated by isobaric cooling under pressure (i.e., IA) are rather limited 34 , 42 , 43 , 45 , 64 , 67 .…”

Section: Summary and Discussionmentioning

confidence: 99%

“…In particular, we note that the IA may play a relevant role in important technological applications, such as cryo-electron microscopy (cryoEM) 58 – 60 , cryopreservation techniques 61 – 64 , and x-ray experiments of protein crystals 65 , 66 . While vitrification of water under pressure is not uncommon in cryoEM experiments, experimental/computational studies characterizing the properties of amorphous ices generated by isobaric cooling under pressure (i.e., IA) are rather limited 34 , 42 , 43 , 45 , 64 , 67 . Indeed, most experimental studies exploring the phase behavior of amorphous ice are based on LDA and HDA forms that are produced by isothermal compression/decompression of ice I h , LDA, and HDA; vitrification of water has been mostly limited to P = 0.1 MPa 32 , 33 .…”

Section: Summary and Discussionmentioning

confidence: 99%

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A continuum of amorphous ices between low-density and high-density amorphous ice

Eltareb,

Lopez,

Giovambattista

2024

Commun Chem

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Amorphous ices are usually classified as belonging to low-density or high-density amorphous ice (LDA and HDA) with densities ρLDA ≈ 0.94 g/cm3 and ρHDA ≈ 1.15−1.17 g/cm3. However, a recent experiment crushing hexagonal ice (ball-milling) produced a medium-density amorphous ice (MDA, ρMDA ≈ 1.06 g/cm3) adding complexity to our understanding of amorphous ice and the phase diagram of supercooled water. Motivated by the discovery of MDA, we perform computer simulations where amorphous ices are produced by isobaric cooling and isothermal compression/decompression. Our results show that, depending on the pressure employed, isobaric cooling can generate a continuum of amorphous ices with densities that expand in between those of LDA and HDA (briefly, intermediate amorphous ices, IA). In particular, the IA generated at P ≈ 125 MPa has a remarkably similar density and average structure as MDA, implying that MDA is not unique. Using the potential energy landscape formalism, we provide an intuitive qualitative understanding of the nature of LDA, HDA, and the IA generated at different pressures. In this view, LDA and HDA occupy specific and well-separated regions of the PEL; the IA prepared at P = 125 MPa is located in the intermediate region of the PEL that separates LDA and HDA.

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Section: Summary and Discussionmentioning

confidence: 99%

Section: Summary and Discussionmentioning

confidence: 99%

A continuum of amorphous ices between low-density and high-density amorphous ice

Eltareb,

Lopez,

Giovambattista

2024

Commun Chem

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“…For example, in the cryopreservation of biomolecules and cells, a major problem is the formation of ice crystals which can damage the sample of interest . In such cases, any water volume in the sample needs to be kept in a glassy state . Most computational studies of glassy water have been performed employing (i) classical MD simulations using (ii) rigid water models, such as SPC/E, ST2, , and TIP4P/2005. , In these studies, the properties of LDA/HDA and the phenomenology associated with the LDA-HDA transformation are reproduced qualitatively well, relative to experiments, but differences among the studied water models can be relevant. , Importantly, classical MD simulations neglect the quantum fluctuations due to the nuclear quantum effects (NQE; i.e., delocalization of atoms) at low temperatures.…”

Section: Introductionmentioning

confidence: 99%

The Importance of Nuclear Quantum Effects on the Thermodynamic and Structural Properties of Low-Density Amorphous Ice: A Comparison with Hexagonal Ice

2023

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We study the nuclear quantum effects (NQE) on the thermodynamic properties of low-density amorphous ice (LDA) and hexagonal ice (I h ) at P = 0.1 MPa and T ≥ 25 K. Our results are based on path-integral molecular dynamics (PIMD) and classical MD simulations of H 2 O and D 2 O using the q-TIP4P/F water model. We show that the inclusion of NQE is necessary to reproduce the experimental properties of LDA and ice I h . While MD simulations (no NQE) predict that the density ρ(T) of LDA and ice I h increases monotonically upon cooling, PIMD simulations indicate the presence of a density maximum in LDA and ice I h . MD and PIMD simulations also predict a qualitatively different Tdependence for the thermal expansion coefficient α P (T) and bulk modulus B(T) of both LDA and ice I h . Remarkably, the ρ(T), α P (T), and B(T) of LDA are practically identical to those of ice I h . The origin of the observed NQE is due to the delocalization of the H atoms, which is identical in LDA and ice I h . H atoms delocalize considerably (over a distance ≈ 20−25% of the OH covalent-bond length) and anisotropically (preferentially perpendicular to the OH covalent bond), leading to less linear hydrogen bonds HB (larger HOO angles and longer OO separations) than observed in classical MD simulations.

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Protein hydration water: Focus on low density and high density local structures upon cooling

Camisasca

Tenuzzo

Gallo

2023

Journal of Molecular Liquids

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The role of high-density and low-density amorphous ice on biomolecules at cryogenic temperatures: a case study with polyalanine

Abstract: Experimental techniques, such as cryo-electron microscopy, require biological samples to be recovered at cryogenic temperatures (T ≈ 100 K) with water being in an amorphous ice state. However, (bulk) water...

Cited by 3 publications

References 58 publications

A continuum of amorphous ices between low-density and high-density amorphous ice

A continuum of amorphous ices between low-density and high-density amorphous ice

The Importance of Nuclear Quantum Effects on the Thermodynamic and Structural Properties of Low-Density Amorphous Ice: A Comparison with Hexagonal Ice

Protein hydration water: Focus on low density and high density local structures upon cooling

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