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Brown SM, Mayer-Bacon C, Freeland S. Xeno Amino Acids: A Look into Biochemistry as We Do Not Know It. Life (Basel) 2023; 13:2281. [PMID: 38137883 PMCID: PMC10744825 DOI: 10.3390/life13122281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Would another origin of life resemble Earth's biochemical use of amino acids? Here, we review current knowledge at three levels: (1) Could other classes of chemical structure serve as building blocks for biopolymer structure and catalysis? Amino acids now seem both readily available to, and a plausible chemical attractor for, life as we do not know it. Amino acids thus remain important and tractable targets for astrobiological research. (2) If amino acids are used, would we expect the same L-alpha-structural subclass used by life? Despite numerous ideas, it is not clear why life favors L-enantiomers. It seems clearer, however, why life on Earth uses the shortest possible (alpha-) amino acid backbone, and why each carries only one side chain. However, assertions that other backbones are physicochemically impossible have relaxed into arguments that they are disadvantageous. (3) Would we expect a similar set of side chains to those within the genetic code? Many plausible alternatives exist. Furthermore, evidence exists for both evolutionary advantage and physicochemical constraint as explanatory factors for those encoded by life. Overall, as focus shifts from amino acids as a chemical class to specific side chains used by post-LUCA biology, the probable role of physicochemical constraint diminishes relative to that of biological evolution. Exciting opportunities now present themselves for laboratory work and computing to explore how changing the amino acid alphabet alters the universe of protein folds. Near-term milestones include: (a) expanding evidence about amino acids as attractors within chemical evolution; (b) extending characterization of other backbones relative to biological proteins; and (c) merging computing and laboratory explorations of structures and functions unlocked by xeno peptides.
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2
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Barakovic M, Pizzolato M, Tax CMW, Rudrapatna U, Magon S, Dyrby TB, Granziera C, Thiran JP, Jones DK, Canales-Rodríguez EJ. Estimating axon radius using diffusion-relaxation MRI: calibrating a surface-based relaxation model with histology. Front Neurosci 2023; 17:1209521. [PMID: 37638307 PMCID: PMC10457121 DOI: 10.3389/fnins.2023.1209521] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023] Open
Abstract
Axon radius is a potential biomarker for brain diseases and a crucial tissue microstructure parameter that determines the speed of action potentials. Diffusion MRI (dMRI) allows non-invasive estimation of axon radius, but accurately estimating the radius of axons in the human brain is challenging. Most axons in the brain have a radius below one micrometer, which falls below the sensitivity limit of dMRI signals even when using the most advanced human MRI scanners. Therefore, new MRI methods that are sensitive to small axon radii are needed. In this proof-of-concept investigation, we examine whether a surface-based axonal relaxation process could mediate a relationship between intra-axonal T2 and T1 times and inner axon radius, as measured using postmortem histology. A unique in vivo human diffusion-T1-T2 relaxation dataset was acquired on a 3T MRI scanner with ultra-strong diffusion gradients, using a strong diffusion-weighting (i.e., b = 6,000 s/mm2) and multiple inversion and echo times. A second reduced diffusion-T2 dataset was collected at various echo times to evaluate the model further. The intra-axonal relaxation times were estimated by fitting a diffusion-relaxation model to the orientation-averaged spherical mean signals. Our analysis revealed that the proposed surface-based relaxation model effectively explains the relationship between the estimated relaxation times and the histological axon radius measured in various corpus callosum regions. Using these histological values, we developed a novel calibration approach to predict axon radius in other areas of the corpus callosum. Notably, the predicted radii and those determined from histological measurements were in close agreement.
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Affiliation(s)
- Muhamed Barakovic
- Translational Imaging in Neurology (ThINk) Basel, Department of Biomedical Engineering, University Hospital Basel and University of Basel, Basel, Switzerland
- Department of Neurology, University Hospital Basel, Basel, Switzerland
- Cardiff University Brain Research Imaging Centre, Cardiff University, Cardiff, Wales, United Kingdom
- Signal Processing Laboratory 5 (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, Basel, Switzerland
| | - Marco Pizzolato
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Chantal M. W. Tax
- Cardiff University Brain Research Imaging Centre, Cardiff University, Cardiff, Wales, United Kingdom
- Image Sciences Institute, University Medical Center Utrecht, Utrecht, Netherlands
| | - Umesh Rudrapatna
- Cardiff University Brain Research Imaging Centre, Cardiff University, Cardiff, Wales, United Kingdom
| | - Stefano Magon
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, Basel, Switzerland
| | - Tim B. Dyrby
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
- Danish Research Centre for Magnetic Resonance (DRCMR), Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager and Hvidovre, Copenhagen, Denmark
| | - Cristina Granziera
- Translational Imaging in Neurology (ThINk) Basel, Department of Biomedical Engineering, University Hospital Basel and University of Basel, Basel, Switzerland
- Department of Neurology, University Hospital Basel, Basel, Switzerland
- Research Center for Clinical Neuroimmunology and Neuroscience Basel (RC2NB), University Hospital Basel and University of Basel, Basel, Switzerland
| | - Jean-Philippe Thiran
- Signal Processing Laboratory 5 (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Radiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
- Centre d’Imagerie Biomédicale (CIBM), EPFL, Lausanne, Switzerland
| | - Derek K. Jones
- Cardiff University Brain Research Imaging Centre, Cardiff University, Cardiff, Wales, United Kingdom
| | - Erick J. Canales-Rodríguez
- Signal Processing Laboratory 5 (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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3
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Malik R, Chandra A, Das B, Chandra A. Temperature Dependence of Non-Condon Effects in Two-Dimensional Vibrational Spectroscopy of Water. J Phys Chem B 2023; 127:2488-2498. [PMID: 36893383 DOI: 10.1021/acs.jpcb.2c06794] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Non-Condon effects in vibrational spectroscopy refers to the dependence of a molecule's vibrational transition dipole and polarizability on the coordinates of the surrounding environment. Earlier studies have shown that such effects can be pronounced for hydrogen-bonded systems like liquid water. Here, we present a theoretical study of two-dimensional vibrational spectroscopy under the non-Condon and Condon approximations at varying temperatures. We have performed calculations of both two-dimensional infrared and two-dimensional vibrational Raman spectra to gain insights into the temperature dependence of non-Condon effects in nonlinear vibrational spectroscopy. The two-dimensional spectra are calculated for the OH vibration of interest in the isotopic dilution limit where the coupling between the oscillators is ignored. Generally, both the infrared and Raman line shapes undergo red shifts with decrease in temperature due to strengthening of hydrogen bonds and decrease in the fraction of OH modes with weaker or no hydrogen bonds. The infrared line shape is further red-shifted under the non-Condon effects at a given temperature, while the Raman line shape does not show any such red shift due to non-Condon effects. The spectral dynamics becomes slower on decrease of temperature due to slower hydrogen bond relaxation and, for a given temperature, the spectral diffusion occurs at a faster rate upon inclusion of non-Condon effects. The time scales of spectral diffusion extracted from different metrics agree well with each other and also with experiments. The changes in the spectrum due to non-Condon effects are found to be more significant at lower temperatures.
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Affiliation(s)
- Ravi Malik
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Abhilash Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Banshi Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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4
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Solhi L, Guccini V, Heise K, Solala I, Niinivaara E, Xu W, Mihhels K, Kröger M, Meng Z, Wohlert J, Tao H, Cranston ED, Kontturi E. Understanding Nanocellulose-Water Interactions: Turning a Detriment into an Asset. Chem Rev 2023; 123:1925-2015. [PMID: 36724185 PMCID: PMC9999435 DOI: 10.1021/acs.chemrev.2c00611] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Modern technology has enabled the isolation of nanocellulose from plant-based fibers, and the current trend focuses on utilizing nanocellulose in a broad range of sustainable materials applications. Water is generally seen as a detrimental component when in contact with nanocellulose-based materials, just like it is harmful for traditional cellulosic materials such as paper or cardboard. However, water is an integral component in plants, and many applications of nanocellulose already accept the presence of water or make use of it. This review gives a comprehensive account of nanocellulose-water interactions and their repercussions in all key areas of contemporary research: fundamental physical chemistry, chemical modification of nanocellulose, materials applications, and analytical methods to map the water interactions and the effect of water on a nanocellulose matrix.
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Affiliation(s)
- Laleh Solhi
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Valentina Guccini
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Katja Heise
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Iina Solala
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Elina Niinivaara
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland.,Department of Wood Science, University of British Columbia, Vancouver, British ColumbiaV6T 1Z4, Canada
| | - Wenyang Xu
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland.,Laboratory of Natural Materials Technology, Åbo Akademi University, TurkuFI-20500, Finland
| | - Karl Mihhels
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Marcel Kröger
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Zhuojun Meng
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland.,Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou325001, China
| | - Jakob Wohlert
- Wallenberg Wood Science Centre (WWSC), Department of Fibre and Polymer Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 10044Stockholm, Sweden
| | - Han Tao
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
| | - Emily D Cranston
- Department of Wood Science, University of British Columbia, Vancouver, British ColumbiaV6T 1Z4, Canada.,Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British ColumbiaV6T 1Z3, Canada
| | - Eero Kontturi
- Department of Bioproducts and Biosystems, Aalto University, EspooFI-00076, Finland
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5
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Wang J, Zheng Y, Zhang H, Ye H. Machine learning-generated TIP4P-BGWT model for liquid and supercooled water. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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6
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Fernández-Fernández ÁM, Pérez-Rodríguez M, Piñeiro MM. Molecular dynamics of fluoromethane type I hydrates. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116720] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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7
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Song J. Adenosine triphosphate energy-independently controls protein homeostasis with unique structure and diverse mechanisms. Protein Sci 2021; 30:1277-1293. [PMID: 33829608 PMCID: PMC8197423 DOI: 10.1002/pro.4079] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 02/06/2023]
Abstract
Proteins function in the crowded cellular environments with high salt concentrations, thus facing tremendous challenges of misfolding/aggregation which represents a pathological hallmark of aging and an increasing spectrum of human diseases. Recently, intrinsically disordered regions (IDRs) were recognized to drive liquid-liquid phase separation (LLPS), a common principle for organizing cellular membraneless organelles (MLOs). ATP, the universal energy currency for all living cells, mysteriously has concentrations of 2-12 mM, much higher than required for its previously-known functions. Only recently, ATP was decoded to behave as a biological hydrotrope to inhibit protein LLPS and aggregation at mM. We further revealed that ATP also acts as a bivalent binder, which not only biphasically modulates LLPS driven by IDRs of human and viral proteins, but also bind to the conserved nucleic-acid-binding surfaces of the folded proteins. Most unexpectedly, ATP appears to act as a hydration mediator to antagonize the crowding-induced destabilization as well as to enhance folding of proteins without significant binding. Here, this review focuses on summarizing the results of these biophysical studies and discussing their implications in an evolutionary context. By linking triphosphate with unique hydration property to adenosine, ATP appears to couple the ability for establishing hydrophobic, π-π, π-cation and electrostatic interactions to the capacity in mediating hydration of proteins, which is at the heart of folding, dynamics, stability, phase separation and aggregation. Consequently, ATP acquired a category of functions at ~mM to energy-independently control protein homeostasis with diverse mechanisms, thus implying a link between cellular ATP concentrations and protein-aggregation diseases.
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Affiliation(s)
- Jianxing Song
- Department of Biological Sciences, Faculty of ScienceNational University of SingaporeSingaporeSingapore
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8
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Ye HF, Wang J, Zheng YG, Zhang HW, Chen Z. Machine learning for reparameterization of four-site water models: TIP4P-BG and TIP4P-BGT. Phys Chem Chem Phys 2021; 23:10164-10173. [PMID: 33951125 DOI: 10.1039/d0cp05831a] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Parameterizing an effective water model is a challenging issue because of the difficulty in maintaining a comprehensive balance among the diverse physical properties of water with a limited number of parameters. The advancement in machine learning provides a promising path to search for a reliable set of parameters. Based on the TIP4P water model, hence, about 6000 molecular dynamics (MD) simulations for pure water at 1 atm and in the range of 273-373 K are conducted here as the training data. The back-propagation (BP) neural network is then utilized to construct an efficient mapping between the model parameters and four crucial physical properties of water, including the density, vaporization enthalpy, self-diffusion coefficient and viscosity. Without additional time-consuming MD simulations, this mapping operation could result in sufficient and accurate data for high-population genetic algorithm (GA) to optimize the model parameters as much as possible. Based on the proposed parameterizing strategy, TIP4P-BG (a conventional four-site water model) and TIP4P-BGT (an advanced model with temperature-dependent parameters) are established. Both the water models exhibit excellent performance with a reasonable balance among the four crucial physical properties. The relevant mean absolute percentage errors are 3.53% and 3.08%, respectively. Further calculations on the temperature of maximum density, isothermal compressibility, thermal expansion coefficient, radial distribution function and surface tension are also performed and the resulting values are in good agreement with the experimental values. Through this water modeling example, the potential of the proposed data-driven machine learning procedure has been demonstrated for parameterizing a MD-based material model.
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Affiliation(s)
- Hong-Fei Ye
- International Research Center for Computational Mechanics, State Key Laboratory of Structural Analysis for Industrial Equipment, Department of Engineering Mechanics, Faculty of Vehicle Engineering and Mechanics, Dalian University of Technology, Dalian 116024, P. R. China.
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9
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Çınaroğlu SS, Biggin PC. Evaluating the Performance of Water Models with Host-Guest Force Fields in Binding Enthalpy Calculations for Cucurbit[7]uril-Guest Systems. J Phys Chem B 2021; 125:1558-1567. [PMID: 33538161 DOI: 10.1021/acs.jpcb.0c11383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Computational prediction of thermodynamic components with computational methods has become increasingly routine in computer-aided drug design. Although there has been significant recent effort and improvements in the calculation of free energy, the prediction of enthalpy (and entropy) remains underexplored. Furthermore, there has been relatively little work reported so far that attempts to comparatively assess how well different force fields and water models perform in conjunction with each other. Here, we report a comprehensive assessment of force fields and water models using host-guest systems that mimic many features of protein-ligand systems. These systems are computationally inexpensive, possibly because of their small size compared to protein-ligand systems. We present absolute enthalpy calculations using the multibox approach on a set of 25 cucurbit[7]uril-guest pairs. Eight water models were considered (TIP3P, TIP4P, TIP4P-Ew, SPC, SPC/E, OPC, TIP5P, Bind3P), along with five force fields commonly used in the literature (GAFFv1, GAFFv2, CGenFF, Parsley, and SwissParam). We observe that host-guest binding enthalpies are strongly sensitive to the selection of force field and water model. In terms of water models, we find that TIP3P and its derivative Bind3P are the best performing models for this particular host-guest system. The performance is generally better for aliphatic compounds than for aromatic ones, suggesting that aromaticity remains a difficult property to include accurately in these simple force fields.
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Affiliation(s)
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
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10
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Andreani C, Romanelli G, Parmentier A, Senesi R, Kolesnikov AI, Ko HY, Calegari Andrade MF, Car R. Hydrogen Dynamics in Supercritical Water Probed by Neutron Scattering and Computer Simulations. J Phys Chem Lett 2020; 11:9461-9467. [PMID: 33108193 DOI: 10.1021/acs.jpclett.0c02547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this work, an investigation of supercritical water is presented combining inelastic and deep inelastic neutron scattering experiments and molecular dynamics simulations based on a machine-learned potential of ab initio quality. The local hydrogen dynamics is investigated at 250 bar and in the temperature range of 553-823 K, covering the evolution from subcritical liquid to supercritical gas-like water. The evolution of libration, bending, and stretching motions in the vibrational density of states is studied, analyzing the spectral features by a mode decomposition. Moreover, the hydrogen nuclear momentum distribution is measured, and its anisotropy is probed experimentally. It is shown that hydrogen bonds survive up to the higher temperatures investigated, and we discuss our results in the framework of the coupling between intramolecular modes and intermolecular librations. Results show that the local potential affecting hydrogen becomes less anisotropic within the molecular plane in the supercritical phase, and we attribute this result to the presence of more distorted hydrogen bonds.
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Affiliation(s)
- Carla Andreani
- Dipartimento di Fisica and NAST Centre, Università degli Studi di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Roma, Italy
- CNR-IPCF, Istituto per i Processi Chimico-Fisici del CNR di Messina, Viale F. Stagno dAlcontres 37, 98158 Messina, Italy
| | - Giovanni Romanelli
- ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom
| | | | - Roberto Senesi
- Dipartimento di Fisica and NAST Centre, Università degli Studi di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Roma, Italy
- CNR-IPCF, Istituto per i Processi Chimico-Fisici del CNR di Messina, Viale F. Stagno dAlcontres 37, 98158 Messina, Italy
| | - Alexander I Kolesnikov
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Hsin-Yu Ko
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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11
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Abstract
Proteinaceous liquid-liquid phase separation (LLPS) occurs when a polypeptide coalesces into a dense phase to form a liquid droplet (i.e., condensate) in aqueous solution. In vivo, functional protein-based condensates are often referred to as membraneless organelles (MLOs), which have roles in cellular processes ranging from stress responses to regulation of gene expression. Late embryogenesis abundant (LEA) proteins containing seed maturation protein domains (SMP; PF04927) have been linked to storage tolerance of orthodox seeds. The mechanism by which anhydrobiotic longevity is improved is unknown. Interestingly, the brine shrimp Artemia franciscana is the only animal known to express such a protein (AfrLEA6) in its anhydrobiotic embryos. Ectopic expression of AfrLEA6 (AWM11684) in insect cells improves their desiccation tolerance and a fraction of the protein is sequestered into MLOs, while aqueous AfrLEA6 raises the viscosity of the cytoplasm. LLPS of AfrLEA6 is driven by the SMP domain, while the size of formed MLOs is regulated by a domain predicted to engage in protein binding. AfrLEA6 condensates formed in vitro selectively incorporate target proteins based on their surface charge, while cytoplasmic MLOs formed in AfrLEA6-transfected insect cells behave like stress granules. We suggest that AfrLEA6 promotes desiccation tolerance by engaging in two distinct molecular mechanisms: by raising cytoplasmic viscosity at even modest levels of water loss to promote cell integrity during drying and by forming condensates that may act as protective compartments for desiccation-sensitive proteins. Identifying and understanding the molecular mechanisms that govern anhydrobiosis will lead to significant advancements in preserving biological samples.
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12
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Elgabarty H, Kühne TD. Tumbling with a limp: local asymmetry in water's hydrogen bond network and its consequences. Phys Chem Chem Phys 2020; 22:10397-10411. [DOI: 10.1039/c9cp06960g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ab initio molecular dynamics simulations of ambient liquid water and energy decomposition analysis have recently shown that water molecules exhibit significant asymmetry between the strengths of the two donor and/or the two acceptor interactions.
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Affiliation(s)
- Hossam Elgabarty
- Dynamics of Condensed Matter and Center for Sustainable Systems Design
- Chair of Theoretical Chemistry
- University of Paderborn
- Paderborn
- Germany
| | - Thomas D. Kühne
- Dynamics of Condensed Matter and Center for Sustainable Systems Design
- Chair of Theoretical Chemistry
- University of Paderborn
- Paderborn
- Germany
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13
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Li S, Schmidt B. Replica exchange MD simulations of two-dimensional water in graphene nanocapillaries: rhombic versus square structures, proton ordering, and phase transitions. Phys Chem Chem Phys 2019; 21:17640-17654. [PMID: 31364628 DOI: 10.1039/c9cp00849g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The hydrogen bond patterns, proton ordering, and phase transitions of monolayer ice in two-dimensional hydrophobic confinement are fundamentally different from those found for bulk ice. To investigate the behavior of quasi-2D ice, we perform molecular dynamics simulations of water confined between fixed graphene plates at a distance of 0.65 nm. While experimental results are still limited and theoretical investigations are often based on a single, often empirically based force field model, this work presents a systematic study modeling the water-graphene interaction by effective Lennard-Jones potentials previously derived from high-level ab initio CCSD(T) calculations of water adsorbed on graphene [Phys. Chem. Chem. Phys., 2013, 15, 4995]. For the water-water interaction different water force fields, i.e. SPCE, TIP3P, TIP4P, TIP4P/ICE, and TIP5P, are used. The water occupancy of the graphene capillary at a pressure of 1000 MPa is determined to be between 13.5 and 13.9 water molecules per square nanometer, depending on the choice of the water force field. Based on these densities, we explore the structure and dynamics of quasi-2D water for temperatures ranging from 200 K to about 600 K for each of the five force fields. To ensure complete sampling of the configurational space and to overcome the barriers separating metastable structures, these simulations are based on the replica exchange molecular dynamics technique. We report different tetragonal hydrogen bond patterns, which are classified as nearly square or as rhombic. While many of these arrangements are essentially flat, in some cases puckered arrangements are found, too. Also the proton ordering of the quasi-2D water structures is considered, allowing us to identify them as ferroelectric, ferrielectric or antiferroelectric. For temperatures between 200 K and 400 K we find several second-order phase transitions from one ice structure to another, changing in many cases both the arrangements of the oxygen atoms and the proton ordering. For temperatures between 400 K and 600 K there are melting-like transitions from a monolayer of ice to a monolayer of liquid water. These first-order phase transitions have a latent heat between 3.4 and 4.0 kJ mol-1. Both the values of the transition temperatures and of the latent heats display considerable model dependence for the five different water models investigated here.
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Affiliation(s)
- Shujuan Li
- Institute for Mathematics, Freie Universität Berlin, Arnimallee 6, D-14195 Berlin, Germany.
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14
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Kripotou S, Zafeiris K, Culebras-Martínez M, Gallego Ferrer G, Kyritsis A. Dynamics of hydration water in gelatin and hyaluronic acid hydrogels. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2019; 42:109. [PMID: 31444585 DOI: 10.1140/epje/i2019-11871-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 07/18/2019] [Indexed: 06/10/2023]
Abstract
We employed broadband dielectric spectroscopy (BDS), for the investigation of the water dynamics in partially hydrated hyaluronic acid (HA), and gelatin (Gel), enzymatically crosslinked hydrogels, in the water fraction ranges [Formula: see text]. Our results indicate that at low hydrations ([Formula: see text]), where the dielectric response of the hydrogels is identical during cooling and heating, water plasticizes strongly the polymeric matrix and is organized in clusters giving rise to [Formula: see text]-process, secondary water relaxation and to an additional slower relaxation process. This later process has been found to be related with the dc charge conductivity and can be described in terms of the conduction current relaxation mechanism. At slightly higher hydrations, however, always below the hydration level where ice is formed during cooling, we have recorded in HA hydrogel a strong water dielectric relaxation process, [Formula: see text], which has Arrhenius-like temperature dependence and large time scale resembling relaxation processes recorded in bulk low density amorphous solid water structures. This relaxation process shows a strong-to-fragile transition at [Formula: see text]C and our data suggest that the VTF-like process recorded at [Formula: see text]C is controlled by the same molecular process like long range charge transport. In addition, our data imply that the crossover temperature is related with the onset of structural rearrangements (increase in configurational entropy) of the macromolecules. In partially crystallized hydrogels ([Formula: see text]) HA exhibits at low temperatures the ice dielectric process consistent with the bulk hexagonal ice, whereas Gel hydrogel exhibits as main low temperature process a slow relaxation process that refers to open tetrahedral structures of water similar to low density amorphous ice structures and to bulk cubic ice. Regarding the water secondary relaxation processes, we have shown that the [Formula: see text]-process and the [Formula: see text] process are activated in water hydrogen bond networks with different structures.
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Affiliation(s)
- Sotiria Kripotou
- National Technical University of Athens, Physics Department, Iroon Polytechneiou 9, Zografou Campus, 15780, Athens, Greece
| | - Konstantinos Zafeiris
- National Technical University of Athens, Physics Department, Iroon Polytechneiou 9, Zografou Campus, 15780, Athens, Greece
| | - Maria Culebras-Martínez
- Centre for Biomaterials and Tissue Engineering (CBIT), Universitat Politècnica de València, Camino de vera s/n, 46022, Valencia, Spain
| | - Gloria Gallego Ferrer
- Centre for Biomaterials and Tissue Engineering (CBIT), Universitat Politècnica de València, Camino de vera s/n, 46022, Valencia, Spain
- Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Valencia, Spain
| | - Apostolos Kyritsis
- National Technical University of Athens, Physics Department, Iroon Polytechneiou 9, Zografou Campus, 15780, Athens, Greece.
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15
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Zhou L, Mernagh TP, Le Losq C. Observation of the Chemical Structure of Water up to the Critical Point by Raman Spectroscopic Analysis of Fluid Inclusions. J Phys Chem B 2019; 123:5841-5847. [PMID: 31188605 DOI: 10.1021/acs.jpcb.9b02129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Raman spectra were obtained simultaneously from the liquid and vapor phases of pure water trapped at the critical density (322 kg·m-3) within synthetic inclusions in quartz. As these inclusions are heated up to the critical temperature (373.946 °C), the liquid phase decreases in density and the maximum of the Raman OH-stretching band increases in wavenumber. Conversely, as the vapor phase increases in density, the maximum of the Raman OH-stretching band decreases in wavenumber. The Raman bands of the liquid and vapor phases converge to a single band at the critical point of water, where the fluid exists as a single phase. A comparison of the band centroids for the vapor and liquid phases of water indicates respective increases and decreases in the amount of hydrogen bonding in these phases as a function of increasing and decreasing density. These effects were further quantified by peak-fitting the Raman OH-stretching peak with five Gaussian components. All the Gaussian components of the liquid phase decrease in amplitude with increasing temperature with the exception of the double donor-single acceptor (H2O)4 cluster, which increases in amplitude and becomes the most intense component at temperatures above 300 °C. The Raman spectra of the vapor phase are dominated by the free OH component at temperatures below 300 °C, but, above this temperature, the double donor-single acceptor (H2O)4 cluster is again the most intense band. The results indicate that a significant quantity of water clusters is present in both liquid and vapor water at high temperatures and that supercritical water can be considered as a mixture of small water clusters [(H2O)n, n = 1-4] dominated by the double donor-single acceptor (H2O)4 cluster.
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Affiliation(s)
- Li Zhou
- Key Laboratory of High-temperature and High-pressure Study of the Earth's Interior, Institute of Geochemistry , Chinese Academy of Sciences , Guiyang 550002 , China
| | - Terrence Patrick Mernagh
- Key Laboratory of High-temperature and High-pressure Study of the Earth's Interior, Institute of Geochemistry , Chinese Academy of Sciences , Guiyang 550002 , China.,Research School of Earth Sciences , The Australian National University , Acton , Australian Capital Territory 2601 , Australia
| | - Charles Le Losq
- Research School of Earth Sciences , The Australian National University , Acton , Australian Capital Territory 2601 , Australia
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16
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Elgabarty H, Kaliannan NK, Kühne TD. Enhancement of the local asymmetry in the hydrogen bond network of liquid water by an ultrafast electric field pulse. Sci Rep 2019; 9:10002. [PMID: 31292493 PMCID: PMC6620291 DOI: 10.1038/s41598-019-46449-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 06/27/2019] [Indexed: 11/18/2022] Open
Abstract
Condensed phase electron decomposition analysis based on density functional theory has recently revealed an asymmetry in the hydrogen-bond network in liquid water, in the sense that a significant population of water molecules are simultaneously donating and accepting one strong hydrogen-bond and another substantially weaker one. Here we investigate this asymmetry, as well as broader structural and energetic features of water's hydrogen-bond network, following the application of an intense electric field square pulse that invokes the ultrafast reorientation of water molecules. We find that the necessary field-strength required to invoke an ultrafast alignment in a picosecond time window is on the order of 108 Vm-1. The resulting orientational anisotropy imposes an experimentally measurable signature on the structure and dynamics of the hydrogen-bond network, including its asymmetry, which is strongly enhanced. The dependence of the molecular reorientation dynamics on the field-strength can be understood by relating the magnitude of the water dipole-field interaction to the rotational kinetic energy, as well as the hydrogen-bond energy.
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Affiliation(s)
- Hossam Elgabarty
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, Warburger Str. 100, D-33098, Paderborn, Germany
| | - Naveen Kumar Kaliannan
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, Warburger Str. 100, D-33098, Paderborn, Germany
| | - Thomas D Kühne
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, Warburger Str. 100, D-33098, Paderborn, Germany.
- Paderborn Center for Parallel Computing and Institute for Lightweight Design, University of Paderborn, Warburger Str. 100, D-33098, Paderborn, Germany.
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17
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Carnevale D, Pelupessy P, Bodenhausen G. Cross-term Splittings Due to the Orientational Inequivalence of Proton Magnetic Shielding Tensors: Do Water Molecules Trapped in Crystals Hop or Tunnel? J Phys Chem Lett 2019; 10:3224-3231. [PMID: 31059264 DOI: 10.1021/acs.jpclett.9b00914] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Water molecules trapped in crystals of barium chlorate monohydrate have been investigated by magic-angle spinning (MAS) proton NMR spectroscopy in the temperature range 110-300 K. At high temperatures, a single spinning sideband pattern is observed. Below 150 K, however, two interleaved spinning sideband manifolds appear, with distinct centerbands that do not coincide with the average isotropic chemical shift seen at high temperatures. This hitherto unknown "cross-term splitting" results from the interplay of the homonuclear dipole-dipole coupling and two anisotropic proton shielding tensors that have identical principal components but nonequivalent orientations. The resulting cross terms cannot be averaged out by rotation about the magic angle. The analysis of the exchange-induced broadening, coalescence, and narrowing of the cross-term splitting in MAS spectra allows one to estimate the rate of exchange of the two protons between 140 and 190 K. The experimental data is compared with 2H and 1H NMR studies of the same sample reported in the literature. Density functional theory methods are utilized to estimate the thermal activation energy for a 2-fold hopping process of proton exchange about the H-O-H bisector. The Bell-Limbach model allows one to take into account contributions due to incoherent quantum tunneling in the low-temperature regime.
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Affiliation(s)
- Diego Carnevale
- Laboratoire des Biomolécules, LBM, Département de Chimie , École Normale Supérieure , PSL University, Sorbonne Université, CNRS, 75005 Paris , France
| | - Philippe Pelupessy
- Laboratoire des Biomolécules, LBM, Département de Chimie , École Normale Supérieure , PSL University, Sorbonne Université, CNRS, 75005 Paris , France
| | - Geoffrey Bodenhausen
- Laboratoire des Biomolécules, LBM, Département de Chimie , École Normale Supérieure , PSL University, Sorbonne Université, CNRS, 75005 Paris , France
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18
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Teplukhin AV. Monte Carlo Simulation of the Local Ordering of Water Molecules. II. Spatial Correlations and Hydrogen Bonds. J STRUCT CHEM+ 2018. [DOI: 10.1134/s0022476618070144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Schweser F, Zivadinov R. Quantitative susceptibility mapping (QSM) with an extended physical model for MRI frequency contrast in the brain: a proof-of-concept of quantitative susceptibility and residual (QUASAR) mapping. NMR IN BIOMEDICINE 2018; 31:e3999. [PMID: 30246892 PMCID: PMC6296773 DOI: 10.1002/nbm.3999] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/21/2018] [Accepted: 06/28/2018] [Indexed: 05/12/2023]
Abstract
Quantitative susceptibility mapping (QSM) aims to calculate the tissue's magnetic susceptibility distribution from its perturbing effect on the MRI static main magnetic field. The method is increasingly being applied to study iron and myelin in clinical and preclinical settings. However, recent experimental and theoretical findings have challenged the fundamental theoretical assumptions that form the basis of current numerical implementations of QSM algorithms. The present work introduces a new class of susceptibility mapping algorithms, termed quantitative susceptibility and residual mapping (QUASAR), which takes into account frequency contributions not related to the spatial variation of bulk magnetic susceptibility in the Lorentz sphere model. We present a simple proof-of-concept QUASAR algorithm that, unlike most of the QSM algorithms currently used widely, results in an improved anatomical accuracy of the susceptibility distribution without any a priori assumptions about the susceptibility distribution during the field-to-source inversion. The algorithm was evaluated both in silico and in vivo in the preclinical setting. Our preliminary application of QUASAR in rodents provides the first in vivo evidence that the susceptibility-field model traditionally used in the QSM field cannot fully explain the frequency contrast in brain tissues. Only when an additional local frequency contribution is added to the physical model can the frequency contrast in the brain be related properly to the underlying anatomy.
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Affiliation(s)
- Ferdinand Schweser
- University at Buffalo, The State University of New York, Department of Neurology, Jacobs School of Medicine and Biomedical Sciences, New York, United States
| | - Robert Zivadinov
- University at Buffalo, The State University of New York, Department of Neurology, Jacobs School of Medicine and Biomedical Sciences, New York, United States
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20
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21
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Liu Y, Ojamäe L. Clathrate ice sL: a new crystalline phase of ice with ultralow density predicted by first-principles phase diagram computations. Phys Chem Chem Phys 2018. [DOI: 10.1039/c8cp00699g] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A new crystalline ice phase (clathrate ice sL) with ultralow density under negative pressure predicted by the first-principles phase diagram computations.
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Affiliation(s)
- Yuan Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- China
- Department of Chemistry
| | - Lars Ojamäe
- Department of Chemistry
- IFM
- Linköping University
- SE-58 183 Linköping
- Sweden
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22
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Riveros-Perez E, Riveros R. Water in the human body: An anesthesiologist's perspective on the connection between physicochemical properties of water and physiologic relevance. Ann Med Surg (Lond) 2017; 26:1-8. [PMID: 29904607 PMCID: PMC5904784 DOI: 10.1016/j.amsu.2017.12.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 11/10/2017] [Accepted: 12/12/2017] [Indexed: 12/13/2022] Open
Abstract
The unique structure and multifaceted physicochemical properties of the water molecule, in addition to its universal presence in body compartments, make water a key player in multiple biological processes in human physiology. Since anesthesiologists deal with physiologic processes where water molecules are critical at different levels, and administer medications whose pharmacokinetics and pharmacodynamics depend on interaction with water molecules, we consider that exploration of basic science aspects related to water and its role in physiology and pharmacology is relevant to the practice of anesthesiology. The purpose of this paper is to delineate the physicochemical basis of water that are critical in enabling it to support various homeostatic processes. The role of water in the formation of solutions, modulation of surface tension and in homeostasis of body temperature, acid-base status and osmolarity, is analyzed. Relevance of molecular water interactions to the anesthesiologist is not limited to the realm of physiology and pathophysiology. Deep knowledge of the importance of water in volatile anesthetic effects on neurons opens a window to a new comprehensive understanding of complex cellular mechanisms underlying the practice of anesthesiology.
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Affiliation(s)
- Efraín Riveros-Perez
- Department of Anesthesiology and Perioperative Medicine, Augusta University, USA
| | - Ricardo Riveros
- Pediatric Anesthesiologist Nemours Children's Health System, Orlando, FL, USA
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23
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24
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Abstract
Szent-Győrgi called water the "matrix of life" and claimed that there was no life without it. This statement is true, as far as we know, on our planet, but it is not clear whether it must hold throughout the cosmos. To evaluate that question requires a close consideration of the many varied and subtle roles that water plays in living cells-a consideration that must be free of both an assumed essentialism that gives water an almost mystical life-giving agency and a traditional tendency to see it as a merely passive solvent. Water is a participant in the "life of the cell," and here I describe some of the features of that active agency. Water's value for molecular biology comes from both the structural and dynamic characteristics of its status as a complex, structured liquid as well as its nature as a polar, protic, and amphoteric reagent. Any discussion of water as life's matrix must, however, begin with an acknowledgment that our understanding of it as both a liquid and a solvent is still incomplete.
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25
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Elliott GD, Wang S, Fuller BJ. Cryoprotectants: A review of the actions and applications of cryoprotective solutes that modulate cell recovery from ultra-low temperatures. Cryobiology 2017; 76:74-91. [DOI: 10.1016/j.cryobiol.2017.04.004] [Citation(s) in RCA: 180] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 04/07/2017] [Accepted: 04/16/2017] [Indexed: 02/08/2023]
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26
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Shi R, Huang X, Su Y, Lu HG, Li SD, Tang L, Zhao J. Which Density Functional Should Be Used to Describe Protonated Water Clusters? J Phys Chem A 2017; 121:3117-3127. [DOI: 10.1021/acs.jpca.7b00058] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ruili Shi
- Key
Laboratory of Materials Modification by Laser, Ion and Electron Beams, Dalian University of Technology, Ministry of Education, Dalian, 116024, China
| | - Xiaoming Huang
- School
of Ocean Science and Technology, Dalian University of Technology, Panjin Campus, Panjin, 124221, China
| | - Yan Su
- Key
Laboratory of Materials Modification by Laser, Ion and Electron Beams, Dalian University of Technology, Ministry of Education, Dalian, 116024, China
| | - Hai-Gang Lu
- Key
Laboratory of Chemical Biology and Molecular Engineering of the Education
Ministry, Institute of Molecular Science, Shanxi University, Taiyuan, 030006, China
| | - Si-Dian Li
- Key
Laboratory of Chemical Biology and Molecular Engineering of the Education
Ministry, Institute of Molecular Science, Shanxi University, Taiyuan, 030006, China
| | - Lingli Tang
- College
of Science, Dalian Nationalities University, Dalian 116600, China
| | - Jijun Zhao
- Key
Laboratory of Materials Modification by Laser, Ion and Electron Beams, Dalian University of Technology, Ministry of Education, Dalian, 116024, China
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27
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Lebre PH, De Maayer P, Cowan DA. Xerotolerant bacteria: surviving through a dry spell. Nat Rev Microbiol 2017; 15:285-296. [DOI: 10.1038/nrmicro.2017.16] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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28
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Dhabal D, Wikfeldt KT, Skinner LB, Chakravarty C, Kashyap HK. Probing the triplet correlation function in liquid water by experiments and molecular simulations. Phys Chem Chem Phys 2017; 19:3265-3278. [DOI: 10.1039/c6cp07599a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three-body information of liquid water is extracted using X-ray diffraction experiment as well as in molecular simulations via isothermal pressure derivative of structure factor term.
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Affiliation(s)
- Debdas Dhabal
- Department of Chemistry
- Indian Institute of Technology Delhi
- New Delhi
- India
| | | | | | | | - Hemant K. Kashyap
- Department of Chemistry
- Indian Institute of Technology Delhi
- New Delhi
- India
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29
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Henchman RH. Water's dual nature and its continuously changing hydrogen bonds. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:384001. [PMID: 27447299 DOI: 10.1088/0953-8984/28/38/384001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A model is proposed for liquid water that is a continuum between the ordered state with predominantly tetrahedral coordination, linear hydrogen bonds and activated dynamics and a disordered state with a continuous distribution of multiple coordinations, multiple types of hydrogen bond, and diffusive dynamics, similar to that of normal liquids. Central to water's heterogeneous structure is the ability of hydrogen to donate to either one acceptor in a conventional linear hydrogen bond or to multiple acceptors as a furcated hydrogen. Linear hydrogen bonds are marked by slow, activated kinetics for hydrogen-bond switching to more crowded acceptors and sharp first peaks in the hydrogen-oxygen radial distribution function. Furcated hydrogens, equivalent to free, broken, dangling or distorted hydrogens, have barrierless, rapid kinetics and poorly defined first peaks in their hydrogen-oxygen radial distribution function. They involve the weakest donor in a local excess of donors, such that barrierless whole-molecule vibration rapidly swaps them between the linear and furcated forms. Despite the low number of furcated hydrogens and their transient existence, they are readily created in a single hydrogen-bond switch and free up the dynamics of numerous surrounding molecules, bringing about the disordered state. Hydrogens in the ordered state switch with activated dynamics to make the non-tetrahedral coordinations of the disordered state, which can also combine to make the ordered state. Consequently, the ordered and disordered states are both connected by diffusive dynamics and differentiated by activated dynamics, bringing about water's continuous heterogeneity.
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Affiliation(s)
- Richard H Henchman
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK. School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
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30
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Prasad S, Chakravarty C. Tuning the tetrahedrality of the hydrogen-bonded network of water: Comparison of the effects of pressure and added salts. J Chem Phys 2016; 144:234509. [DOI: 10.1063/1.4953796] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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31
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Leutritz T, Hilfert L, Busse U, Smalla K, Speck O, Zhong K. Contribution of iron and protein contents from rat brain subcellular fractions to MR phase imaging. Magn Reson Med 2016; 77:2028-2039. [DOI: 10.1002/mrm.26288] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 12/14/2022]
Affiliation(s)
- T. Leutritz
- Dept. Biomedical Magnetic ResonanceOtto‐von‐Guericke UniversityMagdeburg Germany
| | - L. Hilfert
- Institute for ChemistryOtto‐von‐Guericke UniversityMagdeburg Germany
| | - U. Busse
- Institute of Apparatus and Environmental EngineeringOtto‐von‐Guericke UniversityMagdeburg Germany
| | - K.‐H. Smalla
- Center for Behavioral Brain Sciences Magdeburg
- Leibniz Institute for NeurobiologyMagdeburg Germany
| | - O. Speck
- Dept. Biomedical Magnetic ResonanceOtto‐von‐Guericke UniversityMagdeburg Germany
- Center for Behavioral Brain Sciences Magdeburg
- Leibniz Institute for NeurobiologyMagdeburg Germany
- German Center for Neurodegenerative Disease (DZNE)Site Magdeburg Germany
| | - K. Zhong
- Dept. Biomedical Magnetic ResonanceOtto‐von‐Guericke UniversityMagdeburg Germany
- High Magnetic Field Lab, Chinese Academy of SciencesHefei China
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32
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Changes in hydration structure are necessary for collective motions of a multi-domain protein. Sci Rep 2016; 6:26302. [PMID: 27193111 PMCID: PMC4872039 DOI: 10.1038/srep26302] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 04/25/2016] [Indexed: 01/27/2023] Open
Abstract
Conformational motions of proteins are necessary for their functions. To date, experimental studies measuring conformational fluctuations of a whole protein structure have revealed that water molecules hydrating proteins are necessary to induce protein functional motions. However, the underlying microscopic mechanism behind such regulation remains unsolved. To clarify the mechanism, multi-domain proteins are good targets because it is obvious that water molecules between domains play an important role in domain motions. Here, we show how changes in hydration structure microscopically correlate with large-amplitude motions of a multi-domain protein, through molecular dynamics simulation supported by structural analyses and biochemical experiments. We first identified collective domain motions of the protein, which open/close an active-site cleft between domains. The analyses on changes in hydration structure revealed that changes in local hydration in the depth of the cleft are necessary for the domain motion and vice versa. In particular, ‘wetting’/‘drying’ at a hydrophobic pocket and ‘adsorption’/‘dissociation’ of a few water molecules at a hydrophilic crevice in the cleft were induced by dynamic rearrangements of hydrogen-bond networks, and worked as a switch for the domain motions. Our results microscopically demonstrated the importance of hydrogen-bond networks of water molecules in understanding energy landscapes of protein motions.
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33
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Amann-Winkel K, Bellissent-Funel MC, Bove LE, Loerting T, Nilsson A, Paciaroni A, Schlesinger D, Skinner L. X-ray and Neutron Scattering of Water. Chem Rev 2016; 116:7570-89. [DOI: 10.1021/acs.chemrev.5b00663] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Katrin Amann-Winkel
- Department
of Physics, AlbaNova University Center, Stockholm University, SE-106
91, Stockholm, Sweden
| | | | - Livia E. Bove
- IMPMC, CNRS-UMR 7590, Université P&M Curie, 75252 Paris, France
- Institute
of Condensed Matter Physics, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Thomas Loerting
- Institute
of Physical Chemistry, University of Innsbruck, 6020 Innsbruck, Austria
| | - Anders Nilsson
- Department
of Physics, AlbaNova University Center, Stockholm University, SE-106
91, Stockholm, Sweden
| | - Alessandro Paciaroni
- Dipartimento
di Fisica e Geologia, Università di Perugia, Via Alessandro
Pascoli, I-06123 Perugia, Italy
| | - Daniel Schlesinger
- Department
of Physics, AlbaNova University Center, Stockholm University, SE-106
91, Stockholm, Sweden
| | - Lawrie Skinner
- Mineral
Physics Institute, Stony Brook University, Stony Brook, New York 11794-2100, United States
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34
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Kolesnikov AI, Reiter GF, Choudhury N, Prisk TR, Mamontov E, Podlesnyak A, Ehlers G, Seel AG, Wesolowski DJ, Anovitz LM. Quantum Tunneling of Water in Beryl: A New State of the Water Molecule. PHYSICAL REVIEW LETTERS 2016; 116:167802. [PMID: 27152824 DOI: 10.1103/physrevlett.116.167802] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Indexed: 05/15/2023]
Abstract
Using neutron scattering and ab initio simulations, we document the discovery of a new "quantum tunneling state" of the water molecule confined in 5 Å channels in the mineral beryl, characterized by extended proton and electron delocalization. We observed a number of peaks in the inelastic neutron scattering spectra that were uniquely assigned to water quantum tunneling. In addition, the water proton momentum distribution was measured with deep inelastic neutron scattering, which directly revealed coherent delocalization of the protons in the ground state.
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Affiliation(s)
- Alexander I Kolesnikov
- Chemical and Engineering Materials Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - George F Reiter
- Physics Department, University of Houston, Houston, Texas 77204, USA
| | - Narayani Choudhury
- Math and Science Division, Lake Washington Institute of Technology, Kirkland, Washington 98034, USA; School of Science, Technology, Engineering and Math, University of Washington, Bothell, Washington 98011, USA
| | - Timothy R Prisk
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Eugene Mamontov
- Chemical and Engineering Materials Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Andrey Podlesnyak
- Quantum Condensed Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - George Ehlers
- Quantum Condensed Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Andrew G Seel
- ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, United Kingdom
| | - David J Wesolowski
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Lawrence M Anovitz
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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35
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Maynard-Casely HE. Water, a very short introduction. CRYSTALLOGR REV 2016. [DOI: 10.1080/0889311x.2016.1141901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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36
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Dhabal D, Singh M, Wikfeldt KT, Chakravarty C. Triplet correlation functions in liquid water. J Chem Phys 2015; 141:174504. [PMID: 25381528 DOI: 10.1063/1.4898755] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Triplet correlations have been shown to play a crucial role in the transformation of simple liquids to anomalous tetrahedral fluids [M. Singh, D. Dhabal, A. H. Nguyen, V. Molinero, and C. Chakravarty, Phys. Rev. Lett. 112, 147801 (2014)]. Here we examine triplet correlation functions for water, arguably the most important tetrahedral liquid, under ambient conditions, using configurational ensembles derived from molecular dynamics (MD) simulations and reverse Monte Carlo (RMC) datasets fitted to experimental scattering data. Four different RMC data sets with widely varying hydrogen-bond topologies fitted to neutron and x-ray scattering data are considered [K. T. Wikfeldt, M. Leetmaa, M. P. Ljungberg, A. Nilsson, and L. G. M. Pettersson, J. Phys. Chem. B 113, 6246 (2009)]. Molecular dynamics simulations are performed for two rigid-body effective pair potentials (SPC/E and TIP4P/2005) and the monatomic water (mW) model. Triplet correlation functions are compared with other structural measures for tetrahedrality, such as the O-O-O angular distribution function and the local tetrahedral order distributions. In contrast to the pair correlation functions, which are identical for all the RMC ensembles, the O-O-O triplet correlation function can discriminate between ensembles with different degrees of tetrahedral network formation with the maximally symmetric, tetrahedral SYM dataset displaying distinct signatures of tetrahedrality similar to those obtained from atomistic simulations of the SPC/E model. Triplet correlations from the RMC datasets conform closely to the Kirkwood superposition approximation, while those from MD simulations show deviations within the first two neighbour shells. The possibilities for experimental estimation of triplet correlations of water and other tetrahedral liquids are discussed.
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Affiliation(s)
- Debdas Dhabal
- Department of Chemistry, Indian Institute of Technology-Delhi, New Delhi 110016, India
| | - Murari Singh
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | | | - Charusita Chakravarty
- Department of Chemistry, Indian Institute of Technology-Delhi, New Delhi 110016, India
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37
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Matsuoka D, Sugiyama S, Murata M, Matsuoka S. Molecular Dynamics Simulations of Heart-type Fatty Acid Binding Protein in Apo and Holo Forms, and Hydration Structure Analyses in the Binding Cavity. J Phys Chem B 2014; 119:114-27. [DOI: 10.1021/jp510384f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Daisuke Matsuoka
- JST ERATO, Lipid Active
Structure Project, ‡Department of Chemistry, Graduate
School of Science, and §Project Research Center for Fundamental Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Shigeru Sugiyama
- JST ERATO, Lipid Active
Structure Project, ‡Department of Chemistry, Graduate
School of Science, and §Project Research Center for Fundamental Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Michio Murata
- JST ERATO, Lipid Active
Structure Project, ‡Department of Chemistry, Graduate
School of Science, and §Project Research Center for Fundamental Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Shigeru Matsuoka
- JST ERATO, Lipid Active
Structure Project, ‡Department of Chemistry, Graduate
School of Science, and §Project Research Center for Fundamental Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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Bonnet N, Marzari N. Static dielectric permittivity of ice from first principles. PHYSICAL REVIEW LETTERS 2014; 113:245501. [PMID: 25541777 DOI: 10.1103/physrevlett.113.245501] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Indexed: 06/04/2023]
Abstract
The static permittivity of ice is computed from first principles as a function of the electric field, together with the generalized Kirkwood factor. The molecular dipole in ice is unambiguously obtained by an original method combining a slab approach and Berry phase calculations, and the fluctuations of the polarization are sampled by Monte Carlo runs using first-principles model Hamiltonians for different proton configurations. Common approximations in the exchange-correlation functionals overestimate the dielectric permittivity and enhance ferroelectric configurations and the Kirkwood factor, whereas dielectric saturation effects compare well with experiment.
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Affiliation(s)
- Nicéphore Bonnet
- Department of Materials Science and Engineering, MIT, Cambridge, Massachusetts 02139, USA
| | - Nicola Marzari
- Theory and Simulation of Materials (THEOS), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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40
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Soper AK. Disordered Atom Molecular Potential for Water Parameterized against Neutron Diffraction Data. Application to the Structure of Ice Ih. J Phys Chem B 2014; 119:9244-53. [DOI: 10.1021/jp509909w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alan K. Soper
- ISIS Facility, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, U.K
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41
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Izadi S, Anandakrishnan R, Onufriev AV. Building Water Models: A Different Approach. J Phys Chem Lett 2014; 5:3863-3871. [PMID: 25400877 PMCID: PMC4226301 DOI: 10.1021/jz501780a] [Citation(s) in RCA: 577] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 10/16/2014] [Indexed: 05/19/2023]
Abstract
Simplified classical water models are currently an indispensable component in practical atomistic simulations. Yet, despite several decades of intense research, these models are still far from perfect. Presented here is an alternative approach to constructing widely used point charge water models. In contrast to the conventional approach, we do not impose any geometry constraints on the model other than the symmetry. Instead, we optimize the distribution of point charges to best describe the "electrostatics" of the water molecule. The resulting "optimal" 3-charge, 4-point rigid water model (OPC) reproduces a comprehensive set of bulk properties significantly more accurately than commonly used rigid models: average error relative to experiment is 0.76%. Close agreement with experiment holds over a wide range of temperatures. The improvements in the proposed model extend beyond bulk properties: compared to common rigid models, predicted hydration free energies of small molecules using OPC are uniformly closer to experiment, with root-mean-square error <1 kcal/mol.
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Affiliation(s)
- Saeed Izadi
- Department of Biomedical Engineering and Mechanics, Department of Computer Science, and Departments of Computer
Science and Physics, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Ramu Anandakrishnan
- Department of Biomedical Engineering and Mechanics, Department of Computer Science, and Departments of Computer
Science and Physics, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Alexey V. Onufriev
- Department of Biomedical Engineering and Mechanics, Department of Computer Science, and Departments of Computer
Science and Physics, Virginia Tech, Blacksburg, Virginia 24060, United States
- E-mail:
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Ni Y, Skinner JL. Ultrafast pump-probe and 2DIR anisotropy and temperature-dependent dynamics of liquid water within the E3B model. J Chem Phys 2014; 141:024509. [DOI: 10.1063/1.4886427] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Yicun Ni
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - J. L. Skinner
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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44
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Martiniano HFMC, Galamba N, Cabral BJC. Ab initio calculation of the electronic absorption spectrum of liquid water. J Chem Phys 2014; 140:164511. [PMID: 24784291 DOI: 10.1063/1.4871740] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The electronic absorption spectrum of liquid water was investigated by coupling a one-body energy decomposition scheme to configurations generated by classical and Born-Oppenheimer Molecular Dynamics (BOMD). A Frenkel exciton Hamiltonian formalism was adopted and the excitation energies in the liquid phase were calculated with the equation of motion coupled cluster with single and double excitations method. Molecular dynamics configurations were generated by different approaches. Classical MD were carried out with the TIP4P-Ew and AMOEBA force fields. The BLYP and BLYP-D3 exchange-correlation functionals were used in BOMD. Theoretical and experimental results for the electronic absorption spectrum of liquid water are in good agreement. Emphasis is placed on the relationship between the structure of liquid water predicted by the different models and the electronic absorption spectrum. The theoretical gas to liquid phase blue-shift of the peak positions of the electronic absorption spectrum is in good agreement with experiment. The overall shift is determined by a competition between the O-H stretching of the water monomer in liquid water that leads to a red-shift and polarization effects that induce a blue-shift. The results illustrate the importance of coupling many-body energy decomposition schemes to molecular dynamics configurations to carry out ab initio calculations of the electronic properties in liquid phase.
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Affiliation(s)
- Hugo F M C Martiniano
- Grupo de Física Matemática da Universidade de Lisboa, Av. Professor Gama Pinto 2, 1649-003 Lisboa, Portugal
| | - Nuno Galamba
- Grupo de Física Matemática da Universidade de Lisboa, Av. Professor Gama Pinto 2, 1649-003 Lisboa, Portugal
| | - Benedito J Costa Cabral
- Grupo de Física Matemática da Universidade de Lisboa, Av. Professor Gama Pinto 2, 1649-003 Lisboa, Portugal
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45
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Angulo-Sherman A, Mercado-Uribe H. Water under inner pressure: a dielectric spectroscopy study. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:022406. [PMID: 25353481 DOI: 10.1103/physreve.89.022406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Indexed: 06/04/2023]
Abstract
Water is the most studied substance on Earth. However, it is not completely understood why its structural and dynamical properties give rise to some anomalous behaviors. Some of them emerge when experiments at low temperatures and/or high pressures are performed. Here we report dielectric measurements on cold water under macroscopically constrained conditions, i.e., water in a large container at constant volume that cannot freeze below the melting point. The inner pressure in these conditions shifts the α relaxation peak to similar frequencies as seen in ice Ih. At 267 K we observe a peculiar response possibly due to the Grotthuss mechanism. At 251 K (the triple point) ice III forms.
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A systematic method for analysing the protein hydration structure of T4 lysozyme. J Mol Recognit 2013; 26:479-87. [DOI: 10.1002/jmr.2290] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 06/07/2013] [Accepted: 06/08/2013] [Indexed: 11/07/2022]
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Kyakuno H, Matsuda K, Nakai Y, Fukuoka T, Maniwa Y, Nishihara H, Kyotani T. Amorphous water in three-dimensional confinement of zeolite-templated carbon. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.04.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Yigzawe TM, Sadus RJ. Thermodynamic properties of liquid water from a polarizable intermolecular potential. J Chem Phys 2013; 138:044503. [DOI: 10.1063/1.4779295] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Colosi C, Costantini M, Barbetta A, Cametti C, Dentini M. Anomalous Debye-like dielectric relaxation of water in micro-sized confined polymeric systems. Phys Chem Chem Phys 2013; 15:20153-60. [DOI: 10.1039/c3cp52902a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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50
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Mills MJL, Hawe GI, Handley CM, Popelier PLA. Unified approach to multipolar polarisation and charge transfer for ions: microhydrated Na+. Phys Chem Chem Phys 2013; 15:18249-61. [DOI: 10.1039/c3cp53204f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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