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Effect of hemoglobin hydration on the physical properties of erythrocyte cytoplasm and whole blood. Electrochim Acta 2022. [DOI: 10.1016/j.electacta.2022.141560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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2
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Henao A, Angulo-García D, Cuello GJ, Negrier P, Pardo LC. Investigating disordered phases of C2Cl6 using an information theory approach. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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3
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Reich V, Majumdar A, Müller M, Busch S. Comparison of molecular dynamics simulations of water with neutron and X-ray scattering experiments. EPJ WEB OF CONFERENCES 2022. [DOI: 10.1051/epjconf/202227201015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The atomistic structure and dynamics obtained from molecular dynamics (MD) simulations with the example of TIP3P (rigid and flexible) and TIP4P/2005 (rigid) water is compared to neutron and X-ray scattering data at ambient conditions. Neutron and X-ray diffractograms are calculated from the simulations for four isotopic substitutions as well as the incoherent intermediate scattering function for neutrons. The resulting curves are compared to each other and to published experimental data. Differences between simulated and measured intermediate scattering functions are quantified by fitting an analytic model to the computed values. The sensitivity of the scattering curves to the parameters of the MD simulations is demonstrated on the example of two parameters, bond length and angle.
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4
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Ki H, Choi S, Kim J, Choi EH, Lee S, Lee Y, Yoon K, Ahn CW, Ahn DS, Lee JH, Park J, Eom I, Kim M, Chun SH, Kim J, Ihee H, Kim J. Optical Kerr Effect of Liquid Acetonitrile Probed by Femtosecond Time-Resolved X-ray Liquidography. J Am Chem Soc 2021; 143:14261-14273. [PMID: 34455778 DOI: 10.1021/jacs.1c06088] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Optical Kerr effect (OKE) spectroscopy is a method that measures the time-dependent change of the birefringence induced by an optical laser pulse using another optical laser pulse and has been used often to study the ultrafast dynamics of molecular liquids. Here we demonstrate an alternative method, femtosecond time-resolved X-ray liquidography (fs-TRXL), where the microscopic structural motions related to the OKE response can be monitored using a different type of probe, i.e., X-ray solution scattering. By applying fs-TRXL to acetonitrile and a dye solution in acetonitrile, we demonstrate that different types of molecular motions around photoaligned molecules can be resolved selectively, even without any theoretical modeling, based on the anisotropy of two-dimensional scattering patterns and extra structural information contained in the q-space scattering data. Specifically, the dynamics of reorientational (libration and orientational diffusion) and translational (interaction-induced motion) motions are captured separately by anisotropic and isotropic scattering signals, respectively. Furthermore, the two different types of reorientational motions are distinguished from each other by their own characteristic scattering patterns and time scales. The measured time-resolved scattering signals are in excellent agreement with the simulated scattering signals based on a molecular dynamics simulation for plausible molecular configurations, providing the detailed structural description of the OKE response in liquid acetonitrile.
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Affiliation(s)
- Hosung Ki
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Seungjoo Choi
- Department of Chemistry, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Jungmin Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Eun Hyuk Choi
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Seonggon Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Yunbeom Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Kihwan Yoon
- Department of Chemistry, The Catholic University of Korea, Bucheon 14662, Republic of Korea
| | - Chi Woo Ahn
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Doo-Sik Ahn
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Jae Hyuk Lee
- Pohang Accelerator Laboratory, Pohang 37673, Republic of Korea
| | - Jaeku Park
- Pohang Accelerator Laboratory, Pohang 37673, Republic of Korea
| | - Intae Eom
- Pohang Accelerator Laboratory, Pohang 37673, Republic of Korea
| | - Minseok Kim
- Pohang Accelerator Laboratory, Pohang 37673, Republic of Korea
| | - Sae Hwan Chun
- Pohang Accelerator Laboratory, Pohang 37673, Republic of Korea
| | - Joonghan Kim
- Department of Chemistry, The Catholic University of Korea, Bucheon 14662, Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Jeongho Kim
- Department of Chemistry, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
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Yu CH, Lo CC, Chen KH, Chang YR, Chen CW, Wen CY. Self-assembly nuclei with a preferred orientation at the extended hydrophobic surface toward textured growth of ZnO nanorods in aqueous chemical bath deposition. NANOTECHNOLOGY 2021; 32:175603. [PMID: 33455957 DOI: 10.1088/1361-6528/abdc8c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Textured growth of ZnO nanorods with no restriction of the substrate material is beneficial to their applications. The approaches to grow ZnO nanorods with texture are based on preparing suitable surface structure on the growth substrate, e.g. using a crystalline substrate with a specific surface structures or pre-depositing seed layers by high-temperature annealing of precursors. In the aqueous nutrient solution of the chemical bath deposition (CBD) process for ZnO growth, the concentration of Zn2+ ions at the extended hydrophobic surface is sufficiently high for forming self-assembly nuclei with a preferred orientation, resulting in the subsequent textured growth of ZnO nanorods. In this research, the hydrophobic surface is prepared by modifying Si surface with a self-assembly octadecyltrimethoxysilane (OTMS) monolayer. The formation mechanism of the nuclei on this hydrophobic surface for the textured growth of ZnO nanorods is investigated. It is shown that the nuclei form at the beginning of the CBD process and later transform into the Wurtzite structure to seed ZnO growth. An alternative approach to prepare seed layers is therefore involved in the aqueous CBD process, which is applicable to a range of hydrophobic substrates for textured growth of ZnO nanorods.
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Affiliation(s)
- Chia-Hao Yu
- Department of Materials Science and Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Chang-Chen Lo
- Department of Materials Science and Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Kuan-Hung Chen
- Department of Materials Science and Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Yih-Ren Chang
- Department of Materials Science and Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Chun-Wei Chen
- Department of Materials Science and Engineering, National Taiwan University, Taipei 10617, Taiwan
- Center of Atomic Initiative for New Materials, National Taiwan University, Taipei 10617, Taiwan
- International Graduate Program of Molecular Science and Technology, National Taiwan University, Taipei 10617, Taiwan
| | - Cheng-Yen Wen
- Department of Materials Science and Engineering, National Taiwan University, Taipei 10617, Taiwan
- Center of Atomic Initiative for New Materials, National Taiwan University, Taipei 10617, Taiwan
- International Graduate Program of Molecular Science and Technology, National Taiwan University, Taipei 10617, Taiwan
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Henao A, Salazar-Rios JM, Guardia E, Pardo LC. Structure and dynamics of water plastic crystals from computer simulations. J Chem Phys 2021; 154:104501. [PMID: 33722053 DOI: 10.1063/5.0038762] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Water has a rich phase diagram with several crystals, as confirmed by experiments. High-pressure and high-temperature water is of interest for Earth's mantle and exoplanetary investigations. It is in this region of the phase diagram of water that new plastic crystal phases of water have been revealed via computer simulations by both classical forcefields and ab initio calculations. However, these plastic phases still remain elusive in experiments. Here, we present a complete characterization of the structure, dynamics, and thermodynamics of the computational plastic crystal phases of water using molecular dynamics and the two-phase thermodynamic method and uncover the interplay between them. The relaxation times of different reorientational correlation functions are obtained for the hypothetical body-centered-cubic and face-centered-cubic plastic crystal phases of water at T = 440 K and P = 8 GPa. Results are compared to a high pressure liquid and ice VII phases to improve the understanding of the plastic crystal phases. Entropy results indicate that the fcc crystal is more stable compared to the bcc structure under the studied conditions.
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Affiliation(s)
- Andrés Henao
- Grup de Simulació per Ordinador en Matèria Condensada, Departament de Física, B4-B5 Campus Nord, Universitat Politècnica de Catalunya, E-08034 Barcelona, Catalonia, Spain
| | | | - Elvira Guardia
- Grup de Simulació per Ordinador en Matèria Condensada, Departament de Física, B4-B5 Campus Nord, Universitat Politècnica de Catalunya, E-08034 Barcelona, Catalonia, Spain
| | - Luis C Pardo
- Grup de Caracterització de Materials, Departament de Física, EEBE, Universitat Politècnica de Catalunya, Avgda. Eduard Maristany 16, E-080197 Barcelona, Catalonia, Spain
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Geist N, Kulke M, Schulig L, Link A, Langel W. Replica-Based Protein Structure Sampling Methods II: Advanced Hybrid Solvent TIGER2hs. J Phys Chem B 2019; 123:5995-6006. [PMID: 31265293 DOI: 10.1021/acs.jpcb.9b03134] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In many cases, native states of proteins may be predicted with sufficient accuracy by molecular dynamics simulations (MDSs) with modern force fields. Enhanced sampling methods based on MDS are applied for exploring the phase space of a protein sequence and to overcome barriers on rough conformational energy landscapes. The minimum free energy state is obtained with sampling algorithms providing sufficient convergence and accuracy. A reliable but computationally very expensive method is replica exchange molecular dynamics, with many modifications to this approach presented in the past. Recently, we demonstrated how our temperature intervals with global exchange of replicas hybrid (TIGER2h) solvent sampling algorithm made a good compromise between efficiency and accuracy. There, all states are sampled under full explicit solvent conditions with a freely chosen number of replicas, whereas an implicit solvent is used during the swap decisions. This hybrid method yielded a much better approximation to the agreement with calculations in an explicit solvent than fully implicit solvent simulations. Here, we present an extension of TIGER2h and add a few layers of explicit water molecules around the peptide for the energy calculations, whereas the dynamics in fully explicit water is maintained. We claim that these water layers better reproduce steric effects, the polarization of the solvent, and the resulting reaction field energy than typical implicit solvent models. By investigating the protein-solvent interactions across comprehensive thermodynamic state ensembles, we found a strong conformational dependence of this reaction field energy. All simulations were performed with nanoscale molecular dynamics on two peptides, the α-helical peptide (AAQAA)3 and the β-hairpin peptide HP7. A production-ready TIGER2hs implementation is supplied, approaching the accuracy of full explicit solvent sampling at a fraction of computational resources.
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Affiliation(s)
- Norman Geist
- Institut für Biochemie , Universität Greifswald , Felix-Hausdorff-Straße 4 , 17487 Greifswald , Germany
| | - Martin Kulke
- Institut für Biochemie , Universität Greifswald , Felix-Hausdorff-Straße 4 , 17487 Greifswald , Germany
| | - Lukas Schulig
- Institut für Pharmazie , Universität Greifswald , Friedrich-Ludwig-Jahn-Straße 17 , 17487 Greifswald , Germany
| | - Andreas Link
- Institut für Pharmazie , Universität Greifswald , Friedrich-Ludwig-Jahn-Straße 17 , 17487 Greifswald , Germany
| | - Walter Langel
- Institut für Biochemie , Universität Greifswald , Felix-Hausdorff-Straße 4 , 17487 Greifswald , Germany
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8
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Abstract
The idea that water is a mixture of two distinct states is analyzed in some detail. It is shown that the known compressibility of water is in fact sufficiently small that for a volume of water of size 1 nm3, the density fluctuations are of order 4% of the average density. This is much smaller than the ≈25% density fluctuations that would be required for significant regions of high and low density water to occur on this volume scale. It is also pointed out that the density fluctuations in water are, if anything, smaller than those that occur in other common liquids which do not have the anomalous properties of water. It is shown that if the distribution of density fluctuations is unimodal, the system is in the one-phase region, and if bimodal, it is in the two-phase region. None of the liquid or amorphous phases of water explored in this work give any sign of being in the two-phase region. Existing neutron and X-ray scattering data on water in the amorphous phases, and in the stable liquid phases as a function pressure and temperature, are subject to a new set of empirical potential structure refinement simulations. These simulations are interrogated for their configurational entropy, using a spherical harmonic reconstruction of the full orientational pair correlation function. It is shown that the excess pair entropy derived from this function, plus the known perfect gas contributions, give a reasonable account of the total entropy of water, within the likely errors. This estimated entropy follows the expected declining trend with decreasing temperature. Evidence that higher density water will have higher entropy than lower density water emerges, in accordance with what is expected from the negative thermal expansion coefficient of water at low temperatures. However, this entropy increase is not large and goes through a maximum before declining at yet higher densities and pressures, in a manner reminiscent of what has been previously observed in the diffusion coefficient as a function of pressure. There is no evidence that ambient water can be regarded as patches of high density, high entropy and low density, low entropy liquid, as some have claimed, since high density water has a similar entropy to low density water. There is some evidence that the distinction between these two states will become more pronounced as the temperature is lowered. Extensive discussion of the use of order parameters to describe water structure is given, and it is pointed out that these indices generally cannot be used to infer two-state behavior.
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Affiliation(s)
- A K Soper
- ISIS Facility, UKRI-STFC Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire OX11 0QX, United Kingdom
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10
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Douberly GE, Miller RE, Xantheas SS. Formation of Exotic Networks of Water Clusters in Helium Droplets Facilitated by the Presence of Neon Atoms. J Am Chem Soc 2017; 139:4152-4156. [DOI: 10.1021/jacs.7b00510] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gary E. Douberly
- Department
of Chemistry, University of Georgia, Athens, Georgia 30602-2556, United States
| | - Roger E. Miller
- Department
of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Sotiris S. Xantheas
- Physical
Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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11
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Gu Q, Su P, Xia Y, Yang Z, Trindle CO, Knee JL. Quantitative probing of subtle interactions among H-bonds in alpha hydroxy carboxylic acid complexes. Phys Chem Chem Phys 2017; 19:24399-24411. [DOI: 10.1039/c7cp03917d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The alpha OH stretching frequency may be affected upon complexing with water and formic acid.
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Affiliation(s)
- Quanli Gu
- School of Basic Medical Sciences
- Xinxiang Medical University
- Xinxiang
- China
- Chemistry Department
| | - Peifeng Su
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
- China
| | - Yong Xia
- State Key Laboratory of Precision Spectroscopy
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
- China
| | - Zhijun Yang
- School of Basic Medical Sciences
- Xinxiang Medical University
- Xinxiang
- China
| | - Carl O. Trindle
- Chemistry Department
- University of Virginia
- Charlottesville
- USA
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