151
|
Wilkins DM, Manolopoulos DE, Pipolo S, Laage D, Hynes JT. Nuclear Quantum Effects in Water Reorientation and Hydrogen-Bond Dynamics. J Phys Chem Lett 2017; 8:2602-2607. [PMID: 28530836 DOI: 10.1021/acs.jpclett.7b00979] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We combine classical and ring polymer molecular dynamics simulations with the molecular jump model to provide a molecular description of the nuclear quantum effects (NQEs) on water reorientation and hydrogen-bond dynamics in liquid H2O and D2O. We show that while the net NQE is negligible in D2O, it leads to a ∼13% acceleration in H2O dynamics compared to a classical description. Large angular jumps-exchanging hydrogen-bond partners-are the dominant reorientation pathway (just as in a classical description); the faster reorientation dynamics arise from the increased jump rate constant. NQEs do not change the jump amplitude distribution, and no significant tunneling is found. The faster jump dynamics are quantitatively related to decreased structuring of the OO radial distribution function when NQEs are included. This is explained, via a jump model analysis, by competition between the effects of water's librational and OH stretch mode zero-point energies on the hydrogen-bond strength.
Collapse
Affiliation(s)
- David M Wilkins
- Laboratory of Computational Science and Modeling, IMX, École Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | - David E Manolopoulos
- Physical and Theoretical Chemistry Laboratory, University of Oxford , South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Silvio Pipolo
- PASTEUR, Département de Chimie, École Normale Supérieure, UPMC Univ Paris 06, CNRS, PSL Research University , 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR , 75005 Paris, France
| | - Damien Laage
- PASTEUR, Département de Chimie, École Normale Supérieure, UPMC Univ Paris 06, CNRS, PSL Research University , 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR , 75005 Paris, France
| | - James T Hynes
- PASTEUR, Département de Chimie, École Normale Supérieure, UPMC Univ Paris 06, CNRS, PSL Research University , 75005 Paris, France
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States
| |
Collapse
|
152
|
Alford RF, Leaver-Fay A, Jeliazkov JR, O’Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL, Das R, Baker D, Kuhlman B, Kortemme T, Gray JJ. The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design. J Chem Theory Comput 2017; 13:3031-3048. [PMID: 28430426 PMCID: PMC5717763 DOI: 10.1021/acs.jctc.7b00125] [Citation(s) in RCA: 776] [Impact Index Per Article: 110.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Over the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation of low-resolution structural data to design of nanomaterials, protein therapeutics, and vaccines. Central to Rosetta's success is the energy function: a model parametrized from small-molecule and X-ray crystal structure data used to approximate the energy associated with each biomolecule conformation. This paper describes the mathematical models and physical concepts that underlie the latest Rosetta energy function, called the Rosetta Energy Function 2015 (REF15). Applying these concepts, we explain how to use Rosetta energies to identify and analyze the features of biomolecular models. Finally, we discuss the latest advances in the energy function that extend its capabilities from soluble proteins to also include membrane proteins, peptides containing noncanonical amino acids, small molecules, carbohydrates, nucleic acids, and other macromolecules.
Collapse
Affiliation(s)
- Rebecca F. Alford
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Andrew Leaver-Fay
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
| | - Jeliazko R. Jeliazkov
- Program in Molecular Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Matthew J. O’Meara
- Department of Pharmaceutical Chemistry, University of California at San Francisco, 1700 Fourth Street, San Francisco, California 94158, United States
| | - Frank P. DiMaio
- Department of Biochemistry, University of Washington, J-Wing Health Sciences Building, Box 357350, Seattle, Washington 98195, United States
| | - Hahnbeom Park
- Department of Biochemistry, University of Washington, Molecular Engineering and Sciences, Box 357350, 4000 15 Ave NE, Seattle, Washington 98195, United States
| | - Maxim V. Shapovalov
- Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111, United States
| | - P. Douglas Renfrew
- Department of Biology, Center for Genomics and Systems Biology, New York University, 100 Washington Square East, New York, New York 10003
- Center for Computational Biology, Flatiron Institute, Simons Foundation, 162 5 Avenue, New York, New York 10010, United States
| | - Vikram K. Mulligan
- Department of Biochemistry, University of Washington, Molecular Engineering and Sciences, Box 357350, 4000 15 Ave NE, Seattle, Washington 98195, United States
| | - Kalli Kappel
- Biophysics Program, Stanford University, 450 Serra Mall, Stanford, California 94305, United States
| | - Jason W. Labonte
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Michael S. Pacella
- Department of Biomedical Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Richard Bonneau
- Department of Biology, Center for Genomics and Systems Biology, New York University, 100 Washington Square East, New York, New York 10003
- Center for Computational Biology, Flatiron Institute, Simons Foundation, 162 5 Avenue, New York, New York 10010, United States
| | - Philip Bradley
- Computational Biology Program, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, United States
| | - Roland L. Dunbrack
- Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111, United States
| | - Rhiju Das
- Biophysics Program, Stanford University, 450 Serra Mall, Stanford, California 94305, United States
| | - David Baker
- Department of Biochemistry, University of Washington, Molecular Engineering and Sciences, Box 357350, 4000 15 Ave NE, Seattle, Washington 98195, United States
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, California 94158, United States
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
| |
Collapse
|
153
|
Unravelling the influence of quantum proton delocalization on electronic charge transfer through the hydrogen bond. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.04.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
154
|
Hidden role of intermolecular proton transfer in the anomalously diffuse vibrational spectrum of a trapped hydronium ion. Proc Natl Acad Sci U S A 2017; 114:E4706-E4713. [PMID: 28566495 DOI: 10.1073/pnas.1705089114] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We report the vibrational spectra of the hydronium and methyl-ammonium ions captured in the C3v binding pocket of the 18-crown-6 ether ionophore. Although the NH stretching bands of the CH3NH3+ ion are consistent with harmonic expectations, the OH stretching bands of H3O+ are surprisingly broad, appearing as a diffuse background absorption with little intensity modulation over 800 cm-1 with an onset ∼400 cm-1 below the harmonic prediction. This structure persists even when only a single OH group is present in the HD2O+ isotopologue, while the OD stretching region displays a regular progression involving a soft mode at about 85 cm-1 These results are rationalized in a vibrationally adiabatic (VA) model in which the motion of the H3O+ ion in the crown pocket is strongly coupled with its OH stretches. In this picture, H3O+ resides in the center of the crown in the vibrational zero-point level, while the minima in the VA potentials associated with the excited OH vibrational states are shifted away from the symmetrical configuration displayed by the ground state. Infrared excitation between these strongly H/D isotope-dependent VA potentials then accounts for most of the broadening in the OH stretching manifold. Specifically, low-frequency motions involving concerted motions of the crown scaffold and the H3O+ ion are driven by a Franck-Condon-like mechanism. In essence, vibrational spectroscopy of these systems can be viewed from the perspective of photochemical interconversion between transient, isomeric forms of the complexes corresponding to the initial stage of intermolecular proton transfer.
Collapse
|
155
|
Marsalek O, Markland TE. Quantum Dynamics and Spectroscopy of Ab Initio Liquid Water: The Interplay of Nuclear and Electronic Quantum Effects. J Phys Chem Lett 2017; 8:1545-1551. [PMID: 28296422 DOI: 10.1021/acs.jpclett.7b00391] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Understanding the reactivity and spectroscopy of aqueous solutions at the atomistic level is crucial for the elucidation and design of chemical processes. However, the simulation of these systems requires addressing the formidable challenges of treating the quantum nature of both the electrons and nuclei. Exploiting our recently developed methods that provide acceleration by up to 2 orders of magnitude, we combine path integral simulations with on-the-fly evaluation of the electronic structure at the hybrid density functional theory level to capture the interplay between nuclear quantum effects and the electronic surface. Here we show that this combination provides accurate structure and dynamics, including the full infrared and Raman spectra of liquid water. This allows us to demonstrate and explain the failings of lower-level density functionals for dynamics and vibrational spectroscopy when the nuclei are treated quantum mechanically. These insights thus provide a foundation for the reliable investigation of spectroscopy and reactivity in aqueous environments.
Collapse
Affiliation(s)
- Ondrej Marsalek
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Thomas E Markland
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| |
Collapse
|
156
|
Yurenko YP, Novotný J, Marek R. Weak Supramolecular Interactions Governing Parallel and Antiparallel DNA Quadruplexes: Insights from Large-Scale Quantum Mechanics Analysis of Experimentally Derived Models. Chemistry 2017; 23:5573-5584. [PMID: 28225208 DOI: 10.1002/chem.201700236] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Indexed: 12/30/2022]
Abstract
The topology and energetics of guanine (G) quadruplexes is governed by supramolecular interactions within their strands. In this work, an extensive quantum mechanical (QM) study has been performed to analyze supramolecular interactions that shape the stems of (4+0) parallel (P) and (2+2) antiparallel (AP) quadruplex systems. The large-scale (≈400 atoms) models of P and AP were constructed from high-quality experimental structures. The results provide evidence that each of the P and AP structures is shaped by a distinct network of supramolecular interactions. Analysis of electron topological characteristics of hydrogen bonds in P and AP systems indicates that the P model benefits from stronger intratetrad hydrogen bonding. For intertetrad stacking interactions, both noncovalent interaction plot and energy decomposition analysis approaches suggest that the stem of the P quadruplex benefits more from stacking than that of the AP stem; the difference in energetic stabilization for the two topologies is about 10 %. Stronger hydrogen-bonding and stacking interactions in the stem of the P quadruplex, relative to those in the AP system, can be an important indicator to explain the experimental observations that guanine-rich oligonucleotides tend to form all-parallel stems with an all-anti orientation of nucleobases. However, in addition to intrinsic stabilization, partial desolvation effects, which affect the energetics and dynamics of the G-quadruplex folding process, call for further investigations.
Collapse
Affiliation(s)
- Yevgen P Yurenko
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5/A4, 625 00, Brno, Czech Republic
| | - Jan Novotný
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5/A4, 625 00, Brno, Czech Republic
| | - Radek Marek
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5/A4, 625 00, Brno, Czech Republic
| |
Collapse
|
157
|
Sappati S, Hassanali A, Gebauer R, Ghosh P. Nuclear quantum effects in a HIV/cancer inhibitor: The case of ellipticine. J Chem Phys 2017; 145:205102. [PMID: 27908111 DOI: 10.1063/1.4968046] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Ellipticine is a natural product that is currently being actively investigated for its inhibitory cancer and HIV properties. Here we use path-integral molecular dynamics coupled with excited state calculations to characterize the role of nuclear quantum effects on the structural and electronic properties of ellipticine in water, a common biological solvent. Quantum effects collectively enhance the fluctuations of both light and heavy nuclei of the covalent and hydrogen bonds in ellipticine. In particular, for the ellipticine-water system, where the proton donor and acceptor have different proton affinities, we find that nuclear quantum effects (NQEs) strengthen both the strong and the weak H bonds. This is in contrast to what is observed for the cases where the proton affinity of the donors and acceptors is same. These structural fluctuations cause a significant red-shift in the absorption spectra and an increase in the broadening, bringing it into closer agreement with the experiments. Our work shows that nuclear quantum effects alter both qualitatively and quantitatively the optical properties of this biologically relevant system and highlights the importance of the inclusion of these effects in the microscopic understanding of their optical properties. We propose that isotopic substitution will produce a blue shift and a reduction in the broadening of the absorption peak.
Collapse
Affiliation(s)
- Subrahmanyam Sappati
- Department of Chemistry, Indian Institute of Science Education and Research, Pune 411008, India
| | - Ali Hassanali
- Condensed Matter and Statistical Physics Section, The Abdus Salam International Centre for Theoretical Physics, I-34151 Trieste, Italy
| | - Ralph Gebauer
- Condensed Matter and Statistical Physics Section, The Abdus Salam International Centre for Theoretical Physics, I-34151 Trieste, Italy
| | - Prasenjit Ghosh
- Department of Chemistry, Indian Institute of Science Education and Research, Pune 411008, India
| |
Collapse
|
158
|
Guo J, Bian K, Lin Z, Jiang Y. Perspective: Structure and dynamics of water at surfaces probed by scanning tunneling microscopy and spectroscopy. J Chem Phys 2017; 145:160901. [PMID: 27802647 DOI: 10.1063/1.4964668] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The detailed and precise understanding of water-solid interaction largely relies on the development of atomic-scale experimental techniques, among which scanning tunneling microscopy (STM) has proven to be a noteworthy example. In this perspective, we review the recent advances of STM techniques in imaging, spectroscopy, and manipulation of water molecules. We discuss how those newly developed techniques are applied to probe the structure and dynamics of water at solid surfaces with single-molecule and even submolecular resolution, paying particular attention to the ability of accessing the degree of freedom of hydrogen. In the end, we present an outlook on the directions of future STM studies of water-solid interfaces as well as the challenges faced by this field. Some new scanning probe techniques beyond STM are also envisaged.
Collapse
Affiliation(s)
- Jing Guo
- International Center for Quantum Materials, School of Physics, Peking University, Beijing 100871, People's Republic of China
| | - Ke Bian
- International Center for Quantum Materials, School of Physics, Peking University, Beijing 100871, People's Republic of China
| | - Zeren Lin
- International Center for Quantum Materials, School of Physics, Peking University, Beijing 100871, People's Republic of China
| | - Ying Jiang
- International Center for Quantum Materials, School of Physics, Peking University, Beijing 100871, People's Republic of China
| |
Collapse
|
159
|
Drechsel-Grau C, Marx D. Collective proton transfer in ordinary ice: local environments, temperature dependence and deuteration effects. Phys Chem Chem Phys 2017; 19:2623-2635. [DOI: 10.1039/c6cp05679b] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Ordinary ice at low temperature: what about collective nuclear quantum effects in its chiral six rings?
Collapse
Affiliation(s)
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
| |
Collapse
|
160
|
Pylaeva SA, Elgabarty H, Sebastiani D, Tolstoy PM. Symmetry and dynamics of FHF− anion in vacuum, in CD2Cl2 and in CCl4. Ab initio MD study of fluctuating solvent–solute hydrogen and halogen bonds. Phys Chem Chem Phys 2017; 19:26107-26120. [DOI: 10.1039/c7cp04493c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Asymmetric solvation of FHF− by halogen- and hydrogen-bonding solvents breaks the symmetry of the anion.
Collapse
Affiliation(s)
- S. A. Pylaeva
- Institute of Chemistry, Martin-Luther Universität Halle-Wittenberg
- Germany
| | - H. Elgabarty
- Institute of Chemistry, Martin-Luther Universität Halle-Wittenberg
- Germany
| | - D. Sebastiani
- Institute of Chemistry, Martin-Luther Universität Halle-Wittenberg
- Germany
| | - P. M. Tolstoy
- Center for Magnetic Resonance, St. Petersburg State University
- Russia
| |
Collapse
|
161
|
Tao Y, Zou W, Jia J, Li W, Cremer D. Different Ways of Hydrogen Bonding in Water - Why Does Warm Water Freeze Faster than Cold Water? J Chem Theory Comput 2016; 13:55-76. [PMID: 27996255 DOI: 10.1021/acs.jctc.6b00735] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The properties of liquid water are intimately related to the H-bond network among the individual water molecules. Utilizing vibrational spectroscopy and modeling water with DFT-optimized water clusters (6-mers and 50-mers), 16 out of a possible 36 different types of H-bonds are identified and ordered according to their intrinsic strength. The strongest H-bonds are obtained as a result of a concerted push-pull effect of four peripheral water molecules, which polarize the electron density in a way that supports charge transfer and partial covalent character of the targeted H-bond. For water molecules with tetra- and pentacoordinated O atoms, H-bonding is often associated with a geometrically unfavorable positioning of the acceptor lone pair and donor σ*(OH) orbitals so that electrostatic rather than covalent interactions increasingly dominate H-bonding. There is a striking linear dependence between the intrinsic strength of H-bonding as measured by the local H-bond stretching force constant and the delocalization energy associated with charge transfer. Molecular dynamics simulations for 1000-mers reveal that with increasing temperature weak, preferentially electrostatic H-bonds are broken, whereas the number of strong H-bonds increases. An explanation for the question why warm water freezes faster than cold water is given on a molecular basis.
Collapse
Affiliation(s)
- Yunwen Tao
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University , 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Wenli Zou
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University , 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Junteng Jia
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, P. R. China
| | - Wei Li
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, P. R. China
| | - Dieter Cremer
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University , 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| |
Collapse
|
162
|
He L, Zou X, Wang T, Zheng Q, Liao J, Xu C, Liu Y, Lin D. Cation-Induced Variation of Micromorphology and Luminescence Properties of Tungstate Phosphors by a Hydrothermal Method. Inorg Chem 2016; 55:12944-12952. [DOI: 10.1021/acs.inorgchem.6b02352] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lihua He
- College of Chemistry
and Materials Science, Sichuan Normal University, Chengdu 610066, China
| | - Xiao Zou
- College of Chemistry
and Materials Science, Sichuan Normal University, Chengdu 610066, China
| | - Tao Wang
- College of Chemistry
and Materials Science, Sichuan Normal University, Chengdu 610066, China
| | - Qiaoji Zheng
- College of Chemistry
and Materials Science, Sichuan Normal University, Chengdu 610066, China
| | - Jie Liao
- College of Chemistry
and Materials Science, Sichuan Normal University, Chengdu 610066, China
| | - Chenggang Xu
- College of Chemistry
and Materials Science, Sichuan Normal University, Chengdu 610066, China
| | - Yongfu Liu
- Ningbo Institute of Materials Technology
and Engineering, Chinese Academy of Sciences, Ningbo 315201, China
| | - Dunmin Lin
- College of Chemistry
and Materials Science, Sichuan Normal University, Chengdu 610066, China
| |
Collapse
|
163
|
Kong X, Brinkmann A, Terskikh V, Wasylishen RE, Bernard GM, Duan Z, Wu Q, Wu G. Proton Probability Distribution in the O···H···O Low-Barrier Hydrogen Bond: A Combined Solid-State NMR and Quantum Chemical Computational Study of Dibenzoylmethane and Curcumin. J Phys Chem B 2016; 120:11692-11704. [PMID: 27782387 DOI: 10.1021/acs.jpcb.6b08091] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a combined solid-state (1H, 2H, 13C, 17O) NMR and plane-wave density functional theory (DFT) computational study of the O···H···O low-barrier hydrogen bonds (LBHBs) in two 1,3-diketone compounds: dibenzoylmethane (1) and curcumin (2). In the solid state, both 1 and 2 exist in the cis-keto-enol tautomeric form, each exhibiting an intramolecular LBHB with a short O···O distance (2.435 Å in 1 and 2.455 Å in 2). Whereas numerous experimental (structural and spectroscopic) and computational studies have been reported for the enol isomers of 1,3-diketones, a unified picture about the proton location within an LBHB is still lacking. This work reports for the first time the solid-state 17O NMR data for the O···H···O LBHBs in 1,3-diketones. The central conclusion of this work is that detailed information about the probability density distribution of the proton (nuclear zero-point motion) across an LBHB can be obtained from a combination of solid-state NMR and plane-wave DFT computations (both NMR parameter calculations and ab initio molecular dynamics simulations). We propose that the precise proton probability distribution across an LBHB should provide a common basis on which different and sometimes seemingly contradicting experimental results obtained from complementary techniques, such as X-ray diffraction, neutron diffraction, and solid-state NMR, can be reconciled.
Collapse
Affiliation(s)
- Xianqi Kong
- Department of Chemistry, Queen's University , 90 Bader Lane, Kingston, Ontario, Canada K7L 3N6
| | - Andreas Brinkmann
- Measurement Science and Standards, National Research Council Canada , 1200 Montreal Road, M-40, Ottawa, Ontario, Canada K1A 0R6
| | - Victor Terskikh
- Department of Chemistry, Queen's University , 90 Bader Lane, Kingston, Ontario, Canada K7L 3N6.,Department of Chemistry, University of Ottawa , 10 Marie Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | | | - Guy M Bernard
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
| | - Zhuang Duan
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
| | - Qichao Wu
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
| | - Gang Wu
- Department of Chemistry, Queen's University , 90 Bader Lane, Kingston, Ontario, Canada K7L 3N6
| |
Collapse
|
164
|
Requist R, Gross EKU. Exact Factorization-Based Density Functional Theory of Electrons and Nuclei. PHYSICAL REVIEW LETTERS 2016; 117:193001. [PMID: 27858424 DOI: 10.1103/physrevlett.117.193001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Indexed: 06/06/2023]
Abstract
The ground state energy of a system of electrons (r=r_{1},r_{2},…) and nuclei (R=R_{1},R_{2},…) is proven to be a variational functional of the electronic density n(r,R) and paramagnetic current density j_{p}(r,R) conditional on R, the nuclear wave function χ(R), an induced vector potential A_{μ}(R) and a quantum geometric tensor T_{μν}(R). n, j_{p}, A_{μ} and T_{μν} are defined in terms of the conditional electronic wave function Φ_{R}(r). The ground state (n,j_{p},χ,A_{μ},T_{μν}) can be calculated by solving self-consistently (i) conditional Kohn-Sham equations containing effective scalar and vector potentials v_{s}(r) and A_{xc}(r) that depend parametrically on R, (ii) the Schrödinger equation for χ(R), and (iii) Euler-Lagrange equations that determine T_{μν}. The theory is applied to the E⊗e Jahn-Teller model.
Collapse
Affiliation(s)
- Ryan Requist
- Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle, Germany
| | - E K U Gross
- Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle, Germany
| |
Collapse
|
165
|
Pham TA, Ogitsu T, Lau EY, Schwegler E. Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations. J Chem Phys 2016; 145:154501. [DOI: 10.1063/1.4964865] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Tuan Anh Pham
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94551, USA
| | - Tadashi Ogitsu
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94551, USA
| | - Edmond Y. Lau
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94551, USA
| | - Eric Schwegler
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94551, USA
| |
Collapse
|
166
|
Heres M, Wang Y, Griffin PJ, Gainaru C, Sokolov AP. Proton Conductivity in Phosphoric Acid: The Role of Quantum Effects. PHYSICAL REVIEW LETTERS 2016; 117:156001. [PMID: 27768354 DOI: 10.1103/physrevlett.117.156001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Indexed: 05/07/2023]
Abstract
Phosphoric acid has one of the highest intrinsic proton conductivities of any known liquids, and the mechanism of this exceptional conductivity remains a puzzle. Our detailed experimental studies discovered a strong isotope effect in the conductivity of phosphoric acids caused by (i) a strong isotope shift of the glass transition temperature and (ii) a significant reduction of the energy barrier by zero-point quantum fluctuations. These results suggest that the high conductivity in phosphoric acids is caused by a very efficient proton transfer mechanism, which is strongly assisted by quantum effects.
Collapse
Affiliation(s)
- M Heres
- Department of Chemical and Biomolecular Engineering, University of Tennessee Knoxville, Knoxville, Tennessee 37996, USA
| | - Y Wang
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - P J Griffin
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - C Gainaru
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, Tennessee 37996, USA
| | - A P Sokolov
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, Tennessee 37996, USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| |
Collapse
|
167
|
Schreck S, Wernet P. Isotope effects in liquid water probed by transmission mode x-ray absorption spectroscopy at the oxygen K-edge. J Chem Phys 2016; 145:104502. [PMID: 27634266 DOI: 10.1063/1.4962237] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Simon Schreck
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Philippe Wernet
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| |
Collapse
|
168
|
Rossi M, Gasparotto P, Ceriotti M. Anharmonic and Quantum Fluctuations in Molecular Crystals: A First-Principles Study of the Stability of Paracetamol. PHYSICAL REVIEW LETTERS 2016; 117:115702. [PMID: 27661700 DOI: 10.1103/physrevlett.117.115702] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Indexed: 06/06/2023]
Abstract
Molecular crystals often exist in multiple competing polymorphs, showing significantly different physicochemical properties. Computational crystal structure prediction is key to interpret and guide the search for the most stable or useful form, a real challenge due to the combinatorial search space, and the complex interplay of subtle effects that work together to determine the relative stability of different structures. Here we take a comprehensive approach based on different flavors of thermodynamic integration in order to estimate all contributions to the free energies of these systems with density-functional theory, including the oft-neglected anharmonic contributions and nuclear quantum effects. We take the two main stable forms of paracetamol as a paradigmatic example. We find that anharmonic contributions, different descriptions of van der Waals interactions, and nuclear quantum effects all matter to quantitatively determine the stability of different phases. Our analysis highlights the many challenges inherent in the development of a quantitative and predictive framework to model molecular crystals. However, it also indicates which of the components of the free energy can benefit from a cancellation of errors that can redeem the predictive power of approximate models, and suggests simple steps that could be taken to improve the reliability of ab initio crystal structure prediction.
Collapse
Affiliation(s)
- Mariana Rossi
- Laboratory of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Piero Gasparotto
- Laboratory of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Michele Ceriotti
- Laboratory of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| |
Collapse
|
169
|
Agmon N, Bakker HJ, Campen RK, Henchman RH, Pohl P, Roke S, Thämer M, Hassanali A. Protons and Hydroxide Ions in Aqueous Systems. Chem Rev 2016; 116:7642-72. [PMID: 27314430 DOI: 10.1021/acs.chemrev.5b00736] [Citation(s) in RCA: 287] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the structure and dynamics of water's constituent ions, proton and hydroxide, has been a subject of numerous experimental and theoretical studies over the last century. Besides their obvious importance in acid-base chemistry, these ions play an important role in numerous applications ranging from enzyme catalysis to environmental chemistry. Despite a long history of research, many fundamental issues regarding their properties continue to be an active area of research. Here, we provide a review of the experimental and theoretical advances made in the last several decades in understanding the structure, dynamics, and transport of the proton and hydroxide ions in different aqueous environments, ranging from water clusters to the bulk liquid and its interfaces with hydrophobic surfaces. The propensity of these ions to accumulate at hydrophobic surfaces has been a subject of intense debate, and we highlight the open issues and challenges in this area. Biological applications reviewed include proton transport along the hydration layer of various membranes and through channel proteins, problems that are at the core of cellular bioenergetics.
Collapse
Affiliation(s)
- Noam Agmon
- The Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Huib J Bakker
- FOM Institute AMOLF , Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - R Kramer Campen
- Fritz Haber Institute of the Max Planck Society , Faradayweg 4-6, 14195 Berlin, Germany
| | - Richard H Henchman
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom
| | - Peter Pohl
- Johannes Kepler University Linz , Institute of Biophysics, Gruberstrasse 40, 4020 Linz, Austria
| | - Sylvie Roke
- Laboratory for Fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), and Institute of Material Science (IMX), School of Engineering (STI), and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015, Lausanne, Switzerland
| | - Martin Thämer
- Fritz Haber Institute of the Max Planck Society , Faradayweg 4-6, 14195 Berlin, Germany.,Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago , Chicago, Illinois 60637, United States
| | - Ali Hassanali
- CMSP Section, The Abdus Salaam International Center for Theoretical Physics , I-34151 Trieste, Italy
| |
Collapse
|
170
|
Cheng B, Behler J, Ceriotti M. Nuclear Quantum Effects in Water at the Triple Point: Using Theory as a Link Between Experiments. J Phys Chem Lett 2016; 7:2210-2215. [PMID: 27203358 DOI: 10.1021/acs.jpclett.6b00729] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
One of the most prominent consequences of the quantum nature of light atomic nuclei is that their kinetic energy does not follow a Maxwell-Boltzmann distribution. Deep inelastic neutron scattering (DINS) experiments can measure this effect. Thus, the nuclear quantum kinetic energy can be probed directly in both ordered and disordered samples. However, the relation between the quantum kinetic energy and the atomic environment is a very indirect one, and cross-validation with theoretical modeling is therefore urgently needed. Here, we use state of the art path integral molecular dynamics techniques to compute the kinetic energy of hydrogen and oxygen nuclei in liquid, solid, and gas-phase water close to the triple point, comparing three different interatomic potentials and validating our results against equilibrium isotope fractionation measurements. We will then show how accurate simulations can draw a link between extremely precise fractionation experiments and DINS, therefore establishing a reliable benchmark for future measurements and providing key insights to increase further the accuracy of interatomic potentials for water.
Collapse
Affiliation(s)
- Bingqing Cheng
- Laboratory of Computational Science and Modelling, Institute of Materials, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | - Jörg Behler
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum , 44801 Bochum, Germany
| | - Michele Ceriotti
- Laboratory of Computational Science and Modelling, Institute of Materials, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| |
Collapse
|
171
|
Fang W, Chen J, Rossi M, Feng Y, Li XZ, Michaelides A. Inverse Temperature Dependence of Nuclear Quantum Effects in DNA Base Pairs. J Phys Chem Lett 2016; 7:2125-31. [PMID: 27195654 PMCID: PMC4933496 DOI: 10.1021/acs.jpclett.6b00777] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Despite the inherently quantum mechanical nature of hydrogen bonding, it is unclear how nuclear quantum effects (NQEs) alter the strengths of hydrogen bonds. With this in mind, we use ab initio path integral molecular dynamics to determine the absolute contribution of NQEs to the binding in DNA base pair complexes, arguably the most important hydrogen-bonded systems of all. We find that depending on the temperature, NQEs can either strengthen or weaken the binding within the hydrogen-bonded complexes. As a somewhat counterintuitive consequence, NQEs can have a smaller impact on hydrogen bond strengths at cryogenic temperatures than at room temperature. We rationalize this in terms of a competition of NQEs between low-frequency and high-frequency vibrational modes. Extending this idea, we also propose a simple model to predict the temperature dependence of NQEs on hydrogen bond strengths in general.
Collapse
Affiliation(s)
- Wei Fang
- Thomas Young Centre, London Centre for Nanotechnology, Department of Chemistry, and Department of
Physics and Astronomy, University College
London, London WC1E 6BT, United Kingdom
| | - Ji Chen
- Thomas Young Centre, London Centre for Nanotechnology, Department of Chemistry, and Department of
Physics and Astronomy, University College
London, London WC1E 6BT, United Kingdom
| | - Mariana Rossi
- Physical
and Theoretical Chemistry Lab, University
of Oxford, South Parks
Road, OX1 3QZ Oxford, United Kingdom
| | - Yexin Feng
- School
of Physics and Electronics, Hunan University, Changsha 410082, People’s Republic of China
| | - Xin-Zheng Li
- International
Center for Quantum Materials, School of Physics and Collaborative
Innovation Center of Quantum Matter, Peking
University, Beijing 100871, People’s Republic of China
- E-mail: (X.-Z.L.)
| | - Angelos Michaelides
- Thomas Young Centre, London Centre for Nanotechnology, Department of Chemistry, and Department of
Physics and Astronomy, University College
London, London WC1E 6BT, United Kingdom
- E-mail: (A.M.)
| |
Collapse
|
172
|
Guo J, Lü JT, Feng Y, Chen J, Peng J, Lin Z, Meng X, Wang Z, Li XZ, Wang EG, Jiang Y. Nuclear quantum effects of hydrogen bonds probed by tip-enhanced inelastic electron tunneling. Science 2016; 352:321-5. [PMID: 27081066 DOI: 10.1126/science.aaf2042] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 03/14/2016] [Indexed: 01/28/2023]
Abstract
We report the quantitative assessment of nuclear quantum effects on the strength of a single hydrogen bond formed at a water-salt interface, using tip-enhanced inelastic electron tunneling spectroscopy based on a scanning tunneling microscope. The inelastic scattering cross section was resonantly enhanced by "gating" the frontier orbitals of water via a chlorine-terminated tip, so the hydrogen-bonding strength can be determined with high accuracy from the red shift in the oxygen-hydrogen stretching frequency of water. Isotopic substitution experiments combined with quantum simulations reveal that the anharmonic quantum fluctuations of hydrogen nuclei weaken the weak hydrogen bonds and strengthen the relatively strong ones. However, this trend can be completely reversed when a hydrogen bond is strongly coupled to the polar atomic sites of the surface.
Collapse
Affiliation(s)
- Jing Guo
- International Center for Quantum Materials, School of Physics, Peking University, Beijing 100871, P. R. China
| | - Jing-Tao Lü
- School of Physics and Wuhan National High Magnetic Field Center, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| | - Yexin Feng
- International Center for Quantum Materials, School of Physics, Peking University, Beijing 100871, P. R. China. School of Physics and Electronics, Hunan University, Changsha 410082, P. R. China
| | - Ji Chen
- International Center for Quantum Materials, School of Physics, Peking University, Beijing 100871, P. R. China
| | - Jinbo Peng
- International Center for Quantum Materials, School of Physics, Peking University, Beijing 100871, P. R. China
| | - Zeren Lin
- International Center for Quantum Materials, School of Physics, Peking University, Beijing 100871, P. R. China
| | - Xiangzhi Meng
- International Center for Quantum Materials, School of Physics, Peking University, Beijing 100871, P. R. China
| | - Zhichang Wang
- International Center for Quantum Materials, School of Physics, Peking University, Beijing 100871, P. R. China
| | - Xin-Zheng Li
- School of Physics, Peking University, Beijing 100871, P. R. China. Collaborative Innovation Center of Quantum Matter, Beijing 100871, P. R. China.
| | - En-Ge Wang
- International Center for Quantum Materials, School of Physics, Peking University, Beijing 100871, P. R. China. Collaborative Innovation Center of Quantum Matter, Beijing 100871, P. R. China.
| | - Ying Jiang
- International Center for Quantum Materials, School of Physics, Peking University, Beijing 100871, P. R. China. Collaborative Innovation Center of Quantum Matter, Beijing 100871, P. R. China.
| |
Collapse
|
173
|
Ceriotti M, Fang W, Kusalik PG, McKenzie RH, Michaelides A, Morales MA, Markland TE. Nuclear Quantum Effects in Water and Aqueous Systems: Experiment, Theory, and Current Challenges. Chem Rev 2016; 116:7529-50. [DOI: 10.1021/acs.chemrev.5b00674] [Citation(s) in RCA: 339] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Michele Ceriotti
- Laboratory
of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Wei Fang
- Thomas
Young Centre, London Centre for Nanotechnology and Department of Physics
and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Peter G. Kusalik
- Department
of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Ross H. McKenzie
- School
of Mathematics and Physics, University of Queensland, Brisbane, 4072 Queensland Australia
| | - Angelos Michaelides
- Thomas
Young Centre, London Centre for Nanotechnology and Department of Physics
and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Miguel A. Morales
- Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Thomas E. Markland
- Department
of Chemistry, Stanford University, 333 Campus Drive, Stanford, California 94305, United States
| |
Collapse
|
174
|
Chen Y, Okur HI, Gomopoulos N, Macias-Romero C, Cremer PS, Petersen PB, Tocci G, Wilkins DM, Liang C, Ceriotti M, Roke S. Electrolytes induce long-range orientational order and free energy changes in the H-bond network of bulk water. SCIENCE ADVANCES 2016; 2:e1501891. [PMID: 27152357 PMCID: PMC4846452 DOI: 10.1126/sciadv.1501891] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 03/06/2016] [Indexed: 05/05/2023]
Abstract
Electrolytes interact with water in many ways: changing dipole orientation, inducing charge transfer, and distorting the hydrogen-bond network in the bulk and at interfaces. Numerous experiments and computations have detected short-range perturbations that extend up to three hydration shells around individual ions. We report a multiscale investigation of the bulk and surface of aqueous electrolyte solutions that extends from the atomic scale (using atomistic modeling) to nanoscopic length scales (using bulk and interfacial femtosecond second harmonic measurements) to the macroscopic scale (using surface tension experiments). Electrolytes induce orientational order at concentrations starting at 10 μM that causes nonspecific changes in the surface tension of dilute electrolyte solutions. Aside from ion-dipole interactions, collective hydrogen-bond interactions are crucial and explain the observed difference of a factor of 6 between light water and heavy water.
Collapse
Affiliation(s)
- Yixing Chen
- Laboratory for fundamental BioPhotonics, Institutes of Bioengineering and Materials Science and Engineering, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Halil I. Okur
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Nikolaos Gomopoulos
- Laboratory for fundamental BioPhotonics, Institutes of Bioengineering and Materials Science and Engineering, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Carlos Macias-Romero
- Laboratory for fundamental BioPhotonics, Institutes of Bioengineering and Materials Science and Engineering, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Paul S. Cremer
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Poul B. Petersen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Gabriele Tocci
- Laboratory for fundamental BioPhotonics, Institutes of Bioengineering and Materials Science and Engineering, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Laboratory of Computational Science and Modeling, Institute of Materials Science and Engineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - David M. Wilkins
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Chungwen Liang
- Laboratory of Computational Science and Modeling, Institute of Materials Science and Engineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Michele Ceriotti
- Laboratory of Computational Science and Modeling, Institute of Materials Science and Engineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Sylvie Roke
- Laboratory for fundamental BioPhotonics, Institutes of Bioengineering and Materials Science and Engineering, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Corresponding author. E-mail:
| |
Collapse
|
175
|
Amini S, Masic A, Bertinetti L, Teguh JS, Herrin JS, Zhu X, Su H, Miserez A. Textured fluorapatite bonded to calcium sulphate strengthen stomatopod raptorial appendages. Nat Commun 2016; 5:3187. [PMID: 24476684 DOI: 10.1038/ncomms4187] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 01/02/2014] [Indexed: 11/09/2022] Open
Abstract
Stomatopods are shallow-water crustaceans that employ powerful dactyl appendages to hunt their prey. Deployed at high velocities, these hammer-like clubs or spear-like devices are able to inflict substantial impact forces. Here we demonstrate that dactyl impact surfaces consist of a finely-tuned mineral gradient, with fluorapatite substituting amorphous apatite towards the outer surface. Raman spectroscopy measurements show that calcium sulphate, previously not reported in mechanically active biotools, is co-localized with fluorapatite. Ab initio computations suggest that fluorapatite/calcium sulphate interfaces provide binding stability and promote the disordered-to-ordered transition of fluorapatite. Nanomechanical measurements show that fluorapatite crystalline orientation correlates with an anisotropic stiffness response and indicate significant differences in the fracture tolerance between the two types of appendages. Our findings shed new light on the crystallochemical and microstructural strategies allowing these intriguing biotools to optimize impact forces, providing physicochemical information that could be translated towards the synthesis of impact-resistant functional materials and coatings.
Collapse
Affiliation(s)
- Shahrouz Amini
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Admir Masic
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, Research Campus Potsdam-Golm, 14424 Potsdam, Germany
| | - Luca Bertinetti
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, Research Campus Potsdam-Golm, 14424 Potsdam, Germany
| | - Jefri Sanusi Teguh
- School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Jason S Herrin
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Xi Zhu
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Haibin Su
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Ali Miserez
- 1] School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore [2] School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| |
Collapse
|
176
|
Wilkins DM, Manolopoulos DE, Dang LX. Nuclear quantum effects in water exchange around lithium and fluoride ions. J Chem Phys 2016; 142:064509. [PMID: 25681925 DOI: 10.1063/1.4907554] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We employ classical and ring polymer molecular dynamics simulations to study the effect of nuclear quantum fluctuations on the structure and the water exchange dynamics of aqueous solutions of lithium and fluoride ions. While we obtain reasonably good agreement with experimental data for solutions of lithium by augmenting the Coulombic interactions between the ion and the water molecules with a standard Lennard-Jones ion-oxygen potential, the same is not true for solutions of fluoride, for which we find that a potential with a softer repulsive wall gives much better agreement. A small degree of destabilization of the first hydration shell is found in quantum simulations of both ions when compared with classical simulations, with the shell becoming less sharply defined and the mean residence time of the water molecules in the shell decreasing. In line with these modest differences, we find that the mechanisms of the exchange processes are unaffected by quantization, so a classical description of these reactions gives qualitatively correct and quantitatively reasonable results. We also find that the quantum effects in solutions of lithium are larger than in solutions of fluoride. This is partly due to the stronger interaction of lithium with water molecules, partly due to the lighter mass of lithium and partly due to competing quantum effects in the hydration of fluoride, which are absent in the hydration of lithium.
Collapse
Affiliation(s)
- David M Wilkins
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - David E Manolopoulos
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Liem X Dang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 93352, USA
| |
Collapse
|
177
|
Lehmkühler F, Forov Y, Büning T, Sahle CJ, Steinke I, Julius K, Buslaps T, Tolan M, Hakala M, Sternemann C. Intramolecular structure and energetics in supercooled water down to 255 K. Phys Chem Chem Phys 2016; 18:6925-30. [PMID: 26881494 DOI: 10.1039/c5cp07721d] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We studied the structure and energetics of supercooled water by means of X-ray Raman and Compton scattering. Under supercooled conditions down to 255 K, the oxygen K-edge measured by X-ray Raman scattering suggests an increase of tetrahedral order similar to the conventional temperature effect observed in non-supercooled water. Compton profile differences indicate contributions beyond the theoretically predicted temperature effect and provide a deeper insight into local structural changes. These contributions suggest a decrease of the electron mean kinetic energy by 3.3 ± 0.7 kJ (mol K)(-1) that cannot be modeled within established water models. Our surprising results emphasize the need for water models that capture in detail the intramolecular structural changes and quantum effects to explain this complex liquid.
Collapse
Affiliation(s)
- Felix Lehmkühler
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
178
|
|
179
|
Angeloski A, Hook JM, Bhadbhade M, Baker AT, McDonagh AM. Intramolecular H⋯S interactions in metal di-(isopropyl)dithiocarbamate complexes. CrystEngComm 2016. [DOI: 10.1039/c6ce01475e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Intramolecular C–H⋯S interactions create restricted rotation of groups within di(isopropyl)dithiocarbate complexes.
Collapse
Affiliation(s)
- Alexander Angeloski
- School of Mathematical and Physical Sciences
- University of Technology Sydney
- Ultimo, Australia
| | - James M. Hook
- NMR Facility
- Mark Wainwright Analytical Centre
- The University of New South Wales
- Sydney, Australia
| | - Mohan Bhadbhade
- School of Chemistry
- The University of New South Wales
- Sydney, Australia
| | - Anthony T. Baker
- College of Science, Health and Engineering
- La Trobe University
- Melbourne, Australia
| | - Andrew M. McDonagh
- School of Mathematical and Physical Sciences
- University of Technology Sydney
- Ultimo, Australia
| |
Collapse
|
180
|
Baldauf C, Rossi M. Going clean: structure and dynamics of peptides in the gas phase and paths to solvation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:493002. [PMID: 26598600 DOI: 10.1088/0953-8984/27/49/493002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The gas phase is an artificial environment for biomolecules that has gained much attention both experimentally and theoretically due to its unique characteristic of providing a clean room environment for the comparison between theory and experiment. In this review we give an overview mainly on first-principles simulations of isolated peptides and the initial steps of their interactions with ions and solvent molecules: a bottom up approach to the complexity of biological environments. We focus on the accuracy of different methods to explore the conformational space, the connections between theory and experiment regarding collision cross section evaluations and (anharmonic) vibrational spectra, and the challenges faced in this field.
Collapse
Affiliation(s)
- Carsten Baldauf
- Fritz Haber Institute, Faradayweg 4-6, 14195 Berlin, Germany
| | | |
Collapse
|
181
|
Rossi M, Fang W, Michaelides A. Stability of Complex Biomolecular Structures: van der Waals, Hydrogen Bond Cooperativity, and Nuclear Quantum Effects. J Phys Chem Lett 2015; 6:4233-8. [PMID: 26722963 DOI: 10.1021/acs.jpclett.5b01899] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Biomolecules are complex systems stabilized by a delicate balance of weak interactions, making it important to assess all energetic contributions in an accurate manner. However, it is a priori unclear which contributions make more of an impact. Here, we examine stacked polyglutamine (polyQ) strands, a peptide repeat often found in amyloid aggregates. We investigate the role of hydrogen bond (HB) cooperativity, van der Waals (vdW) dispersion interactions, and quantum contributions to free energies, including anharmonicities through density functional theory and ab initio path integral simulations. Of these various factors, we find that the largest impact on structural stabilization comes from vdW interactions. HB cooperativity is the second largest contribution as the size of the stacked chain grows. Competing nuclear quantum effects make the net quantum contribution small but very sensitive to anharmonicities, vdW, and the number of HBs. Our results suggest that a reliable treatment of these systems can only be attained by considering all of these components.
Collapse
Affiliation(s)
- Mariana Rossi
- Physical and Theoretical Chemistry Lab, University of Oxford , South Parks Road, OX1 3QZ Oxford, United Kingdom
- St. Edmund Hall , Queen's Lane, OX1 4AR Oxford, United Kingdom
| | - Wei Fang
- Thomas Young Centre, London Centre for Nanotechnology, and Department of Chemistry, University College London , 17-19 Gordon Street, WC1H 0AH London, United Kingdom
| | - Angelos Michaelides
- Thomas Young Centre, London Centre for Nanotechnology, and Department of Chemistry, University College London , 17-19 Gordon Street, WC1H 0AH London, United Kingdom
| |
Collapse
|
182
|
Poltavsky I, Tkatchenko A. Modeling quantum nuclei with perturbed path integral molecular dynamics. Chem Sci 2015; 7:1368-1372. [PMID: 29910893 PMCID: PMC5975916 DOI: 10.1039/c5sc03443d] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 10/28/2015] [Indexed: 11/25/2022] Open
Abstract
Here we combine perturbation theory with the Feynman–Kac imaginary-time path integral approach to quantum mechanics for modeling quantum nuclear effects.
The quantum nature of nuclear motions plays a vital role in the structure, stability, and thermodynamics of molecules and materials. The standard approach to model nuclear quantum fluctuations in chemical and biological systems is to use path-integral molecular dynamics. Unfortunately, conventional path-integral simulations can have an exceedingly large computational cost due to the need to employ an excessive number of coupled classical subsystems (beads) for quantitative accuracy. Here, we combine perturbation theory with the Feynman–Kac imaginary-time path integral approach to quantum mechanics and derive an improved non-empirical partition function and estimators to calculate converged quantum observables. Our perturbed path-integral (PPI) method requires the same ingredients as the conventional approach, but increases the accuracy and efficiency of path integral simulations by an order of magnitude. Results are presented for the thermodynamics of fundamental model systems, an empirical water model containing 256 water molecules within periodic boundary conditions, and ab initio simulations of nitrogen and benzene molecules. For all of these examples, PPI simulations with 4 to 8 classical beads recover the nuclear quantum contribution to the total energy and heat capacity at room temperature within a 3% accuracy, paving the way toward seamless modeling of nuclear quantum effects in realistic molecules and materials.
Collapse
Affiliation(s)
- Igor Poltavsky
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 Berlin , Germany .
| | - Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 Berlin , Germany .
| |
Collapse
|
183
|
Ogata Y, Kawashima Y, Takahashi K, Tachikawa M. Theoretical vibrational spectra of OH(-)(H2O)2: the effect of quantum distribution and vibrational coupling. Phys Chem Chem Phys 2015; 17:25505-15. [PMID: 26365920 DOI: 10.1039/c5cp03632a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We performed ab initio path integral molecular dynamics simulations for the hydroxide-water cluster, OH(-)(H2O)2, at 50 K, 100 K, and 150 K to investigate its flexible structure. From our simulations, we found that nuclear quantum effects enhance hydroxide hydrogen atom inversion and the conformational change between isomers occurs by simultaneous rotation of the free hydrogen atom. We propose the importance of including the transition state conformer with C2 symmetry, for the description of this system at temperatures realized in predissociation experiments. Temperature dependence of relative populations of each conformer along with multidimensional vibrational calculations were used to simulate the vibrational spectra and compare with the experimental spectra of Johnson and coworkers. We assign the doublet peaks seen in the experiment at 2500 to 3000 cm(-1), as the mixture of the ionic hydrogen bonded OH stretching overtone, ionic hydrogen bonded OH bending overtone, and the combination band of the ionic hydrogen bonded OH stretch and bend, which are modulated by the van der Waals OO vibrations. We concluded that for OH(-)(H2O)2, the vibrational couplings between the ionic hydrogen bonded motion and floppy modes contribute to the broadening of peaks observed in the 2500 to 3000 cm(-1) region.
Collapse
Affiliation(s)
- Yudai Ogata
- Graduate school of Nanobioscience, Yokohama City University, Yokohama 236-0027, Japan.
| | | | | | | |
Collapse
|
184
|
van der Post ST, Hsieh CS, Okuno M, Nagata Y, Bakker HJ, Bonn M, Hunger J. Strong frequency dependence of vibrational relaxation in bulk and surface water reveals sub-picosecond structural heterogeneity. Nat Commun 2015; 6:8384. [PMID: 26382651 PMCID: PMC4595750 DOI: 10.1038/ncomms9384] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/17/2015] [Indexed: 02/07/2023] Open
Abstract
Because of strong hydrogen bonding in liquid water, intermolecular interactions between water molecules are highly delocalized. Previous two-dimensional infrared spectroscopy experiments have indicated that this delocalization smears out the structural heterogeneity of neat H2O. Here we report on a systematic investigation of the ultrafast vibrational relaxation of bulk and interfacial water using time-resolved infrared and sum-frequency generation spectroscopies. These experiments reveal a remarkably strong dependence of the vibrational relaxation time on the frequency of the OH stretching vibration of liquid water in the bulk and at the air/water interface. For bulk water, the vibrational relaxation time increases continuously from 250 to 550 fs when the frequency is increased from 3,100 to 3,700 cm(-1). For hydrogen-bonded water at the air/water interface, the frequency dependence is even stronger. These results directly demonstrate that liquid water possesses substantial structural heterogeneity, both in the bulk and at the surface.
Collapse
Affiliation(s)
| | - Cho-Shuen Hsieh
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands.,Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Masanari Okuno
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Yuki Nagata
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Huib J Bakker
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Mischa Bonn
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Johannes Hunger
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| |
Collapse
|
185
|
Gao L, Zhang X, Meng L, Zeng Y. Enhancing the hydrogen bond between the bridged hydrogen atom of diborane and ammonia. J Mol Model 2015; 21:233. [PMID: 26271730 DOI: 10.1007/s00894-015-2776-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Accepted: 07/27/2015] [Indexed: 10/23/2022]
Abstract
The character of the bridged hydrogen atom (Hb) of B2H6 has become a hot issue in recent years. In this work, the complexes B2H6 · · · NH3, B2H2X4 · · · nNH3 (n = 1, 2) and 2HF · · · B2H2X4 · · · 2NH3 (X = Cl, Br, I) were constructed and studied based on the M06-2X calculations to investigate how to enhance the Hb · · · N hydrogen-bonded interaction. When the terminal hydrogen atoms (Ht) of B2H6 were replaced by X (X = Cl, Br, I) atoms, the Hb · · · N hydrogen bond were strengthened. According to the electrostatic potentials in B2H2X4, two HF molecules were added to the interspace of the B-H-B-H four-membered ring of the B2H2X4 · · · 2NH3 complexes, and H · · · X hydrogen bond formed, resulting in further enhancing effect of Hb · · · N hydrogen bond. As a result, the positive cooperative effect of Hb · · · N hydrogen bond and H · · · X hydrogen bond do enhance the interactions of each other. The two measures not only enhance the strength of Hb · · · N hydrogen bond, but also achieve the goal to make the Hb · · · N hydrogen bond perpendicular to B · · · B direction.
Collapse
Affiliation(s)
- Lei Gao
- Institute of Computational Quantum Chemistry, College of Chemistry and Material Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | | | | | | |
Collapse
|
186
|
McKenzie RH, Athokpam B, Ramesh SG. Isotopic fractionation in proteins as a measure of hydrogen bond length. J Chem Phys 2015; 143:044309. [DOI: 10.1063/1.4927391] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Ross H. McKenzie
- School of Mathematics and Physics, University of Queensland, Brisbane 4072, Australia
| | - Bijyalaxmi Athokpam
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Sai G. Ramesh
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India
| |
Collapse
|
187
|
Huang YL, Zhang X, Ma Z, Zhou G, Sun CQ, Gong YY. Potential Paths for the Hydrogen-Bond Relaxing With (H 2O) NCluster Size. J Phys Chem A 2015. [DOI: 10.1021/acs.jpca.5b03921] [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]
|
188
|
Huang YL, Zhang X, Ma Z, Zhou G, Sun CQ, Gong YY. Potential Paths for the Hydrogen-Bond Relaxing With (H 2O) N Cluster Size. J Phys Chem A 2015; 119:16962-16971. [PMID: 26119068 DOI: 10.1021/acs.jpcc.5b03921] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Relaxation of the inter- and intra-molecular interactions for the hydrogen bond (O:H-O) between undercoordinated molecules determines the unusual behavior of water nanodroplets and nanobubbles. However, probing such potentials remains unreality. Here we show that the Lagrangian solution [Huang et al., J. Phys. Chem. B, 2013. 117: 13639] transforms the observed H-O bond (x = H) and O:H nonbond (x = L) lengths and phonon frequencies (dx, x) [Sun et al., J. Phys. Chem. Lett., 2013. 4: 2565] into the respective force constants and bond energies (kx, Ex) and hence enables the mapping of the potential paths for the O:H-O bond relaxing with water cluster size. Results show that molecular undercoordination not only reduces the molecular size (dH) with enhanced H-O energy from the bulk value of 3.97 to 5.10 eV for a H2O monomer, but also enlarges the molecular separation (dL) with reduced O:H energy from 95 to 35 meV for a dimer. The H-O energy gain raises the melting point from bulk value 273 to 310 K for the skin and the O:H energy loss lowers the freezing temperature from bulk value 258 to 202 K for 1.4 nm sized droplet, by dispersing the quasisolid phase boundaries.
Collapse
|
189
|
Chen J, Ren X, Li XZ, Alfè D, Wang E. On the room-temperature phase diagram of high pressure hydrogen: an ab initio molecular dynamics perspective and a diffusion Monte Carlo study. J Chem Phys 2015; 141:024501. [PMID: 25028021 DOI: 10.1063/1.4886075] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-art DMC results as benchmark, comparisons of the energy differences between structures generated from the MD and PIMD simulations, with molecular and dissociated hydrogens, respectively, in the weak molecular layers of phase IV, indicate that standard functionals in DFT tend to underestimate the dissociation barrier of the weak molecular layers in this mixed phase. Because of this underestimation, inclusion of the quantum nuclear effects (QNEs) in PIMD using electronic structures generated with these functionals leads to artificially dissociated hydrogen layers in phase IV and an error compensation between the neglect of QNEs and the deficiencies of these functionals in standard ab initio MD simulations exists. This analysis partly rationalizes why earlier ab initio MD simulations complement so well the experimental observations. The temperature and pressure dependencies for the stability of phase IV were also studied in the end and compared with earlier results.
Collapse
Affiliation(s)
- Ji Chen
- International Center for Quantum Materials, Peking University, Beijing 100871, People's Republic of China
| | - Xinguo Ren
- Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei 230026, Anhui, People's Republic of China
| | - Xin-Zheng Li
- School of Physics, Peking University, Beijing 100871, People's Republic of China
| | - Dario Alfè
- London Centre for Nanotechnology, University College London, London WC1H 0AH, United Kingdom
| | - Enge Wang
- International Center for Quantum Materials, Peking University, Beijing 100871, People's Republic of China
| |
Collapse
|
190
|
Zen A, Luo Y, Mazzola G, Guidoni L, Sorella S. Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo. J Chem Phys 2015; 142:144111. [PMID: 25877566 DOI: 10.1063/1.4917171] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems.
Collapse
Affiliation(s)
- Andrea Zen
- Dipartimento di Fisica, “La Sapienza” - Università di Roma, piazzale Aldo Moro 5, 00185 Rome, Italy
- London Centre for Nanotechnology, University College London, London WC1E 6BT, United Kingdom
| | - Ye Luo
- SISSA–International School for Advanced Studies, Via Bonomea 26, 34136 Trieste, Italy
- Democritos Simulation Center CNR–IOM Istituto Officina dei Materiali, 34151 Trieste, Italy
| | - Guglielmo Mazzola
- SISSA–International School for Advanced Studies, Via Bonomea 26, 34136 Trieste, Italy
- Democritos Simulation Center CNR–IOM Istituto Officina dei Materiali, 34151 Trieste, Italy
| | - Leonardo Guidoni
- Dipartimento di Fisica, “La Sapienza” - Università di Roma, piazzale Aldo Moro 5, 00185 Rome, Italy
- Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi dell’ Aquila, via Vetoio, 67100 L’ Aquila, Italy
| | - Sandro Sorella
- SISSA–International School for Advanced Studies, Via Bonomea 26, 34136 Trieste, Italy
- Democritos Simulation Center CNR–IOM Istituto Officina dei Materiali, 34151 Trieste, Italy
| |
Collapse
|
191
|
Biswal HS, Bhattacharyya S, Bhattacherjee A, Wategaonkar S. Nature and strength of sulfur-centred hydrogen bonds: laser spectroscopic investigations in the gas phase and quantum-chemical calculations. INT REV PHYS CHEM 2015. [DOI: 10.1080/0144235x.2015.1022946] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
192
|
Kirichek O, Soper A, Dzyuba B, Callear S, Fuller B. Strong isotope effects on melting dynamics and ice crystallisation processes in cryo vitrification solutions. PLoS One 2015; 10:e0120611. [PMID: 25815751 PMCID: PMC4376522 DOI: 10.1371/journal.pone.0120611] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 02/02/2015] [Indexed: 11/18/2022] Open
Abstract
The nucleation and growth of crystalline ice during cooling, and further crystallization processes during re-warming are considered to be key processes determining the success of low temperature storage of biological objects, as used in medical, agricultural and nature conservation applications. To avoid these problems a method, termed vitrification, is being developed to inhibit ice formation by use of high concentration of cryoprotectants and ultra-rapid cooling, but this is only successful across a limited number of biological objects and in small volume applications. This study explores physical processes of ice crystal formation in a model cryoprotective solution used previously in trials on vitrification of complex biological systems, to improve our understanding of the process and identify limiting biophysical factors. Here we present results of neutron scattering experiments which show that even if ice crystal formation has been suppressed during quench cooling, the water molecules, mobilised during warming, can crystallise as detectable ice. The crystallisation happens right after melting of the glass phase formed during quench cooling, whilst the sample is still transiting deep cryogenic temperatures. We also observe strong water isotope effects on ice crystallisation processes in the cryoprotectant mixture. In the neutron scattering experiment with a fully protiated water component, we observe ready crystallisation occurring just after the glass melting transition. On the contrary with a fully deuteriated water component, the process of crystallisation is either completely or substantially supressed. This behaviour might be explained by nuclear quantum effects in water. The strong isotope effect, observed here, may play an important role in development of new cryopreservation strategies.
Collapse
Affiliation(s)
- Oleg Kirichek
- ISIS facility, STFC, Rutherford Appleton Laboratory, Harwell Oxford Campus, Didcot, Oxon, United Kingdom
- * E-mail:
| | - Alan Soper
- ISIS facility, STFC, Rutherford Appleton Laboratory, Harwell Oxford Campus, Didcot, Oxon, United Kingdom
| | - Boris Dzyuba
- South Bohemian Research Center of Aquaculture and Hydrocenoses, University of South Bohemia in Ceske Budejovice, Zatisi, Vodnany, Czech Republic
| | - Sam Callear
- ISIS facility, STFC, Rutherford Appleton Laboratory, Harwell Oxford Campus, Didcot, Oxon, United Kingdom
| | - Barry Fuller
- Department of Surgery & Liver Transplant Unit, University College London, UCL Royal Free Campus, London, United Kingdom
| |
Collapse
|
193
|
|
194
|
|
195
|
Spura T, Elgabarty H, Kühne TD. “On-the-fly” coupled cluster path-integral molecular dynamics: impact of nuclear quantum effects on the protonated water dimer. Phys Chem Chem Phys 2015; 17:14355-9. [DOI: 10.1039/c4cp05192k] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
“On-the-fly” coupled cluster-based path-integral molecular dynamics simulations predict that the effective potential of the protonated water–dimer has a single-well only.
Collapse
Affiliation(s)
- Thomas Spura
- Department of Chemistry
- University of Paderborn
- D-33098 Paderborn
- Germany
| | - Hossam Elgabarty
- Institute for Physical Chemistry
- University of Mainz
- D-55128 Mainz
- Germany
| | - Thomas D. Kühne
- Department of Chemistry
- University of Paderborn
- D-33098 Paderborn
- Germany
- Institute for Physical Chemistry
| |
Collapse
|
196
|
Flitcroft JM, Molinari M, Brincat NA, Storr MT, Parker SC. Hydride ion formation in stoichiometric UO2. Chem Commun (Camb) 2015; 51:16209-12. [DOI: 10.1039/c5cc04799d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigated hydrogen solubility in UO2 using DFT and predicted that hydrogen species energetically prefers to exist as a hydride ion rather than a proton in a hydroxyl group and on diffusion hydrogen's charge state will change.
Collapse
Affiliation(s)
| | - M. Molinari
- Department of Chemistry
- University of Bath
- Bath
- UK
| | | | | | | |
Collapse
|
197
|
Gonçalves RF, Cavalcante LS, Nogueira IC, Longo E, Godinho MJ, Sczancoski JC, Mastelaro VR, Pinatti IM, Rosa ILV, Marques APA. Rietveld refinement, cluster modelling, growth mechanism and photoluminescence properties of CaWO4:Eu3+microcrystals. CrystEngComm 2015. [DOI: 10.1039/c4ce02279c] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
198
|
Lee JH, Bristowe NC, Bristowe PD, Cheetham AK. Role of hydrogen-bonding and its interplay with octahedral tilting in CH3NH3PbI3. Chem Commun (Camb) 2015; 51:6434-7. [DOI: 10.1039/c5cc00979k] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Computed Kohn–Sham energies as a function of torsion angle for three rotational modes of the methylammonium group in orthorhombic CH3NH3PbI3.
Collapse
Affiliation(s)
- Jung-Hoon Lee
- Department of Materials Science and Metallurgy
- University of Cambridge
- Cambridge
- UK
| | | | - Paul D. Bristowe
- Department of Materials Science and Metallurgy
- University of Cambridge
- Cambridge
- UK
| | - Anthony K. Cheetham
- Department of Materials Science and Metallurgy
- University of Cambridge
- Cambridge
- UK
| |
Collapse
|
199
|
Majerz I, Gutmann MJ. Intermolecular OHN hydrogen bond with a proton moving in 3-methylpyridinium 2,6-dichloro-4-nitrophenolate. RSC Adv 2015. [DOI: 10.1039/c5ra06733b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Temperature-dependent changes in the strong OHN hydrogen bond in 3-methylpyridinium 2,6-dichloro-4-nitrophenolate are used to discuss the proton transfer mechanism.
Collapse
Affiliation(s)
- Irena Majerz
- Faculty of Pharmacy
- Wroclaw Medical University
- 50-556 Wroclaw
- Poland
| | | |
Collapse
|
200
|
Roca RA, Sczancoski JC, Nogueira IC, Fabbro MT, Alves HC, Gracia L, Santos LPS, de Sousa CP, Andrés J, Luz GE, Longo E, Cavalcante LS. Facet-dependent photocatalytic and antibacterial properties of α-Ag2WO4crystals: combining experimental data and theoretical insights. Catal Sci Technol 2015. [DOI: 10.1039/c5cy00331h] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We have combined experimental results and calculations with new paths to explain the photocatalytic and antibacterial activities of α-Ag2WO4crystals.
Collapse
Affiliation(s)
- R. A. Roca
- DQ-Universidade Federal de São Carlos
- 13565-905 São Carlos
- Brazil
| | | | - I. C. Nogueira
- Instituto Federal do Maranhão
- Química e PPG em Engenharia de Materiais
- São Luís
- Brazil
| | - M. T. Fabbro
- DQ-Universidade Federal de São Carlos
- 13565-905 São Carlos
- Brazil
- Instituto Federal do Maranhão
- Química e PPG em Engenharia de Materiais
| | - H. C. Alves
- Programa de Pós-Graduação em Biotecnologia
- São Carlos
- Brazil
| | - L. Gracia
- Departamento de Química Física y Analítica
- Universitat Jaume I (UJI)
- Castelló 12071
- Spain
| | - L. P. S. Santos
- Instituto Federal do Maranhão
- Química e PPG em Engenharia de Materiais
- São Luís
- Brazil
| | - C. P. de Sousa
- Programa de Pós-Graduação em Biotecnologia
- São Carlos
- Brazil
| | - J. Andrés
- Departamento de Química Física y Analítica
- Universitat Jaume I (UJI)
- Castelló 12071
- Spain
| | - G. E. Luz
- PPGQ-GERATEC-CCN-DQ
- Universidade Estadual do Piauí
- João Cabral
- N. 2231
- 64002-150 Teresina
| | - E. Longo
- CDMF-Universidade Estadual Paulista
- Araraquara
- Brazil
| | - L. S. Cavalcante
- PPGQ-GERATEC-CCN-DQ
- Universidade Estadual do Piauí
- João Cabral
- N. 2231
- 64002-150 Teresina
| |
Collapse
|