1
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Zhang S, Du M, Ge H, Rong S, Chen Y, Guo L. Sulfur migration mechanism of pig manure in supercritical water: A combined experimental and DFT study. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134376. [PMID: 38657503 DOI: 10.1016/j.jhazmat.2024.134376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 04/16/2024] [Accepted: 04/19/2024] [Indexed: 04/26/2024]
Abstract
Pig manure (PM) is a high concentration organic waste rich in sulfur, and its biofuel contains various sulfur-containing pollutants, which reduces the safety of the products. Supercritical water (SCW) can dissolve most organic matter, which is a technology worthy of further study. In order to reduce sulfur pollution in the process of PM resource utilization and better control the conversion path of sulfur, it is necessary to explore the migration mechanism of sulfur in the whole PM-SCW gasification process. The experimental results indicated that H2S was the only gaseous product. Only inorganic compounds (S2-, S2O32- and SO42-) were detected in the liquid. Sulfur in the solid mainly included thiol/thioether, thiophene and sulfone. The influence of different reaction conditions (temperature, residence time, PM concentration and catalysts) on sulfur migration was studied in a batch reactor. It was worth noting that the catalysts had a significant effect on H2S absorption. The lowest H2S yield was 3.2 * 10-4 mol/kg and more than 70% of the sulfur was distributed in the liquid under the condition of addition of K2CO3. While, the RTH2110 fixed most of the sulfur of PM (the maximum value reached 50.94%) in the solid. Thus, adding the catalysts flexibly can choose composition of the products. Furthermore, six possible pathways of sulfur migration in the solid were designed and the kinetic parameters were calculated by density functional theory (DFT). The results provided a basis for controlling sulfur in PM. Subsequently, the sulfur migration pathways during PM-SCW gasification process were comprehensively summarized through the combination of experiment and DFT. It provided a method for sulfur treatment in PM, which had guiding significance for the realization of pollution-free treatment of PM.
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Affiliation(s)
- Shuyuan Zhang
- State Key Laboratory of Multiphase Flow in Power Engineering, Xi'an Jiaotong University, China
| | - Mingming Du
- State Key Laboratory of Multiphase Flow in Power Engineering, Xi'an Jiaotong University, China
| | - Hui Ge
- State Key Laboratory of Multiphase Flow in Power Engineering, Xi'an Jiaotong University, China
| | - Siqi Rong
- State Key Laboratory of Multiphase Flow in Power Engineering, Xi'an Jiaotong University, China
| | - Yunan Chen
- State Key Laboratory of Multiphase Flow in Power Engineering, Xi'an Jiaotong University, China; Xinjin Weihua Institute of Clean Energy Research, Nanhai District, Foshan City, Guangdong Province, China.
| | - Liejin Guo
- State Key Laboratory of Multiphase Flow in Power Engineering, Xi'an Jiaotong University, China
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2
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Zhu YC, Yang S, Zeng JX, Fang W, Jiang L, Zhang DH, Li XZ. Accurate calculation of tunneling splittings in water clusters using path-integral based methods. J Chem Phys 2023; 158:2895223. [PMID: 37290067 DOI: 10.1063/5.0146562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/03/2023] [Indexed: 06/10/2023] Open
Abstract
Tunneling splittings observed in molecular rovibrational spectra are significant evidence for tunneling motion of hydrogen nuclei in water clusters. Accurate calculations of the splitting sizes from first principles require a combination of high-quality inter-atomic interactions and rigorous methods to treat the nuclei with quantum mechanics. Many theoretical efforts have been made in recent decades. This Perspective focuses on two path-integral based tunneling splitting methods whose computational cost scales well with the system size, namely, the ring-polymer instanton method and the path-integral molecular dynamics (PIMD) method. From a simple derivation, we show that the former is a semiclassical approximation to the latter, despite that the two methods are derived very differently. Currently, the PIMD method is considered to be an ideal route to rigorously compute the ground-state tunneling splitting, while the instanton method sacrifices some accuracy for a significantly smaller computational cost. An application scenario of such a quantitatively rigorous calculation is to test and calibrate the potential energy surfaces of molecular systems by spectroscopic accuracy. Recent progress in water clusters is reviewed, and the current challenges are discussed.
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Affiliation(s)
- Yu-Cheng Zhu
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Frontier Science Center for Nano-optoelectronics and School of Physics, Peking University, Beijing 100871, People's Republic of China
- Interdisciplinary Institute of Light-Element Quantum Materials, Research Center for Light-Element Advanced Materials, and Collaborative Innovation Center of Quantum Materials, Peking University, Beijing 100871, People's Republic of China
| | - Shuo Yang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Jia-Xi Zeng
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Frontier Science Center for Nano-optoelectronics and School of Physics, Peking University, Beijing 100871, People's Republic of China
- Interdisciplinary Institute of Light-Element Quantum Materials, Research Center for Light-Element Advanced Materials, and Collaborative Innovation Center of Quantum Materials, Peking University, Beijing 100871, People's Republic of China
| | - Wei Fang
- Department of Chemistry, Fudan University, Shanghai 200438, People's Republic of China
| | - Ling Jiang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People's Republic of China
| | - Dong H Zhang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People's Republic of China
| | - Xin-Zheng Li
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Frontier Science Center for Nano-optoelectronics and School of Physics, Peking University, Beijing 100871, People's Republic of China
- Interdisciplinary Institute of Light-Element Quantum Materials, Research Center for Light-Element Advanced Materials, and Collaborative Innovation Center of Quantum Materials, Peking University, Beijing 100871, People's Republic of China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu 226010, People's Republic of China
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3
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Sangeetha T, Sahana R, Mounica P, Elangovan A, Shanmugam R, Arivazhagan G. H – Bond interactions in water multimers and water multimers – Pyridine complexes: Natural bond orbital and reduced density gradient isosurface analyses. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
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4
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König HF, Hausmann H, Schreiner PR. Assessing the Experimental Hydrogen Bonding Energy of the Cyclic Water Dimer Transition State with a Cyclooctatetraene-Based Molecular Balance. J Am Chem Soc 2022; 144:16965-16973. [PMID: 35998326 DOI: 10.1021/jacs.2c06141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have conducted an experimental and computational study of cyclooctatetraene-1,4/1,6-dimethanol (1,4 and 1,6) as a molecular balance with the goal in mind to determine the otherwise inaccessible hydrogen bonding energy (HBE) of the cyclic water dimer, which constitutes a transition state. The 1,4/1,6 folding equilibrium is governed by an intramolecular hydrogen bond in the folded 1,6-isomer, in which the OH groups adopt a cyclic planar geometry, akin to the structure of the cyclic water dimer transition state. We characterized hydrogen bonding in 1,6 and reference complexes utilizing SAPT2 + (3)δMP2/aug-cc-pVTZ and selected quantum theory of atoms in molecule descriptors at M06-2XD3(0)/ma-def2-TZVPP. Additionally, we computed HBEs at the DLPNO-CCSD(T)/aug-cc-pVQZ level of theory. We find that hydrogen bonding in 1,6 is very similar to the interaction in the Ci symmetric cyclic water dimer TS, both in magnitude and character. We experimentally determined the Gibbs free energy of the folding process (ΔGeq) in a variety of organic solvents via nuclear magnetic resonance spectroscopy measurements at room temperature. By combining experimentally obtained ΔGeq values with corrections derived from accurate computational methods, we provide estimates for the HBE of cyclic water dimers and the cyclic water dimer TS, as the most stable cyclic water dimer.
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Affiliation(s)
- Henrik Ferdinand König
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Heike Hausmann
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
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5
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Nandi A, Qu C, Houston PL, Conte R, Yu Q, Bowman JM. A CCSD(T)-Based 4-Body Potential for Water. J Phys Chem Lett 2021; 12:10318-10324. [PMID: 34662138 DOI: 10.1021/acs.jpclett.1c03152] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
High-level, ab initio calculations find that the 4-body (4-b) interaction is needed to account for near-100% of the total interaction energy for water clusters as large as the 21-mer. Motivated by this, we report a permutationally invariant polynomial potential energy surface (PES) for the 4-body interaction. This machine-learned PES is a fit to 2119 symmetry-unique, CCSD(T)-F12a/haTZ 4-b interaction energies. Configurations for these come from tetramer direct-dynamics calculations, fragments from an MD water simulation at 300 K, and tetramer fragments in a variety of water clusters. The PIP basis is purified to ensure that the PES goes rigorously to zero in monomer+trimer and dimer+dimer dissociations. The 4-b energies of isomers of the hexamer calculated with the new PES are shown to be in better agreement with benchmark CCSD(T) results than those from the MB-pol potential. Tests on larger clusters further validate the high-fidelity of the PES. The PES is shown to be fast to evaluate, taking 2.4 s for 105 evaluations on a single core of 2.4 GHz Intel Xeon processor, and significantly faster using a parallel version of the PES.
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Affiliation(s)
- Apurba Nandi
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Chen Qu
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Riccardo Conte
- Dipartimento di Chimica, Università Degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Qi Yu
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Joel M Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
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6
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Hartweg S, Garcia GA, Nahon L. Photoelectron Spectroscopy of the Water Dimer Reveals Unpredicted Vibrational Structure. J Phys Chem A 2021; 125:4882-4887. [PMID: 34028282 DOI: 10.1021/acs.jpca.1c03201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogen bonds and proton transfer reactions can be considered as being at the very heart of aqueous chemistry and of utmost importance for many processes of biological relevance. Nevertheless, these processes are not yet well understood, even in seemingly simple model systems like small water clusters. We present a study of the photoelectron spectrum of the water dimer, revealing previously unresolved vibrational structure with 10-30 meV (80-242 cm-1) typical splitting, in disagreement with a previous theoretical photoionization study predicting an apparent main vibrational progression with an ∼130 meV spacing [Kamarchik et al.; J. Chem. Phys. 2010, 132, 194311]. The observed vibrational structure and its deviation from the theoretical prediction is discussed in terms of known difficulties with calculations of strongly coupled anharmonic systems involving large amplitude motions. Potential contributions of the nonzero vibrational energy of the neutral water dimer at a finite experimental internal temperature are addressed. The internal temperature is estimated from the breakdown diagram associated with the dissociative ionization of the water dimer to be around to 130 K. This analysis also provides two additional, independently measured values for the 0 K appearance energy of the hydronium ion (H3O+) from dissociative ionization of the water dimer.
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Affiliation(s)
- Sebastian Hartweg
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin BP 48, 91192 Gif sur Yvette Cedex, France
| | - Gustavo A Garcia
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin BP 48, 91192 Gif sur Yvette Cedex, France
| | - Laurent Nahon
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin BP 48, 91192 Gif sur Yvette Cedex, France
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7
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Kuwahata K, Tachikawa M. Nuclear Quantum Effect on the Geometry of NH4+(H2O). BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20200120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kazuaki Kuwahata
- Yokohama National University, 9-5 Tokiwadai, Hodogaya-ku, Yokohama, Kanagawa 240-8501, Japan
| | - Masanori Tachikawa
- Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa 236-0027, Japan
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8
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9
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Lee VGM, Vetterli NJ, Boyer MA, McCoy AB. Diffusion Monte Carlo Studies on the Detection of Structural Changes in the Water Hexamer upon Isotopic Substitution. J Phys Chem A 2020; 124:6903-6912. [DOI: 10.1021/acs.jpca.0c05686] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Victor G. M. Lee
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Nicholas J. Vetterli
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Mark A. Boyer
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Anne B. McCoy
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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10
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Schwan R, Qu C, Mani D, Pal N, Schwaab G, Bowman JM, Tschumper GS, Havenith M. Observation of the Low‐Frequency Spectrum of the Water Trimer as a Sensitive Test of the Water‐Trimer Potential and the Dipole‐Moment Surface. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Raffael Schwan
- Physical Chemistry II Department of Chemistry and Biochemistry Ruhr-Universität Bochum Bochum Germany
| | - Chen Qu
- Department of Chemistry Biochemistry University of Maryland College Park MD 20742 USA
| | - Devendra Mani
- Physical Chemistry II Department of Chemistry and Biochemistry Ruhr-Universität Bochum Bochum Germany
| | - Nitish Pal
- Physical Chemistry II Department of Chemistry and Biochemistry Ruhr-Universität Bochum Bochum Germany
| | - Gerhard Schwaab
- Physical Chemistry II Department of Chemistry and Biochemistry Ruhr-Universität Bochum Bochum Germany
| | - Joel M. Bowman
- Cherry L. Emerson Center for Scientific Computations and Department of Chemistry Emory University Atlanta GA 30322 USA
| | - Gregory S. Tschumper
- Department of Chemistry and Biochemistry University of Mississippi University MS 38677 USA
| | - Martina Havenith
- Physical Chemistry II Department of Chemistry and Biochemistry Ruhr-Universität Bochum Bochum Germany
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11
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Schwan R, Qu C, Mani D, Pal N, Schwaab G, Bowman JM, Tschumper GS, Havenith M. Observation of the Low-Frequency Spectrum of the Water Trimer as a Sensitive Test of the Water-Trimer Potential and the Dipole-Moment Surface. Angew Chem Int Ed Engl 2020; 59:11399-11407. [PMID: 32307809 PMCID: PMC7383990 DOI: 10.1002/anie.202003851] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Indexed: 12/03/2022]
Abstract
Intermolecular interactions in bulk water are dominated by pairwise and non‐pairwise cooperative interactions. While accurate descriptions of the pairwise interactions are available and can be tested by precise low‐frequency spectra of the water dimer up to 550 cm−1, the same does not hold for the three‐body interactions. Here, we report the first comprehensive spectrum of the water trimer in the frequency region from 70 to 620 cm−1 using helium‐nanodroplet isolation and free‐electron lasers. By comparison to accompanying high‐level quantum calculations, the experimentally observed intermolecular bands can be assigned. The transition frequencies of the degenerate translation, the degenerate in‐plane and the non‐degenerate out‐of‐plane libration, as well as additional bands of the out‐of‐plane librational mode are reported for the first time. These provide a benchmark for state‐of‐the‐art water potentials and dipole‐moment surfaces, especially with respect to three‐body interactions.
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Affiliation(s)
- Raffael Schwan
- Physical Chemistry II, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - Chen Qu
- Department of Chemistry Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Devendra Mani
- Physical Chemistry II, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - Nitish Pal
- Physical Chemistry II, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - Gerhard Schwaab
- Physical Chemistry II, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - Joel M Bowman
- Cherry L. Emerson Center for Scientific Computations and Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Gregory S Tschumper
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS, 38677, USA
| | - Martina Havenith
- Physical Chemistry II, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
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12
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Rubinson KA, Mountain RD. Ion and water transport reasonably involves rotation and pseudorotation: measurement and modeling the temperature dependence of small-angle neutron scattering from aqueous SrI 2. Phys Chem Chem Phys 2020; 22:13479-13488. [PMID: 32525150 DOI: 10.1039/d0cp02088e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
X-ray and neutron scattering have provided insight into the short range (<8 Å) structures of ionic solutions for over a century. For longer distances, single scattering bands have, however, been seen. For the non-hydrolyzing salt SrI2 in aqueous (D2O) solution, a structure sufficient to scatter slow neutrons has been seen to persist down to a concentration of 0.1 mol L-1 where the measured average spacing between scatterers is over 20 Å. Theoretical studies of such long distance solution structures are difficult, and these difficulties are discussed. The width of the distribution in distances between the scatterers (ions, ion pairs, etc.) remains less than 10 Å, which approximates the average size of the ions and their first hydration shell. Here, we measure the temperature dependence from 10 °C to 90 °C of the small angle neutron scattering (SANS) by a 0.5 molar SrI2 solution in D2O and find that this surprisingly narrow distribution of the distances remains constant within experimental uncertainty. This structure of the ions in the solution appears to endure because changes in interion distances along any single spatial dimension require displacements near the size of a water molecule. Together, the experimental measurements support a rotatory mechanism for simultaneous ion transport and water countertransport. Since rotation minimizes displacement of the solution framework, it is suggested that water transport alone also involves rotation of multimolecular structures, and that the interpretation of single-molecule water rotation is confounded by pseudorotation that results from paired picosecond proton exchanges. It is pointed out that NMR-determined millisecond to microsecond proton exchange times of chelated-metal-ion bound waters and the much faster chelate rotational correlation times around 10 picoseconds, both of which require making and breaking of hydrogen bonds, are difficult to impossible to reconcile.
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Affiliation(s)
- Kenneth A Rubinson
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH 45435, USA. and NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
| | - Raymond D Mountain
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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13
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Tiwari A, Honingh C, Ensing B. Accurate calculation of zero point energy from molecular dynamics simulations of liquids and their mixtures. J Chem Phys 2019; 151:244124. [PMID: 31893925 DOI: 10.1063/1.5131145] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The two-phase thermodynamic (2PT) method is used to compute the zero point energy (ZPE) of several liquids and their mixtures. The 2PT method uses the density of states (DoS), which is computed from the velocity autocorrelation (VAC) function obtained from a short classical molecular dynamics trajectory. By partitioning the VAC and the DoS of a fluid into solid and gaslike components, quantum mechanical corrections to thermodynamical properties can be computed. The ZPE is obtained by combining the partition function of the quantum harmonic oscillator with the vibrational part of the solidlike DoS. The resulting ZPE is found to be in excellent agreement with both experimental and ab initio results. Solvent effects such as hydrogen bonding and polarization can be included by the utilization of ab initio density functional theory based molecular dynamics simulations. It is found that these effects significantly influence the DoS of water molecules. The obtained results demonstrate that the 2PT model is a powerful method for efficient ZPE calculations, in particular, to account for solvent effects and polarization.
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Affiliation(s)
- A Tiwari
- Van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - C Honingh
- Van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - B Ensing
- Van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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14
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Schwan R, Qu C, Mani D, Pal N, van der Meer L, Redlich B, Leforestier C, Bowman JM, Schwaab G, Havenith M. Observation of the Low‐Frequency Spectrum of the Water Dimer as a Sensitive Test of the Water Dimer Potential and Dipole Moment Surfaces. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Raffael Schwan
- Physical Chemistry II Department of Chemistry and Biochemistry Ruhr-Universität Bochum Bochum Germany
| | - Chen Qu
- Cherry L. Emerson Center for Scientific Computations and Department of Chemistry Emory University Atlanta Georgia 30322 USA
| | - Devendra Mani
- Physical Chemistry II Department of Chemistry and Biochemistry Ruhr-Universität Bochum Bochum Germany
| | - Nitish Pal
- Physical Chemistry II Department of Chemistry and Biochemistry Ruhr-Universität Bochum Bochum Germany
| | - Lex van der Meer
- Radboud University Institute for Molecules and Materials, FELIX Laboratory 6525 ED Nijmegen The Netherlands
| | - Britta Redlich
- Radboud University Institute for Molecules and Materials, FELIX Laboratory 6525 ED Nijmegen The Netherlands
| | - Claude Leforestier
- Institut Charles Gerhardt, UMR 5253 CNRS-UM-ENSCM Université de Montpellier Place Eugène Bataillon 34090 Montpellier France
| | - Joel M. Bowman
- Cherry L. Emerson Center for Scientific Computations and Department of Chemistry Emory University Atlanta Georgia 30322 USA
| | - Gerhard Schwaab
- Physical Chemistry II Department of Chemistry and Biochemistry Ruhr-Universität Bochum Bochum Germany
| | - Martina Havenith
- Physical Chemistry II Department of Chemistry and Biochemistry Ruhr-Universität Bochum Bochum Germany
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15
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Schwan R, Qu C, Mani D, Pal N, van der Meer L, Redlich B, Leforestier C, Bowman JM, Schwaab G, Havenith M. Observation of the Low-Frequency Spectrum of the Water Dimer as a Sensitive Test of the Water Dimer Potential and Dipole Moment Surfaces. Angew Chem Int Ed Engl 2019; 58:13119-13126. [PMID: 31350942 PMCID: PMC7687217 DOI: 10.1002/anie.201906048] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/23/2019] [Indexed: 11/12/2022]
Abstract
Using the helium nanodroplet isolation setup at the ultrabright free-electron laser source FELIX in Nijmegen (BoHeNDI@FELIX), the intermolecular modes of water dimer in the frequency region from 70 to 550 cm-1 were recorded. Observed bands were assigned to donor torsion, acceptor wag, acceptor twist, intermolecular stretch, donor torsion overtone, and in-plane and out-of-plane librational modes. This experimental data set provides a sensitive test for state-of-the-art water potentials and dipole moment surfaces. Theoretical calculations of the IR spectrum are presented using high-level quantum and approximate quasiclassical molecular dynamics approaches. These calculations use the full-dimensional ab initio WHHB potential and dipole moment surfaces. Based on the experimental data, a considerable increase of the acceptor switch and a bifurcation tunneling splitting in the librational mode is deduced, which is a consequence of the effective decrease in the tunneling barrier.
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Affiliation(s)
- Raffael Schwan
- Physical Chemistry II, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - Chen Qu
- Cherry L. Emerson Center for Scientific Computations and Department of Chemistry, Emory University, Atlanta, Georgia, 30322, USA
| | - Devendra Mani
- Physical Chemistry II, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - Nitish Pal
- Physical Chemistry II, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - Lex van der Meer
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, 6525 ED, Nijmegen, The Netherlands
| | - Britta Redlich
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, 6525 ED, Nijmegen, The Netherlands
| | - Claude Leforestier
- Institut Charles Gerhardt, UMR 5253 CNRS-UM-ENSCM, Université de Montpellier, Place Eugène Bataillon, 34090, Montpellier, France
| | - Joel M Bowman
- Cherry L. Emerson Center for Scientific Computations and Department of Chemistry, Emory University, Atlanta, Georgia, 30322, USA
| | - Gerhard Schwaab
- Physical Chemistry II, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - Martina Havenith
- Physical Chemistry II, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
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16
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Kumar N, Khullar S, Mandal SK. Encapsulation of a Water Octamer Chain in a Chiral 2D Sheetlike Supramolecular Coordination Network Composed of Dinickel-Dicarboxylate Subunits. ACS OMEGA 2018; 3:11062-11070. [PMID: 31459215 PMCID: PMC6645534 DOI: 10.1021/acsomega.8b01355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 08/23/2018] [Indexed: 05/25/2023]
Abstract
Four new chiral supramolecular coordination networks of Ni(II) of general formula [Ni2(Hhissal)2(dicarboxylate)(H2O)2]·nH2O (where Hhissal = histidinesalicylate; dicarboxylate = adipate; n = 8 for 1, succinate; n = 4 for 2, maleate; n = 4 for 3, fumarate; and n = 6 for 4) are reported. On the basis of the single-crystal X-ray study, an unprecedented zig-zag chain structure of water octamer encapsulated in 1 has been identified. The supramolecular network of the dimetal subunits is formed through hydrogen bonding interactions between the amine N-H of Hhissal and the oxygen atom of the coordinated water molecule of one subunit with the uncoordinated oxygen atom and the coordinated oxygen atom of the carboxylate group of Hhissal of the next subunit, respectively. The strength of hydrogen bonding within this water cluster (the range of O···O distances is 2.702-2.760 Å) is similar to that found in ice. These networks are further characterized by elemental analysis, IR spectroscopy, powder X-ray diffraction, polarimetry, UV-vis/diffuse reflectance and circular dichroism spectroscopy, and thermogravimetric analysis. A comparison of their properties indicates that these are isostructural with a variation of encapsulated water clusters.
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Affiliation(s)
- Navnita Kumar
- Department
of Chemical Sciences, Indian Institute of
Science Education and Research Mohali, Sector 81, Manauli PO, S.A.S.
Nagar, Mohali, Punjab 140306, India
| | - Sadhika Khullar
- Department
of Chemistry, DAV University, Jalandhar-Pathankot NH44, Jalandhar, Punjab 144012, India
| | - Sanjay K. Mandal
- Department
of Chemical Sciences, Indian Institute of
Science Education and Research Mohali, Sector 81, Manauli PO, S.A.S.
Nagar, Mohali, Punjab 140306, India
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17
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Yin J, Landau DP. Wang–Landau approach to the simulation of water clusters. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1506119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Junqi Yin
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - David P. Landau
- Center for Simulational Physics, The University of Georgia, Athens, GA, USA
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18
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Heßelmann A. Correlation effects and many-body interactions in water clusters. Beilstein J Org Chem 2018; 14:979-991. [PMID: 29977369 PMCID: PMC6009095 DOI: 10.3762/bjoc.14.83] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/11/2018] [Indexed: 11/23/2022] Open
Abstract
Background: The quantum-chemical description of the interactions in water clusters is an essential basis for deriving accurate and physically sound models of the interaction potential for water to be used in molecular simulations. In particular, the role of many-body interactions beyond the two-body interactions, which are often not explicitly taken into account by empirical force fields, can be accurately described by quantum chemistry methods on an adequate level, e.g., random-phase approximation electron correlation methods. The relative magnitudes of the different interaction energy contributions obtained by accurate ab initio calculations can therefore provide useful insights that can be exploited to develop enhanced force field methods. Results: In line with earlier theoretical studies of the interactions in water clusters, it has been found that the main contribution to the many-body interactions in clusters with a size of up to N = 13 molecules are higher-order polarisation interaction terms. Compared to this, many-body dispersion interactions are practically negligible for all studied sytems. The two-body dispersion interaction, however, plays a significant role in the formation of the structures of the water clusters and their stability, since it leads to a distinct compression of the cluster sizes compared to the structures optimized on an uncorrelated level. Overall, the many-body interactions amount to about 13% of the total interaction energy, irrespective of the cluster size. The electron correlation contribution to these, however, amounts to only about 30% to the total many-body interactions for the largest clusters studied and is repulsive for all structures considered in this work. Conclusion: While this shows that three- and higher-body interactions can not be neglected in the description of water complexes, the electron correlation contributions to these are much smaller in comparison to the two-body electron correlation effects. Efficient quantum chemistry approaches for describing intermolecular interactions between water molecules may therefore describe higher-body interactions on an uncorrelated Hartree-Fock level without a serious loss in accuracy.
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Affiliation(s)
- Andreas Heßelmann
- Lehrstuhl für Theoretische Chemie, Universität Erlangen-Nürnberg, Egerlandstr. 3, 91058 Erlangen, Germany
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19
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Egan CK, Paesani F. Assessing Many-Body Effects of Water Self-Ions. I: OH–(H2O)n Clusters. J Chem Theory Comput 2018. [DOI: 10.1021/acs.jctc.7b01273] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Colin K. Egan
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
- Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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20
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Hartweg S, Yoder BL, Garcia GA, Nahon L, Signorell R. Size-Resolved Photoelectron Anisotropy of Gas Phase Water Clusters and Predictions for Liquid Water. PHYSICAL REVIEW LETTERS 2017; 118:103402. [PMID: 28339280 DOI: 10.1103/physrevlett.118.103402] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Indexed: 05/05/2023]
Abstract
We report the first measurements of size-resolved photoelectron angular distributions for the valence orbitals of neutral water clusters with up to 20 molecules. A systematic decrease of the photoelectron anisotropy is found for clusters with up to 5-6 molecules, and most remarkably, convergence of the anisotropy for larger clusters. We suggest the latter to be the result of a local short-range scattering potential that is fully described by a unit of 5-6 molecules. The cluster data and a detailed electron scattering model are used to predict the anisotropy of slow photoelectrons in liquid water. Reasonable agreement with experimental liquid jet data is found.
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Affiliation(s)
- Sebastian Hartweg
- Department of Chemistry and Applied Biosciences, Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Bruce L Yoder
- Department of Chemistry and Applied Biosciences, Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Gustavo A Garcia
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP 48, 91192 Gif sur Yvette, France
| | - Laurent Nahon
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP 48, 91192 Gif sur Yvette, France
| | - Ruth Signorell
- Department of Chemistry and Applied Biosciences, Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
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21
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Elahi SM, Rajasekharan MV. Alkali Ion - Ce 3+- DipicH 2System : Coordination Networks and Water Clusters. ChemistrySelect 2016. [DOI: 10.1002/slct.201601351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Syed M. Elahi
- School of Chemistry; University of Hyderabad; Hyderabad 500 046 India
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22
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Mallory JD, Mandelshtam VA. Diffusion Monte Carlo studies of MB-pol (H2O)2−6 and (D2O)2−6 clusters: Structures and binding energies. J Chem Phys 2016. [DOI: 10.1063/1.4960610] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Joel D. Mallory
- Department of Chemistry, University of California, Irvine, California 92697, USA
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23
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Affiliation(s)
- Matúš Dubecký
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University Olomouc, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Lubos Mitas
- Department
of Physics and CHiPS, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Petr Jurečka
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University Olomouc, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
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24
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Gillan MJ, Alfè D, Michaelides A. Perspective: How good is DFT for water? J Chem Phys 2016; 144:130901. [DOI: 10.1063/1.4944633] [Citation(s) in RCA: 478] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Michael J. Gillan
- London Centre for Nanotechnology, Gordon St., London WC1H 0AH, United Kingdom
- Thomas Young Centre, University College London, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Dario Alfè
- London Centre for Nanotechnology, Gordon St., London WC1H 0AH, United Kingdom
- Thomas Young Centre, University College London, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
- Department of Earth Sciences, University College London, London WC1E 6BT, United Kingdom
| | - Angelos Michaelides
- London Centre for Nanotechnology, Gordon St., London WC1H 0AH, United Kingdom
- Thomas Young Centre, University College London, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
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25
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Ng YH, Bettens RPA. Comparing Vibrationally Averaged Nuclear Shielding Constants by Quantum Diffusion Monte Carlo and Second-Order Perturbation Theory. J Phys Chem A 2016; 120:1297-306. [PMID: 26835785 DOI: 10.1021/acs.jpca.6b00036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using the method of modified Shepard's interpolation to construct potential energy surfaces of the H2O, O3, and HCOOH molecules, we compute vibrationally averaged isotropic nuclear shielding constants ⟨σ⟩ of the three molecules via quantum diffusion Monte Carlo (QDMC). The QDMC results are compared to that of second-order perturbation theory (PT), to see if second-order PT is adequate for obtaining accurate values of nuclear shielding constants of molecules with large amplitude motions. ⟨σ⟩ computed by the two approaches differ for the hydrogens and carbonyl oxygen of HCOOH, suggesting that for certain molecules such as HCOOH where big displacements away from equilibrium happen (internal OH rotation), ⟨σ⟩ of experimental quality may only be obtainable with the use of more sophisticated and accurate methods, such as quantum diffusion Monte Carlo. The approach of modified Shepard's interpolation is also extended to construct shielding constants σ surfaces of the three molecules. By using a σ surface with the equilibrium geometry as a single data point to compute isotropic nuclear shielding constants for each descendant in the QDMC ensemble representing the ground state wave function, we reproduce the results obtained through ab initio computed σ to within statistical noise. Development of such an approach could thereby alleviate the need for any future costly ab initio σ calculations.
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Affiliation(s)
- Yee-Hong Ng
- Department of Chemistry, National University of Singapore , 3 Science Drive 3, 117543 Singapore
| | - Ryan P A Bettens
- Department of Chemistry, National University of Singapore , 3 Science Drive 3, 117543 Singapore
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26
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27
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Saha S, Sastry GN. Quantifying cooperativity in water clusters: an attempt towards obtaining a generalised equation. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1072648] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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28
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Tang HY, Wang XH, Feng L, Cao ZX, Liu XC. Theoretical study on the interactions between the lignite monomer and water molecules. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2015. [DOI: 10.1134/s0036024415090137] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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29
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Kuang Y, Yang B, Pan J, Meng X, Xiao F. Two Self-assembled Water Clusters Stabilized by Cu-containing Compounds Based on MoO 42-. Z Anorg Allg Chem 2015. [DOI: 10.1002/zaac.201500082] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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30
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Mallory JD, Brown SE, Mandelshtam VA. Assessing the Performance of the Diffusion Monte Carlo Method As Applied to the Water Monomer, Dimer, and Hexamer. J Phys Chem A 2015; 119:6504-15. [PMID: 26001418 DOI: 10.1021/acs.jpca.5b02511] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The diffusion Monte Carlo (DMC) method is applied to the water monomer, dimer, and hexamer using q-TIP4P/F, one of the most simple empirical water models with flexible monomers. The bias in the time step (Δτ) and population size (Nw) is investigated. For the binding energies, the bias in Δτ cancels nearly completely, whereas a noticeable bias in Nw remains. However, for the isotope shift (e.g, in the dimer binding energies between (H2O)2 and (D2O)2), the systematic errors in Nw do cancel. Consequently, very accurate results for the latter (within ∼0.01 kcal/mol) are obtained with moderate numerical effort (Nw ∼ 10(3)). For the water hexamer and its (D2O)6 isotopomer, the DMC results as a function of Nw are examined for the cage and prism isomers. For a given isomer, the issue of the walker population leaking out of the corresponding basin of attraction is addressed by using appropriate geometric constraints. The population size bias for the hexamer is more severe, and to maintain accuracy similar to that of the dimer, Nw must be increased by ∼2 orders of magnitude. Fortunately, when the energy difference between the cage and prism is taken, the biases cancel, thereby reducing the systematic errors to within ∼0.01 kcal/mol when using a population of Nw = 4.8 × 10(5) walkers. Consequently, a very accurate result for the isotope shift is also obtained. Notably, both the quantum and isotope effects for the prism-cage energy difference are small.
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Affiliation(s)
- Joel D Mallory
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - Sandra E Brown
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - Vladimir A Mandelshtam
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
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31
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Shilpi V, Kaur SP, Ramachandran C. Revisiting the structural pattern and the stability of (H2O)20 clusters using the dispersion corrected density functional method. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.02.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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32
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Temelso B, Renner CR, Shields GC. Importance and Reliability of Small Basis Set CCSD(T) Corrections to MP2 Binding and Relative Energies of Water Clusters. J Chem Theory Comput 2015; 11:1439-48. [DOI: 10.1021/ct500944v] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Berhane Temelso
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Carla R. Renner
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - George C. Shields
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
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33
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Liu F, Wang F, Jia G, Huang K. Molecular dynamics simulation of the cooperative effect by different force fields in monosodium glutamate aqueous solution. RSC Adv 2015. [DOI: 10.1039/c4ra11328d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Different force fields (GROMOS and OPLS) in conjunction with different water (SPC, SPCE, TIP3P, TIP4P and TIP5P) were assessed using molecular dynamics simulations of monosodium glutamate (MSG) aqueous solution.
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Affiliation(s)
- Fenghai Liu
- Sichuan University
- College of Electronic and Information Engineering
- Cheng Du
- China
| | - Feng Wang
- Sichuan Normal University
- College of Physics and Electronic Engineering
- Cheng Du
- China
| | - Guozhu Jia
- Sichuan Normal University
- College of Physics and Electronic Engineering
- Cheng Du
- China
| | - Kama Huang
- Sichuan University
- College of Electronic and Information Engineering
- Cheng Du
- China
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34
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Fedorov DG, Asada N, Nakanishi I, Kitaura K. The use of many-body expansions and geometry optimizations in fragment-based methods. Acc Chem Res 2014; 47:2846-56. [PMID: 25144610 DOI: 10.1021/ar500224r] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conspectus Chemists routinely work with complex molecular systems: solutions, biochemical molecules, and amorphous and composite materials provide some typical examples. The questions one often asks are what are the driving forces for a chemical phenomenon? How reasonable are our views of chemical systems in terms of subunits, such as functional groups and individual molecules? How can one quantify the difference in physicochemical properties of functional units found in a different chemical environment? Are various effects on functional units in molecular systems additive? Can they be represented by pairwise potentials? Are there effects that cannot be represented in a simple picture of pairwise interactions? How can we obtain quantitative values for these effects? Many of these questions can be formulated in the language of many-body effects. They quantify the properties of subunits (fragments), referred to as one-body properties, pairwise interactions (two-body properties), couplings of two-body interactions described by three-body properties, and so on. By introducing the notion of fragments in the framework of quantum chemistry, one obtains two immense benefits: (a) chemists can finally relate to quantum chemistry, which now speaks their language, by discussing chemically interesting subunits and their interactions and (b) calculations become much faster due to a reduced computational scaling. For instance, the somewhat academic sounding question of the importance of three-body effects in water clusters is actually another way of asking how two hydrogen bonds affect each other, when they involve three water molecules. One aspect of this is the many-body charge transfer (CT), because the charge transfers in the two hydrogen bonds are coupled to each other (not independent). In this work, we provide a generalized view on the use of many-body expansions in fragment-based methods, focusing on the general aspects of the property expansion and a contraction of a many-body expansion in a formally two-body series, as exemplified in the development of the fragment molecular orbital (FMO) method. Fragment-based methods have been very successful in delivering the properties of fragments, as well as the fragment interactions, providing insights into complex chemical processes in large molecular systems. We briefly review geometry optimizations performed with fragment-based methods and present an efficient geometry optimization method based on the combination of FMO with molecular mechanics (MM), applied to the complex of a subunit of protein kinase 2 (CK2) with a ligand. FMO results are discussed in comparison with experimental and MM-optimized structures.
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Affiliation(s)
- Dmitri G. Fedorov
- NRI, National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan
| | - Naoya Asada
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Isao Nakanishi
- Department of Pharmaceutical Sciences, Kinki University, 3-4-1,
Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Kazuo Kitaura
- Graduate
School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
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35
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36
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Wang K, Li W, Li S. Generalized Energy-Based Fragmentation CCSD(T)-F12a Method and Application to the Relative Energies of Water Clusters (H2O)20. J Chem Theory Comput 2014; 10:1546-53. [DOI: 10.1021/ct401060m] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kedong Wang
- School
of Physics and Electronical Engineering, Henan Normal University, Xinxiang, 453007, People’s Repubic of China
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37
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Wu DH. Three-dimensional hydrogen-bonded assembly in 2,2′-disulfanylidene-5,5′-biimidazolidinylidene-4,4′-dione–dimethylformamide–water (3/2/4). Acta Crystallogr C 2013; 69:1545-8. [DOI: 10.1107/s0108270113031521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 11/19/2013] [Indexed: 11/10/2022] Open
Abstract
The title compound, 3C6H4N4O2S2·2C3H7NO·4H2O, comprises three 2,2′-disulfanylidene-5,5′-biimidazolidinylidene-4,4′-dione molecules, two dimethylformamide molecules and four water molecules arranged around a crystallographic inversion centre. The non-H atoms within the 5,5′-biimidazolidinylidene molecule are coplanar and these molecules aggregate through N—H...S hydrogen-bonding interactions with cyclic motifs [graph setR22(8)], giving two-dimensional ribbon structures which are close to being parallel. The two independent water molecules associate to form centrosymmetric cyclic hydrogen-bonded (H2O)4tetrameric units [graph setR44(8)]. The ribbon structures extend along theaaxis and are linked through the water tetramers and the dimethylformamide molecules by a combination of two- and three-centre hydrogen bonds, giving an overall three-dimensional structure.
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38
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Affiliation(s)
- Branko Ruscic
- Chemical
Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States, and Computation Institute, University of Chicago, Chicago, Illinois 60637, United
States
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39
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Samanta AK, Ch’ng LC, Reisler H. Imaging bond breaking and vibrational energy transfer in small water containing clusters. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.05.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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40
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Shukla M, Kharediya B, Srivastava N, Saha S, Sunkari S. Water square (uudd) in novel CuII framework structures built from isomeric (aminomethyl)pyridines and oxalate: Synthesis, structure, spectral and DFT studies. Polyhedron 2013. [DOI: 10.1016/j.poly.2013.02.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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41
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Walewski Ł, Forbert H, Marx D. Revealing the Subtle Interplay of Thermal and Quantum Fluctuation Effects on Contact Ion Pairing in Microsolvated HCl. Chemphyschem 2012; 14:817-26. [DOI: 10.1002/cphc.201200695] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 10/23/2012] [Indexed: 11/07/2022]
Affiliation(s)
- Łukasz Walewski
- Lehrstuhl für Theoretische Chemie, Ruhr‐Universität Bochum, Universitätsstrasse 150, 44801 Bochum (Germany), Fax: (+49) 234‐32‐14045
| | - Harald Forbert
- Lehrstuhl für Theoretische Chemie, Ruhr‐Universität Bochum, Universitätsstrasse 150, 44801 Bochum (Germany), Fax: (+49) 234‐32‐14045
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr‐Universität Bochum, Universitätsstrasse 150, 44801 Bochum (Germany), Fax: (+49) 234‐32‐14045
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42
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Fujita T, Tanaka S, Fujiwara T, Kusa MA, Mochizuki Y, Shiga M. Ab initio path integral Monte Carlo simulations for water trimer with electron correlation effects. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.07.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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43
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44
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Perez C, Muckle MT, Zaleski DP, Seifert NA, Temelso B, Shields GC, Kisiel Z, Pate BH. Structures of Cage, Prism, and Book Isomers of Water Hexamer from Broadband Rotational Spectroscopy. Science 2012; 336:897-901. [DOI: 10.1126/science.1220574] [Citation(s) in RCA: 335] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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45
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Rocher-Casterline BE, Ch'ng LC, Mollner AK, Reisler H. Communication: determination of the bond dissociation energy (D0) of the water dimer, (H2O)2, by velocity map imaging. J Chem Phys 2012; 134:211101. [PMID: 21663337 DOI: 10.1063/1.3598339] [Citation(s) in RCA: 163] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The bond dissociation energy (D(0)) of the water dimer is determined by using state-to-state vibrational predissociation measurements following excitation of the bound OH stretch fundamental of the donor unit of the dimer. Velocity map imaging and resonance-enhanced multiphoton ionization (REMPI) are used to determine pair-correlated product velocity and translational energy distributions. H(2)O fragments are detected in the ground vibrational (000) and the first excited bending (010) states by 2 + 1 REMPI via the C̃ (1)B(1) (000) ← X̃ (1)A(1) (000 and 010) transitions. The fragments' velocity and center-of-mass translational energy distributions are determined from images of selected rovibrational levels of H(2)O. An accurate value for D(0) is obtained by fitting both the structure in the images and the maximum velocity of the fragments. This value, D(0) = 1105 ± 10 cm(-1) (13.2 ± 0.12 kJ/mol), is in excellent agreement with the recent theoretical value of D(0) = 1103 ± 4 cm(-1) (13.2 ± 0.05 kJ∕mol) suggested as a benchmark by Shank et al. [J. Chem. Phys. 130, 144314 (2009)].
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Wei YL, Li JB, Song WC, Zang SQ. Five-fold interpenetrating diamondlike 3D metal-organic frameworks constructed from the rigid 1,2-di(pyridin-4-yl)ethane-1,2-diol ligand and aromatic carboxylate. INORG CHEM COMMUN 2012. [DOI: 10.1016/j.inoche.2011.09.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Kaneko T, Akimoto T, Yasuoka K, Mitsutake A, Zeng XC. Size-Dependent Phase Changes in Water Clusters. J Chem Theory Comput 2011; 7:3083-7. [DOI: 10.1021/ct200458m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | | | | | | | - Xiao Cheng Zeng
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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Patrone M, Mella M. Sequential growth simulation of (NH3)n clusters (n=2–8) in ultracold superfluid environment. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.07.086] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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49
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Li XZ, Walker B, Michaelides A. Quantum nature of the hydrogen bond. Proc Natl Acad Sci U S A 2011; 108:6369-6373. [PMCID: PMC3081025 DOI: 10.1073/pnas.1016653108] [Citation(s) in RCA: 269] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023] Open
Abstract
Hydrogen bonds are weak, generally intermolecular bonds, which hold much of soft matter together as well as the condensed phases of water, network liquids, and many ferroelectric crystals. The small mass of hydrogen means that they are inherently quantum mechanical in nature, and effects such as zero-point motion and tunneling must be considered, though all too often these effects are not considered. As a prominent example, a clear picture for the impact of quantum nuclear effects on the strength of hydrogen bonds and consequently the structure of hydrogen bonded systems is still absent. Here, we report ab initio path integral molecular dynamics studies on the quantum nature of the hydrogen bond. Through a systematic examination of a wide range of hydrogen bonded systems we show that quantum nuclear effects weaken weak hydrogen bonds but strengthen relatively strong ones. This simple correlation arises from a competition between anharmonic intermolecular bond bending and intramolecular bond stretching. A simple rule of thumb is provided that enables predictions to be made for hydrogen bonded materials in general with merely classical knowledge (such as hydrogen bond strength or hydrogen bond length). Our work rationalizes the influence of quantum nuclear effects, which can result in either weakening or strengthening of the hydrogen bonds, and the corresponding structures, across a broad range of hydrogen bonded materials. Furthermore, it highlights the need to allow flexible molecules when anharmonic potentials are used in force field-based studies of quantum nuclear effects.
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Affiliation(s)
- Xin-Zheng Li
- London Centre for Nanotechnology and Department of Chemistry, University College London, London WC1E 6BT, United Kingdom
| | - Brent Walker
- London Centre for Nanotechnology and Department of Chemistry, University College London, London WC1E 6BT, United Kingdom
| | - Angelos Michaelides
- London Centre for Nanotechnology and Department of Chemistry, University College London, London WC1E 6BT, United Kingdom
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Nedić M, Wassermann TN, Larsen RW, Suhm MA. A combined Raman- and infrared jet study of mixed methanol-water and ethanol-water clusters. Phys Chem Chem Phys 2011; 13:14050-63. [PMID: 21491035 DOI: 10.1039/c1cp20182d] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The vibrational dynamics of vacuum-isolated hydrogen-bonded complexes between water and the two simplest alcohols is characterized at low temperatures by Raman and FTIR spectroscopy. Conformational preferences during adaptive aggregation, relative donor/acceptor strengths, weak secondary hydrogen bonding, tunneling processes in acceptor lone pair switching, and thermodynamic anomalies are elucidated. The ground state tunneling splitting of the methanol-water dimer is predicted to be larger than 2.5 cm(-1). Two types of alcohol-water trimers are identified from the spectra. It is shown that methanol and ethanol are better hydrogen bond donors than water, but even more so better hydrogen bond acceptors. As a consequence, hydrogen bond induced red shifts of OH modes behave non-linearly as a function of composition and the resulting cluster excess quantities correspond nicely to bulk excess enthalpies at room temperature. The effects of weak C-H···O hydrogen bonds are quantified in the case of mixed ethanol-water dimers.
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Affiliation(s)
- Marija Nedić
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstr. 6, 37077 Göttingen, Germany
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