1
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Zhu Z, Zhu J, Chang C, Qi C, Zhu Z, Zhao H, Zhang D, Zeng XC, Wang C. Tunable Surface Wettability via Terahertz Electrowave Controlled Vicinal Subnanoscale Water Layer. NANO LETTERS 2024; 24:3243-3248. [PMID: 38427592 DOI: 10.1021/acs.nanolett.4c00248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Achieving timely, reversible, and long-range remote tunability over surface wettability is highly demanded across diverse fields, including nanofluidic systems, drug delivery, and heterogeneous catalysis. Herein, using molecular dynamic simulations, we show, for the first time, a theoretical design of electrowetting to achieve remotely controllable surface wettability via using a terahertz wave. The key idea driving the design is the unique terahertz collective vibration identified in the vicinal subnanoscale water layer, which is absent in bulk water, enabling efficient energy transfer from the terahertz wave to the rotational motion of the vicinal subnanoscale water layer. Consequently, a frequency-specific alternating terahertz electric field near the critical strength can significantly affect the local hydrogen-bonding network of the contact water layer on the solid surface, thereby achieving tunable surface wettability.
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Affiliation(s)
- Zhi Zhu
- College of Optical-Electrical and Computer Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Junquan Zhu
- College of Optical-Electrical and Computer Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Chao Chang
- Innovation Laboratory of Terahertz Biophysics, National Innovation Institute of Defense Technology, Beijing 100071, China
- School of Physics, Peking University, Beijing 100871, China
| | - Chonghai Qi
- School of Physical and Intelligent Engineering, Jining University, Qufu 273155, China
| | - Zhongjie Zhu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Hongwei Zhao
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Dengsong Zhang
- International Joint Laboratory of Catalytic Chemistry, College of Sciences, Shanghai University, Shanghai 200444, China
| | - Xiao Cheng Zeng
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, 999077, Hong Kong
| | - Chunlei Wang
- International Joint Laboratory of Catalytic Chemistry, College of Sciences, Shanghai University, Shanghai 200444, China
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2
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Kolesár V, Dubecký M. Accuracy of Noncovalent Interactions Involving d-Elements by the 1-Determinant Fixed-Node Diffusion Monte Carlo Method with Effective Core Potentials. J Chem Theory Comput 2023; 19:1170-1176. [PMID: 36751996 DOI: 10.1021/acs.jctc.2c00872] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
A critical assessment of effective core potential (ECP)-based single-determinant (SD) fixed-node diffusion quantum Monte Carlo (FNDMC) accuracy in prototypical noncovalent closed-shell systems involving d-elements is presented. Careful analysis of biases and elimination of possible bias sources leads to two findings of practical importance for SD FNDMC in these systems. First, in some systems (HCu:HCu, HCu:CuH), SD FNDMC reveals large biases of interaction energy differences (significantly exceeding the target 2% relative error) vs a reliable coupled-cluster CCSD(T)/CBS (complete basis set) reference. Second, the leading error of SD FNDMC with ECPs was attributed to a higher nuclear charge Z of d-group (pseudo) atoms, when compared to sp elements, in line with a previously reported finding that aggregate SD FNDMC bias tends to increase in systems with higher electronic densities. Therefore, SD FNDMC should only be used with caution in systems with a large Z.
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Affiliation(s)
- Vladimír Kolesár
- Department of Physics, Faculty of Science, University of Ostrava, 30. dubna 22, 701 03 Ostrava, Czech Republic
| | - Matúš Dubecký
- Department of Physics, Faculty of Science, University of Ostrava, 30. dubna 22, 701 03 Ostrava, Czech Republic.,ATRI, Faculty of Materials Science and Technology in Trnava, Slovak University of Technology in Bratislava, J. Bottu 25, 917 24 Trnava, Slovakia
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3
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Neklyudov V, Freger V. Putting together the puzzle of ion transfer in single-digit carbon nanotubes: mean-field meets ab initio. NANOSCALE 2022; 14:8677-8690. [PMID: 35671158 DOI: 10.1039/d1nr08073c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Nature employs channel proteins to selectively pass water across cell membranes, which inspires the search for bio-mimetic analogues. Carbon nanotube porins (CNTPs) are intriguing mimics of water channels, yet ion transport in CNTPs still poses questions. As an alternative to continuum models, here we present a molecular mean-field model that transparently describes ion coupling, yet unlike continuum models, computes ab initio all required thermodynamic quantities for the KCl salt and H+ and OH- ions present in water. Starting from water transfer, the model considers the transfer of free ions, along with ion-pair formation as a proxy of non-mean-field ion-ion interactions. High affinity to hydroxide, suggested by experiments, making it a dominant charge carrier in CNTPs, is revealed as an exceptionally favorable transfer of KOH pairs. Nevertheless, free ions, coexisting with less mobile ion-pairs, apparently control ion transport. The model well explains the observed effects of salt concentration and pH on conductivity, transport numbers, anion permeation and its activation energies, and current rectification. The proposed approach is extendable to other sub-nanochannels and helps design novel osmotic materials and devices.
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Affiliation(s)
- Vadim Neklyudov
- Wolfson Department of Chemical Engineering, Technion - IIT, Haifa 32000, Israel.
| | - Viatcheslav Freger
- Wolfson Department of Chemical Engineering, Technion - IIT, Haifa 32000, Israel.
- Russel Berrie Nanotechnology Institute, Technion - IIT, Haifa 32000, Israel
- Grand Technion Energy Program, Technion - IIT, Haifa 32000, Israel
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4
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Song Y, Sun Z, Fan G, Yang L, Li F. Regulating Surface‐Interface Structures of Zn‐Incorporated LiAl‐LDH Supported Ru Catalysts for Efficient Benzene Hydrogenation to Produce Cyclohexene. ChemCatChem 2022. [DOI: 10.1002/cctc.202200125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yihui Song
- Beijing University of Chemical Technology State Key Laboratory of Chemical Resource Engineering CHINA
| | - Zhi Sun
- Beijing University of Chemical Technology State Key Laboratory of Chemical Resource Engineering CHINA
| | - Guoli Fan
- Beijing University of Chemical Technology State Key Laboratory of Chemical Resource Engineering CHINA
| | - Lan Yang
- Beijing University of Chemical Technology Post-Publication Corresponding Author CHINA
| | - Feng Li
- Beijing University of Chemical Technology State Key Laboratory of Chemical Resource Engineering POB 98 100029 Beijing CHINA
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5
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Rostkowski M, Schürner HKV, Sowińska A, Vasquez L, Przydacz M, Elsner M, Dybala-Defratyka A. Isotope Effects on the Vaporization of Organic Compounds from an Aqueous Solution-Insight from Experiment and Computations. J Phys Chem B 2021; 125:13868-13885. [PMID: 34908428 PMCID: PMC8724799 DOI: 10.1021/acs.jpcb.1c05574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
An isotope fractionation
analysis of organic groundwater pollutants
can assess the remediation at contaminated sites yet needs to consider
physical processes as potentially confounding factors. This study
explores the predictability of water–air partitioning isotope
effects from experiments and computational predictions for benzene
and trimethylamine (both H-bond acceptors) as well as chloroform (H-bond
donor). A small, but significant, isotope fractionation of different
direction and magnitude was measured with ε = −0.12‰
± 0.07‰ (benzene), εC = 0.49‰
± 0.23‰ (triethylamine), and εH = 1.79‰
± 0.54‰ (chloroform) demonstrating that effects do not
correlate with expected hydrogen-bond functionalities. Computations
revealed that the overall isotope effect arises from contributions
of different nature and extent: a weakening of intramolecular vibrations
in the condensed phase plus additional vibrational modes from a complexation
with surrounding water molecules. Subtle changes in benzene contrast
with a stronger coupling between intra- and intermolecular modes in
the chloroform–water system and a very local vibrational response
with few atoms involved in a specific mode of triethylamine. An energy
decomposition analysis revealed that each system was affected differently
by electrostatics and dispersion, where dispersion was dominant for
benzene and electrostatics dominated for chloroform and triethylamine.
Interestingly, overall stabilization patterns in all studied systems
originated from contributions of dispersion rather than other energy
terms.
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Affiliation(s)
- Michał Rostkowski
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Heide K V Schürner
- Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Elisabeth-Winterhalter-Weg 6, 81377 Munich, Germany
| | - Agata Sowińska
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Luis Vasquez
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Martyna Przydacz
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Martin Elsner
- Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Elisabeth-Winterhalter-Weg 6, 81377 Munich, Germany
| | - Agnieszka Dybala-Defratyka
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
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6
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Queiroz MH, Alves TV, Rivelino R. A theoretical screening of the O H⋅⋅⋅π interaction between water and benzene using density-functional approaches: Effects of nonlocal exchange and long-range dispersion corrections in the true minimum. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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Andersen J, Larsen RW, Ceponkus J, Uvdal P, Nelander B. Far-Infrared Investigation of the Benzene–Water Complex: The Identification of Large-Amplitude Motion and Tunneling Pathways. J Phys Chem A 2019; 124:513-519. [DOI: 10.1021/acs.jpca.9b01497] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. Andersen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800 Kgs. Lyngby, Denmark
| | - R. Wugt Larsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800 Kgs. Lyngby, Denmark
| | - J. Ceponkus
- Department of General Physics and Spectroscopy, Vilnius University, Sauletekio 9, LT-10007 Vilnius, Lithuania
| | - P. Uvdal
- Chemical Physics, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - B. Nelander
- Chemical Physics, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
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8
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Choudhary A, Chandra A. An ab initio molecular dynamics study of benzene in water at supercritical conditions: Structure, dynamics, and polarity of hydration shell water and the solute. J Chem Phys 2019; 151:044508. [PMID: 31370512 DOI: 10.1063/1.5094570] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Anisotropic structure and dynamics of the hydration shell of a benzene solute in supercritical water are investigated by means of ab initio molecular dynamics simulations. The polarity and structural distortion of the benzene solute in supercritical water are also investigated in this study. Calculations are done at 673 K for three different densities of the solvent. The simulations are carried out using the Becke-Lee-Yang-Parr (BLYP) and also the Becke-Lee-Yang-Parr functional including dispersion corrections of Grimme (BYLP-D). The structural anisotropy is found to exist even at supercritical conditions as elucidated by the radial distribution functions of different conical regions and also by angular and spatial distribution functions. The benzene-water πH-bond and also the water-water hydrogen bonds are found to exist even at the supercritical temperature of 673 K. However, the numbers of these hydrogen bonds are reduced substantially with a decrease in water density. The water molecules in the axial region of benzene are found to be preferably oriented with one OH vector pointing toward the benzene ring, whereas the water molecules located in the equatorial region are found to orient their dipoles mostly parallel to the ring plane. The orientational distributions, however, are found to be rather broad at the supercritical temperature due to thermal fluctuations. Although the water molecules have faster dynamics at these supercritical conditions, a slight difference is observed in the dynamics of the solvation shell and bulk molecules. The conformational flexibility of the ring is found to be enhanced which causes an increase in polarity of the benzene solute in water under supercritical conditions.
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Affiliation(s)
- Ashu Choudhary
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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9
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Dubecký M, Jurečka P, Mitas L, Ditte M, Fanta R. Toward Accurate Hydrogen Bonds by Scalable Quantum Monte Carlo. J Chem Theory Comput 2019; 15:3552-3557. [DOI: 10.1021/acs.jctc.9b00096] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matúš Dubecký
- Department of Physics, University of Ostrava, 30. dubna 22, 701 03 Ostrava, Czech Republic
- ATRI, Slovak University of Technology, Paulínska 16, 917 24 Trnava, Slovakia
| | - Petr Jurečka
- Department of Physical Chemistry, Palackỳ 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
| | - Matej Ditte
- Department of Physics, University of Ostrava, 30. dubna 22, 701 03 Ostrava, Czech Republic
| | - Roman Fanta
- Department of Physics, University of Ostrava, 30. dubna 22, 701 03 Ostrava, Czech Republic
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10
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DFT study of small gas molecules adsorbed on undoped and N-, Si-, B-, and Al-doped graphene quantum dots. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2428-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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11
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Brandenburg JG, Zen A, Fitzner M, Ramberger B, Kresse G, Tsatsoulis T, Grüneis A, Michaelides A, Alfè D. Physisorption of Water on Graphene: Subchemical Accuracy from Many-Body Electronic Structure Methods. J Phys Chem Lett 2019; 10:358-368. [PMID: 30615460 DOI: 10.1021/acs.jpclett.8b03679] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Wet carbon interfaces are ubiquitous in the natural world and exhibit anomalous properties, which could be exploited by emerging technologies. However, progress is limited by lack of understanding at the molecular level. Remarkably, even for the most fundamental system (a single water molecule interacting with graphene), there is no consensus on the nature of the interaction. We tackle this by performing an extensive set of complementary state-of-the-art computer simulations on some of the world's largest supercomputers. From this effort a consensus on the water-graphene interaction strength has been obtained. Our results have significant impact for the physical understanding, as they indicate that the interaction is weaker than predicted previously. They also pave the way for more accurate and reliable studies of liquid water at carbon interfaces.
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Affiliation(s)
- Jan Gerit Brandenburg
- Department of Physics and Astronomy , University College London , Gower Street , London WC1E 6BT , United Kingdom
- Thomas Young Centre and London Centre for Nanotechnology , 17-19 Gordon Street , London WC1H 0AH , United Kingdom
| | - Andrea Zen
- Department of Physics and Astronomy , University College London , Gower Street , London WC1E 6BT , United Kingdom
- Thomas Young Centre and London Centre for Nanotechnology , 17-19 Gordon Street , London WC1H 0AH , United Kingdom
| | - Martin Fitzner
- Department of Physics and Astronomy , University College London , Gower Street , London WC1E 6BT , United Kingdom
- Thomas Young Centre and London Centre for Nanotechnology , 17-19 Gordon Street , London WC1H 0AH , United Kingdom
| | - Benjamin Ramberger
- University of Vienna , Faculty of Physics and Center for Computational Materials Sciences , Sensengasse 8/12 , 1090 Wien , Austria
| | - Georg Kresse
- University of Vienna , Faculty of Physics and Center for Computational Materials Sciences , Sensengasse 8/12 , 1090 Wien , Austria
| | - Theodoros Tsatsoulis
- Institute for Theoretical Physics , Vienna University of Technology , Wiedner Hauptstrasse 8-10 , 1040 Vienna , Austria
- Max Planck Institute for Solid State Research , Heisenbergstrasse 1 , 70569 Stuttgart , Germany
| | - Andreas Grüneis
- Institute for Theoretical Physics , Vienna University of Technology , Wiedner Hauptstrasse 8-10 , 1040 Vienna , Austria
- Max Planck Institute for Solid State Research , Heisenbergstrasse 1 , 70569 Stuttgart , Germany
| | - Angelos Michaelides
- Department of Physics and Astronomy , University College London , Gower Street , London WC1E 6BT , United Kingdom
- Thomas Young Centre and London Centre for Nanotechnology , 17-19 Gordon Street , London WC1H 0AH , United Kingdom
| | - Dario Alfè
- Thomas Young Centre and London Centre for Nanotechnology , 17-19 Gordon Street , London WC1H 0AH , United Kingdom
- Department of Earth Sciences , University College London , Gower Street , London WC1E 6BT , United Kingdom
- Dipartimento di Fisica Ettore Pancini , Università di Napoli Federico II , Monte S. Angelo, I-80126 Napoli , Italy
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12
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Ospadov E, Rothstein SM, Baer R. Quantum Monte Carlo assessment of density functionals for π-electron molecules: ethylene and bifuran. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1517905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Egor Ospadov
- Department of Chemistry, The University of Western Ontario, London, ON, Canada
| | | | - Roi Baer
- Fritz Haber Center for Molecular Dynamics and Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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13
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Choudhary A, Chandra A. Dynamics of water in conical solvation shells around a benzene solute under different thermodynamic conditions. Phys Chem Chem Phys 2018; 20:18328-18339. [PMID: 29938274 DOI: 10.1039/c7cp08109j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Water molecules in different parts of the anisotropic hydration shell of an aromatic molecule experience different interactions. In the present study, we investigate the anisotropic dynamics of water molecules in different non-overlapping conical shells around a benzene solute at sub- and supercritical conditions by means of molecular dynamics simulations using both non-polarizable and polarizable models. In addition to the dynamical properties, the effects of polarizability on the hydration structure of benzene at varying thermodynamic conditions are also investigated in the current study. The presence of πH-bonding in the solvation shell is found to be an important factor that influences the anisotropic dynamics of the benzene hydration shell. The water molecules located axial to the benzene plane are found to be maximally influenced by the πH-bonding. The extent of πH-bonding is found to be somewhat reduced on inclusion of polarizability. The πH-bonded water molecules are found to reorient through large-amplitude angular jumps where the jump-angle amplitude increases at higher temperatures and lower densities. For both non-polarizable and polarizable models, it is found that the water molecules in the axial conical shells possess faster orientational and hydrogen bond dynamics compared to those in the equatorial plane. Water molecules in the axial conical shells are also found to diffuse at a faster rate than bulk molecules due to the relatively weaker benzene-water πH-bonding interactions in the axial region of the hydration shell. The residence dynamics of water molecules in different conical solvation shells around the solute is also investigated in the current study.
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Affiliation(s)
- Ashu Choudhary
- Department of Chemistry, Indian Institute of Technology Kanpur, 208016, India.
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14
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Yu XL, Li Y, Xin SM, Yuan PQ, Yuan WK. Partial Hydrogenation of Benzene to Cyclohexene on Ru@XO2 (X = Ti, Zr, or Si). Ind Eng Chem Res 2018. [DOI: 10.1021/acs.iecr.7b04642] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xue-Lian Yu
- State
Key Laboratory of Chemical Engineering and ‡School of Chemistry and Molecular
Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yan Li
- State
Key Laboratory of Chemical Engineering and ‡School of Chemistry and Molecular
Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Shuang-Mei Xin
- State
Key Laboratory of Chemical Engineering and ‡School of Chemistry and Molecular
Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Pei-Qing Yuan
- State
Key Laboratory of Chemical Engineering and ‡School of Chemistry and Molecular
Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wei-Kang Yuan
- State
Key Laboratory of Chemical Engineering and ‡School of Chemistry and Molecular
Engineering, East China University of Science and Technology, Shanghai 200237, China
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15
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Dubecký M. Noncovalent Interactions by Fixed-Node Diffusion Monte Carlo: Convergence of Nodes and Energy Differences vs Gaussian Basis-Set Size. J Chem Theory Comput 2017; 13:3626-3635. [DOI: 10.1021/acs.jctc.7b00537] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matúš Dubecký
- Department of Physics, Faculty of Science, University of Ostrava, 30. dubna 22, 701
03 Ostrava, Czech Republic
- ATRI, Faculty of Materials
Science and Technology, Slovak University of Technology, Paulínska
16, 917 24 Trnava, Slovakia
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16
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Ingenmey J, von Domaros M, Kirchner B. Predicting miscibility of binary liquids from small cluster QCE calculations. J Chem Phys 2017; 146:154502. [PMID: 28433040 DOI: 10.1063/1.4980032] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Johannes Ingenmey
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
| | - Michael von Domaros
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
| | - Barbara Kirchner
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
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17
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Dubecký M. Bias cancellation in one-determinant fixed-node diffusion Monte Carlo: Insights from fermionic occupation numbers. Phys Rev E 2017; 95:033308. [PMID: 28415179 DOI: 10.1103/physreve.95.033308] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Indexed: 06/07/2023]
Abstract
The accuracy of the fixed-node diffusion Monte Carlo (FNDMC) depends on the node location of the supplied trial state Ψ_{T}. The practical FNDMC approaches available for large systems rely on compact yet effective Ψ_{T}, most often containing an explicitly correlated single Slater determinant (SD). However, SD nodes may be better suited to one system than to another, which may possibly lead to inaccurate FNDMC energy differences. It remains a challenge how to estimate nonequivalence or appropriateness of SDs. Here we use the differences of a measure based on the Euclidean distance between the natural orbital occupation number (NOON) vector of the SD and the exact solution in the NOON vector space, which can be viewed as a measure of SD nonequivalence and as a qualitative measure of the expected degree of nondynamic-correlation-related bias in FNDMC energy differences. This is explored on a set of small noncovalent complexes and covalent bond breaking of Si_{2} vs N_{2}. It turns out that NOON-based measures well reflect the magnitude and sign of the bias present in the data available, thus providing insights into the nature of bias cancellation in SD FNDMC energy differences.
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Affiliation(s)
- Matúš Dubecký
- Department of Physics, Faculty of Science, University of Ostrava, 30. dubna 22, 701 03 Ostrava, Czech Republic and ATRI, Faculty of Materials Science and Technology, Slovak University of Technology, Paulínska 16, 917 24 Trnava, Slovakia
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18
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Hayashi S, Sugibayashi Y, Nakanishi W. Behavior of interactions between hydrogen chalcogenides and an anthracene π-system elucidated by QTAIM dual functional analysis with QC calculations. RSC Adv 2017. [DOI: 10.1039/c7ra04224h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The nature of the interactions between chalcogenides and the anthracene p-system, EH2-*-p(C14H10), is predicted to be close to that of EH2-*-p(C10H8), although the partial structures around the central rings can be found in EH2-*-p(C6H6).
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Affiliation(s)
- Satoko Hayashi
- Department of Material Science and Chemistry
- Faculty of Systems Engineering
- Wakayama University
- Wakayama
- 640-8510 Japan
| | - Yuji Sugibayashi
- Department of Material Science and Chemistry
- Faculty of Systems Engineering
- Wakayama University
- Wakayama
- 640-8510 Japan
| | - Waro Nakanishi
- Department of Material Science and Chemistry
- Faculty of Systems Engineering
- Wakayama University
- Wakayama
- 640-8510 Japan
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19
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20
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Sharma D, Sameera WMC, Andersson S, Nyman G, Paterson MJ. Computational Study of the Interactions between Benzene and Crystalline Ice Ih: Ground and Excited States. Chemphyschem 2016; 17:4079-4089. [DOI: 10.1002/cphc.201600660] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Indexed: 01/06/2023]
Affiliation(s)
- Divya Sharma
- Institute of Chemical Sciences; School of Engineering and Physical Sciences; Heriot Watt University Edinburgh EH14 4AS United Kingdom
| | - W. M. C. Sameera
- Fukui Institute for Fundamental Chemistry; Kyoto University; Kyoto 606-8103 Japan
- University of Gothenburg; Department of Chemistry and Molecular Biology; Kemigården 4 412 96 Gothenburg Sweden
| | - Stefan Andersson
- University of Gothenburg; Department of Chemistry and Molecular Biology; Kemigården 4 412 96 Gothenburg Sweden
- SINTEF Materials and Chemistry; P.O. Box 4760 7465 Trondheim Norway
| | - Gunnar Nyman
- University of Gothenburg; Department of Chemistry and Molecular Biology; Kemigården 4 412 96 Gothenburg Sweden
| | - Martin J. Paterson
- Institute of Chemical Sciences; School of Engineering and Physical Sciences; Heriot Watt University Edinburgh EH14 4AS United Kingdom
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21
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Mishra P, Verma K, Bawari D, Viswanathan KS. Does borazine-water behave like benzene-water? A matrix isolation infrared and ab initio study. J Chem Phys 2016; 144:234307. [PMID: 27334162 DOI: 10.1063/1.4953793] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Borazine is isoelectronic with benzene and is popularly referred to as inorganic benzene. The study of non-covalent interactions with borazine and comparison with its organic counterpart promises to show interesting similarities and differences. The motivation of the present study of the borazine-water interaction, for the first time, stems from such interesting possibilities. Hydrogen-bonded complexes of borazine and water were studied using matrix isolation infrared spectroscopy and quantum chemical calculations. Computations were performed at M06-2X and MP2 levels of theory using 6-311++G(d,p) and aug-cc-pVDZ basis sets. At both the levels of theory, the complex involving an N-H⋯O interaction, where the N-H of borazine serves as the proton donor to the oxygen of water was found to be the global minimum, in contrast to the benzene-water system, which showed an H-π interaction. The experimentally observed infrared spectra of the complexes corroborated well with our computations for the complex corresponding to the global minimum. In addition to the global minimum, our computations also located two local minima on the borazine-water potential energy surface. Of the two local minima, one corresponded to a structure where the water was the proton donor to the nitrogen of borazine, approaching the borazine ring from above the plane of the ring; a structure that resembled the global minimum in the benzene-water H-π complex. The second local minimum corresponded to an interaction of the oxygen of water with the boron of borazine, which can be termed as the boron bond. Clearly the borazine-water system presents a richer landscape than the benzene-water system.
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Affiliation(s)
- P Mishra
- Department of Chemistry, Indian Institute of Science Education and Research, Sector 81, Mohali, Punjab 140306, India
| | - K Verma
- Department of Chemistry, Indian Institute of Science Education and Research, Sector 81, Mohali, Punjab 140306, India
| | - D Bawari
- Department of Chemistry, Indian Institute of Science Education and Research, Sector 81, Mohali, Punjab 140306, India
| | - K S Viswanathan
- Department of Chemistry, Indian Institute of Science Education and Research, Sector 81, Mohali, Punjab 140306, India
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22
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Hayashi S, Sugibayashi Y, Nakanishi W. Dynamic and static behavior of the H...π and E...π interactions in EH₂ adducts of benzene π-system (E = O, S, Se and Te), elucidated by QTAIM dual functional analysis. Phys Chem Chem Phys 2016; 18:9948-60. [PMID: 26818845 DOI: 10.1039/c5cp06062a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dynamic and static behavior of the interactions in the EH2 adducts of a benzene π-system (E = O, S, Se and Te) is elucidated by applying QTAIM-DFA (QTAIM dual functional analysis). Two types of H-*-π and E-*-π interactions are detected in the adducts, where the asterisk (*) emphasizes the existence of the bond critical point (BCP) on the interaction in question. Total electron energy densities Hb(rc) are plotted versus Hb(rc) -Vb(rc)/2 [=(ℏ(2)/8m)∇(2)ρb(rc)] at BCPs in QTAIM-DFA, where Vb(rc) are the potential energy densities at BCPs. Data from the fully optimized structures are analyzed by polar (R, θ) coordinate representation. Each plot for an interaction, containing data from the perturbed structures with those of the fully optimized one, shows a specific curve, which provides important information. The plot is expressed by (θp, κp): θp corresponds to the tangent line for the plot and κp is the curvature. θ and θp are measured from the y-axis and y-direction, respectively. Moreover, (R, θ) corresponds to the static nature, (θp, κp) represents the dynamic nature of interactions. While θ classifies the interaction in question, θp characterizes it. Both values are less than 90° for all H-*-π and E-*-π interactions examined in this study; therefore, they are all classified by the pure closed-shell interactions and predicted to have the character of vdW nature. However, it is suggested that E-*-π has the nature of the stronger interaction than the case of H-*-π for dynamic behavior in the same species evaluated at the MP2 and M06-2X levels. The nature of the interactions is well analyzed and specified by applying QTAIM-DFA.
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Affiliation(s)
- Satoko Hayashi
- Department of Material Science and Chemistry, Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan.
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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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Pykal M, Jurečka P, Karlický F, Otyepka M. Modelling of graphene functionalization. Phys Chem Chem Phys 2016; 18:6351-72. [DOI: 10.1039/c5cp03599f] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This perspective describes the available theoretical methods and models for simulating graphene functionalization based on quantum and classical mechanics.
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Affiliation(s)
- Martin Pykal
- Regional Centre of Advanced Technologies and Materials
- Department of Physical Chemistry
- Faculty of Science
- Palacký University Olomouc
- 771 46 Olomouc
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials
- Department of Physical Chemistry
- Faculty of Science
- Palacký University Olomouc
- 771 46 Olomouc
| | - František Karlický
- Regional Centre of Advanced Technologies and Materials
- Department of Physical Chemistry
- Faculty of Science
- Palacký University Olomouc
- 771 46 Olomouc
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials
- Department of Physical Chemistry
- Faculty of Science
- Palacký University Olomouc
- 771 46 Olomouc
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26
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Exploration of Brueckner orbital trial wave functions in diffusion Monte Carlo calculations. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2015.11.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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27
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Gillan MJ, Alfè D, Manby FR. Energy benchmarks for methane-water systems from quantum Monte Carlo and second-order Møller-Plesset calculations. J Chem Phys 2015; 143:102812. [PMID: 26374005 DOI: 10.1063/1.4926444] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The quantum Monte Carlo (QMC) technique is used to generate accurate energy benchmarks for methane-water clusters containing a single methane monomer and up to 20 water monomers. The benchmarks for each type of cluster are computed for a set of geometries drawn from molecular dynamics simulations. The accuracy of QMC is expected to be comparable with that of coupled-cluster calculations, and this is confirmed by comparisons for the CH4-H2O dimer. The benchmarks are used to assess the accuracy of the second-order Møller-Plesset (MP2) approximation close to the complete basis-set limit. A recently developed embedded many-body technique is shown to give an efficient procedure for computing basis-set converged MP2 energies for the large clusters. It is found that MP2 values for the methane binding energies and the cohesive energies of the water clusters without methane are in close agreement with the QMC benchmarks, but the agreement is aided by partial cancelation between 2-body and beyond-2-body errors of MP2. The embedding approach allows MP2 to be applied without loss of accuracy to the methane hydrate crystal, and it is shown that the resulting methane binding energy and the cohesive energy of the water lattice agree almost exactly with recently reported QMC values.
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Affiliation(s)
- M J Gillan
- London Centre for Nanotechnology, University College London, Gordon St., London WC1H 0AH, United Kingdom
| | - D Alfè
- London Centre for Nanotechnology, University College London, Gordon St., London WC1H 0AH, United Kingdom
| | - F R Manby
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
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28
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Al-Hamdani YS, Alfè D, von Lilienfeld OA, Michaelides A. Water on BN doped benzene: a hard test for exchange-correlation functionals and the impact of exact exchange on weak binding. J Chem Phys 2015; 141:18C530. [PMID: 25399195 DOI: 10.1063/1.4898356] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Density functional theory (DFT) studies of weakly interacting complexes have recently focused on the importance of van der Waals dispersion forces, whereas the role of exchange has received far less attention. Here, by exploiting the subtle binding between water and a boron and nitrogen doped benzene derivative (1,2-azaborine) we show how exact exchange can alter the binding conformation within a complex. Benchmark values have been calculated for three orientations of the water monomer on 1,2-azaborine from explicitly correlated quantum chemical methods, and we have also used diffusion quantum Monte Carlo. For a host of popular DFT exchange-correlation functionals we show that the lack of exact exchange leads to the wrong lowest energy orientation of water on 1,2-azaborine. As such, we suggest that a high proportion of exact exchange and the associated improvement in the electronic structure could be needed for the accurate prediction of physisorption sites on doped surfaces and in complex organic molecules. Meanwhile to predict correct absolute interaction energies an accurate description of exchange needs to be augmented by dispersion inclusive functionals, and certain non-local van der Waals functionals (optB88- and optB86b-vdW) perform very well for absolute interaction energies. Through a comparison with water on benzene and borazine (B3N3H6) we show that these results could have implications for the interaction of water with doped graphene surfaces, and suggest a possible way of tuning the interaction energy.
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Affiliation(s)
- Yasmine S Al-Hamdani
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Dario Alfè
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - O Anatole von Lilienfeld
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Angelos Michaelides
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
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29
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Al-Hamdani YS, Ma M, Alfè D, von Lilienfeld OA, Michaelides A. Communication: Water on hexagonal boron nitride from diffusion Monte Carlo. J Chem Phys 2015; 142:181101. [PMID: 25978876 DOI: 10.1063/1.4921106] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Despite a recent flurry of experimental and simulation studies, an accurate estimate of the interaction strength of water molecules with hexagonal boron nitride is lacking. Here, we report quantum Monte Carlo results for the adsorption of a water monomer on a periodic hexagonal boron nitride sheet, which yield a water monomer interaction energy of -84 ± 5 meV. We use the results to evaluate the performance of several widely used density functional theory (DFT) exchange correlation functionals and find that they all deviate substantially. Differences in interaction energies between different adsorption sites are however better reproduced by DFT.
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Affiliation(s)
- Yasmine S Al-Hamdani
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Ming Ma
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Dario Alfè
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - O Anatole von Lilienfeld
- Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials, Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Angelos Michaelides
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
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30
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Wu Y, Wagner LK, Aluru NR. The interaction between hexagonal boron nitride and water from first principles. J Chem Phys 2015; 142:234702. [DOI: 10.1063/1.4922491] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Yanbin Wu
- Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Lucas K. Wagner
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3080, USA
| | - Narayana R. Aluru
- Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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31
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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.
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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
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32
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Cox SJ, Towler MD, Alfè D, Michaelides A. Benchmarking the performance of density functional theory and point charge force fields in their description of sI methane hydrate against diffusion Monte Carlo. J Chem Phys 2015; 140:174703. [PMID: 24811651 DOI: 10.1063/1.4871873] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
High quality reference data from diffusion Monte Carlo calculations are presented for bulk sI methane hydrate, a complex crystal exhibiting both hydrogen-bond and dispersion dominated interactions. The performance of some commonly used exchange-correlation functionals and all-atom point charge force fields is evaluated. Our results show that none of the exchange-correlation functionals tested are sufficient to describe both the energetics and the structure of methane hydrate accurately, while the point charge force fields perform badly in their description of the cohesive energy but fair well for the dissociation energetics. By comparing to ice Ih, we show that a good prediction of the volume and cohesive energies for the hydrate relies primarily on an accurate description of the hydrogen bonded water framework, but that to correctly predict stability of the hydrate with respect to dissociation to ice Ih and methane gas, accuracy in the water-methane interaction is also required. Our results highlight the difficulty that density functional theory faces in describing both the hydrogen bonded water framework and the dispersion bound methane.
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Affiliation(s)
- Stephen J Cox
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Michael D Towler
- Department of Earth Sciences, University College London Gower Street, London WC1E 6BT, United Kingdom
| | - Dario Alfè
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Angelos Michaelides
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
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33
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Hussain HB, Wilson KA, Wetmore SD. Serine and Cysteine π-Interactions in Nature: A Comparison of the Frequency, Structure, and Stability of Contacts Involving Oxygen and Sulfur. Aust J Chem 2015. [DOI: 10.1071/ch14598] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Despite many DNA–protein π-interactions in high-resolution crystal structures, only four X–H···π or X···π interactions were found between serine (Ser) or cysteine (Cys) and DNA nucleobase π-systems in over 100 DNA–protein complexes (where X = O for Ser and X = S for Cys). Nevertheless, 126 non-covalent contacts occur between Ser or Cys and the aromatic amino acids in many binding arrangements within proteins. Furthermore, Ser and Cys protein–protein π-interactions occur with similar frequencies and strengths. Most importantly, due to the great stability that can be provided to biological macromolecules (up to –20 kJ mol–1 for neutral π-systems or –40 kJ mol–1 for cationic π-systems), Ser and Cys π-interactions should be considered when analyzing protein stability and function.
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34
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Wang C, Jiang Y, Zhang R, Lin Z. Intermolecular π/π and H/π interactions in dimers researched by different computational methods. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2014. [DOI: 10.1142/s0219633614500576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The analysis of π/π and H /π interactions in complexes are a challenging aspect of theoretical research. Due to the different approximations of different levels of theory, results tend to be inconsistent. We compared the reliabilities of HF, SVWN, M06L, PW91, BLYP, B3LYP, BHandHLYP, B97D, MP2, and DFTB-D approaches in researching π/π and H /π interactions by calculating the binding energies of five benzene-containing dimers. The effects of 6-31+G**, 6-311++G** and 6-311++G(2df,2p) basis sets on the results were analyzed too. We found that the DFTB-D and B97D methods combined with the 6-311++G** basis set perform well for dimers that contain π/π and H /π interactions. With high efficiency and satisfactory precision, DFTB-D is helpful for the calculation of complexes containing π/π and H /π stacking. We further calculated the structures and properties of phenylalanine-containing dimers using the DFTB-D and B97D methods. The properties of low energy conformers such as rotational constants, dipole moments and molecular orbitals were also analyzed. These data should be helpful for research into systems that contain π/π and H /π stacking.
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Affiliation(s)
- Cuihong Wang
- School of Science, TianJin ChengJian University, Tianjin 300384, P. R. China
| | - Yue Jiang
- School of Science, TianJin ChengJian University, Tianjin 300384, P. R. China
| | - Ruiqin Zhang
- Department of Physics and Materials Science, City University of Hong Kong, Hong Kong, P. R. China
| | - Zijing Lin
- Department of Physics & Collaborative Innovation Center of Suzhou Nano Science and Technology, University of Science and Technology of China, Hefei 230026, P. R. China
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35
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Gadre SR, Yeole SD, Sahu N. Quantum chemical investigations on molecular clusters. Chem Rev 2014; 114:12132-73. [PMID: 25341561 DOI: 10.1021/cr4006632] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Shridhar R Gadre
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208 016, India
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36
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Dubecký M, Derian R, Jurečka P, Mitas L, Hobza P, Otyepka M. Quantum Monte Carlo for noncovalent interactions: an efficient protocol attaining benchmark accuracy. Phys Chem Chem Phys 2014; 16:20915-23. [DOI: 10.1039/c4cp02093f] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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38
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Gillan MJ, Alfè D, Bartók AP, Csányi G. First-principles energetics of water clusters and ice: A many-body analysis. J Chem Phys 2013; 139:244504. [DOI: 10.1063/1.4852182] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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39
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Dubecký M, Jurečka P, Derian R, Hobza P, Otyepka M, Mitas L. Quantum Monte Carlo Methods Describe Noncovalent Interactions with Subchemical Accuracy. J Chem Theory Comput 2013; 9:4287-92. [DOI: 10.1021/ct4006739] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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
| | - 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
| | - René Derian
- Institute
of Physics, Slovak Academy of Sciences, Dúbravská cesta 9, 845
11 Bratislava, Slovakia
| | - Pavel Hobza
- 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
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo
nám. 2, 166 10 Prague 6, Czech Republic
| | - Michal Otyepka
- 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
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40
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Xu J, Deible MJ, Peterson KA, Jordan KD. Correlation Consistent Gaussian Basis Sets for H, B–Ne with Dirac–Fock AREP Pseudopotentials: Applications in Quantum Monte Carlo Calculations. J Chem Theory Comput 2013; 9:2170-8. [DOI: 10.1021/ct300983b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jiawei Xu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania
15218, United States
| | - Michael J. Deible
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania
15218, United States
| | - Kirk A. Peterson
- Department
of Chemistry, Washington State University, Pullman, Washington 99164,
United States
| | - Kenneth D. Jordan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania
15218, United States
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41
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Granatier J, Dubecký M, Lazar P, Otyepka M, Hobza P. Spin-Crossing in an Organometallic Pt–Benzene Complex. J Chem Theory Comput 2013; 9:1461-8. [DOI: 10.1021/ct400016c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Jaroslav Granatier
- Institute of Organic Chemistry and
Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo
nám. 2, 166 10 Prague 6, Czech Republic
| | - 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
- Institute of Electrical
Engineering, Slovak Academy of Sciences, Dúbravská cesta
9, 841 04 Bratislava, Slovakia
| | - Petr Lazar
- 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
| | - Michal Otyepka
- 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
| | - Pavel Hobza
- Institute of Organic Chemistry and
Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo
nám. 2, 166 10 Prague 6, Czech Republic
- 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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42
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Wu Y, Dai X, Huang N, Zhao L. A partition function-based weighting scheme in force field parameter development usingab initiocalculation results in global configurational space. J Comput Chem 2013; 34:1271-82. [DOI: 10.1002/jcc.23249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 01/16/2013] [Accepted: 01/20/2013] [Indexed: 11/09/2022]
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43
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Zhang M, Zhao J, Liu J, Zhou L, Bu Y. Coexistence of solvated electron and benzene-centered valence anion in the negatively charged benzene-water clusters. J Chem Phys 2013; 138:014310. [PMID: 23298044 DOI: 10.1063/1.4773398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a combined M06 functional calculation and ab initio molecular dynamics simulation study of an excess electron (EE) in a microhydrated aromatic complex (modeled by benzene (Bz)-water binary clusters, Bz(H(2)O)(n)). Calculated results illustrate that Bz ring and water clusters are indeed linked through the π···HO interactions in the neutral Bz(H(2)O)(n) (n = 1-8) clusters, and the size of the water cluster does not influence the nature of its interaction with the π system for the oligo-hydrated complexes. The states and the dynamics of an EE trapped in such Bz-water clusters were also determined. All of possible localized states for the EE can be roughly classified into two types: (i) single, ring-localized states (the Bz-centered valence anions) in which an EE occupies the LUMO of the complexes originating from the LUMO (π*) of the Bz ring, and the π···HO interactions are enhanced for increase of electron density of the Bz ring. In this mode, the carbon skeleton of the Bz part is significantly deformed due to increase of electron density and nonsymmetric distribution of electron density induced by the interacting H-O bonds; (ii) solvated states, in which an EE is trapped directly as a surface state by the dangling hydrogen atoms of water molecules or as a solvated state in a mixed cavity formed by Bz and water cluster. In the latter case, Bz may also participate in capturing an EE using its C-H bonds in the side edge of the aromatic ring as a part of the cavity. In general, a small water cluster is favorable to the Bz-centered valence anion state, while a large one prefers a solvated electron state. Fluctuations and rearrangement of water molecules can sufficiently modify the relative energies of the EE states to permit facile conversion from the Bz-centered to the water cluster-centered state. This indicates that aromatic Bz can be identified as a stepping stone in electron transfer and the weak π···HO interaction plays an important role as the driving force in conversion of the two states.
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Affiliation(s)
- Meng Zhang
- The Center for Modeling and Simulation Chemistry, Institute of Theoretical Chemistry, Shandong University, Jinan 250100, People's Republic of China
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44
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Oltean M, Mile G, Vidrighin M, Leopold N, Chiş V. Weakly bound PTCDI and PTCDA dimers studied by using MP2 and DFT methods with dispersion correction. Phys Chem Chem Phys 2013; 15:13978-90. [DOI: 10.1039/c3cp44644a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Gao W, Jiao J, Feng H, Xuan X, Chen L. Natures of benzene-water and pyrrole-water interactions in the forms of σ and π types: theoretical studies from clusters to liquid mixture. J Mol Model 2012. [DOI: 10.1007/s00894-012-1659-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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46
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Tkatchenko A, Alfè D, Kim KS. First-Principles Modeling of Non-Covalent Interactions in Supramolecular Systems: The Role of Many-Body Effects. J Chem Theory Comput 2012; 8:4317-22. [DOI: 10.1021/ct300711r] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195,
Berlin, Germany
- Department
of Chemistry, Pohang University of Science and Technology, Pohang
790−784, South Korea
| | - Dario Alfè
- London Centre for Nanotechnology, University College London, London WC1E 6BT, United
Kingdom
| | - Kwang S. Kim
- Department
of Chemistry, Pohang University of Science and Technology, Pohang
790−784, South Korea
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47
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Gillan MJ, Manby FR, Towler MD, Alfè D. Assessing the accuracy of quantum Monte Carlo and density functional theory for energetics of small water clusters. J Chem Phys 2012; 136:244105. [DOI: 10.1063/1.4730035] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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48
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Albertí M, Faginas Lago N, Pirani F. Benzene water interaction: From gaseous dimers to solvated aggregates. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2011.08.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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49
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Copeland KL, Tschumper GS. Hydrocarbon/Water Interactions: Encouraging Energetics and Structures from DFT but Disconcerting Discrepancies for Hessian Indices. J Chem Theory Comput 2012; 8:1646-56. [DOI: 10.1021/ct300132e] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Kari L. Copeland
- Department
of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677-1848 United
States
| | - Gregory S. Tschumper
- Department
of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677-1848 United
States
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50
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Prakash M, Gopalsamy K, Subramanian V. Studies on the structure, stability, and spectral signatures of hydride ion-water clusters. J Chem Phys 2012; 135:214308. [PMID: 22149793 DOI: 10.1063/1.3663708] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The gas-phase structure, stability, spectra, and electron density topography of H(-)W(n) clusters (where n = 1-8) have been calculated using coupled-cluster CCSD(T) and Møller-Plesset second-order perturbation (MP2) theory combined with complete basis set (CBS) approaches. The performance of various density functional theory (DFT) based methods such as B3LYP, M05-2X, M06, M06-L, and M06-2X using 6-311++G(d,p), and aug-cc-pVXZ (aVXZ, where X = D, T, and Q) basis sets has also been assessed by considering values calculated using CCSD(T)/CBS limit as reference. The performance of the functionals has been ranked based on the mean signed/unsigned error. The comparison of geometrical parameters elicits that the geometrical parameters predicted by B3LYP/aVTZ method are in good agreement with those values obtained at MP2/aVTZ level of theory. Results show that M05-2X functional outperform other functionals in predicting the energetics when compared to CCSD(T)/CBS value. On the other hand, values predicted by M06-2X, and M06 methods, are closer to those values obtained from MP2/CBS approach. It is evident from the calculations that H(-)W(n) (where n = 5-8) clusters adopt several interesting structural motifs such as pyramidal, prism, book, Clessidra, cubic, cage, and bag. The important role played by ion-water (O-H···H(-)) and water-water (O-H···O) interactions in determining the stability of the clusters has also been observed. Analysis of the results indicates that the most stable cluster is made up of minimum number of O-H···H(-) interaction in conjugation with the maximum number of O-H···O interactions. The Bader theory of atoms in molecules (AIM) and natural bond orbital (NBO) analyses has also been carried out to characterize the nature of interactions between hydride ion and water molecules. It can be observed from the vibrational spectra of H(-)W(n) clusters, the stretching frequencies involving ion-water interaction always exhibit larger redshift and intensities than that of water-water (inter solvent) interactions.
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Affiliation(s)
- M Prakash
- Chemical Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai 600 020, India
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