51
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Ouyang W, Azuri I, Mandelli D, Tkatchenko A, Kronik L, Urbakh M, Hod O. Mechanical and Tribological Properties of Layered Materials under High Pressure: Assessing the Importance of Many-Body Dispersion Effects. J Chem Theory Comput 2019; 16:666-676. [DOI: 10.1021/acs.jctc.9b00908] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wengen Ouyang
- School of Chemistry and The Sackler Center for Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ido Azuri
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovoth 76100, Israel
| | - Davide Mandelli
- Istituto Italiano di Tecnologia, Via Morego, 30, 16163 Genova, Italy
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Leeor Kronik
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovoth 76100, Israel
| | - Michael Urbakh
- School of Chemistry and The Sackler Center for Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Oded Hod
- School of Chemistry and The Sackler Center for Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv 6997801, Israel
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52
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Gu J, Huang L, Liu S. Ultralow lattice thermal conductivity and high thermoelectric performance of monolayer KCuTe: a first principles study. RSC Adv 2019; 9:36301-36307. [PMID: 35540616 PMCID: PMC9074958 DOI: 10.1039/c9ra07828b] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/01/2019] [Indexed: 12/17/2022] Open
Abstract
Monolayer KCuTe is a new-type of two-dimensional (2D) semiconductor material with high carrier mobility and large power energy conversion efficiencies, suggesting its potential application in thermoelectric (TE) and photoelectric fields. Based on the density functional theory (DFT) and semiclassical Boltzmann transport equation, the electronic and phonon transport properties of monolayer KCuTe are systematically studied. Our results show that it possesses an ultralow lattice thermal conductivity value of nearly ∼0.13 W m−1 K−1 at 300 K, mainly attributed to its small phonon group velocity, large Grüneisen parameters, and strong phonon–phonon scattering. Furthermore, the intralayer opposite phonon vibrations greatly restrict the heat transport. Monolayer KCuTe shows an ideal direct band gap of ∼1.21 eV, and a high twofold degeneracy appearing at the Γ point gives a high Seebeck coefficient of ∼2070 μV K−1, leading to high TE performance. Using the transport coefficients together with constant electron relaxation time, the figure of merit (ZT) can reach 2.71 at 700 K for the p-type doping, which is comparable to the well-known TE material SnSe (2.6 ± 0.3 at 935 K). Our theoretical studies may provide perspectives to TE applications of monolayer KCuTe and stimulate further experimental synthesis. The excellent thermoelectric performance of monolayer KCuTe is discovered by first-principles study for the first time.![]()
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Affiliation(s)
- Jinjie Gu
- Hunan Provincial Key Laboratory of Finance & Economics Big Data Science and Technology, School of Information Technology and Management, Hunan University of Finance and Economics Changsha 410205 P. R. China
| | - Lirong Huang
- Hunan Provincial Key Laboratory of Finance & Economics Big Data Science and Technology, School of Information Technology and Management, Hunan University of Finance and Economics Changsha 410205 P. R. China
| | - Shengzong Liu
- Hunan Provincial Key Laboratory of Finance & Economics Big Data Science and Technology, School of Information Technology and Management, Hunan University of Finance and Economics Changsha 410205 P. R. China
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53
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Xu W, Wang R, Zheng B, Wu X, Xu H. Two-Dimensional Li-Based Ternary Chalcogenides for Photocatalysis. J Phys Chem Lett 2019; 10:6061-6066. [PMID: 31537065 DOI: 10.1021/acs.jpclett.9b02340] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Motivated by fundamental interest and practical applications, the investigations of two-dimensional photocatalysts are fascinating subjects in clean energy. Herein, we propose that two-dimensional Li-based ternary chalcogenides LiXY2 (X = Al, Ga, In; Y = S, Se, Te) have intrinsic polarization and direct band gaps. Our results show that LiXY2 materials possess optical absorption spectra covering the visible and ultraviolet range. We show that these materials possess extremely high electron mobility (∼103 cm2 V-1 s-1), providing great potential in overall water splitting. Furthermore, LiAlS2 and LiGaS2 can facilitate overall water splitting regardless of their energy gaps because of the large differences of surface electronic potentials of LiXY2. Importantly, it is feasible to exfoliate the layered LiAlTe2 from its bulk counterpart in experiments. Our findings open an exotic pathway to realizing promising photocatalytic applications in two-dimensional ternary materials.
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Affiliation(s)
- Wangping Xu
- Department of Physics , Chongqing University , Chongqing 401331 , China
- Department of Physics and Institute for Quantum Science and Engineering , Southern University of Science and Technology , Shenzhen 518055 , China
| | - Rui Wang
- Department of Physics , Chongqing University , Chongqing 401331 , China
| | - Baobing Zheng
- Department of Physics and Institute for Quantum Science and Engineering , Southern University of Science and Technology , Shenzhen 518055 , China
| | - Xiaozhi Wu
- Department of Physics , Chongqing University , Chongqing 401331 , China
| | - Hu Xu
- Department of Physics and Institute for Quantum Science and Engineering , Southern University of Science and Technology , Shenzhen 518055 , China
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54
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Lokhande PKM, Patil DS, Kadam MM, Sekar N. Theoretical Investigation of Optical and Nonlinear Optical (NLO) Properties of 3‐Azabenzanthrone Analogues : DFT and TD‐DFT Approach. ChemistrySelect 2019. [DOI: 10.1002/slct.201901681] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Prerana K M. Lokhande
- Department of Dyestuff TechnologyInstitute of Chemical Technology, Matunga Mumbai- 400 019 India
| | - Dinesh S. Patil
- Department of Dyestuff TechnologyInstitute of Chemical Technology, Matunga Mumbai- 400 019 India
| | - Mayuri M Kadam
- Department of Dyestuff TechnologyInstitute of Chemical Technology, Matunga Mumbai- 400 019 India
| | - Nagaiyan Sekar
- Department of Dyestuff TechnologyInstitute of Chemical Technology, Matunga Mumbai- 400 019 India
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55
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Apostolidou C. OH radical in water from ab initio molecular dynamics simulation employing hybrid functionals. J Chem Phys 2019. [DOI: 10.1063/1.5107479] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Christina Apostolidou
- Mulliken Center for Theoretical Chemistry, Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
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56
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Abstract
Calculations on the Cu24(m-BDC)24 (m-BDC = 1,3-benzenedicarboxylate) polyoxometalate (POM) cage with 0, 12, 24, and 40 methane molecules inside were made using the M06 exchange/correlation functional. During filling of the cage with 40 CH4 molecules, the 12 strongest binding CH4 molecules are those to the coordination unsaturated sites (CUS) to the inwardly directed Cu(+2) centers via agostic interactions. The next 12 CH4 molecules are less tightly bound followed by the next 16 CH4 molecules with average binding energies of 8.27, 7.88, and 7.36 kcal/mol per CH4, respectively. A section of the Cu24(m-BDC)24 cage was taken with the formula Cu4(m-BDC)(BC)6 (BC = benezenecarboxylate) in order to estimate zero-point, thermal, and entropy corrections of the larger cage. Estimating free energies at 1 bar, the Cu24(m-BDC)24 POM is predicted to lose 16, 12, and 12 CH4 molecules at 67, 123, and 171 °C, respectively. The 40CH4@Cu24(m-BDC)24 cage, which is isostructural to the main cavity of HKUST-1 with 40 CH4 molecules inside, is predicted to have a loading of 224 cm3(STP) cm-3 at 1 bar.
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Affiliation(s)
- Michael L McKee
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
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57
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Lenchuk O, Adelhelm P, Mollenhauer D. Comparative study of density functionals for the description of lithium-graphite intercalation compounds. J Comput Chem 2019; 40:2400-2412. [PMID: 31254474 DOI: 10.1002/jcc.26017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/17/2019] [Accepted: 06/14/2019] [Indexed: 01/18/2023]
Abstract
The lack of description of van der Waals interactions in layered materials such as graphite and binary graphite intercalation compounds remains a main drawback of conventional density functional theory. Two fundamentally different approaches to overcome this issue are the employment of semiempirical dispersion correction scheme such as Grimme dispersion correction or nonlocal density functionals. We carefully compare these two approaches for the description of the geometric structure and the thermodynamic stability of pure graphite and Li-GICs at different lithium concentrations and stages. Based on the computed formation energies, we also evaluate the lithium-graphite intercalation potential. We find that PBE-D3(BJ) accurately reproduces the lattice parameters and the interlayer binding energy of graphite, although it underestimates the thermodynamic stability of stage-II Li-GICs mainly due to overbinding of carbon atoms in pure graphite. The nonlocal van der Waals functionals optB88-vdW, optB86b-vdW, and revPBE-vdW show a good agreement with experiments concerning stability of Li-GICs of different stages, although they overestimate the van der Waals interactions in graphite. The experimentally determined decreasing step-function behavior of Li-graphite intercalation potential can be qualitatively reproduced only by employing the revPBE van der Waals functional, whereas the other density functionals fail in the description. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Olena Lenchuk
- Institute of Physical Chemistry, Heinrich-Buff-Ring 17, Justus-Liebig-University Giessen, 35392, Giessen, Germany.,Center for Materials Research (LaMa), Justus-Liebig-University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
| | - Philipp Adelhelm
- Institute of Technical Chemistry and Environmental Chemistry, CEEC Jena, Friedrich-Schiller University Jena, 07743, Jena, Germany
| | - Doreen Mollenhauer
- Institute of Physical Chemistry, Heinrich-Buff-Ring 17, Justus-Liebig-University Giessen, 35392, Giessen, Germany.,Center for Materials Research (LaMa), Justus-Liebig-University Giessen, Heinrich-Buff-Ring 16, 35392, Giessen, Germany
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58
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Besrour H, Tangour B, Linguerri R, Hochlaf M. Encapsulation of anticancer drug doxorubicin inside dendritic macromolecular cavities: First-principles benchmarks. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 217:278-287. [PMID: 30952094 DOI: 10.1016/j.saa.2019.03.083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 03/24/2019] [Indexed: 06/09/2023]
Abstract
By using first-principles approaches based on Density Functional Theory, we explore the possibility of using dendritic macromolecular structures as carriers of the doxorubicin anticancer drug. In particular, we consider macromolecular cavities of different sizes composed of phenylene-, thiophene-, phenyl-cored thiophen- and thioazole-based dendrimers. The comparison between the optimized molecular geometries of the monomers and of the host-guest complexes reveals that only slight structural changes are observed in doxorubicin upon complexation. Also, the encapsulation energies for the host-guest complexes suggest that these systems are of potential use for pharmacology applications in vivo. The interaction of the guest doxorubicin with the macromolecular cavities exploits different types of weak intermolecular forces including σ, π and hydrogen bond interactions. The electronic structure of these complexes is discussed, with particular emphasis placed on the role of the charge distribution and the nature of the frontier molecular orbitals in the encapsulation process. Spectroscopic properties of these complexes are derived to facilitate their detection in laboratory and in vivo. These include IR vibrational frequencies, absorption wavelengths and relative oscillator strengths for the main transitions in the UV-Vis spectrum.
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Affiliation(s)
- Hatem Besrour
- Université de Tunis Al Manar, Research Unit of Modeling in Fundamental Sciences and Didactic Team of Theoretical Chemistry, Tunis 1060, Tunisia
| | - Bahoueddine Tangour
- Université de Tunis Al Manar, Research Unit of Modeling in Fundamental Sciences and Didactic Team of Theoretical Chemistry, Tunis 1060, Tunisia
| | - Roberto Linguerri
- Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallée, France
| | - Majdi Hochlaf
- Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallée, France.
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59
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Xu W, Wang R, Zheng B, Wu X, Xu H. New Family of Two-Dimensional Ternary Photoelectric Materials. ACS APPLIED MATERIALS & INTERFACES 2019; 11:14457-14462. [PMID: 30912921 DOI: 10.1021/acsami.9b00969] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Screening unique two-dimensional (2D) materials with high mobility and applicable band gaps is motivated by not only the interest in basic science but also the practical applications for photoelectric materials. In this work, we have systematically studied a new family of 2D ternary quintuple layers (QLs), named ABC (A = Na, K, and Rb; B = Cu, Ag, and Au; C = S, Se, and Te). Our results indicate that the QLs of KCuTe, KAgS, KAgSe, KAuTe, RbCuTe, RbAgSe, and RbAgTe host direct band gaps. Moreover, KCuTe, RbCuTe, and RbAgTe QLs show extremely high mobilities of ∼104 cm2 V-1 s-1. Interestingly, the linear scaling between exciton binding energy and quasiparticle band gap for ABC QLs exhibits an unexpected deviation with the 1/4 law. In addition, KAgSe, KAgS, RbAgSe, and RbAgTe show outstanding power energy conversion efficiencies of up to 21.5%, suggesting that they are good potential donor materials. Our results provide many potential candidates for applications in photoelectric materials, which may be realized in experiments due to the possible exfoliation from their parent compounds.
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Affiliation(s)
- Wangping Xu
- Department of Physics , Chongqing University , Chongqing 401331 , China
- Department of Physics & Shenzhen Key Laboratory of Quantum Science and Engineering , Southern University of Science and Technology , Shenzhen 518055 , China
| | - Rui Wang
- Department of Physics , Chongqing University , Chongqing 401331 , China
| | - Baobing Zheng
- Department of Physics & Shenzhen Key Laboratory of Quantum Science and Engineering , Southern University of Science and Technology , Shenzhen 518055 , China
- College of Physics and Optoelectronic Technology & Advanced Titanium Alloys and Functional Coatings Cooperative Innovation Center , Baoji University of Arts and Sciences , Baoji 721016 , China
| | - Xiaozhi Wu
- Department of Physics , Chongqing University , Chongqing 401331 , China
| | - Hu Xu
- Department of Physics & Shenzhen Key Laboratory of Quantum Science and Engineering , Southern University of Science and Technology , Shenzhen 518055 , China
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60
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Cassone G, Kruse H, Sponer J. Interactions between cyclic nucleotides and common cations: an ab initio molecular dynamics study. Phys Chem Chem Phys 2019; 21:8121-8132. [PMID: 30932112 DOI: 10.1039/c8cp07492e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We present the first, to the best of our knowledge, ab initio molecular dynamics (AIMD) investigation on three aqueous solutions where an abasic cyclic nucleotide model is solvated in the presence of distinct cations (i.e., Na+, K+ and Mg2+). We elucidate the typical modalities of interaction between those ionic species and the nucleotide moiety by first-principles numerical simulations, starting from an inner-shell binding configuration on a time scale of 100 ps (total simulation time of ∼600 ps). Whereas the strong "structure-maker" Mg2+ is permanently bound to one of the two oxygen atoms of the phosphate group of the nucleotide model, Na+ and K+ show binding times τb of 65 ps and 10-15 ps, respectively, thus reflecting their chemical nature in aqueous solutions. Furthermore, we qualitatively relate these findings to approximate free-energy barriers of the cations' unbinding obtained by means of exploratory well-tempered metadynamics. With the aim of shedding light on the features of commonly employed force-fields (FFs), classical MD simulations (almost 200 trajectories with a total simulation time of ∼18 μs) using the biomolecular AMBER FF are also reported. By choosing several combinations of the parametrization for the water environment (i.e., TIP3P, SPC/E and OPC) and cations (i.e., Joung-Cheatham, Li-Merz 12-6 and Li-Merz 12-6-4), we found significant differences in the radial distribution functions and residence times compared to the ab initio results. The Na+ and K+ ions wrongly show quasi-identical radial distribution functions and the Li & Merz 12-6-4 Lennard-Jones parameters for Mg2+ were found to be essential in quickly reaching the binding state consistent with AIMD.
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Affiliation(s)
- Giuseppe Cassone
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i, Královopolská 135, 61265 Brno, Czech Republic.
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61
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Xavier S, Narayanan S, Anjali C, Sreekumar K. Theoretical design, synthesis and studies on the solvatochromic behaviour of low band gap phenylenevinylene based copolymers. Eur Polym J 2019. [DOI: 10.1016/j.eurpolymj.2019.01.071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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62
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Boydas EB, Tanriver G, D'hooghe M, Ha HJ, Van Speybroeck V, Catak S. Theoretical insight into the regioselective ring-expansions of bicyclic aziridinium ions. Org Biomol Chem 2019; 16:796-806. [PMID: 29323389 DOI: 10.1039/c7ob02253k] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Transient bicyclic aziridinium ions are known to undergo ring-expansion reactions, paving the way to functionalized nitrogen-containing heterocycles. In this study, the regioselectivity observed in the ring-expansion reactions of 1-azoniabicyclo[n.1.0]alkanes was investigated from a computational viewpoint to study the ring-expansion pathways of two bicyclic systems with different ring sizes. Moreover, several nucleophiles leading to different experimental results were investigated. The effect of solvation was taken into account using both explicit and implicit solvent models. This theoretical rationalization provides valuable insight into the observed regioselectivity and may be used as a predictive tool in future studies.
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Affiliation(s)
- Esma B Boydas
- Bogazici University, Department of Chemistry, Bebek, 34342 Istanbul, Turkey.
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63
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Kozłowska J, Schwilk M, Roztoczyńska A, Bartkowiak W. Assessment of DFT for endohedral complexes' dipole moment: PNO-LCCSD-F12 as a reference method. Phys Chem Chem Phys 2018; 20:29374-29388. [PMID: 30451255 DOI: 10.1039/c8cp05928d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a systematic evaluation of the performance of a wide range of exchange-correlation functionals and related dispersion correction schemes for the computation of dipole moments of endohedral complexes, formed through the encapsulation of an AB molecule (AB = LiF, HCl) inside carbon nanotubes (CNTs) of different diameter. The consistency and accuracy of (i) generalized gradient approximation, (ii) meta GGA, (iii) global hybrid, and (iv) range-separated hybrid density functionals are assessed. In total, 37 density functionals are tested. The results obtained using the highly accurate pair natural orbitals based explicitly correlated local coupled cluster singles doubles (PNO-LCCSD-F12) method of Werner and co-workers [Schwilk et al., J. Chem. Theory Comput., 2017, 13, 3650; Ma et al., J. Chem. Theory Comput., 2017, 13, 4871] with the aug-cc-pVTZ basis set serve as a reference. The static electric dipole moment is computed via the finite field response or, when possible, as the expectation value of the dipole operator. Among others, it is shown that functionals belonging to the class of range-separated hybrids, provide results closest to the coupled cluster reference data. In particular, the ωB97X as well as the M11 functional may be considered as a promising choice for computing electric properties of noncovalent endohedral complexes. On the other hand, the worst performance was found for the functionals which do not include the Hartree-Fock exchange. The analysis of both the coupled cluster and the DFT results indicates a strong coupling of dispersion and polarization that may also explain why lower level DFT methods, as well as Hartree-Fock and MP2, cannot yield dipole moments beyond a qualitative agreement with the higher order reference data. Interestingly, the much smaller and less systematically constructed basis sets of Pople of moderate size provide results of accuracy at least comparable with the extended Dunning's aug-cc-pVTZ basis set.
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Affiliation(s)
- Justyna Kozłowska
- Department of Physical and Quantum Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, PL-50370 Wrocław, Poland.
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64
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Mohbiya DR, Sekar N. Electronic structure and spectral properties of indole based fluorescent styryl dyes: Comprehensive study on linear and non-linear optical properties by DFT/TDDFT method. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.07.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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65
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Cassone G, Creazzo F, Saija F. Ionic diffusion and proton transfer of MgCl2 and CaCl2 aqueous solutions: an ab initio study under electric field. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1513650] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Giuseppe Cassone
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Fabrizio Creazzo
- Université d'Evry val d'Essonne-Université Paris-Saclay, Evry, France
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66
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Kleshchonok A, Tkatchenko A. Tailoring van der Waals dispersion interactions with external electric charges. Nat Commun 2018; 9:3017. [PMID: 30069005 PMCID: PMC6070553 DOI: 10.1038/s41467-018-05407-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 07/05/2018] [Indexed: 11/09/2022] Open
Abstract
van der Waals (vdW) dispersion interactions strongly impact the properties of molecules and materials. Often, the description of vdW interactions should account for the coupling with pervasive electric fields, stemming from membranes, ionic channels, liquids, or nearby charged functional groups. However, this quantum-mechanical effect has been omitted in atomistic simulations, even in widely employed electronic-structure methods. Here, we develop a model and study the effects of an external charge on long-range vdW correlations. We show that a positive external charge stabilizes dispersion interactions, whereas a negative charge has an opposite effect. Our analytical results are benchmarked on a series of (bio)molecular dimers and supported by calculations with high-level correlated quantum-chemical methods, which estimate the induced dispersion to reach up to 35% of intermolecular binding energy (4 kT for amino-acid dimers at room temperature). Our analysis bridges electrostatic and electrodynamic descriptions of intermolecular interactions and may have implications for non-covalent reactions, exfoliation, dissolution, and permeation through biological membranes.
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Affiliation(s)
- Andrii Kleshchonok
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Alexandre Tkatchenko
- Physics and Materials Science Research Unit, University of Luxembourg, Luxembourg City, L-1511, Luxembourg.
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67
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Cassone G, Šponer J, Saija F, Di Mauro E, Marco Saitta A, Šponer JE. Stability of 2',3' and 3',5' cyclic nucleotides in formamide and in water: a theoretical insight into the factors controlling the accumulation of nucleic acid building blocks in a prebiotic pool. Phys Chem Chem Phys 2018; 19:1817-1825. [PMID: 28000820 DOI: 10.1039/c6cp07993h] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Synthesis of the first RNAs represents one of the cornerstones of the emergence of life. Recent studies demonstrated powerful scenarios of prebiotic synthesis of cyclic nucleotides in aqueous and formamide environments. This raised a question about their thermodynamic stability, a decisive factor determining their accumulation in a prebiotic pool. Here we performed ab initio molecular dynamics simulations at various temperatures in formamide and water to study the relative stabilities of the 2',3' and 3',5' isomers of cyclic nucleotides. The computations show that in an aqueous environment 2',3' cyclic nucleotides are more stable than their 3',5' counterparts at all temperatures up to the boiling point. In contrast, in formamide higher temperatures favor the accumulation of the 3',5' cyclic form, whereas below about 400 K the 2',3' cyclic form becomes more stable. The latter observation is consistent with a formamide-based origin scenario, suggesting that 3',5' cyclic nucleotides accumulated at higher temperatures subsequently allowed oligomerization reactions after fast cooling to lower temperatures. A statistical analysis of the geometrical parameters of the solutes indicates that thermodynamics of cyclic nucleotides in aqueous and formamide environments are dictated by the floppiness of the molecules rather than by the ring strain of the cyclic phosphodiester linkages.
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Affiliation(s)
- Giuseppe Cassone
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic.
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic. and Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17. Listopadu, 1192/12, 771 46 Olomouc, Czech Republic
| | - Franz Saija
- CNR-IPCF, Viale Ferdinando Stagno d'Alcontres 37, 98158 Messina, Italy
| | - Ernesto Di Mauro
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Via San Camillo De Lellis, 01100 Viterbo, Italy
| | - A Marco Saitta
- Sorbonne Universités, Université Pierre et Marie Curie Paris 6, CNRS, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d'Histoire Naturelle, Institut de Recherche pour le Développement, UMR 7590, F-75005 Paris, France
| | - Judit E Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic.
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68
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Jadhav AG, Rhyman L, Alswaidan IA, Ramasami P, Sekar N. Spectroscopic and DFT approach for structure property relationship of red emitting rhodamine analogues: A study of linear and nonlinear optical properties. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.03.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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69
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Lao KU, Herbert JM. Atomic Orbital Implementation of Extended Symmetry-Adapted Perturbation Theory (XSAPT) and Benchmark Calculations for Large Supramolecular Complexes. J Chem Theory Comput 2018; 14:2955-2978. [DOI: 10.1021/acs.jctc.8b00058] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ka Un Lao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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70
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Saikia N, Karna SP, Pandey R. Theoretical study of gas and solvent phase stability and molecular adsorption of noncanonical guanine bases on graphene. Phys Chem Chem Phys 2018. [PMID: 28627546 DOI: 10.1039/c7cp02944f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The gas and solvent phase stability of noncanonical (Gua)n nucleobases is investigated in the framework of dispersion-corrected density functional theory (DFT). The calculated results strongly support the high tendency for the dimerization of (Gua)n bases in both gas and solvent phases. An interplay between intermolecular and bifurcated H-bonds is suggested to govern the stability of (Gua)n bases which bears a correlation with the description of dispersion correction terms employed in the DFT calculations. For example, a higher polarity is predicted for (Gua)n bases by the dispersion-corrected DFT in contrast to the non-polar nature of (Gua)3 and (Gua)4 predicted by the hybrid meta-GGA calculations. This distinct variation becomes significant under physiological conditions as polar (Gua)n is likely to exhibit greater stabilization in the gas phase compared to solvated (Gua)n. Graphene acting as a substrate induces modification in base configurations via maximization of π-orbital overlap between the base and substrate. In solvent, the substrate-induced effects are further heightened with lowering of the dipole moments of (Gua)n as also displayed by the corresponding isosurface of the electrostatic potential. The graphene-induced stability in both gas and solvent phases appears to fulfill one of the prerequisite criteria for molecular self-assembly. The DFT results therefore provide atomistic insights into the stability and molecular assembly of free-standing noncanonical (Gua)n nucleobases which can be extended to understanding the self-assembly process of functional biomolecules on 2D materials for potential biosensing applications.
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Affiliation(s)
- Nabanita Saikia
- Department of Physics, Michigan Technological University, Houghton, Michigan, USA.
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71
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Claudot J, Kim WJ, Dixit A, Kim H, Gould T, Rocca D, Lebègue S. Benchmarking several van der Waals dispersion approaches for the description of intermolecular interactions. J Chem Phys 2018; 148:064112. [DOI: 10.1063/1.5018818] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Julien Claudot
- Université de Lorraine, CRM2, UMR 7036, 54506 Vandœuvre-lès-Nancy, France
| | - Won June Kim
- CNRS, CRM2, UMR 7036, 54506 Vandœuvre-lès-Nancy, France
| | - Anant Dixit
- Université de Lorraine, CRM2, UMR 7036, 54506 Vandœuvre-lès-Nancy, France
| | - Hyungjun Kim
- Department of Chemistry and Graduate School of EEWS, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Tim Gould
- QLD Micro- and Nanotechnology Centre, Griffith University, Nathan, QLD 4111, Australia
| | - Dario Rocca
- Université de Lorraine and CNRS, CRM2, UMR 7036, 54506 Vandœuvre-lès-Nancy, France
| | - Sébastien Lebègue
- Université de Lorraine and CNRS, CRM2, UMR 7036, 54506 Vandœuvre-lès-Nancy, France
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72
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Fekete A, Komáromi I. Modeling the archetype cysteine protease reaction using dispersion corrected density functional methods in ONIOM-type hybrid QM/MM calculations; the proteolytic reaction of papain. Phys Chem Chem Phys 2018; 18:32847-32861. [PMID: 27883128 DOI: 10.1039/c6cp06869c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A proteolytic reaction of papain with a simple peptide model substrate N-methylacetamide has been studied. Our aim was twofold: (i) we proposed a plausible reaction mechanism with the aid of potential energy surface scans and second geometrical derivatives calculated at the stationary points, and (ii) we investigated the applicability of the dispersion corrected density functional methods in comparison with the popular hybrid generalized gradient approximations (GGA) method (B3LYP) without such a correction in the QM/MM calculations for this particular problem. In the resting state of papain the ion pair and neutral forms of the Cys-His catalytic dyad have approximately the same energy and they are separated by only a small barrier. Zero point vibrational energy correction shifted this equilibrium slightly to the neutral form. On the other hand, the electrostatic solvation free energy corrections, calculated using the Poisson-Boltzmann method for the structures sampled from molecular dynamics simulation trajectories, resulted in a more stable ion-pair form. All methods we applied predicted at least a two elementary step acylation process via a zwitterionic tetrahedral intermediate. Using dispersion corrected DFT methods the thioester S-C bond formation and the proton transfer from histidine occur in the same elementary step, although not synchronously. The proton transfer lags behind (or at least does not precede) the S-C bond formation. The predicted transition state corresponds mainly to the S-C bond formation while the proton is still on the histidine Nδ atom. In contrast, the B3LYP method using larger basis sets predicts a transition state in which the S-C bond is almost fully formed and the transition state can be mainly featured by the Nδ(histidine) to N(amid) proton transfer. Considerably lower activation energy was predicted (especially by the B3LYP method) for the next amide bond breaking elementary step of acyl-enzyme formation. Deacylation appeared to be a single elementary step process in all the methods we applied.
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Affiliation(s)
- Attila Fekete
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Nagyerdei krt. 98., Debrecen, Hungary.
| | - István Komáromi
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Nagyerdei krt. 98., Debrecen, Hungary.
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73
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Solid-State Testing of a Van-Der-Waals-Corrected Exchange-Correlation Functional Based on the Semiclassical Atom Theory. COMPUTATION 2018. [DOI: 10.3390/computation6010007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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74
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Xu WP, Xu H. Role of surface adsorption in tuning the properties of black phosphorus. Phys Chem Chem Phys 2018; 20:112-117. [DOI: 10.1039/c7cp06576k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synergetic effect of O2and H2O during the oxidation of black phosphorus (BP) at the atomic level is revealed, and the effects of H2O and/or O2on the properties of BP are also investigated.
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Affiliation(s)
- W. P. Xu
- Department of Physics
- Southern University of Science and Technology
- Shenzhen 518055
- China
| | - H. Xu
- Department of Physics
- Southern University of Science and Technology
- Shenzhen 518055
- China
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75
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Gionda A, Macetti G, Loconte L, Rizzato S, Orlando AM, Gatti C, Lo Presti L. A variable-temperature X-ray diffraction and theoretical study of conformational polymorphism in a complex organic molecule (DTC). RSC Adv 2018; 8:38445-38454. [PMID: 35559076 PMCID: PMC9090575 DOI: 10.1039/c8ra08063a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/07/2018] [Indexed: 11/28/2022] Open
Abstract
Two conformational crystal polymorphs of 3-diethylamino-4-(4-methoxyphenyl)-1,1-dioxo-4H-1λ6,2-thiazete-4-carbonitrile (DTC) have been analyzed in the 100 K-room temperature range by single crystal X-ray diffraction and high quality DFT calculations. DTC has strongly polar as well as aliphatic substituents but no hydrogen bonding groups, and thus qualifies as a test molecule for the relative importance of electrostatic vs. dispersion–repulsion terms. The two polymorphs have the same P21/n space group and differ by a flipping of the –OCH3 group, the two conformations being almost equi-energetic and separated by a low barrier. The system is monotropic in the observed temperature range with nearly identical thermal expansion coefficients and energy–temperature slopes, one phase consistently predicted to be more stable in agreement with the relative ease of appearance. Energy decompositions show that the electrostatic term is dominant and stabilizes with decreasing temperature. Dispersion and repulsion show the expected behavior, the former becoming more stabilizing at lower temperature in contrast with increasing repulsion at higher density. Absolute values and trends are very similar in the two phases, explaining the small total energy difference. Geometrical analyses of intermolecular contacts using fingerprint plots, as well as the study of molecular dipole moments as a function of T in the framework of the Quantum Theory of Atoms in Molecules, reveal more details of phase stability. A small conformational change in the asymmetric unit has a significant effect on how non-covalent interactions determine (i) the crystal packing and (ii) the effect of T on the relative balance of electrostatics and dispersion–repulsions.![]()
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Affiliation(s)
- Andrea Gionda
- Università degli Studi di Milano
- Department of Chemistry
- Italy
| | - Giovanni Macetti
- Università degli Studi di Milano
- Department of Chemistry
- Italy
- Centre for Materials Crystallography
- Århus University
| | - Laura Loconte
- Università degli Studi di Milano
- Department of Chemistry
- Italy
| | - Silvia Rizzato
- Università degli Studi di Milano
- Department of Chemistry
- Italy
| | | | - Carlo Gatti
- Centre for Materials Crystallography
- Århus University
- Denmark
- Istituto di Scienze e Tecnologie Molecolari
- Italian CNR
| | - Leonardo Lo Presti
- Università degli Studi di Milano
- Department of Chemistry
- Italy
- Centre for Materials Crystallography
- Århus University
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76
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Kuusik I, Berholts M, Kruusma J, Kisand V, Tõnisoo A, Lust E, Nõmmiste E. Valence electronic structure of [EMIM][BF4] ionic liquid: photoemission and DFT+D study. RSC Adv 2018; 8:30298-30304. [PMID: 35546846 PMCID: PMC9085424 DOI: 10.1039/c8ra05865b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 08/22/2018] [Indexed: 11/21/2022] Open
Abstract
The ultraviolet photoelectron spectrum (UPS) of the [EMIM][BF4] ionic liquid was recorded and analyzed. Together with the gas-phase UPS spectrum of the [EMIM][BF4] vapor and ab initio calculation methods, detailed insight into the electronic structure of this simple ionic liquid is possible. The low binding energy tail in the UPS spectrum is about 7.4 eV, in agreement with previous estimations of the HOMO–LUMO gap of the [EMIM][BF4] ion-pair. The bulk ab initio calculations are able to explain most of the features in the spectrum. However, DFT consistently lacks accuracy in the description of the top of the valence band. The dispersion corrected PBE calculation (PBE-D3) did offer very good agreement with the experimental structure, but the recently-developed vdW-DF functionals C09, optPBE, optB88 and CX were found to offer the best agreement in terms of the electronic structure. The ultraviolet photoelectron spectrum (UPS) of the [EMIM][BF4] ionic liquid was recorded and compared to previously measured vapor phase UPS spectrum.![]()
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Affiliation(s)
- I. Kuusik
- Institute of Physics
- University of Tartu
- 50411 Tartu
- Estonia
| | - M. Berholts
- Institute of Physics
- University of Tartu
- 50411 Tartu
- Estonia
- Dept. of Physics and Astronomy
| | - J. Kruusma
- Institute of Chemistry
- University of Tartu
- 50411 Tartu
- Estonia
| | - V. Kisand
- Institute of Physics
- University of Tartu
- 50411 Tartu
- Estonia
| | - A. Tõnisoo
- Institute of Physics
- University of Tartu
- 50411 Tartu
- Estonia
| | - E. Lust
- Institute of Chemistry
- University of Tartu
- 50411 Tartu
- Estonia
| | - E. Nõmmiste
- Institute of Physics
- University of Tartu
- 50411 Tartu
- Estonia
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77
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Rosbottom I, Toroz D, Hammond RB, Roberts KJ. Conformational and structural stability of the single molecule and hydrogen bonded clusters of para aminobenzoic acid in the gas and solution phases. CrystEngComm 2018. [DOI: 10.1039/c8ce00908b] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structures of α- and β-para aminobenzoic acid are deconstructed into their hydrogen bonding molecular structural building blocks, where they are analysed usingab initioquantum mechanical calculations of their conformation and cluster stability in solution.
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Affiliation(s)
- Ian Rosbottom
- Centre for Digital Drug Product Design
- School of Chemical and Process Engineering
- Leeds
- UK
| | - Dimitrios Toroz
- Centre for Digital Drug Product Design
- School of Chemical and Process Engineering
- Leeds
- UK
- Department of Chemistry
| | - Robert B. Hammond
- Centre for Digital Drug Product Design
- School of Chemical and Process Engineering
- Leeds
- UK
| | - Kevin J. Roberts
- Centre for Digital Drug Product Design
- School of Chemical and Process Engineering
- Leeds
- UK
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78
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The influence of the dispersion corrections on the performance of DFT method in modeling HNgY noble gas molecules and their complexes. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2017.11.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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79
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Abstract
Combining Hirshfeld surface analysis with single molecule electrostatic property calculations allows rationalizing crystalline packing motifs of organic semiconductors.
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Affiliation(s)
- M. Klues
- Fachbereich Physik
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
| | - G. Witte
- Fachbereich Physik
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
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80
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Zhu C, Wang Q, Yun J, Hu Q, Yang G. Non-covalent interactions for carbonaceous materials: impacts of doping, curving and their combination. Phys Chem Chem Phys 2018; 20:22228-22240. [DOI: 10.1039/c8cp02286k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Non-covalent interactions and their influencing factors are addressed after studying the binding of ion pairs with graphene (doped, curved and combination).
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Affiliation(s)
- Chang Zhu
- College of Resources and Environment & Chongqing Key Laboratory of Soil Multi-scale Interfacial Process
- Southwest University
- Chongqing 400715
- China
| | - Qian Wang
- College of Resources and Environment & Chongqing Key Laboratory of Soil Multi-scale Interfacial Process
- Southwest University
- Chongqing 400715
- China
| | - Jiena Yun
- College of Resources and Environment & Chongqing Key Laboratory of Soil Multi-scale Interfacial Process
- Southwest University
- Chongqing 400715
- China
| | - Qiaoli Hu
- College of Resources and Environment & Chongqing Key Laboratory of Soil Multi-scale Interfacial Process
- Southwest University
- Chongqing 400715
- China
| | - Gang Yang
- College of Resources and Environment & Chongqing Key Laboratory of Soil Multi-scale Interfacial Process
- Southwest University
- Chongqing 400715
- China
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81
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Metal-catalyzed rearrangement of allenylsulfides to furan: A theoretical mechanistic approach. MOLECULAR CATALYSIS 2017. [DOI: 10.1016/j.mcat.2017.09.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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82
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Avhad K, Jadhav A, Sekar N. Fluorescent vinyl and styryl coumarins: A comprehensive DFT study of structural, electronic and NLO properties. J CHEM SCI 2017. [DOI: 10.1007/s12039-017-1392-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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83
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Torres A, Amaya Suárez J, R. Remesal E, Márquez AM, Fernández Sanz J, Rincón Cañibano C. Adsorption of Prototypical Asphaltenes on Silica: First-Principles DFT Simulations Including Dispersion Corrections. J Phys Chem B 2017; 122:618-624. [DOI: 10.1021/acs.jpcb.7b05188] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Arturo Torres
- Department of Physical Chemistry, Universidad de Sevilla, 41012 Sevilla, Spain
| | - Javier Amaya Suárez
- Department of Physical Chemistry, Universidad de Sevilla, 41012 Sevilla, Spain
| | - Elena R. Remesal
- Department of Physical Chemistry, Universidad de Sevilla, 41012 Sevilla, Spain
| | - Antonio M. Márquez
- Department of Physical Chemistry, Universidad de Sevilla, 41012 Sevilla, Spain
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84
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Krajčí M, Kameoka S, Tsai AP. Understanding the catalytic activity of nanoporous gold: Role of twinning in fcc lattice. J Chem Phys 2017; 147:044713. [DOI: 10.1063/1.4994701] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Marian Krajčí
- Institute of Physics, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84511 Bratislava, Slovak Republic
| | - Satoshi Kameoka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - An-Pang Tsai
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
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85
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86
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Berland K, Jiao Y, Lee JH, Rangel T, Neaton JB, Hyldgaard P. Assessment of two hybrid van der Waals density functionals for covalent and non-covalent binding of molecules. J Chem Phys 2017. [DOI: 10.1063/1.4986522] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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87
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Akimbekov Z, Katsenis AD, Nagabhushana GP, Ayoub G, Arhangelskis M, Morris AJ, Friščić T, Navrotsky A. Experimental and Theoretical Evaluation of the Stability of True MOF Polymorphs Explains Their Mechanochemical Interconversions. J Am Chem Soc 2017; 139:7952-7957. [DOI: 10.1021/jacs.7b03144] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Zamirbek Akimbekov
- Peter
A. Rock Thermochemistry Laboratory and NEAT ORU, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Athanassios D. Katsenis
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Canada H3A
0B8
| | - G. P. Nagabhushana
- Peter
A. Rock Thermochemistry Laboratory and NEAT ORU, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Ghada Ayoub
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Canada H3A
0B8
| | - Mihails Arhangelskis
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Canada H3A
0B8
| | - Andrew J. Morris
- Cavendish
Laboratory, University of Cambridge, 19 J. J. Thomson Avenue, Cambridge CB3 0HE, U.K
- Department
of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Tomislav Friščić
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Canada H3A
0B8
| | - Alexandra Navrotsky
- Peter
A. Rock Thermochemistry Laboratory and NEAT ORU, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
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88
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Ruiz Pestana L, Mardirossian N, Head-Gordon M, Head-Gordon T. Ab initio molecular dynamics simulations of liquid water using high quality meta-GGA functionals. Chem Sci 2017; 8:3554-3565. [PMID: 30155200 PMCID: PMC6092720 DOI: 10.1039/c6sc04711d] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 02/24/2017] [Indexed: 01/23/2023] Open
Abstract
We have used ab initio molecular dynamics (AIMD) to characterize water properties using two meta-generalized gradient approximation (meta-GGA) functionals, M06-L-D3 and B97M-rV, and compared their performance against a standard GGA corrected for dispersion, revPBE-D3, at ambient conditions (298 K, and 1 g cm-3 or 1 atm). Simulations of the equilibrium density, radial distribution functions, self-diffusivity, the infrared spectrum, liquid dipole moments, and characterizations of the hydrogen bond network show that all three functionals have overcome the problem of the early AIMD simulations that erroneously found ambient water to be highly structured, but they differ substantially among themselves in agreement with experiment on this range of water properties. We show directly using water cluster data up through the pentamer that revPBE-D3 benefits from a cancellation of its intrinsic functional error by running classical trajectories, whereas the meta-GGA functionals are demonstrably more accurate and would require the simulation of nuclear quantum effects to realize better agreement with all cluster and condensed phase properties.
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Affiliation(s)
- Luis Ruiz Pestana
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , USA .
| | - Narbe Mardirossian
- Kenneth S. Pitzer Center for Theoretical Chemistry , Department of Chemistry , University of California , Berkeley , USA
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry , Department of Chemistry , University of California , Berkeley , USA
| | - Teresa Head-Gordon
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , USA .
- Kenneth S. Pitzer Center for Theoretical Chemistry , Department of Chemistry , University of California , Berkeley , USA
- Departments of Chemistry , Bioengineering , Chemical and Biomolecular Engineering , University of California , Berkeley , USA
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89
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90
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Hermann J, DiStasio RA, Tkatchenko A. First-Principles Models for van der Waals Interactions in Molecules and Materials: Concepts, Theory, and Applications. Chem Rev 2017; 117:4714-4758. [PMID: 28272886 DOI: 10.1021/acs.chemrev.6b00446] [Citation(s) in RCA: 267] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Noncovalent van der Waals (vdW) or dispersion forces are ubiquitous in nature and influence the structure, stability, dynamics, and function of molecules and materials throughout chemistry, biology, physics, and materials science. These forces are quantum mechanical in origin and arise from electrostatic interactions between fluctuations in the electronic charge density. Here, we explore the conceptual and mathematical ingredients required for an exact treatment of vdW interactions, and present a systematic and unified framework for classifying the current first-principles vdW methods based on the adiabatic-connection fluctuation-dissipation (ACFD) theorem (namely the Rutgers-Chalmers vdW-DF, Vydrov-Van Voorhis (VV), exchange-hole dipole moment (XDM), Tkatchenko-Scheffler (TS), many-body dispersion (MBD), and random-phase approximation (RPA) approaches). Particular attention is paid to the intriguing nature of many-body vdW interactions, whose fundamental relevance has recently been highlighted in several landmark experiments. The performance of these models in predicting binding energetics as well as structural, electronic, and thermodynamic properties is connected with the theoretical concepts and provides a numerical summary of the state-of-the-art in the field. We conclude with a roadmap of the conceptual, methodological, practical, and numerical challenges that remain in obtaining a universally applicable and truly predictive vdW method for realistic molecular systems and materials.
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Affiliation(s)
- Jan Hermann
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6, 14195 Berlin, Germany
| | - Robert A DiStasio
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6, 14195 Berlin, Germany.,Physics and Materials Science Research Unit, University of Luxembourg , L-1511 Luxembourg, Luxembourg
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91
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Jia L, Zhang Z, Qiao Y, Pedersen CM, Ge H, Wei Z, Deng T, Ren J, Liu X, Wang Y, Hou X. Product Distribution Control for Glucosamine Condensation: Nuclear Magnetic Resonance (NMR) Investigation Substantiated by Density Functional Calculations. Ind Eng Chem Res 2017. [DOI: 10.1021/acs.iecr.6b05057] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Lingyu Jia
- Shanxi
Engineering Research Center of Biorefinery, Institute of Coal Chemistry, Chinese Academy of Sciences, Taiyuan, People’s Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Zhenzhou Zhang
- Graduate University of Chinese Academy of Sciences, Beijing, People’s Republic of China
- State
Key Laboratory of Coal Conversion, Institute of Coal Chemistry, Chinese Academy of Sciences, Taiyuan, People’s Republic of China
| | - Yan Qiao
- State
Key Laboratory of Coal Conversion, Institute of Coal Chemistry, Chinese Academy of Sciences, Taiyuan, People’s Republic of China
| | - Christian Marcus Pedersen
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Hui Ge
- State
Key Laboratory of Coal Conversion, Institute of Coal Chemistry, Chinese Academy of Sciences, Taiyuan, People’s Republic of China
| | - Zhihong Wei
- State
Key Laboratory of Coal Conversion, Institute of Coal Chemistry, Chinese Academy of Sciences, Taiyuan, People’s Republic of China
| | - Tiansheng Deng
- Shanxi
Engineering Research Center of Biorefinery, Institute of Coal Chemistry, Chinese Academy of Sciences, Taiyuan, People’s Republic of China
| | - Jun Ren
- College
of Chemical Engineering and Environment, North University of China, Taiyuan 030051, China
| | - Xingchen Liu
- State
Key Laboratory of Coal Conversion, Institute of Coal Chemistry, Chinese Academy of Sciences, Taiyuan, People’s Republic of China
| | - Yingxiong Wang
- Shanxi
Engineering Research Center of Biorefinery, Institute of Coal Chemistry, Chinese Academy of Sciences, Taiyuan, People’s Republic of China
| | - Xianglin Hou
- Shanxi
Engineering Research Center of Biorefinery, Institute of Coal Chemistry, Chinese Academy of Sciences, Taiyuan, People’s Republic of China
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92
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Mou Z, Tian YH, Kertesz M. Validation of density functionals for pancake-bonded π-dimers; dispersion is not enough. Phys Chem Chem Phys 2017; 19:24761-24768. [DOI: 10.1039/c7cp04637e] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
π-Stacking pancake bonding between radicals poses special challenges to density functional theories (DFTs) due to their shorter than van der Waals contact distances, their multireference singlet ground states and the concurrently important dispersion interactions.
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Affiliation(s)
- Zhongyu Mou
- Department of Chemistry and the Institute of Soft Matter Synthesis and Metrology
- Georgetown University
- Washington
- USA
| | - Yong-Hui Tian
- College of Life Sciences
- Research Center of Analytical Instrumentation
- Sichuan University
- Chengdu
- P. R. China
| | - Miklos Kertesz
- Department of Chemistry and the Institute of Soft Matter Synthesis and Metrology
- Georgetown University
- Washington
- USA
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93
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Cassone G, Creazzo F, Giaquinta PV, Sponer J, Saija F. Ionic diffusion and proton transfer in aqueous solutions of alkali metal salts. Phys Chem Chem Phys 2017; 19:20420-20429. [DOI: 10.1039/c7cp03663a] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We report on a series of ab initio molecular dynamics investigations on LiCl, NaCl, and KCl aqueous solutions under the effect of static electric fields.
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Affiliation(s)
- Giuseppe Cassone
- Institute of Biophysics, Czech Academy of Sciences
- 61265 Brno
- Czech Republic
| | - Fabrizio Creazzo
- Université d'Evry val d'Essonne-Université Paris-Saclay
- 91025 Evry
- France
| | - Paolo V. Giaquinta
- Università degli Studi di Messina
- Dipartimento di Scienze Matematiche e Informatiche
- Scienze Fisiche e Scienze della Terra
- 98166 Messina
- Italy
| | - Jiri Sponer
- Institute of Biophysics, Czech Academy of Sciences
- 61265 Brno
- Czech Republic
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94
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Marianski M, Supady A, Ingram T, Schneider M, Baldauf C. Assessing the Accuracy of Across-the-Scale Methods for Predicting Carbohydrate Conformational Energies for the Examples of Glucose and α-Maltose. J Chem Theory Comput 2016; 12:6157-6168. [DOI: 10.1021/acs.jctc.6b00876] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Mateusz Marianski
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Adriana Supady
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Teresa Ingram
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Markus Schneider
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Carsten Baldauf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
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95
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Montero-Cabrera LA, Pérez-Badell Y, Piris M, Montero-Alejo AL, García de la Vega JM, Varandas AJ. Similarity measures between excited singlet and triplet electron densities in linear acenes: an application to singlet fission. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1255799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Luis A. Montero-Cabrera
- Facultad de Química, Universidad de La Habana, La Habana, Cuba
- Department of Chemistry, Johns Hopkins University, Baltimore, MA, USA
| | | | - Mario Piris
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), and Donostia International Physics Center (DIPC), Donostia, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Ana L. Montero-Alejo
- Facultad de Química, Universidad de La Habana, La Habana, Cuba
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Ñuñoa, Chile
| | - José M. García de la Vega
- Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - António J.C. Varandas
- Departamento de Química and Centro de Química, Universidade de Coimbra, Coimbra, Portugal
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96
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Takanabe A, Tanaka M, Johmoto K, Uekusa H, Mori T, Koshima H, Asahi T. Optical Activity and Optical Anisotropy in Photomechanical Crystals of Chiral Salicylidenephenylethylamines. J Am Chem Soc 2016; 138:15066-15077. [DOI: 10.1021/jacs.6b09633] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Akifumi Takanabe
- Department
of Advanced Science and Engineering, Graduate School of Advanced Science
and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Masahito Tanaka
- Research
Institute for Measurement and Analytical Instrumentation, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Kohei Johmoto
- Department
of Chemistry and Materials Science, Graduate School of Science and
Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Hidehiro Uekusa
- Department
of Chemistry and Materials Science, Graduate School of Science and
Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Tadashi Mori
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1
Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Hideko Koshima
- Researh Organization for Nano & Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
| | - Toru Asahi
- Department
of Advanced Science and Engineering, Graduate School of Advanced Science
and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Researh Organization for Nano & Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
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97
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Jin X, Qi P, Yang H, Zhang Y, Li J, Chen H. Enhanced hydrogen adsorption on Li-coated B 12C 6N 6. J Chem Phys 2016; 145:164301. [PMID: 27802626 DOI: 10.1063/1.4964394] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The hydrogen storage property of Li-coated B12C6N6 is investigated by density functional theory calculations. B12C6N6 is an electron deficient fullerene. Li atoms can be strongly bound to this cage by donating their valance electrons to the virtual 2p orbitals of carbon in the cluster. The binding energy (-2.90 eV) is much larger than the cohesive energy (1.63 eV) of bulk Li, and it prevents the Li atoms from aggregation. The coated Li atoms have large positive charges and the adsorbed hydrogen molecules can be moderately polarized by the Li+ ions. The computation shows that each Li atom coated on B12C6N6 can hold 2-3 H2 molecules with adsorption energies in the range of 0.21-0.24 eV/H2. The B12C6N6Li8 can adsorb 16 H2 and achieve a gravimetric hydrogen density of 8.63 wt. %. The present results indicate that alkali-metal atoms coated on electron deficient fullerenes can serve as hydrogen storage materials that can operate at ambient temperatures with high recycling storage capacity.
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Affiliation(s)
- Xueling Jin
- College of Physics and Electronic Engineering, Northwest Normal University, Lanzhou 730070, China
| | - Pengtang Qi
- Lanzhou Institute of Technology, Lanzhou 730050, China
| | - Huihui Yang
- College of Physics and Electronic Engineering, Northwest Normal University, Lanzhou 730070, China
| | - Yan Zhang
- College of Physics and Electronic Engineering, Northwest Normal University, Lanzhou 730070, China
| | - Jinyun Li
- College of Physics and Electronic Engineering, Northwest Normal University, Lanzhou 730070, China
| | - Hongshan Chen
- College of Physics and Electronic Engineering, Northwest Normal University, Lanzhou 730070, China
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98
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Kim WJ, Kim M, Lee EK, Lebègue S, Kim H. Failure of Density Functional Dispersion Correction in Metallic Systems and Its Possible Solution Using a Modified Many-Body Dispersion Correction. J Phys Chem Lett 2016; 7:3278-3283. [PMID: 27487413 DOI: 10.1021/acs.jpclett.6b00916] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Previous density functional dispersion corrections to density functional theory lead to an unphysical description of metallic systems, as exemplified by alkali and alkaline earth compounds. We demonstrate that it is possible to remedy this limitation by including screening effects into the form of interacting smeared-out dipoles in the many-body expansion of the interaction. Our new approach, called the coupled fluctuating smeared dipole model, describes equally well noncovalent systems, such as molecular pairs and crystals, and metallic systems.
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Affiliation(s)
| | | | | | - Sébastien Lebègue
- Laboratoire de Cristallographie, Résonance Magnétique et Modélisations (CRM2, UMR CNRS 7036), Institut Jean Barriol, Université de Lorraine, BP 239, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
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99
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100
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Zaffran J, Caspary Toroker M. Benchmarking Density Functional Theory Based Methods To Model NiOOH Material Properties: Hubbard and van der Waals Corrections vs Hybrid Functionals. J Chem Theory Comput 2016; 12:3807-12. [PMID: 27420033 DOI: 10.1021/acs.jctc.6b00657] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
NiOOH has recently been used to catalyze water oxidation by way of electrochemical water splitting. Few experimental data are available to rationalize the successful catalytic capability of NiOOH. Thus, theory has a distinctive role for studying its properties. However, the unique layered structure of NiOOH is associated with the presence of essential dispersion forces within the lattice. Hence, the choice of an appropriate exchange-correlation functional within Density Functional Theory (DFT) is not straightforward. In this work, we will show that standard DFT is sufficient to evaluate the geometry, but DFT+U and hybrid functionals are required to calculate the oxidation states. Notably, the benefit of DFT with van der Waals correction is marginal. Furthermore, only hybrid functionals succeed in opening a bandgap, and such methods are necessary to study NiOOH electronic structure. In this work, we expect to give guidelines to theoreticians dealing with this material and to present a rational approach in the choice of the DFT method of calculation.
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Affiliation(s)
- Jeremie Zaffran
- Department of Materials Science and Engineering, Technion - Israel Institute of Technology , Haifa 3200003, Israel
| | - Maytal Caspary Toroker
- Department of Materials Science and Engineering, Technion - Israel Institute of Technology , Haifa 3200003, Israel
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