151
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Valero R, Morales-García Á, Illas F. Theoretical Modeling of Electronic Excitations of Gas-Phase and Solvated TiO 2 Nanoclusters and Nanoparticles of Interest in Photocatalysis. J Chem Theory Comput 2018; 14:4391-4404. [PMID: 30011198 DOI: 10.1021/acs.jctc.8b00651] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The optical absorption spectra of (TiO2) n, nanoclusters ( n = 1-20) and nanoparticles ( n = 35, 84) have been calculated from the frequency-dependent dielectric function in the independent particle approximation under the framework of density functional theory. The PBE generalized gradient approach based functional, the so-called PBE+ U method and the PBE0 and PBEx hybrid functionals-containing 25% and 12.5% of nonlocal Fock exchange, respectively-have been used. The simulated spectra have been obtained in the gas phase and in water on previously PBE0 optimized atomic structures. The effect of the solvent has been accounted for by using an implicit water solvation model. For the smallest nanoclusters, the spectra show discrete peaks, whereas for the largest nanoclusters and for the nanoparticles they resemble a continuum absorption band. In the gas phase and for a given density functional, the onset of the absorption (optical gap, Ogap) remains relatively constant for all nanoparticle sizes although it increases with the percentage of nonlocal Fock exchange, as expected. For all tested functionals, the tendency of Ogap in water is very similar to that observed in the gas phase with an almost constant upshift. For comparison, the optical gap has also been calculated at the TD-DFT level with the PBEx functional in the gas phase and in water. Both approaches agree reasonably well although the TD-DFT gap values are lower than those derived from the dielectric-function. Overall, the position of the spectral maxima and the width of the spectra are relatively constant and independent of particle size which may have implications in the understanding of photocatalysis by TiO2.
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Affiliation(s)
- Rosendo Valero
- Departament de Ciència de Materials i Química Física & Institut de Química Teórica i Computacional (IQTCUB) , Universitat de Barcelona , c/Martí i Franquès 1 , 08028 , Barcelona , Spain
| | - Ángel Morales-García
- Departament de Ciència de Materials i Química Física & Institut de Química Teórica i Computacional (IQTCUB) , Universitat de Barcelona , c/Martí i Franquès 1 , 08028 , Barcelona , Spain
| | - Francesc Illas
- Departament de Ciència de Materials i Química Física & Institut de Química Teórica i Computacional (IQTCUB) , Universitat de Barcelona , c/Martí i Franquès 1 , 08028 , Barcelona , Spain
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152
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Wang H, An W, Liu X, Heath Turner C. Oxygen reduction reaction on Pt(1 1 1), Pt(2 2 1), and Ni/Au1Pt3(2 2 1) surfaces: Probing scaling relationships of reaction energetics and interfacial composition. Chem Eng Sci 2018. [DOI: 10.1016/j.ces.2018.03.054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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153
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Cantu DC, Padmaperuma AB, Nguyen MT, Akhade SA, Yoon Y, Wang YG, Lee MS, Glezakou VA, Rousseau R, Lilga MA. A Combined Experimental and Theoretical Study on the Activity and Selectivity of the Electrocatalytic Hydrogenation of Aldehydes. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00858] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- David C. Cantu
- Institute for Integrated Catalysis, Pacific Northwest National Laboratory, Richland Washington 99352, United States
| | - Asanga B. Padmaperuma
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland Washington 99352, United States
| | - Manh-Thuong Nguyen
- Institute for Integrated Catalysis, Pacific Northwest National Laboratory, Richland Washington 99352, United States
| | - Sneha A. Akhade
- Institute for Integrated Catalysis, Pacific Northwest National Laboratory, Richland Washington 99352, United States
| | - Yeohoon Yoon
- Institute for Integrated Catalysis, Pacific Northwest National Laboratory, Richland Washington 99352, United States
| | - Yang-Gang Wang
- Institute for Integrated Catalysis, Pacific Northwest National Laboratory, Richland Washington 99352, United States
| | - Mal-Soon Lee
- Institute for Integrated Catalysis, Pacific Northwest National Laboratory, Richland Washington 99352, United States
| | - Vassiliki-Alexandra Glezakou
- Institute for Integrated Catalysis, Pacific Northwest National Laboratory, Richland Washington 99352, United States
| | - Roger Rousseau
- Institute for Integrated Catalysis, Pacific Northwest National Laboratory, Richland Washington 99352, United States
| | - Michael A. Lilga
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland Washington 99352, United States
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154
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Basdogan Y, Keith JA. A paramedic treatment for modeling explicitly solvated chemical reaction mechanisms. Chem Sci 2018; 9:5341-5346. [PMID: 30155232 PMCID: PMC6011202 DOI: 10.1039/c8sc01424h] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/28/2018] [Indexed: 12/17/2022] Open
Abstract
We report a static quantum chemistry modeling treatment to study how solvent molecules affect chemical reaction mechanisms without dynamics simulations. This modeling scheme uses a global optimization procedure to identify low energy intermediate states with different numbers of explicit solvent molecules and then the growing string method to locate sequential transition states along a reaction pathway. Testing this approach on the acid-catalyzed Morita-Baylis-Hillman (MBH) reaction in methanol, we found a reaction mechanism that is consistent with both recent experiments and computationally intensive dynamics simulations with explicit solvation. In doing so, we explain unphysical pitfalls that obfuscate computational modeling that uses microsolvated reaction intermediates. This new paramedic approach can promisingly capture essential physical chemistry of the complicated and multistep MBH reaction mechanism, and the energy profiles found with this model appear reasonably insensitive to the level of theory used for energy calculations. Thus, it should be a useful and computationally cost-effective approach for modeling solvent mediated reaction mechanisms when dynamics simulations are not possible.
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Affiliation(s)
- Yasemin Basdogan
- Department of Chemical and Petroleum Engineering , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , USA .
| | - John A Keith
- Department of Chemical and Petroleum Engineering , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , USA .
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155
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Coons MP, Herbert JM. Quantum chemistry in arbitrary dielectric environments: Theory and implementation of nonequilibrium Poisson boundary conditions and application to compute vertical ionization energies at the air/water interface. J Chem Phys 2018; 148:222834. [DOI: 10.1063/1.5023916] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Marc P. Coons
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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156
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Steinmann SN, Ferreira De Morais R, Götz AW, Fleurat-Lessard P, Iannuzzi M, Sautet P, Michel C. Force Field for Water over Pt(111): Development, Assessment, and Comparison. J Chem Theory Comput 2018; 14:3238-3251. [PMID: 29660272 DOI: 10.1021/acs.jctc.7b01177] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Metal/water interfaces are key in many natural and industrial processes, such as corrosion, atmospheric, or environmental chemistry. Even today, the only practical approach to simulate large interfaces between a metal and water is to perform force-field simulations. In this work, we propose a novel force field, GAL17, to describe the interaction of water and a Pt(111) surface. GAL17 builds on three terms: (i) a standard Lennard-Jones potential for the bonding interaction between the surface and water, (ii) a Gaussian term to improve the surface corrugation, and (iii) two terms describing the angular dependence of the interaction energy. The 12 parameters of this force field are fitted against a set of 210 adsorption geometries of water on Pt(111). The performance of GAL17 is compared to several other approaches that have not been validated against extensive first-principles computations yet. Their respective accuracy is evaluated on an extended set of 802 adsorption geometries of H2O on Pt(111), 52 geometries derived from icelike layers, and an MD simulation of an interface between a c(4 × 6) Pt(111) surface and a water layer of 14 Å thickness. The newly developed GAL17 force field provides a significant improvement over previously existing force fields for Pt(111)/H2O interactions. Its well-balanced performance suggests that it is an ideal candidate to generate relevant geometries for the metal/water interface, paving the way to a representative sampling of the equilibrium distribution at the interface and to predict solvation free energies at the solid/liquid interface.
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Affiliation(s)
- Stephan N Steinmann
- Univ Lyon, Ecole Normale Supérieure de Lyon , CNRS Université Lyon 1, Laboratoire de Chimie UMR 5182 , 46 allée d'Italie , F-69364 Lyon , France
| | - Rodrigo Ferreira De Morais
- Univ Lyon, Ecole Normale Supérieure de Lyon , CNRS Université Lyon 1, Laboratoire de Chimie UMR 5182 , 46 allée d'Italie , F-69364 Lyon , France
| | - Andreas W Götz
- San Diego Supercomputer Center , University of California San Diego , La Jolla , California 92093 , United States
| | - Paul Fleurat-Lessard
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB, UMR 6302, CNRS) , Université de Bourgogne Franche-Comté , 9 Avenue Alain Savary , 21078 Dijon , France
| | - Marcella Iannuzzi
- Institut für Chemie , University of Zurich , Winterthurerstrasse 190 , CH-8057 Zurich , Switzerland
| | | | - Carine Michel
- Univ Lyon, Ecole Normale Supérieure de Lyon , CNRS Université Lyon 1, Laboratoire de Chimie UMR 5182 , 46 allée d'Italie , F-69364 Lyon , France
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157
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Groß A. Fundamental Challenges for Modeling Electrochemical Energy Storage Systems at the Atomic Scale. Top Curr Chem (Cham) 2018; 376:17. [DOI: 10.1007/s41061-018-0194-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 03/23/2018] [Indexed: 10/17/2022]
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158
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Sundararaman R, Letchworth-Weaver K, Schwarz KA. Improving accuracy of electrochemical capacitance and solvation energetics in first-principles calculations. J Chem Phys 2018; 148:144105. [DOI: 10.1063/1.5024219] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ravishankar Sundararaman
- Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, 110 8th St., Troy, New York 12180, USA
| | - Kendra Letchworth-Weaver
- Center for Nanoscale Materials, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, Illinois 60439, USA
| | - Kathleen A. Schwarz
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, Maryland 20899, USA
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159
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Womack JC, Anton L, Dziedzic J, Hasnip PJ, Probert MIJ, Skylaris CK. DL_MG: A Parallel Multigrid Poisson and Poisson-Boltzmann Solver for Electronic Structure Calculations in Vacuum and Solution. J Chem Theory Comput 2018; 14:1412-1432. [PMID: 29447447 DOI: 10.1021/acs.jctc.7b01274] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The solution of the Poisson equation is a crucial step in electronic structure calculations, yielding the electrostatic potential-a key component of the quantum mechanical Hamiltonian. In recent decades, theoretical advances and increases in computer performance have made it possible to simulate the electronic structure of extended systems in complex environments. This requires the solution of more complicated variants of the Poisson equation, featuring nonhomogeneous dielectric permittivities, ionic concentrations with nonlinear dependencies, and diverse boundary conditions. The analytic solutions generally used to solve the Poisson equation in vacuum (or with homogeneous permittivity) are not applicable in these circumstances, and numerical methods must be used. In this work, we present DL_MG, a flexible, scalable, and accurate solver library, developed specifically to tackle the challenges of solving the Poisson equation in modern large-scale electronic structure calculations on parallel computers. Our solver is based on the multigrid approach and uses an iterative high-order defect correction method to improve the accuracy of solutions. Using two chemically relevant model systems, we tested the accuracy and computational performance of DL_MG when solving the generalized Poisson and Poisson-Boltzmann equations, demonstrating excellent agreement with analytic solutions and efficient scaling to ∼109 unknowns and 100s of CPU cores. We also applied DL_MG in actual large-scale electronic structure calculations, using the ONETEP linear-scaling electronic structure package to study a 2615 atom protein-ligand complex with routinely available computational resources. In these calculations, the overall execution time with DL_MG was not significantly greater than the time required for calculations using a conventional FFT-based solver.
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Affiliation(s)
- James C Womack
- Department of Chemistry , University of Southampton , Highfield, Southampton SO17 1BJ , United Kingdom
| | - Lucian Anton
- Cray U.K. Ltd. , Broad Quay House, Prince Street , Bristol BS1 4DJ , United Kingdom
| | - Jacek Dziedzic
- Department of Chemistry , University of Southampton , Highfield, Southampton SO17 1BJ , United Kingdom.,Faculty of Applied Physics and Mathematics , Gdańsk University of Technology , Gdańsk 80-233 , Poland
| | - Phil J Hasnip
- Department of Physics , University of York , Heslington, York YO10 5DD , United Kingdom
| | - Matt I J Probert
- Department of Physics , University of York , Heslington, York YO10 5DD , United Kingdom
| | - Chris-Kriton Skylaris
- Department of Chemistry , University of Southampton , Highfield, Southampton SO17 1BJ , United Kingdom
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160
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Celebioglu A, Kayaci-Senirmak F, İpek S, Durgun E, Uyar T. Polymer-free nanofibers from vanillin/cyclodextrin inclusion complexes: high thermal stability, enhanced solubility and antioxidant property. Food Funct 2018; 7:3141-53. [PMID: 27353870 DOI: 10.1039/c6fo00569a] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Vanillin/cyclodextrin inclusion complex nanofibers (vanillin/CD-IC NFs) were successfully obtained from three modified CD types (HPβCD, HPγCD and MβCD) in three different solvent systems (water, DMF and DMAc) via an electrospinning technique without using a carrier polymeric matrix. Vanillin/CD-IC NFs with uniform and bead-free fiber morphology were successfully produced and their free-standing nanofibrous webs were obtained. The polymer-free CD/vanillin-IC-NFs allow us to accomplish a much higher vanillin loading (∼12%, w/w) when compared to electrospun polymeric nanofibers containing CD/vanillin-IC (∼5%, w/w). Vanillin has a volatile nature yet, after electrospinning, a significant amount of vanillin was preserved due to complex formation depending on the CD types. Maximum preservation of vanillin was observed for vanillin/MβCD-IC NFs which is up to ∼85% w/w, besides, a considerable amount of vanillin (∼75% w/w) was also preserved for vanillin/HPβCD-IC NFs and vanillin/HPγCD-IC NFs. Phase solubility studies suggested a 1 : 1 molar complexation tendency between guest vanillin and host CD molecules. Molecular modelling studies and experimental findings revealed that vanillin : CD complexation was strongest for MβCD when compared to HPβCD and HPγCD in vanillin/CD-IC NFs. For vanillin/CD-IC NFs, water solubility and the antioxidant property of vanillin was improved significantly owing to inclusion complexation. In brief, polymer-free vanillin/CD-IC NFs are capable of incorporating a much higher loading of vanillin and effectively preserve volatile vanillin. Hence, encapsulation of volatile active agents such as flavor, fragrance and essential oils in electrospun polymer-free CD-IC NFs may have potential for food related applications by integrating the particularly large surface area of NFs with the non-toxic nature of CD and inclusion complexation benefits, such as high temperature stability, improved water solubility and an enhanced antioxidant property, etc.
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Affiliation(s)
- Asli Celebioglu
- Institute of Materials Science & Nanotechnology, Bilkent University, Ankara, 06800, Turkey. and UNAM-National Nanotechnology Research Center, Bilkent University, Ankara, 06800, Turkey
| | - Fatma Kayaci-Senirmak
- Institute of Materials Science & Nanotechnology, Bilkent University, Ankara, 06800, Turkey. and UNAM-National Nanotechnology Research Center, Bilkent University, Ankara, 06800, Turkey
| | - Semran İpek
- UNAM-National Nanotechnology Research Center, Bilkent University, Ankara, 06800, Turkey and Department of Engineering Physics, Istanbul Medeniyet University, Istanbul, 34700, Turkey
| | - Engin Durgun
- Institute of Materials Science & Nanotechnology, Bilkent University, Ankara, 06800, Turkey. and UNAM-National Nanotechnology Research Center, Bilkent University, Ankara, 06800, Turkey
| | - Tamer Uyar
- Institute of Materials Science & Nanotechnology, Bilkent University, Ankara, 06800, Turkey. and UNAM-National Nanotechnology Research Center, Bilkent University, Ankara, 06800, Turkey
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161
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Yoo SH, Todorova M, Neugebauer J. Selective Solvent-Induced Stabilization of Polar Oxide Surfaces in an Electrochemical Environment. PHYSICAL REVIEW LETTERS 2018; 120:066101. [PMID: 29481276 DOI: 10.1103/physrevlett.120.066101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/10/2017] [Indexed: 06/08/2023]
Abstract
The impact of an electrochemical environment on the thermodynamic stability of polar oxide surfaces is investigated for the example of ZnO(0001) surfaces immersed in water using density functional theory calculations. We show that solvation effects are highly selective: They have little effect on surfaces showing a metallic character, but largely stabilize semiconducting structures, particularly those that have a high electrostatic penalty in vacuum. The high selectivity is shown to have direct consequences for the surface phase diagram and explains, e.g., why certain surface structures could be observed only in an electrochemical environment.
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Affiliation(s)
- Su-Hyun Yoo
- Department of Computational Materials Design, Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Str. 1, D-40237 Düsseldorf, Germany
| | - Mira Todorova
- Department of Computational Materials Design, Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Str. 1, D-40237 Düsseldorf, Germany
| | - Jörg Neugebauer
- Department of Computational Materials Design, Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Str. 1, D-40237 Düsseldorf, Germany
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162
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Fumanal M, Capdevila-Cortada M, Novoa JJ. Understanding room-temperature π-dimerisation of radical ions: intramolecular π-[TTF] 22+ in functionalised calix[4]arenes. Phys Chem Chem Phys 2018; 19:3807-3819. [PMID: 28102383 DOI: 10.1039/c6cp07794c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Long, multicentre π-dimers of radical ions are weakly bound and can only be observed in solution at low temperature. However, recent supramolecular approaches induce the extra stabilisation required to preserve them at room temperature, by different means depending on the approach. In particular, π-[TTF]22+ dimers (TTF = tetrathiafulvalene) were detected upon oxidation of a TTF-based calix[4]arene in acetonitrile solution at room temperature, manifesting intramolecular [R-TTF]˙+[R-TTF]˙+ interactions (Chem. Commun. 2006, 2, 2233). In this work, the reasons behind the remarkable formation of these π-dimers in the calix[4]arene, [calix], molecule are unravelled by means of DFT calculations. We first demonstrate that the properties of the π-[R-TTF]22+ dimers are preserved in the [calix]2+. Most importantly, our results show that the π-dimerised and non-dimerised forms of the [calix]2+ are isoenergetic at room temperature, and that the activation energy for this process is ca. 9.5 kcal mol-1. Hence, both forms coexist in equilibrium at 298 K, as the intramolecular nature of the interaction ensures a high reaction rate. The role of the Na+ cation in preventing the π-[R-TTF]22+ dimerisation of the [calix]2+ receptor is also examined, unveiling that this effect is mostly due to the electrostatic repulsion induced by the cation. Finally, we provide a revision on room-temperature stable supramolecular long, multicentre π-dimers of radical ions, a class of systems with great potential as molecular switches.
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Affiliation(s)
- Maria Fumanal
- Departament de Química Física and IQTCUB, Universitat de Barcelona, Av. Diagonal 645, 08028, Barcelona, Spain.
| | - Marçal Capdevila-Cortada
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007 Tarragona, Spain.
| | - Juan J Novoa
- Departament de Química Física and IQTCUB, Universitat de Barcelona, Av. Diagonal 645, 08028, Barcelona, Spain.
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163
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Gerosa M, Bottani CE, Di Valentin C, Onida G, Pacchioni G. Accuracy of dielectric-dependent hybrid functionals in the prediction of optoelectronic properties of metal oxide semiconductors: a comprehensive comparison with many-body GW and experiments. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:044003. [PMID: 29087359 DOI: 10.1088/1361-648x/aa9725] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Understanding the electronic structure of metal oxide semiconductors is crucial to their numerous technological applications, such as photoelectrochemical water splitting and solar cells. The needed experimental and theoretical knowledge goes beyond that of pristine bulk crystals, and must include the effects of surfaces and interfaces, as well as those due to the presence of intrinsic defects (e.g. oxygen vacancies), or dopants for band engineering. In this review, we present an account of the recent efforts in predicting and understanding the optoelectronic properties of oxides using ab initio theoretical methods. In particular, we discuss the performance of recently developed dielectric-dependent hybrid functionals, providing a comparison against the results of many-body GW calculations, including G 0 W 0 as well as more refined approaches, such as quasiparticle self-consistent GW. We summarize results in the recent literature for the band gap, the band level alignment at surfaces, and optical transition energies in defective oxides, including wide gap oxide semiconductors and transition metal oxides. Correlated transition metal oxides are also discussed. For each method, we describe successes and drawbacks, emphasizing the challenges faced by the development of improved theoretical approaches. The theoretical section is preceded by a critical overview of the main experimental techniques needed to characterize the optoelectronic properties of semiconductors, including absorption and reflection spectroscopy, photoemission, and scanning tunneling spectroscopy (STS).
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Affiliation(s)
- M Gerosa
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, United States of America
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164
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Stellato F, Calandra M, D'Acapito F, De Santis E, La Penna G, Rossi G, Morante S. Multi-scale theoretical approach to X-ray absorption spectra in disordered systems: an application to the study of Zn(ii) in water. Phys Chem Chem Phys 2018; 20:24775-24782. [DOI: 10.1039/c8cp04355h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We develop a multi-scale theoretical approach aimed at calculating from first principles X-ray absorption spectra of liquid solutions and disordered systems.
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Affiliation(s)
| | - Matteo Calandra
- Sorbonne Université
- CNRS, Institut des Nanosciences de Paris
- UMR7588
- Paris
- France
| | - Francesco D'Acapito
- CNR-IOM-OGG c/o European Synchrotron Radiation Facility
- F-38043 Grenoble
- France
| | - Emiliano De Santis
- Dipartimento di Fisica, Università di Roma “Tor Vergata”
- I-00133 Roma
- Italy
| | - Giovanni La Penna
- INFN, Sezione di Roma 2
- I-00133 Roma
- Italy
- CNR – Institute for Chemistry of Organometallic Compounds
- Sesto Fiorentino
| | - Giancarlo Rossi
- INFN, Sezione di Roma 2
- I-00133 Roma
- Italy
- Dipartimento di Fisica, Università di Roma “Tor Vergata”
- I-00133 Roma
| | - Silvia Morante
- INFN, Sezione di Roma 2
- I-00133 Roma
- Italy
- Dipartimento di Fisica, Università di Roma “Tor Vergata”
- I-00133 Roma
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165
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Maheshwari S, Li Y, Agrawal N, Janik MJ. Density functional theory models for electrocatalytic reactions. ADVANCES IN CATALYSIS 2018. [DOI: 10.1016/bs.acat.2018.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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166
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Gatto P, Lipparini F, Stamm B. Computation of forces arising from the polarizable continuum model within the domain-decomposition paradigm. J Chem Phys 2017; 147:224108. [DOI: 10.1063/1.5008329] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Paolo Gatto
- Mathematics Division, Center for Computational Engineering Science, RWTH Aachen University, Aachen, Germany
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benjamin Stamm
- Mathematics Division, Center for Computational Engineering Science, RWTH Aachen University, Aachen, Germany
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167
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Giannozzi P, Andreussi O, Brumme T, Bunau O, Buongiorno Nardelli M, Calandra M, Car R, Cavazzoni C, Ceresoli D, Cococcioni M, Colonna N, Carnimeo I, Dal Corso A, de Gironcoli S, Delugas P, DiStasio RA, Ferretti A, Floris A, Fratesi G, Fugallo G, Gebauer R, Gerstmann U, Giustino F, Gorni T, Jia J, Kawamura M, Ko HY, Kokalj A, Küçükbenli E, Lazzeri M, Marsili M, Marzari N, Mauri F, Nguyen NL, Nguyen HV, Otero-de-la-Roza A, Paulatto L, Poncé S, Rocca D, Sabatini R, Santra B, Schlipf M, Seitsonen AP, Smogunov A, Timrov I, Thonhauser T, Umari P, Vast N, Wu X, Baroni S. Advanced capabilities for materials modelling with Quantum ESPRESSO. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:465901. [PMID: 29064822 DOI: 10.1088/1361-648x/aa8f79] [Citation(s) in RCA: 1493] [Impact Index Per Article: 213.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Quantum EXPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches. Quantum EXPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.
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Affiliation(s)
- P Giannozzi
- Department of Mathematics, Computer Science, and Physics, University of Udine, via delle Scienze 206, I-33100 Udine, Italy
| | - O Andreussi
- Institute of Computational Sciences, Università della Svizzera Italiana, Lugano, Switzerland
- Theory and Simulation of Materials (THEOS), and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - T Brumme
- Wilhelm-Ostwald-Institute of Physical and Theoretical Chemistry, Leipzig University, Linnéstr. 2, D-04103 Leipzig, Germany
| | - O Bunau
- IMPMC, UMR CNRS 7590, Sorbonne Universités-UPMC University Paris 06, MNHN, IRD, 4 Place Jussieu, F-75005 Paris, France
| | - M Buongiorno Nardelli
- Department of Physics and Department of Chemistry, University of North Texas, Denton, TX, United States of America
| | - M Calandra
- IMPMC, UMR CNRS 7590, Sorbonne Universités-UPMC University Paris 06, MNHN, IRD, 4 Place Jussieu, F-75005 Paris, France
| | - R Car
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States of America
| | - C Cavazzoni
- CINECA-Via Magnanelli 6/3, I-40033 Casalecchio di Reno, Bologna, Italy
| | - D Ceresoli
- Institute of Molecular Science and Technologies (ISTM), National Research Council (CNR), I-20133 Milano, Italy
| | - M Cococcioni
- Theory and Simulation of Materials (THEOS), and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - N Colonna
- Theory and Simulation of Materials (THEOS), and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - I Carnimeo
- Department of Mathematics, Computer Science, and Physics, University of Udine, via delle Scienze 206, I-33100 Udine, Italy
| | - A Dal Corso
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, I-34136 Trieste, Italy
- CNR-IOM DEMOCRITOS, Istituto Officina dei Materiali, Consiglio Nazionale delle Ricerche, Italy
| | - S de Gironcoli
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, I-34136 Trieste, Italy
- CNR-IOM DEMOCRITOS, Istituto Officina dei Materiali, Consiglio Nazionale delle Ricerche, Italy
| | - P Delugas
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, I-34136 Trieste, Italy
| | - R A DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, United States of America
| | - A Ferretti
- CNR Istituto Nanoscienze, I-42125 Modena, Italy
| | - A Floris
- School of Mathematics and Physics, College of Science, University of Lincoln, United Kingdom
| | - G Fratesi
- Dipartimento di Fisica, Università degli Studi di Milano, via Celoria 16, I-20133 Milano, Italy
| | - G Fugallo
- ETSF, Laboratoire des Solides Irradiés, Ecole Polytechnique, F-91128 Palaiseau cedex, France
| | - R Gebauer
- The Abdus Salam International Centre for Theoretical Physics (ICTP), Strada Costiera 11, I-34151 Trieste, Italy
| | - U Gerstmann
- Department Physik, Universität Paderborn, D-33098 Paderborn, Germany
| | - F Giustino
- Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH, United Kingdom
| | - T Gorni
- IMPMC, UMR CNRS 7590, Sorbonne Universités-UPMC University Paris 06, MNHN, IRD, 4 Place Jussieu, F-75005 Paris, France
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, I-34136 Trieste, Italy
| | - J Jia
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, United States of America
| | - M Kawamura
- The Institute for Solid State Physics, Kashiwa, Japan
| | - H-Y Ko
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States of America
| | - A Kokalj
- Department of Physical and Organic Chemistry, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - E Küçükbenli
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, I-34136 Trieste, Italy
| | - M Lazzeri
- IMPMC, UMR CNRS 7590, Sorbonne Universités-UPMC University Paris 06, MNHN, IRD, 4 Place Jussieu, F-75005 Paris, France
| | - M Marsili
- Dipartimento di Fisica e Astronomia, Università di Padova, via Marzolo 8, I-35131 Padova, Italy
| | - N Marzari
- Theory and Simulation of Materials (THEOS), and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - F Mauri
- Dipartimento di Fisica, Università di Roma La Sapienza, Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - N L Nguyen
- Theory and Simulation of Materials (THEOS), and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - H-V Nguyen
- Institute of Physics, Vietnam Academy of Science and Technology, 10 Dao Tan, Hanoi, Vietnam
| | - A Otero-de-la-Roza
- Department of Chemistry, University of British Columbia, Okanagan, Kelowna BC V1V 1V7, Canada
| | - L Paulatto
- IMPMC, UMR CNRS 7590, Sorbonne Universités-UPMC University Paris 06, MNHN, IRD, 4 Place Jussieu, F-75005 Paris, France
| | - S Poncé
- Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH, United Kingdom
| | - D Rocca
- Université de Lorraine, CRM2, UMR 7036, F-54506 Vandoeuvre-lès-Nancy, France
- CNRS, CRM2, UMR 7036, F-54506 Vandoeuvre-lès-Nancy, France
| | - R Sabatini
- Orionis Biosciences, Newton, MA 02466, United States of America
| | - B Santra
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States of America
| | - M Schlipf
- Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH, United Kingdom
| | - A P Seitsonen
- Institut für Chimie, Universität Zurich, CH-8057 Zürich, Switzerland
- Département de Chimie, École Normale Supérieure, F-75005 Paris, France
| | - A Smogunov
- SPEC, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-Sur-Yvette, France
| | - I Timrov
- Theory and Simulation of Materials (THEOS), and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - T Thonhauser
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109, United States of America
| | - P Umari
- Dipartimento di Fisica e Astronomia, Università di Padova, via Marzolo 8, I-35131 Padova, Italy
- CNR-IOM DEMOCRITOS, Istituto Officina dei Materiali, Consiglio Nazionale delle Ricerche, Italy
| | - N Vast
- Laboratoire des Solides Irradiés, École Polytechnique, CEA-DRF-IRAMIS, CNRS UMR 7642, Université Paris-Saclay, F-91120 Palaiseau, France
| | - X Wu
- Department of Physics, Temple University, Philadelphia, PA 19122-1801, United States of America
| | - S Baroni
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, I-34136 Trieste, Italy
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168
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Sundararaman R, Letchworth-Weaver K, Schwarz KA, Gunceler D, Ozhabes Y, Arias T. JDFTx: software for joint density-functional theory. SOFTWAREX 2017; 6:278-284. [PMID: 29892692 PMCID: PMC5992620 DOI: 10.1016/j.softx.2017.10.006] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Density-functional theory (DFT) has revolutionized computational prediction of atomic-scale properties from first principles in physics, chemistry and materials science. Continuing development of new methods is necessary for accurate predictions of new classes of materials and properties, and for connecting to nano- and mesoscale properties using coarse-grained theories. JDFTx is a fully-featured open-source electronic DFT software designed specifically to facilitate rapid development of new theories, models and algorithms. Using an algebraic formulation as an abstraction layer, compact C++11 code automatically performs well on diverse hardware including GPUs (Graphics Processing Units). This code hosts the development of joint density-functional theory (JDFT) that combines electronic DFT with classical DFT and continuum models of liquids for first-principles calculations of solvated and electrochemical systems. In addition, the modular nature of the code makes it easy to extend and interface with, facilitating the development of multi-scale toolkits that connect to ab initio calculations, e.g. photo-excited carrier dynamics combining electron and phonon calculations with electromagnetic simulations.
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Affiliation(s)
- Ravishankar Sundararaman
- Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180
| | | | - Kathleen A. Schwarz
- National Institute of Standards and Technology, Material Measurement Laboratory, Gaithersburg, MD, 20899
| | - Deniz Gunceler
- Department of Physics, Cornell University, Ithaca, NY 14853
| | - Yalcin Ozhabes
- Department of Physics, Cornell University, Ithaca, NY 14853
| | - T.A. Arias
- Department of Physics, Cornell University, Ithaca, NY 14853
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169
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Howard JC, Womack JC, Dziedzic J, Skylaris CK, Pritchard BP, Crawford TD. Electronically Excited States in Solution via a Smooth Dielectric Model Combined with Equation-of-Motion Coupled Cluster Theory. J Chem Theory Comput 2017; 13:5572-5581. [DOI: 10.1021/acs.jctc.7b00833] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. Coleman Howard
- Department
of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - James C. Womack
- Department
of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K
| | - Jacek Dziedzic
- Department
of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K
- Faculty
of Applied Physics and Mathematics, Gdańsk University of Technology, Gdańsk 80-233, Poland
| | - Chris-Kriton Skylaris
- Department
of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K
| | - Benjamin P. Pritchard
- Molecular Sciences Software Institute, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - T. Daniel Crawford
- Department
of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
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170
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Sinstein M, Scheurer C, Matera S, Blum V, Reuter K, Oberhofer H. Efficient Implicit Solvation Method for Full Potential DFT. J Chem Theory Comput 2017; 13:5582-5603. [PMID: 28910530 DOI: 10.1021/acs.jctc.7b00297] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
With the advent of efficient electronic structure methods, effective continuum solvation methods have emerged as a way to, at least partially, include solvent effects into simulations without the need for expensive sampling over solvent degrees of freedom. The multipole moment expansion (MPE) model, while based on ideas initially put forward almost 100 years ago, has recently been updated for the needs of modern electronic structure calculations. Indeed, for an all-electron code relying on localized basis sets and-more importantly-a multipole moment expansion of the electrostatic potential, the MPE method presents a particularly cheap way of solving the macroscopic Poisson equation to determine the electrostatic response of a medium surrounding a solute. In addition to our implementation of the MPE model in the FHI-aims electronic structure theory code [ Blum , V. ; Comput. Phys. Commun. 2009 , 180 , 2175 - 2196 , DOI: 10.1016/j.cpc.2009.06.022 ], we describe novel algorithms for determining equidistributed points on the solvation cavity-defined as a charge density isosurface-and the determination of cavity surface and volume from just this collection of points and their local density gradients. We demonstrate the efficacy of our model on an analytically solvable test case, against high-accuracy finite-element calculations for a set of ≈140000 2D test cases, and finally against experimental solvation free energies of a number of neutral and singly charged molecular test sets [ Andreussi , O. ; J. Chem. Phys. 2012 , 136 , 064102 , DOI: 10.1063/1.3676407 ; Marenich , A. V. ; Minnesota Solvation Database , Version 2012; University of Minnesota : Minneapolis, MN, USA , 2012 . ]. In all test cases we find that our MPE approach compares very well with given references at computational overheads < 20% and sometimes much smaller compared to a plain self-consistency cycle.
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Affiliation(s)
- Markus Sinstein
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München , Lichtenbergstraße 4, D-85747 Garching, Germany
| | - Christoph Scheurer
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München , Lichtenbergstraße 4, D-85747 Garching, Germany
| | - Sebastian Matera
- Institut für Mathematik, Freie Universität Berlin , Arnimallee 9, D-14195 Berlin, Germany
| | - Volker Blum
- Department of Mechanical Engineering and Materials Science, Duke University , Durham, North Carolina 27708, United States
| | - Karsten Reuter
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München , Lichtenbergstraße 4, D-85747 Garching, Germany
| | - Harald Oberhofer
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München , Lichtenbergstraße 4, D-85747 Garching, Germany
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171
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Pinna E, Melis C, Antidormi A, Cardia R, Sechi E, Cappellini G, d'Ischia M, Colombo L, Mula G. Deciphering Molecular Mechanisms of Interface Buildup and Stability in Porous Si/Eumelanin Hybrids. Int J Mol Sci 2017; 18:E1567. [PMID: 28753933 PMCID: PMC5536055 DOI: 10.3390/ijms18071567] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/05/2017] [Accepted: 07/11/2017] [Indexed: 01/28/2023] Open
Abstract
Porous Si/eumelanin hybrids are a novel class of organic-inorganic hybrid materials that hold considerable promise for photovoltaic applications. Current progress toward device setup is, however, hindered by photocurrent stability issues, which require a detailed understanding of the mechanisms underlying the buildup and consolidation of the eumelanin-silicon interface. Herein we report an integrated experimental and computational study aimed at probing interface stability via surface modification and eumelanin manipulation, and at modeling the organic-inorganic interface via formation of a 5,6-dihydroxyindole (DHI) tetramer and its adhesion to silicon. The results indicated that mild silicon oxidation increases photocurrent stability via enhancement of the DHI-surface interaction, and that higher oxidation states in DHI oligomers create more favorable conditions for the efficient adhesion of growing eumelanin.
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Affiliation(s)
- Elisa Pinna
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. 8 km 0.700, 09042 Monserrato, Italy.
- Istituto Officina dei Materiali CNR-IOM, Unità di Cagliari SLACS, Cittadella Universitaria di Monserrato, S.P. 8 km 0.700, 09042 Monserrato, Italy.
| | - Claudio Melis
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. 8 km 0.700, 09042 Monserrato, Italy.
- Istituto Officina dei Materiali CNR-IOM, Unità di Cagliari SLACS, Cittadella Universitaria di Monserrato, S.P. 8 km 0.700, 09042 Monserrato, Italy.
| | - Aleandro Antidormi
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. 8 km 0.700, 09042 Monserrato, Italy.
- Istituto Officina dei Materiali CNR-IOM, Unità di Cagliari SLACS, Cittadella Universitaria di Monserrato, S.P. 8 km 0.700, 09042 Monserrato, Italy.
| | - Roberto Cardia
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. 8 km 0.700, 09042 Monserrato, Italy.
| | - Elisa Sechi
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. 8 km 0.700, 09042 Monserrato, Italy.
| | - Giancarlo Cappellini
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. 8 km 0.700, 09042 Monserrato, Italy.
| | - Marco d'Ischia
- Department of Organic Chemistry and Biochemistry, University of Naples "Federico II", Via Cintia 4, 80126 Naples, Italy.
| | - Luciano Colombo
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. 8 km 0.700, 09042 Monserrato, Italy.
- Istituto Officina dei Materiali CNR-IOM, Unità di Cagliari SLACS, Cittadella Universitaria di Monserrato, S.P. 8 km 0.700, 09042 Monserrato, Italy.
| | - Guido Mula
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. 8 km 0.700, 09042 Monserrato, Italy.
- Istituto Officina dei Materiali CNR-IOM, Unità di Cagliari SLACS, Cittadella Universitaria di Monserrato, S.P. 8 km 0.700, 09042 Monserrato, Italy.
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172
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Sheng S, Miller M, Wu J. Molecular Theory of Hydration at Different Temperatures. J Phys Chem B 2017; 121:6898-6908. [DOI: 10.1021/acs.jpcb.7b04264] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shijie Sheng
- Department of Chemical and
Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Michael Miller
- Department of Chemical and
Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Jianzhong Wu
- Department of Chemical and
Environmental Engineering, University of California, Riverside, California 92521, United States
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173
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Fisicaro G, Genovese L, Andreussi O, Mandal S, Nair NN, Marzari N, Goedecker S. Soft-Sphere Continuum Solvation in Electronic-Structure Calculations. J Chem Theory Comput 2017. [DOI: 10.1021/acs.jctc.7b00375] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Giuseppe Fisicaro
- Department
of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
| | - Luigi Genovese
- Laboratoire
de simulation atomistique (L_Sim), SP2M, INAC, CEA-UJF, F-38054 Grenoble, France
| | - Oliviero Andreussi
- Institute
of Computational Science, Università della Svizzera Italiana, Via Giuseppe Buffi 13, CH-6904 Lugano, Switzerland
- Theory
and Simulations of Materials (THEOS) and National Centre for Computational
Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, Station 12, CH-1015 Lausanne, Switzerland
| | - Sagarmoy Mandal
- Department
of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Nisanth N. Nair
- Department
of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Nicola Marzari
- Theory
and Simulations of Materials (THEOS) and National Centre for Computational
Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, Station 12, CH-1015 Lausanne, Switzerland
| | - Stefan Goedecker
- Department
of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
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174
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Iyemperumal SK, Deskins NA. Evaluating Solvent Effects at the Aqueous/Pt(111) Interface. Chemphyschem 2017; 18:2171-2190. [DOI: 10.1002/cphc.201700162] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 04/11/2017] [Indexed: 11/08/2022]
Affiliation(s)
| | - N. Aaron Deskins
- Department of Chemical Engineering Worcester Polytechnic Institute Massachusetts 01609 USA
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175
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Chen J, Sit PHL. Density Functional Theory and Car–Parrinello Molecular Dynamics Study of the Hydrogen-Producing Mechanism of the Co(dmgBF2)2 and Co(dmgH)2 Cobaloxime Complexes in Acetonitrile–Water Solvent. J Phys Chem A 2017; 121:3515-3525. [DOI: 10.1021/acs.jpca.7b00163] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jinfan Chen
- School of Energy and Environment, City University of Hong Kong, Hong Kong Special Administrative Region
| | - Patrick H.-L. Sit
- School of Energy and Environment, City University of Hong Kong, Hong Kong Special Administrative Region
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176
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Goncalves TJ, Arnold U, Plessow PN, Studt F. Theoretical Investigation of the Acid Catalyzed Formation of Oxymethylene Dimethyl Ethers from Trioxane and Dimethoxymethane. ACS Catal 2017. [DOI: 10.1021/acscatal.7b00701] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tiago J. Goncalves
- Institute
of Catalysis Research and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Ulrich Arnold
- Institute
of Catalysis Research and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Philipp N. Plessow
- Institute
of Catalysis Research and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Felix Studt
- Institute
of Catalysis Research and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Institute
for Chemical Technology and Polymer Chemistry, Karlsruhe Institute of Technology, Engesserstrasse 18, 76131 Karlsruhe, Germany
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177
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Aytac Z, Ipek S, Durgun E, Tekinay T, Uyar T. Antibacterial electrospun zein nanofibrous web encapsulating thymol/cyclodextrin-inclusion complex for food packaging. Food Chem 2017; 233:117-124. [PMID: 28530556 DOI: 10.1016/j.foodchem.2017.04.095] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/11/2017] [Accepted: 04/12/2017] [Indexed: 10/19/2022]
Abstract
Thymol (THY)/γ-Cyclodextrin(γ-CD) inclusion complex (IC) encapsulated electrospun zein nanofibrous webs (zein-THY/γ-CD-IC-NF) were fabricated as a food packaging material. The formation of THY/γ-CD-IC (1:1 and 2:1) was proved by experimental (X-ray diffraction (XRD), thermal gravimetric analysis (TGA), 1H NMR) and computational techniques. THY/γ-CD-IC (2:1) exhibited higher preservation rate and stability than THY/γ-CD-IC (1:1). It is worth mentioning that zein-THY/γ-CD-IC-NF (2:1) preserved much more THY as observed in TGA and stability of THY/γ-CD-IC (2:1) was higher, as shown by a modelling study. Therefore, much more THY was released from zein-THY/γ-CD-IC-NF (2:1) than zein-THY-NF and zein-THY/γ-CD-IC-NF (1:1). Similarly, antibacterial activity of zein-THY/γ-CD-IC-NF (2:1) was higher than zein-THY-NF and zein-THY/γ-CD-IC-NF (1:1). It was demonstrated that zein-THY/γ-CD-IC-NF (2:1) was most effective in inhibiting the growth of bacteria on meat samples. These webs show potential application as an antibacterial food packaging material.
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Affiliation(s)
- Zeynep Aytac
- Institute of Materials Science & Nanotechnology, UNAM-National Nanotechnology Research Center, Bilkent University, Ankara 06800, Turkey
| | - Semran Ipek
- Department of Engineering Physics, Istanbul Medeniyet University, Istanbul 34700, Turkey
| | - Engin Durgun
- Institute of Materials Science & Nanotechnology, UNAM-National Nanotechnology Research Center, Bilkent University, Ankara 06800, Turkey
| | - Turgay Tekinay
- Life Sciences Application and Research Center, Gazi University, Ankara 06830, Turkey; Faculty of Medicine, Department of Medical Biology and Genetics, Gazi University, Ankara 06560, Turkey
| | - Tamer Uyar
- Institute of Materials Science & Nanotechnology, UNAM-National Nanotechnology Research Center, Bilkent University, Ankara 06800, Turkey.
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178
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Ringe S, Oberhofer H, Reuter K. Transferable ionic parameters for first-principles Poisson-Boltzmann solvation calculations: Neutral solutes in aqueous monovalent salt solutions. J Chem Phys 2017; 146:134103. [DOI: 10.1063/1.4978850] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Stefan Ringe
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Harald Oberhofer
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Karsten Reuter
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Lichtenbergstr. 4, D-85747 Garching, Germany
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179
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Methanol Oxidation on Pt(111) from First-Principles in Heterogeneous and Electrocatalysis. Electrocatalysis (N Y) 2017. [DOI: 10.1007/s12678-017-0370-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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180
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Sundararaman R, Goddard WA, Arias TA. Grand canonical electronic density-functional theory: Algorithms and applications to electrochemistry. J Chem Phys 2017; 146:114104. [DOI: 10.1063/1.4978411] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Ravishankar Sundararaman
- Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
- Joint Center for Artificial Photosynthesis, California Institute of Technology, Pasadena, California 91125, USA
| | - William A. Goddard
- Joint Center for Artificial Photosynthesis, California Institute of Technology, Pasadena, California 91125, USA
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, USA
| | - Tomas A. Arias
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, USA
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181
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Sundararaman R, Schwarz K. Evaluating continuum solvation models for the electrode-electrolyte interface: Challenges and strategies for improvement. J Chem Phys 2017; 146:084111. [PMID: 28249432 PMCID: PMC5569893 DOI: 10.1063/1.4976971] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Ab initio modeling of electrochemical systems is becoming a key tool for understanding and predicting electrochemical behavior. Development and careful benchmarking of computational electrochemical methods are essential to ensure their accuracy. Here, using charging curves for an electrode in the presence of an inert aqueous electrolyte, we demonstrate that most continuum models, which are parameterized and benchmarked for molecules, anions, and cations in solution, undersolvate metal surfaces, and underestimate the surface charge as a function of applied potential. We examine features of the electrolyte and interface that are captured by these models and identify improvements necessary for realistic electrochemical calculations of metal surfaces. Finally, we reparameterize popular solvation models using the surface charge of Ag(100) as a function of voltage to find improved accuracy for metal surfaces without significant change in utility for molecular and ionic solvation.
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Affiliation(s)
- Ravishankar Sundararaman
- Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, 110 8th St, Troy, NY 12180 (USA)
| | - Kathleen Schwarz
- National Institute of Standards and Technology, Material Measurement Laboratory, 100 Bureau Dr, Gaithersburg, MD, 20899 (USA)
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182
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Gray CM, Saravanan K, Wang G, Keith JA. Quantifying solvation energies at solid/liquid interfaces using continuum solvation methods. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2016.1273525] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Corinne M. Gray
- Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh, PA, USA
| | - Karthikeyan Saravanan
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Guofeng Wang
- Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - John A. Keith
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, USA
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183
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Existence, bifurcation, and geometric evolution of quasi-bilayers in the multicomponent functionalized Cahn-Hilliard equation. J Math Biol 2017; 75:443-489. [PMID: 28040877 DOI: 10.1007/s00285-016-1089-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 08/20/2016] [Indexed: 10/20/2022]
Abstract
Multicomponent bilayer structures arise as the ubiquitous plasma membrane in cellular biology and as blends of amphiphilic copolymers used in electrolyte membranes, drug delivery, and emulsion stabilization within the context of synthetic chemistry. We present the multicomponent functionalized Cahn-Hilliard (mFCH) free energy as a model which allows competition between bilayers with distinct composition and between bilayers and higher codimensional structures, such as co-dimension two filaments and co-dimension three micelles. We construct symmetric and asymmetric homoclinic bilayer profiles via a billiard limit potential and show that co-dimensional bifurcation is driven by the experimentally observed layer-by-layer pearling mechanism. We investigate the stability and slow geometric evolution of multicomponent bilayer interfaces within the context of an [Formula: see text] gradient flow of the mFCH, addressing the impact of aspect ratio of the amphiphile (lipid or copolymer unit) on the intrinsic curvature and the codimensional bifurcation. In particular we derive a Canham-Helfrich sharp interface energy whose intrinsic curvature arises through a Melnikov parameter associated to amphiphile aspect ratio.
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184
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Blumenthal L, Kahk JM, Sundararaman R, Tangney P, Lischner J. Energy level alignment at semiconductor–water interfaces from atomistic and continuum solvation models. RSC Adv 2017. [DOI: 10.1039/c7ra08357b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Efficient electronic energy level alignment at solid–liquid interfaces with continuum solvation models.
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Affiliation(s)
- Lars Blumenthal
- Imperial College London
- Department of Physics
- London SW7 2AZ
- UK
- Thomas Young Centre for Theory and Simulation of Materials
| | - Juhan Matthias Kahk
- Imperial College London
- Department of Materials
- Royal School of Mines
- London SW7 2AZ
- UK
| | | | - Paul Tangney
- Imperial College London
- Department of Physics
- London SW7 2AZ
- UK
- Imperial College London
| | - Johannes Lischner
- Imperial College London
- Department of Physics
- London SW7 2AZ
- UK
- Imperial College London
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185
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Ab Initio Molecular Dynamics Simulation of Infrared Absorption Spectra of H3O+ and H5O+2 in Nonaqueous Solutions of Trifluoromethanesulfonic Acid Hydrates. J SOLUTION CHEM 2016. [DOI: 10.1007/s10953-016-0503-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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186
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Aytac Z, Yildiz ZI, Kayaci-Senirmak F, San Keskin NO, Kusku SI, Durgun E, Tekinay T, Uyar T. Fast-Dissolving, Prolonged Release, and Antibacterial Cyclodextrin/Limonene-Inclusion Complex Nanofibrous Webs via Polymer-Free Electrospinning. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:7325-7334. [PMID: 27616160 DOI: 10.1021/acs.jafc.6b02632] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We have proposed a new strategy for preparing free-standing nanofibrous webs from an inclusion complex (IC) of a well-known flavor/fragrance compound (limonene) with three modified cyclodextrins (HPβCD, MβCD, and HPγCD) via electrospinning (CD/limonene-IC-NFs) without using a polymeric matrix. The experimental and computational modeling studies proved that the stoichiometry of the complexes was 1:1 for CD/limonene systems. MβCD/limonene-IC-NF released much more limonene at 37, 50, and 75 °C than HPβCD/limonene-IC-NF and HPγCD/limonene-IC-NF because of the greater amount of preserved limonene. Moreover, MβCD/limonene-IC-NF has released only 25% (w/w) of its limonene, whereas HPβCD/limonene-IC-NF and HPγCD/limonene-IC-NF released 51 and 88% (w/w) of their limonene in 100 days, respectively. CD/limonene-IC-NFs exhibited high antibacterial activity against E. coli and S. aureus. The water solubility of limonene increased significantly and CD/limonene-IC-NFs were dissolved in water in a few seconds. In brief, CD/limonene-IC-NFs with fast-dissolving character enhanced the thermal stability and prolonged the shelf life along with antibacterial properties could be quite applicable in food and oral care applications.
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Affiliation(s)
- Zeynep Aytac
- Institute of Materials Science & Nanotechnology, Bilkent University , Ankara 06800, Turkey
- UNAM-National Nanotechnology Research Center, Bilkent University , Ankara 06800, Turkey
| | - Zehra Irem Yildiz
- Institute of Materials Science & Nanotechnology, Bilkent University , Ankara 06800, Turkey
- UNAM-National Nanotechnology Research Center, Bilkent University , Ankara 06800, Turkey
| | - Fatma Kayaci-Senirmak
- Institute of Materials Science & Nanotechnology, Bilkent University , Ankara 06800, Turkey
- UNAM-National Nanotechnology Research Center, Bilkent University , Ankara 06800, Turkey
| | - Nalan Oya San Keskin
- UNAM-National Nanotechnology Research Center, Bilkent University , Ankara 06800, Turkey
- Department of Biology, Polatlı Faculty of Literature and Science, Gazi University , Ankara 06900, Turkey
- Life Sciences Application and Research Center, Gazi University , Ankara 06830, Turkey
| | - Semran Ipek Kusku
- UNAM-National Nanotechnology Research Center, Bilkent University , Ankara 06800, Turkey
- Department of Engineering Physics, Istanbul Medeniyet University , Istanbul 34700, Turkey
| | - Engin Durgun
- Institute of Materials Science & Nanotechnology, Bilkent University , Ankara 06800, Turkey
- UNAM-National Nanotechnology Research Center, Bilkent University , Ankara 06800, Turkey
| | - Turgay Tekinay
- Life Sciences Application and Research Center, Gazi University , Ankara 06830, Turkey
- Department of Medical Biology and Genetics, Faculty of Medicine, Gazi University , Ankara 06560, Turkey
| | - Tamer Uyar
- Institute of Materials Science & Nanotechnology, Bilkent University , Ankara 06800, Turkey
- UNAM-National Nanotechnology Research Center, Bilkent University , Ankara 06800, Turkey
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187
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Dziedzic J, Mao Y, Shao Y, Ponder J, Head-Gordon T, Head-Gordon M, Skylaris CK. TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field. J Chem Phys 2016; 145:124106. [DOI: 10.1063/1.4962909] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Jacek Dziedzic
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, Gdańsk, Poland
| | - Yuezhi Mao
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yihan Shao
- Q-Chem Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Jay Ponder
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Teresa Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
- Department of Bioengineering, University of California, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
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188
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Chen LD, Urushihara M, Chan K, Nørskov JK. Electric Field Effects in Electrochemical CO2 Reduction. ACS Catal 2016. [DOI: 10.1021/acscatal.6b02299] [Citation(s) in RCA: 293] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Leanne D. Chen
- SUNCAT
Center for Interface Science and Catalysis, Department of Chemical
Engineering, Stanford University, Stanford, California 94305−5025, United States
- SUNCAT
Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Makoto Urushihara
- SUNCAT
Center for Interface Science and Catalysis, Department of Chemical
Engineering, Stanford University, Stanford, California 94305−5025, United States
- Central
Research Institute, Mitsubishi Materials Corporation, 1002−14
Mukohyama, Naka, Ibaraki 311−0102, Japan
| | - Karen Chan
- SUNCAT
Center for Interface Science and Catalysis, Department of Chemical
Engineering, Stanford University, Stanford, California 94305−5025, United States
- SUNCAT
Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Jens K. Nørskov
- SUNCAT
Center for Interface Science and Catalysis, Department of Chemical
Engineering, Stanford University, Stanford, California 94305−5025, United States
- SUNCAT
Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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189
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La Penna G, Mori Y, Kitahara R, Akasaka K, Okamoto Y. Modeling 15N NMR chemical shift changes in protein backbone with pressure. J Chem Phys 2016; 145:085104. [DOI: 10.1063/1.4961507] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Giovanni La Penna
- Institute for Chemistry of Organo–Metallic Compounds (ICCOM), National Research Council of Italy (Cnr), Via Madonna del Piano 10, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Yoshiharu Mori
- Theoretical and Computational Molecular Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki, 444-8585, Japan
| | - Ryo Kitahara
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu 525-8577, Japan
| | - Kazuyuki Akasaka
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, Kyoto 606-8522, Japan
| | - Yuko Okamoto
- Department of Physics, School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya, Aichi 464-8602, Japan
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190
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Rosa M, Micciarelli M, Laio A, Baroni S. Sampling Molecular Conformers in Solution with Quantum Mechanical Accuracy at a Nearly Molecular-Mechanics Cost. J Chem Theory Comput 2016; 12:4385-9. [DOI: 10.1021/acs.jctc.6b00470] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marta Rosa
- SISSA − Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34136 Trieste, Italy
| | - Marco Micciarelli
- SISSA − Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34136 Trieste, Italy
| | - Alessandro Laio
- SISSA − Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34136 Trieste, Italy
| | - Stefano Baroni
- SISSA − Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34136 Trieste, Italy
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191
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Montemore MM, Andreussi O, Medlin JW. Hydrocarbon adsorption in an aqueous environment: A computational study of alkyls on Cu(111). J Chem Phys 2016; 145:074702. [PMID: 27544118 DOI: 10.1063/1.4961027] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Hydrocarbon chains are important intermediates in various aqueous-phase surface processes, such as CO2 electroreduction, aqueous Fischer-Tropsch synthesis, and aqueous phase reforming of biomass-derived molecules. Further, the interaction between water and adsorbed hydrocarbons represents a difficult case for modern computational methods. Here, we explore various methods for calculating the energetics of this interaction within the framework of density functional theory and explore trade-offs between the use of low water coverages, molecular dynamics approaches, and minima hopping for identification of low energy structures. An effective methodology for simulating low temperature processes is provided by using a unit cell in which the vacuum space is filled with water, employing the minima hopping algorithm to search for low-lying minima, and including dispersion (van der Waals) interactions. Using this methodology, we show that a high coverage of adsorbed alkyls is destabilized by the presence of water, while a low coverage of alkyls is stabilized. Solvation has a small effect on the energetics of hydrocarbon chain growth, generally decreasing its favorability at low temperatures. We studied higher temperatures by running molecular dynamics simulations starting at the minima found by the minima hopping algorithm and found that increased temperatures facilitate chain growth. The self-consistent continuum solvation method effectively describes the alkyl-water interaction and is in general agreement with the explicit solvation results in most cases, but care should be taken at high alkyl coverage.
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Affiliation(s)
- Matthew M Montemore
- Department of Mechanical Engineering, University of Colorado Boulder, UCB 427, Boulder, Colorado 80309, USA
| | - Oliviero Andreussi
- Faculty of Informatics, Institute of Computational Science, Università della Svizzera Italiana, Via G. Buffi 13, 6904 Lugano, Switzerland
| | - J Will Medlin
- Department of Chemical and Biological Engineering, University of Colorado Boulder, UCB 596, Boulder, Colorado 80309, USA
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192
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Timrov I, Micciarelli M, Rosa M, Calzolari A, Baroni S. Multimodel Approach to the Optical Properties of Molecular Dyes in Solution. J Chem Theory Comput 2016; 12:4423-9. [DOI: 10.1021/acs.jctc.6b00417] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Iurii Timrov
- SISSA − Scuola Internazionale
Superiore di Studi Avanzati, Via Bonomea
265, 34136 Trieste, Italy
| | - Marco Micciarelli
- SISSA − Scuola Internazionale
Superiore di Studi Avanzati, Via Bonomea
265, 34136 Trieste, Italy
| | - Marta Rosa
- SISSA − Scuola Internazionale
Superiore di Studi Avanzati, Via Bonomea
265, 34136 Trieste, Italy
| | - Arrigo Calzolari
- CNR-NANO, Istituto Nanoscienze, Centro S3, Via Campi 213A, 41125 Modena, Italy
| | - Stefano Baroni
- SISSA − Scuola Internazionale
Superiore di Studi Avanzati, Via Bonomea
265, 34136 Trieste, Italy
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193
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Sakong S, Groß A. The Importance of the Electrochemical Environment in the Electro-Oxidation of Methanol on Pt(111). ACS Catal 2016. [DOI: 10.1021/acscatal.6b00931] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sung Sakong
- Institute
of Theoretical Chemistry, Ulm University, 89069 Ulm, Germany
| | - Axel Groß
- Institute
of Theoretical Chemistry, Ulm University, 89069 Ulm, Germany
- Electrochemical
Energy Storage, Helmholtz Institute Ulm (HIU), 89069 Ulm, Germany
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194
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Ringe S, Oberhofer H, Hille C, Matera S, Reuter K. Function-Space-Based Solution Scheme for the Size-Modified Poisson-Boltzmann Equation in Full-Potential DFT. J Chem Theory Comput 2016; 12:4052-66. [PMID: 27323006 DOI: 10.1021/acs.jctc.6b00435] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The size-modified Poisson-Boltzmann (MPB) equation is an efficient implicit solvation model which also captures electrolytic solvent effects. It combines an account of the dielectric solvent response with a mean-field description of solvated finite-sized ions. We present a general solution scheme for the MPB equation based on a fast function-space-oriented Newton method and a Green's function preconditioned iterative linear solver. In contrast to popular multigrid solvers, this approach allows us to fully exploit specialized integration grids and optimized integration schemes. We describe a corresponding numerically efficient implementation for the full-potential density-functional theory (DFT) code FHI-aims. We show that together with an additional Stern layer correction the DFT+MPB approach can describe the mean activity coefficient of a KCl aqueous solution over a wide range of concentrations. The high sensitivity of the calculated activity coefficient on the employed ionic parameters thereby suggests to use extensively tabulated experimental activity coefficients of salt solutions for a systematic parametrization protocol.
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Affiliation(s)
- Stefan Ringe
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München , Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Harald Oberhofer
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München , Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Christoph Hille
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München , Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Sebastian Matera
- Fachbereich f. Mathematik u. Informatik, Freie Universität Berlin , Otto-von-Simson-Str. 19, D-14195 Berlin, Germany
| | - Karsten Reuter
- Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München , Lichtenbergstr. 4, D-85747 Garching, Germany
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195
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Lipparini F, Mennucci B. Perspective: Polarizable continuum models for quantum-mechanical descriptions. J Chem Phys 2016; 144:160901. [DOI: 10.1063/1.4947236] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Filippo Lipparini
- Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, D55128 Mainz, Germany
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
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196
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Aytac Z, Kusku SI, Durgun E, Uyar T. Encapsulation of gallic acid/cyclodextrin inclusion complex in electrospun polylactic acid nanofibers: Release behavior and antioxidant activity of gallic acid. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2016; 63:231-9. [PMID: 27040215 DOI: 10.1016/j.msec.2016.02.063] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Revised: 02/03/2016] [Accepted: 02/22/2016] [Indexed: 01/05/2023]
Abstract
Cyclodextrin-inclusion complexes (CD-ICs) possess great prominence in food and pharmaceutical industries due to their enhanced ability for stabilization of active compounds during processing, storage and usage. Here, CD-IC of gallic acid (GA) with hydroxypropyl-beta-cyclodextrin (GA/HPβCD-IC) was prepared and then incorporated into polylactic acid (PLA) nanofibers (PLA/GA/HPβCD-IC-NF) using electrospinning technique to observe the effect of CD-ICs in the release behavior of GA into three different mediums (water, 10% ethanol and 95% ethanol). The GA incorporated PLA nanofibers (PLA/GA-NFs) were served as control. Phase solubility studies showed an enhanced solubility of GA with increasing amount of HPβCD. The detailed characterization techniques (XRD, TGA and (1)H-NMR) confirmed the formation of inclusion complex between GA and HPβCD. Computational modeling studies indicated that the GA made an efficient complex with HPβCD at 1:1 either in vacuum or aqueous system. SEM images revealed the bead-free and uniform morphology of PLA/GA/HPβCD-IC-NF. The release studies of GA from PLA/GA/HPβCD-IC-NF and PLA/GA-NF were carried out in water, 10% ethanol and 95% ethanol, and the findings revealed that PLA/GA/HPβCD-IC-NF has released much more amount of GA in water and 10% ethanol system when compared to PLA/GA-NF. In addition, GA was released slowly from PLA/GA/HPβCD-IC-NF into 95% ethanol when compared to PLA/GA-NF. It was also observed that electrospinning process had no negative effect on the antioxidant activity of GA when GA was incorporated in PLA nanofibers.
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Affiliation(s)
- Zeynep Aytac
- Institute of Materials Science & Nanotechnology, Bilkent University, Ankara 06800, Turkey; UNAM-National Nanotechnology Research Center, Bilkent University, Ankara 06800, Turkey
| | - Semran Ipek Kusku
- UNAM-National Nanotechnology Research Center, Bilkent University, Ankara 06800, Turkey; Department of Engineering Physics, Istanbul Medeniyet University, Göztepe 34700, Istanbul, Turkey
| | - Engin Durgun
- Institute of Materials Science & Nanotechnology, Bilkent University, Ankara 06800, Turkey; UNAM-National Nanotechnology Research Center, Bilkent University, Ankara 06800, Turkey
| | - Tamer Uyar
- Institute of Materials Science & Nanotechnology, Bilkent University, Ankara 06800, Turkey; UNAM-National Nanotechnology Research Center, Bilkent University, Ankara 06800, Turkey.
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197
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Garcia-Ratés M, López N. Multigrid-Based Methodology for Implicit Solvation Models in Periodic DFT. J Chem Theory Comput 2016; 12:1331-41. [PMID: 26771105 DOI: 10.1021/acs.jctc.5b00949] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Continuum solvation models have become a widespread approach for the study of environmental effects in Density Functional Theory (DFT) methods. Adding solvation contributions mainly relies on the solution of the Generalized Poisson Equation (GPE) governing the behavior of the electrostatic potential of a system. Although multigrid methods are especially appropriate for the solution of partial differential equations, up to now, their use is not much extended in DFT-based codes because of their high memory requirements. In this Article, we report the implementation of an accelerated multigrid solver-based approach for the treatment of solvation effects in the Vienna ab initio Simulation Package (VASP). The stated implicit solvation model, named VASP-MGCM (VASP-Multigrid Continuum Model), uses an efficient and transferable algorithm for the product of sparse matrices that highly outperforms serial multigrid solvers. The calculated solvation free energies for a set of molecules, including neutral and ionic species, as well as adsorbed molecules on metallic surfaces, agree with experimental data and with simulation results obtained with other continuum models.
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Affiliation(s)
- Miquel Garcia-Ratés
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology , Avinguda dels Països Catalans 16, 43007 Tarragona, Spain
| | - Núria López
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology , Avinguda dels Països Catalans 16, 43007 Tarragona, Spain
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198
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Bani-Hashemian MH, Brück S, Luisier M, VandeVondele J. A generalized Poisson solver for first-principles device simulations. J Chem Phys 2016; 144:044113. [DOI: 10.1063/1.4940796] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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199
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Barnard AS. Challenges in modelling nanoparticles for drug delivery. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:023002. [PMID: 26682622 DOI: 10.1088/0953-8984/28/2/023002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Although there have been significant advances in the fields of theoretical condensed matter and computational physics, when confronted with the complexity and diversity of nanoparticles available in conventional laboratories a number of modeling challenges remain. These challenges are generally shared among application domains, but the impacts of the limitations and approximations we make to overcome them (or circumvent them) can be more significant one area than another. In the case of nanoparticles for drug delivery applications some immediate challenges include the incompatibility of length-scales, our ability to model weak interactions and solvation, the complexity of the thermochemical environment surrounding the nanoparticles, and the role of polydispersivity in determining properties and performance. Some of these challenges can be met with existing technologies, others with emerging technologies including the data-driven sciences; some others require new methods to be developed. In this article we will briefly review some simple methods and techniques that can be applied to these (and other) challenges, and demonstrate some results using nanodiamond-based drug delivery platforms as an exemplar.
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Affiliation(s)
- Amanda S Barnard
- CSIRO Virtual Nanoscience Laboratory, 343 Royal Parade, Parkville, Victoria 3052, Australia
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Fisicaro G, Genovese L, Andreussi O, Marzari N, Goedecker S. A generalized Poisson and Poisson-Boltzmann solver for electrostatic environments. J Chem Phys 2016; 144:014103. [DOI: 10.1063/1.4939125] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- G. Fisicaro
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - L. Genovese
- University of Grenoble Alpes, CEA, INAC-SP2M, L_Sim, F-38000 Grenoble, France
| | - O. Andreussi
- Institute of Computational Science, Università della Svizzera Italiana, Via Giuseppe Buffi 13, CH-6904 Lugano, Switzerland
- Theory and Simulations of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, Station 12, CH-1015 Lausanne, Switzerland
| | - N. Marzari
- Theory and Simulations of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, Station 12, CH-1015 Lausanne, Switzerland
| | - S. Goedecker
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
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