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Pisani WA, Jenness GR, Schutt TC, Larson SL, Shukla MK. Preferential Adsorption of Prominent Amino Acids in the Urease Enzyme of Sporosarcina pasteurii on Arid Soil Components: A Periodic DFT Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:13414-13428. [PMID: 36279412 DOI: 10.1021/acs.langmuir.2c01854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The urease enzyme is commonly used in microbially induced carbonate precipitation (MICP) and enzyme-induced carbonate precipitation (EICP) to heal and strengthen soil. Improving our understanding of the adsorption of the urease enzyme with various soil surfaces can lead to advancements in the MICP and EICP engineering methods as well as other areas of soil science. In this work, we use density functional theory (DFT) to investigate the urease enzyme's binding ability with four common arid soil components: quartz, corundum, albite, and hematite. As the urease enzyme cannot directly be simulated with DFT due to its size, the amino acids comprising at least 5% of the urease enzyme were simulated instead. An adsorption model incorporating the Gibbs free energy was used to determine the existence of amino acid-mineral binding modes. It was found that the nine simulated amino acids bind preferentially to the different soil components. Alanine favors corundum, glycine and threonine favor hematite, and aspartic acid favors albite. It was found that, under the standard environmental conditions considered here, amino acid binding to quartz is unfavorable. In the polymeric form where the side chains would dominate the binding interactions, hematite favors aspartic acid through its R-OH group and corundum favors glutamic acid through its R-Ket group. Overall, our model predicts that the urease enzyme produced by Sporosarcina pasteurii can bind to various oxides found in arid soil through its alanine, glycine, aspartic/glutamic acid, or threonine residues.
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Affiliation(s)
- William A Pisani
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee37830, United States
- Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, Mississippi39180, United States
| | - Glen R Jenness
- Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, Mississippi39180, United States
| | - Timothy C Schutt
- Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, Mississippi39180, United States
| | - Steven L Larson
- Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, Mississippi39180, United States
| | - Manoj K Shukla
- Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, Mississippi39180, United States
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2
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Li C, Zhu N, Yang S, He X, Zheng S, Sun Z, Dionysiou DD. A review of clay based photocatalysts: Role of phyllosilicate mineral in interfacial assembly, microstructure control and performance regulation. CHEMOSPHERE 2021; 273:129723. [PMID: 33524745 DOI: 10.1016/j.chemosphere.2021.129723] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/01/2021] [Accepted: 01/16/2021] [Indexed: 06/12/2023]
Abstract
Over the past decades, inspired by the outstanding properties of clay minerals such as abundance, low-cost, environmental benignity, high stability, and regularly arranged silica-alumina framework, researchers put much efforts on the interface assembly and surface modification of natural minerals with bare photocatalysts, i.e. TiO2, g-C3N4, ZnO, MoS2, etc. The clay-based hybrid photocatalysts have resulted in a rich database for their tailor-designed microstructures, characterizations, and environmental-related applications. Therefore, in this study, we took a brief introduction of three representative minerals, i.e. kaolinite, montmorillonite and rectorite, and discussed their basic merits in photocatalysis applications. After that, we summarized the recent advances in construction of stable visible-light driven photocatalysts based on these minerals. The structure-activity relationships between the properties of clay types, pore structure, distribution/dispersion and light absorption, carrier separation efficiency as well as redox performance were illustrated in detail. Such representative information would provide theoretical basis and scientific support for the application of clay based photocatalysts. Finally, we pointed out the major challenges and future directions at the end of this review. Undoubtedly, control and preparation of novel photocatalysts based on clays will continue to witness many breakthroughs in the arena of solar-driven technologies.
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Affiliation(s)
- Chunquan Li
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing, 100083, PR China
| | - Ningyuan Zhu
- Zigui Ecological Station for Three Gorges Dam Project, State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Sciences, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008, China
| | - Shanshan Yang
- School of Earth and Space Sciences, Peking University, Beijing, 100871, PR China
| | - Xuwen He
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing, 100083, PR China
| | - Shuilin Zheng
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing, 100083, PR China
| | - Zhiming Sun
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing, 100083, PR China.
| | - Dionysios D Dionysiou
- Department of Chemical and Environmental Engineering (DCEE), University of Cincinnati, Cincinnati, OH, 45221-0012, USA
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Yamada SA, Hung ST, Shin JY, Fayer MD. Complex Formation and Dissociation Dynamics on Amorphous Silica Surfaces. J Phys Chem B 2021; 125:4566-4581. [DOI: 10.1021/acs.jpcb.1c01225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Steven A. Yamada
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Samantha T. Hung
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Jae Yoon Shin
- Department of Advanced Materials Chemistry, Korea University, Sejong, Korea
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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4
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Bag S, Rauwolf S, Suyetin M, Schwaminger SP, Wenzel W, Berensmeier S. Buffer Influence on the Amino Acid Silica Interaction. Chemphyschem 2020; 21:2347-2356. [PMID: 32794279 PMCID: PMC7702087 DOI: 10.1002/cphc.202000572] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/11/2020] [Indexed: 12/11/2022]
Abstract
Protein-surface interactions are exploited in various processes in life sciences and biotechnology. Many of such processes are performed in presence of a buffer system, which is generally believed to have an influence on the protein-surface interaction but is rarely investigated systematically. Combining experimental and theoretical methodologies, we herein demonstrate the strong influence of the buffer type on protein-surface interactions. Using state of the art chromatographic experiments, we measure the interaction between individual amino acids and silica, as a reference to understand protein-surface interactions. Among all the 20 proteinogenic amino acids studied, we found that arginine (R) and lysine (K) bind most strongly to silica, a finding validated by free energy calculations. We further measured the binding of R and K at different pH in presence of two different buffers, MOPS (3-(N-morpholino)propanesulfonic acid) and TRIS (tris(hydroxymethyl)aminomethane), and find dramatically different behavior. In presence of TRIS, the binding affinity of R/K increases with pH, whereas we observe an opposite trend for MOPS. These results can be understood using a multiscale modelling framework combining molecular dynamics simulation and Langmuir adsorption model. The modelling approach helps to optimize buffer conditions in various fields like biosensors, drug delivery or bio separation engineering prior to the experiment.
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Affiliation(s)
- Saientan Bag
- Institute of Nanotechnology (INT)Karlsruhe Institute of Technology (KIT)KarlsruheGermany
| | - Stefan Rauwolf
- Bioseparation Engineering GroupDepartment of Mechanical EngineeringTechnical University of Munich(TUM)GarchingGermany
| | - Mikhail Suyetin
- Institute of Nanotechnology (INT)Karlsruhe Institute of Technology (KIT)KarlsruheGermany
| | - Sebastian P. Schwaminger
- Bioseparation Engineering GroupDepartment of Mechanical EngineeringTechnical University of Munich(TUM)GarchingGermany
| | - Wolfgang Wenzel
- Institute of Nanotechnology (INT)Karlsruhe Institute of Technology (KIT)KarlsruheGermany
| | - Sonja Berensmeier
- Bioseparation Engineering GroupDepartment of Mechanical EngineeringTechnical University of Munich(TUM)GarchingGermany
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Nakamura S, Tsuji Y, Yoshizawa K. Role of Hydrogen-Bonding and OH-π Interactions in the Adhesion of Epoxy Resin on Hydrophilic Surfaces. ACS OMEGA 2020; 5:26211-26219. [PMID: 33073147 PMCID: PMC7557942 DOI: 10.1021/acsomega.0c03798] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/22/2020] [Indexed: 05/14/2023]
Abstract
Epoxy resin adhesives are widely used for joining metal alloys in various industrial fields. To elucidate the adhesion mechanism microscopically, we investigated the interfacial interactions of epoxy resin with hydroxylated silica (0 0 1) and γ-alumina (0 0 1) surfaces using periodic density functional theory calculations as well as density of states (DOS) and crystal orbital Hamilton population (COHP) analyses. To better understand the interfacial interactions, we employed and analyzed water and benzene molecules as hydrophilic and hydrophobic adsorbates, respectively. Structural features and calculated adhesion energies reveal that these small adsorbates have a higher affinity for the γ-alumina surface than that for the silica surface, while a fragmentary model for the epoxy resin exhibits a strong interaction with the silica surface. This discrepancy suggests that the structural features of the hydroxylated silica surface dictate its affinity to a specific species. Partial DOS and COHP curves provide evidence for the presence of OH-π interactions between the OH groups on the surfaces and the benzene rings of the epoxy resin fragments. The orbital interaction energies of the H-bonding and OH-π interactions evaluated from the integrated COHP indicate that the OH-π interaction is a nonnegligible origin of the adhesion interaction, even when polymers with hydrophobic benzene rings are adsorbed on hydroxylated surfaces.
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Dang Y, Yao Y, Liu Y, Wei B, Feng X, Chen X, Yang C. Diffusion properties of aromatic hydrocarbons in mesoporous alumina: A molecular dynamics study. Chem Eng Sci 2019. [DOI: 10.1016/j.ces.2019.04.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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7
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Musa MSM, Sulaiman WRW, Majid ZA, Majid ZA, Idris AK, Rajaei K. Application of henna extract in minimizing surfactant adsorption on quartz sand in saline condition: A sacrificial agent approach. SN APPLIED SCIENCES 2019. [DOI: 10.1007/s42452-019-0870-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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8
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Molpeceres G, Rimola A, Ceccarelli C, Kästner J, Ugliengo P, Maté B. Silicate-mediated interstellar water formation: A theoretical study. MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY 2019; 482:5389-5400. [PMID: 31156274 PMCID: PMC6544534 DOI: 10.1093/mnras/sty3024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Water is one of the most abundant molecules in the form of solid ice phase in the different regions of the interstellar medium (ISM). This large abundance cannot be properly explained by using only traditional low temperature gas-phase reactions. Thus, surface chemical reactions are believed to be major synthetic channels for the formation of interstellar water ice. Among the different proposals, hydrogenation of atomic O (i.e., 2H + O → H2O) is a chemically "simple" and plausible reaction toward water formation occurring on the surfaces of interstellar grains. Here, novel theoretical results concerning the formation of water adopting this mechanism on the crystalline (010) Mg2SiO4 surface (a unequivocally identified interstellar silicate) are presented. The investigated reaction aims to simulate the formation of the first water ice layer covering the silicate core of dust grains. Adsorption of the atomic O as a first step of the reaction has been computed, results indicating that a peroxo (O 2 2 - ) group is formed. The following steps involve the adsorption, diffusion and reaction of two successive H atoms with the adsorbed O atom. Results indicate that H diffusion on the surface has barriers of 4-6 kcal mol-1, while actual formation of OH and H2O present energy barriers of 22-23 kcal mol-1. Kinetic study results show that tunneling is crucial for the occurrence of the reactions and that formation of OH and H2O are the bottlenecks of the overall process. Several astrophysical implications derived from the theoretical results are provided as concluding remarks.
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Affiliation(s)
- Germán Molpeceres
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 123, E-28006, Madrid, Spain
| | - Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Cecilia Ceccarelli
- Univ. Grenoble Alpes, CNRS, Institut de Planétologie et d’Astrophysique de Grenoble (IPAG), 38000 Grenoble, France
| | - Johannes Kästner
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS), Università degli Studi di Torino, Via P. Giuria 7, 10125 Torino, Italy
| | - Belén Maté
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 123, E-28006, Madrid, Spain
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9
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Pantaleone S, Ugliengo P, Sodupe M, Rimola A. When the Surface Matters: Prebiotic Peptide-Bond Formation on the TiO 2 (101) Anatase Surface through Periodic DFT-D2 Simulations. Chemistry 2018; 24:16292-16301. [PMID: 30212609 DOI: 10.1002/chem.201803263] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Indexed: 12/13/2022]
Abstract
The mechanism of the peptide-bond formation between two glycine (Gly) molecules has been investigated by means of PBE-D2* and PBE0-D2* periodic simulations on the TiO2 (101) anatase surface. This is a process of great relevance both in fundamental prebiotic chemistry, as the reaction univocally belongs to one of the different organizational events that ultimately led to the emergence of life on Earth, as well as from an industrial perspective, since formation of amides is a key reaction for pharmaceutical companies. The efficiency of the surface catalytic sites is demonstrated by comparing the reactions in the gas phase and on the surface. At variance with the uncatalyzed gas-phase reaction, which involves a concerted nucleophilic attack and dehydration step, on the surface these two steps occur along a stepwise mechanism. The presence of surface Lewis and Brönsted sites exerts some catalytic effect by lowering the free energy barrier for the peptide-bond formation by about 6 kcal mol-1 compared to the gas-phase reaction. Moreover, the co-presence of molecules acting as proton-transfer assistants (i.e., H2 O and Gly) provide a more significant kinetic energy barrier decrease. The reaction on the surface is also favorable from a thermodynamic standpoint, involving very large and negative reaction energies. This is due to the fact that the anatase surface also acts as a dehydration agent during the condensation reaction, since the outermost coordinatively unsaturated Ti atoms strongly anchor the released water molecules. Our theoretical results provide a comprehensive atomistic interpretation of the experimental results of Martra et al. (Angew. Chem. Int. Ed. 2014, 53, 4671), in which polyglycine formation was obtained by successive feedings of Gly vapor on TiO2 surfaces in dry conditions and are, therefore, relevant in a prebiotic context envisaging dry and wet cycles occurring, at mineral surfaces, in a small pool.
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Affiliation(s)
- Stefano Pantaleone
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS), Inter-Departmental centre, Università degli Studi di Torino, Via P. Giuria 7, 10125, Torino, Italy
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain
| | - Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain
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10
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The Adhesion Mechanism of Marine Mussel Foot Protein: Adsorption of L-Dopa onα- and β-Cristobalite Silica Using Density Functional Theory. J CHEM-NY 2017. [DOI: 10.1155/2017/8756519] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Marine mussels strongly adhere to various surfaces and endure their attachment under a variety of conditions. In order to understand the basic mechanism involved, we study the adsorption of L-dopa molecule on hydrophilic geminal and terminal isolated silanols of silica (001) surface. High content of modified amino acid L-dopa is found in the glue-like material secreted by the mussels through which it sticks to various surfaces under water. To understand the adsorption behavior, we have made use of periodic Density Functional Theory (DFT) study. The L-dopa molecule adheres to silica surfaces terminated with geminal and terminal silanols via its catechol part. In both cases, the adhesion is achieved through the formation of 4 H-bonds. A binding energy of 29.48 and 31.67 kcal/mol has been estimated, after the inclusion of dispersion energy, for geminal and terminal silanols of silica, respectively. These results suggest a relatively stronger adhesion of dopa molecule for surface with terminal isolated silanols.
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11
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Influence of Defects in Boron Nitride Nanotubes in the Adsorption of Molecules. Insights from B3LYP-D2* Periodic Simulations. CRYSTALS 2016. [DOI: 10.3390/cryst6050063] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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12
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Halo M, Ferrari AM, Berlier G, Miletto I, Casassa S. Experimental and first-principles IR characterization of quercetin adsorbed on a silica surface. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1854-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Enrique-Romero J, Rimola A, Ceccarelli C, Balucani N. The (impossible?) formation of acetaldehyde on the grain surfaces: insights from quantum chemical calculations. ACTA ACUST UNITED AC 2016. [DOI: 10.1093/mnrasl/slw031] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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14
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Pandey KK. Does hydrohalic acid HX (X = F, Cl) form true N-protonated twisted amide salts? Effects of anions on the ion-pair interactions and on the amide moiety in N-protonated tricyclic twisted amide salts. NEW J CHEM 2016. [DOI: 10.1039/c6nj01342b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The [BF4]− and [RSO3]− anions interact with N-protonated amide cations through N–H⋯F and N–H⋯O strong hydrogen bonds and hydrohalic acids form very weak N⋯H–X hydrogen bonds.
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Affiliation(s)
- Krishna K. Pandey
- School of Chemical Sciences
- Devi Ahilya University Indore
- Indore-452017
- India
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15
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Mian SA, Khan Y, Ahmad U, Khan MA, Rahman G, Ali S. Investigating the adsorption mechanism of glycine in comparison with catechol on cristobalite surface using density functional theory for bio-adhesive materials. RSC Adv 2016. [DOI: 10.1039/c6ra20683b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Amino acid proteins exist in Mussel's adhesive (mefp's) of which glycine has a significant amount. A density functional theory simulation study was performed in a belief that all the proteins in mefp's are responsible for the versatile adhesion.
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Affiliation(s)
- Shabeer Ahmad Mian
- Department of Physics
- University of Peshawar
- 25120 Peshawar
- Pakistan
- Department of Physics
| | - Younas Khan
- Department of Physics
- University of Peshawar
- 25120 Peshawar
- Pakistan
| | - Uzair Ahmad
- Department of Physics
- Islamia College Peshawar
- 25120 Peshawar
- Pakistan
| | | | - Gul Rahman
- Institute of Chemical Sciences
- University of Peshawar
- 25120 Peshawar
- Pakistan
| | - Shahid Ali
- Department of Physics
- University of Peshawar
- 25120 Peshawar
- Pakistan
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16
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Pandey KK. Structure and bonding analysis of germanones [(Eind) 2 Ge O], [((Tbt))(Tip)Ge O] and [R 2 Ge O] (R = Me, Ph): Significance of the dispersion interactions. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.09.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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Rutigliano M, Sanna N, Palma A. Multiple approach to model unpaired spin density effects in H-ZSM5 zeolite with extra-framework O atom: H-abstraction reaction from methane. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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18
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Theoretical insights into M–SO bonds in transition metal-sulfur monoxide complexes [{N(SPMe2)2}2M(SO)] (M = Fe, Ru, Os): Assessment of density functionals and dispersion interactions. Polyhedron 2015. [DOI: 10.1016/j.poly.2015.09.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Scott AM, Burns EA, Lafferty BJ, Hill FC. Theoretical predictions of thermodynamic parameters of adsorption of nitrogen containing environmental contaminants on kaolinite. J Mol Model 2015; 21:21. [DOI: 10.1007/s00894-015-2577-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 01/07/2015] [Indexed: 10/24/2022]
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20
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Pandey KK. Theoretical insights into structure, bonding, reactivity and importance of ion-pair interactions in Kirby's tetrafluoroboric acid salts of twisted amides. RSC Adv 2015. [DOI: 10.1039/c5ra22792e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The hydrolysis of amide 1 is more exothermic and is more favorable than amides 2 and 3 with bridgehead methyl.
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Affiliation(s)
- Krishna K. Pandey
- School of Chemical Sciences
- D. A. University Indore
- Indore 452 017
- India
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21
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Krawczuk RA, Tierney S, Mitchell W, McDouall JJW. Computational investigation of hole mobilities in organic semiconductors: comparison of single crystal structures and surface adsorbed clusters. Faraday Discuss 2014; 174:281-96. [PMID: 25315989 DOI: 10.1039/c4fd00082j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report hole mobilities obtained computationally based on both single crystal geometries and those obtained from crystal fragments optimised on a model surface. Such computational estimates can differ considerably from experimentally measured thin film mobilities. One source of this discrepancy is due to a difference in the morphology of the thin film compared with that of the crystal. Here, predictions of thin film hole mobilities based on optimised structures are given. A model surface is used to provide an inert geometric platform for the formation of an organic monolayer. The model is tested on pentacene and TIPS-pentacene for which experimental information of the surface morphology exists. The model has also been applied to four previously uninvestigated structures. Two of the compounds studied had fairly low predicted mobilities in their single crystal structures, which were vastly improved post-optimisation. This is in accord with experiment.
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Affiliation(s)
- Rose A Krawczuk
- School of Chemistry, The University of Manchester, Manchester, M13 9PL, UK.
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Zwitterionic versus canonical amino acids over the various defects in zeolites: a two-layer ONIOM calculation. Sci Rep 2014; 4:6594. [PMID: 25307449 PMCID: PMC4194432 DOI: 10.1038/srep06594] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 09/17/2014] [Indexed: 12/01/2022] Open
Abstract
Defects are often considered as the active sites for chemical reactions. Here a variety of defects in zeolites are used to stabilize zwitterionic glycine that is not self-stable in gas phase; in addition, effects of acidic strengths and zeolite channels on zwitterionic stabilization are demonstrated. Glycine zwitterions can be stabilized by all these defects and energetically prefer to canonical structures over Al and Ga Lewis acidic sites rather than Ti Lewis acidic site, silanol and titanol hydroxyls. For titanol (Ti-OH), glycine interacts with framework Ti and hydroxyl sites competitively, and the former with Lewis acidity predominates. The transformations from canonical to zwitterionic glycine are obviously more facile over Al and Ga Lewis acidic sites than over Ti Lewis acidic site, titanol and silanol hydroxyls. Charge transfers that generally increase with adsorption energies are found to largely decide the zwitterionic stabilization effects. Zeolite channels play a significant role during the stabilization process. In absence of zeolite channels, canonical structures predominate for all defects; glycine zwitterions remain stable over Al and Ga Lewis acidic sites and only with synergy of H-bonding interactions can exist over Ti Lewis acidic site, while automatically transform to canonical structures over silanol and titanol hydroxyls.
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23
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Gas-Phase and Microsolvated Glycine Interacting with Boron Nitride Nanotubes. A B3LYP-D2* Periodic Study. INORGANICS 2014. [DOI: 10.3390/inorganics2020334] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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24
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Delle Piane M, Vaccari S, Corno M, Ugliengo P. Silica-Based Materials as Drug Adsorbents: First Principle Investigation on the Role of Water Microsolvation on Ibuprofen Adsorption. J Phys Chem A 2014; 118:5801-7. [DOI: 10.1021/jp411173k] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Massimo Delle Piane
- Università di Torino, Dipartimento di Chimica and NIS (Nanostructured Interfaces
and Surfaces) Centre, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Stefano Vaccari
- Università di Torino, Dipartimento di Chimica and NIS (Nanostructured Interfaces
and Surfaces) Centre, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Marta Corno
- Università di Torino, Dipartimento di Chimica and NIS (Nanostructured Interfaces
and Surfaces) Centre, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Piero Ugliengo
- Università di Torino, Dipartimento di Chimica and NIS (Nanostructured Interfaces
and Surfaces) Centre, Via Pietro Giuria 7, 10125 Torino, Italy
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Rimola A, Costa D, Sodupe M, Lambert JF, Ugliengo P. Silica surface features and their role in the adsorption of biomolecules: computational modeling and experiments. Chem Rev 2013; 113:4216-313. [PMID: 23289428 DOI: 10.1021/cr3003054] [Citation(s) in RCA: 328] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Spain
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26
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Pandey KK, Patidar SK, Patidar P, Vishwakarma R, Bariya PK. Accurate Structure and Bonding Description of the Transition Metal-Disulfur Monoxide Complexes [(PMe3)2M(S2O)] (M= Ni, Pd, Pt): Grimme Dispersion Corrected DFT Study. Z Anorg Allg Chem 2013. [DOI: 10.1002/zaac.201300415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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27
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Alí-Torres J, Rimola A, Rodríguez-Rodríguez C, Rodríguez-Santiago L, Sodupe M. Insights on the Binding of Thioflavin Derivative Markers to Amyloid-Like Fibril Models from Quantum Chemical Calculations. J Phys Chem B 2013; 117:6674-80. [DOI: 10.1021/jp402807g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jorge Alí-Torres
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra
08193, Barcelona, Spain
| | - Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra
08193, Barcelona, Spain
| | - Cristina Rodríguez-Rodríguez
- Medicinal Inorganic Chemistry
Group, University of British Columbia,
2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Luis Rodríguez-Santiago
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra
08193, Barcelona, Spain
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra
08193, Barcelona, Spain
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28
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Delle Piane M, Corno M, Ugliengo P. Does Dispersion Dominate over H-Bonds in Drug-Surface Interactions? The Case of Silica-Based Materials As Excipients and Drug-Delivery Agents. J Chem Theory Comput 2013; 9:2404-15. [PMID: 26583731 DOI: 10.1021/ct400073s] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Amorphous silica is widely employed in pharmaceutical formulations both as a tableting, anticaking agent and as a drug delivery system, whereas MCM-41 mesoporous silica has been recently proposed as an efficient support for the controlled release of drugs. Notwithstanding the relevance of this topic, the atomistic details about the specific interactions between the surfaces of the above materials and drugs and the energetic of adsorption are almost unknown. In this work, we resort to a computational ab initio approach, based on periodic Density Functional Theory (DFT), to study the adsorption behavior of two popular drugs (aspirin and ibuprofen) on two models of an amorphous silica surface characterized by different hydrophilic/hydrophobic properties due to different SiOH surface groups' density. Particular effort was devoted to understand the role of dispersive (vdW) interactions in the adsorption mechanism and their interplay with H-bond interactions. On the hydrophilic silica surface, the H-bond pattern of the Si-OH groups rearranges to comply with the formation of new H-bond interactions triggered by the adsorbed drug. The interaction energy of ibuprofen with the hydrophilic model of the silica surface is computed to be very close to the sublimation energy of the ibuprofen molecular crystal, accounting for the experimental evidence of ibuprofen crystal amorphization induced by the contact with the mesoporous silica material. For both surface models, dispersion interactions play a crucial role in dictating the features of the drug/silica system, and they become dominant for the hydrophobic surface. It was proved that a competition may exist between directional H-bonds and nonspecific dispersion driven interactions, with important structural and energetic consequences for the adsorption. The results of this work emphasize the inadequacy of plain DFT methods to model adsorption processes involving inorganic surfaces and drugs of moderate size, due to the missing term accounting for London dispersion interactions.
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Affiliation(s)
- Massimo Delle Piane
- Università di Torino, Dipartimento di Chimica and NIS (Nanostructured Interfaces and Surfaces) Centre of Excellence, via P. Giuria 7, 10125 Torino, Italy
| | - Marta Corno
- Università di Torino, Dipartimento di Chimica and NIS (Nanostructured Interfaces and Surfaces) Centre of Excellence, via P. Giuria 7, 10125 Torino, Italy
| | - Piero Ugliengo
- Università di Torino, Dipartimento di Chimica and NIS (Nanostructured Interfaces and Surfaces) Centre of Excellence, via P. Giuria 7, 10125 Torino, Italy
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29
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Rimola A, Sodupe M. Physisorption vs. chemisorption of probe molecules on boron nitride nanomaterials: the effect of surface curvature. Phys Chem Chem Phys 2013; 15:13190-8. [DOI: 10.1039/c3cp51728d] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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30
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Johnson ER, Otero-de-la-Roza A. Adsorption of Organic Molecules on Kaolinite from the Exchange-Hole Dipole Moment Dispersion Model. J Chem Theory Comput 2012; 8:5124-31. [DOI: 10.1021/ct3006375] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Erin R. Johnson
- Chemistry and Chemical Biology, School of
Natural Sciences, University of California, Merced, 5200 North Lake Road,
Merced, California 95343, United States
| | - Alberto Otero-de-la-Roza
- Chemistry and Chemical Biology, School of
Natural Sciences, University of California, Merced, 5200 North Lake Road,
Merced, California 95343, United States
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31
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Rimola A, Aschi M, Orlando R, Ugliengo P. Does adsorption at hydroxyapatite surfaces induce peptide folding? Insights from large-scale B3LYP calculations. J Am Chem Soc 2012; 134:10899-910. [PMID: 22680347 DOI: 10.1021/ja302262y] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Large-scale periodic quantum mechanical calculations (509 atoms, 7852 atomic orbitals) based on the hybrid B3LYP functional focused on the peptide folding induced by the adsorption on the (001) and (010) hydroxyapatite (HA) surfaces give interesting insights on the role of specific interactions between surface sites and the peptide, which stabilize the helix conformation over the "native" random coil ones for in silico designed model peptides. The two peptides were derived from the 12-Gly oligomer, with one (P1, C-tGGKGGGGGGEGGN-t) and two (P2, C-tGGKGGKEGGEGGN-t) glutamic acid (E) and lysine (K) residue mutations. The most stable gas-phase "native" conformation for both peptides resulted in a random coil (RC) structure, with the helix (H) conformation being ≈100 kJ mol(-1) higher in free energy. The two peptide conformations interact with the HA (001) and (010) surfaces by C═O groups via Ca(2+) ions, by hydrogen bond between NH(2) groups and the basic PO(4)(3-) groups and by a relevant fraction due to dispersion forces. Peptide adsorption was studied on the dry (001) surface, the wet one envisaging 2 H(2)O per surface Ca(2+) and, on the latter, also considering the adsorption of microsolvated peptides with 4 H(2)O molecules located at sites responsible of the interaction with the surface. The P1 mutant does prefer to be adsorbed as a random coil by ≈160 kJ/mol, whereas the reverse is computed for P2, preferring the helix conformation by ≈50 kJ/mol. Adsorption as helix of both P1 and P2 mutants brings about proton transfer toward the HA surfaces with a large charge transfer component to the interaction energy.
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Affiliation(s)
- Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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Mignon P, Sodupe M. Theoretical study of the adsorption of DNA bases on the acidic external surface of montmorillonite. Phys Chem Chem Phys 2012; 14:945-54. [DOI: 10.1039/c1cp22454a] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Marom N, Tkatchenko A, Rossi M, Gobre VV, Hod O, Scheffler M, Kronik L. Dispersion Interactions with Density-Functional Theory: Benchmarking Semiempirical and Interatomic Pairwise Corrected Density Functionals. J Chem Theory Comput 2011; 7:3944-51. [PMID: 26598340 DOI: 10.1021/ct2005616] [Citation(s) in RCA: 186] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a comparative assessment of the accuracy of two different approaches for evaluating dispersion interactions: interatomic pairwise corrections and semiempirical meta-generalized-gradient-approximation (meta-GGA)-based functionals. This is achieved by employing conventional (semi)local and (screened-)hybrid functionals, as well as semiempirical hybrid and nonhybrid meta-GGA functionals of the M06 family, with and without interatomic pairwise Tkatchenko-Scheffler corrections. All of those are tested against the benchmark S22 set of weakly bound systems, a representative larger molecular complex (dimer of NiPc molecules), and a representative dispersively bound solid (hexagonal boron nitride). For the S22 database, we also compare our results with those obtained from the pairwise correction of Grimme (DFT-D3) and nonlocal Langreth-Lundqvist functionals (vdW-DF1 and vdW-DF2). We find that the semiempirical kinetic-energy-density dependence introduced in the M06 functionals mimics some of the nonlocal correlation needed to describe dispersion. However, long-range contributions are still missing. Pair-wise interatomic corrections, applied to conventional semilocal or hybrid functionals, or to M06 functionals, provide for a satisfactory level of accuracy irrespectively of the underlying functional. Specifically, screened-hybrid functionals such as the Heyd-Scuseria-Ernzerhof (HSE) approach reduce self-interaction errors in systems possessing both localized and delocalized orbitals and can be applied to both finite and extended systems. Therefore, they serve as a useful underlying functional for dispersion corrections.
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Affiliation(s)
- Noa Marom
- Department of Materials and Interfaces, Weizmann Institute of Science , Rehovoth 76100, Israel.,Center for Computational Materials, Institute for Computational Engineering and Sciences, University of Texas at Austin , Austin, Texas 78712, United States
| | - Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6, 14195 Berlin, Germany
| | - Mariana Rossi
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6, 14195 Berlin, Germany
| | - Vivekanand V Gobre
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6, 14195 Berlin, Germany
| | - Oded Hod
- School of Chemistry, The Sackler Faculty of Exact Sciences, Tel Aviv University , Tel Aviv 69978, Israel
| | - Matthias Scheffler
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6, 14195 Berlin, Germany
| | - Leeor Kronik
- Department of Materials and Interfaces, Weizmann Institute of Science , Rehovoth 76100, Israel
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Musso F, Ugliengo P, Sodupe M. Do H-bond features of silica surfaces affect the H2O and NH3 adsorption? Insights from periodic B3LYP calculations. J Phys Chem A 2011; 115:11221-8. [PMID: 21895017 DOI: 10.1021/jp203988j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The adsorption of a single H(2)O and NH(3) molecule on different fully hydroxylated α-quartz, cristobalite, and tridymite surfaces has been studied at the B3LYP level of theory, within a periodic approach using basis sets of polarized triple-ζ quality and accounting for basis set superposition error (BSSE). Fully hydroxylated crystalline silica exhibits SiOH as terminal groups whose distribution and H-bond features depend on both the considered silica polymorph and the crystallographic plane, which gives rise to isolated, H-bond interacting SiOH pairs or infinitely connected H-bond chains. A key point of the present study is to understand how the H-bond features of a dry crystalline silica surface influence its adsorption properties. Results reveal that the silica-adsorbate (H(2)O and NH(3)) interaction energy anticorrelates with the density of SiOH groups at the surface. This counterintuitive observation arises from the fact that pre-existing H-bonds of the dry surface need to be broken to establish new H-bonds between the surface and the adsorbate, which manifests in a sizable energy cost due to surface deformation. A simple method is also proposed to estimate the strength of the pre-existing H-bonds at the dry surfaces, which is shown to anticorrelate with the adsorbate interaction energy, in agreement with the above trends.
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Affiliation(s)
- Federico Musso
- Departament de Quimica, Universitat Autònoma de Barcelona, Bellaterra, Spain
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Maschio L. Local MP2 with Density Fitting for Periodic Systems: A Parallel Implementation. J Chem Theory Comput 2011; 7:2818-30. [PMID: 26605473 DOI: 10.1021/ct200352g] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A parallel implementation is presented for the evaluation of local second-order Møller-Plesset perturbation theory (LMP2) energies in periodic, nonconducting crystalline systems with a density-fitting approximation of two-electron repulsion integrals. Peculiarities of the periodic case with respect to parallel LMP2 implementations in molecular codes, such as the use of translational and point symmetry, impose different strategies in order to achieve good parallel performance. The implementation is benchmarked on a few systems, representing a choice of the most interesting solid state quantum-chemistry problems where the MP2 approach can be decisive. Good parallel efficiency of the algorithms is demonstrated for up to 54 processors. Test systems include a metal organic framework (MOF-5) 3D crystalline structure with a triple-ζ-quality basis set: this is the largest calculation performed so far with 106 atoms, 532 correlated electrons, and 2884 atomic orbitals per unit cell.
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Affiliation(s)
- Lorenzo Maschio
- Dipartimento di Chimica IFM and Centre of Excellence NIS (Nanostructured Interfaces and Surfaces), Università di Torino , via P. Giuria 5, I-10125 Torino, Italy
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36
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Dispersion energy effects on methane interaction within zeolite straight micropores: A computational investigation. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.04.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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37
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Mian SA, Gao X, Nagase S, Jang J. Adsorption of catechol on a wet silica surface: density functional theory study. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-0982-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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38
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Civalleri B, Maschio L, Ugliengo P, Zicovich-Wilson CM. Role of dispersive interactions in the CO adsorption on MgO(001): periodic B3LYP calculations augmented with an empirical dispersion term. Phys Chem Chem Phys 2010; 12:6382-6. [DOI: 10.1039/c001192d] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Tosoni S, Sauer J. Accurate quantum chemical energies for the interaction of hydrocarbons with oxide surfaces: CH4/MgO(001). Phys Chem Chem Phys 2010; 12:14330-40. [DOI: 10.1039/c0cp01261k] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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