1
|
Sharma K, Sonu, Sudhaik A, Ahamad T, Kaya S, Nguyen LH, Maslov MM, Le QV, Nguyen VH, Singh P, Raizada P. Unraveling the synergism mechanistic insight of O-vacancy and interfacial charge transfer in WO 3-x decorated on Ag 2CO 3/BiOBr for photocatalysis of water pollutants: Based on experimental and density functional theory (DFT) studies. ENVIRONMENTAL RESEARCH 2024; 260:119610. [PMID: 39004393 DOI: 10.1016/j.envres.2024.119610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/28/2024] [Accepted: 07/11/2024] [Indexed: 07/16/2024]
Abstract
Photocatalysis has been widely used as one of the most promising approaches to remove various pollutants in liquid or gas phases during the last decade. The main emphasis of the study is on the synergy of vacancy engineering and heterojunction formation, two widely used modifying approaches, to significantly alter photocatalytic performance. The vacancy-induced Ag2CO3/BiOBr/WO3-x heterojunction system has been fabricated using a co-precipitation technique to efficiently abate methylene blue (MB) dye and doxycycline (DC) antibiotic. The as-fabricated Ag2CO3/BiOBr/WO3-x heterojunction system displayed improved optoelectronic characteristic features because of the rational combination of dual charge transferal route and defect modulation. The Ag2CO3/BiOBr/WO3-x system possessed 97% and 74% photodegradation efficacy for MB and DC, respectively, with better charge isolation and migration efficacy. The ternary photocatalyst possessed a multi-fold increase in the reaction rate for both MB and DC, i.e., 0.021 and 0.0078 min-1, respectively, compared to pristine counterparts. Additionally, more insightful deductions about the photodegradation routes were made possible by the structural investigations of MB and DC using density functional theory (DFT) simulations. This study advances the understanding of the mechanisms forming visible light active dual Z-scheme heterojunction for effective environmental remediation.
Collapse
Affiliation(s)
- Kusum Sharma
- School of Advanced Chemical Sciences, Faculty of Basic Sciences, Shoolini University, Solan, HP, India, 173229
| | - Sonu
- School of Advanced Chemical Sciences, Faculty of Basic Sciences, Shoolini University, Solan, HP, India, 173229
| | - Anita Sudhaik
- School of Advanced Chemical Sciences, Faculty of Basic Sciences, Shoolini University, Solan, HP, India, 173229
| | - Tansir Ahamad
- Department of Chemistry, College of Science, King Saud University, Saudi Arabia
| | - Savas Kaya
- Department of Chemistry, Faculty of Science, Sivas Cumhuriyet University, 58140, Sivas, Turkey
| | - Lan Huong Nguyen
- Faculty of Biology and Environment, Ho Chi Minh City University of Industry and Trade (HUIT), 140 Le Trong Tan Street, Tay Thanh Ward, Tan Phu District, Ho Chi Minh City, Viet Nam
| | - Mikhail M Maslov
- Nanoengineering in Electronics, Spintronics and Photonics Institute, National Research Nuclear University "MEPhl", Kashirskoe Shosse 31, Moscow, 115409, Russia
| | - Quyet Van Le
- Department of Materials Science and Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Van-Huy Nguyen
- Centre for Herbal Pharmacology and Environmental Sustainability, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, 603103, Tamil Nadu, India.
| | - Pardeep Singh
- School of Advanced Chemical Sciences, Faculty of Basic Sciences, Shoolini University, Solan, HP, India, 173229
| | - Pankaj Raizada
- School of Advanced Chemical Sciences, Faculty of Basic Sciences, Shoolini University, Solan, HP, India, 173229.
| |
Collapse
|
2
|
Kjellgren ER, Reinholdt P, Fitzpatrick A, Talarico WN, Jensen PWK, Sauer SPA, Coriani S, Knecht S, Kongsted J. The variational quantum eigensolver self-consistent field method within a polarizable embedded framework. J Chem Phys 2024; 160:124114. [PMID: 38533884 DOI: 10.1063/5.0190594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/10/2024] [Indexed: 03/28/2024] Open
Abstract
We formulate and implement the Variational Quantum Eigensolver Self Consistent Field (VQE-SCF) algorithm in combination with polarizable embedding (PE), thereby extending PE to the regime of quantum computing. We test the resulting algorithm, PE-VQE-SCF, on quantum simulators and demonstrate that the computational stress on the quantum device is only slightly increased in terms of gate counts compared to regular VQE-SCF. On the other hand, no increase in shot noise was observed. We illustrate how PE-VQE-SCF may lead to the modeling of real chemical systems using a simulation of the reaction barrier of the Diels-Alder reaction between furan and ethene as an example.
Collapse
Affiliation(s)
- Erik Rosendahl Kjellgren
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | | | - Walter N Talarico
- Algorithmiq Ltd., Kanavakatu 3C, FI-00160 Helsinki, Finland
- Department of Applied Physics, QTF Centre of Excellence, Center for Quantum Engineering, Aalto University School of Science, FIN-00076 AALTO Espoo, Finland
| | - Phillip W K Jensen
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Sonia Coriani
- DTU Chemistry - Department of Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Stefan Knecht
- Algorithmiq Ltd., Kanavakatu 3C, FI-00160 Helsinki, Finland
- ETH Zürich, Department of Chemistry and Applied Life Sciences, Vladimir-Prelog-Weg 1-5/10, CH-8093 Zürich, Switzerland
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| |
Collapse
|
3
|
Bancone N, Pantaleone S, Ugliengo P, Rimola A, Corno M. Adsorption of HCN on cosmic silicates: a periodic quantum mechanical study. Phys Chem Chem Phys 2023; 25:26797-26812. [PMID: 37781958 DOI: 10.1039/d3cp01459b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Hydrogen cyanide (HCN) represents a small but widely distributed fraction of the interstellar molecules, and it has been observed in all the environments characterizing the formation of a new planetary system. HCN can polymerize to form biomolecules, including adenine (H5C5N5), and it has drawn attention as a possible precursor of several building blocks of life due to the presence of its polymerization products in meteorites, comets and other asteroidal bodies. To elucidate the potential catalytic role that cosmic silicates have played in these processes, we have investigated, at DFT-PBE level inclusive of a posteriori dispersion correction, the energetic and spectroscopic features of the adsorption of HCN molecules on the most relevant crystalline surfaces of the mineral forsterite (Mg2SiO4), a common silicate constituent of the interstellar core grains and planetary rocky bodies. The results reveal that HCN adsorbs both in molecular and dissociative ways, within a wide range of adsorption energies (-29.4 to -466.4 kJ mol-1). Thermodynamic and kinetic results show that dissociative adsorption is dominant already at low temperatures, a fact particularly relevant at the protoplanetary conditions (i.e., the latest stages in the star system formation process). The simulated spectroscopic features of the studied adducts show a wide range of different degrees of perturbation of C-H and CN bonds. This finding agrees with previous experimental works, and our results confirm that a complex chemistry is observed when this astrochemically-relevant molecule interacts with Mg2SiO4, which may be associated with a considerable potential reactivity towards the formation of relevant prebiotic compounds.
Collapse
Affiliation(s)
- Niccolò Bancone
- Dipartimento di Chimica and NIS - Nanostructured Interfaces and Surfaces - Centre, Università degli Studi di Torino, via P. Giuria 7, 10125, Torino, Italy.
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Stefano Pantaleone
- Dipartimento di Chimica and NIS - Nanostructured Interfaces and Surfaces - Centre, Università degli Studi di Torino, via P. Giuria 7, 10125, Torino, Italy.
| | - Piero Ugliengo
- Dipartimento di Chimica and NIS - Nanostructured Interfaces and Surfaces - Centre, Università degli Studi di Torino, via P. Giuria 7, 10125, Torino, Italy.
| | - Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Marta Corno
- Dipartimento di Chimica and NIS - Nanostructured Interfaces and Surfaces - Centre, Università degli Studi di Torino, via P. Giuria 7, 10125, Torino, Italy.
| |
Collapse
|
4
|
Nemati M, Farajzadeh MA, Altunay N, Tuzen M, Kaya S, Maslov MM, Mogaddam MRA. Combination of doped amorphous carbon based dispersive solid phase extraction with ionic liquid-based DLLME for the extraction of aromatic amines from leather industries wastewater; Theoretical and experimental insights. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
|
5
|
Khoubnasabjafari M, Altunay N, Tuzen M, Kaya S, Katin KP, Farajzadeh MA, Hosseini M, Mogaddam MRA, Jouyban A. Experimental and theoretical observations in a mixed mode dispersive solid phase extraction of exogenous surfactants from exhaled breath condensate prior to HPLC-MS/MS analysis. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
6
|
Yildiz S, Topal Canbaz G, Kaya S, Maslov MM. A Combined Study on Degradation Mechanism of Reactive Orange 16 through Fenton‐like Process: Experimental Studies and Density Functional Theoretical Findings. ChemistrySelect 2022. [DOI: 10.1002/slct.202202292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Sayiter Yildiz
- Sivas Cumhuriyet University Engineering Faculty Department of Environmental Engineering 58140 Sivas Turkey
| | - Gamze Topal Canbaz
- Sivas Cumhuriyet University Engineering Faculty Department of Chemical Engineering 58140 Sivas Turkey
| | - Savaş Kaya
- Sivas Cumhuriyet University Health Services Vocational School Department of Pharmacy 58140 Sivas/ Turkey
| | - Mikhail M. Maslov
- Department of Condensed Matter Physics National Research Nuclear University “MEPhI” Kashirskoe Shosse 31 Moscow 115409 Russia
| |
Collapse
|
7
|
Experimental and Density Functional Theoretical Analyses on Degradation of Acid Orange 7 via UV Irradiation and Ultrasound enhanced by Fenton Process. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
8
|
Gimaldinova MA, Maslov MM, Katin KP. Energy and Electronic Properties of Nanostructures Based on the CL-20 Framework with the Replacement of the Carbon Atoms by Silicon and Germanium: A Density Functional Theory Study. MATERIALS (BASEL, SWITZERLAND) 2022; 15:6577. [PMID: 36233924 PMCID: PMC9572965 DOI: 10.3390/ma15196577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/14/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
We consider SinCL-20 and GenCL-20 systems with carbon atoms replaced by silicon/germanium atoms and their dimers. The physicochemical properties of the silicon/germanium analogs of the high-energy molecule CL-20 and its dimers were determined and studied using density functional theory with the B3LYP/6-311G(d,p) level of theory. It was found that the structure and geometry of SinCL-20/GenCL-20 molecules change dramatically with the appearance of Si-/Ge-atoms. The main difference between silicon- or germanium-substituted SinCL-20/GenCL-20 molecules and the pure CL-20 molecule is that the NO2 functional groups make a significant rotation relative to the starting position in the classical molecule, and the effective diameter of the frame of the systems increases with the addition of Si-/Ge-atoms. Thus, the effective framework diameter of a pure CL-20 molecule is 3.208 Å, while the effective diameter of a fully silicon-substituted Si6CL-20 molecule is 4.125 Å, and this parameter for a fully germanium-substituted Ge6CL-20 molecule is 4.357 Å. The addition of silicon/germanium atoms to the system leads to a decrease in the binding energy. In detail, the binding energies for CL-20/Si6CL-20/Ge6CL-20 molecules are 4.026, 3.699, 3.426 eV/atom, respectively. However, it has been established that the framework maintains stability, with an increase in the number of substituting silicon or germanium atoms. In addition, we designed homodesmotic reactions for the CL-20 molecule and its substituted derivatives Si6CL-20/Ge6CL-20, and then determined the strain energy to find out in which case more energy would be released when the framework breaks. Further, we also studied the electronic properties of systems based on CL-20 molecules. It was found that the addition of germanium or silicon atoms instead of carbon leads to a decrease in the size of the HOMO-LUMO gap. Thus, the HOMO-LUMO gaps of the CL-20/Si6CL-20/Ge6CL-20 molecules are 5.693, 5.339, and 5.427 eV, respectively. A similar dependence is also observed for CL-20 dimers. So, in this work, we have described in detail the dependence of the physicochemical parameters of CL-20 molecules and their dimers on the types of atoms upon substitution.
Collapse
Affiliation(s)
- Margarita A. Gimaldinova
- Nanoengineering in Electronics, Spintronics and Photonics Institute, National Research Nuclear University “MEPhI”, Kashirskoe Shosse 31, 115409 Moscow, Russia
| | - Mikhail M. Maslov
- Nanoengineering in Electronics, Spintronics and Photonics Institute, National Research Nuclear University “MEPhI”, Kashirskoe Shosse 31, 115409 Moscow, Russia
- Laboratory of Computational Design of Nanostructures, Nanodevices, and Nanotechnologies, Research Institute for the Development of Scientific and Educational Potential of Youth, Aviatorov Str. 14/55, 119620 Moscow, Russia
| | - Konstantin P. Katin
- Nanoengineering in Electronics, Spintronics and Photonics Institute, National Research Nuclear University “MEPhI”, Kashirskoe Shosse 31, 115409 Moscow, Russia
- Laboratory of Computational Design of Nanostructures, Nanodevices, and Nanotechnologies, Research Institute for the Development of Scientific and Educational Potential of Youth, Aviatorov Str. 14/55, 119620 Moscow, Russia
| |
Collapse
|
9
|
Marzi Khosrowshahi E, Afshar Mogaddam MR, Javadzadeh Y, Altunay N, Tuzen M, Kaya S, Ghalkhani M, Farajzadeh MA, Nemati M. Experimental and density functional theoretical modeling of triazole pesticides extraction by Ti2C nanosheets as a sorbent in dispersive solid phase extraction method before HPLC-MS/MS analysis. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107331] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
10
|
Çetinkaya HF, Cebeci MS, Kaya S, Jalbani NS, Maslov MM, Marzouki R. Removal of erythrosine B dye from wastewater using chitosan boric acid composite material: Experimental and density functional theory findings. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Hüseyin Fatih Çetinkaya
- Department of Environmental Engineering, Faculty of Engineering Sivas Cumhuriyet University Sivas Turkey
| | - Meltem Sarıoğlu Cebeci
- Department of Environmental Engineering, Faculty of Engineering Sivas Cumhuriyet University Sivas Turkey
| | - Savaş Kaya
- Department of Pharmacy, Health Services Vocational School Sivas Cumhuriyet University Sivas Turkey
| | - Nida Shams Jalbani
- National Center of Excellence in Analytical Chemistry University of Sindh Jamshoro Pakistan
| | - Mikhail M. Maslov
- Department of Condensed Matter Physics National Research Nuclear University “MEPhI” Moscow Russian Federation
| | - Riadh Marzouki
- Chemistry Department, College of Science King Khalid University Abha Saudi Arabia
- Chemistry Department, Faculty of Sciences of Sfax University of Sfax Sfax Tunisia
| |
Collapse
|
11
|
Serra-Peralta M, Domínguez-Dalmases C, Rimola A. Water formation on interstellar silicates: the role of Fe 2+/H 2 interactions in the O + H 2 → H 2O reaction. Phys Chem Chem Phys 2022; 24:28381-28393. [DOI: 10.1039/d2cp04051d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Water formation by reaction of H2 and O on silicate surfaces as a first step towards the generation of interstellar ice mantles is possible thanks to the activation of H2 inferred by Fe2+ ions and quantum tunnelling effects.
Collapse
Affiliation(s)
- Marc Serra-Peralta
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalonia, Spain
| | | | - Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalonia, Spain
| |
Collapse
|
12
|
Thorhallsson AT, Bjornsson R. The E 2 state of FeMoco: Hydride Formation versus Fe Reduction and a Mechanism for H 2 Evolution. Chemistry 2021; 27:16788-16800. [PMID: 34541722 PMCID: PMC9293435 DOI: 10.1002/chem.202102730] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Indexed: 11/27/2022]
Abstract
The iron‐molybdenum cofactor (FeMoco) is responsible for dinitrogen reduction in Mo nitrogenase. Unlike the resting state, E0, reduced states of FeMoco are much less well characterized. The E2 state has been proposed to contain a hydride but direct spectroscopic evidence is still lacking. The E2 state can, however, relax back the E0 state via a H2 side‐reaction, implying a hydride intermediate prior to H2 formation. This E2→E0 pathway is one of the primary mechanisms for H2 formation under low‐electron flux conditions. In this study we present an exploration of the energy surface of the E2 state. Utilizing both cluster‐continuum and QM/MM calculations, we explore various classes of E2 models: including terminal hydrides, bridging hydrides with a closed or open sulfide‐bridge, as well as models without. Importantly, we find the hemilability of a protonated belt‐sulfide to strongly influence the stability of hydrides. Surprisingly, non‐hydride models are found to be almost equally favorable as hydride models. While the cluster‐continuum calculations suggest multiple possibilities, QM/MM suggests only two models as contenders for the E2 state. These models feature either i) a bridging hydride between Fe2 and Fe6 and an open sulfide‐bridge with terminal SH on Fe6 (E2‐hyd) or ii) a double belt‐sulfide protonated, reduced cofactor without a hydride (E2‐nonhyd). We suggest both models as contenders for the E2 redox state and further calculate a mechanism for H2 evolution. The changes in electronic structure of FeMoco during the proposed redox‐state cycle, E0→E1→E2→E0, are discussed.
Collapse
Affiliation(s)
- Albert Th Thorhallsson
- Science Institute, University of Iceland, Dunhagi 3, 107, Reykjavik, Iceland.,Department of Inorganic Spectroscopy, Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Ragnar Bjornsson
- Science Institute, University of Iceland, Dunhagi 3, 107, Reykjavik, Iceland.,Department of Inorganic Spectroscopy, Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| |
Collapse
|
13
|
Ásgeirsson V, Birgisson BO, Bjornsson R, Becker U, Neese F, Riplinger C, Jónsson H. Nudged Elastic Band Method for Molecular Reactions Using Energy-Weighted Springs Combined with Eigenvector Following. J Chem Theory Comput 2021; 17:4929-4945. [PMID: 34275279 DOI: 10.1021/acs.jctc.1c00462] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The climbing image nudged elastic band method (CI-NEB) is used to identify reaction coordinates and to find saddle points representing transition states of reactions. It can make efficient use of parallel computing as the calculations of the discretization points, the so-called images, can be carried out simultaneously. In typical implementations, the images are distributed evenly along the path by connecting adjacent images with equally stiff springs. However, for systems with a high degree of flexibility, this can lead to poor resolution near the saddle point. By making the spring constants increase with energy, the resolution near the saddle point is improved. To assess the performance of this energy-weighted CI-NEB method, calculations are carried out for a benchmark set of 121 molecular reactions. The performance of the method is analyzed with respect to the input parameters. Energy-weighted springs are found to greatly improve performance and result in successful location of the saddle points in less than a thousand energy and force evaluations on average (about a hundred per image) using the same set of parameter values for all of the reactions. Even better performance is obtained by stopping the calculation before full convergence and complete the saddle point search using an eigenvector following method starting from the location of the climbing image. This combination of methods, referred to as NEB-TS, turns out to be robust and highly efficient as it reduces the average number of energy and force evaluations down to a third, to 305. An efficient and flexible implementation of these methods has been made available in the ORCA software.
Collapse
Affiliation(s)
- Vilhjálmur Ásgeirsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Benedikt Orri Birgisson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Ragnar Bjornsson
- Max-Planck-Institute for Chemical Energy Conversion, Mülheim an der Ruhr 45470, Germany
| | - Ute Becker
- Max-Planck-Institute for Kohlenforschung, Mülheim an der Ruhr 45470, Germany
| | - Frank Neese
- Max-Planck-Institute for Kohlenforschung, Mülheim an der Ruhr 45470, Germany
| | | | - Hannes Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
| |
Collapse
|
14
|
Potapov A, McCoustra M. Physics and chemistry on the surface of cosmic dust grains: a laboratory view. INT REV PHYS CHEM 2021. [DOI: 10.1080/0144235x.2021.1918498] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Alexey Potapov
- Laboratory Astrophysics Group of the Max Planck Institute for Astronomy at the Friedrich Schiller University Jena, Jena, Germany
| | - Martin McCoustra
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh, UK
| |
Collapse
|
15
|
Response surface methodology based on central composite design for optimizing temperature-controlled ionic liquid-based microextraction for the determination of histamine residual in canned fish products. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.103807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
16
|
Ruthenium‐Catalyzed Secondary Amine Formation Studied by Density Functional Theory. ChemCatChem 2021. [DOI: 10.1002/cctc.202001588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
17
|
Maslov MM, Elik A, Demirbaş A, Katin KP, Altunay N. Theoretical and experimental studies aimed at the development of vortex-assisted supramolecular solvent microextraction for determination of nickel in plant samples by FAAS. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
18
|
All-Nitrogen Cages and Molecular Crystals: Topological Rules, Stability, and Pyrolysis Paths. COMPUTATION 2020. [DOI: 10.3390/computation8040091] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We combined ab initio molecular dynamics with the intrinsic reaction coordinate in order to investigate the mechanisms of stability and pyrolysis of N4 ÷ N120 fullerene-like nitrogen cages. The stability of the cages was evaluated in terms of the activation barriers and the activation Gibbs energies of their thermal-induced breaking. We found that binding energies, bond lengths, and quantum-mechanical descriptors failed to predict the stability of the cages. However, we derived a simple topological rule that adjacent hexagons on the cage surface resulted in its instability. For this reason, the number of stable nitrogen cages is significantly restricted in comparison with their carbon counterparts. As a rule, smaller clusters are more stable, whereas the earlier proposed large cages collapse at room temperature. The most stable all-nitrogen cages are the N4 and N6 clusters, which can form the van der Waals crystals with densities of 1.23 and 1.36 g/cm3, respectively. The examination of their band structures and densities of electronic states shows that they are both insulators. Their power and sensitivity are not inferior to the modern advanced high-energy nanosystems.
Collapse
|
19
|
Seritan S, Bannwarth C, Fales BS, Hohenstein EG, Isborn CM, Kokkila‐Schumacher SIL, Li X, Liu F, Luehr N, Snyder JW, Song C, Titov AV, Ufimtsev IS, Wang L, Martínez TJ. TeraChem
: A graphical processing unit
‐accelerated
electronic structure package for
large‐scale
ab initio molecular dynamics. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1494] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Stefan Seritan
- Department of Chemistry and the PULSE Institute Stanford University Stanford California USA
- SLAC National Accelerator Laboratory Menlo Park California USA
| | - Christoph Bannwarth
- Department of Chemistry and the PULSE Institute Stanford University Stanford California USA
- SLAC National Accelerator Laboratory Menlo Park California USA
| | - Bryan S. Fales
- Department of Chemistry and the PULSE Institute Stanford University Stanford California USA
- SLAC National Accelerator Laboratory Menlo Park California USA
| | - Edward G. Hohenstein
- Department of Chemistry and the PULSE Institute Stanford University Stanford California USA
- SLAC National Accelerator Laboratory Menlo Park California USA
| | - Christine M. Isborn
- Department of Chemistry University of California Merced Merced California USA
| | | | - Xin Li
- Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health KTH Royal Institute of Technology Stockholm Sweden
| | - Fang Liu
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| | | | | | - Chenchen Song
- Department of Physics University of California Berkeley Berkeley California USA
- Molecular Foundry Lawrence Berkeley National Laboratory Berkeley California USA
| | | | - Ivan S. Ufimtsev
- Department of Structural Biology Stanford University School of Medicine Stanford California USA
| | - Lee‐Ping Wang
- Department of Chemistry University of California Davis Davis California USA
| | - Todd J. Martínez
- Department of Chemistry and the PULSE Institute Stanford University Stanford California USA
- SLAC National Accelerator Laboratory Menlo Park California USA
| |
Collapse
|
20
|
Katin KP, Javan MB, Kochaev AI, Soltani A, Maslov MM. Kinetic Stability and Reactivity of Silicon and Fluorine‐Containing CL‐20 Derivatives. ChemistrySelect 2019. [DOI: 10.1002/slct.201902583] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Konstantin P. Katin
- Nanoengineering in Electronics, Spintronics and Photonics InstituteNational Research Nuclear University “MEPhI” Kashirskoe Shosse 31 Moscow 115409 Russia
- Laboratory of Computational Design of Nanostructures, Nanodevices, and NanotechnologiesResearch Institute for the Development of Scientific and Educational Potential of Youth Aviatorov str. 14/55 Moscow 119620 Russia
| | - Masoud B. Javan
- Physics Department, Faculty of SciencesGolestan University Shahid Beheshti St. Gorgan 15759-49138 Golestan Iran
| | - Alexey I. Kochaev
- Department of PhysicsUlyanovsk State Technical University Severny Venets str. 32 Ulyanovsk 432027 Russia
| | - Alireza Soltani
- Golestan Rheumatology Research CenterGolestan University of Medical Science Azar 10, 5-th Azar St. 4917774979 Gorgan Iran
| | - Mikhail M. Maslov
- Nanoengineering in Electronics, Spintronics and Photonics InstituteNational Research Nuclear University “MEPhI” Kashirskoe Shosse 31 Moscow 115409 Russia
- Laboratory of Computational Design of Nanostructures, Nanodevices, and NanotechnologiesResearch Institute for the Development of Scientific and Educational Potential of Youth Aviatorov str. 14/55 Moscow 119620 Russia
| |
Collapse
|
21
|
Nutho B, Mulholland AJ, Rungrotmongkol T. The reaction mechanism of Zika virus NS2B/NS3 serine protease inhibition by dipeptidyl aldehyde: a QM/MM study. Phys Chem Chem Phys 2019; 21:14945-14956. [PMID: 31236554 DOI: 10.1039/c9cp02377a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Zika virus (ZIKV) infection has become a global public health problem, associated with microcephaly in newborns and Guillain-Barré syndrome in adults. Currently, there are no commercially available anti-ZIKV drugs. The viral protease NS2B/NS3, which is involved in viral replication and maturation, is a potential drug target. Peptidomimetic aldehyde inhibitors bind covalently to the catalytic S135 of the NS3 protease. Here, we apply hybrid quantum mechanics/molecular mechanics (QM/MM) free-energy simulations at the PDDG-PM3/ff14SB level to investigate the inhibition mechanism of the ZIKV protease by a dipeptidyl aldehyde inhibitor (acyl-KR-aldehyde). The results show that proton transfer from the catalytic S135 to H51 occurs in concert with nucleophilic addition on the aldehyde warhead by S135. The anionic covalent complex between the dipeptidyl aldehyde and the ZIKV protease is analogous to the tetrahedral intermediate for substrate hydrolysis. Spontaneous protonation by H51 forms the hemiacetal. In addition, we use correlated ab initio QM/MM potential energy path calculations at levels up to LCCSD(T)/(aug)-cc-pVTZ to obtain accurate potential energy profiles of the reaction, which also support a concerted mechanism. These results provide detailed insight into the mechanism of ZIKV protease inhibition by a peptidyl aldehyde inhibitor, which will guide in the design of inhibitors.
Collapse
Affiliation(s)
- Bodee Nutho
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
| | - Thanyada Rungrotmongkol
- Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand. and Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| |
Collapse
|
22
|
Salem MA, Gimaldinova MA, Kochaev AI, Katin KP, Ryzhuk RV, Kargin NI, Maslov MM. Nitro Derivatives of Silaprismanes as High-Energy Compounds: Theoretical Study. INTERNATIONAL JOURNAL OF NANOSCIENCE 2019. [DOI: 10.1142/s0219581x19400477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We present ab initio study of structures and properties of silaprismanes Si[Formula: see text]H[Formula: see text] and their nitro derivatives Si[Formula: see text]H[Formula: see text]NO2 ([Formula: see text]–10). We found that silaprismane Si[Formula: see text]H9NO2 possesses the highest stability among all studied cages. Attached NO2 group results in weak decreasing of the HOMO–LUMO gap. The smaller prismanes bind with NO2 groups more strongly. The comparison between silaprismanes and carbon prismanes is also discussed.
Collapse
Affiliation(s)
- M. A. Salem
- Department of Condensed Matter Physics, National Research Nuclear University “MEPhI”, Kashirskoe Shosse 31, 115409 Moscow, Russia
- Department of Physics, Faculty of Science, Zagazig University, Zagazig 44519, Sharkia, Egypt
| | - M. A. Gimaldinova
- Department of Condensed Matter Physics, National Research Nuclear University “MEPhI”, Kashirskoe Shosse 31, 115409 Moscow, Russia
| | - A. I. Kochaev
- Department of Physics, Ulyanovsk State Technical University, Severny Venets Street 32, 432027 Ulyanovsk, Russia
| | - K. P. Katin
- Department of Condensed Matter Physics, National Research Nuclear University “MEPhI”, Kashirskoe Shosse 31, 115409 Moscow, Russia
| | - R. V. Ryzhuk
- Department of Condensed Matter Physics, National Research Nuclear University “MEPhI”, Kashirskoe Shosse 31, 115409 Moscow, Russia
| | - N. I. Kargin
- Department of Condensed Matter Physics, National Research Nuclear University “MEPhI”, Kashirskoe Shosse 31, 115409 Moscow, Russia
| | - M. M. Maslov
- Department of Condensed Matter Physics, National Research Nuclear University “MEPhI”, Kashirskoe Shosse 31, 115409 Moscow, Russia
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Katin KP, Maslov MM. Thermal stability of carbon [n,5] prismanes (n = 2–4): a molecular dynamics study. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1434720] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Konstantin P. Katin
- Department of Condensed Matter Physics, National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Moscow, Russia
- Laboratory of Computational Design of Nanostructures, Nanodevices and Nanotechnologies, Research Institute for the Development of Scientific and Educational Potential of Youth, Moscow, Russia
| | - Mikhail M. Maslov
- Department of Condensed Matter Physics, National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Moscow, Russia
- Laboratory of Computational Design of Nanostructures, Nanodevices and Nanotechnologies, Research Institute for the Development of Scientific and Educational Potential of Youth, Moscow, Russia
| |
Collapse
|
25
|
Gimaldinova MA, Maslov MM, Katin KP. Electronic and reactivity characteristics of CL-20 covalent chains and networks: a density functional theory study. CrystEngComm 2018. [DOI: 10.1039/c8ce00763b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The low-dimensional nanostructures built with CL-20 units were studied in order to investigate the possibility of creating covalent CL-20 crystals.
Collapse
Affiliation(s)
- Margarita A. Gimaldinova
- Department of Condensed Matter Physics
- National Research Nuclear University “MEPhI”
- Moscow 115409
- Russia
| | - Mikhail M. Maslov
- Department of Condensed Matter Physics
- National Research Nuclear University “MEPhI”
- Moscow 115409
- Russia
- Laboratory of Computational Design of Nanostructures
| | - Konstantin P. Katin
- Department of Condensed Matter Physics
- National Research Nuclear University “MEPhI”
- Moscow 115409
- Russia
- Laboratory of Computational Design of Nanostructures
| |
Collapse
|
26
|
Lim JYC, Marques I, Félix V, Beer PD. Enantioselective Anion Recognition by Chiral Halogen-Bonding [2]Rotaxanes. J Am Chem Soc 2017; 139:12228-12239. [PMID: 28777563 DOI: 10.1021/jacs.7b06144] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The application of chiral interlocked host molecules for discrimination of guest enantiomers has been largely overlooked, which is surprising given their unique three-dimensional binding cavities capable of guest encapsulation. Herein, we combined the stringent linear geometric interaction constraints of halogen bonding (XB), the noncovalent interaction between an electrophilic halogen atom and a Lewis base, with highly preorganized and conformationally restricted chiral cavities of [2]rotaxanes to achieve enantioselective anion recognition. Representing the first detailed investigation of the use of chiral XB rotaxanes for this purpose, extensive 1H NMR binding studies and molecular dynamics (MD) simulation experiments revealed that the chiral rotaxane cavity significantly enhances enantiodiscrimination compared to the non-interlocked free axle and macrocycle components. Furthermore, by examining the enantioselectivities of a family of structurally similar XB [2]rotaxanes containing different combinations of chiral and achiral macrocycle and axle components, the dominant influence of the chiral macrocycle in our rotaxane design for determining the effectiveness of chiral discrimination is demonstrated. MD simulations reveal the crucial geometric roles played by the XB interactions in orientating the bound enantiomeric anion guests for chiral selectivity, as well as the critical importance of the anions' hydration shells in governing binding affinity and enantiodiscrimination.
Collapse
Affiliation(s)
- Jason Y C Lim
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford , Mansfield Road, Oxford, OX1 3TA U.K
| | | | | | - Paul D Beer
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford , Mansfield Road, Oxford, OX1 3TA U.K
| |
Collapse
|
27
|
Ómarsson B, Bjornsson R, Ingólfsson O. Proton Shuttling and Reaction Paths in Dissociative Electron Attachment to o- and p-Tetrafluorohydroquinone, an Experimental and Theoretical Study. J Phys Chem A 2017; 121:5580-5585. [PMID: 28695738 DOI: 10.1021/acs.jpca.7b05010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Here we present a combined experimental and theoretical study on the fragmentation of o- and p-tetrafluorohydroquinone upon low energy electron attachment. Despite an identical ring-skeleton and identical functional groups in these constitutional isomers, they show distinctly different fragmentation patterns, a phenomenon that cannot be explained by distinct resonances or different thermochemistry. Using high-level quantum chemical calculations with the computationally affordable domain localized pair natural orbital approach, DLPNO-CCSD(T), we are able to provide a complete and accurate description of the respective reaction dynamics, revealing proton shuttling and transition states for competing channels as the explanation for the different behavior of these isomers. The results represent a "schoolbook example" of how the combination of experiment and modern high-level theory may today provide a thorough understanding of complex reaction dynamics by computationally affordable means.
Collapse
Affiliation(s)
- Benedikt Ómarsson
- Science Institute and Department of Chemistry, University of Iceland , Dunhagi 3, 107 Reykjavík, Iceland
| | - Ragnar Bjornsson
- Science Institute and Department of Chemistry, University of Iceland , Dunhagi 3, 107 Reykjavík, Iceland
| | - Oddur Ingólfsson
- Science Institute and Department of Chemistry, University of Iceland , Dunhagi 3, 107 Reykjavík, Iceland
| |
Collapse
|
28
|
Meisner J, Markmeyer MN, Bohner MU, Kästner J. Comparison of classical reaction paths and tunneling paths studied with the semiclassical instanton theory. Phys Chem Chem Phys 2017; 19:23085-23094. [DOI: 10.1039/c7cp03722h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Comparison of classical reaction paths and semiclassical instanton paths for a proton transfer reaction mechanism.
Collapse
Affiliation(s)
- Jan Meisner
- Institute for Theoretical Chemistry
- University of Stuttgart
- Pfaffenwaldring 55
- Stuttgart
- Germany
| | - Max N. Markmeyer
- Institute for Theoretical Chemistry
- University of Stuttgart
- Pfaffenwaldring 55
- Stuttgart
- Germany
| | - Matthias U. Bohner
- Institute for Theoretical Chemistry
- University of Stuttgart
- Pfaffenwaldring 55
- Stuttgart
- Germany
| | - Johannes Kästner
- Institute for Theoretical Chemistry
- University of Stuttgart
- Pfaffenwaldring 55
- Stuttgart
- Germany
| |
Collapse
|
29
|
|
30
|
Oueslati I, Kerkeni B, Bromley ST. Trends in the adsorption and reactivity of hydrogen on magnesium silicate nanoclusters. Phys Chem Chem Phys 2015; 17:8951-63. [DOI: 10.1039/c4cp05128a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigate the potential role of ultrasmall silicate grains in interstellar hydrogen-based chemistry by modelling H adsorption and H2 formation/dissociation on nanosilicates.
Collapse
Affiliation(s)
- Ichraf Oueslati
- Faculté des Sciences de Tunis
- Département de Physique
- (LPMC)
- Université de Tunis El Manar
- Tunisia
| | - Boutheïna Kerkeni
- Faculté des Sciences de Tunis
- Département de Physique
- (LPMC)
- Université de Tunis El Manar
- Tunisia
| | - Stefan T. Bromley
- Department de Química Física & Institut de Química Teòrica i Computacional
- Universitat de Barcelona
- E-08028 Barcelona
- Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)
| |
Collapse
|
31
|
Abad E, Rommel JB, Kästner J. Reaction mechanism of the bicopper enzyme peptidylglycine α-hydroxylating monooxygenase. J Biol Chem 2014; 289:13726-38. [PMID: 24668808 DOI: 10.1074/jbc.m114.558494] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Peptidylglycine α-hydroxylating monooxygenase is a noninteracting bicopper enzyme that stereospecifically hydroxylates the terminal glycine of small peptides for its later amidation. Neuroendocrine messengers, such as oxytocin, rely on the biological activity of this enzyme. Each catalytic turnover requires one oxygen molecule, two protons from the solvent, and two electrons. Despite this enzyme having been widely studied, a consensus on the reaction mechanism has not yet been found. Experiments and theoretical studies favor a pro-S abstraction of a hydrogen atom followed by the rebinding of an OH group. However, several hydrogen-abstracting species have been postulated; because two protons are consumed during the reaction, several protonation states are available. An electron transfer between the copper atoms could play a crucial role for the catalysis as well. This leads to six possible abstracting species. In this study, we compare them on equal footing. We perform quantum mechanics/molecular mechanics calculations, considering the glycine hydrogen abstraction. Our results suggest that the most likely mechanism is a protonation of the abstracting species before the hydrogen abstraction and another protonation as well as a reduction before OH rebinding.
Collapse
Affiliation(s)
- Enrique Abad
- From the Computational Biochemistry Group, Institute of Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Judith B Rommel
- From the Computational Biochemistry Group, Institute of Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Johannes Kästner
- From the Computational Biochemistry Group, Institute of Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| |
Collapse
|
32
|
Navarro-Ruiz J, Ugliengo P, Rimola A, Sodupe M. B3LYP periodic study of the physicochemical properties of the nonpolar (010) Mg-pure and fe-containing olivine surfaces. J Phys Chem A 2014; 118:5866-75. [PMID: 24517343 DOI: 10.1021/jp4118198] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
B3LYP periodic simulations have been carried out to study some physicochemical properties of the bulk structures and the corresponding nonpolar (010) surfaces of Mg-pure and Fe-containing olivine systems; i.e., Mg2SiO4 (Fo) and Mg1.5Fe0.5SiO4 (Fo75). A detailed structural analysis of the (010) Fo and Fo75 surface models shows the presence of coordinatively unsaturated metal cations (Mg(2+) and Fe(2+), respectively) with shorter metal-O distances compared to the bulk ones. Energetic analysis devoted to the Fe(2+) electronic spin configuration and to the ion position in the surfaces reveals that Fe(2+) in its quintet state and placed at the outermost positions of the slab constitutes the most stable Fe-containing surface, which is related to the higher stability of high spin states when Fe(2+) is coordinatively unsaturated. Comparison of the simulated IR and the corresponding reflectance spectra indicates that Fe(2+) substitution induces an overall bathochromic shift of the spectra due to the larger mass of Fe compared to Mg cation. In contrast, the IR spectra of the surfaces are shifted to upper values and exhibit more bands compared to the corresponding bulk systems due to the shorter metal-O distances given in the coordinatively unsaturated metals and to symmetry reduction which brings nonequivalent motions between the outermost and the internal modes, respectively.
Collapse
Affiliation(s)
- Javier Navarro-Ruiz
- Departament de Química, Universitat Autònoma de Barcelona , 08193 Bellaterra, Barcelona, Spain
| | | | | | | |
Collapse
|
33
|
Karssemeijer LJ, de Wijs GA, Cuppen HM. Interactions of adsorbed CO2 on water ice at low temperatures. Phys Chem Chem Phys 2014; 16:15630-9. [DOI: 10.1039/c4cp01622j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
34
|
Schmidt TC, Paasche A, Grebner C, Ansorg K, Becker J, Lee W, Engels B. QM/MM investigations of organic chemistry oriented questions. Top Curr Chem (Cham) 2014; 351:25-101. [PMID: 22392477 DOI: 10.1007/128_2011_309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
About 35 years after its first suggestion, QM/MM became the standard theoretical approach to investigate enzymatic structures and processes. The success is due to the ability of QM/MM to provide an accurate atomistic picture of enzymes and related processes. This picture can even be turned into a movie if nuclei-dynamics is taken into account to describe enzymatic processes. In the field of organic chemistry, QM/MM methods are used to a much lesser extent although almost all relevant processes happen in condensed matter or are influenced by complicated interactions between substrate and catalyst. There is less importance for theoretical organic chemistry since the influence of nonpolar solvents is rather weak and the effect of polar solvents can often be accurately described by continuum approaches. Catalytic processes (homogeneous and heterogeneous) can often be reduced to truncated model systems, which are so small that pure quantum-mechanical approaches can be employed. However, since QM/MM becomes more and more efficient due to the success in software and hardware developments, it is more and more used in theoretical organic chemistry to study effects which result from the molecular nature of the environment. It is shown by many examples discussed in this review that the influence can be tremendous, even for nonpolar reactions. The importance of environmental effects in theoretical spectroscopy was already known. Due to its benefits, QM/MM can be expected to experience ongoing growth for the next decade.In the present chapter we give an overview of QM/MM developments and their importance in theoretical organic chemistry, and review applications which give impressions of the possibilities and the importance of the relevant effects. Since there is already a bunch of excellent reviews dealing with QM/MM, we will discuss fundamental ingredients and developments of QM/MM very briefly with a focus on very recent progress. For the applications we follow a similar strategy.
Collapse
Affiliation(s)
- Thomas C Schmidt
- Institut für Phys. und Theor. Chemie, Emil-Fischer-Strasse 42, Campus Hubland Nord, 97074, Würzburg, Germany
| | | | | | | | | | | | | |
Collapse
|
35
|
Lee MW, Meuwly M. Diffusion of atomic oxygen relevant to water formation in amorphous interstellar ices. Faraday Discuss 2014; 168:205-22. [DOI: 10.1039/c3fd00160a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Molecular dynamics (MD) simulations together with accurate physics-based force fields are employed to determine the mobility of atomic oxygen in amorphous ice at low temperatures, characteristic for conditions in interstellar ices. From the simulations it is found that the mobility of atomic oxygen ranges from 60 to 480 Å2 ns−1 in amorphous ice at temperatures between 50 and 200 K. Hence, the simulations establish that atomic oxygen is mobile to a certain degree and a chemical mechanism for water formation involving oxygen mobility is a realistic scenario. This is also confirmed by the computed migration barriers for oxygen diffusion by multiple umbrella sampling simulations, which yield barriers for diffusion in the range of 0.7–1.9 kcal mol−1. The physics-based force field – based on a multipolar expansion of the electrostatic interactions – yields more pronounced energetics for oxygen migration pathways compared to the conventional point-charge models employed in typical simulations. Once formed, the computed solvation free energy suggests that atomic oxygen thermodynamically prefers to be localized inside amorphous ice and is available for chemical reaction, which may be relevant to water formation in and on grains.
Collapse
Affiliation(s)
- Myung Won Lee
- Department of Chemistry
- University of Basel
- 4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry
- University of Basel
- 4056 Basel, Switzerland
| |
Collapse
|
36
|
Cuppen HM, Karssemeijer LJ, Lamberts T. The kinetic Monte Carlo method as a way to solve the master equation for interstellar grain chemistry. Chem Rev 2013; 113:8840-71. [PMID: 24187949 PMCID: PMC3934372 DOI: 10.1021/cr400234a] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Indexed: 01/21/2023]
Affiliation(s)
- H. M. Cuppen
- Theoretical
Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen , 6525 AJ Nijmegen, The Netherlands
| | - L. J. Karssemeijer
- Theoretical
Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen , 6525 AJ Nijmegen, The Netherlands
| | - T. Lamberts
- Theoretical
Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen , 6525 AJ Nijmegen, The Netherlands
- Sackler
Laboratory for Astrophysics, Leiden Observatory, Leiden University, 2300
RA Leiden, The Netherlands
| |
Collapse
|
37
|
Bohner MU, Meisner J, Kästner J. A Quadratically-Converging Nudged Elastic Band Optimizer. J Chem Theory Comput 2013; 9:3498-504. [DOI: 10.1021/ct400323z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Matthias U. Bohner
- Computational Biochemistry
Group, Institute of Theoretical
Chemistry, University of Stuttgart, Pfaffenwaldring
55, 70569 Stuttgart, Germany
| | - Jan Meisner
- Computational Biochemistry
Group, Institute of Theoretical
Chemistry, University of Stuttgart, Pfaffenwaldring
55, 70569 Stuttgart, Germany
| | - Johannes Kästner
- Computational Biochemistry
Group, Institute of Theoretical
Chemistry, University of Stuttgart, Pfaffenwaldring
55, 70569 Stuttgart, Germany
| |
Collapse
|
38
|
Metz S, Kästner J, Sokol AA, Keal TW, Sherwood P. C
hem
S
hell—a modular software package for
QM
/
MM
simulations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1163] [Citation(s) in RCA: 252] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sebastian Metz
- Scientific Computing DepartmentSTFC Daresbury LaboratoryDaresburyWarringtonUK
| | - Johannes Kästner
- Institute of Theoretical ChemistryUniversity of StuttgartStuttgartGermany
| | | | - Thomas W. Keal
- Scientific Computing DepartmentSTFC Daresbury LaboratoryDaresburyWarringtonUK
| | - Paul Sherwood
- Scientific Computing DepartmentSTFC Daresbury LaboratoryDaresburyWarringtonUK
| |
Collapse
|
39
|
Vattuone L, Smerieri M, Savio L, Asaduzzaman AM, Muralidharan K, Drake MJ, Rocca M. Accretion disc origin of the Earth's water. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2013; 371:20110585. [PMID: 23734050 DOI: 10.1098/rsta.2011.0585] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Earth's water is conventionally believed to be delivered by comets or wet asteroids after the Earth formed. However, their elemental and isotopic properties are inconsistent with those of the Earth. It was thus proposed that water was introduced by adsorption onto grains in the accretion disc prior to planetary growth, with bonding energies so high as to be stable under high-temperature conditions. Here, we show both by laboratory experiments and numerical simulations that water adsorbs dissociatively on the olivine {100} surface at the temperature (approx. 500-1500 K) and water pressure (approx. 10⁻⁸ bar) expected for the accretion disc, leaving an OH adlayer that is stable at least up to 900 K. This may result in the formation of many Earth oceans, provided that a viable mechanism to produce water from hydroxyl exists. This adsorption process must occur in all disc environments around young stars. The inevitable conclusion is that water should be prevalent on terrestrial planets in the habitable zone around other stars.
Collapse
Affiliation(s)
- Luca Vattuone
- Dipartimento di Fisica dell'Università di Genova and IMEM-CNR, Unità operativa di Genova, Via Dodecaneso 33, 16146 Genova, Italy.
| | | | | | | | | | | | | |
Collapse
|
40
|
Asaduzzaman AM, Laref S, Deymier PA, Runge K, Cheng HP, Muralidharan K, Drake MJ. A first-principles characterization of water adsorption on forsterite grains. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2013; 371:20110582. [PMID: 23734049 DOI: 10.1098/rsta.2011.0582] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Numerical simulations examining chemical interactions of water molecules with forsterite grains have demonstrated the efficacy of nebular gas adsorption as a viable mechanism for water delivery to the terrestrial planets. Nevertheless, a comprehensive picture detailing the water-adsorption mechanisms on forsterite is not yet available. Towards this end, using accurate first-principles density functional theory, we examine the adsorption mechanisms of water on the (001), (100), (010) and (110) surfaces of forsterite. While dissociative adsorption is found to be the most energetically favourable process, two stable associative adsorption configurations are also identified. In dual-site adsorption, the water molecule interacts strongly with surface magnesium and oxygen atoms, whereas single-site adsorption occurs only through the interaction with a surface Mg atom. This results in dual-site adsorption being more stable than single-site adsorption.
Collapse
Affiliation(s)
- Abu Md Asaduzzaman
- Lunar and Planetary Laboratory, University of Arizona, Tucson, AZ 85721, USA
| | | | | | | | | | | | | |
Collapse
|
41
|
Downing CA, Ahmady B, Catlow CRA, de Leeuw NH. The interaction of hydrogen with the {010} surfaces of Mg and Fe olivine as models for interstellar dust grains: a density functional theory study. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2013; 371:20110592. [PMID: 23734054 PMCID: PMC3682719 DOI: 10.1098/rsta.2011.0592] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
There is no consensus as yet to account for the significant presence of water on the terrestrial planets, but suggested sources include direct hydrogen adsorption from the parent molecular cloud after the planets' formation, and delivery of hydrous material via comets or asteroids external to the zone of the terrestrial planets. Alternatively, a more recent idea is that water may have directly adsorbed onto the interstellar dust grains involved in planetary formation. In this work, we use electronic structure calculations based on the density functional theory to investigate and compare the bulk and {010} surface structures of the magnesium and iron end-members of the silicate mineral olivine, namely forsterite and fayalite, respectively. We also report our results on the adsorption of atomic hydrogen at the mineral surfaces, where our calculations show that there is no activation barrier to the adsorption of atomic hydrogen at these surfaces. Furthermore, different surface sites activate the atom to form either adsorbed hydride or proton species in the form of hydroxy groups on the same surface, which indicates that these mineral surfaces may have acted as catalytic sites in the immobilization and reaction of hydrogen atoms to form dihydrogen gas or water molecules.
Collapse
Affiliation(s)
- C A Downing
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AH, UK.
| | | | | | | |
Collapse
|
42
|
Chaabouni H, Minissale M, Manicò G, Congiu E, Noble JA, Baouche S, Accolla M, Lemaire JL, Pirronello V, Dulieu F. Water formation through O2 + D pathway on cold silicate and amorphous water ice surfaces of interstellar interest. J Chem Phys 2012; 137:234706. [PMID: 23267497 DOI: 10.1063/1.4771663] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- H Chaabouni
- LERMA, UMR 8112 du CNRS, de l'Observatoire de Paris et de l'Université de Cergy Pontoise, 5 mail Gay Lussac, 95000 Cergy Pontoise Cedex, France.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Meisner J, Rommel JB, Kästner J. Kinetic isotope effects calculated with the instanton method. J Comput Chem 2011; 32:3456-63. [DOI: 10.1002/jcc.21930] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 07/30/2011] [Accepted: 08/01/2011] [Indexed: 01/18/2023]
|
44
|
Keal TW, Sherwood P, Dutta G, Sokol AA, Catlow CRA. Characterization of hydrogen dissociation over aluminium-doped zinc oxide using an efficient massively parallel framework for QM/MM calculations. Proc Math Phys Eng Sci 2011. [DOI: 10.1098/rspa.2010.0613] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A task-farm parallelization framework has been implemented in the ChemShell computational chemistry environment to provide a facility for parallelizing common chemical calculations, including finite-difference Hessian evaluation, the nudged elastic band method for reaction path optimization, and population-based methods for global optimization. The optimization methods are provided by a parallel interface to the DL-FIND optimization library. As ChemShell can already exploit parallel external programs for energy and gradient evaluations, the new methods result in a two-level approach to parallelization that gives significantly improved performance for massively parallel calculations. For typical systems, speed-up factors of five to eight times have been observed compared with non-task-farmed calculations. The task-farming version of ChemShell has been used to study the heterolytic dissociation of a hydrogen molecule over a polar oxygen-terminated surface of aluminium-doped zinc oxide using an embedded cluster hybrid QM/MM approach. We calculate a 42 kcal mol
−1
heat of reaction and a 30 kcal mol
−1
activation energy, which is equivalent to a high backward reaction barrier of 72 kcal mol
−1
per H
2
molecule, in close agreement with temperature programmed desorption experiments. The dissociation path includes a stable intermediate comprising a hydride ion in an oxygen vacancy and physisorbed atomic hydrogen.
Collapse
Affiliation(s)
- Thomas W. Keal
- Computational Science and Engineering Department, STFC Daresbury Laboratory, Daresbury, Warrington WA4 4AD, UK
| | - Paul Sherwood
- Computational Science and Engineering Department, STFC Daresbury Laboratory, Daresbury, Warrington WA4 4AD, UK
| | - Gargi Dutta
- Department of Chemistry, University College London, Kathleen Lonsdale Materials Chemistry, 20 Gordon Street, London WC1H 0AJ, UK
| | - Alexey A. Sokol
- Department of Chemistry, University College London, Kathleen Lonsdale Materials Chemistry, 20 Gordon Street, London WC1H 0AJ, UK
| | - C. Richard A. Catlow
- Department of Chemistry, University College London, Kathleen Lonsdale Materials Chemistry, 20 Gordon Street, London WC1H 0AJ, UK
| |
Collapse
|
45
|
He J, Frank P, Vidali G. Interaction of hydrogen with surfaces of silicates: single crystal vs. amorphous. Phys Chem Chem Phys 2011; 13:15803-9. [DOI: 10.1039/c1cp21601e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
46
|
Kästner J, Sherwood P. The ribosome catalyzes peptide bond formation by providing high ionic strength. Mol Phys 2010. [DOI: 10.1080/00268970903446764] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
47
|
Kästner J, Carr JM, Keal TW, Thiel W, Wander A, Sherwood P. DL-FIND: an open-source geometry optimizer for atomistic simulations. J Phys Chem A 2010; 113:11856-65. [PMID: 19639948 DOI: 10.1021/jp9028968] [Citation(s) in RCA: 370] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Geometry optimization, including searching for transition states, accounts for most of the CPU time spent in quantum chemistry, computational surface science, and solid-state physics, and also plays an important role in simulations employing classical force fields. We have implemented a geometry optimizer, called DL-FIND, to be included in atomistic simulation codes. It can optimize structures in Cartesian coordinates, redundant internal coordinates, hybrid-delocalized internal coordinates, and also functions of more variables independent of atomic structures. The implementation of the optimization algorithms is independent of the coordinate transformation used. Steepest descent, conjugate gradient, quasi-Newton, and L-BFGS algorithms as well as damped molecular dynamics are available as minimization methods. The partitioned rational function optimization algorithm, a modified version of the dimer method and the nudged elastic band approach provide capabilities for transition-state search. Penalty function, gradient projection, and Lagrange-Newton methods are implemented for conical intersection optimizations. Various stochastic search methods, including a genetic algorithm, are available for global or local minimization and can be run as parallel algorithms. The code is released under the open-source GNU LGPL license. Some selected applications of DL-FIND are surveyed.
Collapse
Affiliation(s)
- Johannes Kästner
- Computational Science and Engineering Department, STFC Daresbury Laboratory, Daresbury, Warrington WA4 4AD, United Kingdom.
| | | | | | | | | | | |
Collapse
|