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Nakata H, Filatov Gulak M, Choi CH. Accelerated Deep Learning Dynamics for Atomic Layer Deposition of Al(Me) 3 and Water on OH/Si(111). ACS APPLIED MATERIALS & INTERFACES 2022; 14:26116-26127. [PMID: 35608478 DOI: 10.1021/acsami.2c01768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Knowledge of the detailed mechanism behind the atomic layer deposition (ALD) can greatly facilitate the optimization of the manufacturing process. Computational modeling can potentially foster the understanding; however, the presently available capabilities of the accurate ab initio computational techniques preclude their application to modeling surface processes occurring on a long time scale, such as ALD. Although the situation can be greatly improved using machine learning (ML), this technique requires an enormous amount of data for training datasets. Here, we propose an iterative protocol for optimizing ML training datasets and apply ML-assisted ab initio calculations to model surface reactions occurring during the Al(Me)3/H2O ALD process on the OH-terminated Si (111) surface. The protocol uses a recently developed low-dimensional projection technique (TDUS), greatly reducing the amount of information required to achieve high accuracy (ca. 1 kcal/mol or less) of the developed ML models. The resulting free energy landscapes reveal fine details of various aspects of the target ALD process, such as the surface proton transfer, zwitterionic surface configurations, elimination-addition/addition-elimination, and SN2 reactions as well as the role of the surface entropic and temperature effects. Simulations of adsorption dynamics predict that the maximum physisorption rate of ca. 70% is achieved at the incidence velocity urms of the reactants in the range of 15-20 Å/ps. Hence, the proposed protocol furnishes a very effective tool to study complex chemical reaction dynamics at a much reduced computational cost.
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Affiliation(s)
- Hiroya Nakata
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | | | - Cheol Ho Choi
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
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2
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Kontkanen OV, Biriukov D, Futera Z. Reorganization Free Energy of Copper Proteins in Solution, in Vacuum, and on Metal Surfaces. J Chem Phys 2022; 156:175101. [DOI: 10.1063/5.0085141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Metalloproteins, known to efficiently transfer electronic charge in biological systems, recently found their utilization in nanobiotechnological devices where the protein is placed into direct contact with metal surfaces. The feasibility of oxidation/reduction of the protein redox sites is affected by the reorganization free energies, one of the key parameters determining the transfer rates. While their values have been measured and computed for proteins in their native environments, i.e., in aqueous solution, the reorganization free energies of dry proteins or proteins adsorbed to metal surfaces remain unknown. Here, we investigate the redox properties of blue copper protein azurin, a prototypical redox-active metalloprotein previously probed by various experimental techniques both in solution and on metal/vacuum interfaces. We used a hybrid QM/MM computational technique based on DFT to explore protein dynamics, flexibility, and corresponding reorganization free energies in aqueous solution, vacuum, and on vacuum gold interfaces. Somewhat surprisingly, the reorganization free energy only slightly decreases when azurin is dried because the loss of the hydration shell leads to larger flexibility of the protein near its redox site. At the vacuum gold surfaces, the energetics of the structure relaxation depends on the adsorption geometry, however, significant reduction of the reorganization free energy was not observed. These findings have important consequences for the charge transport mechanism in vacuum devices, showing that the free energy barriers for protein oxidation remain significant even under ultra-high vacuum conditions.
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Affiliation(s)
| | - Denys Biriukov
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences, Czech Republic
| | - Zdenek Futera
- University of South Bohemia in Ceske Budejovice Faculty of Science, Czech Republic
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3
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Formation of bifunctional cross-linked products due to reaction of NAMI-A with DNA bases – a DFT study. Struct Chem 2022. [DOI: 10.1007/s11224-022-01897-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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4
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Zimmermann T, Šebesta F, Burda JV. A new grand-canonical potential for the thermodynamic description of the reactions in solutions with constant pH. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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5
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Alshaikh H. Synthesis of Dowex functionalised half-sandwich Ru (II) (η6-p-cymene) complex as effective and selective hydrogenation of furfural to levulinic acid. JOURNAL OF POLYMER RESEARCH 2021. [DOI: 10.1007/s10965-021-02454-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Šebesta F, Šebera J, Sychrovský V, Tanaka Y, Burda JV. QM and QM/MM umbrella sampling MD study of the formation of Hg(II)-thymine bond: Model for evaluation of the reaction energy profiles in solutions with constant pH. J Comput Chem 2020; 41:1509-1520. [PMID: 32208552 DOI: 10.1002/jcc.26194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/24/2020] [Accepted: 02/28/2020] [Indexed: 01/01/2023]
Abstract
The formation of the Hg-N3(T) bond between the 1-methylthymine (T) molecule and the hydrated Hg2+ cation was explored with the combined quantum mechanics/molecular mechanics (QM/MM) method including Free Energy Perturbation corrections. The thermodynamic properties were determined in the whole pH range, when these systems were explicitly investigated and considered as the QM part: (1) T + [Hg(H2 O)6 ]2+ , (2) T + [Hg(H2 O)5 (OH)]+ , (3) T + Hg(H2 O)4 (OH)2 , and (4) N3-deprotonated T + Hg(H2 O)4 (OH)2 . The MM part contained only solvent molecules and counterions. As a result, the dependence of Gibbs-Alberty reaction free energy on pH was obtained along the reaction coordinate. We found that an endoergic reaction in acidic condition up to pH < 4-5 becomes exoergic for a higher pH corresponding to neutral and basic solutions. The migration of the Hg2+ cation between N3 and O4/2 positions in dependence on pH is discussed as well. For the verification, DFT calculations of stationary points were performed confirming the qualitative trends of QM/MM MD simulations and NMR parameters were determined for them.
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Affiliation(s)
- Filip Šebesta
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Jakub Šebera
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Yoshiyuki Tanaka
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Japan
| | - Jaroslav V Burda
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
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8
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Nakata H, Choi CH. Low-dimensional projection approach for efficient sampling of molecular recognition and polymer aggregation. Phys Chem Chem Phys 2020; 22:6953-6963. [PMID: 32182309 DOI: 10.1039/c9cp06964j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The one-dimensional projection (ODP) approach is extended to two-dimensional umbrella sampling (TDUS) and is applied to three different complex systems in combination with a reactive force field (ReaxFF). TDUS is capable of showing detailed features of the free-energy surface (FES) of the double-proton transfer of the acetic acid dimer. It also revealed the direct relationship between the types of hydrogen bonding and binding strengths in the case of adrenaline molecular recognition by SIVSF (Serine, Isoleucine, Valine, Cysteine, and Phenylalanine). The study of polymer aggregation using TDUS shows that aggregation is preferred with a less-polar solvent, which is also consistent with the experimental observation of a tape-casting process. Therefore, TDUS can be generally useful in FES explorations from simple chemical reactions to complex processes of molecular recognition and polymer aggregation.
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Affiliation(s)
- Hiroya Nakata
- Kyocera Corporation, Research Institute for Advanced Materials and Devices, 3-5-3 Hikaridai, Seika-cho, Soraku-gun, Kyoto 619-0237, Japan.
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Exploration of selected electronic characteristics of half-sandwich organoruthenium(II) β-diketonate complexes. J Mol Model 2018; 24:98. [DOI: 10.1007/s00894-018-3598-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 01/26/2018] [Indexed: 12/11/2022]
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Spinello A, Magistrato A. An omics perspective to the molecular mechanisms of anticancer metallo-drugs in the computational microscope era. Expert Opin Drug Discov 2017; 12:813-825. [DOI: 10.1080/17460441.2017.1340272] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Angelo Spinello
- CNR-IOM-DEMOCRITOS c/o International School for Advanced Studies (SISSA/ISAS), Trieste, Italy
| | - Alessandra Magistrato
- CNR-IOM-DEMOCRITOS c/o International School for Advanced Studies (SISSA/ISAS), Trieste, Italy
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Šebesta F, Sláma V, Melcr J, Futera Z, Burda JV. Estimation of Transition-Metal Empirical Parameters for Molecular Mechanical Force Fields. J Chem Theory Comput 2016; 12:3681-8. [DOI: 10.1021/acs.jctc.6b00416] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Filip Šebesta
- Department of Chemical Physics
and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
| | - Vladislav Sláma
- Department of Chemical Physics
and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
| | - Josef Melcr
- Department of Chemical Physics
and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
| | - Zdeněk Futera
- Department of Chemical Physics
and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
| | - Jaroslav V. Burda
- Department of Chemical Physics
and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
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Zábojníková T, Cajzl R, Kljun J, Chval Z, Turel I, Burda JV. Interactions of the "piano-stool" [ruthenium(II)(η(6) -arene)(quinolone)Cl](+) complexes with water; DFT computational study. J Comput Chem 2016; 37:1766-80. [PMID: 27185047 DOI: 10.1002/jcc.24373] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 02/23/2016] [Accepted: 02/24/2016] [Indexed: 12/12/2022]
Abstract
Full optimizations of stationary points along the reaction coordinate for the hydration of several quinolone Ru(II) half-sandwich complexes were performed in water environment using the B3PW91/6-31+G(d)/PCM/UAKS method. The role of diffuse functions (especially on oxygen) was found crucial for correct geometries along the reaction coordinate. Single-point (SP) calculations were performed at the B3LYP/6-311++G(2df,2pd)/DPCM/saled-UAKS level. In the first part, two possible reaction mechanisms-associative and dissociative were compared. It was found that the dissociative mechanism of the hydration process is kinetically slightly preferred. Another important conclusion concerns the reaction channels. It was found that substitution of chloride ligand (abbreviated in the text as dechlorination reaction) represents energetically and kinetically the most feasible pathway. In the second part the same hydration reaction was explored for reactivity comparison of the Ru(II)-complexes with several derivatives of nalidixic acid: cinoxacin, ofloxacin, and (thio)nalidixic acid. The hydration process is about four orders of magnitude faster in a basic solution compared to neutral/acidic environment with cinoxacin and nalidixic acid as the most reactive complexes in the former and latter environments, respectively. The explored hydration reaction is in all cases endergonic; nevertheless the endergonicity is substantially lower (by ∼6 kcal/mol) in basic environment. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Tereza Zábojníková
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague 2, 121 16, Czech Republic
| | - Radim Cajzl
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague 2, 121 16, Czech Republic
| | - Jakob Kljun
- Faculty of Chemistry and Chemical Technologyn University of Ljubljana, Večna pot 113, Ljubljana, 1000, Slovenia
| | - Zdeněk Chval
- Department of Laboratory Methods and Information Systems, Faculty of Health and Social Studies, University of South Bohemia, J. Boreckého 27, České Budějovice, 370 11, Czech Republic
| | - Iztok Turel
- Faculty of Chemistry and Chemical Technologyn University of Ljubljana, Večna pot 113, Ljubljana, 1000, Slovenia
| | - Jaroslav V Burda
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague 2, 121 16, Czech Republic
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Guan S, Zhao L, Jin H, Shan N, Han W, Wang S, Shan Y. Binding modes of phosphotriesterase-like lactonase complexed with δ-nonanoic lactone and paraoxon using molecular dynamics simulations. J Biomol Struct Dyn 2016; 35:273-286. [DOI: 10.1080/07391102.2016.1142899] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Shanshan Guan
- National Engineering Laboratory For AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Li Zhao
- National Engineering Laboratory For AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Hanyong Jin
- National Engineering Laboratory For AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Ning Shan
- Editorial Department of Journal of Jilin University (Science Edition), Changchun, China
| | - Weiwei Han
- National Engineering Laboratory For AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Song Wang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Yaming Shan
- National Engineering Laboratory For AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
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Šebesta F, Burda JV. Reduction Process of Tetraplatin in the Presence of Deoxyguanosine Monophosphate (dGMP): A Computational DFT Study. Chemistry 2015; 22:1037-47. [PMID: 26663432 DOI: 10.1002/chem.201503555] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 10/15/2015] [Indexed: 01/01/2023]
Abstract
The reduction mechanism of [Pt(IV) (dach)Cl4 ] (dach=diaminocyclohexyl) in the presence of dGMP was studied. The first step is substitution of a chloro ligand by dGMP, followed by nucleophilic attack of a phosphate or sugar oxygen atom to the C8-position of guanine. Subsequent reduction forms the [Pt(II) (dach)Cl2 ] complex. The whole process is completed by a hydrolysis. Two different pathways for the substitution reaction were examined: a direct associative and a Basolo-Pearson autocatalytic mechanism. All the explored structures were optimized at the B3LYP-D3/6-31G(d) level and by using the COSMO solvation model with Klamt's radii. Single-point energetics was determined at the B3LYP-GD3BJ/6-311++G(2df,2pd)/PCM/scaled-UAKS level. Activation barriers were used for an estimation of the rate constants and these were compared with experimental values. It was found that the rate-determining step is the nucleophilic attack with a slightly faster performance in the 3'-dGMP branch than in the case of 5'-dGMP with activation barriers of 21.1 and 20.4 kcal mol(-1) (experimental: 23.8 and 23.2 kcal mol(-1) ). The reduction reaction is connected with an electron flow from guanine. The product of the reduction reaction is a chelate structure, which dissociates within the last reaction step, that is, a hydrolysis reaction. The whole redox process (substitution, reduction, and hydrolysis) is exergonic by 34 and 28 kcal mol(-1) for 5'-dGMP and 3'-dGMP, respectively.
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Affiliation(s)
- Filip Šebesta
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16, Prague 2, Czech Republic
| | - Jaroslav V Burda
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16, Prague 2, Czech Republic.
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Characterization of Aspartate Kinase from Corynebacterium pekinense and the Critical Site of Arg169. Int J Mol Sci 2015; 16:28270-84. [PMID: 26633359 PMCID: PMC4691045 DOI: 10.3390/ijms161226098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 11/10/2015] [Accepted: 11/11/2015] [Indexed: 11/21/2022] Open
Abstract
Aspartate kinase (AK) is the key enzyme in the biosynthesis of aspartate-derived amino acids. Recombinant AK was efficiently purified and systematically characterized through analysis under optimal conditions combined with steady-state kinetics study. Homogeneous AK was predicted as a decamer with a molecular weight of ~48 kDa and a half-life of 4.5 h. The enzymatic activity was enhanced by ethanol and Ni2+. Moreover, steady-state kinetic study confirmed that AK is an allosteric enzyme, and its activity was inhibited by allosteric inhibitors, such as Lys, Met, and Thr. Theoretical results indicated the binding mode of AK and showed that Arg169 is an important residue in substrate binding, catalytic domain, and inhibitor binding. The values of the kinetic parameter Vmax of R169 mutants, namely, R169Y, R169P, R169D, and R169H AK, with l-aspartate as the substrate, were 4.71-, 2.25-, 2.57-, and 2.13-fold higher, respectively, than that of the wild-type AK. Furthermore, experimental and theoretical data showed that Arg169 formed a hydrogen bond with Glu92, which functions as the entrance gate. This study provides a basis to develop new enzymes and elucidate the corresponding amino acid production.
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Torras J. Multiple active zones in hybrid QM/MM molecular dynamics simulations for large biomolecular systems. Phys Chem Chem Phys 2015; 17:9959-72. [DOI: 10.1039/c5cp00905g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new QM/MM molecular dynamics approach that can deal with the dynamics of large real systems involving several simultaneous active zones is presented.
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Affiliation(s)
- Juan Torras
- Department of Chemical Engineering
- EEI
- Universitat Politècnica de Catalunya
- Igualada 08700
- Spain
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Das D, Mondal P. Interaction of ruthenium(ii) antitumor complexes with d(ATATAT)2 and d(GCGCGC)2: a theoretical study. NEW J CHEM 2015. [DOI: 10.1039/c4nj02118e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have investigated the interaction of three ruthenium(ii) complexes with d(ATATAT)2 and d(GCGCGC)2 sequences by using the molecular docking and quantum mechanics/molecular mechanics (QM/MM) hybrid method.
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Affiliation(s)
- Dharitri Das
- Department of Chemistry
- Assam University
- Silchar 788011
- India
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