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Valencia J, Rubio V, Puerto G, Vasquez L, Bernal A, Mora JR, Cuesta SA, Paz JL, Insuasty B, Abonia R, Quiroga J, Insuasty A, Coneo A, Vidal O, Márquez E, Insuasty D. QSAR Studies, Molecular Docking, Molecular Dynamics, Synthesis, and Biological Evaluation of Novel Quinolinone-Based Thiosemicarbazones against Mycobacterium tuberculosis. Antibiotics (Basel) 2022; 12:antibiotics12010061. [PMID: 36671262 PMCID: PMC9854539 DOI: 10.3390/antibiotics12010061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
In this study, a series of novel quinolinone-based thiosemicarbazones were designed in silico and their activities tested in vitro against Mycobacterium tuberculosis (M. tuberculosis). Quantitative structure-activity relationship (QSAR) studies were performed using quinolinone and thiosemicarbazide as pharmacophoric nuclei; the best model showed statistical parameters of R2 = 0.83; F = 47.96; s = 0.31, and was validated by several different methods. The van der Waals volume, electron density, and electronegativity model results suggested a pivotal role in antituberculosis (anti-TB) activity. Subsequently, from this model a new series of quinolinone-thiosemicarbazone 11a-e was designed and docked against two tuberculosis protein targets: enoyl-acyl carrier protein reductase (InhA) and decaprenylphosphoryl-β-D-ribose-2'-oxidase (DprE1). Molecular dynamics simulation over 200 ns showed a binding energy of -71.3 to -12.7 Kcal/mol, suggesting likely inhibition. In vitro antimycobacterial activity of quinolinone-thiosemicarbazone for 11a-e was evaluated against M. bovis, M. tuberculosis H37Rv, and six different strains of drug-resistant M. tuberculosis. All compounds exhibited good to excellent activity against all the families of M. tuberculosis. Several of the here synthesized compounds were more effective than the standard drugs (isoniazid, oxafloxacin), 11d and 11e being the most active products. The results suggest that these compounds may contribute as lead compounds in the research of new potential antimycobacterial agents.
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Affiliation(s)
- Jhesua Valencia
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
| | - Vivian Rubio
- Grupo de Micobacterias, Red TB Colombia, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Gloria Puerto
- Grupo de Micobacterias, Red TB Colombia, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Luisa Vasquez
- Grupo de Micobacterias, Red TB Colombia, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Anthony Bernal
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
| | - José R. Mora
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 170157, Ecuador
| | - Sebastian A. Cuesta
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 170157, Ecuador
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - José Luis Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Cercado de Lima 15081, Peru
| | - Braulio Insuasty
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, A. A., Cali 25360, Colombia
| | - Rodrigo Abonia
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, A. A., Cali 25360, Colombia
| | - Jairo Quiroga
- Research Group of Heterocyclic Compounds, Department of Chemistry, Universidad del Valle, A. A., Cali 25360, Colombia
| | - Alberto Insuasty
- Grupo de Investigación en Materiales Funcionales Nanoestructurados, Universidad CESMAG, Pasto 520003, Colombia
| | - Andres Coneo
- Medicine Department, Division of Health Sciences, Universidad del Norte, Barranquilla 081007, Colombia
| | - Oscar Vidal
- Medicine Department, Division of Health Sciences, Universidad del Norte, Barranquilla 081007, Colombia
| | - Edgar Márquez
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
- Correspondence: (E.M.); (D.I.)
| | - Daniel Insuasty
- Grupo de Investigación en Química y Biología, Universidad del Norte, Km 5 vía Puerto Colombia, Barranquilla 081007, Colombia
- Correspondence: (E.M.); (D.I.)
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Liang Y, Zheng W, Xie H, Zha X, Wang T. A quantum chemistry study on C–H homolytic bond dissociation enthalpies of five-membered and six-membered heterocyclic compounds. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Palanisamy K, Rubavathy SME, Prakash M, Thilagavathi R, Hosseini-Zare MS, Selvam C. Antiviral activities of natural compounds and ionic liquids to inhibit the Mpro of SARS-CoV-2: a computational approach. RSC Adv 2022; 12:3687-3695. [PMID: 35425367 PMCID: PMC8979281 DOI: 10.1039/d1ra08604a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/30/2021] [Indexed: 12/14/2022] Open
Abstract
The recalcitrant spread of the COVID-19 pandemic produced by the novel coronavirus SARS-CoV-2 is one of the most destructive occurrences in history. Despite the availability of several effective vaccinations and their widespread use, this line of immunization often faces questions about its long-term efficacy. Since coronaviruses rapidly change, and multiple SARS-CoV-2 variants have emerged around the world. Therefore, finding a new target-based medication became a priority to prevent and control COVID-19 infections. The main protease (Mpro) is a salient enzyme in coronaviruses that plays a vital role in viral replication, making it a fascinating therapeutic target for SARS-CoV-2. We screened 0.2 million natural products against the Mpro of SARS-CoV-2 using the Universal Natural Product Database (UNPD). As well, we studied the role of ionic liquids (ILs) on the structural stabilization of Mpro. Cholinium-based ILs are biocompatible and used for a variety of biomedical applications. Molecular docking was employed for the initial screening of natural products and ILs against Mpro. To predict the drug-likeness features of lead compounds, we calculated the ADMET properties. We performed MD simulations for the selected complexes based on the docking outcomes. Using MM/PBSA approaches, we conclude that compounds NP-Hit2 (-25.6 kcal mol-1) and NP-Hit3 (-25.3 kcal mol-1) show stronger binding affinity with Mpro. The hotspot residues of Thr25, Leu27, His41, Met49, Cys145, Met165, and Gln189 strongly interacted with the natural compounds. Furthermore, naproxenate, ketoprofenate, and geranate, cholinium-based ILs strongly interact with Mpro and these ILs have antimicrobial properties. Our findings will aid in the development of effective Mpro inhibitors.
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Affiliation(s)
- Kandhan Palanisamy
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology Kattankulathur-603203 Chennai Tamil Nadu India
| | - S M Esther Rubavathy
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology Kattankulathur-603203 Chennai Tamil Nadu India
| | - Muthuramalingam Prakash
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology Kattankulathur-603203 Chennai Tamil Nadu India
| | - Ramasamy Thilagavathi
- Department of Biotechnology, Faculty of Engineering, Karpagam Academy of Higher Education Coimbatore India
| | - Maryam S Hosseini-Zare
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University Houston TX-77004 USA
| | - Chelliah Selvam
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University Houston TX-77004 USA
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Xu H, Li B, Liu Z, Dang Y. Mechanistic Origins of Stereodivergence in Asymmetric Cascade Allylation and Cyclization Reactions Enabled by Synergistic Cu/Ir Catalysis. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02270] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hui Xu
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Department of Chemistry, Tianjin University, Tianjin 300072, China
| | - Bo Li
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Department of Chemistry, Tianjin University, Tianjin 300072, China
| | - Zheyuan Liu
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Department of Chemistry, Tianjin University, Tianjin 300072, China
| | - Yanfeng Dang
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Department of Chemistry, Tianjin University, Tianjin 300072, China
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Sen R, González-Espinoza CE, Zech A, Dreuw A, Wesolowski TA. Benchmark of the Extension of Frozen-Density Embedding Theory to Nonvariational Correlated Methods: The Embedded-MP2 Case. J Chem Theory Comput 2021; 17:4049-4062. [PMID: 34137597 DOI: 10.1021/acs.jctc.1c00228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The extension of the frozen-density embedding theory for nonvariational methods [J. Chem. Theory Comput. 2020, 16, 6880] was utilized to evaluate intermolecular interaction energies for complexes in the Zhao-Truhlar basis set. In the applied method (FDET-MP2-FAT-LDA), the same auxiliary system is used to evaluate the correlation energy by means of the second-order Møller-Plesset perturbation theory (MP2), as in our previous work [J. Chem. Phys. 2019, 150, 121101]. Local density approximation is used for ExcTnad[ρA,ρB] in both cases. Additionally, the contribution to the energy due to the neglected correlation potential was evaluated and analyzed. The domain of applicability of the local density approximation for ExcTnad[ρA,ρB] was determined based on deviations from the interaction energies from the conventional MP2 calculations. The local density approximation for ExcTnad[ρA,ρB] performs well for hydrogen- or dipole-bound complexes. The relative errors in the interaction energy lie within 3-30%. While for charge-transfer complexes, this approximation fails consistently, and for other types of complexes, the performance of this approximation is not systematic. The sources of error are discussed in detail.
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Affiliation(s)
- Reena Sen
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University Heidelberg, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | | | - Alexander Zech
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University Heidelberg, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Tomasz A Wesolowski
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland
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Maiyelvaganan KR, Ravva MK, Prakash M, Subramanian V. Benchmark studies on protonated benzene (BZH+) and water (Wn, n = 1–6) clusters: a comparison of hybrid DFT with MP2/CBS and CCSD(T)/CBS methods. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02660-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Palanisamy V, Sanphui P, Prakash M, Chernyshev V. Multicomponent solid forms of the uric acid reabsorption inhibitor lesinurad and cocrystal polymorphs with urea: DFT simulation and solubility study. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2019; 75:1102-1117. [PMID: 31380793 DOI: 10.1107/s2053229619008829] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 06/20/2019] [Indexed: 11/11/2022]
Abstract
Lesinurad (systematic name: 2-{[5-bromo-4-(4-cyclopropylnaphthalen-1-yl)-4H-1,2,4-triazol-3-yl]sulfanyl}acetic acid, C17H14BrN3O2S) is a selective uric acid reabsorption inhibitor related to gout, which exhibits poor aqueous solubility. High-throughput solid-form screening was performed to screen for new solid forms with improved pharmaceutically relevant properties. During polymorph screening, we obtained two solvates with methanol (CH3OH) and ethanol (C2H5OH). Binary systems with caffeine (systematic name: 3,7-dihydro-1,3,7-trimethyl-1H-purine-2,6-dione, C8H10N4O2) and nicotinamide (C6H6N2O), polymorphs with urea (CH4N2O) and eutectics with similar drugs, like allopurinol and febuxostat, were prepared using the crystal engineering approach. All these novel solid forms were confirmed by XRD, DSC and FT-IR. The crystal structures were solved by single-crystal and powder X-ray diffraction. The crystal structures indicate that the lesinurad molecule is highly flexible and the triazole moiety, along with the rotatable thioacetic acid (side chain) and cyclopropane ring, is almost perpendicular to the planar naphthalene moiety. The carboxylic acid-triazole heterosynthon in the drug is interrupted by the presence of methanol and ethanol molecules in their crystal structures and forms intermolecular macrocyclic rings. The caffeine cocrystal maintains the consistency of the acid-triazole heterosynthons as in the drug and, in addition, they are bound by several auxiliary interactions. In the binary system of nicotinamide and urea, the acid-triazole heterosynthon is replaced by an acid-amide synthon. Among the urea cocrystal polymorphs, Form I (P-1, 1:1) consists of an acid-amide (urea) heterodimer, whereas in Form II (P21/c, 2:2), both acid-amide heterosynthons and urea-urea dimers co-exist. Density functional theory (DFT) calculations further support the experimentally observed synthon hierarchies in the cocrystals. Aqueous solubility experiments of lesinurad and its binary solids in pH 5 acetate buffer medium indicate the apparent solubility order lesinurad-urea Form I (43-fold) > lesinurad-caffeine (20-fold) > lesinurad-allopurinol (12-fold) ≃ lesinurad-nicotinamide (11-fold) > lesinurad, and this order is correlated with the crystal structures.
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Affiliation(s)
- Vasanthi Palanisamy
- Department of Chemistry, SRM Institute of Science and Technology, Kattankulathur 603 203, India
| | - Palash Sanphui
- Department of Chemistry, SRM Institute of Science and Technology, Kattankulathur 603 203, India
| | - Muthuramalingam Prakash
- Department of Chemistry, SRM Institute of Science and Technology, Kattankulathur 603 203, India
| | - Vladimir Chernyshev
- Department of Chemistry, M. V. Lomonosov Moscow State University, 1-3 Leninskie Gory, Moscow 119991, Russian Federation
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Tian T, Sun X, Weiske T, Cai Y, Geng C, Li J, Schwarz H. Reassessment of the Mechanisms of Thermal C-H Bond Activation of Methane by Cationic Magnesium Oxides: A Critical Evaluation of the Suitability of Different Density Functionals. Chemphyschem 2019; 20:1812-1821. [PMID: 31120181 DOI: 10.1002/cphc.201900508] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 05/22/2019] [Indexed: 12/24/2022]
Abstract
The mechanisms of the thermal reactions of the two iconic magnesium oxide cations MgO.+ and Mg2 O2 .+ with methane have been re-evaluated at the CCSD(T)/CBS//CCSD/def2-TZVP level of theory. For the reaction of MgO.+ with CH4 , only the classical hydrogen-atom transfer (HAT) was found; in contrast, for the Mg2 O2 .+ /CH4 couple, both HAT and proton-coupled electron-transfer (PCET) exist as mechanistic variants. In order to evaluate the suitability of density functional theory (DFT) methods, the reactions were computed by using 27 density functionals. The results obtained demonstrate that the various DFT methods often deliver rather different results for both geometric and energetic features. As to the prediction of the apparent barriers, pure functionals give the largest mean absolute errors. BMK, ωB97XD, and the double-hybrid functional mPW2PLYP were confirmed to come closest to the results provided by CCSD(T)/CBS. Thus, mechanistic conclusions based on a single DFT method should be viewed with great caution. In summary, this study may assist in the selection of a suitable quantum chemical method to unravel the mechanistic details of C-H bond activation by charged metal oxides.
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Affiliation(s)
- Tian Tian
- Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, People's Republic of China
| | - Xiaoli Sun
- Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, People's Republic of China
| | - Thomas Weiske
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 115, 10623, Berlin, Germany
| | - Yuxi Cai
- Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, People's Republic of China
| | - Caiyun Geng
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 115, 10623, Berlin, Germany
| | - Jilai Li
- Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, People's Republic of China.,Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 115, 10623, Berlin, Germany
| | - Helmut Schwarz
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 115, 10623, Berlin, Germany
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Balamurugan K, Prakash M, Subramanian V. Theoretical Insights into the Role of Water Molecules in the Guanidinium-Based Protein Denaturation Process in Specific to Aromatic Amino Acids. J Phys Chem B 2019; 123:2191-2202. [PMID: 30672268 DOI: 10.1021/acs.jpcb.8b08968] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Noncovalent interactions between the guanidinium cation (Gdm+) and aromatic amino acids (AAs) in the water molecules have been studied using quantum chemical calculation and molecular dynamics (MD) simulations. Our studies show that there are two different modes of interactions between Gdm+ and AAs with and without water molecules. It is observed that nonhydrated Gdm+ interacts with AAs through N-H···π interactions, whereas hydrated clusters of Gdm+ are stabilized by stacking interactions with the help of the water-mediated hydrogen bond. Thus, different hydration patterns have significant effects on the predominant cation···π interactions in AAs-Gdm+ complexes. Findings from MD simulation elicit that the interaction pattern of Gdm+ with AAs varies as Phe < Tyr < Trp. Both the QM and MD calculations show a similar trend in the interaction of AAs with Gdm+. Moreover, the interaction of AAs with Gdm+ depends on the spatial orientation of AAs in the protein and the concomitant local structure, that is, the AAs present in the unstructured region of protein such as coils and bends exhibit higher binding for Gdm+ when compared to the AAs present in the structured region of the protein such as the α-helix and the β-sheet. Our study clearly reveals that H-bonded water molecules and the hydration pattern of Gdm+ as well as the positional presence of these AAs in the protein structure context play determining roles in the denaturation of protein by the Gdm+ cation.
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Affiliation(s)
- Kanagasabai Balamurugan
- Chemical Laboratory , CSIR-Central Leather Research Institute , Adyar, Chennai 600 020 , India
| | - Muthuramalingam Prakash
- Chemical Laboratory , CSIR-Central Leather Research Institute , Adyar, Chennai 600 020 , India
| | - Venkatesan Subramanian
- Chemical Laboratory , CSIR-Central Leather Research Institute , Adyar, Chennai 600 020 , India.,Academy of Scientific and Innovative Research (AcSIR) , CSIR-CLRI Campus , Chennai 600 020 , India
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Kruse H, Banáš P, Šponer J. Investigations of Stacked DNA Base-Pair Steps: Highly Accurate Stacking Interaction Energies, Energy Decomposition, and Many-Body Stacking Effects. J Chem Theory Comput 2018; 15:95-115. [DOI: 10.1021/acs.jctc.8b00643] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Pavel Banáš
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17 Listopadu 12, 77146 Olomouc, Czech Republic
| | - Jiřı́ Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17 Listopadu 12, 77146 Olomouc, Czech Republic
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Klahr K, Schlüns D, Neugebauer J. Geometry Optimizations in a Subsystem Density Functional Theory Formalism: A Benchmark Study. J Chem Theory Comput 2018; 14:5631-5644. [DOI: 10.1021/acs.jctc.8b00475] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kevin Klahr
- Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Danny Schlüns
- Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Johannes Neugebauer
- Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
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Interaction energy profile for diphenyl diselenide in complex with δ-aminolevulinic acid dehydratase enzyme using quantum calculations and a molecular fragmentation method. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.comtox.2018.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Insights into the bonding between tributylphosphine chalcogenides and zinc(II). Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2245-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Calbo J, Sancho-García JC, Ortí E, Aragó J. Quantum-Chemical Insights into the Self-Assembly of Carbon-Based Supramolecular Complexes. Molecules 2018; 23:molecules23010118. [PMID: 29316675 PMCID: PMC6017611 DOI: 10.3390/molecules23010118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/02/2018] [Accepted: 01/03/2018] [Indexed: 12/28/2022] Open
Abstract
Understanding how molecular systems self-assemble to form well-organized superstructures governed by noncovalent interactions is essential in the field of supramolecular chemistry. In the nanoscience context, the self-assembly of different carbon-based nanoforms (fullerenes, carbon nanotubes and graphene) with, in general, electron-donor molecular systems, has received increasing attention as a means of generating potential candidates for technological applications. In these carbon-based systems, a deep characterization of the supramolecular organization is crucial to establish an intimate relation between supramolecular structure and functionality. Detailed structural information on the self-assembly of these carbon-based nanoforms is however not always accessible from experimental techniques. In this regard, quantum chemistry has demonstrated to be key to gain a deep insight into the supramolecular organization of molecular systems of high interest. In this review, we intend to highlight the fundamental role that quantum-chemical calculations can play to understand the supramolecular self-assembly of carbon-based nanoforms through a limited selection of supramolecular assemblies involving fullerene, fullerene fragments, nanotubes and graphene with several electron-rich π-conjugated systems.
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Affiliation(s)
- Joaquín Calbo
- Institute of Molecular Science, University of Valencia, 46980 Paterna (Valencia), Spain.
| | | | - Enrique Ortí
- Institute of Molecular Science, University of Valencia, 46980 Paterna (Valencia), Spain.
| | - Juan Aragó
- Institute of Molecular Science, University of Valencia, 46980 Paterna (Valencia), Spain.
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Wang Y, Wei D, Zhang W. Recent Advances on Computational Investigations ofN-Heterocyclic Carbene Catalyzed Cycloaddition/Annulation Reactions: Mechanism and Origin of Selectivities. ChemCatChem 2017. [DOI: 10.1002/cctc.201701119] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yang Wang
- The College of Chemistry and Molecular Engineering; Zhengzhou University; 100 Science Avenue Zhengzhou Henan Province 450001 P.R. China
| | - Donghui Wei
- The College of Chemistry and Molecular Engineering; Zhengzhou University; 100 Science Avenue Zhengzhou Henan Province 450001 P.R. China
| | - Wenjing Zhang
- The College of Chemistry and Molecular Engineering; Zhengzhou University; 100 Science Avenue Zhengzhou Henan Province 450001 P.R. China
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Ashwin BCMA, Herculin Arun Baby A, Prakash M, Hochlaf M, Muthu Mareeswaran P. A combined experimental and theoretical study on p-
sulfonatocalix[4]arene encapsulated 7-methoxycoumarin. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3788] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | | | - Muthuramalingam Prakash
- SRM Research Institute and Department of Chemistry; SRM University; Kattankulathur Tamil Nadu India
| | - Majdi Hochlaf
- Laboratoire Modélisation et Simulation Multi-Echelle, UMR 8208 CNRS; University Paris-Est; Marne la Vallée Cedex 2 France
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Radhika R, Shankar R, Vijayakumar S, Kolandaivel P. Role of 6-Mercaptopurine in the potential therapeutic targets DNA base pairs and G-quadruplex DNA: insights from quantum chemical and molecular dynamics simulations. J Biomol Struct Dyn 2017; 36:1369-1401. [PMID: 28436311 DOI: 10.1080/07391102.2017.1323013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The theoretical studies on DNA with the anticancer drug 6-Mercaptopurine (6-MP) are investigated using theoretical methods to shed light on drug designing. Among the DNA base pairs considered, 6-MP is stacked with GC with the highest interaction energy of -46.19 kcal/mol. Structural parameters revealed that structure of the DNA base pairs is deviated from the planarity of the equilibrium position due to the formation of hydrogen bonds and stacking interactions with 6-MP. These deviations are verified through the systematic comparison between X-H bond contraction and elongation and the associated blue shift and red shift values by both NBO analysis and vibrational analysis. Bent's rule is verified for the C-H bond contraction in the 6-MP interacted base pairs. The AIM results disclose that the higher values of electron density (ρ) and Laplacian of electron density (∇2ρ) indicate the increased overlap between the orbitals that represent the strong interaction and positive values of the total electron density show the closed-shell interaction. The relative sensitivity of the chemical shift values for the DNA base pairs with 6-MP is investigated to confirm the hydrogen bond strength. Molecular dynamics simulation studies of G-quadruplex DNA d(TGGGGT)4 with 6-MP revealed that the incorporation of 6-MP appears to cause local distortions and destabilize the G-quadruplex DNA.
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Affiliation(s)
- R Radhika
- a Department of Physics , Bharathiar University , Coimbatore , India
| | - R Shankar
- a Department of Physics , Bharathiar University , Coimbatore , India
| | - S Vijayakumar
- b Department of Medical Physics , Bharathiar University , Coimbatore , India
| | - P Kolandaivel
- a Department of Physics , Bharathiar University , Coimbatore , India
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20
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Schlüns D, Franchini M, Götz AW, Neugebauer J, Jacob CR, Visscher L. Analytical gradients for subsystem density functional theory within the slater-function-based amsterdam density functional program. J Comput Chem 2016; 38:238-249. [DOI: 10.1002/jcc.24670] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/14/2016] [Accepted: 10/19/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Danny Schlüns
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster; Corrensstraße 40 Münster 48149 Germany
| | - Mirko Franchini
- Amsterdam Center for Multiscale Modeling; Vrije Universiteit Amsterdam; De Boelelaan 1083 HV Amsterdam 1081 The Netherlands
- Scientific Computing & Modelling NV; Vrije Universiteit; Theoretical Chemistry, De Boelelaan 1083 HV Amsterdam 1081 The Netherlands
| | - Andreas W. Götz
- San Diego Supercomputer Center; University of California San Diego; 9500 Gilman Drive La Jolla, California 92093-0505 USA
| | - Johannes Neugebauer
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster; Corrensstraße 40 Münster 48149 Germany
| | - Christoph R. Jacob
- Institute of Physical and Theoretical Chemistry; TU Braunschweig, Hans-Sommer-Straße 10 Braunschweig 38106 Germany
| | - Lucas Visscher
- Amsterdam Center for Multiscale Modeling; Vrije Universiteit Amsterdam; De Boelelaan 1083 HV Amsterdam 1081 The Netherlands
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21
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Prakash M, Subramanian V. Ab initio and density functional theory (DFT) studies on triflic acid with water and protonated water clusters. J Mol Model 2016; 22:293. [PMID: 27888404 DOI: 10.1007/s00894-016-3158-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 11/08/2016] [Indexed: 02/04/2023]
Abstract
The structure, stability and infrared spectral signatures of triflic acid (TA) with water clusters (Wn) and protonated water clusters (TAH+Wn, n = 1 - 6) were computed using DFT and MP2 methods. Our calculations show that a minimum of three water molecules are necessary to stabilize the dissociated zwitterionic form of TA. It can be seen from the results that there is no significant movement of protons in smaller (n = 1 and 2) and linear (n = 1 - 6) types of water clusters. Further, the geometries of TAWn clusters first form a neutral pair (NP) to contact ion pair (CIP), then form a solvent separated ion pair (SSIP) in a water hexamer. These findings reveal that proton transfer may take place through NP to CIP and then CIP to SSIP. The calculated binding energies (BEs) of ion pair clusters is always higher than that of NP clusters (i.e., more stable than the NP). Existing excess proton linear chain clusters transfer a proton to adjacent water molecules via a Grotthuss mechanism, whereas the same isomers in the branched motifs do not conduct protons. Examination of geometrical parameters and infrared frequencies reveals hydronium ion (H3O+ also called Eigen cation) formation in both TAWn and protonated TAWn clusters. The stability of Eigen water clusters is three times higher than that of other non-Eigen water clusters. Our study shows clearly that formation of ion pairs in TAWn and TAH+Wn clusters greatly favors proton transfer to neighboring water molecules and also enhances the stability of these complexes.
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Affiliation(s)
- M Prakash
- Department of Chemistry and Research Institute, SRM University, Kattankulathur, 603203, Tamil Nadu, India
- Chemical Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai, 600 020, India
| | - V Subramanian
- Chemical Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai, 600 020, India.
- Academy of Scientific and Innovative Research (AcSIR), CSIR-CLRI Campus, Chennai, 600 020, India.
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22
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Jambrec D, Haddad R, Lauks A, Gebala M, Schuhmann W, Kokoschka M. DNA Intercalators for Detection of DNA Hybridisation: SCS(MI)-MP2 Calculations and Electrochemical Impedance Spectroscopy. Chempluschem 2016; 81:604-612. [DOI: 10.1002/cplu.201600173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 05/18/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Daliborka Jambrec
- Analytical Chemistry-Center for Electrochemical Sciences (CES); Ruhr-Universität Bochum; Universitätstrasse 150 44780 Bochum Germany
| | - Raoudha Haddad
- Analytical Chemistry-Center for Electrochemical Sciences (CES); Ruhr-Universität Bochum; Universitätstrasse 150 44780 Bochum Germany
| | - Anna Lauks
- Analytical Chemistry-Center for Electrochemical Sciences (CES); Ruhr-Universität Bochum; Universitätstrasse 150 44780 Bochum Germany
| | - Magdalena Gebala
- Analytical Chemistry-Center for Electrochemical Sciences (CES); Ruhr-Universität Bochum; Universitätstrasse 150 44780 Bochum Germany
- Department of Biochemistry; Stanford University; Stanford CA 94305 USA
| | - Wolfgang Schuhmann
- Analytical Chemistry-Center for Electrochemical Sciences (CES); Ruhr-Universität Bochum; Universitätstrasse 150 44780 Bochum Germany
| | - Malte Kokoschka
- Analytical Chemistry-Center for Electrochemical Sciences (CES); Ruhr-Universität Bochum; Universitätstrasse 150 44780 Bochum Germany
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23
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Tuna D, Udvarhelyi A, Sobolewski AL, Domcke W, Domratcheva T. Onset of the Electronic Absorption Spectra of Isolated and π-Stacked Oligomers of 5,6-Dihydroxyindole: An Ab Initio Study of the Building Blocks of Eumelanin. J Phys Chem B 2016; 120:3493-502. [PMID: 27005558 DOI: 10.1021/acs.jpcb.6b01793] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Eumelanin is a naturally occurring skin pigment which is responsible for developing a suntan. The complex structure of eumelanin consists of π-stacked oligomers of various indole derivatives, such as the monomeric building block 5,6-dihydroxyindole (DHI). In this work, we present an ab initio wave-function study of the absorption behavior of DHI oligomers and of doubly and triply π-stacked species of these oligomers. We have simulated the onset of the electronic absorption spectra by employing the MP2 and the linear-response CC2 methods. Our results demonstrate the effect of an increasing degree of oligomerization of DHI and of an increasing degree of π-stacking of DHI oligomers on the onset of the absorption spectra and on the degree of red-shift toward the visible region of the spectrum. We find that π-stacking of DHI and its oligomers substantially red-shifts the onset of the absorption spectra. Our results also suggest that the optical properties of biological eumelanin cannot be simulated by considering the DHI building blocks alone, but instead the building blocks indole-semiquinone and indole-quinone have to be considered as well. This study contributes to advancing the understanding of the complex photophysics of the eumelanin biopolymer.
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Affiliation(s)
- Deniz Tuna
- Department of Chemistry, Technische Universität München , 85747 Garching, Germany
| | - Anikó Udvarhelyi
- Department of Biomolecular Mechanisms, Max-Planck-Institut für Medizinische Forschung , 69120 Heidelberg, Germany
| | | | - Wolfgang Domcke
- Department of Chemistry, Technische Universität München , 85747 Garching, Germany
| | - Tatiana Domratcheva
- Department of Biomolecular Mechanisms, Max-Planck-Institut für Medizinische Forschung , 69120 Heidelberg, Germany
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24
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Gurtu S, Rai S, Ehara M, Priyakumar UD. Ability of density functional theory methods to accurately model the reaction energy pathways of the oxidation of CO on gold cluster: A benchmark study. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1852-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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25
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Boulmene R, Boussouf K, Prakash M, Komiha N, Al-Mogren MM, Hochlaf M. Ab Initio and DFT Studies on CO2Interacting with Znq+-Imidazole (q=0, 1, 2) Complexes: Prediction of Charge Transfer through σ- or π-Type Models. Chemphyschem 2016; 17:994-1005. [DOI: 10.1002/cphc.201501185] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Reda Boulmene
- Université Paris-Est; Laboratoire Modélisation et Simulation Multi-Échelle, MSME UMR 8208 CNRS; 5 bd Descartes 77454 Marne-la-Vallée France
| | - Karim Boussouf
- Université Paris-Est; Laboratoire Modélisation et Simulation Multi-Échelle, MSME UMR 8208 CNRS; 5 bd Descartes 77454 Marne-la-Vallée France
| | - Muthuramalingam Prakash
- Université Paris-Est; Laboratoire Modélisation et Simulation Multi-Échelle, MSME UMR 8208 CNRS; 5 bd Descartes 77454 Marne-la-Vallée France
| | - Najia Komiha
- LS3 ME-Team of theoretical chemistry and modeling; Faculty of Sciences; University Mohammed V; Rabat Morocco
| | - Muneerah M. Al-Mogren
- Chemistry Department; Faculty of Science; King Saud University; P.O. Box 2455 Riyadh 11451 Kingdom of Saudi Arabia
| | - Majdi Hochlaf
- Université Paris-Est; Laboratoire Modélisation et Simulation Multi-Échelle, MSME UMR 8208 CNRS; 5 bd Descartes 77454 Marne-la-Vallée France
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26
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Boulmène R, Prakash M, Hochlaf M. Microscopic investigations of site and functional selectivity of triazole for CO2 capture and catalytic applications. Phys Chem Chem Phys 2016; 18:29709-29720. [DOI: 10.1039/c6cp04650a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ab initio and DFT studies on CO2 interacting with different tautomers and isomers of triazole (TZ) are carried out to understand the adsorption mechanism, site selectivity and their mutual preferential attracting sites.
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Affiliation(s)
- Reda Boulmène
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 5 Bd Descartes
- 77454 Marne- La-Vallée
| | - Muthuramalingam Prakash
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 5 Bd Descartes
- 77454 Marne- La-Vallée
| | - Majdi Hochlaf
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 5 Bd Descartes
- 77454 Marne- La-Vallée
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27
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Dułak M, Kamiński JW, Wesołowski TA. Equilibrium Geometries of Noncovalently Bound Intermolecular Complexes Derived from Subsystem Formulation of Density Functional Theory. J Chem Theory Comput 2015; 3:735-45. [PMID: 26627391 DOI: 10.1021/ct600367t] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The subsystem formulation of density functional theory is used to obtain equilibrium geometries and interaction energies for a representative set of noncovalently bound intermolecular complexes. The results are compared with literature benchmark data. The range of applicability of two considered approximations to the exchange-correlation- and nonadditive kinetic energy components of the total energy is determined. Local density approximation, which does not involve any empirical parameters, leads to excellent intermolecular equilibrium distances for hydrogen-bonded complexes (maximal error 0.13 Å for NH3-NH3). It is a method of choice for a wide class of weak intermolecular complexes including also dipole-bound and the ones formed by rare gas atoms or saturated hydrocarbons. The range of applicability of the chosen generalized gradient approximation, which was shown in our previous works to lead to good interaction energies in such complexes, where π-electrons are involved in the interaction, remains limited to this group because it improves neither binding energies nor equilibrium geometries in the wide class of complexes for which local density approximation is adequate. An efficient energy minimization procedure, in which optimization of the geometry and the electron density of each subsystem is made simultaneously, is proposed and tested.
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Affiliation(s)
- Marcin Dułak
- Département de Chimie Physique, Université de Genève, 30, quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland, and Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Jakub W Kamiński
- Département de Chimie Physique, Université de Genève, 30, quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland, and Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Tomasz A Wesołowski
- Département de Chimie Physique, Université de Genève, 30, quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland, and Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
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28
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Zhao Y, Truhlar DG. Density Functionals for Noncovalent Interaction Energies of Biological Importance. J Chem Theory Comput 2015; 3:289-300. [PMID: 26627172 DOI: 10.1021/ct6002719] [Citation(s) in RCA: 466] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Forty density functionals and one wavefunction method are assessed against a recently published database of accurate noncovalent interaction energies of biological importance. The comparison shows that two newly developed density functional theory (DFT) methods, PWB6K and M05-2X, give the best performance for this benchmark database of 22 noncovalent complexes, including both hydrogen-bonding and dispersion-dominated complexes. In contrast, the more popular B3LYP and PBEh functionals fail to describe the interactions in the dispersion-dominated complexes. The local spin density approximation and BHandH functionals give good performance for dispersion-dominated interactions at the expense of a large error for hydrogen bonding. PWB6K and M05-2X constitute a new generation of DFT methods based on simultaneously optimized exchange and correlation functionals that include kinetic energy density in both the exchange and correlation functional, and the present study confirms that they have greatly improved performance for noncovalent interactions as compared to previous DFT methods. We interpret this as being due to an improved treatment of medium-range correlation effects by the exchange-correlation functional. We recommend the PWB6K and M05-2X methods for investigating large biological systems and soft materials.
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Affiliation(s)
- Yan Zhao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
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29
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Radoń M, Srebro M, Broclawik E. Conformational Stability and Spin States of Cobalt(II) Acetylacetonate: CASPT2 and DFT Study. J Chem Theory Comput 2015; 5:1237-44. [PMID: 26609714 DOI: 10.1021/ct800571y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electronic structure and conformation of bis(acetylacetonate) cobalt(II), Co(acac)2, a prototypical mediator in controlled radical polymerization of olefins, is reinvestigated. The ab initio multiconfigurational CASSCF/CASPT2 method is used to resolve the doubts stemming from density functional theory results. We assign the quartet ground state for a single molecule and point at tetrahedral conformation as the preferred one. Several density functionals are tested against the ab initio calculations, and their performance is assessed. The strength of intermolecular interactions in the crystal structure composed of square-planar Co(acac)2 molecules ( Burgess , J. ; et al. Acta Crystallogr. 2000 , C56 , 649 - 650 ) is estimated to be sufficient for their planarization (suggested by Matyjaszewski , K. ; et al. Chem.-Eur. J. 2007 , 13 , 2480 - 2492 ).
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Affiliation(s)
- Mariusz Radoń
- Department of Theoretical Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Kraków, Poland, and Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Kraków, Poland
| | - Monika Srebro
- Department of Theoretical Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Kraków, Poland, and Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Kraków, Poland
| | - Ewa Broclawik
- Department of Theoretical Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Kraków, Poland, and Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Kraków, Poland
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30
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Boussouf K, Khairat T, Prakash M, Komiha N, Chambaud G, Hochlaf M. Structure, Spectroscopy, and Bonding within the Zn(q+)-Imidazole(n) (q = 0, 1, 2; n = 1-4) Clusters and Implications for Zeolitic Imidazolate Frameworks and Zn-Enzymes. J Phys Chem A 2015; 119:11928-40. [PMID: 26565743 DOI: 10.1021/acs.jpca.5b09500] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using density functional theory (DFT) with dispersion correction and ab initio post Hartree-Fock methods, we treat the bonding, the structure, the stability, and the spectroscopy of the complexes between Zn(q+) and imidazole (Im), Zn(q+)Imn (where q = 0, 1 and 2; n = 1-4). These entities are subunits of zeolitic imidazolate frameworks (ZIFs) and Zn-enzymes, which possess relevant roles in industrial and biological domains, respectively. We also investigate the Imn (n = 2-4) clusters for comparison. For each species, we determine several new structures that were not found previously. Our calculations show a competition between atomic metal solvation, by either σ-type interactions or π-stacking type interaction, and proton transfer through hydrogen bonding (H-bonding) in charged species. This results in several geometrical environments around the metal. These are connected with structural properties and the functional role of Zn cation within ZIFs and Zn-enzymes. Moreover, we show that the Zn(2+)Imn subunits do not absorb in the visible domain, which may be related to the photostability of ZIFs. Our findings are important for the development of new applications of ZIFs and metalloenzymes.
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Affiliation(s)
- K Boussouf
- LS3ME-Equipe de Chimie Théorique et Modélisation, Faculté des Sciences Rabat, Université Mohamed V , Rabat, Morocco.,Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est , 5 bd Descartes, 77454 Marne-la-Vallée, France
| | - T Khairat
- LS3ME-Equipe de Chimie Théorique et Modélisation, Faculté des Sciences Rabat, Université Mohamed V , Rabat, Morocco
| | - M Prakash
- Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est , 5 bd Descartes, 77454 Marne-la-Vallée, France
| | - N Komiha
- LS3ME-Equipe de Chimie Théorique et Modélisation, Faculté des Sciences Rabat, Université Mohamed V , Rabat, Morocco
| | - G Chambaud
- Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est , 5 bd Descartes, 77454 Marne-la-Vallée, France
| | - M Hochlaf
- Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est , 5 bd Descartes, 77454 Marne-la-Vallée, France
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31
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Hill DE, Holland JP. Computational studies on hypervalent iodonium(III) compounds as activated precursors for 18F radiofluorination of electron-rich arenes. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.05.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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32
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Abstract
The article reviews the significant contributions to, and the present status of, applications of computational methods for the characterization and prediction of protein-carbohydrate interactions. After a presentation of the specific features of carbohydrate modeling, along with a brief description of the experimental data and general features of carbohydrate-protein interactions, the survey provides a thorough coverage of the available computational methods and tools. At the quantum-mechanical level, the use of both molecular orbitals and density-functional theory is critically assessed. These are followed by a presentation and critical evaluation of the applications of semiempirical and empirical methods: QM/MM, molecular dynamics, free-energy calculations, metadynamics, molecular robotics, and others. The usefulness of molecular docking in structural glycobiology is evaluated by considering recent docking- validation studies on a range of protein targets. The range of applications of these theoretical methods provides insights into the structural, energetic, and mechanistic facets that occur in the course of the recognition processes. Selected examples are provided to exemplify the usefulness and the present limitations of these computational methods in their ability to assist in elucidation of the structural basis underlying the diverse function and biological roles of carbohydrates in their dialogue with proteins. These test cases cover the field of both carbohydrate biosynthesis and glycosyltransferases, as well as glycoside hydrolases. The phenomenon of (macro)molecular recognition is illustrated for the interactions of carbohydrates with such proteins as lectins, monoclonal antibodies, GAG-binding proteins, porins, and viruses.
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Affiliation(s)
- Serge Pérez
- Department of Molecular Pharmacochemistry, CNRS, University Grenoble-Alpes, Grenoble, France.
| | - Igor Tvaroška
- Department of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic; Department of Chemistry, Faculty of Natural Sciences, Constantine The Philosopher University, Nitra, Slovak Republic.
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33
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Momeni Z, Ebrahimi A. Investigation of the effect of π–π stacking interaction on the properties of –CONH2 functional group of benzamide. Struct Chem 2015. [DOI: 10.1007/s11224-015-0615-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Tian G, Li H, Ma W, Wang Y. Substituent Effects in π-Stacking of Histidine on Functionalized-SWNT and Graphene. COMPUT THEOR CHEM 2015; 1062:44-49. [PMID: 25914869 DOI: 10.1016/j.comptc.2015.03.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adsorptions of histidine on the functionalized (10,0) single-walled carbon nanotube (SWNT) and graphene were investigated using density function theory methods, M05-2x and DFT-D. The results show that the binding of the histidine ring to the functionalized SWNT is weaker than that to the pristine SWNT for both singlet and triplet complexes, regardless of the electron-donating (-OH, -NH2) or electron-withdrawing (-COOH) character and their attached sites. The present decreased binding is opposite to the well-known enhanced binding in the substituted benzene dimers. Since the atoms of the histidine are distant from the substituent atoms by over 6Å, there would be no direct interaction between histidine and the substituent as in the case of the substituted benzene systems. The decreased binding can be mainly driven by the aromaticity of the functionalized SWNT. The nucleus-independent chemical shift (NICS) index analysis for the functionalized SWNTs in deed shows that local aromaticity of SWNT is decreased because of the electron redistribution induced by functional groups, and the π-π stacking between the histidine ring and functionalized-SWNT is therefore decreased as compared to the pristine SWNT. However, the above trend does not remain for the binding between the histidine and graphene. The binding of the histidine to the functionalized graphene with -OH and -NH2 is just slightly weaker than that to the pristine graphene, while its binding to COOH-SWNT becomes a little bit stronger.
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Affiliation(s)
- Ge Tian
- School of Chemistry and Pharmaceutical Engineering, Qilu University of Technology, Jinan, Shandong 250353, China ; Department of Natural Science, Albany State University, Albany, GA 31705, USA
| | - Huifang Li
- Department of Natural Science, Albany State University, Albany, GA 31705, USA ; Department of Chemistry, Gannan Normal University, GanZhou, JiangXi 341000, China
| | - Wanyong Ma
- School of Chemistry and Pharmaceutical Engineering, Qilu University of Technology, Jinan, Shandong 250353, China
| | - Yixuan Wang
- Department of Natural Science, Albany State University, Albany, GA 31705, USA
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35
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Liang J, Su Q, Wang Y, Geng Z. SN2 Reaction of IO− + CH3Cl: An Ab Initio and DFT Benchmark Study. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2015. [DOI: 10.1246/bcsj.20140194] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Junxi Liang
- Gansu Key Laboratory of Environmental Friendly Composites and Biomass Utilization, College of Chemical Engineering, Northwest University for Nationalities
| | - Qiong Su
- Gansu Key Laboratory of Environmental Friendly Composites and Biomass Utilization, College of Chemical Engineering, Northwest University for Nationalities
| | - Yanbin Wang
- Gansu Key Laboratory of Environmental Friendly Composites and Biomass Utilization, College of Chemical Engineering, Northwest University for Nationalities
| | - Zhiyuan Geng
- Gansu Key Laboratory of Polymer Materials, College of Chemistry and Chemical Engineering, Key Laboratory of Eco-environment-related Polymer Materials, Ministry of Education, Northwest Normal University
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36
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Schlüns D, Klahr K, Mück-Lichtenfeld C, Visscher L, Neugebauer J. Subsystem-DFT potential-energy curves for weakly interacting systems. Phys Chem Chem Phys 2015; 17:14323-41. [DOI: 10.1039/c4cp04936e] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Subsystem DFT for weakly interacting systems: good at reference geometries, but not necessarily good for potential-energy curves.
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Affiliation(s)
- Danny Schlüns
- Theoretische Organische Chemie
- Organisch-Chemisches Institut and Center for Multiscale Theory and Computation
- 48149 Münster
- Germany
| | - Kevin Klahr
- Theoretische Organische Chemie
- Organisch-Chemisches Institut and Center for Multiscale Theory and Computation
- 48149 Münster
- Germany
| | - Christian Mück-Lichtenfeld
- Theoretische Organische Chemie
- Organisch-Chemisches Institut and Center for Multiscale Theory and Computation
- 48149 Münster
- Germany
| | - Lucas Visscher
- Amsterdam Center for Multiscale Modeling
- Vrije Universiteit Amsterdam
- 1081 HV Amsterdam
- The Netherlands
| | - Johannes Neugebauer
- Theoretische Organische Chemie
- Organisch-Chemisches Institut and Center for Multiscale Theory and Computation
- 48149 Münster
- Germany
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37
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Gopalakrishnan R, Azhagiya Singam ER, Vijaya Sundar J, Subramanian V. Interaction of collagen like peptides with gold nanosurfaces: a molecular dynamics investigation. Phys Chem Chem Phys 2015; 17:5172-86. [DOI: 10.1039/c4cp04969a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, an attempt has been made to understand the interaction between collagen like peptides (CPs) with a gold nanosurface (AuNS) using a classical molecular dynamics simulation.
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Affiliation(s)
- R. Gopalakrishnan
- Chemical laboratory
- Council of Scientific and Industrial Research
- Central Leather Research Institute
- Chennai-600020
- India
| | - E. R. Azhagiya Singam
- Chemical laboratory
- Council of Scientific and Industrial Research
- Central Leather Research Institute
- Chennai-600020
- India
| | - J. Vijaya Sundar
- Chemical laboratory
- Council of Scientific and Industrial Research
- Central Leather Research Institute
- Chennai-600020
- India
| | - V. Subramanian
- Chemical laboratory
- Council of Scientific and Industrial Research
- Central Leather Research Institute
- Chennai-600020
- India
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38
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Rai S, Singh H, Priyakumar UD. Binding to gold nanoclusters alters the hydrogen bonding interactions and electronic properties of canonical and size-expanded DNA base pairs. RSC Adv 2015. [DOI: 10.1039/c5ra04668h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Structural perturbations, in terms of size expansion and metal binding, lead to exciting electronic properties which can be exploited in designing novel nano-electronic devices.
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Affiliation(s)
- Sandhya Rai
- Center for Computational Natural Science and Bioinformatics
- International Institute of Information Technology
- Hyderabad
- India
| | - Harjinder Singh
- Center for Computational Natural Science and Bioinformatics
- International Institute of Information Technology
- Hyderabad
- India
| | - U. Deva Priyakumar
- Center for Computational Natural Science and Bioinformatics
- International Institute of Information Technology
- Hyderabad
- India
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39
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Huang PQ, Lai CH. Computational study of unsaturated and saturated cyclic (alkyl) (amino) carbene borane complexes. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.10.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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40
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Hill DE, Vasdev N, Holland JP. Evaluating the accuracy of density functional theory for calculating 1H and 13C NMR chemical shifts in drug molecules. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.11.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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41
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Boussouf K, Boulmene R, Prakash M, Komiha N, Taleb M, Mogren Al-Mogren M, Hochlaf M. Characterization of Znq+–imidazole (q = 0, 1, 2) organometallic complexes: DFT methods vs. standard and explicitly correlated post-Hartree–Fock methods. Phys Chem Chem Phys 2015; 17:14417-26. [DOI: 10.1039/c4cp06108j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Benchmarking DFts for the characterization of the Znq+–imidazole (q= 0, 1, 2) complexes.
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Affiliation(s)
- K. Boussouf
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
| | - R. Boulmene
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
| | - M. Prakash
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
| | - N. Komiha
- LS3ME-Equipe de Chimie Théorique et Modélisation
- Université Mohamed
- Faculté des Sciences
- Rabat
- Maroc
| | - M. Taleb
- Laboratoire LIMME
- Université Sidi Med Ben Abdellah
- Fac des Sciences Dhar El Mehrez
- Fès
- Maroc
| | - M. Mogren Al-Mogren
- Chemistry Department
- Faculty of Science
- King Saud University
- Riyadh 11451
- Kingdom of Saudi Arabia
| | - M. Hochlaf
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
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42
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Prakash M, Chambaud G, Al-Mogren MM, Hochlaf M. Role of size and shape selectivity in interaction between gold nanoclusters and imidazole: a theoretical study. J Mol Model 2014; 20:2534. [PMID: 25488624 DOI: 10.1007/s00894-014-2534-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 11/17/2014] [Indexed: 11/26/2022]
Abstract
We present a theoretical study on the structure, stability, spectra and electronic properties of imidazole (Im) adsorbed on gold nanoclusters (Aun, n = 2, 4, 6, 8, 10, and 20). These computations were performed using various density functional theories with and without inclusion of Grimme's (D3) dispersion correction. For small clusters, we also carried out wavefunction-based ab initio (MP2 and SCS-MP2) computations for comparison. Vibrational, atoms in molecules (AIM) and natural bond orbital (NBO) analyses clearly reveal the occurrence of charge transfer (CT) through covalent (N1-Au) and noncovalent interactions that play important roles in the stability of the Im@Aun complexes with anchor assisted H-bonds (Cα-H · Au). Therefore, gold clusters can act as H-bond acceptors with biomolecules for development of new materials and applications. Our study establishes also the ability and reliability of PBE0 and M05-2X functionals compared to B3LYP and PBE for an accurate description of covalent and noncovalent interactions between Im and gold clusters since they lead to close agreement with MP2. Finally, we show that the Au8 cluster may be viewed as large enough to mimic the 3D gold surface.
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Affiliation(s)
- Muthuramalingam Prakash
- Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR, Université Paris-Est, 8208 CNRS, 5 bd Descartes, 77454, Marne-la-Vallée, France
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43
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Valdés H, Poyatos M, Ujaque G, Peris E. Experimental and theoretical approaches to the influence of the addition of pyrene to a series of Pd and Ni NHC-based complexes: catalytic consequences. Chemistry 2014; 21:1578-88. [PMID: 25413787 DOI: 10.1002/chem.201404618] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Indexed: 11/12/2022]
Abstract
A series of Ni and Pd complexes with three different N-heterocyclic carbene (NHC)-based ligands (imidazolylidene, benzimidazolylidene and pyrene-imidazolylidene) has been prepared and fully characterized. The influence of the addition of pyrene to solutions containing these complexes is studied by means of NMR and UV/Vis spectroscopies and by cyclic voltammetry. The addition of pyrene to the pyrene-NHC-containing Pd and Ni complexes gives rise to the formation of adducts by π-π stacking interactions between pyrene and the pyrene group of the NHC ligand. This interaction causes a modification of the electronic properties of the metal, as demonstrated by cyclic voltammetric studies of the Ni-NHC complexes. Theoretical calculations support this type of π-interactions, and justify the higher interactions observed with the pyrene-NHC containing complexes. The catalytic activities of the complexes were tested in the Suzuki-Miyaura C-C coupling and in the α-arylation of ketones. The addition of pyrene as an external π-stacking additive does not affect the activities of the complexes in the Suzuki-Miyaura coupling, but this observation may be justified due to the fact that the process is heterogeneously catalyzed, as indicated by the mercury-drop test. The addition of pyrene to the catalytic α-arylation of ketones results in a decrease in the activity of the reactions catalyzed by the pyrene-imidazolylidene palladium complex, whereas the other two catalysts do not modify their activity in the presence of this π-stacking additive.
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Affiliation(s)
- Hugo Valdés
- Dpto. de Química Inorgánica y Orgánica, Universitat Jaume I, Avda. Sos Baynat, 12071 Castellón (Spain)
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44
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Arefi HH, Nolan M, Fagas G. Density functional theory with van der waals corrections study of the adsorption of alkyl, alkylthiol, alkoxyl, and amino-alkyl chains on the H:Si(111) surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:13255-13265. [PMID: 25260071 DOI: 10.1021/la502488c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Surface modification of silicon with organic monolayers tethered to the surface by different linkers is an important process in realizing future miniaturized electronic and sensor devices. Understanding the roles played by the nature of the linking group and the chain length on the adsorption structures and stabilities of these assemblies is vital to advance this technology. This paper presents a density functional theory (DFT) study of the hydrogen passivated Si(111) surface modified with alkyl chains of the general formula H:Si-(CH2)n-CH2 and H:Si-X-(CH2)n-CH3, where X = NH, O, S and n = (0, 1, 3, 5, 7, 9, 11), at half coverage. For (X)-hexane and (X)-dodecane functionalization, we also examined various coverages up to full monolayer grafting in order to validate the result of half covered surface and the linker effect on the coverage. We find that it is necessary to take into account the van der Waals interaction between the alkyl chains. The strongest binding is for the oxygen linker, followed by S, N, and C, irrespective of chain length. The result revealed that the sequence of the stability is independent of coverage; however, linkers other than carbon can shift the optimum coverage considerably and allow further packing density. For all linkers apart from sulfur, structural properties, in particular, surface-linker-chain angles, saturate to a single value once n > 3. For sulfur, we identify three regimes, namely, n = 0-3, n = 5-7, and n = 9-11, each with its own characteristic adsorption structures. Where possible, our computational results are shown to be consistent with the available experimental data and show how the fundamental structural properties of modified Si surfaces can be controlled by the choice of linking group and chain length.
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Affiliation(s)
- Hadi H Arefi
- Tyndall National Institute, Lee Maltings, and ‡Department of Electrical Engineering, University College Cork , Cork, Ireland
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45
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Mikulski D, Eder K, Molski M. Quantum-chemical study on stacking interactions between bioactive polyphenols (trans-resveratrol, trans-piceatannol) and ribonucleosides. Insight into minimum energy geometries of π–π stacked systems. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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46
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47
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Jacob CR, Neugebauer J. Subsystem density-functional theory. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2014. [DOI: 10.1002/wcms.1175] [Citation(s) in RCA: 229] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Christoph R. Jacob
- Center for Functional Nanostructures and Institute of Physical Chemistry; Karlsruhe Institute of Technology (KIT); Karlsruhe Germany
| | - Johannes Neugebauer
- Theoretische Organische Chemie, Organisch-Chemisches Institut; Westfälische Wilhelms-Universität Münster; Münster Germany
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49
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Paytakov G, Gorb L, Stepanyugin A, Samiylenko S, Hovorun D, Leszczynski J. Homodimers of Cytosine and 1-MethylCytosine. A DFT study of geometry, relative stability and H-NMR shifts in gas-phase and selected solvents. J Mol Model 2014; 20:2115. [DOI: 10.1007/s00894-014-2115-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 12/13/2013] [Indexed: 12/07/2022]
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50
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Rai S, Ranjan S, Singh H, Priyakumar UD. Modulation of structural, energetic and electronic properties of DNA and size-expanded DNA bases upon binding to gold clusters. RSC Adv 2014. [DOI: 10.1039/c4ra03753g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A strong modulation in electronic properties, indicating that such complexes have the potential to serve as scaffolds for building nano electronic devices.
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Affiliation(s)
- Sandhya Rai
- Center for Computational Natural Sciences and Bioinformatics
- International Institute of Information Technology
- Hyderabad, India
| | - Supriya Ranjan
- Center for Computational Natural Sciences and Bioinformatics
- International Institute of Information Technology
- Hyderabad, India
| | - Harjinder Singh
- Center for Computational Natural Sciences and Bioinformatics
- International Institute of Information Technology
- Hyderabad, India
| | - U. Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics
- International Institute of Information Technology
- Hyderabad, India
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