1
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Fan WJ, Shi H, Chen J, Tan D. Novel conjugated microporous polymers for efficient tetracycline adsorption: insights from theoretical investigations. J Mol Graph Model 2024; 126:108655. [PMID: 37907057 DOI: 10.1016/j.jmgm.2023.108655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 11/02/2023]
Abstract
This paper presents a detailed theoretical understanding of the noncovalent interactions between antibiotics tetracycline and conjugated microporous polymer (CMP), which is important to understand the recent experimental finding of efficient removal of antibiotics by CMP materials. We show that the co-work of π-π and H-π interactions determines the final equilibrium structures, when a tetracycline molecule spontaneously adsorbs to the surface or within the pores of the CMP network at physisorption distances. The binding energies for tetracycline/CMP systems are calculated to be -0.31 ∼ -1.15 eV, demonstrating the reliability of the adsorption. The electronic structures of CMP nanostructures remain basically undamaged upon the tetracycline adsorption. The replacement of benzothiadiazole unit with S and N heteroatoms to the phenyl moiety in the linker effectively enhanced the molecular polarity of CMP molecule and increases the interaction area between tetracycline and CMP network, consequently enhancing the average binding energies notably. Our calculations provide useful theoretical guidance for design of novel carbon-based porous adsorbents with good adsorption performance to remove residual tetracycline and other antibiotics in water.
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Affiliation(s)
- Wen-Jie Fan
- College of Marine Science and Environment Engineering, Dalian Ocean University, Dalian, 116023, PR China.
| | - Hua Shi
- College of Marine Science and Environment Engineering, Dalian Ocean University, Dalian, 116023, PR China
| | - Jinghe Chen
- College of Marine Science and Environment Engineering, Dalian Ocean University, Dalian, 116023, PR China
| | - Dazhi Tan
- Experimental Center of Chemistry, Dalian University of Technology, Dalian, 116024, PR China
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2
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Adhav VA, Pananghat B, Saikrishnan K. Probing the Directionality of S···O/N Chalcogen Bond and Its Interplay with Weak C-H···O/N/S Hydrogen Bond Using Molecular Electrostatic Potential. J Phys Chem B 2022; 126:7818-7832. [PMID: 36179131 DOI: 10.1021/acs.jpcb.2c03745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The directionality of the chalcogen bond (Ch-bond) formed by S and its interplay with other weak interactions have important chemical and biological implications. Here, dimers made of CH3-S-X and O/N containing nucleophiles are studied and found to be stabilized by coexisting S···O/N and C-H···O/N interactions. Based on experimentally accessible electron density and molecular electrostatic potentials (MESPs), we showed that reciprocity between S···O/N and C-H···O/N interactions in the stability of cumulative molecular interaction (ΔE) was dependent on the strength of the σ-hole on S (Vs,max). Direct correlation between ΔE of dimers with Vs,max of S supports the electrostatic nature of the Ch-bond. Such interplay of the Ch-bond is necessary for its directionality in complex nucleophiles (carbonyl groups) with multiple electron-rich centers, which is explained using MESP. A correlation between the MESP minima in the π-region and the strength of the S-π interaction explains the directional selectivity of the Ch-bond.
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Affiliation(s)
- Vishal Annasaheb Adhav
- Department of Biology, Indian Institute of Science Education and Research, Pune411008, India
| | - Balanarayan Pananghat
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Mohali140306, India
| | - Kayarat Saikrishnan
- Department of Biology, Indian Institute of Science Education and Research, Pune411008, India
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3
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Fan WJ, Liu N, Zhu WQ, Mao YB, Tan DZ. Design of novel conjugated microporous polymers for efficient adsorptive desulfurization of small aromatic sulfur molecules. J Mol Graph Model 2020; 101:107734. [PMID: 32931981 DOI: 10.1016/j.jmgm.2020.107734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/23/2020] [Accepted: 08/31/2020] [Indexed: 11/29/2022]
Abstract
This paper presents a computational study of the adsorptive desulfurization of small aromatic sulfur compounds by conjugated microporous polymers (CMPs). The density-functional tight-binding method augmented with an R-6 dispersion correction is employed to investigate the physisorption binding mechanism and electronic properties of the CMP-aromatic sulfur complexes. We show that the widely extended π conjugation in the CMP skeletons is favorable for the non-covalent adsorption of aromatic thiophene and dibenzothiophene via π-π, H-π, and S-π interactions. The average binding energies are calculated to be -6.2 ∼ -15.2 kcal/mol for CMP- thiophene/dibenzothiophene systems. For the dibenzothiophene molecule with larger size and more extended conjugation, it binds more than twice stronger to CMP than the thiophene molecule. We show that the replacement of quinoline unit to the phenylene group in the network linker effectively enhances the average binding capacities by around 0.8-1.8 kcal/mol. Our calculations theoretically demonstrate that CMPs materials are kind of promising candidates for the adsorptive desulfurization of small aromatic sulfur compounds. This paper provides useful theoretical guidance for design of novel carbon-based adsorbents for adsorptive desulfurization.
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Affiliation(s)
- Wen-Jie Fan
- College of Marine Science and Environment Engineering, Dalian Ocean University, Dalian, 116023, People's Republic of China.
| | - Na Liu
- College of Marine Science and Environment Engineering, Dalian Ocean University, Dalian, 116023, People's Republic of China
| | - Wei-Qiang Zhu
- College of China & New Zealand Collaboration, Dalian Ocean University, Dalian, 116023, People's Republic of China
| | - Yin-Bu Mao
- College of China & New Zealand Collaboration, Dalian Ocean University, Dalian, 116023, People's Republic of China
| | - Da-Zhi Tan
- Experimental Centre of Chemistry, Faculty of Chemical, Environmental and Biological, Dalian University of Technology, Dalian, 116024, People's Republic of China.
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4
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Polášek J, Paciorek J, Stošek J, Semrád H, Munzarová M, Mazal C. Stereoselective Bromoboration of Acetylene with Boron Tribromide: Preparation and Cross-Coupling Reactions of ( Z)-Bromovinylboronates. J Org Chem 2020; 85:6992-7000. [PMID: 32436705 DOI: 10.1021/acs.joc.0c00341] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanism of acetylene bromoboration in neat boron tribromide was studied carefully by means of experiment and theory. Besides the syn-addition mechanism through a four-center transition state, radical and polar anti-addition mechanisms are postulated, both triggered by HBr, which is evidenced also to take part in the Z/E isomerization of the product. The proposed mechanism is well supported by ab initio calculations at the MP2/6-31+G* level with Ahlrichs' SVP all-electron basis for Br. Implicit solvation in CH2Cl2 has been included using the PCM and/or SMD continuum solvent models. Comparative case studies have been performed involving the B3LYP/6-31+G* with Ahlrichs' SVP for Br and MP2/Def2TZVPP levels. The mechanistic studies resulted in development of a procedure for stereoselective bromoboration of acetylene yielding E/Z mixtures of dibromo(bromovinyl)borane with the Z-isomer as a major product (up to 85%). Transformation to the corresponding pinacol and neopentyl glycol boronates and stereoselective decomposition of their E-isomer provided pure (Z)-(2-bromovinyl)boronates in 57-60% overall yield. Their reactivity in a Negishi cross-coupling reaction was tested. An example of the one-pot reaction sequence of Negishi and Suzuki-Miyaura cross-couplings for synthesis of combretastatin A4 is also presented.
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Affiliation(s)
- Jan Polášek
- Department of Chemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Jan Paciorek
- Department of Chemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Jakub Stošek
- Department of Chemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Hugo Semrád
- Department of Chemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Markéta Munzarová
- Department of Chemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Ctibor Mazal
- Department of Chemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
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5
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Ponce-Vargas M, Lefebvre C, Boisson JC, Hénon E. Atomic Decomposition Scheme of Noncovalent Interactions Applied to Host–Guest Assemblies. J Chem Inf Model 2019; 60:268-278. [DOI: 10.1021/acs.jcim.9b01016] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Miguel Ponce-Vargas
- Institut de Chimie Moléculaire de Reims UMR CNRS 7312, Université de Reims Champagne-Ardenne, Moulin de la Housse, 51687 Reims Cedex 02 BP39, France
| | - Corentin Lefebvre
- Institut de Chimie Moléculaire de Reims UMR CNRS 7312, Université de Reims Champagne-Ardenne, Moulin de la Housse, 51687 Reims Cedex 02 BP39, France
| | - Jean-Charles Boisson
- CRESTIC EA 3804, Université de Reims Champagne-Ardenne, Moulin de la Housse, 51687 Reims Cedex 02 BP39, France
| | - Eric Hénon
- Institut de Chimie Moléculaire de Reims UMR CNRS 7312, Université de Reims Champagne-Ardenne, Moulin de la Housse, 51687 Reims Cedex 02 BP39, France
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Abstract
In addition to the underlying basic concepts and early recognition of halogen bonding, this paper reviews the conflicting views that consistently appear in the area of noncovalent interactions and the ability of covalently bonded halogen atoms in molecules to participate in noncovalent interactions that contribute to packing in the solid-state. It may be relatively straightforward to identify Type-II halogen bonding between atoms using the conceptual framework of σ-hole theory, especially when the interaction is linear and is formed between the axial positive region (σ-hole) on the halogen in one monomer and a negative site on a second interacting monomer. A σ-hole is an electron density deficient region on the halogen atom X opposite to the R–X covalent bond, where R is the remainder part of the molecule. However, it is not trivial to do so when secondary interactions are involved as the directionality of the interaction is significantly affected. We show, by providing some specific examples, that halogen bonds do not always follow the strict Type-II topology, and the occurrence of Type-I and -III halogen-centered contacts in crystals is very difficult to predict. In many instances, Type-I halogen-centered contacts appear simultaneously with Type-II halogen bonds. We employed the Independent Gradient Model, a recently proposed electron density approach for probing strong and weak interactions in molecular domains, to show that this is a very useful tool in unraveling the chemistry of halogen-assisted noncovalent interactions, especially in the weak bonding regime. Wherever possible, we have attempted to connect some of these results with those reported previously. Though useful for studying interactions of reasonable strength, IUPAC’s proposed “less than the sum of the van der Waals radii” criterion should not always be assumed as a necessary and sufficient feature to reveal weakly bound interactions, since in many crystals the attractive interaction happens to occur between the midpoint of a bond, or the junction region, and a positive or negative site.
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7
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Is the Fluorine in Molecules Dispersive? Is Molecular Electrostatic Potential a Valid Property to Explore Fluorine-Centered Non-Covalent Interactions? Molecules 2019; 24:molecules24030379. [PMID: 30678158 PMCID: PMC6384640 DOI: 10.3390/molecules24030379] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 01/15/2019] [Accepted: 01/18/2019] [Indexed: 11/23/2022] Open
Abstract
Can two sites of positive electrostatic potential localized on the outer surfaces of two halogen atoms (and especially fluorine) in different molecular domains attract each other to form a non-covalent engagement? The answer, perhaps counterintuitive, is yes as shown here using the electronic structures and binding energies of the interactions for a series of 22 binary complexes formed between identical or different atomic domains in similar or related halogen-substituted molecules containing fluorine. These were obtained using various computational approaches, including density functional and ab initio first-principles theories with M06-2X, RHF, MP2 and CCSD(T). The physical chemistry of non-covalent bonding interactions in these complexes was explored using both Quantum Theory of Atoms in Molecules and Symmetry Adapted Perturbation Theories. The surface reactivity of the 17 monomers was examined using the Molecular Electrostatic Surface Potential approach. We have demonstrated inter alia that the dispersion term, the significance of which is not always appreciated, which emerges either from an energy decomposition analysis, or from a correlated calculation, plays a structure-determining role, although other contributions arising from electrostatic, exchange-repulsion and polarization effects are also important. The 0.0010 a.u. isodensity envelope, often used for mapping the electrostatic potential is found to provide incorrect information about the complete nature of the surface reactive sites on some of the isolated monomers, and can lead to a misinterpretation of the results obtained.
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8
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Hooker LV, Neufeldt SR. Ligation state of nickel during C-O bond activation with monodentate phosphines. Tetrahedron 2018; 74:6717-6725. [PMID: 31105349 PMCID: PMC6516790 DOI: 10.1016/j.tet.2018.10.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The oxidative addition of phenolic electrophiles at Ni(0) in the presence of monodentate phosphine ligands was studied with both dispersion-free and dispersion-containing DFT methods. With the popular bulky ligand PCy3, consideration of dispersion has a striking effect on the predicted ligation state of nickel during oxidative addition of aryl sulfamates. Dispersioncontaining methods such as M06L indicate a clear preference for a bis-phosphine ligated transition state (TS), while dispersion free methods like B3LYP strongly favor a monophosphine ligated TS. This discrepancy in predicted ligation state is also found with small phosphines (PMe3) in combination with some aryl electrophiles (carbamates, acetates, pivalates, chlorides), but a bis-PMe3-ligated TS is predicted regardless of dispersion for other electrophiles (sulfamates, mesylates, tosylates). DFT calculations that include dispersion also offer a possible explanation for the observed poor efficacy of P t Bu3 as a ligand in Ni-catalyzed cross-coupling reactions.
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Affiliation(s)
- Leidy V. Hooker
- Department of Chemistry and Biochemistry, Montana State University, 103 Chemistry & Biochemistry Bldg., Bozeman, MT 59717, USA
| | - Sharon R. Neufeldt
- Department of Chemistry and Biochemistry, Montana State University, 103 Chemistry & Biochemistry Bldg., Bozeman, MT 59717, USA
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9
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Fekete A, Komáromi I. Modeling the archetype cysteine protease reaction using dispersion corrected density functional methods in ONIOM-type hybrid QM/MM calculations; the proteolytic reaction of papain. Phys Chem Chem Phys 2018; 18:32847-32861. [PMID: 27883128 DOI: 10.1039/c6cp06869c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A proteolytic reaction of papain with a simple peptide model substrate N-methylacetamide has been studied. Our aim was twofold: (i) we proposed a plausible reaction mechanism with the aid of potential energy surface scans and second geometrical derivatives calculated at the stationary points, and (ii) we investigated the applicability of the dispersion corrected density functional methods in comparison with the popular hybrid generalized gradient approximations (GGA) method (B3LYP) without such a correction in the QM/MM calculations for this particular problem. In the resting state of papain the ion pair and neutral forms of the Cys-His catalytic dyad have approximately the same energy and they are separated by only a small barrier. Zero point vibrational energy correction shifted this equilibrium slightly to the neutral form. On the other hand, the electrostatic solvation free energy corrections, calculated using the Poisson-Boltzmann method for the structures sampled from molecular dynamics simulation trajectories, resulted in a more stable ion-pair form. All methods we applied predicted at least a two elementary step acylation process via a zwitterionic tetrahedral intermediate. Using dispersion corrected DFT methods the thioester S-C bond formation and the proton transfer from histidine occur in the same elementary step, although not synchronously. The proton transfer lags behind (or at least does not precede) the S-C bond formation. The predicted transition state corresponds mainly to the S-C bond formation while the proton is still on the histidine Nδ atom. In contrast, the B3LYP method using larger basis sets predicts a transition state in which the S-C bond is almost fully formed and the transition state can be mainly featured by the Nδ(histidine) to N(amid) proton transfer. Considerably lower activation energy was predicted (especially by the B3LYP method) for the next amide bond breaking elementary step of acyl-enzyme formation. Deacylation appeared to be a single elementary step process in all the methods we applied.
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Affiliation(s)
- Attila Fekete
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Nagyerdei krt. 98., Debrecen, Hungary.
| | - István Komáromi
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Nagyerdei krt. 98., Debrecen, Hungary.
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10
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Wong ZC, Fan WY, Chwee TS. Computational modelling of singlet excitation energy transfer: a DFT/TD-DFT study of the ground and excited state properties of a syn bimane dimer system using non-empirically tuned range-separated functionals. NEW J CHEM 2018. [DOI: 10.1039/c8nj02920b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Range-tuned DFT/TD-DFT improves predicted properties for the sequence of events leading to excitation energy transfer (EET) in bimanes.
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Affiliation(s)
- Z. C. Wong
- Institute of High Performance Computing
- Agency for Science, Technology and Research (A*STAR)
- Singapore
- NUS Graduate School for Integrative Sciences and Engineering
- National University of Singapore
| | - W. Y. Fan
- Department of Chemistry
- National University of Singapore
- Singapore
| | - T. S. Chwee
- Institute of High Performance Computing
- Agency for Science, Technology and Research (A*STAR)
- Singapore
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11
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Yang B, Liu S, Lin Z. Computational study on single molecular spectroscopy of tyrosin-glycine, tryptophane-glycine and glycine-tryptophane. Sci Rep 2017; 7:15869. [PMID: 29158576 PMCID: PMC5696477 DOI: 10.1038/s41598-017-16234-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/09/2017] [Indexed: 12/29/2022] Open
Abstract
Quantum chemistry calculations play a fundamental role in revealing the molecular structures observed in gas-phase spectroscopic measurements. The supersonic jet cooling widely used in single molecular spectroscopy experiment is a non-equilibrium process and often causes confusion on the theoretical and experimental comparison. A computational approach is proposed here to account for the effect of the non-equilibrium cooling on the experimental spectra and applied to the cases of tyrosin-glycine (YG), tryptophane-glycine (WG) and glycine-tryptophane (GW). The low energy conformers of YG, WG and GW are obtained through thorough conformational searches. The structural features and equilibrium distributions of conformations and the energy barriers for conformer conversions are then determined. Three classes of transition energy barriers, high, medium and low, are found for the conversions among conformers with distinctly different, similar and the same structural types, respectively. The final conformation populations are determined by assuming an initial temperature of about 450 K and allowing for only the conformation conversion with a low energy barrier to occur during the rapid cooling process. The results provide a natural explanation for the numbers of YG, WG and GW conformations observed experimentally. The theoretical conformation assignments are also in good agreement with the experimental IR data.
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Affiliation(s)
- Bing Yang
- Hefei National Laboratory for Physical Sciences at Microscale & CAS Key Laboratory of Strongly-Coupled Quantum Matter Physics, Department of Physics, University of Science and Technology of China, Hefei, 230026, China
| | - Shixue Liu
- Department of Nanotechnology for Sustainable Energy, Kwansei Gakuin University, Gakuen 2-1, Sanda, Hyogo, 669-1337, Japan
| | - Zijing Lin
- Hefei National Laboratory for Physical Sciences at Microscale & CAS Key Laboratory of Strongly-Coupled Quantum Matter Physics, Department of Physics, University of Science and Technology of China, Hefei, 230026, China.
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12
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Fong CW. Cisplatin cyclodextrin complexes as potential free radical chemoradiosensitizers for enhanced cisplatin treatment of cancers: a quantum mechanical study. J INCL PHENOM MACRO 2017. [DOI: 10.1007/s10847-017-0760-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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13
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14
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Testing the CP-correction procedure with different DFT methods on H-bonding complexes of κ-carrabiose with water molecules. J Mol Model 2017; 23:31. [PMID: 28091888 DOI: 10.1007/s00894-016-3199-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/16/2016] [Indexed: 10/20/2022]
Abstract
Interaction of water molecules with κ-carrabiose disaccharide, within three H-bonding complexes, was investigated. Particular interest was focused on the way with which the BSSE correction has to be performed. Two strategies were used, either performing BSSE correction during or after optimization. For this aim, several DFT-functionals (hybrid GGA and hybrid meta-GGA) and 6-31 + G* basis set were considered. The results demonstrated the uselessness of including of BSSE-CP correction during optimization for all complexes. From a structural point of view, a proper H-bonding description was obtained using the PBE0 functional for all complexes. The basis set effect on the BSSE using B3LYP functional was also investigated. The reliability of B3LYP/6-31 + G** and B3LYP/6-31++G** models for the complexes involving one or two water molecules was reported while the use of B3LYP/6-311 + G** or B3LYP/6-311++G** levels was shown to be more appropriate for larger complexes equivalent to that involving three water molecules. CP-corrected interaction energies were demonstrated to be closer to CBS-4 M interaction energies than the uncorrected ones. Graphical abstract Functional and basis set effects on BSSE.
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15
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Baggioli A, Cavallotti CA, Famulari A. Exploring short intramolecular interactions in alkylaromatic substrates. Phys Chem Chem Phys 2016; 18:29616-29628. [PMID: 27753437 DOI: 10.1039/c6cp03323g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
From proteins and peptides to semiconducting polymers, aliphatic chains on aromatic groups are recurring motifs in macromolecules from very diverse application fields. Fields in which molecular folding and packing determine the macroscopic physical properties that make such advanced materials appealing in the first place. Within each macromolecule, the intrinsic structure of each unit defines how it interacts with its neighbours, ultimately opening up or denying certain backbone conformations. This eventually also determines how macromolecules interact with each other. This account deals specifically with the conformational problem of many common alkylaromatic units, examining the features of an intramolecular interaction involving a side chain with as few as three methylene groups. A set of 23 model compounds featuring an intramolecular interaction between an aliphatic X-H (X = C, N, O, and S) bond and an aromatic ring was considered. Quantitative computational analysis was made possible, thanks to complete basis set extrapolated CCSD(T) calculations and NCI topological analysis, the latter of which revealed an elaborate network of dispersive and steric interactions leading to somewhat unintuitive and unexpected results, such as the higher energetic stability of certain twisted conformational isomers over those with extended side chains. Vicinal covalent effects from polarizing groups and various heteroatoms, along with the occurrence of non-dispersive phenomena, were also investigated. The conclusions drawn from the investigation include a comprehensive set of guidelines intended to aid in the prediction of the most stable conformation for this class of building blocks. Our findings affect a variety of different research fields, including the tailoring of functional materials for organic electronics and photovoltaics, with insights into a rational treatment of conformational disorder, and the study of protein- and peptide-folding preferences, putting an emphasis on peculiar interactions between the backbone and aromatic residues.
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Affiliation(s)
- Alberto Baggioli
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "G. Natta", Politecnico di Milano, via Mancinelli 7, I-20131 Milano, Italy.
| | - Carlo A Cavallotti
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "G. Natta", Politecnico di Milano, via Mancinelli 7, I-20131 Milano, Italy.
| | - Antonino Famulari
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "G. Natta", Politecnico di Milano, via Mancinelli 7, I-20131 Milano, Italy.
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16
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Tran F, Stelzl J, Blaha P. Rungs 1 to 4 of DFT Jacob’s ladder: Extensive test on the lattice constant, bulk modulus, and cohesive energy of solids. J Chem Phys 2016; 144:204120. [DOI: 10.1063/1.4948636] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Fabien Tran
- Institute of Materials Chemistry, Vienna University of Technology, Getreidemarkt 9/165-TC, A-1060 Vienna, Austria
| | - Julia Stelzl
- Institute of Materials Chemistry, Vienna University of Technology, Getreidemarkt 9/165-TC, A-1060 Vienna, Austria
| | - Peter Blaha
- Institute of Materials Chemistry, Vienna University of Technology, Getreidemarkt 9/165-TC, A-1060 Vienna, Austria
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17
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Nazarski RB, Wałejko P, Witkowski S. Multi-conformer molecules in solutions: an NMR-based DFT/MP2 conformational study of two glucopyranosides of a vitamin E model compound. Org Biomol Chem 2016; 14:3142-58. [DOI: 10.1039/c5ob01865j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Overall geometries of both glucosyl derivatives of PMC were found on the basis of their NMR spectra in CDCl3and relatedδH,C/nJHHIEF-PCM(UFF,CHCl3)/DFT calculational results.
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Affiliation(s)
- Ryszard B. Nazarski
- University of Łódź
- Faculty of Chemistry
- Department of Theoretical and Structural Chemistry
- 90-236 Łódź
- Poland
| | - Piotr Wałejko
- University of Białystok
- Institute of Chemistry
- 15-245 Białystok
- Poland
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18
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Zhang G, Li H, Weinhold F, Chen D. 3c/4e -type long-bonding competes with ω-bonding in noble-gas hydrides HNgY (Ng = He, Ne, Ar, Kr, Xe, Rn; Y = F, Cl, Br, I): a NBO/NRT perspective. Phys Chem Chem Phys 2016; 18:8015-26. [DOI: 10.1039/c5cp07965a] [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
Novel resonance bonding for the HNgY molecule is demonstrated based on natural resonance theory analyses. Ng/Y affects the ω-bonding vs. long-bonding propensity in each of the HNgY molecules.
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Affiliation(s)
- Guiqiu Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Hong Li
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Frank Weinhold
- Department of Chemistry
- University of Wisconsin
- Madison
- USA
| | - Dezhan Chen
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
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19
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Fan WJ, Yang GJ, Chi JW, Yu Y, Tan DZ. Theoretical study of the physisorption of organic molecules on conjugated microporous polymers: the critical role of skeleton structures on binding strength. RSC Adv 2016. [DOI: 10.1039/c6ra05955d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
By enlarging the size (area) in the linker or adding substituent group in the node, the binding energy between CMPs and adsorbates will increase significantly, which demonstrates the critical role of skeleton structures on binding strength.
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Affiliation(s)
- Wen-Jie Fan
- College of Science
- Dalian Ocean University
- Dalian 116023
- P. R. China
| | - Gui-Juan Yang
- College of Science
- Dalian Ocean University
- Dalian 116023
- P. R. China
| | - Jian-Wei Chi
- College of Science
- Dalian Ocean University
- Dalian 116023
- P. R. China
| | - You Yu
- College of Science
- Dalian Ocean University
- Dalian 116023
- P. R. China
| | - Da-Zhi Tan
- Experimental Center of Chemistry
- Faculty of Chemical, Environmental and Biological Science and Technology
- Dalian University of Technology
- Dalian 116024
- P. R. China
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20
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Huttmann F, Martínez-Galera AJ, Caciuc V, Atodiresei N, Schumacher S, Standop S, Hamada I, Wehling TO, Blügel S, Michely T. Tuning the van der Waals Interaction of Graphene with Molecules via Doping. PHYSICAL REVIEW LETTERS 2015; 115:236101. [PMID: 26684126 DOI: 10.1103/physrevlett.115.236101] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Indexed: 06/05/2023]
Abstract
We use scanning tunneling microscopy to visualize and thermal desorption spectroscopy to quantitatively measure that the binding of naphthalene molecules to graphene, a case of pure van der Waals interaction, strengthens with n and weakens with p doping of graphene. Density-functional theory calculations that include the van der Waals interaction in a seamless, ab initio way accurately reproduce the observed trend in binding energies. Based on a model calculation, we propose that the van der Waals interaction is modified by changing the spatial extent of graphene's π orbitals via doping.
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Affiliation(s)
- Felix Huttmann
- II. Physikalisches Institut, Universität zu Köln, Zülpicher Straße 77, 50937 Köln, Germany
| | | | - Vasile Caciuc
- Peter Grünberg Institute and Institute for Advanced Simulation, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Nicolae Atodiresei
- Peter Grünberg Institute and Institute for Advanced Simulation, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Stefan Schumacher
- II. Physikalisches Institut, Universität zu Köln, Zülpicher Straße 77, 50937 Köln, Germany
| | - Sebastian Standop
- II. Physikalisches Institut, Universität zu Köln, Zülpicher Straße 77, 50937 Köln, Germany
| | - Ikutaro Hamada
- International Center for Materials Nanoarchitectonics (WPI-MANA) and Global Research Center for Environment and Energy based on Nanomaterials Science (GREEN), National Institute for Materials Science, 1-1 Namiki, Tsukuba 305-0044, Japan
| | - Tim O Wehling
- Bremen Center for Computational Material Science (BCCMS), Universität Bremen, Am Fallturm 1a, 28359 Bremen, Germany
| | - Stefan Blügel
- Peter Grünberg Institute and Institute for Advanced Simulation, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Thomas Michely
- II. Physikalisches Institut, Universität zu Köln, Zülpicher Straße 77, 50937 Köln, Germany
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21
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Xie NZ, Du QS, Li JX, Huang RB. Exploring Strong Interactions in Proteins with Quantum Chemistry and Examples of Their Applications in Drug Design. PLoS One 2015; 10:e0137113. [PMID: 26339784 PMCID: PMC4560430 DOI: 10.1371/journal.pone.0137113] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 08/12/2015] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES Three strong interactions between amino acid side chains (salt bridge, cation-π, and amide bridge) are studied that are stronger than (or comparable to) the common hydrogen bond interactions, and play important roles in protein-protein interactions. METHODS Quantum chemical methods MP2 and CCSD(T) are used in calculations of interaction energies and structural optimizations. RESULTS The energies of three types of amino acid side chain interactions in gaseous phase and in aqueous solutions are calculated using high level quantum chemical methods and basis sets. Typical examples of amino acid salt bridge, cation-π, and amide bridge interactions are analyzed, including the inhibitor design targeting neuraminidase (NA) enzyme of influenza A virus, and the ligand binding interactions in the HCV p7 ion channel. The inhibition mechanism of the M2 proton channel in the influenza A virus is analyzed based on strong amino acid interactions. CONCLUSION (1) The salt bridge interactions between acidic amino acids (Glu- and Asp-) and alkaline amino acids (Arg+, Lys+ and His+) are the strongest residue-residue interactions. However, this type of interaction may be weakened by solvation effects and broken by lower pH conditions. (2) The cation- interactions between protonated amino acids (Arg+, Lys+ and His+) and aromatic amino acids (Phe, Tyr, Trp and His) are 2.5 to 5-fold stronger than common hydrogen bond interactions and are less affected by the solvation environment. (3) The amide bridge interactions between the two amide-containing amino acids (Asn and Gln) are three times stronger than hydrogen bond interactions, which are less influenced by the pH of the solution. (4) Ten of the twenty natural amino acids are involved in salt bridge, or cation-, or amide bridge interactions that often play important roles in protein-protein, protein-peptide, protein-ligand, and protein-DNA interactions.
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Affiliation(s)
- Neng-Zhong Xie
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
| | - Qi-Shi Du
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
- Gordon Life Science Institute, 53 South Cottage Road, Belmont, MA, 02478, United States of America
| | - Jian-Xiu Li
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
- Life Science and Biotechnology College, Guangxi University, Nanning, Guangxi, 530004, China
| | - Ri-Bo Huang
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
- Life Science and Biotechnology College, Guangxi University, Nanning, Guangxi, 530004, China
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22
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Fong CW. Binding energies of tyrosine kinase inhibitors: Error assessment of computational methods for imatinib and nilotinib binding. Comput Biol Chem 2015; 58:40-54. [PMID: 26025598 DOI: 10.1016/j.compbiolchem.2015.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 05/09/2015] [Accepted: 05/13/2015] [Indexed: 11/30/2022]
Abstract
The binding energies of imatinib and nilotinib to tyrosine kinase have been determined by quantum mechanical (QM) computations, and compared with literature binding energy studies using molecular mechanics (MM). The potential errors in the computational methods include these critical factors. Errors in X-ray structures such as structural distortions and steric clashes give unrealistically high van der Waals energies, and erroneous binding energies.MM optimization gives a very different configuration to the QM optimization for nilotinib, whereas the imatinib ion gives similar configurations. Solvation energies are a major component of the overall binding energy. The QM based solvent model (PCM/SMD) gives different values from those used in the implicit PBSA solvent MM models. A major error in inhibitor—kinase binding lies in the non-polar solvation terms. Solvent transfer free energies and the required empirical solvent accessible surface area factors for nilotinib and imatinib ion to give the transfer free energies have been reverse calculated. These values differ from those used in the MM PBSA studies.An intertwined desolvation—conformational binding selectivity process is a balance of thermodynamic desolvation and intramolecular conformational kinetic control.The configurational entropies (TΔS) are minor error sources.
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23
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Miliordos E, Xantheas SS. On the validity of the basis set superposition error and complete basis set limit extrapolations for the binding energy of the formic acid dimer. J Chem Phys 2015; 142:094311. [DOI: 10.1063/1.4913766] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Evangelos Miliordos
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, USA
| | - Sotiris S. Xantheas
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, USA
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24
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Medveď M, Budzák Š, Laurent AD, Jacquemin D. Direct and Indirect Effects of Dispersion Interactions on the Electric Properties of Weakly Bound Complexes. J Phys Chem A 2015; 119:3112-24. [DOI: 10.1021/acs.jpca.5b00842] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Miroslav Medveď
- Department
of Chemistry, Faculty of Natural Sciences, Matej Bel University, Tajovského 40, SK-97400 Banská Bystrica, Slovak Republic
| | - Šimon Budzák
- Department
of Chemistry, Faculty of Natural Sciences, Matej Bel University, Tajovského 40, SK-97400 Banská Bystrica, Slovak Republic
| | - Adèle D. Laurent
- CEISAM,
UMR CNRS 6230, BP 92208, Université de Nantes, 2, rue de
la Houssinière 44322 Nantes Cedex 3, France
| | - Denis Jacquemin
- CEISAM,
UMR CNRS 6230, BP 92208, Université de Nantes, 2, rue de
la Houssinière 44322 Nantes Cedex 3, France
- Institut Universitaire de France, 103, bd Saint-Michel, F-75005 Paris Cedex 05, France
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25
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Shee A, Knecht S, Saue T. A theoretical benchmark study of the spectroscopic constants of the very heavy rare gas dimers. Phys Chem Chem Phys 2015; 17:10978-86. [DOI: 10.1039/c5cp01094b] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The binding energy of the superheavy dimer Uuo2 is considerably larger than that of its lighter homologues, despite a 40% reduction due to spin-other orbit interaction.
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Affiliation(s)
- Avijit Shee
- Laboratoire de Chimie et Physique Quantiques (UMR 5626)
- CNRS/Université Toulouse III – Paul Sabatier
- F-31062 Toulouse cedex
- France
| | - Stefan Knecht
- Laboratory of Physical Chemistry
- ETH Zürich
- 8093 Zürich
- Switzerland
| | - Trond Saue
- Laboratoire de Chimie et Physique Quantiques (UMR 5626)
- CNRS/Université Toulouse III – Paul Sabatier
- F-31062 Toulouse cedex
- France
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26
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Sahu D, Ganguly B. In silico studies on the origin of selective uptake of carbon dioxide with cucurbit[7]uril amorphous material. RSC Adv 2015. [DOI: 10.1039/c5ra13394g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The efficient capture and storage of flue gases is of current interest due to environmental problems. The DFT calculation demonstrates the origin of the physisorption of flue gases (CO2, N2and CH4) on amorphous solid cucurbit[7]uril.
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Affiliation(s)
- Debashis Sahu
- Computation and Simulation Unit
- Analytical Discipline & Centralized Instrument Facility, and Academy of Scientific and Innovative Research
- CSIR-Central Salt and Marine Chemicals Research Institute
- Bhavnagar
- India
| | - Bishwajit Ganguly
- Computation and Simulation Unit
- Analytical Discipline & Centralized Instrument Facility, and Academy of Scientific and Innovative Research
- CSIR-Central Salt and Marine Chemicals Research Institute
- Bhavnagar
- India
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28
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29
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Pohl G, Plumley JA, Dannenberg JJ. The interactions of phenylalanines in β-sheet-like structures from molecular orbital calculations using density functional theory (DFT), MP2, and CCSD(T) methods. J Chem Phys 2014; 138:245102. [PMID: 23822281 DOI: 10.1063/1.4811712] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present density functional theory calculations designed to evaluate the importance of π-stacking interactions to the stability of in-register Phe residues within parallel β-sheets, such as amyloids. We have used a model of a parallel H-bonded tetramer of acetylPheNH2 as a model and both functionals that were specifically designed to incorporate dispersion effects (DFs), as well as, several traditional functionals which have not been so designed. None of the functionals finds a global minimum for the π-stacked conformation, although two of the DFs find this to be a local minimum. The stacked phenyls taken from the optimized geometries calculated for each functional have been evaluated using MP2 and CCSD(T) calculations for comparison. The results suggest that π-stacking does not make an important contribution to the stability of this system and (by implication) to amyloid formation.
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Affiliation(s)
- Gabor Pohl
- Department of Chemistry, City University of New York-Hunter College and the Graduate School, 695 Park Avenue, New York, New York 10065, USA
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30
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A simple and efficient dispersion correction to the Hartree–Fock theory. Bioorg Med Chem Lett 2014; 24:1037-42. [DOI: 10.1016/j.bmcl.2014.01.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 01/08/2014] [Accepted: 01/08/2014] [Indexed: 11/18/2022]
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31
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Pohl G, Asensio A, Dannenberg JJ. Capping parallel β-sheets of acetyl(Ala)6NH2 with an acetyl(Ala)5ProNH2 can arrest the growth of the sheet, suggesting a potential for curtailing amyloid growth. An ONIOM and density functional theory study. Biochemistry 2014; 53:617-23. [PMID: 24422496 PMCID: PMC3985835 DOI: 10.1021/bi401366w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present ONIOM calculations using B3LYP/d95(d,p) as the high level and AM1 as the medium level on parallel β-sheets containing four strands of Ac-AAAAAA-NH2 capped with either Ac-AAPAAA-NH2 or Ac-AAAPAA-NH2. Because Pro can form H-bonds from only one side of the peptide linkage (that containing the C═O H-bond acceptor), only one of the two Pro-containing strands can favorably add to the sheet on each side. Surprisingly, when the sheet is capped with AAPAAA-NH2 at one edge, the interaction between the cap and sheet is slightly more stabilizing than that of another all Ala strand. Breaking down the interaction enthalpies into H-bonding and distortion energies shows the favorable interaction to be due to lower distortion energies in both the strand and the four-stranded sheet. Because another strand would be inhibited for attachment to the other side of the capping (Pro-containing) strand, we suggest the possible use of Pro residues in peptides designed to arrest the growth of many amyloids.
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Affiliation(s)
- Gabor Pohl
- Department of Chemistry, City University of New York, Hunter College and the Graduate School , 695 Park Avenue, New York, New York 10065, United States
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32
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Maranzana A, Giordana A, Indarto A, Tonachini G, Barone V, Causà M, Pavone M. Density functional theory study of the interaction of vinyl radical, ethyne, and ethene with benzene, aimed to define an affordable computational level to investigate stability trends in large van der Waals complexes. J Chem Phys 2013; 139:244306. [DOI: 10.1063/1.4846295] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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33
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Tran F, Hutter J. Nonlocal van der Waals functionals: The case of rare-gas dimers and solids. J Chem Phys 2013; 138:204103. [DOI: 10.1063/1.4807332] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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34
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35
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Zohar G, Baer R, Rabani E. Multiexciton Generation in IV-VI Nanocrystals: The Role of Carrier Effective Mass, Band Mixing, and Phonon Emission. J Phys Chem Lett 2013; 4:317-322. [PMID: 26283441 DOI: 10.1021/jz301892z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We study the role of the effective mass, band mixing, and phonon emission on multiexciton generation in IV-VI nanocrystals. A four-band k · p effective mass model, which allows for an independent variation of these parameters, is adopted to describe the electronic structure of the nanocrystals. Multiexciton generation efficiencies are calculated using a Green's function formalism, providing results that are numerically similar to impact excitation. We find that multiexciton generation efficiencies are maximized when the effective mass of the electron and hole are small and similar. Contact with recent experimental results for multiexciton generation in PbS and PbSe is made.
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Affiliation(s)
| | - Roi Baer
- ‡Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, Hebrew University, Jerusalem 91904, Israel
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36
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Marianski M, Asensio A, Dannenberg JJ. Comparison of some dispersion-corrected and traditional functionals as applied to peptides and conformations of cyclohexane derivatives. J Chem Phys 2012; 137:044109. [PMID: 22852599 DOI: 10.1063/1.4737517] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We compare the energetic and structural properties of fully optimized α-helical and antiparallel β-sheet polyalanines and the energetic differences between axial and equatorial conformations of three cyclohexane derivatives (methyl, fluoro, and chloro) as calculated using several functionals designed to treat dispersion (B97-D, ωB97x-D, M06, M06L, and M06-2X) with other traditional functionals not specifically parametrized to treat dispersion (B3LYP, X3LYP, and PBE1PBE) and with experimental results. Those functionals developed to treat dispersion significantly overestimate interaction enthalpies of folding for the α-helix and predict unreasonable structures that contain Ramachandran φ and ψ and C = O...N H-bonding angles that are out of the bounds of databases compiled the β-sheets. These structures are consistent with overestimation of the interaction energies. For the cyclohexanes, these functionals overestimate the stabilities of the axial conformation, especially when used with smaller basis sets. Their performance improves when the basis set is improved from D95∗∗ to aug-cc-pVTZ (which would not be possible with systems as large as the peptides).
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Affiliation(s)
- Mateusz Marianski
- Department of Chemistry, City University of New York - Hunter College and the Graduate School, 695 Park Avenue, New York, New York 10065, USA
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37
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Ali-Torres J, Dannenberg JJ. The folding of acetyl(Ala)28NH2 and acetyl(Ala)40NH2 extended strand peptides into antiparallel β-sheets. A density functional theory study of β-sheets with β-turns. J Phys Chem B 2012; 116:14017-22. [PMID: 23157432 DOI: 10.1021/jp3094947] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report ONIOM calculations using B3LYP/D95** and AM1 on β-sheet formation from acetyl(Ala)(N)NH(2) (N = 28 or 40). The sheets contain from one to four β-turns for N = 28 and up to six for N = 40. We have obtained four types of geometrically optimized structures. All contain only β-turns. They differ from each other in the types of β-turns formed. The unsolvated sheets containing two turns are most stable. Aqueous solvation (using the SM5.2 and CPCM methods) reduces the stabilities of the folded structures compared to the extended strands.
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Affiliation(s)
- Jorge Ali-Torres
- Department of Chemistry, City University of New York - Hunter College and the Graduate School, New York 10065, United States
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