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Kužela T, Bondarev D, Kutálková E, Benková Z, Hrnčiřík J, Ingr M. Study of absorption and emission spectra of substituted terthiophene compounds by methods of theoretical chemistry. J Comput Chem 2024; 45:1404-1418. [PMID: 38436207 DOI: 10.1002/jcc.27336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 01/16/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024]
Abstract
Terthiophene derivatives attract interest due to their prospective applications in optoelectronic or sensor devices. Due to their nontoxicity they can be considered as suitable candidates in biological applications. Supramolecular organization of the matter is one of the most interesting topics in contemporary materials science. Amphiphilic chromophores based on substituted terthiophenes are capable of self-assembly into supramolecular architectures. In this work, we aim at simulation of the spectral properties of terthiophene with oligo(ethylene oxide) substituents by the methods of quantum chemistry and molecular dynamics (MD). The potential energy surface (PES) of this molecule was determined by the methods of density functional theory (DFT) for the ground state and time-dependent density-functional theory (TD-DFT) for the excited state. MD simulations in water than revealed the most frequented molecular conformations in both these states. Absorption and fluorescence spectra were determined for all these conformations, including the surrounding water molecules, using TD-DFT and averaged over the conformation space to obtain the final absorption and fluorescence spectrum. The calculated spectra were compared with their experimental counterparts and the differences were discussed in context of the supramolecular structure revealed by confocal microscopy. In spite of its simplicity, this approach provides a satisfactory approximation of absorption and fluorescent spectra of these molecules obtained by computational methods.
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Affiliation(s)
- Tomáš Kužela
- Faculty of Technology, Department of Physics and Materials Engineering, Tomas Bata University in Zlín, Zlín, Czech Republic
| | - Dmitrij Bondarev
- Polymer Institute, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Eva Kutálková
- Faculty of Technology, Department of Physics and Materials Engineering, Tomas Bata University in Zlín, Zlín, Czech Republic
| | - Zuzana Benková
- Polymer Institute, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Josef Hrnčiřík
- Faculty of Technology, Department of Physics and Materials Engineering, Tomas Bata University in Zlín, Zlín, Czech Republic
| | - Marek Ingr
- Faculty of Technology, Department of Physics and Materials Engineering, Tomas Bata University in Zlín, Zlín, Czech Republic
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Benková Z, Čakánek P, Cordeiro MNDS. Adsorption of Peptides onto Carbon Nanotubes Grafted with Poly(ethylene Oxide) Chains: A Molecular Dynamics Simulation Study. Nanomaterials (Basel) 2022; 12:3795. [PMID: 36364570 PMCID: PMC9655739 DOI: 10.3390/nano12213795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/17/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Carbon nanotubes (CNTs) display exceptional properties that predispose them to wide use in technological or biomedical applications. To remove the toxicity of CNTs and to protect them against undesired protein adsorption, coverage of the CNT sidewall with poly(ethylene oxide) (PEO) is often considered. However, controversial results on the antifouling effectiveness of PEO layers have been reported so far. In this work, the interactions of pristine CNT and CNT covered with the PEO chains at different grafting densities with polyglycine, polyserine, and polyvaline are studied using molecular dynamics simulations in vacuum, water, and saline environments. The peptides are adsorbed on CNT in all investigated systems; however, the adsorption strength is reduced in aqueous environments. Save for one case, addition of NaCl at a physiological concentration to water does not appreciably influence the adsorption and structure of the peptides or the grafted PEO layer. It turns out that the flexibility of the peptide backbone allows the peptide to adopt more asymmetric conformations which may be inserted deeper into the grafted PEO layer. Water molecules disrupt the internal hydrogen bonds in the peptides, as well as the hydrogen bonds formed between the peptides and the PEO chains.
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Affiliation(s)
- Zuzana Benková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 41 Bratislava, Slovakia
| | - Peter Čakánek
- Polymer Institute, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 41 Bratislava, Slovakia
| | - Maria Natália D. S. Cordeiro
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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Benková Z, Cordeiro MNDS. Structural behavior of monomer of SARS-CoV-2 spike protein during initial stage of adsorption on graphene. Mater Today Chem 2021; 22:100572. [PMID: 34485782 PMCID: PMC8405511 DOI: 10.1016/j.mtchem.2021.100572] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 08/22/2021] [Accepted: 08/26/2021] [Indexed: 05/14/2023]
Abstract
Spike glycoprotein of the SARS-CoV-2 virus and its structure play a crucial role in the infections of cells containing angiotensin-converting enzyme 2 (ACE2) as well as in the interactions of this virus with surfaces. Protection against viruses and often even their deactivation is one of the great varieties of graphene applications. The structural changes of the non-glycosylated monomer of the spike glycoprotein trimer (denoted as S-protein in this work) triggered by its adsorption onto graphene at the initial stage are investigated by means of atomistic molecular dynamics simulations. The adsorption of the S-protein happens readily during the first 10 ns. The shape of the S-protein becomes more prolate during the adsorption, but this trend, albeit less pronounced, is observed also for the freely relaxing S-protein in water. The receptor-binding domain (RBD) of the free and adsorbed S-protein manifests itself as the most rigid fragment of the whole S-protein. The adsorption even enhances the rigidity of the whole S-protein as well as its subunits. Only one residue of the RBD involved in the specific interactions with ACE2 during the cell infection is involved in the direct contact of the adsorbed S-protein with the graphene. The new intramolecular hydrogen bonds formed during the S-protein adsorption replace the S-protein-water hydrogen bonds; this trend, although less apparent, is observed also during the relaxation of the free S-protein in water. In the initial phase, the secondary structure of the RBD fragment specifically interacting with ACE2 receptor is not affected during the S-protein adsorption onto the graphene.
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Affiliation(s)
- Z Benková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 41 Bratislava, Slovakia
| | - M N D S Cordeiro
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, University of Porto, Rua Do Campo Alegre 687, 4168-007 Porto, Portugal
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Benková Z, Rišpanová L, Cifra P. Conformation of Flexible and Semiflexible Chains Confined in Nanoposts Array of Various Geometries. Polymers (Basel) 2020; 12:E1064. [PMID: 32384748 PMCID: PMC7284769 DOI: 10.3390/polym12051064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/27/2020] [Accepted: 04/29/2020] [Indexed: 01/17/2023] Open
Abstract
The conformation and distribution of a flexible and semiflexible chain confined in an array of nanoposts arranged in parallel way in a square-lattice projection of their cross-section was investigated using coarse-grained molecular dynamics simulations. The geometry of the nanopost array was varied at the constant post diameter dp and the ensuing modifications of the chain conformation were compared with the structural behavior of the chain in the series of nanopost arrays with the constant post separation Sp as well as with the constant distance between two adjacent post walls (passage width) wp. The free energy arguments based on an approximation of the array of nanopost to a composite of quasi-channels of diameter dc and quasi-slits of height wp provide semiqualitative explanations for the observed structural behavior of both chains. At constant post separation and passage width, the occupation number displays a monotonic decrease with the increasing geometry ratio dc/wp or volume fraction of posts, while a maximum is observed at constant post diameter. The latter finding is attributed to a relaxed conformation of the chains at small dc/wp ratio, which results from a combination of wide interstitial volumes and wide passage apertures. This maximum is approximately positioned at the same dc/wp value for both flexible and semiflexible chains. The chain expansion from a single interstitial volume into more interstitial volumes also starts at the same value of dc/wp ratio for both chains. The dependence of the axial chain extension on the dc/wp ratio turns out to be controlled by the diameter of the interstitial space and by the number of monomers in the individual interstitial volumes. If these two factors act in the same way on the axial extension of chain fragments in interstitial volumes the monotonic increase of the axial chain extension with the dc/wp in the nanopost arrays is observed. At constant wp, however, these two factors act in opposite way and the axial chain extension plotted against the dc/wp ratio exhibits a maximum. In the case of constant post diameter, the characteristic hump in the single chain structure factor whose position correlates with the post separation is found only in the structure factor of the flexible chain confined in the nanopost array of certain value of Sp. The structure factor of the flexible chain contains more information on the monomer organization and mutual correlations than the structure factor of the semiflexible chain. The stiffer chain confined in the nanopost array is composed of low number of statistical segments important for the presence of respective hierarchical regimes in the structure factor.
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Affiliation(s)
- Zuzana Benková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia; (L.R.); (P.C.)
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Rišpanová L, Benková Z, Cifra P. Block Copolymer of Flexible and Semi-Flexible Block Confined in Nanopost Array. Polymers (Basel) 2018; 10:E1301. [PMID: 30961226 PMCID: PMC6401765 DOI: 10.3390/polym10121301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 11/19/2018] [Accepted: 11/21/2018] [Indexed: 11/28/2022] Open
Abstract
Coarse-grained molecular dynamics simulations of a diblock copolymer consisting of a flexible and semi-flexible block in a dense array of parallel nanoposts with a square lattice packing were performed. The mutual interactions between the two blocks of the confined diblock chain were investigated through a comparison of their size, structure, and penetration among nanoposts with the corresponding separate chains. The geometry of a nanopost array was varied at constant post separation or at constant width of the passage between nanoposts. The size of a single interstitial volume was comparable to or smaller than the size of the diblock chain. A comparison of the blocks with their separate analogous chains revealed that the mutual interactions between the blocks were shielded by the nanoposts and, thus, the blocks behaved independently. At constant passage width, competitive effects of the axial chain extension in interstitial volumes and the lateral chain expansion among interstitial volumes led to a nonmonotonic behavior of the axial span. The position of the maximum in the span plotted against the filling fraction for a diblock chain was dictated by the semi-flexible block. The semi-flexible block penetrates among the nanoposts more readily and the expansion of the whole diblock copolymer is governed by the semiflexible block. The main findings were explained using the free energy arguments when an interstitial volume was approximated by a channel geometry and a passage aperture by a slit geometry. Detail knowledge of controlled conformational behavior in a compartmentalized environment can contribute to new processes in the storage and retrieval of information.
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Affiliation(s)
- Lucia Rišpanová
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia.
| | - Zuzana Benková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia.
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre 687, 4168-007 Porto, Portugal.
| | - Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia.
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Benková Z, Rišpanová L, Cifra P. Correction: Benková, Z.; et al. Structural Behavior of a Semiflexible Polymer Chain in an Array of Nanoposts Polymers 2017, 9, 313. Polymers (Basel) 2017; 9:665. [PMID: 31305793 PMCID: PMC6418585 DOI: 10.3390/polym9120665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 11/30/2017] [Indexed: 11/22/2022] Open
Abstract
[This corrects the article DOI: 10.3390/polym9080313.].
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Affiliation(s)
- Zuzana Benková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 41 Bratislava, Slovakia; (L.R.); (P.C.)
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre 687, 4168-007 Porto, Portugal
| | - Lucia Rišpanová
- Polymer Institute, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 41 Bratislava, Slovakia; (L.R.); (P.C.)
| | - Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 41 Bratislava, Slovakia; (L.R.); (P.C.)
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Benková Z, Rišpanová L, Cifra P. Effect of chain stiffness for semiflexible macromolecules in array of cylindrical nanoposts. J Chem Phys 2017; 147:134907. [DOI: 10.1063/1.4991649] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Zuzana Benková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre 687, 4168-007 Porto, Portugal
| | - Lucia Rišpanová
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia
| | - Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia
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Benková Z, Rišpanová L, Cifra P. Structural Behavior of a Semiflexible Polymer Chain in an Array of Nanoposts. Polymers (Basel) 2017; 9:E313. [PMID: 30970991 PMCID: PMC6418663 DOI: 10.3390/polym9080313] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 07/24/2017] [Accepted: 07/25/2017] [Indexed: 11/27/2022] Open
Abstract
The structural properties of a flexible and semiflexible circular chain confined in an array of parallel nanoposts with a square lattice cross-sectional projection were studied using coarse-grained molecular dynamics simulations. To address the effect of the circular topology, a comparison with linear analogs was also carried out. In the interpretation of the chain structural properties, the geometry of the post array is considered as a combination of a channel approximating the interstitial volume with the diameter dc and a slit approximating the passage aperture with the width wp. The number of interstitial volumes occupied by a chain monotonically increases with the decreasing ratio dc/wp regardless of the way the geometry of the post array is varied. However, depending on how the array geometry is modified, the chain span along the posts displays a monotonic (constant post separation) or a non-monotonic behavior (constant passage width) when plotted as a function of the post diameter. In the case of monotonic trend, the width of interstitial spaces increases with the increasing chain occupation number, while, in the case of non-monotonic trend, the width of interstitial spaces decreases with the increasing chain occupation number. In comparison with linear topology, for circular topology, the stiffness affects more significantly the relative chain extension along the posts and less significantly the occupation number. The geometrical parameters of the post arrays are stored in the single-chain structure factors. The characteristic humps are recognized in the structure factor which ensue from the local increase in the density of segments in the circular chains presented in an interstitial volume or from the correlation of parallel chain fragments separated by a row of posts. Although the orientation correlations provide qualitative information about the chain topology and the character of confinement within a single interstitial volume, information about the array periodicity is missing.
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Affiliation(s)
- Zuzana Benková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 41 Bratislava, Slovakia.
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre 687, 4168-007 Porto, Portugal.
| | - Lucia Rišpanová
- Polymer Institute, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 41 Bratislava, Slovakia.
| | - Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 41 Bratislava, Slovakia.
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Benková Z, Námer P, Cifra P. Comparison of a stripe and slab confinement for ring and linear macromolecules in nanochannel. Soft Matter 2016; 12:8425-8439. [PMID: 27722460 DOI: 10.1039/c6sm01507g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The combined effects of the channel asymmetry and the closed chain topology on the chain extension, structure factor, and the orientation correlations were studied using coarse-grained molecular dynamics simulations for moderate chain lengths. These effects are related to applications in linearization experiments with a DNA molecule in nanofluidic devices. According to the aspect ratio, the channels are classified as a stripe or slabs. The chain segments do not have any freedom to move in the direction of the narrowest stripe size, being approximately the same size as the segment size. The chains of both ring and linear topologies are extended more in a stripe than in a slab; this effect is strengthened for a ring. For a ring in a stripe, the extension-confinement strength dependence leads to effective Flory exponents even larger than 3/4, which is characteristic for a self-avoiding two-dimensional chain. While the chain extension-confinement strength dependence for both topologies conforms to the de Gennes regime in a stripe, a linear chain undergoes gradual transition to the pseudoideal regime as the slab height increases in the slab-like confinement. For a confined circle, the onset of the pseudoideal regime is shifted to larger slab heights. The structure factor confirms the absence of the pseudoideal and extended de Gennes regime in a stripe and the transition from the extended to the pseudoideal regime of a circular and linear chain upon increasing the slab heights.
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Affiliation(s)
- Zuzana Benková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia. and LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre 687, 4168-007 Porto, Portugal
| | - Pavol Námer
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia.
| | - Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia.
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Bhandary D, Benková Z, Cordeiro MNDS, Singh JK. Molecular dynamics study of wetting behavior of grafted thermo-responsive PNIPAAm brushes. Soft Matter 2016; 12:3093-3102. [PMID: 26898416 DOI: 10.1039/c5sm02684a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In this work, the effect of temperature on the contact angle of a water droplet on grafted thermo-responsive poly-(N-isopropylacrylamide) (PNIPAAm) polymer brushes is studied using all-atom molecular dynamics simulations in the temperature range of 270-330 K. A shift from 55° to 65° in contact angle values is observed as the temperature increases from 300 K to 310 K, which is in line with the experimental reports. The behavior of a water droplet on PNIPAAm brushes is analyzed using hydrogen bond analysis, water diffusion, radial distribution functions, the potential of mean force, excess entropy and the second virial coefficient (B2). The thermo-responsive behavior of PNIPAAm brushes, quantified using the excess entropy and B2 of PNIPAAm-water and water-water interactions, is mainly governed by polymer-water interactions. In particular, the excess entropy and B2 of PNIPAAm resulting from the PNIPAAm-water interactions are found to increase with increasing temperature. The dehydration of PNIPAAm brushes and the increase in the contact angle of water were confirmed to be entropy driven processes.
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Affiliation(s)
- Debdip Bhandary
- Department of Chemical Engineering, Indian Institute of Technology Kanpur, UP 208016, India.
| | - Zuzana Benková
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, University of Porto, 4169-007 Portugal and Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia
| | - M Natália D S Cordeiro
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, University of Porto, 4169-007 Portugal
| | - Jayant K Singh
- Department of Chemical Engineering, Indian Institute of Technology Kanpur, UP 208016, India.
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Benková Z, Cordeiro MNDS. Molecular Dynamics Simulations of Poly(ethylene oxide) Grafted onto Silica Immersed in Melt of Homopolymers. Langmuir 2015; 31:10254-10264. [PMID: 26273751 DOI: 10.1021/acs.langmuir.5b01890] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Tuning of surface properties plays an important role in applications ranging from material engineering to biomedicine/chemistry. The interactions of chains grafted to a solid support and exposed to a matrix of chemically identical chains represent an intriguing issue. In this work, the behavior of poly(ethylene oxide) (PEO) chains grafted irreversibly onto an amorphous silica and immersed in the matrix of free PEO chains of different polymerization degree is studied using molecular dynamics simulations. The density distributions of grafted and free PEO chains, the height of the grafted layer, overlap parameters, and orientation order parameters depend not only on the grafting density but also on the length of free chains which confirm the entropic nature of the interactions between the grafted and free chains. In order to achieve a complete expulsion of the free chains from the grafted layer, a grafting density as high as 3.5 nm(-2) is necessary. Free PEO chains of 9 monomers leave the grafted layer at lower grafting densities than the longer PEO chains of 18 monomers in contrast with the theoretical predictions. The height of the grafted layer evolves with the grafting density in the presence of free chains in qualitative agreement with the theoretical phase diagram.
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Affiliation(s)
- Zuzana Benková
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto , Rua do Campo Alegre 687, 4168-007 Porto, Portugal
- Polymer Institute, Slovak Academy of Sciences , Dúbravská cesta 9, 845 41 Bratislava, Slovakia
| | - M Natália D S Cordeiro
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto , Rua do Campo Alegre 687, 4168-007 Porto, Portugal
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Abstract
We investigated the recently suggested advantageous analysis of chain linearization experiments with macromolecules confined in a stripe-like channel (Huang and Battacharya, EPL, 2014, 106, 18004) using Monte Carlo simulations. The enhanced chain extension in a stripe, which is due to the significant excluded volume interactions between the monomers in two dimensions, weakens considerably on transition to an experimentally feasible slit-like channel. Based on the chain extension-confinement strength dependence and the structure factor behavior for a chain in a stripe, we infer the excluded volume regime (de Gennes regime) typical for two-dimensional systems. On widening of the stripe in a direction perpendicular to the stripe plane, i.e. on the transition to the slab geometry, the advantageous chain extension decreases and a Gaussian regime is observed for not very long semiflexible chains. The evidence for pseudo-ideality in confined chains is based on four indicators: the extension curves, variation of the extension with the persistence length P, estimated limits for the regimes in the investigated systems, and the structure factor behavior. The slab behavior can be observed when the two-dimensional stripe (originally of a one-monomer thickness) reaches a reduced thickness D larger than approximately D/P ≈ 0.2 in the third dimension. This maximum height of a slab at which the advantage of a stripe is retained is very low and has implications for DNA linearization experiments.
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Affiliation(s)
- Zuzana Benková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia.
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Affiliation(s)
- Zuzana Benková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská
cesta 9, 845 41 Bratislava, Slovakia
- REQUIMTE, Chemistry Department, University of Porto, Rua do Campo Alegre 687, 4169-007
Porto, Portugal
| | - Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, Dúbravská
cesta 9, 845 41 Bratislava, Slovakia
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Benková Z, Szefczyk B, D. S. Cordeiro MN. Molecular Dynamics Study of Hydrated Poly(ethylene oxide) Chains Grafted on Siloxane Surface. Macromolecules 2011. [DOI: 10.1021/ma200233g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zuzana Benková
- REQUIMTE, Department of Chemistry, University of Porto, Rua do Campo Alegre 687, 4168-007 Porto, Portugal
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia
| | - Borys Szefczyk
- REQUIMTE, Department of Chemistry, University of Porto, Rua do Campo Alegre 687, 4168-007 Porto, Portugal
- Institute of Physical and Theoretical Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - M. Natália D. S. Cordeiro
- REQUIMTE, Department of Chemistry, University of Porto, Rua do Campo Alegre 687, 4168-007 Porto, Portugal
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Abstract
The influence of confinement on the persistence length of dsDNA molecules under a high ionic strength environment was explored by coarse-grained Monte Carlo simulations in channels of different profiles. It was found that under confinement three definitions of the persistence length of DNA molecules were not equivalent and represented different properties. In case of the global quantities, the projection and the WLC persistence lengths, the apparent values up to several hundred nanometres are observed for DNA confined in narrow channels. The orientational correlation function cos theta(s) of confined DNA shows a complex pattern, distinctive for semiflexible polymers. At weak and moderate confinements the function cos theta(s) suggests an unexpected increase in the apparent DNA flexibility. The orientational persistence length computed from the initial slope of the function cos theta(s) mirrors only short-scale correlations and gives the value close to the intrinsic persistence length of DNA. The simulation data of direct relevance to experimental studies of DNA in microfluidic devices are compared with analytical theories for stiff chains.
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Affiliation(s)
- Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 842 36 Bratislava, Slovakia
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Affiliation(s)
- Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 842 36 Bratislava, Slovakia
| | - Zuzana Benková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 842 36 Bratislava, Slovakia
| | - Tomáš Bleha
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 842 36 Bratislava, Slovakia
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Almássy A, Benková Z, Horváth B, Boháč A. Fluxional behavior of methyl-substituted tricarbonyl(tropone)iron complexes and their different reactivity. J Organomet Chem 2008. [DOI: 10.1016/j.jorganchem.2008.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Affiliation(s)
- Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 842 36 Bratislava, Slovakia
| | - Zuzana Benková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 842 36 Bratislava, Slovakia
| | - Tomáš Bleha
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 842 36 Bratislava, Slovakia
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Cifra P, Benková Z, Bleha T. Effect of confinement on properties of stiff biological macromolecules. Faraday Discuss 2008; 139:377-92; discussion 399-417, 419-20. [DOI: 10.1039/b716546c] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Benková Z, Černušák I, Zahradník P. Basis set and electron correlation effects on static electric properties of 1,3-thiazoles and 1,3-benzothiazoles as potential fragments in push–pull NLO chromophores. Mol Phys 2006. [DOI: 10.1080/00268970600652979] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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