Papers by Konstantinos Kotsis
Physical Chemistry Chemical Physics, 2016
We present a comparative Density Functional Theory (DFT) and Density Functional Tight Binding (DF... more We present a comparative Density Functional Theory (DFT) and Density Functional Tight Binding (DFTB) study of geometries and electronic structures of arginine (Arg), arginine adsorbed on the anatase (101) surface of titania in several adsorption configurations, and of an arginine-rich cell penetrating peptide TAT and its adsorption on the surface of TiO 2. Two DFTB parameterizations are considered, tiorg-0-1/mio-1-1 and matsci-0-3. While there is good agreement in the structures and relative energies of Arg and peptide conformers between DFT and DFTB, both adsorption geometries and energies are noticeably different for Arg adsorbed on TiO 2. The tiorg-0-1/mio-1-1 parameterization performs better than matsci-0-3. We relate this difference to the difference in electronic structures resulting from the two methods (DFT and DFTB) and specifically to the band alignment between the molecule and the oxide. We show that the band alignment of TAT and of TiO 2 modeled with DFTB is qualitatively correct but that with DFT using the PBE functional is not. This is specific to the modeling of large molecules where the HOMO is close to the conduction band of the oxide. We therefore report a case where the approximate DFT-based method-DFTB (with which the correct band structure can be effectively obtained)-performs better than the DFT itself with a functional approximation
Proceedings of the 2nd World Congress on Recent Advances in Nanotechnology, Apr 1, 2022
Nanomaterials (NMs) and nanoparticles (NPs) lie at the core of many technological applications in... more Nanomaterials (NMs) and nanoparticles (NPs) lie at the core of many technological applications in medicine and pharmacology, as well as in the food, agriculture, electronics, and energy industries. They are also released in the environment through natural and incidental pathways. Despite our heavy reliance on NMs, the potential risk they pose to the environment and to the biological systems is still of major concern [1]. In this work, we evaluate intrinsic and extrinsic NM descriptors to aid in the prediction of biomolecular interactions at the surface of NMs and development of structure-activity relationships between their physicochemical characteristics and their toxicity [2]. Intrinsic properties are solely based on the molecular and electronic structure of the NM, while the extrinsic properties describe a NM that comes in contact with a protein in a solvent. The NM models for the calculation of intrinsic descriptors are associated with the core of the NM that is described as a periodic bulk material [2]. In this work, we present a database of calculated descriptors for several common NMs. The provided list contained various samples of NP (metals, oxides, minerals, polymers, and carbon-based compounds such as carbon nanotubes (CNTs) and graphene sheets) that were used in toxicological experiments. The intrinsic descriptors are evaluated by different theoretical approaches. The bandgap values of all bulk NMs were calculated using density functional theory (DFT) implemented in the SIESTA package [3]. The density of states obtained from the DFT calculation at the generalized gradient approximation is used to estimate the size of the bandgap. The heat of formation, absolute hardness, electronegativity, dispersion energy, the dipole moment, the Mulliken electronegativity, the Parr and Pople absolute hardness, and polarizability descriptors were calculated using the semi-empirical PM6-D3 [4] with the MOPAC package [5]. The extrinsic (interfacial) descriptor is a quantity that describes the relative hydrophilicity/ hydrophobicity of a periodic surface NM slab (e.g. metals, metal oxides, and carbon-based NMs) in water and octanol based on the relative enthalpy of immersion. In this work, we also employ molecular dynamics with the GROMACS [6] package using e.g. CHARMM force fields [7] in order to obtain the enthalpies of the NM slab, of the solvent (water or octanol) and of the solvated slab metals, metal oxides, and carbon-based compounds.
Proceedings of the 2nd World Congress on Recent Advances in Nanotechnology, Apr 1, 2022
Nature Nanotechnology
The varied transcriptomic response to nanoparticles has hampered the understanding of the mechani... more The varied transcriptomic response to nanoparticles has hampered the understanding of the mechanism of action. Here, by performing a meta-analysis of a large collection of transcriptomics data from various engineered nanoparticle exposure studies, we identify common patterns of gene regulation that impact the transcriptomic response. Analysis identifies deregulation of immune functions as a prominent response across different exposure studies. Looking at the promoter regions of these genes, a set of binding sites for zinc finger transcription factors C2H2, involved in cell stress responses, protein misfolding and chromatin remodelling and immunomodulation, is identified. The model can be used to explain the outcomes of mechanism of action and is observed across a range of species indicating this is a conserved part of the innate immune system.
Toxicogenomics aims at characterising the mechanism of action (MOA) of environmental exposures, a... more Toxicogenomics aims at characterising the mechanism of action (MOA) of environmental exposures, and often relies on transcriptomics to investigate the responses of exposed biological systems. However, the identification of shared toxicogenomics-derived signatures across exposed biological systems is hampered by the complexity and heterogeneity of transcriptomics data. Given the lack of a clear transcriptomic signature of exposure, we hypothesise that common patterns of gene regulation could explain the response to engineered nanomaterials (ENM) across biological systems, disentangling the complexity of their MOA. We performed meta-analysis of a large collection of transcriptomics data from various ENM exposure studies and identified deregulation of immune functions as a prominent response across different ENM exposures. This pattern of transcriptional deregulation differed significantly from exposure to drugs. By investigating the promoter regions of genes frequently altered both in...
Physical Review B, Oct 30, 2014
Noncontact atomic force microscopy (NC-AFM) and Kelvin probe force microscopy (KPFM) have become ... more Noncontact atomic force microscopy (NC-AFM) and Kelvin probe force microscopy (KPFM) have become important tools for nanotechnology; however, their contrast mechanisms on the atomic scale are not entirely understood. Here we used chlorine vacancies in NaCl bilayers on Cu(111) as a model system to investigate atomic contrast as a function of applied voltage, tip height, and tip functionalization. We demonstrate that the AFM contrast on the atomic scale decisively depends on both the tip termination and the sample voltage. On the contrary, the local contact potential difference (LCPD) acquired with KPFM showed the same qualitative contrast for all tip terminations investigated, which resembled the contrast of the electric field of the sample. We find that the AFM contrast stems mainly from electrostatic interactions but its tip dependence cannot be explained by the tip dipole alone. With the aid of a simple electrostatic model and by density functional theory we investigate the underlying contrast mechanisms.
MRS Advances, 2016
ABSTRACTIn search for effective negative electrodes for Mg- and K-ion batteries, we investigate t... more ABSTRACTIn search for effective negative electrodes for Mg- and K-ion batteries, we investigate the potential of glassy amorphous carbon by means of density functional theory calculations. Specifically, we provide the energetics for Mg and K insertion in two different structures of amorphous carbon. The insertion sites are found to be well distributed in energy, with insertion energies Ef vs. the cohesive energies of respectively Mg and K ranging from -1.1 to 2.8 eV for Mg and from -1.0 to 3.7 eV for K. To compare amorphous carbon to the most common structure of carbon (graphite), we study in addition the energetics associated with the insertion of Mg and K in graphite, for which two different stackings are considered for the two layers intercalating the Mg/K atom: the AB stacking which is most stable at the initial state of charge (in pure graphite) and the AA stacking which is most stable at the known final state of charge of K (KxC, x = 1/8). Already at the low concentration cons...
Proceedings of the 7th World Congress on Recent Advances in Nanotechnology
Nanomaterials (NMs) and nanoparticles (NPs) lie at the core of many technological applications in... more Nanomaterials (NMs) and nanoparticles (NPs) lie at the core of many technological applications in medicine and pharmacology, as well as in the food, agriculture, electronics, and energy industries. They are also released in the environment through natural and incidental pathways. Despite our heavy reliance on NMs, the potential risk they pose to the environment and to the biological systems is still of major concern [1]. In this work, we evaluate intrinsic and extrinsic NM descriptors to aid in the prediction of biomolecular interactions at the surface of NMs and development of structure-activity relationships between their physicochemical characteristics and their toxicity [2]. Intrinsic properties are solely based on the molecular and electronic structure of the NM, while the extrinsic properties describe a NM that comes in contact with a protein in a solvent. The NM models for the calculation of intrinsic descriptors are associated with the core of the NM that is described as a periodic bulk material [2]. In this work, we present a database of calculated descriptors for several common NMs. The provided list contained various samples of NP (metals, oxides, minerals, polymers, and carbon-based compounds such as carbon nanotubes (CNTs) and graphene sheets) that were used in toxicological experiments. The intrinsic descriptors are evaluated by different theoretical approaches. The bandgap values of all bulk NMs were calculated using density functional theory (DFT) implemented in the SIESTA package [3]. The density of states obtained from the DFT calculation at the generalized gradient approximation is used to estimate the size of the bandgap. The heat of formation, absolute hardness, electronegativity, dispersion energy, the dipole moment, the Mulliken electronegativity, the Parr and Pople absolute hardness, and polarizability descriptors were calculated using the semi-empirical PM6-D3 [4] with the MOPAC package [5]. The extrinsic (interfacial) descriptor is a quantity that describes the relative hydrophilicity/ hydrophobicity of a periodic surface NM slab (e.g. metals, metal oxides, and carbon-based NMs) in water and octanol based on the relative enthalpy of immersion. In this work, we also employ molecular dynamics with the GROMACS [6] package using e.g. CHARMM force fields [7] in order to obtain the enthalpies of the NM slab, of the solvent (water or octanol) and of the solvated slab metals, metal oxides, and carbon-based compounds.
Proceedings of the 7th World Congress on Recent Advances in Nanotechnology
Physical Chemistry Chemical Physics, 2021
We present a multiscale computational approach for the first-principles study of bio-nano interac... more We present a multiscale computational approach for the first-principles study of bio-nano interactions. Using titanium dioxide as a case study, we evaluate the affinity of titania nanoparticles to water and biomolecules through atomistic and coarse-grained techniques.
Chemical Physics Letters, 2016
MRS Advances, 2016
The adsorption 2-anthroic acid on titania has been shown to result in an interfacial charge trans... more The adsorption 2-anthroic acid on titania has been shown to result in an interfacial charge transfer band, which makes this a promising interface for dye-sensitized solar cells with direct injection. Here, we model the adsorption of 2-anthroic acid on a TiO2 nanocluster exhibiting a (101)-like interface and compute light absorption properties of this system using for the first time a hybrid functional. The band alignment and the formation of interfacial charge transfer bands proposed in previous experimental and lower-level computational works are confirmed.
Bulletin of the American Physical Society, Mar 5, 2015
First-principles study of amorphous carbon: a promising candidate for Na-ion batteries KONSTANTIN... more First-principles study of amorphous carbon: a promising candidate for Na-ion batteries KONSTANTINOS KOTSIS, FLEUR LEGRAIN, SERGEI MANZHOS, National University of Singapore -The perspective of a widespread use of clean but intermittent sources of electricity (wind and solar) as well as that of hybrid electric vehicles calls for alternatives to Li-ion batteries as Li resources are limited. Na being abundant, cheap, and a relatively light and small atom, Na-ion batteries have attracted a lot of interest the past few years. However, while most of the Na-ion batteries studies focus on the positive electrode, the negative electrode remains little investigated and an efficient anode providing all a good capacity, a high cycle life, and a descent rate of charge/discharge, is still not available. The efficient electrode materials for Li, in particular diamond Si and graphite C, have been shown to not allow the intercalation of Na [1, 2]. Computational studies report positive intercalation energies [3, 4] and therefore suggest that the insertion of Na into the crystalline framework (C and Si) is thermodynamically not favored: Na atoms prefer to gather into Na clusters rather than to intercalate into the crystalline phase. Amorphization of Si was found to be a valid strategy to improve the interaction between Si and Na [3]. We investigate here the effects of amorphization of C on its storage properties vis-à-vis Na (as well as Li for reference).
Angewandte Chemie, 2007
Die Aktivierung von CO 2 ist eines der wichtigsten Themen in der Katalyse.1 So wurden zum Beispie... more Die Aktivierung von CO 2 ist eines der wichtigsten Themen in der Katalyse.1 So wurden zum Beispiel zur Hydratation von CO 2 durch Carboanhydrase, einem der einfachen durch Zinkenzyme katalysierten Prozesse, umfangreiche mechanistische und theoretische Studien ...
Journal of the American Chemical Society, Nov 1, 2009
In a combined theoretical and experimental study, an efficient catalytic reaction featuring epoxi... more In a combined theoretical and experimental study, an efficient catalytic reaction featuring epoxide opening and tetrahydrofuran formation through homolytic substitution reactions at C-O and Ti-O bonds was devised. The performance of these two key steps of the catalytic cycle was studied and could be adjusted by modifying the electronic properties of the catalysts through introduction of electron-donating or -withdrawing substituents to the titanocene catalysts. By regarding both steps as single electron versions of oxidative addition and reductive elimination, a mechanism-based platform for the design of catalysts and reagents for electron transfer reactions evolved that opens broad perspectives for further investigations.
Pccp Physical Chemistry Chemical Physics, 2006
O1s XPS-Spektren wurden mit wellenfunktionsbasierten, quantenchemischen ab initio Methoden berech... more O1s XPS-Spektren wurden mit wellenfunktionsbasierten, quantenchemischen ab initio Methoden berechnet. Die experimentellen O1s XPS-Spektren von der H2O/ ZnO(000-1)-Oberfläche sind nur mit der (1 × 1) Oberflächenstruktur für die O terminierte ZnO(000-1)-Oberfläche kompatibel, und nicht mit der (2 × 1) Struktur, die aus theoretischen Argumenten als die stabilere gilt. O1s XPS-Rechnungen für die Adsorption eines CO2-Moleküls auf der nicht polaren ZnO(10-10)-Oberfläche deuten auf eine starke Adsorption und die Bildung eines CO32--Anions auf der Oberfläche hin. Experimentell ist nur die CO2-Insertion in die Zn-H Bindung von Alkoxyzink-hydriden (molekulare Modelle für ZnO- Katalysatoren) beobachtet worden. CO inseriert dagegen nicht. DFT-Rechnungen belegen die experimentelle Aussage. Der Vergleich von harmonischen Frequenzen mit DRIFTS-Spektren zeigt, dass die CO2-Insertion nur dann möglich ist, wenn O mit einer cis- oder trans-Anordnung einer Formiat-Gruppe (HCO2) zum Zn koordiniert ist.
A multidimensional wave packet IR-spectroscopic approach that resumes the coupling between a dege... more A multidimensional wave packet IR-spectroscopic approach that resumes the coupling between a degenerate vibrational mode and a non-degenerate vibrational mode by simple linear transformation of the vibrational displacement modes within the HF-Schwinger variational method for the electron scattering states and the Chase approximation for the nuclei including quantum nuclear effects in an OpenMP/MPI and a GPU scattering code developed by S. Vellas. Texas A&M University, Faculty of Science.
Dyson orbital relaxation in the ionic state, the molecular cationic structure and vibrational mod... more Dyson orbital relaxation in the ionic state, the molecular cationic structure and vibrational modes of the ionic state within VCC as well as vibrational relaxation (vibronic close coupling) were considered in the present study. Final state effects, as orbital relaxation and Cooper minima, are significant in the strong field ionization of the cyanogen halides, XCN (X=F, Cl, Br, I). Texas A&M University, Faculty of Science
The near threshold photoelectron angular distributions (PAD) of the molecular oxygen anion are ty... more The near threshold photoelectron angular distributions (PAD) of the molecular oxygen anion are typical (serve as a paradigma) to a weak breakdown in the Franck-Condon approximation versus a strong vibronic coupling due to the breakdown in the Born-Oppenheimer approximation. The ab initio PAD are in agreement with TDDFT & MCTDHF PAD and the observed PAD (Mabbs et al. 2010). Texas A&M University, Faculty of Science
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Papers by Konstantinos Kotsis