Density-functional Tight-binding Method Research Articles

Simulation and experimental study of fluorescence labeled polyphosphate in microthrix parvicella

To study the binding mechanism of 4′,6-diamidino-2-phenylindole (DAPI) and polyphosphate (Poly-P) and find fluorescent dyes which can dye Poly-P better, the interaction model of DAPI and Poly-P was calculated by the self-consistent-charge, density functional tight-binding (SCC-DFTB-D) method, and the binding sites of DAPI and Poly-P were analyzed. Further, Cy3, Rhodamine 6G and Fluorescein, which are structurally similar to DAPI, were selected to analyze their interactions with Poly-P. The binding energies and frontier orbital properties of the complexes were analyzed. These four fluorescent dyes were further used to dye the activated sludge smear and observe the fluorescence property. The Simulation results show that the N-containing indole ring structures in DAPI plays an important role in the interaction with Poly-P; the binding energies for DAPI, Cy3, Rhodamine 6G and Fluorescein with Poly-P are −42.6, −165.4, −34.7 and −28.9 kcal/mol, respectively. The frontier orbital properties for the complexes were studied, which further indicates that the interactions between Cy3, Rhodamine 6G and Poly-P are stronger than that of Fluorescein and Poly-P. The experimental results showed that Cy3 had excellent dyeing effect on Poly-P and could recognize them, while Fluorescein could not dye Poly-P. The experimental results were in good agreement with those predicted by simulation, which verified the correctness of our calculation method and provided a new strategy for finding more reliable, more sensitive and more economical fluorescent dyes capable of dyeing Poly-P.

Multiscale simulations of the hydration shells surrounding spherical Fe3O4 nanoparticles and effect on magnetic properties.

Iron oxide magnetic nanoparticles (NPs) are excellent systems in catalysis and in nanomedicine, where they are mostly immersed in aqueous media. Even though the NP solvation by water is expected to play an active role, the detailed structural insight at the nanostructure oxide/water interface is still missing. Here, based on our previous efforts to obtain accurate models of dehydrated Fe3O4 NPs and of their magnetic properties and through multiscale molecular dynamics simulations combining the density functional tight binding method and force field, we unravel the atomistic details of the short range (chemical) and long range (physical) interfacial effects when magnetite nanoparticles are immersed in water. The influence of the first hydration shell on the structural, electronic and magnetic properties of Fe3O4 NPs is revealed by high-level hybrid density functional calculations. Hydrated Fe3O4 NPs possess larger magnetic moment than dehydrated ones. This work bridges the large gap between experimental studies on solvated Fe3O4 NPs and theoretical investigations on flat Fe3O4 surfaces covered with water and paves the way for further study of Fe3O4 NPs in biological environments.

Energy stability and electronic properties of carbon nanotorus at a localized breaking of interatomic bonds: computer modeling

This paper is devoted to the study of the dynamic processes that occur in the carbon nanotorus during localized breaking of interatomic bonds, and to the analysis of the influence of these processes on the electronic properties of carbon nanotorus. The object of research is a carbon nanotorus with chirality indices (13, 0) with a diameter of 20 nm and a thickness of 1 nm obtained as a result of defect-free folding of a zigzag carbon nanotube of appropriate geometric dimensions into a ring. The behavior of the nanotorus is modeled by the molecular dynamics method using a modified Brenner potential to describe the interaction between atoms. It is shown that over time, the nanotorus straightens into a nanotube, while maintaining energy stability. It is found that the process of nanotorus straightening is accompanied by the appearance of deformation wave-like bends propagating at a speed of 200 m/s along the atomic network of the structure. These bends lead to deformation of the nanotorus and numerous local breaks in the bonds between atoms. However, broken bonds are restored within a few femtoseconds before the structure relaxes in energy, therefore, in general, the atomic framework of the nanotorus remains defect-free after rectification. The results of calculating the distribution of the density of electronic states (DOS) of a nanotorus by the self-consistent charge density functional tight-binding (SCC-DFTB) quantum method showed that at the moment of localized breaking of interatomic bonds around the circumference of the tubular framework, the nanotorus loses its semiconductor properties, becoming a gapless conductor. The discovered physical phenomenon explains the process of nanotorus formation during synthesis accompanied by multiple ruptures of the nanotori and reverse closure of the nanotubes into the nanotori.

Photoinduced charge-transfer in chromophore-labeled gold nanoclusters: quantum evidence of the critical role of ligands and vibronic couplings.

The electron flow between a metallic aggregate and an organic molecule after excitation with light is a crucial step on which hybrid photovoltaic nanomaterials are based. So far, designing such devices with the help of theoretical approaches has been heavily limited by the computational cost of quantum dynamics models able to track the evolution of the excited states over time. In this article, we present the first application of the time-dependent density functional tight-binding (TD-DFTB) method for an experimental nanometer-sized gold-organic system consisting of a hexyl-protected Au25 cluster labelled with a pyrene fluorophore, in which the fluorescence quenching of the pyrene is attributed to the electron transfer from the metallic cluster to the dye. The full quantum rationalization of the electron transfer is attained through quantum dynamics simulations, highlighting the crucial role of the protecting ligand shell in electron transfer, as well as the coupling with nuclear movement. This work paves the way towards the fast and accurate theoretical design of optoelectronic nanodevices.

Theoretical study of the structural and energetic properties of platinum clusters with up to 60 atoms

Applying a theoretical approach that combines an efficient and fast global optimization based on genetic algorithms (GA) to search in structure space and the parameterized density-functional tight-binding (DFTB) method for the calculation of the energy for a given structure, the structures of neutral and isolated Ptn clusters are determined with size n from 4 up to 60 atoms. For the analysis of the structural, energetic, and electronic properties of Ptn as a function of n, a series of descriptors are employed, including a stability function, the HOMO-LUMO energy gap, and atomic radial distances of the atoms, as well as a similarity function. The results demonstrate that the structural motifs change from planar to shell-like structures with low-symmetry. In addition, the growth patterns of Ptn clusters also are analyzed using these descriptors, suggesting that meta-stable isomers also play a role in the growth process. Studying the impact of zero-point vibration and of temperature on the energetic properties of the different isomers, we found only very small effects, implying that properties found for T = 0 are relevant also at elevated temperatures. On the other hand, even though Pt is the neighbor to Au in the periodic table, the properties of Ptn clusters differ markedly from those of Aun clusters, and it can therefore be expected that the properties of AuPt nanoalloys will not resemble those of the pure clusters.

Thermochemical stabilities of giant fullerenes using density functional tight binding theory and isodesmic-type reactions.

We present a systematic assessment of the density functional tight binding (DFTB) method for calculating heats of formation of fullerenes with isodesmic-type reaction schemes. We show that DFTB3-D/3ob can accurately predict Δf H values of the 1812 structural isomers of C60 , reproduce subtle trends in Δf H values for 24 isolated pentagon rule (IPR) isomers of C84 , and predict Δf H values of giant fullerenes that are in effectively exact agreement with benchmark DSD-PBEP86/def2-QZVPP calculations. For fullerenes up to C320 , DFTB Δf H values are within 1.0 kJ mol-1 of DSD-PBEP86/def2-QZVPP values per carbon atom, and on a per carbon atom basis DFTB3-D/3ob yields exactly the same numerical trend of (Δf H [per carbon] = 722n-0.72 + 5.2 kJ mol-1 ). DFTB3-D/3ob is therefore an accurate replacement for high-level DHDFT and composite thermochemical methods in predicting of thermochemical stabilities of giant fullerenes and analogous nanocarbon architectures.

Theoretical study of the formation of C18H and C18H2 molecules by low energy irradiation with atomic and molecular hydrogen

We study the formation of C18H and C18H2 by irradiating a cyclo [18]carbon molecule with atomic and molecular hydrogen at impact energy, E, in the range of 0.5–25 eV. We utilize the density-functional tight-binding method to perform molecular dynamics simulations to emulate the interaction of a carbon ring when colliding with atomic or molecular hydrogen. From our results, the formation of the C18H molecules is likely to occur upon irradiating by H atoms at E<10 eV and by H2 molecules at 2<E<15 eV center of mass energy. Formation of C18H2 molecules is only observed at around E=2 eV. Our results show that the absorption of hydrogen is more prone in atomic than in molecular hydrogen atmosphere. Thus, we find that the probability of physio-absorption reaches up to 80% for atomic projectiles with E<5 eV but only up to 10% for the molecular ones. Our analysis shows that the deformation of the carbon ring due to the hydrogen bonding produces transition from sp to sp2 hybridization. The angle between the carbon atoms at the locations near to the H bond in the resulting ring is not 120° but instead 110° degrees. No molecular fragmentation of the C18 ring is observed.

Encapsulation ability of silicon carbide and boron nitride nanotubes for spilanthol molecule

We apply the Self-consistent-charge density-functional tight-binding method to study the encapsulation behavior of spilanthol in the armchair (n,n) (n = 4, 5, 6, 7, and 8) silicon carbide (SiC) and boron nitride (BN) nanotubes. Depending on the chirality, one can classify the interactions as physisorption or chemisorption. In addition, one distributes spilanthol in a linear or helical way along the axis of the nanotube. In systems containing BN nanotubes, one can modulate the charge transfer via changing the chirality of the system. The strongest interaction occurs when one traps a spilanthol molecule inside of (5,5) SiC nanotube. Our results show that the properties of the Spilanthol–carrier complexes are suitable for applications in medicine and also for electronics.

Initial Decomposition of Condensed-Phase 1,3,5-Triamino-2,4,6-trinitrobenzene under High Temperature

ABSTRACT We have performed quantum-based molecular dynamics (MD) simulations to investigate the initial chemical processes of the TATB under different temperatures. A self-consistent charge density-functional tight-binding (SCC-DFTB) method was employed.The results show that a large number of clusters (such as C12H12O8N10, C12H12O12N12, C12H12O6N9, C18H18O16N17) formed in the initial reaction process, which indicates that the initial heating mainly results in the binding of TATB adjacent molecules rather than their decomposition. Moreover, the stability sequence of bonds is C-C > N-H > C-NH2 > C-NO2 in our research, C-NO2 is the main reaction path at 1500 K, and C-NO2 and C-NH2 are the main reaction path at 2000 K. When temperature increase to 2500 K and 3000 K, the homolytic cleavage of the N-NO2 and C-NH2 bonds is suppressed, and the C-H bond dissociation becomes the primary pathway for TATB decomposition in its early stages.

Computational studies of energetics, electronic structure, and vibrational spectra of PETN nanoparticles

The density functional tight binding method was used to explore the energetics, electronic structure, and vibrational spectra of pentaerythritol tetranitrate (PETN) nanoparticles (NPs). The surface energy of the PETN NP is anisotropic and its extra energy decreases with the increase of size. The energy bands of the NPs are significantly expanded and the band gaps are narrowed, thus reducing the stability due to nanometer size effect. The surface of the NP is mainly covered by the NO2 group. The high-energy surface may play a role in triggering chemical decomposition. The vibration frequencies of the PETN NPs present a wider distribution than those of the gas and solid phase PETN, which will increase the probability of energy transfer to the molecules in the system and promote the decomposition of PETN. Our results provide a basic understanding from a molecular perspective to the energy properties of nano explosives.

DFTB/MM Molecular Dynamics Simulations of the FMO Light-Harvesting Complex

Because of the size of light-harvesting complexes and the involvement of electronic degrees of freedom, computationally these systems need to be treated with a combined quantum-classical description. To this end, Born-Oppenheimer molecular dynamics simulations have been employed in a quantum mechanics/molecular mechanics (QM/MM) fashion for the ground state followed by excitation energy calculations again in a QM/MM scheme for the Fenna-Matthews-Olson (FMO) complex. The self-consistent-charge density functional tight-binding (DFTB) method electrostatically coupled to a classical description of the environment was applied to perform the ground-state dynamics. Subsequently, long-range-corrected time-dependent DFTB calculations were performed to determine the excitation energy fluctuations of the individual bacteriochlorophyll a molecules. The spectral densities obtained using this approach show an excellent agreement with experimental findings. In addition, the fluctuating site energies and couplings were used to estimate the exciton transfer dynamics.

Theoretical studies of size effects on surfacial properties for CL-20 and NTO nanoparticles

Nanoparticles (NPs) possess the unique physical and chemical properties compared with gas-phase molecule and bulk crystal. Hence, the energetics, electronic structure, and vibrational properties of CL-20 and NTO NPs were investigated by the combinational strategy based on density-functional tight-binding (DFTB) and density-functional theory (DFT) methods. The results show that NPs possess quite different features from the isolated state molecule and the bulk crystal. The excess energies, surface energies, and enthalpy of sublimation for the NPs are predicted. The surface-induced surface states of the CL-20 and NTO NPs result in the significant decrease on the energy gaps and the formation of active sites on the surfaces. The vibrational properties related to the decomposition pathways for both CL-20 and NTO NPs, gas molecules, and bulk crystals are discussed and compared with previous theoretical and experimental values. Our results are expected to provide basic insights into the understandings of the surface effect of nano-sized energetic materials.

Quantum Mechanics/Molecular Mechanics Study on Caspase-2 Recognition by Peptide Inhibitors

For a variety of biological and medical reasons, the ongoing development of humane caspase-2 inhibitors is of vital importance. Herein, a hybrid (Quantum Mechanics/Molecular Mechanics - QM/MM), two-layered molecular model is derived in order to understand better the affinity and specificity of peptide inhibitor interaction with caspase-2. By taking care of both the unique structural features and the catalytic activity of human caspase-2, the critical enzyme residues (E217, R378, N379, T380, and Y420) with the peptide inhibitor are treated at QM level (the Self-Consistent-Charge Density-Functional Tight-Binding method with the Dispersion correction (SCC-DFTB-D)), while the remaining part of the complex is treated at MM level (AMBER force field). The QM/MM binding free energies (BFEs) are well-correlated with the experimental observations and indicate that caspase-2 uniquely prefers a penta-peptide such as VDVAD. The sequence of VDVAD is varied in a systematic fashion by considering the physicochemical properties of every constitutive amino acid and its substituent, and the corresponding BFE with the inhibition constant (Ki) is evaluated. The values of Ki for several caspase-2:peptide complexes are found to be within the experimental range (between 0.01 nM and 1 ?M). The affinity order is: VELAD (Ki=0.081 nM) > VDVAD (Ki=0.23 nM) > VEIAD (Ki=0.61 nM) > VEVAD (Ki=3.7 nM) > VDIAD (Ki=4.5 nM) etc. An approximate condition needed to be satisfied by the kinetic parameters (the Michaelis constant - KM and the specificity constant - kcat/KM) for competitive inhibition is reported. The estimated values of kcat/KM, being within the experimentally established range (between 10-4 and 10-1 ?M-1 s-1), indicate that VELAD and VDVAD are most specific to caspase-2. These two particular peptides are nearly 1.5, 3 and 4 times more specific to the receptor than VEIAD, VEVAD and VDIAD respectively. Additional kinetic threshold, aimed to discriminate tightly bound inhibitors, is given.

Reduced graphene oxide/NH2-MIL-125(Ti) composite: Selective CO2 photoreduction to methanol under visible light and computational insights into charge separation

Abstract The development of visible-light active photocatalysts is highly desirable for CO2 reduction to hydrocarbons and alcohols using sunlight. Here, we report the metal-organic frameworks (MOF) of amino-benzene dicarboxylate with titanium oxocluster center (NH2-MIL-125(Ti)) and modified with reduced graphene oxide (RGO), RGO-NH2-MIL-125(Ti), ideal for the visible-light-driven photocatalytic reduction of CO2 to hydrocarbons and methanol. The catalyst provides high quantum efficiency and selectivity for methanol. The cluster model and self-consistent charge density functional tight binding methods were used to investigate the photogenerated charge separation for NH2-MIL-125(Ti). The quantum modelling suggests that holes were accumulated in the central ring Ti8O8(OH)4, where strongly adsorbed electron donor, triethanolamine, undergoes photooxidation while electrons were located in the organic ligand of MOF including the NH2 group. The binding affinity of NH2 reaction sites to CO2 possibly work to improve the photocatalytic reduction of CO2 to methanol. The RGO also play an important role for charge separation and better photocatalytic reduction with RGO-NH2-MIL-125(Ti).

Design of novel conjugated microporous polymers for efficient adsorptive desulfurization of small aromatic sulfur molecules

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.

Improving the Sensory Properties of Layered Phospholipid-Graphene Films Due to the Curvature of Graphene Layers.

This article is devoted to the in silico study of the sensory properties of mono- and bilayer phospholipid-graphene films with planar and curved graphene sheets. The DPPC (dipalmitoylphosphatidylcholine) molecules are considered as phospholipid structures. These molecules are part of lipid bilayers, liposomes and cell membranes. To find a way to improve the sensory properties of phospholipid-graphene films, we studied the effect of the curvature of the graphene sheet on the charge transfer and electrical conductivity of the films. The distribution of the electron charge density over the film atoms was calculated using the self-consistent-charge density-functional tight-binding method (SCC-DFTB). The calculation of the current through phospholipid-graphene films was carried out within the framework of the Landauer–Buttiker formalism using the Keldysh nonequilibrium Green function technique. As a result of the calculations, the optimal configuration of the arrangement of DPPC molecules between two graphene layers was established. This configuration provides the maximum possible increase in current to 1 μA at low voltages of ~0.2 V and is achieved for curved graphene with a radius of curvature of ~2.7 nm at individual points of graphene atomic network.

Theorectical Studies on Surface-Induced Energetic, Electronic, and Vibrational Properties of Triamino-trinitrobenzene Nanoparticles

The energetics, electronic features, and vibrational properties of a series of triamino-trinitrobenzene (TATB) nanoparticles (NPs) were investigated by density functional theory (DFT) with density functional tight binding (DFTB) methods. The surface energies, enthalpy of sublimation, and melt point for different TATB NPs were compared. The surface-related electronic states in the NPs narrower the energy gap and provide the active sites at surfaces. The vibrational properties of the TATB NPs were carefully compared with those of the gaseous and solid phase TATB. The correlation between the surface molecules in the TATB NPs and initial decomposition was discussed. Our results provide insights into the comprehensive understandings of high activity of nano explosives at the atomic and electronic levels.

Finite-temperature-based time-dependent density-functional theory method for static electron correlation systems.

In this study, we developed a time-dependent density-functional theory (TDDFT) with a finite-temperature (FT) scheme, denoted as FT-TDDFT. We introduced the concept of fractional occupation numbers for random phase approximation equation and evaluated the excited-state electronic entropy terms with excited-state occupation number. The orbital occupation numbers for the excited state were evaluated from the change in the ground-state electron configuration with excitation and deexcitation coefficients. Furthermore, we extended the FT formulation to the time-dependent density-functional tight-binding (TDDFTB) method for larger systems, denoted as FT-TDDFTB. Numerical assessment for the FT-(TD)DFT method showed smooth potential curves for double-bond rotation of ethylene in both ground and excited states. Excited-state calculations based on the FT-TDDFTB method were applied to the uniform π-stacking columns composed of trioxotriangulene, possessing neutral radicals in strong correlation systems.

Non-adiabatic molecular dynamics with divide-and-conquer type large-scale excited-state calculations.

Many of the non-adiabatic processes in the condensed phase are affected by the interaction with the environment, as exemplified by Marcus theory. However, non-adiabatic molecular dynamics simulations with explicitly including the environment are computationally expensive because of the extended system size, suggesting the need for an efficient scheme applicable to huge systems. In this work, time-derivative non-adiabatic coupling (TDNAC) calculation algorithms were developed in the framework of the divide-and-conquer (DC) time-dependent (TD) density-functional tight-binding (DFTB) method, which is an extension of the TD-DFTB for larger systems based on the fragmentation-based DC scheme. The developed algorithms were incorporated into a fewest-switches trajectory surface hopping (FSSH) routine. The calculated TDNAC and the FSSH results were sufficiently accurate compared to the conventional TD-DFTB results. Use of the DC-TD-DFTB provided a significant reduction in the central processing unit (CPU) time vs that of the TD-DFTB, where the CPU time remained constant irrespective of the total system size. It was also confirmed that the present method is not only efficient but also improves the numerical stability of TDNAC calculations.

Bandgap modulation of low-dimensional γ-graphyne-1 under uniform strain

Graphyne sheets and nanotubes (GyNTs) are known as novel low-dimensional, i.e., two-dimensional (2D) and one-dimensional (1D), semiconducting carbon allotropes that can be used in nanoelectronics and therefore merit fundamental investigation. Among such materials, attention is currently focused on γ-graphyne-1, a member of the graphyne family that exhibits a maximum cohesive energy of −8.37 eV and chemical stabilityhas been focused. In this research density functional tight binding (DFTB) method in the investigation of electrical property under geometrical variation is reported and a detailed description of electrical as well as stability properties for γ-graphyne-1 in uniform strain is illustrated. It is concluded that the γ-graphyne-1 family of materials exhibit semiconducting properties with large bandgap values from 1.34 eV for the sheet structure to 1.93 eV for (3,0) armchair γ-graphyne-1 nanotubes. The γ-graphyne-1 family also displays elastic properties, enabling the modulation of the bandgap and engineering of the effective mass using homogeneous strain. These properties, along with the nonmetallic behavior of GyNTs, make them perfect materials for the design of novel electronic devices.