DFT Molecular Dynamics Simulations Research Articles

Effects of Internal Electron-Withdrawing Moieties in D-A-π-A Organic Sensitizers on Photophysical Properties for DSSCs: A Computational Study.

D–A−π–A dyes differ from the traditional D−π–A framework having several merits in dye-sensitized solar cell (DSSC) applications. With regard to D−π–A dyes, D–A−π–A dyes red-shift absorption spectra and show particular photostability. Nevertheless, the effects of internal acceptor on the charge transfer (CT) probability are unclear. We employed density functional theory (DFT), time-dependent DFT (TD-DFT), and TD-DFT molecular dynamics (MD) simulations to investigate the effects of internal acceptor on the photophysical properties of D–A−π–A dyes on DSSCs. Our calculations show the absorption bands of D–A−π–A dyes with strong electron-withdrawing internal acceptors exhibiting significant characteristics of dual CT; the excited electron density is transferred to the internal and terminal acceptors simultaneously. Particularly, the internal acceptor traps a significant amount of electron density upon photoexcitation. The TD-DFT MD simulations at 300 K show that only a small amount of excited electron density is pushing and pulling between the internal acceptor and terminal acceptor moieties; the thermal energy is not high enough to drive the electron density from the internal acceptor to the terminal acceptor. Our study reveals the nature of CT bands of D–A−π–A dyes providing a theoretical basis for further rational engineering.

Ultrafast interfacial charge transfer from the LUMO+1 in ruthenium(ii) polypyridyl quinoxaline-sensitized solar cells.

This paper describes the implementation of robust and modular sensitizers containing aromatic-amphiphilic ligands to provide new insights into the relationship between the molecular structure and electron injection process governing the efficiency of dye-sensitized solar cells (DSSCs). The significance of this work lies in the combination of favorable experimental and theoretical results in a new class of Ru(ii) polypyridyl complexes with the molecular formula of [Ru(E101)(Dicnq)x(Y)] which is named M101-M104 when X = 1 and Y = bpy, X = 1 and Y = phen, X = 2, and X = 1 and Y = 2 NCS, respectively. E101 and Dicnq ligands are 1,10-phenanthroline-5,6 heptan ammin and 6,7-dicyanodipyrido[2,2-d:2',3'-f]quinoxaline, respectively. The good agreement between the experimental and the time-dependent density functional theory (TDDFT)-calculated absorption spectra of the M101-104 sensitizers allowed us to provide a detailed assignment of the main spectral features of the investigated dyes. M102 which contained phen as an ancillary ligand had the best photovoltaic performance which can be attributed to the higher light harvesting of M102 in the visible light region. A DSSC based on complex M102 without the E101 ligand did not show any observable power conversion efficiency (PCE), indicating the importance of the amphiphilic ligand, E101. Transient absorption studies indicated that the ratio of kreg/krec (krec = the rate constant of the recombination of the dye and kreg = the rate constant of regeneration in the presence of the electrolyte) for M101-104 is 1.1, 2.9, 1.3, and 1.2, clearly confirming a weak competition between dye regeneration and recombination. Therefore, because this ratio for M101, 103, and 104 is small, kreg ≈ krec, the operation of the device has been limited by back electron transports, subsequently enhancing the recombination process. However, the rate of recombination is relatively normal for an efficient DSSC, while the rate of regeneration is very low. Subsequently, the PCE will be poor, confirming the role of aliphatic chains in reducing the recombination process. To obtain a deeper insight into the charge transfer process in the investigated devices, ab initio DFT molecular dynamics simulations and quantum dynamics of electronic relaxation were carried out, clearly showing that the interfacial electron transfer (IET) time scale particularly depends on the type of ancillary ligand. The IET results substantially proved that M102 has the fast lifetime of 2.3 ps and 90 fs for the LUMO and LUMO+1, respectively, indicating the experimentally higher PCE of M102 compared to the other three investigated sensitizers.

Adsorption properties of graphene towards the ephedrine – A frequently used molecule in sport

Adsorption properties of graphene nanosheet (GNS) towards the ephedrine (EPH) molecule, which belongs to a group of the most frequently used active components in sport supplements, have been investigated in details in this study. Different approaches within computational molecular modeling, including density functional theory (DFT), periodic DFT, time dependent DFT (TD-DFT) calculations and molecular dynamics (MD) simulations, have been applied. The study encompassed calculations of binding energies and detailed analysis of noncovalent interactions formed between GNS and EPH. Analysis of density of states and charge distribution was used in order to confirm that the physisorption mechanism is principally responsible for the EPH adsorption by GNS. MD simulations were used in order to determine which hydrogen atom of EPH had more important role in terms of interactivity with GNS. Spectroscopic properties were calculated and simulated in order to identify the most important changes occurring as a consequence of interactions between GNS and EPH. Obtained computational results indicate significant potential of GNS for practical applications for detection, delivery or removal of EPH.

Influence of Mg2+, SO[formula omitted] and Na+ ions of sea water in crude oil recovery: DFT and ab initio molecular dynamics simulations

A detailed understanding of surface interaction between crude oil molecule and calcite can pave a way to explain several fundamental challenges of wettability alteration of calcite surface and hence provide a guidance for further enhancement of crude oil recovery. In the enhanced crude oil recovery stage, additives, Mg2+ and SO42− ions of sea water alter the relative wettability characteristics (from oil-wet to less oil-wet) of calcite surface that enhances the crude oil recovery. In this paper, we consider naphthenic acid is a model compound of crude oil molecule, perform Density Functional Theory (DFT) and ab initio molecular dynamics simulations and checking its relative binding energy (i.e. the binding energy difference between water and oil molecule) is an indication of relative wettability alteration of calcite surface. Ab initio molecular dynamics simulations suggest that Mg2+ ion replaces Ca2+ of calcite and then SO42− ion replaces CO32− of calcite. The relative binding energy of oil molecule is larger on modified calcite.MgSO4 surface than on pure calcite surface, providing an indication of less oil wet calcite surface. Ab initio molecular results also show that few Na+ ions of sea water reach to the calcite surface as a precipitate and form Na naphthenates that make oil molecule more sticker (more oil-wet) to the rock surface. Combined study of DFT and ab initio molecular dynamics simulations can help to understand the surface interaction between oil molecule and calcite surface in aqueous sea water environment that has global impact on crude oil recovery from calcite oil reservoirs.

Effect of Surface Symmetry on the Dissociative Adsorption of Water on Gallium Oxynitride

Recently, gallium oxynitride was shown to be a promising material for photoelectrochemical water-splitting applications. Herein, we perform density functional theory (DFT) calculations to study the effect of surface symmetry and chemistry on the adsorption and dissociation processes of water molecules on spinel type gallium oxonitride (Ga3O3N). We found strong dissociative adsorption of water molecules for both N- and O-rich surfaces with different surface symmetries (i.e., (100), (010), (001), and (111)). In addition, DFT molecular dynamics simulations reveal that water molecules undergo dissociation on all considered Ga3O3N surfaces at room temperature. These interesting findings indicate a promising potential of Ga3O3N for water-splitting applications.

Assessment of DFT Calculations and Molecular Dynamics Simulation on the Application of Zinc Oxide Nanotube as Hydrogen Cyanide Gas Sensor

In this study, to providing the valuable insights into the develop a novel gas sensor for the detection of hydrogen cyanide (HCN), we have employed the molecular dynamics simulation in order to examine the adsorption of carbon monoxide (CO), nitrous oxide (N2O), nitrogen (N2) and HCN gas molecules on the surface of zinc oxide nanotube (ZnONT). More tendencies of the HCN molecules for the adsorption on the nanotube surface contrary to the other considered gases in the simulation study indicate that ZnONT can be a suitable sensor for the HCN gas molecule. Moreover, the detailed studies about the effect of the HCN adsorption on the electronic properties of ZnONT are performed by the density functional theory (DFT) calculation. The negative values of the adsorption energies (Eads) and the small transferred charge from ZnONT to the gas molecule indicate that the adsorption of the HCN gas on the surface of the nanotube is weak. The atom in molecules (AIM) analysis reveals the partially covalent nature of the intermolecular interaction between HCN gas molecule and the nanotube.

Hydrogen bonding and vibrational energy relaxation of interfacial water: A full DFT molecular dynamics simulation.

The air-water interface has been a subject of extensive theoretical and experimental studies due to its ubiquity in nature and its importance as a model system for aqueous hydrophobic interfaces. We report on the structure and vibrational energy transfer dynamics of this interfacial water system studied with equilibrium and non-equilibrium molecular dynamics simulations employing a density functional theory -based description of the system and the kinetic energy spectral density analysis. The interfacial water molecules are found to make fewer and weaker hydrogen (H)-bonds on average compared to those in the bulk. We also find that (i) the H-bonded OH groups conjugate to the free OH exhibit rather low vibrational frequencies (3000-3500 cm-1); (ii) the presence of a significant fraction (>10%) of free and randomly oriented water molecules at the interface ("labile water"), neither of whose OH groups are strong H-bond donors; (iii) the inertial rotation of free OH groups, especially from the labile water, contribute to the population decay of excited free OH groups with comparable rate and magnitude as intramolecular energy transfer between the OH groups. These results suggest that the labile water, which might not be easily detectable by the conventional vibrational sum frequency generation method, plays an important role in the surface water dynamics.

Finite Temperature Properties of NiTi from First Principles Simulations: Structure, Mechanics, and Thermodynamics.

We present a procedure to determine temperature-dependent thermodynamic properties of crystalline materials from density functional theory molecular dynamics (DFT-MD). Finite temperature properties (structural, thermal, and mechanical properties) of the phases (ground state monoclinic B33, martensitic B19', and austenitic B2) of the shape memory alloy NiTi are investigated. Fluctuation formulas and numerical derivatives are used to evaluate mechanical and thermal properties. A modified version of thermodynamic upsampling is used to enable simulations with lower DFT convergence thresholds. In addition, a thermodynamic integration expression is developed to compute free energies from isobaric DFT-MD simulations that accounts for volume changes. Structural parameters, elastic constants, volume expansion, and specific heats as a function of temperature are evaluated. Phase transitions between B2 and B19' and between B19' and B33 are characterized according to their thermal energy, entropy, and free energy differences as well as their latent heats. Anharmonic effects are shown to play a large role in both stabilizing the austenite B2 phase as well as suppressing the martensitic phase transition. The quasiharmonic approximation to the free energy results in large errors in estimating the martensitic transition temperature by neglecting these large anharmonic components.

Effect of surface termination on ion intercalation selectivity of bilayer Ti3C2T2 (T = F, O and OH) MXene

Using density functional theory (DFT) calculations we study the effect of surface functionalization on the response of bilayer Ti3C2T2 (T=F, O and OH) MXene to intercalating ions. In the case of pristine MXene, interlayer spacing (d) increases with introducing both anions and cations. The response of the system to the intercalating ions changes significantly after the surface functionalization: interlayer spacing increases in response to anions, whereas cation intercalation results in the contraction of d. The interplanar distance decreases further with increasing the charge state of the cations, the effect which becomes more pronounced in the case of Ti3C2O2. Such dynamic response of the system to the intercalating ions is also confirmed in both DFT and ReaxFF force field-based molecular dynamics simulations. These results show the importance of surface functionalization to water applications of MXene.

On the influence of junction structures on the mechanical and thermal properties of carbon honeycombs

Carbon honeycomb is a 3-dimensional carbon allotrope experimentally discovered recently, but its lattice structure has not been well identified. In this paper, we perform density-functional theory (DFT) calculations to examine the stability of carbon honeycombs with different configurations (chirality and sidewall width). We find that graphene nanoribbons with both zigzag edges and armchair edges can form stable carbon honeycombs if sp3 carbon-carbon bonding is formed in the junction. We further study the mechanical properties and the thermal conductivity of carbon honeycombs with different chirality and the sidewall widths using both DFT calculations and molecular dynamics simulations. All these stable carbon honeycombs exhibit superior mechanical properties (large strength and ductility) and high thermal conductivity (larger than 100 W/m K) with a density as low as 0.5 g/cm3. Light-weight carbon honeycombs could be promising functional materials for many engineering applications.

First-principles simulations of warm dense lithium fluoride.

We perform first-principles path integral Monte Carlo (PIMC) and density functional theory molecular dynamics (DFT-MD) calculations to explore warm dense matter states of LiF. Our simulations cover a wide density-temperature range of 2.08-15.70gcm^{-3} and 10^{4}-10^{9} K. Since PIMC and DFT-MD accurately treat effects of atomic shell structure, we find a pronounced compression maximum and a shoulder on the principal Hugoniot curve attributed to K-shell and L-shell ionization. The results provide a benchmark for widely used EOS tables, such as SESAME, LEOS, and models. In addition, we compute pair-correlation functions that reveal an evolving plasma structure and ionization process that is driven by thermal and pressure ionization. Finally, we compute electronic density of states of liquid LiF from DFT-MD simulations and find that the electronic gap can remain open with increasing density and temperature to at least 15.7 gcm^{-3}.

DFT Calculations and Molecular Dynamics Simulation Study on the Adsorption of 5-Fluorouracil Anticancer Drug on Graphene Oxide Nanosheet as a Drug Delivery Vehicle

In this work, we have studied the calculations for the interaction of 5-fluorouracil (5-FU) anticancer drug with graphene oxide nanosheet (GONS) using density functional theory (DFT) and molecular dynamics (MD) simulation. The structural and electronic properties of 5-FU molecule interacting with GONS are investigated by DFT methods. The process of 5-FU drug adsorption on different functional groups of GONS is exothermic and the optimized geometries are stable. The interaction energy values indicate that 5-FU molecule can be physically adsorbed on the GONS. It is found that at the most stable structure of 5-FU/GONS complexes, the hydrogen bond (HB) interactions between 5-FU molecule and the functional group of GONS predominate. As well as, the reliable assessment of dynamics drug adsorption on the GO surface is examined by complementing traditional analyses of MD simulations in the water solution at various temperatures (250, 300, 350 and 400 K). MD simulation results show that 5-FU drugs are strongly adsorbed on the Graphene oxide surface by increasing the temperature from 250 to 400 K, as reflected by the most negative van der Waals (vdW) interaction energy and a high number of hydrogen bonds between GONS and drug molecules.

Towards the new heterocycle based molecule: Synthesis, characterization and reactivity study

4-Chloro-2-(3-fluorophenyl)-2,3-dihydro-1H-pyrrolo[3,4-c]pyridin-1-one (CFPDPPO) have been synthesized by hydride transfer from Et3SiH to carbenium ions(reduction reaction), which is formed by reaction between 4-chloro-2-(3-fluorophenyl)-3-hydroxy-2,3-dihydro-1H-pyrrolo[3,4-c]pyridin-1-one with TFA, the single crystals were grown in acetonitrile by slow evaporation technique at room temperature and characterized by single crystal X-ray diffraction, FT-IR, FT-Raman, 1H NMR, 13C NMR and ESI-MS. The experimental vibrational spectra were compared with the calculated spectra and each vibrational wavenumber was assigned on the basis of potential energy distribution (PED). Gauge-including atomic orbital 1H NMR and 13C NMR chemical shifts calculations were carried out and compared with experimental data. The HOMO and LUMO analysis is used to determine the charge transfer within the molecule. The stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analysed using NBO analysis. First hyperpolarizability is calculated in order to find its role in non-linear optics. Besides molecular electrostatic potential (MEP), global reactivity descriptors, thermodynamic properties, and Mullikan charge analysis of the title compound were computed with the same method in gas phase, theoretically. Further, employing combination of DFT calculations and molecular dynamics (MD) simulations, we have investigated in detail reactive properties of the title molecule. Investigation of local reactive properties encompassed calculations of average local ionization energies (ALIE) and Fukui functions. Stability in water has been investigated by calculations of radial distribution functions (RDF), while sensitivity towards the mechanism of autoxidation has been investigated by calculations of bond dissociation energies (BDE). The docked ligand forms a stable complex with human alpha9 nicotinic acetylcholine receptor antagonist and can be a lead compound for developing new anti-cancerous drug.

New quinolone derivative: Spectroscopic characterization and reactivity study by DFT and MD approaches

The spectral characterization of ethyl-4-hydroxy-2-oxo-1, 2-dihydroquinoline-3-carboxylate (EHODQ3C) was performed by FT-IR and FT-Raman spectroscopic techniques and density functional theory computations have been carried using B3LYP/6–311++G(d,p) method. On the basis of potential energy distribution the vibrational assignments of the wavenumbers were proposed. Splitting of the NH stretching mode and downshifted from the computed value which indicates the weakening of the NH bond. NBO analysis was performed to study donor acceptor interactions. DFT calculations and molecular dynamics (MD) simulations have been combined in order to investigate fundamental reactive properties of the title molecule. To determine important reactive molecule sites we have calculated average local ionization energies (ALIE) and Fukui functions. Sensitivity towards autoxidation mechanism has been investigated by calculation of bond dissociation energies, while stability of title molecule in water has been investigated by calculation of radial distribution functions (RDF) after (MD) simulations. EHODQ3C exhibits inhibitory activity against ACP reductase and appears to be highly selective.

Structure and Fluxionality of B13+ Probed by Infrared Photodissociation Spectroscopy.

We use cryogenic ion vibrational spectroscopy to characterize the structure and fluxionality of the magic number boron cluster B13+ . The infrared photodissociation (IRPD) spectrum of the D2 -tagged all-11 B isotopologue of B13+ is reported in the spectral range from 435 to 1790 cm-1 and unambiguously assigned to a planar boron double wheel structure based on a comparison to simulated IR spectra of low energy isomers from density-functional-theory (DFT) computations. Born-Oppenheimer DFT molecular dynamics simulations show that B13+ exhibits internal quasi-rotation already at 100 K. Vibrational spectra derived from these simulations allow extracting the first spectroscopic evidence from the IRPD spectrum for the exceptional fluxionality of B13+ .

Vibrational spectroscopic analysis of cyanopyrazine-2-carboxamide derivatives and investigation of their reactive properties by DFT calculations and molecular dynamics simulations

Using density functional theory technique in the B3LYP approximation and cc-pVDZ (5D, 7F) basis set, the molecular structural parameters and vibrational wave numbers of two cyanopyrazine-2-carboxamide derivatives have been investigated. On the basis of potential energy distribution detailed vibrational assignments of observed FT-IR and FT-Raman bands have been proposed. Using molecular electrostatic potential map relative reactivities towards electrophilic and nucleophilic attack are predicted. The first and second hyperpolarizabilities are calculated and the first hyperpolarizability of the title compounds are greater than that of the standard NLO material urea. Molecular studies reveal that the predicted binding affinities of the best poses were −8.7 kcal/mol for BACPC, −9.0 kcal/mol for CBACPC, and −8.8 kcal/mol for the original inhibitor. Efforts were made in order to investigate local reactivity properties of title compounds as well. In order to do so we have calculated average local ionization energy (ALIE) surfaces, Fukui functions, bond dissociation energies (BDE) (within the framework of DFT calculations) and radial distribution functions (RDF) (within the molecular dynamics simulations). ALIE surfaces and Fukui functions gave us initial information on the site reactivity towards electrophilic and nucleophilic attacks. BDE indicated locations that might be prone to autoxidation mechanism, while RDF indicated which atoms of title molecules are having pronounced interactions with water.

Spectroscopic characterization of 1-[3-(1H-imidazol-1-yl)propyl]-3-phenylthiourea and assessment of reactive and optoelectronic properties employing DFT calculations and molecular dynamics simulations

IR and Raman spectra of 1-[3-(1H-imidazol-1-yl)propyl]-3-phenylthiourea (HIPPT) have been recorded in the solid phase and the vibrational wave numbers are calculated theoretically by B3LYP/6-31G(d,p) (6D, 7F) method. All the fundamental vibrational modes have been assigned using potential energy distribution values and the molecular structure was analyzed in terms of parameters like bond length, bond angles and dihedral angles. The ring breathing mode of the phenyl ring is observed at 1016 cm−1 in the IR spectrum, 1014 cm−1 in the Raman spectrum and at 1014 cm−1 theoretically. The values of polarizability and hyperpolarizabilities were calculated and nonlinear optical properties are discussed. The HOMO-LUMO plot reveals the charge transfer possibilities in the molecule. The NBO analysis was computed and possible transitions were correlated with the electronic transitions. In the title compound, the imidazole ring and CH2 groups are tilted from each other and the thiourea group is tilted from the phenyl ring. Using MEP plot the electrophilic and nucleophilic regions are identified. Local reactivity properties were investigated by analysis of ALIE surfaces and Fukui functions. Oxidation and degradation properties were initially assessed by calculation of bond dissociation energies of all single acyclic bonds. Determination of atoms with pronounced interactions with water molecules was performed by calculation of radial distribution functions after molecular dynamics simulations. Chargehopping rates were calculated within Marcus semi-empiric approach, employing both DFT calculations and MD simulations. The molecular docking computational predictions were complemented by the in vitro antibacterial activity evaluation.

Theoretical investigation of loratadine reactivity in order to understand its degradation properties: DFT and MD study.

Antihistamines are frequently used pharmaceuticals that treat the symptoms of allergic reactions. Loratadine (LOR) is an active component of the second generation of selective antihistaminic pharmaceutical usually known as Claritin. Frequent usage of this type of pharmaceuticals imposes the need for understanding their fundamental reactive properties. In this study we have theoretically investigated reactive properties of LOR using both density functional theory (DFT) calculations and molecular dynamics (MD) simulations. DFT study is used for collecting information related to the molecule stability, structure, frontier molecular orbitals, quantum molecular descriptors, charge distribution, molecular electrostatic potential surfaces, charge polarization, and local reactivity properties according to average local ionization energy surfaces. Based on these results, N24 atom of pyridine ring and oxygen atom O1 were identified with nucleophilic nature. In order to collect the information necessary for the proposition of degradation compounds we also calculated bond dissociation energies (BDE) for hydrogen abstraction and single acyclic bonds as well. According to BDE, the oxidation is likely to occur in the piperidine and cycloheptane rings. MD simulations were used in order to understand the interactions with water through radial distribution functions (RDF). Based on RDFs the most important interactions with solvent are determined for carbon atom C5, chlorine atom Cl15, and oxygen atom O1. Collected results based on DFT calculations and MD simulations provided information important for suggestion of possible degradation compounds. Covalent and noncovalent interactions between LOR and (•)OH have also been investigated.

Spectroscopic characterization of 4-[2-(5-Ethylpyridin-2-yl)ethoxy]benzaldehyde oxime and investigation of its reactive properties by DFT calculations and molecular dynamics simulations

The molecular structure, vibrational wave numbers, NLO, NBO, MEP and HOMO, LUMO analysis of 4-[2-(5-Ethylpyridin-2-yl)ethoxy]benzaldehyde oxime were reported. The theoretically predicted geometrical parameters are in agreement with the XRD data. Using NBO analysis the change in the electron density in the anti-bonding orbital and stabilization energies have been calculated to give clear evidence of stabilization in the hyper-conjugation of hydrogen bonded interactions. The calculated first hyperpolarizability is 46.761 times that of the standard NLO material urea. From molecular electrostatic potential plot, phenyl ring, pyridine ring and oxygen atoms are the most electronegative regions and the hydrogen atom in the OH group is the most electropositive region. ALIE surfaces and Fukui functions have been calculated in order to obtain information related to the local reactivity properties of the title molecule. Intra-molecular non-covalent interactions have also been searched for. In order to investigate autoxidation and degradation properties we have calculated bond dissociation energies for all single acyclic bonds. To determine which atoms have the most pronounced interactions with water molecules we have conducted molecular dynamics simulations and calculated radial distribution functions. Molecular docking studies suggest that the title compound can be a lead compound for developing new anti-cancerous drug.

Phonon-Enabled Carrier Transport of Localized States at Non-Polar Semiconductor Surfaces: A First-Principles-Based Prediction.

Electron-phonon coupling can hamper carrier transport either by scattering or by the formation of mass-enhanced polarons. Here, we use time-dependent density functional theory-molecular dynamics simulations to show that phonons can also promote the transport of excited carriers. Using nonpolar InAs (110) surface as an example, we identify phonon-mediated coupling between electronic states close in energy as the origin for the enhanced transport. In particular, the coupling causes localized excitons in the resonant surface states to propagate into bulk with velocities as high as 10(6) cm/s. The theory also predicts temperature enhanced carrier transport, which may be observable in ultrathin nanostructures.