Level Density Functional Theory Calculations Research Articles

Insights from Density Functional Theory on the Feasibility of Modified Reactive Dyes as Dye Sensitizers in Dye-Sensitized Solar Cell Applications

Recently, reactive dyes have attracted a lot of attention for dye-sensitized solar cell applications. This study endeavors to design dye sensitizers with enhanced efficiency for photovoltaic cells by modifying the reactive blue 5 (RB 5) and reactive brown 10 (RB 10) dyes. Three different strategies were used to design the sensitizers, and their efficiency was compared using the density functional theory (DFT). The optimized geometry, bang gap values, the density of states, electrostatic potential surface analysis, and theoretical FT-IR absorption spectra of the sensitizers were obtained. In the first strategy, functional groups (electron-donating (C2H5), electron-withdrawing (–NO2) groups) were anchored onto dye molecules, and their effect on the charge transport properties was evaluated using the DFT analysis. The latter two designs were based on a donor-π-acceptor strategy. The second design consisted of intramolecular donor-acceptor regions separated by a benzodithiophene-based π-spacer. In the third strategy, an external acceptor unit was attached to the dye molecules through the benzodithiophene-based π-spacer. The electron-donating strengths of donor moieties in the donor-π-acceptor systems were studied using B3LYP/6-31G level DFT calculations. The quantum chemical analysis of the three designs revealed that the anchoring of functional groups (–NO2 and C2H5) on the dye molecules showed no impact on the charge transport properties. The introduction of a benzodithiophene-based π-spacer improved the conjugation of the dye sensitizers, which enhanced the electron transport properties. The electron transport properties further improved when an external acceptor unit was attached to the dye molecule containing a π-spacer. It was thus concluded that attaching an external acceptor unit to the donor dye molecule containing a π-spacer produced desired results for both of the dyes.

Interplay of lattice distortion and electronic structure in BaBiO3

We investigate room temperature core level and valence band spectra of BaBiO3 using x-ray photoemission spectroscopy and band structure calculations. The features in the valence band spectrum were studied using density functional theory (DFT) under local density approximation (LDA) and Tran Blaha modified Becke Johnson (TB mBJ) exchange potential. The calculations were performed for three different structural parameters; monoclinic, cubic and monoclinic (M). Our results of the core level spectrum and DFT calculations rule out charge disproportionation of the Bi ions. The valence band spectrum displays gap at the Fermi edge and fine structures in the region close to the Fermi edge. The DFT calculation under TB mBJ for the monoclinic structure is able to generate gap and match the energy positions of the fine structure in a better way. Our calculation results show that there are holes in the O 2 states and unequal transfer of electrons to the states of the Bi ions. Such mechanism could lead to bond disproportionation and its association with the fine structures in the valence band. The current results reveal the significance of strong link between the lattice distortion and electronic structure and hence to its physical properties.

New insights into the vibrational spectroscopic investigation on S-cis & S-trans forms of 2-Methoxy benzoyl chloride

The conformal stability of 2-Methoxy benzoyl chloride (2MBC) in its S-cis and S-trans forms was investigated using Density Functional Theory (DFT) calculations and Potential energy surface scan analysis. The experimental (FT-IR and FT-Raman) spectra were recorded in the condensed phase in order to perform detailed vibrational analysis. Different basis sets were adopted during optimization procedure and the suitable method was identified from the results obtained. The optimized geometry and vibrational wavenumbers were determined by using B3P86/6-31++G(d,p) level Density Functional Theory calculations and was found to be the most suitable one. The effect of scaling on the calculated wavenumbers was analyzed by employing unscaled, uniform scaling and selective scaling procedures. A detailed comparative analysis of the effect of hydrogen bonding on the geometry and structural parameters of both the conformers has been carried out using the results obtained from DFT level calculations. The results from the above studies reveal that, the presence of intramolecular hydrogen bond in S-cis conformer of 2MBC has significantly altered the geometrical parameters and hence the vibrational wavenumbers. The difference in electron transfer mechanism of the two different environments (S-cis and S-trans) was thoroughly investigated using Natural Bond Orbital analysis.

New insights into the conformal stability, influence of hydrogen bonding and vibrational analysis of 2,6- and 3,5-Dihydroxyacetophenone – A comparative study

The conformal stability of 2,6-Dihydroxyacetophenone (DHAP I) and 3,5-Dihydroxyacetophenone (DHAP II) were investigated using Potential Energy Surface scan studies and B3LYP/6-31G** level Density Functional Theory(DFT) calculations. The experimental (FT-IR and FT-Raman) spectra were recorded in the condensed phase in order to perform detailed vibrational analysis. The optimized geometry and vibrational wavenumbers were determined by using B3LYP/6-31G** level Density Functional Theory calculations. The effect of scaling on the calculated wavenumbers was analyzed by employing unscaled, uniform scaling and selective scaling procedures. A detailed comparative analysis on the effect of hydrogen bonding on the geometry, structural parameters and vibrational wavenumbers has been carried out using the results obtained from PES scan and DFT level calculations. The results from the above studies reveals that, the presence of strong intramolecular hydrogen bond in DHAP I has significantly altered the geometrical parameters and hence the vibrational wavenumbers. The hydrogen bonding in DHAP I is strong enough to make it more stable compared to that of DHAP II.

Embedded-cluster calculations in a numeric atomic orbital density-functional theory framework.

We integrate the all-electron electronic structure code FHI-aims into the general ChemShell package for solid-state embedding quantum and molecular mechanical (QM/MM) calculations. A major undertaking in this integration is the implementation of pseudopotential functionality into FHI-aims to describe cations at the QM/MM boundary through effective core potentials and therewith prevent spurious overpolarization of the electronic density. Based on numeric atomic orbital basis sets, FHI-aims offers particularly efficient access to exact exchange and second order perturbation theory, rendering the established QM/MM setup an ideal tool for hybrid and double-hybrid level density functional theory calculations of solid systems. We illustrate this capability by calculating the reduction potential of Fe in the Fe-substituted ZSM-5 zeolitic framework and the reaction energy profile for (photo-)catalytic water oxidation at TiO2(110).

New crystalline salt forms of levofloxacin: conformational analysis and attempts towards the crystal structure prediction of the anhydrous form

Structural information on the anhydrous forms of levofloxacin, a broad spectrum fluoroquinolone antibiotic drug, is limited as it readily converts into the more stable hemihydrate form. Obtaining single crystals of the anhydrous form will be a challenge in this situation. Herein, we report six novel carboxylic acid salt forms of levofloxacin and our attempts towards the crystal structure prediction of its anhydrous form. In-depth analysis of various possible conformations of levofloxacin was performed with the help of high level density functional theory calculations. Useful structural insights obtained from crystal structure analysis of two known hydrates and six new salt forms of levofloxacin were utilized to identify the most probable supramolecular synthons. Synthon information obtained from these crystalline forms was used in the re-ranking of computationally generated crystal structures to arrive at a set of most probable crystal structures for the anhydrous form. A comparison of the crystal structures of the two hydrate forms with the predicted anhydrous form of levofloxacin was performed to understand the hydration–dehydration behaviour.

Density-functional study on the equilibria in the ThDP activation

The equilibria among the various ionization and tautomeric states involved in the activation of ThDP is addressed using high level density functional theory calculations, X3LYP/6-311++G(d,p)//X3LYP(PB)/6-31++G(d,p). This study provides the first theoretically derived thermodynamic data for the internal equilibria in the activation of ThDP. The role of the medium polarity on the geometry and thermodynamics of the diverse equilibria of ThDP is addressed. The media chosen are cyclohexane and water, as paradigms of apolar and polar media. The results suggest that all ionization and tautomeric states are accessible during the catalytic cycle, even in the absence of substrate, being APH(+) the form required to interconvert the AP and IP tautomers; and the generation of the ylide proceeds via the formation of the IP form. Additionally, the calculated ΔG° values allow to calculate all the equilibrium constants, including the pK(C2) for the thiazolium C2 atom whose ionization is believed to initiate the catalytic cycle.

Exploring the bond topological and electrostatic properties of benzimidazole molecule via experimental and theoretical charge density study

The experimental electron density distribution of benzimidazole has been determined from multipole refinement model using accurate high resolution X-ray diffraction intensity data collected at 100 K. The theoretical charge density distribution was calculated from high level Density functional theory calculations, using B3LYP method with the basis set 6-311G **. The bond topological analysis of the experimental electron density shows the difference of charge density distribution between homo and hetero-atomic bonds in the molecule. Further, the difference of molecular charge density between theory and experiment explicitly reveals the influence of crystal field effect in the experimental electron density distribution. The isosurface of molecular electrostatic potential shows the electro positive and negative regions of the molecule. A large negative potential found at the vicinity of nitrogen atom. The bond topological parameters of N H⋯N intermolecular hydrogen bonding interaction confirm the strength of this interaction.

Synthesis and formation mechanism of hydrogenated boron clusters B12Hn with controlled hydrogen content

We present the formation of hydrogen-content-controlled B(12)H(n) (+) clusters through the decomposition and ion-molecule reactions of the decaborane (B(10)H(14)) and diborane (B(2)H(6)) molecules in an external quadrupole static attraction ion trap. The hydrogen- and boron-contents of the B(10-y)H(x) (+) cluster are controlled by charge transfer from ambient gas ions. In the process of ionization, a certain number of hydrogen and boron atoms are detached from decaborane ions by the energy caused by charge transfer. The energy caused by the ion-molecule reactions also induces H atom detachment. Ambient gas of Ar leads to the selective generation of B(10)H(6) (+). The B(10)H(6) (+) clusters react with B(2)H(6) molecules, resulting in the selective formation of B(12)H(8) (+) clusters. Ambient gas of Ne (He) leads to the generation of B(10-y)H(x) (+) clusters with x=4-10 and y=0-1 (with x=2-10 and y=0-2), resulting in the formation of B(12)H(n) (+) clusters with n=4-8 (n=2,4-8). The introduction of ambient gas also increases the production of clusters. PBE0/6-311+G(d)//B3LYP/6-31G(d)-level density functional theory calculations are conducted to investigate the structure and the mechanism of formation of B(10-y)H(x) (+) and B(12)H(n) (+) clusters.

Multiple ionization and fragmentation of fullerene dimers by highly charged ion impact

We have studied the stabilities of multiply charged van der Waals dimers in slow Xe30+ + [C60]2([C60C70], [C70]2) → Xe(30-s)+ + [C60]2r+([C60C70]r+, [C70]2r+) + (r-s)e-electron-transfer collisions (v = 0.4 a.u. and r ≤ 7). The relative ionization cross sections display even-odd variations as functions of r for [C60]2r+, [C60C70]r+, and [C70]2r+. This is in clear contrast to the typical smooth decreasing behavior of the cross sections for multiple ionization of fullerene monomers, which can be explained within the framework of the classical over-the-barrier model. In addition, we report the branching ratios and the kinetic energy releases for the dominant fragmentation processes that yield intact fullerenes. The experimental results are discussed in view of a simple electrostatic model for dimer ionization and recent results from high level density functional theory calculations.

Trans-1,2-Dicyano-cyclopropane and other cyano-cyclopropane derivatives

In this work we present the experimental vibrational absorption (VA), vibrational circular dichroism (VCD) and Raman spectra for (+)-trans-1(S),2(S)-dicyanocyclopropane and its dideuterio derivative, trans-1(S),2(S)-dicyano-1(S),2(S)-dideuteriocyclopropane, along with VA, VCD, Raman and Raman optical activity (ROA) spectral simulations. Here we investigate the applicability of various local and non-local exchange-correlation (XC) functionals, hybrids and meta-hybrids to reproduce the vibrational spectra of this strained ring system, which also bears two cyano groups. At the highest level of theory, B3PW91/ aug-cc-pVTZ, we also investigated the trans-, cis- and gem-dicyanocyclopropane (trans-, cis-, and gem-DCCP), cyanocyclopropane (CCP) and the parent molecule cyclopropane (CP). In doing so we have investigated the electronic effects (coupling) between the cyano groups and the cyclopropane ring. In addition to providing an interpretation of the experimentally observed vibrational spectra for these molecules, this work also provides benchmark calculations for other methods, especially semi-empirical based wave function and density functional theory (DFT) based methods, such as SCC-DFTB and PM6. For the semi-empirical DFT based methods to be used for 3-membered ring systems, one ought to document their reliability for systems which were not used in the parameterization. The small 3- and 4-membered ring systems are good test systems because they contain non-standard bonding, which may be difficult to determine accurately with the approximations used in the SCC-DFTB and other semi-empirical methods. Like molecular mechanics force fields, semi-empirical methods, based on DFT and wave function quantum mechanics (WFQM), must be benchmarked against high level ab initio and DFT calculations and experimental data. In addition to bonding, the changes in the electric dipole moment, magnetic dipole moment, electric dipole-electric dipole polarizability, electric dipole-magnetic dipole polarizability and electric dipole-electric quadrupole polarizability with respect to nuclear displacement and nuclear velocity can be determined by the VA, VCD, Raman and ROA intensities. Hence it is important that the semi-empirical based DFT and wave function methods not only be parameterized to determine energies, gradients and Hessians, but also the electric and magnetic moments and their derivatives that determine the electronic and magnetic properties of these molecules and their interactions with matter and radiation. This will allow biochemists, biophysicists, molecular biologists, and physical biologists to use experimental and theoretical VA, VCD, Raman and ROA spectroscopies to probe biophysical and biochemical function and processes at the molecular level.

Spiroleucettadine: synthetic studies and investigations towards structural revision

Synthetic efforts towards spiroleucettadine are described, including the enantioselective synthesis of the presumed biosynthetic precursor. High level density functional theory calculations were used to predict the 13C NMR shifts of possible alternative structures and, along with a re-evaluation of the available NMR data, allow the proposal of revised structures for this spirocyclic alkaloid.

Mg-Based Nanocomposites with High Capacity and Fast Kinetics for Hydrogen Storage

Magnesium and its alloys have shown a great potential in effective hydrogen storage due to their advantages of high volumetric/gravimetric hydrogen storage capacity and low cost. However, the use of these materials in fuel cells for automotive applications at the present time is limited by high hydrogenation temperature and sluggish sorption kinetics. This paper presents the recent results of design and development of magnesium-based nanocomposites demonstrating the catalytic effects of carbon nanotubes and transition metals on hydrogen adsorption in these materials. The results are promising for the application of magnesium materials for hydrogen storage, with significantly reduced absorption temperatures and enhanced ab/desorption kinetics. High level Density Functional Theory calculations support the analysis of the hydrogenation mechanisms by revealing the detailed atomic and molecular interactions that underpin the catalytic roles of incorporated carbon and titanium, providing clear guidance for further design and development of such materials with better hydrogen storage properties.

Identification, Structure, and Spectroscopy of Neutral Vanadium Oxide Clusters

Neutral vanadium oxide clusters are studied by photoionization time-of-flight (TOF) mass spectroscopy, electronic spectroscopy, and density functional theory (DFT) calculations. Mass spectra of vanadium oxide clusters are observed by photoionization with lasers of three different wavelengths: 118, 193, and 355 nm. Mechanisms of 118 nm single photon ionization and 193 and 355 nm multiphoton ionization/fragmentation of vanadium oxide clusters are discussed on the basis of observed mass spectral patterns and line widths of the mass spectral features. Only the 118 nm laser light can ionize vanadium oxide neutral species by single photon ionization without fragmentation. The stable vanadium oxide neutral clusters under saturated oxygen growth conditions are found to be of the form (VO2)x(V2O5)y. Structures of the first few members of this series of clusters are determined through high level DFT calculations. Fragmentation of this series of clusters through 355 and 193 nm multiphoton ionization processes is discussed in light of these calculated structures. The B(2)B2 <-- X(2)A1 transition is observed for the VO2 neutral species, and nu1 and nu2 vibrations are assigned for both electronic states. From this spectrum, the VO2 rotational and vibrational temperatures are found to be approximately 50 and approximately 700 K, respectively.

Design of 2-cyclopentenone derivatives with enhanced NF-κB: DNA binding inhibitory properties

In this work we derived a series of new inhibitors for the association between nuclear factor kappa B (NF-κB) and the corresponding κB site in DNA. They were derived through optimization of the lead compound 2-cyclopentenone (CP), which corresponds to the reactive unit of natural product 15-Deoxy-Δ 12,14-prostaglandin J 2 (PGJ2). Both CP and PGJ2 possess demonstrated inhibitory efficiency for this and other biological important systems. We began by studying the docking of CP to NF-κB. Subsequently, a set of rational strategies were derived to insert substituents into CP which increase its association to NF-κB, in terms of both the affinity and the specificity. Molecular mechanics calculations have been performed to decide on the suitability of the substitutions, and to evaluate the energies of association with NF-κB. One of the important chemical properties of CP is that it is a weak electrophile, hence it selects attacking nucleophilic sites in proteins, rather than the nucleic acids. To assure that the designed compounds were not substantially more reactive than CP we performed high level density functional theory calculations. Important conclusions have been obtained concerning the optimization of this inhibitor; namely, a set of methodologies for rational drug design have been derived to enhance the affinity of the CP derivatives to NF-κB. The efficacy of these methodologies has been demonstrated by generating a set of substituted CPs, exhibiting increased affinity for NF-κB, and opening new ways to broaden the therapeutic applications of this class of drugs.

Interaction of MSn (MRu, Rh, Pd) dimers with CH2 and CF2: A density functional study

AbstractThe importance of Sn to improve the performance of noble metal‐based catalysts has been extensively discussed in the literature. However, a detailed discussion about the effect of Sn on the electronic structure of the metals has not been reported so far. In this work, density functional theory (DFT) calculations have been performed on the M2 and MSn (MRu, Rh, Pd, Sn) dimers and their interaction with CH2 and CF2 carbenes. The electronic structure, geometry, and harmonic frequencies are reported and compared with the available experimental data and to the previous published high level ab initio and DFT calculations. The calculated values of M2 are in good agreement with the experimental and theoretical results. The exception is the binding energy of the Sn dimer, which can be different from the experimental estimates as much as 16 kcal · mol−1. It has been stressed that this difficulty is related to the atomic energy reference used to estimate the binding energy. Transition metal elements are still a difficult task for DFT methods. Calculations on MSnCH2 and MSnCF2 species with different multiplicities and conformations have been performed. Bonding analyses on the MSn metal dimers showed that carbenes prefer to adsorb in bridge sites favoring a donating/backdonating mechanism of interaction that is enhanced with the presence of the Sn atom. The MSnCH2 binding energy is predicted to be 40% smaller than the MSnCF2 binding energy, following the same trends observed for the first‐row transition‐metal MCH2 and MCF2 complexes. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 95: 164–176, 2003

Substituent Effects on Enthalpies of Formation: Benzene Derivatives

High level density functional theory calculations have been carried out for a benchmark set of benzene derivatives, including methyl, ethyl, n-propyl, i-propyl, tert-butyl, phenyl, and benzyl groups as substituents. Geometries were obtained using the B3LYP method and three basis set expansions, namely 6-31G(d), 6-311G(d,p), and 6-311++G(d,p). Final energies were calculated in B3LYP/6-311+G(3df,2p) single-point calculations. Based on these calculations the performance of different theoretical schemes aiming at reproducing substituent effects on enthalpies of formation has been assessed. The poorest performance is obtained when atomization energies or isodesmic reactions are used. No significant improvement is found when using homodesmotic processes. A significant improvement is achieved when the isodesmic processes used involve the unsubstituted parent compound. That means that this procedure can be a good alternative to explore substituent effects on the enthalpies of formation, although the absolute values of this thermodynamical magnitude have still a significant error. The best performance is obtained when different atom equivalent schemes are used, the correlation coefficient of the linear relationship between calculated and experimental values being greater than 0.999.

A Density Functional Theory Investigation of the Simmons−Smith Cyclopropanation Reaction: Examination of the Insertion Reaction of Zinc into the C−I Bond of CH2I2 and Subsequent Cyclopropanation Reactions

The insertion reaction of zinc into the C-I bond of CH(2)I(2) and subsequent cyclopropanation reactions with CH(2)CH(2) have been investigated using B3LYP level density functional theory calculations. The Simmons-Smith cyclopropanation reaction of olefins does not proceed easily due to the relatively large barriers on the insertion and cyclopropanation pathways. The computed results indicate that the IZnCH(2)I molecule is the active reagent in the Simmons-Smith reaction. This is consistent with the IZnCH(2)I reactive species being generated from diiodomethane and a Zn-Cu couple as proposed by several other research groups. The Simmons-Smith IZnCH(2)I carbenoid and CH(2)I-I carbenoid cyclopropanation reactions with olefins are compared. The reactions of olefins with the radicals from the decomposition of the IZnCH(2)I and CH(2)I-I species were also compared. We found that the chemical reactivity of the carbenoid species is dependent on its electrophilic behavior, steric effects, the leaving group character and the mechanism of the cyclopropanation reactions.

Cr +(H 2) n clusters: Asymmetric bonding from a symmetric ion

Equilibrium methods were used to measure ΔH T °, ΔS T ° and ΔH 0° for the sequential clustering of up to 6 H 2 ligands to a 3d 5 6S Cr + core ion. The binding energies are the weakest yet measured for a d n ion, averaging 4.5 kcal mol −1 and ranging from ∼9 kcal mol −1 for n = 2 down to ∼1 kcal mol −1 for n = 6. High level density functional theory calculations were performed to provide structural information and to help analyse and interpret the data. One definite result is that detailed covalent interactions between the “spherical” 3d 5 Cr + ion and the H 2 ligands are required to explain the data. Both the vacant 4s orbital and, to a lesser extent, the high energy 4p orbitals are involved in hybridization of the 3d orbitals in order to minimize dσ repulsion, maximize σ donation by the H 2 ligands, and maximize back donation into the σ ∗ orbitals of the H 2 ligands. A stable planar D 3h ion appears for n = 3 and again as the core of a trigonal bipyramid for n = 5. Comparisons with results from other first row transition metal ions are made.