Employing DFT Calculations Research Articles

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.

The Electronic Spectrum of the Fulvenallenyl Radical

AbstractThe fulvenallenyl radical was produced in 6 K neon matrices after mass‐selective deposition of C7H5− and C7H5+ generated from organic precursors in a hot cathode ion source. Absorption bands commencing at λ=401.3 nm were detected as a result of photodetachment of electrons from the deposited C7H5− and also by neutralization of C7H5+ in the matrix. The absorption system is assigned to the 1 2B1←X 2B1 transition of the fulvenallenyl radical on the basis of electronic excitation energies calculated with the MS‐CASPT2 method. The vibrational excitation bands detected in the spectrum concur with the structure of the fulvenallenyl radical. Employing DFT calculations, it is found that the fulvenallenyl anion and its radical are the global minima on the potential energy surface among plausible structures of C7H5.

The Electronic Spectrum of the Fulvenallenyl Radical.

The fulvenallenyl radical was produced in 6 K neon matrices after mass-selective deposition of C7H5(-) and C7H5(+) generated from organic precursors in a hot cathode ion source. Absorption bands commencing at λ=401.3 nm were detected as a result of photodetachment of electrons from the deposited C7H5(-) and also by neutralization of C7H5(+) in the matrix. The absorption system is assigned to the 1 (2)B1 ←X (2)B1 transition of the fulvenallenyl radical on the basis of electronic excitation energies calculated with the MS-CASPT2 method. The vibrational excitation bands detected in the spectrum concur with the structure of the fulvenallenyl radical. Employing DFT calculations, it is found that the fulvenallenyl anion and its radical are the global minima on the potential energy surface among plausible structures of C7H5.

Theoretical investigation on homoleptic Yttrium tri-guanidinates

The electronic and molecular structures of the homoleptic Yttrium tris-guanidinates complexes Y[(NiPr)2CNR1R2]3, [R1=R2=Me, Et and iPr] have been investigated employing DFT calculations in order to understand the structures, bonding and energies of the interactions between Yttrium metal and guanidinate ligands. The effect of the substitution on nitrogen position of guanidinate in these complexes has been also investigated employing DFT and TDDFT calculations for six kinds of models obtained by alternative substitution of alkyl on nitrogen of the guanidinate ligands. The results reveal that the substitution position plays a crucial role in the geometric structure by affecting the torsion angle and the HOMO–LUMO transitions. The energy decomposition analysis indicates a majority of ionic bonding in all systems; the exception is in the M4 (Y[(NYR)2CNCR1R2]3; R=Et and R1=R2=H) which present a significant degree of covalency.

Design of an organic redox mediator and optimization of an organic counter electrode for efficient transparent bifacial dye-sensitized solar cells

A new thiolate/disulfide mediator was designed and synthesized by employing DFT calculations as a guide. It possesses high transparency to visible light, a very attractive feature for bifacially active transparent DSCs that require a highly transparent counter electrode (CE). Compared to the reported and most promising thiolate/disulfide mediator T(-)/T(2), this new analogous mediator produced a major enhancement in open circuit potential (V(OC)) by about 40 mV and correspondingly a higher power conversion efficiency (η) for DSCs. Furthermore, a highly uniform and transparent (transmittance > 91%) poly(3,4-ethylenedioxythiophene) (PEDOT(BE)) CE was prepared and could efficiently catalyze the reduction of the disulfide. Based on the novel transparent redox couple and PEDOT(BE) CE, a new type of iodine-free and Pt-free transparent bifacial DSC was successfully fabricated. This new bifacial device could not only yield a promising front-illuminated η of 6.07%, but also produce an attractive η as high as 4.35% for rear-side irradiation, which exceeds the rear-illuminated η of 3.93% achieved for the same type of device, employing the dark-colored I(-)/I(3)(-) electrolyte.

Origin of improved visible photocatalytic activity of nitrogen/hydrogen codoped cubic In2O3: first-principles calculations

We have employed DFT calculations to carry out an accurate analysis of the effect of N- and NH-doping on the visible photocatalytic activity in the cubic In(2)O(3). In the substitutional N-doped In(2)O(3), the 2p impurity states of N induce a red shift in the optical absorption, while in the interstitial N-doping the red shift is dominantly caused by the localized π antibonding states of NO. When a H atom is accompanied by a N impurity in the lattice, the H atom acts as a charge donor and compensates the hole state created by N-doping, thus the energy level of the impurity states is reduced. As a result, the mixing of impurity states and the valence band is enhanced. At the same nitrogen dopant concentration, NH-codoping yields a larger band gap narrowing, especially for the interstitial NH-codoping. The theoretical calculations presented in this work explain well the previous experimental results of the enhanced visible photocatalytic activity in NH-codoped cubic In(2)O(3).

Designing Structural Motifs for Clickamers: Exploiting the 1,2,3‐Triazole Moiety to Generate Conformationally Restricted Molecular Architectures

Noncovalent interactions, especially hydrogen-bonding interactions as well as electrostatic forces, confined within one macromolecule are the key to designing foldamers that adopt well-defined conformations in solution. In the context of significant recent activities in the area of triazole-connected foldamers, so-called clickamers, we present a fundamental study that compares various model compounds that bear adjacent N-, O-, or F-heteroatom substituents. The interplay of attractive and repulsive interactions leads to rotational constraints around the single bonds attached to both the 1- and 4-positions of the 1,2,3-triazole moiety and should therefore be able to induce well-defined conformational preferences in higher oligomers and polymers, that is, foldamers. Various compounds were synthesized and characterized with regard to their preferred conformations in all three aggregation states--that is, in the gas phase, in solution as well as in the solid state--by employing DFT calculations, NMR spectroscopic experiments, and X-ray crystallography, respectively. On the basis of the thus-obtained general understanding of the conformational behavior of the individual connection motifs, heterostructures were prepared from different motifs without affecting their distinct folding characteristics. Therefore, this work provides a kind of foldamer construction kit, which should enable the design of various clickamers with specific shape and incorporated functionality.

A one step/one pot synthesis of N, N-bis(phosphonomethyl)amino acids and their effects on adipogenic and osteogenic differentiation of human mesenchymal stem cells

The one pot reaction of amino acids with diethylphosphite and formaldehyde yielded N, N-bis(phosphonomethyl)amino acids. This synthetic route does not require harsh reagents to cleave the ester group. The molecular structures of the new compounds were determined by X-ray diffraction methods. By employing DFT calculations the hydrolysis of the intermediate phosphonic esters to the respective acids could be explained by the decreasing P–OEt bond strength for C α-bisalkylated amino acids. Biological evaluation on the adipogenic and osteogenic differentiation of mesenchymal stem cells revealed no modification of the adipocyte differentiation, but inhibition of osteoblast formation at concentrations without detectable cytotoxicity.

Probing the influence of pH dependent citric acid towards the morphology of rock salt: a computational study

The influence of citric acid under different pH conditions towards the morphology of sodium chloride was investigated employing DFT calculations. Prior to any analysis, conformational search of citric acid and its three dissociated forms was performed with molecular mechanics MM2* and DFT (B3LYP/6-31+G*) methods in the gas and aqueous phase. The low energy conformers generated in the aqueous phase were found to be in good agreement with the available crystal structures. The calculated higher composition of citric acid at natural pH = 0.75 i.e., α0 = 0.99 is not effective for the habit modification of sodium chloride. Quantum chemically derived molecular electrostatic potential (MESP) showed the possible sites of citric acid and its dissociated forms with the estimated deepest Vmin values and their magnitudes provide an insight for their interaction with the crystal surfaces of sodium chloride. The composition analysis and MESP derived data suggest that the dissociated forms of citric acid at higher pH values are responsible for the change in habit of sodium chloride from cubes to octahedrons. Further, slab model calculations performed to mimic the surfaces of sodium chloride with DFT methods using a conductor-like screening model in the aqueous phase (COSMO) for the interactions of citric acid and dihydrogen citrate validates that there is no preference for the {111} plane of NaCl with citric acid. However, a significant preference was seen with dihydrogen citrate, which quantifies the MESP analysis and corroborates the dependence of morphology on the pH of the solution.

First-principles study of the hydrogen doping influence on the geometric and electronic structures of N-doped TiO 2

We employed DFT calculations to study the geometric and electronic structures of N- and NH-doped anatase TiO 2 systems. With N dopant concentrations of 2.1% and 1.0%, the substitutional NH-doping resulted in bandgap narrowings of 0.12 and 0.13 eV, respectively, very close to that resulted from substitutional N-doping (0.12 and 0.11 eV). For interstitial N- and NH-doping with a nitrogen concentration of 2.1%, only NH-doping resulted in a bandgap narrowing of 0.07 eV. For both substitutional and interstitial NH-doping configurations, the crystalline structure adjacent to the NH dopants was heavily distorted, which might enhance the photocatalytic efficiency.

Conformational evaluation and detailed 1H and 13C NMR assignments of flavoxate, a urinary tract antispasmodic agent

1H and 13C NMR chemical shift assignments for the urinary tract antispasmodic flavoxate ( 1) and flavoxate hydrochloride ( 2) were obtained from one- and two-dimensional measurements. A Monte Carlo random search using molecular mechanics, followed by geometry optimization of each minimum energy structure employing DFT calculations at the B3LYP/6-31G* level, and a Boltzmann analysis of the total energies, provided accurate molecular models which describe the conformational behavior of flavoxate ( 1). The electron density surfaces for the global minimum and the second minimum conformers 1a and 1b of this L-type Ca 2+ channel inhibitor were calculated. The presence of both conformers in solution was demonstrated in full agreement with 2D NOESY data and NOE difference spectroscopy.

Cyano- and Isocyanotris(trifluoromethyl)borates: Syntheses, Spectroscopic Properties, and Solid State Structures of K[(CF3)3BCN] and K[(CF3)3BNC

A two step synthesis to the isocyanotris(trifluoromethyl)borate anion, [(CF3)3BNC]-, and its isomerization to the cyanotris(trifluoromethyl)borate anion, [(CF3)3BCN]-, at temperatures above 150 degrees C are presented. In the first step (CF3)3BNCH was obtained by reacting (CF3)3BCO with hydrogen cyanide followed by deprotonation of the HCN adduct with Li[N(SiMe3)2] in toluene. The thermal behavior of K[(CF3)3BNC] and K[(CF3)3BCN] were investigated by differential scanning calorimetry (DSC), and K[BF4] was identified as a major solid decomposition product. The enthalpy of the isocyanide-cyanide rearrangement, deltaH(iso) = -35 +/- 4 kJ mol(-1), was obtained from DSC measurements, and the activation energy, E(a) = 180 +/- 20 kJ mol(-1), from kinetic measurements. The isomerization was modeled as an intramolecular reaction employing DFT calculations at the B3LYP/6-311+G(d) level of theory yielding a reaction enthalpy of deltaH(iso) = -36.1 kJ mol(-1) and an activation energy of E(a) = 155.7 kJ mol(-1). The solid-state structures of K[(CF3)3BNC] and K[(CF3)3BCN] were determined by single-crystal X-ray diffraction. Both salts are isostructural and crystallize in the orthorhombic space group Pnma (no. 62). In the crystals the borate anions possess C(s) symmetry, while for the energetic minimum C3 symmetry is predicted by DFT calculations. The borate anions have been characterized by IR and Raman spectroscopy as well as by NMR spectroscopy. The assignment of the IR and Raman bands is supported by their calculated wavenumbers and intensities. The spectroscopic and structural properties of both borate anions are compared to the properties of the isoelectronic borane carbonyl (CF3)3BCO and the [B(CF3)4]- anion as well as to those of other related species.

Infrared Spectra and Structure of C60 Heterocyclic Derivatives

Infrared spectra of a number of C60 cycloaddition products, namely, fullerenopyrroline and fullerenopyrazolines with the substituents in the heterocyclic fragments have been studied experimentally and employing DFT calculations. Complete vibrational assignment is proposed.