Absorption and fluorescence emission spectroscopic characters of naphtho‐homologated yy‐DNA bases and effect of methanol solution and base pairing

A comprehensive theoretical study of electronic transitions of naphtho‐homologated base analogs, namely, yy‐T , yy‐C , yy‐A , and yy‐G , was performed. The nature of the low‐lying excited states is discussed, and the results are compared with those from experiment and also with those of y‐bases. Geometrical characteristics of the lowest excited singlet ππ* and nπ* states were explored using the CIS method, and the effects of methanol solution and paring with their complementary natural bases on the relevant absorption and emission spectra of these modified bases were examined. The calculated excitation and emission energies agree well with the measured data, where experimental results are available. In methanol solution, the fluorescence from yy‐A and yy‐G would be expected to occur around 539 and 562 nm, respectively, suggesting that yy‐A is a green‐colored fluorophore, whereas yy‐G is a yellow‐colored fluorophore. The methanol solution was found to red‐shift both the absorption and emission maxima of yy‐A , yy‐T , and yy‐C , but blue‐shift those for yy‐G . Generally, though base pairing has no significant effects on the absorption and fluorescence maxima of yy‐A , yy‐C , and yy‐T , it blue‐shifts those for yy‐G . © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Characterization of electronic structure and physicochemical properties of antiparasitic nifurtimox analogues: A theoretical study

American trypanosomiasis, also known as Chagas' disease, is caused by Trypanosoma cruzi (T. cruzi). It is well known that trypanosomes, and particularly T. cruzi, are highly sensitive towards oxidative stress, i.e., to compounds than are able to produce free radicals. Generally, nifurtimox (NFX) and benznidazol are most effective in the acute phase of the disease; therefore, nitroheterocycles constitute good models to design other nitrocompounds with specific biological characteristics. Thus, we have performed an ab initio study at the Hartree‐Fock and Density Functional Theory levels of theory of several NFX analogues recently synthesized, to characterize them by obtaining their electronic, structural, and physicochemical properties, which might be linked to the observed antichagasic activity. The antitrypanosomal activity scale previously reported for the NFX analogues studied in this work is in good agreement with our theoretical results, from which we can conclude that the activity seems to be related to the reactivity along with the acidity observed for the most active molecules. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Variation of spectral, structural, and vibrational properties within the intrinsically fluorescent proteins family: a density functional study

We report an extensive (time-dependent) density functional study of the whole series of the chromophores within the Intrinsically Fluorescent Protein family, in the relevant conformations and protonation states. Over 30 structures are considered, including three newly discovered chromophores (zFP, Kaede, and the Orange variant of DsRed). Ab initio calculations on selected structures are also performed in order to assess the performances of TDDFT along the family. The use of a uniform scheme for all structures allows to establish relationships between the absorption energy and electrostatic, structural or vibrational properties of the chromophores.     

A theoretical study of porphyrin isomers and their core-modified analogues: cis-trans isomerism, tautomerism and relative stabilities

Semiempirical (AM1 and PM3) and density functional theory (DFT) calculations were performed on about 50 porphyrin isomers with 25 each of 1,2 (syn) and 1,3 (anti) tautomeric forms. The corresponding oxa-and thia-core-modified analogues were also computed. The variations of relative energies and stabilities of the core-modified analogues were compared with parent porphyrin1 and the corresponding oxa-and thia-analogues. The trends in relative energies are not significantly changed while going from parent system to oxa-and thia-core-modified porphyrins in case of bothsyn andanti tautomers. Isomers of types [2·2·0·0], [3·0·1·0], [3·1·0·0], and [4·0·0·0] are destabilized due to the absence of methine bridge, which results in angle strain for tetrapyrroles. Isomers having [2·1·1·0], [2·1·0·1], [2·0·2·0] and [2·2·0·0] connectivity, the Z isomers, are more stable compared to the correspondingE isomers in bothsyn andanti forms of parent and core-modified analogues.     

Solvent effects on the geometry,electronic structure,and bonding style of Zn(N5)2: A theoretical study

Nitrogen-rich compounds involving the cyclo-pentazole anion (cyclo-N₅⁻) have attracted extensive attention due to higher energy release and environmental friendliness than traditional high energy density materials (HEDMs). However, the synthesis of stable HEDMs with cyclo-N₅⁻ is still a challenge. In this study, the effect of nine solvents on the geometrical and electronic structures and solvation energies of Zn(N₅)₂, one of the recently synthesized nitrogen-rich compounds, was studied using the density functional theory and the polarized continuum model. The results indicated an increase in the stability of Zn(N₅)₂ in the solution phase compared to the vacuum phase, and the stability of Zn(N₅)₂ increases with increasing dielectric constants. The energy gap of frontier molecular orbitals and the absolute value of total energy in water are the largest, revealing that Zn(N₅)₂ is more stable in water than in other solvents. To understand the stabilization mechanism of Zn(N₅)₂ by water, further studies were performed with the natural bond orbital (NBO) analysis and the quantum theory of atoms in molecules (QTAIM) analysis using the explicit solvent model. The charge transfer and the hydrogen bonds are observed between Zn(N₅)₂ and water, which are beneficial to improvement of the stability of Zn(N₅)₂. This may indicate the solvents that have strong interactions with the cyclo-N₅⁻ candidate may improve the possibility of success of synthesis.     

Synthesis,Photophysical and Electrochemical Properties,and Self‐assembly Behavior of Two Hexaazatriphenylene Derivatives: A Single Bond Makes a Big Difference

A hexaazatriphenylene (HAT) derivative (compound 1 ) that bears four n‐octyl chains and two thienyl groups was designed and synthesized. Further light‐induced oxidation coupling reaction led to thienyl‐fused compound 2 . Their photophysical and electrochemical properties and self‐assembly behavior have been investigated by UV/Vis, fluorescence, and ¹H NMR spectroscopies, cyclic voltammetry (CV), scanning electron microscopy (SEM), and powder X‐ray diffraction (PXRD). Although the difference in compounds 1 and 2 only lie in one single bond that connects the two thienyl segments, they displayed remarkably different properties, revealing an interesting structure–property relationship.     

Structural and solvent effects on the spectroscopic properties of 1, 8‐naphthalimide derivatives: A density functional study

The molecular structures of 1, 8‐naphthalimide derivatives were investigated at density functional theory level within framework of PBE1PBE/6‐31G*. The vertical ionization potential and their delocalization energy of the X‐ray solid structure and gas‐phase optimized structure were explored. The configuration difference between them was attributed to the π‐π interaction of the solid effect, which has negligible effect on their absorption spectra. Solid effect also weakens the intramolecular interaction. Their absorption and luminescent spectra in gas and solvent phase were calculated by time‐dependent density functional theory (TDDFT) and conductor polarizable continuum models (CPCM)‐TDDFT approaches. Obvious red shifts from the solvent effect were found. Substituents on the imides will not improve their spectra properties a lot, whereas substituents on the naphthalene of naphthalimide would modify their properties to emit different spectra. Systematical deviation of vertical excitation energy from absorption and emission spectra, obtained by CPCM‐PBEPBE/6‐31G* and CIS‐CPCM‐PBEPBE/6‐31G* models, were about 0.05 eV and 0.02 eV compared with the experimental values. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Electronic structure and optical properties of isolated and TiO2-grafted free base porphyrins for water oxidation: A challenging test case for DFT and TD-DFT

Seven free base porphyrins employed in dye-sensitized photoelectrosynthetic cells are investigated with the aim of benchmarking the ability of different density functional theory (DFT) and time-dependent DFT approaches in reproducing their structure, vertical, and E_0-0 excitation energies and the energy levels alignment (red-ox properties) at the interface with the TiO₂. We find that both vertical and E_0-0 excitation energies are accurately reproduced by range-separated functionals, among which the ω B97X-D delivers the lowest absolute deviations from experiments. When the dye/TiO₂ interface is modeled, the physical interfacial energetics is only obtained when the B3LYP functional is employed; on the other hand, M06-2X (54% of exchange) and the two long-range corrected approaches tested (CAM-B3LYP and ω B97X-D) excessively destabilize the semiconductor conduction band levels with respect to the dye's lowest unoccupied molecular orbitals (LUMOs), predicting no pathway for electron injection. © 2019 Wiley Periodicals, Inc.     

A theoretical study of electronic and vibrational properties of neutral,cationic, and anionic B24 clusters

The equilibrium geometries, electronic and vibrational properties, and static polarizability of B₂₄, B, and B clusters are reported here. First‐principles calculations based on density functional theory predict the staggered double‐ring configuration to be the ground state for B₂₄, B, and B, in contrast to the quasi‐planar structure observed in small neutral and ionized B_n clusters with n ≤ 15. Furthermore, the (4 × B₆) tubular structure is found to be relatively stable in comparison to the 3D cage structure. The presence of delocalized π and multicentered σ bonds appears to be the cause of the stability of the double‐ring and tubular isomers. For the ground state of B₂₄, the lower and upper bound of the electron affinity is 2.67 and 2.81 eV, respectively, and the vertical ionization potential is 6.88 eV. Analysis of the frequency spectrum of the double‐ring and tubular isomers reveals the characteristic vibrational modes typically observed in carbon nanotubes. The corresponding IR spectrum also reflects the presence of some of these characteristic modes in the neutral and ionized B₂₄, suggesting that double‐ring and tubular structures can be considered as the building blocks of boron nanotubes. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Simultaneous studies of pressure effect on charge transport and photophysical properties in organic semiconductors: A theoretical investigation

High-mobility and strong luminescent materials are essential as an important component of organic photodiodes, having received extensive attention in the field of organic optoelectronics. Beyond the conventional chemical synthesis of new molecules, pressure technology, as a flexible and efficient method, can tune the electronic and optical properties reversibly. However, the mechanism in organic materials has not been systematically revealed. Here, we theoretically predicted the pressure-depended luminescence and charge transport properties of high-performance organic optoelectronic semiconductors, 2,6-diphenylanthracene (DPA), by first-principle and multi-scale theoretical calculation methods. The dispersion-corrected density functional theory (DFT-D) and hybrid quantum mechanics/molecular mechanics (QM/MM) method were used to get the electronic structures and vibration properties under pressure. Furthermore, the charge transport and luminescence properties were calculated with the quantum tunneling method and thermal vibration correlation function. We found that the pressure could significantly improve the charge transport performance of the DPA single crystal. When the applied pressure increased to 1.86 GPa, the hole mobility could be doubled. At the same time, due to the weak exciton coupling effect and the rigid flat structure, there is neither fluorescence quenching nor obvious emission enhancement phenomenon. The DPA single crystal possesses a slightly higher fluorescence quantum yield ～ 0.47 under pressure. Our work systematically explored the pressure-dependence photoelectric properties and explained the inside mechanism. Also, we proposed that the external pressure would be an effective way to improve the photoelectric performance of organic semiconductors.     

Conformational analysis,tautomeric preference,intramolecular hydrogen bonding,and solvent effect on dinitrosamine: A quantum chemical study

HF, B3LYP, and MP2 methods with the standard basis set, 6‐311++G(d,p), were used to study various aspects of dinitrosamine. These results were compared with the outcomes of G2 and CBS‐QB3 methods. First, the conformational analysis and characterization of equilibrium conformations, especially global minima, were performed. On the basis of relative energies, we found that the dinitroso tautomers are more stable than the nitroso‐hydroxy (NH) ones. This preference is well‐interpreted in terms of tautomerization process and nitrosamine resonance. Furthermore, the nature of O? H···O intramolecular hydrogen bond (IMHB), in chelated forms of NH (NH‐11 and NH‐13) was comprehensively studied to evaluate the effect of hetero atoms (N) on the characteristic of IMHB systems. According to the results of isodesmic reaction method, the hydrogen bond energy of NH‐11 is greater than the malonaldehyde (MA) and NH‐13, whereas the electron density analysis and energy‐geometry correlation methods clearly predict that the hydrogen bond of NH‐11 is weaker than the MA. Additionally, the geometrical, atoms in molecules (AIM) and natural bond orbital's (NBO) parameters also emphasize on the MA as a chelated form with the strongest hydrogen bond. Finally, the solvent effects on the relative stability of selected dinitrosamine conformers are evaluated by different continuum (polarizable‐continuum model, isodensity polarizable continuum model, and self‐consistent isodensity polarizable continuum model), discrete and mixed solvent models. Theoretical results readily show that the potential energy surface of dinitrosamine, especially global minima, is strongly affected by the solvent. © 2012 Wiley Periodicals, Inc.     

Solvent effect on the synthesis of clarithromycin: A molecular dynamics study

Clarithromycin (6-O-methylerythromycin A) is a 14-membered macrolide antibiotic which is active in vitro against clinically important gram-positive and gram-negative bacteria. The selectivity of the methylation of the C-6 OH group is studied on erythromycin A derivatives. To understand the effect of the solvent on the methylation process, detailed molecular dynamics (MD) simulations are performed in pure DMSO, pure THF and DMSO:THF (1:1) mixture by using the anions at the C-6, C-11 and C-12 positions of 2',4"-[O-bis(TMS)]erythromycin A 9-[O-(dimethylthexylsilyl)oxime] under the assumption that the anions are stable on the sub-nanosecond time scale. The conformations of the anions are not affected by the presence of the solvent mixture. The radial distribution functions are computed for the distribution of different solvent molecules around the 'O-' of the anions. At distances shorter than 5 A, DMSO molecules are found to cluster around the C-11 anion, whereas the anion at the C-12 position is surrounded by the THF molecules. The anion at the C-6 position is not blocked by the solvent molecules. The results are consistent with the experimental finding that the methylation yield at the latter position is increased in the presence of a DMSO:THF (1:1) solvent mixture. Thus, the effect of the solvent in enhancing the yield during the synthesis is not by changing the conformational properties of the anions, but rather by creating a suitable environment for methylation at the C-6 position.     

A novel and synthetically facile coumarin-thiophene-derived Schiff base for selective fluorescent detection of cyanide anions in aqueous solution: Synthesis,anion interactions,theoretical study and DNA-binding properties

A colorimetric and fluorescent chemosensor (chemosensor 2) for the detection of cyanide anions in aqueous solution has been designed and synthesized in high yield. The sensing mechanism of the chemosensor was verified via UV–vis, fluorimetric, and NMR titrations, and was theoretically explained using DFT and TD-DFT calculations. The chemosensor could optically discriminate the presence of fluoride ions over other anions by a color change from yellow to red with an enhancement of pink fluorescence in DMSO. However, it showed strong green fluorescence when CN^? was added to a mixture of DMSO/water (6:4 v/v). Thus, the chemosensor can be employed in selective detecting of CN^? besides other interference anions (F^?, AcO^? and H₂PO₄^?) in aqueous solution. Moreover, 2 can be used to detect CN^? at a concentration as low as 0.32?μM, which is lower than the WHO guideline (2.7?μM) for cyanide. A low quantity of CN^? (1.08?μM) can be detected and quantified using the prepared chemosensor. Moreover, the UV–vis and fluorescence spectroscopy studies of the interactions between 2 and dublex DNA revealed intercalative binding of calf thymus DNA to the chemosensor.     

Substituent effect of halogen (F, Cl and Br) on uracil tetrad: A theoretical study

In this paper, the substituted uracil tetrad XU4 (X=F, Cl and Br) where X replace the H atoms at five sites of uracils have been investigated using density functional theory method. Geometries, energies and electrostatic potential energy surfaces have been discussed in detail. The outcomes show that when XU take place of U, the preferred symmetry of the tetrad changed from C₄ to S₄. Stabilization energies indicate that the XU substituted tetrads becomes more and more unstable as from F to Br. ESP maps suggest that U4 could bind a cation while XU4 could not. All the tetrads adopt a nonplanar structure that is not suitable for stacking.     

Scaling and structural properties of a polymer in a simple solvent: A study based on integral equations

We present a statistical mechanical theory for polymer–solvent systems based on integral equations derived from the polymer Kirkwood hierarchy. Integral equations for pair monomer–monomer, monomer–solvent, and solvent–solvent correlation functions yield polymer–solvent distribution, chain conformation in three dimensions, and scaling properties associated with polymer swell and collapse in athermal, good, and poor solvents. Variation of polymer properties with solvent density and solvent quality is evaluated for chains having up to 100 bonds. In good solvents, the scaling exponent v has a constant value of about 0.61 at different solvent densities computed. For the athermal solvent case, the gyration radius and scaling exponent decrease with solvent density. In a poor solvent, the chain size scales as N^v with the value of the exponent being about 0.3, compared with the mean field value of ⅓. © 1998 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 36: 3025–3033, 1998     

MP2, DFT‐D,and PCM study of the HMB–TCNE complex: Thermodynamics,electric properties,and solvent effects

Geometry, thermodynamic, and electric properties of the π‐EDA complex between hexamethylbenzene (HMB) and tetracyanoethylene (TCNE) are investigated at the MP2/6‐31G* and, partly, DFT‐D/6‐31G* levels. Solvent effects on the properties are evaluated using the PCM model. Fully optimized HMB–TCNE geometry in gas phase is a stacking complex with an interplanar distance 2.87 × 10^?10 m and the corresponding BSSE corrected interaction energy is ?51.3 kJ mol^?1. As expected, the interplanar distance is much shorter in comparison with HF and DFT results. However the crystal structures of both (HMB)₂–TCNE and HMB–TCNE complexes have interplanar distances somewhat larger (3.18 and 3.28 × 10^?10 m, respectively) than our MP2 gas phase value. Our estimate of the distance in CCl₄ on the basis of PCM solvent effect study is also larger (3.06–3.16 × 10^?10 m). The calculated enthalpy, entropy, Gibbs energy, and equilibrium constant of HMB–TCNE complex formation in gas phase are: ΔH⁰ = ?61.59 kJ mol^?1, ΔS = ?143 J mol^?1 K^?1, ΔG⁰ = ?18.97 kJ mol^?1, and K = 2,100 dm³ mol^?1. Experimental data, however, measured in CCl₄ are significantly lower: ΔH⁰ = ?34 kJ mol^?1, ΔS = ?70.4 J mol^?1 K^?1, ΔG⁰ = ?13.01 kJ mol^?1, and K = 190 dm³ mol^?1. The differences are caused by solvation effects which stabilize more the isolated components than the complex. The total solvent destabilization of Gibbs energy of the complex relatively to that of components is equal to 5.9 kJ mol^?1 which is very close to our PCM value 6.5 kJ mol^?1. MP2/6‐31G* dipole moment and polarizabilities are in reasonable agreement with experiment (3.56 D versus 2.8 D for dipole moment). The difference here is due to solvent effect which enlarges interplanar distance and thus decreases dipole moment value. The MP2/6‐31G* study supplemented by DFT‐D parameterization for enthalpy calculation, and by the PCM approach to include solvent effect seems to be proper tools to elucidate the properties of π‐EDA complexes. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Photophysical and optoelectronic properties of a platinum(II) complex and its derivatives,designed as a highly efficient OLED emitter: A theoretical study

New platinum(II) complex with picolinate (pic) and 2-phenyl naphtothiazole (pntl) ligand as the guest material has been designed and its capability for OLED applications have been examined. Also, we have studied the effects of different substitutions (ie, electron-withdrawing and electron donating groups) on naphtothiazole moiety on optovoltaic characters. We have employed density functional theoretical (B3LYP/DFT) methods to reveal the photophysical and structure properties relationships with the typical host material. The valence MO energies, vertical and adiabatic triplet energy, reorganization energy, and triplet exciton generation fraction (χ _T) have been extensively studied to exploring high phosphorescence efficiency in OLEDs. It has been predicted that substituted systems are good candidates for OLED applications as well as their parent system.     

A comparative study on the preparation methods and properties of coal-based fluorescent carbon nanoparticles

Fluorescent carbon nanoparticles (FCNPs) have broad application prospects in the fields of bioimaging, ion detection, and photocatalysis. In this paper, coal-based FCNPs were prepared by using mixed acid oxidation, hydrogen peroxide etching, and organic solvent extraction methods (marked as FCNPs-AO, FCNPs-HE, and FCNPs-OS, respectively), and the structures and properties of the as-prepared products were compared. It was found that the coal-based FCNPs obtained by three kinds of methods are all aromatic structural nanomaterials linked with oxygen-containing groups. Among them, FCNPs-AO is a kind of hollow annular spherical particles and FCNPs-HE and FCNPs-OS are solid spherical particles. These FCNPs not only have similar fluorescence properties as traditional quantum dots, but also can be photoexcited to generate photogenerated electrons and holes, and it can also suppress the recombination of photogenerated electrons and holes by using its own surface defects. In particular, the electron transport capability of the FCNPs-AO is stronger than that of FCNPs-HE and FCNPs-OS because of its lower charge transfer impedance, so it can be excited to generate more photogenerated electrons and has the best photogenerated carrier separation efficiency.     

A theoretical study of the structural,thermoelectric, and spin-orbit coupling influenced optoelectronic properties of CsTmCl3 halide perovskite

This first principles study explores the structural, electronic, optical, and thermoelectric properties of the CsTmCl₃ halide perovskite using density functional theory. The structural and thermoelectric properties are calculated without considering the spin-orbit coupling (SOC), while both the electronic and optical properties are calculated with and without the SOC effect. A comparison of the results obtained with and without SOC reveals that inclusion of the SOC effect reduces the band gap from 1.18 to 0.99 eV due to shifting of the Tm-d states toward the Fermi level. However, direct nature of the band gap remains the same in both the cases. The effect of SOC on the optical properties is, however, only visible in shifting of the third characteristic peak to lower energies. Strong optical absorption in the visible and ultraviolet regions shows effectiveness of CsTmCl₃ in the optical devices working in these regions. Moreover, the calculated transport properties reveal CsTmCl₃ as a useful thermoelectric material at room temperature.