Nonempirical (double-hybrid) density functionals applied to atomic excitation energies: A systematic basis set investigation

We investigate here the lowest-energy (spin-conserving) excitation energies for the set of He-Ne atoms, with the family of nonempirical PBE, PBE0, PBE0-1/3, PBE0-DH, PBE-CIDH, PBE-QIDH, and PBE0-2 functionals, after employing a wide variety of basis sets systematically approaching the basis set limit: def2-nVP(D), cc-pVnZ, aug-cc-pVnZ, and d-aug-cc-pVnZ. We find that an accuracy (ie, mean unsigned error) of 0.3 to 0.4 eV for time-dependent density functional theory (DFT) atomic excitation energies can be robustly achieved with modern double-hybrid methods, which are also stable with respect to the addition of a double set of diffuse functions, contrarily to hybrid versions, in agreement with recent findings employing sophisticated multiconfigurational DFT methods.     

Ab initio theoretical calculations of the electronic excitation energies of small water clusters

A direct ab initio molecular dynamics method has been applied to a water monomer and water clusters (H(2)O)(n) (n = 1-3) to elucidate the effects of zero-point energy (ZPE) vibration on the absorption spectra of water clusters. Static ab initio calculations without ZPE showed that the first electronic transitions of (H(2)O)(n), (1)B(1)←(1)A(1), are blue-shifted as a function of cluster size (n): 7.38 eV (n = 1), 7.58 eV (n = 2) and 8.01 eV (n = 3). The inclusion of the ZPE vibration strongly affects the excitation energies of a water dimer, and a long red-tail appears in the range of 6.42-6.90 eV due to the structural flexibility of a water dimer. The ultraviolet photodissociation of water clusters and water ice surfaces is relevant to these results.     

Thiacalix[4]arenes: Extraction of palladium and the electronic structure

The extractability of palladium nitro complexes with the charge state of sulfur and oxygen atoms in thiacalix[4]arenas in the cone and 1,3-alternate conformations are compared. The results of X-ray photoelectron and X-ray emission studies indicate the presence of considerable electron density on the bridging sulfur atoms, which is due to the contribution of the sulfur 3p AO to the upper occupied MOs of molecules. A series of changes in the electron density on sulfur atoms in the order calixarene thioethers > thiacalixarenes > dialkylsulfides ((C₁₀H₂₁)₂S) > (C₆H₅)₂S not completely coincide with changes in their extrability, which can be caused by different nature and stoichiometry of the formed palladium complexes.     

XPS,XES, and quantum chemical investigation of the electronic structure of thiacalix[4]arenes and calix[4]arene thioesters

The X-ray photoelectron and X-ray emission spectra as well as the charge state of thiacalix[4]arenes in the cone and 1,3-alternate conformations and calix[4]arene thioesters were studied. The donor ability of sulfur bridging atoms in the studied compounds was shown to be close to that in dialkyl sulfides. The internal X-ray transitions (K _α and K _β) were described by the energy of Kohn-Sham orbitals calculated by DFT method with relaxation corrections.     

Optimized geometry,electronic structure and Ag adsorption property of nanosheet graphene with different symmetry shapes: a theoretical investigation

Optimized geometries and electronic structures of three different symmetry shapes of nanosheet graphenes with armchair and zig-zag edges were generated by using the generalized gradient approximation/Perdew–Burke–Ernzerhof (GGA/PBE) method of density function theory (DFT) with the double-zeta polarized (DZP) basis set. Based on the results, the calculated HOMO–LUMO energy gap (Eg = LUMO–HOMO) with different symmetry shapes, and nanosheet size for with zig-zag and armchair edges were also presented. Because the p _π orbital was widely localized over the sheet surface, the calculated E _g decreased with increasing the sheet size. Further, the quantum mechanics calculation was used to investigate the adsorption property of the Ag atom adsorbed to the nanosheet graphene (expressed by C₉₀H₃₀) surface. The calculations show that the Ag atom binds to the bridge site (B site) of triangular nanosheet graphene (C₉₀H₃₀) as it is the most stable adsorption site compared with others, and since it has higher formation energy (ΔE) with shorter distance between the Ag atom and the graphene surface. Above all, calculations suggest that the Ag-adsorbed nanosheet graphene is a good option as an adsorbent in environmental research.     

Spatial structure of Au8: Importance of basis set completeness and geometry relaxation

The relative stabilities of the lowest energy structures are calculated for the gold octamer, Au8, employing highly correlated ab initio methods. The question of dimensionality of these clusters is addressed, and a guideline for future structural studies of such systems is provided. In particular, the importance of geometry relaxation beyond the MP2 level of theory as well as the need for basis sets toward the complete limit (CBS) are discussed. The planar D(4h) symmetric structure of Au8 is the lowest energy structure. At the CCSD(T)/CBS limit, it is separated by 16 kJ mol(-1) from the next higher Td symmetric isomer.     

Racemization mechanisms and electronic circular dichroism of [4]heterohelicenium dyes: a theoretical study

Triarylmethylium cations with the three rings linked by two bridging groups constitute a special class of [4]heterohelicenium dyes that combine high configurational stability with the optical properties of classic dye compounds. The racemization barriers and electronic circular dichroism of seven [4]heterohelicenium analogues are investigated with density functional theory to consider different design strategies. The racemization barriers are examined with the B3LYP functional utilizing the basis set 6-31+G* with respect to bridging heteroatoms in the helicenium motif and with different bulky substituents in the helix pitch. The racemization barriers of the [4]heterohelicenium are found to be highly dependent on the relative size of the bridging atom. Nucleophilic attack at the carbenium ion leads to formation of center adducts for which the racemization barriers are found to be lowered by 8-12 kJ/mol. This finding of a nucleophilic racemization catalysis may be rationalized by the loss of conjugation upon formation of an sp(3)-hybridized carbon in the center adducts. The effect of the heteroatom substitution and center adduct formation is reflected in the electronic properties of the compound calculated with the Coulomb-attenuated method CAM-B3LYP with the basis set 6-311++G**. The excitation energies are found to be highly dependent on the twisting of the helicenium framework and only weakly influenced by the electronic nature of the bridging substituent. The electronic circular dichroism is evaluated, as the rotational strength is found to be highly dependent on both the overall molecular structure and substitution pattern but with no simple correlation between structure and circular dichroism (CD) response. The calculations reveal that the magnitude of rotational strength in most cases is dominated by the angle between the electronic and magnetic transition dipole moments. Finally, it is found that computational screening of many different structures and substituents might be needed to find target structures with maximized rotational strength.     

Experimental and theoretical investigation of the electronic structure of 5-fluorouracil compounds

We present a comparison between experimental and theoretical X-ray absorption spectroscopy (XAS) and X-ray emission spectroscopy (XES) of 5-fluorouracil compounds, with an emphasis on the effects of the inclusion of nickel in the structure. By focusing on the 1s thresholds of carbon, nitrogen, oxygen, and fluorine it was possible to provide a complete picture of the occupied and unoccupied partial density of states of the 5-fluorouracil systems. Spectra calculated using density functional theory are compared to experimental results. Most experimental results agree well with our theoretical calculations for the XAS and XES of the compounds. All spectral features are assigned. Our results reveal that the nickel in the compound is coordinated with the nitrogen sites of the 5-fluorouracil ligands.     

Synthesis, reactivity, and electronic structure of [n]vanadoarenophanes: an experimental and theoretical study

An optimized procedure for the selective dimetalation of [V(eta (6)-C 6H 6) 2] by BuLi/tmeda allowed for the isolation and characterization of [V(eta (6)-C 6H 5Li) 2].tmeda. X-ray diffraction of its thf solvate [V(eta (6)-C 6H 5Li) 2].(thf) 7 revealed an unsymmetrical, dimeric composition in the solid state, in which both subunits are connected by three bridging lithium atoms. Treatment with several element dihalides facilitated the isolation of [ n]vanadoarenophanes ( n = 1, 2) with boron and silicon in the bridging positions. In agreement with the number and covalent radii of the bridging elements, these derivatives exhibit molecular ring strain to a greater or lesser extent. The B-B bond of the [2]bora species [V(eta (6)-C 6H 5) 2B 2(NMe 2) 2] was readily cleaved by [Pt(PEt 3) 3] to afford the corresponding oxidative addition product. Subsequently, [V(eta (6)-C 6H 5) 2B 2(NMe 2) 2] was employed as a diborane(4) precursor in the diboration of 2-butyne under stoichiometric, homogeneous, and heterogeneous catalysis conditions. This transformation is facilitated by the reduction of molecular ring strain, which was confirmed by a decrease of the tilt angle alpha observed in the corresponding solid-state structures. EPR spectroscopy was used to probe the electronic structure of strained [ n]vanadoarenophanes and revealed an obvious correlation between the degree of molecular distortion and the observed hyperfine coupling constant a iso. State-of-the-art DFT calculations were able to reproduce the measured isotropic vanadium hyperfine couplings and the coupling anisotropies. The calculations confirmed the decrease of the absolute isotropic hyperfine couplings with increasing tilt angle. Closer analysis showed that this is mainly due to increased positive contributions to the spin density at the vanadium nucleus from the spin polarization of doubly occupied valence orbitals of vanadium-ligand sigma-antibonding character. The latter are destabilized and thus made more polarizable in the bent structures.     

Terminal ligand influence on the electronic structure and intrinsic redox properties of the [Fe4S4]2+ cubane clusters

We used photoelectron spectroscopy (PES) to study how the terminal ligands influence the electronic structure and redox properties of the [4Fe-4S] cubane in several series of ligand-substituted analogue complexes: [Fe(4)S(4)Cl(4-x)(CN)(x)](2-), [Fe(4)S(4)Cl(4-x)(SCN)(x)](2-), [Fe(4)S(4)Cl(4-x)(OAc)(x)](2-), [Fe(4)S(4)(SC(2)H(5))(4-x)(OPr)(x)](2-), and [Fe(4)S(4)(SC(2)H(5))(4-x)Cl(x)](2-) (x = 0-4). All the ligand-substituted complexes gave similar PES spectral features as the parents, suggesting that the mixed-ligand coordination does not perturb the electronic structure of the cubane core significantly. The terminal ligands, however, have profound effects on the electron binding energies of the cubane and induce significant shifts of the PES spectra, increasing in the order SC(2)H(5)(-) --> Cl(-) --> OAc(-)/OPr(-) --> CN(-) --> SCN(-). A linear relationship between the electron binding energies and the substitution number x was observed for each series, indicating that each ligand contributes independently and additively to the total binding energy. The electron binding energies of the gaseous complexes represent their intrinsic oxidation energies; the observed linear dependence on x is consistent with similar observations on the redox potentials of mixed-ligand cubane complexes in solution. The current study reveals the electrostatic nature of the interaction between the [4Fe-4S] cubane core and its coordination environment and provides further evidence for the electronic and structural stability of the cubane core and its robustness as a structural and functional unit in Fe-S proteins.     

Conformational isomerism of electroactive calix[4]arenes: influence of the electronic state in the flexibility of thiophene-containing calix[4]arene

The cone-to-paco conformational isomerism of 11,23-bis(thiophen-5-yl)-26,28-dimethoxycalix[4]arene-25,27-diol, a calix[4]arene with thiophene substituents in para position with respect to the hydroxyl groups, has been investigated using ab initio and DFT quantum mechanical methods. This compound models a molecular device constituted by small oligomers of thiophene and calix[4]arene units, whose actuation mechanism is promoted by the conformational flexibility of the latter. To examine the influence of the electronic structure of this electroactive calix[4]arene, three different states have been considered: (i) neutral state; (ii) oxidized state, in which one electron is extracted from each thiophene ring; and (iii) oxidized-deprotonated state, in which the two hydroxyl groups of the oxidized compound are deprotonated. Results are discussed and compared with those obtained for the same molecule but without thiophene substituents, 25,27-dihydroxy-26,28-dimethoxycalix[4]arene. Although the influence of the thiophene substituents is negligible in the neutral state, they play a crucial role in the rotational isomerism of both the oxidized and deprotonated-oxidized states.     

Effects of global orbital cutoff value and numerical basis set size on accuracies of theoretical atomization energies

Numerical basis sets are known for their rapid convergence in density functional theory calculations. The selections of global orbital cutoff values and numerical basis set sizes are important to the computational accuracies and efficiencies. In this study, the effects of global orbital cutoff values and numerical basis set sizes on the theoretical atomization energies (D ₀) were investigated using density functional theory with the generalized gradient approximation. Our results on the total energies of seven atoms and D ₀ of a set of 44 molecules demonstrate that the numerical orbital cutoff value should be larger than 6.5 Å to get the converged energetic properties. Through comparing the D ₀ of these 44 molecules obtained by using four kinds of different numerical basis sets, DN, DND, DNP, and TNP, it demonstrates that the DNP basis set is good enough to predict accurate D ₀ with affordable computational cost.     

Molecular structure and electronic properties of a series of oligoalkylthiophenes: A theoretical investigation

Molecular geometries and electronic properties of 3-alkylthiophenes (ATs) and their oligomers (OATs) are studied by the density functional theory (DFT). Calculations are performed on the oligomers formed by n repeating units, where n ranges from 1 to 6, using the B3LYP/6-31G** level of theory. The results obtained show that the doped oligomers have more satisfactory structural and electronic characteristics for the conducting polymers. The conjugated system in the doped oligomers has more aromaticity, with expanded and planar chains. The calculated energy gap values between the frontal orbitals and also the ionization potential values for the oligomers indicate that with increase in the oligomer chain length, the conductive band gap decreases. Furthermore, our calculations suggest that an electron-donating alkyl substituent at position 3 of the thiophene ring plays an important role in the structural and electronic properties of the polymers.     

Experimental and theoretical investigation of the molecular and electronic structure of anticancer drug camptothecin

The Fourier Transform Infrared spectrum of (S)-4 ethyl-4-hydroxy-1H-pyrano [3',4':6,7]-indolizino-[1,2-b-quinoline-3,14-(4H,12H)-dione] [camptothecin] was recorded in the region 4000-400 cm(-1). The Fourier Transform Raman spectrum of camptothecin (CPT) was also recorded in the region 3500-50 cm(-1). Quantum chemical calculations of geometrical structural parameters and vibrational frequencies of CPT were carried out by MP2/6-31G(d,p) and density functional theory DFT/B3LYP/6-311++G(d,p) methods. The assignment of each normal mode has been made using the observed and calculated frequencies, their IR and Raman intensities. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FT-IR and FT-Raman spectra. Most of the computed frequencies were found to be in good agreement with the experimental observations. The isotropic chemical shifts computed by (13)C and (1)H NMR analysis also show good agreement with experimental observations. Comparison of calculated spectra with the experimental spectra provides important information about the ability of computational method to describe the vibrational modes of large sized organic molecule.     

Theoretical and experimental study of the vertical excitation energies in the ionic and tautomeric forms of 4-aminomethylpyridine

4-Aminomethylpyridine (4-PAM) has been widely used as a model compound to elucidate the mechanisms of biological and biomedical action of the amino derivatives of vitamin B₆. By virtue of the presence of two ionizable groups (viz. a pyridine nitrogen and an amino function) in its structure, 4-PAM in solution occurs as various ionic and tautomeric forms in equilibrium. In this work, we optimized the geometries of such forms and found the protonation status of the ionizable groups in 4-PAM to affect the molecular geometry and frontier orbitals. In addition, we determined the experimental electronic excitation energies for each molecular species of 4-PAM from deconvoluted UV–vis spectra. The results thus obtained were compared with their theoretical counterparts as determined from TD-DFT calculations. Based on the outcome, the theoretical methodology used affords correct simulation of electronic excitation energies. The theoretical and experimental results showed that the deprotonation of the pyridine nitrogen has no effect on the energy of the first electronic transition, however it affects its intensity. Additionally, the deprotonation of both pyridine nitrogen and methylamino group increases the number of bands, by increasing the n–π^* transitions.