Theoretical study of excited states of DNA base dimers and tetramers using optimally tuned range‐separated density functional theory

Excited states of various DNA base dimers and tetramers including Watson‐Crick H‐bonding and stacking interactions have been investigated by time‐dependent density functional theory using nonempirically tuned range‐separated exchange (RSE) functionals. Significant improvements are found in the prediction of excitation energies and oscillator strengths, with results comparable to those of high‐level coupled‐cluster (CC) models (RI‐CC2 and EOM‐CCSD(T)). The optimally‐tuned RSE functional significantly outperforms its non‐tuned (default) version and widely‐used B3LYP functional. Compared to those high‐level CC benchmarks, the large mean absolute deviations of conventional functionals can be attributed to their inappropriate amount of exact exchange and large delocalization errors which can be greatly eliminated by tuning approach. Furthermore, the impacts of H‐bonding and π‐stacking interactions in various DNA dimers and tetramers are analyzed through peak shift of simulated absorption spectra as well as corresponding change of absorption intensity. The result indicates the stacking interaction in DNA tetramers mainly contributes to the hypochromicity effect. The present work provides an efficient theoretical tool for accurate prediction of optical properties and excited states of nucleobase and other biological systems. © 2015 Wiley Periodicals, Inc.     

A new nonempirical tuning scheme with single self‐consistent field calculation: Comparison with global and IP‐tuned range‐separated functional

System‐dependent nonempirical tuning of range‐separated functional provides a way to minimize the delocalization error of the system. However, existing nonempirical tuning method requires the computation of several ΔSCF calculations to determine the optimal μ value. In this article, we have defined a scheme to evaluate the optimal μ value with single self‐consistent field calculation. Our method is based on the evaluation of the spherically symmetric average Electron localization function (ELF) region. According to this scheme, the radius of the spherically symmetric average ELF region gives is a measure of the distance at which the long‐range part of the range‐separated functional becomes dominant. Numerical results indicate that our method improves the reproduction of HOMO energies and HOMO‐LUMO gap in comparison to global and IP‐tuned range‐separated functional. Moreover, in case of HOMO energies, maximum error of the ELF‐tuned functional is considerably smaller than the global and IP‐tuned functional. Furthermore, our method gives considerably smaller deviation of HOMO energies from ΔSCF IP than global range‐separated functional. © 2017 Wiley Periodicals, Inc.     

Multi‐state multi‐reference Møller–Plesset second‐order perturbation theory for molecular calculations

This work presents multi‐state multi‐reference Møller–Plesset second‐order perturbation theory as a variant of multi‐reference perturbation theory to treat electron correlation in molecules. An effective Hamiltonian is constructed from the first‐order wave operator to treat several strongly interacting electronic states simultaneously. The wave operator is obtained by solving the generalized Bloch equation within the first‐order interaction space using a multi‐partitioning of the Hamiltonian based on multi‐reference Møller–Plesset second‐order perturbation theory. The corresponding zeroth‐order Hamiltonians are nondiagonal. To reduce the computational effort that arises from the nondiagonal generalized Fock operator, a selection procedure is used that divides the configurations of the first‐order interaction space into two sets based on the strength of the interaction with the reference space. In the weaker interacting set, only the projected diagonal part of the zeroth‐order Hamiltonian is taken into account. The justification of the approach is demonstrated in two examples: the mixing of valence Rydberg states in ethylene, and the avoided crossing of neutral and ionic potential curves in LiF. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Implementation of nuclear gradients of range‐separated hybrid density functionals and benchmarking on rotational constants for organic molecules

We have implemented the nuclear gradient for several range‐separated hybrid density functionals in the general quantum chemistry code ORCA. To benchmark the performance, we have used a recently published set of back‐corrected gas phase rotational constants, which we extended by three molecules. In our evaluation, CAM‐B3LYP‐D3 and ωB97X‐D3 show great accuracy, and are surpassed by B2PLYP‐D3 only. Lower‐cost alternatives to quadruple‐ζ basis set‐based calculations, among them a smaller basis set and the use of resolution‐of‐the‐identity approaches, are assessed and shown to yield acceptable deviations. In addition, the Hartree‐Fock‐based back‐correction method is compared to a density functional theory alternative, which largely shows consistency between the two. A new, well‐performing, spin‐component scaled MP2 variant is designed and discussed, as well. © 2014 Wiley Periodicals, Inc.     

Prediction of excited‐state properties of oligoacene crystals using polarizable continuum model‐tuned range‐separated hybrid functional approach

A methodology combining the polarizable continuum model and optimally‐tuned range‐separated (RS) hybrid functional was proposed for the quantitative characterization of the excited‐state properties in oligoacene (from anthracene to hexacene) crystals. We show that it provides lowest vertical singlet and triplet excitation energies, singlet‐triplet gap, and exciton binding energies in very good agreement with the available experimental data. We further find that it significantly outperforms its non‐tuned RS counterpart and the widely used B3LYP functional, and even many‐body perturbation theory within the GW approximation (based on a PBE starting point). Hence, this approach provides an easily applicable and computationally efficient tool to study the excited‐state properties of organic solids of complexity. © 2017 Wiley Periodicals, Inc.     

Assessment of range‐separated exchange functionals and nonempirical functional tuning for calculating the static second hyperpolarizabilities of streptocyanines

DFT method can severely overestimate the response properties for π‐conjugation systems. The range‐separated exchange and recently developed optimal IP‐tuning process are evaluated on the prediction of static second hyperpolarizabilities of streptocyanines of increasing molecular length. The finite field results have shown that the exact exchange at midium and long distance can relieve only a part of the overshooting but still beyond satisfaction. The exact exchange at short distance has the oppsite effects showing the failure of converntional hGGA. The optimal tuned range‐separated exchange functionals show little improvements performing worse than the default ones. Importantly, the electronic structure–property relationship, bond order alternation‐γ , is not well established with DFT method. © 2017 Wiley Periodicals, Inc.     

Description of high‐spin restricted open‐shell molecules with the Piris natural orbital functional

The Piris natural orbital functional (PNOF) based on a new approach for the two‐electron cumulant is considered for the case of high‐spin restricted open‐shell systems. The theory is applied to the calculation of molecular energies, dipole moments, vertical ionization potentials (IP), and electron affinities (EA) of 10 open‐shell molecules. Vertical values of IP and EA were used to evaluate the hardness. It was observed that the results obtained using the PNOF method are comparable to the corresponding results obtained using CCSD(T) in the case of energies and dipole moments. Best agreement between theory and experiment is achieved by PNOF for EA and hardness values. The calculated PNOF values for the mentioned properties are in good agreement with the available experimental data, considering the basis sets used (6–31 ++G**). © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

On the performance of long‐range‐corrected density functional theory and reduced‐size polarized LPol‐n basis sets in computations of electric dipole (hyper)polarizabilities of π‐conjugated molecules

Static longitudinal electric dipole (hyper)polarizabilities are calculated for six medium‐sized π‐conjugated organic molecules using recently developed LPol‐n basis set family to assess their performance. Dunning's correlation‐consistent basis sets of triple‐ζ quality combined with MP2 method and supported by CCSD(T)/aug‐cc‐pVDZ results are used to obtain the reference values of analyzed properties. The same reference is used to analyze (hyper)polarizabilities predicted by selected exchange‐correlation functionals, particularly those asymptotically corrected. © 2012 Wiley Periodicals, Inc.     

Generalized Gaussian reference curve measurement model for high‐performance liquid chromatography with diode array detector separation and its solution by multi‐target intermittent particle swarm optimization

In order to separate a high‐performance liquid chromatography with diode array detector (HPLC‐DAD) data set to chromatogram peaks and spectra for all compounds, a separation method based on the model of generalized Gaussian reference curve measurement (GGRCM) and the algorithm of multi‐target intermittent particle swarm optimization (MIPSO) is proposed in this paper. A parameter θ is constructed to generate a reference curve r(θ) for a chromatogram peak based on its physical principle. The GGRCM model is proposed to calculate the fitness ε(θ) for every θ, which indicates the possibility for the HPLC‐DAD data set to contain a chromatogram peak similar to the r(θ). The smaller the fitness is, the higher the possibility. The algorithm of MIPSO is then introduced to calculate the optimal parameters by minimizing the fitness mentioned earlier. Finally, chromatogram peaks are constructed based on these optimal parameters, and the spectra are calculated by an estimator. Through the simulations and experiments, the following conclusions are drawn: (i) the GGRCM‐MIPSO method can extract chromatogram peaks from simulation data set without knowing the number of the compounds in advance even when a severe overlap and white noise exist and (ii) the GGRCM‐MIPSO method can be applied to the real HPLC‐DAD data set. Copyright © 2014 John Wiley & Sons, Ltd.     

Absorption spectra of azobenzenes simulated with time‐dependent density functional theory

Using time‐dependent density functional theory and the polarizable continuum model, we have simulated the absorption spectra of an extended series of azobenzene dyes. First, we have determined a theoretical level optimal for this important class of dyes, and it turned out that a C‐PCM‐CAM‐B3LYP/6‐311+G(d,p)//C‐PCM‐B3LYP/6‐311G(d,p) approach represents an effective compromise between chemical accuracy and computational cost. In a second stage, we have compared the theoretical and experimental transition energies for 46 n → π^☆ and 141 π → π^☆ excitations. For the full set, that spans over a 302–565 nm domain, we obtained a mean absolute deviation of 13 nm (0.10 eV) and a linear correlation coefficient of 0.95, illustrating the accuracy of our approach, though some significant outliers pertained. In a last step, the impact of several modifications, that is, trans/cis isomerization, variation of the acidity of the medium and azo/hydrazo tautomerism have been modeled with two functionals. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Time‐dependent density functional theory study on the absorption spectrum of Coumarin 102 and its hydrogen‐bonded complexes

The effect of both solvent polarity and hydrogen bonding (HB) on the electronic transition energy of Coumarin 102 (C102) has been examined using the time‐dependent density functional theory (TDDFT). Solvent effect on both geometry and electronic transition energy is evaluated using the polarizable continuum model (PCM). A linear relation of the absorption maximum of C102 with the solvent polarity function Δf is found using the TDDFT‐PCM method for all solvents except dimethyl sulfoxide. The solvent polarity and the type B HB between the carbonyl oxygen and solvent hydrogen atom make the absorption wavelength redshift, whereas the type A HB between the amino nitrogen atom and solvent hydrogen atom has an opposite effect on the absorption wavelength. The calculated absorption wavelengths of C102 with two type B HB between the carbonyl oxygen and solvent hydrogen atom are in excellent agreement with experimental measurements. The solvatochromism of C102 is analyzed in terms of the Kamlet–Taft equation and the parameters s and a are discussed. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011.     

The self‐consistent charge density functional tight‐binding theory study of carbon adatoms using tuned Hubbard U parameters

The self‐consistent charge density functional tight‐binding (DFTB) theory is a useful tool for realizing the electronic structures of large molecular complex systems. In this study, the electronic structure of C₆₁ formed by fullerene C₆₀ with a carbon adatom is analyzed, using the fully localized limit and pseudo self‐interaction correction methods of DFTB to adjust the Hubbard U parameter (DFTB + U). The results show that both the methods used to adjust U can significantly reduce the molecular orbital energy of occupied states localized on the defect carbon atom and improve the gap between highest occupied molecular orbital(HOMO) and lowest unoccupied molecular orbital(LUMO) of C₆₁. This work will provide a methodological reference point for future DFTB calculations of the electronic structures of carbon materials.     

Synthesis of 8‐hydroxyquinolium chloroacetate and synthesis of complexes derived from 8‐hydroxyquinoline,and characterization,density functional theory and biological studies

8‐Hydroxyquinolium chloroacetate ( L¹ ) was synthesized and characterized. The results suggest that L¹ loses ethyl chloroacetate ion on coordination at low pH (2–5) and consequently it behaves as 8‐hydoxyquinoline ( L² ). Cu²⁺, Co²⁺, Pt⁴⁺, Pd²⁺, Au³⁺, Ag⁺ and Nd³⁺ complexes derived from L² have been synthesized and characterized using spectral, magnetic and thermal measurements. L² acts as a neutral bidentate ligand in the case of Cu²⁺, Co²⁺, Pt⁴⁺, Pd²⁺ and Nd³⁺ complexes and as a mononegative bidentate ligand in the case of Au³⁺ and Ag⁺ complexes. Octahedral geometry is proposed for Cu²⁺, Co²⁺ (grey) and Pt⁴⁺ complexes and square‐planar for Co²⁺ (green), Pd²⁺ and Au³⁺ complexes. The bond lengths, bond angles, chemical reactivities, binding energies and dipole moments for all compounds were evaluated using density functional theory and molecular electrostatic potential for L¹ . Superoxide dismutase radical scavenger‐like activity and cytotoxic activity of the complexes towards HepG2 liver cancer cells has been screened. Cytotoxicity measurements show that Ag⁺ and Pd²⁺ complexes have the highest cytotoxic activity while L¹ , Cu²⁺, Co²⁺ (grey), Co²⁺ (green), Pt⁴⁺ and Nd³⁺ complexes have no cytotoxic activity. Copyright © 2015 John Wiley & Sons, Ltd.     

Time‐dependent density functional theory studies of the electronic absorption spectra of metallophthalocyanines of group IVA

Time‐dependent density functional theory (TD‐DFT) calculations were carried out in a comparative study of the electronic absorption spectra of lead(II) phthalocyaninate (PbPc), tin(II) phthalocyaninate (SnPc), tin(IV) dichlorophalocyaninate (PcSnCl₂), germanium(II) phthalocyaninate (GePc), and germanium (IV) dichlorophalocyaninate (PcGeCl₂) with the B3LYP method and LANL2DZ basis set. Our calculated bands correspond well with the experimental results. The electronic natures of all the bands in the absorption spectra are assigned and analyzed comparatively according to the calculated electronic transition contributions. With the increase of the dielectric constant from CHCl₃ to DMSO, all the electronic absorption bands are somewhat red shift, consistent with the shift rules measured experimentally. The radius of the central metals has great influence to the absorption spectra, especially for the B bands. The influence of the radius of the central metals to the absorption spectra of PcSnCl₂ and PcGeCl₂ is smaller than to the spectra of the nonplanar MPcs (M = Pb, Sn, and Ge). Axial ligands also greatly changed the electronic absorption spectra due to the change of the orbital energy level and the molecular symmetry. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Time‐dependent density functional theory study of electronic spectrum property for carbazolyl–pyridinyl alternating copolymers

Three A‐B‐type fluorescent copolymers comprised of alternating carbazolyl and pyridinyl units, poly[(2,7‐(N‐(2‐ethylhexyl)carbazolyl)‐alt‐(3,5‐pyridinyl))](PEHCP‐35), poly[(2,7‐(N‐(2‐ethylhexyl)carbazolyl)‐alt‐(2,6‐pyridinyl))] (PEHCP‐26) and poly[(2,7‐(N‐(2‐ethyl‐hexyl)carbazolyl)‐alt‐(2,5‐pyridinyl))] (PEHCP‐25), are studied by means of the density functional theory (DFT/B3LYP/6‐31G). Based on the optimized geometries, the optical properties are calculated by employing time‐dependent density functional theory (TD‐DFT). The bandgaps and optical properties are saturated quickly in PEHCP‐35 and PEHCP‐26. It is known from experiment that PEHCP‐25 is actually an oligomer with a polymerization degree of 4. So the tetramers of PEHCP‐35, PEHCP‐26, and PEHCP‐25 are adopted to study the electronic and optical properties, and the calculated results are in close agreement with experiment. The calculated bandgaps of copolymers obtained from two ways, i.e., HOMO–LUMO gaps and the lowest excitation energies, decrease in the following order PEHCP‐35 > PEHCP‐26 > PEHCP‐25, the same trend as the data obtained from the edge of the electric band but different from the electrochemically obtained data from experiment (PEHCP‐25 > PEHCP‐26 > PEHCP‐35). The outcomes showed that, when excited, a charge transfer from carbazolyl unit to pyridinyl unit occurs, and the lumophor is mainly carbazolyl units. The UV absorption and emission wavelengths both exhibit bathochromic shifts: PEHCP‐35 < PEHCP‐26 < PEHCP‐25. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Response to “comment on density functional theory study of 1,2‐dioxetanone decomposition in condensed phase”

Roca‐Sanjuan et al. commented on our paper “Density Functional Theory Study of 1,2‐Dioxetanone Decomposition in Condensed Phase”, by criticizing the use of a closed‐shell approach and the differences encountered regarding other previous studies. However, our suggested reaction mechanism was in line with experimental findings, contrary to other computational studies. Moreover, we have presented data to support our use of a closed‐shell approach. © 2012 Wiley Periodicals, Inc.     

Structural properties and the effect of 2,6‐diaminoanthraquinone on G‐tetrad,non‐G‐tetrads,and mixed tetrads—A density functional theory study

Telomerase inhibitor causes the attrition of telomere length and consequently leading to senescence which require a lag period for cancer cells to stop proliferating. Telomeric sequences form quadruplex structures stabilized by tetrads. The structural and electronic properties related with interaction of 2,6‐diaminoanthraquinone and tetrads are the key step to elucidate the anticancer activity. The present study has been focused on the stability of the isolated tetrads and the effect of interaction of 2,6‐diaminoanthraquinone with G‐tetrad, non‐G‐tetrads, and mixed tetrads using density functional theory method in both gas and aqueous phases. The solvent interaction with the molecular systems has increased the stability of the isolated tetrads and complexes. The sharing of electron density between the interacting molecules is shown through electron density difference maps. The atoms in molecules theory and natural bond orbital analysis have been performed to study the nature of hydrogen bonds in the inhibitor interacting complexes. The linear correlation is shown between electron density [ρ(r)], and its Laplacian [(²ρ(r)] at the bond critical points. The strong binding nature of 2,6‐diaminoanthraquinone with studied tetrads reveals that this inhibitor is suitable to stabilize the above tetrads and inhibit the telomerase activity. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Gas‐phase reaction mechanism of Pd+ with CH3CHO: A density functional theoretical study

Details on the reactions of: (1) Pd⁺ + CH₃CHO → PdCO⁺ + CH₄ and (2) Pd⁺ + CH₃CHO → PdH + CH₃CO⁺ in the gas phase were investigated using density functional theory (B3LYP), in conjunction with the LANL2DZ+6‐311+G(d) basis set. Three encounter complexes were located on the potential energy surfaces and the calculations indicated that both the C? C and aldehyde C? H bond activation of acetaldehyde could lead to the dominant demethanation reaction. The charge transfer process for PdH abstraction was caused by an intramolecular PdH rearrangement of the newly found η¹‐aldehyde attached complex. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011