Basis Set Effects Research Articles

Could the description on polynuclear superhalogens by DFT be comparable with high-level ab initio results? A comparison between DFT and CCSD(T).

A systematic density functional theory study including 17 exchange-correlation functionals was performed on different types of superhalogens with high level coupled-cluster single double including perturbative triple excitations (CCSD(T)) results as the reference. The superhalogens selected here cover the ranges from mononuclear to polynuclear structures and from structures with halogen-atom ligands to those with non-halogen ligands, e.g., [MgX3](-), [Mg2X5](-), and [Mg3X7](-) (X = F, Cl, CN). It is clearly indicated that three double-hybrid functionals B2T-PLYP, B2GP-PLYP, B2K-PLYP as well as the range-separated hybrid functional ωB97X are capable of providing results which approach the accuracy at the CCSD(T) level. The basis set effect is usually moderate and, in most cases, it is enough to utilize the basis set of triple-ξ quality, e.g., Def2-TZVP. In addition, the results of the HF and MP2 method are also acceptable here, especially for polynuclear superhalogens where CCSD(T) is probably unpractical.

Benchmark Theoretical and Experimental Study on (15)N NMR Shifts of Oxidatively Damaged Guanine.

The (15)N NMR shifts of 9-ethyl-8-oxoguanine (OG) were calculated and measured in liquid DMSO and in crystal. The OG molecule is a model for oxidatively damaged 2'-deoxyguanosine that occurs owing to oxidative stress in cell. The DNA lesion is repaired with human 8-oxoguanine glycosylase 1 (hOGG1) base-excision repair enzyme, however, the exact mechanism of excision of damaged nucleobase with hOGG1 is currently unknown. This benchmark study on (15)N NMR shifts of OG aims their accurate structural interpretation and calibration of the calculation protocol utilizable in future studies on mechanism of hOGG1 enzyme. The effects of NMR reference, DFT functional, basis set, solvent, structure, and dynamics on calculated (15)N NMR shifts were first evaluated for OG in crystal to calibrate the best performing calculation method. The effect of large-amplitude motions on (15)N NMR shifts of OG in liquid was calculated employing molecular dynamics. The B3LYP method with Iglo-III basis used for B3LYP optimized geometry with 6-311++G(d,p) basis and including effects of solvent and molecular dynamic was the calculation protocol used for calculation of (15)N NMR shifts of OG. The NMR shift of N9 nitrogen of OG was particularly studied because the atom is involved in an N-glycosidic bond that is cleaved with hOGG1. The change of N9 NMR shift owing to oxidation of 9-ethylguanine (G) measured in liquid was -27.1 ppm. The calculated N9 NMR shift of OG deviated from experiment in crystal and in liquid by 0.45 and 0.65 ppm, respectively. The calculated change of N9 NMR shift owing to notable N9-pyramidalization of OG in one previously found polymorph was 20.53 ppm. We therefore assume that the pyramidal geometry of N9 nitrogen that could occur for damaged DNA within hOGG1 catalytic site might be detectable with (15)N NMR spectroscopy. The calculation protocol can be used for accurate structural interpretation of (15)N NMR shifts of oxidatively damaged guanine DNA residue.

Predicting (17)O NMR chemical shifts of polyoxometalates using density functional theory.

We have investigated the computation of (17)O NMR chemical shifts of a wide range of polyoxometalates using density functional theory. The effects of basis sets and exchange-correlation functionals are explored, and whereas pure DFT functionals generally predict the chemical shifts of terminal oxygen sites quite well, hybrid functionals are required for the prediction of accurate chemical shifts in conjunction with linear regression. By using PBE0/def2-tzvp//PBE0/cc-pvtz(H-Ar), lanl2dz(K-) we have computed the chemical shifts of 37 polyoxometalates, corresponding to 209 (17)O NMR signals. We also show that at this level of theory the protonation-induced pH dependence of the chemical shift of the triprotic hexaniobate Lindqvist anion, [HxNb6O19]((8-x)), can be reproduced, which suggests that hypotheses regarding loci of protonation can be confidently tested.

Lowest ionisation and excitation energies of biologically important heterocyclic planar molecules

ABSTRACTWe calculate the lowest ionisation and excitation energies in a variety of biologically important molecules, i.e. π-conjugated systems like DNA and RNA bases and isomers plus related heterocyclic molecules. For approximately half of these molecules, there are no experimental and theoretical/numerical data in the literature, as far as we know. These electronic transitions are mainly but not exclusively of π and π–π* character, respectively. We perform symmetry-constrained density functional theory (DFT) geometry optimisation at the B3LYP/6-311++G** level of theory. At the DFT-obtained ground-state geometries, we calculate vertical ionisation energies with ionisation potential coupled cluster with singles and doubles (IP-EOMCCSD) and vertical excitation energies with the completely renormalised equation of motion coupled cluster with singles, doubles, and non-iterative triples (CR-EOMCCSD(T)) method. We also investigate whether a simple semi-empirical Hückel-type model approach with novel parametrisation could provide reasonable estimates of the lowest π ionisation and π–π* excitation energies. Our coupled cluster (CC) results are in very good agreement with experimental data, while the Hückel-type model predictions generally follow the trends with some deviation. Finally, we investigate the effect of basis set in IP-EOMCCSD energies and we compare our CR-EOMCCSD(T) results with time-dependent DFT (TDDFT) ones.

Toward Relatively General and Accurate Quantum Chemical Predictions of Solid-State (17)O NMR Chemical Shifts in Various Biologically Relevant Oxygen-Containing Compounds.

Oxygen is an important element in most biologically significant molecules, and experimental solid-state (17)O NMR studies have provided numerous useful structural probes to study these systems. However, computational predictions of solid-state (17)O NMR chemical shift tensor properties are still challenging in many cases, and in particular, each of the prior computational works is basically limited to one type of oxygen-containing system. This work provides the first systematic study of the effects of geometry refinement, method, and basis sets for metal and nonmetal elements in both geometry optimization and NMR property calculations of some biologically relevant oxygen-containing compounds with a good variety of XO bonding groups (X = H, C, N, P, and metal). The experimental range studied is of 1455 ppm, a major part of the reported (17)O NMR chemical shifts in organic and organometallic compounds. A number of computational factors toward relatively general and accurate predictions of (17)O NMR chemical shifts were studied to provide helpful and detailed suggestions for future work. For the studied kinds of oxygen-containing compounds, the best computational approach results in a theory-versus-experiment correlation coefficient (R(2)) value of 0.9880 and a mean absolute deviation of 13 ppm (1.9% of the experimental range) for isotropic NMR shifts and an R(2) value of 0.9926 for all shift-tensor properties. These results shall facilitate future computational studies of (17)O NMR chemical shifts in many biologically relevant systems, and the high accuracy may also help the refinement and determination of active-site structures of some oxygen-containing substrate-bound proteins.

Multireference configuration interaction study of dichlorocarbene

Dichlorocarbene is an important reactive chemical intermediate, which has received much investigation. However, the energy, structure, and dynamics of the excited states are not well understood. Here, we investigated the equilibrium geometries and energies of seven electronic states, X̃1A1, Ã1B1, ã3B1, B̃1A2, b̃3A2, C̃1B2 and c̃3B2 of CCl2 using internally contracted multireference configuration interaction method including Davidson correction (icMRCI+Q) with different basis sets aug-cc-pV(X+d)Z(X=T,Q,5), and the effects of different basis sets on the geometries and energies. For the first time, the theoretical studies of high excited singlet and triplet states of CCl2 that are related to the lowest three dissociation limits were carried out at the icMRCI+Q/aug-cc-pV(5+d)Z level. The results were compared with the previous experimental and theoretical data where available. Our results will add some understanding and shed some light on the structures and dynamics of electronic states of CCl2 radical.

TD-DFT Benchmark on Inorganic Pt(II) and Ir(III) Complexes

We report in the present paper a comprehensive investigation of representative Pt(II) and Ir(III) complexes with special reference to their one-photon absorption spectra employing methods rooted in density functional theory and its time dependent extension. We have compared nine different functionals ranging from generalized gradient approximation (GGA) to global or range-separated hybrids, and two different basis sets, including pseudopotentials for 4 iridium and 7 platinum complexes. It turns out that hybrid functionals with the same exchange part give comparable results irrespective of the specific correlation functional (i.e., B3LYP is very close to B3PW91 and PBE0 is very close to MPW1PW91). More recent functionals, such as CAM-B3LYP and M06-2X, overestimate excitation energies, whereas local functionals (BP86 -GGA-, M06-L -Meta GGA-) strongly underestimate transition energies with respect to experimental results. As expected, basis set effects are weak, and the use of a triple-ζ polarized (def2-TZVP) basis set does not significantly improve the computed excitation energies with respect to a classical double-ζ basis set (LANL2DZ) augmented by polarization functions, but it significantly raises the computational effort.

Molecular structure, IR spectra, and chemical reactivity of cisplatin and transplatin: DFT studies, basis set effect and solvent effect

Three different density functional theory (DFT) methods were employed to study the molecular structures of cis-diamminedichloroplatinum(II) (CDDP) and trans-diamminedichloroplatinum(II) (TDDP). The basis set effect on the structure was also investigated. By comparing the optimized structures with the experimental data, a relatively more accurate method was chosen for further study of the IR spectra and other properties as well as the solvent effect. Nineteen characteristic vibrational bands of the title compounds were assigned and compared with available experimental data. The number of characteristic peaks for the asymmetric stretching and deformation vibrations of N–H can serve as a judgment for the isomer between CDDP and TDDP. Significant solvent effect was observed on the molecular structures and IR spectra. The reduced density gradient analysis was performed to study the intramolecular interactions of CDDP and TDDP, and the nature of changes in the structures caused by the solvent was illustrated. Several descriptors determined from the energies of frontier molecular orbitals (HOMO and LUMO) were applied to describe the chemical reactivity of the title compounds. The molecular electrostatic potential (MESP) surfaces showed that the amino groups were the most favorable sites that nucleophilic reagents tend to attack, and CDDP was easier to be attacked by nucleophilic reagents than TDDP.

Relativistic coupled-cluster calculations on XeF6: Delicate interplay between electron-correlation and basis-set effects

A systematic relativistic coupled-cluster study is reported on the harmonic vibrational frequencies of the O(h), C(3v), and C(2v) conformers of XeF6, with scalar-relativistic effects efficiently treated using the spin-free exact two-component theory in its one-electron variant (SFX2C-1e). Atomic natural orbital type basis sets recontracted for the SFX2C-1e scheme have been shown to provide rapid basis-set convergence for the vibrational frequencies. SFX2C-1e as well as complementary pseudopotential based computations consistently predicts that both O(h) and C(3v) structures are local minima on the potential energy surface, while the C(2v) structure is a transition state. Qualitative disagreement between the present results for the O(h) structure and those from CCSD(T)-F12b calculations [Peterson et al., J. Phys. Chem. A 116, 9777 (2012)], which yielded a triply degenerate imaginary frequency for the O(h) structure, is attributed here to the high sensitivity of the computed harmonic frequencies of the t(1u) bending modes to the basis-set effects of triples contributions.

Active space and basis set effects in CASPT2 models of the 1,3‐butadiene‐ethene cycloaddition and the 1,3‐butadiene dimerization

The first step of the asynchronous biradical, stepwise biradical, and concerted mechanisms of the 1,3‐butadiene Diels–Alder reactions with both ethene and itself was studied using CASPT2 to determine the influence of basis set and active space on reaction barriers. CASPT2(6,6) with the cc‐pVDZ, 6‐311+G(3df,2p) and cc‐pVTZ basis sets provided the best results with average errors below 3.1 kJ mol−1 with respect to the experimental result. Increasing the active space size also had little effect on the calculated reaction barriers. With respect to experimental results, uncontracted multireference averaged quadratic coupled cluster (MRAQCC) produced superior barriers than internally contracted MRAQCC by 16.1–39.3 kJ mol−1. The inability of CASSCF to locate transition states for some of the cycloadditions across the butadiene‐ethene and butadiene dimerization reactions is also rationalized. CASPT2 suggests a preference for the concerted mechanism of the butadiene‐ethene reaction, however, no basis set yielded a preference for any of the butadiene dimerization pathways. © 2015 Wiley Periodicals, Inc.

First-Principles Calculations of the Energy and Width of the (2)A(u) Shape Resonance in p-Benzoquinone: A Gateway State for Electron Transfer.

Quinones are versatile biological electron acceptors and mobile electron carriers in redox processes. We present the first ab initio calculations of the width of the (2)A(u) shape resonance in the para-benzoquinone anion, the simplest member of the quinone family. This resonance state located at 2.5 eV above the ground state of the anion is believed to be a gateway state for electron attachment in redox processes involving quinones. We employ the equation-of-motion coupled-cluster method for electron affinity augmented by a complex-absorbing potential (CAP-EOM-EA-CCSD) to calculate the resonance position and width. The calculated width, 0.013 eV, is in excellent agreement with the width of the resonant peak in the photodetachment spectrum, thus supporting the assignment of the band to resonance excitation to the autodetaching (2)A(u) state. The methodological aspects of CAP-EOM-EA-CCSD calculations of resonances positions and widths in medium-sized molecules, such as basis set and CAP box size effects, are also discussed.

Toward selection of efficient density functionals for van der Waals molecular complexes: comparative study of C-H···π and N-H···π interactions.

We have evaluated the performance of two of the recently developed density functionals (M06-2X and B2PLYP-D), which are widely used, by considering three important prototype systems, including benzene-acetylene, benzene-methane, and benzene-ammonia, possessing C-H···π or N-H···π interactions. Computational results are compared with the available experimental data. Considered density functionals are from two different classes: hybrid meta density functional (M06-2X) and double hybrid density functional (B2PLYP-D). The performance of a range of basis sets (6-31G(d), 6-31+G(d), 6-31+G(d,p), 6-311G(d,p), 6-311+G(d,p), aug-cc-pVXZ (X = D, T, Q)) with the above-mentioned two density functionals was evaluated. Comparison of the results includes Pople's basis sets versus Dunning's correlation consistent basis sets with the M06-2X and B2PLYP-D functionals considered in this study. The basis set effect on geometrical parameters, dissociation energies, and selected vibrational frequency shifts was thoroughly analyzed. We have addressed whether the counterpoise corrections with geometry optimizations and vibrational frequencies are important. Our computational study reveals that calculations carried out with smaller basis sets very well reproduce the reported experimental values of dissociation energies. The present study also shows that using the very large Dunning's correlation consistent basis set worsens the results. The necessity of including counterpoise correction for binding energies depends on the system and the type of method used. In general, vibrational frequency calculations using these DFT functionals generate characteristic red shifts for the C-H···π or N-H···π interactions in the complexes.

DFT Studies on the Mechanism of Palladium(IV)-Mediated C–H Activation Reactions: Oxidant Effect and Regioselectivity

A series of density functional theory calculations have been employed to study the PdIV-mediated C–H activation in CD3CN solvent. B3LYP/DZVP, B3LYP/BS1, and B3LYP-D3/DZVP were comparatively employed to locate the geometric parameters of possible stationary points, with IDSCRF radii constituting the cavity. The novel reaction mechanism provided was divided into three distinct steps: oxidation addition, ligand substitution, and C–H activation. The distinct chemical behaviors of different oxidants have been addressed with Bader’s atoms-in-molecules wave function analysis, providing a reasonable explanation for the experimental observation. Regioselectivity was dynamically controlled by the rate-determining oxidation step. At the same time, the basis set effect was also discussed for this PdII → PdIV transformation.

Computation of Electron Affinities with the Second Order Multireference Perturbation Theory

Electron affinities of F, Cl, OH, SH, CN, CH2, and NH2 have been computed with the second order multireference perturbation theory. The effects of basis set and size of the complete active space on accuracy of electron affinity have also been investigated. The results are compared with calculations performed with CASSCF, CASPT2, CCSD, CCSD(T), B3 LYP, X3 LYP, M06, HCTH, TPSS, B97D3,mPW2PLYP, and B2PLYP. The overall performance of the second order multireference perturbation theory is best at the level of basis sets used in this study.

Estimating the Impact of an All-Electron Basis Set and Scalar Relativistic Effects on the Structure, Stability, and Reactivity of Small Copper Clusters

Basis sets of valence double and quadruple zeta qualities and the Douglas-Kroll-Hess (DKH) approximation are used to estimate the impact of an all-electron basis set and scalar relativistic effects on the structure, stability, and electronic properties of small neutral copper clusters (Cun, n ≤ 8). At the Becke three-parameter for exchange and Perdew-Wang 91 for correlation (B3PW91) non-relativistic and relativistic levels of theory, the bond length, binding energy, ionization potential, electron affinity, chemical potential, chemical hardness, and electrophilicity index are calculated. The results show that the agreement with experiment improves significantly when the DKH Hamiltonian combined with an all-electron relativistic basis set is used. Polarizabilities and hyperpolarizability are also reported. At the B3PW91 level, all-electron basis sets are shown to be more reliable than effective core potential valence basis sets in the determination of the second hyperpolarizability of copper clusters.

Two-photon absorption properties of novel charge transfer molecules with divinyl sulfide/sulfone center

Organic materials with strong two-photon absorption response have attracted a great deal of interest in recent years for their many potential applications such as two-photon fluorescence microscopy, optical limiting, photodynamic therapy, and so on. Theoretical study on the relationships between molecular structure and two-photon absorption property has great importance in guiding the experimental design and synthesis of functional materials. Nowadays, quantum chemical calculations become very useful and popular tools in investigating the structure-property relations. At the same computational level, the two-photon absorption properties of different compounds can be compared accurately, and thus provide reasonable structure-property relations. Recently, a series of novel divinyl sulfides/sulfonesbased molecules have been synthesized and it is found that their photophysical properties behave like quadrupolar charge-transfer chromophores. In order to explore their potential two-photon absorption applications, in this paper, the two-photon absorption properties of these new molecules are calculated by using quantum chemical methods. Their molecular geometries are optimized at the hybrid B3LYP level with 6-31+g(d, p) basis set in the Gaussian 09 program. The two-photon absorption cross sections are calculated by response theory using the B3LYP functional with 6-31g(d) and 6-31+g(d) basis sets respectively in the Dalton program. In response theory, the single residue of the quadratic response function is used to identify the two-photon transition matrix element. Using the same methods, the two-photon absorption properties of distyrylbenzene compounds are computed for comparison. The basis set effects on excitation energies and two-photon absorption cross sections have been checked. It is found that the use of large basis sets could probably provide better numerical results, but the overall property trends would not change. Calculations show that the molecule with a triphenylamine group has the largest cross-section due to its strong donor groups. The divinyl sulfones-based dyes have larger cross-sections than the corresponding sulfides-based ones, because divinyl sulfones have stronger capability to accept electrons and at the same time the torsional angles between benzene rings in sulfones-based molecules are smaller than in the sulfides-based molecules. In the applicable wavelength range, these new dyes exhibit large two-photon absorption cross-sections which have the same order of magnitude as the strong two-photon absorption molecules with similar conjugation length. The largest cross section comes to 1613.3 GM calculated by using 6-31g(d) basis set. Molecular orbitals involved in the strongest two-photon absorption excitations are plotted and the charge transfer process is analyzed at length. The divinyl sulfide and sulfone centers behave as electron withdrawing groups and can form effective charge transfer molecules. On the basis of these new molecules, the structure inducing two-photon absorption enhancement is designed by employing isomerism effect. When the benzene rings of carbazole groups are connected with the molecular center, the planarity and charge transfer intensity are increased, and then the two-photon absorption cross-section can be improved dramatically. This study provides theoretical guidelines for the synthesis of new type of active two-photon absorption materials.

Absorption and fluorescence spectra of poly(p-phenylenevinylene) (PPV) oligomers: an ab initio simulation.

The absorption and fluorescence spectra of poly(p-phenylenevinylene) (PPV) oligomers with up to seven repeat units were theoretically investigated using the algebraic diagrammatic construction method to second order, ADC(2), combined with the resolution-of-the-identity (RI) approach. The ground and first excited state geometries of the oligomers were fully optimized. Vertical excitation energies and oscillator strengths of the first four transitions were computed. The vibrational broadening of the absorption and fluorescence spectra was studied using a semiclassical nuclear ensemble method. After correcting for basis set and solvent effects, we achieved a balanced description of the absorption and fluorescence spectra by means of the ADC(2) approach. This fact is documented by the computed Stokes shift along the PPV series, which is in good agreement with the experimental values. The experimentally observed band width of the UV absorption and fluorescence spectra is well reproduced by the present simulations showing that the nuclear ensemble generated should be well suitable for consecutive surface hopping dynamics simulations.

Hydrogen Abstraction Reaction of Hydroxyl Radical with 1,1-Dibromoethane and 1,2-Dibromoethane Studied by Using Semi-Classical Transition State Theory

The hydrogen abstraction reaction by OH radical from CH2BrCH2Br (R1) and CH₃CHBr2 (R2) is investigated theoretically by semi-classical transition state theory. The stationary points for both reactions are located by using ωB97X-D and KMLYP density functional methods along with cc-pVTZ basis. Single-point energy calculations are performed at the QCISD(T) and CCSD(T) levels of theory with different basis sets. The results show that the activation energies are very sensitive to effects of electron correlation and basis set. In order to correct basis set effects on the calculated energetic, a correction factor (CF) is determined from the energy difference between the MP2/cc-pVTZ and MP2/aug-cc-pVTZ levels. xij vibrational anharmonicity coefficients, needed for semi-classical transition state theory, are calculated at the KMLYP/cc-pVTZ level of theory. Thermal rate coefficients are computed over the temperature range from 200 to 3000 K and they are shown to be in accordance with available experimental data. The computed rate constants for the reactions R1 and R2 are fitted to the equation k(T)=A T^n exp[-E(T+T_0 )/(T^2+ T_0^2 ) ].

Experimental and theoretical characterization of the 2-(4-bromobenzyl)-5-ethylsulphonyl-1,3-benzoxazole

Synthesis, crystal structure, Fourier transform infrared spectroscopy (FT-IR) and quantum mechanical studies of the 2-(4-bromobenzyl)-5-ethylsulphonyl-1,3-benzoxazole (C16H14NO3SBr) have been reported. The molecular structure obtained from X-ray single-crystal analysis of the investigated compound in the ground state has been compared using Hartree–Fock (HF) and density functional theory (DFT) with the functional B3LYP and B1B95 using the 6-311++G(d,p) basis set. In addition to the optimized geometrical structures, atomic charges, molecular electrostatic potential (MEP), natural bond orbital (NBO), nonlinear optical (NLO) effects and thermodynamic properties of the compound have been investigated by using DFT. The potential energy surface (PES) scans about four important torsion angles are performed by using B3LYP/6-311++G(d,p) level of theoretical approximation for the compound. The experimental (FT-IR) and calculated vibrational frequencies (using DFT) of the title compound have been compared. The total molecular dipole moment (μ), linear polarisability (α), and the first-order hyperpolarisability (β) were predicted by using DFT with different basis sets 6-31G(d), 6-31+G(d,p), 6-31++G(d,p), 6-311+G(d) and 6-311++G(d,p) for investigating the effects of basis sets on the NLO properties. Our computational results yield that βtot for the title compound is greater than those of urea. The standard thermodynamic functions were obtained for the title compound with the temperature ranging from 200 to 450K.

A first-principles examination of the asymmetric induction model in the binap/Rh(I)-catalysed 1,4-addition of phenylboronic acid to cyclic enones by density functional theory calculations.

First-principles modelling of the diastereomeric transition states in the enantiodiscrimination stage of the catalytic cycle can reveal intimate details about the mechanism of enantioselection. This information can be invaluable for further improvement of the catalytic protocols by rational design. Herein, we present a density functional theory (IEFPCM/PBE0/DGDZVP level of theory) modelling of the carborhodation step for the asymmetric 1,4-arylation of cyclic α,β-unsaturated ketones mediated by a [(binap)Rh(I)] catalyst. The calculations completely support the older, qualitative, pictorial model predicting the sense of the asymmetric induction for both the chelating diphosphane (binap) and the more recent chiral diene (Phbod) ligands, while also permitting quantification of the enantiomeric excess (ee). The effect of dispersion interaction correction and basis sets has been also investigated. Dispersion-corrected functionals and solvation models significantly improve the predicted ee values.