Density Functional Theory Procedures Research Articles

On the Nature of DNA‐Duplex Stability

The unwinding free energy of 128 DNA octamers was correlated with the sum of interaction energies among DNA bases and their solvation energies. The former energies were determined by using the recently developed density functional theory procedure augmented by London dispersion energy (RI-DFT-D) that provides accurate hydrogen-bonding and stacking energies highly comparable with CCSD(T)/complete basis set limit benchmark data. Efficient tight-binding DFT covering dispersion energy was also used and yielded satisfactory results. The latter method can be used for extended systems. The solvation energy was determined by using a C-PCM continuum solvent at HF level calculations. Various models were adopted to correlate theoretical energies with experimental unwinding free energies. Unless all energy components (hydrogen-bonding, intra- and interstrand-stacking, and solvation energies) were included and weighted individually, no satisfactory correlation resulted. The most advanced model yielded very close correlation (RMSE=0.32 kcal mol(-1)) fully comparable with the entirely empirical correlation introduced in the original paper. Analysis of the theoretical results shows the importance of inter- and intramolecular stacking energies, and especially the latter term plays a key role in determining DNA-duplex stabilization.

Electronic excitation in a syn-tetrasilane: 1,1,2,2,3,3, 4,4-octamethyltetrasilacyclopentane

We present a multistate complete active space second-order perturbation theory (MS-CASPT2) study of the low-lying valence excited states of a peralkylated tetrasilacyclopentane, c-(CH2Si4Me8) (1). The lowest-lying calculated valence excited states are located in the 37,400–50,500 cm−1 region, in perfect agreement with experimental observations, 38,600–50,000 cm−1. The MS-CASPT2 results provide a very good description of the nature, intensity, and position of the observed absorption bands, including the recently detected fourth electronic transition. The computational results have been used as a benchmark for evaluating a time-dependent density functional theory (TD-DFT) procedure suitable for calculations on longer oligosilanes.

Theoretical study of neutral and reduced hexacyanobutadiene

The molecular structure and the electronic densities of neutral and anionic hexacyanobutadiene (HCBD), trans-C 4(CN) 6, as well as the electron affinity (EA) of HCBD have been studied using density functional theory (DFT) and perturbation theory (MP2) procedures. The optimized geometries showed that the HCBD molecule is not planar, with a 140° torsion angle about the central C–C bond. While the optimized geometries are not very sensitive to the choice of either the method or the basis set, the adiabatic electron affinity varies significantly with both. All the DFT computed electron affinities overestimate the experimental value, the best results being obtained with the BLYP functional, whereas the MP2 calculations heavily underestimate it. At the MP2 level, the EA value obtained after projecting out the major spin contaminating component (PMP2) is a good estimate of the EA, within 0.11 eV of the experiment. Although other studies suggested that single-point PMP2 calculations over DFT-optimized geometries could be a valuable alternative for the study of larger systems at low computational effort, our results indicate that this approach can increase the spin contamination and should be used with caution.

Extended treatment of charge response kernel comprising the density functional theory and charge regulation procedures

We propose an extended treatment of the charge response kernel (CRK), (partial differential Q(a)/partial differential V(b)), which describes the response of partial charges on atomic sites to external electrostatic potential, on the basis of the density functional theory (DFT) via the coupled perturbed Kohn-Sham equations. The present CRK theory incorporates regulation procedures in the definition of partial charges to avoid unphysical large fluctuation of the CRK on "buried" sites. The CRKs of some alcohol and organic molecules, methanol, ethanol, propanol, butanol, dimethylsulfoxide (DMSO), and tetrahydrofuran (THF) were calculated, demonstrating that the new CRK model at the DFT level has greatly improved the performance of accuracy in comparison with that at the Hartree-Fock level previously proposed. The CRK model was also applied to investigate spatial nonlocality of the charge response through alkyl chain sequences. The CRK model at the DFT level enables us to construct a nonempirical strategy for polarizable molecular modeling, with practical reliability and robustness.

An Assessment of Theoretical Procedures for Predicting the Thermochemistry and Kinetics of Hydrogen Abstraction by Methyl Radical from Benzene

The reaction enthalpy (298 K), barrier (0 K), and activation energy and preexponential factor (600-800 K) have been examined computationally for the abstraction of hydrogen from benzene by the methyl radical, to assess their sensitivity to the applied level of theory. The computational methods considered include high-level composite procedures, including W1, G3-RAD, G3(MP2)-RAD, and CBS-QB3, as well as conventional ab initio and density functional theory (DFT) methods, with the latter two classes employing the 6-31G(d), 6-31+G(d,p) and/or 6-311+G(3df,2p) basis sets, and including ZPVE/thermal corrections obtained from 6-31G(d) or 6-31+G(d,p) calculations. Virtually all the theoretical procedures except UMP2 are found to give geometries that are suitable for subsequent calculation of the reaction enthalpy and barrier. For the reaction enthalpy, W1, G3-RAD, and URCCSD(T) give best agreement with experiment, while the large-basis-set DFT procedures slightly underestimate the endothermicity. The reaction barrier is slightly more sensitive to the choice of basis set and/or correlation level, with URCCSD(T) and the low-cost BMK method providing values in close agreement with the benchmark G3-RAD value. Inspection of the theoretically calculated rate parameters reveals a minor dependence on the level of theory for the preexponential factor. There is more sensitivity for the activation energy, with a reasonable agreement with experiment being obtained for the G3 methods and the hybrid functionals BMK, BB1K, and MPW1K, especially in combination with the 6-311+G(3df,2p) basis set. Overall, the high-level G3-RAD composite procedure, URCCSD(T), and the cost-effective DFT methods BMK, BB1K, and MPW1K give the best results among the methods assessed for calculating the thermochemistry and kinetics of hydrogen abstraction by the methyl radical from benzene.

Transfer hydrogenation between ethane and ethene: a critical assessment of theoretical procedures§

The prototypical transfer-hydrogenation reaction between ethane and ethene has been examined with quantum chemistry procedures. Methods used include high-level single-reference procedures such as CCSD(T), BD(T) and CCSDT, high-level multi-reference procedures such as CASPT2, CAS-ACPF and CAS-AQCC, and less computationally demanding density functional theory procedures such as B3-LYP, MPWB1K and BMK. The concerted pathway for this reaction is clearly favoured over the stepwise process. The best prediction of the concerted barrier is 210 kJ mol–1. An anti transition structure for the stepwise pathway lies 70 kJ mol–1 higher in energy. It is found that the concerted transition structure has relatively little biradical character but that incorporation of dynamic correlation is very important for its accurate theoretical description. The stepwise transition structure has considerable biradical character and, among traditional methods, either high-level multi-reference procedures (e.g. CAS-AQCC) or broken-spin-symmetry single-reference procedures (e.g. UBD(T) or UCCSD(T)) are required for reliable results. Broken-spin-symmetry density functional theory methods such as UMPWB1K and UBMK provide a cost-effective alternative for examining both pathways. § In celebration of the 60th birthday of Professor Michael Robb and in recognition of Mike's contributions to science.

An Evaluation of Various Computational Methods for the Treatment of Organoselenium Compounds

A reliable computational method for the prediction of organoselenium geometries and bond dissociation energies (BDEs) has been determined on the basis of the performance of density functional theory (DFT: B3LYP and B3PW91) and ab initio molecular orbital procedures (Hartree-Fock (HF)) in conjunction with various Pople basis sets including (but not limited to) the 6-31G(d), 6-31G(d,p), 6-311G(d), 6-311G(d,p), 6-311G(2df,p), and 6-311G(3df,3pd) sets. Predicted geometries and BDEs are compared with available experimental data and quadratic configuration interaction including single and double substitutions (QCISD) results. The B3PW91/6-311G(2df,p) level of theory is recommended for the prediction of the geometries and energetics of organoselenium compounds.

Modeling β-Scission Reactions of Peptide Backbone Alkoxy Radicals: Backbone C−C Bond Fission

To model the C-C β-scission reactions of backbone peptide alkoxy radicals, enthalpies and barriers for the fragmentation of four substituted alkoxy radicals have been calculated with a variety of ab initio molecular orbital theory and density functional theory procedures. The high-level methods examined include CBS-QB3, variants of the G3 family, and W1. Simpler methods include HF, MP2, QCISD, B3-LYP, BMK, and MPW1K with a range of basis sets. We find that good accuracy can be achieved with the G3(MP2)//B3-LYP and G3X(MP2)-RAD methods. Lower-cost methods producing reasonable results are single-point energy calculations with UB3-LYP/6-311+G(3df,2p), RB3-LYP/6-311+G(3df,2p), UBMK/6-311+G(3df,2p), and RBMK/6-311+G(3df,2p) on geometries optimized with UB3-LYP/6-31G(d) or UBMK/6-31G(d). Heats of formation at 0 K for the alkoxy radicals and their fragmentation products were also calculated. We predict ΔfH0 values for the alkoxy radicals of -71.4 ((•)OCH2CH [Formula: see text] O), -102.5 ((•)OCH(CH3)CH [Formula: see text] O), -176.6 ((•)OCH(CH3)C(NH2) [Formula: see text] O), and -264.6 ((•)OC(CH3)(NHCH [Formula: see text] O)CH [Formula: see text] O) kJ mol(-)(1). For the fragmentation products NH2C((•)) [Formula: see text] O and CH( [Formula: see text] O)NHC(CH3) [Formula: see text] O, we predict ΔfH0 values of -5.9 kJ mol(-)(1) and -352.8 kJ mol(-)(1).

Ab initio analysis of electron currents in thioalkanes

AbstractA combined density functional theory and Green's function procedure is used to calculate the electrical characteristics of a group of alkanethiols representing possible experimental settings. It is found that the current running through the molecule is the sum of the contributions from all molecular orbitals each presenting a barrier to electron transport equal to their energy difference from the Fermi level of the contacts. For the alkanethiols the location of these intrinsic barriers are at 0.78 eV (highest occupied molecular orbital [HOMO] and HOMO‐1), 1.99 eV (HOMO‐2 and HOMO‐3), 2.07 eV (LUMO and LUMO+1), and 2.67 eV (HOMO‐4). However, barriers obtained through fittings to known models do not bear any physical meaning at the molecular level, as they are sort of exponential average of the intrinsic barriers. We have also found that the exponential dependence of the current with the length of the alkane is practically independent of the contact nature, perhaps due to the large resistance of the alkanes. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005

A theoretical study of neutral and reduced tetracyano- p-quinodimethane (TCNQ)

The molecular structure of neutral, anionic, and dianionic tetracyano- p-quinodimethane (TCNQ), as well as the electron affinity of TCNQ, have been studied with HF, MP2, and different density functional theory (DFT) procedures. The optimized geometries compare well with the available experimental data, although the C N bond distance is not correctly described at the MP2 level. The calculated parameters are rather insensitive to the basis set employed, and the addition of diffuse functions does not yield significant changes. When the extra electrons are added, the central ring of TCNQ progressively becomes more aromatic. Compared with the CCSD(T) estimate, the value of the adiabatic electron affinity is overestimated at the DFT level. The B3P86 functional leads to the largest deviations, higher than 1 eV, whereas the BLYP functional affords the best results. At the MP2 level, the value obtained after projection of the major spin contaminating component (PMP2) is in good agreement with the CCSD(T) result. Single-point PMP2 calculations over DFT-optimized geometries are suggested as a low-cost alternative strategy to study more extended systems.

Molecular Orbital Calculations of Water Clusters on Counterpoise-Corrected Potential Energy Surfaces

Water dimer and the cyclic trimer and tetramer are calculated using the Hartree−Fock (HF), second-order Møller−Plesset (MP2), and two density functional theory (DFT) methods, B3PW91 and B3LYP for a wide variety of different basis sets. The interaction energies and O···O distances as calculated on the normal and counterpoise (CP) corrected potential energy surfaces (PES) are compared as a function of basis set quality (as measured by the energies for optimized water monomer) for each of the four methods. The HF and DFT procedures lead to reasonably rapid conversion to the large basis set values for both interaction energies and O···O distances. Even moderate basis sets can be used to obtain results similar to the extrapolated values when optimizations are performed on the CP-corrected PES's. For MP2, these energies and distances converge to the extrapolated values much more slowly. Basis set superposition error (BSSE) remains significant even for the best basis sets used (aug-cc-pVQz and aug-cc-pVTZ). Nevertheless, the extrapolated MP2 interaction energies could also be reproduced with moderate sized basis sets on the CP-corrected PES, although the calculated O···O distances were less well reproduced with moderate sized basis sets. We calculated the CP using the procedure where each fragment is calculated in the basis if the entire aggregate. The results show this procedure to be well-behaved, as the normal and CP-optimized calculations converged systematically to the same values as the basis set improved for all four methods used. The advantages of this practice over a proposed hierarchical procedure for calculating the CP are discussed. A misconception about the supposed superiority of the latter procedure is remedied.

Interactions between Neutral Molecules and Ca2+: An Assessment of Theoretical Procedures

The performance of a selection of theoretical procedures in describing the binding of Ca2+ to ammonia and formaldehyde has been assessed. Geometries and vibrational frequencies were obtained using the density functional theory procedures, B3-LYP and G96-LYP, as well as with CCSD(T) with a variety of basis sets, with the CCSD(T)/cc-pWCVQZ-optimized structures being used as a reference. Binding energies, including the consideration of basis set superposition errors, were additionally obtained with variants of the G3, W1C, and W2C methods, with the W2C values providing benchmark values in this case. We find that Ca−X (X = N, O) bond lengths for the [Ca−NH3]2+ and [Ca−OCH2]2+ complexes show some sensitivity both to the size of the basis set and to the theoretical procedure employed. In general, the Ca−X lengths decrease as the basis set is systematically enlarged. The B3-LYP and G96-LYP methods yield Ca−X distances that are slightly shorter than the CCSD(T) values obtained with the same basis set. As a consequence of these two factors, B3-LYP/cc-pWCVTZ and B3-LYP/6-311+G(3df,2p) give very reasonable geometries for the two complexes. The B3-LYP/cc-pWCVTZ and G96-LYP/cc-pWCVQZ approaches provide a good compromise between accuracy and computational cost in the calculation of binding energies. Ca2+ is predicted to bind more strongly to formaldehyde than to ammonia, in contrast to the ordering of proton and Li+ affinities for the two molecules.

Theoretical study of the molecular structure and the stability of neutral and reduced tetracyanoethylene

The molecular structure and the stability of neutral, anionic, and dianionic tetracyanoethylene (TCNE) have been studied with MP2, coupled-cluster (CC), and density functional theory (DFT) procedures. The optimized geometries are in agreement with the available experimental data, although significant deviations for the CN bond distance have been obtained at the MP2 level. The adiabatic electron affinity of TCNE calculated with the B3LYP method is overestimated by 0.32 eV. In the light of the CC results, the source of such an overestimation is suggested to lie on the theoretical approach, rather than on a too low experimental value.

Excitation energies of a molecule close to a metal surface

A model for the calculation of excitation energies of molecules close to a metal surface is presented. The molecule is treated at the density functional theory (DFT) or Hartree–Fock (HF) level and the excitation energies are calculated through a time dependent DFT (TDDFT) or time dependent HF (TDHF) procedure. The metal is treated as a continuous body characterized by its frequency dependent dielectric constant, taken from experiments, in the case modified to take into account nonlocal effects in the response to the metal. Such effects are accounted for by using the specular reflection model and a hydrodynamic correction to the dielectric constant. The presence of a solvent is described with the Polarizable Continuum Model. The (quasi-)electrostatic interactions between the molecule and the metal–solvent environment are treated by exploiting the integral equation formalism, numerically solved through a boundary element method. Applications of the method are given to show its numerical accuracy and the dependence of the results on the various parameters of the model (e.g., nature of the molecule, solvent, chemical nature of the metal, metal–molecule distance).

On the direct exchange energy in 2. Co 2+ doped ZnCo lattices

In our previous work [J. Mol. Struct. (THEOCHEM) (2002)] we reported the Co–Co direct exchange energies in Co doped films. In efforts to try to understand the internuclear interaction we present the results of our simulations (on Zn 0.85Co 0.15O film as an example) and quantum chemical calculations on the direct exchange energies between a d 10 atom (Zn) and Co. Whereas for the Co–Co system, the B3PW91 method was the only density functional theory procedure capable of producing reasonable results (compared to empirical findings), in the Zn–Co system, the B1LYP, B3P86, and B3PW91 yield favorable results, however, the HF and B3LYP (which produce similar results within 4 kcal mol −1 from one another) fail to correlate with previous experimental and theoretical values.

Hydrogen-Bonding Interactions between Formic Acid and Pyridine

The structure, energetics, vibrations, and barrier to internal rotation around the N···H−O hydrogen bond of the binary pyridine−formic acid complex are calculated using one properly selected hybrid density functional theory procedure. The calculations demonstrate that the most stable isomer of the complex has a strong N···H−O hydrogen-bonding interaction, whose strength is enhanced by the presence of an agostic interaction between the carbonylic oxygen and the α hydrogen of the pyridine. Rotation around N···H−O, which prevents such an agostic interaction to occur, results in a decrease of the bonding energy of the complex from 11.1 kcal/mol to 6.43 kcal/mol. Additionally, a normal-mode analysis of the vibrations of the two most stable complexes characterized has been carried out and compared with the experimental vibrational frequencies of the pyridine-acetic acid complex. Furthermore, the effect of the specific solvation by one more formic acid molecule and one methanol molecule has also been considered....

Methodologies for Computational Studies of Quininoidal Diiminediyls: Biradical vs Dinitrene Behavior

Density functional and post Hartree−Fock ab initio computations were carried out on the lowest singlet, triplet, and quintet states of 1,4-phenylenedinitrene, biphenyl-4,4‘-dinitrene, (E)-stilbene-4,4‘-dinitrene, and (E,E)-1,4-bis(4-nitrenophenyl)-1,3-butadiene, and (E,E,E)-1,6-bis(4-nitrenophenyl)-1,3,5-hexatriene. Near-degenerate singlet and triplet quinonoidal ground states were found for all systems using CASSCF methodology, with a slight favoring of the singlet, in accord with experimental results. The aromatic quintet dinitrene states lie much higher in energy. Restricted B3LYP hybrid density functional theory (DFT) methods give artifactually high biradical singlet state energies relative to the triplet biradical states, but unrestricted (mixed-state) B3LYP methods correctly give singlet energies that lie somewhat below the triplet state energies, as well as giving geometric results that compare well to the best CASSCF results we could achieve for these biradical states. Appropriate guidelines for selecting CASSCF versus DFT procedures in such cases are suggested in light of comparisons of computed to experimental results.

Infrared and Raman spectra and theoretical study of methyl trifluoromethyl sulfone, CF 3SO 2CH 3

The infrared and Raman spectra were obtained for liquid CF 3SO 2CH 3, as well as the infrared spectrum of the gaseous substance. The molecular geometry was optimized by means of the Hartree–Fock (HF), second order electron correlation (MP2) and density functional theory (DFT) procedures of quantum chemistry, resulting in a structure with C s symmetry. The wavenumbers corresponding to the normal modes of vibration were calculated using the DFT (B3LYP/6-31G**) approximation and their agreement with the measured values improved after scaling of the associated force field. An assignment of bands is proposed on the basis of such calculations and the comparison with related molecules.

Cyanovinyl radical: an illustration of the poor performance of unrestricted perturbation theory and density functional theory procedures in calculating radical stabilization energies

Stabilization energies for the 1-cyanovinyl radical (CH2=CCN) have been calculated using a variety of conventional ab initio (Moller–Plesset, quadratic configuration interaction and coupled-cluster) and density functional theory (B-LYP, B3-LYP) procedures, as well as with a range of compound methods. Compared with a high-level benchmark value (that predicts a stabilization energy of 17.1 kJ mol−1), UMP2 and UMP4 give the wrong sign and magnitude of the stabilization energy (both methods predicting desta- bilization instead of stabilization), while B-LYP and B3-LYP overestimate the degree of stabilization. The RMP2, RMP4, QCISD(T) and CCSD(T) techniques, and several, but not all, variants of G2 and CBS theories give radical stabilization energies in good agreement with the benchmark value.

Density-functional calculation of the inner-shell spectra for two stable enol tautomers: acetylacetone and malonaldehyde

Abstract In this paper we report results from our theoretical studies on two β-diketones which exist as stable enol tautomers: acetylacetone and malonaldehyde. We found that density functional theory (DFT) with Becke's exchange functional and Perdew's correlation functional can accurately predict the core–electron binding energies (CEBEs) of both molecules. The oxygen 1 s →π* inner-shell excitation spectra (ISES) of both tautomers have also been studied using our DFT procedure. The CEBEs for the corresponding carbons and oxygens of the CO and C–OH groups of malonaldehyde are larger than those of acetylacetone. The first term values corresponding to a core-hole on the carbonyl oxygen were found to be larger than those with a core-hole on the enol oxygen. The observation indicates that the effect of a core-hole in the proximity of π* orbital has a stronger effect on increasing the electron affinity of the core-ionized cation.