B97D Functionals Research Articles

Molecular Structure, Vibrational Spectrum and Conformational Properties of 4-(4-Tritylphenoxy)phthalonitrile-Precursor for Synthesis of Phthalocyanines with Bulky Substituent.

By DFT method with B3LYP, PBE, CAM-B3LYP, and B97D functionals, it was found that the molecule 4-(4-tritylphenoxy)phthalonitrile (TPPN) has four conformers. The geometric structure, vibrational frequencies, electronic characteristics, and thermodynamic functions of conformers, as well as the structure and energy of transition states, were determined. IR spectrum of TPPN film contains vibrational bands belonging to different conformers. The assignment of bands was performed basing the distribution of normal vibration energy on internal coordinates. A synchronous electron diffraction/mass spectrometric experiment was performed to determine the structure of conformers in a saturated TPPN vapor. The elemental composition of the ions recorded in the mass spectrum indicates the thermal stability of TPPN at least up to T = 200 °C. The difference in the structure of tetrasubstituted metal phthalocyanines, which can be synthesized from different TPPN conformers, has been shown.

Comparison of the accuracy of DFT methods for reactions with relevance to nitrogenase

We have studied the accuracy of 16 different density functional theory methods to reproduce experimental data for bond lengths, angles, vibrational frequencies, as well as enthalpies and entropies for the binding of N2, H2, CO and hydride ions to various transition-metal complexes (with Fe, Ni, Cr, Mo and W) with relation to nitrogenase. We show that generalized gradient approximation functionals give better structure-related parameters, whereas hybrid functionals often give better energies. However, the BLYP and B97D functionals seem to give reasonably accurate results for both types of properties. Geometries and entropies are converged with split-valence basis sets, but energies and vibrational frequencies (and therefore also thermal corrections) in general require a basis set of triple-zeta quality. Dispersion corrections are important to obtain accurate energies (contributing by up to 57 kJ mol−1), as well as structures.

Is the VCD spectrum a fingerprint of the conformational population? The conformation of perezone in the spotlight

Abstract The M06–2X, B3LYP, ωB97XD and B97D functionals with the 6–311++G(2d,2p) and DGDZVP basis sets were used to describe the stationary points of minimum energy of the potential energy surface of perezone. The inability of theoretical methods to predict a consistent conformational order, including the effects of zero point energy and dielectric constant was highlighted. Perezone was used as a model of study since it is known that weak interactions are involved in its conformation and represent a challenge of study for theoretical methods. Each level of theory here employed generated a significantly different conformational population, ranging from 75% participation of folded conformers (where a π/π stabilizing interaction was predicted) to less than 5%, without producing a uniform conformational order. Surprisingly, in every case, the constructed Vibrational Circular Dichroism (VCD) spectrum with each level of theory was able to reproduce the experimental spectrum with high level of confidence. The correct R configuration of the stereogenic center of perezone was predicted in all cases.

Interaction of positional isomers of dimethylbenzene with graphite

The optimized geometries and interaction energies of the intermolecular heterodimers of coronene with o-, m-, and p-dimethylbenzenes (xylenes) calculated by DFT in the PBE0 and B97D functionals were compared. The applicability of coronene as a model for qualitative assessment of the interaction of mononuclear aromatic compounds with the graphite surface was demonstrated. The necessity of including long-range dispersion interactions in DFT calculations of the dimerization energies of aromatic systems was shown. The sorption enthalpies of p- and m-xylenes were shown to be almost equal irrespective of the conditions of the chromatographic experiment. The preferred sorption of p- over m-xylene on graphite is solely due to the entropy factor.

Analysis of the structural and thermodynamic parameters of the hydrogen bond in complementary pairs of DNA and RNA bases

Density functional methods involving the B3LYP functional and M062X, WB97XD, and B97D ones optimized for calculations of long-range interactions are used to carry out theoretical analysis of the structural and thermodynamic parameters of complementary adenine-thymine, adenine-uracil, and guanine-cytosine base pairs with hydrogen bonds. The calculated values of the structural and thermodynamic parameters are corrected according to the basis superposition error. The enthalpy factor is demonstrated to prevail over the entropy one during the formation of the guanine—cytosine complex, indicating that the equilibrium constant is of great importance. It is discussed whether the M062X, WB97XD, and B97D functionals can be applied to describe hydrogen-bonded systems.

A DFT study on the role of long range correlation interaction and solvent effects in homochiral and heterochiral cyclic trimerization of imidazole based heterocyclic amino acids.

Using B3LYP and B97D functionals of density functional theory (DFT), homochiral and heterochiral cyclic trimerization of imidazole based heterocyclic amino acids are studied in gas phase and solvent phase, i. e., Acetonitrile. Both the functionals show that formation of homochiral cyclic tripeptide is thermodynamically and kinetically favorable over its heterochiral counterpart in gas phase. The functional, B97D, decreases the height of reaction barriers significantly compared to those predicted by the functional B3LYP. The reaction pathways explored using PCM implicit solvent model show reduced kinetic favorability for formation of the homochiral cyclic tripeptide over its heterochiral counterpart. The results are substantiated by structural aspects.

On the thermodynamic stability of the intermolecular association between Lewis acids and Lewis bases: a DFT study

The intermolecular association of twelve combinations of six different Lewis acids and Lewis bases (i.e., R 3 A–BR′3 where A = B and Al; B = N and P; R = H, F, and C6F5; R′ = H, CH3, and C(CH3)3) was theoretically described by means of DFT calculations using the dispersion-corrected ωB97x-D and B97D functionals in conjunction with the 6-311++G(2d,2p) basis set including toluene as solvent through the PCM-SMD implicit solvent scheme. All the studied Lewis pairs appeared to be stable on the basis of computed BSSE-corrected interaction energies; however, the free energies of formation computed in solution (ΔG solv) indicate that three Lewis acid–base combinations can be considered frustrated Lewis pairs (FLPs). Besides, the four features that characterize FLPs are: (1) large distances between the acid and base centers, (2) negligible changes in the geometry of the acid, (3) weak interaction energies, and (4) non-covalent dispersion energy contributing to almost the entire interaction energy. In the present work, we introduce two ad hoc indexes intended to quantify separately the electronic and steric factors, which have a direct effect in the intermolecular association of Lewis acids and Lewis bases and can be used to distinguished FLPs from classical Lewis adducts. Based on the aforementioned ad hoc indexes, the existence of a new kind of complexes that are “intermediate” between classical complexes and FLPs is proposed.

Acidity and metal (Mg2+, Ca2+, Zn2+) affinity of l-γ-carboxyglutamic acid and its peptide analog

Density functional theory methods with the B3LYP and B97D functionals with triple-zeta 6-311++G(d,p) basis set have been used to study the acidity, basicity and metal affinity of l-γ-carboxyglutamic acid (GLA) and its peptide derivative [2-acetylamino-3-(methylamino)-3-oxopropyl]malonic acid (AMD-GLA). The Gibbs interaction energies of the GLA2−…M2+ and AMD-GLA2−…M2+ (M=Mg, Ca, Zn) complexes show an increasing binding affinity in the order Ca2+<Mg2+<Zn2+ The transition metal Zn2+ is most effectively recognized by the dianions of GLA and AMD-GLA. Of the dianions studied the AMD-GLA dianion is the strongest Lewis base. Computations that include the effect of solvation showed that in water the relative stability of GLA2−…M2+ and AMD-GLA2−…M2+ ionic bonds is rapidly diminished. The computed interaction Gibbs energy in water is small and negative.

Structure of clusters of pentacene molecules and their polarizabilities

We calculate and compare the ground state structures of one, two and three pentacene molecule clusters, using B3LYP and B97-D density functionals, and polarizabilities in the ground state structure to examine the extent of anisotropy for applications in electronic device fabrication. B3LYP and B97-D functionals perform sufficiently well for a single pentacene molecule, but for two and three molecule clusters, the inclusion of dispersive interactions through B97-D becomes necessary. For two and three molecule clusters the energy landscape near ground state is flat in molecular coordinates, implying multiple related structures may be accessible at room temperature. Further, for the ground state structures, the polarizability along the long axis of the molecule is larger than the other two directions. This may make it possible to explain the beneficial effect of applying an electric field during processing of pentacene films in electronic devices, as observed experimentally; specifically, in this context, the structural and polarizability data presented could allow for development of models for nucleation and growth of pentacene films.

Halogen bonds with benzene: An assessment of DFT functionals

The performance of an extensive set of density functional theory functionals has been tested against CCSD(T) and MP2 results, extrapolated to the complete basis set (CBS) limit, for the interaction of either DCl or DBr (D = H, HCC, F, and NC) with the aromatic system of benzene. It was found that double hybrid functionals explicitly including dispersion, that is, B2PLYPD and mPW2PLYPD, provide the better agreement with the CCSD(T)/CBS results on both energies and equilibrium geometry, indicating the importance of dispersive contributions in determining this interaction. Among the less expensive functionals, the better performance is provided by the ωB97X and M062X functionals, while the ωB97XD and B97D functionals are shown to work very well for bromine complexes but not so well for chlorine complexes.

Side Chain Flexibility in Perfluorosulfonic Acid Ionomers: An ab Initio Study

Side chain flexibility in perfluorosulfonic acid (PFSA) ionomers has been explored through ab initio electronic structure calculations. Three different PFSA side chain fragments were considered with a CF3CFCF3 backbone representation: Nafion (-OCF2CF(CF3)O(CF2)2SO3H), Aquivion or the short side chain (SSC) (-O(CF2)2SO3H), and the 3M PFSA (-O(CF2)4SO3H). Rotational potential energy surfaces for each bond along the length of the side chains were obtained using density functional theory with the B3LYP and the dispersion-corrected B97D functionals with and without the inclusion of a solvation model. Solvent effects were found to have minimal effect on bond rotations close to the tetrafluoroethylene backbone but had greater impact near the terminal sulfonic acid group. The carbon-sulfur bond was found to be the most flexible portion of the side chain in each of the fragments which was further enhanced with the inclusion of the solvent. Complete rotation about either the O-CF2 or CF-O bond in the Nafion side chain resulted in fairly high energetic barriers, but significant portions of these rotational surfaces had energetic penalties less than 1.5 kcal/mol indicating substantial conformational freedom. Fully extended and folded conformations of the Nafion side chain exhibit considerable contraction in side chain end-to-end distance and were observed to be nearly isoenergetic using B3LYP, but the folded structures with the ether oxygen atoms in gauche conformations were ~1.5 kcal/mol lower in energy using B97D. Below the second ether linkage of the Nafion side chain, the rotational potential energy profiles were identical to that determined for the SSC side chain. The 3M side chain was generally found to be the most rigid with barriers for complete rotation about the central carbon-carbon bonds of approximately 7 kcal/mol. These results indicate that minor differences in side chain length and chemistry may have a pronounced effect on the rotational potential energy surfaces, particularly those involving rotation about different carbon-carbon bonds with distinctly different character.

On UV–Vis spectra and structure of the anticancer drug camptothecin in solutions

UV–Vis spectra of camptothecin (CPT) in toluene, acetone, ethanol, acetonitrile, dimethylsulfoxide and aqueous solutions are investigated by UV–Vis spectroscopy and DFT calculations. The structures of CPT and its π-dimer have been optimized using B3LYP and B97D functionals with cc-pVDZ basis sets. Solvent effects were estimated using the Integral Equation Formalism Polarizable Continuum Model. Electron transitions in the studied systems were evaluated by TD-DFT treatment. Whereas the strong peak at the highest wavelength corresponds to the CPT monomer, the existence of the blue shifted one may be explained by its π-dimers formation instead of CPT hydrogen bonding with water molecules.

Influences of dispersion and long‐range corrections on molecular structures of three types of lithium phthalocyanine dimer

AbstractWe report here the results from theoretical calculations of the potential energy curves for three dimers of lithium phthalocyanine (LiPc) using nine types of functionals: the M06‐2x, M06L, B97D, ωB97, ωB97X, ωB97XD, CAM‐B3LYP, LC‐ωPBE, and LC‐BLYP. The results were discussed in comparison with those obtained for the dimers of magnesium phthalocyanine (MgPc). The dispersive and long‐range interactions were considered in part by using these functionals. The mechanism whereby the dispersive and long‐range interactions affect the geometric structures of the LiPc and MgPc dimers is discussed. The calculated results provide insight into the computational methods for both open‐ and closed‐shell metal phthalocyanine (MPc) dimers: Although it is difficult for the CAM‐B3LYP, LC‐ωPBE, and LC‐BLYP functionals only with the long‐range corrections to evaluate weak dispersion interactions appropriately, the M06‐families, ωB97‐families, and B97D functionals can estimate a weak dispersion interaction well in both open‐ and closed‐shell MPc dimers. However, the results should be used with caution against overestimation of the relative stabilities for the results of functionals considering despersion correction. © 2012 Wiley Periodicals, Inc.

Theoretical study of CO adsorption on the surface of BN, AlN, BP and AlP nanotubes

Behavior of CO adsorption on the surface of BN, AlN, BP, and AlP nanotubes was investigated using density functional theory calculations, by means of B3LYP and B97D functionals. It was found that energetic feasibility of this process depends on several factors including LUMO energy level of tubes, electron density, and length of the surrounding bonds of adsorbing atoms plus their hybridization. These factors compete against each other to specify the adsorption behavior of the tubes. Frontier molecular orbital theory (FMO) and structural analyses show that high energy level of LUMO and short bond lengths of the tube surfaces prevent the adsorption of CO on BN nanotubes. The results suggest that the AlN nanotubes are energetically the most favorable cases toward the CO adsorption. It was found that B97D functional changes the absolute energy values of B3LYP results, but it doesn't change their relative-order of magnitudes.

The shape of gaseousn-butylbenzene: Assessment of computational methods and comparison with experiments

Conformational landscape of neutral and ionized n-butylbenzene has been examined. Geometries have been optimized at the B3LYP/6-31G(d), B3LYP/6-31+G(d,p), B3LYP-D/6-31+G(d,p), B2PLYP/6-31+G(d,p), B2PLYP-D/6-31+G(d,p), B97-D/6-31+G(d,p), and M06-2X/6-31+G(d,p) levels. This study is complemented by energy computations using 6-311++G(3df,2p) basis set and CBS-QB3 and G3MP2B3 composite methods to obtain accurate relative enthalpies. Five distinguishable conformers have been identified for both the neutral and ionized systems. Comparison with experimentally determined rotational constants shows that the best geometrical parameters are provided by B3LYP-D and M06-2X functionals, which include an explicit treatment of dispersion effects. Composite G3MP2B3 and CBS-QB3 methods, and B2PLYP-D, B3LYP-D, B97-D, and M06-2X functionals, provide comparable relative energies for the two sets of neutral and ionized conformers of butyl benzene. An exception is noted however for conformer V(+) the stability of which being overestimated by the B3LYP-D and B97-D functionals. The better stability of neutral conformers I, III, and IV, and of cation I(+) , demonstrated by our computations, is in perfect agreement with conclusions based on micro wave, fluorescence, and multiphoton ionization experiments.

A DFT study of substituent effects in corannulene dimers

Corannulene dimers made up of corannulene monomers with different curvature and substituents were studied using M06-2X, B97D and ωB97XD functionals and 6-31+G* basis set. Corannulene molecules were substituted with five alternating Br, Cl, CH(3), C(2)H or CN units. Geometric results showed that substituents gave rise to small changes in the curvature of corannulene bowls. So, there was not a clear relationship between the curvature of bowls and the changes on interaction energy generated by addition of substituents in the bowl. Electron withdrawing substituents gave rise to a more positive molecular electrostatic potential (MEP) of the bowl, which was able to get a strong interaction with the negative MEP at the surface of a fullerene. Substitution with CN caused the largest effect, giving rise to the most positive MEP and to a large interaction energy of -24.64 kcal mol(-1), at the ωB97XD/6-31+G* level. Dispersive effects must be taken into account to explain the catching ability of the different substituted corannulenes. For unsubstituted dimers, calculations with DFT-D methods employing ωB97XD and B97D functionals led to similar results to those previously reported at the SCS-MP2/cc-pVTZ level for corannulene dimers (A. Sygula and S. Saebø, Int. J. Quant. Chem., 2009, 109, 65). In particular, the ωB97XD functional led to a difference of only 0.35 kcal mol(-1), regarding MP2 interaction energy for corannulene dimers. On the other hand, the M06-2X functional showed a general considerable underestimation of interaction energies. This functional worked quite well to study trends, but not to obtain absolute interaction energies.

Performance of the Empirical Dispersion Corrections to Density Functional Theory: Thermodynamics of Hydrocarbon Isomerizations and Olefin Monomer Insertion Reactions.

Most of the commonly used approximate density functionals have systematic errors in the description of the stability of hydrocarbons. This poses a challenge for the realistic modeling of reactions involving hydrocarbons, such as olefin polymerization. Practical remedies have been proposed, including the application to usual black-box DFT of additional empirical correction CR(-6) terms for the van der Waals interaction (termed DFT-D), or introducing additional pseudopotentials that introduce some medium-to-long-range attraction (C-Pot). In this Article, we use the DFT-D scheme as realized in our BOptimize package to evaluate the performance of a range of commonly used DFT functionals (combinations of xPBE, B88, OPTX with LYP and cPBE GGAs and hybrids) for the modeling of the thermodynamics of reactions of the growth of common polyolefins. We also review and reproduce some of the previously done benchmarks in the area: alkane branching and relative stability of C12H12 and C10H16 isomers. In addition to the common DFT methods, computations with correlated wave function methods (MP2) and the new functionals B97-D and M06-L were performed. The performance of the special density functionals B97-D and M06-L is, in general, similar to the best DFT-D corrected regular functionals (BPBE-D and PBE-D). The results show that (1) the DFT-D correction is sufficient to describe alkane branching, but its performance depends on the parametrization; (2) inclusion of the correction is essential for a proper description of the thermodynamics of reactions of polymer growth; and (3) not all approximate density functionals perform effectively for the description of hydrocarbons even with the correction. The C-Pot method for the B3LYP functional shows quantitatively correct results for our test cases. The enthalpies of hydrocarbon reactions were analyzed in terms of the repulsion characteristics of a given DFT method. PBE is the least repulsive, while OLYP is the most. However, there are cases where the failure of a DFT method cannot be correlated with its repulsive character. A striking example is the performance of B3LYP and BLYP for caged molecules with small carbocycles, such as the [D3d]-octahedrane. The stability of [D3d]-octahedrane is underestimated by the B3LYP, BLYP, and B97-D functionals, but not by DFT methods that contain either B88 exchange or LYP correlation functionals separately. While DFT-D cannot amend the performance of the former functionals for the octahedrane, C-Pot for B3LYP does.