The assessment and application of an approach to noncovalent interactions: the energy decomposition analysis (EDA) in combination with DFT of revised dispersion correction (DFT-D3) with Slater-type orbital (STO) basis set

An assessment study is presented about energy decomposition analysis (EDA) in combination with DFT including revised dispersion correction (DFT-D3) with Slater-type orbital (STO) basis set. There has been little knowledge about the performance of the EDA?+?DFT-D3 concerning STOs. In this assessment such an approach was applied to calculate noncovalent interaction energies and their corresponding components. Complexes in S22 set were used to evaluate the performance of EDA in conjunction with four representative types of GGA-functionals of DFT-D3 (BP86-D3, BLYP-D3, PBE-D3 and SSB-D3) with three STO basis sets ranging in complexity from DZP, TZ2P to QZ4P. The results showed that the approach of EDA?+?BLYP-D3/TZ2P has a better performance not only in terms of calculating noncovalent interaction energy quantitatively but also in analyzing corresponding energy components qualitatively. This approach (EDA?+?BLYP-D3/TZ2P) was thus applied further to two representative large-system complexes including porphine dimers and fullerene aggregates to gain a better insight into binding characteristics.     

d(A)<Subscript>3</Subscript>d(T)<Subscript>3</Subscript> and d(G)<Subscript>3</Subscript>d(C)<Subscript>3</Subscript> B-DNA mini-helixes: the DFT/M06-2x and DFT/B97-D3 comparison of geometrical and energetic characteristics

We report the comprehensive DFT based comparison of geometrical and energetic parameters of the d(A)₃·d(T)₃ and d(G)₃·d(C)₃ nucleic acid mini-helixes performed at B97-D3 and M06-2× levels of theory. We studied the ability of mini-helixes to retain the conformation of B-DNA in the gas phase and under the influence of water bulk, uncompensated charges, and counter-ions. The def2-SV(P) and 6-31G(d,p) basis sets have been used for B97-D3 and M06-2× calculations, correspondently. To estimate basis set superposition error, the recently developed semi-empirical procedure that calls geometrical counterpoise type correction for inter- and intra—molecular basis set superposition error (gcp) has been used in the case of def2-SV(P) basis set. We found that both considered DFT functionals predict very similar results for geometrical ad energetic characteristics. We also found that in contrast to average classical molecular dynamics and data of simple geometrical models, both considered DFT functionals predict the existence of duplex specific geometries. A prediction of interaction energies of d(A)₃d(T)₃ and d(G)₃d(C)₃ duplexes accomplished in this study also verifies the applied models and confirms reliability of the new computational gcp technique.     

Effects of local protein environment on the binding of diatomic molecules to heme in myoglobins. DFT and dispersion-corrected DFT studies

The heme-AB binding energies (AB = CO, O₂) in a wild-type myoglobin (Mb) and two mutants (H64L, V68N) of Mb have been investigated in detail with both DFT and dispersion-corrected DFT methods, where H64L and V68N represent two different, opposite situations. Several dispersion correction approaches were tested in the calculations. The effects of the local protein environment were accounted for by including the five nearest surrounding residues in the calculated systems. The specific role of histidine-64 in the distal pocket was examined in more detail in this study than in other studies in the literature. Although the present calculated results do not change the previous conclusion that the hydrogen bonding by the distal histidine-64 residue plays a major role in the O₂/CO discrimination by Mb, more details about the interaction between the protein environment and the bound ligand have been revealed in this study by comparing the binding energies of AB to a porphyrin and the various myoglobins. The changes in the experimental binding energies from one system to another are well reproduced by the calculations. Without constraints on the residues in geometry optimization, the dispersion correction is necessary, since it improves the calculated structures and energetic results significantly.     

MP2, DFT and DFT-D study of the dimers of diazanaphthalenes: a comparative study of their structures,stabilisation and binding energies

Diazanaphthalenes (DAPs) are a broad class of N-heteroaromatic compounds with several technological and biological applications. Some of these applications are attributed to the ability of DAP molecules to form associated dimers through non-covalent interactions. A study of the types and strength of the interactions involved is crucial for understanding the preferred geometries and energetics of the dimers. In this study, the dimers of five DAPs are investigated by means of Møller–Plesset second order perturbation theory, hybrid meta-GGA [density functional theory methods (DFT): DFT/MPWB1K, DFT/M05-2X and DFT/M06-2X] and DFT dispersion-corrected (DFT-D/ωB97XD) methods to elucidate their dimers' preferred geometries, relative energies and nature of the interactions between monomer units. The results indicate that the monomer units of the dimers are held by either intermolecular hydrogen bonds or π…π stacking interactions, and that the preferred dimers are those in which the monomer units interact through π…π stacking interactions. A comparison across structures suggests that the position of the N atom in the ring has significant role in determining the relative energy and binding strength of the dimers. A comparison among the different methods utilised for the study indicates that DFT/M06-2X method provides binding energies that are close to those of DFT-CCSD(T) correction scheme and could therefore be considered as the best method for describing the binding properties of DAP dimers.     

On the performance of semiempirical MO theory for dipole moments of dye molecules

The dipole moments of a set of 71 simple dye molecules calculated at the ab initio, DFT, and semiempirical levels have been compared. The DFT dipole moments are on average 16% larger than those obtained by MP2/6-31G**. AM1 and PM3 modified with an empirical correction procedure yield dipole moments essentially at the same level of accuracy as the results of non-empirical calculations. INDO/S and CNDO/S are considerably less accurate. Among different versions of spectral methods, the CISD scheme gives the best performance.Electronic Supplementary Material available.     

Problems,successes and challenges for the application of dispersion-corrected density-functional theory combined with dispersion-based implicit solvent models to large-scale hydrophobic self-assembly and polymorphism

The recent advent of dispersion-corrected density-functional theory (DFT) methods allows for quantitative modelling of molecular self-assembly processes, and we consider what is required to develop applications to the formation of large self-assembled monolayers (SAMs) on hydrophobic surfaces from organic solution. Focus is on application of the D3 dispersion correction of Grimme combined with the solvent dispersion model of Floris, Tomasi and Pascual–Ahuir to simulate observed scanning-tunnelling microscopy (STM) images of various polymorphs of tetraalkylporphyrin SAMs on highly oriented pyrolytic graphite surfaces. The most significant problem is identified as the need to treat SAM structures that are incommensurate with those of the substrate, providing a challenge to the use of traditional periodic-imaging boundary techniques. Using nearby commensurate lattices introduces non-systematic errors into calculated lattice constants and free energies of SAM formation that are larger than experimental uncertainties and polymorph differences. Developing non-periodic methods for polymorph interface simulation also remains a challenge. Despite these problems, existing methods can be used to interpret STM images and SAM atomic structures, distinguishing between multiple feasible polymorph types. They also provide critical insight into the factors controlling polymorphism. All this stems from a delicate balance that the intermolecular D3 and solvent Floris, Tomasi and Pascual–Ahuir corrections provide. Combined optimised treatments should yield fully quantitative approaches in the future.     

Calculation of conformational energies and optical rotation of the most simple chiral alkane

Quantum chemical calculations have been performed to investigate the conformer distribution of 4-ethyl-4-methyloctane and its optical rotation. With the reference methods MP2 and SCS-MP2, the energies of seven conformers are found within a range of about 1.5 kcal mol(-1). It is demonstrated that the relative energies cannot be reliably predicted with conventional GGA or hybrid density functionals, Hartree-Fock, semiempirical AM1, and classical force field (MM3) calculations. An empirical dispersion correction to GGA (PBE-D), hybrid (B3LYP-D), or double hybrid (B2PLYP-D) functionals corrects these errors and results in very good agreement with the reference energies. Optical rotations have been calculated for all seven conformers at the TDDFT(BHLYP/aTZV2P) level. The computed macroscopic rotation is derived from a classical Boltzmann average. The result (1.9-3.2 deg dm(-1) (g/mL)(-1)) is very close to the experimental value of 0.2 deg dm(-1) (g/mL)(-1) for the (R)-enantiomer and has the right sign. Because six conformers are significantly populated at room temperature and the rotations of individual conformers differ in sign and magnitude, the calculated average rotation is rather sensitive to the conformer population used. From the electronic structure point of view, this example emphasizes the effect of long-range dispersion effects for the evaluation of population averaged quantities in large molecules. Computations based on free enthalpies are in worse agreement with experiment that is attributed to artefacts of the harmonic approximation used to compute the vibrational entropy terms.     

Calculating the geometry and Raman spectrum of physiological bis(<Emphasis Type="SmallCaps">l</Emphasis>-histidinato)copper(II): an assessment of DFT functionals for aqueous and isolated systems

Reliable density functional theory (DFT) calculations can be performed in conjuction with spectroscopic measurements to elucidate the structural properties of physiologically important bis(amino acidato)copper(II) compounds in solutions. They can provide insight into the influence of intermolecular interactions on the molecular geometry in the crystal lattice or solution when compared with a DFT gas-phase minimum. Our previous paper [Markovi? et al. (2014) Eur J Inorg Chem 198] reported the DFT-determined geometries and Raman spectra for different conformers of physiological bis(l-histidinato)copper(II) with 20 explicit water molecules, as calculated using the B3LYP functional. The present study examined the reliability of those B3LYP results by applying the M06 functional instead, as it should better account for noncovalent interactions. The water molecules were positioned more compactly around the complex by M06 than by B3LYP. The accuracies of the two functionals when compared to relevant experimental data showed that M06 was better at reproducing in-plane Cu?N bond lengths but B3LYP gave more accurate axial Cu?O distances. Both functionals reproduced the experimental Raman spectrum at pH 8 to similar levels of accuracy and provided precise information on the Cu(II) coordination mode and conformation in aqueous solution. Additionally, we assessed several DFT and DFT-D functionals (BP86, B3LYP, B3LYP-D, M06, M06 L, wB97XD, mPW2PLYPD) by using them to model the geometries of experimental bis(l-histidinato)copper(II) crystalline conformations as isolated systems, and then benchmarking the results against those from high-level second-order pertubation Møller–Plesset (MP2) calculations. Although this assessment resulted in an equivocal conclusion because the MP2 results for the isolated complex were inconsistent with the corresponding DFT outcomes, it does provide new information on future benchmark options.     

Theoretical study of electronic absorptions in aminopyridines – TCNE CT complexes by quantum chemical methods, including solvent

The geometric and electronic structure of donor-acceptor complexes of TCNE with aniline, o-, m- and p- aminopyridines and pyridine has been studied in gas phase and in solution using CC2, TDDFT and CIS methods. Concerning interaction energy between particular donor and TCNE acceptor it is fairly described by both CC2 (MP2) and DFT-D approaches. Transition energies in gas phase calculated by CC2 approach are in good agreement with available experimental data for aniline. TDDFT calculations with LC-BLYP functional (with standard value of range separation factor μ?=?0.47) gives transition energies too high although not as high as CIS. The red solvent shifts, calculated by PCM model with CIS method are qualitative correct, but error in the range of 0.1-0.2 eV should be expected.     

Tetrahydroisoquinolines acting as dopaminergic ligands. A molecular modeling study using MD simulations and QM calculations

A molecular modeling study on 16 1-benzyl tetrahydroisoquinolines (BTHIQs) acting as dopaminergic ligands was carried out. By combining molecular dynamics simulations with ab initio and density functional theory (DFT) calculations, a simple and generally applicable procedure to evaluate the binding energies of BTHIQs interacting with the human dopamine D2 receptor (D2 DR) is reported here, providing a clear picture of the binding interactions of BTHIQs from both structural and energetic viewpoints. Molecular aspects of the binding interactions between BTHIQs and the D2 DR are discussed in detail. A significant correlation between binding energies obtained from DFT calculations and experimental pKi values was obtained, predicting the potential dopaminergic effect of non-synthesized BTHIQs.     

DFT study of the interaction between the conjugated fluorescein and dabcyl system, using fluorescene quenching method

Molecular beacon is a DNA probe containing a sequence complementary to the target that is flanked by self-complementary termini, and carries a fluorophore and a quencher at the ends. We used the fluorescein and dabcyl as fluorophore and quencher respectively, and studied with DFT calculations at the GGA/DNP level, and taking into account DFT dispersion corrections by the Grimme and Tkatchenko-Scheffler (TS) schemes, the distance, where the most favorable energetic interaction between the fluorophore and quencher in conjugated form occurs. This distance occurs at a separation distance of 29.451?? between the centers of Dabcyl and fluorescein employing the TS DFT dispersion correction scheme, indicating FRET efficiency around 94.28?%. The calculated emission spectra of the conjugated pair in water indicated that the emission and absorption spectrum overlap completely and thus no fluorescence can be observed due to the fluorescence resonance energy transfer (FRET) effect. The DFT results confirmed the experimentally observing fluorescence quenching of the fluorescein-dabcyl conjugated system by FRET.     

Simple benzene derivatives adsorption on defective single-walled carbon nanotubes: a first-principles van der Waals density functional study

We have investigated the interaction between open-ended zig-zag single-walled carbon nanotube (SWCNT) and a few benzene derivatives using the first-principles van der Waals density functional (vdW-DF) method, involving full geometry optimization. Such sp ²-like materials are typically investigated using conventional DFT methods, which significantly underestimate non-local dispersion forces (vdW interactions), therefore affecting interactions between respected molecules. Here, we considered the vdW forces for the interacting molecules that originate from the interacting π electrons of the two systems. The ?0.54 eV adsorption energy reveals that the interaction of benzene with the side wall of the SWCNT is typical of the strong physisorption and comparable with the experimental value for benzene adsorption onto the graphene sheet. It was found that aromatics are physisorbed on the sidewall of perfect SWCNTs, as well as at the edge site of the defective nanotube. Analysis of the electronic structures shows that no orbital hybridization between aromatics and nanotubes occurs in the adsorption process. The results are relevant in order to identify the potential applications of noncovalent functionalized systems.

Theoretical investigation of cyromazine tautomerism using density functional theory and Møller–Plesset perturbation theory methods

A computational chemistry analysis of six unique tautomers of cyromazine, a pesticide used for fly control, was performed with density functional theory (DFT) and canonical second-order Møller–Plesset perturbation theory (MP2) methods to gain insight into the contributions of molecular structure to detection properties. Full geometry optimisation using the 6-311++G** basis set provided energetic properties, natural charges, frontier orbitals and vibrational modes. Excitation energies were obtained using time-dependent DFT. Hydrogen location and bond order contribute significantly to the electronic properties. The common cyromazine tautomer possesses the lowest energy, highest band gap energy and highest excitation energy. B3LYP/6-31G** dynamics simulations indicate each tautomer possesses a stable structure with limited rotation about the single bonds. Tautomerisation involving intramolecular hydrogen transfer influences the natural charges of neighbouring atoms and the frontier orbital properties. The excitation energies are highly correlated with band gap energies of the frontier orbitals. The calculated infrared and Raman spectra are suitable for vibrational assignments associated with the chemical structure. The tautomeric forms of cyromazine possess similar spatial properties and significant variation in electronic properties.     

Simulations on the possibility of formation of complexes between fluorouracil drug and cucurbit[n]urils: ab initio van der Waals DFT study

The binding geometry of fluorouracil/cucurbit[n]urils (CB[n]s) complexes with n?=?5–8 is investigated using the first-principles van der Waals density functional (vdW-DF) method, involving full geometry optimization. Such host-guest complexes are typically calculated using conventional DFT method, which significantly underestimates non-local dispersion forces (or vdW contributions) and therefore affects interactions between respected entities. We address here the role of vdW forces for the fluorouracil and CB[n]s molecules which can form directional hydrogen bonds with each other. It was found that the inclusion of dispersion interactions significantly affects the host-guest binding properties and the hydrogen bonding between the molecules provides the main binding mechanism, while results in the same geometries for the considered complexes. The 0.84 eV binding energy, for the thermodynamically favorable state, reveals that the interaction of fluorouracil with CB[n]s is an exothermic interaction and typical for strong hydrogen bonding. Furthermore, we have investigated the binding nature of these host-guest systems in aqueous solution with ab initio MD simulations adopting vdW-DF method. These findings afford evidence for the applicability of the vdW-DF approach and provide a realistic benchmark for the investigation of the host-guest complexes.

Computational simulation study on the anion recognition properties of functionalized tetraphenyl porphyrins

Dedicated bond force constant and bulk modulus of C _n fullerenes (n = 20, 28, 36, 50, 60) are computed using density functional theory (DFT). DFT predicts bond force constants of 611, 648, 675, 686, and 691 N/m, for C₂₀, C₂₈, C₃₆, C₅₀, and C₆₀, respectively, indicating that the bond force constant increases for larger fullerenes. The bulk modulus predicted by DFT increases with decreased fullerene diameter, from 0.874 TPa for C₆₀ to 1.830 TPa for C₂₀. The bond force constants predicted by DFT are then used as an input for finite element analysis (FEA) of the fullerenes, considered as spatial frames in structural models where the bond stiffness is represented by the DFT-computed bond force constant. In agreement with DFT, FEA predicts that smaller fullerenes are stiffer, and underestimates the bulk modulus with respect to DFT. The difference between the FEA and DFT predictions of the bulk modulus decreases as the size of the fullerene increases, from 20.9 % difference for C₂₀ to only 4 % difference for C₆₀. Thus, it is concluded that knowing the appropriate bond force constant, FEA can be used as a plausible approximation to model the elastic behavior of small fullerenes.

     

Molecular mechanics:the cross-conjugated carbonyl group in heterocyclic compounds. 3. Parameterisation (MM2) of the adjacent C=C bond: evaluation tests

In the MM2 force field, the definition of a new type of carbon (carbonyl atom, when it is cross-conjugated) has led to the reestimation of the mechanical parameters of the adjacent C(O)-O and C(O)-N bonds in fully-conjugated cyclic compouds: !-pyrones, '-lactones, and conjugated "lactams". New parameters, based on the study of 97 bonds, are presented here for the similar adjacent C(O)-C bond in the same compounds. Comparison of calculated bond lengths to experimental X-ray bond lengths shows that, statistically, the results are substantially improved but the dispersion remains large. Full optimisation of the molecules concerned shows that in some cases the errors accumulate on the C(O)-O bond which is more sensitive to errors in the evaluation of its own ? bond order. The origins of the discrepancies are discussed. Using caffeine as a test molecule, the MM2 method with the parameters proposed here, appears less acurate than the ab initio and DFT methods (both with 6-31G**basis) but still better than the semi-empirical methods (AM1-PM3).     

First-principles investigation on structural,elastic, electronic and thermodynamic properties of filled skutterudite PrFe4P12 compound for thermoelectric applications

Filled skutterudite compound PrFe₄P₁₂ is studied using the full potential linear muffin-tin orbital method with the local density approximation for the exchange correlation potential to investigate the systematic trends for structural and elastic properties of the cubic PrFe₄P₁₂ skutterudite. The calculated ground state quantities such as the lattice constant and internal free parameters are in fairly good agreement with the available experimental data. The elastic constants and their pressure dependence are obtained by calculating the total energy versus volume-conserving strains using the Mehl model. Pressure and temperature effects on the lattice constant, bulk modulus, thermal expansion coefficient, Debye temperature and heat capacity are obtained in the range of 0–30 GPa and 0–1000 K. Reduction of bulk modulus and Debye temperature with temperature essentially indicates the thermal softening of the rare earth-filled skutterudites lattice.     

Atomic solvation parameters in the analysis of protein-protein docking results.

Several sets of amino acid surface areas and transfer free energies were used to derive a total of nine sets of atomic solvation parameters (ASPs). We tested the accuracy of each of these sets of parameters in predicting the experimentally determined transfer free energies of the amino acid derivatives from which the parameters were derived. In all cases, the calculated and experimental values correlated well. We then chose three parameter sets and examined the effect of adding an energetic correction for desolvation based on these three parameter sets to the simple potential function used in our multiple start Monte Carlo docking method. A variety of protein-protein interactions and docking results were examined. In the docking simulations studied, the desolvation correction was only applied during the final energy calculation of each simulation. For most of the docking results we analyzed, the use of an octanol-water-based ASP set marginally improved the energetic ranking of the low-energy dockings, whereas the other ASP sets we tested disturbed the ranking of the low-energy dockings in many of the same systems. We also examined the correlation between the experimental free energies of association and our calculated interaction energies for a series of proteinase-inhibitor complexes. Again, the octanol-water-based ASP set was compatible with our standard potential function, whereas ASP sets derived from other solvent systems were not.     

Study of semiconducting nanomaterials under pressure

The pressure induced structural and mechanical properties of nanocrystalline ZnO, ZnS, ZnSe, GaN, CoO, CdSe, CeO(2), SnO(2), SiC, c-BC(2)N, and β-Ga(2)O(3) with different grain sizes have been analyzed under high pressures. The molecular dynamics simulation model has been used to compute isothermal equation of state, volume collapse and bulk modulus of these materials in nano and bulk phases at ambient and high pressures and compared with the experimental data. It is evident from these calculations that the change in particle size affects directly the phase transition pressure and bulk modulus. The values of phase transition pressure and bulk modulus increase with decrease in grain size of the material. The equilibrium cell volume and volume collapse in parent phase is directly proportional to the grain size of the materials. Present results are in good agreement with experimental data. The model is able to explain these thermodynamic properties at varying temperatures and pressures successfully.