Assessment of the Performance of DFT and DFT-D Methods for Describing Distance Dependence of Hydrogen-Bonded Interactions

Theoretical investigation of the coupling between hydrogen-atom transfer and stacking interaction in adenine-thymine dimers

Three different dimers of the adenine-thymine (A-T) base pair are studied to point out the changes of important properties (structure, atomic charge, energy and so on) induced by coupling between the movement of the atoms in the hydrogen bonds and the stacking interaction. The comparison of these results with those for the A-T monomer system explains the role of the stacking interaction in the hydrogen-atom transfer in this biologically important base pair. The results support the idea that this coupling depends on the exact dimer considered and is different for the N-N and N-O hydrogen bonds. In particular, the correlation between the hydrogen transfer and the stacking interaction is more relevant for the N-N bridge than for the N-O one. Also, the two different mechanisms of two-hydrogen transfer (step by step and concerted) can be modified by the stacking interaction between the base pairs.

Chiral discrimination by vibrational spectroscopy utilizing local modes

Chiral discrimination of homochiral and heterochiral H-bonded complexes is a challenge for both experimentalists and computational chemists. It is demonstrated that a two-pronged approach based on far-infrared vibrational spectroscopy and the calculation of local mode frequencies facilitates the chiral discrimination of H-bonded dimers. The local H-bond stretching frequencies identify the strongest H-bonds and by this the dominating chiral diastereomer. This is shown in the case of peroxide, trioxide, hydrazine, glycidol, and butan-2-ol dimers as well as propylene oxide···glycidol complexes investigated with the help of second-order Møller-Plesset perturbation, coupled cluster, and density functional theory calculations where, in the latter case, the ωB97X-D functional was used for an improved description of H-bonding. In some cases, additional intermolecular interactions overrule the important role of H-bonding, which is found by calculating chirodiastaltic energies.

Quantum-mechanical analysis of the energetic contributions to π stacking in nucleic acids versus rise, twist, and slide

Symmetry-adapted perturbation theory (SAPT) is applied to pairs of hydrogen-bonded nucleobases to obtain the energetic components of base stacking (electrostatic, exchange-repulsion, induction/polarization, and London dispersion interactions) and how they vary as a function of the helical parameters Rise, Twist, and Slide. Computed average values of Rise and Twist agree well with experimental data for B-form DNA from the Nucleic Acids Database, even though the model computations omitted the backbone atoms (suggesting that the backbone in B-form DNA is compatible with having the bases adopt their ideal stacking geometries). London dispersion forces are the most important attractive component in base stacking, followed by electrostatic interactions. At values of Rise typical of those in DNA (3.36 Å), the electrostatic contribution is nearly always attractive, providing further evidence for the importance of charge-penetration effects in π-π interactions (a term neglected in classical force fields). Comparison of the computed stacking energies with those from model complexes made of the "parent" nucleobases purine and 2-pyrimidone indicates that chemical substituents in DNA and RNA account for 20-40% of the base-stacking energy. A lack of correspondence between the SAPT results and experiment for Slide in RNA base-pair steps suggests that the backbone plays a larger role in determining stacking geometries in RNA than in B-form DNA. In comparisons of base-pair steps with thymine versus uracil, the thymine methyl group tends to enhance the strength of the stacking interaction through a combination of dispersion and electrosatic interactions.

Surface interactions of C and C(3) polyols with γ-Al2O3 and the role of coadsorbed water

The formation of surface species from two- and three-carbon polyols on γ-Al(2)O(3) in the presence and absence of coadsorbed water is investigated. Aqueous-phase adsorption isotherms indicate that competitive adsorption between water and polyol inhibits the uptake of the polyol molecules on γ-Al(2)O(3) and that the polyol with the most hydroxyl groups, glycerol, experienced the greatest uptake. Deuterium solid echo pulse NMR measurements support the fact that glycerol strongly interacts with γ-Al(2)O(3) in the presence of physisorbed water and that ethylene glycol interacts with γ-Al(2)O(3) only after the physisorbed water has been removed. In situ high-vacuum FT-IR analysis combined with DFT simulations demonstrate that glycerol readily forms a multidentate alkoxy species through its primary hydroxyl groups with coordinatively unsaturated Al atoms of γ-Al(2)O(3) in the presence of physisorbed water. This surface species exhibits a bridging alkoxy bond from one of its primary hydroxyl groups and a strong interaction with the remaining primary hydroxyl group. FT-IR analysis of 1,3-propanediol on γ-Al(2)O(3) also demonstrates the formation of a multidentate alkoxy species in the presence of coadsorbed water. In contrast, polyols with hydroxyl groups only on the one- and two-carbon atoms, ethylene glycol, and 1,2-propanediol do not form alkoxy bonds with the γ-Al(2)O(3) surface when coadsorbed water is present. These polyols will form alkoxy bonds to γ-Al(2)O(3) when coadsorbed water is removed, and these alkoxy species are removed when water is readsorbed on the sample. The formation of strongly bound, stable multidentate alkoxy species by ethylene glycol and 1,2-propanediol on γ-Al(2)O(3) is prevented by steric limitations of vicinal alcohol groups.

Assessment of ten DFT methods in predicting structures of sheet silicates: importance of dispersion corrections

The performance of ten density functional theory (DFT) methods in a prediction of the structure of four clay minerals, in which non-bonding interactions dominate in the layer stacking (dispersive forces in talc and pyrophyllite, and hydrogen bonds in lizardite and kaolinite), is reported. In a set of DFT methods following functionals were included: standard local and semi-local (LDA, PW91, PBE, and RPBE), dispersion corrected (PW91-D2, PBE-D2, RPBE-D2, and vdW-TS), and functionals developed specifically for solids and solid surfaces (PBEsol and AM05). We have shown that the standard DFT functionals fail in the correct prediction of the structural parameters, for which non-bonding interactions are important. The remarkable improvement leading to very good agreement with experimental structures is achieved if the dispersion corrections are included in the DFT calculations. In such cases the relative error for the most sensitive lattice vector c dropped below 1%. Very good performance was also observed for both DFT functionals developed for solids. Especially, the results achieved with the PBEsol are qualitatively similar to those with DFT-D2.

Microsolvation and hydration enthalpies of CaC₂O₄(H₂O) n (n=0-16) and C₂O₄²⁻(H₂O) n (n=0-14): an ab initio study

We studied hydrated calcium oxalate and its ions at the restricted Hartree-Fock RHF/6-31G* level of theory. Performing a configurational search seems to improve the fit of the HF/6-31G* level to experimental data. The first solvation shell of calcium oxalate contains 13 water molecules, while the first solvation shell of oxalate ion is formed by 14 water molecules. The first solvation shell of Ca(II) is formed by six water molecules, while the second shell contains five. At 298.15 K, we estimate the asymptotic limits (infinite dilution) of the total standard enthalpies of hydration for Ca(II), oxalate ion and calcium oxalate as -480.78, -302.78 and -312.73 kcal mol(-1), resp. The dissociation of hydrated calcium oxalate is an endothermic process with an asymptotic limit of +470.84 kcal mol(-1).

Ab initio molecular dynamics study of water at constant pressure using converged basis sets and empirical dispersion corrections

It is generally believed that studies of liquid water using the generalized gradient approximation to density functional theory require dispersion corrections in order to obtain reasonably accurate structural and dynamical properties. Here, we report on an ab initio molecular dynamics study of water in the isothermal-isobaric ensemble using a converged discrete variable representation basis set and an empirical dispersion correction due to Grimme [J. Comp. Chem. 27, 1787 (2006)]. At 300 K and an applied pressure of 1 bar, the density obtained without dispersion corrections is approximately 0.92 g/cm(3) while that obtained with dispersion corrections is 1.07 g/cm(3), indicating that the empirical dispersion correction overestimates the density by almost as much as it is underestimated without the correction for this converged basis. Radial distribution functions exhibit a loss of structure in the second solvation shell. Comparison of our results with other studies using the same empirical correction suggests the cause of the discrepancy: the Grimme dispersion correction is parameterized for use with a particular basis set; this parameterization is sensitive to this choice and, therefore, is not transferable to other basis sets.

Factors that distort the heme structure in Heme-Nitric Oxide/OXygen-Binding (H-NOX) protein domains. A theoretical study

DFT and dispersion-corrected DFT calculations were carried out to probe the factors that distort the heme structure in Heme-Nitric oxide/OXygen-binding (H-NOX) protein domains. Various model systems that include heme, heme+surrounding residues, and heme+surrounding residues+additional protein environment were examined; the latter system was calculated with a quantum mechanics/molecular mechanics (QM/MM) method. The computations were extended to a myoglobin (Mb) protein, in which the heme structure is quite planar, in contrast to that in H-NOX. The natural tendency of the heme is to be planar. The strong structural distortion in H-NOX is mainly brought about by the intermolecular interactions between the whole heme molecule (heme ring plus its peripheral substituents) and the surrounding residues, among which the polar residues (Tyr140, Pro115, Mse98) play major roles in distorting the heme structure. The two peripheral propionate substituents that are oriented on the same side of the heme plane can also make the molecule distort, but the distortion caused by this factor is not significant. In Mb, the surrounding residues considered are all nonpolar and do not cause a structural distortion. The different structural features of the heme macrocycle in the different proteins (H-NOX and Mb) are reproduced by the calculations. The dispersion correction is necessary, since it improves the calculated structures. The effects of the distortion on the binding affinity of the axial ligand to the heme were also examined.

On the use of pH titration to quantitatively characterize colloidal nanoparticles

Functional nanoparticles (NPs) for bioapplications have been achieved, thanks to synthesis providing high quality nanocrystals, efficient procedures for transfer in water, and further conjugation of (bio)active molecules. However, these nanomaterials are still subjected to batch-to-batch variability and investigations of their physicochemical properties and chemical reactivity are still in their infancy. This may be due to lack of a routine, cost-effective, and readily available quantitative method for characterizing functional NPs. In this work, we show that pH titrations can be a powerful tool for investigating the surface properties of charged NPs and quantifying their surface functionalities. We demonstrate how this method can be useful in characterizing the colloidal and chemical stability, composition, and purity of the nanomaterial. The method also shows potential for the optimization of conjugation conditions.

Quantum mechanical calculations for the misincorporation of nucleotides opposite mutagenic 3,N4-ethenocytosine

The ubiquitous nature and persistence of exocyclic DNA adducts suggest their involvement as initiators of carcinogenesis. We have investigated the misincorporation properties of the exocyclic DNA adduct, 3,N(4)-ethenocytosine, using DFT and DFT-D methods. Computational investigations have been carried out by using the B3LYP, M062X, and wB97XD methods with the 6-31+G* basis set to determine the hydrogen bonding strengths, binding energy, and physical parameters. The single point energy calculations have been carried out at MP2/6-311++G** on corresponding optimized geometries. The energies were compared among the 3,N(4)-ethenocytosine adduct with DNA bases to find the most stable conformer. The solvent phase calculations have also been carried out using the CPCM model. The computed reaction enthalpy values provide computational insights to the earlier experimental observation in in vitro, E.coli, and mammalian cells of a high level of substitution mutation in which C → A transversion results from εC-T pairing [εC-T3 and εC-T4] in the adduct containing DNA sequence.

MOLECULAR BIOLOGY AT THE QUANTUM LEVEL: CAN MODERN DENSITY FUNCTIONAL THEORY FORGE THE PATH?

Recent years have seen vast improvements in the ability of rigorous quantum-mechanical methods to treat systems of interest to molecular biology. In this review article, we survey common computational methods used to study such large, weakly bound systems, starting from classical simulations and reaching to quantum chemistry and density functional theory. We sketch their underlying frameworks and investigate their strengths and weaknesses when applied to potentially large biomolecules. In particular, density functional theory — a framework that can treat thousands of atoms on firm theoretical ground — can now accurately describe systems dominated by weak van der Waals interactions. This newfound ability has rekindled interest in using this tried-and-true approach to investigate biological systems of real importance. In this review, we focus on some new methods within the density functional theory that allow for accurate inclusion of the weak interactions that dominate binding in biological macromolecules. Recent work utilizing these methods to study biologically relevant systems will be highlighted, and a vision for the future of density functional theory within molecular biology will be discussed.

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.

Nature of a hydride-halogen bond. A SAPT-, QTAIM-, and NBO-based study

The nature of a hydride-halogen bond is investigated by means of high-level quantum mechanical calculations expended with symmetry-adapted perturbation theory (SAPT), quantum theory of atoms in molecules (QTAIM), and natural bond orbital (NBO) methods. As model hydride-halogen bonded systems complexes between either LiH or HBeH and either XCF(3) or XCCH (X = F, Cl, Br, I) are used. It is shown that the formation of a hydride-halogen bond leads to the elongation of the R(δ+)-H(δ-) hydride bond, which is accompanied by the blue shift of the ν(R-H) stretching vibration frequency and the increase of the IR intensity of this mode. All these effects, although untypical in the case of, e.g., hydrogen bonds, can be considered as rather typical for hydride-halogen bonded systems. The decomposition of the interaction energy based on the SAPT method clearly indicates the dominant role of the induction term, thus the inductive nature of a hydride-halogen bond in opposition to previous findings. NBO-based analysis indicates the charge transfer from the hydride molecule to the more remote parts of the halogen donor and that the elongation of the R-H bond is caused by the charge outflow from the σ(RH) bonding orbital.