Inclusion Of Dispersion Interactions Research Articles

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.

Dynamics of supercritical methanol of varying density from first principles simulations: Hydrogen bond fluctuations, vibrational spectral diffusion, and orientational relaxation

A first principles study of the dynamics of supercritical methanol is carried out by means of ab initio molecular dynamics simulations. In particular, the fluctuation dynamics of hydroxyl stretch frequencies, hydrogen bonds, dangling hydroxyl groups, and orientation of methanol molecules are investigated for three different densities at 523 K. Apart from the dynamical properties, various equilibrium properties of supercritical methanol such as the local density distributions and structural correlations, hydrogen bonding aspects, frequency-structure correlations, and dipole distributions of methanol molecules are also investigated. In addition to the density dependence of various equilibrium and dynamical properties, their dependencies on dispersion interactions are also studied by carrying out additional simulations using a dispersion corrected density functional for all the systems. It is found that the hydrogen bonding between methanol molecules decreases significantly as we move to the supercritical state from the ambient one. The inclusion of dispersion interactions is found to increase the number of hydrogen bonds to some extent. Calculations of the frequency-structure correlation coefficient reveal that a statistical correlation between the hydroxyl stretch frequency and the nearest hydrogen-oxygen distance continues to exist even at supercritical states of methanol, although it is weakened with increase of temperature and decrease of density. In the supercritical state, the frequency time correlation function is found to decay with two time scales: One around or less than 100 fs and the other in the region of 250-700 fs. It is found that, for supercritical methanol, the times scales of vibrational spectral diffusion are determined by an interplay between the dynamics of hydrogen bonds, dangling OD groups, and inertial rotation of methanol molecules and the roles of these various components are found to vary with density of the supercritical solvent. Effects of system size on the calculated structural and dynamical properties are also investigated in the present study.

Methanol Adsorption on Graphene

The adsorption energies and orientation of methanol on graphene are determined from first‐principles density functional calculations. We employ the well‐tested vdW‐DF method that seamlessly includes dispersion interactions with all of the more close‐ranged interactions that result in bonds like the covalent and hydrogen bonds. The adsorption of a single methanol molecule and small methanol clusters on graphene is studied at various coverages. Adsorption in clusters or at high coverages (less than a monolayer) is found to be preferable, with the methanol C‐O axis approximately parallel to the plane of graphene. The adsorption energies calculated with vdW‐DF are compared with previous DFT‐D and MP2‐based calculations for single methanol adsorption on flakes of graphene (polycyclic aromatic hydrocarbons). For the high coverage adsorption energies, we also find reasonably good agreement with previous desorption measurements.

Mechanistic Studies on the Transformation of Ethanol into Ethene over Fe‐ZSM‐5 Zeolite

Ethanol, through the utilization of bioethanol as a chemical resource, has received considerable industrial attention as it provides an alternative route to produce more valuable hydrocarbons. Using a density functional theory approach incorporating the M06-L functional, which includes dispersion interactions, a large 34T nanocluster model of Fe-ZSM-5 zeolite in which T is a Si or Al atom is employed to examine both the stepwise and concerted mechanisms of the transformation of ethanol into ethene. For the stepwise mechanism, ethanol dehydration commences from the first hydrogen abstraction of the ethanol OH group to form the ethoxide-hydroxide intermediate with a low activation energy of 17.7 kcal mol(-1). Consequently, the ethoxide-hydroxide intermediate is decomposed into ethene through hydrogen abstraction from the ethoxide methyl carbon to either the OH group of hydroxide or the oxygen of the ethoxide group with high activation energies of 64.8 and 63.5 kcal mol(-1), respectively. For the concerted mechanism, ethanol transformation into the ethene product occurs in a single step without intermediate formation, with an activation energy of 32.9 kcal mol(-1).

A Self-Consistent Polarization Potential Model for Describing Excess Electrons Interacting with Water Clusters

A new polarization model potential for describing the interaction of an excess electron with water clusters is presented. This model, which allows for self-consistent electron–water and water–water polarization, including dispersion interactions between the excess electron and the water monomers, gives electron binding energies in excellent agreement with high-level ab initio calculations for both surface-bound and cavity-bound states of (H(2)O)(n)(-) clusters. By contrast, model potentials that do not allow for a self-consistent treatment of electron–water and water–water polarization are less successful at predicting the relative stability of surface-bound and cavity-bound excess electron states.

A Density Functional Theory Study of Cytosine on Au(111)

The adsorption of cytosine on Au(111) is investigated using density functional theory with the nonlocal van der Waals density functional. Test calculations performed on the benzene stacked dimer and on a benzene molecule adsorbed on Au(111) allow us to assess the methodology and reveal the accuracy and predictivity of the van der Waals density funcional relative to experimental outcome. Our results for cytosine on Au(111) indicate that the inclusion of dispersion interactions is crucial for the treatment of this system. In fact, such terms enhance the value of the adsorption energy and also affect the cytosine bonding geometry: in particular, we find that a tilted geometry is always favorable relative to a parallel geometry, which was not found in standard density functional theory investigations. The combined new data for energetics and geometry lead to conclusions that contrast the common opinion that the surface–molecule interaction is negligible in the process of monolayer formation.

Theoretical Study of Asymmetric Transfer Hydrogenation of Ketones Catalyzed by Amino Acid‐Derived Rhodium Complexes

AbstractDensity functional theory calculations are employed to study the asymmetric transfer hydrogenation of ketones catalyzed by rhodium–arene complexes containing hydroxamic acid‐functionalized amino acid ligands. Firstly, the ligand–metal binding is investigated and it is shown that both the N,N and O,O binding modes Are viable. For each of these, the full free energy profile for the transfer hydrogenation is calculated according to the outer‐sphere reaction mechanism. Three factors are demonstrated to influence the stereoselectivity of the process, namely the energy difference between the metal–ligand binding modes, the energy difference between the intermediate hydrogenated catalyst, and the existence of a stabilizing CH–π interaction between the Cp* ligand of the catalyst and the phenyl moiety of the substrate. Theoretical reproduction of the selectivity of a slightly modified ligand that is shown experimentally to yield the opposite enantioselectivity corroborates these results. Finally, a technical observation made is that inclusion of dispersion interactions (using the B3LYP‐D2 correction or the M06 functional) proved to be very important for reproducing the enantioselectivity.

Pentagonal tiling with buckybowls: pentamethylcorannulene on Cu(111)

We present scanning tunnelling microscopy studies and first principles calculation on the 2D crystallization of pentagonal pentamethylcorannulene on a Cu(111) surface under ultrahigh vacuum in the temperature range of 50 K to 400 K. The observed 2D crystal phases and their packing densities are compared to tiling options of hard pentagons. Temperature change-induced reversible phase transitions reveal entropic effects in 2D crystallization. Only inclusion of dispersion interactions into density functional theory yields structures observed experimentally at low temperatures.

On the Accuracy of DFT Methods in Reproducing Ligand Substitution Energies for Transition Metal Complexes in Solution: The Role of Dispersive Interactions

The performance of a series of density functionals when tested on the prediction of the phosphane substitution energy of transition metal complexes is evaluated. The complexes Fe-BDA and Ru-COD (BDA=benzylideneacetone, COD=cyclooctadiene) serve as reference systems, and calculated values are compared with the experimental values in THF as obtained from calorimetry. Results clearly indicate that functionals specifically developed to include dispersion interactions usually outperform other functionals when BDA or COD substitution is considered. However, when phosphanes of different sizes are compared, functionals including dispersion interactions, at odd with experimental evidence, predict that larger phosphanes bind more strongly than smaller phosphanes, while functionals not including dispersion interaction reproduce the experimental trends with reasonable accuracy. In case of the DFT-D functionals, inclusion of a cut-off distance on the dispersive term resolves this issue, and results in a rather robust behavior whatever ligand substitution reaction is considered.

Noncovalent Interactions between Modified Cytosine and Guanine DNA Base Pair Mimics Investigated by Terahertz Spectroscopy and Solid-State Density Functional Theory

Modified cytosine and guanine nucleobases cocrystallize in a hydrogen bonding configuration similar to that observed in native DNA. The noncovalent interactions binding these base pairs in the crystalline solid were investigated using terahertz (THz) spectroscopy and solid-state density functional theory (DFT). While stronger hydrogen bonding interactions are responsible for the general molecular orientations in the crystalline state, it is the weaker dipole-dipole and dispersion forces that determine the overall packing arrangement. The inclusion of dispersion interactions in the DFT calculations was found to be necessary to accurately simulate the unit cell structure and THz vibrational spectrum. Using properly modeled intermolecular potentials, the lattice vibrational motions of the cytosine and guanine derivatives were calculated. The vibrational characters of the modes exhibited by the DNA base pair mimic in the THz region were primarily rotational motions and are indicative of the energies and the nature of vibrations that would likely be observed between similar base pairs in DNA molecules.

Adsorption and Diffusion of Fructose in Zeolite HZSM-5: Selection of Models and Methods for Computational Studies

The adsorption and protonation of fructose in HZSM-5 have been studied for the assessment of models for accurate reaction energy calculations and the evaluation of molecular diffusivity. The adsorption and protonation were calculated using 2T, 5T, and 46T clusters as well as a periodic model. The results indicate that the reaction thermodynamics cannot be predicted correctly using small cluster models, such as 2T or 5T, because these small cluster models fail to represent the electrostatic effect of a zeolite cage, which provides additional stabilization to the ion pair formed upon the protonation of fructose. Structural parameters optimized using the 46T cluster model agree well with those of the full periodic model; however, the calculated reaction energies are in significant error due to the poor account of dispersion effects by density functional theory. The dispersion effects contribute −30.5 kcal/mol to the binding energy of fructose in the zeolite pore based on periodic model calculations that include dispersion interactions. The protonation of the fructose ternary carbon hydroxyl group was calculated to be exothermic by 5.5 kcal/mol with a reaction barrier of 2.9 kcal/mol using the periodic model with dispersion effects. Our results suggest that the internal diffusion of fructose in HZSM-5 is very likely to be energetically limited and only occurs at high temperature due to the large size of the molecule.

Methane adsorption on graphene from first principles including dispersion interaction

The methane–graphene interaction is studied using density functional theory complemented with a semiempirical dispersion correction scheme (DFT-D), an ab initio van der Waals density functional (vdW-DF) ansatz as well as using Møller Plesset perturbation theory (MP2). The adsorption energy of 0.17 eV and the molecular distance of 3.28 Å obtained from the MP2 calculations are close to the experimental data, while the vdW-DF scheme results either in a realistic adsorption energy or a realistic adsorption geometry, depending on the underlying exchange-correlation functional. The present implementation of DFT-D overbinds about as much as bare DFT calculations underbind, but yields a meaningful adsorption height.

Mechanistic differences between methanol and dimethyl ether carbonylation in side pockets and large channels of mordenite

The activity and selectivity towards carbonylation presented by Brønsted acid sites located inside the 8MR pockets or in the main 12MR channels of mordenite is studied by means of quantum-chemical calculations, and the mechanistic differences between methanol and DME carbonylation are investigated. The selectivity towards carbonylation is higher inside the 8MR pockets, where the competitive formation of DME and hydrocarbons that finally leads to catalyst deactivation is sterically impeded. Moreover, inclusion of dispersion interactions in the calculations leads to agreement between the calculated activation barriers for the rate determining step and the experimentally observed higher reactivity of methoxy groups located inside the 8MR channels.

Density Functional Theory Study of Catechol Adhesion on Silica Surfaces

It has been speculated that the catechol (1,2-dihydroxybenzene) functionality of marine mussels is responsible for its strong and versatile adhesion on various wet surfaces. To elucidate features of this adhesion, we performed a periodic density functional theory calculation for catechol adsorption on silica surfaces. We obtained its binding energy and geometry on two representative hydroxylated surfaces of cristobalite, which mimic amorphous silica. Catechol strongly adhered to both surfaces by making three or four hydrogen bonds. Catechol achieved versatility in adhesion via torsion of its hydroxyls. The binding energy of catechol, which amounts to 14 kcal/mol, was larger than that of water, irrespective of the surface. With the inclusion of dispersion interaction, the binding energy of catechol further increased up to 33 kcal/mol, and its preferential adsorption over water became evident. Both the hydroxyls and phenylene ring of catechol contribute to its strong adhesion due to hydrogen bonds and dispe...

Assessment of the performance of common density functional methods for describing the interaction energies of (H2O)6 clusters

Localized molecular orbital energy decomposition analysis and symmetry-adapted perturbation theory (SAPT) calculations are used to analyze the two- and three-body interaction energies of four low-energy isomers of (H(2)O)(6) in order to gain insight into the performance of several popular density functionals for describing the electrostatic, exchange-repulsion, induction, and short-range dispersion interactions between water molecules. The energy decomposition analyses indicate that all density functionals considered significantly overestimate the contributions of charge transfer to the interaction energies. Moreover, in contrast to some studies that state that density functional theory (DFT) does not include dispersion interactions, we adopt a broader definition and conclude that for (H(2)O)(6) the short-range dispersion interactions recovered in the DFT calculations account about 75% or more of the net (short-range plus long-range) dispersion energies obtained from the SAPT calculations.

Computing dispersion interactions in density functional theory

In this article techniques for including dispersion interactions within density functional theory are examined. In particular comparisons are made between four popular methods: dispersion corrected DFT, pseudopotential correction schemes, symmetry adapted perturbation theory, and a non-local density functional — the so called Rutgers–Chalmers van der Waals density functional (vdW-DF). The S22 benchmark data set is used to evaluate the relative accuracy of these methods and factors such as scalability and transferability are also discussed. We demonstrate that vdW-DF presents an excellent compromise between computational speed and accuracy and lends most easily to full scale application in solid materials. This claim is supported through a brief discussion of a recent large scale application to H2 in a prototype metal organic framework material (MOF), Zn2BDC2TED. The vdW-DF shows overwhelming promise for first-principles studies of physisorbed molecules in porous extended systems; thereby having broad applicability for studies as diverse as molecular adsorption and storage, battery technology, catalysis and gas separations.

Including dispersion interactions in the ONETEP program for linear-scaling density functional theory calculations

While density functional theory (DFT) allows accurate quantum mechanical simulations from first principles in molecules and solids, commonly used exchange-correlation density functionals provide a very incomplete description of dispersion interactions. One way to include such interactions is to augment the DFT energy expression by damped London energy expressions. Several variants of this have been developed for this task, which we discuss and compare in this paper. We have implemented these schemes in the ONETEP program, which is capable of DFT calculations with computational cost that increases linearly with the number of atoms. We have optimized all the parameters involved in our implementation of the dispersion correction, with the aim of simulating biomolecular systems. Our tests show that in cases where dispersion interactions are important this approach produces binding energies and molecular structures of a quality comparable with high-level wavefunction-based approaches.

Unraveling Solvent-Driven Equilibria between α- and 310-Helices through an Integrated Spin Labeling and Computational Approach

In this work we present an effective and flexible computational approach, which is the result of an ongoing development in our groups, allowing the complete a priori simulation of the ESR spectra of complex systems in solution. The usefulness and reliability of the method are demonstrated on the very demanding playground represented by the tuning of the equilibrium between 3(10)- and alpha-helices of polypeptides by different solvents. The starting point is the good agreement between computed and X-ray diffraction structures for the 3(10)-helix adopted by the double spin-labelled heptapeptide Fmoc-(Aib-Aib-TOAC)2-Aib-OMe. Next, density functional computations, including dispersion interactions and bulk solvent effects, suggest another energy minimum corresponding to an alpha-helix in polar solvents, which, eventually, becomes the most stable structure. Computation of magnetic and diffusion tensors provides the basic ingredients for the building of complete spectra by methods rooted in the Stochastic Liouville Equation (SLE). The remarkable agreement between computed and experimental spectra at different temperatures allowed us to identify helical structures in the various solvents. The generality of the computational strategy and its implementation in effective and user-friendly computer codes pave the route toward systematic applications in the field of biomolecules and other complex systems.

The Mid-IR Spectra of 9-Ethyl Guanine, Guanosine, and 2-Deoxyguanosine

We present the mid-IR (400-1800 cm(-1)) spectra of 9-ethyl guanine, guanosine, and 2-deoxyguanosine measured by IR-UV double-resonance spectroscopy. We compare the recorded mid-IR spectra with the spectra of the most stable structures obtained from RI-MP2 and RI-DFT-D calculations. The results confirm the enol form for all structures and demonstrate the efficacy of a new approach to DFT calculations that includes dispersion interactions.

First-Principles Description of Correlation Effects in Layered Materials

We present a first-principles description of anisotropic materials characterized by having both weak (dispersionlike) and strong covalent bonds, based on the adiabatic-connection fluctuation-dissipation theorem with density functional theory. For hexagonal boron nitride the in-plane and out-of-plane bonding as well as vibrational dynamics are well described both at equilibrium and when the layers are pulled apart. Bonding in covalent and ionic solids is also described. The formalism allows us to ping down the deficiencies of common exchange-correlation functionals and provides insight toward the inclusion of dispersion interactions into the correlation functional.