Including Dispersion Corrections Research Articles

A molecular study of tetrakis(p -methoxyphenyl)porphyrin and its Zn(II) complex as discotic liquid crystals

A theoretical study has been carried out on two methoxyphenyl derivatives (tetrakis-(p-methoxyphenyl)- porphyrin and the Zn-containing complex), which are the reduced size representation of the alkyl peripheral substituent systems. The aim is to study the electronic interactions on these aromatic cores which is one of the most important properties in discotic liquid crystals. Their face-to-face dimeric conformation systems were studied in order to evaluate charge transport properties, by assessing the intermolecular charge transfer integrals “t” in the context of the Marcus electron transfer theory. The intermolecular transfer integral has been calculated from the matrix elements of the Kohn–Sham Hamiltonian including dispersion correction for noncovalent interacting systems. The results indicate that the effect of the Zn center in these porphyrins is nearly negligible and both studied systems can act as electron carriers, which are also seen in the bonding interaction of the LUMO orbitals. © 2013 Wiley Periodicals, Inc.

The Melatonin Conformer Space: Benchmark and Assessment of Wave Function and DFT Methods for a Paradigmatic Biological and Pharmacological Molecule

Reference quality conformational energies have been obtained for the 52 unique conformers of melatonin by means of explicitly correlated ab initio methods as well as the ccCA composite method. These data have then been used to evaluate more approximate methods, including a variety of density functionals both on their own and paired with various empirical dispersion corrections. Owing to the presence of internal contacts of the C-H···O and C-H···N variety, basis set convergence is much slower than for alkane conformers, for example, and basis sets of aug-cc-pVQZ or def2-QZVP quality seem to be required to obtain firm estimates of the basis set limit. Not just HF, but also many DFT functionals, will transpose the two lowest conformers unless empirical dispersion corrections are added. Somewhat surprisingly, many DFT functionals reproduce the reference data to fairly high accuracy when combined with the D3BJ empirical dispersion correction or the "nonlocal" Vydrov-Van Voorhis dispersion model. The two best performers including dispersion corrections are the double hybrids DSD-PBEP86-D3BJ and B2GP-PLYP-D; if no such correction is permitted, then M06-2X puts in the best performance. Of lower-cost ab initio-like models, MP2.5 yields the best performance, followed by SCS-MP2.

Theoretical and experimental study of montmorillonite intercalated with tetramethylammonium cation

Structural and vibrational features of Na-montmorillonite and montmorillonite intercalated with tetramethylammonium cation (TMA+) were characterized theoretically and experimentally. Theoretical study was performed using density functional theory with inclusion of dispersion corrections. The analysis of the hydrogen bonds in the calculated models has shown that the Na+ cations coordinated by six water molecules (Na-M model) are bound to montmorillonite layers by moderate hydrogen bonds between water molecules and basal oxygen atoms of the tetrahedral sheets. Hydrated Na+ cations are stabilized by relatively strong hydrogen bonds among water molecules. In the intercalate model, the TMA+ cation is fixed in the interlayer space by weak hydrogen bonds between the methyl groups and basal oxygen atoms of montmorillonite layers. The calculated vibrational spectra are in a good agreement with the measured infrared spectra. The detailed analysis of the simulated vibrational spectra allowed unambiguous identification of corresponding bands in the measured spectra and their assignment to the particular vibrational modes. For example, calculations clearly distinguished between AlMgOH and AlAlOH stretching vibrations and also between the coupled vibrations of the methyl groups of the TMA+ cations.

From clusters to liquid: what are the preferred ways for benzene and pyrrole to interact?

The various interactions occurring between pyrrole and benzene are a particularly appropriate model, as they are viewed as better X–H···π examples. A combined and sequential use of Quantum Mechanical (QM) calculations and Molecular Dynamics (MD) simulations was applied to investigate the different intermolecular interactions for benzene and pyrrole as clusters and its liquid mixture. All the cluster structures were fully optimized by the B2PLYP-D methods (including dispersion correction) with jun-cc-pVTZ (a revised aug-cc-pVTZ basis set). MD simulation with OPLS-AA force field was used to study the liquid mixture of benzene/pyrrole at different temperatures. Two types of N–H···π hydrogen bonds are preferred interactions compared with C–H···π interactions, either as clusters or as its liquid mixture. Based on the QM results, we clarify the difference in red-shifts of N–H bond of N–H···π hydrogen bonds observed by Jet FT-IR (Phys Chem Chem Phys 10: 2827, 2008). Meanwhile, the nature of various X–H···π interactions is unveiled by atoms in molecules (AIM), natural bond orbital and energy decomposition analysis (EDA). Furthermore, in light of QM results, MD simulation results further characterize the behavior and structural properties of these interactions. Finally, we proposed an original idea to explain the strength variation of different N–H···π hydrogen bond in liquid mixture based on AIM and EDA analysis.

Dynamics of hydrogen bonds and vibrational spectral diffusion in liquid methanol from first principles simulations with dispersion corrected density functional

The effects of dispersion interactions on the dynamics of hydrogen bonds and vibrational spectral diffusion in liquid methanol are investigated through first principles simulations with a dispersion corrected density functional. Calculations are done at two different temperatures of 300 and 350K and the results are compared with those of an earlier study where no such dispersion corrections were included. It is found that inclusion of dispersion interactions slightly increases the number of molecules held through non-hydrogen-bonded dispersion interactions in the neighborhood which, in turn, makes the dynamics faster. The inclusion of dispersion corrections gives rise to a faster hydrogen bond dynamics compared to the case when no such dispersion corrections are made. Also, the time scale of vibrational spectral diffusion obtained with the dispersion corrected density functional is found to be in better agreement with experiments.

Effect of interlayer counterions on the structures of dry montmorillonites with Si4+/Al3+ substitution

Density functional theory calculations were performed to study the intercalating behaviors of positively charged counterions in montmorillonites (MMTs) with Si4+/Al3+ substitution in their first internal layer. The substitution has great influence on the interaction between the counterions and the internal surface as well as on the MMT lattice structures. The intercalated counterions are characterized by their strong bonding with the six-oxygen-ring (SOR) on the substituted layer and with the O atoms on the opposite surface. The cations with smaller radii or higher charge have stronger interaction with the surface atoms. The inclusion of dispersion correction in the calculations leads to small changes to the lattice structures.

Incipient chemical bond formation of Xe to a cationic silicon cluster: Vibrational spectroscopy and structure of the Si4Xe+ complex

The size-selective vibrational spectrum of Si4Xe+ in the 240–500cm−1 range has been recorded using infrared (IR) multiple photon dissociation spectroscopy. Comparison to linear IR absorption spectra of Si4+ and Si4Xe+ calculated using density functional theory including dispersion corrections reveals an important influence of the Xe ligand on the structure of the cluster, involving significant charge transfer and formation of an incipient chemical Si–Xe bond with De = 0.3eV.

Quantum Chemical Calculations of Side-Group Stacking and Electronic Properties in Thiophene–Quinoxaline Polymers

Organic bulk heterojunction (BHJ) solar cells offer a viable source of solar energy. Structural organization is crucial in BHJ cells but hard to achieve and assess due to limitations in experimental methodology. Quantum chemical methods have here been used to gain further insight into the geometric and optical properties of a promising light-harvesting polymer, poly[2,3-bis(3-octyloxyphenyl)quinoxaline-5,8-diyl-alt-thiophene-2,5-diyl] (TQ1). Calculations show that favorable positions of the two alkoxyphenyl side groups on each TQ1 monomer allow nonbonded side-group stacking interactions with the neighboring units in both directions. This yields a unique, helical geometry with enhanced intramolecular ordering that promotes extensive electronic conjugation. Adequate description of this effect requires computational methods that include dispersion corrections. A strategy based on such side-group interactions is proposed for designing new polymers.

Effect of dispersion correction on the Au(1 1 1)-H2O interface: A first-principles study

A theoretical study of the H(2)O-Au(1 1 1) interface based on first principles density functional theory (DFT) calculations with and without inclusion of dispersion correction is reported. Three different computational approaches are considered. First, the standard generalized gradient approximation (GGA) functional PBE is employed. Second, an additional energy term is further included that adds a semi-empirically derived dispersion correction (PBE-D2), and, finally, a recently proposed functional that includes van der Waals (vdW) interactions directly in its functional form (optB86b-vdW) was used to represent the state-of-the art of DFT functionals. The monomeric water adsorption was first considered in order to explore the dependency of geometry on the details of the model slab used to represent it (size, thickness, coverage). When the dispersion corrections are included the Au-H(2)O interaction is stronger, as manifested by the smaller d(Au-O) and stronger adsorption energies. Additionally, the interfacial region between Au(1 1 1) slab surfaces and a liquid water layer was investigated with Born-Oppenheimer molecular dynamics (BOMD) using the same functionals. Two or three interfacial orientations can be determined, depending on the theoretical methodology applied. Closest to the surface, H(2)O is adsorbed O-down, whereas further away it is oriented with one OH bond pointing to the surface and the molecular plane parallel to the normal direction. For the optB86b-vdW functional a third orientation is found where one H atom points into the bulk water layer and the second OH bond is oriented parallel to the metal surface. As for the water density in the first adsorption layer we find a very small increase of roughly 8%. From the analysis of vibrational spectra a weakening of the H-bond network is observed upon the inclusion of the Au(1 1 1) slab, however, no disruption of H-bonds is observed. While the PBE and PBE-D2 spectra are very similar, the optB86b-vdW spectrum shows that the H-bonds are even more weakened.

Quantum Chemical Parametrization and Spectroscopic Characterization of the Frenkel Exciton Hamiltonian for a J-Aggregate Forming Perylene Bisimide Dye

Quantum chemical and quantum dynamical calculations are performed for a bay-substituted perylene bisimide dye up to its hexameric aggregate. The aggregate structure is determined by employing the self-consistent charge density functional tight-binding (SCC-DFTB) approach including dispersion corrections. It is characterized by a stabilization via two chains of hydrogen bonds facilitated by amide functionalities. Focusing on the central embedded dimer, the Coulomb coupling for this J-aggregate is determined by means of the time-dependent density functional theory (TDDFT) to be -514 cm(-1). Exciton vibrational coupling is treated within the shifted oscillator model from which five strongly coupled modes per monomer are selected for inclusion into a minimal dynamic model. Performing wave packet propagations for a model employing up to 7 electronic states and 30 vibrational modes using the multiconfiguration time-dependent Hartree method, aggregate absorption spectra are obtained and compared to experiment.

A theoretical study of N–H ··· π H-bond interaction of pyrrole: from clusters to the liquid

The N–H ··· π H-bond interactions of clusters and liquid formed by pyrrole molecules were investigated by Quantum Mechanics (QM) and classical Molecular Dynamics (MD), respectively. Based on the optimized geometry at the B97-D/aug-cc-pVTZ level of theory including dispersion correction, the nature and the origin of N–H ··· π H-bond interactions were unveiled by atoms in molecules (AIM), natural bond orbital (NBO), and energy decomposition analysis (EDA). Among them, the AIM analysis gives evidence to the presence of N–H ··· π H-bond interactions, the NBO examination reveals that π → σ* donor-acceptor orbital interaction is of great importance. EDA study indicates that N–H ··· π interactions are governed by the electrostatic and dispersion term. Meanwhile, MD simulation with OPLS-AA (optimized potentials for liquid simulations all-atom) was applied to study the pure liquid pyrrole at different temperature. The results confirm the existence of the N–H ··· π H-bond in the pure liquid pyrrole, and further characterized the structures of this H-bond which is somewhat different to the clusters.

Phase transition and chemical decomposition of shocked CO–N2 mixture

Using quantum molecular dynamics simulations based on density functional theory including dispersion corrections (DFT-D), we have studied the thermophysical properties of liquid carbon monoxide and nitrogen (CO-N(2)) mixture under extreme conditions. Density functional theory (DFT) method significantly overestimates the pressure as compared to DFT-D. It is demonstrated that the van der Waals (vdW) interaction has a negative contribution to the pressure and tends to reduce the overestimation of the equilibrium volume. We also demonstrate that a negative slope of Hugoniot curve could possibly be caused by both the absorption of dissociation energy and the uncertainties in composition. As density and temperature increase along the Hoguniot curve, the system appears to undergo a continuous transition and provides for a much richer set of dissociation products. The influence of dissociated carbon and oxygen atoms on nitrogen molecules is also discussed.

Theoretical Study of the Cytochrome P450 Mediated Metabolism of Phosphorodithioate Pesticides.

The toxicity of phosphorodithioate pesticides is due to the formation of the active oxane product through desulfurization by cytochrome P450 enzymes, both in humans and insects. During this desulfurization, inhibition of cytochrome P450 and a loss of heme has been observed. Here, we study the mechanism of desulfurization and inhibition with density functional theory, using the B3LYP functional with and without dispersion correction. The results show that a reaction mechanism initiated by sulfur oxidation is most likely, with a reaction barrier of 47 kJ/mol. The sulfur oxidation is followed by a ring-closing mechanism with a barrier of 28 kJ/mol relative to the sulfur-oxidized intermediate. The enzymatic contribution to the ring-closing is very small. It is also shown that the apparent loss of heme might be due to the formation of a previously unknown inhibition complex, which changes the aromatic conjugation of the porphyrin ring. We also show that including dispersion correction has significant effects on a ring closure transition state (∼30 kJ/mol), whereas effects on the other steps in the reaction are relatively small (4-15 kJ/mol).

Adsorption of methane on carbon models of coal surface studied by the density functional theory including dispersion correction (DFT-D3)

The density functional theory including dispersion correction (DFT-D3) has been used to investigate the adsorption of methane on carbon models of coal surface, including C6H8, pyrene, and coronene. For the small model complex C6H8–CH4, the interaction energies obtained using four kinds of the functionals, BLYP-D3, TPSS-D3, BP86-D3, and PBE-D3, were benchmarked against the best available result that was provided by the complete basis set (CBS) limit of CCSD(T) method, and the BLYP-D3 functional with the best performance was selected to treat the remained larger systems. Several adsorption positions and orientations of CH4 on the hydrocarbon clusters were systematically considered. Our results indicated that the interaction energy in the complex increases as the size of the complex increases and the up configuration of CH4 (with the hydrogen tripod directed to the surface) adsorbed on pyrene and coronene is greatly preferred when compared with both the down and bidentate configurations. The center adsorption site above the six-membered ring is preferred by the methane molecule adsorbed on coronene. It was shown that in coronene–methane model the interaction energies of −3.17 to −3.32kcal/mol and the molecular distances of 3.36–3.39Å obtained from the BLYP-D3 calculations are close to the values available in experiment for the binding of methane on graphite and can provide the accurate prediction to those in the coal surface–methane complex.

Amino acid analogues bind to carbon nanotube via π-π interactions: Comparison of molecular mechanical and quantum mechanical calculations

Understanding the interaction between carbon nanotubes (CNTs) and biomolecules is essential to the CNT-based nanotechnology and biotechnology. Some recent experiments have suggested that the π-π stacking interactions between protein's aromatic residues and CNTs might play a key role in their binding, which raises interest in large scale modeling of protein-CNT complexes and associated π-π interactions at atomic detail. However, there is concern on the accuracy of classical fixed-charge molecular force fields due to their classical treatments and lack of polarizability. Here, we study the binding of three aromatic residue analogues (mimicking phenylalanine, tyrosine, and tryptophan) and benzene to a single-walled CNT, and compare the molecular mechanical (MM) calculations using three popular fixed-charge force fields (OPLSAA, AMBER, and CHARMM), with quantum mechanical (QM) calculations using the density-functional tight-binding method with the inclusion of dispersion correction (DFTB-D). Two typical configurations commonly found in π-π interactions are used, one with the aromatic rings parallel to the CNT surface (flat), and the other perpendicular (edge). Our calculations reveal that compared to the QM results the MM approaches can appropriately reproduce the strength of π-π interactions for both configurations, and more importantly, the energy difference between them, indicating that the various contributions to π-π interactions have been implicitly included in the van der Waals parameters of the standard MM force fields. Meanwhile, these MM models are less accurate in predicting the exact structural binding patterns (matching surface), meaning there are still rooms to be improved. In addition, we have provided a comprehensive and reliable QM picture for the π-π interactions of aromatic molecules with CNTs in gas phase, which might be used as a benchmark for future force field developments.

Ab initio studies of the crystal structure of cellulose triacetate I

ABSTRACTWe have investigated crystal structure of cellulose triacetate I (CTA I) by using first principal density functional theory (DFT) calculation. The results are in good agreement with the experimentally obtained crystal structure when we used the cutoff energy higher than 70 Ry. However, the cell parameters calculated without dispersion correction are overestimated the results compared to the experimental value. Contrary, with the inclusion of dispersion correction, the cell parameters were calculated slightly smaller than the experimental one. The smaller cell parameter can be considered to be reasonable because the effect of the thermal expansion is not included in the density functional calculation. That is, inclusion of the dispersion term is important in the calculation of this crystal structure of CTA I.

Structures and hydrogen adsorption of [formula omitted] ([formula omitted]) clusters

According to the charge polarization mechanism, high charges carried on metal ions are favorable to improve hydrogen storage capacity. This can be achieved by linking light metal atoms such as Mg with light molecules having large electron affinity such as NCN. Using first-principles calculations based on density functional theory including dispersion corrections, we investigate the geometries, electronic structures, and hydrogen adsorption properties of (MgCN2)n (n=1–4) clusters. The results show that these small clusters exhibit moderate affinity to hydrogen with the average adsorption energy in the range of 0.10–0.20 eV. The gravimetric storage densities for (MgCN2)2 and (MgCN2)3 are 5.9 wt%, suggesting that these clusters can be used as building blocks for assembling hydrogen storage materials or introduced to porous structures for enhancing H2 adsorption capacity.

Overcoming lability of extremely long alkane carbon–carbon bonds through dispersion forces

Steric effects in chemistry are a consequence of the space required to accommodate the atoms and groups within a molecule, and are often thought to be dominated by repulsive forces arising from overlapping electron densities (Pauli repulsion). An appreciation of attractive interactions such as van der Waals forces (which include London dispersion forces) is necessary to understand chemical bonding and reactivity fully. This is evident from, for example, the strongly debated origin of the higher stability of branched alkanes relative to linear alkanes and the possibility of constructing hydrocarbons with extraordinarily long C-C single bonds through steric crowding. Although empirical bond distance/bond strength relationships have been established for C-C bonds (longer C-C bonds have smaller bond dissociation energies), these have no present theoretical basis. Nevertheless, these empirical considerations are fundamental to structural and energetic evaluations in chemistry, as summarized by Pauling as early as 1960 and confirmed more recently. Here we report the preparation of hydrocarbons with extremely long C-C bonds (up to 1.704 Å), the longest such bonds observed so far in alkanes. The prepared compounds are unexpectedly stable--noticeable decomposition occurs only above 200 °C. We prepared the alkanes by coupling nanometre-sized, diamond-like, highly rigid structures known as diamondoids. The extraordinary stability of the coupling products is due to overall attractive dispersion interactions between the intramolecular H•••H contact surfaces, as is evident from density functional theory computations with and without inclusion of dispersion corrections.

Theoretical studies on the dimerization of substituted paraphenylenediamine radical cations

Organic radical cations form dicationic dimers in solution, observed experimentally as diamagnetic species in temperature-dependent EPR and low temperature UV/Vis spectroscopy. Dimerization of paraphenylenediamine, N,N-dimethyl-paraphenylenediamine and 2,3,5,6-tetramethyl-paraphenylenediamine radical cation in ethanol/diethylether mixture was investigated theoretically according to geometry, energetics and UV/Vis spectroscopy. Density Functional Theory including dispersion correction describes stable dimers after geometry optimization with conductor-like screening model of solvation and inclusion of the counter-ion. Energy corrections were done on double-hybrid Density Functional Theory with perturbative second-order correlation (B2PLYP-D) including basis set superposition error (BSSE), and multireference Møller-Plesset second-order perturbation theory method (MRMP2) based on complete active space method (CASSCF(2,2)) single point calculation, respectively. All three dication π-dimers exhibit long multicenter π-bonds around 2.9 ± 0.1 Å with strongly interacting orbitals. Substitution with methyl groups does not influence the dimerization process substantially. Dispersion interaction and electrostatic attraction from counter-ion play an important role to stabilize the dication dimers in solution. Dispersion-corrected double hybrid functional B2PLYP-D and CASSCF(2,2) can describe the interaction energetics properly. Vertical excitations were computed with Tamm-Dancoff approximation for time-dependent Density Functional Theory (TDA-DFT) at the B3LYP level with the cc-pVTZ basis set including ethanol solvent molecules explicitly. A strong interaction of the counter-ion and the solvent ethanol with the monomeric species is observed, whereas in the dimers the strong interaction of both radical cation species is the dominating factor for the additional peak in UV/Vis spectra.

First-Principles Study of Water Confined in Single-Walled Silicon Carbide Nanotubes

In the present work, water molecules confined inside single-walled silicon carbide nanotubes (SiCNTs) are studied using density functional theory calculations. A set of periodic boundary condition models are established for segments of single-file water chains, infinite single-file water chains, and infinite multifiled water networks encapsulated within the periodic armchair and zigzag SiCNTs with (5,5), (6,6), (8,0), (9,0), and (10,0) chiralities. Two hybrid density functionals with and without dispersion correction, ωB97XD and B3LYP, respectively, are employed in all calculations for structure, interaction energy, and charge analysis. Although the silicon carbide surface is essentially hydrophilic, water molecules within SiCNTs have structures and properties that resemble those in the hydrophobic single-walled carbon nanotube since both are controlled by the geometry confinement. It is necessary to include dispersion corrections to describe the weak interactions between the water molecules and the SiCNT wall which arise mainly from van der Waals interactions and a slight charge transfer from SiCNT to the enclosed water molecules.