Dispersion-corrected Density Functional Theory Calculations Research Articles

Prediction of Water Adsorption in Copper-Based Metal–Organic Frameworks Using Force Fields Derived from Dispersion-Corrected DFT Calculations

We develop transferable force fields describing water adsorption in copper-based metal–organic frameworks (MOFs) by combining dispersion-corrected density functional theory (DFT) calculations and classical atomistic simulations. The DFT-D2 approach was found to give reasonable agreement with high level quantum chemistry results for the interaction between water and CuBTC. A classical force field for water adsorption in CuBTC including Lennard-Jones (LJ), Coulombic interactions, and a water–copper distance-dependent correction term was then developed on the basis of 1200 DFT-D2 calculations that probed the full range of accessible volume in CuBTC via random sampling. Good agreement was obtained between adsorption isotherms predicted with our first-principles-derived force field and experiments. Other commonly used models such as simple combinations of LJ and Coulomb potentials cannot adequately describe the interaction between water and CuBTC due to the chemical bonding between water oxygen and copper atom...

IR spectroscopy of crystalline polymers from ab initio calculations: Nylon 6,6

The IR spectrum of Nylon 6,6 in the crystalline α phase is computed by means of dispersion-corrected density functional theory calculations carried out with periodic boundary conditions on the crystal. The results are carefully compared to experimental spectra through a detailed analysis of different frequency regions and focusing on the spectroscopic markers of crystallinity or regularity (i.e. of the regular conformation of the polymer chain). The previous assignments, based exclusively on experimental or semi-empirical investigations, are critically revised, demonstrating that state of the art computational methods in solid state chemistry can provide tools to obtain an unambiguous description of the vibrational properties of the crystalline phases of macromolecular materials. In particular, the ambiguities related to the assignment of some debated bands of crystallinity/regularity are solved. The structural and vibrational properties are interpreted on the basis of the peculiar intra and intermolecular interactions occurring in polyamides.

Binding of Polyvinylpyrrolidone to Ag Surfaces: Insight into a Structure-Directing Agent from Dispersion-Corrected Density Functional Theory

We use dispersion-corrected density functional theory (DFT) to resolve the role of polyvinylpyrrolidone (PVP) in the shape-selective synthesis of Ag nanostructures by probing the interaction of its 2-pyrrolidone (2P) ring with Ag(100) and Ag(111). We employ two different semiempirical methods for including van der Waals (vdW) interactions in DFT calculations: DFT+vdWsurf and DFT-D2. We find that DFT-D2, in its original parametrization, overestimates the Ag metal dispersion interaction and causes an unphysical herringbone-like reconstruction of Ag(100). This can be remedied in DFT-D2 by using modified vdW parameters for Ag that account for many-body screening effects. The results obtained using DFT-D2 with the modified parameters agree well with experiment and with DFT+vdWsurf results. We find that 2P binds more strongly to Ag(100) than Ag(111), consistent with experiment. We analyze the origins of the surface-sensitive binding and find that vdW attraction is stronger on Ag(111), but the direct chemical bonding of 2P is stronger on Ag(100). We also study the influence of strain on binding energies and find that tension tends to lower the vdW interaction with the surfaces, while increasing the direct chemical-bonding interaction, consistent with the d-band center model. Overall, our work indicates that strain has little impact on the structure-directing capabilities of PVP, which is consistent with the fact that strained, 5-fold twinned Ag nanowires have extensive {100} facets and relative small {111} facets.

Influence of accompanying anions on supramolecular assembly and coordination geometry in HgII complexes with 8-aminoquinoline: experimental and theoretical studies

To investigate the effect of counterions on crystalline networks, we have designed and synthesized a series of HgII complexes, [Hg(8-aq)Cl2] (1), [Hg(8-aq)Br2] (2) and [Hg5(8-aq)2I10]n (3), via a reaction between 8-aminoquinoline (8-aq) with HgX2 (X = Cl, Br, I). They have been characterized by elemental analyses, IR, 1H- and 13C-NMR spectroscopy and two of the compounds (X = Br and I) have been structurally determined by single crystal X-ray diffraction analysis. These studies revealed that compound 2 is mononuclear with the metal centre exhibiting a distorted tetragonal geometry while compound 3 is a one-dimensional coordination polymer where the bridging iodide ligands and the metal centres exhibit distorted tetragonal and octahedral geometries. The non-covalent interactions responsible for the crystalline network of 2 and 3 have been studied using theoretical methods by means of dispersion-corrected density functional theory (DFT-D) calculations. The binding energies associated with the different non-covalent interactions indicate hydrogen bonds, stacking and X⋯X interactions govern the network formation of complexes 2 and 3.

DFT Study of Furfural Conversion to Furan, Furfuryl Alcohol, and 2-Methylfuran on Pd(111)

Dispersion-corrected density functional theory calculations were performed to investigate the adsorption of furan, furfural, furfuryl alcohol, and 2-methylfuran as well as the reaction barriers for their interconversion. The most stable configuration for furan, furfural, furfuryl alcohol, and 2-methylfuran entails the furan ring lying flat on the surface, centered over a hollow site. We performed an elementary step analysis for the reaction of furfural to furan, furfuryl alcohol, and 2-methylfuran. Thermodynamics favors the production of furan and CO. The activation energy for furfural reduction to furfuryl alcohol is lower than that for its decarbonylation to furan. The formation of 2-methylfuran occurs via dehydration of furfuryl alcohol or a dehydrogenation pathway through a methoxy intermediate. Our findings are in agreement with recently reported experimental results.

Reinterpretation of the monohydrate of clarithromycin from X-ray powder diffraction data as a trihydrate

Noguchi, Fujiki, Iwao, Miura & Itai [Acta Cryst. (2012), E68, o667-o668] recently reported the crystal structure of clarithromycin monohydrate from synchrotron X-ray powder diffraction data. Voids in the crystal structure suggested the possible presence of two more water molecules. After successful location of the two additional water molecules, the Rietveld refinement still showed minor problems. These were resolved by noticing that one of the chiral centres in the molecule had been inverted. The corrected crystal structure of clarithromycin trihydrate, refined against the original data, is now reported. Dispersion-corrected density functional theory calculations were used to check the final crystal structure and to position the H atoms.

Dispersion-Corrected Density Functional Theory and Classical Force Field Calculations of Water Loading on a Pyrophyllite(001) Surface

Water adsorption on the (001) surface of pyrophyllite [Al(OH)(Si2O5)] was investigated using density functional theory (DFT) with dispersion corrections and force field calculations. The DFT calculations show that a water molecule can bind either to one or to two basal oxygen atoms of the surface, with adsorption energies varying from −0.10 to −0.19 eV depending on the binding configuration and binding site. Because the water–water interactions are stronger than the water–surface interactions, the energetically preferred structures with two or more molecules on the surface are clusters reminiscent of their gas-phase counterparts. The trend in water–surface binding energies with the number of water molecules obtained from force field calculations qualitatively agrees with that predicted by the dispersion-corrected DFT calculations. However, the force field calculations give a low-energy structural motif with a water molecule coordinated to a hydroxyl group associated with the octahedral layer of the pyroph...

Gold anion catalysis of methane to methanol

The oxidation of CH4 has been investigated in the presence and absence of the atomic Au− ion catalyst. We have employed the first principles density functional theory (DFT) and dispersion-corrected DFT calculations for the transition state on the Au− ion and analyzed the thermodynamics properties of the reactions as well. Our results demonstrate that atomic gold anions could be used to catalyze CH4 into valuable industrial products without the emission of CO2, thereby making gold extremely valuable. The fundamental mechanism involves breaking the C–H bond through the formation of the anionic Au−(CH4) molecular complex permitting the oxidation of CH4 to methanol at the temperature of 325 K which is below that of CO2 emission. Potentially, this could significantly impact the quality of our environment.

Three Types of Induced Tryptophan Optical Activity Compared in Model Dipeptides: Theory and Experiment

The tryptophan (Trp) aromatic residue in chiral matrices often exhibits a large optical activity and thus provides valuable structural information. However, it can also obscure spectral contributions from other peptide parts. To better understand the induced chirality, electronic circular dichroism (ECD), vibrational circular dichroism (VCD), and Raman optical activity (ROA) spectra of Trp-containing cyclic dipeptides c-(Trp-X) (where X = Gly, Ala, Trp, Leu, nLeu, and Pro) are analyzed on the basis of experimental spectra and density functional theory (DFT) computations. The results provide valuable insight into the molecular conformational and spectroscopic behavior of Trp. Whereas the ECD is dominated by Trp π-π* transitions, VCD is dominated by the amide modes, well separated from minor Trp contributions. The ROA signal is the most complex. However, an ROA marker band at 1554 cm(-1) indicates the local χ(2) angle value in this residue, in accordance with previous theoretical predictions. The spectra and computations also indicate that the peptide ring is nonplanar, with a shallow potential so that the nonplanarity is primarily induced by the side chains. Dispersion-corrected DFT calculations provide better results than plain DFT, but comparison with experiment suggests that they overestimate the stability of the folded conformers. Molecular dynamics simulations and NMR results also confirm a limited accuracy of the dispersion-DFT model in nonaqueous solvents. Combination of chiral spectroscopies with theoretical analysis thus significantly enhances the information that can be obtained from the induced chirality of the Trp aromatic residue.

Prediction of CO2 Adsorption Properties in Zeolites Using Force Fields Derived from Periodic Dispersion-Corrected DFT Calculations

We demonstrate a new approach to develop transferable force fields describing molecular adsorption in zeolites by combining dispersion-corrected density functional theory (DFT) calculations and classical atomistic simulations. This approach is illustrated with the adsorption of CO2 in zeolites. Multiple dispersion-corrected DFT methods were tested for describing CO2 adsorption in sodium-exchanged ferrierite. The DFT-D2 approach was found to give the best agreement with high level quantum chemistry results and experimental data. A classical force field for CO2 adsorption in siliceous zeolites was then developed on the basis of hundreds of DFT-D2 calculations that probed the full range of accessible volume in purely siliceous chabazite (Si-CHA) via random sampling. We independently performed experiments with Si-CHA measuring CO2 isotherms and heats of adsorption by microcalorimetry. Excellent agreement was obtained between adsorption isotherms predicted with our first-principles-derived force field and our experiments. The transferability of this force field was examined using available adsorption isotherms for CO2 in siliceous MFI and DDR zeolites, again with reasonably good agreement between calculated and experimental results. The methods demonstrated by these calculations will be broadly applicable in using molecular simulations to predict properties of adsorbed molecules in zeolites and other nanoporous materials.

Assessment of a variety of dispersion-corrected density functional theory calculations used in molecular crystal structure prediction

For a long time, the prediction of molecular crystal structures from first principles has been one of the most challenging computational problems. Because of the large number of degrees of freedom, methods with low computational effort have to be used. The price for this efficiency is, however, a loss of accuracy. In recent years, important progress has been made in the development of dispersion corrections [1-3], which raise the accuracy of density functional theory (DFT) calculations to a much higher level. Based on these developments, the software package GRACE [4] was the first program ever to correctly predict all four crystal structures at the 4th crystal structure prediction blind test, organized by G. M. Day and the Cambridge Crystallographic Data Centre in 2007 [5]. GRACE uses dispersion-corrected density functional theory calculations (DFT-D) to generate reference data to which a tailor-made force field (TMFF) is fitted for each respective molecule [6]. Crystal structures are generated with a Monte-Carlo parallel-tempering algorithm that uses the TMFF for the evaluation of lattice energies. Only the most stable crystal structures according to the TMFF are then re-optimized and re-ranked using DFT-D. The DFT calculations are performed using an interface to the two common ab-inito programs VASP [7] and QuantumESPRESSO [8]. In the most recent, 5th blind test, organized in 2010, the excellent agreement between experimental and predicted structures for small, neutral molecules was confirmed. However, it turned out that the crystal structure prediction of molecular salts and hydrates is still a challenging task. The inability of DFT without exact exchange to describe anions properly, as recently published by Jensen [9], suggests that the inclusion of the Hartree-Fock exchange should improve the accuracy for molecular salts and hydrates. Therefore, we will present an assessment of a variety of current density functionals, in which the dispersion-correction parameters were fitted with respect to a minimization of the deviation between experimental and computed crystal structures.

π-Hydrogen Bonding Wins over Conventional Hydrogen Bonding Interaction: A Jet-Cooled Study of Indole···Furan Heterodimer

In this study, we have explored the conformational landscape of the indole···furan dimer in a supersonic jet by using resonant two-photon ionization (R2PI) and IR-UV double-resonance spectroscopic techniques combined with dispersion-corrected density functional theory (DFT) calculations. Only one conformer of the dimer has been observed in the experiment. DFT/B97-D level calculation shows that N-H···π hydrogen-bonded conformer (T') is energetically more stable than the N-H···O hydrogen-bonded conformer (HB). Natural bond orbital (NBO) calculation also shows that the hydrogen-bonding interaction in the HB conformer is very weak. Finally, the structure of the observed dimer has been determined to be tilted T-shaped N-H···π hydrogen-bonded (T') from very excellent agreement between experimental and theoretical N-H stretch frequency. The most significant finding of this study is the first-time observation of a N-H···π bound conformer of a dimer, which wins over a conventional hydrogen-bonded conformer of the dimer.

Adsorption of CO2 on a PdO(101) Thin Film

We investigated the adsorption of CO2 on PdO(101) using temperature-programmed desorption (TPD) and dispersion-corrected density functional theory calculations (DFT-D3). We find that CO2 desorbs from PdO(101) in two main TPD peaks (e1 and e2) centered at ∼176 and 120 K and estimate that the average binding energies in the e1 and e2 states are 54 ± 8 and 37 ± 5 kJ/mol, respectively. The CO2 layer saturates on PdO(101) at a total coverage of ∼0.47 monolayer (ML), with the CO2 molecules distributed nearly evenly between the two adsorbed states. TPD experiments of CO2 adsorption onto preadsorbed layers of pure 18O2 and H2O provide evidence that the e1 and e2 states correspond to CO2 molecules adsorbed on the coordinatively unsaturated (cus) vs saturated (4f) Pd sites of the PdO(101) surface, respectively. DFT-D3 calculations predict CO2 saturation coverages and binding energies on PdO(101) that agree well with our experimental estimates. The calculations suggest that CO2 prefers to adsorb initially on a cus-P...

Van der Waals forces in the perfluorinated metal–organic framework zinc 1,2-bis(4-pyridyl)ethane tetrafluoroterephthalate

Traditional density functional theory (DFT) and dispersion-corrected DFT calculations are performed to investigate the metal-organic framework zinc 1,2-bis(4-pyridyl)ethane tetrafluoroterephthalate (Znbpetpa). Without dispersion correction, straightening of the zigzag C-O-Zn chain connecting the secondary building units across the diagonal of the unit cell is observed, accompanied by a large anisotropic expansion of the structure along one cell parameter. The results show that van der Waals dispersion forces and specifically Zn-C equatorial interactions and the resulting effects on the zigzag chain play an important role in maintaining key structural features which match with experimental observations. It is suggested that the pore volume of the framework could be controlled by substituting the Zn metal centre with another transition element of different polarizability, while maintaining functional linkers.

Pathways for C–H bond cleavage of propane σ-complexes on PdO(101)

We used dispersion-corrected density functional theory (DFT-D3) calculations to investigate the initial C-H bond cleavage of propane σ-complexes adsorbed on the PdO(101) surface. The calculations predict that propane molecules adsorbed in η(1) configurations can undergo facile C-H bond cleavage on PdO(101), where the energy barrier for C-H bond activation is lower than that for desorption for each molecular complex. The preferred pathway for propane dissociation on PdO(101) corresponds to cleavage of a primary C-H bond of a so-called staggered p-2η(1) complex which initially coordinates with the surface by forming two H-Pd dative bonds, one at each CH(3) group. Among all of the adsorbed propane complexes, the staggered p-2η(1) complex has the highest binding energy and must overcome the lowest energy barrier for C-H bond scission. Analysis of the atomic charges reveals that propane C-H bond cleavage occurs heterolytically on PdO(101), and suggests that primary C-H bond activation is favored because a more stabilizing charge distribution develops within the 1-propyl transition state structures. Lastly, we conducted kinetic simulations using microkinetic models derived from the DFT-D3 structures, and find that the models reproduce the apparent activation energy for propane dissociation on PdO(101) to within 14% of that determined experimentally. We show that the entropic contributions of the adsorbed transition structures greatly exceed those predicted by the harmonic oscillator model, and that quantitative agreement with the apparent dissociation pre-factor may be obtained by approximating two of the frustrated adsorbate motions as free motions while treating the remaining modes as harmonic vibrations.

An experimental screen for quinoline/fumaric acid salts and co-crystals

An experimental screen has been carried out for salts and co-crystals of quinoline (C9H7N) and fumaric acid (C4H4O4), including solution-based co-crystallisation from a variety of solvents, solvent-assisted and solvent-free co-grinding, and direct co-crystallisation of the starting materials. Characterised products include the previously published 1 : 1 salt, C9H8N+·C4H3O4−, and a new 2 : 1 quinoline/fumaric acid co-crystal, (C9H7N)2·C4H4O4. Attempts to influence the crystallisation outcome by addition of 6-methylquinoline yielded a second co-crystal, also with an inherent 2 : 1 quinoline/fumaric acid ratio, as a solid solution containing ca. 75% 6-methylquinoline and 25% quinoline. The corresponding co-crystal with pure 6-methylquinoline, (C10H9N)2·C4H4O4, was prepared, but the analogous structure with pure quinoline could not be obtained. Energy minimisation using dispersion-corrected density functional theory (DFT-D) calculations suggests that the hypothetical polymorph of the 2 : 1 quinoline/fumaric acid co-crystal derived from the structure of the 2 : 1 6-methylquinoline/fumaric acid co-crystal is ca. 8 kJ mol−1 less stable than the structure that is actually observed.

Synthesis and Molecular Structure of Gold Triarylcorroles

A number of third-row transition-metal corroles have remained elusive as synthetic targets until now, notably osmium, platinum, and gold corroles. Against this backdrop, we present a simple and general synthesis of β-unsubstituted gold(III) triarylcorroles and the first X-ray crystal structure of such a complex. Comparison with analogous copper and silver corrole structures, supplemented by extensive scalar-relativistic, dispersion-corrected density functional theory calculations, suggests that "inherent saddling" may occur for of all coinage metal corroles. The degree of saddling, however, varies considerably among the three metals, decreasing conspicuously along the series Cu > Ag > Au. The structural differences reflect significant differences in metal-corrole bonding, which are also reflected in the electrochemistry and electronic absorption spectra of the complexes. From Cu to Au, the electronic structure changes from noninnocent metal(II)-corrole(•2-) to relatively innocent metal(III)-corrole(3-).

System‐Dependent Dispersion Coefficients for the DFT‐D3 Treatment of Adsorption Processes on Ionic Surfaces

Dispersion-corrected density functional theory calculations (DFT-D3) were performed for the adsorption of CO on MgO and C(2) H(2) on NaCl surfaces. An extension of our non-empirical scheme for the computation of atom-in-molecules dispersion coefficients is proposed. It is based on electrostatically embedded M(4)X(4) (M=Na, Mg) clusters that are used in TDDFT calculations of dynamic dipole polarizabilities. We find that the C(MM)(6) dispersion coefficients for bulk NaCl and MgO are reduced by factors of about 100 and 35 for Na and Mg, respectively, compared to the values of the free atoms. These are used in periodic DFT calculations with the revPBE semi-local density functional. As demonstrated by calculations of adsorption potential energy curves, the new C(6) coefficients lead to much more accurate energies (E(ads)) and molecule-surface distances than with previous DFT-D schemes. For NaCl/C(2) H(2) we obtained at the revPBE-D3(BJ) level a value of E(ads) =-7.4 kcal mol(-1) in good agreement with experimental data (-5.7 to -7.1 kcal mol(-1)). Dispersion-uncorrected DFT yields an unbound surface state. For the MgO/CO system, the computed revPBE-D3(BJ) value of E(ads) =-4.1 kcal mol(-1) is also in reasonable agreement with experimental results (-3.0 kcal mol(-1)) when thermal corrections are taken into account. Our new dispersion correction also improves computed lattice constants of the bulk systems significantly compared to plain DFT or previous DFT-D results. The extended DFT-D3 scheme also provides accurate non-covalent interactions for ionic systems without empirical adjustments and is suggested as a general tool in surface science.

Dispersion-corrected density functional theory comparison of hydrogen adsorption on boron-nitride and carbon nanotubes

One of the main challenges for the future hydrogen economy is finding a safe and efficient way to store hydrogen. Materials with large surface areas, like carbon nanotubes and their analogues boron-nitride nanotubes, are being studied as potential candidates for this purpose. We perform density functional theory (DFT) and dispersion-corrected DFT (DFT-D) calculations of the adsorption of molecular hydrogen on graphene and boron-nitride sheets and compare the results against M\o{}ller-Plesset perturbation theory (MP2 and MP2.5). Our results indicate that DFT underestimates the binding energies, while DFT-D gives a very good agreement with the higher-order theory. Within DFT-D, we show that the binding energy of molecular hydrogen to the outer walls of carbon nanotubes is more than 40% larger than that of boron-nitride nanotubes.

Commensurate-incommensurate phase transition in bilayer graphene

A commensurate-incommensurate phase transition in bilayer graphene is investigated in the framework of the Frenkel-Kontorova model extended to the case of two interacting chains of particles. Analytic expressions are derived to estimate the critical unit elongation of one of the graphene layers at which the transition to the incommensurate phase takes place, the length and formation energy of incommensurability defects (IDs) and the threshold force required to start relative motion of the layers on the basis of dispersion-corrected density functional theory calculations of the interlayer interaction energy as a function of the relative position of the layers. These estimates are confirmed by atomistic calculations using the DFT-D based classical potential. The possibility to measure the barriers for relative motion of graphene layers by the study of formation of IDs in bilayer graphene is discussed.