Ota Bludský

Investigation of the benzene-dimer potential energy surface: DFT/CCSD(T) correction scheme.

A novel method, designated as the density functional theory/coupled-cluster with single and double and perturbative triple excitation [DFT/CCSD(T)] correction scheme, was developed for precise calculations of weakly interacting sp(2) hydrocarbon molecules and applied to the benzene dimer. The DFT/CCSD(T) interaction energies are in excellent agreement with the estimated CCSD(T)/complete basis set interaction energies. The tilted T-shaped structure having C(s) symmetry was determined to be a global minimum on the benzene-dimer potential energy surface (PES), approximately 0.1 kcal/mol more stable than the parallel-displaced structure. A fully optimized set of ten stationary points on the benzene-dimer PES is proposed for the evaluation of the reliability of methods for the description of weakly interacting systems.

Amino groups in nucleic acid bases, aniline, aminopyridines, and aminotriazine are nonplanar: Results of correlated ab initio quantum chemical calculations and anharmonic analysis of the aniline inversion motion

The amino group nonplanarity in nucleic acid bases, aniline, aminopyridines, and aminotriazine was investigated by ab initio methods with and without inclusion of correlation energy utilizing medium and extended basis sets. For all the systems studied, the amino group was found to be nonplanar and the coupled cluster method [CCSD(T)] ‘‘nonplanarities’’ and inversion barriers slightly higher than their second‐order many‐body perturbation‐theory (MP2) counterparts. To assess the reliability of the calculations, inversion splittings for aniline and aniline‐ND2 were evaluated by solving a two‐dimensional vibrational Schrodinger equation for the large‐amplitude inversion and torsion motions, while respecting the role of small‐amplitude C–N stretching and H–N–H bending motions. Because a large number of points is required for the description of the aniline potential energy surface, the Hartree–Fock (HF) method with 6‐31G* basis set was utilized. The vibrational calculations were performed within the framework o...

DFT/CC investigation of physical adsorption on a graphite (0001) surface

The physical adsorption of molecules (C(2)H(2), C(2)H(4), C(2)H(6), C(6)H(6), CH(4), H(2), H(2)O, N(2), NH(3), CO, CO(2), Ar) on a graphite substrate has been investigated at the DFT/CC level of theory. The calculated DFT/CC interaction energies were compared with the available experimental data at the zero coverage limit. The differences between the DFT/CC results and experiment are within a few tenths of kJ mol(-1) for the most accurate experimental estimates (Ar, H(2), N(2), CH(4)) and within 1-2 kJ mol(-1) for the other systems (C(2)H(2), C(2)H(4), C(2)H(6), C(6)H(6), CO, CO(2)). For water-graphite and ammonia-graphite complexes, DFT/CC predicts interaction energies of 13 kJ mol(-1) in good accord with the DF-DFT-SAPT and DFT-D calculations. The relevance of the results obtained with the coronene model for the description of the physisorption on graphite surface was also studied.

The vibrational dynamics of carbon monoxide in a confined space—CO in zeolites

Based on theoretical calculations, and a survey of infrared spectra of CO adsorbed on different cation exchanged zeolites, a model is proposed to explain the influence of the zeolite framework on the vibrational behaviour of CO confined into small void spaces (zeolite channels and cavities). The concepts developed should help to understand a number of details relevant to both, precise interpretation of IR spectra and a better understanding of the vibrational dynamics of small molecules in a confined space.

Combined DFT/CC and IR spectroscopic studies on carbon dioxide adsorption on the zeolite H-FER

Adsorption of carbon dioxide on H-FER zeolite (Si:Al = 8:1) was investigated by means of a combined methodology involving variable-temperature infrared spectroscopy and DFT/CC calculations on periodic zeolite models. The experimentally found value of adsorption enthalpy was ΔH0 = −30 kJ mol−1. According to calculations, adsorption complexes on isolated Si(OH)Al Bronsted acid sites (single sites) involve an adsorption enthalpy in the range of −33 to −36 kJ mol−1, about half of which is due to weak intermolecular interactions between CO2 and the zeolite framework. Calculations show clearly the significant role played by weak intermolecular interactions; adsorption enthalpies calculated with standard GGA type exchange-correlation functionals are about 13 kJ mol−1 underestimated with respect to experimental results. Good agreement was also found between calculated and experimentally observed stretching frequencies for these complexes. Calculations revealed that CO2 adsorption complexes involving two neighbouring Bronsted acid sites (dual sites) can be formed, provided that the dual site has the required geometry. However, no clear evidence of CO2 adsorption complexes on dual sites was experimentally found.

Accurate description of argon and water adsorption on surfaces of graphene-based carbon allotropes.

Accurate interaction energies of nonpolar (argon) and polar (water) adsorbates with graphene-based carbon allotropes were calculated by means of a combined density functional theory (DFT)-ab initio computational scheme. The calculated interaction energy of argon with graphite (-9.7 kJ mol(-1)) is in excellent agreement with the available experimental data. The calculated interaction energy of water with graphene and graphite is -12.8 and -14.6 kJ mol(-1), respectively. The accuracy of combined DFT-ab initio methods is discussed in detail based on a comparison with the highly precise interaction energies of argon and water with coronene obtained at the coupled-cluster CCSD(T) level extrapolated to the complete basis set (CBS) limit. A new strategy for a reliable estimate of the CBS limit is proposed for systems where numerical instabilities occur owing to basis-set near-linear dependence. The most accurate estimate of the argon and water interaction with coronene (-8.1 and -14.0 kJ mol(-1), respectively) is compared with the results of other methods used for the accurate description of weak intermolecular interactions.

Anharmonic treatment of the lowest-energy conformers of glycine: A theoretical study

The structure and energetics of the four lowest-energy conformers of glycine were determined at the MP2/aug-cc-pVDZ level of theory. The optimized structural parameters for these conformers agree with previous theoretical results obtained by highly correlated ab initio methods and with available experimental data. The only structure with planar heavy atom arrangement is conformer I (global minimum), the other conformers have nonplanar heavy atom arrangements. In accordance with temperature dependence studies of the vibrational spectra in various rare gas environments, conformers III and IV have small interconversion barriers to conformer I (940 and 740 cm−1). Our calculations have shown that full-dimensional anharmonic treatment is required for an accurate description of the vibrational modes in various glycine conformers. The most pronounced effect has been observed for conformer II with the intramolecular O–H⋅⋅⋅N bond. The theoretical results obtained at the MP2/aug-cc-pVDZ level reproduce quantitativel...

Reliable theoretical treatment of molecular clusters: Counterpoise-corrected potential energy surface and anharmonic vibrational frequencies of the water dimer

Structure, properties and energetics of the water dimer were determined by counterpoise (CP)-corrected gradient optimization which apriori eliminates the basis set superposition error (BSSE). Calculations were carried out at the MP2 level with various basis sets up to the aug-cc-pVQZ one. Besides harmonic vibrational frequencies twelve-dimensional anharmonic frequencies were also determined using the second-order perturbation treatment. Harmonic and anharmonic frequencies were based on CP-corrected Hessians. The equilibrium geometry of the dimer differs from that determined by a standard optimization and the difference becomes small only for the largest basis set (aug-cc-pVQZ). The best theoretical estimate of the intermolecular oxygen–oxygen distance (2.92 A) is shorter than the experimental result of 2.95 A. An estimate of the complete basis set limit of the stabilization energy was obtained by extrapolating the stabilization energies as a function of the reciprocal size of the basis set; this value (21.05 kJ mol-1) is slightly smaller than other literature estimates. Adding the changes due to zero-point energy and temperature-dependent enthalpy terms (determined using anharmonic frequencies obtained from the CP-corrected Hessian) we obtain an estimate to the theoretical stabilization enthalpy at 375 K (12.76 kJ mol-1) which is by 0.8–1.3 kJ mol-1 smaller than the literature results. Our theoretical value supports the very low limit of the experimental value. Red shift of the O–H stretching frequency accompanying formation of the dimer was determined at various theoretical levels and best agreement with the experimental value was found for anharmonic frequencies calculated with CP-corrected Hessians.

Calculations of the site specific stretching frequencies of CO adsorbed on Li+/ZSM-5

Interaction of the CO molecule with Li+ within ZSM-5 was investigated by means of the combined quantum mechanics/interaction potential function method. Both, C-on and O-on species were considered. The scaling method based on the linear correlation between CO bond length and stretching frequency has been applied to calculate CO frequencies in CO(OC)–Li+/ZSM-5 adsorption complexes. Three types of C-on adsorption complexes with different r(CO) bond lengths, ν(CO) frequencies, and CO binding energies were identified. The calculated IR spectra of CO adsorbed on the Li+/ZSM-5 system show three distinctive bands at about 2194 cm−1, 2187 cm−1 and 2183 cm−1 for C-on complexes and at about 2116 cm−1, 2114 cm−1 and 2104 cm−1 for O-on complexes, in excellent agreement with experimental data. Calculated adsorption energies and CO stretching frequencies were used for the simulation of the IR spectra at various CO coverages.

Investigation of the Benzene–Naphthalene and Naphthalene–Naphthalene Potential Energy Surfaces: DFT/CCSD(T) Correction Scheme

The potential energy surfaces of the naphthalene dimer and benzene-naphthalene complexes are investigated using the recently developed DFT/CCSD(T) correction scheme [J. Chem. Phys. 2008, 128, 114 102]. One and three minima are located on the PES of the benzene-naphthalene and the naphthalene dimer complexes, respectively, all of which are of the parallel-displaced type. The stabilities of benzene-naphthalene and the naphthalene dimer are -4.2 and -6.2 kcal mol(-1), respectively. Unlike the benzene dimer, where the T-shaped complex is the global minimum, the lowest-energy T-shaped structure is about 0.2 and 1.6 kcal mol(-1) above the global minimum on the benzene-naphthalene and the naphthalene dimer potential energy surfaces, respectively.