Robert Sedlak

MP2.5 and MP2.X: approaching CCSD(T) quality description of noncovalent interaction at the cost of a single CCSD iteration.

The performance of the second-order Møller-Plesset perturbation theory MP2.5 and MP2.X methods, tested on the S22, S66, X40, and other benchmark datasets is briefly reviewed. It is found that both methods produce highly accurate binding energies for the complexes contained in these data sets. Both methods also provide reliable potential energy curves for the complexes in the S66 set. Among the routinely used wavefunction methods, the only other technique that consistently produces lower errors, both for stabilization energies and geometry scans, is the spin-component-scaled coupled-clusters method covering iterative single- and double-electron excitations, which is, however, substantially more computationally intensive. The structures originated from full geometrical gradient optimizations at the MP2.5 and MP2.X level of theory were confirmed to be the closest to the CCSD(T)/CBS (coupled clusters covering iterative single- and double-electron excitations and perturbative triple-electron excitations performed at the complete basis set limit) geometries among all the tested methods (e.g. MP3, SCS(MI)-MP2, MP2, M06-2X, and DFT-D method evaluated with the TPSS functional). The MP2.5 geometries for the tested complexes deviate from the references almost negligibly. Inclusion of the scaled third-order correlation energy results in a substantial improvement of the ability to accurately describe noncovalent interactions. The results shown here serve to support the notion that MP2.5 and MP2.X are reasonable alternative methods for benchmark calculations in cases where system size or (lack of) computational resources preclude the use of CCSD(T)/CBS computations. MP2.X allows for the use of smaller basis sets (i.e. 6-31G*) with results that are nearly identical to those of MP2.5 with larger basis sets, which dramatically decreases computation times and makes calculations on much larger systems possible.

On the Nature of the Stabilization of Benzene⋅⋅⋅Dihalogen and Benzene⋅⋅⋅Dinitrogen Complexes: CCSD(T)/CBS and DFT‐SAPT Calculations

The structure and stabilization energies of benzene (and methylated benzenes)···X(2) (X=F, Cl, Br, N) complexes were investigated by performing CCSD(T)/complete basis set limit and density functional theory/symmetry-adapted perturbation theory (DFT-SAPT) calculations. The global minimum of the benzene···dihalogen complexes corresponds to the T-shaped structure, whereas that of benzene···dinitrogen corresponds to the sandwich one. The different binding motifs of these complexes arise from the different quadrupole moments of dihalogens and dinitrogen. The different sign of the quadrupole moments of these diatomics is explained based on the electrostatic potential (ESP). Whereas all dihalogens, including difluorine, possess a positive σ hole, such a positive area of the ESP is completely missing in the case of dinitrogen. Moreover, benzene···X(2) (X=Br, Cl) complexes are stronger than benzene···X(2) (X=F, N) complexes. When analyzing DFT-SAPT electrostatic, dispersion, induction, and δ(Hartree-Fock) energies, we recapitulate that the former complexes are stabilized mainly by dispersion energy, followed by electrostatic energy, whereas the latter complexes are stabilized mostly by the dispersion interaction. The charge-transfer energy of benzene···dibromine complexes, and surprisingly, also of methylated benzenes···dibromine complexes is only moderate, and thus, not responsible for their stabilization. Benzene···dichlorine and benzene···dibromine complexes can thus be characterized merely as complexes with a halogen bond rather than as charge-transfer complexes.

Density functional theory-symmetry adapted perturbation treatment energy decomposition of nucleic acid base pairs taken from DNA crystal geometry

First- and second-order perturbation energies for H-bonded and stacked structures of nucleic acid base pairs in DNA crystal geometries were determined using the density functional theory symmetry adapted perturbation treatment method. Considerably larger stabilization of the former pairs is due to electrostatic and induction energies. Total E(1) energies for both pairs are, however, similar and the same is true for dispersion energy.

Hydrogen-Bonded Complexes of Phenylacetylene with Water, Methanol, Ammonia, and Methylamine. The Origin of Methyl Group-Induced Hydrogen Bond Switching

The infrared spectra in the acetylenic C-H stretching region for the complexes of phenylacetylene with water, methanol, ammonia, and methylamine are indicative of change in the intermolecular structure upon substitution with a methyl group. High-level ab initio calculations at CCSD(T)/aug-cc-pVDZ level indicate that the observed complexes of water and ammonia are energetically the most favored structures, and electrostatics play a dominant role in stabilizing these structures. The ability of the pi electron density of the benzene ring to offer a larger cross-section for the interaction and the increased polarizability of the O-H and N-H groups in methanol and methylamine favor the formation of pi hydrogen-bonded complexes, in which dispersion is the dominant force. Further, the observed phenylacetylene-methylamine complex can be tentatively assigned to a kinetically trapped higher energy structure. The observed methyl group-induced hydrogen bond switching in the phenylacetylene complexes can be attributed to the switching of the dominant interaction from electrostatic to dispersion.

Interactions of Boranes and Carboranes with Aromatic Systems: CCSD(T) Complete Basis Set Calculations and DFT-SAPT Analysis of Energy Components

The noncovalent interactions of heteroboranes with aromatic systems have only recently been acknowledged as a source of stabilization in supramolecular complexes. The physical basis of these interactions has been studied in several model complexes using advanced computational methods. The highly accurate CCSD(T)/complete basis set (CBS) value of the interaction energy for the model diborane···benzene complex in a stacking geometry exhibiting a B(2)H···π hydrogen bond was calculated to be -4.0 kcal·mol(-1). The DFT-SAPT/CBS approach, which is shown to reproduce the CCSD(T)/CBS data reliably asserted that the major stabilizing component was dispersion, followed by electrostatics. Furthermore, the effect of the benzene heteroatom- and exosubstitutions was studied and found to be small. Next, when aromatic molecules were changed to cyclic aliphatic ones, van der Waals complexes stabilized by the dispersion term only were formed. As the last step, interactions of two larger icosahedral borane cages with benzene were explored. The complex of the monoanionic CB(11)H(12)(-) exhibited two minima: the first stacked above the plane of the benzene ring with a C-H···π hydrogen bond and the second planar, in which the carborane cage bound to benzene via five B-H···H-C dihydrogen bonds. The DFT-SAPT/CBS calculations revealed that both of these binding motifs were stabilized by dispersion followed by electrostatic terms, with the planar complex being 1.4 kcal·mol(-1) more stable than the stacked one. The dianionic B(12)H(12)(2-) interacted with benzene only in the planar geometry, similarly as smaller anions do. The large stabilization energy of 11.0 kcal·mol(-1) was composed of dominant attractive dispersion and slightly smaller electrostatic and induction terms. In summary, the borane/carborane···aromatic interaction is varied both in the complex geometries and in the stabilizing energy components. The detailed insight derived from high-level quantum chemical computations can help us understand such important processes as host-guest complexation or carborane···biomolecule interactions.

Infrared-optical double resonance spectroscopic measurements and high level ab initio calculations on a binary complex between phenylacetylene and borane-trimethylamine. Understanding the role of C-H center dot center dot center dot pi interactions

The structure of the binary complex between phenylacetylene and borane-trimethylamine has been elucidated using IR-UV double resonance spectroscopy in combination with high level ab initio calculations at the CCSD(T) level. Borane-trimethylamine interacts primarily through multiple C-H...pi interactions with the pi electron density of the benzene ring in phenylacetylene. CCSD(T) level calculations provide reliable estimates for the interaction energy and free energy, which are in accord with the experimental observations. The DFT-SAPT calculations point out that the dispersion interaction plays a major role in the formation of the experimentally observed complex, along with a sizable contribution from electrostatics.

Polar flattening and the strength of halogen bonding.

The effect of polar flattening on the stability of 32 halogen-bonded complexes was investigated by utilizing CCSD(T)/CBS, DFT, and DFT-SAPT/CBS methods. It is shown that the value of polar flattening increases with the decreasing value of studied isodensity. For the complexes investigated, the polar flattening based on the isodensity of 0.001 au reaches 0.2-0.3 Å and 10-15% in absolute and relative values, respectively. These geometrical changes induce differences in the stabilization energy up to 20%.

Why Is the L-Shaped Structure of X2···X2 (X = F, Cl, Br, I) Complexes More Stable Than Other Structures?

Five different structures (L- and T-shaped (LS, TS), parallel (P), parallel-displaced (PD), and linear (L)) of (X2)2 dimers (X = F, Cl, Br, I, N) have been investigated at B97-D3, M06-2X, DFT-SAPT, and CCSD(T) levels. The Qzz component of the quadrupole moment of all dihalogens, which coincides with the main rotational axis of the symmetry of the molecule, has been shown to be positive, whereas that of dinitrogen is negative. All of these values correlate well with the most positive value of the electrostatic potential, which, for dihalogens, reflects the magnitude of the σ-hole. The LS structure is the most stable structure for all dihalogen dimers. This trend is the most pronounced in the case of iodine and bromine; for dinitrogen dimer, the LS, TS, and PD structures are comparably stable. The dominant stabilization energy for dihalogen dimers is dispersion energy, followed by Coulomb energy. In the case of dinitrogen dimer, it is only the dispersion energy. At short distances, the Coulomb (polarization) energy for dihalogen dimers is more attractive for the LS structure; at larger distances, the TS structure is more favorable, as dispersion and induction energies are systematically more stable for the TS structure. For all dimers and all distances, the long-range electrostatic energy covering the interactions of multipole moments is the most attractive for the TS structure. In the case of dihalogen dimers, the preference of the LS structure over the others, resulting from the concert action of Coulomb, dispersion, and induction energies, is explained by the presence of a σ-hole. In the case of dinitrogen, comparable stability of LS, TS, and PD structures is obtained, as all are dominantly stabilized by dispersion energy.

Differences in the sublimation energy of benzene and hexahalogenbenzenes are caused by dispersion energy.

The crystals of benzene and hexahalogenbenzenes have been studied by means of the density functional theory augmented by an empirical dispersion correction term as well as by the symmetry-adapted perturbation theory. In order to elucidate the nature of noncovalent binding, pairwise interactions have been investigated. It has been demonstrated that the structures of dimers with the highest stabilization energy differ notably along the crystals. It has been shown that the differences in the experimental sublimation energies might be attributed to the dispersion interaction. To our surprise, the dihalogen bonding observed in the hexachloro- and hexabromobenzenes plays a rather minor role in structure stabilization because it is energetically comparable with the other binding motifs. However, the dihalogen bond is by far the most frequent binding motif in hexachloro- and hexabromobenzenes.

H-Bonding Cooperativity Effects in Amyloids: Quantum Mechanical and Molecular Mechanics Study

Abstract The cooperativity effects have been evaluated on three model systems, the formamide, (formylamino)acetamide and amyloidic-layer oligomers with an increasing size of the monomer units (6, 13 and 214 atoms). In the last model, each layer is a dimer of the amino-acid sequence GNNQQNY in one-letter amino-acid abbreviations. The series of oligomers for each model system of up to six monomers have been constructed. For the calculation of the strength of a particular H-bond formed between various sub-oligomers within an oligomer, different wave function, density functional and semi-empirical quantum mechanical methods as well as empirical force fields have been used. Semi-empirical methods are found to be a reasonable compromise between accuracy and computational cost. These methods are able to describe the cooperativity effects with an accuracy almost comparable to that of the ab initio methods. On the contrary, the empirical force-field methods for all of the model systems mostly failed to describe the H-bonding cooperativity effects properly. Based on the results obtained in this work, we recommend using semi-empirical methods. For the systems where this is impossible, we agree to use polarizable force fields with some reservations. Generally, the more flexible the oligomer chain is (the less steric the repulsion or rigid motifs are), the larger the cooperativity that can be achieved. With the increasing number of monomers in a sequence connected via H-bonds, the cooperativity effects appear to be growing, but relatively soon (at 3–4 monomer units) they tend to become saturated.