Accurate computations of the structures and binding energies of the imidazole⋯benzene and pyrrole⋯benzene complexes

Competition Between Halogen Atom and Ring of Halobenzenes as Hydrogen Bond Electron Donor Sites

A halobenzene molecule contains several sites that are capable of acting in an electron-donating capacity within a H-bond. One set of such sites comprise the lone electron pairs of the halogen (X) atoms on the periphery of the ring. The π-electron system above the ring plane can also fulfill this function in many cases. DFT calculations are applied to compare and contrast the propensity of these two site types to engage in such a H-bond within the context of mono, di, tri, tetra, and hexasubstituted halobenzenes. The X atoms chosen for study comprise the full set: F, Cl, Br, and I. It is found that even when the electrostatic potential of the X lone pair is more negative than that above the ring, it is the latter position which is the preferred binding site of HCl in most cases. This preference switches over to the X lone pair only for higher order of substitution, with n=4 or 6. This pattern is explained in large measure by the higher contribution of dispersion when the proton donor is located above the ring.

Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions

The interactions of amino acid side-chains confer diverse energetic contributions and physical properties to a protein's stability and function. Various computational tools estimate the effect of changing a given amino acid on the protein's stability based on parametrized (free) energy functions. When parametrized for the prediction of protein stability in water, such energy functions can lead to suboptimal results for other solvents, such as ionic liquids (IL), aqueous ionic liquids (aIL), or salt solutions. However, to our knowledge, no comprehensive data are available describing the energetic effects of aIL on intramolecular protein interactions. Here, we present the most comprehensive set of potential of mean force (PMF) profiles of pairwise protein-residue interactions to date, covering 50 relevant interactions in water, the two biotechnologically relevant aIL [BMIM/Cl] and [BMIM/TfO], and [Na/Cl]. These results are based on a cumulated simulation time of >1 ms. aIL and salt ions can weaken, but also strengthen, specific residue interactions by more than 3 kcal mol^-1, depending on the residue pair, residue-residue configuration, participating ions, and concentration, necessitating considering such interactions specifically. These changes originate from a complex interplay of competitive or cooperative noncovalent ion-residue interactions, changes in solvent structural dynamics, or unspecific charge screening effects and occur at the contact distance but also at larger, solvent-separated distances. This data provide explanations at the atomistic and energetic levels for complex IL effects on protein stability and should help improve the prediction accuracies of computational tools that estimate protein stability based on (free) energy functions.

Exploring Avenues beyond Revised DSD Functionals: II. Random-Phase Approximation and Scaled MP3 Corrections

For revDSD double hybrids, the Görling–Levy second-order perturbation theory component is an Achilles’ heel when applied to systems with significant near-degeneracy (“static”) correlation. We have explored its replacement by the direct random phase approximation (dRPA), inspired by the SCS-dRPA75 functional of Kállay and co-workers. The addition to the final energy of both a D4 empirical dispersion correction and of a semilocal correlation component lead to significant improvements, with DSD-PBEdRPA₇₅-D4 approaching the performance of revDSD-PBEP86-D4 and the Berkeley ωB97M(2). This form appears to be fairly insensitive to the choice of the semilocal functional but does exhibit stronger basis set sensitivity than the PT2-based double hybrids (due to much larger prefactors for the nonlocal correlation). As an alternative, we explored adding an MP3-like correction term (in a medium-sized basis set) to a range-separated ωDSD-PBEP86-D4 double hybrid and found it to have significantly lower WTMAD2 (weighted mean absolute deviation) for the large and chemically diverse GMTKN55 benchmark suite; the added computational cost can be mitigated through density fitting techniques.

Range-separated double-hybrid density-functional theory with coupled-cluster and random-phase approximations

We construct range-separated double-hybrid (RSDH) schemes which combine coupled-cluster or random-phase approximations (RPAs) with a density functional based on a two-parameter Coulomb-attenuating-method-like decomposition of the electron-electron interaction. We find that the addition of a fraction of short-range electron-electron interaction in the wave-function part of the calculation is globally beneficial for the RSDH scheme involving a variant of the RPA with exchange terms. Even though the latter scheme is globally as accurate as the corresponding scheme employing only second-order Møller-Plesset perturbation theory for atomization energies, reaction barrier heights, and weak intermolecular interactions of small molecules, it is more accurate for the more complicated case of the benzene dimer in the stacked configuration. The present RSDH scheme employing a RPA thus represents a new member in the family of double hybrids with minimal empiricism which could be useful for general chemical applications.

Accuracy of Frequencies Obtained with the Aid of Explicitly Correlated Wave Function Based Methods

We asses the basis set convergence of harmonic frequencies using different explicitly correlated wave function based methods. All commonly available CCSD(T) variants as well as MP2-F12 and MP4(F12*) are considered, and a hierarchy of the different approaches is established. As for reaction and atomization energies, CCSD(F12*)(T*) is a close approximation to CCSD(F12)(T*) and clearly superior to the other tested approximations. The used scaling for the triples correction enhances the accuracy relative to CCSD(F12*)(T) especially for small basis sets and is very attractive since no additional computational costs are added. However, this scaling slightly breaks size consistency, and therefore we additionally study the accuracy of CCSD(F12*)(T*) and CCSD(F12*)(T) in the context of calculating anharmonic frequencies to check if this causes problems in the generation of the potential energy surface (PES). We find a fast basis set convergence for harmonic and anharmonic frequencies. Already in the cc-pVDZ-F12 basis, the RMSD to the CBS limit is only around 4-5 cm^-1.

Interplay among Electrostatic, Dispersion, and Steric Interactions: Spectroscopy and Quantum Chemical Calculations of π-Hydrogen Bonded Complexes

π-Hydrogen bonding interactions are ubiquitous in both materials and biology. Despite their relatively weak nature, great progress has been made in their investigation by experimental and theoretical methods, but this becomes significantly more complicated when secondary intermolecular interactions are present. In this study, the effect of successive methyl substitution on the supramolecular structure and interaction energy of indole⋅⋅⋅methylated benzene (ind⋅⋅⋅n-mb, n=1-6) complexes is probed through a combination of supersonic jet experiments and benchmark-quality quantum chemical calculations. It is demonstrated that additional secondary interactions introduce a subtle interplay among electrostatic and dispersion forces, as well as steric repulsion, which fine-tunes the overall structural motif. Resonant two-photon ionization and IR-UV double-resonance spectroscopy techniques are used to probe jet-cooled ind⋅⋅⋅n-mb (n=2, 3, 6) complexes, with redshifting of the N-H IR stretching frequency showing that increasing the degree of methyl substitution increases the strength of the primary N-H⋅⋅⋅π interaction. Ab initio harmonic frequency and binding energy calculations confirm this trend for all six complexes. Electronic spectra of the three dimers are broad and structureless, with quantum chemical calculations revealing that this is likely to be due to multiple tilted conformations of each dimer possessing similar stabilization energies.

A computationally efficient double hybrid density functional based on the random phase approximation

A new double hybrid density functional (PWRB95) based on GGA orbitals and RPA is presented and its performance is investigated compared to standard DFT and wavefunction methods.

Nanofibrous polymeric beads from aramid fibers for efficient bilirubin removal

Polymer based hemoperfusion has been developed as an effective therapy to remove the extra bilirubin from patients.

First UHF Implementation of the Incremental Scheme for Open-Shell Systems

The incremental scheme makes it possible to compute CCSD(T) correlation energies to high accuracy for large systems. We present the first extension of this fully automated black-box approach to open-shell systems using an Unrestricted Hartree-Fock (UHF) wave function, extending the efficient domain-specific basis set approach to handle open-shell references. We test our approach on a set of organic and metal organic structures and molecular clusters and demonstrate standard deviations from canonical CCSD(T) values of only 1.35 kJ/mol using a triple ζ basis set. We find that the incremental scheme is significantly more cost-effective than the canonical implementation even for relatively small systems and that the ease of parallelization makes it possible to perform high-level calculations on large systems in a few hours on inexpensive computers. We show that the approximations that make our approach widely applicable are significantly smaller than both the basis set incompleteness error and the intrinsic error of the CCSD(T) method, and we further demonstrate that incremental energies can be reliably used in extrapolation schemes to obtain near complete basis set limit CCSD(T) reaction energies for large systems.

Toluene Valence and Rydberg Excitations as Studied by ab initio Calculations and Vacuum Ultraviolet (VUV) Synchrotron Radiation

The electronic spectroscopy of isolated toluene in the gas phase has been investigated using high-resolution photoabsorption spectroscopy in the 4.0-10.8 eV energy range, with absolute cross-section measurements derived. We present the first set of ab initio calculations (vertical energies and oscillator strengths), which we use in the assignment of valence and Rydberg transitions of the toluene molecule. The spectrum reveals several new features not previously reported in the literature, with particular relevance to 7.989 and 8.958 eV, which are here tentatively assigned to the π*(17a') ← σ(15a') and 1π*(10a″) ← 1π(14a') transitions, respectively. The measured absolute photoabsorption cross sections have been used to calculate the photolysis lifetime of toluene in the upper stratosphere (20-50 km).