Benzene, aromatic rings, van der Waals molecules, and crystals of aromatic molecules in molecular mechanics (MM3)

Physical binding energies using the electron localization function in 4-hydroxyphenylboronic acid co-crystals with aza donors

Binding energies are traditionally simulated using cluster models by computation of each synthon for each individual co-crystal former. However, our investigation of the binding strengths using the electron localization function (ELF) reveals that these can be determined directly from the crystal supercell computations. We propose a new modeling protocol for the computation of physical binding energies directly from bulk simulations using ELF analysis. In this work, we establish a correlation between ELF values and binding energies calculated for co-crystals of 4-hydroxyphenylboronic acid (4HPBA) with four different aza donors using density functional theory with varying descriptions of dispersion. Boronic acids are gaining significant interest in the field of crystal engineering, but theoretical studies on their use in materials are still very limited. Here, we present a systematic investigation of the non-covalent interactions in experimentally realized co-crystals. Prior diffraction studies on these complexes have shown the competitive nature between the boronic acid functional group and the para-substituted phenolic group forming heteromeric interactions with aza donors. We determine the stability of the co-crystals by simulating their lattice energies, and the different dispersion descriptions show similar trends in lattice energies and lattice parameters. Our study bolsters the experimental observation of the boronic acid group as a competitive co-crystal former in addition to the well-studied phenolic group. Further research on correlating ELF values for physical binding could potentially transform this approach to a viable alternative for the computation of binding energies.

Competitive adsorption characteristics of gasoline evaporated VOCs in microporous activated carbon by molecular simulation

The activated carbon in the vehicle's carbon canister needs to adsorb a variety of VOCs (Volatile Organic Compounds) emitted by gasoline evaporation, while the difference in gas adsorption capacity can lead to adsorption competition phenomena. In this study, three typical VOCs (toluene, cyclohexane, and ethanol) were selected to study the adsorption competition characteristics between multi-component gases at different pressures by molecular simulation method. In addition, the effect of temperature on adsorption competition was also investigated. The results show that the selectivity of activated carbon to toluene is negatively correlated with the adsorption pressure, but the opposite is true for ethanol, and the change of cyclohexane is not significant. The competitive order of the three VOCs is toluene > cyclohexane > ethanol at low pressure, which becomes ethanol > toluene > cyclohexane at high pressure. With increasing pressure, the interaction energy decreases from 12.87 kcal/mol to 11.87 kcal/mol, where the electrostatic interaction energy increases from 1.97 kcal/mol to 2.54 kcal/mol. In microporous activated carbon, the competition is mainly manifested in that ethanol preempts the low-energy adsorption sites of toluene in the pore size of 10 Å to 18 Å, while gas molecules near the surface of activated carbon or in smaller pore sizes are stably adsorbed without competition. Despite the fact that high temperature decreases the total adsorption capacity, activated carbon selectivity for toluene increases instead, while the competitiveness of polar ethanol decreases significantly.

Uniaxial strain tuning of organic molecule single photon sources

Organic fluorophores are excellent single photon sources, combining high brightness, lifetime-limited linewidths and useful emission wavelengths. A key factor in their performance as photon emitters is their dynamic frequency tunability, which can be used to render the emission from multiple molecules indistinguishable. In this work we demonstrate dynamic tuning of dibenzoterrylene molecules embedded in anthracene crystals through the application of uniaxial strain fields. By bending a piezoelectric strip in two opposite directions in linear steps, we impose an escalating compressive or tensile strain on the molecular crystals, resulting in two opposite dynamic detunings of the dopant dibenzoterrylene emission wavelength. To validate that the tuning mechanism is strain, we performed a similar measurement using an identical strip that was depolarised by annealing in which the tuning was absent. Finally, we simulated the effect of strain on the dopant dibenzoterrylene emission wavelength by combining molecular dynamics and density functional theory techniques to determine the strain tuning rate which matched well with that found experimentally.

The unique features of non-competitive vs. competitive sorption: Tests against single volatile aromatic hydrocarbons and their quaternary mixtures

The adsorption characteristics of four aromatic hydrocarbons (i.e., benzene, toluene, xylene, and styrene) onto ground-activated carbon were investigated both independently and as a mixture of the four at <10 Pa partial pressures (e.g., 0-100 ppm concentration range). The maximum sorption capacities for benzene, toluene, styrene, and xylene were measured both as a sole component and as a mixture (at 10 Pa). In the former, the values were approximately 123, 184, 272, and 238 mg g^-1, respectively. In contrast, the latter values were 5, 52, 222, and 248 mg g^-1 respectively, showing dramatic reduction in lighter compounds (below C7) relative to heavier ones (above C8). The mechanistic detail of sorption has been explained in terms of Henry's law and Langmuir, Freundlich, Dubinin-Radushkevich, and Elovich isotherm models. The linearized Langmuir adsorption isotherm analysis showed three sorption pressure regions: low (<1 Pa, retrograde), intermediate (1-4 Pa), and high (4-10 Pa). As such, the outcome of this study offers a unique opportunity to acquire detailed information on the dramatic and dynamic effects of the sorptive interaction between competing sorbates, along with a common sorption process between sorbent and sorbate at 298 K.

Quantum mechanical polarizable force field (QMPFF3): refinement and validation of the dispersion interaction for aromatic carbon

The authors have recently introduced a general, polarizable force field QMPFF fitted solely to high-level quantum mechanical data for simulations of biomolecular systems. Here the authors demonstrate using an advanced version QMPFF3 how the problem of insufficient accuracy of the MP2-based training set for the aromatic carbon atom type can be effectively solved by a simple model correction using state-of-the-art CCSD(T) data. The approach demonstrates excellent transferability, which is confirmed for three phases of matter by accurate calculations of the second virial coefficient for benzene vapor and various properties of liquid benzene and polyaromatic hydrocarbon crystals.

Ab initiocalculations of structures and interaction energies of toluene dimers including CCSD(T) level electron correlation correction

The intermolecular interaction energy of the toluene dimer has been calculated with the ARS-F model (a model chemistry for the evaluation of intermolecular interaction energy between ARomatic Systems using Feller's method), which was formerly called as the AIMI model III. The CCSD(T) (coupled cluster calculations with single and double substitutions with noniterative triple excitations) interaction energy at the basis set limit has been estimated from the second-order Moller-Plesset perturbation interaction energy at the basis set limit obtained by Feller's method and the CCSD(T) correction term obtained using a medium-size basis set. The cross (C(2)) dimer has the largest (most negative) interaction energy (-4.08 kcal/mol). The antiparallel (C(2h)) and parallel (C(S)) dimers (-3.77 and -3.41 kcal/mol, respectively) are slightly less stable. The dispersion interaction is found to be the major source of attraction in the toluene dimer. The dispersion interaction mainly determines the relative stability of the stacked three dimers. The electrostatic interaction of the stacked three dimers is repulsive. Although the T-shaped and slipped-parallel benzene dimers are nearly isoenergetic, the stacked toluene dimers are substantially more stable than the T-shaped toluene dimer (-2.62 kcal/mol). The large dispersion interaction in the stacked toluene dimers is the cause of their enhanced stability.

Updating the asymmetric osmium-catalyzed dihydroxylation (AD) mnemonic: Q2MM modeling and new kinetic measurements

The mnemonic device for predicting stereoselectivities in the Sharp-less asymmetric dihydroxylation (AD) reaction has been updated based on extensive computational studies. Kinetic measurements from competition reactions validate the new proposal. The interactions responsible for the high stereoselectivity in the title reaction are analyzed in detail and mapped onto the mnemonic device.

Origin of attraction and directionality of the pi/pi interaction: model chemistry calculations of benzene dimer interaction

A model chemistry for the evaluation of intermolecular interaction between aromatic molecules (AIMI Model) has been developed. The CCSD(T) interaction energy at the basis set limit has been estimated from the MP2 interaction energy near the basis set limit and the CCSD(T) correction term obtained by using a medium size basis set. The calculated interaction energies of the parallel, T-shaped,and slipped-parallel benzene dimers are -1.48, -2.46, and -2.48 kcal/mol, respectively. The substantial attractive interaction in benzene dimer, even where the molecules are well separated, shows that the major source of attraction is not short-range interactions such as charge-transfer but long-range interactions such as electrostatic and dispersion. The inclusion of electron correlation increases attraction significantly. The dispersion interaction is found to be the major source of attraction in the benzene dimer. The orientation dependence of the dimer interaction is mainly controlled by long-range interactions. Although electrostatic interaction is considerably weaker than dispersion interaction, it is highly orientation dependent. Dispersion and electrostatic interactions are both important for the directionality of the benzene dimer interaction.

Structural investigation of helices II, III, and IV of B. megaterium 5S ribosomal RNA by molecular dynamics calculations

The structures of the helices II-III region and the helix IV region of B. megaterium 5S rRNA have been examined by means of energy minimization and molecular dynamics calculations. Calculated distances between neighboring hydrogen-bonded imino protons in helices II, III, and IV were between 3.5 and 4.5 A. The overall axis for the helices II-III region is warped rather than straight. Formation of additional Watson-Crick base pairs in loop B and loop C was not evident from the atomic positions calculated by molecular dynamics. Bases in loop C are well stacked, showing no significant change during dynamics. Bulge migration in helix III does not seem to be possible; the helices II-III region prefers one conformation. Helix II is more stable than helix III. Five base pairs in helix IV were sufficiently stable to establish that helix IV is terminated by a hairpin loop of three nucleotides. U87 protrudes from loop D. Structures of the helices II-III segment and the helix IV segment of B. megaterium 5S rRNA obtained by molecular dynamics were generally consistent with the solution structure inferred from high-field proton nmr spectroscopy.

Pi-pi interactions: the geometry and energetics of phenylalanine-phenylalanine interactions in proteins

The geometries of aromatic-aromatic interactions between phenylalanine residues in proteins are analysed in detail and correlated with energy calculations. A new definition of the interplanar angle is important for distinguishing favourable edge-to-face and unfavourable face-to-face orientations. The experimental observations are scattered over a wide range of conformational space, with no strongly preferred single orientation. However, Phe-Phe interactions occur almost exclusively in electrostatically attractive geometries: electrostatically unfavourable regions are only sparsely populated. Electrostatics dominate the geometry of interaction, while van der Waals' interactions are less significant, probably due to the hydrophobic environment of the protein core. The observations on proteins support the Hunter-Sanders rules for pi-pi interactions. In particular, offset stacked geometries, which theory predicts to be favourable, are observed experimentally. For monocyclic aromatics, use of a C-H dipole, the approach used in molecular mechanics calculations, accounts well for these aromatic-aromatic interactions. Comparison with the results obtained from the small molecules database indicates that the protein and small molecule crystal environments are very different.

Molecular modelling of poly(aryl ether ketones). I. Aryl..aryl interactions in crystal structures

Non-bonded potentials for the aryl..aryl interaction have been derived using crystal structure data of a number of small aromatic molecules. The potentials, based on atom-centered interactions, give an accurate reproduction of the benzene crystal geometry and sublimation energy when used in conjunction with coulombic energies evaluated using point atomic charges. An examination of the charge distribution on benzene suggested values of 0.13e (H) and -0.13e (C) to be suitable. The transferability of the potentials has been shown by prediction of crystal geometries and sublimation energies of other hydrocarbon molecules and, with additional interactions for the oxygen atom included, preliminary polymer crystal structure calculations have been carried out. These demonstrate the validity of the derived parameters by successfully predicting crystallographic unit cell dimensions and ring conformations in the poly(phenylene oxide) and poly(aryl ether ketone) crystals.