CASCI-DFT study of the phenalenyl radical system

We present ab initio complete-active-space configuration interaction (CASCI) density functional theory (DFT) study of the phenalenyl radical systems. Our approach employed in this study is based on the assumption that one-electron per one phenalenyl unit is responsible for magnetic properties of the phenalenyl radical dimeric compounds and that the residual correlation effects can be covered by DFT correlation potential for CASCI[2,2] wavefunction. The effective exchange integrals and lowest-lying excited energies of several phenalenyl dimeric compounds are calculated by CASCI[2,2]-DFT method. The implication of the computational results are discussed in relation with those of spin unrestricted Hartree–Fock (UHF), hybrid DFT, and pure DFT, and the experimental ones.     

QSAR and 3D-QSAR studies of the diacyl-hydrazine derivatives containing furan rings based on the density functional theory

QSAR studies of 27 diacyl-hydrazine derivatives containing furan rings were conducted and compared with the DFT method and AM1-MOPAC method. q ² values of 0.61 and 0.40 validated the predictability and reliability of eq. (5) from the DFT method were higher than those of eq. (6) from the AM1-MOPAC method. The DFT-optimized conformations and ESP-fitting charges of the target compounds were also used for 3D-QSAR analysis, including CoMFA and CoMSIA. The leave-one-out cross-validation correlation coefficient and the good correlation between the predicted and experimental activities of excluded test compounds revealed that CoMFA and CoMSIA models were robust. The QSAR results were consistent with the 3D-QSAR results, indicating that the electrostatic and hydrophobic properties of the target compounds were significant to the biological activity. These models are useful tools for predicting the larvicidal activities of new compounds and designing new specific insect growth regulators.     

Stabilization of non-standard conformations of the annulene rings in cyclobutadiene-framed [<Emphasis Type="Italic">n</Emphasis>]annulenes (<Emphasis Type="Italic">n</Emphasis> = 8, 10, 12, 14) and their beryllium sandwich-like complexes: a quantum chemical study

The structures of a series of polycyclic derivatives of [n]annulenes (n = 8, 10, 12, 14) functionalized with peripheral cyclobutadiene rings were studied using the DFT B3LYP/6-311+G(3df,2p) and M062X/6-311+G(3df,2p) methods. The compounds with n = 8 and 10 have the planar and those with n = 12, 14 saddle-shaped conformations of the central rings. Stabilization of non-standard planar forms of the hydrocarbons with central 12- and 14-membered conjugated rings may be achieved through π-complexation of C=C bonds of the cyclobutadiene fragments with beryllium atoms to afford the sandwich-like complexes with circular arrangement of beryllium centers around the perimeter of a ligand.     

Biradicaloid character of phenalenyl-based aromatic compounds with a small HOMO–LUMO gap

Biradicaloid character of three Kekulé aromatic compounds containing two phenalenyl moieties is discussed on the basis of the theoretical and experimental results. DFT calculation of the compounds reveals a small HOMO–LUMO gap with a large spatial overlap between them, leading to a singlet biradical character in a ground state and an excited triplet biradical state with a small ΔE_S–T. Singlet biradical character for 1 (see Fig. 1) is indicated by the X-ray crystallographic analysis, which shows dimeric pairs with substantially short non-bonding contacts of ∼3.1 Å. The ESR measurements for 1 and 3 give typical spectra for triplet species and the temperature dependence of the half-field signal indicates the thermal excitation to the triplet states.     

Quantum chemical exploration of formaldehyde clusters (H2CO)n (n = 2–4)

Global exploration of equilibrium structures and interconversion pathways on the quantum chemical potential energy surface (PES) is performed for (H₂CO)n (n = 2–4) by using the Scaled Hypersphere Search‐Anharmonic Downward Distortion Following (SHS‐ADDF) method. Density functional theoretical (DFT) calculations with empirical dispersion corrections (D3) yielded comparable results for formaldehyde dimer in comparison with recent detailed studies at CCSD(T) levels. Based on DFT‐D3 calculations, trimer and tetramer structures and their stabilities were studied. For tetramer, a highly symmetrical S₄ structure was found as the most stable form in good accordance with experimentally determined tetramer unit in the formaldehyde crystal. © 2018 Wiley Periodicals, Inc.     

Strong Pancake 2e/12c Bond in π-Stacking Phenalenyl Derivatives Avoiding Bond Conversion

The nature of the 2e/12c bond and its conversion to a carbon-carbon single bond in phenalenyl dimers have prompted a great deal of interests recently. In this work, we theoretically investigated a series of π-stacking phenalenyl derivatives with 2e/12c bonding character by density functional theory (DFT) calculations to elucidate origin of this unusual bond conversion. Results show that bond-conversion of the phenalenyl dimer easily occurs at room-temperature both dynamically and thermodynamically. However, bond-conversion of hetero π-stacking adducts, in which the two center carbon atoms were substituted by boron and nitrogen atoms, respectively, is much more difficult, because the 2e/12c bond is stabilized by its charge transfer character. Consequently, the bond-conversion is an endothermic process, albeit with a low conversion barrier. Interestingly, Lewis acid-base interactions would be induced by substitution of the center nitrogen atom to phosphorus atom. The 2e/12c bond is further stabilized by 5.9 kcal mol⁻¹ and its conversion is also thermodynamically unfavorable.     

An improved theoretical approach to the empirical corrections of density functional theory

An empirical correction to density functional theory (DFT) has been developed in this study. The approach, called correlation corrected atomization–dispersion (CCAZD), involves short- and long-range terms. Short-range correction consists of bond (1,2-) and angle (1,3-) interactions, which remedies the deficiency of DFT in describing the proto-branching stabilization effects. Long-range correction includes a Buckingham potential function aiming to account for the dispersion interactions. The empirical corrections of DFT were parameterized to reproduce reported ΔH _f values of the training set containing alkane, alcohol and ether molecules. The ΔH _f of the training set molecules predicted by the CCAZD method combined with two different DFT methods, B3LYP and MPWB1K, with a 6-31G* basis set agreed well with the experimental data. For 106 alkane, alcohol and ether compounds, the average absolute deviations (AADs) in ΔH _f were 0.45 and 0.51 kcal/mol for B3LYP- and MPWB1K-CCAZD, respectively. Calculations of isomerization energies, rotational barriers and conformational energies further validated the CCAZD approach. The isomerization energies improved significantly with the CCAZD treatment. The AADs for 22 energies of isomerization reactions were decreased from 3.55 and 2.44 to 0.55 and 0.82 kcal/mol for B3LYP and MPWB1K, respectively. This study also provided predictions of MM4, G3, CBS-QB3 and B2PLYP-D for comparison. The final test of the CCAZD approach on the calculation of the cellobiose analog potential surface also showed promising results. This study demonstrated that DFT calculations with CCAZD empirical corrections achieved very good agreement with reported values for various chemical reactions with a small basis set as 6-31G*.     

2-Aryl substituted 3-oxophenalenoxyl radicals: π-Spin structures and properties evaluated by dimer structure

We recently demonstrated that 6- and 4-oxophenalenoxyl radicals possess high stability in air due to extensive π-spin delocalization and steric protection of active sites. In sharp contrast, 3-oxophenalenoxyl radicals were found to be not stable enough to be isolated as an open-shell species, and easily dimerized with each other at 2-positions. The radicals were generated by thermal bond cleavage of the dimers in a solution state and their electronic structures were probed by ESR techniques. In this study, we have revealed a sterically hindered structure of the dimer of 2-(p-methoxyphenyl)-3-oxophenalenoxyl in terms of both X-ray crystal structure analysis and variable temperature ¹H NMR studies. DFT calculations of the radicals indicate that π-spin densities dominantly exist at the 2-position, giving a rationale for the dimerized position of the radicals. These studies demonstrate that the lower stability of 3-oxophenalenoxyl is due to smaller π-spin delocalization into the whole phenalenyl skeleton than 6- and 4-oxophenalenoxyl radicals.     

A resonating broken-symmetry CI study of cationic states of phenalenyl dimeric compounds

We investigated several phenalenyl cationic dimer systems using ab initio methods. First, we examine the through-space cation dimer. The B3LYP method fails to describe the correct dissociation as in the case of usual cation dimers. On the other hand, the resonating broken symmetry configuration interaction (Res-BS CI) method based on unrestricted Hartree–Fock solutions yields the correct potential surface and correct charge distributions. Furthermore, we investigated though-bond interactions of the phenalenyl cationic dimer via acetylene and ethylene bridges. The results are considerably different from those of the though-space case, implying that these bridging units play important roles to determine charge and spin distributions. Judging from these results, different bridges-or-stacks lead to different hole behaviors, indicating the possibility of various electronic functionalities of hole-doped phenalenyl compounds. In particular, the acetylene bridge is expected to enhance the conductivity of the hole-doped phenalenyl compounds.     

Reaction of tetracyanoethylene with aldehydes. Synthesis of 6-imino-2,7-dioxabicyclo[3.2.1]octane-4,4,5-tricarbonitriles

It was discovered by means of dynamic NMR that the 1-(cis-1-methylprop-1-en-1-yl)-1,2-dimethyl-acenaphthylenonium ion generated under conditions of “long life” for carbocations underwent fast (ΔG^#35.8 kJ mol^?1 at ?103°C) degenerate 1,2-shift of the cis-dimethylvinyl group. Quantum-chemical calculations by DFT method predict lower rate of 1,2-shift for the trans-dimethylvinyl group compared to cis-dimethylvinyl group and dependence on the cations conformation of the rates of these processes and of the rearrangement mechanism into the ions of phenalenyl type.     

Intermolecular covalent pi-pi bonding interaction indicated by bond distances, energy bands, and magnetism in biphenalenyl biradicaloid molecular crystal

Density-functional theory (DFT) calculations were performed for energy band structure and geometry optimizations on the stepped pi-chain, the isolated molecule and (di)cations of the chain, and various related molecules of a neutral biphenalenyl biradicaloid (BPBR) organic semiconductor 2. The dependence of the geometries on crystal packing provides indirect evidence for the intermolecular covalent pi-pi bonding interaction through space between neighboring pi-stacked phenalenyl units along the chain. The two phenalenyl electrons on each molecule, occupying the singly occupied molecular orbitals (SOMOs), are participating in the intermolecular covalent pi-pi bonding making them partially localized on the phenalenyl units and less available for intramolecular delocalization. The band structure shows a relatively large bandwidth and small band gap indicative of good pi-pi overlap and delocalization between neighboring pi-stacked phenalenyl units. A new interpretation is presented for the magnetism of the stepped pi-chain of 2 using an alternating Heisenberg chain model, which is consistent with DFT total energy calculations for 2 and prevails against the previous interpretation using a Bleaney-Bowers dimer model. The obtained transfer integrals and the magnetic exchange parameters fit well into the framework of a Hubbard model. All presented analyses on molecular geometries, energy bands, and magnetism provide a coherent picture for 2 pointing toward an alternating chain with significant intermolecular through-space covalent pi-pi bonding interactions in the molecular crystal. Surprisingly, both the intermolecular transfer integrals and exchange parameters are larger than the intramolecular through-bond values indicating the effectiveness of the intermolecular overlap of the phenalenyl SOMO electrons.     

Synthesis,characterisation, mesomorphic investigation and temperature-dependent Raman study of a novel calamitic liquid crystal: methyl 4-(4′-n-alkoxybenzylideneamino)benzoate

A new series of Schiff base calamitic liquid crystal; methyl 4-(4′-n-alkoxybenzylideneamino)benzoate (MABAB), H_2n+1C _n OC₆H₄C(H)=NC₆H₄COOCH₃ (n = 6, 8, 10, 12, 14, 16) has been synthesised and characterised by elemental analyses, Fourier transform infrared spectroscopy (FT-IR), ¹H and ¹³C Nuclear Magnetic Resonance (NMR) spectroscopy. The mesomorphic properties of these compounds were studied by differential scanning calorimetry (DSC) and polarising optical microscopy (POM). All members of the series exhibit enantiotropic smectic A (SmA) mesophase. Temperature-dependent micro-Raman study of one of the members, MABAB-10 has been employed to identify phase transitions and the molecular rearrangement therein. Analysis of Raman marker bands; C–H in-plane bending, C–C stretching of phenyl rings and –C(H)=N– linking group of core confirms the transitions clearly as observed through DSC and POM. An in situ Raman measurement of C–H in-plane bending mode has also been performed to visualise the molecular changes more clearly. The Raman study gives an evidence of induced co-planarity of rings at Cr→SmA phase transition. The density functional theoretical (DFT) optimisation of monomer, dimer and rotational conformer of MABAB-10 also support the induced co-planarity at Cr→SmA phase transition.     

Rearrangements of 1-(1-methylprop-1-en-1-yl)-1,2-dimethylacenaphtyylenonium ions

It was discovered by means of dynamic NMR that the 1-(cis-1-methylprop-1-en-1-yl)-1,2-dimethylacenaphthylenonium ion generated under conditions of “long life” for carbocations underwent fast (ΔG^#35.8 kJ mol^?1 at ?103°C) degenerate 1,2-shift of the cis-dimethylvinyl group. Quantum-chemical calculations by DFT method predict lower rate of 1,2-shift for the trans-dimethylvinyl group compared to cis-dimethylvinyl group and dependence on the cations conformation of the rates of these processes and of the rearrangement mechanism into the ions of phenalenyl type.     

Stability and structure of singly-charged argon clusters Ar n + ,n=3–27. A Monte-Carlo simulation

Monte-Carlo calculations have been performed for positively charged argon clusters in the temperature range between 10 K and 40 K using two different models (one with a dimer ion core, the other one with a trimer ion). The argon-argon interaction potential stems from empirical data, the ion-neutral atoms potential is determined by ab initio MRD-CI calculations. Special stability is found for clusters sizesn=13, 19, 23 and 25/26 atoms using the ‘trimeric core model’ and for those withn=14,n=17,n=20 using the ‘dimeric core model’. The geometrical structure of the clusters is given and the construction principles are discussed in light of the interactions among neutral argon atoms and the ion-neutral atoms interaction.     

The relative stability of nano-“chromic wheels” [Crn(OCH3)2n(CH3COO)n] depending on the number of their coordination units

The relative stability of [Cr_n(OCH₃)_2n(CH₃COO)_n] depending on the number n of its interior groups (n = 4, 6, 8, 10, 12 and 14) has been studied by means of Hartree–Fock (HF) and Density Functional Theory (DFT) calculations. The calculation schemes employ atom-centered localized basis orbitals. As the first step, the structures of the molecules were optimized by means of quantum-chemistry and molecular mechanics approaches. All the molecules were found to have a lower energy in the anti-ferromagnetic state than in the ferromagnetic one; the total energy per one coordination section E_tot/n was calculated for further discussions. The relative stability of [Cr_n(OCH₃)_2n(CH₃COO)_n] molecules for different n, as estimated by the DFT, correlates with a structural rule, which allows the prediction of the relative stability of different ‘wheel’-type compounds by using a simple formula. This study demonstrates that computational chemistry can be useful for theoretical forecasting of new stable molecules of the ‘wheel’-type. This approach can be used for the rational design of molecular systems possessing magnetic properties.     

An HF and DFT ab initio Study on the Mechanism of ortho‐Directed Lithiation of Hydric and Nonhydric Aromatic Compounds Incorporating Aggregation and Discrete Solvation: The Role of N,N,N′,N′‐Tetramethylethane‐1,2‐diamine (TMEDA) in Lithiation Reactions

An HF and DFT ab initio study was set up to decipher the roles of aggregation and solvation in the ortho‐directed lithiation of aromatics (hydric and nonhydric), as well as to shed light on the much debated question of precomplexation in the mechanism of lithiation. Ab initio (HF/6‐31‐G*) calculations on the lithiation of non‐hydric aromatics have uncovered several competitive routes operating as a function of the aggregation state of the organolithium base used. Specifically, two competitive routes were found for the lithiation of the anisole model 2 by organolithium dimers 1‐dim , namely the so‐called cyclic‐dimer and open‐dimer routes, whereas, for organolithium tetramers 1‐tet , the corresponding cyclic route is the only one operative, and, for monomers 1‐mon , several optional routes seem to be available. Precomplexation is, in all cases, a requirement. According to the computational data presented, the mysterious rate acceleration experimentally observed for lithiations carried out in TMEDA can be assigned to an aggregation effect on the intermediate open‐dimer species, which subsidiarily give rise to several so‐called s‐monomer routes, of which the dimerization‐driven s‐monomer route s‐m_3b is the one having the lowest energy barrier. The relevant species characteristic of both the open‐dimer and s‐monomer routes are the so‐called open dimers, i.e., high‐energy intermediates (actually, spiro dimeric aggregates), resulting from cleavage‐induced associative complexation of the aromatic substrate upon the fully solvated organolithium dimer. DFT calculations (B3LYP/6‐31+G*) also revealed that the peri‐lithiation (i.e., Li at C(8)) of 1‐naphthol model 3 is a slow process taking place preferentially through the open‐dimer route.     

Fluorine spin–spin coupling constants of pentafluorobenzene revisited at the ab initio correlated levels

All possible spin–spin coupling constants, ¹⁹F–¹⁹F, ¹⁹F–¹³C, and ¹⁹F–¹H, of pentafluorobenzene were calculated at five different levels of theory, HF, DFT, SOPPA (CCSD), CCSD, and the SOPPA (CCSD)-based composite scheme with taking into account solvent, vibrational, relativistic, and correlation corrections. Most corrections were next to negligible for the long-range couplings but quite essential for the one-bond carbon–fluorine coupling constants. Hartree–Fock calculations were found to be entirely unreliable, while DFT results were comparable in accuracy with the data obtained using the wave function-based methods.     

Third-order nonlinear optical properties of open-shell supermolecular systems composed of acetylene linked phenalenyl radicals

The third-order nonlinear optical (NLO) properties, at the molecular level, the static second hyperpolarizabilities, γ, of supermolecular systems composed of phenalenyl and pyrene rings linked by acetylene units are investigated by employing the long-range corrected spin-unrestricted density functional theory, LC-UBLYP, method. The phenalenyl based superethylene, superallyl, and superbutadiene in their lowest spin states have intermediate diradical characters and exhibit larger γ values than the closed-shell pyrene based superpolyene systems. The introduction of a positive charge into the phenalenyl based superallyl radical changes the sign of γ and enhances its amplitude by a factor of 35. Although such sign inversion is also observed in the allyl radical and cation systems in their ground state equilibrium geometries, the relative amplitude of γ is much different, that is, |γ(regular allyl cation)/γ(regular allyl radical)| = 0.61 versus |γ(phenalenyl based superallyl cation)/γ(phenalenyl based superallyl radical)| = 35. In contrast, the model ethylene, allyl radical/cation, and butadiene systems with stretched carbon-carbon bond lengths (2.0 ?), having intermediate diradical characters, exhibit similar γ features to those of the phenalenyl based superpolyene systems. This exemplifies that the size dependence of γ as well as its sign change by introducing a positive charge on the phenalenyl based superpolyene systems originate from their intermediate diradical characters. In addition, the change from the lowest to the highest π-electron spin states significantly reduces the γ amplitudes of the neutral phenalenyl based superpolyene systems. For phenalenyl based superallyl cation, the sign inversion of γ (from negative to positive) is observed upon switching between the singlet and triplet states, which is predicted to be associated with a modification of the balance between the positive and negative contributions to γ. The present study paves the way toward designing a variety of open-shell NLO supermolecular systems composed of phenalenyl radical building blocks.     

Interaction of positional isomers of dimethylbenzene with graphite

The optimized geometries and interaction energies of the intermolecular heterodimers of coronene with o-, m-, and p-dimethylbenzenes (xylenes) calculated by DFT in the PBE0 and B97D functionals were compared. The applicability of coronene as a model for qualitative assessment of the interaction of mononuclear aromatic compounds with the graphite surface was demonstrated. The necessity of including long-range dispersion interactions in DFT calculations of the dimerization energies of aromatic systems was shown. The sorption enthalpies of p- and m-xylenes were shown to be almost equal irrespective of the conditions of the chromatographic experiment. The preferred sorption of p- over m-xylene on graphite is solely due to the entropy factor.