High-Level ab Initio Calculations of Torsional Potential of Phenol, Anisole, and o-Hydroxyanisole: Effects of Intramolecular Hydrogen Bond

OPLS/2020 Force Field for Unsaturated Hydrocarbons, Alcohols, and Ethers

The OPLS all-atom force field was updated and applied to modeling unsaturated hydrocarbons, alcohols, and ethers. Testing has included gas-phase conformational energetics, properties of pure liquids, and free energies of hydration. Monte Carlo statistical mechanics (MC) calculations were used to model 60 liquids. In addition, a robust, automated procedure was devised to compute the free energies of hydration with high precision via free-energy perturbation (FEP) calculations using double annihilation. Testing has included larger molecules than in the past, and parameters are reported for the first time for some less common groups including alkynes, allenes, dienes, and acetals. The average errors in comparison with experimental data for the computed properties of the pure liquids were improved with the modified force field (OPLS/2020). For liquid densities and heats of vaporization, the average unsigned errors are 0.01 g/cm3 and 0.2 kcal/mol. The average error and signed error for free energies of hydration are both 1.2 kcal/mol. As noted before, this reflects a systematic overestimate of the hydrophobicity of organic molecules when the parametrization is done to minimize the errors for properties of pure liquids. Implications for the modeling of biomolecular systems with standard force fields are considered.

Torsional Potentials of Glyoxal, Oxalyl Halides, and Their Thiocarbonyl Derivatives: Challenges for Popular Density Functional Approximations

The reliability of popular density functionals was studied for the description of torsional profiles of 36 molecules: glyoxal, oxalyl halides, and their thiocarbonyl derivatives. HF and 18 functionals of varying complexity, from local density to range-separated hybrid approximations and double-hybrid, have been considered and benchmarked against CCSD(T)-level rotational profiles. For molecules containing heavy halogens, most functionals fail to reproduce barrier heights accurately and a number of functionals introduce spurious minima. Dispersion corrections show no improvement. Calibrated torsion-corrected atom-centered potentials rectify the shortcomings of PBE and also improve on σ-hole based intermolecular binding in dimers and crystals.

Validating an optimized GAFF force field for liquid crystals: TNI predictions for bent-core mesogens and the first atomistic predictions of a dark conglomerate phase

Atomistic simulations of bent core mesogens provide excellent T_NI predictions and show the formation of a dark conglomerate phase.

Excited state deactivation pathways of neutral/protonated anisole and p-fluoroanisole: a theoretical study

The potential energy profiles of neutral and protonated anisole and p-fluoroanisole at different electronic states have been investigated extensively by the RI-MP2 and RI-CC2 methods. The calculations reveal that the relaxation dynamics in protonated anisole and p-fluoroanisole are essentially different from those of the neutral analogues. In neutral anisole/p-fluoroanisole, the (1)πσ* state plays a vital relaxation role along the O-CH3 coordinate, yielding the CH3 radical. For both of these molecules, the calculations indicate conical intersections (CIs) between the ground and excited state potential energy (PE) curves, hindered by a small barrier, and providing non-adiabatic gates for radiation-less deactivation to the ground state. Nevertheless, for the protonated cases, besides the prefulvenic deformation of the benzene ring, it has been predicted that the lowest (1)(σ,n)π* state along the C-O-C bond angle plays an important role in photochemistry and the relaxation dynamics. The S1, S0 PE profiles of protonated anisole along with the former reaction coordinate (out-of-plane deformation) show a barrierless relaxation pathway, which can be responsible for the ultrafast deactivation of excited systems to the ground state via the low-lying S1/S0 conical intersection. Moreover, the later reaction coordinate in protonated species (C-O-C angle from 120°-180°) is consequently accompanied with the bond cleavage of C-OCH3 at the (1)(σ,n)π* state, hindered by a barrier of ∼0.51 eV, and can be responsible for the relaxation of excited systems with significant excess energy (hν≥ 5 eV). Furthermore, according to the RI-CC2 calculated results, different effects on the S1-S0 electronic transition energy of anisole and p-fluoroanisole upon protonation have been predicted. The first electronic transitions of anisole and p-fluoroanisole shift by ∼0.3 and 1.3 eV to the red respectively due to protonation.

Environment-related properties of polyhydroxylated dibenzo-p-dioxins

Polyhydroxylated dibenzo-p-dioxins (PHODDs) are important metabolic and synthetic products of polychlorinated dibenzo-p-dioxins (PCDDs). Two types of hydrogen bonds exist in PHODD molecules: one between a hydroxyl group (HO) and an oxygen atom of the ether bond, and the other between two ortho hydroxyls of a benzene ring. By fully optimized calculation with density functional theory (DFT), their bond energies were ascertained to be approximately 9-14 kJ/mol and 15-19 kJ/mol respectively by the comparison of standard Gibbs energy of formation (Δ(f)G(θ)) between different molecules, which was experimentally verified. The two types of hydrogen bonds affect the hydrophilicity and stability of the molecules. The torsional potential of hydroxyls and the orientation making the congener most stable were obtained. The octanol-water partition coefficients (logK(ow)s) were calculated based on the group contribution method, and the standard state entropy (S(θ)), standard enthalpy (Δ(f)H(θ)) of formation and Δ(f)G(θ) were obtained from the combination of DFT calculation and isodesmic reaction for the stable PHODD congeners. The number and position of hydroxyl substitution (N(PHOS)) were employed as descriptors to establish quantitative structure-property relationship (QSPR) models. Although the hydrophilicity of PHODDs increases with the number of hydroxyl groups, it is impaired by the intramolecular hydrogen bonds. The logK(ow)s of PHODDs are much smaller than those of PCDDs, and the variation trend with the number of substituents is different. In addition, the relative stability order of PHODD congeners was theoretically proposed, which is quite different from that of PCDDs. Considering the ionization in water, first-order ionization constants of PHODDs were calculated according to the results of SMD method of Self-Consistent Reaction Field Theory (SCRF), and they were influenced by the hydrogen bonds.

The structure, methyl rotation reflected in inelastic and quasielastic neutron scattering and vibrational spectra of 1,2,3,5-tetramethoxybenzene and its 2:1 complex with 1,2,4,5-tetracyanobenzene

X-ray diffraction studies show that molecules of the 1,2,3,5-tetramethoxybenzene (TMOB)(2) x 1,2,4,5-tetracyanobenzene complex form ...CCDCCDCC... columns with the short distances between molecular planes of C and D molecules equal to 3.186 A. The vibrational spectra recorded by using the inelastic neutron scattering, Raman, IR, and quasielastic neutron scattering (QENS) techniques aided by density functional theory calculations for the isolated molecules and the crystalline state enabled all four inequivalent librational modes, ascribed to the methoxy groups, to be analyzed. A rather good consistency was found between the experimental frequencies and those calculated for the crystal. The consistency was also achieved between the experimental structure of molecules and the theoretically reproduced one. A close similarity of the structures of the TMOB molecule isolated and in the complex is taken as a sign of dominating intramolecular interaction. The QENS spectra contain three Lorentzians of relative intensities of 1:1:2. Thus the two most strongly hindered of the four inequivalent methoxy groups in the crystalline lattice are characterized by rather similar barrier heights in good agreement with the packing analysis.

Integrated computational approach to vibrationally resolved electronic spectra: anisole as a test case

A new general and effective procedure to compute Franck-Condon spectra from first principles is exploited to elucidate the subtle features of the vibrationally resolved optical spectra of anisole. Methods based on the density functional theory and its time-dependent extension for electronic excited states [B3LYP6-311+G(d,p) and TD-B3LYP6-311+G(d,p)] have been applied to geometry optimizations and harmonic frequency calculations. Perturbative anharmonic frequencies [J. Chem. Phys. 122, 014108 (2005)] have been calculated for the ground state, and the Duschinsky matrix elements have been used to evaluate the corresponding anharmonic corrections for the first excited electronic state. The relative energetics of both electronic states has been refined by single point calculations at the coupled clusters (CC) level with the aug-cc-pVDZ basis set. Theoretical spectra have been evaluated using a new optimized implementation for the effective computation of Franck-Condon factors. The remarkable agreement between theoretical and experimental spectra allowed for revision of some assignments of fundamental vibrations in the S(1) state of anisole.

High resolution electronic spectra of anisole and anisole-water in the gas phase: hydrogen bond switching in the S1 state

Rotationally resolved S(1)<--S(0) electronic spectra of anisole and its hydrogen bonded complex containing one water molecule have been obtained. The results provide evidence for an "in-plane" complex in which the water molecule is attached via two hydrogen bonds to the anisole molecule, a donor O-H- - -O(CH(3)) bond and an acceptor H-O- - -H(ring) bond. Analysis of the subbands that appear in the spectrum of the complex suggests that hydrogen bond "switching" occurs when the complex absorbs light. The former O-H- - -O(CH(3)) bond is stronger in the ground (S(0)) state, whereas the latter H-O- - -H(ring) bond is stronger in the excited (S(1)) state. Dynamical consequences of this phenomenon are discussed.

Dual Fluorescence of 2-Methoxyanthracene Derivatives

The time-resolved emission properties of selected anthracene derivatives, namely anthracene (1a), 2-methylanthracene (1b), 2-chloroanthracene (1c), 2-methoxyanthracene (1d), 2-methoxy-6-methylanthracene (1e), 2-(N,N'-dicyclohexylureidocarbonyl)-6-methoxyanthrace ne (1f), 2-(6-methoxyanthr-2-yl)-4,4-dimethyl-2-oxazoline (1g), 2-(6-methoxyanthr-2-yl)-pyridine (1h), and N-cyclohexylanthracene-2-carboxamide (1i) were investigated. In contrast to anthracene (1a), 1b, and 1c, the 2-methoxy-substituted anthracene derivatives 1d-1h exhibit two emission lifetimes. The determination of the lifetimes at different emission wavelengths and additional time-resolved emission spectroscopy (TRES) reveal that the dual emission originates from two different, interconvertible emissive species, with the s-cis and s-trans conformation relative to the exocyclic C2-O bond. The energy difference between the two emissive species is very small (<0.1 eV) both in the ground and in the excited state. The larger energy difference between the conformers in the excited-state is responsible for the interconversion within the singlet excited-state lifetimes of the s-cis into the s-trans conformations leading to coupled decay kinetics. The proposed mechanism for the dual emission was qualitatively supported by theoretical studies on CASSCF and DFT level. In addition, the emission lifetimes of the fluoride- and pH-sensitive fluorescent probes 1f and 1g change upon addition of fluoride or acid, respectively, so that in these cases the detection of the fluorescence lifetime may be used complementary to the steady-state fluorimetric detection of these analytes.

The microwave and infrared spectroscopy of benzaldehyde: conflict between theory and experimental deductions

Recently, it has been proposed that ab initio calculations cannot accurately treat molecules comprised of a benzene ring with a pi-conjugated substituent, for example, benzaldehyde. Theoretical predictions of the benzaldehyde barrier to internal rotation are typically a factor of 2 too high in comparison to the experimental values of 4.67 (infared) and 4.90 (microwave) kcal mol(-1). However, both experiments use Pitzer's 1946 model to compute the reduced moment of inertia and employ the experimentally observed torsional frequency to deduce benzaldehyde's rotational barrier. When Pitzer's model is applied to a system with a nonconjugated functional group, such as phenol, the model and theoretical values are in close agreement. Therefore, we conclude the model may not account for conjugation between the substituent and the pi-system of benzene. The experimental values of the benzaldehyde rotational barrier are therefore misleading. The true rotational barrier lies closer to the theoretically extrapolated limit of 7.7 kcal mol(-1), based on coupled cluster theory.

Large Raman-scattering activities for the low-frequency modes of substituted benzenes: Induced polarizability and stereo-specific ring-substituent interactions

The large nonresonant Raman-scattering activities of the out-of-plane bending and torsional modes of monosubstituted benzene analogs are studied by low-frequency Raman experiments and B3LYP6-31++G(d,p) calculations. Electronic interactions between the sigma orbitals of the substituent and the pi orbitals of the ring are found to enhance the Raman activities, depending on the substituent and its conformation. In the case of tert-butylbenzene [C6H5C(CH3)3] and trimethylphenylsilane [C6H5Si(CH3)3], three single bonds which are linked to the alpha atom of the substituent have low rotational barriers around the joint bond. Nearly free rotation of the substituents leads to a significant probability for one of the single bonds to occupy a conformation close to the vertical configuration with respect to the ring at room temperature. The resultant sigma-pi electronic interaction gives rise to the large Raman activities. In contrast, those possessing a single bond in a coplanar (or nearly coplanar) configuration at the most stable equilibrium state, i.e., anisole (C6H5OCH3), thioanisole (C6H5SCH3), and N-methylaniline (C6H5NHCH3), display no prominent Raman bands for the low-frequency vibrational modes. In these molecules, the sigma-pi conjugation does not take place due to the orthogonal orientation of the orbitals. Strong conformational dependence of the sigma-pi Raman enhancement is clearly obtained for the metastable vertical conformer of thioanisole, for which Raman activities are one-order magnitude greater than those of the coplanar conformer.

Molecular Structure and Internal Rotation in 2,3,5,6-Tetrafluoroanisole as Studied by Gas-Phase Electron Diffraction and Quantum Chemical Calculations

The geometric structure of 2,3,5,6-tetrafluoroanisole and the potential function for internal rotation around the C(sp2)-O bond were determined by gas electron diffraction (GED) and quantum chemical calculations. Analysis of the GED intensities with a static model resulted in near-perpendicular orientation of the O-CH3 bond relative to the benzene plane with a torsional angle around the C(sp2)-O bond of tau(C-O) = 67(15) degrees. With a dynamic model, a wide single-minimum potential for internal rotation around the C(sp2)-O bond with perpendicular orientation of the methoxy group [tau(C-O) = 90 degrees] and a barrier of 2.7 +/- 1.6 kcal/mol at planar orientation [tau(C-O) = 0 degrees] was derived. Calculated potential functions depend strongly on the computational method (HF, MP2, or B3LYP) and converge adequately only if large basis sets are used. The electronic energy curves show internal structure, with local minima appearing because of the interplay between electron delocalization, changes in the hybridization around the oxygen atom, and the attraction between the positively polarized hydrogen atoms in the methyl group and the fluorine atom at the ortho position. The internal structure of the electronic energy curves mostly disappears if zero-point energies and thermal corrections are added. The calculated free energy barrier at 298 K is 2.0 +/- 1.0 kcal/mol, in good agreement with the experimental determination.

Matrix isolation infrared and ab initio study of the hydrogen bonding between formic acid and water

The infrared spectra of the formic acid-water complexes isolated in argon matrices are reported. Both supersonic jet expansion and a conventional effusive source followed by trapping in solid argon at 10K are used to obtain the matrices. The experimental IR spectra are compared to the data obtained from high level ab initio (MP2) and DFT (B3LYP) calculations with 6-311++G(d,p) and aug-cc-pVTZ basis sets. The complex formation results in red shifts in the C=O and O-H stretching vibrations and a blue shift in the C-O stretching vibration of formic acid. The O-H stretching modes of water also exhibit pronounced red shifts. Both the MP2 and B3LYP calculations located three minima corresponding to cyclic HCOOH...H2O complexes with two hydrogen bond interactions. The binding energies are -10.3, -5.1, and -3.5 kcal mol(-1), respectively, for the three complexes at the MP2/ aug-cc-pVTZ level, corrected for the basis set superposition error (BSSE) using the Boys-Bernardi counterpoise scheme. Comparison of the calculated frequencies of the three complexes with the matrix IR spectrum reveals that the lowest energy complex is formed. In addition, a complex of formic acid with two water molecules is observed.

Structural Isomerism in Crystals of Redox-Active Secondaryortho-Diamides: The Role of Competing Intra- and Intermolecular Hydrogen Bonds in Directing Crystalline Topologies

The solid-state chemistry of a series of seven ortho-bis(alkylamido)ethylenedithiotetrathiafulvalene derivatives EDT-TTF-(CONHR)2 (R=Me, 1; Et, 2; Pr, 3; Bu, 4; Pent, 5; Hex, 6; and Bz, 7), in their neutral and one-electron-oxidized, radical cation states, was investigated with an eye on the topology of intra- and intermolecular hydrogen-bond motifs. In the case of neutral, monomolecular solids, an intramolecular N--H.O hydrogen bond seals a constrained seven-membered ring for 1, 2, 3, and 7, which is disrupted in butyl derivative 4 in favor of an antiparallel ladder at the expense of any intramolecular hydrogen bond. In the solid-state, the competition between intra- and intermolecular hydrogen bonding observed in solution depends on the packing of the molecules. Electrocrystallization of methyl derivative 1 with ReO4- or ClO4-, two anions of different volumes but otherwise identical charge and symmetry, revealed a fine sensitivity of the constrained seven-membered ring to the internal chemical pressure exerted by the anion. [1]2 *+ReO4 (sigmaRT=8.5 S cm(-1), activation energy Delta=600 K at high temperature) and beta"-[1]2 *+ClO4 (sigmaRT=0.03 S cm(-1), Delta=1600 K; under pressure at room temperature, the conductivity increases by three orders of magnitude up to 17 kbar with a linear variation of the activation energy with pressure, Delta=aP with a=0.202 10(6) K kbar(-1)) have vastly different architectures, dimensionalities, electronic structures, and collective properties, a consequence of the presence of the closed or open structural isomers in one or the other. This exemplifies the flexibility of functionalized TTF derivatives, even when the functional group is directly attached to the electro-active core. This allows an analogy to be drawn with tetrafunctionalized metallocenes, in which such flexibility has already been observed. The experimental data are supported by theoretical calculations of the energy profile of a model molecule on rotation of the amido groups.