Benzvalyne: Real or imaginary?

Benzvalyne (C6H4) is a bicyclic structural isomer of o-benzyne that some typically trusted levels of theory do not report as a minimum on the potential energy surface (PES). The structure was found to be a C2v minimum at the MCSCF, MP2, coupled-cluster single double, coupled-cluster single double triple (CCSDT)-1b, and CCSDT-2 levels of theory. Density functionals at the B3LYP-D3, B2PLYP-D3, and M06-D3 levels also produced a minimum structure. On the other hand, the CCSD(T), CCSD(T)-F12, and CCSDT-1a methods produced a single imaginary frequency for benzvalyne. However, the increase in the correlation for the CCSDT-1b and CCSDT-2 methods implies that benzvalyne is, in fact, a true, if highly strained, minimum on the PES. The C-C≡C bond angle was found to be only 108°; this angle is 180° for an unstrained C-C≡C triple bond moiety. As a result, the strain energy is notably high at 159 kcal mol-1. Comparing the strain energy of the rest of the molecule gives a strain energy of 92 kcal mol-1 for this triple bond region alone. The computed harmonic frequencies contain normal modes consisting of two hindered rotations of the C≡C diatomic part of the molecule, suggesting that the dissociation of this diatomic from the bicylobutane moiety may be important in the chemistry of this molecule. Because the putative C2v minimum is predicted to have a significant dipole moment (2.6 D), benzvalyne may be detectable in TMC-1, where the related o-benzyne molecule has recently been observed by radio astronomy.

Noncovalent Interactions between Trimethylamine N-Oxide (TMAO), Urea, and Water.

Trimethylamine N-oxide (TMAO) and urea are two important osmolytes with their main significance to the biophysical field being in how they uniquely interact with proteins. Urea is a strong protein destabilizing agent, whereas TMAO is known to counteract urea's deleterious effects. The exact mechanisms by which TMAO stabilizes and urea destabilizes folded proteins continue to be debated in the literature. Although recent evidence has suggested that urea binds directly to amino acid side chains to make protein folding less thermodynamically favored, it has also been suggested that urea acts indirectly to denature proteins by destabilizing the surrounding hydrogen bonding water networks. Here, we elucidate the molecular level mechanism of TMAO's unique ability to counteract urea's destabilizing nature by comparing Raman spectroscopic frequency shifts to the results of electronic structure calculations of microsolvated molecular clusters. Experimental and computational data suggest that the addition of TMAO into an aqueous solution of urea induces blue shifts in urea's H-N-H symmetric bending modes, which is evidence for direct interactions between the two cosolvents.

Noncovalent interactions in microsolvated networks of trimethylamine N-oxide.

The effects of the formation of hydrogen-bonded networks on the important osmolyte trimethylamine N-oxide (TMAO) are explored in a joint Raman spectroscopic and electronic structure theory study. Spectral shifts in the experimental Raman spectra of TMAO and deuterated TMAO microsolvated with water, methanol, ethanol, and ethylene glycol are compared with the results of electronic structure calculations on explicit hydrogen-bonded molecular clusters. Very good agreement between experiment and theory suggests that it is the local hydrogen-bonded geometry at TMAO's oxygen atom that dominates the structure of the extended hydrogen-bonded networks and that TMAO's unique stabilizing abilities are a result of the "indirect effect" model. Natural bonding orbital (NBO) calculations further reveal that hyperconjugation results in vibrational blue shifts in TMAO's C-H stretching region when solvated and a red shift in methanol's C-H stretching region when hydrogen bonding with TMAO.

Theoretical study of the pre- and post-translational effects of adenine and thymine tautomers and methyl derivatives.

The study of pre-translational effects (ionization, tautomerization) and post-translational effects (methylation) of adenine and thymine has only recently been the focus of some studies. These effects can potentially help regulate gene expression as well as potentially disrupt normal gene function. Because of this wide array of roles, greater insight into these effects in deoxyribonucleic acids (DNA) are paramount. There has been considerable research of each phenomenon (tautomerization, methylation and ionization) individually. In this work, we attempt to shed light upon the pre-translational effects and post translational effects of adenine and thymine by investigating the electron affinities (EAs) and ionization potentials (IPs) of the major and minor tautomers and their methyl derivatives. We performed all calculations using the density functional theory (DFT) B3LYP functional accompanied with 6-311G(d,p), 6-311+G(d,p) and 6-311++G(df,pd) basis sets. Our results reveal that the thymine tautomer has a higher EA and IP than the adenine tautomers. The higher EA suggests that an electron that attaches to the AT base pair would predominately attach to the thymine instead of adenine. The higher IP would suggest that an electron that is removed from the AT base pair would be predominately removed from the adenine within the base pair. Understanding how tautomerization, ionization and methylation differences change effects, discourages, or promotes one another is lacking. In this work, we begin the steps of integrating these effects with one another, to gain a greater understanding of molecular changes in DNA bases.

Conventional strain energies of azetidine and phosphetane: can density functional theory yield reliable results?

The conventional strain energies for azetidine and phosphetane are determined within the isodesmic, homodesmotic, and hyperhomodesmotic models. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies and zero-point vibrational energies are computed for all pertinent molecular systems using self-consistent field theory, second-order perturbation theory, and density functional theory and using the correlation consistent basis sets cc-pVDZ, cc-pVTZ, and cc-pVQZ. Single point fourth-order perturbation theory, CCSD, and CCSD(T) calculations using the cc-pVTZ and the cc-pVQZ basis sets are computed using the MP2/cc-pVTZ and MP2/cc-pVQZ optimized geometries, respectively, to ascertain the contribution of higher order correlation effects and to determine if the quadruple-zeta valence basis set is needed when higher order correlation is included. In the density functional theory study, eight different functionals are used including B3LYP, wB97XD, and M06-2X to determine if any functional can yield results similar to those obtained at the CCSD(T) level.

Raman spectroscopic signatures of noncovalent interactions between trimethylamine N-oxide (TMAO) and water.

The effects of hydration on vibrational normal modes of trimethylamine N-oxide (TMAO) are investigated by Raman spectroscopy and electronic structure computations. Microsolvated networks of water are observed to induce either red or blue shifts in the normal modes of TMAO with increasing water concentration and to also exhibit distinct spectral signatures. By taking advantage of the selective and gradual nature of the water-induced shifts and using comparisons to theoretical predictions, the assignments of TMAO's normal modes are re-examined and the structure of the hydrogen-bonded network in the vicinity of TMAO is elucidated. Agreement between experiment and theory suggests that the oxygen atom in TMAO accepts on average at least three hydrogen bonds from neighboring water molecules and that water molecules are likely not directly interacting with TMAO's methyl groups.

Structure and reactivity of TNT and related species: application of spectroscopic approaches and quantum-chemical approximations toward understanding transformation mechanisms.

This paper presents our latest findings regarding the structure and reactivity of the nitroaromatics, TNT and selected derivatives, within their environmental context. We also demonstrate the useful and proactive role of combined computational chemistry and spectroscopy tools in studying competing transformation mechanisms, particularly those with toxic potential. TNT and selected derivatives were reacted via alkaline hydrolysis as well as via free radical initiators through monochromatic irradiation and through Fenton reactions in complex competing transformation mechanisms. Only alkaline hydrolysis produced consistent and effective transformation intermediate and final products in this research. However, irradiation of the product generated by alkaline hydrolysis at 450 nm (wavelength of maximum absorption) caused complete disappearance of the spectra.

Application of quantum-chemical approximations to environmental problems: Prediction of physical and chemical properties of TNT and related species.

This paper presents accurate predictions of ecologically important properties of nitroaromatic compounds and their derivatives, including vapor pressure, Henry's law constants, water solubility, octanol/water partition coefficients, heats of formation and ionization potentials. The proposed technique of calculations was based on quantum-chemical methods. The relationship between the chemical structure and mentioned physico-chemical parameters of such widespread military produced contaminants as trinitrotoluene and its derivatives was considered. We revealed that the DFT level of theory combined with the COSMO-RS technique is able to predict the studied parameters with an accuracy that results in error bars of less then one logarithmic unit.

Conventional strain energy in dimethyl-substituted cyclobutane and the gem-dimethyl effect.

The gem-dimethyl effect is the acceleration of cyclization by substituents in the chain and is often used in organic synthesis as a ring-closing effect. Calculations on cyclobutane, methylcyclobutane, and 1,1-dimethylcyclobutane are performed. 1,1-Dimethylcyclobutane is a four-membered carbon ring with gem-dimethyl substituents. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies are computed for all pertinent molecular systems using SCF theory, density functional theory (DFT), and second-order perturbation theory (MP2) with two triple-zeta quality basis sets, 6-311G(d,p) and 6-311G+(2df,2pd). Additional single-point calculations are performed using the optimized MP2/6-311G+(2df,2pd) geometries and coupled-cluster theory including single and double excitations and noniterative, linear triple excitations (CCSD(T)). Calculations indicate that 1,1-dimethylcyclobutane is more than 8 kcal mol-1 less strained than cyclobutane, that is, there is at least some thermodynamic component to the gem-dimethyl effect.

Stability and thermal rearrangement of (E,E)-1,3-cycloheptadiene and trans-bicyclo[3.2.0]hept-6-ene.

The highly strained (E,E)-1,3-cycloheptadiene was shown to be a minimum on the potential energy surface; two structural isomers were found at the MP2 level, but multiconfiguration self-consistent field calculations show that only one is a true minimum. The isomerization of (E,E)-1,3-cycloheptadiene was investigated through double bond rotation, and electrocyclic ring closure. The first pathway gives (E,Z)-1,3-cycloheptadiene, with a barrier of 7.2 kcal x mol(-1), and the second pathway gives the trans isomer of bicyclo[3.2.0]hept-6-ene with a barrier of 13.0 kcal x mol(-1). The strain energy of (E,E)-1,3-cycloheptadiene was calculated using homodesmotic reactions and found to be about 96 kcal x mol(-1) whereas that for (E,Z)-1,3-cycloheptadiene was only 38 kcal x mol(-1), implying that the second trans double bond imparts an additional 58 kcal x mol(-1) in strain energy. The trans isomer of bicyclo[3.2.0]hept-6-ene was calculated to have a strain energy of 69 kcal x mol(-1) and a barrier of 27 kcal x mol(-1) for isomerization to (Z,Z)-1,3-cycloheptadiene. Although many of the structures reported here could be described using a single determinant wave function, several could not, making a multireference method necessary for a complete description of the potential energy surface.