Conformational Study of Monomeric 2,3-Butanediols by Matrix-Isolation Infrared Spectroscopy and DFT Calculations

Photochemical Generation and Characterization of C-Aminophenyl-Nitrilimines: Insights on Their Bond-Shift Isomers by Matrix-Isolation IR Spectroscopy and Density Functional Theory Calculations

The intriguing ability of C-phenyl-nitrilimine to co-exist as allenic and propargylic bond-shift isomers motivated us to investigate how substituents in the phenyl ring influence this behavior. Building on our previous work on the meta- and para-OH substitution, here we extended this investigation to explore the effect of the NH2 substitution. For this purpose, C-(4-aminophenyl)- and C-(3-aminophenyl)-nitrilimines were photogenerated in an argon matrix at 15 K by narrowband UV-light irradiation (λ = 230 nm) of 5-(4-aminophenyl)- and 5-(3-aminophenyl)-tetrazole, respectively. The produced nitrilimines were further photoisomerized to carbodiimides via 1H-diazirines by irradiations at longer wavelengths (λ = 380 or 330 nm). Combining IR spectroscopic measurements and DFT calculations, it was found that the para-NH2-substituted nitrilimine exists as a single isomeric structure with a predominant allenic character. In contrast, the meta-NH2-substituted nitrilimine co-exists as two bond-shift isomers characterized by propargylic and allenic structures. To gain further understanding of the effects of phenyl substitution on the bond-shift isomerism of the nitrilimine fragment, we compared geometric and charge distribution data derived from theoretical calculations performed for C-phenyl-nitrilimine with those performed for the derivatives resulting from NH2 (electron-donating group) and NO2 (electron-withdrawing group) phenyl substitutions.

Structural, optimization of and mechanistic insights into a new thiosemicarbazone derivative as a highly sensitive and selective chemosensor for Hg2+ recognition using DFT, COSMO-RS, RSM, and molecular dynamics simulation approaches

A new thiosemicarbazone derivative, N-(2-hydroxyphenyl)-2-[1-(pyridin-4-yl)ethylidene]hydrazinecarbothioamide (HPEH), has been synthesized, characterized, and further developed as a highly selective and sensitive colorimetric chemosensor for Hg2+ recognition in environmental water samples. Structural conformers of HPEH were successfully identified using a combination of the potential energy surface (PES) and time-dependent density functional theory (TD-DFT) methods. The synthesized HPEH was successfully characterized further and analyzed based on its harmonic vibrational frequencies, NMR spectra, and electronic transitions using the DFT approach. Sigma profiles were generated using the COSMO-RS approach to identify a compatible medium for HPEH to act as a chemosensor. The conditions for the highly sensitive and selective detection of Hg2+ by HPEH were successfully optimized using the statistical response surface methodology approach. The optimum sensing of HPEH occurred in an 8:2 v/v DMSO/pH 7.8 solution at a 20:60 μM HPEH/Hg2+ concentration and after a reaction time of 18 min, with statistically significant independent variables (p < 0.05) for all parameters. Under optimal conditions, the lowest Hg2+ concentration detected by HPEH was 3.56 µM, indicating that HPEH can serve as an alternative and comparable probe for the detection of Hg2+ in aqueous systems. Using the optimized results, the interaction between HPEH and Hg2+ in the chemosensor system was successfully modeled, and the model was subsequently used with the TD-DFT, non-covalent interaction-reduced density gradient (NCI-RDG), and molecular dynamics approaches to gain mechanistic insights into the interaction. The results showed that the newly synthesized HPEH, in addition to being cost-effective, could serve as a suitable alternative and comparable chemosensor for Hg2+ recognition in water samples, with the advantages of being efficient, portable, and eco-friendly, and offering rapid analysis without the need of specialized training.

A journey across dopamine Metabolism: A rotational study of DOPAC

DOPAC, a relevant scaffold in dopamine metabolism, was probed in the gas phase and interrogated by high-resolution rotational spectroscopy. Herein, three distinct conformers were isolated in a supersonic jet and identified for the first time through an examination of the trend of the rotational constants and the dipole moment selection rules. Additionally, we examined the plausible relaxation pathways of the low-energy conformers of DOPAC, which helped us to claim the indirect detection of two additional conformers, providing conclusive experimental evidence of the flexible nature of this biomolecule. The current investigation sheds some light on the differences between jet-cooled rotational experiments and matrix-isolation infrared spectroscopy.

Subtle hydrogen bonds: benchmarking with OH stretching fundamentals of vicinal diols in the gas phase

The theoretical description of spectral signatures for weakly bound hydrogen contacts between alcohol groups is challenging and remains poorly characterised. By combining Raman jet spectroscopy with appropriately scaled harmonic DFT predictions and relaxation path analyses for 16 vicinal diols (ethylene glycol (ethane-1,2-diol), propane-1,2-diol, 3,3,3-trifluoro-propane-1,2-diol, rac-butane-2,3-diol, 2-methyl-propane-1,2-diol, 2-methyl-butane-2,3-diol, pinacol (2,3-dimethyl-butane-2,3-diol), 3-butene-1,2-diol, 1-phenyl-ethane-1,2-diol, trans-cyclobutane-1,2-diol, trans-cyclopentane-1,2-diol, trans-cyclohexane-1,2-diol, trans-cycloheptane-1,2-diol, cis-cyclohexane-1,2-diol, 1-(1-hydroxy-1-methylethyl)-cyclopentanol and [1,1'-bicyclopentyl]-1,1'-diol), 69 conformational assignments become possible in a two-tier approach with a 5 diol training and an 11 diol test set. The latter reveals systematic deviations for ring strain and secondary π interactions, but otherwise a remarkably robust correction and correlation model based on hybrid DFT with a minimally augmented triple-zeta basis set is obtained, whereas GGA functionals perform significantly worse. Raw experimental data in the 3560-3700 cm^-1 wavenumber range as well as computed geometries of all conformations invite further vibrational and structural benchmarking at the onset of hydrogen bonding. Beyond this diol-probed threshold, the accurate prediction of hydrogen bond induced shifts of different magnitudes remains one of the challenges for DFT functionals.

Conformational Space, IR-Induced, and UV-Induced Chemistry of Carvacrol Isolated in a Low-Temperature Argon Matrix

In this work, monomers of carvacrol (5-isopropyl-2-methylphenol), a natural monoterpene exhibiting wide range bioactivity, were trapped in a cryogenic argon matrix and characterized by infrared spectroscopy, while quantum chemical calculations at the B3LYP and MP2 levels were employed to characterize the conformational landscape of the isolated molecule. Four conformers have been localized on the potential energy surface, and the factors accounting for their relative stability were analyzed. The two most stable conformers of carvacrol, differing in the relative orientation of the isopropyl group and both having the OH group pointing away from the vicinal methyl fragment, were identified in the cryomatrix for the first time. The individual spectral signatures of the two conformers were distinguished based on the change in their relative abundance induced by exposing the matrix to broadband infrared light. Matrix-isolated carvacrol was also irradiated with broadband UV light (λ > 200 nm), which resulted in the cleavage of the OH group. Recombination of the released H atom at the ortho- or para-position of the ring resulted in the formation of alkyl-substituted cyclohexadienones. These were found to undergo subsequent valence and open-ring isomerizations, leading, respectively, to the formation of a Dewar isomer and open-chain conjugated ketenes. Decarbonylation of the photoproducts was also observed for longer irradiation times. A mechanistic analysis of the observed photochemical transformations is presented.

UV-induced radical formation and isomerization of 4-methoxyindole and 5-methoxyindole

Monomers of 4-methoxyindole and 5-methoxyindole trapped in low-temperature xenon matrices (15-16 K) were characterized by IR spectroscopy, in separate experiments. Each compound was shown to adopt the most stable 1H-tautomeric form. The photochemistry of the matrix-isolated compounds was then investigated by exciting the matrices with narrowband UV light with λ ≤ 305 nm. Two main photoproducts, similar for each compound, have been detected: (1) 4-methoxy- or 5-methoxy-indolyl radical, resulting from cleavage of the N-H bond; (2) 3H-tautomers (4-methoxy- or 5-methoxy-) with the released hydrogen atom reconnected at the C3 ring carbon atom. The presence of the two types of photoproducts in the UV-irradiated matrices was confirmed by comparison of their B3LYP/6-311++G(d,p) calculated IR spectra with the experimental spectra emerging upon the irradiations. The mechanism of the observed phototransformations was elucidated by Natural Bond Orbital and Natural Resonance Theory computations on the methoxy-substituted indolyl radicals resulting from the N-H bond cleavage. The highest natural atomic spin densities were predicted at the C3 and N1 positions of the indolyl ring, corresponding to a predominance of the resonance structures with the radical centres located at these two atoms. As a whole, the obtained experimental and theoretical data allowed establishing a general pattern for the photochemistry of methoxyindoles under matrix-isolation conditions.

Toward Fully Unsupervised Anharmonic Computations Complementing Experiment for Robust and Reliable Assignment and Interpretation of IR and VCD Spectra from Mid-IR to NIR: The Case of 2,3-Butanediol and trans-1,2-Cyclohexanediol

The infrared (IR) and vibrational circular dichroism (VCD) spectra of 2,3-butanediol and trans-1,2-cyclohexanediol from 900 to 7500 cm^–1 (including mid-IR, fundamental CH and OH stretchings, and near-infrared regions) have been investigated by a combined experimental and computational strategy. The computational approach is rooted in density functional theory (DFT) computations of harmonic and leading anharmonic mechanical, electrical, and magnetic contributions, followed by a generalized second-order perturbative (GVPT2) evaluation of frequencies and intensities for all the above regions without introducing any ad hoc scaling factor. After proper characterization of large-amplitude motions, all resonances plaguing frequencies and intensities are taken into proper account. Comparison of experimental and simulated spectra allows unbiased assignment and interpretation of the most interesting features. The reliability of the GVPT2 approach for OH stretching fundamentals and overtones is confirmed by the remarkable agreement with a local mode model purposely tailored for the latter two regions. Together with the specific interest of the studied molecules, our results confirm that an unbiased assignment and interpretation of vibrational spectra for flexible medium-size molecules can be achieved by means of a nearly unsupervised reliable, robust, and user-friendly DFT/GVPT2 model.

The reduced cohesion of homoconfigurational 1,2-diols

Homochiral encounters of vicinal diols are blocked from relaxing to the heterochiral global minimum dimer structure in supersonic jet expansions.

Anharmonic calculations of frequencies and intensities of OH stretching vibrations of (R)-1,3-butanediol conformers in the fundamentals and first overtones by density functional theory

The frequencies and absorption intensities of the five kinds of conformers of 1,3-butanediol with the same carbon skeleton (GG') were calculated by anharmonic calculation for the fundamentals and first overtones of OH stretching vibrations. The four kinds of conformers form intramolecular hydrogen bonds and one conformer did not. Intramolecular hydrogen bond formation shifted the frequency of fundamental and first overtone of H-bonding OH stretching vibration to the lower frequency. The absorption intensities of the fundamentals as well as the vibrational anharmonicities increased upon hydrogen bond formation, while the intensities of first overtones decreased. The differences of conformers were clearly seen in the frequencies of the first overtones of free OH.

Association of symmetrical alkane diols with pyridine: DFT/GIAO calculation of 1 H NMR chemical shifts

Proton nuclear magnetic resonance (NMR) shifts of the free diol and of its 1 : 1 and 1 : 2 hydrogen-bonded complexes with pyridine have been computed for five symmetrical alkane diols on the basis of density functional theory, by applying the gauge-including atomic orbital method to geometry-optimized conformers. For certain conformers, intramolecular OH···OH interactions, evidenced by high NMR OH proton shifts, are further enhanced on going from the free diol to the corresponding 1 : 1 diol/pyridine complex. This is confirmed by atoms-in-molecules and non-covalent interaction plots. The computed OH and CH proton shifts for the diol and the two complexes correlate well with values obtained by analysing data from the NMR titration of the diols in benzene against pyridine. Shift values for the diols in neat pyridine are calculated by weighting the shifts of the various protons in the three forms (free diol, 1 : 1 and 1 : 2 diol/pyridine complexes) according to the experimentally determined association constants. The results are in good agreement with those observed, and after empirical scaling, the root mean square difference is 0.18 ppm. Copyright © 2016 John Wiley & Sons, Ltd.

The Interplay Between Conformation and Absolute Configuration in Chiral Electron Dynamics of Small Diols

A competition between chiral characteristics alternatively attributable to either conformation or to absolute configuration is identified. Circular dichroism associated with photoexcitation of the outer orbital of configurational enantiomers of 1,3- and 2,3-butanediols has been examined with a focus on the large changes in electron chiral asymmetry produced by different molecular conformations. Experimental gas-phase measurements offer support for the theoretical modeling of this chiroptical effect. A surprising prediction is that a conformationally produced pseudo-enantiomerism in 1,3-butanediol generates a chiral response in the frontier electron dynamics that outweighs the influence of the permanent configurational handedness established at the asymmetrically substituted carbon. Induced conformation, and specifically induced conformational chirality, may thus be a dominating factor in chiral molecular recognition in such systems.

Synthesis, Spectroscopic, Structural and Quantum Chemical Studies of a New Imine Oxime and Its Palladium(II) Complex: Hydrolysis Mechanism

In this work, we report synthesis, crystallographic, spectroscopic and quantum chemical studies of a new imine oxime, namely (4-nitro-phenyl)-(1-phenyl-ethylimino)-acetaldehyde oxime (nppeieoH). Spectroscopic and X-ray diffraction studies showed that nppeieoH is hydrolyzed in aqueous solution, forming nitroisonitrosoacetophenone (ninap) and the hydrolysis product binds to Pd(II) to yield [Pd(nppeieo)(ninap)]. The mechanism of the hydrolysis reaction has been theoretically investigated in detail, using density functional theory (DFT) with the B3LYP method. The vibrational and the electronic spectra of nppeieoH and its Pd(II) complex, the HOMO and LUMO analysis, Mulliken atomic charges and molecular electrostatic potential were also performed. The predicted nonlinear optical properties of both compounds are higher than those of urea.

Conformational preferences of 3,4-dihydroxyphenylacetic acid (DOPAC)

The conformational space of 3,4-dihydroxyphenylacetic acid (DOPAC), an important dopamine metabolite, has been investigated by quantum chemical methods (B3LYP and MP2, with the 6-311++G(d,p) basis set) and matrix-isolation infrared spectroscopy. Detailed analysis of the calculated potential energy surfaces of the molecule led to identification of thirteen unique conformers, all of them showing the acetic acid side chain out of the aromatic ring plane by 60-95°. According to the calculated Gibbs energies, the five lowest energy conformers make up 99.7% of the conformational mixture at 298.15K, exhibiting individual populations falling between 16% and 24%. The main conformational trends of this molecule were interpreted on the grounds of a thorough analysis of the structural parameters and by the application of the Natural Bond Orbital theory. The role of the intramolecular interactions on the relative stability and structure of the conformers was also investigated. The infrared spectrum of DOPAC was registered after isolation of its monomers in argon and xenon matrices. Only one of DOPAC forms populated in the gas phase could be trapped in both matrix gases. This result is in agreement with the predicted low energy barriers for conformational isomerization and is also supported by annealing experiments. The spectra of matrix-isolated model compounds, phenylacetic acid and catechol, were studied under the same experimental conditions. These data were used as references and assisted in the interpretation of the results obtained for DOPAC.

Conformations of n-butyl imidazole: matrix isolation infrared and DFT studies

Conformations of n-butyl imidazole (B-IMID) were studied using matrix isolation infrared spectroscopy by trapping in argon, xenon and nitrogen matrixes using an effusive nozzle source. The experimental studies were supported by DFT computations performed at the B3LYP/6-311++G(d,p) level. Computations identified nine unique minima for B-IMID, corresponding to conformers with tg(±)tt, tg(±)g(∓)t, tg(±)g(±)t, tg(±)tg(±), tg(±)tg(∓), tg(±)g(∓)g(∓), tg(±)g(±)g(±), tg(±)g(∓)g(±) and tg(±)g(±)g(∓) structures, given in order of increasing energy. Computations of the transition state structures connecting the higher energy conformers to the global minimum, tg(±)tt structure were carried out. The barriers for the conformer inter-conversion were found to be ∼2 kcal/mol. Natural Bond Orbital (NBO) analysis was performed to understand the reasons for conformational preferences in B-IMID.

A combined experimental and theoretical investigation of a new imineoxime and its palladium(II) and platinum(II) complexes: synthesis, structural characterization and spectroscopic properties

A new imineoxime compound {(1E,2E)-(2-hydroxy-ethylimino)-naphthalene-2yl-ethanal oxime (heineoH)} and its palladium(II) and platinum(II) complexes ([M(heineo)2]) have been synthesized and characterized by IR, NMR, UV-vis, elemental analysis, mass spectra and X-ray single crystal diffraction. [Pt(heineo)2] was obtained as a single crystal, while [Pd(heineo)2] was synthesized as a polycrystalline powder. The X-ray diffraction analysis of the [Pt(heineo)2] indicated that the platinum(II) ion is coordinated by two heineo ligands in a distorted square-planar geometry. DFT (B3LYP/6-311++G(d,p) and LANL2DZ) calculations on the ligand and its complexes were carried out to correlate the geometry and vibrational and electronic properties. Additionally, heineoH is fluorescent in EtOH at room temperature, but the fluorescence is quenched in the case of the metal complexes.

Structure of isolated 1,4-butanediol: combination of MP2 calculations, NBO analysis, and matrix-isolation infrared spectroscopy

Theoretical calculations at the MP2 level, NBO and AIM analysis, and matrix-isolation infrared spectroscopy have been used to investigate the structure of the isolated molecule of 1,4-butanediol (1,4-BDO). Sixty-five structures were found to be minima on the potential energy surface, and the three most stable forms are characterized by a folded backbone conformation leading to the formation of an intramolecular H-bond. To better characterize the intramolecular interactions and particularly the hydrogen bonds, natural bond orbital analysis (NBO) was performed for the four most stable conformers, and was further complemented with an atoms-in-molecules (AIM) topological analysis. Infrared spectra of 1,4-BDO isolated in low-temperature argon and xenon matrixes show a good agreement with a population-weighted mean theoretical spectrum, and the spectral features of the conformers expected to be trapped in the matrixes were observed experimentally. Annealing the xenon matrix from 20 to 60 K resulted in significant spectral changes, which were interpreted based on the barriers to intramolecular rotation. An estimation of the intramolecular hydrogen bond energy was carried out following three different methodologies.

1H NMR spectra of ethane-1,2-diol and other vicinal diols in benzene: GIAO/DFT shift calculations

The proton NMR spectra of several 1,2-diols in benzene have been analysed so as to associate each magnetically nonequivalent proton with its chemical shift. The shifts and coupling constants of the OH and methylene protons of ethane-1,2-diol have been determined in a wide range of solvents. The conformer distribution and the proton NMR shifts of these 1,2-diols in benzene have been computed on the basis of density functional theory. The solvent is included using the integral-equation-formalism polarizable continuum model implemented in Gaussian 09. Relative Gibbs energies for all stable conformers are calculated at the Perdew, Burke and Enzerhof (PBE)0/6-311 + G(d,p) level, and shifts are calculated using the gauge-including atomic orbital method with the PBE0/6-311 + G(d,p) geometry but using the cc-pVTZ basis set. Previous calculations on ethane-1,2-diol and propane-1,2-diol have been corrected and extended. New calculations on tert-butylethane-1,2-diol, phenylethane-1,2-diol, butane-2,3-diols (dl and meso) and cyclohexane-1,2-diols (cis and trans) are presented. Overall, the computed NMR shifts are in good agreement with experimental values for the OH protons but remain systematically high for CH protons. Some results based on the Gaussian 03 solvation model are included for comparison.