Infrared laser induced conformational and structural changes of glycine and glycine·water complex in low-temperature matrices

Rapid detection of hepatitis B virus DNA level based on interval-point data fusion of infrared spectra

Hepatitis B is an infectious disease cause by the hepatitis B virus (HBV). In recent years, HBV-DNA level clinically gets more attention for its detailed information than other serological markers. Unfortunately, common clinical method for HBV-DNA level detection is limited for its hours consuming. This study combined infrared spectroscopy with machine learning to investigate the feasibility of near-infrared (NIR) and mid-infrared (MIR) spectra for rapid detection of HBV-DNA level. Based on partial least squares-discriminant analysis (PLS-DA) modeling method, the optimal NIR and MIR models and traditional data fusion models were constructed, respectively. Considering inequal weight between interval and point data in machine learning, interval-point data fusion method was used to compare with other traditional date fusion methods. The results of the study illustrate that interval-point data fusion of NIR and MIR spectra combined with PLS-DA modeling can provide a rapid method for HBV-DNA level detection.

Benchmark ab initio proton affinity and gas-phase basicity of α-alanine based on coupled-cluster theory and statistical mechanics

We determine the proton affinity (PA) and gas-phase basicity (GB) of amino acid α-alanine at a chemically accurate level by performing explicitly-correlated CCSD(T)-F12b/aug-cc-pVDZ geometry optimizations and normal mode vibrational frequency calculations as well as CCSD(T)-F12b/aug-cc-pVTZ energy computations at the possible neutral and protonated geometries. Temperature effects at 298.15 K considering translational, rotational, and vibrational enthalpy and entropy corrections are obtained via standard statistical mechanics utilizing the molecular geometries and the harmonic vibrational energy levels. Both the amino nitrogen (N) and the carbonyl oxygen (O) atoms are proven to be potential protonation sites and a systematic conformational search reveals 3 N- and 9 O-protonated conformers in the 0.00-7.88 and 25.43-30.43 kcal/mol energy ranges at 0 K, respectively. The final computed PA and GB values at (0)298.15 K in case of N-protonation are (214.47)216.80 and 207.07 kcal/mol, respectively, whereas the corresponding values for O-protonation are (189.04)190.63 and 182.31 kcal/mol. The results of the benchmark high-level coupled-cluster computations are utilized to assess the accuracy of several lower-level cost-effective methods such as MP2 and density functional theory with various functionals (SOGGA11-X, M06-2X, PBE0, B3LYP, M06, TPSS).

MULTIMODE Calculations of Vibrational Spectroscopy and 1d Interconformer Tunneling Dynamics in Glycine Using a Full-Dimensional Potential Energy Surface

A full-dimensional, permutationally invariant polynomial potential energy surface for glycine recently reported (R. Conte et al., J. Chem. Phys. 2020, 153, 244301) is used with the code MULTIMODE to determine the IR absorption spectra for Conformers I and II using a new separable dipole moment function. The calculated spectra agree well with the experimental ones. The full-dimensional nature of the potential allows us also to examine dynamical results, such as tunneling rates. Remarkably, using a one-dimensional path based on the potential energy surface to estimate the tunneling rate from Conformer VI to Conformer I, good agreement is found with the recent experimental measurement. Finally a brief comparison of our potential energy surface with a recently reported sGDML one is made.

Bond-Breaking/Bond-Forming Reactions by Vibrational Excitation: Infrared-Induced Bidirectional Tautomerization of Matrix-Isolated Thiotropolone

Infrared vibrational excitation is a promising approach for gaining exceptional control of chemical reactions, in ways that cannot be attained via thermal or electronic excitation. Here, we report an unprecedented example of a bond-breaking/bond-forming reaction by vibrational excitation under matrix isolation conditions. Thiotropolone monomers were isolated in cryogenic argon matrices and characterized by infrared spectroscopy and vibrational computations (harmonic and anharmonic). Narrowband near-infrared irradiations tuned at frequencies of first CH stretching overtone (5940 cm^-1) or combination modes (5980 cm^-1) of the OH tautomer, the sole form of the compound that exists in the as-deposited matrices, led to its conversion into the SH tautomer. The tautomerization in the reverse direction was achieved by vibrational excitation of the SH tautomer with irradiation at 5947 or 5994 cm^-1, corresponding to the frequencies of its CH stretching combination and overtone modes. This pioneer demonstration of bidirectional hydroxyl ↔ thiol tautomerization controlled by vibrational excitation creates prospects for new advances in vibrationally induced chemistry.

Conformational isomerizations triggered by vibrational excitation of second stretching overtones

Vibrational excitation using frequency-tunable IR laser light has been developed as a powerful tool for selective manipulation of molecular conformations. In this methodology, vibrational excitation has been typically applied to the first stretching overtones (∼80 kJ mol^-1) but also to the fundamental modes (∼40 kJ mol^-1). Here, we demonstrate that selective conformational isomerizations are also achieved using excitation to second stretching overtones (∼120 kJ mol^-1). The extremely weak absorptions of the second stretching overtones of molecules isolated in low-temperature matrices were measured for the first time; here using three prototype molecules: hydroxyacetone (HA), glycolic acid (GAc) and glycolamide (GAm). Benchmarking of computed anharmonic IR spectra showed that the B3LYP/SNSD method provides the best agreement with experimental frequencies of the ν(OH), 2ν(OH) and 3ν(OH) modes for the studied molecules in argon matrices. Selective irradiation at the 3ν(OH) frequencies (9850-10 500 cm^-1) of HA, GAc and GAm monomers in argon matrices at 15 K successfully triggers their conformational isomerization. These results open the door to extend control over conformations separated by higher barriers and to induce other transformations not energetically accessible by excitation to the fundamental or first stretching overtone modes.

The infrared study of fluoroform + methyl fluoride mixtures in argon and nitrogen matrices. Evidence of nonlinear blue-shifting complex formation

The FTIR spectra of fluoroform + methyl fluoride mixtures trapped in argon and nitrogen matrices are studied at T~10-30 K. Spectroscopic changes observed in the region of the CH stretching mode of fluoroform are typical for weak blue shifting H - bonds of CH⋯F type. The degeneracy lifting effect found on E - type bands of fluoroform interacted with methyl fluoride suggests the complex formation of a nonlinear form. The experimental results are confirmed by ab initio calculations of fluoroform + methyl fluoride based on the second order Møller-Plesset theory of perturbations utilizing advanced basis set. Nonlinear complexes are stabilized by the basic CH⋯F interaction and additionally by van der Waals-type CD⋯FC contacts between deuterated methyl fluoride and fluoroform.

Nunes C, Fausto R, Reva I. Conformational control over an aldehyde fragment by selective vibrational excitation of interchangeable remote antennas

We apply vibrational antennas (OH or NH₂ group) to achieve unprecedented conformational control over the heavy aldehyde fragment in 2-formyl-2H-azirine, using selective vibrational excitations of the OH or NH₂ stretching overtones and combination modes.