Cα−H Bond-Stretching Frequency in Alcohols as a Probe of Hydrogen-Bonding Strength: A Combined Vibrational Spectroscopic and Theoretical Study of n-[1-D]Propanol

Modulating dual carrier-transfer channels and band structure in carbon nitride to amplify ROS storm for enhanced cancer photodynamic therapy

Graphite carbon nitride (CN) eliminates cancer cells by converting H2O2 to highly toxic •OH under visible light. However, its in vivo applications are constrained by insufficient endogenous H2O2, accumulation of OH- and finite photocarriers. We designed Fe/NV-CN, co-modified CN with nitrogen vacancies (NV) and ferric ions (Fe3+). NV and Fe3+, not only adjust the band structure of CN through quantum confinement effect and the altered coupled oscillations of atomic orbitals to facilitates •OH production by oxidizing OH-, but also construct dual carrier-transfer channels for electrons and holes to respective active sites by introducing stepped electrostatic potential and shortening three-electron bonds, thereby involving more carriers in •OH production. Fe/NV-CN, the novel reactor, effectually produces vast •OH under illumination by expanding OH- as the raw material of •OH and augmenting carriers at active sites, which induces cancer cell apoptosis by disrupting mitochondrial function for significant shrinkage of Cal27 cell-induced tumor under illumination. This work provides not only an effective photosensitizer avoiding the accumulation of OH- for cancer therapy but also a novel strategy by constructing dual carrier-transfer channels on semiconductor photosensitizers for improving the therapeutic effect of photodynamic therapy.

An approximation to the vibrational coupled-cluster method for CH-stretching of large molecules: application to naphthalene and anthracene

We propose an approximation to the vibrational coupled-cluster method (VCCM) to describe the CH-stretching region of the vibrational spectrum of large molecules. The vibrational modes of a molecule are divided into two sets: the target set and the bath set. The target set includes the CH stretches and the modes that are strongly coupled with the CH stretches and/or involve strong Fermi resonances with a CH stretch fundamental. The rest of the modes are in the bath set. First, the effective harmonic oscillator (EHO) approximation is invoked for the whole system to obtain the zeroth-order frequencies and modified potentials. The effects of interaction between the bath set and the target sets are included in the modified potential from the EHO calculation. The VCCM equations are constructed with the modified potential from the EHO calculations and for the target set only. The transition energies and intensities are calculated using such a truncated VCCM approximation. The proposed method is applied to calculate the IR spectra of naphthalene and anthracene. The results with three different criteria for selecting the modes in the target set are compared with the experimental IR spectra.

Understanding of the C-H stretch region of infra-red spectroscopy: an analysis of the final state wavefunctions

The nature of the wavefunctions associated with the final states in the CH stretching region of several medium sized molecules is analysed. The number of optically bright transitions is much larger than the number of CH oscillators present in the molecule, and they are spread over a range of about 300 cm^-1. Several of them are clustered together within about 5 cm^-1 with near equal intensities. The final states of all these transitions are superpositions of multiple zeroth order states. In almost all of such superpositions, no single zeroth order state has more than 50% weight. Several multiquantum states, with three to four quanta of excitation dominate the final states, with the CH chromophore contributing only a small weightage. Thus the band structure of the CH stretch region is due to several optically bright transitions whose final states are superpositions of low frequency multiquantum states with the CH chromophore contributing only a small weight to make them spectroscopically active.

Cβ–H stretching vibration as a new probe for conformation of n-propanol in gaseous and liquid states

The CH₂ symmetric stretching mode at the β-carbon position can be used as a new probe for the five conformations of n-propanol.

Mechanistic insights into RNA transphosphorylation from kinetic isotope effects and linear free energy relationships of model reactions

Phosphoryl transfer reactions are ubiquitous in biology and the understanding of the mechanisms whereby these reactions are catalyzed by protein and RNA enzymes is central to reveal design principles for new therapeutics. Two of the most powerful experimental probes of chemical mechanism involve the analysis of linear free energy relations (LFERs) and the measurement of kinetic isotope effects (KIEs). These experimental data report directly on differences in bonding between the ground state and the rate-controlling transition state, which is the most critical point along the reaction free energy pathway. However, interpretation of LFER and KIE data in terms of transition-state structure and bonding optimally requires the use of theoretical models. In this work, we apply density-functional calculations to determine KIEs for a series of phosphoryl transfer reactions of direct relevance to the 2'-O-transphosphorylation that leads to cleavage of the phosphodiester backbone of RNA. We first examine a well-studied series of phosphate and phosphorothioate mono-, di- and triesters that are useful as mechanistic probes and for which KIEs have been measured. Close agreement is demonstrated between the calculated and measured KIEs, establishing the reliability of our quantum model calculations. Next, we examine a series of RNA transesterification model reactions with a wide range of leaving groups in order to provide a direct connection between observed Brønsted coefficients and KIEs with the structure and bonding in the transition state. These relations can be used for prediction or to aid in the interpretation of experimental data for similar non-enzymatic and enzymatic reactions. Finally, we apply these relations to RNA phosphoryl transfer catalyzed by ribonuclease A, and demonstrate the reaction coordinate-KIE correlation is reasonably preserved. A prediction of the secondary deuterium KIE in this reaction is also provided. These results demonstrate the utility of building up knowledge of mechanism through the systematic study of model systems to provide insight into more complex biological systems such as phosphoryl transfer enzymes and ribozymes.

Cα-H carries information of a hydrogen bond involving the geminal hydroxyl group: a case study with a hydrogen-bonded complex of 1,1,1,3,3,3-hexafluoro-2-propanol and tertiary amines

Experimental measurement of the contribution of H-bonding to intermolecular and intramolecular interactions that provide specificity to biological complex formation is an important aspect of macromolecular chemistry and structural biology. However, there are very few viable methods available to determine the energetic contribution of an individual hydrogen bond to binding and catalysis in biological systems. Therefore, the methods that use secondary deuterium isotope effects analyzed by NMR or equilibrium or kinetic isotope effect measurements are attractive ways to gain information on the H-bonding properties of an alcohol system, particularly in a biological environment. Here, we explore the anharmonic contribution to the C-H group when the O-H group of 1,1,1,3,3,3-hexafluoro-2-propanol (HFP) forms an intermolecular H-bond with the amines by quantum mechanical calculations and by experimentally measuring the H/D effect by NMR. Within the framework of density functional theory, ab initio calculations were carried out for HFP in its two different conformational states and their H-bonded complexes with tertiary amines to determine the (13)C chemical shielding, change in their vibrational equilibrium distances, and the deuterium isotope effect on (13)C2 (secondary carbon) of HFP upon formation of complexes with tertiary amines. When C2-OH was involved in hydrogen bond formation (O-H as hydrogen donor), it weakened the geminal C2-H bond; it was reflected in the NMR chemical shift, coupling constant, and the equilibrium distances of the C-H bond. The first derivative of nuclear shielding at C2 in HFP was -48.94 and -50.73 ppm Å(-1) for anti and gauche conformations, respectively. In the complex, the values were -50.28 and -50.76 ppm Å(-1), respectively. The C-H stretching frequency was lower than the free monomer, indicating enhanced anharmonicity in the C-H bond in the complex form. In chloroform, HFP formed a complex with the amine; δC2 was 69.107 ppm for HFP-triethylamine and 68.766 ppm for HFP-d2-triethylamine and the difference in chemical shift, the ΔδC2 was 341 ppb. The enhanced anharmonicity in the hydrogen-bonded complex resulted in a larger vibrational equilibrium distance in C-H/D bonds. An analysis with the Morse potential function indicated that the enhanced anharmonicity encountered in the bond was the origin of a larger isotope effect and the equilibrium distances. Change in vibrational equilibrium distance and the deuterium isotope effect, as observed in the complex, could be used as parameters in monitoring the strength of the H-bond in small model systems with promising application in biomacromolecules.

Fourier Transform Raman and DFT Study of Blue Shift C–H Stretching Vibration of Diazines on Hydrogen Bond Formation

Diazines form various types of hydrogen bonds with water, wherein C–H groups are sometimes involved directly and sometimes indirectly. On hydrogen bond formation, the wavenumber of C–H stretching vibration are usually red shifted (normal hydrogen bond) but blue shift of C–H modes (anomalous hydrogen bond) is also possible in some cases. The Raman spectra of the C–H stretching bands of three diazines; pyrimidine, pyridazine, and pyrazine in pure form and at many concentrations in mole fractions of diazines in the mixture of diazines + water have been measured to analyze the wavenumber shifts experimentally. Theoretical wavenumber shifts have been calculated and NBO analysis has been performed using DFT methods to understand the cause of the shifts. All the four C–H stretching bands of diazines are blue shifted on dilution with water both experimentally and theoretically. The NBO calculations reveal that the cause of the shift is decrease in the charge density in the antibonding orbital of C–H bond on complex formation.

Weak Hydrogen Bonds Make a Difference: Dimers of Jet-Cooled Halogenated Ethanols

Hydrogen-bonded clusters of fluorinated and chlorinated ethanols exhibit rich isomerism in terms of monomer conformation, secondary contacts between the OH and CH groups and the halogen atoms, hydrogen bond topology, chirality recognition and acceptor lone electron pair choice. By expanding the six alcohols involving one to three fluorine or chlorine atoms at the methyl group in a supersonic slit jet expansion and by probing their monomer, dimer and trimer IR spectra between 800 and 4000 cm−1, this isomerism is unravelled in substantial detail. Argon relaxation experiments and complementary cluster Raman spectroscopy provide further information on the individual dimer conformations and on trimer assignments. Energy sequences, helicity- and topology-dependent OH red-shifts, differences between fluorine and chlorine, the influence of dispersion-like interactions and halogen number trends are uncovered and compared to systematic quantum-chemical calculations up to MP2/6–311+G* level. The experimental data provide rigorous reference values for an accurate and balanced quantum-mechanical description of weak hydrogen bond interactions to halogens in the presence of a strong hydrogen bond between oxygen atoms.

Characterization of the unimolecular water elimination reaction from 1-propanol, 3,3,3-propan-1-ol-d3, 3,3,3-trifluoropropan-1-ol, and 3-chloropropan-1-ol

The unimolecular reactions of 1-propanol, 3,3,3-propan-1-ol-d3, 3,3,3-trifluoropropan-1-ol, and 3-chloropropan-1-ol have been studied by the chemical activation technique. The recombination of CH3, CD3, CF3, and CH2Cl radicals with CH2CH2OH radicals at room temperature was used to generate vibrationally excited CH3CH2CH2OH, CD3CH2CH2OH, CF3CH2CH2OH, and CH2ClCH2CH2OH molecules. The principal unimolecular reaction for propanol and propanol-d3 with 90 kcal mol(-1) of vibrational energy is 1,2-H2O elimination with rate constants of 3.4 x 10(5) and 1.4 x 10(5) s(-1), respectively. For CH2ClCH2CH2OH also with 90 kcal mol(-1) of energy, 2,3-HCl elimination with a rate constant of 3.0 x 10(7) s(-1) is more important than 1,2-H2O elimination; the branching fractions are 0.95 and 0.05. For CF3CH2CH2OH with an energy of 102 kcal mol(-1), 1,2-H2O elimination has a rate constant of 7.9 x 10(5) and 2,3-HF elimination has a rate constant of 2.6 x 10(5) s(-1). Density functional theory was used to obtain models for the molecules and their transition states. The frequencies and moments of inertia from these models were used to calculate RRKM rate constants, which were used to assign threshold energies by comparing calculated and experimental rate constants. This comparison gives the threshold energy for H2O elimination from 1-propanol as 64 kcal mol(-1). The threshold energies for 1,2-H2O and 2,3-HCl elimination from CH2ClCH2CH2OH were 59 and 54 kcal mol(-1), respectively. The threshold energies for H2O and HF elimination from CF3CH2CH2OH are 62 and 70 kcal mol(-1), respectively. The structures of the transition states for elimination of HF, HCl, and H2O are compared.

Origin of the Blue Shift of the CH Stretching Band for 2-Butoxyethanol in Water

The blue shift of the isolated CD stretching band of 2-butoxyethanol (C4E1), which is observed for the aqueous solution during the dilution process, has been investigated by infrared (IR) spectroscopy and quantum chemical calculations. Mono-deuterium-labeled C4E1's were employed to remove the severe overlapping among the CH stretching bands. The isolated CD stretching mode of the alpha-methylene in the butoxy group shows a large blue shift, while those of the beta-methylene and methyl groups are not largely shifted. The spectral simulation results for the C4E1/H2O complexes indicate that the large blue shift of the CD stretching band of the butoxy group arises mainly from the hydration of the ether oxygen atom.

Preferred Conformers and Photochemical (λ > 200 nm) Reactivity of Serine and 3,3-Dideutero-Serine In the Neutral Form

A systematic investigation of the conformational potential energy surface of neutral serine [HOCH2CHNH2COOH] and 3,3-dideutero-serine [HOCD2CHNH2COOH] was undertaken, revealing the existence of 61 different minima. The structures and vibrational spectra of the most stable conformers, which were estimated to have relative energies within 7 kJ mol(-1) and account for ca. 93% of the total conformational population at room temperature, were calculated at both the MP2 and DFT/BLYP levels of theory with the 6-311++G(d,p) basis-set and used to interpret the spectroscopic data obtained for the compounds isolated in low-temperature inert matrixes. The assignment of the main spectral infrared features observed in the range 4000-400 cm(-1) to the most stable conformers of serine was undertaken. In addition, UV irradiation (lambda > 200 nm) of the matrix-isolated compounds was also performed, leading to decarboxylation, which was found to be strongly dependent on the conformation assumed by the reactant molecule.