Juan Zhao

Mode-specific intramolecular vibrational energy redistribution is a key elementary process in the earliest molecular response of energetic materials, yet a quantitative, mode-resolved description of its microscopic driving forces remains challenging. Here we combine density functional theory (DFT), ab initio molecular dynamics (AIMD), normal-mode projection, spectral energy density analysis (SED), and a perturbative mode-coupling model to resolve vibrational energy flow in isolated nitromethane after selective excitation of individual normal modes. The simulations reveal a nonrandom, hierarchical energy-flow network in which low- and midfrequency modes funnel energy toward a small set of accepting modes. Spectral fingerprints of acceptor-mode momenta show that most primary transfer channels are not fundamental-fundamental resonances but overtone-fundamental resonances mediated by cubic anharmonicity. This mechanism naturally explains apparently cross-symmetry transfer: the overtone of an A″ mode transforms as A′ and can therefore couple to A′ acceptor fundamentals. A simplified Fermi’s Golden Rule model, parametrized by bilinear and third-order anharmonic force constants and finite-time Lorentzian detuning factors, predicts the dominant primary acceptors observed in AIMD. The isolated molecule exhibits coherent quantum-beating-like energy oscillations whose periods are governed by the detuning of the corresponding resonance condition. These results recast vibrational energy transfer in nitromethane as a symmetry-filtered anharmonic resonance network and provide a transferable framework for identifying early energy-flow bottlenecks in energetic molecules.

The microscopic unfolding process of a cytosine-rich DNA forming i-motif by hemi-protonated base pairs is related to gene regulation. However, the detailed thermal unfolding mechanism and the protonation/deprotonation status of site-specific cytosine in DNA in a physiological environment are still obscure. To address this issue, a vibration-enhanced CC probe tagged on 5′E terminal cytosine of human telomere i-motif DNA was examined using linear and nonlinear infrared (IR) spectroscopies and quantum-chemistry calculations. The CC probe extended into the major groove of the i-motif was found using nonlinear IR results only to introduce a minor steric effect on both steady-state structure and local structure dynamics; however, its IR absorption profile effectively reports the cleavage of the hemi-protonated base pair of C₁–C₁₃ upon the unfolding with C₁ remaining protonated. The temperature mid-point (T_m) of the local transition reported using the CC tag was slightly lower than the T_m of global transition, and the enthalpy of the former exceeds 60% of the global transition. It is shown that the base-pair unraveling is noncooperative, with outer base pairs breaking first and being likely the rate limiting step. Our results offered an in-depth understanding of the macroscopic unfolding characteristics of the i-motif DNA and provided a nonlinear IR approach to monitoring the local structural transition and dynamics of DNA and its complexes.

The time-dependent quantum wave packet (TDWP) and quasi-classical trajectory (QCT) are the basic research methods of reaction dynamics. Utilizing these two methods, the total reaction probability (J = 0), integral cross section (ICS), and rate parameter for the C⁺(²P) + SH(X²Π)(v = 0, 1, 2, 3) → H(²S) + CS⁺(X²Σ⁺) reactions are calculated on an accurate potential energy surface [Zhang et al. Phys. Chem. Chem. Phys. 2022, 24, 1007]. The results of QCT are slightly different from those of the TDWP in value, but the trend is consistent. They are also weakly dependent on the initial vibrational excitation of SH. The state-to-state reaction probability and ICS at fixed collision energies (0.1, 0.3, 0.5, and 0.7 eV) are first calculated using QCT methods. It is hoped that our work can attract experimentalists to study the dynamics of this interesting but rarely discussed system.

The “specific” interaction between metal cations (Na⁺, Ca²⁺, Mg²⁺, and Zn²⁺) and the charged COO⁻ group, and the “non-specific” interaction between these cations and the peptide backbone of a zwitterionic trialanine (Ala3) in aqueous solutions were examined in detail, using linear infrared (IR) absorptions of the COO⁻ symmetric stretching and the amide-II (mainly the C–N stretching) modes as IR probes. Different IR spectral changes in peak positions and intensities of the two IR probes clearly demonstrate their sensitivities to nearby cation distributions in distance and population. Quantum chemistry calculations and molecular dynamics simulations were used to describe the cation–peptide interaction picture. These combined results suggest that Na⁺ and Ca²⁺ tend to bind to the COO⁻ group in the bidentate form, while Mg²⁺ and Zn²⁺ tend to bind to the COO⁻ group in the pseudo-bridging form. The results also show that while all three divalent cations indirectly interact with the peptide backbone with large population, Ca²⁺ and Mg²⁺ can be sometimes distributed very close to the backbone. Such a non-specific cation interaction can be moderately sensed by the C–N stretching of the amide-II mode when cations approach the polar amide CO group, and is also influenced by the NH₃ ⁺ charge group located at the N-terminus. The results suggest that the experimentally observed complication of the Hofmeister cation series shall be understood as a combined specific and non-specific cation–peptide interactions.

Microemulsions are transparent, thermodynamically stable liquid mixtures of oil, water and surfactant. They typically exist in the form of micellar and bicontinuous structures, which appear to be equilibrium systems but are actually complex in structure and are difficult to characterize at the molecular level. In this work, potassium ferrocyanide [K₄Fe(CN)₆] and tungsten hexacarbonyl [W(CO)₆] were chosen as two probe molecules for water and organic phases respectively to simultaneously explore the structures and dynamics of commonly prepared reverse micellar and bicontinuous microemulsion structures using aerosol OT (AOT) as the surfactant and isooctane as the oil phase. Even though these two structures have quite different solvent environments due to the varying geometry and boundary conditions, the steady-state infrared spectra of the CN⁻ stretching mode in the water phase are quite similar, and so are those of the CO stretching mode in the oil phase. However, vibrational and anisotropic relaxation dynamics obtained from infrared pump–probe spectroscopy and spectral diffusion dynamics extracted from two-dimensional infrared spectroscopy of the two infrared chromophores in the two probe molecules are found to be quite sensitive to whether the probe molecules are in pure solvent or in a restricted microemulsion environment. The results in the water phase and oil phase are discussed separately. Our work demonstrated that ultrafast nonlinear infrared spectroscopy can be used to differentiate the structural details at the molecular level for different microemulsion systems.

The vibrational spectra of uracil and thymine in the frequency range of 1600 − 1800 cm ⁻¹ , which mainly contains the C=C and C=O stretching vibration modes, are found to be distinct due to a simple insertion of a methyl group. The nature of these vibrational modes in both molecules was examined through linear infrared spectroscopy and DFT calculations. Anharmonic calculation reveals a generally stronger couplings between pair‐wise C=O modes and also between C=O and C=C modes in uracil than in thymine, agreeing reasonably with previously reported two‐dimensional infrared experimental results. Vibrational transition density cube and vibrational potential energy distributions analyses suggest that methylation causes more localization of the carbonyl stretching modes in thymine, which is the main reason of the observed spectral differences between the two molecules.

Vibrational energy transfer in transition metal complexes with flexible structures in condensed phases is of central importance to catalytical chemistry processes. In this work, two molecules with different metal atoms, M(CO)₅Br (where M = Mn, Re), were used as model systems, and their axial and radial carbonyl stretching modes as infrared probes. The central-metal effect on intramolecular vibrational energy redistribution (IVR) in M(CO)₅Br was investigated in polar and nonpolar solvents. The linear infrared (IR) peak splitting between carbonyl vibrations increases as the metal atom changes from Mn to Re. The waiting-time dependent two-dimensional infrared diagonal- and off-diagonal peak amplitudes reveal a faster IVR process in Re(CO)₅Br than in Mn(CO)₅Br. With the aid of density functional theory (DFT) calculations, the central-metal effect on IVR time linearly correlates with the vibrational coupling strength between the two involved modes. In addition, the polar solvent is found to accelerate the IVR process by affecting the anharmonic vibrational potentials of a solute vibration mode.

In this work, the anionic effect on water structure and on the peptide backbone and water interaction was investigated directly in aqueous solution using thin-layer transmission infrared spectroscopy. The chaotropic anions were found to weaken the water hydrogen-bonding strength and red shift the HOH bending frequency, while the kosmotropic anions were found to strengthen the water hydrogen-bonding network and blue shift the HOH bending frequency. The kosmotropes, especially F^–, blue shift the vibrational frequencies of both amide II and amide III bands of N-methylacetamide (NMA), indicating NMA is in the “salting-in” state; while the chaotropes (Cl^–, NO₃^–, Br^–, I^–, and SCN^–) red shift the frequencies of the two normal modes, indicating NMA is in the “salting-out” state. Furthermore, the changes of the vibrational frequencies of the HOH bending, amide II and III bands were found to generally follow the Hofmeister anionic series. Our results suggest that hydrated anion influences the peptide backbone mainly through the N–H group, but a weak and indirect effect through the amide C═O group also contributes. Thus, these amide modes can be used as vibrational measures of anionic influences on peptide backbone’s hydration state. Our work also suggests that deuteration of the amide unit decreases the sensitivity of the amide II and III vibrational modes in this regard.