Kwang-Im Oh

Understanding how solutes drive water restructuring between crystallization and vitrification remains a central challenge in cryopreservation. Here, we quantitatively compare how two common cryoprotectants, dimethyl sulfoxide (DMSO) and ethylene glycol (EG), modulate water structure at low temperatures. Cryogenic IR spectroscopy of the O–D stretching mode combined with global spectral decomposition reveals a sequential transition from liquid water to vitreous water (VW) to crystalline ice, enabling direct extraction of phase populations as a function of composition and temperature. Both solutes follow this common pathway, with VW emerging as a shared intermediate. The key difference lies in VW stabilization: DMSO induces heterogeneous hydration in which hydrophilic S═O and hydrophobic methyl groups sample distinct local environments, promoting DMSO-rich microdomains that stabilize VW and fully suppress ice formation at 47 wt %. EG maintains a more homogeneous hydration environment, resulting in a smaller VW fraction and partial crystallization. Despite these different macroscopic outcomes, both cryoprotectants employ the same hydrophilic and hydrophobic interactions operating within different molecular architectures. These findings demonstrate that vitrification behavior can be understood at the level of individual molecular architectures, where the spatial arrangement of hydrophilic and hydrophobic motifs shapes local hydration topology, providing a topology-informed basis for rational cryoprotectant design.

In operando monitoring of chemical reactions is crucial for understanding reaction kinetics and mechanisms. Conventional attenuated total reflection (ATR)-IR probes offer real-time measurement capabilities but are limited by shallow penetration depths of the evanescent wave, restricting detection mainly to high-concentration species and surface-localized events. To overcome these limitations, we built an endoscopic Fourier-transform infrared spectroscopy (FT-IR) probe for in operando chemical analysis and direct observation of chemical reactions proceeding inside reaction vessels. An endoscopic probe constructed with hollow-core optical fibers enables transmittance measurements inside reactors and real-time acquisition of mid-IR absorption spectra from the initiation to the endpoint continuously. A key feature of this endoscopic probe is its adjustable optical path length, which allows absorbance optimization across a wide dynamic range, including under dilute conditions. The probe's performance was validated by measuring the C ═ O bond absorbance in acetone solutions across varying pathlengths and concentrations, demonstrating compliance with the Beer-Lambert law. To demonstrate its applicability for reaction monitoring, the probe was applied to monitor the Schiff base formation reaction between acetone and benzylamine in real time, capturing the transformation from C ═ O to C ═ N bonds and the appearance of the O-H stretching modes associated with water formation. Reaction time-resolved IR spectra were further analyzed using two-dimensional correlation spectroscopy (2D-COS), which revealed that water formation precedes imine stabilization, providing mechanistic insight into the condensation process. This compact and modular probe demonstrates high spectral accuracy and full compatibility with conventional FT-IR spectrometers. It offers a promising approach for real-time quantitative monitoring of chemical reactions, particularly for detecting low-concentration intermediates and elucidating reaction kinetics and mechanisms.

In aqueous media, lignin β-O-4 linkages undergo photooxidation via the stepwise plasmon-driven hydrogen atom abstraction and degradation (p-HAADe) mechanism, leading to cleavage of C_α–C_β and C–O bonds into two distinct subunits.

Distal-less 3 (Dlx3) is a homeobox-containing transcription factor and plays a crucial role in the development and differentiation process. Human Dlx3 consists of two transactivation domains and a homeobox domain (HD) that selectively binds to the consensus site (5′-TAATT-3′) of the DNA duplex. Here, we performed chemical shift perturbation experiments on Dlx3-HD in a complex with a 10-base-paired (10-bp) DNA duplex under various salt conditions. We also acquired the imino proton spectra of the 10-bp DNA to monitor the changes in base-pair stabilities during titration with Dlx3-HD. Our study demonstrates that Dlx3-HD selectively recognizes its consensus DNA sequences through the α3 helix and L1 loop regions with a unique dynamic feature. The dynamic properties of the binding of Dlx3-HD to its consensus DNA sequence can be modulated by varying the salt concentrations. Our study suggested that this unique structural and dynamic feature of Dlx3-HD plays an important role in target DNA recognition, which might be associated with tricho-dento-osseous syndrome.

Chemically modified nucleobases are thought to be important for therapeutic purposes as well as diagnosing genetic diseases and have been widely involved in research fields such as molecular biology and biochemical studies. Many artificially modified nucleobases, such as methyl, halogen, and aryl modifications of purines at the C8 position and pyrimidines at the C5 position, are widely studied for their biological functions. DNA containing these modified nucleobases can form non-canonical helical structures such as Z-DNA, G-quadruplex, i-motif, and triplex. This review summarizes the synthesis of chemically modified nucleotides: (i) methylation, bromination, and arylation of purine at the C8 position and (ii) methylation, bromination, and arylation of pyrimidine at the C5 position. Additionally, we introduce the non-canonical structures of nucleic acids containing these modifications.

Carr–Purcell–Meiboom–Gill (CPMG) relaxation dispersion spectroscopy is commonly used for quantifying conformational changes of protein in μs-to-ms timescale transitions. To elucidate the dynamics and mechanism of protein binding, parameters implementing CPMG relaxation dispersion results must be appropriately determined. Building an analytical model for multi-state transitions is particularly complex. In this study, we developed a new global search algorithm that incorporates a random search approach combined with a field-dependent global parameterization method. The robust inter-dependence of the parameters carrying out the global search for individual residues (GSIR) or the global search for total residues (GSTR) provides information on the global minimum of the conformational transition process of the Zα domain of human ADAR1 (hZα_ADAR1)–DNA complex. The global search results indicated that a α-helical segment of hZα_ADAR1 provided the main contribution to the three-state conformational changes of a hZα_ADAR1—DNA complex with a slow B–Z exchange process. The two global exchange rate constants, k_ex and k_ZB, were found to be 844 and 9.8 s⁻¹, respectively, in agreement with two regimes of residue-dependent chemical shift differences—the “dominant oscillatory regime” and “semi-oscillatory regime”. We anticipate that our global search approach will lead to the development of quantification methods for conformational changes not only in Z-DNA binding protein (ZBP) binding interactions but also in various protein binding processes.

Aqueous cosolvent systems (ACoSs) are mixtures of small polar molecules such as amides, alcohols, dimethyl sulfoxide, or ions in water. These liquids have been the focus of fundamental studies due to their complex intermolecular interactions as well as their broad applications in chemistry, medicine, and materials science. ACoSs are fully miscible at the macroscopic level but exhibit nanometer-scale spatial heterogeneity. ACoSs have recently received renewed attention within the chemical physics community as model systems to explore the relationship between intermolecular interactions and microscopic liquid–liquid phase separation. In this perspective, we provide an overview of ACoS spatial segregation, dynamic heterogeneity, and multiscale relaxation dynamics. We describe emerging approaches to characterize liquid microstructure, H-bond networks, and dynamics using modern experimental tools combined with molecular dynamics simulations and network-based analysis techniques.