Carbonyl stretching band in amides as Lorentz oscillator. Insights into anharmonicity and local environment in the liquid phase from NIR and MIR spectra of N-methylformamide and di-N,N-methylformamide.

We investigated the anharmonicity and intermolecular interactions of N-methylformamide (NMF) and di-N,N-methylformamide (DMF) in the neat liquid phase with particular interest in the amide bands. The vibrational spectra, complex refractive index, and complex electric permittivity were determined in in the mid- (MIR) and near-infrared (NIR) regions (11,500-560 cm-1; 870-17857 nm). Dispersion analysis was based on the Classical Damped Harmonic Oscillator (CDHO) and simultaneous modelling of the real and imaginary components of the spectra. This data delivered insights into the vibrational energy dissipation and self-association in liquid amides. Identification of the MIR and NIR bands was based on anharmonic GVPT2//B3LYP/6-311++G(d,p) calculations. DMF and NMF follow distinct self-association, evidenced in the MIR fingerprint by the two components of the νCO, the analog of the Amide I band. These conclusions are supported by the structural information derived from the NIR spectra. Furthermore, the contribution of overtones and combination bands in the MIR spectra of amides was examined. The conclusions on molecular interactions and structural dynamics of NMF and DMF contribute to a deeper understanding of the effects of changes in the local environment of the amide group.

Unraveling the complexity: Advanced methods in analyzing DNA, RNA, and protein interactions.

Exploring the intricate interplay within and between nucleic acids, as well as their interactions with proteins, holds pivotal significance in unraveling the molecular complexities steering cancer initiation and progression. To investigate these interactions, a diverse array of highly specific and sensitive molecular techniques has been developed. The selection of a particular technique depends on the specific nature of the interactions. Typically, researchers employ an amalgamation of these different techniques to obtain a comprehensive and holistic understanding of inter- and intramolecular interactions involving DNA-DNA, RNA-RNA, DNA-RNA, or protein-DNA/RNA. Examining nucleic acid conformation reveals alternative secondary structures beyond conventional ones that have implications for cancer pathways. Mutational hotspots in cancer often lie within sequences prone to adopting these alternative structures, highlighting the importance of investigating intra-genomic and intra-transcriptomic interactions, especially in the context of mutations, to deepen our understanding of oncology. Beyond these intramolecular interactions, the interplay between DNA and RNA leads to formations like DNA:RNA hybrids (known as R-loops) or even DNA:DNA:RNA triplex structures, both influencing biological processes that ultimately impact cancer. Protein-nucleic acid interactions are intrinsic cellular phenomena crucial in both normal and pathological conditions. In particular, genetic mutations or single amino acid variations can alter a protein's structure, function, and binding affinity, thus influencing cancer progression. It is thus, imperative to understand the differences between wild-type (WT) and mutated (MT) genes, transcripts, and proteins. The review aims to summarize the frequently employed methods and techniques for investigating interactions involving nucleic acids and proteins, highlighting recent advancements and diverse adaptations of each technique.

Insight into the effects of ultrasound-assisted intermittent tumbling on the gelation properties of myofibrillar proteins: Conformational modifications, intermolecular interactions, rheological properties and microstructure.

The aim of the present study was to evaluate the effects of ultrasound-assisted intermittent tumbling (UT) at 300 W, 20 kHz and 40 min on the conformation, intermolecular interactions and aggregation of myofibrillar proteins (MPs) and its induced gelation properties at various tumbling times (4 and 6 h). Raman results showed that all tumbling treatments led the helical structure of MPs to unfold. In comparison to the single intermittent tumbling treatment (ST), UT treatment exerted more pronounced effects on strengthening the intermolecular hydrogen bonds and facilitating the formation of an ordered ß-sheet structure. When the tumbling time was the same, UT treatment caused higher surface hydrophobicity, fluorescence intensity and disulfide bond content in the MPs, inducing the occurrence of hydrophobic interaction and disulfide cross-linking between MPs molecules, thus forming the MPs aggregates. Additionally, results from the solubility, particle size, atomic force microscopy and SDS-PAGE further indicated that, relative to the ST treatment, UT treatment was more potent in promoting the polymerization of myosin heavy chain. The MPs aggregates in the UT group were more uniform than those in the ST group. During the gelation process, the pre-formed MPs aggregates in the UT treatment increased the thermal stability of myosin, rendering it more resistant to heat-induced unfolding of the myosin rod region. Furthermore, they improved the protein tail-tail interaction, resulting in the formation of a well-structured gel network with higher gel strength and cooking yield compared to the ST treatment.

Theoretical study on multi-perspective interaction analysis of ADN and ADN-H2O-CH3OH solutions.

CONTEXT: Revealing the mechanism of intermolecular interactions in dinitroamine ammonium (ADN)-based liquid propellants and exploring the reasons for their performance changes, multi-perspective interaction analyses of ADN and ADN-water (H2O)-methanol (CH3OH) solutions have been conducted via theoretical methods. The band structure, density of states (DOS), surface electrostatic potential (ESP), Hirshfeld surface, reduced density gradient (RDG), AIM topological analysis, and detonation performance were studied and the results showed that both the ADN and ADN-H2O-CH3OH solutions had hydrogen bonds and van der Waals interactions. By introducing the small molecules H2O and CH3OH, the detonation performance of the ADN-H2O-CH3OH solution slightly decreased, but its sensitivity also decreased. Overall, the comprehensive performance of the ADN-H2O-CH3OH solution has improved, and the application range has expanded. These results are helpful for obtaining a deeper understanding of ADN-based liquid propellants at the atomic level and contribute to the development of new liquid propellants. METHODS: The ADN and ADN-H2O-CH3OH solutions were constructed by Amorphous cell module and optimized via GGA with PBE methods in the Dmol3 module of the Materials Studio, and their electronic properties were calculated. Hirshfeld surfaces were generated with CrystalExplorer 3.0. A topological analysis of a variety of molecular clusters was performed via QTAIM. The QTAIM and RDG analyses in this work were generated by Multiwfn 3.0.

Thermodynamic and Kinetic Behaviors of Electrolytes Mediated by Intermolecular Interactions Enabling High-Performance Lithium-Ion Batteries.

Electrolyte solvation chemistry regulated by lithium salts, solvents, and additives has garnered significant attention since it is the most effective strategy for designing high-performance electrolytes in lithium-ion batteries (LIBs). However, achieving a delicate balance is a persistent challenge, given that excessively strong or weak Li+-solvent coordination markedly undermines electrolyte properties, including thermodynamic redox stability and Li+-desolvation kinetics, limiting the practical applications. Herein, we elucidate the crucial influence of solvent-solvent interactions in modulating the Li+-solvation structure to enhance electrolyte thermodynamic and kinetic properties. As a paradigm, by combining strongly coordinated propylene carbonate (PC) with weakly coordinated cyclopentylmethyl ether (CPME), we identified intermolecular interactions between PC and CPME using 1H-1H correlation spectroscopy. Experimental and computational findings underscore the crucial role of solvent-solvent interactions in regulating Li+-solvent/anion interactions, which can enhance both the thermodynamic (i.e., antireduction capability) and kinetic (i.e., Li+-desolvation process) aspects of electrolytes. Additionally, we introduced an interfacial model to reveal the intricate relationship between solvent-solvent interactions, electrolyte properties, and electrode interfacial behaviors at a molecular scale. This study provides valuable insights into the critical impact of solvent-solvent interactions on electrolyte properties, which are pivotal for guiding future efforts in functionalized electrolyte engineering for metal-ion batteries.

Low-Temperature and High-Rate Rechargeable Aluminum Batteries Enabled by Ternary Eutectic Electrolytes.

Rechargeable aluminum batteries (RABs) have garnered extensive scientific attention as a promising alternative chemistry due to the inherent advantages associated with aluminum (Al) metal anodes, including their high theoretical capacities, cost-effectiveness, environmental friendliness, and inherent non-flammable properties. Nonetheless, the practical energy density of RABs is constrained by the electrolytes that support lower operational voltage windows. Herein, we report a ternary eutectic electrolyte composed of 1-ethyl-3-methylimidazolium chloride ([C2C1im]Cl):1-butyl-3-methylimidazolium chloride ([C4C1im]Cl):aluminum chloride (AlCl3) for the application of RABs. The electrolyte exhibits a high operational potential window (~3V vs. Al/Al3+ on SS 316) and high ionic conductivity (~8.3 mS.cm-1) while exhibiting only a low temperature glass transition at -65 oC suitable for all-climate conditions. Al||graphene nanoplatelets cell delivers a high capacity of ~117 mAh/g, and ~43 mAh/g at a very high current densities of 1A/g and 5A/g, respectively. The cells render a reversible capacity of 20 mAh/g at -20 oC and 17 mAh/g at -40 oC, indicating their suitability for operation under extreme environmental conditions. We comprehensively evaluated the design and optimization of carbon paper-based battery systems. The ternary eutectic electrolyte demonstrates exceptional electrochemical performance, thus signifying its substantial potential for utilization in high-performance energy storage systems in all climates.

Molecular dynamics simulation of salt diffusion in constituting phosphazene-based polymer electrolyte.

A growing demand to visualize polymer models in liquid poses a computational challenge in molecular dynamics (MD) simulation, as this requires emerging models under suitable force fields (FFs) to capture the underlying molecular behaviour accurately. In our present study, we have employed TIP3P potential on water and all atomistic optimized potentials for liquid simulations FFs to study the liquid electrolyte behavior of phosphazene-based polymer by considering its potential use in lithium-ion polymer batteries. We have explored the polymer's local structure, chain packing, wettability, and hydrophobic tendencies against the silicon surface using a combination of a pseudocontinuum model in MD simulation, and surface-sensitive sum frequency generation (SFG) vibrational spectroscopy. The finding yields invaluable insights into the molecular architecture of phosphazene. This approach identifies the importance of hydrophobic interactions with air and hydrophilic units with water molecules in understanding the behavior and properties of phosphazene-based polymers at interfaces, contributing to its advancements in materials science. The MD study uniquely captures traces of the polymer-ion linkage, which is observed to become more pronounced with the increase in polymer weight fraction. The theoretical observation of this linkage's influence on lithium-ion diffusion motion offers valuable insights into the fundamental physics governing the behavior of atoms and molecules within phosphazene-based polymer electrolytes in aqueous environments. Further these predictions are corroborated in the molecular-level depiction at the air-aqueous interface, as evidenced from the OH-oscillator strength variation measured by the SFG spectroscopy.The fundamental findings from this study open new avenues for utilizing MD simulation as a versatile methodology to gain profound insights into intermolecular interactions of polymer. It could be useful in the application of biomedical and energy-related research, such as polymer lithium-ion batteries, fuel cells, and organic solar cells.

Tailored Metal-Porphyrin Based Molecular Electrocatalysts for Enhanced Artificial Nitrogen Fixation to Green Ammonia.

Electrochemical nitrogen reduction (E-NRR) is one of the most promising approaches to generate green NH3. However, scarce ammonia yields and Faradaic efficiencies (FE) still limit their use on a large scale. Thus, efforts are focusing on different E-NRR catalyst structures and formulations. Among present strategies, molecular electrocatalysts such as metal-porphyrins emerge as an encouraging option due to their planar structures which favor the interaction involving the metal center, responsible for adsorption and activation of nitrogen. Nevertheless, the high hydrophobicity of porphyrins limits the aqueous electrolyte-catalyst interaction lowering yields. This work introduces a new class of metal-porphyrin based catalysts, bearing hydrophilic tris(ethyleneglycol) monomethyl ether chains (metal = Cu(II) and CoII)). Experimental results show that the presence of hydrophilic chains significantly increases ammonia yields and FE, supporting the relevance of fruitful catalyst-electrolyte interactions. This study also investigates the use of hydrophobic branched alkyl chains for comparison, resulting in similar performances with respect to the unsubstituted metal-porphyrin, taken as a reference, further confirming that the appropriate design of electrocatalysts carrying peripheral hydrophilic substituents is able to improve device performances in the generation of green ammonia.

Relating solvatochromism and solvatomorphism in organic dyes using high pressure.

By using complementary experimental methods including in situ high-pressure single-crystal X-ray diffraction and UV-Vis spectroscopy, the intricate connection between solvatochromism and solvatomorphism has been elucidated in a recent publication [Sobczak & Katrusiak (2024). IUCrJ, 11, 528-537]. The connection was demonstrated for an important pigment - Reichardt's dye - with potential applications in nonlinear optoelectronics and molecular pressure sensor development.

Exploring crystal structure-physical property relationships with pressure.

From its conception, X-ray crystallography has provided a unique understanding of the structure, bonding and electronic state of materials, which, in turn, unlocks a means of examining the properties and function of crystalline systems. Using state-of-the-art single-crystal X-ray diffraction, along with UV-Vis spectroscopy and DFT calculations, Zwolenik et al. [(2024). IUCrJ, 11, 519-527] have provided a comprehensive study of the structure-optical property relationship of 1,3-diacetylpyrene with methodologies that are increasingly accessible to non-specialist laboratories.

Comparative Study of Two Spectral Methods for Estimating the Excited State Dipole Moment of Non-Fluorescent Molecules.

The electronic absorption spectral characteristics of cycloimmonium ylids with a zwitterionic structure have been analyzed in forty-three solvents with different hydrogen bonding abilities. The two ylids lack fluorescence emission but are very dynamic in electronic absorption spectra. Using the maximum of the ICT band, the goal was to establish an accurate relationship between the shift of the ICT visible band and the solvent parameters and to estimate two of the descriptors of the first (the) excited state: the dipole moment and the polarizability. Two procedures were involved: the variational method and the relationships of the Abe model. The results indicate that the excited state dipole moment of the two methylids decreases in the absorption process in comparison with the ground state. The introduction of a correction term in the Abe model that neglects the intermolecular H-bonding interactions leads to a more accurate determination of the two descriptors. The strong solvatochromic response of both ylids has been further applied in distinguishing the solvents as a function of their specific parameters. Principal component analysis was applied to five selected properties, including the maximum of the charge transfer band. The results were further applied to discriminate several binary solvent mixtures.

Modulation of the high concentration viscosity of IgG1 antibodies using clinically validated Fc mutations.

The self-association of therapeutic antibodies can result in elevated viscosity and create problems in manufacturing and formulation, as well as limit delivery by subcutaneous injection. The high concentration viscosity of some antibodies has been reduced by variable domain mutations or by the addition of formulation excipients. In contrast, the impact of Fc mutations on antibody viscosity has been minimally explored. Here, we studied the effect of a panel of common and clinically validated Fc mutations on the viscosity of two closely related humanized IgG1, κ antibodies, omalizumab (anti-IgE) and trastuzumab (anti-HER2). Data presented here suggest that both Fab-Fab and Fab-Fc interactions contribute to the high viscosity of omalizumab, in a four-contact model of self-association. Most strikingly, the high viscosity of omalizumab (176 cP) was reduced 10.7- and 2.2-fold by Fc modifications for half-life extension (M252Y:S254T:T256E) and aglycosylation (N297G), respectively. Related single mutations (S254T and T256E) each reduced the viscosity of omalizumab by ~6-fold. An alternative half-life extension Fc mutant (M428L:N434S) had the opposite effect in increasing the viscosity of omalizumab by 1.5-fold. The low viscosity of trastuzumab (8.6 cP) was unchanged or increased by ≤2-fold by the different Fc variants. Molecular dynamics simulations provided mechanistic insight into the impact of Fc mutations in modulating electrostatic and hydrophobic surface properties as well as conformational stability of the Fc. This study demonstrates that high viscosity of some IgG1 antibodies can be mitigated by Fc mutations, and thereby offers an additional tool to help design future antibody therapeutics potentially suitable for subcutaneous delivery.

Probing the interfacial behaviors of interfacially active and non-active asphaltenes and their impact on emulsion stability.

HYPOTHESIS: Asphaltenes subfractions with distinct interfacial behaviors may play different roles in stabilizing oil-water emulsions. EXPERIMENTS: In this work, whole asphaltenes were separated into interfacially active asphaltenes (IAA) and interfacially non-active asphaltenes (INAA). Employing advanced nanomechanical techniques, we have explored the compositions, morphologies, sizes, adsorption, and interfacial behaviors of IAA and INAA. FINDINGS: IAA exhibits a high and unevenly distributed oxygen content, distinguishing it from INAA. In toluene, the diameters of IAA and INAA are about 60 nm and 6 nm, respectively. When adsorbed irreversibly on mica surfaces, the thickness of the IAA and INAA film was measured at âˆ¼5.5 nm or 1 nm, respectively; while in a toluene solution, the film thickness reached âˆ¼46 nm and 3.1 nm for IAA and INAA, respectively. IAA demonstrates superior interfacial activity, and elastic/viscous moduli compared to INAA at the water-toluene interface. Quantified surface force measurements reveal that IAA stabilizes water droplets in toluene at a concentration of only 10 mg/L, while INAA requires a higher concentration of 100 mg/L. This work provides the first comprehensive investigation into the adsorption and interfacial behaviors of asphaltene subfractions and provides useful insights into the asphaltenes-stabilization mechanism of emulsions.

Lignin nanoparticle as a vehicle to load, release, and improve the stability and antioxidant activity of curcumin: Comparison between dropping and pouring regimes.

Curcumin (Cur) was loaded in lignin nanoparticles (LNP) via an antisolvent method by pouring (P-) and dropping (D-) regimes, respectively, and Cur-loaded LNP (Cur/LNP) were comparatively characterized. The results indicated that P-Cur/LNP (62-92 nm) was much smaller than D-Cur/LNP (134-139 nm). For both regimes, their maximum loading efficiencies were comparable (91 ± 3%), while dropping regime (236.2 mg/g) demonstrated a higher loading capacity than pouring regime (174.6 mg/g). In both regimes, Cur was loaded in an amorphous form via the hydrophobic, hydrogen-bonding, and π-π interactions with lignin matrix and it demonstrated a controlled release in in vitro digestion test. In comparison, Cur in D-Cur/LNP showed higher stabilities against photodegradation, thermal treatment, and 30-d storage than that in P-Cur/LNP, while P-Cur/LNP concluded a higher antioxidant activity than D-Cur/LNP. The present findings attested that LNP was a valuable tool to stabilize and controlled release of lipophilic phytochemicals as well as improve their bioactivities.

Temperature-dependent Raman spectroscopy and thermodynamic behaviors of energetic NTO crystal.

The vibrational and thermodynamic properties of energetic materials (EMs) are critical to understand their structure responses at finite temperature. In this work, the zero-point energy and temperature effects are incorporated into dispersion-corrected density functional theory to improve the calculated accuracy for vibrational responses and thermodynamic behaviors of 3-nitro-1,2,4-triazole-5-one (NTO). Based on temperature-dependent Raman spectroscopy, the emergence and disappearance of new peaks as well as discontinuous Raman shifts indicate the distinct changes of molecular configuration and intermolecular interactions within the temperature of 250-350 K. From Hirshfeld surface and structure analysis, the subtle changes of intermolecular hydrogen bonds (HBs) related with the shrinkage of thermal expansion coefficient, are treated as an essential step of a potential structural transformation of NTO. Moreover, the calculated heat capacity, entropy and bulk moduli could reflect the softening behavior of NTO and further enrich the thermodynamic data set of EMs. These results demonstrate the evolution of NTO molecules controlled by non-covalent interactions and provide vital insights into the thermodynamic behaviors at finite temperature.

A comparative study of the effect of high-pressure and low temperature on the crystal structure of lithium xanthinate hydrate.

The crystal structure of lithium xanthinate hydrate was studied by single crystal X-ray diffraction and Raman spectroscopy on cooling to 100 K and under compression to 5.3 GPa. A phase transition at ∼4 GPa is observed. No phase transitions occur on cooling. Anisotropy of lattice strain and changes in intermolecular interactions are compared.

Influence of Solvent Selection on the Crystallizability and Polymorphic Selectivity Associated with the Formation of the "Disappeared" Form I Polymorph of Ritonavir.

The comparative crystallizability and polymorphic selectivity of ritonavir, a novel protease inhibitor for the treatment of acquired immune-deficiency syndrome, as a function of solvent selection are examined through an integrated and self-consistent experimental and computational molecular modeling study. Recrystallization at high supersaturation by rapid cooling at 283.15 K is found to produce the metastable "disappeared" polymorphic form I from acetone, ethyl acetate, acetonitrile, and toluene solutions in contrast to ethanol which produces the stable form II. Concomitant crystallization of the other known solid forms is not found under these conditions. Isothermal crystallization studies using turbidometric detection based upon classical nucleation theory reveal that, for an equal induction time, the required driving force needed to initiate solution nucleation decreases with solubility in the order of ethanol, acetone, acetonitrile, ethyl acetate, and toluene consistent with the expected desolvation behavior predicted from the calculated solute solvation free energies. Molecular dynamics simulations of the molecular and intermolecular chemistry reveal the presence of conformational interplay between intramolecular and intermolecular interactions within the solution phase. These encompass the solvent-dependent formation of intramolecular O-H...O hydrogen bonding between the hydroxyl and carbamate groups coupled with differing conformations of the hydroxyl's shielding phenyl groups. These conformational preferences and their relative interaction propensities, as a function of solvent selection, may play a rate-limiting role in the crystallization behavior by not only inhibiting to different degrees the nucleation process but also restricting the assembly of the optimal intermolecular hydrogen bonding network needed for the formation of the stable form II polymorph.

Precisely Regulating Intermolecular Interactions and Molecular Packing of Nonfused-Ring Electron Acceptors via Halogen Transposition for High-Performance Organic Solar Cells.

The structure of molecular aggregates is crucial for charge transport and photovoltaic performance in organic solar cells (OSCs). Herein, the intermolecular interactions and aggregated structures of nonfused-ring electron acceptors (NFREAs) are precisely regulated through a halogen transposition strategy, resulting in a noteworthy transformation from a 2D-layered structure to a 3D-interconnected packing network. Based on the 3D electron transport pathway, the binary and ternary devices deliver outstanding power conversion efficiencies (PCEs) of 17.46 % and 18.24 %, respectively, marking the highest value for NFREA-based OSCs.

Crystalline Porous Organic Cage Membranes Constructed Using Fortified Intermolecular Interactions for Molecular Sieving.

Among the various types of materials with intrinsic porosity, porous organic cages (POCs) are distinctive as discrete molecules that possess intrinsic cavities and extrinsic channels capable of facilitating molecular sieving. However, the fabrication of POC membranes remains highly challenging due to the weak noncovalent intermolecular interactions and most reported POCs are powders. In this study, we constructed crystalline free-standing porous organic cage membranes by fortifying intermolecular interactions through the induction of intramolecular hydrogen bonds, which was confirmed by single-crystal X-ray analysis. To elucidate the driving forces behind, a series of terephthaldehyde building blocks containing different substitutions were reacted with flexible triamine under different conditions via interfacial polymerization (IP). Furthermore, density functional theory (DFT) calculations suggest that intramolecular hydrogen bonding can significantly boost the intermolecular interactions. The resulting membranes exhibited fast solvent permeance and high rejection of dyes not only in water, but also in organic solvents. In addition, the membrane demonstrated excellent performance in precise molecular sieving in organic solvents. This work opens an avenue to designing and fabricating free-standing membranes composed of porous organic materials for efficient molecular sieving.

From X-ray crystallographic structure to intrinsic thermodynamics of protein-ligand binding using carbonic anhydrase isozymes as a model system.

Carbonic anhydrase (CA) was among the first proteins whose X-ray crystal structure was solved to atomic resolution. CA proteins have essentially the same fold and similar active centers that differ in only several amino acids. Primary sulfonamides are well defined, strong and specific binders of CA. However, minor variations in chemical structure can significantly alter their binding properties. Over 1000 sulfonamides have been designed, synthesized and evaluated to understand the correlations between the structure and thermodynamics of their binding to the human CA isozyme family. Compound binding was determined by several binding assays: fluorescence-based thermal shift assay, stopped-flow enzyme activity inhibition assay, isothermal titration calorimetry and competition assay for enzyme expressed on cancer cell surfaces. All assays have advantages and limitations but are necessary for deeper characterization of these protein-ligand interactions. Here, the concept and importance of intrinsic binding thermodynamics is emphasized and the role of structure-thermodynamics correlations for the novel inhibitors of CA IX is discussed - an isozyme that is overexpressed in solid hypoxic tumors, and thus these inhibitors may serve as anticancer drugs. The abundant structural and thermodynamic data are assembled into the Protein-Ligand Binding Database to understand general protein-ligand recognition principles that could be used in drug discovery.