Molecular dynamics simulations on the interactions between nucleic acids and a phospholipid bilayer

Recently,lipid nanoparticles(LNPs)have been extensively investigated as non-viral carriers of nucleic acid vaccines due to their high transport efficiency,safety,and straightforward production and scalability.However,the molecular mechanism underlying the interactions between nucleic acids and phospholipid bilayers within LNPs remains elusive.In this study,we employed the all-atom molecular dynamics simulation to investigate the interactions between single-stranded nucleic acids and a phospholipid bilayer.Our findings revealed that hydrophilic bases,specifically G in single-stranded RNA(ssRNA)and single-stranded DNA(ssDNA),displayed a higher propensity to form hydrogen bonds with phospholipid head groups.Notably,ssRNA exhibited stronger binding energy than ssDNA.Furthermore,divalent ions,particularly Ca2+,facilitated the binding of ssRNA to phospholipids due to their higher binding energy and lower dissociation rate from phospholipids.Overall,our study provides valuable insights into the molecular mechanisms underlying nucleic acidphospholipid interactions,with potential implications for the nucleic acids in biotherapies,particularly in the context of lipid carriers.

Viral-host molecular interactions and metabolic modulation:Strategies to inhibit flaviviruses pathogenesis

Flaviviruses,which include globally impactful pathogens,such as West Nile virus,yellow fever virus,Zika virus,Japanese encephalitis virus,and dengue virus,contribute significantly to human infections.Despite the ongoing emergence and resurgence of flavivirus-mediated pathogenesis,the absence of specific therapeutic options remains a challenge in the prevention and treatment of flaviviral infections.Through the intricate processes of fusion,transcription,replication,and maturation,the complex interplay of viral and host metabolic interactions affects pathophysiology.Crucial interactions involve metabolic molecules,such as amino acids,glucose,fatty acids,and nucleotides,each playing a pivotal role in the replication and maturation of flaviviruses.These viral-host metabolic molecular interactions hijack and modulate the molecular mechanisms of host metabolism.A comprehensive understanding of these intricate metabolic pathways offers valuable insights,potentially unveiling novel targets for therapeutic interventions against flaviviral pathogenesis.This review emphasizes promising avenues for the development of therapeutic agents that target specific metabolic molecules,such as amino acids,glucose,fatty acids,and nucleotides,which interact with flavivirus replication and are closely linked to the modulation of host metabolism.The clinical limitations of current drugs have prompted the development of new inhibitory strategies for flaviviruses based on an understanding of the molecular interactions between the virus and the host.

Tailoring Light–Matter Interactions in Overcoupled Resonator for Biomolecule Recognition and Detection

Plasmonic nanoantennas provide unique opportunities for precise control of light–matter coupling in surface-enhanced infrared absorption(SEIRA)spectroscopy,but most of the resonant systems realized so far suffer from the obstacles of low sensitivity,narrow bandwidth,and asymmetric Fano resonance perturbations.Here,we demonstrated an overcoupled resonator with a high plasmon-molecule coupling coefficient(μ)(OC-Hμresonator)by precisely controlling the radiation loss channel,the resonator-oscillator coupling channel,and the frequency detuning channel.We observed a strong dependence of the sensing performance on the coupling state,and demonstrated that OC-Hμresonator has excellent sensing properties of ultra-sensitive(7.25%nm^(−1)),ultra-broadband(3–10μm),and immune asymmetric Fano lineshapes.These characteristics represent a breakthrough in SEIRA technology and lay the foundation for specific recognition of biomolecules,trace detection,and protein secondary structure analysis using a single array(array size is 100×100μm^(2)).In addition,with the assistance of machine learning,mixture classification,concentration prediction and spectral reconstruction were achieved with the highest accuracy of 100%.Finally,we demonstrated the potential of OC-Hμresonator for SARS-CoV-2 detection.These findings will promote the wider application of SEIRA technology,while providing new ideas for other enhanced spectroscopy technologies,quantum photonics and studying light–matter interactions.

T cell interactions with microglia in immune-inflammatory processes of ischemic stroke

The primary mechanism of secondary injury after cerebral ischemia may be the brain inflammation that emerges after an ischemic stroke,which promotes neuronal death and inhibits nerve tissue regeneration.As the first immune cells to be activated after an ischemic stroke,microglia play an important immunomodulatory role in the progression of the condition.After an ischemic stroke,peripheral blood immune cells(mainly T cells)are recruited to the central nervous system by chemokines secreted by immune cells in the brain,where they interact with central nervous system cells(mainly microglia)to trigger a secondary neuroimmune response.This review summarizes the interactions between T cells and microglia in the immune-inflammatory processes of ischemic stroke.We found that,during ischemic stroke,T cells and microglia demonstrate a more pronounced synergistic effect.Th1,Th17,and M1 microglia can co-secrete proinflammatory factors,such as interferon-γ,tumor necrosis factor-α,and interleukin-1β,to promote neuroinflammation and exacerbate brain injury.Th2,Treg,and M2 microglia jointly secrete anti-inflammatory factors,such as interleukin-4,interleukin-10,and transforming growth factor-β,to inhibit the progression of neuroinflammation,as well as growth factors such as brain-derived neurotrophic factor to promote nerve regeneration and repair brain injury.Immune interactions between microglia and T cells influence the direction of the subsequent neuroinflammation,which in turn determines the prognosis of ischemic stroke patients.Clinical trials have been conducted on the ways to modulate the interactions between T cells and microglia toward anti-inflammatory communication using the immunosuppressant fingolimod or overdosing with Treg cells to promote neural tissue repair and reduce the damage caused by ischemic stroke.However,such studies have been relatively infrequent,and clinical experience is still insufficient.In summary,in ischemic stroke,T cell subsets and activated microglia act synergistically to regulate inflammatory progression,mainly by secreting inflammatory factors.In the future,a key research direction for ischemic stroke treatment could be rooted in the enhancement of anti-inflammatory factor secretion by promoting the generation of Th2 and Treg cells,along with the activation of M2-type microglia.These approaches may alleviate neuroinflammation and facilitate the repair of neural tissues.

Molecular Structure Tailoring of Organic Spacers for High‑Performance Ruddlesden–Popper Perovskite Solar Cells

Layer-structured Ruddlesden–Popper(RP)perovskites(RPPs)with decent stability have captured the imagination of the photovoltaic research community and bring hope for boosting the development of perovskite solar cell(PSC)technology.However,two-dimensional(2D)or quasi-2D RP PSCs are encountered with some challenges of the large exciton binding energy,blocked charge transport and poor film quality,which restrict their photovoltaic performance.Fortunately,these issues can be readily resolved by rationally designing spacer cations of RPPs.This review mainly focuses on how to design the molecular structures of organic spacers and aims to endow RPPs with outstanding photovoltaic applications.We firstly elucidated the important roles of organic spacers in impacting crystallization kinetics,charge transporting ability and stability of RPPs.Then we brought three aspects to attention for designing organic spacers.Finally,we presented the specific molecular structure design strategies for organic spacers of RPPs aiming to improve photovoltaic performance of RP PSCs.These proposed strategies in this review will provide new avenues to develop novel organic spacers for RPPs and advance the development of RPP photovoltaic technology for future applications.

Decoding molecular mechanisms:brain aging and Alzheimer's disease

The complex morphological,anatomical,physiological,and chemical mechanisms within the aging brain have been the hot topic of research for centuries.The aging process alters the brain structure that affects functions and cognitions,but the worsening of such processes contributes to the pathogenesis of neurodegenerative disorders,such as Alzheimer's disease.Beyond these observable,mild morphological shifts,significant functional modifications in neurotransmission and neuronal activity critically influence the aging brain.Understanding these changes is important for maintaining cognitive health,especially given the increasing prevalence of age-related conditions that affect cognition.This review aims to explore the age-induced changes in brain plasticity and molecular processes,differentiating normal aging from the pathogenesis of Alzheimer's disease,thereby providing insights into predicting the risk of dementia,particularly Alzheimer's disease.

Molecular simulation study of the microstructures and properties of pyridinium ionic liquid[HPy][BF_(4)]mixed with acetonitrile

The microstructures and thermodynamic properties of mixed systems comprising pyridinium ionic liquid[HPy][BF_(4)]and acetonitrile at different mole fractions were studied using molecular dynamics simulation in this work.The following properties were determined:density,self-diffusion coefficient,excess molar volume,and radial distribution function.The results show that with an increase in the mole fraction of[HPy][BF_(4)],the self-diffusion coefficient decreases.Additionally,the excess molar volume initially decreases,reaches a minimum,and then increases.The rules of radial distribution functions(RDFs)of characteristic atoms are different.With increasing the mole fraction of[HPy][BF_(4)],the first peak of the RDFs of HA1-F decreases,while that of CT6-CT6 rises at first and then decreases.This indicates that the solvent molecules affect the polar and non-polar regions of[HPy][BF_(4)]differently.

Molecular Dynamics Simulations of the Interactions Between Konjac Glucomannan and Soy Protein Isolate

The interactions between konjac glucomannan（KGM） and soy protein isolate （SPI） were studied with the method of molecular dynamics simulation. Part representative structures segments of KGM and SPI were used as mode, and the force-field was FF03. The stability and sites of KGM/SPI interactions in water were researched at 363 K with the following results： the potential energy （EPOT） of the mixed gel dropped, while that of single KGM gel increased. The surface area （SA） of KGM in the mixed system was decreased to 401.41 from 1 267.54 Az, and that of SPI to 484.94 from 1 943.28 A2. The sum potential energy of KGM and soy protein in the mixed system was decreased to -13 402.41 from -5 768.56 kcal mol^-1. The variations of two parameters showed that the stability of compound gel KGM/SPI was improved, which was consistent with the previous studies. The sites of interactions in the mixed gel were the -OH groups on C（2） in KGM mannose and glucose, and the amide linkage group on Histidine, Asparagine and Leucine in SPI. The hydrogen bond was formed directly or indirectly by the bridge of waters.

Molecular Dynamics Simulations of the Interactions between Konjac Glucomannan and Carrageenan

The interactions between konjac glucomannan and carrageenan were studied with the method of molecular dynamics simulation. Part representative structure segments of KGM and two unit structures of κ-carrageenan （Fig. 2） were used as mode, and the force-field was AMBER2. The stability and sites of konjac glucomannan/carrageenan interactions in water were researched at 373 K with the following results： the potential energy （EPOT） of the mixed gel was dropped, while those of single-konjac glucomannan gel and single carrageenan were increased. The surface area （SA） of KGM in the mixed system was decreased to 1002.2A^°^2, and that of carrageenan to 800.9 A^°^2. The variations of two parameters showed that the stability of compound gel konjac glucomannan/carrageenan was improved, which is consistent with the previous studies. The sites of interactions in the mixed gel were the -OH groups on C（2）, C（4） and C（6）, the acetyl group in KGM mannose, and the -OH group on C（6） in carrageenan. The hydrogen bond was formed directly or indirectly by the bridge of waters.

Torsional Characteristics of Single Walled Carbon Nanotube with Water Interactions by Using Molecular Dynamics Simulation

The torsional characteristics of single walled carbon nanotube(SWCNT) with water interactions are studied in this work using molecular dynamics simulation method. The torsional properties of carbon nanotubes(CNTs) in a hydrodynamic environment such as water are critical for its key role in determining the lifetime and stability of CNT based nano-fluidic devices. The effect of chirality, defects and the density of water encapsulation is studied by subjecting the SWCNT to torsion. The findings show that the torsional strength of SWCNT decreases due to interaction of water molecules and presence of defects in the SWCNT. Additionally,for the case of water molecules encapsulated inside SWCNT, the torsional response depends on the density of packing of water molecules. Our findings and conclusions obtained from this paper is expected to further compliment the potential applications of CNTs as promising candidates for applications in nano-biological and nano-fluidic devices.

Molecular Simulation of CO2/H2 Mixture Separation in Metal-organic Frameworks： Effect of Catenation and Electrostatic Interactions

In this work grand canonical Monte Carlo simulations were performed to study gas separation in three pairs of isoreticular metal-organic frameworks (IRMOFs) with and without catenation at room temperature.Mixture composed of CO2 and H2 was selected as the model system to separate.The results show that CO2 selectivity in catenated MOFs with multi-porous frameworks is much higher than their non-catenated counterparts.The simulations also show that the electrostatic interactions are very important for the selectivity,and the contributions of different electrostatic interactions are different,depending on pore size,pressure and mixture composition.In fact,changing the electrostatic interactions can even qualitatively change the adsorption behavior.A general conclusion is that the electrostatic interactions between adsorbate molecules and the framework atoms play a dominant role at low pressures,and these interactions in catenated MOFs have much more pronounced effects than those in their non-catenated counterparts,while the electrostatic interactions between adsorbate molecules become evident with increasing pressure,and eventually dominant.

Probing Molecular Interactions in 1-Butyl-3-methylimidazolium Chloride-Water and 2,6-Dimethoxyphenol Mixtures Using Attenuated Total Reflection Infrared Spectroscopy

Molecular interactions of the ternary mixtures of 1-butyl-3-methylimidazolium chloride （[C4C1im]Cl）-water-2,6-dimethoxyphenol （2,6-DMP, a phenolic monomer lignin model compound） were investigated in comparison with the [C4C1im]Cl-water binary systems through attenuated total reflection infrared spectroscopy. Results indicated that the microstructures of water and [C4C1im]Cl changed with varying mole fraction of [C4C1im]Cl （xIL） from 0.01 to 1.0. This change was mainly attributed to the interactions of [C4C1im]Cl-water and the self-aggregation of [C4C1im]Cl through hydrogen bonding. The band shifts of C-H on imidazolium ring and the functional groups in 2,6-DMP indicated that the occurrence of intermolecular interactions by different mechanisms （i.e., hydrogen bonding or π-π stacking） resulted in 2,6-DMP dissolution. In the case of xIL=0.12, the slightly hydrogen-bonded water was fully destroyed and [C4C1im]Cl existed in the form of hydrated ion pairs. Interestingly, the maximum 2,6-DMP solubility （238.5 g/100 g） was achieved in this case. The interactions and microstructures of [C4C1im]Cl-water mixtures influenced the dissolution behavior of 2,6-DMP.

Theoretical Studies on Intermolecular Hydrogen-bond Interactions between Hexamethylenetetramine and Nitric Acid

The structures of the complexes generated by hexamethylenetetramine and nitric acid have been fully optimized by B3LYP method at the 6-311＋＋G＊＊ and aug-cc-pVTZ levels. The intermolecular hydrogen-bonding interactions have been calculated by the B3LYP/6-311＋＋G＊＊, B3LYP/aug-cc-pVTZ, MP2（full）/6-311＋＋G＊＊ and CCSD（T）/6-311＋＋G＊＊ methods, respectively. The NBO （nature bond orbital）, AIM （atom in molecule）, temperature effect and solvation effect have been analyzed to reveal the origin of the interactions. The results indicate that the stable hydrogen-bonded complexes could be generated by hexamethylenetetramine and nitric acid. The interactions follow the order of （a）（e）（b）（c）（d）（f）（g）. The C–N bonds which are adjacent to the methylene involving the hydrogen bonds tend to break in the chemical reaction. Due to the exothermic process, low temperature is conducive to the formation of the composition, which tallies with the experimental result.

A New Three-dimensional Supramolecular Polymer Built from Non-covalent Bonding Interactions

A new complex, [Ni2（L）4（H2O）8]（1, L1 = 4-（1H-imidazol-4-yl）benzoic acid）, has been hydrothermally prepared and characterized by single-crystal X-ray diffraction, IR spectroscopy, elemental analysis and PXRD. Complex 1 crystallizes in monoclinic, space group P21/c with α = 22.281（2）, b = 7.3959（7）, c = 24.978（3） ？, β = 90.876（10）, V = 4115.6（7） ？3, Z = 8, C20H22N4O8Ni, Mr = 505.13, Dc = 1.630 g/cm3, μ = 1.001 mm-1, S = 1.080, F（000） = 2096, the final R = 0.452 and wR = 0.1152 for 9380 observed reflections （I 〉 2σ（I））. The result of X-ray diffraction analysis revealed three different kinds of Ni（II） centre mononuclear molecules in the asymmetric unit. The independent mononuclear units are bridged to form a three-dimensional supramolecular polymer by extensive hydrogen bonds and C–H… non-covalent bonding interactions.

Refractometric Studies on Molecular Interactions in Six Binary Liquid Mixtures

Refractive indices of the six binary mixtures between N-Butyl bromide with Aniline, Benzene, Xylene, Carbon tetrachloride, n-Heptane and Toluene for the entire concentration range have been measured at 303.15 K. Furthermore, deviation in refractive indices from ideal mixture, molar refraction, deviation in molar refraction from ideal values for these mixtures has also been evaluated. The results are discussed in term of molecular interactions between the components of the binary mixtures.

A Molecular Dynamics Study on the Dust-Plasma/Wall Interactions in the EAST Tokamak

The interactions between the W nano-dust and deuterium plasma at different lo- cations of the EAST tokamak are simulated using a molecular dynamics code. It is shown that nano-dust particles, with the radius, Rd, ~5 nm, can exist for at least several nano-seconds under the interactions from the ions without being ablated in some specific places of the tokamak edge plasma, while those with Rd ≥~25 nm may be ablated if the plasma temperature T~ 50 eV and density n^10^19 m-3. In addition, the collisions of tungsten nano-dust grains with a tungsten wall at 100 m/s or I000 m/s impinging speeds are simulated. It is demonstrated that the dust will stick to the wall, and the collision will not cause substantial damage to the wall, but it may be able to cause partial destruction of the dust grains themselves depending on their incident speeds.

Intermolecular Interactions, Thermodynamic Properties, Detonation Performance, and Sensitivity of TNT/CL-20 Cocrystal Explosive

Intermolecular interactions and properties of TNT（2,4,6-trinitrotoluene）/CL-20（2,4,6,8,10,12-hexanitrohexaazaisowurtzitane） cocrystal were studied by density functional theory（DFT） methods. Binding energy, natural bond orbital（NBO）, and atom in molecules（AIM） analysis were performed to investigate the intermolecular interactions in the cocrystal. Results show that the unconventional CH···O type hydrogen bond plays a key role in forming the cocrystal. The variation tendency of entropy and enthalpy shows that the formation of the cocrystal is an exothermic process and low temperature will be benefit for the assembling of complexes. The calculated detonation velocity of the cocrystal agrees well with the experimental value which is higher than that of the physical mixture of TNT and CL-20. In addition, bond dissociation energies（BDEs） of the weakest trigger bond in TNT/CL-20 complex were calculated and the results show that the TNT/CL-20 complex is thermally stable. Finally, first-principles calculations were performed and analysis of the nitro group Mulliken charge indicates that the cocrystal is less sensitive than pure CL-20.

Intermolecular Interactions in Self-Assembly Process of Sodium Dodecyl Sulfate by Vertically Polarized Raman Spectra

Molecular self-assembly is extremely important in many fields, but the characterization of their corresponding intermolecular interactions is still lacking. The C-H stretching Raman band can reflect the hydrophobic interactions during the self-assembly process of sodium dodecyl sulfate （SDS） in aqueous solutions. However, the Raman spectra in this region are seriously overlapped by the OH stretching band of water. In this work, vertically polarized Raman spectra were used to improve the detection sensitivity of spectra of C-H region for the first time. The spectral results showed that the first critical micelle concentration and the second critical micelle concentration of SDS in water were 8.5 and 69 mmol/L, respectively, which were consistent with the results given by surface tension measurements. Because of the high sensitivity of vertically polarized Raman spectra, the critical micelle concentration of SDS in a relatively high concentration of salt solution could be obtained in our experiment. The two critical concentrations of SDS in 100 mmol/L NaCl solution were recorded to be 1.8 and 16.5 mmol/L, respectively. Through comparing the spectra and surface tension of SDS in water and in NaCl solution, the self-assembly process in bulk phase and at interface were discussed. The interactions among salt ions, SDS and water molecules were also analyzed. These results demonstrated the vertically polarized Raman spectra could be employed to study the self-assembly process of SDS in water.

Influence of Small Amphiphiles on Aqueous Dispersions of <i>β</i>-Lactoglobulin A and Bovine Serum Albumin: (1) Intermolecular Interactions

Hydrophilic and hydrophobic (φ) interactions among amphiphiles play critical roles in interfacial properties of proteins and other smaller amphiphiles and affect the creation and stability of foams and emulsions in food systems. Contribution of small amphiphiles on H-bonding and hydrophobic (φ) interactions at a model interface comprising of a water-hydrophobized surface interface as reflected by contact angle (θ) of fatty acid free bovine serum albumin (FAF-BSA), bovine serum albumin (BSA), and β-lactoglobulin variant A (β-LGA) was investigated. Amphiphiles were used with either protein in neutral water or α-bromonaphtalene (α-BrN) (22°C) to obtain θ-H2O and θ-α-BrN measurements, respectively. θ-α-BrN reflected influence of φ-interactions on θ since α-BrN molecules do not partake significantly in H-bonding. Ionic nature of the amphiphiles had no significant effect. Dramatic difference was between zwitterionic Z8 and Z12. At 1%, Z8 significantly increased H-bonding in BSA and β-LGA by 26% and 55%, respectively, whereas Z12, which is more hydrophobic, decreased it by 50% and 21%. At the same concentration, φ-interactions were enhanced by Z8 for BSA by 37% and by all amphiphiles except Z12 for FAF-BSA.

Theoretical Study on the Intermolecular Interactions of Tetrazole Dimers

Tetrazole monomers （Ⅰ, Ⅱ） and all of their possible stable dimers （1, 2, 3, 4, 5, 6, 7 and 8） were fully optimized by DFT method at the B3LYP/6-311＋＋G^＊＊ level. Among the eight dimers, there were two 1H-tetrazole dimers, three 2H-tetrazole dimers and three hetero dimers of 1H-tetrazole and 2H-tetrazole. Vibrational frequencies were calculated to ascertain that each structure was stable （no imaginary frequencies）. The basis set superposition errors （BSSE） are 2.78, 2.28, 2.97, 2.75, 2.74, 2.18, 1.23 and 3.10 kJ/mol, and the zero point energy （ZPE） corrections for the interaction energies are 4.88, 4.18, 3.87, 3.65, 3.54, 3.22, 2.87 and 4.34 kJ/mol for 1, 2, 3, 4, 5, 6, 7 and 8, respectively. After BSSE and ZPE corrections, the greatest corrected intermolecular interaction energy of the dimers is -43.71 kJ/mol. The charge redistribution mainly occurs on the adjacent N-H…N atoms between submolecules. The charge transfer between two subsystems is very small. Natural bond orbital （NBO） analysis was performed to reveal the origin of the interaction. Based on the statistical thermodynamic method, the standard thermodynamic functions, heat capacities （C^0P）, entropies （S^0T） and thermal corrections to enthalpy （H^0T）, and the changes of thermodynamic properties from monomer to dimer in the temperature range of 200.00 K to 700 K have been obtained. 1H-tetrazole monomer can spontaneously turn into two stable dimers at 298.15 K.