Molecular Structure Research Articles

Teaching hydrogen bridges: it is not FON anymore!

Abstract Teaching hydrogen bridges (H-bridges) in introductory chemistry courses is either oversimplified or dogmatically taught; the heuristic that ‘only fluorine, oxygen and nitrogen (FON) form H-bridges’ is commonly used, for example. This rule limits choices, does not match reality, and does not clarify the difference between H-bridge donors (HBD) and H-bridge acceptors (HBA) nor intermolecular versus intramolecular cases. Hydrogen fluoride is a significant HBD but a poor HBA. Oxygen is not always an HBD or HBA. Ammonia is a significant HBA but a poor HBD. There are many examples of H-bridges that do not contain these three elements. All examples of H-bridges should be shown in a way to provide symbolic and molecular structures. Is it necessary to ‘explain’ H-bridges in introductory classes? We conclude not, but it might be necessary to increase the total amount of time to present the material so that students do not rely on superficial rules.

Acetonitrile real gas phase behavior from quasi-ideal gas to nanodroplets: A microscopical view.

We have applied a recently developed general purpose acetonitrile force field based on first-principles calculations to simulate acetonitrile in the gas phase at different temperatures and densities. These conditions range from nearly ideal to real gas phase behavior and condensation. The molecular dynamics simulation results agree fairly well with the experimental studies available in the literature on the gas samples. The structural analysis of aggregates and their associated interaction energies is examined and related to the early model proposed on molecular association and equilibrium determining the non-ideal behavior. The formation of dimers is mainly responsible for the non-ideal behavior of the gas at very low density, confirming suggested models based on previous experimental studies. However, when the density of the sample rises, the level of aggregation increases and the simple concept of dimerization does not hold anymore. The real behavior adopted by the gas is related to the distribution of molecular structures observed. The macroscopical view of a real gas as a generic interparticle interaction system without a defined form may then be rationalized on the basis of a defined molecular association originated by a distribution of aggregates at the low density regime. The sample with the highest density (∼1.4 × 103 molm-3) at the lowest temperature exhibits a massive aggregation where most of the acetonitrile (ACN) molecules in the simulation box form a big cluster. Its radial distribution function is similar to that of the liquid ACN. This strongly inhomogeneous distribution in the box can be considered a condensation in the gas phase under specific density-T conditions. This formation opens the door to the potential tuning of its solvent properties as a function of its size in these nanodroplets that in turn are controlled by the density-T conditions.

Micronization induced gelatinization of tapioca starch and its effects on starch physicochemical and structural properties.

The vibrating superfine mill (VSM) is a machine that belongs to the micronization technique. In this study, VSM was employed to produce micronized tapioca starch by varying micronization times (15, 30, 45, and 60min). The structural and physicochemical properties of the micronized starch were then examined. Scanning electron microscopy studies revealed that micronized starch was partially gelatinized, and the granule size dramatically increased when micronization time increased. X-ray diffraction patterns showed that the relative crystallinity was decreased from 24.67% (native) to 4.13% after micronization treatment for 15min and slightly decreased after that. The solubility of micronized starch significantly increased as the micronization time increased, which was associated with the destruction of the starch crystalline structure. Differential scanning calorimetry investigations confirmed that micronized starch was "partly gelatinized," and the degree of gelatinization increased to 81.27% when the micronization time was 60min. The weight-average molar mass was reduced by 15.0% (15min), 30.9% (30min), 55.7% (45min), and 70.5% (60min), respectively, indicating that the molecular structure was seriously degraded. The results demonstrated that the physicochemical changes of micronized starch granules were related to the destruction of the starch structure. These observations would provide details on micronized starch and its potential applications. PRACTICAL APPLICATION: These observations would provide details on micronized starch and its potential applications. Moreover, we believe that when the structures of starches were known, it is probable that the effect of VSM on the structural and physicochemical properties change of other starches might be predicted by adjusting the processing time.

HMMF: a hybrid multi-modal fusion framework for predicting drug side effect frequencies

BackgroundThe identification of drug side effects plays a critical role in drug repositioning and drug screening. While clinical experiments yield accurate and reliable information about drug-related side effects, they are costly and time-consuming. Computational models have emerged as a promising alternative to predict the frequency of drug-side effects. However, earlier research has primarily centered on extracting and utilizing representations of drugs, like molecular structure or interaction graphs, often neglecting the inherent biomedical semantics of drugs and side effects.ResultsTo address the previously mentioned issue, we introduce a hybrid multi-modal fusion framework (HMMF) for predicting drug side effect frequencies. Considering the wealth of biological and chemical semantic information related to drugs and side effects, incorporating multi-modal information offers additional, complementary semantics. HMMF utilizes various encoders to understand molecular structures, biomedical textual representations, and attribute similarities of both drugs and side effects. It then models drug-side effect interactions using both coarse and fine-grained fusion strategies, effectively integrating these multi-modal features.ConclusionsHMMF exhibits the ability to successfully detect previously unrecognized potential side effects, demonstrating superior performance over existing state-of-the-art methods across various evaluation metrics, including root mean squared error and area under receiver operating characteristic curve, and shows remarkable performance in cold-start scenarios.

Competition between O-H and S-H Intermolecular Interactions in Conformationally Complex Systems: The 2-Phenylethanethiol and 2-Phenylethanol Dimers.

Noncovalent interactions involving sulfur centers play a relevant role in biological and chemical environments. Yet, detailed molecular descriptions are scarce and limited to very simple model systems. Here we explore the formation of the elusive S-H···S hydrogen bond and the competition between S-H···O and O-H···S interactions in pure and mixed dimers of the conformationally flexible molecules 2-phenylethanethiol (PET) and 2-phenylethanol (PEAL), using the isolated and size-controlled environment of a jet expansion. The structure of both PET-PET and PET-PEAL dimers was unraveled through a comprehensive methodology that combined rotationally resolved microwave spectroscopy, mass-resolved isomer-specific infrared laser spectroscopy, and quantum chemical calculations. This synergic experimental-computational approach offered unique insights into the potential energy surface, conformational equilibria, molecular structure, and intermolecular interactions of the dimers. The results show a preferential order for establishing hydrogen bonds following the sequence S-H···S < S-H···O ≲ O-H···S < O-H···O, despite the hydrogen bond only accounting for a fraction of the total interaction energy.

Isomerization Pathways of a Mismatched Base Pair of A:8OG in Free Duplex DNA.

The A:8OG base pair (bp) is the outcome of DNA replication of the mismatched C:8OG bp. A high A:8OG bp population increases the C/G to A/T transversion mutation, which is responsible for various diseases. MutY is an important enzyme in the error-proof cycle and reverts A:8OG to C:8OG bp by cleaving adenine from the A:8OG bp. Several X-ray crystallography studies have determined the structure of MutY during the lesion scanning and lesion recognition stages. Interestingly, glycosidic bond (χ) angles of A:8OG bp in those two lesion recognition structures were found to differ, which implies that χ-torsion isomerization should occur during the lesion recognition process. In this study, as a first step to understanding this isomerization process, we characterized the intrinsic dynamic features of A:8OG in free DNAs by a free energy landscape simulation at the all-atom level. In this study, four isomerization states were assigned in the order of abundance: Aanti:8OGsyn > Aanti:8OGanti > Asyn:8OGanti ≈ Asyn:8OGsyn. Of these bp states, only 8OG in Asyn:8OGanti was located in the extrahelical space, whereas the purine bases (A and 8OG) in the other bp states remained inside the DNA helix. Also, free energy landscapes showed that the isomerization processes connecting these four bp states proceeded mostly in the intrahelical space via successive single glycosidic bond rotations of either A or 8OG.

Energy band engineering in GaS/InS and GaSe/InS van der Waals bilayers by interlayer stacking design and applied vertical electric field - An ab-initio theoretical calculation based approach

In this work, for the first time, an extensive theoretical investigation of the structural and electronic properties of the van der Waals (vdW) bilayer heterostructures of two-dimensional (2D) Gallium Sulphide (GaS)/Indium Sulphide (InS) and Gallium Selenide (GaSe)/Indium Sulphide (InS), is performed using density functional theory calculation. In this context, the effects of natural and artificial interlayer stacking configurations, and externally applied out-of-plane direction electric field are emphasized. The structural, thermal, and dynamic stabilities of individual bilayers are assessed from the cohesive energy/interlayer interaction energy, phonon spectrum, and molecular dynamics evolution, respectively. The effects of the vdW bilayer environment on the in-plane structural parameters like lattice vector, bond length, and bond angle of the constituent monolayers are comprehensively investigated. The electronic properties are estimated from the band edge energy, the density of states, energy bandgap, and interlayer energy band alignment, which are systematically analysed from the interlayer interactions in terms of interlayer distance, out-of-plane charge distribution, and interlayer charge transfer. The key findings demonstrate that the interlayer stacking engineering and applied out-of-plane electric field can induce unique and tailor-made modulations in the overall electronic properties of GaS/InS and GaSe/InS bilayer, which can be exploited in favour of electronic/optoelectronic applications.

Comparative study on physical properties of bio-based PA56 fibers and wearability of their fabrics

Abstract Bio-based polyamide 56 (PA56) has significant advantages in reducing oil dependence and reducing carbon emissions. This study compared the physical properties of bio-based PA56 and conventional polyamide 66 (PA66) fibers and their fabrics. The results showed that due to the odd arrangement structure of carbon atoms in PA56 fiber molecules, its crystallinity and orientation were lower than those of PA66. At the same time, PA56 had a higher degradation rate and coloring rate due to its smaller crystallinity and higher moisture content and gave PA56 fabrics better instantaneous cooling and moisture absorption and drying properties. In addition, the molecular structure characteristics of PA56 also lead to a lower stiffness and soft feel of the fabric, which is beneficial for improving the curling phenomenon of the fabric. Overall, bio-based PA56 fibers can meet the applications in the textile and clothing field and can largely replace PA66, which is worthy of further research and utilization.

Probiotic-derived amphiphilic exopolysaccharide self-assembling adjuvant delivery platform for enhancing immune responses

Enhancing immune response activation through the synergy of effective antigen delivery and immune enhancement using natural, biodegradable materials with immune-adjuvant capabilities is challenging. Here, we present NAPSL.p that can activate the Toll-like receptor 4 (TLR4) pathway, an amphiphilic exopolysaccharide, as a potential self-assembly adjuvant delivery platform. Its molecular structure and unique properties exhibited remarkable self-assembly, forming a homogeneous nanovaccine with ovalbumin (OVA) as the model antigen. When used as an adjuvant, NAPSL.p significantly increased OVA uptake by dendritic cells. In vivo imaging revealed prolonged pharmacokinetics of NAPSL. p-delivered OVA compared to OVA alone. Notably, NAPSL.p induced elevated levels of specific serum IgG and isotype titers, enhancing rejection of B16-OVA melanoma xenografts in vaccinated mice. Additionally, NAPSL.p formulation improved therapeutic effects, inhibiting tumor growth, and increasing animal survival rates. The nanovaccine elicited CD4+ and CD8+ T cell-based immune responses, demonstrating the potential for melanoma prevention. Furthermore, NAPSL.p-based vaccination showed stronger protective effects against influenza compared to Al (OH)3 adjuvant. Our findings suggest NAPSL.p as a promising, natural self-adjuvanting delivery platform to enhance vaccine design across applications.

Ab initio molecular dynamics study on the local structures and solid/liquid interface in liquid Al-Ti and Al-B-Ti alloys

High-purity aluminum, owing to its excellent physical and chemical properties, finds extensive applications across various fields. A comprehensive understanding of the local structure of liquid Al-based alloys and the characteristics of solute atoms at the forefront of the solid-liquid interface is highly advantageous for the purification of aluminum. Ab initio molecular dynamics (AIMD) simulations were employed to study the local structures, element interactions and electronic structures in Al-Ti and Al-B-Ti melts, together with the behaviors of Ti atom and B-Ti atom pair at the solid/liquid interface forefront of Al. In the Al-B-Ti ternary melt, there are stronger interactions between B and Ti atoms than those between Al and B atoms as well as between Al and Ti atoms. The introduction of B atoms leads to the disruption of Al-Ti bonds and the formation of B-Ti bonds, thereby altering the state of Ti atoms in the melt and then influencing their diffusion properties. The dynamic process of B-Ti bond formation in the melt has been elucidated. The bond angle distribution function shows that the geometric configuration around Ti atoms in the Al melt undergoes significant changes with the addition of B atoms. A strong hybridization occurs between the 3d orbital of Ti atom and the 2p orbital of B atom. Moreover, a notable charge accumulation between B and Ti atoms, indicates the strong interaction between them. The addition of Ti atom can promote the migration of the Al solid/liquid interface. The B-Ti bond is very stable at the forefront of the Al solid/liquid interface, and the formation of B-Ti bond significantly drag the migration of the Al solid/liquid interface.

19.36% Efficiency Organic Solar Cells Based on Low‐Cost Terpolymer Donors with Simple Molecular Structures

AbstractLow cost and high performance are key elements for the industrialization of organic solar cells (OSCs). In view of this, developing highly‐efficient organic photovoltaic molecules with simple chemical structure is one of the most effective countermeasures. Herein, three simple‐structure terpolymers PTQ12‐5, PTQ12‐10, and PTQ12‐15 are designed and synthesized, by embedding difluoro‐substituted bithiophene (2T‐2F) unit into the backbone of low‐cost and high‐efficiency polymer PTQ10. The synthesis of three terpolymers contains only two‐step synthetic routes and over 85% synthetic yields from cheap raw compounds, thus exhibiting distinctly low‐cost characteristic. Remarkably, PTQ12‐5 shows significantly higher absorbance coefficient and hole mobility than PTQ10. Consequently, PTQ12‐5‐based OSCs shows more efficient exciton dissociation and charge transfer, suppressed carrier recombination, tighter molecular π‐π stacking, and faster and more balanced charge transport, thus demonstrates a significantly improved efficiency of 18.77% than that of PTQ10‐based device (18.03%). Moreover, an outstanding efficiency of 19.36% is achieved in PTQ12‐5‐based ternary device by further modulating the energy level alignment and blending features of photoactive molecules, which is the highest efficiency of OSCs based on low‐cost polymers to date. This work has significant implications for guiding the design of low‐cost and high‐performance organic photovoltaic materials.

Steric Effects of Alcohols on the [Mn4O4] Cubane-Type Structures

[M4O4] (M = 3d transition metal) represents an interesting class of compounds featuring cubane-type molecular structures, and particularly, [Mn4O4] cubanes or their derivatives attract much attention by virtue of their potential applications as single-molecule magnets (SMMs) or catalysts. However, the rational design of desired cubane-related structures is still a challenging subject due to the lack of readily available methods to effectively tune the construction patterns of the molecule assembly. In this work, we report the employment of different alcohols to prepare three cubane-related molecules, Mn2(dhd)4(iPrOH)2 (1), Mn4(dhd)4(OEt)4(EtOH)4 (2) and Mn4(dhd)6(OMe)2(MeOH)2 (3) (dhd = 5,5-dimethyl-2,4-hexanedione). Interestingly, the bulkiest iPrOH leads to simple rhombic dimer molecule 1. It can be deemed a rudimentary structure oftetranuclear [Mn4O4] cubane 2, which can be realized by the use of less bulky EtOH. In addition, the least bulky MeOH promotes the assembly of the cubanes, eventually bringing about defective dicubane molecular cluster 3. The accurate crystal structures of 1–3 were modeled by single-crystal X-ray diffraction, and their electronic structures were investigated through absorption spectroscopy coupled with theoretical calculations. Overall, this work demonstrates a systematic study on controlling cubane-type structures of Mn-based compounds by applying different solvents, which provides a new means to design functional molecules for specific applications.

Exploring the effects of mono-bromination on hole-electron transport and distribution in dibenzofuran and dibenzothiophene isomers: a first-principles study.

This study delves into hole-electron transport and distribution properties inherent in mono-brominated dibenzofuran (DBF) and dibenzothiophene (DBT) isomers. As determined by frontier molecular orbitals, all brominated structures have narrower bandgaps than their primary structures. The TD-DFT calculation showed that 2BDBT had the highest absorption wavelength of all molecules at 315.35nm. Notably, the study unveils remarkably low electron and hole reorganization energies due to bromine substitution in DBF and DBT molecules. Specifically, the 4BDBF has the lowest hole reorganization energy of all DBF configurations, 0.229eV. In addition, 3BDBF has 0.226eV less electron reorganization energy than all other molecules. Compared to DBT, 3BDBT has the lowest electron reorganization energy of 0.254eV. Overall, this research sheds significant light on the fundamental electronic and hole transport characteristics of bromine-substituted DBF and DBT isomers, highlighting their promising role in polymer design as donors/acceptors for advanced organic electronic applications. Molecular structures were optimized using Density Functional Theory (DFT) B3LYP/6-311 + + G (d, p) level of theory, and the study further elucidates these molecules' energy levels and absorption spectra through Time-Dependent Density Functional Theory TD-DFT; these calculations were performed using Gaussian 09W software package. The key parameters such as reorganization energies, Electron Localization Function map, Laplacian Bond Order, and NCI-RDG were meticulously examined for the molecules with the results of DFT calculations were analyzed and displayed by utilizing the software packages VMD 1.9.4 and Multiwfn 3.8, aiming to comprehend their charge transport and distribution properties.

Toward the Reconciliation of Inconsistent Molecular Structures from Biochemical Databases.

Information on the structure of molecules, retrieved via biochemical databases, plays a pivotal role in various disciplines, including metabolomics, systems biology, and drug discovery. No such database can be complete and it is often necessary to incorporate data from several sources. However, the molecular structure for a given compound is not necessarily consistent between databases. This article presents StructRecon, a novel tool for resolving unique molecular structures from database identifiers. Currently, identifiers from BiGG, ChEBI, Escherichia coli Metabolome Database (ECMDB), MetaNetX, and PubChem are supported. StructRecon traverses the cross-links between entries in different databases to construct what we call identifier graphs. The goal of these graphs is to offer a more complete view of the total information available on a given compound across all the supported databases. To reconcile discrepancies met during the traversal of the databases, we develop an extensible model for molecular structure supporting multiple independent levels of detail, which allows standardization of the structure to be applied iteratively. In some cases, our standardization approach results in multiple candidate structures for a given compound, in which case a random walk-based algorithm is used to select the most likely structure among incompatible alternatives. As a case study, we applied StructRecon to the EColiCore2 model. We found at least one structure for 98.66% of its compounds, which is more than twice as many as possible when using the databases in more standard ways not considering the complex network of cross-database references captured by our identifier graphs. StructRecon is open-source and modular, which enables support for more databases in the future.

Formulation of Chicken Sausages Enriched with Clove (Syzygium Aromaticum) Powder and Sesame (Sesamum Indicum L.) Flour during the Fermentation Stage

The study evaluated the combined effect of clove and sesame flour during the fermentation stage. The impact of the incorporation of sesame flour in S1 batch (sausages with 80% chicken filet, 17% veal fat, 2% sesame flour, and 1% cloves) and S2 batch (sausages with 80% chicken filet, 16% veal fat and 2% sesame flour, and 2% cloves) compared to Control batch (80% chicken filet, 18% veal fat, and 2% sesame flour) on the physico-chemical, color and molecular structure during the fermentation stage. Results showed that the incorporation of clove in the chicken dry sausages significantly increased the moisture and protein contents since it passed from 14.82 on day 1 in the Control at 30.23 ± 0.90% for S2 on day 1, respectively. The results obtained also showed that clove is a source of antioxidants, since the oxidation indicator parameters decreased with the level of addition of clove. The results demonstrated the potential of using fluorescence spectroscopy for monitoring the quality of sausages, since principal component analysis and factorial discriminant analysis (applied to fluorescence spectra allowed to discriminate between samples according to the level of clove addition (97.22% of correct classification).

Exploring different classification-dependent QSAR modelling strategies for HDAC3 inhibitors in search of meaningful structural contributors.

Histone deacetylase 3 (HDAC3), a Zn2+-dependent class I HDACs, contributes to numerous disorders such as neurodegenerative disorders, diabetes, cardiovascular disease, kidney disease and several types of cancers. Therefore, the development of novel and selective HDAC3 inhibitors might be promising to combat such diseases. Here, different classification-based molecular modelling studies such as Bayesian classification, recursive partitioning (RP), SARpy and linear discriminant analysis (LDA) were conducted on a set of HDAC3 inhibitors to pinpoint essential structural requirements contributing to HDAC3 inhibition followed by molecular docking study and molecular dynamics (MD) simulation analyses. The current study revealed the importance of hydroxamate function for Zn2+ chelation as well as hydrogen bonding interaction with Tyr298 residue. The importance of hydroxamate function for higher HDAC3 inhibition was noticed in the case of Bayesian classification, recursive partitioning and SARpy models. Also, the importance of substituted thiazole ring was revealed, whereas the presence of linear alkyl groups with carboxylic acid function, any type of ester function, benzodiazepine moiety and methoxy group in the molecular structure can be detrimental to HDAC3 inhibition. Therefore, this study can aid in the design and discovery of effective novel HDAC3 inhibitors in the future.

Orchestrated Octuple C–H Activation: A Bottom‐Up Topology Engineering Approach toward Stimuli‐Responsive Double‐Heptagon‐Embedded Wavy Polycyclic Heteroaromatics

Curiosity‐driven innovations on the design and synthesis of nonplanar polycyclic aromatic/heteroaromatic compounds with new molecular topologies unfold exciting opportunities for harnessing their intriguing supramolecular properties and thereby the development of novel functional organic materials. This work presents such an innovative synthetic concept of a bottom‐up molecular topology engineering through a unique orchestrated octuple C–H activation reaction, toward the rapid synthesis of a novel class of double heptagon‐incorporated nitrogen‐doped laterally‐fused polycyclic compounds with rarely reported wavy structural configuration. The profound impact of the molecular wavy structures of these compounds on their properties is manifested by weak and tunable solid‐state intermolecular interactions controlling the electronic properties of the materials, leading to reversibly switchable fluorochromism in the solid state and thin films with mechanical force and solvent vapors as external stimuli, thereby indicating their potential applicability in rewritable fluorescent optical recording media, security papers, mechanosensors, volatile organic compound (VOC) sensors etc.

Orchestrated Octuple C-H Activation: A Bottom-Up Topology Engineering Approach toward Stimuli-Responsive Double-Heptagon-Embedded Wavy Polycyclic Heteroaromatics.

Curiosity-driven innovations on the design and synthesis of nonplanar polycyclic aromatic/heteroaromatic compounds with new molecular topologies unfold exciting opportunities for harnessing their intriguing supramolecular properties and thereby the development of novel functional organic materials. This work presents such an innovative synthetic concept of a bottom-up molecular topology engineering through a unique orchestrated octuple C-H activation reaction, toward the rapid synthesis of a novel class of double heptagon-incorporated nitrogen-doped laterally-fused polycyclic compounds with rarely reported wavy structural configuration. The profound impact of the molecular wavy structures of these compounds on their properties is manifested by weak and tunable solid-state intermolecular interactions controlling the electronic properties of the materials, leading to reversibly switchable fluorochromism in the solid state and thin films with mechanical force and solvent vapors as external stimuli, thereby indicating their potential applicability in rewritable fluorescent optical recording media, security papers, mechanosensors, volatile organic compound (VOC) sensors etc.

Synthesis of graphitic carbon nitride (g-C3N4) by high-temperature condensation for electrochemical evaluation of dichlorophen and thymol in environmental trials

The work deals with synthesizing carbon-based nanomaterial, i.e., graphitic carbon nitride, which was carried out using the high-temperature condensation method. Graphitic carbon nitride is characterized by cost efficiency, increased thermal resilience, a two-dimensional molecular layer structure, biocompatibility and stability. These properties can be used in the electrochemical investigations of fungicides such as dichlorophen and thymol. The synthesized nanomaterial was first characterized using XRD, SEM, UV-DRS, BET, FTIR, CV and EIS investigations. The cyclic voltammetry behavior of dichlorophen and thymol shows the proton-coupled irreversible electron transfer process at a modified carbon paste electrode with the participation of same number of protons and electrons. The developed sensor exhibited good detection limits for the dichlorophen and thymol as low as 15.3 nM and 12.0 nM with the sensitivity of 126.8 µA·µM−1·cm−2 and 59.2 µA·µM−1·cm−2, respectively. The applicability of the developed sensor was tested in spiked soil and water samples, and good recoveries were achieved with a % RSD of 1.67 and 1.30, respectively. The anti-interference responses to metal ions demonstrate the selectivity (qualitative) of the developed sensor in the electrochemical detection of dichlorophen and thymol. In the future, the sensor developed would offer the potential to sensitively and selectively detect other pesticide molecules in environmental samples.

Different lateral packing stress in acyl chains alters KcsA orientation and structure in lipid membranes.

The molecular structures of the various intrinsic lipids in membranes regulate lipid-protein interactions. These different lipid structures with unique volumes produce different lipid molecular packing stresses/lateral stresses in lipid membranes. Most studies examining lipid packing effects have used phosphatidylcholine and phosphatidylethanolamine (PE), which are the main phospholipids of eukaryotic cell membranes. In contrast, Gram-negative or Gram-positive bacterial membranes are composed primarily of phosphatidylglycerol (PG) and PE, and the physical and thermodynamic properties of each acyl chain in PG at the molecular level remain unresolved. In this study, we used 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG, 16:0-18:1 PG) and 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (PAPG, 16:0-20:4 PG) to prepare lipid bilayers (liposome) with the rod-type fluorescence probe DPH. We measured the lipid packing conditions by determining the rotational freedom of DPH in POPG or PAPG bilayers. Furthermore, we investigated the effect of different monoacyl chains on a K+ channel (KcsA) structure when embedded in POPG or PAPG membranes. The results revealed that differences in the number of double bonds and carbon chain length in the monoacyl chain at sn-2 affected the physicochemical properties of the membrane and the structure and orientation of KcsA.