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Molecules

Molecules is a leading international, peer-reviewed, open access journal of chemistry published semimonthly online by MDPI.
Indexed in PubMed | Quartile Ranking JCR - Q2 (Biochemistry and Molecular Biology | Chemistry, Multidisciplinary)

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Accurate quantification in LC–MS experiments becomes challenging when analytes overlap both chromatographically and in mass spectra, as conventional extracted ion chromatogram-based methods can yield biased results by double-counting shared isotope signals. This limitation is particularly relevant for oligonucleotides, where degradation products and synthetic impurities frequently co-elute with the intended full-length product, complicating relative quantification. To address this, we developed DECAF, a straightforward and computationally efficient procedure for deconvoluting overlapping isotope patterns directly from MS1 data. The method models experimental isotope distributions as mixtures of theoretical templates across retention time, generating deconvoluted ion chromatograms whose peak areas accurately reflect the contributions of individual components. We demonstrate the utility of DECAF on two pharmaceutically relevant oligonucleotide mixture datasets, where it reliably estimated mixing proportions and enabled visualisation of component-specific elution profiles. Analysis of a typical sample required one to two minutes, underscoring the method’s practical efficiency. DECAF provides a transparent and accessible alternative to existing commercial software, with promising applications in pharmaceutical analysis and quality control.

6 February 2026

The traditional method of LC-MS1 signal quantification—XIC integration—is invalid in the presence of chromatographically and mass-overlapping compounds. (A,B) Theoretical isotope distributions of two oligonucleotides (strands B and C) with molecular weights differing by 4 Da. The short vertical grey lines surrounding the pink peaks are intervals used for aligning experimental isotopes against theoretical ones. (C) Experimental isotope distribution of a 1:1 mixture of overlapping strands B and C. The green and pink arrows indicate the range for traditional XIC-based quantification. (D) Both XICs consider the overlapping m/z region, so their sum will greatly exceed the mixture XIC. (E) Traditionally calculated XICs based on a sample without strand B contribution. And yet, the strand B XIC gives rise to a large peak. Extraction windows as in (D).

This study describes a single-laboratory validation of an ultra-high-performance liquid chromatographic (UHPLC) method for the determination of key compounds like hericenones, hericenes, erinacines, and ergosterol in Hericium erinaceus (H. erinaceus, Lion’s Mane) raw materials and finished products. The expanding market for Hericium erinaceus (Lion’s Mane) has increased the need for practical, routine-ready analytical methods that can quantify characteristic marker compounds and strengthen quality control across both raw materials and finished products. In this study, an ultra-high-performance liquid chromatographic (UHPLC) separation method was developed for the determination of hericenones, hericenes, erinacines, and ergosterol in Hericium erinaceus raw materials and finished products. Under the optimized conditions, the major target analytes—hericenones, hericenes, erinacine A, and ergosterol—were fully resolved (Rs > 1.5) within 38 min using an HSS T3 column at 30 °C. All the peaks in the LC chromatogram of Hericium erinaceus samples and standard solutions were structurally confirmed by LC–UV-MS/MS based on the possible mass spectra. The quantitative calibration curves were linear, covering a range of 10–300 μg/mL for hericenone C, D and E, and hericene A, D and C; 3–100 μg/mL for deacylhericenone and deacylhericene; 1–50 μg/mL for erinacine A, and 5–200 μg/mL for ergosterol. Limits of quantification (LOQs) for hericenone C, D, and E and for hericene A, D, and C were approximately 9.263, 4.545, 4.650, 1.854, 10.72, and 11.18 µg/mL, respectively, while LOQs for deacylhericenone and deacylhericene were 1.083 and 2.109 µg/mL. Erinacine A and ergosterol showed LOQs of 0.642 and 8.352 µg/mL, respectively. The recovery of ergosterol was evaluated for the method at two different levels: 91.6~93.9% for 0.2% spiking and 93.0~102.6% for 0.08% spiking. The method was successfully validated, demonstrating inter-day Relative Standard Deviation (RSD) values between 1.1% and 5.7% for detected analytes across diverse matrices. This validated method provides a consistent quantification of hericenones, hericenes, erinacine A, and ergosterol across a range of commercial products and raw Hericium erinaceus materials, providing a sensitive and reliable tool for product characterization and quality control. This method provides QC laboratories with a robust, UV-based tool for standardized product characterization without requiring mass spectrometry.

6 February 2026

Fruit body and mycelium of H. erinaceus and chemical structures of major hericenones and hericenes, erinacine A and ergosterol.

Bamboo powder waste generated from bamboo processing serves as an ideal feedstock for biochar (BC). This study employed potassium hydroxide (KOH) to modify biochar derived from bamboo powder waste, activating it at different temperatures (700 °C, 800 °C, and 900 °C) to yield samples designated KBC-700, KBC-800, and KBC-900, respectively. The physicochemical properties and pore structures of the modified biochar were characterized using SEM, specific surface area and pore size analysis, FT-IR, Raman spectroscopy, XRD, and zeta potential measurements. The adsorption performance of the modified biochar toward PFOA was investigated using kinetic and thermodynamic models, examining the effects of the solution pH, adsorbent dosage, and temperature. Results indicate that KBC-900 exhibits a significantly enhanced specific surface area (up to 2924.7 m2 g−1), reduced surface oxygen-containing functional groups, increased carbon skeleton aromatization, and expanded mesoporous channels. Under initial conditions of pH = 3 and reaction temperature of 298 K, KBC-900 achieved a PFOA adsorption capacity of 366.7 mg g−1 with a removal efficiency of 91.67%. The adsorption process conformed to pseudo-first-order and pseudo-second-order kinetic models as well as the Freundlich model. The adsorption equilibrium was reached within 12 h, indicating multi-layer adsorption dominated by chemisorption on a heterogeneous surface. Thermodynamic parameters indicate the adsorption reaction is an exothermic process. After five cycles of regeneration, KBC-900 maintained a removal efficiency of 75.69%. This study provides an efficient and reliable solution for removing PFOA from water.

6 February 2026

Three-dimensional structure diagram of PFOA.

The global challenge of antimicrobial resistance (AMR) has been framed primarily in terms of genetic resistance mechanisms. Nevertheless, bacteria can also survive antimicrobial stress through phenotypic plasticity, resulting in transient, non-genetic states such as tolerance, persistence, and population-level resilience. These phenotypic states complicate diagnostic efforts, diminish antibiotic efficacy, and contribute to the chronic nature of infections even in the absence of heritable resistance. This review evaluates phenotypic plasticity as a significant yet underrecognized factor in AMR, with a focus on responses to oxidative and photodynamic stress. Key manifestations of plasticity are discussed, including morphological and metabolic remodeling such as filamentation, small-colony variants, and metabolic rewiring, as well as envelope- and biofilm-associated heterogeneity and regulatory flexibility mediated by gene networks and horizontal regulatory transfer. The review highlights plastic responses elicited by reactive oxygen species-mediated stress and antimicrobial photodynamic inactivation, where single-cell heterogeneity, biofilm and mucus barriers, and light-dependent cues influence bacterial survival. Case studies are presented to demonstrate how photodynamic strategies can induce transient protective states and act synergistically with antibiotics, revealing mechanisms of action that extend beyond conventional single-target therapeutic models. Drawing on evidence from single-cell analyses, biofilm ecology, and experimental evolution, this review establishes phenotypic plasticity as a central element in the chemical biology of AMR. Enhanced understanding of plasticity is essential for advancing diagnostics, informing the development of adjuvant therapies, and predicting bacterial responses to novel antimicrobial interventions.

6 February 2026

Bacterial survival strategies beyond classical genetic resistance. Phenotypic plasticity involves cue-dependent, reversible adaptations (e.g., filamentation, biofilm formation, metabolic shifts), whereas bet-hedging generates stochastic, cue-independent variants such as persister cells. External cues, including antibiotics, reactive oxygen species (ROS), or photoinactivation, can induce phenotypic plasticity, while bet-hedging arises independently of such stimuli. Both strategies are non-heritable and distinct from genetic resistance, yet can promote bacterial survival during antimicrobial exposure and thereby facilitate the eventual emergence of genetic resistance.

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Molecules - ISSN 1420-3049