Complex Biomolecules Research Articles

Electrochemical halogen-atom transfer alkylation via α-aminoalkyl radical activation of alkyl iodides

Alkyl halides, widely recognized as important building blocks and reagents in organic synthesis, can serve as versatile alkyl radical precursors in radical-based transformations. However, generating alkyl radicals directly from unactivated alkyl halides under mild conditions remains a challenge due to their extremely low reduction potentials. To address this issue, α-aminoalkyl radicals were employed as efficient halogen-atom transfer (XAT) reagents in the photoredox activation of unactivated alkyl halides. Here, we report an effective electrooxidation strategy for generating alkyl radicals from unactivated alkyl iodides via an electrochemical halogen-atom transfer (e-XAT) process under mild conditions. The α-aminoalkyl radicals generated by anodic oxidation are demonstrated to be efficient XAT reagents in these transformations. This facile electricity-driven strategy obviates the need for sacrificial anodes and external chemical oxidants. The method successfully applies to a wide variety of alkyl iodides, including primary, secondary, and tertiary, as well as structurally diverse olefins, exhibiting excellent functional group tolerance. Moreover, we further demonstrate the utility of this strategy by rapidly functionalizing complex molecules and biomolecules.

Evidence of H/D Exchange within Metal-Adducted Carbohydrates after Ion/Ion-Dissociation Reactions.

Tandem mass spectrometry (MS/MS) using fragmentation has become one of the most effective methods for gaining sequence and structural information on biomolecules. Ion/ion reactions are competitive reactions, where either proton transfer (PT) or electron transfer (ET) can occur from interactions between multiply charged cations and singly charged anions. Utilizing ion/ion reactions with fluoranthene has offered a unique method of fragment formation for the structural elucidation of biomolecules. Fluoranthene is considered an ideal anion reagent because it selectively causes electron-transfer dissociation (ETD) and minimizes PT when interacting with peptides. However, limited investigations have sought to understand how fluoranthene─the primary, commercially available anion reagent─interacts with other biomolecules. Here, we apply deuterium labeling to investigate ion/ion reaction mechanisms between fluoranthene and divalent, metal-adducted carbohydrates (Ca2+, Mg2+, Co2+, and Ni2+). Deuterium labeling of carbohydrates allowed us to observe evidence of hydrogen/deuterium exchange (HDX) occurring after ion/ion dissociation reactions. The extent of deuterium loss is dependent on several factors, including the physical properties of the metal ion and the fragment structure. Based on the deuterium labeling data, we have proposed ETD, PTD, and intermolecular PT─also described as HDX─mechanisms. This research provides a fundamental perspective of ion/ion and ion/molecule reaction mechanisms and illustrates properties that impact ion/ion and ion/molecule reactions for carbohydrates. Together, this could improve the capability to distinguish complex and heterogeneous biomolecules, such as carbohydrates.

Imaging of N-Linked Glycans in Biological Tissue Sections Using Nanospray Desorption Electrospray Ionization (nano-DESI) Mass Spectrometry.

N-linked glycans are complex biomolecules vital to cellular functions that have been linked to a wide range of pathological conditions. Mass spectrometry imaging (MSI) has been used to study the localization of N-linked glycans in cells and tissues. However, their structural diversity presents a challenge for MSI techniques, which stimulates the development of new approaches. In this study, we demonstrate for the first time spatial mapping of N-linked glycans in biological tissues using nanospray desorption electrospray ionization mass spectrometry imaging (nano-DESI MSI). Nano-DESI MSI is an ambient ionization technique that has been previously used for imaging of metabolites, lipids, and proteins in biological tissue samples without special sample pretreatment. N-linked glycans are released from glycoproteins using an established enzymatic digestion with peptide N-glycosidase F, and their spatial localization is examined using nano-DESI MSI. We demonstrate imaging of N-linked glycans in formalin-fixed paraffin-embedded human hepatocellular carcinoma and human prostate tissues in both positive and negative ionization modes. We examine the localization of 38 N-linked glycans consisting of high mannose, hybrid fucosylated, and sialyated glycans. We demonstrate that negative mode nano-DESI MSI is well-suited for imaging of underivatized sialylated N-linked glycans. On-tissue MS/MS of different adducts of N-linked glycans proves advantageous for elucidation of the glycan sequence. This study demonstrates the applicability of liquid extraction techniques for spatial mapping of N-linked glycans in biological samples, providing an additional tool for glycobiology research.

Divalent transition metal coatings for an effective protein-nanoparticle conjugation

Magnetic nanoparticles (MNPs) are widely used for immobilizing complex biomolecules such as proteins due to their high loading capacity, biocompatibility, and easy magnetic harvesting. However, there is not a universal solution to achieve the oriented immobilization of the protein of interest. One common strategy involves the selective binding of poly-histidine-tagged (His-tag) proteins to divalent transition metal centers (TM2+) chelated by organic molecules like nitrilotriacetic acid (NTA). This article describes an innovative procedure to functionalize MNPs by simply growing of a thin layer of TM2+ hydroxides on the MNP surface, which increases the number of coordination centers and enhances the surface interaction with the protein surface. The immobilization yields of two sets of MNPs coated with Co2+, Ni2+ and Cu2+ hydroxides were compared to the conventional coating using the same inorganic cores but coated and functionalized with NTA-TM2+ moieties. It is shown that the one-step Co coated MNPs showed the highest selectivity and specificity towards His-tags. Thus, this coating not only reduce the functionalization steps to drive an oriented protein binding but also achieve an increment of immobilization yields over 1.5-fold respect to NTA-Co2+ analogous for his-tagged proteins with different 3D complexity while preserving similar or even higher enzymatic activity.

Orientation-Controllable Enzyme Cascade on Electrode for Bioelectrocatalytic Chain Reaction.

The accomplishment of concurrent interenzyme chain reaction and direct electric communication in a multienzyme-electrode is challenging since the required condition of multienzymatic binding conformation is quite complex. In this study, an enzyme cascade-induced bioelectrocatalytic system has been constructed using solid binding peptide (SBP) as a molecular binder that coimmobilizes the invertase (INV) and flavin adenine dinucleotide (FAD)-dependent glucose dehydrogenase gamma-alpha complex (GDHγα) cascade system on a single electrode surface. The SBP-fused enzyme cascade was strategically designed to induce diverse relative orientations of coupling enzymes while enabling efficient direct electron transfer (DET) at the FAD cofactor of GDHγα and the electrode interface. The interenzyme relative orientation was found to determine the intermediate delivery route and affect overall chain reaction efficiency. Moreover, interfacial DET between the fusion GDHγα and the electrode was altered by the binding conformation of the coimmobilized enzyme and fusion INVs. Collectively, this work emphasizes the importance of interenzyme orientation when incorporating enzymatic cascade in an electrocatalytic system and demonstrates the efficacy of SBP fusion technology as a generic tool for developing cascade-induced direct bioelectrocatalytic systems. The proposed approach is applicable to enzyme cascade-based bioelectronics such as biofuel cells, biosensors, and bioeletrosynthetic systems utilizing or producing complex biomolecules.

Protocol for the development of coarse-grained structures for macromolecular simulation using GROMACS.

Coarse-grained simulations have emerged as a valuable tool in the study of large and complex biomolecular systems. These simulations, which use simplified models to represent complex biomolecules, reduce the computational cost of simulations and enable the study of larger systems for longer periods of time than traditional atomistic simulations. GROMACS is a widely used software package for performing coarse-grained simulations of biomolecules, and several force fields have been developed specifically for this purpose. In this protocol paper, we explore the advantages of using coarse-grained simulations in the study of biomolecular systems, focusing specifically on simulations performed using GROMACS. We discuss the force fields required for these simulations and the types of research questions that can be addressed using coarse-grained simulations. We also highlight the potential benefits of coarse-grained simulations for the development of new force fields and simulation methodologies. We then discuss the expected results from coarse-grained simulations using GROMACS and the various techniques that can be used to analyze these results. We explore the use of trajectory analysis tools, as well as thermodynamic and structural analysis techniques, to gain insight into the behavior of biomolecular systems.

Hydrolytic and thermal stability of urea‐formaldehyde resins based on tannin and betaine bio‐fillers

AbstractIn this work, betaine (trimethyl glycine) and tannin (complex biomolecules of polyphenolic nature) were used as bio‐fillers. Urea‐formaldehyde (UF) resin with a molar ratio of formaldehyde versus urea (FA/U) of 0.8 was synthesized in situ with tannin and betaine as bio‐fillers, to obtain UF resin with reduced free FA content and increased hydrolytic and thermal stability by the principles of sustainability. The samples TUF (with tannin) and BUF (with betaine) were characterized by using X‐ray diffraction analysis (XRD), non‐isothermal thermogravimetric analysis (TGA), and differential thermal analysis (DTA), supported by data from Fourier Transform Infrared spectroscopy (FTIR) and Scanning electron microscopy (SEM). The percentage of free FA in modified BUF resin is 0.1%, while the percentage of free FA in tannin‐modified resin is 0.8%. The hydrolytic stability of the modified UF resins was determined by measuring the concentration of liberated FA in the modified UF resins, after acid hydrolysis. The modified BUF resin is hydrolytically more stable because the content of released FA is 3.6% compared to the modified TUF resin, where it was 7.4%. Based on the value for T5%, the more thermally stable resin is the modified TUF resin (T5% = 123.1°C), while the value of the T5% for the BUF resin is 83.1°C. This work showed how UF bio‐composite with reduced free FA content and increased hydrolytic and thermal stability can be obtained using tannin and betaine as bio‐fillers.

Comprehensive Approach to Simulating Large Scale Conformational Changes in Biological Systems Utilizing a Path Collective Variable and New Barrier Restraint.

Conformational sampling of complex biomolecules is an emerging frontier in drug discovery. Advances in lab-based structural biology and related computational approaches like AlphaFold have made great strides in obtaining static protein structures for biologically relevant targets. However, biology is in constant motion, and many important biological processes rely on conformationally driven events. Conventional molecular dynamics (MD) simulations run on standard hardware are impractical for many drug design projects, where conformationally driven biological events can take microseconds to milliseconds or longer. An alternative approach is to focus the search on a limited region of conformational space defined by a putative reaction coordinate (i.e., path collective variable). The search space is typically limited by applying restraints, which can be guided by insights about the underlying biological process of interest. The challenge is striking a balance between the degree to which the system is constrained and still allowing for natural motions along the path. A plethora of restraints exist to limit the size of conformational search space, although each has drawbacks when simulating complex biological motions. In this work, we present a three-stage procedure to construct realistic path collective variables (PCVs) and introduce a new kind of barrier restraint that is particularly well suited for complex conformationally driven biological events, such as allosteric modulations and conformational signaling. The PCV presented here is all-atom (as opposed to C-alpha or backbone only) and is derived from all-atom MD trajectory frames. The new restraint relies on a barrier function (specifically, the scaled reciprocal function), which we show is particularly beneficial in the context of molecular dynamics, where near-hard-wall restraints are needed with zero tolerance to restraint violation. We have implemented our PCV and barrier restraint within a hybrid sampling framework that combines well-tempered metadynamics and extended-Lagrangian adaptive biasing force (meta-eABF). We use three particular examples of high pharmaceutical interest to demonstrate the value of this approach: (1) sampling the distance from ubiquitin to a protein of interest within the supramolecular cullin-RING ligase complex, (2) stabilizing the wild-type conformation of the oncogenic mutant JAK2-V617F pseudokinase domain, and (3) inducing an activated state of the stimulator of interferon genes (STING) protein observed upon ligand binding. For examples 2 and 3, we present statistical analysis of meta-eABF free energy estimates and, for each case, code for reproducing this work.

1H-detected characterization of carbon–carbon networks in highly flexible protonated biomolecules using MAS NMR

In the last three decades, the scope of solid-state NMR has expanded to exploring complex biomolecules, from large protein assemblies to intact cells at atomic-level resolution. This diversity in macromolecules frequently features highly flexible components whose insoluble environment precludes the use of solution NMR to study their structure and interactions. While High-resolution Magic-Angle Spinning (HR-MAS) probes offer the capacity for gradient-based 1H-detected spectroscopy in solids, such probes are not commonly used for routine MAS NMR experiments. As a result, most exploration of the flexible regime entails either 13C-detected experiments, the use of partially perdeuterated systems, or ultra-fast MAS. Here we explore proton-detected pulse schemes probing through-bond 13C–13C networks to study mobile protein sidechains as well as polysaccharides in a broadband manner. We demonstrate the use of such schemes to study a mixture of microtubule-associated protein (MAP) tau and human microtubules (MTs), and the cell wall of the fungus Schizophyllum commune using 2D and 3D spectroscopy, to show its viability for obtaining unambiguous correlations using standard fast-spinning MAS probes at high and ultra-high magnetic fields.

Synthesis and applications of mirror-image proteins.

The homochirality of biomolecules in nature, such as DNA, RNA, peptides and proteins, has played a critical role in establishing and sustaining life on Earth. This chiral bias has also given synthetic chemists the opportunity to generate molecules with inverted chirality, unlocking valuable new properties and applications. Advances in the field of chemical protein synthesis have underpinned the generation of numerous 'mirror-image' proteins (those comprised entirely of D-amino acids instead of canonical L-amino acids), which cannot be accessed using recombinant expression technologies. This Review seeks to highlight recent work on synthetic mirror-image proteins, with a focus on modern synthetic strategies that have been leveraged to access these complex biomolecules as well as their applications in protein crystallography, drug discovery and the creation of mirror-image life.

Ligand-Enabled Gold-Catalyzed C(sp2)–O Cross-Coupling Reactions

Reported herein is a ligand-enabled gold-catalyzed C(sp2)–O cross-coupling reaction of aryl iodides and aliphatic alcohols. The synthesis of a variety of aryl alkyl ethers including complex biomolecules and various medicinally relevant motifs has been achieved to demonstrate the usefulness of the method. The importance of gold catalysis has been highlighted by overcoming the selectivity issues that are in general observed for C–O cross-coupling reactions when other transition metals are used as catalysts.

Solid Lipid Nanoparticles: Multitasking Nano-Carriers for Cancer Treatment.

Despite all the advances seen in recent years, the severe adverse effects and low specificity of conventional chemotherapy are still challenging problems regarding cancer treatment. Nanotechnology has helped to address these questions, making important contributions in the oncological field. The use of nanoparticles has allowed the improvement of the therapeutic index of several conventional drugs and facilitates the tumoral accumulation and intracellular delivery of complex biomolecules, such as genetic material. Among the wide range of nanotechnology-based drug delivery systems (nanoDDS), solid lipid nanoparticles (SLNs) have emerged as promising systems for delivering different types of cargo. Their solid lipid core, at room and body temperature, provides SLNs with higher stability than other formulations. Moreover, SLNs offer other important features, namely the possibility to perform active targeting, sustained and controlled release, and multifunctional therapy. Furthermore, with the possibility to use biocompatible and physiologic materials and easy scale-up and low-cost production methods, SLNs meet the principal requirements of an ideal nanoDDS. The present work aims to summarize the main aspects related to SLNs, including composition, production methods, and administration routes, as well as to show the most recent studies about the use of SLNs for cancer treatment.

Potential use of LIAD time-of-flight mass spectrometry for the detection of biomolecules: An example of detecting nucleobases in DNA

Deoxyribonucleic acid (DNA) carries the genetic information necessary for the synthesis of RNA and proteins; it is a biological macromolecule essential for the development and proper functioning of living organisms and is composed of nucleobases, deoxyribose, and phosphate. The four nucleobases in DNA are adenine (AD), guanine (GU), thymine (TY), and cytosine (CY). Abnormal concentrations of these four nucleobases in an organism have a significant impact on disease diagnosis. Therefore, the qualitative and quantitative detection of these DNA nucleobases in organisms is helpful to diagnose certain diseases. In this work, we report the simultaneous determination of purine (AD, GU) and pyrimidine (TY, CY) nucleobases in DNA using laser-induced acoustic desorption (LIAD) with electron ionization (EI)/time-of-flight mass spectrometry (TOFMS). The purine (MW 120 Da) samples were used as model compounds to assess the sensitivity and quantitative performance of the instrument. Its limits of detection assessed using the LIAD/EI/MS method were ∼0.5–1.2 pg under optimal conditions, and their calibration curves exhibited good linearity (R2 = 0.98). The LIAD/TOFMS was successfully applied in the simultaneous detection of AD, GU, TY, and CY in real DNA samples. The advantage of this technique is simple, fast, and without complex pre-treatment processes. In addition, a quartz-enhanced LIAD (QE-LIAD) source was used to improve the signal strength. The desorption for complex biomolecules shows that the QE-LIAD is still a “gentle” desorption source.

Facilitating the structural characterisation of non-canonical amino acids in biomolecular NMR.

Peptides and proteins containing non-canonical amino acids (ncAAs) are a large and important class of biopolymers. They include non-ribosomally synthesised peptides, post-translationally modified proteins, expressed or synthesised proteins containing unnatural amino acids, and peptides and proteins that are chemically modified. Here, we describe a general procedure for generating atomic descriptions required to incorporate ncAAs within popular NMR structure determination software such as CYANA, CNS, Xplor-NIH and ARIA. This procedure is made publicly available via the existing Automated Topology Builder (ATB) server (https://atb.uq.edu.au, last access: 17 February 2023) with all submitted ncAAs stored in a dedicated database. The described procedure also includes a general method for linking of sidechains of amino acids from CYANA templates. To ensure compatibility with other systems, atom names comply with IUPAC guidelines. In addition to describing the workflow, 3D models of complex natural products generated by CYANA are presented, including vancomycin. In order to demonstrate the manner in which the templates for ncAAs generated by the ATB can be used in practice, we use a combination of CYANA and CNS to solve the structure of a synthetic peptide designed to disrupt Alzheimer-related protein-protein interactions. Automating the generation of structural templates for ncAAs will extend the utility of NMR spectroscopy to studies of more complex biomolecules, with applications in the rapidly growing fields of synthetic biology and chemical biology. The procedures we outline can also be used to standardise the creation of structural templates for any amino acid and thus have the potential to impact structural biology more generally.

Posttranslational, site-directed photochemical fluorine editing of protein sidechains to probe residue oxidation state via 19F-nuclear magnetic resonance.

The fluorination of amino acid residues represents a near-isosteric alteration with the potential to report on biological pathways, yet the site-directed editing of carbon-hydrogen (C-H) bonds in complex biomolecules to carbon-fluorine (C-F) bonds is challenging, resulting in its limited exploitation. Here, we describe a protocol for the posttranslational and site-directed alteration of native γCH2 to γCF2 in protein sidechains. This alteration allows the installation of difluorinated sidechain analogs of proteinogenic amino acids, in both native and modified states. This chemical editing is robust, mild, fast and highly efficient, exploiting photochemical- and radical-mediated C-C bonds grafted onto easy-to-access cysteine-derived dehydroalanine-containing proteins as starting materials. The heteroaryl-sulfonyl reagent required for generating the key carbon-centered C• radicals that install the sidechain can be synthesized in two to six steps from commercially available precursors. This workflow allows the nonexpert to create fluorinated proteins within 24 h, starting from a corresponding purified cysteine-containing protein precursor, without the need for bespoke biological systems. As an example, we readily introduce three γCF2-containing methionines in all three progressive oxidation states (sulfide, sulfoxide and sulfone) as D-/L- forms into histone eH3.1 at site 4 (a relevant lysine to methionine oncomutation site), and each can be detected by 19F-nuclear magnetic resonance of the γCF2 group, as well as the two diastereomers of the sulfoxide, even when found in a complex protein mixture of all three. The site-directed editing of C-H→C-F enables the use of γCF2 as a highly sensitive, 'zero-size-zero-background' label in protein sidechains, which may be used to probe biological phenomena, protein structures and/or protein-ligand interactions by 19F-based detection methods.

Accurate and Cost-Effective NMR Chemical Shift Predictions for Nucleic Acids Using a Molecules-in-Molecules Fragmentation-Based Method.

We have developed, implemented, and assessed an efficient protocol for the prediction of NMR chemical shifts of large nucleic acids using our molecules-in-molecules (MIM) fragment-based quantum chemical approach. To assess the performance of our approach, MIM-NMR calculations are calibrated on a test set of three nucleic acids, where the structure is derived from solution-phase NMR studies. For DNA systems with multiple conformers, the one-layer MIM method with trimer fragments (MIM1trimer) is benchmarked to get the lowest energy structure, with an average error of only 0.80 kcal/mol with respect to unfragmented full molecule calculations. The MIMI-NMRdimer calibration with respect to unfragmented full molecule calculations shows a mean absolute deviation (MAD) of 0.06 and 0.11 ppm, respectively, for 1H and 13C nuclei, but the performance with respect to experimental NMR chemical shifts is comparable to the more expensive MIM1-NMR and MIM2-NMR methods with trimer subsystems. To compare with the experimental chemical shifts, a standard protocol is derived using DNA systems with Protein Data Bank (PDB) IDs 1SY8, 1K2K, and 1KR8. The effect of structural minimizations is employed using a hybrid mechanics/semiempirical approach and used for computations in solution with implicit and explicit-implicit solvation models in our MIM1-NMRdimer methodology. To demonstrate the applicability of our protocol, we tested it on seven nucleic acids, including structures with nonstandard residues, heteroatom substitutions (F and B atoms), and side chain mutations with a size ranging from ∼300 to 1100 atoms. The major improvement for predicted MIM1-NMRdimer calculations is obtained from structural minimizations and implicit solvation effects. A significant improvement with the explicit-implicit solvation model is observed only for two smaller nucleic acid systems (1KR8 and 7NBK), where the expensive first solvation shell is replaced by the microsolvation model, in which a single water molecule is added for each solvent-exposed amino and imino protons, along with the implicit solvation. Overall, our target accuracy of ∼0.2-0.3 ppm for 1H and ∼2-3 ppm for 13C has been achieved for large nucleic acids. The proposed MIM-NMR approach is accurate and cost-effective (linear scaling with system size), and it can aid in the structural assignments of a wide range of complex biomolecules.

Click'n lock: rapid exchange between unsymmetric tetrazines and thiols for reversible, chemoselective functionalisation of biomolecules with on-demand bioorthogonal locking.

The late-stage functionalisation and diversification of complex structures including biomolecules is often achieved with the help of click chemistry. Besides employing irreversible click-like reactions, many synthetic applications benefit from reversible click reaction strategies, so called de-/trans-click approaches. Yet, the combination of both, reversible and irreversible click chemistry - while still respecting the stringent criteria of click transformations - remains so far elusive for modifications of biomolecular structures. Here, we report click'n lock as a concept that enables reversible click reactions and on-demand locking of chemical entities, thus switching from reversible to irreversible modifications of complex biomolecules. For this purpose, we employ the tetrazine-thiol exchange (TeTEx) reaction as a fully traceless click reaction with second order rate constants k2 higher than 2 M-1 s-1 within aqueous environments. Employing TeTEx as a reversible click reaction for the chemoselective modification of biomolecules is made possible by the use of 3,6-disubstituted 1,2,4,5-tetrazines bearing a single sulfide residue. The inherent reactivity of tetrazines towards inverse electron demand Diels-Alder (IEDDA) reactions allows to stabilize the clicked structure, switching from reversible to irreversible systems (click'n lock).

Unveiling Microbial Chemical Interactions Based on Metabolomics Approaches.

Microorganisms are ubiquitous in diverse habitats and studying their chemical interactions with the environment and comprehend its complex relations with both hosts and environment, are crucial for the development of strategies to control microbial diseases. This chapter discusses the importance of studying microorganisms with agricultural benefits, using specialized metabolites as examples. Herein we highlight the challenges and opportunities in utilizing microorganisms as alternatives to synthetic pesticides and fertilizers in agriculture. Genome-guided investigations and improved analytical methodologies are necessary to characterize diverse and complex biomolecules produced by microorganisms. Predicting and isolating bioproducts based on genetic information have become a focus for researchers, aided by tools like antiSMASH, BiG-SCAPE, PRISM, and others. However, translating genomic data into practical applications can be complex. Therefore,integrating genomics, transcriptomics, and metabolomics enhances chemical characterization, aiding in discovering new metabolic pathways and specialized metabolites. Additionally,elicitation is one promising strategy to enhance beneficial metabolite production. Finally, identify and characterize microbial secondary metabolites remain challenging due to their low production, complex chemical structure characterization and different environmental factors necessary for metabolite in vitroproduction.

Transition state searching for complex biomolecules: Algorithms and machine learning

Transition state is a key concept for chemists to understand and fine-tune the conformational changes of large biomolecules. Due to its short residence time, it is difficult to capture a transition state via experimental techniques. Characterizing transition states for a conformational change therefore is only achievable via physics-driven molecular dynamics simulations. However, unlike chemical reactions which involve only a small number of atoms, conformational changes of biomolecules depend on numerous atoms and therefore the number of their coordinates in our 3D space. The searching for their transition states will inevitably encounter the curse of dimensionality, i.e. the reaction coordinate problem, which invokes the invention of various algorithms for solution. Recent years, new machine learning techniques and the incorporation of some of them into the transition state searching methods emerged. Here, we first review the design principle of representative transition state searching algorithms, including the collective-variable (CV)-dependent gentlest ascent dynamics, finite temperature string, fast tomographic, travelling-salesman based automated path searching, and the CV-independent transition path sampling. Then, we focus on the new version of TPS that incorporates reinforcement learning for efficient sampling, and we also clarify the suitable situation for its application. Finally, we propose a new paradigm for transition state searching, a new dimensionality reduction technique that preserves transition state information and combines gentlest ascent dynamics.

Lipid Analysis by Mass Spectrometry coupled with Laser Light

AbstractLipids are small but complex biomolecules that feature an immense structural and functional diversity. The molecular structure and biological functions of lipids are intricately linked. Therefore, modern lipid analysis strives for complete structural elucidation and spatial mapping of individual species in tissues. Mass spectrometry is the uncontested key technology in lipidomics but cannot achieve this goal as a standalone technique. In particular, the distinction between frequently occurring isomers constitutes a major challenge. A promising step towards complete structural analysis of lipids consists in the coupling of mass spectrometry with laser light. Here we review recent advances in lipidomics applications employing laser‐induced ultraviolet and infrared photodissociation and ion spectroscopy, which substantially increase the gain in structural information. Fundamental concepts, instrumentation and promises of these powerful emerging techniques for future lipid analysis are outlined.