PFAS-Biomolecule Interactions: Case Study Using Asclepios Nodes and Automated Workflows in KNIME for Drug Discovery and Toxicology.

The Asclepios suite of KNIME nodes represents an innovative solution for conducting cheminformatics and computational chemistry tasks, specifically tailored for applications in drug discovery and computational toxicology. This suite has been developed using open-source and publicly accessible software. In this chapter, we introduce and explore the Asclepios suite through the lens of a case study. This case study revolves around investigating the interactions between per- and polyfluorinated alkyl substances (PFAS) and biomolecules, such as nuclear receptors. The objective is to characterize the potential toxicity of PFAS and gain insights into their chemical mode of action at the molecular level. The Asclepios KNIME nodes have been designed as versatile tools capable of addressing a wide range of computational toxicology challenges. Furthermore, they can be adapted and customized to accomodate the specific needs of individual users, spanning various domains such as nanoinformatics, biomedical research, and other related applications. This chapter provides an in-depth examination of the technical underpinnings and foundations of these tools. It is accompanied by a practical case study that demonstrates the utilization of Asclepios nodes in a computational toxicology investigation. This showcases the extendable functionalities that can be applied in diverse computational chemistry contexts. By the end of this chapter, we aim for readers to have a comprehensive understanding of the effectiveness of the Asclepios node functions. These functions hold significant potential for enhancing a wide spectrum of cheminformatics applications.

Influence of Pnictogen and Ligand Framework on the Lewis Acidity and Steric Environment in Pnictogen Pincer Complexes.

Pnictogen pincer complexes are a fascinating class of compounds due to their dynamic molecular and electronic structures, and valuable stoichiometric or catalytic reactivity. As recognition of their unique chemistry has grown, so too has the library of pincer ligands employed and pnictogen centres engaged to prepare them. Here we computationally study how the choice of pincer ligand framework and pnictogen influence the electronic and steric outcomes of the complexes obtained. The most relevant electronic parameter is the pnictogen-centred electrophilicity, which has been quantified by fluoride ion affinities and LUMO energies, while the most relevant steric parameter is the crowding around the central pnictogen, which has been quantified by the %Vbur values and visualized using steric maps. The resulting trends are analyzed with reference to binding pocket size, acceptor orbital type, electronic delocalization, π-donor strengths, and heteroatom incorporation. Thus, considering 16 ligand frameworks and 4 heavy pnictogen centres, this study provides a broad-spectrum view of stereo-electronic variation in pnictogen pincer complexes, which, together with a recent study on geometric variation in the same family, provides a substantial dataset to guide future molecular design and reactivity studies.

The radiative efficiency and global warming potential of HCFC-132b.

Hydro-chloro-fluoro-carbons (HCFCs) are potent greenhouse gases which strongly absorb the infrared (IR) radiation within the 8 - 12 µm atmospheric windows. Despite international policies schedule their phasing out by 2020 for developed countries and 2030 globally, HCFC-132b (CH2ClCClF2) has been recently detected with significant atmospheric concentration. In this scenario, detailed climate metrics are of paramount importance for understanding the capacity of anthropogenic pollutants to contribute to global warming. In this work, the radiative efficiency (RE) of HCFC-132b is experimentally measured for the first time and used to determine its global warming potential (GWP) over 20-, 100- and 500-year time horizon. Vibrational- and rotational-spectroscopic properties of this molecule are first characterized by exploiting a synergism between Fourier-transform IR (FTIR) spectroscopy experiments and quantum chemical calculations. Equilibrium geometry, rotational parameters and vibrational properties predicted theoretically beyond the double-harmonic approximation, are employed to assist the vibrational assignment  of the experimental trace. Finally, FTIR spectra measured over a range of pressures are used to determine HCFC-132b absorption cross section spectrum from 150 to 3000 cm-1, from which istantaneous and effective REs are derived and, in turn, used for GWP evaluation.

Alpinia Officinarum Hance Essential Oil as Potent Antipseudomonal Agent: Chemical Profile, Antibacterial Activity, and Computational Study.

Alpinia officinarum Hance, is an aromatic and medicinal herb with a very interesting history and prominent chemical and biological prospects. We aimed to investigate the antibacterial activity of Alpinia officinarum essential oil and the preferred molecular targets of its constituents together with their pharmacokinetic properties and toxicity profile. According to GC-MS analysis, eucalyptol was the main compound (27.52%) identified in Alpinia officinarum essential oil, followed by α-terpineol, and ß-sesquiphellandrene. As opposed to the weak antiradical activity estimated by DPPH and ABTS tests, the essential oil caused inhibition of all the bacteria following well-diffusion and microdilution methods, especially the gram-negative Pseudomonas aeruginosa and Escherichia coli. It displayed exceptionally remarkable activity against Pseudomonas aeruginosa by totally inhibiting its growth on the agar plate exceeding the effect of chloramphenicol standard. This bactericidal effect was confirmed by very low MIC and MBC values of 0.82 and 6.562 µg/mL, respectively. The molecular docking showed interesting binding affinity between the major compounds and various drug targets in Pseudomonas aeruginosa, also good pharmacokinetic and toxicity behavior. These encouraging findings are particularly relevant in light of the increasingly pressing challenge to find alternative substances with antibacterial aptitude to address the issue of antibiotic resistance among infectious bacteria.

Reconstruction of quality marker system for Ginkgo Folium tablet using UHPLC-Q-Orbitrap MS, quantum chemical calculation, network pharmacology, and molecular simulation.

INTRODUCTION: Ginkgo Folium tablet (GFT) is a patented traditional Chinese medicine prepared from Ginkgo biloba leaves extract (GBE). However, the current quality indicators for GFT or GBE as designated by the Chinese Pharmacopoeia are insufficient in preventing counterfeit events. OBJECTIVE: This study aimed to putatively identify compounds in GFT and to further develop a quality marker (Q-marker) system for GFT. METHODS: A novel strategy utilizing database-aided ultrahigh-performance liquid chromatography-quadrupole-orbitrap mass spectrometry was employed to analyze the lyophilized aqueous powder of GFT. Subsequently, the identified compounds underwent quantum chemical calculations, network pharmacology, and molecular simulations through in silico approaches to evaluate the Q-marker principles of traceability, specificity, and efficiency-relevance. RESULTS: The results revealed the putative identification of a total of 66 compounds, including 36 flavonoids, 7 phenolic acids and derivatives, 5 terpene lactones, 4 fatty acids and derivatives, 3 alkaloids, 1 amino acid, and 10 other compounds. Particularly, 16 compounds were unexpectedly observed, and seven compounds met the Q-marker principles. CONCLUSION: This study recommends the seven compounds, namely, (-)-gallocatechin, matrine, (-)-epicatechin, ginkgolide C, ginkgolide A, ginkgolide B, and curdione, as the anti-counterfeiting pharmacopoeia Q-markers for GFT. The reconstruction of the Q-marker system for GFT not only enhances the understanding of the compounds in GFT and other GBE-based preparations but also provides valuable recommendations for the Pharmacopoeia Commission.

Determinants of Product Outcome in Two Sesquiterpene Synthases from the Thermotolerant Bacterium Rubrobacter radiotolerans.

Rubrobacter radiotolerans nerolidol synthase (NerS) and trans-α-bergamotene synthase (BerS) are among the first terpene synthases (TSs) discovered from thermotolerant bacteria, and, despite sharing the same substrate, make terpenoid products with different carbon scaffolds. Here, the potential thermostability of NerS and BerS was investigated, and NerS was found to retain activity up to 55 °C. A library of 22 NerS and BerS variants was designed to probe the differing reaction mechanisms of NerS and BerS, including residues putatively involved in substrate sequestration, cation-π stabilisation of reactive intermediates, and shaping of the active site contour. Two BerS variants showed improved in vivo titres vs the WT enzyme, and also yielded different ratios of the related sesquiterpenoids (E)-ß-farnesene and trans-α-bergamotene. BerS-L86F was proposed to encourage substrate isomerisation by cation-π stabilisation of the first cationic intermediate, resulting in a greater proportion of trans-α-bergamotene. By contrast, BerS-S82L significantly preferred (E)-ß-farnesene formation, attributed to steric blocking of the isomerisation step, consistent with what has been observed in several plant TSs. Our work highlights the importance of isomerisation as a key determinant of product outcome in TSs, and shows how a combined computational and experimental approach can characterise TSs and variants with improved and altered functionality.

Solvent-Controlled Separation of Integratively Self-Sorted Pd2LA2LB2 Coordination Cages.

The integrative implementation of multiple different components into metallosupramolecular self-assemblies requires sophisticated strategies to avoid the formation of statistical mixtures. Previously, the key focus was set on thermodynamically driven reactions of simple homoleptic into complex heteroleptic structures. Using Pd2LA2LB2-type coordination cages, we herein show that integrative self-sorting can be reversed by a change of solvent (from DMSO to MeCN) to favor narcissistic re-segregation into coexisting homoleptic species Pd2LA4 and Pd3LB6. Full separation ("unsorting") back to a mixture of the homoleptic precursors was finally achieved by selective precipitation of Pd3LB6with anionic guest G1 from MeCN, keeping pure Pd2LA4 in solution. When a mixture of homoleptic Pd3LB6 and heteroleptic Pd2LA2LB2 is exposed to a combination of two different di-anions (G1 and G2) in DMSO, selective guest uptake gives rise to two defined coexisting host-guest complexes. A joint experimental and deep theoretical investigation via liquid-state integral equation theory of the reaction thermodynamics on a molecular level accompanied by solvent distribution analysis hints at solvent expulsion from Pd2LA4 to favor the formation of Pd2LA2LB2 in DMSO as the key entropic factor for determining the solvent-specific modulation of the cage conversion equilibrium.

Target Fisher: a Consensus Structure-Based Target Prediction Tool, and its Application in the Discovery of Selective MAO-B Inhibitors.

In this work we introduce Target Fisher, a consensus structure-based target prediction tool that integrates molecular docking and machine learning with the aim to aid in the identification of potential biological targets and the optimization of the use of bioassays. Target Fisher uses per-residue energy decomposition profiles extracted from docking poses as fingerprints to train target-specific machine learning models. It provides predictions for a curated set of 37 protein targets, covering a diverse range of biological entities, and offers a user-friendly interface accessible via a web server (https://gqc.quimica.unlp.edu.ar/targetfisher/). In this sense, Target Fisher is a valuable tool to aid organic and medicinal chemistry groups in target identification, drug discovery and drug repurposing. As a case study, we demonstrate the efficacy of Target Fisher by screening a small library of assorted natural products for targets relevant to neurodegenerative diseases, which resulted in the identification and experimental validation of selective inhibitors of monoamine oxidase B (MAO-B).

The Evolution of the Acylation Mechanism in ß-Lactamase and Rapid Protein Dynamics.

ß-Lactamases are a class of well-studied enzymes that are known to have existed since billions of years ago, starting as a defense mechanism to stave off competitors and are now enzymes responsible for antibiotic resistance. Using ancestral sequence reconstruction, it is possible to study the crystal structure of a laboratory resurrected 2-3 billion year-old ß-lactamase. Comparing the ancestral enzyme to its modern counterpart, a TEM-1 ß-lactamase, the structural changes are minor, and it is probable that dynamic effects play an important role in the evolution of function. We used molecular dynamics simulations and employed transition path sampling methods to identify the presence of rate-enhancing dynamics at the femtosecond level in both systems, found that these fast motions are more efficiently coordinated in the modern enzyme, and examined how specific dynamics can pinpoint evolutionary effects that are essential for improving enzymatic catalysis.

Adsorbate Resonance Induces Water-Metal Bonds in Electrochemical Interfaces.

This study delves into the intricate interactions between surface-near species, OH and H2O, on electrodes in electrochemical interfaces. These species are an inevitable part of many electrocatalytic energy conversion reactions such as the oxygen reduction reaction. In our modeling, we utilize high statistics on a dataset of complex solid solutions with high atomic variability to show the emergence of H2O-metal covalent bonds under specific conditions. Based on density functional theory (DFT) calculations of adsorption energies on many thousands of different surface compositions, we provide a quantifiable physical understanding of this induced water covalency, which is rooted in simple quantum mechanics. Directional hydrogen bonding between surface-near H2O and OH, enables surface bonding electrons to delocalize mediated by near-symmetrical adsorbate resonance structures. The different adsorbate resonance structures differ by surface coordination explaining the induced H2O-metal bonding.

Electrosynthesis of dimeric butenolides by C-C-homocoupling in the oxidation of 2,4-diarylfurans under aqueous conditions.

Fast and efficient galvanostatic conversion of 2,4-diarylfurans into dimeric furan-2(5H)-ones is now possible in one pot and good yields at room temperature in sustainable aqueous organic solvent. Recent applications of these highly desired structures demand our attention since they are a versatile alternative to acrylates in polymerization to achieve green materials. The reaction mechanism proposal, supported by density functional theory (DFT) theoretical calculations, involves furanoxy radicals, detected by electron paramagnetic resonance (EPR), as the last intermediate before a homocoupling step that affords butenolides. The process can be successfully extended to an array of electron-donating and electron-withdrawing substituents on the aromatic ring. The proposed pathways to explain the formation of the products are rationalized and discussed. A concomitant oxidation of water to hydroxyl radicals is not discarded, particularly with electron-withdrawing substituents at the aromatic ring. In addition, the biological activity as biocides of the obtained compounds was tested, and they showed promising activity against Staphylococcus aureus.

An influence of electronic structure theory method, thermodynamic and implicit solvation corrections on the organic carbonates conformational and binding energies.

An impact of an electronic structure or force field method, gas-phase thermodynamic correction, and continuum solvation model on organic carbonate clusters (S)n conformational and binding energies is explored. None of the tested force field (GFN-FF, GAFF, MMFF94) and standard semiempirical methods (PM3, AM1, RM1, PM6, PM6-D3, PM6-D3H4, PM7) can reproduce reference RI-SCS-MP2 conformational energies. Tight-binding GFNn-xTB methods provide more realistic conformational energies which are accurate enough to discard the least stable conformers. The effect of thermodynamic correction is moderate and can be ignored if the gas phase conformational stability ranking is a goal. The influence of continuum solvation is stronger, especially if reinforced with the Gibbs free energy thermodynamic correction, and results in the reduced spread of conformational energies. The cluster formation binding energies strongly depend on a particular approach to vibrational thermochemistry with the difference between traditional harmonic and modified scaled rigid - harmonic oscillator approximations reaching 10 kcal mol-1.

Design and Biophysical Characterization of Second-Generation cyclic peptide LAG-3 inhibitors for cancer immunotherapy.

Lymphocyte activation gene 3 (LAG-3) is an inhibitory immune checkpoint crucial for suppressing the immune response against cancer. Blocking LAG-3 interactions enables T cells to recover their cytotoxic capabilities and diminishes the immunosuppressive effects of regulatory T cells. A cyclic peptide (Cys-Val-Pro-Met-Thr-Tyr-Arg-Ala-Cys, disulfide bridge: 1-9) was recently reported as a LAG-3 inhibitor. Based on this peptide, we designed 19 derivatives by substituting tyrosine residue to maximize LAG-3 inhibition. Screening via TR-FRET assay identified 8 outperforming derivatives, with cyclic peptides 12 [Tyr6(L-3-CN-Phe)], 13 [Tyr6(L-4-NH2-Phe)], and 17 [Tyr6(L-3,5-DiF-Phe)] as top candidates. Cyclic peptide 12 exhibited the highest inhibition (IC50 = 4.45 ± 1.36 µM). MST analysis showed cyclic peptides 12 and 13 bound LAG-3 with KD values of 2.66 ± 2.06 µM and 1.81 ± 1.42 µM, respectively, surpassing the original peptide (9.94 ± 4.13 µM). Docking simulations revealed that cyclic peptide 12 exhibited significantly enhanced binding, with a docking score of -7.236 kcal/mol, outperforming the original peptide (-5.236 kcal/mol) and cyclic peptide 5 (L-4-CN-Phe) (-5.131 kcal/mol). A per-residue decomposition of the interaction energy indicated that the 3-cyano group in cyclic peptide 12 contributes to a more favorable conformation, yielding an interaction energy of -9.22 kcal/mol with Phe443 of MHC-II, compared to -6.03 kcal/mol and -5.619 kcal/mol for cyclic peptides 0 and 5, respectively. Despite promising in vitro results, cyclic peptide 12 failed to inhibit tumor growth in vivo, underscoring the importance of dual immunotherapies targeting several immune checkpoints to achieve anti-tumor efficacy.

Computational study of the supramolecular complexation of azocompounds with cucurbit[7]uril: effects on the production and release of free radicals.

CONTEXT: An inclusion complex between 2,2'-azobis(2-methylpropionamidine) dihydrochloride (AAPH), a widely employed azocompound, and cucurbit[7]util (CB[7]), has shown an increased yield of radicals derived from the homolytic cleavage of the azo bond. Aimed to get insights about the formation of complexes and their effect on the yield of radicals production, complexes of CB[7] with seven azocompounds were studied by computational methods. Molecular electrostatic surfaces and structural analysis showed that the inclusion of symmetrical azocompounds inside of CB[7] depends mainly on the charge density and position of the functional groups at the main chain of the azoderivative. Analysis of non-covalent interactions and thermodynamic outcomes revealed that positively charged azocompounds with amidinium or imidazolium groups presented strong favorable interactions (multiple hydrogen bonds) with the oxygens of CB[7] portals. Additionally, carbon-centered radicals generated from the complexes (azocompounds@CB[7]) were corroborated using the electron localization function (ELF). Results evidenced that the strength of the interactions and the level of inclusion (partial or complete) between the azocompound and CB[7] determined the final orientation of the radicals (located out- or inside of the CB[7] cavity). Obtained results could be employed to design new supramolecular systems based on the properties of azocomplound@CB[7] complexes for new scientific or industrial applications. METHODS: First-principles calculations at B3LYP-D3BJ/6-311g(d,p) level theory in the gas phase and in solvent (PCM, water) were performed in Gaussian 16 software package. The dispersion energy correction was included through the Grimme's dispersion with Becke-Johnson damping D3(BJ). Thermodynamical data and the minimum character of all structures were obtained from vibrational frequency calculations. NBO, Multiwfn, Chemcraft, and NCIPLOT software were used to perform population analysis, analyze outcomes, visualize data, and display non-covalent interactions respectively.

Exploring and Re-Assessing Reverse Anomeric Effect in 2-Iminoaldoses Derived from Mono- and Polynuclear Aromatic Aldehydes.

A curious and noticeable structural feature in Schiff bases from 2-aminoaldoses is the fact that imino tautomers arranged equatorially in the most stable ring conformation exhibit a counterintuitive reverse anomeric effect (RAE) in the mutarotational equilibrium, i.e., the most stable and abundant anomer is the equatorial one (ß). As shown by our very recent research, this effect arises from the total or partial inhibition of the exo-anomeric effect due to the presence of an intramolecular hydrogen bond between the anomeric hydroxyl and the iminic nitrogen in the axial anomer (α). When the Schiff base adopts either an enamine structure or the imino group is protonated, the exo-anomeric effect is restored, and the axial α-anomer becomes the most stable species. Although the intramolecular H-bonding should appropriately be interpreted as a genuine stereoelectronic effect, the magnitude of the RAE could be affected by other structural parameters. Herein and through a comprehensive analysis of benzylidene, cinnamylidene, naphthalene, phenanthrene, and anthracene aldehydes, we show the robustness of the RAE effect, which is similar in extent to simple aldehydes screened so far, irrespective of the size and/or hydrophobicity of the substituent at the nitrogen atom.

Green synthesis and two-step chromatographic separation of thiocanthal and thiocanthol: Two novel biologically active sulfur derivatives of oleocanthal and oleacein from extra virgin olive oil.

Oleocanthal and oleacein are the two major secoiridoids exclusively present in extra virgin olive oil (EVOO). Both compounds exert important pharmacological activities, including anti-inflammatory, anti-tumoral, neuro- and cardiovascular protective effects. Due to their enormous potential as possible drugs the extraction of these two bioactive natural products from EVOO has been extensively investigated in the last years and is generally supported by the use of organic chemistry. It is quite difficult to produce large quantities of these two compounds, either by organic solvent extraction and purification or by chemical synthesis, and furthermore organic processes such as cleaning, defatting, and extraction of EVOO pose a threat to the environment and are potentially harmful to workers. In this work we set up a novel aqueous extraction and isolation method from EVOO by transforming oleocanthal and oleacein into two water-soluble sulfonated products. The two derived compounds, here named thiocanthal and thiocanthol, were isolated by a two-step organic free chromatographic strategy, chemically characterized, and evaluated for their inhibitory activity on cyclooxygenase (COX). The results demonstrate that thiocanthal and thiocanthol possess anti-inflammatory effect, which is comparable to their precursors and higher than the well-known non-steroidal anti-inflammatory drug ibuprofen. Computational docking studies were performed to obtain and analyse putative models of the interaction of thiocanthal and thiocanthol with COX-1 and COX-2 binding sites. Predicted binding energy values suggested that both compounds might preferentially bind COX-2, which may have a significant pharmacological impact. Therefore, thiocanthal and thiocanthol, obtained by this novel green process, are extremely interesting both as new bioactive compounds per se and as lead compounds for the development of novel non-steroidal anti-inflammatory drugs (NSAIDs).

Improving rigor and reproducibility in western blot experiments with the blotRig analysis.

Western blot is a popular biomolecular analysis method for measuring the relative quantities of independent proteins in complex biological samples. However, variability in quantitative western blot data analysis poses a challenge in designing reproducible experiments. The lack of rigorous quantitative approaches in current western blot statistical methodology may result in irreproducible inferences. Here we describe best practices for the design and analysis of western blot experiments, with examples and demonstrations of how different analytical approaches can lead to widely varying outcomes. To facilitate best practices, we have developed the blotRig tool for designing and analyzing western blot experiments to improve their rigor and reproducibility. The blotRig application includes functions for counterbalancing experimental design by lane position, batch management across gels, and analytics with covariates and random effects.

Migration of para-Nitrophenyl Groups in Methyl Pyranosides: Configuration and Conformation Determine the Kinetics.

para-Nitrophenyl (PNP) ethers of glycosides are important building blocks en route to functional carbohydrates. They are stable in neutral media, however, under basic conditions such as during the Zemplén deacylation of sugars, aryl migration is frequently observed. We have employed a library of O-PNP-substituted methyl glycosides of the manno-, galacto-, gluco- and altro-series to study the kinetics of aryl migration in MeOH/sodium methoxide using NMR spectroscopy revealing that migration between cis-oriented OH groups is faster than between trans-oriented ones. The rate constants of migration decrease in the order of Alt>Man>Gal>Glc and are related to the energy barriers of chair conformation inversion. The energy profile of the 3 to 4-PNP migration in methyl mannoside was calculated using DFT methods suggesting the Meisenheimer complex is an intermediate of PNP migration and that coordination of the sodium cation has a major impact on the energy profile.

Pyrolytic conversion of glucose into hydroxymethylfurfural and furfural: Benchmark quantum-chemical calculations.

Quantum chemical methods have been intensively applied to study the pyrolytic conversion of glucose into hydroxymethylfurfural (HMF) and furfural (FF). Herein, we collect the most relevant mechanistic proposals from the recent literature and organize them into a single reaction network. All the transition structures (TSs) and intermediates are characterized using highly accurate ab initio methods and the possible reaction pathways are assessed in terms of the Gibbs energies of the TSs and intermediates with respect to ß-glucopyranose, selecting a 2D ideal-gas standard state at 773 K to represent the pyrolysis conditions. Several pathways can lead to the formation of both HMF and FF passing through rate-determining TSs that have ΔG‡ values of ~49-50 kcal/mol. Both water-assisted mechanisms and nonspecific environmental effects have a minor impact on the Gibbs energy profiles. We find that the HMF → FF + CH2O fragmentation has a small ΔrxnG value and an accessible ΔG‡ barrier. Our computational results, which are in consonance with the kinetic parameters derived from lumped models, the results of isotopic labeling experiments and the reported HMF/FF molecular ratios, could be useful for modeling studies including on nonequilibrium kinetic effects that may render more information about product yields and the relevance of the various pathways.

Fast vibrational analysis of molecular systems.

The development of infrared difference spectroscopy provides unprecedented insights on structures of complex molecules like metalloproteins. However, the relevant information can be hard to find among the many bands of the vibrational spectra. The ab initio modeling is very helpful to assign the frequencies to vibrational modes but it is a challenge to process the huge quantity of data into descriptors useful for experimentalists. To this end, we developed a new tool called VIBMOL allowing to analyze vibrational modes of molecules from hessian matrices calculated with common quantum chemistry codes. VIBMOL program runs on Unix machines. Through a new graphical interface, the users can calculate the normal modes of molecules, visualize them, simulate infrared spectra, and explore the Potential Energy Distribution of normal modes among any set of vibration coordinates. It is combined with an interface program (gosdmu) formatting relevant data from the GAUSSIAN program. VIBMOL code is available upon request to the authors. A discussion is provided to help the readers to choose between a large choice of different software and it shows how VIBMOL can make the IR assignment easier in the context of collaborations with experimentalists.