Luc Patiny

• Swiss Federal Institute of Technology in Lausanne

The browser has become an indispensable tool for a variety of everyday tasks, yet its potential in scientific data processing remains underexplored and is often perceived as slow. This paper presents four examples of advanced web applications that we have developed during the last 20 years and demonstrates the browser’s ability to compete with trad...

Despite the soaring popularity of e‐cigarettes among teenagers and young adults, our understanding of the full extent of their health hazards have remained limited. This is due to the vast complexities of e‐cigarette aerosols and the difficulty in their full characterisation. Conventional mass spectrometry methods of e‐cigarette analysis, though pi...

NMRium is the first web-based software that allows displaying, processing, interpretation, and teaching of 1D and 2D NMR data in a user-friendly interface. It can import the most common data formats (e.g., JCAMP-DX, Bruker, Varian, and Jeol). While the scope for the use of NMRium encompasses a variety of applications such as being a component in da...

Over the past two decades, significant advancements in educational technology have revolutionized the field of chemical education. This publication presents our contributions using web-based tools that have been developed over this period, enabling chemistry students to engage with exercises that closely mirror real-world scenarios encountered in t...

Large amounts of data are generated in chemistry labs—nearly all instruments record data in a digital form, yet a considerable proportion is also captured non-digitally and reported in ways non-accessible to both humans and their computational agents. Chemical research is still largely centred around paper-based lab notebooks, and the publication o...

Although genomic DNA is the primary target of anticancer platinum-based drugs, interactions with proteins also play a significant role in their overall activity. In this study, competitive binding of cisplatin with an oligonucleotide and two peptides corresponding to segments of H2A and H2B histone proteins was investigated by mass spectrometry. Fo...

Protein Recycling In article number 2104581, Sebastian Josef Maerkl, Francesco Stellacci, and co-workers introduce an idealized representation of nature-inspired circular-economy recycling (NaCRe) for proteins, a recycling approach where generic mixtures of protein-based materials are depolymerized into their constituent amino acids, which in turn...

Infrared spectroscopy (IR) is a staple structural elucidation and characterization technique due to its ability to identify functional groups and its ease of use. Interestingly, it allows capturing electronic effects via their influence on the bond strength of "probes" such as the carbonyl group and also offers a wealth of examples for discussion o...

Infrared spectroscopy (IR) is a staple structural elucidation and characterization technique due to its ability to identify functional groups and its ease of use. Interestingly, it allows capturing electronic effects via their influence on the bond strength of "probes" such as the carbonyl group and also offers a wealth of examples for discussion o...

The billion tons of synthetic‐polymer‐based materials (i.e. plastics) produced yearly are a great challenge for humanity. Nature produces even more natural polymers, yet they are sustainable. Proteins are sequence‐defined natural polymers that are constantly recycled when living systems feed. Digestion is the protein depolymerization into amino aci...

Nowadays, computer simulations and experiments are closely interlocked. However, the data and analysis workflows are often barred into "silos" of knowledge — even for routine simulations. Here, we show how a typical electronic laboratory notebook (ELN) environment can be seamlessly integrated with a computational modelling infrastructure. We develo...

Nowadays, computer simulations and experiments are closely interlocked. However, the data and analysis workflows are often barred into "silos" of knowledge — even for routine simulations. Here, we show how a typical electronic laboratory notebook (ELN) environment can be seamlessly integrated with a computational modelling infrastructure. We develo...

Nowadays, computer simulations and experiments are closely interlocked. However, the data and analysis workflows are often barred into "silos" of knowledge — even for routine simulations. Here, we show how a typical electronic laboratory notebook (ELN) environment can be seamlessly integrated with a computational modelling infrastructure. We develo...

Nowadays, computer simulations and experiments are closely interlocked. However, the data and analysis workflows are often barred into "silos" of knowledge — even for routine simulations. Here, we show how a typical electronic laboratory notebook (ELN) environment can be seamlessly integrated with a computational modelling infrastructure. We develo...

According to the World Drug Report 2020, cocaine and ecstasy are the most consumed stimulant drugs, with 19 and 27 million estimated users in 2018. In this context, large efforts are being made to design fast and cost-effective analytical methods to track and monitor the distribution networks of these synthetic drugs. Here, we share two datasets of...

In 2070, 10 ¹² Kg of polymer-based materials ( i.e. plastics) might be produced yearly, posing one of the greatest challenges that humanity has to face. Even though natural polymers, such as proteins and nucleic acids, are more abundant than synthetic ones, they are sustainable. The key property of such natural polymers is that they are sequence-de...

Rationale The Analysis of Oligonucleotide Modifications from Mass Spectra (Aom²S) was created to support the analysis of oligonucleotide mass spectra. This application complements the existing software tools by providing a comprehensive analysis of oligonucleotide fragments from high‐resolution tandem mass spectrometry (HR‐MS/MS) data in a flexible...

The cellular level of nicotinamide adenine dinucleotide (NAD+), through its different functions, affects cellular metabolism and signalling1–3. A decrease in the NAD+ content has been associated with various pathologies and physiological aging4,5, while strategies to boost cellular NAD+ levels have been shown to be effective against age-related dis...

Teaching spectra analysis and structure elucidation requires students to get trained on real problems. This involves solving exercises of increasing complexity and when necessary using computational tools. Although desktop software packages exist for this purpose, nmr.cheminfo.org platform offers students an online alternative. It provides a set of...

NMR is a mature technique that is well established and adopted in a wide range of research facilities from laboratories to hospitals. This accounts for large amounts of valuable experimental data that may be readily exported into a standard and open format. Yet the publication of these data faces an important issue: raw data are not made available;...

Background: We present "Ask Ernö", a self-learning system for the automatic analysis of NMR spectra, consisting of integrated chemical shift assignment and prediction tools. The output of the automatic assignment component initializes and improves a database of assigned protons that is used by the chemical shift predictor. In turn, the predictions...

Following their detection and seizure by police and border guard authorities, false identity and travel documents are usually scanned, producing digital images. This research investigates the potential of these images to classify false identity documents, highlight links between documents produced by a same modus operandi or same source, and thus s...

We present a method for the automatic assignment of small molecules' NMR spectra. The method includes an automatic and novel self-consistent peak-picking routine that validates NMR peaks in each spectrum against peaks in the same or other spectra that are due to the same resonances. The auto-assignment routine used is based on branch-and-bound opti...

Nuclear magnetic resonance (NMR) assignment of small molecules is presented as a typical example of a combinatorial optimization problem in chemical physics. Three strategies that help improve the efficiency of solution search by the branch and bound method are presented: 1. reduction of the size of the solution space by resort to a condensed struc...

This article contributes a highly accurate model for predicting the melting points (MPs) of medicinal chemistry compounds. The model was developed using the largest published data set, comprising more than 47k compounds. The distributions of MPs in drug-like and drug lead sets showed that >90% of molecules melt within [50,250]°C. The final model ca...

For many drugs, finding the balance between efficacy and toxicity requires monitoring their concentrations in the patient's blood. Quantifying drug levels at the bedside or at home would have advantages in terms of therapeutic outcome and convenience, but current techniques require the setting of a diagnostic laboratory. We have developed semisynth...

A methodology based on spectral similarity is presented that allows to compare NMR predictors without the recourse to assigned experimental spectra, thereby making the task of benchmarking NMR predictors less tedious, faster, and less prone to human error. This approach was used to compare four popular NMR predictors using a dataset of 1000 molecul...

Web services, as an aspect of cloud computing, are becoming an important part of the general IT infrastructure, and scientific computing is no exception to this trend. We propose a simple approach to develop chemical web services, through which servers could expose the essential data manipulation functionality that students and researchers need for...

The analysis of spectroscopic data to elucidate chemical structures requires intensive practice. A Web portal is described that allows uploading, storing, simulating, and sharing of spectroscopic data. The Web portal can also be used to create, embed, and solve exercises online. This tool and a demo course for Moodle are available online at no cost...

The Online Chemical Modeling Environment is a web-based platform that aims to automate and simplify the typical steps required for QSAR modeling. The platform consists of two major subsystems: the database of experimental measurements and the modeling framework. A user-contributed database contains a set of tools for easy input, search and modifica...

The Online Chemical Modeling Environment is a unique platform on the Web that aims to automate and simplify the typical steps required for QSAR modeling. The platform consists of two major subsystems: the database of experimental measurements and the modeling framework. The database is user-contributed and contains a set of tools for easy input, se...

The computational cost for the simulation of NMR spectra grows exponentially with the number of nuclei. Today, the memory available to store the Hamiltonian limits the size of the system that can be studied. Modern computers enable to tackle systems containing up to 13 spins [1], which obviously does not allow to study most molecules of interest in...

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

C19H30N2O3, Mr = 334.45, monoclinic, Pc, a = 9.933(2), b = 6.485(2), c = 14.869(2)Å, β = 99.82(2)°, V = 943.8(3)Å3, Z= 2, Dx= 1.18g.cm−3, CuKα radiation (λ = 1.54178Å). The final R indice is 0.042 for 1539 observed reflections.

C12H19BrO3, Mr = 291.18, monoclinic, P21/a, a = 12.063(4), b = 19.751(4), c = 12.300(3)Å, β = 115.86(3), V = 2637(1)Å3, Z = 8, Dx = 1.48g.cm−3, MoKα radiation (λ = 0.71069Å). The final R indice is 0.11 for 1641 observed reflections.

C13H15IO2, Mr = 330.15, orthorhombic, P212121, a = 6.139(1), b = 10.047(2), c = 21.134(5)Å, V = 1303.5(5)Å3, Z = 4, Dx= 1.68g.cm−3, MoKα radiation (λ = 0.71069Å). The final R indice is 0.044 for 1735 observed reflections

C20H23NO, Mr = 293.39, monoclinic, C2/c, a = 19.541(2), b = 7.159(1), c = 24.147(2)Å, β = 92.65(1), V = 3374.4(5)Å3, Z = 8, Dx = 1.16g.cm−3, CuKα radiation (λ = 1.54178Å). The final R indice is 0.055 for 2416 observed reflections.

C66H68O10, Mr = 1021.2, orthorhombic, P212121, a = 11.038(4), b = 14.183(6), c = 18.358(7)Å, V = 2874(2)Å3, Z = 2, Dx = 1.18g.cm−3, MoKα radiation (λ = 0.71069Å). The final R indice is 0.080 for 1033 observed reflections

The synthesis of nine nostocarboline derivatives with substitutions of the 2-methyl group by alkyl, aryl and functionalized residues, 10 symmetrical bis cationic dimers linking 6-Cl-norharmane through the 2-position and fifteen derivatives of the marine alkaloids eudistomin N and O is reported. These compounds were evaluated in vitro against four p...

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Functional groups are prerequisites for the assembly of building blocks to more elaborate structures for research work in the life sciences field. Functionalization can be most conveniently and efficaciously accomplished by generating an organometallic deriv. of the arom. or heterocyclic starting material and subsequently treating it with the elect...

NMR spectroscopy is certainly the analytical methodology that provides the most information about a molecule but the long-term vision of this information is often lacking. We present here two innovative tools accessible free from the web. NMR assigner allows a chemical structure to be assigned to the corresponding NMR spectrum by simply drawing lin...

A novel post-synthesis analysis tool is presented which evaluates quality of the organic preparation based on yield, cost, safety, conditions and ease of workup/purification. The proposed approach is based on assigning a range of penalty points to these parameters. This semi-quantitative analysis can easily be modified by other synthetic chemists w...

New insights into the structure-activity relationship of the peptide hormone oxytocin are presented. Incorporation of the novel cis-prolyl mimic 2,2-dimethyl-1,3-thiazolidine-4-carboxylic acid (pseudoproline, PsiPro) at position 7 of the hormone yielded the analogue [Cys(Psi(Me,Me)pro)]7oxytocin (1) that showed a 92-95% induction of the cis peptide...

This paper describes a convenient synthesis of protected hydrazine derivatives, i.e. 1,2-bis-Boc-hydrazinoacetic acid, and its application for hydrazone ligation techniques in convergent template assembled synthetic protein (TASP) synthesis.

Peptide mit einem Schaltelement S erlauben die gezielte Induktion von Konformationsübergängen – und damit von Struktur und Funktion – unter physiologischen Bedingungen (siehe Schema). Dies eröffnet erstmals den direkten Zugang zu molekularen Prozessen, die z. B. bei Alzheimer-Erkrankungen eine Rolle spielen.

A novel concept for triggering conformational transitions, and thus changes in structure and function, in peptides with a switching element S provides intriguing perspectives for studying molecular processes (see scheme) that play a key role, for example, in early events of Alzheimer's disease.

The selective and reversible insertion of pseudo-proline (? Pro) systems in cyclosporin C (CsC) featuring different C(2) substituents at the oxazolidine ring and its impact on the conformational and biological properties is described. The presence of a 5-membered ring exerts drastic effects upon the backbone conformation of CsC as demonstrated by N...

The chemical synthesis, conformational analysis and receptor binding studies of novel constrained cyclosporin A (CsA) analogues are described. The selective insertion of pseudo-proline (PsiPro) systems featuring different 2-C-substituents at the oxazolidine ring exerts dramatic effects upon the backbone conformation as demonstrated by NMR analysis....

Nicotine is the main culprit for dependence on tobacco-containing products, which in turn are a major etiologic factor for cardiovascular diseases and cancer. This publication describes a vaccine, which elicits antibodies against nicotine. The antibodies in the blood stream intercept the nicotine molecule on its way to its receptors and greatly dim...

The direct conversion of cysteine (Cys) containing peptides into conformationally constrained pseudo-proline (ΨPro) derivatives by intraresidual N,S-acetalisation has been achieved. This post-synthetic modification represents a versatile tool in structure–activity studies of bioactive peptides as exemplified for the immunosuppressive cyclosporine A...

Analogues of the opioid peptides [D-Phe(3)]morphiceptin (H-Tyr-Pro-D-Phe-Pro-NH(2)) and endomorphin-2 (H-Tyr-Pro-Phe-Phe-NH(2)) containing the pseudoproline (Psi Pro) (4R)-thiazolidine-4-carboxylic acid (Cys[Psi(R1,R2)pro]) or (4S)-oxazolidine-4-carboxylic acid (Ser[Psi(R1,R2)pro]) in place of Pro(2) were synthesized. The pseudoproline ring in thes...

A novel methodology for the reversible competitive condensation of peptide loops to chemoreactive topological templates is presented.

We propose that various bonds (see figure below) used for specification of absolute configuration, e.g. the two types (I and II) of solid wedge and broken wedge representation most frequently seen in literature, can be replaced by only one kind of wedge, namely the solid wedge (III and IV). Only one wedge should be used when representing a quadriva...

The insertion of acetals that exhibit variable structural features into complex peptides such as cyclosporin C (CsC) results in oxazolidine derivatives (pseudoprolines, psiPro) of tailored physico-chemical and biological properties. N,O-Acetalation of the 2-threonine hydroxyl group and the preceding amide nitrogen of CsC is achieved by treating the...

Cis-prolyl conformations are recently found to play significant roles in recognition processes among proteins. Here, we present several applications in which pseudoprolines (ΨPro) were used to experimentally target hypothetical bioactive cis conformations. The pseudoproline 2,2-dimethyl-1,3-thiazolidine-4-carboxylic acid (Cys(ΨMe,Mepro), I) represe...

Specific protein-protein interactions are essential facets in cellular communication and the formation and specific assembly of multicomponent protein complexes often is regulated by binding to proline (Pro)-rich peptide sequences. Pro-rich ligands adopt a left-handed polyproline II helical conformation (PPII, all trans amide bonds) and bind to a h...

Cycloaddition of activated furans 10 to 4-methoxycyclopent-2-enone was unexpectedly found to take place with a regioselectivity opposed to that predicted by FMO theory. The reaction represents a direct route towards polyfunctionalised cis-hydrindanones which are key intermediates for the synthesis of ottelione A, a potent inhibitor of tubulin polym...

Since the discovery of the immunosuppresive activity of Cyclosporin A (CsA), considerable work has been devoted to the chemical synthesis of analogues. More recently, the finding of potential anti-HIV I activity of CsA evoked interest for the design of more selective cyclosporins active against HIV I but devoid of immunosuppresive activity. Based o...

Cycloaddition of activated furans 10 to 4-methoxycyclopent-2-enone was unexpectedly found to take place with a regioselectivity opposed to that predicted by FMO theory. The reaction represents a direct route towards polyfunctionalised cis-hydrindanones which are key intermediates for the synthesis of ottelione A, a potent inhibitor of tubulin polym...

The specific recognition of cis peptide bonds is possible with antibodies that are directed against cyclic and linear peptide antigens derived from the V3 loop of the HIV-1 protein gp120, into which a thiazolidine derivative (pseudoproline) has been introduced (see schematic representation). This extension of the pseudoproline concept may help to d...

Experimental data of organic synthesis and compound analysis is very precious chemical information. The monthly chemistry journal Molecules (http://www.mdpi.org/molecules/) started to publish a new column of MolBank in April 1997. The intention is to preserve a large amount of experimental data of organic synthesis and structural characterization o...

Series of substrates derivatives of peptide deformylase were systematically synthesized and studied for their capacities to undergo hydrolysis. Data analysis indicated the requirement for a hydrophobic first side chain and for at least two main chain carbonyl groups in the substrate. For instance, Fo-Met-OCH3 and Fo-Nle-OCH3 were the minimal substr...

Disubstituted-α-chloroenamines are useful synthetic intermediates which had earlier been prepared by the reaction of tertiary amides with phosgene. The toxicity of the latter led us to systematically investigate new synthetic routes towards α-chloro- and α-bromoenamines. The reactions of various halogenating agents (SOCl2, diphosgene, triphosgene,...

A symposium report. Since the discovery of the immunosuppressive activity of cyclosporine A (CsA), considerable work has been devoted to the chem. synthesis of potent analogs. More recently, the finding of potential anti-HIV I activity of CsA raised interest for the design of CsA-derived compds. devoid of immunosuppressive activity. With this objec...