Gigahertz streaking and compression of low-energy electron pulses.

Although radio frequency (RF) technology is routinely employed for controlling high-energy pulses of electrons, corresponding technology has not been developed at beam energies below several kiloelectronvolts. In this work, we demonstrate transverse and longitudinal phase-space manipulation of low-energy electron pulses using RF fields. A millimeter-sized photoelectron gun is combined with synchronized streaking and compression cavities driven at frequencies of 0.5 and 2.5 GHz, respectively. The phase-controlled acceleration and deceleration of photoelectron pulses is characterized in the energy range of 50-100 eV. Deflection from a transient space-charge cloud at a metal grid is used to measure a fourfold compression of 80-eV electron pulses, from τ=34 to τ=8 ps pulse duration.

From the Automated Calculation of Potential Energy Surfaces to Accurate Infrared Spectra.

Advances in the development of quantum chemical methods and progress in multicore architectures in computer science made the simulation of infrared spectra of isolated molecules competitive with respect to established experimental methods. Although it is mainly the multidimensional potential energy surface that controls the accuracy of these calculations, the subsequent vibrational structure calculations need to be carefully converged in order to yield accurate results. As both aspects need to be considered in a balanced way, we focus on approaches for molecules of up to 12-15 atoms with respect to both parts, which have been automated to some extent so that they can be employed in routine applications. Alternatives to machine learning will be discussed, which appear to be attractive, as long as local regions of the potential energy surface are sufficient. The automatization of these methods is still in its infancy, and the generalization to molecules with large amplitude motions or molecular clusters is far from trivial, but many systems relevant for astrophysical studies are already in reach.

The first HyDRA challenge for computational vibrational spectroscopy.

Vibrational spectroscopy in supersonic jet expansions is a powerful tool to assess molecular aggregates in close to ideal conditions for the benchmarking of quantum chemical approaches. The low temperatures achieved as well as the absence of environment effects allow for a direct comparison between computed and experimental spectra. This provides potential benchmarking data which can be revisited to hone different computational techniques, and it allows for the critical analysis of procedures under the setting of a blind challenge. In the latter case, the final result is unknown to modellers, providing an unbiased testing opportunity for quantum chemical models. In this work, we present the spectroscopic and computational results for the first HyDRA blind challenge. The latter deals with the prediction of water donor stretching vibrations in monohydrates of organic molecules. This edition features a test set of 10 systems. Experimental water donor OH vibrational wavenumbers for the vacuum-isolated monohydrates of formaldehyde, tetrahydrofuran, pyridine, tetrahydrothiophene, trifluoroethanol, methyl lactate, dimethylimidazolidinone, cyclooctanone, trifluoroacetophenone and 1-phenylcyclohexane-cis-1,2-diol are provided. The results of the challenge show promising predictive properties in both purely quantum mechanical approaches as well as regression and other machine learning strategies.

Ab Initio Rovibrational Spectroscopy of the Acetylide Anion.

In this work the rovibrational spectrum of the acetylide anion HCC- is investigated using high-level electronic structure methods and variational rovibrational calculations. Using a composite approach the potential energy surface and dipole surface is constructed from explicitly correlated coupled-cluster accounting for corrections due to core-valence correlation, scalar relativistic effects and higher-order excitation effects. Previous approaches for approximating the latter are critically evaluated. Employing the composite potential, accurate spectroscopic parameters determined from variational calculations are presented. In comparison to the few available reference data the present results show excellent agreement with ground state rotational constants within 0.005% of the experimental value. Intensities determined from the variational calculations suggest the bending fundamental transition ν2 around 510 cm-1 to be the best target for detection. The rather weak CD stretching fundamental ν1 in deuterated isotopologues show a second-order resonance with the (0,20,1) state and the consequences are discussed in some detail. The spectroscopic parameters and band intensities provided for a number of vibrational bands in isotopologues of the acetylide anion should facilitate future spectroscopic investigations.

Comprehensive quantum chemical analysis of the (ro)vibrational spectrum of thiirane and its deuterated isotopologue.

The (ro)vibrational spectra of thiirane, c-C2H4S, and its fully deuterated isotopologue, c-C2D4S, have been studied by means of vibrational configuration interaction theory, VCI, its incremental variant, iVCI, and subsequent variational rovibrational calculations, RVCI, which rely on multidimensional potential energy surfaces of coupled-cluster quality including up to four-mode coupling terms. Accurate geometrical parameters, fundamental vibrational transitions and first overtones, rovibrational spectra and rotational spectroscopic constants have been determined from these calculations and were compared with experimental results whenever available. A number of tentative misassignments in the vibrational spectra could be resolved and most results for the deuterated thiirane are high-level predictions, which may guide experiments to come. Besides this, a new implementation of infrared intensities within the iVCI framework has been tested for the transitions of the title compounds and are compared with results obtained from standard VCI calculations.

Combining grating-coupled illumination and image recognition for stable and localized optical scanning tunneling microscopy.

Combining scanning tunneling microscopy (STM) and optical excitation has been a major objective in STM for the last 30 years to study light-matter interactions on the atomic scale. The combination with modern pulsed laser systems even made it possible to achieve a temporal resolution down to the femtosecond regime. A promising approach toward a truly localized optical excitation is featured by nanofocusing via an optical antenna spatially separated from the tunnel junction. Until now, these experiments have been limited by thermal instabilities introduced by the laser. This paper presents a versatile solution to this problem by actively coupling the laser and STM, bypassing the vibration-isolation without compromising it. We utilize optical image recognition to monitor the position of the tunneling junction and compensate for any movement of the microscope relative to the laser setup with up to 10 Hz by adjusting the beamline. Our setup stabilizes the focus position with high precision (<1 µm) on long timescales (>1 h) and allows for high resolution STM under intense optical excitation with femtosecond pulses.

High-dimensional neural network potentials for accurate vibrational frequencies: the formic acid dimer benchmark.

In recent years, machine learning potentials (MLP) for atomistic simulations have attracted a lot of attention in chemistry and materials science. Many new approaches have been developed with the primary aim to transfer the accuracy of electronic structure calculations to large condensed systems containing thousands of atoms. In spite of these advances, the reliability of modern MLPs in reproducing the subtle details of the multi-dimensional potential-energy surface is still difficult to assess for such systems. On the other hand, moderately sized systems enabling the application of tools for thorough and systematic quality-control are nowadays rarely investigated. In this work we use benchmark-quality harmonic and anharmonic vibrational frequencies as a sensitive probe for the validation of high-dimensional neural network potentials. For the case of the formic acid dimer, a frequently studied model system for which stringent spectroscopic data became recently available, we show that high-quality frequencies can be obtained from state-of-the-art calculations in excellent agreement with coupled cluster theory and experimental data.

Determination of spectroscopic constants from rovibrational configuration interaction calculations.

Rotational constants and centrifugal distortion constants of a molecule are the essence of its rotational or rovibrational spectrum (e.g., from microwave, millimeter wave, and infrared experiments). These parameters condense the spectroscopic characteristics of a molecule and, thus, are a valuable resource in terms of presenting and communicating spectroscopic observations. While spectroscopic parameters are obtained from experimental spectra by fitting an effective rovibrational Hamiltonian to transition frequencies, the ab initio calculation of these parameters is usually done within vibrational perturbation theory. In the present work, we investigate an approach related to the experimental fitting procedure, but relying solely on ab initio data obtained from variational calculations, i.e., we perform a nonlinear least squares fit of Watson's A- and S-reduced rotation-vibration Hamiltonian to rovibrational state energies (resp. transition frequencies) from rotational-vibrational configuration interaction calculations. We include up to sextic centrifugal distortion constants. By relying on an educated guess of spectroscopic parameters from vibrational configuration interaction and vibrational perturbation theory, the fitting procedure is very efficient. We observe excellent agreement with experimentally derived parameters.

Comparison of body definitions for incremental vibrational configuration interaction theory (iVCI).

Within incremental vibrational configuration interaction theory (iVCI), the vibrational state energy is determined by means of a many-body expansion, i.e., it is a sum of terms of increasing order, which allow for an embarrassingly parallel evaluation. The convergence of this expansion depends strongly on the definition of the underlying bodies, which essentially decompose the correlation space into fragments. The different definitions considered here comprise mode-based bodies, excitation level-based bodies, and energy-based bodies. An analysis of the convergence behavior revealed that accounting for resonances within these definitions is mandatory and leads to a substantial improvement of the convergence, that is, the expansions can be truncated at lower orders. Benchmark calculations and systematic comparisons of the different body definitions for a small set of molecules, i.e., ketene, ethene, and diborane, have been conducted to study the overall performance of these iVCI implementations with respect to accuracy and central processing unit time.

Non-alcoholic fatty liver disease in type 2 diabetes - A specific entity?

Individuals with obesity or type 2 diabetes (T2D) have an increased risk of developing non-alcoholic fatty liver disease (NAFLD). In insulin-resistant states, altered adipose tissue function may be the initial abnormality underlying NAFLD. Hepatic lipid oversupply interferes with insulin signalling and mitochondrial function. In obese individuals, adaptation of hepatic mitochondrial respiration fails with the progression of NAFLD and can activate pro-inflammatory pathways. T2D as well as type 1 diabetes are associated with altered hepatic mitochondrial function. Screening for NAFLD remains challenging especially in those with diabetes because liver enzymes are often in the normal range and the performance of NAFLD scores is limited. Patients with T2D and severe insulin-resistant diabetes (SIRD) have the highest prevalence of NAFLD at diagnosis and the greatest risk of progression. In this subgroup, the single-nucleotide-polymorphism (SNP) rs738409(G) of the patatin-like phospholipase domain-containing protein 3 (PNPLA3) gene is associated with high liver fat content and adipose tissue insulin resistance. This frequent SNP is also known to be associated with lean NAFLD so that genetic testing for this and other SNPs could improve future screening strategies to identify high-risk individuals. Although lifestyle modifications are effective, this approach is limited owing to difficulties with compliance and several classes of drugs are being tested to treat NAFLD. Antihyperglycaemic drugs such as glucagon-like peptide 1 receptor agonists (GLP-1 RA), sodium-glucose cotransporter 2 inhibitors (SGLT2i) and pioglitazone are promising and halt the progression of NAFLD. In conclusion, although NAFLD in diabetes may not be a separate entity, there are specific features to its pathogenesis and clinical management.

Incremental vibrational configuration interaction theory, iVCI: Implementation and benchmark calculations.

The implementation of an algorithm for the determination of vibrational state energies based on a many-body expansion within the framework of configuration interaction theory is presented. An efficient evaluation of the increments within this approach is realized by an iterative configuration selection scheme. The new algorithm is characterized by low memory demands and an embarassingly parallel workload. The convergence of the expansion has been studied for a series of small molecules of increasing size, namely, formaldehyde, ketene, ethylene, and diborane. A threshold function has been employed to reduce the number of increments for high orders of the expansion. Benchmark calculations with respect to customary configuration-selective vibrational configuration interaction calculations are provided.

Methyl-Shifted Farnesyldiphosphate Derivatives Are Substrates for Sesquiterpene Cyclases.

New sesquiterpene backbones are accessible after biotransformation of presilphiperfolan-8ß-ol synthase (BcBOT2), a fungal sesquiterpene synthase, with non-natural farnesyldiphosphates in which methyl groups are shifted by one position toward the diphosphate terminus. One of the macrocycles formed, a new germacrene A derivative, undergoes a Cope rearrangement to iso-ß-elemene. Three of the new terpenoids show olfactoric properties that range from an intense peppery note to a citrus, ozone-like, and fruity scent.

High-Level Rovibrational Calculations on Ketenimine.

From an astrochemical point of view ketenimine (CH2CNH) is a complex organic molecule (COM) and therefore likely to be a building block for biologically relevant molecules. Since it has been detected in the star-forming region Sagittarius B2(N), it is of high relevance in this field. Although experimental data are available for certain bands, for some energy ranges such as above 1200 cm-1 reliable data virtually do not exist. In addition, high-level ab initio calculations are neither reported for ketenimine nor for one of its deuterated isotopologues. In this paper, we provide for the first time data from accurate quantum chemical calculations and a thorough analysis of the full rovibrational spectrum. Based on high-level potential energy surfaces obtained from explicitly correlated coupled-cluster calculations including up to 4-mode coupling terms, the (ro)vibrational spectrum of ketenimine has been studied in detail by variational calculations relying on rovibrational configuration interaction (RVCI) theory. Strong Fermi resonances were found for all isotopologues. Rovibrational infrared intensities have been obtained from dipole moment surfaces determined from the distinguishable cluster approximation. A comparison of the spectra of the CH2CNH molecule with experimental data validates our results, but also reveals new insight about the system, which shows very strong Coriolis coupling effects.

Perfluoro Alkyl Hypofluorites and Peroxides Revisited.

A more convenient synthesis of the perfluoro alkyl hypofluorite (F3 C)3 COF as well as the hitherto unknown (C2 F5 )(F3 C)2 COF compound is reported. Both hypofluorites can be prepared by use of the corresponding tertiary alcohols RF OH and elemental fluorine in the presence of CsF. An appropriate access to these highly reactive hypofluorites is crucial. The hypofluorites are then transferred into their corresponding perfluoro bisalkyl peroxides RF OORF [RF =(F3 C)3 C, (C2 F5 )(F3 C)2 C] by treatment with partially fluorinated silver wool. NMR, gas-phase infrared, and solid-state Raman spectra of the perfluoro bisalkyl peroxides are presented and their chemical properties are discussed.

Low-barrier hydrogen bonds in enzyme cooperativity.

The underlying molecular mechanisms of cooperativity and allosteric regulation are well understood for many proteins, with haemoglobin and aspartate transcarbamoylase serving as prototypical examples1,2. The binding of effectors typically causes a structural transition of the protein that is propagated through signalling pathways to remote sites and involves marked changes on the tertiary and sometimes even the quaternary level1-5. However, the origin of these signals and the molecular mechanism of long-range signalling at an atomic level remain unclear5-8. The different spatial scales and timescales in signalling pathways render experimental observation challenging; in particular, the positions and movement of mobile protons cannot be visualized by current methods of structural analysis. Here we report the experimental observation of fluctuating low-barrier hydrogen bonds as switching elements in cooperativity pathways of multimeric enzymes. We have observed these low-barrier hydrogen bonds in ultra-high-resolution X-ray crystallographic structures of two multimeric enzymes, and have validated their assignment using computational calculations. Catalytic events at the active sites switch between low-barrier hydrogen bonds and ordinary hydrogen bonds in a circuit that consists of acidic side chains and water molecules, transmitting a signal through the collective repositioning of protons by behaving as an atomistic Newton's cradle. The resulting communication synchronizes catalysis in the oligomer. Our studies provide several lines of evidence and a working model for not only the existence of low-barrier hydrogen bonds in proteins, but also a connection to enzyme cooperativity. This finding suggests new principles of drug and enzyme design, in which sequences of residues can be purposefully included to enable long-range communication and thus the regulation of engineered biomolecules.

New geldanamycin derivatives with anti Hsp properties by mutasynthesis.

Mutasynthetic supplementation of the AHBA blocked mutant strain of S. hygroscopicus, the geldanamycin producer, with 21 aromatic and heteroaromatic amino acids provided new nonquinoid geldanamycin derivatives. Large scale (5 L) fermentation provided four new derivatives in sufficient quantity for full structural characterisation. Among these, the first thiophene derivative of reblastatin showed strong antiproliferative activity towards several human cancer cell lines. Additionally, inhibitory effects on human heat shock protein Hsp90α and bacterial heat shock protein from H. pylori HpHtpG were observed, revealing strong displacement properties for labelled ATP and demonstrating that the ATP-binding site of Hsps is the target site for the new geldanamycin derivatives.

From Polyhalides to Polypseudohalides: Chemistry Based on Cyanogen Bromide.

Pseudohalogens are defined as molecular entities that resemble the halogens in their chemistry. While our understanding of polyhalogen chemistry has increased over the last years, research on polypseudohalogen compounds is lacking. The pseudohalogen BrCN possesses a highly pronounced σ-hole at the bromine side of the molecule, inducing strong halogen bonding. This allows the synthesis and characterization of new polypseudohalogen anions, as shown by the single-crystal X-ray diffraction of [PNP][Br(BrCN)] and [PNP][Br(BrCN)3 ]. Both the nearly linear anion [Br(BrCN)]- and the distorted pyramidal anion [Br(BrCN)3 ]- were characterized by Raman spectroscopy and quantum-chemical calculations. The behavior of the polypseudohalogen compounds in solution and as room-temperature ionic liquids (RT-ILs) using the [NBu4 ]+ cation was studied by 13 C and 15 N NMR spectroscopy. These types of ILs are capable of dissolving elemental gold and offer themselves as promising compounds in metal recycling.

Strained hydrogen bonding in imidazole trimer: a combined infrared, Raman, and theory study.

In this work, a careful analysis of anharmonic couplings in NH and some CH stretch modes of imidazole is carried out. This includes IR and Raman spectra of the isolated molecule and aggregates up to the trimer, together with two different theoretical approaches to the calculation of anharmonic shifts and absolute band positions. The imidazole dimer is vibrationally characterized for the first time in vacuum isolation under supersonic jet conditions, showing substantial shifts from previous helium droplet experiments and evidence for Fermi resonance for the hydrogen-bonded NH stretch. The most stable imidazole trimer structure is unambiguously shown to be cyclic with three non-equivalent, highly strained hydrogen bonds. This contrasts the helium droplet observation of a chain trimer involving two unstrained hydrogen bonds. These experimental conclusions are strongly corroborated by theory, including vibrational perturbation theory and anharmonic normal mode analysis. Systematic error compensation in some of these methods is emphasized. Intramolecular anharmonic coupling constants from perturbation theory are validated by Raman hot band jet spectroscopy of the monomer. Imidazole aggregation is shown to provide valuable benchmarking opportunities for electronic structure and in particular for anharmonic vibrational methods, covering the field of strong and strongly distorted hydrogen bonding.

Stretching our understanding of C3: Experimental and theoretical spectroscopy of highly excited nν1 + mν3 states (n ≤ 7 and m ≤ 3).

We present the high resolution infrared detection of fifteen highly vibrationally excited nν1 + mν3 combination bands (n ≤ 7 and m ≤ 3) of C3 produced in a supersonically expanding propyne plasma, of which fourteen are reported for the first time. The fully resolved spectrum, around 3 µm, is recorded using continuous wave cavity ring-down spectroscopy. A detailed analysis of the resulting spectra is provided by ro-vibrational calculations based on an accurate local ab initio potential energy surface for C3 (X̃1Σg+). The experimental results not only offer a significant extension of the available data set, extending the observed number of quanta v1 to 7 and v3 to 3, but also a vital test to the fundamental understanding of this benchmark molecule. The present variational calculations give remarkable agreement compared to experimental values with typical accuracies of ∼0.01% for the vibrational frequencies and ∼0.001% for the rotational parameters, even for high energy levels around 10 000 cm-1.

Exploiting the Synthetic Potential of Sesquiterpene Cyclases for Generating Unnatural Terpenoids.

The substrate flexibility of eight purified sesquiterpene cyclases was evaluated using six new heteroatom-modified farnesyl pyrophosphates, and the formation of six new heteroatom-modified macrocyclic and tricyclic sesquiterpenoids is described. GC-O analysis revealed that tricyclic tetrahydrofuran exhibits an ethereal, peppery, and camphor-like olfactoric scent.