High-Pressure Reaction Profiles and Activation Volumes of 1,3-Cyclohexadiene Dimerizations Computed by the Extreme Pressure-Polarizable Continuum Model (XP-PCM)

Quantum chemical calculations are reported for the thermal dimerizations of 1,3-cyclohexadiene at 1 atm and high pressures up to the GPa range. Computed activation enthalpies of plausible dimerization pathways at 1 atm agree well with the experiment activation energies and the values from previous calculations. High-pressure reaction profiles, computed by the recently developed extreme pressure-polarizable continuum model (XP-PCM), show that the reduction of reaction barrier is more profound in concerted reactions than in stepwise reactions, which is rationalized on the basis of the volume profiles of different mechanisms. A clear shift of the transition state towards the reactant under pressure is revealed for the [6+4]-ene reaction by the calculations. The computed activation volumes by XP-PCM agree excellently with the experimental values, confirming the existence of competing mechanisms in the thermal dimerization of 1,3-cyclohexadiene.     

La3B6O13(OH): The First Acentric High-Pressure Borate Displaying Edge-Sharing BO4 Tetrahedra

La₃B₆O₁₃(OH) was obtained by a high-pressure/high-temperature experiment at 6 GPa and 1673 K. The compound crystallizes in the space group P2₁ (no. 4) with the lattice parameters a=4.785(2), b=12.880(4), c=7.433(3) Å, and β=90.36(10)°, and is built up of corner- as well as edge-sharing BO₄ tetrahedra. It represents the first acentric high-pressure borate containing these B₂O₆ entities. The compound develops borate layers of „sechser“-rings with the La³⁺ cations positioned between the layers. Single-crystal and powder X-ray diffraction, vibrational and MAS NMR spectroscopy, second-harmonic generation (SHG) and thermoanalytical measurements, as well as computational methods were used to affirm the proposed structure and the B₂O₆ entities.     

The Chemical Shift Baseline for High‐Pressure NMR Spectra of Proteins

High‐pressure (HP) NMR spectroscopy is an important method for detecting rare functional states of proteins by analyzing the pressure response of chemical shifts. However, for the analysis of the shifts it is mandatory to understand the origin of the observed pressure dependence. Here we present experimental HP NMR data on the ¹⁵N‐enriched peptide bond model, N‐methylacetamide (NMA), in water, combined with quantum‐chemical computations of the magnetic parameters using a pressure‐sensitive solvation model. Theoretical analysis of NMA and the experimentally used internal reference standard 4,4‐dimethyl‐4‐silapentane‐1‐sulfonic (DSS) reveal that a substantial part of observed shifts can be attributed to purely solvent‐induced electronic polarization of the backbone. DSS is only marginally responsive to pressure changes and is therefore a reliable sensor for variations in the local magnetic field caused by pressure‐induced changes of the magnetic susceptibility of the solvent.     

Dynamic Stereochemistry of a Biphenyl-Bisprolineamide Model Catalyst and its Imidazolidinone Intermediates

In this study, we characterize the dynamic stereochemistry of a biphenyl-2,2’-bis(proline amide) catalyst in chloroform and DMSO as representative weakly and strongly hydrogen bonding solvents. Using vibrational circular dichroism (VCD) spectroscopy and density functional theory (DFT) based spectra calculations, we show that the preferred axial stereochemistry of the catalyst is determined by solute-solvent interactions. Explicitly considering solvation with DMSO molecules is found to be essential to correctly predict the conformational preferences of the catalyst. Furthermore, we investigate the stereochemistry of the corresponding enamines and imidazolidinones that are formed upon reaction with isovaleraldehyde. The enamines are found to rapidly convert to endo-imidazolidinones and the thermodynamically favored exo-imidazolidinones are formed only slowly. The present study demonstrates that the stereochemistry of these imidazolidinones can be deduced directly from the VCD spectra analysis without any further detailed analysis of NMR spectra. Hence, we herein exemplify the use of VCD spectroscopy for an in situ characterization of intermediates relevant in asymmetric catalysts.     

Spectral Signatures of Hydrogen Thioperoxide (HOSH) and Hydrogen Persulfide (HSSH): Possible Molecular Sulfur Sinks in the Dense ISM

For decades, sulfur has remained underdetected in molecular form within the dense interstellar medium (ISM), and somewhere a molecular sulfur sink exists where it may be hiding. With the discovery of hydrogen peroxide (HOOH) in the ISM in 2011, a natural starting point may be found in sulfur-bearing analogs that are chemically similar to HOOH: hydrogen thioperoxide (HOSH) and hydrogen persulfide (HSSH). The present theoretical study couples the accuracy in the anharmonic fundamental vibrational frequencies from the explicitly correlated coupled cluster theory with the accurate rotational constants provided by canonical high-level coupled cluster theory to produce rovibrational spectra for use in the potential observation of HOSH and HSSH. The ν6 mode for HSSH at 886.1 cm−1 is within 0.2 cm−1 of the gas-phase experiment, and the B0 rotational constant for HSSH of 6979.5 MHz is within 9.0 MHz of the experimental benchmarks, implying that the unknown spectral features (such as the first overtones and combination bands) provided herein are similarly accurate. Notably, a previous experimentally-attributed 2ν1 mode, at 7041.8 cm−1, has been reassigned to the ν1+ν5 combination band based on the present work’s ν1+ν5 value at 7034.3 cm−1. The most intense vibrational transitions for each molecule are the torsions, with HOSH having a more intense transition of 72 km/mol compared to HSSH’s intensity of 14 km/mol. Furthermore, HOSH has a larger net dipole moment of 1.60 D compared to HSSH’s 1.15 D. While HOSH may be the more likely candidate of the two for possible astronomical observation via vibrational spectroscopy due to the notable difference in their intensities, both HSSH and HOSH have large enough net dipole moments to be detectable by rotational spectroscopy to discover the role these molecules may have as possible molecular sulfur sinks in the dense ISM.     

Multi‐Resolution Simulation of Biomolecular Systems: A Review of Methodological Issues

Theoretical‐computational modeling with an eye to explaining experimental observations in regard to a particular chemical phenomenon or process requires choices concerning essential degrees of freedom and types of interactions and the generation of a Boltzmann ensemble or trajectories of configurations. Depending on the degrees of freedom that are essential to the process of interest, for example, electronic or nuclear versus atomic, molecular or supra‐molecular, quantum‐ or classical‐mechanical equations of motion are to be used. In multi‐resolution simulation, various levels of resolution, for example, electronic, atomic, supra‐atomic or supra‐molecular, are combined in one model. This allows an enhancement of the computational efficiency, while maintaining sufficient detail with respect to particular degrees of freedom. The basic challenges and choices with respect to multi‐resolution modeling are reviewed and as an illustration the differential catalytic properties of two enzymes with similar folds but different substrates with respect to these substrates are explored using multi‐resolution simulation at the electronic, atomic and supra‐molecular levels of resolution.     

Complexes of Formaldehyde and α-Dicarbonyls with Hydroxylamine: FTIR Matrix Isolation and Theoretical Study

The interactions of formaldehyde (FA), glyoxal (Gly) and methylglyoxal (MGly) with hydroxylamine (HA) isolated in solid argon and nitrogen were studied using FTIR spectroscopy and ab initio methods. The spectra analysis indicates the formation of two types of hydrogen-bonded complexes between carbonyl and hydroxylamine in the studied matrices. The cyclic planar complexes are stabilized by O–H⋯O(C), and C–H⋯N interactions and the nonplanar complexes are stabilized by O–H⋯O(C) bond. Formaldehyde was found to form with hydroxylamine, the cyclic planar complex and methylglyoxal, the nonplanar one in both argon and nitrogen matrices. In turn, glyoxal forms with hydroxylamine the most stable nonplanar complex in solid argon, whereas in solid nitrogen, both types of the complex are formed.     

Structural Isomerization of the Gas‐Phase 2‐Norbornyl Cation Revealed with Infrared Spectroscopy and Computational Chemistry

In an attempt to produce the 2‐norbornyl cation (2NB⁺) in the gas phase, protonation of norbornene was accomplished in a pulsed discharge ion source coupled with a supersonic molecular beam. The C₇H₁₁⁺ cation was size‐selected in a time‐of‐flight mass spectrometer and investigated with infrared laser photodissociation spectroscopy using the method of “tagging” with argon. The resulting vibrational spectrum, containing sharp bands in the C? H stretching and fingerprint regions, was compared to that predicted by computational chemistry. However, the measured spectrum did not match that of 2NB⁺, prompting a detailed computational study of other possible isomers of C₇H₁₁⁺. This study finds five isomers more stable than 2NB⁺. The spectrum obtained corresponds to the 1,3‐dimethylcyclopentenyl cation, the global minimum‐energy structure for C₇H₁₁⁺, which is produced through an unanticipated ring‐opening rearrangement path.     

Gas‐Phase Infrared Spectroscopy of Substituted Cyanobutadiynes: Roles of the Bromine Atom and Methyl Group as Substituents

The IR spectra of 5‐bromo‐2,4‐pentadiynenitrile (Br?C≡C?C≡C?CN) and 2,4‐hexadiynenitrile (CH₃?C≡C?C≡C?CN), a compound of interstellar interest, have been recorded within the 4000–500 cm^?1 spectral region and calculated by means of high‐level ab initio and density functional calculations. Although the calculated structures of both compounds are rather similar, there are very subtle differences, mainly in the strength of the C≡C bond not directly bound to the substituent. These subtle bonding differences are reflected in small, but not negligible, differences in the electron density at the corresponding bond critical points, and, more importantly, are reflected in the IR spectra. Indeed, the IR spectrum for the bromine derivative presents two well‐differentiated strong bands around 2250 cm^?1, whereas for the methyl derivative both absorptions coalesce in a single band. These bands correspond in both cases to the coupling between C≡C and C≡N stretching displacements. A third, very weak, band also associated with C≡C and C≡N coupled stretches is observed for the bromine derivative, but not for the methyl one, owing to its extremely low intensity.     

Gas‐Phase Infrared Spectra of Three Compounds of Astrochemical Interest: Vinyl,Allenyl, and Propargyl Isocyanides

Isocyanides, isomers of the cyanides detected in the interstellar medium, are also possible components of this medium. The infrared spectra (5000–500 cm^?1) of gaseous vinyl isocyanide, allenyl isocyanide, and propargyl isocyanide have been recorded at 0.1 cm^?1 resolution. When prepared on a gram scale to produce a partial pressure of 10 mbar after evaporation in the cell, these three isocyanides, which have previously been reported to be kinetically unstable, do not display any sign of decomposition when recording the spectra. Geometry optimizations and harmonic and anharmonic vibrational frequencies were calculated using the LCCSD(T) method with the cc‐pVTZ basis set. Anharmonic frequencies of fundamental, overtone, and combination transitions were calculated using a variational approach implemented in the P Anhar.v2.0 code, to assign the experimental data for each compound. These results improve our knowledge of these under‐investigated compounds and pave the way for other physicochemical studies on functionalized isocyanides.     

Modeling the Electrochemical Response of Mesoporous Materials Toward Its Application to Biomolecular Detection

The performance of an electrochemical sensor based on the ability of a probe to cross a mesoporous membrane partially blocked by an analyte is predicted using a numerical model. The system comprehends a membrane placed close to the working electrode and the signal is generated by applying square wave voltammetry. The digital simulation allows comparing the responses for different situations regarding the way in which the membrane is blocked by the sample. The developed model is compared with experimental results. The effect of the sizes of the pore, analyte and probe on the system response is evaluated.     

Bioorganometallic Chemistry with IspG and IspH: Structure,Function, and Inhibition of the [Fe4S4] Proteins Involved in Isoprenoid Biosynthesis

Enzymes of the methylerythritol phosphate pathway of isoprenoid biosynthesis are attractive anti‐infective drug targets. The last two enzymes of this pathway, IspG and IspH, are [Fe₄S₄] proteins that are not produced by humans and catalyze 2 H⁺/ 2 e^? reductions with novel mechanisms. In this Review, we summarize recent advances in structural, mechanistic, and inhibitory studies of these two enzymes. In particular, mechanistic proposals involving bioorganometallic intermediates are presented, and compared with other mechanistic possibilities. In addition, inhibitors based on substrate analogues as well as developed by rational design and compound‐library screening, are discussed. The results presented support bioorganometallic catalytic mechanisms for IspG and IspH, and open up new routes to anti‐infective drug design targeting [Fe₄S₄] clusters in proteins.     

Matrix Isolation FTIR and Theoretical Study of Weakly Bound Complexes of Isocyanic Acid with Nitrogen

Weak complexes of isocyanic acid (HNCO) with nitrogen were studied computationally employing MP2, B2PLYPD3 and B3LYPD3 methods and experimentally by FTIR matrix isolation technique. The results show that HNCO interacts specifically with N₂. For the 1:1 stoichiometry, three stable minima were located on the potential energy surface. The most stable of them involves a weak, almost linear hydrogen bond from the NH group of the acid molecule to nitrogen molecule lone pair. Two other structures are bound by van der Waals interactions of N⋯N and C⋯N types. The 1:2 and 2:1 HNCO complexes with nitrogen were computationally tracked as well. Similar types of interactions as in the 1:1 complexes were found in the case of the higher stoichiometry complexes. Analysis of the HNCO/N₂/Ar spectra after deposition indicates that the 1:1 hydrogen-bonded complex is prevalent in argon matrices with a small amount of the van der Waals structures also present. Upon annealing, complexes of the 1:2 and 2:1 stoichiometry were detected as well.