Conformational analysis of cycloalkanes

[2+2]-Photocycloadditions of 1,4-Naphthoquinone Under Batch and Continuous-Flow Conditions

A series of [2+2]-photocycloadditions of 1,4-naphthoquinone with various alkenes and diphenylacetylene were investigated under batch and continuous-flow conditions. Acetone-sensitization furnished the corresponding photoadducts in good to excellent yields and purities. Compared to batch operations that demanded exhaustive irradiation times of 10-13 h, the flow process generally gave superior conversions and subsequently yields with a residence time of just 60 min. The structures of several photoaddition products were further determined by crystal structure analysis.

ConfRank: Improving GFN-FF Conformer Ranking with Pairwise Training

Conformer ranking is a crucial task for drug discovery, with methods for generating conformers often based on molecular (meta)dynamics or sophisticated sampling techniques. These methods are constrained by the underlying force computation regarding runtime and energy ranking accuracy, limiting their effectiveness for large-scale screening applications. To address these ranking limitations, we introduce ConfRank, a machine learning-based approach that enhances conformer ranking using pairwise training. We demonstrate its performance using GFN-FF-generated conformer ensembles, leveraging the DimeNet++ architecture trained on pairs of 159 760 uncharged organic compounds from the GEOM data set with r2SCAN-3c reference level. Instead of predicting only on single molecules, this approach captures relative energy differences between conformers, leading to a significant improvement of the overall conformational ranking, outperforming GFN-FF and GFN2-xTB. Thereby, the pairwise RMSD of the relative energy difference of two conformers can be reduced from 5.65 to 0.71 kcal mol-1 on the test data set, allowing to correctly identify up to 81% of all lowest lying conformers correctly (GFN-FF: 10%, GFN2-xTB: 47%). The ConfRank approach is cost-effective, allowing for scalable deployment on both CPU and GPU, achieving runtime accelerations by up to 2 orders of magnitude compared to GFN2-xTB. Out-of-sample investigations on CREST-generated conformer ensembles from the QM9 data set and conformers taken from an extended GMTKN55 data set show promising results for the robustness of this approach. Thereby, ranking correlation coefficient such as Spearman can be improved to 0.90 (GFN-FF: 0.39, GFN2-xTB: 0.84) reducing the probability of an incorrect sign flip in pairwise energy comparison from 32 to 7%. On the extended GMTKN55 subsets the pairwise MAD (RMSD) could be reduced on almost all subsets by up to 62% (58%) with an average improvement of 30% (29%). Moreover, an exemplary case study on vancomycin shows similar performance, indicating applicability to larger (bio)molecular structures. Furthermore, we motivate the usage of the pairwise training approach from a theoretical perspective, highlighting that while pairwise training can lead to a decline in single sample prediction of absolute energies for ML models, it significantly enhances conformer ranking performance. The data and models used in this study are available at https://github.com/grimme-lab/confrank.

Thermodynamics of Micelle Formation of Selected Homologous 7-Alkyl Derivatives of Na-Cholate in Aqueous Solution: Steroid Skeleton and the Alkyl Chain Conformation

Bile acid salts are steroid biosurfactants that build relatively small micelles compared to surfactants with an alkyl chain due to the rigid conformation of the steroid skeleton. In order to increase the capacity of micellar solubilization of the hydrophobic molecular guest, certain C7 alkyl derivatives were synthesized. Namely, introducing an alkyl group in the C7 position of the steroid skeleton results in a more effective increase in the micelle's hydrophobic domain (core) than the introduction in the C3 position. In comparison, fewer synthetic steps are required than if alkyl groups are introduced into the C12 position of cholic acid in the Grignard reaction. Here, the thermodynamic parameters of micellization (demicellization) of C7 alkyl (number of C atoms in the alkyl group: 2, 3, 4, and 8) derivatives of cholic acid anion in an aqueous solution without additives are examined (which have not yet been determined) in the temperature interval T (10-40) °C. The critical micellar concentration and the change in the standard molar enthalpy of demicellization (∆hdemic0) are determined by isothermal calorimetric titration (ICT). From the temperature dependence of ∆hdemic0, the change in the standard molar heat capacity of demicellization is obtained (∆Cdemic0), the value of which is proportional to the hydrophobic surface of the monomer, which in the micellar state is protected from hydrophobic hydration. The values of ∆Cdemic0 indicate that in the case of C7-alkyl derivatives of cholic acid anion with butyl and octyl chains, parts of the steroid skeleton and alkyl chain remain shielded from hydration after disintegration of the micelle. Conformational analysis can show that starting from the C7 butyl chain in the alkyl chain, sequences with gauche conformation are also possible without the formation of steric repulsive strain between the alkyl chain and the steroid skeleton so that the C7 alkyl chain takes an orientation above the convex surface of the steroid skeleton instead of an elongated conformation toward the aqueous solution. This is a significant observation, namely, if the micelle is used as a carrier of a hydrophobic drug and after the breakdown of the micelle in the biological system, the released drug has a lower tendency to associate with the monomer if its hydrophobic surface is smaller, i.e., the alkyl chain is oriented towards the angular methyl groups of the steroid skeleton (the ideal monomer increases the hydrophobic domain of the micelle, but in aqueous solution, it adopts a conformation with the as small hydrophobic surface as possible oriented towards the aqueous solution)-which then does not disturb the passage of the drug through the cell membrane.

Ka-Band Rotational Spectroscopy of Succinimide and N-Chlorosuccinimide

Succinimide and its derivatives are cyclic five-membered rings that appear in a variety of natural products and are widely used in organic synthesis. From a structural standpoint, succinimide contains an NH group in the ring which interacts with two adjacent carbonyl groups, pushing the ring structure toward planarity at the expense of increasing ring strain and eclipsing interactions among the out-of-plane hydrogen atoms in the two CH2 groups. Previous quantum chemical calculations at different levels of theory have predicted both a nonplanar C2 structure and a planar C2v structure, the latter of which is the most consistent with gas-phase electron diffraction measurements. Here, we report the pure rotational spectra of succinimide and N-chlorosuccinimide in the 26.5-40.0 GHz range using chirped-pulse Fourier transform microwave spectroscopy, supported by coupled cluster and density functional theory quantum chemical calculations. The spectra were fit to Watson's A-reduced effective Hamiltonian, including both 35Cl and 37Cl isotopologues of N-chlorosuccinimide as well as the N and Cl quadrupole hyperfine interactions. On the basis of the agreement with quantum chemical calculations and the measured inertial defects, we find that the rotational spectra are consistent with a planar ring structure, with a maximum out-of-plane angle of ≤5°.

Direct Visualization of Molecular Stacking in Quasi-2D Hexagonal Ice

Understanding ice nucleation and growth is of great interest to researchers due to its importance in the biological, cryopreservation, and environmental fields. However, microstructural investigations of ice on the molecular scale are still lacking. In this paper, a simple method is proposed to prepare quasi-2-dimensional ice Ih films, which have been characterized via cryogenic transmission electron microscope. The intersecting stacking faults of basal (BSF) and prismatic (PSF) types have been directly visualized and resolved with a notable first-time report of PSF in ice Ih. Moreover, the possible growth pathways of BSF, namely, the Ic phase, were elucidated by the theoretical calculations and the chair conformation of H2O molecules. This study offers valuable insights that can enhance researchers' understanding of the growth kinetics of crystalline ice.

Nuciferol C, a new sesquineolignan dimer from Cocos nucifera L.: bioactivity and theoretical investigation

Nuciferol C (NC), an undescribed dimer of nuciferol B (NB), was isolated from the endocarp of Cocos nucifera L. The planar structure of NC was determined using 1D- and 2D-NMR spectroscopy as well as high resolution MS spectrometry. The absolute configuration was concluded based on analysis of NOESY spectra. NC showed cytotoxic activity against colon cancer cells (CaCo-2) with an IC50 value of 76 μM, and significantly decreased the expression of human epidermal growth factor receptor (EGFR) and tumor necrosis factor alpha (TNF-α) in CaCo-2 as compared with untreated cells by 39% and 33%, respectively (p < 0.05). In addition, NC exhibited anti-herpes simplex virus (HSV-I) activity with an IC50 value of 23 μM. In silico study of NC was implemented at three levels: density functional theory (DFT) was used to study its electronic properties, molecular mechanics was used to estimate the docking results, and finally, molecular dynamic simulation was used to study the behavior and stability of NC inside the active site of the target protein of HSV-1.

8-Bicycloalkyl-CPFPX derivatives as potent and selective tools for in vivo imaging of the A1 adenosine receptor

Imaging of the A1 adenosine receptor (A1R) by positron emission tomography (PET) with 8-cyclopentyl-3-(3-[18F]fluoropropyl)-1-propyl-xanthine ([18F]CPFPX) has been widely used in preclinical and clinical studies. However, this radioligand suffers from rapid peripheral metabolism and subsequent accumulation of radiometabolites in the vascular compartment. In the present work, we prepared four derivatives of CPFPX by replacement of the cyclopentyl group with norbornane moieties. These derivatives were evaluated by competition binding studies, microsomal stability assays and LC-MS analysis of microsomal metabolites. In addition, the 18F-labeled isotopologue of 8-(1-norbornyl)-3-(3-fluoropropyl)-1-propylxanthine (1-NBX) as the most promising candidate was prepared by radiofluorination of the corresponding tosylate precursor and the resulting radioligand ([18F]1-NBX) was evaluated by permeability assays with Caco-2 cells and in vitro autoradiography in rat brain slices. Our results demonstrate that 1-NBX exhibits significantly improved A1R affinity and selectivity when compared to CPFPX and that it does not give rise to lipophilic metabolites expected to cross the blood-brain-barrier in microsomal assays. Furthermore, [18F]1-NBX showed a high passive permeability (Pc = 6.9 ± 2.9 × 10-5 cm/s) and in vitro autoradiography with this radioligand resulted in a distribution pattern matching A1R expression in the brain. Moreover, a low degree of non-specific binding (5%) was observed. Taken together, these findings identify [18F]1-NBX as a promising candidate for further preclinical evaluation as potential PET tracer for A1R imaging.

Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory

We selected 145 reference organic molecules that include model fragments used in computer-aided drug design. We calculated 158 conformational energies and barriers using force fields, with wide applicability in commercial and free softwares and extensive application on the calculation of conformational energies of organic molecules, e.g. the UFF and DREIDING force fields, the Allinger's force fields MM3-96, MM3-00, MM4-8, the MM2-91 clones MMX and MM+, the MMFF94 force field, MM4, ab initio Hartree-Fock (HF) theory with different basis sets, the standard density functional theory B3LYP, the second-order post-HF MP2 theory and the Domain-based Local Pair Natural Orbital Coupled Cluster DLPNO-CCSD(T) theory, with the latter used for accurate reference values. The data set of the organic molecules includes hydrocarbons, haloalkanes, conjugated compounds, and oxygen-, nitrogen-, phosphorus- and sulphur-containing compounds. We reviewed in detail the conformational aspects of these model organic molecules providing the current understanding of the steric and electronic factors that determine the stability of low energy conformers and the literature including previous experimental observations and calculated findings. While progress on the computer hardware allows the calculations of thousands of conformations for later use in drug design projects, this study is an update from previous classical studies that used, as reference values, experimental ones using a variety of methods and different environments. The lowest mean error against the DLPNO-CCSD(T) reference was calculated for MP2 (0.35 kcal mol-1), followed by B3LYP (0.69 kcal mol-1) and the HF theories (0.81-1.0 kcal mol-1). As regards the force fields, the lowest errors were observed for the Allinger's force fields MM3-00 (1.28 kcal mol-1), ΜΜ3-96 (1.40 kcal mol-1) and the Halgren's MMFF94 force field (1.30 kcal mol-1) and then for the MM2-91 clones MMX (1.77 kcal mol-1) and MM+ (2.01 kcal mol-1) and MM4 (2.05 kcal mol-1). The DREIDING (3.63 kcal mol-1) and UFF (3.77 kcal mol-1) force fields have the lowest performance. These model organic molecules we used are often present as fragments in drug-like molecules. The values calculated using DLPNO-CCSD(T) make up a valuable data set for further comparisons and for improved force field parameterization.

Cooperative Nitrile Coordination Using Nickel and a Boron-Containing Secondary Coordination Sphere

Metal-ligand cooperation has emerged as a versatile tool for substrate activation in chemical reactivity. Herein, we provide the synthesis and characterization of a monoboranyl-containing analogue of the ubiquitous bulky diphosphine ligand, 1,2-bis(di-tert-butylphosphino)ethane, whose reactivity has been examined using nickel. Together, the pairing of nickel and boron provides a platform that allows for the cooperative coordination of organonitriles, giving unusual examples of intermolecularly bound dinickelacycles.

Triple Thorpe-Ingold Effect in the Synthesis of 18-Membered C3 Symmetric Lactams Stacking as Endless Supramolecular Tubes

Three C₃ symmetric macrolactams were very efficiently cyclized from their linear precursors. Adequately located substituents are responsible for the enhancement of reactivity that is not observed in the unsubstituted parent. DFT calculations show that the properly folded cyclization precursor, the reactive conformer, is more populated than other conformers, leading to a decrease of free energy of activation. The crystal structure of the ring substituted with three very bulky esters indicates that tubular stacking is preserved.

The Nitrate and Nitrocarbamate of 1,3,5-Trinitrocyclohexane-trimethanol and Selected Salts

With 1,3,5-trinitrocyclohexane-1,3,5-triyl trimethanol as a precursor, available from 1,3,5-trinitrobenzene, two further nitro-containing molecules were synthesized. Via modification of the hydroxyl groups, new oxygen-rich compounds were obtained, the corresponding trinitrate and trinitrocarbamate. From the latter, various salts were obtained by treatment with bases. All compounds were fully characterized by NMR and IR spectroscopy, X-ray diffraction, and elemental and differential thermal analyses. Moreover, the sensitivity toward friction and impact was determined according to BAM standard techniques and the energetic properties were calculated by using the EXPLO5 computer code.

Theoretical Exploitation of 1,2,3,4,5,6-Hexachloro- and 1,2,3,4,5,6-Hexafluorocyclohexane Isomers as Biologically Active Compounds

Hexachlorocyclohexanes (HCHs) have been widely explored as biological compounds during the last century. However, most of them were banned due to their potential toxicity in humans, animals, and the environment. Revisiting HCHs to explore their biological activity while improving key features is valuable and may lead to a new class of pesticides that utilizes the biological response of HCHs without their toxic characteristics. In this sense, the fluorine atom can be a possible alternative since a large number of therapeutics and agrochemicals have been developed with this halogen in their structure. We have evaluated herein the conformational behavior of HCHs and their bioisosteric fluorinated compounds, namely, hexafluorocyclohexanes (HFHs), through quantum-chemical calculations. We also explored the potential of the HCH and HFH isomers as biological compounds by docking them inside three possible targets. It was demonstrated that HCH and HFH have similar ligand-protein interactions with three pockets: the picrotoxin and barbiturate sites of the GABA_A receptor and the ryanodine receptor. The results support HFHs as possible alternatives for HCHs since the replacement of Cl with F does not forfeit the main ligand-protein interactions. Finally, we demonstrated that HFHs have a lower log P than HCHs by almost two logarithmic units. This result highlights the role of fluorine in distribution and bioaccumulation.

Conformations of Steroid Hormones: Infrared and Vibrational Circular Dichroism Spectroscopy

Steroid hormone molecules may exhibit very different functionalities based on the associated functional groups and their 3D arrangements in space, i.e., absolute configurations and conformations. Infrared (IR) and vibrational circular dichroism (VCD) spectra of four different steroid hormones, namely dehydroepiandrosterone (DHEA), 17α-methyltestosterone (MTTT), (16α,17)-epoxyprogesterone (Epoxy-P4), and dehydroepiandrosterone acetate (AcO-DHEA), were measured in deuterated dimethyl sulfoxide and some also in carbon tetrachloride. Extensive conformational searches were carried out using the recent developed conformer-rotamer ensemble sampling tool (CREST) which also accounts for solvent effects using an implicit solvation model. All the CREST conformational candidates were then reoptimized at the B3LYP-D3BJ/def2-TZVPD with the PCM of solvent. The good agreements between the experimental IR and VCD spectra and the theoretical simulations provide a conclusive information about their conformational distribution and absolute configurations. The experimental and theoretical IR and VCD spectra of AcO-DHEA in the carbonyl and alkene stretching region showed some discrepancies, and the possible causes related to solvent effects, large amplitude motions and levels of theory used in the modelling were explored in detail. As part of the investigation, additional calculations at the B3LYP-D3BJ/6-31++G (2d,p) and B3LYP-D3BJ/cc-pVTZ levels, as well as some 'mixed' calculations with the double-hybrid functional B2PLYP-D3 were also carried out. The results indicate that the double-hybrid functional is important for predicting the correct IR band pattern in the carbonyl and alkene stretching region.

Automotive Diesel Fuel Internal Stability Testing with the Use of UV and Temperature as Degradation Factors

Diesel fuel stability can be considered from many points of view, of which the two considered most important are stability in contact with the environment and internal stability. Fuel stability in touch with the environment is often defined as oxidation stability, of which measurement procedures are well developed. The presented paper shows that fuel's internal stability can also be important. The internal stability of diesel fuel with the local use of thermal and ultraviolet radiation (UV) as degradation factors and fluorescence signals as a probe is presented in this paper. We show that the internal degradation of fuel with temperature use differs from that with UV and simultaneous both factors use. Our study shows that using temperature as a degradation factor introduces significant fluorescence fading. Moreover, the fluorescence signal restores significantly later than the sample stabilizes at room temperature. The novelty proposed based on examination is hybrid degradation and an examination cycle that enables the simultaneous use of degradation factors and fluorescence reading. For this purpose, a dedicated measurement setup of signal control and processing was constructed and programmed. The measurement procedure of the data series for specific wavelength enables calculation of signal shifts that allow the internal stability classification of diesel fuel samples in less than 30 min with the cost of a single disposable capillary probe and one polymer plug. Premium and regular fuel examination results show that internal fuel stability can be related to polycyclic aromatic hydrocarbons (PAH) concentrations and can be modified with dedicated additives.

Conformational Panorama of Cycloundecanone: A Rotational Spectroscopy Study

The conformational landscape of the medium-size cyclic ketone cycloundecanone has been investigated using chirped-pulse Fourier transform microwave spectroscopy and computational calculations. Nine conformations were observed in the rotational spectrum and identified from the comparison of experimental and theoretical rotational constants as well as the observed and predicted types of rotational transitions. All singly substituted ¹³C isotopologues were observed for the most abundant conformer, which allowed the determination of partial substitution and effective structures. The most abundant conformer dominates the rotational spectrum and is almost 40 times more abundant than the least abundant conformer. Conformational preferences are governed by the combination of transannular H···H and eclipsed HCCH interactions.

Induced Fit and Mobility of Cycloalkanes within Nanometer-Sized Confinements at 5 K

Host-guest architectures provide ideal systems for investigating site-specific physical and chemical effects. Condensation events in nanometer-sized confinements are particularly interesting for the investigation of intermolecular and molecule-surface interactions. They may be accompanied by conformational adjustments representing induced fit packing patterns. Here, we report that the symmetry of small clusters formed upon condensation, their registry with the substrate, their lateral packing, and their adsorption height are characteristically modified by the packing of cycloalkanes in confinements. While cyclopentane and cycloheptane display cooperativity upon filling of the hosting pores, cyclooctane and to a lesser degree cyclohexane diffusively redistribute to more favored adsorption sites. The dynamic behavior of cyclooctane is surprising at 5 K given the cycloalkane melting point of >0 °C. The site-specific modification of the interaction and behavior of adsorbates in confinements plays a crucial role in many applications of three-dimensional porous materials as gas storage agents or catalysts/biocatalysts.

Hydrocarbon Macrocycle Conformer Ensembles and 13 C-NMR Spectra

NMR as a routine analytical method provides important three-dimensional structure information of compounds in solution. Here we apply the recently released CRENSO computational workflow for the automated generation of conformer ensembles to the quantum mechanical calculation of ¹³ C-NMR spectra of a series of flexible cycloalkanes up to C₂₀ H₄₀ . We evaluate the computed chemical shifts in comparison with corresponding experimental data in chloroform. It is shown that accurate and properly averaged theoretical NMR data can be obtained in about a day of computation time on a standard workstation computer. The excellent agreement between theory and experiment enables one to deduce preferred conformations of large, non-rigid macrocycles under ambient conditions from our automated procedure.

Polymer Structure Predictor (PSP): A Python Toolkit for Predicting Atomic-Level Structural Models for a Range of Polymer Geometries

Three-dimensional atomic-level models of polymers are the starting points for physics-based simulation studies. A capability to generate reasonable initial structural models is highly desired for this purpose. We have developed a python toolkit, namely, polymer structure predictor (psp), to generate a hierarchy of polymer models, ranging from oligomers to infinite chains to crystals to amorphous models, using a simplified molecular-input line-entry system (SMILES) string of the polymer repeat unit as the primary input. This toolkit allows users to tune several parameters to manage the quality and scale of models and computational cost. The output structures and accompanying force field (GAFF2/OPLS-AA) parameter files can be used for downstream ab initio and molecular dynamics simulations. The psp package includes a Colab notebook where users can go through several examples, building their own models, visualizing them, and downloading them for later use. The psp toolkit, being a first of its kind, will facilitate automation in polymer property prediction and design.

Dynamics and Entropy of Cyclohexane Rings Control pH-Responsive Reactivity

Activation entropy (ΔS ^‡) is not normally considered the main factor in determining the reactivity of unimolecular reactions. Here, we report that the intramolecular degradation of six-membered ring compounds is mainly determined by the ΔS ^‡, which is strongly influenced by the ring-flipping motion and substituent geometry. Starting from the unique difference between the pH-dependent degradation kinetics of geometric isomers of 1,2-cyclohexanecarboxylic acid amide (1,2-CHCAA), where only the cis isomer can readily degrade under weakly acidic conditions (pH < 5.5), we found that the difference originated from the large difference in ΔS ^‡ of 16.02 cal·mol^-1·K^-1. While cis-1,2-CHCAA maintains a preference for the classical chair cyclohexane conformation, trans-1,2-CHCAA shows dynamic interconversion between the chair and twisted boat conformations, which was supported by both MD simulations and VT-NMR analysis. Steric repulsion between the bulky 1,2-substituents of the trans isomer is one of the main reasons for the reduced energy barrier between ring conformations that facilitates dynamic ring inversion motions. Consequently, the more dynamic trans isomer exhibits much a larger loss in entropy during the activation process due to the prepositioning of the reactant than the cis isomer, and the pH-dependent degradation of the trans isomer is effectively suppressed. When the ring inversion motion is inhibited by an additional methyl substituent on the cyclohexane ring, the pH degradability can be dramatically enhanced for even the trans isomer. This study shows a unique example in which spatial arrangement and dynamic properties can strongly influence molecular reactivity in unimolecular reactions, and it will be helpful for the future design of a reactive structure depending on dynamic conformational changes.

Seven Conformations of the Macrocycle Cyclododecanone Unveiled by Microwave Spectroscopy

The physicochemical properties and reactivity of macrocycles are critically shaped by their conformations. In this work, we have identified seven conformations of the macrocyclic ketone cyclododecanone using chirped-pulse Fourier transform microwave spectroscopy in combination with ab initio and density functional theory calculations. Cyclododecanone is strongly biased towards adopting a square configuration of the heavy atom framework featuring three C-C bonds per side. The substitution and effective structures of this conformation have been determined through the observation of its ¹³C isotopologues. The minimisation of transannular interactions and, to a lesser extent, HCCH eclipsed configurations drive conformational preferences. Our results contribute to a better understanding of the intrinsic forces mediating structural choices in macrocycles.

1-Methyl-8-phenyl-1,3-diazaspiro[4.5]decane-2,4-dione

A simple, fast and cost-effective three-step synthesis of 1-methyl-8-phenyl-1,3-diazaspiro[4.5]decane-2,4-dione has been developed. The reactions described herein proceed readily, with high yields and no further purification. Therefore, the proposed method, with an overall yield of 60%, offers a facile pathway to the synthesis of N-1 monosubstituted spiro carbocyclic imidazolidine-2,4-diones (hydantoins), which constitute a privileged class of heterocyclic scaffolds with pharmacological interest.

Energetic Descriptors of Steric Hindrance in Real Space: An Improved IQA Picture*

Steric hindrance (SH) plays a central role in the modern chemical narrative, lying at the core of chemical intuition. As it however happens with many successful chemical concepts, SH lacks an underlying physically sound root, and multiple mutually inconsistent approximations have been devised to relate this fuzzy concept to computationally derivable descriptors. We here argue that being SH related to spatial as well as energetic features of interacting systems, SH can be properly handled if we chose a real space energetic stance like the Interacting Quantum Atoms (IQA) approach. Drawing on previous work by Popelier and coworkers (ChemistryOpen 8, 560, 2019) we build an energetic estimator of SH, referred to as E_ST . We show that the rise in the self-energy of a fragment that accompanies steric congestion is a faithful proxy for the chemist's SH concept if we remove the effect of charge transfer. This can be done rigorously, and the E_ST here defined provides correct sterics even for hydrogen atoms, where the plain use of deformation energies leads to non-chemical results. The applicability of E_ST is validated in several chemical scenarios, going from atomic compressions to archetypal S_N2 reactions. E_ST is shown to be a robust steric hindrance descriptor.

Stability, relaxometric and computational studies on Mn2+ complexes with ligands containing a cyclobutane scaffold

The stability constants of Mn²⁺ complexes with ligands containing a trans-1,2-cyclobutanediamine spacer functionalized with picolinate and/or carboxylate functions were determined using potentiometric titrations (25 °C, 0.1 M KCl). The stability constant of the complex with a hexadentate ligand containing four acetate groups (L1^4-, log K_MnL = 10.26) is improved upon replacing one (L2^4-, log K_MnL = 14.71) or two (L3^4-, log K_MnL = 15.81) carboxylate groups with picolinates. The [Mn(L1)]^2- complex contains a water molecule coordinated to the metal ion in aqueous solutions, as evidenced by ¹H NMRD studies and ¹⁷O chemical shifts and transverse relaxation rates. The ¹H relaxivities determined at 60 MHz (3.3 and 2.4 mM^-1 s^-1 at 25 and 37 °C, respectively) are comparable to those of monohydrated complexes such as [Mn(edta)]^2-. The exchange rate of the inner-sphere water molecule (k = 248 × 10⁶ s^-1) is slightly lower than that of the edta^4- analogue. DFT calculations (M11/def2-TZVP) suggest that the water exchange reaction follows a dissociatively activated mechanism, providing activation parameters in reasonably good agreement with the experimental data. DFT calculations also show that the ¹⁷O hyperfine coupling constant A/ℏ is affected slightly by changes in the Mn-O_water distance and the orientation of the water molecule with respect to the Mn-O vector.

Conformational analysis of two new organotin(IV) structures completed with a CSD survey

The conformational flexibilities are studied in two new organotin(IV) complexes, namely, trans-dichloridodimethylbis[N,N',N''-tris(2-chlorobenzyl)phosphoric triamide]tin(IV), [Sn(CH₃)₂(C₂₁H₂₁Cl₃N₃OP)₂Cl₂] or Sn(CH₃)₂Cl₂{OP[NHCH₂C₆H₄(2-Cl)]₃}₂, (I), and bis(dipropylammonium) tetrachloridodimethylstannate(IV), [(CH₃CH₂CH₂)₂NH₂]₂[Sn(CH₃)₂Cl₄], (II), and their analogous structures from the Cambridge Structural Database (CSD). The conformations are considered based on the N-P=O-Sn torsion angles for (I) and the C-C-C-N, C-C-N-C, C-N-C-C and N-C-C-C torsion angles for the two symmetry-independent [CH₃CH₂CH₂NH₂CH₂CH₂CH₃]⁺ cations in (II), and the ±ac±sp±ac (ac = anticlinal and sp = synperiplanar) and ±ap±ap±ap±ap (ap = antiperiplanar) conformations are observed, respectively. In both structures, the four atoms in the corners of the square-planar segment of the octahedral shape around the Sn atom participate in normal hydrogen-bonding interactions as acceptors, which include two O and two Cl atoms for (I), and four Cl atoms for (II). However, the phosphoric triamide ligands block the environment around the Sn atom and limit the hydrogen-bond pattern to form a supramolecular ribbon assembly, while in the presence of small organic cations in (II), a two-dimensional hydrogen-bonded architecture is achieved. The weak interactions π-π, C-H...π and C-Cl...π in (I), and C-H...Cl in (II) do not change the dimensionality of the hydrogen-bond pattern. The 62 CSD structures analogous to (I), i.e. with an SnOPN₃ segment (including 83 entries) fall into four categories of conformations based on the N-P=O-Sn torsion angles. The 132 [(CH₃CH₂CH₂)₂NH₂]⁺ cations from 85 CSD structures are classified into seven groups based on the torsion angles noted for (II). Most of the CSD structures adopt the same associated conformations noted for (I) and (II). 15 [Sn(CH₃)₂Cl₄]^2- anions extracted from the CSD are compared with the structure of (II).

Detailed kinetics of hydrogen abstraction from trans-decalin by OH radicals: the role of hindered internal rotation treatment

In this study, the detailed kinetic mechanism of the trans-decalin + OH reaction is firstly investigated for a wide range of conditions (i.e., T = 200-2000 K & P = 0.76-76 000 Torr) using the M06-2X/aug-cc-pVTZ level and stochastic Rice-Ramsperger-Kassel-Marcus based master equation (RRKM-ME) rate model, which includes corrections of the hindered internal rotor (HIR) and tunneling effects. Our predicted global rate constant excellently matches with the scarce experimental measurement (R. Atkinson, et al. Int. J. Chem. Kinet., 1983, 15, 37-50). The H-abstraction channel from Cα of trans-decalin is found to be dominant at low temperatures. A U-shaped temperature-dependent behavior and slightly positive pressure-dependence at low temperatures (e.g., T ≤ 400 K & P = 760 Torr) of the total rate constants are also observed. Detailed analysis reveals that the HIR treatment is essential to capture the kinetic behavior while the tunneling correction only plays a minor role.

Effect of molecular constitution and conformation on positron binding and annihilation in alkanes

The model-potential approach previously developed by the authors to study positron interactions with molecules is used to calculate the positron binding energy for n-alkanes (C_nH_2n+2) and the corresponding cycloalkanes (C_nH_2n). For n-alkanes, the dependence of the binding energy on the conformation of the molecule is investigated, with more compact structures showing greater binding energies. As a result, thermally averaged binding energies for larger alkanes (n ≳ 9) show a strong temperature dependence in the range of 100 K-600 K. This suggests that positron resonant annihilation can be used as a probe of rotational (trans-gauche) isomerization of n-alkanes. In particular, the presence of different conformers leads to shifts and broadening of vibrational Feshbach resonances in the annihilation rate, as observed with a trap-based low-energy positron beam.

Recent Advances in the Total Synthesis of Natural Products Containing Eight-Membered Carbocycles (2009-2019)

Natural products containing eight-membered carbocycles constitute a class of structurally intriguing and biologically important molecules such as the famous diterpenes taxol and vinigrol. Such natural products are being increasingly investigated because of their fascinating architectural features and potent medicinal properties. However, synthesis of natural products with cyclooctane moieties has proved to be highly challenging. This review highlights the recently completed total syntheses of natural products with eight-membered carbocycles with a focus on strategic considerations. A collection of 27 representative studies from the literature covering the decade from 2009 to 2019 is described in chronological order with relevant studies grouped together, including syntheses of the same natural product by different research groups using different strategies. Finally, a summary and outlook including a discussion of the major features of each strategy used in the syntheses are presented. This review illustrates the diversity and creativity in the elegant synthetic designs of eight-membered carbocycles. We hope this review will provide timely illumination and beneficial guidance for future synthetic efforts for organic chemists who are interested in this area.

Systematic description of molecular deformations with Cremer-Pople puckering and deformation coordinates utilizing analytic derivatives: Applied to cycloheptane, cyclooctane, and cyclo[18]carbon

The conformational properties of ring compounds such as cycloalkanes determine to a large extent their stability and reactivity. Therefore, the investigation of conformational processes such as ring inversion and/or ring pseudorotation has attracted a lot of attention over the past decades. An in-depth conformational analysis of ring compounds requires mapping the relevant parts of the conformational energy surface at stationary and also at non-stationary points. However, the latter is not feasible by a description of the ring with Cartesian or internal coordinates. We provide in this work, a solution to this problem by introducing a new coordinate system based on the Cremer-Pople puckering and deformation coordinates. Furthermore, analytic first- and second-order derivatives of puckering and deformation coordinates, i.e., B-matrices and D-tensors, were developed simplifying geometry optimization and frequency calculations. The new coordinate system is applied to map the potential energy surfaces and reaction paths of cycloheptane (C₇H₁₄), cyclooctane (C₈H₁₆), and cyclo[18]carbon (C₁₈) at the quantum chemical level and to determine for the first time all stationary points of these ring compounds in a systematic way.

Stability of Hierarchically Formed Titanium(IV) Tris(catecholate ester) Helicates with Cyclohexyl Substituents in DMSO

A cyclohexyl substituent strongly prefers the chair conformation with large substituents in equatorial positions, while other cycloalkyls are structurally more flexible. In hierarchically formed dimeric titanium(IV) tris(catecholates) equatorial versus axial connection of the cyclohexane to the ester results in either a more compact (axial) or more expanded (equatorial) structure. In DMSO solution the axial position results in a compact structure which minimizes solvophobic effects, leading to higher stability. However, computational investigations indicate that additionally intramolecular London dispersion interactions significantly contribute to the stability of the dimer. Thus, weak side-chain-side-chain interactions are responsible for the high stability of cyclohexyl ester derivatives with axial compared to equatorial ester connection.

Unveiling the role of intra and interatomic interactions in the energetics of reaction schemes: a quantum chemical topology analysis

In this work we present a detailed analysis of selected reaction schemes in terms of the atomic components of the electronic energy defined by the quantum theory of atoms in molecules and the interacting quantum atoms method. The aim is to provide an interpretation tool for the energy change involved in a chemical reaction by means of the atomic and interaction contributions to the energies of the molecules involved. Ring strain in cyclic alkanes, the resonance energy of aromatic and antiaromatic molecules, local aromaticity in polycyclic aromatic hydrocarbons, intermolecular bonding in hydrogen fluoride clusters, and hydration of d-block metal dications were selected for the study. It was found that in addition to the changes in the strong C-C interactions in the carbon skeleton of the organic molecular rings, other contributions not usually considered to be important such as those between C and H atoms (either bonded or not) need to be considered in order to account for the net energy changes. The analysis unveils the role of the ionic and covalent contributions to the hydrogen bonding in HF clusters and the energetic origin and extent of cooperative effects involved. Moreover, the "double-hump" behavior observed for the hydration energy trend of [M(H2O)6]2+ complexes is explained in terms of the deformation energy of the metal cation and the increasingly covalent metal-water interactions. In addition, proper comparisons with the description provided by other methodologies are briefly discussed. The topological approach proposed in this contribution proves to be useful for the description of energy changes of apposite reaction schemes in chemically meaningful terms.

Magnetic Field-Sensitive Radical Pair Dynamics in Polymethylene Ether-Bridged Donor-Acceptor Systems

Donor-acceptor systems forming exciplexes are versatile models for the study of magnetic field effects (MFEs) on charge recombination reactions. The MFEs originate from singlet-triplet interconversion within transient radical ion pairs (RIPs), which exist in a dynamic equilibrium with the exciplexes. Here, we describe the synthesis and MFEs of the chain-linked N,N-dimethylaniline (DMA)/9-methylanthracene (MAnt) donor-acceptor system MAnt-(CH2) n -O-CH2-CH2-DMA for n = 6, 8, 10, and 16. The MFEs are found to increase with increasing chain length. Effects as large as 37.5% have been observed for the long-chain compound with n = 16. The solvent dependence of the MFEs at magnetic field intensity 75 mT is reported. For the range of solvent static dielectric constants εs = 6.0-36.0, the MFEs go through a maximum for intermediate polarities, for which the direct formation of RIPs prevails and their dissociation and reencounter are balanced. Field-resolved measurements (MARY spectra) are reported for solutions in butyronitrile. The MARY spectra reveal that for n = 8, 10, 16, the average exchange interaction is negligible during the coherent lifetime of the radical pair. However, singlet-triplet dephasing broadens the lineshape; the shorter the linker, the more pronounced this effect is. For n = 6, a dip in the fluorescence intensity reveals a nonzero average exchange coupling of the order of ±5 mT. We discuss the field-dependence in the framework of the semiclassical theory taking spin-selective recombination, singlet-triplet dephasing, and exchange coupling into account. Singlet recombination rates of the order of 0.1 ns-1 and various degrees of singlet-triplet dephasing govern the spin dynamics. In addition, because of a small free energy gap between the exciplex and the locally excited fluorophore quencher pair, a fully reversible interconversion between the RIP, exciplex, and locally excited fluorophore is revealed by spectrally resolved MFE measurements for the long-chain systems (n = 10, 16).

Adaptive responses of sterically confined intramolecular chalcogen bonds

The existence of intramolecular chalcogen bonds (IChBs) in 2,6-disubstituted arylchalcogen derivatives is determined by the substituents and the sigma hole donor behavior of the chalcogen atom in the molecule.

The responsive behavior of an entity towards its immediate surrounding is referred to as an adaptive response. The adaptive responses of a noncovalent interaction at the molecular scale are reflected from its structural and functional roles. Intramolecular chalcogen bonding (IChB), an attractive interaction between a heavy chalcogen E (E = Se or Te) centered sigma hole and an ortho-heteroatom Lewis base donor D (D = O or N), plays an adaptive role in defining the structure and reactivity of arylchalcogen compounds. In this perspective, we describe the adaptive roles of a chalcogen centered Lewis acid sigma hole and a proximal Lewis base (O or N) in accommodating built-in steric stress in 2,6-disubstituted arylchalcogen compounds. From our perspective, the IChB components (a sigma hole and the proximal Lewis base) act in synergism to accommodate the overwhelming steric force. The adaptive responses of the IChB components are inferred from the observed molecular structures and reactivity. These include (a) adaptation of a conformation without IChBs, (b) adaptation of a conformation with weak IChBs, (c) twisting the skeletal aryl ring while maintaining IChBs, (d) ionization of the E–X bond (e.g., X = Br) to relieve stress and (e) intramolecular cyclization to relieve steric stress. A comprehensive approach, involving X-ray data analysis, density functional theory (DFT) calculations, reaction pattern analysis and principal component analysis (PCA), has been employed to rationalize the adaptive behaviors of IChBs in arylchalcogen compounds. We believe that the perception of ChB as an adaptive/stimulus responsive interaction would profit the futuristic approaches that would utilise ChB as self-assembly and molecular recognition tools.

Quantitative Theoretical Predictions and Qualitative Bonding Analysis of the Divinylborinium System and Its Al, Ga, In, and Tl Congeners

A substituted divinylborinium cation was synthesized recently and characterized crystallographically as a gauche structure with a 153° C1-C2-C3-C4 dihedral angle. A full theoretical geometrical optimization of the bis(2-mesityl-1,2-diphenylvinyl)-borane cation shows excellent agreement with the crystal structure. However, for the parent unsubstituted divinylborinium cation, we predict a nearly 90° C1-C2-C3-C4 dihedral angle using the CCSD(T)/cc-pVTZ coupled cluster method. The cis and trans planar geometries (0° and 180° for the C1-C2-C3-C4 dihedral angle) proved to be transition states with energy barriers of 2.8 and 2.3 kcal/mol, respectively, with respect to unimolecular conversion to the gauche equilibrium. The structures of the heavier boron group cations (Al, Ga, In, and Tl) have also been investigated here, finding even lower energy barriers (0.3-0.7 kcal/mol). After the ZPVE corrections, the barriers are further decreased. The torsional angles for the unknown Al, Ga, In, and Tl dimesityl substituted compounds should be somewhat less than 153°. Many of these findings may be understood in terms of qualitative electronic structure theory. The torsional folding of borane complex, including cationic divinylborinium and elementary vinylborane (C₂H₃BH₂) or chlorovinylborane (C₂H₃BHCl) precursors, are investigated with natural bond orbital (NBO) analysis to unveil the electronic origins of the torsional properties. The NBO-based descriptors are employed to systematically deconstruct complex torsional dependence into a balanced portrayal of hyperconjugative and steric effects.