Measures of pyramidalization

Tuning the steric hindrance of alkylamines: a predictive model of steric editing of planar amines

Amines are one of the most prevalent functional groups in chemistry. Perhaps even more importantly, amines represent one of the most ubiquitous moieties within the realm of bioactive natural products and life-saving pharmaceuticals. The archetypal geometrical property of amines is their sp3 hybridization with the lone pair of nitrogen occupying the apex of the pyramid. Herein, we present a blueprint for quantifying the properties of extremely sterically hindered alkylamines. These amines reach planarity around the nitrogen atom due to the excessive steric hindrance, which results in a conformational re-modeling of the amine moiety. Crucially, the steric properties of amines are characterized by the %V Bur index, which we show is a general predictive parameter for evaluating the properties of sterically hindered amines. Computational studies on the acidic nature and the reactivity of organometallic Au and Pd complexes are outlined. Density functional theory calculations permit for predictive catalysis, ordering the mapping of extremely hindered tertiary amines by employing artificial intelligence via machine learning. Overall, the study outlines the correlation between the unusual geometry and the key thermodynamic and kinetic properties of extremely hindered alkylamines. The steric hindrance, as quantified by %V Bur, is the crucial factor influencing the observed trends and the space required to accommodate sterically hindered tertiary amines.

Substrate Plasticity Enables Group-Selective Transmetalation: Catalytic Stereospecific Cross-Couplings of Tertiary Boronic Esters

Activation of enantiomerically enriched tertiary alkylboronic esters with adamantyllithium generated in situ enables stereoretentive boron-to-copper transmetalation. The resulting alkylcopper species can undergo cross-coupling reactions with an array of electrophiles to furnish synthetically useful compounds bearing quaternary stereocenters. DFT calculations of the transmetalation process provide insights for reactivity and selectivity.

Schiff Bases and Stereocontrolled Formation of Fused 1,3-Oxazolidines from 1-Amino-2-Indanol: A Systematic Study on Structure and Mechanism

This paper thoroughly explores the formation of Schiff bases derived from salicylaldehydes and a conformationally restricted amino alcohol (1-amino-2-indanol), as well as the generation of 1,3-oxazolidines, a key heterocyclic core present in numerous bioactive compounds. We provide enough evidences, both experimental-including crystallographic analyses and DFT-based calculations on imine/enamine tautomerism in the solid state and solution. In the course of imine formation, a pentacyclic oxazolidine-oxazine structure could be isolated with complete stereocontrol, whose configuration has been determined by merging theory and experiment. Mechanistic studies reveal that, although oxazolidines can be obtained under kinetic conditions, the prevalence of imines obeys to thermodynamic control as they are the most stable structures. The stereochemical outcome of imine cyclization under acylating conditions leads to formation of 2,4-trans-oxazolidines.

Unified Access to Pyrimidines and Quinazolines Enabled by N-N Cleaving Carbon Atom Insertion

Given the ubiquity of heterocycles in biologically active molecules, transformations with the capacity to modify such molecular skeletons with modularity remain highly desirable. Ring expansions that enable interconversion of privileged heterocyclic motifs are especially interesting in this regard. As such, the known mechanisms for ring expansion and contraction determine the classes of heterocycle amenable to skeletal editing. Herein, we report a reaction that selectively cleaves the N–N bond of pyrazole and indazole cores to afford pyrimidines and quinazolines, respectively. This chlorodiazirine-mediated reaction provides a unified route to a related pair of heterocycles that are otherwise typically prepared by divergent approaches. Mechanistic experiments and DFT calculations support a pathway involving pyrazolium ylide fragmentation followed by cyclization of the ring-opened diazahexatriene intermediate to yield the new diazine core. Beyond enabling access to valuable heteroarenes from easily prepared starting materials, we demonstrate the synthetic utility of skeletal editing in the synthesis of a Rosuvastatin analog as well as in an aryl vector-adjusting direct scaffold hop.

Steric and Electronic Origins of Fluorescence in GFP and GFP-like Proteins

Fluorescent proteins have become routine tools for biological imaging. However, their nanosecond lifetimes on the excited state present computational hurdles to a full understanding of these photoactive proteins. In this work, we simulate approximately 0.5 nanoseconds of ab initio molecular dynamics to elucidate steric and electronic features responsible for fluorescent protein behavior. Using green fluorescent protein (GFP) and Dronpa2─widely used fluorescent proteins with contrasting functionality─as case studies, we leverage previous findings in the gas phase and solution to explore the deactivation mechanisms available to these proteins. Starting with ground-state analyses, we identify steric (the distribution of empty pockets near the chromophore) and electronic (electric fields exerted on chromophore moieties) factors that offer potential avenues for rational design. Picosecond timescale simulations on the excited state reveal that the chromophore can access twisted structures in Dronpa2, while the chromophore is largely confined to planarity in GFP. We couple ab initio multiple spawning (AIMS) and enhanced sampling simulations to discover and characterize conical intersection seams that facilitate internal conversion, which is a rare event in both systems. Our AIMS simulations correctly capture the relative fluorescence profiles of GFP and Dronpa2 within the first few picoseconds, and we attribute the diminished fluorescence intensity of Dronpa2, relative to GFP, to flexible chromophore intermediates on the excited state. Furthermore, we predict that twisted chromophore intermediates produce red-shifted intensities in the Dronpa2 fluorescence spectrum. If confirmed experimentally, this spectroscopic signature would provide valuable insights when screening and developing novel fluorescent proteins.

Resolving the ultrafast dynamics of the anionic green fluorescent protein chromophore in water

The chromophore of the green fluorescent protein (GFP) is critical for probing environmental influences on fluorescent protein behavior. Using the aqueous system as a bridge between the unconfined vacuum system and a constricting protein scaffold, we investigate the steric and electronic effects of the environment on the photodynamical behavior of the chromophore. Specifically, we apply ab initio multiple spawning to simulate five picoseconds of nonadiabatic dynamics after photoexcitation, resolving the excited-state pathways responsible for internal conversion in the aqueous chromophore. We identify an ultrafast pathway that proceeds through a short-lived (sub-picosecond) imidazolinone-twisted (I-twisted) species and a slower (several picoseconds) channel that proceeds through a long-lived phenolate-twisted (P-twisted) intermediate. The molecule navigates the non-equilibrium energy landscape via an aborted hula-twist-like motion toward the one-bond-flip dominated conical intersection seams, as opposed to following the pure one-bond-flip paths proposed by the excited-state equilibrium picture. We interpret our simulations in the context of time-resolved fluorescence experiments, which use short- and long-time components to describe the fluorescence decay of the aqueous GFP chromophore. Our results suggest that the longer time component is caused by an energetically uphill approach to the P-twisted intersection seam rather than an excited-state barrier to reach the twisted intramolecular charge-transfer species. Irrespective of the location of the nonadiabatic population events, the twisted intersection seams are inefficient at facilitating isomerization in aqueous solution. The disordered and homogeneous nature of the aqueous solvent environment facilitates non-selective stabilization with respect to I- and P-twisted species, offering an important foundation for understanding the consequences of selective stabilization in heterogeneous and rigid protein environments.

Transition-State-like Planar Structures for Amine Inversion with Ultralong C-C Bonds in Diamino-o-carborane and Diamino-o-dodecahedron

Umbrella-like inversion of pyramidalized amines proceed through a planar transition state (TS). Stabilization of the TS through N(lone-pair) → σ*(C-C) "negative hyperconjugation" in diamino-o-carborane (1) causes rapid inversion in the amine, which results in the observation of a planarized -NH₂ from the X-ray crystal structure. This proceeds through quantum mechanical tunneling across the small and narrow barrier (low pyramidalization). Tuning this secondary orbital (donor-acceptor) interaction for various derivatives of 1 and diamino-o-dodecahedron (2) provides a rational approach toward increasing d_C-C to as large as 2.001, 2.011, and 1.807 Å for 1b (amino oxide-o-carborane), 1i (di-N,N-dimethylamino-o-carborane), and 2g (di-N,N-diisopropylamino-o-dodecahedron), respectively.

Stereochemistry of bistricyclic aromatic enes and related polycyclic systems

Bistricyclic aromatic enes (BAEs) and related polycyclic systems are a class of molecular materials that display a rich variety of conformations, dynamic stereochemistry and switchable chirality, color, and spectroscopic properties. This is due to the a subtle interplay of the inherent preference for planarity of aromatic systems and the competing necessity of non-planarity due to intramolecular overcrowding in the fjord regions built into the general molecular structure of BAEs. The conformational, dynamic, and spectroscopic properties may be designed and fine-tuned, e.g., by variation of the bridging groups X and Y, the overcrowding in the fjord regions, extensions of the aromatic system, or other modifications of the general BAE structure, based on the fundamental understanding of the structure-property relationships (SPR). The present review provides an analysis of the conformational spaces and the dynamic stereochemistry of overcrowded bistricyclic aromatic enes applying fundamental symmetry considerations. The symmetry analysis presented here allows deeper insight into the conformations, chirality, and the mechanisms of the dynamic stereochemistry, and will be instrumental in future computational studies.

On the origin of the solid-state thermochromism and thermal fatigue of polycyclic overcrowded enes

Aimed at unraveling the relative contribution of the folding, twisting and bending in the mechanism of the solid-state thermochromism of overcrowded polycyclic aromatic enes (PAEs), the structures of two typical heteromeric and homomeric representatives, 2-(thioxanthen-9-ylidene)indane-1,3-dione (1) and 9,9'-bi-9(10H)-anthracenylidene-10,10'-dione (bianthrone, 2), were studied by temperature-resolved single crystal X-ray diffraction (120-530 K) and solid-state UV-visible spectroscopy. Aside from negligibly small unfolding of the tricyclic moiety of 1, this first direct diffraction study of the high-temperature structures of solid PAEs did not unravel any significant and detectable changes in the time- and space-averaged intramolecular structures, thus, showing that the PAE-type thermochromism is not due to phase transitions or to major and permanent molecular distortions of a large portion of the material that would be caused by folding, twisting and/or bending. Instead, the experimental observations and theoretical modeling indicated that the color change is probably due to a dynamic process, where the absorption spectrum changes as a result of enhanced thermal oscillations of the two halves of the molecules around the central bridge. In addition to the reversible coloration, we also observed irreversible processes of thermal fatigue that afford stable chemical products that absorb in the visible region. We showed that the stable products are conductive and they act electrocatalytically toward oxidation of several biomarkers.

Spectral-structural effects of the keto-enol-enolate and phenol-phenolate equilibria of oxyluciferin

The effects of environmental polarity on the enolization of the keto form and the deprotonation of the enol, and the role of the neutral and ionized 6'-OH group in the fluorescence of the firefly emitter, oxyluciferin, were assessed through a detailed study of the structure and absorption and fluorescence spectra of its 6'-dehydroxylated analogue. It was found that the deprotonated 6'-O(-) group is a necessary, albeit insufficient, factor in accounting for the observed yellow-green and red emissions of oxyluciferin. Its negative charge is essential for effective excited-state charge transfer, which lowers the emission energy and broadens the emission spectrum. Deprotonation of the 6'-OH group changes its effect on the emission energy from blue- to red-shifting. Furthermore, the combination of these opposite effects and resonance stabilization of the phenolate-keto form causes switching of the order of maximum emission wavelengths of the three species involved in the keto-enol-enolate equilibrium from enol << keto < enolate in absence of 6'-OH to keto < enol << enolate with 6'-OH, to enol < enolate < keto with 6'-O(-). If only the keto-enol-enolate equilibrium is considered, solvents of medium polarity are the most effective in decreasing the excited-state energy. Polar or very polar environments also stimulate shift of the ground-state equilibrium toward the enol form. Under such circumstances, the enol group can be partly or completely deprotonated in the ground state or from the excited state: a polar environment facilitates the ionization, while a less polar environment requires the presence of a stronger base. In the absence of bases, the ground-state keto form exists only in solvents of very weak to medium polarity, but with stronger bases, it can also exist in a nonpolar or very weakly polar environment, usually together with the enolate anion. The phenol-enolate form of oxyluciferin, a species that could not be experimentally detected prior to this study, was identified as a yellow-emitting species.

Fulvalenes, Fulvenes, and Related Molecules: An ab Initio Study

Ab initio calculations using conventional (HF/6-31G and MP2/6-31G) and density functional theory (B-LYP/6-31G) methods have been used to determine the structures of the [n]fulvene and [n,m]fulvalene (n, m = 3, 5, 7) series of molecules, with particular emphasis on heptafulvalene (n = m = 7: 12). Calculations have also been performed on the parent cycloalkenes: cyclopropene, cyclopentadiene, and cycloheptatriene (1-3, respectively). All the fulvenes (n = 3, 5, 7: 4-6, respectively) and the smaller fulvalenes (n = 3, m= 3, 5, 7: 7-9, respectively, and n = m = 5: 10) are found to be planar. Pentaheptafulvalene (n = 5, m = 7: 11) adopts a very slightly nonplanar C(s)() arrangement of the five- and seven-membered rings. Heptafulvalene (12) is predicted to have an anti-folded C(2)(h)() structure, in accord with the X-ray crystal structure. We propose that the underlying reason for 11 and 12 adopting nonplanar conformations is the proximity of the H(2) and H(2)(') hydrogen atoms which promotes a distortion of the rings away from planarity at the central fulvalenic C=C double bond. In the process, pi-overlap is lost but this is partially regained by pyramidalization of the carbon centers in the seven-membered ring(s). The degree of folding is substantially more pronounced in 12 than in 11. Our calculated dipole moments, pi-electron distributions, bond alternation parameters, and energy comparisons indicate that the unknown smallest fulvalene, triafulvalene (7), is highly destabilized with localized bonding while triapentafulvalene (8), which is also unknown, is predicted to be stabilized and quite delocalized, consistent with Hückel 4n + 2 considerations.