An n→π* Interaction in the Bound Substrate of Aspartic Proteases Replicates the Oxyanion Hole

N···C═O n → π* Interaction: Gas-Phase Electronic and Vibrational Spectroscopy Combined with Quantum Chemistry Calculations

Herein, we have used gas-phase electronic and vibrational spectroscopic techniques for the first time to study the N···C═O n → π* interaction in ethyl 2-(2-(dimethylamino) phenyl) acetate (NMe2-Ph-EA). We have measured the electronic spectra of NMe2-Ph-EA in the mass channels of its two distinct fragments of m/z = 15 and 192 using a resonant two-photon ionization technique as there was extensive photofragmentation of NMe2-Ph-EA. Identical electronic spectra obtained in the mass channels of both fragments confirm the dissociation of NMe2-Ph-EA in the ionic state, and hence, the electronic spectrum of the fragment represents that of NMe2-Ph-EA only. UV-UV hole-burning spectroscopy proved the presence of a single conformer of NMe2-Ph-EA in the experiment. Detailed quantum chemistry calculations reveal the existence of a N···C═O n → π* interaction in all six low-energy conformers of NMe2-Ph-EA. A comparison of the IR spectrum of NMe2-Ph-EA acquired from the gas-phase experiment with those obtained from theoretical calculations indicates that the experimentally observed conformer has a N···C═O n → π* interaction. The present finding might be further valuable in drug design and their recognition based on the N···C═O n → π* interaction.

Extracellular proteolysis in cancer: Proteases, substrates, and mechanisms in tumor progression and metastasis

A vast ensemble of extracellular proteins influences the development and progression of cancer, shaped and reshaped by a complex network of extracellular proteases. These proteases, belonging to the distinct classes of metalloproteases, serine proteases, cysteine proteases, and aspartic proteases, play a critical role in cancer. They often become dysregulated in cancer, with increases in pathological protease activity frequently driven by the loss of normal latency controls, diminished regulation by endogenous protease inhibitors, and changes in localization. Dysregulated proteases accelerate tumor progression and metastasis by degrading protein barriers within the extracellular matrix (ECM), stimulating tumor growth, reactivating dormant tumor cells, facilitating tumor cell escape from immune surveillance, and shifting stromal cells toward cancer-promoting behaviors through the precise proteolysis of specific substrates to alter their functions. These crucial substrates include ECM proteins and proteoglycans, soluble proteins secreted by tumor and stromal cells, and extracellular domains of cell surface proteins, including membrane receptors and adhesion proteins. The complexity of the extracellular protease web presents a significant challenge to untangle. Nevertheless, technological strides in proteomics, chemical biology, and the development of new probes and reagents are enabling progress and advancing our understanding of the pivotal importance of extracellular proteolysis in cancer.

Catalytic Effects of Active Site Conformational Change in the Allosteric Activation of Imidazole Glycerol Phosphate Synthase

Imidazole glycerol phosphate synthase (IGPS) is a class-I glutamine amidotransferase (GAT) that hydrolyzes glutamine. Ammonia is produced and transferred to a second active site, where it reacts with N1-(5'-phosphoribosyl)-formimino-5-aminoimidazole-4-carboxamide ribonucleotide (PrFAR) to form precursors to purine and histidine biosynthesis. Binding of PrFAR over 25 Å away from the active site increases glutaminase efficiency by ∼4500-fold, primarily altering the glutamine turnover number. IGPS has been the focus of many studies on allosteric communication; however, atomic details for how the glutamine hydrolysis rate increases in the presence of PrFAR are lacking. We present a density functional theory study on 237-atom active site cluster models of IGPS based on crystallized structures representing the inactive and allosterically active conformations and investigate the multistep reaction leading to thioester formation and ammonia production. The proposed mechanism is supported by similar, well-studied enzyme mechanisms, and the corresponding energy profile is consistent with steady-state kinetic studies of PrFAR + IGPS. Additional active site models are constructed to examine the relationship between active site structural change and transition-state stabilization via energy decomposition schemes. The results reveal that the inactive IGPS conformation does not provide an adequately formed oxyanion hole structure and that repositioning of the oxyanion strand relative to the substrate is vital for a catalysis-competent oxyanion hole, with or without the hVal51 dihedral flip. These findings are valuable for future endeavors in modeling the IGPS allosteric mechanism by providing insight into the atomistic changes required for rate enhancement that can inform suitable reaction coordinates for subsequent investigations.

Carbon-Bonding Metal Catalysis (CBMC): A Supramolecular Complex Directs Structural-Isomer Selection in Gold-Catalyzed Reactions

Carbon is a primary element to constitute organic molecules, while metal catalysis is a basic tool in organic synthesis. The establishment of a link between the ubiquitous carbon bonding and metal catalysis is thus a fundamentally important problem. However, there is yet no experimental example to introduce the role of carbon bonding in a metal catalysis process. Herein, we merged the topics of carbon bonding and metal catalysis together and demonstrated that a supramolecular carbon-bonding metal complex can not only give rise to catalytic activity but, more remarkably, direct structural-isomer selection events in gold-catalyzed reactions. The experimental results unveil the fact that the imposing of weak carbon-bonding interactions on a gold complex can alter the carbene as well as the Lewis acid property of these catalysts. These results illustrate a non-negligible role of weak carbon-bonding interactions in the modulation of metal catalysis. As such, carbon-bonding metal catalysis is suggested to be used as a routine tool not only in the development of reactions but more frequently in analyzing reaction processes in metal catalysis.

Modulation of n → π* Interaction in the Complexes of p-Substituted Pyridines with Aldehydes: A Theoretical Study

n → π* interaction is analogous to the hydrogen bond in terms of the delocalization of the electron density between the two orbitals. Studies on the intermolecular complexes stabilized by the n → π* interaction are scarce in the literature. Herein, we have studied intermolecular N···C═O n → π* interactions in the complexes of p-substituted pyridines (p-R-Py) with formaldehyde (HCHO), formyl chloride (HCOCl), and acetaldehyde (CH₃CHO) using quantum chemistry calculations. We have shown that the strength of the n → π* interaction can be modulated by varying the electronic substituents at the donor and acceptor sites in the complexes. Variation of the substituents at the para position of the pyridine ring from the electron-withdrawing groups (EWGs) to the electron-donating groups (EDGs) results in a systematic increase in the strength of the n → π* interaction. The strength of this interaction is also modulated by tuning the electron density toward the carbonyl bond by substituting the hydrogen atom of HCHO with the methyl and chloro groups. The modulation of this interaction due to the electronic substitutions at the n → π* donor and acceptor sites in the complexes is monitored by probing the relevant geometrical parameters, binding energies, C═O frequency redshift, NBO energies, and electron density for this interaction derived from QTAIM and NCI index analyses. Energy decomposition analysis reveals that the electrostatic interaction dominates the binding energies of these complexes, while the charge transfer interaction, which is representative of the n → π* interaction, also has a significant contribution to these.

Double n→π* Interactions with One Electron Donor: Structural and Mechanistic Insights

Double n→π* interactions between one common electron donor of the carbonyl oxygen and two individual acceptor aldehyde/imine units are presented. The structural and mechanistic insights were revealed through a collection of experimental and computational evidence. The orientation and further energetic dependence of orbital interactions were facilely regulated by the size of cyclic urea scaffolds, the bulkiness of aldehydes/imines, and the flexibility of imine macrocycles.

Understanding the n → π* non-covalent interaction using different experimental and theoretical approaches

Herein, a perspective on the recent understanding of weak n → π* interaction obtained using different experimental and theoretical approaches is presented. This interaction is purely an orbital interaction that involves the delocalization of the lone pair electrons (n) on nitrogen, oxygen, and sulfur to the π* orbitals of CO, CN, and aromatic rings. The n → π* interaction has been found to profoundly influence the stabilization of peptides, proteins, drugs, and various small molecules. Although the functional properties of this non-covalent interaction are still quite underestimated, there are recent demonstrations of applying this interaction to the regulation of synthetic chemistry, catalysis, and molecular recognition. However, the identification and quantification of the n → π* interaction remain a demanding task as this interaction is quite weak and based on the electron delocalization between the two orbitals, while hyperconjugation interactions between neighboring atoms and the group involved in the n → π* interaction are simultaneously present. This review provides a comprehensive picture of understanding the n → π* interaction using different experimental approaches such as the X-ray diffraction technique, and electronic, NMR, microwave, and IR spectroscopy, in addition to quantum chemistry calculations. A detailed understanding of the n → π* interaction can help in modulating the strength of this interaction, which will be further helpful in designing efficient drugs, synthetic peptides, peptidomimetics, etc.

nN → π*Ar interactions stabilize the E-ac isomers of arylhydrazides and facilitate their SNAr autocyclizations

We describe a novel mechanism of stabilization of the E-ac isomer of an arylhydrazide via n_N → π*_Ar interactions. We further show that when a leaving group (F) is present at the ortho-position of the carbonyl group of such an arylhydrazide, the n_N → π*_Ar interaction facilitates an S_NAr autocyclization reaction to produce indazolone, an important heterocycle with biological activity. Faster autocyclization of arylhydrazide is observed when an electron withdrawing group is present in the aryl ring, which is a characteristic of S_NAr reactions.

Mapping of N-C Bond Formation from a Series of Crystalline Peri-Substituted Naphthalenes by Charge Density and Solid-State NMR Methodologies

A combination of charge density studies and solid state nuclear magnetic resonance (NMR) 1 JNC coupling measurements supported by periodic density functional theory (DFT) calculations is used to characterise the transition from an n-π* interaction to bond formation between a nucleophilic nitrogen atom and an electrophilic sp2 carbon atom in a series of crystalline peri-substituted naphthalenes. As the N⋅⋅⋅C distance reduces there is a sharp decrease in the Laplacian derived from increasing charge density between the two groups at ca. N⋅⋅⋅C = 1.8 Å, with the periodic DFT calculations predicting, and heteronuclear spin-echo NMR measurements confirming, the 1 JNC couplings of ≈3-6 Hz for long C-N bonds (1.60-1.65 Å), and 1 JNC couplings of <1 Hz for N⋅⋅⋅C >2.1 Å.

Catalysis with Supramolecular Carbon-Bonding Interactions

Herein, we describe a new catalysis platform, supramolecular carbon-bonding catalysis, which exploits the highly directional weak interactions between carbon centers of catalysts and electron donors to drive chemical reactions. To demonstrate this catalysis approach, we discovered a class of cyclopropane derivatives incorporated with carbonyl, ester and cyano groups as catalysts which showed general catalysis capability in different types of benchmark reactions. Among these typical examples, a challenging tail-to-head terpene cyclization can be achieved by supramolecular carbon-bonding catalysis. The co-crystal structures of catalyst and electron donors, comparison experiments, and titrations support a catalysis mode of carbon-bonding activation of Lewis basic reactants.

Stereoelectronic power of oxygen in control of chemical reactivity: the anomeric effect is not alone

Although carbon is the central element of organic chemistry, oxygen is the central element of stereoelectronic control in organic chemistry. Generally, a molecule with a C-O bond has both a strong donor (a lone pair) and a strong acceptor (e.g., a σ*_C-O orbital), a combination that provides opportunities to influence chemical transformations at both ends of the electron demand spectrum. Oxygen is a stereoelectronic chameleon that adapts to the varying situations in radical, cationic, anionic, and metal-mediated transformations. Arguably, the most historically important stereoelectronic effect is the anomeric effect (AE), i.e., the axial preference of acceptor groups at the anomeric position of sugars. Although AE is generally attributed to hyperconjugative interactions of σ-acceptors with a lone pair at oxygen (negative hyperconjugation), recent literature reports suggested alternative explanations. In this context, it is timely to evaluate the fundamental connections between the AE and a broad variety of O-functional groups. Such connections illustrate the general role of hyperconjugation with oxygen lone pairs in reactivity. Lessons from the AE can be used as the conceptual framework for organizing disjointed observations into a logical body of knowledge. In contrast, neglect of hyperconjugation can be deeply misleading as it removes the stereoelectronic cornerstone on which, as we show in this review, the chemistry of organic oxygen functionalities is largely based. As negative hyperconjugation releases the "underutilized" stereoelectronic power of unshared electrons (the lone pairs) for the stabilization of a developing positive charge, the role of orbital interactions increases when the electronic demand is high and molecules distort from their equilibrium geometries. From this perspective, hyperconjugative anomeric interactions play a unique role in guiding reaction design. In this manuscript, we discuss the reactivity of organic O-functionalities, outline variations in the possible hyperconjugative patterns, and showcase the vast implications of AE for the structure and reactivity. On our journey through a variety of O-containing organic functional groups, from textbook to exotic, we will illustrate how this knowledge can predict chemical reactivity and unlock new useful synthetic transformations.

Hydrogen Bonds and n → π* Interactions in the Acetylation of Propranolol Catalyzed by Candida antarctica Lipase B: A QTAIM Study

Enzyme-substrate interactions play a crucial role in enzymatic catalysis. Quantum theory of atoms in molecules (QTAIM) calculations are extremely useful in computational studies of these interactions because they provide very detailed information about the strengths and types of molecular interactions. QTAIM also provides information about the intramolecular changes that occur in the catalytic reaction. Here, we analyze the enzyme-substrate interactions and the topological properties of the electron density in the enantioselective step of the acylation of (R,S)-propranolol, an aminoalcohol with therapeutic applications, catalyzed by Candida antarctica lipase B. Eight reaction paths (four for each enantiomer) are investigated and the energies, atomic charges, hydrogen bonds, and n → π* interactions of propranolol, the catalytic triad (composed of D187, H224, and S105), and the oxyanion hole are analyzed. It is found that D187 acts as an electron density reservoir for H224, and H224 acts as an electron density reservoir for the active site of the protein. It releases electron density when the tetrahedral intermediate is formed from the Michaelis complex and receives it when the enzyme-product complex is formed. Hydrogen bonds can be grouped into noncovalent and covalent hydrogen bonds. The latter are stronger and more important for the reaction than the former. We also found weak n → π* interactions, which are characterized by QTAIM and the natural bond orbital (NBO) analysis.

Structural basis for the hyperthermostability of an archaeal enzyme induced by succinimide formation

Stability of proteins from hyperthermophiles (organisms existing under boiling water conditions) enabled by a reduction of conformational flexibility is realized through various mechanisms. A succinimide (SNN) arising from the post-translational cyclization of the side chains of aspartyl/asparaginyl residues with the backbone amide -NH of the succeeding residue would restrain the torsion angle Ψ and can serve as a new route for hyperthermostability. However, such a succinimide is typically prone to hydrolysis, transforming to either an aspartyl or β-isoaspartyl residue. Here, we present the crystal structure of Methanocaldococcus jannaschii glutamine amidotransferase and, using enhanced sampling molecular dynamics simulations, address the mechanism of its increased thermostability, up to 100°C, imparted by an unexpectedly stable succinimidyl residue at position 109. The stability of SNN109 to hydrolysis is seen to arise from its electrostatic shielding by the side-chain carboxylate group of its succeeding residue Asp110, as well as through n → π^∗ interactions between SNN109 and its preceding residue Glu108, both of which prevent water access to SNN. The stable succinimidyl residue induces the formation of an α-turn structure involving 13-atom hydrogen bonding, which locks the local conformation, reducing protein flexibility. The destabilization of the protein upon replacement of SNN with a Φ-restricted prolyl residue highlights the specificity of the succinimidyl residue in imparting hyperthermostability to the enzyme. The conservation of the succinimide-forming tripeptide sequence (E(N/D)(E/D)) in several archaeal GATases strongly suggests an adaptation of this otherwise detrimental post-translational modification as a harbinger of thermostability.

Mechanisms of Proteolytic Enzymes and Their Inhibition in QM/MM Studies

Experimental evidence for enzymatic mechanisms is often scarce, and in many cases inadvertently biased by the employed methods. Thus, apparently contradictory model mechanisms can result in decade long discussions about the correct interpretation of data and the true theory behind it. However, often such opposing views turn out to be special cases of a more comprehensive and superior concept. Molecular dynamics (MD) and the more advanced molecular mechanical and quantum mechanical approach (QM/MM) provide a relatively consistent framework to treat enzymatic mechanisms, in particular, the activity of proteolytic enzymes. In line with this, computational chemistry based on experimental structures came up with studies on all major protease classes in recent years; examples of aspartic, metallo-, cysteine, serine, and threonine protease mechanisms are well founded on corresponding standards. In addition, experimental evidence from enzyme kinetics, structural research, and various other methods supports the described calculated mechanisms. One step beyond is the application of this information to the design of new and powerful inhibitors of disease-related enzymes, such as the HIV protease. In this overview, a few examples demonstrate the high potential of the QM/MM approach for sophisticated pharmaceutical compound design and supporting functions in the analysis of biomolecular structures.

Spectroscopic evidence of n → π* interactions involving carbonyl groups

n → π* has emerged as an important noncovalent interaction that can affect the conformations of both small- and macromolecules including peptides and proteins. Carbonyl-carbonyl (COCO) n → π* interactions involving CO groups are well studied. Recent studies have shown that the COCO n → π* interactions are the most abundant secondary interactions in proteins with a frequency of 33 interactions per 100 residues and, among the various secondary interactions, n → π* interactions are expected to provide the highest enthalpic contributions to the conformational stability of globular proteins. However, n → π* interactions are relatively weak and provide an average stabilization of about 0.25 kcal mol-1 per interaction in proteins. The strongest n → π* interaction could be as strong as a moderate hydrogen bond. Therefore, it is challenging to detect and quantify these weak interactions, especially in solution in the presence of perturbation from other intermolecular interactions. Accordingly, spectroscopic investigations that can provide direct evidence of n → π* interaction are limited, and the majority of papers published in this area have relied on X-ray crystallography and/or theoretical calculations to establish the presence of this interaction. The aim of this perspective is to discuss the studies where a spectroscopic signature in support of n → π* interaction was observed. As the "n → π* interaction" is a relatively new terminology, there remains the possibility of there being earlier studies where spectroscopic evidence for n → π* interactions was obtained but it was not discussed in light of the n → π* terminology. We noticed several such studies and, as can be expected, these studies were often overlooked in the discussion of n → π* interactions in the recent literature. In this perspective, we have also discussed these studies and provided computational support for the presence of n → π* interaction.

Effects of n → π* Orbital Interactions on Molecular Rotors: The Control and Switching of Rotational Pathway and Speed

The role of n → π* orbital interactions in the rotational pathway and barrier of biaryl-based molecular rotors was elucidated through a combined experimental and computational study. The n → π* interaction in the transition state can lead to the acceleration of rotors. The competition between the n → π* interaction and hydrogen bonding further enabled the reversal of the pathway and greasing/braking the rotor in response to acid/base stimuli, thereby creating a switchable molecular rotor.

Visualizing Tetrahedral Oxyanion Bound in HIV-1 Protease Using Neutrons: Implications for the Catalytic Mechanism and Drug Design

HIV-1 protease is indispensable for virus propagation and an important therapeutic target for antiviral inhibitors to treat AIDS. As such inhibitors are transition-state mimics, a detailed understanding of the enzyme mechanism is crucial for the development of better anti-HIV drugs. Here, we used room-temperature joint X-ray/neutron crystallography to directly visualize hydrogen atoms and map hydrogen bonding interactions in a protease complex with peptidomimetic inhibitor KVS-1 containing a reactive nonhydrolyzable ketomethylene isostere, which, upon reacting with the catalytic water molecule, is converted into a tetrahedral intermediate state, KVS-1_TI. We unambiguously determined that the resulting tetrahedral intermediate is an oxyanion, rather than the gem-diol, and both catalytic aspartic acid residues are protonated. The oxyanion tetrahedral intermediate appears to be unstable, even though the negative charge on the oxyanion is delocalized through a strong n → π* hyperconjugative interaction into the nearby peptidic carbonyl group of the inhibitor. To better understand the influence of the ketomethylene isostere as a protease inhibitor, we have also examined the protease structure and binding affinity with keto-darunavir (keto-DRV), which similar to KVS-1 includes the ketomethylene isostere. We show that keto-DRV is a significantly less potent protease inhibitor than DRV. These findings shed light on the reaction mechanism of peptide hydrolysis catalyzed by HIV-1 protease and provide valuable insights into further improvements in the design of protease inhibitors.

n → π* interactions as a versatile tool for controlling dynamic imine chemistry in both organic and aqueous media

The imine bond holds a prominent place in supramolecular chemistry and materials science, and one issue is the stability of imines due to their electrophilic nature. Here we introduced ortho-carboxylate groups into a series of aromatic aldehydes/imines for dictating imine dynamic covalent chemistry (DCC) through n → π* interactions, one class of widespread and yet underused non-covalent interactions. The thermodynamically stabilizing role of carboxylate-aldehyde/imine n → π* interactions in acetonitrile was elucidated by the movement of the imine exchange equilibrium and further supported by crystal analysis. Computational studies provided mechanistic insights for n → π* interactions, the strength of which can surpass that of CH hydrogen bonding and is dependent on the orientation of interacting sites based on natural bond orbital analysis. Moreover, the substituent effect and the combination of recognition sites allowed additional means for modulation. Finally, to show the relevance of our findings ortho-carboxylate containing aldehydes were used to regulate imine formation/exchange in water, and modification of the N-terminus of amino acids and peptides was achieved in a neutral buffer. This work represents the latest example of weak interactions governing DCC and sets the stage for assembly and application studies.

Chiral Restructuring of Peptide Enantiomers on Gold Nanomaterials

The use of biomolecules has been invaluable at generating and controlling optical chirality in nanomaterials; however, the structure and properties of the chiral biotemplate are not well understood due to the complexity of peptide-nanoparticle interactions. In this study, we show that the complex interactions between d-peptides and gold nanomaterials led to a chiral restructuring of peptides as demonstrated by circular dichroism and proteolytic cleavage of d-peptides via gold-mediated inversion of peptide chirality. The gold nanoparticles synthesized using d-peptide produce a highly ordered atomic surface and restructured peptide bonds for enzyme cleavage. Differences in gold nanoparticle catalyzed reduction of 4-nitrophenol were observed on the basis of the chiral peptide used in nanoparticle synthesis. Notably, the proteolytic cleavage of d-peptides on gold provides an opportunity for designing nanoparticle based therapeutics to treat peptide venoms, access new chemistries, or modulate the catalytic activity of nanomaterials.

Interplay between n→π* Interactions and Dynamic Covalent Bonds: Quantification and Modulation by Solvent Effects

Orbital donor-acceptor interactions play critical roles throughout chemistry, and hence, their regulation and functionalization are of great significance. Herein we demonstrate for the first time the investigation of n→π* interactions through the strategy of dynamic covalent chemistry (DCC), and we further showcase its use in the stabilization of imine. The n→π* interaction between donor X and acceptor aldehyde/imine within 2-X-2'-formylbiphenyl derivatives was found to significantly influence the thermodynamics of imine exchange. The orbital interaction was then quantified through imine exchange, the equilibrium of which was successfully correlated with the difference in natural bond orbital stabilization energy of n→π* interactions of aldehyde and its imine. Moreover, the examination of solvent effects provided insights into the distinct feature of the modulation of n→π* interaction with aprotic and protic solvents. The n→π* interaction involving imine was enhanced in protic solvents due to hydrogen bonding with the solvent. This finding further enabled the stabilization of imine in purely aqueous solution. The strategies and results reported should find application in many fields, including molecular recognition, biological labeling, and asymmetric catalysis.