Conformational Isomers Research Articles

Detection and characterisation of oxocyclohexan[b]indoles by combined application of vibrational spectroscopy and mass spectrometry

The vibrational and mass spectra of a representative set of nine oxocyclohexan[b]indoles (tricyclic indoles with a 6,5,6 ring pattern) with a carbonyl group in each of the four positions of the third non-aromatic ring and up to two methyl substituent(s) attached to the carbon atoms in the other positions of this ring are reported and discussed. Particular attention is focused on the use of infrared spectroscopy to determine whether these compounds may best be described as ketoindoles or hydroxyindolenines. Most of these spectra indicate that the tricyclic heterocycles exist preferentially at ketoindoles, but the solid state infrared spectra of oxocyclohexan[b]indoles with the oxygen function in the 4-position are highly unusual, giving the initial impression that these compounds are hydroxyindolenines. Computational modelling supports the interpretation that the 4-ketoindole tautomer has a lower energy than either of its most stable isomeric indolenines conformers. Mass spectrometry is shown to provide valuable confirmatory evidence to differentiate the isomeric ionised oxocyclohexan[b]indoles, which dissociate via distinctive and informative fragmentation routes, in which the stability of intermediate distonic ions appears to be profoundly influenced by participation of the lone pair of electrons on the nitrogen atom. Many of these fragmentations are better described by stepwise mechanisms, rather than as concerted cycloreversions.

Molecular Conformational Isomerization: An Efficient Way to Design Novel Emitters with Dual-Thermally Activated Delayed Fluorescence Characteristics and Their Optoelectronic and Bioimaging Applications

Molecular Conformational Isomerization: An Efficient Way to Design Novel Emitters with Dual-Thermally Activated Delayed Fluorescence Characteristics and Their Optoelectronic and Bioimaging Applications

Conformer-Specific Desorption in Propanol Ices Probed by Chirped-Pulse Millimeter-Wave Rotational Spectroscopy.

We present a new technique for the detection of molecules desorbed from an ice surface using broad-band millimeter-wave rotational spectroscopy. The approach permits interrogation of molecules that have undergone the slow warmup process of temperature-programmed desorption (TPD), analogous to the warmup phase of icy grains in the interstellar medium as they approach the central protostar. The detection is conformer- and isomer-specific and quantitative, as afforded by chirped-pulse rotational spectroscopy. To achieve this, we combine ice TPD with buffer gas cooling, followed by detection in the millimeter-wave regime. In this report we examine the TPD profiles of n- and i-propanol, the former of which may be in five different conformational isomeric forms, and which display distinct desorption profiles. The limited conformational isomerization and temperature-dependent relative yields of n-propanol conformers observed show that the desorption is highly conformer-specific.

Isomeric separation of native N-glycans using nano zwitterionic- hydrophilic interaction liquid chromatography column

Changes in the expression of glycan isomers have been implicated in the development and progression of several diseases. However, the analysis of structurally diverse isomeric N-glycans by LC−MS/MS is still a major analytical challenge, particularly due to their large number of possible isomeric conformations. Common approaches derivatized the N-glycans to increase their hydrophobicity and to gain better detection in the MS system. Unfortunately, glycan derivatization is time-consuming and, in many cases, adds complexity because of the multiple reaction and cleaning steps, incomplete chemical labeling, possible degradation, and unwanted side reactions. Thus, analysis of native glycans, especially for samples with low abundance by LC−MS/MS, is desirable. Normal phase chromatography, which employs HILIC stationary phase, has been commonly employed for the identification and separation of labeled glycans. In this study, we focused on achieving efficient isomeric separation of native N-glycans using a nano ZIC-HILIC column commonly employed to separate labeled glycans and glycopeptides. Underivatized sialylated and oligomannose N-glycans derived from bovine fetuin and Ribonuclease B were initially utilized to optimize chromatographic conditions, including column temperature, pH of mobile phases, and gradient elution time. The optimized condition was then applied for the isomeric separation of native N-glycans derived from alpha-1 acid glycoprotein, as well as from biological samples. Finally, we confirmed the stability and reproducibility of the ZIC-HILIC column by performing run-to-run comparisons of the full width at half height (FWHM) and retention time on different N-glycans. The variability in FWHM was less than 0.5 min, while that of retention time was less than 1.0 min with %RSD less than 1.0%.

Synthesis and Conformational Analysis of Fullerene Torsion Balances for Assessing the Contribution of Dispersion and Anionic Character in Non-Covalent Arene-Fullerene Interactions.

We employ a molecular torsion balance displaying bifurcated conformational isomerism to quantitatively evaluate the non-covalent interactions between the fullerene surface and substituted arene moieties containing elements with high atomic numbers, as well as the thermodynamic processes involved in the folding equilibrium using nuclear magnetic resonance spectroscopy. The interaction between fullerene and haloaryl groups was stronger in cases where the introduced halogen had a higher atomic number, indicating that dispersion forces play a significant role in the interaction between fullerenes and 4-haloaryl groups. The dispersion term also significantly contributed to the interaction between fullerene and the 4-mercaptophenyl group. Moreover, the addition of an appropriate base to the 4-mercaptophenyl-appended torsion balance formed the corresponding thiophenolate anion, resulting in a large negative change in the folding free energy in CDCl3 . Detailed analysis suggested that the observed attractive anionic arene-fullerene interactions predominantly originated from solvation effects.

Solving the crystal structure of heterocyclic Poly(arylene benzimidazole) via model compound single crystal and theoretical calculations

Heterocyclic aramid containing benzimidazole units has demonstrated to be one of the strongest fibers. Due to positional isomerism of asymmetric benzimidazole and conformational isomerism of phenylamide, solving the crystal structure of poly(arylene benzimidazole) (PABI) aramid was a prominent challenge. Herein, we first reported the crystal structure of PABI aramid. First, the model compound: N-(4-(5-benzamido-1H-benzo[d] imidazole-2-yl) phenyl) benzamide (PBA) was cultured into single crystal: the molecules took a perfect ross-tenon-mortise interlocking conformation, in which the hydrogen bonding made a giant three-dimensional network. The PABI crystals with PBA crystal stacking feature were subsequently constructed and optimized through theoretical quantum calculation, disclosing a monoclinic unit cell with the parameters (a = 8.56 Å; b = 5.05 Å; and c = 36.78 Å; and β = 91.4°) and Pn space group. Their plausibility and validity were verified, since the simulated XRD and 2D-WAXD patterns reproduced the experimental XRD patterns. Our strategy of linking model compound PBA single crystals to obtain higher PABI crystals, paved the way to solving asymmetrical heterocyclic macromolecules crystals composed of easily isomerized chemical structures.

Isolated and solvated chiroptical behavior in conformationally flexible butanamines.

The nonresonant optical activity of two highly flexible aliphatic amines, (2R)-3-methyl-2-butanamine (R-MBA) and (2R)-(3,3)-dimethyl-2-butanamine (R-DMBA), has been probed under isolated and solvated conditions to examine the roles of conformational isomerism and to explore the influence of extrinsic perturbations. The optical rotatory dispersion (ORD) measured in six solvents presented uniformly negative rotatory powers over the 320-590 nm region, with the long-wavelength magnitude of chiroptical response growing nearly monotonically as the dielectric constant of the surroundings diminished. The intrinsic specific optical rotation, (in deg dm-1 [g/mL]-1 ), extracted for ambient vapor-phase samples of R-MBA [-11.031(98) and -2.29 (11)] and R-DMBA [-9.434 (72) and -1.350 (48)] at 355 and 633 nm were best reproduced by counterintuitive solvents of high polarity (yet low polarizability) like acetonitrile and methanol. Attempts to interpret observed spectral signatures quantitatively relied on the linear-response frameworks of density-functional theory (B3LYP, cam-B3LYP, and dispersion-corrected analogs) and coupled-cluster theory (CCSD), with variants of the polarizable continuum model (PCM) deployed to account for the effects of implicit solvation. Building on the identification of several low-lying equilibrium geometries (nine for R-MBA and three for R-DMBA), ensemble-averaged ORD profiles were calculated at T = 300K by means of the independent-conformer ansatz, which enabled response properties predicted for the optimized structure of each isomer to be combined through Boltzmann-weighted population fractions derived from corresponding relative internal-energy or free-energy values, the latter of which stemmed from composite CBS-APNO and G4 analyses. Although reasonable accord between theory and experiment was realized for the isolated (vapor-phase) species, the solution-phase results were less satisfactory and tended to degrade progressively as the solvent polarity increased. These trends were attributed to solvent-mediated changes in structural parameters and energy metrics for the transition states that separate and putatively isolate the equilibrium conformations supported by the ground electronic potential-energy surface, with the resulting displacement of barrier locations and/or decrease of barrier heights compromising the underlying premise of the independent-conformer ansatz.

MassCCS: A High-Performance Collision Cross-Section Software for Large Macromolecular Assemblies.

Ion mobility mass spectrometry (IM-MS) techniques have become highly valued as a tool for structural characterization of biomolecular systems since they yield accurate measurements of the rotationally averaged collision cross-section (CCS) against a buffer gas. Despite its enormous potential, IM-MS data interpretation is often challenging due to the conformational isomerism of metabolites, lipids, proteins, and other biomolecules in the gas phase. Therefore, reliable and fast CCS calculations are needed to help interpret IM-MS data. In this work, we present MassCCS, a parallelized open-source code for computing CCS of molecules ranging from small organic compounds to massive protein assemblies at the trajectory method level of description using atomic and molecular buffer gas particles. The performance of the code is comparable to other available software for small molecules and proteins but is significantly faster for larger macromolecular assemblies. We performed extensive tests regarding accuracy, performance, and scalability with system size and number of CPU cores. MassCCS has proven highly accurate and efficient, with execution times under a few minutes, even for large (84.87 MDa) virus capsid assemblies with very modest computational resources. MassCCS is freely available at https://github.com/cces-cepid/massccs.

Discrimination of GLUTs by Fructose Isomers Enables Simultaneous Screening of GLUT5 and GLUT2 Activity in Live Cells.

Facilitative carbohydrate transporters (GLUTs, SLC2 gene family) are transmembrane proteins transporting hexoses and other sugars based on cellular metabolic demands. While a direct link between GLUTs and metabolic disorders has framed them as important biological and medicinal targets, targeting disease-relevant GLUTs remains challenging. In this study, we aimed to identify substrate-GLUT interactions that would discriminate between major fructose transporters. We examined the uptake distribution for conformational and configurational isomers of fructose using the corresponding conformationally locked fluorescently labeled mimetics as probes for assessing GLUT preferences in real time. Through comparative analysis of the uptake of the probes in the yeast-based single GLUT expression systems and the multi-GLUT mammalian cell environment, we established the ability of fructose transporters to discriminate between fructose conformers and epimers. We demonstrated that recreating the conformational and configurational mixture of fructose with molecular probes allows for the specific probe distribution, with fructofuranose mimetic being taken up preferentially through GLUT5 and β-d-fructopyranose mimetic passing through GLUT2. The uptake of α-d-fructopyranose mimetic was found to be independent of GLUT5 or GLUT2. The results of this study provide a new approach to analyzing GLUT5 and GLUT2 activity in live cells, and the findings can be used as a proof-of-concept for multi-GLUT activity screening in live cells. The research also provides new knowledge on substrate-GLUT interactions and new tools for monitoring alterations in GLUT activities.

Non‐symmetric Half‐Fused B←N Coordinated Diketopyrrolopyrrole Building Block for n‐type Semiconducting Polymers

AbstractThe development of conjugated polymers with high semiconducting performance and high reliability is of great significance for flexible electronics. Herein, we developed a new type of electron‐accepting building block; i.e., non‐symmetric half‐fused B←N coordinated diketopyrrolopyrrole (DPP) (HBNDPP), for amorphous conjugated polymers toward flexible electronics. The rigid B←N fusion part of HBNDPP endows the resulting polymers with decent electron transport, while its non‐symmetric structure causes the polymer to exhibit multiple conformation isomers with flat torsional potential energies. Thus, it gets packed in an amorphous manner in solid state, ensuring good resistance to bending strain. Combined with hardness and softness, the flexible organic field‐effect transistor devices exhibit n‐type charge properties with decent mobility, good bending resistance, and good ambient stability. The preliminary study makes this building block a potential candidate for future design of conjugated materials for flexible electronic devices.

Non-symmetric Half-Fused B←N Coordinated Diketopyrrolopyrrole Building Block for n-type Semiconducting Polymers.

The development of conjugated polymers with high semiconducting performance and high reliability is of great significance for flexible electronics. Herein, we develop a new type of electron-accepting building block; ie., non-symmetric half-fused B←N coordinated diketopyrrolopyrrole (DPP) (HBNDPP),for amorphous conjugated polymers towards flexible electronics. The rigid B←N fusion part of HBNDPP endows the resulting polymers with decent electron transport, while the non-symmetric structure of HBNDPP causes the polymer to exhibit multiple conformation isomers with flat torsional potential energies.Thus, it gets packed in anamorphous mannerin solid state, ensuring good resistance to bending strain. Combined with hardness and softness, the flexible OFET devices exhibit n-type charge properties with decent mobility, good bending resistance, and good ambient stability. The preliminary study makes this building block a potential candidate for future design of conjugated materials for flexible electronic devices.

Effects of different conformations of polylysine on the anti-tumor efficacy of methotrexate nanoparticles

Drug delivery systems require that carrier materials have good biocompatibility, degradability, and constructability. Poly(amino acids), a substance with a distinctive secondary structure, not only have the basic features of the carrier materials but also have several reactive functional groups in the side chain, which can be employed as drug carriers to deliver anticancer drugs. The conformation of isomers of drug carriers has some influence on the preparation, morphology, and efficacy of nanoparticles. In this study, two isomers of polylysine, including ε-polylysine (ε-PL) and α-polylysine (α-PL), were used as drug carriers to entrap methotrexate (MTX) and construct nano-drug delivery systems. ε-PL/MTX nanoparticles with the morphology of helical nanorods presented a small particle size (115.0 nm), and relative high drug loading content (57.8 %). The anticancer effect of ε-PL/MTX nanoparticles was 1.3-fold and 2.6-fold stronger than that of α-PL/MTX nanoparticles in vivo and in vitro, respectively. ε-PL is an ideal drug carrier with potential clinical application prospects.

Conserved Conformational Dynamics Reveal a Key Dynamic Residue in the Gatekeeper Loop of Human Cyclophilins.

Cyclophilins are ubiquitous human enzymes that catalyze peptidyl-prolyl cis-trans isomerization in protein substrates. Of the 17 unique isoforms, five closely related isoforms (CypA-E) are found in various environments and participate in diverse cellular processes, yet all have similar structures and the same core catalytic function. The question is what key residues are behind the conserved function of these enzymes. Here, conformational dynamics are compared across these isoforms to detect conserved dynamics essential for the catalytic activity of cyclophilins. A set of key dynamic residues, defined by the most dynamically conserved positions, are identified in the gatekeeper 2 region. The highly conserved glycine (Gly80) in this region is predicted to underlie the local flexibility, which is further tested by molecular dynamics simulations performed on mutants (G80A) of CypE and CypA. The mutation leads to decreased flexibility of CypE and CypA during substrate binding but increased flexibility during catalysis. Dynamical changes occur in the mutated region and a distal loop downstream of the mutation site in sequence. Examinations of the mutational effect on catalysis show that both mutated CypE and CypA exhibit shifted binding free energies of the substrate under distinct isomer conformations. The results suggest a loss of function in the mutated CypE and CypA. These catalytic changes by the mutation are likely independent of the substrate sequence, at least in CypA. Our work presents a method to identify function-related key residues in proteins.

Sterically crowded di-indazolyl-pyridines: Iron(II) complexation studies

Abstract 4-(2,6-Di(2H-indazol-2-yl)pyridin-4-yl)benzoic acid (1) and 10-(2,6-di(1H-pyrazol-1-yl)pyridin-4-yl)anthracene-9-carboxylic acid (2) were required for adsorption studies on Ag(111), with a view to subsequent iron(II) complexation and formation of well-ordered spin-responsive self-assembled monolayers. While the generation of these compounds has remained elusive, several intermediates and by-products were obtained, potentially useful as dipyrazolylpyridine-related derivatives and for metal ion coordination. 3,5-Dichloro-2,6-diindazolylpyridine-4-amine, which forms as a mixture of regioisomers, was synthesised, the mixture separated, and the components characterised (3,5-dichloro-2,6-di(2H-indazol-2-yl)pyridin-4-amine; 3,5-dichloro-2-(1H-indazol-1-yl)-6-(2H-indazol-2-yl)pyridin-4-amine; 3,5-dichloro-2,6-di(1H-indazol-1-yl)pyridin-4-amine). Their iron(II) complexes have been prepared and fully characterised, including single crystal X-ray structure determination. The complexes are instructive examples of the influence of ligand design (“steric jamming”) on the spin-crossover (SCO) activity of FeII centres. Bulky substitution, which entails twisted ligand conformation, increases intramolecular crowding. This prevents contraction of the metal coordination sphere, which would be a prerequisite for thermally inducible SCO. Mössbauer spectroscopy has revealed that the complexes remain predominantly high-spin (HS) between 20 and 200 K, and that a mixture of conformational HS isomers is present in the microcrystalline solid.

Control of dynamic sp3-C stereochemistry

Stereogenic sp3-hybridized carbon centres are fundamental building blocks of chiral molecules. Unlike dynamic stereogenic motifs, such as sp3-nitrogen centres or atropisomeric biaryls, sp3-carbon centres are usually fixed, requiring intermolecular reactions to undergo configurational changes. Here we report the internal enantiomerization of fluxional carbon cages and the consequences of their adaptive configurations for the transmission of stereochemical information. The sp3-carbon stereochemistry of the rigid tricyclic cages is inverted through strain-assisted Cope rearrangements, emulating the low-barrier configurational dynamics typical for sp3-nitrogen inversion or conformational isomerism. This dynamic enantiomerization can be stopped, restarted or slowed by external reagents, while the configuration of the cage is controlled by neighbouring, fixed stereogenic centres. As part of a phosphoramidite–olefin ligand, the fluxional cage acts as a conduit to transmit stereochemical information from the ligand while also transferring its dynamic properties to chiral-at-metal coordination environments, influencing catalysis, ion pairing and ligand exchange energetics.

Unraveling the Nature and Strength of Non-covalent Interactions on the Surface of Fullerenes.

The nature and strength of the noncovalent intermolecular interactions on the surface of fullerenes must be understood for the application of these molecules in pharmaceuticals and materials chemistry. Consequently, experimental and theoretical evaluations of such weak interactions have been conducted in parallel. Nevertheless, the nature of these interactions remains a topic of ongoing debate. In this context, this concept article summarizes recent advances in experimental and theoretical efforts aimed at characterizing the nature and strength of non-covalent interactions on fullerene surfaces. Specifically, this article summarizes recent studies conducted on host-guest chemistry based on various macrocycles and on catalyst chemistry based on conjugated molecular catalysts composed of fullerenes and amines. In addition, conformational isomerism analyses performed using fullerene-based molecular torsion balances and state-of-the-art computational chemistry are reviewed. These studies have enabled a comprehensive evaluation of the contributions of electrostatic, dispersive, and polar interactions on the surface of fullerenes.

INTERACTION OF IONIC LIQUIDS BASED ON BIS(TRIFLUOROMETHYLSULFONIL)IMIDE ANION WITH HALLOYSITE NANOTUBES ACCORDING TO FT-IR SPECTROSCOPY

In this work, FT-IR spectroscopy was used to study the interactions in ionogels of the composition х[X]+[TFSI]−/(100 - x)НNT, where [TFSI]– is the bis(trifluoromethylsulfonyl)imide anion, the cation [X]+ = [BMPip]+ (1-butyl-1-methylpiperidinium), [BMPyr]+ (1-butyl-1-methylpyrrolidinium), and [BMIm]+ (1-butyl-3-methylimidazolium), HNT are halloysite nanotubes, х = (55.2±0.5) wt.%. A comparison of the spectra of the starting compounds and the resulting ionogels showed that the characteristic frequency of the stretching vibrations of OH bonds of adsorbed water molecules, observed in the spectra of pure halloysite, practically vanishes in the spectra of ionogel sts. The stretching vibrations of the C-H bond atoms of the cation, ν(CH), and the stretching vibrations of the C-F bond atoms of the CF3 group of the anion, ν(CF3), in the spectra of limited ionic liquids are shifted to the high frequency region by 1-3 cm-1. The ratio of the intensities of the asymmetric bending vibrations of the S=O bond atoms of the SO2 group, I(δasopSO2)/I(δasipSO2), which correspond to two different conformational isomers of the anion, increases by (15-19)%. As a result, it was found that the H2O molecules of halloysite are replaced by molecules of the ionic liquid due to the electrostatic interaction of the cation with the negatively charged outer siloxane (–Si–O–Si–) surface of the nanotubes and hydrogen bonds (CH···OSi), and due to the electrostatic interaction of the anion with a positively charged internal aluminol (–Al–OH) surface and hydrogen bonds (CF···HO–Al, SO···HO–Al). The restriction of the ionic liquid in the internal cavity of the HNT causes a conformational rearrangement of the [TFSI]− anion. The results obtained are of fundamental importance, make a certain contribution to understanding the effects in ionogels based on ionic liquids and nanoporous natural minerals, and can be used to develop quasi-solid electrolytes in the production of various electrochemical devices. For citation: Ramenskaya L.M., Grishina E.P., Kudryakova N.O. Interaction of ionic liquids based on bis(trifluoromethylsulfonil)imide anion with halloysite nanotubes according to FT-IR spectroscopy. ChemChemTech [Izv. Vyssh. Uchebn. Zaved. Khim. Khim. Tekhnol.]. 2023. V. 66. N 3. P. 36-44. DOI: 10.6060/ivkkt.20236603.6752.

Cation controlled rotation in anionic pillar[5]arenes and its application for fluorescence switch

Controlling molecular motion is one of hot topics in the field of chemistry. Molecular rotors have wide applications in building nanomachines and functional materials, due to their controllable rotations. Hence, the development of novel rotor systems, controlled by external stimuli, is desirable. Pillar[n]arenes, a class of macrocycles, have a unique planar chirality, in which two stable conformational isomers pR and pS would interconvert by oxygen-through-the-annulus rotations of their hydroquinone rings. We observe the differential kinetic traits of planar chirality transformation in sodium carboxylate pillar[5]arene (WP5-Na) and ammonium carboxylate pillar[5]arene (WP5-NH4), which inspire us to construct a promising rotary platform in anionic pillar[5]arenes (WP5) skeletons. Herein, we demonstrate the non-negligible effect of counter cations on rotational barriers of hydroquinone rings in WP5, which enables a cation grease/brake rotor system. Applications of this tunable rotor system as fluorescence switch and anti-counterfeiting ink are further explored.

Rotamerism and tautomerism in hydrazone derivatives of ethylacetoacetate: Spectroscopic features, Hammett relationships, and computational calculations

AbstractHydrazone derivatives of β‐dicarbonyl compounds illustrate an integrated configurational and conformational changes, which make them be considered as probe in disclosing H‐bonding importance in hydrogen transfer and switching. The ethyl‐3‐oxo‐butanoate derivatized hydrazones were synthesized by Japp–Klingemann reaction and were characterized in view of chromatographic and spectroscopic behavior employing thin layer chromatography, infrared (IR), ultraviolet‐visible (UV‐vis), and 1H and 13C nuclear magnetic resonance (NMR) techniques. Conformational isomerization between two possible rotamers along with their tautomeric forms was identified and investigated in detail regarding to resonance‐assisted H‐bonding (RAHB) concept by the referred spectroscopic measurements. Furthermore, substituent impacts were assessed using the acquired spectroscopic data and evaluated for structure–property correlation on the base of Hammett relationships. All of the hydrazone derivatives were found to equilibrate in acetone solution, and more of them existed in one rotameric form in solid state. The aryl substituents influence the intermolecular and intramolecular interactions differently, because the derivatives could be isolated as two distinct crystals only in a few members. Moreover, the RAHB concept was found to stabilize the conformational isomers of the hydrazone derivatives to different degrees leading to distinct equilibrium constant. Quantum chemical calculations (DFT/B3LYP) were also used to characterize the nature of the RAHB and examine the rotameric transformation process and substituent impacts on the rotamerization equilibrium.

Computational and Experimental Evidence for Templated Macrocyclization: The Role of a Hydrogen Bond Network in the Quantitative Dimerization of 24-Atom Macrocycles.

In the absence of preorganization, macrocyclization reactions are often plagued by oligomeric and polymeric side products. Here, a network of hydrogen bonds was identified as the basis for quantitative yields of macrocycles derived from the dimerization of monomers. Oligomers and polymers were not observed. Macrocyclization, the result of the formation of two hydrazones, was hypothesized to proceed in two steps. After condensation to yield the monohydrazone, a network of hydrogen bonds formed to preorganize the terminal acetal and hydrazine groups for cyclization. Experimental evidence for preorganization derived from macrocycles and acyclic models. Solution NMR spectroscopy and single-crystal X-ray diffraction revealed that the macrocycles isolated from the cyclization reaction were protonated twice. These protons contributed to an intramolecular network of hydrogen bonds that engaged distant carbonyl groups to realize a long-range order. DFT calculations showed that this network of hydrogen bonds contributed 8.7 kcal/mol to stability. Acyclic models recapitulated this network in solution. Condensation of an acetal and a triazinyl hydrazine, which adopted a number of conformational isomers, yielded a hydrazone that adopted a favored rotamer conformation in solution. The critical hydrogen-bonded proton was also evident. DFT calculations of acyclic models showed that the rotamers were isoenergetic when deprotonated. Upon protonation, however, energies diverged with one low-energy rotamer adopting the conformation observed in the macrocycle. This conformation anchored the network of hydrogen bonds of the intermediate. Computation revealed that the hydrogen-bonded network in the acyclic intermediate contributed up to 14 kcal/mol of stability and preorganized the acetal and hydrazine for cyclization.