Search Results (21)

Although the harmonic oscillator model has found wide use in physics and chemistry, there are more interesting potential energy functions (PEFs) which can tell us a great deal about molecular structure and energetics. In the present work, we show that for selected systems simple one- and two-dimensional potential functions can be used to very accurately fit detailed spectroscopic data and provide extensive additional information. Results for molecular inversion, ring puckering, the anomeric effect, pseudorotation, triplet-state puckering, internal rotation, and π-type hydrogen bonding in ground and excited electronic states are presented. Full article

Aflatoxin B₁ (AFB₁) and sterigmatocystin (ST) are mycotoxins that pose significant threats to human and animal health owing to their mutagenic, carcinogenic, and toxic properties. They are structurally similar and widely believed to exert their biological effects via the generation of DNA-damaging epoxides at their respective terminal furan rings. Despite structural identity in the warhead portion of each toxin, this work shows that distal parts of each molecule are responsible for the distinctive mutational fingerprints seen in gptΔ C57BL/6J mouse embryo fibroblasts (MEFs). The two toxins differ structurally in the puckered cyclopentenone ring of AFB₁ and in the planar xanthone functionality of ST. While both toxins mainly induce GC→TA mutations, the aforementioned differences in structure apparently trigger unique patterns of mutations, as revealed by high-resolution duplex sequencing of MEF genomes. AFB₁ is more mutagenic than ST and displays its transversion mutations in a pattern with primary and secondary hotspots (underscored) in 5′-CGC-3′ and 5′-CGG-3′ contexts, respectively. ST displays a modest 5′-CGG-3′ hotspot while its other GC→TA transversions are more uniformly distributed in a pattern resembling established oxidative stress mutational spectra. This research delineates the mutational spectra of AFB₁ and ST, establishing these patterns as possible early-onset biomarkers of exposure. Full article

The conformation of tetrahydrofuran (THF) molecules in vapor has been the subject of considerable computational and experimental studies, the most recent by Park and Kwon stated that the difference between the most stable, twisted C₂ conformer and the bent C_s conformer is 17 ± 15 cm⁻¹. Because of low symmetry, all modes from both conformers are allowed in the Raman and infrared spectra. In 1982, Aleksanyan and Antipov observed the emergence of two Raman bands at 249 and 303 cm⁻¹ at 20 K, while only one band at 293 cm⁻¹ was present in solid THF at 142. They assigned the 249 cm⁻¹ band to the restricted pseudorotational motion of THF in the solid state, because on heating, the band diminishes and is too weak to be observed near melting point (at 142 K). Cadioli et al. reported a study of the vibrational spectrum of tetrahydrofuran, giving a complete assignment of all bands including those present in the low-temperature Raman spectrum at 85 K and infrared bands observed at 90 K. They assigned the band at 242 cm⁻¹ in the Raman spectrum at 85 K as an overtone of the lowest normal mode (pseudorotational mode), while the 299 cm⁻¹ band in the same spectrum was assigned as a radial mode. In the following, low-temperature Raman spectra of solid THF together with the Raman matrix isolated spectrum of THF in air will be presented and compared to published data. Our results indicate that the band observed at 245 cm⁻¹ at 10 K is too strong to be assigned as an overtone, since its intensity is of the same magnitude as the 299 cm⁻¹ band. Full article

Hydrated H-Apophyllite (HH-Apo) and H-carletonite (H-Car) were synthesized at 0 °C by leaching an apophyllite and a carletonite single crystal in a large surplus of 1.2 molar hydrochloric acid. The XRD powder patterns of HH-Apo and H-Car were indexed with space group symmetries of P4/ncc and I4/mcm and lattice parameters of a = 8.4872(2) Å, c = 16.8684(8) Å and a = 13.8972(3) Å, c = 20.4677(21) Å, respectively. The crystal structures were solved based on model building of the structures of the precursors and a physico-chemical characterization. Rietveld structure refinements confirmed the structure models. HH-Apo and H-Car are among the very few crystalline silicic acids whose structures have been determined and confirmed based on a structure refinement. The structure of HH-Apo contains thin silicate monolayers that can be regarded as constructed by rings of interconnected [SiO₃OH] tetrahedra which form a puckered silicate layer. A sheet of water molecules is intercalated between the silicate layers. There are no direct hydrogen bonds between the silanol groups, but there are hydrogen bonds of different strengths between the terminal O atoms of the silicate layers and the intercalated water molecules. The ¹H MAS NMR spectrum presents a strong signal at 4.9 ppm related to the aforementioned bonds and interactions between the water molecules, as well as a small signal at 22.5 ppm corresponding to an extremely strong hydrogen bond with d(O...O) ≈ 2.2 Å. The structure of H-Car is free of structural water and consists exclusively of microporous silicate double-layers with 4-connected [SiO₄] and 3-connected [SiO₃OH] tetrahedra in a ratio of 1:1 and a thickness of 9.2 Å. Neighboring layers are connected to each other by medium–strong hydrogen bonds with O...O distances of 2.56 Å. The structure of HH-Apo decays within several hours while H-Car is stable. A topotactic condensation reaction applied to H-Car forms an irregularly condensed silicate which still contains the layers in a distorted form as building blocks. Full article

Novel antiepileptic drugs have been developed at an unparalleled rate during the past 15 years. Gabapentin (GBP), which was approved for the treatment of refractory localization-related epilepsies in the U.K. and Europe in 1993, was one of the first drugs to come out of this era. Since then, GBP has become well-known across the world, not only for its antiepileptic qualities but also for its effectiveness in the treatment of chronic pain disorders, particularly neuropathic pain. In this review, the crystal structures of GBP and GBP-related compounds have been analyzed and compared. Particular attention has been paid to the polymorphism of GBP and its hydrates, their thermodynamic stability, and conformational differences. In addition, the puckering parameters for the cyclohexane ring of a total of 118 molecules of GBP found in the analyzed crystal structures have been calculated and analyzed. The results of recent high-pressure crystallization studies and quantum chemical calculations indicate that the entire landscape of GBP has not been revealed yet. Full article

[5.5.5.5]hexaene is a [12]annulene ring with a symmetrically bound carbon atom in its center. This is the smallest hydrocarbon with a hyperbolic paraboloid shape. [5.5.5.5]hexaene and related hydrocarbons are important building blocks in organic and materials chemistry. For example, penta-graphene—a puckered 2D allotrope of carbon—is comprised of similar repeating subunits. Here, we investigate the thermochemical and kinetic properties of [5.5.5.5]hexaene at the CCSD(T) level by means of the G4 thermochemical protocol. We find that this system is energetically stable relative to its isomeric forms. For example, isomers containing a phenyl ring with one or more acetylenic side chains are higher in energy by ∆H₂₉₈ = 17.5–51.4 kJ mol⁻¹. [5.5.5.5]hexaene can undergo skeletal inversion via a completely planar transition structure; however, the activation energy for this process is ∆H^‡₂₉₈ = 249.2 kJ mol⁻¹ at the G4 level. This demonstrates the high configurational stability of [5.5.5.5]hexaene towards skeletal inversion. [5.5.5.5]hexaene can also undergo a π-bond shift reaction which proceeds via a relatively low-lying transition structure with an activation energy of ∆H^‡₂₉₈ = 67.6 kJ mol⁻¹. Therefore, this process is expected to proceed rapidly at room temperature. Full article

Large amplitude motions (LAMs) form a fundamental phenomenon that demands the development of specific theoretical and Hamiltonian models. In recent years, along with the strong progress in instrumental techniques on high-resolution microwave spectroscopy and computational capacity in quantum chemistry, studies on LAMs have become very diverse. Larger and more complex molecular systems have been taken under investigation, ranging from series of heteroaromatic molecules from five- and six-membered rings to polycyclic-aromatic-hydrocarbon derivatives. Such systems are ideally suited to create families of molecules in which the positions and the number of LAMs can be varied, while the heteroatoms often provide a sufficient dipole moment to the systems to warrant the observation of their rotational spectra. This review will summarize three types of LAMs: internal rotation, inversion tunneling, and ring puckering, which are frequently observed in aromatic five-membered rings such as furan, thiophene, pyrrole, thiazole, and oxazole derivatives, in aromatic six-membered rings such as benzene, pyridine, and pyrimidine derivatives, and larger combined rings such as naphthalene, indole, and indan derivatives. For each molecular class, we will present the representatives and summarize the recent insights on the molecular structure and internal dynamics and how they help to advance the field of quantum mechanics. Full article

In this study we investigate the Diels–Alder reaction between methyl acrylate and butadiene, which is catalyzed by BF${}_3$ Lewis acid in explicit water solution, using URVA and Local Mode Analysis as major tools complemented with NBO, electron density and ring puckering analyses. We considered four different starting orientations of methyl acrylate and butadiene, which led to 16 DA reactions in total. In order to isolate the catalytic effects of the BF${}_3$ catalyst and those of the water environment and exploring how these effects are synchronized, we systematically compared the non-catalyzed reaction in gas phase and aqueous solution with the catalyzed reaction in gas phase and aqueous solution. Gas phase studies were performed at the B3LYP/6-311+G(2d,p) level of theory and studies in aqueous solution were performed utilizing a QM/MM approach at the B3LYP/6-311+G(2d,p)/AMBER level of theory. The URVA results revealed reaction path curvature profiles with an overall similar pattern for all 16 reactions showing the same sequence of CC single bond formation for all of them. In contrast to the parent DA reaction with symmetric substrates causing a synchronous bond formation process, here, first the new CC single bond on the CH${}_2$ side of methyl acrylate is formed followed by the CC bond at the ester side. As for the parent DA reaction, both bond formation events occur after the TS, i.e., they do not contribute to the energy barrier. What determines the barrier is the preparation process for CC bond formation, including the approach diene and dienophile, CC bond length changes and, in particular, rehybridization of the carbon atoms involved in the formation of the cyclohexene ring. This process is modified by both the BF${}_3$ catalyst and the water environment, where both work in a hand-in-hand fashion leading to the lowest energy barrier of 9.06 kcal/mol found for the catalyzed reaction R1 in aqueous solution compared to the highest energy barrier of 20.68 kcal/mol found for the non-catalyzed reaction R1 in the gas phase. The major effect of the BF${}_3$ catalyst is the increased mutual polarization and the increased charge transfer between methyl acrylate and butadiene, facilitating the approach of diene and dienophile and the pyramidalization of the CC atoms involved in the ring formation, which leads to a lowering of the activation energy. The catalytic effect of water solution is threefold. The polar environment leads also to increased polarization and charge transfer between the reacting species, similar as in the case of the BF${}_3$ catalyst, although to a smaller extend. More important is the formation of hydrogen bonds with the reaction complex, which are stronger for the TS than for the reactant, thus stabilizing the TS which leads to a further reduction of the activation energy. As shown by the ring puckering analysis, the third effect of water is space confinement of the reacting partners, conserving the boat form of the six-member ring from the entrance to the exit reaction channel. In summary, URVA combined with LMA has led to a clearer picture on how both BF${}_3$ catalyst and aqueous environment in a synchronized effort lower the reaction barrier. These new insights will serve to further fine-tune the DA reaction of methyl acrylate and butadiene and DA reactions in general. Full article

The conformational properties of carbohydrates can contribute to protein structure directly through covalent conjugation in the cases of glycoproteins and proteoglycans and indirectly in the case of transmembrane proteins embedded in glycolipid-containing bilayers. However, there continue to be significant challenges associated with experimental structural biology of such carbohydrate-containing systems. All-atom explicit-solvent molecular dynamics simulations provide a direct atomic resolution view of biomolecular dynamics and thermodynamics, but the accuracy of the results depends on the quality of the force field parametrization used in the simulations. A key determinant of the conformational properties of carbohydrates is ring puckering. Here, we applied extended system adaptive biasing force (eABF) all-atom explicit-solvent molecular dynamics simulations to characterize the ring puckering thermodynamics of the ten common pyranose monosaccharides found in vertebrate biology (as represented by the CHARMM carbohydrate force field). The results, along with those for idose, demonstrate that the CHARMM force field reliably models ring puckering across this diverse set of molecules, including accurately capturing the subtle balance between ⁴C₁ and ¹C₄ chair conformations in the cases of iduronate and of idose. This suggests the broad applicability of the force field for accurate modeling of carbohydrate-containing vertebrate biomolecules such as glycoproteins, proteoglycans, and glycolipids. Full article

The results of structural studies on a series of halogen-substituted derivatives of 2-deoxy-D-glucose (2-DG) are reported. 2-DG is an inhibitor of glycolysis, a metabolic pathway crucial for cancer cell proliferation and viral replication in host cells, and interferes with D-glucose and D-mannose metabolism. Thus, 2-DG and its derivatives are considered as potential anticancer and antiviral drugs. X-ray crystallography shows that a halogen atom present at the C2 position in the pyranose ring does not significantly affect its conformation. However, it has a noticeable effect on the crystal structure. Fluorine derivatives exist as a dense 3D framework isostructural with the parent compound, while Cl- and I-derivatives form layered structures. Analysis of the Hirshfeld surface shows formation of hydrogen bonds involving the halogen, yet no indication for the existence of halogen bonds. Density functional theory (DFT) periodic calculations of cohesive and interaction energies (at the B3LYP level of theory) have supported these findings. NMR studies in the solution show that most of the compounds do not display significant differences in their anomeric equilibria, and that pyranose ring puckering is similar to the crystalline state. For 2-deoxy-2-fluoro-D-glucose (2-FG), electrostatic interaction energies between the ligand and protein for several existing structures of pyranose 2-oxidase were also computed. These interactions mostly involve acidic residues of the protein; single amino-acid substitutions have only a minor impact on binding. These studies provide a better understanding of the structural chemistry of halogen-substituted carbohydrates as well as their intermolecular interactions with proteins determining their distinct biological activity. Full article

The conformations of 2-cyclopenten-1-ol (2CPOL) have been investigated by high-level theoretical computations and infrared spectroscopy. The six conformational minima correspond to specific values of the ring-puckering and OH internal rotation coordinates. The conformation with the lowest energy possesses intramolecular π-type hydrogen bonding. A second conformer with weaker hydrogen bonding has somewhat higher energy. Ab initio coupled-cluster theory with single and double excitations (CCSD) was used with the cc-pVTZ (triple-ζ) basis set to calculate the two-dimensional potential energy surface (PES) governing the conformational dynamics along the ring-puckering and internal rotation coordinates. The two conformers with the hydrogen bonding lie about 300 cm⁻¹ (0.8 kcal/mole) lower in energy than the other four conformers. The lowest energy conformation has a calculated distance of 2.68 Å from the hydrogen atom on the OH group to the middle of the C=C double bond. For the other conformers, this distance is at least 0.3 Å longer. The infrared spectrum in the O-H stretching region agrees well with the predicted frequency differences between the conformers and shows the conformers with the hydrogen bonding to have the lowest values. The infrared spectra in other regions arise mostly from the two hydrogen-bonded species. Full article

Glycosaminoglycans (GAGs) are the linear carbohydrate components of proteoglycans (PGs) and are key mediators in the bioactivity of PGs in animal tissue. GAGs are heterogeneous, conformationally complex, and polydisperse, containing up to 200 monosaccharide units. These complexities make studying GAG conformation a challenge for existing experimental and computational methods. We previously described an algorithm we developed that applies conformational parameters (i.e., all bond lengths, bond angles, and dihedral angles) from molecular dynamics (MD) simulations of nonsulfated chondroitin GAG 20-mers to construct 3-D atomic-resolution models of nonsulfated chondroitin GAGs of arbitrary length. In the current study, we applied our algorithm to other GAGs, including hyaluronan and nonsulfated forms of dermatan, keratan, and heparan and expanded our database of MD-generated GAG conformations. Here, we show that individual glycosidic linkages and monosaccharide rings in 10- and 20-mers of hyaluronan and nonsulfated dermatan, keratan, and heparan behave randomly and independently in MD simulation and, therefore, using a database of MD-generated 20-mer conformations, that our algorithm can construct conformational ensembles of 10- and 20-mers of various GAG types that accurately represent the backbone flexibility seen in MD simulations. Furthermore, our algorithm efficiently constructs conformational ensembles of GAG 200-mers that we would reasonably expect from MD simulations. Full article

Glycosaminoglycans (GAGs) are linear, structurally diverse, conformationally complex carbohydrate polymers that may contain up to 200 monosaccharides. These characteristics present a challenge for studying GAG conformational thermodynamics at atomic resolution using existing experimental methods. Molecular dynamics (MD) simulations can overcome this challenge but are only feasible for short GAG polymers. To address this problem, we developed an algorithm that applies all conformational parameters contributing to GAG backbone flexibility (i.e., bond lengths, bond angles, and dihedral angles) from unbiased all-atom explicit-solvent MD simulations of short GAG polymers to rapidly construct models of GAGs of arbitrary length. The algorithm was used to generate non-sulfated chondroitin 10- and 20-mer ensembles which were compared to MD-generated ensembles for internal validation. End-to-end distance distributions in constructed and MD-generated ensembles have minimal differences, suggesting that our algorithm produces conformational ensembles that mimic the backbone flexibility seen in simulation. Non-sulfated chondroitin 100- and 200-mer ensembles were constructed within a day, demonstrating the efficiency of the algorithm and reduction in time and computational cost compared to simulation. Full article

Six examples of 2-(1-arylimino)ethyl-9-arylimino-5,6,7,8-tetrahydrocycloheptapyridine-cobalt(II) chloride complexes, [2-(1-ArN)C₂H₃-9-ArN-5,6,7,8-C₅H₈C₅H₃N]CoCl₂, (Ar = 2-(C₅H₉)-6-MeC₆H₃ Co1, 2-(C₆H₁₁)-6-MeC₆H₃ Co2, 2-(C₈H₁₅)-6-MeC₆H₃ Co3, 2-(C₅H₉)-4,6-Me₂C₆H₂ Co4, 2-(C₆H₁₁)-4,6-Me₂C₆H₂ Co5, and 2-(C₈H₁₅)-4,6-Me₂C₆H₂ Co6), were synthesized by the direct reaction of the corresponding ortho-cycloalkyl substituted carbocyclic-fused bis(arylimino)pyridines (L1–L6) and cobalt(II) chloride in ethanol with good yields. All the synthesized ligands (L1–L6) and their corresponding cobalt complexes (Co1–Co6) were fully characterized by FT-IR, ¹H/¹³C-NMR spectroscopy and elemental analysis. The crystal structure of Co2 and Co3 revealed that the ring puckering of both the ortho-cyclohexyl/cyclooctyl substituents and the one pyridine-fused seven-membered ring; a square-based pyramidal geometry is conferred around the metal center. On treatment with either methylaluminoxane (MAO) or modified methylaluminoxane (MMAO), all the six complexes showed high activities (up to 4.09 × 10⁶ g of PE mol⁻¹ (Co) h⁻¹) toward ethylene polymerization at temperatures between 20 °C and 70 °C with the catalytic activities correlating with the type of ortho-cycloalkyl substituent: Cyclopentyl (Co1 and Co4) > cyclohexyl (Co2 and Co5) > cyclooctyl (Co3 and Co6) for either R = H or Me and afforded strictly linear polyethylene (T_m > 130 °C). The narrow unimodal distributions of the resulting polymers are consistent with single-site active species for the precatalyst. Furthermore, compared to the previously reported cobalt analogues, the titled precatalysts exhibited good thermo-stability (up to 70 °C) and possessed longer lifetime along with a higher molecular weight of PE (M_w: 9.2~25.3 kg mol⁻¹). Full article

Alkali-metal phosphanides can be embedded into a [3]ferrocenophane scaffold giving rise to bicyclic ferrocenophanes [MFe(C₅H₄PtBu)₂P] (M = Li, Na, K). Coordination of the alkali-metal ions takes place via the terminal phosphorus atoms adopting a puckered P₃M four-membered ring. All compounds were characterized via single-crystal X-ray diffraction and multinuclear NMR spectroscopy (¹H, ³¹P, ⁷Li), whereas ¹³C NMR data could only be recorded for the Li derivative, owing to the limited solubility of its heavier congeners in unreactive solvents. Full article