Structural non-rigidity of six-membered aromatic rings

Direct Elucidation of the Vibrationally Averaged Structure of Benzene: A Path Integral Molecular Dynamics Study

Path integral molecular dynamics (PIMD) simulations for C₆H₆, C₆D₆, and C₆T₆ have been carried out to directly estimate the distribution of projected C-H(D,T) bond lengths onto the principal axis plane. The average values of raw C-H(D,T) bond lengths obtained from PIMD simulations are in the order of ⟨R_C-H⟩ > ⟨R_C-D⟩ > ⟨R_C-T⟩ due to the anharmonicity of the potential energy curve. However, the projected C-H(D,T) bond lengths are almost the same as those reported by Hirano et al. [J. Mol. Struct. 2021, 1243, 130537]. Our PIMD simulations directly and strongly support the explanation by Hirano et al. for the experimental observations that almost the same projected C-H(D) bond lengths are found for C₆H₆ and C₆D₆. The PIMD simulations also predicted the same projected bond lengths for C₆T₆ as those of C₆H(D)₆. In addition to the previous local mode analysis, the present PIMD simulations predicted, for benzene isotopologues, that the vibrationally averaged structure is planar but non-flat.

Impact of Deuteration and Temperature on Furan Ring Dynamics

Despite significant progress in conformational analysis of cyclic molecules, the number of computational studies is still limited while most of that available in the literature data have been obtained long time ago with outdated methods. In present research, we have studied temperature driven conformational changes of the furan ring at three different temperatures. Additionally, the effect of deuteration on the ring dynamics is discussed; in addition, the aromaticity indices following the Bird and HOMA schemes are computed along all trajectories. Our ab initio molecular dynamic simulations revealed that deuteration has changed the furan ring dynamics and the obvious consequences; in addition, the shape and size of molecule are expected to be different.

Spectroscopic characterization of C-4 substituted 3,5-dichloro-4H-1,2,6-thiadiazines

The effect of C-4 substitution with electron withdrawing groups on the structure and electronic properties of three 3,5-dichloro-4H-1,2,6-thiadiazines is characterized using resonance Raman, absorption and photoluminescence spectroscopies.

Entropy versus aromaticity in the conformational dynamics of aromatic rings

Comparison of the results of Car-Parrinello molecular dynamics simulations of isolated benzene, pyrimidine and 1,2,4-triazine molecules reveals that the unusually low population of planar geometry of the benzene ring is caused by entropy effects despite its high aromaticity. The decrease in symmetry of the molecule results in smaller changes in entropy and Gibbs free energy due to out-of-plane deformations of the ring, leading to an increase in the population of planar geometry of the ring. This leads to differences in the topology of potential energy and Gibbs free energy surfaces.

Crystallographic snapshots of tyrosine phenol-lyase show that substrate strain plays a role in C-C bond cleavage

The key step in the enzymatic reaction catalyzed by tyrosine phenol-lyase (TPL) is reversible cleavage of the Cβ-Cγ bond of L-tyrosine. Here, we present X-ray structures for two enzymatic states that form just before and after the cleavage of the carbon-carbon bond. As for most other pyridoxal 5'-phosphate-dependent enzymes, the first state, a quinonoid intermediate, is central for the catalysis. We captured this relatively unstable intermediate in the crystalline state by introducing substitutions Y71F or F448H in Citrobacter freundii TPL and briefly soaking crystals of the mutant enzymes with a substrate 3-fluoro-L-tyrosine followed by flash-cooling. The X-ray structures, determined at ~2.0 Å resolution, reveal two quinonoid geometries: "relaxed" in the open and "tense" in the closed state of the active site. The "tense" state is characterized by changes in enzyme contacts made with the substrate's phenolic moiety, which result in significantly strained conformation at Cβ and Cγ positions. We also captured, at 2.25 Å resolution, the X-ray structure for the state just after the substrate's Cβ-Cγ bond cleavage by preparing the ternary complex between TPL, alanine quinonoid and pyridine N-oxide, which mimics the α-aminoacrylate intermediate with bound phenol. In this state, the enzyme-ligand contacts remain almost exactly the same as in the "tense" quinonoid, indicating that the strain induced by the closure of the active site facilitates elimination of phenol. Taken together, structural observations demonstrate that the enzyme serves not only to stabilize the transition state but also to destabilize the ground state.

Quantification of thermal ring flexibilities of aromatic and heteroaromatic compounds

The consequences of thermal fluctuations occurring at room temperatures on the aromatic character of a broad group of compounds were analyzed in three distinct ways. First of all, the ring deformations were modeled along normal coordinates coming from quantum thermo-chemistry computations. The amplitudes of vibrations were estimated according to absorbed energies at room temperature. Alternatively, in-plane and out-of-plane ring deformations were modeled via scanning procedure with partial relaxation of the molecular geometry. The influence of ring deformations on π-electron delocalization was expressed in terms of HOMA values. Besides, the ring deformability was defined as the averaged change of bond angles or dihedral angles constituting the ring that was associated with 1.5 kcal mol(-1) increase of the system energy. The molecules structures adopted during vibrations at room temperature can lead to significant heterogeneity of structural index of aromaticity. The broad span of HOMA values was obtained for analyzed five- or six-membered aromatic and heteroaromatic rings. However, the averaged values obtained for such fluctuations almost perfectly match HOMA values of molecule in the ground state. It has been demonstrated that the ring deformability imposed by bond angle changes is much smaller than for dihedral angles with the same rise of system energy. Interestingly in the case of out-of-plane vibrations modeled by scanning procedure there is observed linear correlation between ring deformability and HOMA values. Proposed method for inclusion of thermal vibrations in the framework of π-electron delocalization provides natural shift of the way of thinking about aromaticity from a static quantity to a dynamic and heterogeneous one due to inclusion of a more realistic object of analysis - thermally deformed structures. From this perspective the thermal fluctuations are supposed to be non-negligible contributions to aromaticity phenomenon.

Revisiting the planarity of nucleic acid bases: Pyramidilization at glycosidic nitrogen in purine bases is modulated by orientation of glycosidic torsion

We describe a novel, fundamental property of nucleobase structure, namely, pyramidilization at the N1/9 sites of purine and pyrimidine bases. Through a combined analyses of ultra-high-resolution X-ray structures of both oligonucleotides extracted from the Nucleic Acid Database and isolated nucleotides and nucleosides from the Cambridge Structural Database, together with a series of quantum chemical calculations, molecular dynamics (MD) simulations, and published solution nuclear magnetic resonance (NMR) data, we show that pyramidilization at the glycosidic nitrogen is an intrinsic property. This property is common to isolated nucleosides and nucleotides as well as oligonucleotides—it is also common to both RNA and DNA. Our analysis suggests that pyramidilization at N1/9 sites depends in a systematic way on the local structure of the nucleoside. Of note, the pyramidilization undergoes stereo-inversion upon reorientation of the glycosidic bond. The extent of the pyramidilization is further modulated by the conformation of the sugar ring. The observed pyramidilization is more pronounced for purine bases, while for pyrimidines it is negligible. We discuss how the assumption of nucleic acid base planarity can lead to systematic errors in determining the conformation of nucleotides from experimental data and from unconstrained MD simulations.

Interplay of pi-electron delocalization and strain in [n](2,7)pyrenophanes

The geometries of a series of [n](2,7)pyrenophanes (n = 6-12) were optimized at the B3LYP/6-311G** DFT level. The X-ray crystal structures determined for the [9](2,7)- and [10](2,7)pyrenophanes agreed excellently with the computed structures. The degree of nonplanarity of the pyrene moiety depends on the number of CH2 groups in the aliphatic bridge and, as analyzed theoretically, influences the strain energy and the extent of pi-electron delocalization in the pyrene fragment. Various indices, e.g., the relative aromatic stabilization energies (DeltaASE), magnetic susceptibility exaltations (Lambda), nucleus-independent chemical shifts (NICS), and the harmonic oscillator model of aromaticity (HOMA) were used to quantify the change in aromatic character of the pyrene fragment. DeltaASE and relative Lambda values (with respect to planar pyrene) were evaluated by homodesmotic equations comparing the bent pyrene unit with its bent quinoid dimethylene-substituted analog. The bend angle, alpha, DeltaASE, and Lambda were linearly related. The aromaticity decreases smoothly and regularly over a wide range of bending, but the magnitude of the change is not large. The differences between planar pyrene (alpha = 0 degrees) and the most distorted pyrene unit (alpha = 39.7 degrees in [6](2,7)pyrenophane) are only 15.8 kcal/mol (DeltaASE) and 18.8 cgs-ppm (Lambda). Also, the geometry-based HOMA descriptor changes by only 0.07 unit. The local NICS descriptors of aromatic character also correlate very well with the global indices of aromaticity. In line with the known reactivity of pyrenophanes, the variations of NICS(1), a measure of pi-electron delocalization, were largest for the outer, biphenyl-type rings. The strain energies of the pyrene fragments were much larger and varied more than those evaluated for the bridge. Both strain energies were interrelated (correlation coefficient R = 0.979) and depend on the bend angle, alpha.

Aromaticity of Distorted Benzene Rings: Exploring the Validity of Different Indicators of Aromaticity

The effect of three in-plane (bond length alternation, bond length elongation, and clamping) and three out-of-plane deformations (boatlike, chairlike, and pyramidalization) on the aromaticity of the benzene molecule has been analyzed employing seven widely used indicators of aromaticity. It is shown that only the aromatic fluctuation index (FLU) is able to indicate the expected loss of aromaticity because of distortion from the equilibrium geometry in all deformations analyzed. As FLU has been shown previously to fail in other particular situations, we conclude that there is not yet a single indicator of aromaticity that works properly for all cases. Therefore, to reach safer conclusions, aromaticity analyses should be carried out employing a set of aromaticity descriptors on the basis of different physical manifestations of aromaticity.

Are Isolated Nucleic Acid Bases Really Planar? A Car−Parrinello Molecular Dynamics Study

Car-Parrinello molecular dynamics simulations of the flexibility of isolated DNA bases have been carried out. The comparison of lowest ring out-of-plane vibrations calculated by using MP2/cc-pvdz and BLYP/PW methods reveals that the DFT method with the plane wave basis set reasonably reproduces out-of-plane deformability of the pyrimidine ring in nucleic acid bases and could be used for reliable modeling of conformational flexibility of nucleobases. The conformational phase space of pyrimidine rings in thymine, cytosine, guanine, and adenine has been investigated by using the ab initio Car-Parrinello molecular dynamics method. It is demonstrated that all nucleic acid bases are highly flexible molecules and possess a nonplanar effective conformation of the pyrimidine ring despite the fact that the planar geometry corresponds to a minimum on the potential energy surface. The population of the planar geometry of the pyrimidine ring does not exceed 30%. Among the nonplanar conformations of the pyrimidine rings, the boat-like and half-chair conformations are the most populated.

Low-temperature FTIR spectra and hydrogen bonds in polycrystalline adenosine and uridine

FTIR spectra of polycrystalline samples of adenosine and uridine, pure and containing small (<10%) quantity of N(O)H or N(O)D groups, were measured in KBr pellets from 4000 to 400 cm(-1) at temperatures from 300 to 20 K. For the first time, the bands of narrow isotopically decoupled proton stretching vibration nu1 mode of NH- and OH- groups were found and assigned to ordered hydrogen bonds according to crystal structural data for both nucleosides. The FTIR adenosine spectra in the out-of-plane bending proton nu4 mode range (lower than 1000 cm(-1)) of N(O)H groups revealed at low temperature at least twice more bands, than in the nu1 range, which are influenced by isotopic exchange and (or) cooling. Almost all of them have their counterparts in the N(O)D substance spectrum with an isotopic frequency ratio of 1.30-1.40. These bands were assigned to the differently H-bound disordered NH and OH protons, which could not be seen with crystal structural methods. The energy and length of different H-bonds were estimated from peak positions of both mode bands (as the red shift of nu1 or blue shift of nu4 relatively free molecules) with well-established empirical correlations between spectral, thermodynamic and structural parameters of hydrogen bonds. The results were compared with independent experimental data.