MNDO calculations applied to structural changes in 1,2,4-oxadiazole substituents

MNDO calculations on several substituted 1,2,4-oxadiazole compounds are discussed. Changes in geometry, atomic charge distribution, rotational barriers and molecular orbital energies are examined. A correlation exists between the thermal stability of the heterocycle and the excess electronic charge accumulated inside the ring as well as its distribution. For the case of phenylated derivatives, the nonplanar conformation is energetically more stable than the corresponding planar one, which might explain the relative decrease in thermal stability of phenylated derivatives. It is observed that as the planar conformation starts being populated, a greater amount of electrons are donated to the 1,2, 4-oxadiazole ring.     

Ethyl 3‐amino‐6‐phenyl‐4‐tolylthieno[2,3‐b]pyridine‐2‐carboxylate

In the title compound, C₂₃H₂₀N₂O₂S, the central thieno­pyridine ring system is essentially planar, the dihedral angle between the planes of the two rings being 0.3 (2)°. The terminal ethyl carboxyl­ate group is twisted by 26.7 (3)° away from the central ring system. A short intramolecular hydrogen bond involving the amino N atom and the carbonyl O atom [N⋯O = 2.806 (4) Å] forms a pseudo‐six‐membered ring. Significant intermolecular C—H⋯N, C—H⋯O and C—H⋯π interactions contribute strongly to the stability of the structure, along with weak π–π‐stacking interactions.     

2,3,12,13‐Tetrabromo‐5,10,15,20‐tetrakis(4‐butoxyphenyl)porphyrin 1,2‐dichloroethane solvate

Nonmesogenic 2,3,12,13‐tetrabromo‐5,10,15,20‐tetrakis(4‐butoxyphenyl)porphyrin crystallizes as the title 1,2‐dichloroethane solvate, C₆₀H₅₈Br₄N₄O₄·C₂H₄Cl₂. The porphyrin ring shows a nonplanar conformation, with an average mean plane displacement of the β‐pyrrole C atoms from the 24‐atom (C₂₀N₄) core of ±0.50 (3) Å. The 1,2‐dichloroethane solvent is incorporated between the porphyrin units and induces the formation of one‐dimensional chains via interhalogen Cl...Br and butyl–aryl C—H...π interactions. These chains are oriented along the unit‐cell a axis, with the macrocyclic ring planes lying almost parallel to the (010) plane. The chains are arranged in an offset fashion by aligning the butoxy chains approximately above or below the faces of the adjacent porphyrin core, resulting in decreased interporphyrin π–π interactions, and they are held together by weak intermolecular (C—Br...π, C—H...π and C—H...Br) interactions. The nonplanar geometry of the macrocyclic ring is probably due to the weak interporphyrin interactions induced by the solvent molecule and the peripheral butoxy groups. The nonplanarity of the mesogens could influence the mesogenic behaviour differently relative to planar porphyrin mesogens.     

Conformations of methoxy(hydroxy)-substituted benzenes and benzaldehydes in the gas phase

The electronic structure ofo-methoxy(hydroxy)-substituted benzenes has been investigated by the combined use of photoelectron spectroscopy and molecular orbital calculations by means of the semi-empirical AM1 method. Absorption bands in the PE spectra have been assigned, the dependence of someπ-orbital energies on the molecular conformation has been found, and the estimation of the mean torsion angle of the OCH₃-group with the plane of the benzene ring has been carried out. The results obtained show that the gas-phase conformations of the heavy-atom framework of guaiacol and vanillin molecules are planar. For veratrole and veratraldehyde, nonplanar conformations with mean torsion angles ϕ ≈ 80° and 55°, respectively, have been observed. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 1757–1760, October, 1993.     

Microwave spectrum and conformational composition of 1-vinylimidazole

The microwave spectrum of 1-vinylimidazole has been investigated in the 21-80 GHz spectral region. The spectra of two conformers have been assigned. One of these forms is planar, while the other is nonplanar with the imidazole ring and the vinyl group forming an angle of 15(4)° from coplanarity. The planar form is found to be 5.7(7) kJ/mol more stable than the nonplanar rotamer by relative intensity measurements. The spectra of 10 vibrationally excited states of the planar form and one excited-state spectrum of the nonplanar form were assigned. The vibrational frequencies of several of these states were determined by relative intensity measurements. The microwave work has been augmented by quantum chemical calculations at the CCSD/cc-pVTZ, MP2/cc-pVTZ, and B3LYP/cc-pVTZ levels of theory. The B3LYP calculations predict erroneously that both forms of 1-vinylimidazole are planar, whereas the MP2 and CCSD calculations correctly predict the existence of a planar and a nonplanar conformer of this compound.     

The influence of hydrophobic amino acid side groups on the acidity of the aromatic imidazole ring of histidine: A theoretical study

In this study we have calculated the acidity constant (pKa) of imidazole ring in Histidine‐Hydrophobic amino acid dipeptides using the quantum chemistry and continuum solvation methods. Density functional theory calculations with the large basis sets are used to determine the Gibbs free energy of deprotonate in the gas and liquid phases. Based on our results ΔG_S values are located between ?69.38 and ?18.82 kcal mol^?1 which are related to His⁺–Gly and His forms, respectively. pKa of the dipeptides in the aqueous phase was obtained from the calculated gas‐phase and solvation free energies through a thermodynamic cycle and the solvation model chemistry of Martin Karplus et al. Solvation effects are treated using a self‐consistent reaction field formalism involving polarized continuum models. According to our calculations pKa values are between 5.50 and 8.19 that are belong to His⁺–ILe and His⁺–Ala forms, respectively. Natural bond orbital analysis of dipeptides reveals that the electron delocalization in imidazole ring is the most effective factor in determination of acidity order for these compounds. Structural analysis confirmed that the orientation of carbonyl group with respect to imidazole ring is an effective factor in imidazole ring stability. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

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.     

Ab initio studies on calicene

Optimum geometries of planar and 90°-twisted C_2v calicene are calculated with single-configuration STO-3G and 3-21-G wavefunctions. The barrier to ring–ring rotation is computed. Bond alternation is pronounced in the planar form and decreases in the twisted form, while dipolar character increases on twisting.     

Molecular modeling study of tubulosine and other related ipecac alkaloids

A molecular modeling study of two alkaloids, tubulosine and psychotrine, isolated from the sap of Pogonopus speciosus, and other related ipecac alkaloids, showed that these flexible alkaloids favor a nonplanar structure. The biologically active compounds had conformations with a similar angle between aromatic ring A, the nitrogen in ring B, and ring D. This angle was related to the biological activity reported for these compounds. Our results support the hypothesis of two different types of receptor interactions, one for the nonplanar compounds and another for the planar compounds.     

Electronic nature of planar cyclobutenyl dication derivatives

The cyclobutadiene dication was not experimentally characterized to the date. However, some of its derivatives were. Most of them have planar geometry, but tetramethylcyclobutadiene dication has a nonplanar geometry according to ab initio calculations. From the atoms in molecules (AIM) theoretical analysis, common electronic features for the planar and puckered cyclobutenyl dication derivatives were observed. The planar cyclobutenyl dication derivatives have bond order of chemical bonds in the ring close to unity and relatively small electronic density in the ring. The puckered cyclobutadiene dication and its puckered derivatives have relatively high electronic density in the ring.     

Complexes of Formaldehyde and α-Dicarbonyls with Hydroxylamine: FTIR Matrix Isolation and Theoretical Study

The interactions of formaldehyde (FA), glyoxal (Gly) and methylglyoxal (MGly) with hydroxylamine (HA) isolated in solid argon and nitrogen were studied using FTIR spectroscopy and ab initio methods. The spectra analysis indicates the formation of two types of hydrogen-bonded complexes between carbonyl and hydroxylamine in the studied matrices. The cyclic planar complexes are stabilized by O–H⋯O(C), and C–H⋯N interactions and the nonplanar complexes are stabilized by O–H⋯O(C) bond. Formaldehyde was found to form with hydroxylamine, the cyclic planar complex and methylglyoxal, the nonplanar one in both argon and nitrogen matrices. In turn, glyoxal forms with hydroxylamine the most stable nonplanar complex in solid argon, whereas in solid nitrogen, both types of the complex are formed.     

Vibrational and electronic spectra of benzophenone in different phase states: Ab initio calculations and experiment

An ab initio method has been used to perform quantum mechanical calculations of the formation energy of different conformers of benzophenone: planar molecule, twisted molecule, planar molecule dimer, twisted molecule dimer; electronic and vibrational spectra of these conformers were also obtained. An assessment of the medium (solvent) influence on the optimal geometry, dipole moment and stability of different forms of benzophenone was performed in the self-consistent reaction field approximation. It is shown that the twisted conformer is more stable than the planar one (the difference of free energies is 32 kJ/mol for free molecules) and it becomes even more stable with the increase in solvent polarity. The calculated electronic and vibrational spectra agree well with the experimental data and properly reflect the complication of the vibrational spectrum when passing from the gaseous phase to the condensed state of benzophenone. The difference between spectral properties of the two dimer forms allows their identification from the spectra and qualitative explanation of the observed peculiarities of phosphorescence of the amorphous phase of benzophenone by the stabilization of different conformers.     

3‐Hydro­xy­benz­aldehyde

The title compound, C₇H₆O₂, forms infinite chains where the mol­ecules are hydrogen bonded via the hydroxyl and aldehyde groups, with an O?O distance of 2.719 (3) Å. Interchain interactions are weak. The geometry of the ring differs from the ideal form due to the effect of the substituents. Abinitio (Hartree–Fock self‐consistent field–molecular orbital and density functional theory) calculations for the free mol­ecule reproduce well the observed small distortions of the ring. In the crystal, the geometry deviates from the ideal C_s symmetry of the free mol­ecule, as given by the ab initio calculations. The aldehyde and hydroxyl groups are twisted around the single bonds which join them to the ring as a result of the intermolecular hydrogen‐bond interactions. These are also responsible for an elongation of the hydroxy C—OH bond compared with that calculated for the free mol­ecule.     

Dysobinin,a tetranortriterpenoid

The planar furan ring in the title compound (6β‐acetoxy­aza­dirone, C₃₀H₃₈O₆) is twisted with respect to the steroid D ring. The crystal structure is stabilized by C—H?O hydrogen bonds and van der Waals interactions.     

Reversible Redox Reaction Between Antiaromatic and Aromatic States of 32π‐Expanded Isophlorins

32π‐antiaromatic expanded isophlorins with a varying number of thiophene and furan rings adopt either planar, ring‐inverted, or twisted conformations depending on the number of furan rings in the macrocycle. However, they exhibit identical reactivity with respect to their oxidation to aromatic 30π‐dicationic species under acidic conditions. These 32π‐antiaromatic macrocycles can also be oxidized with [Et₃O⁺SbCl₆^?]and NOBF₄ to generate dications, thus confirming ring oxidation of macrocycles. Furthermore, they can be reduced back to their parent 32π‐antiaromatic state by triethylamine, Zn, or FeCl₂. Single‐crystal X‐ray diffraction analysis confirmed a figure‐eight conformation for a hexafuran system, which opens to a planar structure upon oxidation.     

13C NMR Investigation of Si-alkylsubstituted 1,3,5-Trisilacyclohexanes

¹³C NMR spectra of Si-alkylsubstituted derivatives of 1,3,5-trisilacyclohexanes have been recorded and analyzed. A systematic preparation of alkyl derivatives with mixed substituents made it possible to evaluate substituent-induced chemical shift (SCS) values for the ring carbon atoms in β and δ position. It is found that the β_e effect decreases in the order Me > Et > i-Pr > t-Bu. For the alkyl groups Me, Et, and i-Pr the β_a effect is smaller than the β_e effect. Axial SCS values for the t-Bu group are not accessible because chair conformations with an axial t-Bu group are unfavourable and tend to escape into a twisted boat form. The observed δ effects are small and do not show any obvious tendencies.     

Conformational studies on somep-dimethylaminostyryl dyes

PCILO computations have been carried out on the conformations of five p-dimethylaminostyryl dyes derived from quinoline-4 (I), quinoline-2 (II), pyridine-4 (III), pyridine-2 (IV) and benzothiazole (V). The stable conformations of I–IV are found to be nonplanar, while V is almost planar. The results have been explained in terms of various possible steric interactions.     

The Molecular Structure of gauche‐1,3‐Butadiene: Experimental Establishment of Non‐planarity

The planarity of the second stable conformer of 1,3‐butadiene, the archetypal diene for the Diels–Alder reaction in which a planar conjugated diene and a dienophile combine to form a ring, is not established. The most recent high level calculations predicted the species to adopt a twisted, gauche structure owing to steric interactions between the inner terminal hydrogens rather than a planar, cis structure favored by the conjugation of the double bonds. The structure cis‐1,3‐butadiene is unambiguously confirmed experimentally to indeed be gauche with a substantial dihedral angle of 34°, in excellent agreement with theory. Observation of two tunneling components indicates that the molecule undergoes facile interconversion between two equivalent enantiomeric forms. Comparison of experimentally determined structures for gauche‐ and trans‐butadiene provides an opportunity to examine the effects of conjugation and steric interactions.     

Hybrid QM/MM studies on energetics of malonaldehyde in condensed phase

Energetics of eight enol isomers of a malonaldehyde (MA) at the ground state in CCl₄ solvent environment have been investigated using a hybrid quantum mechanical (QM)/molecular mechanics (MM) method. It is found that relative energies of the isomers slightly change due to interactions between MA and surrounding atoms. In an isolated environment all eight isomers have stable planar structure. On the other hand, most of the isomers have nonplanar structure in CCl₄ whose interactions with the solute molecules are, however, weak. Mainly, structural changes are found in the H? O? C?C dihedral angle ?_{H? O? C?C}, i.e., a hydrogen atom that is connected directly with an oxygen atom, is located at a nonplanar position, and other atoms remain almost planar. Vertical excitation energies of low‐lying excited states at the resultant optimized structure of each isomer are evaluated. The vertical excitation energies in CCl₄ are almost the same as those in the isolated environment, but some changes were found in the triplet excitation states. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004