Nonlinear dielectric effect (NDE) and molecular orbital study of the conformational equilibrium in 1,4-dimethoxybenzene in benzene solution

The conformational equilibrium in 1,4-dimethoxybenzene (1,4-DMB) in benzene solutions has been studied. On the basis of experimental values of the nonlinear dielectric effect (NDE) parameter, electric permittivity and density, determined in this work, and applying the general statistical theory of NDE, the contributions of the syn-anti and syn-syn conformers and the electric dipole moment of the polar syn-syn conformer were calculated. The molecular orbital method (PM3) has also been applied for calculation of the dipole moments and energies of particular conformers. The results of the NDE study and PM3 calculations are consistent and they reveal the existence of two conformers (syn-anti and syn-syn) of comparable energy values, but different values of dipole moments, and the predominance of the polar form (syn-syn) of the mole fraction in benzene. Moreover, the energies of intermolecular interactions have been determined from the concentration dependence of linear and nonlinear polarisability.     

A comparative semi-empirical study of the effect of ring ortho-substitution on the conformation of diphenylamine

An extensive theoretical study of the structural and energy properties of diphenylamine (DPA) and derivatives was carried out. The effect of ring substitution on geometrical parameters, inversion barriers and ionisation potentials was investigated for rings containing methyl, methoxy and chloro groups. The dihedral angles between phenyl rings and pyramidality of the nitrogen atom were also studied. Results were compared to the optimised geometry of the unsubstituted DPA. Calculations were carried out using the AM1 semi-empirical method.     

A molecular mechanics and ab initio prediction of the 1H chemical shifts of pinanes

Molecular mechanics calculations plus the application of a refined Karplus equation gave the conformations of 19 pinanes. These range from a Y‐shaped geometry in the apopinene and α‐pinene series to a pseudo chair conformation in β‐pinene, nopinone and verbanone, a flattened chair in pinocarvone and the pinocarveols and a distorted Y shape for iso‐verbanone. These structures were then used as input to predict the ¹H chemical shifts of these compounds by semi‐empirical (¹H‐NMR spectra (HSPEC)) and ab initio gauge‐invariant atomic orbital (GIAO) calculations, the latter at the B3LYP hybrid density functional theory level using 6‐31++G** basis set. The two methods gave generally good agreement with the 184 observed shifts with root mean square (RMS) errors 0.07 ppm (HSPEC) and 0.10 ppm (GIAO), but the GIAO calculations gave several significant (>0.25 ppm) errors. One was for the H₃ proton in apopinenone and other α,β unsaturated ketones; the others occurred for protons in close proximity to hydroxyl groups. To provide more information, smaller analogues of known geometry and chemical shifts were subject to the same analysis. In cyclopentenone, the Gaussian geometry gave good agreement with the observed shifts, but the MMFF94, MMX and MM3 geometries all gave errors for different protons. These results show clearly that the molecular geometries of the α,β unsaturated ketones are responsible for the errors. The errors for the alcohols were examined using ethanol as model and were shown to be due to the different possible conformations of the OH group. Similar GIAO calculations on substituted methanes gave good agreement for the methyl compounds but poor agreement for di and tri halosubstituted methanes. The aforementioned method of molecular mechanics plus GIAO calculations is shown to be a very useful tool for the investigation of molecular geometries and conformations. However, multihalogen compounds may require different basis sets for accurate calculations. Copyright © 2017 John Wiley & Sons, Ltd.     

Dynamic NMR study on the trans-fused eight-membered ether ring model representing G ring of brevetoxin A

Conformational analysis of the trans-fused eight-membered ether ring model (2) representing G ring of brevetoxin A (1) was carried out by dynamic NMR study in combination with molecular mechanics calculations.     

Electronic and steric substituent influences on the conformational equilibria of cyclohexyl esters: the anomeric effect is not anomalous!

The cyclohexyl esters of a series of carboxylic acids, RCO₂H, spanning a range of electronegativities and quotients of steric hindrance for the R substituent (R=Me, Et, iPr, tBu, CF₃, CH₂Cl, CHCl₂, CCl₃, CH₂Br, CHBr₂, and CBr₃) were prepared. Their conformational equilibria in CD₂Cl₂ were examined by low‐temperature ¹H NMR spectroscopy to study the axial or equatorial orientation of the ester functionality with respect to the adopted chair conformation of the cyclohexane ring. The ab initio and DFT geometry‐optimized structures and relative free energies of the axial and equatorial conformers were also calculated at the HF/6‐311G**, MP2/6‐311G**, and B3LYP/6‐31G** levels of theory, both in the gas phase and in solution. In the latter case, a self‐consistent isodensity polarized continuum model was employed. Only by including electron correlation in the modeling calculations for the solvated molecules was it possible to obtain a reasonable correlation between ΔG°_calcd and ΔG°_exp. Both the structures and the free energy differences of the axial and equatorial conformers were evaluated with respect to the factors normally influencing conformational preference, namely, 1,3‐diaxial steric interactions in the axial conformer and hyperconjugation. It was assessed that hyperconjugative interactions, σ_{C? C}/σ_{C? H} and σ*_{C? O}, together with a steric effect—the destabilization of the equatorial conformer with increasing bulk of the R group—were the determinant factors for the position of the conformational equilibria. Thus, because hyperconjugation is held responsible as the mitigating factor for the anomeric effect in 2‐substituted, six‐membered saturated heterocyclic rings, and since it is also similarly responsible, at least partly, in these monosubstituted cyclohexanes for a preferential shift towards the axial conformer, the question is therefore raised: can the anomeric effect really be construed as anomalous?     

A quantum mechanics/molecular mechanics study of the protein-ligand interaction for inhibitors of HIV-1 integrase

Human immunodeficiency virus type-1 integrase (HIV-1 IN) is an essential enzyme for effective viral replication. Diketo acids such as L-731,988 and S-1360 are potent and selective inhibitors of HIV-1 IN. In this study, we used molecular dynamics simulations, within the hybrid quantum mechanics/molecular mechanics (QM/MM) approach, to determine the protein-ligand interaction energy between HIV-1 IN and L-731,988 and 10 of its derivatives and analogues. This hybrid methodology has the advantage that it includes quantum effects such as ligand polarisation upon binding, which can be very important when highly polarisable groups are embedded in anisotropic environments, as for example in metal-containing active sites. Furthermore, an energy decomposition analysis was performed to determine the contributions of individual residues to the enzyme-inhibitor interactions on averaged structures obtained from rather extensive conformational sampling. Analysis of the results reveals first that there is a correlation between protein-ligand interaction energy and experimental strand transfer into human chromosomes and secondly that the Asn-155, Lys-156 and Lys-159 residues and the Mg(2+) ion are crucial to anti-HIV IN activity. These results may explain the available experimental data.     

Electrostatic effects in enzyme catalysis: a quantum mechanics/molecular mechanics study of the nucleophilic substitution reaction in haloalkane dehalogenase

Combined quantum mechanics/molecular mechanics molecular dynamics simulations have been carried out to study the cleavage of the carbon–chlorine bond in 1,2-dichloroethane catalysed by haloalkane dehalogenase from Xanthobacter Autotrophicus GJ10. The process has been compared with an adequate counterpart in aqueous solution, the nucleophilic attack of acetate anion on 1,2-dichloroethane. Within the limitations of the model, mainly due to the use of a semiempirical Hamiltonian, our results reproduce the magnitude and characteristics of the catalytic effect. Comparisons of the enzymatic and in solution potentials of mean force reveal that, irrespective of the reference state, the enzyme shows a larger affinity for the transition state. The origin of this increased affinity is found in the differences in the electrostatic pattern created by the environment in aqueous solution and in the enzyme.Proceedings of the 11th International Congress of Quantum Chemistry satellite meeting in honor of Jean-Louis Rivail     

Energy‐resolved mass spectrometry for differentiation of the fluorine substitution position on the phenyl ring of fluoromethcathinones

A reliable method for structural analysis is crucial for the forensic investigation of new psychoactive substances (NPSs). Towards this end, mass spectrometry is one of the most efficient and facile methods for the identification of NPSs. However, the differentiation among 2‐, 3‐, and 4‐fluoromethcathinones (o‐, m‐, and p‐FMCs), which are ring‐fluorinated positional isomers part of the major class of NPSs referred to as synthetic cathinones, remains a challenge. This is mostly due to their similar retention properties and nearly identical full scan mass spectra, which hinder their identification. In this study, we describe a novel and practical method for differentiating the fluorine substitution position on the phenyl ring of FMCs, based on energy‐resolved mass spectrometry (ERMS) using an electron ionization‐triple quadrupole mass spectrometer. ERMS measurements showed that the three FMC positional isomers exhibited differences in relative abundances of both the fluorophenyl cation (m/z 95) and the fluorobenzoyl cation (m/z 123). The logarithmic plots of the abundance ratio of these two cations (m/z 95 to m/z 123) as a function of the collision energy (CE) followed the order of o‐FMC < p‐FMC < m‐FMC at each CE, which allowed the three isomers to be unambiguously and reliably differentiated. The theoretical dissociation energy calculations confirmed the relationship obtained by ERMS analyses, and additional ERMS measurements of methylmethcathinone positional isomers showed that the differences in abundance among the FMCs were attributed to the differences in their collision‐induced dissociation reactivities arising from the halogen‐induced resonance effects on the phenyl ring. Moreover, the method for differentiation described herein was successfully applied to the actual samples containing seized drugs. We expect that the described methodology will also contribute significantly to the reliable and accurate structural identification of NPSs in the fields of therapeutic, clinical, and forensic toxicology.     

Effect of hetero atom on the conformational stability of the forming ring in the transition structures of Type-II ene cyclization: a theoretical study

The chair conformation of the forming ring in the transition structure, for its high stability, is usually considered for the determination of the overall stereoselectivity in a type-II ene cyclization reaction. However, present theoretical investigation reveals that the presence of a heteroatom like oxygen or nitrogen in the tether of type-II carbonyl ene cyclization stabilizes the transition structure, in which the forming ring adopts a boat conformation. Due to such stability of the boat conformer the overall stereoselectivity of some type-II reactions may differ from the expected one.     

Polar substituent effect of the ester group on conformational equilibria of O-mono-substituted cyclohexanes—the para-substituent effect in cyclohexyl benzoates

Together with the nonsubstituted reference compound, para-methoxy- and para-nitro cyclohexyl benzoates have been synthesized and their conformational equilibria studied by low temperature NMR spectroscopy and theoretical DFT calculations. The free energy differences ΔG° between axial and equatorial conformers were examined with respect to polar substituent influences on the conformational equilibrium of O-mono-substituted cyclohexane.     

The effect of thiophene ring substitution position on the properties and electrochemical behaviour of alkyne-dicobaltcarbonylthiophene complexes

A large number of Co₂(CO)_6^- and Co₂(CO)₄(L-L)-substituted alkyne complexes (L-L = dppa and dmpm) have been prepared, characterized and studied by cyclic and square-wave voltammetry. In this paper we report a comparative electrochemical study of 2,5-, 2,4-, 3,4- and 2,3-bis(trimethylsilylethynyl)thiophene dicobalt substituted alkyne complexes, in order to evaluate the extent of the electronic interaction between the “Co₂C₂” redox centres depending on the position of the alkynyl substituent on the thiophene ring.     

An ab initio study of the conformational preferences of Hoechst 33258 in gas-phase and aqueous solution environments

A quantum mechanical study of the conformational preferences of Hoechst 33258, a synthetic minor groove-binding drug, has been performed in both gas-phase and aqueous solution. Gas-phase calculations were performed at the HF/6-31G(d) and MP2/6-31G(d) levels of theory, whereas calculations in the aqueous solution phase were performed using the PCM model with the 6-31G(d) basis set. The molecule was divided into three fragments, which were submitted to a systematic and detailed conformational study. The results clearly indicate that Hoechst 33258 does not adopt a planar conformation in either the gas-phase or aqueous solution. Thus, a folded conformation is not induced by binding of the molecule to DNA, but is an intrinsic property of the compound. Received: 3 March 1998 / Accepted: 29 May 1998 / Published online 19 August 1998     

The subtle electronic effects of alkyl groups on the conformational equilibria and intramolecular hydrogen-bond strength in cis-3-alkoxycyclohexanols

(1)H NMR data for cis-3-n-propoxycyclohexanol (cis-3-PCH) and cis-3-isopropoxy-cyclohexanol (cis-3-ICH) show that a concentration increase shifts the conformational equilibrium from the diaxial (aa) conformer, stabilized by an intramolecular hydrogen bond (IAHB), to the diequatorial (ee) conformer [X(ee)=42% and 21% (at 0.01molL(-1)) to 58% and 56% (at 0.40molL(-1)), in CCl(4,) respectively] due to intermolecular hydrogen bonds (IEHB), as confirmed by IR data. The Deltanu values, obtained by IR spectra, indicated that increasing the size of the OR group [R=CH(3), CH(2)CH(2)CH(3) and CH(CH(3))(2)], increases the IAHB strength, due to an increase in the inductive effect of R group, which makes the oxygen lone pairs more available for an IAHB with OH group, in opposition to the steric effect. The percentage of ee conformer increases with the solvent basicity for cis-3-PCH and cis-3-ICH, from 48% and 36% in CCl(4) to 97% and 96% in DMSO, respectively. Values of 4.58, 6.06 and 6.33kcalmol(-1) for the IAHB strength in cis-3-PCH, cis-3-ICH and cis-3-TCH (cis-3-tert-butoxycyclohexanol), respectively, were obtained, from the theoretical data through the CBS-4M method, confirming the experimental results and indicating that the IAHB strength increases with the increasing bulk of OR substituent in this series of compounds.     

Theoretical investigation into the influence of conformational equilibria on the water-exchange process in magnetic resonance imaging contrast agents

The conformational behavior in aqueous solution of four complexes of the Eu(III) ion with bis (R–amide) derivatives (R=H, methyl, ethyl, butyl) of diethylentriamine pentacetate ligands has been characterized at the ab initio level to rationalize the experimentally observed influence of alkyl substituents on the rate of the exchange process of the water molecule coordinated to the ion with the bulk water. Calculations were performed in vacuo and for aqueous solution, the latter by using the polarizable continuum model. Geometry optimizations provide, for each system, four isomers as stable conformations, all presenting a distorted tricapped trigonal prism coordination geometry around the ion. No significant influence of the alkyl substitution on the coordination geometry, nor on the europium–water distance, was observed. Moreover, increasing the length of the alkyl chain had no significant effect on the relative isomer population in solution. Thus, these results lead us to suppose that other effects, like those deriving from lateral chain folding in solution, should be considered to explain the increased rate of the water-exchange process with alkyl chain lengthening.Contribution to the Jacopo Tomasi Honorary Issue     

(±)Alkyl 3-hydroxy-1-azabicyclo[2.2.2]octane-3-carboxylates: conformational preferences of the alkoxycarbonyl group

Molecular mechanics, ab initio (RHF) and density functional (DFT/B3LYP) methods are applied to investigate the conformational preferences of the methoxycarbonyl group of the (±)methyl 3-hydroxy-1-azabicyclo[2.2.2]octane-3-carboxylate. ¹H and ¹³C chemical shifts are also calculated by the GIAO/DFT approach and compared with experimental values. Both theoretical and experimental data account for almost eclipsed conformations with different degrees of distortion from the ideal geometry. It is found that calculations at the B3LYP/6-311G(d,p) level are relatively more reliable to explain the behaviour of the alkoxycarbonyl moiety of 2-hydroxyesters derived from the (±)3-hydroxy-1-azabicyclo[2.2.2]octane-3-carboxylic acid.     

Solvent effect on the syn/anti conformational stability: A comparison between conformational bias Monte Carlo and molecular dynamics methods

The solvent effect on the syn/anti population ratio of the mesityl oxide (MOx) was investigated using a new implementation of conformational bias Monte Carlo (CBMC) and molecular dynamics (MD) methods. It was observed by a previous theoretical work (Theor. Chem. Acc. (2012) 131:1214) that in gas-phase the MOx exists dominantly in syn-form and in aqueous solution in anti-form. The syn/anti free energy difference in the gas phase was used in the intramolecular parametrization and a rotational barrier of approximately 10 kcal mol⁻¹ was found. Molecular systems with barriers of this order of magnitude have been studied by experimental techniques. However, they have not been discussed yet comparing CBMC and MD simulations. In this work, we show that the intramolecular geometrical information such as bond lengths, angles and torsional angles sampled with CBMC and MD methods are equivalent. Nonetheless, only the CBMC simulations sample appropriately the syn/anti population ratio. With the CBMC configurations in gas phase, it was obtained 95% in syn-form and 5% in anti-form regardless the initial conformation. An inversion of the population was found in water, 25% in syn-form and 75% in anti-form. Comparing the gas phase and in-water CBMC sampling, it was observed that the MOx spends typically approximately 110 successive MC cycles in anti-form and approximately 2300 in syn-form in gas phase. While it was much larger with explicit water, approximately 400 times more for anti-form and approximately 6 times more for syn-form. We argue that this strong stabilization of the anti-form in aqueous solution, does not come from the MOx-water hydrogen bonds interactions, because they are the same for both conformations. Instead, the stabilization comes from the dipole-dipole interaction caused by a larger dipole moment of the MOx in the anti-form, 7.2 D, than in the syn-form, 5.2 D. With the MD sampled configurations in both conditions, we observe that the syn/anti conformational change is a very rare event due to the rotational barrier, which is approximately 17 times larger than the thermal energy. Therefore, the MD sampling of the MOx is not appropriated because it is strongly dependent on the initial conformation even for large simulations with 150 ns up to 400 ns for the isolated solute and for solute–solvent systems.     

In situ FT-IR spectroscopic study on the conformational changes of isotactic polypropylene in the presence of supercritical CO2

The conformational changes of isotactic polypropylene (iPP) under supercritical CO₂ condition with different pressure and temperature have been carefully studied by in situ Fourier-transform infrared spectroscopy (FT-IR). Analysis of the corresponding spectra shows that the conformational ordering by supercritical CO₂ results in the intensity enhancement of the regularity bands of iPP. Due to the high CO₂ concentration and strong intermolecular interaction, iPP can reach an equilibrium state in a short time at high CO₂ pressure. The equilibrium time increases with soaking temperature. After supercritical CO₂ treatment, two mechanisms, the formation of short helix from amorphous phase and the extension of short helix into long one, happen simultaneously. The latter mechanism undergoes quickly at the beginning of induced conformational changes and then slows down, resulting in the slight increase of crystallinity. At the same time, the conformational ordering in amorphous phase happens continuously until a thermodynamic equilibrium. In summary, in the presence of supercritical CO₂, the conformational ordering of iPP chains occurs exclusively in the amorphous region, with no impact on the crystal part.     

Effect of substitution on the bonding in He dimer confined within dodecahedrane: A computational study

The effect of substitution in the dodecahedrane (C₂₀H₂₀) cage on bonding in the confined He dimer is analyzed. The He He distances inside the halogenated dodecahedrane C₂₀X₂₀ (X = F Br) cages are found to be less than half of that in the free He dimer. Comparing the equilibrium structure of He₂@C₂₀H₂₀ with He₂@C₂₀X₂₀ at ωB97XD/def2-TZVPP level, it is found that the He-He distances are relatively larger in the latter cases indicating the influence of halogen groups on the interaction between the cage and the trapped He pair. The viability of the He₂@C₂₀X₂₀ complexes is reflected in the presence of a very high activation energy barrier against the thermochemically feasible dissociation process producing free He₂ and C₂₀X₂₀. Quantum theory of atoms in molecules (QTAIM) approach reveals a partial covalent interaction between He pair.