Selective Binding of Imidazolium Cations in Building Multi‐Component Layers

Addition of 1‐alkyl‐3‐methylimidazolium (C_n‐mim) cations 3 – 5 to a mixture of bis‐phosphonium cation 2 and sodium p‐sulfonatocalix[4]arene ( 1 ) in the presence of lanthanide ions results in the selective binding of an imidazolium cation into the cavity of the calixarene. The result is a multi‐layered solid material with an inherently flexible interplay of the components. Incorporating ethyl‐, n‐butyl‐ or n‐hexyl‐mim cations into the multi‐layers results in significant perturbation of the structure, the most striking effect is the tilting of the plane of the bowl‐shaped calixarene relative to the plane of the multi‐layer, with tilt angles of 7.2, 28.9 and 65.5°, respectively. The lanthanide ions facilitate complexation, but are not incorporated into the structures and, in all cases, the calixarene takes on a 5? charge, with one of the lower‐rim phenolic groups deprotonated. ROESY NMR experiments and other ¹H NMR spectroscopy studies establish the formation of 1:1 supermolecules of C_n‐mim and calixarene, regardless of the ratio of the two components, and indicate that the supermolecules undergo rapid exchange on the NMR spectroscopy timescale.     

Synthesis by ring closing metathesis and properties of an electroactive calix[6]arene [2]catenane

Abstract

Tris-(N-phenylureido)-calix[6]arenes are heteroditopic non-symmetric molecular wheels that, in apolar media, bind viologen-based molecular axles in a pseudorotaxane-type fashion. Because of the precise kinetic requirements associated with the threading process, in apolar solvents, the dicationic portion of the axle enters the calixarene annulus exclusively from the upper rim. With the general aim to develop new prototypes of molecular devices and machines whose functions could be governed through a wider set of control elements, we envisaged that the unique properties of these calixarene wheels could be transferred to the synthesis of new catenanes for the construction of unidirectional rotary motors. Herein, we describe the synthesis of a tris(N-phenylureido)calix[6]arene-based catenane by applying the intramolecular ring-closing metathesis reaction for the catenation step on a pre-formed pseudorotaxane.     

Fluorescent chemosensors based on a new type of lower rim-dansylated and bridge-substituted calix[4]arenes

The synthesis, structural and chemosensing properties of several lower rim-dansylated calix[4]arenes bearing different methylene bridge substituents are described. Compared to bridge-unsubstituted pendants neither the conformational nor the fluorescence characteristics of the calixarene core are perceptibly influenced by the bridge substituent. X-ray structure as well as NMR measurements indicates the lower rim-propoxylated and-dansylated calixarenes to adopt the cone conformation capable of the complexation of Cu²⁺ ions at micromolar level. Fluorescent measurements point to selective 1:2 calixarene: Cu²⁺ complex formation with sensing parameters being of a suitable level to make the use as a potentially immobilisable chemosensor for the detection of Cu²⁺ ions promising.     

Intramolecular co-operative hydrogen bond in calix[<Emphasis Type="Italic">n</Emphasis>]arenes (<Emphasis Type="Italic">n</Emphasis> = 4, 6, 8) bearing bulky substituents

Based on the Fourier transform IR spectroscopy together with the published NMR and X-ray data, it was shown that cyclic co-operative intramolecular hydrogen bond in calix[n]arene (n = 4, 6, 8) molecules is mainly responsible for their conformational state irrespective of the presence or absence of bulky substituents at the upper rim of the molecules. In accordance with the size of a macrocycle (n = 4, 6, 8), the stable conformation, secured by such a hydrogen bond, constitutes a cone, a pinched cone, and a pleated loop, respectively. The new, potentially competing system of hydrogen bonds in calix[6]arenes with 3-carboxymethyl-1-adamantyl substituents does not affect the conformational state of the macrocycle and its H-bonding. Six carboxy groups at the upper rim form in pairs three cyclic dimers, which does not disturb the hydrogen bonds of the hydroxy groups and the conformation of the macrocycle. In addition, the cavity of the molecule is considerably enlarged. The removal or rearrangement of the guest molecules in the solid calixarene by heating up to 180 °C only slightly affects the conformational state of macrocycles bearing bulky substituents, whereas in calixarenes devoid of such substituents, the similar procedure leads to somewhat of a distortion of the macrocycles (judging from the IR spectral indications of hydrogen bonding). Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1062–1068, June, 2007.     

Electronic Transitions in Conformationally Controlled Peralkylated Hexasilanes

The photophysical properties of oligosilanes show unique conformational dependence due to σ‐electron delocalization. The excited states of the SAS, AAS, and AEA conformations of peralkylated n‐hexasilanes, in which the SiSiSiSi dihedral angles are controlled into a syn (S), anti (A), or eclipsed (E) conformation, were investigated by using UV absorption, magnetic circular dichroism (MCD), and linear dichroism spectroscopy. Simultaneous Gaussian fitting of all three spectra identified a minimal set of transitions and the wavenumbers, oscillator strengths, and MCD B terms in all three compounds. The results compare well with those obtained by using the symmetry‐adapted‐cluster configuration interaction method and almost as well with those obtained by time‐dependent density functional theory with the PBE0 functional. The conformational dependence of the transition energies and other properties of free‐chain permethylated n‐hexasilane, n‐Si₆Me₁₄, was also examined as a function of dihedral angles, and the striking effects found were attributed to avoided crossings between configurations of σσ* and σπ* character.     

Quantum mechanical calculations of conformationally relevant 1H and 13C NMR chemical shifts of N-, O-, and S-substituted calixarene systems

QM GIAO calculations of (13)C and (1)H chemical shift values of the ArCH(2)Ar group in N-, O-, and S-substituted calixarene systems were performed with a hybrid DFT functional MPW1PW91 and 6-31G(d,p) basis set. A good reproduction of experimental data was obtained for some representative calixarenes and for a series of simplified calixarene models. This allowed the derivation of chemical shift surfaces versus phi and chi dihedral angles. The applicability of chemical shift surfaces in the study of calixarene conformational features is illustrated.     

Prediction of drug solubility from molecular structure using a drug-like training set

Using a training set of 191 drug-like compounds extracted from the AQUASOL database a quantitative structure-property relationship (QSPR) study was conducted employing a set of simple structural and physicochemical properties to predict aqueous solubility. The resultant regression model comprised five parameters (ClogP, molecular weight, indicator variable for aliphatic amine groups, number of rotatable bonds and number of aromatic rings) and demonstrated acceptable statistics (r ² = 0.87, s = 0.51, F = 243.6, n = 191). The model was applied to two test sets consisting of a drug-like set of compounds (r ² = 0.80, s = 0.68, n = 174) and a set of agrochemicals (r ² = 0.88, s = 0.65, n = 200). Using the established general solubility equation (GSE) on the training and drug-like test set gave poorer results than the current study. The agrochemical test set was predicted with equal accuracy using the GSE and the QSPR equation. The results of this study suggest that increasing molecular size, rigidity and lipophilicity decrease solubility whereas increasing conformational flexibility and the presence of a non-conjugated amine group increase the solubility of drug-like compounds. Indeed, the proposed structural parameters make physical sense and provide simple guidelines for modifying solubility during lead optimisation.     

Force-field parametrization and molecular dynamics simulations of p-menthan-3,9-diols: a family of amphiphilic compounds derived from terpenoids

A set of amphiphilic p-menthan-3,9-diols have been investigated by molecular dynamics simulations. These are four stereoisomers than can be specifically obtained from two terpenoids widely used in biorganic chemistry. For this purpose, the p-menthan-3,9-diols have been explicitly parametrized using both semiempirical and ab initio quantum mechanical calculations. The reliability of these parameters has been validated by predicting different molecular and thermodynamic properties. Molecular dynamics simulations in aqueous solution have been performed with the new parameters. The results provide useful insights about the conformational properties of this family of compounds and the formation of intra- and intermolecular hydrogen bonds.     

Quantum mechanical calculations of conformationally relevant 1H and 13C NMR chemical shifts of calixarene systems

[graphs: see text] QM GIAO calculations of 13C and 1H chemical shift values of the ArCH2Ar group have been performed, using the hybrid DFT functional MPW1PW91 and the 6-31G(d,p) basis set, on some representative calixarenes and on a series of simplified calixarene models allowing derivation of chemical shift surfaces versus phi and chi dihedral angles. A good reproduction of experimental data was obtained. The applicability of chemical shift surfaces in the study of calixarene conformational features is illustrated.     

MC(JBW): Simple but smart Monte Carlo algorithm for free energy simulations of multiconformational molecules

Many of the most common molecular simulation methods, including Monte Carlo (MC) and molecular or stochastic dynamics (MD or SD), have significant difficulties in sampling the space of molecular potential energy surfaces characterized by multiple conformational minima and significant energy barriers. In such cases improved sampling can be obtained by special techniques that lower such barriers or somehow direct search steps toward different low energy regions of space. We recently described a hybrid MC/SD algorithm [MC(JBW)/SD] incorporating such a technique that directed MC moves of selected torsion and bond angles toward known low energy regions of conformational space. Exploration of other degrees of freedom was left to the SD part of the hybrid algorithm. In the work described here, we develop a related but simpler simulation algorithm that uses only MC to sample all degrees of freedom (e.g., stretch, bend, and torsion). We term this algorithm MC(JBW). Using simulations on various model potential energy surfaces and on simple molecular systems (n-pentane, n-butane, and cyclohexane), MC(JBW) is shown to generate ensembles of states that are indistinguishable from the canonical ensembles generated by classical Metropolis MC in the limit of very long simulations. We further demonstrate the utility of MC(JBW) by evaluating the room temperature free energy differences between conformers of various substituted cyclohexanes and the larger ring hydrocarbons cycloheptane, cyclooctane, cyclononane, and cyclodecane. The results compare favorably with available experimental data and results from previously reported MC(JBW)/SD conformational free energy calculations. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1736–1745, 1998     

The application of molecular mechanics to the structures of carbohydrates

A study is reported of the accuracy with which the geometries of pyranose and methyl pyranoside molecules are predicted by molecular mechanics. Calculations of the conformational energies of the model compounds dihydroxymethane, methoxymethanol, and dimethoxymethane, made with the program MMI, produced results that compare well with previous ab initio molecular orbital calculations. This indicates that MMI gives a satisfactory account of the energetic and conformational aspects of the anomeric effect, a conclusion further supported by calculations on 2-methoxytetrahydropyran. The prediction of the observed preferred conformations of the primary alcohol group in aldohexopyranoses appears to be less satisfactory. MMI-CARB, a version of MMI with changes in some of the equilibrium C? O bond lengths of the program, has been used to calculate the geometries of 13 pyranose and methyl pyranoside molecules, the crystal structures of which have been studied by neutron diffraction. When the C? C? O? H torsion angles are constrained to approximately the values observed in the crystal structures, good agreement is obtained between the theoretical and experimental molecular geometries. The rms deviation for C? C and C? O bonds, excluding those significantly affected by thermal motion in the crystal structure determinations, is 0.005 Å. Corresponding figures for the valence angles that do not involve hydrogen atoms and for the ring torsion angles are 1.2° and 2.0°, respectively. The Cremer and Pople puckering parameters for the pyranose rings are reproduced within 0.026 Å in Q and 5.4° in θ.     

Synthesis of a Novel Class of Carbohydrate‐Containing Calix[4]resorcinarene Adopting an Asymmetrical Diamond Structure

A novel type of calixsugars, containing sugar moieties at the methine bridges of the calixarene is introduced. These calixsugars were prepared via a nonconvergent stepwise fragment condensation. Four new stereogenic centers were formed simultaneously, and only one diastereoisomer 5 was isolated. The condensation procedure is remarkably mild allowing for a large diversity of labile groups to be used. The solution structure of calixarene 5 with two D ‐glucose and two hexyl moieties was determined by NMR spectroscopy by means of NOEs and coupling constants for molecular dynamics (MD). Chemical shifts were used to validate the conformation with the least NOE and J violations. The structure of calixsugar 5 has the configuration rctc referring to one sugar residue (r=reference, c=cis, t=trans) and adopts a diamond conformation for the macrocyclic backbone with the two sugar moieties axial on opposite sides of the macrocyclic ring and the two hexyl groups on the same side.     

Synthesis and characterization of new calixarene-chitosan polymers

Triflate Ester of Calix[n]arene (n = 4, 6, 8) (TEC[n] (n = 4, 6, 8)) were synthesized based on a new synthetic route, then TEC[n] (n = 4, 6, 8) were further modified by reacting with low molecular weight Chitosan (CS) to get three kinds of new Calix[n]arene-Chitosan polymers (n = 4, 6, 8) (C[n]CSP (n = 4, 6, 8)) through Buchwald-Hartwig cross coupling reaction. The structures of the polymers were characterized by FT-IR, SEM, Elemental analyzer and ¹³C SSNMR. And the results found that Chitosan was successfully introduced to Calix[n]arene (n = 4, 6, 8) (C[n] (n = 4, 6, 8)) without any long-chain alkyl between Chitosan and Calixarene. These new polymers are partially substituted calixarene. The substitute degree of C[4]CSP, C[6]CSP and C[8]CSP is 17.75%, 21.08% and 54.53% respectively. And the optimal preparation conditions were discussed and the results were listed as following, molar ratio (1:2), catalyst (0.05 mmol), solvent ratio (1:1.5 (10 mL?1.0 mmol^?1)) and reaction time (5h).     

Third-order interaction approximation for linear polymer chains

Third-order interactions imposed by a pair of atoms separated by five bonds are taken into account in computations of the mean-square end-to-end distance and the mean-square radius of gyration for linear polymer chains. The statistical weight matrices are established on the basis of the rotational isomeric state model. The conformational energy of n-hexane is calculated as a function of the C? C bond rotation angles. The third-order interaction energy is obtained by comparison with that of n-pentane. The characteristic ratio of polymethylene is 6.6 in the third-order interaction approximation, which is in agreement with experimental data.     

Alternative expressions for energies and forces due to angle bending and torsional energy

We have derived alternative expressions for computing the energies and forces associated with angle bending and torsional energy terms commonly used in molecular mechanics and molecular dynamics computer programs. Our expressions address the problems of singularities that are intrinsic in popular angle energy functions and that occur from other chain rule derivations of force expressions. Most chain rule derivations of expressions for Cartesian forces due to angle energies make use of relations such as where ? is a bond or torsion angle, E(?) is energy, and ?/?x represents a derivative with respect to some Cartesian coordinate. This expression leads to singularities from the middle term, ?1/sin ?, when ? is 0 or π. This is a problem that prevents the use of torsional energy expressions that have phase angles, ?°, other than 0 or π, such as in E(?) = κ[1 + cos(n? ? phsi;°)]. Our derivations make use of a different, but equivalent, form of the chain rule: This form still possesses singularities for the bond angle forces since the last factor is undefined when ? is 0 or π. However, the alternate form may be used to great advantage for the torsional angle forces where no such problem arises. The new expressions are necessary if one desires the use of torsional energy expressions with general phase angles. Even for energy expressions in common use, i.e., with phase angles of 0 or π, our force expressions are as computationally efficient as the standard ones. The new expressions are applicable to all molecular simulations that employ restrained, or phase-shifted, torsional angle energy expressions.     

A Method to Explore Protein Side Chain Conformational Variability Using Experimental Data

Experimentally measured values of molecular properties or observables of biomolecules such as proteins are generally averages over time and space, which do not contain su?cient information to determine the underlying conformational distribution of the molecules in solution. The relationship between experimentally measured NMR ³J‐coupling values and the corresponding dihedral angle values is a particularly complicated case due to its nonlinear, multiple‐valued nature. Molecular dynamics (MD) simulations at constant temperature can generate Boltzmann ensembles of molecular structures that are free from a priori assumptions about the nature of the underlying conformational distribution. They suffer, however, from limited sampling with respect to time and conformational space. Moreover, the quality of the obtained structures is dependent on the choice of force ?eld and solvation model. A recently proposed method that uses time‐averaging with local‐elevation (LE) biasing of the conformational search provides an elegant means of overcoming these three problems. Using a set of side chain ³J‐coupling values for the FK506 binding protein (FKBP), we ?rst investigate the uncertainty in the angle values predicted theoretically. We then propose a simple MD‐based technique to detect inconsistencies within an experimental data set and identify degrees of freedom for which conformational averaging takes place or for which force ?eld parameters may be de?cient. Finally, we show that LE MD is the best method for producing ensembles of structures that, on average, ?t the experimental data.     

The chain configurational properties of novolak p-cresol–formaldehyde resins

Rotational isomeric state chain configurational analysis has been applied to the p-cresol–form-aldehyde chain structure. Steric interference allows the chain to be considered by using a twofold potential energy barrier. The bond rotational angles and conformational energies were set empirically to fit existing experimental dipole moment data, and the conformational angles were ±45° with a 132 cal/mole energy barrrier separating the g^±g^± from the g^±g^± rotational states. The data predict the existence of a cyclic tetramer in support of other researchers' experimental work. The limiting dipole moment ratio and characteristic ratio were computed to be 5.87 and 21.23, respectively. Support for this structure will have to wait for experimental data from higher-molecular-weight materials.     

Molecular modeling studies of novel heteroarotinoids

The molecular structure and conformational properties of structurally related oxo and thio heteroarotinoids have been calculated by employing AM1 molecular orbital and both MM2P and Chem-X “optimize” molecular mechanics methods, and the results have been compared with crystal structure data. For the cis and trans oxo heteroarotinoids, MM2P gives values of the bridge torsion angles ?₁ and ?₂ in closest agreement with the crystal structure, and all three computational methods yield values of ?₁ and ?₂ within about 10° of that found in the crystal structures. All three computational methods locate a minimum-energy conformation for the trans isomer corresponding to the two bridged aryl rings being mutually perpendicular, in agreement with the crystal structure and similar to that found for the structurally analogous trans-stilbene. The calculated heteroring geometries also reproduce the twist-sofa conformation observed for the crystal structure. Calculated conformational energies versus ?₁ and ?₂ indicate broad energy wells about the minimum-energy conformation with barriers to rotation at the planar and perpendicular conformations, and with higher barriers found for the more sterically congested cis isomer. The corresponding cis and trans thio heteroarotinoids exhibit conformational properties similar to their oxo analogues. Both AM1 and MM2P fare poorly in reproducing the crystal structure values of the sulfur-containing bond lengths and bond angles. The C-S bonds found in these thio heteroarotinoids may possess more double-bond character than accounted for in the calculations. Also, the results suggest that the MM2P sulfur-related force-field parameters adopted for these calculations may require further refinement.