MM2 Force Research Articles

Comparison of gas–solid chromatography and MM2 force field molecular binding energies for greenhouse gases on a carbonaceous surface

Gas–solid chromatography was used to determine B 2s (gas–solid virial coefficient) values for eight molecular adsorbates interacting with a carbon powder (Carbopack B, Supelco). B 2s values were determined by multiple size variant injections within the temperature range of 313–553 K. The molecular adsorbates included: carbon dioxide (CO 2); tetrafluoromethane (CF 4); hexafluoroethane (C 2F 6); 1,1-difluoroethane (C 2H 4F 2); 1-chloro-1,1-difluoroethane (C 2H 3ClF 2); dichlorodifluoromethane (CCl 2F 2); trichlorofluoromethane (CCl 3F); and 1,1,1-trichloroethane (C 2H 3Cl 3). Two of these molecules are of special interest because they are “super greenhouse gases”. The global warming potential, GWP, for CF 4 is 6500 and for C 2F 6 is 9200 relative to the reference value of 1 for CO 2. The GWP index considers both radiative blocking and molecular lifetime. For these and other industrial greenhouse gases, adsorptive trapping on a carbonaceous solid, which depends on molecule–surface binding energy, could avoid atmospheric release. The temperature variations of the gas–solid virial coefficients in conjunction with van’t Hoff plots were used to find the experimental adsorption energy or binding energy values ( E *) for each adsorbate. A molecular mechanics based, rough-surface model was used to calculate the molecule–surface binding energy (Ecal *) using augmented MM2 parameters. The surface model consisted of parallel graphene layers with two separated nanostructures each containing 17 benzene rings arranged in linear strips. The separation of the parallel nanostructures had been optimized in a prior study to appropriately represent molecule–surface interactions for Carbopack B. Linear regressions of E * versus Ecal * for the current data set of eight molecules and the same surface model gave E * = 0.926Ecal * and r 2=0.956. A combined set of the current and prior Carbopack B adsorbates studied (linear alkanes, branched alkanes, cyclic alkanes, ethers, and halogenated hydrocarbons) gave a data set with 33 molecules and a regression of E * = 0.991Ecal * and r 2=0.968. These results indicated a good correlation between the experimental and the MM2 computed molecule–surface binding energies.

Molecular Simulation Study of Hexane Diffusion in Dynamic Metal‐Organic Frameworks

AbstractThe modified MM3 force field for describing flexible IRMOF‐1 was extended to include other IRMOFs, and a molecular dynamics simulation study was performed on hexane diffusion in IRMOF‐1 and IRMOF‐16. The self‐diffusion coefficients and diffusion pathways of hexane, as well as the mobility of the frameworks were investigated, as a function of both temperature and loading. The results revealed that the diffusion pathway of hexane was largely influenced by loading, and the flexibility of IRMOF‐16 was much larger than that of IRMOF‐1. The microscopic information obtained is useful for understanding the diffusion mechanism of chain molecules in dynamic MOF.

Ionic Hydrogen-Bond Networks and Ion Solvation. 1. An Efficient Monte Carlo/Quantum Mechanical Method for Structural Search and Energy Computations: Ammonium/Water

Hydrogen-bond networks about solvated ions can form many alternative structures, requiring extensive conformational searches with accurate but affordable energy computation. For this purpose we are combining Monte Carlo searches with a computationally efficient density-functional-based tight-binding (DFTB+) method. The approach is tested for the stepwise hydration energies of the ammonium ion in NH(4)(+)(H(2)O)(n) clusters (n = 1-8), for which experimental data are available. For each cluster size n, we perform Monte Carlo searches, where for each conformation we calculate the minimized energy using the DFTB+ method (and, for comparison, using MM3 or OPLS-AA force field). The Monte Carlo/DFTB+ search identifies the lowest energy structure that can be reoptimized with other quantum mechanical methods (here with HF, B3LYP, B3PW91, MP2, DFT, and CBS-Q, CBS-QB3, and CBS-APNO methods). Calculated geometries and charge densities for the clusters are also presented. The results show that the binding energies calculated by the DFTB+ method reproduce the values measured experimentally and predicted by highly correlated, but significantly more computationally intensive, ab initio quantum chemical methods. The encouraging results suggest that the Monte Carlo/DFTB+ approach is a computationally efficient quantum chemical method for relatively large solvated systems, as demonstrated here for cluster ions.

キラルリチウムアミド反応剤を用いた２-シクロヘキセン-１-オールの立体選択的不斉合成反応の反応中間体および遷移状態の構造：ＭＭ３分子力場による立体選択性の理論的予測

キラルリチウムアミド反応剤を用いた２-シクロヘキセン-１-オールの立体選択的不斉合成反応の反応中間体および遷移状態の構造：ＭＭ３分子力場による立体選択性の理論的予測

A theoretical IR spectroscopic study based on DFT calculations for free mn-15S 2O 3 maleonitrile-dithiacrown ether compound

The theoretically possible stable conformers of free mn-15S 2O 3 maleonitrile-dithiacrown ether molecule were searched by means of a conformational study which consists of molecular dynamics and energy minimization calculations performed with MM2 force field and successive geometry optimization + frequency calculations performed first at B3LYP/3-21G and then at B3LYP/6-31G(d) levels of theory. The obtained calculation results have clearly indicated that the free molecule in electronic ground state is very flexible and accordingly has many possible stable conformers of different conformational properties at room temperature; among them, the one having a macrocyclic ring structure in which all of the ether units oriented toward the center of the ring was determined the energetically most preferable conformer. In addition, the equilibrium geometrical parameters, vibrational normal modes and associated IR spectral data of the determined most stable three conformers of the molecule were calculated at B3LYP/6-31+G(d) and B3LYP/6-31++G(d,p) levels of theory. A successful assignment of the fundamental bands observed in the recorded experimental solid phase and solution phase IR spectra of the molecule was achieved in the light of the theoretical data obtained from these DFT calculations. To fit the calculated harmonic wavenumbers to the experimental ones, two different scaling procedures, referred to as “Scaled Quantum Mechanical Force Field (SQM FF) methodology” and “Scaling wavenumbers with empirical dual scale factors”, were proceeded independently.

Application of the ONIOM-Molecular Dynamics Method to the Organometallic Reaction Cis-(H)2Pt(PR3)2 → H2 + Pt(PR3)2 (R = H, Me, Ph, and t-Bu). An Insight into the Dynamical Environmental Effects

The ONIOM-molecular dynamics (MD) method, which we recently developed, is applied to one of representative organometallic reactions, cis-(H)2Pt(PR3)2 --> H2 + Pt(PR3)2(R=H, Me, Ph, and t-Bu) to give an insight into the dynamical effects of the environment on the reaction. We adopted the two-layered ONIOMmethodology and divided the system into the inner part of cis-(H)2Pt(PH3)2 and the outer part of the others.The inner and outer parts are treated by the quantum mechanics (QM) method at the HF level of theory and the molecular mechanics (MM) method with the MM3 force field, respectively. The ONIOM-MD simulations how that the thermal motion of the outer part increases the magnitude of the energy fluctuations of the inner part and promotes the H2 elimination reaction. These dynamical environmental effects increase in the order,t-Bu > Ph > Me > H, indicating that the reactivity of cis-(H)2Pt(PR3)2 increases in the same order. These results are also supported by an equation derived from the Arrhenius' equation (Matsubara's equation). The snapshots of the reaction for R=t-Bu clearly indicate the new feature of the H2 elimination process

Molecular mechanics models for tetracycline analogs

Tetracyclines (Tcs) are an important family of antibiotics that bind to the ribosome and several proteins. To model Tc interactions with protein and RNA, we have developed a molecular mechanics force field for 12 tetracyclines, consistent with the CHARMM force field. We considered each Tc variant in its zwitterionic tautomer, with and without a bound Mg(2+). We used structures from the Cambridge Crystallographic Data Base to identify the conformations likely to be present in solution and in biomolecular complexes. A conformational search by simulated annealing was undertaken, using the MM3 force field, for tetracycline, anhydrotetracycline, doxycycline, and tigecycline. Resulting, low-energy structures were optimized with an ab initio method. We found that Tc and its analogs all adopt an extended conformation in the zwitterionic tautomer and a twisted one in the neutral tautomer, and the zwitterionic-extended state is the most stable in solution. Intermolecular force field parameters were derived from a standard supermolecule approach: we considered the ab initio energies and geometries of a water molecule interacting with each Tc analog at several different positions. The final, rms deviation between the ab initio and force field energies, averaged over all forms, was 0.35 kcal/mol. Intramolecular parameters were adopted from either the standard CHARMM force field, the ab initio structure, or the earlier, plain Tc force field. The model reproduces the ab initio geometry and flexibility of each Tc. As tests, we describe MD and free energy simulations of a solvated complex between three Tcs and the Tet repressor protein.

Porous Network Structure of Octacyano-Metal-Free Phthalocyanine on the Basal Plane of Highly Oriented Pyrolytic Graphite

We report the formation of a porous network structure of octacyno-metal-free phthalocyanine (H2Pc(CN)8) on a highly oriented pyrolytic graphite surface. The porous structure shows a quadratic packing with one void per unit cell and an average void area of 3 nm2 due to the interaction of cyano groups. The nature of the molecule−molecule interaction was established by a tip-induced molecular rearrangement and force-field simulations. Typical point (filling) defects in the porous structure suggest that this molecular layer might be used as a template for other organic molecules. Regions with high point defect densities are seen to form a close-packed phase, which is found to be developing in small islands. A modified MM2 force field was employed on different quadratic unit cells in which the azimuthal orientation and the intermolecular distance of the molecular lattice were changed to find the minimum-energy structure. Both porous network structure and close-packed phases are found in the calculations, corresponding to two minimum-energy structures in the force-field calculations. The adsorption geometries of molecules in the porous and the close-packed phases are understood by simulating them on the graphene sheet and from the calculated scanning tunneling microscope images.

Prolonged α-Tocopherol Deficiency Decreases Oxidative Stress and Unmasks α-Tocopherol-dependent Regulation of Mitochondrial Function in the Brain

Vitamin E is the major lipid-soluble chain-breaking antioxidant in mammals and plays an important role in normal development and physiology. Deficiency (whether dietary or genetic) results in primarily nervous system pathology, including cerebellar neurodegeneration and progressive ataxia (abnormal gait). However, despite the widely acknowledged antioxidant properties of vitamin E, only a few studies have directly correlated levels of reactive oxygen species with vitamin E availability in animal models. We explored the relationship between vitamin E and reactive oxygen species in two mouse models of vitamin E deficiency: dietary deficiency and a genetic model (tocopherol transfer protein, Ttp-/- mice). Both groups of mice developed nearly complete depletion of alpha-tocopherol (the major tocopherol in vitamin E) in most organs, but not in the brain, which was relatively resistant to loss of alpha-tocopherol. F4-neuroprostanes, an index of lipid peroxidation, were unexpectedly lower in brains of deficient mice compared with controls. In vivo oxidation of dihydroethidium by superoxide radical was also significantly lower in brains of deficient animals. Superoxide production by brain mitochondria isolated from vitamin E-deficient and Ttp-/- mice, measured by electron paramagnetic resonance spectroscopy, demonstrated a biphasic dependence on exogenously added alpha-tocopherol. At low concentrations, alpha-tocopherol enhanced superoxide flux from mitochondria, a response that was reversed at higher concentrations. Here we propose a mechanism, supported by molecular modeling, to explain decreased superoxide production during alpha-tocopherol deficiency and speculate that this could be a beneficial response under conditions of alpha-tocopherol deficiency.

Autoxidation of a 4-iminoimidazolidin-2-one with a tertiary 5-hydrogen to its 5-hydroxy derivative

Chemoselective autoxidation of 4-imino-1,5-dimethyl-3-(4-nitrophenyl)imidazolidin-2-one (1b) to its 5-hydroxy derivative 2 occurred in solutions of DMSO-d6, acetonitrile-d3 or refluxing ethanol. Also bis(imidazolidin-5-yl) peroxide 5 was isolated as a minor product. It crystallizes as a 1:1 mixture of R*, R* and R*, S* diastereomers, whereas the NMR spectra of the reaction solution in DMSO-d6 showed unequal amounts of the two isomers. Molecular mechanics modeling studies with the MM3 force field indicate the R*,S* diastereomer as the more stable one. The 5-unsubstituted and the 5,5-dimethyl substituted imines 1a and 1c, respectively, were found stable against autoxidation; the difference in reactivity of 1b is attributed to the single 5methyl group enhancing the population of the enamine tautomer. The 5-hydroxy-4-imino-1,5dimethylimidazolidin-2-one (2) underwent acid hydrolysis to form 5-hydroxyhydantoin 4.

Conformational Analysis of Bisphosphonate/Calcium Complex

Conformational analysis of three types of pamidronate/calcium (Ca) complex model was performed using a molecular mechanics method with a standard MM3 force field. Three types of pamidronate/Ca-complexes were designed. Namely, one calcium atom was connected to two oxygen atoms of different P-O bonds [Ca-complex (I)], one calcium atom was connected to two oxygen atoms of the same P-O bond at one end of the molecule [Ca-complex (II)], and one calcium atom was connected to two oxygen atoms of the same P-O bond at both ends of the molecule [Ca-complex (III)]. Three-dimensional imaging clearly showed the steric conformation of each compound. Ca-complex (I) showed the lowest steric energy and Ca-complex (III) showed the highest steric energy among the three types of Ca-complexes. The Ca-O bond lengths of Ca-complexes (II) and (III) were shorter than that of Ca-complex (I). The P-O bond lengths of Ca-complexes (II) and (III) were longer than that of Ca-complex (I). The O-Ca-O dihedral angles of Ca-complexes (II) and (III) decreased approximately 30% from that of Ca-complex (I). These data suggested that the Ca-complex (I) was most stable and that the structure of Ca-complex (I) had the highest possibility when pamidronate reacted with a calcium atom. The structure of Ca-complex (III) has the lowest possibility. The present results revealed the stable structures of Ca-complexes using molecular mechanics calculations, a useful tool for obtaining geometrical information about molecules.

MM3 force field prediction of the enantioselective preference in the asymmetric synthesis of a chiral 2-cyclohexen-1-ol using a chiral lithium amide reagent

Enantioselective preference in the asymmetric synthesis where cyclohexene oxide is transformed enantioselectively to chiral ( S)- or ( R)-2-cyclohexen-1-ol by the reaction with the appropriate chiral lithium amide reagent has been evaluated theoretically using the MM3 force field. The plausible possible structures for each precursor (reaction intermediate complex) leading to a ( S)- or ( R)-2-cyclohexen-1-ol have been optimized with the extended MM3 force field applicable to the lithium amide functional group, and the populations of their ( S)- or ( R)-reaction intermediate complexes at an ambient temperature (298 K) were calculated. The initial structure for evaluating the reaction intermediates of this asymmetric synthesis was constructed on the basis of the optimized ab initio transition state structure (MP2/6-31+G ∗) comprising lithium amide LiNH 2 and propene oxide. To the thus obtained transition state structure composed of LiNH 2 and propene oxide, the other remaining Cartesian coordinates for the actual reaction intermediates composed of the chiral lithium amides and cyclohexene oxide were added to make the reaction intermediate structure. The conformational search for the reaction intermediate has been carried out by using the Stochastic search Algorithm, and the optimized geometries and their conformational energies (steric energies) have been calculated by the MM3 force field. The populations calculated from the conformational energies of the reaction intermediate leading to the ( S)- or ( R)-2-cyclohexen-1-ol were shown to be linearly well correlated with the experimentally reported enantiomer excess (% ee) values. The critical factors to control the enantioselectivity were investigated on the basis of the optimized structures of the reaction intermediate complexes. The MM3 force field approach was shown to be applicable to the theoretical evaluation of the enantioselectivity and be useful for designing a new functional chiral lithium amide reagent for the asymmetric synthesis.

Influence of electronic and steric effects on stability constants and electrochemical reversibility of divalent ion complexes with glycine and sarcosine: A glass electrode potentiometric, sampled direct current polarographic, virtual potentiometric, and molecular modelling study

Cd II complexes with glycine (gly) and sarcosine (sar) were studied by glass electrode potentiometry, direct current polarography, virtual potentiometry, and molecular modelling. The electrochemically reversible Cd II–glycine–OH labile system was best described by a model consisting of M(HL), ML, ML 2, ML 3, ML(OH) and ML 2(OH) (M = Cd II, L = gly) with the overall stability constants, as log β, determined to be 10.30 ± 0.05, 4.21 ± 0.03, 7.30 ± 0.05, 9.84 ± 0.04, 8.9 ± 0.1, and 10.75 ± 0.10, respectively. In case of the electrochemically quasi-reversible Cd II–sarcosine–OH labile system, only ML, ML 2 and ML 3 (M = Cd II, L = sar) were found and their stability constants, as log β, were determined to be 3.80 ± 0.03, 6.91 ± 0.07, and 8.9 ± 0.4, respectively. Stability constants for the ML complexes, the prime focus of this work, were thus established with an uncertainty smaller than 0.05 log units. The observed departure from electrochemical reversibility for the Cd–sarcosine–OH system was attributed mainly to the decrease in the transfer coefficient α. The MM2 force field, supplemented by additional parameters, reproduced the reported crystal structures of diaqua-bis(glycinato-O,N)nickel(II) and fac-tri(glycinato)-nickelate(II) very well. These parameters were used to predict structures of all possible isomers of (i) [Ni(H 2O) 4(gly)] + and [Ni(H 2O) 4(sar)] +; and (ii) [Ni(H 2O) 3(IDA)] and [Ni(H 2O) 3(MIDA)] (IDA = iminodiacetic acid, MIDA = N-methyl iminodiacetic acid) by molecular mechanics/simulated annealing methods. The change in strain energy, Δ U str, that accompanies the substitution of one ligand by another (ML + L′ → ML′ + L), was computed and a strain energy Δ U str = +0.28 kcal mol −1 for the reaction [Ni(H 2O) 4(gly)] + + sar → [Ni(H 2O) 4(sar)] + + gly was found. This predicts the monoglycine complex to be marginally more stable. By contrast, for the reaction [Ni(H 2O) 3IDA] + MIDA → [Ni(H 2O) 3MIDA] + IDA, Δ U str = −0.64 kcal mol −1, and the monoMIDA complex is predicted to be more stable. This correlates well with (i) stability constants for Cd–gly and Cd–sar reported here; and (ii) known stability constants of ML complex for glycine, sarcosine, IDA, and MIDA.

Sc(III) porphyrins. The molecular structure of two Sc(III) porphyrins and a re-evaluation of the parameters for the molecular mechanics modelling of Sc(III) porphyrins

The crystal structures of two new Sc(III) porphyrins, [Sc(TPP)Cl]·2.5(1-chloronaphthalene), (5,10,15,20-tetraphenylporphyrin)-chloro-scandium(III)·2.5(1-chloronaphthalene) solvate, (Mo Kα, 0.71073 Å, triclinic system P 1 ¯ , a = 9.9530(2) Å, b = 15.4040(3) Å, c = 17.7770(3) Å, α = 86.5190(10)°, β = 89.7680(10)°, γ = 86.9720(10)°, 13101 independent reflections, R 1 = 0.0712) and the dimeric [μ 2-(OH) 2(Sc(TPP)) 2], bis-(μ-hydroxo)-(5,10,15,20-tetraphenylporphyrin) scandium(III) (Mo Kα, 0.71073 Å, monoclinic system C2, a = 24.2555(16) Å, b = 11.1598(7) Å, c = 25.6468(17) Å, β = 91.980(2)°, 13084 independent reflections, R 1 = 0.0485) are reported. In [Sc(TPP)Cl] the metal is five-coordinate and the porphyrin is domed with the metal displaced by 0.63 Å from the mean porphyrin towards the axial Cl − ligand. The average Sc–N bond length is 2.143(3) Å, which is shorter than the average bond length of previously reported structures. Two of the phenyl rings are nearly orthogonal to the porphyrin core and the other two are significantly tilted because of contacts with 1-chloronaphthalene solvent molecules, and the phenyl rings of neighbouring porphyrins. In [μ 2-(OH) 2(Sc(TPP)) 2] both porphyrins are domed, with the metal displaced from the mean porphyrin plane towards the bridging hydroxo ligands. The average Sc–N bond length is 2.197(12) Å, which is in the upper range of Sc–N bond lengths in known Sc(III) porphyrins but not dissimilar to the average Sc–N bond lengths in another other bis-μ 2-hydroxo Sc(III) porphyrin, [μ 2-(OH) 2(Sc(OEP)) 2]. One porphyrin is rotated relative to the upper porphyrin by 25° due to steric contacts between the phenyl substituents. We have used these new structures to re-evaluated our previously reported molecular mechanics force field parameters for modelling Sc(III) porphyrins using the MM2 force field; the training set was augmented from two to seven structures by using all available Sc(III) porphyrin structures and the two new structures. The modelling reproduces the porphyrin core very accurately; bond lengths are reproduced to within 0.01 Å, bond angles to within 0.5° and torsional angles to within 2°. The optimum parameters for modelling the Sc(III)–N bond lengths, determined by finding the minimum difference between the crystallographic and modelling mean bond lengths with the aid of artificial neural network architectures, were found to be 0.90 ± 0.03 mdyn Å −1 for the bond force constant and2.005 ± 0.005 Å for the strain-free bond length. Modelling the seven Sc(III) porphyrins with the new parameters gives an average Sc–N bond length of 2.182 ± 0.018 Å, indistinguishable from the crystallographic mean of 2.181 ± 0.024 Å.

Fluorescent amino-β-cyclodextrin derivative as a receptor for various types of alcohols having cyclic and macrocyclic rings

The cyclic- and macrocyclic-alcohol sensing in aqueous solution by an amino-β-cyclodextrin (amino-β-CDx), 1, bearing a naphthalene fluorophore has been investigated by fluorescent and induced circular dichroism (ICD) spectrophotometry. The host-guest 1:1 stoichiometric binding was confirmed mainly by fluorescent titration method. The binding constants ( K f) of the 1:1 host-guest inclusion complexes were found to be in the range of 10 2–10 5 mol −1 dm 3, depending on the shape and size of hydrophobic moiety of alcohol molecules. This indicates that the β-CDx cavity takes part in the guest sensing and the partially self-included naphthalene probe of 1 would extrude from the cavity upon binding with guest molecules. Addition of guests to the host 1 solution causes appreciable changes both in fluorescent and ICD intensity. The geometry of the inclusion complexes and the inclusion process were simulated by molecular mechanics using MM2 force field. The optimized steric-energy differences of the various inclusion complexes indicate that the nonbonded van der Waals (non-1,4-VDW) interaction between host and guest play a significant role in the induced-fit inclusion process.

Self‐Assembly of Molecular Nanoball: Design, Synthesis and Characterization.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.

Cumulative π‐π interaction triggers unusually high stabilization of linear hydrocarbons inside the single‐walled carbon nanotube

AbstractThe interactions of linear hydrocarbons C2nH4 and C2nH2 (n = 1–4) with a finite‐length armchair (5,5) single‐walled carbon nanotube have been investigated using HF and MP2 methods in conjunction with 6‐31G(d) basis set, and molecular mechanics (MM) with MM2 force field. In all cases, the results obtained at MP2/6‐31G(d) level show stabilization of these supramolecular systems, contrary to the repulsive interactions obtained with the HF method. The interaction energies computed using MM with MM2 force field are in close agreement with the results obtained using the MP2/6‐31G(d) level. They increase gradually as the length of linear hydrocarbon chain increases. The present study indicates that cumulative π‐π interaction is the origin for the exceptionally high stabilization of the long nanotube‐hydrocarbon complexes. Mulliken population analysis reveals a very small charge transfer between the nanotube and the guest. Essentially there is no change in HOMO‐LUMO energy gap by the insertion of linear hydrocarbons. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007

Excited state intramolecular proton transfer (ESIPT) in a dioxotetraamine derived schiff base and its complexation with Fe(III) and Cr(III)

The excited state intramolecular proton transfer (ESIPT) process in a symmetric Schiff base derived from dioxotetraamine and salicylaldehyde, N, N′-Bis{2-[(2-hydroxybenzylidine)amino]ethyl}malonamide (BHAEM) has been investigated experimentally by the fluorescent method and a two step proton transfer mechanism from dienol to ketoenol and then to diketo tautomer has been proposed on the basis of the theoretical evidence obtained through semi-empirical MO/CI calculations using the AM1 Hamiltonian. BHAEM on interaction with Fe(III) and Cr(III), in an aqueous medium of 0.1N ionic strength and 25 ± 1 °C forms monomeric metal complexes of the type ML and MLH −2 with both metal ions, whereas with Cr(III) it forms two more additional species, MLH and MLH −1. The stabilities of these metal complexes have been evaluated using potentiometric and spectrophotometric methods and the relative stabilities of the complexes formed with this ligand are rationalized. At low pH, the ligand coordinates to the metal ions through bis-imine nitrogen and bis-phenolate oxygen atoms but with an increase of pH, further coordination occurs through two amide nitrogen atoms of the ionized amide groups. The structures of the metal complexes were predicted from minimum strain energy calculations employing molecular mechanics using the MM3 force field and from their theoretical electronic spectra obtained through semi-empirical AM1/ZINDO method.

Structural, energetic, and dynamical properties of rotaxanes constituted of α-cyclodextrins and an azobenzene chain

The [3]rotaxane synthesised as a single isomer constituted of two cyclodextrins (CDs) and an azobenzene chain [M.R. Craig, T.D.W. Claridge, M.G. Hutchings, H.L. Anderson, Synthesis of a cyclodextrin azo dye [3]rotaxane as a single isomer, Chem. Commun. 16 (1999) 1537–1538] has been investigated using molecular mechanics (MM) and dynamics (MD) with the MM3 force field in order to evaluate the stability of various configurations of the complex in the isolated and solvated states. The influence of the blocking groups and the presence of energy barriers along the azo chain were first investigated through the calculation of an energy profile. It revealed that the CD could translate along the chain at room temperature without any decomplexation. Next, MD simulations of three different types of configurations, i.e., head-to-head, head-to-tail, and tail-to-tail, of the [3]rotaxane were carried out. The non-solvated phase simulations showed structures with the CDs close to each other while the solvated ones showed structures with CDs separated by larger distances. This separation occurs due to the solute–solvent interactions. When the systems are in isolated state, the observed structure of the complexes are less stable due to an unfavourable arrangement of the hydroxyls groups of the adjacent CD faces. When considering solvation, energies of the three configurations are roughly identical due to the large distance between the faces of the CDs.

Self-Assembly of Molecular Nanoball: Design, Synthesis, and Characterization

The design and self-assembly of two new flexible supramolecular nanoballs are described. These assemblies incorporate two flexible tritopic amide and ester building blocks and were prepared in excellent yields (96-97%) via coordination driven self-assembly. The first resulted from the reaction of 4 equiv of a new tritopic ester ligand N,N',N' '-tris(4-pyridylmethyl) trimesic ester and 3 equiv of C4 symmetric Pd(NO3)2. The second analogous structure was obtained by the self-assembly of a flexible N,N',N' '-tris(3-pyridylmethyl) trimesic amide and Pd(NO3)2. The assemblies were characterized with multinuclear NMR spectroscopy, electrospray ionization mass spectroscopy, elemental analysis, and TGA. Mass spectrometry along with NMR data and TEM view confirms the existence of the two assemblies. MM2 force field simulations of the cages showed a ball shape with the diameter of the inner cavity of about 2.1 and 1.8 nm for 2a and 2b, respectively, which were also corroborated by TEM analysis.