Ab initio molecular dynamics — Applications to the molecular and solid state physics of phosphorus

Summary We review combined molecular dynamics (MD) and density functional (DF) simulations and their applicability in chemistry and physics. This method (also termedab initio MD, first principles MD or Car-Parrinello method) exhibits characteristic strengths and weaknesses, and we demonstrate both in a set of typical example applications from molecular physics (phosphorus clusters) and solid state physics/chemistry (liquid phosphorus). Dynamical, finite temperature, simulations deriving interatomic forces from state-of-the-art density functional calculations represent a substantial advance over both (i) traditional pointwise total energy and electronic band structure calculations and (ii) classical MD simulations with empirical or semi-empirical forces, and have already yielded qualitatively new insights in several fields.     

Electron–phonon interactions in atomic and molecular devices

Electron–phonon interactions are extremely important for understanding charge transport, inelastic processes, heating, and heat dissipation in nanoscale molecular and atomic devices. In molecular electronics Inelastic Electron Tunneling Spectroscopy (IETS) has recently emerged as one of the premier methods for characterizing molecular-scale junctions and devices. This method provides a distinct chemical fingerprint for identifying molecules within a junction, and has allowed for clear demonstrations of single molecule devices, the effects of electric field on molecular orbitals, the importance of molecular configuration on conductance, as well as information about the charge transport mechanism. In this review we will discuss the use of Point Contact (PC) and IET spectroscopies on molecular and atomic systems, discuss the basic principles involved in inelastic transport for these spectroscopic methods to function, and focus on the experimental techniques involved and the important conclusions drawn from the experiments performed to date.     

Transport property of polyaniline and its molecular weight dependence

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Nanoscale segregation,molecular recognition and fluorophobic effect – from molecular design towards complex mesophase morphologies

Mesomorphic structure formation of hydrogen-bonded complexes of amino substituted 1,3,5-triazines with complementary (semiperfluoro)alkoxybenzoic acids is presented. The substitution pattern of both components was modified systematically in order to elucidate the influence of molecular parameters on the mesophase morphologies of the binary mixed systems. The phase sequence of the triazines, and of their associates with the acids, spans the range from smectic layer structures to discontinuous cubic phases composed of closed inverted micelles. Columnar phases with various two-dimensional lattice symmetries and bicontinuous cubic phases were found as intermediates. The mesophase morphologies are discussed in terms of the microsegregation of rigid polar, lipophilic and fluorinated molecular blocks in different sub-spaces along with tailoring the shape of (curved) aggregates by the space requirement of incompatible molecular fragments.     

The molecular structure and conformation of 1,1′-dimethyl-bicyclopropyl

The molecular structure and conformation of 1,1′-dimethyl-bicyclopropyl have been studied by the gas electron diffraction method, extended by normal coordinate and molecular mechenics calculations. The experimental data are in accordance with all molecules having the gauche conformation, with a dihedral angle of 58°.     

Investigating cyclic peptides inhibiting CD2–CD58 interactions through molecular dynamics and molecular docking methods

The CD2–CD58 protein–protein interaction is known to favor the recognition of antigen presenting cells by T cells. The structural, energetics, and dynamical properties of three known cyclic CD58 ligands, named P6, P7, and RTD-c, are studied through molecular dynamics (MD) simulations and molecular docking calculations. The ligands are built so as to mimic the C and F β-strands of protein CD2, connected via turn inducers. The MD analyses focus on the location of the ligands with respect to the experimental binding site and on the direct and water-mediated hydrogen bonds (H bonds) they form with CD58. Ligand P6, with a sequence close to the experimental β-strands of CD2, presents characteristics that explain its higher experimental affinity, e.g., the lower mobility and flexibility at the CD58 surface, and the larger number and occurrence frequency of ligand-CD58 H bonds. For the two other ligands, the structural modifications lead to changes in the binding pattern with CD58 and its dynamics. In parallel, a large set of molecular docking calculations, carried out with various search spaces and docking algorithms, are compared to provide a consensus view of the preferred ligand binding modes. The analysis of the ligand side chain locations yields results that are consistent with the CD2–CD58 crystal structure and suggests various binding modes of the experimentally identified hot spot of the ligands, i.e., Tyr86. P6 is shown to form a number of contacts that are also present in the experimental CD2–CD58 structure.     

NMR studies of conformations and molecular recognition of pyridinio-appended and nicotinamide-appended β-cyclodextrin

Abstract

The conformations of pyridinio-appended β-cyclodextrin (CDP⁺) and nicotinamide-appended β-cyclodextrin (CDNA⁺) were studied by NMR spectroscopy. The orientations of the pyridine residue of CDP⁺ and the nicotinamide residue of CDNA⁺ were determined by using a combination of NMR spectroscopic techniques. NMR spectra indicate that the shapes of the cavities of CDP⁺ and CDNA⁺ were changed after forming complexes. This change depended on the shape of the guest. CDNA⁺ could separate the ¹H resonances at the Cβ position of racemic tryptophan into two sets of resonances for each enantiomer.     

Solubility and molecular modeling of triflumizole-β-cyclodextrin inclusion complexes

Solubility enhancement of the fungicide triflumicole by-cyclodextrin is explained using a thermodynamic approach. The influence of organic cosolvents on the overall equilibrium constants of triflumizole complexation with-cyclodextrin in aqueous solutions has been investigated. Their variance in mixed solvents is only partly explained by a competitive inclusion of substrate and cosolvent molecules in-cyclodextrin. The geometries of host-guest complexes have been estimated by molecular mechanics calculations. Their broad structural variety caused by the flexibility of host and guest molecules and different association possibilities of triflumizole have been analysed by a dynamic Monte Carlo docking method. The hydrophobic effect has been simulated by cominimization of the hydrophobic contributions to the solvation energy, calculated from the solvent accessible surface area of the complex and the conformational (potential) energy.     

Crystal and molecular structure of nitrophenyl 2,3,4-tri-O-acetyl-β-d-xylopyranosides

Comprehensive structural analyses were performed for o-, m-, and p-nitrophenyl 2,3,4-tri-O-acetyl-β-d-xylopyranosides. Single-crystal X-ray diffraction data were collected and revealed that meta isomer undergoes temperature-dependent polymorph transition (crystal structures of two polymorphs were obtained). This transition was verified by differential scanning calorimetry. The number of molecules in the independent part of the crystal unit cells of the compounds under investigation was in agreement with the number of resonances in solid-state ¹³C and ¹⁵N NMR spectra. The o- and p-nitrophenyl 2,3,4-tri-O-acetyl-β-d-xylopyranosides exist as single polymorph at room temperature, as confirmed by powder X-ray diffraction measurements.     

Photophysical and electrochemical properties of π-extended molecular 2,1,3-benzothiadiazoles

The reaction of 4,7-dibromo-2,1,3-benzothiadiazole with arylboronic acids (phenyl, 1-naphthyl, 4-methoxyphenyl, 4-chlorophenyl and 4-trifluoromethylphenyl) in the presence of catalytic amounts of a NCP-pincer palladacycle affords photoluminescent π-extended 4,7-diaryl-2,1,3-benzothiadiazoles 4a-e in high yields. These 4,7-diaryl-2,1,3-benzothiadiazoles exhibit high fluorescent quantum yields, high electron affinities and adequate band gap values for testing as OLEDs. The 4,7-bis-naphthyl-2,1,3-benzothiadiazole 4b presents two different lifetimes (bi-exponential decay) due to the presence of two atropisomers. The Sonogashira coupling reaction of 4,7-diethynyl-2,1,3-benzothiadiazole 6 with the corresponding halo-aryl compounds (iodobenzene, 1-bromonaphthalene, 4-iodoanisole, 4-bromo-N,N-dimethylaniline and 2-bromopyridine) afforded the photoluminescent π-extended 4,7-bis-alkynylaryl-2,1,3-benzothiadiazoles 7a-e, also in high yields. These 4,7-diethynyl-2,1,3-benzothiadiazoles also present high fluorescent quantum yields, high electron affinities and adequate band gap values for testing as OLEDs. The 4,7-disubstituted-2,1,3-benzothiadiazoles 4a-e and 7a-e exhibit different electrochemical behavior. The presence of two ethynyl spacers in 2,1,3-benzothiadiazoles 7a-e shifts the reduction potentials to less cathodic values and also results in two well-defined and distinct reduction processes.     

Study on multimers and their structures in molecular association mixture

Self-association system of(R)-1,3-butanediol in dilute carbon tetrachloride(CCl4)solution is studied as a model of molecular association mixture.Analysis methods including FSMWEFA(fixed-size moving window evolving factor analysis)combined with PCA(principal component analysis),SIMPLISMA (simple-to-use interactive self-modeling mixture analysis),and ITTFA(iterative target transformation factor analysis)are adopted to resolve infrared spectra of(R)-1,3-butanediol solution.Association number and equilibrium constant are computed.(R)-1,3-butanediol in dilute inert solution is determined as a monomer-trimer equilibrium system.Theoretical investigation of trimer structures is carried out with DFT(density functional theory),and structural factors are analyzed.     

Spectroscopic study of molecular associations between FMN and β-carbolines

The spectrophotometric and thermodynamic properties of molecular complexes of flavin mononucleotide (FMN) (riboflavin 5′-phosphate) with some β-carboline derivatives have been investigated in aqueous solution. The molecular associations have been examined by means of electronic absorption spectra, since in each a new charge-transfer band has been located, and also the variation of the fluorescence emission of FMN on the solutions has been observed. The formation constants for the molecular complexes were determined from absorption data using the Foster—Hammick—Wardley method. The quenching phenomenon observed in FMN fluorescence is related to the concentration of the β-carboline derivatives, allowing the calculation of the quenching constants for FMN-β-carboline complexes. Thermodynamic parameters have been determined from the values of association constants for the molecular complexes at various temperatures. The influence of substituents in the β-carboline molecule on the stability of the complexes formed was also investigated.     

Crystal and molecular structure of β-piperidinopropioamidoxime monochloroacetate and hydrochlorides of its O-benzoylation products

The structures of -piperidinopropioamidoxime monochloroacetate and O-benzoyl- and O-para-toluyl--piperidinopropioamidoxime hydrochlorides have been determined. The geometry of these compounds is analyzed. The N-O bond is in the syn-planar position in -piperidinopropioamidoxime monochloroacetate, but adopts an anti-orientation relative to the C(2)-C(3) bond of the propioamidoxime fragment in the other two compounds. In -piperidinopropioamidoxime monochloroacetate crystals, the cation-anion pairs are joined by intermolecular hydrogen bonds into chains; the latter are linked by van der Waals contacts. The crystals of the O-benzoyl- and O-para-toluyl--piperidinopropioamidoxime hydrochlorides are characterized by the same system of hydrogen bonds; the cations and anions are linked by hydrogen bonds into layers, and the latter make van der Waals contacts in the structure.Original Russian Text Copyright © 2004 by K. M. Beketov, J. T. Welch, P. Toskano, L. A. Kayukova, A. L. Akhelova, and K. D. PralievTranslated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 3, pp. 535–543, May–June 2004.     

Structure and stability of molecular and ionic complexes of AlCl3 with pyrazine and 4,4′-bipyridyl

Structural and thermodynamic characteristics of molecular and ionic complexes of aluminum trichloride with pyrazine (pyz) and 4,4′-bipyridyl (bipy) are calculated at the RI-BP86/def2-SVP level. It is found that for molecular 2AlCl₃·3L and 4AlCl₃·3L complexes an energy difference between isomers does not exceed 4 kJ/mol, and the rotation barrier of the AlCl₃ moiety relative to the N-Al-N bond does not exceed 24 kJ/mol. A comparison of the stability of molecular and ionic complexes of aluminum in the gas phase shows that the maximum energy difference is ～60 kJ/mol. For L = pyz the molecular complex is more stable whereas for L = bipy it is the ionic one.     

Mass spectrometry and molecular modeling studies on the inclusion complexes between alendronate and β-cyclodextrin

Complexation of alendronate sodium (AlnNa) with β-cyclodextrin (β-CD) was studied by means of ESI-mass spectrometry. The experimental results show that stable 1:1 inclusion complexes between selected bisphosphonates and β-CD were formed. In addition, complexes with different stoichiometry were observed. DFT/B3LYP calculations were performed to elucidate the different inclusion behavior between alendronate and β-CD. Molecular modeling showed that the inclusion complex of Aln-β-CD where the two phosphonate groups bound to the central carbon atom of bisphosphonate were inserted into the cavity of β-CD from its “top” side was thermodynamically more favorable than when they were inserted from its “bottom” side; the complexation energy was ?74.05 versus ?60.85 kcal/mol. The calculations indicated that the formation of conventional hydrogen bonds was the main factor for non-covalent β-CD:Aln complex formation and stabilization in the gas phase.     

Construction of molecular nanotubes with precise length,diameter and chirality

<正>Molecular nanotubes are nanoscale organic materials with tubular architecture, that show potential applications in molecular recognition/separation, cross-membrane transportation, catalysis in confined spaces, and nanoelectronics [1]. However, the precise construction of molecular nanotubes with well-defined cavity sizes and shapes is non-trivial.     

Topography of scalar fields: molecular clusters and π-conjugated systems

The pioneering works due to Bader and co-workers have generated widespread interest in the study of the topography of molecular scalar fields, the first step of which is the identification and characterization of the corresponding critical points (CPs). The topography of a molecular system becomes successively richer in going from the bare nuclear potential (BNP) to the molecular electrostatic potential (MESP) through the molecular electron density (MED). The present work clearly demonstrates, through the study of some π-conjugated test molecules as well as molecular clusters, that the CPs could be economically located by following this path within ab initio level theory. Further, the topography mapping of large molecules, especially at a higher level of theory, is known to be a demanding task. However, it is rendered possible by following the above sequential mapping assisted by a divide-and-conquer-type method termed as the molecular tailoring approach (MTA). This is demonstrated with the topography mapping of β-carotene and benzene nonamer at MP2 and a (H(2)O)(32) cluster at the HF level of theory, which are rather challenging problems with contemporary off-the-shelf computer hardware.     

Conformational behaviour and molecular similarity of some β1-adrenergic ligands

Summary The conformational behaviour of a series of aryloxypropanolamines was investigated by means of a new procedure which allows the sampling of the molecular torsional surface in a very efficient way. The combination of such a procedure with the standard molecular mechanics algorithms for the geometry optimization gives, as a result, the definition of a powerful computational scheme for the detailed analysis of the potential energy surface of complex molecules. The compounds studied show a remarkable tendency to form intramolecular hydrogen bonds, which seem to play a key role in determining the lowest energy structures. The indices of molecular similarity proposed by Carbó, computed for the most stable conformers, do not account for differences between diastereoisomers, and, as a consequence, can hardly be used to attempt a structure-activity correlation.     

Bis-β-cyclodextrinyl- and bis-cellobiosyl-diazacrowns: synthesis and molecular complexation behaviors toward Busulfan anticancer agent and two basic aminoacids

The one-step synthesis of two C₂-symmetric receptors including two β-cyclodextrin cores or two disaccharidyl units connected by urea linkers to a diazacrown ether organizing platform is reported. The X-ray structure of the peracetylated bis-ureidocellobiosyl podand could be determined. These molecular systems, long thought to be potent selective carriers for chiral/achiral organic guests at the supramolecular level, were found to be efficient complexing tools toward the Busulfan anticancer agent but also toward l-arginine and l-lysine basic aminoacids.