BODIL: a molecular modeling environment for structure-function analysis and drug design

BODIL is a molecular modeling environment geared to help the user to quickly identify key features of proteins critical to molecular recognition, especially (1) in drug discovery applications, and (2) to understand the structural basis for function. The program incorporates state-of-the-art graphics, sequence and structural alignment methods, among other capabilities needed in modern structure–function–drug target research. BODIL has a flexible design that allows on-the-fly incorporation of new modules, has intelligent memory management, and fast multi-view graphics. A beta version of BODIL and an accompanying tutorial are available at http://www.abo.fi/fak/mnf/bkf/research/johnson/bodil.html     

d-Xylose-based surfactants: Synthesis,characterization and molecular modeling studies

Pentose-derived surfactants were easily synthesized and fully characterized through classical analytical methods. The interfacial behaviors revealed the importance of both the length of the hydrophobic chain and the nature of the anomeric form. Finally, the spatial conformation of four xylosides was obtained by molecular modeling with software Hyperchem^® 4 using the semi-empirical method PM3, which demonstrated the role of hydrophobic interactions in the stability of the compounds.     

Mechanism and control of molecular energy flow: a modeling perspective

 Vibrational energy flow in organic molecules occurs by a multiple-time-scale mechanism that can be modeled by a single exponential only in its initial stages. The mechanism is a consequence of the hierarchical structure of the vibrational Hamiltonian, which leads to diffusion of vibrational wavepackets on a manifold with far fewer than the 3N−6 dimensions of the full vibrational state space. The dynamics are controlled by a local density of states, which does not keep increasing with molecular size. In addition, the number of vibrational coordinates severely perturbed during chemical reaction is small, leading to preservation of the hierarchical structure at chemically interesting energies. This regularity opens up the possibility of controlling chemical reactions by controlling the vibrational energy flow. Computationally, laser control of intramolecular vibrational energy redistribution can be modeled by quantum-classical, or by purely quantum-mechanical models of the molecule and control field. Received: 26 July 2002 / Accepted: 30 September 2002 / Published online: 2 December 2002 Electronic Supplementary Material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00214-002-0394-2. Acknowledgements. This work was supported by NSF grant CHE 9986670. Correspondence to: M. Gruebele e-mail: gruebele@scs.uiuc.edu     

Hapten design and indirect competitive immunoassay for parathion determination: correlation with molecular modeling and principal component analysis

A novel procedure for parathion hapten design is described. The optimal antigen for parathion was selected after molecular modeling studies of six types of potentially immunizing haptens with the aim to identify the best mimicking target analyte. Heterologous competitive indirect enzyme-linked immunosorbent assay (ELISA) was developed after screening a battery of competitors as coating antigens. The relationship between the heterology degree of the competitor and the resulting immunoassay detectability was investigated according to the electronic similarities of the competitor haptens and the target analyte. Molecular modeling and principal component analysis were performed to understand the electronic distribution and steric parameters of the haptens at their minimum energetic levels. The results suggested that the competitors should have a high heterology to produce assays with good detectability values. An indirect competitive ELISA was finally selected for further investigation. The immunoassay had an IC₅₀ value of 4.79 ng mL⁻¹ and a limit of detection of 0.31 ng mL⁻¹. There was little or no cross-reactivity to similar compounds tested except for the insecticide parathion-methyl, which showed a cross-reactivity of 7.8%.     

SYNPHOS®, a new chiral diphosphine ligand: synthesis, molecular modeling and application in asymmetric hydrogenation

A new optically active diphosphine ligand, [(5,6),(5′,6′)-bis(ethylenedioxy)biphenyl-2,2′-diyl]bis(diphenylphosphine) (SYNPHOS®) has been synthesized and used in ruthenium-catalyzed asymmetric hydrogenation. This new ligand has been compared to other diphosphines (BINAP and MeO-BIPHEP), regarding their dihedral angles and the enantioselectivity in the ruthenium mediated hydrogenation reaction.     

Separation of triphenyl atropisomers of a pharmaceutical compound on a novel mixed mode stationary phase: a case study involving dynamic chromatography, dynamic NMR and molecular modeling

Analysis of atropisomers is of considerable interest in the pharmaceutical industry. For complex chiral molecules with several chiral centers hindered axial rotation can lead to formation of interconverting diastereomers that should be separable on achiral stationary phases. However, achieving the actual separation may be difficult as the on-column separation speed must match or be faster then the rate of isomer interconversion. Often, this requirement can be satisfied by using low-temperature conditions and by improving selectivity via use of chiral stationary phases. In the current study, we present an alternative approach utilizing an Obelisc R column, a novel mixed mode stationary phase that provided acceptable separation of triphenyl atropisomers inside a conventional HPLC temperature range. The separation was investigated under various chromatographic conditions. The interconversion chromatograms exhibited classic peak-plateau-peak behavior indicating the simultaneous atropisomer separation and interconversion. The elution profiles were integrated in order to deconvolute the peak areas of the "pure" (non-exchanged) and interconverted species; these data were used to obtain kinetic information. Analysis of retention data rendered thermodynamic information on the mechanism of retention and selectivity. Chromatographic kinetic data were complemented with variable-temperature NMR and molecular modeling studies, which provided additional support and insights into the energetics of the interconversion process.     

Correlation of thermodynamic modeling and molecular simulations for liquid-liquid equilibrium of ternary polymer mixtures based on a phenomenological scaling method

In our previous study [S.Y. Oh, Y.C. Bae, J. Phys. Chem. B 114 (2010) 8948-8953], we presented a new method to predict liquid-liquid equilibria in ternary simple liquid mixtures by using a combination of a thermodynamic model and molecular simulations. As a continuation of that effort, we extend our previously developed method to ternary polymer systems. In the simulations, we used the dummy atoms to calculate the pair interaction energy values between the polymer segments and the solvent molecules. Furthermore, a thermodynamic model scaling concept is introduced to consider the chain length dependence of the energy parameters. This method was applied to ternary mixtures incorporating low to high molecular weight polymers. The method presented here well described the experimental observations using one or no adjustable parameters.     

The generalized hybrid orbital method for combined quantum mechanical/molecular mechanical calculations: formulation and tests of the analytical derivatives

 Hybrid quantum mechanical (QM) and molecular mechanical (MM) potentials are becoming increasingly important for studying condensed-phase systems but one of the outstanding problems in the field has been how to treat covalent bonds between atoms of the QM and MM regions. Recently, we presented a generalized hybrid orbital (GHO) method that was designed to tackle this problem for hybrid potentials using semiempirical QM methods [Gao et al. (1998) J Phys Chem A 102: 4714–4721]. We tested the method on some small molecules and showed that it performed well when compared to the purely QM or MM potentials. In this article, we describe the formalism for the determination of the GHO energy derivatives and then present the results of more tests aimed at validating the model. These tests, involving the calculation of the proton affinities of some model compounds and a molecular dynamics simulation of a protein, indicate that the GHO method will prove useful for the application of hybrid potentials to solution-phase macromolecular systems. Received: 4 October 1999 / Accepted: 18 December 1999 / Published online: 5 June 2000     

Computer-aided molecular modeling study of enantioseparation of iodiconazole and structurally related triadimenol analogues by capillary electrophoresis: Chiral recognition mechanism and mathematical model for predicting chiral separation

Chiral separation of iodiconazole, a new antifungal drug, and 12 new structurally related triadimenol analogues had been developed by capillary electrophoresis (CE) using hydroxypropyl-γ-cyclodextrin (HP-γ-CD) as the chiral selector. The effect of structural features of analytes on Δt and R_s was studied under the optimum separation conditions. Using molecular docking technique and binding energy calculations, the inclusion process between HP-γ-CD and enantiomers was investigated and chiral recognition mechanisms were discussed. The results suggest that hydrogen bonding between fluorine at position 4 of the phenyl group beside the chiral carbon and the hydroxyl group on the HP-γ-CD rim and face to face π–π interactions between two phenyl rings highly contributed to the enantiorecognition process between HP-γ-CD and iodiconazole. The N-methyl group beside chiral carbon also played an important role in enantiomeric separation. Additionally, the big difference in binding energy (ΔΔE) highly contributed to good separation in the presence of HP-γ-CD chiral selector, which may be a helpful initial guide for chiral selector selection and predicting the result of enantioseparation. Furthermore, the new mathematical equation established based on the results of molecular mechanics calculations exhibited good capability in predicting chiral separation of these triadimenol analogues using HP-γ-CD mediated CE.     

Ultrafast vibrational spectroscopy and relaxation in polyatomic molecules: Potential for molecular parallel computing

The feasibility of controlled ultrafast pumping in the mid IR and the probe of the subsequent intramolecular dynamics is illustrated for vibrational excitation of the two metal carbonyls W(CO)₆ and Mn(CO)₅Br in solution. Pumping and probing is performed by short, 130 fs, pulses centered at about 2000 cm⁻¹. Frequency resolved measurements of the time delayed probe pulse are performed. Measured two dimensional spectra are fitted by a kinetic scheme that models the vibrational dynamics. Fast relaxation is solvent induced with the solvent acting also as a heat bath. The (several) probe signals in the experiment can be thought of as the response of a finite state logic machine. This suggests that the molecular machine can act as an ultrafast (petaHertz) processor. The number of internal (memory) states of the machine is determined by the number of vibrational states in the kinetic scheme that can fit the observed relaxation. The number of outputs of the machine is the number of the several different available probe signals. It is shown that the machine is massively parallel because in each (sub ps) time step it produces an entire vector as an output and that each component of the output vector is, by itself, a transform over the input. Beyond that, the machine can produce a (finite number of) different output vectors in sequential time steps.     

An integrated computational tool for the study of the optical properties of nanoscale devices: application to solar cells and molecular wires

We present a combined computational strategy for the study of the optical properties of nanoscale systems, using a combination of codes and techniques based on Density Functional Theory (DFT) and its Time Dependent extension (TDDFT). In particular, we describe the use of Car–Parrinello molecular dynamics simulations for the study of nanoscale devices and show the integration of the obtained results with available quantum chemistry codes for the calculation of TDDFT excitation energies, including solvation effects by continuum solvation models. We review some prototypical applications of this integrated computational strategy, ranging from the interaction of dye sensitizers with TiO₂ nanoparticles, of interest in the field of dye-sensitized solar cells, to transition metal molecular wires exceeding 3 nm length.     

PRIRODA-04: a quantum-chemical program suite. New possibilities in the study of molecular systems with the application of parallel computing

Main characteristics are described of the PRIRODA quantum-chemical program suite designed for the study of complex molecular systems by the density functional theory, at the MP2, MP3, and MP4 levels of multiparticle perturbation theory, and by the coupled-cluster single and double excitations method (CCSD) with the application of parallel computing. A number of examples of calculations are presented.__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 804–810, March, 2005.     

A chemosensor showing discriminating fluorescent response for highly selective and nanomolar detection of Cu and Zn and its application in molecular logic gate

A fluorescent based receptor (4Z)-4-(4-diethylamino)-2-hydroxybenzylidene amino)-1,2dihydro-1,5-dimethyl-2-phenylpyrazol-3-one (receptor 3) was developed for the highly selective and sensitive detection of Cu²⁺ and Zn²⁺ in semi-aqueous system. The fluorescence of receptor 3 was enhanced and quenched, respectively, with the addition of Zn²⁺ and Cu²⁺ ions over other surveyed cations. The receptor formed host-guest complexes in 1:1 stoichiometry with the detection limit of 5 nM and 15 nM for Cu²⁺ and Zn²⁺ ions, respectively. Further, we have effectively utilized the two metal ions (Cu²⁺ and Zn²⁺) as chemical inputs for the manufacture of INHIBIT type logic gate at molecular level using the fluorescence responses of receptor 3 at 450 nm.     

Molecular structure of phenylsilane: a study by gas-phase electron diffraction and ab initio molecular orbital calculations

The molecular structure of phenylsilane has been determined accurately by gas-phase electron diffraction and ab initio MO calculations at the MP2(f.c.)/6-31G* level. The calculations indicate that the perpendicular conformation of the molecule, with a Si–H bond in a plane orthogonal to the plane of the benzene ring, is the potential energy minimum. The coplanar conformation, with a Si–H bond in the plane of the ring, corresponds to a rotational transition state. However, the difference in energy is very small, 0.13 kJ mol⁻¹, implying free rotation of the substituent at the temperature of the electron diffraction experiment (301 K). Important bond lengths from electron diffraction are: <r_g(C–C)>=1.403±0.003 Å, r_g(Si–C)=1.870±0.004 Å, and r_g(Si–H)=1.497±0.007 Å. The calculations indicate that the C_ipso–C_ortho bonds are 0.010 Å longer than the other C–C bonds. The internal ring angle at the ipso position is 118.1±0.2° from electron diffraction and 118.0° from calculations. This confirms the more than 40-year old suggestion of a possible angular deformation of the ring in phenylsilane, in an early electron diffraction study by F.A. Keidel, S.H. Bauer, J. Chem. Phys. 25 (1956) 1218.     

Molecular modeling study for a novel structured oligomer subunit selection: the example of 2-aminomethyl-phenyl-acetic acid

Oligomers derived from dipeptide mimics were selected by computational study for their suitability to fold in ordered structures. After selection of a monomeric unit, short oligomers were synthesized and analyzed by NMR and IR. Oligomers built from 2-aminomethyl-phenyl-acetic acid were shown to adopt a helical structure stabilized by 10-membered ring hydrogen bonds.     

Quantum computation of the properties of helium using two-body and three-body intermolecular potentials: a molecular dynamics study

We have performed the molecular dynamics simulation to obtain energy, pressure, and self-diffusion coefficient of helium at different temperatures and densities using Lennard–Jones (LJ), Hartree–Fock dispersion-Individual damping (HFD-ID) potential, and the HFD-like potential which has been obtained with an inversion of viscosity data at zero pressure supplemented by quantum corrections following the Feynman–Hibbs approach. The contribution of three-body interactions using an accurate simple relationship reported by Wang and Sadus between two-body and three-body interactions has been also involved for non-effective potentials (HFD-ID and HFD-like) in simulation. Our results show a good agreement with corresponding experimental data. A comparison of our simulated results with other molecular simulations using different potentials is also included.     

Molecular structural investigations of quinoxaline derivatives through 3D-QSAR,molecular docking,ADME prediction and pharmacophore modeling studies for the search of novel antimalarial agent

In the present article, a dataset of 63 quinoxaline derivatives were taken for antimalarial activity and pharmacophore were developed. Atom based method was used to develop a three dimensional quantitative structure activity relationship (3D-QSAR) model. On comparison of all statistical parameters, model AHRRR23 was found to be the most effective and predictive QSAR model as it satisfied all statistical parameters of a good model. The model AHRRR23 showed an adequate R² value for the training set 0.9446, good predictive power with Q² of 0.6409, good F- value, low SD 0.1218 value and outstanding Pearson-R values and low RMSE 0.2779 values of the model. The docking studies also gives very good results with good RMSD values. 3D QSAR, docking and ADME studies exhibits that the developed model could be employed as a potential lead for further study as antimalarial drug.     

A study of the interaction energy between a glycoluril molecular clip and dihydroxybenzenes or diaminobenzenes: a justification for easy separation by affinity chromatography

Theoretical calculations were performed to determine the interaction energy between a glycoluril (GL) molecular clip and hydroxybenzenes (HBs) and aminobenzenes (ABs). The theoretical calculations on the GL and its interactions were carried out using the hybrid functional closed-shell RB3LYP and the 6-31G* basis set, employing gaussian 03. The stability in energy of the guest inside the GL, ΔE_T(1), was in the following order: m-DHB-GL > o-DHB-GL > m-THB-GL > m-DAB-GL > o-THB-GL. The geometric parameters, in particular the bond lengths are discussed for the host molecule GL and guest molecules DHB and DAB and their parameters are compared with the host-guest molecules DHB-GL and DAB-GL, respectively.     

Chiral diaminopyrrolic receptors for selective recognition of mannosides, part 2: a 3D view of the recognition modes by X-ray, NMR spectroscopy, and molecular modeling

The structural features of a representative set of five complexes of octyl α- and β-mannosides with some members of a new generation of chiral tripodal diaminopyrrolic receptors, namely, (R)-5 and (S)- and (R)-7, have been investigated in solution and in the solid state by a combined X-ray, NMR spectroscopy, and molecular modeling approach. In the solid state, the binding arms of the free receptors 7 delimit a cleft in which two solvent molecules are hydrogen bonded to the pyrrolic groups and to the benzenic scaffold. In a polar solvent (CD(3)CN), chemical shift and intermolecular NOE data, assisted by molecular modeling calculations, ascertained the binding modes of the interaction between the receptor and the glycoside for these complexes. Although a single binding mode was found to adequately describe the complex of the acyclic receptor 5 with the α-mannoside, for the complexes of the cyclic receptors 7 two different binding modes were required to simultaneously fit all the experimental data. In all cases, extensive binding through hydrogen bonding and CH-π interactions is responsible for the affinities measured in the same solvent. Furthermore, the binding modes closely account for the recognition preferences observed toward the anomeric glycosides and for the peculiar enantiodiscrimination properties exhibited by the chiral receptors.