GridMol2.0: Implementation and application of linear-scale quantum mechanics methods and molecular visualization

GridMol is a “one-stop” platform for molecular structure building, scientific computing, and molecular visualization aided by a high-performance computing environment. GridMol version 2.0 introduces two unique features: the first is fragment-based linear-scaling quantum chemistry methods, such as molecular fractionation with conjugate caps and fragment molecular orbital methods; the second is that GridMol enables users to visualize molecular geometries along a geometry optimization and an intrinsic reaction coordinate calculation. Compared with version 1.0, fragment-based linear-scaling quantum chemistry methods implemented in GridMol version 2.0 can be used as a useful tool for performing quantum calculations for large molecular systems to explore the mechanisms involved in protein-ligand or targeted drug interactions.     

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.     

Native and substituted cyclodextrins as chiral selectors for capillary electrophoresis enantioseparations: Structures,features, application,and molecular modeling

CDs are cyclic oligosaccharides consisting of α-d -glucopyranosyl units linked through 1,4-linkages, which are obtained from enzymatic degradation of starch. The coexistence of hydrophilic and hydrophobic regions in the same structure makes these macrocycles extremely versatile as complexing host with application in food, cosmetics, environmental, agriculture, textile, pharmaceutical, and chemical industries. Due to their inherent chirality, CDs have been also successfully used as chiral selectors in enantioseparation science, in particular, for CE enantioseparations. In the last decades, multidisciplinary approaches based on CE, NMR spectroscopy, X-ray crystallography, microcalorimetry, and molecular modeling have shed light on some aspects of recognition mechanisms underlying enantiodiscrimination. With the ever growing improvement of computer facilities, hardware and software, computational techniques have become a useful tool to model at molecular level the dynamics of diastereomeric associate formation to sample low-energy conformations, the binding energies between the enantiomer and the CD, and to profile noncovalent interactions contributing to the stability of CD/enantiomer association. On this basis, the aim of this review is to provide the reader with a critical overview on the applications of CDs in CE. In particular, the contemporary theory of the electrophoretic technique and the main structural features of CDs are described, with a specific focus on techniques, methods, and approaches to model CE enantioseparations promoted by native and substituted CDs. A systematic compilation of all published literature has not been attempted.     

Identification of novel Plasmodium falciparum PI4KB inhibitors as potential anti-malarial drugs: Homology modeling,molecular docking and molecular dynamics simulations

The current study was set to discover selective Plasmodium falciparum phosphatidylinositol-4-OH kinase type III beta (pfPI4KB) inhibitors as potential antimalarial agents using combined structure-based and ligand-based drug discovery approach. A comparative model of pfPI4KB was first constructed and validated using molecular docking techniques. Performance of Autodock4.2 and Vina4 software in predicting the inhibitor-PI4KB binding mode and energy was assessed based on two Test Sets: Test Set I contained five ligands with resolved crystal structures with PI4KB, while Test Set II considered eleven compounds with known IC50 value towards PI4KB. The outperformance of Autodock as compared to Vina was reported, giving a correlation coefficient (R²) value of 0.87 and 0.90 for Test Set I and Test Set II, respectively. Pharmacophore-based screening was then conducted to identify drug-like molecules from ZINC database with physicochemical similarity to two potent pfPI4KB inhibitors –namely cpa and cpb. For each query inhibitor, the best 1000 hits in terms of TanimotoCombo scores were selected and subjected to molecular docking and molecular dynamics (MD) calculations. Binding energy was then estimated using molecular mechanics–generalized Born surface area (MM-GBSA) approach over 50 ns MD simulations of the inhibitor-pfPI4KB complexes. According to the calculated MM-GBSA binding energies, ZINC78988474 and ZINC20564116 were identified as potent pfPI4KB inhibitors with binding energies better than those of cpa and cpb, with ΔG_binding ≥ −34.56 kcal/mol. The inhibitor-pfPI4KB interaction and stability were examined over 50 ns MD simulation; as well the selectivity of the identified inhibitors towards pfPI4KB over PI4KB was reported.     

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%.     

Acetylcholinesterase inhibitory activities and bioguided fractionation of the Ocotea percoriacea extracts: HPLC-DAD-MS/MS characterization and molecular modeling of their alkaloids in the active fraction

In vitro acetylcholinesterase activities of the hexane, dichloromethane, ethyl acetate, n-butanol and aqueous extracts of leaves of Ocotea percoriacea Kosterm. (Lauraceae) were evaluated. The bioguided fractionation of the most active extract (dichloromethane) using silica gel open-column chromatography led to an active alkaloidal fraction composed of isocorydine N-oxide, isocorydine N-oxide derivative, palmatine, roemerine and roemerine N-Oxide. The identification of the chemical structure of these compounds was carried out with high-performance liquid chromatography coupled to electrospray ionization multiple-stage mass spectrometry (HPLC-ESI-MS/MS). Aiming to understand their inhibitory activities, these alkaloids were docked into a 3D model of Electrophorus electricus Acetylcholinesterase (EelAChE) built in the Modeller 9.18 employing homology modeling approach. The results suggest that the alkaloids had the same binding mode and, possibly, the inhibition mechanism of classic drugs (ex. tacrine and donepezil). The structural difference of these compounds opens a new opportunity for the optimization of leading compounds.     

Evaluation of the separation mechanism of electrokinetic chromatography with a microemulsion and cyclodextrins using NMR and molecular modeling

Electrokinetic chromatography (EKC) allows the separation of closely related substances by the detection of fine effects in analyte-separation system interactions. With the goal of understanding the fine effects involved in separation using a dual cyclodextrin-microemulsion EKC system, an integrated study of NMR and molecular modeling was carried out. The above dual cyclodextrin-microemulsion system was previously used in the separation of clemastine and its related substances and was prepared by the addition of methyl-β-cyclodextrin (MβCD) and heptakis(2,6-di-O-methyl)-β-cyclodextrin (DMβCD) to an oil-in-water microemulsion. The use of DMβCD was shown to be essential in the separation of clemastine from one of its related substance (I(B) ). A molecular modeling study allowed the different affinities of clemastine and I(B) for the two cyclodextrins to be explained. Furthermore, rotating-frame Overhauser effect spectroscopy NMR experiments clearly indicated that besides the primary pseudostationary phase, namely the ionic microemulsion, cyclodextrins acted as a secondary pseudostationary phase. In addition, it was shown that inclusion complexation of sodium dodecyl sulfate (SDS) monomers into the cyclodextrins cavity occurs; differently, the oil (n-heptane) used in the preparation of microemulsion system resulted to be not included into the macrocycle cavity. These experimental results were supported by molecular modeling, which highlighted the preferential inclusion of SDS into DMβCD. On the basis of these results, it was confirmed that, besides its primary role as the ionic carrier in EKC, SDS is involved in inclusion equilibria toward CDs, which can be effective in increasing the system selectivity.     

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.     

N-glycosylation and ubiquitinylation of PD-L1 do not restrict interaction with BMS-202: A molecular modeling study

The Programmed cell Death protein-1/Ligand 1 (PD-1/L1) checkpoint is a major target in oncology. Monoclonal antibodies targeting PD-1 or PD-L1 are used to treat different types of solid tumors and lymphoma. PD-L1-binding small molecules are also actively searched. The lead compound is the biphenyl drug BMS-202 which stabilizes PD-L1 protein dimers and displays a potent antitumor activity in experimental models. Here we have investigated the effect of N-glycosylation (at N35, N192, N200 and N219) and mono-ubiquitination (at K178) of PD-L1 on the interaction with BMS-202 by molecular modeling. Two complementary tridimensional models of PD-L1, based on available crystallographic structures, were constructed with BMS-202 bound. The structures were glycosylated, with a fucosylated bi-antennary N-glycan and ubiquitinated. Model 1 refers to glycoPD-L1 bearing 16 N-glycans, with or without 4 ubiquitin residues. Model 2 presents 8 N-glycans and 2 ubiquitin residues. In both cases, BMS-202 was bound to the protein interface, stabilizing a PD-L1 dimer. The incorporation of the N-glycans or the ubiquitins did not significantly alter the drug-protein recognition. The interface of the drug-stabilized protein dimer is unaffected by the glycosylation or ubiquitination. Calculations of the binding energies indicated that the glycosylation slightly reduces the stability of the drug-protein complexes but does not prevent the drug binding process. Our modeling study suggests that the drug can target efficiently the different forms of PD-L1 in cells, glycosylated, ubiquitinated or not. These models of N-glycosylated and ubiquitinated PD-L1 will be useful to study other PD-L1 protein complexes.     

New potential DNA intercalators of the carbazole series from indole-2,3-quinodimethanes: Synthesis,crystal structure,and molecular modeling with a watson-crick mini-helix

Summary 1-Alkylpyrano[3,4-b]indol-3-ones3 react via a Diels-Alder step with an aryne or N-phenylmaleimide to furnish the new [b]annellated carbazoles4–10 in a one-pot process. In an analogous procedure, the in situ generated N-benzoylindole-2,3-quinodimethane (13) reacted with quinones to furnish the dioxocarbazoles14–16. Compounds4–8 and14–16 with a coplanar skeleton are members of a class of potential DNA intercalators, as has been shown for5 and8 by X-ray structural analysis. On the basis of the geometries determined by X-ray crystallography, the intercalative binding of these molecules with a Watson-Crick mini-helix was predicted by molecular modeling methods.

---

Neue potentielle DNA-Interkalatoren der Carbazol-Reihe aus Indol-2,3-chinodimethanen: Synthese, Kristallstruktur und Molecular Modeling mit einer Watson-Crick Minihelix

Zusammenfassung 1-Alkylpyrano[3,4-b]indol-3-one3 reagieren über einen Diels-Alder-Schritt mit Arin oder N-Phenylmaleinimid zu [b]annellierten Carbazolen4–10 in einer Einstufenreaktion. In analoger Weise reagiert ein in situ erzeugtes N-Benzoylindol-2,3-chinodimethan13 mit Chinonen zu den Dioxocarbazolen14–16. Die Verbindungen4–8 und14–16 gehören infolge ihrer coplanaren Struktur zur Klasse potentieller DNA-Interkalatoren. Auf der Basis von Röntgenstrukturanalysen von5 und8 wird die interkalative Bindung mit einer Watson-Crick Minihelix durch Molecular Modeling vorhergesagt.

     

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.