Sample records for hueckel calculations ligand

  1. Behavior of molecules on interstellar grains - Application of the Langevin equation and iterative extended Hueckel (United States)

    Aronowitz, S.; Chang, S.


    The Langevin equation was used to explore an adsorbate desorption mechanism. Calculations were performed using iterative extended Hueckel on a silica model site with various small adsorbates, e.g., H, CH, OH, NO, CO. It was found that barriers to free traversal from one site to another are substantial (about 3-10 eV). A bootstrap desorption mechanism for some molecules in the process of forming at a site also became apparent from the calculations. The desorption mechanisms appear to be somewhat balanced by a counterforce - the attraction of sites for the newly desorbed molecule. The order of attraction to a silica grain site for the diatomic molecules considered was OH greater than CH greater than CO greater than NO, when these entities were sufficiently distant. The nature of the silica grain and that of the 'cold' desorption mechanism, when considered together, suggest that the abundance of very small grains might be less common than anticipated.

  2. PDB ligand conformational energies calculated quantum-mechanically. (United States)

    Sitzmann, Markus; Weidlich, Iwona E; Filippov, Igor V; Liao, Chenzhong; Peach, Megan L; Ihlenfeldt, Wolf-Dietrich; Karki, Rajeshri G; Borodina, Yulia V; Cachau, Raul E; Nicklaus, Marc C


    We present here a greatly updated version of an earlier study on the conformational energies of protein-ligand complexes in the Protein Data Bank (PDB) [Nicklaus et al. Bioorg. Med. Chem. 1995, 3, 411-428], with the goal of improving on all possible aspects such as number and selection of ligand instances, energy calculations performed, and additional analyses conducted. Starting from about 357,000 ligand instances deposited in the 2008 version of the Ligand Expo database of the experimental 3D coordinates of all small-molecule instances in the PDB, we created a "high-quality" subset of ligand instances by various filtering steps including application of crystallographic quality criteria and structural unambiguousness. Submission of 640 Gaussian 03 jobs yielded a set of about 415 successfully concluded runs. We used a stepwise optimization of internal degrees of freedom at the DFT level of theory with the B3LYP/6-31G(d) basis set and a single-point energy calculation at B3LYP/6-311++G(3df,2p) after each round of (partial) optimization to separate energy changes due to bond length stretches vs bond angle changes vs torsion changes. Even for the most "conservative" choice of all the possible conformational energies-the energy difference between the conformation in which all internal degrees of freedom except torsions have been optimized and the fully optimized conformer-significant energy values were found. The range of 0 to ~25 kcal/mol was populated quite evenly and independently of the crystallographic resolution. A smaller number of "outliers" of yet higher energies were seen only at resolutions above 1.3 Å. The energies showed some correlation with molecular size and flexibility but not with crystallographic quality metrics such as the Cruickshank diffraction-component precision index (DPI) and R(free)-R, or with the ligand instance-specific metrics such as occupancy-weighted B-factor (OWAB), real-space R factor (RSR), and real-space correlation coefficient

  3. CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application. (United States)

    Jo, Sunhwan; Jiang, Wei; Lee, Hui Sun; Roux, Benoît; Im, Wonpil


    Advanced free energy perturbation molecular dynamics (FEP/MD) simulation methods are available to accurately calculate absolute binding free energies of protein-ligand complexes. However, these methods rely on several sophisticated command scripts implementing various biasing energy restraints to enhance the convergence of the FEP/MD calculations, which must all be handled properly to yield correct results. Here, we present a user-friendly Web interface, CHARMM-GUI Ligand Binder ( ), to provide standardized CHARMM input files for calculations of absolute binding free energies using the FEP/MD simulations. A number of features are implemented to conveniently set up the FEP/MD simulations in highly customizable manners, thereby permitting an accelerated throughput of this important class of computations while decreasing the possibility of human errors. The interface and a series of input files generated by the interface are tested with illustrative calculations of absolute binding free energies of three nonpolar aromatic ligands to the L99A mutant of T4 lysozyme and three FK506-related ligands to FKBP12. Statistical errors within individual calculations are found to be small (~1 kcal/mol), and the calculated binding free energies generally agree well with the experimental measurements and the previous computational studies (within ~2 kcal/mol). Therefore, CHARMM-GUI Ligand Binder provides a convenient and reliable way to set up the ligand binding free energy calculations and can be applicable to pharmaceutically important protein-ligand systems.

  4. Quantum mechanical calculation of nanomaterial-ligand interaction energies by molecular fractionation with conjugated caps method (United States)

    Zhang, Dawei


    Molecular fractionation with conjugate caps (MFCC) method is introduced for the efficient estimation of quantum mechanical (QM) interaction energies between nanomaterial (carbon nanotube, fullerene, and graphene surface) and ligand (charged and neutral). In the calculations, nanomaterials are partitioned into small fragments and conjugated caps that are properly capped, and the interaction energies can be obtained through the summation of QM calculations of the fragments from which the contribution of the conjugated caps is removed. All the calculations were performed by density functional theory (DFT) and dispersion contributions for the attractive interactions were investigated by dispersion corrected DFT method. The predicted interaction energies by MFCC at each computational level are found to give excellent agreement with full system (FS) calculations with the mean energy deviation just a fractional kcal/mol. The accurate determination of nanomaterial-ligand interaction energies by MFCC suggests that it is an effective method for performing QM calculations on nanomaterial-ligand systems.

  5. Quantum mechanical calculation of nanomaterial-ligand interaction energies by molecular fractionation with conjugated caps method (United States)

    Zhang, Dawei


    Molecular fractionation with conjugate caps (MFCC) method is introduced for the efficient estimation of quantum mechanical (QM) interaction energies between nanomaterial (carbon nanotube, fullerene, and graphene surface) and ligand (charged and neutral). In the calculations, nanomaterials are partitioned into small fragments and conjugated caps that are properly capped, and the interaction energies can be obtained through the summation of QM calculations of the fragments from which the contribution of the conjugated caps is removed. All the calculations were performed by density functional theory (DFT) and dispersion contributions for the attractive interactions were investigated by dispersion corrected DFT method. The predicted interaction energies by MFCC at each computational level are found to give excellent agreement with full system (FS) calculations with the mean energy deviation just a fractional kcal/mol. The accurate determination of nanomaterial-ligand interaction energies by MFCC suggests that it is an effective method for performing QM calculations on nanomaterial-ligand systems. PMID:28300179

  6. Thermodynamics calculation of protein-ligand interactions by QM/MM polarizable charge parameters. (United States)

    Wang, Jinan; Shao, Qiang; Cossins, Benjamin P; Shi, Jiye; Chen, Kaixian; Zhu, Weiliang


    The calculation of protein-ligand binding free energy (ΔG) is of great importance for virtual screening and drug design. Molecular dynamics (MD) simulation has been an attractive tool to investigate this scientific problem. However, the reliability of such approach is affected by many factors including electrostatic interaction calculation. Here, we present a practical protocol using quantum mechanics/molecular mechanics (QM/MM) calculations to generate polarizable QM protein charge (QMPC). The calculated QMPC of some atoms in binding pockets was obviously different from that calculated by AMBER ff03, which might significantly affect the calculated ΔG. To evaluate the effect, the MD simulations and MM/GBSA calculation with QMPC for 10 protein-ligand complexes, and the simulation results were then compared to those with the AMBER ff03 force field and experimental results. The correlation coefficient between the calculated ΔΔG using MM/GBSA under QMPC and the experimental data is .92, while that with AMBER ff03 force field is .47 for the complexes formed by streptavidin or its mutants and biotin. Moreover, the calculated ΔΔG with QMPC for the complexes formed by ERβ and five ligands is positively related to experimental result with correlation coefficient of .61, while that with AMBER ff03 charge is negatively related to experimental data with correlation coefficient of .42. The detailed analysis shows that the electrostatic polarization introduced by QMPC affects the electrostatic contribution to the binding affinity and thus, leads to better correlation with experimental data. Therefore, this approach should be useful to virtual screening and drug design.

  7. Improving the LIE Method for Binding Free Energy Calculations of Protein-Ligand Complexes. (United States)

    Miranda, Williams E; Noskov, Sergei Yu; Valiente, Pedro A


    In this work, we introduced an improved linear interaction energy (LIE) method parameterization for computations of protein–ligand binding free energies. The protocol, coined LIE-D, builds on the linear relationship between the empirical coefficient γ in the standard LIE scheme and the D parameter, introduced in our work. The D-parameter encompasses the balance (difference) between electrostatic (polar) and van der Waals (nonpolar) energies in protein–ligand complexes. Leave-one-out cross-validation showed that LIE-D reproduced accurately the absolute binding free energies for our training set of protein–ligand complexes ( = 0.92 kcal/mol, SDerror = 0.66 kcal/mol, R(2) = 0.90, QLOO(2) = 0.89, and sPRESS(LOO) = 1.28 kcal/mol). We also demonstrated LIE-D robustness by predicting accurately the binding free energies for three different protein–ligand systems outside the training data set, where the electrostatic and van der Waals interaction energies were calculated with different force fields.

  8. Blinded evaluation of farnesoid X receptor (FXR) ligands binding using molecular docking and free energy calculations (United States)

    Selwa, Edithe; Elisée, Eddy; Zavala, Agustin; Iorga, Bogdan I.


    Our participation to the D3R Grand Challenge 2 involved a protocol in two steps, with an initial analysis of the available structural data from the PDB allowing the selection of the most appropriate combination of docking software and scoring function. Subsequent docking calculations showed that the pose prediction can be carried out with a certain precision, but this is dependent on the specific nature of the ligands. The correct ranking of docking poses is still a problem and cannot be successful in the absence of good pose predictions. Our free energy calculations on two different subsets provided contrasted results, which might have the origin in non-optimal force field parameters associated with the sulfonamide chemical moiety.

  9. Use of the FACTS solvation model for protein-ligand docking calculations. Application to EADock. (United States)

    Zoete, Vincent; Grosdidier, Aurélien; Cuendet, Michel; Michielin, Olivier


    Protein-ligand docking has made important progress during the last decade and has become a powerful tool for drug development, opening the way to virtual high throughput screening and in silico structure-based ligand design. Despite the flattering picture that has been drawn, recent publications have shown that the docking problem is far from being solved, and that more developments are still needed to achieve high successful prediction rates and accuracy. Introducing an accurate description of the solvation effect upon binding is thought to be essential to achieve this goal. In particular, EADock uses the Generalized Born Molecular Volume 2 (GBMV2) solvent model, which has been shown to reproduce accurately the desolvation energies calculated by solving the Poisson equation. Here, the implementation of the Fast Analytical Continuum Treatment of Solvation (FACTS) as an implicit solvation model in small molecules docking calculations has been assessed using the EADock docking program. Our results strongly support the use of FACTS for docking. The success rates of EADock/FACTS and EADock/GBMV2 are similar, i.e. around 75% for local docking and 65% for blind docking. However, these results come at a much lower computational cost: FACTS is 10 times faster than GBMV2 in calculating the total electrostatic energy, and allows a speed up of EADock by a factor of 4. This study also supports the EADock development strategy relying on the CHARMM package for energy calculations, which enables straightforward implementation and testing of the latest developments in the field of Molecular Modeling.

  10. How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations. (United States)

    Kaus, Joseph W; Harder, Edward; Lin, Teng; Abel, Robert; McCammon, J Andrew; Wang, Lingle


    Recent advances in improved force fields and sampling methods have made it possible for the accurate calculation of protein–ligand binding free energies. Alchemical free energy perturbation (FEP) using an explicit solvent model is one of the most rigorous methods to calculate relative binding free energies. However, for cases where there are high energy barriers separating the relevant conformations that are important for ligand binding, the calculated free energy may depend on the initial conformation used in the simulation due to the lack of complete sampling of all the important regions in phase space. This is particularly true for ligands with multiple possible binding modes separated by high energy barriers, making it difficult to sample all relevant binding modes even with modern enhanced sampling methods. In this paper, we apply a previously developed method that provides a corrected binding free energy for ligands with multiple binding modes by combining the free energy results from multiple alchemical FEP calculations starting from all enumerated poses, and the results are compared with Glide docking and MM-GBSA calculations. From these calculations, the dominant ligand binding mode can also be predicted. We apply this method to a series of ligands that bind to c-Jun N-terminal kinase-1 (JNK1) and obtain improved free energy results. The dominant ligand binding modes predicted by this method agree with the available crystallography, while both Glide docking and MM-GBSA calculations incorrectly predict the binding modes for some ligands. The method also helps separate the force field error from the ligand sampling error, such that deviations in the predicted binding free energy from the experimental values likely indicate possible inaccuracies in the force field. An error in the force field for a subset of the ligands studied was identified using this method, and improved free energy results were obtained by correcting the partial charges assigned to the

  11. NMR shielding calculations across the periodic table: diamagnetic uranium compounds. 2. Ligand and metal NMR. (United States)

    Schreckenbach, Georg


    In this and a previous article (J. Phys. Chem. A 2000, 104, 8244), the range of application for relativistic density functional theory (DFT) is extended to the calculation of nuclear magnetic resonance (NMR) shieldings and chemical shifts in diamagnetic actinide compounds. Two relativistic DFT methods are used, ZORA ("zeroth-order regular approximation") and the quasirelativistic (QR) method. In the given second paper, NMR shieldings and chemical shifts are calculated and discussed for a wide range of compounds. The molecules studied comprise uranyl complexes, [UO(2)L(n)](+/-)(q); UF(6); inorganic UF(6) derivatives, UF(6-n)Cl(n), n = 0-6; and organometallic UF(6) derivatives, UF(6-n)(OCH(3))(n), n = 0-5. Uranyl complexes include [UO(2)F(4)](2-), [UO(2)Cl(4)](2-), [UO(2)(OH)(4)](2-), [UO(2)(CO(3))(3)](4-), and [UO(2)(H(2)O)(5)](2+). For the ligand NMR, moderate (e.g., (19)F NMR chemical shifts in UF(6-n)Cl(n)) to excellent agreement [e.g., (19)F chemical shift tensor in UF(6) or (1)H NMR in UF(6-n)(OCH(3))(n)] has been found between theory and experiment. The methods have been used to calculate the experimentally unknown (235)U NMR chemical shifts. A large chemical shift range of at least 21,000 ppm has been predicted for the (235)U nucleus. ZORA spin-orbit appears to be the most accurate method for predicting actinide metal chemical shifts. Trends in the (235)U NMR chemical shifts of UF(6-n)L(n) molecules are analyzed and explained in terms of the calculated electronic structure. It is argued that the energy separation and interaction between occupied and virtual orbitals with f-character are the determining factors.

  12. Protein-Ligand Binding Potential of Mean Force Calculations with Hamiltonian Replica Exchange on Alchemical Interaction Grids

    CERN Document Server

    Minh, David D L


    A binding potential of mean force (BPMF) is a free energy of noncovalent association in which one binding partner is flexible and the other is rigid. I have developed a method to calculate BPMFs for protein-ligand systems. The method is based on replica exchange sampling from multiple thermodynamic states at different temperatures and protein-ligand interaction strengths. Protein-ligand interactions are represented by interpolating precomputed electrostatic and van der Waals grids. Using a simple estimator for thermodynamic length, thermodynamic states are initialized at approximately equal intervals. The method is demonstrated on the Astex diverse set, a database of 85 protein-ligand complexes relevant to pharmacy or agriculture. Fifteen independent simulations of each complex were started using poses from crystallography, docking, or the lowest-energy pose observed in the other simulations. Benchmark simulations completed within three days on a single processor. Overall, protocols initialized using the ther...

  13. Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis. (United States)

    Wang, Changhao; Nguyen, Peter H; Pham, Kevin; Huynh, Danielle; Le, Thanh-Binh Nancy; Wang, Hongli; Ren, Pengyu; Luo, Ray


    Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) methods have become widely adopted in estimating protein-ligand binding affinities due to their efficiency and high correlation with experiment. Here different computational alternatives were investigated to assess their impact to the agreement of MMPBSA calculations with experiment. Seven receptor families with both high-quality crystal structures and binding affinities were selected. First the performance of nonpolar solvation models was studied and it was found that the modern approach that separately models hydrophobic and dispersion interactions dramatically reduces RMSD's of computed relative binding affinities. The numerical setup of the Poisson-Boltzmann methods was analyzed next. The data shows that the impact of grid spacing to the quality of MMPBSA calculations is small: the numerical error at the grid spacing of 0.5 Å is already small enough to be negligible. The impact of different atomic radius sets and different molecular surface definitions was further analyzed and weak influences were found on the agreement with experiment. The influence of solute dielectric constant was also analyzed: a higher dielectric constant generally improves the overall agreement with experiment, especially for highly charged binding pockets. The data also showed that the converged simulations caused slight reduction in the agreement with experiment. Finally the direction of estimating absolute binding free energies was briefly explored. Upon correction of the binding-induced rearrangement free energy and the binding entropy lost, the errors in absolute binding affinities were also reduced dramatically when the modern nonpolar solvent model was used, although further developments were apparently necessary to further improve the MMPBSA methods. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  14. Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015. (United States)

    Deng, Nanjie; Flynn, William F; Xia, Junchao; Vijayan, R S K; Zhang, Baofeng; He, Peng; Mentes, Ahmet; Gallicchio, Emilio; Levy, Ronald M


    We describe binding free energy calculations in the D3R Grand Challenge 2015 for blind prediction of the binding affinities of 180 ligands to Hsp90. The present D3R challenge was built around experimental datasets involving Heat shock protein (Hsp) 90, an ATP-dependent molecular chaperone which is an important anticancer drug target. The Hsp90 ATP binding site is known to be a challenging target for accurate calculations of ligand binding affinities because of the ligand-dependent conformational changes in the binding site, the presence of ordered waters and the broad chemical diversity of ligands that can bind at this site. Our primary focus here is to distinguish binders from nonbinders. Large scale absolute binding free energy calculations that cover over 3000 protein-ligand complexes were performed using the BEDAM method starting from docked structures generated by Glide docking. Although the ligand dataset in this study resembles an intermediate to late stage lead optimization project while the BEDAM method is mainly developed for early stage virtual screening of hit molecules, the BEDAM binding free energy scoring has resulted in a moderate enrichment of ligand screening against this challenging drug target. Results show that, using a statistical mechanics based free energy method like BEDAM starting from docked poses offers better enrichment than classical docking scoring functions and rescoring methods like Prime MM-GBSA for the Hsp90 data set in this blind challenge. Importantly, among the three methods tested here, only the mean value of the BEDAM binding free energy scores is able to separate the large group of binders from the small group of nonbinders with a gap of 2.4 kcal/mol. None of the three methods that we have tested provided accurate ranking of the affinities of the 147 active compounds. We discuss the possible sources of errors in the binding free energy calculations. The study suggests that BEDAM can be used strategically to discriminate

  15. Sequestering uranium from UO2(CO3)3(4-) in seawater with amine ligands: density functional theory calculations. (United States)

    Guo, Xiaojing; Huang, Liangliang; Li, Cheng; Hu, Jiangtao; Wu, Guozhong; Huai, Ping


    The polystyrene-supported primary amine -CH2NH2 has shown an at least 3-fold increase in uranyl capacity compared to a diamidoxime ligand on a polystyrene support. This study aims to understand the coordination of substitution complexes from UO2(CO3)3(4-) and amines using density functional theory calculations. Four kinds of amines (diethylamine (DEA), ethylenediamine (EDA), diethylenetriamine (DETA) and triethylenetetramine (TETA)) were selected because they belong to different classes and have different chain lengths. The geometrical structures, electronic structures and the thermodynamic stabilities of various substitution complexes, as well as the trends in their calculated properties were investigated at equilibrium. In these optimized complexes, DEA groups bind to uranyl as monodentate ligands; EDA groups serve as monodentate and bidentate ligands; DETA groups act as monodentate and tridentate ligands; while TETA groups serve as monodentate, bidentate and tridentate ligands. The thermodynamic analysis confirmed that the primary amines coordinate to uranyl more strongly than does the secondary amine. The stabilities of substitution complexes with primary amines were calculated to decrease with increasing chain length of the amine, except for UO2(L2)(2+). Of the complexes analyzed, only UO2L(CO3)2(2-) (L = EDA and DETA) and UO2L2CO3 (L = EDA) were predicted to form from the substitution reactions with UO2(CO3)3(4-) and protonated amines as reactants in aqueous solution. Amines were calculated to be comparable to, or sometimes weaker than, amidoximate in replacing CO3(2-) in UO2(CO3)3(4-) to coordinate to uranium. Therefore, the coordination mechanism, in which amines replace carbonates to bind to uranyl, is not primarily responsible for the experimentally observed 3-fold or greater increase in uranyl capacity of primary amines compared to a diamidoxime ligand. Based on the results of our calculations, we believe that the cation exchange mechanism, in which the

  16. Importance of the ligand basis set in ab initio thermochemical calculations of transition metal species (United States)

    Plascencia, Cesar; Wang, Jiaqi; Wilson, Angela K.


    The impact of basis set choice has been considered for a series of transition metal (TM) species. The need for higher level correlation consistent basis sets on both the metal and ligand has been investigated, and permutations in the pairings of basis set used for TM's and basis set used for ligands can lead to effective routes to complete basis set (CBS) limit extrapolations of thermochemical energetics with little change in thermochemical predictions as compared to those resulting from the use of traditional basis set pairings, while enabling computational cost savings. Basis set superposition errors (BSSE) that can arise have also been considered.

  17. Structure simulation into a lamellar supramolecular network and calculation of the metal ions/ligands ratio

    Directory of Open Access Journals (Sweden)

    Visa Aurelia


    Full Text Available Abstract Background Research interest in phosphonates metal organic frameworks (MOF has increased extremely in the last two decades, because of theirs fascinating and complex topology and structural flexibility. In this paper we present a mathematical model for ligand/metal ion ratio of an octahedral (Oh network of cobalt vinylphosphonate (Co(vP·H2O. Results A recurrent relationship of the ratio between the number of ligands and the number of metal ions in a lamellar octahedral (Oh network Co(vP·H2O, has been deducted by building the 3D network step by step using HyperChem 7.52 package. The mathematical relationship has been validated using X ray analysis, experimental thermogravimetric and elemental analysis data. Conclusions Based on deducted recurrence relationship, we can conclude prior to perform X ray analysis, that in the case of a thermogravimetric analysis pointing a ratio between the number of metal ions and ligands number around 1, the 3D network will have a central metal ion that corresponds to a single ligand. This relation is valid for every type of supramolecular network with divalent metal central ion Oh coordinated and bring valuable information with low effort and cost.

  18. NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary

    Energy Technology Data Exchange (ETDEWEB)

    Yilmaz, Emel Maden; Güntert, Peter, E-mail: [Goethe University Frankfurt am Main, Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry (Germany)


    An algorithm, CYLIB, is presented for converting molecular topology descriptions from the PDB Chemical Component Dictionary into CYANA residue library entries. The CYANA structure calculation algorithm uses torsion angle molecular dynamics for the efficient computation of three-dimensional structures from NMR-derived restraints. For this, the molecules have to be represented in torsion angle space with rotations around covalent single bonds as the only degrees of freedom. The molecule must be given a tree structure of torsion angles connecting rigid units composed of one or several atoms with fixed relative positions. Setting up CYANA residue library entries therefore involves, besides straightforward format conversion, the non-trivial step of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is compatible with this tree structure. This can be done manually for small numbers of ligands but the process is time-consuming and error-prone. An automated method is necessary in order to handle the large number of different potential ligand molecules to be studied in drug design projects. Here, we present an algorithm for this purpose, and show that CYANA structure calculations can be performed with almost all small molecule ligands and non-standard amino acid residues in the PDB Chemical Component Dictionary.

  19. Improved Ligand-Field Calculation of Energy Spectrum and R-Line Thermal Shift of MgO:Cr3+

    Institute of Scientific and Technical Information of China (English)

    ZHANG Zheng-Jie; MA Dong-Ping


    Traditional ligand-field theory has to be improved by taking into account both pure electronic contribution and electron-phonon interaction one (including lattice-vibrational relaxation energy). By means of improved ligand-field theory, the R-line, t322T1 lines, t22(3T1)e4T2, and t22(3T1)e4T1 bands, ground-state g factor, four strain-induced levelsplittings, and R-line thermalshift of MgO:Cr3+ have been calculated. The results are in very good agreement with the experimental data. It is found that for MgO:Cr3+, the contributions due to electron-phonon interaction (EPI) come from the first-order term. In thermal shift of R-line of MgO:Cr3+, the temperature-dependent contribution due to EPI is dominant.

  20. Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets. (United States)

    Feinstein, Wei P; Brylinski, Michal


    Computational approaches have emerged as an instrumental methodology in modern research. For example, virtual screening by molecular docking is routinely used in computer-aided drug discovery. One of the critical parameters for ligand docking is the size of a search space used to identify low-energy binding poses of drug candidates. Currently available docking packages often come with a default protocol for calculating the box size, however, many of these procedures have not been systematically evaluated. In this study, we investigate how the docking accuracy of AutoDock Vina is affected by the selection of a search space. We propose a new procedure for calculating the optimal docking box size that maximizes the accuracy of binding pose prediction against a non-redundant and representative dataset of 3,659 protein-ligand complexes selected from the Protein Data Bank. Subsequently, we use the Directory of Useful Decoys, Enhanced to demonstrate that the optimized docking box size also yields an improved ranking in virtual screening. Binding pockets in both datasets are derived from the experimental complex structures and, additionally, predicted by eFindSite. A systematic analysis of ligand binding poses generated by AutoDock Vina shows that the highest accuracy is achieved when the dimensions of the search space are 2.9 times larger than the radius of gyration of a docking compound. Subsequent virtual screening benchmarks demonstrate that this optimized docking box size also improves compound ranking. For instance, using predicted ligand binding sites, the average enrichment factor calculated for the top 1 % (10 %) of the screening library is 8.20 (3.28) for the optimized protocol, compared to 7.67 (3.19) for the default procedure. Depending on the evaluation metric, the optimal docking box size gives better ranking in virtual screening for about two-thirds of target proteins. This fully automated procedure can be used to optimize docking protocols in order to

  1. Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS software. (United States)

    Riniker, Sereina; Christ, Clara D; Hansen, Halvor S; Hünenberger, Philippe H; Oostenbrink, Chris; Steiner, Denise; van Gunsteren, Wilfred F


    The calculation of the relative free energies of ligand-protein binding, of solvation for different compounds, and of different conformational states of a polypeptide is of considerable interest in the design or selection of potential enzyme inhibitors. Since such processes in aqueous solution generally comprise energetic and entropic contributions from many molecular configurations, adequate sampling of the relevant parts of configurational space is required and can be achieved through molecular dynamics simulations. Various techniques to obtain converged ensemble averages and their implementation in the GROMOS software for biomolecular simulation are discussed, and examples of their application to biomolecules in aqueous solution are given.

  2. Synthesis, spectroscopic, DFT calculations and biological activity studies of ruthenium carbonyl complexes with 2-picolinic acid and a secondary ligand (United States)

    Shohayeb, Shahera M.; Mohamed, Rania G.; Moustafa, H.; El-Medani, Samir M.


    Thermal reaction of [Ru3(CO)12] with 2-picolinic acid (Hpic) in the absence and presence of a secondary ligand (pyridine, Py, bipyridine, Bipy, or thiourea, Tu) was investigated. Four complexes with molecular formulae: [Ru(CO)3(Hpic)], 1, [Ru2(CO)5(Hpic)(Py)], 2, [Ru2(CO)5(Hpic)(Tu)], 3 and [Ru2(CO)4(Hpic)(Bipy)], 4, were isolated. All complexes were characterized based on elemental analyses, IR, 1H NMR, magnetic studies, mass spectrometry and thermal analysis. The ligand and its complexes have been screened for antibacterial activities. Density Functional Theory (DFT) calculations at the B3LYP/6-311G (d,p)_ level of theory have been carried out to investigate the equilibrium geometry of the ligands. The optimized geometry parameters of the complexes were evaluated using B3LYP method and LANL2DZ basis set. The extent of natural charge population (core, valence and rydberg), exact electronic configuration, total Lewis and total non-Lewis are estimated and discussed in terms of natural bond orbitals (NBO) analysis.

  3. Free energy calculations on Transthyretin dissociation and ligand binding from Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Sørensen, Jesper; Hamelberg, Donald; McCammon, J. Andrew

    experimental results have helped to explain this aberrant behavior of TTR, however, structural insights of the amyloidgenic process are still lacking. Therefore, we have used all-atom molecular dynamics simulation and free energy calculations to study the initial phase of this process. We have calculated...... the free energy changes of the initial tetramer dissociation under different conditions and in the presence of thyroxine....

  4. Free energy calculations on Transthyretin dissociation and ligand binding from Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Sørensen, Jesper; Hamelberg, Donald; McCammon, J. Andrew

    experimental results have helped to explain this aberrant behavior of TTR, however, structural insights of the amyloidgenic process are still lacking. Therefore, we have used all-atom molecular dynamics simulation and free energy calculations to study the initial phase of this process. We have calculated...... the free energy changes of the initial tetramer dissociation under different conditions and in the presence of thyroxine....

  5. Numerical calculation of protein-ligand binding rates through solution of the Smoluchowski equation using smooth particle hydrodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Wenxiao; Daily, Michael D.; Baker, Nathan A.


    We demonstrate the accuracy and effectiveness of a Lagrangian particle-based method, smoothed particle hydrodynamics (SPH), to study diffusion in biomolecular systems by numerically solving the time-dependent Smoluchowski equation for continuum diffusion. The numerical method is first verified in simple systems and then applied to the calculation of ligand binding to an acetylcholinesterase monomer. Unlike previous studies, a reactive Robin boundary condition (BC), rather than the absolute absorbing (Dirichlet) boundary condition, is considered on the reactive boundaries. This new boundary condition treatment allows for the analysis of enzymes with "imperfect" reaction rates. Rates for inhibitor binding to mAChE are calculated at various ionic strengths and compared with experiment and other numerical methods. We find that imposition of the Robin BC improves agreement between calculated and experimental reaction rates. Although this initial application focuses on a single monomer system, our new method provides a framework to explore broader applications of SPH in larger-scale biomolecular complexes by taking advantage of its Lagrangian particle-based nature.

  6. Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions. (United States)

    Singh, Nidhi; Warshel, Arieh


    Calculating the absolute binding free energies is a challenging task. Reliable estimates of binding free energies should provide a guide for rational drug design. It should also provide us with deeper understanding of the correlation between protein structure and its function. Further applications may include identifying novel molecular scaffolds and optimizing lead compounds in computer-aided drug design. Available options to evaluate the absolute binding free energies range from the rigorous but expensive free energy perturbation to the microscopic linear response approximation (LRA/beta version) and related approaches including the linear interaction energy (LIE) to the more approximated and considerably faster scaled protein dipoles Langevin dipoles (PDLD/S-LRA version) as well as the less rigorous molecular mechanics Poisson-Boltzmann/surface area (MM/PBSA) and generalized born/surface area (MM/GBSA) to the less accurate scoring functions. There is a need for an assessment of the performance of different approaches in terms of computer time and reliability. We present a comparative study of the LRA/beta, the LIE, the PDLD/S-LRA/beta, and the more widely used MM/PBSA and assess their abilities to estimate the absolute binding energies. The LRA and LIE methods perform reasonably well but require specialized parameterization for the nonelectrostatic term. The PDLD/S-LRA/beta performs effectively without the need of reparameterization. Our assessment of the MM/PBSA is less optimistic. This approach appears to provide erroneous estimates of the absolute binding energies because of its incorrect entropies and the problematic treatment of electrostatic energies. Overall, the PDLD/S-LRA/beta appears to offer an appealing option for the final stages of massive screening approaches.

  7. Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations. (United States)

    Jiang, Wei; Roux, Benoît


    Free Energy Perturbation with Replica Exchange Molecular Dynamics (FEP/REMD) offers a powerful strategy to improve the convergence of free energy computations. In particular, it has been shown previously that a FEP/REMD scheme allowing random moves within an extended replica ensemble of thermodynamic coupling parameters "lambda" can improve the statistical convergence in calculations of absolute binding free energy of ligands to proteins [J. Chem. Theory Comput. 2009, 5, 2583]. In the present study, FEP/REMD is extended and combined with an accelerated MD simulations method based on Hamiltonian replica-exchange MD (H-REMD) to overcome the additional problems arising from the existence of kinetically trapped conformations within the protein receptor. In the combined strategy, each system with a given thermodynamic coupling factor lambda in the extended ensemble is further coupled with a set of replicas evolving on a biased energy surface with boosting potentials used to accelerate the inter-conversion among different rotameric states of the side chains in the neighborhood of the binding site. Exchanges are allowed to occur alternatively along the axes corresponding to the thermodynamic coupling parameter lambda and the boosting potential, in an extended dual array of coupled lambda- and H-REMD simulations. The method is implemented on the basis of new extensions to the REPDSTR module of the biomolecular simulation program CHARMM. As an illustrative example, the absolute binding free energy of p-xylene to the nonpolar cavity of the L99A mutant of T4 lysozyme was calculated. The tests demonstrate that the dual lambda-REMD and H-REMD simulation scheme greatly accelerates the configurational sampling of the rotameric states of the side chains around the binding pocket, thereby improving the convergence of the FEP computations.

  8. Oxidation of phenyl and hydride ligands of bis(pentamethylcyclopentadienyl)hafnium derivatives by nitrous oxide via selective oxygen atom transfer reactions: insights from quantum chemistry calculations. (United States)

    Xie, Hujun; Liu, Chengcheng; Yuan, Ying; Zhou, Tao; Fan, Ting; Lei, Qunfang; Fang, Wenjun


    The mechanisms for the oxidation of phenyl and hydride ligands of bis(pentamethylcyclopentadienyl)hafnium derivatives (Cp* = η(5)-C5Me5) by nitrous oxide via selective oxygen atom transfer reactions have been systematically studied by means of density functional theory (DFT) calculations. On the basis of the calculations, we investigated the original mechanism proposed by Hillhouse and co-workers for the activation of N2O. The calculations showed that the complex with an initial O-coordination of N2O to the coordinatively unsaturated Hf center is not a local minimum. Then we proposed a new reaction mechanism to investigate how N2O is activated and why N2O selectively oxidize phenyl and hydride ligands of . Frontier molecular orbital theory analysis indicates that N2O is activated by nucleophilic attack by the phenyl or hydride ligand. Present calculations provide new insights into the activation of N2O involving the direct oxygen atom transfer from nitrous oxide to metal-ligand bonds instead of the generally observed oxygen abstraction reaction to generate metal-oxo species.

  9. Specific interactions between lactose repressor protein and DNA affected by ligand binding: ab initio molecular orbital calculations. (United States)

    Ohyama, Tatsuya; Hayakawa, Masato; Nishikawa, Shin; Kurita, Noriyuki


    Transcription mechanisms of gene information from DNA to mRNA are essentially controlled by regulatory proteins such as a lactose repressor (LacR) protein and ligand molecules. Biochemical experiments elucidated that a ligand binding to LacR drastically changes the mechanism controlled by LacR, although the effect of ligand binding has not been clarified at atomic and electronic levels. We here investigated the effect of ligand binding on the specific interactions between LacR and operator DNA by the molecular simulations combined with classical molecular mechanics and ab initio fragment molecular orbital methods. The results indicate that the binding of anti-inducer ligand strengthens the interaction between LacR and DNA, which is consistent with the fact that the binding of anti-inducer enhances the repression of gene transcription by LacR. It was also elucidated that hydrating water molecules existing between LacR and DNA contribute to the specific interactions between LacR and DNA. Copyright © 2011 Wiley Periodicals, Inc.

  10. Computational prediction of binding affinity for CYP1A2-ligand complexes using empirical free energy calculations

    DEFF Research Database (Denmark)

    Poongavanam, Vasanthanathan; Olsen, Lars; Jørgensen, Flemming Steen


    , and methods based on statistical mechanics. In the present investigation, we started from an LIE model to predict the binding free energy of structurally diverse compounds of cytochrome P450 1A2 ligands, one of the important human metabolizing isoforms of the cytochrome P450 family. The data set includes both...... substrates and inhibitors. It appears that the electrostatic contribution to the binding free energy becomes negligible in this particular protein and a simple empirical model was derived, based on a training set of eight compounds. The root mean square error for the training set was 3.7 kJ/mol. Subsequent......Predicting binding affinities for receptor-ligand complexes is still one of the challenging processes in computational structure-based ligand design. Many computational methods have been developed to achieve this goal, such as docking and scoring methods, the linear interaction energy (LIE) method...

  11. Ruthenium(II) bipyridine complexes bearing new keto-enol azoimine ligands: synthesis, structure, electrochemistry and DFT calculations. (United States)

    Al-Noaimi, Mousa; Awwadi, Firas F; Mansi, Ahmad; Abdel-Rahman, Obadah S; Hammoudeh, Ayman; Warad, Ismail


    The novel azoimine ligand, Ph-NH-N=C(COCH3)-NHPh(C≡CH) (H2L), was synthesized and its molecular structure was determined by X-ray crystallography. Catalytic hydration of the terminal acetylene of H2L in the presence of RuCl3·3H2O in ethanol at reflux temperature yielded a ketone (L1=Ph-N=N-C(COCH3)=N-Ph(COCH3) and an enol (L2=Ph-N=N-C(COCH3)=N-PhC(OH)=CH2) by Markovnikov addition of water. Two mixed-ligand ruthenium complexes having general formula, trans-[Ru(bpy)(Y)Cl2] (1-2) (where Y=L1 (1) and Y=L2 (2), bpy is 2.2'-bipyrdine) were achieved by the stepwise addition of equimolar amounts of (H2L) and bpy ligands to RuCl3·3H2O in absolute ethanol. Theses complexes were characterized by elemental analyses and spectroscopic (IR, UV-Vis, and NMR (1D (1)H NMR, (13)C NMR, (DEPT-135), (DEPT-90), 2D (1)H-(1)H and (13)C-(1)H correlation (HMQC) spectroscopy)). The two complexes exhibit a quasi-reversible one electron Ru(II)/Ru(III) oxidation couple at 604 mV vs. ferrocene/ferrocenium (Cp2Fe(0/+)) couple along with one electron ligand reduction at -1010 mV. The crystal structure of complex 1 showed that the bidentate ligand L1 coordinates to Ru(II) by the azo- and imine-nitrogen donor atoms. The complex adopts a distorted trans octahedral coordination geometry of chloride ligands. The electronic spectra of 1 and 1+ in dichloromethane have been modeled by time-dependent density functional theory (TD-DFT). Copyright © 2014 Elsevier B.V. All rights reserved.

  12. Minimum-energy configurations of metallic clusters obtained by simulated annealing molecular dynamics using an Extended-Hueckel Hamiltonian

    Energy Technology Data Exchange (ETDEWEB)

    Rincon, Luis [Universidad de Los Andes, Merida (Venezuela)


    Semiempirical simulated annealing molecular dynamics method using a fictitious Lagrangian has been developed for the study of structural and electronic properties of micro- and nano-clusters. As an application of the present scheme, we study the structure of Na{sub n} clusters in the range of n=2-100, and compared the present calculation with some ab-initio model calculation. [Spanish] Se desarrollo un metodo de Dinamica Molecular-Recocido simulado usando un Lagrangiano ficticio para estudiar las propiedades electronicas y estructurales de micro- y nano-agregados. Como una aplicacion del presente esquema, se estudio la estructura de agregados de Na{sub n} en el rango entre n=2-100, y se compararon los resultados con algunos calculos ab-initio modelo.

  13. Toward Quantitatively Accurate Calculation of the Redox-Associated Acid-Base and Ligand Binding Equilibria of Aquacobalamin. (United States)

    Johnston, Ryne C; Zhou, Jing; Smith, Jeremy C; Parks, Jerry M


    Redox processes in complex transition metal-containing species are often intimately associated with changes in ligand protonation states and metal coordination number. A major challenge is therefore to develop consistent computational approaches for computing pH-dependent redox and ligand dissociation properties of organometallic species. Reduction of the Co center in the vitamin B12 derivative aquacobalamin can be accompanied by ligand dissociation, protonation, or both, making these properties difficult to compute accurately. We examine this challenge here by using density functional theory and continuum solvation to compute Co-ligand binding equilibrium constants (Kon/off), pKas, and reduction potentials for models of aquacobalamin in aqueous solution. We consider two models for cobalamin ligand coordination: the first follows the hexa, penta, tetra coordination scheme for Co(III), Co(II), and Co(I) species, respectively, and the second model features saturation of each vacant axial coordination site on Co(II) and Co(I) species with a single, explicit water molecule to maintain six directly interacting ligands or water molecules in each oxidation state. Comparing these two coordination schemes in combination with five dispersion-corrected density functionals, we find that the accuracy of the computed properties is largely independent of the scheme used, but including only a continuum representation of the solvent yields marginally better results than saturating the first solvation shell around Co throughout. PBE performs best, displaying balanced accuracy and superior performance overall, with RMS errors of 80 mV for seven reduction potentials, 2.0 log units for five pKas and 2.3 log units for two log Kon/off values for the aquacobalamin system. Furthermore, we find that the BP86 functional commonly used in corrinoid studies suffers from erratic behavior and inaccurate descriptions of Co-axial ligand binding, leading to substantial errors in predicted pKas and

  14. [Mo2(CN)11]:5- A detailed description of ligand-field spectra and magnetic properties by first-principles calculations. (United States)

    Hendrickx, Marc F A; Clima, S; Chibotaru, L F; Ceulemans, A


    An ab initio multiconfigurational approach has been used to calculate the ligand-field spectrum and magnetic properties of the title cyano-bridged dinuclear molybdenum complex. The rather large magnetic coupling parameter J for a single cyano bridge, as derived experimentally for this complex by susceptibility measurements, is confirmed to a high degree of accuracy by our CASPT2 calculations. Its electronic structure is rationalized in terms of spin-spin coupling between the two constituent hexacyano-monomolybdate complexes. An in-depth analysis on the basis of Anderson's kinetic exchange theory provides a qualitative picture of the calculated CASSCF antiferromagnetic ground-state eigenvector in the Mo dimer. Dynamic electron correlations as incorporated into our first-principles calculations by means of the CASPT2 method are essential to obtain quantitative agreement between theory and experiment.

  15. Molecular recognition in a diverse set of protein-ligand interactions studied with molecular dynamics simulations and end-point free energy calculations. (United States)

    Wang, Bo; Li, Liwei; Hurley, Thomas D; Meroueh, Samy O


    End-point free energy calculations using MM-GBSA and MM-PBSA provide a detailed understanding of molecular recognition in protein-ligand interactions. The binding free energy can be used to rank-order protein-ligand structures in virtual screening for compound or target identification. Here, we carry out free energy calculations for a diverse set of 11 proteins bound to 14 small molecules using extensive explicit-solvent MD simulations. The structure of these complexes was previously solved by crystallography and their binding studied with isothermal titration calorimetry (ITC) data enabling direct comparison to the MM-GBSA and MM-PBSA calculations. Four MM-GBSA and three MM-PBSA calculations reproduced the ITC free energy within 1 kcal·mol(-1) highlighting the challenges in reproducing the absolute free energy from end-point free energy calculations. MM-GBSA exhibited better rank-ordering with a Spearman ρ of 0.68 compared to 0.40 for MM-PBSA with dielectric constant (ε = 1). An increase in ε resulted in significantly better rank-ordering for MM-PBSA (ρ = 0.91 for ε = 10), but larger ε significantly reduced the contributions of electrostatics, suggesting that the improvement is due to the nonpolar and entropy components, rather than a better representation of the electrostatics. The SVRKB scoring function applied to MD snapshots resulted in excellent rank-ordering (ρ = 0.81). Calculations of the configurational entropy using normal-mode analysis led to free energies that correlated significantly better to the ITC free energy than the MD-based quasi-harmonic approach, but the computed entropies showed no correlation with the ITC entropy. When the adaptation energy is taken into consideration by running separate simulations for complex, apo, and ligand (MM-PBSAADAPT), there is less agreement with the ITC data for the individual free energies, but remarkably good rank-ordering is observed (ρ = 0.89). Interestingly, filtering MD snapshots by prescoring

  16. Synthesis, structural characterization and DFT calculation on a square-planar Ni(II) complex of a compartmental Schiff base ligand (United States)

    Biswas, Surajit; Dolai, Malay; Dutta, Arpan; Ali, Mahammad


    Reaction of a symmetric compartmental Schiff-base ligand, (H2L) with nickel(II) perchlorate hexahydrate in 1:1 M ratio in methanol gives rise to a mononuclear nickel(II) compound, NiL (1). The compound has been characterized by C, H, N microanalyses and UV-Vis spectra. The single crystal X-ray diffraction studies reveal a square planar geometry around the Ni(II) center. The compound crystallizes in monoclinic system with space group C2/c with a = 21.6425(6), b = 9.9481(3), c = 13.1958(4) Å, β = 107.728(2)°, V = 2706.16(14) Å3 and Z = 4. Ground state DFT optimization and TDDFT calculations on the ligand and complex were performed to get their UV-Vis spectral pattern.

  17. A new mixed-ligand copper(II) complex of (E)-N";-(2-hydroxybenzylidene) acetohydrazide: Synthesis, characterization, NLO behavior, DFT calculation and biological activities (United States)

    Yousef Ebrahimipour, S.; Sheikhshoaie, Iran; Crochet, Aurelien; Khaleghi, Moj; Fromm, Katharina M.


    A tridentate hydrazone Schiff base ligand, (E)-N";-(2-hydroxybenzylidene)acetohydrazide [HL], and its mixed-ligand Cu(II) complex [CuL(phen)], have been synthesized and characterized by elemental analyses, FT-IR, molar conductivity, UV-Vis spectroscopy. The structure of the complex has been determined by X-ray diffraction. This complex has square pyramidal geometry and the positions around central atom are occupied with donor atoms of Schiff base ligand and two nitrogens of 1,10-phenanthroline. Computational studies of compounds were performed by using DFT calculations. The linear polarizabilities and first hyperpolarizabilities of the studied molecules indicate that these compounds can be good candidates of nonlinear optical materials. It is in accordance with experimental data. In addition, invitro antimicrobial results show that these compounds specially [CuL(phen)] have great potential of antibacterial activity against Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, Listeria monocytogenes bacteria and antifungal activity against Candida Albicans in comparison to some standard drugs.

  18. Synthesis, spectral characterization, computational calculations and biological activity of complexes designed from NNO donor Schiff-base ligand. (United States)

    El-Gammal, Ola A; Abu El-Reash, G M; Yousef, T A; Mefreh, M


    A new series of Co(II), Ni(II) and Cu(II) complexes of (Z)-2-oxo-2-(phenylamino)-N'-(1-(pyridin-2-yl)ethylidene)acetohydrazide (H2OPPAH) have been prepared and characterized by conventional techniques. The spectral data indicated that the ligand acts as neutral or mononegative NNO tridentate. On the basis of magnetic and electronic spectral data an octahedral geometry for Ni(II) and Cu(II) complexes and a tetrahedral geometry for Co(II) complex have been proposed. The molecular modeling using DFT method are drawn showing the bond length, bond angle, chemical reactivity, energy components (kcal/mol) and binding energy (kcal/mol) for all title compounds. The Kinetic parameters were determined for each thermal degradation stages of the ligand and its complexes using Coats-Redfern and Horowitz-Metzger methods. Also, the compounds were screened for antioxidant activity using ABTS free radical, anti-hemolytic, and in vitro cytotoxic assay. H2OPPAH showed the potent antioxidant activity followed by Co(II) and Cu(II) complexes. On the other hand Ni(II) complex exhibited weak antioxidant activity using ABTS free radical and Erlich and strong erythrocyte hemolysis activity.

  19. Synthesis, spectral characterization, computational calculations and biological activity of complexes designed from NNO donor Schiff-base ligand (United States)

    El-Gammal, Ola A.; El-Reash, G. M. Abu; Yousef, T. A.; Mefreh, M.


    A new series of Co(II), Ni(II) and Cu(II) complexes of (Z)-2-oxo-2-(phenylamino)-N‧-(1-(pyridin-2-yl)ethylidene)acetohydrazide (H2OPPAH) have been prepared and characterized by conventional techniques. The spectral data indicated that the ligand acts as neutral or mononegative NNO tridentate. On the basis of magnetic and electronic spectral data an octahedral geometry for Ni(II) and Cu(II) complexes and a tetrahedral geometry for Co(II) complex have been proposed. The molecular modeling using DFT method are drawn showing the bond length, bond angle, chemical reactivity, energy components (kcal/mol) and binding energy (kcal/mol) for all title compounds. The Kinetic parameters were determined for each thermal degradation stages of the ligand and its complexes using Coats-Redfern and Horowitz-Metzger methods. Also, the compounds were screened for antioxidant activity using ABTS free radical, anti-hemolytic, and in vitro cytotoxic assay. H2OPPAH showed the potent antioxidant activity followed by Co(II) and Cu(II) complexes. On the other hand Ni(II) complex exhibited weak antioxidant activity using ABTS free radical and Erlich and strong erythrocyte hemolysis activity.

  20. High-throughput calculation of protein-ligand binding affinities: modification and adaptation of the MM-PBSA protocol to enterprise grid computing. (United States)

    Brown, Scott P; Muchmore, Steven W


    We have developed a system for performing computations on an enterprise grid using a freely available package for grid computing that allows us to harvest unused CPU cycles off of employee desktop computers. By modifying the traditional formulation of Molecular Mechanics with Poisson-Boltzmann Surface Area (MM-PBSA) methodology, in combination with a coarse-grain parallelized implementation suitable for deployment onto our enterprise grid, we show that it is possible to produce rapid physics-based estimates of protein-ligand binding affinities that have good correlation to experimental data. This is demonstrated by examining the correlation of our calculated binding affinities to experimental data and also by comparison to the correlation obtained from the binding-affinity calculations using traditional MM-PBSA that are reported in the literature.

  1. Synthesis, Characterization, Properties and DFT Calculations of 2-(Benzo[b]thiophen-2-yl)pyridine-based Iridium(III) Complexes with Different Ancillary Ligands. (United States)

    Li, Gao-Nan; Zeng, Yong-Pi; Li, Kai-Xiu; Chen, Hao-Hua; Xie, Hui; Zhang, Fu-Lin; Chen, Guang-Ying; Niu, Zhi-Gang


    A series of new cyclometalated btp-based iridium(III) complexes with three different ancillary ligands, Ir(btp)2(bozp) (3a), Ir(btp)2(btzp) (3b) and Ir(btp)2(izp) (3c) (btp = 2-(benzo[b]thiophen-2-yl)pyridine, bozp =2-(benzo[d]oxazol-2-yl)phenol, btzp =2-(benzo[d]thiazol-2-yl)phenol, izp = 2-(2 H-indazol-2-yl)phenol), have been synthesized and fully characterized. The crystal structure of 3b has been determined by single crystal X-ray diffraction analysis. A comparative study has been carried out for complexes 3a - 3c by UV-vis absorption spectroscopy, photoluminescence spectroscopy, cyclic voltammetry and DFT calculations. This observation illustrates that the substitution of N or S in ancillary ligand can lead to a marked bathochromic shift of absorption and emission wavelengths. The spectroscopic characterisation of these complexes has been complemented by DFT and TD-DFT calculations, supporting the assignment of (3)MLCT/(3)LC to the lowest energy excited state.

  2. Mixed ligand Cu(II)N2O2 complexes: biomimetic synthesis, activities in vitro and biological models, theoretical calculations. (United States)

    Li, Chen; Yin, Bing; Kang, Yifan; Liu, Ping; Chen, Liang; Wang, Yaoyu; Li, Jianli


    Three new mixed ligand Cu(II)N2O2 complexes, namely, [Cu(II)(2-A-6-MBT)2(m-NB)2] (1), [Cu(II)(2-ABT)2(m-NB)2] (2), and [Cu(II)(2-ABT)2(o-NB)2] (3), (2-A-6-MBT = 2-amino-6-methoxybenzothiazole, m-NB = m-nitrobenzoate, 2-ABT = 2-aminobenzothiazole, and o-NB = o-nitrobenzoate), have been prepared by the biomimetic synthesis strategy, and their structures were determined by X-ray crystallography studies and spectral methods. These complexes exhibited the effective superoxide dismutase (SOD) activity and catecholase activity. On the basis of the experimental data and computational studies, the structure-activity relationship for these complexes was investigated. The results reveal that electron-accepting abilities of these complexes and coordination geometries have significant effects on the SOD activity and catecholase activity. Then, we found that 1 and 2 exerted potent intracellular antioxidant capacity in the model of H2O2-induced oxidative stress based on HeLa cervical cancer cells, which were screened out by the cytotoxicity assays of different kinds of cells. Furthermore, 1-3 showed the favorable biocompatibility in two different biological models: Saccharomyces cerevisiae and human vascular endothelial cells. These biological experimental data are indicative of the promising application potential of these complexes in biology and pharmacology.

  3. Charge and Spin States in Schiff Base Metal Complexes with a Disiloxane Unit Exhibiting a Strong Noninnocent Ligand Character: Synthesis, Structure, Spectroelectrochemistry, and Theoretical Calculations. (United States)

    Cazacu, Maria; Shova, Sergiu; Soroceanu, Alina; Machata, Peter; Bucinsky, Lukas; Breza, Martin; Rapta, Peter; Telser, Joshua; Krzystek, J; Arion, Vladimir B


    Mononuclear nickel(II), copper(II), and manganese(III) complexes with a noninnocent tetradentate Schiff base ligand containing a disiloxane unit were prepared in situ by reaction of 3,5-di-tert-butyl-2-hydroxybenzaldehyde with 1,3-bis(3-aminopropyl)tetramethyldisiloxane followed by addition of the appropriate metal(II) salt. The ligand H2L resulting from these reactions is a 2:1 condensation product of 3,5-di-tert-butyl-2-hydroxybenzaldehyde with 1,3-bis(3-aminopropyl)tetramethyldisiloxane. The resulting metal complexes, NiL·0.5CH2Cl2, CuL·1.5H2O, and MnL(OAc)·0.15H2O, were characterized by elemental analysis, spectroscopic methods (IR, UV-vis, X-band EPR, HFEPR, (1)H NMR), ESI mass spectrometry, and single crystal X-ray diffraction. Taking into account the well-known strong stabilizing effects of tert-butyl groups in positions 3 and 5 of the aromatic ring on phenoxyl radicals, we studied the one-electron and two-electron oxidation of the compounds using both experimental (chiefly spectroelectrochemistry) and computational (DFT) techniques. The calculated spin-density distribution and localized orbitals analysis revealed the oxidation locus and the effect of the electrochemical electron transfer on the molecular structure of the complexes, while time-dependent DFT calculations helped to explain the absorption spectra of the electrochemically generated species. Hyperfine coupling constants, g-tensors, and zero-field splitting parameters have been calculated at the DFT level of theory. Finally, the CASSCF approach has been employed to theoretically explore the zero-field splitting of the S = 2 MnL(OAc) complex for comparison purposes with the DFT and experimental HFEPR results. It is found that the D parameter sign strongly depends on the metal coordination geometry.

  4. Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation. (United States)

    Reif, Maria M; Oostenbrink, Chris


    The calculation of binding free energies of charged species to a target molecule is a frequently encountered problem in molecular dynamics studies of (bio-)chemical thermodynamics. Many important endogenous receptor-binding molecules, enzyme substrates, or drug molecules have a nonzero net charge. Absolute binding free energies, as well as binding free energies relative to another molecule with a different net charge will be affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). In the present study, charging contributions to binding free energies of small oligoatomic ions to a series of model host cavities functionalized with different chemical groups are calculated with classical atomistic molecular dynamics simulation. Electrostatic interactions are treated using a lattice-summation scheme or a cutoff-truncation scheme with Barker-Watts reaction-field correction, and the simulations are conducted in boxes of different edge lengths. It is illustrated that the charging free energies of the guest molecules in water and in the host strongly depend on the applied methodology and that neglect of correction terms for the artifacts introduced by the finite size of the simulated system and the use of an effective electrostatic interaction function considerably impairs the thermodynamic interpretation of guest-host interactions. Application of correction terms for the various artifacts yields consistent results for the charging contribution to binding free energies and is thus a prerequisite for the valid interpretation or prediction of experimental data via molecular dynamics simulation. Analysis and correction of electrostatic artifacts according to the scheme proposed in the present study should therefore be considered an integral part of careful free-energy calculation studies if changes in the net charge are involved.

  5. Luminescence investigation on Eu–pillar[5]arene-based diglycolamide (DGA) complexes: Nature of the complex, Judd–Ofelt calculations and effect of ligand structure

    Energy Technology Data Exchange (ETDEWEB)

    Sengupta, Arijit, E-mail: [Radiochemistry Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Wu, Lei; Feng, Wen; Yuan, Lihua [College of Chemistry, Key Laboratory for Radiation Physics and Technology of Ministry of Education, Institute of Nuclear Science and Technology, Sichuan, University, Chengdu 610064 (China); Natarajan, V. [Radiochemistry Division, Bhabha Atomic Research Centre, Mumbai 400085 (India)


    An attempt was made to understand the insight of complexation of Eu{sup 3+} ion with three different structurally modified pillar[5]arene-based diglycolamides (P5DGA) and a comparison was also made with their molecular identity, TODGA. {sup 7}F{sub 0}-{sup 5}D{sub 2}, {sup 5}G{sub 2,3,4}, {sup 5}L{sub 6} transitions were observed in the absorption profiles while {sup 5}D{sub 0}-{sup 7}F{sub 0,1,2,3,4} transitions for emission spectra. Number of water molecules present in the primary coordination sphere of Eu{sup 3+} and the number of species were calculated from the life time measurement of the complexes under investigation. From the splitting pattern of the luminescence spectra of Eu{sup 3+} complex the point group symmetry around Eu{sup 3+} was found to be C4v. Judd-Offelt parameters (Ω{sub λ}, λ=2,4) were calculated for the complexes and correlated with the covalency of metal ligand bonds and long range ordering, respectively. It was demonstrated that preorganization of ligating moieties on the platform of pillararenes favoured the covalency of the metal–ligand bond in diglycolamides. Different photo physical properties such as radiative and non radiative life time, magnetic and electric dipole transition probabilities, branching ratio values for different transitions, quantum efficiency were evaluated for all the Eu{sup 3+}-diglycolamide complexes. - Highlights: • The complexation of Eu{sup 3+} with pillar[5]arene-based diglycolamides (P5DGA) • Comparison with the molecular identity, TODGA. • Absorption spectra assigned as {sup 7}F{sub 0}-{sup 5}D{sub 2}, {sup 5}G{sub 2,3,4}, {sup 5}L{sub 6} transitions • Emission spectra assigned as {sup 5}D{sub 0}-{sup 7}F{sub 0,1,2,3,4} transitions • Number of inner sphere water molecules and number of species were calculated from the life time measurement • The point group symmetry around Eu{sup 3+} was found to be C4v. • Judd-Offelt parameters (Ω{sub λ}, λ=2,4) were calculated for the complexes.

  6. Calculation of vibrational shifts of nitrile probes in the active site of ketosteroid isomerase upon ligand binding. (United States)

    Layfield, Joshua P; Hammes-Schiffer, Sharon


    The vibrational Stark effect provides insight into the roles of hydrogen bonding, electrostatics, and conformational motions in enzyme catalysis. In a recent application of this approach to the enzyme ketosteroid isomerase (KSI), thiocyanate probes were introduced in site-specific positions throughout the active site. This paper implements a quantum mechanical/molecular mechanical (QM/MM) approach for calculating the vibrational shifts of nitrile (CN) probes in proteins. This methodology is shown to reproduce the experimentally measured vibrational shifts upon binding of the intermediate analogue equilinen to KSI for two different nitrile probe positions. Analysis of the molecular dynamics simulations provides atomistic insight into the roles that key residues play in determining the electrostatic environment and hydrogen-bonding interactions experienced by the nitrile probe. For the M116C-CN probe, equilinen binding reorients an active-site water molecule that is directly hydrogen-bonded to the nitrile probe, resulting in a more linear C≡N--H angle and increasing the CN frequency upon binding. For the F86C-CN probe, equilinen binding orients the Asp103 residue, decreasing the hydrogen-bonding distance between the Asp103 backbone and the nitrile probe and slightly increasing the CN frequency. This QM/MM methodology is applicable to a wide range of biological systems and has the potential to assist in the elucidation of the fundamental principles underlying enzyme catalysis.

  7. Three green luminescent cadmium complexes containing 8-aminoquinoline ligands: Syntheses, crystal structures, emission spectra and DFT calculations

    Energy Technology Data Exchange (ETDEWEB)

    Xu Heng; Huang Liangfang; Guo Limin; Zhang Yuanguang [Anhui Key Laboratory for Functional Coordination Compounds, Anqing Normal College, Anqing 246011 (China); Ren Xiaoming [Anhui Key Laboratory for Functional Coordination Compounds, Anqing Normal College, Anqing 246011 (China); Department of Applied Chemistry, Science College, Nanjing University of Technology, 5 Xin Mo Fan Road, Nanjing 210009 (China)], E-mail:; Song You [Coordination Chemistry Institute and State Key Laboratory, Nanjing University, Nanjing 210093 (China); Xie Jingli [School of Chemistry and Bio21 Institute, The University of Melbourne, Parkville, VIC 3010 (Australia)


    Three complexes, Cd(8-aminoql){sub 2}x{sub 2} (8-aminoql=8-aminoquinoline; X{sup -}=ClO{sub 4}{sup -}, SCN{sup -}, 1 and 2, respectively) and Cd(8-aminoql)(N{sub 3}){sub 2} (3), were synthesized and structurally characterized. For each complex, the Cd{sup 2+} ion exhibits distorted octahedral coordination geometry. Two 8-aminoquinoline molecules and two counter-anions are coordinated to the Cd{sup 2+} center to form a mononuclear species with two trans-ClO{sub 4}{sup -} anions for 1, while two SCN{sup -} anions adopt a cis-configuration for 2. The intermolecular H-bonding interactions between the -NH{sub 2} groups and the O atom (1) and the S atom (2) result in the formation of a 2-D layered structure. In the crystal of 3, the N{sub 3}{sup -} anions bridging the neighboring Cd(8-aminoql){sup 2+} units form a 1-D coordination polymer. The three complexes emit green luminescence. The emission bands possess a broad asymmetric feature, which can be assigned to L'LCT transitions based on DFT and TDDFT calculations.

  8. Novel polycarboxylated EDTA-type cyclodextrins as ligands for lanthanide binding: study of their luminescence, relaxivity properties of Gd(iii) complexes, and PM3 theoretical calculations. (United States)

    Maffeo, Davide; Lampropoulou, Maria; Fardis, Michael; Lazarou, Yannis G; Mavridis, Irene M; Mavridou, Despoina A I; Urso, Elena; Pratsinis, Harris; Kletsas, Dimitris; Yannakopoulou, Konstantina


    Novel -type cyclodextrin (CD) derivatives, , and , bearing 6, 7 and 8 bis(carboxymethyl)amino (iminodiacetic acid) groups, respectively, were prepared, and their complexation with Eu(iii), Tb(iii) and Gd(iii) ions was studied. Luminescence titrations and mass spectrometry showed formation of multimetal complexes ( 2 to 3, mainly 3 and exactly 4 metal ions), whereas luminescence lifetime measurements revealed the presence of exchangeable water molecules. Semiempirical quantum mechanical calculations, performed by the PM3 method and assessed by DFT calculations on model ligands, indicated efficient multi-metal complexation, in agreement with the experiment. The structures showed coordination of the metal ions in the outer primary side of the CDs via 4 carboxylate O atoms, 2 N atoms and a glucopyranose O atom per metal ion. Coordination of water molecules was also predicted, in accordance with experimental results. Calculated bond lengths and angles were in agreement with literature experimental values of lanthanide complexes. Calculated energies showed that complex stability decreases in the order > > . (1)H NMR molecular relaxivity measurements for the Gd(iii) complexes of , or in water afforded values 4 to 10 times higher than the relaxivity of a commercial contrast agent at 12 MHz, and 6 to 20 times higher at 100 MHz. Solutions of and Gd(iii) complexes in human blood plasma displayed relaxivity values at 100 MHz 7 and 12 times, respectively, higher than the commercial agent. MTT tests of the Gd(iii) complexes using human skin fibroblasts did not show toxicity. Attempts to supramolecularly sensitize the luminescence of the lanthanide complexes using various aromatic CD guests were ineffective, evidently due to large guest-metal distances and inefficient inclusion. The described lanthanide complexes, could be useful as contrast agents in MRI.

  9. Preparation, crystal structure, thermal decomposition, quantum chemical calculations on [K(ZTO)ṡH2O]∞ and its ligand ZTO (United States)

    Ma, Cong; Huang, Jie; Ma, Hai-Xia; Xu, Kang-Zhen; Lv, Xing-Qiang; Song, Ji-Rong; Zhao, Ning-Ning; He, Jian-Yun; Zhao, Yi-Sha


    A novel potassium complex has been synthesized and characterized under the non-isothermal conditions by DSC and TG-DTG method. The 4,4-azo-1,2,4-triazol-5-one (ZTO) has the molecular formula C4H4N8O2. The thermodynamic parameters, HOMO-LUMO energy gap, total energy and electrostatic potential (MEP) of ZTO are conducted by density functional theory DFT/B3LYP calculation method with 6-311G basis set. In the coordination polymer, with the ligand anion (ZTO-) as space linkers, two types of potassium atoms centers are joined together to form three-dimensional frameworks. The enthalpy, apparent activation energy and pre-exponential factor of the second exothermic decomposition reaction are 85.43 kJ mol-1, 414.4 kJ mol-1and 1037.92 s-1, respectively. The critical temperature of thermal explosion (Tb) for [K(ZTO)ṡH2O]∞ is 275.08 °C. [K(ZTO)ṡH2O]∞ CCDC: 902339.

  10. Ligand field density functional theory calculation of the 4f2→ 4f15d1 transitions in the quantum cutter Cs2KYF6:Pr3+. (United States)

    Ramanantoanina, Harry; Urland, Werner; Cimpoesu, Fanica; Daul, Claude


    Herein we present a Ligand Field Density Functional Theory (LFDFT) based methodology for the analysis of the 4f(n)→ 4f(n-1)5d(1) transitions in rare earth compounds and apply it for the characterization of the 4f(2)→ 4f(1)5d(1) transitions in the quantum cutter Cs2KYF6:Pr(3+) with the elpasolite structure type. The methodological advances are relevant for the analysis and prospection of materials acting as phosphors in light-emitting diodes. The positions of the zero-phonon energy corresponding to the states of the electron configurations 4f(2) and 4f(1)5d(1) are calculated, where the praseodymium ion may occupy either the Cs(+)-, K(+)- or the Y(3+)-site, and are compared with available experimental data. The theoretical results show that the occupation of the three undistorted sites allows a quantum-cutting process. However size effects due to the difference between the ionic radii of Pr(3+) and K(+) as well as Cs(+) lead to the distortion of the K(+)- and the Cs(+)-site, which finally exclude these sites for quantum-cutting. A detailed discussion about the origin of this distortion is also described.

  11. Synthesis and characterization of a new zinc(II) complex with tetradentate azo-thioether ligand: X-ray structure, DNA binding study and DFT calculation (United States)

    Mondal, Apurba Sau; Pramanik, Ajoy Kumar; Patra, Lakshman; Manna, Chandan Kumar; Mondal, Tapan Kumar


    A new zinc(II) complex, [Zn(L)(H2O)](ClO4) (1) with azo-thioether containing NSNO donor ligand, 3-(2-(2-((pyridin-2-ylmethyl)thio)phenyl)hydrazono)pentane-2,4-dione (HL) is synthesized and characterized by several spectroscopic techniques. The distorted square based pyramidal (DSBP) geometry is confirmed by single crystal X-ray structure. The ability of the complex to bind with CT DNA is investigated by UV-vis method and the binding constant is found to be 4.16 × 104 M-1. Competitive binding study with ethidium bromide (EB) by fluorescence method suggests that the zinc(II) complex efficiently displaces EB from EB-DNA. The Stern-Volmer dynamic quenching constant, Ksv is found to be 1.2 × 104 M-1. Theoretical calculations by DFT and TDDFT/CPCM methods are used to interpret the electronic structure and UV-vis spectrum of the complex.

  12. Electrochemical, linear optical, and nonlinear optical properties and interpretation by density functional theory calculations of (4-N,N-dimethylaminostyryl)-pyridinium pendant group associated with polypyridinic ligands and respective multifunctional metal complexes (Ru(II) or Zn(II)). (United States)

    Dumur, Frédéric; Mayer, Cédric R; Hoang-Thi, Khuyen; Ledoux-Rak, Isabelle; Miomandre, Fabien; Clavier, Gilles; Dumas, Eddy; Méallet-Renault, Rachel; Frigoli, Michel; Zyss, Joseph; Sécheresse, Francis


    The synthesis, linear optical and nonlinear optical properties, as well as the electrochemical behavior of a series of pro-ligands containing the 4-(4-N,N-dimethylaminostyryl)-1-methyl pyridinium (DASP(+)) group as a push-pull moiety covalently linked to terpyridine or bipyridine as chelating ligands are reported in this full paper. The corresponding multifunctional Ru(II) and Zn(II) complexes were prepared and investigated. The structural, electronic, and optical properties of the pro-ligands and the ruthenium complexes were investigated using density functional theory (DFT) and time-dependent (TD) DFT calculations. A fairly good agreement was observed between the experimental and the calculated electronic spectra of the pro-ligands and their corresponding ruthenium complexes. A quenching of luminescence was evidenced in all ruthenium complexes compared with the free pro-ligands but even the terpyridine-functionalized metal complexes exhibited detectable luminescence at room temperature. Second order nonlinear optical (NLO) measurements were performed by Harmonic Light Scattering and the contribution of the DASP(+) moieties (and their relative ordering) and the metal-polypyridyl core need to be considered to explain the nonlinear optical properties of the metal complexes.

  13. Chiral vanadium(V) complexes with 2-aminoglucose Schiff-base ligands and their solution configurations: synthesis, structures, and DFT calculations. (United States)

    Mohammadnezhad, Gholamhossein; Böhme, Michael; Geibig, Daniel; Burkhardt, Anja; Görls, Helmar; Plass, Winfried


    The sugar-modified Schiff-base ligands derived from benzyl 2-deoxy-2-salicylideneamino-α-D-glucopyranoside (H2L(5-Br) and H2L(3-OMe)) were used to prepare the chiral oxidovanadium(V) complexes [VO(L(5-Br))(OMe)] (1) and [VO(L(3-OMe))(OMe)] (2) which can be isolated from a methanol solution as the six-coordinate complexes with an additional methanol ligand [VO(L(5-Br))(OMe)(MeOH)] (1-MeOH) and [VO(L(3-OMe))(OMe) (MeOH)] (2-MeOH). Both complexes crystallize in the orthorhombic space group P2(1)2(1)2(1) together with two solvent molecules of methanol as 1-MeOH·2MeOH and 1-MeOH·2MeOH. In both crystal structures, only diastereomers with A configuration at the chiral vanadium centre (OC-6-24-A) are observed which corresponds to an cis configuration of the oxido group at the vanadium centre and the benzyl group at the anomeric carbon of the sugar backbone. Upon recrystallization of 2-MeOH from chloroform, the five-coordinate complex 2 was obtained which crystallizes in the monoclinic space group P2(1) with one co-crystallized chloroform molecule (2·CHCl3). For the chiral vanadium centre in 2·CHCl3, a C configuration (SPY-5-43-C) is observed which corresponds to an trans structure as far as the orientations of the oxido and benzyl groups are concerned. (1)H and (51)V NMR spectra of 1 and 2 indicate the presence of two diastereomers in solution. Their absolute configurations can be assigned based on the magnetic anisotropy effect of the oxidovanadium group. This effect leads to significant differences for the (1)H NMR chemical shifts of the H-2 (1.1 ppm) and H-3 protons (0.3 ppm) of the glucose backbone of the two diastereomers, with the downfield shift observed for the H-2 proton of the C-configured and the H-3 proton of the A-configured diastereomer at the vanadium centre. For 1 and 2 the difference between the (51)V NMR chemical shifts of the two diastereomers is 30 and 28 ppm, respectively. Also in the (13)C NMR significant chemical shift differences between the

  14. Bonding Study on the Chemical Separation of Am(III) from Eu(III) by S-, N-, and O-Donor Ligands by Means of All-Electron ZORA-DFT Calculation. (United States)

    Kaneko, Masashi; Miyashita, Sunao; Nakashima, Satoru


    We performed a theoretical investigation for the selectivity of Eu(III)/Am(III) ions depending on the donor atoms by means of all-electron ZORA-DFT calculation. We estimated their selectivity as the relative stability in the complex formation reaction. The B2PLYP functional reproduced the experimental selectivity in which S- and N-donor ligands favor Am(III) ion, but O-donor ligand favors Eu(III) ion. Mulliken's bond overlap population analysis revealed that the contribution of the f orbital to the bonding was small or zero for Eu complex, whereas it was large for Am complex. The bonding nature of the f orbital for Am ion was the bonding type to S- and N-donor ligands, while it was the antibonding type to O-donor ligand. It was suggested that the difference in the bonding nature between the f orbital in the metal and the donor atoms determines the selectivity of Eu(III)/Am(III) by donor ligands.

  15. Synthesis, characterization, DFT calculation and biological activity of square-planar Ni(II) complexes with tridentate PNO ligands and monodentate pseudohalides. Part II. (United States)

    Milenković, Milica; Pevec, Andrej; Turel, Iztok; Vujčić, Miroslava; Milenković, Marina; Jovanović, Katarina; Gligorijević, Nevenka; Radulović, Siniša; Swart, Marcel; Gruden-Pavlović, Maja; Adaila, Kawther; Cobeljić, Božidar; Anđelković, Katarina


    Three square-planar complexes of Ni(II) with condensation derivative of 2-(diphenylphosphino)benzaldehyde and 4-phenylsemicarbazide and monodentate pseudohalides have been synthesized and characterized on the basis of the results of X-ray, NMR and IR spectroscopy and elemental analysis. Investigated complexes exhibited moderate antibacterial and cytotoxic activity. The most pronounced cytotoxic activity (in the range of cisplatin) to HeLa cell line was observed for ligand and all the complexes. Azido complex and ligand induced concentration dependent cell cycle arrest in the S phase, as well as decrease of percentage of cells in G1 phase, without significant increase of apoptotic fraction of cells. The interaction of the azido complex and ligand with CT-DNA results in changes in UV-Vis spectra typical for non-covalent bonding. The observed intrinsic binding constant of azido complex-CT-DNA and ligand-CT-DNA were 3.22 × 10(5) M(-1) and 2.79 × 10(5) M(-1). The results of DNA cleavage experiments showed that azido complex nicked supercoiled plasmid DNA.

  16. Synthesis, characterization, DFT calculations and biological studies of Mn(II), Fe(II), Co(II) and Cd(II) complexes based on a tetradentate ONNO donor Schiff base ligand (United States)

    Abdel-Rahman, Laila H.; Ismail, Nabawia M.; Ismael, Mohamed; Abu-Dief, Ahmed M.; Ahmed, Ebtehal Abdel-Hameed


    This study highlights synthesis and characterization of a tetradentate ONNO Schiff base ligand namely (1, 1‧- (pyridine-2, 3-dimethyliminomethyl) naphthalene-2, 2‧-diol) and hereafter denotes as "HNDAP″ and selected metal complexes including Mn(II), Fe(II), Co(II) and Cd(II) as a central metal. HNDAP was synthesized from 1:2 M ratio condensation of 2, 3-diaminopyridine and 2- hydroxy-1-naphthaldhyde, respectively. The stoichiometric ratios of the prepared complexes were estimated using complementary techniques such as; elemental analyses (-C, H, N), FT-IR, magnetic measurements and molar conductivity. Furthermore, their physicochemical studies were carried out using thermal TGA, DTA and kinetic-thermodynamic studies along with DFT calculations. The results of elemental analyses showed that these complexes are present in a 1:1 metal-to- ligand molar ratio. Moreover, the magnetic susceptibilities values at room temperature revealed that Mn(II), Fe(II) and Co(II) complexes are paramagnetic in nature and have an octahedral (Oh) geometry. In contrast, Cd(II) is diamagnetic and stabilizes in square planar sites. The molar conductivity measurements indicated that all complexes are nonelectrolytes in dimethyl formamide. Spectral data suggested that the ligand is as tetradentate and coordinated with Co(II) ion through two phenolic OH and two azomethine nitrogen. However, for Mn(II), Fe(II) and Cd(II) complexes, the coordination occurred through two phenolic oxygen and two azomethine nitrogen with deprotonation of OH groups. The proposed chemical structures have been validated by quantum mechanics calculations. Antimicrobial activities of both the HNDAP Schiff base ligand and its metal complexes were tested against strains of Gram (-ve) E. coli and Gram (+ve) B. subtilis and S. aureus bacteria and C. albicans, A. flavus and T. rubrum fungi. All the prepared compounds showed good results of inhibition against the selected pathogenic microorganisms. The investigated

  17. Analysis of macromolecules, ligands and macromolecule-ligand complexes (United States)

    Von Dreele, Robert B [Los Alamos, NM


    A method for determining atomic level structures of macromolecule-ligand complexes through high-resolution powder diffraction analysis and a method for providing suitable microcrystalline powder for diffraction analysis are provided. In one embodiment, powder diffraction data is collected from samples of polycrystalline macromolecule and macromolecule-ligand complex and the refined structure of the macromolecule is used as an approximate model for a combined Rietveld and stereochemical restraint refinement of the macromolecule-ligand complex. A difference Fourier map is calculated and the ligand position and points of interaction between the atoms of the macromolecule and the atoms of the ligand can be deduced and visualized. A suitable polycrystalline sample of macromolecule-ligand complex can be produced by physically agitating a mixture of lyophilized macromolecule, ligand and a solvent.

  18. Probing the Properties of Polynuclear Superhalogens without Halogen Ligand via ab Initio Calculations: A Case Study on Double-Bridged [Mg2 (CN)5 ](-1) Anions. (United States)

    Li, Jin-Feng; Li, Miao-Miao; Bai, Hongcun; Sun, Yin-Yin; Li, Jian-Li; Yin, Bing


    An ab initio study of the superhalogen properties of eighteen binuclear double-bridged [Mg2 (CN)5 ](-1) clusters is reported herein by using various theoretical methods. High-level CCSD(T) results indicate that all the clusters possess strong superhalogen properties owing to their high vertical electron detachment energies (VDEs), which exceed 6.8 eV (highest: 8.15 eV). The outer valence Green's function method provides inaccurate relative VDE values; hence, this method is not suitable for this kind of polynuclear superhalogens. Both the HF and MP2 results are generally consistent with the CCSD(T) level regarding the relative VDE values and-especially interesting-the average values of the HF and MP2 VDEs are extremely close to the CCSD(T) results. The distributions of the extra electrons of the anions are mainly aggregated into the terminal CN units. These distributions are apparently different from those of previously reported triple-bridged isomers and may be the reason for the decreased VDE values of the clusters. In addition, comparisons of the VDEs of binuclear and mononuclear superhalogens as well as studies of the thermodynamic stabilities with respect to the detachment of various CN(-1) ligands are also performed. These results confirm that polynuclear structures with pseudohalogen ligands can be considered as probable new superhalogens with enhanced properties. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Theoretical calculations, DNA interaction, topoisomerase I and phosphatidylinositol-3-kinase studies of water soluble mixed-ligand nickel(II) complexes. (United States)

    Gurumoorthy, Perumal; Mahendiran, Dharmasivam; Kalilur Rahiman, Aziz


    Eight water soluble mixed-ligand nickel(II) complexes of the type [NiL(1-4)(diimine)H2O]·(ClO4)2, (1-8) where L(1-4) = 2-((2-(piperazin-1-yl)ethylimino)methyl)-4-substituted phenols, and diimine = 2,2'-bipyridyl (bpy) or 1,10-phenanthroline (phen) were synthesized and characterized by elemental analysis and spectroscopic methods. The uncoordinated perchlorate anions was ascertained form IR spectra of the complexes, and the absorption spectra reveal the octahedron geometry around nickel(II) ion with tridentate Schiff base ligand, diimine and a coordinated water molecule. Cyclic voltammograms of the complexes indicate the one-electron irreversible processes in the cathodic and anodic region. In vitro antioxidant activity proved the significant radical scavenging activity of the complexes against DPPH radical. The groove/electrostatic binding nature of complexes with CT-DNA (calf thymus deoxyribonucleic acid) were affirmed by absorption, hydrodynamic and voltammetric titration experiments and docking analysis. All the complexes exhibit significant cleavage activity on plasmid DNA via hydrolytic and oxidatively, in which the oxidative mechanism involves hydroxyl radicals and supports the possibility of minor-groove binding. The complex 4 shows significant topoisomerase I (Topo-I) inhibitory activity. The molecular modeling analysis of complexes with phosphatidylinositol-3-kinase (PI3K) receptor indicate the hydrogen bonding with Met1039, Asp837 and Leu1027, and hydrophobic interactions with Ser488, Asn498, Asp500, Gln662, Lys668, Ile844, Ile847, Ile850, Val941, Leu942, Leu1020, Met1034, Leu1035, Thr1037, Met1039, Gln1041 and Ile1051 of subdomain IIA of BSA. The complexes show σ-π interaction between diimines and amino groups of Leu1030 and Arg839.

  20. Crystal Structures and Theoretical Calculation of Zn(Ⅱ) and Cu(Ⅱ) Supramolecular Complexes Based on Macrocyclic Triamine Ligand 1 ,4,7-Triazacyclodecane (tacd)

    Institute of Scientific and Technical Information of China (English)

    QUO,Hui; ZHU,Hai-Yan; HE,Xian-Ling; SU,Zhen-Ping; LI,Jun; ZHANG,Feng-Xing


    Two supramolecular complexes [Zn(tacd)2](C6H8O4)·6H2O (1) and [Cu(tacd)2]Cl2·4H2O (2) were synthesized and characterized by elemental analysis, IR spectra, TGA and single-crystal X-ray diffraction analysis. The crystal structure showed that the metal ions in complexes 1 and 2 had similar coordination circumstance. But for the complex 2, it formed a novel two-dimensional supramolecular network with 12-membered rings and four-membered rings via hydrogen bond interaction. The thermal gravimetric analyses indicated that the two complexes had similar steps of weight-loss. On the basis of experiment, the two complexes were calculated by DFT-B3LYP/6-31G(d) in Gaussian 03. The results of calculation are in good agreement with the experiment.

  1. Synthesis, characterization, EPR spectroelectrochemistry studies and theoretical calculations of manganese(II) complexes with the ligands H{sub 3}bpeten and H{sub 3}bnbpeten

    Energy Technology Data Exchange (ETDEWEB)

    Romanowski, Stela Maris de M.; Friedermann, Geraldo R.; Mangrich, Antonio S.; Hermann, Monique de F.; Nakagaki, Shirley, E-mail: shirley@quimica.ufpr.b [Universidade Federal do Parana (UFPR), Curitiba, PR (Brazil). Dept. de Quimica; Machado, Sergio P.; Lima, Hugo Orofino [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Inst. de Quimica


    The synthesis and characterization of the manganese(II) complexes [Mn{sup II}(Hbpeten)] and [Mn{sup II}(Hbnbpeten)], where H{sub 3}bpeten and H{sub 3}bnbpeten are respectively [N,N'-bis-(2-hydroxybenzyl)- N-(2-pyridylmethyl)-N'-(2-hydroxyethyl)ethane-1,2-diamine] and [N,N'-bis-(5-nitro-2- hydroxybenzyl)-N'-(2-hydroxyethyl)ethane-1,2-diamine], are reported. The characterization was carried out by elemental analyses, cyclic voltammetry, spectroscopic methods (UV-Vis, FTIR, {sup 1}H NMR), electronic paramagnetic resonance spectroelectrochemistry (EPR) and theoretical DFT calculations. The electrochemistry and EPR spectroelectrochemistry data were consistent with the reduction of one of the nitro groups in free H{sub 3}bnbpeten and in the respective manganese(II) complex. These results were supported by DFT calculations, which showed that only one nitro group contributes to the LUMO. The theoretical data appear to be suitable to describe the electronic properties of the compounds. (author)

  2. Synthesis, characterization, X-ray crystal structure, DFT calculation, DNA binding, and antimicrobial assays of two new mixed-ligand copper(II) complexes (United States)

    Ebrahimipour, S. Yousef; Sheikhshoaie, Iran; Mohamadi, Maryam; Suarez, Sebastian; Baggio, Ricardo; Khaleghi, Moj; Torkzadeh-Mahani, Masoud; Mostafavi, Ali


    Two new Cu(II) complexes, [Cu(L)(phen)] (1), [Cu(L)(bipy)] (2), where L2- = (3-methoxy-2oxidobenzylidene)benzohydrazidato, phen = 1,10 phenanthroline, and bipy = 2,2‧ bipyridine, were prepared and fully characterized using elemental analyses, FT-IR, molar conductivity, and electronic spectra. The structures of both complexes were also determined by X-ray diffraction. It was found that, both complexes possessed square pyramidal coordination environment in which, Cu(II) ions were coordinated by donor atoms of HL and two nitrogens of heterocyclic bases. Computational studies were performed using DFT calculations at B3LYP/6-311+G(d,p) level of theory. DNA binding activities of these complexes were also investigated using electronic absorption, competitive fluorescence titration and cyclic voltammetry studies. The obtained results indicated that binding of the complexes to DNA was of intercalative mode. Furthermore, antimicrobial activities of these compounds were screened against microorganisms.

  3. Co(II), Ni(II), Cu(II) and Zn(II) complexes of tridentate ONO donor Schiff base ligand: Synthesis, characterization, thermal, non-isothermal kinetics and DFT calculations (United States)

    Kusmariya, Brajendra S.; Mishra, A. P.


    We report here four mononuclear Co(II), Ni(II), Cu(II) and Zn(II) coordination compounds of general formula [M(L)2] {L = dcp; M = CoII, CuII & ZnII} and [M(L)(H2O)]·H2O {L = dcp; M = NiII} derived from tridentate 2,4-dichloro-6-{[(3-chloro-2-hydroxy-5-nitrophenyl)imino]methyl}phenol (dcp) ligand. These compounds were synthesized and characterized by elemental analysis, FT-IR, uv-vis, 1H NMR, molar conductance, magnetic moment, thermal, PXRD and SEM-EDX. The Powder X-ray Diffraction patterns and SEM analyses showed the crystalline nature of synthesized compounds. The peak broadening was explained in terms of crystallite size and the lattice strain using Scherrer and Williamson-Hall method. Thermogravimetric analysis was performed to determine the thermal stability of synthesized compounds under nitrogen atmosphere up to 820 K at 10 Kmin-1 heating rate. The kinetic and thermodynamic parameters of thermal decomposition were calculated using Coats-Redfern (C-R), Piloyan-Novikova (P-N) and Horowitz-Metzger (H-M) methods assuming first order degradation. The calculated optical band gap values of complexes were found to be in semiconducting range. To support the experimental findings, and derive some fruitful information viz. frequency calculations, HOMO-LUMO, energy gap (ΔE), molecular electrostatic potential (MEP), spin density, absorption spectra etc.; theoretical calculations by means of DFT and TD-DFT at B3LYP level were incorporated.

  4. Copper(II) and nickel(II) complexes of tetradentate Schiff base ligand: UV-Vis and FT-IR spectra and DFT calculation of electronic, vibrational and nonlinear optical properties (United States)

    Zarei, Seyed Amir; Khaledian, Donya; Akhtari, Keivan; Hassanzadeh, Keyumars


    The experimental fourier transform infrared (FT-IR) and ultraviolet-visible (UV-Vis) spectra of copper(II) and nickel(II) complexes of the deprotonated tetradentate Schiff base ligand N,N‧-bis(2-hydroxybenzylidene)-2,2-dimethyl-1,3-propanediamine (H2L) are compared with their corresponding theoretical ones. The applied theoretical method is based on the density functional theory and time-dependent density functional theory at the UPBE0/PBE0 levels using Def2-TZVP basis set. The computational optimised geometric parameters of the complexes are in good agreement with their corresponding experimental data. The FT-IR and UV-Vis spectra of the complexes were reproduced on the basis of their optimised structures. The vibrational assignments of some fundamental modes of the complexes are performed. The highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies are calculated. The analyses of the calculated electronic absorption spectra of the complexes are carried out to elucidate the electronic transitions assignments and their characters. Second-order nonlinear optical property of the complexes is evaluated by the above-mentioned theoretical method that implies much greater values for the complexes in comparison with the corresponding value of urea.

  5. Ligand photo-isomerization triggers conformational changes in iGluR2 ligand binding domain.

    Directory of Open Access Journals (Sweden)

    Tino Wolter

    Full Text Available Neurological glutamate receptors bind a variety of artificial ligands, both agonistic and antagonistic, in addition to glutamate. Studying their small molecule binding properties increases our understanding of the central nervous system and a variety of associated pathologies. The large, oligomeric multidomain membrane protein contains a large and flexible ligand binding domains which undergoes large conformational changes upon binding different ligands. A recent application of glutamate receptors is their activation or inhibition via photo-switchable ligands, making them key systems in the emerging field of optochemical genetics. In this work, we present a theoretical study on the binding mode and complex stability of a novel photo-switchable ligand, ATA-3, which reversibly binds to glutamate receptors ligand binding domains (LBDs. We propose two possible binding modes for this ligand based on flexible ligand docking calculations and show one of them to be analogues to the binding mode of a similar ligand, 2-BnTetAMPA. In long MD simulations, it was observed that transitions between both binding poses involve breaking and reforming the T686-E402 protein hydrogen bond. Simulating the ligand photo-isomerization process shows that the two possible configurations of the ligand azo-group have markedly different complex stabilities and equilibrium binding modes. A strong but slow protein response is observed after ligand configuration changes. This provides a microscopic foundation for the observed difference in ligand activity upon light-switching.

  6. New Fe(III) complex with 8-(4-chlorophenyl)-3-butyl-3H-imidazo[4‧,5‧:3,4]benzo[1,2-c]isoxazol-5-amine (5-AIBI) ligand: Synthesis, spectroscopic characterization and DFT calculations (United States)

    Agheli, Zahra; Pordel, Mehdi; Beyramabadi, S. Ali


    The new heterocyclic ligand 8-(4-chlorophenyl)-3-butyl-3H-imidazo[4‧,5‧:3,4]benzo [1,2-c]isoxazol-5-amine (5-AIBI) was synthesized from the reduction of 3-butyl-8-(4-chlorophenyl)-5-nitro-3H-imidazo[4‧,5‧:3,4]benzo[1,2-c]isoxazole in high yield. The coordination ability of the ligand with some cations was examined by spectrophotometric method at rt condition. Results showed that only the absorption spectra of the Fe3+-5-AIBI complex show a high redshift of the absorption maximum in the aqueous ethanol solution. The effect of pH on the absorption spectrum of the green iron-5-AIBI complex was also investigated. In addition, density functional theory (DFT) calculations are performed to provide the optimized geometries, structural parameters, calculated chemical shifts and vibrational frequencies of the investigated Fe(III) complex.

  7. Visualization of Metal-to-Ligand and Ligand-to-Ligand Charge Transfer in Metal-Ligand Complexes

    Institute of Scientific and Technical Information of China (English)

    Yong Ding; Jian-xiu Guo; Xiang-si Wang; Sha-sha Liu; Feng-cai Ma


    Three methods including the atomic resolved density of state, charge difference density, and the transition density matrix are used to visualize metal to ligand charge transfer (MLCT) in ruthenium(Ⅱ) ammine complex. The atomic resolved density of state shows that there is density of Ru on the HOMOs. All the density is localized on the ammine, which reveals that the excited electrons in the Ru complex are delocalized over the ammine ligand. The charge difference density shows that all the holes are localized on the Ru and the electrons on the ammine. The localization explains the MLCT on excitation. The transition density matrix shows that there is electron-hole coherence between Ru and ammine. These methods are also used to examine the MLCT in Os(bpy)(p0p)Cl ("Osp0p"; bpy=2,2'-bipyridyl; p0p=4,4'-bipyridyl) and the ligand-to-ligand charge transfer (LLCT) in Alq3. The calculated results show that these methods are powerful to examine MLCT and LLCT in the metal-ligand system.

  8. A new class of PN3-pincer ligands for metal–ligand cooperative catalysis

    KAUST Repository

    Li, Huaifeng


    Work on a new class of PN3-pincer ligands for metal-ligand cooperative catalysis is reviewed. While the field of the pyridine-based PN3-transition metal pincer complexes is still relatively young, many important applications of these complexes have already emerged. In several cases, the PN3-pincer complexes for metal-ligand cooperative catalysis result in significantly improved or unprecedented activities. The synthesis and coordination chemistry of PN3-pincer ligands are briefly summarized first to cover the synthetic routes for their preparation, followed by a focus review on their applications in catalysis. A specific emphasis is placed on the later section about the role of PN3-pincer ligands\\' dearomatization-rearomatization steps during the catalytic cycles. The mechanistic insights from density functional theory (DFT) calculations are also discussed.

  9. Distribution of unselectively bound ligands along DNA. (United States)

    Lando, Dmitri Y; Nechipurenko, Yury D


    Unselective and reversible adsorption of ligands on DNA for a model of binding proposed by Zasedatelev, Gursky, and Volkenshtein is considered. In this model, the interaction between neighboring ligands located at the distance of i binding centers is characterized by the statistical weight ai. Each ligand covers L binding centers. For this model, expressions for binding averages are represented in a new simple form. This representation is convenient for the calculation of the fraction of inter-ligand distances of i binding centers fd(i) and the fraction of binding centers included in the distances of i binding centers fbc(i) for various types of interaction between bound ligands. It is shown that, for non-cooperative binding, contact cooperativity and long-range cooperativity, the fraction of the zero inter-ligand distance fd(0) is maximal at any relative concentration of bound ligands (r). Calculations demonstrate that, at low r, fd(0) approximately, and fd(i) approximately r at 11/r-L, then fd(i) rapidly decreases with i at any r for all types of inter-ligand interaction. At high ligand concentration (r is close to rmax=L(-1)), fd(0) is close to unity and fd(i) rapidly decreases with i for any type of inter-ligand interaction. For strong contact cooperativity, fd(0) is close to unity in a much lager r interval ((0.5-1).rmax), and fd(1) approximately ao(-1) at r approximately 0.5.rmax. In the case of long-range interaction between bound ligands, the dependence fd(i) is more complex and has a maximum at i approximately (1/r-L)1/2 for anti-cooperative binding. fbc(i) is maximal at i approximately 1/r-L for all types of binding except the contact cooperativity. A strong asymmetry in the influence of contact cooperativity and anticooperativity on the ligand distribution along DNA is demonstrated.

  10. Analysis of molecular structure, spectroscopic properties (FT-IR, micro-Raman and UV-vis) and quantum chemical calculations of free and ligand 2-thiopheneglyoxylic acid in metal halides (Cd, Co, Cu, Ni and Zn). (United States)

    Gökce, Halil; Bahçeli, Semiha


    In this study, molecular geometries, experimental vibrational wavenumbers, electronic properties and quantum chemical calculations of 2-thiopheneglyoxylic acid molecule, (C6H4O3S), and its metal halides (Cd, Co, Cu, Ni and Zn) which are used as pharmacologic agents have been investigated experimentally by FT-IR, micro-Raman and UV-visible spectroscopies and elemental analysis. Meanwhile the vibrational calculations were verified by DFT/B3LYP method with 6-311++G(d,p) and LANL2DZ basis sets in the ground state, for free TPGA molecule and its metal halide complexes, respectively, for the first time. The calculated fundamental vibrational frequencies for the title compounds are in a good agreement with the experimental data.

  11. Tight-Binding and Hueckel Models of Molecular Clusters (United States)


    Chem. Phys. Lett. 163, 323 (1989); Phys. Rev. Lett. 64, 551 (1990). 16. H. Kupka and K. Jug, Chem. Phys. 130, 23 (1989). 17. Y. Wang , T. F. George...D. M. Lindsay and A. C. Beri, J. Chem. Phys. 86, 3493 (1987). 18. D. M. Lindsay, Y. Wang and T. F. George, J. Chem. Phys. 86, 3500 (1987). 23 Table 1...Department of Chemistry Northwestern University University of California Evanston, IL 60208 Irvine, CA 92717 Professor Frank DiSalvo Professor Roald Hoffmann

  12. Ligand modeling and design

    Energy Technology Data Exchange (ETDEWEB)

    Hay, B.P. [Pacific Northwest National Lab., Richland, WA (United States)


    The purpose of this work is to develop and implement a molecular design basis for selecting organic ligands that would be used in the cost-effective removal of specific radionuclides from nuclear waste streams. Organic ligands with metal ion specificity are critical components in the development of solvent extraction and ion exchange processes that are highly selective for targeted radionuclides. The traditional approach to the development of such ligands involves lengthy programs of organic synthesis and testing, which in the absence of reliable methods for screening compounds before synthesis, results in wasted research effort. The author`s approach breaks down and simplifies this costly process with the aid of computer-based molecular modeling techniques. Commercial software for organic molecular modeling is being configured to examine the interactions between organic ligands and metal ions, yielding an inexpensive, commercially or readily available computational tool that can be used to predict the structures and energies of ligand-metal complexes. Users will be able to correlate the large body of existing experimental data on structure, solution binding affinity, and metal ion selectivity to develop structural design criteria. These criteria will provide a basis for selecting ligands that can be implemented in separations technologies through collaboration with other DOE national laboratories and private industry. The initial focus will be to select ether-based ligands that can be applied to the recovery and concentration of the alkali and alkaline earth metal ions including cesium, strontium, and radium.

  13. Ligand modeling and design

    Energy Technology Data Exchange (ETDEWEB)

    Hay, B. [Pacific Northwest Lab., Richland, WA (United States)


    The purpose of this work is to develop and implement a molecular design basis for selecting organic ligands that would be used tin applications for the cost-effective removal of specific radionuclides from nuclear waste streams.

  14. Chemometric analysis of ligand receptor complementarity: identifying Complementary Ligands Based on Receptor Information (CoLiBRI). (United States)

    Oloff, Scott; Zhang, Shuxing; Sukumar, Nagamani; Breneman, Curt; Tropsha, Alexander


    We have developed a novel structure-based chemoinformatics approach to search for Complimentary Ligands Based on Receptor Information (CoLiBRI). CoLiBRI is based on the representation of both receptor binding sites and their respective ligands in a space of universal chemical descriptors. The binding site atoms involved in the interaction with ligands are identified by the means of a computational geometry technique known as Delaunay tessellation as applied to X-ray characterized ligand-receptor complexes. TAE/RECON multiple chemical descriptors are calculated independently for each ligand as well as for its active site atoms. The representation of both ligands and active sites using chemical descriptors allows the application of well-known chemometric techniques in order to correlate chemical similarities between active sites and their respective ligands. We have established a protocol to map patterns of nearest neighbor active site vectors in a multidimensional TAE/RECON space onto those of their complementary ligands and vice versa. This protocol affords the prediction of a virtual complementary ligand vector in the ligand chemical space from the position of a known active site vector. This prediction is followed by chemical similarity calculations between this virtual ligand vector and those calculated for molecules in a chemical database to identify real compounds most similar to the virtual ligand. Consequently, the knowledge of the receptor active site structure affords straightforward and efficient identification of its complementary ligands in large databases of chemical compounds using rapid chemical similarity searches. Conversely, starting from the ligand chemical structure, one may identify possible complementary receptor cavities as well. We have applied the CoLiBRI approach to a data set of 800 X-ray characterized ligand-receptor complexes in the PDBbind database. Using a k nearest neighbor (kNN) pattern recognition approach and variable selection

  15. Predicting Nanocrystal Shape through Consideration of Surface-Ligand Interactions

    KAUST Repository

    Bealing, Clive R.


    Density functional calculations for the binding energy of oleic acid-based ligands on Pb-rich {100} and {111} facets of PbSe nanocrystals determine the surface energies as a function of ligand coverage. Oleic acid is expected to bind to the nanocrystal surface in the form of lead oleate. The Wulff construction predicts the thermodynamic equilibrium shape of the PbSe nanocrystals. The equilibrium shape is a function of the ligand surface coverage, which can be controlled by changing the concentration of oleic acid during synthesis. The different binding energy of the ligand on the {100} and {111} facets results in different equilibrium ligand coverages on the facets, and a transition in the equilibrium shape from octahedral to cubic is predicted when increasing the ligand concentration during synthesis. © 2012 American Chemical Society.

  16. Calculation of dramatic differences in the activation energy of phenyl migratory insertion in the isomers of [Rh(PMe3)2Cl(CO)(Ph)H]: important effects from both the ligand trans to Ph and the ligand trans to CO. (United States)

    Hasanayn, Faraj; Abu-el-Ez, Dina


    trans,trans-[RhL(2)(Ph)(CO)HCl] (2a) and trans,trans-[RhL(2)(Ph)Cl(CO)H] (2b) are known to form as major products in the reaction between benzene and a photoexcited state of trans-[RhL(2)(CO)Cl] (1; L = PMe(3)). In the presence of carbon monoxide, these species are believed to ultimately lead to catalytic photocarbonylation of benzene. At the B3LYP level of theory the calculated free energy of activation for the concerted transition state (TS) of phenyl to CO migration in 2b (TSb) is 39 kcal/mol. In contrast, the barrier of insertion in the trans,trans-[RhL(2)(Ph)H(CO)Cl] isomer (2c) which is 7.4 kcal/mol higher in energy than 2b is only 15 kcal/mol. The calculated geometries of the reactants and TSs indicate that the disparity in the given barriers arises from a combination of two factors. First, the orientation of H trans to the migrating Ph group in 2c favors the TS because it weakens the Rh-Ph bond and thus makes it easier to begin migration of the phenyl group in comparison with 2b where the phenyl is trans to the chloride. Second, the orientation of the hydride trans to CO in 2b appears to strongly disfavor the reaction compared to 2c where CO is trans to Cl. Specifically, the calculations give strong evidence that the Rh-H bond in 2b is substantially weakened in TSb, and this should add to the increased barrier of this isomer. These propositions are supported by calculations on the reaction of the cis-Rh(PMe(3))(2) isomers of 2 and other related octahedral complexes.

  17. New bisphosphomide ligands, 1,3-phenylenebis((diphenylphosphino)methanone) and (2-bromo-1,3-phenylene)bis((diphenylphosphino)methanone): synthesis, coordination behavior, DFT calculations and catalytic studies. (United States)

    Kumar, Pawan; Siddiqui, Mujahuddin M; Reddi, Yerrnaidu; Mague, Joel T; Sunoj, Raghavan B; Balakrishna, Maravanji S


    )}AuCl] (19), in good yield. The structures of complexes 5, 7-10, 12 and 14a were confirmed by single-crystal X-ray diffraction studies. DFT calculations were performed in order to gain additional insights into the structure and bonding of the pincer complexes. An additional analysis of the orbital interactions in the case of palladium complex 9 is also included. The in situ generated rhodium complex of bisphosphomide 1 showed moderate to good selectivity in the hydroformylation of hex-1-ene and styrene derivatives.

  18. Declination Calculator (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Declination is calculated using the current International Geomagnetic Reference Field (IGRF) model. Declination is calculated using the current World Magnetic Model...

  19. Identification of VDR Antagonists among Nuclear Receptor Ligands Using Virtual Screening

    Directory of Open Access Journals (Sweden)

    Kelly Teske


    Full Text Available Herein, we described the development of two virtual screens to identify new vitamin D receptor (VDR antagonists among nuclear receptor (NR ligands. Therefore, a database of 14330 nuclear receptor ligands and their NR affinities was assembled using the online available “Binding Database.” Two different virtual screens were carried out in conjunction with a reported VDR crystal structure applying a stringent and less stringent pharmacophore model to filter docked NR ligand conformations. The pharmacophore models were based on the spatial orientation of the hydroxyl functionalities of VDR's natural ligands 1,25(OH2D3 and 25(OH2D3. The first virtual screen identified 32 NR ligands with a calculated free energy of VDR binding of more than -6.0 kJ/mol. All but nordihydroguaiaretic acid (NDGA are VDR ligands, which inhibited the interaction between VDR and coactivator peptide SRC2-3 with an IC50 value of 15.8 μM. The second screen identified 162 NR ligands with a calculated free energy of VDR binding of more than -6.0 kJ/mol. More than half of these ligands were developed to bind VDR followed by ERα/β ligands (26%, TRα/β ligands (7%, and LxRα/β ligands (7%. The binding between VDR and ERα ligand H6036 as well as TRα/β ligand triiodothyronine and a homoserine analog thereof was confirmed by fluorescence polarization.

  20. Ligand fitting with CCP4 (United States)


    Crystal structures of protein–ligand complexes are often used to infer biology and inform structure-based drug discovery. Hence, it is important to build accurate, reliable models of ligands that give confidence in the interpretation of the respective protein–ligand complex. This paper discusses key stages in the ligand-fitting process, including ligand binding-site identification, ligand description and conformer generation, ligand fitting, refinement and subsequent validation. The CCP4 suite contains a number of software tools that facilitate this task: AceDRG for the creation of ligand descriptions and conformers, Lidia and JLigand for two-dimensional and three-dimensional ligand editing and visual analysis, Coot for density interpretation, ligand fitting, analysis and validation, and REFMAC5 for macromolecular refinement. In addition to recent advancements in automatic carbohydrate building in Coot (LO/Carb) and ligand-validation tools (FLEV), the release of the CCP4i2 GUI provides an integrated solution that streamlines the ligand-fitting workflow, seamlessly passing results from one program to the next. The ligand-fitting process is illustrated using instructive practical examples, including problematic cases such as post-translational modifications, highlighting the need for careful analysis and rigorous validation. PMID:28177312

  1. LigandRNA: computational predictor of RNA-ligand interactions. (United States)

    Philips, Anna; Milanowska, Kaja; Lach, Grzegorz; Bujnicki, Janusz M


    RNA molecules have recently become attractive as potential drug targets due to the increased awareness of their importance in key biological processes. The increase of the number of experimentally determined RNA 3D structures enabled structure-based searches for small molecules that can specifically bind to defined sites in RNA molecules, thereby blocking or otherwise modulating their function. However, as of yet, computational methods for structure-based docking of small molecule ligands to RNA molecules are not as well established as analogous methods for protein-ligand docking. This motivated us to create LigandRNA, a scoring function for the prediction of RNA-small molecule interactions. Our method employs a grid-based algorithm and a knowledge-based potential derived from ligand-binding sites in the experimentally solved RNA-ligand complexes. As an input, LigandRNA takes an RNA receptor file and a file with ligand poses. As an output, it returns a ranking of the poses according to their score. The predictive power of LigandRNA favorably compares to five other publicly available methods. We found that the combination of LigandRNA and Dock6 into a "meta-predictor" leads to further improvement in the identification of near-native ligand poses. The LigandRNA program is available free of charge as a web server at

  2. Ligand-Receptor Interactions

    CERN Document Server

    Bongrand, Pierre


    The formation and dissociation of specific noncovalent interactions between a variety of macromolecules play a crucial role in the function of biological systems. During the last few years, three main lines of research led to a dramatic improvement of our understanding of these important phenomena. First, combination of genetic engineering and X ray cristallography made available a simultaneous knowledg of the precise structure and affinity of series or related ligand-receptor systems differing by a few well-defined atoms. Second, improvement of computer power and simulation techniques allowed extended exploration of the interaction of realistic macromolecules. Third, simultaneous development of a variety of techniques based on atomic force microscopy, hydrodynamic flow, biomembrane probes, optical tweezers, magnetic fields or flexible transducers yielded direct experimental information of the behavior of single ligand receptor bonds. At the same time, investigation of well defined cellular models raised the ...

  3. Therapeutic androgen receptor ligands


    Allan, George F.; Sui, Zhihua


    In the past several years, the concept of tissue-selective nuclear receptor ligands has emerged. This concept has come to fruition with estrogens, with the successful marketing of drugs such as raloxifene. The discovery of raloxifene and other selective estrogen receptor modulators (SERMs) has raised the possibility of generating selective compounds for other pathways, including androgens (that is, selective androgen receptor modulators, or SARMs).

  4. Imidazoline receptors ligands

    Directory of Open Access Journals (Sweden)

    Agbaba Danica


    Full Text Available Extensive biochemical and pharmacological studies have determined three different subtypes of imidazoline receptors: I1-imidazoline receptors (I1-IR involved in central inhibition of sympathicus that produce hypotensive effect; I2-imidazoline receptors (I2-IR modulate monoamine oxidase B activity (MAO-B; I3-imidazoline receptors (I3-IR regulate insulin secretion from pancreatic β-cells. Therefore, the I1/I2/I3 imidazoline receptors are selected as new, interesting targets for drug design and discovery. Novel selective I1/I2/I3 agonists and antagonists have been recently developed. In the present review, we provide a brief update to the field of imidazoline research, highlighting some of the chemical diversity and progress made in the 2D-QSAR, 3D-QSAR and quantitative pharmacophore development studies of I1-IR and I2-IR imidazoline receptor ligands. Theoretical studies of I3-IR ligands are not yet performed because of insufficient number of synthesized I3-IR ligands.

  5. Bexarotene ligand pharmaceuticals. (United States)

    Hurst, R E


    Bexarotene (LGD-1069), from Ligand, was the first retinoid X receptor (RXR)-selective, antitumor retinoid to enter clinical trials. The company launched the drug for the treatment of cutaneous T-cell lymphoma (CTCL), as Targretin capsules, in the US in January 2000 [359023]. The company filed an NDA for Targretin capsules in June 1999, and for topical gel in December 1999 [329011], [349982] specifically for once-daily oral administration for the treatment of patients with early-stage CTCL who have not tolerated other therapies, patients with refractory or persistent early stage CTCL and patients with refractory advanced stage CTCL. The FDA approved Targretin capsules at the end of December 1999 for once-daily oral treatment of all stages of CTCL in patients refractory to at least one prior systemic therapy, at an initial dose of 300 mg/m2/day. After an NDA was submitted in December 1999 for Targretin gel, the drug received Priority Review status for use as a treatment of cutaneous lesions in patients with stage IA, IB or IIA CTCL [354836]. The FDA issued an approvable letter in June 2000, and granted marketing clearance for CTCL in the same month [370687], [372768], [372769], [373279]. Ligand had received Orphan Drug designation for this indication [329011]. At the request of the FDA, Ligand agreed to carry out certain post-approval phase IV and pharmacokinetic studies [351604]. The company filed an MAA with the EMEA for Targretin Capsules to treat lymphoma in November 1999 [348944]. The NDA for Targretin gel is based on a multicenter phase III trial that was conducted in the US, Canada, Europe and Australia involving 50 patients and a multicenter phase I/II clinical program involving 67 patients. Targretin gel was evaluated for the treatment of patients with early stage CTCL (IA-IIA) who were refractory to, intolerant to, or reached a response plateau for at least 6 months on at least two prior therapies. Efficacy results exceeded the protocol-defined response

  6. Melatonin: functions and ligands. (United States)

    Singh, Mahaveer; Jadhav, Hemant R


    Melatonin is a chronobiotic substance that acts as synchronizer by stabilizing bodily rhythms. Its synthesis occurs in various locations throughout the body, including the pineal gland, skin, lymphocytes and gastrointestinal tract (GIT). Its synthesis and secretion is controlled by light and dark conditions, whereby light decreases and darkness increases its production. Thus, melatonin is also known as the 'hormone of darkness'. Melatonin and analogs that bind to the melatonin receptors are important because of their role in the management of depression, insomnia, epilepsy, Alzheimer's disease (AD), diabetes, obesity, alopecia, migraine, cancer, and immune and cardiac disorders. In this review, we discuss the mechanism of action of melatonin in these disorders, which could aid in the design of novel melatonin receptor ligands.

  7. Macrocyclic G-quadruplex ligands

    DEFF Research Database (Denmark)

    Nielsen, M C; Ulven, Trond


    G-quadruplex stabilizing compounds have recently received increased interest due to their potential application as anticancer therapeutics. A significant number of structurally diverse G-quadruplex ligands have been developed. Some of the most potent and selective ligands currently known are macr...

  8. SuperLigands – a database of ligand structures derived from the Protein Data Bank

    Directory of Open Access Journals (Sweden)

    Preissner Robert


    Full Text Available Abstract Background Currently, the PDB contains approximately 29,000 protein structures comprising over 70,000 experimentally determined three-dimensional structures of over 5,000 different low molecular weight compounds. Information about these PDB ligands can be very helpful in the field of molecular modelling and prediction, particularly for the prediction of protein binding sites and function. Description Here we present an Internet accessible database delivering PDB ligands in the MDL Mol file format which, in contrast to the PDB format, includes information about bond types. Structural similarity of the compounds can be detected by calculation of Tanimoto coefficients and by three-dimensional superposition. Topological similarity of PDB ligands to known drugs can be assessed via Tanimoto coefficients. Conclusion SuperLigands supplements the set of existing resources of information about small molecules bound to PDB structures. Allowing for three-dimensional comparison of the compounds as a novel feature, this database represents a valuable means of analysis and prediction in the field of biological and medical research.

  9. SuperLigands – a database of ligand structures derived from the Protein Data Bank (United States)

    Michalsky, Elke; Dunkel, Mathias; Goede, Andrean; Preissner, Robert


    Background Currently, the PDB contains approximately 29,000 protein structures comprising over 70,000 experimentally determined three-dimensional structures of over 5,000 different low molecular weight compounds. Information about these PDB ligands can be very helpful in the field of molecular modelling and prediction, particularly for the prediction of protein binding sites and function. Description Here we present an Internet accessible database delivering PDB ligands in the MDL Mol file format which, in contrast to the PDB format, includes information about bond types. Structural similarity of the compounds can be detected by calculation of Tanimoto coefficients and by three-dimensional superposition. Topological similarity of PDB ligands to known drugs can be assessed via Tanimoto coefficients. Conclusion SuperLigands supplements the set of existing resources of information about small molecules bound to PDB structures. Allowing for three-dimensional comparison of the compounds as a novel feature, this database represents a valuable means of analysis and prediction in the field of biological and medical research. PMID:15943884

  10. Calculator calculus

    CERN Document Server

    McCarty, George


    How THIS BOOK DIFFERS This book is about the calculus. What distinguishes it, however, from other books is that it uses the pocket calculator to illustrate the theory. A computation that requires hours of labor when done by hand with tables is quite inappropriate as an example or exercise in a beginning calculus course. But that same computation can become a delicate illustration of the theory when the student does it in seconds on his calculator. t Furthermore, the student's own personal involvement and easy accomplishment give hi~ reassurance and en­ couragement. The machine is like a microscope, and its magnification is a hundred millionfold. We shall be interested in limits, and no stage of numerical approximation proves anything about the limit. However, the derivative of fex) = 67.SgX, for instance, acquires real meaning when a student first appreciates its values as numbers, as limits of 10 100 1000 t A quick example is 1.1 , 1.01 , 1.001 , •••• Another example is t = 0.1, 0.01, in the functio...

  11. Glutamate receptor ligands

    DEFF Research Database (Denmark)

    Guldbrandt, Mette; Johansen, Tommy N; Frydenvang, Karla Andrea;


    Homologation and substitution on the carbon backbone of (S)-glutamic acid [(S)-Glu, 1], as well as absolute stereochemistry, are structural parameters of key importance for the pharmacological profile of (S)-Glu receptor ligands. We describe a series of methyl-substituted 2-aminoadipic acid (AA......-ray crystallographic analyses, chemical correlation, and CD spectral analyses. The effects of the individual stereoisomers at ionotropic and metabotropic (S)-Glu receptors (iGluRs and mGluRs) were characterized. Compounds with S-configuration at the alpha-carbon generally showed mGluR2 agonist activity of similar...... limited effect on pharmacology. Structure-activity relationships at iGluRs in the rat cortical wedge preparation showed a complex pattern, some compounds being NMDA receptor agonists [e.g., EC(50) =110 microM for (2S,5RS)-5-methyl-AA (6a,b)] and some compounds showing NMDA receptor antagonist effects [e...

  12. Tris(pyrazolyl)phosphine oxide and Tris(triazolyl)phosphine oxide scorpion ligands

    NARCIS (Netherlands)

    Tazelaar, Cornelis G J; Lyaskovskyy, Volodymyr; Van Doorn, Ilana M.; Schaapkens, Xander; Lutz, Martin; Ehlers, Andreas W.; Slootweg, Jack; Lammertsma, Koop


    DFT calculations were performed on copper(I) complexes of neutral scorpion ligands based on either pyrazolyl (Pz) or triazolyl (Tz) rings with both methane and phosphine oxide apexes, that is, HC(Pz)3, OP(Pz)3, HC(Tz)3, and OP(Tz)3. The analyses reveal that all four ligands have similar donor proper

  13. Tris(pyrazolyl)phosphine oxide and Tris(triazolyl)phosphine oxide scorpion ligands

    NARCIS (Netherlands)

    Tazelaar, Cornelis G J; Lyaskovskyy, Volodymyr; Van Doorn, Ilana M.; Schaapkens, Xander; Lutz, Martin; Ehlers, Andreas W.; Slootweg, Jack; Lammertsma, Koop


    DFT calculations were performed on copper(I) complexes of neutral scorpion ligands based on either pyrazolyl (Pz) or triazolyl (Tz) rings with both methane and phosphine oxide apexes, that is, HC(Pz)3, OP(Pz)3, HC(Tz)3, and OP(Tz)3. The analyses reveal that all four ligands have similar donor proper

  14. Predicting Efficient Antenna Ligands for Tb(III) Emission

    Energy Technology Data Exchange (ETDEWEB)

    Samuel, Amanda P.S.; Xu, Jide; Raymond, Kenneth


    A series of highly luminescent Tb(III) complexes of para-substituted 2-hydroxyisophthalamide ligands (5LI-IAM-X) has been prepared (X = H, CH{sub 3}, (C=O)NHCH{sub 3}, SO{sub 3}{sup -}, NO{sub 2}, OCH{sub 3}, F, Cl, Br) to probe the effect of substituting the isophthalamide ring on ligand and Tb(III) emission in order to establish a method for predicting the effects of chromophore modification on Tb(III) luminescence. The energies of the ligand singlet and triplet excited states are found to increase linearly with the {pi}-withdrawing ability of the substituent. The experimental results are supported by time-dependent density functional theory (TD-DFT) calculations performed on model systems, which predict ligand singlet and triplet energies within {approx}5% of the experimental values. The quantum yield ({Phi}) values of the Tb(III) complex increases with the triplet energy of the ligand, which is in part due to the decreased non-radiative deactivation caused by thermal repopulation of the triplet. Together, the experimental and theoretical results serve as a predictive tool that can be used to guide the synthesis of ligands used to sensitize lanthanide luminescence.

  15. Conformational dynamics of a ligand-free adenylate kinase.

    Directory of Open Access Journals (Sweden)

    Hyun Deok Song

    Full Text Available Adenylate kinase (AdK is a phosphoryl-transfer enzyme with important physiological functions. Based on a ligand-free open structure and a ligand-bound closed structure solved by crystallography, here we use molecular dynamics simulations to examine the stability and dynamics of AdK conformations in the absence of ligands. We first perform multiple simulations starting from the open or the closed structure, and observe their free evolutions during a simulation time of 100 or 200 nanoseconds. In all seven simulations starting from the open structure, AdK remained stable near the initial conformation. The eight simulations initiated from the closed structure, in contrast, exhibited large variation in the subsequent evolutions, with most (seven undergoing large-scale spontaneous conformational changes and approaching or reaching the open state. To characterize the thermodynamics of the transition, we propose and apply a new sampling method that employs a series of restrained simulations to calculate a one-dimensional free energy along a curved pathway in the high-dimensional conformational space. Our calculated free energy profile features a single minimum at the open conformation, and indicates that the closed state, with a high (∼13 kcal/mol free energy, is not metastable, consistent with the observed behaviors of the unrestrained simulations. Collectively, our simulations suggest that it is energetically unfavorable for the ligand-free AdK to access the closed conformation, and imply that ligand binding may precede the closure of the enzyme.

  16. Hydrophobic contribution to the free energy of complexation of aromatic ligands with DNA

    Directory of Open Access Journals (Sweden)

    Evstigneev M. P.


    Full Text Available The hydrophobic component of complexation energy of double-stranded DNA with biologically active aromatic compounds was calculated using two semi-empirical methods – correlations of hydrophobic energy with changes of a heat capacity (DCp and solvent-accessible surface area (SASA. These surface areas were calculated for free ligands and DNA oligomers, unwound DNA duplexes and DNA-ligand complexes. The changes of polar and non-polar SASAs of molecules upon binding ligands to DNA were found. The hydrophobic contribution at both complexation stages were calculated. It was shown that the calculation of hydrophobic energy by SASA method is more correct than (DCp method for DNA-binding ligands.

  17. Controlling Nanocrystal Superlattice Symmetry and Shape-Anisotropic Interactions through Variable Ligand Surface Coverage

    KAUST Repository

    Choi, Joshua J.


    The assembly of colloidal nanocrystals (NCs) into superstructures with long-range translational and orientational order is sensitive to the molecular interactions between ligands bound to the NC surface. We illustrate how ligand coverage on colloidal PbS NCs can be exploited as a tunable parameter to direct the self-assembly of superlattices with predefined symmetry. We show that PbS NCs with dense ligand coverage assemble into face-centered cubic (fcc) superlattices whereas NCs with sparse ligand coverage assemble into body-centered cubic (bcc) superlattices which also exhibit orientational ordering of NCs in their lattice sites. Surface chemistry characterization combined with density functional theory calculations suggest that the loss of ligands occurs preferentially on {100} than on reconstructed {111} NC facets. The resulting anisotropic ligand distribution amplifies the role of NC shape in the assembly and leads to the formation of superlattices with translational and orientational order. © 2011 American Chemical Society.

  18. Ligand Binding Thermodynamics in Drug Discovery: Still a Hot Tip? (United States)

    Geschwindner, Stefan; Ulander, Johan; Johansson, Patrik


    The use of ligand binding thermodynamics has been proposed as a potential success factor to accelerate drug discovery. However, despite the intuitive appeal of optimizing binding enthalpy, a number of factors complicate routine use of thermodynamic data. On a macroscopic level, a range of experimental parameters including temperature and buffer choice significantly influence the observed thermodynamic signatures. On a microscopic level, solute effects, structural flexibility, and cooperativity lead to nonlinear changes in enthalpy. This multifactorial character hides essential enthalpy contributions of intermolecular contacts, making them experimentally nonobservable. In this perspective, we present three case studies, reflect on some key factors affecting thermodynamic signatures, and investigate their relation to the hydrophobic effect, enthalpy-entropy compensation, lipophilic ligand efficiency, and promiscuity. The studies highlight that enthalpy and entropy cannot be used as direct end points but can together with calculations increase our understanding of ligand binding and identify interesting outliers that do not behave as expected.

  19. Ligand-based virtual screening under partial shape constraints (United States)

    von Behren, Mathias M.; Rarey, Matthias


    Ligand-based virtual screening has proven to be a viable technology during the search for new lead structures in drug discovery. Despite the rapidly increasing number of published methods, meaningful shape matching as well as ligand and target flexibility still remain open challenges. In this work, we analyze the influence of knowledge-based sterical constraints on the performance of the recently published ligand-based virtual screening method mRAISE. We introduce the concept of partial shape matching enabling a more differentiated view on chemical structure. The new method is integrated into the LBVS tool mRAISE providing multiple options for such constraints. The applied constraints can either be derived automatically from a protein-ligand complex structure or by manual selection of ligand atoms. In this way, the descriptor directly encodes the fit of a ligand into the binding site. Furthermore, the conservation of close contacts between the binding site surface and the query ligand can be enforced. We validated our new method on the DUD and DUD-E datasets. Although the statistical performance remains on the same level, detailed analysis reveal that for certain and especially very flexible targets a significant improvement can be achieved. This is further highlighted looking at the quality of calculated molecular alignments using the recently introduced mRAISE dataset. The new partial shape constraints improved the overall quality of molecular alignments especially for difficult targets with highly flexible or different sized molecules. The software tool mRAISE is freely available on Linux operating systems for evaluation purposes and academic use (see

  20. Ligand-based virtual screening under partial shape constraints (United States)

    von Behren, Mathias M.; Rarey, Matthias


    Ligand-based virtual screening has proven to be a viable technology during the search for new lead structures in drug discovery. Despite the rapidly increasing number of published methods, meaningful shape matching as well as ligand and target flexibility still remain open challenges. In this work, we analyze the influence of knowledge-based sterical constraints on the performance of the recently published ligand-based virtual screening method mRAISE. We introduce the concept of partial shape matching enabling a more differentiated view on chemical structure. The new method is integrated into the LBVS tool mRAISE providing multiple options for such constraints. The applied constraints can either be derived automatically from a protein-ligand complex structure or by manual selection of ligand atoms. In this way, the descriptor directly encodes the fit of a ligand into the binding site. Furthermore, the conservation of close contacts between the binding site surface and the query ligand can be enforced. We validated our new method on the DUD and DUD-E datasets. Although the statistical performance remains on the same level, detailed analysis reveal that for certain and especially very flexible targets a significant improvement can be achieved. This is further highlighted looking at the quality of calculated molecular alignments using the recently introduced mRAISE dataset. The new partial shape constraints improved the overall quality of molecular alignments especially for difficult targets with highly flexible or different sized molecules. The software tool mRAISE is freely available on Linux operating systems for evaluation purposes and academic use (see

  1. Molecular Recognition and Ligand Association (United States)

    Baron, Riccardo; McCammon, J. Andrew


    We review recent developments in our understanding of molecular recognition and ligand association, focusing on two major viewpoints: (a) studies that highlight new physical insight into the molecular recognition process and the driving forces determining thermodynamic signatures of binding and (b) recent methodological advances in applications to protein-ligand binding. In particular, we highlight the challenges posed by compensating enthalpic and entropic terms, competing solute and solvent contributions, and the relevance of complex configurational ensembles comprising multiple protein, ligand, and solvent intermediate states. As more complete physics is taken into account, computational approaches increase their ability to complement experimental measurements, by providing a microscopic, dynamic view of ensemble-averaged experimental observables. Physics-based approaches are increasingly expanding their power in pharmacology applications.

  2. Why mercury prefers soft ligands

    Energy Technology Data Exchange (ETDEWEB)

    Riccardi, Demian M [ORNL; Guo, Hao-Bo [ORNL; Gu, Baohua [ORNL; Parks, Jerry M [ORNL; Summers, Anne [University of Georgia, Athens, GA; Miller, S [University of California, San Francisco; Liang, Liyuan [ORNL; Smith, Jeremy C [ORNL


    Mercury (Hg) is a major global pollutant arising from both natural and anthropogenic sources. Defining the factors that determine the relative affinities of different ligands for the mercuric ion, Hg2+, is critical to understanding its speciation, transformation, and bioaccumulation in the environment. Here, we use quantum chemistry to dissect the relative binding free energies for a series of inorganic anion complexes of Hg2+. Comparison of Hg2+ ligand interactions in the gaseous and aqueous phases shows that differences in interactions with a few, local water molecules led to a clear periodic trend within the chalcogenide and halide groups and resulted in the well-known experimentally observed preference of Hg2+ for soft ligands such as thiols. Our approach establishes a basis for understanding Hg speciation in the biosphere.

  3. Development of a protein-ligand-binding site prediction method based on interaction energy and sequence conservation. (United States)

    Tsujikawa, Hiroto; Sato, Kenta; Wei, Cao; Saad, Gul; Sumikoshi, Kazuya; Nakamura, Shugo; Terada, Tohru; Shimizu, Kentaro


    We present a new method for predicting protein-ligand-binding sites based on protein three-dimensional structure and amino acid conservation. This method involves calculation of the van der Waals interaction energy between a protein and many probes placed on the protein surface and subsequent clustering of the probes with low interaction energies to identify the most energetically favorable locus. In addition, it uses amino acid conservation among homologous proteins. Ligand-binding sites were predicted by combining the interaction energy and the amino acid conservation score. The performance of our prediction method was evaluated using a non-redundant dataset of 348 ligand-bound and ligand-unbound protein structure pairs, constructed by filtering entries in a ligand-binding site structure database, LigASite. Ligand-bound structure prediction (bound prediction) indicated that 74.0 % of predicted ligand-binding sites overlapped with real ligand-binding sites by over 25 % of their volume. Ligand-unbound structure prediction (unbound prediction) indicated that 73.9 % of predicted ligand-binding residues overlapped with real ligand-binding residues. The amino acid conservation score improved the average prediction accuracy by 17.0 and 17.6 points for the bound and unbound predictions, respectively. These results demonstrate the effectiveness of the combined use of the interaction energy and amino acid conservation in the ligand-binding site prediction.

  4. Implicit ligand theory: rigorous binding free energies and thermodynamic expectations from molecular docking. (United States)

    Minh, David D L


    A rigorous formalism for estimating noncovalent binding free energies and thermodynamic expectations from calculations in which receptor configurations are sampled independently from the ligand is derived. Due to this separation, receptor configurations only need to be sampled once, facilitating the use of binding free energy calculations in virtual screening. Demonstrative calculations on a host-guest system yield good agreement with previous free energy calculations and isothermal titration calorimetry measurements. Implicit ligand theory provides guidance on how to improve existing molecular docking algorithms and insight into the concepts of induced fit and conformational selection in noncovalent macromolecular recognition.

  5. A race for RAGE ligands. (United States)

    Schleicher, Erwin D


    In experimental animals a causal involvement of the multiligand receptor for advanced glycation end products (RAGE) in the development of diabetic vascular complications has been demonstrated. However, the nature of RAGE ligands present in patients with diabetic nephropathy has not yet been defined; this leaves open the relevance of the RAGE system to the human disease.

  6. Role of strain and ligand effects in the modification of the electronic and chemical properties of bimetallic surfaces

    DEFF Research Database (Denmark)

    Kitchin, J.R.; Nørskov, Jens Kehlet; Barteau, M.A.;


    Periodic density functional calculations are used to illustrate how the combination of strain and ligand effects modify the electronic and surface chemical properties of Ni, Pd, and Pt monolayers supported on other transition metals. Strain and the ligand effects are shown to change the width...

  7. Controlled-deactivation cannabinergic ligands. (United States)

    Sharma, Rishi; Nikas, Spyros P; Paronis, Carol A; Wood, Jodianne T; Halikhedkar, Aneetha; Guo, Jason Jianxin; Thakur, Ganesh A; Kulkarni, Shashank; Benchama, Othman; Raghav, Jimit Girish; Gifford, Roger S; Järbe, Torbjörn U C; Bergman, Jack; Makriyannis, Alexandros


    We report an approach for obtaining novel cannabinoid analogues with controllable deactivation and improved druggability. Our design involves the incorporation of a metabolically labile ester group at the 2'-position on a series of (-)-Δ(8)-THC analogues. We have sought to introduce benzylic substituents α to the ester group which affect the half-lives of deactivation through enzymatic activity while enhancing the affinities and efficacies of individual ligands for the CB1 and CB2 receptors. The 1'-(S)-methyl, 1'-gem-dimethyl, and 1'-cyclobutyl analogues exhibit remarkably high affinities for both CB receptors. The novel ligands are susceptible to enzymatic hydrolysis by plasma esterases in a controllable manner, while their metabolites are inactive at the CB receptors. In further in vitro and in vivo experiments key analogues were shown to be potent CB1 receptor agonists and to exhibit CB1-mediated hypothermic and analgesic effects.

  8. Passivating ligand and solvent contributions to the electronic properties of semiconductor nanocrystals

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, S.; Crotty, A.; Kilina, S.; Ivanov, I.; Tretiak, S


    We examine in detail the impact of passivating ligands (i.e., amines, phosphines, phosphine oxides and pyridines) on the electronic and optical spectra of Cd{sub 33}Se{sub 33} quantum dots (QDs) using density functional theory (DFT) and time-dependent DFT (TDDFT) quantum-chemical methodologies. Most ligand orbitals are found deep inside in the valence and conduction bands of the QD, with pyridine being an exception by introducing new states close to the conduction band edge. Importantly, all ligands contribute states which are highly delocalized over both the QD surface and ligands, forming hybridized orbitals rather than ligand-localized trap states. In contrast, the states close to the band gap are delocalized over the QD atoms only and define the lower energy absorption spectra. The random detachment of one of ligands from the QD surface results in the appearance of a highly localized unoccupied state inside the energy gap of the QD. Such changes in the electronic structure are correlated with the respective QD-ligand binding energy and steric ligand-ligand interactions. Polar solvent significantly reduces both effects leading to delocalization and stabilization of the surface states. Thus, trap and surface states are substantially eliminated by the solvent. Polar solvent also blue-shifts (e.g., 0.3-0.4 eV in acetonitrile) the calculated absorption spectra. This shift increases with an increase of the dielectric constant of the solvent. We also found that the approximate single-particle Kohn-Sham (KS) approach is adequate for calculating the absorption spectra of the ligated QDs. Besides a systematic blue-shift, the KS spectra are in very good agreement with their respective counterparts calculated with the more accurate TDDFT method.

  9. Privileged chiral ligands and catalysts

    CERN Document Server

    Zhou, Qi-Lin


    This ultimate ""must have"" and long awaited reference for every chemist working in the field of asymmetric catalysis starts with the core structure of the catalysts, explaining why a certain ligand or catalyst is so successful. It describes in detail the history, the basic structural characteristics, and the applications of these ""privileged catalysts"". A novel concept that gives readers a much deeper insight into the topic.

  10. Tumor targeting via integrin ligands

    Directory of Open Access Journals (Sweden)

    Udaya Kiran eMarelli


    Full Text Available Selective and targeted delivery of drugs to tumors is a major challenge for an effective cancer therapy and also to overcome the side effects associated with current treatments. Overexpression of various receptors on tumor cells is a characteristic structural and biochemical aspect of tumors and distinguishes them from physiologically normal cells. This abnormal feature is therefore suitable for selectively directing anticancer molecules to tumors by using ligands that can preferentially recognize such receptors. Several subtypes of integrin receptors that are crucial for cell adhesion, cell signaling, cell viability and motility have been shown to have an upregulated expression on cancer cells. Thus, ligands that recognize specific integrin subtypes represent excellent candidates to be conjugated to drugs or drug carrier systems and be targeted to tumors. In this regard, integrins recognizing the RGD cell adhesive sequence have been extensively targeted for tumor specific drug delivery. Here we review key recent examples on the presentation of RGD-based integrin ligands by means of distinct drug delivery systems, and discuss the prospects of such therapies to specifically target tumor cells.

  11. Shaping the cavity of the macrocyclic ligand in metallocalix[4]arenes: the role of the ligand sphere. (United States)

    Radius, U


    The coordination form of calix[4]arene ligands and therefore the cavity of the macrocyclic ligand can be controlled by other ligands in transition metal calix[4]arene complexes, if strong directing coligands such as oxo groups are used. This paper describes the synthesis and characterization of the d(0) transition metal complexes [Cax(OMe)(2)O(2)TiCl(2)] 1 (monoclinic, space group P2(1)/c, lattice constants a = 21.639(4), b = 20.152(3), c = 12.750(3) A, beta = 95.68(3), V = 5532.6(19) A(3)) and [Cax(OMe)(2)O(2)MoO(2)] 2 (monoclinic, space group P2/c, lattice constants a = 12.433(3), b = 16.348(3), c = 24.774(5) A, beta = 99.15(3), V = 4971.6(17) A(3)). Whereas in 1 the calix[4]arene ligand adopts an elliptically distorted cone conformation, the macrocyclic ligand binds in a paco-like conformation to the metal center of 2, in the solid state and in solution. This was predicted by density functional theory calculations on models of different isomers of 1 and 2: cis,cone-1',2', trans,cone-1',2', and cis,paco-1',2'. According to these calculations, the energetic difference of 72.9 kJ/mol between both cis-dioxomolybdenum compounds is quite pronounced in favor of the cis,paco isomer, and 28.0 kJ/mol for the titanium compounds in favor of the cis,cone isomer.

  12. Synthesis and Characterization of Dinuclear Metal Complexes Stabilized by Tetradentate Schiff Base Ligands

    Directory of Open Access Journals (Sweden)

    Eid A. Abdalrazaq


    Full Text Available Problem statement: The synthesis, spectroscopic properties and theoretical calculations of acetylacetonimine and acetylacetanilidimine Schiff-base ligands, L1H and L2H, respectively and their dinuclear complexes of the type [M2LnCl2(H2O2], where n = 1 or 2, M = Co(II, Ni(II, Cu(II, Zn(II and Cd(II are described. Approach: The new tetradentate dianion Schiff base ligand which was used as stabilizers for the complexes were prepared by condensation of hydrazine with acetylacetone or acetylacetanilide. The dinuclear complexes of theses ligands were synthesized by treating an ethanolic solution of the prepared ligand with hydrated metal salts in molar ratio of 1:2 (L:M. Results: The ligand and their dinuclear metal complexes were characterized by CHN elemental analysis, FT-IR, UV-Vis, 1HNMR (for the ligands, conductivity, magnetic susceptibility and theoretical calculation by using MM2 modeling program. Conclusion: The reaction of these ligands in a 1:2 (L:M afford dinuclear M(II metal complexes with tetrahedral arrangement around Co(II, Zn(II and Cd(II and square planar around Ni(II and Cu(II.

  13. Thiopyridazine-Based Copper Boratrane Complexes Demonstrating the Z-type Nature of the Ligand. (United States)

    Holler, Stefan; Tüchler, Michael; Belaj, Ferdinand; Veiros, Luis F; Kirchner, Karl; Mösch-Zanetti, Nadia C


    In Z-type ligands the electrons for the coordination bond are formally provided by the metal. They represent an important addition to the much more extensively used L- and X-type σ-donor ligands for the development of transition metal complexes with new reactivities. We report here a new boron Z-type ligand with three tethering thiopyridazinyl donors forming exclusively complexes that feature a metal boron bond. Rational substitution pattern in the backbone of the pyridazinyl heterocycle led to a well-behaved ligand system that allowed preparation of a series of copper boratrane complexes in high yields. They are found to be more soluble in common organic solvents allowing reactivity studies in contrast to previous complexes with this type of ligand. Thus, copper complexes [Cu{B(Pn(Me,tBu))3}X] with X = Cl, OTf, N3, and κN-NCS are reported. Solution behavior was explored, and the molecular structures were determined by single-crystal X-ray diffraction analyses. The thiocyanate ligand is found to coordinate via its nitrogen atom pointing to a high oxidation state of the copper. Density functional theory calculations indicate a high positive charge on copper and a strong copper-boron interaction. Thus, here reported complexes deliver synthetic evidence for the Z-type nature of the ligand. These findings are important for further dissemination of these types of ligands in coordination chemistry.

  14. Lead Generation and Optimization Based on Protein-Ligand Complementarity

    Directory of Open Access Journals (Sweden)

    Koji Ogata


    Full Text Available This work proposes a computational procedure for structure-based lead generation and optimization, which relies on the complementarity of the protein-ligand interactions. This procedure takes as input the known structure of a protein-ligand complex. Retaining the positions of the ligand heavy atoms in the protein binding site it designs structurally similar compounds considering all possible combinations of atomic species (N, C, O, CH3, NH,etc. Compounds are ranked based on a score which incorporates energetic contributions evaluated using molecular mechanics force fields. This procedure was used to design new inhibitor molecules for three serine/threonine protein kinases (p38 MAP kinase, p42 MAP kinase (ERK2, and c-Jun N-terminal kinase 3 (JNK3. For each enzyme, the calculations produce a set of potential inhibitors whose scores are in agreement with IC50 data and Ki values. Furthermore, the native ligands for each protein target, scored within the five top-ranking compounds predicted by our method, one of the top-ranking compounds predicted to inhibit JNK3 was synthesized and his inhibitory activity confirmed against ATP hydrolysis. Our computational procedure is therefore deemed to be a useful tool for generating chemically diverse molecules active against known target proteins.

  15. Synthesis, spectral, thermal and biological studies of mixed ligand complexes with newly prepared Schiff base and 1,10-phenanthroline ligands (United States)

    Abd El-Halim, Hanan F.; Mohamed, Gehad G.; Khalil, Eman A. M.


    A series of mixed ligand complexes were prepared from the Schiff base (L1) as a primary ligand, prepared by condensation of oxamide and furan-2-carbaldehyde, and 1,10-phenanthroline (1,10-phen) as a secondary ligand. The Schiff base ligand and its mixed ligand chelates were characterized based on elemental analysis, IR, 1H NMR, thermal analysis, UV-Visible, mass, molar conductance, magnetic moment. X-ray diffraction, solid reflectance and ESR also have been studied. The mixed ligand complexes were found to have the formulae of [M(L1) (1,10-phen)]Clm.nH2O (M = Cr(III) and Fe(III) (m = 3) (n = 0); M = Mn(II), Cu(II) and Cd(II) (m = 2) (n = 0); and M = Co(II) (m = 2) (n = 1), Ni(II) (m = 2) (n = 2) and Zn(II) (m = 2) (n = 3)) and that the geometrical structure of the complexes were octahedral. The parameters of thermodynamic using Coats-Redfern and Horowitz-Metzger equations were calculated. The synthesized Schiff base ligand, 1,10-phenanthroline ligand and Their mixed ligand complexes were also investigated for their antibacterial and antifungal activity against bacterial species (Gram-Ve bacteria: Pseudomonas aeruginosa and Escherichia coli) and (Gram + Ve bacteria: Bacillus subtilis and Streptococcus pneumonia) and fungi (Aspergillus fumigates and Candida albicans). The anticancer activity of the new compounds had been tested against breast (MFC7) and colon (HCT-116) cell lines. The results showed high activity for the synthesized compounds.

  16. Ligand placement based on prior structures: the guided ligand-replacement method

    Energy Technology Data Exchange (ETDEWEB)

    Klei, Herbert E. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Bristol-Myers Squibb, Princeton, NJ 08543-4000 (United States); Moriarty, Nigel W., E-mail:; Echols, Nathaniel [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Terwilliger, Thomas C. [Los Alamos National Laboratory, Los Alamos, NM 87545-0001 (United States); Baldwin, Eric T. [Bristol-Myers Squibb, Princeton, NJ 08543-4000 (United States); Natural Discovery LLC, Princeton, NJ 08542-0096 (United States); Pokross, Matt; Posy, Shana [Bristol-Myers Squibb, Princeton, NJ 08543-4000 (United States); Adams, Paul D. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); University of California at Berkeley, Berkeley, CA 94720-1762 (United States)


    A new module, Guided Ligand Replacement (GLR), has been developed in Phenix to increase the ease and success rate of ligand placement when prior protein-ligand complexes are available. The process of iterative structure-based drug design involves the X-ray crystal structure determination of upwards of 100 ligands with the same general scaffold (i.e. chemotype) complexed with very similar, if not identical, protein targets. In conjunction with insights from computational models and assays, this collection of crystal structures is analyzed to improve potency, to achieve better selectivity and to reduce liabilities such as absorption, distribution, metabolism, excretion and toxicology. Current methods for modeling ligands into electron-density maps typically do not utilize information on how similar ligands bound in related structures. Even if the electron density is of sufficient quality and resolution to allow de novo placement, the process can take considerable time as the size, complexity and torsional degrees of freedom of the ligands increase. A new module, Guided Ligand Replacement (GLR), was developed in Phenix to increase the ease and success rate of ligand placement when prior protein–ligand complexes are available. At the heart of GLR is an algorithm based on graph theory that associates atoms in the target ligand with analogous atoms in the reference ligand. Based on this correspondence, a set of coordinates is generated for the target ligand. GLR is especially useful in two situations: (i) modeling a series of large, flexible, complicated or macrocyclic ligands in successive structures and (ii) modeling ligands as part of a refinement pipeline that can automatically select a reference structure. Even in those cases for which no reference structure is available, if there are multiple copies of the bound ligand per asymmetric unit GLR offers an efficient way to complete the model after the first ligand has been placed. In all of these applications, GLR

  17. Versatile rare earth hexanuclear clusters for the design and synthesis of highly-connected ftw-MOFsElectronic supplementary information (ESI) available: Materials and methods, synthesis of ligands, NMR spectra, synthesis of MOFs, additional structural figures, PXRD, TGA, low and high pressure gas adsorption isotherms, Qst analysis and IAST calculation. CCDC 1050062-1050064. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c5sc00614g

    National Research Council Canada - National Science Library

    Luebke, Ryan; Belmabkhout, Youssef; Weseli ski, ukasz J; Cairns, Amy J; Alkordi, Mohamed; Norton, George; Wojtas, ukasz; Adil, Karim; Eddaoudi, Mohamed


    .... Examination of the gas adsorption properties of these compounds showed that the ftw -MOF-2 analogues, constructed from rigid ligands with a phenyl, naphthyl, or anthracene core exhibited a relatively...

  18. Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein-Ligand Binding Free Energy. (United States)

    Duan, Lili; Liu, Xiao; Zhang, John Z H


    Efficient and reliable calculation of protein-ligand binding free energy is a grand challenge in computational biology and is of critical importance in drug design and many other molecular recognition problems. The main challenge lies in the calculation of entropic contribution to protein-ligand binding or interaction systems. In this report, we present a new interaction entropy method which is theoretically rigorous, computationally efficient, and numerically reliable for calculating entropic contribution to free energy in protein-ligand binding and other interaction processes. Drastically different from the widely employed but extremely expensive normal mode method for calculating entropy change in protein-ligand binding, the new method calculates the entropic component (interaction entropy or -TΔS) of the binding free energy directly from molecular dynamics simulation without any extra computational cost. Extensive study of over a dozen randomly selected protein-ligand binding systems demonstrated that this interaction entropy method is both computationally efficient and numerically reliable and is vastly superior to the standard normal mode approach. This interaction entropy paradigm introduces a novel and intuitive conceptual understanding of the entropic effect in protein-ligand binding and other general interaction systems as well as a practical method for highly efficient calculation of this effect.

  19. Evaluation of the novel algorithm of flexible ligand docking with moveable target-protein atoms. (United States)

    Sulimov, Alexey V; Zheltkov, Dmitry A; Oferkin, Igor V; Kutov, Danil C; Katkova, Ekaterina V; Tyrtyshnikov, Eugene E; Sulimov, Vladimir B


    We present the novel docking algorithm based on the Tensor Train decomposition and the TT-Cross global optimization. The algorithm is applied to the docking problem with flexible ligand and moveable protein atoms. The energy of the protein-ligand complex is calculated in the frame of the MMFF94 force field in vacuum. The grid of precalculated energy potentials of probe ligand atoms in the field of the target protein atoms is not used. The energy of the protein-ligand complex for any given configuration is computed directly with the MMFF94 force field without any fitting parameters. The conformation space of the system coordinates is formed by translations and rotations of the ligand as a whole, by the ligand torsions and also by Cartesian coordinates of the selected target protein atoms. Mobility of protein and ligand atoms is taken into account in the docking process simultaneously and equally. The algorithm is realized in the novel parallel docking SOL-P program and results of its performance for a set of 30 protein-ligand complexes are presented. Dependence of the docking positioning accuracy is investigated as a function of parameters of the docking algorithm and the number of protein moveable atoms. It is shown that mobility of the protein atoms improves docking positioning accuracy. The SOL-P program is able to perform docking of a flexible ligand into the active site of the target protein with several dozens of protein moveable atoms: the native crystallized ligand pose is correctly found as the global energy minimum in the search space with 157 dimensions using 4700 CPU ∗ h at the Lomonosov supercomputer.

  20. CB receptor ligands from plants. (United States)

    Woelkart, Karin; Salo-Ahen, Outi M H; Bauer, Rudolf


    Advances in understanding the physiology and pharmacology of the endogenous cannabinoid system have potentiated the interest of cannabinoid receptors as potential therapeutic targets. Cannabinoids have been shown to modulate a variety of immune cell functions and have therapeutic implications on central nervous system (CNS) inflammation, chronic inflammatory conditions such as arthritis, and may be therapeutically useful in treating autoimmune conditions such as multiple sclerosis. Many of these drug effects occur through cannabinoid receptor signalling mechanisms and the modulation of cytokines and other gene products. Further, endocannabinoids have been found to have many physiological and patho-physiological functions, including mood alteration and analgesia, control of energy balance, gut motility, motor and co-ordination activities, as well as alleviation of neurological, psychiatric and eating disorders. Plants offer a wide range of chemical diversity and have been a growing domain in the search for effective cannabinoid ligands. Cannabis sativa L. with the known plant cannabinoid, Delta(9-)tetrahydrocannabinol (THC) and Echinacea species with the cannabinoid (CB) receptor-binding lipophilic alkamides are the best known herbal cannabimimetics. This review focuses on the state of the art in CB ligands from plants, as well their possible therapeutic and immunomodulatory effects.

  1. Docking validation resources: protein family and ligand flexibility experiments. (United States)

    Mukherjee, Sudipto; Balius, Trent E; Rizzo, Robert C


    A database consisting of 780 ligand-receptor complexes, termed SB2010, has been derived from the Protein Databank to evaluate the accuracy of docking protocols for regenerating bound ligand conformations. The goal is to provide easily accessible community resources for development of improved procedures to aid virtual screening for ligands with a wide range of flexibilities. Three core experiments using the program DOCK, which employ rigid (RGD), fixed anchor (FAD), and flexible (FLX) protocols, were used to gauge performance by several different metrics: (1) global results, (2) ligand flexibility, (3) protein family, and (4) cross-docking. Global spectrum plots of successes and failures vs rmsd reveal well-defined inflection regions, which suggest the commonly used 2 Å criteria is a reasonable choice for defining success. Across all 780 systems, success tracks with the relative difficulty of the calculations: RGD (82.3%) > FAD (78.1%) > FLX (63.8%). In general, failures due to scoring strongly outweigh those due to sampling. Subsets of SB2010 grouped by ligand flexibility (7-or-less, 8-to-15, and 15-plus rotatable bonds) reveal that success degrades linearly for FAD and FLX protocols, in contrast to RGD, which remains constant. Despite the challenges associated with FLX anchor orientation and on-the-fly flexible growth, success rates for the 7-or-less (74.5%) and, in particular, the 8-to-15 (55.2%) subset are encouraging. Poorer results for the very flexible 15-plus set (39.3%) indicate substantial room for improvement. Family-based success appears largely independent of ligand flexibility, suggesting a strong dependence on the binding site environment. For example, zinc-containing proteins are generally problematic, despite moderately flexible ligands. Finally, representative cross-docking examples, for carbonic anhydrase, thermolysin, and neuraminidase families, show the utility of family-based analysis for rapid identification of particularly good or bad

  2. Measurement of protein-ligand complex formation. (United States)

    Lowe, Peter N; Vaughan, Cara K; Daviter, Tina


    Experimental approaches to detect, measure, and quantify protein-ligand binding, along with their theoretical bases, are described. A range of methods for detection of protein-ligand interactions is summarized. Specific protocols are provided for a nonequilibrium procedure pull-down assay, for an equilibrium direct binding method and its modification into a competition-based measurement and for steady-state measurements based on the effects of ligands on enzyme catalysis.

  3. Aromatic interactions at the ligand-protein interface: Implications for the development of docking scoring functions. (United States)

    Brylinski, Michal


    The ability to design and fine-tune non-covalent interactions between organic ligands and proteins is indispensable to rational drug development. Aromatic stacking has long been recognized as one of the key constituents of ligand-protein interfaces. In this communication, we employ a two-parameter geometric model to conduct a large-scale statistical analysis of aromatic contacts in the experimental and computer-generated structures of ligand-protein complexes, considering various combinations of aromatic amino acid residues and ligand rings. The geometry of interfacial π-π stacking in crystal structures accords with experimental and theoretical data collected for simple systems, such as the benzene dimer. Many contemporary ligand docking programs implicitly treat aromatic stacking with van der Waals and Coulombic potentials. Although this approach generally provides a sufficient specificity to model aromatic interactions, the geometry of π-π contacts in high-scoring docking conformations could still be improved. The comprehensive analysis of aromatic geometries at ligand-protein interfaces lies the foundation for the development of type-specific statistical potentials to more accurately describe aromatic interactions in molecular docking. A Perl script to detect and calculate the geometric parameters of aromatic interactions in ligand-protein complexes is available at The dataset comprising experimental complex structures and computer-generated models is available at © 2017 John Wiley & Sons A/S.

  4. A comparative study of actinide complexation in three ligand systems with increasing complexity (United States)

    Jeanson, A.; Dahou, S.; Guillaumont, D.; Moisy, P.; Den Auwer, C.; Scheinost, A.; Hennig, C.; Vidaud, C.; Subra, G.; Solari, P. L.


    The complexation of thorium, neptunium and plutonium at oxidation state +IV with three ligands of increasing complexity has been investigated. These ligands are relevant for bio inorganic systems. The first ligand is the small nitrilotriacetic acid that often play the role of protecting ligands against hydrolysis. EXAFS results for the Th to Pu series have been correlated to quantum chemical calculations and show an homogeneous behavior of the actinide at oxidation state +IV. For larger ligands, steric effects may become significant and one can ask how the ligand may accommodate the large actinide cation coordination sphere. Model pentapeptides have been synthesized and tested as complexing agents. Comparison with NTA shows that the molecular arrangements are radically different. The third ligand system is transferrin, a diferric metalloptrotein that is well known to coordinate a large variety of cations from transition metals of f-elements. Metalloproteins bear primary, secondary and tertiary structures that all play a crucial role in bonding. At a given oxidation state (+IV), but for various atomic numbers (Th, Np, Pu) EXAFS data at the cation LIII edge exhibit significant coordination discrepancies that are related to a changes in protein geometry. In that sense, the metalloprotein may be viewed as a complex system.

  5. High-affinity multivalent wheat germ agglutinin ligands by one-pot click reaction

    Directory of Open Access Journals (Sweden)

    Henning S. G. Beckmann


    Full Text Available A series of six mono-, di-, and trivalent N,N’-diacetylchitobiose derivatives was conveniently prepared by employing a one-pot procedure for Cu(II-catalyzed diazo transfer and Cu(I-catalyzed azide–alkyne cycloaddition (CuAAC starting from commercially available amines. These glycoclusters were probed for their binding potencies to the plant lectin wheat germ agglutinin (WGA from Triticum vulgaris by an enzyme-linked lectin assay (ELLA employing covalently immobilized N-acetylglucosamine (GlcNAc as a reference ligand. IC50 values were in the low micromolar/high nanomolar range, depending on the linker between the two disaccharides. Binding enhancements β up to 1000 for the divalent ligands and 2800 for a trivalent WGA ligand, compared to N,N’-diacetylchitobiose as the corresponding monovalent ligand, were observed. Molecular modeling studies, in which the chitobiose moieties were fitted into crystallographically determined binding sites of WGA, correlate the binding enhancements of the multivalent ligands with their ability to bind to the protein in a chelating mode. The best WGA ligand is a trivalent cluster with an IC50 value of 220 nM. Calculated per mol of contained chitobiose, this is the best WGA ligand known so far.

  6. A comparative study of actinide complexation in three ligand systems with increasing complexity

    Energy Technology Data Exchange (ETDEWEB)

    Jeanson, A; Dahou, S; Guillaumont, D; Moisy, P; Auwer, C Den [CEA Marcoule, DEN/DRCP/SCPS, 30207 Bagnols sur Ceze (France); Scheinost, A; Hennig, C [Forschungszentrum Dresden-Rossendorf, 01314 Dresden (Germany); Vidaud, C [CEA Marcoule DSV/iBEB/SBTN, 30207 Bagnols sur Ceze (France); Subra, G [Institut des Biomolecules Max Mousseron, CNRS UMR-5247, Universite Montpellier I-II, 34093 Montpellier (France); Solari, P L, E-mail: Christophe.denauwer@cea.f [Synchrotron SOLEIL, MARS beam line, 91192 Gif sur Yvette (France)


    The complexation of thorium, neptunium and plutonium at oxidation state +IV with three ligands of increasing complexity has been investigated. These ligands are relevant for bio inorganic systems. The first ligand is the small nitrilotriacetic acid that often play the role of protecting ligands against hydrolysis. EXAFS results for the Th to Pu series have been correlated to quantum chemical calculations and show an homogeneous behavior of the actinide at oxidation state +IV. For larger ligands, steric effects may become significant and one can ask how the ligand may accommodate the large actinide cation coordination sphere. Model pentapeptides have been synthesized and tested as complexing agents. Comparison with NTA shows that the molecular arrangements are radically different. The third ligand system is transferrin, a diferric metalloptrotein that is well known to coordinate a large variety of cations from transition metals of f-elements. Metalloproteins bear primary, secondary and tertiary structures that all play a crucial role in bonding. At a given oxidation state (+IV), but for various atomic numbers (Th, Np, Pu) EXAFS data at the cation L{sub III} edge exhibit significant coordination discrepancies that are related to a changes in protein geometry. In that sense, the metalloprotein may be viewed as a complex system.

  7. Magnetic Field Calculator (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Magnetic Field Calculator will calculate the total magnetic field, including components (declination, inclination, horizontal intensity, northerly intensity,...

  8. Investigations of Takeout proteins' ligand binding and release mechanism using molecular dynamics simulation. (United States)

    Zhang, Huijing; Yu, Hui; Zhao, Xi; Liu, Xiaoguang; Feng, Xianli; Huang, Xuri


    Takeout (To) proteins exist in a diverse range of insect species. They are involved in many important processes of insect physiology and behaviors. As the ligand carriers, To proteins can transport the small molecule to the target tissues. However, ligand release mechanism of To proteins is unclear so far. In this contribution, the process and pathway of the ligand binding and release are revealed by conventional molecular dynamics simulation, steered molecular dynamics simulation and umbrella sampling methods. Our results show that the α4-side of the protein is the unique gate for the ligand binding and release. The structural analysis confirms that the internal cavity of the protein has high rigidity, which is in accordance with the recent experimental results. By using the potential of mean force calculations in combination with residue cross correlation calculation, we concluded that the binding between the ligand and To proteins is a process of conformational selection. Furthermore, the conformational changes of To proteins and the hydrophobic interactions both are the key factors for ligand binding and release.

  9. Fixed-charge phosphine ligands to explore gas-phase coinage metal-mediated decarboxylation reactions. (United States)

    Vikse, Krista; Khairallah, George N; McIndoe, J Scott; O'Hair, Richard A J


    A combination of multistage mass spectrometry experiments and density functional theory (DFT) calculations were used to examine the decarboxylation reactions of a series of metal carboxylate complexes bearing a fixed-charge phosphine ligand, [(O3SC6H4)(C6H5)2PM(I)O2CR](-) (M = Cu, Ag, Au; R = Me, Et, benzyl, Ph). Collision-induced dissociation (CID) of these complexes using an LTQ linear ion mass spectrometer results in three main classes of reactions being observed: (1) decarboxylation; (2) loss of the phosphine ligand; (3) loss of carboxylic acid. The gas-phase unimolecular chemistry of the resultant decarboxylated organometallic ions, [(O3SC6H4)(C6H5)2PM(I)R](-), were also explored using CID experiments, and fragment primarily via loss of the phosphine ligand. Energy-resolved CID experiments on [(O3SC6H4)(C6H5)2PM(I)O2CR](-) (M = Cu, Ag, Au; R = Me, Et, benzyl, Ph) using a Q-TOF mass spectrometer were performed to gain a more detailed understanding of the factors influencing coinage metal-catalyzed decarboxylation and DFT calculations on the major fragmentation pathways aided in interpretation of the experimental results. Key findings are that: (1) the energy required for loss of the phosphine ligand follows the order Ag phosphine ligand on decarboxylation is also considered in comparison with previous studies on metal carboxylates that do not contain a phosphine ligand.

  10. Stereochemical Properties of Multidentate Nitrogen Donor Ligands and Their Copper Complexes by Electronic CD and DFT. (United States)

    Poopari, Mohammad Reza; Dezhahang, Zahra; Xu, Yunjie


    UV-Vis and electronic circular dichroism (ECD) spectroscopy, complemented with Density Functional Theory (DFT) calculations, were used to elucidate the structural diversities of three multidentate nitrogen donor ligands and two associated copper complexes in solution directly. The three chiral salen ligands all consist of trans-cyclohexane-1,2-diamine as a chiral scaffold and also of pyridine rings as chromophores, differing only in the linking groups between the two functional groups mentioned above. Very different ECD intensities and somewhat different ECD patterns were observed for these ligands and satisfactorily interpreted theoretically. For the geometry optimization and spectral simulation of the open-shell metal complexes, the LANL2DZ basis set with effective core potential for the Cu and Cl atoms and pure cc-pVTZ for the rest of the atoms was utilized. The performance of the same calculations with the polarization functions (f,g) from the cc-pVTZ basis added to the LANL2DZ basis was compared. While the three ligands exhibit different conformational flexibility, the associated copper complexes show great rigidity imposed by the metal-ligand coordination, taking on a single structure in each case. In addition, dispersion interactions were shown to change the conformational stability ordering of the ligands noticeably and to exert considerable influence on the simulated UV-Vis and ECD spectra. Chirality 28:545-555, 2016. © 2016 Wiley Periodicals, Inc.

  11. Reductive Cleavage of CO2 by Metal-Ligand-Cooperation Mediated by an Iridium Pincer Complex. (United States)

    Feller, Moran; Gellrich, Urs; Anaby, Aviel; Diskin-Posner, Yael; Milstein, David


    A unique mode of stoichiometric CO2 activation and reductive splitting based on metal-ligand-cooperation is described. The novel Ir hydride complexes [((t)Bu-PNP*)Ir(H)2] (2) ((t)Bu-PNP*, deprotonated (t)Bu-PNP ligand) and [((t)Bu-PNP)Ir(H)] (3) react with CO2 to give the dearomatized complex [((t)Bu-PNP*)Ir(CO)] (4) and water. Mechanistic studies have identified an adduct in which CO2 is bound to the ligand and metal, [((t)Bu-PNP-COO)Ir(H)2] (5), and a di-CO2 iridacycle [((t)Bu-PNP)Ir(H)(C2O4-κC,O)] (6). DFT calculations confirm the formation of 5 and 6 as reversibly formed side products, and suggest an η(1)-CO2 intermediate leading to the thermodynamic product 4. The calculations support a metal-ligand-cooperation pathway in which an internal deprotonation of the benzylic position by the η(1)-CO2 ligand leads to a carboxylate intermediate, which further reacts with the hydride ligand to give complex 4 and water.

  12. Using robotics to fold proteins and dock ligands. (United States)

    Brutlag, Douglas; Apaydin, Serkan; Guestrin, Carlos; Hsu, David; Varma, Chris; Singh, Amit; Latombe, Jean-Claude


    The problems of protein folding and ligand docking have been explored largely using molecular dynamics or Monte Carlo methods. These methods are very compute intensive because they often explore a much wider range of energies, conformations and time than necessary. In addition, Monte Carlo methods often get trapped in local minima. We initially showed that robotic motion planning permitted one to determine the energy of binding and dissociation of ligands from protein binding sites (Singh et al., 1999). The robotic motion planning method maps complicated three-dimensional conformational states into a much simpler, but higher dimensional space in which conformational rearrangements can be represented as linear paths. The dimensionality of the conformation space is of the same order as the number of degrees of conformational freedom in three-dimensional space. We were able to determine the relative energy of association and dissociation of a ligand to a protein by calculating the energetics of interaction for a few thousand conformational states in the vicinity of the protein and choosing the best path from the roadmap. More recently, we have applied roadmap planning to the problem of protein folding (Apaydin et al., 2002a). We represented multiple conformations of a protein as nodes in a compact graph with the edges representing the probability of moving between neighboring states. Instead of using Monte Carlo simulation to simulate thousands of possible paths through various conformational states, we were able to use Markov methods to calculate the steady state occupancy of each conformation, needing to calculate the energy of each conformation only once. We referred to this Markov method of representing multiple conformations and transitions as stochastic roadmap simulation or SRS. We demonstrated that the distribution of conformational states calculated with exhaustive Monte Carlo simulations asymptotically approached the Markov steady state if the same Boltzman

  13. Ligand effects on the structure and vibrational properties of the thiolated Au18 cluster

    Institute of Scientific and Technical Information of China (English)

    Alfredo; Tlahuice-Flores


    Most of the studies devoted to thiolated gold clusters suppose that their core and Au-S framework do not suffer from distortion independently of the protecting ligands (-SR) and it is assumed as correct to simplify the ligand as SCH3. In this work is delivered a systematic study of the structure and vibrational properties (IR and Raman) of the Au18(SR)14 cluster. The pursued goal is to understand the dependency of the displayed vibrational properties of the thiolated Au18 cluster with the ligands type. A set of six ligands was considered during calculations of the vibrational properties based on density functional theory (DFT) and in its dispersion-corrected approach (DFT-D).

  14. Ligand effects on the structure and vibrational properties of the thiolated Au18 cluster

    Directory of Open Access Journals (Sweden)

    Alfredo Tlahuice-Flores


    Full Text Available Most of the studies devoted to thiolated gold clusters suppose that their core and Au-S framework do not suffer from distortion independently of the protecting ligands (-SR and it is assumed as correct to simplify the ligand as SCH3. In this work is delivered a systematic study of the structure and vibrational properties (IR and Raman of the Au18(SR14 cluster. The pursued goal is to understand the dependency of the displayed vibrational properties of the thiolated Au18 cluster with the ligands type. A set of six ligands was considered during calculations of the vibrational properties based on density functional theory (DFT and in its dispersion-corrected approach (DFT-D.

  15. Electronic structures of ruthenium complexes encircling non-innocent ligand assembly

    Indian Academy of Sciences (India)

    Amit Das; Dipanwita Das; Tanaya Kundu; Goutam Kumar Lahiri


    Electronic structural forms of selected mononuclear and dinuclear ruthenium complexes encompassing redox non-innocent terminal as well as bridging ligands have been addressed. The sensitive valence and spin situations of the complexes have been established in the native and accessible redox states via detailed analysis of their crystal structures, electrochemistry, UV/VIS/NIR spectroelectrochemistry, EPR signatures at the paramagnetic states and DFT calculations. Mononuclear complexes exhibit significant variations in valence and spin distribution processes based on the simple modification of the non-innocent ligand frameworks as well as electronic nature of the co-ligands, -donating or -accepting. Dinuclear complexes with modified pyrazine, -quinone and azo-derived redox-active bridging ligands show complex features including redoxinduced electron-transfer (RIET), remote metal to metal spin-interaction in a three-spin metal-bridge-metal arrangement as well as electron-transfer driven chemical transformation (EC).

  16. Cofactor-Controlled Chirality of Tropoisomeric Ligand

    NARCIS (Netherlands)

    Théveau, L.; Bellini, R.; Dydio, P.; Szabo, Z.; van der Werf, A.; Sander, R.A.; Reek, J.N.H.; Moberg, C.


    A new tropos ligand with an integrated anion receptor receptor site has been prepared. Chiral carboxylate and phosphate anions that bind in the anion receptor unit proved capable of stabilizing chiral conformations of the achiral flexible bidentate biaryl phosphite ligand, as shown by variable

  17. Flexible Ligand Docking Using Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Thomsen, Rene


    The docking of ligands to proteins can be formulated as a computational problem where the task is to find the most favorable energetic conformation among the large space of possible protein–ligand complexes. Stochastic search methods such as evolutionary algorithms (EAs) can be used to sample large...

  18. Flexible Ligand Docking Using Differential Evolution

    DEFF Research Database (Denmark)

    Thomsen, René


    the most favorable energetic conformation among the large space of possible protein-ligand complexes. Stochastic search methods, such as evolutionary algorithms (EAs), can be used to sample large search spaces effectively and is one of the preferred methods for flexible ligand docking. The differential...

  19. Rhodium olefin complexes of diiminate type ligands

    NARCIS (Netherlands)

    Willems, Sander Theodorus Hermanus


    The mono-anionic beta-diiminate ligand (ArNC(CH3)CHC(CH3)NAr) on several previous occasions proved useful in stabilising low coordination numbers for both early and late transition metals. In this thesis the reactivity of the rhodium olefin complexes of one of these beta-diiminate ligands (Ar = 2,6-

  20. Ligand sphere conversions in terminal carbide complexes

    DEFF Research Database (Denmark)

    Morsing, Thorbjørn Juul; Reinholdt, Anders; Sauer, Stephan P. A.


    Metathesis is introduced as a preparative route to terminal carbide complexes. The chloride ligands of the terminal carbide complex [RuC(Cl)2(PCy3)2] (RuC) can be exchanged, paving the way for a systematic variation of the ligand sphere. A series of substituted complexes, including the first exam...

  1. Using AutoDock for ligand-receptor docking. (United States)

    Morris, Garrett M; Huey, Ruth; Olson, Arthur J


    This unit describes how to set up and analyze ligand-protein docking calculations using AutoDock and the graphical user interface, AutoDockTools (ADT). The AutoDock scoring function is a subset of the AMBER force field that treats molecules using the United Atom model. The unit uses an X-ray crystal structure of Indinavir bound to HIV-1 protease taken from the Protein Data Bank (UNIT 1.9) and shows how to prepare the ligand and receptor for AutoGrid, which computes grid maps needed by AutoDock. Indinavir is prepared for AutoDock, adding the polar hydrogens, and partial charges, and defining the rotatable bonds that will be explored during the docking. The input files for AutoGrid and AutoDock are created, and then the grid map calculation run, followed by the docking calculation in AutoDock. Finally, this unit describes some of the ways the results can be analyzed using AutoDockTools. Copyright 2008 by John Wiley & Sons, Inc.

  2. Observation of Protein Structural Vibrational Mode Sensitivity to Ligand Binding (United States)

    Niessen, Katherine; Xu, Mengyang; Snell, Edward; Markelz, Andrea


    We report the first measurements of the dependence of large-scale protein intramolecular vibrational modes on ligand binding. These collective vibrational modes in the terahertz (THz) frequency range (5-100 cm-1) are of great interest due to their predicted relation to protein function. Our technique, Crystals Anisotropy Terahertz Microscopy (CATM), allows for room temperature, table-top measurements of the optically active intramolecular modes. CATM measurements have revealed surprisingly narrowband features. CATM measurements are performed on single crystals of chicken egg-white lysozyme (CEWL) as well as CEWL bound to tri-N-acetylglucosamine (CEWL-3NAG) inhibitor. We find narrow band resonances that dramatically shift with binding. Quasiharmonic calculations are performed on CEWL and CEWL-3NAG proteins with CHARMM using normal mode analysis. The expected CATM response of the crystals is then calculated by summing over all protein orientations within the unit cell. We will compare the CATM measurements with the calculated results and discuss the changes which arise with protein-ligand binding. This work is supported by NSF grant MRI 2 grant DBI2959989.

  3. Asymmetric catalysis based on tropos ligands. (United States)

    Aikawa, Kohsuke; Mikami, Koichi


    All enantiopure atropisomeric (atropos) ligands essentially require enantiomeric resolution or synthetic transformation from a chiral pool. In sharp contrast, the use of tropos (chirally flexible) ligands, which are highly modular, versatile, and easy to synthesize without enantiomeric resolution, has recently been the topic of much interest in asymmetric catalysis. Racemic catalysts bearing tropos ligands can be applied to asymmetric catalysis through enantiomeric discrimination by the addition of a chiral source, which preferentially transforms one catalyst enantiomer into a highly activated catalyst enantiomer. Additionally, racemic catalysts bearing tropos ligands can also be utilized as atropos enantiopure catalysts obtained via the control of chirality by a chiral source followed by the memory of chirality. In this feature article, our results on the asymmetric catalysis via the combination of various central metals and tropos ligands are summarized.

  4. Ligand binding mechanics of maltose binding protein. (United States)

    Bertz, Morten; Rief, Matthias


    In the past decade, single-molecule force spectroscopy has provided new insights into the key interactions stabilizing folded proteins. A few recent studies probing the effects of ligand binding on mechanical protein stability have come to quite different conclusions. While some proteins seem to be stabilized considerably by a bound ligand, others appear to be unaffected. Since force acts as a vector in space, it is conceivable that mechanical stabilization by ligand binding is dependent on the direction of force application. In this study, we vary the direction of the force to investigate the effect of ligand binding on the stability of maltose binding protein (MBP). MBP consists of two lobes connected by a hinge region that move from an open to a closed conformation when the ligand maltose binds. Previous mechanical experiments, where load was applied to the N and C termini, have demonstrated that MBP is built up of four building blocks (unfoldons) that sequentially detach from the folded structure. In this study, we design the pulling direction so that force application moves the two MBP lobes apart along the hinge axis. Mechanical unfolding in this geometry proceeds via an intermediate state whose boundaries coincide with previously reported MBP unfoldons. We find that in contrast to N-C-terminal pulling experiments, the mechanical stability of MBP is increased by ligand binding when load is applied to the two lobes and force breaks the protein-ligand interactions directly. Contour length measurements indicate that MBP is forced into an open conformation before unfolding even if ligand is bound. Using mutagenesis experiments, we demonstrate that the mechanical stabilization effect is due to only a few key interactions of the protein with its ligand. This work illustrates how varying the direction of the applied force allows revealing important details about the ligand binding mechanics of a large protein.

  5. Synthesis, spectroscopic, thermogravimetric and antimicrobial studies of mixed ligands complexes (United States)

    Mahmoud, Walaa H.; Mahmoud, Nessma F.; Mohamed, Gehad G.; El-Sonbati, Adel Z.; El-Bindary, Ashraf A.


    An interesting series of mixed ligand complexes have been synthesized by the reaction of metal chloride with guaifenesin (GFS) in the presence of 2-aminoacetic acid (HGly) (1:1:1 molar ratio). The elemental analysis, magnetic moments, molar conductance, spectral (UV-Vis, IR, 1H NMR and ESR) and thermal studies were used to characterize the isolated complexes. The molecular structure of GFS is optimized theoretically and the quantum chemical parameters are calculated. The IR showed that the ligand (GFS) acts as monobasic tridentate through the hydroxyl, phenoxy etheric and methoxy oxygen atoms and co-ligand (HGly) as monobasic bidentate through the deprotonated carboxylate oxygen atom and nitrogen atom of amino group. The molar conductivities showed that all the complexes are non-electrolytes except Cr(III) complex is electrolyte. Electronic and magnetic data proposed the octahedral structure for all complexes under investigation. ESR spectrum for Cu(II) revealed data which confirm the proposed structure. Antibacterial screening of the compounds were carried out in vitro on gram positive (Bacillus subtilis and Staphylococcus aureus), gram negative (Escherichia coli and Neisseria gonorrhoeae) bacteria and for in vitro antifungal activity against Candida albicans organism. However, some complexes showed more chemotherapeutic efficiency than the parent GFS drug. The complexes were also screened for their in vitro anticancer activity against the breast cell line (MFC7) and the results obtained showed that they exhibit a considerable anticancer activity.

  6. The ligand binding domain controls glucocorticoid receptor dynamics independent of ligand release. (United States)

    Meijsing, Sebastiaan H; Elbi, Cem; Luecke, Hans F; Hager, Gordon L; Yamamoto, Keith R


    Ligand binding to the glucocorticoid receptor (GR) results in receptor binding to glucocorticoid response elements (GREs) and the formation of transcriptional regulatory complexes. Equally important, these complexes are continuously disassembled, with active processes driving GR off GREs. We found that co-chaperone p23-dependent disruption of GR-driven transcription depended on the ligand binding domain (LBD). Next, we examined the importance of the LBD and of ligand dissociation in GR-GRE dissociation in living cells. We showed in fluorescence recovery after photobleaching studies that dissociation of GR from GREs is faster in the absence of the LBD. Furthermore, GR interaction with a target promoter revealed ligand-specific exchange rates. However, using covalently binding ligands, we demonstrated that ligand dissociation is not required for receptor dissociation from GREs. Overall, these studies showed that activities impinging on the LBD regulate GR exchange with GREs but that the dissociation of GR from GREs is independent from ligand dissociation.

  7. Understanding ligand effects in gold clusters using mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Grant E.; Laskin, Julia


    This review summarizes recent research on the influence of phosphine ligands on the size, stability, and reactivity of gold clusters synthesized in solution. Sub-nanometer clusters exhibit size- and composition-dependent properties that are unique from those of larger nanoparticles. The highly tunable properties of clusters and their high surface-to-volume ratio make them promising candidates for a variety of technological applications. However, because “each-atom-counts” toward defining cluster properties it is critically important to develop robust synthesis methods to efficiently prepare clusters of predetermined size. For decades phosphines have been known to direct the size-selected synthesis of gold clusters. Despite the preparation of numerous species it is still not understood how different functional groups at phosphine centers affect the size and properties of gold clusters. Using electrospray ionization mass spectrometry (ESI-MS) it is possible to characterize the effect of ligand substitution on the distribution of clusters formed in solution at defined reaction conditions. In addition, ligand exchange reactions on preformed clusters may be monitored using ESI-MS. Collision induced dissociation (CID) may also be employed to obtain qualitative insight into the fragmentation of mixed ligand clusters and the relative binding energies of differently substituted phosphines. Quantitative ligand binding energies and cluster stability may be determined employing surface induced dissociation (SID) in a custom-built Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR-MS). Rice-Ramsperger-Kassel-Marcus (RRKM) based modeling of the SID data allows dissociation energies and entropy values to be extracted that may be compared with the results of high-level theoretical calculations. The charge reduction and reactivity of atomically precise gold clusters, including partially ligated species generated in the gas-phase by in source CID, on well

  8. Comparative evaluation of the acceptor properties of quinone derivatized polypyridinic ligands

    Energy Technology Data Exchange (ETDEWEB)

    Norambuena, Ester [Departamento de Quimica, Facultad de Ciencias Basicas, Universidad Metropolitana de Ciencias de la Educacion, Santiago (Chile); Olea-Azar, Claudio [Facultad de Ciencias Quimicas y Farmaceuticas, Universidad de Chile, Santiago (Chile); Delgadillo, Alvaro [Departamento de Quimica, Facultad de Ciencias, Universidad de La Serena, Casilla 599, La Serena (Chile); Barrera, Mauricio [Facultad de Quimica, Pontificia Universidad Catolica de Chile, Casilla 306, Santiago (Chile); Loeb, Barbara, E-mail: [Facultad de Quimica, Pontificia Universidad Catolica de Chile, Casilla 306, Santiago (Chile)


    The reduction properties of four acceptor polipyridyl ligands modified with quinones were studied by different experimental methods, as cyclic voltammetry and ESR spectroscopy, and by theoretical calculations. ESR spectra for the reduced ligands show different patterns among them, suggesting that the quinone moiety plays an important role in the delocalization of the received electron. The hyperfine coupling constants calculated for the magnetic nucleus were in good agreement with experimental data. The results were additionally interpreted with the help of two theoretical predictors: the electrophilicity index and the Fukui function obtained through the spin density. The results suggest that 12,17-dihydronaphtho-[2,3-h]dipyrido[3,2-a:2',3'-c]-phenazine-12,17-dione, Aqphen, shows the most promising behavior to be employed as an acceptor ligand in complexes with potential application in NLO devices.

  9. Stochastic description of the ligand-receptor interaction of biologically active substances at extremely low doses. (United States)

    Gurevich, Konstantin G; Agutter, Paul S; Wheatley, Denys N


    Signalling molecules can be effective at extraordinarily low concentrations (down to attomolar levels). To handle such cases, probabilistic methods have been used to describe the formal kinetics of action of biologically active substances in these low doses, although it has been necessary to review what is meant by such a term. The mean numbers of transformed/degraded molecules and their dispersions were calculated for the possible range of ligand-receptor binding schemes. We used both analytical equations and numerical simulations to calculate the coefficients of variation (ratio of standard deviation to mean) and demonstrated that the distribution of the coefficient is highly dependent on the reaction scheme. It may, therefore, be used as an additional factor for discriminating between cooperative and noncooperative models of ligand-receptor interaction over extreme ranges of ligand dilution. The relevance to signalling behaviour is discussed.

  10. Correcting ligands, metabolites, and pathways

    Directory of Open Access Journals (Sweden)

    Vriend Gert


    Full Text Available Abstract Background A wide range of research areas in bioinformatics, molecular biology and medicinal chemistry require precise chemical structure information about molecules and reactions, e.g. drug design, ligand docking, metabolic network reconstruction, and systems biology. Most available databases, however, treat chemical structures more as illustrations than as a datafield in its own right. Lack of chemical accuracy impedes progress in the areas mentioned above. We present a database of metabolites called BioMeta that augments the existing pathway databases by explicitly assessing the validity, correctness, and completeness of chemical structure and reaction information. Description The main bulk of the data in BioMeta were obtained from the KEGG Ligand database. We developed a tool for chemical structure validation which assesses the chemical validity and stereochemical completeness of a molecule description. The validation tool was used to examine the compounds in BioMeta, showing that a relatively small number of compounds had an incorrect constitution (connectivity only, not considering stereochemistry and that a considerable number (about one third had incomplete or even incorrect stereochemistry. We made a large effort to correct the errors and to complete the structural descriptions. A total of 1468 structures were corrected and/or completed. We also established the reaction balance of the reactions in BioMeta and corrected 55% of the unbalanced (stoichiometrically incorrect reactions in an automatic procedure. The BioMeta database was implemented in PostgreSQL and provided with a web-based interface. Conclusion We demonstrate that the validation of metabolite structures and reactions is a feasible and worthwhile undertaking, and that the validation results can be used to trigger corrections and improvements to BioMeta, our metabolite database. BioMeta provides some tools for rational drug design, reaction searches, and

  11. An improvement to the ligand optimisation method (LOM) for measuring the apparent dissociation constant and ligand purity in Ca2+ and Mg2+ buffer solutions. (United States)

    McGuigan, John A S; Kay, James W; Elder, Hugh Y


    In Ca(2+)/Mg(2+) buffers the calculated ionised concentrations ([X(2+)]) can vary by up to a factor of seven. Since there are no defined standards it is impossible to check calculated [X(2+)], making measurement essential. The ligand optimisation method (LOM) is an accurate method to measure [X(2+)] in Ca(2+)/Mg(2+) buffers; independent estimation of ligand purity extends the method to pK(/) buffers, to calculate electrode and buffer characteristics as a function of Σ. Ca(2+)-electrodes have a Σ buffers. These results demonstrated that it is pK(/) that is normally distributed. Until defined standards are available, [X(2+)] in Ca(2+)/Mg(2+) buffers have to be measured. The most appropriate method is to use Ca(2+)/Mg(2) electrodes combined with the Excel programs SALE or AEC. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. Supervised Machine Learning Methods Applied to Predict Ligand- Binding Affinity. (United States)

    Heck, Gabriela S; Pintro, Val O; Pereira, Richard R; de Ávila, Mauricio B; Levin, Nayara M B; de Azevedo, Walter F


    Calculation of ligand-binding affinity is an open problem in computational medicinal chemistry. The ability to computationally predict affinities has a beneficial impact in the early stages of drug development, since it allows a mathematical model to assess protein-ligand interactions. Due to the availability of structural and binding information, machine learning methods have been applied to generate scoring functions with good predictive power. Our goal here is to review recent developments in the application of machine learning methods to predict ligand-binding affinity. We focus our review on the application of computational methods to predict binding affinity for protein targets. In addition, we also describe the major available databases for experimental binding constants and protein structures. Furthermore, we explain the most successful methods to evaluate the predictive power of scoring functions. Association of structural information with ligand-binding affinity makes it possible to generate scoring functions targeted to a specific biological system. Through regression analysis, this data can be used as a base to generate mathematical models to predict ligandbinding affinities, such as inhibition constant, dissociation constant and binding energy. Experimental biophysical techniques were able to determine the structures of over 120,000 macromolecules. Considering also the evolution of binding affinity information, we may say that we have a promising scenario for development of scoring functions, making use of machine learning techniques. Recent developments in this area indicate that building scoring functions targeted to the biological systems of interest shows superior predictive performance, when compared with other approaches. Copyright© Bentham Science Publishers; For any queries, please email at

  13. Ligand fishing with functionalized magnetic nanoparticles coupled with mass spectrometry for herbal medicine analysis: ligand fishing for herbal medicine analysis. (United States)

    Qing, Lin-Sen; Xue, Ying; Deng, Wen-Long; Liao, Xun; Xu, Xue-Min; Li, Bo-Gang; Liu, Yi-Ming


    The chemical composition of herbal medicines is very complex, and their therapeutic effects are determined by multi-components with sophisticated synergistic and/or suppressive actions. Therefore, quality control of herbal medicines has been a formidable challenge. In this work, we describe a fast analytical method that can be used for quality assessment of herbal medicines. The method is based on ligand fishing using human-serum-albumin-functionalized magnetic nanoparticles (HSA-MNPs) and mass spectrometry. To demonstrate the applicability of the proposed method, eight samples of Dioscorea panthaica were analyzed. The sampled plants were of both wild and cultivated origins. They grew at different geographical locations and were harvested at different times. The ligands bound to HSA-MNPs were isolated from the plant extracts and detected by using direct infusion electrospray ionization mass spectrometry (DI-ESI-MS). Chemical identity has been confirmed for five of the ligands isolated. From more than 15 peaks in the ESI-MS spectrum, 11 common peaks were selected for calculating the correlation coefficient and cosine ratio. The values of correlation coefficient and cosine ratio were >0.9824 and >0.9988, respectively, for all the samples tested. The results indicated a high level of similarity among the eight D. panthaica samples. Compared with chromatographic fingerprint analysis, the proposed HSA-MNP-based DI-ESI-MS/MS approach was not only fast and easy to carry out but also biological-activity-oriented, promising a more effective data interpretation and thus reliable assessment conclusions.

  14. Multicomponent mixtures for cryoprotection and ligand solubilization

    Directory of Open Access Journals (Sweden)

    Lidia Ciccone


    Full Text Available Mixed cryoprotectants have been developed for the solubilization of ligands for crystallization of protein–ligand complexes and for crystal soaking. Low affinity lead compounds with poor solubility are problematic for structural studies. Complete ligand solubilization is required for co-crystallization and crystal soaking experiments to obtain interpretable electron density maps for the ligand. Mixed cryo-preserving compounds are needed prior to X-ray data collection to reduce radiation damage at synchrotron sources. Here we present dual-use mixes that act as cryoprotectants and also promote the aqueous solubility of hydrophobic ligands. Unlike glycerol that increases protein solubility and can cause crystal melting the mixed solutions of cryo-preserving compounds that include precipitants and solubilizers, allow for worry-free crystal preservation while simultaneously solubilizing relatively hydrophobic ligands, typical of ligands obtained in high-throughput screening. The effectiveness of these mixture has been confirmed on a human transthyretin crystals both during crystallization and in flash freezing of crystals.

  15. Coordinate unsaturation with fluorinated ligands

    Energy Technology Data Exchange (ETDEWEB)

    Rack, J.L.; Hurlburt, P.K.; Anderson, O.P.; Strauss, S.H. [Colorado State Univ., Ft. Collins, CO (United States)


    The preparation and characterization of Zn(OTeF{sub 5}){sub 2} has resulted in a model compound with which to explore the concept of coordinative unsaturation. The coordination of solvents of varying donicity and dielectric constant to the Zn(II) ions in Zn(OTeF{sub 5}){sub 2} was studied by vapor phase monometry, NMR and IR spectroscopy, conductimetry, and X-Ray crystallography. The structures of [Zn(C{sub 6}H{sub 5}NO{sub 2}){sub 2}(OTeF{sub 5})2]2 and Zn(C{sub 6}H{sub 5}NO{sub 2}){sub 3}(OTEF{sub 5}){sub 2} demonstrate the electronic flexibility of some weakly coordinating solvents in that nitrobenzene can function as either an {eta}{sup 1}O or {eta}{sup 2}O,O`-ligand. The dependence of the number of bound solvent molecules and the degree of OTeF{sub 5}{minus} dissociation on solvent donor number and dielectric constant will be presented.

  16. Flexible Mental Calculation. (United States)

    Threlfall, John


    Suggests that strategy choice is a misleading characterization of efficient mental calculation and that teaching mental calculation methods as a whole is not conducive to flexibility. Proposes an alternative in which calculation is thought of as an interaction between noticing and knowledge. Presents an associated teaching approach to promote…

  17. Geochemical Calculations Using Spreadsheets. (United States)

    Dutch, Steven Ian


    Spreadsheets are well suited to many geochemical calculations, especially those that are highly repetitive. Some of the kinds of problems that can be conveniently solved with spreadsheets include elemental abundance calculations, equilibrium abundances in nuclear decay chains, and isochron calculations. (Author/PR)

  18. Autistic Savant Calendar Calculators. (United States)

    Patti, Paul J.

    This study identified 10 savants with developmental disabilities and an exceptional ability to calculate calendar dates. These "calendar calculators" were asked to demonstrate their abilities, and their strategies were analyzed. The study found that the ability to calculate dates into the past or future varied widely among these…

  19. ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites. (United States)

    Konc, Janez; Miller, Benjamin T; Štular, Tanja; Lešnik, Samo; Woodcock, H Lee; Brooks, Bernard R; Janežič, Dušanka


    Proteins often exist only as apo structures (unligated) in the Protein Data Bank, with their corresponding holo structures (with ligands) unavailable. However, apoproteins may not represent the amino-acid residue arrangement upon ligand binding well, which is especially problematic for molecular docking. We developed the ProBiS-CHARMMing web interface by connecting the ProBiS ( ) and CHARMMing ( ) web servers into one functional unit that enables prediction of protein-ligand complexes and allows for their geometry optimization and interaction energy calculation. The ProBiS web server predicts ligands (small compounds, proteins, nucleic acids, and single-atom ligands) that may bind to a query protein. This is achieved by comparing its surface structure against a nonredundant database of protein structures and finding those that have binding sites similar to that of the query protein. Existing ligands found in the similar binding sites are then transposed to the query according to predictions from ProBiS. The CHARMMing web server enables, among other things, minimization and potential energy calculation for a wide variety of biomolecular systems, and it is used here to optimize the geometry of the predicted protein-ligand complex structures using the CHARMM force field and to calculate their interaction energies with the corresponding query proteins. We show how ProBiS-CHARMMing can be used to predict ligands and their poses for a particular binding site, and minimize the predicted protein-ligand complexes to obtain representations of holoproteins. The ProBiS-CHARMMing web interface is freely available for academic users at

  20. Understanding ligand-protein interactions in affinity membrane chromatography for antibody purification. (United States)

    Boi, Cristiana; Busini, Valentina; Salvalaglio, Matteo; Cavallotti, Carlo; Sarti, Giulio C


    Affinity chromatography with Protein A beads has become the conventional unit operation for the primary capture of monoclonal antibodies. However, Protein A activated supports are expensive and ligand leakage is an issue to be considered. In addition, the limited production capabilities of the chromatographic process drive the research towards feasible alternatives. The use of synthetic ligands as Protein A substitutes has been considered in this work. Synthetic ligands, that mimic the interaction between Protein A and the constant fragment (Fc) of immunoglobulins, have been immobilized on cellulosic membrane supports. The resulting affinity membranes have been experimentally characterized with pure immunoglobulin G (IgG). The effects of the membrane support and of the spacer arm on the ligand-ligate interaction have been studied in detail. Experimental data have been compared with molecular dynamic simulations with the aim of better understanding the interaction mechanisms. Molecular dynamic simulations were performed in explicit water, modelling the membrane as a matrix of overlapped glucopyranose units. Electrostatic charges of the ligand and spacer were calculated through ab initio methods to complete the force field used to model the membrane. The simulations enabled to elucidate how the interactions of surface, spacer and ligand with IgG, contribute to the formation of the bond between protein and affinity membrane.

  1. Molecular modeling of sigma 1 receptor ligands: a model of binding conformational and electrostatic considerations. (United States)

    Gund, Tamara M; Floyd, Jie; Jung, Dawoon


    We have performed molecular modeling studies on several sigma 1 specific ligands, including PD144418, spipethiane, haloperidol, pentazocine, and others to develop a pharmacophore for sigma 1 receptor-ligand binding, under the assumption that all the compounds interact at the same receptor binding site. The modeling studies have investigated the conformational and electrostatic properties of the ligands. Superposition of active molecules gave the coordinates of the hypothetical 5-point sigma 1 pharmacophore, as follows: R1 (0.85, 7.26, 0.30); R2 (5.47, 2.40, -1.51); R3 (-2.57, 4.82, -7.10); N (-0.71, 3.29, -6.40); carbon centroid (3.16, 4.83, -0.60), where R1, R2 were constructed onto the aromatic ring of each compound to represent hydrophobic interactions with the receptor; and R3 represents a hydrogen bond between the nitrogen atom and the receptor. Additional analyses were used to describe secondary binding sites to electronegative groups such as oxygen or sulfur atom. Those coordinates are (2.34, 5.08, -4.18). The model was verified by fitting other sigma 1 receptor ligands. This model may be used to search conformational databases for other possibly active ligands. In conjunction with rational drug design techniques the model may be useful in design and synthesis of novel sigma 1 ligands of high selectivity and potency. Calculations were performed using Sybyl 6.5.

  2. NMR and theoretical study on interactions between diperoxovanadate complex and pyrazole-like ligands. (United States)

    Yu, Xianyong; Liu, Ronghua; Peng, Hongliang; Huang, Haowen; Li, Xiaofang; Zheng, Baishu; Yi, Pinggui; Chen, Zhong


    To understand the effects of pyrazole substitution on reaction equilibrium, the interactions between a series of pyrazole-like ligands and [OV(O(2))(2)(D(2)O)](-)/[OV(O(2))(2)(HOD)](-) were explored by using multinuclear ((1)H, (13)C, and (51)V) magnetic resonance, HSQC, and variable temperature NMR in 0.15 mol/L NaCl ionic medium mimicking physiological conditions. These results show that the relative reactivities among the pyrazole-like ligands are 3-methyl-1H-pyrazole approximately 4-methyl-1H-pyrazole approximately 1H-pyrazole>1-methyl-1H-pyrazole. As a result, the main factor which affects the reaction equilibrium is the steric effect instead of the electronic effect of the methyl group of these ligands. A pair of isomers has been formed resulting from the coordination of 3-methyl-1H-pyrazole and a vanadium complex, which is attributed to different types of coordination between the vanadium atom and the ligands. Thus, the competitive coordination leads to the formation of a series of six-coordinate peroxovanadate species [OV(O(2))(2)L](-) (L, pyrazole-like ligands). Moreover, the results of density functional calculations provided a reasonable explanation on the relative reactivity of the pyrazole-like ligands as well as the important role of solvation in these reactions.

  3. How Do Calculators Calculate Trigonometric Functions? (United States)

    Underwood, Jeremy M.; Edwards, Bruce H.

    How does your calculator quickly produce values of trigonometric functions? You might be surprised to learn that it does not use series or polynomial approximations, but rather the so-called CORDIC method. This paper will focus on the geometry of the CORDIC method, as originally developed by Volder in 1959. This algorithm is a wonderful…

  4. Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations (United States)

    Liu, Kai; Watanabe, Etsurou; Kokubo, Hironori


    The binding mode prediction is of great importance to structure-based drug design. The discrimination of various binding poses of ligand generated by docking is a great challenge not only to docking score functions but also to the relatively expensive free energy calculation methods. Here we systematically analyzed the stability of various ligand poses under molecular dynamics (MD) simulation. First, a data set of 120 complexes was built based on the typical physicochemical properties of drug-like ligands. Three potential binding poses (one correct pose and two decoys) were selected for each ligand from self-docking in addition to the experimental pose. Then, five independent MD simulations for each pose were performed with different initial velocities for the statistical analysis. Finally, the stabilities of ligand poses under MD were evaluated and compared with the native one from crystal structure. We found that about 94% of the native poses were maintained stable during the simulations, which suggests that MD simulations are accurate enough to judge most experimental binding poses as stable properly. Interestingly, incorrect decoy poses were maintained much less and 38-44% of decoys could be excluded just by performing equilibrium MD simulations, though 56-62% of decoys were stable. The computationally-heavy binding free energy calculation can be performed only for these survived poses.

  5. Towards a Dithiocarbamate Ligand for CdS Nanoparticle-based Photocatalysis (United States)

    O'Hara, Andrew; Lacroix, Andrew D.; Pantelides, Sokrates T.; MacDonald, Janet E.

    Photocatalysis of water into H2 and O2 presents a clean, renewable route for energy storage and production. Traditionally, most semiconducting nanoparticle research on photocatalysis has focused on the ability to reduce chemical systems using the photoexcited electron. Here we employ a combination of theory and experiments to develop a possible route towards the oxidation of chemical systems via the hole from photoexcitation using an asymmetric bipyridine ligand with conjugated dithiocarbamate ligand bound to the surface of cadmium sulfide nanorods. In particular, we use density functional theory to calculate the electronic levels and optical absorption of the designer ligand, free from the cadmium sulfide surface as well as attached to the surface, with and without the copper center. These calculations are compared with experimental UV/VIS absorption and fluorescence spectroscopy measurements to understand the role of copper chelation. Furthermore, theoretical comparisons are made with a related ligand known to oxidize water under an applied potential bias. Finally, we discuss whether we expect photocatalysis from the ligand and possible improvements to its design.

  6. Ligand mapping on protein surfaces by the 3D-RISM theory: toward computational fragment-based drug design. (United States)

    Imai, Takashi; Oda, Koji; Kovalenko, Andriy; Hirata, Fumio; Kidera, Akinori


    In line with the recent development of fragment-based drug design, a new computational method for mapping of small ligand molecules on protein surfaces is proposed. The method uses three-dimensional (3D) spatial distribution functions of the atomic sites of the ligand calculated using the molecular theory of solvation, known as the 3D reference interaction site model (3D-RISM) theory, to identify the most probable binding modes of ligand molecules. The 3D-RISM-based method is applied to the binding of several small organic molecules to thermolysin, in order to show its efficiency and accuracy in detecting binding sites. The results demonstrate that our method can reproduce the major binding modes found by X-ray crystallographic studies with sufficient precision. Moreover, the method can successfully identify some binding modes associated with a known inhibitor, which could not be detected by X-ray analysis. The dependence of ligand-binding modes on the ligand concentration, which essentially cannot be treated with other existing computational methods, is also investigated. The results indicate that some binding modes are readily affected by the ligand concentration, whereas others are not significantly altered. In the former case, it is the subtle balance in the binding affinity between the ligand and water that determines the dominant ligand-binding mode.

  7. Multiple ligand detection and affinity measurement by ultrafiltration and mass spectrometry analysis applied to fragment mixture screening. (United States)

    Qin, Shanshan; Ren, Yiran; Fu, Xu; Shen, Jie; Chen, Xin; Wang, Quan; Bi, Xin; Liu, Wenjing; Li, Lixin; Liang, Guangxin; Yang, Cheng; Shui, Wenqing


    Binding affinity of a small molecule drug candidate to a therapeutically relevant biomolecular target is regarded the first determinant of the candidate's efficacy. Although the ultrafiltration-LC/MS (UF-LC/MS) assay enables efficient ligand discovery for a specific target from a mixed pool of compounds, most previous analysis allowed for relative affinity ranking of different ligands. Moreover, the reliability of affinity measurement for multiple ligands with UF-LC/MS has hardly been strictly evaluated. In this study, we examined the accuracy of K(d) determination through UF-LC/MS by comparison with classical ITC measurement. A single-point K(d) calculation method was found to be suitable for affinity measurement of multiple ligands bound to the same target when binding competition is minimized. A second workflow based on analysis of the unbound fraction of compounds was then developed, which simplified sample preparation as well as warranted reliable ligand discovery. The new workflow implemented in a fragment mixture screen afforded rapid and sensitive detection of low-affinity ligands selectively bound to the RNA polymerase NS5B of hepatitis C virus. More importantly, ligand identification and affinity measurement for mixture-based fragment screens by UF-LC/MS were in good accordance with single ligand evaluation by conventional SPR analysis. This new approach is expected to become a valuable addition to the arsenal of high-throughput screening techniques for fragment-based drug discovery.

  8. Light-Controlled Release and Uptake of Zinc Ions in Solution by a Photochromic Terthiazole-Based Ligand. (United States)

    Guérin, Juliette; Léaustic, Anne; Berthet, Jérôme; Métivier, Rémi; Guillot, Régis; Delbaere, Stéphanie; Nakatani, Keitaro; Yu, Pei


    We have synthesized and fully characterized a photochromic zinc complex with a terphenylthiazole-based ligand with a salen-like cavity. The solution stability of the complex was found to be greatly dependent on the state of the photochromic ligand and an interesting photo-triggered release and uptake of zinc ions was found as well as monitored by its fluorescence. The contrasting stability difference of the zinc complex between its two isomeric states was rationalized by DFT calculations.

  9. Automated design of ligands to polypharmacological profiles (United States)

    Besnard, Jérémy; Ruda, Gian Filippo; Setola, Vincent; Abecassis, Keren; Rodriguiz, Ramona M.; Huang, Xi-Ping; Norval, Suzanne; Sassano, Maria F.; Shin, Antony I.; Webster, Lauren A.; Simeons, Frederick R.C.; Stojanovski, Laste; Prat, Annik; Seidah, Nabil G.; Constam, Daniel B.; Bickerton, G. Richard; Read, Kevin D.; Wetsel, William C.; Gilbert, Ian H.; Roth, Bryan L.; Hopkins, Andrew L.


    The clinical efficacy and safety of a drug is determined by its activity profile across multiple proteins in the proteome. However, designing drugs with a specific multi-target profile is both complex and difficult. Therefore methods to rationally design drugs a priori against profiles of multiple proteins would have immense value in drug discovery. We describe a new approach for the automated design of ligands against profiles of multiple drug targets. The method is demonstrated by the evolution of an approved acetylcholinesterase inhibitor drug into brain penetrable ligands with either specific polypharmacology or exquisite selectivity profiles for G-protein coupled receptors. Overall, 800 ligand-target predictions of prospectively designed ligands were tested experimentally, of which 75% were confirmed correct. We also demonstrate target engagement in vivo. The approach can be a useful source of drug leads where multi-target profiles are required to achieve either selectivity over other drug targets or a desired polypharmacology. PMID:23235874

  10. Ligand inducible assembly of a DNA tetrahedron. (United States)

    Dohno, Chikara; Atsumi, Hiroshi; Nakatani, Kazuhiko


    Here we show that a small synthetic ligand can be used as a key building component for DNA nanofabrication. Using naphthyridinecarbamate dimer (NCD) as a molecular glue for DNA hybridization, we demonstrate NCD-triggered formation of a DNA tetrahedron.

  11. Nye ligander for Pt-MOF strukturer


    Jakobsen, Søren


    Metalorganic frameworks (MOFs) are a new type of compounds which have been intensely investigated during the last few years. They have been synthesized using a wide variety of metals and ligands constructing a vast number of 1, 2 and 3 dimensional structures, some of which possess zeolite-type physics and chemistry. Our approach is to incorporate platinum metal sites into the structures making them bimetallic and potentially catalytically active. Therefore a number of N-N-type ligands (dii...

  12. SnapShot: GPCR-Ligand Interactions. (United States)

    Ghosh, Eshan; Nidhi, Kumari; Shukla, Arun K


    G-protein-coupled receptors enable cells to recognize numerous external stimuli and to transmit corresponding signals across the plasma membrane to trigger appropriate cellular responses. Crystal structures of a number of these receptors have now been determined in inactive and active conformations bound to chemically and functionally distinct ligands. These crystal structures illustrate overall receptor organization and atomic details of ligand-receptor interactions. Copyright © 2014 Elsevier Inc. All rights reserved.

  13. Core calculations of JMTR

    Energy Technology Data Exchange (ETDEWEB)

    Nagao, Yoshiharu [Japan Atomic Energy Research Inst., Oarai, Ibaraki (Japan). Oarai Research Establishment


    In material testing reactors like the JMTR (Japan Material Testing Reactor) of 50 MW in Japan Atomic Energy Research Institute, the neutron flux and neutron energy spectra of irradiated samples show complex distributions. It is necessary to assess the neutron flux and neutron energy spectra of an irradiation field by carrying out the nuclear calculation of the core for every operation cycle. In order to advance core calculation, in the JMTR, the application of MCNP to the assessment of core reactivity and neutron flux and spectra has been investigated. In this study, in order to reduce the time for calculation and variance, the comparison of the results of the calculations by the use of K code and fixed source and the use of Weight Window were investigated. As to the calculation method, the modeling of the total JMTR core, the conditions for calculation and the adopted variance reduction technique are explained. The results of calculation are shown. Significant difference was not observed in the results of neutron flux calculations according to the difference of the modeling of fuel region in the calculations by K code and fixed source. The method of assessing the results of neutron flux calculation is described. (K.I.)

  14. Structural criteria for the rational design of selective ligands. 2. Effect of alkyl substitution on metal ion complex stability with ligands bearing ethylene-bridged ether donors

    Energy Technology Data Exchange (ETDEWEB)

    Hay, B.P.; Zhang, D.; Rustad, J.R. [Pacific Northwest National Laboratory, Richland, WA (United States)


    A novel approach is presented for the application and interpretation of molecular methanics calculations in ligand structural design. The methodology yields strain energies that (i) provide a yardstick for the measurements of ligand binding site organization for metal ion complexation and (ii) allow the comparison of any two ligands independent of either the number and type of donor atoms or the identity of the metal ion. Application of this methodology is demonstrated in a detailed examination of the influence of alkyl substitution on the structural organization of ethylene-bridged, bidentate, ether donor ligands for the alkali and alkaline earth cations. Nine cases are examined, including the unsubstituted ethylene bridge (dimethoxyethane), all possible arrangements of individual alkyl groups (monoalkylation, gem-dialkylation, meso-dialkylation, d,l-dialkylation, trialkylation, and tetraalkylation), and both cis and trans attachments of the cyclohexyl group. The calculated degree of binding site organization for metal ion complexation afforded by these connecting structures is shown to correlate with known changes in complex stability caused by alkyl substitution of crown ether macrocycles.

  15. A versatile dinucleating ligand containing sulfonamide groups

    DEFF Research Database (Denmark)

    Sundberg, Jonas; Witt, Hannes; Cameron, Lisa


    Copper, iron, and gallium coordination chemistries of the new pentadentate bis-sulfonamide ligand 2,6-bis(N-2-pyridylmethylsulfonamido)-4-methylphenol (psmpH3) were investigated. PsmpH3 is capable of varying degrees of deprotonation, and notably, complexes containing the fully trideprotonated...... ligand can be prepared in aqueous solutions using only divalent metal ions. Two of the copper(II) complexes, [Cu2(psmp)(OH)] and [Cu2(psmp)(OAc)2]-, demonstrate the anticipated 1:2 ligand/metal stoichiometry and show that the dimetallic binding site created for exogenous ligands possesses high inherent...... flexibility since additional one- and three-atom bridging ligands bridge the two copper(II) ions in each complex, respectively. This gives rise to a difference of 0.4 Å in the Cu···Cu distances. Complexes with 2:3 and 2:1 ligand/metal stoichiometries for the divalent and trivalent metal ions, respectively...

  16. Designer TGFβ superfamily ligands with diversified functionality.

    Directory of Open Access Journals (Sweden)

    George P Allendorph

    Full Text Available Transforming Growth Factor--beta (TGFβ superfamily ligands, including Activins, Growth and Differentiation Factors (GDFs, and Bone Morphogenetic Proteins (BMPs, are excellent targets for protein-based therapeutics because of their pervasiveness in numerous developmental and cellular processes. We developed a strategy termed RASCH (Random Assembly of Segmental Chimera and Heteromer, to engineer chemically-refoldable TGFβ superfamily ligands with unique signaling properties. One of these engineered ligands, AB208, created from Activin-βA and BMP-2 sequences, exhibits the refolding characteristics of BMP-2 while possessing Activin-like signaling attributes. Further, we find several additional ligands, AB204, AB211, and AB215, which initiate the intracellular Smad1-mediated signaling pathways more strongly than BMP-2 but show no sensitivity to the natural BMP antagonist Noggin unlike natural BMP-2. In another design, incorporation of a short N-terminal segment from BMP-2 was sufficient to enable chemical refolding of BMP-9, without which was never produced nor refolded. Our studies show that the RASCH strategy enables us to expand the functional repertoire of TGFβ superfamily ligands through development of novel chimeric TGFβ ligands with diverse biological and clinical values.

  17. LigandRFs: random forest ensemble to identify ligand-binding residues from sequence information alone

    KAUST Repository

    Chen, Peng


    Background Protein-ligand binding is important for some proteins to perform their functions. Protein-ligand binding sites are the residues of proteins that physically bind to ligands. Despite of the recent advances in computational prediction for protein-ligand binding sites, the state-of-the-art methods search for similar, known structures of the query and predict the binding sites based on the solved structures. However, such structural information is not commonly available. Results In this paper, we propose a sequence-based approach to identify protein-ligand binding residues. We propose a combination technique to reduce the effects of different sliding residue windows in the process of encoding input feature vectors. Moreover, due to the highly imbalanced samples between the ligand-binding sites and non ligand-binding sites, we construct several balanced data sets, for each of which a random forest (RF)-based classifier is trained. The ensemble of these RF classifiers forms a sequence-based protein-ligand binding site predictor. Conclusions Experimental results on CASP9 and CASP8 data sets demonstrate that our method compares favorably with the state-of-the-art protein-ligand binding site prediction methods.

  18. Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand.

    Directory of Open Access Journals (Sweden)

    Samuel DeLuca

    Full Text Available RosettaLigand has been successfully used to predict binding poses in protein-small molecule complexes. However, the RosettaLigand docking protocol is comparatively slow in identifying an initial starting pose for the small molecule (ligand making it unfeasible for use in virtual High Throughput Screening (vHTS. To overcome this limitation, we developed a new sampling approach for placing the ligand in the protein binding site during the initial 'low-resolution' docking step. It combines the translational and rotational adjustments to the ligand pose in a single transformation step. The new algorithm is both more accurate and more time-efficient. The docking success rate is improved by 10-15% in a benchmark set of 43 protein/ligand complexes, reducing the number of models that typically need to be generated from 1000 to 150. The average time to generate a model is reduced from 50 seconds to 10 seconds. As a result we observe an effective 30-fold speed increase, making RosettaLigand appropriate for docking medium sized ligand libraries. We demonstrate that this improved initial placement of the ligand is critical for successful prediction of an accurate binding position in the 'high-resolution' full atom refinement step.

  19. Labview virtual instruments for calcium buffer calculations. (United States)

    Reitz, Frederick B; Pollack, Gerald H


    Labview VIs based upon the calculator programs of Fabiato and Fabiato (J. Physiol. Paris 75 (1979) 463) are presented. The VIs comprise the necessary computations for the accurate preparation of multiple-metal buffers, for the back-calculation of buffer composition given known free metal concentrations and stability constants used, for the determination of free concentrations from a given buffer composition, and for the determination of apparent stability constants from absolute constants. As implemented, the VIs can concurrently account for up to three divalent metals, two monovalent metals and four ligands thereof, and the modular design of the VIs facilitates further extension of their capacity. As Labview VIs are inherently graphical, these VIs may serve as useful templates for those wishing to adapt this software to other platforms.

  20. A ligand field series for the 4f-block from experimental and DFT computed Ce(IV/III) electrochemical potentials. (United States)

    Bogart, Justin A; Lewis, Andrew J; Boreen, Michael A; Lee, Heui Beom; Medling, Scott A; Carroll, Patrick J; Booth, Corwin H; Schelter, Eric J


    Understanding of the sensitivity of the reduction potential of cerium(IV) cations to ligand field strength has yet to benefit from systematic variation of the ligand environment. Detailed analyses for a series of seven cerium(IV) tetrakis(pyridyl-nitroxide) compounds and their cerium(III) analogues in varying ligand field strengths are presented. Electrochemical, spectroscopic, and computational results reveal a close correlation of electronic properties with ligand substituents. Together with electrochemical data for reported eight-coordinate compounds, DFT calculations reveal a broad range of the cerium(IV/III) redox potentials correlated to ligand field strengths, establishing a semiempirical, predictive model for the modulation of cerium redox thermodynamics and ligand field strengths. Applications over a variety of scientific disciplines make use of the fundamental redox thermodynamics of cerium. Such applications will benefit from a combined experimental and theoretical approach for assessing redox cycling of cerium compounds.

  1. Calculating correct compilers

    DEFF Research Database (Denmark)

    Bahr, Patrick; Hutton, Graham


    In this article, we present a new approach to the problem of calculating compilers. In particular, we develop a simple but general technique that allows us to derive correct compilers from high-level semantics by systematic calculation, with all details of the implementation of the compilers...... falling naturally out of the calculation process. Our approach is based upon the use of standard equational reasoning techniques, and has been applied to calculate compilers for a wide range of language features and their combination, including arithmetic expressions, exceptions, state, various forms...

  2. Radar Signature Calculation Facility (United States)

    Federal Laboratory Consortium — FUNCTION: The calculation, analysis, and visualization of the spatially extended radar signatures of complex objects such as ships in a sea multipath environment and...

  3. Electrical installation calculations basic

    CERN Document Server

    Kitcher, Christopher


    All the essential calculations required for basic electrical installation workThe Electrical Installation Calculations series has proved an invaluable reference for over forty years, for both apprentices and professional electrical installation engineers alike. The book provides a step-by-step guide to the successful application of electrical installation calculations required in day-to-day electrical engineering practice. A step-by-step guide to everyday calculations used on the job An essential aid to the City & Guilds certificates at Levels 2 and 3Fo

  4. Electrical installation calculations advanced

    CERN Document Server

    Kitcher, Christopher


    All the essential calculations required for advanced electrical installation workThe Electrical Installation Calculations series has proved an invaluable reference for over forty years, for both apprentices and professional electrical installation engineers alike. The book provides a step-by-step guide to the successful application of electrical installation calculations required in day-to-day electrical engineering practiceA step-by-step guide to everyday calculations used on the job An essential aid to the City & Guilds certificates at Levels 2 and 3For apprentices and electrical installatio

  5. Electronics Environmental Benefits Calculator (United States)

    U.S. Environmental Protection Agency — The Electronics Environmental Benefits Calculator (EEBC) was developed to assist organizations in estimating the environmental benefits of greening their purchase,...

  6. Protein ligand interactions. Part 5: Isoquinoline alkaloids as inhibitors of acetylcholinesterase from Electrophorus electricus. (United States)

    Whiteley, C G; Daya, S


    Kinetic analysis has shown that papaverine, berberine and isoquinoline alkaloids acts as reversible competitive inhibitors of acetylcholinesterase with respect to the substrate, acetylthiocholine chloride. The inhibitor constants (Ki) vary from 3.5 microM to 88 microM. With time they act as irreversible covalent inhibitors with papaverine producing 85% inactivation after 40 min. Pseudo first-order kinetics are observed with the rate constant being proportional to the concentration of the ligand and the order of reaction being equal to one. Spectrophotometry was used to study the binding of the ligands with acetylcholinesterase and Scatchard analysis used to calculate the respective dissociation constants and the number of binding sites.

  7. Infrared spectra and structures of anionic complexes of cobalt with carbon dioxide ligands. (United States)

    Knurr, Benjamin J; Weber, J Mathias


    We present infrared photodissociation spectra of [Co(CO2)n](-) ions (n = 3-11) in the wavenumber region 1000-2400 cm(-1), interpreted with the aid of density functional theory calculations. The spectra are dominated by the signatures of a core ion showing bidentate interaction of two CO2 ligands with the Co atom, each forming C-Co and O-Co bonds. This structural motif is very robust and is only weakly affected by solvation with additional CO2 solvent molecules. The Co atom is in oxidation state +1, and both CO2 ligands carry a negative charge.

  8. Computational titration analysis of a multiprotic HIV-1 protease-ligand complex. (United States)

    Spyrakis, Francesca; Fornabaio, Micaela; Cozzini, Pietro; Mozzarelli, Andrea; Abraham, Donald J; Kellogg, Glen E


    A new computational method for analyzing the protonation states of protein-ligand complexes with multiple ionizable groups is applied to the structurally characterized complex between the peptide Glu-Asp-Leu and HIV-1 protease. This complex has eight ionizable groups at the active site: four from the ligand and four Asp residues on the protein. Correlation, with an error of ca. 0.6 kcal mol-1, is made between the calculated titration curve and the experimental titration curve. The analysis suggests that between four and five of the eight ionizable groups are protonated at the pH of crystallization.

  9. Catechol versus bisphosphonate ligand exchange at the surface of iron oxide nanoparticles: towards multi-functionalization (United States)

    Guénin, Erwann; Lalatonne, Yoann; Bolley, Julie; Milosevic, Irena; Platas-Iglesias, Carlos; Motte, Laurence


    We report an investigation of the ligand exchange at the surface of iron oxide nanoparticles in water. For this purpose we compared two strong chelating agents on the iron oxide surface containing catechol and bisphosphonate moieties. Interactions between the coating agents (catechol/bisphosphonate) and the nanoparticle's surface were studied by FTIR and DFT calculations. Ligand exchange experiments were performed using sonication and the exchange yield was characterized by FTIR and EDX. This methodology allowed introducing bisphosphonates with various functionalities (alkyne or biotin) permitting multi-functionalization.

  10. Activation of Aromatic C-C Bonds of 2,2'-Bipyridine Ligands. (United States)

    Fombona, Sergio; Espinal-Viguri, Maialen; Huertos, Miguel A; Díaz, Jesús; López, Ramón; Menéndez, M Isabel; Pérez, Julio; Riera, Lucía


    4,4'-Disubstituted-2,2'-bipyridine ligands coordinated to Mo(II) and Re(I) cationic fragments become dearomatized by an intramolecular nucleophilic attack from a deprotonated N-alkylimidazole ligand in cis disposition. The subsequent protonation of these neutral complexes takes place on a pyridine carbon atom rather than at nitrogen, weakening an aromatic C-C bond and affording a dihydropyridyl moiety. Computational calculations allowed for the rationalization of the formation of the experimentally obtained products over other plausible alternatives.

  11. Synthesis and characterization of mixed ligand chiral nanoclusters

    KAUST Repository

    Guven, Zekiye P.


    Chiral mixed ligand silver nanoclusters were synthesized in the presence of a chiral and an achiral ligand. While the chiral ligand led mostly to the formation of nanoparticles, the presence of the achiral ligand drastically increased the yield of nanoclusters with enhanced chiral properties. © 2016 The Royal Society of Chemistry.

  12. Synthesis of Imine-Naphthol Tripodal Ligand and Study of Its Coordination Behaviour towards Fe(III, Al(III, and Cr(III Metal Ions

    Directory of Open Access Journals (Sweden)

    Kirandeep Kaur


    Full Text Available A hexadentate Schiff base tripodal ligand is synthesized by the condensation of tris (2-aminoethyl amine with 2-hydroxy-1-naphthaldehyde and characterized by various spectroscopic techniques like UV-VIS, IR, NMR, MASS, and elemental analysis. The solution studies by potentiometric and spectrophotometric methods are done at 25 ± 1°C, µ=0.1 M KCl, to calculate the protonation constants of the ligand and formation constants of metal complexes formed by the ligand with Fe(III, Al(III, and Cr(III metal ions. The affinity of the ligand towards Fe(III is compared with deferiprone (a drug applied for iron intoxication and transferrin (the main Fe(III binding protein in plasma. Structural analysis of the ligand and the metal complexes was done using semiempirical PM6 method. Electronic and IR spectra are calculated by semiempirical methods and compared with experimental one.

  13. Synthesis of Imine-Naphthol Tripodal Ligand and Study of Its Coordination Behaviour towards Fe(III), Al(III), and Cr(III) Metal Ions. (United States)

    Kaur, Kirandeep; Baral, Minati


    A hexadentate Schiff base tripodal ligand is synthesized by the condensation of tris (2-aminoethyl) amine with 2-hydroxy-1-naphthaldehyde and characterized by various spectroscopic techniques like UV-VIS, IR, NMR, MASS, and elemental analysis. The solution studies by potentiometric and spectrophotometric methods are done at 25 ± 1°C, µ = 0.1 M KCl, to calculate the protonation constants of the ligand and formation constants of metal complexes formed by the ligand with Fe(III), Al(III), and Cr(III) metal ions. The affinity of the ligand towards Fe(III) is compared with deferiprone (a drug applied for iron intoxication) and transferrin (the main Fe(III) binding protein in plasma). Structural analysis of the ligand and the metal complexes was done using semiempirical PM6 method. Electronic and IR spectra are calculated by semiempirical methods and compared with experimental one.

  14. Calculators and Polynomial Evaluation. (United States)

    Weaver, J. F.

    The intent of this paper is to suggest and illustrate how electronic hand-held calculators, especially non-programmable ones with limited data-storage capacity, can be used to advantage by students in one particular aspect of work with polynomial functions. The basic mathematical background upon which calculator application is built is summarized.…

  15. New polypyridine anchoring ligands for coordination complexes and surface functionalization


    Müller, Steffen


    This PhD thesis focuses on the synthesis of new polypyridine anchoring ligands and several dfferent applications. The ligands consist of a coordinating part, a flexible linker and an anchoring group. Due to the fact that different anchoring groups were used, the ligands can be applied for several types of surface-materials. Using these anchoring ligands, several coordination complexes were synthesized. Ruthenium-based complexes, bearing an ion-sensitive ligand, were tested towards...

  16. Multiple ligand simultaneous docking: orchestrated dancing of ligands in binding sites of protein. (United States)

    Li, Huameng; Li, Chenglong


    Present docking methodologies simulate only one single ligand at a time during docking process. In reality, the molecular recognition process always involves multiple molecular species. Typical protein-ligand interactions are, for example, substrate and cofactor in catalytic cycle; metal ion coordination together with ligand(s); and ligand binding with water molecules. To simulate the real molecular binding processes, we propose a novel multiple ligand simultaneous docking (MLSD) strategy, which can deal with all the above processes, vastly improving docking sampling and binding free energy scoring. The work also compares two search strategies: Lamarckian genetic algorithm and particle swarm optimization, which have respective advantages depending on the specific systems. The methodology proves robust through systematic testing against several diverse model systems: E. coli purine nucleoside phosphorylase (PNP) complex with two substrates, SHP2NSH2 complex with two peptides and Bcl-xL complex with ABT-737 fragments. In all cases, the final correct docking poses and relative binding free energies were obtained. In PNP case, the simulations also capture the binding intermediates and reveal the binding dynamics during the recognition processes, which are consistent with the proposed enzymatic mechanism. In the other two cases, conventional single-ligand docking fails due to energetic and dynamic coupling among ligands, whereas MLSD results in the correct binding modes. These three cases also represent potential applications in the areas of exploring enzymatic mechanism, interpreting noisy X-ray crystallographic maps, and aiding fragment-based drug design, respectively.

  17. Immobilisation of ligands by radio-derivatized polymers; Immobilisering av ligander med radioderiverte polymerer

    Energy Technology Data Exchange (ETDEWEB)

    Varga, J.M.; Fritsch, P.


    The invention relates to radio-derivatized polymers and a method of producing them by contacting non-polymerizable conjugands with radiolysable polymers in the presence of irradiation. The resulting radio-derivatized polymers can be further linked with ligand of organic or inorganic nature to immobilize such ligands. 2 figs., 5 tabs.

  18. Organotellurium ligands - designing and complexation reactions

    Indian Academy of Sciences (India)

    Ajai K Singh


    A variety of tellurium ligands has been designed and studied for their complexation reactions in the last decade. Of these hybrid telluroethers, halotellurium ligands and polytellurides are the most notable ones. RTe- and polytelluride ions have also been used to design clusters. Ligation of ditelluroethers and several hybrid telluroethers is extensively studied in our laboratories. The ditelluroether ligand RTeCH2TeR (where R = 4-MeOC6H4) (1), similar to dppm [1,2-bis(diphenylphosphino) methane], has been synthesized in good yield (∼80 %) by reacting CHCl3 with RTe- (generated in situ by borohydride reduction of R2Te2). Iodine reacts with 1 to give tetra-iodo derivative, which has intermolecular Te$\\cdots$I interactions resulting in a macro structure containing rectangular Te-I$\\cdots$Te bridges. 1 readily forms four membered rings with Pd(II) and Ru(II). On the formation of this chelate ring, the signal in 125Te NMR spectra shifts significantly upfield (50-60 ppm). The bridging mode of 1 has been shown in [Ru(-cymene)Cl2](-1)[Ru(-cymene)Cl2]. The hybrid telluroether ligands explored are of the types (Te, S), (Te, N) and (Te, O). The tellurium donor site has strong trans influence, which is manifested more strongly in square planar complexes of palladium(II). The morpholine N-donor site has been found to have weaker donor characteristics in (Te, N) ligands than pyridine and alkylamine donor sites of analogous ligands. The singlet oxygen readily oxidises the coordinated Te. This oxidation follows first order kinetics. The complexation reaction of RuCl3.H2O with N-[2-(4-methoxyphenyltelluro)ethyl]phthalimide (2) results in a novel (Te, N, O)-heterocycle, Te-chloro,Te-anisyl-1a-aza-4-oxa-3-tellura-1H, 2H, 4aH-9 fluorenone. The (Te, O) ligands can be used as hemilabile ligands, the oxygen atom temporarily protects the vacant coordination site before the arrival of the substrate. The chelate shifts observed in 125Te NMR spectra of metal complexes of Te-ligands have

  19. Modifications of the chromophore of Spinach aptamer based on QM:MM calculations. (United States)

    Skúpa, Katarína; Urban, Ján


    Spinach aptamer was developed as an RNA analog of the green fluorescent protein. The aptamer interacts with its ligand and modifies its electronic spectrum so that it fluoresces brightly at the wavelength of 501 nm. Song et al. investigated modifications of the ligand in their experimental study and found a molecule emitting at 523 nm upon creating a complex with the Spinach aptamer. The crystal structure of the aptamer in complex with its original ligand has been published, which enabled us to study the system computationally. In this article, we suggest several new modifications of the ligand that shift the emission maximum of the complex to even longer wavelengths. Our results are based on combined quantum mechanical/molecular mechanical calculations with DFT method used for geometry optimization and TD-DFT for calculations of absorption and emission energies.

  20. Dockomatic - automated ligand creation and docking

    Directory of Open Access Journals (Sweden)

    Hampikian Greg


    Full Text Available Abstract Background The application of computational modeling to rationally design drugs and characterize macro biomolecular receptors has proven increasingly useful due to the accessibility of computing clusters and clouds. AutoDock is a well-known and powerful software program used to model ligand to receptor binding interactions. In its current version, AutoDock requires significant amounts of user time to setup and run jobs, and collect results. This paper presents DockoMatic, a user friendly Graphical User Interface (GUI application that eases and automates the creation and management of AutoDock jobs for high throughput screening of ligand to receptor interactions. Results DockoMatic allows the user to invoke and manage AutoDock jobs on a single computer or cluster, including jobs for evaluating secondary ligand interactions. It also automates the process of collecting, summarizing, and viewing results. In addition, DockoMatic automates creation of peptide ligand .pdb files from strings of single-letter amino acid abbreviations. Conclusions DockoMatic significantly reduces the complexity of managing multiple AutoDock jobs by facilitating ligand and AutoDock job creation and management.

  1. Dockomatic - automated ligand creation and docking. (United States)

    Bullock, Casey W; Jacob, Reed B; McDougal, Owen M; Hampikian, Greg; Andersen, Tim


    The application of computational modeling to rationally design drugs and characterize macro biomolecular receptors has proven increasingly useful due to the accessibility of computing clusters and clouds. AutoDock is a well-known and powerful software program used to model ligand to receptor binding interactions. In its current version, AutoDock requires significant amounts of user time to setup and run jobs, and collect results. This paper presents DockoMatic, a user friendly Graphical User Interface (GUI) application that eases and automates the creation and management of AutoDock jobs for high throughput screening of ligand to receptor interactions. DockoMatic allows the user to invoke and manage AutoDock jobs on a single computer or cluster, including jobs for evaluating secondary ligand interactions. It also automates the process of collecting, summarizing, and viewing results. In addition, DockoMatic automates creation of peptide ligand .pdb files from strings of single-letter amino acid abbreviations. DockoMatic significantly reduces the complexity of managing multiple AutoDock jobs by facilitating ligand and AutoDock job creation and management.

  2. Sliding tethered ligands add topological interactions to the toolbox of ligand-receptor design (United States)

    Bauer, Martin; Kékicheff, Patrick; Iss, Jean; Fajolles, Christophe; Charitat, Thierry; Daillant, Jean; Marques, Carlos M.


    Adhesion in the biological realm is mediated by specific lock-and-key interactions between ligand-receptor pairs. These complementary moieties are ubiquitously anchored to substrates by tethers that control the interaction range and the mobility of the ligands and receptors, thus tuning the kinetics and strength of the binding events. Here we add sliding anchoring to the toolbox of ligand-receptor design by developing a family of tethered ligands for which the spacer can slide at the anchoring point. Our results show that this additional sliding degree of freedom changes the nature of the adhesive contact by extending the spatial range over which binding may sustain a significant force. By introducing sliding tethered ligands with self-regulating length, this work paves the way for the development of versatile and reusable bio-adhesive substrates with potential applications for drug delivery and tissue engineering.

  3. A density functional theory investigation of the interaction of the tetraaqua calcium cation with bidentate carbonyl ligands. (United States)

    Quattrociocchi, Daniel Garcez S; Meuser, Marcos Vinicius Monsores; Ferreira, Glaucio Braga; de M Carneiro, José Walkimar; Stoyanov, Stanislav R; da Costa, Leonardo Moreira


    Calcium complexes with bidentate carbonyl ligands are important in biological systems, medicine and industry, where the concentration of Ca(2+) is controlled using chelating ligands. The exchange of two water molecules of [Ca(H2O)6](2+) for one bidentate monosubstituted and homo disubstituted dicarbonyl ligand was investigated using the B3LYP/6-311++G(d,p) method. The ligand substituents NH2, OCH3, OH, CH3, H, F, Cl, CN and NO2 are functional groups with distinct electron-donating and -withdrawing effects that bond directly to the sp(2) C atom of the carbonyl group. The geometry, charge and energy characteristics of the complexes were analyzed to help understand the effects of substituents, spacer length and chelation. Coordination strength was quantified in terms of the enthalpy and free energy of the exchange reaction. The most negative enthalpies were calculated for the coordination of bidentate ligands containing three to five methylene group spacers between carbonyls. The chelate effect contribution was analyzed based on the thermochemistry. The electronic character of the substituent modulates the strength of binding to the metal cation, as ligands containing electron-donor substituents coordinate stronger than those with electron-acceptor substituents. This is reflected in the geometric (bond length and chelating angle), electronic (atomic charges) and energetic (components of the total interacting energy) characteristics of the complexes. Energy decomposition analysis (EDA)-an approach for partitioning of the energy into its chemical origins-shows that the electrostatic component of the coordination is predominant, and yields relevant contribution of the covalent term, especially for the electron-withdrawing substituted ligands. The chelate effect of the bidentate ligands was noticeable when compared with substitution by two monodentate ligands. Graphical abstract The affinity of 18 bidentate carbonyl ligands toward the [Ca(H2O)4](2+) cation is evaluated in

  4. Cyclometalated platinum(II) with ethynyl-linked azobenzene ligands: an original switching mode. (United States)

    Savel, Paul; Latouche, Camille; Roisnel, Thierry; Akdas-Kilig, Huriye; Boucekkine, Abdou; Fillaut, Jean-Luc


    The photophysical properties of 6-phenyl-2,2'-bipyridyl platinum(ii) complexes bearing different σ-alkynyl-linked azobenzene ancillary ligands were investigated. These complexes exhibited strong, broad, structureless charge-transfer bands in the visible region, which were red-shifted when the electron-donating ability of the para substituent on the azo-acetylide ligand increased. When excited at the charge-transfer absorption band, the complexes exhibited weak green emission, which was assigned to a triplet metal-to-ligand charge transfer/interligand charge transfer emission ((3)MLCT/(3)L'LCT). The presence of an amino substituent in the azobenzene moiety opened the possibility of protonation, which led to the formation of an azonium based derivative and resulted in drastic perturbations of the molecular orbitals and photophysical properties of the Pt-acetylide complex. These studies are fully supported by DFT and TD-DFT calculations.

  5. Improved Ligand-Field Theory with Effect of Electron-Phonon Interaction

    Institute of Scientific and Technical Information of China (English)

    MA Dong-Ping; CHEN Ju-Rong


    Traditional ligand-field theory has to be improved by taking into account both "pure electronic" contribution and electron-phonon interaction one (including lattice-vibrational relaxation energy). By means of improved ligand-field theory, R1, R2, R'3, R'2, and R'1 lines, U band, ground-state zero-field-splitting (GSZFS), and ground-state g factors of ruby and/or GSGG: Cr3+ as well as thermal shifts of GSZFS, R1 line and R2 line of ruby have been calculated.The results are in very good agreement with the experimental data. Moreover, it is found that the value of cubic-field parameter given by traditional ligand-field theory is inappropriately large. For thermal shifts of GSZFS, R1 line and R2 line of ruby, several conclusions have also been obtained.

  6. Structural characterization of Am(III) formate complexes. Combining EXAFS spectroscopy with DFT and thermodynamical calculations

    Energy Technology Data Exchange (ETDEWEB)

    Rossberg, Andre [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Molecular Structures; Froehlich, D.R. [Heidelberg Univ. (Germany). Physikalisch-Chemisches Inst.


    We used iterative transformation factor analysis (ITFA) in order to isolate the EXAFS spectral contributions of the complexing ligand from a Am(III)/formate pH-series. Thermodynamic calculations were used as constraint for ITFA and for density functional theory (DFT) calculations to identify the coordination mode within the formed complexes.

  7. Ligand-induced changes in estrogen receptor conformation as measured by site-directed spin labeling. (United States)

    Hurth, Kyle M; Nilges, Mark J; Carlson, Kathryn E; Tamrazi, Anobel; Belford, R Linn; Katzenellenbogen, John A


    Site-directed spin labeling (SDSL), the site-specific incorporation of nitroxide spin-labels into a protein, has allowed us to investigate ligand-induced conformational changes in the ligand-binding domain of human estrogen receptor alpha (hERalpha-LBD). EPR (electron paramagnetic resonance) spectroscopy of the nitroxide probe attached to ER produces different spectra depending upon the identity of the bound ligand; these differences are indicative of changes in the type and degree of motional character of the spin-label induced by different ligand-induced conformations of labeled ER. Visual inspection of EPR spectra, construction of B versus C cross-correlation plots, and cross-comparison of spectral pairs using a relative squared difference (RSD) calculation allowed receptor-ligand complexes to be profiled according to their conformational character. Plotting B and C parameters allowed us to evaluate the liganded receptor according to the motional characteristics of the attached spin-label, and they were particularly illustrative for the receptor labeled at position 530, which had motion between the fast and intermediate regimes. RSD analysis allowed us to directly compare the similarity or difference between two different spectra, and these comparisons produced groupings that paralleled those seen in B versus C cross-correlation plots, again relating meaningfully with the pharmacological nature of the bound ligand. RSD analysis was also particularly useful for qualifying differences seen with the receptor labeled at position 417, which had motion between the intermediate and slow motional regimes. This work demonstrates that B and C formulas from EPR line shape theory are useful for qualitative analysis of spectra with differences subtler than those that are often analyzed by EPR spectroscopists. This work also provides evidence that the ER can exist in a range of conformations, with specific conformations resulting from preferential stabilization of ER by the

  8. Cationic ruthenium alkylidene catalysts bearing phosphine ligands. (United States)

    Endo, Koji; Grubbs, Robert H


    The discovery of highly active catalysts and the success of ionic liquid immobilized systems have accelerated attention to a new class of cationic metathesis catalysts. We herein report the facile syntheses of cationic ruthenium catalysts bearing bulky phosphine ligands. Simple ligand exchange using silver(i) salts of non-coordinating or weakly coordinating anions provided either PPh3 or chelating Ph2P(CH2)nPPh2 (n = 2 or 3) ligated cationic catalysts. The structures of these newly reported catalysts feature unique geometries caused by ligation of the bulky phosphine ligands. Their activities and selectivities in standard metathesis reactions were also investigated. These cationic ruthenium alkylidene catalysts reported here showed moderate activity and very similar stereoselectivity when compared to the second generation ruthenium dichloride catalyst in ring-closing metathesis, cross metathesis, and ring-opening metathesis polymerization assays.

  9. Flexible Ligand Docking Using Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Thomsen, Rene


    The docking of ligands to proteins can be formulated as a computational problem where the task is to find the most favorable energetic conformation among the large space of possible protein–ligand complexes. Stochastic search methods such as evolutionary algorithms (EAs) can be used to sample large...... search spaces effectively and is one of the commonly used methods for flexible ligand docking. During the last decade, several EAs using different variation operators have been introduced, such as the ones provided with the AutoDock program. In this paper we evaluate the performance of different EA...... settings such as choice of variation operators, population size, and usage of local search. The comparison is performed on a suite of six docking problems previously used to evaluate the performance of search algorithms provided with the AutoDock program package. The results from our investigation confirm...

  10. Interval arithmetic in calculations (United States)

    Bairbekova, Gaziza; Mazakov, Talgat; Djomartova, Sholpan; Nugmanova, Salima


    Interval arithmetic is the mathematical structure, which for real intervals defines operations analogous to ordinary arithmetic ones. This field of mathematics is also called interval analysis or interval calculations. The given math model is convenient for investigating various applied objects: the quantities, the approximate values of which are known; the quantities obtained during calculations, the values of which are not exact because of rounding errors; random quantities. As a whole, the idea of interval calculations is the use of intervals as basic data objects. In this paper, we considered the definition of interval mathematics, investigated its properties, proved a theorem, and showed the efficiency of the new interval arithmetic. Besides, we briefly reviewed the works devoted to interval analysis and observed basic tendencies of development of integral analysis and interval calculations.

  11. Unit Cost Compendium Calculations (United States)

    U.S. Environmental Protection Agency — The Unit Cost Compendium (UCC) Calculations raw data set was designed to provide for greater accuracy and consistency in the use of unit costs across the USEPA...


    Institute of Scientific and Technical Information of China (English)



    This paper presents a procedure for calculating the effective discharge for rivers with alluvial channels.An alluvial river adjusts the bankfull shape and dimensions of its channel to the wide range of flows that mobilize the boundary sediments. It has been shown that time-averaged river morphology is adjusted to the flow that, over a prolonged period, transports most sediment. This is termed the effective discharge.The effective discharge may be calculated provided that the necessary data are available or can be synthesized. The procedure for effective discharge calculation presented here is designed to have general applicability, have the capability to be applied consistently, and represent the effects of physical processes responsible for determining the channel, dimensions. An example of the calculations necessary and applications of the effective discharge concept are presented.

  13. Calculativeness and trust

    DEFF Research Database (Denmark)

    Frederiksen, Morten


    Williamson’s characterisation of calculativeness as inimical to trust contradicts most sociological trust research. However, a similar argument is found within trust phenomenology. This paper re-investigates Williamson’s argument from the perspective of Løgstrup’s phenomenological theory of trust....... Contrary to Williamson, however, Løgstrup’s contention is that trust, not calculativeness, is the default attitude and only when suspicion is awoken does trust falter. The paper argues that while Williamson’s distinction between calculativeness and trust is supported by phenomenology, the analysis needs...... to take actual subjective experience into consideration. It points out that, first, Løgstrup places trust alongside calculativeness as a different mode of engaging in social interaction, rather conceiving of trust as a state or the outcome of a decision-making process. Secondly, the analysis must take...

  14. Magnetic Field Grid Calculator (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Magnetic Field Properties Calculator will computes the estimated values of Earth's magnetic field(declination, inclination, vertical component, northerly...

  15. LIBSA--a method for the determination of ligand-binding preference to allosteric sites on receptor ensembles. (United States)

    Hocker, Harrison J; Rambahal, Nandini; Gorfe, Alemayehu A


    Incorporation of receptor flexibility into computational drug discovery through the relaxed complex scheme is well suited for screening against a single binding site. In the absence of a known pocket or if there are multiple potential binding sites, it may be necessary to do docking against the entire surface of the target (global docking). However no suitable and easy-to-use tool is currently available to rank global docking results based on the preference of a ligand for a given binding site. We have developed a protocol, termed LIBSA for LIgand Binding Specificity Analysis, that analyzes multiple docked poses against a single or ensemble of receptor conformations and returns a metric for the relative binding to a specific region of interest. By using novel filtering algorithms and the signal-to-noise ratio (SNR), the relative ligand-binding frequency at different pockets can be calculated and compared quantitatively. Ligands can then be triaged by their tendency to bind to a site instead of ranking by affinity alone. The method thus facilitates screening libraries of ligand cores against a large library of receptor conformations without prior knowledge of specific pockets, which is especially useful to search for hits that selectively target a particular site. We demonstrate the utility of LIBSA by showing that it correctly identifies known ligand binding sites and predicts the relative preference of a set of related ligands for different pockets on the same receptor.

  16. AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking. (United States)

    Uehara, Shota; Tanaka, Shigenori


    Water plays a significant role in the binding process between protein and ligand. However, the thermodynamics of water molecules are often underestimated, or even ignored, in protein-ligand docking. Usually, the free energies of active-site water molecules are substantially different from those of waters in the bulk region. The binding of a ligand to a protein causes a displacement of these waters from an active site to bulk, and this displacement process substantially contributes to the free energy change of protein-ligand binding. The free energy of active-site water molecules can be calculated by grid inhomogeneous solvation theory (GIST), using molecular dynamics (MD) and the trajectory of a target protein and water molecules. Here, we show a case study of the combination of GIST and a docking program and discuss the effectiveness of the displacing gain of unfavorable water in protein-ligand docking. We combined the GIST-based desolvation function with the scoring function of AutoDock4, which is called AutoDock-GIST. The proposed scoring function was assessed employing 51 ligands of coagulation factor Xa (FXa), and results showed that both scoring accuracy and docking success rate were improved. We also evaluated virtual screening performance of AutoDock-GIST using FXa ligands in the directory of useful decoys-enhanced (DUD-E), thus finding that the displacing gain of unfavorable water is effective for a successful docking campaign.

  17. Synthesis, structural, thermal studies and biological activity of a tridentate Schiff base ligand and their transition metal complexes. (United States)

    Abd El-halim, Hanan F; Omar, M M; Mohamed, Gehad G


    Schiff base (L) ligand is prepared via condensation of pyridine-2,6-dicarboxaldehyde with -2-aminopyridine. The ligand and its metal complexes are characterized based on elemental analysis, mass, IR, solid reflectance, magnetic moment, molar conductance, and thermal analyses (TG, DTG and DTA). The molar conductance reveals that all the metal chelates are non-electrolytes. IR spectra shows that L ligand behaves as neutral tridentate ligand and bind to the metal ions via the two azomethine N and pyridine N. From the magnetic and solid reflectance spectra, it is found that the geometrical structures of these complexes are octahedral (Cr(III), Fe(III), Co(II), Ni(II), Cu(II), and Th(IV)) and tetrahedral (Mn(II), Cd(II), Zn(II), and UO2(II)). The thermal behaviour of these chelates shows that the hydrated complexes losses water molecules of hydration in the first step followed immediately by decomposition of the anions and ligand molecules in the subsequent steps. The activation thermodynamic parameters, such as, E*, ΔH*, ΔS* and ΔG* are calculated from the DTG curves using Coats-Redfern method. The synthesized ligand, in comparison to their metal complexes also was screened for its antibacterial activity against bacterial species, Escherichia coli, Pseudomonas aeruginosa, Staphylococcus pyogones and Fungi (Candida). The activity data shows that the metal complexes to be more potent/antibacterial than the parent Schiff base ligand against one or more bacterial species.

  18. Ligand-receptor affinities computed by an adapted linear interaction model for continuum electrostatics and by protein conformational averaging. (United States)

    Nunes-Alves, Ariane; Arantes, Guilherme Menegon


    Accurate calculations of free energies involved in small-molecule binding to a receptor are challenging. Interactions between ligand, receptor, and solvent molecules have to be described precisely, and a large number of conformational microstates has to be sampled, particularly for ligand binding to a flexible protein. Linear interaction energy models are computationally efficient methods that have found considerable success in the prediction of binding free energies. Here, we parametrize a linear interaction model for implicit solvation with coefficients adapted by ligand and binding site relative polarities in order to predict ligand binding free energies. Results obtained for a diverse series of ligands suggest that the model has good predictive power and transferability. We also apply implicit ligand theory and propose approximations to average contributions of multiple ligand-receptor poses built from a protein conformational ensemble and find that exponential averages require proper energy discrimination between plausible binding poses and false-positives (i.e., decoys). The linear interaction model and the averaging procedures presented can be applied independently of each other and of the method used to obtain the receptor structural representation.

  19. pK(a) based protonation states and microspecies for protein-ligand docking. (United States)

    ten Brink, Tim; Exner, Thomas E


    In this paper we present our reworked approach to generate ligand protonation states with our structure preparation tool SPORES (Structure PrOtonation and REcognition System). SPORES can be used for the preprocessing of proteins and protein-ligand complexes as e.g. taken from the Protein Data Bank as well as for the setup of 3D ligand databases. It automatically assigns atom and bond types, generates different protonation, tautomeric states as well as different stereoisomers. In the revised version, pKa calculations with the ChemAxon software MARVIN are used either to determine the likeliness of a combinatorial generated protonation state or to determine the titrable atoms used in the combinatorial approach. Additionally, the MARVIN software is used to predict microspecies distributions of ligand molecules. Docking studies were performed with our recently introduced program PLANTS (Protein-Ligand ANT System) on all protomers resulting from the three different selection methods for the well established CCDC/ASTEX clean data set demonstrating the usefulness of especially the latter approach.

  20. Multivalent ligand-receptor-mediated interaction of small filled vesicles with a cellular membrane (United States)

    Zhdanov, Vladimir P.


    The ligand-receptor-mediated contacts of small sub-100-nm-sized lipid vesicles (or nanoparticles) with the cellular membrane are of interest in the contexts of cell-to-cell communication, endocytosis of membrane-coated virions, and drug (RNA) delivery. In all these cases, the interior of vesicles is filled by biologically relevant content. Despite the diversity of such systems, the corresponding ligand-receptor interaction possesses universal features. One of them is that the vesicle-membrane contacts can be accompanied by the redistribution of ligands and receptors between the contact and contact-free regions. In particular, the concentrations of ligands and receptors may become appreciably higher in the contact regions and their composition may there be different compared to that in the suspended state in the solution. A statistical model presented herein describes the corresponding distribution of various ligands and receptors and allows one to calculate the related change of the free energy with variation of the vesicle-engulfment extent. The results obtained are used to clarify the necessary conditions for the vesicle-assisted pathway of drug delivery.

  1. A computational study of ligand binding affinities in iron(III) porphine and protoporphyrin IX complexes. (United States)

    Durrant, Marcus C


    The search for novel anti-malarial drugs that can disrupt biomineralization of ferriprotoporphyrin IX to haemozoin requires an understanding of the fundamental chemistry of the porphyrin's iron(iii) centre at the water-lipid interface. Towards this end, the binding affinities for a diverse set of 31 small ligands with iron(iii) porphine have been calculated using density functional theory, in the gas phase and also with implicit solvent corrections for both water and n-octanol. In addition, the binding of hydroxide, chloride, acetate, methylamine and water to ferriprotoporphyrin IX has been studied, and very similar trends are observed for the smaller and larger models. Anionic ligands generally give stronger binding than neutral ones; the strongest binding is observed for RO(-) and OH(-) ligands, whilst acetate binds relatively weakly among the anions studied. Electron-rich nitrogen donors tend to bind more strongly than electron-deficient ones, and the weakest binding is found for neutral O and S donors such as oxazole and thiophene. In all cases, ligand binding is stronger in n-octanol than in water, and the differences in binding energies for the two solvents are greater for ionic ligands than for neutrals. Finally, dimerization of ferriprotoporphyrin IX by means of iron(iii)-carboxylate bond formation has been modelled. The results are discussed in terms of haemozoin crystal growth and its disruption by known anti-malarial drugs.

  2. Directed Ligand Passage Over the Surface of Diffusion-Controlled Enzymes: A Cellular Automata Model

    CERN Document Server

    Ghaemi, M; Sarbolouki, M N; Ghaemi, Mehrdad; Rezaei-Ghaleh, Nasrollah; Sarbolouki, Mohammad-Nabi


    The rate-limiting step of some enzymatic reactions is a physical step, i.e. diffusion. The efficiency of such reactions can be improved through an increase in the arrival rate of the substrate molecules, e.g. by a directed passage of substrate (ligand) to active site after its random encounter with the enzyme surface. Herein, we introduce a cellular automata model simulating the ligand passage over the protein surface to its destined active site. The system is simulated using the lattice gas automata with probabilistic transition rules. Different distributions of amino acids over the protein surface are examined. For each distribution, the hydration pattern is achieved and the mean number of iteration steps needed for the ligand to arrive at the active site calculated. Comparison of results indicates that the rate at which ligand arrives at the active site is clearly affected by the distribution of amino acids outside the active side. Such a process can facilitate the ligand diffusion towards the active site ...

  3. pKa based protonation states and microspecies for protein-ligand docking (United States)

    ten Brink, Tim; Exner, Thomas E.


    In this paper we present our reworked approach to generate ligand protonation states with our structure preparation tool SPORES (Structure PrOtonation and REcognition System). SPORES can be used for the preprocessing of proteins and protein-ligand complexes as e.g. taken from the Protein Data Bank as well as for the setup of 3D ligand databases. It automatically assigns atom and bond types, generates different protonation, tautomeric states as well as different stereoisomers. In the revised version, pKa calculations with the ChemAxon software MARVIN are used either to determine the likeliness of a combinatorial generated protonation state or to determine the titrable atoms used in the combinatorial approach. Additionally, the MARVIN software is used to predict microspecies distributions of ligand molecules. Docking studies were performed with our recently introduced program PLANTS (Protein-Ligand ANT System) on all protomers resulting from the three different selection methods for the well established CCDC/ASTEX clean data set demonstrating the usefulness of especially the latter approach.

  4. CHARMM Force Field Parameterization of Peroxisome Proliferator-Activated Receptor γ Ligands (United States)

    Mottin, Melina; Souza, Paulo C. T.; Ricci, Clarisse G.; Skaf, Munir S.


    The peroxisome proliferator-activated receptor γ (PPARγ) ligands are important therapeutic drugs for the treatment of type 2 diabetes, obesity and cardiovascular diseases. In particular, partial agonists and non-agonists are interesting targets to reduce glucose levels, presenting few side effects in comparison to full agonists. In this work, we present a set of CHARMM-based parameters of a molecular mechanics force field for two PPARγ ligands, GQ16 and SR1664. GQ16 belongs to the thiazolidinedione class of drugs and it is a PPARγ partial agonist that has been shown to promote the “browning” of white adipose tissue. SR1664 is the precursor of the PPARγ non-agonist class of ligands that activates PPARγ in a non-classical manner. Here, we use quantum chemical calculations consistent with the CHARMM protocol to obtain bonded and non-bonded parameters, including partial atomic charges and effective torsion potentials for both molecules. The newly parameterized models were evaluated by examining the behavior of GQ16 and SR1664 free in water and bound to the ligand binding pocket of PPARγ using molecular dynamics simulations. The potential parameters derived here are readily transferable to a variety of pharmaceutical compounds and similar PPARγ ligands. PMID:28025495

  5. Passivating ligand and solvent contribution to the electronics properties of semiconductor nanocrystals

    Energy Technology Data Exchange (ETDEWEB)

    Tretiak, Sergei [Los Alamos National Laboratory; Crotty, Angela [Los Alamos National Laboratory; Fischer, Sean [Los Alamos National Laboratory; Kilina, Svetlana [NON LANL


    Expanding on previous work, we examine in detail the impact passivating ligands have on the electronic properties of CdSe quantum dots (QDs). We also explore the importance of the inclusion of solvent in simulating passivated QDs. Most ligand states are found well removed from the band edges, with pyridine being the exception and contributing states that sit right on the conduction band edge. Localized trap states are found for trimethylphosphine and pyridine capped QDs, with solvent helping to eliminate these. The effect of losing a ligand on the electronic properties of the system is observed to vary in proportion with the binding energy and steric bulk of the ligand. More disruption of the electronic properties is seen for tight-binding, sterically large ligands. We also look at the validity of using the single-particle Kohn-Sham (KS) representation to approximate optical absorption spectra. Besides a systematic blue-shift relative to the time-dependent density functional theory spectra, the KS spectra are in very good agreement with the more accurate method for these systems. Such agreement here justifies the use of the KS approach for calculating absorption spectra of QD systems.

  6. An Accurate Method for Determination of Receptor-Ligand and Enzyme-Inhibitor Dissociation Constants from Displacement Curves (United States)

    Horovitz, Amnon; Levitzki, Alexander


    Receptor-ligand dissociation constants are usually calculated from the displacement curve of a radioactively labeled ligand bound to the receptor. The formula used is restricted to cases in which the concentration of receptor is negligible compared to the concentration of both the displacing ligand and the radioactive ligand used. In this study, we rigorously derive a simple equation that can be used for calculating receptor-ligand dissociation constants for any set of experimental conditions. A linearized form of this equation provides a convenient plot from which the dissociation constant of the displacing ligand can be directly obtained. The plot is also a test for the competitive mode of binding. This exact equation now allows us to estimate the error incurred by the conventionally used equations. Similarly, we show that for competitive inhibition in enzymology, one can derive the analogous formula. Our new formula is free of the usual restrictions--namely, that the enzyme concentration is very small compared to the concentration of both the substrate and the inhibitor. It may therefore be applied to any set of experimental conditions.

  7. Scientific calculating peripheral

    Energy Technology Data Exchange (ETDEWEB)

    Ethridge, C.D.; Nickell, J.D. Jr.; Hanna, W.H.


    A scientific calculating peripheral for small intelligent data acquisition and instrumentation systems and for distributed-task processing systems is established with a number-oriented microprocessor controlled by a single component universal peripheral interface microcontroller. A MOS/LSI number-oriented microprocessor provides the scientific calculating capability with Reverse Polish Notation data format. Master processor task definition storage, input data sequencing, computation processing, result reporting, and interface protocol is managed by a single component universal peripheral interface microcontroller.

  8. Current interruption transients calculation

    CERN Document Server

    Peelo, David F


    Provides an original, detailed and practical description of current interruption transients, origins, and the circuits involved, and how they can be calculated Current Interruption Transients Calculationis a comprehensive resource for the understanding, calculation and analysis of the transient recovery voltages (TRVs) and related re-ignition or re-striking transients associated with fault current interruption and the switching of inductive and capacitive load currents in circuits. This book provides an original, detailed and practical description of current interruption transients, origins,

  9. Shielding calculations for SSC

    Energy Technology Data Exchange (ETDEWEB)

    Van Ginneken, A.


    Monte Carlo calculations of hadron and muon shielding for SSC are reviewed with emphasis on their application to radiation safety and environmental protection. Models and algorithms for simulation of hadronic and electromagnetic showers, and for production and transport of muons in the TeV regime are briefly discussed. Capabilities and limitations of these calculations are described and illustrated with a few examples. 12 refs., 3 figs.

  10. Geometric unsharpness calculations

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, D.J. [International Training and Education Group (INTEG), Oakville, Ontario (Canada)


    The majority of radiographers' geometric unsharpness calculations are normally performed with a mathematical formula. However, a majority of codes and standards refer to the use of a nomograph for this calculation. Upon first review, the use of a nomograph appears more complicated but with a few minutes of study and practice it can be just as effective. A review of this article should provide enlightenment. (author)

  11. Source and replica calculations

    Energy Technology Data Exchange (ETDEWEB)

    Whalen, P.P.


    The starting point of the Hiroshima-Nagasaki Dose Reevaluation Program is the energy and directional distributions of the prompt neutron and gamma-ray radiation emitted from the exploding bombs. A brief introduction to the neutron source calculations is presented. The development of our current understanding of the source problem is outlined. It is recommended that adjoint calculations be used to modify source spectra to resolve the neutron discrepancy problem.

  12. INVAP's Nuclear Calculation System


    Ignacio Mochi


    Since its origins in 1976, INVAP has been on continuous development of the calculation system used for design and optimization of nuclear reactors. The calculation codes have been polished and enhanced with new capabilities as they were needed or useful for the new challenges that the market imposed. The actual state of the code packages enables INVAP to design nuclear installations with complex geometries using a set of easy-to-use input files that minimize user errors due to confusion or mi...

  13. Probing interaction of a fluorescent ligand with HIV TAR RNA (United States)

    Qi, Liang; Zhang, Jing; He, Tian; Huo, Yuan; Zhang, Zhi-Qi


    Trans-activator of Transcription (Tat) antagonists could block the interaction between Tat protein and its target, trans-activation responsive region (TAR) RNA, to inhibit Tat function and prevent human immunodeficiency virus type 1 (HIV-1) replication. For the first time, a small fluorescence ligand, ICR 191, was found to interact with TAR RNA at the Tat binding site and compete with Tat. It was also observed that the fluorescence of ICR 191 could be quenched when binding to TAR RNA and recovered when discharged via competition with Tat peptide or a well-known Tat inhibitor, neomycin B. The binding parameters of ICR 191 to TAR RNA were determined through theoretical calculations. Mass spectrometry, circular dichroism and molecular docking were used to further confirm the interaction of ICR 191 with TAR RNA. Inspired by these discoveries, a primary fluorescence model for the discovery of Tat antagonists was built using ICR 191 as a fluorescence indicator and the feasibility of this model was evaluated. This ligand-RNA interaction could provide a new strategy for research aimed at discovering Tat antagonists.

  14. Calculation of Absolute Protein-Ligand Binding Affinity Using Path and Endpoint Approaches (United States)


    an explicit solvent layer width of 10 Å. The hybrid solvent model (35) involves encapsulating a biological solute by a layer of water molecules...of cyclodextrin binding affinities: energy, entropy, and implications for drug design. Biophys. J. 87:3035–3049. 42. Janezic, D., R. M. Venable, and

  15. Ligand Intermediates in Metal-Catalyzed Reactions

    Energy Technology Data Exchange (ETDEWEB)

    Gladysz, John A.


    The longest-running goal of this project has been the synthesis, isolation, and physical chemical characterization of homogeneous transition metal complexes containing ligand types believed to be intermediates in the metal-catalyzed conversion of CO/H{sub 2}, CO{sub 2}, CH{sub 4}, and similar raw materials to organic fuels, feedstocks, etc. In the current project period, complexes that contain unusual new types of C{sub x}(carbide) and C{sub x}O{sub y} (carbon oxide) ligands have been emphasized. A new program in homogeneous fluorous phase catalysis has been launched as described in the final report.

  16. Efficient chemoenzymatic synthesis of chiral pincer ligands. (United States)

    Felluga, Fulvia; Baratta, Walter; Fanfoni, Lidia; Pitacco, Giuliana; Rigo, Pierluigi; Benedetti, Fabio


    Chiral, nonracemic pincer ligands based on the 6-phenyl-2-aminomethylpyridine and 2-aminomethylbenzo[h]quinoline scaffolds were obtained by a chemoenzymatic approach starting from 2-pyridyl and 2-benzoquinolyl ethanone. In the enantiodifferentiating step, secondary alcohols of opposite absolute configuration were obtained by a baker's yeast reduction of the ketones and by lipase-mediated dynamic kinetic resolution of the racemic alcohols. Their transformation into homochiral 1-methyl-1-heteroarylethanamines occurred without loss of optical purity, giving access to pincer ligands used in enantioselective catalysis.

  17. CLiBE: a database of computed ligand binding energy for ligand-receptor complexes. (United States)

    Chen, X; Ji, Z L; Zhi, D G; Chen, Y Z


    Consideration of binding competitiveness of a drug candidate against natural ligands and other drugs that bind to the same receptor site may facilitate the rational development of a candidate into a potent drug. A strategy that can be applied to computer-aided drug design is to evaluate ligand-receptor interaction energy or other scoring functions of a designed drug with that of the relevant ligands known to bind to the same binding site. As a tool to facilitate such a strategy, a database of ligand-receptor interaction energy is developed from known ligand-receptor 3D structural entries in the Protein Databank (PDB). The Energy is computed based on a molecular mechanics force field that has been used in the prediction of therapeutic and toxicity targets of drugs. This database also contains information about ligand function and other properties and it can be accessed at The computed energy components may facilitate the probing of the mode of action and other profiles of binding. A number of computed energies of some PDB ligand-receptor complexes in this database are studied and compared to experimental binding affinity. A certain degree of correlation between the computed energy and experimental binding affinity is found, which suggests that the computed energy may be useful in facilitating a qualitative analysis of drug binding competitiveness.

  18. Equilibria and kinetics for pH-dependent axial ligation of bromomethyl(aquo)cobaloxime by aliphatic amine ligands

    Indian Academy of Sciences (India)

    M Bhoopal; N Ravi Kumar Reddy; S Satyanarayana


    Kinetics and equilibria of axial ligation of bromomethyl(aquo) cobaloxime by a series of straight chain primary amines (methylamine, ethylamine, propylamine, butylamine, pentylamine, hexylamine), cycloamines (cyclopentylamine, cyclohexylamine, cycloheptylamine) and secondary amines (N,N-dimethylamine, N,N-diethylamine) have been measured as functions of pH by spectrophotometric technique in aqueous solution, ionic strength 1 M (KCl) at 25°C. The rate of substitution of H2O varies with the Ka of incoming ligand, thus establishing nucleophilic participation of the ligand in the transition state. Binding and kinetic data are interpreted based on the basicity and steric influence of the entering ligand. To compare the rate constants of the entering ligands, pH independent second-order rate constants (on) are calculated.

  19. Theoretical studies of molecular structure, electronic structure, spectroscopic properties and the ancillary ligand effect: A comparison of tris-chelate ML 3-type and ML 2X-type species for gallium(III) complexes with N, O-donor phenolic ligand, 2-(2-hydroxyphenyl)benzothiazole (United States)

    Tong, Yi-Ping; Lin, Yan-Wen


    Two Ga(III) complexes with main ligand, 2-(2-hydroxyphenyl)benzothiazole (HL'), namely mixed-ligand ML 2X-type [GaL' 2X'] ( 1) (HX' = acetic acid, as ancillary ligand) and the meridianal tris-chelate [GaL' 3] ( 2) have been investigated by the density functional theory (DFT/TDDFT) level calculations. Both 1 and 2 can be presented as a similar "mixed-ligand ML 2X-type" species. The molecular geometries, electronic structures, metal-ligand bonding property of Ga-O (N) (main ligand), Ga-O (N) (ancillary ligand) interactions, and the ancillary ligand effect on their HOMO-LUMO gap, their absorption/emission property, and their absorption/emission wavelengths/colors for them have been discussed in detail based on the orbital interactions, the partial density of states (PDOS), and so on. The current investigation also indicates that it is quite probable that by introduction of different ancillary ligands, a series of new mixed-ligand ML 2X-type complexes for group 13 metals can be designed with their absorption/emission property and the absorption/emission wavelengths and colors being tuned.

  20. Ultrafast infrared studies of complex ligand rearrangements in solution

    Energy Technology Data Exchange (ETDEWEB)

    Payne, Christine K. [Univ. of California, Berkeley, CA (United States)


    The complete description of a chemical reaction in solution depends upon an understanding of the reactive molecule as well as its interactions with the surrounding solvent molecules. Using ultrafast infrared spectroscopy it is possible to observe both the solute-solvent interactions and the rearrangement steps which determine the overall course of a chemical reaction. The topics addressed in these studies focus on reaction mechanisms which require the rearrangement of complex ligands and the spectroscopic techniques necessary for the determination of these mechanisms. Ligand rearrangement is studied by considering two different reaction mechanisms for which the rearrangement of a complex ligand constitutes the most important step of the reaction. The first system concerns the rearrangement of a cyclopentadienyl ring as the response of an organometallic complex to a loss of electron density. This mechanism, commonly referred to as ''ring slip'', is frequently cited to explain reaction mechanisms. However, the ring slipped intermediate is too short-lived to be observed using conventional methods. Using a combination of ultrafast infrared spectroscopy and electronic structure calculations it has been shown that the intermediate exists, but does not form an eighteen-electron intermediate as suggested by traditional molecular orbital models. The second example examines the initial steps of alkyne polymerization. Group 6 (Cr, Mo, W) pentacarbonyl species are generated photolytically and used to catalyze the polymerization of unsaturated hydrocarbons through a series of coordination and rearrangement steps. Observing this reaction on the femto- to millisecond timescale indicates that the initial coordination of an alkyne solvent molecule to the metal center results in a stable intermediate that does not rearrange to form the polymer precursor. This suggests that polymerization requires the dissociation of additional carbonyl ligands before

  1. Ligand-protected gold clusters: the structure, synthesis and applications (United States)

    Pichugina, D. A.; Kuz'menko, N. E.; Shestakov, A. F.


    Modern concepts of the structure and properties of atomic gold clusters protected by thiolate, selenolate, phosphine and phenylacetylene ligands are analyzed. Within the framework of the superatom theory, the 'divide and protect' approach and the structure rule, the stability and composition of a cluster are determined by the structure of the cluster core, the type of ligands and the total number of valence electrons. Methods of selective synthesis of gold clusters in solution and on the surface of inorganic composites based, in particular, on the reaction of Aun with RS, RSe, PhC≡C, Hal ligands or functional groups of proteins, on stabilization of clusters in cavities of the α-, β and γ-cyclodextrin molecules (Au15 and Au25) and on anchorage to a support surface (Au25/SiO2, Au20/C, Au10/FeOx) are reviewed. Problems in this field are also discussed. Among the methods for cluster structure prediction, particular attention is given to the theoretical approaches based on the density functional theory (DFT). The structures of a number of synthesized clusters are described using the results obtained by X-ray diffraction analysis and DFT calculations. A possible mechanism of formation of the SR(AuSR)n 'staple' units in the cluster shell is proposed. The structure and properties of bimetallic clusters MxAunLm (M=Pd, Pt, Ag, Cu) are discussed. The Pd or Pt atom is located at the centre of the cluster, whereas Ag and Cu atoms form bimetallic compounds in which the heteroatom is located on the surface of the cluster core or in the 'staple' units. The optical properties, fluorescence and luminescence of ligand-protected gold clusters originate from the quantum effects of the Au atoms in the cluster core and in the oligomeric SR(AuSR)x units in the cluster shell. Homogeneous and heterogeneous reactions catalyzed by atomic gold clusters are discussed in the context of the reaction mechanism and the nature of the active sites. The bibliography includes 345 references.

  2. Ultrafast infrared studies of complex ligand rearrangements in solution

    Energy Technology Data Exchange (ETDEWEB)

    Payne, Christine K.


    The complete description of a chemical reaction in solution depends upon an understanding of the reactive molecule as well as its interactions with the surrounding solvent molecules. Using ultrafast infrared spectroscopy it is possible to observe both the solute-solvent interactions and the rearrangement steps which determine the overall course of a chemical reaction. The topics addressed in these studies focus on reaction mechanisms which require the rearrangement of complex ligands and the spectroscopic techniques necessary for the determination of these mechanisms. Ligand rearrangement is studied by considering two different reaction mechanisms for which the rearrangement of a complex ligand constitutes the most important step of the reaction. The first system concerns the rearrangement of a cyclopentadienyl ring as the response of an organometallic complex to a loss of electron density. This mechanism, commonly referred to as ''ring slip'', is frequently cited to explain reaction mechanisms. However, the ring slipped intermediate is too short-lived to be observed using conventional methods. Using a combination of ultrafast infrared spectroscopy and electronic structure calculations it has been shown that the intermediate exists, but does not form an eighteen-electron intermediate as suggested by traditional molecular orbital models. The second example examines the initial steps of alkyne polymerization. Group 6 (Cr, Mo, W) pentacarbonyl species are generated photolytically and used to catalyze the polymerization of unsaturated hydrocarbons through a series of coordination and rearrangement steps. Observing this reaction on the femto- to millisecond timescale indicates that the initial coordination of an alkyne solvent molecule to the metal center results in a stable intermediate that does not rearrange to form the polymer precursor. This suggests that polymerization requires the dissociation of additional carbonyl ligands before

  3. Protein-Ligand Binding from Distancefield Distances and Hamiltonian Replica Exchange Simulations. (United States)

    de Ruiter, Anita; Oostenbrink, Chris


    The calculation of protein-ligand binding free energies is an important goal in the field of computational chemistry. Applying path-sampling methods for this purpose involves calculating the associated potential of mean force (PMF) and gives insight into the binding free energy along the binding process. Without a priori knowledge about the binding path, sampling reversible binding can be difficult to achieve. To alleviate this problem, we introduce the distancefield (DF) as a reaction coordinate for such calculations. DF is a grid-based method in which the shortest distance between the binding site and a ligand is determined avoiding routes that pass through the protein. Combining this reaction coordinate with Hamiltonian replica exchange molecular dynamics (HREMD) allows for the reversible binding of the ligand to the protein. A comparison is made between umbrella sampling using regular distance restraints and HREMD with DF restraints to study aspirin binding to the protein phospholipase A2. Although the free energies of binding are similar for both methods, the increased sampling with HREMD has a significant influence on the shape of the PMF. A remarkable agreement between the calculated binding free energies from the PMF and the experimental estimate is obtained.

  4. Theoretical investigation of interaction between the set of ligands and α7 nicotinic acetylcholine receptor (United States)

    Glukhova, O. E.; Prytkova, T. R.; Shmygin, D. S.


    Nicotinic acetylcholine receptors (nAChRs) are neuron receptor proteins that provide a transmission of nerve impulse through the synapses. They are composed of a pentametric assembly of five homologous subunits (5 α7 subunits for α7nAChR, for example), oriented around the central pore. These receptors might be found in the chemical synapses of central and peripheral nervous system, and also in the neuromuscular synapses. Transmembrane domain of the one of such receptors constitutes ion channel. The conductive properties of ion channel strongly depend on the receptor conformation changes in the response of binding with some molecule, f.e. acetylcholine. Investigation of interaction between ligands and acetylcholine receptor is important for drug design. In this work we investigate theoretically the interaction between the set of different ligands (such as vanillin, thymoquinone, etc.) and the nicotinic acetylcholine receptor (primarily with subunit of the α7nAChR) by different methods and packages (AutodockVina, GROMACS, KVAZAR, HARLEM, VMD). We calculate interaction energy between different ligands in the subunit using molecular dynamics. On the base of obtained calculation results and using molecular docking we found an optimal location of different ligands in the subunit.

  5. Synthesis, Characterization and Solvatochromism Investigation of Mixed Ligand Chelate Copper(Ⅱ) Complexes with Acetyleacetonate and Three Diamine Ligands

    Institute of Scientific and Technical Information of China (English)

    Golchoubian Hamid; Afshar Zahra Mohseni; Moayyedi Golasa; Bruno Giuseppe; Rudbari Hadi Amiri


    The syntheses of three mixed ligand chelate copper(II) complexes of the type [Cu(L)(acac)(H2O)]BPh4 where acac=acetyleacetonate; L=N,N-dimethyl,N′-benzylethane-1,2-diamine (L1), N,N-dimethyl, N′-2-methylbenzylethane-1,2-diamine (L2) or N,N-dimethyl,N′-2-chlorobenzylethane-1,2-diamine (L3) are reported and characterized by elemental analyses, spectroscopic and molar conductance measurements. The X-ray structure of complex 1 shows that the central copper atom is placed in a distorted square pyramidal geometry made by acac and diamine chelate in the base and a H2O molecule on the apex. The prepared complexes are fairly soluble in a large number of organic solvents and show positive solvatochromism. Calculations of SMLR (stepwise multiple linear regression) method was utilized to find the best model explaining the observed solvatochromic behavior and showed that among different solvent parameters, donor number (DN) is a dominant factor responsible for the shift in the d-d absorption band of the complexes to the lower wavenumber with increasing its values. The importance of substituent effect in diamine ligand on the spectral and SMLR measurements is also discussed.

  6. How wet should be the reaction coordinate for ligand unbinding?

    CERN Document Server

    Tiwary, Pratyush


    We use a recently proposed method called Spectral Gap Optimization of Order Parameters (SGOOP) (Tiwary and Berne, Proc. Natl. Acad. Sci 2016, 113, 2839 (2016)), to determine an optimal 1-dimensional reaction coordinate (RC) for the unbinding of a bucky-ball from a pocket in explicit water. This RC is estimated as a linear combination of the multiple available order parameters that collectively can be used to distinguish the various stable states relevant for unbinding. We pay special attention to determining and quantifying the degree to which water molecules should be included in the RC. Using SGOOP with under-sampled biased simulations, we predict that water plays a distinct role in the reaction coordinate for unbinding in the case when the ligand is sterically constrained to move along an axis of symmetry. This prediction is validated through extensive calculations of the unbinding times through metadynamics, and by comparison through detailed balance with unbiased molecular dynamics estimate of the bindin...

  7. Synthesis, characterization, and photophysical and electroluminescent properties of blue-emitting cationic iridium(III) complexes bearing nonconjugated ligands. (United States)

    Zhang, Fuli; Ma, Dongxin; Duan, Lian; Qiao, Juan; Dong, Guifang; Wang, Liduo; Qiu, Yong


    The development of pure-blue-to-deep-blue-emitting ionic phosphors is an ultimate challenge for full-color displays and white-light sources. Herein we report two series of short-wavelength light-emitting cationic iridium(III) complexes with nonconjugated ancillary and cyclometalating ligands, respectively. In the first series, nonconjugated 1-[(diphenylphosphino)methyl]-3-methylimidazolin-2-ylidene-C,C2' (dppmmi) is used as the ancillary ligand and 2-phenylpyridine (ppy), 2-(2,4-difluorophenyl)pyridine (dfppy), and 1-(2,4-difluorophenyl)-1H-pyrazole (dfppz) are used as cyclometalating ligands. In the second one, nonconjugated 2,4-difluorobenzyl-N-pyrazole (dfbpz) is used as the cyclometalating ligand and 3-methyl-1-(2-pyridyl)benzimidazolin-2-ylidene-C,C(2)' (pymbi) as the ancillary ligand. The synthesis and photophysical and electrochemical properties, together with the X-ray crystal structures of these complexes, have been investigated. At room temperature, blue-emitting complexes [Ir(ppy)2(dppmmi)]PF6 (1) and [Ir(dfppy)2(dppmmi)]PF6 (2; PF6(-) is hexafluorophosphate) show much larger photoluminescence quantum yields of 24% and 46%, respectively. On the contrary, for complexes [Ir(dfppz)2(dppmmi)]PF6 (3) and [Ir(dfbpz)2(pymbi)]PF6 (4), deep-blue luminescence is only observed at low temperature (77 K). Density functional theory calculations are used to rationalize the differences in the photophysical behavior observed upon changes of the ligands. It is shown that the electronic transition dipoles of cationic iridium complexes 1 and 2 are mainly confined to cyclometalated ligands ((3)MLCT and LC (3)π-π*) and those of complex 3 are confined to all of the ligands ((3)MLCT, LC (3)π-π*, and (3)LLCT) because of the high LUMO energy level of dfppz. The emission of 4 mainly originates from the central iridium(III) ion and cyclometalated ligand to ancillary ligand charge transfer ((3)MLCT and (3)LLCT), in contrast to commonly designed cationic complexes using carbene

  8. Calculations in apheresis. (United States)

    Neyrinck, Marleen M; Vrielink, Hans


    It's important to work smoothly with your apheresis equipment when you are an apheresis nurse. Attention should be paid to your donor/patient and the product you're collecting. It gives additional value to your work when you are able to calculate the efficiency of your procedures. You must be capable to obtain an optimal product without putting your donor/patient at risk. Not only the total blood volume (TBV) of the donor/patient plays an important role, but also specific blood values influence the apheresis procedure. Therefore, not all donors/patients should be addressed in the same way. Calculation of TBV, extracorporeal volume, and total plasma volume is needed. Many issues determine your procedure time. By knowing the collection efficiency (CE) of your apheresis machine, you can calculate the number of blood volumes to be processed to obtain specific results. You can calculate whether you need one procedure to obtain specific results or more. It's not always needed to process 3× the TBV. In this way, it can be avoided that the donor/patient is needless long connected to the apheresis device. By calculating the CE of each device, you can also compare the various devices for quality control reasons, but also nurses/operators.

  9. DFT modeling and spectroscopic study of metal ligand bonding in La(III) complex of coumarin-3-carboxylic acid (United States)

    Mihaylov, Tz.; Trendafilova, N.; Kostova, I.; Georgieva, I.; Bauer, G.


    The binding mode of coumarin-3-carboxylic acid (HCCA) to La(III) is elucidated at experimental and theoretical level. The complexation ability of the deprotonated ligand (CCA -) to La(III) is studied using elemental analysis, DTA and TGA data as well as FTIR, 1H NMR and 13C NMR spectra. The experimental data suggest the complex formula La(CCA) 2(NO 3)(H 2O) 2. B3LYP, BHLYP, B3P86, B3PW91, PW91P86 and MPW1PW91 functionals are tested for geometry and frequency calculations of the neutral ligand and all of them show bond length deviations bellow 1%. B3LYP/6-31G(d) level combined with large quasi-relativistic effective core potential for lanthanum is selected to describe the molecular, electronic and vibrational structures as well as the conformational behavior of HCCA, CCA - and La-CCA complex. The metal-ligand binding mode is predicted through molecular modeling and energy estimation of different La-CCA structures. The calculated atomic charges and the bonding orbital polarizations point to strong ionic metal-ligand bonding in La-CCA complex and insignificant donor acceptor interaction. Detailed vibrational analysis of HCCA, CCA - and La(CCA) 2(NO 3)(H 2O) 2 systems based on both calculated and experimental frequencies confirms the suggested metal-ligand binding mode.

  10. [Functional selectivity of opioid receptors ligands]. (United States)

    Audet, Nicolas; Archer-Lahlou, Elodie; Richard-Lalonde, Mélissa; Piñeyro-Filpo, Graciela


    Opiates are the most effective analgesics available for the treatment of severe pain. However, their clinical use is restricted by unwanted side effects such as tolerance, physical dependence and respiratory depression. The strategy to develop new opiates with reduced side effects has mainly focused on the study and production of ligands that specifically bind to different opiate receptors subtypes. However, this strategy has not allowed the production of novel therapeutic ligands with a better side effects profile. Thus, other research strategies need to be explored. One which is receiving increasing attention is the possibility of exploiting ligand ability to stabilize different receptor conformations with distinct signalling profiles. This newly described property, termed functional selectivity, provides a potential means of directing the stimulus generated by an activated receptor towards a specific cellular response. Here we summarize evidence supporting the existence of ligand-specific active conformations for two opioid receptors subtypes (delta and mu), and analyze how functional selectivity may contribute in the production of longer lasting, better tolerated opiate analgesics. double dagger.

  11. Ligand Exchange Kinetics of Environmentally Relevant Metals

    Energy Technology Data Exchange (ETDEWEB)

    Panasci, Adele Frances [Univ. of California, Davis, CA (United States)


    The interactions of ground water with minerals and contaminants are of broad interest for geochemists but are not well understood. Experiments on the molecular scale can determine reaction parameters (i.e. rates of ligand exchange, activation entropy, activation entropy, and activation volume) that can be used in computations to gain insight into reactions that occur in natural groundwaters. Experiments to determine the rate of isotopic ligand exchange for three environmentally relevant metals, rhodium (Rh), iron (Fe), and neptunium (Np), are described. Many environmental transformations of metals (e.g. reduction) in soil occur at trivalent centers, Fe(III) in particular. Contaminant ions absorb to mineral surfaces via ligand exchange, and the reversal of this reaction can be dangerous, releasing contaminants into the environment. Ferric iron is difficult to study spectroscopically because most of its complexes are paramagnetic and are generally reactive toward ligand exchange; therefore, Rh(III), which is diamagnetic and less reactive, was used to study substitution reactions that are analogous to those that occur on mineral oxide surfaces. Studies on both Np(V) and Np(VI) are important in their own right, as 237Np is a radioactive transuranic element with a half-life of 2 million years.

  12. Ligand iron catalysts for selective hydrogenation (United States)

    Casey, Charles P.; Guan, Hairong


    Disclosed are iron ligand catalysts for selective hydrogenation of aldehydes, ketones and imines. A catalyst such as dicarbonyl iron hydride hydroxycyclopentadiene) complex uses the OH on the five member ring and hydrogen linked to the iron to facilitate hydrogenation reactions, particularly in the presence of hydrogen gas.

  13. Supramolecular architectures constructed using angular bipyridyl ligands

    CERN Document Server

    Barnett, S A


    This work details the synthesis and characterization of a series of coordination frameworks that are formed using bidentate angular N-donor ligands. Pyrimidine was reacted with metal(ll) nitrate salts. Reactions using Cd(NO sub 3) sub 2 receive particular focus and the analogous reactions using the linear ligand, pyrazine, were studied for comparison. In all cases, two-dimensional coordination networks were prepared. Structural diversity is observed for the Cd(ll) centres including metal-nitrate bridging. In contrast, first row transition metal nitrates form isostructural one-dimensional chains with only the bridging N-donor ligands generating polymeric propagation. The angular ligand, 2,4-bis(4-pyridyl)-1,3,5-triazine (dpt), was reacted with Cd(NO sub 3) sub 2 and Zn(NO sub 3) sub 2. Whereas Zn(NO sub 3) sub 2 compounds exhibit solvent mediated polymorphism, a range of structures were obtained for the reactions with Cd(NO sub 3) sub 2 , including the first example of a doubly parallel interpenetrated 4.8 sup...

  14. Receptor Binding Ligands to Image Infection

    NARCIS (Netherlands)

    Chianelli, M.; Boerman, O. C.; Malviya, G.; Galli, F.; Oyen, W. J. G.; Signore, A.


    The current gold standard for imaging infection is radiolabeled white blood cells. For reasons of safety, simplicity and cost, it would be desirable to have a receptor-specific ligand that could be used for imaging infection and that would allow a differential diagnosis between sterile and septic in


    Directory of Open Access Journals (Sweden)

    Malte BETHKE


    Full Text Available A food calculator for elderly people was elaborated by Centiv GmbH, an active partner in the European FP7 OPTIFEL Project, based on the functional requirement specifications and the existing recommendations for daily allowances across Europe, data which were synthetized and used to give aims in amounts per portion. The OPTIFEL Personalised Nutritional Calculator is the only available online tool which allows to determine on a personalised level the required nutrients for elderly people (65+. It has been developed mainly to support nursing homes providing best possible (personalised nutrient enriched food to their patients. The European FP7 OPTIFEL project “Optimised Food Products for Elderly Populations” aims to develop innovative products based on vegetables and fruits for elderly populations to increase length of independence. The OPTIFEL Personalised Nutritional Calculator is recommended to be used by nursing homes.

  16. INVAP's Nuclear Calculation System

    Directory of Open Access Journals (Sweden)

    Ignacio Mochi


    Full Text Available Since its origins in 1976, INVAP has been on continuous development of the calculation system used for design and optimization of nuclear reactors. The calculation codes have been polished and enhanced with new capabilities as they were needed or useful for the new challenges that the market imposed. The actual state of the code packages enables INVAP to design nuclear installations with complex geometries using a set of easy-to-use input files that minimize user errors due to confusion or misinterpretation. A set of intuitive graphic postprocessors have also been developed providing a fast and complete visualization tool for the parameters obtained in the calculations. The capabilities and general characteristics of this deterministic software package are presented throughout the paper including several examples of its recent application.

  17. Calculating Quenching Weights

    CERN Document Server

    Salgado, C A; Salgado, Carlos A.; Wiedemann, Urs Achim


    We calculate the probability (``quenching weight'') that a hard parton radiates an additional energy fraction due to scattering in spatially extended QCD matter. This study is based on an exact treatment of finite in-medium path length, it includes the case of a dynamically expanding medium, and it extends to the angular dependence of the medium-induced gluon radiation pattern. All calculations are done in the multiple soft scattering approximation (Baier-Dokshitzer-Mueller-Peign\\'e-Schiff--Zakharov ``BDMPS-Z''-formalism) and in the single hard scattering approximation (N=1 opacity approximation). By comparison, we establish a simple relation between transport coefficient, Debye screening mass and opacity, for which both approximations lead to comparable results. Together with this paper, a CPU-inexpensive numerical subroutine for calculating quenching weights is provided electronically. To illustrate its applications, we discuss the suppression of hadronic transverse momentum spectra in nucleus-nucleus colli...

  18. Some new IIB group complexes of an imidazolidine ligand: Synthesis, spectral characterization, electrochemical, thermal and antimicrobial propert

    Indian Academy of Sciences (India)

    Morteza Montazerozohori; Sayed Alireza Musavi; Asghar Naghiha; Somayeh Veyseh


    An imidazolidine Schiff base ligand, (E)-N-(4-nitrobenzylidene)-2-(2-(4-nitrophenyl) imidazolidine-1-yl) ethaneamine (L) has been synthesized by a condensation reaction between N'-(2-aminoethyl)-ethane-1,2-diamine and 4-nitrobenzaldehyde in 1:2 ratio and then characterized by physical and spectral data. Some new complexes with general formula of MLX2(wherein M is Zn(II),Cd(II) and Hg(II) and X is chloride, bromide and/or iodide) have been prepared and characterized by physical and spectroscopic studies such as elemental analysis, molar conductance measurements, FT-IR, 1H and 13C NMR and UV-Visible electronic spectra. The spectral data indicate that the ligand is coordinated to zinc(II) as a bidentate ligand in imidazolidine form but it binds to other metal salts as bis-imine tridentate ligand. Furthermore, cyclic voltammetry technique was applied for recording the electrochemical behaviour of the ligand and its complexes. Cyclic voltamogram of the ligand showed that it is reduced at four cathodic potentials and then oxidized only in two anodic potentials in reverse direction. The electrochemical behaviour of ligand is affected by coordination. Thermal analysis of ligand and its complexes revealed that they are decomposed via 3-4 thermal steps. Moreover, some activation thermodynamic parameters such as A, E∗, H∗, S∗ and G∗ were calculated based on TG/DTA plots using Coats-Redfern relation. The Schiff base ligand and its complexes have also been tested in vitro to evaluate their antimicrobial activities.

  19. A strategy for the incorporation of water molecules present in a ligand binding site into a three-dimensional quantitative structure--activity relationship analysis. (United States)

    Pastor, M; Cruciani, G; Watson, K A


    Water present in a ligand binding site of a protein has been recognized to play a major role in ligand-protein interactions. To date, rational drug design techniques do not usually incorporate the effect of these water molecules into the design strategy. This work represents a new strategy for including water molecules into a three-dimensional quantitative structure-activity relationship analysis using a set of glucose analogue inhibitors of glycogen phosphorylase (GP). In this series, the structures of the ligand-enzyme complexes have been solved by X-ray crystallography, and the positions of the ligands and the water molecules at the ligand binding site are known. For the structure-activity analysis, some water molecules adjacent to the ligands were included into an assembly which encompasses both the inhibitor and the water involved in the ligand-enzyme interaction. The mobility of some water molecules at the ligand binding site of GP gives rise to differences in the ligand-water assembly which have been accounted for using a simulation study involving force-field energy calculations. The assembly of ligand plus water was used in a GRID/GOLPE analysis, and the models obtained compare favorably with equivalent models when water was excluded. Both models were analyzed in detail and compared with the crystallographic structures of the ligand-enzyme complexes in order to evaluate their ability to reproduce the experimental observations. The results demonstrate that incorporation of water molecules into the analysis improves the predictive ability of the models and makes them easier to interpret. The information obtained from interpretation of the models is in good agreement with the conclusions derived from the structural analysis of the complexes and offers valuable insights into new characteristics of the ligands which may be exploited for the design of more potent inhibitors.

  20. Spin Resonance Strength Calculations (United States)

    Courant, E. D.


    In calculating the strengths of depolarizing resonances it may be convenient to reformulate the equations of spin motion in a coordinate system based on the actual trajectory of the particle, as introduced by Kondratenko, rather than the conventional one based on a reference orbit. It is shown that resonance strengths calculated by the conventional and the revised formalisms are identical. Resonances induced by radiofrequency dipoles or solenoids are also treated; with rf dipoles it is essential to consider not only the direct effect of the dipole but also the contribution from oscillations induced by it.

  1. Spin resonance strength calculations

    Energy Technology Data Exchange (ETDEWEB)



    In calculating the strengths of depolarizing resonances it may be convenient to reformulate the equations of spin motion in a coordinate system based on the actual trajectory of the particle, as introduced by Kondratenko, rather than the conventional one based on a reference orbit. It is shown that resonance strengths calculated by the conventional and the revised formalisms are identical. Resonances induced by radiofrequency dipoles or solenoids are also treated; with rf dipoles it is essential to consider not only the direct effect of the dipole but also the contribution from oscillations induced by it.

  2. Detection and quantification of affinity ligand leaching and specific antibody fragment concentration within chromatographic fractions using surface plasmon resonance. (United States)

    Thillaivinayagalingam, Pranavan; Newcombe, Anthony R; O'Donovan, Kieran; Francis, Richard; Keshavarz-Moore, Eli


    Rapid analyses of chromatographic steps within a biopharmaceutical manufacturing process are often desirable to evaluate column performance, provide mass balance data and to permit accurate calculations of yields and recoveries. Using SPR (surface plasmon resonance) biosensor (Biacore) technology, we have developed a sandwich immunoassay to quantify polyclonal anti-digoxin Fab fragments used for the production of the FDA (Food and Drug Administration)-approved biotherapeutic DigiFab. The results show that specific Fab may be quantified in all affinity process streams and accurate yield and mass balance data calculated. Control experiments using sheep Fab and Fc indicate that the assay is specific to DigiFab. The quantification of potential leached ligand within chromatographic fractions may also be technically challenging, particularly when low-molecular-mass ligands are covalently coupled with an affinity absorbent. Typical methods to assess ligand leakage such as DDMA (digoxin-dicarboxymethoxylamine; digoxin analogue) often involve the use of labelled ligands and relatively complex and labour-intensive analytical techniques. Using the same analytical methodologies, an assay to detect leached or eluted ligand off the column was developed. The results indicate minimal levels of leached ligand in all chromatographic fractions, with total levels of leached DDMA calculated to be 1.52 microg. This is less than 0.01% of the total amount of DDMA coupled with the laboratory-scale affinity column. The SPR methods described in the present study may be applicable for the rapid in-process analysis of specific polyclonal Fab fragments (within a polyclonal mixture) and to rapidly assess leakage of small molecule ligands covalently attached to chromatographic supports.

  3. Dissociation of Multisubunit Protein-Ligand Complexes in the Gas Phase. Evidence for Ligand Migration (United States)

    Zhang, Yixuan; Deng, Lu; Kitova, Elena N.; Klassen, John S.


    The results of collision-induced dissociation (CID) experiments performed on gaseous protonated and deprotonated ions of complexes of cholera toxin B subunit homopentamer (CTB5) with the pentasaccharide (β-D-Gal p-(1→3)-β-D-Gal pNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Gal p-(1→4)-β-D-Glc p (GM1)) and corresponding glycosphingolipid (β-D-Gal p-(1→3)-β-D-Gal pNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Gal p-(1→4)-β-D-Glc p-Cer (GM1-Cer)) ligands, and the homotetramer streptavidin (S4) with biotin (B) and 1,2-dipalmitoyl- sn-glycero-3-phosphoethanolamine-N-(biotinyl) (Btl), are reported. The protonated (CTB5 + 5GM1)n+ ions dissociated predominantly by the loss of a single subunit, with the concomitant migration of ligand to another subunit. The simultaneous loss of ligand and subunit was observed as a minor pathway. In contrast, the deprotonated (CTB5 + 5GM1)n- ions dissociated preferentially by the loss of deprotonated ligand; the loss of ligand-bound and ligand-free subunit were minor pathways. The presence of ceramide (Cer) promoted ligand migration and the loss of subunit. The main dissociation pathway for the protonated and deprotonated (S4 + 4B)n+/- ions, as well as for deprotonated (S4 + 4Btl)n- ions, was loss of the ligand. However, subunit loss from the (S4 + 4B)n+ ions was observed as a minor pathway. The (S4 + 4Btl)n+ ions dissociated predominantly by the loss of free and ligand-bound subunit. The charge state of the complex and the collision energy were found to have little effect on the relative contribution of the different dissociation channels. Thermally-driven ligand migration between subunits was captured in the results of molecular dynamics simulations performed on protonated (CTB5 + 5GM1)15+ ions (with a range of charge configurations) at 800 K. Notably, the migration pathway was found to be highly dependent on the charge configuration of the ion. The main conclusion of this study is that the dissociation pathways of multisubunit protein-ligand

  4. Communication: Free energy of ligand-receptor systems forming multimeric complexes (United States)

    Di Michele, Lorenzo; Bachmann, Stephan J.; Parolini, Lucia; Mognetti, Bortolo M.


    Ligand-receptor interactions are ubiquitous in biology and have become popular in materials in view of their applications to programmable self-assembly. Although complex functionalities often emerge from the simultaneous interaction of more than just two linker molecules, state of the art theoretical frameworks enable the calculation of the free energy only in systems featuring one-to-one ligand/receptor binding. In this Communication, we derive a general formula to calculate the free energy of systems featuring simultaneous direct interaction between an arbitrary number of linkers. To exemplify the potential and generality of our approach, we apply it to the systems recently introduced by Parolini et al. [ACS Nano 10, 2392 (2016)] and Halverson and Tkachenko [J. Chem. Phys. 144, 094903 (2016)], both featuring functionalized Brownian particles interacting via three-linker complexes.

  5. Improving the calculation of magnetic coupling constants in MRPT methods. (United States)

    Spivak, Mariano; Angeli, Celestino; Calzado, Carmen J; de Graaf, Coen


    The magnetic coupling in transition metal compounds with more than one unpaired electron per magnetic center has been studied with multiconfigurational perturbation theory. The usual shortcomings of these methodologies (severe underestimation of the magnetic coupling) have been overcome by describing the Slater determinants with a set of molecular orbitals that maximally resemble the natural orbitals of a high-level multiconfigurational reference configuration interaction calculation. These orbitals have significant delocalization tails onto the bridging ligands and largely increase the coupling strengths in the perturbative calculation.

  6. Targeting Ligand-Dependent and Ligand-Independent Androgen Receptor Signaling in Prostate Cancer (United States)


    Award Number: W81XWH-12-1-0288 TITLE: Targeting Ligand-Dependent and Ligand-Independent Androgen Receptor Signaling in Prostate Cancer...average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed...and completing and reviewing this collection of information. Send comments regarding this burden estimate or any other aspect of this collection of

  7. Quantum.Ligand.Dock: protein-ligand docking with quantum entanglement refinement on a GPU system. (United States)

    Kantardjiev, Alexander A


    Quantum.Ligand.Dock (protein-ligand docking with graphic processing unit (GPU) quantum entanglement refinement on a GPU system) is an original modern method for in silico prediction of protein-ligand interactions via high-performance docking code. The main flavour of our approach is a combination of fast search with a special account for overlooked physical interactions. On the one hand, we take care of self-consistency and proton equilibria mutual effects of docking partners. On the other hand, Quantum.Ligand.Dock is the the only docking server offering such a subtle supplement to protein docking algorithms as quantum entanglement contributions. The motivation for development and proposition of the method to the community hinges upon two arguments-the fundamental importance of quantum entanglement contribution in molecular interaction and the realistic possibility to implement it by the availability of supercomputing power. The implementation of sophisticated quantum methods is made possible by parallelization at several bottlenecks on a GPU supercomputer. The high-performance implementation will be of use for large-scale virtual screening projects, structural bioinformatics, systems biology and fundamental research in understanding protein-ligand recognition. The design of the interface is focused on feasibility and ease of use. Protein and ligand molecule structures are supposed to be submitted as atomic coordinate files in PDB format. A customization section is offered for addition of user-specified charges, extra ionogenic groups with intrinsic pK(a) values or fixed ions. Final predicted complexes are ranked according to obtained scores and provided in PDB format as well as interactive visualization in a molecular viewer. Quantum.Ligand.Dock server can be accessed at

  8. Dynamics Calculation of Spoke

    Institute of Scientific and Technical Information of China (English)


    Compared with ellipse cavity, the spoke cavity has many advantages, especially for the low and medium beam energy. It will be used in the superconductor accelerator popular in the future. Based on the spoke cavity, we design and calculate an accelerator

  9. Haida Numbers and Calculation. (United States)

    Cogo, Robert

    Experienced traders in furs, blankets, and other goods, the Haidas of the 1700's had a well-developed decimal system for counting and calculating. Their units of linear measure included the foot, yard, and fathom, or six feet. This booklet lists the numbers from 1 to 20 in English and Haida; explains the Haida use of ten, hundred, and thousand…

  10. Curvature calculations with GEOCALC

    Energy Technology Data Exchange (ETDEWEB)

    Moussiaux, A.; Tombal, P.


    A new method for calculating the curvature tensor has been recently proposed by D. Hestenes. This method is a particular application of geometric calculus, which has been implemented in an algebraic programming language on the form of a package called GEOCALC. They show how to apply this package to the Schwarzchild case and they discuss the different results.

  11. Daylight calculations in practice

    DEFF Research Database (Denmark)

    Iversen, Anne; Roy, Nicolas; Hvass, Mette;

    programs can give different results. This can be due to restrictions in the program itself and/or be due to the skills of the persons setting up the models. This is crucial as daylight calculations are used to document that the demands and recommendations to daylight levels outlined by building authorities...

  12. Fusion of ligand-coated nanoparticles with lipid bilayers: effect of ligand flexibility. (United States)

    Van Lehn, Reid C; Alexander-Katz, Alfredo


    Amphiphilic, monolayer-protected gold nanoparticles (AuNPs) have recently been shown to insert into and fuse with lipid bilayers, driven by the hydrophobic effect. The inserted transmembrane state is stabilized by the "snorkeling" of charged ligand end groups out of the bilayer interior. This snorkeling process is facilitated by the backbone flexibility of the alkanethiol ligands that comprise the monolayer. In this work, we show that fusion is favorable even in the absence of backbone flexibility by modeling the ligands as rigid rods. For rigid ligands, snorkeling is still accommodated by rotations of the ligand with respect to the grafting point, but the process incurs a more significant free energy penalty than if the backbone were fully flexible. We show that the rigid rod model predicts similar trends in the free energy change for insertion as the previous flexible model when the size of the AuNPs is varied. However, the rigidity of the ligand backbone reduces the overall magnitude of the free energy change compared to that of the flexible model. These results thus generalize previous findings to systems with hindered backbone flexibility due to either structural constraints or low temperature.

  13. Structure-based Drug Screening and Ligand-Based Drug Screening Toward Protein-Compound Network (United States)

    Fukunishi, Yoshifumi


    We developed two new methods to improve the accuracy of molecular interaction data using a protein-compound affinity matrix calculated by a protein-compound docking software. One method is a structure-based in silico drug screening method and another method is a ligand-based in silico drug screening method. These methods were applied to enhance the database enrichment of in silico drug screening and in silico target protein screening.

  14. Prediction of Decomposition Temperature for Lanthanide Complexes Involving Cyclopentadienyl and Benzohydroxamic Acid Ligand by ANNs

    Institute of Scientific and Technical Information of China (English)

    孙益民; 凌青; 万玉宝; 王修然; 宇海银


    The decomposition temperatures of the lanthanide organic complexes(η5-C5H5)2Ln(C6H5CONHO)involving cyclopentadienyl and benzohydroxamic acid ligands were calculated and predicted by the model based on ANNs(artificial neural netowrks)method.The comparison was carried out between results from ANNs method and traditinal regression method.It is proved that ANNs could be used more efficiently for the prediction of decomposition temperature of lanthanide organic complexes.

  15. Prediction of Decomposition Temperature for Lanthanide Complexes Involving Cyclopentadienyl and Benzohydroxamic Acid Ligand by ANNs

    Institute of Scientific and Technical Information of China (English)

    SUN,Yi-Min(孙益民); LING,Qing(凌青); WAN,Yu-Bao(万玉宝); WANG,Xiu-Ran(王修然); YU,Hai-Yin(宇海银)


    The decomposition temperatures of the lanthanide organic complexes (η5-C5H5)2Ln(C6H5CONHO) involving cyclopentadienyl and benzohydroxamic acid ligands were calculated and predicted by the model based on ANNs (artificial neural networks)method. The comparison was carried out between results from ANNs method and traditional regression method. It is proved that ANNs could be used more efficiently for the prediction of decomposition temperature of lanthanide organic complexes.

  16. Separation of lanthanides and actinides(III) using tridentate benzimidazole, benzoxazole and benzothiazole ligands

    Energy Technology Data Exchange (ETDEWEB)

    Drew, M.G.B.; Hudson, M.J.; Iveson, P.B.; Vaillant, L.; Youngs, T.G.A. [Reading Univ. (United Kingdom). Dept. of Chemistry; Hill, C.; Madic, Ch. [CEA Valrho, Dir. de l' Energie Nucleaire, Departement RadioChimie et Procedes, Service de Chimie des Procedes de Separation (DEN/DRCP/SCPS/LCSE), 30 - Marcoule (France)


    The ability of new hydrophobic tridentate ligands based on 2,6-bis(benzimidazole-2-yl)pyridine, 2,6-bis(benzoxazole-2-yl)pyridine and 2,6-bis(benzothiazole-2-yl)pyridine to selectively extract americium(III) from europium(III) was measured. The most promising ligand - 2,6-bis(benzoxazole-2-yl)-4-(2-decyl-1-tetra-decyl-oxy)pyridine L{sup 9} was found to give separation factors (SF{sub Am/Eu}) of up to 70 when used to extract cations from 0.02-0.10 M HNO{sub 3} into TPH in synergy with 2-bromo-decanoic acid. Six structures of lanthanide complexes with 2,6-bis(benzoxazole-2-yl)pyridine L{sup 6} were then determined to evaluate the types of species that are likely to be involved in the separation process. Three structural types were observed, namely [LnL{sup 6}(NO{sub 3}){sub 3}(H{sub 2}O){sub 2}), 11-coordinate only for La, [LnL{sup 6}(NO{sub 3})3 (CH{sub 3}CN)], 10-coordinate for Pr, Nd and Eu and [LnL{sup 6}(NO{sub 3}){sub 3}(H{sub 2}O)], L 10-coordinate for Eu and Gd. Quantum Mechanics calculations were carried out on the tridentate ligands to elucidate the conformational preferences of the ligands in the free state and protonated and di-protonated forms and to assess the electronic properties of the ligands for comparison with other ter-dentate ligands used in lanthanide/actinide separation processes. (authors)

  17. Amino Acids in Nine Ligand-Prefer Ramachandran Regions

    Directory of Open Access Journals (Sweden)

    Chen Cao


    Full Text Available Several secondary structures, such as π-helix and left-handed helix, have been frequently identified at protein ligand-binding sites. A secondary structure is considered to be constrained to a specific region of dihedral angles. However, a comprehensive analysis of the correlation between main chain dihedral angles and ligand-binding sites has not been performed. We undertook an extensive analysis of the relationship between dihedral angles in proteins and their distance to ligand-binding sites, frequency of occurrence, molecular potential energy, amino acid composition, van der Waals contacts, and hydrogen bonds with ligands. The results showed that the values of dihedral angles have a strong preference for ligand-binding sites at certain regions in the Ramachandran plot. We discovered that amino acids preceding the ligand-prefer ϕ/ψ box residues are exposed more to solvents, whereas amino acids following ligand-prefer ϕ/ψ box residues form more hydrogen bonds and van der Waals contacts with ligands. Our method exhibited a similar performance compared with the program Ligsite-csc for both ligand-bound structures and ligand-free structures when just one ligand-binding site was predicted. These results should be useful for the prediction of protein ligand-binding sites and for analysing the relationship between structure and function.

  18. Open-shell organometallics: reactivity at the ligand

    NARCIS (Netherlands)

    W.I. Dzik; B. de Bruin


    The purpose of this review is to show that (cooperative) ligand radical reactivity can be effectively employed in synthetic organometallic chemistry and catalysis to achieve selectivity in radical-type transformations. The ‘redox non-innocence’ of ligands, and the controlled reactivity of ‘ligand ra

  19. Triple Bioaffinity Mass Spectrometry Concept for Thyroid Transporter Ligands

    NARCIS (Netherlands)

    Aqai, P.; Fryganas, C.; Mizuguchi, M.; Haasnoot, W.; Nielen, M.W.F.


    For the analysis of thyroid transporter ligands, a triple bioaffinity mass spectrometry (BioMS) concept was developed, with the aim at three different analytical objectives: rapid screening of any ligand, confirmation of known ligands in accordance with legislative requirements, and identification o

  20. Structural, DFT and biological studies on Co(II) complexes of semi and thiosemicarbazide ligands derived from diketo hydrazide (United States)

    Yousef, T. A.; El-Gammal, O. A.; Ahmed, Sara F.; Abu El-Reash, G. M.


    Three ligands have been prepared by addition ethanolic suspension of 2-hydrazino-2-oxo-N-phenyl-acetamide to phenyl isocyanate (H2PAPS), phenyl isothiocyanate (H2PAPT) and benzoyl isothiocyanate (H2PABT). The Co(II) chloride complexes were prepared and characterized by conventional techniques. The isolated complexes were assigned the formulaes, [Co(HPAPS)Cl(H2O)2]H2O, [Co(HPAPT)Cl]H2O and [Co(H2PABT)Cl2], respectively. The IR spectra of complexes shows that H2PAPS behaves as a mononegative tridentate via CO of hydrazide moiety and enolized CO of hydrazide moiety and CN (azomethine) group due to enolization of CO isocyanate moiety. H2PAPT behaves as mononegative tridentate via one CO of hydrazide moiety and thiol CS and NH groups and finally H2PABT behaves as neutral tetradentate via one CO of hydrazide moiety, CO of benzoyl moiety, Cdbnd S due to enolization of the second CO of hydrazide moiety and new CN (azomethine) groups. The vibrational frequencies of the IR spectra of ligands which were determined experimentally are compared with those obtained theoretically from DFT calculations. Also, the bond lengths, bond angles, HOMO, LUMO and dipole moments have been calculated. The calculated HOMO-LUMO energy gap reveals that charge transfer occurs within the ligand molecules. The calculated values of binding energies indicates the stability of metal complexes is higher that of ligand. Also, the kinetic and thermodynamic parameters for the different thermal degradation steps of the complexes were determined by Coats-Redfern and Horowitz-Metzger methods. The antibacterial activities were also tested against Bacillus subtilis and Escherichia coli bacteria. The free ligands showed a higher antibacterial effect than their Co(II) complexes except [Co(HPAPS)Cl(H2O)2]H2O which shows higher activity than corresponding ligand. The antitumor activities of the Ligands and their Co(II) complexes have been evaluated against liver (HePG2) and breast (MCF-7) cancer cells. All ligands

  1. Molecular evolution of a peptide GPCR ligand driven by artificial neural networks.

    Directory of Open Access Journals (Sweden)

    Sebastian Bandholtz

    Full Text Available Peptide ligands of G protein-coupled receptors constitute valuable natural lead structures for the development of highly selective drugs and high-affinity tools to probe ligand-receptor interaction. Currently, pharmacological and metabolic modification of natural peptides involves either an iterative trial-and-error process based on structure-activity relationships or screening of peptide libraries that contain many structural variants of the native molecule. Here, we present a novel neural network architecture for the improvement of metabolic stability without loss of bioactivity. In this approach the peptide sequence determines the topology of the neural network and each cell corresponds one-to-one to a single amino acid of the peptide chain. Using a training set, the learning algorithm calculated weights for each cell. The resulting network calculated the fitness function in a genetic algorithm to explore the virtual space of all possible peptides. The network training was based on gradient descent techniques which rely on the efficient calculation of the gradient by back-propagation. After three consecutive cycles of sequence design by the neural network, peptide synthesis and bioassay this new approach yielded a ligand with 70fold higher metabolic stability compared to the wild type peptide without loss of the subnanomolar activity in the biological assay. Combining specialized neural networks with an exploration of the combinatorial amino acid sequence space by genetic algorithms represents a novel rational strategy for peptide design and optimization.

  2. Radioprotection calculations for MEGAPIE. (United States)

    Zanini, L


    The MEGAwatt PIlot Experiment (MEGAPIE) liquid lead-bismuth spallation neutron source will commence operation in 2006 at the SINQ facility of the Paul Scherrer Institut. Such an innovative system presents radioprotection concerns peculiar to a liquid spallation target. Several radioprotection issues have been addressed and studied by means of the Monte Carlo transport code, FLUKA. The dose rates in the room above the target, where personnel access may be needed at times, from the activated lead-bismuth and from the volatile species produced were calculated. Results indicate that the dose rate level is of the order of 40 mSv h(-1) 2 h after shutdown, but it can be reduced below the mSv h(-1) level with slight modifications to the shielding. Neutron spectra and dose rates from neutron transport, of interest for possible damage to radiation sensitive components, have also been calculated.

  3. Synthesis, spectral, thermal, potentiometric and antimicrobial studies of transition metal complexes of tridentate ligand

    Directory of Open Access Journals (Sweden)

    Sarika M. Jadhav


    Full Text Available A series of metal complexes of Cu(II, Ni(II, Co(II, Fe(III and Mn(II have been synthesized with newly synthesized biologically active tridentate ligand. The ligand was synthesized by condensation of dehydroacetic acid (3-acetyl-6-methyl-(2H pyran-2,4(3H-dione or DHA, o-phenylene diamine and fluoro benzaldehyde and characterized by elemental analysis, molar conductivity, magnetic susceptibility, thermal analysis, X-ray diffraction, IR, 1H-NMR, UV–Vis spectroscopy and mass spectra. From the analytical data, the stoichiometry of the complexes was found to be 1:2 (metal:ligand with octahedral geometry. The molar conductance values suggest the non-electrolyte nature of metal complexes. The IR spectral data suggest that the ligand behaves as a dibasic tridentate ligand with ONN donor atoms sequence towards central metal ion. Thermal behaviour (TG/DTA and kinetic parameters calculated by the Coats–Redfern and Horowitz–Metzger method suggest more ordered activated state in complex formation. To investigate the relationship between stability constants of metal complexes and antimicrobial activity, the dissociation constants of Schiff bases and stability constants of their binary metal complexes have been determined potentiometrically in THF–water (60:40% solution at 25 ± 1 °C and at 0.1 M NaClO4 ionic strength. The potentiometric study suggests 1:1 and 1:2 complexation. Antibacterial and antifungal activities in vitro were performed against Staphylococcus aureus, Escherichia coli and Aspergillus niger, Trichoderma, respectively. The stability constants of the metal complexes were calculated by the Irving–Rosotti method. A relation between the stability constant and antimicrobial activity of complexes has been discussed. It is observed that the activity enhances upon complexation and the order of antifungal activity is in accordance with stability order of metal ions.

  4. PIC: Protein Interactions Calculator. (United States)

    Tina, K G; Bhadra, R; Srinivasan, N


    Interactions within a protein structure and interactions between proteins in an assembly are essential considerations in understanding molecular basis of stability and functions of proteins and their complexes. There are several weak and strong interactions that render stability to a protein structure or an assembly. Protein Interactions Calculator (PIC) is a server which, given the coordinate set of 3D structure of a protein or an assembly, computes various interactions such as disulphide bonds, interactions between hydrophobic residues, ionic interactions, hydrogen bonds, aromatic-aromatic interactions, aromatic-sulphur interactions and cation-pi interactions within a protein or between proteins in a complex. Interactions are calculated on the basis of standard, published criteria. The identified interactions between residues can be visualized using a RasMol and Jmol interface. The advantage with PIC server is the easy availability of inter-residue interaction calculations in a single site. It also determines the accessible surface area and residue-depth, which is the distance of a residue from the surface of the protein. User can also recognize specific kind of interactions, such as apolar-apolar residue interactions or ionic interactions, that are formed between buried or exposed residues or near the surface or deep inside.

  5. Glycomimetic ligands for the human asialoglycoprotein receptor. (United States)

    Mamidyala, Sreeman K; Dutta, Sanjay; Chrunyk, Boris A; Préville, Cathy; Wang, Hong; Withka, Jane M; McColl, Alexander; Subashi, Timothy A; Hawrylik, Steven J; Griffor, Matthew C; Kim, Sung; Pfefferkorn, Jeffrey A; Price, David A; Menhaji-Klotz, Elnaz; Mascitti, Vincent; Finn, M G


    The asialoglycoprotein receptor (ASGPR) is a high-capacity galactose-binding receptor expressed on hepatocytes that binds its native substrates with low affinity. More potent ligands are of interest for hepatic delivery of therapeutic agents. We report several classes of galactosyl analogues with varied substitution at the anomeric, C2-, C5-, and C6-positions. Significant increases in binding affinity were noted for several trifluoromethylacetamide derivatives without covalent attachment to the protein. A variety of new ligands were obtained with affinity for ASGPR as good as or better than that of the parent N-acetylgalactosamine, showing that modification on either side of the key C3,C4-diol moiety is well tolerated, consistent with previous models of a shallow binding pocket. The galactosyl pyranose motif therefore offers many opportunities for the attachment of other functional units or payloads while retaining low-micromolar or better affinity for the ASGPR.

  6. Leaching behavior of butanedionedioxime as gold ligand

    Institute of Scientific and Technical Information of China (English)


    Butanedionedioxime, a small organic compound with low-toxicity and good chemical stability, has been proposed as an effective gold ligand in gold extraction. The result of experiment shows that: 1) highly effective gold lixiviantcan be composed of butanedionedioxime (BDM) with many oxidants, especially potassium permanganate; 2)in the leaching system of BD M- K M nO4 the suitable Ox/Lig(ratio of oxidants to gold ligands) tange is 0.20 ~ 0. 50, optimally 0.25 ~0.45 at the pH range of 7 ~ 11; 3) BDM-KMnO4 extraction of gold from an oxide ore is similar to cyanide(cyanide-O2)extraction, but the leaching rate of gold by BDM-KMnO4 is faster than that by cyanide-O2; 4) gold may readily be recov-ered by carbon adsorption and zinc precipitation

  7. Mechanics, thermodynamics, and kinetics of ligand binding to biopolymers. (United States)

    Jarillo, Javier; Morín, José A; Beltrán-Heredia, Elena; Villaluenga, Juan P G; Ibarra, Borja; Cao, Francisco J


    Ligands binding to polymers regulate polymer functions by changing their physical and chemical properties. This ligand regulation plays a key role in many biological processes. We propose here a model to explain the mechanical, thermodynamic, and kinetic properties of the process of binding of small ligands to long biopolymers. These properties can now be measured at the single molecule level using force spectroscopy techniques. Our model performs an effective decomposition of the ligand-polymer system on its covered and uncovered regions, showing that the elastic properties of the ligand-polymer depend explicitly on the ligand coverage of the polymer (i.e., the fraction of the polymer covered by the ligand). The equilibrium coverage that minimizes the free energy of the ligand-polymer system is computed as a function of the applied force. We show how ligands tune the mechanical properties of a polymer, in particular its length and stiffness, in a force dependent manner. In addition, it is shown how ligand binding can be regulated applying mechanical tension on the polymer. Moreover, the binding kinetics study shows that, in the case where the ligand binds and organizes the polymer in different modes, the binding process can present transient shortening or lengthening of the polymer, caused by changes in the relative coverage by the different ligand modes. Our model will be useful to understand ligand-binding regulation of biological processes, such as the metabolism of nucleic acid. In particular, this model allows estimating the coverage fraction and the ligand mode characteristics from the force extension curves of a ligand-polymer system.

  8. ABS-Scan: In silico alanine scanning mutagenesis for binding site residues in protein-ligand complex. (United States)

    Anand, Praveen; Nagarajan, Deepesh; Mukherjee, Sumanta; Chandra, Nagasuma


    Most physiological processes in living systems are fundamentally regulated by protein-ligand interactions. Understanding the process of ligand recognition by proteins is a vital activity in molecular biology and biochemistry. It is well known that the residues present at the binding site of the protein form pockets that provide a conducive environment for recognition of specific ligands. In many cases, the boundaries of these sites are not well defined. Here, we provide a web-server to systematically evaluate important residues in the binding site of the protein that contribute towards the ligand recognition through in silico alanine-scanning mutagenesis experiments. Each of the residues present at the binding site is computationally mutated to alanine. The ligand interaction energy is computed for each mutant and the corresponding ΔΔG values are calculated by comparing it to the wild type protein, thus evaluating individual residue contributions towards ligand interaction. The server will thus provide a ranked list of residues to the user in order to obtain loss-of-function mutations. This web-tool can be freely accessed through the following address:

  9. Synthesis, crystal structure and luminescence properties of acenaphthene benzohydrazide based ligand and its zinc(II) complex (United States)

    Kumar, Mukesh; Roy, Soumyabrata; Faizi, Md. Serajul Haque; Kumar, Santosh; Singh, Mantu Kumar; Kishor, Shyam; Peter, Sebastian C.; John, Rohith P.


    The complex compound of zinc(II) supported by (Z)-2-hydroxy-N‧-(1-oxoacenaphthylen-2(1H) ylidene)benzohydrazide ligand (H2L1) has been reported and discussed. The reaction of zinc acetate with H2L1 ligand leads to the formation of a mononuclear zinc(ii) complex, [Zn(HL1)2H2O]. The ligand, H2L1 has been characterized by elemental analysis, 1H, 13C and 1Hsbnd COSY -NMR, IR and ESI-MS, while the complex was characterized by elemental analysis, IR, and ESI-MS. The crystal structures of the free ligand H2L1 and the complex have also been determined by single crystal X-ray diffraction. The ligand chelates with metal centre with a nitrogen atom of imino moiety and an oxygen atom of enolic group. The complex shows distorted trigonal bipyramidal geometry around the metal centre with oxygen atoms lying in the equatorial plane and imino nitrogen atoms along the axial direction. The DFT/TD-DFT calculations were performed on both the ligand and its zinc complex to get insight into the structural, electronic and optical properties. The photoluminescence, fluorescence properties of the complex have been investigated.

  10. Pt(II) diimine complexes bearing carbazolyl-capped acetylide ligands: synthesis, tunable photophysics and nonlinear absorption. (United States)

    Liu, Rui; Chen, Hongbin; Chang, Jin; Li, Yuhao; Zhu, Hongjun; Sun, Wenfang


    A series of new Pt(II) diimine complexes with different carbazolyl-capped acetylide ligands (Pt-1–Pt-5) were synthesized and characterized. Their photophysical properties were investigated systematically via spectroscopic and theoretical methods. All complexes exhibit ligand-centered 1π,π* transitions in the UV region, and broad, structureless metal-to-ligand charge transfer (1MLCT)/ligand-to-ligand charge transfer (1LLCT) absorption bands in the visible spectral region. All complexes are emissive in solution at room temperature, with the emitting state being tentatively assigned to the 3MLCT/3LLCT states for Pt-1–Pt-4, and the emitting state of Pt-5 exhibiting a switch from the 3π,π* state in high-polarity solvents to the 3MLCT state in low-polarity solvents. Complexes Pt-1–Pt-5 all exhibit moderate triplet transient absorption (TA) from the visible to the NIR region, where reverse saturable absorption (RSA) could occur. The spectroscopic studies and theoretical calculations indicate that the photophysical properties of these Pt complexes can be tuned drastically by the carbazolyl-capped acetylide ligand, which would be useful for rational design of transition-metal complexes with high emission quantum yield, long excited-state lifetime, broadband excited-state absorption, and strong nonlinear transmittance for organic light-emitting and/or broadband nonlinear transmission applications.

  11. Metal-ligand cooperative activation of nitriles by a ruthenium complex with a de-aromatized PNN pincer ligand

    NARCIS (Netherlands)

    Eijsink, Linda E; Perdriau, Sébastien C P; de Vries, Johannes G; Otten, Edwin


    The pincer complex (PNN)RuH(CO), with a de-aromatized pyridine in the ligand backbone, is shown to react with nitriles in a metal-ligand cooperative manner. This leads to the formation of a series of complexes with new Ru-N(nitrile) and C(ligand)-C(nitrile) bonds. The initial nitrile cycloaddition

  12. Metal-ligand cooperative activation of nitriles by a ruthenium complex with a de-aromatized PNN pincer ligand

    NARCIS (Netherlands)

    Eijsink, Linda E; Perdriau, Sébastien C P; de Vries, Johannes G; Otten, Edwin


    The pincer complex (PNN)RuH(CO), with a de-aromatized pyridine in the ligand backbone, is shown to react with nitriles in a metal-ligand cooperative manner. This leads to the formation of a series of complexes with new Ru-N(nitrile) and C(ligand)-C(nitrile) bonds. The initial nitrile cycloaddition p

  13. Protein-ligand binding affinity determination by the waterLOGSY method: An optimised approach considering ligand rebinding (United States)

    Huang, Renjie; Bonnichon, Arnaud; Claridge, Timothy D. W.; Leung, Ivanhoe K. H.


    WaterLOGSY is a popular ligand-observed NMR technique to screen for protein-ligand interactions, yet when applied to measure dissociation constants (KD) through ligand titration, the results were found to be strongly dependent on sample conditions. Herein, we show that accurate KDs can be obtained by waterLOGSY with optimised experimental setup.

  14. Targeting Selectins and Their Ligands in Cancer

    Directory of Open Access Journals (Sweden)

    Alessandro eNatoni


    Full Text Available Aberrant glycosylation is a hallmark of cancer cells with increased evidence pointing to a role in tumor progression. In particular, aberrant sialylation of glycoproteins and glycolipids have been linked to increased immune cell evasion, drug evasion, drug resistance, tumor invasiveness, and vascular dissemination leading to metastases. Hypersialylation of cancer cells is largely the result of overexpression of sialyltransferases. Humans differentially express twenty different sialyltransferases in a tissue-specific manner, each of which catalyze the attachment of sialic acids via different glycosidic linkages (2-3; 2-6 or 2-8 to the underlying glycan chain. One important mechanism whereby overexpression of sialyltransferases contributes to an enhanced metastatic phenotype is via the generation of selectin ligands. Selectin ligand function requires the expression of sialyl-Lewis X and its structural-isomer sialyl-Lewis A, which are synthesized by the combined action of alpha 1-3-fucosyltransferases, 2-3-sialyltransferases, 1-4-galactosyltranferases, and N-acetyl--glucosaminyltransferases. The α2-3-sialyltransferases ST3Gal4 and ST3Gal6 are critical to the generation of functional E- and P-selectin ligands and overexpression of these sialyltransferases have been linked to increased risk of metastatic disease in solid tumors and poor outcome in multiple myeloma. Thus, targeting selectins and their ligands as well as the enzymes involved in their generation, in particular sialyltransferases, could be beneficial to many cancer patients. Potential strategies include sialyltransferase inhibition and the use of selectin antagonists, such as glycomimetic drugs and antibodies. Here, we review ongoing efforts to optimize the potency and selectivity of sialyltransferase inhibitors, including the potential for targeted delivery approaches, as well as evaluate the potential utility of selectin inhibitors, which are now in early clinical

  15. The ligands of CXCR4 in vascularization


    Tuchscheerer, Nancy


    The formation of a functional and integrated vascular network is a basic process in the growth and maintenance of tissues and can be established by two forms of blood vessel growth in adults: angiogenesis and arteriogenesis. In this study, the ligands of the chemokine receptor CXCR4 and its role in angiogenesis (represented by the experimental myocardial infarction) and arteriogenesis (represented by the murine hind limb ischemia model) was investigated. The first approach identified the CXCL...

  16. Dockomatic - automated ligand creation and docking


    Hampikian Greg; McDougal Owen M; Jacob Reed B; Bullock Casey W; Andersen Tim


    Abstract Background The application of computational modeling to rationally design drugs and characterize macro biomolecular receptors has proven increasingly useful due to the accessibility of computing clusters and clouds. AutoDock is a well-known and powerful software program used to model ligand to receptor binding interactions. In its current version, AutoDock requires significant amounts of user time to setup and run jobs, and collect results. This paper presents DockoMatic, a user frie...

  17. Selective oxoanion separation using a tripodal ligand

    Energy Technology Data Exchange (ETDEWEB)

    Custelcean, Radu; Moyer, Bruce A.; Rajbanshi, Arbin


    The present invention relates to urea-functionalized crystalline capsules self-assembled by sodium or potassium cation coordination and by hydrogen-bonding water bridges to selectively encapsulate tetrahedral divalent oxoanions from highly competitive aqueous alkaline solutions and methods using this system for selective anion separations from industrial solutions. The method involves competitive crystallizations using a tripodal tris(urea) functionalized ligand and, in particular, provides a viable approach to sulfate separation from nuclear wastes.

  18. galectin-3 ligand — EDRN Public Portal (United States)

    Galectin-3 is an endogenous lectin that binds glycan epitopes of cell membrane and some extracellular glycoproteins such as integrins and laminin. Galectin-3 is involved in several biological activities including regulation of cellular cycle, modulation of adhesion and tumor progression and metastasis. Serum galectin-3 ligands have been shown to modulate the immune reaction against tumors and viruses and their level increases in sera of several neoplastic diseases.

  19. RAGE and its ligands in retinal disease. (United States)

    Barile, Gaetano R; Schmidt, Ann M


    RAGE, the receptor for advanced glycation endproducts (AGEs), is a multiligand signal transduction receptor of the immunoglobulin superfamily of cell surface molecules that has been implicated in the pathogenesis of diabetic complications, neurodegenerative diseases, inflammatory disorders, and cancer. These diverse biologic disorders reflect the multiplicity of ligands capable of cellular interaction via RAGE that include, in addition to AGEs, amyloid-beta (Abeta) peptide, the S100/calgranulin family of proinflammatory cytokines, and amphoterin, a member of the High Mobility Group Box (HMGB) DNA-binding proteins. In the retina, RAGE expression is present in neural cells, the vasculature, and RPE cells, and it has also been detected in pathologic cellular retinal responses including epiretinal and neovascular membrane formation. Ligands for RAGE, in particular AGEs, have emerged as relevant to the pathogenesis of diabetic retinopathy and age-related macular disease. While the understanding of RAGE and its role in retinal dysfunction with aging, diabetes mellitus, and/or activation of pro-inflammatory pathways is less complete compared to other organ systems, increasing evidence indicates that RAGE can initiate and sustain significant cellular perturbations in the inner and outer retina. For these reasons, antagonism of RAGE interactions with its ligands may be a worthwhile therapeutic target in such seemingly disparate, visually threatening retinal diseases as diabetic retinopathy, age-related macular degeneration, and proliferative vitreoretinopathy.

  20. Assessment of accuracy and precision in speciation analysis by competitive ligand equilibration-cathodic stripping voltammetry (CLE-CSV) and application to Antarctic samples

    Energy Technology Data Exchange (ETDEWEB)

    Monticelli, Damiano, E-mail: [Dipartimento di Scienze Chimiche e Ambientali, Universita degli Studi dell' Insubria - sede di Como, via Valleggio 11 22100 Como (Italy); Dossi, Carlo; Castelletti, Alessio [Dipartimento di Scienze Chimiche e Ambientali, Universita degli Studi dell' Insubria - sede di Como, via Valleggio 11 22100 Como (Italy)


    The analytical performances of Competitive Ligand Equilibration with Cathodic Stripping Voltammetric detection of the labile fraction (CLE-CSV) were assessed. This speciation method enables the concentration of natural ligand(s) and their conditional stability constants for the complexation of the investigated metal to be determined through thermodynamic considerations. Literature data were discussed and general trends in the precision of the determined parameters identified: ligand concentrations were affected, on average, by a 10% relative percentage standard deviation (RSD%), whereas conditional stability constants showed much lower precision, with an average RSD% of 50%. New experimental data were collected to obtain a complete assessment of accuracy and precision attainable for the determination of strong ligands at the ultra trace level, enabling the whole protocol to be evaluated. Firstly, the side reaction coefficient alpha for the formation of the complex between the added ligand and the investigated metal ({alpha}{sub CuL}) was determined. The method was subsequently applied to the analysis of solution containing ligand at trace levels (5-50 nM) with known complexing characteristics. Copper was used as the model metal ion and ethylenediaminetetraacetic acid (EDTA) and diethylenetriaminepentaacetic acid (DTPA) as the model ligands. Results evidenced that the CLE-CSV protocol is not affected by systematic errors in the determination of both ligand concentration and the conditional stability constants. Good precision is obtained for ligand concentrations, with an average relative standard deviation (RSD%) of 5%; an average RSD% of 23% was calculated for the conditional stability constants. Including the contribution of the uncertainty in the value of {alpha}{sub CuL} in the evaluation of the uncertainty in the latter parameter increased the RSD% up to 40%. The CLE-CSV protocol was subsequently applied to the detection of strong ligands in water samples

  1. Assessment of accuracy and precision in speciation analysis by competitive ligand equilibration-cathodic stripping voltammetry (CLE-CSV) and application to Antarctic samples. (United States)

    Monticelli, Damiano; Dossi, Carlo; Castelletti, Alessio


    The analytical performances of Competitive Ligand Equilibration with Cathodic Stripping Voltammetric detection of the labile fraction (CLE-CSV) were assessed. This speciation method enables the concentration of natural ligand(s) and their conditional stability constants for the complexation of the investigated metal to be determined through thermodynamic considerations. Literature data were discussed and general trends in the precision of the determined parameters identified: ligand concentrations were affected, on average, by a 10% relative percentage standard deviation (RSD%), whereas conditional stability constants showed much lower precision, with an average RSD% of 50%. New experimental data were collected to obtain a complete assessment of accuracy and precision attainable for the determination of strong ligands at the ultra trace level, enabling the whole protocol to be evaluated. Firstly, the side reaction coefficient alpha for the formation of the complex between the added ligand and the investigated metal (alpha(CuL)) was determined. The method was subsequently applied to the analysis of solution containing ligand at trace levels (5-50 nM) with known complexing characteristics. Copper was used as the model metal ion and ethylenediaminetetraacetic acid (EDTA) and diethylenetriaminepentaacetic acid (DTPA) as the model ligands. Results evidenced that the CLE-CSV protocol is not affected by systematic errors in the determination of both ligand concentration and the conditional stability constants. Good precision is obtained for ligand concentrations, with an average relative standard deviation (RSD%) of 5%; an average RSD% of 23% was calculated for the conditional stability constants. Including the contribution of the uncertainty in the value of alpha(CuL) in the evaluation of the uncertainty in the latter parameter increased the RSD% up to 40%. The CLE-CSV protocol was subsequently applied to the detection of strong ligands in water samples collected in

  2. EGF receptor ligands: recent advances [version 1; referees: 3 approved

    Directory of Open Access Journals (Sweden)

    Bhuminder Singh


    Full Text Available Seven ligands bind to and activate the mammalian epidermal growth factor (EGF receptor (EGFR/ERBB1/HER1: EGF, transforming growth factor-alpha (TGFA, heparin-binding EGF-like growth factor (HBEGF, betacellulin (BTC, amphiregulin (AREG, epiregulin (EREG, and epigen (EPGN. Of these, EGF, TGFA, HBEGF, and BTC are thought to be high-affinity ligands, whereas AREG, EREG, and EPGN constitute low-affinity ligands. This focused review is meant to highlight recent studies related to actions of the individual EGFR ligands, the interesting biology that has been uncovered, and relevant advances related to ligand interactions with the EGFR.


    Institute of Scientific and Technical Information of China (English)

    张建军; 丁尔迅; 王强; 陈学云; 付志仁


    To investigate the expression of Fas ligand in human colon carcinoma cell lines. Methods: A total of six human colon cancer cell lines were examined for the expression of Fas ligand mRNA and cell surface protein by using RT-PCR and flow cytometry respectively. Results: The results showed that Fas ligand mRNA was expressed in all of the six cancer cell lines and Fas ligand cell surface protein was expressed in part of them. Conclusion: These data suggest that Fas ligand was expressed, at least in part, in human colon cancer cell lines and might facilitate to escape from immune surveillance of the host.

  4. Quantum chemical assessment of the ligand effect on the properties and structure of protected gold clusters (United States)

    Nikitina, N. A.; Pichugina, D. A.; Kuz'menko, N. E.


    A procedure based on density functional theory is proposed for calculation of Au20(XCH3)16 (X = S, Se, Te) isomers. It is established that the most stable isomer for all X has a core‒shell structure: Au7@(AuXCH3)8(XCH3(AuXCH3)3)(XCH3AuXCH3)2. Optical and IR spectra, ionization potential, and electron affinity are calculated for the first time for all clusters. It is shown that a cluster protected by thiolate ligands has the greatest electronic and thermodynamic stability.

  5. Dipole moments of ligands and Stark splitting of rare earth ion levels

    CERN Document Server

    Chumachkova, M M


    A model for description the polarization and relaxation of ions-ligands at impurity defects in crystals is proposed and tested. The approach is based on introduction of effective electrical dipole moments, taken into consideration as fundamental parameters of crystals and determined from experimental data on the energy structure of impurity ions. Calculations show that the rare-earth ion energy structure essentially depends on the value of effective electric dipole moments of surrounding matrix ions. Parameters of the theory are found. The calculation results coincide with experimental data available. Possibilities of the approach proposed in investigating crystals containing impurities (dielectrics and semiconductors) are discussed

  6. Bis(methylpyridine)-EDTA derivative as a potential ligand for PET imaging: synthesis, complexation, and biological evaluation. (United States)

    Singh, Pooja; Aggarwal, Swati; Tiwari, Anjani K; Kumar, Vikas; Pratap, Ramendra; Chuttani, Krishna; Mishra, Anil K


    A novel transitional metal ligand derivatized from EDTA-conjugated 2-amino-4-methyl pyridine, an acyclic vehicle (EDTA-Mepy2 ) was designed, synthesized, and characterized for PET imaging with ⁶⁸Ga. The drug likeliness and appropriate lipophilicity were first analyzed by molecular docking studies which shows interactive property of ligand with serum albumin protein (HSA: PDB 1E78), at Lys199, Arg257, and His242 residues, which make it more appropriate in transportation as a specific ligand for PET imaging. As a confirmation, binding constant of the ligand with human serum albumin was calculated at λex = 350 nm which was found to be 4.9 × 10³ m⁻¹. The pharmacokinetics of (68) Ga-EDTA-Mepy2 was analyzed by blood kinetics (t(1/2) slow: 3 h 56 min and t(1/2) fast: 32 min) and biodistribution (maximum % ID/g was found in kidney at 1 h). Further the capability of this ligand was analyzed as optical marker also, by recording λex = 380 nm, RFU = 8000; 710 nm, RFU = 1000 units at fixed λem = 280 nm. Additionally, in physiological conditions where its stability was calculated, suggests 15-20 times selectivity over the endogenously present metal ions (KG aL /KZ nL = 14.3, KG aL /KC uL = 18.1).

  7. Structural Analysis and Reactivity of Tetramethylcopper(III Complex towards Nitrogen Donor Ligands by Density Functional Theory

    Directory of Open Access Journals (Sweden)

    Perumal Balu


    Full Text Available DFT studies are carried out on some ligand substitution reactions of tetramethylcuprate(III (TMC complex with five different nitrogen donor ligands as probe ligands. The geometry optimization of the possible nine model systems and the frequency calculations are carried out at DFT level using LANL2DZ basis set. The selected structural parameters of optimized model systems of Cu(III complexes are reported and discussed. The change in the M-C bond distance in TMC due to substitution by probe ligands is explained. Natural population analysis (NPA has been carried out for these complexes to establish the charge of copper in these complexes. A detailed population analysis of valence orbitals of copper complexes supports the existence of d8 configuration for metal in complexes and there is evidence for the transmission of electrons from the nitrogen donor atom to dxy, dx2-y2, and 4s orbitals. Bond order calculations have been performed for all the complexes to probe the interaction between Cu(III and the ligand. The stability of the complexes is ascertained from the computed chemical hardness. In order to understand the nature of Cu(III-L (L = N donors and Cu(III-Me bonds in different complexes, Energy Decomposition Analysis (EDA has been carried out for all the complexes chosen in the theoretical study. Thermodynamic feasibility of these reactions is investigated in terms of free energy changes of these reactions.

  8. Estimating Mercury-Binding Ligand Concentrations in Freshwater Wetland Porewaters Using the “Tin-Reducible-Mercury” Titration Method (United States)

    Creswell, J. E.; Babiarz, C.; Shafer, M. M.; Armstrong, D. E.


    Wetland environments are recognized as active regions of mercury methylation and may represent the primary source of methylmercury to many aquatic systems. Thus understanding the methylation process in these systems is vital to efforts at prediction of methylmercury accumulation at higher trophic levels. Strong mercury-binding ligands in porewaters can limit methylation in wetlands because large ligands and charged Hg-complexes are not bioavailable to methylating bacteria. Following the method developed by Lamborg and colleagues (2003), we used tin(II) chloride, a weak reductant, to reduce and measure labile Hg in porewater samples (i.e. the fraction not bound to strong ligands). We further titrated samples with Hg(II) to determine the Hg concentration at which the naturally occurring ligands were saturated - thus providing a measure of mercury-binding ligand concentrations. To our knowledge, this is the first extensive use of this technique on porewater samples. In an effort to differentiate between inorganic- and organic-complexed Hg, we modeled the inorganic speciation of Hg using MINEQL+, an aqueous speciation modeling program. Measurements of total mercury, methylmercury, sulfide, sulfate, chloride, carbonate, pH, dissolved organic carbon, phosphate, bromide, and major ions in sample porewaters were used as inputs to the model. Using the inorganic speciation calculated by the model, and the ligand concentrations measured in our laboratory experiment, we calculated conditional stability constants for mercury-ligand binding in this system. Although modeling predicts that mercury speciation will be dominated by sulfide at the concentrations present in this system, mercury methylation rate measurements show a stronger correlation with dissolved organic carbon concentrations than with sulfide. This correlation suggests that dissolved organic carbon plays an important role in mercury speciation, even in the presence of sulfide. Porewaters were extracted from

  9. The Recognition of Identical Ligands by Unrelated Proteins. (United States)

    Barelier, Sarah; Sterling, Teague; O'Meara, Matthew J; Shoichet, Brian K


    The binding of drugs and reagents to off-targets is well-known. Whereas many off-targets are related to the primary target by sequence and fold, many ligands bind to unrelated pairs of proteins, and these are harder to anticipate. If the binding site in the off-target can be related to that of the primary target, this challenge resolves into aligning the two pockets. However, other cases are possible: the ligand might interact with entirely different residues and environments in the off-target, or wholly different ligand atoms may be implicated in the two complexes. To investigate these scenarios at atomic resolution, the structures of 59 ligands in 116 complexes (62 pairs in total), where the protein pairs were unrelated by fold but bound an identical ligand, were examined. In almost half of the pairs, the ligand interacted with unrelated residues in the two proteins (29 pairs), and in 14 of the pairs wholly different ligand moieties were implicated in each complex. Even in those 19 pairs of complexes that presented similar environments to the ligand, ligand superposition rarely resulted in the overlap of related residues. There appears to be no single pattern-matching "code" for identifying binding sites in unrelated proteins that bind identical ligands, though modeling suggests that there might be a limited number of different patterns that suffice to recognize different ligand functional groups.

  10. Zero Temperature Hope Calculations

    Energy Technology Data Exchange (ETDEWEB)

    Rozsnyai, B F


    The primary purpose of the HOPE code is to calculate opacities over a wide temperature and density range. It can also produce equation of state (EOS) data. Since the experimental data at the high temperature region are scarce, comparisons of predictions with the ample zero temperature data provide a valuable physics check of the code. In this report we show a selected few examples across the periodic table. Below we give a brief general information about the physics of the HOPE code. The HOPE code is an ''average atom'' (AA) Dirac-Slater self-consistent code. The AA label in the case of finite temperature means that the one-electron levels are populated according to the Fermi statistics, at zero temperature it means that the ''aufbau'' principle works, i.e. no a priory electronic configuration is set, although it can be done. As such, it is a one-particle model (any Hartree-Fock model is a one particle model). The code is an ''ion-sphere'' model, meaning that the atom under investigation is neutral within the ion-sphere radius. Furthermore, the boundary conditions for the bound states are also set at the ion-sphere radius, which distinguishes the code from the INFERNO, OPAL and STA codes. Once the self-consistent AA state is obtained, the code proceeds to generate many-electron configurations and proceeds to calculate photoabsorption in the ''detailed configuration accounting'' (DCA) scheme. However, this last feature is meaningless at zero temperature. There is one important feature in the HOPE code which should be noted; any self-consistent model is self-consistent in the space of the occupied orbitals. The unoccupied orbitals, where electrons are lifted via photoexcitation, are unphysical. The rigorous way to deal with that problem is to carry out complete self-consistent calculations both in the initial and final states connecting photoexcitations, an enormous computational task

  11. Linewidth calculations and simulations

    CERN Document Server

    Strandberg, Ingrid


    We are currently developing a new technique to further enhance the sensitivity of collinear laser spectroscopy in order to study the most exotic nuclides available at radioactive ion beam facilities, such as ISOLDE at CERN. The overall goal is to evaluate the feasibility of the new method. This report will focus on the determination of the expected linewidth (hence resolution) of this approach. Different effects which could lead to a broadening of the linewidth, e.g. the ions' energy spread and their trajectories inside the trap, are studied with theoretical calculations as well as simulations.

  12. Acute calculous cholecystitis


    Angarita, Fernando A.; University Health Network; Acuña, Sergio A.; Mount Sinai Hospital; Jimenez, Carolina; University of Toronto; Garay, Javier; Pontificia Universidad Javeriana; Gömez, David; University of Toronto; Domínguez, Luis Carlos; Pontificia Universidad Javeriana


    Acute calculous cholecystitis is the most important cause of cholecystectomies worldwide. We review the physiopathology of the inflammatory process in this organ secondary to biliary tract obstruction, as well as its clinical manifestations, workup, and the treatment it requires. La colecistitis calculosa aguda es la causa más importante de colecistectomías en el mundo. En esta revisión de tema se resume la fisiopatología del proceso inflamatorio de la vesículabiliar secundaria a la obstru...

  13. Calculations in furnace technology

    CERN Document Server

    Davies, Clive; Hopkins, DW; Owen, WS


    Calculations in Furnace Technology presents the theoretical and practical aspects of furnace technology. This book provides information pertinent to the development, application, and efficiency of furnace technology. Organized into eight chapters, this book begins with an overview of the exothermic reactions that occur when carbon, hydrogen, and sulfur are burned to release the energy available in the fuel. This text then evaluates the efficiencies to measure the quantity of fuel used, of flue gases leaving the plant, of air entering, and the heat lost to the surroundings. Other chapters consi

  14. Full-electron ligand-to-ligand charge transfer in a compact Re(I) complex. (United States)

    Yue, Yuankai; Grusenmeyer, Tod; Ma, Zheng; Zhang, Peng; Schmehl, Russell H; Beratan, David N; Rubtsov, Igor V


    Ligand-to-ligand charge transfer (LLCT) states in transition metal complexes are often characterized by fractional electron transfer due to coupling of the LLCT state with many other states via the metal. We designed and characterized a compact Re(I) complex that displays essentially full-electron charge transfer in the LLCT excited state. The complex, [Re(DCEB)(CO)3(L)](+) (DCEB = 4,4'-dicarboxyethyl-2,2'-bipyridine), referred to as ReEBA, features two redox active ligands with strong electron accepting (DCEB) and electron donating (L is 3-dimethylaminobenzonitrile (3DMABN)) properties. The lowest energy excited state formed with a ca. 10 ps time constant and was characterized as the full-electron 3DMABN → DCEB LLCT state using time-resolved infrared spectroscopy (TRIR), transient absorption spectroscopy, and DFT computations. Analysis of a range of vibrational modes helped to assign the charge transfer characteristics of the complex. The LLCT state lifetime in ReEBA shows a strong dependence on the solvent polarity and features solvent dependent frequency shifts for several vibrational reporters. The formation of a full-electron LLCT state (∼92%) was enabled by tuning the redox properties of the electron accepting ligand (DCEB) and simultaneously decoupling the redox active group of the electron donating ligand (3DMABN) from the metal center. This strategy is generally applicable for designing compact transition metal complexes that have full-electron LLCT states.

  15. Separation of tryptophan enantiomers by ligand-exchange chromatography with novel chiral ionic liquids ligand. (United States)

    Qing, Haiqun; Jiang, Xinyu; Yu, Jingang


    Chiral ionic liquids (CILs) with amino acids as cations have been applied as novel chiral ligands coordinated with Cu(2+) to separate tryptophan enantiomers in ligand exchange chromatography. Four kinds of amino acid ionic liquids, including [L-Pro][CF3COO], [L-Pro][NO3], [L-Pro]2[SO4], and [L-Phe][CF3COO] were successfully synthesized and used for separation of tryptophan enantiomers. To optimize the separation conditions, [L-Pro][CF3COO] was selected as the model ligand. Some factors influencing the efficiency of chiral separation, such as copper ion concentration, CILs concentration, methanol ratio (methanol/H2O, v/v), and pH, were investigated. The obtained optimal separation conditions were as follows: 8.0 mmol/L Cu(OAc)2, 4.0 mmol/L [L-Pro][CF3COO], and 20% (v/v) methanol at pH 3.6. Under the optimum conditions, acceptable enantioseparation of tryptophan enantiomers could be observed with a resolution of 1.89. The results demonstrate the good applicability of CILs with amino acids as cations for chiral separation. Furthermore, a comparative study was also conducted for exploring the mechanism of the CILs as new ligands in ligand exchange chromatography. © 2014 Wiley Periodicals, Inc.

  16. Steric Maps to Evaluate the Role of Steric Hindrance on the IPr NHC Ligand

    KAUST Repository

    Poater, Albert


    Density functional theory (DFT) calculations were used to predict and rationalize the effect of the modification of the structure of the prototype 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene) (IPr) N-heterocyclic carbene (NHC) ligand. The modification consists in the substitution of the methyl groups of ortho isopropyl substituent with phenyl groups, and here we plan to describe how such significant changes effect the metal environment and therefore the related catalytic behaviour by simple steric maps. Bearing in mind that there is a significant structural difference between IPr and IPr* ligands, that translated in different reactivity for several olefin metathesis reactions, here by means of DFT we characterize where the NHC ligand plays a more active role and where it is a simple spectator, or at least its modification does not significantly change its catalytic role/performance. Furthermore, this communication endeavours to modify further the skeleton of the IPr NHC ligand. The optimization of these bulky new systems go to the limits of the DFT computational method.

  17. Binding capacity of ER-α ligands and SERMs: comparison of the human, dog and cat. (United States)

    Toniti, Waraphan; Suthiyotha, Nareuthorn; Puchadapirom, Pranom; Jenwitheesuk, Ekachai


    The estrogen molecule is the major risk factor related to mammary gland tumors, with estrogen receptor alpha (ER- α) as the important target stimulating growth. Therefore one alternative approach to treatment of breast cancer is to use selective estrogen receptor modulator (SERM), hormonal therapy. In this study, the structures of ER- α in humans, dogs and cats were predicted using the amino acid sequencing data bank and corrected for general protein structures, receptor sites and docking by adding 2,344 ligands with 15 SERMs into the database and calculating estimated inhibition constants (Ki). Thereby, ranking of best ligands of SERMs in humans, dogs and cats could be achieved. The results show that the shapes of ER- α differ between species but the major pocket sites are the same. Bazedoxifene, a new SERM proved to be the best estrogen antagonist and ER- α inhibitor in all species (human, dog, cat) with the lowest Ki. The other good ligands for dogs and cats are Neohesperidin, Dihydrochalcone, and Schreiber2. The differences in these protein structures may explain why there are only a few SERMs or other ligands which can be used as anti-cancer drugs.

  18. Dissolved and labile concentrations of Cd, Cu, Pb, and Zn in the South Fork Coeur d'Alene River, Idaho: Comparisons among chemical equilibrium models and implications for biotic ligand models (United States)

    Balistrieri, L.S.; Blank, R.G.


    In order to evaluate thermodynamic speciation calculations inherent in biotic ligand models, the speciation of dissolved Cd, Cu, Pb, and Zn in aquatic systems influenced by historical mining activities is examined using equilibrium computer models and the diffusive gradients in thin films (DGT) technique. Several metal/organic-matter complexation models, including WHAM VI, NICA-Donnan, and Stockholm Humic model (SHM), are used in combination with inorganic speciation models to calculate the thermodynamic speciation of dissolved metals and concentrations of metal associated with biotic ligands (e.g., fish gills). Maximum dynamic metal concentrations, determined from total dissolved metal concentrations and thermodynamic speciation calculations, are compared with labile metal concentrations measured by DGT to assess which metal/organic-matter complexation model best describes metal speciation and, thereby, biotic ligand speciation, in the studied systems. Results indicate that the choice of model that defines metal/organic-matter interactions does not affect calculated concentrations of Cd and Zn associated with biotic ligands for geochemical conditions in the study area, whereas concentrations of Cu and Pb associated with biotic ligands depend on whether the speciation calculations use WHAM VI, NICA-Donnan, or SHM. Agreement between labile metal concentrations and dynamic metal concentrations occurs when WHAM VI is used to calculate Cu speciation and SHM is used to calculate Pb speciation. Additional work in systems that contain wide ranges in concentrations of multiple metals should incorporate analytical speciation methods, such as DGT, to constrain the speciation component of biotic ligand models. ?? 2008 Elsevier Ltd.

  19. OECD Maximum Residue Limit Calculator (United States)

    With the goal of harmonizing the calculation of maximum residue limits (MRLs) across the Organisation for Economic Cooperation and Development, the OECD has developed an MRL Calculator. View the calculator.

  20. Yada: a novel tool for molecular docking calculations (United States)

    Piotto, S.; Di Biasi, L.; Fino, R.; Parisi, R.; Sessa, L.; Concilio, S.


    Molecular docking is a computational method employed to estimate the binding between a small ligand (the drug candidate) and a protein receptor that has become a standard part of workflow in drug discovery. Generally, when the binding site is known and a molecule is similar to known ligands, the most popular docking methods are rather accurate in the prediction of the geometry. Unfortunately, when the binding site is unknown, the blind docking analysis requires large computational resources and the results are often not accurate. Here we present Yada, a new tool for molecular docking that is capable to distribute efficiently calculations onto general purposes computer grid and that combines biological and structural information of the receptor. Yada is available for Windows and Linux and it is free to download at >

  1. Calculating Speed of Sound (United States)

    Bhatnagar, Shalabh


    Sound is an emerging source of renewable energy but it has some limitations. The main limitation is, the amount of energy that can be extracted from sound is very less and that is because of the velocity of the sound. The velocity of sound changes as per medium. If we could increase the velocity of the sound in a medium we would be probably able to extract more amount of energy from sound and will be able to transfer it at a higher rate. To increase the velocity of sound we should know the speed of sound. If we go by the theory of classic mechanics speed is the distance travelled by a particle divided by time whereas velocity is the displacement of particle divided by time. The speed of sound in dry air at 20 °C (68 °F) is considered to be 343.2 meters per second and it won't be wrong in saying that 342.2 meters is the velocity of sound not the speed as it's the displacement of the sound not the total distance sound wave covered. Sound travels in the form of mechanical wave, so while calculating the speed of sound the whole path of wave should be considered not just the distance traveled by sound. In this paper I would like to focus on calculating the actual speed of sound wave which can help us to extract more energy and make sound travel with faster velocity.

  2. Multilayer optical calculations

    CERN Document Server

    Byrnes, Steven J


    When light hits a multilayer planar stack, it is reflected, refracted, and absorbed in a way that can be derived from the Fresnel equations. The analysis is treated in many textbooks, and implemented in many software programs, but certain aspects of it are difficult to find explicitly and consistently worked out in the literature. Here, we derive the formulas underlying the transfer-matrix method of calculating the optical properties of these stacks, including oblique-angle incidence, absorption-vs-position profiles, and ellipsometry parameters. We discuss and explain some strange consequences of the formulas in the situation where the incident and/or final (semi-infinite) medium are absorptive, such as calculating $T>1$ in the absence of gain. We also discuss some implementation details like complex-plane branch cuts. Finally, we derive modified formulas for including one or more "incoherent" layers, i.e. very thick layers in which interference can be neglected. This document was written in conjunction with ...

  3. Stability Constants of Mixed Ligand Complexes of Transition Metal(II Ions with Salicylidene-4-methoxyaniline as Primary Ligand and 5-Bromosalicylidene-4-nitroaniline as Secondary Ligand

    Directory of Open Access Journals (Sweden)

    N. G. Nadkarni


    Full Text Available Binary and ternary complexes of the type M-Y and M-X-Y [M = Mn(II, Ni(II, Cu(II and Zn(II; X = salicylidene-4-methoxyaniline and Y=5-bromosalicylidene-4-nitroaniline] have been examined pH-metrically at 27±0.5 °C and at constant ionic strength, μ= 0.1 M (KCl in 75 : 25(v/v 1,4-dioxne-water medium. The stability constants for binary (M-Y and ternary (M-X-Y systems were calculated. The relative stability (Δ log KT values of the ternary complexes with corresponding binary complexes for all the metal(II ions in the present study found to be negative indicating that ternary 1:1:1 (M-X-Y complexes are less stable than binary 1:1 (M-Y complexes. In the ternary system studied, the order of stability constants of mixed ligand complexes with respect to the metal ions was found to be Cu(II > NI(II > Mn(II > Zn(II; which is same as in the corresponding binary (M-Y systems.

  4. Ligand-specific conformational changes in the alpha1 glycine receptor ligand-binding domain

    DEFF Research Database (Denmark)

    Pless, Stephan Alexander; Lynch, Joseph W


    indicate that channel opening is accompanied by conformational rearrangements in both beta-sheets. In an attempt to resolve ligand-dependent movements in the ligand-binding domain, we employed voltage-clamp fluorometry on alpha1 glycine receptors to compare changes mediated by the agonist, glycine......, and by the antagonist, strychnine. Voltage-clamp fluorometry involves labeling introduced cysteines with environmentally sensitive fluorophores and inferring structural rearrangements from ligand-induced fluorescence changes. In the inner beta-sheet, we labeled residues in loop 2 and in binding domain loops D and E....... At each position, strychnine and glycine induced distinct maximal fluorescence responses. The pre-M1 domain responded similarly; at each of four labeled positions glycine produced a strong fluorescence signal, whereas strychnine did not. This suggests that glycine induces conformational changes...

  5. Interaction of calreticulin with CD40 ligand, TRAIL and Fas ligand

    DEFF Research Database (Denmark)

    Duus, K; Pagh, R T; Holmskov, U;


    found to bind calreticulin strongly. A low level or no binding was observed for adiponectin, tumour necrosis factor-alpha (TNF-alpha), CD30L, surfactant protein-A and -D and collagen VIII. The interaction with calreticulin required a conformational change in CD40L, TRAIL and FasL and showed the same...... is utilized by many other functionally diverse molecules and in this work the interaction of calreticulin with C1q and structurally similar molecules was investigated. In addition to C1q and MBL, CD40 ligand (CD40L), tumour necrosis factor-related apoptosis-inducing ligand (TRAIL) and Fas ligand (FasL) were...... characteristics as calreticulin's interaction with C1q and MBL: a time-dependent saturable binding to immobilized protein, which was initially sensitive to salt but gradually developed into a salt-insensitive interaction. Thus, the interaction requires a structural change in the interaction partner and leads...

  6. Molecular Dynamics Calculations (United States)


    The development of thermodynamics and statistical mechanics is very important in the history of physics, and it underlines the difficulty in dealing with systems involving many bodies, even if those bodies are identical. Macroscopic systems of atoms typically contain so many particles that it would be virtually impossible to follow the behavior of all of the particles involved. Therefore, the behavior of a complete system can only be described or predicted in statistical ways. Under a grant to the NASA Lewis Research Center, scientists at the Case Western Reserve University have been examining the use of modern computing techniques that may be able to investigate and find the behavior of complete systems that have a large number of particles by tracking each particle individually. This is the study of molecular dynamics. In contrast to Monte Carlo techniques, which incorporate uncertainty from the outset, molecular dynamics calculations are fully deterministic. Although it is still impossible to track, even on high-speed computers, each particle in a system of a trillion trillion particles, it has been found that such systems can be well simulated by calculating the trajectories of a few thousand particles. Modern computers and efficient computing strategies have been used to calculate the behavior of a few physical systems and are now being employed to study important problems such as supersonic flows in the laboratory and in space. In particular, an animated video (available in mpeg format--4.4 MB) was produced by Dr. M.J. Woo, now a National Research Council fellow at Lewis, and the G-VIS laboratory at Lewis. This video shows the behavior of supersonic shocks produced by pistons in enclosed cylinders by following exactly the behavior of thousands of particles. The major assumptions made were that the particles involved were hard spheres and that all collisions with the walls and with other particles were fully elastic. The animated video was voted one of two

  7. Evaluation of small ligand-protein interaction by ligation reaction with DNA-modified ligand. (United States)

    Sugita, Rie; Mie, Masayasu; Funabashi, Hisakage; Kobatake, Eiry


    A method for the evaluation of interactions between protein and ligand using DNA-modified ligands, including signal enhancement of the DNA ligation reactions, is described. For proof of principle, a DNA probe modified by biotin was used. Two DNA probes were prepared with complementary sticky-ends. While one DNA probe was modified at the 5'-end of the sticky-end, the other was not modified. The probes could be ligated together by T4 DNA ligase along the strand without biotin modification. However, in the presence of streptavidin or anti-biotin Fab, the ligation reaction joining the two probes could not occur on either strand.

  8. Impact cratering calculations (United States)

    Ahrens, Thomas J.; Okeefe, J. D.; Smither, C.; Takata, T.


    In the course of carrying out finite difference calculations, it was discovered that for large craters, a previously unrecognized type of crater (diameter) growth occurred which was called lip wave propagation. This type of growth is illustrated for an impact of a 1000 km (2a) silicate bolide at 12 km/sec (U) onto a silicate half-space at earth gravity (1 g). The von Misses crustal strength is 2.4 kbar. The motion at the crater lip associated with this wave type phenomena is up, outward, and then down, similar to the particle motion of a surface wave. It is shown that the crater diameter has grown d/a of approximately 25 to d/a of approximately 4 via lip propagation from Ut/a = 5.56 to 17.0 during the time when rebound occurs. A new code is being used to study partitioning of energy and momentum and cratering efficiency with self gravity for finite-sized objects rather than the previously discussed planetary half-space problems. These are important and fundamental subjects which can be addressed with smoothed particle hydrodynamic (SPH) codes. The SPH method was used to model various problems in astrophysics and planetary physics. The initial work demonstrates that the energy budget for normal and oblique impacts are distinctly different than earlier calculations for silicate projectile impact on a silicate half space. Motivated by the first striking radar images of Venus obtained by Magellan, the effect of the atmosphere on impact cratering was studied. In order the further quantify the processes of meteor break-up and trajectory scattering upon break-up, the reentry physics of meteors striking Venus' atmosphere versus that of the Earth were studied.

  9. Charting the mechanism and reactivity of zirconium oxalate with hydroxamate ligands using density functional theory: implications in new chelate design. (United States)

    Holland, Jason P; Vasdev, Neil


    The reaction of [(89)Zr(C2O4)4](4-) with the tris-hydroxamate ligand desferrioxamine B (DFO) provides the basis of radiolabelling biological vectors such as antibodies and proteins with the radionuclide (89)Zr for positron emission tomography imaging. In this work, density functional theory methods were used to investigate the mechanism of reaction from [Zr(C2O4)4](4-) to Zr(MeAHA)4 by ligand substitution with N-methyl acetohydroxamate (MeAHA). Calculations were performed under simulated basic and acidic conditions. Ligand substitution under basic conditions was found to be thermodynamically feasible with an overall calculated change in solvation free energy, ΔGsol = -97 kJ mol(-1) using the B3LYP/DGDZVP methodology and a water continuum solvation model. In contrast, an acid-mediated mechanism of ligand substitution was found to be thermodynamically non-feasible. Molecular orbital analysis provides a rationale for the difference in thermodynamic stability between [Zr(C2O4)4](4-) and Zr(MeAHA)4. Overall, the DFT calculations are consistent with observed experimental (89)Zr-radiolabelling reactions and suggest that computational methods may prove useful in designing novel chelates for increasing the thermodynamic and kinetic stability of (89)Zr-complexes in vivo.

  10. Landscape of protein-small ligand binding modes. (United States)

    Kasahara, Kota; Kinoshita, Kengo


    Elucidating the mechanisms of specific small-molecule (ligand) recognition by proteins is a long-standing conundrum. While the structures of these molecules, proteins and ligands, have been extensively studied, protein-ligand interactions, or binding modes, have not been comprehensively analyzed. Although methods for assessing similarities of binding site structures have been extensively developed, the methods for the computational treatment of binding modes have not been well established. Here, we developed a computational method for encoding the information about binding modes as graphs, and assessing their similarities. An all-against-all comparison of 20,040 protein-ligand complexes provided the landscape of the protein-ligand binding modes and its relationships with protein- and chemical spaces. While similar proteins in the same SCOP Family tend to bind relatively similar ligands with similar binding modes, the correlation between ligand and binding similarities was not very high (R(2)  = 0.443). We found many pairs with novel relationships, in which two evolutionally distant proteins recognize dissimilar ligands by similar binding modes (757,474 pairs out of 200,790,780 pairs were categorized into this relationship, in our dataset). In addition, there were an abundance of pairs of homologous proteins binding to similar ligands with different binding modes (68,217 pairs). Our results showed that many interesting relationships between protein-ligand complexes are still hidden in the structure database, and our new method for assessing binding mode similarities is effective to find them.

  11. Thermal, spectroscopic, and solvent influence studies on mixed-ligand copper(II) complexes containing the bulky ligand: Bis[ N-( p-tolyl)imino]acenaphthene (United States)

    El-Ayaan, Usama; Gabr, I. M.


    Four mixed-ligand copper(II) complexes containing the rigid bidentate nitrogen ligand bis[ N-( p-tolyl)imino]acenaphthene (abb. p-Tol-BIAN) ligand are reported. These complexes, namely [Cu( p-Tol-BIAN) 2](ClO 4) 21, [Cu( p-Tol-BIAN)(acac)](ClO 4) 2, [Cu( p-Tol-BIAN)Cl 2] 3 and [Cu( p-Tol-BIAN)(AcOH) 2](ClO 4) 24 (where acac, acetylacetonate and AcOH, acetic acid) have been prepared and characterized by elemental analysis, spectroscopic, magnetic and molar conductance measurements. ESR spectra suggest a square planar geometry for complexes 1 and 2. In complexes 3 and 4, a distorted tetrahedral arrangement around copper(II) centre was suggested. Solvatochromic behavior of all studied complexes indicates strong solvatochromism of their solutions. The observed solvatochromism is mainly due to the solute-solvent interaction between the chelate cation and the solvent molecules. Thermal properties and decomposition kinetics of all complexes are investigated. The kinetic parameters ( E, A, Δ H, Δ S and Δ G) of all thermal decomposition stages have been calculated using the Coats-Redfern and other standard equations.

  12. Integrin receptors and ligand-gated channels. (United States)

    Morini, Raffaella; Becchetti, Andrea


    Plastic expression of different integrin subunits controls the different stages of neural development, whereas in the adult integrins regulate synaptic stability. Evidence of integrin-channel crosstalk exists for ionotropic glutamate receptors. As is often the case in other tissues, integrin engagement regulates channel activity through complex signaling pathways that often include tyrosine phosphorylation cascades. The specific pathways recruited by integrin activation depend on cerebral region and cell type. In turn, ion channels control integrin expression onto the plasma membrane and their ligand binding affinity. The most extensive studies concern the hippocampus and suggest implications for neuronal circuit plasticity. The physiological relevance of these findings depends on whether adhesion molecules, aside from determining tissue stability, contribute to synaptogenesis and the responsiveness of mature synapses, thus contributing to long-term circuit consolidation. Little evidence is available for other ligand-gated channels, with the exception of nicotinic receptors. These exert a variety of functions in neurons and non neural tissue, both in development and in the adult, by regulating cell cycle, synaptogenesis and synaptic circuit refinement. Detailed studies in epidermal keratinocytes have shed some light on the possible mechanisms through which ACh can regulate cell motility, which may be of general relevance for morphogenetic processes. As to the control of mature synapses, most results concern the integrinic control of nicotinic receptors in the neuromuscular junction. Following this lead, a few studies have addressed similar topics in adult cerebral synapses. However, pursuing and interpreting these results in the brain is especially difficult because of the complexity of the nicotinic roles and the widespread contribution of nonsynaptic, paracrine transmission. From a pathological point of view, considering the well-known contribution of both

  13. Polydentate cyclotriphosphazene ligands: Design, synthesis and bioactivity

    Institute of Scientific and Technical Information of China (English)

    Le Wang; Yong Ye; Shang Bin Zhong; Yu Fen Zhao


    Five multinuelear cyclotriphosphazene ligands were synthesized and tested for their cleavage activities to plasmid DNA. All of these new compounds were confirmed by MS, 1H NMR, 31p NMR, 13C NMR and IR. Preliminary studies on the cleavage of pUC19 DNA in the presence of metal complexes were performed. The results revealed that these complexes could act as powerful catalysts under physiological conditions. The complexes 3b + Cu can effectively cleave DNA to nicked form, giving hydrolysis rate constant of 0.08/h under physiological conditions. An acid-base catalyzed DNA phosphate-diester hydrolysis mechanism was also proposed.

  14. Thermal melting studies of ligand DNA interactions. (United States)

    Guédin, Aurore; Lacroix, Laurent; Mergny, Jean-Louis


    A simple thermal melting experiment may be used to demonstrate the stabilization of a given structure by a ligand (usually a small molecule, sometimes a peptide). Preparation of the sample is straightforward, and the experiment itself requires an inexpensive apparatus. Furthermore, reasonably low amounts of sample are required. A qualitative analysis of the data is simple: An increase in the melting temperature (T(m)) indicates preferential binding to the folded form as compared to the unfolded form. However, it is perilous to derive an affinity constant from an increase in T(m) as other factors play a role.

  15. Computer-aided design of GPCR ligands. (United States)

    Gutiérrez-de-Terán, Hugo; Keränen, Henrik; Azuaje, Jhonny; Rodríguez, David; Åqvist, Johan; Sotelo, Eddy


    The recent availability of several GPCR crystal structures now contributes decisively to the perspective of structure-based ligand design. In this context, computational approaches are extremely helpful, particularly if properly integrated in drug design projects with cooperation between computational and medicinal chemistry teams. Here, we present the pipelines used in one such project, devoted to the design of novel potent and selective antagonists for the different adenosine receptors. The details of the computational strategies are described, and particular attention is given to explain how these procedures can effectively guide the synthesis of novel chemical entities.

  16. A strategy of designing the ligand of antibody affinity chromatography based on molecular dynamics simulation. (United States)

    Dai, Lu; Li, Weikang; Sun, Fei; Li, Baizhi; Li, Hongrui; Zhang, Hongxing; Zheng, Qingchuan; Liang, Chongyang


    Designing affinity ligands has always been the development focus of affinity chromatography. Previous antibody affinity ligand designs were mostly based on the crystal structure of protein A (UniProt code number: P38507), and the antibody-binding domains were modified according to the properties of amino acid residues. Currently, more effective bioinformatic prediction and experimental validation has been used to improve the design of antibody affinity ligands. In the present study, the complex crystal structure (the domain D of protein A and the Fab segment of IgM, PDB code: 1DEE) was used as the model. The vital site that inhibits the binding between domain D and IgM was estimated by means of molecular dynamics (MD) simulation, then MM-GBSA calculations were used to design a mutant of domain D (K46E) for improving affinity on the above vital site. The binding analysis using Biacore showed the association and dissociation parameters of K46E mutant that were optimized with IgM. The affinity increase of K46E mutant preferred for IgM, the affinity order is K46E tetramer (KD=6.02×10(-9)M)>K46E mutant (KD=6.66×10(-8)M)>domain D (KD=2.17×10(-7)M). Similar results were obtained when the optimized ligands were immobilized to the chromatography medium. A complete designing strategy was validated in this study, which will provide a novel insight into designing new ligands of antibody affinity chromatography media.

  17. Consistent two-dimensional visualization of protein-ligand complex series

    Directory of Open Access Journals (Sweden)

    Stierand Katrin


    Full Text Available Abstract Background The comparative two-dimensional graphical representation of protein-ligand complex series featuring different ligands bound to the same active site offers a quick insight in their binding mode differences. In comparison to arbitrary orientations of the residue molecules in the individual complex depictions a consistent placement improves the legibility and comparability within the series. The automatic generation of such consistent layouts offers the possibility to apply it to large data sets originating from computer-aided drug design methods. Results We developed a new approach, which automatically generates a consistent layout of interacting residues for a given series of complexes. Based on the structural three-dimensional input information, a global two-dimensional layout for all residues of the complex ensemble is computed. The algorithm incorporates the three-dimensional adjacencies of the active site residues in order to find an universally valid circular arrangement of the residues around the ligand. Subsequent to a two-dimensional ligand superimposition step, a global placement for each residue is derived from the set of already placed ligands. The method generates high-quality layouts, showing mostly overlap-free solutions with molecules which are displayed as structure diagrams providing interaction information in atomic detail. Application examples document an improved legibility compared to series of diagrams whose layouts are calculated independently from each other. Conclusions The presented method extends the field of complex series visualizations. A series of molecules binding to the same protein active site is drawn in a graphically consistent way. Compared to existing approaches these drawings substantially simplify the visual analysis of large compound series.

  18. Comparison of ligand- and structure-based virtual screening on the DUD data set. (United States)

    von Korff, Modest; Freyss, Joel; Sander, Thomas


    Several in-house developed descriptors and our in-house docking tool ActDock were compared with virtual screening on the data set of useful decoys (DUD). The results were compared with the chemical fingerprint descriptor from ChemAxon and with the docking results of the original DUD publication. The DUD is the first published data set providing active molecules, decoys, and references for crystal structures of ligand-target complexes. The DUD was designed for the purpose of evaluating docking programs. It contains 2950 active compounds against a total of 40 target proteins. Furthermore, for every ligand the data set contains 36 structurally dissimilar decoy compounds with similar physicochemical properties. We extracted the ligands from the target proteins to extend the applicability of the data set to include ligand based virtual screening. From the 40 target proteins, 37 contained ligands that we used as query molecules for virtual screening evaluation. With this data set a large comparison was done between four different chemical fingerprints, a topological pharmacophore descriptor, the Flexophore descriptor, and ActDock. The Actelion docking tool relies on a MM2 forcefield and a pharmacophore point interaction statistic for scoring; the details are described in this publication. In terms of enrichment rates the chemical fingerprint descriptors performed better than the Flexophore and the docking tool. After removing molecules chemically similar to the query molecules the Flexophore descriptor outperformed the chemical descriptors and the topological pharmacophore descriptors. With the similarity matrix calculations used in this study it was shown that the Flexophore is well suited to find new chemical entities via "scaffold hopping". The Flexophore descriptor can be explored with a Java applet at in the submenu Tools-->Flexophore. Its usage is free of charge and does not require registration.

  19. Estimating the acidity of transition metal hydride and dihydrogen complexes by adding ligand acidity constants. (United States)

    Morris, Robert H


    A simple equation (pKa(THF) = ∑AL + Ccharge + Cnd + Cd6) can be used to obtain an estimate of the pKa of diamagnetic transition metal hydride and dihydrogen complexes in tetrahydrofuran, and, by use of conversion equations, in other solvents. It involves adding acidity constants AL for each of the ligands in the 5-, 6-, 7-, or 8-coordinate conjugate base complex of the hydride or dihydrogen complex along with a correction for the charge (Ccharge = -15, 0 or 30 for x = +1, 0 or -1 charge, respectively) and the periodic row of the transition metal (Cnd = 0 for 3d or 4d metal, 2 for 5d metal) as well as a correction for d(6) octahedral acids (Cd6 = 6 for d(6) metal ion in the acid, 0 for others) that are not dihydrogen complexes. Constants AL are provided for 13 commonly occurring ligand types; of these, nine neutral ligands are correlated with Lever's electrochemical ligand parameters EL. This method gives good estimates of the over 170 literature pKa values that range from less than zero to 50 with a standard deviation of 3 pKa units for complexes of the metals chromium to nickel, molybdenum, ruthenium to palladium, and tungsten to platinum in the periodic table. This approach allows a quick assessment of the acidity of hydride complexes found in nature (e.g., hydrogenases) and in industry (e.g., catalysis and hydrogen energy applications). The pKa values calculated for acids that have bulky or large bite angle chelating ligands deviate the most from this correlation. The method also provides an estimate of the base strength of the deprotonated form of the complex.

  20. MBPT calculations with ABINIT (United States)

    Giantomassi, Matteo; Huhs, Georg; Waroquiers, David; Gonze, Xavier


    Many-Body Perturbation Theory (MBPT) defines a rigorous framework for the description of excited-state properties based on the Green's function formalism. Within MBPT, one can calculate charged excitations using e.g. Hedin's GW approximation for the electron self-energy. In the same framework, neutral excitations are also well described through the solution of the Bethe-Salpeter equation (BSE). In this talk, we report on the recent developments concerning the parallelization of the MBPT algorithms available in the ABINIT code ( In particular, we discuss how to improve the parallel efficiency thanks to a hybrid version that employs MPI for the coarse-grained parallelization and OpenMP (a de facto standard for parallel programming on shared memory architectures) for the fine-grained parallelization of the most CPU-intensive parts. Benchmark results obtained with the new implementation are discussed. Finally, we present results for the GW corrections of amorphous SiO2 in the presence of defects and the BSE absorption spectrum. This work has been supported by the Prace project (PaRtnership for Advanced Computing in Europe,

  1. The autoxidation activity of new mixed-ligand manganese and iron complexes with tripodal ligands

    NARCIS (Netherlands)

    van Gorkum, R.; Berding, J.; Tooke, D.M.; Spek, A.L.; Reedijk, J.; Bouwman, E.


    The activity of new manganese and iron complexes of dianionic tripodal ligands in the autoxidation of ethyl linoleate (EL) is reported. EL consumption rates were monitored using time-resolved FTIR and the degree of oligomerisation was determined by SEC. Almost all complexes showed the same trend in

  2. Ligand binding by the tandem glycine riboswitch depends on aptamer dimerization but not double ligand occupancy. (United States)

    Ruff, Karen M; Strobel, Scott A


    The glycine riboswitch predominantly exists as a tandem structure, with two adjacent, homologous ligand-binding domains (aptamers), followed by a single expression platform. The recent identification of a leader helix, the inclusion of which eliminates cooperativity between the aptamers, has reopened the debate over the purpose of the tandem structure of the glycine riboswitch. An equilibrium dialysis-based assay was combined with binding-site mutations to monitor glycine binding in each ligand-binding site independently to understand the role of each aptamer in glycine binding and riboswitch tertiary interactions. A series of mutations disrupting the dimer interface was used to probe how dimerization impacts ligand binding by the tandem glycine riboswitch. While the wild-type tandem riboswitch binds two glycine equivalents, one for each aptamer, both individual aptamers are capable of binding glycine when the other aptamer is unoccupied. Intriguingly, glycine binding by aptamer-1 is more sensitive to dimerization than glycine binding by aptamer-2 in the context of the tandem riboswitch. However, monomeric aptamer-2 shows dramatically weakened glycine-binding affinity. In addition, dimerization of the two aptamers in trans is dependent on glycine binding in at least one aptamer. We propose a revised model for tandem riboswitch function that is consistent with these results, wherein ligand binding in aptamer-1 is linked to aptamer dimerization and stabilizes the P1 stem of aptamer-2, which controls the expression platform.

  3. LASSO-ligand activity by surface similarity order: a new tool for ligand based virtual screening. (United States)

    Reid, Darryl; Sadjad, Bashir S; Zsoldos, Zsolt; Simon, Aniko


    Virtual Ligand Screening (VLS) has become an integral part of the drug discovery process for many pharmaceutical companies. Ligand similarity searches provide a very powerful method of screening large databases of ligands to identify possible hits. If these hits belong to new chemotypes the method is deemed even more successful. eHiTS LASSO uses a new interacting surface point types (ISPT) molecular descriptor that is generated from the 3D structure of the ligand, but unlike most 3D descriptors it is conformation independent. Combined with a neural network machine learning technique, LASSO screens molecular databases at an ultra fast speed of 1 million structures in under 1 min on a standard PC. The results obtained from eHiTS LASSO trained on relatively small training sets of just 2, 4 or 8 actives are presented using the diverse directory of useful decoys (DUD) dataset. It is shown that over a wide range of receptor families, eHiTS LASSO is consistently able to enrich screened databases and provides scaffold hopping ability.

  4. Exploring the Hydrolytic Behavior of the Platinum(IV) Complexes with Axial Acetato Ligands. (United States)

    Zhao, Jian; Xu, Zichen; Lin, Jing; Gou, Shaohua


    Platinum(IV) complexes are generally thought to be kinetically inert, and are expected to be stable enough to resist premature aquation before entering the cancer cells. Nevertheless, in this work, complex 2 with axial acetato ligands can hydrolyze relatively quickly under biologically relevant conditions with a half-life of 91.7 min, resulting in the loss of the equatorial chlorido ligand. Further study indicated that the fast hydrolysis of complex 2 may be attributed to the strong σ-donor ability of N-isopropyl-1R,2R-diaminocyclohexane, and an increasing σ-donor ability of the amine group can promote the hydrolysis rate of the corresponding platinum(IV) complex. The experiment results were proven by the corresponding DFT calculation. Our study can help to re-evaluate the aqueous properties of the platinum(IV) complexes with axial acetate, which may be less inert to hydrolysis than expected under biologically relevant conditions.

  5. A Novel Cobalt(Ⅲ) Complex with Macrocyclic Triamine Ligand for High Capacity Hydrogen Adsorption

    Institute of Scientific and Technical Information of China (English)

    ZHU Hai-Yan; GUO Hui; LI Sai


    The coordination complex of Co(Ⅲ) based on a macrocyclic triamine ligand 1,4-diacetate-1,4,7-triazacyclodecane (L) has been synthesized and characterized. The metal cation is bonded with three nitrogen atoms and two oxygen atoms of L and one chloride ion to form a distorted octahedral geometry. This complex coordinated with macrocyclic ligand possesses large pore volume that will be contributed to observe high H2 adsorption. With respect to the first-principles electronic structure calculations, the feasibility to store hydrogen in the complex is explored. Indeed, the complex has shown a very high total H2 adsorption of 7.2 wt% (wt% = (weight of adsorbed H2)/(weight of host material)), with a binding energy of 0.03 eV/H2

  6. Importance of Many-Body Effects in the Kernel of Hemoglobin for Ligand Binding (United States)

    Weber, Cédric; O'Regan, David D.; Hine, Nicholas D. M.; Littlewood, Peter B.; Kotliar, Gabriel; Payne, Mike C.


    We propose a mechanism for binding of diatomic ligands to heme based on a dynamical orbital selection process. This scenario may be described as bonding determined by local valence fluctuations. We support this model using linear-scaling first-principles calculations, in combination with dynamical mean-field theory, applied to heme, the kernel of the hemoglobin metalloprotein central to human respiration. We find that variations in Hund’s exchange coupling induce a reduction of the iron 3d density, with a concomitant increase of valence fluctuations. We discuss the comparison between our computed optical absorption spectra and experimental data, our picture accounting for the observation of optical transitions in the infrared regime, and how the Hund’s coupling reduces, by a factor of 5, the strong imbalance in the binding energies of heme with CO and O2 ligands.

  7. Increased accuracy of ligand sensing by receptor internalization

    CERN Document Server

    Aquino, Gerardo


    Many types of cells can sense external ligand concentrations with cell-surface receptors at extremely high accuracy. Interestingly, ligand-bound receptors are often internalized, a process also known as receptor-mediated endocytosis. While internalization is involved in a vast number of important functions for the life of a cell, it was recently also suggested to increase the accuracy of sensing ligand as the overcounting of the same ligand molecules is reduced. Here we show, by extending simple ligand-receptor models to out-of-equilibrium thermodynamics, that internalization increases the accuracy with which cells can measure ligand concentrations in the external environment. Comparison with experimental rates of real receptors demonstrates that our model has indeed biological significance.

  8. Ligands of Therapeutic Utility for the Liver X Receptors

    Directory of Open Access Journals (Sweden)

    Rajesh Komati


    Full Text Available Liver X receptors (LXRs have been increasingly recognized as a potential therapeutic target to treat pathological conditions ranging from vascular and metabolic diseases, neurological degeneration, to cancers that are driven by lipid metabolism. Amidst intensifying efforts to discover ligands that act through LXRs to achieve the sought-after pharmacological outcomes, several lead compounds are already being tested in clinical trials for a variety of disease interventions. While more potent and selective LXR ligands continue to emerge from screening of small molecule libraries, rational design, and empirical medicinal chemistry approaches, challenges remain in minimizing undesirable effects of LXR activation on lipid metabolism. This review provides a summary of known endogenous, naturally occurring, and synthetic ligands. The review also offers considerations from a molecular modeling perspective with which to design more specific LXRβ ligands based on the interaction energies of ligands and the important amino acid residues in the LXRβ ligand binding domain.

  9. Remarkable catalytic activity of dinitrogen-bridged dimolybdenum complexes bearing NHC-based PCP-pincer ligands toward nitrogen fixation (United States)

    Eizawa, Aya; Arashiba, Kazuya; Tanaka, Hiromasa; Kuriyama, Shogo; Matsuo, Yuki; Nakajima, Kazunari; Yoshizawa, Kazunari; Nishibayashi, Yoshiaki


    Intensive efforts for the transformation of dinitrogen using transition metal-dinitrogen complexes as catalysts under mild reaction conditions have been made. However, limited systems have succeeded in the catalytic formation of ammonia. Here we show that newly designed and prepared dinitrogen-bridged dimolybdenum complexes bearing N-heterocyclic carbene- and phosphine-based PCP-pincer ligands [{Mo(N2)2(PCP)}2(μ-N2)] (1) work as so far the most effective catalysts towards the formation of ammonia from dinitrogen under ambient reaction conditions, where up to 230 equiv. of ammonia are produced based on the catalyst. DFT calculations on 1 reveal that the PCP-pincer ligand serves as not only a strong σ-donor but also a π-acceptor. These electronic properties are responsible for a solid connection between the molybdenum centre and the pincer ligand, leading to the enhanced catalytic activity for nitrogen fixation.

  10. Determining PPARγ-ligand binding affinity using fluorescent assay with cis-parinaric acid as a probe

    Institute of Scientific and Technical Information of China (English)

    GAO Zhenting; LUO Haibin; CHEN Lili; SHEN Jianhua; CHEN Kaixian; JIANG Hualiang; SHEN Xu


    Upon the study of small-molecules binding to proteins, the traditional methods for calculating dissociation constants (Kd and Ki) have shortcomings in dealing with the single binding site models. In this paper, two equations have been derived to solve this problem. These two equations are independent of the total concentration or initial degree of saturation of receptor and the activity of the competitive molecule. Through nonlinear fitting against these two equations, Kd value of a probe can be obtained by binding assay, and Ki value of a ligand can be obtained by competitive assay. Moreover, only the total concentrations of receptor([R]t), ligand([L]t) and probe([P]t) are required for the data fitting. In this work, Ki values of some typical ligands of PPARγ were successfully determined by use of our equations, among which the Ki value of PPARγ-LY171883 was reported for the first time.

  11. Singular Value Decomposition and Ligand Binding Analysis

    Directory of Open Access Journals (Sweden)

    André Luiz Galo


    Full Text Available Singular values decomposition (SVD is one of the most important computations in linear algebra because of its vast application for data analysis. It is particularly useful for resolving problems involving least-squares minimization, the determination of matrix rank, and the solution of certain problems involving Euclidean norms. Such problems arise in the spectral analysis of ligand binding to macromolecule. Here, we present a spectral data analysis method using SVD (SVD analysis and nonlinear fitting to determine the binding characteristics of intercalating drugs to DNA. This methodology reduces noise and identifies distinct spectral species similar to traditional principal component analysis as well as fitting nonlinear binding parameters. We applied SVD analysis to investigate the interaction of actinomycin D and daunomycin with native DNA. This methodology does not require prior knowledge of ligand molar extinction coefficients (free and bound, which potentially limits binding analysis. Data are acquired simply by reconstructing the experimental data and by adjusting the product of deconvoluted matrices and the matrix of model coefficients determined by the Scatchard and McGee and von Hippel equation.

  12. Do organic ligands affect calcite dissolution rates? (United States)

    Oelkers, Eric H.; Golubev, Sergey V.; Pokrovsky, Oleg S.; Bénézeth, Pascale


    Steady state Iceland-spar calcite dissolution rates were measured at 25 °C in aqueous solutions containing 0.1 M NaCl and up to 0.05 M dissolved bicarbonate at pH from 7.9 to 9.1 in the presence of 13 distinct dissolved organic ligands in mixed-flow reactors. The organic ligands considered in this study include those most likely to be present in either (1) aquifers at the conditions pertinent to CO 2 sequestration or (2) soil/early diagenetic environments: acetate, phthalate, citrate, EDTA 4-, succinate, D-glucosaminate, L-glutamate, D-gluconate, 2,4-dihydroxybenzoate, 3,4-dihydroxybenzoate, fumarate, malonate, and gallate. Results show that the presence of extract, humic acid, pectin, and gum xanthan. In no case did the presence of <100 ppm of these organics change calcite dissolution rates by more than a factor of 2.5. Results obtained in this study suggest that the presence of aqueous organic anions negligibly affects calcite forward dissolution rates in most natural environments. Some effect on calcite reactivity may be observed, however, by the presence of organic anions if they change substantially the chemical affinity of the fluid with respect to calcite.

  13. Continuous microfluidic assortment of interactive ligands (CMAIL) (United States)

    Hsiao, Yi-Hsing; Huang, Chao-Yang; Hu, Chih-Yung; Wu, Yen-Yu; Wu, Chung-Hsiun; Hsu, Chia-Hsien; Chen, Chihchen


    Finding an interactive ligand-receptor pair is crucial to many applications, including the development of monoclonal antibodies. Biopanning, a commonly used technique for affinity screening, involves a series of washing steps and is lengthy and tedious. Here we present an approach termed continuous microfluidic assortment of interactive ligands, or CMAIL, for the screening and sorting of antigen-binding single-chain variable antibody fragments (scFv) displayed on bacteriophages (phages). Phages carrying native negative charges on their coat proteins were electrophoresed through a hydrogel matrix functionalized with target antigens under two alternating orthogonal electric fields. During the weak horizontal electric field phase, phages were differentially swept laterally depending on their affinity for the antigen, and all phages were electrophoresed down to be collected during the strong vertical electric field phase. Phages of different affinity were spatially separated, allowing the continuous operation. More than 105 CFU (colony forming unit) antigen-interacting phages were isolated with ~100% specificity from a phage library containing 3 × 109 individual members within 40 minutes of sorting using CMAIL. CMAIL is rapid, sensitive, specific, and does not employ washing, elution or magnetic beads. In conclusion, we have developed an efficient and cost-effective method for isolating and sorting affinity reagents involving phage display.

  14. Hydrothermal reactions: From the synthesis of ligand to new lanthanide 3D-coordination polymers

    Energy Technology Data Exchange (ETDEWEB)

    Silva, Fausthon Fred da; Fernandes de Oliveira, Carlos Alberto; Lago Falcão, Eduardo Henrique [Laboratório de Terras Raras, Departamento de Química Fundamental, Universidade Federal de Pernambuco (DQF-UFPE), 50590-470 Recife, PE (Brazil); Gatto, Claudia Cristina [Laboratório de Síntese Inorgânica e Cristalografia, Instituto de Química, Universidade de Brasília (IQ-UnB), 70904-970 Brasilia, DF (Brazil); Bezerra da Costa, Nivan; Oliveira Freire, Ricardo [Pople Computational Chemistry Laboratory, Departamento de Química, Universidade Federal de Sergipe, São Cristóvão-SE 49100-000 (Brazil); Chojnacki, Jarosław [Department of Inorganic Chemistry, Gdansk University of Technology, 80-233 Gdansk (Poland); Alves Júnior, Severino, E-mail: [Laboratório de Terras Raras, Departamento de Química Fundamental, Universidade Federal de Pernambuco (DQF-UFPE), 50590-470 Recife, PE (Brazil)


    The organic ligand 2,5-piperazinedione-1,4-diacetic acid (H{sub 2}PDA) was synthesized under hydrothermal conditions starting from the iminodiacetic acid and catalyzed by oxalic acid. The X-ray powder diffraction data indicates that the compound crystallizes in the P2{sub 1}/c monoclinic system as reported in the literature. The ligand was also characterized by elemental analysis, magnetic nuclear resonance, infrared spectroscopy and thermogravimetric analysis. Two new coordination networks based on lanthanide ions were obtained with this ligand using hydrothermal reaction. In addition to single-crystal X-ray diffraction, the compounds were characterized by infrared spectroscopy, thermogravimetric analysis, scanning electron microscopy and elemental analysis. Single-crystal XRD showed that the compounds are isostructural, crystallizing in P2{sub 1}/n monoclinic system with chemical formula [Ln(PDA){sub 1.5}(H{sub 2}O)](H{sub 2}O){sub 3} (Ln=Gd{sup 3+}(1) and Eu{sup 3+}(2)).The luminescence properties of both compounds were studied. In the compound (1), a broad emission band was observed at 479 nm, redshifted by 70 nm in comparison of the free ligand. In (2), the typical f–f transition was observed with a maximum peak at 618 nm, related with the red emission of the europium ions. Computational methods were performed to simulate the crystal structure of (2). The theoretical calculations of the intensity parameters are in good agreement with the experimental values. - Graphical abstract: Scheme of obtaining the ligand 2,5-piperazinedione-1,4-diacetic acid (H{sub 2}PDA) and two new isostructural 3D-coordination polymers [Ln(PDA){sub 1.5}(H{sub 2}O)](H{sub 2}O){sub 3} (Ln=Gd{sup 3+} and Eu{sup 3+}) by hydrothermal synthesis. Display Omitted - Highlights: • The ligand 2,5-piperazinedione-1,4-diacetic acid was synthetized using the hydrothermic method and characterized. • Two new 3D-coordination polymers with this ligand containing Gd{sup 3+} and Eu{sup 3+} ions

  15. Quantifying Rosette Formation Mediated by Receptor-ligand Interactions

    Institute of Scientific and Technical Information of China (English)


    1 IntroductionRosetting is a simple assay for specific cell-cell adhesion, in which receptor- (or ligand-) coated RBCs form the rosettes with ligand- (or receptor-) expressed nucleated cells~([1]). Although routinely used by immunologists to examine the functionality of the interacting receptors and ligands, however, it has not been regarded as a quantitative method, as the measured rosette fraction has not been quantitatively related to the underlying molecular properties.Recently, we have solved probabili...

  16. Magnetic levitation as a platform for competitive protein-ligand binding assays. (United States)

    Shapiro, Nathan D; Soh, Siowling; Mirica, Katherine A; Whitesides, George M


    This paper describes a method based on magnetic levitation (MagLev) that is capable of indirectly measuring the binding of unlabeled ligands to unlabeled protein. We demonstrate this method by measuring the affinity of unlabeled bovine carbonic anhydrase (BCA) for a variety of ligands (most of which are benzene sulfonamide derivatives). This method utilizes porous gel beads that are functionalized with a common aryl sulfonamide ligand. The beads are incubated with BCA and allowed to reach an equilibrium state in which the majority of the immobilized ligands are bound to BCA. Since the beads are less dense than the protein, protein binding to the bead increases the overall density of the bead. This change in density can be monitored using MagLev. Transferring the beads to a solution containing no protein creates a situation where net protein efflux from the bead is thermodynamically favorable. The rate at which protein leaves the bead for the solution can be calculated from the rate at which the levitation height of the bead changes. If another small molecule ligand of BCA is dissolved in the solution, the rate of protein efflux is accelerated significantly. This paper develops a reaction-diffusion (RD) model to explain both this observation, and the physical-organic chemistry that underlies it. Using this model, we calculate the dissociation constants of several unlabeled ligands from BCA, using plots of levitation height versus time. Notably, although this method requires no electricity, and only a single piece of inexpensive equipment, it can measure accurately the binding of unlabeled proteins to small molecules over a wide range of dissociation constants (K(d) values within the range from ~10 nM to 100 μM are measured easily). Assays performed using this method generally can be completed within a relatively short time period (20 min-2 h). A deficiency of this system is that it is not, in its present form, applicable to proteins with molecular weight greater

  17. The rating reliability calculator

    Directory of Open Access Journals (Sweden)

    Solomon David J


    Full Text Available Abstract Background Rating scales form an important means of gathering evaluation data. Since important decisions are often based on these evaluations, determining the reliability of rating data can be critical. Most commonly used methods of estimating reliability require a complete set of ratings i.e. every subject being rated must be rated by each judge. Over fifty years ago Ebel described an algorithm for estimating the reliability of ratings based on incomplete data. While his article has been widely cited over the years, software based on the algorithm is not readily available. This paper describes an easy-to-use Web-based utility for estimating the reliability of ratings based on incomplete data using Ebel's algorithm. Methods The program is available public use on our server and the source code is freely available under GNU General Public License. The utility is written in PHP, a common open source imbedded scripting language. The rating data can be entered in a convenient format on the user's personal computer that the program will upload to the server for calculating the reliability and other statistics describing the ratings. Results When the program is run it displays the reliability, number of subject rated, harmonic mean number of judges rating each subject, the mean and standard deviation of the averaged ratings per subject. The program also displays the mean, standard deviation and number of ratings for each subject rated. Additionally the program will estimate the reliability of an average of a number of ratings for each subject via the Spearman-Brown prophecy formula. Conclusion This simple web-based program provides a convenient means of estimating the reliability of rating data without the need to conduct special studies in order to provide complete rating data. I would welcome other researchers revising and enhancing the program.

  18. Riboswitch Structure: an Internal Residue Mimicking the Purine Ligand

    Energy Technology Data Exchange (ETDEWEB)

    Delfosse, V.; Bouchard, P; Bonneau, E; Dagenais, P; Lemay, J; Lafontaine, D; Legault, P


    The adenine and guanine riboswitches regulate gene expression in response to their purine ligand. X-ray structures of the aptamer moiety of these riboswitches are characterized by a compact fold in which the ligand forms a Watson-Crick base pair with residue 65. Phylogenetic analyses revealed a strict restriction at position 39 of the aptamer that prevents the G39-C65 and A39-U65 combinations, and mutational studies indicate that aptamers with these sequence combinations are impaired for ligand binding. In order to investigate the rationale for sequence conservation at residue 39, structural characterization of the U65C mutant from Bacillus subtilis pbuE adenine riboswitch aptamer was undertaken. NMR spectroscopy and X-ray crystallography studies demonstrate that the U65C mutant adopts a compact ligand-free structure, in which G39 occupies the ligand-binding site of purine riboswitch aptamers. These studies present a remarkable example of a mutant RNA aptamer that adopts a native-like fold by means of ligand mimicking and explain why this mutant is impaired for ligand binding. Furthermore, this work provides a specific insight into how the natural sequence has evolved through selection of nucleotide identities that contribute to formation of the ligand-bound state, but ensures that the ligand-free state remains in an active conformation.

  19. Competitive antagonism of AMPA receptors by ligands of different classes

    DEFF Research Database (Denmark)

    Hogner, Anders; Greenwood, Jeremy R; Liljefors, Tommy


    that ATPO and DNQX stabilize an open form of the ligand-binding core by different sets of interactions. Computational techniques are used to quantify the differences between these two ligands and to map the binding site. The isoxazole moiety of ATPO acts primarily as a spacer, and other scaffolds could......-(phosphonomethoxy)-4-isoxazolyl]propionic acid (ATPO) in complex with the ligand-binding core of the receptor. Comparison with the only previous structure of the ligand-binding core in complex with an antagonist, 6,7-dinitro-2,3-quinoxalinedione (DNQX) (Armstrong, N.; Gouaux, E. Neuron 2000, 28, 165-181), reveals...

  20. Design of targeting ligands in medicinal inorganic chemistry. (United States)

    Storr, Tim; Thompson, Katherine H; Orvig, Chris


    This tutorial review will highlight recent advances in medicinal inorganic chemistry pertaining to the use of multifunctional ligands for enhanced effect. Ligands that adequately bind metal ions and also include specific targeting features are gaining in popularity due to their ability to enhance the efficacy of less complicated metal-based agents. Moving beyond the traditional view of ligands modifying reactivity, stabilizing specific oxidation states, and contributing to substitution inertness, we will discuss recent work involving metal complexes with multifunctional ligands that target specific tissues, membrane receptors, or endogenous molecules, including enzymes.

  1. Structural basis for ligand recognition of incretin receptors

    DEFF Research Database (Denmark)

    Underwood, Christina Rye; Parthier, Christoph; Reedtz-Runge, Steffen


    been solved recently by X-ray crystallography. The crystal structures reveal a similar fold of the ECD and a similar mechanism of ligand binding, where the ligand adopts an α-helical conformation. Residues in the C-terminal part of the ligand interact directly with the ECD and hydrophobic interactions...... appear to be the main driving force for ligand binding to the ECD of incretin receptors. Obviously, the-still missing-structures of full-length incretin receptors are required to construct a complete picture of receptor function at the molecular level. However, the progress made recently in structural...

  2. Superior serum half life of albumin tagged TNF ligands

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, Nicole [Division of Molecular Internal Medicine, Department of Internal Medicine II, University Hospital Wuerzburg, Roentgenring 11, 97070 Wuerzburg (Germany); Schneider, Britta; Pfizenmaier, Klaus [Institute of Cell Biology and Immunology, University of Stuttgart, Allmandring 31, 70569 Stuttgart (Germany); Wajant, Harald, E-mail: [Division of Molecular Internal Medicine, Department of Internal Medicine II, University Hospital Wuerzburg, Roentgenring 11, 97070 Wuerzburg (Germany)


    Due to their immune stimulating and apoptosis inducing properties, ligands of the TNF family attract increasing interest as therapeutic proteins. A general limitation of in vivo applications of recombinant soluble TNF ligands is their notoriously rapid clearance from circulation. To improve the serum half life of the TNF family members TNF, TWEAK and TRAIL, we genetically fused soluble variants of these molecules to human serum albumin (HSA). The serum albumin-TNF ligand fusion proteins were found to be of similar bioactivity as the corresponding HSA-less counterparts. Upon intravenous injection (i.v.), serum half life of HSA-TNF ligand fusion proteins, as determined by ELISA, was around 15 h as compared to approximately 1 h for all of the recombinant control TNF ligands without HSA domain. Moreover, serum samples collected 6 or 24 h after i.v. injection still contained high TNF ligand bioactivity, demonstrating that there is only limited degradation/inactivation of circulating HSA-TNF ligand fusion proteins in vivo. In a xenotransplantation model, significantly less of the HSA-TRAIL fusion protein compared to the respective control TRAIL protein was required to achieve inhibition of tumor growth indicating that the increased half life of HSA-TNF ligand fusion proteins translates into better therapeutic action in vivo. In conclusion, our data suggest that genetic fusion to serum albumin is a powerful and generally applicable mean to improve bioavailability and in vivo activity of TNF ligands.

  3. Group epitope mapping considering relaxation of the ligand (GEM-CRL): Including longitudinal relaxation rates in the analysis of saturation transfer difference (STD) experiments (United States)

    Kemper, Sebastian; Patel, Mitul K.; Errey, James C.; Davis, Benjamin G.; Jones, Jonathan A.; Claridge, Timothy D. W.


    In the application of saturation transfer difference (STD) experiments to the study of protein-ligand interactions, the relaxation of the ligand is one of the major influences on the experimentally observed STD factors, making interpretation of these difficult when attempting to define a group epitope map (GEM). In this paper, we describe a simplification of the relaxation matrix that may be applied under specified experimental conditions, which results in a simplified equation reflecting the directly transferred magnetisation rate from the protein onto the ligand, defined as the summation over the whole protein of the protein-ligand cross-relaxation multiplied by with the fractional saturation of the protein protons. In this, the relaxation of the ligand is accounted for implicitly by inclusion of the experimentally determined longitudinal relaxation rates. The conditions under which this "group epitope mapping considering relaxation of the ligand" (GEM-CRL) can be applied were tested on a theoretical model system, which demonstrated only minor deviations from that predicted by the full relaxation matrix calculations (CORCEMA-ST) [7]. Furthermore, CORCEMA-ST calculations of two protein-saccharide complexes (Jacalin and TreR) with known crystal structures were performed and compared with experimental GEM-CRL data. It could be shown that the GEM-CRL methodology is superior to the classical group epitope mapping approach currently used for defining ligand-protein proximities. GEM-CRL is also useful for the interpretation of CORCEMA-ST results, because the transferred magnetisation rate provides an additional parameter for the comparison between measured and calculated values. The independence of this parameter from the above mentioned factors can thereby enhance the value of CORCEMA-ST calculations.

  4. Ultrafast heme-ligand recombination in truncated hemoglobin HbO from Mycobacterium tuberculosis: A ligand cage (United States)

    Jasaitis, Audrius; Ouellet, Hugues; Lambry, Jean-Christophe; Martin, Jean-Louis; Friedman, Joel M.; Guertin, Michel; Vos, Marten H.


    Truncated hemoglobin HbO from Mycobacterium tuberculosis displays very slow exchange of diatomic ligands with its environment. Using femtosecond spectroscopy, we show that upon photoexcitation, ligands rebind with unusual speed and efficiency. Only ˜1% O2 can escape from the heme pocket and less than 1% NO. Most remarkably, CO rebinding occurs for 95%, predominantly in 1.2 ns. The general CO rebinding properties are unexpectedly robust against changes in the interactions with close by aromatic residues Trp88 (G8) and Tyr36 (CD1). Molecular dynamics simulations of the CO complex suggest that interactions of the ligand with structural water molecules as well as its rotational freedom play a role in the high reactivity of the ligand and the heme. The slow exchange of ligands between heme and environment may result from a combination of hindered ligand access to the heme pocket by the network of distal aromatic residues, and low escape probability from the pocket.

  5. PET imaging for receptor occupancy: meditations on calculation and simplification. (United States)

    Zhang, Yumin; Fox, Gerard B


    This invited mini-review briefly summarizes procedures and challenges of measuring receptor occupancy with positron emission tomography. Instead of describing the detailed analytic procedures of in vivo ligand-receptor imaging, the authors provide a pragmatic approach, along with personal perspectives, for conducting positron emission tomography imaging for receptor occupancy, and systematically elucidate the mathematics of receptor occupancy calculations in practical ways that can be understood with elementary algebra. The authors also share insights regarding positron emission tomography imaging for receptor occupancy to facilitate applications for the development of drugs targeting receptors in the central nervous system.

  6. A new copper(II) Schiff base complex containing asymmetrical tetradentate N2O2 Schiff base ligand: Synthesis, characterization, crystal structure and DFT study (United States)

    Grivani, Gholamhossein; Baghan, Sara Husseinzadeh; Vakili, Mohammad; Khalaji, Aliakbar Dehno; Tahmasebi, Vida; Eigner, Václav; Dušek, Michal


    A new copper (II) Schiff base complex, CuL1, was prepared from the reaction of asymmetrical Schiff base ligand of L1 and Cu(OAC)2 (L1 = salicylidene imino-ethylimino-pentan-2-one). The Schiff base ligand, L1, and its copper (II) complex, CuL1, have been characterized by elemental analysis (CHN) and FT-IR and UV-vis spectroscopy. In addition, 1H NMR was employed for characterization of the ligand. Thermogrametric analysis of the CuL1 reveals its thermal stability and its decomposition pattern shows that it is finally decomposed to the copper oxide (CuO). The crystal structure of CuL1 was determined by the single crystal X-ray analysis. The CuL1 complex crystallizes in the monoclinic system, with space group P21/n and distorted square planar coordination around the metal ion. The Schiff base ligand of L1 acts as a chelating ligand and coordinates via two nitrogen and two oxygen atoms to the copper (II) ion with C1 symmetry. The structure of the CuL1 complex was also studied theoretically at different levels of DFT and basis sets. According to calculated results the Csbnd O bond length of the salicylate fragment is slightly higher than that in the acetylacetonate fragment of ligand, which could be interpreted by resonance increasing between phenyl and chelated rings in ligand in relative to the acetylacetonate fragment.

  7. Chirality Inversion of CdSe and CdS Quantum Dots without Changing the Stereochemistry of the Capping Ligand. (United States)

    Choi, Jung Kyu; Haynie, Benjamin E; Tohgha, Urice; Pap, Levente; Elliott, K Wade; Leonard, Brian M; Dzyuba, Sergei V; Varga, Krisztina; Kubelka, Jan; Balaz, Milan


    L-cysteine derivatives induce and modulate the optical activity of achiral cadmium selenide (CdSe) and cadmium sulfide (CdS) quantum dots (QDs). Remarkably, N-acetyl-L-cysteine-CdSe and L-homocysteine-CdSe as well as N-acetyl-L-cysteine-CdS and L-cysteine-CdS showed "mirror-image" circular dichroism (CD) spectra regardless of the diameter of the QDs. This is an example of the inversion of the CD signal of QDs by alteration of the ligand's structure, rather than inversion of the ligand's absolute configuration. Non-empirical quantum chemical simulations of the CD spectra were able to reproduce the experimentally observed sign patterns and demonstrate that the inversion of chirality originated from different binding arrangements of N-acetyl-L-cysteine and L-homocysteine-CdSe to the QD surface. These efforts may allow the prediction of the ligand-induced chiroptical activity of QDs by calculating the specific binding modes of the chiral capping ligands. Combined with the large pool of available chiral ligands, our work opens a robust approach to the rational design of chiral semiconducting nanomaterials.

  8. Computational understanding and experimental characterization of twice-as-smart quadruplex ligands as chemical sensors of bacterial nucleotide second messengers (United States)

    Zhou, Jie; Roembke, Benjamin T.; Paragi, Gabor; Laguerre, Aurélien; Sintim, Herman O.; Fonseca Guerra, Célia; Monchaud, David


    A twice-as-smart ligand is a small molecule that experiences a structural switch upon interaction with its target (i.e., smart ligand) that concomitantly triggers its fluorescence (i.e., smart probe). Prototypes of twice-as-smart ligands were recently developed to track and label G-quadruplexes: these higher-order nucleic acid structures originate in the assembly of four guanine(G)-rich DNA or RNA strands, whose stability is imparted by the formation and the self-assembly of G-quartets. The first prototypes of twice-as-smart quadruplex ligands were designed to exploit the self-association of quartets, being themselves synthetic G-quartets. While their quadruplex recognition capability has been thoroughly documented, some doubts remain about the precise photophysical mechanism that underlies their peculiar spectroscopic properties. Here, we uncovered this mechanism via complete theoretical calculations. Collected information was then used to develop a novel application of twice-as-smart ligands, as efficient chemical sensors of bacterial signaling pathways via the fluorescent detection of naturally occurring extracellular quadruplexes formed by cyclic dimeric guanosine monophosphate (c-di-GMP). PMID:27667717

  9. Axial Ligand Effects on the Structures of Self-Assembled Gallium-Porphyrin Monolayers on Highly Oriented Pyrolytic Graphite. (United States)

    Kamm, Judith M; Iverson, Cameron P; Lau, Wing-Yeung; Hopkins, Michael D


    Monolayers of five-coordinate gallium octaethylporphyrin complexes (Ga(OEP)X; X = Cl, Br, I, O3SCF3, CCPh) on highly oriented pyrolytic graphite were studied at the solid-liquid (1-phenyloctane) interface using scanning tunneling microscopy (STM) to probe the dependence of their properties on the nature of the axial X ligand. Density functional theory calculations of the gas-phase structures of the free molecules reveal that the gallium atom is positioned above the plane of the porphyrin macrocycle, with this pyramidal distortion increasing in magnitude according to X = O3SCF3 (displacement = 0.35 Å) monolayers are sensitive to the nature of the axial ligand: the monolayers of Ga(OEP)(O3SCF3) and Ga(OEP)(CCPh) exhibit damage during the STM experiment upon repeated scanning and upon toggling the sign of the bias potential, but monolayers of Ga(OEP)Cl, Ga(OEP)Br, and Ga(OEP)I do not. A second important ligand-influenced property is that Ga(OEP)I forms bilayer structures, whereas the other Ga(OEP)X compounds form monolayers exclusively under identical conditions. The top layer of the Ga(OEP)I bilayer is oriented with the iodo ligand directed away from the surface, like the bottom layer, but the molecules pack in a square, lower-density geometry. The comparatively large polarizability of the iodo ligand is suggested to be important in stabilizing the bilayer structure.

  10. LFP: A PC-program for ligand-field analysis of 3d(n) ions in Oh and lower symmetries (United States)



    A modular and efficient version of PC program for calculating ligand-field parameters, i.e. crystal-field model (CFM) and angular overlap model (AOM) is presented. The LFP program is designed to calculate the ligand-field parameters of low symmetry transition metal complexes. It is based on the general method for the analysis of central ion states distortion using group theory. The program has not closed form. It will be extended, according to spectroscopic studies in our laboratory. It is written in FORTRAN language.

  11. Ruthenium(II) Complexes Containing Lutidine-Derived Pincer CNC Ligands: Synthesis, Structure, and Catalytic Hydrogenation of C-N bonds. (United States)

    Hernández-Juárez, Martín; López-Serrano, Joaquín; Lara, Patricia; Morales-Cerón, Judith P; Vaquero, Mónica; Álvarez, Eleuterio; Salazar, Verónica; Suárez, Andrés


    A series of Ru complexes containing lutidine-derived pincer CNC ligands have been prepared by transmetalation with the corresponding silver-carbene derivatives. Characterization of these derivatives shows both mer and fac coordination of the CNC ligands depending on the wingtips of the N-heterocyclic carbene fragments. In the presence of tBuOK, the Ru-CNC complexes are active in the hydrogenation of a series of imines. In addition, these complexes catalyze the reversible hydrogenation of phenantridine. Detailed NMR spectroscopic studies have shown the capability of the CNC ligand to be deprotonated and get involved in ligand-assisted activation of dihydrogen. More interestingly, upon deprotonation, the Ru-CNC complex 5 e(BF4 ) is able to add aldimines to the metal-ligand framework to yield an amido complex. Finally, investigation of the mechanism of the hydrogenation of imines has been carried out by means of DFT calculations. The calculated mechanism involves outer-sphere stepwise hydrogen transfer to the C-N bond assisted either by the pincer ligand or a second coordinated H2 molecule.

  12. Design of Ligands for Affinity Purification of G-CSF Based on Peptide Ligands Derived from a Peptide Library

    Institute of Scientific and Technical Information of China (English)


    Combinatorial peptide libraries have become powerful tools to screen functional ligands by the principle of affinity selection. We screened in a phage peptide library to investigate potential peptide affinity ligands for the purification of human granulocyte colony-stimulation factor(hG-CSF). Peptide ligands will be promising to replace monoclonal antibodies as they have advantages of high stability, efficiency, selectivity and low price.

  13. mRAISE: an alternative algorithmic approach to ligand-based virtual screening (United States)

    von Behren, Mathias M.; Bietz, Stefan; Nittinger, Eva; Rarey, Matthias


    Ligand-based virtual screening is a well established method to find new lead molecules in todays drug discovery process. In order to be applicable in day to day practice, such methods have to face multiple challenges. The most important part is the reliability of the results, which can be shown and compared in retrospective studies. Furthermore, in the case of 3D methods, they need to provide biologically relevant molecular alignments of the ligands, that can be further investigated by a medicinal chemist. Last but not least, they have to be able to screen large databases in reasonable time. Many algorithms for ligand-based virtual screening have been proposed in the past, most of them based on pairwise comparisons. Here, a new method is introduced called mRAISE. Based on structural alignments, it uses a descriptor-based bitmap search engine (RAISE) to achieve efficiency. Alignments created on the fly by the search engine get evaluated with an independent shape-based scoring function also used for ranking of compounds. The correct ranking as well as the alignment quality of the method are evaluated and compared to other state of the art methods. On the commonly used Directory of Useful Decoys dataset mRAISE achieves an average area under the ROC curve of 0.76, an average enrichment factor at 1 % of 20.2 and an average hit rate at 1 % of 55.5. With these results, mRAISE is always among the top performing methods with available data for comparison. To access the quality of the alignments calculated by ligand-based virtual screening methods, we introduce a new dataset containing 180 prealigned ligands for 11 diverse targets. Within the top ten ranked conformations, the alignment closest to X-ray structure calculated with mRAISE has a root-mean-square deviation of less than 2.0 Å for 80.8 % of alignment pairs and achieves a median of less than 2.0 Å for eight of the 11 cases. The dataset used to rate the quality of the calculated alignments is freely available at

  14. Azomethines of N-aminobenzazoles- a new ligand system

    Energy Technology Data Exchange (ETDEWEB)

    Kuznetsova, L.I.; Kolodyazhnyj, Yu.V.; Blotskaya, O.A.; Chikina, N.L.; Kuz' menko, V.V.; Garnovskij, A.D. (Rostovskij-na-Donu Gosudarstvennyj Univ. (USSR); Rostovskij-na-Donu Gosudarstvennyj Univ. (USSR). Nauchno-Issledovatel' skij Inst. Fizicheskoj i Organicheskoj Khimii; Rostovskij-na-Donu Inst. Sel' skokhozyajstvennogo Mashinostroeniya (USSR))


    Azomethines of 1-aminobensimidazole (2) have been used for the first time as ligands. It is shown that their complexing properties differ from the previously studied azomethines of 2-aminobenzazoles (1) and are determined by specificity of spatial and electron structure of compounds 2. On the basis of comparison of experimental and calculated according to the vector scheme values of dipole momenta suppositions U on stereochemistry of molecules 2 and mechanism of electron effect transfer in them are made. It is established that in contrast to 2-aminoderivatives of azomethines 1, coordination interaction 2 with metal salts is realized first of all according to N/sub 3/-donor centre of heterofragment and not according to azomethine bond -N=C=. The result agrees with the highest value of negative charge and basicity constants pKsub(a) of N/sub 3/-heteroatom. On the basis of the data of element analysis and IR spectroscopy it is shown that 2 with transition and non-transition metal salts (CdCl/sub 2/, in particular) can form coordination compounds of adduct type, metal-chelate complexes and polynuclear systems of mixed metal-chelate and molecular types.

  15. Ligand "Brackets" for Ga-Ga Bond. (United States)

    Fedushkin, Igor L; Skatova, Alexandra A; Dodonov, Vladimir A; Yang, Xiao-Juan; Chudakova, Valentina A; Piskunov, Alexander V; Demeshko, Serhiy; Baranov, Evgeny V


    The reactivity of digallane (dpp-Bian)Ga-Ga(dpp-Bian) (1) (dpp-Bian = 1,2-bis[(2,6-diisopropylphenyl)imino]acenaphthene) toward acenaphthenequinone (AcQ), sulfur dioxide, and azobenzene was investigated. The reaction of 1 with AcQ in 1:1 molar ratio proceeds via two-electron reduction of AcQ to give (dpp-Bian)Ga(μ2-AcQ)Ga(dpp-Bian) (2), in which diolate [AcQ](2-) acts as "bracket" for the Ga-Ga bond. The interaction of 1 with AcQ in 1:2 molar ratio proceeds with an oxidation of the both dpp-Bian ligands as well as of the Ga-Ga bond to give (dpp-Bian)Ga(μ2-AcQ)2Ga(dpp-Bian) (3). At 330 K in toluene complex 2 decomposes to give compounds 3 and 1. The reaction of complex 2 with atmospheric oxygen results in oxidation of a Ga-Ga bond and affords (dpp-Bian)Ga(μ2-AcQ)(μ2-O)Ga(dpp-Bian) (4). The reaction of digallane 1 with SO2 produces, depending on the ratio (1:2 or 1:4), dithionites (dpp-Bian)Ga(μ2-O2S-SO2)Ga(dpp-Bian) (5) and (dpp-Bian)Ga(μ2-O2S-SO2)2Ga(dpp-Bian) (6). In compound 5 the Ga-Ga bond is preserved and supported by dithionite dianionic bracket. In compound 6 the gallium centers are bridged by two dithionite ligands. Both 5 and 6 consist of dpp-Bian radical anionic ligands. Four-electron reduction of azobenzene with 1 mol equiv of digallane 1 leads to complex (dpp-Bian)Ga(μ2-NPh)2Ga(dpp-Bian) (7). Paramagnetic compounds 2-7 were characterized by electron spin resonance spectroscopy, and their molecular structures were established by single-crystal X-ray analysis. Magnetic behavior of compounds 2, 5, and 6 was investigated by superconducting quantum interference device technique in the range of 2-295 K.

  16. Characterizing mixed phosphonic acid ligand capping on CdSe/ZnS quantum dots using ligand exchange and NMR spectroscopy. (United States)

    Davidowski, Stephen K; Lisowski, Carmen E; Yarger, Jeffery L


    The ligand capping of phosphonic acid functionalized CdSe/ZnS core-shell quantum dots (QDs) was investigated with a combination of solution and solid-state (31) P nuclear magnetic resonance (NMR) spectroscopy. Two phosphonic acid ligands were used in the synthesis of the QDs, tetradecylphosphonic acid and ethylphosphonic acid. Both alkyl phosphonic acids showed broad liquid and solid-state (31) P NMR resonances for the bound ligands, indicative of heterogeneous binding to the QD surface. In order to quantify the two ligand populations on the surface, ligand exchange facilitated by phenylphosphonic acid resulted in the displacement of the ethylphosphonic acid and tetradecylphosphonic acid and allowed for quantification of the free ligands using (31) P liquid-state NMR. After washing away the free ligand, two broad resonances were observed in the liquids' (31) P NMR corresponding to the alkyl and aromatic phosphonic acids. The washed samples were analyzed via solid-state (31) P NMR, which confirmed the ligand populations on the surface following the ligand exchange process. Copyright © 2015 John Wiley & Sons, Ltd.

  17. New Arsenic Cross Section Calculations

    Energy Technology Data Exchange (ETDEWEB)

    Kawano, Toshihiko [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)


    This report presents calculations for the new arsenic cross section. Cross sections for 73,74,75 As above the resonance range were calculated with a newly developed Hauser-Feshbach code, CoH3.

  18. Cosmological Calculations on the GPU

    CERN Document Server

    Bard, Deborah; Allen, Mark T; Yepremyan, Hasmik; Kratochvil, Jan M


    Cosmological measurements require the calculation of nontrivial quantities over large datasets. The next generation of survey telescopes (such as DES, PanSTARRS, and LSST) will yield measurements of billions of galaxies. The scale of these datasets, and the nature of the calculations involved, make cosmological calculations ideal models for implementation on graphics processing units (GPUs). We consider two cosmological calculations, the two-point angular correlation function and the aperture mass statistic, and aim to improve the calculation time by constructing code for calculating them on the GPU. Using CUDA, we implement the two algorithms on the GPU and compare the calculation speeds to comparable code run on the CPU. We obtain a code speed-up of between 10 - 180x faster, compared to performing the same calculation on the CPU. The code has been made publicly available.

  19. Equilibria and kinetics for H-dependent axial ligation of alkyl(aquo) cobaloximes with aromatic and aliphatic N-donor ligands

    Indian Academy of Sciences (India)

    V Sridhar; D Sudarshan Reddy; N Ravikumar Reddy; S Satyanarayana


    Equilibria and kinetics of the reaction of bromomethyl(aquo) cobaloxime with histamine, histidine, glycine and ethyl glycine ester and iodomethyl(aquo) cobaloxime with cyanide, imidazole and substituted imidazoles were studied as a function of H at 25°C, 1.0 M ionic strength (KCl) by spectrophotometry technique. The rate of substitution of H2O varies with the of the incoming ligand, thus establishing the existence of nucleophilic participation of the ligand in the transition state. Dissociation kinetic reactions were also studied as a function of H. Binding and kinetic data were interpreted based on the basicity, steric crowd of the entering ligand and HSAB principle. To compare the rate constants of the entering ligands H independent second-order rate constants were calculated.

  20. "Long-range" metal-ligand cooperation in H2 activation and ammonia-promoted hydride transfer with a ruthenium-acridine pincer complex. (United States)

    Gunanathan, Chidambaram; Gnanaprakasam, Boopathy; Iron, Mark A; Shimon, Linda J W; Milstein, David


    The acridine-based pincer complex 1 exhibits an unprecedented mode of metal-ligand cooperation involving a "long-range" interaction between the distal acridine C9 position and the metal center. Reaction of 1 with H(2)/KOH results in H(2) splitting between the Ru center and C9 with concomitant dearomatization of the acridine moiety. DFT calculations show that this process involves the formation of a Ru dihydride intermediate bearing a bent acridine ligand in which C9 is in close proximity to a hydride ligand followed by through-space hydride transfer. Ammonia induces transfer of a hydride from the Ru center of 1 to C9 of the flexible acridine pincer ligand, forming an unusual dearomatized fac-acridine PNP complex.

  1. Phosphinothiolates as ligands for polyhydrido copper nanoclusters. (United States)

    Huertos, Miguel A; Cano, Israel; Bandeira, Nuno A G; Benet-Buchholz, Jordi; Bo, Carles; van Leeuwen, Piet W N M


    The reaction of [CuI(HSC6 H4 PPh2 )]2 with NaBH4 in CH2 Cl2 /EtOH led to air- and moisture-stable copper hydride nanoparticles (CuNPs) containing phosphinothiolates as new ligands, one of which was isolated by crystallization. The X-ray crystal structure of [Cu18 H7 L10 I] (L=(-) S(C6 H4 )PPh2 ) shows unprecedented features in its 28-atom framework (18 Cu and 10 S atoms). Seven hydrogen atoms, in hydride form, are needed for charge balance and were located by density functional theory methods. H2 was released from the copper hydride nanoparticles by thermolysis and visible light irradiation.

  2. Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level. (United States)

    Olsson, Martin A; Söderhjelm, Pär; Ryde, Ulf


    In this article, the convergence of quantum mechanical (QM) free-energy simulations based on molecular dynamics simulations at the molecular mechanics (MM) level has been investigated. We have estimated relative free energies for the binding of nine cyclic carboxylate ligands to the octa-acid deep-cavity host, including the host, the ligand, and all water molecules within 4.5 Å of the ligand in the QM calculations (158-224 atoms). We use single-step exponential averaging (ssEA) and the non-Boltzmann Bennett acceptance ratio (NBB) methods to estimate QM/MM free energy with the semi-empirical PM6-DH2X method, both based on interaction energies. We show that ssEA with cumulant expansion gives a better convergence and uses half as many QM calculations as NBB, although the two methods give consistent results. With 720,000 QM calculations per transformation, QM/MM free-energy estimates with a precision of 1 kJ/mol can be obtained for all eight relative energies with ssEA, showing that this approach can be used to calculate converged QM/MM binding free energies for realistic systems and large QM partitions. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

  3. DFT modeling and spectroscopic study of metal-ligand bonding in La(III) complex of coumarin-3-carboxylic acid

    Energy Technology Data Exchange (ETDEWEB)

    Mihaylov, Tz. [Institute of General and Inorganic Chemistry, Bulgarian Academy of Sciences, 1113 Sofia (Bulgaria); Trendafilova, N. [Institute of General and Inorganic Chemistry, Bulgarian Academy of Sciences, 1113 Sofia (Bulgaria)], E-mail:; Kostova, I. [Department of Chemistry, Faculty of Pharmacy, Medical University, Sofia 1000 (Bulgaria); Georgieva, I. [Institute of General and Inorganic Chemistry, Bulgarian Academy of Sciences, 1113 Sofia (Bulgaria); Bauer, G. [Institute of Chemical Technologies and Analytics, Technical University of Vienna, Vienna A-1060 (Austria)


    The binding mode of coumarin-3-carboxylic acid (HCCA) to La(III) is elucidated at experimental and theoretical level. The complexation ability of the deprotonated ligand (CCA{sup -}) to La(III) is studied using elemental analysis, DTA and TGA data as well as FTIR, {sup 1}H NMR and {sup 13}C NMR spectra. The experimental data suggest the complex formula La(CCA){sub 2}(NO{sub 3})(H{sub 2}O){sub 2}. B3LYP, BHLYP, B3P86, B3PW91, PW91P86 and MPW1PW91 functionals are tested for geometry and frequency calculations of the neutral ligand and all of them show bond length deviations bellow 1%. B3LYP/6-31G(d) level combined with large quasi-relativistic effective core potential for lanthanum is selected to describe the molecular, electronic and vibrational structures as well as the conformational behavior of HCCA, CCA{sup -} and La-CCA complex. The metal-ligand binding mode is predicted through molecular modeling and energy estimation of different La-CCA structures. The calculated atomic charges and the bonding orbital polarizations point to strong ionic metal-ligand bonding in La-CCA complex and insignificant donor acceptor interaction. Detailed vibrational analysis of HCCA, CCA{sup -} and La(CCA){sub 2}(NO{sub 3})(H{sub 2}O){sub 2} systems based on both calculated and experimental frequencies confirms the suggested metal-ligand binding mode.

  4. Isolation of atomically precise mixed ligand shell PdAu24 clusters (United States)

    Sels, Annelies; Barrabés, Noelia; Knoppe, Stefan; Bürgi, Thomas


    Exposure of PdAu24(2-PET)18 (2-PET: 2-phenylethylthiolate) to BINAS (1,1-binaphthyl-2,2-dithiol) leads to species of composition PdAu24(2-PET)18-2x(BINAS)x due to ligand exchange reactions. The BINAS adsorbs in a specific mode that bridges the apex and one core site of two adjacent S(R)-Au-S(R)-Au-S(R) units. Species with different compositions of the ligand shell can be separated by HPLC. Furthermore, site isomers can be separated. For the cluster with exactly one BINAS in its ligand shell only one isomer is expected due to the symmetry of the cluster, which is confirmed by High-Performance Liquid Chromatography (HPLC). Addition of a second BINAS to the ligand shell leads to several isomers. In total six distinguishable isomers are possible for PdAu24(2-PET)14(BINAS)2 including two pairs of enantiomers concerning the adsorption pattern. At least four distinctive isomers are separated by HPLC. Calculations indicate that one of the six possibilities is energetically disfavoured. Interestingly, diastereomers, which have an enantiomeric relationship concerning the adsorption pattern of chiral BINAS, have significantly different stabilities. The relative intensity of the observed peaks in the HPLC does not reflect the statistical weight of the different isomers. This shows, as supported by the calculations, that the first adsorbed BINAS molecule influences the adsorption of the second incoming BINAS ligand. In addition, experiments with the corresponding Pt doped gold cluster reveal qualitatively the same behaviour, however with slightly different relative abundances of the corresponding isomers. This finding points towards the influence of electronic effects on the isomer distribution. Even for clusters containing more than two BINAS ligands a limited number of isomers were found, which is in contrast to the corresponding situation for monothiols, where the number of possible isomers is much larger.Exposure of PdAu24(2-PET)18 (2-PET: 2-phenylethylthiolate) to BINAS (1

  5. Investigating silver coordination to mixed chalcogen ligands. (United States)

    Knight, Fergus R; Randall, Rebecca A M; Wakefield, Lucy; Slawin, Alexandra M Z; Woollins, J Derek


    Six silver(I) coordination complexes have been prepared and structurally characterised. Mixed chalcogen-donor acenaphthene ligands L1-L3 [Acenap(EPh)(E'Ph)] (Acenap = acenaphthene-5,6-diyl; E/E' = S, Se, Te) were independently treated with silver(I) salts (AgBF₄/AgOTf). In order to keep the number of variables to a minimum, all reactions were carried out using a 1:1 ratio of Ag/L and run in dichloromethane. The nature of the donor atoms, the coordinating ability of the respective counter-anion and the type of solvent used in recrystallisation, all affect the structural architecture of the final silver(I) complex, generating monomeric, silver(I) complexes {[AgBF₄(L)₂] (1 L = L1; 2 L = L2; 3 L = L3), [AgOTf(L)₃] (4 L = L1; 5 L = L3), [AgBF₄(L)₃] (2a L = L1; 3a L = L3)} and a 1D polymeric chain {[AgOTf(L3)](n) 6}. The organic acenaphthene ligands L1-L3 adopt a number of ligation modes (bis-monodentate μ₂-η²-bridging, quasi-chelating combining monodentate and η⁶-E(phenyl)-Ag(I) and classical monodentate coordination) with the central silver atom at the centre of a tetrahedral or trigonal planar coordination geometry in each case. The importance of weak interactions in the formation of metal-organic structures is also highlighted by the number of short non-covalent contacts present within each complex.

  6. Investigating Silver Coordination to Mixed Chalcogen Ligands

    Directory of Open Access Journals (Sweden)

    J. Derek Woollins


    Full Text Available Six silver(I coordination complexes have been prepared and structurally characterised. Mixed chalcogen-donor acenaphthene ligands L1–L3 [Acenap(EPh(E'Ph] (Acenap = acenaphthene-5,6-diyl; E/E' = S, Se, Te were independently treated with silver(I salts (AgBF4/AgOTf. In order to keep the number of variables to a minimum, all reactions were carried out using a 1:1 ratio of Ag/L and run in dichloromethane. The nature of the donor atoms, the coordinating ability of the respective counter-anion and the type of solvent used in recrystallisation, all affect the structural architecture of the final silver(I complex, generating monomeric, silver(I complexes {[AgBF4(L2] (1 L = L1; 2 L = L2; 3 L = L3, [AgOTf(L3] (4 L = L1; 5 L = L3, [AgBF4(L3] (2a L = L1; 3a L = L3} and a 1D polymeric chain {[AgOTf(L3]n 6}. The organic acenaphthene ligands L1-L3 adopt a number of ligation modes (bis-monodentate μ2-η2-bridging, quasi-chelating combining monodentate and η6-E(phenyl-Ag(I and classical monodentate coordination with the central silver atom at the centre of a tetrahedral or trigonal planar coordination geometry in each case. The importance of weak interactions in the formation of metal-organic structures is also highlighted by the number of short non-covalent contacts present within each complex.

  7. Development and Application of Ligand-Exchange Reaction Method ...

    African Journals Online (AJOL)


    Methods: The method is based on ligand-exchange reaction. ... Clonazepam, Ligand-exchange reaction, Kinetic spectrometry, Validation, Pharmaceutical ... sensitive and selective analytical method for ... does not need sophisticated instruments or ..... of clonazepam in human serum ("Lytorol N) by standard addition method.

  8. Polymerization catalysts containing electron-withdrawing amide ligands (United States)

    Watkin, John G.; Click, Damon R.


    The present invention describes methods of making a series of amine-containing organic compounds which are used as ligands for group 3-10 and lanthanide metal compounds. The ligands have electron-withdrawing groups bonded to them. The metal compounds, when combined with a cocatalyst, are catalysts for the polymerization of olefins.

  9. Functionalized pyrazines as ligands for minor actinide extraction and catalysis

    NARCIS (Netherlands)

    Nikishkin, N.


    The research presented in this thesis concerns the design of ligands for a wide range of applications, from nuclear waste treatment to catalysis. The strategies employed to design actinide-selective extractants, for instance, comprise the fine tuning of the ligand electronic properties as well as

  10. a review of cyclopentadienyl type ligands in group 4 metallocene ...

    African Journals Online (AJOL)

    Neil Grimmer

    metal, ligand and bridge choice has on polymerisation activity and the physical properties of the polymer ... It is the ligands bonded to a metal atom(s) that strongly influence the course of a ...... The indenyl framework also lends itself to .... capable of producing an amorphous polymer.151,162 The reason is proposed to relate.

  11. Soluble CD40 ligand in acute coronary syndromes

    NARCIS (Netherlands)

    C. Heeschen (Christopher); S. Dimmeler (Stefanie); C.W. Hamm (Christian); A.M. Zeiher (Andreas); M.L. Simoons (Maarten); M.J.B.M. van den Brand (Marcel); H. Boersma (Eric)


    textabstractBACKGROUND: CD40 ligand is expressed on platelets and released from them on activation. We investigated the predictive value of soluble CD40 ligand as a marker for clinical outcome and the therapeutic effect of glycoprotein IIb/IIIa receptor inhibition in patients with acute coronary syn

  12. Functionalized pyrazines as ligands for minor actinide extraction and catalysis

    NARCIS (Netherlands)

    Nikishkin, N.


    The research presented in this thesis concerns the design of ligands for a wide range of applications, from nuclear waste treatment to catalysis. The strategies employed to design actinide-selective extractants, for instance, comprise the fine tuning of the ligand electronic properties as well as us

  13. 1,8-Dimethylnaphthalene-bridged diphosphine ligands

    DEFF Research Database (Denmark)

    Bellabarba, Ronan M; Hammond, Colin; Forman, Grant S


    The synthesis of a new series of ligands with a 1,8-dimethylnaphthalene backbone is reported, 1,8-(R2PCH2)2C10H6, where R = (t)Bu 1 (dbpn), (i)Pr 2 (dippn), Cy 3 (dchpn) and Ph 4 (dphpn). The ligand 1 is structurally characterised by X-ray crystallography. A comparative structural study...

  14. Dynamic Ligand Reactivity in a Rhodium Pincer Complex

    NARCIS (Netherlands)

    Tang, Zhou; Otten, Edwin; Reek, Joost N H; van der Vlugt, Jarl Ivar; de Bruin, Bas


    Ligand cooperativity provides (transition) metal complexes with new reactivities in substrate activation and catalytic reactions, but usually the ligand acts as an internal (Brønsted) base, while the metal acts as a (Lewis) acid. We describe the synthesis and stepwise activation of a new phosphane-p

  15. Ligand-modified metal clusters for gas separation and purification

    Energy Technology Data Exchange (ETDEWEB)

    Okrut, Alexander; Ouyang, Xiaoying; Runnebaum, Ron; Gates, Bruce C.; Katz, Alexander


    Provided is an organic ligand-bound metal surface that selects one gaseous species over another. The species can be closely sized molecular species having less than 1 Angstrom difference in kinetic diameter. In one embodiment, the species comprise carbon monoxide and ethylene. Such organic ligand-bound metal surfaces can be successfully used in gas phase separations or purifications, sensing, and in catalysis.

  16. Interaction of calreticulin with CD40 ligand, TRAIL and Fas ligand. (United States)

    Duus, K; Pagh, R T; Holmskov, U; Højrup, P; Skov, S; Houen, G


    The molecular chaperone calreticulin has been shown to bind C1q and mannan-binding lectin (MBL), which are constituents of the innate immune defence system. C1q and MBL do not share a large sequence identity but have a similar overall molecular architecture: an N-terminal triple-helical collagen-like domain and a C-terminal globular domain with ligand-binding properties. C1q is a hetero-trimer, while MBL is a homo-trimer, but due to the presence of N-terminal cysteines they both form higher order oligomers of trimers, which are the mature functional molecules. The same molecular architecture is utilized by many other functionally diverse molecules and in this work the interaction of calreticulin with C1q and structurally similar molecules was investigated. In addition to C1q and MBL, CD40 ligand (CD40L), tumour necrosis factor-related apoptosis-inducing ligand (TRAIL) and Fas ligand (FasL) were found to bind calreticulin strongly. A low level or no binding was observed for adiponectin, tumour necrosis factor-alpha (TNF-alpha), CD30L, surfactant protein-A and -D and collagen VIII. The interaction with calreticulin required a conformational change in CD40L, TRAIL and FasL and showed the same characteristics as calreticulin's interaction with C1q and MBL: a time-dependent saturable binding to immobilized protein, which was initially sensitive to salt but gradually developed into a salt-insensitive interaction. Thus, the interaction requires a structural change in the interaction partner and leads to a conformational change in calreticulin itself. The implications of these results are that calreticulin may function as a general response modifier for a whole group of immunologically important proteins.

  17. The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities (United States)

    Genheden, Samuel; Ryde, Ulf


    Introduction: The molecular mechanics energies combined with the Poisson–Boltzmann or generalized Born and surface area continuum solvation (MM/PBSA and MM/GBSA) methods are popular approaches to estimate the free energy of the binding of small ligands to biological macromolecules. They are typically based on molecular dynamics simulations of the receptor–ligand complex and are therefore intermediate in both accuracy and computational effort between empirical scoring and strict alchemical perturbation methods. They have been applied to a large number of systems with varying success. Areas covered: The authors review the use of MM/PBSA and MM/GBSA methods to calculate ligand-binding affinities, with an emphasis on calibration, testing and validation, as well as attempts to improve the methods, rather than on specific applications. Expert opinion: MM/PBSA and MM/GBSA are attractive approaches owing to their modular nature and that they do not require calculations on a training set. They have been used successfully to reproduce and rationalize experimental findings and to improve the results of virtual screening and docking. However, they contain several crude and questionable approximations, for example, the lack of conformational entropy and information about the number and free energy of water molecules in the binding site. Moreover, there are many variants of the method and their performance varies strongly with the tested system. Likewise, most attempts to ameliorate the methods with more accurate approaches, for example, quantum-mechanical calculations, polarizable force fields or improved solvation have deteriorated the results. PMID:25835573

  18. Enthalpy of ligand substitution in cis organopalladium complexes with monodentate ligands. (United States)

    Salas, Gorka; Casares, Juan A; Espinet, Pablo


    The enthalpy for the substitution reaction cis-[PdRf(2)(THF)(2)] + 2 L -->cis-[PdRf(2)L(2)] + 2THF (THF = tetrahydrofuran) has been measured in THF by calorimetric methods for Rf = 3,5-dichloro-2,4,6-trifluorophenyl, L = PPh(3), AsPh(3), SbPh(3), PMePh(2), PCyPh(2), PMe(3), AsMePh(2), or L(2) = dppe (1,2-bis(diphenylphosphino)ethane), dppf (1,1'-bis(diphenylphosphino)ferrocene). The values determined show that the substitution enthalpy has a strong dependence on the electronic and steric properties of the ligand. The study of the consecutive substitution reactions cis-[PdRf(2)(THF)(2)] + L -->cis-[PdRf(2)L(THF)] + THF, and cis-[PdRf(2)L(THF)] + L -->cis-[PdRf(2)L(2)] + THF has been carried our for L = PPh(3) and L = PCyPh(2). The first substitution is clearly more favorable for the bulkier leaving ligand, but the second gives practically the same DeltaH value for both cases, indicating that the differences in steric hindrance happen to compensate the electronic differences for both ligands. The X-ray structures of cis-[PdRf(2)(PMePh(2))(2)], cis-[PdRf(2)(dppe)] and cis-[PdRf(2)(dppf)] are reported.

  19. Improving binding mode and binding affinity predictions of docking by ligand-based search of protein conformations: evaluation in D3R grand challenge 2015 (United States)

    Xu, Xianjin; Yan, Chengfei; Zou, Xiaoqin


    The growing number of protein-ligand complex structures, particularly the structures of proteins co-bound with different ligands, in the Protein Data Bank helps us tackle two major challenges in molecular docking studies: the protein flexibility and the scoring function. Here, we introduced a systematic strategy by using the information embedded in the known protein-ligand complex structures to improve both binding mode and binding affinity predictions. Specifically, a ligand similarity calculation method was employed to search a receptor structure with a bound ligand sharing high similarity with the query ligand for the docking use. The strategy was applied to the two datasets (HSP90 and MAP4K4) in recent D3R Grand Challenge 2015. In addition, for the HSP90 dataset, a system-specific scoring function (ITScore2_hsp90) was generated by recalibrating our statistical potential-based scoring function (ITScore2) using the known protein-ligand complex structures and the statistical mechanics-based iterative method. For the HSP90 dataset, better performances were achieved for both binding mode and binding affinity predictions comparing with the original ITScore2 and with ensemble docking. For the MAP4K4 dataset, although there were only eight known protein-ligand complex structures, our docking strategy achieved a comparable performance with ensemble docking. Our method for receptor conformational selection and iterative method for the development of system-specific statistical potential-based scoring functions can be easily applied to other protein targets that have a number of protein-ligand complex structures available to improve predictions on binding.

  20. Ligand-Induced Stability of Gold Nanoclusters: Thiolate versus Selenolate. (United States)

    Kurashige, Wataru; Yamaguchi, Masaki; Nobusada, Katsuyuki; Negishi, Yuichi


    Thiolate-protected gold nanoclusters have attracted considerable attention as building blocks for new functional materials and have been extensively researched. Some studies have reported that changing the ligand of these gold nanoclusters from thiolate to selenolate increases cluster stability. To confirm this, in this study, we compare the stabilities of precisely synthesized [Au25(SC8H17)18](-) and [Au25(SeC8H17)18](-) against degradation in solution, thermal dissolution, and laser fragmentation. The results demonstrate that changing the ligand from thiolate to selenolate increases cluster stability in reactions involving dissociation of the gold-ligand bond but reduces cluster stability in reactions involving intramolecular dissociation of the ligand. These results reveal that using selenolate ligands makes it possible to produce gold clusters that are more stable against degradation in solution than thiolate-protected gold nanoclusters.

  1. Development of chiral sulfoxide ligands for asymmetric catalysis. (United States)

    Trost, Barry M; Rao, Meera


    Nitrogen-, phosphorus-, and oxygen-based ligands with chiral backbones have been the historic workhorses of asymmetric transition-metal-catalyzed reactions. On the contrary, sulfoxides containing chirality at the sulfur atom have mainly been used as chiral auxiliaries for diastereoselective reactions. Despite several distinct advantages over traditional ligand scaffolds, such as the proximity of the chiral information to the metal center and the ability to switch between S and O coordination, these compounds have only recently emerged as a versatile class of chiral ligands. In this Review, we detail the history of the development of chiral sulfoxide ligands for asymmetric catalysis. We also provide brief descriptions of metal-sulfoxide bonding and strategies for the synthesis of enantiopure sulfoxides. Finally, insights into the future development of this underutilized ligand class are discussed.

  2. Polypharmacology: in silico methods of ligand design and development. (United States)

    McKie, Samuel A


    How to design a ligand to bind multiple targets, rather than to a single target, is the focus of this review. Rational polypharmacology draws on knowledge that is both broad ranging and hierarchical. Computer-aided multitarget ligand design methods are described according to their nested knowledge level. Ligand-only and then receptor-ligand strategies are first described; followed by the metabolic network viewpoint. Subsequently strategies that view infectious diseases as multigenomic targets are discussed, and finally the disease level interpretation of medicinal therapy is considered. As yet there is no consensus on how best to proceed in designing a multitarget ligand. The current methodologies are bought together in an attempt to give a practical overview of how polypharmacology design might be best initiated.

  3. Predicting protein-ligand affinity with a random matrix framework. (United States)

    Lee, Alpha A; Brenner, Michael P; Colwell, Lucy J


    Rapid determination of whether a candidate compound will bind to a particular target receptor remains a stumbling block in drug discovery. We use an approach inspired by random matrix theory to decompose the known ligand set of a target in terms of orthogonal "signals" of salient chemical features, and distinguish these from the much larger set of ligand chemical features that are not relevant for binding to that particular target receptor. After removing the noise caused by finite sampling, we show that the similarity of an unknown ligand to the remaining, cleaned chemical features is a robust predictor of ligand-target affinity, performing as well or better than any algorithm in the published literature. We interpret our algorithm as deriving a model for the binding energy between a target receptor and the set of known ligands, where the underlying binding energy model is related to the classic Ising model in statistical physics.

  4. Protein ligand interactions: alkylated pyridinium salts as inhibitors of acetylcholinesterase from Electrophorus electricus. (United States)

    Whiteley, C G; Ngwenya, D S


    The interaction of alkyl-quaternary pyridinium hydrochloride salts on acetylcholinesterase (AChE, E.C. has been investigated. Kinetic analysis has shown that they reflect a competitive inhibition with Ki values in the range 5-12 microM and 7-17 microM for ethyl- and methyl-substituted salts, respectively. Spectrophotometry was used to study the binding of the ligands with the enzyme and Scatchard analysis used to calculate the respective dissociation constants (Kd) and the number of binding sites. The substitution position of the alkyl group on the pyridine ring also influenced the binding capacity and the Ki values.

  5. Protein ligand interactions 7 halogenated pyridinium salts as inhibitors of acetylcholinesterase from Electrophorus electricus. (United States)

    Whiteley, C G; Ngwenya, D S


    The interaction of halo-quaternary pyridinium hydrochloride salts on acetylcholinesterase (AChE, E.C. has been investigated. Kinetic analysis has shown that they reflect a non-competitive inhibition with Ki values in the range 8-13 microM and 5-34 microM for chloro- and bromo-substituted salts respectively. Spectrophotometry was used to study the binding of the ligands with the enzyme and Scatchard analysis used to calculate the respective dissociation constants (Kd) and the number of binding sites. The substitution position of the halogen on the pyridine ring also influenced the binding capacity and the Ki values.

  6. Determining the size-dependent structure of ligand-free gold-cluster ions. (United States)

    Schooss, Detlef; Weis, Patrick; Hampe, Oliver; Kappes, Manfred M


    Ligand-free metal clusters can be prepared over a wide size range, but only in comparatively small amounts. Determining their size-dependent properties has therefore required the development of experimental methods that allow characterization of sample sizes comprising only a few thousand mass-selected particles under well-defined collision-free conditions. In this review, we describe the application of these methods to the geometric structural determination of Au(n)(+) and Au(n)(-) with n = 3-20. Geometries were assigned by comparing experimental data, primarily from ion-mobility spectrometry and trapped ion electron diffraction, to structural models from quantum chemical calculations.

  7. Ligand induced circular dichroism and circularly polarized luminescence in CdSe quantum dots. (United States)

    Tohgha, Urice; Deol, Kirandeep K; Porter, Ashlin G; Bartko, Samuel G; Choi, Jung Kyu; Leonard, Brian M; Varga, Krisztina; Kubelka, Jan; Muller, Gilles; Balaz, Milan


    Chiral thiol capping ligands L- and D-cysteines induced modular chiroptical properties in achiral cadmium selenide quantum dots (CdSe QDs). Cys-CdSe prepared from achiral oleic acid capped CdSe by postsynthetic ligand exchange displayed size-dependent electronic circular dichroism (CD) and circularly polarized luminescence (CPL). Opposite CPL signals were measured for the CdSe QDs capped with D- and L-cysteine. The CD profile and CD anisotropy varied with size of CdSe nanocrystals with largest anisotropy observed for CdSe nanoparticles of 4.4 nm. Magic angle spinning solid state NMR (MAS ssNMR) experiments suggested bidentate interaction between cysteine and the surface of CdSe. Time Dependent Density Functional Theory (TDDFT) calculations verified that attachment of L- and D-cysteine to the surface of model (CdSe)13 nanoclusters induces measurable opposite CD signals for the exitonic band of the nanocluster. The origin of the induced chirality is consistent with the hybridization of highest occupied CdSe molecular orbitals with those of the chiral ligand.

  8. Copper(II and lead(II complexation by humic acid and humic-like ligands

    Directory of Open Access Journals (Sweden)



    Full Text Available The stability of metal–humate complexes is an important factor determining and predicting speciation, mobility and bioavailability of heavy metals in the environment. A comparative investigation of the complexation of Cu(II and Pb(II with humic acid and humic-like ligands, such as benzoic and salicylic acid, was performed. The analysis was realized at pH 4.0, a temperature of 25 °C and at an ionic strength of 0.01 mol dm-3 (NaCl using the Schubert ion-exchange method and its modified form. The stability constants were calculated from the experimental data by the Schubert method for complexes with benzoic and humic acid. A modified Schubert method was used for the determination of the stability constants of the complexes with salicylic acid. It was found that Cu(II and Pb(II form mononuclear complexes with benzoic and humic acid while with salicylic acid both metals form polynuclear complexes. The results indicate that Pb(II has a higher binding ability than Cu(II to all the investigated ligands. The Cu(II–salicylate and Pb(II–salicylate complexes showed noticeable higher stability constants compared with their complexes with humic acid, while the stabilities of the complexes with benzoic acid differed less. Salicylic and benzoic acids as humic-like ligands can be used for setting the range of stability constants of humic complexes with Cu(II and Pb(II.

  9. Ambivalent binding between a radical-based pincer ligand and iron. (United States)

    Harriman, Katie L M; Leitch, Alicea A; Stoian, Sebastian A; Habib, Fatemah; Kneebone, Jared L; Gorelsky, Serge I; Korobkov, Ilia; Desgreniers, Serge; Neidig, Michael L; Hill, Stephen; Murugesu, Muralee; Brusso, Jaclyn L


    A complex exhibiting valence delocalization was prepared from 3,5-bis(2-pyridyl)-1,2,4,6-thiatriazinyl (), an inherently redox active pincer-type ligand, coordinated to iron ( ()). Complex can be prepared via two routes, either from the reaction of the neutral radical with FeCl2 or by treatment of the anionic ligand () with FeCl3, demonstrating its unique redox behaviour. Electrochemical studies, solution absorption and solid-state diffuse reflectance measurements along with X-ray crystallography were carried out to elucidate the molecular and solid-state properties. Temperature- and field-dependent Mössbauer spectroscopy coupled with magnetic measurements revealed that exhibits an isolated S = 5/2 ground spin state for which the low-temperature magnetic behaviour is dominated by exchange interactions between neighbouring molecules. This ground state is rationalized on the basis of DFT calculations that predict the presence of strong electronic interactions between the redox active ligand and metal. This interaction leads to the delocalization of β electron density over the two redox active centres and highlights the difficulty in assigning formal charges to .

  10. Searching for new aluminium chelating agents: a family of hydroxypyrone ligands. (United States)

    Toso, Leonardo; Crisponi, Guido; Nurchi, Valeria M; Crespo-Alonso, Miriam; Lachowicz, Joanna I; Mansoori, Delara; Arca, Massimiliano; Santos, M Amélia; Marques, Sérgio M; Gano, Lurdes; Niclós-Gutíerrez, Juan; González-Pérez, Josefa M; Domínguez-Martín, Alicia; Choquesillo-Lazarte, Duane; Szewczuk, Zbigniew


    Attention is devoted to the role of chelating agents in the treatment of aluminium related diseases. In fact, in spite of the efforts that have drastically reduced the occurrence of aluminium dialysis diseases, they so far constitute a cause of great medical concern. The use of chelating agents for iron and aluminium in different clinical applications has found increasing attention in the last thirty years. With the aim of designing new chelators, we synthesized a series of kojic acid derivatives containing two kojic units joined by different linkers. A huge advantage of these molecules is that they are cheap and easy to produce. Previous works on complex formation equilibria of a first group of these ligands with iron and aluminium highlighted extremely good pMe values and gave evidence of the ability to scavenge iron from inside cells. On these bases a second set of bis-kojic ligands, whose linkers between the kojic chelating moieties are differentiated both in terms of type and size, has been designed, synthesized and characterized. The aluminium(III) complex formation equilibria studied by potentiometry, electrospray ionization mass spectroscopy (ESI-MS), quantum-mechanical calculations and (1)H NMR spectroscopy are here described and discussed, and the structural characterization of one of these new ligands is presented. The in vivo studies show that these new bis-kojic derivatives induce faster clearance from main organs as compared with the monomeric analog. © 2013.

  11. Biophysical and physicochemical methods differentiate highly ligand-efficient human D-amino acid oxidase inhibitors. (United States)

    Lange, Jos H M; Venhorst, Jennifer; van Dongen, Maria J P; Frankena, Jurjen; Bassissi, Firas; de Bruin, Natasja M W J; den Besten, Cathaline; de Beer, Stephanie B A; Oostenbrink, Chris; Markova, Natalia; Kruse, Chris G


    Many early drug research efforts are too reductionist thereby not delivering key parameters such as kinetics and thermodynamics of target-ligand binding. A set of human D-Amino Acid Oxidase (DAAO) inhibitors 1-6 was applied to demonstrate the impact of key biophysical techniques and physicochemical methods in the differentiation of chemical entities that cannot be adequately distinguished on the basis of their normalized potency (ligand efficiency) values. The resulting biophysical and physicochemical data were related to relevant pharmacodynamic and pharmacokinetic properties. Surface Plasmon Resonance data indicated prolonged target-ligand residence times for 5 and 6 as compared to 1-4, based on the observed k(off) values. The Isothermal Titration Calorimetry-derived thermodynamic binding profiles of 1-6 to the DAAO enzyme revealed favorable contributions of both ΔH and ΔS to their ΔG values. Surprisingly, the thermodynamic binding profile of 3 elicited a substantially higher favorable contribution of ΔH to ΔG in comparison with the structurally closely related fused bicyclic acid 4. Molecular dynamics simulations and free energy calculations of 1, 3, and 4 led to novel insights into the thermodynamic properties of the binding process at an atomic level and in the different thermodynamic signatures of 3 and 4. The presented holistic approach is anticipated to facilitate the identification of compounds with best-in-class properties at an early research stage.

  12. Towards full Quantum-Mechanics-based Protein-Ligand Binding Affinities. (United States)

    Ehrlich, Stephan; Göller, Andreas H; Grimme, Stefan


    Computational methods play a key role in modern drug design in the pharmaceutical industry but are mostly based on force fields, which are limited in accuracy when describing non-classical binding effects, proton transfer, or metal coordination. Here, we propose a general fully quantum mechanical (QM) scheme for the computation of protein-ligand affinities. It works on a single protein cutout (of about 1000 atoms) and evaluates all contributions (interaction energy, solvation, thermostatistical) to absolute binding free energy on the highest feasible QM level. The methodology is tested on two different protein targets: activated serine protease factor X (FXa) and tyrosine-protein kinase 2 (TYK2). We demonstrate that the geometry of the model systems can be efficiently energy-minimized by using general purpose graphics processing units, resulting in structures that are close to the co-crystallized protein-ligand structures. Our best calculations at a hybrid DFT level (PBEh-3c composite method) for the FXa ligand set result in an overall mean absolute deviation as low as 2.1 kcal mol(-1) . Though very encouraging, an analysis of outliers indicates that the structure optimization level, conformational sampling, and solvation treatment require further improvement.

  13. On the feasibility of designing hyperalkali cations using superalkali clusters as ligands (United States)

    Sun, Wei-Ming; Li, Xiang-Hui; Li, Ying; Liu, Jia-Yuan; Wu, Di; Li, Chun-Yan; Ni, Bi-Lian; Li, Zhi-Ru


    The possibility of using superalkali clusters instead of alkali atoms as ligands to design a class of cationic compounds, referred to as hyperalkali cations, has been examined by using gradient-corrected density functional theory. By taking typical superalkalis (FLi2, OLi3, and NLi4) as examples, a series of hyperalkali cations ML2+ [M = (super)halogen; L = superalkali] have been constructed and investigated. Calculational results show that all the superalkali moieties preserve their geometric and electronic integrity in these proposed cations. The stability of these studied cations is guaranteed by the strong ionic bonds between superalkali ligand and (super)halogen core, as well as their large highest occupied molecular orbital-lowest unoccupied molecular orbital gaps and positive dissociation energies. In particular, all these proposed cations possess lower vertical electron affinities (2.36-3.56 eV) than those of their corresponding cationic superalkali ligands, verifying their hyperalkali nature. We, therefore, hope that this study will provide an approach to obtain new species with excellent reducing capability by utilizing various superalkalis as building blocks.

  14. Lanthanide complexes derived from hexadentate macrocyclic ligand: synthesis, spectroscopic and thermal investigation. (United States)

    Chandra, Sulekh; Tyagi, Monika; Rani, Soni; Kumar, Sumit


    The lanthanide complexes derived from (3,5,13,15-tetramethyl 2,6,12,16,21-22-hexaazatricyclo[15.3.I(1-17)I(7-11)]cosa-1(21),2,5,7,9,11(22),12,15,17,19-decane) were synthesized. The complexes were found to have general composition [Ln(L)X(2).H(2)O]X, where Ln=La(3+), Ce(3+), Nd(3+), Sm(3+) and Eu(3+) and X=NO(3)(-) and Cl(-). The ligand was characterized by elemental analyses, IR, Mass, and (1)H NMR spectral studies. All the complexes were characterized by elemental analyses, molar conductance measurements, magnetic susceptibility measurements, IR, Mass, electronic spectral techniques and thermal studies. The ligand acts as a hexadentate and coordinates through four nitrogen atoms of azomethine groups and two nitrogen of pyridine ring. The lanthanum complexes are diamagnetic while the other Ln(III) complexes are paramagnetic. The spectral parameters i.e. nephelauxetic ratio (beta), covalency factor (b(1/2)), Sinha parameter (delta%) and covalency angular overlap parameter (eta) have been calculated from absorption spectra of Nd(III) and Sm(III) complexes. These parameters suggest the metal-ligand covalent bonding. In the present study, the complexes were found to have coordination number nine.

  15. Bioavailability and Electroreactivity of Zinc Complexed to Strong and Weak Organic Ligands. (United States)

    Kim, Ja-Myung; Baars, Oliver; Morel, François M M


    Laboratory experiments have established the importance of complexation by organic ligands in determining the bioavailability of trace metals to marine phytoplankton, while electrochemical measurements with field samples have demonstrated that a large fraction of bioactive trace metals are complexed to strong organic ligands in seawater. Using the model organic ligands, EDTA and histidine, we show a quantitative correspondence between the bioavailability of Zn to the diatom Thalassiosira weissflogii, and its reduction at -1.2 V (vs Ag/AgCl) on a hanging mercury drop electrode. Equilibrium calculations and polarographic data indicate that Zn bound in inorganic complexes and the 1:1 Zn-histidine complex, but not in the 1:2 Zn-histidine complex or the Zn-EDTA complexes, is taken up by the organism and reduced at the electrode surface, confirming a previous report of the bioavailability of weak Zn complexes. Electrochemical measurements of Zn speciation in seawater do not generally reveal the presence of weak (and potentially bioavailable) complexes; but such measurements (particularly by Anodic Stripping Voltammetry) should nonetheless often provide good estimates of the bioavailable Zn concentrations. These results can likely be generalized to other bioactive divalent trace metals.

  16. Highly Fluorescent Group 13 Metal Complexes with Cyclic, Aromatic Hydroxamic Acid Ligands

    Energy Technology Data Exchange (ETDEWEB)

    Seitz, Michael; Moore, Evan G.; Raymond, Kenneth N.


    The neutral complexes of two ligands based on the 1-oxo-2-hydroxy-isoquinoline (1,2-HOIQO) motif with group 13 metals (Al, Ga, In) show bright blue-violet luminescence in organic solvents. The corresponding transition can be attributed to ligand-centered singlet emission, characterized by a small Stokes shifts of only a few nm combined with lifetimes in the range between 1-3 ns. The fluorescence efficiency is high, with quantum yields of up to 37% in benzene solution. The crystal structure of one of the indium(III) complexes (trigonal space group R-3, a = b = 13.0384(15) {angstrom}, c = 32.870(8) {angstrom}, ? = {beta} = 90{sup o}, {gamma} = 120{sup o}, V = 4839.3(14) {angstrom}{sup 3}, Z = 6) shows a six-coordinate geometry around the indium center which is close to trigonal-prismatic, with a twist angle between the two trigonal faces of 20.7{sup o}. Time-dependent density functional theory (TD-DFT) calculations (Al and Ga: B3LYP/6-31G(d)); In: B3LYP/LANL2DZ of the fac and mer isomers with one of the two ligands indicate that there is no clear preference for either one of the isomeric forms of the metal complexes. In addition, the metal centers do not have a significant influence on the electronic structure, and as a consequence, on the predominant intraligand optical transitions.

  17. Ligand Induced Circular Dichroism and Circularly Polarized Luminescence in CdSe Quantum Dots (United States)

    Tohgha, Urice; Deol, Kirandeep K.; Porter, Ashlin G.; Bartko, Samuel G.; Choi, Jung Kyu; Leonard, Brian M.; Varga, Krisztina; Kubelka, Jan; Muller, Gilles; Balaz, Milan


    Chiral thiol capping ligands L- and D-cysteines induced modular chiroptical properties in achiral cadmium selenide quantum dots (CdSe QDs). Cys-CdSe prepared from achiral oleic acid capped CdSe by post-synthetic ligand exchange displayed size-dependent electronic circular dichroism (CD) and circularly polarized luminescence (CPL). Opposite CPL signals were measured for the CdSe QDs capped with D- and L-cysteine. The CD profile and CD anisotropy varied with size of CdSe nanocrystals with largest anisotropy observed for CdSe nanoparticles of 4.4 nm. Magic angle spinning solid state NMR (MAS ssNMR) experiments suggested bidentate interaction between cysteine and the surface of CdSe. Density functional theory (DFT) calculations verified that attachment of L- and D-cysteine to the surface of model (CdSe)13 nanoclusters induces measurable opposite CD signals for the exitonic band of the nanocluster. The chirality was induced by the hybridization of highest occupied CdSe molecular orbitals with those of the chiral ligand. PMID:24200288

  18. Prediction of the Iron-Based Polynuclear Magnetic Superhalogens with Pseudohalogen CN as Ligands. (United States)

    Ding, Li-Ping; Shao, Peng; Lu, Cheng; Zhang, Fang-Hui; Liu, Yun; Mu, Qiang


    To explore stable polynuclear magnetic superhalogens, we perform an unbiased structure search for polynuclear iron-based systems based on pseudohalogen ligand CN using the CALYPSO method in conjunction with density functional theory. The superhalogen properties, magnetic properties, and thermodynamic stabilities of neutral and anionic Fe2(CN)5 and Fe3(CN)7 clusters are investigated. The results show that both of the clusters have superhalogen properties due to their electron affinities (EAs) and that vertical detachment energies (VDEs) are significantly larger than those of the chlorine element and their ligand CN. The distribution of the extra electron analysis indicates that the extra electron is aggregated mainly into pseudohalogen ligand CN units in Fe2(CN)5(¯) and Fe3(CN)7(¯) cluster. These features contribute significantly to their high EA and VDE. Besides superhalogen properties, these two anionic clusters carry a large magnetic moment just like the Fe2F5(¯) cluster. Additionally, the thermodynamic stabilities are also discussed by calculating the energy required to fragment the cluster into various smaller stable clusters. It is found that Fe(CN)2 is the most favorable fragmentation product for anionic Fe2(CN)5(¯) and Fe3(CN)7(¯) clusters, and both of the anions are less stable against ejection of Fe atoms than Fe(CN)n-x.

  19. The Role of Ligand Packing Frustration in Body-Centered Cubic (bcc) Superlattices of Colloidal Nanocrystals. (United States)

    Goodfellow, Brian W; Yu, Yixuan; Bosoy, Christian A; Smilgies, Detlef-M; Korgel, Brian A


    This paper addresses the assembly of body centered-cubic (bcc) superlattices of organic ligand-coated nanocrystals. First, examples of bcc superlattices of dodecanethiol-capped Au nanocrystals and oleic acid-capped PbS and PbSe nanocrystals are presented and examined by transmission electron microscopy (TEM) and grazing incidence small-angle X-ray scattering (GISAXS). These superlattices tend to orient on their densest (110) superlattice planes and exhibit a significant amount of {112} twinning. The same nanocrystals deposit as monolayers with hexagonal packing, and these thin films can coexist with thicker bcc superlattice layers, even though there is no hexagonal plane in a bcc lattice. Both the preference of bcc in bulk films over the denser face-centered cubic (fcc) superlattice structure and the transition to hexagonal monolayers can be rationalized in terms of packing frustration of the ligands. A model is presented to calculate the difference in entropy associated with capping ligand packing frustration in bcc and fcc superlattices.

  20. A novel method for protein-ligand binding affinity prediction and the related descriptors exploration. (United States)

    Li, Shuyan; Xi, Lili; Wang, Chengqi; Li, Jiazhong; Lei, Beilei; Liu, Huanxiang; Yao, Xiaojun


    In this study, a novel method was developed to predict the binding affinity of protein-ligand based on a comprehensive set of structurally diverse protein-ligand complexes (PLCs). The 1300 PLCs with binding affinity (493 complexes with K(d) and 807 complexes with K(i)) from the refined dataset of PDBbind Database (release 2007) were studied in the predictive model development. In this method, each complex was described using calculated descriptors from three blocks: protein sequence, ligand structure, and binding pocket. Thereafter, the PLCs data were rationally split into representative training and test sets by full consideration of the validation of the models. The molecular descriptors relevant to the binding affinity were selected using the ReliefF method combined with least squares support vector machines (LS-SVMs) modeling method based on the training data set. Two final optimized LS-SVMs models were developed using the selected descriptors to predict the binding affinities of K(d) and K(i). The correlation coefficients (R) of training set and test set for K(d) model were 0.890 and 0.833. The corresponding correlation coefficients for the K(i) model were 0.922 and 0.742, respectively. The prediction method proposed in this work can give better generalization ability than other recently published methods and can be used as an alternative fast filter in the virtual screening of large chemical database. (c) 2008 Wiley Periodicals, Inc.

  1. Specific noncovalent interactions at protein-ligand interface: implications for rational drug design. (United States)

    Zhou, P; Huang, J; Tian, F


    Specific noncovalent interactions that are indicative of attractive, directional intermolecular forces have always been of key interest to medicinal chemists in their search for the "glue" that holds drugs and their targets together. With the rapid increase in the number of solved biomolecular structures as well as the performance enhancement of computer hardware and software in recent years, it is now possible to give more comprehensive insight into the geometrical characteristics and energetic landscape of certain sophisticated noncovalent interactions present at the binding interface of protein receptors and small ligands based on accumulated knowledge gaining from the combination of two quite disparate but complementary approaches: crystallographic data analysis and quantum-mechanical ab initio calculation. In this perspective, we survey massive body of published works relating to structural characterization and theoretical investigation of three kinds of strong, specific, direct, enthalpy-driven intermolecular forces, including hydrogen bond, halogen bond and salt bridge, involved in the formation of protein-ligand complex architecture in order to characterize their biological functions in conferring affinity and specificity for ligand recognition by host protein. In particular, the biomedical implications of raised knowledge are discussed with respect to potential applications in rational drug design.

  2. Spectral and thermal studies with anti-fungal aspects of some organotin(IV) complexes with nitrogen and sulphur donor ligands derived from 2-phenylethylamine (United States)

    Singh, Rajeev; Kaushik, N. K.


    Some complexes of 2-phenylethyl dithiocarbamate, thiohydrazides and thiodiamines with dibenzyltin(IV) chloride, tribenzyltin(IV) chloride and di( para-chlorobenzyl)tin(IV) dichloride have been synthesized and investigated in 1:2 and 1:1 molar ratio. The dithiocarbamate ligand act as monoanionic bidentate and thiohydrazide, thiodiamines act as neutral bidentate ligand. The synthesized complexes have been characterized by elemental analysis and molecular weight determination studies and their bonding pattern suggested on the basis of electronic, infrared, 1H and 13C NMR spectroscopy. Using thermogravimetric (TG) and differential thermal analysis (DTA) various thermodynamic and kinetic parameters viz. reaction order ( n), apparent activation energy ( Ea), apparent activation entropy ( S#) and heat of reaction (Δ H) have been calculated and correlated with the structural aspects for solid-state decomposition of complexes. The ligands and their tin complexes have also been screened for their fungitoxicity activity against Rhizoctonia solanii and Sclerotium rolfsii and their ED 50 values calculated.

  3. Gas adsorption and gas mixture separations using mixed-ligand MOF material (United States)

    Hupp, Joseph T.; Mulfort, Karen L.; Snurr, Randall Q.; Bae, Youn-Sang


    A method of separating a mixture of carbon dioxiode and hydrocarbon gas using a mixed-ligand, metal-organic framework (MOF) material having metal ions coordinated to carboxylate ligands and pyridyl ligands.

  4. Equilibrium calculations of firework mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Hobbs, M.L. [Sandia National Labs., Albuquerque, NM (United States); Tanaka, Katsumi; Iida, Mitsuaki; Matsunaga, Takehiro [National Inst. of Materials and Chemical Research, Tsukuba, Ibaraki (Japan)


    Thermochemical equilibrium calculations have been used to calculate detonation conditions for typical firework components including three report charges, two display charges, and black powder which is used as a fuse or launch charge. Calculations were performed with a modified version of the TIGER code which allows calculations with 900 gaseous and 600 condensed product species at high pressure. The detonation calculations presented in this paper are thought to be the first report on the theoretical study of firework detonation. Measured velocities for two report charges are available and compare favorably to predicted detonation velocities. However, the measured velocities may not be true detonation velocities. Fast deflagration rather than an ideal detonation occurs when reactants contain significant amounts of slow reacting constituents such as aluminum or titanium. Despite such uncertainties in reacting pyrotechnics, the detonation calculations do show the complex nature of condensed phase formation at elevated pressures and give an upper bound for measured velocities.

  5. Global nuclear-structure calculations

    Energy Technology Data Exchange (ETDEWEB)

    Moeller, P.; Nix, J.R.


    The revival of interest in nuclear ground-state octupole deformations that occurred in the 1980's was stimulated by observations in 1980 of particularly large deviations between calculated and experimental masses in the Ra region, in a global calculation of nuclear ground-state masses. By minimizing the total potential energy with respect to octupole shape degrees of freedom in addition to {epsilon}{sub 2} and {epsilon}{sub 4} used originally, a vastly improved agreement between calculated and experimental masses was obtained. To study the global behavior and interrelationships between other nuclear properties, we calculate nuclear ground-state masses, spins, pairing gaps and {Beta}-decay and half-lives and compare the results to experimental qualities. The calculations are based on the macroscopic-microscopic approach, with the microscopic contributions calculated in a folded-Yukawa single-particle potential.

  6. Regulation mechanisms of the FLT3-ligand after irradiation; Mecanismes de regulation du FLT3-ligand apres irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Prat-Lepesant, M


    The hematopoietic compartment is one of the most severely damaged after chemotherapy, radiotherapy or accidental irradiations. Whatever its origin, the resulting damage to the bone marrow remains difficult to evaluate. Thus, it would be of great interest to get a biological indicator of residual hematopoiesis in order to adapt the treatment to each clinical situation. Recent results indicated that the plasma Flt3 ligand concentration was increased in patients suffering from either acquired or induced aplasia, suggesting that Flt3 ligand might be useful as a biological indicator of bone marrow status. We thus followed in a mouse model as well as in several clinical situations the variations in plasma Flt3 ligand concentration, after either homogeneous or heterogeneous irradiations. These variations were correlated to the number of hematopoietic progenitors and to other parameters such as duration and depth of pancytopenia. The results indicated that the concentration of Flt3 ligand in the blood reflects the bone marrow status, and that the follow-up of plasma Flt3 ligand concentration could give predictive information about the bone marrow function and the duration and severity of pancytopenia and thrombocytopenia. Nevertheless, the clinical use of Flt3 ligand as a biological indicator of bone marrow damage require the knowledge of the mechanisms regulating the variations in plasma Flt3 ligand concentration. We thus developed a study in the mouse model. The results indicated that the variations in plasma Flt3 ligand variations were not solely due to a balance between its production by lymphoid cells and its consumption by hematopoietic cells. Moreover, we showed that T lymphocytes are not the main regulator of plasma Flt3 ligand concentration as previously suggested, and that other cell types, possibly including bone marrow stromal cells, might be strongly implicated. These results also suggest that the Flt3 ligand is a main systemic regulator of hematopoiesis

  7. Computational exploration of a protein receptor binding space with student proposed peptide ligands. (United States)

    King, Matthew D; Phillips, Paul; Turner, Matthew W; Katz, Michael; Lew, Sarah; Bradburn, Sarah; Andersen, Tim; McDougal, Owen M


    Computational molecular docking is a fast and effective in silico method for the analysis of binding between a protein receptor model and a ligand. The visualization and manipulation of protein to ligand binding in three-dimensional space represents a powerful tool in the biochemistry curriculum to enhance student learning. The DockoMatic tutorial described herein provides a framework by which instructors can guide students through a drug screening exercise. Using receptor models derived from readily available protein crystal structures, docking programs have the ability to predict ligand binding properties, such as preferential binding orientations and binding affinities. The use of computational studies can significantly enhance complimentary wet chemical experimentation by providing insight into the important molecular interactions within the system of interest, as well as guide the design of new candidate ligands based on observed binding motifs and energetics. In this laboratory tutorial, the graphical user interface, DockoMatic, facilitates docking job submissions to the docking engine, AutoDock 4.2. The purpose of this exercise is to successfully dock a 17-amino acid peptide, α-conotoxin TxIA, to the acetylcholine binding protein from Aplysia californica-AChBP to determine the most stable binding configuration. Each student will then propose two specific amino acid substitutions of α-conotoxin TxIA to enhance peptide binding affinity, create the mutant in DockoMatic, and perform docking calculations to compare their results with the class. Students will also compare intermolecular forces, binding energy, and geometric orientation of their prepared analog to their initial α-conotoxin TxIA docking results.

  8. Reversible dissociation and ligand-glutathione exchange reaction in binuclear cationic tetranitrosyl iron complex with penicillamine. (United States)

    Syrtsova, Lidia; Sanina, Natalia; Lyssenko, Konstantin; Kabachkov, Evgeniy; Psikha, Boris; Shkondina, Natal'ja; Pokidova, Olesia; Kotelnikov, Alexander; Aldoshin, Sergey


    This paper describes a comparative study of the decomposition of two nitrosyl iron complexes (NICs) with penicillamine thiolic ligands [Fe2(SC5H11NO2)2(NO)4]SO4 ·5H2O (I) and glutathione- (GSH-) ligands [Fe2(SC10H17N3O6)2(NO)4]SO4 ·2H2O (II), which spontaneously evolve to NO in aqueous medium. NO formation was measured by a sensor electrode and by spectrophotometric methods by measuring the formation of a hemoglobin- (Hb-) NO complex. The NO evolution reaction rate from (I)  k 1 = (4.6 ± 0.1)·10(-3) s(-1) and the elimination rate constant of the penicillamine ligand k 2 = (1.8 ± 0.2)·10(-3) s(-1) at 25°C in 0.05 M phosphate buffer,  pH 7.0, was calculated using kinetic modeling based on the experimental data. Both reactions are reversible. Spectrophotometry and mass-spectrometry methods have firmly shown that the penicillamine ligand is exchanged for GS(-) during decomposition of 1.5·10(-4) M (I) in the presence of 10(-3) M GSH, with 76% yield in 24 h. As has been established, such behaviour is caused by the resistance of (II) to decomposition due to the higher affinity of iron to GSH in the complex. The discovered reaction may impede S-glutathionylation of the essential enzyme systems in the presence of (I) and is important for metabolism of NIC, connected with its antitumor activity.

  9. Computational Exploration of a Protein Receptor Binding Space with Student Proposed Peptide Ligands (United States)

    King, Matthew D.; Phillips, Paul; Turner, Matthew W.; Katz, Michael; Lew, Sarah; Bradburn, Sarah; Andersen, Tim; Mcdougal, Owen M.


    Computational molecular docking is a fast and effective in silico method for the analysis of binding between a protein receptor model and a ligand. The visualization and manipulation of protein to ligand binding in three-dimensional space represents a powerful tool in the biochemistry curriculum to enhance student learning. The DockoMatic tutorial described herein provides a framework by which instructors can guide students through a drug screening exercise. Using receptor models derived from readily available protein crystal structures, docking programs have the ability to predict ligand binding properties, such as preferential binding orientations and binding affinities. The use of computational studies can significantly enhance complimentary wet chemical experimentation by providing insight into the important molecular interactions within the system of interest, as well as guide the design of new candidate ligands based on observed binding motifs and energetics. In this laboratory tutorial, the graphical user interface, DockoMatic, facilitates docking job submissions to the docking engine, AutoDock 4.2. The purpose of this exercise is to successfully dock a 17-amino acid peptide, α-conotoxin TxIA, to the acetylcholine binding protein from Aplysia californica-AChBP to determine the most stable binding configuration. Each student will then propose two specific amino acid substitutions of α-conotoxin TxIA to enhance peptide binding affinity, create the mutant in DockoMatic, and perform docking calculations to compare their results with the class. Students will also compare intermolecular forces, binding energy, and geometric orientation of their prepared analog to their initial α-conotoxin TxIA docking results. PMID:26537635

  10. Palladium(II) complex with thiazole containing tridentate ONN donor ligand: Synthesis, X-ray structure and DFT computation (United States)

    Biswas, Sujan; Pramanik, Ajoy Kumar; Mondal, Tapan Kumar


    New palladium(II) complex with 2-(2-thiazolyl)-4-methylphenol (TAC) having general formula [Pd(TAC)Cl) (1) has been synthesized and characterized. The complex has been characterized by various spectroscopic techniques. Single crystal X-ray structure shows distorted square planar geometry around palladium(II). Cyclic voltammetric studies shows ligand based irreversible oxidation and reduction peaks. The electronic structure, redox properties and electronic excitations in the complex are interpreted by DFT and TDDFT calculations.

  11. Spectrochemical Series and the Dependence of Racah and 10Dq Parameters on the Metal−Ligand Distance: Microscopic Origin

    DEFF Research Database (Denmark)

    Trueba, A.; Garcia-Fernandez, P.; García Lastra, Juan Maria


    The origin of the spectrochemical series and the different dependence of crystal-field splitting (10Dq) and Racah parameters on the metal−ligand distance, R, is explored through ab initio calculations on Cr3+-doped K2NaScF6, Cs2NaYCl6, Cs2NaYBr6, and Cs2NaYI6 lattices. For this purpose both perio...

  12. Synthesis, characterization, and reactivity of a side-on manganese(iii)-peroxo complex bearing a pentadentate aminopyridine ligand. (United States)

    Du, Junyi; Xu, Daqian; Zhang, Chunxi; Xia, Chungu; Wang, Yong; Sun, Wei


    A manganese(ii) complex has been prepared with a proline-derived pentadentate ligand (Pro3Py), and it can be converted to a peroxomanganese(iii) complex in the presence of H2O2 and triethylamine. The resulting peroxomanganese(iii) complex was well characterised by UV-vis, EPR and ESI-MS techniques, and the geometric structure was discussed based on DFT calculations.

  13. Electronic spectra and photophysics of platinum(II) complexes with alpha-diimine ligands - Solid-state effects. I - Monomers and ligand pi dimers (United States)

    Miskowski, Vincent M.; Houlding, Virginia H.


    Two types of emission behavior for Pt(II) complexes containing alpha-diimine ligands have been observed in dilute solution. If the complex also has weak field ligands such as chloride, ligand field (d-d) excited states become the lowest energy excited states. If only strong field ligands are present, a diimine 3(pi-pi/asterisk/) state becomes the lowest. In none of the cases studied did metal-to-ligand charge transfer excited state lie lowest.

  14. Equilibria and kinetics for pH-dependent axial ligation of ethylester and methylester(aquo)cobaloximes with aromatic and aliphatic N-donor ligands and a molecular mechanistic study of the Co-C bond

    Indian Academy of Sciences (India)

    J V Madhuri; V Malathi; S Satyanarayana


    Equilibrium constants are determined for the reaction of ethylester and methyl ester (aquo) cobaloximes with histamine, histidine, glycine and ethyl glycine ester as a function of pH at 25°C, using spectrophotometric technique. The functional dependence of p on the substitution rate of H2O varies with the p of the incoming ligand, establishing the existence of nucleophilic participation of the ligand in the transition state. This data is interpreted with the help of kinetic data where dissociation kinetic reactions were also studied as a function of pH. Binding and kinetic data were correlated based on the basicity, steric hindrance of the entering ligand and HSAB principle. To compare the rate constants of the entering ligands pH-independent second-order rate constants were calculated. The effect of incoming ligand on Co-C bond is studied using molecular mechanics.

  15. A new bioactive Schiff base ligands derived from propylazo-N-pyrimidin-2-yl-benzenesulfonamides Mn(II) and Cu(II) complexes: synthesis, thermal and spectroscopic characterization biological studies and 3D modeling structures. (United States)

    Tawfik, Abdelrazak M; El-Ghamry, Mosad A; Abu-El-Wafa, Samy M; Ahmed, Naglaa M


    New series of Schiff base ligand H(2)L and their Cu(II) and Mn(II) complexes derived from azosulfapyrimidine were synthesized and characterized by elemental and thermal studies conductance measurements IR, electronic and EPR spectra. 3D modeling of the ligand indicate that azo group does not participate in complex formation and surface potential on one of the ligand under study indicate that electron density around azomethine groups are much higher than the azo group therefore coordination takes place around azomethine groups. The variety in the geometrical structures depends on the nature of both the metal ions and the Schiff base ligands. The thermo kinetic parameters are calculated and discussed. The biological activities of the ligands and complexes have been screened in vitro against some bacteria and fungi to study their capacity to inhibit their growth and to study the toxicity of the compounds.


    Directory of Open Access Journals (Sweden)

    Bogdan Nedic


    Full Text Available The paper presents description methods of metal cutting and calculation of treatment costs based on model that is developed on Faculty of mechanical engineering in Kragujevac. Based on systematization and analysis of large number of calculation models of cutting with unconventional methods, mathematical model is derived, which is used for creating a software for calculation costs of metal cutting. Software solution enables resolving the problem of calculating the cost of laser cutting, comparison' of costs made by other unconventional methods and provides documentation that consists of reports on estimated costs.

  17. Interaction Energies in Complexes of Zn and Amino Acids: A Comparison of Ab Initio and Force Field Based Calculations. (United States)

    Ahlstrand, Emma; Hermansson, Kersti; Friedman, Ran


    Zinc plays important roles in structural stabilization of proteins, enzyme catalysis, and signal transduction. Many Zn binding sites are located at the interface between the protein and the cellular fluid. In aqueous solutions, Zn ions adopt an octahedral coordination, while in proteins zinc can have different coordinations, with a tetrahedral conformation found most frequently. The dynamics of Zn binding to proteins and the formation of complexes that involve Zn are dictated by interactions between Zn and its binding partners. We calculated the interaction energies between Zn and its ligands in complexes that mimic protein binding sites and in Zn complexes of water and one or two amino acid moieties, using quantum mechanics (QM) and molecular mechanics (MM). It was found that MM calculations that neglect or only approximate polarizability did not reproduce even the relative order of the QM interaction energies in these complexes. Interaction energies calculated with the CHARMM-Drude polarizable force field agreed better with the ab initio results, although the deviations between QM and MM were still rather large (40-96 kcal/mol). In order to gain further insight into Zn-ligand interactions, the free energies of interaction were estimated by QM calculations with continuum solvent representation, and we performed energy decomposition analysis calculations to examine the characteristics of the different complexes. The ligand-types were found to have high impact on the relative strength of polarization and electrostatic interactions. Interestingly, ligand-ligand interactions did not play a significant role in the binding of Zn. Finally, analysis of ligand exchange energies suggests that carboxylates could be exchanged with water molecules, which explains the flexibility in Zn binding dynamics. An exchange between carboxylate (Asp/Glu) and imidazole (His) is less likely.


    Directory of Open Access Journals (Sweden)

    Lisnyak Yu. V.


    algorithm. To model the reduction in flexibility of allosteric pocket on modulator binding, the unperturbed normal modes are first calculated for the protein. The calculation is then repeated, each time perturbing one of the pockets in the protein. These results are combined with output from Fpocket in a support vector machine (SVM to predict allosteric pockets on proteins. The AlloSite server is similar to the AlloPred method in that it uses the Fpocket algorithm to elucidate allosteric pockets, whereas AlloPred uses an approach that combines flexibility with the Fpocket output. Results and discussion. By computational solvent mapping method FTSite, we have explored M.tuberculosis urease nonamer surface to find sites that tend to bind small organic molecular probes representing fragments of drug molecules with diverse hydrophobic and hydrophilic properties. The predicted three top ranked binding sites were situated at the interfaces between chains C and A, and chain G of neighbour trimer (and at equivalent locations in symmetrical trimers as well. A mapping of enzymes generally yields the most probable sites situated in a subsite of the enzyme active site. This was not the case for MTU which active sites were inaccessible for probes due to the closed conformation of the covering flap, and predicted binding sites were located not far from them at the entrance into a deep pocket. To explore their possible structural and functional role, we correlated the locations of predicted MTU binding sites and its ancillary pockets (which remain open and solvent exposed even while the flap is closed and indicated their partial overlapping. This overlapping may suggest that predicted sites are likely the intermediate binding sites responsible for recruiting a ligand to another binding site deeply buried in the protein. To examine the possibility that predicted binding sites are the sites for allostery binding we carried out the search for probable sites of allostery binding on MTU

  19. APBSmem: a graphical interface for electrostatic calculations at the membrane.

    Directory of Open Access Journals (Sweden)

    Keith M Callenberg

    Full Text Available Electrostatic forces are one of the primary determinants of molecular interactions. They help guide the folding of proteins, increase the binding of one protein to another and facilitate protein-DNA and protein-ligand binding. A popular method for computing the electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB equation, and there are several easy-to-use software packages available that solve the PB equation for soluble proteins. Here we present a freely available program, called APBSmem, for carrying out these calculations in the presence of a membrane. The Adaptive Poisson-Boltzmann Solver (APBS is used as a back-end for solving the PB equation, and a Java-based graphical user interface (GUI coordinates a set of routines that introduce the influence of the membrane, determine its placement relative to the protein, and set the membrane potential. The software Jmol is embedded in the GUI to visualize the protein inserted in the membrane before the calculation and the electrostatic potential after completing the computation. We expect that the ease with which the GUI allows one to carry out these calculations will make this software a useful resource for experimenters and computational researchers alike. Three examples of membrane protein electrostatic calculations are carried out to illustrate how to use APBSmem and to highlight the different quantities of interest that can be calculated.

  20. Comparison of availability of copper(II) complexes with organic ligands to bacterial cells and to chitin

    Energy Technology Data Exchange (ETDEWEB)

    Vasconcelos, M.T.S.D.; Azenha, M.A.O. [Laquipai, Porto (Portugal). Faculdade de Ciencias do Porto; Cabral, J.P.S. [Inst. de Botanica e Centro de Citologia Experimental U.P., Porto (Portugal)


    Bacterial cells or chitin were exposed to solutions with 100 {micro}M total but only 5 {micro}M free copper, due to the presence of a proper concentration of proline, lysine, cysteine, or ethylenediamine tetraacetate (EDTA). The influence of the nature and concentration of the particles and soluble ligands, on the sorption and on the desorption of the copper, at pH 6.50 and 25.0 C, was investigated. The metal sorbed by the particles and that left in the solution were measured by atomic absorption spectrometry, after different periods of contact between particles and solution. The interpretation of the results was based on the copper(II) speciation calculated through equilibrium approaches applied to homogeneous or heterogeneous systems. A significant fraction of copper bound to the organic ligands was displaced to the bacteria or chitin, and the extent of chemical reaction depended on the nature of both the soluble (or leaving) ligands and sites on the particle surface (or entering ligands), as expected by the equilibrium theory. But with chitin, the uptake of copper in the presence of cysteine or EDTA was higher than expected, which may be due to the adsorption of the soluble copper complexes on the particle surface. In consequence of a competition between soluble and particulate ligands (cells or chitin), the free copper(II) concentration decreased in the solution, even in the presence of very strong chelators. The results indicate that copper availability is not a simple function of the initial free copper concentration in the solution. Desorption of the previously fixed copper, originated by free soluble ligands indicated that the sorption of copper was quasireversible for both particles, though a larger dismissal of the equilibrium position occurred for the cells, probably due to their biological activity.

  1. Exploring the role of water in molecular recognition: predicting protein ligandability using a combinatorial search of surface hydration sites (United States)

    Vukovic, Sinisa; Brennan, Paul E.; Huggins, David J.


    The interaction between any two biological molecules must compete with their interaction with water molecules. This makes water the most important molecule in medicine, as it controls the interactions of every therapeutic with its target. A small molecule binding to a protein is able to recognize a unique binding site on a protein by displacing bound water molecules from specific hydration sites. Quantifying the interactions of these water molecules allows us to estimate the potential of the protein to bind a small molecule. This is referred to as ligandability. In the study, we describe a method to predict ligandability by performing a search of all possible combinations of hydration sites on protein surfaces. We predict ligandability as the summed binding free energy for each of the constituent hydration sites, computed using inhomogeneous fluid solvation theory. We compared the predicted ligandability with the maximum observed binding affinity for 20 proteins in the human bromodomain family. Based on this comparison, it was determined that effective inhibitors have been developed for the majority of bromodomains, in the range from 10 to 100 nM. However, we predict that more potent inhibitors can be developed for the bromodomains BPTF and BRD7 with relative ease, but that further efforts to develop inhibitors for ATAD2 will be extremely challenging. We have also made predictions for the 14 bromodomains with no reported small molecule K d values by isothermal titration calorimetry. The calculations predict that PBRM1(1) will be a challenging target, while others such as TAF1L(2), PBRM1(4) and TAF1(2), should be highly ligandable. As an outcome of this work, we assembled a database of experimental maximal K d that can serve as a community resource assisting medicinal chemistry efforts focused on BRDs. Effective prediction of ligandability would be a very useful tool in the drug discovery process.

  2. Optimized hydrophobic interactions and hydrogen bonding at the target-ligand interface leads the pathways of drug-designing.

    Directory of Open Access Journals (Sweden)

    Rohan Patil

    Full Text Available BACKGROUND: Weak intermolecular interactions such as hydrogen bonding and hydrophobic interactions are key players in stabilizing energetically-favored ligands, in an open conformational environment of protein structures. However, it is still poorly understood how the binding parameters associated with these interactions facilitate a drug-lead to recognize a specific target and improve drugs efficacy. To understand this, comprehensive analysis of hydrophobic interactions, hydrogen bonding and binding affinity have been analyzed at the interface of c-Src and c-Abl kinases and 4-amino substituted 1H-pyrazolo [3, 4-d] pyrimidine compounds. METHODOLOGY: In-silico docking studies were performed, using Discovery Studio software modules LigandFit, CDOCKER and ZDOCK, to investigate the role of ligand binding affinity at the hydrophobic pocket of c-Src and c-Abl kinase. Hydrophobic and hydrogen bonding interactions of docked molecules were compared using LigPlot program. Furthermore, 3D-QSAR and MFA calculations were scrutinized to quantify the role of weak interactions in binding affinity and drug efficacy. CONCLUSIONS: The in-silico method has enabled us to reveal that a multi-targeted small molecule binds with low affinity to its respective targets. But its binding affinity can be altered by integrating the conformationally favored functional groups at the active site of the ligand-target interface. Docking studies of 4-amino-substituted molecules at the bioactive cascade of the c-Src and c-Abl have concluded that 3D structural folding at the protein-ligand groove is also a hallmark for molecular recognition of multi-targeted compounds and for predicting their biological activity. The results presented here demonstrate that hydrogen bonding and optimized hydrophobic interactions both stabilize the ligands at the target site, and help alter binding affinity and drug efficacy.

  3. "Darker-than-black" PbS quantum dots: enhancing optical absorption of colloidal semiconductor nanocrystals via short conjugated ligands. (United States)

    Giansante, Carlo; Infante, Ivan; Fabiano, Eduardo; Grisorio, Roberto; Suranna, Gian Paolo; Gigli, Giuseppe


    Colloidal quantum dots (QDs) stand among the most attractive light-harvesting materials to be exploited for solution-processed optoelectronic applications. To this aim, quantitative replacement of the bulky electrically insulating ligands at the QD surface coming from the synthetic procedure is mandatory. Here we present a conceptually novel approach to design light-harvesting nanomaterials demonstrating that QD surface modification with suitable short conjugated organic molecules permits us to drastically enhance light absorption of QDs, while preserving good long-term colloidal stability. Indeed, rational design of the pendant and anchoring moieties, which constitute the replacing ligand framework leads to a broadband increase of the optical absorbance larger than 300% for colloidal PbS QDs also at high energies (>3.1 eV), which could not be predicted by using formalisms derived from effective medium theory. We attribute such a drastic absorbance increase to ground-state ligand/QD orbital mixing, as inferred by density functional theory calculations; in addition, our findings suggest that the optical band gap reduction commonly observed for PbS QD solids treated with thiol-terminating ligands can be prevalently ascribed to 3p orbitals localized on anchoring sulfur atoms, which mix with the highest occupied states of the QDs. More broadly, we provide evidence that organic ligands and inorganic cores are inherently electronically coupled materials thus yielding peculiar chemical species (the colloidal QDs themselves), which display arising (opto)electronic properties that cannot be merely described as the sum of those of the ligand and core components.

  4. Identification of Soft Matter Binding Peptide Ligands Using Phage Display. (United States)

    Günay, Kemal Arda; Klok, Harm-Anton


    Phage display is a powerful tool for the selection of highly affine, short peptide ligands. While originally primarily used for the identification of ligands to proteins, the scope of this technique has significantly expanded over the past two decades. Phage display nowadays is also increasingly applied to identify ligands that selectively bind with high affinity to a broad range of other substrates including natural and biological polymers as well as a variety of low-molecular-weight organic molecules. Such peptides are of interest for various reasons. The ability to selectively and with high affinity bind to the substrate of interest allows the conjugation or immobilization of, e.g., nanoparticles or biomolecules, or generally, facilitates interactions at materials interfaces. On the other hand, presentation of peptide ligands that selectively bind to low-molecular-weight organic materials is of interest for the development of sensor surfaces. The aim of this article is to highlight the opportunities provided by phage display for the identification of peptide ligands that bind to synthetic or natural polymer substrates or to small organic molecules. The article will first provide an overview of the different peptide ligands that have been identified by phage display that bind to these "soft matter" targets. The second part of the article will discuss the different characterization techniques that allow the determination of the affinity of the identified ligands to the respective substrates.

  5. Study of complexation between two 1,3-alternate calix[4]crown derivatives and alkali metal ions by electrospray ionization mass spectrometry and density functional theory calculations (United States)

    Shamsipur, Mojtaba; Allahyari, Leila; Fasihi, Javad; Taherpour, Avat (Arman); Asfari, Zuhair; Valinejad, Azizollah


    Complexation of two 1,3-alternate calix[4]crown ligands with alkali metals (K+, Rb+ and Cs+) has been investigated by electrospray ionization mass spectrometry (ESI-MS) and density functional theory calculations. The binding selectivities of the ligands and the binding constants of their complexes in solution have been determined using the obtained mass spectra. Also the percentage of each formed complex species in the mixture of each ligand and alkali metal has been experimentally evaluated. For both calix[4]crown-5 and calix[4]crown-6 ligands the experimental and theoretical selectivity of their alkali metal complexes found to follow the trend K+ > Rb+ > Cs+. The structures of ligands were optimized by DFT-B3LYP/6-31G method and the structures of complexes were obtained by QM-SCF-MO/PM6 method and discussed in the text.

  6. Ligand-based identification of environmental estrogens

    Energy Technology Data Exchange (ETDEWEB)

    Waller, C.L. [Environmental Protection Agency, Research Triangle Park, NC (United States); Oprea, T.I. [Los Alamos National Lab., NM (United States); Chae, K. [National Institute of Environmental Health Sciences, Research Triangle Park, NC (United States)] [and others


    Comparative molecular field analysis (CoMFA), a three-dimensional quantitative structure-activity relationship (3D-QSAR) paradigm, was used to examine the estrogen receptor (ER) binding affinities of a series of structurally diverse natural, synthetic, and environmental chemicals of interest. The CoMFA/3D-QSAR model is statistically robust and internally consistent, and successfully illustrates that the overall steric and electrostatic properties of structurally diverse ligands for the estrogen receptor are both necessary and sufficient to describe the binding affinity. The ability of the model to accurately predict the ER binding affinity of an external test set of molecules suggests that structure-based 3D-QSAR models may be used to supplement the process of endocrine disrupter identification through prioritization of novel compounds for bioassay. The general application of this 3D-QSAR model within a toxicological framework is, at present, limited only by the quantity and quality of biological data for relevant biomarkers of toxicity and hormonal responsiveness. 28 refs., 12 figs., 9 tabs.

  7. Mixed ligand complexation of some transition metal ions in solution and solid state: Spectral characterization, antimicrobial, antioxidant, DNA cleavage activities and molecular modeling (United States)

    Shobana, Sutha; Dharmaraja, Jeyaprakash; Selvaraj, Shanmugaperumal


    Equilibrium studies of Ni(II), Cu(II) and Zn(II) mixed ligand complexes involving a primary ligand 5-fluorouracil (5-FU; A) and imidazoles viz., imidazole (him), benzimidazole (bim), histamine (hist) and L-histidine (his) as co-ligands(B) were carried out pH-metrically in aqueous medium at 310 ± 0.1 K with I = 0.15 M (NaClO4). In solution state, the stoichiometry of MABH, MAB and MAB2 species have been detected. The primary ligand(A) binds the central M(II) ions in a monodentate manner whereas him, bim, hist and his co-ligands(B) bind in mono, mono, bi and tridentate modes respectively. The calculated Δ log K, log X and log X' values indicate higher stability of the mixed ligand complexes in comparison to binary species. Stability of the mixed ligand complex equilibria follows the Irving-Williams order of stability. In vitro biological evaluations of the free ligand(A) and their metal complexes by well diffusion technique show moderate activities against common bacterial and fungal strains. Oxidative cleavage interaction of ligand(A) and their copper complexes with CT DNA is also studied by gel electrophoresis method in the presence of oxidant. In vitro antioxidant evaluations of the primary ligand(A), CuA and CuAB complexes by DPPH free radical scavenging model were carried out. In solid, the MAB type of M(II)sbnd 5-FU(A)sbnd his(B) complexes were isolated and characterized by various physico-chemical and spectral techniques. Both the magnetic susceptibility and electronic spectral analysis suggest distorted octahedral geometry. Thermal studies on the synthesized mixed ligand complexes show loss of coordinated water molecule in the first step followed by decomposition of the organic residues subsequently. XRD and SEM analysis suggest that the microcrystalline nature and homogeneous morphology of MAB complexes. Further, the 3D molecular modeling and analysis for the mixed ligand MAB complexes have also been carried out.

  8. Analysis of the magnetic coupling in binuclear systems. III. The role of the ligand to metal charge transfer excitations revisited (United States)

    Calzado, Carmen J.; Angeli, Celestino; Taratiel, David; Caballol, Rosa; Malrieu, Jean-Paul


    In magnetic coordination compounds and solids the magnetic orbitals are essentially located on metallic centers but present some delocalization tails on adjacent ligands. Mean field variational calculations optimize this mixing and validate a single band modelization of the intersite magnetic exchange. In this approach, due to the Brillouin's theorem, the ligand to metal charge transfer (LMCT) excitations play a minor role. On the other hand the extensive configuration interaction calculations show that the determinants obtained by a single excitation on the top of the LMCT configurations bring an important antiferromagnetic contribution to the magnetic coupling. Perturbative and truncated variational calculations show that contrary to the interpretation given in a previous article [C. J. Calzado et al., J. Chem. Phys. 116, 2728 (2002)] the contribution of these determinants to the magnetic coupling constant is not a second-order one. An analytic development enables one to establish that they contribute at higher order as a correlation induced increase in the LMCT components of the wave function, i.e., of the mixing between the ligand and the magnetic orbitals. This larger delocalization of the magnetic orbitals results in an increase in both the ferro- and antiferromagnetic contributions to the coupling constant.

  9. Synthesis, Characterization, and Density Functional Theory Analysis of Uranium and Thorium Complexes Containing Nitrogen-Rich 5-Methyltetrazolate Ligands. (United States)

    Browne, Kevin P; Maerzke, Katie A; Travia, Nicholas E; Morris, David E; Scott, Brian L; Henson, Neil J; Yang, Ping; Kiplinger, Jaqueline L; Veauthier, Jacqueline M


    Two nitrogen-rich, isostructural complexes of uranium and thorium, (C5Me5)2U[η(2)-(N,N')-tetrazolate]2 (7) and (C5Me5)2Th[η(2)-(N,N')-tetrazolate]2 (8), containing 5-methyltetrazolate, have been synthesized and structurally characterized by single-crystal X-ray diffraction, electrochemical methods, UV-visible-near-IR spectroscopy, and variable-temperature (1)H NMR spectroscopy. Density functional theory (DFT) calculations yield favorable free energies of formation (approximately -375 kJ/mol) and optimized structures in good agreement with the experimental crystal structures. Additionally, calculated NMR chemical shifts of 7 and 8 are in good agreement with the variable-temperature (1)H NMR experiments. Time-dependent DFT calculations of both complexes yield UV-visible spectroscopic features that are consistent with experiment and provide assignments of the corresponding electronic transitions. The electronic transitions in the UV-visible spectroscopic region are attributed to C5Me5 ligand-to-metal charge transfer. The low-lying molecular orbitals of the tetrazolate ligands (∼2 eV below the HOMO) do not contribute appreciably to experimentally observed electronic transitions. The combined experimental and theoretical analysis of these new nitrogen-rich uranium and thorium complexes indicates the tetrazolate ligand behaves primarily as a σ-donor.

  10. Database of ligand-induced domain movements in enzymes

    Directory of Open Access Journals (Sweden)

    Hayward Steven


    Full Text Available Abstract Background Conformational change induced by the binding of a substrate or coenzyme is a poorly understood stage in the process of enzyme catalysed reactions. For enzymes that exhibit a domain movement, the conformational change can be clearly characterized and therefore the opportunity exists to gain an understanding of the mechanisms involved. The development of the non-redundant database of protein domain movements contains examples of ligand-induced domain movements in enzymes, but this valuable data has remained unexploited. Description The domain movements in the non-redundant database of protein domain movements are those found by applying the DynDom program to pairs of crystallographic structures contained in Protein Data Bank files. For each pair of structures cross-checking ligands in their Protein Data Bank files with the KEGG-LIGAND database and using methods that search for ligands that contact the enzyme in one conformation but not the other, the non-redundant database of protein domain movements was refined down to a set of 203 enzymes where a domain movement is apparently triggered by the binding of a functional ligand. For these cases, ligand binding information, including hydrogen bonds and salt-bridges between the ligand and specific residues on the enzyme is presented in the context of dynamical information such as the regions that form the dynamic domains, the hinge bending residues, and the hinge axes. Conclusion The presentation at a single website of data on interactions between a ligand and specific residues on the enzyme alongside data on the movement that these interactions induce, should lead to new insights into the mechanisms of these enzymes in particular, and help in trying to understand the general process of ligand-induced domain closure in enzymes. The website can be found at:

  11. Preparation, characterization and cytotoxicity studies of some transition metal complexes with ofloxacin and 1,10-phenanthroline mixed ligand (United States)

    Sadeek, S. A.; El-Hamid, S. M. Abd


    [Zn(Ofl)(Phen)(H2O)2](CH3COO)·2H2O (1), [ZrO(Ofl)(Phen)(H2O)]NO3·2H2O (2) and [UO2(Ofl)(Phen)(H2O)](CH3COO)·H2O (3) complexes of fluoroquinolone antibacterial agent ofloxacin (HOfl), containing a nitrogen donor heterocyclic ligand, 1,10-phenathroline monohydrate (Phen), were prepared and their structures were established with the help of elemental analysis, molar conductance, magnetic properties, thermal studies and different spectroscopic studies like IR, UV-Vis., 1H NMR and Mass. The IR data of HOfl and Phen ligands suggested the existing of a bidentate binding involving carboxylate O and pyridone O for HOfl ligand and two pyridine N atoms for Phen ligand. The coordination geometries and electronic structures are determined from electronic absorption spectra and magnetic moment measurements. From molar conductance studies reveals that metal complexes are electrolytes and of 1:1 type. The calculated bond length and force constant, F(Udbnd O), in the uranyl complex are 1.751 Å and 641.04 Nm-1. The thermal properties of the complexes were investigated by thermogravimetry (TGA) technique. The activation thermodynamic parameters are calculated using Coats-Redfern and Horowitz-Metzger methods. Antimicrobial activity of the compounds was evaluated against some bacteria and fungi species. The activity data show that most metal complexes have antibacterial activity than that of the parent HOfl drug. The in vitro cytotoxicities of ligands and their complexes were also evaluated against human breast and colon carcinoma cells.

  12. Structures of d4 MH3X: a computational study of the influence of the metal and the ligands. (United States)

    Poblador-Bahamonde, Amalia I; Raynaud, Christophe; Eisenstein, Odile


    Density functional theory (DFT, PBE0, and range separated DFT, RSH + MP2) and coupled-cluster with single and double and perturbative triple excitations (CCSD(T)) calculations have been used to probe the structural preference of d(4) MH(3)X(q) (M = Ru, Os, Rh(+), Ir(+), and Re(-); X = H, F, CH(3), CF(3), SiH(3), and SiF(3)) and of MX(4) (M = Ru; X = H, F, CH(3), CF(3), SiH(3), and SiF(3)). Landis et al. have shown that complexes in which the metal is sd(3) hybridized have tetrahedral and non-tetrahedral structures with shapes of an umbrella or a 4-legged piano stool. In this article, the influence of the metal and ligands on the energies of the three isomeric structures of d(4) MH(3)X and MX(4) is established and rationalized. Fluoride and alkyl ligands stabilize the tetrahedral relative to non-tetrahedral structures while hydride and silyl ligands stabilize the non-tetrahedral structures. For given ligands and charge, 4d metal favors more the non-tetrahedral structures than 5d metals. A positive charge increases the preference for the non-tetrahedral structures while a negative charge increases the preference for the tetrahedral structure. The factors that determine these energy patterns are discussed by means of a molecular orbital analysis, based on Extended Hückel (EHT) calculations, and by means of Natural Bond Orbital (NBO) analyses of charges and resonance structures (NRT analysis). These analyses show the presence of through-space interactions in the non-tetrahedral structures that can be sufficiently stabilizing, for specific metals and ligands, to stabilize the non-tetrahedral structures relative to the tetrahedral isomer.

  13. Synthesis of symmetrical and non-symmetrical bivalent neurotransmitter ligands

    DEFF Research Database (Denmark)

    Stuhr-Hansen, Nicolai; Andersen, Jacob; Thygesen, Mikkel Boas


    A novel procedure for synthesis of bivalent neurotransmitter ligands was developed by reacting O-benzyl protected N-nosylated dopamine and serotonin with alkyl- or PEG-linked diols under Fukuyama-Mitsunobu conditions in the presence of DIAD/PPh3 generating three different bivalent neurotransmitter...... ligands in a one-pot reaction. The methodol. establishes a facile route towards bivalent neurotransmitter ligands, and libraries of in total 40 sym. and non-sym. bivalent and monovalent dopamine and serotonin compds. linked through alkyl or PEG spacers of varying length were prepd. Interestingly...

  14. Ligands recognizing the minor groove of DNA: development and applications. (United States)

    Wemmer, D E

    Polyamide ligands comprised of pyrrole, imidazole and hydroxypyrrole rings have been developed over the past decade which can be used to target many different, predetermined DNA sequences through recognition of functional groups in the minor groove. The design principles for these ligands are described with a description of the characterization of their binding. Variations containing linked recognition modules have been described which allow high affinity and specificity recognition of DNA sequences of over 15 base pairs. Recent applications of these ligands in affecting biological response through competition with proteins for DNA binding sites are reviewed. Copyright 2001 John Wiley & Sons, Inc.

  15. Ligands targeting the excitatory amino acid transporters (EAATs). (United States)

    Dunlop, John; Butera, John A


    This review provides an overview of ligands for the excitatory amino acid transporters (EAATs), a family of high-affinity glutamate transporters localized to the plasma membrane of neurons and astroglial cells. Ligand development from the perspective of identifying novel and more selective tools for elucidating transporter subtype function, and the potential of transporter ligands in a therapeutic setting are discussed. Acute pharmacological modulation of EAAT activity in the form of linear and conformationally restricted glutamate and aspartate analogs is presented, in addition to recent strategies aimed more toward modulating transporter expression levels, the latter of particular significance to the development of transporter based therapeutics.

  16. Calculation of Spectra of Solids:

    DEFF Research Database (Denmark)

    Lindgård, Per-Anker


    The Gilat-Raubenheimer method simplified to tetrahedron division is used to calculate the real and imaginary part of the dynamical response function for electrons. A frequency expansion for the real part is discussed. The Lindhard function is calculated as a test for numerical accuracy. The condu...

  17. Calculator. Owning a Small Business. (United States)

    Parma City School District, OH.

    Seven activities are presented in this student workbook designed for an exploration of small business ownership and the use of the calculator in this career. Included are simulated situations in which students must use a calculator to compute property taxes; estimate payroll taxes and franchise taxes; compute pricing, approximate salaries,…

  18. Calculating charged defects using CRYSTAL (United States)

    Bailey, Christine L.; Liborio, Leandro; Mallia, Giuseppe; Tomić, Stanko; Harrison, Nicholas M.


    The methodology for the calculation of charged defects using the CRYSTAL program is discussed. Two example calculations are used to illustrate the methodology: He+ ions in a vacuum and two intrinsic charged defects, Cu vacancies and Ga substitution for Cu, in the chalcopyrite CuGaS2.

  19. Economic calculation in socialist countries

    NARCIS (Netherlands)

    Ellman, M.; Durlauf, S.N.; Blume, L.E.


    In the 1930s, when the classical socialist system emerged, economic decisions were based not on detailed and precise economic methods of calculation but on rough and ready political methods. An important method of economic calculation - particularly in the post-Stalin period - was that of

  20. Evaluation and comparison of n-alkyl chain and polar ligand bonded stationary phases for protein separation in reversed-phase liquid chromatography. (United States)

    Ding, Ling; Guo, Zhimou; Xiao, Yuansheng; Xue, Xingya; Zhang, Xiuli; Liang, Xinmiao


    Protein retention is very sensitive to the change of solvent composition in reversed-phase liquid chromatography for so called "on-off" mechanism, leading to difficulty in mobile phase optimization. In this study, a novel 3-chloropropyl trichlorosilane ligand bonded column was prepared for protein separation. The differences in retention characteristics between the 3-chloropropyl trichlorosilane ligand bonded column and n-alkyl chain modified (C2, C4, C8) stationary phases were elucidated by the retention equation l nk=a+cC(B). Retention parameters (a and c) of nine standard proteins with different molecular weights were calculated by using homemade software. Results showed that retention times of nine proteins were similar on four columns, but the 3-chloropropyl trichlorosilane ligand bonded column obtained the lowest retention parameter values of larger proteins. It meant that their retention behavior affected by acetonitrile concentration would be different due to lower |c| values. More specifically, protein elution windows were broader, and retentions were less sensitive to the change of acetonitrile concentration on the 3-chloropropyl trichlorosilane ligand bonded column than that on other columns. Meanwhile, the 3-chloropropyl trichlorosilane ligand bonded column displayed distinctive selectivity for some proteins. Our results indicated that stationary phase with polar ligand provided potential solutions to the "on-off" problem and optimization in protein separation.

  1. Binary and ternary copper(II) complexes of a tridentate ONS ligand derived from 2-aminochromone-3 carboxaldehyde and thiosemicarbazide: Synthesis, spectral studies and antimicrobial activity (United States)

    Shebl, Magdy; Ibrahim, M. A.; Khalil, Saied M. E.; Stefan, S. L.; Habib, H.


    A tridentate ONS donor ligand, HL, was synthesized by the condensation of 2-aminochromone-3-carboxaldehyde with thiosemicarbazide. The structure of the ligand was elucidated by elemental analyses, IR, 1H and 13C NMR, electronic and mass spectra. Reaction of the ligand with several copper(II) salts, including AcO-, NO3-, SO42-, Cl-, Br- and ClO4- afforded different metal complexes that reflect the non-coordinating or weakly coordinating power of the ClO4- and Br- anions as compared to the strongly coordinating power of AcO-, SO42-, Cl- and NO3- anions. Also, the ligand was allowed to react with Cu(II) ion in the presence of a secondary ligand (L‧) [N,O-donor; 8-hydroxyquinoline or N,N-donor; 1,10-phenanthroline]. Characterization and structure elucidation of the prepared complexes were achieved by elemental and thermal analyses, IR, electronic, mass and EPR spectra as well as conductivity and magnetic susceptibility measurements. The EPR spin Hamiltonian parameters of some complexes were calculated. The metal complexes exhibited octahedral and square planar geometrical arrangements depending on the nature of the anion. The ligand and most of its metal complexes showed antibacterial activity towards Gram-positive bacteria (Staphylococcus aureus and Bacillus subtilis), Gram-negative bacteria (Salmonella typhimurium and Escherichia coli), yeast (Candida albicans) and fungus (Aspergillus fumigatus).

  2. Insights into dehydrogenative coupling of alcohols and amines catalyzed by a (PNN)-Ru(II) hydride complex: unusual metal-ligand cooperation. (United States)

    Zeng, Guixiang; Li, Shuhua


    Density functional theory calculations were performed to elucidate the mechanism of dehydrogenative coupling of primary alcohols and amines mediated by a PNN-Ru(II) hydride complex (PNN = (2-(di-tert-butylphosphinomethyl)-6-(diethylaminomethyl)pyridine)). A plausible reaction pathway was proposed which contains three stages: (1) The alcohol dehydrogenation reaction to generate the aldehyde and H(2); (2) The aldehyde-amine condensation reaction to form the hemiaminal intermediate; (3) The dehydrogenation process of the hemiaminal intermediate to yield the final amide product with the liberation of H(2). The first and third stages occur via a similar pathway: (a) Proton transfer from the substrate to the PNN ligand; (b) Intramolecular rearrangement of the deprotonated substrate to form an anagostic complex; (c) Hydride transfer from the deprotonated substrate to the Ru center to yield the trans-dihydride intermediate and the aldehyde (or amide); (d) Benzylic proton migration from the PNN ligand to the metal center forming a dihydrogen complex and subsequent H(2) liberation to regenerate the catalyst. In all these steps, the metal-ligand cooperation plays an essential role. In proton transfer steps (a) and (d), the metal-ligand cooperation is achieved through the aromatization/dearomatization processes of the PNN ligand. While in steps (b) and (c), their collaboration are demonstrated by the formation of an anagostic interaction between Ru and the C-H bond and two ionic hydrogen bonds supported by the PNN ligand.

  3. Chromium(III) complexes of naturally occurring ligands (United States)

    El-Shahawi, M. S.


    Chromium(III) complexes prepared from CrCl 3Py 3 and anhydrous CrCl 3 with L(-)-threonine, nicotinic acid, glycine, D(-)-penicillamine, L(-)-cysteine and L(-)-cystine have been characterized. The magnetic moments (3.4-4.05 B.M.) are close to the spin only value for a d3 chromium(III) ion in octahedral or pseudo octahedral symmetry. In the electronic spectra two sharp peaks are observed at (15.9-19.8) × 10 3 and (22.0-26.7) × 10 3 cm -1 and are assigned to d-d transitions in the pseudo octahedral configuration. The parameters ( Dq, B, β35) and the interelectronic repulsion parameter with the ionic charge, Z∗, are calculated and place the ligand in the middle of the spectrochemical series. In the circular dichroism spectra three Cotton effects are observed in the forbidden band of the optically active chelates and are assigned to the 2E( 2Eg), 2A 2( 2T 1g) and2E( 2T 1g) while that in the spin allowed band are a result of the splitting of the 4A 2g( 4T 2g) to 4A 1( 4T 2g) and4E( 4T 2g) transitions. The structure of threonine, cystine and cysteine chelates are likely to be fac since strong and well defined Cotton effects are observed. The Cotton effects of penicillamine chelates are weak suggesting formation of the mer structure. Prolonged heating or bubbling air through the solution of CrCl 3Py 3 containing L(-)-threonine, glycine or nicotinic acid for several hours enhances chromium(VI) formation.

  4. Role of ligand-dependent GR phosphorylation and half-life in determination of ligand-specific transcriptional activity. (United States)

    Avenant, Chanel; Ronacher, Katharina; Stubsrud, Elisabeth; Louw, Ann; Hapgood, Janet P


    A central question in glucocorticoid mechanism of action via the glucocorticoid receptor (GR) is what determines ligand-selective transcriptional responses. Using a panel of 12 GR ligands, we show that the extent of GR phosphorylation at S226 and S211, GR half-life and transcriptional response, occur in a ligand-selective manner. While GR phosphorylation at S226 was shown to inhibit maximal transcription efficacy, phosphorylation at S211 is required for maximal transactivation, but not for transrepression efficacy. Both ligand-selective GR phosphorylation and half-life correlated with efficacy for transactivation and transrepression. For both expressed and endogenous GR, in two different cell lines, agonists resulted in the greatest extent of phosphorylation and the greatest extent of GR downregulation, suggesting a link between these functions. However, using phosphorylation-deficient GR mutants we established that phosphorylation of the GR at S226 or S211 does not determine the rank order of ligand-selective GR transactivation. These results are consistent with a model whereby ligand-selective GR phosphorylation and half-life are a consequence of upstream events, such as ligand-specific GR conformations, which are maintained in the phosphorylation mutants.

  5. Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach (United States)

    Lam, Polo C.-H.; Abagyan, Ruben; Totrov, Maxim


    Ligand docking to flexible protein molecules can be efficiently carried out through ensemble docking to multiple protein conformations, either from experimental X-ray structures or from in silico simulations. The success of ensemble docking often requires the careful selection of complementary protein conformations, through docking and scoring of known co-crystallized ligands. False positives, in which a ligand in a wrong pose achieves a better docking score than that of native pose, arise as additional protein conformations are added. In the current study, we developed a new ligand-biased ensemble receptor docking method and composite scoring function which combine the use of ligand-based atomic property field (APF) method with receptor structure-based docking. This method helps us to correctly dock 30 out of 36 ligands presented by the D3R docking challenge. For the six mis-docked ligands, the cognate receptor structures prove to be too different from the 40 available experimental Pocketome conformations used for docking and could be identified only by receptor sampling beyond experimentally explored conformational subspace.

  6. Closure and Sealing Design Calculation

    Energy Technology Data Exchange (ETDEWEB)

    T. Lahnalampi; J. Case


    The purpose of the ''Closure and Sealing Design Calculation'' is to illustrate closure and sealing methods for sealing shafts, ramps, and identify boreholes that require sealing in order to limit the potential of water infiltration. In addition, this calculation will provide a description of the magma that can reduce the consequences of an igneous event intersecting the repository. This calculation will also include a listing of the project requirements related to closure and sealing. The scope of this calculation is to: summarize applicable project requirements and codes relating to backfilling nonemplacement openings, removal of uncommitted materials from the subsurface, installation of drip shields, and erecting monuments; compile an inventory of boreholes that are found in the area of the subsurface repository; describe the magma bulkhead feature and location; and include figures for the proposed shaft and ramp seals. The objective of this calculation is to: categorize the boreholes for sealing by depth and proximity to the subsurface repository; develop drawing figures which show the location and geometry for the magma bulkhead; include the shaft seal figures and a proposed construction sequence; and include the ramp seal figure and a proposed construction sequence. The intent of this closure and sealing calculation is to support the License Application by providing a description of the closure and sealing methods for the Safety Analysis Report. The closure and sealing calculation will also provide input for Post Closure Activities by describing the location of the magma bulkhead. This calculation is limited to describing the final configuration of the sealing and backfill systems for the underground area. The methods and procedures used to place the backfill and remove uncommitted materials (such as concrete) from the repository and detailed design of the magma bulkhead will be the subject of separate analyses or calculations. Post

  7. Multiple binding modes of ibuprofen in human serum albumin identified by absolute binding free energy calculations

    KAUST Repository

    Evoli, Stefania


    Human serum albumin possesses multiple binding sites and transports a wide range of ligands that include the anti-inflammatory drug ibuprofen. A complete map of the binding sites of ibuprofen in albumin is difficult to obtain in traditional experiments, because of the structural adaptability of this protein in accommodating small ligands. In this work, we provide a set of predictions covering the geometry, affinity of binding and protonation state for the pharmaceutically most active form (S-isomer) of ibuprofen to albumin, by using absolute binding free energy calculations in combination with classical molecular dynamics (MD) simulations and molecular docking. The most favorable binding modes correctly reproduce several experimentally identified binding locations, which include the two Sudlow\\'s drug sites (DS2 and DS1) and the fatty acid binding sites 6 and 2 (FA6 and FA2). Previously unknown details of the binding conformations were revealed for some of them, and formerly undetected binding modes were found in other protein sites. The calculated binding affinities exhibit trends which seem to agree with the available experimental data, and drastically degrade when the ligand is modeled in a protonated (neutral) state, indicating that ibuprofen associates with albumin preferentially in its charged form. These findings provide a detailed description of the binding of ibuprofen, help to explain a wide range of results reported in the literature in the last decades, and demonstrate the possibility of using simulation methods to predict ligand binding to albumin.

  8. IC 50-to-K i: a web-based tool for converting IC 50 to K i values for inhibitors of enzyme activity and ligand binding


    Cer, R. Z.; Mudunuri, U.; Stephens, R.; Lebeda, F. J.


    A new web-server tool estimates K i values from experimentally determined IC 50 values for inhibitors of enzymes and of binding reactions between macromolecules (e.g. proteins, polynucleic acids) and ligands. This converter was developed to enable end users to help gauge the quality of the underlying assumptions used in these calculations which depend on the type of mechanism of inhibitor action and the concentrations of the interacting molecular species. Additional calculations are performed...

  9. Water mediated ligand functional group cooperativity: the contribution of a methyl group to binding affinity is enhanced by a COO(-) group through changes in the structure and thermodynamics of the hydration waters of ligand-thermolysin complexes. (United States)

    Nasief, Nader N; Tan, Hongwei; Kong, Jing; Hangauer, David


    Ligand functional groups can modulate the contributions of one another to the ligand-protein binding thermodynamics, producing either positive or negative cooperativity. Data presented for four thermolysin phosphonamidate inhibitors demonstrate that the differential binding free energy and enthalpy caused by replacement of a H with a Me group, which binds in the well-hydrated S2' pocket, are more favorable in presence of a ligand carboxylate. The differential entropy is however less favorable. Dissection of these differential thermodynamic parameters, X-ray crystallography, and density-functional theory calculations suggest that these cooperativities are caused by variations in the thermodynamics of the complex hydration shell changes accompanying the H→Me replacement. Specifically, the COO(-) reduces both the enthalpic penalty and the entropic advantage of displacing water molecules from the S2' pocket and causes a subsequent acquisition of a more enthalpically, less entropically, favorable water network. This study contributes to understanding the important role water plays in ligand-protein binding.

  10. Theoretical investigation of paramagnetic NMR shifts in transition metal acetylacetonato complexes: analysis of signs, magnitudes, and the role of the covalency of ligand-metal bonding. (United States)

    Pritchard, Ben; Autschbach, Jochen


    Ligand chemical shifts are calculated and analyzed for three paramagnetic transition metal tris-acetylacetonato (acac) complexes, namely high-spin Fe(III) and Cr(III), and low-spin Ru(III), using scalar relativistic density functional theory (DFT). The signs and magnitudes of the paramagnetic NMR ligand chemical shifts are directly related to the extent of covalent acac oxygen-to-metal σ donation involving unoccupied metal valence d(σ) acceptor orbitals. The role of delocalization of metal-centered spin density over the ligand atoms plays a minor secondary role. Of particular interest is the origin of the sign and magnitude of the methyl carbon chemical shift in the acac ligands, and the role played by the DFT delocalization error when calculating such shifts. It is found that the α versus β spin balance of oxygen σ donation to metal valence d acceptor orbitals is responsible for the sign and the magnitude of the ligand methyl carbon chemical shift. A problematic case is the methyl carbon shift of Fe(acac)(3). Most functionals produce shifts in excess of 1400 ppm, whereas the experimental shift is approximately 279 ppm. Range-separated hybrid functionals that are optimally tuned for Fe(acac)(3) based on DFT energetic criteria predict a lower limit of about 2000 ppm for the methyl carbon shift of the high-spin electronic configuration. Since the experimental value is based on a very strongly broadened signal it is possibly unreliable.

  11. Aromatic side-chain cluster of biotin binding site of avidin allows circular dichroism spectroscopic investigation of its ligand binding properties. (United States)

    Zsila, Ferenc


    Promiscuous ligand binding by hen egg-white avidin has been demonstrated and studied by using circular dichroism (CD) spectroscopy complemented by molecular docking calculations. It has been shown that the biotin-binding pocket of avidin is able to accommodate a wide variety of chemical compounds including therapeutic drugs (e.g., thalidomide, NSAIDs, antihistamines), natural compounds (bilirubin, myristic acid), and synthetic agents (xanthenone dyes). The cluster of aromatic residues located at the biotin-binding pocket renders the intrinsic CD spectrum of avidin sensitive to ligand binding that results in the increase of the vibronic components of the (1) L(b) transition of the Trp residues. Extrinsic (induced) CD bands measured with chemically diverse avidin ligands are generated by intramolecular coupled oscillator (e.g., bilirubin) or by intermolecular ligand-Trp exciton coupling mechanism [e.g., 2-(4'-hydroxyazobenzene)-benzoic acid (HABA)]. Among the compounds of which avidin-binding affinity constants have been calculated, two novel high-affinity ligands, flufenamic acid and an enzyme inhibitor thiazole derivative have been identified (K(d) ≈ 1 μM). Avidin binding mode of the ligand molecules has been discussed in the light of docking results. The induced CD profile of the thiazole derivative has been correlated with the stereochemistry of its docked conformation. The important role in the ligand binding of a polar side-chain cluster at the bottom of the biotin-binding cavity as well as the analogous avidin-binding mode of HABA and fenamic acid type NSAIDs have been proposed. Copyright © 2011 John Wiley & Sons, Ltd.

  12. Using consensus-shape clustering to identify promiscuous ligands and protein targets and to choose the right query for shape-based virtual screening. (United States)

    Pérez-Nueno, Violeta I; Ritchie, David W


    Ligand-based shape matching approaches have become established as important and popular virtual screening (VS) techniques. However, despite their relative success, many authors have discussed how best to choose the initial query compounds and which of their conformations should be used. Furthermore, it is increasingly the case that pharmaceutical companies have multiple ligands for a given target and these may bind in different ways to the same pocket. Conversely, a given ligand can sometimes bind to multiple targets, and this is clearly of great importance when considering drug side-effects. We recently introduced the notion of spherical harmonic-based "consensus shapes" to help deal with these questions. Here, we apply a consensus shape clustering approach to the 40 protein-ligand targets in the DUD data set using PARASURF/PARAFIT. Results from clustering show that in some cases the ligands for a given target are split into two subgroups which could suggest they bind to different subsites of the same target. In other cases, our clustering approach sometimes groups together ligands from different targets, and this suggests that those ligands could bind to the same targets. Hence spherical harmonic-based clustering can rapidly give cross-docking information while avoiding the expense of performing all-against-all docking calculations. We also report on the effect of the query conformation on the performance of shape-based screening of the DUD data set and the potential gain in screening performance by using consensus shapes calculated in different ways. We provide details of our analysis of shape-based screening using both PARASURF/PARAFIT and ROCS, and we compare the results obtained with shape-based and conventional docking approaches using MSSH/SHEF and GOLD. The utility of each type of query is analyzed using commonly reported statistics such as enrichment factors (EF) and receiver-operator-characteristic (ROC) plots as well as other early performance metrics.

  13. Ligand Discrimination in Myoglobin from Linear-Scaling DFT+U

    CERN Document Server

    Cole, Daniel J; Payne, Mike C


    Myoglobin modulates the binding of diatomic molecules to its heme group via hydrogen-bonding and steric interactions with neighboring residues, and is an important benchmark for computational studies of biomolecules. We have performed calculations on the heme binding site and a significant proportion of the protein environment (more than 1000 atoms) using linear-scaling density functional theory and the DFT+U method to correct for self-interaction errors associated with localized 3d states. We confirm both the hydrogen-bonding nature of the discrimination effect (3.6 kcal/mol) and assumptions that the relative strain energy stored in the protein is low (less than 1 kcal/mol). Our calculations significantly widen the scope for tackling problems in drug design and enzymology, especially in cases where electron localization, allostery or long-ranged polarization influence ligand binding and reaction.

  14. Kinetic consequences of introducing a proximal selenocysteine ligand into cytochrome P450cam. (United States)

    Vandemeulebroucke, An; Aldag, Caroline; Stiebritz, Martin T; Reiher, Markus; Hilvert, Donald


    The structural, electronic, and catalytic properties of cytochrome P450cam are subtly altered when the cysteine that coordinates to the heme iron is replaced with a selenocysteine. To map the effects of the sulfur-to-selenium substitution on the individual steps of the catalytic cycle, we conducted a comparative kinetic analysis of the selenoenzyme and its cysteine counterpart. Our results show that the more electron-donating selenolate ligand has only negligible effects on substrate, product, and oxygen binding, electron transfer, catalytic turnover, and coupling efficiency. Off-pathway reduction of oxygen to give superoxide is the only step significantly affected by the mutation. Incorporation of selenium accelerates this uncoupling reaction approximately 50-fold compared to sulfur, but because the second electron transfer step is much faster, the impact on overall catalytic turnover is minimal. Density functional theory calculations with pure and hybrid functionals suggest that superoxide formation is governed by a delicate interplay of spin distribution, spin state, and structural effects. In light of the remarkably similar electronic structures and energies calculated for the sulfur- and selenium-containing enzymes, the ability of the heavier atom to enhance the rate of spin crossover may account for the experimental observations. Because the selenoenzyme closely mimics wild-type P450cam, even at the level of individual steps in the reaction cycle, selenium represents a unique mechanistic probe for analyzing the role of the proximal ligand and spin crossovers in P450 chemistry.

  15. Controlled Redox Chemistry at Cerium within a Tripodal Nitroxide Ligand Framework. (United States)

    Bogart, Justin A; Lippincott, Connor A; Carroll, Patrick J; Booth, Corwin H; Schelter, Eric J


    Ligand reorganization has been shown to have a profound effect on the outcome of cerium redox chemistry. Through the use of a tethered, tripodal, trianionic nitroxide ligand, [((2-tBuNOH)C6 H4 CH2 )3 N](3-) (TriNOx (3-) ), controlled redox chemistry at cerium was accomplished, and typically reactive complexes of tetravalent cerium were isolated. These included rare cationic complexes [Ce(TriNOx )thf][BAr(F) 4 ], in which Ar(F) =3,5-(CF3 )2 -C6 H3 , and [Ce(TriNOx )py][OTf]. A rare complete Ce-halide series, Ce(TriNOx )X, in which X=F(-) , Cl(-) , Br(-) , I(-) , was also synthesized. The solution chemistry of these complexes was explored through detailed solution-phase electrochemistry and (1) H NMR experiments and showed a unique shift in the ratio of species with inner- and outer-sphere anions with size of the anionic X(-) group. DFT calculations on the series of calculations corroborated the experimental findings.

  16. Role of the Sulfonium Center in Determining the Ligand Specificity of Human S-Adenosylmethionine Decarboxylase

    Energy Technology Data Exchange (ETDEWEB)

    Bale, Shridhar; Brooks, Wesley; Hanes, Jeremiah W.; Mahesan, Arnold M.; Guida, Wayne C.; Ealick, Steven E.; (Moffitt); (Cornell)


    S-Adenosylmethionine decarboxylase (AdoMetDC) is a key enzyme in the polyamine biosynthetic pathway. Inhibition of this pathway and subsequent depletion of polyamine levels is a viable strategy for cancer chemotherapy and for the treatment of parasitic diseases. Substrate analogue inhibitors display an absolute requirement for a positive charge at the position equivalent to the sulfonium of S-adenosylmethionine. We investigated the ligand specificity of AdoMetDC through crystallography, quantum chemical calculations, and stopped-flow experiments. We determined crystal structures of the enzyme cocrystallized with 5{prime}-deoxy-5{prime}-dimethylthioadenosine and 5{prime}-deoxy-5{prime}-(N-dimethyl)amino-8-methyladenosine. The crystal structures revealed a favorable cation-{pi} interaction between the ligand and the aromatic side chains of Phe7 and Phe223. The estimated stabilization from this interaction is 4.5 kcal/mol as determined by quantum chemical calculations. Stopped-flow kinetic experiments showed that the rate of the substrate binding to the enzyme greatly depends on Phe7 and Phe223, thus supporting the importance of the cation-{pi} interaction.

  17. Riding the Wave of Monodentate Ligand Revival: From the A/B Concept to Noncovalent Interactions. (United States)

    Pignataro, Luca; Gennari, Cesare


    The rediscovery of chiral monodentate ligands made in the period 1999-2003 had important consequences in enantioselective transition-metal catalysis, such as the introduction of the A/B concept (i.e., use of monodentate ligand mixtures) and, later, a renewed interest in supramolecular ligands capable of ligand-ligand and ligand-substrate interactions. This Personal Account summarizes the contributions made by our research group in this area in the period 2004-2015, which reflect the abovementioned developments. Within this area, we introduced some original concepts, such as 1) the use of chiral tropos ligand mixtures; 2) the development of new strategies to maximize heterocomplex formation from combinations of simple monodentate ligands; 3) the investigation of new ligand-ligand interactions to achieve selective heterocomplex formation; and 4) the development of highly efficient and synthetically accessible supramolecular ligands. © 2016 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Ligand peptide-grafted PEGylated liposomes using HER2 targeted peptide-lipid derivatives for targeted delivery in breast cancer cells: The effect of serine-glycine repeated peptides as a spacer. (United States)

    Suga, Tadaharu; Fuchigami, Yuki; Hagimori, Masayori; Kawakami, Shigeru


    Ligand peptide-grafted PEGylated liposomes have been widely studied for targeted drug delivery systems. Because ligand peptides are commonly grafted using PEG as a spacer on the surface of PEGylated liposomes, the interaction between ligand peptides and their corresponding receptors can be interrupted by steric hindrance of the PEG layer. Therefore, we aimed to develop ligand peptide-lipid derivatives to enhance the targeting efficiency of ligand peptide-grafted PEGylated liposomes, and designed a new ligand peptide-lipid derivatives having serine-glycine repeats (SG)n as a spacer based on the peptide length calculated by PyMol (v0.99). We selected KCCYSL (KCC) as the ligand peptide for binding to human epidermal growth factor receptor-2 (HER2). We synthesized new KCC-(SG)n-lipid derivatives (n=3, 5, 7) and evaluated their cellular association in breast cancer cells. KCC-(SG)n/PEGylated liposomes dramatically increased cellular association on HER2-positive breast cancer cells. The results suggest that KCC can be grafted on the surface of KCC-(SG)n/PEGylated liposomes prepared from KCC-(SG)n-lipid derivatives (n=3, 5, 7). In summary, we succeeded in developing KCC-(SG)n-lipid derivatives for the preparation of ligand peptide-grafted PEGylated liposomes.

  19. The Foundations of Protein-Ligand Interaction (United States)

    Klebe, Gerhard

    For the specific design of a drug we must first answer the question: How does a drug achieve its activity? An active ingredient must, in order to develop its action, bind to a particular target molecule in the body. Usually this is a protein, but also nucleic acids in the form of RNA and DNA can be target structures for active agents. The most important condition for binding is at first that the active agent exhibits the correct size and shape in order to optimally fit into a cavity exposed to the surface of the protein, the "bindingpocket". It is further necessary for the surface properties of the ligand and protein to be mutually compatible to form specific interactions. In 1894 Emil Fischer compared the exact fit of a substrate for the catalytic centre of an enzyme with the picture of a "lock-and-key". Paul Ehrlich coined in 1913 "Corpora non agunt nisi fixata", literally "bodies do not work when they are not bound". He wanted to imply that active agents that are meant to kill bacteria or parasites must be "fixed" by them, i.e. linked to their structures. Both concepts form the starting point for any rational concept in the development of active pharmaceutical ingredients. In many respects they still apply today. A drug must, after being administered, reach its target and interact with a biological macromolecule. Specific agents have a large affinity and sufficient selectivity to bind to the macromolecule's active site. This is the only way they can develop the desired biological activity without side-effects.

  20. Generating Cu(II)-Oxyl / Cu(III)-Oxo Species from Cu(I)-α-Ketocarboxylate Complexes and O2: In silico Studies on Ligand Effects and C-H-activation Reactivity


    Huber, Stefan M.; Ertem, M. Zahid; Aquilante, Francesco; Gagliardi, Laura; Tolman, William B.; Cramer, Christopher J.


    A mechanism for the oxygenation of Cu(I) complexes with α-ketocarboxylate ligands is elaborated that is based on a combination of density functional theory and multireference second-order perturbation theory (CASSCF/CASPT2) calculations. The reaction proceeds in a manner largely analogous to those of similar Fe(II) α-ketocarboxylate systems, i.e. by initial attack of a coordinated oxygen molecule on a ketocarboxylate ligand with concomitant decarboxylation. Subsequently, two reactive intermed...

  1. Enantioselective catalysis with tropos ligands in chiral ionic liquids. (United States)

    Schmitkamp, Mike; Chen, Dianjun; Leitner, Walter; Klankermayer, Jürgen; Franciò, Giancarlo


    Enantioselective homogeneous rhodium-catalysed hydrogenation using tropoisomeric biphenylphosphine ligands was accomplished in readily available chiral ionic liquids and the catalytic system could be reused after extraction with scCO(2).

  2. Synthesis and Catalytic Activity of Two New Cyclic Tetraaza Ligands

    Directory of Open Access Journals (Sweden)

    Burkhard König


    Full Text Available Two new chiral cyclic tetraaza ligands were synthesized and characterized. Their catalytic activity was tested in the asymmetric addition of diethylzinc to benzaldehyde. The expected secondary alcohol was obtained in moderate yields, but with very low enantioselectivity.

  3. Ligand Binding to Macromolecules: Allosteric and Sequential Models of Cooperativity. (United States)

    Hess, V. L.; Szabo, Attila


    A simple model is described for the binding of ligands to macromolecules. The model is applied to the cooperative binding by hemoglobin and aspartate transcarbamylase. The sequential and allosteric models of cooperative binding are considered. (BB)

  4. Observations on the ligand selectivity of the melanocortin 2 receptor. (United States)

    Veo, Kristopher; Reinick, Christina; Liang, Liang; Moser, Emily; Angleson, Joseph K; Dores, Robert M


    The melanocortin 2 receptor (MC2R) is unique in terms of ligand selectivity and in vitro expression in mammalian cell lines as compared to the other four mammalian MCRs. It is well established that ACTH is the only melanocortin ligand that can activate the ACTH receptor (i.e., melanocortin 2 receptor). Recent studies have provided new insights into the presence of a common binding site for the HFRW motif common to all melanocortin ligands. However, the activation of the melanocortin 2 receptor requires an additional amino acid motif that is only found in the sequence of ACTH. This mini-review will focus on these two topics and provide a phylogenetic perspective on the evolution of MC2R ligand selectivity.

  5. Unique advantages of organometallic supporting ligands for uranium complexes

    Energy Technology Data Exchange (ETDEWEB)

    Diaconescu, Paula L. [Univ. of California, Los Angeles, CA (United States); Garcia, Evan [Univ. of California, Los Angeles, CA (United States)


    The objective of our research project was to study the reactivity of uranium complexes supported by ferrocene-based ligands. In addition, this research provides training of graduate students as the next generation of actinide scientists.

  6. Fluorescent ligand for human progesterone receptor imaging in live cells. (United States)

    Weinstain, Roy; Kanter, Joan; Friedman, Beth; Ellies, Lesley G; Baker, Michael E; Tsien, Roger Y


    We employed molecular modeling to design and then synthesize fluorescent ligands for the human progesterone receptor. Boron dipyrromethene (BODIPY) or tetramethylrhodamine were conjugated to the progesterone receptor antagonist RU486 (Mifepristone) through an extended hydrophilic linker. The fluorescent ligands demonstrated comparable bioactivity to the parent antagonist in live cells and triggered nuclear translocation of the receptor in a specific manner. The BODIPY labeled ligand was applied to investigate the dependency of progesterone receptor nuclear translocation on partner proteins and to show that functional heat shock protein 90 but not immunophilin FKBP52 activity is essential. A tissue distribution study indicated that the fluorescent ligand preferentially accumulates in tissues that express high levels of the receptor in vivo. The design and properties of the BODIPY-labeled RU486 make it a potential candidate for in vivo imaging of PR by positron emission tomography through incorporation of (18)F into the BODIPY core.

  7. Specific activity of radioiodine-labelled human chorionic gonadotropin ligand

    Energy Technology Data Exchange (ETDEWEB)

    Crespi, M. (South African Inst. for Medical Research, Sandringham. National Inst. for Virology); Kay, G.W.; Van der Walt, L.A. (South African Inst. for Medical Research, Johannesburg. Dept. of Pathology)


    The article deals with the determination of the specific activity of radioiodine-labelled human chorionic gonadotropin ligand. The iodiation of human chorionic gonadotropin and the counting efficiency of /sup 125/I are discussed.

  8. Steered molecular dynamics simulations of protein-ligand interactions

    Institute of Scientific and Technical Information of China (English)

    XU; Yechun; SHEN; Jianhua; LUO; Xiaomin; SHEN; Xu; CHEN; Ka


    Studies of protein-ligand interactions are helpful to elucidating the mechanisms of ligands, providing clues for rational drug design. The currently developed steered molecular dynamics (SMD) is a complementary approach to experimental techniques in investigating the biochemical processes occurring at microsecond or second time scale, thus SMD may provide dynamical and kinetic processes of ligand-receptor binding and unbinding, which cannot be accessed by the experimental methods. In this article, the methodology of SMD is described, and the applications of SMD simulations for obtaining dynamic insights into protein-ligand interactions are illustrated through two of our own examples. One is associated with the simulations of binding and unbinding processes between huperzine A and acetylcholinesterase, and the other is concerned with the unbinding process of α-APA from HIV-1 reverse transcriptase.

  9. CD40 ligand immunotherapy in cancer: an efficient approach. (United States)

    Kuwashima, N; Kageyama, S; Eto, Y; Urashima, M


    Cancer cells do not elicit a clinically sufficient anti-tumor immune response that results in tumor rejection. Recently, many investigators have been trying to enhance anti-tumor immunity and encouraging results have been reported. This review will discuss current anti-cancer immunotherapy; interleukin-2 therapy, tumor vaccine secreting Granulocyte macrophage-colony stimulating factor, dendritic cells fused with tumor cells, and CD40 ligand immunotherapy. Moreover, we introduce our two kinds of CD40 ligand immuno-genetherapy; (1) oral CD40 ligand gene therapy against lymphoma using attenuated Salmonella typhimurium (published in BLOOD 2000), (2) cancer vaccine transfected with CD40 ligand ex vivo for neuroblastoma (unpublished). Both approaches resulted in a high degree of protection against the tumor progression and they are simple and safe in the murine system.

  10. Influence of Ancillary Ligands and Isomerism on the Luminescence of Bis-cyclometalated Platinum(IV) Complexes. (United States)

    Juliá, Fabio; García-Legaz, María-Dulce; Bautista, Delia; González-Herrero, Pablo


    The synthesis, characterization, and photophysical properties of a wide variety of bis-cyclometalated Pt(IV) complexes featuring a C2-symmetrical or unsymmetrical {Pt(ppy)2} unit (sym or unsym complexes, respectively; ppy = C-deprotonated 2-phenylpyridine) and different ancillary ligands are reported. Complexes sym-[Pt(ppy)2X2] (X = OTf(-), OAc(-)) were obtained by chloride abstraction from sym-[Pt(ppy)2Cl2] using the corresponding AgX salts, and the triflate derivative was employed to obtain homologous complexes with X = F(-), Br(-), I(-), trifluoroacetate (TFA(-)). Complexes unsym-[Pt(ppy)2(Me)X] (X = OTf(-), F(-)) were prepared by reacting unsym-[Pt(ppy)2(Me)Cl] with AgOTf or AgF, respectively, and the triflate derivative was employed as precursor for the synthesis of the homologues with X = Br(-), I(-), or TFA(-) through its reaction with the appropriate anionic ligands. The previously reported complexes unsym-[Pt(ppy)2X2] (X = Cl(-), Br(-), OAc(-), TFA(-)) are included in the photophysical study to assess the influence of the arrangement of the cyclometalated ligands. Density functional theory (DFT) and time-dependent DFT calculations on selected derivatives were performed for a better interpretation of the observed excited-state properties. Complexes sym-[Pt(ppy)2X2] (except X = I(-)) exhibit phosphorescent emissions in fluid solutions at 298 K arising from essentially (3)LC(ppy) excited states, which are very similar in shape and energy. However, their efficiencies are heavily dependent on the nature of the ancillary ligands, which affect the energy of deactivating ligand-to-ligand charge transfer (LLCT) or ligand-to-metal charge transfer (LMCT) states. The fluoride derivative sym-[Pt(ppy)2F2] shows the highest quantum yield of this series (Φ = 0.398), mainly because the relatively high metal-to-ligand charge transfer admixture in its emitting state leads to a high radiative rate constant. Complexes unsym-[Pt(ppy)2X2] emit from (3)LC(ppy) states in frozen

  11. Tetrapyrroles as Endogenous TSPO Ligands in Eukaryotes and Prokaryotes: Comparisons with Synthetic Ligands

    Directory of Open Access Journals (Sweden)

    Leo Veenman


    Full Text Available The 18 kDa translocator protein (TSPO is highly 0conserved in eukaryotes and prokaryotes. Since its discovery in 1977, numerous studies established the TSPO’s importance for life essential functions. For these studies, synthetic TSPO ligands typically are applied. Tetrapyrroles present endogenous ligands for the TSPO. Tetrapyrroles are also evolutionarily conserved and regulate multiple functions. TSPO and tetrapyrroles regulate each other. In animals TSPO-tetrapyrrole interactions range from effects on embryonic development to metabolism, programmed cell death, response to stress, injury and disease, and even to life span extension. In animals TSPOs are primarily located in mitochondria. In plants TSPOs are also present in plastids, the nuclear fraction, the endoplasmic reticulum, and Golgi stacks. This may contribute to translocation of tetrapyrrole intermediates across organelles’ membranes. As in animals, plant TSPO binds heme and protoporphyrin IX. TSPO-tetrapyrrole interactions in plants appear to relate to development as well as stress conditions, including salt tolerance, abscisic acid-induced stress, reactive oxygen species homeostasis, and finally cell death regulation. In bacteria, TSPO is important for switching from aerobic to anaerobic metabolism, including the regulation of photosynthesis. As in mitochondria, in bacteria TSPO is located in the outer membrane. TSPO-tetrapyrrole interactions may be part of the establishment of the bacterial-eukaryote relationships, i.e., mitochondrial-eukaryote and plastid-plant endosymbiotic relationships.

  12. Tetrapyrroles as Endogenous TSPO Ligands in Eukaryotes and Prokaryotes: Comparisons with Synthetic Ligands. (United States)

    Veenman, Leo; Vainshtein, Alex; Yasin, Nasra; Azrad, Maya; Gavish, Moshe


    The 18 kDa translocator protein (TSPO) is highly 0conserved in eukaryotes and prokaryotes. Since its discovery in 1977, numerous studies established the TSPO's importance for life essential functions. For these studies, synthetic TSPO ligands typically are applied. Tetrapyrroles present endogenous ligands for the TSPO. Tetrapyrroles are also evolutionarily conserved and regulate multiple functions. TSPO and tetrapyrroles regulate each other. In animals TSPO-tetrapyrrole interactions range from effects on embryonic development to metabolism, programmed cell death, response to stress, injury and disease, and even to life span extension. In animals TSPOs are primarily located in mitochondria. In plants TSPOs are also present in plastids, the nuclear fraction, the endoplasmic reticulum, and Golgi stacks. This may contribute to translocation of tetrapyrrole intermediates across organelles' membranes. As in animals, plant TSPO binds heme and protoporphyrin IX. TSPO-tetrapyrrole interactions in plants appear to relate to development as well as stress conditions, including salt tolerance, abscisic acid-induced stress, reactive oxygen species homeostasis, and finally cell death regulation. In bacteria, TSPO is important for switching from aerobic to anaerobic metabolism, including the regulation of photosynthesis. As in mitochondria, in bacteria TSPO is located in the outer membrane. TSPO-tetrapyrrole interactions may be part of the establishment of the bacterial-eukaryote relationships, i.e., mitochondrial-eukaryote and plastid-plant endosymbiotic relationships.

  13. The XChemExplorer graphical workflow tool for routine or large-scale protein-ligand structure determination. (United States)

    Krojer, Tobias; Talon, Romain; Pearce, Nicholas; Collins, Patrick; Douangamath, Alice; Brandao-Neto, Jose; Dias, Alexandre; Marsden, Brian; von Delft, Frank


    XChemExplorer (XCE) is a data-management and workflow tool to support large-scale simultaneous analysis of protein-ligand complexes during structure-based ligand discovery (SBLD). The user interfaces of established crystallographic software packages such as CCP4 [Winn et al. (2011), Acta Cryst. D67, 235-242] or PHENIX [Adams et al. (2010), Acta Cryst. D66, 213-221] have entrenched the paradigm that a `project' is concerned with solving one structure. This does not hold for SBLD, where many almost identical structures need to be solved and analysed quickly in one batch of work. Functionality to track progress and annotate structures is essential. XCE provides an intuitive graphical user interface which guides the user from data processing, initial map calculation, ligand identification and refinement up until data dissemination. It provides multiple entry points depending on the need of each project, enables batch processing of multiple data sets and records metadata, progress and annotations in an SQLite database. XCE is freely available and works on any Linux and Mac OS X system, and the only dependency is to have the latest version of CCP4 installed. The design and usage of this tool are described here, and its usefulness is demonstrated in the context of fragment-screening campaigns at the Diamond Light Source. It is routinely used to analyse projects comprising 1000 data sets or more, and therefore scales well to even very large ligand-design projects.

  14. The role of macrocyclic ligands in the peroxo/superoxo nature of Ni-O2 biomimetic complexes. (United States)

    Zapata-Rivera, Jhon; Caballol, Rosa; Calzado, Carmen J


    The impact of the macrocyclic ligand on the electronic structure of two LNi-O2 biomimetic adducts, [Ni(12-TMC)O2](+) (12-TMC = 1,4,7,10-tetramethyl-1,4,7,10-tetraazacyclododecane) and [Ni(14-TMC)O2](+) (14-TMC = 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane), has been inspected by means of difference-dedicated configuration interaction calculations and a valence bond reading of the wavefunction. The system containing the 12-membered macrocyclic ligand has been experimentally described as a side-on nickel(III)-peroxo complex, whereas the 14-membered one has been characterized as an end-on nickel(II)-superoxide. Our results put in evidence the relationship between the steric effect of the macrocyclic ligand, the O2 coordination mode and the charge transfer extent between the Ni center and the O2 molecule. The 12-membered macrocyclic ligand favors a side-on coordination, a most efficient overlap between Ni 3d and O2 π* orbitals and, consequently, a larger charge transfer from LNi fragment to O2 molecule. The analysis of the ground-state electronic structure shows an enhancement of the peroxide nature of the Ni-O2 interaction for [Ni(12-TMC)O2](+), although a dominant superoxide character is found for both systems.

  15. Practical astronomy with your calculator

    CERN Document Server

    Duffett-Smith, Peter


    Practical Astronomy with your Calculator, first published in 1979, has enjoyed immense success. The author's clear and easy to follow routines enable you to solve a variety of practical and recreational problems in astronomy using a scientific calculator. Mathematical complexity is kept firmly in the background, leaving just the elements necessary for swiftly making calculations. The major topics are: time, coordinate systems, the Sun, the planetary system, binary stars, the Moon, and eclipses. In the third edition there are entirely new sections on generalised coordinate transformations, nutr

  16. The Collective Practice of Calculation

    DEFF Research Database (Denmark)

    Schrøder, Ida

    on the idea that professions are hybrids by introducing the notion of qualculation as an entry point to investigate decision-making in child protection work as an extreme case of calculating on the basis of other elements than quantitative numbers. The analysis reveals that it takes both calculation...... and judgement to reach decisions to invest in social services. The line is not drawn between the two, but between the material arrangements that make decisions possible. This implies that the insisting on qualitatively based decisions gives the professionals agency to collectively engage in practical...... arrangements that affords calculations of both qualitative measures of the individual case and distant accounting numbers....

  17. Novel peptide ligand with high binding capacity for antibody purification

    DEFF Research Database (Denmark)

    Lund, L. N.; Gustavsson, P. E.; Michael, R.


    Small synthetic ligands for protein purification have become increasingly interesting with the growing need for cheap chromatographic materials for protein purification and especially for the purification of monoclonal antibodies (mAbs). Today, Protein A-based chromatographic resins are the most ......-aggregated IgG, indicating that the ligand could be used both as a primary purification step of IgG as well as a subsequent polishing step. (C) 2012 Elsevier B.V. All rights reserved....

  18. Predicting protein-ligand affinity with a random matrix framework


    Lee, Alpha Albert; Brenner, MP; Colwell, Lucy Jane


    Rapid determination of whether a candidate compound will bind to a particular target receptor remains a stumbling block in drug discovery. We use an approach inspired by random matrix theory to decompose the known ligand set of a target in terms of orthogonal "signals" of salient chemical features, and distinguish these from the much larger set of ligand chemical features that are not relevant for binding to that particular target receptor. After removing the noise caused by finite sampling, ...

  19. Reversible Size Control of Silver Nanoclusters via Ligand-exchange

    KAUST Repository

    Bootharaju, Megalamane Siddaramappa


    The properties of atomically monodisperse noble metal nanoclusters (NCs) are intricately intertwined with their precise molecular formula. The vast majority of size-specific NC syntheses start from the reduction of the metal salt and thiol ligand mixture. Only in gold was it recently shown that ligand-exchange could induce the growth of NCs from one atomically precise species to another; a process of yet unknown reversibility. Here, we present a process for the ligand-exchange-induced growth of atomically precise silver NCs, in a biphasic liquid-liquid system, which is particularly of interest because of its complete reversibility and ability to occur at room temperature. We explore this phenomenon in-depth using Ag35(SG)18 [SG= glutathionate] and Ag44(4-FTP)30 [4-FTP= 4-fluorothiophenol] as model systems. We show that the ligand-exchange conversion of Ag35(SG)18 into Ag44(4-FTP)30 is rapid (< 5 min) and direct, while the reverse process proceeds slowly through intermediate cluster sizes. We adapt a recently developed theory of reverse Ostwald ripening to model the NCs’ interconvertibility. The model’s predictions are in good agreement with the experimental observations, and they highlight the importance of small changes in the ligand-metal binding energy in determining the final equilibrium NC size. Based on the insight provided by this model, we demonstrated experimentally that by varying the choice of ligands, ligand-exchange can be used to obtain different sized NCs. The findings in this work establish ligand-exchange as a versatile tool for tuning cluster sizes.

  20. Tailoring the Properties of Metallic Clusters by Ligand Coatings


    Fresch, Barbara


    Tuning the properties of metallic clusters using different protecting ligand shells is an important step toward the application-orientated design of nanoparticles for nano-electronics and catalysis. An attractive property of these materials is the ability to engineer ligand shells composed of different molecules that influence the electronic structure of the system due to their chemical interaction with the metal core. Sometimes properties are not simply additive, and cooperative effects emer...