Theoretical insight into the aggregation induced emission phenomena of diphenyldibenzofulvene: a nonadiabatic molecular dynamics study

The diphenyldibenzofulvene (DPDBF) molecule appears in two forms: ring open and ring closed. The former fluoresces weakly in solution, but it becomes strongly emissive in the solid phase, exhibiting an exotic aggregation-induced emission phenomenon. The latter presents a normal aggregation quenching phenomenon, as is expected. We implement nonadiabatic molecular dynamics based on the combination of time-dependent Kohn-Sham (TDKS) and density functional tight binding (DFTB) methods with Tully's fewest switches surface hopping algorithm to investigate the excited state nonradiative decay processes. From the analysis of the nonadiabatic coupling vectors, it is found that the low frequency twisting motion in the ring open DPDBF couples strongly with the electronic excitation and dissipates the energy efficiently. While in the closed form, such motion is blocked by a chemical bond. This leads to the nonradiative decay rate for the open form (1.4 ps) becoming much faster than the closed form (24.5 ps). It is expected that, in the solid state, the low frequency motion of the open form will be hindered and the energy dissipation pathway by nonradiative decay will be slowed, presenting a remarkable aggregation enhanced emission phenomenon.     

Ultrafast internal dynamics of flexible hydrogen-bonded supramolecular complexes

Supramolecular chemistry is intimately linked to the dynamical interplay between intermolecular forces and intramolecular flexibility. Here, we studied the ultrafast equilibrium dynamics of a supramolecular hydrogen-bonded receptor-substrate complex, 18-crown-6 monohydrate, using Fourier transform infrared (FTIR) and two-dimensional infrared (2DIR) spectroscopy in combination with numerical simulations based on molecular mechanics, density functional theory, and transition state theory. The theoretical calculations suggest that the flexibility of the macrocyclic crown ether receptor is related to an ultrafast crankshaft isomerization occurring on a time scale of several picoseconds and that the OH stretching vibrations of the substrate can serve as internal probes for the receptor's flexibility. The importance of population transfer among the vibrational modes of a given binding motif and of chemical exchange between spectroscopically distinguishable binding motifs for shaping the two-dimensional infrared spectrum and its temporal evolution is discussed.     

Identification of anabolic steroids and derivatives using bioassay-guided fractionation, UHPLC/TOFMS analysis and accurate mass database searching

Biological tests can be used to screen samples for large groups of compounds having a particular effect, but it is often difficult to identify a specific compound when a positive effect is observed. The identification of an unknown compound is a challenge for analytical chemistry in environmental analysis, food analysis, as well as in clinical and forensic toxicology. In this study bioassay-guided fractionation, ultra high performance liquid chromatography combined with time-of-flight mass spectrometry (UHPLC/TOFMS) and accurate mass database searching was tested to detect and identify unknown androgens. Herbal mixtures and sport supplements were tested using an androgen bioassay and modifications in sample preparations were carried out in order to activate inactive pro-androgens, androgen esters and conjugated androgens to enable their detection in the bioassay. Two of the four herbal mixtures tested positive and bioassay-guided fractionation followed by UHPLC/TOFMS of positive fractions resulted in the identification of nortestosterone phenylpropionate, testosterone cyclohexanecarboxylate and methyltestosterone. Three of the four sport supplements reacted toxic in the bioassay or gave inconclusive results and were further investigated using UHPLC/TOFMS in combination with data processing software and an accurate mass database having approximately 40,000 entries. This accurate mass database was derived from the PubChem database on the internet and coupled to the TOFMS software. This resulted in the tentative identification of several androgens, including methylboldenone, testosterone and the androgen esters methyltestosterone propionate or testosterone isobutyrate, testosterone buciclate and methylenetestosterone acetate. The study showed that bioassay-guided fractionation in combination with UHPLC/TOFMS analysis is a useful procedure to detect, isolate and identify unknown androgens in suspected samples. As an alternative, the use of data processing software in combination with an accurate mass database and coupled on-line with the TOFMS instrument software enabled the identification of androgens and androgen esters in the chromatogram even without bioassay-guided fractionation.     

Catalysis on the coastline: theozyme,molecular dynamics,and free energy perturbation analysis of antibody 21D8 catalysis of the decarboxylation of 5-nitro-3-carboxybenzisoxazole

Antibody 21D8 catalyzes the decarboxylation of 5-nitro-3-carboxybenzisoxazole. The hapten used was designed to induce an antibody binding site with anion binders for the carboxylate, plus a nonpolar environment to accelerate decarboxylation. A recent X-ray crystal structure of 21D8 has shown that the binding pocket contains an array of both polar and charged residues. Nevertheless, 21D8 is able to catalyze a reaction that involves a decrease in polarity from reactant to transition state. The origins of this phenomenon were explored using various computational strategies-quantum mechanics, theozyme models, docking, molecular dynamics, free energy perturbation, and linear interaction energy-the combination of which has produced a consistent picture of catalysis. By partially desolvating the charged carboxylate, 21D8 manages to effect "catalysis on the coastline," without burying the carboxylate in a nonpolar region of the binding pocket. The results have implications for that broad class of enzyme and antibody catalyzed reactions that involve the conversion of a substrate with a relatively localized charge into a transition state with a highly dispersed charge.     

Characterization of the Intermediate in and Identification of the Repair Mechanism of (6‐4) Photolesions by Photolyases

Quantum mechanics/molecular mechanics calculations are employed to assign previously recorded experimental spectroscopic signatures of the intermediates occurring during the photo‐induced repair of (6‐4) photolesions by photolyases to specific molecular structures. Based on this close comparison of experiment and theory it is demonstrated that the acting repair mechanism involves proton transfer from the protonated His365 to the N3′ nitrogen of the lesion, which proceeds simultaneously with intramolecular OH transfer along an oxetane‐like transition state.     

Pattern recognition in molecular quantum mechanics

It is shown that the classical concept of an open system does not encompass quantal systems but has to be replaced by the non-Boolean notion of an entangled system. Molecular, chemical, or biological phenomena can be considered to be reduced to a fundamental theory like quantum mechanics only if the fundamental and the phenomenological theories are formally and interpretatively connected, and if the classifications used in the empirical sciences are shown to follow from a single set of fundamental dynamical laws. These conditions enforce a non-statistical and ontic interpretation of quantum mechanics, hence a non-Boolean calculus of propositions. In this interpretation the notion of a world state is well-defined, its Schmidt-decomposition defines a background-dependent model state for molecular systems and creates the phenomena we can observe. To any molecular system there is associated in an objective way a nonnegative number which we call the integrity. The integrity measures the inherent fuzziness of the system concept in a holistic theory, and is used to define recognizable molecular patterns.     

Comparative molecular field analysis (CoMFA) model using a large diverse set of natural, synthetic and environmental chemicals for binding to the androgen receptor

A large number of natural, synthetic and environmental chemicals are capable of disrupting the endocrine systems of experimental animals, wildlife and humans. These so-called endocrine disrupting chemicals (EDCs), some mimic the functions of the endogenous androgens, have become a concern to the public health. Androgens play an important role in many physiological processes, including the development and maintenance of male sexual characteristics. A common mechanism for androgen to produce both normal and adverse effects is binding to the androgen receptor (AR). In this study, we used Comparative Molecular Field Analysis (CoMFA), a three-dimensional quantitative structure-activity relationship (3D-QSAR) technique, to examine AR-ligand binding affinities. A CoMFA model with r2 = 0.902 and q2 = 0.571 was developed using a large training data set containing 146 structurally diverse natural, synthetic, and environmental chemicals with a 10(6)-fold range of relative binding affinity (RBA). By comparing the binding characteristics derived from the CoMFA contour map with these observed in a human AR crystal structure, we found that the steric and electrostatic properties encoded in this training data set are necessary and sufficient to describe the RBA of AR ligands. Finally, the CoMFA model was challenged with an external test data set; the predicted results were close to the actual values with average difference of 0.637 logRBA. This study demonstrates the utility of this CoMFA model for real-world use in predicting the AR binding affinities of structurally diverse chemicals over a wide RBA range.     

Assessing the performance of the g_mmpbsa tools to simulate the inhibition of oseltamivir to influenza virus neuraminidase by molecular mechanics Poisson–Boltzmann surface area methods

The molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) method for GROMACS (g_mmpbsa) is an open-source tool that is capable of reading the trajectories generated by GROMACS and calculating the binding free energy using the MM-PBSA method. However, there are multiple force fields available for users to choose from in the GROMACS software, and there are also different solvent water models to combine with the chosen force fields. These different combinations of parameters may significantly impact the results of g_mmpbsa calculation. Unfortunately, the exact combination of force field and solvent water that can well calculate the free energy of the receptor–ligand binding in GROMACS has not been explored yet. To resolve the above issues, this study mainly explored the molecular dynamics (MD) simulations by GROMACS with the six commonly used force fields and three solvent water models, in combination with g_mmpbsa, to calculate the binding free energies of the influenza virus neuraminidase and its mutants with inhibitor oseltamivir carboxylate and compared the present results with previous published results of Amber software from ours and other researchers. Finally, we provided an optimized calculation model, as well as suggestions that may serve as advice and guidance for future computer-aided designs of drug molecules.     

Dynamic devices. Shape switching and substrate binding in ion-controlled nanomechanical molecular tweezers

As examples of supramolecular devices performing chemical (ionic, molecular) control of binding events and models of related natural systems, two molecular conformational switches are described, which display cation-controlled nanomechanical motion coupled to substrate binding and release. The substrate binding relies on donor/acceptor interactions, provided by intercalation between planar sites located at the extremities of the switching units, whereas cation complexation is responsible for conformational regulation. The terpyridine py-py-py-based receptor is activated toward substrate binding upon complexation of a zinc(II) cation and operates in a two-state process. The replacement of the central pyridine by a 4,6-disubstituted pyridimine as in py-pym-py induces a state reversal and yields a new receptor which binds a substrate in the absence of cation, and releases it when copper(I) is introduced, following a three-step process. These systems represent effector-triggered supramolecular switching devices leading toward multistate nanomechanical chemical systems. These two systems illustrate the use of simple conformational switches in the binding site and allosteric regulation of substrate affinity.     

Modeling of dexmedetomidine conformers and their interactions with alpha2 adrenergic receptor subtypes

Dexmedetomidine (4-[(S)-1-(2,3-dimethyl-phenyl)-ethyl]-1H-imidazole), Dex, is potent agonist acting on α₂-adrenergic receptors (α₂-ARs). It can exist at the physiological pH in both forms: neutral and protonated. The results of receptor-independent and receptor-dependent studies applied to both forms of Dex are reported. A conformational analysis with PM3 semiempirical MO and ab initio HF/6-31G* methods was carried out for both forms of Dex. The calculated geometries of low-energy conformers of Dex were compared with X-ray geometry and those of conformers resulted from molecular docking of Dex in the binding pockets of 3D homology models of the α_2A-, α_2B-, and α_2C-adrenoceptor subtypes. A MM/QM (molecular mechanics/quantum mechanics) docking study was performed to refine and optimize receptor–ligand complex and close contacts between the ligand and amino acids lining the binding cavity. Two-dimensional potential energy surface and docking results suggest that the imidazole ring can easily adopt the best orientation for an efficient interaction with the carboxylate group of Asp3.32 from the binding cavity of alpha2 adrenergic receptor subtypes.     

Synthesis of 7alpha-(fluoromethyl)dihydrotestosterone and 7alpha-(fluoromethyl)nortestosterone, structurally paired androgens designed to probe the role of sex hormone binding globulin in imaging androgen receptors in prostate tumors by positron emission tomography

Although prostate cancer growth is regulated by androgens through the androgen receptor (AR), in vitro assays of AR levels in prostate tumors have limited prognostic value. This might be improved by direct measurement of tumor AR in vivo using positron emission tomography (PET) imaging with fluorine-18-labeled androgens. Most AR PET imaging agents have been designed to limit steroid binding to serum proteins, but there is evidence that binding to sex hormone binding globulin (SHBG) might enhance tumor uptake. To probe the role of SHBG in prostate tumor uptake of PET imaging agents, we have synthesized two fluoro steroids, 7alpha-(fluoromethyl)dihydrotestosterone (7alpha-FM-DHT) and 7alpha-(fluoromethyl)nortestosterone (7alpha-FM-norT), by a route amenable to their labeling with [18F]fluoride ion. Both compounds have high affinity for AR, but 7alpha-FM-norT has much lower affinity for SHBG. Thus, these two fluoro steroids are well matched in terms of their site of fluorine labeling, similarity of structure, and equivalent AR binding affinity-but contrasting SHBG binding-and therefore can be used as agents for evaluating the role of SHBG binding in the target tissue uptake of AR PET imaging agents in humans.     

Two-state model based on the block-localized wave function method

The block-localized wave function (BLW) method is a variant of ab initio valence bond method but retains the efficiency of molecular orbital methods. It can derive the wave function for a diabatic (resonance) state self-consistently and is available at the Hartree-Fock (HF) and density functional theory (DFT) levels. In this work we present a two-state model based on the BLW method. Although numerous empirical and semiempirical two-state models, such as the Marcus-Hush two-state model, have been proposed to describe a chemical reaction process, the advantage of this BLW-based two-state model is that no empirical parameter is required. Important quantities such as the electronic coupling energy, structural weights of two diabatic states, and excitation energy can be uniquely derived from the energies of two diabatic states and the adiabatic state at the same HF or DFT level. Two simple examples of formamide and thioformamide in the gas phase and aqueous solution were presented and discussed. The solvation of formamide and thioformamide was studied with the combined ab initio quantum mechanical and molecular mechanical Monte Carlo simulations, together with the BLW-DFT calculations and analyses. Due to the favorable solute-solvent electrostatic interaction, the contribution of the ionic resonance structure to the ground state of formamide and thioformamide significantly increases, and for thioformamide the ionic form is even more stable than the covalent form. Thus, thioformamide in aqueous solution is essentially ionic rather than covalent. Although our two-state model in general underestimates the electronic excitation energies, it can predict relative solvatochromic shifts well. For instance, the intense pi-->pi* transition for formamide upon solvation undergoes a redshift of 0.3 eV, compared with the experimental data (0.40-0.5 eV).     

Application of an androgen receptor assay for the characterisation of the androgenic or antiandrogenic activity of various phenylurea herbicides and their derivatives.

The potency of different substances for [3H]dihydrotestosterone ([3H]DHT) displacement from the bovine androgen receptor was tested. The phenylurea herbicide linuron and its derivative 3,4-dichloroaniline (3,4-DCA), which are found in sediments and surface waters, are known to displace bound testosterone from the rat androgen receptor. Because 3,4-DCA is rapidly taken up by fish and metabolised into 3,4-dichloroacetanilide (3,4-DCAc), it was investigated whether the displacement effects are attributable to 3,4-DCA or to 3,4-DCAc. The potency of 3,4-DCAc androgen receptor binding was compared with that of several phenylurea compounds. In a radioreceptor assay with calf uterus cytosol as androgen receptor preparation, the specific binding of [3H]DHT, the endogenous ligand, was completely displaceable by increasing concentrations of 3,4-DCAc. The relative binding affinities (RBA) of the various compounds were about 1/10(4) to 1/10(5) of that of DHT. 3,4-DCAc had the relative highest affinity (1.31 x 10(-4)), followed by linuron, 3,4-dichlorophenylurea, flutamide, 3,4-DCA and diuron with the lowest RBA (2.4 x 10(-5)). Hence the metabolism of xenobiotic compounds has to be considered to estimate potential ecotoxiocological effects. This test not only can be used to screen for androgen- and antiandrogen-like substances in environmentally relevant samples such as surface waters, but might also be applied for drug testing and for residue monitoring.     

Computer simulation of the interaction of Cu(I) with cys residues at the binding site of the yeast metallochaperone Cu(I)-Atx1

The copper binding site and electronic structure of the metallochaperone protein Atx1 were investigated using the combination of quantum mechanics methods and molecular mechanics methods in the ONIOM(QM:MM) scheme at the density functional theory (DFT) B3LYP/ 6-31G(d):AMBER level. The residues in the binding site, -Met13-Thr14-Cys15-Cu(I)-Cys18-Gly17-Ser16-, were modeled with QM and the rest of the residues with MM. Our results indicate that the structure for Cu(I)-Atx1 has the copper atom coordinated to two sulfur atoms from Cys15 (2.110 A) and Cys18 (2.141 A) with an angle S-Cu(I) -S of 166 degrees . The potential energy surface of the copper atom is used to estimate its binding energy and the force field for the copper ligands. The potential surface is shallow for the bending mode S-Cu-S, which explains the origin of the disorder observed in crystallographic and nuclear magnetic resonance studies. Using molecular dynamics for Cu(I)-Atx1 in a box of water molecules and in vacuum, with the force field derived in this work, we observed a correlated motion between the side chains of Thr14 and of Lys65 which enhances distortions in the S-Cu-S geometry. The results are compared with recent experiments and the previous models. The vibrational spectra for the copper ligands and for the residues in the binding site were computed. The localized modes for the copper ligands and the amide bands were assigned. The presence of the copper atom affects the amide bands' frequencies of the residues Cys15 and Cys18, giving resolved bands that can be used to sense changes in the binding site upon translocation of copper atom or interaction with target proteins. Furthermore, the EXAFS (extended X-ray absorption fine structure) spectrum of the proposed structure for Cu(I)-Atx1 was calculated and reproduced the experiments fairly well.     

Subtle structural changes in tetrahydroquinolines, a new class of nonsteroidal selective androgen receptor modulators, induce different functions

Tetrahydroquinolines (THQs), a new class of nonsteroidal selective androgen receptor (AR) modulators, have two indispensable functional groups, that is, a hydroxyl group for AR binding and a nitro group for agonistic activity. Interestingly, switching the nitro to a cyano group, the compound acts as an antagonist. To understand this phenomenon, molecular dynamics simulations were applied for dihydrotestosterone (DHT) and representative THQs complexes with AR. Upon ligand binding, the hydroxyl group formed a tight hydrogen-bond (H-bond) with Asn705 on Helix 3 (H3). The immobilization of Asn705 on H3 is helpful in the formation of tight H-bonds with Asp890 on loop 11-12, and this immobilization consequently leads to a stabilization of H12. The difference in the DHT carbonyl isosteres affected the presence or absence of the H-bonds between the hydroxyl group of THQ and Thr877 and the distortion of H12, which is caused by the methyl group of THQ. Thus, the binding, agonist, and antagonist functions were controlled by subtle structural changes in THQ.     

Force-induced prolyl cis-trans isomerization in elastin-like polypeptides

Elastin-like polypeptides (ELPs) are stimulus-responsive polymers that contain repeats of five amino acids, Val-Pro-Gly-Xaa-Gly (VPGXG), where Xaa is a guest residue that can be any amino acid with the exception of proline. While studying the conformational mechanics of ELPs over a range of solvent conditions by single-molecule force spectroscopy, we noticed that some force-extension curves showed temperature-independent, extensional transitions that could not be fitted with a freely jointed chain or worm-like chain model. Here we show that the observed molecular elongation results from the force-induced peptidyl-prolyl cis-trans isomerization in prolines, which are repeated every fifth residue in the main chain of ELPs. Control experiments with poly(L-proline) demonstrate the similarity of the conformational transition between poly(L-proline) and ELPs. In contrast, the force-extension behavior of poly(L-lysine) showed no deviation in the relevant force range. Force-extension curves in hysteresis experiments showed an elongational difference between extension and relaxation pathways that suggests that the cis conformational state of the prolines could be exhausted on the time scale of the experiment. We present further computational evidence for this mechanism by Monte Carlo simulation of the force-extension behavior using an elastically coupled, two-state model. We believe ours is the first demonstration of force-induced prolyl cis-trans isomerization in proline-containing polypeptides. Our results suggest that single-molecule force spectroscopy could provide an alternate means to assay this important conformational transition in polypeptides.     

Quantum Mechanics/Molecular Mechanics Study on the Oxygen Binding and Substrate Hydroxylation Step in AlkB Repair Enzymes

AlkB repair enzymes are important nonheme iron enzymes that catalyse the demethylation of alkylated DNA bases in humans, which is a vital reaction in the body that heals externally damaged DNA bases. Its mechanism is currently controversial and in order to resolve the catalytic mechanism of these enzymes, a quantum mechanics/molecular mechanics (QM/MM) study was performed on the demethylation of the N¹‐methyladenine fragment by AlkB repair enzymes. Firstly, the initial modelling identified the oxygen binding site of the enzyme. Secondly, the oxygen activation mechanism was investigated and a novel pathway was found, whereby the catalytically active iron(IV)–oxo intermediate in the catalytic cycle undergoes an initial isomerisation assisted by an Arg residue in the substrate binding pocket, which then brings the oxo group in close contact with the methyl group of the alkylated DNA base. This enables a subsequent rate‐determining hydrogen‐atom abstraction on competitive σ‐ and π‐pathways on a quintet spin‐state surface. These findings give evidence of different locations of the oxygen and substrate binding channels in the enzyme and the origin of the separation of the oxygen‐bound intermediates in the catalytic cycle from substrate. Our studies are compared with small model complexes and the effect of protein and environment on the kinetics and mechanism is explained.     

Slippage of a Porphyrin Macrocycle over Threads of Varying Bulkiness: Implications for the Mechanism of Threading Polymers through a Macrocyclic Ring

Threading of a polymer through a macrocyclic ring may occur directly, that is, by finding the end of the polymer chain, or by a process in which the polymer chain first folds and then threads through the macrocyclic ring in a hairpin‐like conformation. We present kinetic and thermodynamic studies on the threading of a macrocyclic porphyrin receptor ( H₂1 ) onto molecular threads that are blocked on one side and are open on the other side. The open side is modified by groups that vary in ease of folding and in bulkiness. Additionally, the threads contain a viologen binding site for the macrocyclic receptor, which is located close to the blocking group. The rates of threading of H₂1 were measured under various conditions, by recording as a function of time the quenching of the fluorescence of the porphyrin, which occurs when receptor H₂1 reaches the viologen binding site. The kinetic data suggest that threading is impossible if the receptor encounters an open side that is sterically encumbered in a similar way as a folded polymer chain. This indicates that threading of polymers through macrocyclic compounds through a folded chain mechanism is unlikely.     

The Hexacarbonyl(ethyne)dicobalt Unit: An Androgen Tag

The interaction of estrogens and androgens with their corresponding receptors is known to play an important role in cancers of the breast and prostate. This paper reports the synthesis, characterization, and biochemical properties of a novel organometallic complex derived from 17α‐ethynyltestosterone, namely hexacarbonyl{μ‐[(20,21‐η:20,21‐η)‐(17α)‐17‐hydroxypregn‐4‐en‐20‐yn‐3‐one}dicobalt ([Co₂(CO)₆(17α‐ethynyltestosterone)]). The crystal and molecular structure of this compound was determined by single‐crystal X‐ray diffraction: it crystallizes in the monoclinic space group with a=24.6600(18) Å, b=12.9188(10) Å, c=26.3573(19) Å, β=108.651(2)°, and Z=12. A biochemical study showed that the compound is still recognized by the androgen receptor even when the relative binding affinity (RBA) is quite low (0.5%). This finding can be explained by the recently published 3D structure of the androgen receptor that shows that its binding site cannot accommodate a bulky substituent at the 17α position of the steroid.