Monte Carlo Conformational Search Research Articles

Theoretical Insights into the Ultrafast Deactivation Mechanism and Photostability of a Natural Sunscreen System: Mycosporine Glycine.

In this work, different levels of quantum computational models such as MP2, ADC(2), CASSCF/CASPT2, and DFT/TD-DFT have been employed to investigate the photophysics and photostability of a mycosporine system, mycosporine glycine (MyG). First of all, a molecular mechanics approach based on the Monte Carlo conformational search has been employed to investigate the possible geometry structures of MyG. Then, comprehensive studies on the electronic excited states and deactivation mechanism have been conducted on the most stable conformer. The first optically bright electronic transition responsible for the UV absorption of MyG has been assigned as the S2 (1ππ*) owing to the large oscillator strength (0.450). The first excited electronic state (S1) has been assigned as an optically dark (1nπ*) state. From the nonadiabatic dynamics simulation model, we propose that the initial population in the S2 (1ππ*) state transfers to the S1 state in under 100 fs, through an S2/S1 conical intersection (CI). The barrierless S1 potential energy curves then drive the excited system to the S1/S0 CI. This latter CI provides a significant route for ultrafast deactivation of the system to the ground state via internal conversion.

Molecular Mechanics Simulations and Improved Tight-Binding Hamiltonians for Artificial Light Harvesting Systems: Predicting Geometric Distributions, Disorder, and Spectroscopy of Chromophores in a Protein Environment.

We present molecular mechanics and spectroscopic calculations on prototype artificial light harvesting systems consisting of chromophores attached to a tobacco mosaic virus (TMV) protein scaffold. These systems have been synthesized and characterized spectroscopically, but information about the microscopic configurations and geometry of these TMV-templated chromophore assemblies is largely unknown. We use a Monte Carlo conformational search algorithm to determine the preferred positions and orientations of two chromophores, Coumarin 343 together with its linker and Oregon Green 488, when these are attached at two different sites (104 and 123) on the TMV protein. The resulting geometric information shows that the extent of disorder and aggregation properties and therefore the optical properties of the TMV-templated chromophore assembly are highly dependent on both the choice of chromophores and the protein site to which they are bound. We use the results of the conformational search as geometric parameters together with an improved tight-binding Hamiltonian to simulate the linear absorption spectra and compare with experimental spectral measurements. The ideal dipole approximation to the Hamiltonian is not valid because the distance between chromophores can be very small. We found that using the geometries from the conformational search is necessary to reproduce the features of the experimental spectral peaks.

P,p-Dihydroxydihydrostilbenophanes related to antimitotic combretastatins. Conformational analysis and its relationship to tubulin inhibition.

The structures of a new family of macrocyclic analogues of combretastatins B combining oxygenated substituents on the phenyl rings and indole rings are described. The effects of the stereochemistry, of the length of the spacer linking both aryl groups, and of the decoration of the macrocycles on the kinematics of the system have been studied by means of NMR studies at several temperatures and in different solvents combined with theoretical studies including Monte Carlo conformational searches and molecular dynamics simulations at different temperatures. The new indole macrocycles provide a more rigid view of this kind of macrocycles than that previously held. The tubulin polymerization activity of this new class of macrocycles has been assayed and analyzed.

Role of Dimerization Efficiency of Transmembrane Domains in Activation of Fibroblast Growth Factor Receptor 3

Mutations in transmembrane (TM) domains of receptor tyrosine kinases are shown to cause a number of inherited diseases and cancer development. Here, we use a combined molecular modeling approach to understand molecular mechanism of effect of G380R and A391E mutations on dimerization of TM domains of human fibroblast growth factor receptor 3 (FGFR3). According to results of Monte Carlo conformational search in the implicit membrane and further molecular dynamics simulations, TM dimer of this receptor is able to form a number of various conformations, which differ significantly by the free energy of association in a full-atom model bilayer. The aforementioned mutations affect dimerization efficiency of TM segments and lead to repopulation of conformational ensemble for the dimer. Particularly, both mutations do not change the dimerization free energy of the predominant (putative "non-active") symmetric conformation of TM dimer, while affect dimerization efficiency of its asymmetric ("intermediate") and alternative symmetric (putative "active") models. Results of our simulations provide novel atomistic prospective of the role of G380 and A391E mutations in dimerization of TM domains of FGFR3 and their consecutive contributions to the activation pathway of the receptor.

Proline-mediated formation of novel chroman-4-one tetrahydropyrimidines

Novel tricyclic N-benzylated chroman-4-one tetrahydropyrimidine derivatives have been prepared through a multi-component reaction between various 2-substituted chroman-4-one derivatives, N-methylenebenzylamine and a catalytic amount of proline under mild reaction conditions. The tricyclic structure of 1a was determined by NMR spectroscopy and confirmed by X-ray crystallography. An additional product, 2a, was isolated from the reaction mixture and its structure and conformation were determined by a combination of theoretical (Monte Carlo conformational search) and NMR-based (NOE and 3JHH couplings) conformational analysis. The NMR analysis revealed one preferred geometry for 1a and 2a in CHCl3 solution.

Synthetic Hosts for Molecular Recognition of Ureas

Four hosts (7-10) containing 2,6-bisamidopyridine- and 2,5-bisamidopyrrole-bearing pyridyl or 1,8-naphthyridyl groups have been prepared and their structures studied by a combination of multinuclear NMR spectroscopy and X-ray crystallography. Their behavior in molecular recognition of urea derivatives, including (+)-biotin methyl ester, has been approached by molecular modeling (Monte Carlo conformational search, AMBER force field). The minimum energy values for the complexes are correlated with the experimental binding energies determined by means of (1)H NMR titrations.

Disulfide Cyclized Tripeptide Analogues of Angiotensin IV as Potent and Selective Inhibitors of Insulin-Regulated Aminopeptidase (IRAP)

The insulin-regulated aminopeptidase (IRAP) localized in areas of the brain associated with memory and learning is emerging as a new promising therapeutic target for the treatment of memory dysfunctions. The angiotensin II metabolite angiotensin IV (Ang IV, Val(1)-Tyr(2)-Ile(3)-His(4)-Pro(5)-Phe(6)) binds with high affinity to IRAP and inhibits this aminopeptidase (K(i) = 62.4 nM). Furthermore, Ang IV has been demonstrated to enhance cognition in animal models and is believed to play an important role in cognitive processes. It is herein reported that displacement of the C-terminal tripeptide His(4)-Pro(5)-Phe(6) with a phenylacetic acid functionality combined with a constrained macrocyclic system in the N-terminal affords potent IRAP inhibitors that are less peptidic in character than the hexapeptide Ang IV. Configurational analysis of three pairs of diastereomeric Ang IV analogues was performed using a combination of solution NMR spectroscopic methods, Monte Carlo conformational searches, and NAMFIS calculations. The compounds encompassing l-amino acids only (4, 8, and 12) showed significantly higher bioactivity compared to their lld-epimers (5, 9, and 13). The best inhibitors in the series, compounds 8 and 12, incorporating a 13- and 14-membered disulfide ring system, respectively, and both with a β(3)-homotyrosine residue (β(3)hTyr) replacing Tyr(2), exhibit K(i) values of 3.3 and 5.2 nM, respectively.

Separation and Identification of Phenolic Compounds of Extra Virgin Olive Oil from Olea europaea L. by HPLC-DAD-SPE-NMR/MS. Identification of a New Diastereoisomer of the Aldehydic Form of Oleuropein Aglycone

The phenolic fraction of a monovarietal extra virgin olive oil (EVOO) from Olea europaea L. var. Cornezuelo was studied by the hyphenated HPLC-DAD-SPE-NMR/MS techniques. This survey led to the identification of 25 main compounds. One was identified as a new diastereoisomer of the aldehydic form of oleuropein aglycone (AOA) and characterized by 1D and 2D NMR techniques. The relative configuration of this new AOA was determined as 5R*,8S*,9S* on the basis of the results obtained from the combination of NOE experiments and Monte Carlo conformational search calculations. Assuming, as for the described diastereoisomers, that the new AOA comes from the natural oleuropein aglycone (OA), the absolute configuration was proposed as 5S,8R,9R.

Environmental effects on luminescence of meso-tetra-2-chlorophenylporphyrin

Effects of solvent polarity on the photophysical behaviour of meso-tetra-2-chlorophenylporphyrin have been studied by means of steady-state absorption and fluorescence, as well as time-resolved fluorescence techniques. A non-mirror symmetric absorption and emission spectra due to vibronic borrowing were obtained. Time-resolved fluorescence study indicated the bi-exponential decay kinetics for both the emission bands, observed in steady-state emission spectra. Such findings implied that there exists two emitting species on the photoinduced conformational excursions of the excited-state equilibrium and also that their relative contributions to emission change with solvent polarity. Monte Carlo conformational search based on force-field molecular mechanics was performed to locate equilibrium conformers in the ground state which enable evaluation of the ground-state barrier energies. This was followed by CIS and ZINDO calculations to explore the excited-state barriers.

Binding and Orientation of Tricyclic Antidepressants within the Central Substrate Site of the Human Serotonin Transporter

Tricyclic antidepressants (TCAs) have been used for decades, but their orientation within and molecular interactions with their primary target is yet unsettled. The recent finding of a TCA binding site in the extracellular vestibule of the bacterial leucine transporter 11 A above the central site has prompted debate about whether this vestibular site in the bacterial transporter is applicable to binding of antidepressants to their relevant physiological target, the human serotonin transporter (hSERT). We present an experimentally validated structural model of imipramine and analogous TCAs in the central substrate binding site of hSERT. Two possible binding modes were observed from induced fit docking calculations. We experimentally validated a single binding mode by combining mutagenesis of hSERT with uptake inhibition studies of different TCA analogs according to the paired mutation ligand analog complementation paradigm. Using this experimental method, we identify a salt bridge between the tertiary aliphatic amine and Asp(98). Furthermore, the 7-position of the imipramine ring is found vicinal to Phe(335), and the pocket lined by Ala(173) and Thr(439) is utilized by 3-substituents. These protein-ligand contact points unambiguously orient the TCA within the central binding site and reveal differences between substrate binding and inhibitor binding, giving important clues to the inhibition mechanism. Consonant with the well established competitive inhibition of uptake by TCAs, the resulting binding site for TCAs in hSERT is fully overlapping with the serotonin binding site in hSERT and dissimilar to the low affinity noncompetitive TCA site reported in the leucine transporter (LeuT).

Conformational Analysis of a Model for the trans-Fused FGH Ether Rings in Brevetoxin A

We have applied the Low Mode:Monte Carlo (LM:MC) conformational search method to an investigation of the low energy structures for 3R,4aS,7aR,11aS,12aR)-11a-methyl-3-phenyldecahydro-1H-[1,3]dioxino[5,4-b]pyrano[2,3-g]oxocine, 3, a model for the FGH rings in brevetoxin A, a potent marine toxin. Searches performed using a variety of classical force field-solvent combinations yielded ensembles containing between 30 and 60 structures with the central G-ring adopting the crown, twist-crown, boat-chair, and boat conformations. The lowest energy structure depended on the force field-solvent treatment, and the twist-crown and boat-chair conformers were typically lowest in energy. B3LYP/6-31G** geometry optimizations using the SCRF continuum solvent model confirmed these structures but indicated that the crown was the energetically preferred conformer with the boat-chair lying within 1.4 kcal/mol.

Exploring the Conformational Space for the Interactions of Aromatic Residue Analogs with Biologically Important Saccharides

Proteins interacting with carbohydrate ligands are getting a great deal of attention because of its important role in various biological processes. The crystal structures of several lectin-saccharide complexes have shown the presence of an aromatic residue in the binding site. The C-H hydrophobic patch of saccharide “stacks” against pi-cloud of aromatic residues forming CH-pi interactions, which are governed by dispersive and charge transfer interactions. The energetics of saccharide - aromatic residue interactions are dictated by their mutual position-orientations. It is conceivable that there exist low-energy position-orientations other than those found in the limited number of crystal structures of protein-carbohydrate complexes known to date. Hence, we have explored the conformational space for the interactions of 3-methylindole (3-MeIn), p-hydroxytoluene (p-OHTol) and toluene (Tol) (analogs of tryptophan, tyrosine and phenylalanine, respectively) with six saccharides. A Monte Carlo conformational search method was used to explore the features of the molecular potential energy surfaces. We found that the saccharides are densely populated above and below the pi-cloud of the aromatic ring of the amino acid residue but not along the edges. Clustering of conformers indicate the aromatic residues are spread out when interacting with C-H atoms as compared to that with -OH groups. The saccharides were capable of sliding on the surface of the aromatic residue. Four C-H groups can simultaneously participate in CH-pi interaction in 3-MeIn systems owing to its larger surface area. The β-D-Galactose and β-L-Fucose have been found to interact only through their b- and a-faces, respectively. Our ability to understand molecular flexibility through conformational search will further lead to advances in the design of drugs and to understand the advantages of selective choice of aromatic residues viz., tryptophan, tyrosine or phenylalanine in different carbohydrate binding proteins.

Solvolysis process of organophosphorus compound P-[2-(dimethylamino)ethyl]-N,N-dimethylphosphonamidic fluoride with simple and α-nucleophiles: a DFT study

Density functional theory (DFT) has been used to study the solvolysis process of the organophosphorus compound P-[2-(dimethylamino)ethyl]-N,N-dimethylphosphonamidic fluoride (GV) with simple nucleophile [hydroxide (HO−)] and α-nucleophiles [hydroperoxide (HOO−) and hydroxylamine anion (NH2O−)]. The lowest energy conformer of GV used for the solvolysis process was identified with Monte Carlo conformational search (MCMM) algorithm employing MMFFs force field followed by DFT calculations. The profound effect was found for α-nucleophiles toward the solvolysis of GV compared to normal alkaline hydrolysis. Incorporation of solvent (water) employing SCRF (PCM) model at B3LYP/6-31+G* showed that solvolysis of GV with hydroperoxide (activation energy = 7.6 kcal/mol) is kinetically more favored compared to hydroxide and hydroxylamine anion (activation energy = 11.0 and 9.2 kcal/mol, respectively). The faster solvolysis of GV with hydroperoxide is achieved due to strong intermolecular hydrogen bonding in the transition state geometry compared to similar α-nucleophile hydroxylamine anion. Assistance of a water molecule in solvolysis of GV affects the activation barriers; however, the hydroperoxidolysis remains the preferential process. The topological properties of electron density distributions for (–X–H···O, X = O, N) intermolecular hydrogen bonding bridges have been analyzed in terms of Bader theory of atoms in molecules (AIM). Further, the analysis was extended by natural bond orbital (NBO) methods for the strength of intermolecular hydrogen bonding in the transition state geometries. This study showed that the reactivity of these α-nucleophiles toward the solvolysis of GV is a delicate balance between the nucleophilicity and hydrogen-bond strength. Solvation governs the overall thermodynamics for the destruction of GV, which otherwise is unfavored in the gas phase studies.

Role of Environmental Factors on the Structure and Spectroscopic Response of 5′‐DNA–Porphyrin Conjugates Caused by Changes in the Porphyrin–Porphyrin Interactions

We have explored the utility, strength, and limitation of through-space exciton-coupled circular dichroism in determination of the secondary structure of optically active chromophoric nanoarrays using the example of end-capped porphyrin- and metalloporphyrin-oligodeoxynucleotide conjugates. We put special emphasis on the explanation of the origin and significance of the distinctive multiple bands in the CD spectra (trisignate and tetrasignate CD bands). Such CD profiles are often observed in chiral aggregates or multichromophoric arrays but have never before been studied in detail. We found that variation of temperature and ionic strength has a profound effect on the geometry of the porphyrin-DNA conjugates and thus the nature of electronic interactions. At lower temperatures and in the absence of NaCl all three 5'-DNA-porphyrin conjugates display negative bisignate CD exciton couplets of variable intensity in the Soret region resulting from through-space interaction between the electric transition dipole moments of the two end-capped porphyrins. As the temperature is raised these exciton couplets are transformed into single positive bands originating from the porphyrin-single-strand DNA interactions. At higher ionic strengths and low temperatures, multisignate CD bands are observed in the porphyrin Soret region. These CD signature bands originate from a combination of intermolecular, end-to-end porphyrin-porphyrin stacking between duplexes and porphyrin-DNA interactions. The intermolecular aggregation was confirmed by fluorescence and absorption spectroscopy and resonance light scattering. DeVoe theoretical CD calculations, in conjunction with molecular dynamics simulations and Monte Carlo conformational searches, were used to mimic the observed bisignate exciton-coupled CD spectra as well as multiple CD bands. Calculations correctly predicted the sign and shape of the experimentally observed CD spectra. These studies reveal that the exciton-coupled circular dichroism is a very useful technique for the determination of the structure of optically active arrays.

Influence of the rigid spacer to macrocyclization of poly(thialactones): synthesis and computational analysis

AbstractFormation of macrocyclic lactones 8‐19 by ring‐opening condensation of corresponding stannathianes 1‐4 with diacyl dichlorides 5‐7 was studied experimentally and theoretically. The cyclization reactions afforded mixtures of corresponding monomers (M), dimers (D), and trimers (T). In order to rationalize the influence of type and size of the spacer on the products ratio in the M‐D‐T mixtures we performed a force field based molecular modeling study. Monte Carlo conformational search was conducted and lowest energy conformations in chloroform were determined. Results of the molecular modeling in combination with the assumed kinetic parameters enabled better understanding of the experimentally obtained composition of the M‐D‐T‐mixtures. Copyright © 2008 John Wiley & Sons, Ltd.

Structural Selection of a Native Fold by Peptide Recognition. Insights into the Thioredoxin Folding Mechanism

Thioredoxins (TRXs) are monomeric alpha/beta proteins with a fold characterized by a central twisted beta-sheet surrounded by alpha-helical elements. The interaction of the C-terminal alpha-helix 5 of TRX against the remainder of the protein involves a close packing of hydrophobic surfaces, offering the opportunity of studying a fine-tuned molecular recognition phenomenon with long-range consequences on the acquisition of tertiary structure. In this work, we focus on the significance of interactions involving residues L94, L99, E101, F102, L103 and L107 on the formation of the noncovalent complex between reduced TRX1-93 and TRX94-108. The conformational status of the system was assessed experimentally by circular dichroism, intrinsic fluorescence emission and enzymic activity; and theoretically by molecular dynamics simulations (MDS). Alterations in tertiary structure of the complexes, resulting as a consequence of site specific mutation, were also examined. To distinguish the effect of alanine scanning mutagenesis on secondary structure stability, the intrinsic helix-forming ability of the mutant peptides was monitored experimentally by far-UV CD spectroscopy upon the addition of 2,2,2-trifluoroethanol, and also theoretically by Monte Carlo conformational search and MDS. This evidence suggests a key role of residues L99, F102 and L103 on the stabilization of the secondary structure of alpha-helix 5, and on the acquisition of tertiary structure upon complex formation. We hypothesize that the transition between a partially folded and a native-like conformation of reduced TRX1-93 would fundamentally depend on the consolidation of a cooperative tertiary unit based on the interaction between alpha-helix 3 and alpha-helix 5.

Quantum chemical studies on the potentially important imidates

The conformational space for the imidates 1–5 was explored with the Monte Carlo conformational search varying all the torsional degrees of freedom. Geometry optimization of the most stable conformers of imidates 1–5 were performed at the level B3LYP/6-31+G(d). Computed geometrical parameters were compared with the X-ray reported results. Hydrogen bonding, both intra- and intermolecular with methanol as solvent were computed at different computational levels in gas phase and DMSO. Intramolecular hydrogen bond strength does not exceed the limit of 8.50 kcal/mol due to geometry restrictions while, on the other hand, intermolecular hydrogen bond strength approaches 30.00 kcal/mol. Transition states of the inter-conversion between the most stable conformers (rotamers) were located and activation barrier of the inter-conversion processes was computed at different levels in gas phase and DMSO. Infrared spectra of these compounds were simulated and compared with experimental results. The carbonyl of the ester group shows bond stretching vibrational frequency at 1706–1812 cm −1 which agrees well with the experimentally recorded values at 1708–1740 cm −1.

P-Sulfonatocalix[7]arene: synthesis, protolysis, and binding ability

Water-soluble p -sulfonatocalix[7]arene 1 has been synthesized in good yield through standard procedures and its conformational preferences have been investigated by Monte Carlo conformational searches. The acid–base properties of 1 were investigated by means of potentiometric titration, obtaining p K a values in agreement with those reported for other p -sulfonatocalix[ n ]arene homologs. The binding ability of 1 toward organic quaternary ammonium cations such as Diquat ( 2 ), Paraquat ( 3 ), and Chlormequat ( 4 ) was investigated by means of 1 H NMR titrations in D 2 O at pD=7.3, DOSY NMR measurements, and 2D ROESY NMR spectroscopy. Spectrofluorimetry proved to be a useful method for the determination of trace amounts of 2 and 3 in aqueous solution by using Acridine Orange bound to 1 as a chemical indicator.

β-Cyclodextrin interactions with three drugs used in inflammatory pathologies: An experimental and theoretical study

Abstract Complexation of 5-amino salicylic acid ( 1 ), sulfasalazine ( 2 ) and diflunisal ( 3 ), nonsteroid anti-inflammatory drugs with a wide range of actions, with β-cyclodextrin (βCD) have been studied by means of differential scanning calorimetry and UV–vis spectroscopy. The experimental results have shown the formation of stable inclusion complexes. The molecular modeling study has been carried out to elucidate the different inclusion behaviors. A preliminary Monte Carlo (MC) conformational search of the guest molecules followed by docking and multiple minimization procedure with two force fields, A mber ∗ and P cff , has indicated that drugs forms stable complexes with βCD. The results are in good agreement with the experimental data from measurement of stability constants.

Conformational Preferences of Natural and C3-Modified Epothilones in Aqueous Solution

The conformational properties of the microtubule-stabilizing agent epothilone A ( 1a) and its 3-deoxy and 3-deoxy-2,3-didehydro derivatives 2 and 3 have been investigated in aqueous solution by a combination of NMR spectroscopic methods, Monte Carlo conformational searches, and NAMFIS calculations. The tubulin-bound conformation of epothilone A ( 1a), as previously proposed on the basis of solution NMR data, was found to represent a significant fraction of the ensemble of conformations present for the free ligands in aqueous solution.