A Combined Spectroscopic/Molecular Dynamic Study for Investigating a Methyl-Carboxylated PEI as a Potential Uranium Decorporation Agent

Inorganic Chemistry
Natural uranium has a very limited radioactive dose impact, but its chemical toxicity due to chronic exposure is still a matter of debate. Once inside the human body, the soluble uranium, under its uranyl form (U(VI)), is quickly removed from the blood system, partially excreted from the body, and partially retained in targeted organs, that is, the kidneys and bone matrix essentially. It is then crucial to remove or prevent the incorporation of uranium in these organs to limit the long-term chronic exposure. A lot of small chelating agents such as aminocarboxylates, catecholamides, and hydroxypyridonates have been developed so far. However, they suffer from poor selectivity and targeting abilities. Macromolecules and polymers are known to present a passive accumulation (size related), that is, the so-called enhanced permeability and retention effect, toward the main organs, which can be used as indirect targeting. Very interestingly, the methyl carboxylated polyethylenimine (PEI-MC)...  Read more

Prediction of low-field nuclear singlet lifetimes with molecular dynamics and quantum-chemical property surface

Physical Chemistry Chemical Physics
Molecular dynamics and quantum chemistry methods are implemented to quantify nuclear spin-1/2 pair singlet-state relaxation rates for three molecular systems at low magnetic field and room temperature. Computational methodology is developed for weak interactions, particularly important for singlet states at low field. These include spin-rotation and spin-internal-motion effects, which describe the coupling of the spin-carrying nuclei to fluctuating local magnetic fields induced by the overall and internal molecular fluctuations, respectively. A high-dimensional tensor property surface using Kriging interpolation is developed to circumvent costly quantum-chemical calculations. Together with the intramolecular dipolar relaxation, all the simulated relaxation mechanisms are accounted for with a common theoretical framework. Comparison with experiment indicates that quantitative accuracy is obtained, sufficient to enable guidance in the molecular design of molecules with long-lived...  Read more

Solvent Effects on Ligand Binding to a Serine Protease

Physical Chemistry Chemical Physics
Solvation plays an important role in virtually all biomolecular recognition and binding processes. However, the consequences of changes in solvation conditions often remain elusive. In this work, we combined isothermal titration calorimetry (ITC) and molecular dynamics (MD) simulations to investigate the effect of solvent composition on the thermodynamics of protein-ligand binding. We studied binding of p-aminobenzamidine (PAB) to trypsin in various water/methanol mixtures as a model system for a biomolecular complex. Our ITC experiments show that the free energy of binding changes only very modestly with methanol concentration, and that this small change is due to strong enthalpy-entropy compensation. The MD and free energy simulations not only reproduce the experimental binding free energies, but also provide atomic-level insights into the mechanisms behind the thermodynamic observations. The more favorable binding enthalpy at increased methanol concentrations (as compared to pure...  Read more

Alternative Route Toward Nitrones: Experimental and Theoretical Findings

The Journal of Organic Chemistry
Nitrones are important building blocks for natural and biologically active compounds, used as spin-trap reagents and therapeutic agents. All this makes nitrones intriguing and valuable compounds for fundamental studies and as useful chemicals in various synthetic strategies. Therefore, nitrones are still of great interest and in the limelight of researches. With our initial goal to solve synthetic problems toward 5-phenyl-2,2′-bipyridine (Phbpy), we found that this reaction can proceed through the formation of 6-phenyl-3-(pyridin-2-yl)-1,2,4-triazin-4(3H)-ol (4-OH), which rapidly isomerizes to a 3,4-dihydro-1,2,4-triazine-based nitrone, namely 6-phenyl-3-pyridin-2-yl-2,3-dihydro-1,2,4-triazin-4-oxide (4′), This encouraged us to study condensation of hydrazonophenylacetaldehyde oxime (2), obtained from 2-isonitrosoacetophenone (1), with other aldehydes. The reaction with both salicylaldehyde and p-tolualdehyde leads to the open-chain...  Read more

Agglomeration Behavior of Calcium Hydroxide/Calcium Oxide as Thermochemical Heat Storage Material: A Reactive Molecular Dynamics Study

The Journal of Physical Chemistry C
Thermochemical energy storage is a promising alternation in heat recovery application compared to phase change energy storage. However, cycling instability caused by agglomeration of the reactant particles is the main problem that hinders the application of this system. The present paper focuses on the agglomeration behavior of the calcium hydroxide/calcium oxide particles as a thermochemical energy storage material at the molecular level. Molecular dynamics simulations with the reactive force field were carried out to investigate the agglomeration of two nano-CaO/Ca(OH)2 particles. The results indicated that the agglomeration rate of two Ca(OH)2 particles was faster than that of two CaO particles in the presence of H2O, which was attributed to the greater spatial displacements of atoms in the reactant particles when thermochemical reaction occurred. The present of H2O could accelerate the agglomeration of the CaO particles. Moreover, the...  Read more

Impact of Turn Propensity on the Folding Rates of Z34C Protein: Implications for the Folding of Helix-Turn-Helix Motif

The Journal of Physical Chemistry B
The rate-limiting step for the folding of the helix-turn-helix (HTH) protein, Z34C, involves β-turn region 20DPNL23. This reverse turn has been observed to be part of the transition state in the folding process for Z34C, influencing its folding rates. Molecular dynamics simulations were performed on this turn peptide and its two mutants, D20A and P21A, to study turn formation using GROMOS54A7 force field. We find that this region has a turn propensity of its own, and the highest turn propensity is observed for the wild-type, which correlates well with available experimental results. We also find that a slight unfavorable change in ΔG turn folding causes a drastic change in the folding rates of HTH motif and a mechanistic interpretation is given. Implications of these observations for the folding of the HTH protein Z34C are discussed.Read more

Structural Model of the Tubular Assembly of the Rous Sarcoma Virus Capsid Protein

Journal of the American Chemical Society
The orthoretroviral capsid protein (CA) assembles into polymorphic capsids, whose architecture, assembly, and stability are still being investigated. The N-terminal and C-terminal domains of CA (NTD and CTD, respectively) engage in both homotypic and heterotypic interactions to create the capsid. Hexameric turrets formed by the NTD decorate the majority of the capsid surface. We report nearly complete solid-state NMR (ssNMR) resonance assignments of Rous sarcoma virus (RSV) CA, assembled into hexamer tubes that mimic the authentic capsid. The ssNMR assignments show that, upon assembly, large conformational changes occur in loops connecting helices, as well as the short 310 helix initiating the CTD. The interdomain linker becomes statically disordered. Combining constraints from ssNMR and cryo-electron microscopy (cryo-EM), we establish an atomic resolution model of the RSV CA tubular assembly using molecular dynamics flexible fitting (MDFF) simulations. On the basis of...  Read more

Diabat Interpolation for Polymorph Free-Energy Differences

The Journal of Physical Chemistry Letters
Existing methods to compute free-energy differences between polymorphs use harmonic approximations, advanced non-Boltzmann bias sampling techniques, and/or multistage free-energy perturbations. This work demonstrates how Bennett’s diabat interpolation method (J. Comput. Phys.1976, 22, 245) can be combined with energy gaps from lattice-switch Monte Carlo techniques (Phys. Rev. E2000, 61, 906) to swiftly estimate polymorph free-energy differences. The new method requires only two unbiased molecular dynamics simulations, one for each polymorph. To illustrate the new method, we compute the free-energy difference between face-centered cubic and body-centered cubic polymorphs for a Gaussian core solid. We discuss the justification for parabolic models of the free-energy diabats and similarities to methods that have been used in studies of electron transfer.Read more

The annular tautomerism of lithium 1,2,3-triazolate

New Journal of Chemistry
The annular tautomerism of lithium 1,2,3-triazolate (Li-TR) is experimentally investigated in the solid state by X-ray diffraction and in methanolic solution by NMR spectroscopy. DFT-based ab initio molecular dynamics simulations are additionally carried out to characterize the solvation structure of Li-TR in methanol and to determine the free energy landscape of the two tautomers.Read more

Mapping the sequence–structure relationships of simple cyclic hexapeptides

Physical Chemistry Chemical Physics
Cyclic peptides are promising protein–protein interaction modulators with high binding affinities and specificities, as well as enhanced stabilities and oral availabilities over linear analogs. Despite their relatively small size and cyclic architecture, it is currently difficult to predict the favored conformation(s) of most classes of cyclic peptides. An improved understanding of the sequence–structure relationships for cyclic peptides will offer an avenue for the rational design of cyclic peptides as possible therapeutics. In this work, we systematically explored the sequence–structure relationships for two cyclic hexapeptide systems using molecular dynamics simulation techniques. Starting with an all-glycine cyclic hexapeptide, cyclo-G6, we systematically replaced glycine residues with alanines and characterized the structural ensembles of different variants. The same process was repeated with valines to investigate the effects of larger side...  Read more

Molecular Details of the PH Domain of ACAP1BAR-PH Protein Binding to PIP-Containing Membrane

The Journal of Physical Chemistry B
ACAP1 proteins were previously reported to specifically bind PIP2-containing cell membranes and form well-structured protein lattices in order to conduct membrane tubulation. We carried out molecular dynamics simulations to characterize orientation of the PH domains with respect to the BAR domains inside the protein dimer. Followed by molecular dynamics simulations, we present a comprehensive orientation analysis of PH domain under different states including unbound and bound with lipids. We have examined two binding pockets on the PH domain and present PMF profiles of the two pockets to account for their preference to PIP2 lipids. Combining orientation analysis and studies of binding pockets, our simulations results reveal valuable molecular basis for protein–lipid interactions of ACAP1 proteins during membrane remodeling process.Read more

Molecular Interactions between Graphene and Biological Molecules

Journal of the American Chemical Society
Applications of graphene have extended into areas of nanobio-technology such as nanobio-medicine, nanobio-sensing, as well as nanoelectronics with biomolecules. These applications involve interactions between proteins, peptides, DNA, RNA etc. and graphene, therefore understanding such molecular interactions is essential. For example, many applications based on using graphene and peptides require peptides to interact with (e.g., noncovalently bind to) graphene at one end, while simultaneously exposing the other end to the surrounding medium (e.g., to detect analytes in solution). To control and characterize peptide behavior on a graphene surface in solution is difficult. Here we successfully probed the molecular interactions between two peptides (cecropin P1 and MSI-78(C1)) and graphene in situ and in real-time using sum frequency generation (SFG) vibrational spectroscopy and molecular dynamics (MD) simulation. We demonstrated that the distribution of various planar (including aromatic...  Read more

Effect of Interlayer Spacing on the Activity of Layered Manganese Oxide Bilayer Catalysts for the Oxygen Evolution Reaction

Journal of the American Chemical Society
We investigated the dependence of the electrocatalytic activity for the oxygen evolution reaction (OER) on the interlayer distance of five compositionally distinct layered manganese oxide nanostructures. Each individual electrocatalyst was assembled with a different alkali metal intercalated between two nanosheets (NS) of manganese oxide to form a bilayer structure. Manganese oxide NS were synthesized via the exfoliation of a layered material, birnessite. Atomic force microscopy was used to determine the heights of the bilayer catalysts. The interlayer spacing of the supported bilayers positively correlates with the size of the alkali cation: NS/Cs+/NS > NS/Rb+/NS > NS/K+/NS > NS/Na+/NS > NS/Li+/NS. The thermodynamic origins of these bilayer heights were investigated using molecular dynamics simulations. The overpotential (η) for the OER correlates with the interlayer spacing; NS/Cs+/NS has the lowest η...  Read more

Pharmacophore-Based 3D-QSAR Analysis of Thienyl Chalcones as a New Class of Human MAO-B Inhibitors: Investigation of Combined Quantum Chemical and Molecular Dynamics Approach

The Journal of Physical Chemistry B
Selective monoamine oxidase-B (MAO-B) inhibitors are imperative in the treatment of various neurodegenerative disorders. Herein, we describe the pharmacophore generation and atom-based three-dimensional quantitative structure–activity relationship (3D-QSAR) analyses of previously reported thiophene-based hMAO-B inhibitors by our research group. The aim of this study was to identify the principal structural features that could potentially be responsible for the inhibitory activity of hMAO-B inhibitors. The best pharmacophore model generated was the four-point assay of AHRR.8. The pharmacophore model exhibited good correlation with its predictability of the statistically valid 3D-QSAR analyses. Density functional theory calculations were further employed on the lead molecule (2E)-1-(5-bromothiophen-2-yl)-3-[4-(dimethylamino) phenyl] prop-2-en-1-one (Tb5) to investigate the electrostatic potential surface and analyze the natural bond orbital toward the binding...  Read more

Quantitative Assessment of Molecular Dynamics Sampling for Flexible Systems

Journal of Chemical Theory and Computation
Molecular dynamics (MD) simulation is a natural method for the study of flexible molecules but at the same time is limited by the large size of the conformational space of these molecules. We ask by how much the MD sampling quality for flexible molecules can be improved by two means: the use of diverse sets of trajectories starting from different initial conformations to detect deviations between samples and sampling with enhanced methods such as accelerated MD (aMD) or scaled MD (sMD) that distort the energy landscape in controlled ways. To this end, we test the effects of these approaches on MD simulations of two flexible biomolecules in aqueous solution, Met-Enkephalin (5 amino acids) and HIV-1 gp120 V3 (a cycle of 35 amino acids). We assess the convergence of the sampling quantitatively with known, extensive measures of cluster number Nc and cluster distribution entropy Sc and with two new quantities, conformational overlap...  Read more

Defining the molecular structure of teixobactin analogues and understanding their role in antibacterial activities

Chemical Communications
The discovery of the highly potent antibiotic teixobactin, which kills the bacteria without any detectable resistance, has stimulated interest in its structure–activity relationship. However, a molecular structure–activity relationship has not been established so far for teixobactin. Moreover, the importance of the individual amino acids in terms of their L/D configuration and their contribution to the molecular structure and biological activity are still unknown. For the first time, we have defined the molecular structure of seven teixobactin analogues through the variation of the D/L configuration of its key residues, namely N-Me-D-Phe, D-Gln, D-allo-Ile and D-Thr. Furthermore, we have established the role of the individual D amino acids and correlated this with the molecular structure and biological activity. Through extensive NMR and structural...  Read more

Molecular dynamics simulations of the effect of waviness and agglomeration of CNTs on interface strength of thermoset nanocomposites

Physical Chemistry Chemical Physics
Most existing molecular dynamics simulations in nanoreinforced composites assume carbon nanotubes (CNTs) to be straight and uniformly dispersed within thermoplastics. In reality, however, CNTs are typically curved, agglomerated and aggregated as a result of van der Waal interactions and electrostatic forces. In this paper, we account for both curvature and agglomeration of CNTs in extensive molecular dynamic (MD) simulations. The purpose of these simulations is to evaluate the influence of waviness and agglomeration of these curved and agglomerated CNTs on the interfacial strength of thermoset nanocomposite and upon their load transfer capability. Two aspects of the work were accordingly examined. In the first, realistic carbon nanotubes (CNTs) of the same length but varied curvatures were embedded in thermoset polymer composites and simulations of pull-out tests were conducted to evaluate the corresponding interfacial shear strength (ISS). In the second, the effect of the agglomerate...  Read more

Structure and stability of clusters of β-alanine in the gas phase: importance of the nature of intermolecular interactions

Physical Chemistry Chemical Physics
We present a theoretical study of neutral clusters of β-alanine molecules in the gas phase, (β-ala)nn ≤ 5. Classical molecular dynamics simulations carried out with different internal excitation energies provide information on the clusters formation and their thermal decomposition limits. We also present an assessment study performed with different families of density functionals using the dimer, (β-ala)2, as a benchmark system. The M06-2X functional provides the best agreement in geometries and relative energies in comparison with the reference values computed with the MP2 and CCSD(T) methods. The structure, stability, dissociation energies and vertical ionization potentials of the studied clusters have been investigated using this functional in combination with the 6-311++G(d,p) basis set. An exhaustive analysis of intermolecular interactions is also presented. These results provide new insights into the...  Read more

Novel high-temperature ferroelectric domain morphology in PbTiO3 ultrathin films

Physical Chemistry Chemical Physics
Exotic domain morphologies in ferroic materials are an exciting avenue for the development of novel nanoelectronics. In this work we have used large scale molecular dynamics to construct a strain-temperature phase diagram of the domain morphology of PbTiO3 ultrathin films. Sampling a wide interval of strain values over a temperature range up to the Curie temperature Tc, we found that epitaxial strain induces the formation of a variety of closure- and in-plane domain morphologies. The local strain and ferroelectric–antiferrodistortive coupling at the film surface vary for the strain mediated transition sequence and this could offer a route for experimental observation of the morphologies. Remarkably, we identify a new nanobubble domain morphology that is stable in the high-temperature regime for compressively strained PbTiO3. We demonstrate that the formation mechanism of the nanobubble domains...  Read more

Muropeptide Binding and the X-ray Structure of the Effector Domain of the Transcriptional Regulator AmpR of Pseudomonas aeruginosa

Journal of the American Chemical Society
A complex link exists between cell-wall recycling/repair and the manifestation of resistance to β-lactam antibiotics in many Enterobacteriaceae and Pseudomonas aeruginosa. This process is mediated by specific cell-wall-derived muropeptide products. These muropeptides are internalized into the cytoplasm and bind to the transcriptional regulator AmpR, which controls the cytoplasmic events that lead to expression of β-lactamase, an antibiotic-resistance determinant. The effector-binding domain (EBD) of AmpR was purified to homogeneity. We document that the EBD exists exclusively as a dimer, even at a concentration as low as 1 μM. The EBD binds to the suppressor ligand UDP-N-acetyl-β-d-muramyl-l-Ala-γ-d-Glu-meso-DAP-d-Ala-d-Ala and binds to two activator muropeptides, N-acetyl-β-Read more