Molecular dynamics simulations of hydration shell on montmorillonite (001) in water

Molecular dynamics simulations (MDS) of montmorillonite (001)/water interface system were used for studying the hydration shell on the montmorillonite surface in this work. The study was performed on the simulation of concentration profile and self‐diffusion coefficients. The results have shown that there was a hydration shell on the surface with the thickness of approximately 1.74 nm, which was composed of six ordered water molecule layers, including ordered layers and transition layers. The water molecules in the shell were closely and orderly arranged than those in bulk water, leading to a higher concentration of water molecules. Copyright © 2016 John Wiley & Sons, Ltd.     

Ab initio quantum chemistry and molecular dynamics simulations studies of LiPF6/poly(ethylene oxide) interactions

Ab initio and molecular mechanics studies of LiPF₆ and the interaction of the salt with the poly(ethylene oxide) (PEO) oligomer dimethylether have been performed. Optimized geometries and energies of Li⁺/PF₆^? complexes obtained from quantum chemistry revealed a preference for C_3V symmetry structures for Li⁺–P separations under 2.8 Å, C_2V symmetry for Li⁺–P in the range of 2.8–3.3 Å and C_4V symmetry for Li⁺–P separations larger than 3.3 Å. Electron correlation effects were found to make an insignificant contribution to binding in the Li⁺/PF₆^? complex. By contrast, analogous studies of PF₆^?/PF₆^? and PF₆^?/dimethyl ether complexes revealed important contributions of electron correlation to the complex interaction energy. A molecular mechanics force field for simulations of PEO/LiPF₆ melts was parameterized to reproduce the geometries and energies of Li⁺/PF₆^?, PF₆^?/PF₆^?, PF₆^?/dimethylether complexes. Molecular dynamics simulations of PEO/LiPF₆ melts were performed to validate this quantum chemistry‐based force field. Accurate reproduction of the increase in solution density with addition of salt was found while the electrical conductivity of PEO/LiPF₆ solutions was found to be within an order of magnitude of the experimental values. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 641–654, 2001     

The NMR structure of [Xd(C2)]4 investigated by molecular dynamics simulations

The i‐motif tetrameric structure is built up from two parallel duplexes intercalated in a head‐to‐tail orientation, and held together by hemiprotonated cytosine pairs. Two topologies exist for the i‐motif structure, one with outermost 3′ extremities and the other with outermost 5′ extremities, called the 3′E and 5′E topology, respectively. Since the comparison of sugar and phosphate group interactions between the two topologies is independent of the length of the intercalation motif, the relative stability of the 3′E and 5′E topologies therefore should not depend on this length. Nevertheless, it has been shown that the 3′E topology of the [d(C2)]4 is much more stable than the 5′E topology, and that the former is the only species observed in solution. In order to understand the reason for this atypical behavior, the NMR structure of the [Xd(C2)]4 was determined and analyzed by molecular dynamics simulations. In the NMR structure, the width of the narrow groove is slightly smaller than in previously determined i‐motif structures, which supports the importance of phosphodiester backbone interactions in the structure stability. The simulations show that the stacking of cytosines, essential for the i‐motif stability, is produced by a similar and non‐negative twisting of the phosphodiester backbones. The twisting is induced by an interaction between the backbones; the [Xd(C2)]4 in 5′E topology, exhibiting very limited interaction between the phosphodiester backbones, is thus unstable. Copyright © 2002 John Wiley & Sons, Ltd.     

Computing the (1)H NMR spectrum of a bulk ionic liquid from snapshots of car-parrinello molecular dynamics simulations.

We have investigated the performance of several computational protocols in predicting the NMR spectrum of a molecular ion in a complex liquid phase such as an ionic liquid. To do this, we computed the proton NMR chemical shifts of the 1-ethyl-3-methylimidazolium cation [emim](+) in [emim][Cl]. Environmental effects on the imidazolium ring proton chemical shifts are quite significant and must be taken into account explicitly. Calculations performed on the isolated imidazolium cation as well as on the [emim][Cl] ion pair grossly fail to reproduce the correct spacing between proton signals. In contrast, calculations performed on clusters extracted from the trajectory of a Car-Parrinello molecular dynamics simulation yield very good results.     

A conformational dynamics study of alpha-l-Rhap-(1-->2)[alpha-l-Rhap-(1-->3)]-alpha-l-Rhap-OMe in solution by NMR experiments and molecular simulations

The conformational preference of alpha-l-Rhap-(1-->2)[alpha-l-Rhap-(1-->3)]-alpha-l-Rhap-OMe in solution has been studied by NMR spectroscopy using one-dimensional (1)H,(1)H T-ROESY experiments and measurement of trans-glycosidic (3)J(C,H) coupling constants. Molecular dynamics (MD) simulations with a CHARMM22 type of force field modified for carbohydrates were performed with water as the explicit solvent. The homonuclear cross-relaxation rates, interpreted as effective proton-proton distances, were compared to those obtained from simulation. Via a Karplus torsional relationship, (3)J(C,H) values were calculated from simulation and compared to experimental data. Good agreement was observed between experimental data and the MD simulation, except for one inter-residue T-ROE between protons in the terminal sugar residues. The results show that the trisaccharide exhibits substantial conformational flexibility, in particular along the psi glycosidic torsion angles. Notably, for these torsions, a high degree of correlation (77%) was observed in the MD simulation revealing either psi(2)(+) psi(3)(+) or psi(2)(-)psi(3)(-) states. The simulations also showed that non-exoanomeric conformations were present at the phi torsion angles, but to a limited extent, with the phi(3) state populated to a larger extent than the phi(2) state. Further NMR analysis of the trisaccharide by translational diffusion measurements and (13)C T(1) relaxation experiments quantified global reorientation using an anisotropic model together with interpretation of the internal dynamics via the "model-free" approach. Fitting of the dynamically averaged states to experimental data showed that the psi(2)(+)psi(3)(+) state is present to approximately 49%, psi(2)(-) psi(3)(-) to approximately 39%, and phi(3) (non-exo) to approximately 12%. Finally, using a dynamic and population-averaged model, (1)H,(1)H T-ROE buildup curves were calculated using a full relaxation matrix approach and were found to be in excellent agreement with experimental data, in particular for the above inter-residue proton-proton interaction between the terminal residues.     

First-principles molecular dynamics evaluation of thermal effects on the NMR (1)J(Li,C) spin-spin coupling

Car-Parrinello (CP) molecular dynamics were applied to sample conformations of various models of organolithium aggregates which are chosen to estimate (1)J(Li,C) NMR coupling constants. The results show that the deviations from the values computed using static (optimized) geometries are small provided no large-amplitude motions occur within the timescale of the simulations. In the case of the vinyllithium dimer, for which rotation of the vinyl chain is observed, this approach allows analysis of the various contributions to the experimentally measured constants. For the trisolvated methyllithium monomer, partial decoordination of solvating dimethyl ether is observed and results in a significant shift of (1)J(Li,C). All these results highlight that a varied physicochemical machinery is hidden behind general empirical formulas, such as the Bauer-Winchester-Schleyer rule used experimentally.     

New all-atom force field for molecular dynamics simulation of an AlPO(4)-34 molecular sieve

A force field of the triclinic framework of AlPO(4)-34, important in methanol-hydrocarbon conversion reactions, was developed using an empirical potential function. Molecular dynamics simulation of an AlPO(4)-34 triclinic framework segment of 1216 atoms, containing the template molecules isopropylamine and water, was performed with explicit consideration of atomic charges. The average RMS difference between instantaneous positions of the framework atoms during 1 ns simulation and their positions in the structure determined from single crystal X-ray diffraction was calculated, and the average structure of the flexible framework was determined. The computed Debye-Waller factors and simulated FTIR spectra are in good agreement with the experimental data. The new force field permits detailed molecular dynamics simulations of flexible, charged aluminophosphate molecular sieves which should lead to a better understanding of the catalytic processes and the crucial role played by templating molecules.     

Molecular dynamics of hydrophilic poly(propylene imine) dendrimers in aqueous solutions by 1H NMR relaxation

The local dynamics of three poly(propylene imine) dendrimers with hydrophilic triethylenoxy methyl ether terminal groups were studied in D₂O by the measurement of the ¹H NMR relaxation times, which were treated with the Lipari–Szabo model‐free approach. The results showed that the overall mobility increased with temperature and decreased with increasing dendrimer size. An Arrhenius trend was observed for both overall and local motions. The activation energy of overall tumbling increased from 11.3 to 17.5 kJ/mol with the dendrimer size. The local mobility decreased from the outer part to the inner part of the dendrimer and with the dendrimer size. The spatial restriction of local motions decreased with increasing temperature up to 55 °C and remained constant above 55 °C. Local motions were more restricted when the dendrimer size increased. The results showed that the hydrophilic end groups of the dendrimers were located preferentially at the periphery of the molecules and were extended in the aqueous environment. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 2969–2975, 2003     

Force-field development and molecular dynamics simulations of ferrocene-peptide conjugates as a scaffold for hydrogenase mimics

The increasing importance of hydrogenase enzymes in the new energy research field has led us to examine the structure and dynamics of potential hydrogenase mimics, based on a ferrocene-peptide scaffold, using molecular dynamics (MD) simulations. To enable this MD study, a molecular mechanics force field for ferrocene-bearing peptides was developed and implemented in the CHARMM simulation package, thus extending the usefulness of the package into peptide-bioorganometallic chemistry. Using the automated frequency-matching method (AFMM), optimized intramolecular force-field parameters were generated through quantum chemical reference normal modes. The partial charges for ferrocene were derived by fitting point charges to quantum-chemically computed electrostatic potentials. The force field was tested against experimental X-ray crystal structures of dipeptide derivatives of ferrocene-1,1'-dicarboxylic acid. The calculations reproduce accurately the molecular geometries, including the characteristic C2-symmetrical intramolecular hydrogen-bonding pattern, that were stable over 0.1 micros MD simulations. The crystal packing properties of ferrocene-1-(D)alanine-(D)proline-1'-(D)alanine-(D)proline were also accurately reproduced. The lattice parameters of this crystal were conserved during a 0.1 micros MD simulation and match the experimental values almost exactly. Simulations of the peptides in dichloromethane are also in good agreement with experimental NMR and circular dichroism (CD) data in solution. The developed force field was used to perform MD simulations on novel, as yet unsynthesized peptide fragments that surround the active site of [Ni-Fe] hydrogenase. The results of this simulation lead us to propose an improved design for synthetic peptide-based hydrogenase models. The presented MD simulation results of metallocenes thereby provide a convincing validation of our proposal to use ferrocene-peptides as minimal enzyme mimics.     

MBO(N)D: A multibody method for long‐time molecular dynamics simulations

A modeling approach that can significantly speed up the dynamics simulation of large molecular systems is presented herein. A multigranular modeling approach, whereby different parts of the molecule are modeled at different levels of detail, is enabled by substructuring. Substructuring the molecular system is accomplished by collecting groups of atoms into rigid or flexible bodies. Body flexibility is modeled by a truncated set of body‐based modes. This approach allows for the elimination of the high‐frequency harmonic motion while capturing the low‐frequency anharmonic motion of interest. This results in the use of larger integration step sizes, substantially reducing the computational time required for a given dynamic simulation. The method also includes the use of a multiple time scale (MTS) integration scheme. Speed increases of 5‐ to 30‐fold over atomistic simulations have been realized in various applications of the method. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 159–184, 2000     

Berry pseudorotation mechanism for the interpretation of the 19F NMR spectrum in PF5 by ab initio molecular dynamics simulations.

For the first time, theoretical evidence that confirms the importance of the Berry pseudorotation process in the interpretation of the 19F NMR spectrum of phosphorus pentafluoride (PF5) is presented. Ab initio molecular dynamics simulations have been performed to generate a large number of configurations used for NMR parameter computations at the density functional theory level. Two different temperatures were set to highlight the effect of pseudorotation process on the NMR spectrum. Average 19F chemical shifts and spin-spin coupling constants calculated for the five fluorine atoms converge towards the NMR equivalence of the five atoms when the Berry pseudorotation mechanism is accounted for.     

NMR relaxation and relaxivity parameters of MRI probes revealed by optimal wavelet signal compression of molecular dynamics simulations

The MRI contrast agents (CAs) have been routinely used for detecting tumors at early stages. Currently, the most used CAs in MRI are gadolinium (Gd³⁺) complexes. However, these CAs can be toxic to the body. Thus, this work proposes Ni²⁺ complexes ([Ni(ACAC)₂(H₂O)₂], [Ni(TEA)]²⁺) as promising CAs. For the theoretical prediction, molecular dynamics simulations were carried out and the conformations were selected by the optimal wavelet signal compression algorithm method. The T₁ and T₂ values were obtained directly by means of the spectral density. Our findings showed that the Ni²⁺ complexes can be promising CAs in MRI.     

Liquid properties of dimethyl ether from molecular dynamics simulations using Ab Initio force fields

We have used molecular dynamic simulations to study the structural and dynamical properties of liquid dimethyl ether (DME) with a newly constructed ab initio force field in this article. The ab initio potential energy data were calculated at the second order Møller‐Plesset (MP2) perturbation theory with Dunning's correlation consistent basis sets (up to aug‐cc‐pVQZ). We considered 17 configurations of the DME dime for the orientation sampling. The calculated MP2 potential data were used to construct a 3‐site united atom force field model. The simulation results are compared with those using the empirical force field of Jorgensen and Ibrahim (Jorgensen and Ibrahim, J Am Chem Soc 1981, 103, 3976) and with available experimental measurements. We obtain quantitative agreements for the atom‐wise radial distribution functions, the self‐diffusion coefficients, and the shear viscosities over a wide range of experimental conditions. This force field thus provides a suitable starting point to predict liquid properties of DME from first principles intermolecular interactions with no empirical data input a priori. © 2012 Wiley Periodicals, Inc.     

Probing the dynamics of CO2 and CH4 within the porous zirconium terephthalate UiO-66(Zr): a synergic combination of neutron scattering measurements and molecular simulations

Quasi-elastic neutron scattering (QENS) measurements combined with molecular dynamics (MD) simulations were conducted to deeply understand the concentration dependence of the self- and transport diffusivities of CH(4) and CO(2), respectively, in the humidity-resistant metal-organic framework UiO-66(Zr). The QENS measurements show that the self-diffusivity profile for CH(4) exhibits a maximum, while the transport diffusivity for CO(2) increases continuously at the loadings explored in this study. Our MD simulations can reproduce fairly well both the magnitude and the concentration dependence of each measured diffusivity. The flexibility of the framework implemented by deriving a new forcefield for UiO-66(Zr) has a significant impact on the diffusivity of the two species. Methane diffuses faster than CO(2) over a broad range of loading, and this is in contrast to zeolites with narrow windows, for which opposite trends were observed. Further analysis of the MD trajectories indicates that the global microscopic diffusion mechanism involves a combination of intracage motions and jump sequences between tetrahedral and octahedral cages.     

Coarse‐grained molecular dynamics simulations of stereoregular poly(methyl methacrylate)/poly(vinyl chloride) blends

The stereoregular poly(methyl methacrylate)/poly(vinyl chloride) blends with a wide formulation range are extensively simulated using the coarse‐grained (CG) molecular dynamics (MD) method. To improve the representability, the bonded CG potentials are re‐parameterized against the atomistic simulated melt systems whereas the nonbonded CG potentials are adopted as developed in our previous work. Based on the CG potentials, the MD simulations reproduce all the local distributions of pure systems and the miscibility of mixed systems. Moreover, the global conformational properties are also closer to the target ones than those obtained using the previous CG potentials. The changes in density and volume upon mixing are computed together with the energies of mixing. They are all negative over the entire composition range and indicate stronger intermolecular interactions between distinct components than those between identical components. In particular, it is found that upon mixing the changes in density are insensible to chain tacticity but the changes in volume and the energies of mixing do, which quantitatively confirms that both inter‐molecular interactions and free‐volumes mainly contribute to the observed phase behaviors. Such models and methods reported herein can be used to quickly optimize formulations of polymer blends. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 203–212     

Atomistic insight into chondroitin‐6‐sulfate glycosaminoglycan chain through quantum mechanics calculations and molecular dynamics simulation

Chondroitin‐6‐sulfate (C6S) is a glycosaminoglycan (GAG) constituent in the extracellular matrix, which participates actively in crucial biological processes, as well as in various pathological conditions, such as atherosclerosis and cancer. Molecular interactions involving the C6S chain are therefore of considerable interest. A computational model for atomistic simulation was built. This work describes the design and validation of a force field for a C6S dodecasaccharide chain. The results of an extensive molecular dynamics simulation performed with the new force field provide a novel insight into the structure and dynamics of the C6S chain. The intramolecular H‐bonds in the disaccharide linkage region are suggested to play a major role in determining the chain structural dynamics. Moreover, the unravelling of an additional H‐bond involving the sulfate groups in C6S is interesting as changes in sulfation have been claimed to be an important factor in several diseases. The force field will prove useful for future studies of crucial interactions between C6S and various nanoassemblies. It can also be used as a basis for modeling of other GAGs. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Ergodicity and model quality in template‐restrained canonical and temperature/Hamiltonian replica exchange coarse‐grained molecular dynamics simulations of proteins

Molecular simulations restrained to single or multiple templates are commonly used in protein‐structure modeling. However, the restraints introduce additional barriers, thus impairing the ergodicity of simulations, which can affect the quality of the resulting models. In this work, the effect of restraint types and simulation schemes on ergodicity and model quality was investigated by performing template‐restrained canonical molecular dynamics (MD), multiplexed replica‐exchange molecular dynamics, and Hamiltonian replica exchange molecular dynamics (HREMD) simulations with the coarse‐grained UNRES force field on nine selected proteins, with pseudo‐harmonic log‐Gaussian (unbounded) or Lorentzian (bounded) restraint functions. The best ergodicity was exhibited by HREMD. It has been found that non‐ergodicity does not affect model quality if good templates are used to generate restraints. However, when poor‐quality restraints not covering the entire protein are used, the improved ergodicity of HREMD can lead to significantly improved protein models. © 2017 Wiley Periodicals, Inc.     

An NMR investigation on the phase structure and molecular mobility of the novel exfoliated polyethylene/palygorskite nanocomposites

Novel exfoliated polyethylene (PE)/palygorskite nanocomposites prepared by in situ polymerization are characterized by solid‐state nuclear magnetic resonance (NMR). The phase structure and molecular mobility are investigated by a combination of proton and carbon NMR. The results showed that incorporation of small amounts of palygorskite had great influence on the phase structure and molecular mobility. The incorporated palygorskite hindered the crystallization process and introduced motion‐hindered chains in the NMR crystalline and amorphous phase. ¹³C cross‐polarization and magic‐angle spinning NMR revealed two orthorhombic crystalline phase with different line‐width. The chain mobility of orthorhombic crystalline phase with broad resonance line is obviously hindered compared with the phase with narrow resonance line when the filler is introduced. Additionally, the results of pulsed field gradient NMR technique show those the tortuosities in the nanocomposites are much higher than that in the bulk PE. The self‐diffusion process of probe molecules is also influenced by the palygorksite load. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 1363–1371, 2010