Duplex formation and the onset of helicity in poly d(CG)n oligonucleotides in a solvent-free environment

The gas-phase conformations of a series of cytosine/guanine DNA duplexes were examined by ion mobility and molecular dynamics methods. Deprotonated duplex ions were formed by electrospray ionization, and their collision cross sections measured in helium were compared to calculated cross sections of theoretical models generated by molecular dynamics. The 4-mer (dCGCG) and 6-mer (dCGCGCG) duplexes were found to have globular conformations. Globular and helical structures were observed for the 8-mer (dCGCGCGCG) duplex, with the globular form being the more favored conformer. For the 10-mer (dCGCGCGCGCG), 14-mer (dCGCGCGCGCGCGCG), and 18-mer (dCGCGCGCGCGCGCGCGCG) duplexes, only helical structures were observed in the ion mobility measurements. Theory predicts that the helical structures are less stable than the globular forms in the gas phase and should collapse into the globular form given enough time. However, molecular dynamics simulations at 300 K indicate the helical structures are stable in aqueous solution and will retain their conformations for a limited time in the gas phase. The presence of helical structures in the ion mobility experiments indicates that the duplexes retain "solution structures" in the gas phase on the millisecond time scale.     

Molecular representation of coal-derived asphaltene based on high resolution mass spectrometry

The asphaltene separated by solubility in small molecular alkanes and toluene is the most structurally diverse and complex components in heavy oil, such as vacuum residue and coal tar. The coal-derived asphaltene is always regard as a succession of maltene fraction from small molecules to large molecules, and also a continuum of island- and archipelago-type structures, which is difficult to be identified accurately through current characterization methods. This limits the further study of molecular dynamics and reaction dynamics simulation of asphaltenes. In this work, a representation model of molecular composition and structure for coal-derived asphaltene is developed mainly based on Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) coupled with collision induced dissociation (CID) and traditional methods of nuclear magnetic resonance spectroscopy (¹³C NMR), Fourier transform infrared spectroscopy (FT-IR), X-ray photoelectron spectroscopy (XPS). Island- and archipelago-type structures are considered qualitatively in the representation of asphaltene. The asphaltene molecules are systematic assembled using stochastic algorithms and optimized by simulated annealing algorithm according to the group contribution method. The bulk properties for simulating asphaltenes are in good agreement with the experimental results giving acceptable predictions for the composition and structure of the asphaltenes. Moreover, the representative average structure asphaltene molecules are obtained using the developed molecular similarity function, which could be applied in the further study of molecular aggregation simulation and reaction kinetics simulation.     

温控分子动力学研究微管蛋白活性肽链的折叠机制

运用温控和常温分子动力学方法, 研究了微管蛋白活性部位Pep1-28肽链的折叠机制, 总模拟时间为380.0 ns. 对于温控分子动力学, 逐渐降温可以清晰显示Pep1-28肽链的折叠途径, 发生明显折叠的温度约为550 K, 其折叠和去折叠可逆机制为U(>1200 K)←→I1(1200-1000 K)←→I2(800 K)←→I3(600 K)←→I4(450 K)←→F1(400 K)←→F2(300 K), 其中U为去折叠态构象, I1、I2、I3和I4是折叠过程中的四个重要的中间态构象, F1和F2是两个结构相近的折叠态构象. 对于常温(300 K)分子动力学, 其构象转变和折叠过程相当迅速, 很难观察到有效、稳定的中间态构象. 尤其引人注意的是, 其折叠态结构陷入了能量局域极小点, 与温控(300 K)的有较大差异, 两者能量差高达297.53 kJ·mol-1. 可见, 温控分子动力学方法不仅清晰地显示多肽和蛋白质折叠过程的重要中间态构象, 为折叠和去折叠机制提供直接、可靠的依据, 而且还有助于跨越较高的构象能垒, 促使多肽和蛋白质折叠以形成全局能量最低的稳定结构.     

Conformational search using a molecular dynamics–minimization procedure: Applications to clusters of coulombic charges,Lennard–Jones particles,and waters

A new conformational search method, molecular dynamics–minimization (MDM), is proposed, which combines a molecular dynamics sampling strategy with energy minimizations in the search for low-energy molecular structures. This new method is applied to the search for low energy configurations of clusters of coulombic charges on a unit sphere, Lennard–Jones clusters, and water clusters. The MDM method is shown to be efficient in finding the lowest energy configurations of these clusters. A closer comparison of MDM with alternative conformational search methods on Lennard–Jones clusters shows that, although MDM is not as efficient as the Monte Carlo–minimization method in locating the global energy minima, it is more efficient than the diffusion equation method and the method of minimization from randomly generated structures. Given the versatility of the molecular dynamics sampling strategy in comparison to Monte Carlo in treating molecular complexes or molecules in explicit solution, one anticipates that the MDM method could be profitably applied to conformational search problems where the number of degrees of freedom is much greater. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 60–70, 1998     

Magnetic resonance analysis of capillary formation reaction front dynamics in alginate gels

The formation of heterogeneous structures in biopolymer gels is of current interest for biomedical applications and is of fundamental interest to understanding the molecular level origins of structures generated from disordered solutions by reactions. The cation-mediated physical gelation of alginate by calcium and copper is analyzed using magnetic resonance measurements of spatially resolved molecular dynamics during gel front propagation. Relaxation time and pulse-field gradient methods are applied to determine the impact of ion front motion on molecular translational dynamics. The formation of capillaries in alginate copper gels is correlated to changes in translational dynamics.     

New AMBER force field parameters of heme iron for cytochrome P450s determined by quantum chemical calculations of simplified models

The heme protein, cytochrome P450, is an oxidoreductase that plays an important role in drug metabolism. To model P450s using molecular mechanics methods and classical molecular dynamics simulations, force field parameters and atomic charges are required. Because these parameters are generally obtained by quantum chemical methods, an appropriate simplified model for the iron-porphyrin system was needed. In this study, two models with a five-coordinated Fe(III) mimicking the sextet spin state of P450s are proposed, which are optimized by semiempirical and ab initio unrestricted Hartree-Fock methods. The results produced using the simpler of the two models were similar to those of the more complex model; therefore, the more simplified model of P450 can be used without a loss of accuracy. Furthermore, several quantum chemical calculations were carried out on the simpler model to investigate which method was most suitable for iron-porphyrin systems. The results calculated by hybrid density functional theory (DFT), with the MIDI basis set for iron, reproduced the three-dimensional structures determined by X-ray diffraction and extended X-ray absorption fine-structure experiments. From these results, atomic charges and force-field parameters for molecular mechanics and molecular dynamics calculations were obtained.     

Stability of nucleic acid base pairs in organic solvents: molecular dynamics, molecular dynamics/quenching, and correlated ab initio study

The dynamic structure and potential energy surface of adenine...thymine and guanine...cytosine base pairs and their methylated analogues interacting with a small number (from 1 to 16 molecules) of organic solvents (methanol, dimethylsulfoxide, and chloroform) were investigated by various theoretical approaches starting from simple empirical methods employing the Cornell et al. force field to highly accurate ab initio quantum chemical calculations (MP2 and particularly CCSD(T) methods). After the simple molecular dynamics simulation, the molecular dynamics in combination with quenching technique was also used. The molecular dynamics simulations presented here have confirmed previous experimental and theoretical results from the bulk solvents showing that, whereas in chloroform the base pairs create hydrogen-bonded structures, in methanol, stacked structures are preferred. While methanol (like water) can stabilize the stacked structures of the base pairs by a higher number of hydrogen bonds than is possible in hydrogen-bonded pairs, the chloroform molecule lacks such a property, and the hydrogen-bonded structures are preferred in this solvent. The large volume of the dimethylsulfoxide molecule is an obstacle for the creation of very stable hydrogen-bonded and stacked systems, and a preference for T-shaped structures, especially for complexes of methylated adenine...thymine base pairs, was observed. These results provide clear evidence that the preference of either the stacked or the hydrogen-bonded structures of the base pairs in the solvent is not determined only by bulk properties or the solvent polarity but rather by specific interactions of the base pair with a small number of the solvent molecules. These conclusions obtained at the empirical level were verified also by high-level ab initio correlated calculations.     

Exploring potential energy surfaces for chemical reactions: an overview of some practical methods

Potential energy surfaces form a central concept in the application of electronic structure methods to the study of molecular structures, properties, and reactivities. Recent advances in tools for exploring potential energy surfaces are surveyed. Methods for geometry optimization of equilibrium structures, searching for transition states, following reaction paths and ab initio molecular dynamics are discussed. For geometry optimization, topics include methods for large molecules, QM/MM calculations, and simultaneous optimization of the wave function and the geometry. Path optimization methods and dynamics based techniques for transition state searching and reaction path following are outlined. Developments in the calculation of ab initio classical trajectories in the Born-Oppenheimer and Car-Parrinello approaches are described.     

Conformational analysis of bradykinin by annealed molecular dynamics and comparison to NMR-derived conformations

Conformational analysis of bradykinin (BK), a nonapeptide of the sequence RPPGFSPFR, was accomplished using annealed molecular dynamics (AMD) at 1000 K in BIOGRAF 2.2. One hundred anneal cycles produced 100 conformations over approximately 2000 ps. These conformations were compared to structures derived by nuclear magnetic resonance (NMR) methods for similar shape and energy. Energy minimization of relevant conformations using both BIOGRAF 2.2 and AMBER 3.0a revealed that the AMD-determined conformations are in the same energy range as the NMR-determined structures. Also, the shape of the relevant conformations appeared similar, suggesting that AMD is a good tool for the conformational analysis of small peptide ligands. © 1993 John Wiley & Sons, Inc.     

SAMPL6 host–guest challenge: binding free energies via a multistep approach

In this effort in the SAMPL6 host–guest binding challenge, a combination of molecular dynamics and quantum mechanical methods were used to blindly predict the host–guest binding free energies of a series of cucurbit[8]uril (CB8), octa-acid (OA), and tetramethyl octa-acid (TEMOA) hosts bound to various guest molecules in aqueous solution. Poses for host–guest systems were generated via molecular dynamics (MD) simulations and clustering analyses. The binding free energies for the structures obtained via cluster analyses of MD trajectories were calculated using the MMPBSA method and density functional theory (DFT) with the inclusion of Grimme’s dispersion correction, an implicit solvation model to model the aqueous solution, and the resolution-of-the-identity (RI) approximation (MMPBSA, RI-B3PW91-D3, and RI-B3PW91, respectively). Among these three methods tested, the results for OA and TEMOA systems showed MMPBSA and RI-B3PW91-D3 methods can be used to qualitatively rank binding energies of small molecules with an overbinding by 7 and 37 kcal/mol respectively, and RI-B3PW91 gave the poorest quality results, indicating the importance of dispersion correction for the binding free energy calculations. Due to the complexity of the CB8 systems, all of the methods tested show poor correlation with the experimental results. Other quantum mechanical approaches used for the calculation of binding free energies included DFT without the RI approximation, utilizing truncated basis sets to reduce the computational cost (memory, disk space, CPU time), and a corrected dielectric constant to account for ionic strength within the implicit solvation model.     

Solvent interaction energy calculations on molecular dynamics trajectories: increasing the efficiency using systematic frame selection

End-point methods such as linear interaction energy (LIE) analysis, molecular mechanics generalized Born solvent-accessible surface (MM/GBSA), and solvent interaction energy (SIE) analysis have become popular techniques to calculate the free energy associated with protein-ligand binding. Such methods typically use molecular dynamics (MD) simulations to generate an ensemble of protein structures that encompasses the bound and unbound states. The energy evaluation method (LIE, MM/GBSA, or SIE) is subsequently used to calculate the energy of each member of the ensemble, thus providing an estimate of the average free energy difference between the bound and unbound states. The workflow requiring both MD simulation and energy calculation for each frame and each trajectory proves to be computationally expensive. In an attempt to reduce the high computational cost associated with end-point methods, we study several methods by which frames may be intelligently selected from the MD simulation including clustering and address the question of how the number of selected frames influences the accuracy of the SIE calculations.     

Adsorption of cationic multicharged surfactants at liquid–gas interface

We present the review of the existing methods for describing adsorption at fluid interfaces that may be applicable for multiple charge cationic surfactant structures of various architectures—multiheaded (e.g., dicephalic) structures and multimeric surfactants (e.g., dimeric (so-called gemini), trimeric, tetrameric, etc.). We discuss the role of the prefactor the in the Gibbs adsorption equation originating from the number of charges present in the adsorbed layer and the reasons for the deviation from its thermodynamic value. We present several models of adsorption that can be used to describe surface tension isotherms and appreciate the role of prof. Peter Kralchevski in their development. Application of molecular dynamics methods combined with the approach based on the thermodynamic models of multicharged surfactant adsorption may lead to an explanation of some experimentally observed phenomena and can provide the basis for the development of novel materials designated for a variety of applications.     

Structure and ultrafast dynamics of liquid water: a quantum mechanics/molecular mechanics molecular dynamics simulations study

A quantum mechanics/molecular mechanics molecular dynamics simulation was performed for liquid water to investigate structural and dynamical properties of this peculiar liquid. The most important region containing a central reference molecule and all nearest surrounding molecules (first coordination shell) was treated by Hartree-Fock (HF), post-Hartree-Fock [second-order Moller-Plesset perturbation theory (MP2)], and hybrid density functional B3LYP [Becke's three parameter functional (B3) with the correlation functional of Lee, Yang, and Parr (LYP)] methods. In addition, another HF-level simulation (2HF) included the full second coordination shell. Site to site interactions between oxygen-oxygen, oxygen-hydrogen, and hydrogen-hydrogen atoms of all ab initio methods were compared to experimental data. The absence of a second peak and the appearance of a shoulder instead in the gO-O graph obtained from the 2HF simulation is notable, as this feature has been observed so far only for pressurized or heated water. Dynamical data show that the 2HF procedure compensates some of the deficiency of the HF one-shell simulation, reducing the difference between correlated (MP2) and HF results. B3LYP apparently leads to too rigid structures and thus to an artificial slow down of the dynamics.     

Comparison of approximate quantum simulation methods applied to normal liquid helium at 4 K

The Feynman-Kleinert linearized path integral molecular dynamics (FK-LPI), ring polymer molecular dynamics (RPMD), and centroid molecular dynamics (CMD) methods are applied to the simulation of normal liquid helium. Comparisons of the simulation results at the T = 4 K and rho = 0.01873 A-3 state point are presented. The calculated quantum correlation functions for the three methods show significant differences, both in the short time and in the intermediate regions of the spectrum. Our simulation results are also compared to the recent results of other approximate quantum simulation methods. We find that FK-LPI qualitatively agrees with other approximate quantum simulation results while CMD and RPMD predict a qualitatively different impulsive rebound in the velocity autocorrelation function. Frequency space analysis reveals that RPMD exhibits a broad high-frequency tail similar to that from quantum mode coupling theory and numerical analytic continuation approaches, while FK-LPI provides a somewhat more rapid decay at high frequency than any of these three methods. CMD manifests a high-frequency component that is greatly reduced compared with the other methods.     

Theoretical study of correlations between the coordination structures and catalytic activities in polymer-stabilized au nanocluster catalysts

Au nanoclusters (Au NCs) stabilized by poly(N-vinyl-2-pyrrolidone) and poly(allylamine), abbreviated to Au:PVP and Au:PAA, catalyze the aerobic oxidation of p-hydroxybenzyl alcohols, but the catalytic activity of Au:PVP is much higher than that of Au:PAA. To elucidate the correlations between the catalytic activities and coordination structures of the stabilizing polymer, the substrate accessibility on Au NCs was estimated by density functional theory (DFT) and molecular dynamics (MD) calculations. For MD simulations, we applied a systematic method to optimize the temperature parameters in temperature replica exchange molecular dynamics (T-REMD), and the coordination structures were comprehensively classified by multivariate analysis. The results show that the number of open active sites on the Au NCs is a good index for predicting the catalytic activities. © 2018 Wiley Periodicals, Inc.     

MM and QM/MM Modeling of Threonyl-tRNA Synthetase: Model Testing and Simulations

Aminoacyl-tRNA synthetases are centrally important enzymes in protein synthesis. We have investigated threonyl-tRNA synthetase from E. coli, complexed with reactants, using molecular mechanics and combined quantum mechanical/molecular mechanical (QM/MM) techniques. These modeling methods have the potential to provide molecular level understanding of enzyme catalytic processes. Modeling of this enzyme presents a number of challenges. The procedure of system preparation and testing is described in detail. For example, the number of metal ions at the active site, and their positions, were investigated. Molecular dynamics simulations suggest that the system is most stable when it contains only one magnesium ion, and the zinc ion is removed. Two different QM/MM methods were tested in models based on the findings of MM molecular dynamics simulations. AM1/CHARMM calculations resulted in unrealistic structures for the phosphates in this system. This is apparently due to an error of AM1. PM3/CHARMM calculations proved to be more suitable for this enzyme system. These results will provide a useful basis for future modeling investigations of the enzyme mechanism and dynamics.     

An enantioselective voltammetric sensor for the recognition of propranolol stereoisomers

An enantioselective voltammetric sensor for the recognition of propranolol stereoisomers is developed based on a carbon-paste electrode modified with uracil supramolecular structures and the use of chemometric methods. The conditions for the formation of an enantioselective selector on the surface of graphite (graphene) particles and the selective registration of voltammograms of enantiomers, as well as the possibility of the recognition thereof, are studied by methods of molecular dynamics simulation and voltammetry.     

Silicon monohydride clusters Si(n)H (n = 4-10) and their anions: structures, thermochemistry, and electron affinities

The molecular structures, electron affinities, and dissociation energies of the Si(n)H/Si(n)H- (n = 4-10) species have been examined via five hybrid and pure density functional theory (DFT) methods. The basis set used in this work is of double-zeta plus polarization quality with additional diffuse s- and p-type functions, denoted DZP++. The geometries are fully optimized with each DFT method independently. The three different types of neutral-anion energy separations presented in this work are the adiabatic electron affinity (EA(ad)), the vertical electron affinity (EA(vert)), and the vertical detachment energy (VDE). The first Si-H dissociation energies, D(e)(Si(n)H --> Si(n) + H) for neutral Si(n)H and D(e)(Si(n)H- --> Si(n)- + H) for anionic Si(n)H- species, have also been reported. The structures of the ground states of these clusters are traditional H-Si single-bond forms. The ground-state geometries of Si5H, Si6H, Si8H, and Si9H predicted by the DFT methods are different from previous calculations, such as those obtained by Car-Parrinello molecular dynamics and nonorthogonal tight-binding molecular dynamics schemes. The most reliable EA(ad) values obtained at the B3LYP level of theory are 2.59 (Si4H), 2.84 (Si5H), 2.86 (Si6H), 3.19 (Si7H), 3.14 (Si8H), 3.36 (Si9H), and 3.56 (Si10H) eV. The first dissociation energies (Si(n)H --> Si(n) + H) predicted by all of these methods are 2.20-2.29 (Si4H), 2.30-2.83 (Si5H), 2.12-2.41 (Si6H), 1.75-2.03 (Si7H), 2.41-2.72 (Si8H), 1.86-2.11 (Si9H), and 1.92-2.27 (Si10H) eV. For the negatively charged ion clusters (Si(n)H- --> Si(n)- + H), the dissociation energies predicted are 2.56-2.69 (Si4H-), 2.80-3.01 (Si5H-), 2.86-3.06 (Si6H-), 2.80-3.03 (Si7H-), 2.69-2.92 (Si8H-), 2.92-3.18 (Si9H-), and 2.89-3.25 (Si10H-) eV.