Molecular dynamics simulation of anticancer drug delivery from carbon nanotube using metal nanowires

In this study, we have investigated delivery of cisplatin as the anticancer drug molecules in different carbon nanotubes (CNTs) in the gas phase using molecular dynamics simulation. We examined the shape and composition of the releasing agent by using the different nanowires and nanoclusters. We also investigated the doping effect on the drug delivery process using N-, Si, B-, and Fe-doped CNTs. Different thermodynamics, structural, and dynamical properties have been studied by using the pure and different doped CNTs in this study. Our results show that the doping of the CNT has significant effect on the rate of the drug releasing process regardless of the composition of the releasing agent. © 2019 Wiley Periodicals, Inc.     

Molecular dynamics simulation of potassium along the liquid-vapor coexistence curve

The applicability of pair potential functions to liquid alkali metals is questionable. On the one hand, some recent reports in the literature suggest the validity of two-parameter pair-wise additive Lennard-Jones (LJ) potentials for liquid alkali metals. On the other hand, there are some reports suggesting the inaccuracy of pair potential functions for liquid metals. In this work, we have performed extensive molecular dynamics simulations of vapor-liquid phase equilibria in potassium to check the validity of the proposed LJ potentials and to improve their accuracy by changing the LJ exponents and taking into account the temperaturedependencies of the potential parameters. We have calculated the orthobaric liquid and vapor densities of potassium using LJ (12–6), LJ (8.5–4) and LJ (5–4), effective pair potential energy functions. The results show that using an LJ (8.5–4) potential energy function with temperature-independent parameters, ε and σ, is inadequate to account for the vapor-liquid coexistence properties of potassium. Taking into account the temperature-dependencies of the LJ parameters, ε(T) and σ(T), we obtained the densities of coexisting liquid and vapor potassium in a much better agreement with experimental data. Changing the magnitude of repulsive and attractive contributions to the potential energy function shows that a two-parameter LJ (5–4) potential can well reproduce the densities of liquid and vapor potassium. The results show that LJ (5–4) potential with temperature-dependent parameters produces the densities of liquid and vapor potassium more accurately, compared to the results obtained using LJ (12–6) and LJ (8.5–4) potential energy functions.     

Molecular mechanism of the DNA sequence selectivity of 5-halo-2'-deoxyuridines as potential radiosensitizers

The 5-halo-2'-deoxyuridines bromodeoxyuridine (BrdU) and iododeoxyuridine (IdU) are well-known photosensitizers for inducing DNA/RNA-protein cross-linking and potential radiosensitizers for radiotherapy of cancer. The dependence of the photosensitivity of BrdU and IdU on the DNA sequence has been well-observed, but it is unknown whether there is a similar DNA sequence selectivity in their radiosensitivity. Here we show a new ultrafast electron transfer (UET) mechanism for the likely DNA sequence dependence of the radiosensitivity of BrdU and IdU. Our femtosecond time-resolved transient laser absorption spectroscopic measurements provide the first real-time observation of the UET reactions of BrdU/IdU with the anion states of adenine and guanine. It is shown that the UET between BrdU and dA*(-) (dA(-)) is more effective than that between BrdU and dG*(-). This is related to the recent observation that dG*(-) is highly destructive while dA(-) is long-lived. This mechanistic understanding may lead to the improvement of BrdU and IdU to achieve sufficient radiosensitizing efficacy and the development of more effective radiosensitizers for clinical uses.     

Deciphering the activation sequence of ferrociphenol anticancer drug candidates

The complete oxidation sequence of a model for ferrociphenols, a new class of anticancer drug candidate, is reported. Cyclic voltammetry was used to monitor the formation of oxidation intermediates on different timescales, thereby allowing the electrochemical characterization of both the short-lived and stable species obtained from the successive electron-transfer and deprotonation steps. The electrochemical preparation of the ferrocenium intermediate enabled a stepwise voltammetric determination of the stable oxidation compounds obtained upon addition of a base as well as the electron stoichiometry observed for the overall oxidation process. A mechanism has been established from the electrochemical data, which involves a base-promoted intramolecular electron transfer between the phenol and the ferrocenium cation. The resulting species is further oxidized then deprotonated to yield a stable quinone methide. To further characterize the transient species successively formed during the two-electron oxidation of the ferrociphenol to its quinone methide, EPR was used to monitor the fate of the paramagnetic species generated upon addition of imidazole to the electrogenerated ferrocenium. The study revealed the passage from an iron-centered to a carbon-centered radical, which is then oxidized to yield the quinone methide, namely, the species that interacts with proteins and so forth under biological conditions.     

Molecular simulation of the frictional behavior of polymer-on-polymer sliding

Molecular simulations of the sliding processes of polymer-on-polymer systems were performed to investigate the surface and subsurface deformations and how these affect tribological characteristics of nanometer-scale polymer films. It is shown that a very severe deformation is localized to a band of material about 2.5 nm thick at the interface of the polymer surfaces. Outside of this band, the polymer films experience a uniform shear strain that reaches a finite steady-state value of close to 100%. Only after the polymer films have achieved this steady-state shear strain do the contacting surfaces of the films show significant relative slippage over each other. Because severe deformation is limited to a localized band much thinner than the polymeric films, the thickness of the deformation band is envisaged to be independent of the film thickness and hence frictional forces are expected to be independent of the thickness of the polymer films. A strong dependency of friction on interfacial adhesion, surface roughness, and the shear modulus of the sliding system was observed. Although the simulations showed that frictional forces increase linearly with contact pressure, adhesive forces contribute significantly to the overall friction and must therefore be accounted for in nanometer-scale friction. It is also shown that the coefficient of friction is lower for lower-density polymers as well as for polymers with higher molecular weights.     

Molecular dynamics simulation of thymine glycol-lesioned DNA reveals specific hydration at the lesion

One nanosecond molecular dynamics (MD) simulation of a thymine glycol (TG)-lesioned part of human lymphoblast AG9387 was performed to determine structural changes in DNA molecule caused by the presence of a lesion. These changes can be significant for proper recognition of lesions by a repair enzyme. Thymine glycol is the DNA oxidative lesion formed by addition of OH radicals to C5 and C6 atoms of the thymine base. This lesion is known as causing Cockayne Syndrome-inherited genetic disorder. Distribution of water molecules in a hydration shell around the DNA molecule was analyzed for its contribution to the recognition of the TG lesion by the repair enzyme. The results of MD simulation show there is a specific DNA structural configuration formed at the lesion. After 500 ps the DNA is bent in a kink at the TG site. This change dislocates the glycosyl bond at C5' to a position closer to the DNA surface, and thus its atoms are more exposed to the surrounding water shell. The increased number of water molecules that are close to the TG site indicates that the glycosyl bond may be easily contacted by the repair enzyme. In addition, the higher number of water molecules at the TG site substantiates the importance of water-mediated hydrogen bonds created between the repair enzyme and the DNA upon formation of the complex. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1723-1731, 2001     

Molecular dynamics simulation of mechanical properties of TATB/fluorine-polymer PBXs along different surfaces

TATB (1,3,5-triamino-2,4,6-trinitrobenzene) is the well-known high insensitive explosive. With TATB as the main body (90% and above) the polymer bonded explosives ( PBXs) contain a small amount of poly-mers (5%―10%). The composite materials with good saf…     

On the origin of the DNA sequence selectivity of the azinomycins

Simplified synthetic azinomycins preferentially induce in vitro DNA interstrand cross-links at the same 5'-d(GCC)-3' site as the natural products revealing that non-covalent interactions are relatively unimportant in defining sequence specificity.     

Molecular dynamics simulations of peptide-surface interactions

Proteins, which are bioactive molecules, adsorb on implants placed in the body through complex and poorly understood mechanisms and directly influence biocompatibility. Molecular dynamics modeling using empirical force fields provides one of the most direct methods of theoretically analyzing the behavior of complex molecular systems and is well-suited for the simulation of protein adsorption behavior. To accurately simulate protein adsorption behavior, a force field must correctly represent the thermodynamic driving forces that govern peptide residue-surface interactions. However, since existing force fields were developed without specific consideration of protein-surface interactions, they may not accurately represent this type of molecular behavior. To address this concern, we developed a host-guest peptide adsorption model in the form of a G(4)-X-G(4) peptide (G is glycine, X is a variable residue) to enable determination of the contributions to adsorption free energy of different X residues when adsorbed to functionalized Au-alkanethiol self-assembled monolayers (SAMs). We have previously reported experimental results using surface plasmon resonance (SPR) spectroscopy to measure the free energy of peptide adsorption for this peptide model with X = G and K (lysine) on OH and COOH functionalized SAMs. The objectives of the present research were the development and assessment of methods to calculate adsorption free energy using molecular dynamics simulations with the GROMACS force field for these same peptide adsorption systems, with an oligoethylene oxide (OEG) functionalized SAM surface also being considered. By comparing simulation results to the experimental results, the accuracy of the selected force field to represent the behavior of these molecular systems can be evaluated. From our simulations, the G(4)-G-G(4) and G(4)-K-G(4) peptides showed minimal to no adsorption to the OH SAM surfaces and the G(4)-K-G(4) showed strong adsorption to the COOH SAM surface, which is in agreement with our SPR experiments. Contrary to our experimental results, however, the simulations predicted a relatively strong adsorption of G(4)-G-G(4) peptide to the COOH SAM surface. In addition, both peptides were unexpectedly predicted to adsorb to the OEG surface. These findings demonstrate the need for GROMACS force field parameters to be rebalanced for the simulation of peptide adsorption behavior on SAM surfaces. The developed methods provide a direct means of assessing, modifying, and validating force field performance for the simulation of peptide and protein adsorption to surfaces, without which little confidence can be placed in the simulation results that are generated with these types of systems.     

In silico evolution of substrate selectivity: comparison of organometallic ruthenium complexes with the anticancer drug cisplatin

A comparative quantum chemical approach helps to clarify how the selectivity of anticancer metallopharmaceuticals towards potential biological targets can be controlled by metal and ligands.     

DNA G-quadruplex and its potential as anticancer drug target

G-quadruplex secondary structures are four-stranded globular nucleic acid structures form in the specific DNA and RNA G-rich sequences with biological significance such as human telomeres,oncogene-promoter regions,replication initiation sites,and 5′and 3′-untranslated(UTR)regions.The non-canonical G-quadruplex secondary structures can readily form under physiologically relevant ionic conditions and are considered to be new molecular target for cancer therapeutics.This review discusses the essential progress in our lab related to the structures and functions of biologically relevant DNA G-quadruplexes in human gene promoters and telomeres,and the opportunities presented for the development of G-quadruplex-targeted smallmolecule drugs.     

Molecular dynamics simulation of clustered DNA damage sites containing 8-oxoguanine and abasic site

Clustered DNA damage sites induced by ionizing radiation have been suggested to have serious consequences to organisms, such as cancer, due to their reduced probability to be repaired by the enzymatic repair machinery of the cell. Although experimental results have revealed that clustered DNA damage sites effectively retard the efficient function of repair enzymes, it remains unclear as to what particular factors influence this retardation. In this study, approaches based on molecular dynamics (MD) simulation have been applied to examine conformational changes and energetic properties of DNA molecules containing clustered damage sites consisting of two lesioned sites, namely 7,8-dihydro-8-oxoguanine (8-oxoG) and apurinic/apyrimidinic (AP) site, located within a few base pairs of each other. After 1 ns of MD simulation, one of the six DNA molecules containing a clustered damage site develops specific characteristic features: sharp bending at the lesioned site and weakening or complete loss of electrostatic interaction energy between 8-oxoG and bases located on the complementary strand. From these results it is suggested that these changes would make it difficult for the repair enzyme to bind to the lesions within the clustered damage site and thereby result in a reduction of its repair capacity.     

Molecular dynamics simulation of liquid trimethylphosphine

Structural and dynamical properties of liquid trimethylphosphine (TMP), (CH(3))(3)P, as a function of temperature is investigated by molecular dynamics (MD) simulations. The force field used in the MD simulations, which has been proposed from molecular mechanics and quantum chemistry calculations, is able to reproduce the experimental density of liquid TMP at room temperature. Equilibrium structure is investigated by the usual radial distribution function, g(r), and also in the reciprocal space by the static structure factor, S(k). On the basis of center of mass distances, liquid TMP behaves like a simple liquid of almost spherical particles, but orientational correlation due to dipole-dipole interactions is revealed at short-range distances. Single particle and collective dynamics are investigated by several time correlation functions. At high temperatures, diffusion and reorientation occur at the same time range as relaxation of the liquid structure. Decoupling of these dynamic properties starts below ca. 220 K, when rattling dynamics of a given TMP molecules due to the cage effect of neighbouring molecules becomes important.     

液态水的分子动力学模拟

用分子动力学(MD)模拟方法在150~376K的温度范围内对液态水的微正则系统进行了研究。考察了液态水的结构及其性质。模拟采用了由从头算得出的柔性水-水相互作用势MCYL。对时间和空间的平均得出了液态中水分子几何构型及温度改变所引起的液态水结构变化。对径向分布函数gOH, gOO, gHH及配位数的分析表明, 在所考察的温度范围内, 每个水分子与相邻分子形成的氢键数为2~3, 水分子在参与的2个氢键中同时作为授受体。结合对振动谱的研究表明在低温时液态水形成的网络结构可能随温度的升高而形成小的簇结构。     

Molecular dynamics simulation of semirigid polymers

The chain rigidity of poly(p-hydroxybenzoate) was estimated through the theoretical evaluation of its persistence length (L_p). A non-Brownian molecular dynamics (MD) simulation of an isolated chain with 20 monomeric units was performed. The sampled conformational population was analyzed and the orientational correlation function between monomeric units along the chain was calculated. An algorithm based on the worm-like chain model was applied to evaluate the persistence length. The results were compared with those obtained from equilibrium models like the freely-rotating-chain and the rotational-matrix method with fluctuations. Equilibrium models give different results depending on the degree of accuracy used in describing the monomeric unit. The inclusion of thermal fluctuations is crucial to obtain realistic results. These coincide with those given by MD simulation when only nearest-neighbour orientational correlations are taken into account: inclusion of higher-order correlation terms leads to lower values of the persistence length. The origin of this discrepancy was investigated. The MD simulation results are characterized by an overrepresentation of conformations with a short end-to-end distance resulting from an anomalous energy concentration in the first bending mode of the chain. In analogy with previous simulation results from systems characterized by a week coupling amoung their degrees of freedom, failure in the energy equipartition is proposed as a likely explanation of the anomalous dynamical behaviour.     

Molecular dynamics simulation of LiTFSI-acetamide electrolytes: structural properties

The liquid structures of nonaqueous electrolytes composed of lithium bis(trifluoromethylsulfonyl)imide (LiTFSI) and acetamide, with LiTFSI/acetamide molar ratios of 1:2, 1:4, and 1:6, were studied by molecular dynamics simulations. The simulations indicate that the Li+ cations prefer to be six-coordinate by the sulfonyl oxygen atoms of the TFSI- anions and the carbonyl oxygen atoms of the acetamide molecules, rather than by the most electronegative nitrogen atom of the TFSI- anion. Therefore, close Li+-TFSI- contact pairs exist in the system. The TFSI- anion prefers to provide only one of four possible oxygen atoms to coordinate to the same Li+ cation. Three conformations (cis, trans, and gauche) of the TFSI- anions were found to coexist in the liquid electrolyte. At high salt concentrations, the TFSI- anions mainly adopt the gauche conformation in order to provide more oxygen atoms to coordinate to different Li+ cations, while simultaneously reducing the repulsion among the Li+ cations. On the other hand, the fraction of TFSI- anions adopting the cis conformation is largest for the system with the molar ratio of 1:6, in which many clusters, mainly composed of the Li+ cations and the TFSI- anions, are immersed in the acetamide molecules. The size and charge distribution of clusters were also investigated. In the system with the molar ratio of 1:2, nearly all of the ions in the PBC (periodic boundary conditions) box aggregate into a bulky cluster that gradually disassembles into small clusters with decreasing salt concentration. The addition of acetamide molecules was found to effectively relax the liquid electrolyte structure, and the system with the molar ratio of 1:4 was found to exhibit a more homogeneous liquid structure than the other two electrolyte systems with molar ratios of 1:2 and 1:6.     

Molecular dynamics simulation of solvent-polymer interdiffusion: Fickian diffusion

The interdiffusion of a solvent into a polymer melt has been studied using large scale molecular dynamics and Monte Carlo simulation techniques. The solvent concentration profile and weight gain by the polymer have been measured as a function of time. The weight gain is found to scale as t(1/2), which is expected for Fickian diffusion. The concentration profiles are fit very well assuming Fick's second law with a constant diffusivity. The diffusivity found from fitting Fick's second law is found to be independent of time and equal to the self-diffusion constant in the dilute solvent limit. We separately calculated the diffusivity as a function of concentration using the Darken equation and found that the diffusivity is essentially constant for the concentration range relevant for interdiffusion.     

Molecular dynamics simulation in the grand canonical ensemble

An extended system Hamiltonian is proposed to perform molecular dynamics (MD) simulation in the grand canonical ensemble. The Hamiltonian is similar to the one proposed by Lynch and Pettitt (Lynch and Pettitt, J Chem Phys 1997, 107, 8594), which consists of the kinetic and potential energies for real and fractional particles as well as the kinetic and potential energy terms for material and heat reservoirs interacting with the system. We perform a nonlinear scaling of the potential energy parameters of the fractional particle, as well as its mass to vary the number of particles dynamically. On the basis of the equations of motion derived from this Hamiltonian, an algorithm has been proposed for MD simulation at constant chemical potential. The algorithm has been tested for the ideal gas, for the Lennard-Jones fluid over a wide range of temperatures and densities, and for water. The results for the low-density Lennard-Jones fluid are compared with the predictions from a truncated virial equation of state. In the case of the dense Lennard-Jones fluid and water our predicted results are compared with the results reported using other available methods for the calculation of the chemical potential. The method is also applied to the case of vapor-liquid coexistence point predictions.