Molecular dynamics of minimal B‐DNA

Stable and accurate molecular dynamics (MD) of B‐DNA duplexes can be obtained in inexpensive computational conditions where only the minor groove is filled with water while the bulk solvent is represented implicitly. This model system presents significant theoretical as well as practical interest because, due to its simplicity and exceptional computational performance, it can be employed in simulations of very long DNA fragments. To better understand its properties and clarify the physical background of the effects produced by the limited water shell, dynamics of several different DNA oligomers was studied. It is found that optimal simulation conditions are reached when the explicit water is confined within the minor groove while the major groove is cleaned periodically. The internal solvent mobility appears high enough to observe in the nanosecond time scale spontaneous formation of sequence‐specific hydration patterns known from experiments. It is shown that the model produces stable MD trajectories close to the B‐DNA form regardless of the base pair sequence and that, on the other hand, the dynamics are strongly sequence dependent. Independent observations suggest that B‐DNA with only minor groove hydrated resembles its natural thermodynamic state at low water concentration; therefore, this model system can be tentatively called “minimal B‐DNA.” © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 457–467, 2001     

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.     

Molecular dynamics simulation of DNA‐directed assembly of nanoparticle superlattices using patterned templates

DNA‐directed assembly is a well developed approach in constructing desired nano‐architectures. On the other hand, E‐beam lithography is widely utilized for high resolution nano‐scale patterning. Recently, a new technique combining these two methods was developed to epitaxially grow DNA‐mediated nanoparticle superlattices on patterned substrates. However, defects are observed in epitaxial layers which restricts this technique from building large‐scale superlattices for real applications. Here we use molecular dynamics simulations to study and predict defect formation on adsorbed superlattice monolayers. We demonstrate that this epitaxial growth is energetically driven by maximizing DNA hybridization between the epitaxial layer and the substrate and that the shape anisotropy of the DNA‐mediated template posts leads to structural defects. We also develop design rules to dramatically reduce defects on epitaxial layers. Ultimately, with the assist of the computational study, this technique will open the door to constructing well‐ordered, three‐dimensional novel nanomaterials. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 1687–1692     

Gas‐phase hydration of Mg2+ complexes with deprotonated uracil,thymine, uridine,and thymidine

The gas‐phase hydration of Mg²⁺ complexes with deprotonated uracil ( U ), thymine ( T ), uridine ( U _r , uracil riboside), and thymidine ( T _dr , thymine deoxyriboside) was studied. The aim of the work was to analyze the hydration of product ions (eg, [2 U ‐H+Mg]⁺) formed as a result of the collision induced dissociation of the respective parent ion (eg, [3 U _r ‐H+Mg]⁺). The efficiency of gas‐phase hydration of the ions [2 U ‐H+Mg]⁺ and [2 T ‐H+Mg]⁺ was similar. However, the efficiency of gas‐phase hydration of the ion [ U + U _r ‐H+Mg]⁺ was much higher than that of gas‐phase hydration of the ion [ T + T _dr ‐H+Mg]⁺. On the basis of the mass spectra obtained and the performed molecular modelling, it was concluded that in the ion [ T + T _dr ‐H+Mg]⁺, we deal with a steric hindrance due to the presence of a sugar moiety, which affects water attachment. In the ion [ U + U _r ‐H+Mg]⁺, the position of the sugar moiety does not affect water attachment.     

Molecular mechanics parameters for the FapydG DNA lesion

FapydG is a common oxidative DNA lesion involving opening of the imidazole ring. It shares the same precursor as 8-oxodG and can be excised by the same enzymes as 8-oxodG. However, the loss of the aromatic imidazole in FapydG results in a reduction of the double bond character between C5 and N7, with an accompanying increase in conformational flexibility. Experimental characterization of FapydG is hampered by high reactivity, and thus it is desirable to investigate structural details through computer simulation. We show that the existing Amber force field parameters for FapydG do not reproduce X-ray structural data. We employed quantum mechanics energy profile calculations to derive new molecular mechanics parameters for the rotation of the dihedral angles in the eximidazole moiety. Using these parameters, all-atom simulations in explicit water reproduce the nonplanar conformation of cFapydG in the crystal structure of the complex with L. lactis glycosylase Fpg. We note that the nonplanar structure is stabilized by an acidic residue that is not present in most Fpg sequences. Simulations of the E-->S mutant, as present in E. coli, resulted in a more planar conformation, suggesting that the highly nonplanar form observed in the crystal structure may not have direct biological relevance for FapydG.     

Efficient conversion of thymine glycol into the formamide lesion in oligonucleotides

Oxidation of (5R,6S)-5,6-dihydro-5,6-dihydroxythymidine (thymidine glycol) with sodium periodate efficiently produced N-(2-deoxy-β-d-erythro-pentofuranosyl)formamide, a hydroxyl radical-induced decomposition product of pyrimidine bases in DNA, and this method was successfully applied to the conversion of thymine glycol in oligonucleotides into the formamide lesion.     

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.     

Refinement of the primary hydration shell model for molecular dynamics simulations of large proteins

A realistic representation of water molecules is important in molecular dynamics simulation of proteins. However, the standard method of solvating biomolecules, that is, immersing them in a box of water with periodic boundary conditions, is computationally expensive. The primary hydration shell (PHS) method, developed more than a decade ago and implemented in CHARMM, uses only a thin shell of water around the system of interest, and so greatly reduces the computational cost of simulations. Applying the PHS method, especially to larger proteins, revealed that further optimization and a partial reworking was required and here we present several improvements to its performance. The model is applied to systems with different sizes, and both water and protein behaviors are compared with those observed in standard simulations with periodic boundary conditions and, in some cases, with experimental data. The advantages of the modified PHS method over its original implementation are clearly apparent when it is applied to simulating the 82 kDa protein Malate Synthase G. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009     

甲烷水合物导热机理的分子动力学模拟

甲烷水合物导热系数是甲烷水合物勘探、开采、储运以及其他应用过程中一个十分重要的物理参数.我们采用平衡分子动力学（EMD）方法Green-Kubo理论计算温度203.15～263.15K、压力范围3～100MPa、晶穴占有率为0～1的sI甲烷水合物的导热系数,采用的水分子模型包括TIP4P、TIP4P-Ew、TIP4P-FQ、TIP4P/2005、TIP4P/Ice.研究了主客体分子、外界温压条件等对甲烷水合物导热性能的影响.研究结果显示甲烷水合物的低导热性能由主体分子构建的sI笼型结构决定,而客体分子进入笼型结构后,使得笼型结构导热性能增强,同时进入笼型结构的客体分子越多,甲烷水合物导热性能越强.研究结果还显示在高温区域（T〉TDebye/3）内不同温度作用下,所有sI水合物具有相似的导热规律.压力对导热系数有一定影响,尤其是在较高压力条件下,压力越高,导热系数越大.而在不同温度和不同压力作用过程中,密度的改变对导热系数的增大或减小几乎没有影响.     

Diffusive dynamics of DNA unzipping in a nanopore

When an electric field is applied to an insulating membrane, movement of charged particles through a nanopore is induced. The measured ionic current reports on biomolecules passing through the nanopore. In this work, we explored the kinetics of DNA unzipping in a nanopore using our coarse‐grained model (Stachiewicz and Molski, J. Comput. Chem. 2015, 36, 947). Coarse graining allowed a more detailed analysis for a wider range of parameters than all‐atom simulations. Dependence of the translocation mode (unzipping or distortion) on the pore diameter was examined, and the threshold voltages were estimated. We determined the potential of mean force, position‐dependent diffusion coefficient, and position‐dependent effective charge for the DNA unzipping. The three molecular profiles were correlated with the ionic current and molecular events. On the unzipping/translocation force profile, two energy maxima were found, one of them corresponding to the unzipping, and the other to the translocation barriers. The unzipping kinetics were further explored using Brownian dynamics. © 2015 Wiley Periodicals, Inc.     

Molecular dynamics simulation of copper nano-cluster melting on the graphite substrate

The melting processes of different-sized copper nano-clusters supported on graphite (0001) plane are investigated by the molecular dynamics method. In this work, the melting point is predicted through the caloric curve. The simulation results show that the melting point of the supported copper nano-cluster is higher than that of the isolated one with the same Cu atoms. In the heating process, the copper nano-particle will adhere to the (0001) face of graphite with its (111) face. Pair analysis results show that the copper atoms close to the graphite can keep with order arrangement even when the temperature is higher than the melt point of the isolated nano-cluster.     

金属晶体间微观静摩擦特性的分子动力学模拟研究

以光滑干摩擦接触平面为对象,利用金属晶体间的强体积效应特征,建立了简化计算静摩擦力的界面势能模型.根据第一性原理的方法模拟得出界面分子势能的变化,通过界面分子势能计算出静摩擦力大小,并将数据结果通过通用黏附能量函数计算出的静摩擦力大小进行验证,也将计算结果与超高真空原子力显微镜试验结果进行对比.最后拟合出最大静摩擦力与法向载荷的线性函数关系,得出摩擦力的数值为真实接触面积的函数,并与法向载荷成正比的结论.从微观上对同种金属材料间库伦摩擦定律进行验证与研究.     

A QM/MM Investigation of Thymine Dimer Radical Anion Splitting Catalyzed by DNA Photolyase

On the mend : The repair reaction of the thymine dimer by DNA photolyase (see picture) is studied by hybrid quantum mechanical/molecular mechanical dynamics simulations based on the X‐ray structure of the enzyme–DNA complex. The dynamics of splitting of the thymine dimer radical anion within the DNA photolyase active site is characterized. The model includes the protein environment.

     

分子动力学模拟研究荧光分子芘在磺基甜菜碱胶束中的增溶

采用分子动力学模拟研究了荧光分子芘在磺基甜菜碱两性表面活性剂聚集体中的增溶现象．结果表明,芘分子自发地自溶液中增溶进入胶束疏水内核的栅栏层区域．当胶束溶液中芘分子的局部浓度增大时,两个芘分子可以同时增溶进胶束的栅栏层区域,此时两个芘分子形成π-π共轭堆积的激发态络合物．但是由于荧光分子之间的弱兀．兀相互作用,激发态络合物在胶束中是不稳定的,表现为两个芘分子的多次结合和分离．模拟表明,分子动力学方法可以在分子水平上研究荧光探针分子在表面活性剂胶束中的增溶位点,解释荧光分子在胶束中的动力学现象．     

Molecular dynamics simulation and density functional theory insight into the cocrystal explosive of hexaazaisowurtzitane/nitroguanidine

Theoretical methods involving molecular dynamics (MD) simulation and density functional theory were performed to investigate the different molecular ratios, mechanical Properties, structure, trigger bond, and intermolecular interaction of hexaazaisowurtzitane (CL‐20)/nitroguanidine (NQ) cocrystal explosive. Results of MD simulation show that CL‐20 and NQ packed in ratios of 1:1 present the larger binding energy and better mechanical properties than any other molecular ratios, which indicates 1:1 cocrystal can form the stable crystal structure. Shorter length and larger dissociation energy of trigger bond in composite structure than in isolated CL‐20 component suggests that the cocrystal may exhibit less sensitive than CL‐20. Analyses of atoms in molecules, reduced density gradient, and natural bond orbital confirm that intermolecular interactions are mainly derived from a series of weak hydrogen bond and strong vdW forces, involving of NH···O, CH···O, CH···N, O···N, and O···O. Additionally, composite structures of 2 and 3 bringing us more attractive performance will act as a key role in constructing of CL‐20/NQ cocrystal explosive. © 2015 Wiley Periodicals, Inc.