Biophysical characterization of DNA binding from single molecule force measurements

Single molecule force spectroscopy is a powerful method that uses the mechanical properties of DNA to explore DNA interactions. Here we describe how DNA stretching experiments quantitatively characterize the DNA binding of small molecules and proteins. Small molecules exhibit diverse DNA binding modes, including binding into the major and minor grooves and intercalation between base pairs of double-stranded DNA (dsDNA). Histones bind and package dsDNA, while other nuclear proteins such as high mobility group proteins bind to the backbone and bend dsDNA. Single-stranded DNA (ssDNA) binding proteins slide along dsDNA to locate and stabilize ssDNA during replication. Other proteins exhibit binding to both dsDNA and ssDNA. Nucleic acid chaperone proteins can switch rapidly between dsDNA and ssDNA binding modes, while DNA polymerases bind both forms of DNA with high affinity at distinct binding sites at the replication fork. Single molecule force measurements quantitatively characterize these DNA binding mechanisms, elucidating small molecule interactions and protein function.     

Non-linear protocell models: synchronization and chaos

We consider generic protocells models allowing linear and non-linear kinetics for the main involved chemical reactions. We are interested in understanding if and how the protocell division and the metabolism do synchronise to give rise to sustainable evolution of the protocell.     

The comparative analysis of prebiological evolution models

Several models of prebiological systems are described and analyzed. The following models are characterized: a quasispecies model, a hypercycle model, a syser model (the term "syser" is an abbreviation of SYstem of SElf-Reproduction), a stochastic corrector model, a model of the origin of a primordial genome through spontaneous symmetry breaking. The quasispecies model analyzes the Darwinian evolution of information chains; this evolution is similar to the evolution of RNA molecules. Rather general estimates of the speed and efficiency of evolutionary processes can be obtained in the framework of the quasispecies model. We briefly describe the method for obtaining these estimates and the corresponding results. The hypercycle model considers the interaction of RNA chains and enzymes. The syser model characterizes a rather general scheme of the self-reproducing system, which is similar to the self-reproducing systems of biological cells. Syser includes a polynucleotide sequence, a replication enzyme, a translation enzyme, and other enzymes; these macromolecules are located inside the protocell. The stochastic corrector model describes the process of using a relatively small number of molecules of competing and cooperating replicators in protocells. The model of the origin of a primordial genome through spontaneous symmetry breaking characterizes an interesting and important process of the appearance of genotypes in protocells. This model was proposed and investigated by Takeuchi, Hogeweg, and Kaneko in 2017; we call it further “the THK model.” The current article characterizes and compares all these models.     

石墨烯表面的特征水分子排布及其湿润透明特性的分子动力学模拟

石墨烯因其独特的分子构型、卓越的物理化学性能而受到广泛关注.本文首先利用分子动力学模拟比较了单层石墨烯、铜、二氧化硅三者表面的浸润性,除了接触角的比较,还分析了基底表面的水分子排布,得到石墨烯表面的特征水分子排布为:表面有两层密集的水分子层,其中靠近基底的密集水分子层中O—H键与垂直基底方向夹角集中在90°附近,并且基底表面的氢键几乎都垂直于基底.另一方面,本文研究了石墨烯浸润透明特性,发现在铜和二氧化硅上添加一层石墨烯,对铜的浸润性影响较小,对二氧化硅的浸润性影响很大,不仅使其上接触角显著增大,还使得基底表面的水分子排布呈现出类似单层石墨烯上的规律.本文使用分子动力学模拟方法从微观尺度验证了文献的实验结果,从基底表面水分子排布角度分析了石墨烯独特的浸润透明特性,为进一步开发石墨烯在微结构设计上的应用提供了理论指导.     

First-principles simulations of chemical reactions in an HCl molecule embedded inside a C or BN nanotube induced by ultrafast laser pulses

We show by first-principles simulations that ultrafast laser pulses induce different chemical reactions in a molecule trapped inside a nanotube. A strong laser pulse polarized perpendicular to the tube axis induces a giant bond stretch of an encapsulated HCl molecule in semiconducting carbon nanotube or in a BN nanotube. Depending on the initial orientation of the HCl molecule, the subsequent laser-induced dynamics is different: either complete disintegration or rebonding of the HCl molecule. Radial motion of the nanotube is always observed and a vacancy appears on the tube wall when the HCl is perpendicular to the tube axis. Those results are important to analyze confined nanochemistry and to manipulate molecules and nanostructures encapsulated in organic and inorganic nanotubes.     

用二极管激光探测法研究分子的动力学过程

本文介绍用二极管激光探测法研究分子的光解、碰撞、化学反应及能量转移等动力学过程.以高速原子和分子的碰撞过程为例进行了介绍.二极管激光探测法的分辨率比传统的红外荧光法提高一万倍,速率提高十倍,且灵敏度也较高.即使在有许多分子和众多量子态存在的情况下,该方法也能抓住待测分子或待测态,得到清楚的结果.目前可在3～30μm的范围内适用.     

Nonrigid molecules in solution: Internal potential energy surface for acetone dissolved in carbon disulfide.

In this article molecular properties of acetone dissolved in carbon disulfide are computed. In particular we focus attention on the evaluation of the internal rotation energy surface of the two rotor acetone molecule. The method we employ is Semiclassical, by combining quantum chemical information about molecules of the sample with the pertinent structural statistical data for the solution. Quantum information is based on the CNDO level of approximation, and the solution structure is given by the solute-solvent atom-atom radial distribution functions (rdfs). These two tools (CNDO, rdfs) can be easily coupled to each other in order to build our Semiclassical method for evaluating molecular properties of dissolved molecules. It is worthwhile to point out that results arising from this method are quantitative in the same extent as normal quantum chemical calculations for isolated molecules.     

Inducing all steps of a chemical reaction with the scanning tunneling microscope tip: towards single molecule engineering

All elementary steps of a chemical reaction have been successfully induced on individual molecules with a scanning tunneling microscope (STM) in a controlled step-by-step manner utilizing a variety of manipulation techniques. The reaction steps involve the separation of iodine from iodobenzene by using tunneling electrons, bringing together two resultant phenyls mechanically by lateral manipulation and, finally, their chemical association to form a biphenyl molecule mediated by excitation with tunneling electrons. The procedures presented here constitute an important step towards the assembly of individual molecules out of simple building blocks in situ on the atomic scale.     

FTIR spectroscopy as a tool for nano-material characterization

Covalently grafting functional molecules to carbon nanotubes (CNTs) is an important step to leverage the excellent properties of that nano-fiber in order to exploit its potential in improving the mechanical and thermal properties of a composite material. While Fourier Transform Infra Red (FTIR) spectroscopy can display the various chemical bonding in a material, we found that the existing database in FTIR library does not cover all the bonding information present in functionalized CNTs because the bond between the grafted molecule and the CNT is new in the FTIR study. In order to extend the applicability of FTIR to nano-material, we present a theoretical method to derive FTIR spectroscopy and compare it with our experimental results. In particular, we illustrate a method for the identification of functional molecules grafted on CNTs, and we are able to confirm that the functional molecules are indeed covalently grafted on the CNTs without any alterations to its functional groups.     

Photoinduced reconfiguration cycle in a molecular adsorbate layer studied by femtosecond inner-shell photoelectron spectroscopy

A time-resolved study of core-level chemical shifts in a monolayer of aromatic molecules reveals complex photoinduced reaction dynamics. The combination of electron spectroscopy for chemical analysis and ultrashort pulse excitation in the extreme ultraviolet allows performing time-correlated 4d-core-level spectroscopy of iodine atoms that probe the local chemical environment in the adsorbate molecule. The selectivity of the method unveils metastable molecular configurations that appear about 50 ps after the excitation and are efficiently quenched back to the ground state.     

Modeling the dissociation and ionization of a sputtered organic molecule

The evolution of an organic molecule after sputtering from a gold surface has been analyzed by classical molecular dynamics and ab initio calculations to gain insight into the ionization and fragmentation processes occurring in SIMS. The calculated ionization potential (6.2 eV) of the tetraphenylnaphthalene (TPN) molecule has been found to be close to the unimolecular dissociation energy (5.4 eV) of the most favorable reaction channel involving the loss of a phenyl ring. On the other hand, our calculations show that the internal energies of sputtered TPN molecules can be significantly larger than 5-6 eV. Therefore, it appears energetically possible to relax such excited molecules via both fragmentation and ionization.We propose to virtually decompose the TPN molecule into its basic fragments. The rationale is that, if the molecule is very excited, then separate parts (e.g. pendant phenyl rings) can interact with each other almost independently. The analysis of the molecular motion after emission shows that the oscillations along the phenyl-naphthalene bond direction, expected to induce the molecule fragmentation by the loss of a phenyl ring, are relatively small (they store only about 0.2 eV). On the other hand, the relative energy stored in the inter-phenyl interactions, modulated by their bending and responsible for ionization according to our hypothesis, oscillates over a range of 6-7 eV and favors ionization.     

一种新型双共轭链分子非线性光学性质的理论研究

对实验室合成的双共轭链分子1,4-二(4-二乙胺基苯乙烯基)-2-［4-(N-甲基-N-羟乙基)氨基-4′-硝基偶氮苯］-5-己烷氧基苯(BSBAB)及合成它的单共轭链分子的单光子和双光子吸收特性在从头计算的基础上利用密度泛函理论进行了研究.分子BSBAB的优化结构显示，组成该分子的横链和纵链除了保持各自的共轭面外，几近相互垂直.因此，分子BSBAB较好地继承了两个单共轭链分子的光学特性.计算结果表明，在低能量范围内，分子BSBAB具有三个双光子吸收峰，分别来自于两个单共轭链分子以及两者的耦合作用.从理论上证明了双共轭链分子BSBAB是一种具有宽带强双光子吸收的分子材料.理论结果和实验结果符合得较好.在HF水平上的响应函数方法进一步证实了有限态求和方法计算结果的可靠性.还给出了电荷转移态的电荷迁移过程. 关键词： 双光子吸收 双共轭链有机分子 非线性光学     

An efficientmethod to determine chemical potential of mixtures in the isothermal and isobaric bulk phase with kineticMonte Carlo simulation

A kinetic Monte Carlo (kMC) scheme in the NPT ensemble (constant number of molecules, pressure and temperature) has been developed to determine accurate chemical potentials for all components in a homogeneous mixture. The simulation requires two moves: (1) a displacement move and (2) a volume change move. In the former, the mobility rate of a selected molecule is determined by its interaction with all the other molecules in the system and is moved to a random position within the simulation box, according to the Rosenbluth algorithm, without any rejections (entropic sampling). The volume change move is decided by a comparison between either the instant pressure or the partial average pressure (with long-range correction) and the specified pressure and is carried out much less frequently than the displacement move. We applied this NPT scheme to a number of mixtures in both the gaseous and liquid phases, and show that the derived chemical potentials are accurate and reproducible. The method is recommended for obtaining chemical potentials in mixtures that are required as input in a grand canonical ensemble simulation.     

A priori calculation of rate of dissociation of a molecule in an ionic lattice assuming a phonon relaxation process

The rate of dissociation of the rectangular N₄ ^? ion into two diatomic molecules has been calculated in the ionic KN₃ lattice assuming the initial step is the transfer of three lattice phonons to the internal vibrational states of the molecule causing an internal vibrational excitation of the N₄ ^?. The rate of dissociation of the molecule is then calculated using a stochastic random walk approach which enables a determination of the mean time for the molecule to be vibrationally excited to the dissociative state. The results are in order of magnitude agreement with the measured reaction rates at a number of temperatures suggesting the possible role of phonon relaxation processes in unimolecular chemical reactions in the bulk solid state.     

The Unconventional Influence of a Nearby Molecule onto Transport of Single C_(60) Molecule Transistor

We study the transport property of single C_(60) molecular transistors with special focus on the situation that other molecules are in vicinity. The devices are prepared using electromigration and thermal deposition techniques. Pure single C_(60) molecule transistors show typical coulomb blockade behavior at low temperature. When we increase the coverage of molecules slightly by extending the deposition time, the transport spectrum of devices displays a switching behavior in the general coulomb blockade pattern. We attribute this unconventional phenomenon to the influence from a nearby C_(60) molecule. By analyzing this transport behavior quantitatively based on the parallel-double-quantum-dot model, the interaction from the nearby molecule is proved to be of capacity and tunneling coupling. Thermal stimulation is also applied to the device to investigate the effect of local charging environment variation on intermolecular interaction.     

Nickel cluster functionalised carbon nanotube for CO molecule detection: a theoretical study

Using spin-polarised density functional theory calculation single-walled carbon nanotube (SWCNT) whose sidewall is functionalised with nickel cluster is studied for its possible application in CO molecule sensing. We have chosen (6,0) SWCNT functionalised with Ni₁₃ cluster as the model for nanotube-cluster system. Changes in the properties of nanotube-cluster system brought by the CO molecule are reported. The CO molecule binding is energetically more favourable to the nanotube-cluster system than the pristine nanotube. The electronic properties are investigated in terms of density of states and bandstructure calculations. Pristine carbon nanotubes are intrinsically non-magnetic but nanotubes functionalised with nickel cluster are observed to have a huge magnetic moment which reduced on adsorbing CO molecule. The change in magnetisation upon CO adsorption may be detected using a suitable magnetometer. This result suggests the possibility of using carbon nanotube-cluster system to detect CO molecules. Bader charge analysis shows that CO molecule withdraws electronic charge from the cluster atoms. Nature of chemical bonding is studied with crystal orbital Hamilton population (–COHP) analysis.     

电场作用下P掺杂硅烯选择性吸附CH_4的第一性原理计算

在煤层气中选择性吸附和捕捉甲烷分子,对提高煤矿安全具有十分重要的意义.本文采用第一性原理计算的方法,研究了外加电场作用下P掺杂硅烯对甲烷分子的选择性吸附性能.结果表明:正电场作用下,P掺杂硅烯与甲烷分子之间产生较强的化学吸附,能够快速捕获甲烷分子.当关闭外加电场时,P掺杂硅烯与甲烷分子之间则为微弱的物理吸附,甲烷分子很容易实现脱附.同时还发现,外加电场作用下,P掺杂硅烯与氮气、氧气及水之间的吸附均属于物理吸附,表明P掺杂硅烯可以在这些混合气体中实现甲烷气体的选择性吸附. P掺杂硅烯有望成为选择性好的甲烷传感、捕获新材料.     

氮分子固体中配位环境对其分子振动的影响

研究了孤立氮分子与处于氮分子固体中氮分子之间的振动频率差异.基于α-N_2晶体结构建立了5种不同氮分子数的氮分子固体团簇模型,采用密度泛函理论计算了孤立自由氮分子及各固体模型中氮分子的振动频率,并对它们的频率进行了比较和讨论.比较发现:受集体效应的影响,处于分子固体模型中的所有氮分子的键长较孤立自由氮分子的键长更短,振动频率更高;就固体模型本身而言,分子数越多,平均振动频率越大,而且,内部氮分子的振动频率总是大于表面氮分子的振动频率,整体来说,频率大小关系为v_(内部)v_(表面)v_(孤立).讨论分析认为这种频率差异主要是由于孤立自由氮分子、固体表面和内部分子的配位关系不同引起的;表面分子存在大量配位缺陷,与其相互作用的分子相对较少,氮分子键力较弱,从而频率更低.     

Estimation of friction of a single chemisorbed molecule on a surface using incident atoms

Friction of a single molecule chemisorbed on a surface is a very fundamental property related to the dynamics of the diffusion of the molecule. We used a newly developed method, in which energy-controlled rare gas atoms collide with CO molecules on a stepped surface to displace CO molecules from initial terrace sites to final step sites. The friction coefficient of CO molecules on the surface was determined directly by comparing the experimentally measured increase in the number of CO molecules at step sites with classical molecular dynamics simulation results.