Solvating,manipulating, damaging,and repairing DNA in a computer

This work highlights four different topics in modeling of DNA: (i) the importance of water and ions together with the structure and function of DNA; the hydration structure around the ions appears to be the determining factor in the ion coordination to DNA, as demonstrated in the results of our MD simulations; (ii) how MD simulations can be used to simulate single molecule manipulation experiments as a complement to reveal the structural dynamics of the studied biomolecules; (iii) how damaged DNA can be studied in computer simulations; and (iv) how repair of damaged DNA can be studied theoretically. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

带功能基的全氟烷基乙烯基醚的研究——4.四氟乙烯与全氟-3,6-二氧杂-4-甲基-△~7-辛基磺酰氟溶液共聚反应单体竞聚率的测定

在乙烯-四氟乙烯溶液共聚合体系研究中,我们曾编制了一个简易的计算机程序,用于测定二种单体的共聚竞聚率,这一方法计算方便,而且可以避免原先作图法中的误差,结果较为可靠。前文我们报道了四氟乙烯与两个新的全氟烷基乙烯基醚的共聚合反应,并对其中一个新单体——7,7-二氯-3-氧杂-全氟庚烯-1——与四氟乙烯的共聚进行了单体竞聚率的测定。结果表明,这一新的含氟烯醚单体的聚合活性较其它已有报道的同类单体大。为了验证这一     

Two-photon absorption in quadrupolar pi-conjugated molecules: influence of the nature of the conjugated bridge and the donor-acceptor separation

Quadrupolar-type substitution of pi-conjugated chromophores with donor and acceptor groups has been shown to increase their two-photon absorption (TPA) response by up to two orders of magnitude. Here, we apply highly correlated quantum-chemical calculations to evaluate the impact of the nature of conjugated bridge and the charge-transfer distance on that enhancement. We compare chromophores with phenylenevinylene-, thienylenevinylene-, polyene-, and indenofluorene-type backbones substituted by dimethylamino and cyano groups. In all compounds, we find a strongly TPA-active A(g) state (either 2A(g) or 3A(g)) in the low-energy region, as well as a higher lying TPA-active state (mA(g)) at close to twice the energy of the lowest lying one-photon allowed state; the smaller energy detuning in the mA(g) states results in very large TPA cross sections delta. We also investigate the influence of the degree of ground-state polarization on TPA. Independent of the nature of the backbone and the donor-acceptor separation, delta displays the same qualitative evolution with a maximum before the cyanine-like limit; the highest TPA cross sections are calculated for distirylbenzene- and polyene-based systems.     

Theory of reflectance measurements in quantitative evaluation in TLC and HPTLC. 1. Multilayer model of reflectance and transmittance

In the approach described in this paper, the layer of adsorbent is divided into n sublayers. The radiation density in each sublayer is given by the sum of the transmittance and the reflectance of the adjacent sublayers. Absorption of light by the layer or the substance will diminish this radiation density. Depending upon the factors of reflectance and transmittance some light will pass to the adjacent sublayers. Two polynomials are derived from this readily understood formulation to calculate the reflectance or the transmittance of a layer of finite thickness. The algorithms given describe the reflectance and transmittance encountered in practical measurements with large amounts of substance per spot, as well as with small amounts. There are no restrictions with respect to nonideal scattering or reflection by the adsorbent layer support.     

Qualitative estimation of the dependence of the number of energetic compounds on their oxygen coefficient

The ratio between the numbers of structural formulas of C,H,N,O-containing energetic compounds belonging to the classes of fuels (low values of the oxygen coefficientA), explosives (mediumA), and oxidants (highA values) was studied by a computer generation procedure. The number of the theoretically possible structural formulas was found to decrease rapidly on going from fuels to explosives and then to oxidants; this observation agrees with the data on the numbers of various energetic compounds currently used and proposed. The strategy of the search for new compounds with the specified properties is described in brief, and its applicability to the search for explosives and oxidants with a small (up to 12) number of atoms in a molecule is evaluated. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 7, pp. 1304–1310, July, 1998.     

A new method for predicting conduction anesthesia

A new method for predicting conduction anesthesia has been suggested. The method is based on calculation of theP matrix probabilities of interatomic contacts for each molecule of the compounds considered. TheP matrix enables one to evaluate the main tendencies of atoms and atomic groups to interact in biochemical sorption on the nerve fiber surface. The minimum effective concentrations calculated for 25 compounds are in good agreement with the experimental data. The correlation coefficient between the experimental and calculated values is 0.98 when the standard deviation is 0.1 mmol L⁻¹. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 1781–1784, October, 1997.     

NMR频率综合器的微机控制

为实现ＰＴＳ系列频率综合器的微机控制，设计了一种简单的控制电路。在微机的控制下，通过该电路与微机的并行通讯口，用Ｃ语言编写的控制程序可以很方便的控制频率综合器的输出频率。控制程序采用菜单操作，电路所需的＋５Ｖ电源由微机提供，整个控制系统简单实用，值得推广。     

Møller-Plesset (MP2) perturbation theory for large molecules

Summary A novel formulation of MP2 theory is presented which starts from the Laplace transform MP2 ansatz, and subsequently moves from a molecular orbital (MO) representation to an atomic orbital (AO) representation. Consequently, the new formulation is denoted AO-MP2. As in traditional MP2 approaches electron repulsion integrals still need to be transformed. Strict bounds on the individual MP2 energy contribution of each intermediate four-index quantity allow to screen off numerically insignificant integrals with a single threshold parameter. Implicit in our formulation is a bound to two-particle density matrix elements. For small molecules the computational cost for AO-MP2 calculations is about a factor of 100 higher than for traditional MO-based approaches, but due to screening the computational effort in larger systems will only grow with the fourth power of the size of the system (or less) as is demonstrated both in theory and in application. MP2 calculations on (non-metallic) crystalline systems seem to be a feasible extension of the Laplace transform approach. In large molecules the AO-MP2 ansatz allows massively parallel MP2 calculations without input/output of four-index quantities provided that each processor has in-core memory for a limited number of two-index quantities. Energy gradient formulas for the AO-MP2 approach are derived.Dedicated to Prof. W. Kutzelnigg whose books on theoretical chemistry aroused my interest in this field     

Fine structures of zeolite-Linde-L (LTL): surface structures, growth unit and defects

High-resolution electron microscopy (HREM) has been used to image the surface structure of nano- and micrometer-sized synthetic crystals of zeolite-Linde-L (LTL). Columnar holes and rotational, nano-sized, wheel-like defects were observed within the crystals, where the hole has a minimum size equal to that of the rotational defect. Predictions of surface structure from atomistic computer simulation concur with the observations from HREM and provide insight into the crystal growth mechanism of perfect and defective LTL. Analysis of the energetics of the formation of rotational defect structures reveals that the driving force for defect creation is thermodynamic and furthermore, the rotational defects could be created in high concentrations. Formation of a columnar hole is found to be slightly energetically unfavourable and therefore we speculate that the incidence of both rotational and nano-sized vacancy defects is strongly dependent on kinetic factors and reaction conditions. The morphology of nano- and microcrystalline LTL is contradistinct and we use insights from simulation to propose an explanation of the disparity in crystal shape.     

Mechanical properties of twist grain boundaries in Cu

In a previous paper we studied the Young's and shear modulus of a high-angle twist grain boundary (5) in Cu, using the EAM, and related it to the uniaxial strain derivatives of single crystals. In this paper, we discuss elastic properties of ten additional twist grain boundaries, from 8.8–43.6°. The monolayer Young's modulus at each boundary was calculated and found to be 20–50% higher than the bulk value for all eleven boundaries for both csl and type1 structures. The monolayer shear modulus at each boundary was calculated and found to be 93–98% lower than the bulk value for six grain boundaries with csl structure and found to decrease with increasing twist angle. The critical shear stress was also calculated for eleven boundaries with csl structure and found to roughly decrease with increasing twist angle.