Elongation method with intermediate mechanical and electrostatic embedding for geometry optimizations of polymers

The elongation method with intermediate mechanical and electrostatic embedding (ELG-IMEE) is proposed. The electrostatic embedding uses atomic charges generated by a charge sensitivity analysis (CSA) method and parameterized for three different population analyses, namely, the Merz–Singh–Kollman scheme, the charge model 5, and the atomic polar tensor. The obtained CSA models were tested on two model systems. Test calculations show that the electrostatic embedding provides several times of decrease in the difference of energies of testing and reference calculations in comparison with the conventional elongation approach (ELG). The mechanical embedding is implemented in a combination of the conventional elongation method and the ONIOM approach. Moreover, it was demonstrated that the geometry optimization with the ELG-IMEE reduces the errors in the optimized structures by about one order in root-mean-square deviation, when compared to ELG.     

从静电作用探讨化学键的本质及其教学实践

当前中学的化学键教学中,过分强调Lewis“八隅体结构”,忽视静电作用力,导致学生不能认识到化学键的本质,且传统教学方法中,元素的二分法导致化学键的二分法,不利于学生思维的发展。借鉴国外相关研究,在考虑学生认知水平的基础上,尝试从强调化学键静电作用的本质和引入电负性的角度设计教学内容,帮助学生构建正确的化学键本质观。     

增长法在离域体系纳米线中的应用

本文综述了增长法这样一个原先起源于理论合成非周期性聚合物的方法。通过不同的体系验证了增长法高精度和高效率的特性。通过轨道漂移的处理手段,增长法能成功地应用到离域的p共轭体系。其处理手法是在增长过程中一些离域性特别强的分子轨道被重新指认到活性轨道中去,并与进攻的单元相互作用。增长法也可用来确定离域的卟啉线体系的非线性光学系数。     

Elongation cutoff technique armed with quantum fast multipole method for linear scaling

A linear‐scaling implementation of the elongation cutoff technique (ELG/C) that speeds up Hartree‐Fock (HF) self‐consistent field calculations is presented. The cutoff method avoids the known bottleneck of the conventional HF scheme, that is, diagonalization, because it operates within the low dimension subspace of the whole atomic orbital space. The efficiency of ELG/C is illustrated for two model systems. The obtained results indicate that the ELG/C is a very efficient sparse matrix algebra scheme. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Analyzing Reaction Rates with the Distortion/Interaction‐Activation Strain Model

The activation strain or distortion/interaction model is a tool to analyze activation barriers that determine reaction rates. For bimolecular reactions, the activation energies are the sum of the energies to distort the reactants into geometries they have in transition states plus the interaction energies between the two distorted molecules. The energy required to distort the molecules is called the activation strain or distortion energy. This energy is the principal contributor to the activation barrier. The transition state occurs when this activation strain is overcome by the stabilizing interaction energy. Following the changes in these energies along the reaction coordinate gives insights into the factors controlling reactivity. This model has been applied to reactions of all types in both organic and inorganic chemistry, including substitutions and eliminations, cycloadditions, and several types of organometallic reactions.     

The Role of Molecular Electrostatic Potentials in the Formation of a Halogen Bond in Furan⋅⋅⋅XY and Thiophene⋅⋅⋅XY Complexes

The halogen bonding of furan???XY and thiophene???XY (X=Cl, Br; Y=F, Cl, Br), involving σ‐ and π‐type interactions, was studied by using MP2 calculations and quantum theory of “atoms in molecules” (QTAIM) studies. The negative electrostatic potentials of furan and thiophene, as well as the most positive electrostatic potential (V_S,max) on the surface of the interacting X atom determined the geometries of the complexes. Linear relationships were found between interaction energy and V_S,max of the X atom, indicating that electrostatic interactions play an important role in these halogen‐bonding interactions. The halogen‐bonding interactions in furan???XY and thiophene???XY are weak, “closed‐shell” noncovalent interactions. The linear relationship of topological properties, energy properties, and the integration of interatomic surfaces versus V_S,max of atom X demonstrate the importance of the positive σ hole, as reflected by the computed V_S,max of atom X, in determining the topological properties of the halogen bonds.     

The Origin of the Reactivity of the Criegee Intermediate: Implications for Atmospheric Particle Growth

The electronic structure of the simplest Criegee intermediate, H₂COO, is practically that of a closed shell. On the biradical scale (β), where 0 corresponds to the pure closed shell and 1 to a pure biradical, its β value is only 0.10, suggesting that its ground electronic state is best described as a H₂C=O^δ+?O^δ? zwitterion. However, this picture of a nearly inert closed shell contradicts its rich reactivity in the atmosphere. It is shown that the mixing of its ground state with the first triplet excited state, which is a pure biradical state of the type H₂C^.?O?O^., is responsible for the formation of strongly bound products during reactions inducing atmospheric particle growth.     

Electric field measurement for quantum‐dot cellular automata clocking circuits

Bistable molecules under electric field are being investigated for the concept of quantum‐dot cellular automata (QCA). Different configurations of molecular arrays implement various logic devices and circuits. The electric field emitted from underlying metal wires, which are applied with clock signal, not only enables power gain, but also fulfills pipelining computation. It might be convenient to measure the electric field distribution directly from these metal wires. A pseudo‐quantitative method was developed to map the electric field distribution with electrostatic force microscopy. This method converts the phase signal into the electric field intensity, by which we demonstrated how to use a particular electric field distribution to drive the computation of QCA molecules. Copyright © 2008 John Wiley & Sons, Ltd.     

Elongation method for electronic structure calculations of random DNA sequences

We applied ab initio order‐N elongation (ELG) method to calculate electronic structures of various deoxyribonucleic acid (DNA) models. We aim to test potential application of the method for building a database of DNA electronic structures. The ELG method mimics polymerization reactions on a computer and meets the requirements for linear scaling computational efficiency and high accuracy, even for huge systems. As a benchmark test, we applied the method for calculations of various types of random sequenced A‐ and B‐type DNA models with and without counterions. In each case, the ELG method maintained high accuracy with small errors in energy on the order of 10^?8 hartree/atom compared with conventional calculations. We demonstrate that the ELG method can provide valuable information such as stabilization energies and local densities of states for each DNA sequence. In addition, we discuss the “restarting” feature of the ELG method for constructing a database that exhaustively covers DNA species. © 2015 Wiley Periodicals, Inc.     

Near Infrared Spectral Similarity Combined with Variable Selection Method in the Quality Control of Flos Lonicerae: A Preliminary Study

This paper indicates the possibility to use near infrared (NIR) spectral similarity as a rapid method to estimate the quality of Flos Lonicerae. Variable selection together with modelling techniques is utilized to select representative variables that are used to calculate the similarity. NIR is used to build calibration models to predict the bacteriostatic activity of Flos Lonicerae. For the determination of the bacteriostatic activity, the in vitro experiment is used. Models are built for the Gram‐positive bacteria and also for the Gram‐negative bacteria. A genetic algorithm combined with partial least squares regression (GA‐PLS) is used to perform the calibration. The results of GA‐PLS models are compared to interval partial least squares (iPLS) models, full‐spectrum PLS and full‐spectrum principal component regression (PCR) models. Then, the variables in the two GA‐PLS models are combined and then used to calculate the NIR spectral similarity of samples. The similarity based on the characteristic variables and full spectrum is used for evaluating the fingerprints of Flos Lonicerae, respectively. The results show that the combination of variable selection method, modelling techniques and similarity analysis might be a powerful tool for quality control of traditional Chinese medicine (TCM).     

Silylated Tag-Assisted Peptide Synthesis: Continuous One-Pot Elongation for the Production of Difficult Peptides under Environmentally Friendly Conditions

Addition of the silylated tag (STag) enables peptides to be highly soluble in CPME, allowing them to be used at high concentrations in a coupling reaction to enhance reactivity and achieve effective synthesis of sterically hindered peptides. We described the development of a continuous one-pot STag-assisted peptide synthesis platform as a method that provides near-stoichiometric, speedy, environmentally friendly, and scalable peptide synthesis.     

Evaluating the COSMO‐RS Method for Modeling Hydrogen Bonding in Solution

The ability of the Conductor‐like Screening Model for Realistic Solvation (COSMO‐RS) computational method to model hydrogen bond (HB) formation in solution is examined by comparing computational data with experimental data from literature. This is the first study of this kind where mixed solvents are also involved. Hydrogen bond formation is examined between neutral molecules, between acids and their anions, and between various anion receptor molecules and different anions in a number of aprotic solvents. HB formation equilibrium constants, the corresponding Gibbs’ free energies and, when available from the literature, enthalpies were calculated. The supermolecule (SM) approach and the contact probability (CP) approach were used. Both in the case of the SM and CP approach, good to very good correlations between the experiment and computations are found for complexes formed from neutral species, enabling quantitative predictions. When the HB acceptor is an anion, the correlations are poor and in some cases even qualitative predictions fail.     

Comparative analysis of the applicability of AM1 and CNDO/2 methods for quantitative prediction of the35Cl NQR frequencies of RC-Cl compounds

The³⁵Cl NQR frequencies of a series of RC-Cl compounds were calculated by the AM1 and CNDO/2 methods in the Townes-Dailey approximation. It was shown that neither of these methods can be directly used for the quantitative prediction of NQR frequencies, and their use in the correlation approach is only possible in narrow series. The AM1 method gives better results for saturated compounds.Institute of Organic and Physical Chemistry, Kazan' Scientific Center, Russian Academy of Sciences, 420083 Kazan'. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 5, pp. 1078–1082, May, 1992.     

Ground‐State and Excitation Spectra of a Strongly Correlated Lattice by the Coupled Cluster Method

The coupled cluster method is applied to a strongly correlated lattice Hamiltonian, and the coupled cluster linear response method is extended to the calculation of electronic spectra by finding an approximation to a resolvent operator which describes the spectral response of the coupled cluster solution to excitation operators. In this spectral coupled cluster method, the ground and excited states appear as resonances in the spectra, and the resolvent can be iteratively improved in selected spectral regions. The method is applied to a MnO₂ plane model which corresponds to previous experimental works.     

Atomic Properties of Amino Acids: Computed Atom Types as a Guide for Future Force‐Field Design

The quantum chemical topology (QCT) is able to propose atom types by direct computation rather than by chemical intuition. In previous work, molecular electron densities of 20 amino acids and smaller derived molecules were partitioned into a set of 760 topological atoms. Each atom was characterised by seven atomic properties and subjected to cluster analysis element by element, that is, C, H, O, N, and S. From the respective dendrograms, 21 carbon atom types were distinguished, 7 hydrogen, 2 nitrogen, 6 oxygen, and 6 sulfur atom types. Herein, we contrast the QCT atom types with those of the assisted model building with energy refinement (AMBER) force field. We conclude that in spite of fair agreement between QCT and AMBER atom types, the latter are sometimes underdifferentiated and sometimes overdifferentiated. In summary, we suggest that QCT is a useful guide in designing new force fields or improving existing ones. The computational origin of QCT atom types makes their determination unbiased compared to atom type determination by chemical intuition and a priori assumptions. We provide a list of specific recommendations.     

Quantum‐chemical approach to the solvatochromic transition in polysilane derivatives

We approached the solvatochromic transition observed in polysilane derivatives (poly[bis(4‐propoxybutyl)silylene] (PPBS)) from the standpoint of various quantum chemical treatments. It was found from conventional geometry optimizations at the levels of semiempirical and ab initio molecular orbital methods that a protonation to polysilane oligomers with side chain R = ? OCH₃ results in the conformational change of Si‐backbone to a trans‐zigzag structure. Using the Elongation method, which was developed for efficient calculations of huge systems, it was demonstrated that a protonation could change the conformation of Si‐backbone to a trans‐zigzag structure over 10–14 Si atoms. In addition, ab initio calculations showed that the positive charge of a proton can delocalize into the Si‐backbone through a long side chain in PPBS. Positively charged polysilane oligomers provide a rotational barrier that prefers a trans‐zigzag structure, whereas neutral oligomers have a barrier that results to a random structure. This unique behavior of the charged polysilane oligomers should not be disregarded in understanding the mechanism of the solvatochromic transition in PPBS. In ab initio configuration interaction/Mφller‐Plesset through‐space/bond interaction analysis, it was found that such a unique behavior of the rotational barrier in polysilane oligomers could be explained by the effect of orbital delocalization through σ‐conjugation on the Si‐backbone. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 119–133, 2006