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.     

Fast multipole method for three-dimensional systems with periodic boundary condition in two directions

We derived a new expression for the electrostatic interaction of three-dimensional charge-neutral systems with two-dimensional periodic boundary conditions (slab geometry) using a fast multipole method (FMM). Contributions from all the image cells are expressed as a sum of real and reciprocal space terms, and a self-interaction term. The reciprocal space contribution consists of two parts: zero and nonzero terms of the absolute value of the reciprocal lattice vector. To test the new expressions, electrostatic interactions were calculated for a randomly placed charge distribution in a cubic box and liquid water produced by molecular dynamics calculation. The accuracy could be controlled by the degree of expansion of the FMM. In the present expression, the computational complexity of the electrostatic interaction of N-particle systems is order N, which is superior to that of the conventional two-dimensional periodic Ewald method for a slab geometry and the particle mesh Ewald method with a large empty space at an interface of the unit cell. © 2020 Wiley Periodicals, Inc.     

介孔SBA-15棒负载的Pd3Cl催化剂催化Sonogashira偶联反应（英文）

通过静电吸引策略将具有高度分散性的原子精确纳米团簇[Pd3Cl(PPh2)2(PPh3)3]+(Pd3Cl)负载在介孔SBA-15棒上。结构明确的Pd3Cl/SBA-15催化剂在以水作为溶剂以及温和的反应条件下对催化Sonogashira碳-碳偶联反应展现了较好的催化性能以及循环性。在此基础上,我们研究了Pd3Cl团簇结构与性能之间的关系,并证实内核的Pdδ+(0<δ<2)与配体之间的协同效应是催化反应的关键。     

开尔文滴水起电机在潮湿环境下的实验研究

探讨了开尔文滴水起电机要求环境凉爽、干燥的原因,并对传统的开尔文滴水起电机进行了改进,通过改善传统滴水起电机的表面绝缘性,增大水溶液的离子浓度以及预加初始电荷等方法使其能在潮湿的环境下快速获得较大的高压静电,起电效果明显.     

3‐O‐Sulfation of Heparan Sulfate Enhances Tau Interaction and Cellular Uptake

Prion‐like transcellular spreading of tau in Alzheimer's Disease (AD) is mediated by tau binding to cell surface heparan sulfate (HS). However, the structural determinants for tau–HS interaction are not well understood. Microarray and SPR assays of structurally defined HS oligosaccharides show that a rare 3‐O‐sulfation (3‐O‐S) of HS significantly enhances tau binding. In Hs3st1^?/? (HS 3‐O‐sulfotransferase‐1 knockout) cells, reduced 3‐O‐S levels of HS diminished both cell surface binding and internalization of tau. In a cell culture, the addition of a 3‐O‐S HS 12‐mer reduced both tau cell surface binding and cellular uptake. NMR titrations mapped 3‐O‐S binding sites to the microtubule binding repeat 2 (R2) and proline‐rich region 2 (PRR2) of tau. Tau is only the seventh protein currently known to recognize HS 3‐O‐sulfation. Our work demonstrates that this rare 3‐O‐sulfation enhances tau–HS binding and likely the transcellular spread of tau, providing a novel target for disease‐modifying treatment of AD and other tauopathies.     

Accurate Modelling of Group Electrostatic Potential and Distributed Polarizability in Dipeptides

Within the scope of accurate structure-property correlations in biomolecules, this work investigates how conformations and electronic configurations of biologically relevant macromolecules affect their intermolecular potentials. With the purpose of testing the suitability of a simple and universal model, the dipeptides are made from the assembly of their building blocks, namely the amino acid residuals or, more finely tuned, the individual functional groups. The model makes use of functional-group electrostatic potentials (GEP) and distributed polarizabilities (GDP), which enable an in depth analysis of the correlation between structural features and property build-up. GEPs and GDPs are calculated for various conformers and protonation states of L-alanyl-L-alanine, glycyl-L-alanine, L-alanylglycine, and glycylglycine, which are prototypic molecules to model the pertinent functional groups. The model provides GEPs that reproduce the exact potential to an average accuracy of ca. 0.05 au. The good agreement between the properties estimated with the simple model and those calculated with state-of-the-art quantum chemical methods encourages further testing of the predictive power of this model, simulating for example interaction energies and optoelectronic properties.     

Synthesis,experimental and in silico studies of N‐fluorenylmethoxycarbonyl‐O‐tert‐butyl‐N‐methyltyrosine,coupled with CSD data: a survey of interactions in the crystal structures of Fmoc–amino acids

Recently, fluorenylmethoxycarbonyl (Fmoc) amino acids (e.g. Fmoc–tyrosine or Fmoc–phenylalanine) have attracted growing interest in biomedical research and industry, with special emphasis directed towards the design and development of novel effective hydrogelators, biomaterials or therapeutics. With this in mind, a systematic knowledge of the structural and supramolecular features in recognition of those properties is essential. This work is the first comprehensive summary of noncovalent interactions combined with a library of supramolecular synthon patterns in all crystal structures of amino acids with the Fmoc moiety reported so far. Moreover, a new Fmoc‐protected amino acid, namely, 2‐{[(9H‐fluoren‐9‐ylmethoxy)carbonyl](methyl)amino}‐3‐{4‐[(2‐hydroxypropan‐2‐yl)oxy]phenyl}propanoic acid or N‐fluorenylmethoxycarbonyl‐O‐tert‐butyl‐N‐methyltyrosine, Fmoc‐N‐Me‐Tyr(t‐Bu)‐OH, C₂₉H₃₁NO₅, was successfully synthesized and the structure of its unsolvated form was determined by single‐crystal X‐ray diffraction. The structural, conformational and energy landscape was investigated in detail by combined experimental and in silico approaches, and further compared to N‐Fmoc‐phenylalanine [Draper et al. (2015). CrystEngComm, 42 , 8047–8057]. Geometries were optimized by the density functional theory (DFT) method either in vacuo or in solutio. The polarizable conductor calculation model was exploited for the evaluation of the hydration effect. Hirshfeld surface analysis revealed that H…H, C…H/H…C and O…H/H…O interactions constitute the major contributions to the total Hirshfeld surface area in all the investigated systems. The molecular electrostatic potentials mapped over the surfaces identified the electrostatic complementarities in the crystal packing. The prediction of weak hydrogen‐bonded patterns via Full Interaction Maps was computed. Supramolecular motifs formed via C—H…O, C—H…π, (fluorenyl)C—H…Cl(I), C—Br…π(fluorenyl) and C—I…π(fluorenyl) interactions are observed. Basic synthons, in combination with the Long‐Range Synthon Aufbau Modules, further supported by energy‐framework calculations, are discussed. Furthermore, the relevance of Fmoc‐based supramolecular hydrogen‐bonding patterns in biocomplexes are emphasized, for the first time.     

Net charge changes in the calculation of relative ligand‐binding free energies via classical atomistic molecular dynamics simulation

The calculation of binding free energies of charged species to a target molecule is a frequently encountered problem in molecular dynamics studies of (bio‐)chemical thermodynamics. Many important endogenous receptor‐binding molecules, enzyme substrates, or drug molecules have a nonzero net charge. Absolute binding free energies, as well as binding free energies relative to another molecule with a different net charge will be affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). In the present study, charging contributions to binding free energies of small oligoatomic ions to a series of model host cavities functionalized with different chemical groups are calculated with classical atomistic molecular dynamics simulation. Electrostatic interactions are treated using a lattice‐summation scheme or a cutoff‐truncation scheme with Barker–Watts reaction‐field correction, and the simulations are conducted in boxes of different edge lengths. It is illustrated that the charging free energies of the guest molecules in water and in the host strongly depend on the applied methodology and that neglect of correction terms for the artifacts introduced by the finite size of the simulated system and the use of an effective electrostatic interaction function considerably impairs the thermodynamic interpretation of guest‐host interactions. Application of correction terms for the various artifacts yields consistent results for the charging contribution to binding free energies and is thus a prerequisite for the valid interpretation or prediction of experimental data via molecular dynamics simulation. Analysis and correction of electrostatic artifacts according to the scheme proposed in the present study should therefore be considered an integral part of careful free‐energy calculation studies if changes in the net charge are involved. © 2013 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

On the determination of the basin of attraction of periodic orbits in three- and higher-dimensional systems

The determination of the basin of attraction of a periodic orbit can be achieved using a Lyapunov function. A Lyapunov function can be constructed by approximation of a first-order linear PDE for the orbital derivative via meshless collocation. However, if the periodic orbit is only accessible numerically, a different method has to be used near the periodic orbit. Borg's criterion provides a method to obtain information about the basin of attraction by measuring whether adjacent solutions approach each other with respect to a Riemannian metric. Using a numerical approximation of the periodic orbit and its first variation equation, a suitable Riemannian metric is constructed.     

Comment on “Analytical evaluation for two-center nuclear attraction integrals over Slater type orbitals by using Fourier transform method” by S. ?zcan and E. ?ztekin (J. Math. Chem. DOI 10.1007/s10910-008-9398-z)

S. ?zcan and E. ?ztekin, (J. Math. Chem. doi:) published formulas for evaluating the two-center nuclear attraction integrals over Slater type orbitals. It is shown that the analytical relations for these integrals through the expansion coefficients of the electron charge density for the one-center case and the overlap integrals presented in Sect. 3 of this work can easily be derived by means of a simple algebra from the formulas published in our papers (I.I. Guseinov, J Mol Struct (Theochem) 417:117, 1997; J Math Chem 42:415, 2007 and B.A. Mamedov, Chin J Chem 22:545, 2004). It should be noted that the formulas of overlap integrals presented by E. ?ztekin et al., in previous paper (E. ?ztekin, M. Yavuz, Ş. Atalay, J Mol Struct (Theochem) 544:69, 2001) for the calculation of two-center nuclear attraction integrals also are obtained from our papers (see Comment: I.I. Guseinov, J Mol Struct (Theochem) 638:235, 2003).