Cooperative Effect of CH···O Bonds in Models for Biological Systems

In order to calculate CH···O interactions appearing in biologically important systems, a preliminary study is performed for smaller models. MO bond indices I_XHY are calculated for dimers involving HCN, acetic acid, acetamide, glyoxal and formamide, as well as a ribose33-U35 pair appearing in tRNA^Phe and 3MU-U, also related to RNA. The distance dependence obeys the same pattern for I_OHO, I_NHO and I_CHO. It is shown that the negative I_XHY sign is related to the lengthening of the XH distance; the fluctuation of net charges for the involved atoms is related to the bond index. All results point at a definite cooperative effect.     

Topology of Electron Charge Density for Chemical Bonds from Valence Bond Theory: A Probe of Bonding Types

Covalent, ionic, or something new? A new interpretation of the topology of the electron density at the bond critical point is proposed to characterize covalent, ionic, and charge‐shift bonding from the density point of view (see figure). The topological properties of the density representation confirm the reality of charge‐shift bonds, in which the covalent contribution is weak or repulsive, and most of the bonding is due to the covalent–ionic resonance energy.

     

Film Growth and Surface Roughness with Effective Fluctuating Covalent Bonds in Evaporating Aqueous Solution of Reactive Hydrophobic and Polar Groups: A Computer Simulation Model

Summary: A computer simulation model is proposed to study film growth and surface roughness in aqueous (A) solution of hydrophobic (H) and hydrophilic (P) groups on a simple three dimensional lattice of size with an adsorbing substrate. Each group is represented by a particle with appropriate characteristics occupying a unit cube (i.e., eight sites). The Metropolis algorithm is used to move each particle stochastically. The aqueous constituents are allowed to evaporate while the concentration of H and P is constant. Reactions proceed from the substrate and bonded particles can hop within a fluctuating bond length. The film thickness ( ) and its interface width ( ) are examined for hardcore and interacting particles for a range of temperature ( ). Simulation data show a rapid increase in and followed by its non‐monotonic growth and decay before reaching steady‐state and near equilibrium ( ) in asymptotic time step limit. The growth can be described by power laws, e.g., with a typical value of in initial time regime followed by at . For hardcore system, the equilibrium film thickness ( ) and surface roughness ( ) seem to scale linearly with the temperature, i.e., at low and at higher . For interacting functional groups in contrast, the long time (unsaturated) film thickness and surface roughness, and decay rapidly followed by a slow increase on raising the temperature.

Growth of the average film thickness at a temperature .     

Research on Chemical Reactivity of Nitrotriazolam in Its Process of Preparation

Chemical reaction possibility was described quantitatively for the case of nitrotriazolam preparation with 2-clonazepam by using the data of two quantum chemical reactivity indices: net electrophilicity index and Wiberg bond order. Furthennore, relevant reaction mechanism was derived from tlie aspect of quantum chemistry. The results show that the indices used can quantitatively explain the chemical reactivity and reaction mechanism of the nitrotriazolam preparation. To validate the universal applicability of the proposed approach, the authors continued to use the quantum chemical reactivity indices to describe some classic chemical reactions, expecting to predict major issues related to physical organic chemistry, such as new chemical reactions and their mechanisms.     

Enantioseparation of 5,5′-Dibromo-2,2′-dichloro-3-selanyl-4,4′-bipyridines on Polysaccharide-Based Chiral Stationary Phases: Exploring Chalcogen Bonds in Liquid-Phase Chromatography

The chalcogen bond (ChB) is a noncovalent interaction based on electrophilic features of regions of electron charge density depletion (σ-holes) located on bound atoms of group VI. The σ-holes of sulfur and heavy chalcogen atoms (Se, Te) (donors) can interact through their positive electrostatic potential (V) with nucleophilic partners such as lone pairs, π-clouds, and anions (acceptors). In the last few years, promising applications of ChBs in catalysis, crystal engineering, molecular biology, and supramolecular chemistry have been reported. Recently, we explored the high-performance liquid chromatography (HPLC) enantioseparation of fluorinated 3-arylthio-4,4′-bipyridines containing sulfur atoms as ChB donors. Following this study, herein we describe the comparative enantioseparation of three 5,5′-dibromo-2,2′-dichloro-3-selanyl-4,4′-bipyridines on polysaccharide-based chiral stationary phases (CSPs) aiming to understand function and potentialities of selenium σ-holes in the enantiodiscrimination process. The impact of the chalcogen substituent on enantioseparation was explored by using sulfur and non-chalcogen derivatives as reference substances for comparison. Our investigation also focused on the function of the perfluorinated aromatic ring as a π-hole donor recognition site. Thermodynamic quantities associated with the enantioseparation were derived from van’t Hoff plots and local electron charge density of specific molecular regions of the interacting partners were inspected in terms of calculated V. On this basis, by correlating theoretical data and experimental results, the participation of ChBs and π-hole bonds in the enantiodiscrimination process was reasonably confirmed.     

Bonding and Reactivity in RB-As R Systems(R=H,F,OH,CH_3,CMe_3,CF_3,SiF_3,BO): Substituent Effects

Density functional theory-based calculations have been carried out to study the bonding and reactivity in RB-As R(R=H,F,OH,CH3,CMe_3,CF_3,SiF_3,BO)systems.Our calculations demonstrated that all the studied systems adopted bent geometry(DR-B-As≈180°andDB-As-R≈90°or less).The reason for this bending was explained with the help of a valence-orbital model.The potential energy surfaces for three possible isomers of RB-As R systems were also generated,indicating that the RB-As R isomer was more stable than R_2B-As R when R=SiF_3,CMe_3,and H.The B-As bond character was analyzed using natural bond orbital(NBO)and Wiberg bond index(WBI)calculations.The WBI values for B-As bonds in F3Si B-As SiF_3 and HB-As H were 2.254 and 2.209,respectively,indicating that this bond has some triple-bond character in these systems.While the B centers prefer nucleophilic attack,the As centers prefer electrophilic attack.     

The Topological Analysis of the ELFx Localization Function: Quantitative Prediction of Hydrogen Bonds in the Guanine–Cytosine Pair

In this contribution, we recall and test a new methodology designed to identify the favorable reaction pathway between two reactants. Applied to the formation of the DNA guanine (G) –cytosine (C) pair, we successfully predict the best orientation between the base pairs held together by hydrogen bonds and leading to the formation of the typical Watson Crick structure of the GC pair. Beyond the global minimum, some local stationary points of the targeted pair are also clearly identified.     

Bonding Trends in Molecular Compounds of Lanthanides: The Double‐Bonded Carbene Cations LnCH2+ (Ln=Sc,Y, La–Lu)

Quasi‐relativistic Douglas–Kroll CASPT2 calculations are reported for the title molecules, mainly to provide primary data for a fit of double‐bond covalent radii. Indeed, a well‐developed σ²π² double bond is identified in all cases. For Eu and Yb, however, it is an excited state. The main valence orbitals of all Ln ions are 6s and 5d. In the σ bonds, more 5d than 6s character is found at the Ln. The Ln?C bond lengths show a systematic lanthanide contraction of 13 pm from La to Lu. An agostic symmetry breaking is demonstrated for Ce but its effect on the Ln? C length is small.     

The Nature of the [TTF].+⋅⋅⋅[TTF].+ Interactions in the [TTF]22+ Dimers Embedded in Charged [3]Catenanes: Room‐Temperature Multicenter Long Bonds

The properties of tetrathiafulvalene dimers ([TTF]₂²⁺) and the functionalized ring‐shaped bispropargyl (BPP)‐functionalized TTF dimers, [BPP–TTF]₂²⁺, found at room temperature in charged [3]catenanes, were evaluated by M06L calculations. The results showed that their isolated [TTF]₂²⁺ and [BPP–TTF]₂²⁺ dimers are energetically unstable towards dissociation. When enclosed in the 4⁺‐charged central cyclophane ring of charged [3]catenanes (CBPQT⁴⁺), [TTF]₂²⁺ and [BPP–TTF]₂²⁺ dimers are also energetically unstable with respect to leaving the CBPQT⁴⁺ ring; since the barrier for the exiting process is only about 3 kcal mol^?1, that is, within the reach of thermal energies at room temperature (neutral [TTF]₂⁰ dimers are stable within the CBPQT⁴⁺ ring). However, the [BPP–TTF]₂²⁺ dimers in charged [3]catenanes cannot exit, because this would imply breaking the covalent bonds of the BPP–TTF⁺ macrocycle. Finally, it was shown that the [TTF]₂²⁺, [BPP–TTF]₂²⁺ dimers, and charged [3]catenanes are energetically stable in solution and in crystals of their salts, in the first case due to the interactions with the solvent, and in the second case mostly due to cation–anion interactions. In these environmental conditions at room temperature the TTF units of the [BPP–TTF]₂²⁺ dimers make short contacts, thus allowing their SOMO orbitals to overlap: a room‐temperature multicenter long bond is formed, similar to those previously found in other [TTF]₂²⁺ salts and their solutions.     

ChemInform Abstract: Molecular Structure of C(GeBr3)4 Determined by Gas-Phase Electron Diffraction and Density Functional Theory Calculations: Implications for the Length and Stability of Ge—C Bonds in Crystalline Semiconductor Solids.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.     

Order of stabilities in water nanoclusters: Insight from some recent double‐hybrid functionals

In the present work, the applicability of some of the recently proposed and modern double‐hybrid (DH) models and other density functional theory (DFT) approximations has been analyzed for a difficult test, the order of stability in low‐energy isomers of water nanoclusters. In particular, we aim to systematically investigate for these functionals the role played by several factors such as dispersion correction, integrand functions upon which the DHs are based, and different spin scaling for the perturbative term in DH calculations of the relative energies for various isomers of water nanoclusters (H₂O)₂₀. From the obtained results, the superior performance of DHs with respect to the functionals from previous rungs is confirmed. It is shown that the dispersion corrected DHs perform better than noncorrected counterparts. Plus, the DH models based on cubic integrand (CI) and quadratic integrand (QI) functions are nearly equivalent in performance. We also find that using only contributions of electron pairs with opposite spin for the perturbative correlation part through scaled opposite spin scheme does not represent a significant improvement on accuracy of the results. Putting all the results together, the dispersion corrected parameterized DHs and parameter‐free DH models involving CI and QI functions outperform other approximations for relative energies of water 20‐mers. Altogether, predicting the correct order of the stability in water nanoclusters may be considered as another Achilles' heel in DFT calculations, although more analyses in this context are still needed. © 2016 Wiley Periodicals, Inc.     

On the Paucity of Molecular Actinide Complexes with Unsupported Metal—Metal Bonds: A Comparative Investigation of the Electronic Structure and Metal—Metal Bonding in U2X6 (X: Cl,F, OH,NH2, CH3) Complexes and d‐Block Analogues

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.     

一维[Pd(mnt)2]-自旋体系磁交换作用的密度泛函理论(DFT)分析

4个一维磁链化合物[R-BzPy][Pd(mnt)2](R-BzPy+=对位取代苄基吡啶阳离子;R=Cl(化合物1),Br(化合物2),I(化合物3)和NO2(化合物4))具有相似的晶体堆积结构,即,[Pd(mnt)2]-和R-BzPy+分别形成完全分列的柱状堆积。这一结构特征与其类似化合物[R-BzPy][Ni(mnt)2]相似。但是,[Pd(mnt)2]-和[Ni(mnt)2]-2个系列化合物结构之间存在明显差异:(1)室温下,[R-BzPy][Ni(mnt)2]晶体中[Ni(mnt)2]-和R-BzPy+堆积柱是均匀的;而[R-BzPy][Pd(mnt)2]晶体中[Pd(mnt)2]-和R-BzPy+堆积柱是不均匀的。(2)在两个系列化合物阴离子堆积柱内,相邻[Pd(mnt)2]-分子平面之间距离比相邻[Ni(mnt)2]-分子平面之间距离短。在[Pd(mnt)2]-堆积柱内,[Pd(mnt)2]-离子之间反铁磁交换作用非常强,导致了化合物几乎呈抗磁性。在密度泛函理论框架下,利用对称性破损方法,我们计算了[Pd(mnt)2]-离子之间磁交换常数。在svwn/lanl2dz和bpw91/lanl2dz水平上的计算结果与磁化率拟合结果一致。理论分析揭示,在[Pd(mnt)2]-堆积柱内,[Pd(mnt)2]-离子之间强反铁磁交换与其π-型前线轨道有效重叠密切相关。