The nature of chemical bonding in nitramide

The spatial and electronic structure studies of nitramide NH₂NO₂ suggest that the change in its molecular geometry upon transition from the gas phase to the condensed state is caused by an increase in the contribution of conjugation between functional groups. According to the analysis of the Bader atomic charges, the effects of such conjugation are to a considerable extent governed by intramolecular charge transfer from the amino to the nitro group. From estimation of the contribution of conjugation to the charge transfer it follows that conjugation remains in the isolated molecule. The influence of hydrogen bonding on the increase in the contribution of conjugation and the corresponding charge redistribution in the molecule was considered. Despite the presence of conjugation between functional groups, the planar configuration of the molecule in the crystal is not realized and the crystallographic twofold axis corresponds to superposition of two molecular configurations with C _s symmetry.     

The Transannular Interaction in [2.2]Paracyclophane: Repulsive or Attractive?

The molecular structure and charge density distribution in the crystal of [2.2]paracyclophane derived from the high‐resolution single crystal X‐ray diffraction data at 100 K is reported together with ab initio calculations of this molecule. Analysis of the atomic, anisotropic displacement parameters in a “rigid‐body” model approximation has revealed that the molecule is ordered in the crystal. Topological analysis of the electron density and potential‐energy density‐distribution functions has demonstrated that there is no “through‐space” interaction between the rings in the molecule. The role of the ethylene bridges and distortion of the aromatic desks on the inter‐ring interaction are discussed.     

Novel properties from experimental charge densities: an application to the zwitterionic neurotransmitter taurine

The charge distribution of taurine (2-aminoethane-sulfonic acid) is revisited by using an orbital-based method that describes the density in a fixed molecular orbital basis with variable orbital occupation numbers. A new neutron data set is also employed to explore whether this improves the deconvolution of thermal motion and charge density. A range of molecular properties that are novel for experimentally determined charge densities are computed, including Weinhold population analysis, Mayer bond orders, and local kinetic energy densities, in addition to charge topological analysis and quantum theory of atoms-in-molecules (QTAIM) integrated properties. The ease with which a distributed multipole analysis can be performed on the fitted density matrix makes it straightforward to compute molecular moments, the lattice energy, and the electrostatic interaction energies of molecules removed from the crystal. Results are compared with high-level (QCISD) gas-phase calculations and band structure calculations employing density functional theory. Finally, the avenues available for extending the range of molecular properties that can be calculated from experimental charge densities still further using this approach are discussed.     

Molecular modelling of hyperbranched polyacetylene

Ab initio and density functional theory calculations carried out on linear and dendritic polyacetylenic (PA) oligomers of different size showed that acetylenic dendrimers are less stable than trans‐PA oligomers and that the instability increases with molecular weight reflecting the strain in crowded hyperbranched structures. However, the energy difference between linear and dendritic structure is rather small and tends to a limit with molecular weight. Twisting of the double bonds decreases the conjugation in hyperbranched PA compared to linear trans‐PA. However, the conjugation though less effective than in trans‐PA is extended up to the 4^th or 5^th generation of dendrimers. It was shown that bromine end groups strongly affect the electronic properties of acetylenic dendrimers decreasing even more the conjugation due to the sterical hindrances, however, highly polarizable bromine atoms reduced significantly the adiabatic potentials of ionization to be very close to that for trans‐PA oligomers.     

Structure‐Independent Conductance of Thiophene‐Based Single‐Stacking Junctions

The experimental investigation of intermolecular charge transport in π‐conjugated materials is challenging. Herein, we describe the investigation of charge transport through intermolecular and intramolecular paths in single‐molecule and single‐stacking thiophene junctions by the mechanically controllable break junction (MCBJ) technique. We found that the ability for intermolecular charge transport through different single‐stacking junctions was approximately independent of the molecular structure, which contrasts with the strong length dependence of conductance in single‐molecule junctions with the same building blocks, and the dominant charge‐transport path of molecules with two anchors transited from an intramolecular to an intermolecular path when the degree of conjugation increased. An increase in conjugation further led to higher binding probability owing to the variation in binding energies, as supported by DFT calculations.     

Charge transfer in the TCNQ-sexithiophene complex

Molecular crystals from thiophene molecules can be doped with TCNQ-F4 molecules for use in all-organic optoelectronic and semiconductor devices. The charge transfer and the molecular orbital energy level formation in between these two organic molecules are investigated here by density functional theory calculations. The isolated molecules are calculated nonbonded and bonded together, forming a charge transfer complex (CTC). The relaxed structure of the complex shows essentially coplanar and centered molecules with the alpha-sexithiophene rings tilted alternatingly by 4.8 degrees. The bond formation of these molecules results in a charge transfer of approximately 0.4 e from the alpha-sexithiophene to the TCNQ-F4 molecule. The highest occupied molecular orbital-lowest unoccupied molecular orbital gap width is reduced as compared to the isolated molecules due to the newly formed orbitals in the CTC. Upon adsorption on a Au(111) surface, electrons are transferred onto the molecule complex, thereby causing the molecular levels to align asymmetric with respect to the charge neutrality level. The theoretical results for the single molecule and CTC layer are compared to experimental photoemission and scanning tunneling spectroscopy results.     

Dithiocarbamate anchoring in molecular wire junctions: a first principles study

Recent experimental realization [J. Am. Chem. Soc., 127 (2005) 7328] of various dithiocarbamate self-assembly on gold surface opens the possibility for use of dithiocarbamate linkers to anchor molecular wires to gold electrodes. In this paper, we explore this hypothesis computationally. We computed the electron transport properties of 4,4'-bipyridine (BP), 4,4'-bipyridinium-1,1'-bis(carbodithioate) (BPBC), 4-(4'-pyridyl)-peridium-1-carbodithioate (BPC) molecule junctions based on the density functional theory and nonequilibrium Green's functions. We demonstrated that the stronger molecule-electrode coupling associated with the conjugated dithiocarbamate linker broadens transmission resonances near the Fermi energy. The broadening effect along with the extension of the pi conjugation from the molecule to the gold electrodes lead to enhanced electrical conductance for BPBC molecule. The conductance enhancement factor is as large as 25 at applied voltage bias 1.0 V. Rectification behavior is predicted for BPC molecular wire junction, which has the asymmetric anchoring groups.     

一个新BEDT-TTF电荷转移盐的晶体结构预测

用分子力学方法预测了一个新的电荷转移盐(ET)2FeCl4的晶体结构.用密度泛函理论(DFT)对(ET)2FeCl4系列电荷转移盐的单晶电子能量进行了计算.通过对比相近晶体的晶体结构和电子能量，解释了计算所得晶体结构的合理性.     

Electrostatic Energies in the 1,4‐Dichlorobenzene Polymorph Crystals: the Role of Charge Density Overlap Effects in Crystal Packing Analysis

Electrostatic and polarization energies for the three known polymorphic crystal structures of 1,4‐dichlorobenzene, as well as for one particularly stable virtual crystal structure generated by computer search, were calculated by a new accurate numerical integration method over static molecular charge densities obtained from high level ab initio molecular‐orbital calculations. Results are compared with those from standard empirical atom‐atom force fields. The new electrostatic energies, which include charge density overlap (penetration) effects, are seen to be much larger than and sometimes of opposite sign to those derived from point‐charge models. None of the four polymorphs is substantially more stable than the others on electrostatic‐energy grounds. Molecule‐molecule electrostatic energies have been calculated for the more important molecular pairs in each of the four structures; trends are found to be very different from those indicated by point‐charge energies or by total energies estimated with a parametric atom‐atom force field. Conclusions based exclusively on analysis of intermolecular atom contacts and point‐charge electrostatics may need to be modified in the light of the new kind of calculation.     

Reproducibility and transferability of topological data: experimental charge density study of two modifications of L-alanyl-L-tyrosyl-L-alanine

Two crystalline modifications of the tripeptide L-Ala-L-Tyr-L-Ala, which have different solvent molecules in the crystal structure (water and ethanol for modifications 1 and 2), were the subject of experimental charge density studies based on high resolution X-ray data collected at ultra-low temperatures of 9 K (1) and 20 K (2), respectively. The molecular structures and the intermolecular interactions were found to be rather similar in the two crystal lattices, so that this study allowed the reproducibility of the charge density of a given molecule in different (but widely comparable) crystalline environments to be examined. With respect to bond topological and atomic properties, the agreement between the two modifications of the title tripeptide was in the same range as found from the comparison with the previously reported results of tri-L-alanine. It follows that the reproducibility and transferability of quantitative topological data are comparable and that within the accuracy of experimental charge density work the replacement of the central amino acid residue L-Ala by L-Tyr has no significant influence, neither on bond nor on the atomic properties of the oligopeptide main chain. Intermolecular interactions in the form of hydrogen bonds were characterized quantitatively and qualitatively by topological criteria and by mapping the charge density distribution on the Hirshfeld surface.     

The kinetic energy of molecular charge distributions and molecular stability

This paper examines the relationship between the topographical features of a molecular charge distribution and the kinetic energy of the system. Specifically, the spatial contributions to the kinetic energy are related to the Laplacian of the total charge density and to the gradients of the natural-orbital densities. It is concluded that a necessary requirement for molecular stability is the existence of a net negative curvature for the molecular charge distribution in the internuclear region. It is shown that the charge density accumulated in the internuclear region of a stable molecule is distributed in such a way as to keep the accompanying increase in the kinetic energy to a minimum. A comparison of the contributions to the kinetic energy from the atomic and molecular charge distributions indicates that in the formation of a stable molecule the contribution from the molecular charge density in the binding region is decreased relative to that of the atoms.     

Chemical bonding in the crystal structure of 1-hydrosilatrane

A study has been made of the crystal and molecular structure of 1-hydrosilatrane HSi(OCH_2CH₂)₃N. The quantum chemical calculations of its crystal structure have been carried out. According to an estimate of the energy, the coordination bond N→Si is by 5 kcal mol^?1 stronger than that in the crystal of 1-methylsilatrane. The charge values calculated within the framework of the topological analysis of the electron density demonstrate that the electron density of the coordination bond N→Si is primarily transferred to the region of the equatorial bonds Si—O and, to a lesser extent, to the bond Si—H. On going from the isolated molecule of 1-hydrosilatrane to its crystal, the interatomic distance N—Si decreases, mainly owing to the weak intermolecular interaction C—H...O.     

Molecular and crystal structure of 1-(2-hydroxyethyl)-1,2-dihydro-3,4,6-trimethyl-2-oxopyrimidinium iodide: the N-alkylation product of xymedone

The structure of xymedone iodo methylate is determined by X-ray crystallography. The molecular and crystal structure of the compound is analyzed in comparison with xymedone whose X-ray crystallographic data have been obtained previously. The molecular and electronic structures of both compounds and noncovalent interactions in the ionic pair of xymedone iodo methylate are analyzed using the data of the quantum topological calculations. It is shown that the presence of the iodine anion results in an increase in the delocalization of the π electron density inside the heterocyclic moiety, the charge redistribution inside the molecule, and consequently, in significant distinctions in crystal packings.     

Multifunctional transition metal complexes: Information transfer at the molecular level

Recent investigations from our laboratory have described compelling experimental evidence to the effect that polyacetylenes operate as extremely effective molecular-scale wires for conducting electronic charge between redox-active terminals. The unusually low electronic resistivity of polyacetylenic bridges is derived from their relatively accessible HOMOs and LUMOs, which facilitate electron and hole tunnelling over long distances, and because of the excellent electronic coupling that occurs between adjacent carbon atoms, these being in very close proximity. In order to prevent direct participation of the acetylenic bridge in triplet energy-transfer processes or in light-induced electron-transfer reactions, it is prudent to restrict the conjugation length of the bridge to less than five ethynylene groups. We now consider various synthetic strategies for the engineering of such molecular systems that retain the favorable electronic properties of a polyacetylenic bridge but that include a relay or insulator in the bridging moiety. A convenient way to construct such systems is to use a Pt^II bis-acetylide as the spacer that separates terminal metal oligopyridine complexes. In this case, the central Pt^II complex becomes an insulator. By careful design of the system, this insulatory behavior can be exploited as a means by which to introduce directionality and selectivity into the system, and we demonstrate such effects by using polycyclic hydrocarbons and metalloporphyrins as the photoactive terminals. Similar effects can be obtained with polycyclic hydrocarbons built into the acetylenic wire and, in such cases, the energetics of the bridge can be tuned over an inordinately wide range by varying the extent of conjugation inherent to the aromatic nucleus. A special case is identified in which the polycycle itself possesses vacant coordination sites since the energy of the bridge can be further tuned by external complexation of adventitious cations. In order to provide for an energy gradient along the molecular axis, we have devised a versatile synthetic strategy for attaching different types of ligand to the terminals. This approach also facilitates both extension of the molecular axis and alteration of the molecular shape. The photophysical and electrochemical properties have been recorded for all the molecular systems reported herein and used as a simple experimental means by which to quantify the extent of electronic communication along the molecular axis. For mixed-metal or mixed-ligand systems, rates of intramolecular energy or electron transfer have been measured. In most cases, these rates are extremely fast and testify to the remarkable electronic coupling properties of this family of compounds. Finally, some consideration is given to the preparation of third-generation systems.     

On the interplay between CH...O and OH...O interactions in determining crystal packing and molecular conformation: an experimental and theoretical charge density study of the fungal secondary metabolite austdiol (C12H12O5)

The total experimental electron density rho(r), its Laplacian inverted delta(2)rho(r), the molecular dipole moment, the electrostatic potential phi(r), and the intermolecular interaction energies have been obtained from an extensive set of single-crystal X-ray diffracted intensities, collected at T = 70(1) K, for the fungal metabolite austdiol (1). The experimental results have been compared with theoretical densities from DFT calculations on the isolated molecule and with fully periodic calculations. The crystal structure of (1) consists of zigzag ribbons extended along one cell axis and formed by molecules connected by both OH...O and CH...O interactions, while in a perpendicular direction, adjacent molecules are linked by short CH...O intermolecular contacts. An extensive, quantitative study of all the intra- and intermolecular H...O interactions, based not only on geometrical criteria, but also on the topological analysis of rho(r), as well as on the evaluation of the pertinent energetics, allowed us (i) to assess the mutual role of OH...O and CH...O interactions in determining molecular conformation and crystal packing; (ii) to identify those CH...O contacts which are true hydrogen bonds (HBs); (iii) to determine the relative hydrogen bond strengths. An experimental, quantitative evidence is given that CH...O HBs are very similar to the conventional OH...O HBs, albeit generally weaker. The comparison between experimental and theoretical electric dipole moments indicates that a noticeable charge rearrangement occurs upon crystallization and shows the effects of the mutual cooperation of HBs in the crystal. The total intermolecular interaction energies and the electrostatic energy contribution obtained through different theoretical methods are reported and compared with the experimental results. It is found that the new approach proposed by Spackman, based on the use of the promolecular charge density to approximate the penetration contribution to intermolecular electrostatic energies, predicts the correct relative electrostatic interaction energies in most of the cases.     

外型-1,4-氧桥-环己基-2,3-二羧酸的晶体及分子结构

外型-1,4-氧桥-环己基-2,3-二羧酸晶体属单斜晶系,空间群为P2_1/n;晶胞参数为:α=5.594(3)A,b=11.178(7)A,c=14.675(11)A,β=91.46(5)°;Ζ=4.从直接法得到结构的初始模型,经块矩阵最小二乘修正后,最后的R值为0.072.在晶体中,分子间的O—H…O氢键将分子连接成层型氢键体系.使用自编的CNDO/2程序,计算得电子的能量、分子的总能量、偶极矩及各原子的电荷密度和净电荷.     

The unexpected and large enhancement of the dipole moment in the 3,4-bis(dimethylamino)-3-cyclobutene-1,2-dione (DMACB) molecule upon crystallization: a new role of the intermolecular CH...O interactions.

The molecular dipole moment of the 3,4-bis(dimethylamino)-3-cyclobutene-1,2-dione (DMACB) molecule and its enhancement in the crystal was evaluated by periodic RHF ab initio computations. A discrete boundary partitioning of the electronic density that allows an unambiguous partitioning of the molecular space in the condensed phase was adopted. The resulting molecular dipole in the crystal compares favorably with the experimental value obtained by a multipolar analysis of single-crystal X-ray diffraction data recorded at 20 K, using a fuzzy boundary partitioning of the derived pseudoatom densities. We show that a large and highly significant molecular dipole enhancement may occur upon crystallization, despite the lack of a strongly hydrogen bonded environment in the crystal. The 23 unique C-H...O interactions which are formed upon packing of the DMACB molecule induce an increase in the molecular dipole (over 75%) that is comparable to or greater than that found in systems which are characterized by the stronger O-H...O and N-H...O hydrogen bonds. The DMACB molecule constitutes an excellent system for the study of C-H...O interactions in the condensed phase, since no other kind of competing hydrogen bonds is present in its crystal. A simple and qualitative model for the matrix contribution to the DMACB molecular dipole enhancement in the crystal is proposed. The formation of several weak C-H...O bonds is found to yield a small (about 0.2 e) net flux of electronic charge flowing from the hydrogens of the methyl groups to the carbonyl oxygen atoms. Despite the limited increase of the intramolecular charge transfer upon crystallization, a large molecular dipole enhancement occurs because the centroids of the positive and negative induced charges are quite far apart. This work highlights a new and important role of the C-H...O bond, besides those already known in the literature.     

二[2-(邻羟苄叉胺基)酚]二铁(Ⅱ)配合物分子片模型的电子结构研究

用CNDO/2法计算了二[2-(邻羟苄叉胺基)酚]二(Ⅱ)铁双核铁(Ⅱ)配合物分子片模型的电子结构,研究了该配合物中平面结构单元与结晶水的相互作用。几何结构优化结果表明,结晶水与平面结构单元之间存在3种可能相对取向,“伞式”模型最稳定;这3种相互作用导致体系能级移动,并出现新的能级结构;从原子定域态密度分析看到,这种定域相互作用主要在结晶水分子和平面结构单元中的氧原子之间,具有最近邻相互作用的特征。     

[Co(H2O)4(NCS)2]·(18-C-6)配合物晶体的成键特性理论研究

[Co(H_2O)_4(NCS)_2]·(18-C-6)是本文作者之一最近合成的新王冠醚配合物晶体。我们用CNDO/2方法计算了该配合物原子簇模型的电荷分布, Mulliken键级,电子态密度(DOS)等,研究其成键特性。结果表明, 该配合物中存在稳定的[Co(H_2O)_4(NCS)_2]·(18-C-6)集团, 配合单元[Co(H_2O)_4(NCS)_2]采取四根强度不同的氢键与(18-C-6)相结合, 并较好地解释了实验结果。