Why do the heavy-atom analogues of acetylene E2H2 (E = Si-Pb) exhibit unusual structures?

DFT calculations at BP86/QZ4P have been carried out for different structures of E(2)H(2) (E = C, Si, Ge, Sn, Pb) with the goal to explain the unusual equilibrium geometries of the heavier group 14 homologues where E = Si-Pb. The global energy minima of the latter molecules have a nonplanar doubly bridged structure A followed by the singly bridged planar form B, the vinylidene-type structure C, and the trans-bent isomer D1. The energetically high-lying trans-bent structure D2 possessing an electron sextet at E and the linear form HEEH, which are not minima on the PES, have also been studied. The unusual structures of E(2)H(2) (E = Si-Pb) are explained with the interactions between the EH moieties in the (X(2)Pi) electronic ground state which differ from C(2)H(2), which is bound through interactions between CH in the a(4)Sigma(-) excited state. Bonding between two (X(2)Pi) fragments of the heavier EH hydrides is favored over the bonding in the a(4)Sigma(-) excited state because the X(2)Pi --> a(4)Sigma(-) excitation energy of EH (E = Si-Pb) is significantly higher than for CH. The doubly bridged structure A of E(2)H(2) has three bonding orbital contributions: one sigma bond and two E-H donor-acceptor bonds. The singly bridged isomer B also has three bonding orbital contributions: one pi bond, one E-H donor-acceptor bond, and one lone-pair donor-acceptor bond. The trans-bent form D1 has one pi bond and two lone-pair donor-acceptor bonds, while D2 has only one sigma bond. The strength of the stabilizing orbital contributions has been estimated with an energy decomposition analysis, which also gives the bonding contributions of the quasi-classical electrostatic interactions.     

Molecular Dynamics Simulation Study of ClF in Water: Halogen Bonding Interaction in Liquid

Does the halogen bonding interaction co-exist in liquid when it competes with the hydrogen bonding interaction? The classical molecular dynamics simulations for the solvation properties of ClF molecule in water are performed with the Lennard-Jones plus Coulomb electrostatic potential parameters that are optimized with ab initio interaction energy calculations for the pre-reactive H₂O…ClF complex. We find that the halogen bonding interactions occur between O and Cl atoms and have the comparable strength and population with respect to the hydrogen bonding interactions of Cl…H.     

Combined Crossed Molecular Beams and Ab Initio Study of the Bimolecular Reaction of Ground State Atomic Silicon (Si; 3P) with Germane (GeH4; X1A1)

The chemical dynamics of the elementary reaction of ground state atomic silicon (Si; ³P) with germane (GeH₄; X¹A₁) were unraveled in the gas phase under single collision condition at a collision energy of 11.8±0.3 kJ mol⁻¹ exploiting the crossed molecular beams technique contemplated with electronic structure calculations. The reaction follows indirect scattering dynamics and is initiated through an initial barrierless insertion of the silicon atom into one of the four chemically equivalent germanium-hydrogen bonds forming a triplet collision complex (HSiGeH₃; ³ i1 ). This intermediate underwent facile intersystem crossing (ISC) to the singlet surface (HSiGeH₃; ¹ i1 ). The latter isomerized via at least three hydrogen atom migrations involving exotic, hydrogen bridged reaction intermediates eventually leading to the H₃SiGeH isomer i5 . This intermediate could undergo unimolecular decomposition yielding the dibridged butterfly-structured isomer ¹ p1 (Si(μ-H₂)Ge) plus molecular hydrogen through a tight exit transition state. Alternatively, up to two subsequent hydrogen shifts to i6 and i7 , followed by fragmentation of each of these intermediates, could also form ¹ p1 (Si(μ-H₂)Ge) along with molecular hydrogen. The overall non-adiabatic reaction dynamics provide evidence on the existence of exotic dinuclear hydrides of main group XIV elements, whose carbon analog structures do not exist.     

Theoretical Study of the Interplay between Lithium Bond and Hydrogen Bond in Complexes Involved with HLi and HCN

The lithium‐ and hydrogen‐bonded complex of HLi? NCH? NCH is studied with ab initio calculations. The optimized structure, vibrational frequencies, and binding energy are calculated at the MP2 level with 6‐311++G(2d,2p) basis set. The interplay between lithium bonding and hydrogen bonding in the complex is investigated with these properties. The effect of lithium bonding on the properties of hydrogen bonding is larger than that of hydrogen bonding on the properties of lithium bonding. In the trimer, the binding energies are increased by about 19 % and 61 % for the lithium and hydrogen bonds, respectively. A big cooperative energy (?5.50 kcal mol^?1) is observed in the complex. Both the charge transfer and induction effect due to the electrostatic interaction are responsible for the cooperativity in the trimer. The effect of HCN chain length on the lithium bonding has been considered. The natural bond orbital and atoms in molecules analyses indicate that the electrostatic force plays a main role in the lithium bonding. A many‐body interaction analysis has also been performed for HLi? (NCH)_N (N=2–5) systems.     

Theoretical study on intermolecular interactions in BrF/HnX adducts

Equilibrium geometries, interaction energies, and charge transfer for the intermolecular interactions between BrF and H_nX (HF, H₂O, and NH₃) were studied at the MP2/6-311++G(3d,3p) level. The halogen-bonded geometry and hydrogen-bonded geometry are observed in these interactions. The calculated interaction energies show that the halogen-bonded structures are more stable than the corresponding hydrogen-bonded structures. To study the nature of the intermolecular interactions, symmetry-adapted perturbation theory (SAPT) calculations were carried out and the results indicate that the halogen bonding interactions are dominantly inductive energy in nature, while electrostatic energy governs the hydrogen bonding interactions.     

Dual Role of the 1,2,3‐Triazolium Ring as a Hydrogen‐Bond Donor and Anion–π Receptor in Anion‐Recognition Processes

Several bis(triazolium)‐based receptors have been synthesized as chemosensors for anion recognition. The central naphthalene core features two aryltriazolium side‐arms. NMR experiments revealed differences between the binding modes of the two triazolium rings: one triazolium ring acts as a hydrogen‐bond donor, the other as an anion–π receptor. Receptors 9²⁺?2BF₄ ^? (C₆H₅), 11²⁺?2BF₄ ^? (4‐NO₂?C₆H₄), and 13²⁺?2BF^4? (ferrocenyl) bind HP₂O₇^3? anions in a mixed‐binding mode that features a combination of hydrogen‐bonding and anion–π interactions and results in strong binding. On the other hand, receptor 10²⁺?2 BF₄ ^? (4‐CH₃O?C₆H₄) only displays combined Csp₂?H/anion–π interactions between the two arms of the receptors and the bound anion rather than triazolium (CH)⁺???anion hydrogen bonding. All receptors undergo a downfield shift of the triazolium protons, as well as the inner naphthalene protons, in the presence of H₂PO₄^? anions. That suggests that only hydrogen‐bonding interactions exist between the binding site and the bound anion, and involve a combination of cationic (triazolium) and neutral (naphthalene) C?H donor interactions. Theoretical calculations relate the electronic structure of the substituent on the aromatic group with the interaction energies and provide a minimum‐energy conformation for all the complexes that explains their measured properties.     

超分子2，2′-联咪唑镉(Ⅱ)配聚物的合成与结构表征

以硫氰酸根、叠氮基、二氰胺为桥联配体,分别与2,2'-联咪唑和硝酸镉反应,获得配聚物[Cd(SCN)2(H2biim)]N(1),[Cd(N3)2(H2biim)]n(2)和[Cd2(NO3)(dca)3(H2biim)2.5]n(3),3个化合物通过元素分析、IR、TGA等表征,并测定了它们的晶体结构.结果表明:化合物1和2分别是以μ1.3-SCN-和μ1.1-N3-双桥连接的一维链状结构,化合物3是以μ1.5-dca-和μ3.3-H2biim交叉桥连的二维网状结构.对它们的荧光性质也进行了初步分析.     

Crystal structure,spectroscopic and thermal properties of copper(II) and manganese(II) coordination polymers based on triazole-benzoic acid ligands

Two transition metal coordination polymers {[Cu(tba)₂(H₂O)]·2H₂O} _n (1) and {[Mn(Htta)₂(H₂O)₂]·2H₂O} _n (2) {Htba = 3-[1,2,4]triazol-1-yl-benzoic acid, H₂tta = 2-[1,2,4]triazol-1-yl-terephthalic acid} have been synthesized under solvothermal conditions. Both complexes have been characterized by single-crystal X-ray diffraction, X-ray powder diffraction, elemental analysis and FTIR spectroscopy. Complex 1 has a 1-D chain structure in which Cu(II) atoms are doubly bridged by tba^? ligands, which is further stabilized by hydrogen bonding and π–π stacking interactions to give a 3-D supramolecular framework. In complex 2, Mn(II) atoms are doubly bridged by Htta^? ligands to form 1-D chains, which are further connected by intermolecular hydrogen bonds to form a 3-D supramolecular framework. The electronic spectra and thermal behaviors of complexes 1 and 2 are also reported.     

Time‐dependent density functional theory study on the electronic excited‐state geometric structure,infrared spectra,and hydrogen bonding of a doubly hydrogen‐bonded complex

The geometric structures and infrared (IR) spectra in the electronically excited state of a novel doubly hydrogen‐bonded complex formed by fluorenone and alcohols, which has been observed by IR spectra in experimental study, are investigated by the time‐dependent density functional theory (TDDFT) method. The geometric structures and IR spectra in both ground state and the S₁ state of this doubly hydrogen‐bonded FN‐2MeOH complex are calculated using the DFT and TDDFT methods, respectively. Two intermolecular hydrogen bonds are formed between FN and methanol molecules in the doubly hydrogen‐bonded FN‐2MeOH complex. Moreover, the formation of the second intermolecular hydrogen bond can make the first intermolecular hydrogen bond become slightly weak. Furthermore, it is confirmed that the spectral shoulder at around 1700 cm^?1 observed in the IR spectra should be assigned as the doubly hydrogen‐bonded FN‐2MeOH complex from our calculated results. The electronic excited‐state hydrogen bonding dynamics is also studied by monitoring some vibraitonal modes related to the formation of hydrogen bonds in different electronic states. As a result, both the two intermolecular hydrogen bonds are significantly strengthened in the S₁ state of the doubly hydrogen‐bonded FN‐2MeOH complex. The hydrogen bond strengthening in the electronically excited state is similar to the previous study on the singly hydrogen‐bonded FN‐MeOH complex and play important role on the photophysics of fluorenone in solutions. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009     

A new polymorph of phenylselenium trichloride

A second polymorph of phenylselenium trichloride, PhSeCl₃ or C₆H₅Cl₃Se, is disclosed, which is comprised of asymmetric chlorine‐bridged noncovalent dimer units rather than polymeric chains. These dimers are each weakly bound to an adjacent dimer through noncovalent Se…Cl bonding interactions. Phenyl rings within each dimer are oriented in a syn fashion. Density functional theory (DFT) calculations reveal that the putative anti isomer is within 5 kJ mol^?1 of the experimentally observed form. This structure represents the first additional polymorph discovered for an organoselenium trihalide compound.     

Measuring the Relative Hydrogen‐Bonding Strengths of Alcohols in Aprotic Organic Solvents

Voltammetric experiments with 9,10‐anthraquinone and 1,4‐benzoquinone performed under controlled moisture conditions indicate that the hydrogen‐bond strengths of alcohols in aprotic organic solvents can be differentiated by the electrochemical parameter ΔE_p^red=|E_p^red(1)?E_p^red(2)|, which is the potential separation between the two one‐electron reduction processes. This electrochemical parameter is inversely related to the strength of the interactions and can be used to differentiate between primary, secondary, tertiary alcohols, and even diols, as it is sensitive to both their steric and electronic properties. The results are highly reproducible across two solvents with substantially different hydrogen‐bonding properties (CH₃CN and CH₂Cl₂) and are supported by density functional theory calculations. This indicates that the numerous solvent–alcohol interactions are less significant than the quinone–alcohol hydrogen‐bonding interactions. The utility of ΔE_p^red was illustrated by comparisons between 1) 3,3,3‐trifluoro‐n‐propanol and 1,3‐difluoroisopropanol and 2) ethylene glycol and 2,2,2‐trifluoroethanol.     

The balance between side-chain and backbone-driven association in folding of the α-helical influenza A transmembrane peptide

The correct balance between attractive, repulsive and peptide hydrogen bonding interactions must be attained for proteins to fold correctly. To investigate these important contributors, we sought a comparison of the folding between two 25-residues peptides, the influenza A M2 protein transmembrane domain (M2TM) and the 25-Ala (Ala₂₅). M2TM forms a stable α-helix as is shown by circular dichroism (CD) experiments. Molecular dynamics (MD) simulations with adaptive tempering show that M2TM monomer is more dynamic in nature and quickly interconverts between an ensemble of various α-helical structures, and less frequently turns and coils, compared to one α-helix for Ala₂₅. DFT calculations suggest that folding from the extended structure to the α-helical structure is favored for M2TM compared with Ala₂₅. This is due to CH⋯O attractive interactions which favor folding to the M2TM α-helix, and cannot be described accurately with a force field. Using natural bond orbital (NBO) analysis and quantum theory atoms in molecules (QTAIM) calculations, 26 CH⋯O interactions and 22 NH⋯O hydrogen bonds are calculated for M2TM. The calculations show that CH⋯O hydrogen bonds, although individually weaker, have a cumulative effect that cannot be ignored and may contribute as much as half of the total hydrogen bonding energy, when compared to NH⋯O, to the stabilization of the α-helix in M2TM. Further, a strengthening of NH⋯O hydrogen bonding interactions is calculated for M2TM compared to Ala₂₅. Additionally, these weak CH⋯O interactions can dissociate and associate easily leading to the ensemble of folded structures for M2TM observed in folding MD simulations.     

乙硼烷离子和自由基结构的量子化学研究

用B₃LYP/6-311G(d,p)密度泛函方法对B₂H₅⁺阳离子和B₂H₅^·自由基的几何异构体的空间构型进行了优化,并在此基础上用QCISD(T)/6-311++G(3df,2p)偶合簇法进行了单点能计算和零点能校正.结果表明,B₂H₅⁺单态有2种稳定的几何构型(D_3h,C₁),其中C₁构型是新发现的.B₂H₅⁺三重态阳离子除已知C_s构型外,又发现两种稳定构型(C₁).对于B₂H₅^·自由基体系,共有4种异构体(包括两种新发现的构型C_s),其中,具有单桥结构的C_2v最稳定.用二级多体微扰理论和密度泛函方法对前人所认为稳定的B₂H₅⁺单态的C_2v构型进行了全优化,结果发现该构型始终具有一个虚频,不是稳定构型.对B₂H₅^-阴离子体系的单态和三重态进行的全优化,理论上得出单态时具有C_2v和C_s两种稳定构型,而三重态只有C_2v一种稳定构型.     

Comparison of Hydrogen and Gold Bonding in [XHX]−, [XAuX]−, and Isoelectronic [NgHNg]+, [NgAuNg]+ (X=Halogen,Ng=Noble Gas)

Quantum chemical calculations at the MP2/aug‐cc‐pVTZ and CCSD(T)/aug‐cc‐pVTZ levels have been carried out for the title compounds. The electronic structures were analyzed with a variety of charge and energy partitioning methods. All molecules possess linear equilibrium structures with D_∞h symmetry. The total bond dissociation energies (BDEs) of the strongly bonded halogen anions [XHX]^? and [XAuX]^? decrease from [FHF]^? to [IHI]^? and from [FAuF]^? to [IAuI]^?. The BDEs of the noble gas compounds [NgHNg]⁺ and [NgAuNg]⁺ become larger for the heavier atoms. The central hydrogen and gold atoms carry partial positive charges in the cations and even in the anions, except for [IAuI]^?, in which case the gold atom has a small negative charge of ?0.03 e. The molecular electrostatic potentials reveal that the regions of the most positive or negative charges may not agree with the partial charges of the atoms, because the spatial distribution of the electronic charge needs to be considered. The bonding analysis with the QTAIM method suggests a significant covalent character for the hydrogen bonds to the noble gas atoms in [NgHNg]⁺ and to the halogen atoms in [XHX]^?. The covalent character of the bonding in the gold systems [NgAuNg]⁺ and [XAuX]^? is smaller than in the hydrogen compound. The energy decomposition analysis suggests that the lighter hydrogen systems possess dative bonds X^?→H⁺←X^? or Ng→H⁺←Ng while the heavier homologues exhibit electron sharing through two‐electron, three‐center bonds. Dative bonds X^?→Au⁺←X^? and Ng→Au⁺←Ng are also diagnosed for the lighter gold systems, but the heavier compounds possess electron‐shared bonds.     

Structural analysis and probing the conformational space of dansylamide by means of gas-phase electron diffraction and quantum chemistry

Dansylamide is perhaps the most ubiquitous fluorophore due to its donor-acceptor bifunctionality and its ability to form intra- and intermolecular hydrogen bonding. Among the diversity of its applications is the development of new generation of biosensors for the in vivo monitoring of traces of metals. The structure and conformational stability of dansylamide in the gas phase were investigated for the first time by a combined gas-phase electron diffraction-mass spectrometry (GED/MS), complemented by quantum chemical calculations. GED data indicate that different skewed conformers exist at T?=?464 K, which are characterized by the deviation of two S–N bonds from the perpendicular orientation relative to the naphthalene plane. Maybe the most indicative structural parameters for electronic interactions between the donor-acceptor substituents and the aromatic naphthalene and the subsequent stabilization of the favorable skewed eclipsed-syn conformer are the dihedral angles C₉–C₁–S–N and C₁₀–C₅–N–C with the experimentally determined values of 66.8° (32) and 68.1° (72), respectively. The role of –SO₂NH₂ by forming intramolecular hydrogen bonds was scrutinized by employing the natural bond orbital approach (NBO), quantum theory atoms in molecules (QTAIM), and molecular electrostatic potential (MESP). The non-planarity of the naphthalene skeleton due to the electronic interactions with the substituents and its consequence for the fluorescence activity of dansylamide have been discussed.     

Aqua­di­chloro­(di‐2‐pyridyl­di­azene)copper(II) monohydrate

The crystal structure of the mononuclear title complex, [CuCl₂(C₁₀H₈N₄)(H₂O)]·H₂O, shows an s‐cis/E/s‐trans‐configured di‐2‐pyridyl­diazene ligand, with the square‐pyramidal Cu^II ion coordinated to one pyridyl and one diazene N atom together with two Cl atoms and one aqua ligand. The crystal packing involves both hydrogen‐bonding and π–π interactions. The solvent water mol­ecule links three monomers to one another through hydrogen‐bonding interactions in which two monomers are linked via chloro ligands and the third via the aqua ligand. Face‐to‐face and weak slipped π–π interactions also occur between di‐2‐pyridyl­diazene moieties, and these interactions are responsible for the interchain packing.     

Visualizing lone pairs in compounds containing heavier congeners of the carbon and nitrogen group elements

In this mini-review, I discuss some recent work on the stereochemistry and bonding of lone pairs of electrons in divalent compounds of the heavier carbon group elements (Sn^II , Pb^II) and in trivalent compounds of the heavier nitrogen group elements (Bi^III). Recently developed methods that permit the real-space visualization of bonding patterns on the basis of density functional calculations of electronic structure, reveal details of the nature of s electron lone pairs in compounds of the heavier main group elements — their stereochemistry and their inertness (or lack thereof). An examination of tetragonalP4/nmm SnO, α-PbO and BiOF, and cubic PbS provides a segue into perovskite phases of technological significance, including ferroelectric PbTiO₃ and antiferroelectric/piezoelectric PbZrO₃, in both of which the lone pairs on Pb atoms play a pivotal r?le.     

Theoretical prediction of a graphene-like 2D uranyl material with p-orbital antiferromagnetism

Versatile graphene-like two-dimensional materials with s-, p- and d-block elements have aroused significant interest because of their extensive applications while there is a lack of such materials with f-block elements. Herein we report a unique one composed of the f-block element moiety of uranyl (UO₂²⁺) through a global-minimum structure search. Its geometry is found to be similar to that of graphene with a honeycomb-like hexagonal unit composed of six uranyl ligands, where each uranyl is bridged by two superoxido groups and a pair of hydroxyl ligands. All the uranium and bridging oxygen atoms form an extended planar 2D structure, which shows thermodynamic, kinetic and thermal stabilities due to σ/π bonding as well as electrostatic interactions between ligands. Each superoxido ligand has one unpaired (2p_π*)¹ electron and is antiferromagnetically coupled through uranyl bridges with 2p_π*–5f_δ–2p_π* superexchange interactions, forming a rare type of one-dimensional Heisenberg chain with p-orbital antiferromagnetism, which might become valuable for application in antiferromagnetic spintronics.

An unprecedented graphene-like 2D uranyl material with p-orbital antiferromagnetism is found to be stable by computational investigations.     

(E)‐Methyl 2‐anilinomethylene‐3‐oxobutanoate: X‐ray and density functional theory studies

Molecules of the title compound, C₁₂H₁₃NO₃, are not planar and are stabilized by electrostatic interactions, as the dipole moment of the molecule is 3.76 D. They are also stabilized by intramolecular hydrogen bonds of N...O and C...O types, and by a complicated network of weak intermolecular hydrogen bonds of the C...O type. This paper also reports the theoretical investigation of the hydrogen bonding and electronic structure of the title compound using natural bond orbital (NBO) analysis.     

Incorporating two different chromophores onto a silicon atom: the crystal structure and photophysical properties of 9‐{4‐[(9,9‐dimethyl‐9H‐fluoren‐2‐yl)dimethylsilyl]phenyl}‐9H‐carbazole

The crystal structure of the title bifunctional silicon‐bridged compound, C₃₅H₃₁NSi, (I), has been determined. The compound crystallizes in the centrosymmetric space group P2₁/c. In the crystal structure, the pairs of aryl rings in the two different chromophores, i.e. 9‐phenyl‐9H‐carbazole and 9,9‐dimethyl‐9H‐fluorene, are positioned orthogonally. In the crystal packing, no classical hydrogen bonding is observed. UV–Vis absorption and fluorescence emission spectra show that the central Si atom successfully breaks the electronic conjugation between the two different chromophores, and this was further analysed by density functional theory (DFT) calculations.