Chalcogen- and halogen-bonds involving SX<Subscript>2</Subscript> (X = F,Cl, and Br) with formaldehyde

The capacity of SX₂ (X = F, Cl, and Br) to engage in different kinds of noncovalent bonds was investigated by ab initio calculations. SCl₂ (SBr₂) has two σ-holes upon extension of Cl (Br)?S bonds, and two σ-holes upon extension of S?Cl (Br) bonds. SF₂ contains only two σ-holes upon extension of the F?S bond. Consequently, SCl₂ and SBr₂ form chalcogen and halogen bonds with the electron donor H₂CO while SF₂ forms only a chalcogen bond, i.e., no F···O halogen bond was found in the SF₂:H₂CO complex. The S···O chalcogen bond between SF₂ and H₂CO is the strongest, while the strongest halogen bond is Br···O between SBr₂ and H₂CO. The nature of these two types of noncovalent interaction was probed by a variety of methods, including molecular electrostatic potentials, QTAIM, energy decomposition, and electron density shift maps. Termolecular complexes X₂S···H₂CO···SX′₂ (X = F, Cl, Br, and X′ = Cl, Br) were constructed to study the interplay between chalcogen bonds and halogen bonds. All these complexes contained S···O and Cl (Br)···O bonds, with longer intermolecular distances, smaller values of electron density, and more positive three-body interaction energies, indicating negative cooperativity between the chalcogen bond and the halogen bond. In addition, for all complexes studied, interactions involving chalcogen bonds were more favorable than those involving halogen bonds.

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Graphical Abstract Molecular electrostatic potential and contour map of the Laplacian of the electron density in Cl₂S···H₂CO···SCl₂ complex

     

Theoretical studies on identity SN2 reactions of lithium halide and methyl halide: A microhydration model

Reactions of lithium halide (LiX, X = F, Cl, Br and I) and methyl halide (CH₃X, X = F, Cl, Br and I) have been investigated at the B3LYP/6-31G(d) level of theory using the microhydration model. Beginning with hydrated lithium ion, four or two water molecules have been conveniently introduced to these aqueous-phase halogen-exchange S_N2 reactions. These water molecules coordinated with the center metal lithium ion, and also interacted with entering and leaving halogen anion via hydrogen bond in complexes and transition state, which to some extent compensated hydration of halogen anion. At 298 K the reaction profiles all involve central barriers ΔE _cent which are found to decrease in the order F > Cl > Br > I. The same trend is also found for the overall barriers (ΔE _ovr ) of the title reaction. In the S_N2 reaction of sodium iodide and methyl iodide, the activation energy agrees well with the aqueous conductometric investigation.     

The insertion reactions of the p-complex silylenoid H<Subscript>2</Subscript>SiLiF with Si-X (X=F,Cl, Br,O, N) bonds

The insertion reactions of the silylenoid H₂SiLiF with SiH₃XH_n-1 (X = F, Cl, Br, O, N; n = 1, 1, 1, 2, 3) have been studied by DFT calculations. The results indicate that the insertions proceed in a concerted manner, forming H₃SiSiH₂XH_n-1 and LiF. The essence of H₂SiLiF insertion into Si-X bonds reactions are the donations of the electrons of X into the p orbital on the Si atom in H₂SiLiF and the σ electrons on the Si atom in H₂SiLiF to the positive SiH₃ group. The order of reactivity by H₂SiLiF insertion in vacuum indicates the reaction barriers decrease for the same-row element X from right to left and the same-family element X from up down in the periodic table. The insertion reactions in ether are similar to those in vacuum. The energy barriers in vacuum are higher than those in ether. The silylenoid insertions are thermodynamically exothermic both in vacuum and in ether.     

Bonding,aromaticity, and planar tetracoordinated carbon in Si<Subscript>2</Subscript>CH<Subscript>2</Subscript> and Ge<Subscript>2</Subscript>CH<Subscript>2</Subscript>

Natural bond orbital (NBO) analyses and dissected nucleus-independent chemical shifts (NICS _{π z z} ) were computed to evaluate the bonding (bond type, electron occupation, hybridization) and aromatic character of the three lowest-lying Si₂CH₂ (1-Si, 2-Si, 3-Si) and Ge₂CH₂ (1-Ge, 2-Ge, 3-Ge) isomers. While their carbon C₃H₂ analogs favor classical alkene, allene, and alkyne type bonding, these Si and Ge derivatives are more polarizable and can favor “highly electron delocalized”? and “non-classical”? structures. The lowest energy Si ₂CH₂ and Ge ₂CH₂ isomers, 1-Si and 1-Ge, exhibit two sets of 3–center 2–electron (3c-2e) bonding; a π-3c-2e bond involving the heavy atoms (C–Si–Si and C–Ge–Ge), and a σ-3c-2e bond (Si–H–Si, Ge–H–Ge). Both 3-Si and 3-Ge exhibit π and σ-3c-2e bonding involving a planar tetracoordinated carbon (ptC) center. Despite their highly electron delocalized nature, all of the Si₂CH₂ and Ge₂CH₂ isomers considered display only modest two π electron aromatic character (NICS(0) _{π z z} =--6.2 to –8.9 ppm, computed at the heavy atom ring center) compared to the cyclic-C ₃H₂ (–13.3 ppm).

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Graphical Abstract The three lowest Si2CH2 and Ge2CH2 isomers.

     

Theoretical study of the effects of substituents (F,Cl, Br,CH<Subscript>3</Subscript>, and CN) on the aromaticity of borazine

This paper presents a theoretical study of the effects of substituents (F, Cl, Br, CH₃, and CN) on the aromaticity of borazine (B₃N₃H₆), using density functional theory (DFT) and the Hartree-Fock (HF) method. The calculations to optimize the geometries, structural properties, and vibrational frequencies were performed using the same 6–311G(d,p) and 6–311++G(d,p) basis sets, comparing the methods with experimental results. In the analysis of the NICS_ZZ values, it was found that that replacing the hydrogen atoms by halogen atoms (F, Cl, and Br) and CH₃ reduced the aromaticity of the borazine molecule, while use of the CN group resulted in NICS_ZZ values (0.9–2.0 Å) very close to those of borazine, presenting the following order of increasing aromaticity: B₃N₃H₃-(Br)₃?<?B₃N₃H₃-(Cl)₃?<?B₃N₃H₃-(F)₃?<?B₃N₃H₃-(CH₃)₃?<?B₃N₃H₆ ~ B₃N₃H₃-(CN)₃. All the spectra of the compounds showed only the presence of transition peaks distant from the UV region, reflecting the large energy difference between the HOMO and LUMO orbitals. After the substitution of the borazine ring, all the compounds presented an intensification of the spectrum, with a shift of the maximum absorbance toward red, indicative of a bathochromic effect. There was a direct inverse relation between the energy gap and the maximum wavelength of the compounds.     

Theoretical study of N<Subscript>4</Subscript>X (X = O,S, Se) systems

A series of N₄X (X = O, S, Se) compounds have been examined with ab initio and density functional theory (DFT) methods. To our knowledge, these compounds, except for the C_2v ring and the C_3v towerlike isomers of N₄O, are first reported here. The ring structures are the most energetically favored for N₄X (X = O and S) systems. For N₄Se, the cagelike structure is the most energetically favored. Several decomposition and isomerization pathways for the N₄X species have been investigated. The dissociation of C_2v ring N₄O and N₄S structures via ring breaking and the barrier height are only 1.1 and −0.2 kcal mol⁻¹ at the CCSD(T)/6-311+G*//MP2/6-311+G* level of theory. The dissociation of the cagelike N₄X species is at a cost of 12.1–16.2 kcal mol⁻¹. As for the towerlike and triangle bipyramidal isomers, their decomposition or isomerization barrier heights are all lower than 10.0 kcal mol⁻¹. Although the C_S cagelike N₄S isomer has a moderate isomerization barrier (18.3–29.1 kcal mol⁻¹), the low dissociation barrier (−1.0 kcal mol⁻¹) indicates that it will disappear when going to the higher CCSD(T) level. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Comparison of <Superscript>13</Superscript>CH<Subscript>3</Subscript>, <Superscript>13</Superscript>CH<Subscript>2</Subscript>D,and <Superscript>13</Superscript>CHD<Subscript>2</Subscript> methyl labeling strategies in proteins

A comparison of three labeling strategies for studies involving side chain methyl groups in high molecular weight proteins, using ¹³CH₃,¹³CH₂D, and ¹³CHD₂ methyl isotopomers, is presented. For each labeling scheme, ¹H–¹³C pulse sequences that give optimal resolution and sensitivity are identified. Three highly deuterated samples of a 723 residue enzyme, malate synthase G, with ¹³CH₃,¹³CH₂D, and ¹³CHD₂ labeling in Ile δ1 positions, are used to test the pulse sequences experimentally, and a rationalization of each sequence’s performance based on a product operator formalism that focuses on individual transitions is presented. The HMQC pulse sequence has previously been identified as a transverse relaxation optimized experiment for ¹³CH₃-labeled methyl groups attached to macromolecules, and a zero-quantum correlation pulse scheme (¹³CH₃ HZQC) has been developed to further improve resolution in the indirectly detected dimension. We present a modified version of the ¹³CH₃ HZQC sequence that provides improved sensitivity by using the steady-state magnetization of both ¹³C and ¹H spins. The HSQC and HMQC spectra of ¹³CH₂D-labeled methyl groups in malate synthase G are very poorly resolved, but we present a new pulse sequence, ¹³CH₂D TROSY, that exploits cross-correlation effects to record ¹H–¹³C correlation maps with dramatically reduced linewidths in both dimensions. Well-resolved spectra of ¹³CHD₂-labeled methyl groups can be recorded with HSQC or HMQC; a new ¹³CHD₂ HZQC sequence is described that provides improved resolution with no loss in sensitivity in the applications considered here. When spectra recorded on samples prepared with the three isotopomers are compared, it is clear that the ¹³CH₃ labeling strategy is the most beneficial from the perspective of sensitivity (gains ≥2.4 relative to either ¹³CH₂D or ¹³CHD₂ labeling), although excellent resolution can be obtained with any of the isotopomers using the pulse sequences presented here.     

Theoretical study on the aromaticity from d-AOs in cationic X 3 + (X = Sc,Y, La) clusters

The stable structures and aromatic characters for three cationic X₃⁺ (X = Sc, Y, and La) and three relevant neutral X₃Cl (X = Sc, Y, La) clusters are investigated at the DFT and post HF level of theory. The calculated results show that the X₃⁺ cations each has two stable structures: the regular trigon (D_3h) and the line (D_￥h {{\hbox{D}}_{\infty {\rm{h}}}} ) with the regular trigon (D_3h) being the ground state, while for three neutral X₃Cl clusters, Sc₃Cl has three stable isomers: the trigon-pyramidal (C_3v), bidentate (C_2v-1), and C_2v-2 structures, Y₃Cl and La₃Cl each has only two stable isomers: the trigon-pyramidal (C_3v) and bidentate (C_2v-1) structures. The ground states for three X₃Cl species are all the bidentate (C_2v-1) isomers. The calculations of the resonance energy (RE) and NICS show that trigonal X₃⁺ isomers exhibit higher degree of aromaticity. The detailed molecular orbital analyzes reveal that the isolated trigonal Sc₃⁺ and Y₃⁺ cations each has one delocalized π-type MO and shows single π-aromaticity, while the isolated trigonal La₃⁺ cation has one delocalized σ-type MO and shows single σ-aromaticity. The single π- or σ-aromaticity for X₃⁺ are attributed to the contributions mainly from the d AOs of the corresponding transition metal X atoms. However, when a singly negatively charged counterion Cl^- is added to Sc₃⁺, Y₃⁺, and La₃⁺ cations respectively, the aromatic type for the two Sc₃⁺, Y₃⁺ units in the corresponding neutral Sc₃Cl, Y₃Cl complexes are changed from π-aromaticity into σ-aromaticity, whereas the σ-aromaticity of the La₃⁺ units in the La₃Cl complex keeps unchanged in this process. Thus three Sc₃⁺, Y₃⁺, La₃⁺ units in the corresponding X₃Cl complexes all have only one σ-type MO and exhibit single σ-aromaticity.     

A DFT study of addition reaction between fragment ion (CH<Subscript>2</Subscript>) units and fullerene (C<Subscript>60</Subscript>) molecule

The theoretical study of the interaction between CH₂ and fullerene (C₆₀) suggests the existence of an addition reaction mechanism; this feature is studied by applying an analysis of electronic properties. Several different effects are evident in this interaction as a consequence of the particular electronic transfer which occurs during the procedure. The addition or insertion of the methylene group results in a process, where the inclusion of CH₂ into a fullerene bond produces the formation of several geometric deformations. A simulation of these procedures was carried out, taking advantage of the dynamic semi-classical Born-Oppenheimer approximation. Dynamic aspects were analyzed at different speeds, for the interaction between the CH₂ group and the two bonds: CC (6, 6) and CC (6, 5) respectively on the fullerene (C₆₀) rings. All calculations which involved electrons employed DFT as well as exchange and functional correlation. The results indicate a tendency for the CH₂ fragment to attack the CC (6, 5) bond.     

Quantum chemical topological analysis of hydrogen bonding in HX…HX and CH3X…HX dimers (X = Br,Cl, F)

We present a systematic investigation of the nature and strength of the hydrogen bonding in HX···HX and CH₃X…HX (X = Br, Cl and F) dimers using ab initio MP2/aug-cc-pVTZ calculations in the framework of the quantum theory of atoms in molecules (QTAIM) and electron localisation functions (ELFs) methods. The electron density of the complexes has been characterised, and the hydrogen bonding energy, as well as the QTAIM and ELF parameters, is consistent, providing deep insight into the origin of the hydrogen bonding in these complexes. It was found that in both linear and angular HX…HX and CH₃X…HX dimers, F atoms form stronger HB than Br and Cl, but they need short (～2 Å) X…HX contacts.     

Theoretical study of structural patterns in CH<Subscript>2</Subscript>OP<Subscript>2</Subscript> isomers

DFT calculations have been performed on the derivatives of formula CH₂OP₂ to determine their total energy, the relative energy between the isomers and their geometry. Among compounds with a P-C-P linkage, the most stable one is the 2-hydroxy-1,2-diphosphirene II.1, a three-membered heterocycle with a P=C unsaturation. The phosphavinylidene(oxo)phosphorane HP=C=P(O)H IV.5 (which has the same skeleton as the experimentally obtained Mes*P=C=P(O)Mes*) lies 36.30 kcal mol^-1 above it. The least stable compounds are carbenes; the singlet carbenes are more stable than the triplet ones.     

The Importance of Termites to the CH<Subscript>4</Subscript> Balance of a Tropical Savanna Woodland of Northern Australia

Termites produce methane (CH₄) as a by-product of microbial metabolism of food in their hindguts, and are one of the most uncertain components of the regional and global CH₄ exchange estimates. This study was conducted at Howard Springs near Darwin, and presents the first estimate of CH₄ emissions from termites based on replicated in situ seasonal flux measurements in Australian savannas. Using measured fluxes of CH₄ between termite mounds and the atmosphere, and between soil and the atmosphere across seasons we determined net CH₄ flux within a tropical savanna woodland of northern Australia. By accounting for both mound-building and subterranean termite colony types, and estimating the contribution from tree-dwelling colonies it was calculated that termites were a CH₄ source of +0.24 kg CH₄-C ha⁻¹ y⁻¹ and soils were a CH₄ sink of −1.14 kg CH₄-C ha⁻¹ y⁻¹. Termites offset 21% of CH₄ consumed by soil resulting in net sink strength of −0.90 kg CH₄-C ha⁻¹ y⁻¹ for these savannas. For Microcerotermes nervosus (Hill), the most abundant mound-building termite species at this site, mound basal area explained 48% of the variation in mound CH₄ flux. CH₄ emissions from termites offset 0.1% of the net biome productivity (NBP) and CH₄ consumption by soil adds 0.5% to the NBP of these tropical savannas at Howard Springs.     

Theoretical investigations of the H···π and X (X = F,Cl, Br,I)···π complexes between hypohalous acids and benzene

The H···π and X (X = F, Cl, Br, I)···π interactions between hypohalous acids and benzene are investigated at the MP2/6-311++G(2d,2p) level. Four hydrogen-bonded and three halogen-bonded complexes were obtained. Ab initio calculations indicate that the X···π interaction between HOX and C₆H₆ is mainly electrostatically driven, and there is nearly an equal contribution from both electrostatic and dispersive energies in the case of XOH–C₆H₆ complexes. Natural bond orbital (NBO) analysis reveals that there exists charge transfer from benzene to hypohalous acids. Atom in molecules (AIM) analysis locates bond critical points (BCP) linking the hydrogen or halogen atom and carbon atom in benzene.     

Characteristics and nature of the intermolecular interactions in boron-bonded complexes with carbene as electron donor: an <Emphasis Type="Italic">ab initio</Emphasis>, SAPT and QTAIM study

We report geometries, stabilization energies, symmetry adapted perturbation theory (SAPT) and quantum theory of atoms in molecules (QTAIM) analyses of a series of carbene–BX₃ complexes, where X = H, OH, NH₂, CH₃, CN, NC, F, Cl, and Br. The stabilization energies were calculated at HF, B3LYP, MP2, MP4 and CCSD(T)/aug-cc-pVDZ levels of theory using optimized geometries of all the complexes obtained from B3LYP/aug-cc-pVTZ. Quantitatively, all the complexes indicate the presence of B–C_carbene interaction due to the short B–C_carbene distances. Inspection of stabilization energies reveals that the interaction energies increase in the order NH₂ > OH > CH₃ > F > H > Cl > Br > NC > CN, which is the opposite trend shown in the binding distances. Considering the SAPT results, it is found that electrostatic effects account for about 50% of the overall attraction of the studied complexes. By comparison, the induction components of these interactions represent about 40% of the total attractive forces. Despite falling in a region of charge depletion with ∇² ρ _BCP >0, the B–C_carbene bond critical points (BCPs) are characterized by a reasonably large value of the electron density (ρ _BCP) and H_BCP <0, indicating that the potential energy overcomes the kinetic energy density at BCP and the B–C_carbene bond is a polar covalent bond.     

Emissions of CO<Subscript>2</Subscript>, CH<Subscript>4</Subscript> and N<Subscript>2</Subscript>O from undisturbed,drained and mined peatlands in Estonia

The aim of this study is to estimate emissions of greenhouse gases CO₂, CH₄ and N₂O, and the effects of drainage and peat extraction on these processes, in Estonian transitional fens and ombrotrophic bogs. Closed-chamber-based sampling lasted from January to December 2009 in nine peatlands in Estonia, covering areas with different land-use practices: natural (four study sites), drained (six sites), abandoned peat mining (five sites) and active peat mining areas (five sites). Median values of soil CO₂ efflux were 1,509, 1,921, 2,845 and 1,741 kg CO₂-C ha^?1 year^?1 from natural, drained, abandoned and active mining areas, respectively. Emission of CH₄-C (median values) was 85.2, 23.7, 0.07 and 0.12 kg ha^?1 year^?1, and N₂O-N ?0.05, ?0.01, 0.18 and 0.19 kg ha^?1 year^?1, respectively. There were significantly higher emissions of CO₂ and N₂O from abandoned and active peat mining areas, whereas CH₄ emissions were significantly higher in natural and drained areas. Significant Spearman rank correlation was found between soil temperature and CO₂ flux at all sites, and CH₄ flux with high water level at natural and drained areas. Significant increase in CH₄ flux was detected for groundwater levels above 30 cm.     

Insight into the gas phase dissociation of CF<Subscript>3</Subscript>CH<Subscript>2</Subscript>I and its reactions with H and OH by first principles

The Arrhenius kinetic parameters of dissociation reactions and reactions of CF₃CH₂I with radicals like H, O, and OH are determined using highly accurate first principles calculations. Thermophysical properties like molar heat capacity (C_p), thermal stability index, and the bond dissociation energies are also determined for the CF₃CH₂I molecule under the PBE/DNP formalism. Since, there are no theoretical study or experimental investigation reports available regarding the dissociation reactions of CF₃CH₂I and reactions of this molecule with the H and OH radical, a parallel comparative analysis is done with similar iodoalkanes to ascertain the precision of the results obtained. The atmospheric lifetime of 0.54 years is obtained for this molecule.     

Theoretical study of the reaction mechanism of CH<Subscript>3</Subscript>NO<Subscript>2</Subscript> with NO<Subscript>2</Subscript>, NO and CO: the bimolecular reactions that cannot be ignored

The intriguing decompositions of nitro-containing explosives have been attracting interest. While theoretical investigations have long been concentrated mainly on unimolecular decompositions, bimolecular reactions have received little theoretical attention. In this paper, we investigate theoretically the bimolecular reactions between nitromethane (CH₃NO₂)—the simplest nitro-containing explosive—and its decomposition products, such as NO₂, NO and CO, that are abundant during the decomposition process of CH₃NO₂. The structures and potential energy surface (PES) were explored at B3LYP/6-31G(d), B3P86/6-31G(d) and MP2/6-311?+?G(d,p) levels, and energies were refined using CCSD(T)/cc-pVTZ methods. Quantum chemistry calculations revealed that the title reactions possess small barriers that can be comparable to, or smaller than, that of the initial decomposition reactions of CH₃NO₂. Considering that their reactants are abundant in the decomposition process of CH₃NO₂, we consider bimolecular reactions also to be of great importance, and worthy of further investigation. Moreover, our calculations show that NO₂ can be oxidized by CH₃NO₂ to NO₃ radical, which confirms the conclusion reached formerly by Irikura and Johnson [(2006) J Phys Chem A 110:13974–13978] that NO₃ radical can be formed during the decomposition of nitramine explosives.     

The platinum-olefin binding energy in series of (PH<Subscript>3</Subscript>)<Subscript>2</Subscript>Pt(olefin) complexes - a theoretical study

Theoretical investigation of Pt(0)-olefin organometallic complexes containing tertiary phosphine ligands was focused on the strength of platinum-olefin electronic interaction. DFT theoretical study of electronic effects in a substantial number of ethylene derivatives was evaluated in terms of the Pt-olefin binding energy using MP2 correlation theory. Organometallics bearing coordinated olefins with general formula (R¹R²C = CR³R⁴)Pt(PH₃)₂ [R = various substituents] had been selected, including olefins containing both electron-donor substituents as well as electron-withdrawing groups. The stability of the corresponding complexes increases with a strengthening electron-withdrawal ability of the olefin substituents. Figure Representation of (CH₂ = CHR)Pt(PPh₃)₂ and the stability chart     

Metal-metal bonding and charge localisation in [Ru2X9], X=Cl or Br; n=1, 2, 3, 4. A spectroelectrochemical study

A spectroelectrochemical study of [Ru₂X₉]ⁿ⁻, X=Cl, Br; n=1, 2, 3, 4 has been undertaken. Stable solutions of n=4, 2, 1 can be formed by electrolysis at low temperatures. Analysis of the Vis-NIR spectra of the complexes indicate that the Ru^II---R^III dimers (n=4) have delocalised mixed valence and that the Ru^III---R^III (n=3) dimers have a strong Ru---Ru bond. The more oxidised materials do not form a Ru---Ru bond; the spectroscopic data indicates the Ru^III---R^IV dimers have localised valency.     

Theoretical study of the novel sandwich compound [Au<Subscript>3</Subscript>Cl<Subscript>3</Subscript>Tr<Subscript>2</Subscript>]<Superscript>2+</Superscript>

A theoretical study of a sandwich compound with a metal monolayer sheet between two aromatic ligands is presented. A full geometry optimization of the [Au₃Cl₃Tr₂]²⁺ (1) compound, which is a triangular gold(I) monolayer sheet capped by chlorines and bounded to two cycloheptatrienyl (Tr) ligands was carried out using perturbation theory at the MP2 computational level and DFT. Compound (1) is in agreement with the 18–electron rule, the bonding nature in the complex may be interpreted from the donation interaction coming from the Tr rings to the Au array, and from the back-donation from the latter to the former. NICS calculations show a strong aromatic character in the gold monolayer sheet and Tr ligands; calculations done with HOMA, also report the same aromatic behavior on the cycloheptatrienyl fragments giving us an insight on the stability of (1). The Au –Au bond lengths indicate that an intramolecular aurophilic interaction among the Au(I) cations plays an important role in the bonding of the central metal sheet. Figure (a) Ground state geometry of complex 1; (b) Top view of compound 1 and Wiberg bond orders computed with the MP2/B1 computational method; (c) Lateral view of compound 1 and NICS values calculated with the MP2/B1 method; the values in parenthesis were obtained at the VWN/TZP level