Reactions of palladium (II) chloride with 1,4 - diphenyl - 2,3 - dimethyl - 1,4 - diazabutadiene and 1,4-DI(p-methoxyphenyl)-2,3-dimethyl- 1,4 - diazabutadiene

The reactions of palladium(II) chloride with 1,4 - diphenyl - 2,3 - dimethyl - 1,4 - diazabutadiene and 1,4 - di(p - methoxyphenyl) - 2,3 - dimethyl - 1,4 - diazabutadiene are described. With 1,4 - diphenyl - 2,3 - dimethyl - 1,4 - diazabutadiene diimine fission is produced, giving rise to a product identified by elemental analysis, IR and Raman spectra, and X-ray diffraction, as trans-dichlorobis(aniline) palladium(II). The complex is soluble in dimethylformamide and crystallizes with two molecules of solvent. The substance crystallizes in the monoclinic space group P2₁/n. The X-ray data were refined to R = 0.047 and R_w = 0.046. Final distances are PdN = 2.060(5)Åand PdC1 = 2.299(2)Å. There are two bifurcated intermolecular NH ... C1 and CH... C1 hydrogen bonds which, together with one more intermolecular hydrogen bond NH... O, are responsible for the packing of the molecules. However, when 1,4 - di(p - methoxyphenyl) - 2,3 - dimethyl - 1,4 - diazabutadiene was treated with palladium chloride under the same conditions cis - dichloro - 1,4 - di(p - methoxyphenyl) - 2,3 - dimethyl - 1,4 - diazabutadiene was formed, as deduced from elemental analysis, and IR and Raman spectra.     

Heterolytic Cleavage of Hydrogen by an Iron Hydrogenase Model: An Fe‐H⋅⋅⋅H‐N Dihydrogen Bond Characterized by Neutron Diffraction

Hydrogenase enzymes in nature use hydrogen as a fuel, but the heterolytic cleavage of H? H bonds cannot be readily observed in enzymes. Here we show that an iron complex with pendant amines in the diphosphine ligand cleaves hydrogen heterolytically. The product has a strong Fe‐H???H‐N dihydrogen bond. The structure was determined by single‐crystal neutron diffraction, and has a remarkably short H???H distance of 1.489(10) Å between the protic N‐H^δ+ and hydridic Fe‐H^δ? part. The structural data for [CpFe H (P^tBu₂N^tBu₂ H )]⁺ provide a glimpse of how the H? H bond is oxidized or generated in hydrogenase enzymes. These results now provide a full picture for the first time, illustrating structures and reactivity of the dihydrogen complex and the product of the heterolytic cleavage of H₂ in a functional model of the active site of the [FeFe] hydrogenase enzyme.     

Crystal Structure of the Complex of 1,2-Bis[2-(o-hydroxyphenoxy)ethoxy]ethane with Ammonium Thiocyanate

The complex of the podand 1'2-bis[2-(o-hydroxyphenoxy)ethoxy]ethane (L) with ammoniumthiocyanate, [NH₄(SCN)L], was prepared, studied by single crystal X-ray diffraction. This is a host-guestcomplex; in its molecule the podand L is wrapped around the NH ₄ ⁺ cation, which forms hydrogen bondswith all the six oxygen atoms of the podand and one hydrogen bond with the sulfur atom of the SCN^- anion. The geometric parameters (bond lengths, bond angles, torsion angles, etc.) of the molecule of [NH₄(SCN)L] and packing of the molecules in the crystal were determined. The molecules are linked into infinite polymeric chains by intermolecular hydrogen bonds O-H···NCS.     

Solvatochromism of Heteroaromatic Compounds: VII. Bifurcate Hydrogen Bond in Solvatochromic Complexes of 2-(1,2,2-Tritricyanovinyl)pyrrole

IR and UV spectrosocopy and quantum chemistry were used to reveal a bifurcate (three-center) hydrogen bond in the complexes of 2-(1,2,2-tricyanovinyl)pyrrole with hydrogen-bond acceptors. In the gas phase and aprotic inert solvents this compound exists predominantly as the sp conformer stabilized by intra- molecular hydrogen bond involving an orthogonal system of the nitrile group and the NH hydrogen. The formation of the three-center hydrogen bond with an aprotic protophilic solvent shifts the conformational equilibrium to the ap conformer. As the strength of the intermolecular hydrogen bond increases in the series nitromethane < acetonitrile < dioxane, the fraction of the ap conformer increases and becomes prevailing already in the moderately protophilic THF. Solvatochromism of the long-wave absorption band in the elec- tronic spectra of the sp and ap conformers was studied in detail.     

Effect of Doped Transition Metal on Reversible Hydrogen Release/Uptake from NaAlH4

Storage facility : A dihydrogen complex formed in transition‐metal‐doped NaAlH₄ was found to play important roles in hydrogen release/uptake (see figure). Electronic structure analysis revealed that the electron transfer between hydrogen and Al groups was mediated by the d orbitals of transition metals. Hydrogen release/uptake from the transition‐metal‐doped NaAlH₄ was accompanied by an exchange of Al? H and H? H bond ligands through σ‐bond metathesis.

     

Correlating Boron–Hydrogen Stretching Frequencies with Boron–Hydrogen Bond Lengths in Closoboranes: An Approach Using DFT Calculations

Using harmonic and anharmonic DFT calculations, we have established a general correlation between B–H stretching frequencies and B–H bond lengths valid for the closoboranes (x = 6 – 12), substituted closoboranes B₁₂H_{12 –} (with X = F, Cl, Br and n = 1 – 3 and 9 – 12) and the carboranes and , suggesting that this correlation is also applicable to other similar species. It appears that the average B–H stretching frequency observed around 2500 cm⁻¹ shift by about −100 cm⁻¹ if the average B–H bond length increases by 1 pm. In contrast to , the B–H bond in closoboranes is practically covalent and the correlation evidenced between its stretching frequency and its length proves to be similar to the one observed for the C–H bond.     

Supramolecular amide and thioamide synthons in hydrogen bonding patterns of N-aryl-furamides and N-aryl-thiofuramides

The supramolecular synthon of amide group in the primary and secondary amides is well recognized to be infinite chains of the C(4) type formed by the intermolecular hydrogen bond of the type N–HO=C. On the other hand, there is a lack of structural data for the thioamides. Three compounds belonging to the class of N-aryl-fura-mides (N-(4-bromophenyl)-5-bromo-2-furancarboxamide, N-(4-chlorophenyl)-5-bromo-2-furancarboxamide) and to the class of N-aryl-thiofuramide (N-(4-methoxyphenyl)-2-furanthiocarboxamide) are prepared and characterized by the NMR spectroscopy in solution; molecular and crystal structures in the solid state have been determined by X-ray single crystal diffractometry and the structures in the gas phase by DFT and AM1 calculations. The investigation is carried out in order to establish supramolecular amide and thioamide synthons of hydrogen bonding patterns in these crystal structures. The geometry of the N–HO=C and the N–HS=C type of hydrogen bonds are compared due to the possibility of the N–H amide group to form intramolecular hydrogen bond with the furan oxygen atom, thus, commonly, leading to the three-center hydrogen bond pattern. The competition between the S=C proton acceptor of thioamides and the other proton acceptors (such as methoxy group) for the amide N–H proton donor group has been investigated. In that context, the above-mentioned compounds are correlated with the others of this class, structurally determined, so far.     

Hydride‐Triel Bonds

In this article, we present the results of our comprehensive studies of 72 dimers of the type (X = Si, Ge; Y = B, Al, Ga; R^X = H, Cl, Me; R^Y = H, F, Cl, Me) and featuring hydride‐triel bonds (i.e., charge‐inverted hydrogen bonds). Influence of X and Y atoms as well as R^X and R^Y substituents on various properties of these dimers is investigated in detail. In particular the strength of the H⋯Y hydride‐triel bonds is paid a close attention and it is shown that hydride‐triel bonds can be strong enough to considerably determine structure and properties of molecular systems. In addition, properties of the investigated dimers are largely governed by the charge transfer from the Lewis base to the Lewis acid, which is particularly important if more bulky and polarizable R^Y and Y atoms are present in the molecule. Several excellent linear (R² close to 1) and exponential correlations between pairs of diverse parameters are presented. Few instances are discussed where somewhat unexpected bond paths exist between two atoms featuring partial negative charges (e.g., between hydride hydrogen and halogen and between lateral sides of two halogens) showing that in some cases a bond path prefers to link two closely spaced electron‐rich atoms instead of two atoms that are expected to form a bond. © 2018 Wiley Periodicals, Inc.     

Hydrogen bonds in carbonylated 1,4-dihydropyridines

For H bonds stabilized by π-conjugation in carbonylated 1,4-dihydropyridines, an analysis of the structural data of the Cambridge Structural Databank showed that the hydrogen bond was an essential condition for π-conjugation. It was found that π-delocalization possibly correlated with the bioactivity of drugs that were calcium antagonists. In the presence of two carbonyl groups, hydrogen bonds in crystal are predominantly formed by the carbonyl group that is anti-periplanar to the 1,4-dihydropyridine ring.     

Stereochemistry of Seven-Membered Heterocycles: XLII. A Theoretical Study of Stereochemistry of H Complexes Formed by Conformationally Nonuniform 2-R-1,3-Dioxacyclohept-5-enes with Some Proton Donors

According to semiempirical AM1 calculations, the stability of the boat and twist forms of 2-R-1,3- dioxacyclohept-5-enes depends on the size of substituents at the acetal carbon atom. The twist form gives diastereomeric H complexes with chloroform and methanol of the cis and trans structure, containing monocentered hydrogen bonds, whereas the chair conformation preferably forms complexes with a two-centered hydrogen bond. Based on theoretical data (_{O H}, H, geometry of complexes), the specific features of H complexes of the conformers in electrophilic addition and cycloaddition were revealed. Considerable preferableness of the exo attack of the diastereotopic double bond in the H complex having the chair form is due to the steric accessibility of the exo side, whereas in the complexes of the twist form the facial selectivity is appreciably lower.     

Effect of Hydrogen Bonds on Structures and Glass Transition Temperatures of Maleimide–Isobutene Alternating Copolymers: Molecular Dynamics Simulation Study

The objective of this paper is to use molecular dynamics (MD) simulation to study the influence of hydrogen bonding on the structure and glass transition temperature (T_g) of maleimide–isobutene alternating copolymers (poly(RMI‐alt‐IB)), a promising material used in the optoelectronics industry. The T_g obtained by MD simulation shows that the incorporation of hydrogen bonding increased the T_g for 48 K. The static and dynamic properties of poly(RMI‐alt‐IB)s are examined in this study. All the results prove that intermolecular CO…H O is the main hydrogen bond in the copolymers, while negligible intramolecular hydrogen bonding is observed. The segmental mobility and chain mobility are decreased because of the existance of the hydrogen bonds.

     

Matrix-isolation infrared spectra of 2-, 3- and 4-pyridinecarboxaldehyde before and after UV irradiation

Three structural isomers of pyridinecarboxaldehydes (2-, 3- and 4-pyridinecarboxaldehyde) have been investigated in detail with matrix-isolation infrared spectroscopy in the 3000–600 cm⁻¹ region, combined with the UV photo-excitation and density-functional theory (DFT) calculations. Two rotamers (anti and syn) for 2- and 3-pyridinecarboxaldehyde (2- and 3-PCA, respectively) and one rotamer for 4-pyridinecarboxaldehyde (4-PCA) were identified upon photo-excitation. Most of the observed bands of each rotamer have been assigned. Both the infrared data and the results of the DFT calculations agree that the syn rotamer is a less stable isomer for 2- and 3-PCA. Formation of an intramolecular CH⋯N hydrogen bond in the anti rotamer of 2-PCA results in a shortening of the aldehyde CH bond length. The CO bond length is shortened in the syn rotamer due to the repulsion between the N and aldehyde O atoms. With 2-PCA, both photoinduced rotational isomerism and photolysis were observed upon UV irradiation.     

Kinetics and thermochemistry of the gas phase reaction of methyl ethyl ketone with iodine. I. The resonance energy of the methylacetonyl radical

The gas phase reaction of iodine (2.8–43.3 torr) with methyl ethyl ketone (MEK) (7.4–303.4 torr) has been studied over the temperature range 280–355°C in a static system. The initial rate of disappearance of I₂ is first order in MEK and half order in I₂. The rate-determining step is the abstraction of a secondary hydrogen atom by an iodine atom: where k₁ is given by and θ = 2.303RT in kcal/mole. This activation energy is equivalent to a secondary C? H bond strength of 92.3 ± 1.4 kcal/mole and ΔH of the methylacetonyl radical = -16.8 ± 1.7 kcal/mole. By comparison with 95 kcal/mole for the secondary C? H bond strength, when delocalization of the unpaired electron with a pi bond is not possible, the resonance stabilization of the methylacetonyl radical is calculated to be 2.7 ± 1.7 kcal/mole. This value is 10 kcal/mole less than the stabilization energy of the isoelectronic methylallyl radical. The difference in pi bond energies in the canonical forms of the methylacetonyl radical is shown to account for the variation in stabilization energies.     

Influence of the position of the nitro group on the structural and spectroscopic characteristics of N"-(nitrobenzylidene)isonicotinic hydrazides in the crystalline state

N"-Substituted isonicotinic hydrazides of the general formula Py—C(=O)—N(H)-N"=C(H)—R, where R is o- (1), m- (2), or p-nitrophenyl (3), were studied by IR spectroscopy and X-ray diffraction analysis. The position of the nitro group in these compounds has no effect on the type of the crystal structure. The crystal packings are based on stacks consisting of antiparallel planar molecules. The molecules from the adjacent stacks are linked to each other via the N—H...N_Py hydrogen bonds. Depending on the position of the nitro group, the N...N_Py distance increases in the series 3 > 1 > 2 and the energy of the hydrogen bonds decreases (according to the IR spectroscopic data) from 3.9 to 3.1 kcal mol^–1. Analysis of the IR spectra demonstrated that the intensity of absorption in the (C—H) stretching region of the pyridine ring increases substantially as the the N—H...N_Py hydrogen bond is strengthened. Some regularities of the changes, which are observed for the (NO₂) bands in the spectra of the nitrophenyl-containing conjugated molecules in solutions, persist in the crystalline state.     

Computational reexamination of the eclipsed conformation in cis-2-tert-butyl-5-(tert-butylsulfonyl)-1,3-dioxane

The conformational free energy differences, ΔG° values, for the methyl sulfide, methyl sulfoxide, methyl sulfone, tert-butyl sulfide, tert-butyl sulfoxide, and tert-butyl sulfone groups at C(5) in the 1,3-dioxane ring have been calculated at two different levels, B3LYP/6-31G(d) and B3LYP/6-311++G(d,p). There is good agreement between experimental and calculated values, particularly in the case of data obtained at the lower level of theory, B3LYP/6-31G(d). In order to get information that could help understand the nature of the effects present in the molecules of interest, the charge distribution in representative compounds was analyzed by means of the natural bond orbital (NBO) analysis. NBO calculations indicate the existence of substantial negative charges at oxygen and significant positive charge at sulfur. This observation seems to support the argument the existence of electrostatic, attractive interactions between the endocyclic oxygens and the axial sulfonyl group. From the second order perturbation theory analysis of Fock matrix, two σ _C–C → σ*_S–O delocalizing interactions are observed in the methyl-inside conformer of cis-2-tert-butyl-5-(methylsulfonyl)-1,3-dioxane derivative cis-7. These results are in line with anti-periplanar σ _C–C → σ*_S–O hyperconjugative interactions that help stabilize the methyl-inside conformation of cis-7, as previously found by ¹H NMR analysis. By contrast, NBO analysis does not provide evidence for the existence of σ _C–C → σ*_S–O hyperconjugative interactions that might help stabilize the eclipsed tert-butyl—outside conformation previously found in the solid-state crystallographic structure of analog cis-1. Because of the threshold value of the NBO calculations, if present such syn-periplanar stereoelectronic interaction should be less than 0.5 kcal mol^?1. This observation suggests that an anti-periplanar orientation of the interacting orbitals is more effective relatively to the corresponding syn-periplanar orientation.     

Difference of Electron Capture and Transfer Dissociation Mass Spectrometry on Ni<Superscript>2+</Superscript>-, Cu<Superscript>2+</Superscript>-, and Zn<Superscript>2+</Superscript>-Polyhistidine Complexes in the Absence of Remote Protons

Electron capture dissociation (ECD) and electron transfer dissociation (ETD) in metal-peptide complexes are dependent on the metal cation in the complex. The divalent transition metals Ni²⁺, Cu²⁺, and Zn²⁺ were used as charge carriers to produce metal-polyhistidine complexes in the absence of remote protons, since these metal cations strongly bind to neutral histidine residues in peptides. In the case of the ECD and ETD of Cu²⁺-polyhistidine complexes, the metal cation in the complex was reduced and the recombination energy was redistributed throughout the peptide to lead a zwitterionic peptide form having a protonated histidine residue and a deprotonated amide nitrogen. The zwitterion then underwent peptide bond cleavage, producing a and b fragment ions. In contrast, ECD and ETD induced different fragmentation processes in Zn²⁺-polyhistidine complexes. Although the N–C_α bond in the Zn²⁺-polyhistidine complex was cleaved by ETD, ECD of Zn²⁺-polyhistidine induced peptide bond cleavage accompanied with hydrogen atom release. The different fragmentation modes by ECD and ETD originated from the different electronic states of the charge-reduced complexes resulting from these processes. The details of the fragmentation processes were investigated by density functional theory.

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Graphical Abstract ?

     

Structural and vibrational study on N-(biphenyl-2-thiocarbamoyl)-4-phenylcarboxamide

A new thiourea derivative, N-(biphenyl-2-thiocarbamoyl)-4-phenylcarboxamide, is synthesized and characterized by elemental analysis, FTIR, NMR and the single crystal X-ray diffraction study. The title compound crystallizes with two molecules in the asymmetric unit. The dihedral angle between the two aromatic rings in the biphenyl unit is 47.9(2) and 56.52(19)°, respectively, for the two molecules in the asymmetric unit. The molecular conformation is stabilized by intramolecular NH?O hydrogen bond. The crystal packing shows that the molecules form centrosymmetric dimers connected by NH?S hydrogen bonds. The vibrational properties have been studied by FTIR and FT-Raman spectroscopy along with quantum chemical calculations at the B3LYP/6-311 + G^* level of approximation. The main normal modes related with the thioamide bands are discussed.     

Spatial and Electronic Structure of 2-(2-Furyl)- and 2-(2-Thienyl)pyrroles According to 1H and 13C NMR Data

In 2-(2-furyl)- and 2-(2-thienyl)pyrroles the heterocycles are in efficient ,-conjugation. The presumably possible for this compounds intramolecular hydrogen bond N-H···O or N-H···S is lacking. The COCF₃ group in position 2 of the pyrrole ring is syn-oriented with respect to pyrrole fragment, and the orientation is fixed by an intramolecular hydrogen bond N-H···O. However no bifurcating hydrogen bonds arise in the molecules containing COCF₃ group.     

Conformational Equilibrium of 4-Hydroxy- and 4-Acetoxy-4-(3-aryloxy-1-propynyl)-1-(2-ethoxyethyl)piperidinium Salts in Solution

4-Hydroxy- and 4-acetoxy-4-(3-aryloxy-1-propynyl)-1-(2-ethoxyethyl)piperidine hydroclorides in aprotic solvents give rise to equilibrium mixtures of two epimers. In the case of the acetoxy derivatives (in CDCl₃) the equilibrium is displaced toward the less stable epimer. This may be due to considerable contribution of the skewed boat conformer with intramolecular hydrogen bond.     

Tetrahydro-1,4-epoxynaphthalene-1-carboxylic acid: a chiral derivatizing agent for the determination of the absolute configuration of secondary alcohols

A new chiral derivatizing agent, tetrahydro-1,4-epoxynaphthalene-1-carboxylic acid (THENA), with a represented syn-periplanar disposition of O-C_α-CO as a part of the bicyclic system to lock the aromatic residue conformation and the availability of an internal reference proton for ¹H NMR spectral alignment, is introduced. In the determination of the absolute configuration of chiral secondary alcohols, THENA offered good uniformity of Δδ with high reliability, resulting in unambiguous assignment of the absolute configuration.