The O–H···O, O–H···N and C–H···O hydrogen bonds in 1,4-dimethylpiperazine mono-betaine monohydrate

1,4-Dimethylpiperazine mono-betaine (1-carboxymethyl-1,4-dimethylpiperazinium inner salt, MBPZ) crystallizes as monohydrate. The crystals are orthorhombic, space group Pccn. Two MBPZ molecules and two water molecules form a cyclic oligomer, (MBPZ·H₂O)₂. The O–H···O and O–H···N hydrogen bonds are of 2.769(1) and 2.902(1) Å, respectively. The dimers interact with the neighboring molecules through the C–H···O hydrogen bonds of 3.234(1) Å. The piperazine ring assumes a chair conformation with the N(4)–CH₃ and N⁺(1)–CH₂COO⁻ groups in the equatorial position and the N⁺(1)–CH₃ group in the axial one. The FTIR spectrum is compared with that calculated by the B3LYP/6-31G(d,p) level of theory.     

Intermolecular interactions in group 14 hydrides: Beyond CH···HC contacts

In line with previous work in which we established the factors that enhance attractive C?H···H?C dihydrogen interactions in alkanes, an extended theoretical analysis of noncovalent intermolecular interactions in group 14 hydrides is presented here. Remarkably, these weak interactions may play a major role in determining the crystal structures adopted by several families of molecules. A combined structural and computational analysis at the MP2 level allowed us to identify and characterize different interactions of the type E?H···H?E and E···H?E (E = Si, Ge, Sn, and Pb), and to find also the most suitable scenario for the establishment of each particular type. The nature of the interactions has been analyzed in terms of natural charges of the atoms involved and a topological analysis of the electron density of several dimers confirms the existence of H···H and H···E attractive contacts. We have observed that the interaction strength increases when descending down the periodic group and that silicon has a marked tendency to establish Si···H?Si interactions. A size‐dependent backbone effect that reinforces H···H dihydrogen interactions in polyhedral systems has also been found.     

From Isolated Polyanions to 1‐D Structure: Synthesis and Crystal Structure of Hybrid Fluorides {[(C2H4NH3)3NH]4+}2 · (H3O)+ · [Al7F30]9– and {[(C2H4NH3)3NH]4+}2 · [Al7F29]8– · (H2O)2

Two new hybrid fluorides, {[(C₂H₄NH₃)₃NH]⁴⁺}₂ · (H₃O)⁺ · [Al₇F₃₀]^9– ( I ) and {[(C₂H₄NH₃)₃NH]⁴⁺}₂ · [Al₇F₂₉]^8– · (H₂O)₂ ( II ), are synthesized by solvothermal method. The structure determinations are performed by single crystal technique. The symmetry of both crystals is triclinic, sp. gr. P 1, I : a = 9.1111(6) Å, b = 10.2652(8) Å, c = 11.3302(8) Å, α = 110.746(7)°, β = 102.02(1)°, γ = 103.035(4)°, V = 915.9(3) ų, Z = 1, R = 0.0489, R_w = 0.0654 for 2659 reflections, II : a = 8.438(2) Å, b = 10.125(2) Å, c = 10.853(4) Å, α = 106.56(2)°, β = 96.48(4)°, γ = 94.02(2)°, V = 877.9(9) ų, Z = 1, R = 0.0327, R_w = 0.0411 for 3185 reflections. In I , seven corner‐sharing AlF₆ octahedra form a [Al₇F₃₀]^9– anion with pseudo 3 symmetry; such units are found in the pyrochlore structure. The aluminum atoms lie at the corners of two tetrahedra, linked by a common vertex. In II , similar heptamers are linked in order to build infinite (Al₇F₂₉)_n^8– chains oriented along a axis. In both compounds, organic moieties are tetra protonated and establish a system of hydrogen bonds N–H…F with four Al₇F₃₀^9– heptamers in I and with three inorganic chains in II .     

An insight into CH···N hydrogen bond and stability of the complexes formed by trihalomethanes with ammonia and its monohalogenated derivatives

A theoretical study of the C?H···N hydrogen bond in the interactions of trihalomethanes CHX₃ (X = F, Cl, Br) with ammonia and its halogen derivatives NH₂Y (Y = F, Cl, Br) has been carried out thoroughly. The complexes are quite stable, and their stability increases in going from CHF₃ to CHCl₃ then to CHBr₃ when Y keeps unchanged. With the same CHX₃ proton donor, enhancement of the gas phase basicity of NH₂Y strengthens stability of the CHX₃···NH₂Y complex. The C?H···N hydrogen bond strength is directly proportional to the increase of proton affinity (PA) at N site of NH₂Y and the decrease of deprotonation enthalpy (DPE) of C?H bond in CHX₃. The CHF₃ primarily appears to favor blue shift while the red‐shift is referred to the CHBr₃. The blue‐ or red‐shift of CHCl₃ strongly depends on PA at N site of NH₂Y. We suggest the ratio of DPE/PA as a factor to predict which type of hydrogen bond is observed upon complexation. The SAPT2+ results show that all C?H···N interactions in the complexes are electrostatically driven regardless of the type of hydrogen bond, between 48% and 61% of the total attractive energy, and partly contributed by both induction and dispersion energies.     

17O, 13C and 1H NMR and IR spectral study of crowded ketones: possible intramolecular C—H···O interactions

Unusual behaviour was observed in the study of the ¹⁷O, ¹³C and ¹H NMR and IR spectra of crowded (1‐adamantyl)alkyl ketones. As the size of the alkyl substituent is increased, abnormal upfield chemical shifts in the ¹³C NMR and downfield shifts in the ¹⁷O NMR of the carbonyl group, as well as downfield shifts in the ¹H NMR of the adamantyl γ'‐protons, are found. In the IR spectrum, the ν_C?O stretching frequencies of the ketones with bulky substituents show considerable red shifts. Correlation of the NMR shifts with the number of γ‐carbon atoms of the alkyl substituents and comparison with the IR results indicated that there is an intramolecular through‐space CH···O interaction in crowded ketones. This was supported by the results of ab initio calculations. Copyright © 2002 John Wiley & Sons, Ltd.     

Using Me3Si–F–Al(ORF)3 and Me3Si–Cl as Methylating Agents – Synthesis and Characterization of SeMeCl2[F{Al(ORF)3}2]

Upon reacting SeCl₄ with Me₃Si–F–Al(OR^F)₃, the selenonium salt SeMeCl₂[al‐f‐al] ( 1 ) {[al‐f‐al]^– = [F[Al(OC(CF₃)₃)₃]₂]^–} was obtained and characterized by NMR, IR, and Raman spectroscopy as well as single crystal XRD experiments. Despite the [SeX₃]⁺ (X = F, Cl, Br, I) and [SeR₃]⁺ salts (R = aliphatic organic residue) being well known and thoroughly studied, the mixed cations are scarce. The only previous example of a salt with the [SeMeCl₂]⁺ cation is SeMeCl₂[SbCl₆], which was never structurally characterized and is unstable in solution over hours. Only ¹H‐NMR studies and IR spectra of this compound are known. The unexpected use of Me₃Si–F–Al(OR^F)₃ as a methylating agent was investigated via DFT calculations and NMR experiments of the reaction solution. The reaction of SeCl₃[al‐f‐al] with Me₃Si‐Cl at room temperature in CH₂Cl₂ proved to yield the same product with Me₃Si–Cl acting as a methylating agent.     

Probing Polyoxometalate–Protein Interactions Using Molecular Dynamics Simulations

The molecular interactions between the Ce^IV‐substituted Keggin anion [PW₁₁O₃₉Ce(OH₂)₄]^3? ( CeK ) and hen egg‐white lysozyme (HEWL) were investigated by molecular dynamics simulations. The analysis of CeK was compared with the Ce^IV‐substituted Keggin dimer [(PW₁₁O₃₉)₂Ce]^10? ( CeK₂ ) and the Zr^IV‐substituted Lindqvist anion [W₅O₁₈Zr(OH₂)(OH)]^3? ( ZrL ) to understand how POM features such as shape, size, charge, or type of incorporated metal ion influence the POM???protein interactions. Simulations revealed two regions of the protein in which the CeK anion interacts strongly: cationic sites formed by Arg21 and by Arg45 and Arg68. The POMs chiefly interact with the side chains of the positively charged (arginines, lysines) and the polar uncharged residues (tyrosines, serines, aspargines) via electrostatic attraction and hydrogen bonding with the oxygen atoms of the POM framework. The CeK anion shows higher protein affinity than the CeK₂ and ZrL anions, because it is less hydrophilic and it has the right size and shape for establishing interactions with several residues simultaneously. The larger, more negatively charged CeK₂ anion has a high solvent‐accessible surface, which is sub‐optimal for the interaction, while the smaller ZrL anion is highly hydrophilic and cannot efficiently interact with several residues simultaneously.     

Molecular structure, IR spectra of 2-mercaptobenzothiazole and 2-mercaptobenzoxazole by density functional theory and ab initio Hartree–Fock calculations

Quantum chemistry calculations have been performed using Gaussian03 program to compute optimized geometry, harmonic vibrational frequency along with intensities in IR and Raman spectra and atomic charges at RHF/6-31+G*, B3LYP/6-31+G* and B3LYP/6-31++G* levels for 2-mercaptobenzothiazole (MBT, C₇H₅NS₂) and 2-mercaptobenzoxazole (MBO, C₇H₅NOS) in the ground state. The scaled harmonic vibrational frequencies have been compared with experimental FT-IR and FT-Raman spectra. The results show that the scaled theoretical vibrational frequencies is very good agreement with the experimental values. A detailed interpretation of the infrared and Raman spectra of 2-mercaptobenzothiazole and 2-mercaptobenzoxazole was reported. Comparison of calculated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes.     

Elaboration of modelized surfaces with well defined microtopochemistry–localization of adsorbed proteins

Using microphotolithographic techniques, we have been able to devise silica surfaces bearing two types of microdomains with an average width of 40μm. One of the microdomain types was silanized in order to make them hydrophobic. Fourier transform-infrared (FTIR) and Auger electron spectroscopies (AES) were used to check the presence of the expected chemical groups on the modified silica surface. Silica and silanized surface morphology was studied using Scanning Force Microscopy (SFM). Wetting properties were investigated. Protein adsorption studies were performed using diluted human decalcified plasma. Attention was focused on the topographic distribution of the adsorbed molecules in order to establish a correlation between the protein behaviour and the specific chemistry of each type of microdomain.     

Preparation of Aluminum Alkoxides and Crystal Structures of [Al{(S)-(-)-μ-OC(H)(CH3)C(Ph)2OH}Cl2]2·2Et2O and [(μ-O(CH2)2OPh)AlMe2]2

The reaction of (S)-(-)-1, l-diphenyl-propane-1,2-diol with AlCl₃ in diethyl ether furnishes the product [Al((S)-(-)-μ₂-OC(H)(Me)C(Ph)₂OH)Cl₂]₂ 1, which decomposes slowly above 25 °C. Complex 1·2Et₂O Crystallizes in the non-centrosymmetric monoclinic space group P2₁ with a=10.591(1) Å, b=16.718(1) Å, c = 12.156(2) Å, β=99.30(2)°, V = 2124.1(3) Å₃, z = 4, R = 4.67%, Rw=4.84%, GoF=1.14. The structure of 1 shows a dimer feature, which is hydrogen bonded to two diethyl ether molecules. In the reaction of 2-phenoxyethanol with AlMe₃, the dimeric [(μ-O(CH₂)₂OPh)AlMe₂]₂ is obtained in high yield. 2 crystallizes in the monoclinic space group P2₁/c with a = 7.398(2) Å, b = 7.376(2) Å, c = 20.710(2) Å, β = 90.56(2)°, v = 1129.9(4) ų, z=4, R=5.70%, Rw=7.15%, GoF=1.59.     

Radicals formed in cytosine–hydrochloride(thiocytosine) single crystals: Insights from a DFT study

Specific properties of chlorine interaction with thiocytosine in comparison to chlorine interaction with cytosine in the system formed by the incorporation of small amount of thiocytosine in a cytosine–hydrochloride crystal lattice have been investigated by DFT calculations of the g-tensor of sulfur centered radical. Taking account of the crystal environment of the radical site it has been shown that the main reason for difficulties in interpretation of spectroscopic as well as theoretical results in this model system is the considerable spin density spread on both chlorine and sulfur atoms. From comparison of the results for the proposed model structure with accessible spectroscopic data, the specific direction in which charge transfer in the investigated system may take place has been pointed out.     

C—H···X (X = N,O, S) intramolecular interaction in 1‐vinyl‐2‐(2′‐heteroaryl)pyrroles as monitored by 1H and 13C NMR spectroscopy

¹H and ¹³C NMR spectroscopy of a series of 1‐vinyl‐2‐(2′‐heteroaryl)‐pyrroles were employed for the analysis of their electronic and spatial structure. The C—H···N intramolecular interaction between the α‐hydrogen of the vinyl group and the pyridine nitrogen, a kind of hydrogen bonding, was detected in 1‐vinyl‐2‐(2′‐pyridyl)pyrrole, which disappeared in its iodide methyl derivative. It was shown that this interaction is stronger than the C—H···O and C—H···S interactions in 1‐vinyl‐2‐(2′‐furyl)‐ and ‐2‐(2′‐thienyl)‐pyrroles. Copyright © 2001 John Wiley & Sons, Ltd.     

Zum Verlauf der Hydratation von 3 CaO · Al2O3 in den Primärstadien

On Hydration of 3 CaO · Al₂O₃ in the Initial Stages Differential calorimetric analysis, chemical analysis of liquid phase, x-ray diffraction, DTA, and Kr-adsorption have been used to study the primary hydration of 3 CaO · Al₂O₃. It is shown that the primary hydration is attributed to the formation of a reaction layer on the surface of 3 CaO · Al₂O₃ and that in the time of hydration take place oscillating processes.     

Electronic structure of DNA dimer units,d(AG) · d, (CT), d(TG) · d(CA), · d(GT), and d(GA), in A and B conformations by DV–Xα cluster calculations

The electronic structure of d(AG) · d(CT), d(TG) · d(CA), d(AC) · d(GT), and d(TC) · d(GA), which are stacked base pairs in the DNA double helix, are elucidated for A and B conformations in detail by DV -X α cluster calculations. By using the S?_r values of the O2 (and O3) of each phosphate in the clusters together with those calculated in previous articles, it becomes possible to treat chemical reactivities of phosphates as recognition sites for all DNA fragments. Contour maps of the wave function of the HOMO and LUMO for bases differ subtly among the clusters and show the various fields around the P ion induced by the respective stacking constructed from four kinds of bases. © 1994 John Wiley & Sons, Inc.     

A Light‐Controlled Molecular Brake with Complete ON–OFF Rotation

A light‐controlled molecular machine based on cyclic azobenzenophanes consisting of a dioxynaphthalene rotating unit and a photoisomerizable dioxyazobenzene unit bridged by methylene spacers is reported. In compounds 1 and 2 , 1,5‐ and 2,6‐dioxynaphthalene moieties, respectively, are linked to p‐dioxyazobenzene by different methylene spacers (n=2 in 1 a and 2 ; n=3 in 1 b ), whereas a 1,5‐dioxynaphthalene moiety is bonded to m‐dioxyazobenzene by bismethylene spacers in 3 . In 1 b and 2 , the naphthalene ring can rotate freely in both the trans and cis states at room temperature. The rotation speed can be controlled either by photoinduced reversible trans–cis (E–Z) isomerization of the azobenzene or by keeping the system at low temperature, as is evident from its NMR spectra. Furthermore, for the first time, we demonstrate a light‐controlled molecular brake, wherein the rotation of the naphthalene moiety through the cyclophane is completely OFF in the trans isomer of compound 3 due to its smaller cavity size. Such restricted rotation imparts planar chirality to the molecule, and the corresponding enantiomers could be resolved by chiral HPLC. However, the rotation of the naphthalene moiety is rendered ON in the cis isomer due to its increased cavity size, and it is manifested experimentally by the racemization of the separated enantiomers by photoinduced E–Z isomerization.     

Polysulfonylamine. CLXVI [1] Kristallstrukturen von Metall‐di(methansulfonyl)amiden. 15 [1] Die isotypen Kristallstrukturen von Ammonium‐ und Caesium‐dimesylamid: Kristallographische Kongruenz zwischen Wasserstoffbrücken N—H···O/N und Metall‐Ligand‐Bindungen Cs—O/N

Polysulfonylamines. CLXVI. Crystal Structures of Metal Di(methanesulfonyl)amides. 15. The Isotypic Crystal Structures of Ammonium and Cesium Dimesylamide: Crystallographic Congruency of Hydrogen Bonds N—H···O/N and Metal‐Ligand Interactions Cs—O/N The ammonium salt NH₄[N(SO₂CH₃)₂] and its previously reported cesium analogue Cs[N(SO₂CH₃)₂] are isostructural (monoclinic, space group P2₁/n, Z = 4, V at —140 °C: 0.761 and 0.832 nm³ respectively). The cesium ion adopts an irregular (O₆N)‐heptacoordination by forming close contacts to one (O, N)‐chelating, one (O, O)‐chelating and three κ¹O‐bonding anions, whereas in the ammonium‐based structure each of the seven Cs—O/N interactions is perfectly mimicked by an N—H···O/N hydrogen‐bond component. To this effect, three N—H donors are engaged in asymmetric three‐centre bonds, the fourth in a moderately strong and approximately linear two‐centre bond. The crystal packings consist of anion monolayers that intercalate planar zigzag rows of cations propagating around symmetry centres (Cs···Cs alternatingly 422.5 and 487.5 pm, Cs···Cs···Cs 135.7°; N···N alternatingly 397.4 and 474.1 pm, N···N···N 136.1°). Each cation row is surrounded by and bonded to four translation‐generated anion stacks, and each anion stack connects two cation rows. The net effect is that the packings display congruent three‐dimensional networks of metal‐ligand bonds or hydrogen bonds, respectively. Moreover, close C—H···O/N interanion contacts consistent with weak hydrogen bonding are observed in both structures.     

A density functional study of N NQR parameters of imidazole derivatives and extrapolation to PfHRP2–Fe-PPIX complex

In this paper, density functional theory (DFT) was used to calculate ¹⁴N nuclear quadrupole coupling constants (NQCC), χ, and asymmetry parameters, η, for a series of imidazole derivatives: imidazole, 5-methylimidazole and histidine. These calculations were carried out with the PW91P86 method via the Gaussian 98 package. A systematic theoretical investigation of the different environmental effects on (χ, η) values of amino ¹⁴N1 and imino ¹⁴N2 of imidazole ring of these compounds, reveals that the local surrounding of nitrogen atoms play an important role in determining their χ and η values. Our calculations in solution show that adding explicit solvent molecules to the polarizable continuum model (PCM) has a strong effect on (χ, η) values, thereby indicating that for long-range effects, PCM, is not sufficient to describe the whole solvent effects. We also evaluate the influence of [Fe³⁺ (S = 1/2)] on the (χ, η) values of proximal and remote nitrogens of an axial ligand and compare with those of free ligands. The results show that Fe³⁺ has a strong effect on the (χ, η) values of proximal nitrogen unlike remote nitrogen. Finally, our results predict (χ = 1.56 MHz, η = 0.690) for proximal nitrogen and (χ = 2.75 MHz, η = 0.169) for remote nitrogen in PfHRP2–Fe³⁺-PPIX complex.