MNDO calculations on hydrogen bonds. Modified function for core-core repulsion

The MNDO method has been modified to calculate the properties of the structures involving hydrogen bonds X···H—Y, X, Y = N, O and F. A new method (referred to as MNDO/H) has been tested by calculation of a wide range of molecular systems with weak and strong (ionic) hydrogen bonds. The results obtained are in good agreement with the experimental data. In the cases where direct comparisons are possible, the MNDO/H method seems to give more accurate values of hydrogen bond energy than the ab initio method using STO-4-31G basis set.     

Charge‐Shift Bonding: A New and Unique Form of Bonding

Charge‐shift bonds (CSBs) constitute a new class of bonds different than covalent/polar‐covalent and ionic bonds. Bonding in CSBs does not arise from either the covalent or the ionic structures of the bond, but rather from the resonance interaction between the structures. This Essay describes the reasons why the CSB family was overlooked by valence‐bond pioneers and then demonstrates that the unique status of CSBs is not theory‐dependent. Thus, valence bond (VB), molecular orbital (MO), and energy decomposition analysis (EDA), as well as a variety of electron density theories all show the distinction of CSBs vis‐à‐vis covalent and ionic bonds. Furthermore, the covalent–ionic resonance energy can be quantified from experiment, and hence has the same essential status as resonance energies of organic molecules, e.g., benzene. The Essay ends by arguing that CSBs are a distinct family of bonding, with a potential to bring about a Renaissance in the mental map of the chemical bond, and to contribute to productive chemical diversity.     

Intermolecularly Hydrogen-Bonded Dimeric Helices. Tripyrrindiones

A rare and unusual class of tripyrrolic compounds, violet-colored tripyrrin-1,14-diones, can be prepared easily and in moderately high yields from base (piperidine)-catalyzed condensation of 3-pyrrolin-2-ones with 2,5-diformylpyrroles. Dipyrrinones adopt the all-syn-Z conformation leading to helical, lock-washer like structures, which form dimers that are held together by intermolecular hydrogen bonds in nonpolar solvents and in the crystal. Strong bathochromic spectral shifts of the tripyrrindione ∼480 nm long wavelength UV-visible absorption band are seen with added base: DBU, 615 nm; TFA, 573 nm; and Zn(OAc)₂, 586 nm.     

Metal-metal quadruple bonds: New frontiers for their kith and kin

The entire range of compounds related to, as weil as including those containing, quadruple bonds between metal atoms is reviewed, briefly and historically, and some prospects for future work are considered.     

Physical gelation of melamine formaldehyde resin solutions. II. A combined light-scattering and low-resolution relaxation proton NMR study

The kinetics of physical gelation in aqueous melamine formaldehyde (MF) resin solutions were studied with the aid of low-resolution ¹H NMR T₂ relaxation experiments in combination with both static and dynamic light-scattering measurements. The investigations were conducted on a series of MF resins with increasing degrees of condensation. We show that MF aggregates (aided by hydrogen bonds) were immediately formed upon cooling from reaction to room temperature, that is, storage temperature. Surprisingly, the growth of these aggregates, which eventually led to the formation of a physical gel, did not have a major effect on molecular mobility. By means of light-scattering experiments, we were able to monitor the increase of the size of MF aggregates as a function of storage time. The physically gelled MF solutions were subjected to heating and subsequent cooling runs and again studied by light-scattering and nuclear magnetic resonance (NMR) experiments. MF aggregates were destroyed, depending on the degree of condensation, in the temperature range 35–60 °C according to NMR, and 40–75 °C as determined by light scattering. The process of physical gelation was reversible; upon subsequent cooling, the MF aggregates were formed anew. © 1999 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 37: 3307–3318, 1999     

Zipped-up chain-type coordination polymers: unsymmetrical amide-containing ligands inducing beta-sheet or helical structures. kazu-u@yamaguchi-u.ac.jp

The crystal structures of thirteen AgI coordination polymers involving py-CONH-(CH2)n-py (py=pyridine; n=0, 1) derivatives were determined by means of single-crystal X-ray analyses. All of the compounds form one-dimensional chains composed of AgI atoms and bridging ligands with formulas [[Ag(py-CONH-(CH2)n-py)][X]]n (X=PF6 -, ClO4 -, BF4 -, and NO3 - with solvent molecules). The unsymmetrical coordination environments around AgI atoms induce direction in the chains, that is, -[NH-(CH2)n-py-Ag-py-CO]-, which resembles the alignment of amino acid chains in proteins. In compounds [[Ag(4-pia)][X]]n (1 supersetX; 4-pia=N-(4-pyridyl)isonicotinamide; X=PF6 -, ClO4 -, BF4 -, and NO3 -), [[Ag(4-pmia)][X]]n (2 supersetX; 4-pmia=N-(pyridin-4-ylmethyl)isonicotinamide; X=PF6 -, ClO4 -H2O, and NO3 -H2O), and [[Ag(3-pmia)][X]]n (3 supersetX; 3-pmia=N-(pyridin-3-ylmethyl)isonicotinamide; X=PF6 -, ClO4 -, BF4 -, and NO3 -H2O), each chain is aligned parallel to neighboring chains, but adjacent chains run in the opposite direction. Particularly in [[Ag(3-pmia)][PF6]]n (3 supersetPF6 -), [[Ag(3-pmia)][ClO4]]n (3 supersetClO4 -), and [[Ag(3-pmia)][BF4]]n (3 supersetBF4 -), amide moieties of 3-pmia ligands are complementarily hydrogen bonded to amide moieties in neighboring chains, as in the beta-sheet motif in proteins. On the other hand, in [[Ag(4-pmna)][PF6]MeOH]n (4-pmna=N-(pyridin-4-ylmethyl)nicotinamide), all chains in the crystal form left-handed (4 a supersetPF6 -MeOH) and right-handed (4 b supersetPF6 -MeOH) helical structures with a helical pitch of 28 A. Heterogeneous anion exchanges proceed reversibly in 2, but not in 3, which provides information about the thermal stabilities of the crystals.     

Relative Stability of Multiple Bonds between Germanium and Stibium. A Theoretical Study

Substituent effects on the potential energy surface of XGeSb (X=H, Li, Na, BeH, MgH, BH₂, AlH₂, CH₃, SiH₃, NH₂, PH₂, OH, SH, F, and Cl) were investigated by using B3LYP/Def2‐TZVP, B3PW91/Def2‐ TZVPP CCSD (T)//B3LYP/Def2‐TZVP methods. The isomers include structures with formal double (Ge=SbX) and triple (Xge=Sb) bonds to germanium‐stibium, so a direct comparison of these types of species is possible. Our model calculations indicate that electropositively substituted Ge=SbX species are thermodynamically and kinetically more stable than their isomeric Xge=Sb molecules. Moreover, the theoretical findings suggest that only the organic substitutions (such as CH₃) can make triply bonded Xge=Sb molecule more stable than the doubly bonded Ge=SbX species.     

Reaction of Dess-Martin periodinane with 2-(alkylselenyl)pyridines. Dehydration of primary alcohols under extraordinarily mild conditions

Dess-Martin periodinane oxidizes very rapidly 2-pyridylseleno derivatives RR′CHCH₂SePy in CHCl₃ or CH₂Cl₂ and more chemoselectively than mCPBA. Tetravalent selenanes, RR′CHCH₂Se(OAc)₂Py, seem to be formed. Treatment of these intermediates with aqueous NaHCO₃ gives rise to irreversible hydrolysis and elimination to terminal alkenes. As the OH/SePy exchange can be performed in minutes, the overall process is an exceptionally efficient procedure for the dehydration of primary alcohols.     

Theoretical study of the interaction of fluorinated dimethyl ethers and the ClF and HF molecules. Comparison between halogen and hydrogen bonds

A theoretical study of the halogen‐bonded complexes formed between fluorinated dimethyl ethers (n_F = 0–4) and ClF is carried out using the wB97XD method combined with the 6‐311++G(d,p) basis set. The properties of the complexes are compared with the corresponding properties of the hydrogen‐bonded complexes formed between the same electron donors and HF. The optimized geometries, the interaction energies, relevant natural bonding orbital characteristics along with some vibrational data are calculated. The analyzed properties also include the symmetry adapted perturbation theory decomposition of the energies along with the atoms‐in molecule analysis. For both the halogen and hydrogen bonds, the interaction energies are ruled by the intermolecular hyperconjugation energies. In contrast, the correlations between the binding energies and the basic properties of the ethers or the charge transfer are different for the halogen and hydrogen bonds. The applicability of the Bent's rule to these systems is discussed. © 2016 Wiley Periodicals, Inc.     

Catalysis with Pnictogen,Chalcogen, and Halogen Bonds

Halogen‐ and chalcogen‐based σ‐hole interactions have recently received increased interest in non‐covalent organocatalysis. However, the closely related pnictogen bonds have been neglected. In this study, we introduce conceptually simple, neutral, and monodentate pnictogen‐bonding catalysts. Solution and in silico binding studies, together with high catalytic activity in chloride abstraction reactions, yield compelling evidence for operational pnictogen bonds. The depth of the σ holes is easily varied with different substituents. Comparison with homologous halogen‐ and chalcogen‐bonding catalysts shows an increase in activity from main group VII to V and from row 3 to 5 in the periodic table. Pnictogen bonds from antimony thus emerged as by far the best among the elements covered, a finding that provides most intriguing perspectives for future applications in catalysis and beyond.     

Carboxylic acid to amide hydrogen bonding. 10-Oxo-semirubins

Using their amide (and pyrrole) groups, dipyrrinones act as hydrogen bonding receptors for carboxylic acids, as found in a large number of 10-oxo-semirubins (1-6). The latter can be synthesized readily by Friedel-Crafts coupling of 9-H dipyrrinones with half-ester acid chlorides or diacid dichlorides of α,ω-dicarboxylic acids, ranging from C₂ to C₁₀. With ω-oxo-alkanoic acid chains of C₅ or ≥C₅, intramolecular hydrogen bonding is observed. With acid chains <C₅ hydrogen bonding is not observed. Uncharacteristically (for dipyrrinones), 10-oxo-dipyrrinone acids (1-6) and their corresponding esters (1e-6e) remain monomeric in hydrogen bond promoting solvents.     

Oligonucleotide Analogues with Integrated Bases and Backbone. Part 32

The G[s ]G dinucleoside 6 and the G[s ]G* dinucleoside 8 were prepared by alkylation of the guanosine thiols derived from 2 and 5 , respectively, by the C(8)‐chloromethylated guanosine 4 that was obtained from alcohol 3 . Dinucleosides 6 and 8 were deacylated to 7 and 9 , and fully deprotected to 10 and 11 , respectively. The G[n ]G dinucleoside 16 was obtained by reductive amination of aldehyde 13 with an iminophosphorane derived from azide 14 and deprotection of the resulting dimer 15 . In the solid state of 6 , and in a solution of 6 and 8 in CDCl₃, H? N(1/I) and H? N(1/II) are engaged in intramolecular H‐bonds to the C?O of the isobutyryl protecting groups, and HN of the isobutyryl group of unit I forms an interresidue, intramolecular H‐bond to N(7/II), leading to a syn orientation of the nucleobase at unit I, to a tg orientation of the sulfanyl moiety, and to an orthogonal orientation of the nucleobases, preventing any base pairing. The silylated and isopropylidenated dinucleosides 7 and 9 are present in DMSO solution as solvated monoplexes. Broad ¹H‐NMR signals of the nucleosides 7 and 16 in CHCl₃ solution evidence equilibrating G‐quadruplexes. The quadruplex formation of 7 and 16 was established by ¹H‐NMR spectroscopy (only of 16 ), vapour pressure osmometry, mass spectrometry, and CD spectroscopy. The C(6(I))‐hydroxymethylated analogue 9 in CDCl₃ and the fully deprotected dinucleosides 10 and 11 in H₂O form only weakly π? π stacked associates, but no G‐quadruplexes, as evidenced by CD spectroscopy.     

Oligonucleotide Analogues with Integrated Bases and Backbones. Part 25

The ability of A*[s ]U dinucleosides to gel organic solvents and water is modulated by changing the nature of the substituents at O C(2′) and O C(3′), as evidenced by comparing the gelation of the dinucleosides 7 – 9 and the properties of the gels. A mere extension of the hydrophobic moiety, by replacing the isopropylidene groups of 2 by cyclohexylidene groups, as in 7 , has a small effect, while changing the conformation of the ribose ring and reducing the size of the hydrophobic moiety, as in 8 , has a strong effect on the scope of gelation, the minimum gelation concentration, as low as 0.07% for pentanol and decanol, and the properties of the gel. The fully deprotected dinucleoside 9 gels water at a minimal gelation concentration of 0.6%. A TEM of the corresponding xerogel shows the formation of fibers with a diameter of ca. 30 to 90 nm.