Crystallographic evidence for intermolecular hydrogen bonding between aryl groups and OH groups in silanols

In crystals of the silanols (Me₃Si)₃CSiPh(X)OH (X  I or OMe) there is intermolecular π ⋯ HO bonding between a phenyl group in one molecule and an OH group in another, and there are probably intramolecular π ⋯ HO interactions in two silanols previously reported to show no hydrogen bonding. It is suggested that similar interactions should exist for OH groups attached to other metals or metalloids.     

Crystallographic evidence for chromium-platinum interaction

Heteronuclear Pt-Cr paddlewheel complexes with significant Pt-Cr interaction have been made. They can be interconverted. Upon oxidation, the Pt-Cr distance shortens significantly while other bond lengths remain unchanged. By taking into account the strong axial coordination from the chloride ligand in the oxidized compound, we suspect that the removed electron upon oxidation is probably from a Pt-Cr orbital that is significantly antibonding in nature.     

Computational evidence for methyl-donated hydrogen bonds and hydrogen-bond networking in 1,2-ethanediol-dimethyl sulfoxide

The 1:1 complex of 1,2-ethanediol with dimethyl sulfoxide was studied using density functional theory. A network of three hydrogen bonds holds the complex together, including two in which each methyl group donates to the same hydroxyl oxygen. Four lines of evidence support the existence of methyl-donated hydrogen bonds. The interaction energy is 36 +/- 5 kJ/mol using Becke's three parameter hybrid theory with the 1991 nonlocal correlation functional of Perdew and Wang, and a moderately large basis set (B3PW91/6-311++G**//B3PW91/6-31+G**). To determine the energy of each hydrogen bond, a relaxed potential energy scan was performed in a smaller basis set to break the weaker hydrogen bonds by forced systematic rotation of the methyl groups. Two cross-checking analyses show cooperative effects that cause individual hydrogen bond energies in the network to be nonadditive. When one methyl hydrogen bond is broken, the remaining interactions stabilize the complex by storing an additional 2-3 kJ/mol. With all hydrogen bonds intact, the O[bond]H...O[bond]S hydrogen bond contributes 26 +/- 2 kJ/mol stability, and each weak methyl bond stores 5 +/- 2 kJ/mol.     

Rate constants for hydrogen abstraction from alkoxides by a perfluoroalkyl radical. An oxyanion accelerated process

A combination of laser flash photolysis and competitive kinetic methods has been used to measure the absolute bimolecular rate constants for hydrogen atom abstraction in water from a series of fluorinated alkoxides and aldehyde hydrates by the perfluoroalkyl radical, *CF2CF2OCF2CF2SO3- Na+. The bimolecular rate constants observed for the beta-fluorinated alkoxides were in the 10(5) M(-1) s(-1) range, such rates representing enhancements (relative to the respective alcohols) of between 100 and almost 1000-fold, depending on the reactivity of the alkoxide. Likewise, the monobasic sodium salts of chloral and fluoral hydrate exhibit similar rate enhancements, relative to their respective hydrates.     

An electrostatic model for hydrogen bonds in alcohols

We have measured the Raman spectra of liquid methanol at temperatures between 50° and –77°C. The weak O–H stretching bands appear, under amplification, more and more asymmetric as the temperature is lowered. They can be decomposed into three Gaussian components centered at about 3220, 3310, and 3400 cm^–1. The former, predominant at low temperature, corresponds to single, linear hydrogen bonds (LHB) between two molecules. The other two are assigned to branched hydrogen bonds, respectively bifurcated (BHB), between three molecules, and trifurcated (THB), between four molecules. We conclude that the molecular structure of liquid alcohols is not chain-like, as presumed so far, but a three-dimensional network featuring a mixture of single (LBH), and multiple hydrogen bonds (BHB, and THB). They are mainly electrostatic in nature, their relative proportions and geometry governed by the packing conditions for minimum energy. They form distinct trimers and tetramers in dilute solutions of alcohols in inert solvents and frozen matrices, and the latter even in the vapor.Deceased December 25, 1987.     

Study of hydrogen bonds in N-methylacetamide by DFT calculations of oxygen, nitrogen, and hydrogen solid-state NMR parameters

Solid-state nuclear magnetic resonance (NMR) parameters of ¹⁷O, ¹⁴N/¹⁵N, and ²H/¹H nuclei were evaluated in two available neutron crystalline structures of N-methylacetamide (NMA) at 250 and 276 K, NMA-I and NMA-II, respectively. Density functional theory calculations were performed by B3LYP method and 6-311++G** and IGLO-II type basis sets to calculate the electric field gradient (EFG) and chemical shielding (CS) tensors at the sites of mentioned nuclei. In order to investigate hydrogen bonds (HBs) effects on NMR tensors, calculations were performed on four-model systems of NMA: an optimized isolated gas-phase, crystalline monomers, crystalline dimers, and crystalline trimers. Comparing the calculated results reveal the influence of N–H···O=C and C–H···O=C HB types on the NMR tensors which are observable by the evaluated parameters including quadrupole coupling constant, C _Q, and isotropic CS, σ _iso. Furthermore, the results demonstrate more influence of HB on the EFG and CS tensors of NMA at 276 K rather than that of 250 K.     

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.     

Influence of conjugation of donor and acceptor on the properties of hydrogen bonds of Cis and trans isomers

Cis and trans, and syn and anti. isomers are studied by IR and NMR in acetonitrile-d₃ solutions. Cis and syn isomers form completely intramolecular N⁺H…N⇌N…H⁺N bonds. They show, however, nearly no proton polarizability since the donor and acceptor are electronically conjugated. The trans and anti isomers form intermolecular N⁺H…N⇌N…H⁺N bonds showing large proton polarizability.     

Nitrobenzene as hydrogen acceptor in Pd/C-catalyzed hydrogen transfer reaction

Nitrobenzene was found to work as an efficient hydrogen acceptor in the oxidation of allylic alcohols to give the corresponding enones in high yields.     

Commensurate and incommensurate hydrogen bonds. An exercise in crystal engineering.

Ureas characteristically form one-dimensional hydrogen-bonded alpha-networks with a repeat distance of about 4.60 A. Oxamides form similar alpha-networks with a longer 5.05 A repeat distance. The urea of glycine and the oxamide of glycine were each cocrystallized with a series of four bipyridines, including two urea derivatives and two oxamide derivatives. This series of eight cocrystals was studied by X-ray diffraction in order to see what would happen when molecules that would normally form alpha-networks with incommensurate distances were forced into the same crystal. The two all-urea crystals and the two all-oxamide crystals contained the expected alpha-networks with repeat distances in accordance with normal urea or oxamide values. Four of the crystals were mixed, containing both oxamide and urea molecules. Three consisted of two-dimensional beta-networks with alternating parallel urea and oxamide subnetworks. The repeat distances averaged 4.87 A, a value close to the value expected for oxamides, but shorter than any previously observed examples. In the fourth mixed crystal, the urea alpha-network formed with a normal urea repeat distance, but the oxamide network did not form, the oxamide adopting an unusual molecular conformation that maximizes intramolecular hydrogen bonds instead.     

Fluorine hydrogen short contacts and hydrogen bonds in substituted benzamides

A series of fluorine substituted benzamides 1-10 was synthesised and investigated by spectroscopic methods (NMR, IR, MS) and X-ray structure analysis. The configuration of these compounds strongly depends on solvent, temperature and substitution pattern. Unexpectedly, some of these compounds form weak intramolecular hydrogen bonds/short NH?FC contacts in CDCl₃ solution and in the solid state.     

Evaluation of coarse grained models for hydrogen bonds in proteins

Backbone hydrogen bonds contribute very importantly to the stability of proteins and therefore they must be appropriately represented in protein folding simulations. Simple models are frequently used in theoretical approaches to this process, but their simplifications are often confronted with the need to be true to the physics of the interactions. Here we study the effects of different levels of coarse graining in the modeling of backbone hydrogen bonds. We study three different models taken from the bibliography in a twofold fashion. First, we calculate the hydrogen bonds in 2gb1, an (alpha + beta)-protein, and see how different backbone representations and potentials can mimic the effects of real hydrogen bonds both in helices and sheets. Second, we use an evolutionary method for protein fragment assembly to locate the global energy minimum for a set of small beta-proteins with these models. This way, we assess the effects of coarse graining in hydrogen bonding models and show what can be expected from them when used in simulation experiments.     

Multiple hydrogen bonds in cytosinium zoledronate trihydrate

The asymmetric unit of the title compound [systematic name: 4‐amino‐2‐oxo‐2,3‐dihydropyrimidin‐1‐ium 1‐hydroxy‐2‐(1H,3H‐imidazol‐3‐ium‐1‐yl)ethylidenediphosphonate trihydrate], C₄H₆N₃O⁺·C₅H₉N₂O₇P₂⁻·3H₂O, contains one cytosinium cation, one zoledronate anion and three water molecules. The zoledronate anion has a zwitterionic character, in which each phosphonate group is singly deprotonated and an imidazole N atom is protonated. Furthermore, proton transfer takes place from one of the phosphonic acid groups of the zoledronate anion to one of the N atoms of the cytosinium cation. The cytosinium cation forms a C(6) chain, while the zoledronate anion forms a rectangular‐shaped centrosymmetric dimer through N—H...O hydrogen bonds. The cations and anions are held together by N—H...O and O—H...O hydrogen bonds to form a one‐dimensional polymeric tape. The three water molecules play a crucial role in hydrogen bonding, resulting in a three‐dimensional hydrogen‐bonded network.     

The proton potential in short hydrogen bonds

The state of knowledge of the proton potential in systems for which double minimum and symmetrical, single minimum type curves have been envisaged is critically reviewed. In particular, the proposed model potentials for carboxylic acids, for KDP type ferroelectrics and for the shortest hydrogen bonds are confronted with experimental data, particularly from vibrational spectra. The early attempts at explaining the complex features in the AH stretching region by level splitting in one-dimensional double minimum potentials have not been successful. The interest in the profile of the potential surface is shifted from this aspect to its role in anharmonic interaction based general band-shaping mechanisms.     

Stereoelectronic effects and general trends in hyperconjugative acceptor ability of sigma bonds

A systematic study of general trends in sigma acceptor properties of C-X bonds where X is a main group element from groups IVa-IIa is presented. The acceptor ability of the C-X sigma bonds in monosubstituted ethanes increases when going to the end of a period and down a group. Enhancement of acceptor ability of C-X sigma bonds as one moves from left to right in periods parallels the increase in electronegativity of X, whereas augmentation of acceptor ability in groups is opposite to the changes in electronegativity of X and in the C-X bond polarization, following instead the decrease in the energy of sigma(C)(-)(X) orbitals when one moves from the top to the bottom within a group. This simple picture of acceptor ability of sigma bonds being controlled by electronegativity in periods and by sigma orbital energy in groups is changed in monosubstituted ethenes where the role of electronegativity of the substituent X becomes more important due to increased overlap between sigma orbitals. The combination of several effects of similar magnitude influences acceptor ability of sigma bonds in monosubstituted ethenes in a complex way. As a result, the acceptor ability of sigma bonds can be significantly modified by substitution and is conformer dependent. Stereoelectronic effects displayed by C-X bonds with X from second and third periods are highly anisotropic. For example, C-chalcogen bonds are excellent sigma acceptors at the carbon end but poor sigma acceptors at the chalcogen end. This effect can be relied upon in the design of molecular diodes with sigma bridges with unidirectional electron conductivity. While the general trends revealed in this work should be useful for the qualitative understanding of stereoelectronic effects, one should bear in mind that the magnitude of hyperconjugative effects is extremely sensitive to small variations in structure and in substitution. This advocates for the increased role of theoretical methods in analysis of stereoelectronic effects.