Effects of methyl substituents on the proton chemical shifts in the NMR spectra of the twenty methyl and ethyl substituted hydrazines. Electronegativity values for hydrazyl groups

The C? H proton NMR spectra of the twenty conceivable methyl and ethyl substituted hydrazines are presented and analyzed with respect to effects on chemical shifts of the C? H protons caused by replacement of hydrogen by methyl and ethyl groups on the C? N? N? C chain. Thirteen different methyl substituent effects and six different ethyl substituent effects are identified and evaluated. Most of the effects are shielding and in accordance with an electron-releasing inductive effect of alkyl groups. A deshielding effect (the ‘C? C bond effect’) is observed when a methyl group replaces the hydrogen on the carbon bearing the hydrogen in focus and primary hydrogen on the carbon bearing the hydrogen in focus and primary hydrogens become secondary, as observed in other systems. On the basis of their effects on the chemical shifts of methyl protons in CH₃X, eighteen different hydrazyl groups (× = ? NR₁NR₂R₃) fall into three classes: I (R₁ = H; R₂, R₃ = H or alkyl); II (R₁ = alkyl; R₂ and/or R₃ = H); III (R₁, R₂ and R₃ = alkyl), with slightly different electronegativities: 2·94, 2·83 and 2·74, respectively.     

Strong intramolecular hydrogen bonds and steric effects involving C═S groups: An NMR and computational study

A number of 5-acyl rhodanines and thiorhodanines with bulky acyl groups (pivaloyl and adamantoyl), not previously available, have been synthesized. The compounds are shown to exist in the enol form. Structures have been calculated using both the MP2 approach and the B3LYP-GD3BJ functional and the 6-311++G(d,p) basis set. Hydrogen bond energies are estimated by subtracting energies of a structure with the OH group turned 180° from those of the intramolecularly hydrogen-bonded one. Properties such as OH chemical shifts, two-bond isotope effects on ¹³C chemical shifts, electron densities at the bond critical point from atoms in molecules analysis, and the hydrogen bond energies show that the sterically hindered compounds have stronger hydrogen bonds than methyl or isopropyl derivatives. The combination of oxygen and sulfur derivatives enables a detailed analysis of hydrogen bond energies.     

Comparative study on the nonadditivity of methyl group in lithium bonding and hydrogen bonding

Quantum chemical calculations at the second‐order Moeller–Plesset (MP2) level with 6‐311++G(d,p) basis set have been performed on the lithium‐bonded and hydrogen‐bonded systems. The interaction energy, binding distance, bond length, and stretch frequency in these systems have been analyzed to study the nonadditivity of methyl group in the lithium bonding and hydrogen bonding. In the complexes involving with NH₃, the introduction of one methyl group into NH₃ molecule results in an increase of the strength of lithium bonding and hydrogen bonding. The insertion of two methyl groups into NH₃ molecule also leads to an increase of the hydrogen bonding strength but a decrease of the lithium bonding strength relative to that of the first methyl group. The addition of three methyl groups into NH₃ molecule causes the strongest hydrogen bonding and the weakest lithium bonding. Although the presence of methyl group has a different influence on the lithium bonding and hydrogen bonding, a negative nonadditivity of methyl group is found in both interactions. The effect of methyl group on the lithium bonding and hydrogen bonding has also been investigated with the natural bond orbital and atoms in molecule analyses. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Hydrogen bond stabilization in 1,3-dimethylimidazolium methyl sulfate and 1-butyl-3-methylimidazolium hexafluorophosphate probed by high pressure: the role of charge-enhanced C-H...O interactions in the room-temperature ionic liquid

The hydrogen bonding structures of room-temperature ionic liquids 1,3-dimethylimidazolium methyl sulfate and 1-butyl-3-methylimidazolium hexafluorophosphate have been studied by infrared spectroscopy. High-pressure infrared spectral profiles and theoretical calculations allow us to make a vibrational assignment of these compounds. The imidazolium C-H bands of 1,3-dimethylimidazolium methyl sulfate display anomalous non-monotonic pressure-induced frequency shifts. This discontinuity in frequency shift is related to enhanced C-H...O hydrogen bonding. This behavior is in contrast with the trend of blue shifts in frequency for the methyl C-H stretching mode at ca. 2960 cm(-1). Our results indicated that the imidazolium C-H groups are more favorable sites for hydrogen bonding than the methyl C-H groups in the pure 1,3-dimethylimidazolium methyl sulfate. Nevertheless, both methyl C-H and imidazolium C-H groups are favorable sites for C-H...O hydrogen bonding in a dilute 1,3-dimethylimidazolium methyl sulfate/D(2)O mixture. Hydrogen bond-like C-H...F interactions were observed between PF(6)(-) and H atoms on the alkyl side chains and imidazolium ring for 1-butyl-3-methylimidazolium hexafluorophosphate.     

Solvent-induced polymorphism of three-dimensional hydrogen-bonded networks of hexakis(4-carbamoylphenyl)benzene

The crystal structures for three types of three-dimensional (3-D) hydrogen-bonded networks of hexakis(4-carbamoylphenyl)benzene (1), the network morphologies of which depend greatly on crystallization conditions, have been determined. When this compound is crystallized from hot DMSO, the resulting crystals, 1.12DMSO (orthorhombic, Pca2(1)), showed a 3-D hydrogen-bonded porous network (type A) via 1-D catemer chains as a hydrogen-bonding motif of six primary amide groups. The type A network creates chambers surrounded by six molecules of 1 and channels along the c axis to give the highest porosity among the network polymorphs of 1 investigated here. Crystallization from a boiling mixture of n-PrOH and water gave 1.6n-PrOH (monoclinic, P2(1)/c), which exhibits another type of 3-D hydrogen-bonded porous network (type B) via cyclic dimers as another hydrogen-bonding motif of six primary amide groups. The type B network leads to triangle-like channels along the a axis having a cross section of ca. 9.2 x 9.7 x 9.7 A (including van der Waals radii). The crystal structure of 1.H(2)O (monoclinic, P2(1)/c), which was produced under hydrothermal conditions, showed a nonporous 3-D hydrogen-bonded network chain of amide groups (type C) composed of a mixed hydrogen bonding motif of helical catemer chains/cyclic dimer/catemer. Solvent-induced topological isomerism of these 3-D hydrogen-bonded networks of 1 arises from (i) the guest inclusion ability based on a radially functionalized hexagonal structure of 1, (ii) the correlation between the hydrogen bond donor ability of the syn and anti protons of the primary amide group in host 1 and the hydrogen bond acceptor ability of the oxygen atoms of 1 and guest solvents, and (iii) the polarity of the bulk crystallization solvents.     

Solute-solvent complex switching dynamics of chloroform between acetone and dimethylsulfoxide-two-dimensional IR chemical exchange spectroscopy

Hydrogen bonds formed between C-H and various hydrogen bond acceptors play important roles in the structure of proteins and organic crystals, and the mechanisms of C-H bond cleavage reactions. Chloroform, a C-H hydrogen bond donor, can form weak hydrogen-bonded complexes with acetone and with dimethylsulfoxide (DMSO). When chloroform is dissolved in a mixed solvent consisting of acetone and DMSO, both types of hydrogen-bonded complexes exist. The two complexes, chloroform-acetone and chloroform-DMSO, are in equilibrium, and they rapidly interconvert by chloroform exchanging hydrogen bond acceptors. This fast hydrogen bond acceptor substitution reaction is probed using ultrafast two-dimensional infrared (2D-IR) vibrational echo chemical exchange spectroscopy. Deuterated chloroform is used in the experiments, and the 2D-IR spectrum of the C-D stretching mode is measured. The chemical exchange of the chloroform hydrogen bonding partners is tracked by observing the time-dependent growth of off-diagonal peaks in the 2D-IR spectra. The measured substitution rate is 1/30 ps for an acetone molecule to replace a DMSO molecule in a chloroform-DMSO complex and 1/45 ps for a DMSO molecule to replace an acetone molecule in a chloroform-acetone complex. Free chloroform exists in the mixed solvent, and it acts as a reactive intermediate in the substitution reaction, analogous to a SN1 type reaction. From the measured rates and the equilibrium concentrations of acetone and DMSO, the dissociation rates for the chloroform-DMSO and chloroform-acetone complexes are found to be 1/24 ps and 1/5.5 ps, respectively. The difference between the measured rate for the complete substitution reaction and the rate for complex dissociation corresponds to the diffusion limited rate. The estimated diffusion limited rate agrees well with the result from a Smoluchowski treatment of diffusive reactions.     

Solvent effects on electronic properties from Wannier functions in a dimethyl sulfoxide/water mixture

We present an efficient implementation for the calculation of maximally localized Wannier functions (MLWFs) during parallel Car-Parrinello molecular dynamics simulations. The implementation is based on a block Jacobi method. The calculation of MLWFs results in only a moderate (10%-20%) increase in computer time. Consequently it is possible to calculate MLWFs routinely during Car-Parrinello simulations. The Wannier functions are then applied to derive molecular dipole moments of dimethyl sulfoxide (DMSO) in gas phase and aqueous solution. We observe a large increase of the local dipole moment from 3.97 to 7.39 D. This large solvent effect is caused by strong hydrogen bonding at the DMSO oxygen atom and methyl groups. Decomposing the dipole moment into local contributions from the S-O bond and the methyl groups is used to understand the electrostatic response of DMSO in aqueous solution. A scheme is given to derive charges on individual atoms from the MLWFs using the D-RESP methodology. The charges also display large solvent effects and give insight into the transferability of recent force field models for DMSO.     

Induced crystal G phase through intermolecular hydrogen bonding II. Influence of alkyl chain length of n-alkyl p-hydroxybenzoates on thermal and phase behaviour

A new series of intermolecular hydrogen-bonded complexes have been synthesized using p-n-alkoxybenzoic acid (alkyl chain length varies from propyl- to decyl- and dodecyl-) and methyl p-hydroxybenzoate moieties. The thermal and phase behaviour of these complexes were studied by thermal microscopy and differential scanning calorimetry. Further, the stabilization of intermolecular hydrogen bonding in solution was studied by IR spectroscopy. A detailed IR spectral investigation in the solid and dissolved states suggests that the acid and phenol groups act as proton donor and proton acceptor, respectively. The thermal studies also reveal the inducement of a crystal G phase in the complexes.     

Induced crystal G phase through intermolecular hydrogen bonding II. Influence of alkyl chain length of n-alkyl p-hydroxybenzoates on thermal and phase behaviour

A new series of intermolecular hydrogen-bonded complexes have been synthesized using p-n-alkoxybenzoic acid (alkyl chain length varies from propyl- to decyl- and dodecyl-) and methyl p-hydroxybenzoate moieties. The thermal and phase behaviour of these complexes were studied by thermal microscopy and differential scanning calorimetry. Further, the stabilization of intermolecular hydrogen bonding in solution was studied by IR spectroscopy. A detailed IR spectral investigation in the solid and dissolved states suggests that the acid and phenol groups act as proton donor and proton acceptor, respectively. The thermal studies also reveal the inducement of a crystal G phase in the complexes.     

Coupling of functional hydrogen bonds in pyridoxal-5'-phosphate-enzyme model systems observed by solid-state NMR spectroscopy

We present a novel series of hydrogen-bonded, polycrystalline 1:1 complexes of Schiff base models of the cofactor pyridoxal-5'-phosphate (PLP) with carboxylic acids that mimic the cofactor in a variety of enzyme active sites. These systems contain an intramolecular OHN hydrogen bond characterized by a fast proton tautomerism as well as a strong intermolecular OHN hydrogen bond between the pyridine ring of the cofactor and the carboxylic acid. In particular, the aldenamine and aldimine Schiff bases N-(pyridoxylidene)tolylamine and N-(pyridoxylidene)methylamine, as well as their adducts, were synthesized and studied using 15N CP and 1H NMR techniques under static and/or MAS conditions. The geometries of the hydrogen bonds were obtained from X-ray structures, 1H and 15N chemical shift correlations, secondary H/D isotope effects on the 15N chemical shifts, or directly by measuring the dipolar 2H-15N couplings of static samples of the deuterated compounds. An interesting coupling of the two "functional" OHN hydrogen bonds was observed. When the Schiff base nitrogen atoms of the adducts carry an aliphatic substituent such as in the internal and external aldimines of PLP in the enzymatic environment, protonation of the ring nitrogen shifts the proton in the intramolecular OHN hydrogen bond from the oxygen to the Schiff base nitrogen. This effect, which increases the positive charge on the nitrogen atom, has been discussed as a prerequisite for cofactor activity. This coupled proton transfer does not occur if the Schiff base nitrogen atom carries an aromatic substituent.     

Structure and dynamics of water confined in dimethyl sulfoxide.

We study the structure and dynamics of hydrogen-bonded complexes of H2O/D2O and dimethyl sulfoxide (DMSO) by infrared spectroscopy, NMR spectroscopy and ab initio calculations. We find that single water molecules occur in two configurations. For one half of the water monomers both OH/OD groups form strong hydrogen bonds to DMSO molecules, whereas for the other half only one of the two OH/OD groups is hydrogen-bonded to a solvent molecule. The H-bond strength between water and DMSO is in the order of that in bulk water. NMR deuteron relaxation rates and calculated deuteron quadrupole coupling constants yield rotational correlation times of water. The molecular reorientation of water monomers in DMSO is two-and-a-half times slower than in bulk water. This result can be explained by local structure behavior.     

Effect of methyl groups substitution on the strength of intramolecular hydrogen bonding of naphthazarin: DFT and NBO studies

A density functional theory (DFT) study-based method B3LYP/6-311++G** was carried out to investigate the methyl groups substitution effect on the structure and the strength of intramolecular hydrogen bonding in naphthazarin (NZ) (5,8-dihydroxy-1,4-naphthoquinone). The full geometry optimization of molecular structures, the difference between the energies of hydrogen-bonded and non-hydrogen-bonded rotamers, and the proton chemical shift of the hydroxyl groups in NZ and its methyl substituents obtained at the B3LYP/6-311++G** level. The vibrational frequencies of all samples and their deuterated analogues were calculated at the same theoretical level. The ¹H chemical shifts for NZ and its methyl substituents were computed at the B3LYP/6-311++G** level using the gauge-including atomic orbital method. Furthermore, in order to investigate the changes in bond order, electron density, electron delocalization, and steric effects caused by methyl substituents, natural bond orbital analysis were carried out at the B3LYP/6-311++G** level. After comparing these effective parameters in methyl substituents with those of their parent, NZ, we concluded that, in general, intramolecular hydrogen bonding strength increases by substituting methyl groups in the different positions of NZ.     

Effect of alkyl group size on the mechanism of acid hydrolyses of benzaldehyde acetals

Hydrolyses of benzaldehyde acetals, PhCH(OR)(2), are specific hydrogen-ion catalyzed when R = methyl, n-butyl, but with secondary and tertiary alkyl derivatives, R = i-propyl, s-butyl, t-butyl, t-amyl, hydrolyses are general-acid catalyzed. The Br?nsted alpha values for both secondary and tertiary alkyl groups are in the range: alpha = 0.57-0.61. A simple iterative procedure was developed to estimate the individual rate constants for general-acid catalysis by the diacid and monoacid forms of succinic acid buffer. Plots of log k(obs) (at [buffer] = 0 M) against pH are linear for the secondary and tertiary acetals, and plots of log k(H) for the H(3)O(+)-catalyzed reaction, (13)C and (1)H chemical shifts, and (1)J(CH) coupling constants against the Charton steric parameter, nu, for alkoxy groups are linear. The second-order rate constant, k(H), increases about 100-fold on going from R = Me to R = t-amyl, indicating the significant role of steric effects on reactivity. Steric effects upon (13)C NMR chemical shifts and coupling constants indicate that increasing the bulk of the alkoxy moiety increases the electron density at the carbon reaction center, which accelerates hydrolysis. Analysis of the Jencks-More-O'Ferrall free energy diagram for the reaction provides support for concerted proton transfer and C-O bond breaking in the transition state for hydrolyses of benzaldehyde acetals with secondary and tertiary alkyl groups in contrast to specific hydrogen catalysis with R = Me and n-Bu. All our results are consistent with rate-determining acid hydrolysis of benzaldehyde dialkyl acetals to hemiacetal intermediates that breakdown rapidly to benzaldehyde.     

Understanding the effects of surface chemistry on Q: mechanical energy dissipation in alkyl-terminated (C1-C18) micromechanical silicon resonators

The rate of mechanical energy dissipation in 300-nm-thick, megahertz-range micromechanical silicon resonators is sensitive to single monolayer changes in surface chemistry. Resonators terminated with a single monolayer of methyl groups have significantly higher quality factors (Q's), and thus lower mechanical energy dissipation, than comparable resonators terminated with either long-chain alkyl monolayers (C2H2n+1, n = 2-18) or monolayers of hydrogen atoms. This effect cannot be attributed to mechanical energy dissipation within the alkyl monolayer, as a 9-fold increase in alkyl chain length does not lead to an observable increase in dissipation. Similarly, this effect is not correlated with the chemical structure of the silicon-monolayer interface (e.g., the density of Si-H vs Si-C bonds.) Instead, the chemical trends in resonator quality and stability are consistent with a dissipation mechanism involving the coupling of long-range strain fields to localized, electronically active defects in the monolayer coatings.     

多巴胺盐酸盐与二甲亚砜的相互作用研究

使用核磁共振技术、密度泛函理论(DFT)和分子中原子(AIM)理论,研究了多巴胺盐酸盐(DH)与二甲亚砜(DMSO)的相互作用。结果表明,DH中酚羟基和氨基正离子上的氢原子、苯环上位于酚羟基和侧链之间碳上的氢原子,甚至侧链上与苯环直接相连的亚甲基上的氢原子都可与DMSO中的氧原子形成分子间氢键。     

Intrinsic isotope effects on benzylic hydroxylation by the aromatic amino acid hydroxylases: evidence for hydrogen tunneling, coupled motion, and similar reactivities

Deuterium kinetic isotope effects for hydroxylation of the methyl group of 4-methylphenylalanine have been used as a probe of the relative reactivities of the hydroxylating intermediates in the aromatic amino acid hydroxylases phenylalanine, tyrosine, and tryptophan hydroxylase. When there are three deuterium atoms in the methyl group, all three enzymes exhibit an intrinsic isotope effect of about 13. The temperature dependence of the isotope effect is consistent with moderate tunneling, with the extent of tunneling identical for all three enzymes. In the case of phenylalanine hydroxylase, the presence of the regulatory domain has no effect on the values. The intrinsic primary and secondary isotope effects were determined using 4-methylphenylalanine containing one or two deuterium atoms in the methyl group. With one deuterium atom, the intrinsic primary and secondary effects have average values of 10 and 1.1, respectively. With two deuterium atoms, the primary effects decrease to 7.4 and the secondary effect increases to 1.3, consistent with coupled motion of the primary and secondary hydrogens. The results with all three enzymes are consistent with a hydrogen abstraction mechanism. The similarities of the isotope effects and extent of tunneling establish that the reactivities of the hydroxylating intermediates in the three enzymes are essentially identical.     

Influence of Hydrogen Bonding and Polarity on the Spectral Properties of 4-Aminophthalimide Clusters Formed with Triethylamine and Dimethyl Sulfoxide in Solution

The time-dependent density functional theory (TDDFT) method has been carried out to study the influences of hydrogen bonding and solvent polarity on the spectral properties of 4-aminophthalimide (4AP) clusters formed with hydrogen-accepting solvents triethylamine (TEA) and dimethyl sulfoxide (DMSO). The ground- and S₁-state geometry structure optimizations, hydrogen bond energies, absorption and emission spectra for both the 4AP monomer and its two triply hydrogen-bonded clusters 4AP + (TEA)₃ and 4AP + (DMSO)₃ have been calculated using DFT and TDDFT methods respectively with the hybrid exchange correlation functional PBE1PBE and split-valence basis set 6-311++G(d,p). It has been demonstrated that the two hydrogen bonds I and II formed with the amine group of 4AP are significantly strengthened while the hydrogen bond III formed with the imide group is slightly weakened due to the intramolecular charge transfer from the amine group to the two carbonyl groups of the 4AP molecule upon photoexcitation. In addition, the hydrogen bonds formed by 4AP with DMSO are stronger than those formed with TEA, which together with its strong polarity, should be the main reasons for the more redshifts of both the absorption and the fluorescence spectra of 4AP in solvent DMSO than those in TEA.     

Low-temperature STM images of methyl-terminated Si(111) surfaces

Low-temperature scanning tunneling microscopy (STM) has been used to image CH(3)-terminated Si(111) surfaces that were prepared through a chlorination/alkylation procedure. The STM data revealed a well-ordered structure commensurate with the atop sites of an unreconstructed 1 x 1 overlayer on the silicon (111) surface. Images collected at 4.7 K revealed bright spots, separated by 0.18 +/- 0.01 nm, which are assigned to adjacent H atoms on the same methyl group. The C-H bonds in each methyl group were observed to be rotated by 7 +/- 3 degrees away from the center of an adjacent methyl group and toward an underlying Si atom. Hence, the predominant interaction that determines the surface structure arises from repulsions between hydrogen atoms on neighboring methyl groups, and secondary interactions unique to the surface are also evident.     

Thermosolvatochromism of merocyanine polarity indicators in pure and aqueous solvents: relevance of solvent lipophilicity

The following novel solvatochromic probes were synthesized: 2,6-dibromo-4-[(E)-2-(1-alkylpyridinium-4-yl)ethenyl] phenolate, where the alkyl groups are methyl, n-butyl, n-hexyl, and n-octyl, respectively. Solvatochromism of three of these probes (C(1), C(4), and C(8)) was studied in 36 protic and aprotic solvents. A modified linear solvation energy relationship has been applied to the data obtained at 25 degrees C. Correlation of (empirical) polarities with other solvent properties showed more dependence on lipophilicity than on basicity. A similar conclusion has been reached for a series of other solvatochromic indicators. Exceptions are those that carry acidic hydrogens, being biased toward solvent basicity. Thermosolvatochromism has been studied in mixtures of water with methanol, 1-propanol, acetonitrile, and DMSO. Thermosolvatochromic data have been treated according to a model that explicitly considers the presence in bulk solution of three "species": water, organic component, and solvent-water hydrogen-bonded aggregate. Solvation by the latter is favored over solvation by either of the two precursor solvents (aqueous DMSO is an exception). Temperature increase resulted in desolvation of the probes, due to concomitant decrease of the structures of the component solvents. The above-mentioned modified solvation equation has been successfully applied to solvatochromism in aqueous methanol and aqueous 1-propanol.     

The mass spectrometric fragmentation of n-heptane

The electron impact fragmentation of n-heptane has been investigated using ¹³C labelled derivatives. A mechanism is proposed for the loss of alkyl radicals where the cleavage of a C? C bond is coupled with the rearrangement of a hydrogen atom, thus yielding a secondary alkyl ion that eventually fragments further by a subsequent loss of olefin. For alkyl ions with less than six carbon atoms this consecutive pathway is in competition with formation directly from the molecular ion. The consecutive pathway contributes about 15% to the intensity of the alkyl ions with four and five carbon atoms and 80% for smaller ions. The electron energy dependence was studied.