Amide Molecules Research Articles

An approached method for predict the nature of the reaction mechanism by assessment of the binding chain (CH2)n (n=1, 2 and 3) role to the intramolecular cycloaddition Diels-Alder reaction of triene amide

In this study, we propose a new approach that their purposes to facilitate the theoretical examinations of the intramolecular Diels-Alder (IMDA) reactions of triene amide and other IMDA reactions. In this end, the nature of reaction mechanism (NRM) will be determined by evaluating the contribution of binding chain on the HOMO and LUMO energies of triene amide. During our study, we have used the density functional theory (DFT) combined with B3LYP hybrid and 6-31G(d,p) basis set level. The results found shows that the binding chain has a negligible contribution on the HOMO and LUMO energies of triene amide molecule. Therefore, the diene and dienophile are treated as they were in isolated fragments. Thus the calculation of the NRM reveals that these reactions are at normal electronic demand (NED) in accordance with the results found by charge transfer between fragments in the transition state.

Aqueous solvation of an amide molecule from first principles molecular simulations: Structure, hydrogen bond dynamics and spectral signature

Density functional theory (DFT) based Car–Parrinello molecular dynamics (CPMD) simulations were carried out to investigate the structure and dynamics of aqueous solvation shell of a single formamide (FA) molecule. Vibrational frequency through wavelet analysis and correlation function calculations have been performed to understand the spectral signature of water molecules in the first solvation shell and dynamics of solute–solvent hydrogen bonds, respectively. Structural aspects have been analyzed by calculating various pair correlation functions. FA takes part in more than two hydrogen bonds with water via carbonyl oxygen. Due to the presence of carbonyl group, the solvation through amine group hydrogen atoms is asymmetrical; each hydrogen participates in roughly one hydrogen bond. Carbonyl–water hydrogen bonds are stronger than the water–water hydrogen bonds; amine–water hydrogen bonds are much weaker than other two types of hydrogen bonds.

Fluorescent tags. dansyl amide (CH3)2N–С10Н6–SO2NH2: Reflection of the conformational properties of a free molecule in crystal structures

The conformational properties of a dansyl amide molecule (CH3)2N–C10Н6–SO2NH2, which is widely used for fluorescent labeling of compounds, e.g., amino acids or nucleotides and compounds able to form liquid crystals, are studied. It is found that the molecule has six conformers with relative energies 0/0.13, 1.13/1.38, 0.06/0.06, 0.31/0, 2.95/2.70, 0.31/0 (B3LYP/cc-pVTZ and МР2/cc-pVTZ methods respectively). In all conformers the naphthalene core becomes non-planar under the effect of two substituents. The effect of the nature of substituents on the geometric parameters of the conformers is considered. In terms of the NBO analysis a substantial deviation of the S–N bond in the –SO2NH2 substituent from orthogonality and also the asymmetrical position of the –N(СH3)2 group with respect to the naphthalene core are explained. The paths and barriers of conformational transformations of the dansyl amideа molecule are determined. The structure of the (CH3)2N–C10H6–SO2NН–X moiety in the crystals is analyzed and the relationship between the relative energy of the conformers of a free molecule and the probability of the occurrence of their structures in the crystals is determined.

Understanding water and ion transport behaviour and permeability through poly(amide) thin film composite membrane

Molecular dynamics (MD) together with the adaptive biasing force (ABF) and metadynamics free energy calculation methods was used to investigate the permeation properties of salt water through poly(amide) thin film composite reverse osmosis membranes. The thin films were generated by annealing an amorphous cell of poly(amide) chains through an MD method. The MD results showed they have typical structural properties of the active layer of thin film composite membranes and comparable water diffusivity (2.13×10−5cm2/s for the film with a density of 1.06g/cm3) and permeability (9.27×10−15cm3cm/cm2sPa) to experimental data. The simulations of water permeation through the films under different transmembrane pressures revealed the behaviours of water molecules in the thin films and the dynamic regimes of water permeation, including Brownian diffusion, flush and jump diffusion regimes. The intermolecular interactions of water and ions with poly(amide) chains showed a strong dependence on the local structure of films. The attraction between water and ploy(amide) molecules can be up to 8.5kcal/mol in dense polymer regions and 5kcal/mol in the pores of about 3nm. The ABF and metadynamics simulations produced the profiles of free energy potential of water and ions along the depth of the thin films, which provided important information for quantitatively determining the barrier energy required for water permeation and rejection of ions. The thin film with a density of 1.06g/cm3 and a thickness of 6nm offers a rejection to Na+ but a slight absorption of Cl− (0.25kcal/mol) at 0.3–0.4nm distance to its surface. Water molecules must overcome 63kcal/mol energy to move to the centre of the film. The dependences of the barrier energy and the water–polymer interaction energy on the local free volume size in the thin film were analysed. The simulations of water permeation under high transmembrane pressures showed a nonlinear response of the concentration and distribution of water molecules in the film to the imposed pressure. Compaction of the film segments close to the porous substrate and water congestion in dense regions significantly influenced the water permeation when the membrane was operated under pressures of more than 3.0MPa.

Theoretical study of interaction of amide molecules with kaolinite

In this paper, we have constructed the cluster models Si6O18H12, Al6O24H30 and Si6Al6O42H42 for SiO, AlO surfaces and isolated kaolinite, respectively. All calculations have been performed at the B3LYP (Becke, three-parameter, Lee–Yang–Parr exchange–correlation functional) level using the 6-31G(d) basis set to investigate the various gas phase properties of interaction of amide (including formamide (FA), acetamide (AA), cis-N-methylformamide (NMFA1), trans-N-methylformamide (NMFA2), cis-N-methylacetamide (NMA1) and trans-N-methylacetamide (NMA2)) with kaolinite, such as optimal structures, structural parameters, interaction energies, charge transfer, vibrational frequencies, electrostatic potential, and so on. Moreover, extra calculations have also been performed at the M052X/6-31G(d) level in order to test the effect of van der Waals interactions on the order of stability of complexes in adsorption or intercalation systems. The results show that hydrogen bonds are formed between amide and the hydroxyl groups of the AlO surface or the basal oxygen atoms of the SiO surface in kaolinite. Moreover, the adsorption between amide and AlO surface of kaolinite is stronger than that of amide and SiO surface of kaolinite, and the intercalation interaction is more stable than the adsorption interaction. As for the order of the stability of intercalated kaolinite complexes, there is a slight difference between the order (K–NMFA2>K–FA>K–AA>K–NMA2>K–NMFA1>K–NMA1) calculated at the level of M052X/6-31G(d) and the order (K–NMFA2>K–FA>K–AA>K–NMFA1>K–NMA2>K–NMA1) calculated at the level of B3LYP/6-31G(d), in which K denotes kaolinite. The order is different from that of adsorbed systems at the same computational level.

Densities, viscosities, and excess properties for binary mixtures of ethylene glycol with amides at 308.15 K

The densities, ρ, and viscosities, η, of binary mixtures of ethylene glycol with formamide, N,N-dimethyl formamide and N,N-dimethyl acetamide, have been measured over the entire composition range at 308.15 K. From this experimental data, excess molar volume, $$ V_{\text{m}}^{\text{E}} $$ , deviation in viscosity, Δη, and excess Gibbs free energy of activation of viscous flow, $$ \Delta G^{{ * {\text{E}}}}, $$ have been determined. Negative values of $$ V_{\text{m}}^{\text{E}} $$ , Δη, and $$ \Delta G^{{ * {\text{E}}}} $$ are observed over the entire composition range in the mixtures studied. The observed negative values of various excess and deviation parameters are attributed to the existence of strong interactions, like dipole–dipole interactions, H-bonding between the carbonyl group of amide molecules, and hydroxyl group of glycol molecules, geometrical fitting of smaller molecules into the voids created by larger molecules in the liquid mixtures. The excess properties have been fitted to Redlich–Kister-type polynomial, and the corresponding standard deviations have been calculated. The derived partial molar volumes and excess partial molar volumes also support the $$ V_{\text{m}}^{\text{E}} $$ results. The experimental viscosity data of all of these liquid mixtures have been correlated with four viscosity models.

Topotactic Conversion of β‐Helix‐Layered Silicate into AST‐Type Zeolite through Successive Interlayer Modifications

AST-type zeolite with a plate morphology can be synthesized by topotactic conversion of a layered silicate (β-helix-layered silicate; HLS) by using N,N-dimethylpropionamide (DPA) to control the layer stacking of silicate layers and the subsequent interlayer condensation. Treatment of HLS twice with 1) hydrochloric acid/ethanol and 2) dimethylsulfoxide (DMSO) are needed to remove interlayer hydrated Na ions and tetramethylammonium (TMA) ions in intralayer cup-like cavities (intracavity TMA ions), both of which are introduced during the preparation of HLS. The utilization of an amide molecule is effective for the control of the stacking sequence of silicate layers. This method could be applicable to various layered silicates that cannot be topotactically converted into three-dimensional networks by simple interlayer condensation by judicious choice of amide molecules.

Preferable solvatation of decane and benzene in 1-octanol-N,N-dimethylformamide mixed solvent

Heat effects of the dissolution of decane and benzene in a model system of 1-octanol (OctOH)-N,N-dimethylformamide are measured at 298 and 318 K using a variable temperature calorimeter with an isotermic shell. The state of hydrocarbon molecules in the mixed solvent is studied using an extended coordination model and is compared to earlier data for ethyl acetate (EtOAc), DMF, OctOH, and tetramethyl hematoporphyrin (TMHP). It is shown that the polar carboxylic groups of porphyrin are preferably solvated by amide molecules due to stronger interaction with DMF, while nonpolar aliphatic groups are solvated by alcohol molecules. We conclude that a solvate shell of aromatic benzene is strongly enriched with DMF over the range of compositions, suggesting that the weakening of the preferable solvatation of porphyrin relative to EtOAc is due primarily to the influence of nonpolar substituents.

Electronic transitions in liquid amides studied by using attenuated total reflection far-ultraviolet spectroscopy and quantum chemical calculations

Attenuated total reflection far-ultraviolet (ATR-FUV) spectra in the 140-260 nm region were measured for several types of liquid amides (formamide, FA; N-methylformamide, NMF; N-methylacetamide, NMA; N,N-dimethylformamide, NdMF; and N,N-dimethylacetamide, NdMA) to investigate their electronic transitions in the FUV region. The spectra were compared with the corresponding gas-phase spectra to examine the shift in the major absorption band in the 180-200 nm region going from the gas phase to the liquid phase, and it was found that the peak shift was dependent on the particular amide. FA and NMF, which exhibit intermolecular C=O[ellipsis...H-N hydrogen bonding, show a large shift of ~0.60 eV to lower energy; however, NMA, which also exhibits hydrogen bonding, shows only a small shift. In NdMF and NdMA, C=O groups seem to be coupled, which results in a small peak shift. Two types of quantum chemical calculations, time-dependent density functional theory (TD-DFT) and symmetry-adapted-cluster configuration interaction (SAC-CI) method, were performed to elucidate the origin of the shifts and the band assignments. The shift estimated by the monomer and dimer models with TD-DFT reproduced well the observed shift from the gas phase to the liquid phase. This suggests that the intermolecular hydrogen-bonding interaction significantly affects the magnitude of the shift. The many-body effects were also considered using the larger cluster models (trimer to pentamer). The energy shift calculated using SAC-CI with the monomer and the state-specific polarizable continuum model was also accurate, indicating that the nonlinear polarization effect appears to be important. As for the band assignments, it was found that though the major band can be mainly attributed to the π-π* transition, several types of Rydberg transitions also exist in its vicinity and mixing of orbitals with the same symmetry occurs. The number and type of Rydberg transitions in the spectra depend upon the type of amide molecules. The valence-Rydberg coupling of the π-π* transition is more significant than n-π* transition, which also holds in the pure liquid phase.

Thermochemistry of the dissolution of DL-α-alanyl-DL-norleucine in aqueous solutions of amides at 298.15 K

Enthalpies of the dissolution of DL-α-alanyl-DL-norleucine are determined by calorimetry in aqueous solutions of formamide (FA), N-methylformamide (MFA), N,N-dimethylformamide (DMF), and N,N-dimethylacetamide (DMA) at a concentration of amides of x2 = 0–0.4 molar parts and T = 298.15 K. Standard values of enthalpies of dissolution ΔsolHo and ΔtrHo of DL-α-alanyl-DL-norleucine transfer from water to binary solvent are calculated, along with the enthalpy coefficients of pair interactions hxy of DL-α-alanyl-DL-norleucine with amide molecules. The effect of the composition of water-organic mixtures and the structure of amides on the enthalpy characteristics of dissolution and transition of DL-α-alanyl-DL-norleucine is considered. Quantitative estimates of the contributions to energy from DL-α-alanyl-DL-norleucine-amides pair interactions determined by the polarity, polarizability, and electron acceptor and electron donor ability of organic cosolvents are given using the Kamlet-Taft correlation equation.

ChemInform Abstract: Solvothermal Synthesis of New Open‐Framework Metal Phosphites with Structure‐Directing Agents Generated in situ.

AbstractThe new compounds (III), (IV), and (VI) are solvothermally synthesized using amide molecules and a urea derivative as the source of structure‐directing agents.

Quantum chemical study of free and coordinate molecules and complexes of amides with mercuric acetate propionamide

Electron structures and reactivities of free and coordinated molecules of fatty acid amides and complex of mercury acetate with propionamide have been studied using quantum chemical methods. The geometry and energy parameters have been determined. The conformational change in the molecules of fatty acid amides and complex of mercury acetate with propionamide at complexation has been observed.

Solvothermal synthesis of new open-framework metal phosphites with structure-directing agents generated in situ

By using amide molecules and a urea derivative as the source of structure-directing agents (SDAs), three open-framework metal phosphites, (CH3NH3)2·[Be3(HPO3)4] (1), (CH3CH2NH3)2·[Be3(HPO3)4] (2), and [(CH3)2NH2]1.5·(H3O)0.5·[Al4(HPO3)7(H2O)3]·(H2O)0.5 (3), have been synthesized under solvothermal conditions. Compound 1 has left- and right-handed helical channels running along the [001] directions. Compound 2 possesses zigzag 12-ring channels running along the [001] direction. Compound 3 contains multidirectional 12-ring channels running along the [100], [010], and [110] directions. It is noteworthy that the direct use of methylamine, ethylamine and dimethylamine as SDAs can't produce corresponding single crystals of compounds 1–3, demonstrating the slow release of amines from amide molecules and urea derivative is a key process for the crystal growth.

Rac-[2-(Dicyclohexylphosphanyl)phenyl](phenyl)phosphinic diisopropylamide–borane hemihydrate

In the title compound, C30H48BNOP2·0.5H2O, the water molecule is disordered about an inversion centre. Both phospho­rus atoms shows distortions in their tetra­hedral environments with the cyclo­hexyl substituents disordered over two orientations in a 0.851 (3):0.149 (3) occupancy ratio. The crystal structure is assembled via O—H⋯O inter­actions between pairs of phosphininc amide mol­ecules and water molecules, creating hydrogen-bonded dimers with graph-set R 2 4(8) along [001]. Weak C—H⋯O inter­actions are also observed.

Switching of the Diastereomer Deposited during the Crystallization of N-[(S)-1-Phenylethyl]-2′-carbamoyl-1,1′-binaphthalene-2-carboxylic Acid: Investigation of the Mechanism of Dielectrically Controlled Resolution

Dielectrically controlled resolution (DCR) has been achieved during the crystallization of (S)-1-phenylethylamides of racemic 1,1'-binaphthalene-2,2'-dicarboxylic acid (RS(a),S)-1. For example, a water well-shaped plot is obtained for the diastereomeric excess (de) of the deposited amide versus the solvent permittivity (ε) for the crystallization of (RS(a),S)-1 from three-component mixed solvents, consisting of 25 vol % of dichloromethane and 75 vol % of varying ratios of two solvents (i.e., an alcohol and either hexane or water). The de value drastically changes within two narrow ε ranges and diastereomerically pure crystals of either (R(a),S)-1 (13.9 ≤ ε ≤ 17.9) or (S(a),S)-1·CH(2)Cl(2) (ε ≤ 11.9 and ε ≥ 21.8) deposit, depending on the solvent permittivity. X-ray crystallographic analyses reveal that the major difference between the crystal structures of (S(a),S)-1 and (R(a),S)-1 is the presence of solvent molecules that fill the spatial voids in the (S(a),S)-1 crystals. The ε-dependence of the chemical shifts of (S(a),S)-1 and (R(a),S)-1 suggests that their aggregation states are similar in the same solvents and change discontinuously at two ε values. The ε-dependence of the C═O stretching vibrations suggests that the lower ε is a transition point where the amide molecules, which aggregate through intermolecular hydrogen bonds in low-permittivity solvents, begin to dissociate. An absorption experiment suggests that dichloromethane is easily incorporated into solvent-free (S(a),S)-1 crystals in high-permittivity solvents. On the basis of these observations, a feasible molecular mechanism is proposed for the present DCR phenomenon.

Quantum Chemical Analysis of the Thermodynamics of 2D Cluster Formation of Aliphatic Amides at the Air/Water Interface

The semiempirical quantum chemical PM3 method is used to calculate the thermodynamic and structural parameters of formation and clusterization of aliphatic amides with the general composition CnH2n+1CONH2 (n = 6–16) at 293 and 298 K. Enthalpy, absolute entropy, and Gibbs’ energy of the formation for two stable conformations of monomers are calculated. The correlation dependencies of the calculated parameters on the alkyl chain length are found to be linear. The structures found for the monomers are used to build clusters (dimers, trimers, tetramers). The thermodynamic parameters of formation and clusterization for all cluster series are calculated. The obtained clusterzation parameters show stepwise dependencies on the alkyl chain length. It is demonstrated that the formation of two structurally different 2D films is possible. In the first film, the aliphatic amide molecules are oriented at the angles δ1 = 10° and φ1 = 20.5° to the normal to the sides of the unit cell, and in the second film, the values o...

Organic hydrogen-bonded assembly of asymmetric phenol amide molecules

The significant involvement of weak intermolecular interactions and steric and/or symmetry-related packing features was assessed with supramolecular arrays of 4-hydroxyphenyl amides in the crystal structure. The one-dimensional chain is observed in the aryl substituted 4-hydroxyphenyl amides, while alkyl analogs generate 2D or 3D arrays. A comparison of supramolecular assemblies in the similar 4-hydroxyphenyl amide compounds in the Cambridge Structural Database has been presented. It is correlated with the different steric constraints of aryl and alkyl groups to create chains, 2D sheets and 3D-interpenetrated networks in the asymmetric 4-hydroxyphenyl amides. A comprehensive analysis of crystal packing and energy features of the selected 4-hydroxyphenyl amide derivatives is reported.

Density Functional Theory Study on the Cleavage Mechanism of the Carbonyl Bond in Amides on Flat and Stepped Ru Surfaces: Hydrogen-Induced or Direct C–O Bond Breaking?

We have performed density functional theory (DFT) calculations to investigate the reaction mechanism of the cleavage of the carbonyl bond in amides on both flat and stepped Ru surfaces. The simplest amide molecule, N,N-dimethylacetamide (DMA), was used as the exemplar model molecule. Through the calculations, the most stable transition states (TSs) in all the pathways on both flat and stepped Ru surfaces are identified. Comparing the energy profiles of different reaction pathways, we find that a direct cleavage mechanism is always energetically favored as compared with an alternative hydrogen-induced mechanism on either the flat or stepped Ru surface. It is easier for the dissociation process to occur on the stepped surface than on the flat surface. However, as compared with the terrace, the superiority of step sites boosting the C–O bond dissociation is not as evident as that on CO dissociation.

Unraveling the Hierarchic Formation of Open-porous Bimolecular Networks

The surface-confined formation of bicomponent organic molecular networks providing open pores following hierarchic assembly principles is investigated by low-temperature scanning tunneling microscopy and ab initio theoretical methods. The nanomeshes are realized by codeposition of N,N′-diphenyl oxalic amide and sexiphenyl dicarbonitrile molecules, with the substrate held at room temperature and subsequent cooling to cryogenic temperatures. We find that the formation of mixed molecular networks is generally preferred over phase segregation. Depending on the exact stoichiometry of the constituents, different types of open networks self-assemble on the employed Ag(111) surface. All network types reflect hierarchic architectures, where essential molecular interactions are identical and the noncovalent bonding of sexiphenyl to oxalic amide molecules prevails. The different association motifs are assessed by theoretical modeling to unravel the mechanisms mediating the hierarchic organization, whereby a cooperat...

Amide bond dissociation enthalpies: Effect of substitution on N[sbnd]C bond strength

The amide group plays an important role in the structure of proteins and is one of the major functional groups in organic chemistry. Although a large number of investigations were devoted to understanding the chemical character of the amide bond, little is known about the NC bond dissociation enthalpies (BDEs), which represent one of the fundamental sets of chemical thermodynamic data. In this study, the homolytic NC BDEs have been calculated for 55 amides and the effect of substituents on the strength of NC bond has been investigated using the Gaussian-4 (G4) method. The atomization reaction and isodesmic reaction procedures were used for accurate evaluations of enthalpies of formation of parent molecules and radicals derived from them by the breaking of the amide bond. It is demonstrated that the G4 method reproduces the experimental data with high accuracy in most cases. The large discrepancies between experimental and theoretical values revealed in some cases could be due to possible experimental errors. More reliable enthalpies of formation are recommended for 10 molecules and 9 radicals based on quantum chemical calculations. The accurate and internally consistent values of enthalpies of formation of amide molecules and corresponding radicals were used to calculate the NC BDEs. The trends observed in BDEs are associated with substituents on nitrogen and carbonyl. The electron-donating substituents (C(O), NHC(O), O, N3) on carbonyl increase the BDE; these groups, therefore, have stabilizing effect on amide bond. However, the methyl and phenyl substituents on nitrogen result in a decrease of 10–90kJ/mol in BDEs on going from primary to tertiary amides and, therefore, cause the amide bond to weaken. The observed BDE trends correlate with the NC bond lengths. Nitrogen atomic charges and second-order stabilization energy estimates obtained by NBO analysis can be also used to uncover trends in BDEs and build qualitative descriptions.