Mechanistic insights into the Bazarov synthesis of urea from NH3 and CO2 using electronic structure calculation methods

The mechanism of the noncatalyzed and reagent-catalyzed Bazarov synthesis of urea has extensively been investigated in the gas phase by means of density functional (B3LYP/6-31G(d,p)) and high quality ab initio (CBS-QB3) computational techniques. It was found that the first step of urea formation from NH3(g) and CO2(g) corresponds to a simple addition reaction leading to the carbamic acid intermediate, a process being slightly endothermic. Among the three possible reaction mechanisms considered, the addition-elimination-addition (AEA) and the double addition-elimination (DAE) mechanisms are almost equally favored, while the concerted (C) one was predicted kinetically forbidden. The second step involves the formation of loose adducts between NH3 and carbamic acid corresponding to an ammonium carbamate intermediate, which subsequently dehydrates to urea. The formation of "ammonium carbamate" corresponds to an almost thermoneutral process, whereas its dehydration, which is the rate-determining step, is highly endothermic. The Bazarov synthesis of urea is strongly assisted by the active participation of extra NH3 or H2O molecules (autocatalysis). For all reaction pathways studied the entire geometric and energetic profiles were computed and thoroughly analyzed. The reaction scheme described herein can be related with the formation of both isocyanic acid, H-N=C=O, and carbamic acid, H2N-COOH, as key intermediates in the initial formation of organic molecules, such as urea, under prebiotic conditions.     

Building blocks for coordination polymers: self-assembled cleft-like and planar discrete metallo-macrocyclic complexes

Discrete dinuclear metallo-macrocyclic complexes have been prepared from the flexible amide ligand N-6-[(3-pyridylmethylamino)carbonyl]pyridine-2-carboxylic acid (L1-CH(3)), and its more rigid analogue, N-6-[(3-pyridylamino)carbonyl]pyridine-2-carboxylic acid (L3-CH(3)). With ligands L1-CH(3) and L3-CH(3), discrete dinuclear metallo-macrocyclic complexes with the generic formula [Cu(2)(L1-CH(3))(2)(X)(2)(Y)(2)] (7, X = NO(3); 8, X = Cl, Y = H(2)O; 9, X = ClO(4), Y = CH(3)OH) and [Cu(2)(L3-CH(3))(2)(X)(2)(Y)(2)] (10, X = NO(3), Y = H(2)O; 11, X = ClO(4), Y = CH(3)OH) are obtained. For complexes 7-9, containing the more flexible link L1-CH(3), these complexes are cleft-shaped and hinged at the methylene spacer, which allows the cleft to widen and contract to accommodate different packing modes in the solid-state. In contrast, the rigid link L3-CH(3) gives near planar metallo-macrocyclic structures. These metallo-macrocyclic compounds may be useful building blocks for coordination polymers.     

Investigation of uranyl nitrate ion pairs complexed with amide ligands using electrospray ionization ion trap mass spectrometry and density functional theory

Ion populations formed from electrospray of uranyl nitrate solutions containing different amides vary depending on ligand nucleophilicity and steric crowding at the metal center. The most abundant species were ion pair complexes having the general formula [UO(2)(NO(3))(amide)(n=2,3)](+); however, singly charged complexes containing the amide conjugate base and reduced uranyl UO(2)(+) were also formed as were several doubly charged species. The formamide experiment produced the greatest diversity of species resulting from weaker amide binding, leading to dissociation and subsequent solvent coordination or metal reduction. Experiments using methyl formamide, dimethyl formamide, acetamide, and methyl acetamide produced ion pair and doubly charged complexes that were more abundant and less abundant complexes containing solvent or reduced uranyl. This pattern is reversed in the dimethylacetamide experiment, which displayed lower abundance doubly charged complexes, but augmented reduced uranyl complexes. DFT investigations of the tris-amide ion pair complexes showed that interligand repulsion distorts the amide ligands out of the uranyl equatorial plane and that complex stabilities do not increase with increasing amide nucleophilicity. Elimination of an amide ligand largely relieves the interligand repulsion, and the remaining amide ligands become closely aligned with the equatorial plane in the structures of the bis-amide ligands. The studies show that the phenomenological distribution of coordination complexes in a metal-ligand electrospray experiment is a function of both ligand nucleophilicity and interligand repulsion and that the latter factor begins exerting influence even in the case of relatively small ligands like the substituted methyl-formamide and methyl-acetamide ligands.     

Ab initio studies of structural features not easily amenable to experiment: Part 6. Quantitative estimate of the effect of bond delocalization on structure and hyperconjugative interaction of the amide group

The structural changes, which occur in the amide unit when the NH₂-group is twisted out of plane by rotation about the NC bond, have been determined by comparing the completely relaxed ab initio geometries of planar and perpendicular formamide and acetamide. In the perpendicular conformation, in which the π-electron amide resonance is uncoupled, the NC bond distance is 0.080.09 Å longer than in the planar form; the CO bond distance is about 0.01 Å shorter; NH distances are about 0.01 Å longer; and HNC angles are 510° smaller, whereas the CNO angle is relatively constant. Because of the apparent invariance of CH₃-hyperconjugation effects in planar and perpendicular acetamide, it is tentatively postulated that anomeric orbital interactive effects (involving the lone pair on NH, the CO π-electron pair and antibonding π*-group-orbitals on C(α) in NHC(HR)C(O)), which should be an important factor in determining peptide chain conformation, do not vary significantly with small deviations from amide group planarity.     

甘氨酸从水到酰胺衍生物水溶液中的迁移焓

用RD496-Ⅱ型微量热量计测定了298.15 K甘氨酸在N-甲基甲酰胺（NMF）,N, N-二甲基甲酰胺（DMF）,N-甲基乙酰胺（NMA）,N, N-二甲基乙酰胺（DMA）水溶液中的溶解焓,计算了甘氨酸从水到四种酰胺衍生物水溶液中的迁移焓（ΔtrH）。根据结构水合作用模型讨论了酰胺的结构对甘氨酸迁移焓的影响。实验结果表明：甘氨酸在酰胺衍生物水溶液中的迁移焓均为正值,并且随着溶液浓度增大而增大。比较甘氨酸在甲酰胺（FA）和乙酰胺（AD）水溶液中的迁移焓,发现在不同酰胺水溶液中迁移焓大小为：DMA>NMA>DMF>NMF>AD>FA。甘氨酸与甲酰胺之间以亲水-亲水相互作用为主,与其它酰胺之间以亲水-疏水作用为主。     

A spectroscopic study of model urethanes

The synthesis, far infrared spectra, temperature-dependent mid-infrared spectra in the carbonyl and NH stretching regions and the Fourier transform Raman spectra are reported for polycrystalline samples of three small diurethanes, 1,3-phenyl di(carbamic acid methyl ester),2,6-toluene di(carbamic acid methyl ester) and 2,4-toluene di(carbamic acid methyl ester). An ab initio geometry optimization is reported for methyl N-phenyl carbamate using STO-3G and 3-21G basis sets, and for the three small diurethanes by molecular mechanics methods using the Dreiding I force field. The results suggest that, in isotropic surroundings, only a very small number of the 256 possible conformers of the urethane groups in the three small diurethanes contribute appreciably to the structure.     

Microsolvation of formamide: a rotational study

Microsolvated formamide clusters have been generated in a supersonic jet expansion and characterized using Fourier transform microwave spectroscopy. Three conformers of the monohydrated cluster and one of the dihydrated complex have been observed. Seven monosubstituted isotopic species have been measured for the most stable conformer of formamide...H(2)O, which adopts a closed planar ring structure stabilized by two intermolecular hydrogen bonds (N-H...O(H)-H...O=C). The two higher energy forms of formamide...H(2)O have been observed for the first time. The second most stable conformer is stabilized by a O-H...O=C and a weak C-H...O hydrogen bond, while, in the less stable form, water accepts a hydrogen bond from the anti hydrogen of the amino group. For formamide...(H(2)O)(2), the parent and nine monosubstituted isotopic species have been observed. In this cluster the two water molecules close a cycle with the amide group through three intermolecular hydrogen bonds (N-H...O(H)-H...O(H)-H...O=C), the nonbonded hydrogen atoms of water adopting an up-down configuration. Substitution (r(s)) and effective (r(0)) structures have been determined for formamide, the most stable form of formamide...H(2)O and formamide...(H(2)O)(2). The results on monohydrated formamide clusters can help to explain the observed preferences of bound water in proteins. Clear evidence of sigma-bond cooperativity effects emerges when comparing the structures of the mono- and dihydrated formamide clusters. No detectable structural changes due to pi-bond cooperativity are observed on formamide upon hydration.     

Thermochemical Study of Solvation of Aliphatic Carboxamides in Aqueous Formamide Solutions

The entahlpies of solution of formamide, acetamide, and propionamide in aqueous formamide solutions (formamide concentration 8 mol kg^-1) at 298.15 K were measured. The entahlpies of transfer of amides from water to the mixed aqueous-organic solvent were calculated and compared with published data on the enthalpies of transfer of amides into aqueous urea solutions. The opposite trend in variation of the enthalpies of transfer of amides in these systems with increasing concentration of the nonaqueous component is due to different proton-donor power of formamide and urea relative to water. The enthalpy coefficients of pair interaction of amides with formamide in ternary aqueous solutions were calculated. Their positive values are due to endothermic interaction with formamide of the alkyl groups of amide molecules. The relative hydrophobicity of amides with different degrees of substitution of the amide group was estimated.     

The electronic structure of inorganic benzenes: valence bond and ring-current descriptions

Valence bond (VB) theory and ring-current maps have been used to study the electronic structure of inorganic benzene analogues X(6)H(6) (X = C (1), Si (2)), X(6) (X = N (3), P (4)), X(3)Y(3)H(6) (X,Y = B,N (5), B,P (6), Al,N (7), Al,P (8)), and B(3)Y(3)H(3) (Y = O (9), S (10)). It is shown that the homonuclear compounds possess benzene-like character, with resonance between two Kekulé-like structures and induced diatropic ring currents. Heteronuclear compounds typically show localization of the lone pairs on the electronegative atoms; Kekulé-like structures do not contribute. Of the heteronuclear compounds, only B(3)P(3)H(6) (6) has some benzene-like features with a significant contribution of two Kekulé-like structures to its VB wave function, an appreciable resonance energy, and a discernible diatropic ring current in planar geometry. However, relaxation of 6 to the optimal nonplanar chair conformation is accompanied by the onset of localization of the ring current.     

15N NMR spectroscopy. 30—structure/shift relationships of oligopeptides and copolypeptides,including gramicidin S

The ¹⁵N NMR spectra of various oligopeptide derivatives of the Z? X? Y? Y? OMe structure, where X and Y are variable amino acids and Z is the benzyloxycarbonyl group, were measured in several protic and aprotic solvents. The shift difference of the ¹⁵N of the Y? Y and X? Y bond (neighbouring residue effect) is discussed with respect to the nature of X and Y with respect to the solvent. Oligopeptides of the Z? X? Y? Y? OH and n?H₃? X? Y? Y? OMe structures were compared with the Z-pëptide esters to investigate the spectroscopic influence of the protecting groups. The methyl ester hydrochlorides of the 25 most common amino acids were measured in water and DMSO to elucidate the solvent dependence of the substituent effects. Moreover, the methyl ester hydrochlorides were compared with Z-amino acids and N-acetyl-amino acid methyl esters in DMSO to establish whether the substituent effects depend on the nature of the amino acid derivatives. In this connection the assignments of the serine, threonine and glycine signals are discussed with respect to silk proteins. Furthermore, the assignments of the signals of copolypeptides by comparison with oligo- and homo-polypeptides are discussed. Finally, it was demonstrated that intramolecular H bonds cause downfied shifts of 7–10 ppm of the acceptor amide groups.     

含有脲桥结构的苯氧乙酰胺衍生物的合成与表征

为了开发新型高效低毒杀菌剂,设计合成了5个未见文献报道的含有脲桥结构的苯氧乙酰胺类化合物,其结构经元素分析,1H NMR和IR确证.     

Silylanions: inversion barriers and NMR chemical shifts

Alpha-substituent effects on inversion barriers and NMR chemical shifts have been studied on a set of silyl anions, [X(3-n)Y(n)Si](-) (X, Y=H, CH(3), and SiH(3)). The MP2/6-31+G* optimized structures show a pattern of increasing inversion barriers with augmenting numbers of methyl substituents. The highest barrier of 48.5 kcalmol(-1) is obtained for the (CH(3))(3)Si(-) ion. The silyl group displays the opposite effect by decreasing the inversion barrier to a minimum of 16.3 kcalmol(-1) in (SiH(3))(3)Si(-). The influence of counterions on these barriers is probed by addition of a lithium or potassium cation. In most cases, a decrease of the energy barriers with respect to the bare anions is observed. The (29)Si NMR chemical shifts calculated at the IGLO-DFT and GIAO-MP2 level of theory are also analyzed in view of the substituents and counterions.     

Three New Urea Derivatives from Pliocene‐Fossil Pinus armandii

Three new urea derivatives, isolated from the Pliocene lignified wood of Pinus armandii, were identified as carbonylbis[imino(6‐methyl‐3,1‐phenylene)]bis[carbamic acid] dimethyl ester ( 1 ), and as the corresponding dibutyl ester 2 and bis(2‐methylpropyl) ester 3 . Their structures were elucidated by spectroscopic methods, including MS and 1D‐ and 2D‐NMR techniques.     

Synthesis and crystal structures of the potential tyrosinase inhibitors N‐(4‐acetylphenyl)‐2‐chloroacetamide and 2‐(4‐acetylanilino)‐2‐oxoethyl cinnamate

Substituted benzoic acid and cinnamic acid esters are of interest as tyrosinase inhibitors and the development of such inhibitors may help in diminishing many dermatological disorders. The tyrosinase enzyme has also been linked to Parkinson's disease. In view of hydroxylated compounds having ester and amide functionalities to potentially inhibit tyrosinase, we herein report the synthesis and crystal structures of two amide‐based derivatives, namely N‐(4‐acetylphenyl)‐2‐chloroacetamide, C₁₀H₁₀ClNO₂, (I), and 2‐(4‐acetylanilino)‐2‐oxoethyl cinnamate, C₁₉H₁₇NO₄, (II). In compound (I), the acetylphenyl ring and the N—(C=O)—C unit of the acetamide group are almost coplanar, with a dihedral angle of 7.39 (18)°. Instead of esterification, a cheaper and more efficient synthetic method has been developed for the preparation of compound (II). The molecular geometry of compound (II) is a V‐shape. The acetamide and cinnamate groups are almost planar, with mean deviations of 0.088 and 0.046 Å, respectively; the dihedral angle between these groups is 77.39 (7)°. The carbonyl O atoms are positioned syn and anti to the amide carbonyl O atom. In the crystals of (I) and (II), N—H…O, C—H…O and C—H…π interactions link the molecules into a three‐dimensional network.     

Mechanisms and kinetics for sorption of CO2 on bicontinuous mesoporous silica modified with n-propylamine

We studied equilibrium adsorption and uptake kinetics and identified molecular species that formed during sorption of carbon dioxide on amine-modified silica. Bicontinuous silicas (AMS-6 and MCM-48) were postsynthetically modified with (3-aminopropyl)triethoxysilane or (3-aminopropyl)methyldiethoxysilane, and amine-modified AMS-6 adsorbed more CO(2) than did amine-modified MCM-48. By in situ FTIR spectroscopy, we showed that the amine groups reacted with CO(2) and formed ammonium carbamate ion pairs as well as carbamic acids under both dry and moist conditions. The carbamic acid was stabilized by hydrogen bonds, and ammonium carbamate ion pairs formed preferably on sorbents with high densities of amine groups. Under dry conditions, silylpropylcarbamate formed, slowly, by condensing carbamic acid and silanol groups. The ratio of ammonium carbamate ion pairs to silylpropylcarbamate was higher for samples with high amine contents than samples with low amine contents. Bicarbonates or carbonates did not form under dry or moist conditions. The uptake of CO(2) was enhanced in the presence of water, which was rationalized by the observed release of additional amine groups under these conditions and related formation of ammonium carbamate ion pairs. Distinct evidence for a fourth and irreversibly formed moiety was observed under sorption of CO(2) under dry conditions. Significant amounts of physisorbed, linear CO(2) were detected at relatively high partial pressures of CO(2), such that they could adsorb only after the reactive amine groups were consumed.     

Exploring molecular recognition pathways within a family of gelators with different hydrogen bonding motifs

We report the synthesis of a family of gelators in which alkyl chains are connected to the amino groups of l-lysine methyl ester using a range of different hydrogen bonding linking groups (carbamate, amide, urea, thiourea and diacylhydrazine) using simple synthetic methodology based on isocyanate or acid chloride chemistry. The ability of these compounds to gelate organic solvents such as toluene or cyclohexane can be directly related to the ability of the linking group to form intermolecular hydrogen bonds. In general terms, the ability to structure solvents can be considered as: thiourea<carbamate<amide<urea∼diacylhydrazine. This process has been confirmed by thermal measurements, scanning electron microscopy (SEM) and infrared and circular dichroism spectroscopies. By deprotecting the methyl ester group, we have demonstrated that a balance between hydrophobic and hydrophilic groups is essential—if the system has too much hydrophilicity (e.g., diacylhydrazine, urea) it will not form gels due to low solubility in the organic media. However, the less effective gelators based on amide and carbamate linkages are enhanced by converting the methyl ester to a carboxylic acid. Furthermore, subsequent mixing of the acid with a second component (diaminododecane) further enhances the ability to form networks, and, in the case of the amide, generates a two-component gel, which can immobilise a wide range of solvents of industrial interest including petrol and diesel (fuel oils), olive oil and sunflower oil (renewable food oils) and ethyl laurate, isopropyl myristate and isopropyl palmitate (oils used in pharmaceutical formulation). The gels are all thermoreversible, and may therefore be useful in controlled release/formulation applications.     

Key Role of Intramolecular Metal Chelation and Hydrogen Bonding in the Cobalt‐Mediated Radical Polymerization of N‐Vinyl Amides

This work reveals the preponderance of an intramolecular metal chelation phenomenon in a controlled radical polymerization system involving the reversible trapping of the radical chains by a cobalt complex bis(acetylacetonato)cobalt(II). The cobalt‐mediated radical polymerization (CMRP) of a series of N‐vinyl amides was considered with the aim of studying the effect of the cobalt chelation by the amide moiety of the last monomer unit of the chain. The latter reinforces the cobalt? polymer bond in the order N‐vinylpyrrolidone<N‐vinyl caprolactam<N‐methyl‐N‐vinyl acetamide, and is responsible for the optimal control of the polymerizations observed for the last two monomers. Such a double linkage between the controlling agent and the polymer, through a covalent bond and a dative bond, is unique in the field of controlled radical polymerization and represents a powerful opportunity to fine tune the equilibrium between latent and free radicals. Possible hydrogen bond formation is also taken into account in the case of N‐vinyl acetamide and N‐vinyl formamide. These results are essential for understanding the factors influencing Co? C bond strength in general, and the CMRP mechanism in particular, but also for developing a powerful platform for the synthesis of new precision poly(N‐vinyl amide) materials, which are an important class of polymers that sustain numerous applications today.     

"Amide resonance" correlates with a breadth of C-N rotation barriers

Complete basis set calculations (CBS-QB3) were used to compute the CN rotation barriers for acetamide and eight related compounds, including acetamide enolate and O-protonated acetamide. Natural resonance theory analysis was employed to quantify the "amide resonance" contribution to ground-state electronic structures. A range of rotation barriers, spanning nearly 50 kcal/mol, correlates well to the ground-state resonance weights without the need to account for transition-state effects. Use of appropriate model compounds is crucial to gain an understanding of the structural and electronic changes taking place during rotation of the CN bond in acetamide. The disparate changes in bond length (DeltarCO < DeltarCN) are found to be consonant with the resonance model. Similarly, charge differences are consistent with donation from the nitrogen lone pair electrons into the carbonyl pi* orbital. Despite recent attacks on the resonance model, these findings demonstrate it to be a sophisticated and highly predictive tool in the chemist's arsenal.     

Reactivity of a (mu-oxo)(mu-hydroxo)diiron(III) diamond core with water, urea, substituted ureas, and acetamide

A series of iron(III) complexes of the tetradentate ligand BPMEN (N,N'-dimethyl-N,N'-bis(2-pyridylmethyl)ethane-1,2-diamine) were prepared and structurally characterized. Complex [Fe(2)(mu-O)(mu-OH)(BPMEN)(2)](ClO(4))(3) (1) contains a (mu-oxo)(mu-hydroxo)diiron(III) diamond core. Complex [Fe(BPMEN)(urea)(OEt)](ClO(4))(2) (2) is a rare example of a mononuclear non-heme iron(III) alkoxide complex. Complexes [Fe(2)(mu-O)(mu-OC(NH(2))NH)(BPMEN)(2)](ClO(4))(3) (3) and [Fe(2)(mu-O)(mu-OC(NHMe)NH)(BPMEN)(2)](ClO(4))(3) (4) feature N,O-bridging deprotonated urea ligands. The kinetics and equilibrium of the reactions of 1 with ligands L (L = water, urea, 1-methylurea, 1,1-dimethylurea, 1,3-dimethylurea, 1,1,3,3-tetramethylurea, and acetamide) in acetonitrile solutions were studied by stopped-flow UV-vis spectrophotometry, NMR, and mass spectrometry. All these ligands react with 1 in a rapid equilibrium, opening the four-membered Fe(III)(mu-O)(mu-OH)Fe(III) core and forming intermediates with a (HO)Fe(III)(mu-O)Fe(III)(L) core. The entropy and enthalpy for urea binding through oxygen are DeltaH degrees = -25 kJ mol(-1) and DeltaS degrees = -53.4 J mol(-1) K(-1) with an equilibrium constant of K(1) = 37 L mol(-1) at 25 degrees C. Addition of methyl groups on one of the urea nitrogen did not affect this reaction, but the addition of methyl groups on both nitrogens considerably decreased the value of K(1). An opening of the hydroxo bridge in the diamond core complex [Fe(2)(mu-O)(mu-OH)(BPMEN)(2)] is a rapid associative process, with activation enthalpy of about 60 kJ mol(-1) and activation entropies ranging from -25 to -43 J mol(-1) K(-1). For the incoming ligands with the -CONH(2) functionality (urea, 1-methylurea, 1,1-dimethylurea, and acetamide), a second, slow step occurs, leading to the formation of stable N,O-coordinated amidate diiron(III) species such as 3 and 4. The rate of this ring-closure reaction is controlled by the steric bulk of the incoming ligand and by the acidity of the amide group.     

Unexpected formation of an azetidine-carborane derivative by dehydration of N-(1,12-dicarba-closo-dodecaboran-1-yl)formamide. The first X-ray structure of a 2,3-bis(imino)azetidine

Efforts to dehydrate (1,12-dicarba-closo-dodecaboran(12)-1-yl)formamide (a = 6.685(2) A, b = 12.877(4) A, c = 12.547(4) A, alpha = gamma = 90 degrees, beta = 90.724(11) degrees, V = 1080.8(6) A(3), Z = 4) resulted in the formation of a series of unexpected products. Addition of the Burgess reagent to the formamide, for example, led to the isolation of the corresponding methyl carbamate (a = 11.529(8) A, b = 11.529(8) A, c = 11.402(12) A, alpha = beta = gamma = 90 degrees, V = 1516(2) A(3), Z = 4), while treatment with triphosgene, a well-known dehydrating agent, resulted in the formation of a highly unusual 2,3-bis(p-carboranylimino)azetidine derivative. This particular compound, in the presence of Re(I), was hydrolyzed to give the corresponding amide, which is the first example of a 2,3-bis(imino)azetidine that has been characterized crystallographically (a = 38.496(13) A, b = 11.920(4) A, c = 27.523(10) A, beta = 127.050(5) degrees, V = 10079(6) A(3), Z = 8).