Electrostatic DFT map for the complete vibrational amide band of NMA

An anharmonic vibrational Hamiltonian for the amide I, II, III, and A modes of N-methyl acetamide (NMA), recast in terms of the 19 components of an external electric field and its first and second derivative tensors (electrostatic DFT map), is calculated at the DFT(BPW91/6-31G(d,p)) level. Strong correlations are found between NMA geometry and the amide frequency fluctuations calculated using this Hamiltonian together with the fluctuating solvent electric field obtained from the MD simulations in TIP3 water. The amide I and A frequencies are strongly positively correlated with the C=O and N-H bond lengths. The C=O and C-N amide bond lengths are negatively correlated, suggesting the solvent-induced fluctuations of the contribution of zwitterionic resonance form. Sampling the global electric field in the entire region of the transition charge densities (TCDs) is required for accurate infrared line shape simulations. Collective electrostatic solvent coordinates which represent the fluctuations of the 10 lowest amide fundamental and overtone states are reported. Normal-mode analysis of an NMA-3H(2)O cluster shows that the 660 cm(-1) to 1100 cm(-1) oscillation found in the frequency autocorrelation functions of the amide modes may be ascribed to the two bending vibrations of intermolecular hydrogen bonds with the amide oxygen of NMA.     

Vibrational-exciton couplings for the amide I, II, III, and A modes of peptides

The couplings between all amide fundamentals and their overtones and combination vibrational states are calculated. Combined with the level energies reported previously (Hayashi, T.; Zhuang, W.; Mukamel, S. J. Phys. Chem. A 2005, 109, 9747), we obtain a complete effective vibrational Hamiltonian for the entire amide system. Couplings between neighboring peptide units are obtained using the anharmonic vibrational Hamiltonian of glycine dipeptide (GLDP) at the BPW91/6-31G(d,p) level. Electrostatic couplings between non-neighboring units are calculated by the fourth rank transition multipole coupling (TMC) expansion, including 1/R3 (dipole-dipole), 1/R4 (quadrupole-dipole), and 1/R5 (quadrupole-quadrupole and octapole-dipole) interactions. Exciton delocalization length and its variation with frequency in the various amide bands are calculated. The simulated infrared amide I and II absorptions and CD spectra of 24 residue alpha-helical motifs (SPE3) are in good agreement with experiment.     

A new chiral lithium amide based on (S)-2-[1-(3,3-dimethyl)pyrrolidinylmethyl]pyrrolidine—synthesis,NMR studies and use in the enantioselective deprotonation of cyclohexene oxide

A new chiral lithium amide has been designed starting from (S)-proline. This new chiral lithium amide has been used for asymmetric deprotonation/ring opening of cyclohexene oxide to give (S)-2-cyclohexen-1-ol in 88% yield and 78% enantiomeric excess. NMR studies of the lithium amide and the ligand–substrate complex are also presented.     

5-Perfluoroalkyl bicyclic amide acetals

A new route to a novel class of bicyclic amide acetals, 5-perfluoroalkyl-4,6-dioxa-1-azabicyclo [3.3.0] octanes, is described. These compounds are prepared by the acid catalyzed dehydration of N,N-bis-(2-hydroxyethyl)-perfluoroalkylamides and are characterized by their lack of reactivity with a variety of electrophiles and nucleophiles relative to the very reactive 5-alkyl bicyclic amide acetals.     

Study of the Natural Product Intermediates of Steviolbioside,Steviol, and Isosteviol; O‐ and N‐Acylated Forms of Benzotriazoyl Esters

Glycosides, steviolside, and rubaudioside A, which are extracted from the leaves of Stevia rebaudiana, can be used as sweetener for food additive. Intermediates of steviolbioside, steviol, and isosteviol are very stable compounds obtained from benzotriazol‐1‐yloxtri(pyrrolidinol)phosphonium hexafluorophosphate. They are suitable to be used in amide and amide dimer synthesis. These nature product intermediates possess special characteristics. The spectra data showed two tautomeric groups: an ester form and an amide form. Their nuclear magnetic resonance, mass and chromatographic/mass/mass spectra were examined.     

Hydrogen-bonding dynamics in aqueous solutions of amides and acids: monomer, dimer, trimer, and polymer

Hydrogen-bonding dynamics in aqueous solutions of series of amides and acids have been investigated by means of femtosecond Raman-induced Kerr effect spectroscopy and ab initio quantum chemistry calculation. The amides and acids studied here are acetamide, 1,3-propanedicarboxamide, 1,3,5-pentanetricaroxamide, polyacrylamide with Mw=1500, acetic acid, 1,3-propanedicarboxylic acid, 1,3,5-pentanetricarboxylic acid, and poly(acrylic acid) with Mw=2000. The femtosecond damped transient feature for aqueous amide solutions, which arises from the intermolecular hydrogen bonds of amide and water, becomes clearer with the larger molecular weight of amide. A characteristic vibrational band at about 100 cm(-1) is assigned as the hydrogen-bonding vibrational mode and the ab initio quantum chemistry calculation result indicates that at least two waters, which make up the hydrogen-bonding network with amide, are necessary for this mode. The hydrogen-bonding vibrational mode at about 100 cm(-1) in aqueous amide solutions shifts to the higher frequency with the larger molecular weight amide in consequence of the stronger intermolecular interaction between amide and water. The evidence likely comes from the stronger hydrophobic interaction for polymer than oligomers and monomer. In the picosecond time region, an extra slow relaxation process with a time constant of about 60 ps has been found in the aqueous polymer solutions. The relaxation is assigned as a local motion of the constitutional repeat unit of polymers from comparison with monomer and oligomers.     

The arginine anomaly: arginine radicals are poor hydrogen atom donors in electron transfer induced dissociations

Arginine amide radicals are generated by femtosecond electron transfer to protonated arginine amide cations in the gas phase. A fraction of the arginine radicals formed (2-amino-5-dihydroguanid-1'-yl-pentanamide, 1H) is stable on the 6.7 micros time scale and is detected after collisional reionization. The main dissociation of 1H is loss of a guanidine molecule from the side chain followed by consecutive dissociations of the 2-aminopentanamid-5-yl radical intermediate. Intramolecular hydrogen atom transfer from the guanidinium group onto the amide group is not observed. These results are explained by ab initio and density functional theory calculations of dissociation and transition state energies. Loss of guanidine from 1H is calculated to require a transition state energy of 68 kJ mol(-)(1), which is substantially lower than that for hydrogen atom migration from the guanidine group. The loss of guanidine competes with the reverse migration of the arginine alpha-hydrogen atom onto the guanidyl radical. RRKM calculations of dissociation kinetics predict the loss of guanidine to account for >95% of 1H dissociations. The anomalous behavior of protonated arginine amide upon electron transfer provides an insight into electron capture and transfer dissociations of peptide cations containing arginine residues as charge carriers. The absence of efficient hydrogen atom transfer from charge-reduced arginine onto sterically proximate amide group blocks one of the current mechanisms for electron capture dissociation. Conversely, charge-reduced guanidine groups in arginine residues may function as radical traps and induce side-chain dissociations. In light of the current findings, backbone dissociations in arginine-containing peptides are predicted to involve excited electronic states and proceed by the amide superbase mechanism that involves electron capture in an amide pi* orbital, which is stabilized by through-space coulomb interaction with the remote charge carriers.     

Spectroscopic, semi-empirical and antimicrobial studies of a new amide of monensin A with 4-aminobenzo-15-crown-5 and its complexes with Na cation at 1:1 and 1:2 ratios

A new amide of monensin A with 4-aminobenzo-15-crown-5 (M-AM3) was synthesised and its ability to form complexes with Na⁺ cations was studied by ESIMS, ¹H, ¹³C and ²³Na NMR, FTIR and PM5 semi-empirical methods. ESI mass spectrometry indicates that in the gas phase M-AM3 amide forms complexes of 1:1 and 1:2 stoichiometry with Na⁺ cations. The formation of such complexes is also confirmed in the acetonitrile solution, in which the existence of equilibrium between two structures A and B is found, of which B structure is dominant. The structures of M-AM3 and its 1:1 and 1:2 complexes with Na⁺ cations are stabilised by various intramolecular hydrogen bonds, which are discussed in detail. The in vitro biological tests have demonstrated that the new M-AM3 amide shows good activity towards some strains of Gram-positive bacteria (MIC 25-50 μg/ml).     

Effects of internal hydrogen bonds between amide groups: protonation of alicyclic diamides

The proton affinity (PA) of cyclopentane carboxamide 1, cyclohexane carboxamide 2 and their secondary and tertiary amide derivatives S1, S2, T1 and T2, was determined by the thermokinetic method and the kinetic method [PA(1) = 888 +/- 5 kJ mol(1); PA(2) = 892 +/- 5 kJ mol(1); PA(S1) = 920 +/- 6 kJ mol(1); PA(S2) = 920 +/- 6 kJ mol(1); PA(T1) = 938 +/- 6 kJ mol(1); PA(T2) = 938 +/- 6 kJ mol(1)]. Special entropy effects are not observed. Additionally, the effects of protonation have been studied using an advanced kinetic method for all isomers 37 of cyclopentane dicarboxamides and cyclohexane dicarboxamides (with the exception of cis-cyclopentane-1,2-dicarboxamide) and their bis-tertiary derivatives T3T7 by estimating the PA and the apparent entropy of protonation Delta(DeltaS(app)). Finally, the study was extended to bicyclo[2.2.1]hepta-2,5-diene-2,3-dicarboxamide 8 and its bis-tertiary derivative T8, to all stereoisomers of bicyclo[2.2.1]heptane-2,3-dicarboxamide 9, their secondary and tertiary amide derivatives S9 and T9, and to endoendobicyclo[2.2.1]heptane-2,5-dicarboxamide 10 and the corresponding secondary and tertiary derivatives S10 and T10. Compared with 1 and 2, all alicyclic diamides exhibit a significant increase of the PA (DeltaPA) and special entropy effects on protonation. For alicyclic diamides, which can not accommodate a conformation appropriate for building a proton bridge, the values of DeltaPA and Delta(DeltaS(app)) are small to moderate. This is explained by ion / dipole interactions between the protonated and neutral amide group which stabilize the protonated species but hinder the free rotation of the amide groups. If any of the conformations of the alicyclic diamide allows formation of a proton bridge, DeltaPA and Delta(DeltaS(app)) increase considerably. A spectacular case is cis-cyclohexane-1,4-dicarboxamide 7c which is the most basic monocyclic diamide, although generation of the proton bridge requires the unfavorable boat conformation with both amide substituents at a flagpole position. A pre-orientation of the two amide groups in such a 1,4-position in 10 results in a particularly large PA of < 1000 kJ mol(1). The observation of comparable values for Delta(DeltaS(app)) for linear and monocyclic diamides indicates that a major part of the entropy effects originates from freezing the free rotation of the amide groups by formation of the proton bridge. This is corroborated by observing corresponding effects during the protonation of dicarboxamides containing the rigid bicyclo[2.2.1]heptane carbon skeleton, where the only internal movements of the molecules corresponds to rotation of the amide substituents.     

红外光谱酰胺Ⅲ带用于蛋白质二级结构的测定研究

用甲醇对BSA和RaseA等蛋白质进行变性处理,结合蛋白质酰胺带的拟合结果对酰胺带各二级结构的谱峰进行了初步指认:1330～1290cm^-1为α-螺旋;1295～1265cm^-1为β-转角;1270～1245cm^-1为无规卷曲;1250～1220cm^-1为β-折叠.依据这些谱峰归属,对一些已知二级结构的蛋白质进行了测定,所得结果与X射线衍射数据以及酰胺带的定量结果基本一致.     

A nitrogen-15 NMR study of hydrogen bonding in 1-alkyl-4-imino-1,4-dihydro-3-quinolinecarboxylic acids and related compounds

The title compounds contain groups (amine, amide, imine, carboxylic acid) that are capable of forming intramolecular hydrogen bonds involving a six-membered ring. In compounds where the two interacting functional groups are imine and carboxylic acid, the imine is protonated to give a zwitterion; where the two groups are imine and amide, the amide remains intact and forms a hydrogen bond to the imine nitrogen. The former is confirmed by the iminium 15N signal, which shows the coupling of 1J(15N,1H) -85 to -86.8 Hz and 3J(1H,1H) 3.7-4.2 Hz between the iminium proton and the methine proton of a cyclopropyl substituent on the iminium nitrogen. Hydrogen bonding of the amide is confirmed by its high 1H chemical shift and by coupling of the amide hydrogen to (amide) nitrogen [(1J(15N,1H) -84.7 to -90.7 Hz)] and to ortho carbons of a phenyl substituent. Data obtained from N,N-dimethylanthranilic acid show 15N-1H coupling of (-)8.2 Hz at 223 K (increasing to (-)5.3 Hz at 243 K) consistent with the presence of a N... H-O hydrogen bond.     

Reductive amidation of nitroarenes: a practical approach for the amidation of natural products

A simple and practical approach for the one-pot conversion of nitroarenes into amide derivatives has been developed. Zinc and acetic acid are utilized as a reducing agent, and acyl chloride and triethylamine are used as the acylating agent in DMF with good yield (∼60%) of the amide. This method was applicable to manzamine A (1), where the yield of 6-cyclohexamidemanzamine A (7) was significantly improved (56%) by this approach relative to (17%) by beginning with the amine.     

Raman spectroscopic characterization of secondary structure in natively unfolded proteins: alpha-synuclein

The application of Raman spectroscopy to characterize natively unfolded proteins has been underdeveloped, even though it has significant technical advantages. We propose that a simple three-component band fitting of the amide I region can assist in the conformational characterization of the ensemble of structures present in natively unfolded proteins. The Raman spectra of alpha-synuclein, a prototypical natively unfolded protein, were obtained in the presence and absence of methanol, sodium dodecyl sulfate (SDS), and hexafluoro-2-propanol (HFIP). Consistent with previous CD studies, the secondary structure becomes largely alpha-helical in HFIP and SDS and predominantly beta-sheet in 25% methanol in water. In SDS, an increase in alpha-helical conformation is indicated by the predominant Raman amide I marker band at 1654 cm(-1) and the typical double minimum in the CD spectrum. In 25% HFIP the amide I Raman marker band appears at 1653 cm(-1) with a peak width at half-height of approximately 33 cm(-1), and in 25% methanol the amide I Raman band shifts to 1667 cm(-1) with a peak width at half-height of approximately 26 cm(-1). These well-characterized structural states provide the unequivocal assignment of amide I marker bands in the Raman spectrum of alpha-synuclein and by extrapolation to other natively unfolded proteins. The Raman spectrum of monomeric alpha-synuclein in aqueous solution suggests that the peptide bonds are distributed in both the alpha-helical and extended beta-regions of Ramachandran space. A higher frequency feature of the alpha-synuclein Raman amide I band resembles the Raman amide I band of ionized polyglutamate and polylysine, peptides which adopt a polyproline II helical conformation. Thus, a three-component band fitting is used to characterize the Raman amide I band of alpha-synuclein, phosvitin, alpha-casein, beta-casein, and the non-A beta component (NAC) of Alzheimer's plaque. These analyses demonstrate the ability of Raman spectroscopy to characterize the ensemble of secondary structures present in natively unfolded proteins.     

Rotational spectra and computational analysis of two conformers of leucinamide

Rotational spectra were recorded for two isotopic species of two conformers of the amide derivative of leucine in the range of 10.5-21 GHz and fit to a rigid rotor Hamiltonian. Ab initio calculations at the MP2/6-311++G(d,p) level identified the low energy conformations with different side chain configurations; the rotational spectra were assigned to the two lowest energy ab initio structures. We recorded 16 a- and b-type rotational transitions for conformer 1; the rotational constants of the normal species are A = 2275.6(2), B = 1033.37(2) and C = 911.71(5) MHz. We recorded 23 a- and b-type rotational transitions for conformer 2; the rotational constants of the normal species are A = 2752.775(8), B = 843.502(1) and C = 796.721(1) MHz. The rotational spectra of the (15)N(amide) isotopomer of each conformer were recorded and the atomic coordinates of the amide nitrogen were determined by Kraitchman's method of isotopic substitution. The experimentally observed structures are significantly different from the crystal structures of leucinamide and the gas-phase structures of leucine, and a natural bond orbital analysis revealed the donor-acceptor interactions governing side chain configuration.     

In vitro and in vivo production of new aminocoumarins by a combined biochemical, genetic, and synthetic approach

The aminocoumarin antibiotics clorobiocin, novobiocin, and coumermycin A(1) are inhibitors of bacterial gyrase. Their chemical structures contain amide bonds, formed between an aminocoumarin ring and an aromatic acyl component, which is 3-dimethylallyl-4-hydroxybenzoate in the case of novobiocin and clorobiocin. These amide bonds are formed under catalysis of the gene products of cloL, novL, and couL, respectively. We first examined the substrate specificity of the purified amide synthetases CloL, NovL, and CouL for the various analogs of the prenylated benzoate moiety. We then generated new aminocoumarin antibiotics by feeding synthetic analogs of the 3-dimethylallyl-4-hydroxybenzoate moiety to a mutant strain defective in the biosynthesis of the prenylated benzoate moiety. This resulted in the formation of 32 new aminocoumarin compounds. The structures of these compounds were elucidated using FAB-MS and (1)H-NMR spectroscopy.     

Twisted amide reduction under Wolff-Kishner conditions: synthesis of a benzo-1-aza-adamantane derivative

A synthesis of 4,5-benzo-1-aza-tricyclo[4.3.1.1(3,8)]undecane (1), a benzo-1-aza-adamantane derivative, is described and features a previously unknown application of the Wolff-Kishner reduction of a nonresonance stabilized or "twisted" amide. An intermediate amino ester is converted to a severely "twisted amide", which, when exposed to hydrazine in alcohol, provides the corresponding "twisted" amino hydrazone. Wolff-Kishner conditions (KOH/ethylene glycol, 200 degrees C) provide the reduced target 1 without hydrolysis to amino acid derivatives. These operations are conveniently performed in a single flask in high yield.     

Computation of the amide I band of polypeptides and proteins using a partial Hessian approach

A partial Hessian approximation for the computation of the amide I band of polypeptides and proteins is introduced. This approximation exploits the nature of the amide I band, which is largely localized on the carbonyl groups of the backbone amide residues. For a set of model peptides, harmonic frequencies computed from the Hessian comprising only derivatives of the energy with respect to the displacement of the carbon, oxygen, and nitrogen atoms of the backbone amide groups introduce mean absolute errors of 15 and 10 cm(-1) from the full Hessian values at the Hartree-Fock/STO-3G and density functional theory EDF16-31G(*) levels of theory, respectively. Limiting the partial Hessian to include only derivatives with respect to the displacement of the backbone carbon and oxygen atoms yields corresponding errors of 24 and 22 cm(-1). Both approximations reproduce the full Hessian band profiles well with only a small shift to lower wave number. Computationally, the partial Hessian approximation is used in the solution of the coupled perturbed Hartree-Fock/Kohn-Sham equations and the evaluation of the second derivatives of the electron repulsion integrals. The resulting computational savings are substantial and grow with the size of the polypeptide. At the HF/STO-3G level, the partial Hessian calculation for a polypeptide comprising five tryptophan residues takes approximately 10%-15% of the time for the full Hessian calculation. Using the partial Hessian method, the amide I bands of the constituent secondary structure elements of the protein agitoxin 2 (PDB code 1AGT) are calculated, and the amide I band of the full protein estimated.     

Significant enhancement of electron transfer reduction of NAD(+) analogues by complexation with scandium ion and the detection of the radical intermediate-scandium ion complex

4-Acetyl-N,N-diisopropyl-1-benzylnicotinamidinium ion (ABNA(+)) and 1-benzyl-4-phenylnicotinamidinium ion (PhBNA(+)) were newly synthesized as NAD(+) analogues to examine the electron-transfer reactivity and the effects of metal ions on the reactivity in comparison with those of 1-benzylnicotinamidinium ion (BNA(+)) and 1-methyl-4-phenylpyridinium ion (MPP(+)) which has no amide or acetyl group. A remarkable positive shift in the one-electron reduction potential of ABNA(+) was observed in the presence of Sc(3+) which forms a 1:1 complex with ABNA(+) through both acetyl and amide groups, whereas no such shift in the presence of Sc(3+) was observed for the one-electron reduction of MPP(+) which has no acetyl or amide group. Similar but less positive shifts in the one-electron reduction potentials were observed in the presence of Sc(3+) for the one-electron reduction of BNA(+) and PhBNA(+) both of which have only one amide group. The rate of electron-transfer reduction of ABNA(+) is enhanced significantly by the complexation with Sc(3+) to produce stable ABNA(*)-Sc(3+) complex which has been successfully detected by ESR. The electron self-exchange rates of the MPP(*)/MPP(+) system have been determined from the ESR line width variation and are compared with those of the ABNA(*)/ABNA(+) system.     

Preparation and properties of new poly(amide‐imide)s based on 1,4‐bis(4‐trimellitimidophenoxy)naphthalene and aromatic diamines

A diimide dicarboxylic acid, 1,4‐bis(4‐trimellitimidophenoxy)naphthalene (1,4‐BTMPN), was prepared by condensation of 1,4‐bis(4‐aminophenoxy)naphthalene and trimellitic anhydride at a 1 : 2 molar ratio. A series of novel poly(amide‐imide)s (IIa–k) with inherent viscosities of 0.72 to 1.59 dL/g were prepared by triphenyl phosphite‐activated polycondensation from the diimide‐diacid 1,4‐BTMPN with various aromatic diamines (Ia–k) in a medium consisting of N‐methyl‐2‐pyrrolidinone (NMP), pyridine, and calcium chloride. The poly(amide‐imide)s showed good solubility in NMP, N,N‐dimethylacetamide, and N,N‐dimethylformamide. The thermal properties of the obtained poly(amide‐imide)s were examined with differential scanning calorimetry and thermogravimetry analysis. The synthesized poly(amide‐imide)s possessed glass‐transition temperatures in the range of 215 to 263°C. The poly(amide‐imide)s exhibited excellent thermal stabilities and had 10% weight losses at temperatures in the range of 538 to 569°C under a nitrogen atmosphere. A comparative study of some corresponding poly(amide‐imide)s also is presented. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 1–8, 2000     

Three-dimensional porous coordination polymer functionalized with amide groups based on tridentate ligand: selective sorption and catalysis

To create a functionalized porous compound, amide group is used in porous framework to produce attractive interactions with guest molecules. To avoid hydrogen-bond formation between these amide groups our strategy was to build a three-dimensional (3D) coordination network using a tridentate amide ligand as the three-connector part. From Cd(NO3)2.4H2O and a three-connector ligand with amide groups a 3D porous coordination polymer (PCP) based on octahedral Cd(II) centers, {[Cd(4-btapa)2(NO3)2].6H2O.2DMF}n (1a), was obtained (4-btapa = 1,3,5-benzene tricarboxylic acid tris[N-(4-pyridyl)amide]). The amide groups, which act as guest interaction sites, occur on the surfaces of channels with dimensions of 4.7 x 7.3 A2. X-ray powder diffraction measurements showed that the desolvated compound (1b) selectively includes guests with a concurrent flexible structural (amorphous-to-crystalline) transformation. The highly ordered amide groups in the channels play an important role in the interaction with the guest molecules, which was confirmed by thermogravimetric analysis, adsorption/desorption measurements, and X-ray crystallography. We also performed a Knoevenagel condensation reaction catalyzed by 1a to demonstrate its selective heterogeneous base catalytic properties, which depend on the sizes of the reactants. The solid catalyst 1a maintains its crystalline framework after the reaction and is easily recycled.