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Conformation of Secondary Amides. A Predictive Algorithm That Correlates DFT-Calculated Structures and Experimental Proton Chemical Shifts †
Abstract
The magnetic deshielding caused by the amido group on CON-CHalpha protons of secondary amides can easily be correlated with DFT-based structures at the B3LYP/6-31G level of theory via a novel algorithm that refines previous models, such as the classical McConnell equation. The shift is given by delta = a + 2.16 cos2(alpha - 35)/d, where alpha denotes the virtual dihedral angle resulting from linking the carbonyl and the alpha-carbons and d is the distance (A) between the shifted proton and the carbonyl oxygen. Notably, in this equation a is a parameter that can be optimized for different solvents, namely, CDCl3, DMSO-d6, and D2O. For the development of these correlations, the preferential conformation of amides is taken from the optimized structures in the gas phase obtained at the DFT level. The deshielding on anti and gauche protons in both rotamers of (Z)-acetamides and E/Z isomers of formamides has been evaluated. This methodology has proved to be highly reliable, allowing us to discard ab initio or DFT conformational arrangements when shifts calculated by the above-mentioned equation differ from the experimental values. Thus, the anti disposition between the CHalpha proton and the N-H bond appears to be the more stable conformation of simple amides. For amides bearing only one proton at Calpha, a local syn minimum can equally be characterized. The rotational barriers around the CON-alkyl bond along with the pyramidalization of the amido group have also been reassessed. As the conformation is taken away from anti or local syn minima, the nonplanarity of the amido group appears to increase.
... Overall, the spectral patterns are similar to those observed for 37, nevertheless. Scheme 7 (R = Me, R 1 = Ph) shows the possible rotamers for the benzyl and tertiary acetamido groups [107], along with a visual description of the φ, ϕ, and ψ angles for conformational analyses. The amide-group stereochemistry of 37 in the solid state ( Figure 3) is Z-syn-anti (φ = 0, ϕ = 0, ψ = 180), but the chemical shift of H-2 indicates that the most stable rotamer in the solution must be the Z-anti-syn (φ = 0, ϕ = 180, ψ = 0) conformer [107], since this is the disposition that generates less steric hindrance, being the only one actually detected in both the 1 H and 13 C NMR spectra. ...
... Scheme 7 (R = Me, R 1 = Ph) shows the possible rotamers for the benzyl and tertiary acetamido groups [107], along with a visual description of the φ, ϕ, and ψ angles for conformational analyses. The amide-group stereochemistry of 37 in the solid state ( Figure 3) is Z-syn-anti (φ = 0, ϕ = 0, ψ = 180), but the chemical shift of H-2 indicates that the most stable rotamer in the solution must be the Z-anti-syn (φ = 0, ϕ = 180, ψ = 0) conformer [107], since this is the disposition that generates less steric hindrance, being the only one actually detected in both the 1 H and 13 C NMR spectra. ...
... This behavior has already been described in tertiary amides, in which the CH proton adjacent to the amide group in the Z-anti orientation is shifted downfield, by ca. 1.4 ppm, relative to an E conformation [107,108]. Also, the existence of restricted rotation is evident through the signal shape, small and broad, of the C-2 and CH 2 signals in the benzyl group of the Z-anti conformer. Scheme 7. E/Z rotamers around N-alkyl and acyl amido moieties. ...
This paper explores and revisits in detail the formation and characterization of sugar-based aminonitriles, whose ultimate origin can be traced to the interaction of biomolecules with cyanide. Although the synthesis and spectroscopic data of 2-amino-aldononitriles were reported long ago, there are both contradictory and confusing results among the published data. We have now addressed this concern through an exhaustive structural elucidation of acylated 2-amino- and 2-alkyl(aryl)amino-2-deoxyaldonitriles using mass spectrometry and FT-IR, FT–Raman, and NMR spectroscopies. Several structures could be unambiguously determined through single-crystal X-ray diffraction, which allowed us to correct other misassignments. Moreover, this study unveils how steric and electronic effects influence the acylation outcome of the amino, (alkyl, aryl)amino, or acetamido group at C-2. The chirality at the latter, which was assigned tentatively through optical rotation correlation, and hence the preferential threo stereochemistry generated during the cyanohydrin synthesis of 2-amino-2-deoxy aldononitriles have now been established with confidence.
... A predictive algorithm that correlated DFT-calculated structures and proton chemical shifts of the CHα proton was developed. 17 The analysis of the X-ray crystal structures of simple amides and small peptides indicated that the conformations adopted by the secondary amides in the solid state are very similar in general to the anti conformers found in the gas phase and in solution. 18 In this context, we observed that N-cyclopropylacetamide (1), a small aliphatic secondary amide for which only a very predominant trans rotamer was expected, displayed 19% cis rotamer in CDCl 3 , which is a significant population in comparison to the low or undetectable cis rotamer population reported for other aliphatic secondary amides. ...
... The NMR analysis provided additional insights into the conformational behavior of 1 around the N−cPr bond through the analysis of the NH−CH coupling constant across this bond. Aliphatic acetamides arrange the NH proton in an anti disposition with respect to the CH proton, 16,17 and a large NH−CH coupling constant would be expected according to the Karplus−Altona equation. 23 For instance, the large 3 J HN-HC values measured for 2 (7.4 Hz for both rotamers) and 3 (8.1 and 8.3 Hz for the E-and Z-rotamers respectively) in CDCl 3 are consistent with the predominance of the anti conformer around the N−cPr bond. ...
... Additional information can be extracted from Hα chemical shifts, which have been used as a diagnostic probe for assignment of rotamers in amides because they are sensitive to the carbonyl bond anisotropy. 17 Thus, the difference between the Hα chemical shifts of the Z-and Erotamers reflects the magnetic deshielding generated by the carbonyl bond and can be used to determine the disposition of the Hα relative to the carbonyl moiety. While this chemical shift difference is between 0.4 and 0.5 ppm for 2−5, which is consistent with the Z-anti conformer where the Hα lies in the plane defined by the HN−CO moiety and on the same side as the carbonyl group, the difference is only ca. ...
NMR studies in conjunction with ab initio calculations revealed an unexpected conformational behavior of N-cyclopropylacetamide (1). This secondary amide displays 16-19% E-rotamer (cis) around the carbonyl-nitrogen bond in apolar solvents, in contrast to other aliphatic secondary acetamides in which significant E-rotamer populations are rare due to steric contacts between the substituents on the amide bond. In addition, 1 adopts an ortho conformation around the N─cPr bond instead of the anti conformation generally preferred by secondary acetamides. This distinct conformational behavior was also observed for other secondary N-cyclopropyl amides.
... However, it is known that Narylformamides, amides, carbamates, and ureas prefer to be in the s-trans orientation, eliminating the desired hydrogen bond donor/acceptor conformation. 15 However, 2-pyridylureas, and to a lesser extent 2-pyridylformamides, prefer the s-cis orientation. 16 These preferences are illustrated in the activities shown in Table 1. ...
Glucokinase (GK) is the rate-limiting step for insulin release from the pancreas in response to high levels of glucose. Flux through GK also contributes to reducing hepatic glucose output. Since many individuals with type 2 diabetes appear to have an inadequacy or defect in one or both of these processes, identifying compounds that can allosterically activate GK may address this issue. Herein we report the identification and initial optimization of a novel series of glucokinase activators (GKAs). Optimization led to the identification of 33 as a compound that displayed activity in an oral glucose tolerance test (OGTT) in normal and diabetic mice.
... Moreno, Extremadura (Santa Marta, Badajoz, 1962)148149150. La renovación de la química de azúcares extremeña ya ha tenido lugar con las nuevas generaciones. Los principales intereses de Pedro Cintas son: 1) la estereoquímica, con especial énfasis en reacciones asimétricas usando auxiliares basados en carbohidratos; 2) el desarrollo y la aplicación de tecnologías no convencionales en síntesis orgánica; 3) el uso de los compuestos mesoiónicos (como las isomünchnonas), y 4) la química computacional (veáse su trabajo sobre la conformación de amidas secundarias). ...
It is axiomatic in medicinal chemistry that optimization of the potency of a small molecule at a macromolecular target requires complementarity between the ligand and target. In order to minimize the conformational penalty on binding, both enthalpically and entropically, it is therefore preferred to have the ligand preorganized in the bound conformation. In this Perspective, we highlight the role of allylic strain in controlling conformational preferences. Allylic strain was originally described for carbon-based allylic systems, but the same principles apply to other types of structure with sp2 or pseudo-sp2 arrangements. These systems include benzylic (including heteroaryl methyl) positions, amides, N-aryl groups, aryl ethers, and nucleotides. We have derived torsion profiles from small molecule X-ray structures for these systems. Through multiple examples, we show how these effects have been applied in drug discovery and how they can be used prospectively to influence conformation in the design process.
Intramolecular nucleophilic aromatic substitution (Truce–Smiles rearrangement) of the anions of 2‐benzyl benzanilides leads to triarylmethanes in an operationally simple manner. The reaction succeeds even without electronic activation of the ring that plays the role of electrophile in the SNAr reaction, being accelerated instead by the preferred conformation imposed by the tertiary amide tether. The amide substituent of the product may be removed or transformed into alternative functional groups. A ring‐expanding variant (n to n+4) of the reaction provided a route to doubly benzo‐fused medium ring lactams of 10 or 11 members. Hammett analysis returned a ρ value consistent with the operation of a partially concerted reaction mechanism.
A conformationally accelerated intramolecular arylation provides an operationally simple way to prepare triarylmethanes and their medium‐ring analogues. In situ IR spectroscopy and a Hammett plot revealed mechanistic details of the electronically unactivated SNAr reaction.
Abstract
Intramolecular nucleophilic aromatic substitution (Truce–Smiles rearrangement) of the anions of 2‐benzyl benzanilides leads to triarylmethanes in an operationally simple manner. The reaction succeeds even without electronic activation of the ring that plays the role of electrophile in the SNAr reaction, being accelerated instead by the preferred conformation imposed by the tertiary amide tether. The amide substituent of the product may be removed or transformed into alternative functional groups. A ring‐expanding variant (n to n+4) of the reaction provided a route to doubly benzo‐fused medium ring lactams of 10 or 11 members. Hammett analysis returned a ρ value consistent with the operation of a partially concerted reaction mechanism.
Significance
Many studies have investigated secondary formamides as mixtures of cis and trans isomers. They are widespread in nature, but relatively low energetic barriers to interconversion prevent the isolation and characterization of the pure isomers. Here, we determine hydrophilic differences between the isomers by binding in a water-soluble, synthetic molecular container. The container offers a range of environments from hydrophilic to hydrophobic and distinguishes subtle differences in the polarities of formamide isomers. Using NMR methods, we find that cis formamides are more hydrophobic than the corresponding trans isomers. The conclusion holds for diformamides, where we staged an intramolecular competition between cis and trans formamides within the container. Stable and isolable compounds are not required for the determination with this method.
The conformational preferences of 25 sterically and electronically diverse N-aryl amides were determined using density functional theory (DFT), using the B3LYP functional and 6-31G(d) basis set. For each compound, both the cis and trans conformers were optimized, and the difference in ground state energy calculated. For six of the compounds, the potential energy surface was determined as a function of rotation about the N-aryl bond (by 5° increments) for both cis and trans conformers. An NBO deletion strategy was also employed to determine the extent of the contribution of conjugation to the energies of each of the conformers. By comparing these computational results with previously reported experimental data, an explanation for the divergent conformational preferences of 2° N-aryl amides and 3° N-alkyl-N-aryl amides was formulated. This explanation accounts for the observed relationships of both steric and electronic factors determining the geometry of the optimum conformation, and the magnitude of the energetic difference between cis and trans conformers: Except under the most extreme scenarios, 2° amides maintain a trans conformation, and the N-bound arene lies in the same plane as the amide unless it has ortho substituents; for 3° N-alkyl-N-aryl amides in which the alkyl and aryl substituents are connected in a small ring, trans conformations are also favored, for most cases other than formamides, and the arene and amide remain in conjugation; and for 3° N-alkyl-N-aryl amides in which the alkyl and aryl substituents are not connected in a small ring, allylic strain between the two N-bound substituents forces the aryl substituent to rotate out of the plane of the amide, and the trans conformation is destabilized with respect to the cis conformation due to repulsion between the π system of the arene and the lone pairs on the oxygen atom of the carbonyl. The cis conformation is increasingly more stable than the trans conformation as electron density is increased on the arene because the more electron-rich arenes adopt a more orthogonal arrangement, increasing the interaction with the carbonyl oxygen, while simultaneously increasing the magnitude of the repulsion due to the increased electron density in the π system. The trans conformation is favored for 2° amides even when the arene is orthogonal to the amide, in nearly all cases, because the C-N-C bond angle can expend at the expense of the C-N-H bond angles, while this is not favorable for 3° amides.
To search for new antiestrogens more effective in treating breast cancers, we explored alternatives to the acrylic acid side chain used in many antiestrogens. To facilitate our search, we used a simple adamantyl ligand core that by avoiding stereochemical issues enabled rapid synthesis of acrylate ketone, ester, and amide analogs. All compounds were high affinity estrogen receptor-alpha (ERα) ligands, but displayed a range of efficacies and potencies as antiproliferative and ERα-downregulating agents. There were large differences in activity between compounds having minor structural changes, but antiproliferative and ERα-downregulating efficacies generally paralleled one another. Some compounds with side chain polar groups had particularly high affinities. The secondary carboxamides had the best cellular activities, and the 3-hydroxypropylamide was as efficacious as fulvestrant in suppressing cell proliferation and gene expression. This study has produced structurally novel antiestrogens based on a simple adamantyl core structure with acrylate side chains optimized for cellular antagonist activity.
A convenient approach for the absolute configuration assignment of secondary alcohols in the (8R,1′R,2′S,5′R)-15,25, (8S,1′R,2′S,5′R)-15,25, (8R,1′R)-21–24, and (8S,1′R)-21–24 ester series, and of primary amines in the (8R,1′R)-32–37 and (8S,1′R)-32–37 amide series, by means of ¹H NMR and VCD spectroscopy, using 2-cyano-2-indolylpropanoic acid as a chiral derivatizing agent is presented. DFT calculations were carried out to demonstrate the anisotropic effect of the indole skeleton on the chiral alcohol or the amine fragment. Vibrational circular dichroism (VCD) measurements of the above series indicated a VCD bisignated couplet resulting from the interaction of the ester carbonyl group and the CN group. The absolute configuration assignments were further tested by X-ray diffraction analysis.
N,N′-Diformylethylenediamine derivatives of the general formula R1-N(CHO)-CH2CH2-N(CHO)-R2 [R 1=R2=benzyl (1); R1=benzyl, R2=H (2); R1=benzyl, R2benzoyl (3); R1=R 2H (4); R1=R2=benzoyl (5); R1=H, R2benzoyl (6)] were synthesized and fully characterized by 1H- and 13C-NMR spectroscopy, including NOE experiments. Restricted rotation about the C-N amide bonds determined the existence of E/Z isomers. At room temperature, 1 presented three stereoisomers (48/45/7%), 2 four (5.5/58.3/3/33%), each of 3 or 6 two (60/40 and 88/12%, respectively), but 4 and 5 one species only. The preferred conformations of (benzyl)N-CHO (in 1-3) and HN-CHO (in 2 and 6) moieties were E and Z, respectively.
N-Cinnamoyl-9-aminoanthracenes cyclise with PPA or triflic acid to form novel 2-azahexacyclo[10.6.6.0(1,5).0(6,11).0(13,18).0(19,24)]tetracosa-6(11),7,9,13,15,17,19(24),20,22-nonaen-3-ones. In contrast, both N-cinnamoyl-N-methyl-9-(2-aminomethyl)anthracene and N-cinnamoyl-9-(2-aminoethyl)anthracene undergo an intramolecular Diels-Alder cycloaddition.
1-Hydroxy-9,9a-dihydro-1H-imidazo[1,2-a]indol-2(3H)-ones, as a new type of azaheterocyclic hydroxamic acids, have been synthesized regioselectively from 1-carbamoylmethyl- or 1-(methoxycarbonyl)methyl-2,3,3-trimethyl-3H-indolium salts by reaction with hydroxylamine in the presence of a strong base. The alkylation and reduction with sodium borohydride of these novel heterocycles have been investigated. When treated with protic acids 1-hydroxy- or 1-alkoxy-9,9a-dihydro-1H-imidazo[1,2-a]indol-2(3H)-ones underwent ring opening of the imidazolidine to afford 1-[2-(hydroxyamino)-2-oxoethyl]-2,3,3-trimethyl-3H-indolium salts. The structural assignments are based on extensive 1H, 13C and 15N NMR spectroscopic studies and single crystal X-ray analyses.
This paper describes a general preparation of a series of 1,3-thiazolium-4-olates, each bearing an alkyl group at C-2, through reactions between N-arylthiocarboxamides and alpha-haloacyl halides. Unlike the 2-aryl-substituted derivatives, such alkylated mesoionic compounds exist in equilibria with their non-dipolar tautomers, the corresponding 2-alkylidene-1,3-thiazolidin-4 -ones. The unambiguous characterization of such tautomers and their relative stabilities have now been assessed by spectroscopic and computational studies. The presence of o,o'-disubstituted aryl groups at N-3 of the heterocyclic ring slows down free rotation around the N-Ar bond, thus opening access to a promising class of non-biaryl atropisomers. Finally, treatment of N-arylthioformamides with alpha-haloacyl halides gives rise to N-acylthioformamides instead of the corresponding mesoionic species. (C) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004.
We describe a reliable method for determining the absolute configuration of 2-(2-oxo-3-indolyl)acetamides based on analysis of the 1H NMR spectra of their phenylethylamide diastereomers. The conformational preferences for two diastereomeric amides were calculated by DFT, which matched well with the experimental results. X-ray diffraction analysis allowed us to validate the method.
We have realized for the first time a series of truly water-soluble and tightly coupled porphyrin/C(60) electron-donor-acceptor conjugates in which the charge separation and charge recombination dynamics are controlled by modifying the nature of the dendrimer and/or the choice of the central metal atom.
This paper describes a methodology that correlates experimental chemical shifts (at the alpha proton) of proteins with their geometrical data (both dihedral angles and distances) obtained from 13 representative proteins, which are taken from the Protein Data Bank (PDB) and the BioMagRes Data Bank (BMRB). To this end, the experimentally measured proton chemical shifts of simple amides have been correlated with DFT-based calculated structures, at the B3PW91/6-31G* level. This results in a series of mathematical relationships, which are extrapolated to the above-mentioned proteins giving rise to a modified equation for such skeleta. It is relevant to note that the equation is also supported by a clear comparison with NMR data of a protein beyond the chosen set, such as insulin, even with lower errors. The model also relates the dependence of chemical shifts on hydrophobic and anisotropic effects at the amino acid residues.
The acidities (pK(a) values) of proline amide derivatives are of great importance for understanding the catalytic activity of proline-based organocatalysts. The development of new catalysts could also benefit from the systematic study of the pK(a) values of these compounds. However, only a few pK(a) values of the proline-based organocatalysts are currently available due to the difficulty in experimentally measurements. In this work, we set out to study the pK(a) values of various proline amide derivatives with theoretical calculations. Different theoretical methods were evaluated and the combined method, B3PW91/6-311++G(3df,2p)//B3LYP/6-31+G(d)//HF//CPCM/UA0, was found to be the best one in reproducing the pK(a) values of structurally unrelated amides and amide derivatives in DMSO. The MAD and RMSE of the newly developed theoretical model equal to 0.98 and 1.3 pK units, respectively. The method also enabled the systematically study on various structural effects on pK(a) values of proline amide derivatives, such as the ZE-isomerization, remote substitution, and alpha-substitution effects, for the first time. The pK(a) values of a series of chiral amides were also studied in this work. Finally, we applied the theoretical method to predict a large number of proline-based organocatalysts and established an extensive acidity scale of the compounds.
Interesting anisotropic effects were observed for phenylglyoxamides and their respective mandelamides. Such effects were observed in experimental (1)H and (13)C NMR (in CDCl(3), CD(3)OD, and DMSO-d(6) solvents) and in some cases with good correlation to theoretical (1)H and (13)C NMR DFT-GIAO (B3LYP/6-311++G**//B3LYP/6-31G*) calculations. A systematic conformational analysis of these compounds was performed in a two-step methodology, using PM3 and DFT (B3LYP/6-31G*) calculations; with good accomplishment and computational time economy. It was observed that intramolecular hydrogen bonding plays a significant role in the conformation of such compounds. Finally, a geminal nonequivalence of an N-CH(2) moiety, in one of the alkyl side chain (R1 = R2), was found for the tertiary mandelamides studied.
Reversible encapsulation complexes are applied to the reaction of isonitriles with carboxylic acids. Encapsulation facilitates these reactions by amplifying the concentration of reactants, arranging the acid and isonitrile in the appropriate orientations, isolating intermediates from bulk solution, and providing an organized solvent cage.
Cross-correlation between 15N−1H dipolar interactions and 1HN chemical shift anisotropy (CSA) gives rise to different relaxation rates of the doublet components of 1H−{15N} peptide backbone amides. Two schemes for quantitative measurement of this effect are described and demonstrated for samples of uniformly 15N-enriched ubiquitin and perdeuterated 15N-enriched HIV-1 protease. The degree of relaxation interference correlates with the isotropic 1HN chemical shift, and results indicate that an upfield change of the most shielded principal components of the CSA tensor is correlated with an approximately 2-fold larger downfield shift of the average of the other two components. The magnitude of the relaxation interference is large in β-sheet and considerably smaller in α-helices. This correlation is not dominated by the backbone geometry but reflects the slightly longer hydrogen bond length in helices compared to β-sheet. The smallest relaxation interference effect in ubiquitin is observed for Ser20-HN and Ile36-HN, which are the only two amide protons that are not hydrogen bonded in the crystal structure of ubiquitin, inaccessible to solvent, and not highly mobile.
The infrared spectrum of the water–formamide complex in argon matrices has been recorded from 10 to 4000 cm−1. The interaction energy of the complex forming molecules has been calculated from a theoretical potential. One global and three different local minima have been found for this potential. Intermolecular vibration frequencies have been calculated for each minimum. The results are compared with the experimentally observed far infrared spectrum. In agreement with microwave measurements and ab initio calculations, the global minimum of the complex is found, both from calculations and experiment, to have a cyclic structure with water forming a hydrogen bond to the amide oxygen and receiving a hydrogen bond from an amide hydrogen. In addition to the cyclic complex, we observe one of the local minimum structures of the complex, where water accepts a hydrogen bond from the amide NH on the CH side of the amide.
Knowledge of three-dimensional protein structures is one of the foundations of protein design and protein engineering. Nuclear magnetic resonance spectroscopy was recently introduced as a second method for protein structure determination, in addition to the well-established diffraction techniques with protein single crystals. This new approach enables one to carry out detailed structural studies of proteins in solution and other noncrystalline states, which may be similar or identical to the physiological environment, and promises new insights into the dynamics of protein molecules and the protein-folding problem.
The parameters for a number of models that have been proposed for calculating chemical shifts in proteins and peptides have been optimized using experimental data on CαH shifts for a range of proteins with well-defined crystal structures. These models include the Johnson-Bovey and Haigh-Mallion models for ring-current shifts, magnetic-anisotropy models based on bonds and on the peptide group as a whole, and electric-field models using atomic charges or charge dipoles. The two ring-current models and the two electric-field models are equally good, but the bond-anisotropy model has a slight advantage. Values of the parameters are presented. Although all are physically reasonable, some differ extensively from those proposed previously.
This chapter provides an overview of the results and concepts that have been put forward in the field of in nitro misassembly (coagulation, aggregation). Considering the posttranslational fate of a protein molecule, polypeptide chains that fail to reach the native state are commonly discarded by appropriate cellular mechanisms, either protein turnover or deposition as aggregates. Over the past 30 years, protein chemists have not shown great interest in these side reactions. They merely tried to avoid them because what fully absorbed their curiosity was the structure function relationship of proteins, and function was exactly what aggregates or precipitates were lacking. Lately, the focus has changed for a number of reasons. This chapter summarizes experimental approaches to a deeper understanding of the physicochemical basis of protein misfolding in vitro and with the solution of the protein folding problem still ahead, one may easily predict that another generation of biochemists will be engaged in trying to find the solution to the misfolding problem, with its physical, cell biological, and medical implications.
The microwave spectrum of N-methylformamide has been investigated in the 18–40 GHz frequency range. The rotational spectrum of the conformer with the methyl group cis to the aldehydic oxygen has been assigned. Several rotational transitions of the A sublevel of the ground torsional state have been measured for both normal and N—D isotopic species. The V3 barrier to the methyl group internal rotation has been obtained from the effective pseudo-defect of inertia. The dipole moment and the 14N quadrupole coupling constants have been determined. The results of ab initio calculations performed at the HF and MP2 levels are in agreement with the experimental data
Significant advances have been made in understanding the thermodynamics of the hydrophobic effect and of the reversible unfolding of proteins, although there is still considerable controversy. Recent analyses suggest that the predominant factor in stabilizing the folded states of proteins is intramolecular hydrogen bonding even though in the unfolded state the polar groups form intermolecular hydrogen bonds with water. Van der Waals interactions between non-polar groups also contribute substantially, but perhaps not as much as might have been expected if protein interiors were perfectly close-packed. The role of the solvent seems to be primarily destabilizing, and involves the favourable solvation of both polar and non-polar groups. The effects of added stabilizers and denaturants can be understood on the basis of their alterations of the properties of water and of their interactions with the surfaces of folded and unfolded proteins. Also, their electrostatic interactions between groups involved in salt bridges in folded proteins can be substantial.
Density functional calculations using gradient corrected functionals have been used to explore the factors which determine the strength of the intermolecular interaction in cyclic systems formed by complementary hydrogen bonding between amides. Optimised structures and interaction energies are presented for the simplest amide dimer, diformamide, and the results are compared with experimental and ab initio results available in the literature. Full optimisations are also performed on hydrogen bonded molecular pairs formed from the N-substituted derivatives of formamide, N-methylformamide (NMF) and N-formylformamide (NFF). The total interaction energy is found to decrease in the order NMF·NMF > NFF·NMF > NFF·NFF, the difference between successive pairs being approximately 10 kJ mol–1 in each case. The origin of this trend is traced to electrostatic repulsions between the spectator carbonyl groups in NFF and the carbonyl groups involved in the cyclic hydrogen bonded array.
Configurational and conformational NMR analyses of amido and thioamido groups in pyranoid sugar derivatives are described. Z, E isomers about the N-CX bond were unequivocally identified. Also, the disposition of this functional group with respect to the sugar ring has been determined on the basis of some NMR parameters. A relevant parameter was the chemical shift of the alpha-sugar proton to the amide or thioamide group. The scope and limitations of other H-1 and C-13 NMR data have been studied.
An experiment is presented that allows the quantitative measurement of the cross-correlation rate between 1HN CSA and 1HN−15N dipolar interaction in uniformly 15N-enriched samples. The CSA/DD cross-correlation rate is obtained from the intensity ratio of an experiment in which the CSA/DD cross-correlation is active for a fixed time, τ, with a reference experiment in which it is inactive. The CSA/DD cross-correlation rates of 75 residues of the HU protein from Bacillus stearothermophilus were obtained from the linear fits of CSA/DD to reference ratios recorded for five values of τ and at two different Bo fields. After correction for the mobility of the 1H−15N bond vector the values of (σ − σ)(3 cos2(θ) − 1)/2, containing information about the chemical shielding anisotropy, were derived for individual amide protons. The average value of 13 ± 5 ppm compares well with the results from previous solid state NMR measurements. The data also show a dependence upon hydrogen bonding and secondary structure: residues in α-helical conformation show values of 9 ± 4 ppm, whereas residues in β-sheet conformation show substantially higher values of 16 ± 6 ppm.
The changes that occur during the rotation of the amino group of formamide have been studied in some detail. Geometry optimizations at the MP2/6-31 G* level confirmed the relatively large increase in C-N bond length but small decrease in the C-O length on going from the planar structure to the rotational transition state. A calculation of the force constants for formamide and for the transition state showed that the carbonyl force constant changed relatively little, but the C-N constant changed by about 30%. The path followed in the rotation was studied starting with the saddle point geometry and following it computationally down to the ground state. The geometrical changes are discussed. The electron populations were calculated for a number of structures along the reaction coordinate by numerical integration of the charge density within uniquely defined atomic volumes. The oxygen population was little affected by the rotation and the main charge shift was between carbon and nitrogen. The electrostatic potentials for the structures also were examined and converted to effective charges for spherically symmetrical atoms. All of the analyses indicated that essentially all of the interactions leading to the rotational barrier originate in the C-N bond and that the oxygen does not participate to a significant extent. The direction of the charge shift between C and N was in opposite directions for the electron populations derived by integration of the charge density, and by fitting the electrostatic potentials. However, this was due to the difference in the definition of the atoms, being anisotropic in the first case and spherically symmetrical in the second. All of the observations can be rationalized on the basis of the assumption that stabilization of the lone pair on nitrogen is the most important factor in determining both structures and energies.
The structure of N-formyl, N-acetyl-N-methyl, and N-acetyl glycosylamines has been studied by NMR spectroscopy in solution, single crystal X-ray diffractometry, and corroborated by PM3 semiempirical calculations. The results quite agree with an anti conformation around the glycosydic bond for these substances.
Glycoamidines are readily prepared by a mercury-promoted reaction of the corresponding thioamides with amines. The reaction appears to involve the participation of bidentate mercury complexes with N-monosubstituted thioamides, whereas N,N-disubstituted derivatives form presumably monocoordinated species. In the light of these assumptions, two different mechanistic pathways can be applicable depending on the starting thioamide. In addition, this protocol enhances the versatility of transformations of organosulfur compounds in the presence of transition metal ions and illustrates novel features.
The gauge-independent atomic orbital (GIAO) approach is used within the coupled Hartree-Fock (CHF) approximation to compute the oxygen NMR shielding constant in the carbonyl group for a series of molecules. We apply a correction to account for the correlation effects which is based on the comparison with the experimental results for a few molecules. Our final results enable us to predict the oxygen shielding or interpret the results of the experiment, in particular when the experimental data for the gas phase are not known.
From earlier published enthalpies of solution of various organic compounds in binary solvent systems containing water and N,N-dimethylformamide (DMF), the enthalpic pair interaction coefficients (Bhxy) of these compounds with DMF in water as solvent, and with water in DMF as solvent have been evaluated. The organic solutes comprise urea, alkylsubstituted ureas, amides and alkanols. For water dissolved in DMF, enthalpic interaction coefficients have been obtained from microcalorimetrical dilution experiments. In water and DMF the various results differ considerably. In water a much larger variation in Bhxy is found than in DMF. In the former an almost constant CH2 contribution to Bhx,DMF is found for most homologous series. Branching of the alkyl chain in the organic compound hardly influences Bhx,DMF. The results indicate that hydrophobic interaction plays an important role. In DMF the results are less regular and branching effects are considerable. Hydrogen bonding has a large impact on Bhx,H2O. The relations between the enthalpic pair interaction coefficients on basis of the Savage and Wood additivity approach and the Barone method (square root rule) are tested. When sufficient functional groups are introduced, the Savage and Wood concept seems to work well for a large amount of molecules of different classes in water. The Barone approach seems to be more useful for the interaction between molecules with comparable functional groups.
A solid-state nuclear magnetic resonance (NMR) method for the site-resolved identification of the secondary structure of solid peptides and proteins is presented. This technique exploits the correlation between the backbone conformation and the Cα chemical shift anisotropies (CSA) of proteins. The 13Cα CSAs are measured under fast magic-angle-spinning using a new sequence of sixteen 180° pulses with special timing to reintroduce the CSA interaction selectively. Quantitative values of the shielding anisotropies are determined from the magnetization decay, as demonstrated for several amino acids. To achieve high-resolution spectra, this CSA filter experiment is combined with 2D 15N−13C correlation spectroscopy. Applied to selectively and extensively 13C-labeled and uniformly 15N-labeled ubiquitin at the largest dephasing time, the 2D experiment yields a spectral pattern that corresponds primarily to α-helical residues. This agrees with the previous finding that helical residues have smaller CSAs than sheet residues. However, the quantitative CSA differences between the helical and sheet conformations are less pronounced than indicated by solution-state NMR. This CSA filter technique provides an efficient and site-resolved method for characterizing the secondary structure of extensively isotopically labeled proteins.
A tunable microwave‐sideband CO2 laser has been used with a molecular‐beam electric‐resonance optothermal spectrometer to observe the infrared spectrum of the NH3 umbrella fundamental vibration (ν5 in Cs ) of HOH––NH3 at a resolution of ∼3 MHz. Ground‐ and excited‐state assignments were verified and extended using microwave–infrared double‐resonance spectroscopy, with microwave transitions observed in both the ground and the excited states. The spectrum exhibits numerous perturbations, as evidenced by the observation of a minimum of 13 subbands originating from the (K,m)=(0,0) ground NH3 internal‐rotor state and the (K,m)=(±1,±1) first excited NH3 internal‐rotor state. For an unperturbed spectrum, only four such subbands are expected, two for the symmetric H2O tunneling state and two for the antisymmetric H2O tunneling state. The rotational progressions within the excited states are poorly fit to polynomial series in J(J+1), in contrast to the ground‐state progressions which are well characterized by such series. The B rotational constants in the excited states are smaller than in the ground state, indicating an extension of the hydrogen‐bonding interaction distance upon vibrational excitation. This is consistent with the observed infrared band origin for the (K,m)=(0,0) state of ∼1021 cm−1, which is blue shifted by 71 cm−1 from the hypothetical inversion‐free 950 cm−1 ν2 band origin of uncomplexed NH3. The observed ν5 band origin is also in good agreement with matrix‐isolation results scaled to correct for the matrix shift of the NH3 umbrella frequency found in the recently studied NH3–HCN complex. The complex does not dissociate upon vibrational excitation, implying that the binding energy is greater than the laser frequency of ∼1021 cm−1.
The general nuclear magnetic shielding theory of Ramsey is developed for the case of ``long‐range'' nuclear shieldings. Such shieldings arise from the magnetization induced in molecular electrons localized to groups one or more bond lengths removed from the shielded nucleus. Order‐of‐magnitude calculations indicate that these long‐range shielding fields can make significant contributions to proton chemical shifts in, for example, aromatic hydrocarbons and alkyl halides.
Effects of intermolecular hydrogen-bonding interactions on the amide I mode of N-methylacetamide (NMA) are studied by matrix-isolation infrared (IR) spectroscopy and ab initio molecular orbital calculations. The wavenumbers of the amide I IR bands of NMA in Ar and N2 matrixes with various NMA/matrix gas mixing ratios are compared with those calculated for the monomer, dimers, and trimers of trans-NMA and the monomer and dimer of cis-NMA. The band at 1708 (1706) cm-1 in Ar (N2) matrixes is assigned to the amide I mode of the monomer of trans-NMA. The band observed at 1686 (1681) cm-1 in Ar (N2) matrixes with the NMA/matrix gas mixing ratio larger than 1/500 is assigned to the amide I band due to the dimers of trans-NMA. The bands observed at lower wavenumbers for samples with the NMA/matrix gas mixing ratio as large as 1/100 are assigned to the amide I bands of the trimers and larger clusters of trans-NMA. It is likely that the band observed at 1695 (1693) cm-1 in the Ar (N2) matrix arises from the dimer of cis-NMA, which is as stable as the trans-NMA dimers because of the formation of two hydrogen bonds in a cyclic form. Although there are two amide I modes in an NMA dimer and three in an NMA trimer, only one mode is strongly IR active in each species. The intrinsic amide I wavenumbers of individual peptide groups in NMA clusters, i.e., the amide I wavenumbers in the case where there is no resonant vibrational coupling between the peptide groups, are examined by calculating the amide I wavenumbers for the dimers and trimers whose constituent molecules other than the target molecule have the CO group(s) substituted with 13C and 18O. It is shown that the shifts of the amide I band to lower wavenumbers induced by hydrogen bonding to the CO group are 20−25 cm-1, while those induced by hydrogen bonding to the N−H group are 15−20 cm-1. These shifts are approximately in line with the changes in the CO bond lengths and are approximately additive if both the CO and N−H groups of a peptide group are hydrogen bonded.
The isotropic and anisotropic Raman spectra of neat N-methylacetamide (NMA) at different temperatures between −10 and 60 °C and NMA in acetonitrile were measured in order to spectroscopically compare and characterize the crystallized (T < 28 °C) and liquid states. These plus infrared data were subjected to a self-consistent component band analysis. We found that the amide I band is composed of two subbands in the solid phase and three in the liquid phase. For the former, the subbands at 1633 and 1656 cm-1 arise from transition dipole coupling interactions associated with the Ag and B2g species of the crystal unit cell. Depolarization ratio measurements suggest a departure from strict D2h symmetry. The three subbands in the liquid phase reflect different aggregate structures. The lowest frequency band at 1634 cm-1 results from an NMA oligomer exhibiting a structure similar to that observed in the ordered crystal phase. The most intense subband shows a significant negative noncoincidence effect, its isotropic component appearing at 1650 cm-1 and its anisotropic part at 1655 cm-1. This subband is interpreted as resulting from locally ordered short oligomeric hydrogen-bonded structures. The third subband is at 1675 cm-1 and results from isolated non-hydrogen-bonded NMA molecules or from amide I modes of the terminal groups of the above oligomers. Amide III shows a small but detectable positive noncoincidence effect in the liquid phase (2 cm-1), which is also assignable to transition dipole coupling between adjacent molecules in a locally ordered environment. The Raman bands arising from the symmetric bending modes of the two methyl groups are significantly affected by crystallization; the CCH3 symmetric bending mode becomes depolarized and less intense while the NCH3 symmetric bending mode gains intensity and becomes polarized. Ab initio calculations of torsional distortions of the CH3 groups, caused by interactions between adjacent non-hydrogen-bonded NMA molecules in the crystal, qualitatively reproduce these effects.
The question of planarity and the validity of the amide resonance model have been investigated in formamide on the basis of high-level quantum chemical calculations. Complete geometry optimizations were performed for the equilibrium structure and for the 90°-rotated transition state at the MBPT(2), MBPT(4), CCSD, and CCSD(T) electron correlation levels, with basis sets up to cc-PVTZ. While electron correlation tends to give nonplanar equilibrium, the final result at the CCSD(T)/PVTZ level is an exactly planar structure, as proven by the absence of imaginary vibrational frequencies. The crucial parameter in the geometry, the C−N bond length is calculated at 1.354 Å. For the barrier to internal rotation around the C−N bond our best estimate, including the zero-point-energy correction, is 15.2 ± 0.5 kcal/mol. To check predictions of the resonance model, we have analyzed geometric changes, charge shifts from Mulliken population analysis, and the nature of relevant valence orbitals and also calculated NMR chemical shieldings as a function of internal rotation. In contrast to recent suggestions by Wiberg et al. (J. Am. Chem. Soc. 1987, 109, 5935; 1992, 114, 831; Science 1991, 252, 1266) that π-resonance would not play a significant role in explaining the rotational barrier in formamide, we have found no compelling evidence to doubt the validity of the amide resonance model.
We have developed a polarizable intermolecular potential function (PIPF) for simulation of liquid amides. The PIPF potential includes a pairwise additive component, consisting of the familiar Lennard-Jones and Coulomb form, and a nonadditive polarization term. The empirical parameters were optimized through a series of statistical mechanical Monte Carlo simulations of liquid formamide, N-methylacetamide (NMA), N-methylformamide (NMF), and N,N-dimethylformamide (DMF). In deriving the empirical potential functions, bimolecular complexes of the amides dimers were studied by ab initio molecular orbital calculations using the 6-31G(d) basis set, and the results were compared with the PIPF predictions. The computed heats of vaporization and densities for the liquids using the final parameters are within 2% and 3% of experimental values, respectively. The polarization effects are found to be significant in all liquids, ranging from 6% for DMF to 14% for formamide of the total liquid energy. Electrostatic and polarization components dominate in primary and secondary amides, while the van der Waals contribution is greater than electrostatic terms for the tertiary amide DMF. In the present parameter optimization, polarization energies and induced dipole moments in the liquids are compared with results obtained from separate Monte Carlo simulations employing a combined quantum mechanical and molecular mechanical (QM/MM) approach. In the latter calculation, one amide monomer is treated quantum mechanically by the semiempirical AM1 theory, which is embedded in the liquid of the same amide represented by the empirical OPLS potential. In addition, structural features including hydrogen-bonding interactions and radial distribution functions are examined and found to be in good agreement with the previous computational results.
The amide compounds have been studied, and their parameters have been developed for the MM4 force field. The structures, moments of inertia, vibrational spectra, conformational energies, barriers to internal rotation and dipole moments have been examined for these compounds. The MM4 structures calculated for these compounds were fit to available electron diffraction (ED) and microwave data (MW). Structural parameters were fitted in favor to the MW moments of inertia, which are more accurately determined experimental quantities than ED measured bond lengths. For all of the 15 moments (5 molecules) experimentally known for the amide compounds, the MM4 rms error is 0.62%. For the calculated vibrational spectra of four amide compounds which were fully analyzed, the MM4 rms error from experiment was 27 cm-1 over a total of 108 weighted modes. Heat of formation parameters were optimized for 25 amide compounds whose gas-phase heats of formation were experimentally known. For 18 weighted compounds, the weighted standard deviation between MM4 and experiment was 0.53 kcal mol-1.
Density functional theory DFT(BPW91) level calculations with modified 6-31G(d) basis sets are tested for a small amide, N-methyl acetamide (NMA), as an efficient way for calculating amide I and amide II frequencies that are directly comparable to those commonly measured in solution. The calculational results are compared to experimentally measured FTIR spectra in gas and solution phases. The 6-31G(d) basis set at the DFT level yields vibrational frequencies that have the best agreement with the gas-phase experiment, as compared to amide I and II frequencies calculated with the same basis at the HF, CASSCF, MP2, QCISD, and CCD levels. The DFT(BPW91)/6-31G(d) level calculation for the NMA·3H2O hydrogen-bonded complex with an Onsager or CPCM reaction field yields amide I, II, and III frequencies comparable to the experiment in aqueous solution. The amide I and, to a smaller degree, amide II frequencies are found to be sensitive to the exponent of the d function in the basis set. Use of more diffuse (smaller exponent) d functions in the 6-31G(d) basis set results in a calculated amide I frequency closer to the solution experimental values. Such modified, relatively small basis sets may provide a computationally efficient means of approximating the solvent effects on amide vibrational frequencies.
The known general preference of cis-amide structure in N-methylanilides both in crystal and in solution was studied by ab initio molecular orbital (MO) calculations for acetanilide and N-methylacetanilide. The cis structure was more stable by 3.50 kcal/mol than the trans one in N-methylacetanilide, whereas the traits structure was more stable by 2.15 kcal/mol than the cis one in acetanilide at the 6-31G**//4-31G basis set level. In order to examine the reliability of the result, the basis set dependency of the energy difference between trans- and cis-amide structures was also examined by changing the basis set from 4-31G to 6-31G** in the case of N-methylacetamide. The remarkable cis preference in N-methylanilides seems to be ascribed to destabilization of the trans structure due to steric hindrance between the two methyl groups and to electronic repulsion between the carbonyl lone-pair electrons and the phenyl pi-electrons in the twisted phenyl orientation.
The core ionization energies of three, strained lactams have been measured and compared with those of model lactams, amides, amines, and ketones In general. the high values for N1s and the low values for O1s in planar amide (lactam) linkages compared to those in model amines and ketones are consistent with traditional resonance arguments. The N1s and O1s data for the distorted lactams 1,3-di-tert-butylaziridinone and 1-azabicyclo-[3.3.1]nonan-2-one are consistent with a reduced positive charge on nitrogen and a reduced negative charge on oxygen in accord with the classical resonance viewpoint. They are also consistent with other spectroscopic data for distorted lactams. The carbonyl C 1 s ionization energies are lower in distorted lactams than in planar lactams. The explanation may lie in the relative electronegativities of the nitrogen atoms. ESCA data also suggest the presence of more C+-O- character in ketones than in amides. Although 1-pyrrolidinecarboxaldehyde has a distorted amide linkage, its ESCA data are not unambiguously interpretable in terms of reduced resonance. The dependencies of core electron ionization energies upon different amide distortion modes need to be explored using a much expanded set of amides and lactams. The relationships between the resulting experimental ESCA data with various calculations of atomic charge need to be examined.
Density-functional chemical shielding calculations are reported for the alanine dipeptide with a variety of backbone torsion angles and for methane and N-methylacetamide complexes with rare gases, monatomic ions, water, and other amides. These fragment systems model electrostatic, nonbonded, and hydrogen bonding interactions in proteins and have been investigated at a variety of geometries. The results are compared to empirical formulas that relate intermolecular shielding effects to peptide group magnetic anisotropies, electrostatic polarization of the C−H and N−H bonds, magnetic contributions from C−C and C−H bonds, and close contact effects. Close contacts are found to deshield protons involved in close nonbonded contacts that typically occur in hydrogen bonds. “Lone pair” charges improve the model for electrostatic effects and are important for understanding the angular dependence of shifts for protons involved in hydrogen bonds. C−C and C−H bond anisotropy contributions help to explain the torsional dependence of amide proton shifts in alanine dipeptide. Good agreement is found between the empirical formulas and the quantum chemistry results, allowing a reassessment of empirical formulas that are used in the analysis of chemical shift dispersion in proteins.
The dependence of hydrogen-bond interaction energies between identical amides (two formamides and two N-methylacetamides) on the hydrogen bond length (rO···H), the two hydrogen bond angles (θCOH and θNHO), and the dihedral between the two amides (ΦCNCN) has been assessed by semiempirical calculations (SAM1 with single point transfers to AM1/SM2.1 aqueous solvation calculations). Ab initio calculations (MP2/6-31+G(d,p)//HF/6-31+G(d,p)) at given values of ΦCNCN and θCOH predict the same change in interaction energies with changes in θNHO as the semiempirical calculations. With formamide, hydrogen-bond interaction energies are independent of the dihedral angle ΦCNCN when θCOH and θNHO deviate less than 40° from 180°. Most importantly, the increased interaction energies at θCOH and θNHO below 140° and above 220° are found to be associated with steric interference between the carbonyl oxygen of the hydrogen-bond acceptor and the amide nitrogen of the hydrogen-bond donor. Comparing formamide and N-methylacetamide, the angle requirements (θCOH, θNHO, and ΦCNCN) of favorable hydrogen-bond interaction energies are much more stringent for the latter due to the steric effects of the methyl substituents. In summary, by both semiempirical SAM1 and ab initio MP2/6-31+G(d,p)//HF/6-31+G(d,p) calculations, the strength of amide hydrogen bonding in the absence of steric hindrance is essentially independent of the angles defining the hydrogen bond.
The n.m.r. spectra of thirteen N-monosubstituted aliphatic amides reveals that four of these, N-methylformamide, N-ethylformamide, N-isopropylformamide, and N-t-butylformamide, exist in both the cis and the trans configuration about the central C-N bond. Although the trans form predominates, the percentage of cis isomer increases as the nitrogen substituent becomes more bulky. Studies of the change in chemical shift of the nitrogen substituent upon dilution with benzene are in accord with the peak assignments. Spin coupling constants between the protons on carbon and nitrogen may be found for each isomer in sulfuric acid solutions of the substituted formamides. The remaining nine amides, where the carbonyl substituent was larger than hydrogen, showed the presence of only the trans configuration.
A theoretical framework is given for partitioning the individual elements in the total magnetic susceptibility tensor (χaa, χbb, and χcc) into local contributions. Molecular data are analyzed to give local values of χaa, χbb, and χcc for either atoms or bonds. These values can be added to give the total molecular magnetic tensor elements for a wide range of nonstrained, nonaromatic compounds. The method is used to estimate relative aromaticities, interpret data from Cotton-Mouton experiments, and to gain information about molecular structure. The values given here are also of use in determining neighbor group effects in proton magnetic shielding.
A band in the 1300-1500-cm-1 region has been observed to be enhanced in the UV resonance Raman spectra of peptides and proteins. We show, on the basis of normal-mode analysis of experimental data from N-methylacetamide (NMA) and several conformations of poly(L-glutamic acid), that this band can be definitively assigned to the overtone of the amide V mode. The results of 13C15N isotopic substitution on some NMA analogues support this assignment. The sensitivity of this band to polypeptide chain conformation can make it a new sensitive probe of secondary structure in proteins.
The rotational barriers for N,N-dimethylformamide and N,N-dimethylacetamide have been investigated theoretically and experimentally. Calculations at the G2(MP2) theoretical level followed by correction to 25 degrees C reproduced the experimental gas-phase barriers. An examination of the geometries of these amides showed that the lower barrier for the acetamide resulted mainly from a ground state methyl-methyl repulsive interaction. The rotational barriers for the amides were measured in several solvents using NMR selective inversion-recovery experiments. The effect of solvent on the C-N rotational barriers was examined computationally using reaction field theory. This approach was found to give barriers that are in good agreement with experiment for aprotic, non-aromatic solvents which do not engage in specific interactions with the amides. The effect of a hydrogen bonding solvent, water, was studied via incorporating a water molecule hydrogen bonded to the oxygen and examining this ensemble using reaction field theory.
The C-N rotational barrier for thioformamide is known to be larger than that for formamide. The origin of this barrier has been examined with the aid of ab initio molecular orbital calculations. The larger barrier is reproduced, and it is found that the amino group of thioformamide is less ''floppy'' than that of ordinary amides. In addition, the change in charge density at sulfur on rotation of the amino group in thioformamide is much greater than that at oxygen in formamide. It is concluded that the traditional picture of amide ''resonance'' is more appropriate for thioamides than for amides. The small difference in electronegativity between carbon and sulfur and the larger size of sulfur are the major factors that allow charge transfer from nitrogen to sulfur in thioamides. The effect of replacing the carbonyl oxygen of formamide by =NH, =PH, =CH2, and =SiH2 also was examined. The energies associated with group separation reactions were divided into pi components (the rotational barriers) and a components. The latter were found to increase with increasing electronegativity of the substituent, indicating that they resulted from internal Coulombic stabilization. The pi components were about the same for the corresponding first and second row C=Y groups where Y is the terminal atom or group of the double bond, and they increased with increasing electronegativity of Y.
The ab initio IGLO (individual gauge for localized orbitals) method was used to examine the conformational dependencies of the isotropic C-13 chemical shifts in the model peptide N-acetyl-N'-methylglycinamide. A surface plot of the calculated C-13 isotropic chemical shifts for the Calpha carbon was constructed at 30-degrees grid intervals of the phi and psi angles. These data are used to examine the relationship between chemical shifts and protein secondary structure. The Calpha carbons in alpha-helix and beta-sheet conformations are calculated to be shifted 2.3 ppm downfield and 2.9 ppm to high field, respectively, of the random coil value. Considering the spread in experimental values, especially for the beta-sheet conformations, these secondary shifts are in reasonable agreement with the average experimental values of 3.2 and -1.2 ppm, respectively, for glycyl residues in peptides and proteins. The smaller differences predicted for other types of secondary structures are also consistent with the experimental results. Thus, for the Calpha carbon it is not necessary to include interresidue hydrogen-bonding effects to explain the major chemical shift trends. An analysis of the localized MO contributions (LMOC) shows that all four bonds directly connected to the Calpha carbon are important to the total shift but each of these has a different (phi, psi) angle dependence. The LMOC from the Calpha-C' bond provides the largest contribution to the chemical shift difference between the alpha-helix and the beta-sheet conformations.
Experimental vibrational circular dichroism (VCD) spectra for trans-2,3-dimethylthiirane and its 2,3-d2 isotopomer were measured in the 1600-700-cm-1 region. Ab initio theoretical calculations of VCD using the localized molecular orbital formalism were carried out with the 6-31G* basis set. Similar calculations were also done using the vibronic coupling formalism for trans-2,3-dimethylthiirane, its 2,3-d2 isotopomer, and methylthiirane. A comparison between the theoretical model predictions and the experimental data reveals that the theoretical models are successful in reproducing the experimental VCD spectra. The merits and limitations of the individual models are discussed.
In order to characterize the vibrational dynamics of the hydrogen-bonded N-methylacetamide (NMA) molecule, we have calculated the energies, geometries, and force constants (at the 4-31G* level) of trans-NMA and cis-NMA to which are hydrogen bonded two H2O molecules, one at the NH group and one at the CO group. The force constants for trans-NMA were scaled to experimental frequencies for NMA in aqueous solution and resulted in predicted frequencies within 5 cm-1 of observed bands. Experimental data for cis-NMA are more limited, but transfer of scale factors from the isolated molecule permitted verification of the assignments of two resonance Raman bands proposed to be characteristic of this isomer.
We present an empirical analysis of proton chemical shifts from 17 proteins whose X-ray crystal structures have been determined. The crystal structures are used to estimate the conformation-dependent part of the shift, that is, the difference between the observed shift and that of a "random-coil" linear peptide. The results indicate that a significant improvement over ring-current theories can be made by including the effects of the magnetic anisotropy of the peptide group and estimates of backbone electrostatic contributions. For 5678 protons bonded to carbon, we find a linear correlation coefficient of 0.88 between calculated and observed structural shifts, with a root-mean-square error of 0.23 ppm; contributions from the peptide group are especially noticeable for protons at the C-alpha position. If we consider only side-chain protons in non-heme proteins, the rms error is 0.18 ppm, and methyl protons show an rms error of 0.13 ppm. New estimates of intensity factors for various ring-current contributions are given (including those arising from the heme group) which suggest more nearly equal contributions from various rings than found in earlier studies. Predictions for protons bonded to nitrogen are much poorer than for protons bonded to carbon, but significant qualitative insights can be obtained. Prospects for using calculated chemical shifts in the final refinement of protein solution structures are discussed.
Excitation into the amide pi-pi* transitions of N-methylacetamide (NMA) and small peptides such as di- and triglycine results in the photochemical conversion of the trans-amides into cis-amides with a high quantum yield. The cis form of NMA is easily monitored since its amide II UV Raman cross section is ca. 10-fold larger than that of the trans peptide with 220-nm excitation. We can detect the ca. 1.5% Boltzmann population of the cis form of NMR present at room temperature. The amide II mode of cis peptides differs dramatically from that of trans peptides since it contains much less N-H in-plane bending. This result is inconsistent with previous normal mode calculations which assumed identical geometry and force constants for the cis and trans forms. The pi* excited state of peptides is twisted relative to the ground state in a manner reminiscent of ethylene. We also reinterpret previous studies of N-methylthioacetamide to indicate that its pi* excited state is twisted. Our data clearly indicate the correctness of the assignment of the peptide conformation sensitive band at ca. 1400 cm-1 to the overtone of the amide V vibration for dipeptides and polypeptides. The fact that the overtone of the amide V vibration is not enhanced for NMA and related derivatives indicates a significant difference between the NMA excited-state potential surface and that of dipeptides and polypeptides. This result may signal that the peptide pi* excited state is delocalized over the peptide backbone.
Hydrogen bonding interactions and their effect on the structure and the energetics of the rotation about N-C(alpha) and C(alpha)-C' bonds are studied for N-methylacetamide (NMA) by use of ab initio quantum mechanical calculations. The structure and methyl rotational barriers for isolated NMA have been determined at the Hartree-Fock (HF) level with 6-31G, 6-31G*, and 6-311G** basis sets and at the second-order Moller-Plesset perturbation (MP2) level with a 6-31G* basis set including geometry optimization for the different methyl orientations. The optimized geometries, the hydrogen bonding interaction energies, and the methyl rotational barriers for 11 complexes in which NMA is hydrogen bonded to H2O and/or formamide (FM) [i.e., NMA + H2O (3 complexes), NMA + 2H2O (2 complexes), NMA + 3H2O (1 complex), NMA + FM (2 complexes), NMA + (FM and H2O) (1 complex), NMA + 2FM (1 complex), and NMA + (2FM and 1H2O) (1 complex)] have been calculated at the HF/6-31G level; HF/6-31G* calculations were performed for the 3 NMA + H2O complexes and 1 of the NMA + 2H2O complexes. For isolated NMA, the torsional potentials for both methyl groups are predicted to be very flat and the rotational barriers are only approximately 0.1 kcal/mol. This contrasts with some of the earlier calculations in which larger barriers were obtained due to lack of geometry optimization of the rotated conformers. The barriers in the hydrogen bonded systems are calculated to be significantly larger (0.2-0.9 kcal/mol). The increase of the C'=O bond length from the gas-phase to crystalline-state NMA corresponds to that found in the ab initio calculations with hydrogen bonding ligands, but the difference (0.1 angstrom) in the experimental C'(O)-N bond distance is significantly larger than the calculated value. This suggests that the crystal structure may be in error. In agreement with the crystal structure, the lowest energy conformation in all the hydrogen bonded systems is predicted to have an eclipsed (C')CH3 group and a staggered (N)CH3 group with respect to the C'(O)-N bond; this contrasts with isolated NMA, where the conformations with the different methyl orientations have similar energies with a difference of only approximately 0.1 kcal/mol. In accord with the general trend observed in hydrogen bonding in a crystal data base, the ab initio calculations show that the hydrogen bond distance involving "multiple acceptors" (i.e., the C'=O group that accepts two hydrogen bonds) is 0.02-0.06 angstrom longer than that involving a "single acceptor". The calculated hydrogen bond energy is approximately 0.5-1.5 kcal/mol smaller when two acceptors are present. By contrast, the formation of a hydrogen bond to the NH group reduces the hydrogen bond distance for the hydrogen bond to the C'=O group by approximately 0.02-0.045 angstrom and increases the corresponding hydrogen bond energy by approximately 0.3-0.9 kcal/mol. Correspondingly, the formation of each hydrogen bond to C'=O reduces the hydrogen bond distance for the hydrogen bond to the NH and increases the corresponding hydrogen bond energy by about the same amount. When one ligand is bound to the carbonyl group, the C=O...H(N) angle is nearly linear (approximately 160-degrees-165-degrees), while, for two ligands (i.e., with any additional H2O ligand), the angle is reduced to approximately 130-degrees, in accord with an analysis of structural data. The changes in the geometrical parameters and the increase of the methyl rotational barriers as a result of hydrogen bonding are interpreted in terms of Mulliken populations, and their importance for empirical force fields is briefly discussed.
We have compared force constants of formamide calculated by a wide range of ab initio quantum chemical methods and basis sets. Force fields calculated by local and gradient-corrected density functional theory (DFT) methods were found to be closer to MP2/6-31G** values than Hartree-Fock (HF) values. A comparison of calculated frequencies and infrared intensities with experimental values indicated better performance of the DFT methods over HF and even MP2. Several scaling schemes for interaction force constants were evaluated, as well as the effect of the variation of interaction force constants with theoretical method on the calculated frequencies, IR intensities, and normal modes.
A general method is provided to calculate chemical shifts for protons attached to sp3 carbons (methyl, methylene and methine). the approach is similar to rules developed by J. N. Shoolery in 1959. His rules are extended to allow calculations of proton chemical shifts in molecules that have multiple substituents within three carbons of the calculated proton chemical shifts. Keywords (Audience): Upper-Division Undergraduate
Previous folding studies have shown that equilibrium denaturation of bovine growth hormone (bGH) is a multistate process with stable intermediates. The native and unfolded species are monomeric, but intermediates are both monomeric and associated. In this study, the relative insolubility of an associated intermediate is used to distinguish its presence in equilibrium denaturation and during kinetic refolding. To study the role of the associated intermediate in the refolding pathway, a two-step procedure for its detection was developed. The first step of this procedure is used to populate the associated intermediate, and the second step involves dilution to solvent conditions in which only the associated intermediate precipitates. The amount of precipitate is quantitated either directly by formation of turbidity or indirectly by quantitation of the remaining soluble protein. The results show that an associated species is transiently populated during folding, it is incorrectly folded, and it occurs due to specific interactions of monomeric folding intermediates at moderate to high protein concentrations. This association of intermediates is a competing reaction that decreases the folding rate. The location of this competing reaction in the refolding pathway occurs after the formation of an early framework-type intermediate that contains considerable secondary structure but prior to the rate-limiting formation of the native tertiary structure. When refolding occurs in solutions that solubilize the associated intermediate, then native protein is obtained quantitatively. However, if refolding occurs in solutions that do not solubilize the associated intermediate, then most of the product results in an insoluble protein aggregate. The formation of precipitate that occurs upon refolding is inhibited by addition of fragments 96-133 or 109-133 that are derived from bGH. It is suggested that these fragments prevent precipitation by binding to the framework-type intermediate in a manner that prevents it from participating in the association reaction. The relationship of these results to general pathways of protein precipitation is discussed.
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