Calculation of trans-hydrogen-bond 13C-15N three-bond and other scalar J-couplings in cooperative peptide models. A density functional theory study

We report B3LYP DFT calculations on peptide models that consider the effects of cooperative interactions with proximate H-bonds and local geometry at the H-bonding site upon trans-H-bond (13)C-(15)N three-bond scalar J-couplings. The calculations predict that cooperative interactions with other H-bonds within a H-bonding chain can significantly increase the magnitude of these couplings. Such increases are due to a combination of the presence of the neighboring H-bonds and the slight increase in C=O distances expected for peptide H-bonds near the centers of H-bonding chains. The energies of H-bonds inferred from H-bonding distances, alone, could be significantly in error if the effects of neighboring H-bonds are ignored.     

Cooperative 4-pyridone H-bonds with extraordinary stability. A DFT molecular orbital study

The N-H...O H-bonding enthalpy between 4-pyridones connected in a chain of H-bonds can achieve 23 kcal/mol for the most central H-bonds, while that between two 4-pyridones is 9.90 kcal/mol based upon DFT calculations on the counterpoise-corrected potential energy surfaces. That the range of enthalpies for N-H...O H-bonds can vary from as little as 2 to as much 23 kcal/mol depends primarily upon the polarizability of whatever internally connects the N-H and C=O within the H-bonding molecule, which are two parallel -C=C- entities in 4-pyridone. The contribution of covalent or charge-transfer interactions between the pi-systems of adjacent 4-pyridones is small.     

Attractive strain: the disadvantages of rigid multiple H-bond donors and acceptors. A theoretical analysis of the hydrogen-bonding interactions in complexes of tetraazaanthracenedione with pyridylureas

We report density functional theory calculations at the B3LYP/D95(d,p) level on the hydrogen-bonding complexes of tetraazaanthracenedione, 1, with N-(pyridin-2-yl)urea, 2H, or N-(6-aminopyridin-2-yl)urea, 2N. The interaction energy of the 1-2H complex exceeds that of 1-2N, despite the fact that 1-2N contains a strong N-H...O interaction in place of a weak C-H...O interaction in 1-2H. We show that the 1-2N interaction is weaker than the sum of the four normal individual H-bonding interactions because the steric constraints of the complex prevent the H-bonding donors and acceptors from optimally approaching each other to form the two central H-bonds. This steric phenomenon, which we call attractive strain, is likely present to some extent in most H-bonding systems that contain more than two H-bonds between rigid monomers. Attractive strain is unusually important in 1-2N. Attractive strain can be conceived of as an enthalpic cost for the entropic benefits of freezing the dihedral angles of the multiple H-bond donors and acceptors by designing rigid systems.     

Single-site mutation and secondary structure stability: an isodesmic reaction approach. The case of unnatural amino acid mutagenesis Ala-->Lac

A method is described to evaluate backbone interactions in proteins via computational unnatural amino acid mutagenesis. Several N-acetyl polyalanyl amides (AcA(n)NH(2)) were optimized in the representative helical (3(10)-, 4(13)-, and a "hybrid" kappa-helix, n = 7, 9, 10, 14) and hairpin (two- and three-stranded antiparallel beta-sheets with type I turns betaalphaalphaepsilon, n = 6, 9, 10) conformations, and extended conformers of N-acetyl polyalanyl methylamides (n = 2, 3) were used to derive multistranded beta-sheet fragments. Subsequently, each residue of every model structure was substituted, one at a time, with l-lactic acid. The resulting mutant structures were again optimized, and group-transfer energies DeltaE(GT) were obtained as heats of the isodesmic reactions: AcA(n)NHR + AcOMe --> AcA(x)LacA(y)NHR + AcNHMe (R = H, CH(3)). These group-transfer energies correlate with the degree of charge polarization of the substituted peptide linkages as measured by the difference Deltae in H and O Mulliken populations in HN-C=O and with the H-bond distances in the "wild-type" structures. A good correlation obtains for the HF/3-21G and B3LYP/6-31G* group-transfer energies. The destabilization effects are interpreted in terms of loss of interstrand and intrastrand H-bonds, decrease in Lewis basicity of the C=O group, and O...O repulsion. On the basis of several comparisons of Ala --> Lac DeltaE(GT)'s with heats of the NH --> CH(2) substitutions, the latter contribution is estimated (B3LYP/6-31G*) to range between 1.5 and 2.4 kcal mol(-1), a figure close to the recent experimental DeltaDeltaG(o) value of 2.6 kcal mol(-1) (McComas, C. C.; Crowley, B. M.; Boger, D. L. J. Am.Chem. Soc. 2003, 125, 9314). The partitioning yields the following maximum values of the electronic association energy of H-bonds in the examined sample of model structures (B3LYP/6-31G* estimates): 3(10)-helix D(e) = -1.7 kcal mol(-1), alpha-helix D(e) = -3.8 kcal mol(-1), beta-sheet D(e) = -6.1 kcal mol(-1). The premise of experimental evaluations of the backbone-backbone H-bonding that Ala --> Lac substitution in proteins is isosteric (e.g., Koh, J. T.; Cornish, V. W.; Schultz, P. G. Biochemistry 1997, 36, 11314) is often but not always corroborated. Examination of the integrity of H-bonding pattern and phi(i), psi(i) distribution identified several mutants with significant distortions of the "wild-type" structure resulting inter alia from the transitions between i, i + 3 and i, i + 4 H-bonding in helices, observed previously in the crystallographic studies of depsipeptides (Ohyama, T.; Oku, H.; Hiroki, A.; Maekawa, Y.; Yoshida, M.; Katakai, R. Biopolymers 2000, 54, 375; Karle, I. L.; Das, C.; Balaram, P. Biopolymers 2001, 59, 276). Thus, the isodesmic reaction approach provides a simple way to gauge how conformation of the polypeptide chain and dimensions of the H-bonding network affect the strength of backbone-backbone C=O...HN bonds. The results indicate that the stabilization provided by such interactions increases on going from 3(10)-helix to alpha-helix to beta-sheet.     

Direct probing of sorbent-solvent interactions for amylose tris(3,5-dimethylphenylcarbamate) using infrared spectroscopy, X-ray diffraction, solid-state NMR, and DFT modeling

The sorbent-solvent interactions for amylose tris(3, 5-dimethylphenylcarbamate) (ADMPC) with five commonly used solvents, hexane, methanol, ethanol, 2-propanol (IPA), and acetonitrile (ACN), are studied using attenuated total reflection infrared spectroscopy (ATR-IR) of thin sorbent films, X-ray diffraction (XRD) of thin films, (13)C cross polarization/magic angle spinning (CP/MAS) and MAS solid state NMR of polymer-coated silica beads (commercially termed "Chiralpak AD"), and DFT modeling. The ADMPC-polymer-coated silica beads are used commercially for analytical and preparative scale separations of chiral enantiomers. The polymer forms helical rods with intra- and inter-rod hydrogen bonds (H-bonds). There are various nm-sized cavities formed between the polymer side-chains and rods. The changes in the H-bonding states of the C=O and NH groups of the polymer upon absorption of each of the five solvents at 25 degrees C are determined with ATR-IR. The IR wavenumbers, the H-bonding interaction energies, and the H-bonding distances of the polymer side-chains with each of the solvent molecules are predicted using the DFT/B3LYP/6-311+g(d,p) level of theory. The changes in the polymer crystallinity upon absorption of each solvent are characterized with XRD. The changes in the polymer crystallinity and the H-bonding states of C=O groups are also probed with (13)C CP/MAS solid-state NMR. The changes in the polymer side-chain mobility are detected using (13)C MAS solid-state NMR. The H-bonding states of the polymer change upon absorption of each polar solvent and usually result in an increase in the polymer crystallinity and the side-chain mobility. The polymer rods are reorganized upon solvent absorption, and the distance between the rods increases with the increase in the solvent molecular size. These results have implications for understanding the role of the solvent in modifying the structure and behavior of the polymer sorbents.     

Dissection of complex molecular recognition interfaces

The synthesis of a family of zinc porphyrins and pyridine ligands equipped with peripheral H-bonding functionality has provided access to a wide range of closely related supramolecular complexes featuring between zero and four intramolecular H-bonds. An automated UV/vis titration system was used to characterize 120 different complexes, and these data were used to construct a large of number of different chemical double mutant cycles to quantify the intramolecular H-bonding interactions. The results probe the quantitative structure-activity relationship that governs cooperativity in the assembly of complex molecular recognition interfaces. Specifically, variations in the chemical structures of the complexes have allowed us to change the supramolecular architecture, conformational flexibility, geometric complementarity, the number and nature of the H-bond interactions, and the overall stability of the complex. The free energy contributions from individual H-bonds are additive, and there is remarkably little variation with architecture in the effective molarity for the formation of intramolecular interactions. Intramolecular H-bonds are not observed in complexes where they are geometrically impossible, but there are no cases where excellent geometric complementarity leads to very high affinities. Similarly, changes in conformational flexibility seem to have limited impact on the values of effective molarity (EM). The major variation that was found for all of the 48 intramolecular interactions that were examined using double mutant cycles is that the values of EM for intramolecular carboxylate ester-phenol H-bonds (200 mM) are an order of magnitude larger than those found for phosphonate diester-phenol H-bonds (30 mM). The corresponding intermolecular phosphonate diester-phenol H-bonds are 2 orders of magnitude more stable than carboxylate ester-phenol H-bonds, and the large differences in EM may be due to some kind of compensation effect, where the stronger H-bond is harder to make, because it imposes tighter constraints on the geometry of the complex.     

Direct calculation of trans-hydrogen-bond 13C-15N 3-bond J-couplings in entire polyalanine alpha-helices. A density functional theory study

We present the first trans-H-bond 13C-15N 3-bond J couplings calculated from entire neutral and protonated alpha-helical polyalanines. The neutral helices considered are those of the capped peptides, acetyl(Ala)NNH2, where N = 8, 16, 17, and 18, while the protonated peptides are the uncapped (Ala)17 protonated at three different positions. The calculated J values correlate well with O...H distances and somewhat less well with N...O distances, particularly if the terminal H-bonds are eliminated from the correlation. The J values calculated using the entire helix are about 6% lower in magnitude than those recently reported for H-bonding chains whose geometries were extracted from the same helices. Aqueous solvation favors protonation of the alpha-helix on the terminal COOH. Experimental measurements of the trans-H-bond 13C-15N 3-bond J couplings in acidic solution should be interpreted with this context.     

H-bonding patterns in the platinated guanine-cytosine base pair and guanine-cytosine-guanine-cytosine base tetrad: an electron density deformation analysis and AIM study

The atoms in molecule theory (AIM) and electronic structure analysis are applied together to investigate H-bonding patterns in metalated nucleobase complexes. The influence of Pt on the intra GC base pair H-bonding has been found to reduce intra base pair H-bonding of N4(C)...O6(G) in the platinated GC pair and GCGC tetrad. The relaxation of geometry constrains in metalated nucleobases is found to be decisively important in the formation of novel molecular architectures from nucleobases and metal entities. The incorporation of the platinum in the GCGC tetrad benefits the formation of the unique CH...N (H5(C)...N1(G)) hydrogen bond pattern in the tetrad by offering improved geometric constraints rather than through changing the electronic properties around the H5(C) and N1(G) sites. Platination at the N7 of guanine reduces the deprotonation energy considerably.     

Experimental FTIR and simulation studies on H-bonds of model polyurethane in solutions. I: In dimethylformamide (DMF)

Polyurethane (PU) hard segment is one of the key factors determining the final PU properties whereas dimethylformamide (DMF), with the simplest tertiary amide, is one of the good solvents for PU. In the present paper, both FTIR and molecular simulation (QM/B3LYP) were used to study the hydrogen bonds (H-bonds) of PU model hard segment (PUMHS) in DMF. The FTIR characteristics and the H-bonding interaction between DMF and PUMHS, as well as in DMF and PUMHS themselves have been investigated. The results showed that the H-bonds not only exist in DMF and in PUMHS themselves, but also exist between PUMHS and DMF. Among them, seven H-bonding complexes between DMF and PUMHS were found based on different conformations. The H-bonding properties and the forming probabilities have been obtained and compared. The evolution of H-bonds of PUMHS in DMF with different concentration was qualitatively analyzed.     

Direct NMR observation and pKa determination of the Asp102 side chain in a serine protease

The pK(a) value of aspartic acid in the catalytic triad of serine proteases has been a pivotal element in essentially every mechanism proposed for these enzymes over the past 40 years, but has, until now, eluded direct determination. Here, we have used the multinuclear 3D-NMR pulse programs HCACO and HCCH-TOCSY to directly identify and study the side-chain resonances of the aspartate and glutamate residues in uniformly (13)C-labeled α-lytic protease. Resonances from four of the six residues were detected and assigned, including that of Asp(102), which is notably the weakest of the four. pH titrations have shown all of the carboxylate (13)C signals to have unusually low pK(a) values: 2.0, 3.2, and 1.7 for Glu(129), Glu(174), and Glu(229), respectively, and an upper limit of 1.5 for Asp(102). The multiple H-bonds to Asp(102), long known from X-ray crystal studies, probably account for its unusually low pK(a) value through preferential stabilization of its anionic form. These H-bonds probably also contribute to the weakness of the NMR resonances of Asp(102) by restricting its mobility. The Asp(102)(13)C(γ) atom responds to the ionization of His(57) in the resting enzyme and to the inhibitor-derived oxyanion in a chloromethyl ketone complex, observations that strongly support the assignment. The low pK(a) value of Asp(102) would appear to be incompatible with mechanisms involving strong Asp(102)-His(57) H-bonds or high pK(a) values, but is compatible with mechanisms involving normal Asp(102)-His(57) H-bonds and moving His(57) imidazole rings, such as the reaction-driven ring flip.     

Measurements of carbon to amide-proton distances by C-H dipolar recoupling with 15N NMR detection

A new magic-angle spinning NMR method for measuring internuclear distances between a 13C-labeled site and amide protons is described. The magnetization of the protons evolves under homonuclear decoupling and the recoupled 13C-1H dipolar interaction, which provides simple spin-pair REDOR curves if only one 13C-labeled site is present. The modulation of the amide proton HN is detected via short 1H-15N cross polarization followed by 15N detection. The method is demonstrated on two specifically 13C- and 15N-labeled peptides, with 13C-HN distances from 2.2 to ca. 6 A. This technique promises to be particularly useful for measuring distances between 13C=O and H-15N groups, to identify hydrogen bonds in peptides and proteins.     

A critical examination of H-bonding interactions calculated using the AM1 molecular orbital method

AM 1 calculations for various intermolecular and internally hydrogen-bonding species are compared with experiment. The calculations generally provide a useful, but not perfect, means for modeling H-bonds. The average stabilization energy for 33 gas-phase hydrations of ions was 1.4, whereas that for amination of 10 ions was 4.2 kcal/mol, too weak when compared to experimental results. H-bonding distances have a tendency to be long. The tendency of AM 1 to predict multicentered H-bonds is discussed in the context of recent surveys of crystallographic data banks. Caution is recommended in comparing AM 1 results with inappropriate experiments and inadequate ab initio calculations. © 1992 John Wiley & Sons, Inc.     

Mechanism of RNase T1: concerted triester-like phosphoryl transfer via a catalytic three-centered hydrogen bond

BACKGROUND: The microscopic events of ribonuclease (RNase) catalyzed phosphoryl transfer reactions are still a matter of debate in which the contenders adhere to either the classical concerted acid-base mechanism or a more sequential triester-like mechanism. In the case of RNase A, small thio-effects of the nonbridging oxygens have been invoked in favor of the classical mechanism. However, the RNase T1 catalyzed transphosphorylation of phosphorothioate RNA is highly stereoselective. R(P) thio-substituted RNA is depolymerized 60000 times faster than S(P) thio-substituted RNA by this enzyme, whereas the uncatalyzed cleavage of both substrates occurs at comparable rates. We combined site-directed mutagenesis in the RNase active site and stereospecific thio-substitution of an RNA substrate to probe the intermolecular interactions of the enzyme with the nonbridging pro-S(P) oxygen that bring about this stereoselectivity of RNase T1. RESULTS: Thio-substitution of the nonbridging pro-S(P) oxygen in the substrate afflicts chemical turnover but not ground state binding whereas thio-substitution of the nonbridging pro-R(P) oxygen does not affect the kinetics of RNase T1. Site-directed mutagenesis of the catalytic base Glu58 impairs the enzyme's ability to discriminate both phosphorothioate diastereomers. Glu58Ala RNase T1 cleaves R(P) and S(P) phosphorothioate RNA with similar rates. The dependence of the pro-S(P) thio-effect on the presence of the Glu58 carboxylate evidences a strong rate-limiting interaction between the nonbridging pro-S(P) oxygen and the catalytic base Glu58 in the wild type enzyme. CONCLUSIONS: Based on these results, we put forward a new triester-like mechanism for the RNase T1 catalyzed reaction that involves a three-centered hydrogen bond between the 2'-OH group, the nonbridging pro-S(P) oxygen and one of the carboxylate oxygens of Glu58. This interaction allows nucleophilic attack on an activated phosphate to occur simultaneously with general base catalysis, ensuring concerted phosphoryl transfer via a triester-like mechanism.     

Selenium in Proteins: Conformational Changes Induced by Se Substitution on Methionine,as Studied in Isolated Model Peptides by Optical Spectroscopy and Quantum Chemistry

The side-chain of methionine residues is long enough to establish NH⋯S H-bonds with neighboring carbonyl groups of the backbone, giving rise to so-called intra-residue 6^δ and inter-residue 7^δ H-bonds. The aim of the present article is to document how the substitution of sulfur with a selenium atom affects the H-bonding of the Met system. This was investigated both experimentally and theoretically by conformation-resolved optical spectroscopy, following an isolated molecule approach. The present work emphasizes the similarities of the Met and Sem residues in terms of conformational structures, energetics, NH⋯Se/S H-bond strength and NH stretch spectral shifts, but also reveals subtle behavior differences between them. It provides evidence for the sensitivity of the H-bonding network with the folding type of the Sem/Met side-chains, where a simple flip of the terminal part of the side-chain can induce an extra 50 cm⁻¹ spectral shift of the NH stretch engaged in a 7^δ NH⋯S/Se bond.     

Side-chain and backbone ordering in homopolymers

In order to study the relation between backbone and side-chain ordering in proteins, we have performed multicanonical simulations of deka-peptide chains with various side groups. Glu(10), Gln(10), Asp(10), Asn(10), and Lys(10) were selected to cover a wide variety of possible interactions between the side chains of the monomers. All homopolymers undergo helix-coil transitions. We found that peptides with long side chains that are capable of hydrogen bonding, i.e., Glu(10), and Gln(10), exhibit a second transition at lower temperatures connected with side-chain ordering. This occurs in the gas phase as well as in solvent, although the character of the side-chain structure is different in each case. However, in polymers with short side chains capable of hydrogen bonding, i.e., Asp(10) and Asn(10), side-chain ordering takes place over a wide temperature range and exhibits no phase transition-like character. Moreover, non-backbone hydrogen bonds show enhanced formation and fluctuations already at the helix-coil transition temperature, indicating competition between side-chain and backbone hydrogen bond formation. Again, these results are qualitatively independent of the environment. Side-chain ordering in Lys(10), whose side groups are long and polar, also takes place over a wide temperature range and exhibits no phase transition-like character in both environments. Reasons for the observed chain length threshold and consequences from these results for protein folding are discussed.     

Gas-phase DNA oligonucleotide structures. A QM/MM and atoms in molecules study

QM/MM calculations have been employed to investigate the role of hydrogen bonding and pi-stacking in single- and double-stranded DNA oligonucleotides. DFT calculations and Atoms in Molecules analysis on QM/MM-optimized structures allow characterization and estimation of the energies of pi-stacking and hydrogen-bond interactions. This shows that pi-stacking interactions depend on the number and the nature of the DNA bases for single-stranded nucleotides; for instance, guanines are found to be involved in strong hydrogen bonds, whereas adenines interact mainly via stacking interactions. The role of interbase hydrogen bonding was explored: the -NH2 groups of guanine, adenine, and cytosine participate in N-H...O and N-H...N interactions. These are much stronger in single-strand oligonucleotides, where the -NH2 groups are highly nonplanar. In double-stranded DNA, the strong base-pairing hydrogen bonds of complementary bases lead to more planar -NH2 groups, which tend to be involved in pi-stacking interactions rather than H-bonds. The use of AIM also allows us to evaluate the interplay of pi-stacking and H-bonding, suggesting that cooperativity does occur, but is generally limited to about 1-2 kcal/mol.     

Intramolecular hydrogen bonding and cooperative interactions in carbohydrates via the molecular tailoring approach

In spite of many theoretical and experimental attempts for understanding intramolecular hydrogen bonding (H-bonding) in carbohydrates, a direct quantification of individual intramolecular H-bond energies and the cooperativity among the H-bonded networks has not been reported in the literature. The present work attempts, for the first time, a direct estimation of individual intramolecular O-H...O interaction energies in sugar molecules using the recently developed molecular tailoring approach (MTA). The estimated H-bond energies are in the range of 1.2-4.1 kcal mol(-1). It is seen that the OH...O equatorial-equatorial interaction energies lie between 1.8 and 2.5 kcal mol(-1), with axial-equatorial ones being stronger (2.0-3.5 kcal mol(-1)). The strongest bonds are nonvicinal axial-axial H-bonds (3.0-4.1 kcal mol(-1)). This trend in H-bond energies is in agreement with the earlier reports based on the water-water H-bond angle, solvent-accessible surface area (SASA), and (1)H NMR analysis. The contribution to the H-bond energy from the cooperativity is also estimated using MTA. This contribution is seen to be typically between 0.1 and 0.6 kcal mol(-1) when H-bonds are a part of a relatively weak equatorial-equatorial H-bond network and is much higher (0.5-1.1 kcal mol(-1)) when H-bonds participate in an axial-axial H-bond network.     

The effect of polarization on multiple hydrogen-bond formation in models of self-assembling materials

We report density functional theory calculations at the B3LYP/D95(d,p) level on several different cyclic H-bonding dimers, where the monomers of each are connected by a pair of N-H···O=C H-bonding interactions, and the H-bonding donors and acceptors on each monomer are separated by polarizable spacers. Depending on the structures, the individual H-bonds vary in strength (enthalpy) by over a factor of four, from 2.41 to 10.99 kcal/mol. We attribute most of the variation in interaction energies to differences in the extent of polarization due to each of the H-bonds, which can either combine constructively or destructively. The dipole-dipole interactions between the pair of H-bonds also contribute somewhat to the relative stabilities. The relevance of these results to the design of self-assembling materials is discussed.     

A solvatochromic model calibrates nitriles' vibrational frequencies to electrostatic fields

Electrostatic interactions provide a primary connection between a protein's three-dimensional structure and its function. Infrared probes are useful because vibrational frequencies of certain chemical groups, such as nitriles, are linearly sensitive to local electrostatic field and can serve as a molecular electric field meter. IR spectroscopy has been used to study electrostatic changes or fluctuations in proteins, but measured peak frequencies have not been previously mapped to total electric fields, because of the absence of a field-frequency calibration and the complication of local chemical effects such as H-bonds. We report a solvatochromic model that provides a means to assess the H-bonding status of aromatic nitrile vibrational probes and calibrates their vibrational frequencies to electrostatic field. The analysis involves correlations between the nitrile's IR frequency and its (13)C chemical shift, whose observation is facilitated by a robust method for introducing isotopes into aromatic nitriles. The method is tested on the model protein ribonuclease S (RNase S) containing a labeled p-CN-Phe near the active site. Comparison of the measurements in RNase S against solvatochromic data gives an estimate of the average total electrostatic field at this location. The value determined agrees quantitatively with molecular dynamics simulations, suggesting broader potential for the use of IR probes in the study of protein electrostatics.     

Ferrocene-appended aryl triazole for electrochemical recognition of phosphate ions

A neutral ferrocene-appended aryl triazole receptor 1 for phosphate anions has been synthesized and characterized by X-ray crystal analysis. Among various anions, 1 shows a distinct electrochemical recognition of phosphate anions by its multiple H-bonding (C-H···O) with a tetrahedral anion, which is supported by density functional theory based theoretical calculation and (1)H NMR titration results.