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.     

Signature of mobile hydrogen bonding of lysine side chains from long-range 15N-13C scalar J-couplings and computation

Amino acid side chains involved in hydrogen bonds and electrostatic interactions are crucial for protein function. However, detailed investigations of such side chains in solution are rare. Here, through the combination of long-range (15)N-(13)C scalar J-coupling measurements and an atomic-detail molecular dynamics (MD) simulation, direct insight into the structural dynamic behavior of lysine side chains in human ubiquitin has been gained. On the basis of (1)H/(13)C/(15)N heteronuclear correlation experiments selective for lysine NH(3)(+) groups, we analyzed two different types of long-range (15)N-(13)C J-coupling constants: one between intraresidue (15)Nζ and (13)Cγ nuclei ((3)J(NζCγ)) and the other between (15)Nζ and carbonyl (13)C' nuclei across a hydrogen bond ((h3)J(NζC')). The experimental (3)J(NζCγ) data confirm the highly mobile nature of the χ(4) torsion angles of lysine side chains seen in the MD simulation. The NH(3)(+) groups of Lys29 and Lys33 exhibit measurable (h3)J(NζC') couplings arising from hydrogen bonds with backbone carbonyl groups of Glu16 and Thr14, respectively. When interpreted together with the (3)J(NζCγ)-coupling constants and NMR-relaxation-derived S(2) order parameters of the NH(3)(+) groups, they strongly suggest that hydrogen bonds involving NH(3)(+) groups are of a transient and highly dynamic nature, in remarkably good agreement with the MD simulation results.     

Gas-phase acidity of D-glucose. A density functional theory study

The gas-phase acidity of D-glucopyranose was studied by means of B3LYP calculations combined with 6-31G(d,p) or 6-31+G(d,p) standard basis sets. For each anomer, deprotonation of the various primary and secondary hydroxyl groups was considered. As in solution, the anomeric hydroxyl is found to be the most acidic for both anomers, but only when the 6-31+G(d,p) basis set is used for geometry optimization. Deprotonation of the anomeric hydroxyl induces an important C(1)--O endocyclic bond elongation and subsequently promotes an energetically favored ring-opening process as attested by the very small calculated activation barriers. The results also suggest that interconversion between the various deprotonated alpha- and beta-anomers may easily occur under slightly energetic conditions. B3LYP/6-311+G(2df,2p) calculations led to the an absolute gas-phase acidity of deltaacidGo(298)(alpha-D-glucose) = 1398 kJ mol(-1). This estimate matches well the only experimental value available to date. Finally, this study again confirms that the use of diffuse functions on heavy atoms is necessary to describe anionic systems properly and to achieve good relative and absolute gas-phase acidities.     

Silabutadienes. Internal rotations and pi-conjugation. A density functional theory study

The potential energy surfaces (PESs) for internal rotation around the central single bond of nine silabutadienes, which include all possible mono-, di-, tri-, and tetrasilabutadienes, are investigated computationally by using DFT with the B3LYP functional and the 6-311+G(d,p) basis set. For 1-silabutadiene (3), 2-silabutadiene (4), 1,4-disilabutadiene (5), 2,3-disilabutadiene (6), and 1,3-disilabutadiene (7), the s-trans rotamer is the most stable. For 1,2-disilabutadiene (8), 1,2,3-trisilabutadiene (9), and 1,2,4-trisilabutadiene (10), all having a trans-bent SiSi double bond, the most stable conformers are those having an antiperiplanar (ap) structure. For tetrasilabutadiene (11), the global minimum is the gauche rotamer. The internal rotation barriers (RB) (relative to the global minimum) follow the order (kcal/mol) 5 (10.0) > 3 (7.4) > 1,3-butadiene (12, (6.6)) > 10 (4.9) > or = 7 (4.4) > or = 4 (4.0) approximately = 8 (3.9) > 9 (2.7) approximately = 6 (2.6) > 11 (2.4). The barriers are slightly smaller at CCSD(T)/cc-PVTZ, but the trend remains the same. The size of the rotation barrier is mainly dictated by the length of the central single bond; that is, it is the largest for dienes with the shorter C-C central bond (5, 3, and 12), and it is smaller for dienes with the longer Si-C and Si-Si central bonds. The strength of pi-conjugation in the s-trans conformers of silabutadienes was estimated by resonance stabilization energies (RE) calculated by using the Natural Bond Orbital (NBO) and Block Localized Wave function (BLW) methods and bond separation equations. A linear correlation is found between the barrier heights for internal rotation and pi-conjugation energies. The calculated RBs are significantly smaller than the corresponding REs, indicating that pi-resonance energies are not the only factor that dictate the RB, and therefore, RBs, although suitable for estimating trends in pi-conjugation in a series of compounds, cannot be used for estimating absolute resonance energies.     

A density functional theory study of sulfur poisoning

Density functional theory calculations have been used to investigate the chemisorption of H, S, SH, and H(2)S as well as the hydrogenation reactions S+H and SH+H on a Rh surface with steps, Rh(211), aiming to explain sulfur poisoning effect. In the S hydrogenation from S to H(2)S, the transition state of the first step S+H-->SH is reached when the S moves to the step-bridge and H is on the off-top site. In the second step, SH+H-->H(2)S, the transition state is reached when SH moves to the top site and H is close to another top site nearby. Our results show that it is difficult to hydrogenate S and they poison defects such as steps. In order to address why S is poisoning, hydrogenation of C, N, and O on Rh(211) has also been calculated and has been found that the reverse and forward reactions possess similar barriers in contrast to the S hydrogenation. The physical origin of these differences has been analyzed and discussed.     

A density functional theory study of vibrational coupling in the amide I band of beta-sheet models

We report the first molecular orbital/density functional theory (DFT) calculations on the vibrational frequencies involved in the amide I band of completely geometrically optimized models for beta-sheet peptides based upon (up to 16) glycine residues. These calculations use the B3LYP/D95** level of DFT. The primary means of vibrational coupling occurs through H bond, rather than through space, interactions, which is consistent with a previous report on alpha-helical polyalanines and H-bonding chains of both formamides and 4-pyridones. We decoupled the C=O stretching vibrations using selected 14C substitutions to probe the coupling mechanism and to determine "natural" frequencies for individual 14C=Os. The intermolecular H-bonding interactions affect the geometries of the amide groups. Those near the center of H-bonding chains have long C=O bonds. The C=O bond lengths correlate with these "natural" frequencies, The frequencies obtained from the DFT calculations are generally more coupled, and the most intense are more red shifted than those calculated by transition dipole coupling (TDC). TDC inverts the order of the shifted frequencies compared to DFT in several cases.     

A density functional theory study of the benzene-water complex

The intermolecular interaction of the benzene-water complex is calculated using real-space pseudopotential density functional theory utilizing a van der Waals density functional. Our results for the intermolecular potential energy surface clearly show a stable configuration with the water molecule standing above or below the benzene with one or both of the H atoms pointing toward the benzene plane, as predicted by previous studies. However, when the water molecule is pulled outside the perimeter of the ring, the configuration of the complex becomes unstable, with the water molecule attaching in a saddle point configuration to the rim of the benzene with its O atom adjacent to a benzene H. We find that this structural change is connected to a change in interaction from H (water)/pi cloud (benzene) to O (water)/H (benzene). We compare our results for the ground-state structure with results from experiments and quantum-chemical calculations.     

13C,15N]2-Acetamido-2-deoxy-D-aldohexoses and their methyl glycosides: synthesis and NMR investigations of J-couplings involving 1H, 13C, and 15N

[reaction: see text] A series of 2-amino-2-deoxy-D-[1-13C]aldohexoses and their methyl glycosides was prepared with use of a simplified cyanohydrin reduction route. Four d-aldopentosylamines (arabino, lyxo, ribo, xylo) were prepared from the corresponding D-aldopentoses by reaction with NH3(g) in MeOH solvent, isolated in solid form, and characterized by 13C and 1H NMR. Hydrolysis of beta-D-xylopyranosylamine was studied using 13C-labeled substrates to establish optimal solution conditions for cyanohydrin formation. Major hydrolytic intermediates were observed and identified by time-lapse 1D and 2D NMR analyses of reaction mixtures. The aldopentosylamines were subsequently employed in cyanohydrin reduction reactions with K13CN to yield C2-epimeric [1-13C]2-aminosugars, which were separated by chromatography on ion-exchange columns. N-Acetylation and methyl glycosidation followed by chromatography gave pure 2-acetamido-2-deoxy-D-[1-13C]aldohexopyranosides. J(CH) and J(CC) spin-spin coupling constants involving the labeled anomeric carbon were measured and compared to those observed previously in methyl D-[1-13C]aldohexopyranosides. In parallel studies, theoretical J-couplings were calculated in model N-acetylated aldopyranosides using density functional theory (DFT) to predict the effect of OH vs NHCOCH(3) substitution at C2 on J(CH) and J(CC) values in aldopyranosyl rings. The synthetic method was also modified to accommodate (15)N- and (13)C-labeling within the N-acetyl side-chain, and some J-couplings involving 1H, 13C, and 15N atoms in 2-[1,2-13C2;15N]acetamido-2-deoxy-D-[1-13C]glucose were measured and interpreted.     

CaSO4 and its pressure-induced phase transitions. A density functional theory study

Theoretical investigations concerning possible calcium sulfate, CaSO(4), high-pressure polymorphs have been carried out. Total-energy calculations and geometry optimizations have been performed by using density functional theory at the B3LYP level for all crystal structures considered. The following sequence of pressure-driven structural transitions has been found: anhydrite, Cmcm (in parentheses the transition pressure) → monazite-type, P2(1)/n (5 GPa) → barite-type, Pnma (8 GPa), and scheelite-type, I4(1)/a (8 GPa). The equation of state of the different polymorphs is determined, while their corresponding vibrational properties have been calculated and compared with previous theoretical results and experimental data.     

The Calculation of directly bonded 13C-H and 13C-13C coupling constants using delocalized molecular orbital theory

The Pople-Santry theory of coupling in -electron systems lias been applied to directly bonded CH and CC coupling constants. Calculations on normal hydrocarbons, e.g. CH₄, C₂H₆, C₂H₄, C₂H₂, show that the theory can give a satisfactory explanation of such coupling constants, although the values are sensitive to the parameters used in the calculation. The theory has been applied with varying success to the larger hydrocarbons methylacetylene, butadiene and benzene, and to the strained molecules cyclopropane and ferrocene. No difficulty arises in applying the theory to hetero-atomic systems (pyridine and pyrimidine) and the results are quite satisfactory.

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Zusammenfassung Die Pople-Santry Theory über Koppelung in -Elektronensystemen wurde auf CH und CC Koppelungskonstanten direkt gebundener Atome angewandt. Rechnungen für einfache Kohlenwasserstoffe, z. B. CH₄, C₂H₆, C₂H₄, C₂H₂ zeigen, daß die Theorie eine zufriedenstellende Erklärung solcher Koppelungskonstanten geben kann, obwohl die Werte empfindlich von den in der Rechnung benutzten Parametern abhängen. Die Theorie wurde mit unterschiedlichem Erfolg auf die größeren Kohlenwasserstoffe Methylazetylen, Butadien und Benzol und auf die gespannten Moleküle Cyclopropan und Ferrocen angewandt. Bei Anwendung der Theorie auf Systeme mit Heteroatomen (Pyridin und Pyrimidin) entsteht keine Schwierigkeit und die Ergebnisse sind zufriedenstellend.

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Résumé La théorie de Pople et Santry sur le couplage dans les systèmes d'électrons a été appliquée aux constantes de couplage CH et CC entre atomes liés. Les calcules pour quelques simples hydrocarbures, par example CH₄, C₂H₆, C₂H₄, C₂H₂, montrent que la théorie explique satisfaisamment ces constantes, bien que les valeurs dépendent sensiblement des paramètres du calcul. La théorie a été appliquée avec succès variable aux hydrocarbures plus grandes: methylacetylene, butadiene et benzène et aux molecules tendues: cyclopropane et ferrocène. Des systèmes à hétéroatomes (pyridine et pyrimidine) ne prêtent pas de difficultés, et les résultats sont satisfaisants.

     

A density functional theory study of hydrogen adsorption in MOF-5

Ab initio molecular dynamics in the generalized gradient approximation to density functional theory and ground-state relaxations are used to study the interaction between molecular hydrogen and the metal-organic framework with formula unit Zn4O(O2C-C6H4-CO2)3. Five symmetrically unique adsorption sites are identified, and calculations indicate that the sites with the strongest interaction with hydrogen are located near the Zn4O clusters. Twenty total adsorption sites are found around each Zn4O cluster, but after 16 of these are populated, the interaction energy at the remaining four sites falls off significantly. The adsorption of hydrogen on the pore walls creates an attractive potential well for hydrogen in the center of the pore. The effect of the framework on the physical structure and electronic structure of the organic linker is calculated, suggesting ways by which the interaction between the framework and hydrogen could be modified.     

A density functional theory study of copper-catalyzed aziridination of olefins

Density functional theory calculations are reported for the reaction mechanism of selected XCuNHX(X = Cl, Br, I) with olefins to form three-membered ring products. The copper reagents react with olefins via an asynchronous attack on one CH₂ group of ethylene with a relatively low barrier (<78 kJ/mol). These computational results are in good agreement with experimental results, and this suggests that the nitrene transfer process is favored. The BrCuNHBr is found to be the most reactive reagent in the XCuNHX (X = Cl, Br, I) series of reagents. These results are qualitatively consistent with the agreement between copper-catalyzed species character and experimental conditions needed for efficient reaction.     

Measurement of multiple psi torsion angles in uniformly 13C,15N-labeled alpha-spectrin SH3 domain using 3D 15N-13C-13C-15N MAS dipolar-chemical shift correlation spectroscopy

We demonstrate the simultaneous measurement of several backbone torsion angles psi in the uniformly (13)C,(15)N-labeled alpha-Spectrin SH3 domain using two different 3D 15N-13C-13C-15N dipolar-chemical shift magic-angle spinning (MAS) NMR experiments. The first NCCN experiment utilizes double quantum (DQ) spectroscopy combined with the INADEQUATE type 13C-13C chemical shift correlation. The decay of the DQ coherences formed between 13C'(i) and 13C(alphai) spin pairs is determined by the "correlated" dipolar field due to 15N(i)-13C(alphai) and 13C'(i)-15N(i+1) dipolar couplings and is particularly sensitive to variations of the torsion angle in the regime |psi| > 140 degrees. However, the ability of this experiment to constrain multiple psi-torsion angles is limited by the resolution of the 13C(alpha)-(13)CO correlation spectrum. This problem is partially addressed in the second approach described here, which is an NCOCA NCCN experiment. In this case the resolution is enhanced by the superior spectral dispersion of the 15N resonances present in the 15N(i+1)-13C(alphai) part of the NCOCA chemical shift correlation spectrum. For the case of the 62-residue alpha-spectrin SH3 domain, we determined 13 psi angle constraints with the INADEQUATE NCCN experiment and 22 psi constraints were measured in the NCOCA NCCN experiment.     

A density functional theory study of interaction between formamide and guanine

Hydrogen bonding in complexes formed between formamide and guanine molecules was completely investigated using density functional theory (DFT) at the 6-311++G(d, p) level. For comparison, the HF and MP2 methods were also used. Nine stable cyclic structures stabilized by two hydrogen bonds were found. One of these was a six-membered ring, five were seven-membered rings, and the others were eight-membered rings. The eight-membered ring is preferable to the seven-and six-membered ones as follows from H-bond lengths and interaction energies. The FG4 structure was calculated to be the most stable, and another cyclic structure, FG5, was least stable because of the six-membered ring and the weakest interaction. The infrared spectrum frequencies, intensities, and vibrational frequency shifts are also reported. The text was submitted by the authors in English.     

Calculation of <Superscript>15</Superscript>N NMR chemical shifts of amines in the framework of the density functional theory

The ¹⁵N NMR magnetic shielding constants (followed by recalculation into chemical shifts) in a representative series of amines were calculated in the framework of the density functional theory. The results were compared with experiment. The accuracy factors of this calculation (functional, basis set, solvent effects, and multistandard) were studied. Taking into account all the above factors leads to a noticeable decrease in the average absolute error in the calculation of the ¹⁵N NMR chemical shifts (from 13 to 4 ppm) in a range of their changing in the studies series of compounds of ～60 ppm (which is 6—7% in relative units).     

Structures,stabilities, and IR and 13C-NMR spectra of dihedral fullerenes: A density functional theory study

Dihedral fullerenes are thermodynamically stable molecules with D nd or D nh symmetry.Based on experimental findings,two series of dihedral fullerenes with five-fold(C5) and six-fold(C6) symmetry have been studied using density functional theory(DFT).The DFT calculations showed that for both series the stabilities increased with increasing fullerene size.Structural analyses indicated that the stabilities are related to specific local geometries.In the case of the more abundant C5 series,the presence of approximately planar pentagons and hexagons on the top bowl favors their formation.That is to say,those fullerenes with small dihedral angles within the polygons are readily formed,because planar hexagons lead to strengthened conjugation which lowers average bonding energies(ABE) and increases thermodynamic stabilities.Non-planar hexagons at equatorial positions in tube-shaped fullerenes have an adverse effect on the conjugation and inhibit their formation.Calculations also demonstrated that fullerenes in the two series,including C 50(D 5h),C 60(D 6h),C 80(D 5d),C 96(D 6d),C 110(D 5h),and C 120(D 5d),have thermodynamically stable triplet structures with strong conjugation.The calculated IR and 13 C NMR spectra of the fullerenes show some similarities and regular trends due to their homogenous structures.The electronic structures indicate that short double bonds in hexagons with high electron occupancies are readily attacked by electrophilic agents and can also be coordinated by transition metals.Mechanistic discussions suggested that C 2 additions and C 2 losses constitute reversible processes at high temperature and C 2 additions in pentagonal fusions are crucial to the kinetics of the curvature of structures.C 3 additions lead to the formation of large fullerenes of other types.     

Spin-spin coupling constants 13C-15N and 1H-15N in the investigation of azido-tetrazole tautomerism in a series of 2-azidopyrimidines

A new method was developed for the investigation of an azido-tetrazole equilibrium based on using a complex analysis of ¹³C-¹⁵N and ¹H-¹⁵N spin-spin coupling constants. The use of this approach became possible due to the selective inclusion of ¹⁵N isotopes into the structures of 2-azidopyrimidines and their cyclic analogs tetrazolo[1,5-a]pyrimidines.     

13C-15N spin-spin coupling constants of amides: H-bonding effects in a cyclohexapeptide

The effect of intramolecular H-bonding and solvent acidity on the magnitude of one-bond ¹³C-¹⁵N spin-spin coupling constants has been examined using specifically ¹⁵N-labeled $\text{cyclo}$-(Gly-L-Pro-Gly)₂ and related linear peptides.