Comprehensive conformational analysis of the nucleoside analogue 2'-beta-deoxy-6-azacytidine by DFT and MP2 calculations

A comprehensive conformational analysis of isolated 2'-beta-deoxy-6-azacytidine (d6AC), an analogue of therapeutically active 6-azacytidine (6AC), has been performed by means of ab initio calculations at the MP2/6-311++G(2df,pd)//DFT B3LYP/6-31G(d,p) level of theory. Among the 81 conformers located within a 7.83 kcal/mol Gibbs energy range at T = 298.15 K, 38 contain syn-oriented bases with respect to 2'-deoxyribose; the other conformers include anti-oriented bases. Energetic analysis of these conformers shows that conformational equilibrium of isolated d6AC at T = 298.15 K is shifted to syn conformation with a syn/anti ratio estimated as 61.4%:38.6%. As far as the sugar conformation is concerned, 40 conformers contain north (N) (with 0.3 degrees < or = P < or = 40.1 degrees), and the rest possess south (S) (with 157.1 degrees < or = P < or = 207.0 degrees) puckers, where P is the pseudorotational angle of the furanose ring. The S/N occupancy ratio is estimated as 80.2%:19.8% (T = 298.15 K). The two most stable conformers are energetically quasidegenerate and correspond to both C2'-endo/syn conformers differing only by orientation of the O3'H hydroxyl group. They are both stabilized by means of similar intramolecular H-bonds, i.e., O5'H...O2, C2'H2...O2, and C2'H2...O5'. As examined by AIM criteria, from 1 to 3 H-bonds per conformer were identified among 13 possible interactions: O5'H...O2, O5'H...N6, O3'H...O5', O5'H...O3', C1'H...O2, C2'H2...O2, C2'H2...O5', C3'H...O2, C3'H...N6, C5'H1...O2, C5'H2...O2, C5'H1...N6, and C5'H2...N6. The biological effect of d6AC is conceived as an inhibition of replicative DNA polymerase caused by an unusual orientation of the sugar residue against the base in the only A form DNA-like conformer.     

Ab initio comprehensive conformational analysis of 2'-deoxyuridine, the biologically significant DNA minor nucleoside, and reconstruction of its low-temperature matrix infrared spectrum

A comprehensive conformational analysis of isolated 2'-deoxyuridine (dU), a minor DNA nucleoside, has been performed by means of ab initio calculations at the MP2/6-311++G (d,p)//DFT B3LYP/6-31G (d,p) level of theory. At 298.15 and 420 K, all 94 allowed conformers of dU are within 8.96 and 7.91 kcal/mol Gibbs energy ranges, respectively. Syn orientation for the base and South (S) conformers for the sugar dominate at 298.15 K: syn/anti=62.3%:37.7% and S/N=77.2%:22.8%. At 420 K in the majority of conformers, the base is anti oriented and the population of North (N) sugars increases: syn/anti=39.3%:60.7% and S/N=63.0%:37.0%. Values of all conformational parameters and correlations between them, as well as their correlations with valence bonds, and also correlations between valence bonds and angles were estimated. In general, 14 types of intramolecular H-bonds were detected (1-3 H-bonds per conformer, the total number 175), namely, C1'H...O2 (16 H-bonds), C2'H1...O5' (9), C2'H2...O2 (21), C3'H...O2 (21), C5'H1...O2 (14), C5'H2...O2 (11), C6H...O4' (37), C6H...O5' (22), C3'H...HC6 (4), O5'H...HC6 (2), O3'H...O5' (5), O5'H...O4' (1), O5'H...O3' (4), and O5'H...O2 (8). Geometric, vibrational, structural-topological, and energetic features of the OH...O intramolecular H-bonds in dU conformers were determined. The close similarity between energetic and geometric characteristics of dU and thymidine DNA-like conformers in anti and relevant syn conformations and their transition states of the anti-->syn interconversion implies that mismatch DNA glycosylase discriminates between the two nucleosides, mainly because of the difference in the shapes of their bases. Convolution of calculated IR spectra of all the dU conformers within the limits 3400-3700 cm(-1) appears to be consistent with its low-temperature matrix IR spectrum (Ivanov et al. Spectrochim. Acta, Part A 2003, 59, 1959), wavenumber discrepancy not exceeding 1%. It was concluded that, for a reliable reproduction of the experimental spectrum, the whole set of conformers should be taken into consideration. The suggested method makes reconstruction of the isolated nucleoside IR spectrum at a physiological interval of temperature reasonably possible.     

Conformation and tautomerism of the cimetidine molecule: a theoretical study

The cimetidine molecule conformation and tautomer stability was studied at the ab initio HF/6-31G** level and for single point energies at the MP2/6-31G** level. The most stable N3-H cimetidine tautomer was found to be more stable than the most stable N1-H tautomer by ca. 3.7 and 5.0 kcal/mol, at the HF/6-31G** and MP2/6-31G**//HF/6-31G** level, respectively. At the HF/6-31G** level, the most stable N3-H and 1-H forms are stabilized by the intramolecular N3′-H?N1 hydrogen bond and N1-H?N4′, respectively. However, when the correlation effects are included at the MP2/6-31G**//HF/6-31G** level, the most stable N3-H and N1-H tautomers appeared to be folded forms without hydrogen bonds.     

Estimation on the intramolecular 10-membered ring N-H...O=C hydrogen-bonding energies in glycine and alanine peptides

Computation of accurate intramolecular hydrogen-bonding energies for peptides is of great importance in understanding the conformational stabilities of peptides and developing a more accurate force field for proteins. We have proposed a method to determine the intramolecular seven-membered ring N-H...O=C hydrogen-bonding energies in glycine and alanine peptides. In this article, the method is further applied to evaluate the intramolecular 10-membered ring N-H...O=C hydrogen-bonding energies in peptides. The optimal structures of the intramolecular 10-membered ring N-H...O=C hydrogen bonds in glycine and alanine tripetide molecules are obtained at the MP2 level with 6-31G(d), 6-31G(d,p), and 6-31+G(d,p) basis sets. The intramolecular 10-membered ring N-H...O=C hydrogen-bonding energies are then evaluated based on our method at the MP2/6-311++G(3df,2p) level with basis set superposition error correction. The intramolecular 10-membered ring N-H...O=C hydrogen-bonding energies are calculated to be in the range of -6.84 to -7.66, -4.44 to -4.98, and -6.95 to -7.88 kcal/mol. The method is also applied to estimate the individual intermolecular hydrogen-bonding energies in the dimers of amino-acetaldehyde, 2-amino-acetamide, formamide, and oxalamide, each dimer having two identical intermolecular hydrogen bonds. According to our method, the individual intermolecular hydrogen-bonding energies in the four dimers are calculated to be -1.77, -1.67, -6.35, and -4.82 kcal/mol at the MP2/6-311++G(d,p) level, which are in good agreement with the values of -1.84, -1.72, -6.23, and -4.93 kcal/mol predicted by the supermolecular method.     

Conformational study of the structure of free 18-crown-6

A conformational search was performed for 18-crown-6 using the CONLEX method at the MM3 level. To have a more accurate energy order of the predicted conformations, the predicted conformations were geometry optimized at the HF/STO-3G level and the 198 lowest energy conformations, according to the HF/STO-3G energy order, were geometry optimized at the HF/6-31+G level. In addition, the 47 nonredundant lowest energy conformations, according to the MP2/6-31+G energy order at the HF/6-31+G optimized geometry, hereafter the MP2/6-31+G//HF/6-31+G energy order, were geometry optimized at the B3LYP/6-31+G level. According to the MP2/6-31+G//B3LYP/6-31+G energy order, three conformations had energies lower than the experimentally known Ci conformation of 18c6. At the MP2/6-31+G//B3LYP/6-31+G level, the S6 lowest energy conformation is more stable by 1.96 kcal/mol than this Ci conformation. This was confirmed by results at the MP2/6-31+G level with an energy difference of 1.84 kcal/mol. Comparison between the structure of the S6 conformation of 18c6 and the S4 lowest energy conformation of 12-crown-4, as well as other important conformations of both molecules, is made. It is concluded that the correlation energy is necessary to have an accurate energy order of the predicted conformations. A rationalization of the conformational energy order in terms of the hydrogen bonding and conformational dihedral angles is given. It is also suggested that to have a better energy order of the predicted conformations at the MM3 level, better empirical force fields corresponding to the hydrogen bond interactions are needed.     

A new scheme for determining the intramolecular seven-membered ring N-H...O=C hydrogen-bonding energies of glycine and alanine peptides

In this paper a new scheme was proposed to calculate the intramolecular hydrogen-bonding energies in peptides and was applied to calculate the intramolecular seven-membered ring N-H...O=C hydrogen-bonding energies of the glycine and alanine peptides. The density-functional theory B3LYP6-31G(d) and B3LYP6-311G(d,p) methods and the second-order Moller-Plesset perturbation theory MP26-31G(d) method were used to calculate the optimal geometries and frequencies of glycine and alanine peptides and related structures. MP26-311++G(d,p), MP26-311++G(3df,2p), and MP2/aug-cc-pVTZ methods were then used to evaluate the single-point energies. It was found that the B3LYP6-31G(d), MP26-31G(d), and B3LYP6-311G(d,p) methods yield almost similar structural parameters for the conformers of the glycine and alanine dipeptides. MP2/aug-cc-pVTZ predicts that the intramolecular seven-membered ring N-H...O=C hydrogen-bonding strength has a value of 5.54 kcal/mol in glycine dipeptide and 5.73 and 5.19 kcal/mol in alanine dipeptides, while the steric repulsive interactions of the seven-membered ring conformers are 4.13 kcal/mol in glycine dipeptide and 6.62 and 3.71 kcal/mol in alanine dipeptides. It was also found that MP26-311++G(3df,2p) gives as accurate intramolecular N-H...O=C hydrogen-bonding energies and steric repulsive interactions as the much more costly MP2/aug-cc-pVTZ does.     

Conformational study and electron density analysis of 9-[tetrahydropyran-3-yl]purine derivatives

A conformational analysis was carried out on cis-6-chloro-9-[2-(2-hydroxyethyl)-2,3,5,6-tetrahydro-4H-pyran-3-yl]purine and several related model compounds at the HF/6-31++G(d,p) and B3LYP/6-311++G(2d,2p) levels, and also using the semiempirical methods AM1 and PM3. The result of this analysis shows that the molecule prefers an axial disposition of the purine ring, with an approximate cis orientation of C4-N9-C1′-H1′ dihedral angle. The stability of this conformation comes mainly from the formation of a C-H?O?H-O intramolecular three-center hydrogen bond. In this structure, the tetrahydropyran oxygen acts as an acceptor, while both H8 of the purine ring and the hydroxylic hydrogen of the hydroxyethyl group act as donors. Also, the equatorial disposition of the hydroxyethyl group in this conformer reduces its repulsions with the purine ring and the tetrahydropyran hydrogens. The quantum theory of atoms in molecules was applied to study the electronic effects produced by the conformational changes, bonding between tetrahydropyran and purine rings, chlorine substitution, and intramolecular hydrogen bonding.     

The rate enhancement for prolyl cis-to-trans isomerization of cyclic CPFC peptide is caused by an increase in the vibrational entropy of the transition state

The conformational preferences and prolyl cis-trans isomerization of oxidized and reduced Ac-Cys-Pro-Phe-Cys-NH2 (CPFC peptides) have been carried out using the ab initio HF/6-31+G(d) and hybrid density functional B3LYP/6-311++G(d,p) levels of theory. The most preferred conformations of oxidized and reduced CPFC peptides with the trans prolyl peptide bond have a type-I beta-turn for the Pro-Phe sequence in common. In particular, the transition states for both forms are stabilized by the intramolecular hydrogen bonds between the prolyl nitrogen and the N-H group of the Phe3 residue. The rotational barrier DeltaGct to the cis-to-trans isomerization for the oxidized CPFC peptide is calculated to be 19.37 kcal/mol at the B3LYP/6-311++G(d,p)//HF/6-31+G(d) level of theory, which is lower by 0.88 kcal/mol than that of the reduced CPFC peptide. This may indicate that the rate constant kc-->t of the prolyl cis-to-trans isomerization for the oxidized form is about 4 times larger than that of the reduced form, which is reasonably consistent with the value deduced from NMR experiments. In particular, the increase in vibrational entropy for the transition state of the oxidized form over that of the reduced form contributes to enhance the rate constant for the prolyl cis-to-trans isomerization of the oxidized form.     

Molecular Conformation of 2,2'-Dinitrodiphenylamine According to Dielectric Studies and Ab Initio Quantum Chemical Calculations

According to the results of ab initio calculations employing the HF/6-31G* approach, the isolated 2,2'-dinitrodiphenylamine molecule exists as an sc, sc conformer stabilized by a symmetric intramolecular bifurcated (three-center) hydrogen bond. In protophilic solvents (1,4-dioxane), the conformational equilibrium is also shifted in the direction of this rotational isomer.     

胺对锂电池电解液中小分子的稳定作用

用密度泛函理论(DFT)方法在PBE0/6-31+G(d, p)水平上对乙胺、乙二胺分别与电解液中的小分子H2O、HF分子间的相互作用进行理论计算, 并在PBE/TZP 水平上利用能量分解分析(EDA)方法对胺与HF、H2O 结合的II-1、II-2、III-1和III-2模型进行计算分析. 结果表明, 胺类物质都能与HF、H2O形成N…H—F(O)、F(O)…H—N或F(O)…H—C的稳定氢键. 但HF与胺类物质形成的氢键比H2O与胺形成的氢键强, 故胺类物质在电解液中优先稳定HF. 乙二胺与HF、H2O结合的稳定性比乙胺强. 乙胺、乙二胺与HF(H2O)形成的最稳定构型均由F(O)—H…N 和F(O)…H—C 氢键结合形成.     

The effect of electron correlation on the conformational space of melatonin

The pineal gland hormone melatonin regulates several physiological processes including circadian rhythm and also alleviates oxidative stress‐induced degenerative diseases. In spite of its important biological roles, no high level ab initio conformational study has been conducted to reveal its structural features. In this work, the conformational flexibility of melatonin was investigated using correlated ab initio calculations. Conformers, obtained previously at the Hartree‐Fock level (HF/6‐31G*), were fully optimized using second order Møller‐Plesset perturbation theory applying the frozen core approximation (MP2(FC)/6‐31G*). Furthermore, single‐point MP4(SDQ,FC)/6‐31G*//MP2(FC)/6‐31G* computations were performed to investigate the effect of higher order perturbation terms. The HF and MP2 conformational spaces are considerably different: the initial 128 structures converged into 102 different local minima as confirmed by frequency calculations; 28 new minima appeared and 26 previous HF local minima disappeared; no “all‐trans” C3 side chain conformations are seen at the MP2(FC) level. The MP2 global minimum conformation is stabilized by an aromatic‐side chain interaction. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008     

Conformational stability of a model macrocycle tetraamide: an ab initio study

Ab initio calculations are carried out to investigate the conformational stability of a model macrocyle tetraamide. The four amide groups in the selected model are present in the sequence: -(O=CNH)-Ph-(NHC=O)-CH=CH-(O=CNH)-Ph-(NHC=O)-CH=CH-. In this sequence, two phenyl rings and two ethene groups act as bridges between the amide units. Each amide motif bonds to a phenyl ring through its amide nitrogen and to an ethene group through its amide carbon. Four clearly distinct minimum-energy conformations are found upon full geometry optimization using the B3LYP/6-31+G(d) method. Frequency calculations using the same method confirm that the four conformations are indeed minima in the macrocycle potential energy surface. Relative to the most stable conformer, the other conformations are higher in energy by 0.86, 2.09, and 9.17 kcal/mol, respectively, at the MP2/6-31+G(d,p) level. The stability of the macrocycle conformations is correlated primarily to the existence and strength of intramolecular N-H...O=C hydrogen bonds. Additional stability to the conformations is found to come from weak Ph-H...O=C hydrogen bonding between a carbonyl oxygen and a hydrogen atom of a phenyl group. Solvent effects play an important role in the relative energies of the various conformations, as indicated by the simple SCRF = dipole model calculations for the case of aqueous solution.     

Theoretical study of the conformational energy hypersurface of cyclotrisarcosyl

The multidimensional Conformational Potential Energy Hypersurface (PEHS) of cyclotrisarcosyl was comprehensively investigated at the DFT (B3LYP/6-31G(d), B3LYP/6-31G(d,p) and B3LYP/6-311++G(d,p)), levels of theory. The equilibrium structures, their relative stability, and the Transition State (TS) structures involved in the conformational interconversion pathways were analyzed. Aug-cc-pVTZ//B3LYP/6-311++G(d,p) and MP2/6-31G(d)//B3LYP/6-311++G(d,p) single point calculations predict a symmetric cis-cis-cis crown conformation as the energetically preferred form for this compound, which is in agreement with the experimental data. The conformational interconversion between the global minimum and the twist form requires 20.88 kcal mol-1 at the MP2/6-31G(d)//B3LYP/6-311++G(d,p) level of theory. Our results allow us to form a concise idea about the internal intricacies of the PEHSs of this cyclic tripeptide, describing the conformations as well as the conformational interconversion processes in this hypersurface. In addition, a comparative analysis between the conformational behaviors of cyclotrisarcosyl with that previously reported for cyclotriglycine was carried out     

Hartree-Fock and density functional theory study of alpha-cyclodextrin conformers

Herein, we report the geometry optimization of four conformers of alpha-cyclodextrin (alpha-CD) by means of PM3, HF/STO-3G, HF/3-21G, HF/6-31G(d), B3LYP/6-31G(d), and X3LYP/6-31G(d) calculations. The analysis of several geometrical parameters indicates that all conformers possess bond lengths, angles, and dihedrals that agree fairly well with the crystalline structure of alpha-CD. However, only three of them (1-3) resemble the polar character of CDs and show intramolecular hydrogen-bonding patterns that agree with experimental NMR data. Among them, conformer 3 appears to be the most stable species both in the gas phase and in solution; therefore, it is expected to be the most suitable representative structure for alpha-CD conformation. The purpose of selecting such a species is to identify an appropriate structure to be employed as a starting point for reliable computational studies on complexation phenomena. Our results indicate that the choice of a particular alpha-CD conformer should affect the results of ab initio computational studies on the inclusion complexation with this cyclodextrin since both the direction and the magnitude of the dipole moment depend strongly on the conformation of alpha-CD.     

2-Deoxy-beta-D-erythro-pentofuranose: hydroxymethyl group conformation and substituent effects on molecular structure, ring geometry, and NMR spin-spin coupling constants from quantum chemical calculations.

The effect of hydroxymethyl conformation (gg, gt, and tg rotamers about the C4-C5 bond) on the conformational energies and structural parameters (bond lengths, bond angles, bond torsions) of the 10 envelope forms of the biologically relevant aldopentofuranose, 2-deoxy-beta-D-erythro-pentofuranose (2-deoxy-D-ribofuranose) 2, has been investigated by ab initio molecular orbital calculations at the HF/6-31G level of theory. C4-C5 bond rotation induces significant changes in the conformational energy profile of 2 (2gt and 2tg exhibit one global energy minimum, whereas 2gg exhibits two nearly equivalent energy minima), and structural changes, especially those in bond lengths, are consistent with predictions based on previously reported vicinal, 1,3- and 1,4-oxygen lone pair effects. HF/6-31G-optimized envelope geometries of 2gg were re-optimized using density functional theory (DFT, B3LYP/6-31G), and the resulting structures were used in DFT calculations of NMR spin-spin coupling constants involving 13C (i.e., J(CH) and J(CC) over one, two, and three bonds) in 2gg according to methods described previously. The computed J-couplings were compared to those reported previously in 2gt to assess the effect of C4-C5 bond rotation on scalar couplings within the furanose ring and hydroxymethyl side chain. The results confirm prior predictions of correlations between 2J(CH), 3J(CH), 2J(CC) and 3J(CC), and ring conformation, and verify the usefulness of a concerted application of these couplings (both their magnitudes and signs) in assigning preferred ring and C4-C5 bond conformations in aldopentofuranosyl rings. The new calculated J-couplings in 2gg have particular relevance to related J-couplings in DNA (and RNA indirectly), where the gg rotamer, rather than the gt rotamer, is observed in most native structures. The effects of two additional structural perturbations on 2 were also studied, namely, deoxygenation at C5 (yielding 2,5-dideoxy-beta-D-erythro-pentofuranose 4) and methyl glycosidation at O1 (yielding methyl 2-deoxy-beta-D-erythro-pentofuranoside 5) at the HF/6-31G level. The conformational energy profile of 4 resembles that found for 2gt, not 2gg, indicating that 4 is an inappropriate structural mimic of the furanose ring in DNA. Glycosidation failed to induce differential stabilization of ring conformations containing an axial C1-O1 bond (anomeric effect), contrary to experimental data. The latter discrepancy indicates that either the magnitude of this differential stabilization depends on ring configuration or that solvent effects, which are neglected in these calculations, play a role in promoting this stabilization.     

Intramolecular hydrogen bond in the push–pull CF3-aminoenones: DFT and FTIR study,NBO analysis

Postulated conformers of trifluoromethylated β-aminoenones stabilized by intramolecular NH?O and N?HO bonds were studied by IR and NMR spectroscopy and evaluated with quantum chemical calculations (B3LYP/6-311+G(d,p), MP2/6-311+G(d,p)//B3LYP/6-311+G(d,p) and MP2/6-31G(d,p)) and NBO analysis. The influence of the nature of EWG, substituents at the nitrogen atom and double bond, and of orbital interactions of heteroatoms and double bonds in these structures on the proton affinity of basic and acid centers, strength of hydrogen bonds, and the energy of tautomeric transfers is discussed. The theoretical results agree satisfactorily with the experimental observations.     

DFT and ab initio potential energy scan and hydrogen bond analysis of N-substituted hydrazino acetamides: Characterization of the “hydrazinoturn” hydrogen bonding pattern

We studied a series of model primary amides in gas phase at the DFT (B3LYP) and HF at 6-31+G/6-31+G** levels of theory in order to shed light on their conformation, structure, and intramolecular hydrogen bonding network. A potential energy scan was performed by rotating around the appropriate bond for each molecule studied in this paper. In this manner, it was possible to show that the amidic group of these model compounds acts as H-bond donor and interacts with two different H-bond acceptors which stabilizes a C₈ pseudocycle, the so called “hydrazinoturn”. This study was addressed theoretically in order to understand the conformation adopted by hydrazino acetamides as model compounds for aza-β³-peptides. We thus investigated the conformational analysis of hydrazinoturns computationally and showed that these systems represent a very stabilizing folding driving force, provided that the neighboring molecular functional groups do not imply other competing hydrogen bonding patterns.     

Dimerization of the keto tautomer of acetohydroxamic acid-infrared matrix isolation and theoretical study

Dimerization of the keto tautomer of acetohydroxamic acid has been studied using FTIR matrix isolation spectroscopy and DFT(B3LYP)/6-31+G(d,p) calculations. Analysis of CH3CONHOH/Ar matrix spectra indicates formation of two dimers in which two intramolecular CO...HON bonds within two interacting acetohydroxamic acid molecules are retained. A chain dimer I is stabilized by the intermolecular CO...HN hydrogen bond, whereas the cyclic dimer II is stabilized by two intermolecular NH...O(H)N bonds. Twelve vibrations were identified for dimer I and six vibrations for dimer II; the observed frequency shifts show a good agreement with the calculated ones for the structures I and II. Both dimers have comparable binding energies (DeltaE(ZPE)(CP)I, II=-7.02, -6.34 kcal mol-1) being less stable than calculated structures III and IV (DeltaE(ZPE)(CP)III, IV=-9.50, -8.87 kcal mol-1) in which one or two intramolecular hydrogen bonds are disrupted. In the most stable 10-membered cyclic dimer III, two intermolecular CO...HON hydrogen bonds are formed at expense of intramolecular hydrogen bonds of the same type. The formation of the less stable (AHA)2 dimers in the studied matrixes indicates that the formation of (AHA)2 is kinetically and not thermodynamically controlled.