Monte Carlo simulations on short single-stranded oligonucleotides. I. Application to RNA trimers

Monte Carlo (MC) structural simulation of short RNA sequences has been carried out by random variations of the nucleotide conformational angles (i.e., phosphodiester chain torsional angles and sugar pucker pseudorotational angles). All of the chemical bond lengths and valence angles remained fixed during the structural simulation, except those of the sugar pucker ring. In this article we present the simulated structures of RNA trimers—r(AAA) and r(AAG)—obtained at 11°C and 70°C. The influence of various initial conformations (selected as starting points in the MC simulations) on the equilibrium conformations has been discussed. The simulated conformational angles have been compared with those estimated by nuclear magnetic resonance (NMR) spectroscopy. For both of the oligonucleotides studied here, the most stable structures are helical conformations with stacked bases, at 11°C and 70°C. However, when the starting point is a stretched chain, it is found that r(AAA) adopts a reverse-stacked structure at low temperature (11°C), in which the A3 base is located between the A1 and A2 bases. Although the energies of these conformations (helical and reverse stacked) are very close to each other, the potential barrier between them is extremely high (close to 30 kcal/mol). This hinders the conformational transition from one structure to the other at a given temperature (and in the course of a same MC simulation). However, it is possible to simulate this structural transition by heating the reverse-stacked structure up to 500°C and cooling down progressively to 70°C and 11°C: Canonical helical structures have been obtained by this procedure. © 1994 by john Wiley & Sons, Inc.     

Ab initio studies of structural features not easily amenable to experiment: Part V. Conformational analysis of keto- and enol-acetone

The structures of several conformations of keto- and enol-acetone were determined by unconstrained ab initio geometry refinements using the 4-21G basis set. The geometry of propene was also refined to compare it with enol-acetone. The structural consequences of hyperconjugation for the local geometries of the methyl groups were determined in all conformations. In the most stable form of keto-acetone, one hydrogen atom of each methyl group was found in an eclipsed arrangement with respect to the carbonyl group. The stability of this crowded structure has previously been rationalized in terms of aromatic π-electron delocalization. This result is in contrast to one of two previous gas electron diffraction studies. It is concluded that the electron diffraction data may not contain enough information to determine the exact conformational arrangement of the methyl groups in acetone. The calculated structures are found to be in excellent agreement with experiment. Uncertainties in calculated bond distances and bond angles are on the order of magnitude of 0.01–0.02 Å and 1–2°, respectively.     

Kinetic and thermodynamic characterization of C–N bond rotation by N‐methylacetohydroxamic acid in aqueous media

Hydroxamic acids (HAs) perform tasks in medicine and industry that require bidentate metal binding. The two favored conformations of HAs are related by rotation around the C(=O)–N bond. The conformations are unequal in stability. Recently, we reported that the most stable conformation of a small secondary HA in water places the oxygen atoms anti to one another. The barrier to C–N bond rotation may therefore modulate metal binding by secondary HAs in aqueous media. We have now determined the activation barrier to C–N rotation from major to minor conformation of a small secondary HA in D₂O to be 67.3 kJ/mol. The HA rotational barrier scales with solvent polarity, as is observed in amides, although the HA barrier is less than that of a comparable tertiary amide in aqueous solution. Successful design of new secondary HAs to perform specific tasks requires solid understanding of rules governing HA structural behavior. Results from this work provide a more complete foundation for HA design efforts. Copyright © 2015 John Wiley & Sons, Ltd.     

Evaluation of the origin of conformational and tautomeric preferences in N‐formylformamide – A quantum chemical study

Quantum chemical study of N‐formylformamide (NFF) was carried out at various theoretical levels and the determinate equilibrium conformations were recomputed at the high level ab initio methods such as G2MP2, G2, G3, and complete basis set (CBS)‐QB3. The computational results reveal that the amide resonance and intramolecular hydrogen bonding are two superior factors in determining the most stable conformation of diamide (DA) and amide–imidic (AI) acid tautomers, respectively. The evaluation of hydrogen bond energies predicts that the hydrogen bond (HB( strength of NFF is weaker than the malonaldehyde (MA). But the results of atoms in molecules (AIM(, natural bond orbital (NBO), and geometrical parameters are given a different order, E_HB(NFF) > E_HB(MA). Although the bond average energies of tautomerization process emphasized on more stability of AI tautomer, but our theoretical calculations reveal that the DA conformers are more stable than the AI ones. The population analyses of equilibrium conformations by NBO method also predict that the origin of tautomeric preference is mainly because of the electron delocalization of amide functional group, especially LP(N)→ π*_C?O charge transfer. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

The Conformational Landscape of Nicotinoids: Solving the Conformational Disparity of Anabasine

The conformational landscape of the alkaloid anabasine (neonicotine) has been investigated by using rotational spectroscopy and ab initio calculations. The results allow a detailed comparison of the structural properties of the prototype piperidinic and pyrrolidinic nicotinoids (anabasine vs. nicotine). Anabasine adopts two most stable conformations in isolation conditions, for which we determined accurate rotational and nuclear quadrupole coupling parameters. The preferred conformations are characterized by an equatorial pyridine moiety and additional N–H equatorial stereochemistry at the piperidine ring (eq‐eq; eq=equatorial). The two rings of anabasine are close to a bisecting arrangement, with the observed conformations differing by an approximately 180° rotation of the pyridine subunit, denoted either syn or anti. The preference of anabasine for the eq‐eq‐syn conformation has been established by relative intensity measurements (syn/anti～5(2)). The conformational preferences of free anabasine are directed by a weak N???H? C hydrogen bond interaction between the nitrogen lone pair at piperidine and the closest C? H bond in pyridine, with N???H distances ranging from 2.686 (syn) to 2.667 Å (anti). Supporting ab initio calculations by using MP2 and the recent M05‐2X density functional are provided, evaluating the predictive performance of both methods.     

Ab initio studies of structural features not easily amenable to experiment. 42. Molecular geometries and conformational analysis of methylbutanoate

Conformational energy profiles were calculated for τ₁, the C? C? C?O torsion, and τ₂, the C? C? C? C torsion, of methyl butanoate, using Pulay's ab initio gradient procedure at the 4-21G level with geometry optimization at each point. In addition, the structures of seven conformations were fully relaxed, including the energy minima (τ₁, τ₂) = (0, ?60), (0, 180), (120, 180), (120, ?60), and the maxima (0, 0), (180, 180), and (60, ?60). The calculated geometries confirm the previously formulated rule that, in saturated hydrocarbons, a C? H bond trans to a C? C bond (C? H_s) is consistently shorter than a C? H bond (C? H_a) trans to another C? H bond. Specifically, for X? C(α) (? O)? C(β)? C(γ)? C(δ) systems, the following rules can be formulated, incorporating results from previous studies of butanal, butanoic acid, and 2-pentanone: (1) C(δ)? H_s < C(δ)? H_a in all the conformers in which the δ-methyl group is remote from the ester group; whereas, in all the conformers in which nonbonded interactions are possible between the C(δ)-methyl and the ester groups, the bonding pattern is affected by a C? H ?O?C interaction. (2) In the most stable conformers, (0, 60), C(β)? H_a < C(β)? H_s, and C(γ)? H_a < C(γ)? H_s, regardless of X. (3) The average C? C bonds in the τ₂ = 180° conformers are consistently shorter than those with τ₂ = 60° (compared at τ₁ constant). In the most stable conformations (τ₁ = 0°, τ₂ = 60° or 180°), the bonding sequence is consistently C(α)? C(β) < C(β)? C(γ) < C(γ)? C(δ); whereas, when τ₁ = 120°, C(α)? C(β) < C(β)? C(γ) > C(γ)? C(δ).     

Theoretical studies on structure-property relationships of cellulose and nitrocellulose: I. Conformation,stability and conductivity

The banding and electronic structures of a series of long-chain macromolecules of cellulose, 2-, 3-, 6-mononitrocellulose, 2,3-,2,6-, 3,6-dinitrocellulose and trinitrocellulose as well as their structural units (i.e. single-, double- or three-ring systems) have been calculated by both the EH and CNDO/2 methods. The increase of molecular total energies is consistent with the decrease of their stabilities at the three conformations of gg, gt and tg. The Mulliken bond order of O—NO₂ bond is the smallest in each molecule at any of the three conformations, which indicates that this bond is the weakest, and supports the view of initial homolytic cleavage of O—NO₂ bond on slow thermal decomposition. The band gap at the edge of the first Brillouin zone far surpasses 5 eV for cellulose, and is less than 3 eV for mono-, di-, and trinitrocellulose. The results show that cellulose is a typical insulator, as we know, and it can be predicted that nitrocellulose has electric conductivity similar to that of semiconductor.     

Conformational study of halogen- and hydrogen-substituted polythionylphosphazenes using density functional theory method

The structure and conformational stability of polythionylphosphazenes is investigated by modeling single polymer chains with small mimics. The model compounds are composed of repeat units of the corresponding polythionylphosphazenes. Two of the model compounds have hydrogens and two have chlorines as substituents on phosphorus atoms. The substituents on sulfur may be either fluorine or chlorine. Fully geometry-optimized structures and energies of the stable conformations involving rotations around the P? N bond near the sulfur are obtained using the density functional theory method. The structural and conformational analyses indicate that the rotation around the N? P bond leads to variations in the bond lengths, the SNP bond angle openings, as well as couplings between dihedral angles in different conformations in all model compounds. In addition, the conformational analysis suggests that the minima on the conformational potential energy surface in these compounds may be located in the vicinity of the following values of the NP? NS dihedral angle: -50°, 90° (or 60°), 180°, and 240°. It was found that the values of the conformational energy differences range between less than 1 to 5 kcal/mol. A comparison is made between the structural results obtained using the density functional theory and the ab initio molecular orbital theory for the global minimum structures. © 1995 John Wiley & Sons, Inc.     

Ab initio calculations on phosphorus compounds. II. Effects of disubstitution on ligand apicophilicity in phosphoranes

Geometry optimizations at the HF/3-21G(*) and HF/6-31G* levels of ab initio theory have been carried out for various isomers of model disubstituted phosphoranes PH₃XY(X, Y?OH, CH₃, NH₂, and SH). Reasonable agreement was obtained between the optimized geometries and available crystal structure data for analogous compounds. The isomers were further characterized by frequency calculations. The MP2/6-31G*//6-31G* + ZPE energy data reveal that the interactions between the ligands are relatively small (0–4 kcal mol^?1) for the most stable conformations of the isomers. Hence, for these conformations the apicophilicities (based upon monosubstituted phosphoranes) are approximately additive. The less stable PH₃XY conformations are in general transition states or higher-order saddle points, and their interligand interactions are larger in magnitude (up to 10 kcal mol^?1); the results with these conformations suggest that apicophilicities may not be as additive for some highly substituted phosphoranes. © 1993 John Wiley & Sons, Inc.     

Conformational properties of polar polymers. I. Poly(vinyl chloride)

A recently developed method for including polar bonds in conformational energy calculations is applied to poly(vinyl chloride). Inductive effects on dipole moments and the effects of intervening atoms on electrostatic interaction energies are represented by polarizability centers in conjunction with bond centered dipoles. Solvation energies are estimated by means of a continuum dipole–quadrupole electrostatic model. Calculated energies of a number of conformations of meso and racemic 2,4-dichloropentane and the iso, syndio, and hetero forms of 2,4,6-trichloroheptane give satisfactory representations of isomer and conformer populations. Electrostatic effects are found to be quite important. However they appear to be effectively of sufficiently short range that the calculated conformer energies are found to be fit well by a linear combination of interaction parameters (consisting of gauche, skew chlorine, four-bond CH₂…CH₂, CH₂…Cl, and Cl…Cl interactions) conventional to vinyl polymers and a special four-bond interaction that arises when the bond sequence Cl? CH? CH²? CH? Cl is (nearly) coplanar. These interaction parameters when assembled into statistical weight matrices lead to calculated values of both the characteristic ratio and the dipole moment ratio in satisfactory agreement with experiment. Least energy paths for transitions between the most stable conformations are also calculated.     

Theoretical analysis of fluoroglycine conformers

Seven different optimized conformers of α‐fluoroglycine (H₂NCHFCOOH) were obtained from ab initio calculations. Some of these conformers are exceptionally stable compared to similar conformers of glycine. Conformers in which the lone pair of electrons on the nitrogen atom are antiperiplanar to the C F bond are more stable than conformers that do not have such an arrangement. The stability difference between conformers with such an arrangement and conformers that have the lone pair of electrons synperiplanar to the C F bond is about 27 kJ/mol (calculated at the MP2/6‐31+G* level). Conformers that have the lone pair of electrons antiperiplanar to the C F bond possess a longer C F bond, a shorter C N bond, and sp²‐like amino bond angles. For some conformers an unusual hydrogen bond involving the acidic carboxylic acid hydrogen and the electronegative fluorine atom is observed. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 426–431, 2000     

Ab initio studies of structural features not easily amenable to experiment: Part 20. Structural aspects of ethyl groups

The molecular structures of a number of stable conformations of ethanol, ethylamine, methylethyl ether, methylethylamine and of the ethyl anion have been determined by ab initio geometry optimizations using Pulay's Force method on the 4–21G level. The calculated geometries characterize the extent to which structural groups in a molecule are sensitive to asymmetries in their environment. Characteristic structural trends are consistently found for the CH bond distances and CCH angles in the C₂H₅ groups of trans-ethanol, trans-methylethyl ether and in the ethyl anion. They differ from those previously found for C₂H₅ groups in hydrocarbons. There is qualitative disagreement between the trends calculated for CH bond distances in trans-ethanol and trans-methylethyl ether and those found in the microwave substitution structures of these compounds. Since the substitution parameters are unresolved because of relatively large experimental or model uncertainties, it is presently impossible to decide whether this discrepancy is the result of computational or experimental deficiency. The methyl groups in methylethyl ether and methylethylamine exhibit the characteristic structural distortions which are usually found for CH₃ groups adjacent to electron lone pairs. The CC bond distances in C₂H₅ in the systems studied here are sensitive to the conformational arrangement of ethyl relative to the rest of a system in a way which can be rationalized by orbital interactions involving antibonding orbitals on sp³-hybridized carbon atoms. The calculated conformational stabilities agree qualitatively with experimental trends, except in the case of ethanol where the trans — gauche energy difference is small (about 0.1 kcal mol^?1) and within the uncertainties of the calculations. Our conformational energies for CH₃CH₂NH₂ are in disagreement with a previous ab initio investigation based on a comparison of unoptimized standard geometries. In general, the agreement between calculated structural parameters and corresponding reliable experimental values is very good in all comparable cases.     

Solvent effects on glycine II. Water-assisted tautomerization

The water-assisted tautomerization of glycine has been investigated at the B3LYP/6-31+G** level using supermolecules containing up to six water molecules as well as considering a 1:1 glycine-water complex embedded in a continuum. The conformations of the tautomers in this mechanism do not display an intramolecular H bond, instead the functional groups are bridged by a water molecule. The replacement of the intramolecular H bond by the bridging water reduces the polarity of the N-H bond in the zwitterion and increases that of the O-H bond in the neutral, stabilizing the zwitterion. Both the charge transfer effects and electrostatic interactions stabilize the nonintramolecularly H-bonded zwitterion conformer over the intramolecularly hydrogen bonded one. The nonintramolecularly H-bonded neutral is favored only by charge transfer effects. Although there is no strong evidence whether the intramolecularly hydrogen bonded or non hydrogen bonded structures are favored in the bulk solution represented as a dielectric continuum, it is likely that the latter species are more stable. The free energy of activation of the water-assisted mechanism is higher than the intramolecular proton transfer channel. However, when the presumably higher conformational energy of the zwitterion reacting in the intramolecular mechanism is taken into account, both mechanisms are observed to compete. The various conformers of the neutral glycine may form via multiple proton transfer reactions through several water molecules instead of a conformational rearrangement.     

Ab initio studies of structural features not easily amenable to experiment : Part 40. Structural and conformational investigations of 2-butanone and 2-pentanone

The ab initio gradient refined 4-21G geometries of two conformations of 2-butanone and of six conformations of 2-pentanone are reported. The C---C---C=O torsional energies of both systems were determined with geometry optimization at each point and are compared with those previously calculated for some homologous aldehydes and carboxylic acids. In agreement with the structural trends known for C---H bonds in methyl groups adjacent to C=O, it is found that a C---C bond eclipsing an adjacent C=O bond is more stable and shorter than in a skew position (C---C---C= O = 120°). The sum total of the 4-21G results available for various systems may support the following general rule: in X--- C---C=O systems the C---X bond is relatively short when syn-coplanar with C==O (X---C---C= O = 0°), and relatively long when skew with C=O (X---C---C=O 120°).     

Spannungsenergie und konformation sterisch gehinderter olefine berechnungen von überbrückten derivaten des tetra-tert-butylethylens

Strain energy relaxation by in plane bending is not eflective in tetra-tert-butylethyethylene 1 because of the repulsions between geminal tert-butyl groups. When rings are closed between the geminal tert-butyl groups, the repulsions across the double bond are relieved. The strain energies and conformations of such molecules have been evaluated by empirical force field calculations (molecular mechanics) A close correlation is found between ring size and strain energy: strain increases stepwise with ringsize. In the most stable conformations, the methyl groups adopt a “staggered” arrangement across the double bond. In compounds containing a six-membered ring this can be achieved only in (strongly preferred) twist-boat conformations. The double bond in such molecules is nearly planar when the rings are smaller than 6-membered, but exhibits a torsion of up to 16.5° when 6-membered rings are present.     

The conformations of allylic alcohols in solution from FT-i.r. OH stretching vibration measurements

The distribution of conformations of allylic alcohols in CCl₄ differs from that in the vapour phase and from ab initio calculations. FT-i.r. measurements of the OH stretching vibrations show two peak maxima which can be resolved by band splitting techniques. The predominant conformations of allylic alcohols are intramolecularly hydrogen bonded, with a conformation gauche (G or G′) with respect to rotation about the CO bond and eclipsed (E or E′) with respect to rotation about the CC bond. In contrast with vapour phase data and ab initio calculations, no other hydrogen bonded conformations have been identified.For primary alcohols, the shoulder to the higher wavenumber side can be unequivocally assigned to conformations in which the OH is free, with a trans (T) conformation with respect to rotation about the CO bond.The secondary allylic alcohols exhibit no bands that can be attributed to free OH conformations except in the case of severe steric interaction in the eclipsed (E) conformation.In accordance with our previous work on solvent interactions with the OH group, the contrast with the vapour state assignments are interpreted in terms of an interaction of the solvent with the OH proton which destabilizes the hydrogen bond.     

Theoretical study of CH…O hydrogen bond in proton transfer reaction of glycine

Density functional theory (DFT) calculations are used to study the strength of the CH…O H‐bond in the proton transfer reaction of glycine. Comparison has been made between four proton transfer reactions (ZW1, ZW2, ZW3, SCRFZW) in glycine. The structural parameters of the zwitterionic, transition, and neutral states of glycine are strongly perturbed when the proton transfer takes place. It has been found that the interaction of water molecule at the side chain of glycine is high in the transition state, whereas it is low in the zwitterionic and neutral states. This strongest multiple hydrogen bond interaction in the transition state reduces the barrier for the proton transfer reaction. The natural bond orbital analysis have also been carried out for the ZW2 reaction path, it has been concluded that the amount of charge transfer between the neighboring atoms will decide the strength of H‐bond. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

An ab initio study of the p,π interaction: IV. Interaction of an ether oxygen atom with a carbonyl group

RHF/6-311G(d) calculations were performed for the H₃COCOH molecule with full geometry optimization and at varied angles of rotation of the methoxy group about the C-O bond, with all the other geometric parameters optimized. The molecule can exist in two stable conformations with the dihedral angle O¹C¹O²C² of 0.00° and 179.99°. The influence of the rotation angle on the population of the p _y orbital of the carbonyl oxygen atom in compounds with different types of the adjacent bond is essentially similar. The results obtained are inconsistent with the concept of the p,π conjugation involving the p _y orbitals of the planar molecular fragment (orbitals whose symmetry axes are perpendicular to this fragment).     

Electron spin resonance studies of propagating radicals in polymerization. I. Methacrylate propagating radicals

Ferric chloride-photosensitized free-radical initiation was used to generate propagating radicals in polymerization of methacrylic acid (MAA), allyl methacrylate (AMA), methyl methacrylate (MMA), 1,3-butylene dimethacrylate (1,3-BDMA), hydroxypropyl methacrylate (HPMA), lauryl methacrylate (LMA), hexyl methacrylate (HMA), and methacrylamide (MA) in rigid glasses of methanol or acetone at near liquid nitrogen temperatures. The formation and conformational changes of these propagating radicals at different temperatures were studied by electron spin resonance (ESR) spectroscopy. When methanol was the rigid glass, ·CH₂OH radicals were formed initially and were stable below ?160°C. As the temperature of the rigid glass was increased, the ·CH₂OH radicals reacted with monomer to yield propagating radicals. With the exception of the propagating radical for methacrylamide, the propagating radicals of the methacrylates examined initially generated five-line ESR spectra which gradually changed to nine-line spectra, as temperature of the rigid glass was increased. It was concluded that one type of propagating radical was formed in all cases. However, when the temperature of the rigid glass was increased, the single structural conformation that initially allowed one of the methylene hydrogens and methyl group to interact with the unpaired electron to generate only a five-line spectrum was changed to yield a second conformation that allowed interaction to generate an additional four-line spectrum. Finally, a mixture of the propagating radical for methacrylate monomer in two structural conformations was obtained, and an ESR spectrum consisting of nine lines (5 + 4 lines) was generated. In the case of the propagating radical for methacrylamide this change to yield two structural conformations evidently was hindered, so that only an ESR spectrum consisting of five lines was generated.     

Simulation of the Raman spectra of zwitterionic glycine + nH2O (n = 1, 2, …, 5) by means of DFT calculations and comparison to the experimentally observed Raman spectra of glycine in aqueous medium

Raman spectra of an aqueous solution of glycine (Gly) have been recorded in the range of 400-2000 cm⁻¹. In aqueous solution, glycine molecules exist in their zwitterionic form, having two opposite charged poles, COO⁻ and NH₃⁺. The zwitterionic structure of glycine (ZGly) is stabilized by the hydrogen bond interaction of water (W) molecules. In the present report, we have optimized the ground state geometries of different hydrogen bonded complexes of [ZGly + (W)_n=1-5] in aqueous medium using DFT calculations at the B3LYP/6-311++G(d) level of theory. A comparative discussion on the structural details and binding energies (BEs) of each conformer has been also done. The theoretical Raman spectra were calculated corresponding to the most stable [ZGly + (W)_n=1-5] conformers. The theoretically simulated Raman spectra of each stable conformer were compared with experimentally observed Raman spectra to explore the number of water molecules needed for stabilizing the structure of ZGly. The theoretically simulated Raman spectra corresponding to the most stable conformer of [ZGly + (W)₅] having a BE of −22.8 kcal/mol, are matching nicely with the experimentally observed Raman spectra. Thus, on the basis of the above observations, we conclude that the conformer, [ZGly + (W)₅] is the most probable conformer in the aqueous medium. We also believe that in the conformer, [ZGly + (W)₅] the five water molecules are arranged around the ZGly in such a way that the effect of steric hindrance is less compared to the other conformers. The dipole-dipole interaction potential (DDP) is also calculated corresponding to the strongest hydrogen bond for each [ZGly + (W)_n=1-5] conformer.