Intramolecular hydrogen bonds and conformations of the 1,4-butanediol molecule

IR and Raman spectra of 1,4-butanediol (BD) versus variations in the medium (CCl₄, CH₃CN), concentration, temperature, and phase state were obtained. The observed changes attest to the conformational variety of BD molecules under the experimental conditions. On the basis of the analysis of the v(OH) region it is concluded that both in the gas phase and in CCl₄ solution conformers of BD with free OH groups coexist with conformers with O-H...O intramolecular hydrogen bonds. The difference in enthalpies, H, for the groups of conformers with and without intramolecular hydrogen bonds was found from the temperature dependence of the v(OH)_free and v(OH)_intra band intensities. The structures and energies for 70 possible spectrally and energetically distinguishable conformers of BD that do not take into account intramolecular hydrogen bonds were calculated by molecular mechanics with account of electron lone pairs of oxygen atoms. Using the experimental values of H and the calculated relative conformer energies,E, the intramolecular hydrogen bond energyE _intra= 3.7 kcal mol^–1 was found.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1572–1577, September, 1993.     

Computational study of conformations and of sulfinyl oxygen-induced pentacoordination at silicon in 4-chloro-4-silathiacyclohexane 1-oxide and 4,4-dichloro-4-silathiacyclohexane 1-oxide

Second-order Møller-Plesset theory (MP2) and density functional theory (B3LYP) with the 6-311G(d,p) and 6-311+G(d,p) basis sets have been used to calculate the equilibrium geometries and relative energies of the chair, twist, and boat conformations of 4-chloro-4-silathiacyclohexane 1-oxide and 4,4-dichloro-4-silathiacyclohexane 1-oxide. The chair conformers of the axial sulfoxides are lower in energy than the chair conformers of the corresponding equatorial sulfoxides. MP2/6-311+G(d,p) predicted the chair conformer of axial trans-4-chloro-4-silathiacyclohexane 1-oxide (4a) to be 6.12, 0.44, and 0.45 kcal/mol, respectively, more stable than the corresponding 1,4-twist (4b), 2,5-twist (4c) and 1,4-boat (4d) conformers and 6.93 kcal/mol more stable than the 2,5-boat transition state ([4e]^‡). Structures 4c and 4d are stabilized by intramolecular coordination of the sulfinyl oxygen with silicon that results in trigonal bipyramidal geometry at silicon. The 1,4-boat conformer (7d) of axial 4,4-dichloro-4-silathiacyclohexane 1-oxide is also stabilized by transannular coordination of the sulfinyl oxygen with silicon. The energy difference (E_rel = 4.23 kcal/mol) between the chair conformer (7a) and 7d is larger than that between 4a and 4d. The relatively lower stability of the 1,4-boat conformer (7d) of axial 4,4-dichloro-4-silathiacyclohexane 1-oxide (7a) may be due to repulsive interactions of the axial halogen and sulfinyl oxygen atoms. The relative energies and structures of the conformers and transition states of cis- and trans-4-chloro-4-silathiacyclohexane 1-oxide and 4,4-dichloro-4-silathiacyclohexane 1-oxide are discussed in terms of hyperconjugative interactions, orbital interactions, nonbonded interactions, and intramolecular sulfinyl oxygen-silicon coordination.     

DFT and neutron diffraction study of 1,6-anhydro-β-D-glucopyranose (levoglucosan)

Geometries of 27 generated conformers of levoglucosan were optimized in vacuo at DFT level of theory combining several functionals with high quality basis sets. For the sake of comparison a reference molecular and crystal geometry obtained from 30 K single crystal neutron diffraction data was used. Analysis of the conformers’ geometries revealed that in all stable conformers intramolecular two-or three centre hydrogen bonds were formed. Relative energy of the conformer, which approximated the molecule in the crystal structure the most, was only ∼3 kcal/mol higher, than the energy of the most stable conformer in vacuo. The largest discrepancies between the geometries calculated in vacuo and experimental geometry concentrated in the vicinity of anomeric C1. These differences were reduced by involving O1 to intermolecular hydrogen bond using a simple model of the respective hydrogen bond in the crystal.      

Computational schemes for modeling proton transfer in biological systems: Calculations on the hydrogen bonded complex [CH3OH · H · NH3]+

Different schemes are explored for the calculation of the proton transfer process in the hydrogen bonded cation [CH₃OH · H · NH₃]⁺. Results from ab-initio calculations with the STO-3G, 3-21G and 4-31G basis sets, are compared in search for an efficient reliable scheme to study the potential energy curves for the proton transfer. The curve constructed from the lowest energies calculated with the frozen optimized geometries of the two possible pairs of proton donor and acceptor fragments, (i.e., CH₃OH/NH₃ and CH₃OH/NH) is in good agreement with that obtained when all the fragments of the hydrogen bonded complex are completely optimized simultaneously.     

Ab initio study of the conformational equilibrium of ethylene glycol

Summary The conformational equilibrium of ethylene glycol (CH₂OHCH₂OH) has been examined by performing geometry optimizations at the 6-31G*, MP2/6-31G* and 6-31G** levels. Final energies have been calculated at the MP3 level with the optimized geometries. The two most stable conformers are atGg andgGg but it is verified that the inclusion of electronic correlations reduces their energy difference of 0.6 kcal/mol at the HF level to less than 0.2 kcal/mol. The possible coexistence of the two most stable conformers is in agreement with some previous studies of Frei et al. For thetXg conformer a detailed analysis of the intramolecular potential as a function of rotation around the C-C bond is also reported.     

Ab initio SCF investigation of the intramolecular hydrogen bonding in δ-aminopentanoic acid

The potential energy surface of the neutral form of-aminopentanoic acid was investigated by means of ab initio 4-31G SCF calculations. Four symmetry unique local minima are stabilized by an intramolecular O-H NH₂ hydrogen bond. The geometries, energies, and wave numbers of these conformers are reported. The hydrogen bond is discussed with respect to all reactions of these conformers and in comparison with the homologues glycine,-alanine, and-aminobutyric acid and also with the bimolecular adducts between formic acid, acetic acid, and propionic acid, on the one hand, and ammonia, methylamine, and ethylamine, on the other hand.     

Gas phase conformational behavior of selenomethionine: A computational elucidation

Selenium containing amino acids are known to play numerous key biological roles in various lifesupporting processes. In the current theoretical investigation DFT(B3LYP) and MP2 methods are used to study the gas phase conformers of the selenomethionine molecule in view of their relative stabilities, theoretically predicted harmonic frequencies, HOMO-LUMO energy gaps, rotational constants, and dipole moments. The number and type of intramolecular H-bond interactions existing in the selenomethionine conformers, which play key roles in determining the energy of the conformers, are also analyzed. The predicted geometries as well as the relative stabilities of the conformers suggest that the structural aspects and energies of the conformers may depend on the level of theory and the size of the basis set used. A comparison of the vibrational frequencies furnished in this study with the previous experimental and theoretical results obtained at MP2/6-31++G(d,p) and B3LYP/6-311++G(d,p) levels promotes the interpretation of the vibrational spectroscopy data on biologically relevant molecules.     

Ab initio molecular orbital calculations of 3,4-dihydro-1,2-dioxin, 3,6-dihydro-1,2-dioxin, 4H-1,3-dioxin (1,3-diox-4-ene), and 2,3-dihydro-1,4-dioxin (1,4-dioxene)

Optimized geometries and total energies for 3,4-dihydro-1,2-dioxin ( 1 ), 3,6-dihydro-1,2-dioxin ( 2 ), 4H-1,3-dioxin (1,3-diox-4-ene, 3 ), and 2,3-dihydro-1,4-dioxin (1,4-dioxene, 4 ) were calculated using ab initio 3-21G, 6-31G*, and MP2/6-31G*//6-31G* methods. The half-chair conformers of 1 (C₁), 2 (C₂), 3 (C₁), and 4 (C₂) are more stable than their respective planar structures [ 1 (C_s), 2 (C_2v), 3 (C_s), and 4 (C_2v)]. Among the four isomers 1 – 4 , the half-chair conformer of 3 is the most stable. It is 53.1, 54.6, and 3.4 kcal mol⁻¹ more stable than 1 , 2 , and 4 , respectively. The largest energy difference (19.0 kcal mol⁻¹) is observed between the half-chair and planar conformers of 2 . The boat conformers of 2 and 4 are less stable than their respective half-chair conformers, but are more stable than their planar structures. Hyperconjugative orbital interactions (anomeric effects) contribute to the greater stability of 3 (n_O(3) →σ*_C(2)—O(1), n_O(3)→σ*,n _O(3)→σ*) and of 4 (n_O(1)→ σ*). The ab initio calculated structural features of the half-chair conformations of the dihydrodioxins 1 – 4 are compared with the half-chair conformations of cyclohexene and the chair conformations of cyclohexane, oxacyclohexane (tetrahydropyran), 1,2-dioxacyclohexane (1,2-dioxane), 1,3-dioxacyclohexane (1,3-dioxane), and 1,4-dioxacyclohexane (1,4-dioxane) © 1997 by John Wiley & Sons, Inc. J Comput Chem 18 : 1392–1406, 1997     

Conformational analysis of 2,4,5-trimethyl-1,3,2-dioxaborinane individual stereoisomers

The study of the conformational isomerization of cis- and trans-isomers of 2,4,5-trimethyl-1,3-dioxaborinane I by means of RHF//STO-3G, 3-21G and 6-31G(d) quantumchemical methods led to the conclusion that its route includes equilibrium between sofa conformers with a different steric orientation of substituents at the C-4 and C-5 ring atoms. These conformers are interconverted through the maxima, the conformations of equatorial and axial 2,5-twist-forms. A comparison between experimental ¹H NMR and theoretical vicinal spin-spin coupling constants was used to determine the quantitative conformational composition of stereoisomers and a value of ΔG ⁰ for conformational equilibrium.     

N-Trifyl substituted 1,4-diheterocyclohexanes—stereodynamics and the Perlin effect

The stereodynamic behaviour of 1-(trifluoromethylsulfonyl)piperidine 1, 4-(trifluoromethylsulfonyl)morpholine 2, 1,4-bis(trifluoromethylsulfonyl)piperazine 3 and 4-(trifluoromethylsulfonyl)thiomorpholine 1,1-dioxide 4 was studied by low-temperature ¹H, ¹³C and ¹⁹F NMR spectroscopies. In acetone solution, compounds 1, 2 and 4 were found to exist as mixtures of two conformers in the ratio of 4:1, 4:1 and 8:1, respectively, differing by orientation of the CF₃ group with respect to the ring. Compound 3 exists as a mixture of three conformers in the ratio of 3:28:69 also differing by the orientation of the two CF₃ groups. Unlike the previously studied N-trifyl substituted 1,3,5-triheterocyclohexanes, the preferred conformers of compound 1 and of 1,4-diheterocyclohexanes 2-4 are those with the CF₃ group directed outward from the ring, which is caused by intramolecular interactions of the oxygen atoms of the CF₃SO₂N groups with the equatorial hydrogens in the α-position. B3LYP/6-311+G(d,p) calculations of the energy, geometry and NMR parameters corroborate the experimental data. The calculated Perlin effects for all conformers of compounds 1-4 as well as those measured for the major conformers of compounds 3 and 4 were analyzed by the use of the NBO analysis.     

A theoretical study of α-substituted isopropyl and cyclopropyl anions

Ab initio molecular orbital theory has been used to probe the effect of the substituent X on the structures, strain energies, stabilization energies, inversion barriers, and proton affinities of carbanions CH₃CX CH and cis-C₃H₄X^?, where X = H, F, CN, and NC. All geometries have been optimized with a 3-21G basis set, and the parent anions (X = H) were also optimized with the same basis set with a diffuse function added (i.e. the 3-21 + G basis set). The anions, with the exception of the α-cyanoisopropyl anion, are pyramidal. The out-of-plane angle, α, for the pyramidal anions decreases in the order F > H ≈ NC > CN, and the barriers to inversion follow the same order with the cyclopropyl anions consistently having higher barriers than the isopropyl anions. The substituents strongly stabilize the anions with the stabilization energy following the order CN > NC > F. The cyano group slightly reduces the strain energy of cyclopropane, but the isocyano and fluoro substituents are weakly and strongly destabilizing, respectively. The pyramidal cyclopropyl anions are less strained than the cyclopropanes except when the substituent is a cyano group where the strain energies are reversed but are very similar. The planar anions all have higher strain energies than the cyclopropanes.     

1-(Nitrosoamino)benzimidazoles Containing Electron-acceptor Substituents at the Amine Nitrogen. Theoretical and Experimental Investigation of Conformational Mobility

The previously unknown 1-(N-nitrosoallylamino)- and 1-(N-nitrosopropargylamino)benzimidazoles have been synthesized and they exist in solution as a mixture of the E- and Z-conformers due to hindered rotation around the N-N(O) bond. The activation energies for the EZ transition in these compounds and for the model N-benzyl analog have been determined by a dynamic ¹H NMR method. With a view to studying the effect of a substituent at the amino nitrogen on the EZ isomerization we have carried out 3-21G and 6-31G** type ab initio calculations of the stable conformers of a series of N-nitrosohydrazines.     

Hydrogen bond in 3-acetyl-4-hydroxycoumarin: X-ray diffraction study and quantum-chemical calculations

The proton transfer and the character of the strong intramolecular O--H...O hydrogen bond (O...O 2.442 ) in 3-acetyl-4-hydroxycoumarin were analyzed based on the results of X-ray diffraction study in the temperature range from 100 to 353 K and quantum-chemical B3LYP/6-31G(d,p) calculations. The barrier to proton transfer along the H-bond line is low (2 kcal mol^–1). However, no proton transfer was observed in the crystal at 100 K. Bader's topological analysis of the electron density distribution both in the crystal and in the isolated molecule demonstrated that the hydrogen bond corresponds to an intermediate type of interatomic interactions (E(r) < 0, ²(r) > 0 at the critical point (3, –1)).     

DFT computations,vibrational spectra,monomer, dimer,NBO and NMR analyses of antifungal agent: 3,5-Dibromosalicylic acid

The experimental and theoretical study on the structures and vibrations of 3,5-dibromosalicylic acid (DBSA) are presented. The FT-IR and FT-Raman of the title compound have been recorded. The molecular structures, vibrational wavenumbers, infrared intensities, Raman activities were calculated. The energies of DBSA are obtained for all the eight conformers from density functional theory with 6-311++G(d,p) basis set calculations. From the computational results, C1 or C5 forms are identified as the most stable conformers of DBSA. The spectroscopic and theoretical results are compared with the corresponding properties for DBSA monomer and dimer of C1 (or C5) conformer. Intermolecular hydrogen bonds are discussed in dimer structure of the molecule. NBO analysis is useful to understand the intramolecular hyperconjugative interaction between lone pair O9 and C7O8. The calculated HOMO–LUMO energies reveal charge transfer occurs within the molecule. The polarizability, first hyperpolarizability, anisotropy polarizability invariant has been computed using quantum chemical calculations. The isotopic chemical shift computed by ¹H and ¹³C nuclear magnetic resonance (NMR) chemical shifts of the DBSA molecule, calculated using the gauge invariant atomic orbital (GIAO) method, also shows good agreement with experimental observations.     

Ab initio and density functional study of the conformational space of 1C4 α-L-fucose

The conformational space of ¹C₄ α-L-fucose was searched by the MM2^*-SUMM molecular mechanics conformational search technique. The molecular geometries of the first 17 structures of lowest energy were analyzed at the HF/3-21G, 6-31G(d), and generalized gradient approximation (GGA) DFT levels of theory. © 1997 by John Wiley & Sons, Inc.     

Conformational Analysis of Planar Enol Rotamers of 2,4-Pentanedione: an Ab Initio Study

All conformations among different planar enol conformers (rotamers) of 2,4-pentanedione were studied by means of the Hartree-Fock method using the STO-3G** basis set. The calculations were carried out with the Gaussian-98 program. For each conformation, stationary points with the highest energy on the energy curve were found graphically. Several conformations have low energy barriers and correspond to rotations around single bonds. They describe the spatial motion of only one (in most cases, hydrogen) atom or a small molecular fragment. All low energy barriers are in the interval 13-59 kJ·mol^-1. As would be expected, the lowest energy barrier is exhibited by the conformation that leads to the formation of an enol rotamer having an intramolecular H-bond (so-called -shaped form). On the other hand, conformations in which rotation around a bond leads to a break of the intramolecular hydrogen bond have the highest energy barriers. Conformations in which rotation occurs around the double bond have high energy barriers. The influence of the solvents CHCl₃ and CH₃CN on the intramolecular H-bond has also been studied by means of IPCM at the HF/6-31G** level.     

Molecular structure,conformational stability,energetic and intramolecular hydrogen bonding in ground,and electronic excited state of 3-mercapto propeneselenal

In the present work, a conformational analysis of 3-mercapto propeneselenal is performed using several computational methods, including DFT (B3LYP), MP2, and G2MP2. At the DFT and G2MP2 levels the most stable conformers of title compound are characterized by an extended backbone structure, minimizing the steric repulsions between the sulfur and selenium lone pairs. Two conformers exhibit hydrogen bonding. This feature, although not being the dominant factor in energetic terms, appears to be of foremost importance to define the geometry of the molecule. The influence of the solvent on the stability order of conformers and the strength of intramolecular hydrogen bonding was considered using the PCM, SCI–PCM, and IEF–PCM methods. The results of analysis by quantum theory of “Atoms in Molecules” and natural bond orbital method fairly support the DFT results. The calculated HOMO and LUMO energies showed that charge transfer occurs within the molecule. Further verification of the obtained transition state structures was implemented via intrinsic reaction coordinate analysis. Calculations of the ¹H NMR chemical shift at GIAO/B3LYP/6–311++G** levels of theory are also presented. The excited-state properties of intramolecular hydrogen bonding in hydrogen-bonded systems have been investigated theoretically using the time-dependent density functional theory method.     

Theoretical study of “protonated pyruvate”: A methylhydroxycarbene—carbon dioxide complex—implications for the decarboxylation of pyruvic acid

Two conformers of protonated pyruvate, CH₃C⁺(OH)COO, with the OH group either trans or cis to the methyl group and the carboxylate group in the C? C? C plane have been studied using the ab initio SCF/3-21G method, as well as by some semiempirical AM1 calculations. Both ab initio SCF and AM1 curves for the potential energy as a function of the C? COO distance exhibit a minimum corresponding to a complex of methylhydroxycarbene, CH₃COH, associated with carbon dioxide, but only the AM1 curves predict an inner minimum corresponding to a covalently bonded protonated pyruvate molecule with a C? COO distance of 1.6–1.7 Å. The two models also disagree on the dissociation pathway for pyruvic acid, with the AM1 calculations predicting formation of acetyl and HOCO radicals while the ab initio method predicts dissociation into methylhydroxycarbene and carbon dioxide following an initial intramolecular proton transfer. The weakly bound complexes of methylhydroxycarbene and carbon dioxide have been studied in some detail using ab initio SCF and MP2 methods in conjunction with 6-311G** basis sets, obtaining equilibrium geometries and vibrational frequencies. In addition, the lactone-type isomer of protonated pyruvate, which contains a C? C? O ring, was also studied. The conclusions of these calculations are consistent with those from earlier work using the smaller 3-21G basis set. The most stable complex is predicted to occur between trans-methylhydroxycarbene and carbon dioxide where substantial stabilization is provided by an OH ? OC hydrogen bond. © 1993 John Wiley & Sons, Inc.     

Dipole moments and structure of <Emphasis Type="Italic">ortho</Emphasis>-diphenyl(diethyl)phosphinoyl-substituted benzyl alcohols,phenols, and their derivatives

The method of dipole moments and DFT B3LYP/6-31G* quantum-chemical calculations were used to study the structures of ortho-substituted aryl-and arylmethyldiphenyl(diethyl)phosphine oxides. It was established that methyl ethers of phosphorus-containing benzyl alcohols and phenols exist as equilibrium mixtures of several conformers with prevalence of forms with the weakest steric interactions. Preferred conformers of o-[(diethylphosphinoyl)methyl]benzyl alcohol and i-[(diphenylphosphinoyl)methyl]phenol contain an intramolecular hydrogen bond between the hydroxyl hydrogen atom and phosphinoyl oxygen atom.     

Physical Image vs. Structure Relation. Part 3 [1]. Basic Properties and Protonation Mechanism of Some Tetraaza Macrocyclic Ligands

The protonation constants, log K, for 1,4,7,11-tetraazacyclotetradecane (isocyclam, 2), 1-(2-aminoethyl)-1,4,8,11-tetraazacyclotetradecane (scorpiand, 3), 5,12-dimethyl-1,4,8,11-tetraazacyclotetradecane (Me₂cyclam, 4) and 5,5,7,12,14,14-hexamethyl-1,4,8,11- tetraazacyclotetradecane (Me₆cyclam, 5) were determined pH-metrically. Attempts of correlation of the calculated enthalpy of protonation in the gas phase (AM1 method) with experimental values of the protonation constants for ligands 1, 2, 4–7 were done 1,4,8,11-tetraazacyclotetradecane, cyclam, 1; 1,4,7,10-tetraazacyclotetradecane, cyclen, 6; 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane, (N-Me)₄cyclam, 7. Extensive NMR pH-titrations, i.e., determination of pH vs. chemical shifts (¹H and/or ¹³C) plots, (_X = f(pH), allowed to suggest the most likely protonation schemes of all nitrogen atoms in the cyclic polyamines 1–3. The possibility of the formation-breaking of the intramolecular hydrogen bonds, as well as the change of conformation of these polybasic macrocycles during protonation-deprotonation steps, has been considered on the basis of the supplementary theoretical calculations (MMX/STO-3G study).