Intramolecular hydrogen bonding in structural conformers of 2‐amino methylene malonaldehyde: AIM and NBO studies

The molecular structure and intramolecular hydrogen bond energies of 44 conformers of 2‐Amino methylene malonaldehyde were investigated at MP2 and B3LYP levels of theory using the standard 6‐311++G** basis set and AIM and NBO analysis. The calculated geometrical parameters and conformational analysis in gas phase show that the closed ring via intramolecular hydrogen bonded conformers of this compound are more stable than the other ones. Hydrogen bond energies for H‐bonded conformers were obtained from the related rotamers method (RRM) and Schuster method, and also the nature of H‐bonding of them has been investigated by means of the Bader theory of atoms in molecules, which is based on topological properties of the electron density. Delocalization effects can be identified from the presence of off diagonal elements of the Fock matrix in the NBO basis. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

A DFT study of hydrogen bond interactions between oxidative 2′-deoxyadenosine nucleotides and RNA nucleotides

In this study, the interactions between oxidative 2′-deoxyadenosine nucleotides (2OHA, 8OHA, 8OXOA, fapyA) and canonical ribonucleotides (A, C, G, U) were investigated at B3LYP level with 6-31G(d) basis set. The binding energies calculated were corrected for the basis set superposition error at the same level. The result shows that syn 8OXOA:G complex is the most stable among all the complexes. According to energetic analysis, the species and position of substitution of 2′-deoxyadenosine nucleotide significantly influence the stability of conformers. The intermolecular and intramolecular hydrogen bonds (HBs) were characterized based on atoms in molecules theory (AIM) and natural bond orbital (NBO) analysis, indicating that the type and geometry of HB significantly influence the stability of monomer and complex. Furthermore, in most cases, the intramolecular HBs in monomer and complex exhibit similar properties because they own nearly the same geometry and parameters obtained from AIM and NBO analysis.     

Study of hydrogen-bonded clusters of 2-methoxyphenol–water

Various hydrogen-bonded clusters of 2-methoxyphenol (2MP) with water have been analyzed using ab initio methods and Atoms in Molecules (AIM) theory. The intramolecular hydrogen bond energy (and enthalpy) for 2MP was evaluated from two different methods. The results of rotational barriers method are in better agreement with experimental data. Binding energies, vibrational frequencies and geometrical parameters were examined and compared for these complexes. It was shown that in the most stable complex, water acts both as a donor and an acceptor. The “bifurcated” complex was shown to be relatively stable based on energy values. Atoms in Molecules and Natural Bond Orbital (NBO) analysis were used to confirm the existence of hydrogen bonds and to compare the strengths of them. The results obtained from quantum mechanical, AIM and NBO calculations are in agreement with each other.     

Intramolecular hydrogen bond in 3‐imino‐propenylamine isomers: AIM and NBO studies

The molecular structure and intramolecular hydrogen bond energy of 18 conformers of 3‐imino‐propenyl‐amine were investigated at MP2 and B3LYP levels of theory using the standard 6‐311++G** basis set. The atom in molecules or AIM theory of Bader, which is based on the topological properties of the electron density (ρ), was used additionally and the natural bond orbital (NBO) analysis was also carried out. Furthermore calculations for all possible conformations of 3‐imino‐propenyl‐amin in water solution were also carried out at B3LYP/6‐311++G** and MP2/6‐311++G** levels of theory. The calculated geometrical parameters and conformational analyses in gas phase and water solution show that the imine–amine conformers of this compound are more stable than the other conformers. B3LYP method predicts the IMA‐1 as global minimum. This stability is mainly due to the formation of a strong N? H···N intramolecular hydrogen bond, which is assisted by π‐electrons resonance, and this π‐electrons are established by NH2 functional group. Hydrogen bond energies for all conformers of 3‐imino‐propenyl‐amine were obtained from the related rotamers methods. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Conformational study of monomeric 2,3-butanediols by matrix-isolation infrared spectroscopy and DFT calculations

The FT-IR spectra of two diastereomers of 2,3-butanediol, (R,S) and (S,S), isolated in low-temperature argon and xenon matrixes were studied, allowing the identification of two different conformers for each compound. These conformers were characterized by a +/-gauche arrangement around the O-C-C-O dihedral angle, thus enabling the establishment of a very weak intramolecular hydrogen bond of the O...H-O type. No other forms of these compounds were identified in matrixes, despite the fact that these four conformers had calculated relative energies from 0 to 5.1 kJ mol(-1) and were expected to be thermally populated from 50 to 6% in the gaseous phase of each compound. The nonobservation of additional conformers was explained in terms of low barriers to intramolecular rotation, resulting in the conformational relaxation of the compounds during deposition of the matrixes. The barriers to internal rotation of the OH groups were computed to be less than 4 kJ mol(-1) and are easily overcome in matrixes within the family of conformers with the same heavy atom backbone. The barriers for intramolecular rearrangement of the O-C-C-O dihedral angle in both diastereomers were calculated to range from 20 to 30 kJ mol(-1). Interconversions between the latter conformers were not observed in matrixes, even after annealing up to 65 K. Energy calculations, barriers, and calculated infrared spectra were carried out at the DFT(B3LYP)/6-311++G theory. Additional MP2/6-311++G calculations of energies and vibrational frequencies were performed on the most relevant conformers. Finally, independent estimations of the hydrogen-bond enthalpy in the studied molecules were also obtained based on theoretical structural data and from vibrational frequencies (using well-established empirical correlations). The obtained values for -DeltaH for both diastereomers of 2,3-butanediol amount to ca. 6-8 kJ mol(-1).     

Conformational analysis,tautomeric preference,intramolecular hydrogen bonding,and solvent effect on dinitrosamine: A quantum chemical study

HF, B3LYP, and MP2 methods with the standard basis set, 6‐311++G(d,p), were used to study various aspects of dinitrosamine. These results were compared with the outcomes of G2 and CBS‐QB3 methods. First, the conformational analysis and characterization of equilibrium conformations, especially global minima, were performed. On the basis of relative energies, we found that the dinitroso tautomers are more stable than the nitroso‐hydroxy (NH) ones. This preference is well‐interpreted in terms of tautomerization process and nitrosamine resonance. Furthermore, the nature of O? H···O intramolecular hydrogen bond (IMHB), in chelated forms of NH (NH‐11 and NH‐13) was comprehensively studied to evaluate the effect of hetero atoms (N) on the characteristic of IMHB systems. According to the results of isodesmic reaction method, the hydrogen bond energy of NH‐11 is greater than the malonaldehyde (MA) and NH‐13, whereas the electron density analysis and energy‐geometry correlation methods clearly predict that the hydrogen bond of NH‐11 is weaker than the MA. Additionally, the geometrical, atoms in molecules (AIM) and natural bond orbital's (NBO) parameters also emphasize on the MA as a chelated form with the strongest hydrogen bond. Finally, the solvent effects on the relative stability of selected dinitrosamine conformers are evaluated by different continuum (polarizable‐continuum model, isodensity polarizable continuum model, and self‐consistent isodensity polarizable continuum model), discrete and mixed solvent models. Theoretical results readily show that the potential energy surface of dinitrosamine, especially global minima, is strongly affected by the solvent. © 2012 Wiley Periodicals, Inc.     

A theoretical study of the photodetachment and intramolecular hydrogen-bonding energies of hydrogen maleate anions

Three low-lying conformers of the hydrogen maleate anions (HMAs) regarding cis-HMA(HB) having the O-...HO intramolecular hydrogen bond (HB), cis-HMA(nHB) without the HB, and trans-HMA are studied by density functional theory (B3LYP) combined with natural bond orbital (NBO) and atoms-in-molecules (AIM) analyses. The photoelectron spectra of cis- and trans-HMA conformers recorded by Woo et al. (J. Phys. Chem. A 2005, 109, 10633) are reassigned on the basis of the present electron propagator theory calculations, indicating the significant energy differences between the Dyson orbitals and canonical molecular orbitals due to the electron-correlation and orbital relaxation effects considered in the electron propagator theory. The NBO associated with the natural resonance theory analyses and AIM electron topological study show that the strong O-...HO in cis-HMA(HB) has the remarkable characteristics of three-center four-electron hyperbond, and the bonding strength of ca. 30 kcal/mol is recommended with the reference calculations of the HO-...HOH complex. The further calculations for the microhydrated cis-HMA(HB) clusters indicate that the O-...HO bonding strength decreases in water solution.     

Structure of the 2-isopropylaminoethanol isolated molecule: Conformational analysis and intramolecular interactions

In this paper, a systematic exploration of all the possible conformers of 2-isopropylaminoethanol (2-IPAE) was carried out using the Density Functional Theory (B3LYP) and the 6-311++G(d,p) basis set. At this level, 66 unique conformers within a Gibbs energy range of ca. 31 kJ mol⁻¹ were found in the potential energy surface and their geometrical and thermodynamic properties were determined and discussed. A significant molecular strain was evidenced by the dihedrals and distances between non-bonded hydrogen atoms. According to the geometrical parameters, a O–H···N hydrogen bond was found to be present in the three most stable conformers, representing 68% of the conformational composition at 298.15 K. The energetic and geometrical data derived from the DFT calculations were further complemented by a NBO analysis of the most stable conformers.     

Structural and vibrational characterisation of 3-amino-1-propanol a concerted SCF-MO ab initio, Raman and infrared (matrix isolation and liquid phase) spectroscopy study

Results obtained for the isolated and liquid 3-amino-1-propanol by a concerted molecular orbital and vibrational spectroscopic approach are reported. The relative energies and both structural and vibrational data of the different conformers of the studied compound were calculated using the extended 6-31G* basis set both at the HF-SCF and MP2 ab initio levels of theory and the theoretical results used to interpret Raman and infrared experimental data. In the gaseous phase and for the molecule isolated in an Argon matrix, monomeric 3-amino-1-propanol exists as a mixture of conformers, the first and second lowest energy forms corresponding to conformers which exhibit an intramolecular OH-N hydrogen bond (forms I and II). On the other hand, in the pure liquid, where intermolecular H-bonding occurs, the monomeric unit within the aggregates assumes a conformation similar to that of the third most stable form found for the isolated molecule situation (form III), which is characterised by having a weak intramolecular NH-O bond. The experimental data obtained for the pure liquid also reveals the presence of monomeric form I in this phase, a result that is in consonance with the strongly stabilizing OH-N intramolecular hydrogen bond that is present in this conformer.     

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     

Structural,electronic properties and intramolecular hydrogen bonding of substituted 2-[(E)-imino methyl] benzenethiol in ground and first excited state by quantum chemical methods

Quantum chemical calculations of geometric structure, the intramolecular hydrogen bond, harmonic vibrational frequencies, NMR spin–spin coupling constants, and physical properties such as chemical potential and chemical hardness of the 2-(E)-imino methyl benzenethiol and its nineteen derivatives were carried out using density functional theory (DFT/B3LYP/6-311++G**) method in the gas phase and the water solution. Furthermore, the topological properties of the electron density distributions for S–H···N intramolecular hydrogen bond have been analyzed in terms of the Bader’s theory of atoms in molecules (AIM). Natural bond orbital (NBO) analysis also performed for better understanding the nature of intramolecular interactions, the results of analysis by quantum theory of AIM and NBO method fairly supported the DFT results. Besides, MEP was performed by the DFT method. On the other hand, the aromaticity of the formed ring has been measured using several well-established indices of aromaticity such as nucleus-independent chemical shift, harmonic oscillator models of the aromaticity, para-delocalization index, average two-center indices, and aromatic fluctuation index. Also, the excited-state properties of intramolecular hydrogen bonding in these systems have been investigated theoretically using the time-dependent DFT method.     

Coded amino acids in gas phase: the shape of isoleucine

The solid alpha-amino acid isoleucine has been vaporized by laser ablation and expanded in a supersonic jet, where the molecular conformations of the isolated molecule were probed using Fourier transform microwave spectroscopy. Two conformers of neutral isoleucine have been detected in gas phase, the most stable being stabilized by an intramolecular hydrogen bond N-H...O=C and a cis-COOH arrangement. The higher energy form is stabilized by an intramolecular hydrogen bond N...H-O. The sec-butyl side chain of the amino acid adopts the same configuration in the two observed conformers, with a staggered configuration at Cbeta similar to that observed in valine and a trans arrangement of Calpha and Cdelta. Ab initio calculations at MP2/6-311++G(d,p) level reproduce satisfactorily the experimental results.     

Electronic structure and conformational properties of (carboxy-alkenyl)-phosphonic acids

The general conformational properties and electronic structure of (carboxy-alkenyl)-phosphonic derivatives were determined at RHF/STO-3G^* level. In all the series, low rotation barriers were found for the two C=C/P=O conformers. In the compounds in which the interactions between the carboxylic and phosphonic moieties are smaller, the most stable conformers are the C=C/P=O s-cis ones. In most of the conformers, the C=C/C=O system presents the disposition s-cis. The Z-(2-carboxy-vinyl) and Z-(2-carboxy-propenyl) phosphonic acids present intramolecular hydrogen bonds, existing in at least four conformer with internal hydrogen bonds. These last compounds were more rigorously studied at RHF/3-21G^* and RHF/6-31G^** levels. The most stable conformer shows a trans structure for the C=C/P=O angle, with an intramolecular hydrogen bond located between the hydroxylic hydrogen of phosphonic group and the carbonyl oxygen of carboxylic moiety. A secondary conformer is found with a double intramolecular hydrogen bond between two hydroxylic hydrogens of the phosphonic moiety and the oxygen of carboxylic bond. Another secondary conformer appears with an intramolecular hydrogen bond between the oxygen of the phosphoryl bond and the hydroxylic hydrogen of the carboxylic group. A study of the topology of charge densities is carried out. This analysis reveals bonds with an ionic participation. A very weak π conjugation, variable with the conformers, is found in the C=C/P=O system, as well as a strongly polarized P=O partial triple bond. The intramolecular hydrogen bonds give rise to cyclic structures.     

Conformational study of eugenol by density functional theory method and matrix-isolation infrared spectroscopy

The B3LYP/6-311++G(2d,2p) study of the potential energy surface of eugenol (4-allyl-2-methoxyphenol, 2-methoxy-4-pro-2-emyl-phenol) was performed with the aim of finding all possible conformers of the molecule. Twelve conformers were found belonging to one of three groups differing in the relative orientation of the OH and OCH 3 moieties: SA (syn-anti), AA (antianti) and AG (antigauche). The lowest-energy conformers of eugenol (SAA+, SAA- and SAS) stabilized by the intramolecular hydrogen bond differ only in the arrangement of the allyl group with respect to the aromatic ring. The calculated abundance of all three SA species equals 99.8% whereas the remaining AA and AG show the negligible population of 0.2%. In consonance with theoretical predictions, only syn-anti conformers are present in the low temperature matrices studied. The presented FTIR results allow, for the first time, unequivocal identification and spectral characterization of three SA conformers of the eugenol molecule isolated in solid argon and xenon. The performed studies reveal that conformational cooling (upon increasing the substrate temperature during deposition) takes place in the studied matrices and that the less stable SAA- and SAS species convert into SAA+. This observation appears to be consistent with the theoretically predicted energy barriers of 6.70 and 10.45 kJ/mol for the SAA- --> SAA+ and SAS --> SAA+ interconversions which are low enough to be surpassed during deposition at higher temperatures.     

Influence of intramolecular hydrogen bond strength on OH-stretching overtones

Vapor-phase OH-stretching overtone spectra of 1,3-propanediol and 1,4-butanediol were recorded and compared to the spectra of ethylene glycol to investigate the effect of increased intramolecular hydrogen bond strength on OH-stretching overtone transitions. The spectra were recorded with laser photoacoustic spectroscopy in the second and third OH-stretching overtone regions. The room-temperature spectra of each molecule are dominated by two conformers that show intramolecular hydrogen bonding. Anharmonic oscillator local-mode calculations of the OH-stretching transitions have been performed to aid assignment of the different conformers in the spectra and to illustrate the effect of the intramolecular hydrogen bonding. The hydrogen bond strength increases in the order ethylene glycol, 1,3-propanediol, and 1,4-butanediol. The overtone transitions of the hydrogen-bonded hydroxyl groups are more difficult to observe with increasing intramolecular hydrogen bond strength. We suggest that the bandwidth of these transitions increases with increasing hydrogen bond strength and with increasing overtone and furthermore that these changes are in part responsible for the lack of observed overtone spectra for complexes.     

Matrix-isolated monomeric tryptophan: electrostatic interactions as nontrivial factors stabilizing conformers

An extensive analysis of the conformational space of tryptophan (Trp) was performed at the B3LYP/6-311++G(d,p) level and verified by comparison with the infrared spectra of the compound isolated in low-temperature argon and xenon matrixes. Different types of conformers have been unequivocally identified in the matrixes. Type I exhibits the trans arrangement of the carboxylic group and is stabilized by an O-H...N intramolecular H-bond. Types II and III have the carboxylic group in the cis conformation and feature N-H...O=C and N-H...O-C hydrogen bonds, respectively. Three individual conformers of type I were identified in the matrixes. Other conformational degrees of freedom are related with the Calpha-Cbeta-Cgamma=C and C1-Calpha-Cbeta-Cgamma angles (chi1 and chi2, respectively). In proteins, these two dihedral angles define the conformations of the amino acid residues. In monomeric Trp, chi1 adopts the "+" (ca. +90 degrees ) and "-" (ca. -90 degrees ) orientations, while average values of -67.4, 170.5, and 67.6 degrees ("a", "b", and "c", respectively) were found for chi2. Theoretical analysis revealed two important factors in stabilizing the structures of the Trp conformers: the H-bond type and electrostatic interactions. Classified by the H-bond type, the most stable are forms I, followed by II and III. Out of possible combinations of the chi1 and chi2 dihedral angles, "a+", "b+", and "c-" were theoretically found more stable than their "a-", "b-", and "c+" counterparts. Thus, the stabilizing effect of interactions involving the pyrrole ring (which are possible in Ia+, Ib+, and Ic- conformers) is considerably higher compared to those in which the phenyl ring is engaged (existing in the Ia-, Ib-, and Ic+ forms).     

Conformations, energies, and intramolecular hydrogen bonds in dicarboxylic acids: implications for the design of synthetic dicarboxylic acid receptors

The various conformers of the dicarboxylic acids HO2C--(CH2)n--CO2H, n = 1-4, were obtained using density functional methods (DFT), both in the gas phase and in the aqueous phase using a polarized continuum model (PCM). Several new conformers were identified, particularly for the two larger molecules glutaric (n = 3) and adipic acid (n =4). The PCM results show that the stability of most conformers were affected, many becoming unstable in the aqueous phase; and the energy ordering of conformers is also different. The results suggest that conformational preferences could be important in determining the design and stability of appropriate synthetic receptors for glutaric and adipic acid. Geometry changes between gas and aqueous phases were most marked in those conformers containing an intramolecular hydrogen bond. Additional calculations have probed the strength of intramolecular hydrogen bonds in these dicarboxylic acids. In the cases of glutaric and adipic acid, the strength of the intramolecular hydrogen bond were estimated to be around 28-29 kJ/mol, without any vibrational energy correction. The intramolecular hydrogen bond energies in malonic and succinic acid were also estimated from the calculated H-bond distances using an empirical relationship. Intramolecular H-bond redshifts of 170-250 cm(-1) have been estimated from the results of the harmonic frequency analyses.     

Electronic effects of the functional groups in ortho-Nitrobenzenesulfonic acids on the results of NBO analysis

An NBO analysis of electronic density distribution is performed for gaseous benzenesulfonic acid and its mono- and trinitro-substituted molecules (B3LYP, MP2, HF /cc-pVTZ). The energy of orbital inter-actions of nitro and sulfonic groups with benzene ring orbitals is calculated for the most stable acid conformers, and the contributions of inductive and resonance effects of substituents are determined. The dependences of these contributions on the positions and number of nitro groups in an aromatic ring and the possibility of intramolecular hydrogen bond formation are revealed. The nitro group in nitrobenzene exhibits a stronger electron-acceptor effect than the sulfonic group in benzenesulfonic acid. Under the influence of the strong electron-acceptor properties of the nitrogroups, the sulfonic group has a donating effect in ortho-nitrosubstituted benzenesulfonic acids.     

Conformational behavior of dimethyl 5-methyl-1H,3H-pyrrolo[1,2-c][1,3]thiazole-6,7-dicarboxylate 2,2-dioxide isolated in low-temperature matrixes

The structure of dimethyl 5-methyl-1H,3H-pyrrolo[1,2-c][1,3]thiazole-6,7-dicarboxylate 2,2-dioxide (PTD) was investigated in low-temperature noble gas matrixes (Ar, Kr, Xe), amorphous solid, and the crystalline state by infrared spectroscopy and computational methods. The geometry of PTD conformers is defined by the orientation of two methyl ester groups, which may adopt pseudo-trans or pseudo-cis positions in relation to the pyrrolo-thiazole system. For both methyl ester groups, the latter arrangement was predicted by the calculations to be energetically the most favorable in the isolated molecule. The envelope form of the thiazolidine ring is present in all conformers, with the sulfur atom placed in the apex position, while the pyrrole ring is almost planar. Three types of conformers differing in the orientation of the methyl ester groups relative to the pyrrolo-thiazole system (cis/cis, trans/cis, cis/trans) were identified in the matrixes. The cis/cis forms were found to be the most stable ones in both gaseous state and argon matrixes. On the other hand, the more polar trans/cis forms were found to be stabilized in the more polarizable krypton and xenon matrixes as well as in the neat amorphous and crystalline phases. On the basis of annealing experiments, performed in argon and xenon matrixes up to 35 and 68 K, respectively, conformational changes preceding the aggregation of the compound are suggested.     

Unusual photochemical C-N bond cleavage in the novel methyl 2-chloro-3-methyl-2H-azirine-2-carboxylate

The structure, preferred conformers, vibrational spectrum, and photochemical behavior of the novel azirine, methyl 2-chloro-3-methyl-2H-azirine-2-carboxylate (MCMAC) were investigated in low-temperature matrixes and in the neat solid amorphous state by infrared spectroscopy and quantum-chemical calculations. Two conformers of the compound were observed in argon, krypton, and xenon matrixes, in agreement with the DFT(B3LYP)/6-311++G(d,p) and MP2/6-311++G(d,p) theoretical calculations. Both conformers were found to exhibit the carboxylic ester group in the cis conformation, differing in the arrangement defined by the O=C-C-Cl dihedral angle (cis and trans, for Ct and Cc forms, respectively). The Ct conformer was found to be the most stable conformer in the gaseous phase as well as in both argon and krypton matrixes, whereas the more polar Cc conformer became the most stable form in the xenon matrix and in the neat solid amorphous phase. In situ broadband UV (lambda > 235 nm) excitation of matrix-isolated MCMAC led to azirine ring C-C and C-N bond cleavages, the latter process corresponding to the most efficient reaction channel. The photochemical cleavage of the C-N bond had never been previously observed in the case of aliphatic 2H-azirines. Two electron withdrawing substituents (methoxycarbonyl group and chlorine atom) are connected to the azirine ring in the novel MCMAC azirine. The simultaneous presence of these two groups accelerates intersystem crossing toward the triplet state where cleavage of the C-N bond takes place. The primary photoproducts resulting from the C-N and C-C ring-opening reactions were also found to undergo further photochemical decarbonylation or decarboxylation reactions.