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     

Theoretical study of molecular interactions of sulfur ylide with HSX (X = F, Cl, and Br) molecules

The molecular interactions between sulfur ylide (SY) and HSX molecules (X = F, Cl and Br) were investigated using the MP2 method with the 6-311++G (2d, 2p) basis set. The SY (CH₂=SH₂) have two reactive sites: CH₂ (denoted as C-interaction) and SH₂ (S-interaction) that both could interact with three atoms of HSX molecules. The results show that S···C, X···C, and H···C interactions (C-interactions) is preference over the X···S, H···S, and H···X interactions. Quantum theories of atoms in molecules and natural bond orbitals methods have been applied to analyze the intermolecular interactions. Good correlations have been found between the interaction energies, the second-order perturbation energies E⁽²⁾, and the charge transfer qCT in the studied systems.     

Microwave spectrum of 3-butyne-1-thiol: evidence for intramolecular S-H...pi hydrogen bonding

The microwave spectrum of 3-butyne-1-thiol has been studied by means of Stark-modulation microwave spectroscopy and quantum-chemical calculations employing the B3LYP/6-311++G(3df,2pd), MP2/aug-cc-pVTZ, MP2/6-311++G(3df,2pd), and G3 methods. Rotational transitions attributable to two conformers of this molecule were assigned. One of these conformers possesses an antiperiplanar arrangement of the atoms S-C1-C2-C3, while the other is synclinal and stabilized by the formation of an intramolecular hydrogen bond between the H-atom of the thiol group and the pi-electrons of the C[triple bond]C triple bond. The energy difference between these conformers was estimated to be 1.7(4) kJ mol(-1) by relative intensity measurements, with the hydrogen-bonded conformer being lower in energy. The spectra of five vibrationally excited states of the synclinal conformer were observed, and an assignment of these states to particular vibrational modes was made with the aid of a density functional theory (DFT) calculation of the vibrational frequencies at the B3LYP/6-311++G(3df,2pd) level of theory.     

Intramolecular hydrogen bonding in 3‐imino‐propenylamine: Theoretical investigations

Intramolecular H‐bonds existing for derivatives of 3‐imino‐propenylamine have been studied using the B3LYP/6‐311++G** level of theory. The nature of these interactions, known as resonance‐assisted hydrogen bonds, has been discussed. Vibrational frequencies for α‐derivatives were calculated at the same level of theory. The topological properties of the electron density distributions for N? H···N intramolecular bridges have been analyzed in terms of the Bader theory of atoms in molecules (AIM). Calculation for 3‐imino‐propenylamine derivatives in water solution were also carried out at B3LYP/6‐311++G** level of theory. Finally, the analysis of hydrogen bond in this molecule and their derivatives by quantum theory of natural bond orbital methods fairly support the ab initio results. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Theoretical study of molecular interactions of phosphorus ylide with HF, HCN, and HN3

The molecular interactions between phosphorous ylide (PY) and HX molecules (X?=?F, CN, and N₃) were investigated using the MP2 method at 6-311++G(2d,2p) basis set. Three different patterns including non-classical hydrogen bond H···C, X···P interaction and classical hydrogen bond H···X were found for complex formation between PY and HX molecules. From the predicted models, stability of the H···C type complexes are greater than other types. Quantum theories of atoms in molecules and natural bond orbitals methods have been applied to analyze the intermolecular interactions. Good correlations have been found between the interaction energies (SE), the second-order perturbation energy E ⁽²⁾, and the charge transfer qCT in the studied systems.     

Quantum-chemical study of compounds containing intramolecular O-H…O=C bond

New results of the study of stable intermediates containing an intramolecular hydrogen bond O-H…O=C in the gas phase and solvents, carbon tetrachloride and dioxane, were analyzed. The structural and energy characteristics of the stable conformers of these compounds were determined by a MR2/6-311++G(d, p) method. The most stable is the hydrogen-bonded conformer of 1-hydroxy-1-chloroethyl acetate molecule. The approaches to accounting for the effects of the O-H…O=C intramolecular hydrogen bonding on the molecules reactivity were discussed.     

Conformational analysis and rotation barriers of 2-aminoethanethiol and 2-aminoethanol: An ab initio study

All the possible rotamers of 2-aminoethanol and 2-amino-ethanethiol were fully optimized at the ab initio level using the 6–31G** basis with correlation energy inclusion and zero-point energy evaluation. Thirteen local minima for the former and 14 for the latter compound were found. In both molecules, the gauche′-gauche-gauche′ (g′Gg′) is the prevailing conformation, but in the sulfurated compound, it is accompanied by relevant percentages of other conformers, owing to the very low ΔE values. The stability of the g′Gg′ accommodation derives mainly from the presence of weak hydrogen bridges (O(SINGLE BOND)H···N and S(SINGLE BOND)H···N, respectively). The rotation barriers around the C(SINGLE BOND)C and C(SINGLE BOND)N bonds are higher than those around the C(SINGLE BOND)O and C(SINGLE BOND)S ones. © 1996 John Wiley & Sons, Inc.     

Study of metal ions (Na+, K+) interaction with different conformations of glycine molecule

Interaction of metal ions (Na⁺, K⁺) with different binding sites, such as amino nitrogen, hydroxyl oxygen, and carbonyl oxygen for all gaseous conformers of glycine molecule were investigated using Density Functional Theory (B3LYP/6‐311++G**, B3PW91/6‐311++G**) methods. It was found that the order of stability of the conformers was changed due to the binding of the metal ion. The relative energy values show that the 7p conformer is more stable than the 1p conformer when a metal ion binds with the carbonyl oxygen. The intensity of interaction on hydroxyl oxygen is very low due to the low basicity of hydroxyl oxygen. The binding affinities of the complexes were calculated using the thermochemical properties. The relative energy and chemical hardness values predicted the most stable complex. The calculated condensed Fukui functions predict the favorable reactive site among the three binding sites. It is concluded that the reactivity of each binding site varies for each conformation due to the presence of intramolecular hydrogen bonding. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

The Role of Intramolecular Hydrogen Bonds vs. Other Weak Interactions on the Conformation of Hyponitrous Acid and Its Mono- and Dithio-Derivatives

High level ab initio and density functional theory calculations have been carried out to investigate the relative stability of the different conformers of hyponitrous acid and its mono- and dithio-derivatives. Geometries and vibrational frequencies were obtained at the B3LYP/6-311+G(d,p) level and final energies through B3LYP/6-311++G(3df,2pd) single point calculations. The reliability of this theoretical scheme has been assessed by comparing these DFT results with those obtained at the G3 level of theory, for some suitable cases. The cis conformers of hyponitrous acid and its mono- and dithio-derivatives are systematically more stable than the trans ones because in the cis conformation a dative interaction between the nitrogen-lone pairs and the σ_NX^* antibonding orbital is significantly favored. Quite interestingly, in general, the conformers presenting an intramolecular hydrogen bond (IHB) are not the global minima of the corresponding potential energy surfaces and only for hyponitrous acid the conformer with a OH ⋅s O IHB is slightly more stable than the cis conformer without IHB. The low stability of the tautomers with IHB is closely related with another weak intramolecular interaction which involves the lone-pairs of the chalcogen atoms and the π_NN^* antibondig orbital, and which is significantly perturbed when the IHB is formed.     

Conformational studies of aliphatic secondary ozonides (propene, 1-butene and 1-heptene) by means of FTIR spectroscopy

Ozonization reaction of simple alkenes was studied by means of FT infrared absorption gas spectroscopy. The reaction was performed at 95 K in neat films of the reactants. IR absorption spectra of the gaseous products were recorded. The spectra were analyzed combining experimental results with theoretical calculations performed at B3LYP 6-311++G (3df, 3pd) level. We found that among all theoretically predicted conformers of propene secondary ozonide, only one which has the O-O half-chair configuration for the five membered ring and the radical attached in the equatorial position was present in the sample. Samples of 1-butene and 1-heptene secondary ozonides consist from two conformers of very similar energy (ΔH=0.3 kJ/mol). The most stable conformer for both ozonides is the one with O-O half-chair configuration of the five membered ring and the radical attached in equatorial position and the aliphatic chain in gauche position. The second stable conformer has the aliphatic chain in anti position.     

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.     

A conformational study of ethylene glycol

Ab initio calculations were performed for some different conformers of 1,2-ethanediol in order to reveal their relative energies. The equilibrium conformation is of gauche type with a comparatively weak intramolecular hydrogen bond. The energy of the all-trans conformer is 3 kcal/mol above the minimum.     

Electronic structures, intramolecular interactions, and aromaticity of substituted 1-(2-iminoethylidene) silan amine: a density functional study

The intramolecular hydrogen bond, molecular structure, π electrons delocalization, and vibrational frequencies in 1-(2-iminoethylidene) silan amine and its derivatives have been investigated by means of density functional method with 6-311++G** basis set, in gas phase, water, and carbon tetrachloride solutions. The obtained results showed that the hydrogen bond strength is mainly governed by resonance variations inside the chelate ring induced by the substituent groups. Furthermore, the topological properties of the electron density distributions for N–H···N intramolecular hydrogen bond were analyzed in terms of the Bader's theory of atoms in molecules. On the other hand, the aromaticity of the ring formed is 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, aromatic fluctuation index, and π-fluctuation aromatic index. Natural population analysis data, the electron density and Laplacian properties, as well as γ(NH) and ν(NH) were further used for estimation of the hydrogen bonding interactions and the forces driving their formation.     

Intramolecular hydrogen bonding in chemoselective synthesized 2-substituted pyrrole stable phosphorus ylide: GIAO, AIM, and NBO approaches

The chemoselectivity of geometrically ylide compounds is often hard to assign from experimental techniques, particular system with intramolecular hydrogen bonding (IHB) are even more challenging. Herein, theoretical calculations were performed to investigate whether theoretical results would provide consistent evidence for the existence of IHB to confirm experimental data and to evaluate strength of the N–H···O IHB from geometrical synthesized 2-substituted pyrrole stable phosphorus ylide (dimethyl 2-(1H-pyrrol-2-yl)-3-(triphenylphosphoranylidene) butanedioate in a single chemoselective compound. Topological parameters at the bond critical points (BCP) of intramolecular hydrogen bonds from Bader’s atoms in molecules (AIM) theory and Winhold’s natural bond orbital (NBO) calculations were analyzed at the B3LYP/6-311++g** level in details. A series of gage-including atomic orbital chemical shift (GIAO c.s.) calculations at the HF and DFT levels of theory were carried out to assign the ¹H NMR chemical shifts. The best prediction of the experimental ¹H NMR values was obtained at the mPW1PW91 levels using the 6-31G** basis set. Theoretical results, in agreement with the experimental data, were confirmed the N–H···O IHB was caused the deshielding of the proton to lower field. The barriers in double bond and single bond rotation were theoretically estimated in detailed and the AIM and NPA approaches were confirmed the loss of charge of the hydrogen atom involving in intramolecular N–H···O hydrogen bonding. The geometrical and topological parameters from AIM and NBO analyses were indicated the medium N–H···O IHB.     

Matrix isolation FT-IR spectroscopy and molecular orbital study of sarcosine methyl ester

N-methylglycine methyl ester (sarcosine-Me) has been studied by matrix isolation FT-IR spectroscopy and molecular orbital calculations undertaken at the DFT/B3LYP and MP2 levels of theory with the 6-311++G(d,p) and 6-31++G(d,p) basis set, respectively. Twelve different conformers were located in the potential energy surface of the studied compound, with the ASC conformer being the ground conformational state. This form is analogous to the dimethylglycine methyl ester most stable conformer and is characterized by a NH?O intramolecular hydrogen bond; in this form, the ester group assumes the cis configuration and the OC-C-N and Lp-N-C-C (where Lp is the nitrogen lone electron pair) dihedral angles are ca. −17.8 and 171.3°, respectively. The second most stable conformer (GSC) differs from the ASC conformer essentially in the conformation assumed by the methylamino group, which in this case is gauche (Lp-N-C-C dihedral angle equal to 79.4°). On the other hand, the third most stable conformer (AAC) differs from the most stable form in the conformation of the OC-C-N axis (151.4°). These three forms were predicted to differ in energy by less than ca. 5 kJ mol⁻¹ and represent ≈95% of the total conformational population at room temperature. FT-IR spectra were obtained for sarcosine-Me isolated in argon matrices revealing the presence in the matrices of the three lowest energy conformers predicted by the calculations. The matrices were prepared by deposition of the vapour of the compound using two different nozzle temperatures, 25 and 60 °C. The relative populations of the three conformers trapped in the matrices were found to be consistent with occurrence of conformational cooling during matrix deposition and with a stabilization of the most polar GSC and AAC conformers in the matrices compared to the gas phase. Indeed, like it was previously observed for the methyl ester of dimethylglycine [Phys. Chem. Chem. Phys. 5 (2003) 52] the different strength of the interactions between the conformers and the matrix environment seem to lead to a change in the relative order of stabilities of GSC and ASC upon going from the gas phase to the matrices, with the first conformer becoming the conformational ground state in the latter media. The assignment of the bands observed in the matrix spectra to the three experimentally observed conformers of sarcosine-Me is presented and discussed.     

Reinvestigation of intramolecular hydrogen bond in malonaldehyde derivatives: An ab initio,AIM and NBO study

The RAHB systems in malonaldehyde and its derivatives at MP2/ 6‐311++G(d,p) level of theory were studied and their intramolecular hydrogen bond energies by using the related rotamers method was obtained. The topological properties of electron density distribution in O? H···O intramolecular hydrogen bond have been analyzed in term of quantum theory of atoms in molecules (QTAIM). Correlations between the H‐bond strength and topological parameters are probed. The results of QTAIM clearly showed that the linear correlation between the electron density distribution at HB critical point and RAHB ring critical point with the corresponding hydrogen bond energies was obtained. Moreover, it was found a linear correlation between the electronic potential energy density, V(r_cp), and hydrogen bond energy which can be used as a simple equation for evaluation of HB energy in complex RAHB systems. Finally, the similar linear treatment between the geometrical parameters, such as O···O or O? H distance, and Lp(O)→σ*_OH charge transfer energy with the intramolecular hydrogen bond energy is observed. © 2010 Wiley Periodicals, Inc., Int J Quantum Chem, 2011     

Computational studies on the conformational preference of N-(Thiazol-2-yl) benzamide

N-(Thiazol-2-yl) benzamide 1 substructures are found in some of bioactive compounds. In some of protein/ligand co-crystals, the 1 moiety adopts a conformer in which the amide O and the thiazole S atoms are close. In fact, in the crystalline structure of 1 , the O—S distance is even shorter than Van der Waals radius. Although the natural bond orbital analysis finds a weak stabilizing interaction between O and S atoms, the attractive dipole–dipole interaction between the amide N─H and thiazole N atom seems to play a more significant role. Moreover, an intramolecular O—H hydrogen bonding in dimeric forms found to have an important role in the conformation preference of 1 . Computational details for the stability of conformers have been discussed using quantum theory of atoms in molecules, natural bond orbital (NBO) and noncovalent interaction index analysis.     

INTRAMOLECULAR OH···S HYDROGEN BONDS AND MOLECULAR CONFORMATIONS IN 2-METHYLMERCAPTOETHANOL

Abstract

The infrared absorption spectrum of monomeric 2-methylmercaptoethanol in dilute CC1₄, solution exhibits four overlapped bands in the fundamental OH stretching region. The individual band components were resolved using digital computing techniques [1], and the relative band intensities are temperature dependent. The “free” OH bands at 3634 and 3623 cm correspond to gauche and trans orientations about the C-O bond, respectively, by analogy with similar band components in the infrared spectrum of ethanol in dilute CC1₄, solution. The OH bands at 3539 and 3446 cm^?1 are assigned to gGt and gGg¹ conformers, respectively, each involving an intramolecular OH···S hydrogen bond (conformer notation refers to the orientation about the C-O, C-C and C-S(CH₃) bonds, respectively). A similar interpretation of the matrix isolated infrared spectra of ethylene glycol, involving two conformers with intramolecular OH···O hydrogen bonds and differing principally in the orientation of the proton-acceptor OH group, has been presented recently [2]. The microwave spectrum of 2-mercaptoethanol in the vapour phase arises from an all-gauche conformation with an intramolecular OH···S hydrogen bond [3].     

Theoretical study of molecular interactions of sulfur ylide with HF, HCN, and HN3

The molecular interactions between sulfur ylide (SY) and HX molecules (X = F, CN, and N₃) were investigated using the MP2 method at 6-311++G(2d,2p) basis set. Three different patterns including non-classical hydrogen bond (HB) H···C and classical HB H···X were found for complex formation between SY and HX molecules. Stability of the H···C type complexes are greater than H···X complexes. Quantum theories of atoms in molecules, natural bond orbitals, and energy decomposition analysis methods have been applied to analyze the intermolecular interactions. Good correlations have been found between the interaction energies (SE), the second-order perturbation energy E ⁽²⁾ and the charge transfer qCT in the studied systems.     

Conformational Analysis of N-Alkyl-N-[2-(diphenylphosphoryl)ethyl]amides of Diphenylphosphorylacetic Acid: Dipole Moments,IR Spectroscopy,DFT Study

Experimental and theoretical conformational analysis of N-methyl-N-[2-(diphenylphosphoryl)ethyl]diphenylphosphorylacetamide, N-butyl-N-[2-(diphenylphosphoryl)ethyl]diphenylphosphorylacetamide, and N-octyl-N-[2-(diphenylphosphoryl)ethyl]diphenylphosphorylacetamide was carried out by the methods of dipole moments, IR spectroscopy, and Density Functional Theory (DFT) B3PW91/6-311++G(df,p) calculations. In solution, these N,N-dialkyl substituted bisphosphorylated acetamides exist as a conformational equilibrium of several forms divided into two groups—with Z- or E-configuration of the carbonyl group and alkyl substituent, and syn or anti arrangement of the phosphoryl-containing fragments relative to the amide plane. The substituents at the phosphorus atoms have eclipsed cis- or staggered gauche-orientation relative to the P=O groups, and cis orientation of the substituents is due to the presence of intramolecular H-contacts P=O...H−C_phenyl or p,π conjugation between the phosphoryl group and the phenyl ring. Preferred conformers of acetamides molecules are additionally stabilized by various intramolecular hydrogen contacts with the participation of oxygen atoms of the P=O or C=O groups and hydrogen atoms of the methylene and ethylene bridges, alkyl substituents, and phenyl rings. However, steric factors, such as a flat amide fragment, the bulky phenyl groups, and the configuration of alkyl bridges, make a significant contribution to the realization of preferred conformers.