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

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

β‐Aminoacrolein: An ab initio,AIM and NBO study

The molecular structure and the intramolecular hydrogen bonding of β‐aminoacrolein and its simple derivatives were investigated at the MP2 and B3LYP levels of theory using the standard 6‐311++G(d, p) basis set. The “atoms in molecules” or AIM theory of Bader which is based on topological properties of the electron density (ρ), was used. Additionally, an analysis of the critical points was performed to study the nature hydrogen bonding in these systems. Natural bond orbital (NBO) analysis was also carried out for to better comprehend the nature of the intramolecular interactions in β‐aminoacrolein and its derivatives. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

The effect of spiroadamantane substitution on the conformational preferences of N-Me pyrrolidine and N-Me piperidine: a description based on dynamic NMR spectroscopy and ab initio correlated calculations

Dynamic NMR spectroscopy and ab initio correlated calculations revealed that the attachment of a spiroadamantane entity at the C-2 position of N-methylpyrrolidine or N-methylpiperidine induces a severe steric crowding around nitrogen, which changes the conformational space of the heterocycle resulting in: (a) the complete destabilization of the N-Me(eq) conformer in spiranic structures; in contrast the N-Me(eq) conformer corresponds to the global minimum in N-methylpyrrolidine or N-methylpiperidine. The spiroadamantane structure raises the energy of the equatorial conformer because of the severe van der Waals repulsion between the N-Me(eq) group and adamantane C-H bonds. (b) The interconversion between the only populated enantiomeric N-Me(ax) conformers ax→[eq]→ax′; the interconversion eq→ax between N-Me(eq) and N-Me(ax) conformers, which are both populated, is observed in N-methylpyrrolidine or N-methylpiperidine. (c) The raising of ring and nitrogen inversion barriers ax→ts by ∼4-6 kcal mol⁻¹. The dynamic NMR study provides evidence that the most important process required for the enantiomerization between the axial N-Me conformers in spiropiperidine 4 and spiropyrrolidine 5 are different, i.e., a nitrogen inversion in 5 (9.10 kcal mol⁻¹) and a ring inversion in 4 (15.2 kcal mol⁻¹). While an enantiomerization interconverts N-Me axial conformers in spiropiperidine 5 and spiropyrrolidine 4, substitution of the pyrrolidine ring of 5 with a C-Me group effects a diastereomerization between two N-Me axial conformers and reduces effectively the nitrogen inversion barrier according to the protonation experiments and the calculations. In general, all the calculations levels used, i.e., the MM3, B3LYP/6-31+G^∗∗ and MP2/6-311++G^∗∗//B3LYP/6-31+G^∗∗, predict correctly the different stability of the local minima; however only MP2/6-311++G^∗∗//B3LYP/6-31+G^∗∗ was found to be reliable for the calculation of the nitrogen inversion barriers.     

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     

Comparison of epimeric methyl lithocholate and methyl iso-lithocholate molecules: single crystal X-ray structure of methyl lithocholate, ab initio HF/6-31G* optimized structures and experimental and calculated DFT/B3LYP C NMR chemical shifts

¹³C NMR chemical shifts have been measured and assigned for epimeric methyl 3α/β-hydroxy-5β-cholan-24-oates (methyl lithocholate [3α-OH epimer] and methyl iso-lithocholate [3β-OH epimer]). Their molecular dynamics simulations suggest that for both epimers there exists two predominant gas phase conformations, which have been further forwarded for ab initio/HF optimizations and DFT/GIAO based ¹³C NMR chemical shift calculations. Excellent linear relationships have been observed between experimental and calculated ¹³C NMR chemical shifts for both epimers. For methyl lithocholate (MeLC), the other minimum energy conformation equates very well with the single crystal X-ray structure (orthorhombic, space group P2₁2₁2₁, unit cell ). The crystalline packing of MeLC consists of continuous parallel intermolecular hydrogen bonded [3α-OH?OC24] head-to-tail polymeric chains, which are further cross-linked by many simultaneous weak C(sp³)H?O-type of interactions.     

Theoretical calculations of hypersurfaces of the C chemical shift anisotropy in the COHN hydrogen bond and the benefit for the ab initio structure determination

We investigated the influence of structural changes on the anisotropic part of the carbonyl ¹³C chemical shift tensor in a model complex containing hydrogen bonded cyanuric acid and pyrrole. The model was chosen for its chemical resemblance to cyameluric acid. In the solid state this compound comprises three different hydrogen bonds which are well distinguishable based on the anisotropy parameters δ_aniso and η of the carbonyl ¹³C atoms. The variation of six relevant structural variables in the model system produced hypersurfaces for the isotropic shift, δ_aniso and η. Our goal was to investigate whether such surfaces can be used for the ab initio structure determination of hydrogen bonds. With a medium size basis set it could be shown that although the absolute values differ DFT describes the relative change in δ_aniso and η close to the quality of MP2 calculations. Due to the high dimensionality of the hypersurface we had to reduce the number of variables in our study. We systematically created subsurfaces each described by three of the six variables and investigated their isolated influence on the NMR observables. We identified the most important structure parameters and on this base built a minimal model. For a fixed NO distance the hydrogen bond arrangement was altered by two angular variations and one dihedral distortion. In this model evidence was found that the η surfaces for different NO distances exhibit a uniform shape and can be transformed into one another by a simple shift and multiplication by a mean factor. Furthermore, the experimental parameters δ_aniso and η of cyameluric acid were taken as a base for the extraction of structures from the hypersurfaces. δ_aniso and η unequivocally selected ensembles of similar structure and the COHN arrangement in two of the three cyameluric hydrogen bonds could be predicted with good quality from the theoretical model. Our results show that it is possible to predict the distance and at least qualitatively the orientation in a hydrogen bond environment from an analysis of the anisotropic part of the ¹³C chemical shift tensor.     

DFT and NBO theoretical study of protonation of tri-tert-butoxysilanethiol and its anion

Density functional theory (DFT) calculations of geometry optimization at the B3LYP/6-31+G(d) level have been made for the tri-tert-butoxysilanethiolato anion, i.e. (^tBuO)₃SiS⁻ [coded A], and its O- and S-protonated derivatives: (^tBuO)₃SiSH (B), (^tBuO⁺H)(^tBuO)₂SiS⁻ (C), (^tBuO)₃SiSH₂⁺ (D) and (^tBuO⁺H)(^tBuO)₂SiSH (E). Energy balances for the protonation of silanethiol B in vacuum and the aqueous phase (using the polarized continuum IPCM model) were considered. Based on theoretical calculations, it was found that protonation on the oxygen atom causes Si–S bond shortening, while protonation on the sulfur atoms results in elongation of the bond. Changeability of the Si–S and Si–O bond lengths was analyzed in terms of the natural bond orbital (NBO) method. Principal electronic delocalizations caused by anomeric effects of the sulfur and oxygen lone pairs interaction with the anti-bonding Si–O orbitals were confirmed by the correlation between the shortening of the Si–S bond length and the elongation of the Si–O bond within the structures of the species A–E.     

DFT and ab initio theoretical study for the CF3S + CO reaction

The potential energy surface for the reaction of CF₃S with CO is calculated at the G4//B3LYP/6-311++G(d,p) level of theory. The results show that F-abstraction and addition-elimination mechanisms are involved, and the latter one is dominant thermodynamically and kinetically. The dominant channel is the reactant addition to form CF₃SCO, and then decomposes to CF₃ + OCS. While the direct F-abstraction channel and CF₃SCO isomerization channel are not significant for the title reaction due to higher barriers involved. The comparisons among four reactions of CX₃Y + CO (X = H, F; and Y = O, S) are made to imply the similar and different properties and reactivities of the same family elements and the F- and S-substituted derivatives.     

Why N-methyleneformamide, CH2N–CHO, prefers gauche-conformation? A DFT/NBO study

Three possible stable conformations of N-methyleneformamide were studied using Weinhold's Natural bond orbital method. Wavefunctions for the NBO analysis were obtained using B3LYP hybrid functional with 6-311+G(d,p) extended basis set. gauche conformation was predicted to be more stable than trans conformation by ≈2.3 kcal/mol in agreement with earlier studies. At the same time it was found that this preference is due to the strong π_C1–N2↔π_C3–O4 and σ_C3–H5↔n_σN2 repulsive interactions in the planar conformations, and additional conjugative stabilization of the gauche conformation.     

Search of structure and ligands exchange for palladium(II) complexes with N-allylimidazole; X-ray and solid-state/solution NMR studies

Two coordination compounds of palladium(II) with N-allylimidazole (l) of the general formula [PdL₄]Cl₂ · 3H₂O (1) and trans-[PdL₂Cl₂] (2) have been synthesized. The crystal and molecular structure of complexes 1 and 2 was established by single-crystal X-ray diffraction analysis. The X-ray structural data were supplemented by solid-state ¹³C NMR measurements (CP MAS and PASS 2D). The 1D and 2D NMR studies in solution reveal that complex 1 is unstable at room temperature and undergoes reversible decomposition to 2. The method for how to preserve a complex with four allyl-imidazole ligands in solution is shown.     

Intramolecular hydrogen bonds in the sulfonamide derivatives of oxamide, dithiooxamide, and biuret. FT-IR and DFT study, AIM and NBO analysis

The hydrogen bonding in [(1-arylsulfonylamino-2,2,2-trichloro)ethyl]biuret 1, [(1-arylsulfonylamino-2,2,2-trichloro)ethyl]oxamide 2, and [(1-arylsulfonylamino-2,2,2-trichloro)ethyl]dithiooxamide 3, the sulfonamide derivatives of biuret 4, oxamide 5, and dithiooxamide 6, has been studied by molecular spectroscopy and DFT theoretical calculations including frequency calculations, at the B3LYP/6-311+G(d,p) level of theory. The analysis of the CO?HN and CS?HN intramolecular hydrogen bonds closing the five- and six-membered rings employing the atoms-in-molecules (AIM) method using the MP2(full)/6-311++G(d,p) wave functions has shown that their stability is increased in comparison to the original molecules and is much higher in the thiocarbonyl compounds. The results of the AIM and the NBO analysis of donor-acceptor interactions are in good agreement with each other and with the experimental FT-IR spectroscopy data.     

Study of hydrogen bonds in N-methylacetamide by DFT calculations of oxygen, nitrogen, and hydrogen solid-state NMR parameters

Solid-state nuclear magnetic resonance (NMR) parameters of ¹⁷O, ¹⁴N/¹⁵N, and ²H/¹H nuclei were evaluated in two available neutron crystalline structures of N-methylacetamide (NMA) at 250 and 276 K, NMA-I and NMA-II, respectively. Density functional theory calculations were performed by B3LYP method and 6-311++G** and IGLO-II type basis sets to calculate the electric field gradient (EFG) and chemical shielding (CS) tensors at the sites of mentioned nuclei. In order to investigate hydrogen bonds (HBs) effects on NMR tensors, calculations were performed on four-model systems of NMA: an optimized isolated gas-phase, crystalline monomers, crystalline dimers, and crystalline trimers. Comparing the calculated results reveal the influence of N–H···O=C and C–H···O=C HB types on the NMR tensors which are observable by the evaluated parameters including quadrupole coupling constant, C _Q, and isotropic CS, σ _iso. Furthermore, the results demonstrate more influence of HB on the EFG and CS tensors of NMA at 276 K rather than that of 250 K.     

Mercury(II) cyanide complexes with alkyldiamines: solid-state/solution NMR,computational, and antimicrobial studies

Mercury cyanide complexes of alkyldiamines (1–6), [Hg(L)(CN)₂] (where L?=?en (1,2-diaminoethane), pn (1,3-diaminopropane), N-Me-en, N, N′-Me₂-en, N, N′-Et₂-en, and N, N′-ipr₂-en), have been synthesized and characterized by elemental analysis, IR, ¹³C, and ¹⁵N solution NMR in DMSO-d₆, as well as ¹³C, ¹⁵N, and ¹⁹⁹Hg solid-state NMR spectroscopy. Complexes 1 and 2 have been studied computationally, built and optimized by GAUSSIAN03 using DFT at B3LYP level with LanL2DZ basis set. Binding modes of en and bn (where bn?=?1,4-diaminobutane) toward Hg(CN)₂ are completely different. Complexes with en and pn show chelating binding to Hg(II), while bn behaves as a bridging ligand to form a polymeric structure, [Hg(CN)₂-bn]_∞ [B.A. Al-Maythalony, M. Fettouhi, M.I.M. Wazeer, A.A. Isab. Inorg. Chem. Commun., 12, 540 (2009).]. The solution ¹³C NMR of the complexes demonstrates a slight shift of the ?C≡N (0.9 to 2?ppm) and ?C–NH₂ (0.25 to 6?ppm) carbon resonances, while the other resonances are relatively unaffected. ¹⁵N labeling studies have shown involvement of alkyldiamine ligands in coordination to the metal. The principal components of the ¹³C, ¹⁵N, and ¹⁹⁹Hg shielding tensors have been determined from solid-state NMR data. Antimicrobial activity studies show that the complexes exhibit higher antibacterial activities toward various microorganisms than Hg(CN)₂.     

The spectroscopic (FT-IR, FT-Raman), NCA, first order hyperpolarizability, NBO analysis, HOMO and LUMO analysis of L-cysteine by ab inito HF and density functional method

In this work, we report a combined experimental and theoretical study on molecular structure (monomer, dimer), vibrational spectra, and Natural Bond Orbital (NBO) analysis of non-ionized L-cysteine (LCY). The FT-IR solid phase (4000-400 cm(-1)) and FT-Raman spectra (3500-50 cm(-1)) of LCY was recorded at room temperature. The molecular geometry, harmonic and anharmonic vibrational frequencies and bonding features of LCY in the ground state have been calculated by using the density functional method (B3LYP) with 6-311G(d,p) as basis set. The assignments of the vibrational spectra have been carried out with the help of normal co-ordinate analysis (NCA) following the Scaled Quantum Mechanical Force Field (SQMFF) methodology. The first order hyperpolarizability (β(0)) of this novel molecular system and related properties (β, α(0) and Δα) of LCY are calculated using HF/6-311G(d,p) method on the finite-field approach. Stability of the molecule has been analyzed using NBO analysis. The calculated first hyperpolarizability shows that the molecule is an attractive molecule for future applications in non-linear optics. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. Finally the calculations results were applied to stimulate infrared and Raman spectra of the title compound which show good agreement with observed spectra.     

The first N,N′-ditosyl-substituted cyclic boron cation, stabilized by neighboring-group participation by two sulfonyl groups, and the alternative, stabilized by polar solvents

When 2-bromo-1,3-ditosyl-1,3,2-diazaborolidine was treated with AgSbF₆, a novel cyclic boron cation was formed in CD₂Cl₂, the ¹¹B NMR chemical shift of which appeared at 8.7 ppm. Ab initio calculations were consistent with the cationic boron center being stabilized by neighboring-group participation of the two sulfonyl functions. The reaction in CD₃NO₂ resulted in an alternate formation of a cyclic boron cation species (16.2 ppm), stabilized by coordination to the basic solvents.     

Thermochromism in nickel(II) complexes: thermal, solid state H NMR and single crystal X-ray analysis of bis-(N,N-dimethyl-1,2-ethanediamine) nickel(II) perchlorate

The complex bis-(N,N-dimethyl-1,2-ethanediamine) nickel(II) perchlorate undergoes a first-order thermochromic phase transition at ca. 476 K, changing its color from orange to red. The room temperature X-ray crystal structure determination showed that the nickel ion possesses a square-planar geometry with two five membered chelate rings, in the δλ conformation, forming the NiN₄ chromophore. The broad-line ¹H NMR indicates the onset of a dynamic disorder of diamine chelate rings at the phase transition temperature region, while T₁ measurement of ¹H affords the activation energy of the puckering metal chelate rings to be 26 kJ mol⁻¹. The electronic spectrum revealed that a weakening of ligand field around the nickel is associated with the phase transition.     

Experimental and theoretical study of N-(2-hydroxyethyl)morpholine betaine

N-(2-hydroxyethyl)morpholine betaine (HEMB) has been characterized by a single crystal X-ray analysis, FTIR spectroscopy and DFT calculations. The crystals are monoclinic, space group P2₁/c with a=10.273(2), b=9.360(2), c=9.447(2) Å and β=104.72(3)Å. Two molecules of HEMB form a centrosymmetric dimer (X2) connected by a pair of hydrogen bonds between the CH₂CH₂OH and COO⁻ groups, with the O?O distance of 2.672(2) Å. The morpholine ring adopts a chair conformation with the CH₂CH₂OH group in the axial and the CH₂COO⁻ group in the equatorial position. The structures of the dimer, B2, and two monomers, B1a and B1b, have been optimized by the B3LYP approach using the 6-31G(d,p) basis set. The computed structure of B2, agrees well with the experimental X2. From two stable monomeric conformers the more favored is B1a, with the intramolecular hydrogen bond with the O-H?O distance of 2.566 Å. The effects of hydrogen bonding and electrostatic interactions on the conformation of the molecules investigated have been discussed. The FTIR spectrum shows a broad absorption in the 3300-2600 cm⁻¹ region, typical of moderate O-H?O hydrogen bonds.     

Invertomers at nitrogen in aziridine carboxylates by mltltinuclear (1H,13C,17O,and15N) NMR study

A confrgurational and conformational study of NH, N-acetyl- and N-sulfonylaziridine carboxylates is performed by¹H ,¹³C,¹⁷O, and¹⁵N NMR spectroscopy. The presence of acetyl and su fonyl groups on the ring nitrogen atom seems to reduce greatly the configurational stability at nitrogen.Published in Khimiya Geterotsiklicheskikh Soedinenii, No. 9, pp. 1226–1234, September, 1995.