Molecular and crystal structures of N,N′-propylene- and N,N′-phenylene-diylbis [3-(1-aminoethyl)-6-methyl-2H-pyran-2,4(3H)-dione]

Two macrocyclic ligands, N,N′-propylene-diylbis[3-(1-aminoethyl)-6-methyl-2H-pyran-2,4(3H)-dione] I and N,N′-phenylene-diylbis[3-(1-aminoethyl)-6-methyl-2H-pyran-2,4(3H)-dione] II, have been prepared by the condensation of dehydroacetic acid (3-acetyl-4-hydroxy-6-methyl-2H-pyran-2-one) with 1,2-phenylenediamine and 1,3-propylenediamine. They have been characterized by means of elemental analysis, IR spectroscopy as well as by X-ray crystallography. The molecular structures of the compounds I and II can be described as consisting of two β-enaminone-2-pyrone rings interlaced with either alkyl chain in I or phenyl ring in II. The X-ray studies confirmed the existence of strong N–HO intramolecular hydrogen bonds in both structures. Their lengths are in accordance to lengths of RAHB intramolecular hydrogen bonds in 1,3-diketones, aryl-hydrazones, β-enaminones and related heterodienes (2.5–2.6 Å) [P. Gilli, V. Bertolasi, V. Ferretti and G. Gilli, J. Am. Chem. Soc., 122 (2000) 10405].     

Intramolecular hydrogen bonds with large proton polarizability in semisalts of mono- and di-N-oxides of N,N′-tetraalkyl-o-xylyldiamines

Heteroconjugated NO⁺H … N NO … H⁺N and homoconjugated NO⁺H … ON NO … H⁺ON intramolecular hydrogen bonds formed in semisalts of mono- and di-N-oxides of N,N′-tetraalkyl-o-xylyldiamines were studied by IR and NMR spectroscopy. All these hydrogen bonds show large proton polarizability. In the case of the heteroconjugated hydrogen bonds the proton transfer equilibrium shifts from compounds 1 to 3 to the left hand side since the interaction of the hydrogen bond with the solvent environment decreases in this series of compounds. With compound 1 the hydrogen bonds are slightly weaker and longer, hence the wavenumber dependence of the intensity of the continuum caused by these hydrogen bonds is slightly changed with compound 1 compared with compound 2. In the case of compound 3 the intensity of the continuum decreases because of increasing screening of the hydrogen bonds. In the series of homoconjugated hydrogen bonds, from compound 4 to 6 the intense continuum vanishes, and only the band of the 0–1 proton transition at 950 cm⁻¹ remains. The vanishing of the continuum is caused by increasing screening of the hydrogen bonds against their solvent environments by bulky groups, and thus, this change demonstrates again that the interaction of the hydrogen bond with large proton polarizabilities is a necessary prerequisite for IR continua to appear.     

Molecular structure and vibrational spectra of N-mesylhydroxylamin and N-mesyl-O-methylhydroxylamin by density functional theory and ab initio Hartree–Fock calculations

The molecular geometry and vibrational frequencies of N-mesylhydroxylamin (N-MHN) and N-mesyl-O-methylhydroxylamin (N-MMHN) in the ground state have been calculated using the Hartree–Fock and density functional method (B3LYP) with 6-31G(d) basis set. The optimized geometric band lengths and bond angles obtained by using HF and DFT (B3LYP) show the best agreement with the experimental data. Comparison of the observed fundamental vibrational frequencies of N-MHN and N-MMHN and calculated results by density functional B3LYP and Hartree–Fock methods indicate that B3LYP is superior to the scaled Hartree–Fock approach for molecular vibrational problems.     

Structural and spectral studies on N-(4-chloro)benzoyl-N′-(4-tolyl)thiourea

The crystal and molecular structure of the N-(4-chloro)benzoyl-N′-(4-tolyl)thiourea (C₁₅H₁₃N₂OSCl, M_r=304.79) is determined by X-ray diffraction. The crystal structure is monoclinic, space group: P2₁/n, a=16.097(6), b=4.5989(2), c=19.388(7) Å and β=89.299(6)° V=1434.7(9)ų, Z=4. FTIR and NMR spectra have been characterized. The interactions of intramolecular and intermolecular hydrogen bonds have been discussed. Density functional theory (DFT) (B3LYP) methods have been used to determine the structure and energies of stable conformers. Minimum energy conformations are calculated as a function of the torsion angle θ (C13–N1–C14–N2) varied every 30°. The optimized geometry corresponding to crystal structure is the most stable conformation. This has partly been attributed to intramolecular hydrogen bonds. With the basis sets of the 6-311G* quality, the DFT calculated bond parameters and harmonic vibrations are predicted in a very good agreement with experimental data.     

Spectroscopic characterization and single molecule structures of N,N-bis-(3-phthalimidopropyl)-N-(2-hydroxyethyl)-N-propylammonium salts and their hydrates

N,N-Bis-(3-phthalimidopropyl)-N-(2-hydroxyethyl)-N-propylammonium salts and their hydrates have been characterized by FTIR, Raman and NMR spectroscopy. Also B3LYP and PM5 calculations have been carried out. The optimized bond lengths, bond angles and torsion angles calculated by B3LYP/6-31G(d,p) approach have been compared with the spectroscopic data. The screening constants for ¹³C and ¹H atoms have been calculated by the GIAO/B3LYP/6-31G(d,p) approach and analyzed. Linear correlations between the experimental ¹H and ¹³C chemical shifts and the computed screening constants confirm the optimized geometry.     

Photochemical reactions of electron-deficient olefins with N,N,N′,N′-tetramethylbenzidine via photoinduced electron-transfer

Photoinduced electron transfer reactions of several electron-deficient olefins with N,N,N′,N′-tetramethylbenzidine (TMB) in acetonitrile solution have been studied by using laser flash photolysis technique and steady-state fluorescence quenching method. Laser pulse excitation of TMB yields ³TMB* after rapid intersystem crossing from ¹TMB*. The triplet which located at 480 nm is found to undergo fast quenching with the electron acceptors fumaronitrile (FN), dimethyl fumarate (DMF), diethyl fumarate (DEF), cinnamonitrile (CN), -acetoxyacrylonitrile (AAN), crotononitrile (CrN) and 3-methoxyacrylonitrile (MAN). Substituents binding to olefin molecule own different electron-donating/withdrawing powers, which determine the electron-deficient property (π-cloud density) of olefin molecule as well as control the electron transfer rate constant directly. The detection of ion radical intermediates in the photolysis reactions confirms the proposed electron transfer mechanism, as expected from thermodynamics. The quenching rate constants of triplet TMB by these olefins have been determined at 510 nm to avoid the disturbance of formed TMB cation radical around 475 nm. All the values approach or reach to the diffusion-controlled limit. In addition, fluorescence quenching rate constants have been also obtained by calculating with Stern–Volmer equation. A correlation between experimental electron transfer rate constants and free energy changes has been explained by Marcus theory of adiabatic outer-sphere electron transfer. Disharmonic k_q values for CN and CrN in endergonic region may be the disturbance of exciplexs formation.     

Density functional and multiphoton ionization studies of N,N-dimethylformamide–(methanol)n clusters

The multiphoton ionization of the hydrogen-bonded clusters N,N-dimethylformamide–(methanol)_n (DMF–(CH₃OH)_n) was studied using a time-of-flight mass spectrometer at the wavelengths of 355 and 532 nm. At both wavelengths, a series of protonated DMF–(CH₃OH)_nH⁺ ions was obtained. The clusters were also investigated by density functional theory B3LYP method in conjunction with basis sets 6-31+G(d,p) and 6-311+G(2d,p). Equilibrium geometries of both neutral and ionic DMF–CH₃OH clusters, and dissociation channels and dissociation energies of the ionic clusters are presented. The results show that when DMF–CH₃OH is vertically ionized and dissociated, DMFH⁺ and CH₃O are the dominant products via proton transfer reaction. A high energy barrier makes another channel corresponding to the production of DMFH⁺ and CH₂OH disfavored. In the DMF–(CH₃OH)H⁺ ion, the proton prefers to link with the O atom of DMF molecule. Variation of atomic charges during proton transfer in hydrogen bond of the protonated cluster DMF–(CH₃OH)H⁺ ion is also discussed.     

On the reduced form of (imidazole-N)(N-salicylidene-alaninato-O,N,O′) copper(II)

The geometries of the (imidazole-N³)(N-salicylidene-alaninato-O,N,O′) copper(II) and of its anion as well as of six models of its neutral hydrogenated form with the additional hydrogen at oxygen or nitrogen sites modeling its reduced copper(I) form are optimized using the gaussian 98 program package at B3LYP/6-31G* level of theory. Energy data indicate the highest stability of the structures with additional hydrogen bonded to some of carboxyl oxygens with released (or significantly weakened) Cu–O(carboxyl) bond. Hydrogen atom is inserted into this bond in the second most stable model system (with ca. 1 kJ/mol higher energy).     

Quantitative analysis of transport process of cerium(III) ion through polymer inclusion membrane containing N,N,N′,N′-tetraoctyl-3-oxapentanediamide (TODGA) as carrier

The facilitated transport mechanism of cerium(III) ions through polymer inclusion membrane (PIM) consisting of cellulose triacetate (CTA) as a polymer matrix, 2-nitrophenyl n-octyl ether (NPOE) as a solvent and N,N,N′,N′-tetraoctyl-3-oxapentanediamide (TODGA) as a carrier was studied. In order to evaluate the mass transport phenomena in the PIM, a mathematical model was derived from the Fick's first law and the equations for the extraction and the material balance. Methods to determine the values of the transport parameters such as the diffusion coefficient are described, and the dependency of the flux on the experimental condition was calculated. The model is very useful as a design tool to analyze and optimize the concentration process of low level radioactive wastewater using the PIM.     

Photochemistry of N-acetyl and N-benzoyl carbazoles: photo-Fries rearrangement and photoinduced single electron transfer

The photochemistry of two N-acyl carbazoles, N-acetyl and N-benzoyl carbazole, in different pure and mixed organic solvents is studied. Depending on the properties of the medium, photo-Fries rearrangement and photoinduced single electron transfer (PSET) processes are observed yielding the former 1-acyl and 3-acyl carbazoles and the latter 3-chloro-N-acyl carbazole. k_SV, k_Q and φ for fluorescence emission, conversion of N-acyl carbazole and product formation yields have been measured as well as the properties of the N-acyl carbazole radical cations formed during the PSET process (laser flash photolysis experiments). The Rehm-Weller equation is used in order to evaluate the ΔG°_ET of the PSET processes.     

Intramolecular hydrogen bonds in canonical 2'-deoxyribonucleotides: an atoms in molecules study

The molecular structure and relative stability of different conformers of isolated canonical 2'-deoxyribonucleotides thymidine-5'-phosphate (pdT), 2-deoxycytidine-5'-phosphate (pdC), 2-deoxyadenosine-5'-phosphate (pdA), and 2'-deoxyguanosine-5'-phosphate (pdG) were calculated using the B3LYP/6-31++G(d,p) level of theory. The results of the calculations reveal that, for all nucleotides except pdG, conformers with a syn orientation of the base do not correspond to a minimum on the potential energy surface. In the case of pdA and pdC, conformers with an orthogonal orientation of the nucleobase are located instead, north/syn conformers. These conformers as well as syn conformers of pdG are stabilized by intramolecular N-H...O hydrogen bonds. Analysis of the electron density distribution within the atoms in molecules theory reveals the presence of numerous C-H...O hydrogen bonds in the nucleotides. However, a more detailed consideration of the properties of these bonds demonstrates that many of them should be considered as strong attractive electrostatic interactions rather than true hydrogen bonds. True hydrogen bonds are represented mainly by C6/ C8-H...O5'/O-P in anti conformers and the N-H...O-P bonds in syn conformers. It is demonstrated that the values of ellipticity of the electron density at the bond critical point (BCP) and the distance between BCP and ring critical point are the most reliable indicators for determining the true intramolecular hydrogen bonds.     

A new insight into the understanding of the collapsed form of poly(N-isopropylacrylamide) molecules

Possible collapsed forms of poly(N-isopropylacrylamide) molecules are reviewed on the basis of first principle calculations. Various configurations and associated conformations are detailed. The calculated optimized structures exhibit different possibilities of creating networks of intra-molecular bonds of the hydrogen type. We show that the most remarkable one is able to form a local, self-saturated and well ordered helix. We also indicate in which direction the synthesis of the molecule should be oriented to improve its global behavior in term of hydrophobic/hydrophilic behavior.     

Interpretation of hydrogen bonding in the weak and strong regions using conceptual DFT descriptors

Hydrogen bonding is among the most fundamental interactions in biology and chemistry, providing an extra stabilization of 1-40 kcal/mol to the molecular systems involved. This wide range of stabilization energy underlines the need for a general and comprehensive theory that will explain the formation of hydrogen bonds. While a simple electrostatic model is adequate to describe the bonding patterns in the weak and moderate hydrogen bond regimes, strong hydrogen bonds, on the other hand, require a more complete theory due to the appearance of covalent interactions. In this study, conceptual DFT tools such as local hardness, eta(r) and local softness, s(r), have been used in order to get an alternative view on solving this hydrogen-bonding puzzle as described by Gilli et al. [J. Mol. Struct. 2000, 552, 1]. A series of both homonuclear and heteronuclear resonance-assisted hydrogen bonds of the types O-H...N, N-H...O, N-H...N, and O-H...O with strength varying from weak to very strong have been studied. First of all, DeltaPA and DeltapK(a) values were calculated and correlated to the hydrogen bond energy. Then the electrostatic effects were examined as hard-hard interactions accessible through molecular electrostatic potential, natural population analysis (NPA) charge, and local hardness calculations. Finally, secondary soft-soft interaction effects were entered into the picture described by the local softness values, providing insight into the covalent character of the strong hydrogen bonds.     

Ab initio study of 1,1-(methylphosphinylidene) bis(methanamine) and vibrational assignment of its N,N′-coordinated Pt(II) and Pd(II) chloro complexes

Infrared and Raman spectra of 1,1-(methylphosphinylidene) bis(methanamine) [mpbm, (CH₃)PO(CH₂NH₂)₂] and its N,N′-coordinated Pt(II) and Pd(II) have been studied in the 4000–200 cm⁻¹ frequency range. Ab initio calculations have been carried out for different conformations of the mpbm at HF/6-31G* level of the theory from which structural parameters, conformational stability and predicted infrared and Raman spectra have been obtained. A complete vibrational assignment of the lowest energy conformer, tttg⁻, as well as of its N,N′-coordinated Pt(II) and Pd(II) chloro-complexes was done on the basis of the calculated frequencies, relative infrared intensities, Raman activities and potential energy distribution (PED). The theoretical predictions are compared with the experimental results where appropriate.     

Structural and spectral characterization of two 1-phenyl-1,2-propanedione bis{N(4)-alkylthiosemicarbazones}

1-phenyl-1,2-propanedione bis{N(4)-methyl- and {N(4)-ethylthiosemicarbazone}, H₂Pm4M and H₂Pm4E, respectively, have been prepared, studied spectroscopically (¹H NMR, ultraviolet and infrared) and their crystal structures solved. Intermoiety hydrogen bonding does not occur in H₂Pm4M and H₂Pm4E, in contrast to the analogous bis{N(4)-thiosemicarbazones} prepared from 1-phenylglyoxal. The two thiosemicarbazone moieties are on the opposite side of the carbon–carbon backbone, but the N(4)Hs intramolecularly hydrogen bond to the imine nitrogen for each moiety.     

Hydrogen‐bonded complexes of nicotine with simple alcohols

Ab initio and density functional theory studies have been performed on the hydrogen‐bonded complexes of neutral and protonated nicotine with ethanol, methanol, and trifluromethanol to explore their relative stability in a systematic way. Among all the hydrogen‐bonded nicotine complexes considered here, protonated forms in nicotine–ethanol and nicotine–methanol, and neutral form in nicotine–trifluromethanol complexes have been found to be the most stable. In the former two complexes, the proton attached to the pyrrolidine nitrogen acts as a strong hydrogen bond donor, whereas the pyrrolidine nitrogen atom acts as a hydrogen bond acceptor in the latter case. Neutral complex of nicotine with trifluromethanol has been found to possess a very short hydrogen bond (1.57 Å) and basis set superposition error corrected hydrogen bond energy value of 19 kcal/mol. The nature of the various hydrogen bonds formed has been investigated through topological aspects using Bader's atoms in molecules theory. From the calculated topological results, excellent linear correlation is shown to exist among the hydrogen bond length, electron density, and its Laplacian at the bond critical points for all the complexes considered. The natural bond orbital analysis has been carried out to investigate the charge transfer in the nicotine alcohol complexes. In contrast to the blue shifting behavior that is generally exhibited by other C? H···O hydrogen bonds involving sp³ carbon atom, the C? H···O hydrogen bond in the protonated nicotine–ethanol and methanol complexes has been found to be proper with red shifting in nature. © 2011 Wiley Periodicals, Inc.     

Electronic structure of N-sulfonylimines

The electronic structure of N-sulfonylimines has been studied in detail using ab initio MO and density functional methods. The S–N rotational barriers in HS(O)₂N=CH₂ at G2MP2 and CBS-Q levels have been found to be 3.25 and 3.43 kcal/mol respectively. Complete optimization at HF/6-31+G^*, MP2(full)/6-31+G^* and B3LYP/6-31+G^* levels have shown that synperiplanar arrangement of S–O with respect to C=N is more stable. NBO analysis has been carried out to quantitatively estimate these delocalisations and charge polarization in RS(O)₂N=CH₂ (R=H, Me, Cl, F). The Lewis basic character in N-sulfonylimines is less compared to N-alkylimines due to anomeric interactions that reduce the lone pair electron density on nitrogen in 1.     

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     

Excited state intramolecular charge transfer in N,N-heterocyclic-4-aminobenzonitriles: a DFT study

The excited state intramolecular charge transfer (ICT) reaction in a series of N,N-heterocyclic 4-aminobenzonitriles is investigated theoretically by a combination of density functional theory and multi-reference configuration interaction (DFT/MRCI). Experimentally, increasing ICT emission is observed with increasing ring size. Formation of both a planar and twisted ICT (PICT and TICT) state are energetically unfavorable in the small systems due to high inversion barriers. With increasing ring size, the TICT state is more stabilized than the PICT state. A good agreement of the computed TICT state dipole moment is found with experimental values. The red-shifted fluorescence of all systems is explained by the TICT model due to both arguments.     

Excited‐State Hydrogen Bonding Strengthening and Weakening with Intramolecular Charge Transfer in Resorufin‐Water Complexes: A TD‐DFT Study

The geometric structures, infrared spectra and hydrogen bond binding energies of the various hydrogen‐bonded Res^?‐water complexes in states S0 and S1 have been calculated using the density functional theory (DFT) and time‐dependent density functional theory (TD‐DFT) methods, respectively. Based on the changes of the hydrogen bond lengths and binding energies as well as the spectral shifts of the vibrational mode of the hydroxyl groups, it is demonstrated that hydrogen bonds HB‐II, HB‐III and HB‐IV are strengthened while hydrogen bond HB‐I is weakened in the four singly hydrogen‐bonded Res^?‐Water complexes upon photoexcitation. When the four hydrogen bonds are formed simultaneously between one resorufin anion and four water molecules in the Res^?‐4Water complex, all the hydrogen bonds are weakened in both the ground and excited states compared with those in the corresponding singly hydrogen‐bonded Res^?‐Water complexes. Furthermore, in complex Res^?‐4Water, hydrogen bonds HB‐II and HB‐IV are strengthened while hydrogen bonds HB‐I and HB‐III are weakened after the electronic excitation. The hydrogen bond strengthening and weakening in the various hydrogen‐bonded Res^?‐water complexes should be due to the redistribution of the charges among the four heteroatoms (O_1‐3 and N₁) within the resorufin molecule upon the optical excitation.