Interaction between RNA segment (adenine‐uracil) and model of protein unit (formamide): A density‐functional theory study

Various possible structures of adenine‐uracil‐formamide hydrogen‐bond complexes were optimized at 6‐311++G(d,p) level, and the binding energies of these complexes were also calculated at DFT B3LYP/6‐311++G(d,p) level. Eight stable cyclic structures being involved in the interaction are found on the potential energy surface. By analyzing the structure, NPA charge and interaction energy of complexes, we obtain the most stable geometry structure. The results show that the interactions between formamide and adenine‐uracil (A‐U) base pair affect the stabilities of the base pairs. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Theoretical study of hydrogen‐bonded complexes of benzene with hydrides of astrochemical interest

Post Hartree–Fock and DFT calculations have been performed for studying the possibility for a benzene support to be linked to various hydrides through a quasi Bz···H? A bond. Interaction energy of compounds, including C? H bonds (CH₄, CH₃F, CH₂O, CHN, CHN? O), N? H bonds (NH₃, NH₂F, NHC, NHCO, NH₃O), and O? H bonds (OH₂, OHF, NCOH), were evaluated, taking basis set superposition error (BSSE) and zero point vibrational energy (ZPVE) corrections into account. Numerical convergence of results with respect to the ingredients included at different steps of theory (basis set, DFT functionals, correlation treatments, geometry optimization) was tested mainly on the example of the water adduct and, for comparison, the Bz···H₃O⁺ system containing a cation instead of a neutral molecule. A rather large range of adsorption energies is obtained, from about 1 kcal/mol for methane to more than 6 kcal/mol for cyanic acid, according to the acidic character of the adsorbed species in each family of Bz···H? A bonds. Some consequences for astrophysical problems involving PAHs in the interstellar medium are pointed out. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Density functional theory study of the interaction between formamide and uracil

The hydrogen bonding of complexes formed between the formamide and uracil molecule has been fully investigated in the present study using the density functional theory (DFT) method at varied basis set levels from 6‐31G to 6‐311++G(d,p). Eight stable cyclic structures with two hydrogen bonds involved in the interaction are found on the potential energy surface (PES). The four structures are seven‐membered rings; the others are eight‐membered rings. The eight‐membered ring is preferred over the seven‐membered one by analyzing the hydrogen bond lengths and the interaction energies. The infrared (IR) spectrum frequencies, IR intensities, and the vibrational frequency shifts are reported. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Time‐dependent density functional theory study on the absorption spectrum of Coumarin 102 and its hydrogen‐bonded complexes

The effect of both solvent polarity and hydrogen bonding (HB) on the electronic transition energy of Coumarin 102 (C102) has been examined using the time‐dependent density functional theory (TDDFT). Solvent effect on both geometry and electronic transition energy is evaluated using the polarizable continuum model (PCM). A linear relation of the absorption maximum of C102 with the solvent polarity function Δf is found using the TDDFT‐PCM method for all solvents except dimethyl sulfoxide. The solvent polarity and the type B HB between the carbonyl oxygen and solvent hydrogen atom make the absorption wavelength redshift, whereas the type A HB between the amino nitrogen atom and solvent hydrogen atom has an opposite effect on the absorption wavelength. The calculated absorption wavelengths of C102 with two type B HB between the carbonyl oxygen and solvent hydrogen atom are in excellent agreement with experimental measurements. The solvatochromism of C102 is analyzed in terms of the Kamlet–Taft equation and the parameters s and a are discussed. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011.     

Density functional theory study of nitrogen‐14 nuclear quadrupole coupling parameters of L‐histidine: hydrogen‐bonded system

The calculations of nitrogen‐14 nuclear quadrupole parameters, nuclear quadrupole coupling constant, χ, and asymmetry parameter, η, of L‐His were done in two distinct environments: one as a free fully optimized molecule, an isolated molecule with the geometrical parameters taken from X‐ray, and the other in the orthorhombic and monoclinic solid states. The most probable interacting molecules with the central molecule in the crystalline phase were considered in the hexameric clusters to include hydrogen‐bonding effects in the calculations. The computations were performed with PW91P86/6‐31++G** and B3LYP6‐31++G** methods using the Gaussian 98 program. The good agreement between the nitrogen‐14 quadrupole parameters of the free His and imidazole molecules with their microwave available data demonstrates that the applied level of theory and the 6‐31++G** basis set are suitable to obtain reliable electric field gradient values. In the solid state, the shifts of quadrupole coupling parameters from the monomer to the solid phase are reasonably well reproduced for the amino and imino sites of imidazole ring in a hexameric cluster. That implies the fact that the hexameric cluster worked effectively to generate the results which are compatible with the experiment. The quadrupole coupling constant values of –N⁺H₃ group are in fair agreement with the experiment. This discrepancy is due to the absences of vibrational effects and the rotation of –N⁺H₃ group around N–C(α) bond. Copyright © 2012 John Wiley & Sons, Ltd.     

Density functional studies on hydrogen‐bonded clusters of hydrogen halides and the interaction on halide anions

Density functional theory (DFT) calculations have been performed to study the structures and stability of X^?·(HX)_n=2–5 clusters where X = F, Cl, Br at B3LYP/6‐311++G** level of theory. The presence of halide ions in these clusters disintegrates the hydrogen halide clusters. All the hydrogen halides are then hydrogen bonded to the centrally placed halide ions, thereby forming multiple hydrogen bonds. The interaction energies have been corrected for the basis set superposition error (BSSE) using Boy's counterpoise correction method. Evidence for the destruction of hydrogen bonds in hydrogen halide clusters due to the presence of halide ions is further obtained from topological analysis and natural bond orbital analysis. The chemical hardness and chemical potential have been calculated for all the anion clusters. The above analysis reveals that hydrogen bonding in these systems is not an essentially electrostatic interaction. The nature of the stabilization interactions operative in these multiple hydrogen‐bonded clusters has been explained in terms of many‐body contribution to interaction energies. From these studies, an attempt has been made to understand the nature of the molecular properties resulting from different electronegativities of the halogens. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Time‐dependent density functional theory study on the electronic excited‐state geometric structure,infrared spectra,and hydrogen bonding of a doubly hydrogen‐bonded complex

The geometric structures and infrared (IR) spectra in the electronically excited state of a novel doubly hydrogen‐bonded complex formed by fluorenone and alcohols, which has been observed by IR spectra in experimental study, are investigated by the time‐dependent density functional theory (TDDFT) method. The geometric structures and IR spectra in both ground state and the S₁ state of this doubly hydrogen‐bonded FN‐2MeOH complex are calculated using the DFT and TDDFT methods, respectively. Two intermolecular hydrogen bonds are formed between FN and methanol molecules in the doubly hydrogen‐bonded FN‐2MeOH complex. Moreover, the formation of the second intermolecular hydrogen bond can make the first intermolecular hydrogen bond become slightly weak. Furthermore, it is confirmed that the spectral shoulder at around 1700 cm^?1 observed in the IR spectra should be assigned as the doubly hydrogen‐bonded FN‐2MeOH complex from our calculated results. The electronic excited‐state hydrogen bonding dynamics is also studied by monitoring some vibraitonal modes related to the formation of hydrogen bonds in different electronic states. As a result, both the two intermolecular hydrogen bonds are significantly strengthened in the S₁ state of the doubly hydrogen‐bonded FN‐2MeOH complex. The hydrogen bond strengthening in the electronically excited state is similar to the previous study on the singly hydrogen‐bonded FN‐MeOH complex and play important role on the photophysics of fluorenone in solutions. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009     

Significant glass‐transition‐temperature increase through hydrogen‐bonded copolymers

The role of hydrogen bonding in promoting intermolecular cohesion and higher glass‐transition temperatures of polymer is a subject of longstanding interest. A series of poly(vinylphenol‐co‐vinylpyrrolidone) copolymers were prepared by the free‐radical copolymerization of acetoxystyrene and vinylpyrrolidone; this was followed by the selective removal of the acetyl protective group, with corresponding and significant glass‐transition‐temperature increases after this procedure. The incorporation of acetoxystyrene into poly(vinylpyrrolidone) resulted in lower glass‐transition temperatures because of the reduced dipole interactions in its homopolymers. However, the deacetylation of acetoxystyrene to transform the poly(vinylphenol‐co‐vinylpyrrolidone) copolymer enhanced the higher glass‐transition temperature because of the strong hydrogen bonding in the copolymer chain. The thermal properties and hydrogen bonding of these two copolymers were investigated with differential scanning calorimetry and Fourier transform infrared spectroscopy, and good correlations between the thermal behaviors and IR results were observed. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 2313–2323, 2002     

Density functional study of hydrogen‐bonded acetonitrile–water complex

We report the interaction of acetonitrile with one, two, and three water molecules using the Density Functional Theory method and the 6‐31+G* basis set. Different conformers were studied and the most stable conformer of acetonitrile–(water)_n complex has total energies –209.1922504, –285.6224478, and –362.068728 hartrees with one, two, and three water molecules, respectively. The corresponding binding energy for these three structures is 4.52, 8.34, and 22.48 kcal/mol. The hydrogen‐bonding results in blue, blue, and redshift in C?N stretching mode in acetonitrile with one, two, and three water molecules, respectively, whereas there was a redshift in O? H symmetric stretching mode of water. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Synthesis of main‐chain hydrogen‐bonded supramolecular liquid crystalline complexes: The effects of spacer on thermal behavior of mesophase

Two series of difunctional proton acceptors, stilbazole derivatives 4a – c and 6a – c with different spacers, oligo(methylene) and oligo(ethylene glycol), respectively, were synthesized. Hydrogen‐bonded polymeric complexes 4 / 7 and 6 / 7 and trimeric complexes 4 / 8₂ and 6 / 82 ( 7 and 8 are aromatic dicarboxylic acids and monocarboxylic acids, respectively) were prepared, and their liquid crystallinity was examined. The effects of the spacer in 4 , 6 , and 7 and the terminal group in 8 on the thermal behaviors of hydrogen‐bonded complexes were investigated using differential scanning calorimetry and polarizing optical microscopy. X‐ray diffraction at elevated temperatures was used to verify liquid crystal phases. The study showed that the phase transition temperatures for isotropic to nematic (T_I–Ns) of polymeric complexes 4 / 7 and 6 / 7 in general decreased with the increase in length of spacer in the corresponding proton donors 7 . The increase in length of the proton acceptors 6 led to a drop of T_I–Ns of the corresponding complexes 6 / 7 ; however, the T_I–Ns of complexes 4 / 7 did not show any correlation with the spacer length in 4 . In contrast, the increase in length of the terminal group in 8 resulted in a slight decrease in T_I–Ns of trimeric complexes 4 / 8₂ , but had a negligible effect on the T_I–Ns of 6 / 8₂ because of the presence of the more flexible spacer in the proton acceptors 6 . © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 4731–4743, 2005     

Ab initio prediction of the vibrational spectra of the hydrogen‐bonded complexes between CO and HONO2

The vibrational characteristics (vibrational frequencies and infrared intensities) for free and complexed CO and HONO₂ have been predicted using ab initio calculations at SCF and MP2 levels with different basis sets and B3LYP/6?31G(d,p) calculations. The ab initio calculations show that the complexation between HONO₂ and CO leads to two stable structures: CO … HONO₂ (1A) and OC … HONO₂ (1B). The changes in the vibrational characteristics from free monomers to complexes have been estimated. It was established that the most sensitive to the complexation is the stretching O? H vibration. In agreement with the experiment, its vibrational frequency in the complexes is shifted to lower frequency (Δν = ?123 cm^?1). The magnitude of the wave number shift is indicative of relatively strong hydrogen‐bonded interaction. The ab initio calculations at different levels predict an increase of the infrared intensity of the stretching O? H vibration for structure 1A more than five times and for structure 1B more than nine times. The most consistent agreement between the computed values of the frequency shifts for structure 1B and those experimentally observed suggests that this structure is preferred. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003     

Chiral discrimination in hydrogen‐bonded complexes of hydrogen peroxide with methyl hydroperoxide: Theoretical study

For the first time, the discrimination of different chiral forms of 1:1 complexes with hydrogen peroxide and methyl hydroperoxide have been investigated using density functional theory (DFT) and Møller–Plesset type 2 (MP2) methods at varied basis set levels from 6‐31+G(d,p) to 6‐31++G(2d,2p). Three pairs of chiral enantiomers were considered. The optimized geometric parameters, interaction energies, and chirodiastatic energies for various isomers at different levels are estimated. To take into account the water solvation effect, the polarized continuum model (PCM) method has been used to evaluate the ΔG_solv. The gas phase results show that the heterochiral six‐membered ring complex (structure I) and homochiral five‐membered ring complexes (structures IV and V) are preferred configurations for the three pairs of chiral enantiomers. The solvation effect on six‐membered ring complexes (structures I and II) shows nonsignificant changes in the configurations preferred, but on five‐membered ring complexes, the homo‐/heterochiral preference is found to be inverse in the polar solvent. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

New basis sets for the evaluation of interaction‐induced electric properties in hydrogen‐bonded complexes

Interaction‐induced static electric properties, that is, dipole moment, polarizability, and first hyperpolarizability, of the CO? (HF)_n and N₂? (HF)_n, n = 1–9 hydrogen‐bonded complexes are evaluated within the finite field approach using the Hartree–Fock, density functional theory, Møller–Plesset second‐order perturbation theory, and coupled cluster methods, and the LPol‐n (n = ds, dl, fs, fl) basis sets. To compare the performance of the different methods with respect to the increase of the complex size, we consider as model systems linear chains of the complexes. We analyze the results in terms of the many‐body and cooperative effects. © 2012 Wiley Periodicals, Inc.     

Spacer‐length‐dependent association in polymers with multiple‐hydrogen‐bonded end groups

Herein, we investigate the influence of spacer length on the homoassociation and heteroassociation of end‐functionalized hydrogen‐bonding polymers based on poly(n‐butyl acrylate). Two monofunctional ureido‐pyrimidinone (UPy) end‐functionalized polymers were prepared by atom transfer radical polymerization using self‐complementary UPy‐functional initiators that differ in the spacer length between the multiple‐hydrogen‐bonding group and the chain initiation site. The self‐complementary binding strength (K_dim) of these end‐functionalized polymers was shown to depend critically on the spacer length as evident from ¹H NMR and diffusion‐ordered spectroscopy. In addition, the heteroassociation strength of the end‐functionalized UPy polymers with end‐functionalized polymers containing the complementary 2,7‐diamido‐1,8‐naphthyridine (NaPy) hydrogen‐bond motif is also affected when the aliphatic spacer length is too short. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011     

Density functional theory study of the hydrogen bonding interaction of 1:1 complexes of serine with water

The hydrogen bonding of 1:1 complexes formed between serine and water molecules were completely investigated in the present study employing ab initio and Density Functional Theory (DFT) methods at varied basis set levels from 6‐31g to 6‐311++g (2d,2p). For comparison, we also used the second‐order Moller–Plesset Perturbation (MP2) method at the 6‐31+g(d) level. Twelve reasonable geometries on the potential energy hypersurface of serine and water system were considered with the global minimum, 10 of which are cyclic double‐hydrogen bonded structures and the other two are one‐hydrogen bonded structures. The optimized geometric parameters and interaction energies for various isomers at different levels were estimated. The infrared spectrum frequencies, IR intensities, and the vibrational frequency shifts are reported. Finally, the solvent effects on the geometries of the serine–water complexes were also investigated using self‐consistent reaction‐field (SCRF) calculations at the B3LYP/6‐311++g(d,p) level. The results indicate that the polarity of the solvent played an important role in the structures and relative stabilities of different isomers. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Hydrogen‐bonded chains in three cis‐dichloridoplatinum(II) complexes bearing piperidine and amine ligands

The crystal structures of cis‐dichlorido(ethylamine‐κN)(piperidine‐κN)platinum(II), [PtCl₂(C₂H₇N)(C₅H₁₁N)], (I), cis‐dichlorido(3‐methoxyaniline‐κN)(piperidine‐κN)platinum(II), [PtCl₂(C₅H₁₁N)(C₇H₉NO)], (II), and cis‐dichlorido(piperidine‐κN)(quinoline‐κN)platinum(II), [PtCl₂(C₅H₁₁N)(C₉H₇N)], (III), have been determined at 100 K in order to verify the influence of the nonpiperidine ligand on the geometry and crystal packing. The crystal packing is characterized by N—H...Cl hydrogen bonding, resulting in the formation of chains of molecules connected in a head‐to‐tail fashion. Hydrogen‐bonding interactions play a major role in the packing of (I), where the chains further aggregate into planes, but less so in the case of (II) and (III), where π–π stacking interactions are of greater importance.     

Density functional study of HO(H2O)n (n = 1–3) clusters

The hydrogen bonding complexes HO(H₂O)_n (n = 1–3) were completely investigated in the present study using DFT and MP2 methods at varied basis set levels from 6‐31++G(d,p) to 6‐311++G(2d,2p). For n = 1 two, for n = 2 two, and for n = 3 five reasonable geometries are considered. The optimized geometric parameters and interaction energies for various complexes at different levels are estimated. The infrared spectrum frequencies and IR intensities of the most stable structures are reported. Finally, thermochemistry studies are also carried out. The results indicate that the formation and the number of hydrogen bonding have played an important role in the structures and relative stabilities of different complexes. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005