Solvent effects on the molecular stability,intramolecular hydrogen bond,and π-electron delocalization in the simple RAHB systems with different donors and acceptors: a quantum chemical study

Structural Chemistry - In the present study, solvent effects on the molecular stability, intramolecular hydrogen bond (IMHB), and π-electron delocalization (π-ED) in some of the simple...     

A quantum chemical study of conformational and tautomeric preferences, intramolecular hydrogen bonding and π-electron delocalization on dinitrosomethane; in gas phase and water solution

HF, B3LYP, and MP2 methods with the standard basis set, 6-311++G(d,p), were employed to study various aspects of dinitrosomethane (DNM). These results are compared with the outcomes of G2, G2MP2, G3, and CBS-QB3 methods. In the present study, we first characterized the equilibrium conformations, especially global minima. In general, the nitroso-oxime (NO) tautomers of DNM are stabler than the dioxime and dinitroso ones. Furthermore, it was found that the stablest form of NO tautomer is global minima among the known local minima. Surprisingly, the chelated form of NO tautomer, with O–H···O intramolecular hydrogen bond (IMHB), is less stable than the global minimum. In spite of this instability, we comprehensively studied various aspects of IMHB to evaluate the effect of heteroatom’s (N). The results of open–close and related rotamer models predict that the heteroatoms weaken the hydrogen bond, whereas, the geometric, topologic, and natural bond orbital parameters emphasize on opposite conclusion. The HOMA of aromaticity aromaticity index clearly predicts that the π-electron delocalization of chelated form of NO tautomer is greater than the malonaldehyde. Finally, the solvent effects on the properties of DNM tautomers have been estimated by continuum (PCM, IPCM, and SCIPCM), discrete, and mixed models. Theoretical results clearly show that the potential energy surface of DNM, especially global minima, is strongly affected by the solvent.     

The substituent effect of π-electron delocalization in N-methylamino-nitropyridine derivatives: crystal structure and DFT calculations

Structural Chemistry - The crystal and molecular structures of 3-(N-methylamino)-2-nitropyridine, 5-(N-methylamino)-2-nitropyridine and 2-(N-methylamino)-5-nitropyridine have been characterized by...     

CNDO/2 Molecular orbital calculations on hydrogen bond and charge transfer interactions with π-electron donors

CNDO/2 calculations for hydrogen bond interaction of H₂0 and HF and the charge transfer interaction of chlorine with benzene have been carried out. While the dissociation energies for hydrogen bond interactions are satisfactory, they are large for charge transfer interactions. The axial model for the chlorinebenzene interaction has been found to be more stable.     

Combining crystallographic and quantum chemical data to understand DNA-protein π-interactions in nature

Noncovalent interactions are accepted to be prevalent across biochemical systems, including governing interactions between nucleic acids and proteins. The present review summarizes work done to characterize the abundance, structure and strength of DNA–protein π interactions by combining rigorous searches of experimental X-ray crystal structures of DNA–protein complexes and quantum chemical calculations. Focus is placed on interactions that occur between the π-containing amino acids (W, H, F, Y, R, E, and D) and the canonical DNA nucleobases (A, T, G, and C) or 2′-deoxyribose moiety. These studies highlight the considerable frequency of both DNA–protein π–π and sugar–π interactions in nature, which can involve any π-containing amino acid arranged in many unique binding orientations with respect to any DNA component. When combined with the significant strength predicted for the identified DNA–protein π contacts using density functional theory, these works underscore the potential impact of these interactions on critical biological functions. This conclusion is supported by a review of examples from the recent literature that have acknowledged the role of DNA–protein π interactions in binding, specificity, and catalysis.

     

N?H···S and S?H···N intramolecular hydrogen bond in β‐thioaminoacrolein: A quantum chemical study

The conformational study of β‐thioaminoacrolein was performed at various theoretical levels, HF, B3LYP, and MP2 with 6‐311++G(d,p) basis set, and the equilibrium conformations were determined. To have more reliable energies, the total energies of all conformers were recomputed at high‐level ab initio methods, G2MP2, G3, and CBS‐QB3. According to these calculations, the intramolecular hydrogen bond is accepted as the origin of conformational preference in thialamine (TAA) and thiolimine groups. The hydrogen bond strength in various resonance‐assisted hydrogen bond systems was evaluated by HB energy, geometrical parameters, topological parameters, and charge transfers corresponding to orbital interactions. Furthermore, our results reveal that the TAA tautomer has extra stability with respect to the other tautomers. The population analyses of the possible conformations by NBO predict that the origin of this preference is mainly due to the π‐electron delocalization in framework of TAA forms, especially usual π_C?C → π*_C?S and Lp (N) → π*_C?C charge transfers. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Reaction between ��-phenyl-��-alanine and 4-hydroxy-4-methylpent-2-ynenitrile: a spectroscopic and quantum chemical study

The sequence of isomeric transformations of intermediate adducts formed upon nuceleophilic addition of ??-phenyl-??-alanine to 4-hydroxy-4-methylpent-2-ynenitrile affording a neutral or two alternative zwitterionic forms (with protonated imino or amino groups) of the product was studied quantum chemically by the B3LYP/6-31G(d,p) method and by UV spectroscopy. In the isolated state, the equilibrium is completely shifted toward the neutral form. Taking into account the polyhydrate environment increases the portion of the zwitterionic form bearing a protonated imino group of the dihydrofuran cycle. Protonation of the amino group of amino acid is thermodynamically unfavorable.     

Structural variation, π-charge transfer,and transmission of electronic substituent effects through the carbon-carbon triple bond in β-substituted phenylacetylenes: a quantum chemical study,and a comparison with (E)-β-substituted styrenes

Structural Chemistry - The transmission of electronic substituent effects through a carbon-carbon triple bond has been investigated from the small changes induced by a variable substituent X on the...     

Density functional and chemical model study of the competition between methyl and hydrogen scission of propane and ��-scission of the propyl radical

In this work, we study the competence between the reactions of hydrogen and methyl scission during thermal cracking and combustion of propane, the emergence of the two isomers of the propyl radical, n-propyl and i-propyl, and their subsequent ??-scission reaction to ethene and methyl radical. The purpose of the study was to analyze the accuracy of density functional (DFT) methods as applied on this relatively well-known subset of the reactions implied in the production of propylene oxide from propane and propene. Conventional (B3LYP, B3PW91) and state-of-the-art (PBE0, M06, BMK) DFT methods were employed, and their accuracy checked against experimental data and calculations performed using model chemistries (complete basis set CBS-4M, QB3, and APNO, and G4 methods) and ab initio methods (MP2, CCSD(T) with a large 6-311 ++G(3df,2pd) basis set). The results obtained at the BMK level for the thermodynamics of the reactions are closer to experimental data than those afforded by any other DFT method and very similar actually to CBS or CCSD(T) results, even if a medium size basis set is used. Activation energies determined using two- and three-parameter Arrhenius equations are also very good, but the preexponential factors are incorrect. Tunneling and internal rotation corrections must be applied to obtain semiquantitative results.     

Neutron diffraction study of the HF adducts containing a hydrogen bond F-H?O

Single-crystal structures of HF adducts of acid salts CsH₂PO₃·HF, KH₂PO₄·HF, and CsH₂PO₄·HF were determined by neutron diffraction using the Laue method. In the crystals, HF molecules are connected to anions by means of new type of hydrogen bonds, F-H?O, which are significantly shorter (F?O distances 2.356-2.386(3) Å) than strong O-H?O or O-H?F hydrogen bonds. The H-F distances in the structures of these adducts, 1.020-1.027(5) Å, are compared with those in crystalline HF and hydrofluoride anions.     

Field-induced π-polarization in barrelene derivatives: a computational study based on structural variation

Barrelene, H–C(CH=CH)₃C–H, is an unsaturated polycyclic hydrocarbon containing three isolated double bonds in a non-planar arrangement. We have studied the transmission of field effects through the barrelene framework by analyzing the small structural changes occurring in the phenyl group of many Ph–C(CH=CH)₃C–X molecules, where X is a variable substituent. Molecular geometries have been determined by quantum chemical calculations at the HF/6-31G* and B3LYP/6-311++G** levels of theory. Comparison with the results obtained for the corresponding saturated molecules, the bicyclo[2.2.2]octane derivatives Ph–C(CH₂–CH₂)₃C–X, reveals a small, but significant, field-induced π-polarization of the barrelene cage, especially when the remote substituent is a charged group. Additional evidence of π-polarization is obtained by comparing the electric dipole moments of the two sets of uncharged molecules. The structural variation of the barrelene cage caused by the variable substituent in Ph–C(CH=CH)₃C–X molecules has also been investigated. It is much larger than that of the phenyl group and depends primarily on the electronegativity of the substituent. Particularly pronounced is the concerted variation of the non-bonded distance between the bridgehead carbons of the cage, r(C···C) ₁ ^BARR , and the average of the three C–C–C angles at the cage carbon bonded to the variable substituent, α ₁ ^BARR . A scattergram of r(C···C) ₁ ^BARR versus the corresponding parameter for bicyclo[2.2.2]octane derivatives, r(C···C) ₁ ^BCO , shows that the variation of r(C···C) ₁ ^BARR becomes gradually less pronounced than that of r(C···C) ₁ ^BCO as the electronegativity of the substituent increases.     

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.     

Electronic coupling through intramolecular π-π interactions in biscobaltocenes: a structural, spectroscopic, and magnetic study

The paramagnetic dinuclear complexes 1,8-bis(cobaltocenyl)naphthalene (2) and 1,8-bis[(pentamethyl-η(5)-cyclopentadienyl)(η(5)-cyclopentadiendiyl)cobalt(II)]naphthalene (4) were synthesized. The molecular structures were characterized by X-ray structure analysis and consisted of two cobaltocenes linked through a distorted naphthalene clamp. Electronic interactions between the two cobalt atoms were observed by cyclic voltammetric studies. Superconducting quantum interference device (SQUID) measurements of the pure compounds and diluted in their diamagnetic iron derivatives, as well as variable-temperature NMR spectroscopy experiments in solution are presented. Magnetic measurements revealed an antiferromagnetic coupling of the electrons in complexes 2 and 4. From NMR spectroscopy experiments, Curie behavior in the temperature range from -60 to +60 °C can be deduced. The electronic structure and magnetic behavior is supported by results of broken-symmetry DFT and multireference calculations along with UV/Vis spectroscopic data, which revealed an intramolecular through space π-π interaction between the cobaltocene units.     

Theoretical study of the intermolecular hydrogen bond interaction for furan-HCl and furan-CHCl_3 complexes

The importance of intermolecular interactions in biology and material science has prompted chemists to explore the nature of the variety of such interactions. The strongest of these interac-tions are the hydrogen bonds, which play an important role in determining the molecular confor-mation, crystal packing, and the structure of biological systems such as nucleic acids. Extensive experimental and theoretical efforts[1—5] have been devoted to the studies of this type of interac-tions, such as …