Effects of substituents upon the P···N noncovalent interaction: the limits of its strength

Previous work has documented the ability of the P atom to form a direct attractive noncovalent interaction with a N atom, based in large measure on the charge transfer from the N lone pair into the σ* antibonding orbital of the P-H that is turned away from the N atom. As the systems studied to date include only hydrides, the present work considers how substituents affect the interaction and examines whether P···N might compete with other attractive forces such as H-bonds. It is found that the addition of electron-withdrawing substituents greatly strengthens the P···N interaction to the point where it exceeds that of the majority of H-bonds. The highest interaction energy occurs in the FH(2)P···N(CH(3))(3) complex, amounting to 11 kcal/mol. A breakdown of the individual forces involved attributes the stability of the interaction to approximately equal parts electrostatic and induction energy, with a smaller contribution from dispersion.     

Effect of microhydration on the guanidinium···benzene interaction

The effect of microhydration on the interaction of guanidinium cation with benzene has been studied by employing ab initio calculations. Four different structural arrangements were considered for the guanidinium···benzene interaction to which up to six water molecules were added. T-shaped structures are usually the most stable, but as water molecules are included the energy differences with the parallel structures decrease, reaching a point where parallel complexes are even more stable than T-shaped ones. Therefore, the inclusion of water molecules promotes a change in the structure of the cation···π contact. The analysis reveals that these stability changes are more related with the structure of the hydrating water molecules than to a modulation of the cation···π interaction. Already with three water molecules, one water molecule in the T-shaped complex has to be located in the second solvation shell, whereas in parallel structures this occurs with four water molecules. As a consequence energy differences among structures decrease. The calculations show that the nature of the interaction is almost unaffected in T-shaped structures, whereas an important dispersion increment is observed in parallel ones, though its overall effect is small.     

On the nature of the stabilization of benzene···dihalogen and benzene···dinitrogen complexes: CCSD(T)/CBS and DFT-SAPT calculations

The structure and stabilization energies of benzene (and methylated benzenes)···X(2) (X=F, Cl, Br, N) complexes were investigated by performing CCSD(T)/complete basis set limit and density functional theory/symmetry-adapted perturbation theory (DFT-SAPT) calculations. The global minimum of the benzene···dihalogen complexes corresponds to the T-shaped structure, whereas that of benzene···dinitrogen corresponds to the sandwich one. The different binding motifs of these complexes arise from the different quadrupole moments of dihalogens and dinitrogen. The different sign of the quadrupole moments of these diatomics is explained based on the electrostatic potential (ESP). Whereas all dihalogens, including difluorine, possess a positive σ hole, such a positive area of the ESP is completely missing in the case of dinitrogen. Moreover, benzene···X(2) (X=Br, Cl) complexes are stronger than benzene···X(2) (X=F, N) complexes. When analyzing DFT-SAPT electrostatic, dispersion, induction, and δ(Hartree-Fock) energies, we recapitulate that the former complexes are stabilized mainly by dispersion energy, followed by electrostatic energy, whereas the latter complexes are stabilized mostly by the dispersion interaction. The charge-transfer energy of benzene···dibromine complexes, and surprisingly, also of methylated benzenes···dibromine complexes is only moderate, and thus, not responsible for their stabilization. Benzene···dichlorine and benzene···dibromine complexes can thus be characterized merely as complexes with a halogen bond rather than as charge-transfer complexes.     

Effects of the biological backbone on stacking interactions at DNA-protein interfaces: the interplay between the backbone···π and π···π components

The (gas-phase) MP2/6-31G*(0.25) π···π stacking interactions between the five natural bases and the aromatic amino acids calculated using (truncated) monomers composed of conjugated rings and/or (extended) monomers containing the biological backbone (either the protein backbone or deoxyribose sugar) were previously compared. Although preliminary energetic results indicated that the protein backbone strengthens, while the deoxyribose sugar either strengthens or weakens, the interaction calculated using truncated models, the reasons for these effects were unknown. The present work explains these observations by dissecting the interaction energy of the extended complexes into individual backbone···π and π···π components. Our calculations reveal that the total interaction energy of the extended complex can be predicted as a sum of the backbone···π and π···π components, which indicates that the biological backbone does not significantly affect the ring system through π-polarization. Instead, we find that the backbone can indirectly affect the magnitude of the π···π contribution by changing the relative ring orientations in extended dimers compared with truncated dimers. Furthermore, the strengths of the individual backbone···π contributions are determined to be significant (up to 18 kJ mol(-1)). Therefore, the origin of the energetic change upon model extension is found to result from a balance between an additional (attractive) backbone···π component and differences in the strength of the π···π interaction. In addition, to understand the effects of the biological backbone on the stacking interactions at DNA-protein interfaces in nature, we analyzed the stacking interactions found in select DNA-protein crystal structures, and verified that an additive approach can be used to examine the strength of these interactions in biological complexes. Interestingly, although the presence of attractive backbone···π contacts is qualitatively confirmed using the quantum theory of atoms in molecules (QTAIM), QTAIM electron density analysis is unable to quantitatively predict the additive relationship of these interactions. Most importantly, this work reveals that both the backbone···π and π···π components must be carefully considered to accurately determine the overall stability of DNA-protein assemblies.     

Ab initio excitation spectrum of the weak H···CO interaction

The adiabatic interaction energy (IE) in the van der Waals region of the ground $ {\text{H}}\left( {{}^{2}{\text{S}}} \right) \cdots {\text{CO}}\left( {{\text{X}}^{1} \Upsigma^{ + } } \right) $ and excited $ {\text{H}}\left( {{}^{2}{\text{S}}} \right) \cdots {\text{CO}}\left( {{\text{a}}^{3} \Uppi } \right) $ electronic states of the $ {\text{H}} \cdots {\text{CO}} $ complex is studied in the framework of the supermolecule approach at the RHF-CCSD(T) level of theory. Calculations predict a minimum with β _e = 72°, R _e = 6.89a _o and D _e = 34.10 cm^?1 for the ground X²A′state. For the excited ⁴A′ state the minimum occurs at β _e = 104° and R _e = 5.90a _o with D _e = 75.42 cm^?1. The resulting IE of the excited ⁴A′′ state reveals two minima separated by a saddle point. The most stable configuration occurs at β _e = 132°, R _e = 6.71a _o and D _e = 40.03 cm^?1. The corresponding vertical excitation energies and corresponding shifts with respect to the isolated CO molecule are calculated as a guideline for future theoretical and experimental work. In order to investigate the use of less demanding correlation methods, test density functional theory calculations using the mPW1PW exchange–correlation functional are also presented for comparison.     

Density functional analysis of the magnetic structure of Li3RuO4: importance of the Ru-O···O-Ru spin-exchange interactions and substitutional Ru defects at the Li sites

We evaluated the spin-exchange interactions of Li(3)RuO(4) by performing energy-mapping analysis based on density functional calculations and examined the nature of its magnetic transition at T(1) = 66 K and the divergence of the field-cooled and zero-field-cooled susceptibilities below T(2) = 32 K. Our study shows that T(1) is associated with a three-dimensional antiferromagnetic ordering, in which the two-dimensional antiferromagnetic lattices parallel to the ab plane are antiferromagnetically coupled along the c direction. We examined how the substitutional defects, Ru atoms residing in the Li sites, affect the antiferromagnetic coupling along the c direction to explain why the expected c-axis doubling is not detected from powder neutron diffraction measurements. The susceptibility divergence below T(2) is attributed to a slight spin canting out of the ab plane.     

Internucleotide J-couplings and chemical shifts of the N-H···N hydrogen-bonds in the radiation-damaged guanine-cytosine base pairs

Internucleotide ^2hJ_NN spin‐spin couplings and chemical shifts (δ(¹H) and Δδ(¹⁵N)) of N? H···N H‐bond units in the natural and radiation‐damaged G‐C base pairs were predicted using the appropriate density functional theory calculations with a large basis set. Four possible series of the damaged G‐C pairs (viz., dehydrogenated and deprotonated G‐C pairs, GC^?? and GC^?+ radicals) were discussed carefully in this work. Computational NMR results show that radicalization and anionization of the base pairs can yield strong effect on their ^2hJ_NN spin scalar coupling constants and the corresponding chemical shifts. Thus, variations of the NMR parameters associated with the N? H···N H‐bonds may be taken as an important criterion for prejudging whether the natural G‐C pair is radiation‐damaged or not. Analysis shows that ^2hJ_NN couplings are strongly interrelated with the energy gaps (ΔE_LP→σ*) and the second‐order interaction energies (E(2)) between the donor N lone‐pair (LP_N) and the acceptor σ^*_{N? H} localized NBO orbitals, and also are sensitive to the electron density distributions over the σ*(N? H) orbital, indicating that ^2hJ_NN couplings across the N? H···N H‐bonds are charge‐transfer‐controlled. This is well supported by variation of the electrostatic potential surfaces and corresponding charge transfer amount between G and C moieties. It should be noted that although the NMR spectra for the damaged G‐C pair radicals are unavailable now and the states of the radicals are usually detected by the electron spin resonance, this study provides a correlation of the properties of the damaged DNA species with some of the electronic parameters associated with the NMR spectra for the understanding of the different state character of the damaged DNA bases. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011.     

Quantification of binding affinities of essential sugars with a tryptophan analogue and the ubiquitous role of C-H···π interactions

The role of noncovalent interactions in carbohydrate recognition by aromatic amino acids has long been reported. To develop a molecular understanding of noncovalent interactions in the recognition process, we have examined a series of binary complexes between 3-methylindole (3-MeIn) and sugars. In particular, the geometries and binding affinities of 3-MeIn with α/β-D-glucose, β-D-galactose, α-D-mannose and α/β-L-fucose are obtained using the MP2(full)/6-31G(d,p) and the M06/TZV2D//MP2/6-31G(d,p) level of theories. The conventional hydrogen bonding such as N-H···O and C-H···O as well as nonconventional O-H···π and C-H···π type of interactions is, in general, identified as responsible for the moderately strong interaction energies. Large variations in the position-orientations of 3-MeIn with respect to saccharide are noticed, within the same sugar family, as well as across different sugar series. Furthermore, complexes with large differences in their geometries are recognized as capable of exhibiting very similar interaction energies, underscoring the significance of exhaustive conformation sampling, as carried out in the present study. These observations are readily attributed to the differences in the efficiency of the type of interactions enlisted above. The highest and lowest interaction energies, upon inclusion of 50% BSSE correction, are found to be -16.02 and -6.22 kcal mol(-1), respectively, for α-D-glucose (1a) and α-L-fucose (5j). While more number of prominent conventional hydrogen bonding contacts remains as a characteristic feature of the strongly bound complexes, the lower end of the interaction energy spectrum is dominated by multiple C-H···π interactions. The complexes exhibiting as many as four C-H···π contacts are identified in the case of α/β-D-glucose, β-D-galactose, and α/β-L-fucose with an interaction energy hovering around -8 kcal mol(-1). The presence of effective C-H···π interactions is found to be dependent on the saccharide configuration as well as the area of the apolar patch constituted by the C-H groups. The study offers a comprehensive set of binary complexes, across different saccharides, which serves as an illustration of the significance and ubiquitous nature of C-H···π interactions in carbohydrate binding in saccharide-protein complexes.     

Spin-adduct of the P4 ·− radical anion during the electrochemical reduction of white phosphorus

The radical anion P₄·⁻ was detected and identified by the ESR method as a spin-adduct with nitrone during the electrochemical reduction of white phosphorus in the presence of a spin trap, viz., α-phenyl-N-tert-butylnitrone, in a special electrolysis cell with a helical platinum working electrode in the potentiostatic mode. The character of the behavior of P₄·⁻ and the spin trap during electrochemical reduction was monitored by cyclic voltammetry directly in the electrolysis cell, and the spin-adduct formed was detected by ESR.     

Theoretical study of the N—H···O red-shifted andblue-shifted hydrogen bonds

Theoretical calculations are performed to study the nature of the hydrogen bonds in complexes HCHO···HNO, HCOOH···HNO, HCHO···NH3, HCOOH···NH3, HCHO···NH2F and HCOOH···NH2F. The geomet- ric structures and vibrational frequencies of these six complexes at the MP2/6-31 G(d,p), MP2/6-311 G(d,p), B3LYP/6-31 G(d,p) and B3LYP/6-311 G(d,p) levels are calculated by standard and counterpoise-corrected methods, respectively. The results indicate that in complexes HCHO···HNO and HCOOH···HNO the N—H bond is strongly contracted and N—H···O blue-shifted hydrogen bonds are observed. While in complexes HCHO···NH3, HCOOH···NH3, HCHO···NH2F and HCOOH···NH2F, the N—H bond is elongated and N—H···O red-shifted hydrogen bonds are found. From the natural bond orbital analysis it can be seen that the X—H bond length in the X—H···Y hydrogen bond is controlled by a balance of four main factors in the opposite directions: hyperconjugation, electron density redistribu- tion, rehybridization and structural reorganization. Among them hyperconjugation has the effect of elongating the X—H bond, and the other three factors belong to the bond shortening effects. In complexes HCHO···HNO and HCOOH···HNO, the shortening effects dominate which lead to the blue shift of the N—H stretching frequencies. In complexes HCHO···NH3, HCOOH···NH3, HCHO···NH2F and HCOOH···NH2F where elongating effects are dominant, the N—H···O hydrogen bonds are red-shifted.     

Fragmentation energetics of the phenol(+)···Ar(3) cation cluster

The various dissociation thresholds of phenol(+)···Ar(3) complexes for the consecutive loss of all three Ar ligands were measured in a molecular beam using resonant photoionization efficiency and mass analyzed threshold ionization spectroscopy via excitation of the first excited singlet state (S(1)). The adiabatic ionization energy is derived as 68077 ± 15 cm(-1). The analysis of the dissociation thresholds demonstrate that all three Ar ligands in the neutral phenol···Ar(3) tetramer are attached to the aromatic ring via π-bonding, denoted phenol···Ar(3)(3π). The value of the dissociation threshold for the loss of one Ar ligand from phenol(+)···Ar(3)(3π), ～190 cm(-1), is significantly lower than the binding energy measured for the π-bonded Ar ligand in the phenol(+)···Ar(π) dimer, D(0) = 535 ± 3 cm(-1). This difference is rationalized by an ionization-induced π → H isomerization process occurring prior to dissociation, that is, one Ar atom in phenol(+)···Ar(3)(3π) moves to the OH binding site, leading to a structure with one H-bonded and 2 π-bonded ligands, denoted phenol(+)···Ar(3)(H/2π). The dissociation thresholds for the loss of two and three Ar atoms are also reported as 860 and 1730 cm(-1). From these values, the binding energy of the H-bound Ar atom can be estimated as 870 cm(-1).     

On the weakly C-H···π hydrogen bonded complexes of sevoflurane and benzene

A vibrational assignment of the anaesthetic sevoflurane, (CF(3))(2)CHOCH(2)F, is proposed and its interaction with the aromatic model compound benzene is studied using vibrational spectroscopy of supersonic jet expansions and of cryosolutions in liquid xenon. Ab initio calculations, at the MP2/cc-pVDZ and MP2/aug-cc-pVDZ levels, predict two isomers for the 1?:?1 complex, one in which the near-cis, gauche conformer of sevoflurane is hydrogen bonded through its isopropyl-hydrogen atom, the other in which the same conformer is bonded through a bifurcated hydrogen bond with the fluoromethyl hydrogen atoms. From the experiments it is shown that the two isomers are formed, however with a strong population dominance of the isopropyl-bonded species, both in the jet and liquid phase spectra. The experimental complexation enthalpy in liquid xenon, ΔH(o)(LXe), of this species equals -10.9(2) kJ mol(-1), as derived from the temperature dependent behaviour of the cryosolution spectra. Theoretical complexation enthalpies in liquid xenon were obtained by combining the complete basis set extrapolated complexation energies at the MP2/aug-cc-pVXZ (X = D,T) level with corrections derived from statistical thermodynamics and Monte Carlo Free Energy Perturbation calculations, resulting in a complexation enthalpy of -11.2(3) kJ mol(-1) for the isopropyl-bonded complex, in very good agreement with the experimental value, and of -11.4(4) kJ mol(-1), for the fluoromethyl-bonded complex. The Monte Carlo calculations show that the solvation entropy of the isopropyl-bonded species is considerably higher than that of the fluoromethyl-bonded complex, which assists in explaining its dominance in the liquid phase spectra.     

Intramolecularly coordinated azobenzene selenium derivatives: effect of strength of the Se···N intramolecular interaction on luminescence

A series of selenium derivatives (6-12) of 2-phenylazophenyl have been synthesized using o-lithiation route. The effect of the strength of the intramolecular Se···N interaction on the absorption spectra as well as emission spectra has been studied. The studies suggest that the secondary bonding Se···N interaction give rise to fluorescence, however, the strength of Se···N interaction cannot be directly correlated with the intensity of the fluorescence. TD-DFT calculations show that the main transition involved in the absorption spectra of the compound is the ligand based π-π* type.     

Synthesis of novel O-alkylbenzochromeno-1,5-benzodiazepinones. Study of the N–H····N and CO····HN hydrogen bonding interactions with 2-aminopyridines

A series of novel 6-(O-alky)lbenzochromeno-1,5-benzodiazepin-2-ones 4a–c was prepared through the condensation between the [1]benzopyrano[4,3-c][1,5]benzodiazepin-7(8H)one 1 and a series of alkylalcohols. Scaffold 4 exhibited interesting hydrogen-bonding interaction with 2-aminopyridine derivatives. The so obtained self-assembled systems 5 were fully characterized by 1D/2D-NMR techniques and mass spectrometry. The hydrogen-bonding interaction was supported by IR and Raman spectroscopy and by ¹H NMR titration experiments, and was confirmed by an X-ray crystal structure analysis.     

Observation of a double C-H···π interaction in the CH2ClF···HCCH weakly bound complex

The structure of the CH(2)ClF···HCCH dimer has been determined using both chirped-pulse and resonant cavity Fourier-transform microwave spectroscopy. The complex has C(s) symmetry and contains both a double C-H···π interaction, in which one π-bond acts as acceptor to two hydrogen atoms from the CH(2)ClF donor, and a weak C-H···Cl interaction, with acetylene as the donor. Analysis of the rotational spectra of four isotopologues (CH(2)(35)ClF···H(12)C(12)CH, CH(2)(37)ClF···H(12)C(12)CH, CH(2)(35)ClF···H(13)C(13)CH, and CH(2)(37)ClF-H(13)C(13)CH) has led to a structure with C-H···π distances of 3.236(6) ? and a C-H···Cl distance of 3.207(22) ?, in good agreement with ab initio calculations at the MP2/6-311++G(2d,2p) level. Both weak contacts are longer than those observed in similar complexes containing a single C-H···π interaction that lies in the C(s) plane; however, this appears to be the first double C-H···π contact to be studied by microwave spectroscopy, so there is little data for direct comparison. The rotational and chlorine nuclear quadrupole coupling constants for the most abundant isotopologue are: A = 5262.899(14) MHz, B = 1546.8074(10) MHz, C = 1205.4349(7) MHz, χ(aa) = 28.497(5) MHz, χ(bb) = -65.618(13) MHz, and χ(cc) = 37.121(8) MHz.     

First principle studies toward the design of a new class of carbene superbases involving intramolecular H···π interactions

The higher basicity of carbenes has been exploited with H···π non-bonding interactions to design a new class of organic superbases. This simple molecular architecture gains a basicity comparable to some of the known functionalized nitrogen superbases and phosphazenes.