Intermolecular Components Research Articles

The isomorphous substitution of 2H+ for the Cu2+ cation in the complex of bis(aminoguanidine)copper(II): Crystal structures of (Cu0.61H0.78 Agu 2)B12H12 and (HAgu)2B12H12

An X-ray diffraction study of the (Cu0.61H0.78Agu2)B12H12 (I) mixed crystal and one of its components (HAgu)2B12H12 (II) is performed at 160 K (R = 0.0312 and 0.0345, respectively). Crystals I and II are isostructural. In I, two H+ ions partially substitute the Cu2+ cation, resulting in a combination of [CuAgu2]2+ and (HAgu2)2+ cations in the structure. The cations and polyhedral B12H122− anions have centrosymmetric structures. A square planar environment for the Cu atom is formed by four N atoms of two Agu molecules, which close five-membered chelate cycles [Cu-N, 1.9702(13) and 2.0261(10) A]. The distant apical vertices are occupied by H atoms of the B12H122− anions [Cu…H, 2.805(14) A]. In the dimeric (HAgu2)2+ cations, the proton that substitutes for the Cu2+ cation forms a three-center N(1)-H…N(4),N(4)′ hydrogen bond which consists of intramolecular and an intermolecular components. In crystal II, the N(1)…N(4) and N(1)…N(4)′ distances [2.685(1) and 3.111(1) A] are longer than in I [2.610(2) and 3.027(2) A]. In I, the Cu…H interactions connect [CuAgu2]2+ cations and B12H122− anions into chains. In the cells that contain the (HAgu2)2+ dimeric cation, the chains are retained due to the secondary N-H…(B-H) interactions. Numerous weak secondary interactions between the cations and anions form three-dimensional frameworks in structures I and II.

On the Nature of Intermolecular Interactions in Nucleic Acid Base−Amino Acid Side-Chain Complexes

Twenty hydrogen-bonded complexes composed of nucleic acid base and amino acid side chain have been analyzed using ab initio quantum chemistry methods with the aim of gaining insights into the nature of molecular interactions in these systems. The intermolecular interaction energies were estimated using the second-order Møller-Plesset perturbation theory and coupled clusters approach with single and double excitations, while their components have been determined by means of a hybrid variational-perturbational decomposition scheme. Additionally, the topological analysis of an electron density distribution of the studied complexes has been performed. In the case of all of the studied neutral complexes, the main source of stabilization is the delocalizaction energy associated with the electron density deformation upon the interaction which contributes almost half of the total interaction energy. Furthermore, analysis of the interaction induced difference density maps of complexes containing neutral amino acid side chains reveals that the delocalization component involves the electron density changes localized in the double-hydrogen-bonded ring structures. A relatively good correlation between the sum of densities at hydrogen-bond critical points and the Hartree-Fock intermolecular interaction energy components (electrostatic, delocalization, and exchange) has been observed for the two independently considered sets of complexes, containing positively charged and neutral amino acid side chains.

Structure of liquid n-hexane

The structure of deuterated liquid n-hexane has been investigated at room temperature by neutron diffraction and molecular dynamics simulations. By carrying out a careful analysis of the measurements, experimental data were obtained in very good agreement with the simulated data. This allowed a thorough analysis of the simulation results aiming at the evaluation of the partial, intra-, and intermolecular components of the n-hexane structure. We finally compare the intramolecular differential cross sections calculated from the most probable n-hexane molecular configurations with the measured and simulated data.

How does modification of adenine by hydroxyl radical influence the stability and the nature of stacking interactions in adenine-cytosine complex?

This study reports on ab initio calculations of adenine-cytosine complexes in two different context alignments appearing in B-DNA. The influence of adenine modification by hydroxyl radical on the stability of the complexes is also discussed. The analysis was performed on over 40 crystallographic structures for each of the sequence contexts. In most cases, modification of adenine by hydroxyl radical leads to less negative intermolecular interaction energies. The issue of the influence of alteration of structural base step parameters on the stability of modified and unmodified adenine-cytosine complexes is also addressed. Analysis of the dependence of intermolecular interaction energy on base step parameters reveals that for twist and shift modification of adenine by hydroxyl radical leads to quite different interaction energy profiles in comparison with unmodified complexes. In order to elucidate the physical origins of this phenomenon, i.e. to analyze how the modification of adenine by hydroxyl radical is reflected in the change of intermolecular interaction energy components, a variational-perturbational decomposition scheme was applied at the MP2/aug-cc-pVDZ level of theory.

A comparison of ether- and alkyl-derivatized imidazolium-based room-temperature ionic liquids: a molecular dynamics simulation study

Molecular dynamics simulations of ether-derivatized imidazolium-based room-temperature ionic liquids (EDI-RTILs), [C(5)O(2)mim][TFSI] and [C(5)O(2)mim][BF(4)], have been performed and compared with simulations of alkyl-derivatized analogues (ADI-RTILs). Simulations yield RTIL densities, self-diffusion coefficients and viscosity in excellent agreement with experimental data. Simulations reveal that structure in the EDI-RTILs, quantified by the extent of nanoscale segregation of tails as well as cation-ion and cation-cation correlations, is reduced compared to that observed in the ADI-RTILs. Significant correlation between ether tail oxygen atoms and imidazolium ring hydrogen atoms was observed in the EDI-RTILs. This correlation is primarily intramolecular in origin but has a significant intermolecular component. Competition of ether oxygen atoms with oxygen atoms of TFSI(-) or fluorine atoms of BF(4)(-) for coordination of the ring hydrogen atoms was found to reduce the extent of cation-anion correlation in the EDI-RTILs compared to the ADI-RTILs. The reduction in intermolecular correlation, particularly tail-tail segregation, as well as weakening of cation-anion specific interactions due to the ether tail, may account for the faster dynamics observed in the EDI-RTILs compared to ADI-RTILs.

A review of the computational studies of proton- and metal-exchanged chabazites as media for molecular hydrogen storage performed with the CRYSTAL code

In the present paper, a review of our previously published results about the ab initio modeling on the H 2 interaction with the polarizing centers of proton- and metal-exchanged chabazites performed with the periodic ab initio CRYSTAL code is reported. The paper highlights how ab initio modeling allows to: (i) understand the H 2 interaction with solids at an atomistic level; (ii) infer the potential of zeolites as hydrogen storage materials; (iii) give insights in the design of new H 2 storage materials for applications. The calculations were performed within the periodic approach using the B3LYP functional with all-electron double zeta polarized Gaussian type basis sets. New data are reported using a richer basis set for both zeolite and H 2 , which ensures a better description of the intermolecular interaction components. In all the considered systems, H 2 mainly interacts side-on with zeolites’ charge balancer cations. Geometrical and energetic features were also refined at MP2 level adopting clusters cut out from the chabazite framework in order to gauge the dispersive contribution to the interaction energy, not accounted for by the B3LYP functional. Computed BSSE-free binding energies ( BE c ) showed that H 2 interacts poorly with the protons ( H + ) of the Brønsted sites ( BE c ∼ 5 kJ / mol ) , whereas the interaction with Li + , Na + and K + in metal-exchanged chabazites was stronger, particularly for Li + located in small framework rings ( BE c ∼ 12 kJ / mol ) . When divalent Mg 2 + cation is used as a charge balancer, the BE c becomes ∼ 18 kJ / mol , showing that the interplay between cationic polarization and its spatial position in the zeolite framework is crucial in determining the sorption capacity of the material.

The nature of interactions in uracil dimer: An ab initio study

Abstract The intermolecular interaction energy components for the stacked uracil dimer have been evaluated at the MP2 level of theory using the variational–perturbational intermolecular interaction energy decomposition scheme. It was observed that the dispersion and electrostatic components are most dominant contributions to the stabilization energy. The former component does not exhibit the dependence on the mutual orientation of the uracil monomers, while for the latter strong directional variations have been found.

Molecular structure of complexes with a bifurcated hydrogen bond. 5. Dimers of 3-hydroxy-2-methyl-4-pyrone in inert media

According to the data from IR spectroscopy and quantum-chemical calculations (B3LYP/6-31G**, B3LYP/6-311G*), in the vapor and in dichloroethane the synperiplanar conformer of 3-hydroxy-2-methyl-4-pyrone (maltol) exists in equilibrium with two types of dimers. The hydrogen atom of the hydroxy group of one them participates in the formation of a three-center bifurcated hydrogen bond. The second isomer is formed by means of two such H bonds, the intramolecular component of which is substantially weakened while the intermolecular component is so strong that it approximates in character to a two-center hydrogen bond.

Fluorometric Measurements of Intermolecular Distances between the α- and β-Subunits of the Na+/K+-ATPase

The Na+/K+-ATPase maintains the physiological Na+ and K+ gradients across the plasma membrane in most animal cells. The functional unit of the ion pump is comprised of two mandatory subunits including the alpha-subunit, which mediates ATP hydrolysis and ion translocation, as well as the beta-subunit, which acts as a chaperone to promote proper membrane insertion and trafficking in the plasma membrane. To examine the conformational dynamics between the alpha- and beta-subunits of the Na+/K+-ATPase during ion transport, we have used fluorescence resonance energy transfer, under voltage clamp conditions on Xenopus laevis oocytes, to differentiate between two models that have been proposed for the relative orientation of the alpha- and beta-subunits. These experiments were performed by measuring the time constant of irreversible donor fluorophore destruction with fluorescein-5-maleimide as the donor fluorophore and in the presence or absence of tetramethylrhodamine-6-maleimide as the acceptor fluorophore following labeling on the M3-M4 or M5-M6 loop of the alpha-subunit and the beta-subunit. We have also used fluorescence resonance energy transfer to investigate the relative movement between the two subunits as the ion pump shuttles between the two main conformational states (E1 and E2) as described by the Albers-Post scheme. The results from this study have identified a model for the orientation of the beta-subunit in relation to the alpha-subunit and suggest that the alpha- and beta-subunits move toward each other during the E2 to E1 conformational transition.

On the weak intermolecular interactions and their influence on the optical properties of unsaturated hydrocarbons. Part 1: Two-body interactions†

The systematic ab initio studies of intermolecular interaction energy components in the model unsaturated hydrocarbon complexes have been performed. The influence of the weak intermolecular interactions on the optical properties has been analyzed within the supermolecular approach. The estimated interaction energy components and electric properties of the studied systems indicate the substantial influence of the intermolecular forces on the optical response of the studied systems. The obtained results could be important for understanding the properties of the organic materials exploited for the purposes of the nonlinear optics. †Dedicated to Professor Andrzej Sadlej on the Occasion of his 65th birthday.

Optimal Charges in Lead Progression: A Structure-Based Neuraminidase Case Study

Collective experience in structure-based lead progression has found electrostatic interactions to be more difficult to optimize than shape-based ones. A major reason for this is that the net electrostatic contribution observed includes a significant nonintuitive desolvation component in addition to the more intuitive intermolecular interaction component. To investigate whether knowledge of the ligand optimal charge distribution can facilitate more intuitive design of electrostatic interactions, we took a series of small-molecule influenza neuraminidase inhibitors with known protein cocrystal structures and calculated the difference between the optimal and actual charge distributions. This difference from the electrostatic optimum correlates with the calculated electrostatic contribution to binding (r(2) = 0.94) despite small changes in binding modes caused by chemical substitutions, suggesting that the optimal charge distribution is a useful design goal. Furthermore, detailed suggestions for chemical modification generated by this approach are in many cases consistent with observed improvements in binding affinity, and the method appears to be useful despite discrete chemical constraints. Taken together, these results suggest that charge optimization is useful in facilitating generation of compound ideas in lead optimization. Our results also provide insight into design of neuraminidase inhibitors.

Organization of Calcium Channel β1a Subunits in Triad Junctions in Skeletal Muscle

In skeletal muscle, dihydropyridine receptors (DHPRs) in the plasma membrane interact with the type 1 ryanodine receptor (RyR1) at junctions with the sarcoplasmic reticulum. This interaction organizes junctional DHPRs into groups of four termed tetrads. In addition to the principle alpha1S subunit, the beta1a subunit of the DHPR is also important for the interaction with RyR1. To probe this interaction, we measured fluorescence resonance energy transfer (FRET) of beta1a subunits labeled with cyan fluorescent protein (CFP) and/or yellow fluorescent protein (YFP). Expressed in dysgenic (alpha1S-null) myotubes, YFP-beta1a-CFP and CFP-beta1a-YFP were diffusely distributed in the cytoplasm and highly mobile as indicated by fluorescence recovery after photobleaching. Thus, beta1a does not appear to bind to other cellular proteins in the absence of alpha1S. FRET efficiencies for these cytoplasmic beta1a subunits were approximately 6-7%, consistent with the idea that <10 nm separates the N and C termini. After coexpression with unlabeled alpha1S (in dysgenic or beta1-null myotubes), both constructs produced discrete fluorescent puncta, which correspond to assembled DHPRs in junctions and that did not recover after photobleaching. In beta1-null myotubes, FRET efficiencies of doubly labeled beta1a in puncta were similar to those of the same constructs diffusely distributed in the cytoplasm and appeared to arise intramolecularly, since no FRET was measured when mixtures of singly labeled beta1a (CFP or YFP at the N or C terminus) were expressed in beta1-null myotubes. Thus, DHPRs in tetrads may be arranged such that the N and C termini of adjacent beta1a subunits are located >10 nm from one another.

Proton-bifurcated C—H...(O,O) hydrogen bonds in 2,3-dichloro-6-nitrobenzylaminium chloride

In the crystal structure of the title salt, C7H7Cl2N2O2+.Cl-, the chloride anions participate in extensive hydrogen bonding with the aminium cations and indirectly link the molecules through multiple N+-H...Cl- salt bridges. There are two independent molecules in the asymmetric unit, related by a pseudo-inversion center. The direct intermolecular coupling is established by C-H...O, C-H...Cl and C-Cl...Cl(-) interactions. A rare three-center (donor bifurcated) C-H...(O,O) hydrogen bond is observed between the methylene and nitro groups, with a side-on intramolecular component of closed-ring type and a head-on intermolecular component.

Maximum entropy: A complement to Tikhonov regularization for determination of pair distance distributions by pulsed ESR

Tikhonov regularization (TIKR) has been demonstrated as a powerful and valuable method for the determination of distance distributions of spin-pairs in bi-labeled biomolecules directly from pulsed ESR signals. TIKR is a direct method, which requires no iteration, and, therefore, provides a rapid and unique solution. However, the distribution obtained tends to exhibit oscillatory excursions with negative portions in the presence of finite noise, especially in the peripheral regions of the distribution. The Shannon–Jaynes entropy of a probability distribution provides an intrinsic non-negativity constraint on the probability distribution and an unbiased way of obtaining information from incomplete data. We describe how the maximum entropy regularization method (MEM) may be applied to solve the ill-posed nature of the dipolar signal in pulsed ESR. We make use of it to suppress the negative excursions of the distance distribution and to increase the tolerance to noise in the dipolar signal. Model studies and experimental data are investigated, and they show that, with the initial or “seed” probability distribution that is required for MEM taken as the TIKR result, then MEM is able to provide a regularized solution, subject to the non-negativity constraint, and it is effective in dealing with noise that is problematic for TIKR. In addition we have incorporated into our MEM method the ability to extract the intermolecular dipolar component, which is embedded in the raw experimental data. We find that MEM minimization, which is implemented iteratively, is greatly accelerated using the TIKR result as the seed, and it converges more successfully. Thus we regard the MEM method as a complement to TIKR by securing a positive pair distance distribution and enhancing the accuracy of TIKR.

Intra- and intermolecular components of the ν2 forbidden band of CF4 in pure gas and in He, Ar, Xe and N2 mixtures

Spectra of CF4 as pure gas and in mixtures with gaseous He, Ar, Xe and N2 were obtained in the region of the forbidden ν2 band at pressures from about 1 atm up to 100 atm at ambient temperature. The absorption consists of two components depending on the gas pressure. The first, with an integrated intensity (cm−2 Amagat−1) that is independent of pressure, arises through the Coriolis or intramolecular interactions. The second, varying linearly with the partial pressure, is attributable to additional absorption arising during intermolecular binary collisions. The intensity of each of these components was measured and analysed, and from the results we are able to draw some conclusions concerning the collision-induced mechanisms responsible for the absorption.

Chloro(phenyl)(1H-pyrazole-κN2)(triphenylphosphine-κP)palladium(II)

In the title compound, [Pd(C6H5)Cl(C3H4N2){P(C6H5)3}], PdClPh(pyrazole)(PPh3), the phenyl and Cl ligands lie mutually trans. The compound is the first structurally characterized complex with four monodentate Cl, P, N and (non-carbenoid) C ligands in a squareplanar four-coordinate palladium(II) environment. The pyrazole ligand is coplanar with the latter array. The pyrazole NH group forms a bifurcated hydrogen bond to Cl, with an intra and intermolecular component.

Correlated intermolecular interaction components from asymptotically corrected Kohn-Sham orbitals

The symmetry-adapted perturbation theory (SAPT) that has the ability in decomposition of the total interaction energy into physically meaningful components is used to provide a more fundamental understanding of intermolecular forces. This work was motivated by the difficulty of standard SAPT in computing the intermolecular interactions for large energetic dimer systems. SAPT based on Kohn-Sham orbitals (SAPT(DFT)) proves computationally efficient for these large systems, but has been shown to perform poorly for interaction energy components. The deficiencies of SAPT(DFT) result from wrong asymptotical behaviors of commonly used exchange-correlation potentials. To remove the deficiencies, two asymptotic corrections by means of van Leeuwen and Baerends (LB) model potential and Fermi-Amaldi (FA) type potential were applied into three small test systems comprising He 2 , HF 2 and (N 2 ) 2 and a set of larger nitramide dimers at several separations. The results showed that when utilizing newly developed frequency-dependent density susceptibilities (FDDS) technique for computing dispersion energy, the FA asymptotic correction is very effective to circumvent these deficiencies in SAPT(DFT) and yields a good accuracy over the LB correction. The FA corrected SAPT(DFT) approach is capable of correctly predicting all the quantitative trends in binding energies for all test cases and substantially reduces computational cost as compared with the standard SAPT calculations. The successful application of the approach to nitramide dimer demonstrates that it potentially provides a good means to calculate accurately intermolecular forces in larger system such as energetic systems.

6-Amino-3-methyl-5-nitrosopyrimidine-2,4(1H,3H)-dione forms a three-dimensional hydrogen-bonded framework structure.

Molecules of the title compound, C(5)H(6)N(4)O(3), are linked into a single three-dimensional framework by a two-centre N-H.O hydrogen bond [H.O = 1.92 A, N.O = 2.785 (2) A and N-H.O = 168 degrees ], a two-centre N-H.H hydrogen bond [H.N = 2.19 A, N.N = 3.017 (2) A and N-H.N = 157 degrees ] and the intermolecular component of an effectively planar three-centre N-H.(O)(2) hydrogen bond [H.O = 2.03 and 2.31 A, N.O = 2.645 (2) and 2.957 (2) A, N-H.O = 126 and 130 degrees, and O.H.O = 101 degrees ].

Lone Pairs in Confrontation in [M(S.CS.XR(n))3] Systems. Crystal and Molecular Structure of Tris(N-methyl-N-phenyldithiocarbamato) antimony(III)

Tris(dithiochelate) complexes of metal ions exhibit a diversity of interesting behaviours.[1] The particular ligand form R(n)XCS2 (L) may be varied by changing X sequentially (e.g.) from C (dithiocarboxylate) to N (dithiocarbamate) to O (xanthate) among the first row elements, with a consequent change in electron density at the sulfur atoms. This in turn influences features such as the crystal-field strength experienced at the metal in those complexes where it forms symmetrically bonded chelates. A change in the metal atom may cause a change in bonding mode. For example, trivalent transition metal and group 13 species ML3 exhibit metal core environments of 32 symmetry, whereas with group 15 metals, the core symmetry is degraded to 3 with the bonding in the chelate becoming unsymmetrical, possibly with concomitant effects attributable to a stereochemically active lone pair. In general terms, among the now numerous array of such complexes structurally characterized, a further degradation in symmetry about the metal atom is often found among complexes of the larger metals Sb and Bi where scope for increased coordination number is enhanced with increase in metal size. This leads to the observation of loosely[2] or strongly[3] bonded dimeric forms, due to the effect of M· · ·S intermolecular interactions between the two component molecules. Among the structurally characterized ML3 where M is a trivalent group 15 metal, a number of examples may be identified where the potential threefold symmetry is realized by location of the metal atom on a crystallographic symmetry axis. The majority of such examples, interestingly, are found in space group R3,[4–7] with the implication that molecules so disposed will lie in confrontation with their inversion images. This may be a consequence of the dominance of ‘packing forces’ at the supramolecular level. Alternatively, it may be a manifestation of some tendency towards dimerization by metal–metal bond formation.This raises the possibility of the presence of some interaction competing with the confrontation of any postulated lone pairs, which should lie coincident with the molecular/crystallographic axis, or, alternatively, a diminution in lone-pair/lone-pair repulsion. A vehicle which drew our attention to this curiosity was the observation of apparent rhombohedral symmetry in nicely crystalline, golden specimens of the title compound, [Sb(S2CNMePh)3] (m.p. 216–218◦C. Found: C, 42.9; H, 3.9; N, 6.3%. C24H24N3S6Sb requires: C, 43.1; H, 3.6; N, 6.3%.) prompting us to determine its crystal structure. Our hopes that the molecule would be disposed on a crystallographic 3-axis (indeed, a 3-axis in space group R3) were realized, one third of the molecule comprising the asymmetric unit of the structure, the first example of this type for X=N. The molecule is depicted, together with its inversion image in Figure 1, normal to and down the crystallographic 3-axis, with the phenyl substituents of the ‘tails’of successive pairs interleaving. Sb–S(1,2) are 2.528(2), 3.000(3) A, with S(1)–Sb–S(1) 83.34(7), S(2)–Sb–S(2) 116.75(8)◦, values in which it is of interest to compare with their counterparts in the recently determined structure of [Sb(S2CNMeCy)3],[8] the molecules of which are stacked successively up the symmetry axis in space group P63 (2.530(1), 2.975(1)) A, 87.1(2), 117.2(2)◦). These differences are quite minor, suggesting that the mode of stacking—successive, compared with confrontational—plays little part as a determinant of these values. (Interestingly, the substituent dispositions— methyl versus ring—are interchanged in the two compounds, so that parameter is not constant throughout.) We also note the numerous array of related structures that have been determined which, although not in space group R3 (or of similar centrosymmetric, threefold axis combinations), do crystallize in centrosymmetric space groups with some form of binuclear interaction across the centres. Generally, these are of a lower symmetry with significant M· · ·S intermolecular component, and we do not consider such examples further here. Table 1 marshals relevant parameters for all examples of group 15 [M(S2CXR(n))3] complexes which have been structurally defined as R3 (Z 2 (rhombohedral cell)), these being confined to the cases M=As or Sb. (There is an X=P example,[9] but P is disordered).Although for neither of these is there a complete X= (C,) N, or O array, the examples

Chemical force spectroscopy in heterogeneous systems: intermolecular interactions involving epoxy polymer, mixed monolayers, and polar solvents.

We used chemical force microscopy (CFM) to study adhesive forces between surfaces of epoxy resin and self-assembled monolayers (SAMs) capable of hydrogen bonding to different extents. The influence of the liquid medium in which the experiments were carried out was also examined systematically. The molecular character of the tip, polymer, and liquid all influenced the adhesion. Complementary macroscopic contact angle measurements were used to assist in the quantitative interpretation of the CFM data. A direct correlation between surface free energy and adhesion forces was observed in mixed alcohol-water solvents. An increase in surface energy from 2 to 50 mJ/m(2) resulted in an increase in adhesion from 4-8 nN to 150-300 nN for tips with radii of 50-150 nm. The interfacial surface energy for identical nonpolar surface groups of SAMs was found not to exceed 2 mJ/m(2). An analysis of adhesion data suggests that the solvent was fully excluded from the zone of contact between functional groups on the tip and sample. With a nonpolar SAM, the force of adhesion increased monotonically in mixed solvents of higher water content; whereas, with a polar SAM (one having a hydrogen bonding component), higher water content led to decreased adhesion. The intermolecular force components theory was used for the interpretation of adhesion force measurements in polar solvents. Competition between hydrogen bonding within the solvent and hydrogen bonding of surface groups and the solvent was shown to provide the main contribution to adhesion forces. We demonstrate how the trends in the magnitude of the adhesion forces for chemically heterogeneous systems (solvents and surfaces) measured with CFM can be quantitatively rationalized using the surface tension components approach. For epoxy polymer, inelastic deformations also contributed heavily to measured adhesion forces.