Uracil-water interaction revisited - in search of single H-bonded secondary minima.

Monohydrated uracil (UW) complexes are stabilized by both O⋯HO and NH⋯O hydrogen bonds (H-bonds), simultaneously participating in forming three stable cyclic structures. The role and contribution of these individual H-bonds (O⋯HO and NH⋯O) to the stability of the three UW complexes are still not understood, because of the technical problems in obtaining their optimized structures by standard geometry optimization. The present study explores a non-standard approach to identify three single H-bonded local minima structures without imaginary frequency using DFT (M06-2X, B3LYP and B3LYP-D3), MP2 and CCSD(T) theories and Dunning's correlation-consistent aug-cc-pVTZ basis set, in both vacuum and aqueous media (CPCM method). The results reveal that these new structures are very shallow secondary minima between two deep wells or next to a deep well of primary minima (double H-bonded structures) in the potential energy surface. The H-bond energy of these single H-bonded complexes is found to be less sensitive to a wide range (about 15-20 degrees) of O⋯HO and NH⋯O angles, and the linearity is preferred in the stable three single H-bonded structures. The technical method used to locate such a shallow minimum is described in detail and may be useful for identifying local minima in other cases where consecutive multiple H-bonded structures are global minima. Energy decomposition (using symmetry adapted perturbation theory (SAPT)) of interaction energy, electron redistribution, and relevant vibrational modes are discussed.

N/O→B dative bonds supplemented by N-HN/HC hydrogen bonds make BN-cages an attractive candidate for DNA-nucleobase adsorption - an MP2 prediction.

The response of B12N12-nanocages towards DNA-nucleobases (adenine, guanine, cytosine, and thymine) is investigated using MP2 and DFT (M06-2X) levels of theory with the 6-311+G** basis set. Multiple BN-cage-nucleobase structures for each nucleobase emerged depending on the number of Lewis base centers of nucleobases. The main source of stability of these complexes is the N/O→B dative bond, where the N or O atom of nucleobases donates the lone-pair electron to one of the boron atoms of the nanocage. Nitrogen atoms of the BN-cage, adjacent to the B-site forming dative bond, act as a proton acceptor to form multiple (N-HN and N-HC) hydrogen bonds, where proton-donors NH and CH are part of nucleobases. MP2/6-311+G** adsorption energies are -43.1, -43.4 and -45.3 kcal mol-1 (B12N12-adenine), -37.1, -41.9 and -43.3 kcal mol-1 (B12N12-guanine), -41.3 and -43.4 (B12N12-cytosine), and -29.3 and -31.3 (B12N12-thymine). Similar adsorption energies were recorded for larger BN-fullerenes-nucleobases, namely B16N16 and B24N24. Changes in adsorption energies and structures of these nano-bio-hybrid materials in aqueous media are also discussed. Computationally cost-effective MP2 single point calculations at the M06-2X optimized geometries were found to be reliable in predicting adsorption energies. The effect of the BN-network and H-bonds on the adsorption process is assessed by comparing the results with simple BH3-nucleobase models. BSSE correction to the adsorption energy is not recommended.

Local aromaticity in polyacenes manifested by individual proton and carbon shieldings: DFT mapping of aromaticity.

Exponential dependencies between locally calculated geometric and magnetic indexes of aromaticity, harmonic oscillator model of aromaticity (HOMA) and nucleus independent chemical shifts (NICS)(0), NICS(1) and NICS(1)zz, and the number of conjugated benzene rings in linear acenes, from benzene to decacene were observed at B3LYP/6-311+G** level of theory. Correlations between HOMA and NICS indexes showed exponential dependencies and were fitted with simple three-parameter function. Similar correlations between both indexes of aromaticity and proton and carbon nuclear isotropic shieldings of individual acene rings were observed. Contrary to proton data, the predicted 13 C nuclear isotropic shieldings of carbon atoms belonging to inner rings in polyacenes were less shielded, indicating lower aromaticity and therefore, higher reactivity.

Evaluation of Lignans from Piper cubeba against Schistosoma mansoni Adult Worms: A Combined Experimental and Theoretical Study.

Six dibenzylbutyrolactonic lignans ((-)-hinokinin (1), (-)-cubebin (2), (-)-yatein (3), (-)-5-methoxyyatein (4), dihydrocubebin (5) and dihydroclusin (6)) were isolated from Piper cubeba seed extract and evaluated against Schistosoma mansoni. All lignans, except 5, were able to separate the adult worm pairs and reduce the egg numbers during 24 h of incubation. Lignans 1, 3 and 4 (containing a lactone ring) were the most efficient concerning antiparasitary activity. Comparing structures 3 and 4, the presence of the methoxy group at position 5 appears to be important for this activity. Considering 1 and 3, it is possible to see that the substitution pattern change (methylenedioxy or methoxy groups) in positions 3' and 4' alter the biological response, with 1 being the second most active compound. Computational calculations suggest that the activity of compound 4 can be correlated with the largest lipophilicity value.

How the electron-deficient cavity of heterocalixarenes recognizes anions: insights from computation.

We have quantum chemically analyzed the bonding mechanism behind the affinity of various heterocalixarenes for anions with a range of geometries and net charges, using modern dispersion-corrected density functional theory (DFT-D3BJ). The purpose is to better understand the physical factors that are responsible for the computed affinities and thus to develop principles for a more rational design of anion receptors. Our model systems comprise heterocalixarenes 1-4 as hosts, which are characterized by different bridging heteroatoms (O, N, S) as well as the anionic guests Cl-, Br-, I-, BF4-, CH3CO2-, H2PO4-, HSO4-, NCS-, NO3-, PF6-, and SO42-. We use various analysis schemes (EDA, NCI, and NBO) to elucidate the interactions between the calixarene cavity and the anions to probe the importance of the different bonding modes (anion-π, lone-pair electron-π, σ-complexes, hydrogen bonds, and others) of the interactions. Electrostatic interactions appear to be dominant for heterocalixarenes with oxygen bridges whereas orbital interactions prevail in the case of nitrogen and sulfur bridges. Dispersion interactions are however in all cases non-negligible.

Segmentation and additive approach: A reliable technique to study noncovalent interactions of large molecules at the surface of single-wall carbon nanotubes.

This investigation explores a new protocol, named Segmentation and Additive approach (SAA), to study exohedral noncovalent functionalization of single-walled carbon nanotubes with large molecules, such as polymers and biomolecules, by segmenting the entire system into smaller units to reduce computational cost. A key criterion of the segmentation process is the preservation of the molecular structure responsible for stabilization of the entire system in smaller segments. Noncovalent interaction of linoleic acid (LA, C18 H32 O2 ), a fatty acid, at the surface of a (10,0) zigzag nanotube is considered for test purposes. Three smaller segmented models have been created from the full (10,0)-LA system and interaction energies were calculated for these models and compared with the full system at different levels of theory, namely ωB97XD, LDA. The success of this SAA is confirmed as the sum of the interaction energies is in very good agreement with the total interaction energy. Besides reducing computational cost, another merit of SAA is an estimation of the contributions from different sections of the large system to the total interaction energy which can be studied in-depth using a higher level of theory to estimate several properties of each segment. On the negative side, bulk properties, such as HOMO-LUMO (highest occupied molecular orbital - lowest occupied molecular orbital) gap, of the entire system cannot be estimated by adding results from segment models. © 2016 Wiley Periodicals, Inc.

Site and chirality selective chemical modifications of boron nitride nanotubes (BNNTs) via Lewis acid-base interactions.

The pristine BNNTs contain both Lewis acid (boron) and Lewis base (nitrogen) centers at their surface. Interactions of ammonia and borane molecules, representatives of Lewis base and acid as adsorbates respectively, with matching sites at the surface of BNNTs, have been explored in the present DFT study. Adsorption energies suggest stronger chemisorption (about 15-20 kcal mol(-1)) of borane than ammonia (about 5-10 kcal mol(-1)) in both armchair (4,4) and zigzag (8,0) variants of the tube. NH3 favors (8,0) over the (4,4) tube, whereas BH3 exhibits the opposite preference, indicating some chirality dependence on acid-base interactions. A new feature of bonding is found in BH3/AlH3-BNNTs (at the edge site) complexes, where one hydrogen of the guest molecule is involved in three-center two-electron bonding, in addition to dative covalent bond (N: → B). This interaction causes a reversal of electron flow from borane/alane to BNNT, making the tube an electron acceptor, suggesting tailoring of electronic properties could be possible by varying strength of incoming Lewis acids. On the contrary, BNNTs always behave as electron acceptor in ammonia complexes. IR, XPS and NMR spectra show some characteristic features of complexes and can help experimentalists to identify not only structures of such complexes but also the location of the guest molecules and design second functionalizations. Interaction with several other neutral BF3, BCl3, BH2CH3 and ionic CH3(+) acids as well as amino group (CH3NH2 and NH2COOH) were also studied. The strongest interaction (>100 kcal mol(-1)) is found in BNNT-CH3(+) complexes and H-bonds are the only source of stability of NH2COOH-BNNT complexes.

Pauli-Rydberg-London potential: an accurate pair potential function for diatomic systems.

Based on a molecular-orbital theory for H2(+), we have proposed and tested a pair potential function form for the diatomic systems. The new form has included the Pauli repulsive term, Rydberg potential, and London inverse-sixth-power energy, and is accurate at all relevant distances and simple enough for practical application in all-atom computer simulations. We find that an "approximate" universal reduced potential curve for strongly and weakly bound diatomic molecules may exist.

The polar mechanism for the nitration of benzene with nitronium ion: ab initio structures of intermediates and transition states.

The nitration of benzene by nitronium ion in the gas phase has been re-examined. New features have been revealed; in particular, three transition states have been detected along the reaction coordinate. These have been shown by IRC analysis to connect an initially formed π complex (pi1) to a σ complex (sig1) (via ts1), sig1 to sig2 (via ts2), and finally sig2 to the product (via ts3). Sig2 also connects to another isomeric σ complex sig3 (via sig23ts), which connects to sig4 (via sig34ts).

B3N3 borazine substitution in hexa-peri-hexabenzocoronene: computational analysis and Scholl reaction of hexaphenylborazine.

The doping of graphene molecules by borazine (B(3)N(3)) units may modify the electronic properties favorably. Therefore, the influence of the substitution of the central benzene ring of hexa-peri-hexabenzocoronene (HBC, C(42)H(18)) by an isoelectronic B(3)N(3) ring resulting in C(36)B(3)N(3)H(18) (B3N3HBC) is investigated by computational methods. For comparison, the isoelectronic and isosteric all-B/N molecule B(21)N(21)H(18) (termed BN) and its carbon derivative C(6)B(18)N(18)H(18) (C6BN), obtained by substitution of a central B(3)N(3) by a C(6) ring, are also studied. The substitution of C(6) in the HBC molecule by a B(3)N(3) unit results in a significant change of the computed IR vibrational spectrum between 1400 and 1600 cm(-1) due to the polarity of the borazine core. The properties of the BN molecule resemble those of hexagonal boron nitride, and substitution of the central B(3)N(3) ring by C(6) changes the computed IR vibrational spectrum only slightly. The allowed transitions to excited states associated with large oscillator strengths shift to higher energy upon going from HBC to B3N3HBC, but to lower energy upon going from BN to C6BN. The possibility of synthesis of B3N3HBC from hexaphenylborazine (HPB) using the Scholl reaction (CuCl(2)/AlCl(3) in CS(2)) is investigated. Rather than the desired B3N3HBC an insoluble and X-ray amorphous polymer P is obtained. Its analysis by IR and (11)B magic angle spinning NMR spectroscopy reveals the presence of borazine units. The changes in the (11)B quadrupolar coupling constant C(Q), asymmetry parameter η, and isotropic chemical shift δ(iso)((11)B) with respect to HPB are in agreement with a structural model that includes B3N3HBC-derived monomeric units in polymer P. This indicates that both intra- and intermolecular cyclodehydrogenation reactions take place during the Scholl reaction of HPB.

Analysis of the reactivities of protein C-H bonds to H atom abstraction by OH radical.

Ab initio and density functional theory calculations are used to monitor the process wherein a OH· radical is allowed to approach the various CH groups of a Leu dipeptide, with its CH(2)CH(CH(3))(2) side chain. After forming an encounter complex, the OH· abstracts the pertinent H atom, and the resulting HOH is then dissociated from the complex. The energy barriers for H· abstraction from the ß, γ, and δ CH groups are all less than 8 kcal/mol, but a significantly higher barrier is computed for the C(α)H removal. This higher barrier is the result of the strong H-bonds formed in the encounter complex between the OH· and the NH and C═O groups of the peptide units that surround the C(α) atom. This low-energy complex represents a kinetic trap which raises the energy needed to surmount the ensuing H· transfer barrier.

A novel approach for the design of a highly selective sulfate-ion-selective electrode.

A hydroxyl Schiff base molecule was synthesized from tetraethylenetetramine and 4-nitrosalicylaldehyde and explored as an ionophore with ionic liquid, cation excluder in PVC membranes showing remarkable sulfate selectivity; the optimal recognition site was predicted by density function theory (DFT) simulation.

Borazine and benzene homo- and heterodimers.

The homodimers of benzene and borazine as well as a heterodimer consisting of one benzene (bz) and one borazine (bor) molecule are investigated using MP2, SCS-MP2, and CCSD(T) theories in conjunction with basis sets of up to quadruple-zeta quality. Dimer geometries were completely optimized using the resolution of the identity approximation of MP2 with a QZVPP basis set and characterized by computation of harmonic vibrational frequencies using triple-zeta basis sets. While significant higher order correlation effects beyond MP2 are important for the benzene dimer, these are very small for the borazine dimer and intermediate for the heterodimer. The spin-component scaling (SCS) correction of MP2 produces binding energies for the borazine dimer that are too low but yields very good agreement with CCSD(T) for the heterodimer. The decrease in the intermolecular distance in the sandwich (S) configurations from bz(2) via bz-bor to bor(2) is accompanied by an increased binding energy and a change from second-order stationary points to a minimum for bor(2). The T isomer is less stable than the S configuration for bor(2), but it is preferred over the S and a parallel-displaced (PD) arrangement in the heterodimer. The following order of stability is obtained for the minima at the extrapolated CCSD(T) level: T(bz-bor) > S(bor(2)) > PD(bz-bor) > PD(bor(2)) > T(bor(2)) > PD(bz(2)). The most stable isomer at all levels of theory, T(bz-bor), features a NH...pi interaction.

Theoretical study of the effect of structural modifications on the hyperpolarizabilities of indigo derivatives.

The static first and second hyperpolarizabilities of a number of indigo (In) derivatives, donor-In-donor, acceptor-In-acceptor, and donor-In-acceptor, have been calculated at the B3LYP/6-31+G* level. The various useful relations are obtained from the standard sum-overstate (SOS) expressions with the use of the Thomas-Kuhn (TK) sum rule. The variation of NLO properties, especially the second hyperpolarizability (gamma) of indigo compounds, can be satisfactorily explained in terms of ground-state electric moments, linear polarizability (alpha), and second-order polarizability (beta). The noncentrosymmetry arising from replacement of the ring NH of indigo with O and S atoms and also substitution with donor and acceptor at different ring positions of indigo lead to rather significant modulation of gamma. The appreciable decrease of third-order polarizability on pyramidalization of the NH2 group as explained in the present model is equivalent to the decrease of the dipole moment difference and increase of the transition energy in the two-state model.

Performance of polarization-consistent vs. correlation-consistent basis sets for CCSD(T) prediction of water dimer interaction energy.

Detailed study of Jensen's polarization-consistent vs. Dunning's correlation-consistent basis set families performance on the extrapolation of raw and counterpoise-corrected interaction energies of water dimer using coupled cluster with single, double, and perturbative correction for connected triple excitations (CCSD(T)) in the complete basis set (CBS) limit are reported. Both 3-parameter exponential and 2-parameter inverse-power fits vs. the cardinal number of basis set, as well as the number of basis functions were analyzed and compared with one of the most extensive CCSD(T) results reported recently. The obtained results for both Jensen- and Dunning-type basis sets underestimate raw interaction energy by less than 0.136 kcal/mol with respect to the reference value of - 4.98065 kcal/mol. The use of counterpoise correction further improves (closer to the reference value) interaction energy. Asymptotic convergence of 3-parameter fitted interaction energy with respect to both cardinal number of basis set and the number of basis functions are closer to the reference value at the CBS limit than other fitting approaches considered here. Separate fits of Hartree-Fock and correlation interaction energy with 3-parameter formula additionally improved the results, and the smallest CBS deviation from the reference value is about 0.001 kcal/mol (underestimated) for CCSD(T)/aug-cc-pVXZ calculations. However, Jensen's basis set underestimates such value to 0.012 kcal/mol. No improvement was observed for using the number of basis functions instead of cardinal number for fitting. Graphical Abstract.

Spectroscopic and structural signature of the CH-O hydrogen bond.

It has been observed that the vibrational stretching frequency of a C-H covalent bond commonly shifts to the blue and suffers intensity loss, when the CH engages in a hydrogen bond. However, the shift does not always occur in this direction, and there are cases when a CH blue shift may be present even in the absence of a CH...O interaction. Ab initio quantum calculations are used to analyze the structure, and vibrational and NMR spectra of small model systems containing both conventional and CH...O H-bonds, and thereby identify patterns that unambiguously signal the presence of a CH...O interaction.

Spectroscopy, crystal structure, valance molecular orbital energy level diagram and DFT study of cis-[Cr(2,2'-bipy)2Cl2](Cl)0.38(PF6)0.62.

A new octahedral chromium(III) complex having 2,2'-bipyridine as ligand system was synthesized in methanol. Single crystal X-ray diffraction analysis shows that it possesses non-stoichiometry in its anionic primary covalency. It has also been studied by elemental analyses, optical spectroscopy (UV-vis, IR) and magnetic susceptibility data. DFT calculations (with B3LYP functional and double-xi quality LANLDZ(D95V) basis set) were carried out to interpret the electronic and infrared spectra of the complex. The DFT optimized geometric structure for the complex is compared with the X-ray crystallographic data; the theory-experiment agreement is satisfactory.

Nanoscale stabilization of zintl compounds: 1D ionic Li-P double helix confined inside a carbon nanotube.

One-dimensional (1D) ionic nanowires are extremely rare materials due to the difficulty in stabilizing 1D chains of ions under ambient conditions. We demonstrate here a theoretical prediction of a novel hybrid material, a nanotube encapsulated 1D ionic lithium monophosphide (LiP) chain, featuring a unique double-helix structure, which is very unusual in inorganic chemistry. This nanocomposite has been investigated with density functional theory, including molecular dynamics simulations and electronic structure calculations. We find that the formation of the LiP double-helical nanowire is facilitated by strong interactions between LiP and CNTs resulting in a charge transfer. This work suggests that nanostructured confinement may be used to stabilize other polyphosphide 1D chains, thus opening new ways to study the chemistry of zintl compounds at the nanoscale.

Effect of solvent upon CH...O hydrogen bonds with implications for protein folding.

The series of CH...O bonds formed between CF(n)H(4-n) (n = 0-3) and water are studied by quantum calculations under vacuum and in various solvents, including aqueous environment. The results are compared with the OH...O bond of the water dimer in the same solvents. Increasing polarity of the solvent leads in all cases to a lessening of the H-bond interaction energy, in a uniform fashion such that the CH...O bonds all remain weaker than OH...O in any solvent. These H-bond weakenings are coupled to a shortening of the inter-subunit separation. The contraction of the covalent CH bond to the bridging proton is reduced as the solvent becomes more polar, and the blue shift of its stretching vibration is likewise diminished. A process is considered that simulates protein folding by starting from a pair of noninteracting subunits in aqueous solvent and then goes to a H-bonded pair within the confines of a protein environment. This process is found to be energetically more favorable for some of the CH...O H-bonds than for the nominally stronger conventional OH...O H-bond. This finding suggests that CH...O bonds can make important energetic contributions to protein folding, on par with those made by traditional H-bonds.

Electronic structure and spectroscopic properties of the two structural isomers of donor-acceptor substituted sesquifulvalene in the gas and solution phases-a case study of sudden polarization.

The ground state equilibrium structure and electric properties of two structural isomers of donor-acceptor substituted sesquifulvalene have been calculated at ab initio HF and MP2 levels for different conformations. The electronic properties of low lying excited singlets are calculated by using CI calculations including single excitations only. Isomer I in which the inter-ring charge transfer (CT) is reinforced in the presence of substituents shows sudden polarization in the ground and two lower lying excited states, while isomer II in which the longitudinal CT interaction is attenuated does not exhibit sudden polarization. The phenomenon of sudden polarization has been rationalized in terms of the easy polarization, smaller rotational barrier, and enhanced inter-ring CT on going from the planar to the orthogonal geometry. The appreciably large static second-order polarizability of I stems from its sudden polarized ground state. The solvent (using the conductor-like polarizable continuum model (CPCM)) plays a significant role on the modulation of ground and excited state electronic properties which, in general, predicts blue-shifts for I. However, for molecule II, the two lower energy transitions show a red-shift while the others show a weaker blue-shift at any conformation.