Dissecting Bonding Interactions in Cysteine Dimers.

Neutral (n) and zwitterionic (z) forms of cysteine monomers are combined in this work to extensively explore the potential energy surfaces for the formation of cysteine dimers in aqueous environments represented by a continuum. A simulated annealing search followed by optimization and characterization of the candidate structures afforded a total of 746 structurally different dimers held together via 80 different types of intermolecular contacts in 2894 individual non-covalent interactions as concluded from Natural Bond Orbitals (NBO), Quantum Theory of Atoms in Molecules (QTAIM) and Non-Covalent Interactions (NCI) analyses. This large pool of interaction possibilities includes the traditional primary hydrogen bonds and salt bridges which actually dictate the structures of the dimers, as well as the less common secondary hydrogen bonds, exotic X⋯Y (X = C, N, O, S) contacts, and H⋯H dihydrogen bonds. These interactions are not homogeneous but have rather complex distributions of strengths, interfragment distances and overall stabilities. Judging by their Gibbs bonding energies, most of the structures located here are suitable for experimental detection at room conditions.

A Comprehensive Picture of the Structures, Energies, and Bonding in the Alanine Dimers.

High level quantum mechanical computations and extensive stochastic searches of the potential energy surfaces of the Alanine dimers uncover rich and complex structural and interaction landscapes. A total of 416 strongly bound (up 13.4 kcal mol-1 binding energies at the DLPNO-CCSD(T)/6-311++G(d,p) level corrected by the basis set superposition error and by the zero point vibrational energies over B3LYP-D3 geometries), close energy equilibrium structures were located, bonded via 32 specific types of intermolecular contacts including Y⋅⋅⋅H-X primary and Y⋅⋅⋅H-C secondary hydrogen bonds, H⋅⋅⋅H dihydrogen contacts, and non conventional anti-electrostatic Y δ-⋯ X δ- interactions. The putative global minimum is triply degenerate, corresponding to the structure of the common dimer of a carboxylic acid. All quantum descriptors of chemical bonding point to a multitude of weak individual interactions within each dimer, whose cumulative effect results in large binding energies and in an attractive fluxional wall of non-covalent interactions in the interstitial region between the monomers.

A detailed look at the bonding interactions in the microsolvation of monoatomic cations.

Global and local descriptors of the properties of intermolecular bonding, formally derived from independent methodologies (QTAIM, NCI, NBO, density differences) afford a highly complex picture of the bonding interactions responsible for microsolvation of monoatomic cations. In all cases, the dominant factor dictating geometries and interaction strengths is the electrophilic power of the metal cation. The formal charge disrupts the hydrogen bonding network otherwise present in pristine water clusters, making the hydrogen bonds considerably stronger, even inducing some degree of covalency. All MO interactions are highly ionic, with strengths than in some cases approach that of the reference LiCl bond. Accumulation of electron density in the region connecting MO is observed, thus, ionic bonding in the microsolvation of monoatomic cations is not as simple as an electrostatic interaction between opposing charges.

A combined experimental and computational study of the molecular interactions between anionic ibuprofen and water.

In this work, we report a detailed study of the microsolvation of anionic ibuprofen, Ibu(-). Stochastic explorations of the configurational spaces for the interactions of Ibu(-) with up to three water molecules at the DFT level lead to very rich and complex potential energy surfaces. Our results suggest that instead of only one preponderant structure, a collection of isomers with very similar energies would have significant contributions to the properties of the solvated drug. One of these properties is the shift on the vibrational frequencies of the asymmetric stretching band of the carboxylate group in hydrated Ibu(-) with respect to the anhydrous drug, whose experimental values are nicely reproduced using the weighted contribution of the structures. We found at least three types of stabilizing interactions, including conventional CO2(-)⋯H2O, H2O⋯H2O charge assisted hydrogen bonds (HBs), and less common H2O⋯H-C and H2O⋯π interactions. Biological water molecules, those in direct contact with Ibu(-), prefer to cluster around the carboxylate oxygen atoms via cyclic or bridged charge assisted hydrogen bonds. Many of those interactions are strongly affected by the formal carboxylate charge, resulting in "enhanced" HBs with increased strengths and degree of covalency. We found striking similarities between this case and the microsolvation of dymethylphosphate, which lead us to hypothesize that since microsolvation of phosphatidylcholine depends mainly on the formal charge of its ionic PO2(-) group in the polar head, then microsolvation of anionic ibuprofen and interactions of water molecules with eukaryotic cell membranes are governed by the same types of physical interactions.

Structures, energies, and bonding in the water heptamer.

In this paper we report the geometries and properties of 38 distinct geometrical motifs located on the B3LYP/6-31+G(d), MP2/6-311++G(d, p) potential energy surfaces of the water heptamer. Binding energies of up to 45 kcal/mol are calculated. All motifs fall within 10 kcal/mol of the most stable conformation, with at least 13 structural patterns located no more than 3 kcal/mol above, leading to a very complex potential energy surface, populated by a multitude of motifs each one allowing large numbers of conformations. Cluster stability does not seem to be correlated with the number of hydrogen bonds. Compact structures are energetically favored by electronic energies with zero-point energy corrections, while more open structures are preferred when temperature and entropy are accounted for. The molecular interactions holding the clusters as discrete units lead to large binding energies but are not strong enough to cause significant changes in the geometries of the interacting monomers. Our results indicate that bonding in the water heptamers can be considered as largely non-shared interactions with contributions from intermediate character of increasing covalency.

Structural characterization of the (MeSH)4 potential energy surface.

A random walk on the PES for (MeSH)4 clusters produced 50 structural isomers held together by hydrogen-bonding networks according to calculations performed at the B3LYP/6-311++G** and MP2/6-311++G** levels. The geometric motifs observed are somewhat similar to those encountered for the methanol tetramer, but the interactions responsible for cluster stabilization are quite different in origin. Cluster stabilization is not related to the number of hydrogen bonds. Two distinct, well-defined types of hydrogen bonds scattered over a wide range of distances are predicted.

A detailed look at the reaction mechanisms of substituted carbenes with water.

Two competitive reaction mechanisms for the gas-phase chemical transformation of singlet chlorocarbene into chloromethanol in the presence of one and two water molecules are examined in detail. An analysis of bond orders and bond order derivatives as well as of properties of bond critical points in the electron densities along the intrinsic reaction coordinates (IRCs for intermediates → transition state (TS) → products) suggests that, from the perspective of bond breaking/formation, both reactions should be considered to be highly nonsynchronous, concerted processes. Both transition states are early, resembling the intermediates, yielding rate constants whose magnitudes are mostly influenced by structural changes and to a lesser degree by bond breaking/formation. For the case of one water molecule, most of the energy in the reactants region of the IRC is used for structural changes, while the transition state region encompasses the majority of electron activity, except for the formation of the C-O bond, which extends well into the products region. In the case of two water molecules, very little electron flux and comparatively less work required for structural changes is noticed in the reactants region, leading to an earlier transition state and therefore to a smaller activation energy and to a larger rate constant. This, together with evidence gathered from other sources, allows us to provide plausible explanations for the observed difference in rate constants.

(H3N-BH3)4: the ammonia borane tetramer.

For this special edition of PCCP dealing with prediction of new molecules using quantum mechanical methods, we propose a structure for (H(3)N-BH(3))(4), the isolated ammonia borane tetramer in gas phase, for which there are no experimental reports. The structure, belonging to the S(4) point group, was found at the MP2/6-311++G(d,p) level of theory; the total energy was computed at the CCSD(T) level including BSSE correction, affording a binding energy of 40.1 kcal mol(-1). The tetramer is stabilized by a network of dihydrogen bonds. We study the stabilizing interactions via QTAIM, obtaining eight N-H(δ+)···(δ-)H-B bonding interactions characterized as hydrogen bonds by application of the Koch-Popelier rules; in addition, two highly controversial B-H(δ-)···(δ-)H-B interactions are also predicted by a topological analysis of the electron density.

The Jahn-Teller effect: a case of incomplete theory for d4 complexes?

We present relativistic calculations at the four-component Dirac-DFT level for the geometries of the series of group 9 monoanionic hexafluorides MF(6)(-), M = Co, Rh, Ir. Highly correlated four-component relativistic CCSD(T) energies were also calculated for the optimized geometries. Spin-orbit coupling effects influence the geometrical preferences for molecular structures: relativistic calculations predict ground states with octahedral symmetries O(h)* for all hexafluorides in this study, while at the nonrelativistic limit, a structural deviation toward D(4h) ground state symmetries is predicted. Our findings suggest that relativistic effects have an important role in molecular structure preferences for the title hexafluorides.

Structure and reactivity of the (1)Au6Pt clusters.

In this paper we report the geometries, properties, and reactivity descriptors of 12 structural isomers located on the MP2/SDDALL potential energy surface of the (1)Au(6)Pt binary clusters. A nonplanar, D(3d) symmetry, cyclohexane chairlike structure is predicted to be the global minimum. Binding energies per atom in the range ≈44-51 kcal/mol account for very stable clusters. The relative stability of the clusters is directly related to all global and local reactivity descriptors. All structures are predicted to have large electron affinities. The chemical environment of the Pt atom on the structures plays a central role in the resulting relative stabilities and global and local reactivities. Our results show that more peripheral Pt atoms are more likely to be involved in electron-accepting processes.

Electronic structure calculations on helical conducting polymers.

We present a study of the electronic structure and derived properties of polyfurane (PFu), polypyrrol (PPy), and polythiophene (PTh). Two spatial arrangements are considered: trans chain (tc-PFu, tc-PPy, tc-PTh) and cis α-helical (α-PFu, α-PPy, α-PTh). Even at the small sizes considered here, helical conformations appear to be stable. Band gaps of pure, undoped oligomers fall into the semiconductor range. Density of states (DOS) analysis suggest dense valence and conduction bands. Bond length alternation analysis predicts almost complete delocalization of the π clouds in all spatial arrangements. Doping with electron donors or electron-withdrawing impurities reduces all band gaps close to the metallic regime in addition to increasing the DOS for the valence and conduction bands.

Competitive substituent effects on the reactivity of aromatic rings.

We performed second order perturbation theory calculations of gas phase proton affinities for o, m, p-nitroaniline at all positions and attempted correlations of the thermodynamic stability of the products with several reactivity indices: inductive effects from resonance, partial charges, and frontier orbital related indices such as local nucleophilic and electron-donating powers, global hardness of the products, and the substituent push-pull effect. All protonation reactions at ring positions are predicted to be exothermic. Resonance and charge analysis give inconsistent correlations with proton affinities, while the condensed nucleophilic Fukui function, electron-donating power, global hardness, and push-pull effect show promising trends.

Structural characterization of the (methanol)4 potential energy surface.

In this paper, we report the geometries and properties of the structural isomers obtained from a random walk of the potential energy surface (PES) of the methanol tetramer. Thirty-three structures were obtained after B3LYP/6-31+g* optimization of 94 candidate structures generated from a stochastic search of the PM3 conformational space. The random search was carried out using a recently proposed modified Metropolis acceptance test in the simulated annealing (SA) procedure. Corrections for the basis set superposition error (BSSE) show improvements on the binding energies of the clusters in an average of approximately 2.0 kcal/mol, while geometries are predicted to be less sensitive to BSSE corrections. MP2/aug-cc-pvdz calculations on representative structures did not change the geometries but predicted better binding energies. Highly correlated CCSD(T) energies were calculated on the B3LYP and MP2 stationary points and used to establish relative stabilities. We report several new conformations and group the structures into six distinct geometrical motifs. Only the cyclic tetramers with four primary hydrogen bonds in the same plane are predicted to have significant populations. Secondary hydrogen bonds, those for which the donated proton comes from an alkyl group, lead to a rich conformational space.