Benchmark database on isolated small peptides containing an aromatic side chain: comparison between wave function and density functional theory methods and empirical force field.

A detailed quantum chemical study on five peptides (WG, WGG, FGG, GGF and GFA) containing the residues phenylalanyl (F), glycyl (G), tryptophyl (W) and alanyl (A) -- where F and W are of aromatic character -- is presented. When investigating isolated small peptides, the dispersion interaction is the dominant attractive force in the peptide backbone-aromatic side chain intramolecular interaction. Consequently, an accurate theoretical study of these systems requires the use of a methodology covering properly the London dispersion forces.

Nature and magnitude of aromatic stacking of nucleic acid bases.

This review summarises recent advances in quantum chemical calculations of base-stacking forces in nucleic acids. We explain in detail the very complex relationship between the gas-phase base-stacking energies, as revealed by quantum chemical (QM) calculations, and the highly variable roles of these interactions in nucleic acids. This issue is rarely discussed in quantum chemical and physical chemistry literature.

Adsorption of aromatic hydrocarbons and ozone at environmental aqueous surfaces.

Adsorption of environmentally important aromatic molecules on a water surface is studied by means of classical and ab initio molecular dynamics simulations and by reflection-absorption infrared spectroscopy. Both techniques show strong activity and orientational preference of these molecules at the surface. Benzene and naphthalene, which bind weakly to water surface with a significant contribution of dispersion interactions, prefer to lie flat on water but retain a large degree of orientational flexibility.

A sodium atom in a large water cluster: electron delocalization and infrared spectra.

Ab initio molecular dynamics simulations modeling low-energy collisions of a sodium atom with a cluster with more than 30 water molecules are presented. We follow the dynamics of the atom-cluster interaction and the delocalization of the valence electron of sodium together with the changes in the electron binding energy. This electron tends to be shared by the nascent sodium cation and the water cluster.

Potential-energy and free-energy surfaces of glycyl-phenylalanyl-alanine (GFA) tripeptide: experiment and theory.

The free-energy surface (FES) of glycyl-phenylalanyl-alanine (GFA) tripeptide was explored by molecular dynamics (MD) simulations in combination with high-level correlated ab initio quantum chemical calculations and metadynamics. Both the MD and metadynamics employed the tight-binding DFT-D method instead of the AMBER force field, which yielded inaccurate results. We classified the minima localised in the FESs as follows: a) the backbone-conformational arrangement; and b) the existence of a COOH.

Investigation of the benzene-dimer potential energy surface: DFT/CCSD(T) correction scheme.

A novel method, designated as the density functional theory/coupled-cluster with single and double and perturbative triple excitation [DFT/CCSD(T)] correction scheme, was developed for precise calculations of weakly interacting sp(2) hydrocarbon molecules and applied to the benzene dimer. The DFT/CCSD(T) interaction energies are in excellent agreement with the estimated CCSD(T)/complete basis set interaction energies. The tilted T-shaped structure having C(s) symmetry was determined to be a global minimum on the benzene-dimer potential energy surface (PES), approximately 0.

Origin of the X-Hal (Hal = Cl, Br) bond-length change in the halogen-bonded complexes.

The origin of the X-Hal bond-length change in the halogen bond of the X-Hal...

Specific ion binding to macromolecules: effects of hydrophobicity and ion pairing.

Using molecular dynamics simulations in an explicit aqueous solvent, we examine the binding of fluoride versus iodide to a spherical macromolecule with both hydrophobic and positively charged patches. Rationalizing our observations, we divide the ion association interaction into two mechanisms: (1) poorly solvated iodide ions are attracted to hydrophobic surface patches, while (2) the strongly solvated fluoride and to a minor extent also iodide bind via cation-anion interactions. Quantitatively, the binding affinities vary significantly with the accessibility of the charged groups as well as the surface potential; therefore, we expect the ion-macromolecule association to be modulated by the local surface characteristics of the (bio-)macromolecule.

A DFT-D investigation of the mechanisms for activation of the wild-type and S810L mutated mineralocorticoid receptor by steroid hormones.

In this work, we investigate the mode of binding of several steroid hormones, namely aldosterone, deoxycorticosterone, and progesterone to the wild-type and S810L mutated mineralocorticoid (MR) receptor using the newly formulated density functional theory with an empirical dispersion term (DFT-D) molecular electronic structure method. It is found that the MR agonists, aldosterone and deoxycorticosterone, form tight hydrogen bonds with residues Thr945 and Asn770, which leads to the formation of hydrogen bond networks near the steroid D-ring, allowing for activation of this transcription factor. Progesterone, an MR antagonist, fails to form the necessary hydrogen bonds near the steroid D-ring.

Investigations into the Nature of Halogen Bonding Including Symmetry Adapted Perturbation Theory Analyses.

In recent years it has been recognized that, because of their unique properties, halogen bonds have tremendous potential in the development of new pharmaceutical compounds and materials. In this study we investigate the phenomenon of halogen bonding by carrying out ab initio calculations on the halomethane-formaldehyde complexes as well as the fluorine substituted FnH3-nCX···OCH2 dimers, where the halogen bonding halogens (X) are chlorine, bromine, and iodine. Coupled cluster (CCSD(T)/aug-cc-pVTZ) calculations indicate that the binding energies for these type of interactions lie in the range between -1.

Identifying stabilizing key residues in proteins using interresidue interaction energy matrix.

We are proposing an interresidue interaction energy map (IEM)--a new tool for protein structure analysis and protein bioinformatics. This approach employs the sum of pair-wise interaction energies of a particular residue as a measure of its structural importance. We will show that the IEM can serve as a means for identifying key residues responsible for the stability of a protein.

Performance of the DFT-D method, paired with the PCM implicit solvation model, for the computation of interaction energies of solvated complexes of biological interest.

In this work we investigate the performance of the DFT method, augmented with an empirical dispersion function (DFT-D), paired with the PCM implicit solvation model, for the computation of noncovalent interaction energies of biologically-relevant, solvated model complexes. It is found that this method describes intermolecular interactions within water and ether (protein-like) environments with roughly the same accuracy as in the gas phase. Another important finding is that, when environmental effects are taken into account, the empirical dispersion term associated with the DFT-D method need be modified very little (or not at all), in order to obtain the optimum, most well balanced, performance.

Autoionization at the surface of neat water: is the top layer pH neutral, basic, or acidic?

Autoionization of water which gives rise to its pH is one of the key properties of aqueous systems. Surfaces of water and aqueous electrolyte solutions are traditionally viewed as devoid of inorganic ions; however, recent molecular simulations and spectroscopic experiments show the presence of certain ions including hydronium in the topmost layer. This raises the question of what is the pH (defined using proton concentration in the topmost layer) of the surface of neat water.

Dispersion interactions govern the strong thermal stability of a protein.

Rubredoxin from the hyperthermophile Pyrococcus furiosus (Pf Rd) is an extremely thermostable protein, which makes it an attractive subject of protein folding and stability studies. A fundamental question arises as to what the reason for such extreme stability is and how it can be elucidated from a complex set of interatomic interactions. We addressed this issue first theoretically through a computational analysis of the hydrophobic core of the protein and its mutants, including the interactions taking place inside the core.

Model of peptide bond-aromatic ring interaction: correlated ab initio quantum chemical study.

Aromatic ring-peptide bond interactions (modeled as benzene and formamide, N-methylformamide and N-methylacetamide) are studied by means of advanced computational chemistry methods: second-order Möller-Plesset (MP2), coupled-cluster single and double excitation model [CCSD(T)], and density functional theory with dispersion (DFT-D). The geometrical preferences of these interactions as well as their interaction energy content, in both parallel and T-shaped arrangements, are investigated. The stabilization energy reaches a value of over 5 kcal/mol for the N-methylformamide-benzene complex at the CCSD(T)/complete basis set (CBS) level.

Microsolvation of the dicyanamide anion: [N(CN)(2)(-)](H(2)O)n (n = 0-12).

Photoelectron spectroscopy is combined with ab initio calculations to study the microsolvation of the dicyanamide anion, N(CN)(2)(-). Photoelectron spectra of [N(CN)(2)(-)](H2O)n (n = 0-12) have been measured at room temperature and also at low temperature for n = 0-4. Vibrationally resolved photoelectron spectra are obtained for N(CN)(2)(-), allowing the electron affinity of the N(CN)2 radical to be determined accurately as 4.

Assessment of the MP2 method, along with several basis sets, for the computation of interaction energies of biologically relevant hydrogen bonded and dispersion bound complexes.

In the past several years the MP2 method has been used extensively in studies of noncovalent interactions within biological systems such as proteins, DNA/RNA, and protein-ligand complexes. In this work we assess the performance that can be expected of this method, when paired with several different medium and extended basis sets, for the accurate computation of binding energies of hydrogen bonded and dispersion bound biologically derived complexes. It is found that, overall, the MP2/cc-pVTZ method produces the best, most well balanced, description of noncovalent interactions.

Accurate theoretical determination of the structure of aromatic complexes is complicated: the phenol dimer and phenol...methanol cases.

The structure of the phenol dimer and phenol...

Segregation of inorganic ions at surfaces of polar nonaqueous liquids.

We present a short review of recent computational and experimental studies on surfaces of solutions of inorganic salts in polar nonaqueous solvents. These investigations complement our knowledge of aqueous interfaces and show that liquids such as formamide, liquid ammonia, and ethylene glycol can also surface-segregate large polarizable anions like iodide, albeit less efficiently than water. For liquids whose surfaces are covered with hydrophobic groups (e.

Interaction of heteroboranes with biomolecules. Part 2. The effect of various metal vertices and exo-substitutions.

Icosahedral heteroboranes and especially metallacarboranes, which have recently been shown to act as potent HIV-1 protease inhibitors, are a unique class of chemical compounds with unusual properties, one of which is the formation of dihydrogen bonds with biomolecules. In this study, we investigate the effect of various metal vertices and exo-substitutions on several series of heteroboranes, including 11-vertex carborane cages [nido-7,8-C2B9Hn]n-13(n= 11,12,13), closo-1-SB11H11, closo-1-NB11H12, metal bis(dicarbollides)[3,3'-M (1,2-C2B9H11)2]n(M/n=Fe/2-, Co/1-, Ni/0) and fluoro (F), amino (NH2) and hydroxo (OH) derivatives of the metal bis(dicarbollides). Besides the properties of isolated systems (geometries, electronic properties and hydration), we study their interactions with a tetrapeptide, which models their biomolecular partner.

Stability of nucleic acid base pairs in organic solvents: molecular dynamics, molecular dynamics/quenching, and correlated ab initio study.

The dynamic structure and potential energy surface of adenine...

Hydration and stability of nucleic acid bases and base pairs.

Empirical, quantum chemical calculations and molecular dynamics simulations of the role of a solvent on tautomerism of nucleic acid bases and structure and properties of nucleic acid base pairs are summarized. Attention was paid to microhydrated (by one and two water molecules) complexes, for which structures found by scanning of empirical potential surfaces were recalculated at a correlated ab initio level. Additionally, isolated as well as mono- and dihydrated H-bonded, T-shaped and stacked structures of all possible nucleic acid base pairs were studied at the same theoretical levels.

Resolution of identity density functional theory augmented with an empirical dispersion term (RI-DFT-D): a promising tool for studying isolated small peptides.

Resolution of identity standard density functional theory augmented with a damped empirical dispersion term (RI-DFT-D) calculations have been carried out on a set of lowest energy minima of tryptophyl-glycine (Trp-Gly) and tryptophyl-glycyl-glycine (Trp-Gly-Gly) peptides. RI-DFT-D (TPSS/TZVP) results are in excellent agreement with benchmark data based on the CCSD(T) method. Experimental spectra could be assigned according to the calculated IR frequencies.

Hydrogen-bonded nucleic acid base pairs containing unusual base tautomers: complete basis set calculations at the MP2 and CCSD(T) levels.

The total interaction energies of altogether 15 hydrogen-bonded nucleic acid base pairs containing unusual base tautomers were calculated. The geometry properties of all selected adenine-thymine and guanine-cytosine hydrogen-bonded base pairs enable their incorporation into DNA. Unusual base pairing patterns were compared with Watson-Crick H-bonded structures of the adenine-thymine and guanine-cytosine pairs.