Influence of basis set on the calculated properties of (H3N–HCl)

The structure of (H3N–HCl) is investigated by ab initio calculations using a number of different basis sets ranging from minimal to split valence. The effects of including a diffuse sp shell and d orbitals on Cl are considered as well. The geometries of the complex and the isolated subunits are fully optimized. Minimal basis sets (STO‐3G, STO‐6G, and MINI‐1) lead to an overestimate of the interaction between the subunits. Addition of d functions produces only a marginal improvement. The 3‐21G, 3‐21+G, MIDI‐1, and LP‐31G split‐valence sets erroneously predict an ion pair (H3NH+⋅⋅⋅−Cl) in the equilibrium structure, a conclusion which is reversed by polarization of each basis. On the other hand, both the ion pair and (H3N⋅⋅⋅HCl) complexes are identified as minima in the 4‐31G potential. When this basis set is augmented with d functions, agreement with previous calculations involving large basis sets is quite good

The Potential Energy Surface of (NH3)2

Ab initio calculations at the SCF and correlated levels are carried out to characterize the potential energy surface of the NH3 dimer. The two basis sets used are 4‐31G∗ and a larger one containing two sets of d‐functions on N centers, 6‐31G∗∗ (1p, 2d). The only minimum occurring on the surface is a cyclic C2h structure in which the two H‐bonding protons are displaced 42° from the N‐‐N axis. The surface contains a very shallow valley along the direction leading from this geometry to a single linear H bond although there is no minimum corresponding to this arrangement. Despite the symmetrically nonpolar character of the cyclic geometry, the shallowness of the potential in the direction of the linear structure may allow zero point vibration effects to displace the minimum, thereby leading to the observed small dipole moment and its sensitivity to isotopic substitution

Primary and secondary basis set superposition error at the SCF and MP2 levels. H3N‐‐Li+ and H2O‐‐Li+

The primary basis set superposition error (BSSE) results from the artificial lowering of the energy of each subunit of a pair by the presence of ‘‘ghost orbitals’’ of its partner. In addition, these ghost orbitals perturb the one‐electron properties of the molecule, causing a change in the interaction energy, an effect known as secondary BSSE which is not corrected by the counterpoise procedure. The primary and secondary BSSE are calculated for the interactions of NH3 and H2O with Li+, using a variety of different basis sets. It is found that the 2° BSSE can be quite large, comparable in magnitude to the 1° component at both the SCF and MP2 levels. There is no basis found for the supposition that 2° BSSE improves the calculated interaction energy, nor do the 1° and 2° effects cancel one another in general. While the MP2 BSSE tends to be smaller than the SCF analog, the former can be similar in magnitude to the ‘‘true’’ MP2 contribution to the interaction; failure to remove the BSSE can hence lead to a qualitatively incorrect interpretation of the effects of electron correlation. Comparison with a system in which basis set superposition is rigorously excluded suggests that subtraction of both the full 1° and 2° BSSE is appropriate and does not overcorrect the potential. Addition of a diffuse sp shell, especially if coupled with orbital exponent reoptimization, leads to a lowering of the 1° and 2° BSSE, which moreover take on opposite sign and cancel one another to some extent

Ab initio study of FH–PH3 and ClH–PH3 including the effects of electron correlation

Ab initio calculations are carried out for FH–PH3 and ClH–PH3 using a basis set including two sets of polarization functions. Electron correlation is incorporated via Møller–Plesset perturbation theory to second and (in part) to third orders. The basis set is tested and found to produce satisfactory treatments of subsystem properties including geometries and dipole moments as well as the proton affinity and inversion barrier of PH3. Electron correlation is observed to markedly enhance the interaction between PH3 and the hydrogen halides. Its contribution to the complexation energy is 30% for FH–PH3 and 50% for ClH–PH3. Moreover, the equilibrium geometries of the complexes at correlated levels are quite different than SCF structures

Peptides and Peptidomimetics as Inhibitors of Enzymes Involved in Fibrillar Collagen Degradation

Collagen fibres degradation is a complex process involving a variety of enzymes. Fibrillar collagens, namely type I, II, and III, are the most widely spread collagens in human body, e.g., they are responsible for tissue fibrillar structure and skin elasticity. Nevertheless, the hyperactivity of fibrotic process and collagen accumulation results with joints, bone, heart, lungs, kidneys or liver fibroses. Per contra, dysfunctional collagen turnover and its increased degradation leads to wound healing disruption, skin photoaging, and loss of firmness and elasticity. In this review we described the main enzymes participating in collagen degradation pathway, paying particular attention to enzymes degrading fibrillar collagen. Therefore, collagenases (MMP-1, -8, and -13), elastases, and cathepsins, together with their peptide and peptidomimetic inhibitors, are reviewed. This information, related to the design and synthesis of new inhibitors based on peptide structure, can be relevant for future research in the fields of chemistry, biology, medicine, and cosmeceuticals

Reaction of atomic hydrogen with formic acid

Peer reviewe

Structure, energetics, and vibrational spectrum of H2O–HCl

H2O–HCl is studied using a number of basis sets including 6‐31G∗∗ and variants which are augmented by a diffuse sp shell and a second set of d functions on O and Cl. Optimization of the geometry of the complex is carried out including explicitly electron correlation and counterpoise correction of the basis set superposition error (BSSE) at both the SCF and correlated levels. Correlation strengthens and shortens the H bond while BSSE correction leads to an opposite trend; these two effects are of different magnitude and hence cancel one another only partially. ΔH°(298 K) is calculated to be −4.0 kcal/mol, 1/4 of which is due to correlation. Formation of the complex causes the strong intensification and red shift of the H–Cl stretching band normally associated with H bonding, whereas the internal vibrations of H2O are very little affected, except for a doubling of the intensity of the symmetric stretch. With respect to the intermolecular modes, the bends of the proton donor are of higher frequency than those involving the acceptor. While these intermolecular bends are all of moderate intensity, comparable to the intramolecular modes, the H‐bond stretch νσ is very weak indeed, consistent with a principle involving subunit dipoles. All calculated vibrational data are in excellent agreement with the spectra measured in solid inert gas matrices

Peptide stapling by late-stage Suzuki-Miyaura cross-coupling

The development of peptide stapling techniques to stabilise alpha-helical secondary structure motifs of peptides led to the design of modulators of protein-protein interactions, which had been considered undruggable for a long time. We disclose a novel approach towards peptide stapling utilising macrocyclisation by late-stage Suzuki-Miyaura cross-coupling of bromotryptophan-containing peptides of the catenin-binding domain of axin. Optimisation of the linker length in order to find a compromise between both sufficient linker rigidity and flexibility resulted in a peptide with an increased alpha-helicity and enhanced binding affinity to its native binding partner beta-catenin. An increased proteolytic stability against proteinase K has been demonstrated