Intermolecular potentials for simulations of collisions of SiNCS+ and (CH3)2SiNCS+ ions with fluorinated self-assembled monolayers

The PM6-FGC Method: Improved Corrections for Amines and Amides

Recently, we reported a new approach to develop pairwise analytical corrections to improve the description of noncovalent interactions, by approximate methods of electronic structures, such as semiempirical quantum mechanical (SQM) methods. In particular, and as a proof of concept, we used the PM6 Hamiltonian and we named the method PM6-FGC, where the FGC acronym, corresponding to Functional Group Corrections, emphasizes the idea that the corrections work for specific functional groups rather than for individual atom pairs. The analytical corrections were derived from fits to B3LYP-D3/def2-TZVP (reference). PM6 interaction energy differences, evaluated for a reduced set of small bimolecular complexes, were chosen as representatives of saturated hydrocarbons, carboxylic, amine and, tentatively, amide functional groups. For the validation, the method was applied to several complexes of well-known databases, as well as to complexes of diglycine and dialanine, assuming the transferability of amine group corrections to amide groups. The PM6-FGC method showed great potential but revealed significant inaccuracies for the description of some interactions involving the –NH₂ group in amines and amides, caused by the inadequate selection of the model compound used to represent these functional groups (an NH₃ molecule). In this work, methylamine and acetamide are used as representatives of amine and amide groups, respectively. This new selection leads to significant improvements in the calculation of noncovalent interactions in the validation set.

New Approach for Correcting Noncovalent Interactions in Semiempirical Quantum Mechanical Methods: The Importance of Multiple-Orientation Sampling

A new approach is presented to improve the performance of semiempirical quantum mechanical (SQM) methods in the description of noncovalent interactions. To show the strategy, the PM6 Hamiltonian was selected, although, in general, the procedure can be applied to other semiempirical Hamiltonians and to different methodologies. A set of small molecules were selected as representative of various functional groups, and intermolecular potential energy curves (IPECs) were evaluated for the most relevant orientations of interacting molecular pairs. Then, analytical corrections to PM6 were derived from fits to B3LYP-D3/def2-TZVP reference–PM6 interaction energy differences. IPECs provided by the B3LYP-D3/def2-TZVP combination of the electronic structure method and basis set were chosen as the reference because they are in excellent agreement with CCSD(T)/aug-cc-pVTZ curves for the studied systems. The resulting method, called PM6-FGC (from functional group corrections), significantly improves the performance of PM6 and shows the importance of including a sufficient number of orientations of the interacting molecules in the reference data set in order to obtain well-balanced descriptions.

A Trajectory-Based Method to Explore Reaction Mechanisms

The tsscds method, recently developed in our group, discovers chemical reaction mechanisms with minimal human intervention. It employs accelerated molecular dynamics, spectral graph theory, statistical rate theory and stochastic simulations to uncover chemical reaction paths and to solve the kinetics at the experimental conditions. In the present review, its application to solve mechanistic/kinetics problems in different research areas will be presented. Examples will be given of reactions involved in photodissociation dynamics, mass spectrometry, combustion chemistry and organometallic catalysis. Some planned improvements will also be described.

Intermolecular potential for binding of protonated peptide ions with perfluorinated hydrocarbon surfaces

An analytic potential energy function was developed to model both short-range and long-range interactions between protonated peptide ions and perfluorinated hydrocarbon chains. The potential function is defined as a sum of two-body potentials of the Buckingham form. The parameters of the two-body potentials were obtained by fits to intermolecular potential energy curves (IPECs) calculated for CF4, which represents the F and C atoms of a perfluoroalkane chain, interacting with small molecules chosen as representatives of the main functional groups and atoms present in protonated peptide ions: specifically, CH4, NH3, NH4(+), and HCOOH. The IPECs were calculated at the MP2/aug-cc-pVTZ level of theory, with basis set superposition error (BSSE) corrections. Good fits were obtained for an energy range extending up to about 400 kcal/mol. It is shown that the pair potentials derived from the NH3/CF4 and HCOOH/CF4 fits reproduce acceptably well the intermolecular interactions in HCONH2/CF4, which indicates that the parameters obtained for the amine and carbonyl atoms may be transferable to the corresponding atoms of the amide group. The derived potential energy function may be used in chemical dynamics simulations of collisions of peptide-H(+) ions with perfluorinated hydrocarbon surfaces.