Journal of Computational Chemistry

doi: 10.1002/jcc.26603pmid: N/A

Gallmetzer, Hans Georg; Hofer, Thomas S.

doi: 10.1002/jcc.26830pmid: 35239208

Optimized link bond parameters for the CαCβ bond of 22 different capped amino acid model systems have been determined at SCC DFTB/mio (self‐consistent charge density functional tight‐binding), SCC DFTB/3ob and GFNn‐xTB (n = 0, 1, and 2) level in conjunction with the AMBER 99SB, 14SB, and 19B force fields. The resulting parameter sets have been compared to newly calculated reference data obtained via resolution‐of‐identity 2nd order Møller–Plesset perturbation theory. The data collected in this work suggests that the optimized values in this study provide a more suitable setup of the QM/MM link bonds compared to the use of a single global setting applied to every amino acid fragmented by the QM/MM interface. The results also imply that a transfer of the ideal link bond settings between different levels of theory is not advised. In contrast, virtually identical parameters were obtained in calculations employing different variants of the AMBER force field. Considering the increasing success of tight binding based approaches being inter alia a results of their exceptional accuracy/effort ratio the provided collection of link atoms parameters provides a valuable resource for QM/MM studies of biomacromolecular systems as demonstrated in an exemplary QM/MM MD simulation of the β‐amyloid/Zn2+ complex.

Devi, Kavita; Gorantla, Sai Manoj N. V. T.; Mondal, Kartik Chandra

doi: 10.1002/jcc.26832pmid: 35289411

Binding of dinitrogen (N2) to a transition metal center (M) and followed by its activation under milder conditions is no longer impossible; rather, it is routinely studied in laboratories by transition metal complexes. In contrast, binding of N2 by main group elements has been a challenge for decades, until very recently, an exotic cAAC‐borylene (cAAC = cyclic alkyl(amino) carbene) species showed similar binding affinity to kinetically inert and non‐polar dinitrogen (N2) gas under ambient conditions. Since then, N2 binding by short lived borylene species has made a captivating news in different journals for its unusual features and future prospects. Herein, we carried out different types of DFT calculations, including EDA‐NOCV analysis of the relevant cAAC‐boron‐dinitrogen complexes and their precursors, to shed light on the deeper insight of the bonding secret (EDA‐NOCV = energy decomposition analysis coupled with natural orbital for chemical valence). The hidden bonding aspects have been uncovered and are presented in details. Additionally, similar calculations have been carried out in comparison with a selected stable dinitrogen bridged‐diiron(I) complex. Singlet cAAC ligand is known to be an exotic stable species which, combined with the BAr group, produces an intermediate singlet electron‐deficient (cAAC)(BAr) species possessing a high lying HOMO suitable for overlapping with the high lying π*‐orbital of N2 via effective π‐backdonation. The BN2 interaction energy has been compared with that of the FeN2 bond. Our thorough bonding analysis might answer the unasked questions of experimental chemists about how boron compounds could mimic the transition metal of dinitrogen binding and activation, uncovering hidden bonding aspects. Importantly, Pauling repulsion energy also plays a crucial role and decides the binding efficiency in terms of intrinsic interaction energy between the boron‐center and the N2 ligand.

Khakimov, Dmitry V.; Zelenov, Victor P.; Pivina, Tatyana S.

doi: 10.1002/jcc.26833pmid: 35246991

Simulation of crystal structures of series 1(2)‐R‐1(2)H‐[1,2,3]triazolo[4,5‐e][1,2,3,4]tetrazine 5,7‐dioxides, 1,5,7‐trioxides, 4,6‐dioxides and 3,4,6‐trioxides was carried out using an original technique based on the method of atom‐atom potentials and quantum chemistry. The effect of the position of the substituent in the triazole ring on the change in the crystal structures of these compounds and their thermochemical characteristics was studied for the first time. For some of synthesized compounds, thermochemical characteristics were investigated and differential scanning calorimetry curves were obtained. Detonation parameters were calculated, on the basis of which the prospects for the use of the considered compounds were assessed.

Gallegos, Miguel; Costales, Aurora; Martín Pendás, Ángel

doi: 10.1002/jcc.26834pmid: 35277994

Within substitution reactions, the Bimolecular Nucleophilic Substitution (SN2) reaction mechanism is one of the most frequently found and studied ones. Among other factors, the easiness of the SN2 pathway is classically considered to be determined by steric hindrance. However, the diffuse nature of the latter inevitably darkens these and other arguments holding the pillars of chemical intuition. In this work, we employ the steric energy (EST) descriptor, formulated within the Interacting Quantum Atoms approach, to offer insights regarding this problem. The steric demands of the substrate, nucleophile and leaving group were studied using the gas‐phase SN2 reaction with different organic skeletons (CH3, CH3CH2, (CH3)2CH, (CH3)3C, (CH3)3CCH2) and halogens (F, Cl, and Br) as test‐bed systems. Our results show that, according to EST, the SH experienced along these simple reactions fits, in the general case, the trends predicted by a meticulous and rigorous application of chemical intuition. However, steric clash alone should not be considered as the only argument used to explain the easiness of the SN2 reaction over different electrophiles.

Fernández, Israel; Noonikara‐Poyil, Anurag; Dias, H. V. Rasika

doi: 10.1002/jcc.26835pmid: 35277876

The bonding situation of Ag(I)CO complexes having a Scorpionate ligand directly attached to the transition metal has been analyzed in detail by means of relativistic density functional theory calculations. To this end, different experimentally characterized complexes together with other representative species have been considered to rationalize the observed shift of the corresponding ν(CO) stretching frequencies and the influence of the substituents in the Scorpionate ligand. With the help of the energy decomposition analysis method combined with the natural orbital for chemical valence it is found that the main contribution to the bonding comes from the electrostatic attractions between the LAg(I) and CO fragments. Despite that, the LAg → CO π‐backdonation is also significant in these species as well as in related LCu(I)CO complexes.

Sánchez‐González, Ángel; Grenut, Pierre; Gil, Adrià

doi: 10.1002/jcc.26836pmid: 35297513

The influence of hydrogen bonds in model intercalated systems between guanine‐cytosine and adenine‐thymine DNA base pairs (bps) was analyzed with the popular intercalator 1,10‐phenanthroline (phen) and derivatives obtained by substitution with OH and NH2 groups in positions 4 and 7. Semiempirical and Density Functional Theory (DFT) methods were used both including dispersion effects: PM6‐DH2, M06‐2X and B3LYP‐D3 along with the recently developed near linear‐scaling coupled cluster method DLPNO‐CCSD(T) for benchmark calculations. Our results given by QTAIM and non‐covalent interaction analysis confirmed the existence of hydrogen bonds created by OH and NH2. The trends in the energy decomposition analysis for the interaction energy, ΔEint, showed that the ΔEelstat contributions are equal or even a little bit higher than the values for ΔEdisp. Such important ΔEelstat attractive contribution comes mainly from the conventional hydrogen bonds formed by OH and NH2 functional groups with DNA not only with bps but specially with the sugar and phosphate backbone. This behavior is very different from that of phen and other classical intercalators that cannot form conventional hydrogen bonds, where the ΔEdisp is the most important attractive contribution to the ΔEint. The inclusion of explicit water molecules in molecular dynamics simulations showed, as a general trend, that the hydrogen bonds with the bps disappear during the simulations but those with the sugar and phosphate backbone remain in time, which highlights the important role of the sugar and phosphate backbone in the stabilization of these systems.