Explore the vast range of titles available.

A set of 35 representative neutral and charged tetrel complexes was investigated with the objective of finding the factors that influence the strength of tetrel bonding involving single bonded C, Si, and Ge donors and double bonded C or Si donors. For the first time, we introduced an intrinsic bond strength measure for tetrel bonding, derived from calculated vibrational spectroscopy data obtained at the CCSD(T)/aug-cc-pVTZ level of theory and used this measure to rationalize and order the tetrel bonds. Our study revealed that the strength of tetrel bonds is affected by several factors, such as the magnitude of the σ-hole in the tetrel atom, the negative electrostatic potential at the lone pair of the tetrel-acceptor, the positive charge at the peripheral hydrogen of the tetrel-donor, the exchange-repulsion between the lone pair orbitals of the peripheral atoms of the tetrel-donor and the heteroatom of the tetrel-acceptor, and the stabilization brought about by electron delocalization. Thus, focusing on just one or two of these factors, in particular, the σ-hole description can only lead to an incomplete picture. Tetrel bonding covers a range of −1.4 to −26 kcal/mol, which can be strengthened by substituting the peripheral ligands with electron-withdrawing substituents and by positively charged tetrel-donors or negatively charged tetrel-acceptors.

In this work hydrogen bonding in a diverse set of 36 unnatural and the three natural Watson Crick base pairs adenine (A)–thymine (T), adenine (A)–uracil (U) and guanine (G)–cytosine (C) was assessed utilizing local vibrational force constants derived from the local mode analysis, originally introduced by Konkoli and Cremer as a unique bond strength measure based on vibrational spectroscopy. The local mode analysis was complemented by the topological analysis of the electronic density and the natural bond orbital analysis. The most interesting findings of our study are that (i) hydrogen bonding in Watson Crick base pairs is not exceptionally strong and (ii) the N–H⋯N is the most favorable hydrogen bond in both unnatural and natural base pairs while O–H⋯N/O bonds are the less favorable in unnatural base pairs and not found at all in natural base pairs. In addition, the important role of non-classical C–H⋯N/O bonds for the stabilization of base pairs was revealed, especially the role of C–H⋯O bonds in Watson Crick base pairs. Hydrogen bonding in Watson Crick base pairs modeled in the DNA via a QM/MM approach showed that the DNA environment increases the strength of the central N–H⋯N bond and the C–H⋯O bonds, and at the same time decreases the strength of the N–H⋯O bond. However, the general trends observed in the gas phase calculations remain unchanged. The new methodology presented and tested in this work provides the bioengineering community with an efficient design tool to assess and predict the type and strength of hydrogen bonding in artificial base pairs.

The interplay between FeC and CO bonding in carboxymyoglobin (MbCO) and the role of potential hydrogen bonding between the CO moiety and the side chains of the surrounding protein amino acids have been the subject of numerous experimental and theoretical studies. In this work, we present a quantitative measure for the intrinsic FeC and CO bond strength in MbCO, as well as for CO⋯H bonding, based on the local vibrational mode analysis, originally developed by Konkoli and Cremer. We investigated a gas phase model, two models of the wild-type protein, and 17 protein mutations that change the distal polarity of the heme pocket, as well as two protein mutations of the heme porphyrin ring. Based on local mode force constants, we could quantify for the first time the suggested inverse relationship between the CO and FeC bond strength, the strength of CO⋯H bonding, and how it weakens the CO bond. Combined with the natural orbital analysis, we could also confirm the key role of π back donation between Fe and the CO moiety in determining the FeC bond strength. We further clarified that CO and FeC normal modes couple with other protein motions in the protein environment. Therefore, normal mode frequencies/force constants are not suited as bond strength descriptors and instead their local mode counterparts should be used. Our comprehensive results provide new guidelines for the fine-tuning of existing and the design of MbCO models with specific FeC, CO, and CO⋯H bond strengths. Graphical abstract

In this work, we analyzed five groups of different dihydrogen bonding interactions and hydrogen clusters with an H3+ kernel utilizing the local vibrational mode theory, developed by our group, complemented with the Quantum Theory of Atoms–in–Molecules analysis to assess the strength and nature of the dihydrogen bonds in these systems. We could show that the intrinsic strength of the dihydrogen bonds investigated is primarily related to the protonic bond as opposed to the hydridic bond; thus, this should be the region of focus when designing dihydrogen bonded complexes with a particular strength. We could also show that the popular discussion of the blue/red shifts of dihydrogen bonding based on the normal mode frequencies is hampered from mode–mode coupling and that a blue/red shift discussion based on local mode frequencies is more meaningful. Based on the bond analysis of the H3+(H2)n systems, we conclude that the bond strength in these crystal–like structures makes them interesting for potential hydrogen storage applications.

Experimentalists recently characterized the difficulty in isolating gaseous histidine in its neutral form. To understand the factors which stabilize neutral histidine, the intrinsic nature of the intramolecular hydrogen bonding networks in the four most stable histidine conformers was investigated via density functional theory combined with the local vibrational mode analysis originally introduced by Konkoli and Cremer, quantum theory of atoms in molecules, non-covalent interaction analysis, and natural bond orbital population analysis. Our results show a positive correlation between intramolecular hydrogen bond strength and structural stability, where the presence of the O-H⋯Nα bond type is a major factor.

Over the past two decades, the vibrational Stark effect has become an important tool to measure and analyze the in situ electric field strength in various chemical environments with infrared spectroscopy. The underlying assumption of this effect is that the normal stretching mode of a target bond such as CO or CN of a reporter molecule (termed vibrational Stark effect probe) is localized and free from mass-coupling from other internal coordinates, so that its frequency shift directly reflects the influence of the vicinal electric field. However, the validity of this essential assumption has never been assessed. Given the fact that normal modes are generally delocalized because of mass-coupling, this analysis was overdue. Therefore, we carried out a comprehensive evaluation of 68 vibrational Stark effect probes and candidates to quantify the degree to which their target normal vibration of probe bond stretching is decoupled from local vibrations driven by other internal coordinates. The unique tool we used is the local mode analysis originally introduced by Konkoli and Cremer, in particular the decomposition of normal modes into local mode contributions. Based on our results, we recommend 31 polyatomic molecules with localized target bonds as ideal vibrational Stark effect probe candidates.

Visualizing vibrational motions calculated with different ab initio packages requires dedicated post-processing tools. Here, we present a PyMOL plugin called PyVibMS for visualizing the vibrational motions for both molecular and solid systems calculated by mainstream quantum chemical computer programs including Gaussian, Q–Chem, VASP, and CRYSTAL. Benefiting from the continuing development of the PyMOL platform, PyVibMS provides powerful functionalities and user-friendly interface. PyVibMS was written in Python and its open-source nature makes it flexible and sustainable. As an example, the motions of the Konkoli-Cremer local vibrational modes are shown in this work for the first time. PyVibMS is freely available at https://github.com/smutao/PyVibMS . Graphical abstract In this work, a PyMOL plugin named PyVibMS is developed to visualize molecular and lattice vibrations.

For decades one has strived to synthesize a compound with the longest covalent C−C bond applying predominantly steric hindrance and/or strain to achieve this goal. On the other hand electronic effects have been added to the repertoire, such as realized in the electron deficient ethane radical cation in its D3d form. Recently, negative hyperconjugation effects occurring in diamino-o-carborane analogs such as di-N,N-dimethylamino-o-carborane have been held responsible for their long C−C bonds. In this work we systematically analyzed CC bonding in a diverse set of 53 molecules including clamped bonds, highly sterically strained complexes such as diamondoid dimers, electron deficient species, and di-N,N-dimethylamino-o-carborane to cover the whole spectrum of possibilities for elongating a covalent C−C bond to the limit. As a quantitative intrinsic bond strength measure, we utilized local vibrational CC stretching force constants ka(CC) and related bond strength orders BSO n(CC), computed at the ωB97X-D/aug-cc-pVTZ level of theory. Our systematic study quantifies for the first time that whereas steric hindrance and/or strain definitely elongate a C−C bond, electronic effects can lead to even longer and weaker C−C bonds. Within our set of molecules the electron deficient ethane radical cation, in D3d symmetry, acquires the longest C−C bond with a length of 1.935 Å followed by di-N,N-dimethylamino-o-carborane with a bond length of 1.930 Å. However, the C−C bond in di-N,N-dimethylamino-o-carborane is the weakest with a BSO n value of 0.209 compared to 0.286 for the ethane radical cation; another example that the longer bond is not always the weaker bond. Based on our findings we provide new guidelines for the general characterization of CC bonds based on local vibrational CC stretching force constants and for future design of compounds with long C−C bonds.

Periodic local vibrational modes were calculated with the rev-vdW-DF2 density functional to quantify the intrinsic strength of the X-I⋯OA-type halogen bonding (X = I or Cl; OA: carbonyl, ether and N-oxide groups) in 32 model systems originating from 20 molecular crystals. We found that the halogen bonding between the donor dihalogen X-I and the wide collection of acceptor molecules OA features considerable variations of the local stretching force constants (0.1–0.8 mdyn/Å) for I⋯O halogen bonds, demonstrating its powerful tunability in bond strength. Strong correlations between bond length and local stretching force constant were observed in crystals for both the donor X-I bonds and I⋯O halogen bonds, extending for the first time the generalized Badger’s rule to crystals. It is demonstrated that the halogen atom X controlling the electrostatic attraction between the σ -hole on atom I and the acceptor atom O dominates the intrinsic strength of I⋯O halogen bonds. Different oxygen-containing acceptor molecules OA and even subtle changes induced by substituents can tweak the n → σ ∗ (X-I) charge transfer character, which is the second important factor determining the I⋯O bond strength. In addition, the presence of the second halogen bond with atom X of the donor X-I bond in crystals can substantially weaken the target I⋯O halogen bond. In summary, this study performing the in situ measurement of halogen bonding strength in crystalline structures demonstrates the vast potential of the periodic local vibrational mode theory for characterizing and understanding non-covalent interactions in materials.

The catalytic effects of iridium pincer complexes for the hydrogenation of carbon dioxide were investigated with the Unified Reaction Valley Approach (URVA), exploring the reaction mechanism along the reaction path traced out by the reacting species on the potential energy surface. Further details were obtained with the Local Mode Analysis performed at all stationary points, complemented by the Natural Bond Orbital and Bader’s Quantum Atoms in Molecules analyses. Each of the five reaction paths forming the catalytic cycle were calculated at the DFT level complemented with DLPNO-CCSD(T) single point calculations at the stationary points. For comparison, the non-catalytic reaction was also investigated. URVA curvature profiles identified all important chemical events taking place in the non-catalyzed reaction and in the five reactions forming the catalytic cycle, and their contribution to the activation energy was disclosed. The non-catalytic reaction has a large unfavorable activation energy of 76.3 kcal/mol, predominately caused by HH bond cleave in the H2 reactant. As shown by our study, the main function of the iridium pincer catalyst is to split up the one–step non-catalytic reaction into an energy efficient multistep cycle, where HH bond cleavage is replaced by the cleavage of a weaker IrH bond with a small contribution to the activation energy. The dissociation of the final product from the catalyst requires the cleavage of an IrO bond, which is also weak, and contributes only to a minor extent to the activation energy. This, in summary, leads to the substantial lowering of the overall activation barrier by about 50 kcal/mol for the catalyzed reaction. We hope that this study inspires the community to add URVA to their repertoire for the investigation of catalysis reactions.