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This Feature Article starts highlighting some recent experimental and theoretical advances in the field of IR and Raman spectroscopy, giving a taste of the breadth and dynamics of this striving field. The local mode theory is then reviewed, showing how local vibrational modes are derived from fundamental normal modes. New features are introduced that add to current theoretical efforts: (i) a unique measure of bond strength based on local mode force constants ranging from bonding in single molecules in different environments to bonding in periodic systems and crystals and (ii) a new way to interpret vibrational spectra by pinpointing and probing interactions between particular bond stretching contributions to the normal modes. All of this represents a means to work around the very nature of normal modes, namely that the vibrational motions in polyatomic molecules are delocalized. Three current focus points of the local mode analysis are reported, demonstrating how the local mode analysis extracts important information hidden in vibrational spectroscopy data supporting current experiments: (i) metal-ligand bonding in heme proteins, such as myoglobin and neuroglobin; (ii) disentanglement of DNA normal modes; and (iii) hydrogen bonding in water clusters and ice. Finally, the use of the local mode analysis by other research groups is summarized. Our vision is that in the future local mode analysis will be routinely applied by the community and that this Feature Article serves as an incubator for future collaborations between experiment and theory.

We report a comprehensive investigation of the 5-androstene-3,17-dione to 4-androstene-3,17-dione isomerization in Ketosteroid Isomerase, gas phase and aqueous solution, applying as tools the Unified Reaction Valley Approach (URVA) and the Local Vibrational Mode Analysis. Conformational changes of the steroid rings are monitored via Cremer-Pople puckering coordinates. URVA identifies simultaneous breakage of the C[Formula: see text]–H bond and O–H bond formation with the catalytic acid, leading to an intermediate with the acid positioned over ring [Formula: see text] as the major chemical events of the first reaction step. Via a barrier-less shift, a second intermediate is formed with the acid being positioned over ring [Formula: see text]. Then, according to URVA, breakage of the intermediate O–H bond, the formation of the new C[Formula: see text]–H bond accompanied by a double bond shift in rings [Formula: see text] and [Formula: see text] forms the major chemical events of the second reaction step, which is facilitated by favorable ring puckering. Reactions in protein and gas phase have comparable activation enthalpies, whereas the barrier in aqueous solution is higher, confirming that the major task of the enzyme pocket is to shield the migrating hydrogen atom and the catalyzing acid from interactions with solvent molecules diluting the catalytic power. We do not find exceptional H-bonding with Asp99 and Tyr14, excluding their catalytic activity. There is no strong hydrogen bonding in the TS, which could account for lowering the activation barrier. Our study provides a clear picture of the isomerization process, which will also inspire similar investigations of other important enzymatic reactions.

One of the ultimate goals of chemistry is to understand and manipulate chemical reactions, which implies the ability to monitor the reaction and its underlying mechanism at an atomic scale.

We introduce in this work a unique parameter for the quantitative assessment of the intrinsic strength of the π interaction between two monomers forming a complex. The new parameter is a local intermonomer stretching force constant, based on the local mode theory, originally developed by Konkoli and Cremer, and derived from the set of nine possible intermonomer normal vibrational modes. The new local force constant was applied to a diverse set of more than 70 molecular complexes, which was divided into four groups. Group 1 includes atoms, ions, and small molecules interacting with benzene and substituted benzenes. Group 2 includes transition metal hydrides and oxides interacting with benzene while Group 3 involves ferrocenes, chromocenes, and titanium sandwich compounds. Group 4 presents an extension to oxygen π–hole interactions in comparison with in-plane hydrogen bonding. We found that the strength of the π interactions in these diverse molecular complexes can vary from weak interactions with predominantly electrostatic character, found, e.g., for argon–benzene complexes, to strong interactions with a substantial covalent nature, found, e.g., for ferrocenes; all being seamlessly described and compared with the new intermonomer local mode force constant, which also outperforms other descriptors such as an averaged force constant or a force constant guided by the electron density bond paths. We hope that our findings will inspire the community to apply the new parameter also to other intermonomer π interactions, enriching in this way the broad field of organometallic chemistry with a new efficient assessment tool.

LModeAGen, a new protocol for the automatic determination of a nonredundant, complete set of local vibrational modes is reported, which is based on chemical graph concepts. Whereas local mode properties can be calculated for a selection of parameters targeting specific local modes of interest, a complete set of nonredundant local mode parameters is requested for the adiabatic connection scheme (ACS), relating each local vibrational mode with a normal mode counterpart, and for the decomposition of normal modes (CNM) in terms of local mode contributions, a unique way to analyze vibrational spectra. So far, nonredundant parameter sets have been generated manually following chemical intuition or from a set of redundant parameters in a trial-and-error fashion, which has hampered the study of larger systems with hundreds of parameters. LModeAGen was successfully applied for a test set of 11 systems, ranging from small molecules to the large QM (100 atoms) subsystem of carbomonoxy-neuroglobin protein, described with a hybrid QM/MM method. The ωB97X-D/aug-cc-pVDZ, M06L/def2-TZVP, and QM/MM ωB97X-D/6-31G(d,p)/AMBER model chemistries were adopted for the description of the molecules in the test set. Our new protocol is an important step forward for a routine ACS and CNM analysis of the vibrational spectra of complex and large systems with hundreds of atoms, providing new access to important encoded electronic structure information.

In this work, we investigated bonding features of 15 ruthenium(II) nitrile complexes of the type [Ru(tpy)(L)-(CH3CN)] n+, containing the tridentate tpy ligand (tpy = 2,2′:6′,2″-terpyridine) and various bidentate ancillary ligands L; 12 compounds originally synthesized by Loftus et al. [J. Phys. Chem. C 123, 10291–10299 (2019)] and three new complexes. We utilized local vibrational force constants derived from the local mode theory as a quantitative measure of bond strength complemented with the topological analysis of the electron density and the natural bond orbital analysis. Loftus et al. suggested that nitrile dissociation occurs after light induced singlet–triplet transition of the original complexes and they used as a measure of nitrile release efficiency quantum yields for ligand exchange in water. They observed larger quantum yields for complexes with smaller singlet–triplet energy gaps. The major goal of this work was to assess how the Ru–NC and Ru–L bond strengths in these 15 compounds relate to and explain the experimental data of Loftus et al., particularly focusing on the question whether there is a direct correlation between Ru–NC bond strength and measured quantum yield. Our study provides the interesting result that the compounds with the highest quantum yields also have the strongest Ru–NC bonds suggesting that breaking the Ru–NC bond is not the driving force for the delivery process rather than the change of the metal framework as revealed by first results of a unified reaction valley approach investigation of the mechanism. Compounds with the highest quantum yield show larger electronic structure changes upon singlet–triplet excitation, i.e., larger changes in bond strength, covalency, and difference between the singlet and triplet HOMOs, with exception of the compound 12. In summary, this work provides new insights into the interplay of local properties and experimental quantum yields forming in synergy a useful tool for fine tuning of existing and future design of new nitrile releasing ruthenium compounds. We hope that this work will bring theoretical and experimental studies closer together and serves as an incubator for future collaboration between computational chemists and their experimental colleagues.

Hydroxylation is an effective approach for the synthesis of carbon-oxygen bonds and allylic ethers. The [NHC]Au(I) catalyzed intermolecular hydroalkoxylation of allene was studied at the DFT and Coupled Cluster level of theory. Using the Unified Reaction Valley Approach (URVA), we carry out a comprehensive mechanistic analysis of [NHC]Au(I)-catalyzed and noncatalyzed reactions. The URVA study of several possible reaction pathways reveal that the [NHC]Au(I) catalyst enables the hydroalkoxylation reaction to occur via a two step mechanism based upon the Au ability to switch between π- and σ-complexation. The first step of the mechanism involves the formation of a CO bond after the transition state with no energy penalty. Following the CO bond breakage, the OH bond breaks and CH bond forms during the second step of the mechanism, as the catalyst transforms into the more stable π-Au complex. The URVA results were complemented with local vibrational mode analysis to provide measures of intrinsic bond strength for Au(I)-allene interactions of all stationary points, and NBO analysis was applied in order to observe charge transfer events along the reaction pathway. Overall, the π-Au C═C interactions of the products are stronger than those of the reactants adding to their exothermicity. Our work on the hydroxylation of allene provides new insights for the design of effective reaction pathways to produce allylic ethers and also unravels new strategies to form C-O bonds by activation of C═C bonds.

Two-dimensional infrared spectroscopy has reported highly delocalized in-plane base vibrations in the fingerprint region of nucleotide monophosphates, suggesting the involvement of base pair C=O and C=C ring bonds and considerable interaction between C=O bond stretches. The high delocalization results in congested vibrational spectra, which complicates the assignment of the peaks. This congestion also extends to Watson–Crick base pairs. We applied in this work the characterization of normal mode procedure, a special feature of our local mode analysis, and could for the first time identify the C=O and C=C bonds being engaged in base pair coupling and quantify their contribution to each of the delocalized fingerprint vibration. In addition, a detailed and quantitative description of the hydrogen bonds involved in the Watson–Crick base pairs was provided. Based on the results of this study, we developed a new protocol to elucidate on the assignment of bands in the vibrational spectra of nucleic acids by probing the vibrational space for specific interactions between functional groups prior to and upon base pairing. This protocol will aid to fill the gap between deoxyribonucleic acid structural information and vibrational spectroscopy experiments by facilitating the interpretation of spectra on a quantitative basis.

This work introduces a novel application of generative adversarial networks (GANs) for the prediction of starting geometries in transition state (TS) searches based on the geometries of reactants and products. The multi-dimensional potential energy space of a chemical reaction often complicates the location of a starting TS geometry, leading to the correct TS combining reactants and products in question. The proposed TS-GAN efficiently maps the space between reactants and products and generates reliable TS guess geometries, and it can be easily combined with any quantum chemical software package performing geometry optimizations. The TS-GAN was trained and applied to generate TS guess structures for typical chemical reactions, such as hydrogen migration, isomerization, and transition metal-catalyzed reactions. The performance of the TS-GAN was directly compared to that of classical approaches, proving its high accuracy and efficiency. The current TS-GAN can be extended to any dataset that contains sufficient chemical reactions for training. The software is freely available for training, experimentation, and prediction at https://github.com/ekraka/TS-GAN.

In this work, we investigated the formation of protonated hydrogen cyanide HCNH+ and methylene amine cation CH[Formula: see text] (both identified in Titan's upper atmosphere) from three different pathways which stem from the interaction between CH4 and N+(3P). As a mechanistic tool, we used the Unified Reaction Valley Approach (URVA) complemented with the Local Mode Analysis (LMA) assessing the strength of the CN bonds formed in these reactions. Our URVA studies could provide a comprehensive overview on bond formation/cleavage processes relevant to the specific mechanism of eight reactions R1- R8 that occur across the three pathways. In addition, we could explain the formation of CH[Formula: see text] and the appearance of HCNH+ and CHNH[Formula: see text] along these paths. Although only smaller molecules are involved in these reactions including isomerization, hydrogen atom abstraction, and hydrogen molecule capture, we found a number of interesting features, such as roaming in reaction R3 or the primary interaction of H2 with the carbon atom in HCNH+ in reaction R8 followed by migration of one of the H2 hydrogen atoms to the nitrogen which is more cost effective than breaking the HH bond first; a feature often found in catalysis. In all cases, charge transfer between carbon and nitrogen could be identified as a driving force for the CN bond formation. As revealed by LMA, the CN bonds formed in reactions R1-R8 cover a broad bond strength range from very weak to very strong, with the CN bond in protonated hydrogen cyanide HCNH+ identified as the strongest of all molecules investigated in this work. Our study demonstrates the large potential of both URVA and LMA to shed new light into these extraterrestrial reactions to help better understand prebiotic processes as well as develop guidelines for future investigations involving areas of complex interstellar chemistry. In particular, the formation of CN bonds as a precursor to the extraterrestrial formation of amino acids will be the focus of future investigations. Formation of CN bonds in Titan's atmosphere visualized via the reaction path curvature.

Tetrazoles are well known for their high positive enthalpy of formation which makes them attractive as propellants, explosives, and energetic materials. As a step towards a deeper understanding of the stability of benziodazolotetrazole (BIAT)-based materials compared to their benziodoxole (BIO) counterparts, we investigated in this work electronic structure features and bonding properties of two monovalent iodine precursors: 2-iodobenzoic acid and 5-(2-iodophenyl)tetrazole and eight hypervalent iodine (III) compounds: I-hydroxybenzidoxolone, I-methoxybenziodoxolone, I-ethoxybenziodoxolone, I-iso-propoxybenziodoxolone and the corresponding I-hydroxyben ziodazolotetrazole, I-methoxybenziodazolotetrazole, I-ethoxybenziodazolotetrazole and I-iso- propoxybenziodazolotetrazole. As an efficient tool for the interpretation of the experimental IR spectra and for the quantitative assessment of the I−C, I−N, and I−O bond strengths in these compounds reflecting substituent effects, we used the local vibrational mode analysis, originally introduced by Konkoli and Cremer, complemented by electron density and natural bond orbital analyses. Based on the hypothesis that stronger bonds correlate with increased stability, we predict that, for both series, i.e., substituted benziodoxoles and benziodazolotetrazoles, the stability increases as follows: I-iso-propoxy &lt, I-ethoxy &lt, I-methoxy &lt, I-hydroxy. In particular, the I−N bonds in the benziodazolotetrazoles could be identified as the so-called trigger bonds being responsible for the initiation of explosive decomposition in benziodazolotetrazoles. The new insight gained by this work will allow for the design of new benziodazolotetrazole materials with controlled performance or stability based on the modulation of the iodine bonds with its three ligands. The local mode analysis can serve as an effective tool to monitor the bond strengths, in particular to identify potential trigger bonds. We hope that this article will foster future collaboration between the experimental and computational community being engaged in vibrational spectroscopy.

The Cremer-Pople ring puckering analysis and the Konkoli-Cremer local mode analysis supported by the topological analysis of the electron density were applied for the first comprehensive analysis of the interplay between deoxyribose ring puckering and intramolecular H-bonding in 2'-deoxycytidine, 2'-deoxyadenosine, 2'-deoxythymidine, and 2'-deoxyguanosine. We mapped for each deoxyribonucleoside the complete conformational energy surface and the corresponding pseudorotation path. We found only incomplete pseudorotation cycles, caused by ring inversion, which we coined as pseudolibration paths. On each pseudolibration path a global and a local minimum separated by a transition state were identified. The investigation of H-bond free deoxyribonucleoside analogs revealed that removal of the H-bond does not restore the full conformational flexibility of the sugar ring. Our work showed that ring puckering predominantly determines the conformational energy; the larger the puckering amplitude, the lower the conformational energy. In contrast no direct correlation between conformational energy and H-bond strength was found. The longest and weakest H-bonds are located in the local minimum region, whereas the shortest and strongest H-bonds are located outside the global and local minimum regions at the turning points of the pseudolibration paths, i.e., H-bonding determines the shape and length of the pseudolibration paths. In addition to the H-bond strength, we evaluated the covalent/electrostatic character of the H-bonds applying the Cremer-Kraka criterion of covalent bonding. H-bonding in the puric bases has a more covalent character whereas in the pyrimidic bases the H-bond character is more electrostatic. We investigated how the mutual orientation of the CH2OH group and the base influences H-bond formation via two geometrical parameters describing the rotation of the substituents perpendicular to the sugar ring and their tilting relative to the ring center. According to our results, rotation is more important for H-bond formation. In addition we assessed the influence of the H-bond acceptor, the lone pair (N, respectively O), via the delocalization energy. We found larger delocalization energies corresponding to stronger H-bonds for the puric bases. The global minimum conformation of 2'-deoxyguanosine has the strongest H-bond of all conformers investigated in this work with a bond strength of 0.436 which is even stronger than the H-bond in the water dimer (0.360). The application of our new analysis to DNA deoxyribonucleotides and to unnatural base pairs, which have recently drawn a lot of attention, is in progress.

We systematically investigated iodine–metal and iodine–iodine bonding in van Koten’s pincer complex and 19 modifications changing substituents and/or the transition metal with a PBE0–D3(BJ)/aug–cc–pVTZ/PP(M,I) model chemistry. As a novel tool for the quantitative assessment of the iodine–metal and iodine–iodine bond strength in these complexes we used the local mode analysis, originally introduced by Konkoli and Cremer, complemented with NBO and Bader’s QTAIM analyses. Our study reveals the major electronic effects in the catalytic activity of the M-I-I non-classical three-center bond of the pincer complex, which is involved in the oxidative addition of molecular iodine I2 to the metal center. According to our investigations the charge transfer from the metal to the σ* antibonding orbital of the I-I bond changes the 3c–4e character of the M-I-I three-center bond, which leads to weakening of the iodine I-I bond and strengthening of the metal–iodine M-I bond, facilitating in this way the oxidative addition of I2 to the metal. The charge transfer can be systematically modified by substitution at different places of the pincer complex and by different transition metals, changing the strength of both the M-I and the I2 bonds. We also modeled for the original pincer complex how solvents with different polarity influence the 3c–4e character of the M-I-I bond. Our results provide new guidelines for the design of pincer complexes with specific iodine–metal bond strengths and introduce the local vibrational mode analysis as an efficient tool to assess the bond strength in complexes.

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.

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.

The unified reaction valley approach combined with the local vibrational mode and ring puckering analysis is applied to investigate the hydrogen evolution from water in the presence of small hydrides such as BH3, metal hydrides as AlH3, and their derivatives. We studied a series of reactions involving BH3, AlH3, B2H6, Al2H6, and AlH3BH3 with one- and two-water molecules, considering multiple reaction paths. In addition, the influence of the aqueous medium was examined. A general reaction mechanism was identified for most of the reactions. Those that deviate could be associated with unusually high reaction barriers with no hydrogen release. The charge transfer along the reaction path suggests that a viable hydrogen release is achieved when the catalyst adopts the role of a charge donor during the chemical processes. The puckering analysis showed that twistboat and boat forms are the predominant configurations in the case of an intermediate six-membered ring formation, which influences the activation barrier. The local mode analysis was used as a tool to detect the H-H bond formation as well as to probe catalyst regenerability. Based on the correlation between the activation energy and the change in the charge separation for cleaving O-H and B(Al)-H bonds, two promising subsets of reactions could be identified along with prescriptions for lowering the reaction barrier individually with electron-donating/withdrawing substituents.

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.

11 aryl&ndash, lone pair and three aryl&ndash, anion &pi, &ndash, hole interactions are investigated, along with the argon&ndash, benzene dimer and water dimer as reference compounds, utilizing the local vibrational mode theory, originally introduced by Konkoli and Cremer, to quantify the strength of the &pi, hole interaction in terms of a new local vibrational mode stretching force constant between the two engaged monomers, which can be conveniently used to compare different &pi, hole systems. Several factors have emerged which influence strength of the &pi, hole interactions, including aryl substituent effects, the chemical nature of atoms composing the aryl rings/ &pi, hole acceptors, and secondary bonding interactions between donors/acceptors. Substituent effects indirectly affect the &pi, hole interaction strength, where electronegative aryl-substituents moderately increase &pi, hole interaction strength. N-aryl members significantly increase &pi, hole interaction strength, and anion acceptors bind more strongly with the &pi, hole compared to charge neutral acceptors (lone&ndash, pair donors). Secondary bonding interactions between the acceptor and the atoms in the aryl ring can increase &pi, hole interaction strength, while hydrogen bonding between the &pi, hole acceptor/donor can significantly increase or decrease strength of the &pi, hole interaction depending on the directionality of hydrogen bond donation. Work is in progress expanding this research on aryl &pi, hole interactions to a large number of systems, including halides, CO, and OCH3- as acceptors, in order to derive a general design protocol for new members of this interesting class of compounds.

The field of organometallic chemistry has tremendously grown over the past decades and become an integral part of many areas of chemistry and beyond. Organometallic compounds find a wide use in synthesis, where organometallic compounds are utilized as homogeneous/heterogeneous catalysts or as stoichiometric reagents. In particular, modifying and fine-tuning organometallic catalysts has been at the focus. This requires an in-depth understanding of the complex metal–ligand (ML) interactions which are playing a key role in determining the diverse properties and rich chemistry of organometallic compounds. We introduce in this article the metal–ligand electronic parameter (MLEP), which is based on the local vibrational ML stretching force constant, fully reflecting the intrinsic strength of this bond. We discuss how local vibrational stretching force constants and other local vibrational properties can be derived from the normal vibrational modes, which are generally delocalized because of mode–mode coupling, via a conversion into local vibrational modes, first introduced by Konkoli and Cremer. The MLEP is ideally suited to set up a scale of bond strength orders, which identifies ML bonds with promising catalytic or other activities. The MLEP fully replaces the Tolman electronic parameter (TEP), an indirect measure, which is based on the normal vibrational CO stretching frequencies of [RnM(CO)mL] complexes and which has been used so far in hundreds of investigations. We show that the TEP is at best a qualitative parameter that may fail. Of course, when it was introduced by Tolman in the 1960s, one could not measure the low-frequency ML vibration directly, and our local mode concept did not exist. However, with these two problems solved, a new area of directly characterizing the ML bond has begun, which will open new avenues for enriching organometallic chemistry and beyond.

The Bacillus subtilis chorismate mutase catalysed Claisen rearrangement of chorismate to prephenate is one of the few pericyclic processes in biology, and as such provides a rare opportunity for un...

The unified reaction valley approach (URVA) combined with the local mode, ring puckering and electron density analysis is applied to elucidate the mechanistic differences of the non-catalys...

In this work, we investigated the strength of the $${\hbox {H}}^{-}$$ and $${\hbox {H}}_{2}$$ interaction with the Fe atom of a [NiFe] hydrogenase mimic, and how this interaction can be modulated by changing the Fe ligand in trans-position relative to $${\hbox {H}}^{-}$$ and $${\hbox {H}}_{2}$$ . We used as a quantitative measure of bond strength local vibrational force constants derived from the Konkoli–Cremer local mode analysis, complemented by the topological analysis of the electronic density and the natural bond orbital analysis. Seventeen different ligands were investigated utilizing density functional theory calculations, including $${\sigma }$$ -donor ligands such as $${\hbox {CH}}_{3}^{-}$$ , $${\hbox {C}}_{2}{\hbox {H}}_{5}^{-}$$ , $${\hbox {NH}}_{3}$$ , and $${\hbox {H}}_{2}\hbox {O}$$ , $${\pi }$$ -donor ligands such as $${\hbox {Cl}}^{-}$$ , $${\hbox {F}}^{-}$$ , and $${\hbox {OH}}^{-}$$ , and $${\sigma }$$ -donor/ $${\pi }$$ -acceptor ligands such as $${\hbox {CN}}^{-}$$ and CO. According to the local mode analysis, Fe–H interactions are strengthened by $${\sigma }$$ -donor or $${\pi }$$ -donor ligands and weakened by $${\sigma }$$ -donor/ $${\pi }$$ -acceptor ligands. In contrast, the H–H bond of $${\hbox {H}}_{2}$$ is weakened by $${\sigma }$$ -donor or $${\pi }$$ -donor ligands and strengthened by $${\sigma }$$ -donor/ $${\pi }$$ -acceptor ligands. We also present a new metal–ligand electronic parameter (MLEP) for Fe–H ligands which can be generally applied to evaluate the Fe–H bond strength in iron complexes and iron hydrides. These results form a valuable basis for future [NiFe] hydrogenase-based catalyst design and fine tuning, as well as for the development of efficient biomimetic catalysts for $${\hbox {H}}_{2}$$ generation.

The reaction mechanism of the cycloaddition of 10 1,3-dipoles with the two dipolarphiles ethene and acetylene is investigated and compared using the Unified Reaction Valley Approach in a new form, which is based on a dual-level strategy, an accurate description of the reaction valley far out into the van der Waals region, and a comparative analysis of the electronic properties of the reaction complex. A detailed one-to-one comparison of 20 different 1,3-dipolar cycloadditions is performed, and unknown mechanistic features are revealed. There are significant differences in the reaction mechanisms for the two dipolarophiles that result from the van der Waals complex formation in the entrance channel of the cycloadditions. Hydrogen bonding between the 1,3-dipoles and acetylene is generally stronger, which leads to higher reaction barriers in the acetylene case, but which also facilitates to overcome the problem of a reduced charge transfer from 1,3-dipole to acetylene. Mechanistic differences are found in the prechemical and chemical reaction regions with regard to reactant orientation, preparation for the reaction, charge transfer, charge polarization, rehybridization, and bond formation. It is shown that similarities in the reaction barriers as determined by CCSD(T)-F12/aug-cc-pVTZ calculations result from a fortuitous cancellation of different electronic effects. In general, a caveat must be made with regard to oversimplified descriptions of the reaction mechanism based on orbital theory or energy decomposition schemes.

The unified reaction valley approach (URVA) used for a detailed mechanistic analysis of chemical reactions is improved in three different ways: (i) Direction and curvature of path are analyzed in terms of internal coordinate components that no longer depend on local vibrational modes. In this way, the path analysis is no longer sensitive to path instabilities associated with the occurrences of imaginary frequencies. (ii) The use of third order terms of the energy for a local description of the reaction valley allows an extension of the URVA analysis into the pre- and postchemical regions of the reaction path, which are typically characterized by flat energy regions. (iii) Configurational and conformational processes of the reaction complex are made transparent even in cases where these imply energy changes far less than a kcal/mol by exploiting the topology of the potential energy surface. As examples, the rhodium-catalyzed methanol carbonization, the Diels-Alder reaction between 1,3-butadiene and ethene, and the rearrangement of HCN to CNH are discussed.

The local vibrational mode analysis, originally introduced by Konkoli and Cremer, provides a physically sound platform for a comprehensive analysis of calculated or measured vibrational spectra and for providing detailed insights into chemical bonding and other structural features. In this work, we summarize the essentials of the local vibrational mode theory with a focus on local vibrational force constants and their relationship with compliance and relaxed force constants. Furthermore, we discuss how local vibrational force constants can be used (i) to assess the quality of empirically derived force constants, (ii) to disclose bonding features in large molecules, and (iii) to provide metal ligand force field parameters. Future applications will be suggested.

The relativistic Hamiltonian Normalised Elimination of the Small Component with atomic unitary transformation (NESCau) was used for the first time to calculate geometries and harmonic vibrational f...

Chiral discrimination of homochiral and heterochiral H-bonded complexes is a challenge for both experimentalists and computational chemists. It is demonstrated that a two-pronged approach based on far-infrared vibrational spectroscopy and the calculation of local mode frequencies facilitates the chiral discrimination of H-bonded dimers. The local H-bond stretching frequencies identify the strongest H-bonds and by this the dominating chiral diastereomer. This is shown in the case of peroxide, trioxide, hydrazine, glycidol, and butan-2-ol dimers as well as propylene oxide…glycidol complexes investigated with the help of second-order Moller–Plesset perturbation, coupled cluster, and density functional theory calculations where, in the latter case, the ωB97X-D functional was used for an improved description of H-bonding. In some cases, additional intermolecular interactions overrule the important role of H-bonding, which is found by calculating chirodiastaltic energies. Chirality 25:185–196, 2013. © 2013 Wiley Periodicals, Inc.

High-level ab initio calculations of the NESC/SOC/CCSD(T)/cc-pV5Z type (NESC, Normalized Elimination of the Small Component; SOC, spin-orbit coupling corrections using the Breit-Pauli Hamiltonian) are employed to determine the energetics of the 18 hydrogenation reactions XHn + H2 → XHn+1 + H with X = F, Cl, Br, I, O, S, Se, Te, N, P, As, Sb, Bi, C, Si, Ge, Sn, and Pb. Accurate reaction and activation enthalpies as well as the corresponding free energies are obtained by calculating vibrational, thermochemical, and entropy corrections with a cc-pVTZ basis set. Also calculated are accurate X-H bond dissociation enthalpies at 298 K. The reaction mechanism of all 18 reactions is analyzed using the unified reaction valley approach (URVA) and UMP2/6-31G(d,p) to determine each reaction valley with high accuracy (step size 0.005 to 0.03 amu(1/2) bohr). By analyzing the reaction path curvature, the mechanism can be partitioned into four to six reaction phases, in which the reaction complex XHn···H2 undergoes specific chemical transformations. The fate of the reaction complex is determined at an early stage in the entrance channel. Curvature peaks reflect the strength of the bonds being broken or formed and provide the basis for a quantitative justification of the Hammond-Leffler postulate.

Local stretching modes for 69 different DH single bonds and 58 H···A H-bonds are calculated at the ωB97X-D/aug-cc-pVTZ level of theory to describe the changes in donor D and acceptor A upon forming the hydrogen-bonded complex. The intrinsic strength of the DH and AH interactions is determined utilizing the properties of a well-defined set of local, uncoupled vibrational modes. The local mode stretching force constant ka(HA) provides a unique measure of bond strength for both covalently and electrostatically bonded complexes. Generally applicable bond orders are derived, which can be related to the binding energies of the hydrogen bonded complexes. Although the red shifts in the DH stretching frequencies can be used to detect hydrogen bonding, they are not sufficient to assess the strength of hydrogen bonding. It is demonstrated that the calculated BSSE-corrected binding energies of hydrogen bonded complexes are related to the sum of bond order changes caused by hydrogen bonding. The covalent character of charge assisted hydrogen bonds is explained. Because local mode frequencies can also be derived from experimental normal mode frequencies, a new dimension in the study of hydrogen bonding is gained. © 2012 Wiley Periodicals, Inc.

Recent biochemical studies have identified a cell surface receptor for thyroid and steroid hormones that bind near the arginine-glycine-aspartate (RGD) recognition site on the heterodimeric αvβ3 integrin. To further characterize the intermolecular interactions for a series of hormone analogues, combined quantum mechanical and molecular mechanical (QM/MM) methods were used to calculate their interaction energies. All calculations were performed in the presence of either calcium (Ca2+) or magnesium (Mg2+) ions. These data reveal that 3,5′-triiodothyronine (T3) and 3,5,3′,5′-tetraiodothyroacetic acid (T4ac) bound in two different modes, occupying two alternate sites, one of which is along the Arg side chain of the RGD cyclic peptide site. These orientations differ from those of the other ligands whose alternate binding modes placed the ligands deeper within the RGD binding pocket. These observations are consistent with biological data that indicate the presence of two discrete binding sites that control distinct downstream signal transduction pathways for T3.

The ongoing controversy whether cyclization reactions of conjugated allenes or ketenes follow a pericyclic or a pseudopericyclic mechanism has triggered dozens of investigations, which have led to new valuable synthetic routes. In this work, the mechanism of 10 representative cyclization reactions of hepta-1,2,4,6-tetraenes with different terminal groups is investigated utilizing the unified reaction valley approach that registers all electronic structure changes of the target molecule along the entire reaction pathway. A clear differentiation between a purely pericyclic and a purely pseudopericyclic mechanism is established. Additionally, it is found that, by using suitable functional groups, a pericyclic mechanism can be converted into a pseudopericyclic one, which is associated with a steady decrease of the reaction barrier and a continuous change from one mechanism to the other. The energetics of the reaction are confirmed by coupled cluster calculations of the CCSD(T) type. The mechanistic insight gained is used to design new pseudopericyclic reactions with low or no barrier, which will open new synthetic avenues.