On the origin of cooperativity effects in the formation of self-assembled molecular networks at the liquid/solid interface

In this work we investigate the behaviour of molecules at the nanoscale using scanning tunnelling microscopy in order to explore the origin of the cooperativity in the formation of self-assembled molecular networks (SAMNs) at the liquid/solid interface. By studying concentration dependence of alkoxylated dimethylbenzene, a molecular analogue to 5-alkoxylated isophthalic derivatives, but without hydrogen bonding moieties, we show that the cooperativity effect can be experimentally evaluated even for low-interacting systems and that the cooperativity in SAMN formation is its fundamental trait. We conclude that cooperativity must be a local effect and use the nearest-neighbor Ising model to reproduce the coverage vs. concentration curves. The Ising model offers a direct link between statistical thermodynamics and experimental parameters, making it a valuable tool for assessing the thermodynamics of SAMN formation.

Exploration of biochemical reactivity with a QM/MM growing string method

In this work, we have implemented the single-ended growing string method using a hybrid internal/Cartesian coordinate scheme within our in-house QM/MM package, QoMMMa, representing the first implementation of the growing string method in the QM/MM framework. The goal of the implementation was to facilitate generation of QM/MM reaction pathways with minimal user input, and also to improve the quality of the pathways generated as compared to the widely used adiabatic mapping approach. We have validated the algorithm against a reaction which has been studied extensively in previous computational investigations - the Claisen rearrangement catalysed by chorismate mutase. The nature of the transition state and the height of the barrier was predicted well using our algorithm, where more than 88% of the pathways generated were deemed to be of production quality. Directly compared to using adiabatic mapping, we found that while our QM/MM single-ended growing string method is slightly less efficient, it readily produces reaction pathways with fewer discontinuites and thus minimises the need for involved remapping of unsatisfactory energy profiles.

Highly Ordered Co-Assembly of Bisurea Functionalized Molecular Switches at the Solid-Liquid Interface

Immobilization of stimulus-responsive systems on solid surfaces is beneficial for controlled signal transmission and adaptive behavior while allowing the characterization of the functional interface with high sensitivity and high spatial resolution. Positioning of the stimuli-responsive units with nanometer-scale precision across the adaptive surface remains one of the bottlenecks in the extraction of cooperative function. Nanoscale organization, cooperativity, and amplification remain key challenges in bridging the molecular and the macroscopic worlds. Here we report on the design, synthesis, and scanning tunneling microscopy (STM) characterization of overcrowded alkene photoswitches merged in self-assembled networks physisorbed at the solid-liquid interface. A detailed anchoring strategy that ensures appropriate orientation of the switches with respect to the solid surface through the use of bis-urea groups is presented. We implement a co-assembly strategy that enables the merging of the photoswitches within physisorbed monolayers of structurally similar 'spacer' molecules. The self-assembly of the individual components and the co-assemblies was examined in detail using (sub)molecular resolution STM which confirms the robust immobilization and controlled orientation of the photoswitches within the spacer monolayers. The experimental STM data is supported by detailed molecular mechanics (MM) simulations. Different designs of the switches and the spacers were investigated which allowed us to formulate guidelines that enable the precise organization of the photoswitches in crystalline physisorbed self-assembled molecular networks.

Machine Learning Representations of the Three Lowest Adiabatic Electronic Potential Energy Surfaces for the ArH2+ Reactive System

In this work, we present Gaussian process regression machine learning representations of the three lowest coupled 2A' adiabatic electronic potential energy surfaces of the ArH2+ reactive system in full dimensionality. Additionally, the nonadiabatic coupling matrix elements were calculated. These adiabatic potentials and their nonadiabatic couplings are necessary ingredients in the theoretical investigation of the nonadiabatic reaction dynamics of the Ar + H2+ → ArH+ + H and Ar+ + H2 → ArH+ + H reactions, as well as the competing charge transfer process, Ar + H2+↔ Ar+ + H2. Accurate ab initio electronic structure calculations (ic-MRCI+Q/aug-cc-pVQZ), whereby the effect of spin-orbit coupling in Ar+ has been accounted for through the state interaction method, serve as input for the machine learning training process. The potential energy surfaces are fitted with high accuracies, with root-mean-square errors on the order of 10-7 eV for the three surfaces, which meet the requirements for chemical dynamics at low temperature. It was found that quite a large number of training points (of the order of 5000 ab initio points) are needed in order to achieve these accuracies due to the complex topography of these electronic surfaces.

Molecular structure of soluble vimentin tetramers

Intermediate filaments (IFs) are essential constituents of the metazoan cytoskeleton. A vast family of cytoplasmic IF proteins are capable of self-assembly from soluble tetrameric species into typical 10-12 nm wide filaments. The primary structure of these proteins includes the signature central 'rod' domain of ~ 300 residues which forms a dimeric α-helical coiled coil composed of three segments (coil1A, coil1B and coil2) interconnected by non-helical, flexible linkers (L1 and L12). The rod is flanked by flexible terminal head and tail domains. At present, the molecular architecture of mature IFs is only poorly known, limiting our capacity to rationalize the effect of numerous disease-related mutations found in IF proteins. Here we addressed the molecular structure of soluble vimentin tetramers which are formed by two antiparallel, staggered dimers with coil1B domains aligned (A₁₁ tetramers). By examining a series of progressive truncations, we show that the presence of the coil1A domain is essential for the tetramer formation. In addition, we employed a novel chemical cross-linking pipeline including isotope labelling to identify intra- and interdimeric cross-links within the tetramer. We conclude that the tetramer is synergistically stabilized by the interactions of the aligned coil1B domains, the interactions between coil1A and the N-terminal portion of coil2, and the electrostatic attraction between the oppositely charged head and rod domains. Our cross-linking data indicate that, starting with a straight A₁₁ tetramer, flexibility of linkers L1 and L12 enables 'backfolding' of both the coil1A and coil2 domains onto the tetrameric core formed by the coil1B domains. Through additional small-angle X-ray scattering experiments we show that the elongated A₁₁ tetramers dominate in low ionic strength solutions, while there is also a significant structural flexibility especially in the terminal domains.

Stability profile of vimentin rod domain

Intermediate filaments (IFs) form an essential part of the metazoan cytoskeleton. Despite a long history of research, a proper understanding of their molecular architecture and assembly process is still lacking. IFs self-assemble from elongated dimers, which are defined by their central "rod" domain. This domain forms an α-helical coiled coil consisting of three segments called coil1A, coil1B, and coil2. It has been hypothesized that the structural plasticity of the dimer, including the unraveling of some coiled-coil regions, is essential for the assembly process. To systematically explore this possibility, we have studied six 50-residue fragments covering the entire rod domain of human vimentin, a model IF protein. After creating in silico models of these fragments, their evaluation using molecular dynamics was performed. Large differences were seen across the six fragments with respect to their structural variability during a 100 ns simulation. Next, the fragments were prepared recombinantly, whereby their correct dimerization was promoted by adding short N- or C-terminal capping motifs. The capped fragments were subjected to circular dichroism measurements at varying temperatures. The obtained melting temperatures reveal the relative stabilities of individual fragments, which correlate well with in silico results. We show that the least stable regions of vimentin rod are coil1A and the first third of coil2, while the structures of coil1B and the rest of coil2 are significantly more robust. These observations are in line with the data obtained using other experimental approaches, and contribute to a better understanding of the molecular mechanisms driving IF assembly.

Microscopic Reactivity of Phenylferrate Ions toward Organyl Halides

Despite its practical importance, organoiron chemistry remains poorly understood due to its mechanistic complexity. Here, we focus on the oxidative addition of organyl halides to phenylferrate anions in the gas phase. By mass-selecting individual phenylferrate anions, we can determine the effect of the oxidation state, the ligation, and the nuclearity of the iron complex on its reactions with a series of organyl halides RX. We find that Ph₂ Fe(I)^- and other low-valent ferrates are more reactive than Ph₃ Fe(II)^- ; Ph₄ Fe(III)^- is inert. The coordination of a PPh₃ ligand or the presence of a second iron center lower the reactivity. Besides direct cross-coupling reactions resulting in the formation of RPh, we also observe the abstraction of halogen atoms. This reaction channel shows the readiness of organoiron species to undergo radical-type processes. Complementary DFT calculations afford further insight and rationalize the high reactivity of the Ph₂ Fe(I)^- complex by the exothermicity of the oxidative addition and the low barriers associated with this reaction step. At the same time, they point to the importance of changes of the spin state in the reactions of Ph₃ Fe(II)^- .

An automated method for graph-based chemical space exploration and transition state finding

Algorithms that automatically explore the chemical space have been limited to chemical systems with a low number of atoms due to expensive involved quantum calculations and the large amount of possible reaction pathways. The method described here presents a novel solution to the problem of chemical exploration by generating reaction networks with heuristics based on chemical theory. First, a second version of the reaction network is determined through molecular graph transformations acting upon functional groups of the reacting. Only transformations that break two chemical bonds and form two new ones are considered, leading to a significant performance enhancement compared to previously presented algorithm. Second, energy barriers for this reaction network are estimated through quantum chemical calculations by a growing string method, which can also identify non-octet species missed during the previous step and further define the reaction network. The proposed algorithm has been successfully applied to five different chemical reactions, in all cases identifying the most important reaction pathways.

The Mechanism of Biochemical NO‐Sensing: Insights from Computational Chemistry

The binding of small gas molecules such as NO and CO plays a major role in the signaling routes of the human body. The sole NO‐receptor in humans is soluble guanylyl cyclase (sGC) – a histidine‐ligated heme protein, which, upon NO binding, activates a downstream signaling cascade. Impairment of NO‐signaling is linked, among others, to cardiovascular and inflammatory diseases. In the present work, we use a combination of theoretical tools such as MD simulations, high‐level quantum chemical calculations and hybrid QM/MM methods to address various aspects of NO binding and to elucidate the most likely reaction paths and the potential intermediates of the reaction. As a model system, the H‐NOX protein from Shewanella oneidensis (So H‐NOX) homologous to the NO‐binding domain of sGC is used. The signaling route is predicted to involve NO binding to form a six‐coordinate intermediate heme‐NO complex, followed by relatively facile His decoordination yielding a five‐coordinate adduct with NO on the distal side with possible isomerization to the proximal side through binding of a second NO and release of the first one. MD simulations show that the His sidechain can quite easily rotate outward into solvent, with this motion being accompanied in our simulations by shifts in helix positions that are consistent with this decoordination leading to significant conformational change in the protein.

Effect of solvent motions on the dynamics of the Diels-Alder reaction

How solvent motions affect the dynamics of chemical reactions in which the solute undergoes a substantial shape change is a fundamental but elusive issue. This work utilizes reactive simulation and Grote-Hynes theory to explore the effect of solvent motions on the dynamics of the Diels-Alder reaction (in the reverse direction, this reaction involves very substantial solute expansion) in aprotic solvents. The results reveal that the solvent environment is not sufficiently constraining to influence transition state passage dynamics, with the calculated transmission coefficients being close to unity. Even when solvent motions are suppressed or artificially slowed down, the solvent only affects the reaction dynamics in the transition state region to a very small extent. The only notable effect of solvent occurs far from the transition state region and corresponds to caging of the reactants within the reactant well.

On the Importance of Considering Multinuclear Metal Sites in Homogeneous Catalysis Modeling

In this short review, we provide an account of a number of computational studies of catalytic reaction mechanisms carried out in our groups. We focus in particular on studies in which we came to realize during the course of the investigation that the active catalytic species was a bimetallic complex, rather a monometallic one as previously assumed. In some cases, this realization was in part prompted by experimental observations, but careful exploration based on computation of the speciation of the metal precursor also provided a powerful guide: it is often possible to predict that bimetallic species (intermediates or transition states) lie lower in free energy than a priori competitive monometallic species. In this sense, we argue that in organometallic catalysis, the rule whereby “two is better than one” turns out to be relevant much more often than one might expect.

On the Use of Normalized Metrics for Density Sensitivity Analysis in DFT

In the past years, there has been a discussion about how the errors in density functional theory might be related to errors in the self-consistent densities obtained from different density functional approximations. This, in turn, brings up the discussion about the different ways in which we can measure such errors and develop metrics that assess the sensitivity of calculated energies to changes in the density. It is important to realize that there cannot be a unique metric in order to look at this density sensitivity, simultaneously needing size-extensive and size-intensive metrics. In this study, we report two metrics that are widely applicable to any density functional approximation. We also show how they can be used to classify different chemical systems of interest with respect to their sensitivity to small variations in the density.

The changing incidence of childhood-onset type 1 diabetes in Wales: Effect of gender and season at diagnosis and birth

AIMS

Determinants of the changing incidence of childhood-onset type 1 diabetes remain uncertain. We determined the recent time-trend of type 1 diabetes incidence in Wales and explored the role of vitamin D by evaluating the influence of season both at diagnosis and at birth.

METHODS

Data from all Welsh paediatric units 1990-2019, and from primary care to determine ascertainment.

RESULTS

Log-linear modelling indicated a non-linear secular trend in incidence with peak and subsequent decline. The peak occurred around June 2010: 31∙3 cases/year/100,000 children aged < 15y. It occurred earlier in children younger at diagnosis and earlier in boys. There were more cases in males aged <2y and >12y but more in females aged 9-10 y. More were diagnosed in winter. Also, children born in winter had less risk of future diabetes.

CONCLUSIONS

The risk of developing type 1 diabetes before age 15y in Wales is no longer increasing. The data on season are consistent with a preventative role for vitamin D both during pregnancy and later childhood. Metereological Office data shows increasing hours of sunlight since 1980 likely to increase vitamin D levels with less diabetes. Additional dietary supplementation with vitamin D might further reduce the incidence of type 1 diabetes.

Vibrational Energy Relaxation of Deuterium Fluoride in d-Dichloromethane: Insights from Different Potentials

Vibrationally excited deuterium fluoride (DF) formed by fluorine atom reaction with a solvent was found (Science, 2015, 347, 530) to relax rapidly (less than 10 ps) in acetonitrile-d₃ (CD₃CN) and dichloromethane-d₂ (CD₂Cl₂). However, insights into how CD₂Cl₂ facilitates this energy relaxation have so far been lacking, given the weak interaction between DF and a single CD₂Cl₂. In this work, we report the results of reactive simulations with a two-state reactive empirical valence bond (EVB) potential to study the energy deposited into nascent DF after transition-state passage and of nonequilibrium molecular dynamics simulations using multiple different potential energy functions to model the relaxation dynamics. For these second simulations, we used the standard Merck molecular force field (MMFF) potential, an MMFF-based covalent-ionic empirical valence bond (EVB) potential (EVB^CI), a newly developed potential [referred to as MMFF(rDF)] which extends upon the MMFF potential by making the DF/CD₂Cl₂ interaction depend on the value of the D-F bond stretching coordinate and by taking the anisotropic charge distribution of the solvent molecules into account, the polarizable atomic multipole optimized energetics for biomolecular applications (AMOEBA) potential, and the quantum mechanics/molecular mechanics (QM/MM) potential. The relaxation is revealed to be highly sensitive to the potential used. Neither standard MMFF nor EVB^CI reproduces the experimentally observed rapid relaxation dynamics, and they also fail to provide a good description of the interaction potential between DF and CD₂Cl₂ as calculated using CCSD(T)-F12. This is attributed to the use of a point-charge model for the solute and to failing to model the anisotropic electrostatic properties of CD₂Cl₂. The MMFF(rDF), AMOEBA, and QM/MM potentials all reproduce the CCSD(T)-F12 two-body DF---CD₂Cl₂ interaction potential rather well but only with the QM/MM approach is fast vibrational relaxation obtained (lifetimes of ∼288, ∼186, and ∼8 ps, respectively), which we attribute to differences in the solute-solvent local structure. With QM/MM, a unique "many-body" interaction pattern in which DF is in close contact with two solvent Cl atoms and more than three solvent D atoms is found, but this structure is not seen with other potentials. The QM/MM dynamics also display enhanced solute-solvent interactions with vibrationally excited DF that induce a DF band redshift and hence a resonant overlap with solvent C-D modes, which facilitate the intermolecular energy transfer. Our work also suggests that potentials used to model energy relaxation need to capture the fine structure of solute-solvent interactions and not just the two-body part.

Histidine versus Cysteine-Bearing Heme-Dependent Halogen Peroxidases: Parallels and Differences for Cl- Oxidation

The homodimeric myeloperoxidase (MPO) features a histidine as a proximal ligand and a sulfonium linkage covalently attaching the heme porphyrin ring to the protein. MPO is able to catalyze Cl^- oxidation with about the same efficiency as chloroperoxidase at pH 7.0. In this study, we seek to explore the parallels and differences between the histidine and cysteine heme-dependent halogen peroxidases. Transition states, reaction barriers, and relevant thermodynamic properties are calculated on protein models. Together with electronic structure calculations, it gives an overview of the reaction mechanisms and of the factors that determine the selectivity between one- and two-electron paths. Conclusions point to the innate oxidizing nature of MPO with the ester and sulfonium linkages hiking up the reactivity to enable chloride oxidation. The installation of a deprotonated imidazolate as a proximal ligand does not shift the equilibrium from one- to two-electron events without influencing the chemistry of the oxidation reaction.

Mechanism of the highly effective peptide bond hydrolysis by MOF-808 catalyst under biologically relevant conditions

Efficient and selective hydrolysis of inert peptide bonds is of paramount importance. MOF-808, a metal-organic framework based on Zr₆ nodes, can hydrolyze peptide bonds efficiently under biologically relevant conditions. However, the details of the catalyst structure and of the underlying catalytic reaction mechanism are challenging to establish. By means of DFT calculations we first investigate the speciation of the Zr₆ nodes and identify the nature of ligands that bind to the Zr₆O₈H_4-x core in aqueous conditions. The core is predicted to strongly prefer a Zr₆O₈H₄ protonation state and to be predominantly decorated by bridging formate ligands, giving Zr₆(μ₃-O)₄(μ₃-OH)₄(BTC)₂(HCOO)₆ and Zr₆(μ₃-O)₄(μ₃-OH)₄(BTC)₂(HCOO)₅(OH)(H₂O) as the most favorable structures at physiological pH. The GlyGly peptide can bind MOF in several different ways, with the preferred structure involving coordination through the terminal carboxylate analogously to the binding mode of formate ligand. The pre-reactive binding mode in which the amide carbonyl oxygen coordinates the metal core lies 7 kcal higher in free energy. The preferred reaction pathway is predicted to have two close-lying transition states, either of which could be the rate-determining step: nucleophilic attack on the amide carbon atom and C-N bond breaking, with calculated relative free energies of 31 and 32 kcal mol^-1, respectively. Replacement of formate by water and hydroxide at the Zr₆ node is predicted to be possible, but does not appear to play a role in the hydrolysis mechanism.

Ruthenium-catalyzed cascade C-H activation/annulation of N-alkoxybenzamides: reaction development and mechanistic insight

A highly selective ruthenium-catalyzed C–H activation/annulation of alkyne-tethered N-alkoxybenzamides has been developed. In this reaction, diverse products from inverse annulation can be obtained in moderate to good yields with high functional group compatibility. Insightful experimental and theoretical studies indicate that the reaction to the inverse annulation follows the Ru(ii)–Ru(iv)–Ru(ii) pathway involving N–O bond cleavage prior to alkyne insertion. This is highly different compared to the conventional mechanism of transition metal-catalyzed C–H activation/annulation with alkynes, involving alkyne insertion prior to N–O bond cleavage. Via this pathway, the in situ generated acetic acid from the N–H/C–H activation step facilitates the N–O bond cleavage to give the Ru-nitrene species. Besides the conventional mechanism forming the products via standard annulation, an alternative and novel Ru(ii)–Ru(iv)–Ru(ii) mechanism featuring N–O cleavage preceding alkyne insertion has been proposed, affording a new understanding of transition metal-catalyzed C–H activation/annulation.

A highly selective ruthenium-catalyzed C–H activation/annulation through a pathway involving N–O bond cleavage prior to alkyne insertion is developed.

Computational Chemistry and Non-noble Metal-catalyzed Cross-coupling Reaction Mechanisms

This short overview discusses the contribution that computational methods can make to the study of reaction mechanisms in non-noble-metal-catalyzed cross-coupling reactions. The differences between such reactions and those catalyzed by more traditional noble metals are emphasized, together with the challenge this poses to computation.

Benchmarking quantum mechanical methods for calculating reaction energies of reactions catalyzed by enzymes

To assess the accuracy of different quantum mechanical methods for biochemical modeling, the reaction energies of 20 small model reactions (chosen to represent chemical steps catalyzed by commonly studied enzymes) were calculated. The methods tested included several popular Density Functional Theory (DFT) functionals, second-order Møller Plesset perturbation theory (MP2) and its spin-component scaled variant (SCS-MP2), and coupled cluster singles and doubles and perturbative triples (CCSD(T)). Different basis sets were tested. CCSD(T)/aug-cc-pVTZ results for all 20 reactions were used to benchmark the other methods. It was found that MP2 and SCS-MP2 reaction energy calculation results are similar in quality to CCSD(T) (mean absolute error (MAE) of 1.2 and 1.3 kcal mol−1, respectively). MP2 calculations gave a large error in one case, and are more subject to basis set effects, so in general SCS-MP2 calculations are a good choice when CCSD(T) calculations are not feasible. Results with different DFT functionals were of reasonably good quality (MAEs of 2.5–5.1 kcal mol−1), whereas popular semi-empirical methods (AM1, PM3, SCC-DFTB) gave much larger errors (MAEs of 11.6–14.6 kcal mol−1). These results should be useful in guiding methodological choices and assessing the accuracy of QM/MM calculations on enzyme-catalyzed reactions.

Oxidative Addition of Aryl Halides to a Triphosphine Ni(0) Center to Form Pentacoordinate Ni(II) Aryl Species

Oxidative addition of aryl halides to Ni(0) is a ubiquitous elementary step in cross-coupling and related reactions, usually producing a square-planar Ni(II)-aryl intermediate. Here we show that a triphosphine ligand supports oxidative addition at a tris-ligated Ni(0) center to cleanly form stable five-coordinate Ni(II)-aryl compounds. Kinetic and computational studies support a concerted, two-electron mechanism rather than radical halogen abstraction. These results support the idea that oxidative addition to triphosphine Ni(0) species may be more generally involved in Ni/phosphine catalytic systems.

Spin-Forbidden Reactivity of Transition Metal Oxo Species: Exploring the Potential Energy Surfaces

Spin-forbidden reactions are frequently encountered when transition metal oxo species are involved, particularly in oxygen transfer reactivity. The computational study of such reactions is challenging, because reactants and products are located on different spin potential energy surfaces (PESs). One possible approach to describe these reactions is the so-called minimum energy crossing point (MECP) between the diabatic reactants and products PESs. Alternatively, inclusion of spin-orbit coupling (SOC) effects allows to locate a saddle point on a single adiabatic PES (TS SOC). The TS SOC approach is rarely applied because of its high computational cost. Recently evidence for a TS SOC impact on significantly lowering the activation barrier in dioxygen addition to a carbene-gold(I)-hydride complex reaction (Chem. Sci. 2016, 7, 7034-7039) or even on predicting a qualitatively different reaction mechanism in mercury methylation by cobalt corrinoid (Angew. Chem. Int. Ed. 2016, 55, 11503-11506) has been put forward. Using MECP and TS SOC approaches a systematic analysis is provided here of three prototypical transition metal oxo spin-forbidden processes to investigate their implications on reactivity. Cycloaddition of ethylene to chromyl chloride (CrO₂ Cl₂ +C₂ H₄ ), iron oxide cation insertion into the hydrogen molecule (FeO⁺ +H₂ ) and H-abstraction from toluene by a Mn^V -oxo-porphyrin cation (MnOP(H₂ O)⁺ +C₆ H₅ CH₃ ) are case studies. For all these processes the MECP and TS SOC results are compared, which show that the spin-forbidden reactivity of transition metal oxo species can be safely described by a MECP approach, at least for the first-row transition metals investigated here, where the spin-orbit coupling is relatively weak. However, for the Mn-oxo reactivity, the MECP and TS SOC have been found to be crucial for a correct description of the reaction mechanism. In particular, the TS SOC approach allows to straightforwardly explore detailed features of the adiabatic potential energy surface which in principle could affect the overall reaction rate in cases where the involved diabatic PESs are tricky.

Anatomy of On-Surface Synthesized Boroxine Two-Dimensional Polymers

Synthetic two-dimensional polymers (2DPs) obtained from well-defined monomers via bottom-up fabrication strategies are promising materials that can extend the realm of inorganic 2D materials. The on-surface synthesis of such 2DPs is particularly popular, however the pathway complexity in the growth of such films formed on solid surfaces is poorly understood. In this contribution, we present a straightforward experimental protocol which allows the synthesis of large-area, defect-free 2DPs based on boroxine linkages at room temperature. We focus on unravelling the multiple pathways available to the polymerizing system for the spatial extension of the covalent bonds. Besides the anticipated 2DP, the system can evolve into self-assembled monolayers of partially fused monodisperse reaction products that are difficult to isolate by conventional synthetic methods or remain in the monomeric state. The access to each pathway can be controlled via monomer concentration and the choice of the solvent. Most importantly, the unpolymerized systems do not evolve into the corresponding 2DP upon annealing, indicating the presence of strong kinetic traps. Using high-resolution scanning tunneling microscopy, we show reversibility in the polymerization process where the attachment and the detachment of monomers to 2DP crystallites could be monitored as a function of time. Finally, we show that the way the 2DP grows depends on the choice of the solvent. Using UV-vis absorption and emission spectroscopy, we reveal that the dominant pathway for 2DP growth is via in-plane self-condensation of the monomers, whereas in the case of an aprotic solvent, the favored growth mode is via π stacking of the monomers.

Iron-Catalyzed Reductive Coupling of Alkyl Iodides with Alkynes To Yield cis-Olefins: Mechanistic Insights from Computation

In a recent study, a new procedure for Z-selective olefin synthesis by reductive coupling of alkyl iodides with terminal alkynes in the presence of iron salts is described. This transformation is representative of many newly developed synthetic routes through the involvement of multiple species and phases, which makes mechanistic insight hard to obtain. Here, we report computational work aimed at exploring the possible reaction pathways. DFT calculations lead to two suggested routes, one involving C-I reduction by metallic zinc and radical addition to the alkyne and the other involving addition of two reduced iron species to the alkyne bond followed by reductive elimination. Comparison to experimental results as well as kinetic modeling is used to discuss the likelihood of these and related mechanisms.

Energetics of non-heme iron reactivity: can ab initio calculations provide the right answer?

We use a variety of computational methods to characterize and compare the hydrogen atom transfer (HAT) and epoxidation reaction pathways for oxidation of cyclohexene by an iron(iv)-oxo complex.

Understanding the Reactivity of Mn-Oxo Porphyrins for Substrate Hydroxylation: Theoretical Predictions and Experimental Evidence Reconciled

The Mn-oxo porphyrin (MnOP) mechanism for substrate hydroxylation is computationally studied with the aim to better understand reactivity in these systems. Theoretical studies suggest Mn(V)OP species to be very reactive intermediates with thermally accessible reaction barriers represented by low-spin/high-spin-crossover occurring in the Mn(V)OP oxidant, and kinetics for selected Mn(V)OP species indeed find high reactivity. On the other hand, MnOP complexes lead to modest yields in hydroxylation reactions of several different substrates, implying low rate constants and high reaction barriers. The resolution of this inconsistency is very important to understand the reactivity of Mn-oxo porphyrins and to improve the catalytic conditions. In this work we use the toluene hydroxylation by the Mn(V)OP(H₂O)⁺ complex as a case study to gain deep insight into the reaction mechanism. Minimum energy crossing point (MECP) results on the H-abstraction process from toluene indicate a first crossover from a singlet to a triplet spin state of the Mn(V)OP(H₂O)⁺ species with a thermally accessible barrier, followed by a very facile H-abstraction by the triplet complex. Issues concerning (i) the validation of the level of the density functional theory employed (BP86) to describe the singlet-triplet energy gap in the Mn(V)OP(H₂O)⁺ system versus highly accurate DMRG-CASPT2/CC calculations, and (ii) the influence of the axial ligand (X = none, Cl^-, CH₃CN, OH^-, and O^2-) on MnOP reactivity, which models the different experimental conditions, are addressed. The ligand trans influence mainly controls the reactivity through the singlet-triplet energy gap modulation, with the porphyrin ruffling distortion also finely tuning it. Finally, a stepwise model for the H-abstraction process is proposed which allows a direct comparison between the calculated and experimentally measured Gibbs free activation energy barriers ( Zhang et al. J. Am. Chem. Soc. 2005 , 127 , 6573 - 6582 ). The low yields in catalysis are shown not to be due to low reactivity of Mn(V).

Halogenated building blocks for 2D crystal engineering on solid surfaces: lessons from hydrogen bonding

Halogen bonding has emerged as a promising tool in two-dimensional (2D) crystal engineering. Since halogen bonds are similar to hydrogen bonds in a number of aspects, the existing knowledge of hydrogen bonded systems can be applied to halogenated systems. Here we evaluate the applicability of a retrosynthetic approach based on topological similarity between hydrogen and halogen bonds to obtain predictable halogen bonded networks. The self-assembly of 1,3-dibromo-5-alkoxybenzene derivatives was studied in analogy with well-explored alkoxy isophthalic acids using a combination of experimental and theoretical tools. Scanning tunneling microscopy (STM) characterization of the networks formed at the liquid-graphite interface revealed that while the retrosynthetic approach works at the level of small clusters of molecules within the 2D network, the overall structure of the network deviates from the anticipated structure. The monolayers consist of fractured rows of halogen-bonded modules instead of the expected continuous lamellar structure. Each module consists of a discrete number of halogen-bonded molecules. The interactions responsible for the stabilization of halogen bonded dimers are delineated through detailed density functional theory (DFT) calculations coupled with natural bonding orbitals (NBO) and perturbation analysis. A modified force field that includes an extra charged site to imitate the σ hole on the halogen atom was developed and applied to extract total potential energies of the anticipated and observed networks. Plausible reasons for the deviation from the anticipated structure are discussed. Finally, a modified molecular design that allows successful application of the hydrogen bond-halogen bond analogy was tested experimentally.

Limits of Coupled-Cluster Calculations for Non-Heme Iron Complexes

In a large variety of studies, the coupled-cluster method with singles, doubles, and perturbative triples (CCSD(T)) is used as a reference for benchmarking the performance of density functional theory (DFT) functionals. In the case of open-shell species, this theory can be applied in different forms depending on the restricted or unrestricted treatment of spin. In this study, we show that these different approaches can produce results which deviate by ∼5 kcal/mol for different species on the potential energy surfaces. This was demonstrated for a simple model of the C-H activation carried out by non-heme iron enzymes. Assessing the limits of CCSD(T) prior to its use as a general benchmark tool is warranted. This was done using higher-order coupled-cluster calculations as well as multiconfigurational second-order perturbation theory (CASPT2), since iron-oxo species present some multireference character. Furthermore, we tested two different implementations of the local coupled-cluster method and compared them to the CCSD(T) results, showing that even though these novel approaches are promising, without further developments they appear not to be suitable for describing two-state reactivity of the system investigated in the current study. Additionally, we implemented and assessed the performance of the hotspot approach for the local unrestricted CCSD(T) scheme which aims at reducing the pair error for systems containing transition metals.

Suzuki–Miyaura coupling revisited: an integrated computational study

Computation is used to revisit the mechanism of the Suzuki–Miyaura coupling mechanism.

EVB and polarizable MM study of energy relaxation in fluorine–acetonitrile reactions

Many-body effects can impact on rates of energy transfer from a ‘hot’ DF solute to acetonitrile solvent.

The effect of coordination of alkanes, Xe and CO2 (η1-OCO) on changes in spin state and reactivity in organometallic chemistry: a combined experimental and theoretical study of the photochemistry of CpMn(CO)3

A combined experimental and theoretical study is presented of several ligand addition reactions of the triplet fragment 3CpMn(CO)2 formed upon photolysis of CpMn(CO)3. Experimental data are provided for reactions in n-heptane and perfluoromethylcyclohexane (PFMCH), as well as in PFMCH doped with C2H6, Xe and CO2. In PFMCH we find that the conversion of 3CpMn(CO)2 to 1CpMn(CO)2(PFMCH) is much slower (τ = 18 (±3) ns) than the corresponding reactions in conventional alkanes (τ = 111 (±10) ps). We measure the effect of the coordination ability by doping PFMCH with alkane, Xe and CO2; these doped ligands form the corresponding singlet adducts with significantly variable formation rates. The reactivity as measured by the addition timescale follows the order 1CpMn(CO)2(C5H10) (τ = 270 (±10) ps) > 1CpMn(CO)2Xe (τ = 3.9 (±0.4) ns) ∼ 1CpMn(CO)2(CO2) (τ = 4.7 (±0.5) ns) > 1CpMn(CO)2(C7F14) (τ = 18 (±3) ns). Electronic structure theory calculations of the singlet and triplet potential energy surfaces and of their intersections, together with non-adiabatic statistical rate theory, reproduce the observed rates semi-quantitatively. It is shown that triplet adducts of the ligand and 3CpMn(CO)2 play a role in the kinetics, and account for the variable timescales observed experimentally.

Computational Modelling of Selectivity in Cobalt-Catalyzed Propene Hydroformylation

A mechanistic model for the cobalt-catalyzed hydroformylation of propene, based on density functional theory and coupled cluster electronic structure calculations and transition state theory, is proposed to explain the experimentally observed reactivity and selectivity. The electronic structure calculations provide very accurate energies, which are used with transition state theory to compute rate constants; the kinetics of the network of coupled reactions are then modelled numerically for this organometallic reaction. The model accounts well for the dependence of rate on the concentrations of catalysts and reagents, and also on the temperature, and the agreement with experiment is improved still further upon making small adjustments to the ab initio calculated free energy values. The calculations provide detailed kinetic insight into the mechanism of hydroformylation and the role of various elementary steps in defining reactivity and selectivity.

Mixed Explicit-Implicit Solvation Approach for Modeling of Alkane Complexation in Water-Soluble Self-Assembled Capsules

The host-guest binding properties of a water-soluble resorcinarene-based cavitand are examined using density functional theory methodology. Experimentally, the cavitand has been observed to self-assemble in aqueous solution into both 1:1 and 2:1 host/guest complexes with hydrophobic guests such as n-alkanes. For n-decane, equilibrium was observed between the 1:1 and 2:1 complexes, while 1:1 complexes are formed with shorter n-alkanes and 2:1 complexes are formed with longer ones. These findings are used to assess the standard quantum chemical methodology. It is first shown that a rather advanced computational protocol (B3LYP-D3(BJ)/6-311+G(2d,2p) with COSMO-RS and quasi-rigid-rotor-harmonic-oscillator) gives very large errors. Systematic examination of the various elements of the methodology shows that the error stems from the implicit solvation model. A mixed explicit-implicit solvation protocol is developed that involves a parametrization of the hydration free energy of water such that water cluster formation in water is predicted to be thermoneutral. This new approach is demonstrated to lead to a major improvement in the calculated binding free energies of n-alkanes, reproducing very well the 1:1 versus 2:1 host/guest binding trends.

Toward Highly Accurate Spin State Energetics in First-Row Transition Metal Complexes: A Combined CASPT2/CC Approach

In previous work on the performance of multiconfigurational second-order perturbation theory (CASPT2) in describing spin state energetics in first-row transition metal systems [ Pierloot et al. J. Chem. Theory Comput. 2017 , 13 , 537 - 553 ], we showed that standard CASPT2 works well for valence correlation but does not describe the metal semicore (3s3p) correlation effects accurately. This failure is partially responsible for the well-known bias toward high-spin states of CASPT2. In this paper, we expand our previous work and show that this bias could be partly removed with a combined CASPT2/CC approach: using high-quality CASPT2 with extensive correlation-consistent basis sets for valence correlation and low-cost CCSD(T) calculations with minimal basis sets for the metal semicore (3s3p) correlation effects. We demonstrate that this approach is efficient by studying the spin state energetics of a series of iron complexes modeling important intermediates in oxidative catalytic processes in chemistry and biochemistry. On the basis of a comparison with bare CCSD(T) results from this and previous work, the average error of the CASPT2/CC approach is estimated at around 2 kcal mol^-1 in favor of high spin states.

First Principles Calculation of the Reaction Rates for Ligand Binding to Myoglobin: The Cases of NO and CO

Ligand binding by proteins is among the most fundamental processes in nature. Among these processes the binding of small gas molecules, such as O₂ , CO and NO to heme proteins has traditionally received vivid interest, which was further boosted by their recently recognized significant role in gas sensing in the body. At the heart of the binding of these ligands to the heme group is the spinforbidden reaction between high-spin iron(II) and the ligand yielding a low-spin adduct. We use computational means to address the complete mechanism of CO and NO binding by myoglobin. Considering that it involves several steps occurring on different time scales, molecular dynamics simulations were performed to address the diffusion of the ligand through the enzyme, and DFT calculations in combination with statistical rate calculation to investigate the spin-forbidden reaction. The calculations yielded rate constants in qualitative agreement with experiments and revealed that the bottleneck of NO and CO binding is different; for NO, diffusion was found to be rate-limiting, whereas for CO, the spin-forbidden step is the slowest.

Mechanism and reactivity in the Morita-Baylis-Hillman reaction: the challenge of accurate computations

A systematic density functional theory exploration of various reactive steps together with benchmark coupled cluster results are used to propose an accurate model of the mechanism of the Morita-Baylis-Hillman (MBH) reaction in organic chemistry. This reaction has attracted considerable interest from the synthetic and mechanistic points of view in recent years, with both computational and experimental mechanistic studies. It has recently (R. E. Plata and D. A. Singleton, J. Am. Chem. Soc., 2015, 137, 3811-3826) been correctly pointed out that previous computational studies failed to reproduce known mechanistic features of the reaction. The same study argued that computation is simply not able at the present time to provide accurate models for such reactions. This second claim is shown by our present work to overstate the problem: by using current 'state of the art' methodology, our results are fully consistent with observed behavior within the expected error bars of 1-5 kcal mol^-1, far smaller than the errors reported in Plata and Singleton's study. On the basis of exhaustive calculations reported here, we suggest that our proposed approaches for modeling electronic structure, solvation, and entropy should be able to provide accurate predictions for many more reactions. We also suggest that reactions like the MBH reaction, where solvation and entropy effects are particularly large, are among the hardest for computational mechanistic studies.

QM/MM methods for free energies and photochemistry

Hybrid computational methods describing a small region of a biomolecular system with quantum mechanics and the bulk with molecular mechanics, referred to as QM/MM methods, are now a central part of computational biochemistry. This review considers developments in the QM/MM approach that make it easier to calculate free energies using accurate QM-based potential energy expressions. We also describe techniques to treat electronic coupling between the core region and the MM environment. Polarizability of the protein matrix is important but so is electronic coupling. Applications of these new methods, especially to photochemistry, are discussed.

Computational insight into the origin of unexpected contrast in chiral markers as revealed by STM

Internal substituents can serve the double purpose of generating stereogenic centers and (potentially) being identifiable with Scanning Tunneling Microscopy (STM) in 2D self-assembled molecular layers. We investigate computationally the origin of stark contrast variations in STM images of chirally substituted self-assembled organic films. STM images of alkyl derivatives with secondary -CH₃ and -OH groups have been simulated. Density functional theory calculations reveal bias-dependent contrast reversals in the substituent regions: a lack of local density of states in the relevant energy regime results in 'dark spots' in the simulated STM images, which turn bright upon increasing the bias voltage.

Modelling absorption and emission of a meso-aniline–BODIPY based dye with molecular mechanics

Absorption and emission spectra of 8-(4-dimethylaminophenyl)-1,3,5,7-tetramethyl–BODIPY have been calculated using Coupled Cluster (CC) approaches, Time-Dependent Density Functional Theory (TD-DFT) and a QM-informed MM approach.