On the Nature of the Bonding in Coinage Metal Halides

This article analyzes the nature of the chemical bond in coinage metal halides using high-level ab initio Valence Bond (VB) theory. It is shown that these bonds display a large Charge-Shift Bonding character, which is traced back to the large Pauli pressure arising from the interaction between the bond pair with the filled semicore d shell of the metal. The gold-halide bonds turn out to be pure Charge-Shift Bonds (CSBs), while the copper halides are polar-covalent bonds and silver halides borderline cases. Among the different halogens, the largest CSB character is found for fluorine, which experiences the largest Pauli pressure from its σ lone pair. Additionally, all these bonds display a secondary but non-negligible π bonding character, which is also quantified in the VB calculations.

Theory of quasi-exact fault-tolerant quantum computing and valence-bond-solid codes

In this work, we develop the theory of quasi-exact fault-tolerant quantum (QEQ) computation, which uses qubits encoded into quasi-exact quantum error-correction codes (``quasi codes''). By definition, a quasi code is a parametric approximate code that can become exact by tuning its parameters. The model of QEQ computation lies in between the two well-known ones: the usual noisy quantum computation without error correction and the usual fault-tolerant quantum computation, but closer to the later. Many notions of exact quantum codes need to be adjusted for the quasi setting. Here we develop quasi error-correction theory using quantum instrument, the notions of quasi universality, quasi code distances, and quasi thresholds, etc. We find a wide class of quasi codes which are called valence-bond-solid codes, and we use them as concrete examples to demonstrate QEQ computation.

Extraction of a One-Particle Reduced Density Matrix from a Quantum Monte Carlo Electronic Density: A New Tool for Studying Nondynamic Correlation

In this work, we present a method to build a first order reduced density matrix (1-RDM) of a molecule from variational Quantum Monte Carlo (VMC) computations by means of a given correlated mapping wave function. Such a wave function is modeled on a Generalized Valence Bond plus Complete Active Space Self Configuration Interaction form and fits at best the density resulting from the Slater-Jastrow wave function of VMC. The accuracy of the method proposed has been proved by comparing the resulting kinetic energy with the corresponding VMC value. This 1-RDM is used to analyze the amount of correlation eventually captured in Kohn-Sham calculations performed in an unrestricted approach (UKS-DFT) and with different energy functionals. We performed test calculations on a selected set of molecules that show a significant multireference character. In this analysis, we compared both local and global indicators of nondynamic and dynamic correlation. Moreover, following the natural orbital decomposition of the 1-RDM, we also compared the effective temperatures of the corresponding Fermi-like distributions. Although there is a general agreement between UKS-DFT and VMC, we found the best match with the functional LC-BLYP.

The Essential Functional Interplay of the Catalytic Groups in Acid Phosphatase

Cooperative interplay between the functional devices of a preorganized active site is fundamental to enzyme catalysis. A deepened understanding of this phenomenon is central to elucidating the remarkable efficiency of natural enzymes, and provides an essential benchmark for enzyme design and engineering. Here, we study the functional interconnectedness of the catalytic nucleophile (His18) in an acid phosphatase by analyzing the consequences of its replacement with aspartate. We present crystallographic, biochemical and computational evidence for a conserved mechanistic pathway via a phospho-enzyme intermediate on Asp18. Linear free-energy relationships for phosphoryl transfer from phosphomonoester substrates to His18/Asp18 provide evidence for cooperative interplay between the nucleophilic and general-acid catalytic groups in the wildtype enzyme, and its substantial loss in the H18D variant. As an isolated factor of phosphatase efficiency, the advantage of a histidine compared to an aspartate nucleophile is around 10^4-fold. Cooperativity with the catalytic acid adds ≥10^2-fold to that advantage. Empirical valence bond simulations of phosphoryl transfer from glucose 1-phosphate to His and Asp in the enzyme explain the loss of activity of the Asp18 enzyme through a combination of impaired substrate positioning in the Michaelis complex, as well as a shift from early to late protonation of the leaving group in the H18D variant. The evidence presented furthermore suggests that the cooperative nature of catalysis distinguishes the enzymatic reaction from the corresponding reaction in solution and is enabled by the electrostatic preorganization of the active site. Our results reveal sophisticated discrimination in multifunctional catalysis of a highly proficient phosphatase active site.

ThermoSlope: A Software for Determining Thermodynamic Parameters from Single Steady-State Experiments

The determination of the temperature dependence of enzyme catalysis has traditionally been a labourious undertaking. We have developed a new approach to the classical Arrhenius parameter estimation by fitting the change in velocity under a gradual change in temperature. The evaluation with a simulated dataset shows that the approach is valid. The approach is demonstrated as a useful tool by characterizing the Bacillus pumilus LipA enzyme. Our results for the lipase show that the enzyme is psychrotolerant, with an activation energy of 15.3 kcal/mol for the chromogenic substrate para-nitrophenyl butyrate. Our results demonstrate that this can produce equivalent curves to the traditional approach while requiring significantly less sample, labour and time. Our method is further validated by characterizing three α-amylases from different species and habitats. The experiments with the α-amylases show that the approach works over a wide range of temperatures and clearly differentiates between psychrophilic, mesophilic and thermophilic enzymes. The methodology is released as an open-source implementation in Python, available online or used locally. This method of determining the activation parameters can make studies of the temperature dependence of enzyme catalysis more widely adapted to understand how enzymes have evolved to function in extreme environments. Moreover, the thermodynamic parameters that are estimated serve as functional validations of the empirical valence bond calculations of enzyme catalysis.

Catalytic mechanism of the mitochondrial methylenetetrahydrofolate dehydrogenase/cyclohydrolase (MTHFD2)

Methylenetetrahydrofolate dehydrogenase/cyclohydrolase (MTHFD2) is a new drug target that is expressed in cancer cells but not in normal adult cells, which provides an Achilles heel to selectively kill cancer cells. Despite the availability of crystal structures of MTHFD2 in the inhibitor- and cofactor-bound forms, key information is missing due to technical limitations, including (a) the location of absolutely required Mg2+ ion, and (b) the substrate-bound form of MTHFD2. Using homology modeling and simulation studies, we propose that two magnesium ions are present at the active site whereby (i) Arg233, Asp225, and two water molecules coordinate MgA, while MgA together with Arg233 stabilize the inorganic phosphate (Pi); (ii) Asp168 and three water molecules coordinate MgB, and MgB further stabilizes Pi by forming a hydrogen bond with two oxygens of Pi; (iii) Arg201 directly coordinates the Pi; and (iv) through three water-mediated interactions, Asp168 contributes to the positioning and stabilization of MgA, MgB and Pi. Our computational study at the empirical valence bond level allowed us to elucidate the detailed reaction mechanisms. We found that the dehydrogenase activity features a proton-coupled electron transfer with charge redistribution coupled to the reorganization of the surrounding water molecules which further facilitates the subsequent cyclohydrolase activity. The cyclohydrolase activity then drives the hydration of the imidazoline ring and the ring opening in a concerted way. Furthermore, we have uncovered that two key residues Ser197/Arg233 are key factors in determining the cofactor (NADP+/NAD+) preference of the dehydrogenase activity. Our work sheds new light on the structural and kinetic framework of MTHFD2, which will be helpful to design small molecule inhibitors that can be used for cancer therapy.

Chemical Bonding 2: Modern Theories of Chemical Bonding

Chemical Bonding II: Modern Theories of Chemical Bonding explains four bonding theories related to molecular geometry and bonding. Lewis structures and the Valence-Shell Electron-Pair Repulsion (VSEPR) model are used to describe and predict the electron group geometry, molecular geometry and shapes of molecules. The VSEPR model is then used to predict molecular polarity as a function of shape. This leads to Valence Bond Theory, which uses the principles of orbital overlap and hybridization of atomic orbitals to describe chemical bonding. Finally the Molecular Orbital Theory (MOT) based on electron delocalization is discussed in terms of bonding and anti-bonding molecular orbitals.