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In this chapter we present an overview of what is known today about the reactivity of Ca2+ with different species, both from the theoretical and the experimental points of view. We have paid particular attention to the bonding characteristics of Ca2+ complexes and to the electron density re-distribution undergone by the neutral interacting with this doubly charged metal, due to the quite intense electric...
We present a review of our recent developments in computational modeling of hydrogen-bonding-induced phenomena in a series of biologically relevant bifunctional proton donor–acceptor heteroazaaromatic compounds. Different types of hydrogen-bonded solvates, in which water or alcohol molecules form a bridge connecting the proton donor (pyrrole NH group) and the acceptor (pyridine or quinoline nitrogen)...
Dynamics simulations are an essential step in exploring ultrafast phenomena in photochemistry and photobiology. In this chapter we present results of photodynamics studies for some model compounds for the peptide bond using the on-the-fly surface hopping method. The mechanism of photodissociation of formamide, its protonated forms and methyl substituted derivatives in their lowest singlet excited...
The current decade being a golden era in the history of organocatalysis, designing new organocatalysts for synthetically valuable reactions is of high importance. A fine blend of theoretical techniques and knowledge gathered from the experimental observations can help one design highly selective organocatalysts. The present chapter summarizes our efforts in designing organocatalysts for two synthetically...
Describing chemical reactions is one of the most challenging aspects of current computational approaches to chemistry. In this chapter established (EVB, ReaxFF) and novel (MMPT, ARMD) approaches are discussed that allow to study bond forming and bond breaking processes in a variety of chemical and biological environments. Particular emphasis is put on methods that enable investigating the dynamics...
In this review, the applicability of computational chemistry procedures for modelling of macromolecules and large macromolecular systems is shortly reviewed. In particular, the recent achievements in studying the reactions leading to polymers by quantum chemical and molecular mechanical methods are presented.
The kinetics of chemical reactions characterizes the rates of chemical processes, i.e. distribution of all reactants, intermediates and products over time. This information is of vital importance for all areas of chemistry: chemical technology to control organic or inorganic syntheses, chemical construction of nanomaterials, as well as for the investigation of biochemical processes. The chemical kinetics...
The phenomenon of charge migration in DNA has attracted considerable interest of experimental as well as computational research in the last decade. It poses a huge challenge for simulation, due to the large system size and the long relevant time scales. Simple modeling frameworks may miss or overapproximate several important factors influencing the charge transfer in DNA, most prominently the dynamical...
Computational studies of biological macromolecules are challenging due to large size of biomolecules, their conformational flexibility, and the need in explicit water solvation in order to simulate conditions close to experiment. Under these circumstances studying molecular systems via quantum-mechanical calculations becomes exceedingly difficult. Natural is the attempt to reduce the complex quantum-mechanical...
The role transition structures (TSs) and vectors have played in discussing issues associated to enzyme catalysis is examined with focus on RubisCO; computations belong to standard semi-classic Born-Oppenheimer model with one-electron orbitals located at nuclear position coordinates. Here, theory is brought a step beyond starting from exact quantum schemes to get types of semi-classic Hamiltonians...
The application of molecular dynamics (MD) simulations is now firmly established as a strategy to help understanding the activity of biological systems, being routinely applied to investigate the structure, dynamics and thermodynamics of biological molecules and their complexes. Commonly available biomolecular force fields like AMBER, CHARMM, OPLS, and GROMOS contain sets of molecular mechanical parameters...
Combined quantum mechanical/molecular mechanical (QM/MM) models have been established as efficient approaches to simulate chemical reactions in complex molecular systems including enzymes. The QM/MM Hamiltonian is defined based on partitioning a molecular system into a reactive center and its surrounding, namely, the QM and MM regions. How to properly treat the QM/MM interface, which involves both...
Lactate dehydrogenases, LDH, catalyzed reaction has been used in this chapter as a conductor wire to present the evolution and difficulties on computing methods to model chemical reactions in enzymes, since the early calculations based at semiempirical level carried out in gas phase to the recent sophisticated simulations based on hybrid Quantum Mechanical/Molecular Mechanics Dynamics (QM/MM MD) schemes...
Molecular modelling and simulation are making increasingly important contributions to the study of the structure and function of biological macromolecules. An area of particular current interest and debate is that of enzyme catalysis, and the role of protein dynamics in enzyme-catalysed reactions. Simulations allow enzyme catalytic mechanisms and protein dynamics to be investigated at the atomic level...
Computational approaches at various levels have been used to elucidate the mechanism of the ammonium/ammonia transport process through the Escherichia coli AmtB membrane protein. Molecular dynamics (MD) simulations at the classical molecular mechanical (MM) level confirmed that only NH3 can transport through the highly hydrophobic AmtB channel. Thus, NH4+, which is predominant in solution,...
Many computational methods have become standard techniques in modern drug discovery. However, approaches which employ explicit molecular dynamics simulations still are restricted to special applications, as their extensive computational requirements make it difficult to obtain results within the necessary time scale of industrial drug development projects. Moreover, a high expertise is needed to analyze...
A model is presented which relates kinetic isotope effects and their temperature dependence to physical parameters governing enzymatic carbon–hydrogen cleavage, a reaction that typically exhibits a large isotope effect indicative of tunneling. The model aims to replace the Arrhenius equation, which is not valid for tunneling reactions, and the one-dimensional Bell model, which excludes skeletal vibrations...
The accurate evaluation of quantum effects is of great importance in many reaction processes. Variational transition state theory with multidimensional tunneling is the natural choice for the study of these reactions, because it incorporates quantum effects through a multiplicative transmission coefficient and it can deal with large systems. Currently, the main approximation used for taking into account...
We review the role of dynamics in enzyme catalysed H-tunnelling reactions with particular focus on the integration of computational methods with experimental and numerical modelling studies. We show that H-tunnelling requires compressive motion along the H-transfer coordinate and these reactions can be modelled successfully using vibrationally-coupled H-tunnelling models in which barrier compression...
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