Massimiliano Aschi

A first-principles method to model perturbed electronic wavefunctions : the effect of an external homogeneous electric field

In this Letter, we show that with the use of matrix notation to express the time-independent Schroedinger equation, it is possible to model perturbed electronic wavefunctions. Such a method makes use of first principles of the quantum mechanical theory and hence is rigorous within the only approximation due to the truncation of the perturbed Hamiltonian matrix used. Results show that for three different molecules in vacuo under an electric field, the proposed method provides reliable perturbed electronic wavefunctions at a low computational costs.

Crystal Structure of the Peroxisome Proliferator-Activated Receptor γ (PPARγ) Ligand Binding Domain Complexed with a Novel Partial Agonist: A New Region of the Hydrophobic Pocket Could Be Exploited for Drug Design

The peroxisome proliferator-activated receptors (PPARs) are ligand-dependent transcription factors regulating glucose and lipid metabolism. The search for new PPAR ligands with reduced adverse effects with respect to the marketed antidiabetic agents thiazolidinediones (TZDs) and the dual-agonists glitazars is highly desired. We report the crystal structure and activity of the two enantiomeric forms of a clofibric acid analogue, respectively complexed with the ligand-binding domain (LBD) of PPARgamma, and provide an explanation on a molecular basis for their different potency and efficacy against PPARgamma. The more potent S-enantiomer is a dual PPARalpha/PPARgamma agonist which presents a partial agonism profile against PPARgamma. Docking of the S-enantiomer in the PPARalpha-LBD has been performed to explain its different subtype pharmacological profile. The hypothesis that partial agonists show differential stabilization of helix 3, when compared to full agonists, is also discussed. Moreover, the structure of the complex with the S-enantiomer reveals a new region of the PPARgamma-LBD never sampled before by other ligands.

Experimental and computational study of neutral xenon halides (XeX) in the gas phase for X=F, Cl, Br, and I

We report a combined experimental and theoretical study of the xenon monohalide radicals XeX• (X=F, Cl, Br, and I) together with their cationic and anionic counterparts XeX+ and XeX−. In brief, the XeX+ cations are characterized by reasonably strong chemical bonds with significant charge-transfer stabilization, except for X=F. In contrast, the neutral XeX• radicals as well as the XeX− anions can mostly be described in terms of van der Waals complexes and exhibit bond strengths of only a few tenths of an electron volt. For both XeX• and XeX− the fluorides (X=F) are the most strongly bound among the xenon halides due to significant covalency in the neutral radical, and to the large charge density on fluoride in the XeX− anion, respectively. Mass spectrometric experiments reveal the different behavior of xenon fluoride as compared to the other halides, and in kiloelectron-volt collisions sequential electron transfer according to XeX+→XeX•→XeX− can be achieved allowing one to generate neutral XeX• radicals wi...

A Gas‐Phase Model for the Pt+‐Catalyzed Coupling of Methane and Ammonia

What exactly are the elementary steps in the Pt-catalyzed coupling of methane and ammonia (Degussa process) shown on the right? Mass spectrometry and ab initio theory have been used to probe the mechanistic details of this technically important synthesis of hydrogen cyanide.

Theoretical characterization of electronic states in interacting chemical systems

In this article we characterize, by means of the perturbed matrix method, the response of the electronic states of a chemical system to the perturbing environment. In the theory section we describe in detail the basic derivations and implications of the method, extending its theoretical framework to treat possible excitonic effects, and we show how to characterize the perturbed electronic states. Finally, by using a set of chemical systems interacting with complex atomic-molecular environments, we describe the nature and general features of the electronic state mixing and transitions as caused by atomic and molecular interactions.

Extension of the perturbed matrix method: application to a water molecule

In this Letter we extend the perturbed matrix method by explicitly including the nuclear degrees of freedom and showing how to treat a non-homogeneous electric field. In a previous Letter we showed that this method provides reliable perturbed energies. In the present Letter we evaluate a more sophisticated property such as molecular polarizability for a water molecule.

The Reversible Opening of Water Channels in Cytochrome c Modulates the Heme Iron Reduction Potential

Dynamic protein-solvent interactions are fundamental for life processes, but their investigation is still experimentally very demanding. Molecular dynamics simulations up to hundreds of nanoseconds can bring to light unexpected events even for extensively studied biomolecules. This paper reports a combined computational/experimental approach that reveals the reversible opening of two distinct fluctuating cavities in Saccharomyces cerevisiae iso-1-cytochrome c. Both channels allow water access to the heme center. By means of a mixed quantum mechanics/molecular dynamics (QM/MD) theoretical approach, the perturbed matrix method (PMM), that allows to reach long simulation times, changes in the reduction potential of the heme Fe(3+)/Fe(2+) couple induced by the opening of each cavity are calculated. Shifts of the reduction potential upon changes in the hydration of the heme propionates are observed. These variations are relatively small but significant and could therefore represent a tool developed by cytochrome c for the solvent driven, fine-tuning of its redox functionality.

Theoretical modeling of vibroelectronic quantum states in complex molecular systems: Solvated carbon monoxide, a test case

In this paper we extend the perturbed matrix method by explicitly including the nuclear degrees of freedom, in order to treat quantum vibrational states in a perturbed molecule. In a previous paper we showed how to include, in a simple way, nuclear degrees of freedom for the calculation of molecular polarizability. In the present work we extend and generalize this approach to model vibroelectronic transitions, requiring a more sophisticated treatment.

Conformational fluctuations and electronic properties in myoglobin

In this article we use the recently developed perturbed matrix method (PMM) to investigate the effect of conformational fluctuations on the electronic properties of heme in Myoglobin. This widely studied biomolecule has been chosen as a benchmark for evaluating the accuracy of PMM in a large and complex system. Using a long, 80‐ns, molecular dynamics simulation and unperturbed Configuration Interaction (CISD) calculations in PMM, we reproduced the main spectroscopic features of deoxy‐Myoglobin. Moreover, in line with our previous results on a photosensitive protein, this study reveals a clear dynamical coupling between electronic properties and conformational fluctuations, suggesting that this correlation could be a general feature of proteins.

Mixed Quantum-Classical Methods for Molecular Simulations of Biochemical Reactions With Microwave Fields: The Case Study of Myoglobin

Contradictory data in the huge literature on microwaves bio-effects may result from a poor understanding of the mechanisms of interaction between microwaves and biological systems. Molecular simulations of biochemical processes seem to be a promising tool to comprehend microwave induced bio-effects. Molecular simulations of classical and quantum events involved in relevant biochemical processes enable to follow the dynamic evolution of a biochemical reaction in the presence of microwave fields. In this paper, the action of a microwave signal (1 GHz) on the covalent binding process of a ligand (carbon monoxide) to a protein (myoglobin) has been studied. Our results indicate that microwave fields, with intensities much below the atomic/molecular electric interactions, cannot affect such biochemical process.