Ab initio computational study of positron emission tomography ligands interacting with lipid molecule for the prediction of nonspecific binding

Nonspecific binding is a poorly understood biological phenomenon of relevance in the study of small molecules interactions in vivo and in drug development. Nonspecific binding is thought to be correlated in part to a molecule's lipophilicity, typically estimated by measuring (or calculating) octanol-water partition coefficient. This is, however, a gross simplification of a complex phenomenon. In this article, we present a computational method whose aim is to help identify positron emission tomography (PET) ligands with low nonspecific binding characteristics by investigating the molecular basis of ligand-membrane interaction. We considered a set consisting of 10 well-studied central nervous system PET radiotracers acting on a variety of molecular targets. Quantum mechanical calculations were used to estimate the strength of the interaction between each drug molecule and one phospholipid molecule commonly present in mammalian membranes. The results indicate a correlation between the computed drug-lipid interaction energy and the in vivo nonspecific distribution volume relative to the free tracer plasma concentration, calculated using standard compartmental modeling for the analysis of PET data. Significantly, the drugs whose interaction with the lipid molecule more favorably possessed, in general, a higher nonspecific binding value, whereas for the drugs taken in consideration in this study, the water-octanol partition coefficient, log P, did not show good predictive power of the nonspecific binding. This study also illustrates how ab initio chemical methods may offer meaningful and unbiased insights for the understanding of the underlying chemical mechanisms in biological systems.     

The effect of pH on the photophysics and photochemistry of disulphonated aluminum phthalocyanine

The results of a study of the effect of pH on the photophysics and photochemistry of di-sulphonated aluminum phthalocyanine (AlPcS₂) in aqueous solution are presented. The pH dependence of the triplet quantum yield, fluorescence quantum yield, singlet-oxygen quantum yield, triplet lifetime, fluorescence lifetime and apparent dimerization constants is investigated and the results interpreted in terms of the pH dependence of the nature of the axial ligands. Evidence that the aluminum–axial ligand bond strength, rather than dimer binding energy that determines the extent of dimerization is provided by semi-empirical and ab initio calculations. Possible dimer structures obtained using ab initio calculations are discussed.     

Quantum mechanical map for protein-ligand binding with application to beta-trypsin/benzamidine complex

We report full ab initio Hartree-Fock calculation to compute quantum mechanical interaction energies for beta-trypsin/benzamidine binding complex. In this study, the full quantum mechanical ab initio energy calculation for the entire protein complex with 3238 atoms is made possible by using a recently developed MFCC (molecular fractionation with conjugate caps) approach in which the protein molecule is decomposed into amino acid-based fragments that are properly capped. The present MFCC ab initio calculation enables us to obtain an "interaction spectrum" that provides detailed quantitative information on protein-ligand binding at the amino acid levels. These detailed information on individual residue-ligand interaction gives a quantitative molecular insight into our understanding of protein-ligand binding and provides a guidance to rational design of potential inhibitors of protein targets.     

Determination of the absolute configuration of 1,3,5,7-tetramethyl-1,3-dihydroindol-2-one by optical rotation computation

The absolute configuration of 1,3,5,7-tetramethyl-1,3-dihydroindol-2-one was determined by quantum chemical calculations of specific rotation angles with coupled–perturbed Hartree–Fock methods. The computation used molecular geometries obtained from ab initio calculations as well as from molecular mechanics and semi-empirical optimization. In addition to the dependence on geometry optimization strategies, the basis set dependence of the computed rotation angle was examined.     

A combination of pseudopotentials and density functionals: Results for Cun, Cun, Agn, and Agn clusters (n ≤ 4)

Structures and binding energies have been calculated for neutral and singly ionized Cu and Ag clusters with up to four atoms. The valence-electron system is treated at the ab initio SCF level; core-valence interaction is accounted for by semi-empirical pseudopotentials, corrected for core polarization; valence correlation is included using a local spin-density-functional approximation, corrected for self-interaction. The results are compared to previous calculations for Li, Na and K clusters, and it is shown that, in spite of the different bulk crystal structure, small group 1a and 1b clusters have many properties in common.     

Searching the Chemical Space of Bicyclic Dienes for Molecular Solar Thermal Energy Storage Candidates

Photoswitches are molecular systems that are chemically transformed subsequent to interaction with light and they find potential application in many new technologies. The design and discovery of photoswitch candidates require intricate molecular engineering of a range of properties to optimize a candidate to a specific applications, a task which can be tackled efficiently using quantum chemical screening procedures. In this paper, we perform a large scale screening of approximately half a million bicyclic diene photoswitches in the context of molecular solar thermal energy storage using ab initio quantum chemical methods. We further device an efficient strategy for scoring the systems based on their predicted solar energy conversion efficiency and elucidate potential pitfalls of this approach. Our search through the chemical space of bicyclic dienes reveals systems with unprecedented solar energy conversion efficiencies and storage densities that show promising design guidelines for next generation molecular solar thermal energy storage systems.     

A fully ab initio potential energy surface for C1H_2 reactive system

An ab initio analytical potential energy surface called BW3 for the CIH2 reactive system is presented. The fit of this surface is based on about 1 200 ab initio energy points, computed with multi-reference configuration interaction(MRCI) and scaling external correlation (SEC) method and a very large basis set. The precision in the fit is very high. The BW3 surface could reproduce correctly the dissociation energy of H2 and HCI, and the endothermicity of the Cl H2 abstraction reaction. For the Cl H2 abstraction reaction, the saddle point of BW3 lies in collinear geometries, and the barrier height is 32.84 kJ/mol; for the H CIH exchange reaction, the barrier of BW3 is also linear, with a height of 77.40 kJ/mol.     

A fully ab initio potential energy surface for ClH2 reactive system

An ab initio analytical potential energy surface called BW3 for the ClH2 reactive system is presented. The fit of this surface is based on about 1 200 ab initio energy points, computed with multi-reference configuration interaction(MRCI) and scaling external correlation (SEC) method and a very large basis set. The precision in the fit is very high. The BW3 surface could reproduce correctly the dissociation energy of H2 and HCl, and the endothermicity of the Cl + H2 abstraction reaction. For the Cl + H2 abstraction reaction, the saddle point of BW3 lies in collinear geometries, and the barrier height is 32.84 kJ/mol; for the H + ClH exchange reaction, the barrier of BW3 is also linear, with a height of 77.40 kJ/mol.     

Distribution of reaction products (theory). Investigation of an ab initio energy-surface for F + H2 ⇀ HF + H

Bender, O'Neil, Pearson and Schaefer (BOPS) have computed ab initio energies for 232 collinear configurations of FHH, using extensive configuration interaction. We have fitted these points using an LEPS-type function. Comparison with semi-empirical surfaces for FHH shows that the general form of these surfaces is in good accord with the ab initio findings. Evidence is presented which indicates that the BOPS ab initio surface exhibits too great a drop in energy along the favoured route into the exit valley.     

Modeling the global potential energy surface of the N + N2 reaction from ab initio data

A new global potential energy surface for the N + N2 exchange reaction has been built from ab initio data. To overcome the difficulty of carrying out ab initio calculations for a large set of geometries the alternative strategy of fitting the minimum energy paths of the surface and their angular dependence using a modified LAGROBO functional form has been adopted. In this way we have been able to reproduce all the main features of the potential using a fairly small set of ab initio values.     

Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations

Combined ab initio quantum mechanical and molecular mechanical calculations have been widely used for modeling chemical reactions in complex systems such as enzymes, with most applications being based on the determination of a minimum energy path connecting the reactant through the transition state to the product in the enzyme environment. However, statistical mechanics sampling and reaction dynamics calculations with a combined ab initio quantum mechanical (QM) and molecular mechanical (MM) potential are still not feasible because of the computational costs associated mainly with the ab initio quantum mechanical calculations for the QM subsystem. To address this issue, a reaction path potential energy surface is developed here for statistical mechanics and dynamics simulation of chemical reactions in enzymes and other complex systems. The reaction path potential follows the ideas from the reaction path Hamiltonian of Miller, Handy and Adams for gas phase chemical reactions but is designed specifically for large systems that are described with combined ab initio quantum mechanical and molecular mechanical methods. The reaction path potential is an analytical energy expression of the combined quantum mechanical and molecular mechanical potential energy along the minimum energy path. An expansion around the minimum energy path is made in both the nuclear and the electronic degrees of freedom for the QM subsystem internal energy, while the energy of the subsystem described with MM remains unchanged from that in the combined quantum mechanical and molecular mechanical expression and the electrostatic interaction between the QM and MM subsystems is described as the interaction of the MM charges with the QM charges. The QM charges are polarizable in response to the changes in both the MM and the QM degrees of freedom through a new response kernel developed in the present work. The input data for constructing the reaction path potential are energies, vibrational frequencies, and electron density response properties of the QM subsystem along the minimum energy path, all of which can be obtained from the combined quantum mechanical and molecular mechanical calculations. Once constructed, it costs much less for its evaluation. Thus, the reaction path potential provides a potential energy surface for rigorous statistical mechanics and reaction dynamics calculations of complex systems. As an example, the method is applied to the statistical mechanical calculations for the potential of mean force of the chemical reaction in triosephosphate isomerase.     

Effect of structural relaxation on the binding energy in a molecular complex. The role of relaxation in the formation of intermediate for nucleophilic reactions of carbonyl compounds

The problem of a change in the geometry of interacting molecules, based on harmonic approximation, is considered here, to describe the effect of structural relaxation in the formation of a molecular complex on the binding energy. The correlation between the relaxation and deformation energies found earlier was analyzed with the use of an harmonic model of a molecular complex. To verify the correlation, calculations on the molecular complexes of different kinds were carried out using ab initio and semiempirical AM1 quantum chemical methods. The effect of structural relaxation on the properties of the potential energy surface for reactions of nucleophilic addition to carbonyl compounds is discussed.     

Theoretical studies on hydroquinone-benzene clusters

High-level ab initio calculations were carried out to evaluate the interaction between the hydroquinone and benzene molecules. The intermolecular interaction energy was calculated using the M?ller-Plesset second-order perturbation theory at the complete basis set limit and also at the coupled cluster theory with single, double, and perturbatively triple excitations. The calculated binding energy is larger than the benzene dimer interaction energy. The T-shaped cluster (T-a) and the parallel conformation (P-a) are calculated to be nearly isoenergetic. Owing to the large energy gain in the attraction by electron correlation, the dispersion interaction is important for the attraction.     

Dynamical mean-field theory from a quantum chemical perspective

We investigate the dynamical mean-field theory (DMFT) from a quantum chemical perspective. Dynamical mean-field theory offers a formalism to extend quantum chemical methods for finite systems to infinite periodic problems within a local correlation approximation. In addition, quantum chemical techniques can be used to construct new ab initio Hamiltonians and impurity solvers for DMFT. Here, we explore some ways in which these things may be achieved. First, we present an informal overview of dynamical mean-field theory to connect to quantum chemical language. Next, we describe an implementation of dynamical mean-field theory where we start from an ab initio Hartree-Fock Hamiltonian that avoids double counting issues present in many applications of DMFT. We then explore the use of the configuration interaction hierarchy in DMFT as an approximate solver for the impurity problem. We also investigate some numerical issues of convergence within DMFT. Our studies are carried out in the context of the cubic hydrogen model, a simple but challenging test for correlation methods. Finally, we finish with some conclusions for future directions.     

Quantum dynamics of inelastic excitations and charge transfer processes in the H+ +NO collisions

State-resolved differential cross section, integral cross section, average vibrational energy transfer, and the relative transition probability are computed for the H(+)+NO system using our newly obtained ab initio potential energy surfaces (PES) at the multireference configuration interaction level of accuracy employing the correlation consistent polarized valence triple zeta basis set. The quantum dynamics is treated within the vibrational close-coupling rotational infinite-order sudden approximation using the coupled ground state and first excited state ab initio quasidiabatic PES. The computed collision attributes for the inelastic vibrational excitation are compared with the state-to-state scattering data available at E(c.m.)=9.5 eV and E(c.m.)=29.03 eV and are found to be in overall good agreement with those of the experiments. The results for the vibrational charge transfer processes at these collision energies are also presented.     

Classical trajectory study of collisions of Ar with alkanethiolate self-assembled monolayers: potential-energy surface effects on dynamics

We have investigated collisions between Ar and alkanethiolate self-assembled monolayers (SAMs) using classical trajectory calculations with several potential-energy surfaces. The legitimacy of the potential-energy surfaces is established through comparison with molecular-beam data and ab initio calculations. Potential-energy surfaces used in previous work overestimate the binding of Ar to the SAM, leading to larger energy transfer than found in the experiments. New calculations, based on empirical force fields that better reproduce ab initio calculations, exhibit improved agreement with the experiments. In particular, polar-angle-dependent average energies calculated with explicit-atom potential-energy surfaces are in excellent agreement with the experiments. Polar- and azimuthal-angle-dependent product translational energies are examined to gain deeper insight into the dynamics of Ar+SAM collisions.     

Theoretical study on isotope and temperature effect in hydronium ion using ab initio path integral simulation

We have applied the ab initio path integral molecular dynamics simulation to study hydronium ion and its isotopes, which are the simplest systems for hydrated proton and deuteron. In this simulation, all the rotational and vibrational degrees of freedom are treated fully quantum mechanically, while the potential energies of the respective atomic configurations are calculated "on the fly" using ab initio quantum chemical approach. With the careful treatment of the ab initio electronic structure calculation by relevant choices in electron correlation level and basis set, this scheme is theoretically quite rigorous except for Born-Oppenheimer approximation. This accurate calculation allows a close insight into the structural shifts for the isotopes of hydronium ion by taking account of both quantum mechanical and thermal effects. In fact, the calculation is shown to be successful to quantitatively extract the geometrical isotope effect with respect to the Walden inversion. It is also shown that this leads to the isotope effect on the electronic structure as well as the thermochemical properties.