Accurate interaction energies by spin component scaled Möller-Plesset second order perturbation theory calculations with optimized basis sets (SCS-MP2mod): Development and application to aromatic heterocycles.

The Spin Component Scaled (SCS) MP2 method using a reduced and optimized basis set (SCS-MP2mod) is employed to compute the interaction energies of nine homodimers, formed by aromatic heterocyclic molecules (pyrrole, furan, thiophene, oxazole, isoxazole, pyridine, pyridazine, pyrimidine, and pyrazine). The coefficients of the same-spin and opposite-spin correlation energies and the Gaussian type orbitals (GTO) polarization exponents of the 6-31G** basis set are simultaneously optimized in order to minimize the energy differences with respect to the coupled-cluster with single, double and perturbative triples excitations [CCSD(T)] reference interaction energies, extrapolated to a complete basis set. It is demonstrated that the optimization of the spin scale factors leads to a noticeable improvement of the accuracy with a root mean square deviation less than 0.1 kcal/mol and a largest unsigned deviation smaller than 0.25 kcal/mol. The pyrrole dimer provides an exception, with a slightly higher deviation from the reference data. Given the high benefit in terms of computational time with respect to the CCSD(T) technique and the small loss of accuracy, the SCS-MP2mod method appears to be particularly suitable for extensive sampling of intermolecular potential energy surfaces at a quantum mechanical level. Within this framework, a transferability test of the SCS-MP2mod parameters to a benchmark set of this class of molecules is very promising as the reference interaction energies of several heterocyclic aromatic heterodimers were reproduced with a standard deviation of 0.30 kcal/mol. The SCS-MP2mod remarkably outperforms the value of 1.95 kcal/mol obtained with standard MP2/6-31G**.

A General Treatment to Study Molecular Complexes Stabilized by Hydrogen-, Halogen-, and Carbon-Bond Networks: Experiment and Theory of (CH2 F2 )n ⋠⋠⋠(H2 O)m.

Rotational spectra of several difluoromethane-water adducts have been observed using two broadband chirped-pulse Fourier-transform microwave (CP-FTMW) spectrometers. The experimental structures of (CH2 F2 )⋅⋅⋅(H2 O)2 , (CH2 F2 )2 ⋅⋅⋅(H2 O), (CH2 F2 )⋅⋅⋅(H2 O)3 , and (CH2 F2 )2 ⋅⋅⋅(H2 O)2 were unambiguously identified with the aid of 18 isotopic substituted species. A subtle competition between hydrogen, halogen, and carbon bonds is observed and a detailed analysis was performed on the complex network of non-covalent interactions which stabilize each cluster. The study shows that the combination of stabilizing contact networks is able to reinforce the interaction strength through a cooperative effect, which can lead to large stable oligomers.

The role of the multiconfigurational character of nitronyl-nitroxide in the singlet-triplet energy gap of its diradicals.

While technological applications demand the development of reliable computational techniques and accurate experiments for the characterization of diradicals, these species are still challenging systems for both theory and experiments. The singlet-triplet energy gap, the J-term of the Heisenberg-Dirac-van Vleck spin Hamiltonian, is the most significant quantity; its measurement and computational evaluation may serve for understanding and controlling magnetism at the molecular scale. In this framework, we report a study of three diradicals containing one or two nitronyl-nitroxide species. Using Difference Dedicated Configuration Interaction (DDCI) calculations, we investigate the multiconfigurational character of the O-N-C-N-O fragment of this unit. We find that a computational scheme that takes this nature into account is necessary to confidently obtain reliable values of the spin-spin coupling J. In addition, we show that the reduced DDCI2 scheme with a CAS(2,2) reference, which can reproduce experimental data in some cases, provides quite poor results in the present context.

Quantitative prediction and interpretation of spin energy gaps in polyradicals: the virtual magnetic balance.

Open-shell organic molecules possessing more than two unpaired electrons and sufficient stability even at room temperature are very unusual, but few were recently synthesized that promise a number of fascinating applications. Unfortunately, reliable structural information is not available and only lower limits can be estimated for energy splittings between the different spin states. On these grounds, we introduce here an effective 'virtual magnetic balance', a robust and user-friendly tool purposely tailored for polyradicals and devised to be used in parallel with experimental studies. The main objective of this tool is to provide reliable structures and quantitative splittings of spin states of large, complex molecules. We achieved this objective with reasonable computation times and in a theoretical framework that allows disentanglement of different stereo-electronic effects contributing to the overall experimental result. A recently synthesized tetraradical with remarkable chemical stability was used as a case study.

Magnetic gaps in organic tri-radicals: From a simple model to accurate estimates.

The calculation of the energy gap between the magnetic states of organic poly-radicals still represents a challenging playground for quantum chemistry, and high-level techniques are required to obtain accurate estimates. On these grounds, the aim of the present study is twofold. From the one side, it shows that, thanks to recent algorithmic and technical improvements, we are able to compute reliable quantum mechanical results for the systems of current fundamental and technological interest. From the other side, proper parameterization of a simple Hubbard Hamiltonian allows for a sound rationalization of magnetic gaps in terms of basic physical effects, unraveling the role played by electron delocalization, Coulomb repulsion, and effective exchange in tuning the magnetic character of the ground state. As case studies, we have chosen three prototypical organic tri-radicals, namely, 1,3,5-trimethylenebenzene, 1,3,5-tridehydrobenzene, and 1,2,3-tridehydrobenzene, which differ either for geometric or electronic structure. After discussing the differences among the three species and their consequences on the magnetic properties in terms of the simple model mentioned above, accurate and reliable values for the energy gap between the lowest quartet and doublet states are computed by means of the so-called difference dedicated configuration interaction (DDCI) technique, and the final results are discussed and compared to both available experimental and computational estimates.

Perturbative multireference configuration interaction (CI-MRPT2) calculations in a focused dynamical approach: a computational study of solvatochromism in pyrimidine.

We have investigated solvatochromic effects over a solvent series of increasing polarity on the prototype molecule pyrimidine as a solute species. The line shape profiles, obtained by a time-dependent approach based on quantum mechanical calculations performed over frames sampled from classical molecular dynamics trajectories, were directly compared to the available experimental bands. The multireference configuration interaction second-order perturbation (CI-MRPT2) calculations are in quantitative agreement with the experiment. The results also confirm how nonprotic solvents can be confidently modeled by continuous solvation models as the polarizable continuum model, whereas protic solvents, as water, require the inclusion of explicit solvent molecules to account for the effects of hydrogen bonds.

Transport properties of binuclear metal complexes of the VIII group using a simplified NEGF-DFT approach.

We report on a theoretical study of the electronic transport properties of binuclear complexes of metals of the VIII group bridged by pyrazine. Metal-porphyrazine units have been combined in order to investigate symmetric and non-symmetric species with particular focus on their current rectification properties. Transmission functions and I-V characteristics of the various species have been computed using a Non-Equilibrium Green Function with a simplified treatment of the molecule-lead interaction. The results obtained show an overall moderate asymmetry in the current along the molecules, which is of the donor-σ-acceptor type and follow the trend of the ionization potential of the metals in the binuclear system. The bias-dependent rectification ratio, which is significant in a limited voltage window, can be explained in terms of the alignment of the occupied orbitals of the metallic fragments that contribute to the HOMO and HOMO - 1 of the supermolecule. The possible improvement of the rectification performance of such a class of molecules has also been investigated exploiting suitable substitution by electron-withdrawing groups.

Joyce and Ulysses: integrated and user-friendly tools for the parameterization of intramolecular force fields from quantum mechanical data.

The Joyce program is augmented with several new features, including the user friendly Ulysses GUI, the possibility of complete excited state parameterization and a more flexible treatment of the force field electrostatic terms. A first validation is achieved by successfully comparing results obtained with Joyce2.0 to literature ones, obtained for the same set of benchmark molecules. The parameterization protocol is also applied to two other larger molecules, namely nicotine and a coumarin based dye. In the former case, the parameterized force field is employed in molecular dynamics simulations of solvated nicotine, and the solute conformational distribution at room temperature is discussed. Force fields parameterized with Joyce2.0, for both the dye's ground and first excited electronic states, are validated through the calculation of absorption and emission vertical energies with molecular mechanics optimized structures. Finally, the newly implemented procedure to handle polarizable force fields is discussed and applied to the pyrimidine molecule as a test case.

An automated approach for the parameterization of accurate intermolecular force-fields: pyridine as a case study.

An automated protocol is proposed and validated, which integrates accurate quantum mechanical calculations with classical numerical simulations. Intermolecular force fields, (FF) suitable for molecular dynamics (MD) and Monte Carlo simulations, are parameterized through a novel iterative approach, fully based on quantum mechanical data, which has been automated and coded into the PICKY software, here presented. The whole procedure is tested and validated for pyridine, whose bulk phase, described through MD simulations performed with the specifically parameterized FF, is characterized by computing several of its thermodynamic, structural, and transport properties, comparing them with their experimental counterparts.

Complementary and partially complementary DNA duplexes tethered to a functionalized substrate: a molecular dynamics approach to biosensing.

Molecular dynamics simulations (90 ns) of different DNA complexes attached to a functionalized substrate in solution were performed in order to clarify the behavior of mismatched DNA sequences captured by a tethered DNA probe (biochip). Examination of the trajectories revealed that the substrate influence and a series of cooperative events, including recognition, reorientation and reorganization of the bases, could induce the formation of stable duplexes having non-canonical arrangements. Major adjustment of the structures was observed when the mutated base was located in the end region of the chain close to the surface.

Singlet-triplet energy gap of a diarylnitroxide diradical by an accurate many-body perturbative approach.

We report on the calculation of the spin-spin coupling term J in a diarylnitroxide diradical system which is a slightly simplified version of a recently synthesized stable species with a triplet ground state. We have applied our complementary space perturbative approach using virtual orbitals appropriately modified with the aim of investigating, through molecular fragmentation, the effects of the non-bridge aryls. We show how by using multireference CI techniques it is now possible to obtain accurate and reliable values of J even for large organic radicals, the basic units of longer chain polyradical systems.

Automated Parameterization of Quantum Mechanically Derived Force Fields for Soft Materials and Complex Fluids: Development and Validation.

The reliability of molecular dynamics (MD) simulations in predicting macroscopic properties of complex fluids and soft materials, such as liquid crystals, colloidal suspensions, or polymers, relies on the accuracy of the adopted force field (FF). We present an automated protocol to derive specific and accurate FFs, fully based on ab initio quantum mechanical (QM) data. The integration of the Joyce and Picky procedures, recently proposed by our group to provide an accurate description of simple liquids, is here extended to larger molecules, capable of exhibiting more complex fluid phases. While the standard Joyce protocol is employed to parameterize the intramolecular FF term, a new automated procedure is here proposed to handle the computational cost of the QM calculations required for the parameterization of the intermolecular FF term. The latter is thus obtained by integrating the old Picky procedure with a fragmentation reconstruction method (FRM) that allows for a reliable, yet computationally feasible sampling of the intermolecular energy surface at the QM level. The whole FF parameterization protocol is tested on a benchmark liquid crystal, and the performances of the resulting quantum mechanically derived (QMD) FF were compared with those delivered by a general-purpose, transferable one, and by the third, "hybrid" FF, where only the bonded terms were refined against QM data. Lengthy atomistic MD simulations are carried out with each FF on extended 5CB systems in both isotropic and nematic phases, eventually validating the proposed protocol by comparing the resulting macroscopic properties with other computational models and with experiments. The QMD-FF yields the best performances, reproducing both phases in the correct range of temperatures and well describing their structure, dynamics, and thermodynamic properties, thus providing a clear protocol that may be explored to predict such properties on other complex fluids or soft materials.

Parameterization and validation of an accurate force-field for the simulation of alkylamine functionalized silicon (111) surfaces.

The stretching, bending, and torsional force-field parameters for modelling Si (111) surfaces functionalized with alkylamines have been derived from energies, optimized geometries and harmonic frequencies obtained by accurate quantum mechanical calculations. Addition of inter-chain non-bonded parameters from a literature force field leads to computed energies in good agreement with their quantum mechanical counterparts for a large set of geometrical arrangements. The overall force-field was tested through molecular dynamics simulations performed on several models of Si functionalized surfaces, with different coverage percentages. Preliminary results indicate that the presence of a polar terminal amine group yields a surface coating of around 50%.

Force-field modeling through quantum mechanical calculations: molecular dynamics simulations of a nematogenic molecule in its condensed phases.

Interaction energy of the 4-n-pentyloxy-4'-cyanobiphenyl (5OCB) dimer is computed at MP2 level, for many geometrical arrangements using the Fragmentation Reconstruction Method (FRM). DFT calculations are performed for a number of geometries of the monomer. The resulting database is used to parameterize an atomistic intra- and inter-molecular force-field suitable for classical bulk simulations. Several structural and dynamical properties in 5OCB isotropic and liquid crystalline phases are computed from molecular dynamics simulation mainly in the NPT ensemble. Lengthy runs (more than 70 ns) and large sample sizes (up to 806 molecules) were used to determine the nematic to isotropic transition temperature up to a precision of few K. Good agreement was found in most of the investigated properties, thus validating the accuracy of the proposed model potential, only derived by quantum mechanical calculations.

Sensors for DNA detection: theoretical investigation of the conformational properties of immobilized single-strand DNA.

A major challenge in the design and creation of biomolecular sensors is the development of efficient strategies using both existing synthetic technologies and novel fabrication methods to effectively adsorb and assemble different molecular species on suitable substrates. In order to generate stable and effective biodevices it is fundamental to understand the mechanisms responsible for the formation of the supramolecular structures, to evaluate to what extent the function and conformation of the adsorbed macromolecules are influenced by their interactions with the substrates and the environment and to identify possible causes of disruption, with the ultimate aim of suggesting and selecting appropriate methodologies to design highly efficient systems. Here in silico modeling comes into play, provided that realistic models and reliable computational strategies are employed. This paper is focused on DNA detection systems based on the hybridization between a DNA target and its complementary probe, which is present either in solution or on a solid support. MD simulations of the fully hydrated single strand attached to an allylamine functionalized Si(111) surface in aqueous solution are presented. A reliable and high quality picture of the structural flexibility and dynamic properties of the modified and unmodified DNA segment in solution together with the ability of DNA to rearrange its structure due to environmental effects is given and clarified.

Magnetic interactions in phenyl-bridged nitroxide diradicals: conformational effects by multireference and broken symmetry DFT approaches.

In the present paper we report the key results of a comprehensive computational study aimed at investigating the dependence of the singlet-triplet energy gap in phenyl-bridged bis-nitroxide diradicals, on the basis set and on soft structural parameters like torsion and pyramidalization. We have compared the BS-DFT technique with the post-Hartree-Fock DDCI2 multireference approach. With this latter method we have also studied the different role that sigma and pi core and virtual orbitals have in the resulting singlet-triplet energy gap.The results obtained represent one step forward in the definition of a protocol for an efficient and reliable computation of spin-spin coupling in diradical systems.

Magnetic coupling in bis-nitronylnitroxide radicals: The role of aromatic bridges.

Configuration interaction calculations have been applied to the study of the magnetic coupling in bis-nitronyl nitroxide radicals with benzene bridges. Molecular orbitals obtained with different localization schemes have been considered in the generation of the CI space, with the aim of investigating the role played by the various fragments in the magnetic interaction. The aromatic bridge is found significant, while fragments outside the magnetic-bridge-magnetic moiety can be neglected. Using simplified model molecular species, an accurate analysis of the ferromagnetic/antiferromagnetic coupling in the meta and para diradicals is reported.

Accurate yet feasible post-Hartree-Fock computation of magnetic interactions in large biradicals through a combined variational/perturbative approach: Setup and validation.

We present a scheme for the calculation of the spin-spin coupling term J in diradicals which is quantitatively accurate and computationally cheap. The method exploits the use of modified virtual orbitals and perturbation theory, incorporated in a multireference configuration interaction approach. The results obtained for model diradical species which exhibit ferromagnetic and antiferromagnetic coupling are fully satisfactory and very promising for future applications of the method to larger molecular systems of technological interest in magnetic-based devices.

Development and Validation of Quantum Mechanically Derived Force-Fields: Thermodynamic, Structural, and Vibrational Properties of Aromatic Heterocycles.

A selection of several aromatic molecules, representative of the important class of heterocyclic compounds, has been considered for testing and validating an automated Force Field (FF) parametrization protocol, based only on Quantum Mechanical data. The parametrization is carried out separately for the intra- and intermolecular contributions, employing respectively the Joyce and Picky software packages, previously implemented and refined in our research group. The whole approach is here automated and integrated with a computationally effective yet accurate method, devised very recently ( J. Chem. THEORY: Comput., 2018, 14, 543-556) to evaluate a large number of dimer interaction energies. The resulting quantum mechanically derived FFs are then used in extensive molecular dynamics simulations, in order to evaluate a number of thermodynamic, structural, and dynamic properties of the heterocycle's gas and liquid phases. The comparison with the available experimental data is good and furnishes a validation of the presented approach, which can be confidently exploited for the design of novel and more complex materials.

Interaction Energy Landscapes of Aromatic Heterocycles through a Reliable yet Affordable Computational Approach.

Noncovalent interactions between homodimers of several aromatic heterocycles (pyrrole, furan, thiophene, pyridine, pyridazine, pyrimidine, and pyrazine) are investigated at the ab initio level, employing the Möller-Plesset second-order perturbation theory, coupled with small Gaussian basis sets (6-31G* and 6-31G**) with specifically tuned polarization exponents. The latter are modified using a systematic and automated procedure, the MP2mod approach, based on a comparison with high level CCSD(T) calculations extrapolated to a complete basis set. The MP2mod results achieved with the modified 6-31G** basis set show an excellent agreement with CCSD(T)/CBS reference energies, with a standard deviation less than 0.3 kcal/mol. Exploiting its low computational cost, the MP2mod approach is then used to explore sections of the intermolecular energy of the considered homodimers, with the aim of rationalizing the results. It is found that the direct electrostatic interaction between the monomers electron clouds is at the origin of some observed features, and in many cases multipoles higher than dipole play a relevant role, although often the interplay with other contributions to the noncovalent forces (as for instance induction, π-π or XH-π interactions) makes a simple rationalization rather difficult.