SSIPTools: Software and Methodology for Surface Site Interaction Point (SSIP) Approach and Applications.

We present the SSIPTools suite of programs. SSIPTools is a collection of software modules enabling the use of the Surface Site Interaction Point (SSIP) molecular descriptors, used for the modeling of noncovalent interactions in neutral organic molecules. It contains an implementation of the workflow for the generation of the SSIP descriptors, as well as the Functional Group Interaction Profiles (FGIPs) and Solvent Similarity Indexes (SSIs) applications, based on the SSIMPLE (Surface Site Interaction model for the Properties of Liquids at Equilibria) approach.

Automated parameterization of quantum-mechanically derived force-fields including explicit sigma holes: A pathway to energetic and structural features of halogen bonds in gas and condensed phase.

In classical molecular dynamics, general purpose atomistic force-fields (FFs) often deliver inaccurate results when dealing with halogen bonds (XBs), notwithstanding their crucial role in many fields of science, ranging from material design to drug development. Given the large dimensions of the systems of interest, it would be therefore desirable to increase the FF accuracy maintaining the simplicity of the standard Lennard-Jones (LJ) plus point charge description to avoid an excessive computational cost. A simple yet effective strategy consists in introducing a number of virtual sites able to mimic the so-called "explicit σ-hole." In this work, we present an automated FF parameterization strategy based on a global optimization of both LJ and charge parameters with respect to accurate quantum mechanical data, purposely computed for the system under investigation. As a test case, we report on two homologue series, characterized either by weak or strong XBs, namely, the di-halogenated methanes and the mono-, di-, and tri-substituted acetonitriles, taking into consideration Cl, Br, and I substituents. The resulting quantum mechanically derived FFs are validated for each compound in the gas and in the condensed phase by comparing them to general purpose and specific FFs without virtual sites and to highly accurate reference quantum mechanical data. The results strongly support the adoption of the specific FFs with virtual sites, which overcome the other investigated models in representing both gas phase energetics and the structural patterns of the liquid phase structure related to the presence of XBs.

An Activatable Cancer-Targeted Hydrogen Peroxide Probe for Photoacoustic and Fluorescence Imaging.

Reactive oxygen species play an important role in cancer, however, their promiscuous reactivity, low abundance, and short-lived nature limit our ability to study them in real time in living subjects with conventional noninvasive imaging methods. Photoacoustic imaging is an emerging modality for in vivo visualization of molecular processes with deep tissue penetration and high spatiotemporal resolution. Here, we describe the design and synthesis of a targeted, activatable probe for photoacoustic imaging, which is responsive to one of the major and abundant reactive oxygen species, hydrogen peroxide (H2O2). This bifunctional probe, which is also detectable with fluorescence imaging, is composed of a heptamethine carbocyanine dye scaffold for signal generation, a 2-deoxyglucose cancer localization moiety, and a boronic ester functionality that specifically detects and reacts to H2O2. The optical properties of the probe were characterized using absorption, fluorescence, and photoacoustic measurements; upon addition of pathophysiologic H2O2 concentrations, a clear increase in fluorescence and red-shift of the absorption and photoacoustic spectra were observed. Studies performed in vitro showed no significant toxicity and specific uptake of the probe into the cytosol in breast cancer cell lines. Importantly, intravenous injection of the probe led to targeted uptake and accumulation in solid tumors, which enabled noninvasive photoacoustic and fluorescence imaging of H2O2. In conclusion, the reported probe shows promise for the in vivo visualization of hydrogen peroxide. SIGNIFICANCE: This study presents the first activatable and cancer-targeted hydrogen peroxide probe for photoacoustic molecular imaging, paving the way for visualization of hydrogen peroxide at high spatiotemporal resolution in living subjects.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/79/20/5407/F1.large.jpg.

Understanding the Influence of Surface Solvation and Structure on Polymorph Stability: A Combined Mechanochemical and Theoretical Approach.

We explore the effect of solvent concentration on the thermodynamic stability of two polymorphs of a 1:1 cocrystal of theophylline and benzamide subjected to ball-mill liquid assisted grinding (LAG) and we investigate how this can be related to surface solvent solvation phenomena. In this system, most stable bulk polymorph form II converts to metastable bulk polymorph form I upon neat grinding (NG), while form I can fully or partially transform into form II under LAG conditions, depending on the amount of solvent used. Careful and strict experimental procedures were designed to achieve polymorph equilibrium under ball-mill LAG conditions for 16 different solvents. This allowed us to determine 16 equilibrium polymorph concentration curves as a function of solvent concentration. Ex-situ powder X-ray diffraction (PXRD) was used to monitor the polymorph concentration and crystallite size. The surface site interactions point (SSIP) description of noncovalent interactions was used in conjunction with the SSIMPLE method for calculating solvation energies to determine which functional groups are more or less exposed on the polymorph crystal surfaces. Our results demonstrate that (i) ball-mill LAG equilibrium curves can be successfully achieved experimentally for a cocrystal system; (ii) the equilibrium curves vary from solvent to solvent in onset values and slopes, thus confirming the generality of the interconversion phenomenon that we interpret here in terms of cooperativity; (iii) the concentration required for a switch in polymorphic outcome is dependent on the nature of the solvent; (iv) the SSIP results indicate that the theophylline π-system face is more exposed on the surface of form I while the theophylline N-methyl groups are more exposed in form II; and (v) for some solvents, form II has a significantly smaller crystal size at equilibrium than form I in the investigated solvent concentration range. Therefore, the free energy of the 1:1 cocrystal of theophylline and benzamide polymorphs studied here must be affected by surface solvation under ball-mill LAG conditions.

Electronic absorption spectra of pyridine and nicotine in aqueous solution with a combined molecular dynamics and polarizable QM/MM approach.

The electronic absorption spectra of pyridine and nicotine in aqueous solution have been computed using a multistep approach. The computational protocol consists in studying the solute solvation with accurate molecular dynamics simulations, characterizing the hydrogen bond interactions, and calculating electronic transitions for a series of configurations extracted from the molecular dynamics trajectories with a polarizable QM/MM scheme based on the fluctuating charge model. Molecular dynamics simulations and electronic transition calculations have been performed on both pyridine and nicotine. Furthermore, the contributions of solute vibrational effect on electronic absorption spectra have been taken into account in the so called vertical gradient approximation. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Systematic and Automated Development of Quantum Mechanically Derived Force Fields: The Challenging Case of Halogenated Hydrocarbons.

A robust and automated protocol for the derivation of sound force field parameters, suitable for condensed-phase classical simulations, is here tested and validated on several halogenated hydrocarbons, a class of compounds for which standard force fields have often been reported to deliver rather inaccurate performances. The major strength of the proposed protocol is that all of the parameters are derived only from first principles because all of the information required is retrieved from quantum mechanical data, purposely computed for the investigated molecule. This a priori parametrization is carried out separately for the intra- and intermolecular contributions to the force fields, respectively exploiting the Joyce and Picky programs, previously developed in our group. To avoid high computational costs, all quantum mechanical calculations were performed exploiting the density functional theory. Because the choice of the functional is known to be crucial for the description of the intermolecular interactions, a specific procedure is proposed, which allows for a reliable benchmark of different functionals against higher-level data. The intramolecular and intermolecular contribution are eventually joined together, and the resulting quantum mechanically derived force field is thereafter employed in lengthy molecular dynamics simulations to compute several thermodynamic properties that characterize the resulting bulk phase. The accuracy of the proposed parametrization protocol is finally validated by comparing the computed macroscopic observables with the available experimental counterparts. It is found that, on average, the proposed approach is capable of yielding a consistent description of the investigated set, often outperforming the literature standard force fields, or at least delivering results of similar accuracy.

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.

Absorption and Emission Spectra of a Flexible Dye in Solution: a Computational Time-Dependent Approach.

The spectroscopic properties of the organic chromophore 4-naphthoyloxy-1-methoxy-2,2,6,6-tetramethylpiperidine (NfO-TEMPO-Me) in toluene solution are explored through an integrated computational strategy combining a classical dynamic sampling with a quantum mechanical description within the framework of the time-dependent density functional theory (TDDFT) approach. The atomistic simulations are based on an accurately parametrized force field, specifically designed to represent the conformational behavior of the molecule in its ground and bright excited states, whereas TDDFT calculations are performed through a selected combination of hybrid functionals and basis sets to obtain optical spectra closely matching the experimental findings. Solvent effects, crucial to obtain good accuracy, are taken into account through explicit molecules and polarizable continuum descriptions. Although, in the case of toluene, specific solvation is not fundamental, the detailed conformational sampling in solution has confirmed the importance of a dynamic description of the molecular geometry for a reliable description of the photophysical properties of the dye. The agreement between theoretical and experimental data is established and a robust protocol for the prediction of the optical behaviour of flexible fluorophores in solution is set.

Analytical First and Second Derivatives for a Fully Polarizable QM/Classical Hamiltonian.

In this work, we present the derivation and implementation of analytical first and second derivatives for a fully polarizable QM/MM/PCM energy functional. First derivatives with respect to both QM- and MM-described nuclear coordinates and electric perturbations are derived and implemented, and some preliminary application is shown. Analytical second derivatives with respect to nuclear and electric perturbations are then derived, and some numerical test is presented both for a solvated system and for a cromophore embedded in a biological matrix.