Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field.

We introduce the Open Force Field (OpenFF) 2.0.0 small molecule force field for drug-like molecules, code-named Sage, which builds upon our previous iteration, Parsley. OpenFF force fields are based on direct chemical perception, which generalizes easily to highly diverse sets of chemistries based on substructure queries. Like the previous OpenFF iterations, the Sage generation of OpenFF force fields was validated in protein-ligand simulations to be compatible with AMBER biopolymer force fields. In this work, we detail the methodology used to develop this force field, as well as the innovations and improvements introduced since the release of Parsley 1.0.0. One particularly significant feature of Sage is a set of improved Lennard-Jones (LJ) parameters retrained against condensed phase mixture data, the first refit of LJ parameters in the OpenFF small molecule force field line. Sage also includes valence parameters refit to a larger database of quantum chemical calculations than previous versions, as well as improvements in how this fitting is performed. Force field benchmarks show improvements in general metrics of performance against quantum chemistry reference data such as root-mean-square deviations (RMSD) of optimized conformer geometries, torsion fingerprint deviations (TFD), and improved relative conformer energetics (ΔΔE). We present a variety of benchmarks for these metrics against our previous force fields as well as in some cases other small molecule force fields. Sage also demonstrates improved performance in estimating physical properties, including comparison against experimental data from various thermodynamic databases for small molecule properties such as ΔHmix, ρ(x), ΔGsolv, and ΔGtrans. Additionally, we benchmarked against protein-ligand binding free energies (ΔGbind), where Sage yields results statistically similar to previous force fields. All the data is made publicly available along with complete details on how to reproduce the training results at https://github.com/openforcefield/openff-sage.

Data augmentation using image translation for underwater sonar image segmentation.

In underwater environment, the study of object recognition is an important basis for implementing an underwater unmanned vessel. For this purpose, abundant experimental data to train deep learning model is required. However, it is very difficult to obtain these data because the underwater experiment itself is very limited in terms of preparation time and resources. In this study, the image transformation model, Pix2Pix is utilized to generate data similar to experimental one obtained by our ROV named SPARUS between the pool and reservoir. These generated data are applied to train the other deep learning model, FCN for a pixel segmentation of images. The original sonar image and its mask image have to be prepared for all training data to train the image segmentation model and it takes a lot of effort to do it what if all training data are supposed to be real sonar images. Fortunately, this burden can be released here, for the pairs of mask image and synthesized sonar image are already consisted in the image transformation step. The validity of the proposed procedures is verified from the performance of the image segmentation result. In this study, when only real sonar images are used for training, the mean accuracy is 0.7525 and the mean IoU is 0.7275. When the both synthetic and real data is used for training, the mean accuracy is 0.81 and the mean IoU is 0.7225. Comparing the results, the performance of mean accuracy increase to 6%, performance of the mean IoU is similar value.

Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field.

We present a methodology for defining and optimizing a general force field for classical molecular simulations, and we describe its use to derive the Open Force Field 1.0.0 small-molecule force field, codenamed Parsley. Rather than using traditional atom typing, our approach is built on the SMIRKS-native Open Force Field (SMIRNOFF) parameter assignment formalism, which handles increases in the diversity and specificity of the force field definition without needlessly increasing the complexity of the specification. Parameters are optimized with the ForceBalance tool, based on reference quantum chemical data that include torsion potential energy profiles, optimized gas-phase structures, and vibrational frequencies. These quantum reference data are computed and are maintained with QCArchive, an open-source and freely available distributed computing and database software ecosystem. In this initial application of the method, we present essentially a full optimization of all valence parameters and report tests of the resulting force field against compounds and data types outside the training set. These tests show improvements in optimized geometries and conformational energetics and demonstrate that Parsley's accuracy for liquid properties is similar to that of other general force fields, as is accuracy on binding free energies. We find that this initial Parsley force field affords accuracy similar to that of other general force fields when used to calculate relative binding free energies spanning 199 protein-ligand systems. Additionally, the resulting infrastructure allows us to rapidly optimize an entirely new force field with minimal human intervention.

Driving torsion scans with wavefront propagation.

The parameterization of torsional/dihedral angle potential energy terms is a crucial part of developing molecular mechanics force fields. Quantum mechanical (QM) methods are often used to provide samples of the potential energy surface (PES) for fitting the empirical parameters in these force field terms. To ensure that the sampled molecular configurations are thermodynamically feasible, constrained QM geometry optimizations are typically carried out, which relax the orthogonal degrees of freedom while fixing the target torsion angle(s) on a grid of values. However, the quality of results and computational cost are affected by various factors on a non-trivial PES, such as dependence on the chosen scan direction and the lack of efficient approaches to integrate results started from multiple initial guesses. In this paper, we propose a systematic and versatile workflow called TorsionDrive to generate energy-minimized structures on a grid of torsion constraints by means of a recursive wavefront propagation algorithm, which resolves the deficiencies of conventional scanning approaches and generates higher quality QM data for force field development. The capabilities of our method are presented for multi-dimensional scans and multiple initial guess structures, and an integration with the MolSSI QCArchive distributed computing ecosystem is described. The method is implemented in an open-source software package that is compatible with many QM software packages and energy minimization codes.

Non-bonded force field model with advanced restrained electrostatic potential charges (RESP2).

The restrained electrostatic potential (RESP) approach is a highly regarded and widely used method of assigning partial charges to molecules for simulations. RESP uses a quantum-mechanical method that yields fortuitous overpolarization and thereby accounts only approximately for self-polarization of molecules in the condensed phase. Here we present RESP2, a next generation of this approach, where the polarity of the charges is tuned by a parameter, δ, which scales the contributions from gas- and aqueous-phase calculations. When the complete non-bonded force field model, including Lennard-Jones parameters, is optimized to liquid properties, improved accuracy is achieved, even with this reduced set of five Lennard-Jones types. We argue that RESP2 with δ≈0.6 (60% aqueous, 40% gas-phase charges) is an accurate and robust method of generating partial charges, and that a small set of Lennard-Jones types is good starting point for a systematic re-optimization of this important non-bonded term.

Quantum chemical studies of redox properties and conformational changes of a four-center iron CO2 reduction electrocatalyst.

The CO2 reduction electrocatalyst [Fe4N(CO)12]- (abbrev. 1-) reduces CO2 to HCO2- in a two-electron, one-proton catalytic cycle. Here, we employ ab initio calculations to estimate the first two redox potentials of 1- and explore the pathway of a side reaction involving CO dissociation from 13-. Using the BP86 density functional approximation, the redox potentials were computed with a root mean squared error of 0.15 V with respect to experimental data. High temperature Born-Oppenheimer molecular dynamics was employed to discover a reaction pathway of CO dissociation from 13- with a reaction energy of +10.6 kcal mol-1 and an activation energy of 18.8 kcal mol-1; including harmonic free energy terms, this yields ΔGsep = 1.4 kcal mol-1 for fully separated species and ΔG‡ = +17.4 kcal mol-1, indicating CO dissociation is energetically accessible at ambient conditions. The analogous dissociation pathway from 12- has a reaction energy of 22.1 kcal mol-1 and an activation energy of 22.4 kcal mol-1 (ΔGsep = 12.8 kcal mol-1, ΔG‡ = +18.1 kcal mol-1). Our computed harmonic vibrational analysis of [Fe4N(CO)11]3- or 23- reveals a distinct CO-stretching peak red-shifted from the main CO-stretching band, pointing to a possible vibrational signature of dissociation. Multi-reference CASSCF calculations are used to check the assumptions of the density functional approximations that were used to obtain the majority of the results.