Ultra-Fast Semi-Empirical Quantum Chemistry for High-Throughput Computational Campaigns with Sparrow

Semi-empirical quantum chemical approaches are known to compromise accuracy for feasibility of calculations on huge molecules. However, the need for ultrafast calculations in interactive quantum mechanical studies, high-throughput virtual screening, and for data-driven machine learning has shifted the emphasis towards calculation runtimes recently. This comes with new constraints for the software implementation as many fast calculations would suffer from a large overhead of manual setup and other procedures that are comparatively fast when studying a single molecular structure, but which become prohibitively slow for high-throughput demands. In this work, we discuss the effect of various well-established semi-empirical approximations on calculation speed and relate this to data transfer rates from the raw-data source computer to the results visualization front end. For the former, we consider desktop computers, local high performance computing, as well as remote cloud services in order to elucidate the effect on interactive calculations, for web and cloud interfaces in local applications, and in world-wide interactive virtual sessions. The models discussed in this work have been implemented into our open-source software SCINE Sparrow.Comment: 39 pages, 4 figures, 4 table

Interface of the polarizable continuum model of solvation with semi-empirical methods in the GAMESS program

An interface between semi-empirical methods and the polarized continuum model (PCM) of solvation successfully implemented into GAMESS following the approach by Chudinov et al (Chem. Phys. 1992, 160, 41). The interface includes energy gradients and is parallelized. For large molecules such as ubiquitin a reasonable speedup (up to a factor of six) is observed for up to 16 cores. The SCF convergence is greatly improved by PCM for proteins compared to the gas phase

Stabilizing small particles of lithium hydroxide with adsorbed water molecules: a quantum chemical study

Quantum chemical calculations have been carried out of the energetic and geometric characteristics of the lithium hydroxide molecular models within the frameworks of both semiempirical (the MNDO method) and ab initio (the STO-3G and 6-31G basises being used) approaches. The adsorption of water molecules has been shown to result in stabilizing small particles of the compound. The vibrational spectra of the LiOH microcrystallites have been also examined

An ab initio analytical potential energy surface for the O(3P) + CS(X1Σ+) → CO(X1Σ+) + S(3P) reaction useful for kinetic and dynamical studies

The N(4Su) + NO(X 2Π) → N 2(X 1Σg+) + O( 3Pg) reaction plays an important role in the upper atmosphere chemistry and as a calibration system for discharge flow systems. Surprisingly, very little theoretical and experimental work has been devoted to the characterization of the dynamical features of this system. In this work a Sorbie-Murrell expression for the lowest 3A″ potential energy surface (PES) connecting reactants in their ground electronic states based upon the fitting of an accurate ab initio CI grid of points has been derived. The PES fitted shows no barrier to reaction with respect to the reactants asymptote in accordance with experimental findings and becomes highly repulsive as the NNO angle is varied away from the saddle point geometry. The results of preliminary quasiclassical trajectory calculations on this surface reproduce very well the experimental energy disposal in products, even though the vibrational distribution derived from trajectories seems to be a bit cooler than the experimental data. Moreover, thermal rate constants derived from trajectories are in excellent accordance with experimental value

The bicyclo[2.1.1]hexan-2-one system: a new probe for the experimental and computational study of electronic effects in π-facial selectivity in nucleophilic additions

The remotely substituted 5-exo-bicyclo[2.1.1]hexan-2-one system is introduced as a new probe to study long range electronic effects on π -face selectivity during hydride reduction and a systematic computational study demonstrates good predictability at the semi-empirical level

MLatom 3: Platform for machine learning-enhanced computational chemistry simulations and workflows

Machine learning (ML) is increasingly becoming a common tool in computational chemistry. At the same time, the rapid development of ML methods requires a flexible software framework for designing custom workflows. MLatom 3 is a program package designed to leverage the power of ML to enhance typical computational chemistry simulations and to create complex workflows. This open-source package provides plenty of choice to the users who can run simulations with the command line options, input files, or with scripts using MLatom as a Python package, both on their computers and on the online XACS cloud computing at XACScloud.com. Computational chemists can calculate energies and thermochemical properties, optimize geometries, run molecular and quantum dynamics, and simulate (ro)vibrational, one-photon UV/vis absorption, and two-photon absorption spectra with ML, quantum mechanical, and combined models. The users can choose from an extensive library of methods containing pre-trained ML models and quantum mechanical approximations such as AIQM1 approaching coupled-cluster accuracy. The developers can build their own models using various ML algorithms. The great flexibility of MLatom is largely due to the extensive use of the interfaces to many state-of-the-art software packages and libraries

A Theoretical Study of Silylamides

Silylation is an important reaction in organosilicon and related chemistries. It involves the reversible exchange of an active hydrogen for a silyl group, generally trimethysilyl, which dramatically alters the physical and chemical characteristics of the original molecule. Among the various classes of silylating agents available, the silylamides are the most interesting. This class of silylating agent has demonstrated thermodynamic silylating power which spans over seven orders of magnitude. The structural complexity of these materials appears to be related to their reaotivity and includes both tautomeric and rotameric species. The work presented here, explores this novel class of materials. The hindered rotation of silylamides, the 1,3-migration of silicon between nitrogen and oxygen in these materials, and some of their conformational effects on the silylation process are examined using both semiempirical quantum mechanical methods and ah initio techniques. The computational data presented here, supports what is known about the rotational and tautomeric behaviour of silylamides and silylformamide. We have successfully calculated the torsional barrier for a series of materials and explained some of their unique electronic and chemical characteristics. The activated 5-coordinate intermediate for the 1,3- migration of silicon between nitrogen and oxygen has been characterized and an estimated activation energy for the process given. The reaction of N-silylformamide and 0-silylformimide with water was studied. Those data suggest that the O- silylimidate tautomer is the preferred tautomeric species for the silylation of water. A calculated energy profile for each reaction is given and explained. Several semiempirical molecular orbital methods were evaluated during this work and those findings are described and compared to ab initio results

Vitamin C and Its Radicals: Tautomerism, Electronic Structure and Properties

The biological importance and activity of ascorbic acid and its radicals are briefly reviewed. The quantum mechanical calculations performed on these remarkable compounds are presented in some detail. Particular attention is devoted to structural and electronic features offered by the semiempirical MINDO/3 and MNDO schemes. By making use of the self-consistent charge (SCC-MO) method, the ESCA spectra of the ascorbic acid tautomers are predicted. It is found that the radical anion is more stable than each of the four AA tautomers. This is of importance because the unusual biological protective property of ascorbate against free radical damage is most likely related to the stability of its radical, Ortgins of the enhanced stability of the radical anion are analyzed by the energy partitioning technique