Solvent accessible surface area-assessed molecular basis of osmolyte-induced protein stability.

In solvent-modulated protein folding, under certain physiological conditions, an equilibrium exists between the unfolded and folded states of the protein without any need to break or make a covalent bond. In this process, interactions between various protein groups (peptides) and solvent molecules are known to play a major role in determining the directionality of the chemical reaction. However, an understanding of the mechanism of action of the co(solvent) by a generic theoretical underpinning is lacking.

MoleGuLAR: Molecule Generation Using Reinforcement Learning with Alternating Rewards.

The design of new inhibitors for novel targets is a very important problem especially in the current scenario with the world being plagued by COVID-19. Conventional approaches such as high-throughput virtual screening require extensive combing through existing data sets in the hope of finding possible matches. In this study, we propose a computational strategy for de novo generation of molecules with high binding affinities to the specified target and other desirable properties for druglike molecules using reinforcement learning.

SCONES: Self-Consistent Neural Network for Protein Stability Prediction Upon Mutation.

Engineering proteins to have desired properties by mutating amino acids at specific sites is commonplace. Such engineered proteins must be stable to function. Experimental methods used to determine stability at throughputs required to scan the protein sequence space thoroughly are laborious.

Desolvation of Peptide Bond by O to S Substitution Impacts Protein Stability.

Amino acid side chains are key to fine-tuning the microenvironment polarity in proteins composed of polar amide bonds. Here, we report that substituting an oxygen atom of the backbone amide bond with sulfur atom desolvates the thioamide bond, thereby increasing its lipophilicity. The impact of such local desolvation by O to S substitution in proteins was tested by synthesizing thioamidated variants of Pin1 WW domain.

Multiscale Modeling of Wobble to Watson-Crick-Like Guanine-Uracil Tautomerization Pathways in RNA.

Energetically unfavorable Watson-Crick (WC)-like tautomeric forms of nucleobases are known to introduce spontaneous mutations, and contribute to replication, transcription, and translation errors. Recent NMR relaxation dispersion techniques were able to show that wobble (w) G•U mispair exists in equilibrium with the short-lived, low-population WC-like enolic tautomers. Presently, we have investigated the wG•U → WC-like enolic reaction pathway using various theoretical methods: quantum mechanics (QM), molecular dynamics (MD), and combined quantum mechanics/molecular mechanics (QM/MM).

Polarizable Multipolar Molecular Dynamics Using Distributed Point Charges.

Distributed point charge models (DCM) and their minimal variants (MDCM) have been integrated with tools widely used for condensed-phase simulations, including a virial-based barostat and a slow-growth algorithm for thermodynamic integration. Minimal DCM is further developed in a systematic fashion to reduce fitting errors in the electrostatic interaction energy, and a new fragment-based approach offers considerable speedup of the MDCM fitting process for larger molecules with increased numbers of off-centered charged sites. Finally, polarizable (M)DCM is also introduced in the present work.

Machine Learning for Accurate Force Calculations in Molecular Dynamics Simulations.

The computationally expensive nature of molecular dynamics simulations severely limits its ability to simulate large system sizes and long time scales, both of which are necessary to imitate experimental conditions. In this work, we explore an approach to make use of the data obtained using the quantum mechanical density functional theory (DFT) on small systems and use deep learning to subsequently simulate large systems by taking liquid argon as a test case. A suitable vector representation was chosen to represent the surrounding environment of each Ar atom, and a Δ-NetFF machine learning model, where the neural network was trained to predict the difference in resultant forces obtained by DFT and classical force fields, was introduced.

Transition between [R]- and [S]-stereoisomers without bond breaking.

The fifty-year old proposal of a nondissociative racemization reaction of a tetracoordinated tetrahedral center from one enantiomer to another via a planar transition state by Hoffmann and coworkers has been explored by many research groups over the past five decades. A number of stable molecules with planar tetracoordinated and higher-coordinated centers have been designed and experimentally realized; however, there has not been a single example of a molecular system that can possibly undergo such racemization. Here we show examples of molecular species that undergo inversion of stereochemistry around tetrahedral centers (Si, Al- and P+) either via a planar transition state or an intermediate state using quantum mechanical, ab initio quasi-classical dynamics calculations, and Born-Oppenheimer molecular dynamics (BOMD) simulations.

Urea-aromatic interactions in biology.

Noncovalent interactions are key determinants in both chemical and biological processes. Among such processes, the hydrophobic interactions play an eminent role in folding of proteins, nucleic acids, formation of membranes, protein-ligand recognition, etc..

The Role of Water in the Stability of Wild-type and Mutant Insulin Dimers.

Insulin dimerization and aggregation play important roles in the endogenous delivery of the hormone. One of the important residues at the insulin dimer interface is Phe, which is an invariant aromatic anchor that packs toward its own monomer inside a hydrophobic cavity formed by Val, Leu, Tyr, Cys, and Tyr. Using molecular dynamics and free-energy simulations within explicit solvent, the structural and dynamical consequences of mutations of Phe at position B24 to glycine (Gly), alanine (Ala), and d-Ala and the des-PheB25 variant are quantified.

A Novel, Computationally Efficient Multipolar Model Employing Distributed Charges for Molecular Dynamics Simulations.

A truncated multipole expansion can be re-expressed exactly using an appropriate arrangement of point charges. This means that groups of point charges that are shifted away from nuclear coordinates can be used to achieve accurate electrostatics for molecular systems. We introduce a multipolar electrostatic model formulated in this way for use in computationally efficient multipolar molecular dynamics simulations with well-defined forces and energy conservation in NVE (constant number-volume-energy) simulations.

Limits of the creation of electronic wave packets using time-dependent density functional theory.

Explicitly time-dependent density functional theory (TDDFT) has often been suggested as the method of choice for controlling the correlated dynamics of many electron systems. However, it is not yet clear which control tasks can be achieved reliably and how this depends on the functionals used. In this article, we show that the control task of creating a simple wave packet, having a population of 50% in the excited state, can indeed be achieved if a certain condition is fulfilled.

The Lack of Resonance Problem in Coherent Control with Real-Time Time-Dependent Density Functional Theory.

We will show that adiabatic real-time TDDFT predicts a time- and energy-dependent electronic structure of molecules, which makes it hard to combine TDDFT with coherent control schemes that depend on resonance conditions. In this study, we use sequences of ultrashort pulses, separated by long intervals of field free evolution, to illustrate this phenomenon for two molecules and two functionals. In coherent control scenarios, long laser pulses, with many oscillation periods, excite the system continuously and, in this way produce, a time-dependent electronic structure.

Coherent control and time-dependent density functional theory: towards creation of wave packets by ultrashort laser pulses.

Explicitly time-dependent density functional theory (TDDFT) is a formally exact theory, which can treat very large systems. However, in practice it is used almost exclusively in the adiabatic approximation and with standard ground state functionals. Therefore, if combined with coherent control theory, it is not clear which control tasks can be achieved reliably, and how this depends on the functionals.

Critical Examination of Explicitly Time-Dependent Density Functional Theory for Coherent Control of Dipole Switching.

We compare the performance of explicitly time-dependent density functional theory (DFT) with time-dependent configuration interaction (TDCI) to achieve the control task of a population inversion in LiCN. We assume that if a given pulse achieves the control task when used in TDCI, then there should be a pulse with similar frequency and intensity that achieves the task in time-dependent DFT (TDDFT). The present investigation indicates that this is not the case, if standard functionals are used in the adiabatic approximation.