A newly synthesized small molecule, KTT-1, exhibits kinetically selective inhibition of histone deacetylase 2, HDAC2, over its homologous enzyme, HDAC1. KTT-1 is hard to be released from the HDAC2/KTT-1 complex, compared to the HDAC1/KTT-1 complex and the residence time of KTT-1 in HDAC2 is longer than that in HDAC1. To explore the physical origin of this kinetic selectivity, we performed replica-exchange umbrella sampling molecular dynamics simulations for formation of both complexes. The calculated potentials of mean force suggest that KTT-1 is stably bound to HDAC2 and that it is easily disassociated from HDAC1. In the direct vicinity of the KTT-1 binding site in both enzymes, there exists a conserved loop consisting of four consecutive glycine residues (Gly304-307 for HDAC2; Gly299-302 for HDA1). The difference between the two enzymes comes from a single un-conserved residue behind this loop, namely, Ala268 in HDAC2 and Ser263 in HDAC1. The Ala268 contributes to the tight binding of KTT-1 to HDAC2 by the linear orientation of Ala268, Gly306, and one carbon atom in KTT-1. On the other hand, Ser263 cannot stabilize the binding of KTT-1 to HDAC1, because it is relatively further away from the glycine loop and because the directions of the two forces are not in line.

Increasing the repertoire of available complementary tools to advance the knowledge of protein structures is fundamental for structural biology. The Neighbors Influence of Amino Acids and Secondary Structures (NIAS) is a server that analyzes a protein's conformational preferences of amino acids. NIAS is based on the Angle Probability List, representing the normalized frequency of empirical conformational preferences, such as torsion angles, of different amino acid pairs and their corresponding secondary structure information, as available in the Protein Data Bank. In this work, we announce the updated NIAS server with the data comprising all structures deposited until Sep 2022, 7 years after the initial release. Unlike the original publication, which accounted for only studies conducted with X-ray crystallography, we added data from solid nuclear magnetic resonance (NMR), solution NMR, CullPDB, Electron Microscopy, and Electron Crystallography using multiple filtering parameters. We also provide examples of how NIAS can be applied as a complementary analysis tool for different structural biology works and what are its limitations.

The Molecular Fractionation with Conjugate Caps (MFCC) method is a popular fragmentation method for the quantum-chemical treatment of proteins. However, it does not account for interactions between the amino acid fragments, such as intramolecular hydrogen bonding. Here, we present a combination of the MFCC fragmentation scheme with a second-order many-body expansion (MBE) that consistently accounts for all fragment-fragment, fragment-cap, and cap-cap interactions, while retaining the overall simplicity of the MFCC scheme with its chemically meaningful fragments. We show that with the resulting MFCC-MBE(2) scheme, the errors in the total energies of selected polypeptides and proteins can be reduced by up to one order of magnitude and relative energies of different protein conformers can be predicted accurately.

The alarming increase in the atmospheric CO2 concertation is a global concern today. Thus, the researchers around the globe are finding ways to decrease the amount of CO2 in the atmosphere. Converting CO2 into valuable chemicals like formic acid is one of the best ways to address this issue, but the stability of the CO2 molecule poses a great challenge in its conversion. To date various metal-based and organic catalysts are available for the reduction of CO2 . Still there is a great need for better, robust and economic catalytic systems and the advent of functionalized nanoreactors based on metal organic frame works (MOF) have opened a new dimension in this field. Thus, in the present work UiO-66 MOF functionalized with alanine boronic acid (AB) have been theoretically investigated for the reaction of CO2 with H2 . The density functional theory (DFT) based calculations were carried out to probe the reaction pathway. The result shows that the proposed nanoreactors can efficiently catalyze the CO2 hydrogenation. Further, the periodic energy decomposition analysis (pEDA) unveils important insights about the catalytic action of the nanoreactor.

The structure, chemical bonding, and reactivity of neutral 16 valence electrons (VE) transition metal complexes of beryllium, BeM(PMe3 )2 (1M-Be) and BeM(CO)2 (2M-Be, M = Ni, Pd, and Pt) were studied. The molecular orbital and EDA-NOCV analysis suggest dative quadruple bonds between the transition metal and beryllium, viz., one Be→M σ bond, one Be←M σ bond, and two Be←M π bonds. The strength of these bonding interactions varies based on the ligands coordinated to the transition metal. The Be←M σ bond is stronger than the Be→M σ bond when the ligand is PMe3, whereas the reverse order is observed when the ligand is CO. This is attributed to the higher π acceptor strength of CO as compared to PMe3 . Since these complexes have M-Be dative quadruple bonds, the beryllium center is susceptible to ambiphilic reactivity, as indicated by high proton and hydride affinity values.

The Grand Canonical Monte Carlo (GCMC) ensemble defined by the excess chemical potential, μex , volume, and temperature, in the context of molecular simulations allows for variations in the number of particles in the system. In practice, GCMC simulations have been widely applied for the sampling of rare gasses and water, but limited in the context of larger molecules. To overcome this limitation, the oscillating μex GCMC method was introduced and shown to be of utility for sampling small solutes, such as formamide, propane, and benzene, as well as for ionic species such as monocations, acetate, and methylammonium. However, the acceptance of GCMC insertions is low, and the method is computationally demanding. In the present study, we improved the sampling efficiency of the GCMC method using known cavity-bias and configurational-bias algorithms in the context of GPU architecture. Specifically, for GCMC simulations of aqueous solution systems, the configurational-bias algorithm was extended by applying system partitioning in conjunction with a random interval extraction algorithm, thereby improving the efficiency in a highly parallel computing environment. The method is parallelized on the GPU using CUDA and OpenCL, allowing for the code to run on both Nvidia and AMD GPUs, respectively. Notably, the method is particularly well suited for GPU computing as the large number of threads allows for simultaneous sampling of a large number of configurations during insertion attempts without additional computational overhead. In addition, the partitioning scheme allows for simultaneous insertion attempts for large systems, offering considerable efficiency. Calculations on the BK Channel, a transporter, including a lipid bilayer with over 760,000 atoms, show a speed up of ~53-fold through the use of system partitioning. The improved algorithm is then combined with an enhanced μex oscillation protocol and shown to be of utility in the context of the site-identification by ligand competitive saturation (SILCS) co-solvent sampling approach as illustrated through application to the protein CDK2.

Generalized replica exchange with solute tempering (gREST) is one of the enhanced sampling algorithms for proteins or other systems with rugged energy landscapes. Unlike the replica-exchange molecular dynamics (REMD) method, solvent temperatures are the same in all replicas, while solute temperatures are different and are exchanged frequently between replicas for exploring various solute structures. Here, we apply the gREST scheme to large biological systems containing over one million atoms using a large number of processors in a supercomputer. First, communication time on a multi-dimensional torus network is reduced by matching each replica to MPI processors optimally. This is applicable not only to gREST but also to other multi-copy algorithms. Second, energy evaluations, which are necessary for the multistate bennet acceptance ratio (MBAR) method for free energy estimations, are performed on-the-fly during the gREST simulations. Using these two advanced schemes, we observed 57.72 ns/day performance in 128-replica gREST calculations with 1.5 million atoms system using 16,384 nodes in Fugaku. These schemes implemented in the latest version of GENESIS software could open new possibilities to answer unresolved questions on large biomolecular complex systems with slow conformational dynamics.

Quantum chemical calculations were carried out to investigate the noble gas binding ability of Be3 B+ cluster. Calculations reveal that heavier noble gas atoms (ArXe) form stable complexes with this cluster. Detailed bonding analyses reveal that the noble gas atoms act as donor fragment in the formation of Ng → Be donor-acceptor bonds. Three noble gas atoms can consecutively form bonds with the Be atom of the Be3 B+ cluster.

We describe the development and features of a program called IGMPlot, which is based on the independent gradient model (IGM) and its local descriptor δg . The IGM approach analyzes the gradient of the electron density (ED) in a molecular system to identify regions of space where chemical interactions take place. IGMPlot is intended for use by both experimental scientists and theoretical chemists. It is standalone software written in C++, with versions available for multiple platforms. Some key features are: probing and quantifying interactions between two given molecular fragments, determining bond strength (IBSI), estimating the atomic contributions to an intermolecular interaction and preparing data to build 2D and 3D representations of interaction regions. The software has been updated to include new features: critical point analysis of the ED, assessing ED asymmetry of a given bond (PDA) and a new descriptor called qg designed to enhance the IGM- δg analysis. The program can be found at: http://igmplot.univ-reims.fr.

Spin relaxation is an important aspect of the spin dynamics of free radicals and can have a significant impact on the outcome of their spin-selective reactions. Examples range from the use of radicals as spin qubits in quantum information processing to the radical pair reactions in proteins that may allow migratory birds to sense the direction of the Earth's magnetic field. Accurate modeling of spin relaxation, however, is non-trivial. Bloch-Redfield-Wangsness theory derives a quantum mechanical master equation from system-bath interactions in the Markovian limit that provides a comprehensive framework for describing spin relaxation. Unfortunately, the construction of the master equation is system-specific and often resource-heavy. To address this challenge, we introduce a generalized and efficient implementation of BRW theory as a new feature of the spin dynamics toolkit MolSpin which offers an easy-to-use approach for studying systems of reacting radicals of varying complexity.

The molecular basis underlying the rich phase behavior of globular proteins remains poorly understood. We use atomistic multiscale molecular simulations to model the solution-state conformational dynamics and interprotein interactions of γ D-crystallin and its P23T-R36S mutant, which drastically limits the protein solubility, at both infinite dilution and at a concentration where the mutant fluid phase and crystalline phase coexist. We find that while the mutant conserves the protein fold, changes to the surface exposure of residues in the neighborhood of residue-36 enhance protein-protein interactions and develop specific protein-protein contacts found in the protein crystal lattice.

Stabilizing the exotic chemical species possessing multiple bonds is often extremely challenging due to insufficient orbital overlap, especially involving one heavier element. Bulky aryl groups and/or carbene as ligand have previously stabilized the SiSi, GeGe, and BB triple bonds. Herein, theoretical calculations have been carried out to shed light on the stability and bonding of elusive silaboryne/germaboryne (Si/GeB triple bond) stabilized by donor base ligands ((cAAC)BE(Me)(L); E = Si, L = cAACMe , NHCMe , PMe3 ; E = Ge, L = cAACMe ). The heavier analogues (Sn, Pb) have been further studied for comparison. Additionally, the effects of bulky substituents at the Si and N atoms on the structural parameters and stability of those species have been investigated. Energy decomposition analysis coupled with natural orbital for chemical valence (EDA-NOCV; for Si) showed that cAAC/NHC ligands could stabilize the exotic BSi-Me species more efficiently than PMe3 ligands. The BSi partial triple bond of the corresponding species possesses a mixture of one covalent electron sharing BSi σ-bond and two dative π-bonds (B ← Si, B → Si).

In this work, we investigated the structural evolution, electronic and magnetic properties of Cr2 Gen - clusters for n = 15-20 by using density functional theory (DFT) calculations. Low-energy structures for these clusters were fully searched through a self-developed genetic algorithm code combined with DFT calculations. The calculations show that all the two Cr atoms prefer to stay together to form a strong CrCr bond, which-except for size 20-is shorter than the nearest neighbor distance in Cr bulk. Sizes 15 and 16 adopt a wheel-like structure as the structural motif with the extra Ge atoms capped on the top, while larger sizes (n = 17-20) prefer fullerene-like Cr2 @Ge12 motifs. From the results of the average binding energies of Cr2 Gen - , one can conclude that it is easier to form larger size clusters. In these lowest-lying isomers except for size 16, the two Cr atoms contribute opposite magnetic moments for the total magnetic moments of 1 μB , showing an antiferromagnetic state.

In this study, structural, electronic, optical, thermoelectric, and thermodynamics properties of vacancy-ordered double perovskites Rb2 XCl6 (X = Se, Ti) were explored theoretically. The results revealed that Rb2SeCl6 and Rb2 TiCl6 are indirect band gap (Eg ) semiconductors with Eg values of 2.95 eV, and 2.84 eV respectively. The calculated properties (phonons, elastic constant, Poisson's ratio, and Pugh's ratio) revealed that both materials are dynamically and chemically stable and can exhibit brittle (Rb2 SeCl6 ) and ductile (Rb2 TiCl6 ) nature. From the analysis of optical parameters, it was noticed that the refractive index of the materials has a value of 1.5-2.0 where light absorption was found from the visible to the ultraviolet region. The thermoelectric properties determined by using the BoltzTrap code demonstrated that at room temperature, the Figure of merit (ZT) was found to be 0.74 and 0.76 for Rb2 SeCl6 and Rb2 TiCl6 , respectively. Despite a moderate value of ZT in such materials, further studies might explore effective methods for tuning the electronic band gap and improving the thermoelectric response of the material for practical energy production applications.