An adaptive finite element solver for the numerical calculation of the electrostatic coupling between molecules in a solvent environment is developed and tested. At the heart of the solver is a goal-oriented a posteriori error estimate for the electrostatic coupling, derived and implemented in the present work, that gives rise to an orders of magnitude improved precision and a shorter computational time as compared to standard finite difference solvers. The accuracy of the new solver ARGOS is evaluated by numerical experiments on a series of problems with analytically known solutions. In addition, the solver is used to calculate electrostatic couplings between two chromophores, linked to polyproline helices of different lengths and between the spike protein of SARS-CoV-2 and the ACE2 receptor. All the calculations are repeated by using the well-known finite difference solvers MEAD and APBS, revealing the advantages of the present finite element solver.

In the present paper, the results of the theoretical investigation of the small lithium-chloride clusters are reported. The geometrical structures, electronic and thermodynamic stability of superalkalis, superhalogens, and their single and double charged ions are obtained using efficient and accurate quantum chemistry methods. Further, low-lying isomers of the Lin Cln ( n = 2 - 5 ) clusters and their stability parameters are calculated. Two ways of formation of the Lin Cln clusters, polymerization of LiCl fragments and combination of superalkalis and superhalogen clusters, are compared. By examination the lattice energy and the average Li-Cl bond length in rectangular Lin Cln ( n ≤ 60 ) clusters, it was concluded that already 50 LiCl are enough to mostly resembles the structure and stability of the bulk LiCl.

The goal of the present work is to develop an excited-state distribution function that can be used to calculate electronic transition dipole moment time correlation functions at a considerably low computational cost. An additional merit of the distribution function is its capability to probe the Hertzberg-Teller vibronic coupling effect in terms of the previously reported Condon correlation functions in the literature without having to start from the equilibrium density operator to probe spectral non-Condon effects, thereby exploring Hertzberg-Teller vibronic coupling by building on the Condon regime. It is easily extendable to anharmonic systems. Model calculations are reported to show the high degree of accuracy and computational efficiency of the presented approach. Application to a photosynthetic system such as pheophytin a in triethylamine is provided.

The new compound 2,2'-disulfanediylbis (tetrahydro-4H-cyclo penta[d][1,3,2]dioxaphosphole 2-sulfide), the dimeric form of 2-mercaptotetrahydro-4H-cyclopenta[d] [1,3,2] dioxaphosphole 2-sulfide, has been synthesized and characterized by elemental analysis, molecular weight determination and spectral data (1 H-NMR, 13 C-NMR, 31 P-NMR, FTIR). The molecular geometry was confirmed by single X-Ray crystallography. The ground state property was examined by PBE0 and B3LYP density functionals using aug-cc-pV(Q+d)Z basis set in the gas phase and in DMSO solution. The preference of PBE0 functional was statistically established. Thermodynamic parameters and standard heat of dissociation reaction ( ΔHR(298 K)o ) have been established. The calculated equilibrium constants at different temperatures reflect the stability of the dimer over the monomers at low temperatures and vice versa. Valency and Fukui indices calculations showed that the monomer is more reactive than the dimer. 2D-fingerprint revealed that, while the H…X; [X = H, O and S] nonbonding intermolecular interactions and reciprocals play a crucial role in strengthening of molecules packing in the crystal unit cell while the S…S ones contribute negatively on it.

Since December 2019, coronavirus disease (COVID-19) has claimed the lives of millions of people across the globe. To date, no medicine is available for the responsible virus SARS-CoV-2. 3CLpro, that is, 3-chymotrypsin-like protease, the main protease (Mpro ), has an important role in cleaving pp1a and pp1ab polyproteins. This Mpro serves as an important target in drug designing against COVID-19. Herein, the study includes the investigation, screening, and identification of potent leads from (Withania sps.), against SARS-CoV-2, using virtual screening, molecular docking, and molecular dynamics (MD) simulations. Seventy-three natural compounds from this important medicinal plant were screened. The Binding affinity was used to identify the most probable target to inhibit the Mpro , compounds 27-hydroxywithanolide F (W32, -11.5 kcal/mol), withanolide A (W56, -11.4 kcal/mol), and withacoagulin H (W30, -11.1 kcal/mol) showed highest binding energy. Lipinski's rule, followed by drug-likability and likeness screening, resulted in 36 molecules. Further, MD simulation of 50 ns predicted withacoagulin H possessing strong binding affinity and hydrogen-bonding interactions with the active site. The binding free energy calculation showed the most negative energy of withacoagulin H (-63.463 KJ/mol) compared to other selected compounds. The study also compared the bonding energy of already reported repurposed and newly synthesized drugs. Further, absorption, distribution, metabolism, and excretion predictions were made to found a good balance of potency. Hence the following screened compounds from Withania sps. could serve as the potential leads for drug development against COVID-19.

Photocatalytic water oxidation remains the bottleneck in many artificial photosynthesis devices. The efficiency of this challenging process is inherently linked to the thermodynamic and electronic properties of the chromophore and the water oxidation catalyst (WOC). Computational investigations can facilitate the search for favorable chromophore-catalyst combinations. However, this remains a demanding task due to the requirements on the computational method that should be able to correctly describe different spin and oxidation states of the transition metal, the influence of solvation and the different rates of the charge transfer and water oxidation processes. To determine a suitable method with favorable cost/accuracy ratios, the full catalytic cycle of a molecular ruthenium based WOC is investigated using different computational methods, including density functional theory (DFT) with different functionals (GGA, Hybrid, Double Hybrid) as well as the semi-empirical tight binding approach GFN-xTB. A workflow with low computational cost is proposed that combines GFN-xTB and DFT and provides reliable results. GFN-xTB geometries and frequencies combined with single-point DFT energies give free energy changes along the catalytic cycle that closely follow the full DFT results and show satisfactory agreement with experiment, while significantly decreasing the computational cost. This workflow allows for cost efficient determination of energetic, thermodynamic and dynamic properties of WOCs.

AutoMeKin2021 is an updated version of tsscds2018, a program for the automated discovery of reaction mechanisms (J. Comput. Chem. 2018, 39, 1922). This release features a number of new capabilities: rare-event molecular dynamics simulations to enhance reaction discovery, extension of the original search algorithm to study van der Waals complexes, use of chemical knowledge, a new search algorithm based on bond-order time series analysis, statistics of the chemical reaction networks, a web application to submit jobs, and other features. The source code, manual, installation instructions and the website link are available at: https://rxnkin.usc.es/index.php/AutoMeKin.

The predictive power of density functional theory for materials properties can be improved without increasing the overall computational complexity by extending the generalized gradient approximation (GGA) for electronic exchange and correlation to density functionals depending on the electronic kinetic energy density in addition to the charge density and its gradient, resulting in a meta-GGA. Here, we propose an empirical meta-GGA model that is based both on physical constraints and on experimental and quantum chemistry reference data. The resulting optimized meta-GGA MCML yields improved surface and gas phase reaction energetics without sacrificing the accuracy of bulk property predictions of existing meta-GGA approaches.

Preparing molecular coordinate files for molecular dynamics (MD) simulations can be a very time-consuming process. Herein we present the development of a user-friendly program that drastically reduces the time required to prepare these molecular coordinate files for MD software packages such as AmberTools. Our program, known as charge atomtype naming (CAN), creates and uses a library of structures such as amino acid monomers to update the charge, atom type, and name of atoms in any molecular structure (mol2) file. We demonstrate the utility of this new program by rapidly preparing structural files for MD simulations for polypeptides ranging from small molecules to large protein structures. Both native and non-native amino acid residues are easily handled by this new program.

The design of new two-dimensional (2D) materials with moderate band gaps and high carrier mobility is an important aspiration for materials innovation. Recent studies have shown that boron and oxygen atoms can be integrated into the graphene lattice to form a stable B-C-O monolayer structure. To search for the most energetically stable configuration for 2D B-C-O, here, we theoretically propose two new 2D B-C-O crystal structures with a stoichiometric ratio of 2:1:1, namely monolayer (1 L) C3v - and C2v -B2 CO. Two configurations have 0.09 and 0.03 eV/unit cell lower energies than the reported 1 L Cs -B2 CO configuration (Nanoscale 2016, 8, 8910). This result is further confirmed by particle swarm optimization (PSO) calculations. According to the chemical bonding analysis, 1 L C3v -B2 CO with a quasi-planar configuration has the lowest energy, which is consisted of three strong B'-O σ-bonds, three B″-C σ-bonds, and one B'-C σ-bond. As a result, 2D B2 CO has an ultra-high mechanical strength of ~366 J m-2 , comparable to graphene ~352 J m-2 . In addition, 1 L C3v -B2 CO is a semiconductor with an HSE06 bandgap of 2.57 eV, and it has a high electron mobility of up to ~150 cm2  v-1  s-1 . The high kinetic and thermodynamic stabilities of both 1 L C3v - and C2v -B2 CO were confirmed according to phonon dispersion and molecular dynamic simulation. Comparable to that of crystalline silicon, 1 L C3v -B2 CO also shows a high light absorption intensity in the 400-550 nm region. Therefore, 2D C3v -B2 CO will have promising applications in semiconductor devices and photodetectors.

Temperature accelerated sliced sampling (TASS) is an efficient method to compute high dimensional free energy landscapes. The original TASS method employs the weighted histogram analysis method (WHAM) which is an iterative post-processing to reweight and stitch high dimensional probability distributions in sliced windows that are obtained in the presence of restraining biases. The WHAM necessitates that TASS windows lie close to each other for proper overlap of distributions and span the collective variable space of interest. On the other hand, increase in number of TASS windows implies more number of simulations, and thus it affects the efficiency of the method. To overcome this problem, we propose herein a new mean-force (MF) based reweighting scheme called TASS-MF, which enables accurate computation with a fewer number of windows devoid of the WHAM post-processing. Application of the technique is demonstrated for alanine di- and tripeptides in vacuo to compute their two- and four-dimensional free energy landscapes, the latter of which is formidable in conventional umbrella sampling and metadynamics. The landscapes are computed within a kcal mol-1 accuracy, ensuring a safe usage for broad applications in computational chemistry.

This work is devoted to investigations of the influence of O-H···Se(-) hydrogen bonds on the electronic shells of selenolate R-Se(-) fragment (R═CH3 ). The geometric, energetic and nuclear magnetic resonance (NMR) spectral parameters for various conformers of CH3 Se(-)⋯(H2 O)n clusters with n = 0-6 were calculated at CCSD/aug-cc-pVDZ level of theory. For selenolate anion CH3 Se(-) solvation free energy was calculated, and for water media it is equal to -71.41 kcal/mol. For O-H···Se(-) hydrogen bonds the proportionality coefficients between QTAIM parameters at (3; -1) bond critical point and the strength of an individual hydrogen bond ∆E were proposed. It was shown, that despite a relative weakness of O-H···Se(-) hydrogen bonds, the outer electronic shell of the selenium atom changes significantly upon formation of each hydrogen bond. This, in turn, cause the dramatic change of NMR parameters of selenium nuclei.

A nearly linear scaling implementation of coupled-cluster with singles and doubles excitations (CCSD) can be achieved by means of the domain-based local pair natural orbital (DLPNO) method. The combination of DLPNO-CCSD with implicit solvation methods allows the calculation of accurate energies and chemical properties of solvated systems at an affordable computational cost. We have efficiently implemented different schemes within the conductor-like polarizable continuum model (C-PCM) for DLPNO-CCSD in the ORCA quantum chemistry suite. In our implementation, the overhead due to the additional solvent terms amounts to less than 5% of the time the equivalent gas phase job takes. Our results for organic neutrals and open-shell ions in water show that for most systems, adding solvation terms to the coupled-cluster amplitudes equations and to the energy leads to small changes in the total energy compared to only considering solvated orbitals and corrections to the reference energy. However, when the solute contains certain functional groups, such as carbonyl or nitrile groups, the changes in the energy are larger and estimated to be around 0.04 and 0.02 kcal/mol for each carbonyl and nitrile group in the solute, respectively. For solutes containing metals, the use of accurate CC/C-PCM schemes is crucial to account for correlation solvation effects. Simultaneously, we have calculated the electrostatic component of the solvation energy for neutrals and ions in water for the different DLPNO-CCSD/C-PCM schemes. We observe negligible changes in the deviation between DLPNO-CCSD and canonical-CCSD data. Here, DLPNO-CCSD results outperform those for Hartree-Fock and density functional theory calculations.

In this paper, an improved Poisson-Nernst-Planck ion channel (PNPic) model is presented, along with its effective finite element solver and software package for an ion channel protein in a solution of multiple ionic species. Numerical studies are then done on the effects of boundary value conditions, membrane charges, and bulk concentrations on electrostatics and ionic concentrations for an ion channel protein, a gramicidin A (gA), and five different ionic solvents with up to four species. Numerical results indicate that the cation selectivity property of gA occurs within a central portion of ion channel pore, insensitively to any change of boundary value condition, membrane charge, or bulk concentration. Moreover, a numerical scheme for computing the electric currents induced by ion transports across membrane via an ion channel pore is presented and implemented as a part of the PNPic finite element package. It is then applied to the calculation of current-voltage curves, well validating the PNPic model and finite element package by electric current experimental data.

Recently, two-dimensional organic-inorganic hybrid perovskites have attracted great attention for their outstanding performances in solar energy conversion devices. By using first principles calculations, we explored the structural, electronic and optical properties of recently synthesized (PEA)2 PbI4 and (PEA)2 SnI4 organic-inorganic hybrid perovskites to understand the photovoltaic performances of these systems. Our study reveals that both the perovskites are direct band gap semiconductors and possess desirable band gap for solar energy absorption. We have further extended our study to fluoro-, chloro-, and bromo-functionalized phenethylammonium (PEA) cations based [X(X = F, Cl, Br)PEA]2 A(A = Pb, Sn)I4 perovskite materials. The halogenated benzene moiety confers an ultrahydrophobic character and protects the perovskites from ambient moisture. The halogen functionalized perovskites remain direct band gap semiconductors and all the perovskites show very strong optical absorption (∼7 × 105  cm-1 ) across UV-visible region. We have further calculated the photo-conversion efficiency (PCE) of both arene and functionalized arene based perovskites. The halogen-functionalized PEA-based perovskites also exhibit high PCE as like pristine ones and finally achieve high PCE of up to 24.30%, making them competitive with other previously reported perovskite-based photovoltaic devices.

Metal nanoclusters are an important class of materials for catalytic applications. Sub nanometer clusters are relatively less explored for their catalytic activity on account of undercoordinated surface structure. Taking this into account, we studied platinum-based sub nanometer clusters for their catalytic activity for oxygen reduction reaction (ORR). A comprehensive analysis with global optimization is carried out for structural prediction of the platinum clusters. The energetic and electronic properties of interactions of clusters with reaction intermediates are investigated. The role of structural sensitivity in the dynamics of clusters is unraveled, and unique intermediate specific interactions are identified. ORR energetics is examined, and exceptional activity for sub nanometer clusters are observed. An inverse size versus activity relationship is identified, challenging the conventional trends followed by larger nanoclusters. The principal role of atomicity in governing the catalytic activity of nanoclusters is illustrated. The structural norms governing the sub nanometer cluster activity are shown to be markedly different from larger nanoclusters.

Norcarane hydroxylation by neutral [PorMn(V)O-L] (L═OH- , F- ) and cationic [PorMn(V)O-L]+ (L═H2 O, imidazole) oxoMn(V) porphyrin complex models has been investigated by density functional theory calculations to better understand the reaction mechanism and electronic structure. We found that the energy barriers of norcarane hydroxylation by cationic oxoMn(V) porphyrin complexes are lower than those by neutral oxoMn(V) porphyrin complexes. This indicates that cationic oxoMn(V) porphyrin complexes enhance norcarane hydroxylation compared with neutral oxoMn(V) porphyrin complexes. According to electronic structure analysis, in the C─H activation step, electron transfer occurs through initial interaction between the σCH and rich-oxygen π(Mn═O) orbitals to form real donor orbitals, followed by transfer to the acceptor π*(Mn═O) orbitals. Moreover, single electron shifts from norcarane (CH) to Mn atom during C─H activation. The positive charge of the cationic complex stabilizes the acceptor orbital more than the donor orbital, reducing the energy gap between these orbitals, thus lowering the reaction barrier.

We introduce the HF-R35-D3(BJ) functional combining full nonlocal exact (Hartree-Fock-like, HF) exchange, inexpensive rung-3.5 correlation constructed from nonlocal one-electron operators, and nonlocal D3 dispersion corrections. HF-R35-D3(BJ) is among the first full-exact-exchange functionals offering competitive accuracy for general main-group thermochemistry, kinetics, and noncovalent interactions. HF-R35-D3(BJ) gives weighted mean absolute deviation WTMAD-2 8.5 kcal/mol across the entire GMTKN55 dataset, outperforming most dispersion-corrected semilocal functionals and approaching the accuracy of dispersion-corrected global hybrids. This requires six fitted parameters, three each in the nonlocal correlation and dispersion corrections. Full nonlocal exchange appears to help give accurate binding energies and reasonable energy orderings for water hexamers. These results motivate continued exploration of inexpensive nonlocal correlation corrections to nonlocal exchange.