Recent rsearches have shown that the lengths of the chemical bonds, whether completely or partially covalent or ionic, are sums of the radii of the adjacent atoms and/or ions. On investigating the bond length data for the molecular components of nucleic acids, all were found (for the first time) to be effectively the sums of the covalent radii of the adjacent atoms. This work shows that the bond lengths in caffeine and related molecules are likewise sums of the covalent radii of C, N, O and H. This has enabled arriving at the atomic structures of these molecules, also for the first time.
During the asymptoyic giant branch (AGB) phase, different elements are dredge-up to the stellar surface depending on progenitor mass and metallicity. When the mass loss increases at the end of the AGB, a circumstellar dust shell is formed, where different (C-rich or O-rich) molecules and solid-state compounds are formed. These are further processed in the transition phase between AGB stars and planetary nebulae (PNe) to create more complex organic molecules and inorganic solid-state compounds (e.g., polycyclic aromatic hydrocarbons, fullerenes, and graphene precursors in C-rich environments an…
Polyhalogenated compounds are common in industrial, agricultural, and environmental applications. These compounds contain more halogen bonds than monohalogenated compounds. The presence of coupled σ-holes in the covalent halogen atoms, which demonstrates strong interplay in halogen bonds, should be carefully evaluated in force field optimization. In this study, a polarizable ellipsoidal force field model was successfully applied to many possible halogenated benzenes. The symmetry of the fitted parameters was reproduced without any additional restrictions. The optimized parameters for the aniso…
In our theoretical study in which we combine a nonequilibrium Green's function (NEGF) approach with density functional theory (DFT) we investigate branched compounds containing Ru or Os metal complexes in two branches, which due to their identical or different metal centers are symmetric or asymmetric. In these compounds the metal atoms are connected to pyridyl anchor groups via acetylenic and phenyl spacer groups in a meta-connection. We find there is no destructive quantum interference (DQI) feature in the transmission function near the Fermi level for the investigated molecules regardless o…
We show that by using intuitive and accessible molecular features it is possible to predict the temperature-dependent second virial coefficient of organic and inorganic compounds using Gaussian process regression. In particular, we built a low dimensional representation of features based on intrinsic molecular properties, topology and physical properties relevant for the characterization of molecule-molecule interactions. The featurization was used to predict second virial coefficients in the interpolative regime with a relative error $\lesssim 1\% $ and to extrapolate the prediction to temper…
The present manuscript reports the elemental as well as molecular study of the Green Crackers. Laser-induced breakdown spectroscopy has been used for elemental analysis, UV-Vis and Photoacoustic Spectroscopy (PAS) are used for molecular study of the green crackers. The spectral lines of several elements including heavy/toxic such as Al, Ba, Sr, Cr, Cu are observed in the LIBS spectra of green crackers like present in normal crackers. In addition to this, the electronic bands of diatomic molecules like AlO, SrO, and CaO are also observed in LIB spectra of the green crackers. PAS, which is non-d…
The formation process and composition of the acrylonitrile/urea inclusion compounds (AN/UIC) with different aging times and AN/urea molar feed ratios are studied by differential scanning calorimetry (DSC) and X-ray diffraction (XRD). It is suggested that DSC could be one of the helpful methods to determine the guest/host ratio and the heat of decomposition. Meanwhile, the guest/host ratio and heat of deformation are obtained, which are 1.17 and 5361.53 J/mol, respectively. It is suggested AN molecules included in urea canal lattice may be packed flat against each other. It is found that the fo…
Conjugated organic molecules represent an important area of materials chemistry for both fundamental scientific exploration and technological applications. Using a genetic algorithm to computationally screen up to ~25-50 million molecules for organic photovoltaic properties, we find that our methods find top monomers 6,000-8,000 times faster than brute force search. By testing multiple runs and establishing convergence criteria, we show the computational scaling with search space size, common molecular motifs, and discuss the reliability to choose the same molecules independent of initial data…
To contribute to the understanding of noncovalent binding of halogenated molecules with a biological activity, electrostatic potential (ESP) maps of more than 2,500 compounds were thoroughly analysed. A peculiar region of positive ESP, called $σ$-hole, is a concept of central importance for halogen bonding. We aim at simplifying the view on $σ$-holes and provide general trends in organic drug-like molecules. The results are in fair agreement with crystallographic surveys of small molecules as well as of biomolecular complexes and attempt to improve the intuition of chemists when dealing with h…
We present and discuss carbon-rich compounds of astrochemical interest such as polyynes, acetylenic carbon chains and the related derivative known as monocyanopolyynes and dicyanopolyynes. Fullerenes are now known to be abundant in space, while fulleranes - the hydrogenated fullerenes - and other carbon-rich compounds such as very large polycyclic aromatic hydrocarbons (VLPAHs) and heavy petroleum fractions are suspected to be present in space. We review the synthesis, the infrared spectra as well as the electronic absorption spectra of these four classes of carbon-rich molecules. The existenc…
Designing a molecule with desired properties is one of the biggest challenges in drug development, as it requires optimization of chemical compound structures with respect to many complex properties. To augment the compound design process we introduce Mol-CycleGAN - a CycleGAN-based model that generates optimized compounds with high structural similarity to the original ones. Namely, given a molecule our model generates a structurally similar one with an optimized value of the considered property. We evaluate the performance of the model on selected optimization objectives related to structura…
The combination of modern scientific computing with electronic structure theory can lead to an unprecedented amount of data amenable to intelligent data analysis for the identification of meaningful, novel, and predictive structure-property relationships. Such relationships enable high-throughput screening for relevant properties in an exponentially growing pool of virtual compounds that are synthetically accessible. Here, we present a machine learning (ML) model, trained on a data base of \textit{ab initio} calculation results for thousands of organic molecules, that simultaneously predicts m…
Machine learning (ML) has shown to advance the research field of quantum chemistry in almost any possible direction and has recently also entered the excited states to investigate the multifaceted photochemistry of molecules. In this paper, we pursue two goals: i) We show how ML can be used to model permanent dipole moments for excited states and transition dipole moments by adapting the charge model of [Chem. Sci., 2017, 8, 6924-6935], which was originally proposed for the permanent dipole moment vector of the electronic ground state. ii) We investigate the transferability of our excited-stat…
Molecular design principles provide guidelines for augmenting a molecule with a smaller group of atoms to realize a desired property or function. We demonstrate that these concepts can be used to create an optical cycling center that can be attached to a number of aromatic ligands, allowing the scattering of many photons from the resulting molecules without changing the molecular vibrational states. We provide further design principles that indicate the ability to expand this work. This represents a significant step towards a quantum functional group, which may serve as a generic qubit moiety …
Photo-acid generators (PAGs) are compounds that release acids ($H^+$ ions) when exposed to light. These compounds are critical components of the photolithography processes that are used in the manufacture of semiconductor logic and memory chips. The exponential increase in the demand for semiconductors has highlighted the need for discovering novel photo-acid generators. While de novo molecule design using deep generative models has been widely employed for drug discovery and material design, its application to the creation of novel photo-acid generators poses several unique challenges, such a…
The computational prediction of atomistic structure is a long-standing problem in physics, chemistry, materials, and biology. Within conventional force-field or {\em ab initio} calculations, structure is determined through energy minimization, which is either approximate or computationally demanding. Alas, the accuracy-cost trade-off prohibits the generation of synthetic big data records with meaningful energy based conformational search and structure relaxation output. Exploiting implicit correlations among relaxed structures, our kernel ridge regression model, dubbed Graph-To-Structure (G2S)…
Calculated state-of-the art results for solvation and ionization energies of thousands of organic molecules relevant to battery design
Ecole Polytechnique Fédérale de Lausanne（洛桑联邦理工学院）；University of Vienna（维也纳大学）；Uppsala University（乌普萨拉大学）；Vector Institute for Artificial Intelligence（人工智能向量研究所）；University of Toronto（多伦多大学）；Technische Universität Berlin（柏林工业大学）
In open-shell atoms and ions, processes such as photoionization, combination (Raman) scattering, electron scattering and recombination, are often mediated by many-electron compound resonances. We show that their interference (neglected in the independent-resonance approximation) leads to a coherent contribution, which determines the energy-averaged total cross sections of electron- and photon-induced reactions obtained using the optical theorem. In contrast, the partial cross sections (e.g., electron recombination, or photon Raman scattering) are dominated by the stochastic contributions. Thus…
Evaluating the (dis)similarity of crystalline, disordered and molecular compounds is a critical step in the development of algorithms to navigate automatically the configuration space of complex materials. For instance, a structural similarity metric is crucial for classifying structures, searching chemical space for better compounds and materials, and driving the next generation of machine-learning techniques for predicting the stability and properties of molecules and materials. In the last few years several strategies have been designed to compare atomic coordination environments. In partic…
Organic semiconductors are promising materials for cheap, scalable and sustainable electronics, light-emitting diodes and photovoltaics. For organic photovoltaic cells, it is a challenge to find compounds with suitable properties in the vast chemical compound space. For example, the ionization energy should fit to the optical spectrum of sun light, and the energy levels must allow efficient charge transport. Here, a machine-learning model is developed for rapidly and accurately estimating the HOMO and LUMO energies of a given molecular structure. It is build upon the SchNet model (Schütt et al…
Using first principles calculations, we show the high hydrogen storage capacity of a new class of compounds, metalloboranes. Metalloboranes are transition metal (TM) and borane compounds that obey a novel-bonding scheme. We have found that the transition metal atoms can bind up to 10 H2 molecules.
Accounting for correlations with core electrons by means of the generalized relativistic effective core potentials: Atoms Hg and Pb and their compounds
Comprehensive and confident identifications of metabolites and other chemicals in complex samples will revolutionize our understanding of the role these chemically diverse molecules play in biological systems. Despite recent advances, metabolomics studies still result in the detection of a disproportionate number of features than cannot be confidently assigned to a chemical structure. This inadequacy is driven by the single most significant limitation in metabolomics: the reliance on reference libraries constructed by analysis of authentic reference chemicals. To this end, we have developed th…
A new iterative version of population projection analysis is formulated and applied to determine relativistic effective atomic configurations of superheavy elements Cn and Fl and their lighter homologues (Hg and Pb) in the molecules of their fluorides and oxides. The dependence of the computed populations on the initial reference atomic spinors is completely avoided. The difference in population of atomic spinors with the same orbital angular momentum and different total angular momenta is demonstrated to be essential for understanding the peculiarities of chemical bonding in superheavy elemen…
Recovering molecules from coarse-grained beads: free-energy-conditioned generative backmapping across chemical space
Institute for Theoretical Physics, Heidelberg University（海德堡大学理论物理研究所）；Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University（海德堡大学跨学科科学计算中心）
Method of evaluating chemical shifts of X-ray emission lines for sufficiently heavy atoms (beginning from period 4 elements) in chemical compounds is developed. This method is based on the pseudopotential model and one-center restoration method (to reconstruct the proper electronic structure in heavy-atom cores). The approximations of instantaneous transition and frozen inner core spinors of the atom are used for derivation of an expression for chemical shift as a difference between mean values of some effective operator. The method allows one to avoid evaluating small values (chemical shifts …
