Scientific and modeling feature are contained in the Gaussian package; moreover, calculations are not entangled with any artificial limitations, except for your computing resources and time. Realization of the description of wave functions is done with real-space uniform grids, multigrid methods and the finite-difference approximation FD , atom-centered basis-functions LCAO , and plane-waves PW. GPAW calculations are controlled through scripts written in the programming language Python. GPAW relies on the atomic simulation environment ASE that handles molecular dynamics, analysis, visualization, geometry optimization, and more.
HORTON [24] is a modular quantum chemistry program that allows to carry out various ab initio and DFT calculations following the post-processing options such as atoms- in-molecule analysis including Hirshfeld, extended Hirshfeld, iterative Hirshfeld, Becke, and iterative stockholder; orbital entanglement analysis; and electrostatic potential fitting of atomic charges.
Compounds , 1 HyperChem [25] is an environment that was developed for molecular modeling. The base features of HyperChem are presented in the program as a conjunction of 3D visualization and 3D animation with molecular dynamics, molecular mechanics, and quantum calculations on chemical systems. The program HyperChem is available on computers with Windows as well as Linux operative systems.
In addition, Langevin dynamics and metropolis Monte Carlo simulations are run in the environment. Calculations of free energies, heat capacities, and entropies are accomplished through treatment of vibrational partition, rotational, and translational functions.
JDFTx [26] is a code, developed for plane-wave density-functional theory DFT , and specifically the code that supports of all the standard functionalities presented in electronic DFT software and several semi-local, meta-GGA, and EXX-hybrid exchange- correlation functions, which are available with additional options by linking to the library of exchange-correlation functionals LibXC.
Including van der Waals interactions in calculations is possible in pair potential dispersion corrections. The usage of analytically continued energy functionals allows JDFTx to implement total energy minimization. Before performing the first electronic solution, following straight after the end of initialization, JDFTx carries prints out that present a list for optional features of current relevant citations of the code.
The Maple Quantum Chemistry MQC package [27] is a toolbox, developed for the predictions, research, and design of novel molecules in an available and easy-to-build encirclement. Moreover, the MQC package uses a database that includes nearly 96 million molecules to define molecules; in addition, the package runs quan- tum computations with an approach of electronic structure methods, analyzes molecular energies, and carries out high-quality 2D and 3D plots and animations.
Molcas [28] is a quantum chemistry ab initio software, which presents itself as a package developed on a stable version of OpenMolcas. As the basic idea of code is an ability to consider general electronic structures, the focus of the package is primarily turned to multiconfigurational methods; therefore, the number of approaches is typically connected to the consideration of highly degenerate states. MOLGW [29] is a Gaussian-type orbital GTO code designed to implement a self- consistent mean-field calculation for finite systems clusters, molecules, atoms with a sequent application of a many-body perturbation theory on the system.
The MOLGW code performs the approximation for the optical excitations applying the Bethe—Salpeter equation and, for the self-energy, the code accomplishes the density-functional theory DFT code for preparation of the subsequent many-body perturbation theory MBPT runs. MOLGW is capable of semi-local and standard local approximations of density-functional theory DFT along with several range-separated hybrid and hybrid functionals; moreover, the usage of a Gaussian-type orbitals basis set allows for the entire standard quantum chemistry tools to be reused.
Molpro [30] is a complex system composed of ab initio programs designed for cal- culations on molecular electronic structures. Molpro comprises programs that were well connected in parallel. Standard computational chemistry approaches include the multi- reference wave function methods, state-of-the-art high-level coupled-cluster, density func- tional theory DFT with a large choice of functionals, and so on.
Molpro accomplishes the modules that were developed for computing molecular properties such as further wave function analysis, calculations on harmonic as well as inharmonic vibrational frequencies, and geometry optimization. This allows to minimize errors that might appear owing to incompleteness of the basis set, thus achieving results near to CBS quality using the triple-zeta basis sets. The package allowed to use the improved handling of large biomolecules, including the ability to more easily manipulate macro- molecules, e.
The Massively Parallel Quantum Chemistry MPQC [32] platform is a platform developed as a package for building simulation capable of run ab initio of the electronic structure of periodic solids and other molecules. The package is able to use the Gaussian integrals library Libint embedding, distribution of task-based programming model, and runtime MADWorld, causing the massively parallel tensor framework TiledArray.
Compounds , 1 MRCC [33] is a software that presents itself as a suite developed for quantum chem- istry programs of ab initio and density functional with high-accuracy calculations on an electronic structure.
The approach based on the automated tools of the program allows realizing techniques of high complexity for quantum chemistry mod- els. The applied methods include and compose multi-reference CC approaches, arbitrary coupled-cluster CC taken as a reference and configuration interaction CI methods, arbi- trary perturbative CC approaches, CC and CI energy derivatives, and response functions.
In addition, the number of features that the package implies are capable of availabil- ity with relativistic Hamiltonians, which allows accurate calculations on heavy element systems. The techniques were developed specifically for cost-reduction on calculations; moreover, approaches with local correlation allow high-precision calculations on large- and medium-sized molecules.
It is specified explicitly for the computation for general purpose of the molecular electronic structure calculation. NTChem presents a complex new software of ab initio quantum chemistry; moreover, it contains standard quantum chemistry and original applications.
NWChem [35] is a software package for ab initio computational chemistry, and was designed in a way to include both molecular dynamics and quantum chemical functionality at the same time. The prime focus of NWChem remains to run on parallel supercomputers with high-performance along with conventional workstation clusters.
The aims of the package are to be scale both in its usage of available parallel computing resources, and in its ability to consider efficiently problems. It was developed explicitly for calculations on quantum-mechanical systems.
The prime focus of ONETEP is to improve and apply the overall linear scaling and to control accuracy, keeping it high. The optimization procedures and the density-matrix formulation of density functional theory DFT were both included in the method of code; therefore, the description of the local orbitals or non-orthogonal generalized Wannier functions and for the density-kernel is implemented. Enabling this feature will form chemical bonds among the atoms of a compound.
By default, it forms the single bond between two atoms. You can change single bond to double, triple, or hybrid bonds easily by right clicking on that bond. Moreover, various rendering options are available to represent a chemical structure.
Talking about hydrogen atoms, you can add all hydrogen atoms to the chemical structure with a single click. However, you can also add them one by one manually. Besides this, you can also change the color of an atom. Each of the available calculations can be customized by setting values of different parameters. For convenience, some basic structures of rings and amino acids are provided in the software. You can use these structures directly in your molecular model.
Following are some of the available structures:. MoluCAD is another free chemical drawing software to draw chemical models. It lets you draw chemical structures in both 2D and 3D modes. Some commonly used elements to make a chemical structure are available on the right panel of the software.
Other elements can be added to the chemical model from periodic table. You can launch the periodic table from the View menu. Four different views are available for each chemical structure, namely, top view, front view, side view, and oblique view. You can connect all atoms in a molecule with single, double, triple, or hybrid bonds. Besides this, you can also change any atom or bond of a molecule by right-clicking on it. Render Modes : You will get more than 5 render modes to represent a chemical structure.
MoluCAD comes with a large number of pre-designed molecular structures categorized in different folders:. You can animate your created chemical models. The animation will spin the molecular structures at a speed set by the user.
While the animation is running, you can vary the speed of each axis of the molecular model separately. A method for grafting and refining antibody CDR loops as well as using a knowledge-based approach to scFv fusion protein modeling using the MOE linker application will be described. The course will focus on fragment-based drug design tools in MOE.
Combinatorial fragment design and scaffold replacement in the receptor active site will be covered in detail, along with approaches for fragment linking and growing.
A method for generating a series of closely related derivatives through medicinal chemistry transformations will also be presented. Cryo electron microscopy Cryo EM allows structures to be solved rapidly for a new biological target. Many drug discovery projects now use Cryo EM structures as well as X-ray crystal structures in structure-based design exercises.
The prepared structure is compared with the electron density map to highlight regions of the structure likely to be flexible. Learn More Request a Trial. Molecular Operating Environment. Small Molecules Peptides Biologics. This application offers you the possibility to edit and modify any issues you may have with the structure of the molecular drawing. It searches the molecules for structural problems and once an error is found, the software provides automatically a real-time solution.
BIOVIA Draw is a molecular drawing software that is addressed mainly to chemists and experienced professionals of the chemical industry. It offers scientists a complete set of tools for drawing and modifying complex molecules, chemical reactions and biological sequences.
Its interface is easy to learn, and offers the possibility of viewing, communicating, and archiving of scientific information.
Molecular modeling software 6: MolView. MolView is a modeling software for chemistry with a quite different interface than the other packages mentioned above. Its main difference consists in the fact that it is a free and online web-application. It is a very easy program to use, even if you have no prior experience in kind of 3D modeling software.
This Open-Source web-application can be used both as molecular editor and as a 3D model viewer. With MolView, apart from creating structural formulas, you can also use it for protein display, modeling and simulation of proteins assembly and Chain representation. But keep in mind that the free version of ChemSketch does not include all the features of the commercial version. However, it is a pretty complete software that can be used for educational purposes, either by high school students or by undergraduate chemistry students.
With this software, you can draw organic chemical structures, structures of organometallics, polymers and Markush structures. As a user, you are also given the possibility of calculating molecular properties, such as molecular weight, density, molar refractivity etc..
It is also possible to preview your 2D molecular design in 3D to visualize better the designed structure. If you are interested in getting familiar with molecular modeling software for chemistry, you will eventually find the one that suits you best.
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