UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations
01 Dec 1992-Journal of the American Chemical Society (American Chemical Society)-Vol. 114, Iss: 25, pp 10024-10035
TL;DR: In this article, the Universal force field (UFF) is described, where the force field parameters are estimated using general rules based only on the element, its hybridization, and its connectivity.
Abstract: A new molecular mechanics force field, the Universal force field (UFF), is described wherein the force field parameters are estimated using general rules based only on the element, its hybridization, and its connectivity. The force field functional forms, parameters, and generating formulas for the full periodic table are presented
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TL;DR: This paper presents a meta-modelling procedure called "Continuum Methods within MD and MC Simulations 3072", which automates the very labor-intensive and therefore time-heavy and expensive process of integrating discrete and continuous components into a discrete-time model.
Abstract: 6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072
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TL;DR: The “Activation‐strain TS interaction” (ATS) model of chemical reactivity is reviewed as a conceptual framework for understanding how activation barriers of various types of reaction mechanisms arise and how they may be controlled, for example, in organic chemistry or homogeneous catalysis.
Abstract: We present the theoretical and technical foundations of the Amsterdam Density Functional (ADF) program with a survey of the characteristics of the code (numerical integration, density fitting for the Coulomb potential, and STO basis functions). Recent developments enhance the efficiency of ADF (e.g., parallelization, near order-N scaling, QM/MM) and its functionality (e.g., NMR chemical shifts, COSMO solvent effects, ZORA relativistic method, excitation energies, frequency-dependent (hyper)polarizabilities, atomic VDD charges). In the Applications section we discuss the physical model of the electronic structure and the chemical bond, i.e., the Kohn–Sham molecular orbital (MO) theory, and illustrate the power of the Kohn–Sham MO model in conjunction with the ADF-typical fragment approach to quantitatively understand and predict chemical phenomena. We review the “Activation-strain TS interaction” (ATS) model of chemical reactivity as a conceptual framework for understanding how activation barriers of various types of (competing) reaction mechanisms arise and how they may be controlled, for example, in organic chemistry or homogeneous catalysis. Finally, we include a brief discussion of exemplary applications in the field of biochemistry (structure and bonding of DNA) and of time-dependent density functional theory (TDDFT) to indicate how this development further reinforces the ADF tools for the analysis of chemical phenomena. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 931–967, 2001
8,490 citations
TL;DR: The implementation of Open Babel is detailed, key advances in the 2.3 release are described, and a variety of uses are outlined both in terms of software products and scientific research, including applications far beyond simple format interconversion.
Abstract: A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats. We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org
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6,040 citations
Cites methods from "UFF, a full periodic table force fi..."
...not supported by MMFF94), the UFF force field can be used instead [33]....
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TL;DR: In this paper, a general all-atom force field for atomistic simulation of common organic molecules, inorganic small molecules, and polymers was developed using state-of-the-art ab initio and empirical parametrization techniques.
Abstract: A general all-atom force field for atomistic simulation of common organic molecules, inorganic small molecules, and polymers was developed using state-of-the-art ab initio and empirical parametrization techniques. The valence parameters and atomic partial charges were derived by fitting to ab initio data, and the van der Waals (vdW) parameters were derived by conducting MD simulations of molecular liquids and fitting the simulated cohesive energies and equilibrium densities to experimental data. The combined parametrization procedure significantly improves the quality of a general force field. Validation studies based on large number of isolated molecules, molecular liquids and molecular crystals, representing 28 molecular classes, show that the present force field enables accurate and simultaneous prediction of structural, conformational, vibrational, and thermophysical properties for a broad range of molecules in isolation and in condensed phases. Detailed results of the parametrization and validation f...
4,722 citations
TL;DR: In this paper, a force field for large-scale reactive chemical systems (1000s of atoms) is proposed. But the force field does not have Coulomb and Morse potentials to describe nonbond interactions between all atoms.
Abstract: To make practical the molecular dynamics simulation of large scale reactive chemical systems (1000s of atoms), we developed ReaxFF, a force field for reactive systems. ReaxFF uses a general relationship between bond distance and bond order on one hand and between bond order and bond energy on the other hand that leads to proper dissociation of bonds to separated atoms. Other valence terms present in the force field (angle and torsion) are defined in terms of the same bond orders so that all these terms go to zero smoothly as bonds break. In addition, ReaxFF has Coulomb and Morse (van der Waals) potentials to describe nonbond interactions between all atoms (no exclusions). These nonbond interactions are shielded at short range so that the Coulomb and van der Waals interactions become constant as Rij → 0. We report here the ReaxFF for hydrocarbons. The parameters were derived from quantum chemical calculations on bond dissociation and reactions of small molecules plus heat of formation and geometry data for...
4,455 citations
References
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Book•
01 Jan 1969
6,280 citations
Book•
01 Jan 1972
TL;DR: In this article, the fundamental vibrational frequencies of 109 molecular forms of 38 polyatomic chain molecules consisting of the CH3, CD3, CH2 CD2, CHD, O, and S groups are given as an extension of tables of molecular vibrational frequency published in the NSRDS•NBS publication series and in this journal.
Abstract: Fundamental vibrational frequencies of 109 molecular forms of 38 polyatomic chain molecules consisting of the CH3, CD3, CH2 CD2, CHD, O, and S groups are given as an extension of tables of molecular vibrational frequencies published in the NSRDS‐NBS publication series and in this journal. On preparing the tables in this part, an approach, different from that in the previous parts, based on the calculations of normal vibration frequencies was adopted. A set of force constants which explains all the frequencies of small molecules for which the assignments had been established was obtained and then the frequencies of larger molecules was calculated and compared with the frequencies observed in the infrared and Raman spectra. The tables provide a convenient source of information for those who require vibrational energy levels and related properties in molecular spectroscopy, thermodynamics, analytical chemistry, and other fields of physics and chemistry.
706 citations
TL;DR: In this paper, the Universal Force Field (UFF) was used to predict the structures of a variety of organic molecules, including unstrained and uncongested hydrocarbons, silanes, alkenes, saturated amines, saturated ethers and phosphines.
Abstract: The application of a Universal force field (UFF) to the treatment of organic molecules is described. The ability of the force field to predict the structures of a variety of organic molecules is examined, and the results are compared with the MM2 or MM3 force fields. UFF correctly predicts the structures of unstrained and uncongested hydrocarbons, silanes, alkenes, saturated amines, saturated ethers and phosphines, aromatic systems, and simple unconjugated multiple bond containing compounds such as nitriles, ketones, and imines well
506 citations
TL;DR: In this article, the Universal Force Field (UFF) was used to predict the structures of a variety of organic molecules, including unstrained and uncongested hydrocarbons, silanes, alkenes, saturated amines, saturated ethers and phosphines.
Abstract: The application of a Universal force field (UFF) to the treatment of organic molecules is described. The ability of the force field to predict the structures of a variety of organic molecules is examined, and the results are compared with the MM2 or MM3 force fields. UFF correctly predicts the structures of unstrained and uncongested hydrocarbons, silanes, alkenes, saturated amines, saturated ethers and phosphines, aromatic systems, and simple unconjugated multiple bond containing compounds such as nitriles, ketones, and imines well
63 citations