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...

COMPASS: An ab Initio Force-Field Optimized for Condensed-Phase ApplicationsOverview with Details on Alkane and Benzene Compounds

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...

http://www.wag.caltech.edu/publications/sup/pdf/471.pdf

ReaxFF: A Reactive Force Field for Hydrocarbons

In this study, we present conformational energies for a molecular mechanical model (Parm99) developed for organic and biological molecules using the restrained electrostatic potential (RESP) approach to derive the partial charges. This approach uses the simple "generic" force field model (Parm94), and attempts to add a minimal number of extra Fourier components to the torsional energies, but doing so only when there is a physical justification. The results are quite encouraging, not only for the 34-molecule set that has been studied by both the highest level ab initio model (GVB/LMP2) and experiment, but also for the 55-molecule set for which high-quality experimental data are available. Considering the 55 molecules studied by all the force field models for which there are experimental data, the average absolute errors (AAEs) are 0.28 (this model), 0.52 (MM3), 0.57 (CHARMm (MSI)), and 0.43 kcal/mol (MMFF). For the 34-molecule set, the AAEs of this model versus experiment and ab initio are 0.28 and 0.27 kcal/mol, respectively. This is a lower error than found with MM3 and CHARMm, and is comparable to that found with MMFF (0.31 and 0.22 kcal/mol). We also present two examples of how well the torsional parameters are transferred from the training set to the test set. The absolute errors of molecules in the test set are only slightly larger than in the training set (differences of <0.1 kcal/mol). Therefore, it can be concluded that a simple "generic" force field with a limited number of specific torsional parameters can describe intra- and intermolecular interactions, although all comparison molecules were selected from our 82-compound training set. We also show how this effective two-body

/pdf/how-well-does-a-restrained-electrostatic-potential-resp-5fgytd7p7h.pdf

How Well Does a Restrained Electrostatic Potential (RESP) Model Perform in Calculating Conformational Energies of Organic and Biological Molecules

A potential function is presented that can be used to model both chemical reactions and intermolecular interactions in condensed-phase hydrocarbon systems such as liquids, graphite, and polymers. This potential is derived from a well-known dissociable hydrocarbon force field, the reactive empirical bond-order potential. The extensions include an adaptive treatment of the nonbonded and dihedral-angle interactions, which still allows for covalent bonding interactions. Torsional potentials are introduced via a novel interaction potential that does not require a fixed hybridization state. The resulting model is intended as a first step towards a transferable, empirical potential capable of simulating chemical reactions in a variety of environments. The current implementation has been validated against structural and energetic properties of both gaseous and liquid hydrocarbons, and is expected to prove useful in simulations of hydrocarbon liquids, thin films, and other saturated hydrocarbon systems.

https://www.usna.edu/Users/chemistry/jah/_files/Papers/AIREBO_JCPversion.pdf

A reactive potential for hydrocarbons with intermolecular interactions

The Cologne Database for Molecular Spectroscopy, CDMS: a useful tool for astronomers and spectroscopists

We present an analysis of the data from our Swedish-ESO Submillimetre Telescope molecular line survey in the 1.3 mm band of the N, M, and NW positions in the Sgr B2 molecular cloud. The line emissions from 42 molecular species, and some of their isotopomers, were analyzed assuming a single temperature and a homogeneous source. In cases where a source size much smaller than the antenna beam (23'') could be estimated, optical depth effects were also accounted for. In this way rotation temperatures, molecular column densities, and in several cases also source sizes, were determined. Observed and modeled intensities are presented in rotation diagrams. A few complex molecular species, NH2CHO, CH3CHO, C2H3CN, C2H5CN, and CH3OCHO, mainly in the N source, exhibit anomalously strong intensities in their intrinsically weak b- and c-type lines. We argue that this effect can hardly be explained by high optical depths alone, and therefore propose that the possibility of radiative pumping via the low-lying vibrational states of these molecules should be investigated as an alternative explanation. The highest rotation temperatures, up to about 500 K, were found for large molecules toward Sgr B2(N), closely followed by Sgr B2(M). In Sgr B2(NW), which samples the cloud envelope, the rotation temperatures are 15-50 K. For molecules with too few observed transitions to allow determination of rotation temperatures, the column density was calculated assuming optically thin emission, and we adopted rotation temperatures of 50, 50, and 20 K in M, N, and NW, respectively. Column density ratios of isotopomers were determined. After a critical discussion of the resolution-dependent H2 column density toward the observed positions, abundances relative to H2 were calculated. We discuss the chemical differences between the three observed cloud positions and compare with the hot core, compact ridge, and outflow in Orion A. Hot core-type molecules like CH2NH, NH2CN, CH3CN, C2H3CN, and C2H5CN, as well as H2CS, are more abundant in Sgr B2(N) by factors of 3-8 as compared to the M position. Large oxygen-containing species like CH3OH, CH3CHO, CH3OCHO, CH3OCH3, and NH2CHO, of compact ridge-type, show similar or slightly enhanced abundances in N as compared to M. The C2H5OH abundances are similar in N, M, and also in NW. The SO2 and SO abundances in the M core (4 × 10-7 and 1 × 10-7, respectively) are 13 and 5 times higher than in N and are very enhanced (103 and 102 times) as compared to NW. Such high SO2 and SO abundances are also found in the prominent Orion A outflow source. In M the SO18O and S18O data suggest a 16O/18O ratio of 120. The HOCO+ ion is detected in all three positions and appears to be 3 times more abundant in the NW position. HCNH+ is seen only in NW.

http://iopscience.iop.org/article/10.1086/313376/pdf

A Three-Position Spectral Line Survey of Sagittarius B2 between 218 and 263 GHZ. II. Data Analysis

We completed the first spectral line survey toward a cold, dark cloud TMC-1 (cyanopolyyne peak) in a frequency range between 8.8 and 50.0 GHz by the 45-m radio telescope of Nobeyama Radio Observatory. We detected 414 lines of 38 molecular species including 11 new molecules, such as C6H, CCO, C3O, CCS, C3S, HNCCC, HCCNC, HC3NH + , HCCCHO, CH2CN, and cyclic C3H (c-C3H), which were previously reported; only one significant line, U49536, remains unidentified. 177 out of 414 lines are reported for the first time. Some half of the detected molecules are linear carbon-chain species and their derivatives. We also discovered three new rarer isotopomers: CC34S, C3S, and HDCS. Spectral charts are presented together with the observed line parameters of all detected lines. Improved molecular constants of several carbon-chain molecules obtained during the course of identification are also presented.

A 8.8-50 GHz Complete Spectral Line Survey toward TMC-1: I. Survey Data.

The linear MgNC radical was detected, for the first time, by laboratory microwave spectroscopy, and six unidentified lines in IRC +10216 reported by Guelin et al. (1986) were assigned to the transitions of this radical. The radical was produced in a free space absorption cell by a DC discharge in a mixture of magnesium vapor, argon, and cyanogen. Observed spectral lines in the 250-370 GHz region were analyzed by using the 2 Σ energy level expression, to give the rotational, centrifugal distortion and spin-rotation constants: B 0 = 5966.896(24) MHz, D 0 =0.004 2338(35) MHz, H 0 =0.308(16)×10 −7 MHz, and B 0 =15.219(13) MHz, with one standard deviation in parentheses

Laboratory Spectroscopy of MgNC: The First Radioastronomical Identification of Mg-bearing Molecule

The linear CCS radical has been detected, for the first time, by laboratory microwave spectroscopy, and four unidentified lines including the U45379 line from TMC-1 and seven from Sgr B2 have been assigned to the transitions of this radical. The radical was produced in a free-space absorption cell by a dc glow discharge in a mixture of CS2 and He. Twenty-nine lines were observed in the frequency region up to 300 HGz and were least-squares analyzed to determine the detailed molecular constants. Two strong unidentified lines, U45379 and U22344, were assigned to the F1 components, J(N) = 4(3)-3(2) and 2(1)-1(0), respectively. The J(N) = 2(1)-1(0) transition of CC(S-34) was also observed in TMC-1. The column densities of CCS in Sgr B2 and TMC-1 are estimated to be (6 + or - 1) x 10 to the 13th and (8 + or - 2) x 10 to the 13th per sq cm, respectively. 19 references.

Laboratory detection and astronomical identification of a new free radical, CCS 3Sigma/-/

The successive members of a new sulfur-containing carbon-chain molecule, CCS and C3S, have been detected and identified in the laboratory and in interstellar space. Here, the synthesis of the C3S molecule and the assigning to it of three strong unidentified lines in TMC-1 is reported. The molecular constants of two C3S lines are given along with an estimated value for the column density in TMC-1. 13 references.

Shuji Saito

Papers

A Three-Position Spectral Line Survey of Sagittarius B2 between 218 and 263 GHZ. II. Data Analysis

A 8.8-50 GHz Complete Spectral Line Survey toward TMC-1: I. Survey Data.

Laboratory Spectroscopy of MgNC: The First Radioastronomical Identification of Mg-bearing Molecule

Laboratory detection and astronomical identification of a new free radical, CCS 3Sigma/-/

Laboratory detection of a new carbon-chain molecule C3S and its astronomical identification