A new intermolecular polarizable potential for cis-formic acid. Introduction of many-body interactions in condensed phases

Topology Automated Force-Field Interactions (TAFFI): A Framework for Developing Transferable Force Fields

Force-field development has undergone a revolution in the past decade with the proliferation of quantum chemistry based parametrizations and the introduction of machine learning approximations of the atomistic potential energy surface. Nevertheless, transferable force fields with broad coverage of organic chemical space remain necessary for applications in materials and chemical discovery where throughput, consistency, and computational cost are paramount. Here, we introduce a force-field development framework called Topology Automated Force-Field Interactions (TAFFI) for developing transferable force fields of varying complexity against an extensible database of quantum chemistry calculations. TAFFI formalizes the concept of atom typing and makes it the basis for generating systematic training data that maintains a one-to-one correspondence with force-field terms. This feature makes TAFFI arbitrarily extensible to new chemistries while maintaining internal consistency and transferability. As a demonstration of TAFFI, we have developed a fixed-charge force-field, TAFFI-gen, from scratch that includes coverage for common organic functional groups that is comparable to established transferable force fields. The performance of TAFFI-gen was benchmarked against OPLS and GAFF for reproducing several experimental properties of 87 organic liquids. The consistent performance of these force fields, despite their distinct origins, validates the TAFFI framework while also providing evidence of the representability limitations of fixed-charge force fields.

Polarizable Simulations with Second order Interaction Model (POSSIM) force field: Developing parameters for alanine peptides and protein backbone

A previously introduced POSSIM (POlarizable Simulations with Second order Interaction Model) force field has been extended to include parameters for alanine peptides and protein backbones. New features were introduced into the fitting protocol, as compared to the previous generation of the polarizable force field for proteins. A reduced amount of quantum mechanical data was employed in fitting the electrostatic parameters. Transferability of the electrostatics between our recently developed NMA model and the protein backbone was confirmed. Binding energy and geometry for complexes of alanine dipeptide with a water molecule were estimated and found in a good agreement with high-level quantum mechanical results (for example, the intermolecular distances agreeing within ca. 0.06Å). Following the previously devised procedure, we calculated average errors in alanine di- and tetra-peptide conformational energies and backbone angles and found the agreement to be adequate (for example, the alanine tetrapeptide extended-globular conformational energy gap was calculated to be 3.09 kcal/mol quantim mechanically and 3.14 kcal/mol with the POSSIM force field). However, we have now also included simulation of a simple alpha-helix in both gas-phase and water as the ultimate test of the backbone conformational behavior. The resulting alanine and protein backbone force field is currently being employed in further development of the POSSIM fast polarizable force field for proteins.

Theoretical investigation on the stability of negatively charged formic acid clusters

Recent experimental results on negatively charged formic acid clusters generated by the impact of (252)Cf fission fragments on icy formic acid target are compared to quantum mechanical calculations. Structures for the clusters series, (HCOOH)nOH(-), where 2 < or = n < or = 4, are proposed based on ab initio electronic structure methods. The results show that cluster growth does not have a regular pattern of nucleation. A stability analysis was performed considering the commonly defined stability function. Temporal behavior of the clusters was evaluated by Born-Oppenheimer molecular dynamics to check the mechanism that provides cluster stability. The evaluated temporal profiles indicate the importance of hydrogen atom migration between the formic acid moieties in maintaining the stability of the structures and the water formation due to hydrogen abstraction by the hydroxyl approach.

Theoretical investigation on the stability of ionic formic acid clusters

Recent experimental results on positive charged formic acid clusters generated by the impact of (252)Cf fission fragments (FF) on icy formic acid target are examined in this paper by quantum mechanical calculations. Structures for the clusters series, (HCOOH)(n)H(+) and (HCOOH)(n)H(3)O(+), where 2 < or = n < or = 4, are proposed based on ab initio electronic structure methods. Results show that cluster growth does not present a regular pattern of nucleation. A stability analysis was performed considering the commonly defined stability function, where E is the total electronic energy plus the zero point vibrational energy correction, including the BSSE correction. The stability analysis leads to a picture that is compatible with experimental observations, indicating a decay of the stability with the increase of cluster mass. Temporal behavior of the clusters was evaluated by Born-Oppenheimer molecular dynamics to check the mechanism that provides cluster stability. The evaluated temporal profiles indicate the importance of hydrogen atom migration between the formic acid moieties to maintain the stability of the structures.

Inner-shell excitation spectroscopy and fragmentation of small hydrogen-bonded clusters of formic acid after core excitations at the oxygen K edge

Inner-shell excitation spectra and fragmentation of small clusters of formic acid have been studied in the oxygen K-edge region by time-of-flight fragment mass spectroscopy. In addition to several fragment cations smaller than the parent molecule, we have identified the production of HCOOH.H+ and H3O+ cations characteristic of proton transfer reactions within the clusters. Cluster-specific excitation spectra have been generated by monitoring the partial ion yields of the product cations. Resonance transitions of O1s(C[double bond]O/OH) electrons into pi(CO)* orbital in the preedge region were found to shift in energy upon clusterization. A blueshift of the O1s(C[double bond]O)-->pi(CO)* transition by approximately 0.2 eV and a redshift of the O1s(OH)-->pi(CO)* by approximately 0.6 eV were observed, indicative of strong hydrogen-bond formation within the clusters. The results have been compared with a recent theoretical calculation, which supports the conclusion that the formic-acid clusters consist of the most stable cyclic dimer andor trimer units. Specifically labeled formic acid-d, HCOOD, was also used to examine the core-excited fragmentation mechanisms. These deuterium-labeled experiments showed that HDO+ was formed via site-specific migration of a formyl hydrogen within an individual molecule, and that HD2O+ was produced via the subsequent transfer of a deuterium atom from the hydroxyl group of a nearest-neighbor molecule within a cationic cluster. Deuteron (proton) transfer from the hydroxyl site of a hydrogen-bond partner was also found to take place, producing deuteronated HCOOD.D+ (protonated HCOOH.H+) cations within the clusters.

Does the most stable formic acid tetramer have π stacking or C–H⋯O interactions?

Density functional theory (DFT), Moller-Plesset (MP) perturbation theory, and coupled-cluster calculations are used to examine low-energy minima on the potential energy surface of the formic acid tetramer (HCOOH)(4). The potential energy surface is rather flat with respect to rotation of one of the dimers, relative to the other dimer in an aligned stack, about the axis passing through the inversion centers of the dimers. Our best calculations suggest that an aligned pi-pi stack of two dimers is very likely to be the global minimum but there are two other pi-pi stacks within 0.5 kcal /mol. Moreover, a fourth pi-pi stack, a planar association of two dimers held together by C-H...O interactions, and a bowl structure all lie within 1 kcal /mol of the lowest-energy structure.

New theoretical insight into the interactions and properties of formic acid: Development of a quantum-based pair potential for formic acid

We performed ab initio quantum-chemical studies for the development of intra- and intermolecular interaction potentials for formic acid for use in molecular-dynamics simulations of formic acid molecular crystal. The formic acid structures considered in the ab initio studies include both the cis and trans monomers which are the conformers that have been postulated as part of chains constituting liquid and crystal phases under extreme conditions. Although the cis to trans transformation is not energetically favored, the trans isomer was found as a component of stable gas-phase species. Our decomposition scheme for the interaction energy indicates that the hydrogen-bonded complexes are dominated by the Hartree-Fock forces while parallel clusters are stabilized by the electron correlation energy. The calculated three-body and higher interactions are found to be negligible, thus rationalizing the development of an atom-atom pair potential for formic acid based on high-level ab initio calculations of small formic acid clusters. Here we present an atom-atom pair potential that includes both intra- and inter molecular degrees of freedom for formic acid. The newly developed pair potential is used to examine formic acid in the condensed phase via molecular-dynamics simulations. The isothermal compression under hydrostatic pressure obtained from molecular-dynamics simulations is in good agreement with experiment. Further, the calculated equilibrium melting temperature is found to be in good agreement with experiment.

Structure of Liquid Formic Acid Investigated by First Principle and Classical Molecular Dynamics Simulations

The structure of liquid formic acid has been investigated by Car-Parrinello and classical molecular dynamics simulations, focusing on the characterization of the H-bond network and on the mutual arrangement of pairs of bonded molecules. In agreement with previous computational studies, two levels of H-bonded structures have been found. Small clusters, characterized by O-H...O bonds, are held together by weak C-H...O bonds to form large branched structures. From the ab initio simulation we infer the importance of cyclic H-bond dimer configurations, typical of the gas phase. Most of these dimer structures are however found to be embedded into H-bonded chains. When only O-H...O bonds are taken into account, linear H-bond chains are detected as basic structures of the liquid. More branched structures occur when C-H...O bonds are also considered. Regarding the arrangement of molecular pairs, we observed that O-H...O bonds favor the occurrence of configurations with parallel molecular planes, whereas no preferential orientation is observed for molecules forming C-H...O bonds.

A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulations

We present an approximation, which allows reduction of computational resources needed to explicitly incorporate electrostatic polarization into molecular simulations utilizing empirical force fields. The proposed method is employed to compute three-body energies of molecular complexes with dipolar electrostatic probes, gas-phase dimerization energies, and pure liquid properties for five systems that are important in biophysical and organic simulations-water, methanol, methylamine, methanethiol, and acetamide. In all the cases, the three-body energies agreed with high level ab initio data within 0.07 kcal/mol, dimerization energies-within 0.43 kcal/mol (except for the special case of the CH(3)SH), and computed heats of vaporization and densities differed from the experimental results by less than 2%. Moreover, because the presented method allows a significant reduction in computational cost, we were able to carry out the liquid-state calculations with Monte Carlo technique. Comparison with the full-scale point dipole method showed that the computational time was reduced by 3.5 to more than 20 times, depending on the system in hand and on the desired level of the full-scale model accuracy, while the difference in energetic results between the full-scale and the presented approximate model was not great in the most cases. Comparison with the nonpolarizable OPLS-AA force field for all the substances involved and with the polarizable POL3 and q90 models for water and methanol, respectively, demonstrates that the presented technique allows reduction of computational cost with no sacrifice of accuracy. We hope that the proposed method will be of benefit to research employing molecular modeling technique in the biophysical and physical organic chemistry areas.

Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests

We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model.