AmberTools.

AmberTools is a free and open-source collection of programs used to set up, run, and analyze molecular simulations. The newer features contained within AmberTools23 are briefly described in this Application note.

TeraChem protocol buffers (TCPB): Accelerating QM and QM/MM simulations with a client-server model.

The routine use of electronic structures in many chemical simulation applications calls for efficient and easy ways to access electronic structure programs. We describe how the graphics processing unit (GPU) accelerated electronic structure program TeraChem can be set up as an electronic structure server, to be easily accessed by third-party client programs. We exploit Google's protocol buffer framework for data serialization and communication.

Data for molecular dynamics simulations of cytochrome oxidase with the Amber force field.

Cytochrome -type quinol oxidase is an important metalloenzyme that allows many bacteria to survive in low oxygen conditions. Since oxidase is found in many prokaryotes but not in eukaryotes, it has emerged as a promising bacterial drug target. Examples of organisms containing oxidases include the bacterium that causes tuberculosis (TB) in humans, the bacterium that causes cholera, the bacterium that contributes to antibiotic resistance and sepsis, and the bacterium that causes food poisoning.

Highly Accurate Many-Body Potentials for Simulations of NO in Water: Benchmarks, Development, and Validation.

Dinitrogen pentoxide (NO) is an important intermediate in the atmospheric chemistry of nitrogen oxides. Although there has been much research, the processes that govern the physical interactions between NO and water are still not fully understood at a molecular level. Gaining a quantitative insight from computer simulations requires going beyond the accuracy of classical force fields while accessing length scales and time scales that are out of reach for high-level quantum-chemical approaches.

Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK.

The quantum mechanics/molecular mechanics (QM/MM) approach is an essential and well-established tool in computational chemistry that has been widely applied in a myriad of biomolecular problems in the literature. In this publication, we report the integration of the QUantum Interaction Computational Kernel (QUICK) program as an engine to perform electronic structure calculations in QM/MM simulations with AMBER. This integration is available through either a file-based interface (FBI) or an application programming interface (API).

Relationship between Hydrogen-Bonding Motifs and the 1b Splitting in the X-ray Emission Spectrum of Liquid Water.

The split of the 1b peak observed in the X-ray emission (XE) spectrum of liquid water has been the focus of intense research. Although several hypotheses have been proposed to explain the origin of this split, a consensus has not yet been reached. Here, we introduce a novel theoretical/computation approach which, combining path-integral molecular dynamics simulations with the MB-pol model and time-dependent density functional theory calculations, predicts the 1b splitting in liquid water and not in crystalline ice, in agreement with the experimental observations.

Exploring Coupled Redox and pH Processes with a Force-Field-Based Approach: Applications to Five Different Systems.

Coupled redox and pH-driven processes are at the core of many important biological mechanisms. As the distribution of protonation and redox states in a system is associated with the pH and redox potential of the solution, having efficient computational tools that can simulate under these conditions becomes very important. Such tools have the potential to provide information that complement and drive experiments.

Multidimensional Replica Exchange Simulations for Efficient Constant pH and Redox Potential Molecular Dynamics.

Efficient computational methods that are capable of supporting experimental measures obtained at constant values of pH and redox potential are important tools as they serve to, among other things, provide additional atomic level information that cannot be obtained experimentally. Replica Exchange is an enhanced sampling technique that allows converged results to be obtained faster in comparison to regular molecular dynamics simulations. In this work we report the implementation, also available with GPU-accelerated code, of pH and redox potential (E) as options for multidimensional REMD simulations in AMBER.

Redox potential replica exchange molecular dynamics at constant pH in AMBER: Implementation and validation.

Redox processes are important in chemistry, with applications in biomedicine, chemical analysis, among others. As many redox experiments are also performed at a fixed value of pH, having an efficient computational method to support experimental measures at both constant redox potential and pH is very important. Such computational techniques have the potential to validate experimental observations performed under these conditions and to provide additional information unachievable experimentally such as an atomic level description of macroscopic measures.

Probing the Structures of Solvent-Complexed Ions Formed in Electrospray Ionization Using Cryogenic Infrared Photodissociation Spectroscopy.

The gas-phase infrared photodissociation (IRPD) spectra of solvent-tagged small biomolecules are studied in a cryogenic ion trap at 17 K. In this study para-aminobenzoic acid (PABA) and tyramine molecules are noncovalently tagged with water or acetonitrile in the electrospray ionization (ESI) source. The complexes are then cooled in the cryogenic trap prior to spectroscopic measurements.

Cation-Dependent Conformations in 25-Hydroxyvitamin D3-Cation Adducts Measured by Ion Mobility-Mass Spectrometry and Theoretical Modeling.

Ion mobility-mass spectrometry is a useful tool in separation of biological isomers, including clinically relevant analytes such as 25-hydroxyvitamin D3 (25OHD3) and its epimer, 3-epi-25-hydroxyvitamin D3 (epi25OHD3). Previous research indicates that these epimers adopt different gas-phase sodiated monomer structures, either the "open" or "closed" conformer, which allow 25OHD3 to be readily resolved in mixtures. In the current work, alternative metal cation adducts are investigated for their relative effects on the ratio of "open" and "closed conformers.

Investigating Differences in Gas-Phase Conformations of 25-Hydroxyvitamin D3 Sodiated Epimers using Ion Mobility-Mass Spectrometry and Theoretical Modeling.

Drift tube ion mobility coupled with mass spectrometry was used to investigate the gas-phase structure of 25-hydroxyvitamin D3 (25OHD3) and D2 (25OHD2) epimers, and to evaluate its potential in rapid separation of these compounds. Experimental results revealed two distinct drift species for the 25OHD3 sodiated monomer, whereas only one of these conformations was observed for its epimer (epi25OHD3). The unique species allowed 25OHD3 to be readily distinguished, and the same pattern was observed for 25OHD2 epimers.

Experimental and Theoretical Investigation of Sodiated Multimers of Steroid Epimers with Ion Mobility-Mass Spectrometry.

Ion mobility-mass spectrometry (IM-MS) has recently seen increased use in the analysis of small molecules, especially in the field of metabolomics, for increased breadth of information and improved separation of isomers. In this study, steroid epimers androsterone and trans-androsterone were analyzed with IM-MS to investigate differences in their relative mobilities. Although sodiated monomers exhibited very similar collision cross-sections (CCS), baseline separation was observed for the sodiated dimer species (R = 1.