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1. Analysis of the conformational properties of amine ligands at the gold/water interface with QM, MM and QM/MM simulations

   https://doi.org/10.1039/C7CP06709G  

   Liang, Dongyue ; Hong, Jiewei ; Fang, Dong ; Bennett, Joseph W. ; Mason, Sara E. ; Hamers, Robert J. ; Cui, Qiang ( January 2018 , Physical Chemistry Chemical Physics)

   We describe a strategy of integrating quantum mechanical (QM), hybrid quantum mechanical/molecular mechanical (QM/MM) and MM simulations to analyze the physical properties of a solid/water interface. This protocol involves using a correlated ab initio (CCSD(T)) method to first calibrate Density Functional Theory (DFT) as the QM approach, which is then used in QM/MM simulations to compute relevant free energy quantities at the solid/water interface using a mean-field approximation of Yang et al. that decouples QM and MM thermal fluctuations; gas-phase QM/MM and periodic DFT calculations are used to determine the proper QM size in the QM/MM simulations. Finally, the QM/MM free energy results are compared with those obtained from MM simulations to directly calibrate the force field model for the solid/water interface. This protocol is illustrated by examining the orientations of an alkyl amine ligand at the gold/water interface, since the ligand conformation is expected to impact the chemical properties ( e.g. , charge) of the solid surface. DFT/MM and MM simulations using the INTERFACE force field lead to consistent results, suggesting that the effective gold/ligand interactions can be adequately described by a van der Waals model, while electrostatic and induction effects are largely quenched by solvation. The observed differences among periodic DFT, QM/MM and MM simulations, nevertheless, suggest that explicitly including electronic polarization and potentially charge transfer in the MM model can be important to the quantitative accuracy. The strategy of integrating multiple computational methods to cross-validate each other for complex interfaces is applicable to many problems that involve both inorganic/metallic and organic/biomolecular components, such as functionalized nanoparticles. 

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2. NMR and computational studies of ammonium ion binding to dibenzo-18-crown-6

   Shope B, Magers DB ( July 2022 , Structural chemistry)

   Dibenzo-18-crown-6 (DB18C6) is a single-crown ether that can act as a host for a guest ion. In an effort to illuminate the relationships among structure, dynamics, and thermodynamics of ligand binding in a simple model for understanding the affinity and specificity of ligand interactions, nuclear magnetic resonance (NMR) experiments and density functional theory (DFT) were used to study the interaction of DB18C6 with ammonium ion. 1H-NMR was used to follow the titration of DB18C6 with ammonium chloride in deuterated methanol, a solvent chosen for its amphipathic character. Ammonium ion binds strongly to DB18C6 with a dissociation equilibrium constant at least as low as ~ 10 - 6 M. DFT calculations were used to identify optimized conformations of bound and free DB18C6 and to estimate its binding energy with ammonium ion in implicit solvent. An approach is described that accounts for geometry relaxation in addition to solvation correction and basis set superposition error; to our knowledge, this is the first such report that includes the energy difference from optimizing species geometry. The lowest-energy conformer of free DB18C6 in implicit methanol acquires an open, W-shaped structure that is also the lowest-energy conformer found for the DB18C6-ammonium ion complex. These results form a foundation for further studies of this system by molecular dynamics simulations. 

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3. The effect of solvent on determining highest occupied molecular orbital energies of semiconducting organic molecules: Insight from a combined computational approach

   https://doi.org/10.1002/jcc.27065  

   Kramer, Aaron ; Pachter, Ruth ; Hsu, Julia W. P. ; Vandenberghe, William G. ( January 2023 , Journal of Computational Chemistry)

   Although cyclic voltammetry (CV) measurements in solution have been widely used to determine the highest occupied molecular orbital energy (E_HOMO) of semiconducting organic molecules, an understanding of the experimentally observed discrepancies due to the solvent used is lacking. To explain these differences, we investigate the solvent effects onE_HOMOby combining density functional theory and molecular dynamics calculations for four donor molecules with a common backbone moiety. We compare the experimentalE_HOMOvalues to the calculated values obtained from either implicit or first solvation shell theories. We find that the first solvation shell method can capture theE_HOMOvariation arising from the functional groups in solution, unlike the implicit method. We further applied the first solvation shell method to other semiconducting organic molecules measured in solutions for different solvents. We find that theE_HOMOobtained using an implicit method is insensitive to solvent choice. The first solvation shell, however, producesE_HOMOvalues that are sensitive to solvent choices and agrees with published experimental results. The solvent sensitivity arises from a hierarchy of three effects: (1) the solute electronic state within a surrounding dielectric continuum, (2) ambient temperature or solvent atoms changing the solute geometry, and (3) electronic interactions between the solute and solvents. The implicit method, on the other hand, only captures the effect of a dielectric environment. Our findings suggest thatE_HOMOobtained by CV measurements should account for the influence of solvent when the results are reported, interpreted, or compared to other molecules.

    

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4. CHARMM‐GUI 10 years for biomolecular modeling and simulation

   https://doi.org/10.1002/jcc.24660  

   Jo, Sunhwan ; Cheng, Xi ; Lee, Jumin ; Kim, Seonghoon ; Park, Sang‐Jun ; Patel, Dhilon S. ; Beaven, Andrew H. ; Lee, Kyu Il ; Rui, Huan ; Park, Soohyung ; et al ( November 2016 , Journal of Computational Chemistry)

   CHARMM‐GUI,http://www.charmm-gui.org, is a web‐based graphical user interface that prepares complex biomolecular systems for molecular simulations. CHARMM‐GUI creates input files for a number of programs including CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Since its original development in 2006, CHARMM‐GUI has been widely adopted for various purposes and now contains a number of different modules designed to set up a broad range of simulations: (1)PDB Reader & Manipulator,Glycan Reader, andLigand Reader & Modelerfor reading and modifying molecules; (2)Quick MD Simulator,Membrane Builder,Nanodisc Builder,HMMM Builder,Monolayer Builder,Micelle Builder, andHex Phase Builderfor building all‐atom simulation systems in various environments; (3)PACE CG BuilderandMartini Makerfor building coarse‐grained simulation systems; (4)DEER FacilitatorandMDFF/xMDFF Utilizerfor experimentally guided simulations; (5)Implicit Solvent Modeler,PBEQ‐Solver, andGCMC/BD Ion Simulatorfor implicit solvent related calculations; (6)Ligand Binderfor ligand solvation and binding free energy simulations; and (7)Drude Prepperfor preparation of simulations with the CHARMM Drude polarizable force field. Recently, new modules have been integrated into CHARMM‐GUI, such asGlycolipid Modelerfor generation of various glycolipid structures, andLPS Modelerfor generation of lipopolysaccharide structures from various Gram‐negative bacteria. These new features together with existing modules are expected to facilitate advanced molecular modeling and simulation thereby leading to an improved understanding of the structure and dynamics of complex biomolecular systems. Here, we briefly review these capabilities and discuss potential future directions in the CHARMM‐GUI development project. © 2016 Wiley Periodicals, Inc.

    

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5. The influence of a solvent environment on direct non-covalent interactions between two molecules: A symmetry-adapted perturbation theory study of polarization tuning of π – π interactions by water

   https://doi.org/10.1063/5.0087302  

   Sirianni, Dominic A. ; Zhu, Xiao ; Sitkoff, Doree F. ; Cheney, Daniel L. ; Sherrill, C. David ( May 2022 , The Journal of Chemical Physics)

   High-level quantum chemical computations have provided significant insight into the fundamental physical nature of non-covalent interactions. These studies have focused primarily on gas-phase computations of small van der Waals dimers; however, these interactions frequently take place in complex chemical environments, such as proteins, solutions, or solids. To better understand how the chemical environment affects non-covalent interactions, we have undertaken a quantum chemical study of π– π interactions in an aqueous solution, as exemplified by T-shaped benzene dimers surrounded by 28 or 50 explicit water molecules. We report interaction energies (IEs) using second-order Møller–Plesset perturbation theory, and we apply the intramolecular and functional-group partitioning extensions of symmetry-adapted perturbation theory (ISAPT and F-SAPT, respectively) to analyze how the solvent molecules tune the π– π interactions of the solute. For complexes containing neutral monomers, even 50 explicit waters (constituting a first and partial second solvation shell) change total SAPT IEs between the two solute molecules by only tenths of a kcal mol −1 , while significant changes of up to 3 kcal mol −1 of the electrostatic component are seen for the cationic pyridinium–benzene dimer. This difference between charged and neutral solutes is attributed to large non-additive three-body interactions within solvated ion-containing complexes. Overall, except for charged solutes, our quantum computations indicate that nearby solvent molecules cause very little “tuning” of the direct solute–solute interactions. This indicates that differences in binding energies between the gas phase and solution phase are primarily indirect effects of the competition between solute–solute and solute–solvent interactions. 

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