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Article ; Online: Adsorption of constitutional isomers of cyclic monoterpenes on hydroxylated silica surfaces.

Huang, Liubin / Frank, Elianna S / Riahi, Saleh / Tobias, Douglas J / Grassian, Vicki H

2021 Volume 154, Issue 12, Page(s) 124703

Abstract: We present a study of four monoterpene isomers (limonene, γ-terpinene, terpinolene, and α-pinene) that are prevalent in indoor environments and their interaction with the hydroxylated ... ...

Abstract	We present a study of four monoterpene isomers (limonene, γ-terpinene, terpinolene, and α-pinene) that are prevalent in indoor environments and their interaction with the hydroxylated SiO
Language	English
Publishing date	2021-04-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0042467
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Article ; Online: Heterogeneous Interactions of Prevalent Indoor Oxygenated Organic Compounds on Hydroxylated SiO

Huang, Liubin / Frank, Elianna S / Shrestha, Mona / Riahi, Saleh / Tobias, Douglas J / Grassian, Vicki H

Environmental science & technology

2021 Volume 55, Issue 10, Page(s) 6623–6630

Abstract: Oxygenated organic compounds (OOCs) are widely found in indoor environments and come from either the direct emissions from indoor activities or the subsequent oxidation of nonoxygenated OCs. Adsorption and partitioning of OCs on surfaces are significant ... ...

Abstract	Oxygenated organic compounds (OOCs) are widely found in indoor environments and come from either the direct emissions from indoor activities or the subsequent oxidation of nonoxygenated OCs. Adsorption and partitioning of OCs on surfaces are significant processes in indoor chemistry, yet these interactions specifically involving OOCs are still poorly understood. In this study, we investigate the interactions of three prevalent indoor OOCs (dihydromyrcenol, α-terpineol, and linalool) on an indoor surface proxy (hydroxylated SiO
MeSH term(s)	Adsorption ; Air Pollutants/analysis ; Air Pollution, Indoor/analysis ; Organic Chemicals ; Silicon Dioxide
Chemical Substances	Air Pollutants ; Organic Chemicals ; Silicon Dioxide (7631-86-9)
Language	English
Publishing date	2021-05-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1520-5851
ISSN (online)	1520-5851
DOI	10.1021/acs.est.1c00067
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A novel Hv1 inhibitor reveals a new mechanism of inhibition of a voltage-sensing domain.

Zhao, Chang / Hong, Liang / Riahi, Saleh / Lim, Victoria T / Tobias, Douglas J / Tombola, Francesco

The Journal of general physiology

2021 Volume 153, Issue 9

Abstract: Voltage-gated sodium, potassium, and calcium channels consist of four voltage-sensing domains (VSDs) that surround a central pore domain and transition from a down state to an up state in response to membrane depolarization. While many types of drugs ... ...

Abstract	Voltage-gated sodium, potassium, and calcium channels consist of four voltage-sensing domains (VSDs) that surround a central pore domain and transition from a down state to an up state in response to membrane depolarization. While many types of drugs bind pore domains, the number of organic molecules known to bind VSDs is limited. The Hv1 voltage-gated proton channel is made of two VSDs and does not contain a pore domain, providing a simplified model for studying how small ligands interact with VSDs. Here, we describe a ligand, named HIF, that interacts with the Hv1 VSD in the up and down states. We find that HIF rapidly inhibits proton conduction in the up state by blocking the open channel, as previously described for 2-guanidinobenzimidazole and its derivatives. HIF, however, interacts with a site slowly accessible in the down state. Functional studies and MD simulations suggest that this interaction traps the compound in a narrow pocket lined with charged residues within the VSD intracellular vestibule, which results in slow recovery from inhibition. Our findings point to a "wrench in gears" mechanism whereby side chains within the binding pocket trap the compound as the teeth of interlocking gears. We propose that the use of screening strategies designed to target binding sites with slow accessibility, similar to the one identified here, could lead to the discovery of new ligands capable of interacting with VSDs of other voltage-gated ion channels in the down state.
MeSH term(s)	Ion Channel Gating ; Ion Channels/metabolism ; Potassium ; Protons
Chemical Substances	Ion Channels ; Protons ; Potassium (RWP5GA015D)
Language	English
Publishing date	2021-07-06
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	3118-5
ISSN	1540-7748 ; 0022-1295
ISSN (online)	1540-7748
ISSN	0022-1295
DOI	10.1085/jgp.202012833
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Article ; Online: Surface ID: a geometry-aware system for protein molecular surface comparison.

Riahi, Saleh / Lee, Jae Hyeon / Sorenson, Taylor / Wei, Shuai / Jager, Sven / Olfati-Saber, Reza / Park, Anna / Wendt, Maria / Minoux, Hervé / Qiu, Yu

Bioinformatics (Oxford, England)

2023 Volume 39, Issue 4

Abstract: Motivation: A protein can be represented in several forms, including its 1D sequence, 3D atom coordinates, and molecular surface. A protein surface contains rich structural and chemical features directly related to the protein's function such as its ... ...

Abstract	Motivation: A protein can be represented in several forms, including its 1D sequence, 3D atom coordinates, and molecular surface. A protein surface contains rich structural and chemical features directly related to the protein's function such as its ability to interact with other molecules. While many methods have been developed for comparing the similarity of proteins using the sequence and structural representations, computational methods based on molecular surface representation are limited. Results: Here, we describe "Surface ID," a geometric deep learning system for high-throughput surface comparison based on geometric and chemical features. Surface ID offers a novel grouping and alignment algorithm useful for clustering proteins by function, visualization, and in silico screening of potential binding partners to a target molecule. Our method demonstrates top performance in surface similarity assessment, indicating great potential for protein functional annotation, a major need in protein engineering and therapeutic design. Availability and implementation: Source code for the Surface ID model, trained weights, and inference script are available at https://github.com/Sanofi-Public/LMR-SurfaceID.
MeSH term(s)	Algorithms ; Software ; Membrane Proteins
Chemical Substances	Membrane Proteins
Language	English
Publishing date	2023-04-17
Publishing country	England
Document type	Journal Article
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btad196
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Article ; Online: Impact of Adsorbed Water on the Interaction of Limonene with Hydroxylated SiO

Frank, Elianna S / Fan, Hanyu / Shrestha, Mona / Riahi, Saleh / Tobias, Douglas J / Grassian, Vicki H

The journal of physical chemistry. A

2020 Volume 124, Issue 50, Page(s) 10592–10599

Abstract: The indoor environment is a dynamic one with many variables impacting indoor air quality and indoor air chemistry. These include relative humidity (RH) and the presence of different surfaces. Although it has been suggested that the indoor concentrations ... ...

Abstract	The indoor environment is a dynamic one with many variables impacting indoor air quality and indoor air chemistry. These include relative humidity (RH) and the presence of different surfaces. Although it has been suggested that the indoor concentrations of gas-phase compounds increase at higher relative humidity, because of displacement of these compounds from indoor surfaces, little is known from a molecular perspective about how RH and adsorbed water impact the adsorption of indoor relevant organic compounds such as limonene with indoor relevant surfaces. Herein, we investigate the effects of RH on the adsorption of limonene, a hydrophobic molecule, on hydroxylated SiO
Language	English
Publishing date	2020-12-04
Publishing country	United States
Document type	Journal Article
ISSN	1520-5215
ISSN (online)	1520-5215
DOI	10.1021/acs.jpca.0c08600
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Why can hydrogen sulfide permeate cell membranes?

Riahi, Saleh / Rowley, Christopher N

Journal of the American Chemical Society

2014 Volume 136, Issue 43, Page(s) 15111–15113

Abstract: The high membrane permeability of H2S was studied using polarizable molecular dynamics simulations of a DPPC lipid bilayer. The solubility-diffusion model predicts permeability coefficients of H2S and H2O that are in good agreement with experiment. The ... ...

Abstract	The high membrane permeability of H2S was studied using polarizable molecular dynamics simulations of a DPPC lipid bilayer. The solubility-diffusion model predicts permeability coefficients of H2S and H2O that are in good agreement with experiment. The computed diffusion coefficient profile shows H2S to diffuse at a lower rate than H2O, but the barrier for H2S permeation on the Gibbs energy profile is negligible. The hydrophobicity of H2S allows it to partition into the paraffinic interior of the membrane readily.
MeSH term(s)	1,2-Dipalmitoylphosphatidylcholine/chemistry ; Cell Membrane Permeability ; Hydrogen Sulfide/chemistry ; Hydrogen Sulfide/metabolism ; Lipid Bilayers/chemistry ; Lipid Bilayers/metabolism ; Molecular Dynamics Simulation ; Thermodynamics ; Water/chemistry
Chemical Substances	Lipid Bilayers ; Water (059QF0KO0R) ; 1,2-Dipalmitoylphosphatidylcholine (2644-64-6) ; Hydrogen Sulfide (YY9FVM7NSN)
Language	English
Publishing date	2014-10-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/ja508063s
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Article ; Online: Solvation of hydrogen sulfide in liquid water and at the water-vapor interface using a polarizable force field.

Riahi, Saleh / Rowley, Christopher N

The journal of physical chemistry. B

2014 Volume 118, Issue 5, Page(s) 1373–1380

Abstract: Molecular dynamics (MD) simulations using the Drude polarizable force field are used to study the solution and interfacial properties of hydrogen sulfide (H2S) in water. Pairwise H2O-H2S Lennard-Jones interactions were optimized to the experimental H2S ... ...

Abstract	Molecular dynamics (MD) simulations using the Drude polarizable force field are used to study the solution and interfacial properties of hydrogen sulfide (H2S) in water. Pairwise H2O-H2S Lennard-Jones interactions were optimized to the experimental H2S gas solubility at 298 K. These parameters yield hydration free energies and diffusion coefficients for H2S that are in good agreement with the experiment over 273-323 K and 298-368 K, respectively. H2S is sparingly soluble in water, with a ΔG(hydr)° of -0.5 kcal mol(-1). The free energy perturbation (FEP) calculations and analysis of the radial distribution functions show that H2S has limited hydrogen bonding and electrostatic interactions with the water solvent and generally behaves like a hydrophobic solute. These features were confirmed by ab initio MD simulations. Umbrella sampling simulations were used to calculate the free energy profile of the transition of H2S across the water-vapor interface, which showed that H2S has a sizable surface excess, with a ΔG(surf) of 1.3 kcal mol(-1). This high surface excess is consistent with our calculations of the surface tension, which decreases to 20 dyn cm(-1) under high densities of H2S (g). The dipole moment of H2S increases from its gas phase value of 0.98 to 1.25 D in bulk water as it moves across the interface. Adsorbed H2S tends to be oriented perpendicular to the interface, with the sulfur atom pointing toward the vapor phase.
Language	English
Publishing date	2014-02-06
Publishing country	United States
Document type	Journal Article
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/jp4096198
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The CHARMM-TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics, free energies, and excited state properties.

Riahi, Saleh / Rowley, Christopher N

Journal of computational chemistry

2014 Volume 35, Issue 28, Page(s) 2076–2086

Abstract: The quantum mechanical (QM)/molecular mechanical (MM) interface between Chemistry at HARvard Molecular Mechanics (CHARMM) and TURBOMOLE is described. CHARMM provides an extensive set of simulation algorithms, like molecular dynamics (MD) and free energy ... ...

Abstract	The quantum mechanical (QM)/molecular mechanical (MM) interface between Chemistry at HARvard Molecular Mechanics (CHARMM) and TURBOMOLE is described. CHARMM provides an extensive set of simulation algorithms, like molecular dynamics (MD) and free energy perturbation, and support for mature nonpolarizable and Drude polarizable force fields. TURBOMOLE provides fast QM calculations using density functional theory or wave function methods and excited state properties. CHARMM-TURBOMOLE is well-suited for extended QM/MM MD simulations using first principles methods with large (triple-ζ) basis sets. We demonstrate these capabilities with a QM/MM simulation of Mg(2+) (aq), where the MM outer sphere water molecules are represented using the SWM4-NDP Drude polarizable force field and the ion and inner coordination sphere are represented using QM PBE, PBE0, and MP2 methods. The relative solvation free energies of Mg(2+) and Zn(2+) were calculated using thermodynamic integration. We also demonstrate the features for excited state properties. We calculate the time-averaged solution absorption spectrum of indole, the emission spectrum of the indole 1La excited state, and the electronic circular dichroism spectrum of an oxacepham.
Language	English
Publishing date	2014-10-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	1479181-x
ISSN	1096-987X ; 0192-8651
ISSN (online)	1096-987X
ISSN	0192-8651
DOI	10.1002/jcc.23716
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Article: Why Can Hydrogen Sulfide Permeate Cell Membranes?

Riahi, Saleh / Rowley Christopher N

Journal of the American Chemical Society. 2014 Oct. 29, v. 136, no. 43

2014

Abstract: The high membrane permeability of HâS was studied using polarizable molecular dynamics simulations of a DPPC lipid bilayer. The solubilityâdiffusion model predicts permeability coefficients of HâS and HâO that are in good agreement with ... ...

Abstract	The high membrane permeability of HâS was studied using polarizable molecular dynamics simulations of a DPPC lipid bilayer. The solubilityâdiffusion model predicts permeability coefficients of HâS and HâO that are in good agreement with experiment. The computed diffusion coefficient profile shows HâS to diffuse at a lower rate than HâO, but the barrier for HâS permeation on the Gibbs energy profile is negligible. The hydrophobicity of HâS allows it to partition into the paraffinic interior of the membrane readily.
Keywords	diffusivity ; energy ; hydrogen sulfide ; hydrophobicity ; lipid bilayers ; membrane permeability ; models ; molecular dynamics
Language	English
Dates of publication	2014-1029
Size	p. 15111-15113.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021%2Fja508063s
Database	NAL-Catalogue (AGRICOLA)

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Article: Solvation of Hydrogen Sulfide in Liquid Water and at the WaterâVapor Interface Using a Polarizable Force Field

Riahi, Saleh / Rowley Christopher N

Journal of physical chemistry. 2014 Feb. 06, v. 118, no. 5

2014

Abstract: Molecular dynamics (MD) simulations using the Drude polarizable force field are used to study the solution and interfacial properties of hydrogen sulfide (HâS) in water. Pairwise HâOâHâS Lennard-Jones interactions were optimized to the ... ...

Abstract	Molecular dynamics (MD) simulations using the Drude polarizable force field are used to study the solution and interfacial properties of hydrogen sulfide (HâS) in water. Pairwise HâOâHâS Lennard-Jones interactions were optimized to the experimental HâS gas solubility at 298 K. These parameters yield hydration free energies and diffusion coefficients for HâS that are in good agreement with the experiment over 273â323 K and 298â368 K, respectively. HâS is sparingly soluble in water, with a ÎGâydáµ£Â° of â0.5 kcal molâÂ¹. The free energy perturbation (FEP) calculations and analysis of the radial distribution functions show that HâS has limited hydrogen bonding and electrostatic interactions with the water solvent and generally behaves like a hydrophobic solute. These features were confirmed by ab initio MD simulations. Umbrella sampling simulations were used to calculate the free energy profile of the transition of HâS across the waterâvapor interface, which showed that HâS has a sizable surface excess, with a ÎGâáµ¤áµ£f of 1.3 kcal molâÂ¹. This high surface excess is consistent with our calculations of the surface tension, which decreases to 20 dyn cmâÂ¹ under high densities of HâS (g). The dipole moment of HâS increases from its gas phase value of 0.98 to 1.25 D in bulk water as it moves across the interface. Adsorbed HâS tends to be oriented perpendicular to the interface, with the sulfur atom pointing toward the vapor phase.
Keywords	Gibbs free energy ; diffusivity ; electrostatic interactions ; hydrogen bonding ; hydrogen sulfide ; hydrophobicity ; molecular dynamics ; solubility ; solutes ; solvents ; sulfur ; surface tension ; water vapor
Language	English
Dates of publication	2014-0206
Size	p. 1373-1380.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5207
DOI	10.1021%2Fjp4096198
Database	NAL-Catalogue (AGRICOLA)

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