Ramachandran Gnanasekaran | VIT University (original) (raw)

Papers by Ramachandran Gnanasekaran

Research paper thumbnail of Conformational Stability and Vibrational Relaxation as a Function of Halogen Substitution in Benzene sulfonamides: A Theoretical Study

ChemistrySelect, Jun 3, 2024

Research paper thumbnail of Controlled, Sequential approach to Synthesize Stereogenic Methanesvia in situGenerated Reactive Intermediates

ChemistrySelect, Aug 1, 2016

Research paper thumbnail of Ions as Probes of Sub-PS Water Network Dynamics

mss, Jun 1, 2010

ABSTRACT We present THz measurements of salt solutions which shed new light on the controversy of... more ABSTRACT We present THz measurements of salt solutions which shed new light on the controversy of salts as kosmotropes (structure makers) or chaotropes (structure breakers). We performed concentration dependent narrow-band THz-absorption spectroscopy on fifteen alkali-halide salt solutions around 85 cm-1 (2.5 THz) and wide-band (30-300 cm-1) THz Fourier transform measurements on six alkali halide salt solutions. All solutions show an increased THz-absorption compared to pure water with a linear concentration dependence. Our comprehensive data set is well-described by a model including damped harmonic oscillations (rattling modes) of both anions and cations within the water network. This model well-predicts key features of THz spectra for a variety of salt solutions. Complementary molecular dynamics simulations using the TIP3P water model support experiments and show that the fast sub-ps ionic motions and their surroundings are almost decoupled. These findings provide a complete description of the solute-induced changes in the THz solvation dynamics for the investigated salts and suggests a treatment of the ions as simple defects in an H-bond network. Our results show that THz spectroscopy is a powerful experimental tool to establish a new insights on contributions to the structuring of water by anions and cations.

Research paper thumbnail of The dielectric response to photoexcitation of GFP: A molecular dynamics study

Chemical Physics Letters, Mar 1, 2013

ABSTRACT The dielectric response to photoexcitation of the Green Fluorescent Protein (GFP) chromo... more ABSTRACT The dielectric response to photoexcitation of the Green Fluorescent Protein (GFP) chromophore and contributions to it from water and GFP are computed by molecular simulations using a force field for the chromophore parametrized by ab initio calculations of ground and excited states. The chromophore is embedded in the β-barrel where it is surrounded by about 10 waters, which are found to play a significant role in slow dielectric relaxation. Dynamics of hydrogen bonds between water and GFP is examined and found to be slower and more heterogeneous for hydrogen bonds inside the β-barrel than in the hydration layer around GFP.

Research paper thumbnail of Understanding the Energetic Components Influencing the Thermodynamic Quantities of Carbonic Anhydrase Protein upon Ligand Binding

ChemistrySelect, Feb 22, 2022

We perform structural analysis and calculate the vibrational energy diffusivities, represented as... more We perform structural analysis and calculate the vibrational energy diffusivities, represented as heat‐communication map, between a carbonic anhydrase II and its binding inhibitor benzosulfonamide, to identify critical residues involved in the secondary and tertiary adaptations surrounding the active site, such as HID95, HIE118, HID93, THR197, and HIE198. Notably, the water molecules surrounding the active sites play an essential part in the energy flow. The stability of the docked ligand is assessed using its structural deviation and free energy calculation. Additionally, density functional theory calculations are used to evaluate specific binding energies, resulting in prominent residues such as THR197, THR198, and HIE118 with high binding potential to the benzosulfonamide ligand.

Research paper thumbnail of Molecular dynamics simulation studies of dielectric response and vibrational energy relaxation in photoactive yellow protein and green fluorescent protein

Bulletin of the American Physical Society, Mar 1, 2012

The first step in the photocycle of many proteins involves conformational change of a chromophore... more The first step in the photocycle of many proteins involves conformational change of a chromophore or a charge transfer reaction following photoexcitation. To explore the response of the protein and solvent environment to photoexcitation of the chromophore in photoactive yellow protein (PYP) and green fluorescent protein (GFP) we carried out molecular dynamics simulations of the dielectric response and vibrational energy relaxation (VER) from the chromophore to the protein and solvent. In PYP the time scale of the protein response, mainly contributed by Tyr42 and Glu46, to photoexcitation appears prominently between 0.1 and 0.3 picoseconds. The frequency-dependent VER rate also reveals dynamic coupling between the chromophore and residues that hydrogen bond to it. Resonances in the VER rate appear at frequencies comparable to the oscillations observed in recent fluorescence decay studies. In GFP, which undergoes excited state proton transfer about 10 ps following photoexcitation that may be assisted by specific chromophore vibrations, both the protein and water molecules inside the β-barrel surrounding the chromophore mediate the dielectric response.

Research paper thumbnail of Dielectric response and vibrational energy relaxation in photoactive yellow protein: A molecular dynamics simulation study

Chemical Physics Letters, Nov 1, 2011

Molecular dynamics simulations of the dielectric response and vibrational energy relaxation (VER)... more Molecular dynamics simulations of the dielectric response and vibrational energy relaxation (VER) from the chromophore to the protein and solvent environment following photoexcitation of photoactive yellow protein are presented. The computed protein ...

Research paper thumbnail of Rattling in the Cage: Ions as Probes of Sub-picosecond Water Network Dynamics

Journal of the American Chemical Society, Nov 24, 2009

We present terahertz (THz) measurements of salt solutions that shed new light on the controversy ... more We present terahertz (THz) measurements of salt solutions that shed new light on the controversy over whether salts act as kosmotropes (structure makers) or chaotropes (structure breakers), which enhance or reduce the solvent order, respectively. We have carried out precise measurements of the concentration-dependent THz absorption coefficient of 15 solvated alkali halide salts around 85 cm(-1) (2.5 THz). In addition, we recorded overview spectra between 30 and 300 cm(-1) using a THz Fourier transform spectrometer for six alkali halides. For all solutions we found a linear increase of THz absorption compared to pure water (THz excess) with increasing solute concentration. These results suggest that the ions may be treated as simple defects in an H-bond network. They therefore cannot be characterized as either kosmotropes or chaotropes. Below 200 cm(-1), the observed THz excess of all salts can be described by a linear superposition of the water absorption and an additional absorption that is attributed to a rattling motion of the ions within the water network. By providing a comprehensive set of data for different salt solutions, we find that the solutions can all be very well described by a model that includes damped harmonic oscillations of the anions and cations within the water network. We find this model predicts the main features of THz spectra for a variety of salt solutions. The assumption of the existence of these ion rattling motions on sub-picosecond time scales is supported by THz Fourier transform spectroscopy of six alkali halides. Above 200 cm(-1) the excess is interpreted in terms of a change in the wing of the water network librational mode. Accompanying molecular dynamics simulations using the TIP3P water model support our conclusion and show that the fast sub-picosecond motions of the ions and their surroundings are almost decoupled. These findings provide a complete description of the solute-induced changes in the THz solvation dynamics for the investigated salts. Our results show that THz spectroscopy is a powerful experimental tool to establish a new view on the contributions of anions and cations to the structuring of water.

Research paper thumbnail of The first HyDRA challenge for computational vibrational spectroscopy

Vibrational spectroscopy in supersonic jet expansions is a powerful tool to assess molecular aggr... more Vibrational spectroscopy in supersonic jet expansions is a powerful tool to assess molecular aggregates in close to ideal conditions for the benchmarking of quantum chemical approaches. The low temperatures achieved as well as the absence of environment effects allow for a direct comparison between computed and experimental spectra. This provides potential benchmarking data which can be revisited to hone different computational techniques, and it allows for the critical analysis of procedures under the setting of a blind challenge. In the latter case, the final result is unknown to modellers, providing an unbiased testing opportunity for quantum chemical models. In this work, we present the spectroscopic and computational results for the first HyDRA blind challenge. The latter deals with the prediction of water donor stretching vibrations in monohydrates of organic molecules. This edition features a test set of 10 systems. Experimental water donor OH vibrational wavenumbers for the ...

Research paper thumbnail of CCDC 1558176: Experimental Crystal Structure Determination

An entry from the Cambridge Structural Database, the world's repository for small molecule cr... more An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

Research paper thumbnail of Computational study to understand the energy transfer pathways within amicyanin

Journal of molecular graphics & modelling, 2017

Vibrational energy diffusivities between the residues present in Amicyanin copper protein are cal... more Vibrational energy diffusivities between the residues present in Amicyanin copper protein are calculated and presented in form of communication map. From those results energy flow pathways from the copper metal ion to the inter protein residue Glu31 are identified. Our finding suggests many different pathways are possible and copper metal ion in oxidized and reduced state switches the pathways. Our finding also suggests the cooperative nature of surrounding residues and water molecules towards selecting the pathways. The major transport channels in the oxidised state are, Cu---> MET28---> LYS29---> TYR30---> GLU31 and Cu---> MET98---> TYR30--- > GLU31. And in the reduced state Cu---> CYS9---> TYR30---> GLU31 and Cu---> MET28---> LYS2---> TYR30---> GLU31. We studied further the interaction energies between the copper ion and neighbouring residues using B3LYP/QZVP method. Both the methods complement each other in predicting the energy flow pat...

Research paper thumbnail of A comparison of ab initio quantum-mechanical and experimental D0 binding energies of eleven H-bonded and eleven dispersion-bound complexes

Physical chemistry chemical physics : PCCP, Jan 22, 2015

Dissociation energies (D0) of 11 H-bonded and 11 dispersion-bound complexes were calculated as th... more Dissociation energies (D0) of 11 H-bonded and 11 dispersion-bound complexes were calculated as the sum of interaction energies and the change of zero-point vibrational energies (ΔZPVE). The structures of H-bonded complexes were optimized at the RI-MP2/cc-pVTZ level, at which deformation and harmonic ΔZPVE energies were also calculated. The structures of dispersion-bound complexes were optimized at the DFT-D3 level, and harmonic ΔZPVE energies were determined at the same level as well. For comparison, CCSD(T)/CBS D0 energies were also evaluated for both types of complexes. The CCSD(T)/CBS interaction energy was constructed as the sum of MP2/CBS interaction energy, extrapolated from aug-cc-pVTZ and aug-cc-pVQZ basis sets, and ΔCCSD(T) correction, determined with the aug-cc-pVDZ basis set. The ΔZPVE energies were determined for all complexes at the harmonic level and for selected complexes, these energies were also calculated using second-order vibration perturbation (VPT2) theory. For...

Research paper thumbnail of Analysis of Water and Hydrogen Bond Dynamics at the Surface of an Antifreeze Protein

Journal of Atomic, Molecular, and Optical Physics, 2012

We examine dynamics of water molecules and hydrogen bonds at the water-protein interface of the w... more We examine dynamics of water molecules and hydrogen bonds at the water-protein interface of the wild-type antifreeze protein from spruce budworm Choristoneura fumiferana and a mutant that is not antifreeze active by all-atom molecular dynamics simulations. Water dynamics in the hydration layer around the protein is analyzed by calculation of velocity autocorrelation functions and their power spectra, and hydrogen bond time correlation functions are calculated for hydrogen bonds between water molecules and the protein. Both water and hydrogen bond dynamics from subpicosecond to hundred picosecond time scales are sensitive to location on the protein surface and appear correlated with protein function. In particular, hydrogen bond lifetimes are longest for water molecules hydrogen bonded to the ice-binding plane of the wild type, whereas hydrogen bond lifetimes between water and protein atoms on all three planes are similar for the mutant.

Research paper thumbnail of Normal modes and the Duschinsky mixing of the ground- and excited-state vibrations of the green fluorescent protein chromophore

Chemical Physics Letters, 2013

ABSTRACT

Research paper thumbnail of Understanding the Energetic Components Influencing the Thermodynamic Quantities of Carbonic Anhydrase Protein upon Ligand Binding

Research paper thumbnail of Communication Maps: Exploring Energy Transport through Proteins and Water

Israel Journal of Chemistry, 2014

Research paper thumbnail of The dielectric response to photoexcitation of GFP: A molecular dynamics study

Chemical Physics Letters, 2013

ABSTRACT The dielectric response to photoexcitation of the Green Fluorescent Protein (GFP) chromo... more ABSTRACT The dielectric response to photoexcitation of the Green Fluorescent Protein (GFP) chromophore and contributions to it from water and GFP are computed by molecular simulations using a force field for the chromophore parametrized by ab initio calculations of ground and excited states. The chromophore is embedded in the β-barrel where it is surrounded by about 10 waters, which are found to play a significant role in slow dielectric relaxation. Dynamics of hydrogen bonds between water and GFP is examined and found to be slower and more heterogeneous for hydrogen bonds inside the β-barrel than in the hydration layer around GFP.

Research paper thumbnail of Understanding the Factors Which Affect the Thermodyanamic Quantities of a Protein Upon Ligand Binding

SSRN Electronic Journal, 2021

Vibrational energy diffusivities were calculated between the binding inhibitor benzosulfonamide (... more Vibrational energy diffusivities were calculated between the binding inhibitor benzosulfonamide (ligand) and the rest of the residues of the carbonic anhydrase II complex system. With those results, communication map was prepared. This map enables us to identify the residues like HID95, HIE118, HID93, THR197, HIE198, etc., involved in secondary and tertiary changes surrounding the active site. It is also found that the water molecules surrounding the active sites exchange energies and do play a significant role. From the DFT interaction energy studies, It is found that the residues like THR197, THR198 and HIE118 have high binding capability with the ligand.

Research paper thumbnail of Ions as Probes of Sub-PS Water Network Dynamics

Author Institution: Department of Physical Chemistry II, Ruhr-University Bochum, D-44780 Bochum, ... more Author Institution: Department of Physical Chemistry II, Ruhr-University Bochum, D-44780 Bochum, Germany; Department of Chemistry, Koc University, 34450 Istanbul, Turkey; Department of Chemistry, University of Nevada, 89557 Reno, Nevada, USA

Research paper thumbnail of InCl3 -Assisted Eco-Friendly Approach for N-Fused 1,4-Dihydropyridine Scaffolds via Ring Opening Michael Addition of Cyclic Nitroketene and Iminocoumarin: Synthesis and DFT Studies

Research paper thumbnail of Conformational Stability and Vibrational Relaxation as a Function of Halogen Substitution in Benzene sulfonamides: A Theoretical Study

ChemistrySelect, Jun 3, 2024

Research paper thumbnail of Controlled, Sequential approach to Synthesize Stereogenic Methanesvia in situGenerated Reactive Intermediates

ChemistrySelect, Aug 1, 2016

Research paper thumbnail of Ions as Probes of Sub-PS Water Network Dynamics

mss, Jun 1, 2010

ABSTRACT We present THz measurements of salt solutions which shed new light on the controversy of... more ABSTRACT We present THz measurements of salt solutions which shed new light on the controversy of salts as kosmotropes (structure makers) or chaotropes (structure breakers). We performed concentration dependent narrow-band THz-absorption spectroscopy on fifteen alkali-halide salt solutions around 85 cm-1 (2.5 THz) and wide-band (30-300 cm-1) THz Fourier transform measurements on six alkali halide salt solutions. All solutions show an increased THz-absorption compared to pure water with a linear concentration dependence. Our comprehensive data set is well-described by a model including damped harmonic oscillations (rattling modes) of both anions and cations within the water network. This model well-predicts key features of THz spectra for a variety of salt solutions. Complementary molecular dynamics simulations using the TIP3P water model support experiments and show that the fast sub-ps ionic motions and their surroundings are almost decoupled. These findings provide a complete description of the solute-induced changes in the THz solvation dynamics for the investigated salts and suggests a treatment of the ions as simple defects in an H-bond network. Our results show that THz spectroscopy is a powerful experimental tool to establish a new insights on contributions to the structuring of water by anions and cations.

Research paper thumbnail of The dielectric response to photoexcitation of GFP: A molecular dynamics study

Chemical Physics Letters, Mar 1, 2013

ABSTRACT The dielectric response to photoexcitation of the Green Fluorescent Protein (GFP) chromo... more ABSTRACT The dielectric response to photoexcitation of the Green Fluorescent Protein (GFP) chromophore and contributions to it from water and GFP are computed by molecular simulations using a force field for the chromophore parametrized by ab initio calculations of ground and excited states. The chromophore is embedded in the β-barrel where it is surrounded by about 10 waters, which are found to play a significant role in slow dielectric relaxation. Dynamics of hydrogen bonds between water and GFP is examined and found to be slower and more heterogeneous for hydrogen bonds inside the β-barrel than in the hydration layer around GFP.

Research paper thumbnail of Understanding the Energetic Components Influencing the Thermodynamic Quantities of Carbonic Anhydrase Protein upon Ligand Binding

ChemistrySelect, Feb 22, 2022

We perform structural analysis and calculate the vibrational energy diffusivities, represented as... more We perform structural analysis and calculate the vibrational energy diffusivities, represented as heat‐communication map, between a carbonic anhydrase II and its binding inhibitor benzosulfonamide, to identify critical residues involved in the secondary and tertiary adaptations surrounding the active site, such as HID95, HIE118, HID93, THR197, and HIE198. Notably, the water molecules surrounding the active sites play an essential part in the energy flow. The stability of the docked ligand is assessed using its structural deviation and free energy calculation. Additionally, density functional theory calculations are used to evaluate specific binding energies, resulting in prominent residues such as THR197, THR198, and HIE118 with high binding potential to the benzosulfonamide ligand.

Research paper thumbnail of Molecular dynamics simulation studies of dielectric response and vibrational energy relaxation in photoactive yellow protein and green fluorescent protein

Bulletin of the American Physical Society, Mar 1, 2012

The first step in the photocycle of many proteins involves conformational change of a chromophore... more The first step in the photocycle of many proteins involves conformational change of a chromophore or a charge transfer reaction following photoexcitation. To explore the response of the protein and solvent environment to photoexcitation of the chromophore in photoactive yellow protein (PYP) and green fluorescent protein (GFP) we carried out molecular dynamics simulations of the dielectric response and vibrational energy relaxation (VER) from the chromophore to the protein and solvent. In PYP the time scale of the protein response, mainly contributed by Tyr42 and Glu46, to photoexcitation appears prominently between 0.1 and 0.3 picoseconds. The frequency-dependent VER rate also reveals dynamic coupling between the chromophore and residues that hydrogen bond to it. Resonances in the VER rate appear at frequencies comparable to the oscillations observed in recent fluorescence decay studies. In GFP, which undergoes excited state proton transfer about 10 ps following photoexcitation that may be assisted by specific chromophore vibrations, both the protein and water molecules inside the β-barrel surrounding the chromophore mediate the dielectric response.

Research paper thumbnail of Dielectric response and vibrational energy relaxation in photoactive yellow protein: A molecular dynamics simulation study

Chemical Physics Letters, Nov 1, 2011

Molecular dynamics simulations of the dielectric response and vibrational energy relaxation (VER)... more Molecular dynamics simulations of the dielectric response and vibrational energy relaxation (VER) from the chromophore to the protein and solvent environment following photoexcitation of photoactive yellow protein are presented. The computed protein ...

Research paper thumbnail of Rattling in the Cage: Ions as Probes of Sub-picosecond Water Network Dynamics

Journal of the American Chemical Society, Nov 24, 2009

We present terahertz (THz) measurements of salt solutions that shed new light on the controversy ... more We present terahertz (THz) measurements of salt solutions that shed new light on the controversy over whether salts act as kosmotropes (structure makers) or chaotropes (structure breakers), which enhance or reduce the solvent order, respectively. We have carried out precise measurements of the concentration-dependent THz absorption coefficient of 15 solvated alkali halide salts around 85 cm(-1) (2.5 THz). In addition, we recorded overview spectra between 30 and 300 cm(-1) using a THz Fourier transform spectrometer for six alkali halides. For all solutions we found a linear increase of THz absorption compared to pure water (THz excess) with increasing solute concentration. These results suggest that the ions may be treated as simple defects in an H-bond network. They therefore cannot be characterized as either kosmotropes or chaotropes. Below 200 cm(-1), the observed THz excess of all salts can be described by a linear superposition of the water absorption and an additional absorption that is attributed to a rattling motion of the ions within the water network. By providing a comprehensive set of data for different salt solutions, we find that the solutions can all be very well described by a model that includes damped harmonic oscillations of the anions and cations within the water network. We find this model predicts the main features of THz spectra for a variety of salt solutions. The assumption of the existence of these ion rattling motions on sub-picosecond time scales is supported by THz Fourier transform spectroscopy of six alkali halides. Above 200 cm(-1) the excess is interpreted in terms of a change in the wing of the water network librational mode. Accompanying molecular dynamics simulations using the TIP3P water model support our conclusion and show that the fast sub-picosecond motions of the ions and their surroundings are almost decoupled. These findings provide a complete description of the solute-induced changes in the THz solvation dynamics for the investigated salts. Our results show that THz spectroscopy is a powerful experimental tool to establish a new view on the contributions of anions and cations to the structuring of water.

Research paper thumbnail of The first HyDRA challenge for computational vibrational spectroscopy

Vibrational spectroscopy in supersonic jet expansions is a powerful tool to assess molecular aggr... more Vibrational spectroscopy in supersonic jet expansions is a powerful tool to assess molecular aggregates in close to ideal conditions for the benchmarking of quantum chemical approaches. The low temperatures achieved as well as the absence of environment effects allow for a direct comparison between computed and experimental spectra. This provides potential benchmarking data which can be revisited to hone different computational techniques, and it allows for the critical analysis of procedures under the setting of a blind challenge. In the latter case, the final result is unknown to modellers, providing an unbiased testing opportunity for quantum chemical models. In this work, we present the spectroscopic and computational results for the first HyDRA blind challenge. The latter deals with the prediction of water donor stretching vibrations in monohydrates of organic molecules. This edition features a test set of 10 systems. Experimental water donor OH vibrational wavenumbers for the ...

Research paper thumbnail of CCDC 1558176: Experimental Crystal Structure Determination

An entry from the Cambridge Structural Database, the world's repository for small molecule cr... more An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

Research paper thumbnail of Computational study to understand the energy transfer pathways within amicyanin

Journal of molecular graphics & modelling, 2017

Vibrational energy diffusivities between the residues present in Amicyanin copper protein are cal... more Vibrational energy diffusivities between the residues present in Amicyanin copper protein are calculated and presented in form of communication map. From those results energy flow pathways from the copper metal ion to the inter protein residue Glu31 are identified. Our finding suggests many different pathways are possible and copper metal ion in oxidized and reduced state switches the pathways. Our finding also suggests the cooperative nature of surrounding residues and water molecules towards selecting the pathways. The major transport channels in the oxidised state are, Cu---> MET28---> LYS29---> TYR30---> GLU31 and Cu---> MET98---> TYR30--- > GLU31. And in the reduced state Cu---> CYS9---> TYR30---> GLU31 and Cu---> MET28---> LYS2---> TYR30---> GLU31. We studied further the interaction energies between the copper ion and neighbouring residues using B3LYP/QZVP method. Both the methods complement each other in predicting the energy flow pat...

Research paper thumbnail of A comparison of ab initio quantum-mechanical and experimental D0 binding energies of eleven H-bonded and eleven dispersion-bound complexes

Physical chemistry chemical physics : PCCP, Jan 22, 2015

Dissociation energies (D0) of 11 H-bonded and 11 dispersion-bound complexes were calculated as th... more Dissociation energies (D0) of 11 H-bonded and 11 dispersion-bound complexes were calculated as the sum of interaction energies and the change of zero-point vibrational energies (ΔZPVE). The structures of H-bonded complexes were optimized at the RI-MP2/cc-pVTZ level, at which deformation and harmonic ΔZPVE energies were also calculated. The structures of dispersion-bound complexes were optimized at the DFT-D3 level, and harmonic ΔZPVE energies were determined at the same level as well. For comparison, CCSD(T)/CBS D0 energies were also evaluated for both types of complexes. The CCSD(T)/CBS interaction energy was constructed as the sum of MP2/CBS interaction energy, extrapolated from aug-cc-pVTZ and aug-cc-pVQZ basis sets, and ΔCCSD(T) correction, determined with the aug-cc-pVDZ basis set. The ΔZPVE energies were determined for all complexes at the harmonic level and for selected complexes, these energies were also calculated using second-order vibration perturbation (VPT2) theory. For...

Research paper thumbnail of Analysis of Water and Hydrogen Bond Dynamics at the Surface of an Antifreeze Protein

Journal of Atomic, Molecular, and Optical Physics, 2012

We examine dynamics of water molecules and hydrogen bonds at the water-protein interface of the w... more We examine dynamics of water molecules and hydrogen bonds at the water-protein interface of the wild-type antifreeze protein from spruce budworm Choristoneura fumiferana and a mutant that is not antifreeze active by all-atom molecular dynamics simulations. Water dynamics in the hydration layer around the protein is analyzed by calculation of velocity autocorrelation functions and their power spectra, and hydrogen bond time correlation functions are calculated for hydrogen bonds between water molecules and the protein. Both water and hydrogen bond dynamics from subpicosecond to hundred picosecond time scales are sensitive to location on the protein surface and appear correlated with protein function. In particular, hydrogen bond lifetimes are longest for water molecules hydrogen bonded to the ice-binding plane of the wild type, whereas hydrogen bond lifetimes between water and protein atoms on all three planes are similar for the mutant.

Research paper thumbnail of Normal modes and the Duschinsky mixing of the ground- and excited-state vibrations of the green fluorescent protein chromophore

Chemical Physics Letters, 2013

ABSTRACT

Research paper thumbnail of Understanding the Energetic Components Influencing the Thermodynamic Quantities of Carbonic Anhydrase Protein upon Ligand Binding

Research paper thumbnail of Communication Maps: Exploring Energy Transport through Proteins and Water

Israel Journal of Chemistry, 2014

Research paper thumbnail of The dielectric response to photoexcitation of GFP: A molecular dynamics study

Chemical Physics Letters, 2013

ABSTRACT The dielectric response to photoexcitation of the Green Fluorescent Protein (GFP) chromo... more ABSTRACT The dielectric response to photoexcitation of the Green Fluorescent Protein (GFP) chromophore and contributions to it from water and GFP are computed by molecular simulations using a force field for the chromophore parametrized by ab initio calculations of ground and excited states. The chromophore is embedded in the β-barrel where it is surrounded by about 10 waters, which are found to play a significant role in slow dielectric relaxation. Dynamics of hydrogen bonds between water and GFP is examined and found to be slower and more heterogeneous for hydrogen bonds inside the β-barrel than in the hydration layer around GFP.

Research paper thumbnail of Understanding the Factors Which Affect the Thermodyanamic Quantities of a Protein Upon Ligand Binding

SSRN Electronic Journal, 2021

Vibrational energy diffusivities were calculated between the binding inhibitor benzosulfonamide (... more Vibrational energy diffusivities were calculated between the binding inhibitor benzosulfonamide (ligand) and the rest of the residues of the carbonic anhydrase II complex system. With those results, communication map was prepared. This map enables us to identify the residues like HID95, HIE118, HID93, THR197, HIE198, etc., involved in secondary and tertiary changes surrounding the active site. It is also found that the water molecules surrounding the active sites exchange energies and do play a significant role. From the DFT interaction energy studies, It is found that the residues like THR197, THR198 and HIE118 have high binding capability with the ligand.

Research paper thumbnail of Ions as Probes of Sub-PS Water Network Dynamics

Author Institution: Department of Physical Chemistry II, Ruhr-University Bochum, D-44780 Bochum, ... more Author Institution: Department of Physical Chemistry II, Ruhr-University Bochum, D-44780 Bochum, Germany; Department of Chemistry, Koc University, 34450 Istanbul, Turkey; Department of Chemistry, University of Nevada, 89557 Reno, Nevada, USA

Research paper thumbnail of InCl3 -Assisted Eco-Friendly Approach for N-Fused 1,4-Dihydropyridine Scaffolds via Ring Opening Michael Addition of Cyclic Nitroketene and Iminocoumarin: Synthesis and DFT Studies