Aatto Laaksonen | Stockholm University (original) (raw)
Papers by Aatto Laaksonen
bioRxiv (Cold Spring Harbor Laboratory), Apr 10, 2020
A new betacoronavirus named SARS-CoV-2 has emerged as a new threat to global health and economy. ... more A new betacoronavirus named SARS-CoV-2 has emerged as a new threat to global health and economy. A promising target for both diagnosis and therapeutics treatments of the new disease named COVID-19 is the coronavirus (CoV) spike (S) glycoprotein. By constant-pH Monte Carlo simulations and the PROCEEDpKa method, we have mapped the electrostatic epitopes for four monoclonal antibodies and the angiotensin-converting enzyme 2 (ACE2) on both SARS-CoV-1 and the new SARS-CoV-2 S receptor binding domain (RBD) proteins. We also calculated free energy of interactions and shown that the S RBD proteins from both SARS viruses binds to ACE2 with similar affinities. However, the affinity between the S RBD protein from the new SARS-CoV-2 and ACE2 is higher than for any studied antibody previously found complexed with SARS-CoV-1. Based on physical chemical analysis and free energies estimates, we can shed some light on the involved molecular recognition processes, their clinical aspects, the implications for drug developments, and suggest structural modifications on the CR3022 antibody that would improve its binding affinities for SARS-CoV-2 and contribute to address the ongoing international health crisis.
The Royal Society of Chemistry eBooks, Oct 1, 1985
Chemischer Informationsdienst, Jun 11, 1985
The Royal Society of Chemistry eBooks, Nov 1, 1986
Lecture Notes in Computer Science
Molecular modelling/simulation techniques have in three decades evolved to a powerful tool and sc... more Molecular modelling/simulation techniques have in three decades evolved to a powerful tool and scientific discipline of its own now used in many areas of physics, chemistry, and biology with applications from materials science to biotechnology. These techniques have naturally become applicable for more and complex systems largely thanks to the rapid development in computer technology. However in recent years a variety of new advanced and innovative techniques have been presented to push the time and length scales further towards nano/meso scale applications and soft matter. More efficient computational schemes have been proposed to treat long-ranged interactions, parallel algorithms are proposed to run on high-end fast computers, pc-clusters and heterogeneous GRID environment. Ab initio and hybrid QM/MM methods are becoming routine and developed to treat large systems. Multi-scale modelling schemes across several physical descriptions of matter from quantum mechanical systems with nuclei and electrons all the way to nano/meso/micro/macro levels are maturing rapidly. This minisymposium will highlight several of these latest techniques.
Lecture Notes in Computational Science and Engineering, 2006
The use of general descriptive names, registered names, trademarks, etc. in this publication does... more The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use.
Lecture Notes in Computer Science, 2007
In Memoriam and Dedication Every day we are reminded of the perishables of life and that our indi... more In Memoriam and Dedication Every day we are reminded of the perishables of life and that our individual lives are only a gift for a finite time. Unfortunately, at PARA 2006 this was no exception.
Nuclear Magnetic Resonance
Page 133. 4 Theoretical Aspects of Spin-Spin Couplings BY H. FUKUI AND T. BABA 1 Introduction The... more Page 133. 4 Theoretical Aspects of Spin-Spin Couplings BY H. FUKUI AND T. BABA 1 Introduction The indirect nuclear spin-spin coupling between nuclei is of fundamental importance in nuclear magnetic resonance (NMR) spectroscopy. ...
Chemischer Informationsdienst, 1982
ChemInform Abstract Berechnungen der effektiven Abstände zwischen den Liganden-Kernen und ungepaa... more ChemInform Abstract Berechnungen der effektiven Abstände zwischen den Liganden-Kernen und ungepaarten Elektronenspins des Grundzustandes der paramagnetischen Komplexe (I) und der Hyperfeinkopplungskonstanten sowie Untersuchung der Beziehung zwischen "O-Hyperfeinkopplungen und Abweichungen von der Punktdipol-Näherung.
New Trends in Macromolecular and Supramolecular Chemistry for Biological Applications, 2021
In solving mathematical and physical problems we generally think that the problem can be condense... more In solving mathematical and physical problems we generally think that the problem can be condensed to a well-defined equation which then can be solved either analytically or numerically with the provided input data and, if necessary, applying initial and boundary conditions to limit the amount of solutions to something which makes sense and can be accepted as the correct solution. This is the typical practice in "forward" problem solving. Consequently the solution can be considered as the inverse of the problem. Indeed, it is not uncommon in Science and also in everyday life to have the "solution" without knowing what exactly did "cause" it and "how". We take an illustrative example from Forensics with a case where a lethal crime is committed with a dead body (solution), but at the time of arrival to the crime scene the details to start to investigate are scattered all over the place. The investigators have the difficult task to mentally reverse the time to get good enough picture of the crime (problem) to start to trace the criminal and murder weapon (input) and possibly also the motive (cause). In this Chapter we discuss on how solving of the Inverse Problems is entering in Chemistry and focus on our own inverse computer modelling method to create a model (force field) from the results we already have. We explain how this method, called the Inverse Monte Carlo, can also be used for systematic hierarchical multi-scale modelling based on successive coarse-graining from first-principles to meso-scale and even further by super-coarse-graining. We show several applications of using it and also vision future prospects of hierarchical multi-scale modelling.
The 1H NMR chemical shift of water exhibits non-monotonic dependence on the composition of an aqu... more The 1H NMR chemical shift of water exhibits non-monotonic dependence on the composition of an aqueous mixture of 1-butyl-3-methylimidazolium chloride, [C4mim][Cl], ionic liquid (IL). A clear minimum is observed for the 1H NMR chemical shift at a molar fraction of the IL of 0.34. To scrutinize the molecular mechanism behind this phenomenon, extensive classical molecular dynamics simulations of [C4mim][Cl] IL and its mixtures with water were carried out. A combined quantum mechanics/molecular mechanics approach based on the density functional theory was applied to predict the NMR chemical shifts. The proliferation of strongly hydrogen-bonded complexes between chloride anions and water molecules is found to be the reason behind the increasing 1H NMR chemical shift of water when its molar fraction in the mixture is low and decreasing. The model shows that the chemical shift of water molecules that are trapped in the IL matrix without direct hydrogen bonding to the anions is considerably smaller than the 1H NMR chemical shift predicted for the neat water. The structural features of neat IL and its mixtures with water have also been analyzed in relation to their NMR properties. The 1H NMR spectrum of neat [C4mim][Cl] was predicted and found to be in very reasonable agreement with the experimental data. Finally, the experimentally observed strong dependence of the chemical shift of the proton at position 2 in the imidazolium ring on the composition of the mixture was rationalized.
Binary alcohol + ether liquid mixtures are of significant importance as potential biofuels or add... more Binary alcohol + ether liquid mixtures are of significant importance as potential biofuels or additives for internal combustion engines and attract considerable fundamental interest as model systems containing one strongly H-bonded self-associating component (alcohol) and one that is unable to do so (ether), but that can interact strongly as a H-bond acceptor. In this context, the excess thermodynamic properties of these mixtures, specifically the excess molar enthalpies and volumes (H E and V E), have been extensively measured. Butanol isomer + din -butyl ether (DBE) mixtures received significant attention because of interesting differences in their V E , changing from negative (1-and isobutanol) to positive (2-and tert-butanol) with increasing alkyl group branching. With the aim of shedding light on the differences in alcohol selfassociation and cross-species H-bonding, considered responsible for the observed differences, we studied representative 1-and 2-butanol + DBE mixtures by molecular dynamics simulations and experimental excess property measurements. The simulations reveal marked differences in the self-association of the two isomers and, while supporting the existing interpretations of the H E and V E in a general sense, our results suggest, for the first time, that subtle changes in H-bonded topologies may contribute significantly to the anomalous volumetric properties of these mixtures.
The Journal of Chemical Physics, 2016
Atomistic molecular dynamics simulations have been performed to investigate effective interaction... more Atomistic molecular dynamics simulations have been performed to investigate effective interactions of isolated water molecules dispersed in trihexyltetradecylphosphonium-orthoborate ionic liquids (ILs). The intrinsic free energy changes in solvating one water molecule from gas phase into bulk IL matrices were estimated as a function of temperature, and thereafter, the calculations of potential of mean force between two dispersed water molecules within different IL matrices were performed using umbrella sampling simulations. The systematic analyses of local ionic microstructures, orientational preferences, probability and spatial distributions of dispersed water molecules around neighboring ionic species indicate their preferential coordinations to central polar segments in orthoborate anions. The effective interactions between two dispersed water molecules are partially or totally screened as their separation distance increases due to interference of ionic species in between. These ...
Ionic liquids (ILs) are a special category of molten salts with melting points near ambient tempe... more Ionic liquids (ILs) are a special category of molten salts with melting points near ambient temperatures (or by convention below 100°C). Owing to their numerous valuable physicochemical properties as bulk liquids, solvents, at surfaces and in confined environments, ILs have attracted increasing attention in both academic and industrial communities in a variety of application areas involving physics, chemistry, material science and engineering. Due to their nearly limitless number of combinations of cation-anion pairs and mixtures with cosolvents, a molecular level understanding of their hierarchical structures and dynamics, requiring strategies to connect several length and time scales, is of crucial significance for rational design of ILs with desired properties, and thereafter refining their functional performance in applications. As an invaluable compliment to experiments from synthesis to characterization, computational modeling and simulations have significantly increased our understanding on how physicochemical and structural properties of ILs can be controlled by their underlying chemical and molecular structures. In this chapter, we will give examples from our own modeling work based on selected IL systems, with focus on imidazolium-based and tetraalkylphosphonium-orthoborate ILs, studied at several spatio-temporal scales in different environments and with particular attention to applications of high technological interest. We start by describing studies performed using ab initio methods on force field development for tetraalkylphosphonium-orthoborate ILs, and computational studies on thermal decomposition of these ILs. The delicate interplay between hydrogen bonding and π-type interactions in an imidazolium-orthoborate IL was studied by performing ab initio molecular dynamics simulations. On the atomistic level, atomistic simulations were performed with constructed force field parameters to study intrinsic molecular interactions between residual water molecules and tetraalkylphosphoniumorthoborate ionic species. For a typical trihexyltetradecylphosphonium bis(oxalato) borate IL at varied concentrations, microstructures and dynamics were systematically analyzed as water concentration increases. The liquid viscosities of typical trihexyltetradecylphosphonium-based ILs were estimated through equilibrium atomistic simulations using Green-Kubo relation with charge scaling factors on ionic species.
Biomolecular Simulations in Structure-Based Drug Discovery
Understanding the Structure and Dynamics of Peptides and Proteins Through the Lens of Network Sci... more Understanding the Structure and Dynamics of Peptides and Proteins Through the Lens of Network Science
Journal of Chemical Physics, 1998
Solvation free energy for methane, dissolved both in pure water, water/methane mixture (14 mole %... more Solvation free energy for methane, dissolved both in pure water, water/methane mixture (14 mole % methane) and in aqueous NaCl solution, is calculated using the expanded ensemble molecular dynamics method. Dependencies due to system size and potential model are investigated. Results, using a simple onesite methane model, together with large enough system size, are found in very good agreement with experimental data, while calculations using a flexible fivesite methane model give too high free energies. Also, the solvation energy for 20 different ion pairs of alkali halides is calculated in a systematic study. Very good overall agreement is found for the solvation energies of all the ion pairs. Calculations of solvation free energies provide a sensitive test of the used potential models.
ChemInform, Aug 21, 2010
ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was e... more ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Canadian Journal of Chemistry, Nov 1, 1994
Using molecular dynamics simulations, the motion and intermolecular interactions of the ions of s... more Using molecular dynamics simulations, the motion and intermolecular interactions of the ions of silver nitrate are studied in aqueous solution and compared to the results obtained from simulations of molten AgNO3. The particularly interesting and experimentally frequently studied modes of reorientational motion (in-plane and end-over-end) of the planar nitrate ion have been determined from the simulation results. In accordance with earlier experimental results, the correlation times for the end-over-end rotation in aqueous solution are longer than those for the in-plane rotation, while the opposite is found to hold in the melt. In addition, the rotational motion of the nitrate ion in aqueous solution is experimentally studied using 14N relaxation measurements. Good agreement is found between the reorientational correlation times obtained from MD simulations and from NMR relaxation measurements.
bioRxiv (Cold Spring Harbor Laboratory), Apr 6, 2021
The COVID-19 pandemic has spread widely worldwide. However, as soon as the vaccines were released... more The COVID-19 pandemic has spread widely worldwide. However, as soon as the vaccines were releasedthe only scientifically verified and efficient therapeutic option thus fara few mutations combined into variants of SARS-CoV-2 that are more transmissible and virulent emerged raising doubts about their efficiency. Therefore, this work aims to explain possible molecular mechanisms responsible for the increased transmissibility and the increased rate of hospitalizations related to the new variants. A combination of theoretical methods was employed. Constant-pH Monte Carlo simulations were carried out to quantify the stability of several spike trimeric structures at different conformational states and the free energy of interactions between the receptor binding domain (RBD) and Angiotensin Converting Enzyme 2 (ACE2) for the most worrying variants. Electrostatic epitopes were mapped using the PROCEEDpKa method. These analyses showed that the increased virulence is more likely to be due to the improved stability to the S trimer in the opened state (the one in which the virus can interact with the cellular receptor ACE2) than due to alterations in the complexation RBD-ACE2, once the increased observed in the free energy values is small. Conversely, the South .
bioRxiv (Cold Spring Harbor Laboratory), Apr 10, 2020
A new betacoronavirus named SARS-CoV-2 has emerged as a new threat to global health and economy. ... more A new betacoronavirus named SARS-CoV-2 has emerged as a new threat to global health and economy. A promising target for both diagnosis and therapeutics treatments of the new disease named COVID-19 is the coronavirus (CoV) spike (S) glycoprotein. By constant-pH Monte Carlo simulations and the PROCEEDpKa method, we have mapped the electrostatic epitopes for four monoclonal antibodies and the angiotensin-converting enzyme 2 (ACE2) on both SARS-CoV-1 and the new SARS-CoV-2 S receptor binding domain (RBD) proteins. We also calculated free energy of interactions and shown that the S RBD proteins from both SARS viruses binds to ACE2 with similar affinities. However, the affinity between the S RBD protein from the new SARS-CoV-2 and ACE2 is higher than for any studied antibody previously found complexed with SARS-CoV-1. Based on physical chemical analysis and free energies estimates, we can shed some light on the involved molecular recognition processes, their clinical aspects, the implications for drug developments, and suggest structural modifications on the CR3022 antibody that would improve its binding affinities for SARS-CoV-2 and contribute to address the ongoing international health crisis.
The Royal Society of Chemistry eBooks, Oct 1, 1985
Chemischer Informationsdienst, Jun 11, 1985
The Royal Society of Chemistry eBooks, Nov 1, 1986
Lecture Notes in Computer Science
Molecular modelling/simulation techniques have in three decades evolved to a powerful tool and sc... more Molecular modelling/simulation techniques have in three decades evolved to a powerful tool and scientific discipline of its own now used in many areas of physics, chemistry, and biology with applications from materials science to biotechnology. These techniques have naturally become applicable for more and complex systems largely thanks to the rapid development in computer technology. However in recent years a variety of new advanced and innovative techniques have been presented to push the time and length scales further towards nano/meso scale applications and soft matter. More efficient computational schemes have been proposed to treat long-ranged interactions, parallel algorithms are proposed to run on high-end fast computers, pc-clusters and heterogeneous GRID environment. Ab initio and hybrid QM/MM methods are becoming routine and developed to treat large systems. Multi-scale modelling schemes across several physical descriptions of matter from quantum mechanical systems with nuclei and electrons all the way to nano/meso/micro/macro levels are maturing rapidly. This minisymposium will highlight several of these latest techniques.
Lecture Notes in Computational Science and Engineering, 2006
The use of general descriptive names, registered names, trademarks, etc. in this publication does... more The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use.
Lecture Notes in Computer Science, 2007
In Memoriam and Dedication Every day we are reminded of the perishables of life and that our indi... more In Memoriam and Dedication Every day we are reminded of the perishables of life and that our individual lives are only a gift for a finite time. Unfortunately, at PARA 2006 this was no exception.
Nuclear Magnetic Resonance
Page 133. 4 Theoretical Aspects of Spin-Spin Couplings BY H. FUKUI AND T. BABA 1 Introduction The... more Page 133. 4 Theoretical Aspects of Spin-Spin Couplings BY H. FUKUI AND T. BABA 1 Introduction The indirect nuclear spin-spin coupling between nuclei is of fundamental importance in nuclear magnetic resonance (NMR) spectroscopy. ...
Chemischer Informationsdienst, 1982
ChemInform Abstract Berechnungen der effektiven Abstände zwischen den Liganden-Kernen und ungepaa... more ChemInform Abstract Berechnungen der effektiven Abstände zwischen den Liganden-Kernen und ungepaarten Elektronenspins des Grundzustandes der paramagnetischen Komplexe (I) und der Hyperfeinkopplungskonstanten sowie Untersuchung der Beziehung zwischen "O-Hyperfeinkopplungen und Abweichungen von der Punktdipol-Näherung.
New Trends in Macromolecular and Supramolecular Chemistry for Biological Applications, 2021
In solving mathematical and physical problems we generally think that the problem can be condense... more In solving mathematical and physical problems we generally think that the problem can be condensed to a well-defined equation which then can be solved either analytically or numerically with the provided input data and, if necessary, applying initial and boundary conditions to limit the amount of solutions to something which makes sense and can be accepted as the correct solution. This is the typical practice in "forward" problem solving. Consequently the solution can be considered as the inverse of the problem. Indeed, it is not uncommon in Science and also in everyday life to have the "solution" without knowing what exactly did "cause" it and "how". We take an illustrative example from Forensics with a case where a lethal crime is committed with a dead body (solution), but at the time of arrival to the crime scene the details to start to investigate are scattered all over the place. The investigators have the difficult task to mentally reverse the time to get good enough picture of the crime (problem) to start to trace the criminal and murder weapon (input) and possibly also the motive (cause). In this Chapter we discuss on how solving of the Inverse Problems is entering in Chemistry and focus on our own inverse computer modelling method to create a model (force field) from the results we already have. We explain how this method, called the Inverse Monte Carlo, can also be used for systematic hierarchical multi-scale modelling based on successive coarse-graining from first-principles to meso-scale and even further by super-coarse-graining. We show several applications of using it and also vision future prospects of hierarchical multi-scale modelling.
The 1H NMR chemical shift of water exhibits non-monotonic dependence on the composition of an aqu... more The 1H NMR chemical shift of water exhibits non-monotonic dependence on the composition of an aqueous mixture of 1-butyl-3-methylimidazolium chloride, [C4mim][Cl], ionic liquid (IL). A clear minimum is observed for the 1H NMR chemical shift at a molar fraction of the IL of 0.34. To scrutinize the molecular mechanism behind this phenomenon, extensive classical molecular dynamics simulations of [C4mim][Cl] IL and its mixtures with water were carried out. A combined quantum mechanics/molecular mechanics approach based on the density functional theory was applied to predict the NMR chemical shifts. The proliferation of strongly hydrogen-bonded complexes between chloride anions and water molecules is found to be the reason behind the increasing 1H NMR chemical shift of water when its molar fraction in the mixture is low and decreasing. The model shows that the chemical shift of water molecules that are trapped in the IL matrix without direct hydrogen bonding to the anions is considerably smaller than the 1H NMR chemical shift predicted for the neat water. The structural features of neat IL and its mixtures with water have also been analyzed in relation to their NMR properties. The 1H NMR spectrum of neat [C4mim][Cl] was predicted and found to be in very reasonable agreement with the experimental data. Finally, the experimentally observed strong dependence of the chemical shift of the proton at position 2 in the imidazolium ring on the composition of the mixture was rationalized.
Binary alcohol + ether liquid mixtures are of significant importance as potential biofuels or add... more Binary alcohol + ether liquid mixtures are of significant importance as potential biofuels or additives for internal combustion engines and attract considerable fundamental interest as model systems containing one strongly H-bonded self-associating component (alcohol) and one that is unable to do so (ether), but that can interact strongly as a H-bond acceptor. In this context, the excess thermodynamic properties of these mixtures, specifically the excess molar enthalpies and volumes (H E and V E), have been extensively measured. Butanol isomer + din -butyl ether (DBE) mixtures received significant attention because of interesting differences in their V E , changing from negative (1-and isobutanol) to positive (2-and tert-butanol) with increasing alkyl group branching. With the aim of shedding light on the differences in alcohol selfassociation and cross-species H-bonding, considered responsible for the observed differences, we studied representative 1-and 2-butanol + DBE mixtures by molecular dynamics simulations and experimental excess property measurements. The simulations reveal marked differences in the self-association of the two isomers and, while supporting the existing interpretations of the H E and V E in a general sense, our results suggest, for the first time, that subtle changes in H-bonded topologies may contribute significantly to the anomalous volumetric properties of these mixtures.
The Journal of Chemical Physics, 2016
Atomistic molecular dynamics simulations have been performed to investigate effective interaction... more Atomistic molecular dynamics simulations have been performed to investigate effective interactions of isolated water molecules dispersed in trihexyltetradecylphosphonium-orthoborate ionic liquids (ILs). The intrinsic free energy changes in solvating one water molecule from gas phase into bulk IL matrices were estimated as a function of temperature, and thereafter, the calculations of potential of mean force between two dispersed water molecules within different IL matrices were performed using umbrella sampling simulations. The systematic analyses of local ionic microstructures, orientational preferences, probability and spatial distributions of dispersed water molecules around neighboring ionic species indicate their preferential coordinations to central polar segments in orthoborate anions. The effective interactions between two dispersed water molecules are partially or totally screened as their separation distance increases due to interference of ionic species in between. These ...
Ionic liquids (ILs) are a special category of molten salts with melting points near ambient tempe... more Ionic liquids (ILs) are a special category of molten salts with melting points near ambient temperatures (or by convention below 100°C). Owing to their numerous valuable physicochemical properties as bulk liquids, solvents, at surfaces and in confined environments, ILs have attracted increasing attention in both academic and industrial communities in a variety of application areas involving physics, chemistry, material science and engineering. Due to their nearly limitless number of combinations of cation-anion pairs and mixtures with cosolvents, a molecular level understanding of their hierarchical structures and dynamics, requiring strategies to connect several length and time scales, is of crucial significance for rational design of ILs with desired properties, and thereafter refining their functional performance in applications. As an invaluable compliment to experiments from synthesis to characterization, computational modeling and simulations have significantly increased our understanding on how physicochemical and structural properties of ILs can be controlled by their underlying chemical and molecular structures. In this chapter, we will give examples from our own modeling work based on selected IL systems, with focus on imidazolium-based and tetraalkylphosphonium-orthoborate ILs, studied at several spatio-temporal scales in different environments and with particular attention to applications of high technological interest. We start by describing studies performed using ab initio methods on force field development for tetraalkylphosphonium-orthoborate ILs, and computational studies on thermal decomposition of these ILs. The delicate interplay between hydrogen bonding and π-type interactions in an imidazolium-orthoborate IL was studied by performing ab initio molecular dynamics simulations. On the atomistic level, atomistic simulations were performed with constructed force field parameters to study intrinsic molecular interactions between residual water molecules and tetraalkylphosphoniumorthoborate ionic species. For a typical trihexyltetradecylphosphonium bis(oxalato) borate IL at varied concentrations, microstructures and dynamics were systematically analyzed as water concentration increases. The liquid viscosities of typical trihexyltetradecylphosphonium-based ILs were estimated through equilibrium atomistic simulations using Green-Kubo relation with charge scaling factors on ionic species.
Biomolecular Simulations in Structure-Based Drug Discovery
Understanding the Structure and Dynamics of Peptides and Proteins Through the Lens of Network Sci... more Understanding the Structure and Dynamics of Peptides and Proteins Through the Lens of Network Science
Journal of Chemical Physics, 1998
Solvation free energy for methane, dissolved both in pure water, water/methane mixture (14 mole %... more Solvation free energy for methane, dissolved both in pure water, water/methane mixture (14 mole % methane) and in aqueous NaCl solution, is calculated using the expanded ensemble molecular dynamics method. Dependencies due to system size and potential model are investigated. Results, using a simple onesite methane model, together with large enough system size, are found in very good agreement with experimental data, while calculations using a flexible fivesite methane model give too high free energies. Also, the solvation energy for 20 different ion pairs of alkali halides is calculated in a systematic study. Very good overall agreement is found for the solvation energies of all the ion pairs. Calculations of solvation free energies provide a sensitive test of the used potential models.
ChemInform, Aug 21, 2010
ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was e... more ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Canadian Journal of Chemistry, Nov 1, 1994
Using molecular dynamics simulations, the motion and intermolecular interactions of the ions of s... more Using molecular dynamics simulations, the motion and intermolecular interactions of the ions of silver nitrate are studied in aqueous solution and compared to the results obtained from simulations of molten AgNO3. The particularly interesting and experimentally frequently studied modes of reorientational motion (in-plane and end-over-end) of the planar nitrate ion have been determined from the simulation results. In accordance with earlier experimental results, the correlation times for the end-over-end rotation in aqueous solution are longer than those for the in-plane rotation, while the opposite is found to hold in the melt. In addition, the rotational motion of the nitrate ion in aqueous solution is experimentally studied using 14N relaxation measurements. Good agreement is found between the reorientational correlation times obtained from MD simulations and from NMR relaxation measurements.
bioRxiv (Cold Spring Harbor Laboratory), Apr 6, 2021
The COVID-19 pandemic has spread widely worldwide. However, as soon as the vaccines were released... more The COVID-19 pandemic has spread widely worldwide. However, as soon as the vaccines were releasedthe only scientifically verified and efficient therapeutic option thus fara few mutations combined into variants of SARS-CoV-2 that are more transmissible and virulent emerged raising doubts about their efficiency. Therefore, this work aims to explain possible molecular mechanisms responsible for the increased transmissibility and the increased rate of hospitalizations related to the new variants. A combination of theoretical methods was employed. Constant-pH Monte Carlo simulations were carried out to quantify the stability of several spike trimeric structures at different conformational states and the free energy of interactions between the receptor binding domain (RBD) and Angiotensin Converting Enzyme 2 (ACE2) for the most worrying variants. Electrostatic epitopes were mapped using the PROCEEDpKa method. These analyses showed that the increased virulence is more likely to be due to the improved stability to the S trimer in the opened state (the one in which the virus can interact with the cellular receptor ACE2) than due to alterations in the complexation RBD-ACE2, once the increased observed in the free energy values is small. Conversely, the South .