Dominik Domin - Academia.edu (original) (raw)
Papers by Dominik Domin
Multiple dehydrogenation of fluorene cation and neutral fluorene using the statistical molecular fragmentation model
Physical Chemistry Chemical Physics, 2021
The statistical molecular fragmentation model was used to analyze the 306 fragmentation channels ... more The statistical molecular fragmentation model was used to analyze the 306 fragmentation channels (containing 611 different species) that result from the fluorene (C13H10+) cation losing up to three hydrogen atoms (neutral radicals and/or a proton).
Probing the structural properties of the water solvation shell around gold nanoparticles: A computational study
Journal of Chemical Physics, Jan 28, 2021
While subjected to radiation, gold nanoparticles (GNPs) have been shown to enhance the production... more While subjected to radiation, gold nanoparticles (GNPs) have been shown to enhance the production of radicals when added to aqueous solutions. It has been proposed that the arrangement of water solvation layers near the water–gold interface plays a significant role. As such, the structural and electronic properties of the first water solvation layer surrounding GNPs of varying sizes were compared to bulk water using classical molecular dynamics and quantum and semi-empirical methods. Classical molecular dynamics was used to understand the change in macroscopic properties of bulk water in the presence of different sizes of GNP, as well as by including salt ions. The analysis of these macroscopic properties has led to the conclusion that larger GNPs induce the rearrangement of water molecules to form a 2D hydrogen-bond network at the interface. Quantum methods were employed to understand the electronic nature of the interaction between water molecules and GNPs along with the change in the water orientation and the vibrational density of states. The stretching region of vibrational density of states was found to extend into the higher wavenumber region, as the size of the GNP increases. This extension represents the dangling water molecules at the interface, as a result of reorientation of the water molecules in the first solvation shell. This multi-level study suggests that in the presence of GNP of increasing sizes, the first water solvation shell undergoes a rearrangement to maximize the water–water interactions as well as the water–GNP interactions.
Text (counted by MS Word 2003) 3227 40 References (40+2)*2.3*7.6 735 3 Equations (4+4+4)*7.6 92 5... more Text (counted by MS Word 2003) 3227 40 References (40+2)*2.3*7.6 735 3 Equations (4+4+4)*7.6 92 5 Figures (435+386+122+175+250) 1368 4 Tables 4*((10+2)*7.6) 365
Role of Hydration Shell in the Transesterification Reaction Catalyzed by Subtilisin Carlsberg in Hexane
Recent years have revealed that some enzymes retain their structure and functional activities in ... more Recent years have revealed that some enzymes retain their structure and functional activities in solvents other than their natural aqueous environment. This has lead to enhanced applications in the field of biocatalysis, since reactions that were suppressed in water can be explored. Lipases and proteases family of enzymes have been studied extensively in organic solvents. Proteases catalyze hydroxylation reactions in water however, transesterification reactions are observed in non-aqueous medium. Utilizing Subtilisin Carlsberg (SC), a prototypical serine protease enzyme, we study the role of the residual hydration shell in the transesterification reaction catalyzed by SC in organic solvents. Our goal is to elucidate why the enzymatic activity decreases when the hydration level is decreased. We use hexane as the organic solvent and altering the number of waters hydrating the protein we intend to study the effect of decreasing hydration on the catalytic activity in the first step of t...
Multiple dehydrogenation of fluorene cation and neutral fluorene using the statistical molecular fragmentation model
Physical Chemistry Chemical Physics, 2021
The statistical molecular fragmentation model was used to analyze the 306 fragmentation channels ... more The statistical molecular fragmentation model was used to analyze the 306 fragmentation channels (containing 611 different species) that result from the fluorene (C13H10+) cation losing up to three hydrogen atoms (neutral radicals and/or a proton).
Probing the structural properties of the water solvation shell around gold nanoparticles: A computational study
The Journal of Chemical Physics, 2021
While subjected to radiation, gold nanoparticles (GNPs) have been shown to enhance the production... more While subjected to radiation, gold nanoparticles (GNPs) have been shown to enhance the production of radicals when added to aqueous solutions. It has been proposed that the arrangement of water solvation layers near the water–gold interface plays a significant role. As such, the structural and electronic properties of the first water solvation layer surrounding GNPs of varying sizes were compared to bulk water using classical molecular dynamics and quantum and semi-empirical methods. Classical molecular dynamics was used to understand the change in macroscopic properties of bulk water in the presence of different sizes of GNP, as well as by including salt ions. The analysis of these macroscopic properties has led to the conclusion that larger GNPs induce the rearrangement of water molecules to form a 2D hydrogen-bond network at the interface. Quantum methods were employed to understand the electronic nature of the interaction between water molecules and GNPs along with the change in...
Some Recent Developments of Quantum Monte Carlo to Molecular Systems
AIP Conference Proceedings, 2008
A brief review of recent advances in quantum Monte Carlo for the electronic structure of molecule... more A brief review of recent advances in quantum Monte Carlo for the electronic structure of molecules at the University of California, Berkeley, is given based on an invited talk presented at the Workshop on Nuclear and Mesoscopic Physics.
arXiv (Cornell University), Jul 29, 2022
The VB-QMC method is presented in this chapter. It consists of using in quantum Monte Carlo (QMC)... more The VB-QMC method is presented in this chapter. It consists of using in quantum Monte Carlo (QMC) approaches with a wave function expressed as a usually short expansion of classical Valence-Bond (VB) structures supplemented by a Jastrow factor to account for dynamical correlation. Two variants exist: the VB-VMC (using variational Monte Carlo) and VB-DMC (using diffusion Monte Carlo) methods. QMC algorithms circumvent the notorious non-orthogonality issue of classical VB approaches, and allow highly efficient calculations on massively parallel machines. Calculation of VB weights and resonance energies are possible at the VB-VMC level, which makes VB-VMC a correlated method retaining all the interpretative capabilities of classical VB methods. Several recent applications are shown to illustrate the potential of this method as a modern alternative to classical VB methods to study ground and excited states of molecules. KEYWORDS Valence Bond; non-orthogonal wave functions; chemical bonding; quantum Monte Carlo; variational Monte Carlo; diffusion Monte Carlo; interpretative methods; structure weights; resonance energies; excited states; hypervalency; charge-shift bonding; three-electron bond. GLOSSARY • BOVB Breathing-orbital Valence Bond, a VB method in which each VB structure is allowed to have a different set of orbitals. • CASPT2 Complete-active-space second-order perturbation theory, a standard wavefunction method for both static and dynamical correlation. • CASSCF Complete-active-space self-consistent field, a standard wave-function method for static correlation. • CI Configuration interaction, a standard wave-function method.
Elsevier eBooks, 2022
The VB-QMC method is presented in this chapter. It consists of using in quantum Monte Carlo (QMC)... more The VB-QMC method is presented in this chapter. It consists of using in quantum Monte Carlo (QMC) approaches with a wave function expressed as a usually short expansion of classical Valence-Bond (VB) structures supplemented by a Jastrow factor to account for dynamical correlation. Two variants exist: the VB-VMC (using variational Monte Carlo) and VB-DMC (using diffusion Monte Carlo) methods. QMC algorithms circumvent the notorious non-orthogonality issue of classical VB approaches, and allow highly efficient calculations on massively parallel machines. Calculation of VB weights and resonance energies are possible at the VB-VMC level, which makes VB-VMC a correlated method retaining all the interpretative capabilities of classical VB methods. Several recent applications are shown to illustrate the potential of this method as a modern alternative to classical VB methods to study ground and excited states of molecules. KEYWORDS Valence Bond; non-orthogonal wave functions; chemical bonding; quantum Monte Carlo; variational Monte Carlo; diffusion Monte Carlo; interpretative methods; structure weights; resonance energies; excited states; hypervalency; charge-shift bonding; three-electron bond. GLOSSARY • BOVB Breathing-orbital Valence Bond, a VB method in which each VB structure is allowed to have a different set of orbitals. • CASPT2 Complete-active-space second-order perturbation theory, a standard wavefunction method for both static and dynamical correlation. • CASSCF Complete-active-space self-consistent field, a standard wave-function method for static correlation. • CI Configuration interaction, a standard wave-function method.
Structural Chemistry, Nov 28, 2019
The first steps of the oxidation process of amino acid methionine (Met, CAS 63-68-3) by OH radi... more The first steps of the oxidation process of amino acid methionine (Met, CAS 63-68-3) by OH radicals, leading to Met-OH • adduct and then to Met radical cation, were investigated theoretically over the last few years considering the aqueous environment as a continuum. In this work, following the same procedure that we used for the oxidation of dimethyl sulfide (Domin et al. (2017) J Phys Chem B, 121:9321), discrete water molecules as well as relative positions of the OH radical to Met were taken from Molecular Dynamics calculations. The presence of water molecules strongly modifies the relative energies of Met-OH adducts and cations when water is properly modeled. Depending on the terminal functional groups and on the position of the • OH radical several stable structures were found, however the most stable radical is the N-centered or the SN radical cation. QTAIM analysis and Valence Bond (VB) treatment allowed for the characterization of the 2c3e nature of SN and SOH bonds. VB analysis estimated the probability of the heterolytic rupture of the OH adduct that is modified by the presence of water molecules.
Journal of Chemical Theory and Computation, May 1, 2013
The nature of the multicenter, long bond in ditetracyanoethylene dianion complex [TCNE] 2 2− is e... more The nature of the multicenter, long bond in ditetracyanoethylene dianion complex [TCNE] 2 2− is elucidated using high level ab initio Valence Bond (VB) theory coupled with Quantum Monte Carlo (QMC) methods. This dimer is the prototype of the general family of pancake-bonded dimers with large interplanar separations. Quantitative results obtained with a compact wave function in terms of only six VB structures match the reference CCSD(T) bonding energies. Analysis of the VB wave function shows that the weights of the VB structures are not compatible with a covalent bond between the π* orbitals of the fragments. On the other hand, these weights are consistent with a simple picture in terms of two resonating bonding schemes, one displaying a pair of interfragment three-electron σ bonds and the other displaying intrafragment three-electron π bonds. This simple picture explains at once (1) the long interfragment bond length, which is independent of the countercations but typical of three-electron (3-e) CC σ bonds, (2) the interfragment orbital overlaps which are very close to the theoretical optimal overlap of 1/6 for a 3-e σ bond, and (3) the unusual importance of dynamic correlation, which is precisely the main bonding component of 3-e bonds. Moreover, it is shown that the [TCNE] 2 2− system is topologically equivalent to the square C 4 H 4 2− dianion, a well-established aromatic system. To better understand the role of the cyano substituents, the unsubstituted diethylenic Na + 2 [C 2 H 4 ] 2 2− complex is studied and shown to be only metastable and topologically equivalent to a rectangular C 4 H 4 2− dianion, devoid of aromaticity.
Structural Chemistry, 2019
The first steps of the oxidation process of amino acid methionine (Met, CAS 63-68-3) by OH radi... more The first steps of the oxidation process of amino acid methionine (Met, CAS 63-68-3) by OH radicals, leading to Met-OH • adduct and then to Met radical cation, were investigated theoretically over the last few years considering the aqueous environment as a continuum. In this work, following the same procedure that we used for the oxidation of dimethyl sulfide (Domin et al. (2017) J Phys Chem B, 121:9321), discrete water molecules as well as relative positions of the OH radical to Met were taken from Molecular Dynamics calculations. The presence of water molecules strongly modifies the relative energies of Met-OH adducts and cations when water is properly modeled. Depending on the terminal functional groups and on the position of the • OH radical several stable structures were found, however the most stable radical is the N-centered or the SN radical cation. QTAIM analysis and Valence Bond (VB) treatment allowed for the characterization of the 2c3e nature of SN and SOH bonds. VB analysis estimated the probability of the heterolytic rupture of the OH adduct that is modified by the presence of water molecules.
Journal of Chemical Theory and Computation, 2013
The nature of the multicenter, long bond in ditetracyanoethylene dianion complex [TCNE] 2 2− is e... more The nature of the multicenter, long bond in ditetracyanoethylene dianion complex [TCNE] 2 2− is elucidated using high level ab initio Valence Bond (VB) theory coupled with Quantum Monte Carlo (QMC) methods. This dimer is the prototype of the general family of pancake-bonded dimers with large interplanar separations. Quantitative results obtained with a compact wave function in terms of only six VB structures match the reference CCSD(T) bonding energies. Analysis of the VB wave function shows that the weights of the VB structures are not compatible with a covalent bond between the π* orbitals of the fragments. On the other hand, these weights are consistent with a simple picture in terms of two resonating bonding schemes, one displaying a pair of interfragment three-electron σ bonds and the other displaying intrafragment three-electron π bonds. This simple picture explains at once (1) the long interfragment bond length, which is independent of the countercations but typical of three-electron (3-e) CC σ bonds, (2) the interfragment orbital overlaps which are very close to the theoretical optimal overlap of 1/6 for a 3-e σ bond, and (3) the unusual importance of dynamic correlation, which is precisely the main bonding component of 3-e bonds. Moreover, it is shown that the [TCNE] 2 2− system is topologically equivalent to the square C 4 H 4 2− dianion, a well-established aromatic system. To better understand the role of the cyano substituents, the unsubstituted diethylenic Na + 2 [C 2 H 4 ] 2 2− complex is studied and shown to be only metastable and topologically equivalent to a rectangular C 4 H 4 2− dianion, devoid of aromaticity.
The Journal of Physical Chemistry A, 2008
This study explores the use of breathing orbital valence bond (BOVB) trial wave functions for dif... more This study explores the use of breathing orbital valence bond (BOVB) trial wave functions for diffusion Monte Carlo (DMC). The approach is applied to the computation of the carbon-hydrogen (C-H) bond dissociation energy (BDE) of acetylene. DMC with BOVB trial wave functions yields a C-H BDE of 132.4 (0.9 kcal/mol, which is in excellent accord with the recommended experimental value of 132.8 (0.7 kcal/ mol. These values are to be compared with DMC results obtained with single determinant trial wave functions, using Hartree-Fock orbitals (137.5 (0.5 kcal/mol) and local spin density (LDA) Kohn-Sham orbitals (135.6 (0.5 kcal/mol). † Part of the special section for the "Symposium on Energetics and Dynamics of Molecules, Solids and Surfaces".
The statistical molecular fragmentation model compared to experimental plasma induced hydrocarbon decays
Physical Chemistry Chemical Physics
We compare the predictions of our recently developed statistical molecular fragmentation model wi... more We compare the predictions of our recently developed statistical molecular fragmentation model with experimental results from plasma induced decay of propene and other small hydrocarbons.
Statistical molecular fragmentation: which parameters influence the branching ratios?
Physical Chemistry Chemical Physics
Our recently developed statistical model for molecular fragmentation (SMF) is used to study the d... more Our recently developed statistical model for molecular fragmentation (SMF) is used to study the decomposition of propane and to predict thermodynamically controlled yields of products as a function of excitation energy deposited into propane.
Breaking down cellulose fibrils with a mid-infrared laser
Cellulose
The Journal of Physical Chemistry B
Enzymes are widely used in non-aqueous solvents to catalyze non-natural reactions. While experime... more Enzymes are widely used in non-aqueous solvents to catalyze non-natural reactions. While experimental measurements showed that the solvent nature has a strong effect on the reaction kinetics, the molecular details of the catalytic mechanism in non-aqueous solvents have remained largely elusive. Here we study the transesterification reaction catalyzed by the paradigm subtilisin Carlsberg serine protease in an organic apolar solvent. The rate-limiting acylation step involves a proton transfer between active-site residues and the nucleophilic attack of the substrate to form a tetrahedral intermediate. We design the first coupled valence-bond state model that simultaneously describes both reactions in the enzymatic active site. We develop a new systematic procedure to parameterize this model on high-level ab initio QM/MM free energy calculations that account for the molecular details of the active site and for both substrate and protein conformational fluctuations. Our calculations show that the reaction energy barrier changes dramatically with the solvent and protein conformational fluctuations. We find that the mechanism of the tetrahedral intermediate formation during the acylation step is similar to that determined in aqueous conditions, and that the proton transfer and nucleophilic attack reactions occur concertedly. We identify the reaction coordinate to be mostly due to the rearrangement of some residual water molecules close to the active site.
The Journal of Physical Chemistry B
Oxidative stress of sulfur-containing biological molecules in aqueous environments may lead to th... more Oxidative stress of sulfur-containing biological molecules in aqueous environments may lead to the formation of adduct intermediates that are too short lived to be experimentally detectable. In this study we have modeled the simplest of such oxidative reactions: the attack of dimethyl sulfide (DMS) by a hydroxyl radical (• OH) to form radical adduct, whose subsequent heterolytic dissociation leads to a radical cation (DMS +) that is important for further reactions. We have modeled the aqueous environment with a limited number of discrete water molecules, selected after an original multistep procedure, and further embedded in a polarizable continuum model, to observe the impact of the water configuration on the heterolytic dissociation of the radical adduct. Molecular dynamics and quantum chemical methods (DFT, MP2 and CCSD) were used to elucidate the lowest energy structures resulting from the • OH attack on DMS. Subsequent high level ab initio Valence Bond (BOVB) calculations revealed the possibility for the occurrence of subsequent heterolytic dissociation.
Lawrence Berkeley National Laboratory, Mar 24, 2007
Reaction pathways are presented for hydrogen-mediated isomerization of a five and six member carb... more Reaction pathways are presented for hydrogen-mediated isomerization of a five and six member carbon ring complex on the zigzag edge of a graphene layer. A new reaction sequence that reverses orientation of the ring complex, or "flips" it, was identified. Competition between the flip reaction and "ring separation" was examined. Ring separation is the reverse of the five and six member ring complex formation reaction, previously reported as "ring collision." The elementary steps of the pathways were analyzed using density-functional theory (DFT). Rate coefficients were obtained by solution of the energy master equation and classical transition state theory utilizing the DFT energies, frequencies, and geometries. The results indicate that the flip reaction pathway dominates the separation reaction and should be competitive with other pathways important to the graphene zigzag edge growth in high temperature environments.
Multiple dehydrogenation of fluorene cation and neutral fluorene using the statistical molecular fragmentation model
Physical Chemistry Chemical Physics, 2021
The statistical molecular fragmentation model was used to analyze the 306 fragmentation channels ... more The statistical molecular fragmentation model was used to analyze the 306 fragmentation channels (containing 611 different species) that result from the fluorene (C13H10+) cation losing up to three hydrogen atoms (neutral radicals and/or a proton).
Probing the structural properties of the water solvation shell around gold nanoparticles: A computational study
Journal of Chemical Physics, Jan 28, 2021
While subjected to radiation, gold nanoparticles (GNPs) have been shown to enhance the production... more While subjected to radiation, gold nanoparticles (GNPs) have been shown to enhance the production of radicals when added to aqueous solutions. It has been proposed that the arrangement of water solvation layers near the water–gold interface plays a significant role. As such, the structural and electronic properties of the first water solvation layer surrounding GNPs of varying sizes were compared to bulk water using classical molecular dynamics and quantum and semi-empirical methods. Classical molecular dynamics was used to understand the change in macroscopic properties of bulk water in the presence of different sizes of GNP, as well as by including salt ions. The analysis of these macroscopic properties has led to the conclusion that larger GNPs induce the rearrangement of water molecules to form a 2D hydrogen-bond network at the interface. Quantum methods were employed to understand the electronic nature of the interaction between water molecules and GNPs along with the change in the water orientation and the vibrational density of states. The stretching region of vibrational density of states was found to extend into the higher wavenumber region, as the size of the GNP increases. This extension represents the dangling water molecules at the interface, as a result of reorientation of the water molecules in the first solvation shell. This multi-level study suggests that in the presence of GNP of increasing sizes, the first water solvation shell undergoes a rearrangement to maximize the water–water interactions as well as the water–GNP interactions.
Text (counted by MS Word 2003) 3227 40 References (40+2)*2.3*7.6 735 3 Equations (4+4+4)*7.6 92 5... more Text (counted by MS Word 2003) 3227 40 References (40+2)*2.3*7.6 735 3 Equations (4+4+4)*7.6 92 5 Figures (435+386+122+175+250) 1368 4 Tables 4*((10+2)*7.6) 365
Role of Hydration Shell in the Transesterification Reaction Catalyzed by Subtilisin Carlsberg in Hexane
Recent years have revealed that some enzymes retain their structure and functional activities in ... more Recent years have revealed that some enzymes retain their structure and functional activities in solvents other than their natural aqueous environment. This has lead to enhanced applications in the field of biocatalysis, since reactions that were suppressed in water can be explored. Lipases and proteases family of enzymes have been studied extensively in organic solvents. Proteases catalyze hydroxylation reactions in water however, transesterification reactions are observed in non-aqueous medium. Utilizing Subtilisin Carlsberg (SC), a prototypical serine protease enzyme, we study the role of the residual hydration shell in the transesterification reaction catalyzed by SC in organic solvents. Our goal is to elucidate why the enzymatic activity decreases when the hydration level is decreased. We use hexane as the organic solvent and altering the number of waters hydrating the protein we intend to study the effect of decreasing hydration on the catalytic activity in the first step of t...
Multiple dehydrogenation of fluorene cation and neutral fluorene using the statistical molecular fragmentation model
Physical Chemistry Chemical Physics, 2021
The statistical molecular fragmentation model was used to analyze the 306 fragmentation channels ... more The statistical molecular fragmentation model was used to analyze the 306 fragmentation channels (containing 611 different species) that result from the fluorene (C13H10+) cation losing up to three hydrogen atoms (neutral radicals and/or a proton).
Probing the structural properties of the water solvation shell around gold nanoparticles: A computational study
The Journal of Chemical Physics, 2021
While subjected to radiation, gold nanoparticles (GNPs) have been shown to enhance the production... more While subjected to radiation, gold nanoparticles (GNPs) have been shown to enhance the production of radicals when added to aqueous solutions. It has been proposed that the arrangement of water solvation layers near the water–gold interface plays a significant role. As such, the structural and electronic properties of the first water solvation layer surrounding GNPs of varying sizes were compared to bulk water using classical molecular dynamics and quantum and semi-empirical methods. Classical molecular dynamics was used to understand the change in macroscopic properties of bulk water in the presence of different sizes of GNP, as well as by including salt ions. The analysis of these macroscopic properties has led to the conclusion that larger GNPs induce the rearrangement of water molecules to form a 2D hydrogen-bond network at the interface. Quantum methods were employed to understand the electronic nature of the interaction between water molecules and GNPs along with the change in...
Some Recent Developments of Quantum Monte Carlo to Molecular Systems
AIP Conference Proceedings, 2008
A brief review of recent advances in quantum Monte Carlo for the electronic structure of molecule... more A brief review of recent advances in quantum Monte Carlo for the electronic structure of molecules at the University of California, Berkeley, is given based on an invited talk presented at the Workshop on Nuclear and Mesoscopic Physics.
arXiv (Cornell University), Jul 29, 2022
The VB-QMC method is presented in this chapter. It consists of using in quantum Monte Carlo (QMC)... more The VB-QMC method is presented in this chapter. It consists of using in quantum Monte Carlo (QMC) approaches with a wave function expressed as a usually short expansion of classical Valence-Bond (VB) structures supplemented by a Jastrow factor to account for dynamical correlation. Two variants exist: the VB-VMC (using variational Monte Carlo) and VB-DMC (using diffusion Monte Carlo) methods. QMC algorithms circumvent the notorious non-orthogonality issue of classical VB approaches, and allow highly efficient calculations on massively parallel machines. Calculation of VB weights and resonance energies are possible at the VB-VMC level, which makes VB-VMC a correlated method retaining all the interpretative capabilities of classical VB methods. Several recent applications are shown to illustrate the potential of this method as a modern alternative to classical VB methods to study ground and excited states of molecules. KEYWORDS Valence Bond; non-orthogonal wave functions; chemical bonding; quantum Monte Carlo; variational Monte Carlo; diffusion Monte Carlo; interpretative methods; structure weights; resonance energies; excited states; hypervalency; charge-shift bonding; three-electron bond. GLOSSARY • BOVB Breathing-orbital Valence Bond, a VB method in which each VB structure is allowed to have a different set of orbitals. • CASPT2 Complete-active-space second-order perturbation theory, a standard wavefunction method for both static and dynamical correlation. • CASSCF Complete-active-space self-consistent field, a standard wave-function method for static correlation. • CI Configuration interaction, a standard wave-function method.
Elsevier eBooks, 2022
The VB-QMC method is presented in this chapter. It consists of using in quantum Monte Carlo (QMC)... more The VB-QMC method is presented in this chapter. It consists of using in quantum Monte Carlo (QMC) approaches with a wave function expressed as a usually short expansion of classical Valence-Bond (VB) structures supplemented by a Jastrow factor to account for dynamical correlation. Two variants exist: the VB-VMC (using variational Monte Carlo) and VB-DMC (using diffusion Monte Carlo) methods. QMC algorithms circumvent the notorious non-orthogonality issue of classical VB approaches, and allow highly efficient calculations on massively parallel machines. Calculation of VB weights and resonance energies are possible at the VB-VMC level, which makes VB-VMC a correlated method retaining all the interpretative capabilities of classical VB methods. Several recent applications are shown to illustrate the potential of this method as a modern alternative to classical VB methods to study ground and excited states of molecules. KEYWORDS Valence Bond; non-orthogonal wave functions; chemical bonding; quantum Monte Carlo; variational Monte Carlo; diffusion Monte Carlo; interpretative methods; structure weights; resonance energies; excited states; hypervalency; charge-shift bonding; three-electron bond. GLOSSARY • BOVB Breathing-orbital Valence Bond, a VB method in which each VB structure is allowed to have a different set of orbitals. • CASPT2 Complete-active-space second-order perturbation theory, a standard wavefunction method for both static and dynamical correlation. • CASSCF Complete-active-space self-consistent field, a standard wave-function method for static correlation. • CI Configuration interaction, a standard wave-function method.
Structural Chemistry, Nov 28, 2019
The first steps of the oxidation process of amino acid methionine (Met, CAS 63-68-3) by OH radi... more The first steps of the oxidation process of amino acid methionine (Met, CAS 63-68-3) by OH radicals, leading to Met-OH • adduct and then to Met radical cation, were investigated theoretically over the last few years considering the aqueous environment as a continuum. In this work, following the same procedure that we used for the oxidation of dimethyl sulfide (Domin et al. (2017) J Phys Chem B, 121:9321), discrete water molecules as well as relative positions of the OH radical to Met were taken from Molecular Dynamics calculations. The presence of water molecules strongly modifies the relative energies of Met-OH adducts and cations when water is properly modeled. Depending on the terminal functional groups and on the position of the • OH radical several stable structures were found, however the most stable radical is the N-centered or the SN radical cation. QTAIM analysis and Valence Bond (VB) treatment allowed for the characterization of the 2c3e nature of SN and SOH bonds. VB analysis estimated the probability of the heterolytic rupture of the OH adduct that is modified by the presence of water molecules.
Journal of Chemical Theory and Computation, May 1, 2013
The nature of the multicenter, long bond in ditetracyanoethylene dianion complex [TCNE] 2 2− is e... more The nature of the multicenter, long bond in ditetracyanoethylene dianion complex [TCNE] 2 2− is elucidated using high level ab initio Valence Bond (VB) theory coupled with Quantum Monte Carlo (QMC) methods. This dimer is the prototype of the general family of pancake-bonded dimers with large interplanar separations. Quantitative results obtained with a compact wave function in terms of only six VB structures match the reference CCSD(T) bonding energies. Analysis of the VB wave function shows that the weights of the VB structures are not compatible with a covalent bond between the π* orbitals of the fragments. On the other hand, these weights are consistent with a simple picture in terms of two resonating bonding schemes, one displaying a pair of interfragment three-electron σ bonds and the other displaying intrafragment three-electron π bonds. This simple picture explains at once (1) the long interfragment bond length, which is independent of the countercations but typical of three-electron (3-e) CC σ bonds, (2) the interfragment orbital overlaps which are very close to the theoretical optimal overlap of 1/6 for a 3-e σ bond, and (3) the unusual importance of dynamic correlation, which is precisely the main bonding component of 3-e bonds. Moreover, it is shown that the [TCNE] 2 2− system is topologically equivalent to the square C 4 H 4 2− dianion, a well-established aromatic system. To better understand the role of the cyano substituents, the unsubstituted diethylenic Na + 2 [C 2 H 4 ] 2 2− complex is studied and shown to be only metastable and topologically equivalent to a rectangular C 4 H 4 2− dianion, devoid of aromaticity.
Structural Chemistry, 2019
The first steps of the oxidation process of amino acid methionine (Met, CAS 63-68-3) by OH radi... more The first steps of the oxidation process of amino acid methionine (Met, CAS 63-68-3) by OH radicals, leading to Met-OH • adduct and then to Met radical cation, were investigated theoretically over the last few years considering the aqueous environment as a continuum. In this work, following the same procedure that we used for the oxidation of dimethyl sulfide (Domin et al. (2017) J Phys Chem B, 121:9321), discrete water molecules as well as relative positions of the OH radical to Met were taken from Molecular Dynamics calculations. The presence of water molecules strongly modifies the relative energies of Met-OH adducts and cations when water is properly modeled. Depending on the terminal functional groups and on the position of the • OH radical several stable structures were found, however the most stable radical is the N-centered or the SN radical cation. QTAIM analysis and Valence Bond (VB) treatment allowed for the characterization of the 2c3e nature of SN and SOH bonds. VB analysis estimated the probability of the heterolytic rupture of the OH adduct that is modified by the presence of water molecules.
Journal of Chemical Theory and Computation, 2013
The nature of the multicenter, long bond in ditetracyanoethylene dianion complex [TCNE] 2 2− is e... more The nature of the multicenter, long bond in ditetracyanoethylene dianion complex [TCNE] 2 2− is elucidated using high level ab initio Valence Bond (VB) theory coupled with Quantum Monte Carlo (QMC) methods. This dimer is the prototype of the general family of pancake-bonded dimers with large interplanar separations. Quantitative results obtained with a compact wave function in terms of only six VB structures match the reference CCSD(T) bonding energies. Analysis of the VB wave function shows that the weights of the VB structures are not compatible with a covalent bond between the π* orbitals of the fragments. On the other hand, these weights are consistent with a simple picture in terms of two resonating bonding schemes, one displaying a pair of interfragment three-electron σ bonds and the other displaying intrafragment three-electron π bonds. This simple picture explains at once (1) the long interfragment bond length, which is independent of the countercations but typical of three-electron (3-e) CC σ bonds, (2) the interfragment orbital overlaps which are very close to the theoretical optimal overlap of 1/6 for a 3-e σ bond, and (3) the unusual importance of dynamic correlation, which is precisely the main bonding component of 3-e bonds. Moreover, it is shown that the [TCNE] 2 2− system is topologically equivalent to the square C 4 H 4 2− dianion, a well-established aromatic system. To better understand the role of the cyano substituents, the unsubstituted diethylenic Na + 2 [C 2 H 4 ] 2 2− complex is studied and shown to be only metastable and topologically equivalent to a rectangular C 4 H 4 2− dianion, devoid of aromaticity.
The Journal of Physical Chemistry A, 2008
This study explores the use of breathing orbital valence bond (BOVB) trial wave functions for dif... more This study explores the use of breathing orbital valence bond (BOVB) trial wave functions for diffusion Monte Carlo (DMC). The approach is applied to the computation of the carbon-hydrogen (C-H) bond dissociation energy (BDE) of acetylene. DMC with BOVB trial wave functions yields a C-H BDE of 132.4 (0.9 kcal/mol, which is in excellent accord with the recommended experimental value of 132.8 (0.7 kcal/ mol. These values are to be compared with DMC results obtained with single determinant trial wave functions, using Hartree-Fock orbitals (137.5 (0.5 kcal/mol) and local spin density (LDA) Kohn-Sham orbitals (135.6 (0.5 kcal/mol). † Part of the special section for the "Symposium on Energetics and Dynamics of Molecules, Solids and Surfaces".
The statistical molecular fragmentation model compared to experimental plasma induced hydrocarbon decays
Physical Chemistry Chemical Physics
We compare the predictions of our recently developed statistical molecular fragmentation model wi... more We compare the predictions of our recently developed statistical molecular fragmentation model with experimental results from plasma induced decay of propene and other small hydrocarbons.
Statistical molecular fragmentation: which parameters influence the branching ratios?
Physical Chemistry Chemical Physics
Our recently developed statistical model for molecular fragmentation (SMF) is used to study the d... more Our recently developed statistical model for molecular fragmentation (SMF) is used to study the decomposition of propane and to predict thermodynamically controlled yields of products as a function of excitation energy deposited into propane.
Breaking down cellulose fibrils with a mid-infrared laser
Cellulose
The Journal of Physical Chemistry B
Enzymes are widely used in non-aqueous solvents to catalyze non-natural reactions. While experime... more Enzymes are widely used in non-aqueous solvents to catalyze non-natural reactions. While experimental measurements showed that the solvent nature has a strong effect on the reaction kinetics, the molecular details of the catalytic mechanism in non-aqueous solvents have remained largely elusive. Here we study the transesterification reaction catalyzed by the paradigm subtilisin Carlsberg serine protease in an organic apolar solvent. The rate-limiting acylation step involves a proton transfer between active-site residues and the nucleophilic attack of the substrate to form a tetrahedral intermediate. We design the first coupled valence-bond state model that simultaneously describes both reactions in the enzymatic active site. We develop a new systematic procedure to parameterize this model on high-level ab initio QM/MM free energy calculations that account for the molecular details of the active site and for both substrate and protein conformational fluctuations. Our calculations show that the reaction energy barrier changes dramatically with the solvent and protein conformational fluctuations. We find that the mechanism of the tetrahedral intermediate formation during the acylation step is similar to that determined in aqueous conditions, and that the proton transfer and nucleophilic attack reactions occur concertedly. We identify the reaction coordinate to be mostly due to the rearrangement of some residual water molecules close to the active site.
The Journal of Physical Chemistry B
Oxidative stress of sulfur-containing biological molecules in aqueous environments may lead to th... more Oxidative stress of sulfur-containing biological molecules in aqueous environments may lead to the formation of adduct intermediates that are too short lived to be experimentally detectable. In this study we have modeled the simplest of such oxidative reactions: the attack of dimethyl sulfide (DMS) by a hydroxyl radical (• OH) to form radical adduct, whose subsequent heterolytic dissociation leads to a radical cation (DMS +) that is important for further reactions. We have modeled the aqueous environment with a limited number of discrete water molecules, selected after an original multistep procedure, and further embedded in a polarizable continuum model, to observe the impact of the water configuration on the heterolytic dissociation of the radical adduct. Molecular dynamics and quantum chemical methods (DFT, MP2 and CCSD) were used to elucidate the lowest energy structures resulting from the • OH attack on DMS. Subsequent high level ab initio Valence Bond (BOVB) calculations revealed the possibility for the occurrence of subsequent heterolytic dissociation.
Lawrence Berkeley National Laboratory, Mar 24, 2007
Reaction pathways are presented for hydrogen-mediated isomerization of a five and six member carb... more Reaction pathways are presented for hydrogen-mediated isomerization of a five and six member carbon ring complex on the zigzag edge of a graphene layer. A new reaction sequence that reverses orientation of the ring complex, or "flips" it, was identified. Competition between the flip reaction and "ring separation" was examined. Ring separation is the reverse of the five and six member ring complex formation reaction, previously reported as "ring collision." The elementary steps of the pathways were analyzed using density-functional theory (DFT). Rate coefficients were obtained by solution of the energy master equation and classical transition state theory utilizing the DFT energies, frequencies, and geometries. The results indicate that the flip reaction pathway dominates the separation reaction and should be competitive with other pathways important to the graphene zigzag edge growth in high temperature environments.