Abstract
A Yukawa-field approximation of the electrostatic free energy of a molecular solvation system with an implicit or continuum solvent is constructed. It is argued through the analysis of model molecular systems with spherically symmetric geometries that such an approximation is rational. The construction extends non-trivially that of the Coulomb-field approximation which serves as a basis of the widely used generalized Born model of molecular electrostatics. The electrostatic free energy determines the dielectric boundary force that in turn influences crucially the molecular conformation, stability, and dynamics. An explicit formula of such forces with the Yukawa-field approximation is obtained using local coordinates and shape differentiation.
Keywords: Molecular solvation, electrostatic free energy, Yukawa-field approximation, shape derivative
1 Introduction
Implicit-solvent (or continuum-solvent) modeling is an efficient and widely used approach to the biomolecular solvation [8, 15, 20, 34, 39]. In such a model, the solvent molecules and ions are treated implicitly and their effects are coarse grained. Most of the existing implicit-solvent models are based on various kinds of fixed solute-solvent interfaces, such as the van der Waals surface, solvent-excluded surface, or solvent-accessible surface [13, 14, 27, 32, 33]. Such a predefined interface is used to compute the solvation free energy as the sum of two separate parts. One is the surface energy, proportional to the area of interface. The other is the electrostatic contribution determined by the Poisson–Boltzmann (PB) [1,6,7,16,21–24, 28, 29, 36, 41] or generalized Born (GB) [2, 3, 38] approach in which the solute-solvent interface is used as the dielectric boundary.
In recent years, a new class of implicit-solvent models, termed variational implicit-solvent models (VISM), have emerged [18,19]. Coupled with the robust level-set numerical method, such models allow an efficient and quantitative description of molecular solvation [9,10,12]. Central in the VISM is a free-energy functional of all possible solute-solvent interfaces, or dielectric boundaries, that separate the continuum solvent from all solute atoms. In a simple setting, such a free-energy functional consists of surface energy, solute-solvent van der Waals interaction energy, and continuum electrostatic free energy, all depending solely on a given solute-solvent interface. Minimizing the functional determines the solvation free energy and stable equilibrium solute-solvent interfaces. Initial applications of the level-set VISM to nonpolar molecular systems have demonstrated its success in capturing the hydrophobic interaction, multiple equilibrium states of hydration, and fluctuation between such states [9, 11, 12, 35, 40], all of which are difficult to be captured by a fixed-surface implicit-solvent model.
The present work concerns the electrostatic free energy, more precisely the electrostatic part of solvation free energy, and the resulting dielectric boundary force in the framework of VISM for charged molecules. Our approach is quite uncommon: instead of solving the PB equation or linearized PB equation—the Debye–Hückel equation [30], we use the Yukawa potential to construct an approximation of the electrostatic free energy. The Yukawa potential is the fundamental solution of the Debye–Hückel equation with a uniform dielectric coefficient [31]. It decays as e−κr/r as the distance r to the solute charges becomes large, where κ is the inverse Debye screening length.
Our approximations are made in two steps. Consider a charged solute molecule that carries atomic charges Qi at xi (i = 1,…, N) in the solute region Ω− separated by a solute-solvent interface Γ from the solvent region Ω+. Our first step is to approximate the electric displacement by that corresponds to the Coulomb-field
| (1.1) |
for any spatial point x ∈ Ω− and by
for any x ∈ Ω+. The functions fi(·, κ, Γ) (i = 1,…, N) are constructed to satisfy some basic requirements. They include, for example, the recovery of the known Coulomb-field approximation in the case of κ = 0, the proper decay at the infinity, and the exactness for model systems with special geometries. Through the analysis of some model systems, we propose a formula of the functions fi(x, κ, Γ), cf. (3.5). Our second step is to approximate the electrostatic free energy using the approximated electric displacement. The result is an integral over the solvent region Ω+, cf. (3.2). The dielectric coefficient ε, which equals one constant ε− in the solute region Ω− and another ε+ in the solvent region Ω+, relates the electric field and electric displacement, and hence appears in our final form of the approximate electrostatic free energy.
The Coulomb-field approximation, i.e., the approximation of electric displacement by (1.1), provides a means of computing generalized Born radii in the GB model that has been widely used for biomolecular systems [3, 38]. In our recent work [40], we use the Coulomb-field approximation to construct the electrostatic free energy
| (1.2) |
where ε0 is the vacuum permittivity, and incorporate it into the level-set VISM. Notice that we do not compute generalized Born radii, and hence introduce no additional parameters. Instead we evaluate the integral in (1.2) that is over an arbitrarily shaped domain Ω+ to calculate the approximate electrostatic free energy. The Yukawa-field approximation that we construct here is one step forward. It describes the additional effect from the mobile charges with the same kind of efficiency of the Coulomb-field approximation. Both of these approximations are clearly very attractive due to their high efficiency that is largely demanded in biomolecular modeling. In the meantime, these approximations are very accurate in many cases for large molecular systems, since they capture well the long-range behavior that characterizes the electrostatic interaction.
To see the heuristics behind the Yukawa-field approximation, particularly how the functions fi(x, κ, Γ) are constructed, we consider two simple model systems with spherical symmetry. The first one is a spherical solute molecule with only one charged atom in the center. This system is the same in geometry as that studied by Born in [4] except we include here the ionic charge effect. The second one is a concentric sphere-ring solute with a single charge placed at the center of sphere. For both of these two systems, we solve analytically the boundary-value problem of the Debye–Hückel equation (2.5) to get the corresponding electrostatic potentials. For the second one, we also carry out an asymptotic analysis with respect to the asymptotics κ ⪡ 1 and ε−/ε+ ⪡ 1.
We study next the normal component of the dielectric boundary force that is defined as the negative variational derivative of the electrostatic free energy with respect to the location change of the dielectric boundary Γ. Such a boundary force is crucial in determining the conformation, stability, and dynamics of the solute molecules. It is exactly the electrostatic part of the “normal velocity” in the level-set method for numerically relaxing the free energy functional in VISM. We define and derive the variational derivative of the free energy using two methods. One is the method of local coordinates. After the boundary variation is defined clearly, the calculations using this method are straight forward. The other is the method of shape differentiation. It begins with a systematic definition of boundary variation. The derivation of the shape derivative formula is a bit more involved. But it is connected to the level-set representation of the boundary. Such a connection will be useful in our future level-set numerical calculations. The final result of our calculations is summarized in Proposition 3.1.
The rest of the paper is organized as follows: In Section 2, we describe the mathematical setting of molecular solvation with an implicit solvent, and the electrostatics part of the solvation free energy. In Section 3, we present our formulas of the Yukawa-field approximation of the electrostatic free energy and the related dielectric boundary force. In Section 4 we study two model systems with spherical symmetry. In Sections 5 and 6, we use the method of local coordinates and shape differentiation, respectively, to derive the formula of dielectric boundary force.
2 Electrostatic Free Energy
We consider the electrostatics of a molecular solvation system in the framework of the continuum-solvent description. We denote by Γ a solute-solvent interface or the dielectric boundary that separates the solute molecular region Ω− and the implicit or continuum solvent region Ω+, cf. Figure 1, where n denotes the unit normal of the interface Γ pointing from Ω− to Ω+. We assume that is a smooth, bounded, and open set, with possibly multiple connected components, Γ = ∂Ω− is the boundary of Ω−, and , where an over-line denotes the closure. We assume that there are N atoms of the solute molecules located at x1,…, xN in Ω− and carrying point charges Q1,…, QN, respectively. We denote by ε− and ε+ the dielectric constants (relative permittivities) of the solute region and the solvent region, respectively.
Figure 1.

The geometry of a solvation system with an implicit solvent.
By the Born cycle [4], the electrostatic component of the solvation free energy ΔG of our underlying solvation system is defined to be ΔG = G2 − G1, where G1 is the electrostatic free energy of a reference state and G2 that of the solvated state. By definition,
| (2.1) |
where Ei and Di are the electric field and electrostatic displacement of the ith state, respectively, and dV is the volume element of .
A natural choice of the reference state is the underlying charged solute molecules placed in the entire space with the uniform dielectric constant ε−. The corresponding electrostatic potential ψ1 is
| (2.2) |
where ε0 is the vacuum permittivity. It is the unique solution of the boundary-value problem of the Poisson equation
where δxi denotes the Dirac delta function concentrated at xi. The corresponding electric field E1 and electric displacement D1 are
| (2.3) |
| (2.4) |
In the solvated state, the solute molecules are immersed in the solvent, creating the solute-solvent interface or the dielectric boundary Γ, resulting a large jump of the dielectric coefficient from the solute molecular region to the solvent region, cf. Figure 1. The corresponding electrostatic potential ψ2 is the unique solution of a boundary-value problem of the Poisson–Boltzmann equation. In many cases, particularly when ionic concentrations are low, the linearized Poisson–Boltzmann equation, or the Debye–Hückel equation, is a good approximation. Therefore, we assume that the electrostatic potential ψ2 is the unique solution of the boundary-value problem of the Debye–Hückel equation
| (2.5) |
Here ε is the variable dielectric coefficient of the entire solvation region defined by
χ+ is the characteristic function of the solvent region Ω+ (i.e., χ+(x) = 1 if x ∈ Ω+ and 0 otherwise), and κ > 0 is the inverse Debye screening length, defined by
where kB is the Boltzmann constant, T is the temperature, and and qj are the bulk concentration and charge of the jth ionic species of which a total of M is assumed. Since the boundary Γ can be arbitrarily shaped, there is in general no analytical formula of the solution ψ2. But the corresponding electric field E2 and electrostatic displacement D2 can be still defined as usual by
| (2.6) |
respectively.
Notice that both ψ1 and ψ2 have singularities at points of charges x1,…, xN. Therefore the integrals in the definition of electrostatic energy (2.1) should be understood as those over the entire space minus balls centered at x1,…, xN with a very small cut-off radius. Alternatively, they should be understood as there are no self-interaction energy terms [25]. For instance, in the reference state, these terms are
3 The Yukawa-Field Approximation
Let the solute molecular region Ω−, the solvent region Ω+, the solute-solvent interface or the dielectric boundary Γ, and the positions x1,…, xN ∈ Ω− and point charges Q1,…, QN of the solute atoms be given as above, cf. Figure 1. Let D1 be the electric displacement of the reference state as given in (2.4). Let D2 be the electric displacement of the solvated state as given in (2.6), where ψ2 is the electrostatic potential that solves the boundary-value problem of the Debye–Hückel equation (2.5). We define a Yukawa-field approximation of D2 to be
| (3.1) |
where each fi(·, κ, Γ) depends only on xi, κ, and Γ. We define to be the approximate electric field corresponding to , i.e., cf. (2.6).
With this approximation, the electrostatic free energy becomes
Therefore we define the Yukawa-field approximation of the electrostatic free energy to be
| (3.2) |
Here we use the same symbol ΔG to denote this approximation. We also indicate its dependence on Γ for the given set of data xi and Qi (i = 1,…, N), ε− and ε+, and κ.
We require that the functions satisfy the following conditions:
If κ = 0 then all fi(·, κ, Γ) = 1 identically in Ω+. This means that the Yukawa-field approximation (3.2) recovers the Coulomb-field approximation (1.2);
Each fi(x, κ, Γ) Qi(x − xi)/∣x − xi∣3 decays as e−κr/r as r = ∣x∣ → ∞;
The approximation formula (3.2) becomes exact for a spherical solute with a single charge at the center of sphere.
We now construct the functions fi(x, κ, Γ) (i = 1,…, N). The ideas behind our constructions can be seen from our analysis of two model systems with spherical symmetry that we present in the next section. Fix an arbitrary index i with 1 ≤ i ≤ N. Fix an arbitrary point x ∈ Ω+. Denote by [xi, x] the line segment connecting xi and x, i.e.,
See Figure 2. Define
| (3.3) |
where ∣S∣ denotes the one-dimensional Lebesgue measure along the line [xi, x]. Note that and are the total lengths of line segments [xi, x] in Ω+ and that in Ω−, respectively. We assume that
| (3.4) |
This way, we have defined for each i two smooth functions and . Notice that our assumption (3.4) can be relaxed. For instance, since our electrostatic free energy (3.2) is an integral over Ω+, we need only assume that the three-dimensional Lebesgue measure of the set is zero for all i = 1,…, N. Finally, we define by
| (3.5) |
Clearly, these functions satisfy the conditions (1) and (2) above. We shall see in the next section that they also satisfy the condition (3).
Figure 2.
Definition of the function fi(·, κ, Γ).
We now present our formula of variational derivative δΓΔG[Γ]. Note that the dielectric boundary force is −δΓΔG[Γ]. For each i ∈ {1,…, N} and each x ∈ Ω+, we denote by the intersection of Ω+ and the half line starting from x in the direction from xi to x, i.e.,
| (3.6) |
Proposition 3.1
The variation of ΔG with respect to Γ is a function , and is given by
| (3.7) |
where dl denotes the line element and where for each i ∈ {1,…, N}
| (3.8) |
Notice from (3.4) and (3.5) that
Therefore, if we define , where is the set of all nonnegative real numbers, by
| (3.9) |
then the electrostatic free energy ΔG[Γ] is exactly (cf. (3.2))
Moreover, one verifies that the functions Fi(x) in (3.8) are given by
| (3.10) |
Proposition 3.1 is proved using two different methods in Section 5 and Section 6, respectively. The precise definition of the variation with respect to Γ is also given in the proof.
4 Two Model Systems
4.1 A Spherical Solute
We consider two model systems with spherically symmetric geometry. The first system consists of a single point charge Q at the center of a spherical solute of radius R. Let the center be the origin. Then corresponding to our previous set up, we have now N = 1, x1 = 0, Q1 = Q, and
In this case the solution to the boundary-value problem of Debye–Hückel equation (2.5) is
The corresponding electric displacement is
Clearly, in this case, the Yukawa-field approximation (3.1) with f1(x, κ, Γ) defined in (3.5) is exact, i.e., the condition (3) stated in the previous section is satisfied.
4.2 A Model Sphere-Ring Solute
The second model system consists of a point charge Q at the origin with solute molecular region Ω− and solvent region Ω+ given by
| (4.1) |
| (4.2) |
respectively, for some constants R1, R2, R3 with 0 < R1 < R2 < R3. See Figure 3.
Figure 3.
A spherically symmetric model system. The grey region is the solute molecular region Ω− defined by (4.1). The white region is the solvent region Ω+ defined by (4.2).
With this geometry, the electrostatic potential ψ = ψ2 is radially symmetric: ψ = ψ(r) with r = ∣x∣. (For convenience we write ψ instead of ψ2 in the rest of this section.) It is defined to be the solution to the boundary-value problem of the Debye–Hückel equation (2.5). This is equivalent to the elliptic interface problem
| (4.3) |
where δ is the Dirac delta function concentrated at the origin and ⟦u(r)⟧ = u(r+) − u(r−) for any function u that has both left and right limits at r.
Since ψ = ψ(r) is radially symmetric, the equation Δψ = 0 is an ordinary differential equation and has two linearly independent solutions 1 and 1/r. Similarly, the equation Δψ − κ2ψ = 0 is also an ordinary differential equation and has two linearly independent solutions e−κr/r and eκr/r. Therefore, from the first four equations and the boundary condition ψ(∞) = 0 in (4.3), we obtain
| (4.4) |
where all Ci (i = 1,…, 6) are constants. By the fifth and sixth equations in (4.3), we obtain with some calculations that
This system of linear equations of C1,…, C6 can be solved. Since we are only interested in the corresponding electric displacement, the values of C1 and C4 are not needed. After a series of calculations we obtain the other constants
| (4.5) |
where
| (4.6) |
| (4.7) |
We now calculate the approximation of the electric displacement D = −εε0▽ψ. This is the same as D2 defined in (2.6). Consider first the solute molecular region Ω− defined by r < R1 and R2 < r < R3. It is clear from (4.4) that D(x) = D1(x) if r = ∣x∣ < R1, where D1 is given in (2.4). By Taylor’s expansion and a series of calculations, we obtain from (4.7) that
| (4.8) |
This and (4.5) lead to
Therefore we also get from (4.4) that D(x) ≈ D1(x) if R2 < r < R3. Hence D1 is a good approximation of D2 in the solute molecular region Ω− in this case. This is the reason to have the Yukawa-field approximation (3.1) in Ω−.
We now consider the solvent region Ω+ defined by R1 < r < R2 and r > R3. Notice that typically ε+ ⪢ ε−. Therefore
Consequently we have by (4.5), (4.4), and a series of calculations that for R1 < r < R2
If we only keep the leading term in the numerator and that in the denominator, and use (4.4), we get for R1 < r = ∣x∣ < R2 that
This is the same as the Yukawa-field approximation (3.1) with fi(x, κ, Γ) given in (3.5) with N = 1, Q1 = Q, and x1 = 0.
Now from (4.8) and (4.5) we obtain
This and (4.4) imply that for r > R3
Notice that this is not quiet the same as that in (3.1). But for the function fi(·, κ, Γ) to be continuous we propose to replace R1 for the current system by R3 − R2 + R1. Therefore the modified electric displacement for r > R3 is
This is the same as that in (3.1) with fi(·, κ, Γ) given in (3.5) with N = 1, Q1 = Q, and x1 = 0.
5 Variational Derivative with Local Coordinates
Let all Γ, Ω−, Ω+, xi ∈ Ω− and (i = 1,…, N), ε−, ε+, ε0, and κ be all given as in Section 1 and Section 3, cf. Figure 1. We consider the derivative of the electrostatic free energy functional
with respect to the variation of the boundary Γ, where H(x) = H(x, Γ) is the free energy density—the integrand of the integral in (3.2)—defined on \ {x1,…, xN}.
The variation of the boundary Γ is defined by a family of boundaries Γt, parameterized by t ≥ 0 small, that depend smoothly on the parameter t. These boundaries are small perturbations of the boundary Γ0 = Γ, and are locally graphs of functions near a point of Γ of interest. The boundaries Γt can be viewed as moving surfaces starting from Γ0 = Γ and the parameter t is the time variable. Each point x ∈ Γ moves to x(t) at time t. We denote by v(x) the normal velocity of Γt at t = 0 at x ∈ Γ :
where n is the unit normal to Γ at x pointing from Ω− to Ω+.
Each Γt divides the entire solvation region into the open sets and that are small perturbations of Ω− and Ω+, respectively. In particular, all the points x1,…, xN remain in for all t. If we denote Ht(x) = H(x, Γt) with H0(x) = H(x) then
The derivative, δΓΔG[Γ], of the functional ΔG[Γ] with respect to the variation of Γ in the normal direction at Γ from Ω− to Ω+ is a function defined on Γ such that
where dS is the surface element of Γ.
In the rest of this section, we first derive a general expression of the derivative δΓΔG[Γ]. We then handle our free energy functional ΔG[Γ], proving the main formula (3.7) first for a single solute atom (N = 1) and then for multiple solute atoms (N > 1). We remark that our results can be generalized to those for an ambient space of any dimension d ≥ 3.
5.1 A General Result
With the above setting, we claim that
| (5.1) |
To prove this formula, we let for some p ≥ 1 be a partition of unity of . We assume the open sets U1,…,Up are bounded and smooth (e.g., balls) whose union covers a neighborhood of Γ. The open set U0 is also smooth but is unbounded, covering the complement of a neighborhood of Γ in Ω+. For each i (0 ≤ i ≤ p), and supp (ηi) ⊂ Ui. We also assume that for each i with 1 ≤ i ≤ p all the surfaces Γt ⋂ Ui are locally graphs. Now using the property of the partition of unity that we obtain
| (5.2) |
Since is independent of t > 0 and that supp (η0) ⊂ U0, we have
| (5.3) |
Fix an index i ∈ {1,…, p}. Assume Γ ⋂ Ui and Γt ⋂ Ui are graphs of functions z = u(y) and z = ut(y), respectively, in a local Cartesian coordinate system with and . Assume also that
Extend the functions u(y) and ut(y) continuously onto the entire . Since supp (ηi) ⊂ Ui, the integral of the function ηiHt over is then the same as that over
The normal velocity v = v(x) at a point x = (y, z) ∈ Γ ⋂ Ui is given by
The surface element dS of Γ and the surface element dA of are related by
Since supp (ηi) ⊂ Ui, we have
5.2 Single Solute Atom
We now consider , where F is defined in (3.9). The functions are defined in (3.3). In this subsection, we consider the case of a single solute atom, i.e., N = 1. For convenience, we denote x0 = x1 ∈ Ω− and . We define l+t(x) similar to that of l+(x) but using Γt instead of Γ. By (5.1),
| (5.4) |
Consider the spherical coordinates (ρ, θ) based around x0 with θ = (θ1, θ2) ∈ S2. Assume the set of points x of Γ with normal vector orthogonal to the line through x0 and x has measure zero. Then given x ∈ Γ there exists a neighborhood of x in Γ such that for compactly supported normal velocities v in this neighborhood, Γ and Γt for small enough t can be parameterized in terms of spherical coordinates. This means that Γ and Γt are graphs of functions ρ = u(θ) and ρ = ut(θ), respectively, for θ = (θ1, θ2) ∈ U for some open set U ⊂ S2. A consequence of this is that if x = (ρ, θ) ∈ Ω+ with θ ∉ U then
Otherwise if θ ∈ U then
| (5.5) |
where F1 is the partial derivative of F with respect to the variable α1 = l+(x), cf. (3.10), and where we used the fact that
Further simplification can be made by noticing that the normal velocity of Γt at t = 0 at x = (r, θ) ∈ Γ is
and that the surface measure dS on graph(u) is
where . Thus
| (5.6) |
Now denote by by (3.6) with x0 replacing xi. Denote also by dl the line element on , We have by (5.5) and (5.6) that
Combining this and (5.4), we have
| (5.7) |
5.3 Multiple Solute Atoms
We now consider the general case of N ≥ 1 solute atoms and derive our main formula (3.7). For boundaries Γt that perturb Γ, we denote as before by the corresponding perturbations of Ω+. We also define similar to but using Γt instead of Γ, cf. (3.3). By the general result (5.1), the chain rule, and a similar argument used in deriving (5.7), we obtain
| (5.8) |
where all are defined in (3.6) and Fi is the partial derivative of F = F (u, α1,…, αN) with respect to αi.
We finally prove our main formula (3.7). It follows from (3.2) that
| (5.9) |
where
It is clear from (5.1) that
| (5.10) |
We can express ΔG1[Γ] as
| (5.11) |
with F (u, α1,…, αN) given in (3.9). By (5.8) we obtain that
| (5.12) |
For our function F = F (u, α1,…, αN) in (3.9), we can compute directly its partial derivative Fi = ∂αiF to get (3.8). The main formula (3.7) now follows from (3.8), (3.9), and (5.9), (5.10), and (5.12).
6 Shape Derivative
We first define the shape derivative of the electrostatic free energy with respect to the local perturbation of the dielectric boundary. We then calculate the shape derivative of a functional defined on the boundary Γ in a form more general than our electrostatic free energy functional. Finally, we use our general result to derive the main formula (3.7).
6.1 Shape Derivative via Local Perturbation
Let z ∈ Γ and d > 0. Denote by B(z, d) the open ball in centered at z with radius d. Let be such that V = 0 outside the ball B(z, d). See Figure 4. The vector field V defines the solution map of the dynamical system
for any , where a dot denotes the derivative with respect to t. We shall denote Tt(X) = x(t, X) for all t and X. For each is a diffeomorphism. It maps Ω−, Ω+ and Γ to Tt(Ω−), Tt(Ω+) and Tt(Γ), respectively. We denote Γt = Tt(Γ) for all t ≥ 0. The dependence on V is suppressed. Clearly Γ0 = Γ.
Figure 4.
Local perturbation of the boundary Γ near z ∈ Γ.
Let t0 > 0 and consider the boundaries Γt for t ∈ [0, t0]. We assume both d and t0 are small so that the following hold true:
All the points x1,…, xN lie outside the closed ball . This implies particularly that xi = Tt(xi) ∈ Tt(Ω−) for i = 1,…, N and for all t ≥ 0;
If t ∈ [0, t0] then B(z, d) ⋂ Γt ≠ ∞ and (the ball centered at z with radius d/2);
If X ∈ Ω+ and 1 ≤ i ≤ N, then either [xi, X] ⋂ Γt ⋂ B(z, d) = ∅ for all t ∈ [0, t0] or [xi, X] ⋂ Γt ⋂ B(z, d) contains exactly one point for all t ∈ [0, t0]. This point can depend on t.
For each t > 0 we define the electrostatic free energy ΔG[Γt] by (3.2) with Γt replacing Γ. We define the derivative of the electrostatic free energy ΔG[Γ] with respect to the vector field V to be [5,17,26,37]
This is a surface integral over Γ, or more precisely over Γ ⋂ B(z, d), of the product of V · n and some function that is independent of V, where n is the unit normal along Γ pointing from Ω− to Ω+. We identify this function on Γ ⋂ B(z, d) as the shape derivative of ΔG[Γ] over Γ ⋂ B(z, d) and denote it by δΓΔG[Γ]. In particular, this defines the shape derivative at the arbitrarily chosen point z ∈ Γ.
We recall some properties of the transformation Tt(X) that will be used later [17]. First, by the definition of Tt(X) = x(t, X), we have
| (6.1) |
Denote by ▽Tt(X) the Jacobian matrix of Tt at X defined by , where is the ith component of Tt (i = 1, 2, 3). Denote Jt(X) = det ▽Tt(X). Then
| (6.2) |
For any smooth function and any t ≥ 0, we also have
| (6.3) |
6.2 Shape Derivative of a General Functional
We consider the following functional of Γ which is more general than our free-energy functional ΔG[Γ] defined in (3.2):
Here F is a smooth and integrable function defined on , where denotes the set of all nonnegative real numbers, and are the same as before, cf. Section 3. Here and below dV denotes the volume element and the letter V in dV is not the vector field V. We derive in this section the following formula of the shape derivative:
| (6.4) |
where Fi is the partial derivative of F = F (u, α1,…, αN) with respect to αi and is defined in (3.6).
Notice that with the same argument as in Subsection 5.3 and this formula, we can obtain our main formula (3.7).
Let z ∈ Γ, B(z, d), , and t0 > 0 be given as in the previous subsection. For each i ∈ {1,…, N} and each t ∈ (0, t0], we define in the same way as for but using the boundary Γt = Tt(Γ) instead of Γ. We then have by the change of variable x = Tt(X) that
Consequently, it follows from the chain rule, our notation F = F (u, α1,…, αN), (6.1) and (6.2), and integration by parts that
Note that the minus sign in front of the boundary integral term follows from our convention that the unit normal n along Γ points from Ω− to Ω+.
By the chain rule, (6.3), and (6.1), we have for each i (1 ≤ i ≤ N) that
Therefore,
| (6.5) |
It will be shown later in this section that for each i (1 ≤ i ≤ N)
| (6.6) |
This and (6.5) then imply (6.4).
We now fix i (1 ≤ i ≤ N) and prove (6.6). For convenience, we denote , and . Denote by Λ the open set of points such that [X0, X] ⋂ Γ ⋂ B(z, d) ≠ ∅. Clearly,
Hence
| (6.7) |
where A := B means A is defined to be B.
We proceed in four steps.
Step 1
Let X ∈ Λ ⋂ Ω+. By our assumption on the locality of perturbation (cf. the previous subsection), the line segment [X0, X] and the boundary Γt intersect at exactly 2k − 1 points with some k = k(X) for all t ∈ [0, t0]:
where all sj(X, t) ∈ [0, 1] are smooth functions such that
See Figure 4 where these intersection points are marked by dots. Set s0(X, t) = 0, s2k(X, t) = 1, P0(X, t) = X0, and P2k(X, t) = X for all t ∈ [0, t0]. It then follows from the definition of that
Notice that there exists exactly one index j0 = j0(X) ∈ {1,…, 2k − 1} such that [X0, X] ⋂ Γt ⋂ B(z, d) = {Pj0(X, t)} for all t ∈ [0, t0]. For all other indices j ≠ j0, the intersection points Pj(X, t), and hence the functions sj(X, t) as well, are independent of t ∈ [0, t0]. Therefore ∂tsj(X, 0) = 0 if j ≠ j0. Consequently,
| (6.8) |
Step 2
To calculate ∂tsj,0(X, 0), we set
Clearly, aj0(X,0) = Pj0(X,0) and
Take the derivative with respect to t and then set t = 0 to get by (6.1) that
leading to
| (6.9) |
Let Λ0 denote the cone generated by X0 and Γ ⋂ B(z, d), cf. Figure 4. Precisely, Λ0 is the set of points such that the intersection of the half line {X0 + s(Y − X0) : s ≥ 0} and the set Γ ⋂ B(z, d) contains exactly one point, denoted P (Y). Clearly Λ ⊂ Λ0. For X ∈ Λ ⋂ Ω+ as above, we have P(X) = Pj0(X, 0). Define
For any Y ∈ Λ0, ϕ(Y) = 0 if and only if Y = P(Y) ∈ Γ, i.e., Γ ⋂ B(z, d) is the (zero) level-set of .
Clearly ϕ(aj0(X, t)) = 0. Thus, taking the derivative against t and setting t = 0, we obtain by the chain rule that ▽ϕ(aj0(X, 0)) · ∂taj0(X, 0) = 0. This and (6.9), with the notation P(X) = Pj0(X), then imply
Plugging this into (6.8), we obtain that
| (6.10) |
Notice that ϕ(P(X))/∣ϕ(P(X))∣ is a unit normal at P(X) along Γ. It differs from n(P(X)) by a sign. Observe that j0 = j0(X) is odd if and only if X0 + s(P(X) − X0) ∈ Ω− for s ∈ (0, 1) sufficiently close to 1, cf. Figure 4. Since the unit normal n points from Ω− to Ω+, that j0 is odd then implies ϕ increases at P(X) in the direction n(P(X)), i.e., n(P(X)) · ▽ϕ(P(X)) > 0. Therefore
| (6.11) |
Step 3
Since X ∈ Λ ⋂ Ω+, we have ϕ(X) = ∣X − P(X)∣/∣X − X0∣. Moreover
| (6.12) |
Thus
By taking the partial derivative with respect to Xl for l ∈ {1, 2, 3}, we obtain by the chain rule that
leading to
| (6.13) |
Since ϕ increases in the direction from X0 to X, this particularly implies that (X − X0) · ▽ϕ(P(X)) > 0. Also, ∣ϕ(X)∣ < 1. Hence
| (6.14) |
Now combining (6.13) with (6.10) and then using (6.14) and (6.11), we obtain that
| (6.15) |
Step 4
Denote by the characteristic function of Ω+, i.e., χ+(Y) = 1 if Y ∈ Ω+ and χ+(Y) = 0 if Y ∉ Ω+. Notice that ∣▽ϕ(Y)∣ = ∣▽(1 − ϕ(Y))∣ and that 1 − ϕ(Y) ∈ (0, 1) if Y ∈ Λ. We then have by (6.7) and (6.15), and by an application of the co-area formula that
| (6.16) |
Fix σ ∈ (0, 1). Under the change of variable Y = P(X), the surface {X ∈ Λ : 1−ϕ(X) = σ} is mapped to that defined by ϕ(X) = 0 which is Γ ⋂ B(z, d). Moreover, by (6.12), this change of variable is Y = P(X) = X0 + σ(X − X0). The change of surface element is
where Cof B denotes the cofactor matrix of a matrix B and n(X) is the unit normal along Γ. Therefore, it follows from (6.16) and using X instead of Y that
For any X ∈ Γ ⋂ B(z, d), by parameterizing using Y = X0 + (1/σ)(X − X0) with σ ∈ (0, 1), we get
These two equations together with (6.7) implies the desired (6.6) with our notations.
6.3 Derivation of the Main Formula
By defining ΔG1[Γ] as in (5.11) with F (u, α1,…, αN) given in (3.9), we obtain (5.12) by (6.4). The rest of the derivation is the same as that presented in Subsection 5.3.
Acknowledgment
This work was supported by the US National Science Foundation (NSF) through the grant DMS-0811259 (B. L.), by the NSF Center for Theoretical Biological Physics (CTBP) through the NSF grant PHY-0822283 (B. L.), and by the National Institutes of Health through the grant R01GM096188 (L.-T. C. and B. L.). The authors thank Dr. Jianwei Che, Dr. Joachim Dzubiella, and Dr. Zhongming Wang for helpful discussions.
References
- [1].Andelman D. Electrostatic properties of membranes: The Poisson–Boltzmann theory. In: Lipowsky R, Sackmann E, editors. Handbook of Biological Physics. volume 1. Elsevier; 1995. pp. 603–642. [Google Scholar]
- [2].Baker NA. Improving implicit solvent simulations: a Poisson-centric view. Curr Opin Struct Biol. 2005;15:137–143. doi: 10.1016/j.sbi.2005.02.001. [DOI] [PubMed] [Google Scholar]
- [3].Bashford D, Case DA. Generalized Born models of macromolecular solvation effects. Ann. Rev. Phys. Chem. 2000;51:129–152. doi: 10.1146/annurev.physchem.51.1.129. [DOI] [PubMed] [Google Scholar]
- [4].Born M. Volumen und Hydratationswärme der Ionen. Z. Phys. 1920;1:45–48. [Google Scholar]
- [5].Bucur D, Buttazzo G. Progress in Nonlinear Differential Equations and Their Applications. Birkhäuser, Boston: 2005. Variational Methods in Shape Optimization Problems. [Google Scholar]
- [6].Chapman DL. A contribution to the theory of electrocapillarity. Phil. Mag. 1913;25:475–481. [Google Scholar]
- [7].Che J, Dzubiella J, Li B, McCammon JA. Electrostatic free energy and its variations in implicit solvent models. J. Phys. Chem. B. 2008;112:3058–3069. doi: 10.1021/jp7101012. [DOI] [PubMed] [Google Scholar]
- [8].Chen J, Brooks CL, III, Khandogin J. Recent advances in implicit solvent based methods for biomolecular simulations. Curr. Opin. Struct. Biol. 2008;18:140–148. doi: 10.1016/j.sbi.2008.01.003. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [9].Cheng L-T, Dzubiella J, McCammon JA, Li B. Application of the level-set method to the implicit solvation of nonpolar molecules. J. Chem. Phys. 2007;127:084503. doi: 10.1063/1.2757169. [DOI] [PubMed] [Google Scholar]
- [10].Cheng L-T, Li B, Wang Z. Level-set minimization of potential controlled Hadwiger valuations for molecular solvation. J. Comput. Phys. 2010;229:8497–8510. doi: 10.1016/j.jcp.2010.07.032. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [11].Cheng L-T, Wang Z, Setny P, Dzubiella J, Li B, McCammon JA. Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach. J. Chem. Phys. 2009;131:144102. doi: 10.1063/1.3242274. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [12].Cheng L-T, Xie Y, Dzubiella J, McCammon JA, Che J, Li B. Coupling the level-set method with molecular mechanics for variational implicit solvation of nonpolar molecules. J. Chem. Theory Comput. 2009;5:257–266. doi: 10.1021/ct800297d. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [13].Connolly ML. Analytical molecular surface calculation. J. Appl. Cryst. 1983;16:548–558. [Google Scholar]
- [14].Connolly ML. The molecular surface package. J. Mol. Graphics. 1992;11:139–141. doi: 10.1016/0263-7855(93)87010-3. [DOI] [PubMed] [Google Scholar]
- [15].Cramer CJ, Truhlar DG. Implicit solvation models: Equilibria, structure, spectra, and dynamics. Chem. Rev. 1999;99:2161–2200. doi: 10.1021/cr960149m. [DOI] [PubMed] [Google Scholar]
- [16].Davis ME, McCammon JA. Electrostatics in biomolecular structure and dynamics. Chem. Rev. 1990;90:509–521. [Google Scholar]
- [17].Delfour MC, Zolésio J-P. Shapes and Geometries: Analysis, Differential Calculus, and Optimization. SIAM. 1987 [Google Scholar]
- [18].Dzubiella J, Swanson JMJ, McCammon JA. Coupling hydrophobicity, dispersion, and electrostatics in continuum solvent models. Phys. Rev. Lett. 2006;96:087802. doi: 10.1103/PhysRevLett.96.087802. [DOI] [PubMed] [Google Scholar]
- [19].Dzubiella J, Swanson JMJ, McCammon JA. Coupling nonpolar and polar solvation free energies in implicit solvent models. J. Chem. Phys. 2006;124:084905. doi: 10.1063/1.2171192. [DOI] [PubMed] [Google Scholar]
- [20].Feig M, Brooks CL., III Recent advances in the development and applications of implicit solvent models in biomolecule simulations. Current Opinion in Structure Biology. 2004;14:217–224. doi: 10.1016/j.sbi.2004.03.009. [DOI] [PubMed] [Google Scholar]
- [21].Fixman F. The Poisson–Boltzmann equation and its application to polyelecrolytes. J. Chem. Phys. 1979;70:4995–5005. [Google Scholar]
- [22].Fogolari F, Brigo A, Molinari H. The Poisson–Boltzmann equation for biomolecular electrostatics: a tool for structural biology. J. Mol. Recognit. 2002;15:377–392. doi: 10.1002/jmr.577. [DOI] [PubMed] [Google Scholar]
- [23].Gouy M. Sur la constitution de la charge électrique a la surface d’un électrolyte. J. de Phys. 1910;9:457–468. [Google Scholar]
- [24].Grochowski P, Trylska J. Continuum molecular electrostatics, salt effects and counterion binding—A review of the Poisson–Boltzmann model and its modifications. Biopolymers. 2008;89:93–113. doi: 10.1002/bip.20877. [DOI] [PubMed] [Google Scholar]
- [25].Jackson JD. Classical Electrodynamics. 3rd edition Wiley; New York: 1999. [Google Scholar]
- [26].Kawohl B, Pironneau O, Tartar L, Zolésio J-P. Optimal Shape Design, volume 1740 of Lecture Notes in Mathematics. Springer; 2000. [Google Scholar]
- [27].Lee B, Richards FM. The interpretation of protein structures: Estimation of static accessibility. J. Mol. Biol. 1971;55:379–400. doi: 10.1016/0022-2836(71)90324-x. [DOI] [PubMed] [Google Scholar]
- [28].Li B. Continuum electrostatics for ionic solutions with nonuniform ionic sizes. Nonlinearity. 2009;22:811–833. [Google Scholar]
- [29].Li B. Minimization of electrostatic free energy and the Poisson–Boltzmann equation for molecular solvation with implicit solvent. SIAM J. Math. Anal. 2009;40:2536–2566. [Google Scholar]
- [30].Li B, Zhang Z-F, Cheng X-L. Dielectric boundary force in molecular solvation with the Poisson–Boltzmann free energy: A shape derivative approach. SIAM J. Applied Math. 2011 doi: 10.1137/110826436. (submitted) [DOI] [PMC free article] [PubMed] [Google Scholar]
- [31].Lieb EH, Loss M. Analysis. Amer. Math. Soc. (2nd edition) 2001 [Google Scholar]
- [32].Richards FM. Areas, volumes, packing, and protein structure. Annu. Rev. Biophys. Bioeng. 1977;6:151–176. doi: 10.1146/annurev.bb.06.060177.001055. [DOI] [PubMed] [Google Scholar]
- [33].Richmond TJ. Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect. J. Mol. Biol. 1984;178:63–89. doi: 10.1016/0022-2836(84)90231-6. [DOI] [PubMed] [Google Scholar]
- [34].Roux B, Simonson T. Implicit solvent models. Biophys. Chem. 1999;78:1–20. doi: 10.1016/s0301-4622(98)00226-9. [DOI] [PubMed] [Google Scholar]
- [35].Setny P, Wang Z, Cheng L-T, Li B, McCammon JA, Dzubliella J. Dewetting-controlled binding of ligands to hydrophobic pockets. Phys. Rev. Lett. 2009;103:187801. doi: 10.1103/PhysRevLett.103.187801. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [36].Sharp KA, Honig B. Electrostatic interactions in macromolecules: Theory and applications. Annu. Rev. Biophys. Biophys. Chem. 1990;19:301–332. doi: 10.1146/annurev.bb.19.060190.001505. [DOI] [PubMed] [Google Scholar]
- [37].Sokolowski J, Zolésio J-P. Springer Series in Computational Mathematics. Springer; 1992. Introduction to Shape Optimization: Shape Sensitivity Analysis. [Google Scholar]
- [38].Still WC, Tempczyk A, Hawley RC, Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Amer. Chem. Soc. 1990;112:6127–6129. [Google Scholar]
- [39].Tomasi J, Persico M. Molecular interactions in solution: An overview of methods based on continuous distributions of the solvent. Chem. Rev. 1994;94:2027–2094. [Google Scholar]
- [40].Wang Z, Che J, Cheng L-T, Dzubiella J, Li B, McCammon JA. Level-set variational implicit solvation with the Coulomb-field approximation. J. Chem. Theory Comput. 2011 doi: 10.1021/ct200647j. (submitted) [DOI] [PMC free article] [PubMed] [Google Scholar]
- [41].Zhou S, Wang Z, Li B. Mean-field description of ionic size effects with nonuniform ionic sizes: A numerical approach. Phys. Rev. E. 2011;84:021901. doi: 10.1103/PhysRevE.84.021901. [DOI] [PMC free article] [PubMed] [Google Scholar]



